Multiple sequence alignment - TraesCS3D01G250300

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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 TraesCS3D01G250300 chr3D 100.000 8079 0 0 1 8079 350784736 350792814 0.000000e+00 14920.0
1 TraesCS3D01G250300 chr3D 93.781 2605 80 17 1646 4237 478094648 478092113 0.000000e+00 3838.0
2 TraesCS3D01G250300 chr3D 93.073 2151 93 28 1648 3780 566618226 566620338 0.000000e+00 3096.0
3 TraesCS3D01G250300 chr3D 93.388 242 14 1 7840 8079 349973823 349974064 2.770000e-94 357.0
4 TraesCS3D01G250300 chr3D 77.311 119 26 1 7035 7153 554698529 554698646 1.450000e-07 69.4
5 TraesCS3D01G250300 chr5D 98.222 2925 48 4 4231 7153 310570917 310573839 0.000000e+00 5110.0
6 TraesCS3D01G250300 chr5D 93.727 2184 74 27 2100 4245 478377259 478375101 0.000000e+00 3216.0
7 TraesCS3D01G250300 chr5D 93.617 2162 70 16 2100 4237 288574689 288576806 0.000000e+00 3166.0
8 TraesCS3D01G250300 chr5D 92.966 2175 74 24 2100 4242 123866910 123869037 0.000000e+00 3096.0
9 TraesCS3D01G250300 chr5D 94.922 1418 42 7 2831 4238 321633803 321635200 0.000000e+00 2193.0
10 TraesCS3D01G250300 chr5D 97.551 939 13 2 1 930 310568998 310569935 0.000000e+00 1598.0
11 TraesCS3D01G250300 chr5D 88.278 1092 117 8 5782 6868 22412926 22411841 0.000000e+00 1297.0
12 TraesCS3D01G250300 chr5D 98.000 650 12 1 999 1647 310570279 310570928 0.000000e+00 1127.0
13 TraesCS3D01G250300 chr5D 90.592 287 26 1 5495 5780 22413273 22412987 5.920000e-101 379.0
14 TraesCS3D01G250300 chr5D 85.172 290 24 8 6883 7153 22411371 22411082 6.170000e-71 279.0
15 TraesCS3D01G250300 chr5D 90.683 161 8 2 1426 1580 468291312 468291471 2.950000e-49 207.0
16 TraesCS3D01G250300 chr5D 82.700 237 30 4 6869 7094 350690093 350689857 4.940000e-47 200.0
17 TraesCS3D01G250300 chr5D 77.311 119 26 1 7035 7153 505021385 505021268 1.450000e-07 69.4
18 TraesCS3D01G250300 chr1D 98.397 2683 38 5 4473 7153 471610710 471608031 0.000000e+00 4711.0
19 TraesCS3D01G250300 chr1D 93.059 2651 86 33 1642 4243 122527127 122529728 0.000000e+00 3786.0
20 TraesCS3D01G250300 chr1D 93.672 2165 81 24 2100 4237 458361421 458359286 0.000000e+00 3188.0
21 TraesCS3D01G250300 chr1D 93.167 2210 75 20 1648 3852 30377628 30375490 0.000000e+00 3175.0
22 TraesCS3D01G250300 chr1D 93.694 1554 60 19 2707 4237 78951259 78952797 0.000000e+00 2292.0
23 TraesCS3D01G250300 chr1D 94.522 1424 48 6 2825 4238 396203267 396204670 0.000000e+00 2170.0
24 TraesCS3D01G250300 chr1D 98.452 969 14 1 1 968 471613633 471612665 0.000000e+00 1705.0
25 TraesCS3D01G250300 chr1D 86.965 1005 88 12 5780 6781 416838326 416839290 0.000000e+00 1090.0
26 TraesCS3D01G250300 chr1D 96.769 650 17 3 999 1647 471612469 471611823 0.000000e+00 1081.0
27 TraesCS3D01G250300 chr1D 89.245 437 39 4 6122 6552 421438513 421438947 2.570000e-149 540.0
28 TraesCS3D01G250300 chr1D 99.595 247 1 0 4234 4480 471611831 471611585 1.240000e-122 451.0
29 TraesCS3D01G250300 chr1D 90.446 314 29 1 6555 6868 421439078 421439390 5.830000e-111 412.0
30 TraesCS3D01G250300 chr1D 88.502 287 31 2 5495 5780 416837982 416838267 6.000000e-91 346.0
31 TraesCS3D01G250300 chr1D 83.276 293 38 7 6869 7153 421529598 421529887 8.040000e-65 259.0
32 TraesCS3D01G250300 chr1D 82.432 296 41 2 6869 7153 421439991 421440286 1.740000e-61 248.0
33 TraesCS3D01G250300 chr1D 88.350 206 23 1 5578 5782 421438182 421438387 6.260000e-61 246.0
34 TraesCS3D01G250300 chr1D 83.966 237 27 4 6869 7094 252506590 252506826 4.910000e-52 217.0
35 TraesCS3D01G250300 chr1D 77.972 286 38 20 6869 7153 416840117 416840378 1.090000e-33 156.0
36 TraesCS3D01G250300 chr1D 89.796 98 6 4 6216 6311 421528956 421529051 1.100000e-23 122.0
37 TraesCS3D01G250300 chr2B 94.012 2956 111 28 4238 7157 443271724 443268799 0.000000e+00 4418.0
38 TraesCS3D01G250300 chr2B 97.126 174 5 0 1275 1448 443271967 443271794 2.200000e-75 294.0
39 TraesCS3D01G250300 chr2B 83.793 290 35 11 6871 7154 707259847 707260130 1.730000e-66 265.0
40 TraesCS3D01G250300 chr2B 84.133 271 37 5 6884 7153 250517125 250516860 2.890000e-64 257.0
41 TraesCS3D01G250300 chr2B 92.903 155 10 1 1426 1580 630382141 630381988 2.930000e-54 224.0
42 TraesCS3D01G250300 chr3B 93.982 2958 105 32 4238 7144 26490013 26492948 0.000000e+00 4409.0
43 TraesCS3D01G250300 chr3B 88.853 933 87 11 7152 8079 449202351 449203271 0.000000e+00 1131.0
44 TraesCS3D01G250300 chr3B 91.322 242 19 1 7840 8079 448863847 448864088 6.040000e-86 329.0
45 TraesCS3D01G250300 chr3B 96.316 190 7 0 1259 1448 26489754 26489943 6.090000e-81 313.0
46 TraesCS3D01G250300 chr3B 92.000 175 14 0 6979 7153 299601453 299601627 6.260000e-61 246.0
47 TraesCS3D01G250300 chr3B 92.903 155 10 1 1426 1580 351688476 351688629 2.930000e-54 224.0
48 TraesCS3D01G250300 chr3B 94.872 78 4 0 1570 1647 26489940 26490017 1.100000e-23 122.0
49 TraesCS3D01G250300 chr6D 94.594 2608 105 22 1648 4237 452974593 452972004 0.000000e+00 4002.0
50 TraesCS3D01G250300 chr6D 94.396 2177 66 9 1648 3817 435997465 435995338 0.000000e+00 3293.0
51 TraesCS3D01G250300 chr6D 94.457 2147 82 17 2100 4239 352011085 352013201 0.000000e+00 3271.0
52 TraesCS3D01G250300 chr6D 92.631 1452 43 13 2100 3531 411935087 411936494 0.000000e+00 2030.0
53 TraesCS3D01G250300 chr6D 92.186 1075 38 9 2709 3780 423921899 423922930 0.000000e+00 1478.0
54 TraesCS3D01G250300 chr6D 86.264 546 57 9 6155 6683 408645754 408645210 1.960000e-160 577.0
55 TraesCS3D01G250300 chr6D 93.137 204 14 0 6747 6950 455537888 455538091 4.740000e-77 300.0
56 TraesCS3D01G250300 chr6D 86.585 164 19 2 5601 5763 408646358 408646197 2.320000e-40 178.0
57 TraesCS3D01G250300 chr6D 84.831 178 26 1 5599 5775 455553437 455553614 2.320000e-40 178.0
58 TraesCS3D01G250300 chr6D 95.833 48 0 2 1134 1179 66260198 66260151 8.690000e-10 76.8
59 TraesCS3D01G250300 chr2D 94.359 2606 96 19 1648 4237 412647339 412644769 0.000000e+00 3951.0
60 TraesCS3D01G250300 chr2D 95.478 951 42 1 4831 5780 21223196 21224146 0.000000e+00 1517.0
61 TraesCS3D01G250300 chr2D 93.222 841 20 10 2263 3086 484125758 484124938 0.000000e+00 1203.0
62 TraesCS3D01G250300 chr2D 88.259 1005 96 13 5780 6781 112921500 112922485 0.000000e+00 1182.0
63 TraesCS3D01G250300 chr2D 93.582 779 39 7 5778 6549 21224205 21224979 0.000000e+00 1151.0
64 TraesCS3D01G250300 chr2D 96.377 552 20 0 1 552 188859594 188859043 0.000000e+00 909.0
65 TraesCS3D01G250300 chr2D 90.864 405 26 2 6760 7153 21234724 21235128 4.290000e-147 532.0
66 TraesCS3D01G250300 chr2D 87.167 413 45 3 6747 7152 520556289 520555878 5.710000e-126 462.0
67 TraesCS3D01G250300 chr2D 86.458 288 35 4 5495 5780 112921156 112921441 6.090000e-81 313.0
68 TraesCS3D01G250300 chr2D 96.183 131 5 0 1445 1575 559209926 559209796 1.770000e-51 215.0
69 TraesCS3D01G250300 chr7D 94.100 2627 78 28 1651 4234 465376168 465378760 0.000000e+00 3921.0
70 TraesCS3D01G250300 chr7D 93.687 2598 76 18 1648 4237 232555383 232552866 0.000000e+00 3808.0
71 TraesCS3D01G250300 chr7D 93.879 2173 88 26 2100 4239 179494718 179492558 0.000000e+00 3234.0
72 TraesCS3D01G250300 chr7D 93.683 2153 67 12 2100 4245 167368509 167370599 0.000000e+00 3158.0
73 TraesCS3D01G250300 chr7D 94.863 1538 49 5 2709 4237 232826347 232827863 0.000000e+00 2375.0
74 TraesCS3D01G250300 chr7D 94.460 1426 43 18 1648 3070 530441041 530442433 0.000000e+00 2163.0
75 TraesCS3D01G250300 chr7D 85.978 813 81 10 5006 5789 104219671 104218863 0.000000e+00 839.0
76 TraesCS3D01G250300 chr7D 84.519 239 34 1 5780 6015 480407946 480407708 4.880000e-57 233.0
77 TraesCS3D01G250300 chr5A 96.667 2040 50 5 4966 6987 48734291 48736330 0.000000e+00 3374.0
78 TraesCS3D01G250300 chr5A 94.844 640 18 7 547 1172 48732885 48733523 0.000000e+00 985.0
79 TraesCS3D01G250300 chr5A 87.322 844 80 11 5780 6621 412522069 412522887 0.000000e+00 941.0
80 TraesCS3D01G250300 chr5A 98.168 273 5 0 1176 1448 48733988 48734260 2.040000e-130 477.0
81 TraesCS3D01G250300 chr5A 94.245 139 7 1 1442 1580 687680924 687681061 2.280000e-50 211.0
82 TraesCS3D01G250300 chr5A 85.311 177 25 1 5600 5775 545715028 545715204 1.790000e-41 182.0
83 TraesCS3D01G250300 chr5A 86.335 161 8 4 6993 7153 48736417 48736563 6.490000e-36 163.0
84 TraesCS3D01G250300 chr5A 93.333 105 6 1 6666 6770 412524480 412524583 3.900000e-33 154.0
85 TraesCS3D01G250300 chr5A 92.771 83 6 0 6601 6683 412522897 412522979 3.960000e-23 121.0
86 TraesCS3D01G250300 chr5B 93.467 2250 91 22 4932 7144 676237768 676239998 0.000000e+00 3290.0
87 TraesCS3D01G250300 chr5B 93.357 557 28 6 1 552 532176903 532176351 0.000000e+00 815.0
88 TraesCS3D01G250300 chr5B 94.636 261 13 1 4301 4561 359144540 359144799 3.510000e-108 403.0
89 TraesCS3D01G250300 chr5B 97.403 154 3 1 6876 7028 676239670 676239823 2.240000e-65 261.0
90 TraesCS3D01G250300 chr5B 89.048 210 12 5 547 747 521994841 521995048 4.840000e-62 250.0
91 TraesCS3D01G250300 chr5B 98.571 140 2 0 6167 6306 641793382 641793521 1.740000e-61 248.0
92 TraesCS3D01G250300 chr5B 83.273 275 36 8 6884 7153 321200594 321200325 2.250000e-60 244.0
93 TraesCS3D01G250300 chr5B 91.139 158 10 4 1029 1183 532175176 532175020 2.280000e-50 211.0
94 TraesCS3D01G250300 chr5B 84.746 177 26 1 5600 5775 321201323 321201147 8.330000e-40 176.0
95 TraesCS3D01G250300 chr5B 90.291 103 8 1 5495 5597 377678944 377679044 5.090000e-27 134.0
96 TraesCS3D01G250300 chr4D 94.076 2144 79 16 2100 4235 265377002 265379105 0.000000e+00 3212.0
97 TraesCS3D01G250300 chr4D 86.441 413 47 4 6747 7152 95121079 95120669 2.070000e-120 444.0
98 TraesCS3D01G250300 chr4D 79.514 288 42 12 6871 7153 452849952 452850227 1.070000e-43 189.0
99 TraesCS3D01G250300 chr4D 85.124 121 18 0 5599 5719 95119556 95119436 3.060000e-24 124.0
100 TraesCS3D01G250300 chr4D 84.706 85 12 1 5415 5499 105937239 105937322 5.200000e-12 84.2
101 TraesCS3D01G250300 chr4D 77.311 119 26 1 7035 7153 509205689 509205572 1.450000e-07 69.4
102 TraesCS3D01G250300 chr1B 92.895 1520 71 20 5655 7144 65694368 65692856 0.000000e+00 2174.0
103 TraesCS3D01G250300 chr1B 94.213 553 26 4 3 552 30439716 30439167 0.000000e+00 839.0
104 TraesCS3D01G250300 chr1B 95.228 482 20 2 4906 5384 595344044 595344525 0.000000e+00 760.0
105 TraesCS3D01G250300 chr1B 84.385 301 25 7 4997 5278 463518343 463518640 7.990000e-70 276.0
106 TraesCS3D01G250300 chr1B 87.712 236 23 4 5780 6012 679325004 679325236 3.720000e-68 270.0
107 TraesCS3D01G250300 chr1B 97.403 154 3 1 6876 7028 65693178 65693025 2.240000e-65 261.0
108 TraesCS3D01G250300 chr1B 83.764 271 37 6 6884 7153 679325491 679325755 4.840000e-62 250.0
109 TraesCS3D01G250300 chr1B 82.963 135 20 3 7024 7158 181304162 181304031 1.420000e-22 119.0
110 TraesCS3D01G250300 chr1B 86.667 75 10 0 5299 5373 463518640 463518714 5.200000e-12 84.2
111 TraesCS3D01G250300 chr6B 87.525 1010 99 15 5780 6781 141648379 141649369 0.000000e+00 1142.0
112 TraesCS3D01G250300 chr6B 88.160 777 74 11 5847 6621 75409359 75410119 0.000000e+00 909.0
113 TraesCS3D01G250300 chr6B 87.291 779 79 13 5847 6621 564650717 564651479 0.000000e+00 872.0
114 TraesCS3D01G250300 chr6B 92.818 181 12 1 6601 6781 75410129 75410308 2.240000e-65 261.0
115 TraesCS3D01G250300 chr6B 78.151 119 25 1 7035 7153 159153844 159153961 3.130000e-09 75.0
116 TraesCS3D01G250300 chr6B 91.837 49 4 0 7105 7153 673658952 673659000 1.450000e-07 69.4
117 TraesCS3D01G250300 chr4A 88.413 794 57 18 6389 7153 740881524 740880737 0.000000e+00 924.0
118 TraesCS3D01G250300 chr4A 95.427 328 15 0 4234 4561 563488671 563488344 2.580000e-144 523.0
119 TraesCS3D01G250300 chr4A 94.161 274 12 1 1175 1448 563489008 563488739 1.620000e-111 414.0
120 TraesCS3D01G250300 chr4A 94.981 259 12 1 4303 4561 352589435 352589692 9.760000e-109 405.0
121 TraesCS3D01G250300 chr4A 91.696 289 14 2 681 959 563503433 563503145 7.600000e-105 392.0
122 TraesCS3D01G250300 chr4A 89.862 217 12 5 4559 4770 599348756 599348967 3.720000e-68 270.0
123 TraesCS3D01G250300 chr4A 97.183 142 3 1 6876 7016 740881067 740880926 1.050000e-58 239.0
124 TraesCS3D01G250300 chr4A 92.517 147 8 3 1040 1183 563489609 563489463 2.950000e-49 207.0
125 TraesCS3D01G250300 chr4A 85.311 177 24 2 5600 5775 111079421 111079596 1.790000e-41 182.0
126 TraesCS3D01G250300 chr4A 80.729 192 31 5 6966 7153 111080253 111080442 2.350000e-30 145.0
127 TraesCS3D01G250300 chr4A 92.500 80 4 1 1570 1647 563488742 563488663 6.630000e-21 113.0
128 TraesCS3D01G250300 chrUn 93.370 543 31 4 3 543 235697794 235697255 0.000000e+00 798.0
129 TraesCS3D01G250300 chrUn 93.370 543 31 4 3 543 319354891 319354352 0.000000e+00 798.0
130 TraesCS3D01G250300 chrUn 92.199 423 23 3 547 959 235696817 235696395 2.510000e-164 590.0
131 TraesCS3D01G250300 chrUn 90.000 420 30 4 549 959 22419446 22419862 4.290000e-147 532.0
132 TraesCS3D01G250300 chrUn 89.607 433 23 12 773 1183 235696397 235695965 1.540000e-146 531.0
133 TraesCS3D01G250300 chrUn 89.607 433 23 12 773 1183 248756615 248756183 1.540000e-146 531.0
134 TraesCS3D01G250300 chrUn 89.437 426 32 5 547 959 5426516 5426091 7.180000e-145 525.0
135 TraesCS3D01G250300 chrUn 92.394 355 18 3 547 892 319353914 319353560 1.570000e-136 497.0
136 TraesCS3D01G250300 chrUn 96.350 274 10 0 1175 1448 235695534 235695261 1.240000e-122 451.0
137 TraesCS3D01G250300 chrUn 96.350 274 10 0 1175 1448 248755752 248755479 1.240000e-122 451.0
138 TraesCS3D01G250300 chrUn 96.203 237 9 0 4234 4470 235695193 235694957 9.830000e-104 388.0
139 TraesCS3D01G250300 chrUn 96.203 237 9 0 4234 4470 248755411 248755175 9.830000e-104 388.0
140 TraesCS3D01G250300 chrUn 94.286 140 5 3 1437 1575 64149694 64149831 2.280000e-50 211.0
141 TraesCS3D01G250300 chrUn 84.916 179 22 4 5600 5775 158062491 158062667 8.330000e-40 176.0
142 TraesCS3D01G250300 chrUn 95.000 80 2 1 1570 1647 235695264 235695185 3.060000e-24 124.0
143 TraesCS3D01G250300 chrUn 95.000 80 2 1 1570 1647 248755482 248755403 3.060000e-24 124.0
144 TraesCS3D01G250300 chrUn 86.813 91 8 3 5600 5688 478545784 478545872 1.860000e-16 99.0
145 TraesCS3D01G250300 chrUn 87.671 73 8 1 5427 5499 330485068 330485139 5.200000e-12 84.2
146 TraesCS3D01G250300 chr4B 92.545 550 29 7 3 549 626513687 626514227 0.000000e+00 778.0
147 TraesCS3D01G250300 chr4B 99.076 433 3 1 118 550 667988637 667988206 0.000000e+00 776.0
148 TraesCS3D01G250300 chr4B 93.381 423 18 4 547 959 626514667 626515089 1.150000e-172 617.0
149 TraesCS3D01G250300 chr4B 89.260 419 26 11 773 1172 626515087 626515505 2.600000e-139 507.0
150 TraesCS3D01G250300 chr4B 95.290 276 11 1 1175 1448 626515948 626516223 3.460000e-118 436.0
151 TraesCS3D01G250300 chr4B 95.402 261 12 0 4301 4561 577023501 577023241 4.510000e-112 416.0
152 TraesCS3D01G250300 chr4B 96.203 237 8 1 4231 4467 626516288 626516523 3.540000e-103 387.0
153 TraesCS3D01G250300 chr4B 97.487 199 5 0 1 199 608062503 608062701 2.790000e-89 340.0
154 TraesCS3D01G250300 chr4B 96.154 78 3 0 1570 1647 667987885 667987808 2.370000e-25 128.0
155 TraesCS3D01G250300 chr4B 95.000 80 2 1 1570 1647 626516220 626516299 3.060000e-24 124.0
156 TraesCS3D01G250300 chr7A 87.977 524 59 4 5269 5789 250808871 250808349 4.140000e-172 616.0
157 TraesCS3D01G250300 chr2A 87.977 524 58 5 5269 5789 688572436 688572957 1.490000e-171 614.0
158 TraesCS3D01G250300 chr2A 80.829 193 31 5 6966 7154 726994602 726994792 6.530000e-31 147.0
159 TraesCS3D01G250300 chr6A 86.716 542 58 6 6155 6683 554455256 554454716 2.510000e-164 590.0
160 TraesCS3D01G250300 chr7B 88.599 421 34 7 547 958 33384602 33384187 4.350000e-137 499.0
161 TraesCS3D01G250300 chr7B 86.560 439 48 4 5074 5502 613145049 613144612 2.640000e-129 473.0
162 TraesCS3D01G250300 chr3A 94.466 253 14 0 7827 8079 468516346 468516598 2.730000e-104 390.0
163 TraesCS3D01G250300 chr3A 92.149 242 17 1 7840 8079 468251114 468251355 2.790000e-89 340.0
164 TraesCS3D01G250300 chr1A 90.323 155 14 1 1426 1580 342019678 342019525 1.370000e-47 202.0
165 TraesCS3D01G250300 chr1A 90.411 73 6 1 5427 5499 58252633 58252562 2.400000e-15 95.3
166 TraesCS3D01G250300 chr1A 91.304 46 4 0 7108 7153 29240697 29240742 6.770000e-06 63.9


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 TraesCS3D01G250300 chr3D 350784736 350792814 8078 False 14920.000000 14920 100.000000 1 8079 1 chr3D.!!$F2 8078
1 TraesCS3D01G250300 chr3D 478092113 478094648 2535 True 3838.000000 3838 93.781000 1646 4237 1 chr3D.!!$R1 2591
2 TraesCS3D01G250300 chr3D 566618226 566620338 2112 False 3096.000000 3096 93.073000 1648 3780 1 chr3D.!!$F4 2132
3 TraesCS3D01G250300 chr5D 478375101 478377259 2158 True 3216.000000 3216 93.727000 2100 4245 1 chr5D.!!$R2 2145
4 TraesCS3D01G250300 chr5D 288574689 288576806 2117 False 3166.000000 3166 93.617000 2100 4237 1 chr5D.!!$F2 2137
5 TraesCS3D01G250300 chr5D 123866910 123869037 2127 False 3096.000000 3096 92.966000 2100 4242 1 chr5D.!!$F1 2142
6 TraesCS3D01G250300 chr5D 310568998 310573839 4841 False 2611.666667 5110 97.924333 1 7153 3 chr5D.!!$F5 7152
7 TraesCS3D01G250300 chr5D 321633803 321635200 1397 False 2193.000000 2193 94.922000 2831 4238 1 chr5D.!!$F3 1407
8 TraesCS3D01G250300 chr5D 22411082 22413273 2191 True 651.666667 1297 88.014000 5495 7153 3 chr5D.!!$R4 1658
9 TraesCS3D01G250300 chr1D 122527127 122529728 2601 False 3786.000000 3786 93.059000 1642 4243 1 chr1D.!!$F2 2601
10 TraesCS3D01G250300 chr1D 458359286 458361421 2135 True 3188.000000 3188 93.672000 2100 4237 1 chr1D.!!$R2 2137
11 TraesCS3D01G250300 chr1D 30375490 30377628 2138 True 3175.000000 3175 93.167000 1648 3852 1 chr1D.!!$R1 2204
12 TraesCS3D01G250300 chr1D 78951259 78952797 1538 False 2292.000000 2292 93.694000 2707 4237 1 chr1D.!!$F1 1530
13 TraesCS3D01G250300 chr1D 396203267 396204670 1403 False 2170.000000 2170 94.522000 2825 4238 1 chr1D.!!$F4 1413
14 TraesCS3D01G250300 chr1D 471608031 471613633 5602 True 1987.000000 4711 98.303250 1 7153 4 chr1D.!!$R3 7152
15 TraesCS3D01G250300 chr1D 416837982 416840378 2396 False 530.666667 1090 84.479667 5495 7153 3 chr1D.!!$F5 1658
16 TraesCS3D01G250300 chr1D 421438182 421440286 2104 False 361.500000 540 87.618250 5578 7153 4 chr1D.!!$F6 1575
17 TraesCS3D01G250300 chr2B 443268799 443271967 3168 True 2356.000000 4418 95.569000 1275 7157 2 chr2B.!!$R3 5882
18 TraesCS3D01G250300 chr3B 26489754 26492948 3194 False 1614.666667 4409 95.056667 1259 7144 3 chr3B.!!$F5 5885
19 TraesCS3D01G250300 chr3B 449202351 449203271 920 False 1131.000000 1131 88.853000 7152 8079 1 chr3B.!!$F4 927
20 TraesCS3D01G250300 chr6D 452972004 452974593 2589 True 4002.000000 4002 94.594000 1648 4237 1 chr6D.!!$R3 2589
21 TraesCS3D01G250300 chr6D 435995338 435997465 2127 True 3293.000000 3293 94.396000 1648 3817 1 chr6D.!!$R2 2169
22 TraesCS3D01G250300 chr6D 352011085 352013201 2116 False 3271.000000 3271 94.457000 2100 4239 1 chr6D.!!$F1 2139
23 TraesCS3D01G250300 chr6D 411935087 411936494 1407 False 2030.000000 2030 92.631000 2100 3531 1 chr6D.!!$F2 1431
24 TraesCS3D01G250300 chr6D 423921899 423922930 1031 False 1478.000000 1478 92.186000 2709 3780 1 chr6D.!!$F3 1071
25 TraesCS3D01G250300 chr6D 408645210 408646358 1148 True 377.500000 577 86.424500 5601 6683 2 chr6D.!!$R4 1082
26 TraesCS3D01G250300 chr2D 412644769 412647339 2570 True 3951.000000 3951 94.359000 1648 4237 1 chr2D.!!$R2 2589
27 TraesCS3D01G250300 chr2D 21223196 21224979 1783 False 1334.000000 1517 94.530000 4831 6549 2 chr2D.!!$F2 1718
28 TraesCS3D01G250300 chr2D 484124938 484125758 820 True 1203.000000 1203 93.222000 2263 3086 1 chr2D.!!$R3 823
29 TraesCS3D01G250300 chr2D 188859043 188859594 551 True 909.000000 909 96.377000 1 552 1 chr2D.!!$R1 551
30 TraesCS3D01G250300 chr2D 112921156 112922485 1329 False 747.500000 1182 87.358500 5495 6781 2 chr2D.!!$F3 1286
31 TraesCS3D01G250300 chr7D 465376168 465378760 2592 False 3921.000000 3921 94.100000 1651 4234 1 chr7D.!!$F3 2583
32 TraesCS3D01G250300 chr7D 232552866 232555383 2517 True 3808.000000 3808 93.687000 1648 4237 1 chr7D.!!$R3 2589
33 TraesCS3D01G250300 chr7D 179492558 179494718 2160 True 3234.000000 3234 93.879000 2100 4239 1 chr7D.!!$R2 2139
34 TraesCS3D01G250300 chr7D 167368509 167370599 2090 False 3158.000000 3158 93.683000 2100 4245 1 chr7D.!!$F1 2145
35 TraesCS3D01G250300 chr7D 232826347 232827863 1516 False 2375.000000 2375 94.863000 2709 4237 1 chr7D.!!$F2 1528
36 TraesCS3D01G250300 chr7D 530441041 530442433 1392 False 2163.000000 2163 94.460000 1648 3070 1 chr7D.!!$F4 1422
37 TraesCS3D01G250300 chr7D 104218863 104219671 808 True 839.000000 839 85.978000 5006 5789 1 chr7D.!!$R1 783
38 TraesCS3D01G250300 chr5A 48732885 48736563 3678 False 1249.750000 3374 94.003500 547 7153 4 chr5A.!!$F3 6606
39 TraesCS3D01G250300 chr5A 412522069 412524583 2514 False 405.333333 941 91.142000 5780 6770 3 chr5A.!!$F4 990
40 TraesCS3D01G250300 chr5B 676237768 676239998 2230 False 1775.500000 3290 95.435000 4932 7144 2 chr5B.!!$F5 2212
41 TraesCS3D01G250300 chr5B 532175020 532176903 1883 True 513.000000 815 92.248000 1 1183 2 chr5B.!!$R2 1182
42 TraesCS3D01G250300 chr5B 321200325 321201323 998 True 210.000000 244 84.009500 5600 7153 2 chr5B.!!$R1 1553
43 TraesCS3D01G250300 chr4D 265377002 265379105 2103 False 3212.000000 3212 94.076000 2100 4235 1 chr4D.!!$F2 2135
44 TraesCS3D01G250300 chr4D 95119436 95121079 1643 True 284.000000 444 85.782500 5599 7152 2 chr4D.!!$R2 1553
45 TraesCS3D01G250300 chr1B 65692856 65694368 1512 True 1217.500000 2174 95.149000 5655 7144 2 chr1B.!!$R3 1489
46 TraesCS3D01G250300 chr1B 30439167 30439716 549 True 839.000000 839 94.213000 3 552 1 chr1B.!!$R1 549
47 TraesCS3D01G250300 chr1B 679325004 679325755 751 False 260.000000 270 85.738000 5780 7153 2 chr1B.!!$F3 1373
48 TraesCS3D01G250300 chr6B 141648379 141649369 990 False 1142.000000 1142 87.525000 5780 6781 1 chr6B.!!$F1 1001
49 TraesCS3D01G250300 chr6B 564650717 564651479 762 False 872.000000 872 87.291000 5847 6621 1 chr6B.!!$F3 774
50 TraesCS3D01G250300 chr6B 75409359 75410308 949 False 585.000000 909 90.489000 5847 6781 2 chr6B.!!$F5 934
51 TraesCS3D01G250300 chr4A 740880737 740881524 787 True 581.500000 924 92.798000 6389 7153 2 chr4A.!!$R3 764
52 TraesCS3D01G250300 chr4A 563488344 563489609 1265 True 314.250000 523 93.651250 1040 4561 4 chr4A.!!$R2 3521
53 TraesCS3D01G250300 chrUn 319353560 319354891 1331 True 647.500000 798 92.882000 3 892 2 chrUn.!!$R4 889
54 TraesCS3D01G250300 chrUn 235694957 235697794 2837 True 480.333333 798 93.788167 3 4470 6 chrUn.!!$R2 4467
55 TraesCS3D01G250300 chrUn 248755175 248756615 1440 True 373.500000 531 94.290000 773 4470 4 chrUn.!!$R3 3697
56 TraesCS3D01G250300 chr4B 626513687 626516523 2836 False 474.833333 778 93.613167 3 4467 6 chr4B.!!$F2 4464
57 TraesCS3D01G250300 chr4B 667987808 667988637 829 True 452.000000 776 97.615000 118 1647 2 chr4B.!!$R2 1529
58 TraesCS3D01G250300 chr7A 250808349 250808871 522 True 616.000000 616 87.977000 5269 5789 1 chr7A.!!$R1 520
59 TraesCS3D01G250300 chr2A 688572436 688572957 521 False 614.000000 614 87.977000 5269 5789 1 chr2A.!!$F1 520
60 TraesCS3D01G250300 chr6A 554454716 554455256 540 True 590.000000 590 86.716000 6155 6683 1 chr6A.!!$R1 528

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
251 252 0.608035 CCCCAACACAACATAGCGGT 60.608 55.0 0.0 0.0 0.00 5.68 F
975 1859 1.347817 GCTCGCAGGTCTTCTTGACG 61.348 60.0 0.0 0.0 46.24 4.35 F
2171 3816 2.081425 TTTGCCGTCCATTGTGGTGC 62.081 55.0 0.0 0.0 39.03 5.01 F
2948 4707 0.103937 TCGTGTCGGGTTTTACGGTT 59.896 50.0 0.0 0.0 37.18 4.44 F
4576 7292 0.038166 AGTAGGGGGTTGTCGTCGTA 59.962 55.0 0.0 0.0 0.00 3.43 F
4847 7581 0.478507 CCCTCCCTCTCTCTCTCTCC 59.521 65.0 0.0 0.0 0.00 3.71 F
6297 9300 1.967319 ACACCAGAATTGACGCTTGT 58.033 45.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 3195 1.201424 GTACTCCCTCCGTCCCAAAT 58.799 55.000 0.00 0.0 0.00 2.32 R
2948 4707 0.103937 ACCGTAAAACCCGACACGAA 59.896 50.000 0.00 0.0 36.53 3.85 R
3922 5749 0.940126 CGCTTGCGGATGCTAATCTT 59.060 50.000 12.76 0.0 43.34 2.40 R
4740 7459 1.806247 GCCGATGTCGTTGATGATCCA 60.806 52.381 1.44 0.0 37.74 3.41 R
6335 9339 2.679837 CACAATCCAGCGAGTTTGCTAT 59.320 45.455 0.00 0.0 45.23 2.97 R
6599 9778 4.535526 AAAGTTGACAGCAGTTGGTTTT 57.464 36.364 0.00 0.0 0.00 2.43 R
7224 13011 0.177604 CAAAACCAAGCACAAGGCCA 59.822 50.000 5.01 0.0 46.50 5.36 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
251 252 0.608035 CCCCAACACAACATAGCGGT 60.608 55.000 0.00 0.00 0.00 5.68
723 1215 8.934023 TGTCCATTATTTTCTTAGTTCCACTT 57.066 30.769 0.00 0.00 0.00 3.16
968 1841 3.006323 CCTAATCTATGCTCGCAGGTCTT 59.994 47.826 0.00 0.00 0.00 3.01
970 1843 1.769026 TCTATGCTCGCAGGTCTTCT 58.231 50.000 0.00 0.00 0.00 2.85
972 1845 2.159184 TCTATGCTCGCAGGTCTTCTTG 60.159 50.000 0.00 0.00 0.00 3.02
975 1859 1.347817 GCTCGCAGGTCTTCTTGACG 61.348 60.000 0.00 0.00 46.24 4.35
1018 2166 2.356382 CAGGTCGTTGTTGCTTTTGGTA 59.644 45.455 0.00 0.00 0.00 3.25
1043 2194 4.081142 TCTGCGTTCAAAGGGATCAAGATA 60.081 41.667 0.00 0.00 0.00 1.98
1134 2285 7.175467 TGAGCAATGACATAGACAACATTTTCT 59.825 33.333 0.00 0.00 31.85 2.52
1345 2988 7.945033 TGTAAAGGCAAGAATCAAACAATTC 57.055 32.000 0.00 0.00 36.16 2.17
1453 3096 6.936968 AGTTTATTGTCAACTACTCCCTCT 57.063 37.500 0.00 0.00 32.48 3.69
1588 3231 6.071278 AGGGAGTACTTTACTGATGACACTTC 60.071 42.308 0.00 0.00 39.59 3.01
1693 3338 7.607223 CCATGTTTGGTTTTGGTAATTGATGAT 59.393 33.333 0.00 0.00 38.30 2.45
1759 3404 6.041296 GGATTTGTCCATAGGCATTTCTTGAT 59.959 38.462 0.00 0.00 0.00 2.57
1805 3450 2.452600 ATGTGGTGACCAAGGTGTTT 57.547 45.000 5.57 0.00 34.18 2.83
1811 3456 4.399934 GTGGTGACCAAGGTGTTTTTAAGA 59.600 41.667 5.57 0.00 34.18 2.10
2152 3797 6.657966 TCATGAAGAGATCAAATGCTTGAAGT 59.342 34.615 0.00 0.00 44.64 3.01
2171 3816 2.081425 TTTGCCGTCCATTGTGGTGC 62.081 55.000 0.00 0.00 39.03 5.01
2172 3817 2.983030 GCCGTCCATTGTGGTGCA 60.983 61.111 0.00 0.00 39.03 4.57
2173 3818 2.953821 CCGTCCATTGTGGTGCAC 59.046 61.111 8.80 8.80 39.03 4.57
2174 3819 2.625823 CCGTCCATTGTGGTGCACC 61.626 63.158 29.67 29.67 39.03 5.01
2312 3957 5.457140 GGAGTCAAGATCGTCATCATCTAC 58.543 45.833 0.00 0.00 29.97 2.59
2315 3960 5.009510 AGTCAAGATCGTCATCATCTACCTG 59.990 44.000 0.00 0.00 29.97 4.00
2699 4366 7.229951 TCCCCTACCTCTTCTTACTATAACA 57.770 40.000 0.00 0.00 0.00 2.41
2703 4371 7.288158 CCCTACCTCTTCTTACTATAACAAGCT 59.712 40.741 0.00 0.00 0.00 3.74
2704 4372 8.697292 CCTACCTCTTCTTACTATAACAAGCTT 58.303 37.037 0.00 0.00 0.00 3.74
2705 4373 9.522804 CTACCTCTTCTTACTATAACAAGCTTG 57.477 37.037 24.84 24.84 0.00 4.01
2706 4374 8.135382 ACCTCTTCTTACTATAACAAGCTTGA 57.865 34.615 32.50 12.08 0.00 3.02
2707 4375 8.254508 ACCTCTTCTTACTATAACAAGCTTGAG 58.745 37.037 32.50 20.59 0.00 3.02
2709 4377 9.646427 CTCTTCTTACTATAACAAGCTTGAGTT 57.354 33.333 32.50 19.08 0.00 3.01
2712 4380 8.029642 TCTTACTATAACAAGCTTGAGTTTGC 57.970 34.615 32.50 0.00 39.43 3.68
2771 4460 5.294734 TCATATGCAGAAGTTATGGCAGA 57.705 39.130 0.00 0.00 39.95 4.26
2774 4463 6.429078 TCATATGCAGAAGTTATGGCAGATTC 59.571 38.462 0.00 0.00 36.18 2.52
2817 4506 3.117372 CCGGAGCGGTAGTACTGG 58.883 66.667 11.13 0.00 42.73 4.00
2948 4707 0.103937 TCGTGTCGGGTTTTACGGTT 59.896 50.000 0.00 0.00 37.18 4.44
2949 4708 0.936600 CGTGTCGGGTTTTACGGTTT 59.063 50.000 0.00 0.00 33.27 3.27
2950 4709 1.070643 CGTGTCGGGTTTTACGGTTTC 60.071 52.381 0.00 0.00 33.27 2.78
2951 4710 1.070643 GTGTCGGGTTTTACGGTTTCG 60.071 52.381 0.00 0.00 43.02 3.46
2961 4720 3.721851 CGGTTTCGTGTCGGGTTT 58.278 55.556 0.00 0.00 0.00 3.27
2962 4721 2.016171 CGGTTTCGTGTCGGGTTTT 58.984 52.632 0.00 0.00 0.00 2.43
2963 4722 1.216122 CGGTTTCGTGTCGGGTTTTA 58.784 50.000 0.00 0.00 0.00 1.52
2964 4723 1.070643 CGGTTTCGTGTCGGGTTTTAC 60.071 52.381 0.00 0.00 0.00 2.01
2965 4724 1.070643 GGTTTCGTGTCGGGTTTTACG 60.071 52.381 0.00 0.00 37.85 3.18
2966 4725 1.070643 GTTTCGTGTCGGGTTTTACGG 60.071 52.381 0.00 0.00 37.18 4.02
2967 4726 0.103937 TTCGTGTCGGGTTTTACGGT 59.896 50.000 0.00 0.00 37.18 4.83
2996 4755 2.440817 GCAGTGGGGGCCGTAGTAT 61.441 63.158 0.00 0.00 0.00 2.12
2998 4757 1.046472 CAGTGGGGGCCGTAGTATCA 61.046 60.000 0.00 0.00 0.00 2.15
3169 4991 2.553685 GGGGTAACGGTTGGATTGTTCT 60.554 50.000 3.07 0.00 37.60 3.01
3277 5100 2.501723 TGCTAACTCTCAATCCCTCCAC 59.498 50.000 0.00 0.00 0.00 4.02
3321 5144 4.832823 GGGAAAAGAGAGAGGAGATCTAGG 59.167 50.000 0.00 0.00 38.84 3.02
3331 5154 5.284582 AGAGGAGATCTAGGTCCACATTTT 58.715 41.667 0.00 0.00 36.10 1.82
3420 5246 5.859495 TCTCCTTGTTCTTCCTCTCTTTTC 58.141 41.667 0.00 0.00 0.00 2.29
3600 5426 0.250901 TGAGCTTGTTCCTCTTGGGC 60.251 55.000 0.00 0.00 34.39 5.36
3634 5460 2.203098 CGGTTGGTGGTGTTCGGT 60.203 61.111 0.00 0.00 0.00 4.69
3679 5505 4.699522 GGCAAGCGTCGGGGTCTT 62.700 66.667 0.00 0.00 0.00 3.01
3710 5536 2.279784 GAGATCGCCCCGAGCAAG 60.280 66.667 5.67 0.00 45.07 4.01
3721 5547 1.164041 CCGAGCAAGTTGACGGGTTT 61.164 55.000 24.38 0.00 41.41 3.27
3755 5581 2.748209 AAGGGTTGCCAAAGTGTACT 57.252 45.000 0.00 0.00 0.00 2.73
3915 5742 3.872603 TGTGCCTCCACACCGCTT 61.873 61.111 0.00 0.00 46.51 4.68
3922 5749 0.878523 CTCCACACCGCTTCAAACGA 60.879 55.000 0.00 0.00 0.00 3.85
3940 5767 1.070309 CGAAGATTAGCATCCGCAAGC 60.070 52.381 0.00 0.00 42.27 4.01
4185 6013 3.701532 TTTGTTCAAGCCTAAACCGTG 57.298 42.857 0.00 0.00 0.00 4.94
4576 7292 0.038166 AGTAGGGGGTTGTCGTCGTA 59.962 55.000 0.00 0.00 0.00 3.43
4632 7351 1.207329 GGCCGATCTGTTGTTCCTAGT 59.793 52.381 0.00 0.00 0.00 2.57
4740 7459 2.579241 CTTCATCGACGACGCCGACT 62.579 60.000 8.80 0.00 38.97 4.18
4833 7567 1.342672 TGGTAAGATTCGCCCCCTCC 61.343 60.000 0.00 0.00 0.00 4.30
4847 7581 0.478507 CCCTCCCTCTCTCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
5086 7837 7.938140 TTAGGTTGCAGCTTTATATTTGACT 57.062 32.000 0.00 0.00 0.00 3.41
5112 7863 2.051334 TTGCACTGCAGGTTACTTGT 57.949 45.000 19.93 0.00 40.61 3.16
5478 8238 8.997323 CACCAATCAATATTTCTAGCTCTTAGG 58.003 37.037 0.00 0.00 0.00 2.69
5597 8357 4.433615 ACTACTCAATACCAATCAGTGCG 58.566 43.478 0.00 0.00 0.00 5.34
6012 8927 2.864343 CCTATCGAATCGTTTGGTGTCC 59.136 50.000 1.52 0.00 0.00 4.02
6297 9300 1.967319 ACACCAGAATTGACGCTTGT 58.033 45.000 0.00 0.00 0.00 3.16
6335 9339 7.523415 ACAGGTTGTCCTTAGGATTTTCTTTA 58.477 34.615 3.52 0.00 43.07 1.85
6459 9475 6.071896 AGGCTTTAGATTTTCTGCTGGTTTAC 60.072 38.462 0.00 0.00 0.00 2.01
6579 9758 6.607019 AGATTGTTGTCCTTTAGTTACCCAA 58.393 36.000 0.00 0.00 0.00 4.12
6599 9778 6.555360 ACCCAAACCTTTGTTTTCATGGTATA 59.445 34.615 0.00 0.00 41.92 1.47
6996 12711 6.707161 TGTTGTACTGTAGTTTTGGTATCCAC 59.293 38.462 0.00 0.00 30.78 4.02
7038 12812 8.690840 CCGATTACACTTGAATGTTTCTTTTTC 58.309 33.333 0.00 0.00 33.85 2.29
7096 12883 9.595823 GCTTTCTACTAACTTCACCATTACATA 57.404 33.333 0.00 0.00 0.00 2.29
7103 12890 5.450818 ACTTCACCATTACATACATGGGT 57.549 39.130 0.00 0.00 45.05 4.51
7158 12945 1.524355 CGCTGCCGATCTAGTGAAATG 59.476 52.381 0.00 0.00 36.29 2.32
7167 12954 2.412870 TCTAGTGAAATGTGGTGTGCG 58.587 47.619 0.00 0.00 0.00 5.34
7168 12955 1.464608 CTAGTGAAATGTGGTGTGCGG 59.535 52.381 0.00 0.00 0.00 5.69
7184 12971 2.580276 GGCGGTCGTTGGTGGATA 59.420 61.111 0.00 0.00 0.00 2.59
7186 12973 1.157870 GGCGGTCGTTGGTGGATATG 61.158 60.000 0.00 0.00 0.00 1.78
7187 12974 1.157870 GCGGTCGTTGGTGGATATGG 61.158 60.000 0.00 0.00 0.00 2.74
7188 12975 0.462375 CGGTCGTTGGTGGATATGGA 59.538 55.000 0.00 0.00 0.00 3.41
7189 12976 1.134640 CGGTCGTTGGTGGATATGGAA 60.135 52.381 0.00 0.00 0.00 3.53
7190 12977 2.561569 GGTCGTTGGTGGATATGGAAG 58.438 52.381 0.00 0.00 0.00 3.46
7191 12978 1.940613 GTCGTTGGTGGATATGGAAGC 59.059 52.381 0.00 0.00 0.00 3.86
7192 12979 1.557371 TCGTTGGTGGATATGGAAGCA 59.443 47.619 0.00 0.00 0.00 3.91
7202 12989 3.437052 GGATATGGAAGCAGGTTTCCCAT 60.437 47.826 11.67 10.67 44.93 4.00
7205 12992 1.146774 TGGAAGCAGGTTTCCCATTCA 59.853 47.619 11.67 0.00 44.93 2.57
7210 12997 1.631405 CAGGTTTCCCATTCAAGGCA 58.369 50.000 0.00 0.00 0.00 4.75
7215 13002 3.830192 CCCATTCAAGGCAGGCGC 61.830 66.667 0.00 0.00 37.44 6.53
7234 13021 4.030452 GCGTCAGTGGCCTTGTGC 62.030 66.667 3.32 8.01 40.16 4.57
7250 13037 1.134753 TGTGCTTGGTTTTGTGCTCTG 59.865 47.619 0.00 0.00 0.00 3.35
7255 13042 3.214328 CTTGGTTTTGTGCTCTGGTAGT 58.786 45.455 0.00 0.00 0.00 2.73
7298 13085 2.821810 GCCGAGCCTTGGAGCTTC 60.822 66.667 0.80 0.00 45.15 3.86
7301 13088 0.179097 CCGAGCCTTGGAGCTTCTAC 60.179 60.000 0.00 0.00 45.15 2.59
7344 13131 2.028420 GCATCTGCACATACTGGTGA 57.972 50.000 0.00 0.00 41.32 4.02
7350 13137 1.001974 TGCACATACTGGTGAGTGGTC 59.998 52.381 0.00 0.00 41.32 4.02
7352 13139 2.549992 GCACATACTGGTGAGTGGTCAA 60.550 50.000 0.00 0.00 41.32 3.18
7353 13140 3.329386 CACATACTGGTGAGTGGTCAAG 58.671 50.000 0.00 0.00 41.32 3.02
7355 13142 3.006967 ACATACTGGTGAGTGGTCAAGTC 59.993 47.826 0.00 0.00 33.27 3.01
7356 13143 1.794714 ACTGGTGAGTGGTCAAGTCT 58.205 50.000 0.00 0.00 33.27 3.24
7363 13150 0.603569 AGTGGTCAAGTCTACGCCAG 59.396 55.000 0.00 0.00 0.00 4.85
7373 13160 2.168728 AGTCTACGCCAGATTTTCCTCC 59.831 50.000 0.00 0.00 35.17 4.30
7378 13165 0.922626 GCCAGATTTTCCTCCCTCCT 59.077 55.000 0.00 0.00 0.00 3.69
7382 13169 1.834263 AGATTTTCCTCCCTCCTGTCG 59.166 52.381 0.00 0.00 0.00 4.35
7422 13209 0.533308 TTCAAACCGGTGGTTCTCCG 60.533 55.000 8.52 1.92 46.20 4.63
7425 13212 0.399075 AAACCGGTGGTTCTCCGATT 59.601 50.000 8.52 0.00 46.20 3.34
7439 13226 0.940126 CCGATTCAATGCTTCTCCGG 59.060 55.000 0.00 0.00 0.00 5.14
7441 13228 1.382522 GATTCAATGCTTCTCCGGCA 58.617 50.000 0.00 0.00 44.05 5.69
7447 13234 1.033746 ATGCTTCTCCGGCATGTTGG 61.034 55.000 0.00 0.00 46.85 3.77
7449 13236 1.244019 GCTTCTCCGGCATGTTGGTT 61.244 55.000 0.00 0.00 0.00 3.67
7451 13238 0.109532 TTCTCCGGCATGTTGGTTCA 59.890 50.000 0.00 0.00 0.00 3.18
7457 13244 2.296792 CGGCATGTTGGTTCATATGGA 58.703 47.619 2.13 0.00 0.00 3.41
7483 13270 3.170585 GTCGACTTCCCGTTCGCG 61.171 66.667 8.70 0.00 40.93 5.87
7486 13273 2.017783 CGACTTCCCGTTCGCGAAA 61.018 57.895 25.24 4.71 44.71 3.46
7495 13282 1.635663 CGTTCGCGAAAATCCTGCCT 61.636 55.000 25.24 0.00 44.71 4.75
7497 13284 1.922135 TTCGCGAAAATCCTGCCTGC 61.922 55.000 21.14 0.00 0.00 4.85
7498 13285 2.100991 GCGAAAATCCTGCCTGCG 59.899 61.111 0.00 0.00 0.00 5.18
7506 13293 0.179045 ATCCTGCCTGCGGATAACAC 60.179 55.000 11.88 0.00 39.44 3.32
7512 13299 0.806102 CCTGCGGATAACACGGTCAG 60.806 60.000 0.00 0.00 0.00 3.51
7514 13301 1.217244 GCGGATAACACGGTCAGGT 59.783 57.895 0.00 0.00 0.00 4.00
7520 13307 1.466025 TAACACGGTCAGGTCGGCTT 61.466 55.000 0.00 0.00 0.00 4.35
7587 13374 1.603739 GTGTTGGGTTGGCTCCTCC 60.604 63.158 0.00 0.00 0.00 4.30
7590 13377 4.649705 TGGGTTGGCTCCTCCGGA 62.650 66.667 2.93 2.93 37.80 5.14
7592 13379 2.046217 GGTTGGCTCCTCCGGAAC 60.046 66.667 5.23 0.00 37.80 3.62
7598 13385 2.284699 CTCCTCCGGAACCTGGGT 60.285 66.667 5.23 0.00 0.00 4.51
7605 13392 1.279846 TCCGGAACCTGGGTGTAATTC 59.720 52.381 0.00 0.00 0.00 2.17
7616 13403 3.137544 TGGGTGTAATTCTCAACCTGTGT 59.862 43.478 15.54 0.00 42.57 3.72
7630 13417 3.616219 ACCTGTGTTGTGTGTTGTGTAT 58.384 40.909 0.00 0.00 0.00 2.29
7632 13419 3.625313 CCTGTGTTGTGTGTTGTGTATCA 59.375 43.478 0.00 0.00 0.00 2.15
7633 13420 4.275689 CCTGTGTTGTGTGTTGTGTATCAT 59.724 41.667 0.00 0.00 0.00 2.45
7645 13432 5.815222 TGTTGTGTATCATCGGTTATCCTTG 59.185 40.000 0.00 0.00 0.00 3.61
7667 13454 4.407296 TGTTTATTGAGCTGGGGTGTTTTT 59.593 37.500 0.00 0.00 0.00 1.94
7673 13460 0.597377 GCTGGGGTGTTTTTCGCAAG 60.597 55.000 0.00 0.00 0.00 4.01
7696 13483 8.341903 CAAGAAAACAAAAACAACCTCAAAACT 58.658 29.630 0.00 0.00 0.00 2.66
7701 13488 7.646446 ACAAAAACAACCTCAAAACTAACAC 57.354 32.000 0.00 0.00 0.00 3.32
7764 13553 8.279800 CACTCAAACGTGAATCTATTGTGTAAA 58.720 33.333 0.00 0.00 37.06 2.01
7800 13589 6.375736 TCTTCCGTAGCTCCATATGAATCTAG 59.624 42.308 3.65 0.00 0.00 2.43
7864 13656 0.461870 TGTTATGCTAGCCTGCACGG 60.462 55.000 13.29 0.00 46.33 4.94
7919 13711 2.360475 GTGAAGGACTGCCAGGCC 60.360 66.667 9.17 9.17 46.64 5.19
7957 13749 3.790437 CTGCGCCACCTCCCATCT 61.790 66.667 4.18 0.00 0.00 2.90
8032 13824 4.920112 CACGTTCACCGCCCACCA 62.920 66.667 0.00 0.00 41.42 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 252 2.198287 GCCGAGGATACCGTGGCTA 61.198 63.158 15.33 0.00 42.54 3.93
915 1788 4.963276 TTCAGCCATGTAATGCAAGTAC 57.037 40.909 0.00 0.00 44.97 2.73
991 1880 1.885388 CAACAACGACCTGGACGCA 60.885 57.895 18.00 0.00 0.00 5.24
1018 2166 3.071874 TGATCCCTTTGAACGCAGAAT 57.928 42.857 0.00 0.00 0.00 2.40
1552 3195 1.201424 GTACTCCCTCCGTCCCAAAT 58.799 55.000 0.00 0.00 0.00 2.32
1588 3231 8.677300 ACACCAGCAACTCACAATATAAATAAG 58.323 33.333 0.00 0.00 0.00 1.73
1693 3338 6.558775 AGGCAACCATTAGTCCATAGAGATTA 59.441 38.462 0.00 0.00 37.17 1.75
1759 3404 4.019858 TCCTTGAAACCAACACATGAACA 58.980 39.130 0.00 0.00 0.00 3.18
2152 3797 2.037053 CACCACAATGGACGGCAAA 58.963 52.632 0.84 0.00 40.96 3.68
2231 3876 5.724328 TCGATGAAGACTAGTTGATTGCTT 58.276 37.500 0.00 0.00 0.00 3.91
2312 3957 0.250858 TGCACATGGTCCACTTCAGG 60.251 55.000 0.00 0.00 0.00 3.86
2315 3960 0.883833 CCTTGCACATGGTCCACTTC 59.116 55.000 0.00 0.00 0.00 3.01
2499 4145 6.764379 AGAGAAAAACCAAACAAGAACCAAA 58.236 32.000 0.00 0.00 0.00 3.28
2570 4217 2.729882 CGAGTGAACTCCGTTTTCGATT 59.270 45.455 4.90 0.00 43.79 3.34
2705 4373 4.614946 AGCTTGTTGAATTGAGCAAACTC 58.385 39.130 0.00 0.00 43.76 3.01
2706 4374 4.660789 AGCTTGTTGAATTGAGCAAACT 57.339 36.364 0.00 0.00 37.59 2.66
2707 4375 4.805192 TCAAGCTTGTTGAATTGAGCAAAC 59.195 37.500 25.19 0.00 37.59 2.93
2709 4377 4.613944 CTCAAGCTTGTTGAATTGAGCAA 58.386 39.130 25.19 1.02 41.39 3.91
2718 4407 3.698029 GAGCAAACTCAAGCTTGTTGA 57.302 42.857 24.64 9.05 42.04 3.18
2771 4460 2.105766 ACTACCGCTAGGAAACCGAAT 58.894 47.619 0.00 0.00 41.02 3.34
2774 4463 1.066152 GGTACTACCGCTAGGAAACCG 59.934 57.143 0.00 0.00 41.02 4.44
2817 4506 0.320946 TACCGCTTGTAGCACCCAAC 60.321 55.000 0.00 0.00 42.58 3.77
2948 4707 0.103937 ACCGTAAAACCCGACACGAA 59.896 50.000 0.00 0.00 36.53 3.85
2949 4708 0.955178 TACCGTAAAACCCGACACGA 59.045 50.000 0.00 0.00 36.53 4.35
2950 4709 1.059942 GTACCGTAAAACCCGACACG 58.940 55.000 0.00 0.00 0.00 4.49
2951 4710 2.438868 AGTACCGTAAAACCCGACAC 57.561 50.000 0.00 0.00 0.00 3.67
2952 4711 2.094752 GCTAGTACCGTAAAACCCGACA 60.095 50.000 0.00 0.00 0.00 4.35
2953 4712 2.530177 GCTAGTACCGTAAAACCCGAC 58.470 52.381 0.00 0.00 0.00 4.79
2954 4713 1.476488 GGCTAGTACCGTAAAACCCGA 59.524 52.381 0.00 0.00 0.00 5.14
2955 4714 1.926561 GGCTAGTACCGTAAAACCCG 58.073 55.000 0.00 0.00 0.00 5.28
2965 4724 3.834799 ACTGCCGCGGCTAGTACC 61.835 66.667 45.79 20.24 42.51 3.34
2966 4725 2.582498 CACTGCCGCGGCTAGTAC 60.582 66.667 45.79 21.01 42.51 2.73
2967 4726 3.833645 CCACTGCCGCGGCTAGTA 61.834 66.667 45.79 28.16 42.51 1.82
2996 4755 1.942657 GGTACTACCGCATACGAGTGA 59.057 52.381 0.00 0.00 43.93 3.41
3169 4991 5.378985 AGAAGACCTCCTTATATAGTGGGGA 59.621 44.000 6.52 2.42 34.68 4.81
3277 5100 4.923281 CCCTCAAAAACTAGCAAAAATCCG 59.077 41.667 0.00 0.00 0.00 4.18
3283 5106 6.605594 TCTCTTTTCCCTCAAAAACTAGCAAA 59.394 34.615 0.00 0.00 33.40 3.68
3321 5144 4.853924 AGTGATTGGTGAAAATGTGGAC 57.146 40.909 0.00 0.00 0.00 4.02
3331 5154 5.485353 ACATAGAGGAGAAAGTGATTGGTGA 59.515 40.000 0.00 0.00 0.00 4.02
3380 5203 3.202151 AGGAGAACACCAAGAACTCCAAA 59.798 43.478 0.00 0.00 46.43 3.28
3634 5460 4.321156 GCTTTACACCACAATGATTGAGCA 60.321 41.667 12.80 0.00 0.00 4.26
3679 5505 3.531538 GCGATCTCCACAACCTAATTGA 58.468 45.455 0.00 0.00 41.23 2.57
3710 5536 1.501337 GGTCACCGAAACCCGTCAAC 61.501 60.000 0.00 0.00 36.31 3.18
3735 5561 3.482436 CAGTACACTTTGGCAACCCTTA 58.518 45.455 0.00 0.00 0.00 2.69
3755 5581 3.948719 GGGGCGGTCACTGAACCA 61.949 66.667 0.00 0.00 39.43 3.67
3915 5742 2.607635 GCGGATGCTAATCTTCGTTTGA 59.392 45.455 0.00 0.00 38.39 2.69
3922 5749 0.940126 CGCTTGCGGATGCTAATCTT 59.060 50.000 12.76 0.00 43.34 2.40
3940 5767 2.357327 TGTATCCCGAAGTTCACACG 57.643 50.000 3.32 0.00 0.00 4.49
4117 5945 3.181505 TGACAAGCACAAAACCTACAACG 60.182 43.478 0.00 0.00 0.00 4.10
4185 6013 6.861572 GGGTGAATAGGCGCTTTAAAATAATC 59.138 38.462 7.64 0.00 0.00 1.75
4740 7459 1.806247 GCCGATGTCGTTGATGATCCA 60.806 52.381 1.44 0.00 37.74 3.41
4833 7567 2.387757 CAAAGGGGAGAGAGAGAGAGG 58.612 57.143 0.00 0.00 0.00 3.69
5086 7837 0.467844 ACCTGCAGTGCAAACCATGA 60.468 50.000 20.22 0.00 38.41 3.07
6012 8927 4.574013 GCTGACCATCTCTTCAGTTAATGG 59.426 45.833 0.00 0.00 41.24 3.16
6297 9300 4.262292 GGACAACCTGTACACACTCATACA 60.262 45.833 0.00 0.00 29.61 2.29
6335 9339 2.679837 CACAATCCAGCGAGTTTGCTAT 59.320 45.455 0.00 0.00 45.23 2.97
6459 9475 6.644248 TCAAATGCTCCATGAATCATAAGG 57.356 37.500 0.00 0.00 0.00 2.69
6579 9758 8.896320 GGTTTTATACCATGAAAACAAAGGTT 57.104 30.769 17.35 0.00 46.92 3.50
6599 9778 4.535526 AAAGTTGACAGCAGTTGGTTTT 57.464 36.364 0.00 0.00 0.00 2.43
6924 12546 8.655970 CGATAGTACAACACATTTGAAGAATGA 58.344 33.333 5.82 0.00 0.00 2.57
6996 12711 2.591571 TCGGAGCAAGACATCATCAG 57.408 50.000 0.00 0.00 0.00 2.90
7066 12853 4.591498 TGGTGAAGTTAGTAGAAAGCCAGA 59.409 41.667 0.00 0.00 0.00 3.86
7096 12883 3.078837 GGTTTCAACGATGTACCCATGT 58.921 45.455 7.98 0.00 0.00 3.21
7103 12890 2.406130 GGTGTCGGTTTCAACGATGTA 58.594 47.619 0.00 0.00 42.82 2.29
7167 12954 1.145377 ATATCCACCAACGACCGCC 59.855 57.895 0.00 0.00 0.00 6.13
7168 12955 1.157870 CCATATCCACCAACGACCGC 61.158 60.000 0.00 0.00 0.00 5.68
7173 12960 1.942657 CTGCTTCCATATCCACCAACG 59.057 52.381 0.00 0.00 0.00 4.10
7177 12964 2.736670 AACCTGCTTCCATATCCACC 57.263 50.000 0.00 0.00 0.00 4.61
7220 13007 1.529010 CCAAGCACAAGGCCACTGA 60.529 57.895 5.01 0.00 46.50 3.41
7224 13011 0.177604 CAAAACCAAGCACAAGGCCA 59.822 50.000 5.01 0.00 46.50 5.36
7234 13021 3.214328 ACTACCAGAGCACAAAACCAAG 58.786 45.455 0.00 0.00 0.00 3.61
7279 13066 3.618780 AAGCTCCAAGGCTCGGCAG 62.619 63.158 0.00 0.00 42.24 4.85
7283 13070 0.532573 TGTAGAAGCTCCAAGGCTCG 59.467 55.000 0.00 0.00 42.24 5.03
7334 13121 3.259374 AGACTTGACCACTCACCAGTATG 59.741 47.826 0.00 0.00 0.00 2.39
7340 13127 1.669211 GCGTAGACTTGACCACTCACC 60.669 57.143 0.00 0.00 0.00 4.02
7344 13131 0.603569 CTGGCGTAGACTTGACCACT 59.396 55.000 0.00 0.00 34.59 4.00
7350 13137 3.600388 AGGAAAATCTGGCGTAGACTTG 58.400 45.455 0.00 0.00 38.49 3.16
7352 13139 2.168728 GGAGGAAAATCTGGCGTAGACT 59.831 50.000 0.00 0.00 38.49 3.24
7353 13140 2.552031 GGAGGAAAATCTGGCGTAGAC 58.448 52.381 0.00 0.00 38.49 2.59
7355 13142 1.486726 AGGGAGGAAAATCTGGCGTAG 59.513 52.381 0.00 0.00 0.00 3.51
7356 13143 1.485066 GAGGGAGGAAAATCTGGCGTA 59.515 52.381 0.00 0.00 0.00 4.42
7363 13150 1.744114 GCGACAGGAGGGAGGAAAATC 60.744 57.143 0.00 0.00 0.00 2.17
7382 13169 3.474570 ATCACCTCTCTGGCCGGC 61.475 66.667 21.18 21.18 40.22 6.13
7388 13175 3.190118 GGTTTGAAAGCATCACCTCTCTG 59.810 47.826 1.74 0.00 37.92 3.35
7422 13209 1.382522 TGCCGGAGAAGCATTGAATC 58.617 50.000 5.05 0.00 34.69 2.52
7439 13226 3.023119 TGGTCCATATGAACCAACATGC 58.977 45.455 11.99 0.00 0.00 4.06
7441 13228 5.332743 ACTTTGGTCCATATGAACCAACAT 58.667 37.500 24.63 13.61 41.35 2.71
7442 13229 4.735369 ACTTTGGTCCATATGAACCAACA 58.265 39.130 24.63 14.98 41.35 3.33
7447 13234 4.693566 TCGACAACTTTGGTCCATATGAAC 59.306 41.667 3.65 0.00 31.55 3.18
7449 13236 4.020573 AGTCGACAACTTTGGTCCATATGA 60.021 41.667 19.50 0.00 33.03 2.15
7451 13238 4.553330 AGTCGACAACTTTGGTCCATAT 57.447 40.909 19.50 0.00 33.03 1.78
7476 13263 1.226018 GGCAGGATTTTCGCGAACG 60.226 57.895 23.33 7.09 42.01 3.95
7495 13282 1.216977 CCTGACCGTGTTATCCGCA 59.783 57.895 0.00 0.00 0.00 5.69
7497 13284 0.524816 CGACCTGACCGTGTTATCCG 60.525 60.000 0.00 0.00 0.00 4.18
7498 13285 0.179119 CCGACCTGACCGTGTTATCC 60.179 60.000 0.00 0.00 0.00 2.59
7561 13348 1.407936 CCAACCCAACACATCCACAA 58.592 50.000 0.00 0.00 0.00 3.33
7562 13349 1.112315 GCCAACCCAACACATCCACA 61.112 55.000 0.00 0.00 0.00 4.17
7567 13354 0.251341 GAGGAGCCAACCCAACACAT 60.251 55.000 0.00 0.00 0.00 3.21
7587 13374 2.027561 TGAGAATTACACCCAGGTTCCG 60.028 50.000 0.00 0.00 0.00 4.30
7590 13377 3.397955 AGGTTGAGAATTACACCCAGGTT 59.602 43.478 0.00 0.00 0.00 3.50
7592 13379 3.244911 ACAGGTTGAGAATTACACCCAGG 60.245 47.826 2.59 0.00 0.00 4.45
7616 13403 3.734463 ACCGATGATACACAACACACAA 58.266 40.909 0.00 0.00 0.00 3.33
7630 13417 6.260050 GCTCAATAAACAAGGATAACCGATGA 59.740 38.462 5.15 0.00 41.83 2.92
7632 13419 6.260936 CAGCTCAATAAACAAGGATAACCGAT 59.739 38.462 0.00 0.00 41.83 4.18
7633 13420 5.584649 CAGCTCAATAAACAAGGATAACCGA 59.415 40.000 0.00 0.00 41.83 4.69
7645 13432 4.600692 AAAACACCCCAGCTCAATAAAC 57.399 40.909 0.00 0.00 0.00 2.01
7667 13454 4.561105 AGGTTGTTTTTGTTTTCTTGCGA 58.439 34.783 0.00 0.00 0.00 5.10
7673 13460 9.588774 GTTAGTTTTGAGGTTGTTTTTGTTTTC 57.411 29.630 0.00 0.00 0.00 2.29
7674 13461 9.110502 TGTTAGTTTTGAGGTTGTTTTTGTTTT 57.889 25.926 0.00 0.00 0.00 2.43
7675 13462 8.552865 GTGTTAGTTTTGAGGTTGTTTTTGTTT 58.447 29.630 0.00 0.00 0.00 2.83
7676 13463 7.929245 AGTGTTAGTTTTGAGGTTGTTTTTGTT 59.071 29.630 0.00 0.00 0.00 2.83
7677 13464 7.383843 CAGTGTTAGTTTTGAGGTTGTTTTTGT 59.616 33.333 0.00 0.00 0.00 2.83
7678 13465 7.383843 ACAGTGTTAGTTTTGAGGTTGTTTTTG 59.616 33.333 0.00 0.00 0.00 2.44
7679 13466 7.438564 ACAGTGTTAGTTTTGAGGTTGTTTTT 58.561 30.769 0.00 0.00 0.00 1.94
7684 13471 5.811399 TGACAGTGTTAGTTTTGAGGTTG 57.189 39.130 0.00 0.00 0.00 3.77
7764 13553 3.006967 AGCTACGGAAGAACACACAAGAT 59.993 43.478 0.00 0.00 0.00 2.40
7919 13711 1.070445 GGAGATCGACATGGGCCTG 59.930 63.158 4.53 3.00 0.00 4.85
7967 13759 2.419297 GGATTTGTCTCGCCTCATGACT 60.419 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.