Multiple sequence alignment - TraesCS7D01G470900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G470900 chr7D 100.000 2447 0 0 1 2447 584276343 584278789 0.000000e+00 4519.0
1 TraesCS7D01G470900 chr7D 100.000 2242 0 0 2775 5016 584279117 584281358 0.000000e+00 4141.0
2 TraesCS7D01G470900 chr7D 90.086 1503 106 11 2 1472 584218523 584217032 0.000000e+00 1910.0
3 TraesCS7D01G470900 chr7D 89.059 1572 128 12 1 1541 584604502 584602944 0.000000e+00 1910.0
4 TraesCS7D01G470900 chr7D 91.488 1351 98 9 503 1849 582603355 582602018 0.000000e+00 1842.0
5 TraesCS7D01G470900 chr7D 91.774 1325 90 10 503 1821 582680126 582678815 0.000000e+00 1825.0
6 TraesCS7D01G470900 chr7D 92.321 599 34 5 1852 2447 582678729 582678140 0.000000e+00 841.0
7 TraesCS7D01G470900 chr7D 91.987 599 36 5 1852 2447 582601514 582600925 0.000000e+00 830.0
8 TraesCS7D01G470900 chr7D 93.060 562 38 1 1288 1849 583034546 583033986 0.000000e+00 821.0
9 TraesCS7D01G470900 chr7D 91.304 598 46 3 1852 2447 586107535 586108128 0.000000e+00 811.0
10 TraesCS7D01G470900 chr7D 91.152 599 45 5 1852 2447 586024636 586025229 0.000000e+00 806.0
11 TraesCS7D01G470900 chr7D 90.970 598 48 3 1852 2447 586120034 586120627 0.000000e+00 800.0
12 TraesCS7D01G470900 chr7D 89.901 604 60 1 3776 4378 584590734 584590131 0.000000e+00 776.0
13 TraesCS7D01G470900 chr7D 88.988 563 42 12 4392 4941 234094259 234094814 0.000000e+00 678.0
14 TraesCS7D01G470900 chr7D 91.264 435 33 3 2775 3206 583033633 583033201 5.590000e-164 588.0
15 TraesCS7D01G470900 chr7D 89.631 434 34 8 2775 3206 582600832 582600408 4.420000e-150 542.0
16 TraesCS7D01G470900 chr7D 89.220 436 35 8 2775 3206 582678047 582677620 7.390000e-148 534.0
17 TraesCS7D01G470900 chr7D 85.305 279 40 1 4054 4331 425263528 425263250 2.290000e-73 287.0
18 TraesCS7D01G470900 chr7D 96.629 89 3 0 4928 5016 79517414 79517326 1.130000e-31 148.0
19 TraesCS7D01G470900 chr7D 97.222 72 2 0 3445 3516 582600102 582600031 6.820000e-24 122.0
20 TraesCS7D01G470900 chr7D 93.671 79 4 1 3438 3516 583033207 583033130 3.170000e-22 117.0
21 TraesCS7D01G470900 chr2D 88.901 1829 127 24 1 1798 107839096 107837313 0.000000e+00 2183.0
22 TraesCS7D01G470900 chr2D 90.833 600 45 6 1852 2447 107837168 107836575 0.000000e+00 795.0
23 TraesCS7D01G470900 chr2D 88.414 561 44 13 4392 4938 521590854 521591407 0.000000e+00 656.0
24 TraesCS7D01G470900 chr2D 85.192 574 59 23 4389 4947 605557551 605558113 2.620000e-157 566.0
25 TraesCS7D01G470900 chr2D 84.672 548 53 20 4379 4909 433497825 433498358 7.440000e-143 518.0
26 TraesCS7D01G470900 chr2D 92.531 241 18 0 3203 3443 378729165 378729405 3.720000e-91 346.0
27 TraesCS7D01G470900 chr2D 90.698 129 11 1 3544 3672 107834888 107834761 2.400000e-38 171.0
28 TraesCS7D01G470900 chr2D 95.556 90 4 0 4927 5016 73498617 73498706 1.460000e-30 145.0
29 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577354597 577354686 6.770000e-29 139.0
30 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577358862 577358951 6.770000e-29 139.0
31 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577363138 577363227 6.770000e-29 139.0
32 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577367415 577367504 6.770000e-29 139.0
33 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577371689 577371778 6.770000e-29 139.0
34 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577757996 577757907 6.770000e-29 139.0
35 TraesCS7D01G470900 chr2D 94.505 91 4 1 4926 5016 577762271 577762182 6.770000e-29 139.0
36 TraesCS7D01G470900 chr7B 88.488 1859 139 29 1 1798 708677347 708675503 0.000000e+00 2178.0
37 TraesCS7D01G470900 chr7B 89.462 1338 104 11 1 1310 652402758 652401430 0.000000e+00 1655.0
38 TraesCS7D01G470900 chr7B 89.222 1336 108 10 1 1308 652440994 652439667 0.000000e+00 1637.0
39 TraesCS7D01G470900 chr7B 91.189 1135 86 8 716 1849 652175107 652173986 0.000000e+00 1530.0
40 TraesCS7D01G470900 chr7B 88.281 1297 106 16 43 1318 651874116 651872845 0.000000e+00 1511.0
41 TraesCS7D01G470900 chr7B 89.935 1073 97 10 780 1849 652061227 652060163 0.000000e+00 1373.0
42 TraesCS7D01G470900 chr7B 90.816 882 62 11 445 1318 652256004 652255134 0.000000e+00 1162.0
43 TraesCS7D01G470900 chr7B 90.046 874 75 5 445 1310 652975263 652974394 0.000000e+00 1122.0
44 TraesCS7D01G470900 chr7B 88.023 860 74 8 1 839 656300375 656301226 0.000000e+00 990.0
45 TraesCS7D01G470900 chr7B 88.179 829 68 10 34 839 722090945 722090124 0.000000e+00 961.0
46 TraesCS7D01G470900 chr7B 89.276 718 68 7 3670 4382 652971809 652971096 0.000000e+00 891.0
47 TraesCS7D01G470900 chr7B 89.201 713 68 7 3670 4377 652437033 652436325 0.000000e+00 881.0
48 TraesCS7D01G470900 chr7B 88.982 717 69 8 3670 4381 652398840 652398129 0.000000e+00 878.0
49 TraesCS7D01G470900 chr7B 89.047 703 72 3 3692 4392 652254767 652254068 0.000000e+00 867.0
50 TraesCS7D01G470900 chr7B 92.642 598 38 3 1852 2447 656302479 656303072 0.000000e+00 856.0
51 TraesCS7D01G470900 chr7B 91.514 601 38 8 1852 2447 652057815 652057223 0.000000e+00 815.0
52 TraesCS7D01G470900 chr7B 91.231 593 45 5 1857 2447 652400755 652400168 0.000000e+00 800.0
53 TraesCS7D01G470900 chr7B 91.231 593 45 5 1857 2447 652438940 652438353 0.000000e+00 800.0
54 TraesCS7D01G470900 chr7B 90.970 598 45 4 1852 2447 708675262 708674672 0.000000e+00 797.0
55 TraesCS7D01G470900 chr7B 91.062 593 46 4 1857 2447 652973734 652973147 0.000000e+00 795.0
56 TraesCS7D01G470900 chr7B 89.172 628 51 8 847 1472 722089966 722089354 0.000000e+00 767.0
57 TraesCS7D01G470900 chr7B 88.103 580 50 11 847 1422 656301384 656301948 0.000000e+00 671.0
58 TraesCS7D01G470900 chr7B 85.275 618 52 17 1 586 652175761 652175151 7.190000e-168 601.0
59 TraesCS7D01G470900 chr7B 88.506 435 42 5 2775 3206 652973054 652972625 2.070000e-143 520.0
60 TraesCS7D01G470900 chr7B 87.356 435 38 9 2775 3206 652400075 652399655 2.720000e-132 483.0
61 TraesCS7D01G470900 chr7B 89.059 393 36 4 3670 4058 651872246 651871857 9.770000e-132 481.0
62 TraesCS7D01G470900 chr7B 87.273 440 33 11 2008 2447 652173502 652173086 9.770000e-132 481.0
63 TraesCS7D01G470900 chr7B 91.036 357 22 3 1500 1849 656301982 656302335 1.630000e-129 473.0
64 TraesCS7D01G470900 chr7B 87.436 390 45 2 3670 4058 652167040 652166654 3.560000e-121 446.0
65 TraesCS7D01G470900 chr7B 91.205 307 23 4 1540 1844 652401201 652400897 1.000000e-111 414.0
66 TraesCS7D01G470900 chr7B 86.559 372 35 7 54 410 652975919 652975548 3.640000e-106 396.0
67 TraesCS7D01G470900 chr7B 89.968 309 23 6 1540 1844 652439386 652439082 4.710000e-105 392.0
68 TraesCS7D01G470900 chr7B 87.324 355 25 11 1500 1848 722089356 722089016 6.090000e-104 388.0
69 TraesCS7D01G470900 chr7B 90.406 271 22 4 1540 1808 652974115 652973847 2.220000e-93 353.0
70 TraesCS7D01G470900 chr7B 83.293 413 30 16 1 408 653003337 653002959 1.340000e-90 344.0
71 TraesCS7D01G470900 chr7B 81.099 455 33 22 1 442 652256530 652256116 1.050000e-81 315.0
72 TraesCS7D01G470900 chr7B 90.000 160 16 0 1852 2011 722088825 722088666 1.830000e-49 207.0
73 TraesCS7D01G470900 chr7B 91.200 125 11 0 3544 3668 652053501 652053377 2.400000e-38 171.0
74 TraesCS7D01G470900 chr7B 88.189 127 15 0 3545 3671 708673444 708673318 8.700000e-33 152.0
75 TraesCS7D01G470900 chr7B 91.346 104 9 0 1438 1541 652439650 652439547 5.230000e-30 143.0
76 TraesCS7D01G470900 chr7B 91.346 104 9 0 1438 1541 652974379 652974276 5.230000e-30 143.0
77 TraesCS7D01G470900 chr7B 95.652 46 2 0 4347 4392 652254041 652253996 1.940000e-09 75.0
78 TraesCS7D01G470900 chr7B 93.333 45 3 0 3499 3543 195707247 195707291 3.240000e-07 67.6
79 TraesCS7D01G470900 chr7B 93.333 45 3 0 3499 3543 667983673 667983717 3.240000e-07 67.6
80 TraesCS7D01G470900 chr7B 93.333 45 3 0 3499 3543 670047160 670047204 3.240000e-07 67.6
81 TraesCS7D01G470900 chr7B 96.774 31 1 0 1 31 656298464 656298434 9.000000e-03 52.8
82 TraesCS7D01G470900 chr7A 90.889 1350 104 12 503 1849 674683474 674682141 0.000000e+00 1794.0
83 TraesCS7D01G470900 chr7A 89.306 1253 92 15 1 1223 675870493 675871733 0.000000e+00 1533.0
84 TraesCS7D01G470900 chr7A 89.526 907 62 10 344 1223 675907782 675908682 0.000000e+00 1118.0
85 TraesCS7D01G470900 chr7A 88.323 942 68 18 1 917 708496303 708495379 0.000000e+00 1092.0
86 TraesCS7D01G470900 chr7A 86.279 860 72 15 1 839 677611172 677612006 0.000000e+00 893.0
87 TraesCS7D01G470900 chr7A 91.653 599 43 4 1852 2447 674681957 674681363 0.000000e+00 822.0
88 TraesCS7D01G470900 chr7A 91.400 593 45 3 1852 2442 677441293 677441881 0.000000e+00 808.0
89 TraesCS7D01G470900 chr7A 91.525 531 39 3 1852 2380 677614613 677615139 0.000000e+00 726.0
90 TraesCS7D01G470900 chr7A 90.293 546 43 6 1852 2391 675871799 675872340 0.000000e+00 706.0
91 TraesCS7D01G470900 chr7A 87.629 582 47 5 904 1476 708495356 708494791 0.000000e+00 652.0
92 TraesCS7D01G470900 chr7A 90.805 435 31 6 2775 3206 675874313 675874741 1.570000e-159 573.0
93 TraesCS7D01G470900 chr7A 90.575 435 32 6 2775 3206 675912188 675912616 7.290000e-158 568.0
94 TraesCS7D01G470900 chr7A 90.323 434 34 5 2775 3206 674681270 674680843 3.390000e-156 562.0
95 TraesCS7D01G470900 chr7A 88.969 417 30 6 1 406 675907369 675907780 7.500000e-138 501.0
96 TraesCS7D01G470900 chr7A 88.249 417 35 6 1 410 676975995 676976404 2.100000e-133 486.0
97 TraesCS7D01G470900 chr7A 87.981 416 40 3 1 410 676974696 676975107 2.720000e-132 483.0
98 TraesCS7D01G470900 chr7A 87.949 390 43 3 3670 4058 675875530 675875916 1.650000e-124 457.0
99 TraesCS7D01G470900 chr7A 87.949 390 43 3 3670 4058 675913405 675913791 1.650000e-124 457.0
100 TraesCS7D01G470900 chr7A 87.949 390 43 2 3670 4058 677446782 677447168 1.650000e-124 457.0
101 TraesCS7D01G470900 chr7A 89.859 355 22 6 1500 1849 676993112 676993457 1.280000e-120 444.0
102 TraesCS7D01G470900 chr7A 88.202 356 27 7 1500 1849 677440811 677441157 1.300000e-110 411.0
103 TraesCS7D01G470900 chr7A 89.157 249 26 1 3202 3450 427281585 427281338 4.880000e-80 309.0
104 TraesCS7D01G470900 chr7A 89.922 129 13 0 3544 3672 675875220 675875348 3.110000e-37 167.0
105 TraesCS7D01G470900 chr7A 89.922 129 13 0 3544 3672 675913095 675913223 3.110000e-37 167.0
106 TraesCS7D01G470900 chr7A 85.606 132 19 0 3544 3675 674680336 674680205 6.770000e-29 139.0
107 TraesCS7D01G470900 chr7A 93.671 79 4 1 3438 3516 675874735 675874812 3.170000e-22 117.0
108 TraesCS7D01G470900 chr7A 86.139 101 10 4 3417 3515 637058984 637059082 6.870000e-19 106.0
109 TraesCS7D01G470900 chr7A 89.831 59 6 0 2389 2447 677615739 677615797 5.380000e-10 76.8
110 TraesCS7D01G470900 chr5D 91.747 521 31 11 4426 4941 412969372 412968859 0.000000e+00 713.0
111 TraesCS7D01G470900 chr5D 87.922 563 49 10 4391 4941 287742060 287741505 0.000000e+00 645.0
112 TraesCS7D01G470900 chr5D 91.286 241 21 0 3203 3443 533280930 533281170 3.740000e-86 329.0
113 TraesCS7D01G470900 chr5D 88.341 223 19 3 29 245 51685068 51685289 1.390000e-65 261.0
114 TraesCS7D01G470900 chr5D 87.391 230 24 1 32 256 450172869 450172640 4.980000e-65 259.0
115 TraesCS7D01G470900 chr5D 85.897 234 28 1 29 257 501176255 501176488 1.390000e-60 244.0
116 TraesCS7D01G470900 chr5D 85.185 243 29 3 35 271 277544753 277544512 5.020000e-60 243.0
117 TraesCS7D01G470900 chr5D 91.304 46 4 0 3498 3543 162578240 162578195 4.190000e-06 63.9
118 TraesCS7D01G470900 chr4D 89.840 561 39 10 4392 4941 380952451 380951898 0.000000e+00 704.0
119 TraesCS7D01G470900 chr4D 89.122 524 43 9 4426 4941 3513388 3512871 1.520000e-179 640.0
120 TraesCS7D01G470900 chr4D 87.170 530 52 7 4389 4907 50137545 50138069 5.590000e-164 588.0
121 TraesCS7D01G470900 chr4D 85.891 567 59 14 4392 4950 450485874 450485321 7.240000e-163 584.0
122 TraesCS7D01G470900 chr4D 87.446 231 23 2 32 256 105123121 105122891 1.390000e-65 261.0
123 TraesCS7D01G470900 chr4D 87.281 228 24 1 35 257 478255362 478255135 6.440000e-64 255.0
124 TraesCS7D01G470900 chr4D 85.833 240 28 4 29 263 168061562 168061800 3.000000e-62 250.0
125 TraesCS7D01G470900 chr4D 86.784 227 25 1 35 256 37936724 37936498 1.080000e-61 248.0
126 TraesCS7D01G470900 chr4D 85.106 235 30 1 29 258 203010767 203011001 8.400000e-58 235.0
127 TraesCS7D01G470900 chr4D 84.236 203 26 2 32 228 335353053 335353255 5.120000e-45 193.0
128 TraesCS7D01G470900 chr4D 80.473 169 27 2 88 251 484556426 484556593 1.900000e-24 124.0
129 TraesCS7D01G470900 chr4D 75.845 207 32 10 32 228 54396083 54395885 6.920000e-14 89.8
130 TraesCS7D01G470900 chr4D 83.871 93 9 6 33 121 331446433 331446523 3.220000e-12 84.2
131 TraesCS7D01G470900 chr4D 89.552 67 6 1 29 94 468268652 468268718 3.220000e-12 84.2
132 TraesCS7D01G470900 chr4D 100.000 33 0 0 3511 3543 287338030 287337998 1.510000e-05 62.1
133 TraesCS7D01G470900 chr4D 91.111 45 3 1 3499 3543 146390281 146390324 5.420000e-05 60.2
134 TraesCS7D01G470900 chr4D 91.111 45 3 1 3499 3543 149659309 149659266 5.420000e-05 60.2
135 TraesCS7D01G470900 chr4D 91.111 45 3 1 3499 3543 180028464 180028421 5.420000e-05 60.2
136 TraesCS7D01G470900 chr4D 91.111 45 3 1 3499 3543 284714229 284714186 5.420000e-05 60.2
137 TraesCS7D01G470900 chr4D 92.683 41 3 0 3499 3539 285688021 285688061 5.420000e-05 60.2
138 TraesCS7D01G470900 chr4D 87.755 49 4 1 3499 3545 87667297 87667249 7.020000e-04 56.5
139 TraesCS7D01G470900 chr4A 88.571 525 37 14 4428 4941 675129357 675128845 2.570000e-172 616.0
140 TraesCS7D01G470900 chr4A 87.179 234 24 2 29 257 159363488 159363720 1.390000e-65 261.0
141 TraesCS7D01G470900 chr6B 86.988 561 52 14 4392 4941 635409561 635409011 3.320000e-171 612.0
142 TraesCS7D01G470900 chr6B 85.451 543 46 22 4388 4907 293096799 293096267 7.390000e-148 534.0
143 TraesCS7D01G470900 chr6B 91.736 242 20 0 3202 3443 672097456 672097697 2.240000e-88 337.0
144 TraesCS7D01G470900 chr6B 87.556 225 27 1 35 258 276733567 276733343 4.980000e-65 259.0
145 TraesCS7D01G470900 chr6B 86.638 232 25 3 32 258 488850638 488850868 8.340000e-63 252.0
146 TraesCS7D01G470900 chr1D 86.542 535 54 15 4392 4917 312950536 312950011 1.570000e-159 573.0
147 TraesCS7D01G470900 chr1D 86.920 237 24 3 29 260 351265337 351265571 4.980000e-65 259.0
148 TraesCS7D01G470900 chr1D 86.175 217 25 1 29 240 418715090 418715306 3.910000e-56 230.0
149 TraesCS7D01G470900 chr1D 83.682 239 33 2 29 261 244246781 244247019 2.350000e-53 220.0
150 TraesCS7D01G470900 chr3A 86.278 532 48 14 4388 4905 563520049 563520569 5.670000e-154 555.0
151 TraesCS7D01G470900 chr2B 86.252 531 49 12 4390 4907 140586194 140585675 5.670000e-154 555.0
152 TraesCS7D01G470900 chr2B 84.982 546 60 13 4390 4920 281803029 281802491 7.390000e-148 534.0
153 TraesCS7D01G470900 chr2B 93.671 79 4 1 3438 3516 646109639 646109716 3.170000e-22 117.0
154 TraesCS7D01G470900 chr3D 85.714 511 51 16 4389 4886 339007236 339007737 2.070000e-143 520.0
155 TraesCS7D01G470900 chr3D 86.331 278 33 5 4058 4331 177335478 177335202 1.060000e-76 298.0
156 TraesCS7D01G470900 chr5A 82.941 510 71 12 3014 3515 69321059 69320558 3.560000e-121 446.0
157 TraesCS7D01G470900 chr3B 91.165 249 20 2 3203 3450 225815442 225815195 2.240000e-88 337.0
158 TraesCS7D01G470900 chr3B 91.165 249 20 2 3203 3450 225829641 225829394 2.240000e-88 337.0
159 TraesCS7D01G470900 chr3B 91.165 249 20 2 3203 3450 225865841 225865594 2.240000e-88 337.0
160 TraesCS7D01G470900 chr3B 91.429 245 20 1 3199 3443 25288312 25288069 8.050000e-88 335.0
161 TraesCS7D01G470900 chr3B 87.129 101 11 2 3416 3515 612811019 612810920 4.100000e-21 113.0
162 TraesCS7D01G470900 chr3B 89.011 91 7 2 3438 3528 520760336 520760249 5.310000e-20 110.0
163 TraesCS7D01G470900 chr3B 93.478 46 3 0 3498 3543 78845875 78845830 9.010000e-08 69.4
164 TraesCS7D01G470900 chr4B 91.286 241 21 0 3203 3443 17341556 17341316 3.740000e-86 329.0
165 TraesCS7D01G470900 chr4B 84.746 236 28 4 29 258 558221995 558222228 3.910000e-56 230.0
166 TraesCS7D01G470900 chr4B 84.211 228 31 1 35 257 404566308 404566081 3.040000e-52 217.0
167 TraesCS7D01G470900 chr4B 84.753 223 24 5 35 251 122852189 122851971 1.090000e-51 215.0
168 TraesCS7D01G470900 chr4B 83.122 237 29 7 30 257 51868192 51868426 6.580000e-49 206.0
169 TraesCS7D01G470900 chr4B 95.556 45 2 0 3499 3543 83996659 83996703 6.970000e-09 73.1
170 TraesCS7D01G470900 chr4B 95.455 44 2 0 3500 3543 655843808 655843765 2.510000e-08 71.3
171 TraesCS7D01G470900 chr4B 93.333 45 3 0 3499 3543 415048441 415048397 3.240000e-07 67.6
172 TraesCS7D01G470900 chr6A 88.417 259 25 5 3200 3455 585171235 585170979 1.750000e-79 307.0
173 TraesCS7D01G470900 chr6A 88.417 259 25 5 3200 3455 585183363 585183107 1.750000e-79 307.0
174 TraesCS7D01G470900 chr6A 86.344 227 26 1 35 256 80727523 80727297 5.020000e-60 243.0
175 TraesCS7D01G470900 chr6A 86.026 229 27 1 35 258 290614217 290613989 1.800000e-59 241.0
176 TraesCS7D01G470900 chr6A 85.217 230 29 1 29 253 576392159 576392388 1.090000e-56 231.0
177 TraesCS7D01G470900 chr6A 85.153 229 29 1 35 258 617178712 617178484 3.910000e-56 230.0
178 TraesCS7D01G470900 chr6A 93.333 45 3 0 3499 3543 466488021 466487977 3.240000e-07 67.6
179 TraesCS7D01G470900 chr6D 88.800 250 26 2 3200 3448 13155567 13155319 6.310000e-79 305.0
180 TraesCS7D01G470900 chr6D 85.455 275 39 1 4058 4331 411871247 411871521 8.220000e-73 285.0
181 TraesCS7D01G470900 chr6D 84.746 236 27 6 29 258 14982393 14982625 1.400000e-55 228.0
182 TraesCS7D01G470900 chr6D 83.830 235 32 2 29 258 16776104 16776337 8.450000e-53 219.0
183 TraesCS7D01G470900 chr1B 87.597 258 29 3 3203 3459 564921564 564921819 3.800000e-76 296.0
184 TraesCS7D01G470900 chr1B 85.818 275 38 1 4058 4331 553972220 553971946 1.770000e-74 291.0
185 TraesCS7D01G470900 chr1B 87.255 102 9 4 3416 3515 309119891 309119990 4.100000e-21 113.0
186 TraesCS7D01G470900 chr1B 95.556 45 2 0 3499 3543 42929637 42929681 6.970000e-09 73.1
187 TraesCS7D01G470900 chr1B 95.556 45 2 0 3499 3543 364058328 364058284 6.970000e-09 73.1
188 TraesCS7D01G470900 chr1A 86.404 228 26 1 35 257 31856646 31856419 1.390000e-60 244.0
189 TraesCS7D01G470900 chr1A 86.404 228 26 1 35 257 495491871 495491644 1.390000e-60 244.0
190 TraesCS7D01G470900 chr1A 85.714 231 26 3 29 253 234813206 234813435 2.330000e-58 237.0
191 TraesCS7D01G470900 chr1A 100.000 33 0 0 3511 3543 449661869 449661837 1.510000e-05 62.1
192 TraesCS7D01G470900 chr1A 91.111 45 3 1 3499 3543 136794968 136794925 5.420000e-05 60.2
193 TraesCS7D01G470900 chrUn 89.119 193 16 3 35 222 336901300 336901108 8.400000e-58 235.0
194 TraesCS7D01G470900 chrUn 73.729 236 44 13 33 256 18273879 18273650 5.380000e-10 76.8
195 TraesCS7D01G470900 chrUn 73.729 236 44 13 33 256 18278268 18278039 5.380000e-10 76.8
196 TraesCS7D01G470900 chrUn 87.692 65 8 0 29 93 335108232 335108296 5.380000e-10 76.8
197 TraesCS7D01G470900 chrUn 73.729 236 44 13 33 256 338876569 338876340 5.380000e-10 76.8
198 TraesCS7D01G470900 chrUn 74.528 212 33 12 29 228 1714375 1714577 6.970000e-09 73.1
199 TraesCS7D01G470900 chrUn 74.641 209 32 13 32 228 255004657 255004458 6.970000e-09 73.1
200 TraesCS7D01G470900 chrUn 87.719 57 4 3 19 74 434742487 434742541 4.190000e-06 63.9
201 TraesCS7D01G470900 chrUn 91.111 45 3 1 3499 3543 21858695 21858652 5.420000e-05 60.2
202 TraesCS7D01G470900 chrUn 94.737 38 2 0 40 77 221735173 221735136 5.420000e-05 60.2
203 TraesCS7D01G470900 chrUn 72.609 230 45 12 40 257 224516258 224516035 5.420000e-05 60.2
204 TraesCS7D01G470900 chrUn 97.059 34 1 0 3510 3543 31198948 31198981 1.950000e-04 58.4


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 TraesCS7D01G470900 chr7D 584276343 584281358 5015 False 4330.000000 4519 100.000000 1 5016 2 chr7D.!!$F5 5015
1 TraesCS7D01G470900 chr7D 584217032 584218523 1491 True 1910.000000 1910 90.086000 2 1472 1 chr7D.!!$R3 1470
2 TraesCS7D01G470900 chr7D 584602944 584604502 1558 True 1910.000000 1910 89.059000 1 1541 1 chr7D.!!$R5 1540
3 TraesCS7D01G470900 chr7D 582677620 582680126 2506 True 1066.666667 1825 91.105000 503 3206 3 chr7D.!!$R7 2703
4 TraesCS7D01G470900 chr7D 582600031 582603355 3324 True 834.000000 1842 92.582000 503 3516 4 chr7D.!!$R6 3013
5 TraesCS7D01G470900 chr7D 586107535 586108128 593 False 811.000000 811 91.304000 1852 2447 1 chr7D.!!$F3 595
6 TraesCS7D01G470900 chr7D 586024636 586025229 593 False 806.000000 806 91.152000 1852 2447 1 chr7D.!!$F2 595
7 TraesCS7D01G470900 chr7D 586120034 586120627 593 False 800.000000 800 90.970000 1852 2447 1 chr7D.!!$F4 595
8 TraesCS7D01G470900 chr7D 584590131 584590734 603 True 776.000000 776 89.901000 3776 4378 1 chr7D.!!$R4 602
9 TraesCS7D01G470900 chr7D 234094259 234094814 555 False 678.000000 678 88.988000 4392 4941 1 chr7D.!!$F1 549
10 TraesCS7D01G470900 chr7D 583033130 583034546 1416 True 508.666667 821 92.665000 1288 3516 3 chr7D.!!$R8 2228
11 TraesCS7D01G470900 chr2D 107834761 107839096 4335 True 1049.666667 2183 90.144000 1 3672 3 chr2D.!!$R3 3671
12 TraesCS7D01G470900 chr2D 521590854 521591407 553 False 656.000000 656 88.414000 4392 4938 1 chr2D.!!$F4 546
13 TraesCS7D01G470900 chr2D 605557551 605558113 562 False 566.000000 566 85.192000 4389 4947 1 chr2D.!!$F10 558
14 TraesCS7D01G470900 chr2D 433497825 433498358 533 False 518.000000 518 84.672000 4379 4909 1 chr2D.!!$F3 530
15 TraesCS7D01G470900 chr7B 708673318 708677347 4029 True 1042.333333 2178 89.215667 1 3671 3 chr7B.!!$R11 3670
16 TraesCS7D01G470900 chr7B 651871857 651874116 2259 True 996.000000 1511 88.670000 43 4058 2 chr7B.!!$R4 4015
17 TraesCS7D01G470900 chr7B 652173086 652175761 2675 True 870.666667 1530 87.912333 1 2447 3 chr7B.!!$R6 2446
18 TraesCS7D01G470900 chr7B 652398129 652402758 4629 True 846.000000 1655 89.647200 1 4381 5 chr7B.!!$R8 4380
19 TraesCS7D01G470900 chr7B 652053377 652061227 7850 True 786.333333 1373 90.883000 780 3668 3 chr7B.!!$R5 2888
20 TraesCS7D01G470900 chr7B 652436325 652440994 4669 True 770.600000 1637 90.193600 1 4377 5 chr7B.!!$R9 4376
21 TraesCS7D01G470900 chr7B 656300375 656303072 2697 False 747.500000 990 89.951000 1 2447 4 chr7B.!!$F4 2446
22 TraesCS7D01G470900 chr7B 652253996 652256530 2534 True 604.750000 1162 89.153500 1 4392 4 chr7B.!!$R7 4391
23 TraesCS7D01G470900 chr7B 652971096 652975919 4823 True 602.857143 1122 89.600143 54 4382 7 chr7B.!!$R10 4328
24 TraesCS7D01G470900 chr7B 722088666 722090945 2279 True 580.750000 961 88.668750 34 2011 4 chr7B.!!$R12 1977
25 TraesCS7D01G470900 chr7A 708494791 708496303 1512 True 872.000000 1092 87.976000 1 1476 2 chr7A.!!$R3 1475
26 TraesCS7D01G470900 chr7A 674680205 674683474 3269 True 829.250000 1794 89.617750 503 3675 4 chr7A.!!$R2 3172
27 TraesCS7D01G470900 chr7A 677440811 677441881 1070 False 609.500000 808 89.801000 1500 2442 2 chr7A.!!$F7 942
28 TraesCS7D01G470900 chr7A 675870493 675875916 5423 False 592.166667 1533 90.324333 1 4058 6 chr7A.!!$F4 4057
29 TraesCS7D01G470900 chr7A 677611172 677615797 4625 False 565.266667 893 89.211667 1 2447 3 chr7A.!!$F8 2446
30 TraesCS7D01G470900 chr7A 675907369 675913791 6422 False 562.200000 1118 89.388200 1 4058 5 chr7A.!!$F5 4057
31 TraesCS7D01G470900 chr7A 676974696 676976404 1708 False 484.500000 486 88.115000 1 410 2 chr7A.!!$F6 409
32 TraesCS7D01G470900 chr5D 412968859 412969372 513 True 713.000000 713 91.747000 4426 4941 1 chr5D.!!$R4 515
33 TraesCS7D01G470900 chr5D 287741505 287742060 555 True 645.000000 645 87.922000 4391 4941 1 chr5D.!!$R3 550
34 TraesCS7D01G470900 chr4D 380951898 380952451 553 True 704.000000 704 89.840000 4392 4941 1 chr4D.!!$R10 549
35 TraesCS7D01G470900 chr4D 3512871 3513388 517 True 640.000000 640 89.122000 4426 4941 1 chr4D.!!$R1 515
36 TraesCS7D01G470900 chr4D 50137545 50138069 524 False 588.000000 588 87.170000 4389 4907 1 chr4D.!!$F1 518
37 TraesCS7D01G470900 chr4D 450485321 450485874 553 True 584.000000 584 85.891000 4392 4950 1 chr4D.!!$R11 558
38 TraesCS7D01G470900 chr4A 675128845 675129357 512 True 616.000000 616 88.571000 4428 4941 1 chr4A.!!$R1 513
39 TraesCS7D01G470900 chr6B 635409011 635409561 550 True 612.000000 612 86.988000 4392 4941 1 chr6B.!!$R3 549
40 TraesCS7D01G470900 chr6B 293096267 293096799 532 True 534.000000 534 85.451000 4388 4907 1 chr6B.!!$R2 519
41 TraesCS7D01G470900 chr1D 312950011 312950536 525 True 573.000000 573 86.542000 4392 4917 1 chr1D.!!$R1 525
42 TraesCS7D01G470900 chr3A 563520049 563520569 520 False 555.000000 555 86.278000 4388 4905 1 chr3A.!!$F1 517
43 TraesCS7D01G470900 chr2B 140585675 140586194 519 True 555.000000 555 86.252000 4390 4907 1 chr2B.!!$R1 517
44 TraesCS7D01G470900 chr2B 281802491 281803029 538 True 534.000000 534 84.982000 4390 4920 1 chr2B.!!$R2 530
45 TraesCS7D01G470900 chr3D 339007236 339007737 501 False 520.000000 520 85.714000 4389 4886 1 chr3D.!!$F1 497
46 TraesCS7D01G470900 chr5A 69320558 69321059 501 True 446.000000 446 82.941000 3014 3515 1 chr5A.!!$R1 501

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
283 309 0.248907 GCATGTTGCATGCTAGCCAG 60.249 55.000 20.33 5.65 44.26 4.85 F
708 1198 1.066071 GTTAGCCTGTCCTTCAGTCCC 60.066 57.143 0.00 0.00 42.19 4.46 F
1687 3940 0.536006 AGCCATCGCTCAATTAGGGC 60.536 55.000 0.00 0.00 43.95 5.19 F
2281 7425 0.107410 AAGTTGTTGGGACAGTCGCA 60.107 50.000 16.08 16.08 42.39 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 2082 1.135286 GCTTTCAGCTTGGCATACACC 60.135 52.381 0.00 0.00 38.45 4.16 R
2191 7330 2.129555 AATCAACCACTCAGGCGCCT 62.130 55.000 27.08 27.08 43.14 5.52 R
3012 12239 1.146263 CTCCCATTACGACCAGCCC 59.854 63.158 0.00 0.00 0.00 5.19 R
4123 16724 0.326143 GGCTCCTCTTCTCTCCCCTT 60.326 60.000 0.00 0.00 0.00 3.95 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
201 211 7.913674 TTTTTGTTACAAATTTGGTCAAGCT 57.086 28.000 21.74 2.02 0.00 3.74
236 246 7.513371 TTGACCAAATTTTATACACGGAGTT 57.487 32.000 0.00 0.00 41.61 3.01
240 250 9.550811 GACCAAATTTTATACACGGAGTTAAAG 57.449 33.333 0.00 0.00 41.61 1.85
282 308 1.811195 GCATGTTGCATGCTAGCCA 59.189 52.632 20.33 7.08 44.26 4.75
283 309 0.248907 GCATGTTGCATGCTAGCCAG 60.249 55.000 20.33 5.65 44.26 4.85
345 399 7.942894 GGCCTAATAATAACCTAATCACTGGTT 59.057 37.037 0.00 0.00 46.84 3.67
520 1000 5.796424 ATTATTAGCCTTGCTTTGATGGG 57.204 39.130 0.00 0.00 40.44 4.00
538 1018 3.088532 TGGGGGATCAGAAAATGAAACG 58.911 45.455 0.00 0.00 42.53 3.60
552 1034 3.412981 TGAAACGGAAACACACACATG 57.587 42.857 0.00 0.00 0.00 3.21
708 1198 1.066071 GTTAGCCTGTCCTTCAGTCCC 60.066 57.143 0.00 0.00 42.19 4.46
829 1321 4.940046 CAGACTCTTGTGCTTATGTTGGAT 59.060 41.667 0.00 0.00 0.00 3.41
886 1528 8.531622 TGTTCATGCTTTTATTTTATGGTGTG 57.468 30.769 0.00 0.00 0.00 3.82
1085 1790 6.483307 GGTATGTATGTGCACATGTATGAACT 59.517 38.462 36.72 18.87 39.46 3.01
1151 1863 5.208463 AGTCGTTTTGGCATTAAATTGGT 57.792 34.783 0.00 0.00 0.00 3.67
1349 2082 1.469595 CCAATGGCTACGGTTGCAATG 60.470 52.381 15.95 10.61 0.00 2.82
1397 2131 1.781025 TTTTCTGGCGCTTGTGACGG 61.781 55.000 7.64 0.00 0.00 4.79
1442 2176 4.833478 ACTGCTCCTATGAGATTGTTGT 57.167 40.909 0.00 0.00 41.42 3.32
1489 2223 2.158711 TGATGCAATGATCCTCCCAGTC 60.159 50.000 0.00 0.00 0.00 3.51
1687 3940 0.536006 AGCCATCGCTCAATTAGGGC 60.536 55.000 0.00 0.00 43.95 5.19
1850 4105 7.518731 TTCTTGTGTTGTTACAAATGAAAGC 57.481 32.000 0.00 0.00 39.81 3.51
1855 6576 8.261492 TGTGTTGTTACAAATGAAAGCAAATT 57.739 26.923 0.00 0.00 35.69 1.82
1895 6616 1.915141 AAATCTGAACCTGCCAGTGG 58.085 50.000 4.20 4.20 33.57 4.00
1989 6715 9.495754 GATGTGATACAAATTTTAGAAGCAGAC 57.504 33.333 0.00 0.00 0.00 3.51
2130 7267 4.619973 ACATCACAATTTCGTGCAATGTT 58.380 34.783 0.00 0.00 33.09 2.71
2159 7296 8.139350 ACATTGTTTGGCTAAACTTAAGGTTAC 58.861 33.333 23.82 6.60 45.06 2.50
2173 7310 4.877378 AAGGTTACTTGTATCCACGTCA 57.123 40.909 9.68 0.00 35.09 4.35
2174 7311 4.451629 AGGTTACTTGTATCCACGTCAG 57.548 45.455 9.68 0.00 0.00 3.51
2175 7312 2.928116 GGTTACTTGTATCCACGTCAGC 59.072 50.000 0.00 0.00 0.00 4.26
2182 7321 1.663379 TATCCACGTCAGCTGGACCG 61.663 60.000 15.13 15.83 43.95 4.79
2191 7330 4.424711 GCTGGACCGCCCATTCCA 62.425 66.667 0.00 0.00 45.57 3.53
2254 7396 8.141298 TCACTATTAGTTAACATGAGGTCCAA 57.859 34.615 8.61 0.00 0.00 3.53
2281 7425 0.107410 AAGTTGTTGGGACAGTCGCA 60.107 50.000 16.08 16.08 42.39 5.10
2284 7428 1.336755 GTTGTTGGGACAGTCGCATTT 59.663 47.619 20.21 0.00 42.39 2.32
2328 7472 4.872691 GGTAGATGGTGATGTGAGAAACAG 59.127 45.833 0.00 0.00 43.64 3.16
2357 7501 9.847224 TCCAGAGAACTAGTAAAAAGAACATTT 57.153 29.630 0.00 0.00 0.00 2.32
2861 12087 7.823745 ACGCAGATAAAAATATCCCTCAAAT 57.176 32.000 0.00 0.00 0.00 2.32
2928 12155 7.948357 AGATTGCATGTGCTAATTGACAATAT 58.052 30.769 0.00 0.00 42.66 1.28
2929 12156 9.070179 AGATTGCATGTGCTAATTGACAATATA 57.930 29.630 0.00 0.00 42.66 0.86
2930 12157 9.121517 GATTGCATGTGCTAATTGACAATATAC 57.878 33.333 0.00 0.00 42.66 1.47
2931 12158 7.565323 TGCATGTGCTAATTGACAATATACA 57.435 32.000 0.00 5.36 42.66 2.29
2967 12194 1.565390 TAGCAAGCCCATCACTGCCT 61.565 55.000 0.00 0.00 0.00 4.75
3000 12227 2.234661 TCCGTCAGTGAGCAAGATTCAT 59.765 45.455 0.00 0.00 0.00 2.57
3012 12239 4.021719 AGCAAGATTCATTGTTGGGTCTTG 60.022 41.667 8.19 8.19 41.93 3.02
3068 12300 3.287312 TGCATGCACTAGACTTTTTGC 57.713 42.857 18.46 0.00 35.45 3.68
3218 13197 5.604650 ACTTATGATACTCCCTCCTTCCTTG 59.395 44.000 0.00 0.00 0.00 3.61
3235 13214 6.215636 CCTTCCTTGTATATAGGGCCTAATGT 59.784 42.308 18.91 9.02 33.41 2.71
3236 13215 6.620877 TCCTTGTATATAGGGCCTAATGTG 57.379 41.667 18.91 4.53 33.41 3.21
3242 13221 8.685838 TGTATATAGGGCCTAATGTGTTTTTC 57.314 34.615 18.91 1.39 0.00 2.29
3246 13225 2.163613 GGGCCTAATGTGTTTTTCGAGG 59.836 50.000 0.84 0.00 0.00 4.63
3251 13230 5.163652 GCCTAATGTGTTTTTCGAGGCTAAT 60.164 40.000 2.77 0.00 43.77 1.73
3255 13234 9.191995 CTAATGTGTTTTTCGAGGCTAATTTTT 57.808 29.630 0.00 0.00 0.00 1.94
3281 13260 8.557592 ACCACATGTGAGAGCAATAATATATG 57.442 34.615 27.46 6.35 0.00 1.78
3303 13282 3.705604 ACATGCAAGTTACACAAAGCAC 58.294 40.909 0.00 0.00 34.54 4.40
3319 13298 5.048083 ACAAAGCACACCATCAAATTCGTAT 60.048 36.000 0.00 0.00 0.00 3.06
3323 13302 4.661125 CACACCATCAAATTCGTATGTGG 58.339 43.478 0.00 0.00 34.05 4.17
3333 13312 2.672961 TCGTATGTGGAAGGAGCTTG 57.327 50.000 0.00 0.00 0.00 4.01
3334 13313 1.899814 TCGTATGTGGAAGGAGCTTGT 59.100 47.619 0.00 0.00 0.00 3.16
3402 13381 8.770828 TCTTAACAATAGTCAAAGGAAAACTCG 58.229 33.333 0.00 0.00 0.00 4.18
3408 13387 9.463443 CAATAGTCAAAGGAAAACTCGAAAAAT 57.537 29.630 0.00 0.00 0.00 1.82
3439 13420 4.777896 GCCCTATATACATGGAAGGAGTGA 59.222 45.833 0.00 0.00 0.00 3.41
3440 13421 5.105146 GCCCTATATACATGGAAGGAGTGAG 60.105 48.000 0.00 0.00 0.00 3.51
3441 13422 6.019748 CCCTATATACATGGAAGGAGTGAGT 58.980 44.000 0.00 0.00 0.00 3.41
3443 13424 7.674348 CCCTATATACATGGAAGGAGTGAGTAA 59.326 40.741 0.00 0.00 0.00 2.24
3516 13632 6.110411 AGTAAATGATACTCCCCATTACGG 57.890 41.667 0.00 0.00 33.13 4.02
3517 13633 5.842328 AGTAAATGATACTCCCCATTACGGA 59.158 40.000 0.00 0.00 36.56 4.69
3518 13634 5.640158 AAATGATACTCCCCATTACGGAA 57.360 39.130 0.00 0.00 36.56 4.30
3521 13637 4.806892 TGATACTCCCCATTACGGAAGTA 58.193 43.478 0.00 0.00 46.88 2.24
3539 13655 9.434420 ACGGAAGTAGTATCATACACTAGTATC 57.566 37.037 0.00 0.00 46.88 2.24
3551 15956 7.883311 TCATACACTAGTATCATACAGCTAGCA 59.117 37.037 18.83 0.00 38.88 3.49
3560 15965 1.924731 TACAGCTAGCACCTGACACT 58.075 50.000 18.83 0.00 34.47 3.55
3561 15966 0.319728 ACAGCTAGCACCTGACACTG 59.680 55.000 18.83 5.36 34.47 3.66
3613 16018 1.632589 GGCCAGGTTCAGTTGGAAAT 58.367 50.000 0.00 0.00 37.23 2.17
3835 16435 3.452264 TCTTGCATGTGCTAGTATGTCCT 59.548 43.478 14.34 0.00 42.89 3.85
3844 16444 3.832490 TGCTAGTATGTCCTGTGTGTTCT 59.168 43.478 0.00 0.00 0.00 3.01
3899 16499 1.331756 GACACCTGAGCGGCAATTATG 59.668 52.381 1.45 0.00 35.61 1.90
3900 16500 1.065491 ACACCTGAGCGGCAATTATGA 60.065 47.619 1.45 0.00 35.61 2.15
3935 16535 1.912001 CTTTACCGACGGTTGCGATA 58.088 50.000 27.06 2.13 37.09 2.92
3956 16556 6.454318 CGATAATACATGCGTAGATGAAAGCC 60.454 42.308 0.00 0.00 0.00 4.35
3967 16567 2.696707 AGATGAAAGCCCCGATAACGTA 59.303 45.455 0.00 0.00 37.88 3.57
4017 16617 5.791336 TGCTACTGCTATACATGCTAGTT 57.209 39.130 0.00 0.00 40.48 2.24
4037 16637 5.723295 AGTTTGAGATTGTTGTTGTTGCTT 58.277 33.333 0.00 0.00 0.00 3.91
4042 16642 0.389037 TTGTTGTTGTTGCTTGCGCA 60.389 45.000 5.66 5.66 46.24 6.09
4069 16669 3.668447 ACAACCATGAGAGCAAGTACAG 58.332 45.455 0.00 0.00 0.00 2.74
4205 16808 7.355101 AGATACTATGTAAGAGTGGGAAGTGA 58.645 38.462 0.00 0.00 0.00 3.41
4222 16825 7.836685 TGGGAAGTGAGCCATGTATTAATAAAA 59.163 33.333 0.00 0.00 0.00 1.52
4304 16907 3.638484 TGACAACGTCATATAGCCATCG 58.362 45.455 0.00 0.00 37.67 3.84
4309 16912 8.925039 GACAACGTCATATAGCCATCGGCTAA 62.925 46.154 18.11 8.67 46.50 3.09
4353 16956 0.106819 GCAATGATCCCAGCCTGACT 60.107 55.000 0.00 0.00 0.00 3.41
4403 17082 3.191371 GGCTCTTATGTGTTGGGAAACAG 59.809 47.826 0.00 0.00 32.64 3.16
4421 17100 7.174772 GGGAAACAGTGCATGGAAAATAATTTT 59.825 33.333 0.00 0.00 35.12 1.82
4422 17101 8.567104 GGAAACAGTGCATGGAAAATAATTTTT 58.433 29.630 0.00 0.00 37.75 1.94
4444 17128 2.640346 TTCTACGCACACGCAAGATA 57.360 45.000 0.00 0.00 45.53 1.98
4491 17178 3.627747 GGGGGAGAGTGTGTCTATGTACT 60.628 52.174 0.00 0.00 34.71 2.73
4749 17450 6.661805 ACAAAAATATGACCGAGGGTGTAAAT 59.338 34.615 0.00 0.00 35.25 1.40
4750 17451 7.177744 ACAAAAATATGACCGAGGGTGTAAATT 59.822 33.333 0.00 0.00 35.25 1.82
4751 17452 8.679100 CAAAAATATGACCGAGGGTGTAAATTA 58.321 33.333 0.00 0.00 35.25 1.40
4752 17453 8.810990 AAAATATGACCGAGGGTGTAAATTAA 57.189 30.769 0.00 0.00 35.25 1.40
4889 17605 2.433239 GTCCGAATCCTACTTGGGCTTA 59.567 50.000 0.00 0.00 36.20 3.09
4941 17670 1.857348 CAAGGGGAAGGAAGGGGGT 60.857 63.158 0.00 0.00 0.00 4.95
4944 17673 1.855451 GGGGAAGGAAGGGGGTGAA 60.855 63.158 0.00 0.00 0.00 3.18
4945 17674 1.691823 GGGAAGGAAGGGGGTGAAG 59.308 63.158 0.00 0.00 0.00 3.02
4947 17676 0.845102 GGAAGGAAGGGGGTGAAGGA 60.845 60.000 0.00 0.00 0.00 3.36
4950 17679 1.773541 AGGAAGGGGGTGAAGGAAAT 58.226 50.000 0.00 0.00 0.00 2.17
4951 17680 2.942905 AGGAAGGGGGTGAAGGAAATA 58.057 47.619 0.00 0.00 0.00 1.40
4952 17681 3.485136 AGGAAGGGGGTGAAGGAAATAT 58.515 45.455 0.00 0.00 0.00 1.28
4953 17682 4.652628 AGGAAGGGGGTGAAGGAAATATA 58.347 43.478 0.00 0.00 0.00 0.86
4954 17683 4.415846 AGGAAGGGGGTGAAGGAAATATAC 59.584 45.833 0.00 0.00 0.00 1.47
4955 17684 4.447325 GGAAGGGGGTGAAGGAAATATACC 60.447 50.000 0.00 0.00 0.00 2.73
4961 17690 6.361768 GGGTGAAGGAAATATACCCTAGAG 57.638 45.833 0.00 0.00 45.94 2.43
4962 17691 5.248705 GGGTGAAGGAAATATACCCTAGAGG 59.751 48.000 0.00 0.00 45.94 3.69
4963 17692 5.280062 GGTGAAGGAAATATACCCTAGAGGC 60.280 48.000 0.00 0.00 40.58 4.70
4964 17693 5.307196 GTGAAGGAAATATACCCTAGAGGCA 59.693 44.000 0.00 0.00 40.58 4.75
4965 17694 5.908831 TGAAGGAAATATACCCTAGAGGCAA 59.091 40.000 0.00 0.00 40.58 4.52
4966 17695 6.562608 TGAAGGAAATATACCCTAGAGGCAAT 59.437 38.462 0.00 0.00 40.58 3.56
4967 17696 7.737607 TGAAGGAAATATACCCTAGAGGCAATA 59.262 37.037 0.00 0.00 40.58 1.90
4968 17697 8.520119 AAGGAAATATACCCTAGAGGCAATAA 57.480 34.615 0.00 0.00 40.58 1.40
4969 17698 8.701643 AGGAAATATACCCTAGAGGCAATAAT 57.298 34.615 0.00 0.00 40.58 1.28
4970 17699 9.799223 AGGAAATATACCCTAGAGGCAATAATA 57.201 33.333 0.00 0.00 40.58 0.98
4977 17706 6.970191 ACCCTAGAGGCAATAATAAAGTTGT 58.030 36.000 0.00 0.00 40.58 3.32
4978 17707 7.410991 ACCCTAGAGGCAATAATAAAGTTGTT 58.589 34.615 0.00 0.00 40.58 2.83
4979 17708 7.339466 ACCCTAGAGGCAATAATAAAGTTGTTG 59.661 37.037 0.00 0.00 40.58 3.33
4980 17709 7.339466 CCCTAGAGGCAATAATAAAGTTGTTGT 59.661 37.037 0.00 0.00 0.00 3.32
4981 17710 8.739972 CCTAGAGGCAATAATAAAGTTGTTGTT 58.260 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
236 246 6.363167 TCAGTATTCCCTTCGTTTCCTTTA 57.637 37.500 0.00 0.00 0.00 1.85
240 250 4.571176 GTGATCAGTATTCCCTTCGTTTCC 59.429 45.833 0.00 0.00 0.00 3.13
282 308 0.324943 AGTATTTGGTGAGCACGGCT 59.675 50.000 0.00 0.00 43.88 5.52
283 309 0.727398 GAGTATTTGGTGAGCACGGC 59.273 55.000 0.00 0.00 0.00 5.68
284 310 0.999406 CGAGTATTTGGTGAGCACGG 59.001 55.000 0.00 0.00 0.00 4.94
285 311 1.654105 GTCGAGTATTTGGTGAGCACG 59.346 52.381 0.00 0.00 0.00 5.34
332 386 5.282055 TGATCAGCTAACCAGTGATTAGG 57.718 43.478 6.39 0.00 30.93 2.69
345 399 4.651045 TGAGCTTGGACTAATGATCAGCTA 59.349 41.667 0.09 0.00 0.00 3.32
350 404 4.965814 TGGATGAGCTTGGACTAATGATC 58.034 43.478 0.00 0.00 0.00 2.92
442 810 2.803492 CGGGCTCTTAACCTACTCATGC 60.803 54.545 0.00 0.00 0.00 4.06
455 932 0.251341 ATCTTTGCAACCGGGCTCTT 60.251 50.000 6.32 0.00 34.04 2.85
520 1000 5.161358 GTTTCCGTTTCATTTTCTGATCCC 58.839 41.667 0.00 0.00 32.72 3.85
538 1018 0.385029 TGCTGCATGTGTGTGTTTCC 59.615 50.000 0.00 0.00 0.00 3.13
829 1321 6.099413 TCTCCGATCTTAGTCTCCTAGTGTTA 59.901 42.308 0.00 0.00 0.00 2.41
998 1703 3.066291 TCTTTTCTGAAGGCGCCATTA 57.934 42.857 31.54 13.51 0.00 1.90
1085 1790 5.872617 CGGACAATTCACTTATACTTCCACA 59.127 40.000 0.00 0.00 0.00 4.17
1196 1912 5.505159 GCAAGAACGTGGTTATAATTAGCCC 60.505 44.000 0.00 0.00 0.00 5.19
1349 2082 1.135286 GCTTTCAGCTTGGCATACACC 60.135 52.381 0.00 0.00 38.45 4.16
1370 2103 1.172812 AGCGCCAGAAAAGGTGTTCC 61.173 55.000 2.29 0.00 41.26 3.62
1397 2131 4.578105 AGGAATAGCAGTAGCATTTGAAGC 59.422 41.667 0.00 0.00 45.49 3.86
1489 2223 6.699895 TTATATTTAAGATACACGCGCCAG 57.300 37.500 5.73 0.00 0.00 4.85
1554 2450 6.675413 AACCCCTCCTGGTTATTTAAAAAC 57.325 37.500 0.00 0.00 46.70 2.43
1566 3813 3.411700 GGTGGTAACCCCTCCTGG 58.588 66.667 0.00 0.00 42.63 4.45
1650 3903 3.427161 GCTAGCTGCCCTTTTGTAATG 57.573 47.619 7.70 0.00 35.15 1.90
1821 4076 6.972328 TCATTTGTAACAACACAAGAAAGCTC 59.028 34.615 0.00 0.00 39.46 4.09
1827 4082 6.625362 TGCTTTCATTTGTAACAACACAAGA 58.375 32.000 0.00 0.00 39.46 3.02
1849 4104 8.477984 TTTATGGCTCTAAACATCAAATTTGC 57.522 30.769 13.54 0.00 0.00 3.68
1864 6585 6.264067 GCAGGTTCAGATTTATTTATGGCTCT 59.736 38.462 0.00 0.00 0.00 4.09
1916 6637 6.152661 TCTGTCCCATCATTTTATGGTTTGAC 59.847 38.462 2.43 3.72 44.29 3.18
1989 6715 4.807304 GTGATACTAACACCATTGTACGGG 59.193 45.833 0.00 0.00 33.55 5.28
2130 7267 9.523168 ACCTTAAGTTTAGCCAAACAATGTATA 57.477 29.630 10.39 0.00 45.44 1.47
2191 7330 2.129555 AATCAACCACTCAGGCGCCT 62.130 55.000 27.08 27.08 43.14 5.52
2254 7396 2.306847 GTCCCAACAACTTGGTGTCAT 58.693 47.619 6.08 0.00 45.22 3.06
2281 7425 6.265196 CCGCCATATATAATGCCCATGTAAAT 59.735 38.462 0.00 0.00 0.00 1.40
2284 7428 4.165180 ACCGCCATATATAATGCCCATGTA 59.835 41.667 0.00 0.00 0.00 2.29
2328 7472 5.467705 TCTTTTTACTAGTTCTCTGGACGC 58.532 41.667 0.00 0.00 0.00 5.19
2929 12156 7.713073 GCTTGCTAGAAAGGTCTATTATCTTGT 59.287 37.037 12.62 0.00 35.76 3.16
2930 12157 7.172361 GGCTTGCTAGAAAGGTCTATTATCTTG 59.828 40.741 12.62 0.00 35.76 3.02
2931 12158 7.220740 GGCTTGCTAGAAAGGTCTATTATCTT 58.779 38.462 12.62 0.00 35.76 2.40
2967 12194 3.021695 CACTGACGGATTAGGGACACTA 58.978 50.000 0.00 0.00 0.00 2.74
2979 12206 1.618343 TGAATCTTGCTCACTGACGGA 59.382 47.619 0.00 0.00 0.00 4.69
3000 12227 1.152567 CCAGCCCAAGACCCAACAA 60.153 57.895 0.00 0.00 0.00 2.83
3012 12239 1.146263 CTCCCATTACGACCAGCCC 59.854 63.158 0.00 0.00 0.00 5.19
3068 12300 6.100668 TCATTTAATTGTGTGCCACATCATG 58.899 36.000 0.00 7.28 44.16 3.07
3218 13197 7.658575 TCGAAAAACACATTAGGCCCTATATAC 59.341 37.037 0.00 0.00 0.00 1.47
3235 13214 6.919115 GTGGTAAAAATTAGCCTCGAAAAACA 59.081 34.615 0.00 0.00 0.00 2.83
3236 13215 6.919115 TGTGGTAAAAATTAGCCTCGAAAAAC 59.081 34.615 0.00 0.00 0.00 2.43
3242 13221 5.123186 TCACATGTGGTAAAAATTAGCCTCG 59.877 40.000 25.16 0.00 0.00 4.63
3246 13225 6.030228 GCTCTCACATGTGGTAAAAATTAGC 58.970 40.000 25.16 15.27 0.00 3.09
3251 13230 7.517614 TTATTGCTCTCACATGTGGTAAAAA 57.482 32.000 25.16 14.62 0.00 1.94
3255 13234 9.657419 CATATATTATTGCTCTCACATGTGGTA 57.343 33.333 25.16 12.69 0.00 3.25
3281 13260 3.730715 GTGCTTTGTGTAACTTGCATGTC 59.269 43.478 5.61 0.00 38.61 3.06
3303 13282 5.449041 CCTTCCACATACGAATTTGATGGTG 60.449 44.000 0.00 4.37 0.00 4.17
3319 13298 4.574674 ATCATTACAAGCTCCTTCCACA 57.425 40.909 0.00 0.00 0.00 4.17
3381 13360 7.562454 TTTCGAGTTTTCCTTTGACTATTGT 57.438 32.000 0.00 0.00 0.00 2.71
3393 13372 8.080417 GGGCCTAATATATTTTTCGAGTTTTCC 58.920 37.037 0.84 0.00 0.00 3.13
3395 13374 8.762481 AGGGCCTAATATATTTTTCGAGTTTT 57.238 30.769 2.82 0.00 0.00 2.43
3408 13387 9.615660 CCTTCCATGTATATAGGGCCTAATATA 57.384 37.037 18.91 15.67 0.00 0.86
3410 13389 7.667848 TCCTTCCATGTATATAGGGCCTAATA 58.332 38.462 18.91 13.23 0.00 0.98
3415 13394 4.080863 CACTCCTTCCATGTATATAGGGCC 60.081 50.000 0.00 0.00 0.00 5.80
3416 13395 4.777896 TCACTCCTTCCATGTATATAGGGC 59.222 45.833 0.00 0.00 0.00 5.19
3430 13411 8.790718 TCCGTAATGTATATTACTCACTCCTTC 58.209 37.037 17.18 0.00 44.13 3.46
3447 13556 8.461249 AGTGTATGATACTACTTCCGTAATGT 57.539 34.615 4.03 0.00 0.00 2.71
3521 13637 9.967451 AGCTGTATGATACTAGTGTATGATACT 57.033 33.333 18.83 0.00 46.64 2.12
3526 13642 7.965655 GTGCTAGCTGTATGATACTAGTGTATG 59.034 40.741 17.23 0.00 39.29 2.39
3528 13644 6.430308 GGTGCTAGCTGTATGATACTAGTGTA 59.570 42.308 17.23 0.00 35.58 2.90
3529 13645 5.241949 GGTGCTAGCTGTATGATACTAGTGT 59.758 44.000 17.23 0.00 35.58 3.55
3530 13646 5.475220 AGGTGCTAGCTGTATGATACTAGTG 59.525 44.000 17.23 0.00 35.58 2.74
3531 13647 5.475220 CAGGTGCTAGCTGTATGATACTAGT 59.525 44.000 17.23 0.00 38.80 2.57
3532 13648 5.707764 TCAGGTGCTAGCTGTATGATACTAG 59.292 44.000 17.23 1.60 43.70 2.57
3535 13651 4.038042 TGTCAGGTGCTAGCTGTATGATAC 59.962 45.833 17.23 2.48 43.70 2.24
3536 13652 4.038042 GTGTCAGGTGCTAGCTGTATGATA 59.962 45.833 17.23 10.13 43.70 2.15
3537 13653 3.033909 TGTCAGGTGCTAGCTGTATGAT 58.966 45.455 17.23 0.00 43.70 2.45
3539 13655 2.167281 AGTGTCAGGTGCTAGCTGTATG 59.833 50.000 17.23 9.57 43.70 2.39
3551 15956 2.831770 CTGGCCACAGTGTCAGGT 59.168 61.111 0.00 0.00 39.92 4.00
3600 16005 3.005791 CCCCAAGTGATTTCCAACTGAAC 59.994 47.826 0.00 0.00 31.05 3.18
3613 16018 5.415065 ACATATGATCCTATCCCCAAGTGA 58.585 41.667 10.38 0.00 0.00 3.41
3699 16295 5.312895 TCAATGCCAAAACTTCAGTAGCTA 58.687 37.500 0.00 0.00 0.00 3.32
3703 16299 6.222389 CCAATTCAATGCCAAAACTTCAGTA 58.778 36.000 0.00 0.00 0.00 2.74
3707 16303 4.067192 AGCCAATTCAATGCCAAAACTTC 58.933 39.130 0.00 0.00 0.00 3.01
3788 16388 9.087424 GAACATGGTTAATTAGCCAAAAGATTC 57.913 33.333 22.91 16.81 40.04 2.52
3835 16435 2.276201 GCATACGCCATAGAACACACA 58.724 47.619 0.00 0.00 0.00 3.72
3844 16444 0.950836 GGTTGCATGCATACGCCATA 59.049 50.000 23.37 0.00 37.32 2.74
3880 16480 1.065491 TCATAATTGCCGCTCAGGTGT 60.065 47.619 0.00 0.00 43.70 4.16
3899 16499 1.172812 AAGCCAAAGCACGGTCCTTC 61.173 55.000 0.00 0.00 43.56 3.46
3900 16500 0.755327 AAAGCCAAAGCACGGTCCTT 60.755 50.000 0.00 0.00 43.56 3.36
3935 16535 3.815401 GGGCTTTCATCTACGCATGTATT 59.185 43.478 0.00 0.00 0.00 1.89
3956 16556 1.373748 CGCCCCATACGTTATCGGG 60.374 63.158 0.00 0.00 39.36 5.14
3967 16567 1.750399 GCAGTCACAATCGCCCCAT 60.750 57.895 0.00 0.00 0.00 4.00
4017 16617 3.864583 GCAAGCAACAACAACAATCTCAA 59.135 39.130 0.00 0.00 0.00 3.02
4037 16637 3.490031 ATGGTTGTCTGGGTGCGCA 62.490 57.895 5.66 5.66 0.00 6.09
4042 16642 0.326264 GCTCTCATGGTTGTCTGGGT 59.674 55.000 0.00 0.00 0.00 4.51
4045 16645 2.775890 ACTTGCTCTCATGGTTGTCTG 58.224 47.619 0.00 0.00 0.00 3.51
4047 16647 3.664107 TGTACTTGCTCTCATGGTTGTC 58.336 45.455 0.00 0.00 0.00 3.18
4122 16723 0.829990 GCTCCTCTTCTCTCCCCTTG 59.170 60.000 0.00 0.00 0.00 3.61
4123 16724 0.326143 GGCTCCTCTTCTCTCCCCTT 60.326 60.000 0.00 0.00 0.00 3.95
4205 16808 9.965824 GTTGTGCTATTTTATTAATACATGGCT 57.034 29.630 16.82 0.00 0.00 4.75
4256 16859 7.235606 TGTCATCTATAGCCAAGTTTATAGCCT 59.764 37.037 0.00 0.00 32.42 4.58
4304 16907 4.261197 GCATGGTTAATAGTGCAGTTAGCC 60.261 45.833 0.00 5.92 44.83 3.93
4309 16912 4.080919 TCAGAGCATGGTTAATAGTGCAGT 60.081 41.667 0.00 0.00 39.94 4.40
4313 16916 4.818005 TGCATCAGAGCATGGTTAATAGTG 59.182 41.667 0.00 0.00 40.11 2.74
4444 17128 4.934001 CGTTGCTATGCATCTCCTTGATAT 59.066 41.667 0.19 0.00 38.76 1.63
4522 17209 1.074319 TTCGACTACATCAACCGCGC 61.074 55.000 0.00 0.00 0.00 6.86
4595 17283 0.388520 TCATCGAGCTGAACGTGTGG 60.389 55.000 0.00 0.00 0.00 4.17
4749 17450 3.708544 CGCCCCCTCCACCGTTAA 61.709 66.667 0.00 0.00 0.00 2.01
4941 17670 5.473273 TGCCTCTAGGGTATATTTCCTTCA 58.527 41.667 0.00 0.00 37.43 3.02
4944 17673 8.701643 ATTATTGCCTCTAGGGTATATTTCCT 57.298 34.615 0.00 2.69 37.43 3.36
4951 17680 8.724310 ACAACTTTATTATTGCCTCTAGGGTAT 58.276 33.333 0.00 0.00 37.43 2.73
4952 17681 8.097791 ACAACTTTATTATTGCCTCTAGGGTA 57.902 34.615 0.00 0.00 37.43 3.69
4953 17682 6.970191 ACAACTTTATTATTGCCTCTAGGGT 58.030 36.000 0.00 0.00 37.43 4.34
4954 17683 7.339466 ACAACAACTTTATTATTGCCTCTAGGG 59.661 37.037 0.00 0.00 35.18 3.53
4955 17684 8.281212 ACAACAACTTTATTATTGCCTCTAGG 57.719 34.615 0.00 0.00 38.53 3.02


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

AutoCloner maintained by Alex Coulton.