Multiple sequence alignment - TraesCS1B01G283900

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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 TraesCS1B01G283900 chr1B 100.000 6684 0 0 1 6684 492793331 492786648 0.000000e+00 12344.0
1 TraesCS1B01G283900 chr1B 82.812 192 27 4 5158 5349 631120205 631120020 4.150000e-37 167.0
2 TraesCS1B01G283900 chr2B 99.229 2465 18 1 1564 4027 72965691 72968155 0.000000e+00 4446.0
3 TraesCS1B01G283900 chr2B 84.094 2477 361 30 1566 4025 758138464 758136004 0.000000e+00 2361.0
4 TraesCS1B01G283900 chr2B 98.092 996 19 0 1567 2562 168675605 168676600 0.000000e+00 1735.0
5 TraesCS1B01G283900 chr2B 84.062 320 27 13 6032 6351 484928838 484928543 3.050000e-73 287.0
6 TraesCS1B01G283900 chr2B 83.420 193 29 2 5158 5349 31581363 31581553 6.890000e-40 176.0
7 TraesCS1B01G283900 chr2B 81.865 193 29 5 5157 5349 212558752 212558938 2.500000e-34 158.0
8 TraesCS1B01G283900 chr2B 85.185 135 13 5 5039 5166 91043236 91043370 1.510000e-26 132.0
9 TraesCS1B01G283900 chr6A 99.148 2465 17 3 1565 4027 485775327 485772865 0.000000e+00 4433.0
10 TraesCS1B01G283900 chr6A 80.214 187 33 3 5164 5349 517898405 517898588 3.250000e-28 137.0
11 TraesCS1B01G283900 chr6A 79.894 189 32 5 5164 5349 594863370 594863555 4.210000e-27 134.0
12 TraesCS1B01G283900 chr6A 88.462 52 4 2 5355 5404 351287174 351287123 2.010000e-05 62.1
13 TraesCS1B01G283900 chr3A 98.782 2463 26 2 1566 4027 728251962 728249503 0.000000e+00 4379.0
14 TraesCS1B01G283900 chr3A 84.431 1792 269 8 2239 4027 158535038 158536822 0.000000e+00 1755.0
15 TraesCS1B01G283900 chr3A 83.203 512 81 5 1573 2080 603270336 603270846 1.310000e-126 464.0
16 TraesCS1B01G283900 chr3A 79.154 638 128 5 1607 2242 158505152 158505786 2.860000e-118 436.0
17 TraesCS1B01G283900 chr3A 83.489 321 27 4 6032 6351 625234881 625235176 6.600000e-70 276.0
18 TraesCS1B01G283900 chr3A 83.529 170 24 4 5158 5325 588516479 588516312 8.970000e-34 156.0
19 TraesCS1B01G283900 chr3A 81.347 193 32 3 5158 5349 108032189 108032000 3.230000e-33 154.0
20 TraesCS1B01G283900 chr3A 83.453 139 15 6 5035 5166 38393174 38393311 9.100000e-24 122.0
21 TraesCS1B01G283900 chr3A 88.732 71 6 2 5615 5684 627253719 627253788 1.190000e-12 86.1
22 TraesCS1B01G283900 chr1A 91.312 1600 91 17 1 1565 468608994 468607408 0.000000e+00 2141.0
23 TraesCS1B01G283900 chr1A 94.540 1337 55 9 4033 5356 468607423 468606092 0.000000e+00 2049.0
24 TraesCS1B01G283900 chr1A 89.919 496 34 5 5446 5936 468606081 468605597 5.690000e-175 625.0
25 TraesCS1B01G283900 chr1A 80.846 402 77 0 1141 1542 323643607 323643206 3.890000e-82 316.0
26 TraesCS1B01G283900 chr1A 83.750 320 28 14 6032 6351 557421233 557420938 1.420000e-71 281.0
27 TraesCS1B01G283900 chr1A 88.780 205 21 1 6176 6378 369498107 369498311 4.000000e-62 250.0
28 TraesCS1B01G283900 chr1A 81.250 192 28 5 5160 5349 527790615 527790430 1.500000e-31 148.0
29 TraesCS1B01G283900 chr1A 92.222 90 7 0 5937 6026 468605564 468605475 1.960000e-25 128.0
30 TraesCS1B01G283900 chr1A 97.619 42 1 0 5387 5428 58627962 58627921 9.300000e-09 73.1
31 TraesCS1B01G283900 chr1D 89.951 1622 93 30 1 1565 370016434 370014826 0.000000e+00 2028.0
32 TraesCS1B01G283900 chr1D 94.162 1336 60 8 4036 5356 370014838 370013506 0.000000e+00 2019.0
33 TraesCS1B01G283900 chr1D 93.314 344 16 4 5447 5787 370013494 370013155 1.000000e-137 501.0
34 TraesCS1B01G283900 chr1D 80.597 402 78 0 1141 1542 252529221 252528820 1.810000e-80 311.0
35 TraesCS1B01G283900 chr1D 84.740 308 23 12 6044 6351 246951508 246951225 3.050000e-73 287.0
36 TraesCS1B01G283900 chr1D 82.019 317 33 12 6035 6351 42832022 42831730 1.440000e-61 248.0
37 TraesCS1B01G283900 chr1D 88.281 128 7 6 5036 5155 305226292 305226419 5.400000e-31 147.0
38 TraesCS1B01G283900 chr1D 85.039 127 13 3 5038 5158 341037335 341037461 2.530000e-24 124.0
39 TraesCS1B01G283900 chr1D 82.979 141 17 6 5033 5166 289395014 289395154 3.270000e-23 121.0
40 TraesCS1B01G283900 chr1D 89.773 88 6 2 5080 5166 359723473 359723388 7.090000e-20 110.0
41 TraesCS1B01G283900 chr1D 76.970 165 26 7 5186 5349 484027644 484027797 4.300000e-12 84.2
42 TraesCS1B01G283900 chr1D 82.222 90 12 3 5350 5436 434282789 434282701 2.590000e-09 75.0
43 TraesCS1B01G283900 chr1D 97.561 41 1 0 5388 5428 464798878 464798918 3.340000e-08 71.3
44 TraesCS1B01G283900 chr1D 100.000 35 0 0 5353 5387 127626776 127626810 1.560000e-06 65.8
45 TraesCS1B01G283900 chr5B 92.984 1240 79 6 1971 3208 281371741 281372974 0.000000e+00 1801.0
46 TraesCS1B01G283900 chr5B 94.103 407 18 3 1568 1973 281365881 281366282 1.230000e-171 614.0
47 TraesCS1B01G283900 chr5B 81.583 619 114 0 4096 4714 223984465 223983847 4.620000e-141 512.0
48 TraesCS1B01G283900 chr5B 94.545 275 11 4 3206 3479 281433276 281433547 8.010000e-114 422.0
49 TraesCS1B01G283900 chr5B 92.000 175 12 1 6179 6351 643465047 643464873 1.860000e-60 244.0
50 TraesCS1B01G283900 chr5B 90.909 143 12 1 6027 6168 357173971 357174113 2.460000e-44 191.0
51 TraesCS1B01G283900 chr5B 83.523 176 26 2 5158 5332 633679510 633679683 1.930000e-35 161.0
52 TraesCS1B01G283900 chr5B 85.385 130 11 5 5037 5158 636609304 636609433 1.960000e-25 128.0
53 TraesCS1B01G283900 chr5B 87.500 96 7 4 5350 5443 143720176 143720268 9.170000e-19 106.0
54 TraesCS1B01G283900 chr5B 85.567 97 5 6 5353 5440 354513793 354513697 7.140000e-15 93.5
55 TraesCS1B01G283900 chr5B 88.462 78 5 4 5354 5427 696437526 696437603 2.570000e-14 91.6
56 TraesCS1B01G283900 chr5B 86.076 79 4 5 5355 5427 415802059 415801982 2.000000e-10 78.7
57 TraesCS1B01G283900 chr6B 98.752 641 7 1 1566 2205 319823331 319823971 0.000000e+00 1138.0
58 TraesCS1B01G283900 chr6B 96.303 568 18 3 1567 2134 712653748 712654312 0.000000e+00 929.0
59 TraesCS1B01G283900 chr7A 93.548 620 38 2 3032 3651 589450347 589450964 0.000000e+00 922.0
60 TraesCS1B01G283900 chr7A 89.968 618 50 4 1590 2199 589433698 589434311 0.000000e+00 787.0
61 TraesCS1B01G283900 chr7A 92.578 512 37 1 2195 2706 589435599 589436109 0.000000e+00 734.0
62 TraesCS1B01G283900 chr7A 91.643 347 27 2 2702 3047 589449990 589450335 4.690000e-131 479.0
63 TraesCS1B01G283900 chr7A 93.115 305 20 1 6381 6684 472629425 472629121 4.760000e-121 446.0
64 TraesCS1B01G283900 chr7A 82.143 196 30 5 5156 5349 113455491 113455683 5.360000e-36 163.0
65 TraesCS1B01G283900 chr7A 85.000 80 3 5 5354 5425 191173804 191173882 9.300000e-09 73.1
66 TraesCS1B01G283900 chr5A 81.583 619 114 0 4096 4714 272132568 272131950 4.620000e-141 512.0
67 TraesCS1B01G283900 chr5A 92.857 56 3 1 5388 5443 239529879 239529825 5.560000e-11 80.5
68 TraesCS1B01G283900 chr5D 94.426 305 16 1 6381 6684 470046165 470046469 1.010000e-127 468.0
69 TraesCS1B01G283900 chr5D 94.257 296 17 0 6389 6684 324348123 324348418 2.840000e-123 453.0
70 TraesCS1B01G283900 chr5D 93.603 297 19 0 6388 6684 360902726 360902430 1.710000e-120 444.0
71 TraesCS1B01G283900 chr5D 83.178 321 27 10 6032 6351 360902981 360902687 1.100000e-67 268.0
72 TraesCS1B01G283900 chr5D 95.181 83 4 0 5076 5158 559421122 559421204 1.510000e-26 132.0
73 TraesCS1B01G283900 chr5D 92.391 92 6 1 5076 5166 27353959 27353868 5.440000e-26 130.0
74 TraesCS1B01G283900 chr5D 82.550 149 21 3 5186 5332 450748068 450748213 7.040000e-25 126.0
75 TraesCS1B01G283900 chr5D 78.351 194 37 4 5158 5349 438554254 438554064 3.270000e-23 121.0
76 TraesCS1B01G283900 chr5D 79.661 177 26 6 5158 5332 557938003 557937835 1.180000e-22 119.0
77 TraesCS1B01G283900 chr5D 79.651 172 27 6 5180 5349 497860633 497860798 4.240000e-22 117.0
78 TraesCS1B01G283900 chr5D 79.213 178 28 7 5158 5333 439208838 439209008 1.520000e-21 115.0
79 TraesCS1B01G283900 chr5D 97.619 42 1 0 5387 5428 536900297 536900338 9.300000e-09 73.1
80 TraesCS1B01G283900 chr5D 97.561 41 1 0 5387 5427 386674062 386674022 3.340000e-08 71.3
81 TraesCS1B01G283900 chr5D 92.157 51 1 2 5353 5401 530428429 530428380 1.200000e-07 69.4
82 TraesCS1B01G283900 chr5D 95.122 41 2 0 5387 5427 521497628 521497588 1.560000e-06 65.8
83 TraesCS1B01G283900 chr7D 93.115 305 20 1 6381 6684 471228595 471228291 4.760000e-121 446.0
84 TraesCS1B01G283900 chr7D 83.489 321 28 14 6032 6351 550996413 550996117 6.600000e-70 276.0
85 TraesCS1B01G283900 chr7D 80.220 182 32 4 5169 5349 221000791 221000969 4.210000e-27 134.0
86 TraesCS1B01G283900 chr7D 97.561 41 1 0 5387 5427 556128118 556128078 3.340000e-08 71.3
87 TraesCS1B01G283900 chr7D 89.091 55 2 3 5353 5404 428727632 428727579 1.560000e-06 65.8
88 TraesCS1B01G283900 chr7D 79.381 97 12 6 5338 5429 87504150 87504057 2.010000e-05 62.1
89 TraesCS1B01G283900 chr6D 93.115 305 20 1 6381 6684 462396041 462396345 4.760000e-121 446.0
90 TraesCS1B01G283900 chr6D 84.062 320 27 4 6032 6351 54232816 54233111 3.050000e-73 287.0
91 TraesCS1B01G283900 chr6D 83.699 319 28 2 6033 6351 355269685 355269391 5.100000e-71 279.0
92 TraesCS1B01G283900 chr6D 84.175 297 23 12 6055 6351 390026111 390026383 3.970000e-67 267.0
93 TraesCS1B01G283900 chr6D 81.818 187 30 3 5164 5349 455630464 455630647 3.230000e-33 154.0
94 TraesCS1B01G283900 chr6D 84.138 145 12 5 5032 5166 303059847 303059990 5.440000e-26 130.0
95 TraesCS1B01G283900 chr6D 92.045 88 6 1 5080 5166 410398382 410398295 9.100000e-24 122.0
96 TraesCS1B01G283900 chr6D 88.636 88 9 1 5080 5166 2956175 2956088 9.170000e-19 106.0
97 TraesCS1B01G283900 chr6D 87.640 89 10 1 5080 5167 134289063 134288975 1.190000e-17 102.0
98 TraesCS1B01G283900 chr6D 87.640 89 10 1 5080 5167 134694241 134694153 1.190000e-17 102.0
99 TraesCS1B01G283900 chr6D 88.372 86 8 2 5083 5166 426888329 426888244 1.190000e-17 102.0
100 TraesCS1B01G283900 chr6D 86.364 88 11 1 5080 5166 305362456 305362369 1.980000e-15 95.3
101 TraesCS1B01G283900 chr6D 95.349 43 0 1 5354 5394 419276460 419276502 4.330000e-07 67.6
102 TraesCS1B01G283900 chr6D 100.000 34 0 0 5354 5387 10448545 10448578 5.600000e-06 63.9
103 TraesCS1B01G283900 chr6D 97.297 37 1 0 5355 5391 287751869 287751833 5.600000e-06 63.9
104 TraesCS1B01G283900 chr6D 95.000 40 1 1 5355 5393 181350675 181350714 2.010000e-05 62.1
105 TraesCS1B01G283900 chr6D 91.304 46 3 1 5345 5390 228815610 228815566 2.010000e-05 62.1
106 TraesCS1B01G283900 chr6D 91.304 46 3 1 5345 5390 415236127 415236083 2.010000e-05 62.1
107 TraesCS1B01G283900 chr6D 89.796 49 4 1 5342 5390 416063606 416063559 2.010000e-05 62.1
108 TraesCS1B01G283900 chr6D 89.796 49 4 1 5342 5390 416172467 416172420 2.010000e-05 62.1
109 TraesCS1B01G283900 chr6D 91.304 46 3 1 5342 5387 472850555 472850599 2.010000e-05 62.1
110 TraesCS1B01G283900 chr2D 93.115 305 20 1 6381 6684 586371308 586371612 4.760000e-121 446.0
111 TraesCS1B01G283900 chr2D 92.787 305 21 1 6381 6684 57097576 57097272 2.210000e-119 440.0
112 TraesCS1B01G283900 chr2D 80.208 192 35 2 5158 5349 13988548 13988360 2.510000e-29 141.0
113 TraesCS1B01G283900 chr2D 81.143 175 25 7 5159 5332 522510497 522510330 4.210000e-27 134.0
114 TraesCS1B01G283900 chr2D 95.652 46 2 0 5387 5432 41824948 41824993 2.590000e-09 75.0
115 TraesCS1B01G283900 chr2D 95.652 46 2 0 5387 5432 641579026 641579071 2.590000e-09 75.0
116 TraesCS1B01G283900 chr2D 88.462 52 4 2 5337 5387 152230251 152230301 2.010000e-05 62.1
117 TraesCS1B01G283900 chr3D 92.787 305 21 1 6381 6684 8513042 8512738 2.210000e-119 440.0
118 TraesCS1B01G283900 chr3D 83.706 313 25 14 6041 6351 131490999 131491287 8.540000e-69 272.0
119 TraesCS1B01G283900 chr3D 84.173 139 14 6 5035 5166 29167294 29167431 1.960000e-25 128.0
120 TraesCS1B01G283900 chr3D 86.066 122 12 4 5049 5166 365519225 365519345 7.040000e-25 126.0
121 TraesCS1B01G283900 chr3D 83.088 136 15 4 5039 5166 611218400 611218535 4.240000e-22 117.0
122 TraesCS1B01G283900 chr3D 83.212 137 12 7 5040 5166 447571989 447571854 1.520000e-21 115.0
123 TraesCS1B01G283900 chr3D 97.619 42 1 0 5387 5428 609921400 609921359 9.300000e-09 73.1
124 TraesCS1B01G283900 chr3D 100.000 33 0 0 5355 5387 102348075 102348107 2.010000e-05 62.1
125 TraesCS1B01G283900 chr3D 100.000 33 0 0 5355 5387 161321095 161321127 2.010000e-05 62.1
126 TraesCS1B01G283900 chrUn 84.013 319 27 4 6033 6351 73960524 73960818 1.100000e-72 285.0
127 TraesCS1B01G283900 chrUn 79.545 176 26 7 5164 5332 287949818 287949990 4.240000e-22 117.0
128 TraesCS1B01G283900 chrUn 78.977 176 27 7 5164 5332 287943749 287943921 1.970000e-20 111.0
129 TraesCS1B01G283900 chrUn 83.465 127 13 7 5039 5158 339377878 339378003 1.970000e-20 111.0
130 TraesCS1B01G283900 chrUn 88.312 77 5 2 5354 5427 110336271 110336346 9.230000e-14 89.8
131 TraesCS1B01G283900 chrUn 85.227 88 11 2 5080 5166 248130791 248130705 9.230000e-14 89.8
132 TraesCS1B01G283900 chrUn 85.393 89 5 2 5050 5130 283591444 283591532 1.190000e-12 86.1
133 TraesCS1B01G283900 chrUn 97.561 41 1 0 5387 5427 302640085 302640045 3.340000e-08 71.3
134 TraesCS1B01G283900 chrUn 93.333 45 0 2 5355 5397 310386119 310386162 5.600000e-06 63.9
135 TraesCS1B01G283900 chrUn 97.222 36 1 0 5355 5390 21456930 21456895 2.010000e-05 62.1
136 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 26816114 26816082 2.010000e-05 62.1
137 TraesCS1B01G283900 chrUn 97.222 36 1 0 5355 5390 58768958 58768923 2.010000e-05 62.1
138 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 66416741 66416773 2.010000e-05 62.1
139 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 70024617 70024649 2.010000e-05 62.1
140 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 74064371 74064403 2.010000e-05 62.1
141 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 76500624 76500656 2.010000e-05 62.1
142 TraesCS1B01G283900 chrUn 97.222 36 1 0 5355 5390 77959774 77959739 2.010000e-05 62.1
143 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 95497568 95497600 2.010000e-05 62.1
144 TraesCS1B01G283900 chrUn 100.000 33 0 0 5355 5387 143991119 143991151 2.010000e-05 62.1
145 TraesCS1B01G283900 chrUn 97.222 36 1 0 5355 5390 170437980 170437945 2.010000e-05 62.1
146 TraesCS1B01G283900 chrUn 94.872 39 2 0 5349 5387 358202195 358202233 2.010000e-05 62.1
147 TraesCS1B01G283900 chrUn 92.683 41 3 0 5389 5429 359865660 359865700 7.240000e-05 60.2
148 TraesCS1B01G283900 chr4A 83.125 320 30 3 6032 6351 690120955 690120660 3.070000e-68 270.0
149 TraesCS1B01G283900 chr4A 90.476 147 12 1 6032 6176 626493830 626493976 6.840000e-45 193.0
150 TraesCS1B01G283900 chr4A 80.928 194 30 5 5160 5349 485227713 485227523 5.400000e-31 147.0
151 TraesCS1B01G283900 chr4A 81.818 176 28 3 5158 5332 632589045 632589217 1.940000e-30 145.0
152 TraesCS1B01G283900 chr4A 80.412 194 31 5 5160 5349 485256693 485256503 2.510000e-29 141.0
153 TraesCS1B01G283900 chr4A 88.095 84 5 2 5350 5428 647387560 647387643 1.980000e-15 95.3
154 TraesCS1B01G283900 chr4A 85.714 70 7 1 5355 5421 700422593 700422524 3.340000e-08 71.3
155 TraesCS1B01G283900 chr4D 82.759 319 31 2 6032 6350 482717832 482717538 5.140000e-66 263.0
156 TraesCS1B01G283900 chr4D 81.356 177 28 4 5158 5332 446899222 446899395 9.040000e-29 139.0
157 TraesCS1B01G283900 chr4D 79.381 194 22 14 5158 5347 505973390 505973569 3.270000e-23 121.0
158 TraesCS1B01G283900 chr4D 83.969 131 13 3 5039 5161 420141168 420141038 1.180000e-22 119.0
159 TraesCS1B01G283900 chr4D 82.517 143 16 4 5033 5166 296729552 296729410 4.240000e-22 117.0
160 TraesCS1B01G283900 chr4D 79.412 170 31 3 5164 5332 475965028 475964862 4.240000e-22 117.0
161 TraesCS1B01G283900 chr4D 93.478 46 0 2 5355 5398 124010642 124010686 1.560000e-06 65.8
162 TraesCS1B01G283900 chr4D 88.462 52 4 2 5355 5404 4580928 4580877 2.010000e-05 62.1
163 TraesCS1B01G283900 chr4D 100.000 33 0 0 5355 5387 111762218 111762250 2.010000e-05 62.1
164 TraesCS1B01G283900 chr4D 91.304 46 3 1 5345 5390 143976893 143976849 2.010000e-05 62.1
165 TraesCS1B01G283900 chr4D 92.857 42 2 1 5239 5279 231979020 231978979 7.240000e-05 60.2
166 TraesCS1B01G283900 chr4B 86.667 135 14 3 5035 5166 92547370 92547237 5.400000e-31 147.0
167 TraesCS1B01G283900 chr4B 95.652 46 2 0 5387 5432 542972600 542972555 2.590000e-09 75.0
168 TraesCS1B01G283900 chr4B 81.132 106 7 5 5335 5428 364668384 364668488 9.300000e-09 73.1
169 TraesCS1B01G283900 chr4B 93.617 47 1 1 5354 5398 621424695 621424741 1.200000e-07 69.4
170 TraesCS1B01G283900 chr4B 90.196 51 2 2 5349 5397 509166456 509166505 5.600000e-06 63.9
171 TraesCS1B01G283900 chr3B 84.337 83 5 5 5355 5435 409277961 409278037 2.590000e-09 75.0


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 TraesCS1B01G283900 chr1B 492786648 492793331 6683 True 12344.00 12344 100.000000 1 6684 1 chr1B.!!$R1 6683
1 TraesCS1B01G283900 chr2B 72965691 72968155 2464 False 4446.00 4446 99.229000 1564 4027 1 chr2B.!!$F2 2463
2 TraesCS1B01G283900 chr2B 758136004 758138464 2460 True 2361.00 2361 84.094000 1566 4025 1 chr2B.!!$R2 2459
3 TraesCS1B01G283900 chr2B 168675605 168676600 995 False 1735.00 1735 98.092000 1567 2562 1 chr2B.!!$F4 995
4 TraesCS1B01G283900 chr6A 485772865 485775327 2462 True 4433.00 4433 99.148000 1565 4027 1 chr6A.!!$R2 2462
5 TraesCS1B01G283900 chr3A 728249503 728251962 2459 True 4379.00 4379 98.782000 1566 4027 1 chr3A.!!$R3 2461
6 TraesCS1B01G283900 chr3A 158535038 158536822 1784 False 1755.00 1755 84.431000 2239 4027 1 chr3A.!!$F3 1788
7 TraesCS1B01G283900 chr3A 603270336 603270846 510 False 464.00 464 83.203000 1573 2080 1 chr3A.!!$F4 507
8 TraesCS1B01G283900 chr3A 158505152 158505786 634 False 436.00 436 79.154000 1607 2242 1 chr3A.!!$F2 635
9 TraesCS1B01G283900 chr1A 468605475 468608994 3519 True 1235.75 2141 91.998250 1 6026 4 chr1A.!!$R5 6025
10 TraesCS1B01G283900 chr1D 370013155 370016434 3279 True 1516.00 2028 92.475667 1 5787 3 chr1D.!!$R6 5786
11 TraesCS1B01G283900 chr5B 281371741 281372974 1233 False 1801.00 1801 92.984000 1971 3208 1 chr5B.!!$F3 1237
12 TraesCS1B01G283900 chr5B 223983847 223984465 618 True 512.00 512 81.583000 4096 4714 1 chr5B.!!$R1 618
13 TraesCS1B01G283900 chr6B 319823331 319823971 640 False 1138.00 1138 98.752000 1566 2205 1 chr6B.!!$F1 639
14 TraesCS1B01G283900 chr6B 712653748 712654312 564 False 929.00 929 96.303000 1567 2134 1 chr6B.!!$F2 567
15 TraesCS1B01G283900 chr7A 589433698 589436109 2411 False 760.50 787 91.273000 1590 2706 2 chr7A.!!$F3 1116
16 TraesCS1B01G283900 chr7A 589449990 589450964 974 False 700.50 922 92.595500 2702 3651 2 chr7A.!!$F4 949
17 TraesCS1B01G283900 chr5A 272131950 272132568 618 True 512.00 512 81.583000 4096 4714 1 chr5A.!!$R2 618
18 TraesCS1B01G283900 chr5D 360902430 360902981 551 True 356.00 444 88.390500 6032 6684 2 chr5D.!!$R7 652

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
645 690 0.179006 CCTCAGGAATTAGGCCAGCC 60.179 60.000 5.01 0.0 0.00 4.85 F
822 881 3.508793 CAGATGGTGTTCCTCAATTGCTT 59.491 43.478 0.00 0.0 34.23 3.91 F
3152 4553 3.776731 TGGAGATCCCTGAAACCTAGA 57.223 47.619 0.00 0.0 35.38 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3153 4554 1.340405 GCTGCCAAAGAAGGATGGAGA 60.340 52.381 0.00 0.0 39.12 3.71 R
4031 5438 2.733858 GCGGCAACTGTTTCAAACAAGA 60.734 45.455 4.13 0.0 41.61 3.02 R
6173 7631 0.035317 TCGAGACAATGCAGGCAAGT 59.965 50.000 0.00 0.0 0.00 3.16 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
24 25 2.029073 CCGTGAACAGGTGACGCT 59.971 61.111 0.00 0.00 0.00 5.07
67 68 1.409064 CCCTCGATCCGTTTGATCTGA 59.591 52.381 0.00 0.00 46.52 3.27
68 69 2.159099 CCCTCGATCCGTTTGATCTGAA 60.159 50.000 0.00 0.00 46.52 3.02
71 72 3.259064 TCGATCCGTTTGATCTGAAACC 58.741 45.455 0.00 0.00 46.52 3.27
78 79 4.218417 CCGTTTGATCTGAAACCCAAATCT 59.782 41.667 0.00 0.00 33.04 2.40
120 122 1.238625 GGTAGATCGCCTCGCTAGCT 61.239 60.000 13.93 0.00 31.76 3.32
125 127 1.388065 ATCGCCTCGCTAGCTTCTGT 61.388 55.000 13.93 0.00 0.00 3.41
128 130 1.443802 GCCTCGCTAGCTTCTGTTTT 58.556 50.000 13.93 0.00 0.00 2.43
142 144 3.399330 TCTGTTTTGATCGGTGAACCTC 58.601 45.455 0.00 0.00 0.00 3.85
143 145 3.138304 CTGTTTTGATCGGTGAACCTCA 58.862 45.455 0.00 0.00 0.00 3.86
144 146 3.546724 TGTTTTGATCGGTGAACCTCAA 58.453 40.909 0.00 0.00 31.03 3.02
147 149 3.485463 TTGATCGGTGAACCTCAAGTT 57.515 42.857 0.00 0.00 43.07 2.66
179 202 0.749649 TTGTGCTGTGGGCGAATTTT 59.250 45.000 0.00 0.00 45.43 1.82
192 215 0.598065 GAATTTTGCTGCTCGGTGGT 59.402 50.000 0.00 0.00 0.00 4.16
219 242 0.988145 TCCCTTCCGGAGCATGGAAT 60.988 55.000 3.34 0.00 41.02 3.01
234 257 1.919240 GGAATTTTTCCGGGGTGAGT 58.081 50.000 0.00 0.00 40.59 3.41
256 279 5.426509 AGTGGATGATCTGAGGATGTGTTTA 59.573 40.000 0.00 0.00 31.46 2.01
319 345 3.054802 TGTTCATTTTGCTTTTGTGGGGT 60.055 39.130 0.00 0.00 0.00 4.95
469 508 5.278169 GCTTCCATGCTTAATCTATGTGTGG 60.278 44.000 0.00 0.00 0.00 4.17
497 536 5.234972 GTGATGTCATGATAAGTGCGATTCA 59.765 40.000 0.00 0.00 0.00 2.57
591 633 2.764314 GCGGCATGCCAACTTCGAT 61.764 57.895 34.93 0.00 37.76 3.59
595 637 1.334869 GGCATGCCAACTTCGATTAGG 59.665 52.381 32.08 0.00 35.81 2.69
607 649 2.364632 TCGATTAGGTGCATGTTTGGG 58.635 47.619 0.00 0.00 0.00 4.12
645 690 0.179006 CCTCAGGAATTAGGCCAGCC 60.179 60.000 5.01 0.00 0.00 4.85
822 881 3.508793 CAGATGGTGTTCCTCAATTGCTT 59.491 43.478 0.00 0.00 34.23 3.91
965 1024 7.617041 ACAGAAACTTGCTCTTATACCAATC 57.383 36.000 0.00 0.00 0.00 2.67
1074 1139 5.215160 GTCAAGGTTGTTATTCAGCACAAG 58.785 41.667 0.00 0.00 33.55 3.16
1088 1153 4.828939 TCAGCACAAGATCCTTTGAACATT 59.171 37.500 1.96 0.00 0.00 2.71
1130 1197 5.124457 CCCAAACTAACTGATCACATTCCTG 59.876 44.000 0.00 0.00 0.00 3.86
1291 1358 5.930837 AGAGAGGTATCCTGACTTTGAAG 57.069 43.478 0.00 0.00 31.76 3.02
3152 4553 3.776731 TGGAGATCCCTGAAACCTAGA 57.223 47.619 0.00 0.00 35.38 2.43
3153 4554 4.286813 TGGAGATCCCTGAAACCTAGAT 57.713 45.455 0.00 0.00 35.38 1.98
4027 5434 6.314917 TGGCTTTCCCTCTTCTTTTATTCTT 58.685 36.000 0.00 0.00 0.00 2.52
4028 5435 6.782494 TGGCTTTCCCTCTTCTTTTATTCTTT 59.218 34.615 0.00 0.00 0.00 2.52
4029 5436 7.947890 TGGCTTTCCCTCTTCTTTTATTCTTTA 59.052 33.333 0.00 0.00 0.00 1.85
4030 5437 8.462811 GGCTTTCCCTCTTCTTTTATTCTTTAG 58.537 37.037 0.00 0.00 0.00 1.85
4031 5438 9.015367 GCTTTCCCTCTTCTTTTATTCTTTAGT 57.985 33.333 0.00 0.00 0.00 2.24
4035 5442 9.726438 TCCCTCTTCTTTTATTCTTTAGTCTTG 57.274 33.333 0.00 0.00 0.00 3.02
4036 5443 9.508642 CCCTCTTCTTTTATTCTTTAGTCTTGT 57.491 33.333 0.00 0.00 0.00 3.16
4088 5495 5.278808 GGATAGGGTGGTTGACAACTTTTTC 60.279 44.000 17.52 1.75 36.85 2.29
4089 5496 3.708451 AGGGTGGTTGACAACTTTTTCT 58.292 40.909 17.52 7.00 36.85 2.52
4090 5497 4.093743 AGGGTGGTTGACAACTTTTTCTT 58.906 39.130 17.52 0.00 36.85 2.52
4091 5498 4.530553 AGGGTGGTTGACAACTTTTTCTTT 59.469 37.500 17.52 0.00 36.85 2.52
4198 5605 3.429372 TTTGGACCTTGCTGGCCGT 62.429 57.895 0.00 0.00 40.22 5.68
4297 5704 5.247110 TGTCAGAGACATAAAGGAGAAGCTT 59.753 40.000 0.00 0.00 37.67 3.74
4432 5839 2.122729 AGGTGCCCTGAGGTGCTA 59.877 61.111 12.14 0.00 34.57 3.49
4825 6235 5.833406 TTTCTCAGCATGTTCAACTTTCA 57.167 34.783 0.00 0.00 37.40 2.69
4872 6282 2.107366 CCACTTTCAGTTTGGGTTGGT 58.893 47.619 0.00 0.00 0.00 3.67
5200 6618 7.358066 ACGTATAGTGTTGGTCTTATATGACG 58.642 38.462 11.45 0.00 37.81 4.35
5230 6649 1.090728 TCGAAGTGCTTTTGTGTGCA 58.909 45.000 0.00 0.00 36.79 4.57
5273 6694 0.189574 TCCTAGCTATGCAGAGGCCT 59.810 55.000 3.86 3.86 40.13 5.19
5275 6696 1.047002 CTAGCTATGCAGAGGCCTGT 58.953 55.000 12.00 1.36 42.35 4.00
5290 6711 1.990799 CCTGTTGTGCATGCTCAATG 58.009 50.000 31.10 25.45 39.49 2.82
5305 6726 4.152223 TGCTCAATGTGTTTGTATCGTCTG 59.848 41.667 0.00 0.00 36.65 3.51
5310 6731 3.595173 TGTGTTTGTATCGTCTGGATGG 58.405 45.455 0.00 0.00 36.55 3.51
5364 6785 9.555727 TTTATTGAAAATCTTATACTCCCTCCG 57.444 33.333 0.00 0.00 0.00 4.63
5365 6786 6.555463 TTGAAAATCTTATACTCCCTCCGT 57.445 37.500 0.00 0.00 0.00 4.69
5366 6787 6.555463 TGAAAATCTTATACTCCCTCCGTT 57.445 37.500 0.00 0.00 0.00 4.44
5367 6788 6.579865 TGAAAATCTTATACTCCCTCCGTTC 58.420 40.000 0.00 0.00 0.00 3.95
5368 6789 5.548181 AAATCTTATACTCCCTCCGTTCC 57.452 43.478 0.00 0.00 0.00 3.62
5369 6790 3.675348 TCTTATACTCCCTCCGTTCCA 57.325 47.619 0.00 0.00 0.00 3.53
5370 6791 3.985127 TCTTATACTCCCTCCGTTCCAA 58.015 45.455 0.00 0.00 0.00 3.53
5371 6792 4.355549 TCTTATACTCCCTCCGTTCCAAA 58.644 43.478 0.00 0.00 0.00 3.28
5372 6793 4.778958 TCTTATACTCCCTCCGTTCCAAAA 59.221 41.667 0.00 0.00 0.00 2.44
5373 6794 5.427481 TCTTATACTCCCTCCGTTCCAAAAT 59.573 40.000 0.00 0.00 0.00 1.82
5374 6795 6.612456 TCTTATACTCCCTCCGTTCCAAAATA 59.388 38.462 0.00 0.00 0.00 1.40
5375 6796 5.703730 ATACTCCCTCCGTTCCAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
5376 6797 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
5377 6798 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
5378 6799 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
5379 6800 3.073356 TCCCTCCGTTCCAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
5380 6801 3.439129 CCCTCCGTTCCAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
5381 6802 4.324267 CCTCCGTTCCAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
5382 6803 4.392138 CCTCCGTTCCAAAATAAGTGTCTC 59.608 45.833 0.00 0.00 0.00 3.36
5383 6804 4.963373 TCCGTTCCAAAATAAGTGTCTCA 58.037 39.130 0.00 0.00 0.00 3.27
5384 6805 5.369833 TCCGTTCCAAAATAAGTGTCTCAA 58.630 37.500 0.00 0.00 0.00 3.02
5385 6806 5.237779 TCCGTTCCAAAATAAGTGTCTCAAC 59.762 40.000 0.00 0.00 0.00 3.18
5386 6807 5.238650 CCGTTCCAAAATAAGTGTCTCAACT 59.761 40.000 0.00 0.00 0.00 3.16
5387 6808 6.136071 CGTTCCAAAATAAGTGTCTCAACTG 58.864 40.000 0.00 0.00 0.00 3.16
5388 6809 6.238374 CGTTCCAAAATAAGTGTCTCAACTGT 60.238 38.462 0.00 0.00 0.00 3.55
5389 6810 7.042321 CGTTCCAAAATAAGTGTCTCAACTGTA 60.042 37.037 0.00 0.00 0.00 2.74
5390 6811 7.724305 TCCAAAATAAGTGTCTCAACTGTAC 57.276 36.000 0.00 0.00 0.00 2.90
5391 6812 7.506114 TCCAAAATAAGTGTCTCAACTGTACT 58.494 34.615 0.00 0.00 0.00 2.73
5392 6813 8.644216 TCCAAAATAAGTGTCTCAACTGTACTA 58.356 33.333 0.00 0.00 0.00 1.82
5393 6814 9.268268 CCAAAATAAGTGTCTCAACTGTACTAA 57.732 33.333 0.00 0.00 0.00 2.24
5395 6816 8.535690 AAATAAGTGTCTCAACTGTACTAAGC 57.464 34.615 0.00 0.00 0.00 3.09
5396 6817 5.793030 AAGTGTCTCAACTGTACTAAGCT 57.207 39.130 0.00 0.00 0.00 3.74
5397 6818 5.793030 AGTGTCTCAACTGTACTAAGCTT 57.207 39.130 3.48 3.48 0.00 3.74
5398 6819 5.533482 AGTGTCTCAACTGTACTAAGCTTG 58.467 41.667 9.86 1.57 0.00 4.01
5399 6820 5.302059 AGTGTCTCAACTGTACTAAGCTTGA 59.698 40.000 9.86 0.00 0.00 3.02
5400 6821 5.631512 GTGTCTCAACTGTACTAAGCTTGAG 59.368 44.000 9.86 4.51 37.04 3.02
5401 6822 5.535030 TGTCTCAACTGTACTAAGCTTGAGA 59.465 40.000 9.86 7.05 39.39 3.27
5402 6823 5.859648 GTCTCAACTGTACTAAGCTTGAGAC 59.140 44.000 23.59 23.59 45.21 3.36
5403 6824 5.535030 TCTCAACTGTACTAAGCTTGAGACA 59.465 40.000 9.86 8.91 38.26 3.41
5404 6825 5.773575 TCAACTGTACTAAGCTTGAGACAG 58.226 41.667 23.89 23.89 40.09 3.51
5406 6827 5.793030 ACTGTACTAAGCTTGAGACAGTT 57.207 39.130 24.82 15.15 43.70 3.16
5407 6828 6.896021 ACTGTACTAAGCTTGAGACAGTTA 57.104 37.500 24.82 8.58 43.70 2.24
5408 6829 7.469537 ACTGTACTAAGCTTGAGACAGTTAT 57.530 36.000 24.82 11.55 43.70 1.89
5409 6830 7.897864 ACTGTACTAAGCTTGAGACAGTTATT 58.102 34.615 24.82 11.30 43.70 1.40
5410 6831 8.368668 ACTGTACTAAGCTTGAGACAGTTATTT 58.631 33.333 24.82 11.04 43.70 1.40
5411 6832 9.209175 CTGTACTAAGCTTGAGACAGTTATTTT 57.791 33.333 20.13 0.00 31.70 1.82
5412 6833 8.988934 TGTACTAAGCTTGAGACAGTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
5413 6834 7.440523 ACTAAGCTTGAGACAGTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
5414 6835 5.712152 AAGCTTGAGACAGTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5415 6836 4.985538 AGCTTGAGACAGTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
5416 6837 4.762251 AGCTTGAGACAGTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
5417 6838 4.518970 GCTTGAGACAGTTATTTTGGGACA 59.481 41.667 0.00 0.00 0.00 4.02
5418 6839 5.335191 GCTTGAGACAGTTATTTTGGGACAG 60.335 44.000 0.00 0.00 42.39 3.51
5419 6840 5.560722 TGAGACAGTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
5420 6841 5.551233 TGAGACAGTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
5421 6842 4.911390 AGACAGTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
5422 6843 4.010349 GACAGTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
5423 6844 3.655777 ACAGTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
5424 6845 4.263506 ACAGTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
5437 6858 3.262420 CAGAGGGAGTATTTGTGAACGG 58.738 50.000 0.00 0.00 0.00 4.44
5438 6859 3.056107 CAGAGGGAGTATTTGTGAACGGA 60.056 47.826 0.00 0.00 0.00 4.69
5439 6860 3.195825 AGAGGGAGTATTTGTGAACGGAG 59.804 47.826 0.00 0.00 0.00 4.63
5440 6861 2.236395 AGGGAGTATTTGTGAACGGAGG 59.764 50.000 0.00 0.00 0.00 4.30
5441 6862 2.629051 GGAGTATTTGTGAACGGAGGG 58.371 52.381 0.00 0.00 0.00 4.30
5442 6863 2.235402 GGAGTATTTGTGAACGGAGGGA 59.765 50.000 0.00 0.00 0.00 4.20
5443 6864 3.259902 GAGTATTTGTGAACGGAGGGAC 58.740 50.000 0.00 0.00 0.00 4.46
5444 6865 2.027469 AGTATTTGTGAACGGAGGGACC 60.027 50.000 0.00 0.00 0.00 4.46
5524 6945 3.118223 ACCAAAGAATAGGCCAGTAGCTC 60.118 47.826 5.01 0.00 43.05 4.09
5644 7067 1.174783 TCTCCAAGGCAGAGTACGAC 58.825 55.000 0.00 0.00 32.93 4.34
5692 7115 0.605589 AGTGCTTCTGAAGAGTCGGG 59.394 55.000 21.06 0.00 0.00 5.14
5811 7237 4.302559 AAGGGGTACAGGAAAATCAGTC 57.697 45.455 0.00 0.00 0.00 3.51
5820 7246 3.681897 CAGGAAAATCAGTCTCGGTTCAG 59.318 47.826 0.00 0.00 0.00 3.02
5828 7254 1.694696 AGTCTCGGTTCAGCTTTTCCT 59.305 47.619 0.00 0.00 0.00 3.36
5944 7402 1.602237 CATACTCGTGGCCCTGGTT 59.398 57.895 0.00 0.00 0.00 3.67
5968 7426 6.741109 TGAAATCGTAGTGACACTGAAACTA 58.259 36.000 18.58 1.15 0.00 2.24
5975 7433 2.160417 GTGACACTGAAACTATGCTGCC 59.840 50.000 0.00 0.00 0.00 4.85
5976 7434 2.224499 TGACACTGAAACTATGCTGCCA 60.224 45.455 0.00 0.00 0.00 4.92
6016 7474 1.139947 GCAGCCAGACTAGACGACC 59.860 63.158 0.00 0.00 0.00 4.79
6020 7478 2.044555 CCAGACTAGACGACCGCCA 61.045 63.158 0.00 0.00 0.00 5.69
6050 7508 0.325933 CACATCTGAACCCAGCCTGA 59.674 55.000 0.00 0.00 40.20 3.86
6080 7538 3.751479 AACAGCCTCATATGCGACATA 57.249 42.857 0.00 0.00 0.00 2.29
6101 7559 1.289276 GCAAGTTGTTTGGTTGCCTG 58.711 50.000 4.48 0.00 40.61 4.85
6104 7562 0.175531 AGTTGTTTGGTTGCCTGCAC 59.824 50.000 0.00 0.00 0.00 4.57
6107 7565 1.697284 TGTTTGGTTGCCTGCACATA 58.303 45.000 0.00 0.00 0.00 2.29
6109 7567 1.067635 GTTTGGTTGCCTGCACATAGG 60.068 52.381 0.00 0.00 40.95 2.57
6139 7597 2.507407 TAGGGGATCAACTTTGGCAC 57.493 50.000 0.00 0.00 0.00 5.01
6148 7606 2.029828 TCAACTTTGGCACGTTGTTTGT 60.030 40.909 21.28 0.00 40.88 2.83
6168 7626 2.437359 GCCTGCATTGTCTCGGCT 60.437 61.111 3.76 0.00 37.76 5.52
6169 7627 2.042831 GCCTGCATTGTCTCGGCTT 61.043 57.895 3.76 0.00 37.76 4.35
6170 7628 0.744414 GCCTGCATTGTCTCGGCTTA 60.744 55.000 3.76 0.00 37.76 3.09
6171 7629 1.009829 CCTGCATTGTCTCGGCTTAC 58.990 55.000 0.00 0.00 0.00 2.34
6172 7630 1.675714 CCTGCATTGTCTCGGCTTACA 60.676 52.381 0.00 0.00 0.00 2.41
6173 7631 2.076100 CTGCATTGTCTCGGCTTACAA 58.924 47.619 0.00 0.00 39.73 2.41
6174 7632 1.804151 TGCATTGTCTCGGCTTACAAC 59.196 47.619 0.00 0.00 38.35 3.32
6175 7633 2.076863 GCATTGTCTCGGCTTACAACT 58.923 47.619 0.00 0.00 38.35 3.16
6176 7634 2.484264 GCATTGTCTCGGCTTACAACTT 59.516 45.455 0.00 0.00 38.35 2.66
6177 7635 3.667960 GCATTGTCTCGGCTTACAACTTG 60.668 47.826 0.00 0.00 38.35 3.16
6178 7636 1.508632 TGTCTCGGCTTACAACTTGC 58.491 50.000 0.00 0.00 0.00 4.01
6179 7637 0.796927 GTCTCGGCTTACAACTTGCC 59.203 55.000 0.00 0.00 42.94 4.52
6180 7638 0.685097 TCTCGGCTTACAACTTGCCT 59.315 50.000 0.00 0.00 44.09 4.75
6181 7639 0.798776 CTCGGCTTACAACTTGCCTG 59.201 55.000 0.00 0.00 44.09 4.85
6182 7640 1.210155 CGGCTTACAACTTGCCTGC 59.790 57.895 0.00 0.00 44.09 4.85
6183 7641 1.514678 CGGCTTACAACTTGCCTGCA 61.515 55.000 0.00 0.00 44.09 4.41
6184 7642 0.890683 GGCTTACAACTTGCCTGCAT 59.109 50.000 0.00 0.00 43.05 3.96
6185 7643 1.273327 GGCTTACAACTTGCCTGCATT 59.727 47.619 0.00 0.00 43.05 3.56
6186 7644 2.331194 GCTTACAACTTGCCTGCATTG 58.669 47.619 4.39 4.39 0.00 2.82
6187 7645 2.288395 GCTTACAACTTGCCTGCATTGT 60.288 45.455 13.70 13.70 38.72 2.71
6188 7646 3.568538 CTTACAACTTGCCTGCATTGTC 58.431 45.455 12.84 0.00 36.67 3.18
6189 7647 1.696063 ACAACTTGCCTGCATTGTCT 58.304 45.000 5.51 0.00 29.30 3.41
6190 7648 1.610522 ACAACTTGCCTGCATTGTCTC 59.389 47.619 5.51 0.00 29.30 3.36
6191 7649 0.877071 AACTTGCCTGCATTGTCTCG 59.123 50.000 0.00 0.00 0.00 4.04
6192 7650 0.035317 ACTTGCCTGCATTGTCTCGA 59.965 50.000 0.00 0.00 0.00 4.04
6196 7654 1.206849 TGCCTGCATTGTCTCGACATA 59.793 47.619 0.00 0.00 41.52 2.29
6205 7663 5.220228 GCATTGTCTCGACATACAACTACAC 60.220 44.000 0.00 0.00 41.52 2.90
6206 7664 4.074466 TGTCTCGACATACAACTACACG 57.926 45.455 0.00 0.00 36.21 4.49
6241 7699 1.678101 GCATGGGGTGTGATTAAGAGC 59.322 52.381 0.00 0.00 0.00 4.09
6278 7736 4.701765 AGCACACATGATTAAGAGCTAGG 58.298 43.478 0.00 0.00 0.00 3.02
6283 7741 6.040278 CACACATGATTAAGAGCTAGGAGAGA 59.960 42.308 0.00 0.00 0.00 3.10
6288 7746 5.600484 TGATTAAGAGCTAGGAGAGAAAGGG 59.400 44.000 0.00 0.00 0.00 3.95
6290 7748 1.062505 AGAGCTAGGAGAGAAAGGGGG 60.063 57.143 0.00 0.00 0.00 5.40
6305 7763 2.562296 AGGGGGAGAAGAAATGCAGTA 58.438 47.619 0.00 0.00 0.00 2.74
6308 7766 3.372025 GGGGGAGAAGAAATGCAGTATGT 60.372 47.826 0.00 0.00 39.31 2.29
6309 7767 3.629398 GGGGAGAAGAAATGCAGTATGTG 59.371 47.826 0.00 0.00 39.31 3.21
6320 7778 1.016627 CAGTATGTGCCGAACCATGG 58.983 55.000 11.19 11.19 0.00 3.66
6336 7794 4.344474 GGCGACCGCGGAGGATAG 62.344 72.222 35.90 16.19 45.00 2.08
6337 7795 3.593794 GCGACCGCGGAGGATAGT 61.594 66.667 35.90 7.12 45.00 2.12
6338 7796 2.331805 CGACCGCGGAGGATAGTG 59.668 66.667 35.90 7.71 45.00 2.74
6339 7797 2.728817 GACCGCGGAGGATAGTGG 59.271 66.667 35.90 0.02 45.00 4.00
6340 7798 2.043248 ACCGCGGAGGATAGTGGT 60.043 61.111 35.90 0.68 45.42 4.16
6341 7799 2.728817 CCGCGGAGGATAGTGGTC 59.271 66.667 24.07 0.00 45.00 4.02
6342 7800 2.331805 CGCGGAGGATAGTGGTCG 59.668 66.667 0.00 0.00 0.00 4.79
6343 7801 2.478890 CGCGGAGGATAGTGGTCGT 61.479 63.158 0.00 0.00 0.00 4.34
6344 7802 1.065928 GCGGAGGATAGTGGTCGTG 59.934 63.158 0.00 0.00 0.00 4.35
6345 7803 1.734137 CGGAGGATAGTGGTCGTGG 59.266 63.158 0.00 0.00 0.00 4.94
6346 7804 1.442148 GGAGGATAGTGGTCGTGGC 59.558 63.158 0.00 0.00 0.00 5.01
6347 7805 1.065928 GAGGATAGTGGTCGTGGCG 59.934 63.158 0.00 0.00 0.00 5.69
6348 7806 2.585247 GGATAGTGGTCGTGGCGC 60.585 66.667 0.00 0.00 0.00 6.53
6368 7826 4.451150 GACCATGGCGACTGCGGA 62.451 66.667 13.04 0.00 44.10 5.54
6378 7836 1.384989 CGACTGCGGAGGATAGTGGT 61.385 60.000 9.36 0.00 0.00 4.16
6406 7864 4.760047 GACCATGGCGACTGCGGT 62.760 66.667 13.04 0.00 44.10 5.68
6407 7865 4.329545 ACCATGGCGACTGCGGTT 62.330 61.111 13.04 0.00 44.10 4.44
6408 7866 3.803082 CCATGGCGACTGCGGTTG 61.803 66.667 8.72 8.72 44.10 3.77
6409 7867 2.741985 CATGGCGACTGCGGTTGA 60.742 61.111 17.62 0.00 44.10 3.18
6410 7868 2.108514 CATGGCGACTGCGGTTGAT 61.109 57.895 17.62 0.00 44.10 2.57
6411 7869 0.809636 CATGGCGACTGCGGTTGATA 60.810 55.000 17.62 4.60 44.10 2.15
6412 7870 0.530650 ATGGCGACTGCGGTTGATAG 60.531 55.000 17.62 0.00 44.10 2.08
6413 7871 1.153628 GGCGACTGCGGTTGATAGT 60.154 57.895 17.62 0.00 44.10 2.12
6414 7872 1.421410 GGCGACTGCGGTTGATAGTG 61.421 60.000 17.62 0.00 44.10 2.74
6415 7873 1.421410 GCGACTGCGGTTGATAGTGG 61.421 60.000 17.62 0.00 38.16 4.00
6416 7874 0.108804 CGACTGCGGTTGATAGTGGT 60.109 55.000 7.16 0.00 0.00 4.16
6417 7875 1.671850 CGACTGCGGTTGATAGTGGTT 60.672 52.381 7.16 0.00 0.00 3.67
6418 7876 1.732259 GACTGCGGTTGATAGTGGTTG 59.268 52.381 0.00 0.00 0.00 3.77
6419 7877 1.071699 ACTGCGGTTGATAGTGGTTGT 59.928 47.619 0.00 0.00 0.00 3.32
6420 7878 1.464608 CTGCGGTTGATAGTGGTTGTG 59.535 52.381 0.00 0.00 0.00 3.33
6421 7879 1.070914 TGCGGTTGATAGTGGTTGTGA 59.929 47.619 0.00 0.00 0.00 3.58
6422 7880 1.463444 GCGGTTGATAGTGGTTGTGAC 59.537 52.381 0.00 0.00 0.00 3.67
6423 7881 1.724623 CGGTTGATAGTGGTTGTGACG 59.275 52.381 0.00 0.00 0.00 4.35
6424 7882 2.762745 GGTTGATAGTGGTTGTGACGT 58.237 47.619 0.00 0.00 0.00 4.34
6425 7883 2.735134 GGTTGATAGTGGTTGTGACGTC 59.265 50.000 9.11 9.11 0.00 4.34
6426 7884 2.341318 TGATAGTGGTTGTGACGTCG 57.659 50.000 11.62 0.00 0.00 5.12
6452 7910 2.354821 CGACATGACGAGTATGGAGTCA 59.645 50.000 12.27 0.00 46.99 3.41
6460 7918 2.031595 CGAGTATGGAGTCATGGACGAG 60.032 54.545 0.00 0.00 37.67 4.18
6529 7987 2.310233 TGCTCGCGCAAAGACAGTC 61.310 57.895 8.75 0.00 44.62 3.51
6566 8024 3.564027 GTGCTCGCGCCATGGTAC 61.564 66.667 14.67 4.76 34.43 3.34
6572 8030 2.890474 GCGCCATGGTACCGTCAG 60.890 66.667 14.67 0.00 0.00 3.51
6641 8099 1.682394 CCAGTGTAGTAGGGCGAGAGT 60.682 57.143 0.00 0.00 0.00 3.24
6650 8108 3.844090 GGCGAGAGTGAGGAGGCC 61.844 72.222 0.00 0.00 0.00 5.19
6663 8121 0.755686 GGAGGCCAAGATGATCGACT 59.244 55.000 5.01 0.00 0.00 4.18
6669 8127 1.405463 CCAAGATGATCGACTCCGTCA 59.595 52.381 0.00 0.00 37.05 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.732016 CGTCACCTGTTCACGGGA 59.268 61.111 12.03 0.00 45.36 5.14
54 55 2.940994 TGGGTTTCAGATCAAACGGA 57.059 45.000 0.00 0.00 37.16 4.69
67 68 3.146847 GGAACTCGACAGATTTGGGTTT 58.853 45.455 0.00 0.00 0.00 3.27
68 69 2.105821 TGGAACTCGACAGATTTGGGTT 59.894 45.455 0.00 0.00 0.00 4.11
98 100 0.108019 TAGCGAGGCGATCTACCTGA 59.892 55.000 8.77 0.00 37.77 3.86
120 122 3.813166 GAGGTTCACCGATCAAAACAGAA 59.187 43.478 0.00 0.00 42.08 3.02
125 127 3.815809 ACTTGAGGTTCACCGATCAAAA 58.184 40.909 0.00 0.00 42.08 2.44
142 144 4.265320 GCACAAGAAACCGAAAAGAACTTG 59.735 41.667 0.00 0.00 39.02 3.16
143 145 4.157840 AGCACAAGAAACCGAAAAGAACTT 59.842 37.500 0.00 0.00 0.00 2.66
144 146 3.694566 AGCACAAGAAACCGAAAAGAACT 59.305 39.130 0.00 0.00 0.00 3.01
147 149 3.013921 ACAGCACAAGAAACCGAAAAGA 58.986 40.909 0.00 0.00 0.00 2.52
148 150 3.108144 CACAGCACAAGAAACCGAAAAG 58.892 45.455 0.00 0.00 0.00 2.27
154 177 1.363807 GCCCACAGCACAAGAAACC 59.636 57.895 0.00 0.00 42.97 3.27
179 202 4.641645 CCCAACCACCGAGCAGCA 62.642 66.667 0.00 0.00 0.00 4.41
219 242 0.774908 ATCCACTCACCCCGGAAAAA 59.225 50.000 0.73 0.00 31.18 1.94
234 257 4.849813 AAACACATCCTCAGATCATCCA 57.150 40.909 0.00 0.00 0.00 3.41
325 355 0.404040 AACATTTCGAGGCAAGGGGA 59.596 50.000 0.00 0.00 0.00 4.81
354 384 2.202703 AATCCGCGCACCGTCTAC 60.203 61.111 8.75 0.00 34.38 2.59
361 396 2.526120 GGCACTAGAATCCGCGCAC 61.526 63.158 8.75 0.00 0.00 5.34
458 493 1.131638 ATCACGGGCCACACATAGAT 58.868 50.000 4.39 0.00 0.00 1.98
469 508 2.545526 CACTTATCATGACATCACGGGC 59.454 50.000 0.00 0.00 0.00 6.13
497 536 4.855298 TCCCGATCCCAATTTCTAAAGT 57.145 40.909 0.00 0.00 0.00 2.66
579 621 1.271108 TGCACCTAATCGAAGTTGGCA 60.271 47.619 0.00 0.00 0.00 4.92
583 625 4.082787 CCAAACATGCACCTAATCGAAGTT 60.083 41.667 0.00 0.00 0.00 2.66
591 633 2.390225 AACCCCAAACATGCACCTAA 57.610 45.000 0.00 0.00 0.00 2.69
595 637 0.943673 GCAAAACCCCAAACATGCAC 59.056 50.000 0.00 0.00 34.10 4.57
607 649 0.179137 GCGGATAGCCAAGCAAAACC 60.179 55.000 0.00 0.00 40.81 3.27
672 717 6.399639 TGAAAGTTTTTCTTCCATACACCC 57.600 37.500 3.53 0.00 35.02 4.61
822 881 5.215845 TGTATCTGTCATCTGGTGGGATAA 58.784 41.667 0.00 0.00 0.00 1.75
965 1024 6.115446 TCCTGTAAGAAATCTGCAATGGTAG 58.885 40.000 0.00 0.00 34.07 3.18
1035 1096 0.687920 TGACCATTCCAGTGCCGTTA 59.312 50.000 0.00 0.00 0.00 3.18
1095 1160 5.012664 TCAGTTAGTTTGGGAGAGCATGTTA 59.987 40.000 0.00 0.00 0.00 2.41
1130 1197 0.681175 AAACCAGCCTGCCAAACATC 59.319 50.000 0.00 0.00 0.00 3.06
1291 1358 1.846007 TGCCATGTTCAATGGGGTAC 58.154 50.000 6.50 0.00 39.53 3.34
3152 4553 2.686118 GCTGCCAAAGAAGGATGGAGAT 60.686 50.000 0.00 0.00 39.12 2.75
3153 4554 1.340405 GCTGCCAAAGAAGGATGGAGA 60.340 52.381 0.00 0.00 39.12 3.71
4027 5434 5.646606 GGCAACTGTTTCAAACAAGACTAA 58.353 37.500 4.13 0.00 41.61 2.24
4028 5435 4.201871 CGGCAACTGTTTCAAACAAGACTA 60.202 41.667 4.13 0.00 41.61 2.59
4029 5436 3.427503 CGGCAACTGTTTCAAACAAGACT 60.428 43.478 4.13 0.00 41.61 3.24
4030 5437 2.851824 CGGCAACTGTTTCAAACAAGAC 59.148 45.455 4.13 0.00 41.61 3.01
4031 5438 2.733858 GCGGCAACTGTTTCAAACAAGA 60.734 45.455 4.13 0.00 41.61 3.02
4032 5439 1.587946 GCGGCAACTGTTTCAAACAAG 59.412 47.619 4.13 1.65 41.61 3.16
4033 5440 1.203523 AGCGGCAACTGTTTCAAACAA 59.796 42.857 4.13 0.00 41.61 2.83
4034 5441 0.814457 AGCGGCAACTGTTTCAAACA 59.186 45.000 2.24 2.24 39.52 2.83
4035 5442 1.199624 CAGCGGCAACTGTTTCAAAC 58.800 50.000 1.45 0.00 32.78 2.93
4036 5443 1.098869 TCAGCGGCAACTGTTTCAAA 58.901 45.000 1.45 0.00 38.84 2.69
4037 5444 1.065401 CTTCAGCGGCAACTGTTTCAA 59.935 47.619 1.45 0.00 38.84 2.69
4038 5445 0.662619 CTTCAGCGGCAACTGTTTCA 59.337 50.000 1.45 0.00 38.84 2.69
4039 5446 0.663153 ACTTCAGCGGCAACTGTTTC 59.337 50.000 1.45 0.00 38.84 2.78
4040 5447 1.065551 GAACTTCAGCGGCAACTGTTT 59.934 47.619 1.45 0.00 38.84 2.83
4041 5448 0.663153 GAACTTCAGCGGCAACTGTT 59.337 50.000 1.45 1.92 38.84 3.16
4042 5449 0.463654 TGAACTTCAGCGGCAACTGT 60.464 50.000 1.45 0.00 38.84 3.55
4043 5450 0.040958 GTGAACTTCAGCGGCAACTG 60.041 55.000 1.45 0.00 39.12 3.16
4044 5451 0.179045 AGTGAACTTCAGCGGCAACT 60.179 50.000 1.45 0.00 0.00 3.16
4045 5452 0.040958 CAGTGAACTTCAGCGGCAAC 60.041 55.000 1.45 0.00 0.00 4.17
4046 5453 1.165907 CCAGTGAACTTCAGCGGCAA 61.166 55.000 1.45 0.00 0.00 4.52
4047 5454 1.597854 CCAGTGAACTTCAGCGGCA 60.598 57.895 1.45 0.00 0.00 5.69
4088 5495 2.094894 CGAGCACAATACCTGCAGAAAG 59.905 50.000 17.39 0.15 37.08 2.62
4089 5496 2.076100 CGAGCACAATACCTGCAGAAA 58.924 47.619 17.39 2.32 37.08 2.52
4090 5497 1.275010 TCGAGCACAATACCTGCAGAA 59.725 47.619 17.39 2.75 37.08 3.02
4091 5498 0.894835 TCGAGCACAATACCTGCAGA 59.105 50.000 17.39 0.00 37.08 4.26
4198 5605 7.233553 ATCTTCATTAGATTATCCGTGAGGTCA 59.766 37.037 0.00 0.00 46.45 4.02
4297 5704 0.037590 AATCAAGGGCCACGTAAGCA 59.962 50.000 6.18 0.00 45.62 3.91
4432 5839 2.024655 ACCAACATGAGATGGCTGGAAT 60.025 45.455 14.15 0.00 41.12 3.01
5171 6589 9.006839 CATATAAGACCAACACTATACGTAGGA 57.993 37.037 0.08 0.00 31.96 2.94
5183 6601 4.827692 AGCAACGTCATATAAGACCAACA 58.172 39.130 2.65 0.00 35.07 3.33
5200 6618 3.813529 AGCACTTCGACAAATAGCAAC 57.186 42.857 0.00 0.00 0.00 4.17
5230 6649 2.094286 CACACAACCAACACCAACACAT 60.094 45.455 0.00 0.00 0.00 3.21
5265 6686 1.880894 CATGCACAACAGGCCTCTG 59.119 57.895 0.00 5.97 46.10 3.35
5273 6694 1.682323 ACACATTGAGCATGCACAACA 59.318 42.857 28.97 15.88 36.14 3.33
5275 6696 3.124560 CAAACACATTGAGCATGCACAA 58.875 40.909 28.63 28.63 41.85 3.33
5290 6711 3.596214 ACCATCCAGACGATACAAACAC 58.404 45.455 0.00 0.00 0.00 3.32
5341 6762 7.138054 ACGGAGGGAGTATAAGATTTTCAAT 57.862 36.000 0.00 0.00 0.00 2.57
5343 6764 6.407752 GGAACGGAGGGAGTATAAGATTTTCA 60.408 42.308 0.00 0.00 0.00 2.69
5349 6770 3.675348 TGGAACGGAGGGAGTATAAGA 57.325 47.619 0.00 0.00 0.00 2.10
5350 6771 4.748277 TTTGGAACGGAGGGAGTATAAG 57.252 45.455 0.00 0.00 0.00 1.73
5351 6772 5.703730 ATTTTGGAACGGAGGGAGTATAA 57.296 39.130 0.00 0.00 0.00 0.98
5353 6774 5.191124 ACTTATTTTGGAACGGAGGGAGTAT 59.809 40.000 0.00 0.00 0.00 2.12
5354 6775 4.533311 ACTTATTTTGGAACGGAGGGAGTA 59.467 41.667 0.00 0.00 0.00 2.59
5355 6776 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
5356 6777 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
5357 6778 3.073356 ACACTTATTTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
5358 6779 3.418047 ACACTTATTTTGGAACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
5359 6780 4.324267 AGACACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
5360 6781 4.994852 TGAGACACTTATTTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
5361 6782 4.963373 TGAGACACTTATTTTGGAACGGA 58.037 39.130 0.00 0.00 0.00 4.69
5362 6783 5.238650 AGTTGAGACACTTATTTTGGAACGG 59.761 40.000 0.00 0.00 0.00 4.44
5363 6784 6.136071 CAGTTGAGACACTTATTTTGGAACG 58.864 40.000 0.00 0.00 0.00 3.95
5364 6785 7.027778 ACAGTTGAGACACTTATTTTGGAAC 57.972 36.000 0.00 0.00 0.00 3.62
5365 6786 7.990886 AGTACAGTTGAGACACTTATTTTGGAA 59.009 33.333 0.00 0.00 0.00 3.53
5366 6787 7.506114 AGTACAGTTGAGACACTTATTTTGGA 58.494 34.615 0.00 0.00 0.00 3.53
5367 6788 7.730364 AGTACAGTTGAGACACTTATTTTGG 57.270 36.000 0.00 0.00 0.00 3.28
5369 6790 8.989980 GCTTAGTACAGTTGAGACACTTATTTT 58.010 33.333 0.00 0.00 0.00 1.82
5370 6791 8.368668 AGCTTAGTACAGTTGAGACACTTATTT 58.631 33.333 0.00 0.00 0.00 1.40
5371 6792 7.897864 AGCTTAGTACAGTTGAGACACTTATT 58.102 34.615 0.00 0.00 0.00 1.40
5372 6793 7.469537 AGCTTAGTACAGTTGAGACACTTAT 57.530 36.000 0.00 0.00 0.00 1.73
5373 6794 6.896021 AGCTTAGTACAGTTGAGACACTTA 57.104 37.500 0.00 0.00 0.00 2.24
5374 6795 5.793030 AGCTTAGTACAGTTGAGACACTT 57.207 39.130 0.00 0.00 0.00 3.16
5375 6796 5.302059 TCAAGCTTAGTACAGTTGAGACACT 59.698 40.000 0.00 0.00 0.00 3.55
5376 6797 5.529791 TCAAGCTTAGTACAGTTGAGACAC 58.470 41.667 0.00 0.00 0.00 3.67
5377 6798 5.535030 TCTCAAGCTTAGTACAGTTGAGACA 59.465 40.000 15.59 2.76 45.09 3.41
5378 6799 6.015027 TCTCAAGCTTAGTACAGTTGAGAC 57.985 41.667 15.59 0.00 45.09 3.36
5379 6800 5.535030 TGTCTCAAGCTTAGTACAGTTGAGA 59.465 40.000 15.59 15.59 46.81 3.27
5380 6801 5.773575 TGTCTCAAGCTTAGTACAGTTGAG 58.226 41.667 0.00 12.73 43.61 3.02
5381 6802 5.302059 ACTGTCTCAAGCTTAGTACAGTTGA 59.698 40.000 23.73 6.46 43.63 3.18
5382 6803 5.533482 ACTGTCTCAAGCTTAGTACAGTTG 58.467 41.667 23.73 10.29 43.63 3.16
5383 6804 5.793030 ACTGTCTCAAGCTTAGTACAGTT 57.207 39.130 23.73 13.95 43.63 3.16
5384 6805 5.793030 AACTGTCTCAAGCTTAGTACAGT 57.207 39.130 23.73 23.73 46.95 3.55
5385 6806 8.764524 AAATAACTGTCTCAAGCTTAGTACAG 57.235 34.615 22.80 22.80 40.08 2.74
5386 6807 8.988934 CAAAATAACTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 2.68 0.00 2.90
5387 6808 8.443937 CCAAAATAACTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
5388 6809 7.606456 CCCAAAATAACTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
5389 6810 6.431234 CCCAAAATAACTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
5390 6811 6.655003 TCCCAAAATAACTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
5391 6812 6.430000 GTCCCAAAATAACTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
5392 6813 5.241728 GTCCCAAAATAACTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
5393 6814 4.762251 GTCCCAAAATAACTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
5394 6815 4.518970 TGTCCCAAAATAACTGTCTCAAGC 59.481 41.667 0.00 0.00 0.00 4.01
5395 6816 5.997746 TCTGTCCCAAAATAACTGTCTCAAG 59.002 40.000 0.00 0.00 0.00 3.02
5396 6817 5.935945 TCTGTCCCAAAATAACTGTCTCAA 58.064 37.500 0.00 0.00 0.00 3.02
5397 6818 5.513094 CCTCTGTCCCAAAATAACTGTCTCA 60.513 44.000 0.00 0.00 0.00 3.27
5398 6819 4.938226 CCTCTGTCCCAAAATAACTGTCTC 59.062 45.833 0.00 0.00 0.00 3.36
5399 6820 4.263506 CCCTCTGTCCCAAAATAACTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
5400 6821 4.010349 CCCTCTGTCCCAAAATAACTGTC 58.990 47.826 0.00 0.00 0.00 3.51
5401 6822 3.655777 TCCCTCTGTCCCAAAATAACTGT 59.344 43.478 0.00 0.00 0.00 3.55
5402 6823 4.263506 ACTCCCTCTGTCCCAAAATAACTG 60.264 45.833 0.00 0.00 0.00 3.16
5403 6824 3.916989 ACTCCCTCTGTCCCAAAATAACT 59.083 43.478 0.00 0.00 0.00 2.24
5404 6825 4.302559 ACTCCCTCTGTCCCAAAATAAC 57.697 45.455 0.00 0.00 0.00 1.89
5405 6826 6.652205 AATACTCCCTCTGTCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
5406 6827 6.011981 ACAAATACTCCCTCTGTCCCAAAATA 60.012 38.462 0.00 0.00 0.00 1.40
5407 6828 5.222337 ACAAATACTCCCTCTGTCCCAAAAT 60.222 40.000 0.00 0.00 0.00 1.82
5408 6829 4.105697 ACAAATACTCCCTCTGTCCCAAAA 59.894 41.667 0.00 0.00 0.00 2.44
5409 6830 3.655777 ACAAATACTCCCTCTGTCCCAAA 59.344 43.478 0.00 0.00 0.00 3.28
5410 6831 3.009033 CACAAATACTCCCTCTGTCCCAA 59.991 47.826 0.00 0.00 0.00 4.12
5411 6832 2.571653 CACAAATACTCCCTCTGTCCCA 59.428 50.000 0.00 0.00 0.00 4.37
5412 6833 2.838202 TCACAAATACTCCCTCTGTCCC 59.162 50.000 0.00 0.00 0.00 4.46
5413 6834 4.254492 GTTCACAAATACTCCCTCTGTCC 58.746 47.826 0.00 0.00 0.00 4.02
5414 6835 3.927142 CGTTCACAAATACTCCCTCTGTC 59.073 47.826 0.00 0.00 0.00 3.51
5415 6836 3.306780 CCGTTCACAAATACTCCCTCTGT 60.307 47.826 0.00 0.00 0.00 3.41
5416 6837 3.056107 TCCGTTCACAAATACTCCCTCTG 60.056 47.826 0.00 0.00 0.00 3.35
5417 6838 3.170717 TCCGTTCACAAATACTCCCTCT 58.829 45.455 0.00 0.00 0.00 3.69
5418 6839 3.522553 CTCCGTTCACAAATACTCCCTC 58.477 50.000 0.00 0.00 0.00 4.30
5419 6840 2.236395 CCTCCGTTCACAAATACTCCCT 59.764 50.000 0.00 0.00 0.00 4.20
5420 6841 2.629051 CCTCCGTTCACAAATACTCCC 58.371 52.381 0.00 0.00 0.00 4.30
5421 6842 2.235402 TCCCTCCGTTCACAAATACTCC 59.765 50.000 0.00 0.00 0.00 3.85
5422 6843 3.259902 GTCCCTCCGTTCACAAATACTC 58.740 50.000 0.00 0.00 0.00 2.59
5423 6844 2.027469 GGTCCCTCCGTTCACAAATACT 60.027 50.000 0.00 0.00 0.00 2.12
5424 6845 2.353323 GGTCCCTCCGTTCACAAATAC 58.647 52.381 0.00 0.00 0.00 1.89
5437 6858 0.479378 AGATACTCCCTCGGTCCCTC 59.521 60.000 0.00 0.00 0.00 4.30
5438 6859 0.935194 AAGATACTCCCTCGGTCCCT 59.065 55.000 0.00 0.00 0.00 4.20
5439 6860 1.330234 GAAGATACTCCCTCGGTCCC 58.670 60.000 0.00 0.00 0.00 4.46
5440 6861 1.330234 GGAAGATACTCCCTCGGTCC 58.670 60.000 0.00 0.00 0.00 4.46
5441 6862 2.068834 TGGAAGATACTCCCTCGGTC 57.931 55.000 0.00 0.00 34.22 4.79
5442 6863 2.024273 TCTTGGAAGATACTCCCTCGGT 60.024 50.000 0.00 0.00 34.22 4.69
5443 6864 2.625790 CTCTTGGAAGATACTCCCTCGG 59.374 54.545 0.00 0.00 34.22 4.63
5444 6865 2.625790 CCTCTTGGAAGATACTCCCTCG 59.374 54.545 0.00 0.00 34.22 4.63
5495 6916 3.006752 TGGCCTATTCTTTGGTTGCAAAG 59.993 43.478 3.32 0.00 41.98 2.77
5524 6945 1.550130 TAAACAGCCTCCCCTCCACG 61.550 60.000 0.00 0.00 0.00 4.94
5557 6979 3.310860 AACGCACCGGATCTGGTCC 62.311 63.158 24.03 14.50 41.38 4.46
5562 6984 1.375523 GGAACAACGCACCGGATCT 60.376 57.895 9.46 0.00 0.00 2.75
5607 7030 3.558746 GGAGATCCACATCTGCCATTAGG 60.559 52.174 0.00 0.00 40.74 2.69
5644 7067 3.019003 AATGCCGGGACCAGACTCG 62.019 63.158 2.18 0.00 0.00 4.18
5692 7115 3.319972 GTCCCCTTTGTAAACAACCTTCC 59.680 47.826 0.00 0.00 35.28 3.46
5717 7140 8.417273 TGTACTACTATATATTCTTGGCAGCA 57.583 34.615 0.00 0.00 0.00 4.41
5811 7237 3.550842 CCAAAAGGAAAAGCTGAACCGAG 60.551 47.826 0.00 0.00 0.00 4.63
5820 7246 3.548616 GCAATTGTGCCAAAAGGAAAAGC 60.549 43.478 7.40 0.00 45.68 3.51
5841 7267 2.185867 CACCATGCAAGGCCATGC 59.814 61.111 25.78 25.78 46.58 4.06
5842 7268 2.185867 GCACCATGCAAGGCCATG 59.814 61.111 8.15 3.85 44.26 3.66
5891 7317 4.600692 TGTCGCTTAGGCATACACATAT 57.399 40.909 0.00 0.00 38.60 1.78
5944 7402 5.597806 AGTTTCAGTGTCACTACGATTTCA 58.402 37.500 4.85 0.00 0.00 2.69
6020 7478 4.704833 AGATGTGCACGCGCCCTT 62.705 61.111 13.13 0.00 37.32 3.95
6023 7481 3.422303 TTCAGATGTGCACGCGCC 61.422 61.111 13.13 0.00 37.32 6.53
6026 7484 1.915614 CTGGGTTCAGATGTGCACGC 61.916 60.000 13.13 6.90 43.49 5.34
6027 7485 1.915614 GCTGGGTTCAGATGTGCACG 61.916 60.000 13.13 0.00 43.49 5.34
6028 7486 1.589716 GGCTGGGTTCAGATGTGCAC 61.590 60.000 10.75 10.75 43.49 4.57
6029 7487 1.303561 GGCTGGGTTCAGATGTGCA 60.304 57.895 0.00 0.00 43.49 4.57
6030 7488 1.001641 AGGCTGGGTTCAGATGTGC 60.002 57.895 0.00 0.00 43.49 4.57
6038 7496 1.981256 TTCAAAGTCAGGCTGGGTTC 58.019 50.000 15.73 3.42 0.00 3.62
6080 7538 1.485895 AGGCAACCAAACAACTTGCAT 59.514 42.857 4.18 0.00 41.77 3.96
6084 7542 0.901124 TGCAGGCAACCAAACAACTT 59.099 45.000 0.00 0.00 37.17 2.66
6101 7559 3.004106 CCTAATGCAGAAAGCCTATGTGC 59.996 47.826 0.00 0.00 44.83 4.57
6104 7562 3.152341 CCCCTAATGCAGAAAGCCTATG 58.848 50.000 0.00 0.00 44.83 2.23
6107 7565 1.298953 TCCCCTAATGCAGAAAGCCT 58.701 50.000 0.00 0.00 44.83 4.58
6109 7567 2.936202 TGATCCCCTAATGCAGAAAGC 58.064 47.619 0.00 0.00 45.96 3.51
6113 7571 4.272489 CAAAGTTGATCCCCTAATGCAGA 58.728 43.478 0.00 0.00 0.00 4.26
6139 7597 1.569708 ATGCAGGCAAACAAACAACG 58.430 45.000 0.00 0.00 0.00 4.10
6148 7606 1.865788 GCCGAGACAATGCAGGCAAA 61.866 55.000 6.04 0.00 46.48 3.68
6168 7626 3.221771 AGACAATGCAGGCAAGTTGTAA 58.778 40.909 11.88 0.00 35.15 2.41
6169 7627 2.813754 GAGACAATGCAGGCAAGTTGTA 59.186 45.455 11.88 0.00 35.15 2.41
6170 7628 1.610522 GAGACAATGCAGGCAAGTTGT 59.389 47.619 11.76 11.76 37.49 3.32
6171 7629 1.400629 CGAGACAATGCAGGCAAGTTG 60.401 52.381 0.00 0.00 0.00 3.16
6172 7630 0.877071 CGAGACAATGCAGGCAAGTT 59.123 50.000 0.00 0.00 0.00 2.66
6173 7631 0.035317 TCGAGACAATGCAGGCAAGT 59.965 50.000 0.00 0.00 0.00 3.16
6174 7632 0.445436 GTCGAGACAATGCAGGCAAG 59.555 55.000 0.00 0.00 0.00 4.01
6175 7633 0.250252 TGTCGAGACAATGCAGGCAA 60.250 50.000 3.11 0.00 38.56 4.52
6176 7634 0.036105 ATGTCGAGACAATGCAGGCA 60.036 50.000 10.15 0.00 45.41 4.75
6177 7635 1.594862 GTATGTCGAGACAATGCAGGC 59.405 52.381 10.15 0.00 45.41 4.85
6178 7636 2.892374 TGTATGTCGAGACAATGCAGG 58.108 47.619 10.15 0.00 45.41 4.85
6179 7637 3.928992 AGTTGTATGTCGAGACAATGCAG 59.071 43.478 10.15 0.00 45.41 4.41
6180 7638 3.925379 AGTTGTATGTCGAGACAATGCA 58.075 40.909 10.15 6.80 45.41 3.96
6181 7639 4.862574 TGTAGTTGTATGTCGAGACAATGC 59.137 41.667 10.15 4.44 45.41 3.56
6182 7640 5.003496 CGTGTAGTTGTATGTCGAGACAATG 59.997 44.000 10.15 0.00 45.41 2.82
6183 7641 5.093457 CGTGTAGTTGTATGTCGAGACAAT 58.907 41.667 10.15 2.37 45.41 2.71
6184 7642 4.023792 ACGTGTAGTTGTATGTCGAGACAA 60.024 41.667 10.15 3.91 45.41 3.18
6185 7643 3.499537 ACGTGTAGTTGTATGTCGAGACA 59.500 43.478 8.48 8.48 46.44 3.41
6186 7644 4.075763 ACGTGTAGTTGTATGTCGAGAC 57.924 45.455 0.00 0.00 0.00 3.36
6187 7645 4.754372 AACGTGTAGTTGTATGTCGAGA 57.246 40.909 0.00 0.00 42.39 4.04
6228 7686 4.201763 GCAAGTGCTAGCTCTTAATCACAC 60.202 45.833 26.76 8.78 38.21 3.82
6230 7688 3.935203 TGCAAGTGCTAGCTCTTAATCAC 59.065 43.478 26.76 16.05 42.66 3.06
6264 7722 5.600484 CCCTTTCTCTCCTAGCTCTTAATCA 59.400 44.000 0.00 0.00 0.00 2.57
6266 7724 4.904853 CCCCTTTCTCTCCTAGCTCTTAAT 59.095 45.833 0.00 0.00 0.00 1.40
6267 7725 4.290942 CCCCTTTCTCTCCTAGCTCTTAA 58.709 47.826 0.00 0.00 0.00 1.85
6278 7736 4.522114 CATTTCTTCTCCCCCTTTCTCTC 58.478 47.826 0.00 0.00 0.00 3.20
6283 7741 2.110721 ACTGCATTTCTTCTCCCCCTTT 59.889 45.455 0.00 0.00 0.00 3.11
6288 7746 3.065925 GCACATACTGCATTTCTTCTCCC 59.934 47.826 0.00 0.00 46.29 4.30
6319 7777 4.344474 CTATCCTCCGCGGTCGCC 62.344 72.222 27.15 0.00 37.98 5.54
6320 7778 3.593794 ACTATCCTCCGCGGTCGC 61.594 66.667 27.15 5.16 37.85 5.19
6321 7779 2.331805 CACTATCCTCCGCGGTCG 59.668 66.667 27.15 17.27 0.00 4.79
6322 7780 2.073037 GACCACTATCCTCCGCGGTC 62.073 65.000 27.15 7.22 36.46 4.79
6323 7781 2.043248 ACCACTATCCTCCGCGGT 60.043 61.111 27.15 8.36 0.00 5.68
6324 7782 2.728817 GACCACTATCCTCCGCGG 59.271 66.667 22.12 22.12 0.00 6.46
6325 7783 2.331805 CGACCACTATCCTCCGCG 59.668 66.667 0.00 0.00 0.00 6.46
6326 7784 1.065928 CACGACCACTATCCTCCGC 59.934 63.158 0.00 0.00 0.00 5.54
6327 7785 1.734137 CCACGACCACTATCCTCCG 59.266 63.158 0.00 0.00 0.00 4.63
6328 7786 1.442148 GCCACGACCACTATCCTCC 59.558 63.158 0.00 0.00 0.00 4.30
6329 7787 1.065928 CGCCACGACCACTATCCTC 59.934 63.158 0.00 0.00 0.00 3.71
6330 7788 3.077519 GCGCCACGACCACTATCCT 62.078 63.158 0.00 0.00 0.00 3.24
6331 7789 2.585247 GCGCCACGACCACTATCC 60.585 66.667 0.00 0.00 0.00 2.59
6332 7790 2.585247 GGCGCCACGACCACTATC 60.585 66.667 24.80 0.00 0.00 2.08
6333 7791 4.508128 CGGCGCCACGACCACTAT 62.508 66.667 28.98 0.00 35.47 2.12
6368 7826 3.077519 GCGCCACGACCACTATCCT 62.078 63.158 0.00 0.00 0.00 3.24
6389 7847 4.760047 ACCGCAGTCGCCATGGTC 62.760 66.667 14.67 4.79 33.11 4.02
6390 7848 4.329545 AACCGCAGTCGCCATGGT 62.330 61.111 14.67 0.00 31.46 3.55
6391 7849 3.803082 CAACCGCAGTCGCCATGG 61.803 66.667 7.63 7.63 33.11 3.66
6392 7850 0.809636 TATCAACCGCAGTCGCCATG 60.810 55.000 0.00 0.00 33.11 3.66
6393 7851 0.530650 CTATCAACCGCAGTCGCCAT 60.531 55.000 0.00 0.00 33.11 4.40
6394 7852 1.153647 CTATCAACCGCAGTCGCCA 60.154 57.895 0.00 0.00 33.11 5.69
6395 7853 1.153628 ACTATCAACCGCAGTCGCC 60.154 57.895 0.00 0.00 33.11 5.54
6396 7854 1.421410 CCACTATCAACCGCAGTCGC 61.421 60.000 0.00 0.00 0.00 5.19
6397 7855 0.108804 ACCACTATCAACCGCAGTCG 60.109 55.000 0.00 0.00 0.00 4.18
6398 7856 1.732259 CAACCACTATCAACCGCAGTC 59.268 52.381 0.00 0.00 0.00 3.51
6399 7857 1.071699 ACAACCACTATCAACCGCAGT 59.928 47.619 0.00 0.00 0.00 4.40
6400 7858 1.464608 CACAACCACTATCAACCGCAG 59.535 52.381 0.00 0.00 0.00 5.18
6401 7859 1.070914 TCACAACCACTATCAACCGCA 59.929 47.619 0.00 0.00 0.00 5.69
6402 7860 1.463444 GTCACAACCACTATCAACCGC 59.537 52.381 0.00 0.00 0.00 5.68
6403 7861 1.724623 CGTCACAACCACTATCAACCG 59.275 52.381 0.00 0.00 0.00 4.44
6404 7862 2.735134 GACGTCACAACCACTATCAACC 59.265 50.000 11.55 0.00 0.00 3.77
6405 7863 2.407361 CGACGTCACAACCACTATCAAC 59.593 50.000 17.16 0.00 0.00 3.18
6406 7864 2.034939 ACGACGTCACAACCACTATCAA 59.965 45.455 17.16 0.00 0.00 2.57
6407 7865 1.610038 ACGACGTCACAACCACTATCA 59.390 47.619 17.16 0.00 0.00 2.15
6408 7866 1.983605 CACGACGTCACAACCACTATC 59.016 52.381 17.16 0.00 0.00 2.08
6409 7867 1.338973 ACACGACGTCACAACCACTAT 59.661 47.619 17.16 0.00 0.00 2.12
6410 7868 0.740149 ACACGACGTCACAACCACTA 59.260 50.000 17.16 0.00 0.00 2.74
6411 7869 0.526954 GACACGACGTCACAACCACT 60.527 55.000 17.16 0.00 44.69 4.00
6412 7870 1.922189 GACACGACGTCACAACCAC 59.078 57.895 17.16 0.00 44.69 4.16
6413 7871 4.405762 GACACGACGTCACAACCA 57.594 55.556 17.16 0.00 44.69 3.67
6425 7883 0.445043 TACTCGTCATGTCGGACACG 59.555 55.000 13.92 12.74 37.66 4.49
6426 7884 2.451132 CATACTCGTCATGTCGGACAC 58.549 52.381 13.92 0.00 37.66 3.67
6435 7893 3.319405 GTCCATGACTCCATACTCGTCAT 59.681 47.826 0.00 0.00 46.17 3.06
6497 7955 0.163788 CGAGCACCGCAACTAGTTTG 59.836 55.000 5.07 2.89 38.37 2.93
6498 7956 2.528797 CGAGCACCGCAACTAGTTT 58.471 52.632 5.07 0.00 0.00 2.66
6529 7987 0.820226 TGCATTCTCCTCCTCTGTCG 59.180 55.000 0.00 0.00 0.00 4.35
6566 8024 2.734723 CGTCCACTGCACTGACGG 60.735 66.667 16.20 1.29 45.93 4.79
6572 8030 1.214062 CCTCTCTCGTCCACTGCAC 59.786 63.158 0.00 0.00 0.00 4.57
6612 8070 3.257624 CCCTACTACACTGGAGTCGTTTT 59.742 47.826 0.00 0.00 0.00 2.43
6641 8099 0.755079 CGATCATCTTGGCCTCCTCA 59.245 55.000 3.32 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.