Multiple sequence alignment - TraesCS2B01G159800

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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 TraesCS2B01G159800 chr2B 100.000 5307 0 0 1 5307 133531004 133525698 0.000000e+00 9801.0
1 TraesCS2B01G159800 chr2B 90.943 1060 70 13 2519 3575 133582596 133581560 0.000000e+00 1402.0
2 TraesCS2B01G159800 chr2B 90.815 871 62 11 3622 4481 133580912 133580049 0.000000e+00 1149.0
3 TraesCS2B01G159800 chr2B 91.255 709 49 5 1797 2505 133583347 133582652 0.000000e+00 953.0
4 TraesCS2B01G159800 chr2B 83.416 404 47 12 1 391 407987055 407987451 1.820000e-94 357.0
5 TraesCS2B01G159800 chr2B 82.620 397 42 11 913 1302 133583788 133583412 5.130000e-85 326.0
6 TraesCS2B01G159800 chr2D 96.162 3257 99 11 1275 4523 81388175 81384937 0.000000e+00 5299.0
7 TraesCS2B01G159800 chr2D 88.403 983 73 15 3583 4551 81394402 81393447 0.000000e+00 1146.0
8 TraesCS2B01G159800 chr2D 89.412 595 42 9 2996 3581 81457196 81456614 0.000000e+00 730.0
9 TraesCS2B01G159800 chr2D 90.399 552 46 3 3999 4547 81454304 81453757 0.000000e+00 719.0
10 TraesCS2B01G159800 chr2D 92.191 461 22 5 718 1176 81389150 81388702 1.610000e-179 640.0
11 TraesCS2B01G159800 chr2D 92.771 415 27 1 2001 2412 81807697 81807283 9.840000e-167 597.0
12 TraesCS2B01G159800 chr2D 92.363 419 31 1 2567 2984 81807286 81806868 3.540000e-166 595.0
13 TraesCS2B01G159800 chr2D 94.350 354 20 0 2013 2366 81458495 81458142 1.300000e-150 544.0
14 TraesCS2B01G159800 chr2D 88.978 372 39 1 3622 3993 81456242 81455873 4.840000e-125 459.0
15 TraesCS2B01G159800 chr2D 80.154 650 83 23 1 626 346153357 346152730 1.360000e-120 444.0
16 TraesCS2B01G159800 chr2D 93.750 288 14 2 3298 3581 81418714 81418427 3.800000e-116 429.0
17 TraesCS2B01G159800 chr2D 81.162 568 73 20 74 620 433718868 433719422 4.910000e-115 425.0
18 TraesCS2B01G159800 chr2D 85.146 377 31 12 4918 5271 81384151 81383777 3.910000e-96 363.0
19 TraesCS2B01G159800 chr2D 83.853 353 34 7 4952 5281 81391531 81391179 1.110000e-81 315.0
20 TraesCS2B01G159800 chr2D 92.391 184 13 1 4740 4922 81384414 81384231 1.470000e-65 261.0
21 TraesCS2B01G159800 chr2D 91.813 171 13 1 4558 4727 81384641 81384471 2.470000e-58 237.0
22 TraesCS2B01G159800 chr2D 85.714 224 20 5 1795 2018 81468147 81467936 5.350000e-55 226.0
23 TraesCS2B01G159800 chr2D 82.946 258 25 12 145 391 608563712 608563463 1.160000e-51 215.0
24 TraesCS2B01G159800 chr2D 81.783 258 28 12 145 391 570992934 570993183 1.170000e-46 198.0
25 TraesCS2B01G159800 chr2D 89.474 57 5 1 5251 5307 128890621 128890676 2.650000e-08 71.3
26 TraesCS2B01G159800 chr2D 97.143 35 1 0 2950 2984 81418892 81418858 5.740000e-05 60.2
27 TraesCS2B01G159800 chr2A 88.624 1679 130 24 875 2516 82030764 82029110 0.000000e+00 1986.0
28 TraesCS2B01G159800 chr2A 93.973 896 43 6 3631 4519 82027529 82026638 0.000000e+00 1345.0
29 TraesCS2B01G159800 chr2A 89.007 937 67 15 3622 4551 82034624 82033717 0.000000e+00 1127.0
30 TraesCS2B01G159800 chr2A 91.653 599 33 9 2996 3580 82028496 82027901 0.000000e+00 813.0
31 TraesCS2B01G159800 chr2A 87.656 721 51 12 1795 2505 82050758 82050066 0.000000e+00 804.0
32 TraesCS2B01G159800 chr2A 93.148 540 29 7 4736 5271 82026163 82025628 0.000000e+00 785.0
33 TraesCS2B01G159800 chr2A 95.708 466 16 1 2519 2984 82029059 82028598 0.000000e+00 747.0
34 TraesCS2B01G159800 chr2A 89.526 401 20 10 3200 3581 82035392 82034995 6.180000e-134 488.0
35 TraesCS2B01G159800 chr2A 93.464 306 16 2 2520 2825 82050009 82049708 8.100000e-123 451.0
36 TraesCS2B01G159800 chr2A 84.573 363 36 9 4918 5266 82033518 82033162 5.090000e-90 342.0
37 TraesCS2B01G159800 chr2A 94.712 208 10 1 4503 4710 82026621 82026415 6.630000e-84 322.0
38 TraesCS2B01G159800 chr2A 91.827 208 15 2 2996 3201 82045939 82045732 6.720000e-74 289.0
39 TraesCS2B01G159800 chr2A 92.857 168 12 0 2817 2984 82046393 82046226 1.480000e-60 244.0
40 TraesCS2B01G159800 chr2A 89.524 105 11 0 913 1017 82051153 82051049 3.330000e-27 134.0
41 TraesCS2B01G159800 chr4A 93.132 728 35 7 1 719 685838084 685837363 0.000000e+00 1053.0
42 TraesCS2B01G159800 chr4A 80.407 393 35 20 2 391 182697771 182697418 1.470000e-65 261.0
43 TraesCS2B01G159800 chr4A 90.385 52 5 0 5256 5307 214314406 214314457 9.540000e-08 69.4
44 TraesCS2B01G159800 chr7D 82.746 539 61 18 33 555 603844840 603845362 8.100000e-123 451.0
45 TraesCS2B01G159800 chr7D 82.558 258 26 12 145 391 38275411 38275660 5.390000e-50 209.0
46 TraesCS2B01G159800 chr7D 88.095 168 9 5 1492 1655 578999703 578999543 7.020000e-44 189.0
47 TraesCS2B01G159800 chr6D 81.239 549 63 18 26 555 419656393 419655866 1.780000e-109 407.0
48 TraesCS2B01G159800 chr6D 90.000 180 17 1 1 179 81915663 81915484 1.150000e-56 231.0
49 TraesCS2B01G159800 chr6D 97.619 42 1 0 5266 5307 237751397 237751356 7.370000e-09 73.1
50 TraesCS2B01G159800 chr6D 97.561 41 1 0 5267 5307 113614157 113614117 2.650000e-08 71.3
51 TraesCS2B01G159800 chr6D 97.500 40 1 0 5268 5307 159490484 159490523 9.540000e-08 69.4
52 TraesCS2B01G159800 chr6D 97.368 38 1 0 5270 5307 403969207 403969170 1.230000e-06 65.8
53 TraesCS2B01G159800 chrUn 84.065 433 42 9 185 598 225555889 225556313 4.980000e-105 392.0
54 TraesCS2B01G159800 chrUn 84.075 427 41 9 185 592 228689695 228690113 2.320000e-103 387.0
55 TraesCS2B01G159800 chrUn 85.640 383 36 8 221 592 221383915 221384289 8.340000e-103 385.0
56 TraesCS2B01G159800 chrUn 95.122 41 2 0 5267 5307 37403239 37403279 1.230000e-06 65.8
57 TraesCS2B01G159800 chrUn 95.122 41 2 0 5263 5303 436061852 436061812 1.230000e-06 65.8
58 TraesCS2B01G159800 chrUn 95.122 41 2 0 5263 5303 454147246 454147206 1.230000e-06 65.8
59 TraesCS2B01G159800 chrUn 95.000 40 2 0 5268 5307 15903396 15903357 4.440000e-06 63.9
60 TraesCS2B01G159800 chrUn 95.000 40 2 0 5268 5307 30123192 30123153 4.440000e-06 63.9
61 TraesCS2B01G159800 chrUn 95.000 40 2 0 5268 5307 385915567 385915528 4.440000e-06 63.9
62 TraesCS2B01G159800 chrUn 94.872 39 2 0 5269 5307 26701823 26701861 1.600000e-05 62.1
63 TraesCS2B01G159800 chrUn 92.857 42 3 0 5266 5307 28955432 28955473 1.600000e-05 62.1
64 TraesCS2B01G159800 chrUn 92.857 42 3 0 5266 5307 29029198 29029239 1.600000e-05 62.1
65 TraesCS2B01G159800 chrUn 93.023 43 2 1 5266 5307 348315105 348315147 1.600000e-05 62.1
66 TraesCS2B01G159800 chr7A 79.276 608 74 24 20 598 54940917 54941501 1.400000e-100 377.0
67 TraesCS2B01G159800 chr1B 80.000 480 51 22 1 474 102845732 102845292 3.990000e-81 313.0
68 TraesCS2B01G159800 chr1B 89.560 182 16 2 1 179 438174456 438174275 1.490000e-55 228.0
69 TraesCS2B01G159800 chr1B 95.833 48 1 1 5261 5307 527834231 527834278 5.700000e-10 76.8
70 TraesCS2B01G159800 chr1B 87.097 62 6 2 5247 5307 156593773 156593833 9.540000e-08 69.4
71 TraesCS2B01G159800 chr5A 83.489 321 37 9 3 307 546708235 546708555 8.700000e-73 285.0
72 TraesCS2B01G159800 chr5A 88.485 165 8 5 1492 1652 238862810 238862967 7.020000e-44 189.0
73 TraesCS2B01G159800 chr7B 79.756 410 53 15 3 391 2138487 2138087 2.440000e-68 270.0
74 TraesCS2B01G159800 chr7B 89.024 164 7 5 1492 1652 33503049 33503204 5.420000e-45 193.0
75 TraesCS2B01G159800 chr5D 90.055 181 14 3 3 179 70214370 70214190 1.150000e-56 231.0
76 TraesCS2B01G159800 chr5D 97.561 41 1 0 5267 5307 225584075 225584115 2.650000e-08 71.3
77 TraesCS2B01G159800 chr5D 97.500 40 1 0 5268 5307 88159531 88159492 9.540000e-08 69.4
78 TraesCS2B01G159800 chr6A 88.485 165 8 5 1492 1652 155848137 155848294 7.020000e-44 189.0
79 TraesCS2B01G159800 chr6A 90.196 51 5 0 5257 5307 154040864 154040814 3.430000e-07 67.6
80 TraesCS2B01G159800 chr6A 95.349 43 1 1 5265 5307 457387208 457387167 3.430000e-07 67.6
81 TraesCS2B01G159800 chr4D 88.095 168 9 5 1492 1655 241062049 241061889 7.020000e-44 189.0
82 TraesCS2B01G159800 chr4D 88.485 165 8 5 1492 1652 446960797 446960954 7.020000e-44 189.0
83 TraesCS2B01G159800 chr4D 97.500 40 1 0 5268 5307 307492693 307492654 9.540000e-08 69.4
84 TraesCS2B01G159800 chr4D 93.617 47 2 1 5261 5307 493742346 493742391 9.540000e-08 69.4
85 TraesCS2B01G159800 chr4D 95.238 42 2 0 5266 5307 21876055 21876096 3.430000e-07 67.6
86 TraesCS2B01G159800 chr4D 95.238 42 2 0 5266 5307 47984293 47984334 3.430000e-07 67.6
87 TraesCS2B01G159800 chr4D 95.122 41 2 0 5267 5307 11466056 11466096 1.230000e-06 65.8
88 TraesCS2B01G159800 chr4D 97.368 38 1 0 5270 5307 18692618 18692655 1.230000e-06 65.8
89 TraesCS2B01G159800 chr4D 95.122 41 2 0 5267 5307 82867094 82867054 1.230000e-06 65.8
90 TraesCS2B01G159800 chr4D 95.238 42 1 1 5266 5307 379147281 379147241 1.230000e-06 65.8
91 TraesCS2B01G159800 chr1A 88.485 165 8 5 1492 1652 334094217 334094374 7.020000e-44 189.0
92 TraesCS2B01G159800 chr3A 81.008 258 30 13 145 391 477425789 477426038 2.520000e-43 187.0
93 TraesCS2B01G159800 chr3A 93.617 47 3 0 5261 5307 470843471 470843517 2.650000e-08 71.3
94 TraesCS2B01G159800 chr3A 90.566 53 4 1 5255 5307 620473480 620473531 9.540000e-08 69.4
95 TraesCS2B01G159800 chr3D 97.619 42 1 0 5266 5307 455952348 455952389 7.370000e-09 73.1
96 TraesCS2B01G159800 chr3D 97.500 40 1 0 5268 5307 1767530 1767491 9.540000e-08 69.4
97 TraesCS2B01G159800 chr3D 95.455 44 1 1 5264 5307 67062537 67062495 9.540000e-08 69.4
98 TraesCS2B01G159800 chr3D 93.478 46 3 0 5261 5306 352387157 352387202 9.540000e-08 69.4
99 TraesCS2B01G159800 chr1D 89.474 57 5 1 5251 5307 346659692 346659747 2.650000e-08 71.3
100 TraesCS2B01G159800 chr1D 93.750 48 2 1 5261 5307 394271211 394271164 2.650000e-08 71.3
101 TraesCS2B01G159800 chr4B 90.566 53 2 3 5256 5305 204335861 204335809 3.430000e-07 67.6
102 TraesCS2B01G159800 chr6B 86.667 60 6 2 5250 5307 281611855 281611914 1.230000e-06 65.8


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 TraesCS2B01G159800 chr2B 133525698 133531004 5306 True 9801.000000 9801 100.000000 1 5307 1 chr2B.!!$R1 5306
1 TraesCS2B01G159800 chr2B 133580049 133583788 3739 True 957.500000 1402 88.908250 913 4481 4 chr2B.!!$R2 3568
2 TraesCS2B01G159800 chr2D 81383777 81394402 10625 True 1180.142857 5299 89.994143 718 5281 7 chr2D.!!$R4 4563
3 TraesCS2B01G159800 chr2D 81453757 81458495 4738 True 613.000000 730 90.784750 2013 4547 4 chr2D.!!$R6 2534
4 TraesCS2B01G159800 chr2D 81806868 81807697 829 True 596.000000 597 92.567000 2001 2984 2 chr2D.!!$R7 983
5 TraesCS2B01G159800 chr2D 346152730 346153357 627 True 444.000000 444 80.154000 1 626 1 chr2D.!!$R2 625
6 TraesCS2B01G159800 chr2D 433718868 433719422 554 False 425.000000 425 81.162000 74 620 1 chr2D.!!$F2 546
7 TraesCS2B01G159800 chr2A 82025628 82035392 9764 True 883.888889 1986 91.213778 875 5271 9 chr2A.!!$R1 4396
8 TraesCS2B01G159800 chr2A 82045732 82051153 5421 True 384.400000 804 91.065600 913 3201 5 chr2A.!!$R2 2288
9 TraesCS2B01G159800 chr4A 685837363 685838084 721 True 1053.000000 1053 93.132000 1 719 1 chr4A.!!$R2 718
10 TraesCS2B01G159800 chr7D 603844840 603845362 522 False 451.000000 451 82.746000 33 555 1 chr7D.!!$F2 522
11 TraesCS2B01G159800 chr6D 419655866 419656393 527 True 407.000000 407 81.239000 26 555 1 chr6D.!!$R5 529
12 TraesCS2B01G159800 chr7A 54940917 54941501 584 False 377.000000 377 79.276000 20 598 1 chr7A.!!$F1 578

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
825 937 0.106149 GTTGGGTCAGAGGTGTCGTT 59.894 55.0 0.00 0.0 0.00 3.85 F
875 987 0.253160 TAGATGGTGCCCTTCCCTGT 60.253 55.0 4.24 0.0 0.00 4.00 F
1176 8359 0.322277 AACAGCATCTGGGAGCAGTG 60.322 55.0 0.00 0.0 35.51 3.66 F
1241 8426 0.482446 TCCCAGTTGTTTCATGGCCT 59.518 50.0 3.32 0.0 32.46 5.19 F
3107 14531 0.527169 GGCTAAACTACTCGCGGGAC 60.527 60.0 15.95 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2774 10589 0.323360 TGCCAATGGGTACTCAAGCC 60.323 55.000 0.00 0.0 46.67 4.35 R
2885 14023 2.306805 AGAATGGAGGAGTTGTGCATCA 59.693 45.455 0.00 0.0 0.00 3.07 R
3107 14531 2.048597 TAGCACTCAACCACGCGG 60.049 61.111 12.47 0.0 38.77 6.46 R
3141 14565 8.728337 TGTGTATACTCTTTCTCGTAGTATGT 57.272 34.615 4.17 0.0 37.11 2.29 R
4736 18650 0.686224 TTTACGTACTGGGTGGGTGG 59.314 55.000 0.00 0.0 0.00 4.61 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
38 82 3.848272 ATGCTCCGTTGGTTTGTAATG 57.152 42.857 0.00 0.00 0.00 1.90
39 83 2.577700 TGCTCCGTTGGTTTGTAATGT 58.422 42.857 0.00 0.00 0.00 2.71
40 84 2.952978 TGCTCCGTTGGTTTGTAATGTT 59.047 40.909 0.00 0.00 0.00 2.71
41 85 3.243234 TGCTCCGTTGGTTTGTAATGTTG 60.243 43.478 0.00 0.00 0.00 3.33
42 86 3.243267 GCTCCGTTGGTTTGTAATGTTGT 60.243 43.478 0.00 0.00 0.00 3.32
43 87 4.533222 CTCCGTTGGTTTGTAATGTTGTC 58.467 43.478 0.00 0.00 0.00 3.18
45 89 5.366460 TCCGTTGGTTTGTAATGTTGTCTA 58.634 37.500 0.00 0.00 0.00 2.59
46 90 5.467399 TCCGTTGGTTTGTAATGTTGTCTAG 59.533 40.000 0.00 0.00 0.00 2.43
47 91 5.237779 CCGTTGGTTTGTAATGTTGTCTAGT 59.762 40.000 0.00 0.00 0.00 2.57
48 92 6.238538 CCGTTGGTTTGTAATGTTGTCTAGTT 60.239 38.462 0.00 0.00 0.00 2.24
49 93 6.631238 CGTTGGTTTGTAATGTTGTCTAGTTG 59.369 38.462 0.00 0.00 0.00 3.16
50 94 6.067263 TGGTTTGTAATGTTGTCTAGTTGC 57.933 37.500 0.00 0.00 0.00 4.17
52 96 5.912955 GGTTTGTAATGTTGTCTAGTTGCAC 59.087 40.000 0.00 0.00 0.00 4.57
56 100 0.934496 TGTTGTCTAGTTGCACGCAC 59.066 50.000 0.00 0.00 0.00 5.34
57 101 0.934496 GTTGTCTAGTTGCACGCACA 59.066 50.000 0.00 0.00 0.00 4.57
58 102 1.531149 GTTGTCTAGTTGCACGCACAT 59.469 47.619 0.00 0.00 0.00 3.21
60 104 1.530720 TGTCTAGTTGCACGCACATTG 59.469 47.619 0.00 0.00 0.00 2.82
61 105 1.798223 GTCTAGTTGCACGCACATTGA 59.202 47.619 0.00 0.00 0.00 2.57
63 107 2.416202 TCTAGTTGCACGCACATTGATG 59.584 45.455 0.00 0.00 0.00 3.07
64 108 0.953727 AGTTGCACGCACATTGATGT 59.046 45.000 0.00 0.00 42.84 3.06
65 109 1.337703 AGTTGCACGCACATTGATGTT 59.662 42.857 0.00 0.00 39.39 2.71
67 111 3.004210 AGTTGCACGCACATTGATGTTTA 59.996 39.130 0.00 0.00 39.39 2.01
68 112 3.200294 TGCACGCACATTGATGTTTAG 57.800 42.857 0.00 0.00 39.39 1.85
72 116 3.913763 CACGCACATTGATGTTTAGTTGG 59.086 43.478 0.00 0.00 39.39 3.77
144 190 3.535561 ACTAGTTGCACACATATGCTCC 58.464 45.455 1.58 0.00 46.28 4.70
341 437 3.255642 ACACATATTTTCAGTTGGCGCTT 59.744 39.130 7.64 0.00 0.00 4.68
357 453 4.158949 TGGCGCTTCAATGTAGTCTAGTTA 59.841 41.667 7.64 0.00 0.00 2.24
358 454 4.503370 GGCGCTTCAATGTAGTCTAGTTAC 59.497 45.833 7.64 0.00 0.00 2.50
359 455 5.100259 GCGCTTCAATGTAGTCTAGTTACA 58.900 41.667 0.00 10.71 35.66 2.41
362 458 7.434307 GCGCTTCAATGTAGTCTAGTTACATTA 59.566 37.037 22.86 14.27 45.26 1.90
561 665 3.291584 AGACGAATATGAGGAGCAGTGA 58.708 45.455 0.00 0.00 0.00 3.41
566 670 4.701765 GAATATGAGGAGCAGTGACATGT 58.298 43.478 0.00 0.00 0.00 3.21
737 849 5.570234 AAAACAAAGCTACTCGGAAAACA 57.430 34.783 0.00 0.00 0.00 2.83
738 850 4.813296 AACAAAGCTACTCGGAAAACAG 57.187 40.909 0.00 0.00 0.00 3.16
739 851 4.067972 ACAAAGCTACTCGGAAAACAGA 57.932 40.909 0.00 0.00 0.00 3.41
740 852 3.808174 ACAAAGCTACTCGGAAAACAGAC 59.192 43.478 0.00 0.00 0.00 3.51
741 853 2.349297 AGCTACTCGGAAAACAGACG 57.651 50.000 0.00 0.00 0.00 4.18
743 855 1.347320 CTACTCGGAAAACAGACGGC 58.653 55.000 0.00 0.00 0.00 5.68
744 856 0.963962 TACTCGGAAAACAGACGGCT 59.036 50.000 0.00 0.00 0.00 5.52
747 859 2.556287 GGAAAACAGACGGCTGCG 59.444 61.111 20.90 0.00 46.26 5.18
748 860 2.127232 GAAAACAGACGGCTGCGC 60.127 61.111 20.90 0.00 46.26 6.09
749 861 3.911155 GAAAACAGACGGCTGCGCG 62.911 63.158 20.90 0.00 46.26 6.86
766 878 1.736645 CGTGGGTCTTCGCGTGATT 60.737 57.895 5.77 0.00 36.10 2.57
767 879 1.787847 GTGGGTCTTCGCGTGATTG 59.212 57.895 5.77 0.00 0.00 2.67
768 880 0.669318 GTGGGTCTTCGCGTGATTGA 60.669 55.000 5.77 0.00 0.00 2.57
769 881 0.669318 TGGGTCTTCGCGTGATTGAC 60.669 55.000 18.42 18.42 0.00 3.18
772 884 1.419374 GTCTTCGCGTGATTGACAGT 58.581 50.000 20.46 0.00 31.99 3.55
773 885 1.792949 GTCTTCGCGTGATTGACAGTT 59.207 47.619 20.46 0.00 31.99 3.16
774 886 2.058798 TCTTCGCGTGATTGACAGTTC 58.941 47.619 5.77 0.00 0.00 3.01
777 889 0.179240 CGCGTGATTGACAGTTCAGC 60.179 55.000 0.00 0.00 31.71 4.26
780 892 2.663879 GCGTGATTGACAGTTCAGCTTG 60.664 50.000 0.00 0.00 31.71 4.01
781 893 2.545526 CGTGATTGACAGTTCAGCTTGT 59.454 45.455 0.00 0.00 31.71 3.16
782 894 3.002656 CGTGATTGACAGTTCAGCTTGTT 59.997 43.478 0.00 0.00 31.71 2.83
783 895 4.531332 GTGATTGACAGTTCAGCTTGTTC 58.469 43.478 0.00 0.00 31.71 3.18
784 896 4.274459 GTGATTGACAGTTCAGCTTGTTCT 59.726 41.667 0.00 0.00 31.71 3.01
785 897 4.512944 TGATTGACAGTTCAGCTTGTTCTC 59.487 41.667 0.00 0.00 31.71 2.87
786 898 2.838736 TGACAGTTCAGCTTGTTCTCC 58.161 47.619 0.00 0.00 0.00 3.71
790 902 3.152341 CAGTTCAGCTTGTTCTCCCAAT 58.848 45.455 0.00 0.00 0.00 3.16
791 903 3.057736 CAGTTCAGCTTGTTCTCCCAATG 60.058 47.826 0.00 0.00 0.00 2.82
801 913 3.383229 TCCCAATGGAGACGCGAA 58.617 55.556 15.93 0.00 35.03 4.70
802 914 1.904771 TCCCAATGGAGACGCGAAT 59.095 52.632 15.93 0.00 35.03 3.34
803 915 0.251916 TCCCAATGGAGACGCGAATT 59.748 50.000 15.93 1.33 35.03 2.17
804 916 1.483004 TCCCAATGGAGACGCGAATTA 59.517 47.619 15.93 0.00 35.03 1.40
805 917 2.093394 TCCCAATGGAGACGCGAATTAA 60.093 45.455 15.93 0.00 35.03 1.40
806 918 2.287915 CCCAATGGAGACGCGAATTAAG 59.712 50.000 15.93 0.00 0.00 1.85
807 919 2.936498 CCAATGGAGACGCGAATTAAGT 59.064 45.455 15.93 0.00 0.00 2.24
810 922 2.343101 TGGAGACGCGAATTAAGTTGG 58.657 47.619 15.93 0.00 0.00 3.77
811 923 1.664151 GGAGACGCGAATTAAGTTGGG 59.336 52.381 15.93 5.73 0.00 4.12
812 924 2.344025 GAGACGCGAATTAAGTTGGGT 58.656 47.619 15.93 12.13 0.00 4.51
813 925 2.344025 AGACGCGAATTAAGTTGGGTC 58.656 47.619 24.90 24.90 42.56 4.46
814 926 2.070783 GACGCGAATTAAGTTGGGTCA 58.929 47.619 26.43 0.00 42.03 4.02
816 928 2.289195 ACGCGAATTAAGTTGGGTCAGA 60.289 45.455 15.93 0.00 0.00 3.27
819 931 3.868754 GCGAATTAAGTTGGGTCAGAGGT 60.869 47.826 0.00 0.00 0.00 3.85
820 932 3.684788 CGAATTAAGTTGGGTCAGAGGTG 59.315 47.826 0.00 0.00 0.00 4.00
821 933 4.652822 GAATTAAGTTGGGTCAGAGGTGT 58.347 43.478 0.00 0.00 0.00 4.16
822 934 3.764237 TTAAGTTGGGTCAGAGGTGTC 57.236 47.619 0.00 0.00 0.00 3.67
823 935 0.393077 AAGTTGGGTCAGAGGTGTCG 59.607 55.000 0.00 0.00 0.00 4.35
824 936 0.759436 AGTTGGGTCAGAGGTGTCGT 60.759 55.000 0.00 0.00 0.00 4.34
825 937 0.106149 GTTGGGTCAGAGGTGTCGTT 59.894 55.000 0.00 0.00 0.00 3.85
826 938 0.834612 TTGGGTCAGAGGTGTCGTTT 59.165 50.000 0.00 0.00 0.00 3.60
829 941 2.036733 TGGGTCAGAGGTGTCGTTTTAG 59.963 50.000 0.00 0.00 0.00 1.85
830 942 2.067013 GGTCAGAGGTGTCGTTTTAGC 58.933 52.381 0.00 0.00 0.00 3.09
833 945 2.626266 TCAGAGGTGTCGTTTTAGCTGA 59.374 45.455 0.00 0.00 0.00 4.26
834 946 2.731976 CAGAGGTGTCGTTTTAGCTGAC 59.268 50.000 0.00 0.00 0.00 3.51
836 948 3.825014 AGAGGTGTCGTTTTAGCTGACTA 59.175 43.478 0.00 0.00 33.81 2.59
837 949 4.463186 AGAGGTGTCGTTTTAGCTGACTAT 59.537 41.667 0.00 0.00 33.81 2.12
838 950 5.047235 AGAGGTGTCGTTTTAGCTGACTATT 60.047 40.000 0.00 0.00 33.81 1.73
839 951 5.169295 AGGTGTCGTTTTAGCTGACTATTC 58.831 41.667 0.00 0.00 33.81 1.75
842 954 6.147328 GGTGTCGTTTTAGCTGACTATTCTTT 59.853 38.462 0.00 0.00 33.81 2.52
843 955 7.010023 GTGTCGTTTTAGCTGACTATTCTTTG 58.990 38.462 0.00 0.00 33.81 2.77
846 958 8.160976 GTCGTTTTAGCTGACTATTCTTTGTAC 58.839 37.037 0.00 0.00 0.00 2.90
847 959 7.868922 TCGTTTTAGCTGACTATTCTTTGTACA 59.131 33.333 0.00 0.00 0.00 2.90
849 961 9.204570 GTTTTAGCTGACTATTCTTTGTACAGA 57.795 33.333 0.00 0.00 0.00 3.41
850 962 9.772973 TTTTAGCTGACTATTCTTTGTACAGAA 57.227 29.630 0.00 0.00 37.20 3.02
851 963 9.772973 TTTAGCTGACTATTCTTTGTACAGAAA 57.227 29.630 0.00 0.00 36.36 2.52
853 965 8.089115 AGCTGACTATTCTTTGTACAGAAAAC 57.911 34.615 0.00 0.00 36.36 2.43
854 966 7.715249 AGCTGACTATTCTTTGTACAGAAAACA 59.285 33.333 0.00 0.00 36.36 2.83
855 967 8.507249 GCTGACTATTCTTTGTACAGAAAACAT 58.493 33.333 0.00 0.00 36.36 2.71
866 978 5.414454 TGTACAGAAAACATTAGATGGTGCC 59.586 40.000 0.00 0.00 33.60 5.01
867 979 3.763897 ACAGAAAACATTAGATGGTGCCC 59.236 43.478 0.00 0.00 33.60 5.36
868 980 4.019174 CAGAAAACATTAGATGGTGCCCT 58.981 43.478 0.00 0.00 33.60 5.19
869 981 4.463891 CAGAAAACATTAGATGGTGCCCTT 59.536 41.667 0.00 0.00 33.60 3.95
870 982 4.706962 AGAAAACATTAGATGGTGCCCTTC 59.293 41.667 0.53 0.53 33.60 3.46
871 983 2.736670 ACATTAGATGGTGCCCTTCC 57.263 50.000 4.24 0.00 33.60 3.46
872 984 1.215423 ACATTAGATGGTGCCCTTCCC 59.785 52.381 4.24 0.00 33.60 3.97
873 985 1.496429 CATTAGATGGTGCCCTTCCCT 59.504 52.381 4.24 0.00 0.00 4.20
874 986 0.918983 TTAGATGGTGCCCTTCCCTG 59.081 55.000 4.24 0.00 0.00 4.45
875 987 0.253160 TAGATGGTGCCCTTCCCTGT 60.253 55.000 4.24 0.00 0.00 4.00
876 988 1.142688 AGATGGTGCCCTTCCCTGTT 61.143 55.000 4.24 0.00 0.00 3.16
1083 8263 0.888736 CGCCTGTGTTTCATCCCACA 60.889 55.000 0.00 0.00 39.16 4.17
1110 8290 3.432326 GGGGCGACTTCTTCATCAACTAT 60.432 47.826 0.00 0.00 0.00 2.12
1144 8327 0.815734 ACAGGCATGCTTCATCTTGC 59.184 50.000 18.92 0.00 36.68 4.01
1150 8333 2.681848 GCATGCTTCATCTTGCTACAGT 59.318 45.455 11.37 0.00 35.17 3.55
1176 8359 0.322277 AACAGCATCTGGGAGCAGTG 60.322 55.000 0.00 0.00 35.51 3.66
1191 8376 3.072944 AGCAGTGCATTTTCAGTCTCTC 58.927 45.455 19.20 0.00 0.00 3.20
1202 8387 7.655490 CATTTTCAGTCTCTCCATGTTTTTCT 58.345 34.615 0.00 0.00 0.00 2.52
1218 8403 7.513190 TGTTTTTCTTTCGGTTTTATGTGTG 57.487 32.000 0.00 0.00 0.00 3.82
1241 8426 0.482446 TCCCAGTTGTTTCATGGCCT 59.518 50.000 3.32 0.00 32.46 5.19
1242 8427 1.707989 TCCCAGTTGTTTCATGGCCTA 59.292 47.619 3.32 0.00 32.46 3.93
1246 8431 2.095263 CAGTTGTTTCATGGCCTAACCG 60.095 50.000 3.32 0.00 43.94 4.44
1255 8440 2.477845 TGGCCTAACCGAAAGTTACC 57.522 50.000 3.32 0.00 43.94 2.85
1257 8442 2.289819 TGGCCTAACCGAAAGTTACCTG 60.290 50.000 3.32 0.00 43.94 4.00
1379 9016 1.434696 CCACGCTTGATTGGCATCC 59.565 57.895 0.00 0.00 0.00 3.51
1485 9126 3.988976 ACCCTCTACGTGTACACTCTA 57.011 47.619 23.01 11.36 0.00 2.43
1511 9152 3.181483 GGGAGTCAACCGTAATACGATGT 60.181 47.826 15.03 1.45 46.05 3.06
1686 9331 6.721208 AGCTTCCAATGAATAGGAAACAAGAA 59.279 34.615 0.00 0.00 42.91 2.52
1700 9345 5.011023 GGAAACAAGAAGACCCATGACATTT 59.989 40.000 0.00 0.00 0.00 2.32
1977 9638 3.449018 TGGCTGCAACTTTAACCAAGAAA 59.551 39.130 0.50 0.00 36.21 2.52
2389 10143 9.643693 CAAAAGCTCCTGAAATATTGTATTGTT 57.356 29.630 0.00 0.00 0.00 2.83
2561 10375 4.712051 AGAATCACCAATGCTAGCCATA 57.288 40.909 13.29 0.00 32.67 2.74
2562 10376 5.252586 AGAATCACCAATGCTAGCCATAT 57.747 39.130 13.29 0.00 32.67 1.78
2695 10510 7.360438 GGCTATTAAGTCTATACAATGCAGCAC 60.360 40.741 0.00 0.00 0.00 4.40
2745 10560 2.877786 TGAAGAAAGCATCTCGTTTGCA 59.122 40.909 9.05 0.00 42.62 4.08
2774 10589 2.623889 ACCTCGAATCGATGGAAGGTAG 59.376 50.000 21.62 2.72 34.61 3.18
2885 14023 4.672587 TGTCAGAGTACAAACAAGAGCT 57.327 40.909 0.00 0.00 0.00 4.09
3107 14531 0.527169 GGCTAAACTACTCGCGGGAC 60.527 60.000 15.95 0.00 0.00 4.46
3141 14565 1.605710 GCTACTTCTGGGCGTATACGA 59.394 52.381 28.66 7.22 43.02 3.43
3389 14822 2.702478 CTGTATGCAGATGGGAGGAGAA 59.298 50.000 4.57 0.00 45.28 2.87
3636 15672 5.438761 ACTGCACTATCCAAAACTTTCAC 57.561 39.130 0.00 0.00 0.00 3.18
3638 15674 3.252215 TGCACTATCCAAAACTTTCACCG 59.748 43.478 0.00 0.00 0.00 4.94
3686 15722 8.561738 TTCCCACTCTTGTAGTTTCAAATATC 57.438 34.615 0.00 0.00 35.76 1.63
3817 15853 3.073209 TGTTGGGTTGCTAGTTGGTATGA 59.927 43.478 0.00 0.00 0.00 2.15
3945 15981 8.801882 TTAAGGTACAAATTACATCTCCAAGG 57.198 34.615 0.00 0.00 0.00 3.61
4002 17603 2.497273 ACACCCCTGATTAAGCATTTGC 59.503 45.455 0.00 0.00 42.49 3.68
4234 17838 4.509230 CCCTTCATGTATGATGACAAGACG 59.491 45.833 8.76 0.00 36.56 4.18
4300 17904 5.671329 GCGACTGTTTGTCAATCCTATTGAC 60.671 44.000 20.64 20.64 45.60 3.18
4345 17949 8.099537 GGTATATGAGTGTCCATGAAATCATCT 58.900 37.037 8.54 4.03 33.61 2.90
4348 17952 6.550938 TGAGTGTCCATGAAATCATCTACT 57.449 37.500 0.00 0.00 33.61 2.57
4385 17993 2.775384 ACCCCCGTGCTAATGAAAGATA 59.225 45.455 0.00 0.00 0.00 1.98
4573 18487 6.709018 TGGATTGTAATCATCAGTCGACTA 57.291 37.500 19.57 2.37 37.15 2.59
4616 18530 3.191162 CGATTTTTCTGTCCAATGAGGCA 59.809 43.478 0.00 0.00 37.29 4.75
4656 18570 3.607741 TGTTTTTGAGTGTGGTCCGTTA 58.392 40.909 0.00 0.00 0.00 3.18
4711 18625 0.469144 AATTTGGGTTGCTGGACCGT 60.469 50.000 0.00 0.00 40.75 4.83
4719 18633 3.948719 GCTGGACCGTTCACCCCA 61.949 66.667 0.00 0.00 0.00 4.96
4720 18634 2.032071 CTGGACCGTTCACCCCAC 59.968 66.667 0.00 0.00 0.00 4.61
4723 18637 3.562232 GACCGTTCACCCCACCCA 61.562 66.667 0.00 0.00 0.00 4.51
4724 18638 2.856988 ACCGTTCACCCCACCCAT 60.857 61.111 0.00 0.00 0.00 4.00
4725 18639 2.361104 CCGTTCACCCCACCCATG 60.361 66.667 0.00 0.00 0.00 3.66
4726 18640 3.061848 CGTTCACCCCACCCATGC 61.062 66.667 0.00 0.00 0.00 4.06
4727 18641 3.061848 GTTCACCCCACCCATGCG 61.062 66.667 0.00 0.00 0.00 4.73
4728 18642 4.358841 TTCACCCCACCCATGCGG 62.359 66.667 0.00 0.00 37.81 5.69
4786 18925 4.951715 AGCAGATGAAAATTGCTATGGTGA 59.048 37.500 0.00 0.00 45.67 4.02
4815 18955 8.797438 GGACATTTCTGGAGAAAAAGAAGTATT 58.203 33.333 5.94 0.00 45.81 1.89
4841 18981 6.261118 GTTCAGAATTGCTAATAAGGTGCAG 58.739 40.000 0.00 0.00 38.01 4.41
4941 19165 4.494350 AACATTACTTTCAGCTGCTGTG 57.506 40.909 27.24 18.62 32.61 3.66
5005 19229 2.094675 ACAACACTTGACTGCTGCTTT 58.905 42.857 0.00 0.00 0.00 3.51
5006 19230 2.098117 ACAACACTTGACTGCTGCTTTC 59.902 45.455 0.00 0.00 0.00 2.62
5041 19275 7.254185 CGACGATAAAAATCGAGGGAAACAATA 60.254 37.037 14.13 0.00 46.12 1.90
5049 19283 8.801882 AAATCGAGGGAAACAATAATTGACTA 57.198 30.769 0.00 0.00 0.00 2.59
5066 19300 3.455910 TGACTAAGCATTGCCTATCTGGT 59.544 43.478 4.70 0.00 38.35 4.00
5159 19406 6.364435 CCAAGAAAAAGATGAGCAGTTTTAGC 59.636 38.462 0.00 0.00 0.00 3.09
5162 19409 8.340618 AGAAAAAGATGAGCAGTTTTAGCATA 57.659 30.769 0.00 0.00 0.00 3.14
5274 19521 9.886132 TTTTGTCTGAATATTCCTAAGTACTCC 57.114 33.333 12.90 0.00 0.00 3.85
5275 19522 7.598759 TGTCTGAATATTCCTAAGTACTCCC 57.401 40.000 12.90 0.00 0.00 4.30
5276 19523 7.363031 TGTCTGAATATTCCTAAGTACTCCCT 58.637 38.462 12.90 0.00 0.00 4.20
5277 19524 7.506261 TGTCTGAATATTCCTAAGTACTCCCTC 59.494 40.741 12.90 0.00 0.00 4.30
5278 19525 7.726738 GTCTGAATATTCCTAAGTACTCCCTCT 59.273 40.741 12.90 0.00 0.00 3.69
5279 19526 7.726291 TCTGAATATTCCTAAGTACTCCCTCTG 59.274 40.741 12.90 0.00 0.00 3.35
5280 19527 7.363031 TGAATATTCCTAAGTACTCCCTCTGT 58.637 38.462 12.90 0.00 0.00 3.41
5281 19528 8.508601 TGAATATTCCTAAGTACTCCCTCTGTA 58.491 37.037 12.90 0.00 0.00 2.74
5282 19529 9.364653 GAATATTCCTAAGTACTCCCTCTGTAA 57.635 37.037 3.92 0.00 0.00 2.41
5283 19530 9.725206 AATATTCCTAAGTACTCCCTCTGTAAA 57.275 33.333 0.00 0.00 0.00 2.01
5284 19531 7.663043 ATTCCTAAGTACTCCCTCTGTAAAG 57.337 40.000 0.00 0.00 0.00 1.85
5285 19532 6.398655 TCCTAAGTACTCCCTCTGTAAAGA 57.601 41.667 0.00 0.00 0.00 2.52
5286 19533 6.797707 TCCTAAGTACTCCCTCTGTAAAGAA 58.202 40.000 0.00 0.00 0.00 2.52
5287 19534 7.243824 TCCTAAGTACTCCCTCTGTAAAGAAA 58.756 38.462 0.00 0.00 0.00 2.52
5288 19535 7.899709 TCCTAAGTACTCCCTCTGTAAAGAAAT 59.100 37.037 0.00 0.00 0.00 2.17
5289 19536 9.198475 CCTAAGTACTCCCTCTGTAAAGAAATA 57.802 37.037 0.00 0.00 0.00 1.40
5296 19543 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
5297 19544 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
5298 19545 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
5299 19546 9.319143 CCCTCTGTAAAGAAATATAAGAGTGTG 57.681 37.037 0.00 0.00 0.00 3.82
5300 19547 9.877178 CCTCTGTAAAGAAATATAAGAGTGTGT 57.123 33.333 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 82 0.934496 TGTGCGTGCAACTAGACAAC 59.066 50.000 0.00 0.00 31.75 3.32
39 83 1.877637 ATGTGCGTGCAACTAGACAA 58.122 45.000 0.00 0.00 31.75 3.18
40 84 1.530720 CAATGTGCGTGCAACTAGACA 59.469 47.619 0.00 0.00 31.75 3.41
41 85 1.798223 TCAATGTGCGTGCAACTAGAC 59.202 47.619 0.00 0.00 31.75 2.59
42 86 2.162319 TCAATGTGCGTGCAACTAGA 57.838 45.000 0.00 0.00 31.75 2.43
43 87 2.160219 ACATCAATGTGCGTGCAACTAG 59.840 45.455 0.00 0.00 40.03 2.57
45 89 0.953727 ACATCAATGTGCGTGCAACT 59.046 45.000 0.00 0.00 40.03 3.16
46 90 1.769733 AACATCAATGTGCGTGCAAC 58.230 45.000 0.00 0.00 41.61 4.17
47 91 2.505628 AAACATCAATGTGCGTGCAA 57.494 40.000 0.00 0.00 41.61 4.08
48 92 2.551887 ACTAAACATCAATGTGCGTGCA 59.448 40.909 0.00 0.00 41.61 4.57
49 93 3.201726 ACTAAACATCAATGTGCGTGC 57.798 42.857 0.00 0.00 41.61 5.34
50 94 3.913763 CCAACTAAACATCAATGTGCGTG 59.086 43.478 0.00 0.00 41.61 5.34
52 96 2.916716 GCCAACTAAACATCAATGTGCG 59.083 45.455 0.00 0.00 41.61 5.34
56 100 7.814107 ACATTACAAGCCAACTAAACATCAATG 59.186 33.333 0.00 0.00 0.00 2.82
57 101 7.895759 ACATTACAAGCCAACTAAACATCAAT 58.104 30.769 0.00 0.00 0.00 2.57
58 102 7.283625 ACATTACAAGCCAACTAAACATCAA 57.716 32.000 0.00 0.00 0.00 2.57
60 104 8.040716 ACTACATTACAAGCCAACTAAACATC 57.959 34.615 0.00 0.00 0.00 3.06
61 105 7.883311 AGACTACATTACAAGCCAACTAAACAT 59.117 33.333 0.00 0.00 0.00 2.71
63 107 7.668525 AGACTACATTACAAGCCAACTAAAC 57.331 36.000 0.00 0.00 0.00 2.01
64 108 9.953565 ATTAGACTACATTACAAGCCAACTAAA 57.046 29.630 0.00 0.00 0.00 1.85
65 109 9.953565 AATTAGACTACATTACAAGCCAACTAA 57.046 29.630 0.00 0.00 0.00 2.24
67 111 7.148239 GCAATTAGACTACATTACAAGCCAACT 60.148 37.037 0.00 0.00 0.00 3.16
68 112 6.967199 GCAATTAGACTACATTACAAGCCAAC 59.033 38.462 0.00 0.00 0.00 3.77
72 116 6.961554 GTGTGCAATTAGACTACATTACAAGC 59.038 38.462 0.00 0.00 0.00 4.01
144 190 5.408356 ACTAGACTACATTACAAGCCAACG 58.592 41.667 0.00 0.00 0.00 4.10
341 437 9.850628 GTGTGTAATGTAACTAGACTACATTGA 57.149 33.333 27.23 18.30 45.28 2.57
357 453 8.165239 ACTAAACATCAATGTGTGTGTAATGT 57.835 30.769 0.00 0.00 41.61 2.71
358 454 8.904712 CAACTAAACATCAATGTGTGTGTAATG 58.095 33.333 0.00 0.00 41.61 1.90
359 455 8.081633 CCAACTAAACATCAATGTGTGTGTAAT 58.918 33.333 0.00 0.00 41.61 1.89
362 458 5.735922 GCCAACTAAACATCAATGTGTGTGT 60.736 40.000 0.00 0.00 41.61 3.72
466 562 3.608796 TGCATGTCGAAATTCAGATCCA 58.391 40.909 0.00 0.00 0.00 3.41
614 719 3.303791 GCTCCTGTGGTTAAAAAGACACG 60.304 47.826 0.00 0.00 36.67 4.49
719 831 3.120991 CGTCTGTTTTCCGAGTAGCTTTG 60.121 47.826 0.00 0.00 0.00 2.77
721 833 2.609737 CCGTCTGTTTTCCGAGTAGCTT 60.610 50.000 0.00 0.00 0.00 3.74
722 834 1.067776 CCGTCTGTTTTCCGAGTAGCT 60.068 52.381 0.00 0.00 0.00 3.32
724 836 1.067776 AGCCGTCTGTTTTCCGAGTAG 60.068 52.381 0.00 0.00 0.00 2.57
725 837 0.963962 AGCCGTCTGTTTTCCGAGTA 59.036 50.000 0.00 0.00 0.00 2.59
727 839 1.901650 GCAGCCGTCTGTTTTCCGAG 61.902 60.000 0.00 0.00 42.29 4.63
728 840 1.959226 GCAGCCGTCTGTTTTCCGA 60.959 57.895 0.00 0.00 42.29 4.55
730 842 2.556287 CGCAGCCGTCTGTTTTCC 59.444 61.111 0.00 0.00 42.29 3.13
748 860 1.736645 AATCACGCGAAGACCCACG 60.737 57.895 15.93 0.00 0.00 4.94
749 861 0.669318 TCAATCACGCGAAGACCCAC 60.669 55.000 15.93 0.00 0.00 4.61
750 862 0.669318 GTCAATCACGCGAAGACCCA 60.669 55.000 15.93 0.00 0.00 4.51
751 863 0.669318 TGTCAATCACGCGAAGACCC 60.669 55.000 15.93 0.24 32.27 4.46
755 867 1.792367 TGAACTGTCAATCACGCGAAG 59.208 47.619 15.93 4.76 0.00 3.79
757 869 1.418373 CTGAACTGTCAATCACGCGA 58.582 50.000 15.93 0.00 31.88 5.87
758 870 0.179240 GCTGAACTGTCAATCACGCG 60.179 55.000 3.53 3.53 31.88 6.01
759 871 1.151668 AGCTGAACTGTCAATCACGC 58.848 50.000 0.00 0.00 31.88 5.34
761 873 4.274459 AGAACAAGCTGAACTGTCAATCAC 59.726 41.667 0.00 0.00 31.88 3.06
762 874 4.454678 AGAACAAGCTGAACTGTCAATCA 58.545 39.130 0.00 0.00 31.88 2.57
763 875 4.083590 GGAGAACAAGCTGAACTGTCAATC 60.084 45.833 0.00 0.00 31.88 2.67
766 878 2.485479 GGGAGAACAAGCTGAACTGTCA 60.485 50.000 0.00 0.00 0.00 3.58
767 879 2.147150 GGGAGAACAAGCTGAACTGTC 58.853 52.381 0.00 0.00 0.00 3.51
768 880 1.490490 TGGGAGAACAAGCTGAACTGT 59.510 47.619 0.00 0.00 0.00 3.55
769 881 2.260844 TGGGAGAACAAGCTGAACTG 57.739 50.000 0.00 0.00 0.00 3.16
772 884 2.108075 TCCATTGGGAGAACAAGCTGAA 59.892 45.455 2.09 0.00 38.64 3.02
773 885 1.704628 TCCATTGGGAGAACAAGCTGA 59.295 47.619 2.09 0.00 38.64 4.26
774 886 2.205022 TCCATTGGGAGAACAAGCTG 57.795 50.000 2.09 0.00 38.64 4.24
784 896 0.251916 AATTCGCGTCTCCATTGGGA 59.748 50.000 5.77 0.00 42.29 4.37
785 897 1.948104 TAATTCGCGTCTCCATTGGG 58.052 50.000 5.77 0.00 0.00 4.12
786 898 2.936498 ACTTAATTCGCGTCTCCATTGG 59.064 45.455 5.77 0.00 0.00 3.16
790 902 2.343101 CCAACTTAATTCGCGTCTCCA 58.657 47.619 5.77 0.00 0.00 3.86
791 903 1.664151 CCCAACTTAATTCGCGTCTCC 59.336 52.381 5.77 0.00 0.00 3.71
794 906 2.070783 TGACCCAACTTAATTCGCGTC 58.929 47.619 5.77 0.00 0.00 5.19
795 907 2.073816 CTGACCCAACTTAATTCGCGT 58.926 47.619 5.77 0.00 0.00 6.01
796 908 2.343101 TCTGACCCAACTTAATTCGCG 58.657 47.619 0.00 0.00 0.00 5.87
797 909 2.678336 CCTCTGACCCAACTTAATTCGC 59.322 50.000 0.00 0.00 0.00 4.70
798 910 3.684788 CACCTCTGACCCAACTTAATTCG 59.315 47.826 0.00 0.00 0.00 3.34
799 911 4.652822 ACACCTCTGACCCAACTTAATTC 58.347 43.478 0.00 0.00 0.00 2.17
800 912 4.652822 GACACCTCTGACCCAACTTAATT 58.347 43.478 0.00 0.00 0.00 1.40
801 913 3.306780 CGACACCTCTGACCCAACTTAAT 60.307 47.826 0.00 0.00 0.00 1.40
802 914 2.036733 CGACACCTCTGACCCAACTTAA 59.963 50.000 0.00 0.00 0.00 1.85
803 915 1.616865 CGACACCTCTGACCCAACTTA 59.383 52.381 0.00 0.00 0.00 2.24
804 916 0.393077 CGACACCTCTGACCCAACTT 59.607 55.000 0.00 0.00 0.00 2.66
805 917 0.759436 ACGACACCTCTGACCCAACT 60.759 55.000 0.00 0.00 0.00 3.16
806 918 0.106149 AACGACACCTCTGACCCAAC 59.894 55.000 0.00 0.00 0.00 3.77
807 919 0.834612 AAACGACACCTCTGACCCAA 59.165 50.000 0.00 0.00 0.00 4.12
810 922 2.067013 GCTAAAACGACACCTCTGACC 58.933 52.381 0.00 0.00 0.00 4.02
811 923 2.731976 CAGCTAAAACGACACCTCTGAC 59.268 50.000 0.00 0.00 0.00 3.51
812 924 2.626266 TCAGCTAAAACGACACCTCTGA 59.374 45.455 0.00 0.00 0.00 3.27
813 925 2.731976 GTCAGCTAAAACGACACCTCTG 59.268 50.000 0.00 0.00 0.00 3.35
814 926 2.628657 AGTCAGCTAAAACGACACCTCT 59.371 45.455 4.19 0.00 31.92 3.69
816 928 4.803098 ATAGTCAGCTAAAACGACACCT 57.197 40.909 4.19 0.00 31.92 4.00
819 931 6.704493 ACAAAGAATAGTCAGCTAAAACGACA 59.296 34.615 4.19 0.00 31.92 4.35
820 932 7.118422 ACAAAGAATAGTCAGCTAAAACGAC 57.882 36.000 0.00 0.00 0.00 4.34
821 933 7.868922 TGTACAAAGAATAGTCAGCTAAAACGA 59.131 33.333 0.00 0.00 0.00 3.85
822 934 8.014322 TGTACAAAGAATAGTCAGCTAAAACG 57.986 34.615 0.00 0.00 0.00 3.60
823 935 9.204570 TCTGTACAAAGAATAGTCAGCTAAAAC 57.795 33.333 0.00 0.00 0.00 2.43
824 936 9.772973 TTCTGTACAAAGAATAGTCAGCTAAAA 57.227 29.630 0.00 0.00 31.19 1.52
825 937 9.772973 TTTCTGTACAAAGAATAGTCAGCTAAA 57.227 29.630 0.00 0.00 36.12 1.85
826 938 9.772973 TTTTCTGTACAAAGAATAGTCAGCTAA 57.227 29.630 0.00 0.00 36.12 3.09
829 941 7.861630 TGTTTTCTGTACAAAGAATAGTCAGC 58.138 34.615 0.00 0.00 36.12 4.26
837 949 9.349713 ACCATCTAATGTTTTCTGTACAAAGAA 57.650 29.630 0.00 0.00 34.36 2.52
838 950 8.783093 CACCATCTAATGTTTTCTGTACAAAGA 58.217 33.333 0.00 0.00 0.00 2.52
839 951 7.538678 GCACCATCTAATGTTTTCTGTACAAAG 59.461 37.037 0.00 0.00 0.00 2.77
842 954 5.414454 GGCACCATCTAATGTTTTCTGTACA 59.586 40.000 0.00 0.00 0.00 2.90
843 955 5.880341 GGCACCATCTAATGTTTTCTGTAC 58.120 41.667 0.00 0.00 0.00 2.90
862 974 0.961753 CTTTGAACAGGGAAGGGCAC 59.038 55.000 0.00 0.00 0.00 5.01
866 978 0.875059 GCGTCTTTGAACAGGGAAGG 59.125 55.000 0.00 0.00 0.00 3.46
867 979 1.264288 GTGCGTCTTTGAACAGGGAAG 59.736 52.381 0.00 0.00 0.00 3.46
868 980 1.134220 AGTGCGTCTTTGAACAGGGAA 60.134 47.619 0.00 0.00 0.00 3.97
869 981 0.468226 AGTGCGTCTTTGAACAGGGA 59.532 50.000 0.00 0.00 0.00 4.20
870 982 1.308998 AAGTGCGTCTTTGAACAGGG 58.691 50.000 0.00 0.00 31.57 4.45
871 983 2.287009 GGAAAGTGCGTCTTTGAACAGG 60.287 50.000 10.64 0.00 45.15 4.00
872 984 2.614057 AGGAAAGTGCGTCTTTGAACAG 59.386 45.455 10.64 0.00 45.15 3.16
873 985 2.354510 CAGGAAAGTGCGTCTTTGAACA 59.645 45.455 10.64 0.00 45.15 3.18
874 986 2.287009 CCAGGAAAGTGCGTCTTTGAAC 60.287 50.000 10.64 3.04 45.15 3.18
875 987 1.946768 CCAGGAAAGTGCGTCTTTGAA 59.053 47.619 10.64 0.00 45.15 2.69
876 988 1.140052 TCCAGGAAAGTGCGTCTTTGA 59.860 47.619 10.64 1.21 45.15 2.69
1083 8263 1.371558 GAAGAAGTCGCCCCACACT 59.628 57.895 0.00 0.00 0.00 3.55
1110 8290 2.568062 TGCCTGTAACGGTTCTGGATTA 59.432 45.455 7.20 0.00 0.00 1.75
1144 8327 7.014326 TCCCAGATGCTGTTATTACTACTGTAG 59.986 40.741 13.13 13.13 0.00 2.74
1150 8333 4.653801 TGCTCCCAGATGCTGTTATTACTA 59.346 41.667 0.00 0.00 0.00 1.82
1176 8359 5.382618 AAACATGGAGAGACTGAAAATGC 57.617 39.130 0.00 0.00 0.00 3.56
1191 8376 7.223777 ACACATAAAACCGAAAGAAAAACATGG 59.776 33.333 0.00 0.00 0.00 3.66
1202 8387 5.302059 TGGGATTTCACACATAAAACCGAAA 59.698 36.000 0.00 0.00 31.44 3.46
1218 8403 3.588955 GCCATGAAACAACTGGGATTTC 58.411 45.455 0.00 0.00 33.75 2.17
1379 9016 5.241506 TGTTTGGAAACAGCATTAAGAGGAG 59.758 40.000 0.70 0.00 43.45 3.69
1485 9126 3.571401 CGTATTACGGTTGACTCCCCTAT 59.429 47.826 8.36 0.00 38.08 2.57
1511 9152 1.668751 GCATCGACCGCATTTCCTTTA 59.331 47.619 3.85 0.00 0.00 1.85
1561 9202 3.548818 CGCTCTTTCAGTTTCAACCCTTG 60.549 47.826 0.00 0.00 0.00 3.61
1563 9204 2.158813 TCGCTCTTTCAGTTTCAACCCT 60.159 45.455 0.00 0.00 0.00 4.34
1566 9207 2.545946 AGCTCGCTCTTTCAGTTTCAAC 59.454 45.455 0.00 0.00 0.00 3.18
1567 9208 2.838736 AGCTCGCTCTTTCAGTTTCAA 58.161 42.857 0.00 0.00 0.00 2.69
1568 9209 2.533266 AGCTCGCTCTTTCAGTTTCA 57.467 45.000 0.00 0.00 0.00 2.69
1569 9210 3.318017 TGTAGCTCGCTCTTTCAGTTTC 58.682 45.455 0.00 0.00 0.00 2.78
1570 9211 3.386768 TGTAGCTCGCTCTTTCAGTTT 57.613 42.857 0.00 0.00 0.00 2.66
1571 9212 3.386768 TTGTAGCTCGCTCTTTCAGTT 57.613 42.857 0.00 0.00 0.00 3.16
1572 9213 3.194542 AGATTGTAGCTCGCTCTTTCAGT 59.805 43.478 0.00 0.00 0.00 3.41
1573 9214 3.779759 AGATTGTAGCTCGCTCTTTCAG 58.220 45.455 0.00 0.00 0.00 3.02
1686 9331 5.579047 TGGTTTATCAAATGTCATGGGTCT 58.421 37.500 0.00 0.00 0.00 3.85
1777 9422 7.223777 GCAGAAGAGGTGTCATTAAAGACTATC 59.776 40.741 11.75 7.22 39.27 2.08
1949 9610 1.604604 TAAAGTTGCAGCCACCAGTC 58.395 50.000 0.00 0.00 0.00 3.51
2090 9751 4.081254 TGTCATCCTTTCCTCTGACATCTG 60.081 45.833 0.38 0.00 42.12 2.90
2156 9817 2.540515 CTCAACTATGGTACTGCACGG 58.459 52.381 0.00 0.00 0.00 4.94
2695 10510 3.954258 GTCTCCCCATGGATAAAAAGGTG 59.046 47.826 15.22 5.00 40.80 4.00
2774 10589 0.323360 TGCCAATGGGTACTCAAGCC 60.323 55.000 0.00 0.00 46.67 4.35
2885 14023 2.306805 AGAATGGAGGAGTTGTGCATCA 59.693 45.455 0.00 0.00 0.00 3.07
3107 14531 2.048597 TAGCACTCAACCACGCGG 60.049 61.111 12.47 0.00 38.77 6.46
3141 14565 8.728337 TGTGTATACTCTTTCTCGTAGTATGT 57.272 34.615 4.17 0.00 37.11 2.29
3389 14822 5.515106 ACTCTGGTAGAAGAGAAGTAGCAT 58.485 41.667 8.16 0.00 45.59 3.79
3611 15045 7.422399 GTGAAAGTTTTGGATAGTGCAGTTTA 58.578 34.615 0.00 0.00 0.00 2.01
3629 15665 5.221581 ACACATTAGTACTTCCGGTGAAAGT 60.222 40.000 17.85 11.38 0.00 2.66
3636 15672 5.243207 AGGAAAACACATTAGTACTTCCGG 58.757 41.667 0.00 0.00 38.07 5.14
3638 15674 8.080417 GGAAAAGGAAAACACATTAGTACTTCC 58.920 37.037 0.00 0.00 35.44 3.46
3686 15722 6.404074 GGCTTCTTGGAGATAGTTGTTTGATG 60.404 42.308 0.00 0.00 0.00 3.07
3817 15853 0.613260 TCCTTGGTTGCAGTATCGCT 59.387 50.000 0.00 0.00 0.00 4.93
3876 15912 0.533755 GTGTCACCTCTGCACAAGCT 60.534 55.000 0.00 0.00 42.74 3.74
3945 15981 8.784043 CAAAGGATAAGCAATATAGGTGGTAAC 58.216 37.037 0.00 0.00 0.00 2.50
3961 15999 4.265556 GTGTCGTCGTGATCAAAGGATAAG 59.734 45.833 0.00 0.00 32.67 1.73
4002 17603 1.939934 TCTTTCCACGCTGTGAACAAG 59.060 47.619 9.75 8.39 35.23 3.16
4195 17799 1.888215 AGGGCATGCTGATCGTTATG 58.112 50.000 18.92 0.00 0.00 1.90
4234 17838 2.729156 GCTGCTGAACGTAAAAGCATCC 60.729 50.000 17.02 9.78 45.35 3.51
4300 17904 6.662865 ATACCACATCCTCATGTCTAGAAG 57.337 41.667 0.00 0.00 41.69 2.85
4345 17949 1.079819 GCTGGCGCTTCTGTCAGTA 60.080 57.895 7.64 0.00 0.00 2.74
4348 17952 2.666190 GTGCTGGCGCTTCTGTCA 60.666 61.111 7.64 0.00 36.97 3.58
4364 17972 0.988832 TCTTTCATTAGCACGGGGGT 59.011 50.000 0.00 0.00 0.00 4.95
4385 17993 4.411540 AGCAGATTGGAAGTGTCCTGATAT 59.588 41.667 0.00 0.00 45.22 1.63
4537 18183 7.598278 TGATTACAATCCAAATACACACCAAC 58.402 34.615 0.00 0.00 34.50 3.77
4616 18530 9.991388 CAAAAACAAATGAAAAGATGTGTCATT 57.009 25.926 0.00 0.00 42.38 2.57
4728 18642 4.295199 GGGTGGGTGGGGTGTTCC 62.295 72.222 0.00 0.00 0.00 3.62
4729 18643 3.503839 TGGGTGGGTGGGGTGTTC 61.504 66.667 0.00 0.00 0.00 3.18
4730 18644 2.936721 TACTGGGTGGGTGGGGTGTT 62.937 60.000 0.00 0.00 0.00 3.32
4731 18645 3.429685 TACTGGGTGGGTGGGGTGT 62.430 63.158 0.00 0.00 0.00 4.16
4732 18646 2.530661 TACTGGGTGGGTGGGGTG 60.531 66.667 0.00 0.00 0.00 4.61
4733 18647 2.530916 GTACTGGGTGGGTGGGGT 60.531 66.667 0.00 0.00 0.00 4.95
4734 18648 3.712907 CGTACTGGGTGGGTGGGG 61.713 72.222 0.00 0.00 0.00 4.96
4736 18650 0.686224 TTTACGTACTGGGTGGGTGG 59.314 55.000 0.00 0.00 0.00 4.61
4737 18651 2.547299 TTTTACGTACTGGGTGGGTG 57.453 50.000 0.00 0.00 0.00 4.61
4738 18652 2.806382 CGTTTTTACGTACTGGGTGGGT 60.806 50.000 0.00 0.00 0.00 4.51
4786 18925 5.694995 TCTTTTTCTCCAGAAATGTCCAGT 58.305 37.500 2.59 0.00 42.83 4.00
4815 18955 5.125417 GCACCTTATTAGCAATTCTGAACCA 59.875 40.000 0.00 0.00 0.00 3.67
4841 18981 7.606456 TCCCAGTAGTTGATTTTAGTGTCAATC 59.394 37.037 0.00 0.00 36.79 2.67
4875 19015 6.343716 TGAAGCCTTATTTTGCTGATTTCA 57.656 33.333 0.00 0.00 38.00 2.69
4941 19165 7.120873 TCAGTGTTGTCCTATCTAGTTCTGTAC 59.879 40.741 0.00 0.00 0.00 2.90
4993 19217 5.181056 TCGATTATTTTGAAAGCAGCAGTCA 59.819 36.000 0.00 0.00 0.00 3.41
5005 19229 9.843874 CTCGATTTTTATCGTCGATTATTTTGA 57.156 29.630 13.91 3.70 42.65 2.69
5006 19230 9.092322 CCTCGATTTTTATCGTCGATTATTTTG 57.908 33.333 13.91 0.00 42.65 2.44
5041 19275 5.533903 CCAGATAGGCAATGCTTAGTCAATT 59.466 40.000 4.82 0.00 0.00 2.32
5049 19283 3.659183 AGAACCAGATAGGCAATGCTT 57.341 42.857 4.82 0.00 43.14 3.91
5066 19300 5.483937 AGGACTATGTGAACCATGTGTAGAA 59.516 40.000 0.00 0.00 34.86 2.10
5107 19353 3.492102 AACTGTAGCTCACATGGTTGT 57.508 42.857 0.00 0.00 36.29 3.32
5113 19359 3.594134 GCTCTGAAACTGTAGCTCACAT 58.406 45.455 0.00 0.00 36.29 3.21
5172 19419 8.970859 TCTTTTTCATCTTTTGAGTCTCTCTT 57.029 30.769 0.65 0.00 35.27 2.85
5182 19429 9.777575 AACTGCAATTTTCTTTTTCATCTTTTG 57.222 25.926 0.00 0.00 0.00 2.44
5188 19435 8.606602 GTCTGAAACTGCAATTTTCTTTTTCAT 58.393 29.630 17.19 0.00 34.58 2.57
5271 19518 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
5272 19519 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
5273 19520 9.319143 CACACTCTTATATTTCTTTACAGAGGG 57.681 37.037 0.00 0.00 36.55 4.30
5274 19521 9.877178 ACACACTCTTATATTTCTTTACAGAGG 57.123 33.333 0.00 0.00 32.21 3.69


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

AutoCloner maintained by Alex Coulton.