Multiple sequence alignment - TraesCS3D01G182400

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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 TraesCS3D01G182400 chr3D 100.000 9793 0 0 1 9793 166500201 166490409 0.000000e+00 18085.0
1 TraesCS3D01G182400 chr3D 90.265 226 21 1 11 235 155945255 155945480 2.670000e-75 294.0
2 TraesCS3D01G182400 chr3D 80.337 178 26 7 6141 6314 298589983 298590155 1.030000e-24 126.0
3 TraesCS3D01G182400 chr3A 96.972 5548 121 20 675 6199 204879595 204874072 0.000000e+00 9271.0
4 TraesCS3D01G182400 chr3A 94.136 1944 60 22 7597 9524 204867513 204865608 0.000000e+00 2909.0
5 TraesCS3D01G182400 chr3A 98.062 1290 23 2 6194 7483 204868814 204867527 0.000000e+00 2242.0
6 TraesCS3D01G182400 chr3A 90.055 362 22 6 234 584 95938637 95938995 3.220000e-124 457.0
7 TraesCS3D01G182400 chr3A 81.659 458 60 14 234 676 224354744 224355192 9.350000e-95 359.0
8 TraesCS3D01G182400 chr3A 87.500 320 27 11 234 551 987273 986965 3.360000e-94 357.0
9 TraesCS3D01G182400 chr3A 87.815 238 15 7 9563 9793 204865553 204865323 5.830000e-67 267.0
10 TraesCS3D01G182400 chr3A 91.005 189 16 1 9554 9741 204863015 204862827 4.540000e-63 254.0
11 TraesCS3D01G182400 chr3A 81.006 179 26 7 6141 6314 396616780 396616955 1.720000e-27 135.0
12 TraesCS3D01G182400 chr3A 94.444 36 2 0 5846 5881 204874534 204874499 1.000000e-03 56.5
13 TraesCS3D01G182400 chr2D 96.684 5096 119 18 2249 7305 462486307 462481223 0.000000e+00 8429.0
14 TraesCS3D01G182400 chr2D 88.916 5007 372 90 878 5785 544996673 545001595 0.000000e+00 6002.0
15 TraesCS3D01G182400 chr2D 96.734 1378 42 3 7332 8709 462481226 462479852 0.000000e+00 2292.0
16 TraesCS3D01G182400 chr2D 90.884 1470 122 9 7503 8970 545003190 545004649 0.000000e+00 1962.0
17 TraesCS3D01G182400 chr2D 93.103 1189 66 10 6329 7507 545001604 545002786 0.000000e+00 1727.0
18 TraesCS3D01G182400 chr2D 89.512 410 20 4 8892 9281 462479756 462479350 1.900000e-136 497.0
19 TraesCS3D01G182400 chr2D 90.000 230 20 2 9 235 129270404 129270633 2.670000e-75 294.0
20 TraesCS3D01G182400 chr2D 86.765 204 26 1 9554 9756 462479091 462478888 9.900000e-55 226.0
21 TraesCS3D01G182400 chr2D 87.432 183 23 0 5879 6061 409257238 409257420 2.770000e-50 211.0
22 TraesCS3D01G182400 chr2D 90.476 126 12 0 9324 9449 462479344 462479219 6.080000e-37 167.0
23 TraesCS3D01G182400 chr2D 92.000 50 4 0 5949 5998 120530519 120530470 4.910000e-08 71.3
24 TraesCS3D01G182400 chr2D 94.444 36 2 0 5846 5881 462482799 462482764 1.000000e-03 56.5
25 TraesCS3D01G182400 chr3B 97.279 4925 103 16 732 5652 242202002 242197105 0.000000e+00 8323.0
26 TraesCS3D01G182400 chr3B 95.673 3767 103 30 5780 9515 242196621 242192884 0.000000e+00 5999.0
27 TraesCS3D01G182400 chr3B 88.627 510 36 9 75 584 242202710 242202223 1.410000e-167 601.0
28 TraesCS3D01G182400 chr3B 89.474 228 23 1 9 235 225804272 225804045 4.480000e-73 287.0
29 TraesCS3D01G182400 chr3B 89.655 203 20 1 9554 9755 242172996 242172794 3.510000e-64 257.0
30 TraesCS3D01G182400 chr3B 99.291 141 1 0 5651 5791 242196943 242196803 1.260000e-63 255.0
31 TraesCS3D01G182400 chr3B 97.222 36 1 0 5846 5881 242196869 242196834 2.950000e-05 62.1
32 TraesCS3D01G182400 chr3B 92.857 42 2 1 9514 9554 242173099 242173058 1.060000e-04 60.2
33 TraesCS3D01G182400 chr2A 90.868 3340 234 38 2507 5791 688430919 688427596 0.000000e+00 4412.0
34 TraesCS3D01G182400 chr2A 91.627 1457 112 8 7503 8956 688425771 688424322 0.000000e+00 2006.0
35 TraesCS3D01G182400 chr2A 93.565 1181 68 6 6329 7507 688427593 688426419 0.000000e+00 1753.0
36 TraesCS3D01G182400 chr2A 87.671 876 77 14 1646 2505 688431944 688431084 0.000000e+00 990.0
37 TraesCS3D01G182400 chr2A 87.879 462 41 12 850 1309 688434855 688434407 6.740000e-146 529.0
38 TraesCS3D01G182400 chr2A 83.824 204 25 6 234 434 120449962 120449764 4.670000e-43 187.0
39 TraesCS3D01G182400 chr2B 92.811 1697 96 15 3138 4816 651719974 651721662 0.000000e+00 2435.0
40 TraesCS3D01G182400 chr2B 90.408 1470 119 13 7504 8970 651725194 651726644 0.000000e+00 1914.0
41 TraesCS3D01G182400 chr2B 93.188 1189 69 8 6322 7507 651722583 651723762 0.000000e+00 1736.0
42 TraesCS3D01G182400 chr2B 85.959 1282 120 25 1597 2838 651718146 651719407 0.000000e+00 1315.0
43 TraesCS3D01G182400 chr2B 90.461 933 73 7 4870 5791 651721658 651722585 0.000000e+00 1216.0
44 TraesCS3D01G182400 chr2B 87.171 608 46 19 2837 3419 651719501 651720101 0.000000e+00 662.0
45 TraesCS3D01G182400 chr2B 85.339 457 43 13 850 1303 651717100 651717535 1.500000e-122 451.0
46 TraesCS3D01G182400 chr2B 87.143 280 25 9 234 507 19464923 19464649 3.440000e-79 307.0
47 TraesCS3D01G182400 chr2B 85.652 230 26 5 234 461 579795094 579795318 1.640000e-57 235.0
48 TraesCS3D01G182400 chr2B 84.293 191 25 3 1356 1543 651717550 651717738 2.170000e-41 182.0
49 TraesCS3D01G182400 chr2B 87.662 154 14 5 3261 3411 651719783 651719934 3.640000e-39 174.0
50 TraesCS3D01G182400 chr4A 93.760 609 27 5 7945 8543 554085177 554084570 0.000000e+00 904.0
51 TraesCS3D01G182400 chr4A 79.339 121 15 9 5881 5996 100969850 100969965 1.050000e-09 76.8
52 TraesCS3D01G182400 chr4D 94.311 334 7 6 7945 8267 45311546 45311878 1.470000e-137 501.0
53 TraesCS3D01G182400 chr1D 86.721 369 31 6 234 591 454300337 454299976 2.560000e-105 394.0
54 TraesCS3D01G182400 chr1D 89.912 228 22 1 9 235 413229204 413229431 9.620000e-75 292.0
55 TraesCS3D01G182400 chr1D 86.331 278 24 8 313 581 473706255 473706527 3.460000e-74 291.0
56 TraesCS3D01G182400 chr1D 84.914 232 27 5 9 233 488588082 488588312 2.750000e-55 228.0
57 TraesCS3D01G182400 chr1D 91.667 48 4 0 6263 6310 280682195 280682148 6.350000e-07 67.6
58 TraesCS3D01G182400 chr7A 85.556 360 33 13 234 584 217390669 217390320 9.350000e-95 359.0
59 TraesCS3D01G182400 chr1A 83.978 362 42 10 234 584 13166668 13167024 5.670000e-87 333.0
60 TraesCS3D01G182400 chr1A 89.535 172 14 4 3181 3351 583249131 583249299 2.140000e-51 215.0
61 TraesCS3D01G182400 chr1A 95.918 49 2 0 6262 6310 352852798 352852750 8.150000e-11 80.5
62 TraesCS3D01G182400 chr6D 92.609 230 14 3 9 235 470662824 470663053 2.640000e-85 327.0
63 TraesCS3D01G182400 chr6D 84.426 122 19 0 553 674 136464159 136464280 4.800000e-23 121.0
64 TraesCS3D01G182400 chr4B 88.496 226 24 2 12 235 530233020 530232795 1.250000e-68 272.0
65 TraesCS3D01G182400 chr7D 84.135 208 24 8 9 212 5106595 5106797 1.000000e-44 193.0
66 TraesCS3D01G182400 chr5D 83.030 165 20 7 5879 6039 412468633 412468473 1.030000e-29 143.0
67 TraesCS3D01G182400 chr7B 77.340 203 36 8 6110 6306 666329238 666329040 2.890000e-20 111.0
68 TraesCS3D01G182400 chr7B 77.838 185 26 8 5881 6054 666329929 666329749 6.260000e-17 100.0
69 TraesCS3D01G182400 chr7B 94.872 39 1 1 546 584 133709801 133709838 1.060000e-04 60.2
70 TraesCS3D01G182400 chr1B 95.918 49 2 0 6262 6310 381381872 381381824 8.150000e-11 80.5


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 TraesCS3D01G182400 chr3D 166490409 166500201 9792 True 18085.000000 18085 100.000000 1 9793 1 chr3D.!!$R1 9792
1 TraesCS3D01G182400 chr3A 204874072 204879595 5523 True 9271.000000 9271 96.972000 675 6199 1 chr3A.!!$R2 5524
2 TraesCS3D01G182400 chr3A 204862827 204868814 5987 True 1418.000000 2909 92.754500 6194 9793 4 chr3A.!!$R4 3599
3 TraesCS3D01G182400 chr2D 544996673 545004649 7976 False 3230.333333 6002 90.967667 878 8970 3 chr2D.!!$F3 8092
4 TraesCS3D01G182400 chr2D 462478888 462486307 7419 True 1944.583333 8429 92.435833 2249 9756 6 chr2D.!!$R2 7507
5 TraesCS3D01G182400 chr3B 242192884 242202710 9826 True 3048.020000 8323 95.618400 75 9515 5 chr3B.!!$R3 9440
6 TraesCS3D01G182400 chr2A 688424322 688434855 10533 True 1938.000000 4412 90.322000 850 8956 5 chr2A.!!$R2 8106
7 TraesCS3D01G182400 chr2B 651717100 651726644 9544 False 1120.555556 2435 88.588000 850 8970 9 chr2B.!!$F2 8120
8 TraesCS3D01G182400 chr4A 554084570 554085177 607 True 904.000000 904 93.760000 7945 8543 1 chr4A.!!$R1 598

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
282 283 0.036388 TCCAAGCTCCCGATGACAAC 60.036 55.000 0.00 0.0 0.00 3.32 F
900 975 0.326927 TCCCCATTTCGTCCACTTCC 59.673 55.000 0.00 0.0 0.00 3.46 F
1678 4499 0.029300 CTTGCCACAAAGTGACACGG 59.971 55.000 0.00 0.0 35.23 4.94 F
2080 4927 1.068610 CGTTCCGTTGTGCCAATGATT 60.069 47.619 8.26 0.0 0.00 2.57 F
3403 6752 1.737793 GTGAAGACAAATGCTACCCCG 59.262 52.381 0.00 0.0 0.00 5.73 F
4576 7941 0.534203 GCGTCCTCCCACAGAAACAA 60.534 55.000 0.00 0.0 0.00 2.83 F
5358 8738 1.471119 ATGCCTTGTCAGATGGCTTG 58.529 50.000 12.63 0.0 43.90 4.01 F
6797 10565 1.528129 CAACTGGGAAGCAGGAGAAC 58.472 55.000 0.00 0.0 0.00 3.01 F
8315 14200 2.076863 GGCAGCAACAGAAGTATCGTT 58.923 47.619 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1389 0.609681 GGTCGGACAGGAGTGAGAGT 60.610 60.000 10.76 0.0 0.00 3.24 R
2182 5029 1.176527 TAGCACAGGCCAAAGCAATC 58.823 50.000 5.01 0.0 42.56 2.67 R
3403 6752 2.554142 AGGCAAAGCAAGCAGAAAAAC 58.446 42.857 0.00 0.0 0.00 2.43 R
3734 7097 3.507233 TGTTAGCTCCCAGCAATTTTCTG 59.493 43.478 0.00 0.0 45.56 3.02 R
5358 8738 1.141053 AGTTTATCATGCCGGTCCCTC 59.859 52.381 1.90 0.0 0.00 4.30 R
5494 8879 1.142870 TCTAACCTGCCACAAAGCACT 59.857 47.619 0.00 0.0 38.00 4.40 R
7055 10824 0.807496 GCAGAATGTCAGTTCCCTGC 59.193 55.000 0.00 0.0 39.31 4.85 R
8715 14603 0.031716 AGACAGCTATCCTGGGAGCA 60.032 55.000 19.38 0.0 46.14 4.26 R
9666 18157 0.244994 CTGCACCTGCTAAGTCGTCT 59.755 55.000 0.00 0.0 42.66 4.18 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
47 48 2.821366 CGCCGGAGAGCTTGCAAT 60.821 61.111 5.05 0.00 0.00 3.56
48 49 2.401766 CGCCGGAGAGCTTGCAATT 61.402 57.895 5.05 0.00 0.00 2.32
49 50 1.885871 GCCGGAGAGCTTGCAATTT 59.114 52.632 5.05 0.00 0.00 1.82
50 51 0.457337 GCCGGAGAGCTTGCAATTTG 60.457 55.000 5.05 0.00 0.00 2.32
51 52 0.883833 CCGGAGAGCTTGCAATTTGT 59.116 50.000 0.00 0.00 0.00 2.83
52 53 1.270550 CCGGAGAGCTTGCAATTTGTT 59.729 47.619 0.00 0.00 0.00 2.83
53 54 2.322161 CGGAGAGCTTGCAATTTGTTG 58.678 47.619 0.00 0.00 0.00 3.33
60 61 3.776849 GCAATTTGTTGCGCCGGC 61.777 61.111 19.07 19.07 38.26 6.13
61 62 3.468841 CAATTTGTTGCGCCGGCG 61.469 61.111 43.13 43.13 44.10 6.46
62 63 4.715892 AATTTGTTGCGCCGGCGG 62.716 61.111 45.81 29.29 44.10 6.13
92 93 3.648339 ACAAGGTGTGTGATGAAATGC 57.352 42.857 0.00 0.00 39.72 3.56
112 113 2.939103 GCTCACAAGGTATGATTTCGCT 59.061 45.455 0.00 0.00 0.00 4.93
114 115 3.531538 TCACAAGGTATGATTTCGCTCC 58.468 45.455 0.00 0.00 0.00 4.70
115 116 2.614057 CACAAGGTATGATTTCGCTCCC 59.386 50.000 0.00 0.00 0.00 4.30
119 120 4.236527 AGGTATGATTTCGCTCCCTTTT 57.763 40.909 0.00 0.00 0.00 2.27
120 121 4.600062 AGGTATGATTTCGCTCCCTTTTT 58.400 39.130 0.00 0.00 0.00 1.94
203 204 9.772973 ACTTTGTAGTTTCAGTTATGACACATA 57.227 29.630 0.00 0.00 38.37 2.29
219 220 6.727824 GACACATATATGTCAACTATGGGC 57.272 41.667 15.60 0.65 46.89 5.36
250 251 2.292267 ACAATGATGCCGTTGGAGATC 58.708 47.619 0.00 0.00 42.20 2.75
258 259 1.656652 CCGTTGGAGATCTTGCGAAT 58.343 50.000 0.00 0.00 0.00 3.34
266 267 3.244215 GGAGATCTTGCGAATACCATCCA 60.244 47.826 0.00 0.00 0.00 3.41
269 270 2.288666 TCTTGCGAATACCATCCAAGC 58.711 47.619 0.00 0.00 34.44 4.01
282 283 0.036388 TCCAAGCTCCCGATGACAAC 60.036 55.000 0.00 0.00 0.00 3.32
306 307 2.095768 CGCGCTTGAAAATGGAGAAGAA 60.096 45.455 5.56 0.00 0.00 2.52
313 314 6.349197 GCTTGAAAATGGAGAAGAAGAGGAAG 60.349 42.308 0.00 0.00 0.00 3.46
332 333 3.768468 AGAATCGTCTTCGGAAGAGTC 57.232 47.619 20.23 14.37 43.84 3.36
333 334 2.096174 AGAATCGTCTTCGGAAGAGTCG 59.904 50.000 20.23 19.56 46.39 4.18
334 335 1.735386 ATCGTCTTCGGAAGAGTCGA 58.265 50.000 25.68 25.68 43.69 4.20
335 336 1.516161 TCGTCTTCGGAAGAGTCGAA 58.484 50.000 23.06 12.02 43.69 3.71
336 337 1.875514 TCGTCTTCGGAAGAGTCGAAA 59.124 47.619 23.06 8.70 44.42 3.46
337 338 2.095869 TCGTCTTCGGAAGAGTCGAAAG 60.096 50.000 23.06 10.26 44.42 2.62
338 339 2.095869 CGTCTTCGGAAGAGTCGAAAGA 60.096 50.000 20.23 0.00 44.42 2.52
339 340 3.608707 CGTCTTCGGAAGAGTCGAAAGAA 60.609 47.826 20.23 0.00 44.42 2.52
340 341 3.915569 GTCTTCGGAAGAGTCGAAAGAAG 59.084 47.826 20.23 12.23 44.42 2.85
341 342 3.819337 TCTTCGGAAGAGTCGAAAGAAGA 59.181 43.478 16.19 15.24 44.42 2.87
342 343 3.833545 TCGGAAGAGTCGAAAGAAGAG 57.166 47.619 0.00 0.00 37.15 2.85
343 344 2.488545 TCGGAAGAGTCGAAAGAAGAGG 59.511 50.000 0.00 0.00 37.15 3.69
344 345 2.488545 CGGAAGAGTCGAAAGAAGAGGA 59.511 50.000 0.00 0.00 45.01 3.71
345 346 3.426963 CGGAAGAGTCGAAAGAAGAGGAG 60.427 52.174 0.00 0.00 45.01 3.69
346 347 3.119280 GGAAGAGTCGAAAGAAGAGGAGG 60.119 52.174 0.00 0.00 45.01 4.30
347 348 3.443145 AGAGTCGAAAGAAGAGGAGGA 57.557 47.619 0.00 0.00 45.01 3.71
348 349 3.768878 AGAGTCGAAAGAAGAGGAGGAA 58.231 45.455 0.00 0.00 45.01 3.36
351 352 4.153411 AGTCGAAAGAAGAGGAGGAAGAA 58.847 43.478 0.00 0.00 45.01 2.52
376 377 3.764972 TGATGTGGCATGAATGTTGATGT 59.235 39.130 0.00 0.00 0.00 3.06
389 390 4.134379 TGTTGATGTGCCATTTGTTTGT 57.866 36.364 0.00 0.00 0.00 2.83
395 396 4.134379 TGTGCCATTTGTTTGTGTGAAT 57.866 36.364 0.00 0.00 0.00 2.57
402 403 8.680903 TGCCATTTGTTTGTGTGAATTTTTATT 58.319 25.926 0.00 0.00 0.00 1.40
447 448 6.314152 TGATTTTGAACTATGCCATGCAATTG 59.686 34.615 0.00 0.00 43.62 2.32
466 467 6.204359 CAATTGAACTATGCTATGTTGCTCC 58.796 40.000 0.00 0.00 0.00 4.70
468 469 4.842574 TGAACTATGCTATGTTGCTCCAA 58.157 39.130 0.00 0.00 0.00 3.53
474 475 3.754965 TGCTATGTTGCTCCAACTCTTT 58.245 40.909 9.23 0.00 43.85 2.52
504 505 8.603181 GCACACTTGTTTAAATGTTTGAAAGAT 58.397 29.630 0.00 0.00 0.00 2.40
519 520 8.626526 TGTTTGAAAGATCATGATGGATATGTG 58.373 33.333 14.30 0.00 34.96 3.21
542 543 3.277715 TGATCATATTTGCCAAGCGTCA 58.722 40.909 0.00 0.00 0.00 4.35
563 564 1.556591 CTGCTCGTGCGCACTGTAAA 61.557 55.000 35.27 17.32 43.34 2.01
594 633 4.845580 CTGGAGCAAGCGCCCGAT 62.846 66.667 12.30 0.00 39.83 4.18
596 635 3.880846 GGAGCAAGCGCCCGATTG 61.881 66.667 13.61 13.61 43.50 2.67
624 663 4.687901 AAAAAGGCTATTTTGGTGCTGT 57.312 36.364 0.00 0.00 31.55 4.40
630 669 5.723295 AGGCTATTTTGGTGCTGTAAAATG 58.277 37.500 12.45 6.71 37.16 2.32
640 679 4.385379 GTGCTGTAAAATGAATTTTGCGC 58.615 39.130 0.00 0.00 42.70 6.09
643 682 2.089734 TGTAAAATGAATTTTGCGCGCG 59.910 40.909 28.44 28.44 42.70 6.86
664 703 1.424403 CACGGTTGCGTGTCTATTGA 58.576 50.000 0.00 0.00 35.39 2.57
669 708 3.242091 CGGTTGCGTGTCTATTGAAGATG 60.242 47.826 0.00 0.00 36.36 2.90
671 710 3.251479 TGCGTGTCTATTGAAGATGCT 57.749 42.857 0.00 0.00 36.36 3.79
673 712 3.118992 TGCGTGTCTATTGAAGATGCTCT 60.119 43.478 0.00 0.00 36.36 4.09
692 731 5.476599 TGCTCTTAATAAAGCTCAAAGGCAA 59.523 36.000 0.00 0.00 39.31 4.52
698 737 1.613836 AAGCTCAAAGGCAAGGTCTG 58.386 50.000 0.00 0.00 34.17 3.51
900 975 0.326927 TCCCCATTTCGTCCACTTCC 59.673 55.000 0.00 0.00 0.00 3.46
1068 1147 2.776053 TAACCCTCCGCCCCCTTCTT 62.776 60.000 0.00 0.00 0.00 2.52
1073 1152 4.162690 CCGCCCCCTTCTTCTCCG 62.163 72.222 0.00 0.00 0.00 4.63
1088 1167 2.745100 CCGTCTCCGTCGGTCTCA 60.745 66.667 11.88 0.00 42.62 3.27
1089 1168 2.479650 CGTCTCCGTCGGTCTCAC 59.520 66.667 11.88 3.15 0.00 3.51
1146 1225 3.567797 GGCTGGCTCGAATGCGAC 61.568 66.667 0.00 0.00 42.51 5.19
1164 1243 3.727970 GCGACGGATTTCTGATTGTTTCC 60.728 47.826 0.00 0.00 0.00 3.13
1303 1389 2.365635 GAGGTGAGCCAGCCCCTA 60.366 66.667 1.45 0.00 37.19 3.53
1505 1609 1.003839 CGGCTTGAGGCTTGGTACA 60.004 57.895 2.99 0.00 41.46 2.90
1623 2089 1.202533 CCGGGCTAGATGTAACTGTGG 60.203 57.143 0.00 0.00 0.00 4.17
1678 4499 0.029300 CTTGCCACAAAGTGACACGG 59.971 55.000 0.00 0.00 35.23 4.94
1710 4536 1.955778 TCAAGTGCTGGACAAACATGG 59.044 47.619 1.24 0.00 0.00 3.66
1859 4702 7.669427 TCTTTCATCGGGTTTGTACTTAAGTA 58.331 34.615 11.38 11.38 0.00 2.24
1905 4748 3.452474 CCGTTTTTCTTTTGGATGTGCA 58.548 40.909 0.00 0.00 0.00 4.57
2060 4907 9.875675 TGCACATAATTTGTTTATTTTTGCTTC 57.124 25.926 0.00 0.00 36.00 3.86
2080 4927 1.068610 CGTTCCGTTGTGCCAATGATT 60.069 47.619 8.26 0.00 0.00 2.57
2089 4936 5.233902 CGTTGTGCCAATGATTCTTTTGAAA 59.766 36.000 2.05 0.00 42.31 2.69
2182 5029 5.711976 AGTTTCCAGGGATTTGTATTGACTG 59.288 40.000 0.00 0.00 0.00 3.51
2565 5591 7.921745 GCTCGGAATATTTGAACTAGAAGTACT 59.078 37.037 0.00 0.00 0.00 2.73
2594 5622 7.908193 ACAAAACTTTACGTTTCATTAGCTG 57.092 32.000 0.00 0.00 44.77 4.24
2752 5791 8.860128 GTGAATGCTACTAAAACTATTTTTGCC 58.140 33.333 1.32 0.00 35.62 4.52
2793 5832 5.435686 TTACATTGAAGTATGGTCAGCCT 57.564 39.130 0.00 0.00 35.27 4.58
3337 6682 2.362077 GGTGCTTGTTTGTGTTCCAGAT 59.638 45.455 0.00 0.00 0.00 2.90
3369 6718 7.382898 TGTGTGACATATGCAGACTTTTACTA 58.617 34.615 20.07 4.34 31.49 1.82
3403 6752 1.737793 GTGAAGACAAATGCTACCCCG 59.262 52.381 0.00 0.00 0.00 5.73
3695 7056 4.453819 GGATGCATGAAGGTAATCAGTAGC 59.546 45.833 2.46 0.00 31.76 3.58
3734 7097 7.867752 TGTAAATACAGTAACAGCAAAGGAAC 58.132 34.615 0.00 0.00 0.00 3.62
3881 7245 9.741647 TTTTCTTCAAGCATTTTGTTTTGTTTT 57.258 22.222 0.00 0.00 0.00 2.43
4335 7700 1.876156 GCTGAGCGAAATGGGGATAAG 59.124 52.381 0.00 0.00 0.00 1.73
4576 7941 0.534203 GCGTCCTCCCACAGAAACAA 60.534 55.000 0.00 0.00 0.00 2.83
5094 8460 6.152154 TGAATGCATTCCATAGCCAGATAATG 59.848 38.462 31.35 0.00 35.97 1.90
5358 8738 1.471119 ATGCCTTGTCAGATGGCTTG 58.529 50.000 12.63 0.00 43.90 4.01
5463 8843 3.765511 AGGATAGCAAAGAAAGCAATGCA 59.234 39.130 8.35 0.00 41.18 3.96
5619 9007 6.183360 CCCTATACTTCATCACGTTGTGAAAC 60.183 42.308 12.03 0.00 45.96 2.78
6032 9782 3.848272 AAGGCAATTACAATGGTCACG 57.152 42.857 0.00 0.00 0.00 4.35
6161 9911 5.715439 AGACATTCATTGACCAAGGGATA 57.285 39.130 0.00 0.00 0.00 2.59
6260 10011 1.608590 CAACGACTGCAATTTCAGGGT 59.391 47.619 9.93 4.42 38.36 4.34
6797 10565 1.528129 CAACTGGGAAGCAGGAGAAC 58.472 55.000 0.00 0.00 0.00 3.01
7002 10771 8.046708 TCATACCAAATATGAGCCGCTATATTT 58.953 33.333 15.14 15.14 43.99 1.40
7055 10824 6.780031 TCCCTGGACTTATTTCTCTGATAGAG 59.220 42.308 0.00 0.00 43.64 2.43
7500 11269 2.292918 TGGCCTGTAACTATCTGGACCT 60.293 50.000 3.32 0.00 32.05 3.85
7653 13530 6.446318 TCCTGTCTTTTGTGATAATTTGTGC 58.554 36.000 0.00 0.00 0.00 4.57
7830 13707 7.485810 CAATAAAGATTGTGATGCCAGATTCA 58.514 34.615 0.00 0.00 38.13 2.57
8153 14035 2.588314 GCTCTGGCATCTGCTCCG 60.588 66.667 1.70 0.00 41.70 4.63
8315 14200 2.076863 GGCAGCAACAGAAGTATCGTT 58.923 47.619 0.00 0.00 0.00 3.85
8715 14603 1.663445 CGCTCGTCTCGTCTTTCAAGT 60.663 52.381 0.00 0.00 0.00 3.16
8720 14608 2.062519 GTCTCGTCTTTCAAGTGCTCC 58.937 52.381 0.00 0.00 0.00 4.70
8750 14638 0.450983 GTCTTGCTGATGCTGCTTCC 59.549 55.000 12.33 0.00 40.48 3.46
8759 14647 3.368571 GCTGCTTCCTGTGTGGGC 61.369 66.667 0.00 0.00 36.20 5.36
8848 14738 2.286833 GCCGTTGCATAAGCGATCTTAA 59.713 45.455 0.00 0.00 46.23 1.85
8849 14739 3.058914 GCCGTTGCATAAGCGATCTTAAT 60.059 43.478 0.00 0.00 46.23 1.40
8894 14784 1.134670 GTATCTCTGGCGCCAAGAGTT 60.135 52.381 34.66 30.97 0.00 3.01
8961 14853 1.667830 TTGCTACTGTCTGGCACGC 60.668 57.895 3.22 0.00 35.62 5.34
9204 15117 7.012138 TCTCTGTACTTAGTCCGTATAAGCAAG 59.988 40.741 0.00 0.00 34.25 4.01
9296 15209 4.095610 GCAATAAGCCAATAACACACGAC 58.904 43.478 0.00 0.00 37.23 4.34
9409 15325 3.077359 CAGACTTTGACCATGTCCTTCC 58.923 50.000 0.00 0.00 0.00 3.46
9433 15349 3.791245 CCAGTCAATCTCTTCTGGTAGC 58.209 50.000 0.00 0.00 41.51 3.58
9548 15467 1.232621 GGTGTTTGTCCTGTACCGCC 61.233 60.000 0.00 0.00 0.00 6.13
9568 18059 3.253838 TTCCCCCACCCGACTTGG 61.254 66.667 0.00 0.00 37.55 3.61
9572 18063 2.983592 CCCACCCGACTTGGCAAC 60.984 66.667 0.00 0.00 35.87 4.17
9666 18157 2.045561 TTTGTCTTTGGGCACGAGAA 57.954 45.000 0.00 0.00 0.00 2.87
9685 18176 0.244994 AGACGACTTAGCAGGTGCAG 59.755 55.000 4.48 0.00 45.16 4.41
9689 18180 0.391793 GACTTAGCAGGTGCAGGTCC 60.392 60.000 4.48 0.00 45.16 4.46
9698 18189 3.742640 GCAGGTGCAGGTCCTTATCTTAG 60.743 52.174 0.00 0.00 41.59 2.18
9718 18210 7.657336 TCTTAGCAAGGAAATTTCGACATTTT 58.343 30.769 10.67 0.00 0.00 1.82
9720 18212 6.769608 AGCAAGGAAATTTCGACATTTTTC 57.230 33.333 10.67 7.00 0.00 2.29
9726 18218 6.093404 GGAAATTTCGACATTTTTCCTCCTC 58.907 40.000 10.67 0.00 42.41 3.71
9735 18227 6.350629 ACATTTTTCCTCCTCCTGAAAATG 57.649 37.500 14.68 14.68 39.45 2.32
9780 18272 5.633655 ACGGAGTATTAGAGAAGGAGAGA 57.366 43.478 0.00 0.00 41.94 3.10
9781 18273 6.003859 ACGGAGTATTAGAGAAGGAGAGAA 57.996 41.667 0.00 0.00 41.94 2.87
9782 18274 6.607019 ACGGAGTATTAGAGAAGGAGAGAAT 58.393 40.000 0.00 0.00 41.94 2.40
9783 18275 7.747690 ACGGAGTATTAGAGAAGGAGAGAATA 58.252 38.462 0.00 0.00 41.94 1.75
9784 18276 8.219178 ACGGAGTATTAGAGAAGGAGAGAATAA 58.781 37.037 0.00 0.00 41.94 1.40
9785 18277 9.069082 CGGAGTATTAGAGAAGGAGAGAATAAA 57.931 37.037 0.00 0.00 0.00 1.40
9791 18283 6.056090 AGAGAAGGAGAGAATAAAACACCC 57.944 41.667 0.00 0.00 0.00 4.61
9792 18284 5.548056 AGAGAAGGAGAGAATAAAACACCCA 59.452 40.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.803426 AAGCTCTCCGGCGCTTCG 62.803 66.667 16.44 2.53 42.39 3.79
26 27 3.191539 CAAGCTCTCCGGCGCTTC 61.192 66.667 18.49 0.00 44.06 3.86
30 31 1.926511 AAATTGCAAGCTCTCCGGCG 61.927 55.000 4.94 0.00 37.29 6.46
31 32 0.457337 CAAATTGCAAGCTCTCCGGC 60.457 55.000 4.94 0.00 0.00 6.13
32 33 0.883833 ACAAATTGCAAGCTCTCCGG 59.116 50.000 4.94 0.00 0.00 5.14
33 34 2.322161 CAACAAATTGCAAGCTCTCCG 58.678 47.619 4.94 0.00 0.00 4.63
44 45 3.468841 CGCCGGCGCAACAAATTG 61.469 61.111 38.48 5.99 38.99 2.32
45 46 4.715892 CCGCCGGCGCAACAAATT 62.716 61.111 42.39 0.00 38.24 1.82
60 61 4.781959 CCTTGTGCGCATTGGCCG 62.782 66.667 15.91 0.00 36.38 6.13
61 62 3.683937 ACCTTGTGCGCATTGGCC 61.684 61.111 15.91 0.00 36.38 5.36
62 63 2.431260 CACCTTGTGCGCATTGGC 60.431 61.111 15.91 0.00 0.00 4.52
63 64 1.372004 CACACCTTGTGCGCATTGG 60.372 57.895 15.91 18.47 41.89 3.16
64 65 4.231753 CACACCTTGTGCGCATTG 57.768 55.556 15.91 8.84 41.89 2.82
72 73 3.225104 AGCATTTCATCACACACCTTGT 58.775 40.909 0.00 0.00 39.97 3.16
73 74 3.253921 TGAGCATTTCATCACACACCTTG 59.746 43.478 0.00 0.00 0.00 3.61
81 82 5.355071 TCATACCTTGTGAGCATTTCATCAC 59.645 40.000 0.00 0.00 44.88 3.06
92 93 3.557595 GGAGCGAAATCATACCTTGTGAG 59.442 47.826 0.00 0.00 0.00 3.51
250 251 2.289002 GAGCTTGGATGGTATTCGCAAG 59.711 50.000 0.00 0.00 32.06 4.01
258 259 0.758734 CATCGGGAGCTTGGATGGTA 59.241 55.000 12.31 0.00 35.15 3.25
266 267 1.079127 CCGTTGTCATCGGGAGCTT 60.079 57.895 13.59 0.00 43.68 3.74
269 270 2.885644 CGCCGTTGTCATCGGGAG 60.886 66.667 20.99 3.57 46.90 4.30
282 283 2.875711 CCATTTTCAAGCGCGCCG 60.876 61.111 30.33 20.27 0.00 6.46
284 285 0.109781 TTCTCCATTTTCAAGCGCGC 60.110 50.000 26.66 26.66 0.00 6.86
313 314 2.095532 TCGACTCTTCCGAAGACGATTC 59.904 50.000 15.97 6.88 42.66 2.52
323 324 2.488545 TCCTCTTCTTTCGACTCTTCCG 59.511 50.000 0.00 0.00 0.00 4.30
324 325 3.119280 CCTCCTCTTCTTTCGACTCTTCC 60.119 52.174 0.00 0.00 0.00 3.46
331 332 4.408276 TCTTCTTCCTCCTCTTCTTTCGA 58.592 43.478 0.00 0.00 0.00 3.71
332 333 4.792521 TCTTCTTCCTCCTCTTCTTTCG 57.207 45.455 0.00 0.00 0.00 3.46
333 334 6.293004 TCATCTTCTTCCTCCTCTTCTTTC 57.707 41.667 0.00 0.00 0.00 2.62
334 335 6.215227 ACATCATCTTCTTCCTCCTCTTCTTT 59.785 38.462 0.00 0.00 0.00 2.52
335 336 5.725822 ACATCATCTTCTTCCTCCTCTTCTT 59.274 40.000 0.00 0.00 0.00 2.52
336 337 5.129155 CACATCATCTTCTTCCTCCTCTTCT 59.871 44.000 0.00 0.00 0.00 2.85
337 338 5.358922 CACATCATCTTCTTCCTCCTCTTC 58.641 45.833 0.00 0.00 0.00 2.87
338 339 4.163839 CCACATCATCTTCTTCCTCCTCTT 59.836 45.833 0.00 0.00 0.00 2.85
339 340 3.710677 CCACATCATCTTCTTCCTCCTCT 59.289 47.826 0.00 0.00 0.00 3.69
340 341 3.743899 GCCACATCATCTTCTTCCTCCTC 60.744 52.174 0.00 0.00 0.00 3.71
341 342 2.172293 GCCACATCATCTTCTTCCTCCT 59.828 50.000 0.00 0.00 0.00 3.69
342 343 2.092753 TGCCACATCATCTTCTTCCTCC 60.093 50.000 0.00 0.00 0.00 4.30
343 344 3.272574 TGCCACATCATCTTCTTCCTC 57.727 47.619 0.00 0.00 0.00 3.71
344 345 3.201487 TCATGCCACATCATCTTCTTCCT 59.799 43.478 0.00 0.00 0.00 3.36
345 346 3.548770 TCATGCCACATCATCTTCTTCC 58.451 45.455 0.00 0.00 0.00 3.46
346 347 5.067413 ACATTCATGCCACATCATCTTCTTC 59.933 40.000 0.00 0.00 0.00 2.87
347 348 4.954202 ACATTCATGCCACATCATCTTCTT 59.046 37.500 0.00 0.00 0.00 2.52
348 349 4.533815 ACATTCATGCCACATCATCTTCT 58.466 39.130 0.00 0.00 0.00 2.85
351 352 4.274978 TCAACATTCATGCCACATCATCT 58.725 39.130 0.00 0.00 0.00 2.90
376 377 6.506500 AAAAATTCACACAAACAAATGGCA 57.493 29.167 0.00 0.00 0.00 4.92
395 396 7.497249 CCCAACCAAGTTCATGACAAATAAAAA 59.503 33.333 0.00 0.00 0.00 1.94
402 403 2.692557 CACCCAACCAAGTTCATGACAA 59.307 45.455 0.00 0.00 0.00 3.18
404 405 2.582052 TCACCCAACCAAGTTCATGAC 58.418 47.619 0.00 0.00 0.00 3.06
447 448 4.878397 AGTTGGAGCAACATAGCATAGTTC 59.122 41.667 0.00 0.00 45.66 3.01
474 475 8.087982 TCAAACATTTAAACAAGTGTGCAAAA 57.912 26.923 0.00 0.00 0.00 2.44
504 505 9.969001 AATATGATCAACACATATCCATCATGA 57.031 29.630 0.00 0.00 39.18 3.07
507 508 8.517056 GCAAATATGATCAACACATATCCATCA 58.483 33.333 0.00 0.00 39.18 3.07
519 520 4.032703 ACGCTTGGCAAATATGATCAAC 57.967 40.909 0.00 0.00 0.00 3.18
551 552 2.519002 CGCTAAATTTACAGTGCGCA 57.481 45.000 5.66 5.66 37.13 6.09
556 557 1.396996 CAGGCGCGCTAAATTTACAGT 59.603 47.619 32.29 0.00 0.00 3.55
563 564 3.204827 CCAGCAGGCGCGCTAAAT 61.205 61.111 32.29 12.41 45.49 1.40
608 647 5.719173 TCATTTTACAGCACCAAAATAGCC 58.281 37.500 0.00 0.00 33.66 3.93
616 655 4.447054 CGCAAAATTCATTTTACAGCACCA 59.553 37.500 0.00 0.00 37.86 4.17
618 657 4.385379 GCGCAAAATTCATTTTACAGCAC 58.615 39.130 0.30 0.00 37.86 4.40
619 658 3.120947 CGCGCAAAATTCATTTTACAGCA 59.879 39.130 8.75 0.00 37.86 4.41
624 663 1.651138 CCGCGCGCAAAATTCATTTTA 59.349 42.857 32.61 0.00 37.86 1.52
646 685 3.616560 ATCTTCAATAGACACGCAACCGT 60.617 43.478 0.00 0.00 40.86 4.83
669 708 5.567138 TGCCTTTGAGCTTTATTAAGAGC 57.433 39.130 0.00 1.23 39.17 4.09
671 710 6.010219 ACCTTGCCTTTGAGCTTTATTAAGA 58.990 36.000 0.00 0.00 32.92 2.10
673 712 6.010219 AGACCTTGCCTTTGAGCTTTATTAA 58.990 36.000 0.00 0.00 0.00 1.40
682 721 4.774124 TCATATCAGACCTTGCCTTTGAG 58.226 43.478 0.00 0.00 0.00 3.02
692 731 5.587844 GCTGTGATTGTTTCATATCAGACCT 59.412 40.000 0.00 0.00 36.54 3.85
698 737 5.807011 GGTTTGGCTGTGATTGTTTCATATC 59.193 40.000 0.00 0.00 36.54 1.63
1073 1152 2.698763 GGGTGAGACCGACGGAGAC 61.699 68.421 23.38 11.37 39.83 3.36
1303 1389 0.609681 GGTCGGACAGGAGTGAGAGT 60.610 60.000 10.76 0.00 0.00 3.24
1490 1594 3.820467 TGACATTTGTACCAAGCCTCAAG 59.180 43.478 0.00 0.00 0.00 3.02
1605 2070 1.486726 AGCCACAGTTACATCTAGCCC 59.513 52.381 0.00 0.00 0.00 5.19
1623 2089 4.143305 CGCCAAGCTTATCGTTATCTTAGC 60.143 45.833 0.00 0.00 0.00 3.09
1678 4499 7.370383 TGTCCAGCACTTGAAAAATAAGAATC 58.630 34.615 0.00 0.00 0.00 2.52
1859 4702 4.105697 TCCTTGGAAGGGACAATAACAAGT 59.894 41.667 5.58 0.00 46.47 3.16
1860 4703 4.662278 TCCTTGGAAGGGACAATAACAAG 58.338 43.478 5.58 0.00 46.47 3.16
1905 4748 3.072944 GCAGTTGCTCAGAGAGACAAAT 58.927 45.455 0.00 0.00 38.21 2.32
2080 4927 7.378181 GGACCTGCAAAGATAATTTCAAAAGA 58.622 34.615 0.00 0.00 0.00 2.52
2089 4936 3.480470 CATCCGGACCTGCAAAGATAAT 58.520 45.455 6.12 0.00 0.00 1.28
2182 5029 1.176527 TAGCACAGGCCAAAGCAATC 58.823 50.000 5.01 0.00 42.56 2.67
2752 5791 9.277565 CAATGTAATGACAAATAGTTTTCTCGG 57.722 33.333 0.00 0.00 39.59 4.63
2793 5832 4.592942 AGATCATAAAAGCAGCTGGTTCA 58.407 39.130 29.77 20.82 34.26 3.18
2842 5988 7.804129 GCATGAACACAAAGTATTAAACCGTAA 59.196 33.333 0.00 0.00 0.00 3.18
2843 5989 7.041303 TGCATGAACACAAAGTATTAAACCGTA 60.041 33.333 0.00 0.00 0.00 4.02
2844 5990 6.146898 GCATGAACACAAAGTATTAAACCGT 58.853 36.000 0.00 0.00 0.00 4.83
2845 5991 6.087555 GTGCATGAACACAAAGTATTAAACCG 59.912 38.462 0.00 0.00 40.40 4.44
2846 5992 7.114811 CAGTGCATGAACACAAAGTATTAAACC 59.885 37.037 6.60 0.00 43.23 3.27
2847 5993 7.860373 TCAGTGCATGAACACAAAGTATTAAAC 59.140 33.333 6.60 0.00 43.23 2.01
2848 5994 7.935520 TCAGTGCATGAACACAAAGTATTAAA 58.064 30.769 6.60 0.00 43.23 1.52
2849 5995 7.503521 TCAGTGCATGAACACAAAGTATTAA 57.496 32.000 6.60 0.00 43.23 1.40
2850 5996 7.228507 ACTTCAGTGCATGAACACAAAGTATTA 59.771 33.333 6.60 0.00 43.09 0.98
2851 5997 6.039717 ACTTCAGTGCATGAACACAAAGTATT 59.960 34.615 6.60 0.00 43.09 1.89
2852 5998 5.532406 ACTTCAGTGCATGAACACAAAGTAT 59.468 36.000 6.60 0.00 43.09 2.12
2853 5999 4.881273 ACTTCAGTGCATGAACACAAAGTA 59.119 37.500 6.60 0.00 43.09 2.24
3337 6682 4.020662 TCTGCATATGTCACACAACAGGTA 60.021 41.667 4.29 0.00 31.50 3.08
3403 6752 2.554142 AGGCAAAGCAAGCAGAAAAAC 58.446 42.857 0.00 0.00 0.00 2.43
3695 7056 8.506168 ACTGTATTTACATATTTCACAGTGGG 57.494 34.615 0.00 0.00 42.46 4.61
3734 7097 3.507233 TGTTAGCTCCCAGCAATTTTCTG 59.493 43.478 0.00 0.00 45.56 3.02
4576 7941 5.763204 TCTTAACTTCAGCCTCATTTTCGTT 59.237 36.000 0.00 0.00 0.00 3.85
5094 8460 4.516698 TGAAAAGATCCACTCAAACTCTGC 59.483 41.667 0.00 0.00 0.00 4.26
5358 8738 1.141053 AGTTTATCATGCCGGTCCCTC 59.859 52.381 1.90 0.00 0.00 4.30
5492 8877 2.065899 AACCTGCCACAAAGCACTAA 57.934 45.000 0.00 0.00 38.00 2.24
5494 8879 1.142870 TCTAACCTGCCACAAAGCACT 59.857 47.619 0.00 0.00 38.00 4.40
5619 9007 1.868498 TCTTACCGCCACAACTTTTCG 59.132 47.619 0.00 0.00 0.00 3.46
6032 9782 9.811995 AATTTAGTTTGTAACTTCCCAAAAGAC 57.188 29.630 0.00 0.00 42.81 3.01
6084 9834 4.509616 TGTCTCTTCGTGGAAAGAAACAA 58.490 39.130 0.00 0.00 34.22 2.83
6570 10338 6.489700 TGCCAAGTTAAATCATGAGAAGACAA 59.510 34.615 0.09 0.00 0.00 3.18
6797 10565 5.697633 ACAAGAAATTGCAATAAGCCTTGTG 59.302 36.000 28.22 16.54 43.96 3.33
7002 10771 6.591935 ACTGTTTCTCCTCAGTTAATGACAA 58.408 36.000 0.00 0.00 41.33 3.18
7055 10824 0.807496 GCAGAATGTCAGTTCCCTGC 59.193 55.000 0.00 0.00 39.31 4.85
7286 11055 0.889186 GACGTTTGCCACCCATGACT 60.889 55.000 0.00 0.00 0.00 3.41
7500 11269 7.050377 GTCTCCATATTTTCTCATCAGGTTGA 58.950 38.462 0.00 0.00 0.00 3.18
7621 13496 4.776349 TCACAAAAGACAGGAGTTTAGCA 58.224 39.130 0.00 0.00 0.00 3.49
7653 13530 5.003804 AGCCTGGAAGTACAATAAAGTGTG 58.996 41.667 0.00 0.00 32.75 3.82
7830 13707 7.118825 CACATCAGACAGTATCTTCAAACACAT 59.881 37.037 0.00 0.00 34.41 3.21
8153 14035 4.713792 AAGGATATTGGAGTCCATGTCC 57.286 45.455 21.75 21.75 36.96 4.02
8315 14200 1.141657 AGTGCAGGTTCTTTGCTGAGA 59.858 47.619 0.00 0.00 42.02 3.27
8699 14586 1.716581 GAGCACTTGAAAGACGAGACG 59.283 52.381 0.00 0.00 34.31 4.18
8715 14603 0.031716 AGACAGCTATCCTGGGAGCA 60.032 55.000 19.38 0.00 46.14 4.26
8720 14608 1.483827 TCAGCAAGACAGCTATCCTGG 59.516 52.381 0.00 0.00 44.54 4.45
8750 14638 4.988598 AGTTCGGCGCCCACACAG 62.989 66.667 23.46 5.48 0.00 3.66
8830 14718 8.703604 TCCTATATTAAGATCGCTTATGCAAC 57.296 34.615 0.00 0.00 36.54 4.17
8840 14730 6.628398 GCCAAGACCCTCCTATATTAAGATCG 60.628 46.154 0.00 0.00 0.00 3.69
8848 14738 2.982488 CCAAGCCAAGACCCTCCTATAT 59.018 50.000 0.00 0.00 0.00 0.86
8849 14739 2.408565 CCAAGCCAAGACCCTCCTATA 58.591 52.381 0.00 0.00 0.00 1.31
9171 15084 6.123651 ACGGACTAAGTACAGAGATCTGAAT 58.876 40.000 16.52 0.00 46.59 2.57
9204 15117 8.886816 CTTCATTACAGATACTGAAGCAAAAC 57.113 34.615 5.76 0.00 39.69 2.43
9221 15134 7.594015 CCAGAGATAAATTGCATGCTTCATTAC 59.406 37.037 20.33 6.07 0.00 1.89
9281 15194 0.719465 CCTCGTCGTGTGTTATTGGC 59.281 55.000 0.00 0.00 0.00 4.52
9282 15195 1.990563 GACCTCGTCGTGTGTTATTGG 59.009 52.381 0.00 0.00 0.00 3.16
9283 15196 2.668250 TGACCTCGTCGTGTGTTATTG 58.332 47.619 0.00 0.00 34.95 1.90
9284 15197 3.374220 TTGACCTCGTCGTGTGTTATT 57.626 42.857 0.00 0.00 34.95 1.40
9285 15198 3.374220 TTTGACCTCGTCGTGTGTTAT 57.626 42.857 0.00 0.00 34.95 1.89
9286 15199 2.867287 TTTGACCTCGTCGTGTGTTA 57.133 45.000 0.00 0.00 34.95 2.41
9287 15200 1.931172 CTTTTGACCTCGTCGTGTGTT 59.069 47.619 0.00 0.00 34.95 3.32
9288 15201 1.135527 TCTTTTGACCTCGTCGTGTGT 59.864 47.619 0.00 0.00 34.95 3.72
9296 15209 4.024809 GGAAACTGAACTCTTTTGACCTCG 60.025 45.833 0.00 0.00 0.00 4.63
9409 15325 1.649664 CAGAAGAGATTGACTGGCCG 58.350 55.000 0.00 0.00 0.00 6.13
9568 18059 0.510359 CTGTGAACGAGAGCTGTTGC 59.490 55.000 0.00 0.00 40.05 4.17
9570 18061 2.890808 TTCTGTGAACGAGAGCTGTT 57.109 45.000 0.00 0.00 0.00 3.16
9572 18063 5.635280 TCTTTAATTCTGTGAACGAGAGCTG 59.365 40.000 0.00 0.00 0.00 4.24
9666 18157 0.244994 CTGCACCTGCTAAGTCGTCT 59.755 55.000 0.00 0.00 42.66 4.18
9689 18180 7.974675 TGTCGAAATTTCCTTGCTAAGATAAG 58.025 34.615 12.54 0.00 0.00 1.73
9698 18189 5.915857 GGAAAAATGTCGAAATTTCCTTGC 58.084 37.500 13.89 7.49 44.69 4.01
9718 18210 2.108075 TGTGCATTTTCAGGAGGAGGAA 59.892 45.455 0.00 0.00 0.00 3.36
9720 18212 1.815003 GTGTGCATTTTCAGGAGGAGG 59.185 52.381 0.00 0.00 0.00 4.30
9723 18215 2.608752 GCTTGTGTGCATTTTCAGGAGG 60.609 50.000 0.00 0.00 0.00 4.30
9726 18218 1.269206 ACGCTTGTGTGCATTTTCAGG 60.269 47.619 0.00 0.00 0.00 3.86
9756 18248 6.523840 TCTCTCCTTCTCTAATACTCCGTAC 58.476 44.000 0.00 0.00 0.00 3.67
9757 18249 6.744175 TCTCTCCTTCTCTAATACTCCGTA 57.256 41.667 0.00 0.00 0.00 4.02
9758 18250 5.633655 TCTCTCCTTCTCTAATACTCCGT 57.366 43.478 0.00 0.00 0.00 4.69
9759 18251 8.624367 TTATTCTCTCCTTCTCTAATACTCCG 57.376 38.462 0.00 0.00 0.00 4.63
9765 18257 8.268605 GGGTGTTTTATTCTCTCCTTCTCTAAT 58.731 37.037 0.00 0.00 0.00 1.73
9766 18258 7.236847 TGGGTGTTTTATTCTCTCCTTCTCTAA 59.763 37.037 0.00 0.00 0.00 2.10
9767 18259 6.729100 TGGGTGTTTTATTCTCTCCTTCTCTA 59.271 38.462 0.00 0.00 0.00 2.43
9768 18260 5.548056 TGGGTGTTTTATTCTCTCCTTCTCT 59.452 40.000 0.00 0.00 0.00 3.10
9769 18261 5.805728 TGGGTGTTTTATTCTCTCCTTCTC 58.194 41.667 0.00 0.00 0.00 2.87
9770 18262 5.843019 TGGGTGTTTTATTCTCTCCTTCT 57.157 39.130 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.