Multiple sequence alignment - TraesCS1A01G319900

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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 TraesCS1A01G319900 chr1A 100.000 2415 0 0 1 2415 510456220 510458634 0.000000e+00 4460.0
1 TraesCS1A01G319900 chr3D 93.923 938 42 5 1485 2415 431339166 431338237 0.000000e+00 1402.0
2 TraesCS1A01G319900 chr3D 93.343 661 32 5 749 1399 555912758 555912100 0.000000e+00 966.0
3 TraesCS1A01G319900 chr3D 79.394 660 67 38 768 1400 555801559 555800942 3.740000e-108 401.0
4 TraesCS1A01G319900 chr1D 93.783 933 46 8 1486 2415 278100153 278101076 0.000000e+00 1391.0
5 TraesCS1A01G319900 chr1D 93.148 934 53 4 1485 2415 254797674 254796749 0.000000e+00 1360.0
6 TraesCS1A01G319900 chr4D 93.777 932 43 6 1486 2415 481889345 481888427 0.000000e+00 1386.0
7 TraesCS1A01G319900 chr4D 93.362 934 44 5 1484 2415 502728498 502729415 0.000000e+00 1365.0
8 TraesCS1A01G319900 chr4D 84.277 159 15 5 183 332 357533510 357533353 1.930000e-31 147.0
9 TraesCS1A01G319900 chr2D 93.291 939 55 4 1481 2415 498275651 498274717 0.000000e+00 1378.0
10 TraesCS1A01G319900 chr2D 79.872 467 84 8 940 1400 378166220 378166682 1.380000e-87 333.0
11 TraesCS1A01G319900 chr2D 89.005 191 18 2 749 938 378165938 378166126 1.440000e-57 233.0
12 TraesCS1A01G319900 chr2D 90.062 161 15 1 175 334 409309267 409309107 8.750000e-50 207.0
13 TraesCS1A01G319900 chr2A 93.114 944 56 6 1475 2415 496897292 496898229 0.000000e+00 1375.0
14 TraesCS1A01G319900 chr2A 78.112 466 86 12 940 1400 512442286 512442740 5.080000e-72 281.0
15 TraesCS1A01G319900 chr2A 92.994 157 10 1 177 332 15606741 15606585 6.720000e-56 228.0
16 TraesCS1A01G319900 chr6D 93.184 939 50 10 1479 2415 325416552 325417478 0.000000e+00 1367.0
17 TraesCS1A01G319900 chr6D 91.544 272 14 6 480 749 340102779 340102515 1.360000e-97 366.0
18 TraesCS1A01G319900 chr6D 93.011 186 6 3 1 180 340103917 340103733 5.120000e-67 265.0
19 TraesCS1A01G319900 chr6D 89.809 157 13 3 177 332 47784729 47784575 5.270000e-47 198.0
20 TraesCS1A01G319900 chr6D 93.651 63 0 4 333 394 340103743 340103684 9.190000e-15 91.6
21 TraesCS1A01G319900 chr1B 93.162 936 49 5 1485 2415 302007166 302008091 0.000000e+00 1360.0
22 TraesCS1A01G319900 chr1B 94.595 111 6 0 1 111 610358570 610358460 3.190000e-39 172.0
23 TraesCS1A01G319900 chr3B 92.900 662 42 3 749 1406 738993059 738992399 0.000000e+00 957.0
24 TraesCS1A01G319900 chr3B 92.760 663 41 4 749 1406 738910961 738910301 0.000000e+00 952.0
25 TraesCS1A01G319900 chr3B 87.288 236 18 4 523 750 805829815 805830046 2.380000e-65 259.0
26 TraesCS1A01G319900 chr3B 90.556 180 13 3 1 180 805829048 805829223 4.010000e-58 235.0
27 TraesCS1A01G319900 chr3B 89.444 180 11 5 749 923 738758607 738758431 1.120000e-53 220.0
28 TraesCS1A01G319900 chr3B 83.696 184 14 8 3 180 733216141 733216314 2.490000e-35 159.0
29 TraesCS1A01G319900 chr3B 96.825 63 1 1 333 394 805829213 805829275 1.180000e-18 104.0
30 TraesCS1A01G319900 chr3B 93.651 63 3 1 333 394 733216304 733216366 2.560000e-15 93.5
31 TraesCS1A01G319900 chr3B 97.500 40 1 0 414 453 805829738 805829777 4.310000e-08 69.4
32 TraesCS1A01G319900 chr3B 100.000 28 0 0 947 974 738758426 738758399 4.000000e-03 52.8
33 TraesCS1A01G319900 chr3A 90.090 666 48 7 749 1399 692945481 692944819 0.000000e+00 848.0
34 TraesCS1A01G319900 chr3A 81.288 652 72 30 749 1368 692724091 692723458 1.300000e-132 483.0
35 TraesCS1A01G319900 chr3A 87.898 157 18 1 177 332 642124756 642124912 1.470000e-42 183.0
36 TraesCS1A01G319900 chr3A 95.495 111 5 0 1 111 450703316 450703206 6.860000e-41 178.0
37 TraesCS1A01G319900 chr7D 79.355 465 84 9 940 1400 175443544 175444000 1.390000e-82 316.0
38 TraesCS1A01G319900 chr7D 89.730 185 10 5 1 180 602661840 602662020 6.720000e-56 228.0
39 TraesCS1A01G319900 chr7D 93.694 111 7 0 1 111 412186804 412186914 1.490000e-37 167.0
40 TraesCS1A01G319900 chr7D 95.161 62 1 2 333 393 602662010 602662070 1.980000e-16 97.1
41 TraesCS1A01G319900 chr2B 85.600 250 23 5 522 762 792168609 792168854 1.430000e-62 250.0
42 TraesCS1A01G319900 chr2B 95.495 111 5 0 1 111 10605949 10605839 6.860000e-41 178.0
43 TraesCS1A01G319900 chr2B 96.825 63 1 1 333 394 792167899 792167961 1.180000e-18 104.0
44 TraesCS1A01G319900 chr7A 91.250 160 13 1 177 335 77469191 77469032 1.450000e-52 217.0
45 TraesCS1A01G319900 chr5A 91.139 158 10 3 177 332 540399774 540399929 6.760000e-51 211.0
46 TraesCS1A01G319900 chr6B 93.694 111 7 0 1 111 429706768 429706878 1.490000e-37 167.0
47 TraesCS1A01G319900 chr4A 91.057 123 9 2 212 332 484750765 484750887 5.340000e-37 165.0
48 TraesCS1A01G319900 chr5B 85.443 158 19 4 177 332 111903992 111903837 6.910000e-36 161.0
49 TraesCS1A01G319900 chr6A 92.941 85 6 0 979 1063 14073643 14073727 9.070000e-25 124.0
50 TraesCS1A01G319900 chr6A 88.060 67 8 0 1046 1112 14077128 14077194 1.990000e-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 TraesCS1A01G319900 chr1A 510456220 510458634 2414 False 4460.000000 4460 100.000000 1 2415 1 chr1A.!!$F1 2414
1 TraesCS1A01G319900 chr3D 431338237 431339166 929 True 1402.000000 1402 93.923000 1485 2415 1 chr3D.!!$R1 930
2 TraesCS1A01G319900 chr3D 555912100 555912758 658 True 966.000000 966 93.343000 749 1399 1 chr3D.!!$R3 650
3 TraesCS1A01G319900 chr3D 555800942 555801559 617 True 401.000000 401 79.394000 768 1400 1 chr3D.!!$R2 632
4 TraesCS1A01G319900 chr1D 278100153 278101076 923 False 1391.000000 1391 93.783000 1486 2415 1 chr1D.!!$F1 929
5 TraesCS1A01G319900 chr1D 254796749 254797674 925 True 1360.000000 1360 93.148000 1485 2415 1 chr1D.!!$R1 930
6 TraesCS1A01G319900 chr4D 481888427 481889345 918 True 1386.000000 1386 93.777000 1486 2415 1 chr4D.!!$R2 929
7 TraesCS1A01G319900 chr4D 502728498 502729415 917 False 1365.000000 1365 93.362000 1484 2415 1 chr4D.!!$F1 931
8 TraesCS1A01G319900 chr2D 498274717 498275651 934 True 1378.000000 1378 93.291000 1481 2415 1 chr2D.!!$R2 934
9 TraesCS1A01G319900 chr2D 378165938 378166682 744 False 283.000000 333 84.438500 749 1400 2 chr2D.!!$F1 651
10 TraesCS1A01G319900 chr2A 496897292 496898229 937 False 1375.000000 1375 93.114000 1475 2415 1 chr2A.!!$F1 940
11 TraesCS1A01G319900 chr6D 325416552 325417478 926 False 1367.000000 1367 93.184000 1479 2415 1 chr6D.!!$F1 936
12 TraesCS1A01G319900 chr6D 340102515 340103917 1402 True 240.866667 366 92.735333 1 749 3 chr6D.!!$R2 748
13 TraesCS1A01G319900 chr1B 302007166 302008091 925 False 1360.000000 1360 93.162000 1485 2415 1 chr1B.!!$F1 930
14 TraesCS1A01G319900 chr3B 738992399 738993059 660 True 957.000000 957 92.900000 749 1406 1 chr3B.!!$R2 657
15 TraesCS1A01G319900 chr3B 738910301 738910961 660 True 952.000000 952 92.760000 749 1406 1 chr3B.!!$R1 657
16 TraesCS1A01G319900 chr3A 692944819 692945481 662 True 848.000000 848 90.090000 749 1399 1 chr3A.!!$R3 650
17 TraesCS1A01G319900 chr3A 692723458 692724091 633 True 483.000000 483 81.288000 749 1368 1 chr3A.!!$R2 619

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
326 333 0.106894 ATACTTTAGGCTGGCCTCGC 59.893 55.0 18.06 6.69 44.43 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 2456 0.03392 CATCTATAGGCAGGCACGCA 59.966 55.0 0.0 0.0 0.0 5.24 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
57 58 4.780815 TCGATTAATTCAGCTCCAATGGT 58.219 39.130 0.00 0.00 0.00 3.55
66 67 1.492176 AGCTCCAATGGTGGTATCTGG 59.508 52.381 4.05 0.00 46.11 3.86
204 211 3.921021 CGAAGCTACAAGTTAGTCTGTGG 59.079 47.826 0.00 0.00 0.00 4.17
205 212 3.963428 AGCTACAAGTTAGTCTGTGGG 57.037 47.619 0.00 0.00 0.00 4.61
206 213 2.567615 AGCTACAAGTTAGTCTGTGGGG 59.432 50.000 0.00 0.00 0.00 4.96
207 214 2.302157 GCTACAAGTTAGTCTGTGGGGT 59.698 50.000 0.00 0.00 0.00 4.95
208 215 3.616802 GCTACAAGTTAGTCTGTGGGGTC 60.617 52.174 0.00 0.00 0.00 4.46
209 216 2.404559 ACAAGTTAGTCTGTGGGGTCA 58.595 47.619 0.00 0.00 0.00 4.02
210 217 2.368875 ACAAGTTAGTCTGTGGGGTCAG 59.631 50.000 0.00 0.00 36.85 3.51
211 218 2.368875 CAAGTTAGTCTGTGGGGTCAGT 59.631 50.000 0.00 0.00 36.85 3.41
212 219 2.690840 AGTTAGTCTGTGGGGTCAGTT 58.309 47.619 0.00 0.00 36.85 3.16
213 220 2.368875 AGTTAGTCTGTGGGGTCAGTTG 59.631 50.000 0.00 0.00 36.85 3.16
214 221 2.367567 GTTAGTCTGTGGGGTCAGTTGA 59.632 50.000 0.00 0.00 36.85 3.18
215 222 1.734655 AGTCTGTGGGGTCAGTTGAT 58.265 50.000 0.00 0.00 36.85 2.57
216 223 1.625818 AGTCTGTGGGGTCAGTTGATC 59.374 52.381 0.00 0.00 36.85 2.92
217 224 0.984230 TCTGTGGGGTCAGTTGATCC 59.016 55.000 2.68 2.68 44.64 3.36
222 229 3.558674 GGGTCAGTTGATCCCACAG 57.441 57.895 0.00 0.00 39.44 3.66
223 230 0.693049 GGGTCAGTTGATCCCACAGT 59.307 55.000 0.00 0.00 39.44 3.55
224 231 1.073923 GGGTCAGTTGATCCCACAGTT 59.926 52.381 0.00 0.00 39.44 3.16
225 232 2.489073 GGGTCAGTTGATCCCACAGTTT 60.489 50.000 0.00 0.00 39.44 2.66
226 233 3.222603 GGTCAGTTGATCCCACAGTTTT 58.777 45.455 0.00 0.00 0.00 2.43
227 234 3.636764 GGTCAGTTGATCCCACAGTTTTT 59.363 43.478 0.00 0.00 0.00 1.94
255 262 8.691797 AGAAAATAAGCCTAAAAACACTGTTCA 58.308 29.630 0.00 0.00 0.00 3.18
256 263 8.871686 AAAATAAGCCTAAAAACACTGTTCAG 57.128 30.769 0.00 0.00 0.00 3.02
257 264 7.582667 AATAAGCCTAAAAACACTGTTCAGT 57.417 32.000 0.00 0.00 0.00 3.41
258 265 5.914898 AAGCCTAAAAACACTGTTCAGTT 57.085 34.783 2.47 0.00 0.00 3.16
259 266 8.685838 ATAAGCCTAAAAACACTGTTCAGTTA 57.314 30.769 2.47 0.00 0.00 2.24
260 267 6.373186 AGCCTAAAAACACTGTTCAGTTAC 57.627 37.500 2.47 0.00 0.00 2.50
261 268 6.120220 AGCCTAAAAACACTGTTCAGTTACT 58.880 36.000 2.47 0.00 0.00 2.24
262 269 6.038271 AGCCTAAAAACACTGTTCAGTTACTG 59.962 38.462 5.94 5.94 0.00 2.74
263 270 6.183360 GCCTAAAAACACTGTTCAGTTACTGT 60.183 38.462 12.41 0.00 32.61 3.55
264 271 7.627726 GCCTAAAAACACTGTTCAGTTACTGTT 60.628 37.037 12.41 2.34 32.61 3.16
265 272 8.241367 CCTAAAAACACTGTTCAGTTACTGTTT 58.759 33.333 12.41 7.80 32.61 2.83
270 277 9.609346 AAACACTGTTCAGTTACTGTTTATACT 57.391 29.630 12.41 0.00 32.61 2.12
271 278 8.589335 ACACTGTTCAGTTACTGTTTATACTG 57.411 34.615 12.41 9.75 39.41 2.74
272 279 8.418662 ACACTGTTCAGTTACTGTTTATACTGA 58.581 33.333 12.41 0.00 43.69 3.41
307 314 4.396357 AAAATACCATTGACCCCACAGA 57.604 40.909 0.00 0.00 0.00 3.41
308 315 4.608170 AAATACCATTGACCCCACAGAT 57.392 40.909 0.00 0.00 0.00 2.90
309 316 5.725551 AAATACCATTGACCCCACAGATA 57.274 39.130 0.00 0.00 0.00 1.98
310 317 4.706842 ATACCATTGACCCCACAGATAC 57.293 45.455 0.00 0.00 0.00 2.24
311 318 2.562296 ACCATTGACCCCACAGATACT 58.438 47.619 0.00 0.00 0.00 2.12
312 319 2.919602 ACCATTGACCCCACAGATACTT 59.080 45.455 0.00 0.00 0.00 2.24
313 320 3.333680 ACCATTGACCCCACAGATACTTT 59.666 43.478 0.00 0.00 0.00 2.66
314 321 4.538490 ACCATTGACCCCACAGATACTTTA 59.462 41.667 0.00 0.00 0.00 1.85
315 322 5.126067 CCATTGACCCCACAGATACTTTAG 58.874 45.833 0.00 0.00 0.00 1.85
316 323 4.837093 TTGACCCCACAGATACTTTAGG 57.163 45.455 0.00 0.00 0.00 2.69
317 324 2.504175 TGACCCCACAGATACTTTAGGC 59.496 50.000 0.00 0.00 0.00 3.93
318 325 2.772515 GACCCCACAGATACTTTAGGCT 59.227 50.000 0.00 0.00 0.00 4.58
319 326 2.505819 ACCCCACAGATACTTTAGGCTG 59.494 50.000 0.00 0.00 34.65 4.85
320 327 2.158755 CCCCACAGATACTTTAGGCTGG 60.159 54.545 0.00 0.00 32.82 4.85
321 328 2.565841 CCACAGATACTTTAGGCTGGC 58.434 52.381 0.00 0.00 32.82 4.85
322 329 2.565841 CACAGATACTTTAGGCTGGCC 58.434 52.381 3.00 3.00 32.82 5.36
324 331 2.436173 ACAGATACTTTAGGCTGGCCTC 59.564 50.000 18.06 2.13 44.43 4.70
325 332 1.689273 AGATACTTTAGGCTGGCCTCG 59.311 52.381 18.06 10.13 44.43 4.63
326 333 0.106894 ATACTTTAGGCTGGCCTCGC 59.893 55.000 18.06 6.69 44.43 5.03
339 346 3.610669 CTCGCCGCTGCTCCCTAT 61.611 66.667 0.00 0.00 34.43 2.57
340 347 2.203437 TCGCCGCTGCTCCCTATA 60.203 61.111 0.00 0.00 34.43 1.31
341 348 2.206515 CTCGCCGCTGCTCCCTATAG 62.207 65.000 0.00 0.00 34.43 1.31
342 349 2.659610 GCCGCTGCTCCCTATAGG 59.340 66.667 12.27 12.27 33.53 2.57
343 350 2.210711 GCCGCTGCTCCCTATAGGT 61.211 63.158 17.72 0.00 36.75 3.08
344 351 1.968310 CCGCTGCTCCCTATAGGTC 59.032 63.158 17.72 6.96 36.75 3.85
387 394 6.873605 CCCTGTTATTTTTCCCTTTCACATTC 59.126 38.462 0.00 0.00 0.00 2.67
388 395 7.256296 CCCTGTTATTTTTCCCTTTCACATTCT 60.256 37.037 0.00 0.00 0.00 2.40
389 396 8.150296 CCTGTTATTTTTCCCTTTCACATTCTT 58.850 33.333 0.00 0.00 0.00 2.52
390 397 8.885494 TGTTATTTTTCCCTTTCACATTCTTG 57.115 30.769 0.00 0.00 0.00 3.02
391 398 8.700051 TGTTATTTTTCCCTTTCACATTCTTGA 58.300 29.630 0.00 0.00 0.00 3.02
392 399 8.978539 GTTATTTTTCCCTTTCACATTCTTGAC 58.021 33.333 0.00 0.00 0.00 3.18
393 400 5.529581 TTTTCCCTTTCACATTCTTGACC 57.470 39.130 0.00 0.00 0.00 4.02
394 401 2.778299 TCCCTTTCACATTCTTGACCG 58.222 47.619 0.00 0.00 0.00 4.79
395 402 1.812571 CCCTTTCACATTCTTGACCGG 59.187 52.381 0.00 0.00 0.00 5.28
396 403 2.552155 CCCTTTCACATTCTTGACCGGA 60.552 50.000 9.46 0.00 0.00 5.14
397 404 2.744202 CCTTTCACATTCTTGACCGGAG 59.256 50.000 9.46 0.00 0.00 4.63
399 406 2.455674 TCACATTCTTGACCGGAGTG 57.544 50.000 9.46 3.70 0.00 3.51
400 407 1.967779 TCACATTCTTGACCGGAGTGA 59.032 47.619 9.46 6.09 32.70 3.41
401 408 2.069273 CACATTCTTGACCGGAGTGAC 58.931 52.381 9.46 0.00 0.00 3.67
403 410 3.056821 CACATTCTTGACCGGAGTGACTA 60.057 47.826 9.46 0.00 0.00 2.59
404 411 3.576982 ACATTCTTGACCGGAGTGACTAA 59.423 43.478 9.46 0.00 0.00 2.24
405 412 4.223032 ACATTCTTGACCGGAGTGACTAAT 59.777 41.667 9.46 0.00 0.00 1.73
406 413 5.421056 ACATTCTTGACCGGAGTGACTAATA 59.579 40.000 9.46 0.00 0.00 0.98
408 415 5.515797 TCTTGACCGGAGTGACTAATATG 57.484 43.478 9.46 0.00 0.00 1.78
409 416 4.954202 TCTTGACCGGAGTGACTAATATGT 59.046 41.667 9.46 0.00 0.00 2.29
410 417 4.649088 TGACCGGAGTGACTAATATGTG 57.351 45.455 9.46 0.00 0.00 3.21
411 418 3.181479 TGACCGGAGTGACTAATATGTGC 60.181 47.826 9.46 0.00 0.00 4.57
412 419 2.102588 ACCGGAGTGACTAATATGTGCC 59.897 50.000 9.46 0.00 0.00 5.01
418 1262 5.221641 GGAGTGACTAATATGTGCCATGGTA 60.222 44.000 14.67 5.86 0.00 3.25
446 1290 6.091305 CGTGACAACTATTGCCTATCCATATG 59.909 42.308 0.00 0.00 0.00 1.78
453 1297 6.771267 ACTATTGCCTATCCATATGATGCATG 59.229 38.462 2.46 0.00 33.75 4.06
454 1298 4.579647 TGCCTATCCATATGATGCATGT 57.420 40.909 2.46 0.00 34.76 3.21
457 1301 5.776208 TGCCTATCCATATGATGCATGTTTT 59.224 36.000 2.46 0.00 34.76 2.43
458 1302 6.268158 TGCCTATCCATATGATGCATGTTTTT 59.732 34.615 2.46 0.00 34.76 1.94
491 1335 8.643324 ACAGACATTCCTTATATTAGTCACTCC 58.357 37.037 0.00 0.00 0.00 3.85
539 1384 6.605471 AACTGAAAAGAAAAGGTGGAGTTT 57.395 33.333 0.00 0.00 0.00 2.66
610 1455 9.822185 ATAAATGTATCTTTTCCAATTTGCCTC 57.178 29.630 0.00 0.00 0.00 4.70
623 1468 2.010145 TTGCCTCTATGCACGACTTC 57.990 50.000 0.00 0.00 41.88 3.01
625 1470 1.550524 TGCCTCTATGCACGACTTCTT 59.449 47.619 0.00 0.00 36.04 2.52
665 1511 9.094578 AGCTTATCCATGTAGCTCTCTAATTTA 57.905 33.333 0.00 0.00 41.15 1.40
706 1552 8.140628 ACAAAAACAGCATACATAAACATGACA 58.859 29.630 0.00 0.00 0.00 3.58
724 1570 2.207229 ATATCTACAGGGCGCGGCA 61.207 57.895 34.30 13.23 0.00 5.69
779 1639 5.796350 AAGAAATGATGTACGTAAGCCAC 57.204 39.130 0.00 0.00 45.62 5.01
782 1642 2.665649 TGATGTACGTAAGCCACAGG 57.334 50.000 0.00 0.00 45.62 4.00
1022 1997 2.692824 CCATGGGAGCATGGTGGGA 61.693 63.158 0.00 0.00 45.28 4.37
1086 2061 0.541392 TCATCGCCATGGCTAACTGT 59.459 50.000 33.07 5.66 39.32 3.55
1098 2073 2.224305 GGCTAACTGTGCTCGGGATATT 60.224 50.000 0.00 0.00 0.00 1.28
1108 2083 2.598565 CTCGGGATATTCCTGACTCCA 58.401 52.381 0.00 0.00 46.55 3.86
1128 2103 2.605837 TTGCCAAGAACACTCGTACA 57.394 45.000 0.00 0.00 0.00 2.90
1212 2203 3.716195 CCGGTCATGGGGTGCAGA 61.716 66.667 0.00 0.00 0.00 4.26
1217 2214 0.739813 GTCATGGGGTGCAGACGTAC 60.740 60.000 0.00 0.00 0.00 3.67
1292 2298 0.944386 CACTTGTAACAAGCCGTGCT 59.056 50.000 0.00 0.00 42.56 4.40
1354 2360 2.429058 CTGACCACCTGCTGCTGT 59.571 61.111 0.00 0.00 0.00 4.40
1369 2375 3.561725 GCTGCTGTAAGAAGAACTGTGTT 59.438 43.478 0.00 0.00 45.09 3.32
1402 2414 0.386478 CACGCAGGAGCAGCTTTTTC 60.386 55.000 0.00 0.00 42.27 2.29
1412 2424 2.825861 CAGCTTTTTCTGCCAATGGT 57.174 45.000 0.00 0.00 0.00 3.55
1413 2425 2.409975 CAGCTTTTTCTGCCAATGGTG 58.590 47.619 0.00 0.00 0.00 4.17
1414 2426 2.036217 CAGCTTTTTCTGCCAATGGTGA 59.964 45.455 0.00 0.00 31.67 4.02
1415 2427 2.699846 AGCTTTTTCTGCCAATGGTGAA 59.300 40.909 0.00 3.48 0.00 3.18
1416 2428 3.134442 AGCTTTTTCTGCCAATGGTGAAA 59.866 39.130 14.86 14.86 0.00 2.69
1417 2429 4.067192 GCTTTTTCTGCCAATGGTGAAAT 58.933 39.130 17.85 0.00 31.71 2.17
1418 2430 5.011943 AGCTTTTTCTGCCAATGGTGAAATA 59.988 36.000 17.85 13.92 31.71 1.40
1419 2431 5.700373 GCTTTTTCTGCCAATGGTGAAATAA 59.300 36.000 17.85 14.38 31.71 1.40
1420 2432 6.204495 GCTTTTTCTGCCAATGGTGAAATAAA 59.796 34.615 17.85 11.92 31.71 1.40
1421 2433 7.094677 GCTTTTTCTGCCAATGGTGAAATAAAT 60.095 33.333 17.85 0.00 31.71 1.40
1422 2434 9.434420 CTTTTTCTGCCAATGGTGAAATAAATA 57.566 29.630 17.85 5.70 31.71 1.40
1423 2435 9.784531 TTTTTCTGCCAATGGTGAAATAAATAA 57.215 25.926 17.85 9.85 31.71 1.40
1424 2436 9.784531 TTTTCTGCCAATGGTGAAATAAATAAA 57.215 25.926 17.85 4.66 31.71 1.40
1425 2437 9.956640 TTTCTGCCAATGGTGAAATAAATAAAT 57.043 25.926 14.86 0.00 0.00 1.40
1426 2438 9.598517 TTCTGCCAATGGTGAAATAAATAAATC 57.401 29.630 0.00 0.00 0.00 2.17
1427 2439 8.980596 TCTGCCAATGGTGAAATAAATAAATCT 58.019 29.630 0.00 0.00 0.00 2.40
1428 2440 9.252962 CTGCCAATGGTGAAATAAATAAATCTC 57.747 33.333 0.00 0.00 0.00 2.75
1429 2441 7.920151 TGCCAATGGTGAAATAAATAAATCTCG 59.080 33.333 0.00 0.00 0.00 4.04
1430 2442 7.920682 GCCAATGGTGAAATAAATAAATCTCGT 59.079 33.333 0.00 0.00 0.00 4.18
1431 2443 9.801873 CCAATGGTGAAATAAATAAATCTCGTT 57.198 29.630 0.00 0.00 0.00 3.85
1434 2446 9.716507 ATGGTGAAATAAATAAATCTCGTTTCG 57.283 29.630 0.00 0.00 0.00 3.46
1435 2447 8.937884 TGGTGAAATAAATAAATCTCGTTTCGA 58.062 29.630 0.00 0.00 0.00 3.71
1436 2448 9.931210 GGTGAAATAAATAAATCTCGTTTCGAT 57.069 29.630 0.00 0.00 34.61 3.59
1438 2450 9.843874 TGAAATAAATAAATCTCGTTTCGATCG 57.156 29.630 9.36 9.36 34.61 3.69
1439 2451 8.695355 AAATAAATAAATCTCGTTTCGATCGC 57.305 30.769 11.09 0.00 34.61 4.58
1440 2452 4.356162 AATAAATCTCGTTTCGATCGCG 57.644 40.909 11.09 8.84 34.61 5.87
1441 2453 1.625616 AAATCTCGTTTCGATCGCGT 58.374 45.000 11.09 0.00 38.98 6.01
1442 2454 1.189403 AATCTCGTTTCGATCGCGTC 58.811 50.000 11.09 1.94 38.98 5.19
1457 2469 4.735132 GTCGTGCGTGCCTGCCTA 62.735 66.667 0.00 0.00 0.00 3.93
1458 2470 3.770040 TCGTGCGTGCCTGCCTAT 61.770 61.111 0.00 0.00 0.00 2.57
1459 2471 2.106131 CGTGCGTGCCTGCCTATA 59.894 61.111 0.00 0.00 0.00 1.31
1460 2472 1.951130 CGTGCGTGCCTGCCTATAG 60.951 63.158 0.00 0.00 0.00 1.31
1461 2473 1.441729 GTGCGTGCCTGCCTATAGA 59.558 57.895 0.00 0.00 0.00 1.98
1462 2474 0.034059 GTGCGTGCCTGCCTATAGAT 59.966 55.000 0.00 0.00 0.00 1.98
1463 2475 0.033920 TGCGTGCCTGCCTATAGATG 59.966 55.000 0.00 0.00 0.00 2.90
1464 2476 0.671781 GCGTGCCTGCCTATAGATGG 60.672 60.000 0.00 1.52 0.00 3.51
1479 2491 7.428826 CCTATAGATGGCAAAAAGAACATTCC 58.571 38.462 0.00 0.00 0.00 3.01
1495 2507 2.570415 TTCCTATTGGGCGTGTTTGA 57.430 45.000 0.00 0.00 34.39 2.69
1513 2525 3.558931 TGATTACATTGCCGATCCAGT 57.441 42.857 0.00 0.00 0.00 4.00
1564 2576 1.466856 GTTTGAGGAGATGCATGCCA 58.533 50.000 16.68 3.52 0.00 4.92
1565 2577 1.820519 GTTTGAGGAGATGCATGCCAA 59.179 47.619 16.68 7.22 0.00 4.52
1593 2605 3.719268 ACCCAGATGCACATAGTTTGA 57.281 42.857 0.00 0.00 0.00 2.69
1632 2644 5.280654 AGTTGCATGAGACAACCATTTTT 57.719 34.783 10.06 0.00 46.85 1.94
1635 2647 5.471556 TGCATGAGACAACCATTTTTGAT 57.528 34.783 0.00 0.00 0.00 2.57
1667 2679 2.492773 GCCCGCATTGCATTAGGCT 61.493 57.895 17.14 0.00 45.15 4.58
1853 2865 5.045140 GCCATTGGCTAAATAGGGGATAGTA 60.045 44.000 20.66 0.00 46.69 1.82
1867 2879 3.319972 GGGATAGTACATCGGTGTTGCTA 59.680 47.826 6.64 10.81 39.77 3.49
2118 3145 2.790433 GTGTTCATCAAAGCCCCACTA 58.210 47.619 0.00 0.00 0.00 2.74
2156 3185 4.730657 CAGAATGCAAAGCAAGAACTAGG 58.269 43.478 0.00 0.00 43.62 3.02
2208 3237 5.431765 GCTTCTGATCCAGGATCTTAAACA 58.568 41.667 26.94 8.32 39.56 2.83
2279 3309 5.337169 GGAGTGTCTGAGATTAAACAGCTCT 60.337 44.000 0.00 0.00 38.88 4.09
2298 3328 2.695666 TCTTGTGCAGTCCTAGGATAGC 59.304 50.000 24.04 24.04 37.37 2.97
2315 3345 5.871834 GGATAGCTCCTACTAGAGAACTCA 58.128 45.833 0.00 0.00 38.65 3.41
2331 3361 6.897966 AGAGAACTCATTGAGATGGTACCTTA 59.102 38.462 20.33 0.00 33.93 2.69
2386 3416 1.144298 TGCATAGCCAGCATCTCCAAT 59.856 47.619 0.00 0.00 37.02 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.578282 TGAGTGAGTTTCCTGTATGAGCA 59.422 43.478 0.00 0.00 0.00 4.26
20 21 6.969828 ATTAATCGAACTGAGTGAGTTTCC 57.030 37.500 0.00 0.00 45.48 3.13
57 58 4.080919 CACTTCCATGTCTTCCAGATACCA 60.081 45.833 0.00 0.00 0.00 3.25
66 67 8.352942 AGAAAAATTGTACACTTCCATGTCTTC 58.647 33.333 0.00 0.00 33.85 2.87
139 146 4.142337 CCTCTCCGGTCTAGAGTCTTTTTC 60.142 50.000 15.43 0.00 39.09 2.29
145 152 0.838608 TCCCTCTCCGGTCTAGAGTC 59.161 60.000 15.43 0.00 39.09 3.36
176 183 0.321653 AACTTGTAGCTTCGCCCCTG 60.322 55.000 0.00 0.00 0.00 4.45
177 184 1.207329 CTAACTTGTAGCTTCGCCCCT 59.793 52.381 0.00 0.00 0.00 4.79
179 186 2.094130 AGACTAACTTGTAGCTTCGCCC 60.094 50.000 0.00 0.00 0.00 6.13
180 187 2.924290 CAGACTAACTTGTAGCTTCGCC 59.076 50.000 0.00 0.00 0.00 5.54
181 188 3.365220 CACAGACTAACTTGTAGCTTCGC 59.635 47.826 0.00 0.00 0.00 4.70
182 189 3.921021 CCACAGACTAACTTGTAGCTTCG 59.079 47.826 0.00 0.00 0.00 3.79
183 190 4.246458 CCCACAGACTAACTTGTAGCTTC 58.754 47.826 0.00 0.00 0.00 3.86
184 191 3.008049 CCCCACAGACTAACTTGTAGCTT 59.992 47.826 0.00 0.00 0.00 3.74
185 192 2.567615 CCCCACAGACTAACTTGTAGCT 59.432 50.000 0.00 0.00 0.00 3.32
186 193 2.302157 ACCCCACAGACTAACTTGTAGC 59.698 50.000 0.00 0.00 0.00 3.58
187 194 3.576982 TGACCCCACAGACTAACTTGTAG 59.423 47.826 0.00 0.00 0.00 2.74
188 195 3.576982 CTGACCCCACAGACTAACTTGTA 59.423 47.826 0.00 0.00 39.94 2.41
189 196 2.368875 CTGACCCCACAGACTAACTTGT 59.631 50.000 0.00 0.00 39.94 3.16
190 197 2.368875 ACTGACCCCACAGACTAACTTG 59.631 50.000 0.00 0.00 40.63 3.16
191 198 2.690840 ACTGACCCCACAGACTAACTT 58.309 47.619 0.00 0.00 40.63 2.66
192 199 2.368875 CAACTGACCCCACAGACTAACT 59.631 50.000 0.00 0.00 40.63 2.24
193 200 2.367567 TCAACTGACCCCACAGACTAAC 59.632 50.000 0.00 0.00 40.63 2.34
194 201 2.684943 TCAACTGACCCCACAGACTAA 58.315 47.619 0.00 0.00 40.63 2.24
195 202 2.391926 TCAACTGACCCCACAGACTA 57.608 50.000 0.00 0.00 40.63 2.59
196 203 1.625818 GATCAACTGACCCCACAGACT 59.374 52.381 0.00 0.00 40.63 3.24
197 204 1.339151 GGATCAACTGACCCCACAGAC 60.339 57.143 0.00 0.00 40.63 3.51
198 205 0.984230 GGATCAACTGACCCCACAGA 59.016 55.000 0.00 0.00 40.63 3.41
199 206 3.558674 GGATCAACTGACCCCACAG 57.441 57.895 0.00 0.00 42.78 3.66
204 211 0.693049 ACTGTGGGATCAACTGACCC 59.307 55.000 10.39 0.00 43.51 4.46
205 212 2.568623 AACTGTGGGATCAACTGACC 57.431 50.000 10.39 0.00 0.00 4.02
206 213 4.918810 AAAAACTGTGGGATCAACTGAC 57.081 40.909 10.39 0.00 0.00 3.51
229 236 8.691797 TGAACAGTGTTTTTAGGCTTATTTTCT 58.308 29.630 10.45 0.00 0.00 2.52
230 237 8.865590 TGAACAGTGTTTTTAGGCTTATTTTC 57.134 30.769 10.45 0.00 0.00 2.29
231 238 8.474831 ACTGAACAGTGTTTTTAGGCTTATTTT 58.525 29.630 10.45 0.00 40.75 1.82
232 239 8.007405 ACTGAACAGTGTTTTTAGGCTTATTT 57.993 30.769 10.45 0.00 40.75 1.40
233 240 7.582667 ACTGAACAGTGTTTTTAGGCTTATT 57.417 32.000 10.45 0.00 40.75 1.40
234 241 7.582667 AACTGAACAGTGTTTTTAGGCTTAT 57.417 32.000 10.45 0.00 41.58 1.73
235 242 7.771826 AGTAACTGAACAGTGTTTTTAGGCTTA 59.228 33.333 10.45 3.30 41.58 3.09
236 243 5.914898 AACTGAACAGTGTTTTTAGGCTT 57.085 34.783 10.45 0.00 41.58 4.35
237 244 6.038271 CAGTAACTGAACAGTGTTTTTAGGCT 59.962 38.462 10.45 2.98 41.58 4.58
238 245 6.183360 ACAGTAACTGAACAGTGTTTTTAGGC 60.183 38.462 10.45 0.00 41.58 3.93
239 246 7.316544 ACAGTAACTGAACAGTGTTTTTAGG 57.683 36.000 10.45 6.52 41.58 2.69
244 251 9.609346 AGTATAAACAGTAACTGAACAGTGTTT 57.391 29.630 10.45 18.12 41.58 2.83
245 252 9.042008 CAGTATAAACAGTAACTGAACAGTGTT 57.958 33.333 8.61 8.61 41.58 3.32
246 253 8.418662 TCAGTATAAACAGTAACTGAACAGTGT 58.581 33.333 8.25 0.00 43.90 3.55
247 254 8.812147 TCAGTATAAACAGTAACTGAACAGTG 57.188 34.615 8.25 0.00 43.90 3.66
285 292 4.746466 TCTGTGGGGTCAATGGTATTTTT 58.254 39.130 0.00 0.00 0.00 1.94
286 293 4.396357 TCTGTGGGGTCAATGGTATTTT 57.604 40.909 0.00 0.00 0.00 1.82
287 294 4.608170 ATCTGTGGGGTCAATGGTATTT 57.392 40.909 0.00 0.00 0.00 1.40
288 295 4.726825 AGTATCTGTGGGGTCAATGGTATT 59.273 41.667 0.00 0.00 0.00 1.89
289 296 4.307259 AGTATCTGTGGGGTCAATGGTAT 58.693 43.478 0.00 0.00 0.00 2.73
290 297 3.731431 AGTATCTGTGGGGTCAATGGTA 58.269 45.455 0.00 0.00 0.00 3.25
291 298 2.562296 AGTATCTGTGGGGTCAATGGT 58.438 47.619 0.00 0.00 0.00 3.55
292 299 3.652057 AAGTATCTGTGGGGTCAATGG 57.348 47.619 0.00 0.00 0.00 3.16
293 300 5.126067 CCTAAAGTATCTGTGGGGTCAATG 58.874 45.833 0.00 0.00 0.00 2.82
294 301 4.385310 GCCTAAAGTATCTGTGGGGTCAAT 60.385 45.833 0.00 0.00 0.00 2.57
295 302 3.054655 GCCTAAAGTATCTGTGGGGTCAA 60.055 47.826 0.00 0.00 0.00 3.18
296 303 2.504175 GCCTAAAGTATCTGTGGGGTCA 59.496 50.000 0.00 0.00 0.00 4.02
297 304 2.772515 AGCCTAAAGTATCTGTGGGGTC 59.227 50.000 0.00 0.00 0.00 4.46
298 305 2.505819 CAGCCTAAAGTATCTGTGGGGT 59.494 50.000 0.00 0.00 0.00 4.95
299 306 2.158755 CCAGCCTAAAGTATCTGTGGGG 60.159 54.545 0.00 0.00 0.00 4.96
300 307 2.746472 GCCAGCCTAAAGTATCTGTGGG 60.746 54.545 0.00 0.00 0.00 4.61
301 308 2.565841 GCCAGCCTAAAGTATCTGTGG 58.434 52.381 0.00 0.00 0.00 4.17
302 309 2.171448 AGGCCAGCCTAAAGTATCTGTG 59.829 50.000 10.11 0.00 46.14 3.66
303 310 2.482494 AGGCCAGCCTAAAGTATCTGT 58.518 47.619 10.11 0.00 46.14 3.41
325 332 2.161078 GACCTATAGGGAGCAGCGGC 62.161 65.000 22.91 0.00 40.27 6.53
326 333 0.540830 AGACCTATAGGGAGCAGCGG 60.541 60.000 22.91 0.00 40.27 5.52
327 334 0.885196 GAGACCTATAGGGAGCAGCG 59.115 60.000 22.91 0.00 40.27 5.18
328 335 2.302587 AGAGACCTATAGGGAGCAGC 57.697 55.000 22.91 6.06 40.27 5.25
329 336 3.161866 GGAAGAGACCTATAGGGAGCAG 58.838 54.545 22.91 0.00 40.27 4.24
330 337 2.518407 TGGAAGAGACCTATAGGGAGCA 59.482 50.000 22.91 0.00 40.27 4.26
331 338 3.246416 TGGAAGAGACCTATAGGGAGC 57.754 52.381 22.91 11.47 40.27 4.70
332 339 4.810345 ACTTGGAAGAGACCTATAGGGAG 58.190 47.826 22.91 8.30 40.27 4.30
333 340 4.901785 ACTTGGAAGAGACCTATAGGGA 57.098 45.455 22.91 0.00 40.27 4.20
334 341 5.959583 AAACTTGGAAGAGACCTATAGGG 57.040 43.478 22.91 5.28 40.27 3.53
338 345 8.272889 GGGTAAATAAACTTGGAAGAGACCTAT 58.727 37.037 0.00 0.00 0.00 2.57
339 346 7.460082 AGGGTAAATAAACTTGGAAGAGACCTA 59.540 37.037 0.00 0.00 0.00 3.08
340 347 6.274908 AGGGTAAATAAACTTGGAAGAGACCT 59.725 38.462 0.00 0.00 0.00 3.85
341 348 6.374613 CAGGGTAAATAAACTTGGAAGAGACC 59.625 42.308 0.00 0.00 0.00 3.85
342 349 6.940867 ACAGGGTAAATAAACTTGGAAGAGAC 59.059 38.462 0.00 0.00 0.00 3.36
343 350 7.086685 ACAGGGTAAATAAACTTGGAAGAGA 57.913 36.000 0.00 0.00 0.00 3.10
344 351 7.761038 AACAGGGTAAATAAACTTGGAAGAG 57.239 36.000 0.00 0.00 0.00 2.85
374 381 2.552155 CCGGTCAAGAATGTGAAAGGGA 60.552 50.000 0.00 0.00 0.00 4.20
387 394 5.043903 CACATATTAGTCACTCCGGTCAAG 58.956 45.833 0.00 0.00 0.00 3.02
388 395 4.679639 GCACATATTAGTCACTCCGGTCAA 60.680 45.833 0.00 0.00 0.00 3.18
389 396 3.181479 GCACATATTAGTCACTCCGGTCA 60.181 47.826 0.00 0.00 0.00 4.02
390 397 3.381949 GCACATATTAGTCACTCCGGTC 58.618 50.000 0.00 0.00 0.00 4.79
391 398 2.102588 GGCACATATTAGTCACTCCGGT 59.897 50.000 0.00 0.00 0.00 5.28
392 399 2.102420 TGGCACATATTAGTCACTCCGG 59.898 50.000 0.00 0.00 0.00 5.14
393 400 3.452755 TGGCACATATTAGTCACTCCG 57.547 47.619 0.00 0.00 0.00 4.63
408 415 2.303163 TGTCACGTATACCATGGCAC 57.697 50.000 13.04 6.66 0.00 5.01
409 416 2.235155 AGTTGTCACGTATACCATGGCA 59.765 45.455 13.04 0.00 0.00 4.92
410 417 2.901249 AGTTGTCACGTATACCATGGC 58.099 47.619 13.04 0.00 0.00 4.40
411 418 5.050363 GCAATAGTTGTCACGTATACCATGG 60.050 44.000 11.19 11.19 0.00 3.66
412 419 5.050363 GGCAATAGTTGTCACGTATACCATG 60.050 44.000 0.00 0.00 34.79 3.66
418 1262 5.069914 TGGATAGGCAATAGTTGTCACGTAT 59.930 40.000 0.00 0.00 37.85 3.06
465 1309 8.643324 GGAGTGACTAATATAAGGAATGTCTGT 58.357 37.037 0.00 0.00 0.00 3.41
466 1310 8.642432 TGGAGTGACTAATATAAGGAATGTCTG 58.358 37.037 0.00 0.00 0.00 3.51
467 1311 8.783660 TGGAGTGACTAATATAAGGAATGTCT 57.216 34.615 0.00 0.00 0.00 3.41
468 1312 9.832445 TTTGGAGTGACTAATATAAGGAATGTC 57.168 33.333 0.00 0.00 0.00 3.06
514 1359 6.605471 ACTCCACCTTTTCTTTTCAGTTTT 57.395 33.333 0.00 0.00 0.00 2.43
515 1360 6.605471 AACTCCACCTTTTCTTTTCAGTTT 57.395 33.333 0.00 0.00 0.00 2.66
516 1361 6.605471 AAACTCCACCTTTTCTTTTCAGTT 57.395 33.333 0.00 0.00 0.00 3.16
517 1362 7.898014 ATAAACTCCACCTTTTCTTTTCAGT 57.102 32.000 0.00 0.00 0.00 3.41
530 1375 3.933332 GCATCCGCTATATAAACTCCACC 59.067 47.826 0.00 0.00 34.30 4.61
539 1384 7.987750 TGTAATTTTTGGCATCCGCTATATA 57.012 32.000 0.00 0.00 38.60 0.86
685 1531 9.565090 AGATATGTCATGTTTATGTATGCTGTT 57.435 29.630 0.00 0.00 35.73 3.16
706 1552 1.544825 ATGCCGCGCCCTGTAGATAT 61.545 55.000 0.00 0.00 0.00 1.63
1022 1997 7.710475 GCTTCACTAATAAGCTCTTCTTCATCT 59.290 37.037 0.00 0.00 44.75 2.90
1086 2061 1.964223 GAGTCAGGAATATCCCGAGCA 59.036 52.381 0.00 0.00 37.19 4.26
1098 2073 1.361204 TCTTGGCAATGGAGTCAGGA 58.639 50.000 0.00 0.00 0.00 3.86
1108 2083 3.120321 TGTACGAGTGTTCTTGGCAAT 57.880 42.857 0.00 0.00 0.00 3.56
1212 2203 2.050714 CGTCGCAGGTGTGTACGT 60.051 61.111 0.00 0.00 0.00 3.57
1217 2214 1.347097 CTGATGTCGTCGCAGGTGTG 61.347 60.000 0.00 0.00 0.00 3.82
1276 2282 1.169661 CCCAGCACGGCTTGTTACAA 61.170 55.000 0.00 0.00 36.40 2.41
1292 2298 3.384532 GTCGTACCCTTCCGCCCA 61.385 66.667 0.00 0.00 0.00 5.36
1330 2336 2.224159 GCAGGTGGTCAGGAAGGGA 61.224 63.158 0.00 0.00 0.00 4.20
1354 2360 5.698089 CAGAGCATCAACACAGTTCTTCTTA 59.302 40.000 0.00 0.00 37.82 2.10
1402 2414 9.252962 GAGATTTATTTATTTCACCATTGGCAG 57.747 33.333 1.54 0.00 0.00 4.85
1408 2420 9.716507 CGAAACGAGATTTATTTATTTCACCAT 57.283 29.630 0.00 0.00 0.00 3.55
1409 2421 8.937884 TCGAAACGAGATTTATTTATTTCACCA 58.062 29.630 0.00 0.00 0.00 4.17
1410 2422 9.931210 ATCGAAACGAGATTTATTTATTTCACC 57.069 29.630 0.00 0.00 39.91 4.02
1412 2424 9.843874 CGATCGAAACGAGATTTATTTATTTCA 57.156 29.630 10.26 0.00 39.91 2.69
1413 2425 8.819161 GCGATCGAAACGAGATTTATTTATTTC 58.181 33.333 21.57 0.00 39.91 2.17
1414 2426 7.526186 CGCGATCGAAACGAGATTTATTTATTT 59.474 33.333 21.57 0.00 39.91 1.40
1415 2427 7.001922 CGCGATCGAAACGAGATTTATTTATT 58.998 34.615 21.57 0.00 39.91 1.40
1416 2428 6.143438 ACGCGATCGAAACGAGATTTATTTAT 59.857 34.615 21.57 0.00 39.91 1.40
1417 2429 5.456497 ACGCGATCGAAACGAGATTTATTTA 59.544 36.000 21.57 0.00 39.91 1.40
1418 2430 4.266976 ACGCGATCGAAACGAGATTTATTT 59.733 37.500 21.57 0.00 39.91 1.40
1419 2431 3.795101 ACGCGATCGAAACGAGATTTATT 59.205 39.130 21.57 0.00 39.91 1.40
1420 2432 3.369385 ACGCGATCGAAACGAGATTTAT 58.631 40.909 21.57 0.00 39.91 1.40
1421 2433 2.780014 GACGCGATCGAAACGAGATTTA 59.220 45.455 21.57 0.00 39.91 1.40
1422 2434 1.582502 GACGCGATCGAAACGAGATTT 59.417 47.619 21.57 0.00 39.91 2.17
1423 2435 1.189403 GACGCGATCGAAACGAGATT 58.811 50.000 21.57 0.00 39.91 2.40
1424 2436 2.856089 GACGCGATCGAAACGAGAT 58.144 52.632 21.57 0.00 39.91 2.75
1425 2437 4.354935 GACGCGATCGAAACGAGA 57.645 55.556 21.57 0.00 39.91 4.04
1440 2452 2.622903 TATAGGCAGGCACGCACGAC 62.623 60.000 0.00 0.00 0.00 4.34
1441 2453 2.349969 CTATAGGCAGGCACGCACGA 62.350 60.000 0.00 0.00 0.00 4.35
1442 2454 1.951130 CTATAGGCAGGCACGCACG 60.951 63.158 0.00 0.00 0.00 5.34
1443 2455 0.034059 ATCTATAGGCAGGCACGCAC 59.966 55.000 0.00 0.00 0.00 5.34
1444 2456 0.033920 CATCTATAGGCAGGCACGCA 59.966 55.000 0.00 0.00 0.00 5.24
1445 2457 0.671781 CCATCTATAGGCAGGCACGC 60.672 60.000 0.00 0.00 0.00 5.34
1446 2458 3.521995 CCATCTATAGGCAGGCACG 57.478 57.895 0.00 0.00 0.00 5.34
1454 2466 7.286316 AGGAATGTTCTTTTTGCCATCTATAGG 59.714 37.037 0.00 0.00 0.00 2.57
1455 2467 8.230472 AGGAATGTTCTTTTTGCCATCTATAG 57.770 34.615 0.00 0.00 0.00 1.31
1456 2468 9.866655 ATAGGAATGTTCTTTTTGCCATCTATA 57.133 29.630 0.00 0.00 0.00 1.31
1457 2469 8.773033 ATAGGAATGTTCTTTTTGCCATCTAT 57.227 30.769 0.00 0.00 0.00 1.98
1458 2470 8.469200 CAATAGGAATGTTCTTTTTGCCATCTA 58.531 33.333 0.00 0.00 0.00 1.98
1459 2471 7.325694 CAATAGGAATGTTCTTTTTGCCATCT 58.674 34.615 0.00 0.00 0.00 2.90
1460 2472 6.536224 CCAATAGGAATGTTCTTTTTGCCATC 59.464 38.462 3.64 0.00 36.89 3.51
1461 2473 6.408869 CCAATAGGAATGTTCTTTTTGCCAT 58.591 36.000 3.64 0.00 36.89 4.40
1462 2474 5.279910 CCCAATAGGAATGTTCTTTTTGCCA 60.280 40.000 3.64 0.00 38.24 4.92
1463 2475 5.178061 CCCAATAGGAATGTTCTTTTTGCC 58.822 41.667 3.64 0.00 38.24 4.52
1464 2476 4.631377 GCCCAATAGGAATGTTCTTTTTGC 59.369 41.667 3.64 0.00 38.24 3.68
1465 2477 4.864247 CGCCCAATAGGAATGTTCTTTTTG 59.136 41.667 2.57 2.57 38.24 2.44
1466 2478 4.526650 ACGCCCAATAGGAATGTTCTTTTT 59.473 37.500 0.00 0.00 38.24 1.94
1467 2479 4.082245 CACGCCCAATAGGAATGTTCTTTT 60.082 41.667 0.00 0.00 38.24 2.27
1468 2480 3.443681 CACGCCCAATAGGAATGTTCTTT 59.556 43.478 0.00 0.00 38.24 2.52
1469 2481 3.016736 CACGCCCAATAGGAATGTTCTT 58.983 45.455 0.00 0.00 38.24 2.52
1470 2482 2.026262 ACACGCCCAATAGGAATGTTCT 60.026 45.455 0.00 0.00 38.24 3.01
1471 2483 2.365582 ACACGCCCAATAGGAATGTTC 58.634 47.619 0.00 0.00 38.24 3.18
1472 2484 2.507407 ACACGCCCAATAGGAATGTT 57.493 45.000 0.00 0.00 38.24 2.71
1473 2485 2.491693 CAAACACGCCCAATAGGAATGT 59.508 45.455 0.00 0.00 38.24 2.71
1474 2486 2.752354 TCAAACACGCCCAATAGGAATG 59.248 45.455 0.00 0.00 38.24 2.67
1475 2487 3.080300 TCAAACACGCCCAATAGGAAT 57.920 42.857 0.00 0.00 38.24 3.01
1476 2488 2.570415 TCAAACACGCCCAATAGGAA 57.430 45.000 0.00 0.00 38.24 3.36
1477 2489 2.799126 ATCAAACACGCCCAATAGGA 57.201 45.000 0.00 0.00 38.24 2.94
1478 2490 3.692101 TGTAATCAAACACGCCCAATAGG 59.308 43.478 0.00 0.00 39.47 2.57
1479 2491 4.955925 TGTAATCAAACACGCCCAATAG 57.044 40.909 0.00 0.00 0.00 1.73
1495 2507 3.470709 CAGACTGGATCGGCAATGTAAT 58.529 45.455 0.00 0.00 0.00 1.89
1593 2605 1.152610 CTAGGGGCATGCAGGCAAT 60.153 57.895 26.25 12.34 46.44 3.56
1632 2644 1.234821 GGCAACCAAACGTCAGATCA 58.765 50.000 0.00 0.00 0.00 2.92
1667 2679 4.661222 ACCAAACACCATGTCATATGTGA 58.339 39.130 17.23 0.00 0.00 3.58
1853 2865 1.897133 TGGTAGTAGCAACACCGATGT 59.103 47.619 0.00 0.00 42.46 3.06
1867 2879 4.231890 AGAGGAAGAGGAAGATCTGGTAGT 59.768 45.833 0.00 0.00 0.00 2.73
2012 3039 2.143122 TGACAATGACGCTTGGAAGAC 58.857 47.619 0.00 0.00 0.00 3.01
2118 3145 4.746089 GCATTCTGCATAACTGGATCCTCT 60.746 45.833 14.23 0.00 44.26 3.69
2156 3185 3.518303 ACCCATACTCCACTCAGGTTAAC 59.482 47.826 0.00 0.00 39.02 2.01
2208 3237 4.826183 GGCATTTGGAGCTCTGAAGAATAT 59.174 41.667 14.64 0.00 0.00 1.28
2279 3309 2.695666 GAGCTATCCTAGGACTGCACAA 59.304 50.000 28.71 3.19 0.00 3.33
2298 3328 7.040478 CCATCTCAATGAGTTCTCTAGTAGGAG 60.040 44.444 10.36 0.00 34.61 3.69
2305 3335 6.436027 AGGTACCATCTCAATGAGTTCTCTA 58.564 40.000 15.94 0.00 34.61 2.43
2315 3345 7.872138 TCAGGAAAATAAGGTACCATCTCAAT 58.128 34.615 15.94 0.00 0.00 2.57
2331 3361 4.469469 TTCTTCCACCCTTCAGGAAAAT 57.531 40.909 0.00 0.00 42.91 1.82
2386 3416 0.251916 CCCCGATGGCAAGTTCTACA 59.748 55.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.