Multiple sequence alignment - TraesCS7D01G394100

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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 TraesCS7D01G394100 chr7D 100.000 5296 0 0 1 5296 509561004 509555709 0.000000e+00 9780.0
1 TraesCS7D01G394100 chr7D 81.280 2500 438 23 1202 3680 509614764 509612274 0.000000e+00 1997.0
2 TraesCS7D01G394100 chr7D 89.655 377 38 1 4905 5281 509611328 509610953 3.710000e-131 479.0
3 TraesCS7D01G394100 chr7D 80.206 389 49 17 3823 4187 509612141 509611757 3.140000e-67 267.0
4 TraesCS7D01G394100 chr7D 84.762 105 11 4 361 460 244451453 244451557 3.370000e-17 100.0
5 TraesCS7D01G394100 chr7D 88.333 60 7 0 727 786 70967883 70967942 7.360000e-09 73.1
6 TraesCS7D01G394100 chr7B 94.616 4532 186 23 803 5296 537677327 537672816 0.000000e+00 6964.0
7 TraesCS7D01G394100 chr7B 80.827 2999 452 71 1319 4248 537831109 537828165 0.000000e+00 2239.0
8 TraesCS7D01G394100 chr7B 80.164 2919 458 62 1201 4050 537795902 537793036 0.000000e+00 2071.0
9 TraesCS7D01G394100 chr7B 92.602 392 27 2 4906 5296 537827426 537827036 3.580000e-156 562.0
10 TraesCS7D01G394100 chr7B 90.083 242 15 6 4905 5146 537792089 537791857 6.660000e-79 305.0
11 TraesCS7D01G394100 chr7B 87.143 140 12 3 595 729 537677463 537677325 2.550000e-33 154.0
12 TraesCS7D01G394100 chr7B 86.792 106 8 3 361 460 183308220 183308325 4.330000e-21 113.0
13 TraesCS7D01G394100 chr7A 96.210 3245 104 10 1248 4482 580474482 580471247 0.000000e+00 5293.0
14 TraesCS7D01G394100 chr7A 82.692 2392 369 32 1319 3680 580509399 580507023 0.000000e+00 2082.0
15 TraesCS7D01G394100 chr7A 76.979 2463 505 47 1220 3639 580693866 580696309 0.000000e+00 1351.0
16 TraesCS7D01G394100 chr7A 95.929 786 24 5 4516 5296 580471246 580470464 0.000000e+00 1267.0
17 TraesCS7D01G394100 chr7A 88.571 385 29 10 4905 5281 580506502 580506125 2.250000e-123 453.0
18 TraesCS7D01G394100 chr7A 90.566 318 20 2 803 1116 580475076 580474765 3.820000e-111 412.0
19 TraesCS7D01G394100 chr7A 89.869 306 23 5 1 301 580476184 580475882 2.310000e-103 387.0
20 TraesCS7D01G394100 chr7A 91.698 265 21 1 465 729 580475337 580475074 3.010000e-97 366.0
21 TraesCS7D01G394100 chr7A 96.875 64 2 0 1137 1200 580474658 580474595 2.020000e-19 108.0
22 TraesCS7D01G394100 chr5A 93.723 462 22 3 4076 4537 425486004 425485550 0.000000e+00 686.0
23 TraesCS7D01G394100 chr5A 91.342 462 33 2 4076 4537 44117403 44116949 4.500000e-175 625.0
24 TraesCS7D01G394100 chr3D 93.074 462 25 3 4076 4537 258275023 258275477 0.000000e+00 669.0
25 TraesCS7D01G394100 chr1A 92.791 430 24 3 4108 4537 13962862 13963284 2.710000e-172 616.0
26 TraesCS7D01G394100 chr2B 85.918 490 39 10 4550 5035 126731046 126731509 3.680000e-136 496.0
27 TraesCS7D01G394100 chr2B 95.897 195 7 1 5072 5266 126731509 126731702 1.110000e-81 315.0
28 TraesCS7D01G394100 chr2A 91.620 179 13 1 4076 4252 186437743 186437565 4.100000e-61 246.0
29 TraesCS7D01G394100 chr2A 85.577 104 9 3 361 458 350732382 350732485 2.610000e-18 104.0
30 TraesCS7D01G394100 chr2A 84.615 104 11 4 361 459 267885346 267885449 1.210000e-16 99.0
31 TraesCS7D01G394100 chr5B 87.310 197 25 0 5100 5296 667412452 667412648 5.340000e-55 226.0
32 TraesCS7D01G394100 chr6B 86.111 108 7 5 361 461 153394910 153394804 5.610000e-20 110.0
33 TraesCS7D01G394100 chr4A 85.714 105 9 3 361 459 737468566 737468670 7.250000e-19 106.0
34 TraesCS7D01G394100 chr2D 85.577 104 9 3 361 458 271511873 271511770 2.610000e-18 104.0
35 TraesCS7D01G394100 chr6D 87.234 94 6 3 373 460 80517540 80517447 9.380000e-18 102.0
36 TraesCS7D01G394100 chr5D 82.609 115 13 5 351 460 480858545 480858433 1.570000e-15 95.3


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 TraesCS7D01G394100 chr7D 509555709 509561004 5295 True 9780.000000 9780 100.000000 1 5296 1 chr7D.!!$R1 5295
1 TraesCS7D01G394100 chr7D 509610953 509614764 3811 True 914.333333 1997 83.713667 1202 5281 3 chr7D.!!$R2 4079
2 TraesCS7D01G394100 chr7B 537672816 537677463 4647 True 3559.000000 6964 90.879500 595 5296 2 chr7B.!!$R1 4701
3 TraesCS7D01G394100 chr7B 537827036 537831109 4073 True 1400.500000 2239 86.714500 1319 5296 2 chr7B.!!$R3 3977
4 TraesCS7D01G394100 chr7B 537791857 537795902 4045 True 1188.000000 2071 85.123500 1201 5146 2 chr7B.!!$R2 3945
5 TraesCS7D01G394100 chr7A 580693866 580696309 2443 False 1351.000000 1351 76.979000 1220 3639 1 chr7A.!!$F1 2419
6 TraesCS7D01G394100 chr7A 580470464 580476184 5720 True 1305.500000 5293 93.524500 1 5296 6 chr7A.!!$R1 5295
7 TraesCS7D01G394100 chr7A 580506125 580509399 3274 True 1267.500000 2082 85.631500 1319 5281 2 chr7A.!!$R2 3962
8 TraesCS7D01G394100 chr2B 126731046 126731702 656 False 405.500000 496 90.907500 4550 5266 2 chr2B.!!$F1 716

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
538 964 0.035152 TCCATGATCAGTGGTGGCAC 60.035 55.0 9.7 9.7 37.96 5.01 F
1671 2300 0.037232 GCAACCTCCAGTTACTCGCT 60.037 55.0 0.0 0.0 36.18 4.93 F
2299 2966 0.538057 CTGCACACAGGGGTTCATGT 60.538 55.0 0.0 0.0 40.48 3.21 F
2409 3082 0.615331 ATTCGCACACCACAGAGGAT 59.385 50.0 0.0 0.0 41.22 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2770 0.107410 TGACTGCCCACGACAAGTTT 60.107 50.0 0.00 0.00 0.00 2.66 R
3601 4286 0.438830 GTCAACGGCGATGAACAGTC 59.561 55.0 21.50 5.23 0.00 3.51 R
3963 4897 0.526662 ATCTTGCTGCTGCTGCTTTC 59.473 50.0 27.67 6.29 40.48 2.62 R
4333 5492 0.668535 GACAAAGGCACACCAAGGAC 59.331 55.0 0.00 0.00 39.06 3.85 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
30 31 2.377810 ATCCTCATCAGGGCGCCAA 61.378 57.895 30.85 13.81 40.80 4.52
61 62 0.923358 AGGACACCAAAACACCAGGA 59.077 50.000 0.00 0.00 0.00 3.86
68 69 2.094442 ACCAAAACACCAGGAAACAACG 60.094 45.455 0.00 0.00 0.00 4.10
72 73 0.681564 ACACCAGGAAACAACGGCAA 60.682 50.000 0.00 0.00 0.00 4.52
137 138 3.254166 ACAATCTGCACACAAAGACCATC 59.746 43.478 0.00 0.00 0.00 3.51
142 143 1.069906 GCACACAAAGACCATCGACAC 60.070 52.381 0.00 0.00 0.00 3.67
150 151 2.227968 GACCATCGACACAACGCTGC 62.228 60.000 0.00 0.00 0.00 5.25
157 158 1.845809 GACACAACGCTGCTGGGAAG 61.846 60.000 14.63 8.30 0.00 3.46
172 173 0.667184 GGAAGCATTGCCAAACACGG 60.667 55.000 4.70 0.00 0.00 4.94
189 190 2.476320 GGGCGCATTCCTCTGCTTC 61.476 63.158 10.83 0.00 40.06 3.86
215 216 4.361451 AACTGCAGCATACAAGCATAAC 57.639 40.909 15.27 0.00 37.68 1.89
249 252 4.761739 TGCTTCCATAAACTCCAGTCAAAG 59.238 41.667 0.00 0.00 0.00 2.77
254 257 1.884235 AAACTCCAGTCAAAGCCTCG 58.116 50.000 0.00 0.00 0.00 4.63
281 284 4.004982 GCGTTTTTAACATGGTCCCTCTA 58.995 43.478 0.00 0.00 0.00 2.43
286 289 5.853572 TTTAACATGGTCCCTCTAACCTT 57.146 39.130 0.00 0.00 37.69 3.50
287 290 6.956102 TTTAACATGGTCCCTCTAACCTTA 57.044 37.500 0.00 0.00 37.69 2.69
289 292 2.764572 ACATGGTCCCTCTAACCTTACG 59.235 50.000 0.00 0.00 37.69 3.18
301 304 6.090898 CCTCTAACCTTACGTTTTCACATGAG 59.909 42.308 0.00 0.00 35.79 2.90
303 306 5.924475 AACCTTACGTTTTCACATGAGAG 57.076 39.130 0.00 0.00 0.00 3.20
304 307 4.315803 ACCTTACGTTTTCACATGAGAGG 58.684 43.478 0.00 0.00 0.00 3.69
306 309 4.152402 CCTTACGTTTTCACATGAGAGGTG 59.848 45.833 0.00 0.00 37.60 4.00
309 312 3.181465 ACGTTTTCACATGAGAGGTGAGT 60.181 43.478 0.00 0.00 45.20 3.41
314 317 6.850752 TTTCACATGAGAGGTGAGTGTATA 57.149 37.500 0.00 0.00 45.20 1.47
315 318 6.456795 TTCACATGAGAGGTGAGTGTATAG 57.543 41.667 0.00 0.00 45.20 1.31
316 319 5.510430 TCACATGAGAGGTGAGTGTATAGT 58.490 41.667 0.00 0.00 40.16 2.12
318 321 6.542735 TCACATGAGAGGTGAGTGTATAGTAC 59.457 42.308 0.00 0.00 40.16 2.73
319 322 6.544197 CACATGAGAGGTGAGTGTATAGTACT 59.456 42.308 0.00 0.00 38.54 2.73
320 323 6.768861 ACATGAGAGGTGAGTGTATAGTACTC 59.231 42.308 0.00 9.21 43.73 2.59
321 324 5.682659 TGAGAGGTGAGTGTATAGTACTCC 58.317 45.833 0.00 0.00 43.00 3.85
322 325 5.051409 AGAGGTGAGTGTATAGTACTCCC 57.949 47.826 0.00 12.21 43.00 4.30
323 326 4.727841 AGAGGTGAGTGTATAGTACTCCCT 59.272 45.833 17.65 17.65 42.92 4.20
324 327 5.194132 AGAGGTGAGTGTATAGTACTCCCTT 59.806 44.000 18.16 6.36 41.62 3.95
325 328 5.447757 AGGTGAGTGTATAGTACTCCCTTC 58.552 45.833 0.00 0.00 43.00 3.46
326 329 4.583907 GGTGAGTGTATAGTACTCCCTTCC 59.416 50.000 0.00 7.65 43.00 3.46
327 330 5.198965 GTGAGTGTATAGTACTCCCTTCCA 58.801 45.833 0.00 0.00 43.00 3.53
328 331 5.834204 GTGAGTGTATAGTACTCCCTTCCAT 59.166 44.000 0.00 0.00 43.00 3.41
329 332 6.324254 GTGAGTGTATAGTACTCCCTTCCATT 59.676 42.308 0.00 0.00 43.00 3.16
330 333 6.901300 TGAGTGTATAGTACTCCCTTCCATTT 59.099 38.462 0.00 0.00 43.00 2.32
331 334 7.069578 TGAGTGTATAGTACTCCCTTCCATTTC 59.930 40.741 0.00 0.00 43.00 2.17
332 335 7.133483 AGTGTATAGTACTCCCTTCCATTTCT 58.867 38.462 0.00 0.00 0.00 2.52
333 336 7.288158 AGTGTATAGTACTCCCTTCCATTTCTC 59.712 40.741 0.00 0.00 0.00 2.87
334 337 6.553852 TGTATAGTACTCCCTTCCATTTCTCC 59.446 42.308 0.00 0.00 0.00 3.71
335 338 3.803340 AGTACTCCCTTCCATTTCTCCA 58.197 45.455 0.00 0.00 0.00 3.86
336 339 4.175962 AGTACTCCCTTCCATTTCTCCAA 58.824 43.478 0.00 0.00 0.00 3.53
337 340 3.441500 ACTCCCTTCCATTTCTCCAAC 57.558 47.619 0.00 0.00 0.00 3.77
338 341 2.716424 ACTCCCTTCCATTTCTCCAACA 59.284 45.455 0.00 0.00 0.00 3.33
339 342 3.140144 ACTCCCTTCCATTTCTCCAACAA 59.860 43.478 0.00 0.00 0.00 2.83
340 343 3.760684 CTCCCTTCCATTTCTCCAACAAG 59.239 47.826 0.00 0.00 0.00 3.16
341 344 3.140144 TCCCTTCCATTTCTCCAACAAGT 59.860 43.478 0.00 0.00 0.00 3.16
342 345 4.352595 TCCCTTCCATTTCTCCAACAAGTA 59.647 41.667 0.00 0.00 0.00 2.24
343 346 5.015178 TCCCTTCCATTTCTCCAACAAGTAT 59.985 40.000 0.00 0.00 0.00 2.12
344 347 5.716703 CCCTTCCATTTCTCCAACAAGTATT 59.283 40.000 0.00 0.00 0.00 1.89
345 348 6.211384 CCCTTCCATTTCTCCAACAAGTATTT 59.789 38.462 0.00 0.00 0.00 1.40
346 349 7.256296 CCCTTCCATTTCTCCAACAAGTATTTT 60.256 37.037 0.00 0.00 0.00 1.82
347 350 7.814587 CCTTCCATTTCTCCAACAAGTATTTTC 59.185 37.037 0.00 0.00 0.00 2.29
348 351 7.831691 TCCATTTCTCCAACAAGTATTTTCA 57.168 32.000 0.00 0.00 0.00 2.69
349 352 8.243961 TCCATTTCTCCAACAAGTATTTTCAA 57.756 30.769 0.00 0.00 0.00 2.69
350 353 8.700051 TCCATTTCTCCAACAAGTATTTTCAAA 58.300 29.630 0.00 0.00 0.00 2.69
351 354 9.492973 CCATTTCTCCAACAAGTATTTTCAAAT 57.507 29.630 0.00 0.00 0.00 2.32
355 358 9.748708 TTCTCCAACAAGTATTTTCAAATGAAG 57.251 29.630 0.00 0.00 35.21 3.02
356 359 8.359642 TCTCCAACAAGTATTTTCAAATGAAGG 58.640 33.333 0.00 0.00 35.21 3.46
357 360 7.441017 TCCAACAAGTATTTTCAAATGAAGGG 58.559 34.615 0.00 0.00 35.21 3.95
358 361 7.288852 TCCAACAAGTATTTTCAAATGAAGGGA 59.711 33.333 0.00 0.00 35.21 4.20
359 362 7.599998 CCAACAAGTATTTTCAAATGAAGGGAG 59.400 37.037 0.00 0.00 35.21 4.30
388 391 9.155053 GATCTTAACCGTTGATTTTATTTAGCG 57.845 33.333 0.00 0.00 0.00 4.26
390 393 4.625972 ACCGTTGATTTTATTTAGCGGG 57.374 40.909 0.00 0.00 41.88 6.13
396 402 6.402766 CGTTGATTTTATTTAGCGGGTCTGAA 60.403 38.462 0.00 0.00 0.00 3.02
405 411 6.534475 TTTAGCGGGTCTGAATAACTCTTA 57.466 37.500 0.00 0.00 0.00 2.10
407 413 3.132467 AGCGGGTCTGAATAACTCTTACC 59.868 47.826 0.00 0.00 0.00 2.85
411 417 5.127356 CGGGTCTGAATAACTCTTACCTTCT 59.873 44.000 0.00 0.00 32.83 2.85
418 424 8.075761 TGAATAACTCTTACCTTCTTACCTCC 57.924 38.462 0.00 0.00 0.00 4.30
426 432 3.256704 ACCTTCTTACCTCCCATGTGAA 58.743 45.455 0.00 0.00 0.00 3.18
431 437 5.576563 TCTTACCTCCCATGTGAAAAGAA 57.423 39.130 0.00 0.00 0.00 2.52
432 438 5.560724 TCTTACCTCCCATGTGAAAAGAAG 58.439 41.667 0.00 0.00 0.00 2.85
437 443 3.754965 TCCCATGTGAAAAGAAGAGGTG 58.245 45.455 0.00 0.00 0.00 4.00
438 444 3.394274 TCCCATGTGAAAAGAAGAGGTGA 59.606 43.478 0.00 0.00 0.00 4.02
440 446 3.755378 CCATGTGAAAAGAAGAGGTGAGG 59.245 47.826 0.00 0.00 0.00 3.86
441 447 4.505566 CCATGTGAAAAGAAGAGGTGAGGA 60.506 45.833 0.00 0.00 0.00 3.71
442 448 4.073293 TGTGAAAAGAAGAGGTGAGGAC 57.927 45.455 0.00 0.00 0.00 3.85
443 449 3.711704 TGTGAAAAGAAGAGGTGAGGACT 59.288 43.478 0.00 0.00 0.00 3.85
445 451 5.544176 TGTGAAAAGAAGAGGTGAGGACTAT 59.456 40.000 0.00 0.00 0.00 2.12
446 452 5.872070 GTGAAAAGAAGAGGTGAGGACTATG 59.128 44.000 0.00 0.00 0.00 2.23
447 453 5.544176 TGAAAAGAAGAGGTGAGGACTATGT 59.456 40.000 0.00 0.00 0.00 2.29
448 454 6.043243 TGAAAAGAAGAGGTGAGGACTATGTT 59.957 38.462 0.00 0.00 0.00 2.71
451 457 7.554959 AAGAAGAGGTGAGGACTATGTTAAA 57.445 36.000 0.00 0.00 0.00 1.52
454 460 8.606830 AGAAGAGGTGAGGACTATGTTAAAATT 58.393 33.333 0.00 0.00 0.00 1.82
455 461 8.567285 AAGAGGTGAGGACTATGTTAAAATTG 57.433 34.615 0.00 0.00 0.00 2.32
456 462 6.599638 AGAGGTGAGGACTATGTTAAAATTGC 59.400 38.462 0.00 0.00 0.00 3.56
457 463 6.485171 AGGTGAGGACTATGTTAAAATTGCT 58.515 36.000 0.00 0.00 0.00 3.91
458 464 6.599638 AGGTGAGGACTATGTTAAAATTGCTC 59.400 38.462 0.00 0.00 0.00 4.26
462 468 5.294552 AGGACTATGTTAAAATTGCTCTCGC 59.705 40.000 0.00 0.00 0.00 5.03
485 911 2.467566 TTTCCTTAACTGAGACCGGC 57.532 50.000 0.00 0.00 0.00 6.13
487 913 0.252103 TCCTTAACTGAGACCGGCCT 60.252 55.000 0.00 0.00 0.00 5.19
508 934 1.826385 CTCCTTGTCCACCACCAATC 58.174 55.000 0.00 0.00 0.00 2.67
535 961 1.003464 TGTGTCCATGATCAGTGGTGG 59.997 52.381 18.08 13.32 37.96 4.61
538 964 0.035152 TCCATGATCAGTGGTGGCAC 60.035 55.000 9.70 9.70 37.96 5.01
553 979 1.442017 GCACGTTTGGAATGGCGAC 60.442 57.895 0.00 0.00 0.00 5.19
570 996 1.264288 CGACAAGACCAAAGCACTTCC 59.736 52.381 0.00 0.00 0.00 3.46
579 1005 1.744320 AAAGCACTTCCGCCAAACCC 61.744 55.000 0.00 0.00 0.00 4.11
590 1016 1.334243 CGCCAAACCCGACAAAACTTA 59.666 47.619 0.00 0.00 0.00 2.24
591 1017 2.603652 CGCCAAACCCGACAAAACTTAG 60.604 50.000 0.00 0.00 0.00 2.18
592 1018 2.860971 GCCAAACCCGACAAAACTTAGC 60.861 50.000 0.00 0.00 0.00 3.09
594 1020 3.067601 CCAAACCCGACAAAACTTAGCTT 59.932 43.478 0.00 0.00 0.00 3.74
595 1021 4.276431 CCAAACCCGACAAAACTTAGCTTA 59.724 41.667 0.00 0.00 0.00 3.09
596 1022 5.449304 CAAACCCGACAAAACTTAGCTTAG 58.551 41.667 0.00 0.00 0.00 2.18
597 1023 4.347360 ACCCGACAAAACTTAGCTTAGT 57.653 40.909 0.00 0.00 0.00 2.24
600 1026 4.312443 CCGACAAAACTTAGCTTAGTCCA 58.688 43.478 5.74 0.00 0.00 4.02
601 1027 4.753107 CCGACAAAACTTAGCTTAGTCCAA 59.247 41.667 5.74 0.00 0.00 3.53
605 1031 5.889289 ACAAAACTTAGCTTAGTCCAACCAA 59.111 36.000 5.74 0.00 0.00 3.67
637 1063 8.988934 GTTGATACACTTTCTTTACATCAGACA 58.011 33.333 0.00 0.00 0.00 3.41
638 1064 8.534333 TGATACACTTTCTTTACATCAGACAC 57.466 34.615 0.00 0.00 0.00 3.67
646 1072 9.868277 CTTTCTTTACATCAGACACTAGAAGAT 57.132 33.333 0.00 0.00 0.00 2.40
726 1156 7.537596 TTAACATGGGAAATGAGTTGTTGAT 57.462 32.000 0.00 0.00 0.00 2.57
727 1157 8.642935 TTAACATGGGAAATGAGTTGTTGATA 57.357 30.769 0.00 0.00 0.00 2.15
728 1158 6.515272 ACATGGGAAATGAGTTGTTGATAC 57.485 37.500 0.00 0.00 0.00 2.24
729 1159 6.248433 ACATGGGAAATGAGTTGTTGATACT 58.752 36.000 0.00 0.00 0.00 2.12
730 1160 6.375455 ACATGGGAAATGAGTTGTTGATACTC 59.625 38.462 0.00 0.00 41.86 2.59
731 1161 5.253330 TGGGAAATGAGTTGTTGATACTCC 58.747 41.667 0.00 0.00 41.02 3.85
732 1162 4.640647 GGGAAATGAGTTGTTGATACTCCC 59.359 45.833 0.00 0.00 41.02 4.30
733 1163 5.501156 GGAAATGAGTTGTTGATACTCCCT 58.499 41.667 0.00 0.00 41.02 4.20
734 1164 5.946377 GGAAATGAGTTGTTGATACTCCCTT 59.054 40.000 0.00 0.00 41.02 3.95
735 1165 6.094186 GGAAATGAGTTGTTGATACTCCCTTC 59.906 42.308 0.00 0.00 41.02 3.46
736 1166 5.762179 ATGAGTTGTTGATACTCCCTTCA 57.238 39.130 0.00 0.00 41.02 3.02
737 1167 5.762179 TGAGTTGTTGATACTCCCTTCAT 57.238 39.130 0.00 0.00 41.02 2.57
738 1168 6.867519 TGAGTTGTTGATACTCCCTTCATA 57.132 37.500 0.00 0.00 41.02 2.15
739 1169 7.252612 TGAGTTGTTGATACTCCCTTCATAA 57.747 36.000 0.00 0.00 41.02 1.90
740 1170 7.685481 TGAGTTGTTGATACTCCCTTCATAAA 58.315 34.615 0.00 0.00 41.02 1.40
741 1171 7.824289 TGAGTTGTTGATACTCCCTTCATAAAG 59.176 37.037 0.00 0.00 41.02 1.85
742 1172 7.918076 AGTTGTTGATACTCCCTTCATAAAGA 58.082 34.615 0.00 0.00 34.14 2.52
743 1173 8.383175 AGTTGTTGATACTCCCTTCATAAAGAA 58.617 33.333 0.00 0.00 34.14 2.52
744 1174 9.010029 GTTGTTGATACTCCCTTCATAAAGAAA 57.990 33.333 0.00 0.00 35.40 2.52
745 1175 9.753674 TTGTTGATACTCCCTTCATAAAGAAAT 57.246 29.630 0.00 0.00 35.40 2.17
784 1214 9.654663 AGATCACTAAAGTATTGGTCTAAACAC 57.345 33.333 0.00 0.00 28.37 3.32
785 1215 9.654663 GATCACTAAAGTATTGGTCTAAACACT 57.345 33.333 0.00 0.00 0.00 3.55
787 1217 9.841295 TCACTAAAGTATTGGTCTAAACACTTT 57.159 29.630 13.16 13.16 39.23 2.66
796 1226 8.934023 ATTGGTCTAAACACTTTCTTTATGGA 57.066 30.769 0.00 0.00 0.00 3.41
797 1227 7.979444 TGGTCTAAACACTTTCTTTATGGAG 57.021 36.000 0.00 0.00 0.00 3.86
798 1228 6.940298 TGGTCTAAACACTTTCTTTATGGAGG 59.060 38.462 0.00 0.00 0.00 4.30
799 1229 6.374613 GGTCTAAACACTTTCTTTATGGAGGG 59.625 42.308 0.00 0.00 0.00 4.30
800 1230 7.166167 GTCTAAACACTTTCTTTATGGAGGGA 58.834 38.462 0.00 0.00 0.00 4.20
801 1231 7.334671 GTCTAAACACTTTCTTTATGGAGGGAG 59.665 40.741 0.00 0.00 0.00 4.30
805 1235 5.785940 ACACTTTCTTTATGGAGGGAGTACT 59.214 40.000 0.00 0.00 0.00 2.73
818 1248 7.598248 TGGAGGGAGTACTTGATATTACCTTA 58.402 38.462 0.00 0.00 0.00 2.69
895 1329 4.473444 AGGAAATGTTCAGCTTCCTTTCA 58.527 39.130 11.03 0.00 45.37 2.69
896 1330 4.279420 AGGAAATGTTCAGCTTCCTTTCAC 59.721 41.667 11.03 0.00 45.37 3.18
897 1331 4.279420 GGAAATGTTCAGCTTCCTTTCACT 59.721 41.667 8.36 0.00 36.48 3.41
898 1332 5.221322 GGAAATGTTCAGCTTCCTTTCACTT 60.221 40.000 8.36 0.00 36.48 3.16
929 1367 6.202188 CAGCAAATTTGAAATGTTCAGCTTCT 59.798 34.615 22.31 1.17 41.38 2.85
1009 1447 1.301244 CTTCACGGCAGCTGTCAGT 60.301 57.895 20.11 14.19 0.00 3.41
1051 1489 3.818773 ACTTACCATTTTGACGGAAGGTG 59.181 43.478 0.00 0.00 0.00 4.00
1056 1494 0.749818 TTTTGACGGAAGGTGCAGCA 60.750 50.000 19.63 0.00 0.00 4.41
1066 1504 0.392193 AGGTGCAGCAGAATTCCTCG 60.392 55.000 19.63 0.00 0.00 4.63
1081 1519 1.028905 CCTCGTGGCCTTTTGACAAA 58.971 50.000 3.32 0.00 0.00 2.83
1156 1681 6.767902 ACTTGCTGGATCGTATCATGTTTATT 59.232 34.615 0.00 0.00 0.00 1.40
1195 1720 4.261072 CGCTGATCATGCAAGAAGCTAATT 60.261 41.667 12.36 0.00 45.94 1.40
1200 1725 8.151141 TGATCATGCAAGAAGCTAATTAGAAG 57.849 34.615 16.85 0.00 45.94 2.85
1201 1726 6.369059 TCATGCAAGAAGCTAATTAGAAGC 57.631 37.500 16.85 3.46 45.94 3.86
1269 1874 1.981256 TTGTTCTCCACCTTGCTTCC 58.019 50.000 0.00 0.00 0.00 3.46
1414 2028 1.979155 CTCGACTCTGACCCCAGCA 60.979 63.158 0.00 0.00 40.20 4.41
1606 2235 5.473504 GGTAGCATAATATGGACAAACCCAG 59.526 44.000 2.13 0.00 39.97 4.45
1671 2300 0.037232 GCAACCTCCAGTTACTCGCT 60.037 55.000 0.00 0.00 36.18 4.93
1741 2370 3.447025 CTCCTCCCGGGTCAATCGC 62.447 68.421 22.86 0.00 36.25 4.58
1911 2567 0.739813 GCACTAACACCTACCAGCCG 60.740 60.000 0.00 0.00 0.00 5.52
2106 2770 0.909610 AGAACGCCATGGGAAGGAGA 60.910 55.000 15.13 0.00 0.00 3.71
2299 2966 0.538057 CTGCACACAGGGGTTCATGT 60.538 55.000 0.00 0.00 40.48 3.21
2409 3082 0.615331 ATTCGCACACCACAGAGGAT 59.385 50.000 0.00 0.00 41.22 3.24
2433 3106 3.077359 GTGTGCAGACTCTTGCCTAAAT 58.923 45.455 6.76 0.00 43.43 1.40
2501 3174 2.779430 AGATGGTGTCATTGGCAGGATA 59.221 45.455 0.00 0.00 32.98 2.59
3441 4126 7.669427 AGATTGAGGTTTTGTTGCATAATGAA 58.331 30.769 0.00 0.00 0.00 2.57
3580 4265 0.939577 CGTGGTTGAGGTCGACACTG 60.940 60.000 18.91 0.00 31.82 3.66
3601 4286 1.142748 CCTGCTCCTACAAGCTCCG 59.857 63.158 0.00 0.00 42.94 4.63
3809 4534 8.091449 GCCTTGTAGCTATTACATGTCTTCTAT 58.909 37.037 0.00 0.00 41.72 1.98
3835 4745 5.186198 AGTATTACTTCATTGTGCTCCACC 58.814 41.667 0.00 0.00 32.73 4.61
3872 4782 6.071728 CCTTTGGTTTGAGCACTAATTCATCT 60.072 38.462 0.00 0.00 0.00 2.90
3879 4791 9.415544 GTTTGAGCACTAATTCATCTTGATTTT 57.584 29.630 0.00 0.00 0.00 1.82
3963 4897 2.091541 AGGAAAACATACCACATGGCG 58.908 47.619 0.00 0.00 39.32 5.69
3965 4899 2.490115 GGAAAACATACCACATGGCGAA 59.510 45.455 0.00 0.00 39.32 4.70
4074 5134 1.691434 TGAACTTGGTTGGGCATTTCC 59.309 47.619 0.00 0.00 0.00 3.13
4218 5369 7.375834 TGTCGAACAGATACTAACAGAACAAT 58.624 34.615 0.00 0.00 0.00 2.71
4248 5399 7.643123 AGGTGAATGAATAATAACCTTGGAGT 58.357 34.615 0.00 0.00 33.57 3.85
4252 5403 9.177608 TGAATGAATAATAACCTTGGAGTTGAG 57.822 33.333 0.00 0.00 0.00 3.02
4253 5404 8.525290 AATGAATAATAACCTTGGAGTTGAGG 57.475 34.615 0.00 0.00 39.02 3.86
4255 5406 6.884295 TGAATAATAACCTTGGAGTTGAGGTG 59.116 38.462 0.00 0.00 45.32 4.00
4256 5407 4.993705 AATAACCTTGGAGTTGAGGTGA 57.006 40.909 0.00 0.00 45.32 4.02
4257 5408 2.938956 AACCTTGGAGTTGAGGTGAG 57.061 50.000 0.00 0.00 45.32 3.51
4258 5409 1.807814 ACCTTGGAGTTGAGGTGAGT 58.192 50.000 0.00 0.00 44.40 3.41
4280 5439 9.733556 TGAGTATAATAACAAGAAAGAAAGGCA 57.266 29.630 0.00 0.00 0.00 4.75
4300 5459 7.112452 AGGCATGAAGGGTGAATAAATAAAC 57.888 36.000 0.00 0.00 0.00 2.01
4303 5462 6.559810 CATGAAGGGTGAATAAATAAACGCA 58.440 36.000 0.00 0.00 0.00 5.24
4308 5467 5.810074 AGGGTGAATAAATAAACGCATTTGC 59.190 36.000 0.00 0.00 37.78 3.68
4333 5492 3.181528 GCAAATTTCATTGTCCATGTGCG 60.182 43.478 0.00 0.00 34.06 5.34
4529 5781 6.688073 ATAGATTCCAGATTCCGGTTATGT 57.312 37.500 0.00 0.00 0.00 2.29
4691 5967 8.442632 TTCAGCTAGTCATAAATCATGGAAAG 57.557 34.615 0.00 0.00 35.16 2.62
4692 5968 7.568349 TCAGCTAGTCATAAATCATGGAAAGT 58.432 34.615 0.00 0.00 35.16 2.66
4695 5971 9.331282 AGCTAGTCATAAATCATGGAAAGTAAC 57.669 33.333 0.00 0.00 35.16 2.50
4911 6195 4.026744 TCCCTGTTCTGAGATAAGACTGG 58.973 47.826 2.10 2.10 0.00 4.00
5003 6344 0.543749 AGTGGTTCCTGCTAGGATGC 59.456 55.000 5.83 3.32 45.34 3.91
5022 6363 4.100279 TGCCTCTCATAAGTCCTCGATA 57.900 45.455 0.00 0.00 0.00 2.92
5204 6546 1.375396 CGGCGATTCACCACTTCCA 60.375 57.895 0.00 0.00 0.00 3.53
5286 6636 3.576550 TGTGAACTGTATAGTCAGTGCCA 59.423 43.478 0.00 0.38 46.25 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.507944 GCGCCCTGATGAGGATGT 59.492 61.111 0.00 0.00 42.93 3.06
17 18 3.499737 GTCGTTGGCGCCCTGATG 61.500 66.667 26.77 15.35 38.14 3.07
18 19 4.778143 GGTCGTTGGCGCCCTGAT 62.778 66.667 26.77 0.00 32.73 2.90
30 31 1.367840 GTGTCCTTGCTCTGGTCGT 59.632 57.895 0.00 0.00 0.00 4.34
61 62 0.104120 GCCCTCTTTTGCCGTTGTTT 59.896 50.000 0.00 0.00 0.00 2.83
68 69 1.669604 GTAGCTAGCCCTCTTTTGCC 58.330 55.000 12.13 0.00 0.00 4.52
72 73 1.687297 GCGGGTAGCTAGCCCTCTTT 61.687 60.000 31.20 0.00 43.92 2.52
90 91 6.418956 TGACGAATTCGCAATATTTCTTAGC 58.581 36.000 27.03 0.00 44.43 3.09
96 97 7.218773 CAGATTGTTGACGAATTCGCAATATTT 59.781 33.333 27.77 19.58 44.43 1.40
98 99 6.194463 CAGATTGTTGACGAATTCGCAATAT 58.806 36.000 27.77 24.04 44.43 1.28
100 101 4.406069 CAGATTGTTGACGAATTCGCAAT 58.594 39.130 27.77 25.40 44.43 3.56
101 102 3.809234 CAGATTGTTGACGAATTCGCAA 58.191 40.909 27.03 25.27 44.43 4.85
102 103 2.412716 GCAGATTGTTGACGAATTCGCA 60.413 45.455 27.03 21.44 44.43 5.10
103 104 2.169179 GCAGATTGTTGACGAATTCGC 58.831 47.619 27.03 19.24 44.43 4.70
107 108 2.877786 TGTGTGCAGATTGTTGACGAAT 59.122 40.909 0.00 0.00 0.00 3.34
111 112 4.037690 GTCTTTGTGTGCAGATTGTTGAC 58.962 43.478 0.00 0.00 0.00 3.18
137 138 3.716006 CCCAGCAGCGTTGTGTCG 61.716 66.667 0.00 0.00 0.00 4.35
150 151 0.680618 TGTTTGGCAATGCTTCCCAG 59.319 50.000 4.82 0.00 0.00 4.45
189 190 3.129113 TGCTTGTATGCTGCAGTTTATGG 59.871 43.478 16.64 2.21 32.55 2.74
215 216 1.296392 TGGAAGCACCACCGATCAG 59.704 57.895 0.00 0.00 44.64 2.90
254 257 1.068816 ACCATGTTAAAAACGCTCGGC 60.069 47.619 0.00 0.00 0.00 5.54
261 264 6.008331 AGGTTAGAGGGACCATGTTAAAAAC 58.992 40.000 0.00 0.00 39.71 2.43
281 284 9.730489 TCACCTCTCATGTGAAAACGTAAGGTT 62.730 40.741 0.00 0.00 39.23 3.50
286 289 4.038763 ACTCACCTCTCATGTGAAAACGTA 59.961 41.667 0.00 0.00 41.85 3.57
287 290 3.181465 ACTCACCTCTCATGTGAAAACGT 60.181 43.478 0.00 0.00 41.85 3.99
289 292 4.130118 ACACTCACCTCTCATGTGAAAAC 58.870 43.478 0.00 0.00 41.85 2.43
301 304 5.051409 AGGGAGTACTATACACTCACCTC 57.949 47.826 0.00 0.00 45.81 3.85
303 306 4.583907 GGAAGGGAGTACTATACACTCACC 59.416 50.000 0.00 8.02 45.81 4.02
304 307 5.198965 TGGAAGGGAGTACTATACACTCAC 58.801 45.833 0.00 7.63 45.15 3.51
306 309 6.980416 AATGGAAGGGAGTACTATACACTC 57.020 41.667 0.00 2.36 41.43 3.51
309 312 6.553852 GGAGAAATGGAAGGGAGTACTATACA 59.446 42.308 0.00 0.00 0.00 2.29
314 317 3.803340 TGGAGAAATGGAAGGGAGTACT 58.197 45.455 0.00 0.00 0.00 2.73
315 318 4.262617 GTTGGAGAAATGGAAGGGAGTAC 58.737 47.826 0.00 0.00 0.00 2.73
316 319 3.913799 TGTTGGAGAAATGGAAGGGAGTA 59.086 43.478 0.00 0.00 0.00 2.59
318 321 3.439857 TGTTGGAGAAATGGAAGGGAG 57.560 47.619 0.00 0.00 0.00 4.30
319 322 3.140144 ACTTGTTGGAGAAATGGAAGGGA 59.860 43.478 0.00 0.00 0.00 4.20
320 323 3.500343 ACTTGTTGGAGAAATGGAAGGG 58.500 45.455 0.00 0.00 0.00 3.95
321 324 6.840780 AATACTTGTTGGAGAAATGGAAGG 57.159 37.500 0.00 0.00 0.00 3.46
322 325 8.359642 TGAAAATACTTGTTGGAGAAATGGAAG 58.640 33.333 0.00 0.00 0.00 3.46
323 326 8.243961 TGAAAATACTTGTTGGAGAAATGGAA 57.756 30.769 0.00 0.00 0.00 3.53
324 327 7.831691 TGAAAATACTTGTTGGAGAAATGGA 57.168 32.000 0.00 0.00 0.00 3.41
325 328 8.885494 TTTGAAAATACTTGTTGGAGAAATGG 57.115 30.769 0.00 0.00 0.00 3.16
329 332 9.748708 CTTCATTTGAAAATACTTGTTGGAGAA 57.251 29.630 0.00 0.00 33.07 2.87
330 333 8.359642 CCTTCATTTGAAAATACTTGTTGGAGA 58.640 33.333 0.00 0.00 33.07 3.71
331 334 7.599998 CCCTTCATTTGAAAATACTTGTTGGAG 59.400 37.037 0.00 0.00 33.07 3.86
332 335 7.288852 TCCCTTCATTTGAAAATACTTGTTGGA 59.711 33.333 0.00 0.00 33.07 3.53
333 336 7.441017 TCCCTTCATTTGAAAATACTTGTTGG 58.559 34.615 0.00 0.00 33.07 3.77
334 337 8.143835 ACTCCCTTCATTTGAAAATACTTGTTG 58.856 33.333 0.00 0.00 33.07 3.33
335 338 8.250143 ACTCCCTTCATTTGAAAATACTTGTT 57.750 30.769 0.00 0.00 33.07 2.83
336 339 7.839680 ACTCCCTTCATTTGAAAATACTTGT 57.160 32.000 0.00 0.00 33.07 3.16
337 340 9.231297 TCTACTCCCTTCATTTGAAAATACTTG 57.769 33.333 0.00 0.00 33.07 3.16
338 341 9.981460 ATCTACTCCCTTCATTTGAAAATACTT 57.019 29.630 0.00 0.00 33.07 2.24
339 342 9.620259 GATCTACTCCCTTCATTTGAAAATACT 57.380 33.333 0.00 0.00 33.07 2.12
340 343 9.620259 AGATCTACTCCCTTCATTTGAAAATAC 57.380 33.333 0.00 0.00 33.07 1.89
344 347 9.449719 GTTAAGATCTACTCCCTTCATTTGAAA 57.550 33.333 0.00 0.00 33.07 2.69
345 348 8.047310 GGTTAAGATCTACTCCCTTCATTTGAA 58.953 37.037 0.00 0.00 0.00 2.69
346 349 7.565680 GGTTAAGATCTACTCCCTTCATTTGA 58.434 38.462 0.00 0.00 0.00 2.69
347 350 6.480320 CGGTTAAGATCTACTCCCTTCATTTG 59.520 42.308 0.00 0.00 0.00 2.32
348 351 6.156429 ACGGTTAAGATCTACTCCCTTCATTT 59.844 38.462 0.00 0.00 0.00 2.32
349 352 5.661759 ACGGTTAAGATCTACTCCCTTCATT 59.338 40.000 0.00 0.00 0.00 2.57
350 353 5.209659 ACGGTTAAGATCTACTCCCTTCAT 58.790 41.667 0.00 0.00 0.00 2.57
351 354 4.607239 ACGGTTAAGATCTACTCCCTTCA 58.393 43.478 0.00 0.00 0.00 3.02
352 355 5.126707 TCAACGGTTAAGATCTACTCCCTTC 59.873 44.000 0.00 0.00 0.00 3.46
353 356 5.021458 TCAACGGTTAAGATCTACTCCCTT 58.979 41.667 0.00 0.00 0.00 3.95
354 357 4.607239 TCAACGGTTAAGATCTACTCCCT 58.393 43.478 0.00 0.00 0.00 4.20
355 358 4.996788 TCAACGGTTAAGATCTACTCCC 57.003 45.455 0.00 0.00 0.00 4.30
356 359 7.845066 AAAATCAACGGTTAAGATCTACTCC 57.155 36.000 0.00 0.00 0.00 3.85
367 370 5.647225 ACCCGCTAAATAAAATCAACGGTTA 59.353 36.000 0.00 0.00 37.74 2.85
384 387 4.340381 GGTAAGAGTTATTCAGACCCGCTA 59.660 45.833 0.00 0.00 30.40 4.26
387 390 5.127356 AGAAGGTAAGAGTTATTCAGACCCG 59.873 44.000 0.00 0.00 34.79 5.28
388 391 6.547930 AGAAGGTAAGAGTTATTCAGACCC 57.452 41.667 0.00 0.00 34.79 4.46
390 393 8.751242 AGGTAAGAAGGTAAGAGTTATTCAGAC 58.249 37.037 0.00 0.00 0.00 3.51
396 402 6.509386 TGGGAGGTAAGAAGGTAAGAGTTAT 58.491 40.000 0.00 0.00 0.00 1.89
405 411 2.915869 TCACATGGGAGGTAAGAAGGT 58.084 47.619 0.00 0.00 0.00 3.50
407 413 5.560724 TCTTTTCACATGGGAGGTAAGAAG 58.439 41.667 13.64 6.78 0.00 2.85
411 417 5.514834 CCTCTTCTTTTCACATGGGAGGTAA 60.515 44.000 0.00 0.00 35.66 2.85
418 424 3.755378 CCTCACCTCTTCTTTTCACATGG 59.245 47.826 0.00 0.00 0.00 3.66
426 432 7.554959 TTAACATAGTCCTCACCTCTTCTTT 57.445 36.000 0.00 0.00 0.00 2.52
431 437 6.599638 GCAATTTTAACATAGTCCTCACCTCT 59.400 38.462 0.00 0.00 0.00 3.69
432 438 6.599638 AGCAATTTTAACATAGTCCTCACCTC 59.400 38.462 0.00 0.00 0.00 3.85
437 443 6.938542 CGAGAGCAATTTTAACATAGTCCTC 58.061 40.000 0.00 0.00 0.00 3.71
438 444 6.910536 CGAGAGCAATTTTAACATAGTCCT 57.089 37.500 0.00 0.00 0.00 3.85
456 462 4.315803 TCAGTTAAGGAAAAAGGCGAGAG 58.684 43.478 0.00 0.00 0.00 3.20
457 463 4.039973 TCTCAGTTAAGGAAAAAGGCGAGA 59.960 41.667 0.00 0.00 0.00 4.04
458 464 4.152580 GTCTCAGTTAAGGAAAAAGGCGAG 59.847 45.833 0.00 0.00 0.00 5.03
462 468 3.751698 CCGGTCTCAGTTAAGGAAAAAGG 59.248 47.826 0.00 0.00 0.00 3.11
485 911 1.302832 GTGGTGGACAAGGAGCAGG 60.303 63.158 0.00 0.00 0.00 4.85
487 913 1.640593 TTGGTGGTGGACAAGGAGCA 61.641 55.000 0.00 0.00 0.00 4.26
508 934 3.268330 CTGATCATGGACACACTTGAGG 58.732 50.000 0.00 0.00 0.00 3.86
535 961 1.442017 GTCGCCATTCCAAACGTGC 60.442 57.895 0.00 0.00 0.00 5.34
538 964 0.871722 TCTTGTCGCCATTCCAAACG 59.128 50.000 0.00 0.00 0.00 3.60
553 979 0.040067 GCGGAAGTGCTTTGGTCTTG 60.040 55.000 0.00 0.00 0.00 3.02
570 996 0.101579 AAGTTTTGTCGGGTTTGGCG 59.898 50.000 0.00 0.00 0.00 5.69
579 1005 5.333875 GGTTGGACTAAGCTAAGTTTTGTCG 60.334 44.000 0.00 0.00 32.01 4.35
590 1016 3.584848 ACTGATCTTGGTTGGACTAAGCT 59.415 43.478 2.34 0.00 36.73 3.74
591 1017 3.944087 ACTGATCTTGGTTGGACTAAGC 58.056 45.455 0.00 0.00 36.73 3.09
592 1018 5.551233 TCAACTGATCTTGGTTGGACTAAG 58.449 41.667 18.88 0.00 41.91 2.18
594 1020 5.762179 ATCAACTGATCTTGGTTGGACTA 57.238 39.130 18.88 7.27 41.91 2.59
595 1021 4.647564 ATCAACTGATCTTGGTTGGACT 57.352 40.909 18.88 8.19 41.91 3.85
596 1022 5.122396 GTGTATCAACTGATCTTGGTTGGAC 59.878 44.000 18.88 17.25 41.91 4.02
597 1023 5.013079 AGTGTATCAACTGATCTTGGTTGGA 59.987 40.000 18.88 11.01 41.91 3.53
600 1026 7.227156 AGAAAGTGTATCAACTGATCTTGGTT 58.773 34.615 0.00 0.00 36.05 3.67
601 1027 6.773638 AGAAAGTGTATCAACTGATCTTGGT 58.226 36.000 0.00 0.00 36.05 3.67
605 1031 9.950496 ATGTAAAGAAAGTGTATCAACTGATCT 57.050 29.630 0.00 0.00 36.05 2.75
693 1123 7.235399 ACTCATTTCCCATGTTAAATTCACCTT 59.765 33.333 0.00 0.00 0.00 3.50
698 1128 8.711457 CAACAACTCATTTCCCATGTTAAATTC 58.289 33.333 0.00 0.00 30.48 2.17
758 1188 9.654663 GTGTTTAGACCAATACTTTAGTGATCT 57.345 33.333 0.00 0.00 0.00 2.75
759 1189 9.654663 AGTGTTTAGACCAATACTTTAGTGATC 57.345 33.333 0.00 0.00 0.00 2.92
761 1191 9.841295 AAAGTGTTTAGACCAATACTTTAGTGA 57.159 29.630 6.54 0.00 34.62 3.41
771 1201 8.934023 TCCATAAAGAAAGTGTTTAGACCAAT 57.066 30.769 0.00 0.00 0.00 3.16
772 1202 7.447238 CCTCCATAAAGAAAGTGTTTAGACCAA 59.553 37.037 0.00 0.00 0.00 3.67
773 1203 6.940298 CCTCCATAAAGAAAGTGTTTAGACCA 59.060 38.462 0.00 0.00 0.00 4.02
774 1204 6.374613 CCCTCCATAAAGAAAGTGTTTAGACC 59.625 42.308 0.00 0.00 0.00 3.85
775 1205 7.166167 TCCCTCCATAAAGAAAGTGTTTAGAC 58.834 38.462 0.00 0.00 0.00 2.59
776 1206 7.017254 ACTCCCTCCATAAAGAAAGTGTTTAGA 59.983 37.037 0.00 0.00 0.00 2.10
777 1207 7.168905 ACTCCCTCCATAAAGAAAGTGTTTAG 58.831 38.462 0.00 0.00 0.00 1.85
778 1208 7.086685 ACTCCCTCCATAAAGAAAGTGTTTA 57.913 36.000 0.00 0.00 0.00 2.01
779 1209 5.953571 ACTCCCTCCATAAAGAAAGTGTTT 58.046 37.500 0.00 0.00 0.00 2.83
780 1210 5.584551 ACTCCCTCCATAAAGAAAGTGTT 57.415 39.130 0.00 0.00 0.00 3.32
781 1211 5.785940 AGTACTCCCTCCATAAAGAAAGTGT 59.214 40.000 0.00 0.00 0.00 3.55
782 1212 6.301169 AGTACTCCCTCCATAAAGAAAGTG 57.699 41.667 0.00 0.00 0.00 3.16
783 1213 6.500751 TCAAGTACTCCCTCCATAAAGAAAGT 59.499 38.462 0.00 0.00 0.00 2.66
784 1214 6.947464 TCAAGTACTCCCTCCATAAAGAAAG 58.053 40.000 0.00 0.00 0.00 2.62
785 1215 6.945636 TCAAGTACTCCCTCCATAAAGAAA 57.054 37.500 0.00 0.00 0.00 2.52
786 1216 8.798975 ATATCAAGTACTCCCTCCATAAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
787 1217 8.798975 AATATCAAGTACTCCCTCCATAAAGA 57.201 34.615 0.00 0.00 0.00 2.52
788 1218 9.930693 GTAATATCAAGTACTCCCTCCATAAAG 57.069 37.037 0.00 0.00 0.00 1.85
789 1219 8.877195 GGTAATATCAAGTACTCCCTCCATAAA 58.123 37.037 0.00 0.00 0.00 1.40
790 1220 8.239478 AGGTAATATCAAGTACTCCCTCCATAA 58.761 37.037 0.00 0.00 0.00 1.90
791 1221 7.776745 AGGTAATATCAAGTACTCCCTCCATA 58.223 38.462 0.00 0.00 0.00 2.74
792 1222 6.635021 AGGTAATATCAAGTACTCCCTCCAT 58.365 40.000 0.00 0.00 0.00 3.41
793 1223 6.039415 AGGTAATATCAAGTACTCCCTCCA 57.961 41.667 0.00 0.00 0.00 3.86
794 1224 6.997942 AAGGTAATATCAAGTACTCCCTCC 57.002 41.667 0.00 0.00 0.00 4.30
818 1248 7.443575 GCAGATGGATCACTTTATTGACTGTAT 59.556 37.037 0.00 0.00 0.00 2.29
896 1330 7.473027 ACATTTCAAATTTGCTGACTGAAAG 57.527 32.000 13.54 4.53 38.86 2.62
897 1331 7.548427 TGAACATTTCAAATTTGCTGACTGAAA 59.452 29.630 13.54 7.41 39.56 2.69
898 1332 7.040494 TGAACATTTCAAATTTGCTGACTGAA 58.960 30.769 13.54 0.00 36.59 3.02
929 1367 1.764851 CGCAATTTGCTGACCGAAAA 58.235 45.000 18.57 0.00 42.25 2.29
1009 1447 5.854010 AGTTCTCAGTCAACTCAGTGTAA 57.146 39.130 0.00 0.00 27.00 2.41
1051 1489 1.986575 GCCACGAGGAATTCTGCTGC 61.987 60.000 1.86 0.00 36.89 5.25
1056 1494 2.162681 CAAAAGGCCACGAGGAATTCT 58.837 47.619 5.01 0.00 36.89 2.40
1066 1504 3.791245 TGTCAATTTGTCAAAAGGCCAC 58.209 40.909 5.01 0.00 0.00 5.01
1081 1519 0.887933 GGTGGTTGGCGAATGTCAAT 59.112 50.000 0.00 0.00 42.59 2.57
1156 1681 0.536233 AGCGTGCCATTGTGGTGTAA 60.536 50.000 0.00 0.00 40.46 2.41
1246 1851 2.310538 AGCAAGGTGGAGAACAAAAGG 58.689 47.619 0.00 0.00 0.00 3.11
1414 2028 1.072965 CCAGACAGCAAGGAGGAACTT 59.927 52.381 0.00 0.00 41.55 2.66
1521 2135 3.890674 GACAACTCCGTGGCCATC 58.109 61.111 9.72 1.29 0.00 3.51
1606 2235 1.442148 CGGCTTGTAGGCTAGGGTC 59.558 63.158 0.00 0.00 38.85 4.46
1741 2370 1.077858 GAGCCTTTCCAGAGCCCAG 60.078 63.158 0.00 0.00 0.00 4.45
1911 2567 4.966787 TTGCCGGCCTGGTTGTCC 62.967 66.667 26.77 0.00 41.21 4.02
1922 2581 4.701956 AAGAAAATAGTCATGTTGCCGG 57.298 40.909 0.00 0.00 0.00 6.13
2106 2770 0.107410 TGACTGCCCACGACAAGTTT 60.107 50.000 0.00 0.00 0.00 2.66
2220 2887 0.321564 TTGGGCACTCACAATCGAGG 60.322 55.000 0.00 0.00 37.34 4.63
2299 2966 1.740332 TTCCCGTCACAACTCTGCGA 61.740 55.000 0.00 0.00 0.00 5.10
2409 3082 0.250038 GGCAAGAGTCTGCACACTGA 60.250 55.000 0.00 0.00 44.52 3.41
2501 3174 1.306141 TCTCCTCCTTGCCGTCCAT 60.306 57.895 0.00 0.00 0.00 3.41
3441 4126 3.338249 CAAATCCTCAATGGTGTCGTCT 58.662 45.455 0.00 0.00 37.07 4.18
3580 4265 1.137282 GGAGCTTGTAGGAGCAGGTAC 59.863 57.143 0.00 0.00 45.12 3.34
3601 4286 0.438830 GTCAACGGCGATGAACAGTC 59.561 55.000 21.50 5.23 0.00 3.51
3718 4428 7.655328 TGGTGAAACAATTACCATTCATGAAAC 59.345 33.333 13.09 0.48 39.43 2.78
3809 4534 7.335924 GGTGGAGCACAATGAAGTAATACTTAA 59.664 37.037 5.55 0.00 35.79 1.85
3818 4728 3.614092 CATAGGTGGAGCACAATGAAGT 58.386 45.455 0.00 0.00 35.86 3.01
3819 4729 2.357009 GCATAGGTGGAGCACAATGAAG 59.643 50.000 0.00 0.00 35.86 3.02
3821 4731 1.281577 TGCATAGGTGGAGCACAATGA 59.718 47.619 0.00 0.00 35.86 2.57
3835 4745 6.698766 GCTCAAACCAAAGGATTATTGCATAG 59.301 38.462 0.00 0.00 0.00 2.23
3883 4795 8.491045 AAATATCCTGGGACTTCAAAAAGAAA 57.509 30.769 0.00 0.00 35.40 2.52
3963 4897 0.526662 ATCTTGCTGCTGCTGCTTTC 59.473 50.000 27.67 6.29 40.48 2.62
3965 4899 0.966920 AAATCTTGCTGCTGCTGCTT 59.033 45.000 27.67 13.89 40.48 3.91
4074 5134 8.387190 TGAATTATGACTCATTGCTCTTATGG 57.613 34.615 0.00 0.00 0.00 2.74
4218 5369 9.184523 CAAGGTTATTATTCATTCACCTTACCA 57.815 33.333 1.15 0.00 41.70 3.25
4253 5404 9.989869 GCCTTTCTTTCTTGTTATTATACTCAC 57.010 33.333 0.00 0.00 0.00 3.51
4254 5405 9.733556 TGCCTTTCTTTCTTGTTATTATACTCA 57.266 29.630 0.00 0.00 0.00 3.41
4277 5436 5.977129 CGTTTATTTATTCACCCTTCATGCC 59.023 40.000 0.00 0.00 0.00 4.40
4278 5437 5.458779 GCGTTTATTTATTCACCCTTCATGC 59.541 40.000 0.00 0.00 0.00 4.06
4280 5439 6.767524 TGCGTTTATTTATTCACCCTTCAT 57.232 33.333 0.00 0.00 0.00 2.57
4303 5462 7.839925 CATGGACAATGAAATTTGCATGCAAAT 60.840 33.333 40.04 40.04 46.17 2.32
4308 5467 5.672570 GCACATGGACAATGAAATTTGCATG 60.673 40.000 0.00 0.18 42.59 4.06
4321 5480 0.888736 CCAAGGACGCACATGGACAA 60.889 55.000 0.00 0.00 34.82 3.18
4333 5492 0.668535 GACAAAGGCACACCAAGGAC 59.331 55.000 0.00 0.00 39.06 3.85
4545 5799 1.943340 GCAGCTGTTATCTTGTAGGCC 59.057 52.381 16.64 0.00 0.00 5.19
4640 5916 8.928733 AGACAAATGCATACATGAATTTTGAAC 58.071 29.630 0.00 0.00 42.04 3.18
4691 5967 2.352715 GGCCTGCAAAGGATGTTGTTAC 60.353 50.000 0.00 0.00 0.00 2.50
4692 5968 1.892474 GGCCTGCAAAGGATGTTGTTA 59.108 47.619 0.00 0.00 0.00 2.41
4695 5971 0.680618 TTGGCCTGCAAAGGATGTTG 59.319 50.000 3.32 0.00 0.00 3.33
4955 6296 2.906182 TATTCCTCGTGGCTGCGCAG 62.906 60.000 32.83 32.83 0.00 5.18
4965 6306 5.715753 ACCACTACTTTCTTCTATTCCTCGT 59.284 40.000 0.00 0.00 0.00 4.18
5003 6344 4.216687 GGTGTATCGAGGACTTATGAGAGG 59.783 50.000 0.00 0.00 0.00 3.69
5022 6363 1.062488 AAGAGGGTTCTGCAGGGTGT 61.062 55.000 15.13 0.00 32.79 4.16


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

AutoCloner maintained by Alex Coulton.