Multiple sequence alignment - TraesCS7A01G119400

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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 TraesCS7A01G119400 chr7A 100.000 2644 0 0 1 2644 76955235 76952592 0.000000e+00 4883.0
1 TraesCS7A01G119400 chr7A 86.602 515 62 5 5 516 76972500 76971990 1.780000e-156 562.0
2 TraesCS7A01G119400 chr7A 84.914 232 26 5 507 734 76972050 76971824 2.650000e-55 226.0
3 TraesCS7A01G119400 chr7D 91.299 816 58 5 951 1761 70905451 70904644 0.000000e+00 1101.0
4 TraesCS7A01G119400 chr7D 96.028 428 16 1 1082 1509 73117143 73116717 0.000000e+00 695.0
5 TraesCS7A01G119400 chr7D 89.924 526 30 6 2135 2644 70903615 70903097 0.000000e+00 656.0
6 TraesCS7A01G119400 chr7D 92.273 220 15 2 1921 2139 70903900 70903682 7.110000e-81 311.0
7 TraesCS7A01G119400 chr7D 82.022 356 54 3 29 375 571696897 571696543 7.160000e-76 294.0
8 TraesCS7A01G119400 chr7D 79.945 364 64 2 29 383 100990984 100991347 2.610000e-65 259.0
9 TraesCS7A01G119400 chr7D 77.665 394 71 8 58 435 571238136 571237744 9.520000e-55 224.0
10 TraesCS7A01G119400 chr7D 92.857 84 5 1 809 891 70905819 70905736 1.290000e-23 121.0
11 TraesCS7A01G119400 chr7B 91.184 828 42 18 942 1761 13329716 13328912 0.000000e+00 1096.0
12 TraesCS7A01G119400 chr7B 90.201 847 44 14 812 1633 16135776 16136608 0.000000e+00 1068.0
13 TraesCS7A01G119400 chr7B 85.201 723 60 29 814 1508 14980502 14981205 0.000000e+00 699.0
14 TraesCS7A01G119400 chr7B 88.528 523 40 7 2135 2644 13327415 13326900 1.340000e-172 616.0
15 TraesCS7A01G119400 chr7B 89.905 317 26 4 2328 2644 16137814 16138124 1.140000e-108 403.0
16 TraesCS7A01G119400 chr7B 91.144 271 24 0 1869 2139 13327753 13327483 4.160000e-98 368.0
17 TraesCS7A01G119400 chr7B 92.405 158 12 0 1869 2026 16137659 16137816 2.650000e-55 226.0
18 TraesCS7A01G119400 chr7B 86.473 207 18 9 542 744 16131659 16131859 4.430000e-53 219.0
19 TraesCS7A01G119400 chr7B 74.345 534 115 19 5 516 627296204 627295671 9.590000e-50 207.0
20 TraesCS7A01G119400 chr7B 74.447 497 86 19 47 503 463234378 463234873 2.700000e-40 176.0
21 TraesCS7A01G119400 chr7B 84.375 192 15 7 747 924 13330223 13330033 9.730000e-40 174.0
22 TraesCS7A01G119400 chr4D 83.661 967 101 34 813 1761 415583997 415583070 0.000000e+00 857.0
23 TraesCS7A01G119400 chr4D 80.757 317 57 4 60 372 344859739 344860055 7.310000e-61 244.0
24 TraesCS7A01G119400 chr4B 84.725 910 75 33 814 1696 512335510 512334638 0.000000e+00 852.0
25 TraesCS7A01G119400 chr4B 89.041 73 8 0 389 461 147372327 147372399 1.010000e-14 91.6
26 TraesCS7A01G119400 chr4B 78.788 132 23 4 389 516 665945240 665945110 1.690000e-12 84.2
27 TraesCS7A01G119400 chr4A 83.490 957 99 34 814 1747 48275171 48276091 0.000000e+00 837.0
28 TraesCS7A01G119400 chr4A 96.190 420 16 0 1087 1506 675854935 675855354 0.000000e+00 688.0
29 TraesCS7A01G119400 chr2A 81.044 364 53 8 25 375 688409898 688410258 2.590000e-70 276.0
30 TraesCS7A01G119400 chr2A 76.751 357 55 20 24 372 167945796 167946132 9.730000e-40 174.0
31 TraesCS7A01G119400 chr1D 80.822 365 59 7 23 378 235581784 235582146 2.590000e-70 276.0
32 TraesCS7A01G119400 chr1D 79.592 343 62 6 23 363 134685041 134685377 3.400000e-59 239.0
33 TraesCS7A01G119400 chr5B 79.630 270 50 5 5 269 429099690 429099421 3.470000e-44 189.0
34 TraesCS7A01G119400 chr5B 79.245 106 17 5 415 516 35499304 35499200 4.720000e-08 69.4
35 TraesCS7A01G119400 chr2B 73.506 502 83 21 53 507 145361271 145361769 7.630000e-31 145.0
36 TraesCS7A01G119400 chr2D 85.496 131 16 2 386 513 93650283 93650413 1.650000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G119400 chr7A 76952592 76955235 2643 True 4883.00 4883 100.00000 1 2644 1 chr7A.!!$R1 2643
1 TraesCS7A01G119400 chr7A 76971824 76972500 676 True 394.00 562 85.75800 5 734 2 chr7A.!!$R2 729
2 TraesCS7A01G119400 chr7D 70903097 70905819 2722 True 547.25 1101 91.58825 809 2644 4 chr7D.!!$R4 1835
3 TraesCS7A01G119400 chr7B 14980502 14981205 703 False 699.00 699 85.20100 814 1508 1 chr7B.!!$F1 694
4 TraesCS7A01G119400 chr7B 13326900 13330223 3323 True 563.50 1096 88.80775 747 2644 4 chr7B.!!$R2 1897
5 TraesCS7A01G119400 chr7B 16131659 16138124 6465 False 479.00 1068 89.74600 542 2644 4 chr7B.!!$F3 2102
6 TraesCS7A01G119400 chr7B 627295671 627296204 533 True 207.00 207 74.34500 5 516 1 chr7B.!!$R1 511
7 TraesCS7A01G119400 chr4D 415583070 415583997 927 True 857.00 857 83.66100 813 1761 1 chr4D.!!$R1 948
8 TraesCS7A01G119400 chr4B 512334638 512335510 872 True 852.00 852 84.72500 814 1696 1 chr4B.!!$R1 882
9 TraesCS7A01G119400 chr4A 48275171 48276091 920 False 837.00 837 83.49000 814 1747 1 chr4A.!!$F1 933

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
341 355 0.036164 TTCTGGGTGATTCCGTGTGG 59.964 55.0 0.0 0.0 37.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2281 7720 0.391228 TAGCGGCAGTTTCAGTCACA 59.609 50.0 1.45 0.0 0.0 3.58 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
19 20 2.905996 TTTGGAGGCAGCCCGACAT 61.906 57.895 8.22 0.00 35.76 3.06
21 22 3.785859 GGAGGCAGCCCGACATCA 61.786 66.667 8.22 0.00 35.76 3.07
32 33 2.824041 GACATCAATGCGGGCGGT 60.824 61.111 0.00 0.00 0.00 5.68
67 73 1.213182 TCTCCTGCTCGATCTGGTACT 59.787 52.381 11.35 0.00 0.00 2.73
70 76 1.107114 CTGCTCGATCTGGTACTGGT 58.893 55.000 0.00 0.00 0.00 4.00
121 127 2.216750 CTTTTGCTGGACCATGGCGG 62.217 60.000 13.04 2.31 42.50 6.13
205 219 1.524482 GGAGGAGGTGGATGTGCTC 59.476 63.158 0.00 0.00 0.00 4.26
236 250 1.067212 CGCCAACCGACTTAGATAGCT 59.933 52.381 0.00 0.00 40.02 3.32
237 251 2.292569 CGCCAACCGACTTAGATAGCTA 59.707 50.000 0.00 0.00 40.02 3.32
238 252 3.640592 GCCAACCGACTTAGATAGCTAC 58.359 50.000 0.00 0.00 0.00 3.58
250 264 6.546403 ACTTAGATAGCTACATTTGGTCTCGA 59.454 38.462 0.00 0.00 0.00 4.04
256 270 2.509336 ATTTGGTCTCGAGCGGCG 60.509 61.111 7.81 0.51 42.69 6.46
284 298 4.390584 GCGTCACGCGTCGTTCAC 62.391 66.667 19.53 6.91 44.55 3.18
285 299 3.020105 CGTCACGCGTCGTTCACA 61.020 61.111 9.86 0.00 38.32 3.58
286 300 2.538058 GTCACGCGTCGTTCACAC 59.462 61.111 9.86 0.00 38.32 3.82
292 306 3.698463 CGTCGTTCACACGCCCAC 61.698 66.667 0.00 0.00 46.70 4.61
293 307 2.279918 GTCGTTCACACGCCCACT 60.280 61.111 0.00 0.00 46.70 4.00
294 308 1.007038 GTCGTTCACACGCCCACTA 60.007 57.895 0.00 0.00 46.70 2.74
295 309 1.007336 GTCGTTCACACGCCCACTAG 61.007 60.000 0.00 0.00 46.70 2.57
296 310 1.174078 TCGTTCACACGCCCACTAGA 61.174 55.000 0.00 0.00 46.70 2.43
297 311 0.732880 CGTTCACACGCCCACTAGAG 60.733 60.000 0.00 0.00 40.18 2.43
298 312 0.389948 GTTCACACGCCCACTAGAGG 60.390 60.000 0.00 0.00 0.00 3.69
299 313 0.541063 TTCACACGCCCACTAGAGGA 60.541 55.000 7.92 0.00 0.00 3.71
300 314 0.965866 TCACACGCCCACTAGAGGAG 60.966 60.000 7.92 6.76 0.00 3.69
301 315 0.965866 CACACGCCCACTAGAGGAGA 60.966 60.000 7.92 0.00 0.00 3.71
302 316 0.966370 ACACGCCCACTAGAGGAGAC 60.966 60.000 7.92 0.00 0.00 3.36
303 317 1.749638 ACGCCCACTAGAGGAGACG 60.750 63.158 7.92 10.60 0.00 4.18
304 318 1.749638 CGCCCACTAGAGGAGACGT 60.750 63.158 7.92 0.00 0.00 4.34
305 319 1.716826 CGCCCACTAGAGGAGACGTC 61.717 65.000 7.70 7.70 0.00 4.34
306 320 1.385756 GCCCACTAGAGGAGACGTCC 61.386 65.000 13.01 3.55 44.33 4.79
314 328 2.876219 GGAGACGTCCGTCAGACC 59.124 66.667 20.57 15.83 46.76 3.85
315 329 2.479650 GAGACGTCCGTCAGACCG 59.520 66.667 20.57 0.00 46.76 4.79
316 330 3.664223 GAGACGTCCGTCAGACCGC 62.664 68.421 20.57 1.02 46.76 5.68
317 331 4.773117 GACGTCCGTCAGACCGCC 62.773 72.222 14.48 0.00 43.08 6.13
331 345 4.323477 CGCCGGGTTTCTGGGTGA 62.323 66.667 2.18 0.00 39.84 4.02
332 346 2.355115 GCCGGGTTTCTGGGTGAT 59.645 61.111 2.18 0.00 39.84 3.06
333 347 1.304134 GCCGGGTTTCTGGGTGATT 60.304 57.895 2.18 0.00 39.84 2.57
334 348 1.313091 GCCGGGTTTCTGGGTGATTC 61.313 60.000 2.18 0.00 39.84 2.52
335 349 0.679960 CCGGGTTTCTGGGTGATTCC 60.680 60.000 0.00 0.00 35.76 3.01
336 350 1.024579 CGGGTTTCTGGGTGATTCCG 61.025 60.000 0.00 0.00 37.00 4.30
337 351 0.037734 GGGTTTCTGGGTGATTCCGT 59.962 55.000 0.00 0.00 37.00 4.69
338 352 1.165270 GGTTTCTGGGTGATTCCGTG 58.835 55.000 0.00 0.00 37.00 4.94
339 353 1.544759 GGTTTCTGGGTGATTCCGTGT 60.545 52.381 0.00 0.00 37.00 4.49
340 354 1.535462 GTTTCTGGGTGATTCCGTGTG 59.465 52.381 0.00 0.00 37.00 3.82
341 355 0.036164 TTCTGGGTGATTCCGTGTGG 59.964 55.000 0.00 0.00 37.00 4.17
342 356 1.377202 CTGGGTGATTCCGTGTGGG 60.377 63.158 0.00 0.00 37.00 4.61
343 357 1.836999 CTGGGTGATTCCGTGTGGGA 61.837 60.000 0.00 0.00 45.40 4.37
358 372 2.979649 GGAACCCCTCGTCAGTCC 59.020 66.667 0.00 0.00 0.00 3.85
359 373 2.572284 GAACCCCTCGTCAGTCCG 59.428 66.667 0.00 0.00 0.00 4.79
360 374 1.975407 GAACCCCTCGTCAGTCCGA 60.975 63.158 0.00 0.00 35.22 4.55
361 375 2.210341 GAACCCCTCGTCAGTCCGAC 62.210 65.000 0.00 0.00 41.62 4.79
368 382 2.502080 GTCAGTCCGACGCGACAG 60.502 66.667 15.93 0.00 34.19 3.51
369 383 2.667199 TCAGTCCGACGCGACAGA 60.667 61.111 15.93 0.16 35.07 3.41
370 384 2.502080 CAGTCCGACGCGACAGAC 60.502 66.667 15.93 15.69 35.07 3.51
371 385 4.086178 AGTCCGACGCGACAGACG 62.086 66.667 15.93 10.10 45.66 4.18
390 404 2.672996 GCCCGTGCACACCTTGAT 60.673 61.111 18.64 0.00 37.47 2.57
391 405 1.376683 GCCCGTGCACACCTTGATA 60.377 57.895 18.64 0.00 37.47 2.15
392 406 0.748005 GCCCGTGCACACCTTGATAT 60.748 55.000 18.64 0.00 37.47 1.63
393 407 1.016627 CCCGTGCACACCTTGATATG 58.983 55.000 18.64 0.00 0.00 1.78
394 408 1.406751 CCCGTGCACACCTTGATATGA 60.407 52.381 18.64 0.00 0.00 2.15
395 409 1.935873 CCGTGCACACCTTGATATGAG 59.064 52.381 18.64 0.00 0.00 2.90
396 410 1.935873 CGTGCACACCTTGATATGAGG 59.064 52.381 18.64 1.07 40.24 3.86
397 411 2.292267 GTGCACACCTTGATATGAGGG 58.708 52.381 13.17 0.00 38.65 4.30
398 412 1.212688 TGCACACCTTGATATGAGGGG 59.787 52.381 3.00 3.00 43.59 4.79
401 415 1.972872 CACCTTGATATGAGGGGTGC 58.027 55.000 0.00 0.00 40.44 5.01
402 416 1.492176 CACCTTGATATGAGGGGTGCT 59.508 52.381 0.00 0.00 40.44 4.40
403 417 1.492176 ACCTTGATATGAGGGGTGCTG 59.508 52.381 0.00 0.00 38.65 4.41
404 418 1.202855 CCTTGATATGAGGGGTGCTGG 60.203 57.143 0.00 0.00 0.00 4.85
405 419 1.492176 CTTGATATGAGGGGTGCTGGT 59.508 52.381 0.00 0.00 0.00 4.00
406 420 1.595311 TGATATGAGGGGTGCTGGTT 58.405 50.000 0.00 0.00 0.00 3.67
407 421 2.770447 TGATATGAGGGGTGCTGGTTA 58.230 47.619 0.00 0.00 0.00 2.85
408 422 2.705658 TGATATGAGGGGTGCTGGTTAG 59.294 50.000 0.00 0.00 0.00 2.34
417 431 2.358737 GCTGGTTAGCCTGTGCGT 60.359 61.111 4.47 0.00 44.33 5.24
418 432 1.966451 GCTGGTTAGCCTGTGCGTT 60.966 57.895 4.47 0.00 44.33 4.84
419 433 1.515521 GCTGGTTAGCCTGTGCGTTT 61.516 55.000 4.47 0.00 44.33 3.60
420 434 0.238289 CTGGTTAGCCTGTGCGTTTG 59.762 55.000 0.00 0.00 44.33 2.93
421 435 0.179043 TGGTTAGCCTGTGCGTTTGA 60.179 50.000 0.00 0.00 44.33 2.69
422 436 0.517316 GGTTAGCCTGTGCGTTTGAG 59.483 55.000 0.00 0.00 44.33 3.02
423 437 0.517316 GTTAGCCTGTGCGTTTGAGG 59.483 55.000 0.00 0.00 44.33 3.86
425 439 4.043200 GCCTGTGCGTTTGAGGCC 62.043 66.667 0.00 0.00 45.69 5.19
426 440 3.365265 CCTGTGCGTTTGAGGCCC 61.365 66.667 0.00 0.00 0.00 5.80
427 441 3.726517 CTGTGCGTTTGAGGCCCG 61.727 66.667 0.00 0.00 0.00 6.13
428 442 4.555709 TGTGCGTTTGAGGCCCGT 62.556 61.111 0.00 0.00 0.00 5.28
429 443 3.284449 GTGCGTTTGAGGCCCGTT 61.284 61.111 0.00 0.00 0.00 4.44
430 444 2.517402 TGCGTTTGAGGCCCGTTT 60.517 55.556 0.00 0.00 0.00 3.60
431 445 2.050442 GCGTTTGAGGCCCGTTTG 60.050 61.111 0.00 0.00 0.00 2.93
432 446 2.548295 GCGTTTGAGGCCCGTTTGA 61.548 57.895 0.00 0.00 0.00 2.69
433 447 1.574428 CGTTTGAGGCCCGTTTGAG 59.426 57.895 0.00 0.00 0.00 3.02
434 448 1.852067 CGTTTGAGGCCCGTTTGAGG 61.852 60.000 0.00 0.00 0.00 3.86
435 449 0.536460 GTTTGAGGCCCGTTTGAGGA 60.536 55.000 0.00 0.00 0.00 3.71
436 450 0.250727 TTTGAGGCCCGTTTGAGGAG 60.251 55.000 0.00 0.00 0.00 3.69
437 451 2.436824 GAGGCCCGTTTGAGGAGC 60.437 66.667 0.00 0.00 0.00 4.70
438 452 3.978571 GAGGCCCGTTTGAGGAGCC 62.979 68.421 0.00 7.22 43.50 4.70
441 455 4.016706 CCCGTTTGAGGAGCCCGT 62.017 66.667 0.00 0.00 0.00 5.28
442 456 2.434359 CCGTTTGAGGAGCCCGTC 60.434 66.667 0.00 0.00 0.00 4.79
443 457 2.657237 CGTTTGAGGAGCCCGTCT 59.343 61.111 0.00 0.00 0.00 4.18
444 458 1.738099 CGTTTGAGGAGCCCGTCTG 60.738 63.158 0.00 0.00 0.00 3.51
445 459 1.376037 GTTTGAGGAGCCCGTCTGG 60.376 63.158 0.00 0.00 37.09 3.86
458 472 3.726291 CCGTCTGGGTTGAATTTTTGT 57.274 42.857 0.00 0.00 0.00 2.83
459 473 3.380142 CCGTCTGGGTTGAATTTTTGTG 58.620 45.455 0.00 0.00 0.00 3.33
460 474 3.067461 CCGTCTGGGTTGAATTTTTGTGA 59.933 43.478 0.00 0.00 0.00 3.58
461 475 4.041723 CGTCTGGGTTGAATTTTTGTGAC 58.958 43.478 0.00 0.00 0.00 3.67
462 476 4.368315 GTCTGGGTTGAATTTTTGTGACC 58.632 43.478 0.00 0.00 0.00 4.02
463 477 3.067461 TCTGGGTTGAATTTTTGTGACCG 59.933 43.478 0.00 0.00 0.00 4.79
464 478 2.131972 GGGTTGAATTTTTGTGACCGC 58.868 47.619 0.00 0.00 0.00 5.68
465 479 2.223947 GGGTTGAATTTTTGTGACCGCT 60.224 45.455 0.00 0.00 0.00 5.52
466 480 3.049912 GGTTGAATTTTTGTGACCGCTC 58.950 45.455 0.00 0.00 0.00 5.03
467 481 3.243401 GGTTGAATTTTTGTGACCGCTCT 60.243 43.478 0.00 0.00 0.00 4.09
468 482 3.624326 TGAATTTTTGTGACCGCTCTG 57.376 42.857 0.00 0.00 0.00 3.35
469 483 2.287547 TGAATTTTTGTGACCGCTCTGC 60.288 45.455 0.00 0.00 0.00 4.26
481 495 4.052229 CTCTGCGACCGGACCGTT 62.052 66.667 9.46 0.00 0.00 4.44
482 496 3.966026 CTCTGCGACCGGACCGTTC 62.966 68.421 9.46 7.34 0.00 3.95
491 505 2.746277 GGACCGTTCGCCTGCATT 60.746 61.111 0.00 0.00 0.00 3.56
492 506 2.332654 GGACCGTTCGCCTGCATTT 61.333 57.895 0.00 0.00 0.00 2.32
493 507 1.154225 GACCGTTCGCCTGCATTTG 60.154 57.895 0.00 0.00 0.00 2.32
494 508 1.573829 GACCGTTCGCCTGCATTTGA 61.574 55.000 0.00 0.00 0.00 2.69
495 509 1.135315 CCGTTCGCCTGCATTTGAG 59.865 57.895 0.00 0.00 0.00 3.02
496 510 1.135315 CGTTCGCCTGCATTTGAGG 59.865 57.895 0.00 0.00 0.00 3.86
500 514 3.064324 GCCTGCATTTGAGGCGGT 61.064 61.111 0.00 0.00 46.47 5.68
501 515 2.639327 GCCTGCATTTGAGGCGGTT 61.639 57.895 0.00 0.00 46.47 4.44
502 516 1.966762 CCTGCATTTGAGGCGGTTT 59.033 52.632 0.00 0.00 35.87 3.27
503 517 0.388907 CCTGCATTTGAGGCGGTTTG 60.389 55.000 0.00 0.00 35.87 2.93
504 518 0.388907 CTGCATTTGAGGCGGTTTGG 60.389 55.000 0.00 0.00 32.96 3.28
505 519 1.079888 GCATTTGAGGCGGTTTGGG 60.080 57.895 0.00 0.00 0.00 4.12
506 520 1.591183 CATTTGAGGCGGTTTGGGG 59.409 57.895 0.00 0.00 0.00 4.96
507 521 1.155155 ATTTGAGGCGGTTTGGGGT 59.845 52.632 0.00 0.00 0.00 4.95
508 522 1.184970 ATTTGAGGCGGTTTGGGGTG 61.185 55.000 0.00 0.00 0.00 4.61
509 523 2.575455 TTTGAGGCGGTTTGGGGTGT 62.575 55.000 0.00 0.00 0.00 4.16
510 524 2.671963 GAGGCGGTTTGGGGTGTC 60.672 66.667 0.00 0.00 0.00 3.67
511 525 4.280019 AGGCGGTTTGGGGTGTCC 62.280 66.667 0.00 0.00 0.00 4.02
513 527 4.629523 GCGGTTTGGGGTGTCCGA 62.630 66.667 6.63 0.00 44.86 4.55
514 528 2.667199 CGGTTTGGGGTGTCCGAC 60.667 66.667 0.00 0.00 44.86 4.79
515 529 2.833957 GGTTTGGGGTGTCCGACT 59.166 61.111 0.00 0.00 38.76 4.18
516 530 1.302271 GGTTTGGGGTGTCCGACTC 60.302 63.158 0.00 0.00 38.76 3.36
517 531 1.752833 GTTTGGGGTGTCCGACTCT 59.247 57.895 0.00 0.00 38.76 3.24
518 532 0.602905 GTTTGGGGTGTCCGACTCTG 60.603 60.000 0.00 0.00 38.76 3.35
519 533 2.391724 TTTGGGGTGTCCGACTCTGC 62.392 60.000 0.00 0.00 38.76 4.26
520 534 4.436998 GGGGTGTCCGACTCTGCG 62.437 72.222 0.00 0.00 0.00 5.18
521 535 3.371063 GGGTGTCCGACTCTGCGA 61.371 66.667 0.00 0.00 0.00 5.10
522 536 2.126424 GGTGTCCGACTCTGCGAC 60.126 66.667 0.00 0.00 0.00 5.19
523 537 2.126424 GTGTCCGACTCTGCGACC 60.126 66.667 0.00 0.00 0.00 4.79
524 538 2.596338 TGTCCGACTCTGCGACCA 60.596 61.111 0.00 0.00 0.00 4.02
525 539 2.197605 TGTCCGACTCTGCGACCAA 61.198 57.895 0.00 0.00 0.00 3.67
526 540 1.006571 GTCCGACTCTGCGACCAAA 60.007 57.895 0.00 0.00 0.00 3.28
527 541 1.006571 TCCGACTCTGCGACCAAAC 60.007 57.895 0.00 0.00 0.00 2.93
528 542 2.027625 CCGACTCTGCGACCAAACC 61.028 63.158 0.00 0.00 0.00 3.27
529 543 2.372690 CGACTCTGCGACCAAACCG 61.373 63.158 0.00 0.00 0.00 4.44
530 544 1.300697 GACTCTGCGACCAAACCGT 60.301 57.895 0.00 0.00 0.00 4.83
531 545 0.878961 GACTCTGCGACCAAACCGTT 60.879 55.000 0.00 0.00 0.00 4.44
532 546 0.878961 ACTCTGCGACCAAACCGTTC 60.879 55.000 0.00 0.00 0.00 3.95
533 547 1.886861 CTCTGCGACCAAACCGTTCG 61.887 60.000 0.00 0.00 0.00 3.95
535 549 4.379143 GCGACCAAACCGTTCGCC 62.379 66.667 3.88 0.00 43.03 5.54
536 550 3.719144 CGACCAAACCGTTCGCCC 61.719 66.667 0.00 0.00 0.00 6.13
537 551 2.281276 GACCAAACCGTTCGCCCT 60.281 61.111 0.00 0.00 0.00 5.19
538 552 1.004679 GACCAAACCGTTCGCCCTA 60.005 57.895 0.00 0.00 0.00 3.53
539 553 1.004200 ACCAAACCGTTCGCCCTAG 60.004 57.895 0.00 0.00 0.00 3.02
540 554 2.396157 CCAAACCGTTCGCCCTAGC 61.396 63.158 0.00 0.00 0.00 3.42
552 566 2.264794 CCTAGCGTTTGAGGCGGT 59.735 61.111 0.00 0.00 42.79 5.68
555 569 0.165944 CTAGCGTTTGAGGCGGTTTG 59.834 55.000 0.00 0.00 40.61 2.93
556 570 0.533308 TAGCGTTTGAGGCGGTTTGT 60.533 50.000 0.00 0.00 40.61 2.83
557 571 1.065109 GCGTTTGAGGCGGTTTGTT 59.935 52.632 0.00 0.00 0.00 2.83
561 575 1.323271 TTTGAGGCGGTTTGTTGGCA 61.323 50.000 0.00 0.00 0.00 4.92
566 580 2.622011 GCGGTTTGTTGGCATCCGA 61.622 57.895 15.57 0.00 41.45 4.55
567 581 1.209127 CGGTTTGTTGGCATCCGAC 59.791 57.895 8.93 0.00 41.45 4.79
571 585 0.950836 TTTGTTGGCATCCGACTGTG 59.049 50.000 4.98 0.00 38.66 3.66
584 598 5.644977 TCCGACTGTGGATGCTATAATAG 57.355 43.478 0.00 0.00 31.53 1.73
585 599 5.077564 TCCGACTGTGGATGCTATAATAGT 58.922 41.667 0.00 0.00 31.53 2.12
586 600 6.243148 TCCGACTGTGGATGCTATAATAGTA 58.757 40.000 0.00 0.00 31.53 1.82
590 604 8.176365 CGACTGTGGATGCTATAATAGTAGTAC 58.824 40.741 0.00 0.00 0.00 2.73
613 627 9.869757 GTACAATTTTAAAGTAAATCCAGGCAT 57.130 29.630 0.00 0.00 0.00 4.40
627 641 4.836825 TCCAGGCATAACTCTTCAGAAAG 58.163 43.478 0.00 0.00 0.00 2.62
628 642 3.944015 CCAGGCATAACTCTTCAGAAAGG 59.056 47.826 0.00 0.00 33.03 3.11
629 643 3.376546 CAGGCATAACTCTTCAGAAAGGC 59.623 47.826 0.00 0.00 33.03 4.35
630 644 3.265479 AGGCATAACTCTTCAGAAAGGCT 59.735 43.478 0.00 0.00 33.03 4.58
632 646 4.460731 GGCATAACTCTTCAGAAAGGCTTT 59.539 41.667 13.25 13.25 33.03 3.51
645 660 7.114754 TCAGAAAGGCTTTGATACATCTTGAT 58.885 34.615 18.79 0.00 0.00 2.57
695 711 0.758734 TGATACGGGAGAGGCCAATG 59.241 55.000 5.01 0.00 38.95 2.82
739 2460 4.209307 TCATAGCACGGTCCATTTAACA 57.791 40.909 0.00 0.00 0.00 2.41
742 2463 5.650266 TCATAGCACGGTCCATTTAACATTT 59.350 36.000 0.00 0.00 0.00 2.32
743 2464 4.864704 AGCACGGTCCATTTAACATTTT 57.135 36.364 0.00 0.00 0.00 1.82
744 2465 4.805219 AGCACGGTCCATTTAACATTTTC 58.195 39.130 0.00 0.00 0.00 2.29
821 4686 1.062294 CGTACAGAGTCTACCGCTCAC 59.938 57.143 0.00 0.00 35.55 3.51
959 5127 3.726517 CGCAGAGCACCAAACCCG 61.727 66.667 0.00 0.00 0.00 5.28
982 5153 5.107607 CGTCGTCAATCCTATTTAAATCCCG 60.108 44.000 3.39 0.00 0.00 5.14
1013 5195 0.594110 GAATCCACCACCGCGAAAAA 59.406 50.000 8.23 0.00 0.00 1.94
1017 5199 0.168128 CCACCACCGCGAAAAATCTC 59.832 55.000 8.23 0.00 0.00 2.75
1024 5206 3.125146 CACCGCGAAAAATCTCAATCTCA 59.875 43.478 8.23 0.00 0.00 3.27
1025 5207 3.372206 ACCGCGAAAAATCTCAATCTCAG 59.628 43.478 8.23 0.00 0.00 3.35
1514 5704 1.081108 CGCGCCTAGGCTCTGTATC 60.081 63.158 30.55 9.98 39.32 2.24
1581 5775 2.564947 CTGTAGTTGTCTGCTCCTCCTT 59.435 50.000 0.00 0.00 0.00 3.36
1582 5776 3.764434 CTGTAGTTGTCTGCTCCTCCTTA 59.236 47.826 0.00 0.00 0.00 2.69
1647 5842 7.408756 TCAAATCTCTGGTTTGATAAATGGG 57.591 36.000 2.30 0.00 39.81 4.00
1657 5852 5.240623 GGTTTGATAAATGGGATCACGCATA 59.759 40.000 0.00 0.00 46.37 3.14
1662 5862 7.592938 TGATAAATGGGATCACGCATATTTTC 58.407 34.615 0.00 0.00 46.37 2.29
1740 6024 1.202879 TGTCTGATTTGTGGGTCCACC 60.203 52.381 16.57 0.00 45.63 4.61
1761 6045 6.150474 CCACCGTAAGTAAGAATTCCATTTGT 59.850 38.462 0.65 0.00 0.00 2.83
1762 6046 7.021196 CACCGTAAGTAAGAATTCCATTTGTG 58.979 38.462 0.65 0.00 0.00 3.33
1764 6048 6.348950 CCGTAAGTAAGAATTCCATTTGTGCA 60.349 38.462 0.65 0.00 0.00 4.57
1767 6051 7.472334 AAGTAAGAATTCCATTTGTGCATCT 57.528 32.000 0.65 0.00 0.00 2.90
1768 6052 6.860080 AGTAAGAATTCCATTTGTGCATCTG 58.140 36.000 0.65 0.00 0.00 2.90
1769 6053 4.119442 AGAATTCCATTTGTGCATCTGC 57.881 40.909 0.65 0.00 42.50 4.26
1794 6227 3.229276 AGACTCTGATGTGAAGCGAAG 57.771 47.619 0.00 0.00 0.00 3.79
1811 6254 3.486584 CGAAGTTGCAGATCTTTTGAGC 58.513 45.455 0.00 0.00 34.56 4.26
1825 6268 9.732130 AGATCTTTTGAGCAACTAGTAATTCTT 57.268 29.630 0.00 0.00 37.30 2.52
1832 6283 6.591834 TGAGCAACTAGTAATTCTTTCTGCTC 59.408 38.462 23.88 23.88 42.84 4.26
1837 6334 9.604626 CAACTAGTAATTCTTTCTGCTCAAAAG 57.395 33.333 0.00 0.00 35.49 2.27
1839 6336 9.213799 ACTAGTAATTCTTTCTGCTCAAAAGAG 57.786 33.333 0.00 0.00 42.12 2.85
1880 7233 4.558697 GCAGATTGGTAACTGTTTTCCCAC 60.559 45.833 0.00 0.00 36.62 4.61
1881 7234 4.582656 CAGATTGGTAACTGTTTTCCCACA 59.417 41.667 0.00 0.00 37.61 4.17
1907 7260 4.754114 GTGCTATCAGATCCATGTCTTTCC 59.246 45.833 0.00 0.00 0.00 3.13
1911 7264 3.548770 TCAGATCCATGTCTTTCCATGC 58.451 45.455 0.00 0.00 40.72 4.06
1919 7272 5.036737 CCATGTCTTTCCATGCGTTATTTC 58.963 41.667 0.00 0.00 40.72 2.17
1924 7277 6.150976 TGTCTTTCCATGCGTTATTTCAAGAT 59.849 34.615 0.00 0.00 0.00 2.40
1956 7309 2.110213 GTGGTGCTGGTCGGTTCA 59.890 61.111 0.00 0.00 0.00 3.18
2028 7381 1.224069 CCCGCATACAGATCTTGGCG 61.224 60.000 16.02 16.02 43.68 5.69
2130 7483 7.128976 CAGCTCTTACTCAAACTTTCTTGTTC 58.871 38.462 0.00 0.00 0.00 3.18
2148 7573 4.797471 TGTTCGATGCTTTCATCTTTTGG 58.203 39.130 4.11 0.00 45.32 3.28
2152 7577 6.271488 TCGATGCTTTCATCTTTTGGAAAT 57.729 33.333 4.11 0.00 45.32 2.17
2164 7589 6.418057 TCTTTTGGAAATTACCACTGCAAT 57.582 33.333 0.00 0.00 39.85 3.56
2187 7612 5.474578 TTTGCCTATAGATTCTCAGCGAT 57.525 39.130 0.00 0.00 0.00 4.58
2192 7617 0.319040 TAGATTCTCAGCGATGCGGC 60.319 55.000 0.00 0.00 0.00 6.53
2281 7720 0.400594 GTAGCCCCAGTTTGTCCACT 59.599 55.000 0.00 0.00 0.00 4.00
2300 7739 0.391228 TGTGACTGAAACTGCCGCTA 59.609 50.000 0.00 0.00 0.00 4.26
2307 7746 3.189287 ACTGAAACTGCCGCTAAATTCAG 59.811 43.478 18.62 18.62 45.65 3.02
2314 7753 4.154918 ACTGCCGCTAAATTCAGAAGAAAG 59.845 41.667 0.00 0.00 37.29 2.62
2351 7790 0.892755 TACTGTAACCTGGGAGCACG 59.107 55.000 0.00 0.00 0.00 5.34
2390 7829 6.467723 TGTTCATCTTCTCTTTTAGCGAAC 57.532 37.500 0.00 0.00 0.00 3.95
2412 7851 5.106442 ACACACGTTTTTCTTGGGAATTTC 58.894 37.500 0.00 0.00 0.00 2.17
2456 7897 2.254546 TGGAACAGTTGTGCTGGTAG 57.745 50.000 0.00 0.00 46.91 3.18
2475 7916 5.248477 TGGTAGAAGTCCTTAGAAATGTGCT 59.752 40.000 0.00 0.00 0.00 4.40
2476 7917 6.439375 TGGTAGAAGTCCTTAGAAATGTGCTA 59.561 38.462 0.00 0.00 0.00 3.49
2477 7918 6.981559 GGTAGAAGTCCTTAGAAATGTGCTAG 59.018 42.308 0.00 0.00 0.00 3.42
2478 7919 6.613153 AGAAGTCCTTAGAAATGTGCTAGT 57.387 37.500 0.00 0.00 0.00 2.57
2479 7920 6.402222 AGAAGTCCTTAGAAATGTGCTAGTG 58.598 40.000 0.00 0.00 0.00 2.74
2480 7921 4.508662 AGTCCTTAGAAATGTGCTAGTGC 58.491 43.478 0.00 0.00 40.20 4.40
2485 7926 5.521735 CCTTAGAAATGTGCTAGTGCTAGTG 59.478 44.000 7.90 0.00 40.48 2.74
2504 7945 1.200716 TGCTTGCTGCTTAGCACATTC 59.799 47.619 20.59 3.06 45.32 2.67
2521 7962 7.725251 AGCACATTCCAAATTCTTGTTCTTTA 58.275 30.769 0.00 0.00 0.00 1.85
2560 8001 3.866883 TTCGGCCCTGATTTTCATTTC 57.133 42.857 0.00 0.00 0.00 2.17
2570 8011 7.040548 GCCCTGATTTTCATTTCCAAAAATTCA 60.041 33.333 0.00 0.00 35.72 2.57
2636 8077 5.130477 GGACTACCCAATCATCAGGTTCTTA 59.870 44.000 0.00 0.00 35.02 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.056328 GTCGGGCTGCCTCCAAAC 61.056 66.667 19.68 6.20 0.00 2.93
1 2 2.819984 GATGTCGGGCTGCCTCCAAA 62.820 60.000 19.68 1.31 0.00 3.28
3 4 3.785859 GATGTCGGGCTGCCTCCA 61.786 66.667 19.68 12.75 0.00 3.86
42 48 1.606189 CAGATCGAGCAGGAGATTCGA 59.394 52.381 2.38 0.00 45.96 3.71
121 127 0.739112 CTTCCCACGCTCTTCAGCTC 60.739 60.000 0.00 0.00 44.40 4.09
125 131 1.293498 GCTCTTCCCACGCTCTTCA 59.707 57.895 0.00 0.00 0.00 3.02
186 200 1.977293 GAGCACATCCACCTCCTCCC 61.977 65.000 0.00 0.00 0.00 4.30
187 201 1.524482 GAGCACATCCACCTCCTCC 59.476 63.158 0.00 0.00 0.00 4.30
188 202 1.142748 CGAGCACATCCACCTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
219 233 6.201044 CCAAATGTAGCTATCTAAGTCGGTTG 59.799 42.308 0.00 0.00 0.00 3.77
220 234 6.127140 ACCAAATGTAGCTATCTAAGTCGGTT 60.127 38.462 0.00 0.00 0.00 4.44
223 237 6.740110 AGACCAAATGTAGCTATCTAAGTCG 58.260 40.000 0.00 0.00 0.00 4.18
236 250 0.459585 GCCGCTCGAGACCAAATGTA 60.460 55.000 18.75 0.00 0.00 2.29
237 251 1.741770 GCCGCTCGAGACCAAATGT 60.742 57.895 18.75 0.00 0.00 2.71
238 252 2.802667 CGCCGCTCGAGACCAAATG 61.803 63.158 18.75 0.00 41.67 2.32
269 283 2.538058 GTGTGAACGACGCGTGAC 59.462 61.111 20.70 0.87 39.99 3.67
275 289 2.736343 TAGTGGGCGTGTGAACGACG 62.736 60.000 1.87 0.00 43.10 5.12
276 290 1.007038 TAGTGGGCGTGTGAACGAC 60.007 57.895 1.87 0.00 41.09 4.34
277 291 1.174078 TCTAGTGGGCGTGTGAACGA 61.174 55.000 1.87 0.00 34.64 3.85
278 292 0.732880 CTCTAGTGGGCGTGTGAACG 60.733 60.000 0.00 0.00 0.00 3.95
279 293 0.389948 CCTCTAGTGGGCGTGTGAAC 60.390 60.000 2.68 0.00 0.00 3.18
280 294 0.541063 TCCTCTAGTGGGCGTGTGAA 60.541 55.000 10.89 0.00 0.00 3.18
281 295 0.965866 CTCCTCTAGTGGGCGTGTGA 60.966 60.000 10.89 0.00 0.00 3.58
282 296 0.965866 TCTCCTCTAGTGGGCGTGTG 60.966 60.000 10.89 0.00 0.00 3.82
283 297 0.966370 GTCTCCTCTAGTGGGCGTGT 60.966 60.000 10.89 0.00 0.00 4.49
284 298 1.810532 GTCTCCTCTAGTGGGCGTG 59.189 63.158 10.89 0.51 0.00 5.34
285 299 1.749638 CGTCTCCTCTAGTGGGCGT 60.750 63.158 10.89 0.00 0.00 5.68
286 300 1.716826 GACGTCTCCTCTAGTGGGCG 61.717 65.000 8.70 14.04 0.00 6.13
287 301 1.385756 GGACGTCTCCTCTAGTGGGC 61.386 65.000 16.46 1.81 33.07 5.36
288 302 1.096386 CGGACGTCTCCTCTAGTGGG 61.096 65.000 16.46 4.76 33.79 4.61
289 303 0.392729 ACGGACGTCTCCTCTAGTGG 60.393 60.000 16.46 4.35 33.79 4.00
290 304 1.008329 GACGGACGTCTCCTCTAGTG 58.992 60.000 16.46 0.00 41.57 2.74
291 305 0.612229 TGACGGACGTCTCCTCTAGT 59.388 55.000 23.18 4.59 44.80 2.57
292 306 1.134759 TCTGACGGACGTCTCCTCTAG 60.135 57.143 23.18 12.48 44.80 2.43
293 307 0.900421 TCTGACGGACGTCTCCTCTA 59.100 55.000 23.18 3.63 44.80 2.43
294 308 0.674269 GTCTGACGGACGTCTCCTCT 60.674 60.000 23.18 0.00 44.80 3.69
295 309 1.646624 GGTCTGACGGACGTCTCCTC 61.647 65.000 23.18 7.99 45.35 3.71
296 310 1.674980 GGTCTGACGGACGTCTCCT 60.675 63.158 23.18 0.00 45.35 3.69
297 311 2.876219 GGTCTGACGGACGTCTCC 59.124 66.667 23.18 18.09 45.35 3.71
298 312 2.479650 CGGTCTGACGGACGTCTC 59.520 66.667 23.18 6.69 45.35 3.36
299 313 3.735029 GCGGTCTGACGGACGTCT 61.735 66.667 23.18 0.00 45.35 4.18
300 314 4.773117 GGCGGTCTGACGGACGTC 62.773 72.222 18.16 17.19 45.35 4.34
307 321 2.741211 GAAACCCGGCGGTCTGAC 60.741 66.667 26.32 8.34 43.71 3.51
308 322 2.920912 AGAAACCCGGCGGTCTGA 60.921 61.111 26.32 0.00 43.71 3.27
309 323 2.742372 CAGAAACCCGGCGGTCTG 60.742 66.667 24.66 24.66 43.71 3.51
310 324 4.016706 CCAGAAACCCGGCGGTCT 62.017 66.667 26.32 18.35 43.71 3.85
314 328 3.622060 ATCACCCAGAAACCCGGCG 62.622 63.158 0.00 0.00 0.00 6.46
315 329 1.304134 AATCACCCAGAAACCCGGC 60.304 57.895 0.00 0.00 0.00 6.13
316 330 0.679960 GGAATCACCCAGAAACCCGG 60.680 60.000 0.00 0.00 0.00 5.73
317 331 1.024579 CGGAATCACCCAGAAACCCG 61.025 60.000 0.00 0.00 34.64 5.28
318 332 0.037734 ACGGAATCACCCAGAAACCC 59.962 55.000 0.00 0.00 34.64 4.11
319 333 1.165270 CACGGAATCACCCAGAAACC 58.835 55.000 0.00 0.00 34.64 3.27
320 334 1.535462 CACACGGAATCACCCAGAAAC 59.465 52.381 0.00 0.00 34.64 2.78
321 335 1.544537 CCACACGGAATCACCCAGAAA 60.545 52.381 0.00 0.00 34.64 2.52
322 336 0.036164 CCACACGGAATCACCCAGAA 59.964 55.000 0.00 0.00 34.64 3.02
323 337 1.676968 CCACACGGAATCACCCAGA 59.323 57.895 0.00 0.00 34.64 3.86
324 338 1.377202 CCCACACGGAATCACCCAG 60.377 63.158 0.00 0.00 34.64 4.45
325 339 1.419720 TTCCCACACGGAATCACCCA 61.420 55.000 0.00 0.00 46.27 4.51
326 340 1.377229 TTCCCACACGGAATCACCC 59.623 57.895 0.00 0.00 46.27 4.61
340 354 2.657066 GGACTGACGAGGGGTTCCC 61.657 68.421 0.00 0.00 45.90 3.97
341 355 2.979649 GGACTGACGAGGGGTTCC 59.020 66.667 0.00 0.00 0.00 3.62
342 356 1.975407 TCGGACTGACGAGGGGTTC 60.975 63.158 0.00 0.00 38.06 3.62
343 357 2.116772 TCGGACTGACGAGGGGTT 59.883 61.111 0.00 0.00 38.06 4.11
344 358 2.675772 GTCGGACTGACGAGGGGT 60.676 66.667 0.00 0.00 44.42 4.95
351 365 2.502080 CTGTCGCGTCGGACTGAC 60.502 66.667 18.04 18.04 44.53 3.51
352 366 2.667199 TCTGTCGCGTCGGACTGA 60.667 61.111 10.89 14.73 40.95 3.41
353 367 2.502080 GTCTGTCGCGTCGGACTG 60.502 66.667 29.80 15.13 39.71 3.51
354 368 4.086178 CGTCTGTCGCGTCGGACT 62.086 66.667 32.10 0.00 40.40 3.85
373 387 0.748005 ATATCAAGGTGTGCACGGGC 60.748 55.000 13.13 0.34 41.68 6.13
374 388 1.016627 CATATCAAGGTGTGCACGGG 58.983 55.000 13.13 0.00 0.00 5.28
375 389 1.935873 CTCATATCAAGGTGTGCACGG 59.064 52.381 13.13 0.00 0.00 4.94
376 390 1.935873 CCTCATATCAAGGTGTGCACG 59.064 52.381 13.13 0.00 0.00 5.34
377 391 2.292267 CCCTCATATCAAGGTGTGCAC 58.708 52.381 10.75 10.75 31.51 4.57
378 392 1.212688 CCCCTCATATCAAGGTGTGCA 59.787 52.381 0.00 0.00 31.51 4.57
379 393 1.212935 ACCCCTCATATCAAGGTGTGC 59.787 52.381 1.02 0.00 31.51 4.57
380 394 2.923121 CACCCCTCATATCAAGGTGTG 58.077 52.381 0.00 2.98 42.47 3.82
383 397 1.492176 CAGCACCCCTCATATCAAGGT 59.508 52.381 0.00 0.00 31.51 3.50
384 398 1.202855 CCAGCACCCCTCATATCAAGG 60.203 57.143 0.00 0.00 0.00 3.61
385 399 1.492176 ACCAGCACCCCTCATATCAAG 59.508 52.381 0.00 0.00 0.00 3.02
386 400 1.595311 ACCAGCACCCCTCATATCAA 58.405 50.000 0.00 0.00 0.00 2.57
387 401 1.595311 AACCAGCACCCCTCATATCA 58.405 50.000 0.00 0.00 0.00 2.15
388 402 3.409026 CTAACCAGCACCCCTCATATC 57.591 52.381 0.00 0.00 0.00 1.63
401 415 0.238289 CAAACGCACAGGCTAACCAG 59.762 55.000 0.00 0.00 39.06 4.00
402 416 0.179043 TCAAACGCACAGGCTAACCA 60.179 50.000 0.00 0.00 39.06 3.67
403 417 0.517316 CTCAAACGCACAGGCTAACC 59.483 55.000 0.00 0.00 38.10 2.85
404 418 0.517316 CCTCAAACGCACAGGCTAAC 59.483 55.000 0.00 0.00 38.10 2.34
405 419 2.927004 CCTCAAACGCACAGGCTAA 58.073 52.632 0.00 0.00 38.10 3.09
406 420 4.693532 CCTCAAACGCACAGGCTA 57.306 55.556 0.00 0.00 38.10 3.93
409 423 3.365265 GGGCCTCAAACGCACAGG 61.365 66.667 0.84 0.00 0.00 4.00
410 424 3.726517 CGGGCCTCAAACGCACAG 61.727 66.667 0.84 0.00 0.00 3.66
411 425 4.555709 ACGGGCCTCAAACGCACA 62.556 61.111 0.84 0.00 0.00 4.57
412 426 2.841160 AAACGGGCCTCAAACGCAC 61.841 57.895 0.84 0.00 0.00 5.34
413 427 2.517402 AAACGGGCCTCAAACGCA 60.517 55.556 0.84 0.00 0.00 5.24
414 428 2.050442 CAAACGGGCCTCAAACGC 60.050 61.111 0.84 0.00 0.00 4.84
415 429 1.574428 CTCAAACGGGCCTCAAACG 59.426 57.895 0.84 0.00 0.00 3.60
416 430 0.536460 TCCTCAAACGGGCCTCAAAC 60.536 55.000 0.84 0.00 0.00 2.93
417 431 0.250727 CTCCTCAAACGGGCCTCAAA 60.251 55.000 0.84 0.00 0.00 2.69
418 432 1.374947 CTCCTCAAACGGGCCTCAA 59.625 57.895 0.84 0.00 0.00 3.02
419 433 3.068881 CTCCTCAAACGGGCCTCA 58.931 61.111 0.84 0.00 0.00 3.86
420 434 2.436824 GCTCCTCAAACGGGCCTC 60.437 66.667 0.84 0.00 0.00 4.70
421 435 4.035102 GGCTCCTCAAACGGGCCT 62.035 66.667 0.84 0.00 37.40 5.19
424 438 3.952628 GACGGGCTCCTCAAACGGG 62.953 68.421 0.00 0.00 0.00 5.28
425 439 2.434359 GACGGGCTCCTCAAACGG 60.434 66.667 0.00 0.00 0.00 4.44
426 440 1.738099 CAGACGGGCTCCTCAAACG 60.738 63.158 0.00 0.00 0.00 3.60
427 441 1.376037 CCAGACGGGCTCCTCAAAC 60.376 63.158 0.00 0.00 0.00 2.93
428 442 3.068881 CCAGACGGGCTCCTCAAA 58.931 61.111 0.00 0.00 0.00 2.69
438 452 3.067461 TCACAAAAATTCAACCCAGACGG 59.933 43.478 0.00 0.00 37.81 4.79
439 453 4.041723 GTCACAAAAATTCAACCCAGACG 58.958 43.478 0.00 0.00 0.00 4.18
440 454 4.368315 GGTCACAAAAATTCAACCCAGAC 58.632 43.478 0.00 0.00 0.00 3.51
441 455 3.067461 CGGTCACAAAAATTCAACCCAGA 59.933 43.478 0.00 0.00 0.00 3.86
442 456 3.380142 CGGTCACAAAAATTCAACCCAG 58.620 45.455 0.00 0.00 0.00 4.45
443 457 2.482142 GCGGTCACAAAAATTCAACCCA 60.482 45.455 0.00 0.00 0.00 4.51
444 458 2.131972 GCGGTCACAAAAATTCAACCC 58.868 47.619 0.00 0.00 0.00 4.11
445 459 3.049912 GAGCGGTCACAAAAATTCAACC 58.950 45.455 10.30 0.00 0.00 3.77
446 460 3.730715 CAGAGCGGTCACAAAAATTCAAC 59.269 43.478 18.15 0.00 0.00 3.18
447 461 3.795150 GCAGAGCGGTCACAAAAATTCAA 60.795 43.478 18.15 0.00 0.00 2.69
448 462 2.287547 GCAGAGCGGTCACAAAAATTCA 60.288 45.455 18.15 0.00 0.00 2.57
449 463 2.319472 GCAGAGCGGTCACAAAAATTC 58.681 47.619 18.15 0.00 0.00 2.17
450 464 2.422276 GCAGAGCGGTCACAAAAATT 57.578 45.000 18.15 0.00 0.00 1.82
464 478 3.966026 GAACGGTCCGGTCGCAGAG 62.966 68.421 14.76 0.24 36.95 3.35
465 479 4.047059 GAACGGTCCGGTCGCAGA 62.047 66.667 14.76 0.00 32.79 4.26
474 488 2.332654 AAATGCAGGCGAACGGTCC 61.333 57.895 0.00 0.00 0.00 4.46
475 489 1.154225 CAAATGCAGGCGAACGGTC 60.154 57.895 0.00 0.00 0.00 4.79
476 490 1.577328 CTCAAATGCAGGCGAACGGT 61.577 55.000 0.00 0.00 0.00 4.83
477 491 1.135315 CTCAAATGCAGGCGAACGG 59.865 57.895 0.00 0.00 0.00 4.44
478 492 1.135315 CCTCAAATGCAGGCGAACG 59.865 57.895 0.00 0.00 0.00 3.95
484 498 0.388907 CAAACCGCCTCAAATGCAGG 60.389 55.000 0.00 0.00 0.00 4.85
485 499 0.388907 CCAAACCGCCTCAAATGCAG 60.389 55.000 0.00 0.00 0.00 4.41
486 500 1.664873 CCAAACCGCCTCAAATGCA 59.335 52.632 0.00 0.00 0.00 3.96
487 501 1.079888 CCCAAACCGCCTCAAATGC 60.080 57.895 0.00 0.00 0.00 3.56
488 502 1.184970 ACCCCAAACCGCCTCAAATG 61.185 55.000 0.00 0.00 0.00 2.32
489 503 1.155155 ACCCCAAACCGCCTCAAAT 59.845 52.632 0.00 0.00 0.00 2.32
490 504 1.830408 CACCCCAAACCGCCTCAAA 60.830 57.895 0.00 0.00 0.00 2.69
491 505 2.203422 CACCCCAAACCGCCTCAA 60.203 61.111 0.00 0.00 0.00 3.02
492 506 3.485346 GACACCCCAAACCGCCTCA 62.485 63.158 0.00 0.00 0.00 3.86
493 507 2.671963 GACACCCCAAACCGCCTC 60.672 66.667 0.00 0.00 0.00 4.70
494 508 4.280019 GGACACCCCAAACCGCCT 62.280 66.667 0.00 0.00 34.14 5.52
496 510 4.629523 TCGGACACCCCAAACCGC 62.630 66.667 0.00 0.00 44.19 5.68
497 511 2.667199 GTCGGACACCCCAAACCG 60.667 66.667 2.62 0.00 45.61 4.44
498 512 1.302271 GAGTCGGACACCCCAAACC 60.302 63.158 11.27 0.00 34.14 3.27
499 513 0.602905 CAGAGTCGGACACCCCAAAC 60.603 60.000 11.27 0.00 34.14 2.93
500 514 1.752198 CAGAGTCGGACACCCCAAA 59.248 57.895 11.27 0.00 34.14 3.28
501 515 2.879233 GCAGAGTCGGACACCCCAA 61.879 63.158 11.27 0.00 34.14 4.12
502 516 3.311110 GCAGAGTCGGACACCCCA 61.311 66.667 11.27 0.00 34.14 4.96
503 517 4.436998 CGCAGAGTCGGACACCCC 62.437 72.222 11.27 0.00 0.00 4.95
504 518 3.371063 TCGCAGAGTCGGACACCC 61.371 66.667 11.27 0.00 0.00 4.61
505 519 2.126424 GTCGCAGAGTCGGACACC 60.126 66.667 11.27 1.72 36.95 4.16
506 520 2.126424 GGTCGCAGAGTCGGACAC 60.126 66.667 11.27 3.96 36.95 3.67
507 521 1.740332 TTTGGTCGCAGAGTCGGACA 61.740 55.000 11.27 0.00 36.95 4.02
508 522 1.006571 TTTGGTCGCAGAGTCGGAC 60.007 57.895 0.00 0.00 36.95 4.79
509 523 1.006571 GTTTGGTCGCAGAGTCGGA 60.007 57.895 0.00 0.00 36.95 4.55
510 524 2.027625 GGTTTGGTCGCAGAGTCGG 61.028 63.158 0.00 0.00 36.95 4.79
511 525 2.372690 CGGTTTGGTCGCAGAGTCG 61.373 63.158 0.00 0.00 36.95 4.18
512 526 0.878961 AACGGTTTGGTCGCAGAGTC 60.879 55.000 0.00 0.00 36.95 3.36
513 527 0.878961 GAACGGTTTGGTCGCAGAGT 60.879 55.000 0.00 0.00 36.95 3.24
514 528 1.860078 GAACGGTTTGGTCGCAGAG 59.140 57.895 0.00 0.00 36.95 3.35
515 529 1.952133 CGAACGGTTTGGTCGCAGA 60.952 57.895 0.00 0.00 0.00 4.26
516 530 2.549282 CGAACGGTTTGGTCGCAG 59.451 61.111 0.00 0.00 0.00 5.18
519 533 2.768503 TAGGGCGAACGGTTTGGTCG 62.769 60.000 10.03 3.08 0.00 4.79
520 534 1.004679 TAGGGCGAACGGTTTGGTC 60.005 57.895 10.03 0.05 0.00 4.02
521 535 1.004200 CTAGGGCGAACGGTTTGGT 60.004 57.895 10.03 0.00 0.00 3.67
522 536 2.396157 GCTAGGGCGAACGGTTTGG 61.396 63.158 10.03 0.00 0.00 3.28
523 537 3.174788 GCTAGGGCGAACGGTTTG 58.825 61.111 3.65 3.65 0.00 2.93
533 547 3.195698 CGCCTCAAACGCTAGGGC 61.196 66.667 6.73 0.01 39.43 5.19
534 548 2.511600 CCGCCTCAAACGCTAGGG 60.512 66.667 5.05 5.05 33.17 3.53
535 549 0.953960 AAACCGCCTCAAACGCTAGG 60.954 55.000 0.00 0.00 35.86 3.02
536 550 0.165944 CAAACCGCCTCAAACGCTAG 59.834 55.000 0.00 0.00 0.00 3.42
537 551 0.533308 ACAAACCGCCTCAAACGCTA 60.533 50.000 0.00 0.00 0.00 4.26
538 552 1.381165 AACAAACCGCCTCAAACGCT 61.381 50.000 0.00 0.00 0.00 5.07
539 553 1.065109 AACAAACCGCCTCAAACGC 59.935 52.632 0.00 0.00 0.00 4.84
540 554 0.593773 CCAACAAACCGCCTCAAACG 60.594 55.000 0.00 0.00 0.00 3.60
548 562 2.126502 CGGATGCCAACAAACCGC 60.127 61.111 0.00 0.00 40.77 5.68
552 566 0.950836 CACAGTCGGATGCCAACAAA 59.049 50.000 0.00 0.00 0.00 2.83
555 569 0.392998 ATCCACAGTCGGATGCCAAC 60.393 55.000 4.28 0.00 44.40 3.77
556 570 1.990424 ATCCACAGTCGGATGCCAA 59.010 52.632 4.28 0.00 44.40 4.52
557 571 3.726004 ATCCACAGTCGGATGCCA 58.274 55.556 4.28 0.00 44.40 4.92
566 580 8.935614 TGTACTACTATTATAGCATCCACAGT 57.064 34.615 0.00 0.00 0.00 3.55
586 600 9.084533 TGCCTGGATTTACTTTAAAATTGTACT 57.915 29.630 0.00 0.00 0.00 2.73
601 615 6.560003 TCTGAAGAGTTATGCCTGGATTTA 57.440 37.500 0.00 0.00 0.00 1.40
602 616 5.441718 TCTGAAGAGTTATGCCTGGATTT 57.558 39.130 0.00 0.00 0.00 2.17
605 619 4.323792 CCTTTCTGAAGAGTTATGCCTGGA 60.324 45.833 0.00 0.00 34.71 3.86
606 620 3.944015 CCTTTCTGAAGAGTTATGCCTGG 59.056 47.826 0.00 0.00 34.71 4.45
613 627 7.450074 TGTATCAAAGCCTTTCTGAAGAGTTA 58.550 34.615 0.00 0.00 34.71 2.24
615 629 5.869579 TGTATCAAAGCCTTTCTGAAGAGT 58.130 37.500 0.00 0.00 34.71 3.24
617 631 6.715280 AGATGTATCAAAGCCTTTCTGAAGA 58.285 36.000 0.00 0.00 34.71 2.87
645 660 6.873076 GCTTATCATGTTCCCATTTTTCAACA 59.127 34.615 0.00 0.00 33.42 3.33
655 670 5.508567 TCAATCTTGCTTATCATGTTCCCA 58.491 37.500 0.00 0.00 0.00 4.37
656 671 6.645790 ATCAATCTTGCTTATCATGTTCCC 57.354 37.500 0.00 0.00 0.00 3.97
695 711 4.178540 TCGATGATTTTTACCACGGTCTC 58.821 43.478 0.00 0.00 0.00 3.36
739 2460 3.578282 AGGCATTTTGGTCTTCCGAAAAT 59.422 39.130 4.13 0.00 46.43 1.82
742 2463 1.885887 CAGGCATTTTGGTCTTCCGAA 59.114 47.619 0.00 0.00 35.48 4.30
743 2464 1.202879 ACAGGCATTTTGGTCTTCCGA 60.203 47.619 0.00 0.00 36.30 4.55
744 2465 1.247567 ACAGGCATTTTGGTCTTCCG 58.752 50.000 0.00 0.00 36.30 4.30
851 4717 1.200020 GTGGGGATTCGAGTTTGCAAG 59.800 52.381 0.00 0.00 0.00 4.01
930 4821 1.083784 CTCTGCGCGCGATGATTTC 60.084 57.895 37.18 14.74 0.00 2.17
959 5127 5.333875 GCGGGATTTAAATAGGATTGACGAC 60.334 44.000 0.00 0.00 0.00 4.34
982 5153 1.685148 GTGGATTCCTGGAGAATGGC 58.315 55.000 3.95 0.00 45.52 4.40
1013 5195 4.834496 GGAGATGGAGACTGAGATTGAGAT 59.166 45.833 0.00 0.00 0.00 2.75
1017 5199 4.589798 AGATGGAGATGGAGACTGAGATTG 59.410 45.833 0.00 0.00 0.00 2.67
1024 5206 3.411454 TTGGAGATGGAGATGGAGACT 57.589 47.619 0.00 0.00 0.00 3.24
1025 5207 3.432890 GGTTTGGAGATGGAGATGGAGAC 60.433 52.174 0.00 0.00 0.00 3.36
1532 5722 2.918712 ACATCTAGCGGGATTCAAGG 57.081 50.000 0.00 0.00 0.00 3.61
1581 5775 9.627123 CATTAGAAATACAAGGAGGGAAACATA 57.373 33.333 0.00 0.00 0.00 2.29
1582 5776 7.561356 CCATTAGAAATACAAGGAGGGAAACAT 59.439 37.037 0.00 0.00 0.00 2.71
1657 5852 6.479884 ACAGACCAGAGATTTAGCAGAAAAT 58.520 36.000 0.00 0.00 0.00 1.82
1662 5862 5.083533 AGAACAGACCAGAGATTTAGCAG 57.916 43.478 0.00 0.00 0.00 4.24
1702 5907 1.806542 ACAATCACGCACAACAGATCC 59.193 47.619 0.00 0.00 0.00 3.36
1740 6024 6.607689 TGCACAAATGGAATTCTTACTTACG 58.392 36.000 5.23 0.00 33.67 3.18
1762 6046 0.727970 CAGAGTCTTGCTGCAGATGC 59.272 55.000 20.43 3.09 42.50 3.91
1764 6048 2.236644 ACATCAGAGTCTTGCTGCAGAT 59.763 45.455 20.43 0.00 33.45 2.90
1767 6051 1.345415 TCACATCAGAGTCTTGCTGCA 59.655 47.619 0.00 0.00 33.45 4.41
1768 6052 2.090400 TCACATCAGAGTCTTGCTGC 57.910 50.000 0.00 0.00 33.45 5.25
1769 6053 2.415857 GCTTCACATCAGAGTCTTGCTG 59.584 50.000 0.00 0.00 34.71 4.41
1771 6055 1.392853 CGCTTCACATCAGAGTCTTGC 59.607 52.381 0.00 0.00 0.00 4.01
1811 6254 9.604626 CTTTTGAGCAGAAAGAATTACTAGTTG 57.395 33.333 0.00 0.00 36.45 3.16
1852 6349 6.294731 GGAAAACAGTTACCAATCTGCAGAAT 60.295 38.462 22.50 10.09 35.37 2.40
1857 6354 3.572255 TGGGAAAACAGTTACCAATCTGC 59.428 43.478 10.42 0.00 35.37 4.26
1858 6355 4.582656 TGTGGGAAAACAGTTACCAATCTG 59.417 41.667 10.42 0.00 37.65 2.90
1862 6359 2.683867 CGTGTGGGAAAACAGTTACCAA 59.316 45.455 10.42 0.00 32.19 3.67
1863 6360 2.290464 CGTGTGGGAAAACAGTTACCA 58.710 47.619 10.42 6.12 0.00 3.25
1864 6361 1.605232 CCGTGTGGGAAAACAGTTACC 59.395 52.381 0.00 0.00 38.47 2.85
1865 6362 2.032426 CACCGTGTGGGAAAACAGTTAC 59.968 50.000 0.00 0.00 40.75 2.50
1866 6363 2.290464 CACCGTGTGGGAAAACAGTTA 58.710 47.619 0.00 0.00 40.75 2.24
1867 6364 1.099689 CACCGTGTGGGAAAACAGTT 58.900 50.000 0.00 0.00 40.75 3.16
1880 7233 2.224137 ACATGGATCTGATAGCACCGTG 60.224 50.000 11.68 11.68 41.61 4.94
1881 7234 2.036475 GACATGGATCTGATAGCACCGT 59.964 50.000 0.00 0.00 0.00 4.83
1919 7272 7.489113 GCACCACTGGTTTTGATAAATATCTTG 59.511 37.037 0.00 0.00 31.02 3.02
1924 7277 6.266168 CAGCACCACTGGTTTTGATAAATA 57.734 37.500 0.00 0.00 43.19 1.40
1942 7295 0.818040 AACCTTGAACCGACCAGCAC 60.818 55.000 0.00 0.00 0.00 4.40
1951 7304 1.264288 CGCAACTCTGAACCTTGAACC 59.736 52.381 0.00 0.00 0.00 3.62
1956 7309 0.947244 CTTGCGCAACTCTGAACCTT 59.053 50.000 21.02 0.00 0.00 3.50
2028 7381 6.412072 GTCAAGATAAATACATGCACGCTTTC 59.588 38.462 0.00 0.00 0.00 2.62
2036 7389 7.304735 TGTGTTGTGTCAAGATAAATACATGC 58.695 34.615 0.00 0.00 0.00 4.06
2041 7394 7.686438 ATGCTGTGTTGTGTCAAGATAAATA 57.314 32.000 0.00 0.00 0.00 1.40
2046 7399 3.884693 TGAATGCTGTGTTGTGTCAAGAT 59.115 39.130 0.00 0.00 0.00 2.40
2164 7589 5.276461 TCGCTGAGAATCTATAGGCAAAA 57.724 39.130 0.00 0.00 34.92 2.44
2187 7612 2.124983 GATCAAGAGCTGGCCGCA 60.125 61.111 19.30 1.45 42.61 5.69
2192 7617 1.380524 CTGCCAAGATCAAGAGCTGG 58.619 55.000 0.00 0.00 0.00 4.85
2281 7720 0.391228 TAGCGGCAGTTTCAGTCACA 59.609 50.000 1.45 0.00 0.00 3.58
2300 7739 3.829026 GGCAGTCCCTTTCTTCTGAATTT 59.171 43.478 0.00 0.00 31.56 1.82
2333 7772 1.119574 ACGTGCTCCCAGGTTACAGT 61.120 55.000 0.00 0.00 36.75 3.55
2351 7790 0.109781 AACATTTGCATCACGCCGAC 60.110 50.000 0.00 0.00 41.33 4.79
2390 7829 4.206200 CGAAATTCCCAAGAAAAACGTGTG 59.794 41.667 0.00 0.00 35.09 3.82
2412 7851 0.966920 ACTACCAGAGTCCAACACCG 59.033 55.000 0.00 0.00 29.95 4.94
2456 7897 5.064071 GCACTAGCACATTTCTAAGGACTTC 59.936 44.000 0.00 0.00 41.58 3.01
2475 7916 3.143675 GCAGCAAGCACTAGCACTA 57.856 52.632 0.00 0.00 45.49 2.74
2476 7917 3.978272 GCAGCAAGCACTAGCACT 58.022 55.556 0.00 0.00 45.49 4.40
2531 7972 3.249189 AGGGCCGAAAGCTCCACA 61.249 61.111 0.00 0.00 46.61 4.17
2543 7984 3.979101 TTGGAAATGAAAATCAGGGCC 57.021 42.857 0.00 0.00 0.00 5.80
2560 8001 5.275695 CGACGTTGTCAAGTTGAATTTTTGG 60.276 40.000 7.25 0.00 32.09 3.28
2570 8011 1.931172 CCTGAACGACGTTGTCAAGTT 59.069 47.619 19.60 0.00 32.09 2.66
2574 8015 2.519377 AATCCTGAACGACGTTGTCA 57.481 45.000 19.60 10.12 32.09 3.58


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

AutoCloner maintained by Alex Coulton.