Multiple sequence alignment - TraesCS7D01G311200

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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 TraesCS7D01G311200 chr7D 100.000 2415 0 0 2561 4975 394828750 394831164 0.000000e+00 4460.0
1 TraesCS7D01G311200 chr7D 100.000 2337 0 0 1 2337 394826190 394828526 0.000000e+00 4316.0
2 TraesCS7D01G311200 chr7A 92.798 1680 67 27 2571 4213 448096461 448098123 0.000000e+00 2383.0
3 TraesCS7D01G311200 chr7A 90.849 1814 98 27 560 2337 448094668 448096449 0.000000e+00 2368.0
4 TraesCS7D01G311200 chr7A 96.216 555 13 4 4426 4972 448099596 448100150 0.000000e+00 902.0
5 TraesCS7D01G311200 chr7A 90.345 290 20 5 1 289 448094386 448094668 1.690000e-99 374.0
6 TraesCS7D01G311200 chr7A 93.617 47 2 1 2841 2886 448096690 448096736 8.940000e-08 69.4
7 TraesCS7D01G311200 chr7B 94.655 1422 53 10 533 1946 394398012 394399418 0.000000e+00 2183.0
8 TraesCS7D01G311200 chr7B 94.769 975 41 7 2567 3536 394400070 394401039 0.000000e+00 1509.0
9 TraesCS7D01G311200 chr7B 91.731 774 54 7 3537 4306 394401092 394401859 0.000000e+00 1066.0
10 TraesCS7D01G311200 chr7B 93.151 584 30 9 4397 4975 394401994 394402572 0.000000e+00 848.0
11 TraesCS7D01G311200 chr1B 86.598 97 11 2 431 525 518807884 518807980 6.810000e-19 106.0
12 TraesCS7D01G311200 chr1B 85.149 101 14 1 426 525 519518085 519518185 8.810000e-18 102.0
13 TraesCS7D01G311200 chr1B 84.158 101 15 1 426 525 519505604 519505704 4.100000e-16 97.1
14 TraesCS7D01G311200 chr1B 84.211 95 13 2 431 523 373145576 373145482 1.910000e-14 91.6
15 TraesCS7D01G311200 chr4A 88.372 86 10 0 437 522 690621558 690621643 2.450000e-18 104.0
16 TraesCS7D01G311200 chr1D 85.567 97 14 0 432 528 418194252 418194156 8.810000e-18 102.0
17 TraesCS7D01G311200 chr1D 84.211 95 13 2 431 523 273816401 273816307 1.910000e-14 91.6
18 TraesCS7D01G311200 chr1A 84.536 97 15 0 432 528 515546721 515546625 4.100000e-16 97.1
19 TraesCS7D01G311200 chr2B 85.714 91 12 1 433 522 542916918 542917008 1.470000e-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 TraesCS7D01G311200 chr7D 394826190 394831164 4974 False 4388.00 4460 100.0000 1 4975 2 chr7D.!!$F1 4974
1 TraesCS7D01G311200 chr7A 448094386 448100150 5764 False 1219.28 2383 92.7650 1 4972 5 chr7A.!!$F1 4971
2 TraesCS7D01G311200 chr7B 394398012 394402572 4560 False 1401.50 2183 93.5765 533 4975 4 chr7B.!!$F1 4442

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
81 83 0.112412 ACGTGGGGGAAAGCTTTCAT 59.888 50.000 33.88 5.08 38.92 2.57 F
384 386 0.179045 ACCGATGGCCTAATGAGCAC 60.179 55.000 3.32 0.00 0.00 4.40 F
386 388 0.530650 CGATGGCCTAATGAGCACGT 60.531 55.000 3.32 0.00 0.00 4.49 F
1701 1713 0.543749 GCACCTTCCTCATAGGCACT 59.456 55.000 0.00 0.00 46.37 4.40 F
1702 1714 1.065126 GCACCTTCCTCATAGGCACTT 60.065 52.381 0.00 0.00 41.75 3.16 F
2068 2364 1.348036 ACAGTTTAGGGCCTCAGTGAC 59.652 52.381 21.75 10.74 0.00 3.67 F
2828 3154 0.034863 GGGGGACGCTATTGAAACCA 60.035 55.000 0.00 0.00 38.67 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 1889 1.011968 CGCACTTAGTTGCACGCCTA 61.012 55.000 0.0 0.0 43.15 3.93 R
2211 2532 0.955178 ATCAGCCGACGACCAGATAG 59.045 55.000 0.0 0.0 0.00 2.08 R
2221 2542 2.749621 ACTTCCAAATCAATCAGCCGAC 59.250 45.455 0.0 0.0 0.00 4.79 R
2571 2892 0.032017 AGGCTACTCTAGGTGGGTGG 60.032 60.000 0.0 0.0 0.00 4.61 R
2573 2894 0.711184 ACAGGCTACTCTAGGTGGGT 59.289 55.000 0.0 0.0 0.00 4.51 R
3742 4135 1.422024 TCGTCAACCCAATCCAAAGGA 59.578 47.619 0.0 0.0 35.55 3.36 R
4336 4758 0.030101 CGAGCGATGGAGGAGAAGAC 59.970 60.000 0.0 0.0 0.00 3.01 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
65 66 2.295070 GGTTGTTCCAATGGCTAAACGT 59.705 45.455 0.00 0.00 35.97 3.99
71 72 0.322997 CAATGGCTAAACGTGGGGGA 60.323 55.000 0.00 0.00 0.00 4.81
72 73 0.406361 AATGGCTAAACGTGGGGGAA 59.594 50.000 0.00 0.00 0.00 3.97
73 74 0.406361 ATGGCTAAACGTGGGGGAAA 59.594 50.000 0.00 0.00 0.00 3.13
74 75 0.250989 TGGCTAAACGTGGGGGAAAG 60.251 55.000 0.00 0.00 0.00 2.62
75 76 1.592400 GGCTAAACGTGGGGGAAAGC 61.592 60.000 0.00 0.00 0.00 3.51
81 83 0.112412 ACGTGGGGGAAAGCTTTCAT 59.888 50.000 33.88 5.08 38.92 2.57
82 84 1.256812 CGTGGGGGAAAGCTTTCATT 58.743 50.000 33.88 4.68 38.92 2.57
90 92 3.440173 GGGAAAGCTTTCATTCGACATCA 59.560 43.478 33.88 0.00 38.92 3.07
129 131 1.244816 CGTGATATAGTCCCCAGCGA 58.755 55.000 0.00 0.00 0.00 4.93
156 158 6.893020 AAGTCTACATTAGAGTTTGGGGAT 57.107 37.500 0.00 0.00 43.97 3.85
170 172 2.418083 GGGATTTGGGCGAGCAAGG 61.418 63.158 0.00 0.00 0.00 3.61
273 275 4.888038 GTTGGACAAACTTTACGAAGGT 57.112 40.909 0.00 0.00 37.19 3.50
288 290 4.142038 ACGAAGGTTGGCTTTAGACAAAT 58.858 39.130 0.00 0.00 45.92 2.32
289 291 4.023193 ACGAAGGTTGGCTTTAGACAAATG 60.023 41.667 0.00 0.00 45.92 2.32
290 292 4.023193 CGAAGGTTGGCTTTAGACAAATGT 60.023 41.667 0.00 0.00 45.92 2.71
291 293 5.507315 CGAAGGTTGGCTTTAGACAAATGTT 60.507 40.000 0.00 0.00 45.92 2.71
292 294 6.293735 CGAAGGTTGGCTTTAGACAAATGTTA 60.294 38.462 0.00 0.00 45.92 2.41
293 295 7.539034 AAGGTTGGCTTTAGACAAATGTTAT 57.461 32.000 0.00 0.00 45.92 1.89
294 296 8.644374 AAGGTTGGCTTTAGACAAATGTTATA 57.356 30.769 0.00 0.00 45.92 0.98
295 297 8.051901 AGGTTGGCTTTAGACAAATGTTATAC 57.948 34.615 0.00 0.00 45.92 1.47
296 298 6.964934 GGTTGGCTTTAGACAAATGTTATACG 59.035 38.462 0.00 0.00 45.92 3.06
297 299 6.114221 TGGCTTTAGACAAATGTTATACGC 57.886 37.500 0.00 0.00 0.00 4.42
298 300 5.878116 TGGCTTTAGACAAATGTTATACGCT 59.122 36.000 0.00 0.00 0.00 5.07
299 301 7.042950 TGGCTTTAGACAAATGTTATACGCTA 58.957 34.615 0.00 0.00 0.00 4.26
300 302 7.549842 TGGCTTTAGACAAATGTTATACGCTAA 59.450 33.333 0.00 0.00 0.00 3.09
301 303 8.557029 GGCTTTAGACAAATGTTATACGCTAAT 58.443 33.333 0.00 0.00 0.00 1.73
302 304 9.931210 GCTTTAGACAAATGTTATACGCTAATT 57.069 29.630 0.00 0.00 0.00 1.40
318 320 5.419760 GCTAATTAAAAAGTAGCGGAGGG 57.580 43.478 3.69 0.00 43.86 4.30
319 321 5.121105 GCTAATTAAAAAGTAGCGGAGGGA 58.879 41.667 3.69 0.00 43.86 4.20
320 322 5.236695 GCTAATTAAAAAGTAGCGGAGGGAG 59.763 44.000 3.69 0.00 43.86 4.30
321 323 4.838904 ATTAAAAAGTAGCGGAGGGAGT 57.161 40.909 0.00 0.00 0.00 3.85
322 324 5.945144 ATTAAAAAGTAGCGGAGGGAGTA 57.055 39.130 0.00 0.00 0.00 2.59
323 325 3.606595 AAAAAGTAGCGGAGGGAGTAC 57.393 47.619 0.00 0.00 0.00 2.73
324 326 2.528673 AAAGTAGCGGAGGGAGTACT 57.471 50.000 0.00 0.00 0.00 2.73
325 327 2.528673 AAGTAGCGGAGGGAGTACTT 57.471 50.000 0.00 0.00 32.13 2.24
326 328 2.528673 AGTAGCGGAGGGAGTACTTT 57.471 50.000 0.00 0.00 0.00 2.66
327 329 2.100989 AGTAGCGGAGGGAGTACTTTG 58.899 52.381 0.00 0.00 0.00 2.77
328 330 1.823610 GTAGCGGAGGGAGTACTTTGT 59.176 52.381 0.00 0.00 0.00 2.83
329 331 1.349067 AGCGGAGGGAGTACTTTGTT 58.651 50.000 0.00 0.00 0.00 2.83
330 332 1.697982 AGCGGAGGGAGTACTTTGTTT 59.302 47.619 0.00 0.00 0.00 2.83
331 333 2.901839 AGCGGAGGGAGTACTTTGTTTA 59.098 45.455 0.00 0.00 0.00 2.01
332 334 3.518303 AGCGGAGGGAGTACTTTGTTTAT 59.482 43.478 0.00 0.00 0.00 1.40
333 335 3.621715 GCGGAGGGAGTACTTTGTTTATG 59.378 47.826 0.00 0.00 0.00 1.90
334 336 4.622220 GCGGAGGGAGTACTTTGTTTATGA 60.622 45.833 0.00 0.00 0.00 2.15
335 337 4.868734 CGGAGGGAGTACTTTGTTTATGAC 59.131 45.833 0.00 0.00 0.00 3.06
336 338 5.337330 CGGAGGGAGTACTTTGTTTATGACT 60.337 44.000 0.00 0.00 0.00 3.41
337 339 6.473758 GGAGGGAGTACTTTGTTTATGACTT 58.526 40.000 0.00 0.00 0.00 3.01
338 340 7.578189 CGGAGGGAGTACTTTGTTTATGACTTA 60.578 40.741 0.00 0.00 0.00 2.24
339 341 8.098912 GGAGGGAGTACTTTGTTTATGACTTAA 58.901 37.037 0.00 0.00 0.00 1.85
340 342 9.668497 GAGGGAGTACTTTGTTTATGACTTAAT 57.332 33.333 0.00 0.00 0.00 1.40
372 374 8.391075 ACCAATGACTTAATTTATACCGATGG 57.609 34.615 0.00 0.00 0.00 3.51
373 375 7.040686 ACCAATGACTTAATTTATACCGATGGC 60.041 37.037 0.00 0.00 0.00 4.40
374 376 7.305474 CAATGACTTAATTTATACCGATGGCC 58.695 38.462 0.00 0.00 0.00 5.36
375 377 6.182507 TGACTTAATTTATACCGATGGCCT 57.817 37.500 3.32 0.00 0.00 5.19
376 378 7.305813 TGACTTAATTTATACCGATGGCCTA 57.694 36.000 3.32 0.00 0.00 3.93
377 379 7.737869 TGACTTAATTTATACCGATGGCCTAA 58.262 34.615 3.32 0.00 0.00 2.69
378 380 8.380099 TGACTTAATTTATACCGATGGCCTAAT 58.620 33.333 3.32 0.00 0.00 1.73
379 381 8.561738 ACTTAATTTATACCGATGGCCTAATG 57.438 34.615 3.32 0.00 0.00 1.90
380 382 8.380099 ACTTAATTTATACCGATGGCCTAATGA 58.620 33.333 3.32 0.00 0.00 2.57
381 383 8.786826 TTAATTTATACCGATGGCCTAATGAG 57.213 34.615 3.32 0.00 0.00 2.90
382 384 2.770164 ATACCGATGGCCTAATGAGC 57.230 50.000 3.32 0.00 0.00 4.26
383 385 1.419381 TACCGATGGCCTAATGAGCA 58.581 50.000 3.32 0.00 0.00 4.26
384 386 0.179045 ACCGATGGCCTAATGAGCAC 60.179 55.000 3.32 0.00 0.00 4.40
385 387 1.224069 CCGATGGCCTAATGAGCACG 61.224 60.000 3.32 0.00 0.00 5.34
386 388 0.530650 CGATGGCCTAATGAGCACGT 60.531 55.000 3.32 0.00 0.00 4.49
387 389 1.668419 GATGGCCTAATGAGCACGTT 58.332 50.000 3.32 0.00 0.00 3.99
388 390 2.017049 GATGGCCTAATGAGCACGTTT 58.983 47.619 3.32 0.00 0.00 3.60
389 391 1.904287 TGGCCTAATGAGCACGTTTT 58.096 45.000 3.32 0.00 0.00 2.43
390 392 1.539388 TGGCCTAATGAGCACGTTTTG 59.461 47.619 3.32 0.00 0.00 2.44
391 393 1.539827 GGCCTAATGAGCACGTTTTGT 59.460 47.619 0.00 0.00 0.00 2.83
403 405 4.545823 CACGTTTTGTGTACCAATGACT 57.454 40.909 0.00 0.00 43.88 3.41
404 406 4.915704 CACGTTTTGTGTACCAATGACTT 58.084 39.130 0.00 0.00 43.88 3.01
405 407 6.050454 CACGTTTTGTGTACCAATGACTTA 57.950 37.500 0.00 0.00 43.88 2.24
406 408 6.487960 CACGTTTTGTGTACCAATGACTTAA 58.512 36.000 0.00 0.00 43.88 1.85
407 409 7.136119 CACGTTTTGTGTACCAATGACTTAAT 58.864 34.615 0.00 0.00 43.88 1.40
408 410 7.646130 CACGTTTTGTGTACCAATGACTTAATT 59.354 33.333 0.00 0.00 43.88 1.40
409 411 8.192110 ACGTTTTGTGTACCAATGACTTAATTT 58.808 29.630 0.00 0.00 31.81 1.82
410 412 9.666626 CGTTTTGTGTACCAATGACTTAATTTA 57.333 29.630 0.00 0.00 31.81 1.40
444 446 9.846248 ATTTTTACATTCAAAATTCTCTCTCCG 57.154 29.630 0.00 0.00 31.09 4.63
445 447 7.979444 TTTACATTCAAAATTCTCTCTCCGT 57.021 32.000 0.00 0.00 0.00 4.69
446 448 7.979444 TTACATTCAAAATTCTCTCTCCGTT 57.021 32.000 0.00 0.00 0.00 4.44
447 449 6.487689 ACATTCAAAATTCTCTCTCCGTTC 57.512 37.500 0.00 0.00 0.00 3.95
448 450 5.997746 ACATTCAAAATTCTCTCTCCGTTCA 59.002 36.000 0.00 0.00 0.00 3.18
449 451 6.656693 ACATTCAAAATTCTCTCTCCGTTCAT 59.343 34.615 0.00 0.00 0.00 2.57
450 452 7.824289 ACATTCAAAATTCTCTCTCCGTTCATA 59.176 33.333 0.00 0.00 0.00 2.15
451 453 8.668353 CATTCAAAATTCTCTCTCCGTTCATAA 58.332 33.333 0.00 0.00 0.00 1.90
452 454 7.834068 TCAAAATTCTCTCTCCGTTCATAAG 57.166 36.000 0.00 0.00 0.00 1.73
453 455 7.386851 TCAAAATTCTCTCTCCGTTCATAAGT 58.613 34.615 0.00 0.00 0.00 2.24
454 456 8.528643 TCAAAATTCTCTCTCCGTTCATAAGTA 58.471 33.333 0.00 0.00 0.00 2.24
455 457 9.319143 CAAAATTCTCTCTCCGTTCATAAGTAT 57.681 33.333 0.00 0.00 0.00 2.12
456 458 9.892130 AAAATTCTCTCTCCGTTCATAAGTATT 57.108 29.630 0.00 0.00 0.00 1.89
509 511 9.586435 CTACATATGTAGTGAAATGAGTGAACA 57.414 33.333 27.86 0.00 42.22 3.18
510 512 8.846943 ACATATGTAGTGAAATGAGTGAACAA 57.153 30.769 6.56 0.00 0.00 2.83
511 513 9.283768 ACATATGTAGTGAAATGAGTGAACAAA 57.716 29.630 6.56 0.00 0.00 2.83
512 514 9.546909 CATATGTAGTGAAATGAGTGAACAAAC 57.453 33.333 0.00 0.00 0.00 2.93
513 515 6.993786 TGTAGTGAAATGAGTGAACAAACA 57.006 33.333 0.00 0.00 0.00 2.83
514 516 6.781138 TGTAGTGAAATGAGTGAACAAACAC 58.219 36.000 0.00 0.00 40.60 3.32
515 517 5.895636 AGTGAAATGAGTGAACAAACACA 57.104 34.783 0.00 0.00 42.45 3.72
516 518 5.640732 AGTGAAATGAGTGAACAAACACAC 58.359 37.500 0.00 0.00 42.45 3.82
518 520 6.597672 AGTGAAATGAGTGAACAAACACACTA 59.402 34.615 0.00 0.00 45.54 2.74
519 521 7.120579 AGTGAAATGAGTGAACAAACACACTAA 59.879 33.333 0.00 0.00 45.54 2.24
520 522 7.753132 GTGAAATGAGTGAACAAACACACTAAA 59.247 33.333 0.00 0.00 45.54 1.85
521 523 8.300286 TGAAATGAGTGAACAAACACACTAAAA 58.700 29.630 0.00 0.00 45.54 1.52
522 524 9.134734 GAAATGAGTGAACAAACACACTAAAAA 57.865 29.630 0.00 0.00 45.54 1.94
523 525 9.651913 AAATGAGTGAACAAACACACTAAAAAT 57.348 25.926 0.00 0.00 45.54 1.82
524 526 8.633075 ATGAGTGAACAAACACACTAAAAATG 57.367 30.769 0.00 0.00 45.54 2.32
525 527 7.821652 TGAGTGAACAAACACACTAAAAATGA 58.178 30.769 0.00 0.00 45.54 2.57
526 528 7.967854 TGAGTGAACAAACACACTAAAAATGAG 59.032 33.333 0.00 0.00 45.54 2.90
527 529 7.826690 AGTGAACAAACACACTAAAAATGAGT 58.173 30.769 0.00 0.00 44.06 3.41
528 530 8.303876 AGTGAACAAACACACTAAAAATGAGTT 58.696 29.630 0.00 0.00 44.06 3.01
529 531 9.562583 GTGAACAAACACACTAAAAATGAGTTA 57.437 29.630 0.00 0.00 40.11 2.24
572 574 5.561679 ACTTTCAGTTTCCTAGACCATTCC 58.438 41.667 0.00 0.00 0.00 3.01
585 587 2.939103 GACCATTCCCGAATTCTCACAG 59.061 50.000 3.52 0.00 0.00 3.66
663 666 5.385198 AGGAGGAAAAAGCTACACAAATCA 58.615 37.500 0.00 0.00 0.00 2.57
669 672 8.806146 AGGAAAAAGCTACACAAATCACATAAT 58.194 29.630 0.00 0.00 0.00 1.28
885 891 1.227263 CACCCATCTACGCCCGAAG 60.227 63.158 0.00 0.00 0.00 3.79
1098 1110 3.003173 TCCAAGCCCCACTCCTCG 61.003 66.667 0.00 0.00 0.00 4.63
1699 1711 1.522092 CGCACCTTCCTCATAGGCA 59.478 57.895 0.00 0.00 36.17 4.75
1700 1712 0.811616 CGCACCTTCCTCATAGGCAC 60.812 60.000 0.00 0.00 36.17 5.01
1701 1713 0.543749 GCACCTTCCTCATAGGCACT 59.456 55.000 0.00 0.00 46.37 4.40
1702 1714 1.065126 GCACCTTCCTCATAGGCACTT 60.065 52.381 0.00 0.00 41.75 3.16
1703 1715 2.636830 CACCTTCCTCATAGGCACTTG 58.363 52.381 0.00 0.00 41.75 3.16
1704 1716 2.237143 CACCTTCCTCATAGGCACTTGA 59.763 50.000 0.00 0.00 41.75 3.02
1705 1717 3.118112 CACCTTCCTCATAGGCACTTGAT 60.118 47.826 0.00 0.00 41.75 2.57
1706 1718 4.101585 CACCTTCCTCATAGGCACTTGATA 59.898 45.833 0.00 0.00 41.75 2.15
1758 1771 2.029380 AGTATGTTGCGTCTGTGTGCTA 60.029 45.455 0.00 0.00 0.00 3.49
1791 1804 6.818142 TCGATTACTGAATGACATGTGATTGT 59.182 34.615 15.60 10.26 0.00 2.71
1793 1806 7.427318 CGATTACTGAATGACATGTGATTGTTG 59.573 37.037 15.60 7.46 0.00 3.33
1795 1808 5.072055 ACTGAATGACATGTGATTGTTGGA 58.928 37.500 15.60 0.00 0.00 3.53
1816 1838 1.596603 TGGTGTGTCATGCTGTGAAG 58.403 50.000 0.00 0.00 38.90 3.02
1825 1847 3.127548 GTCATGCTGTGAAGTGGTTATGG 59.872 47.826 0.00 0.00 38.90 2.74
1834 1856 5.428457 TGTGAAGTGGTTATGGGATGATACT 59.572 40.000 0.00 0.00 0.00 2.12
1835 1857 5.760253 GTGAAGTGGTTATGGGATGATACTG 59.240 44.000 0.00 0.00 0.00 2.74
1864 1887 7.260603 GTGGTTTTATCTCGCTTAGGTAGTTA 58.739 38.462 0.00 0.00 0.00 2.24
1865 1888 7.924947 GTGGTTTTATCTCGCTTAGGTAGTTAT 59.075 37.037 0.00 0.00 0.00 1.89
1866 1889 8.480501 TGGTTTTATCTCGCTTAGGTAGTTATT 58.519 33.333 0.00 0.00 0.00 1.40
1867 1890 9.971922 GGTTTTATCTCGCTTAGGTAGTTATTA 57.028 33.333 0.00 0.00 0.00 0.98
1870 1893 5.702349 TCTCGCTTAGGTAGTTATTAGGC 57.298 43.478 0.00 0.00 0.00 3.93
1902 1928 8.258708 ACTAAGTGCGTTTTATCTAGGAGAATT 58.741 33.333 0.00 0.00 0.00 2.17
1910 1936 7.201530 CGTTTTATCTAGGAGAATTGTTCGCTT 60.202 37.037 0.00 0.00 34.02 4.68
1911 1937 8.451748 GTTTTATCTAGGAGAATTGTTCGCTTT 58.548 33.333 0.00 0.00 34.02 3.51
1924 1950 2.161831 CGCTTTTCTGATGTGGCGA 58.838 52.632 0.00 0.00 44.36 5.54
1927 1953 1.470098 GCTTTTCTGATGTGGCGATGT 59.530 47.619 0.00 0.00 0.00 3.06
1932 1958 5.984233 TTTCTGATGTGGCGATGTATTAC 57.016 39.130 0.00 0.00 0.00 1.89
1960 2256 5.522460 GTCCATTTTTGCAATGATCATCTGG 59.478 40.000 9.06 3.23 0.00 3.86
2021 2317 6.009589 TGATTGTTTGGTGGATAGTGTGAAT 58.990 36.000 0.00 0.00 0.00 2.57
2052 2348 4.078639 GGCTGAAGAATGCCTATACAGT 57.921 45.455 0.00 0.00 45.26 3.55
2060 2356 3.790089 ATGCCTATACAGTTTAGGGCC 57.210 47.619 16.46 0.00 37.32 5.80
2068 2364 1.348036 ACAGTTTAGGGCCTCAGTGAC 59.652 52.381 21.75 10.74 0.00 3.67
2079 2375 3.933332 GGCCTCAGTGACTGTTTGTATAC 59.067 47.826 12.93 0.00 32.61 1.47
2089 2385 7.340999 AGTGACTGTTTGTATACTTTTTGGGTT 59.659 33.333 4.17 0.00 0.00 4.11
2093 2389 8.141268 ACTGTTTGTATACTTTTTGGGTTCATG 58.859 33.333 4.17 0.00 0.00 3.07
2111 2407 5.622770 TCATGTATGCAATGATCATCTGC 57.377 39.130 24.18 24.18 36.60 4.26
2151 2447 1.799181 CGGTGAAGCGGTGTAGATGAG 60.799 57.143 0.00 0.00 0.00 2.90
2163 2459 4.009675 GTGTAGATGAGCATTTGGTGGAA 58.990 43.478 0.00 0.00 0.00 3.53
2164 2460 4.095483 GTGTAGATGAGCATTTGGTGGAAG 59.905 45.833 0.00 0.00 0.00 3.46
2165 2461 3.726557 AGATGAGCATTTGGTGGAAGA 57.273 42.857 0.00 0.00 0.00 2.87
2166 2462 4.038271 AGATGAGCATTTGGTGGAAGAA 57.962 40.909 0.00 0.00 0.00 2.52
2167 2463 4.607239 AGATGAGCATTTGGTGGAAGAAT 58.393 39.130 0.00 0.00 0.00 2.40
2168 2464 4.401519 AGATGAGCATTTGGTGGAAGAATG 59.598 41.667 0.00 0.00 34.67 2.67
2211 2532 7.324616 GCATGAGTGACTGTTTGTATTCTTTTC 59.675 37.037 0.00 0.00 0.00 2.29
2221 2542 8.251750 TGTTTGTATTCTTTTCTATCTGGTCG 57.748 34.615 0.00 0.00 0.00 4.79
2223 2544 8.381387 GTTTGTATTCTTTTCTATCTGGTCGTC 58.619 37.037 0.00 0.00 0.00 4.20
2252 2573 2.562298 TGATTTGGAAGTTGATGCCACC 59.438 45.455 0.00 0.00 0.00 4.61
2253 2574 2.380064 TTTGGAAGTTGATGCCACCT 57.620 45.000 0.00 0.00 0.00 4.00
2306 2627 6.233434 AGTAAACTGCTTCTTCATGACATCA 58.767 36.000 0.00 0.00 0.00 3.07
2323 2644 7.912056 TGACATCATGAGTCTTTTTCCTTAG 57.088 36.000 19.39 0.00 36.94 2.18
2324 2645 7.453393 TGACATCATGAGTCTTTTTCCTTAGT 58.547 34.615 19.39 0.00 36.94 2.24
2577 2898 3.814906 CACACACCCACCCACCCA 61.815 66.667 0.00 0.00 0.00 4.51
2578 2899 3.816090 ACACACCCACCCACCCAC 61.816 66.667 0.00 0.00 0.00 4.61
2579 2900 4.596585 CACACCCACCCACCCACC 62.597 72.222 0.00 0.00 0.00 4.61
2580 2901 4.855230 ACACCCACCCACCCACCT 62.855 66.667 0.00 0.00 0.00 4.00
2581 2902 2.530661 CACCCACCCACCCACCTA 60.531 66.667 0.00 0.00 0.00 3.08
2582 2903 2.204090 ACCCACCCACCCACCTAG 60.204 66.667 0.00 0.00 0.00 3.02
2592 2913 0.711184 ACCCACCTAGAGTAGCCTGT 59.289 55.000 0.00 0.00 0.00 4.00
2627 2948 5.696270 GGCCTTGATTTGGAAGTTACTTTTG 59.304 40.000 0.00 0.00 0.00 2.44
2639 2960 3.767131 AGTTACTTTTGTTTGTGGTGGCT 59.233 39.130 0.00 0.00 0.00 4.75
2647 2968 3.096092 TGTTTGTGGTGGCTTCTCTTTT 58.904 40.909 0.00 0.00 0.00 2.27
2662 2983 6.147000 GCTTCTCTTTTAGTATAGAGCATGCC 59.853 42.308 15.66 6.03 38.20 4.40
2788 3114 0.108281 TGACACGTTCACCCGTTCAA 60.108 50.000 0.00 0.00 39.45 2.69
2820 3146 3.849951 CGCTGTGGGGGACGCTAT 61.850 66.667 0.00 0.00 43.80 2.97
2828 3154 0.034863 GGGGGACGCTATTGAAACCA 60.035 55.000 0.00 0.00 38.67 3.67
2839 3165 3.922171 ATTGAAACCAAAACCCAGCAA 57.078 38.095 0.00 0.00 0.00 3.91
2871 3197 1.092348 GGGGACGCTAATGAAACCAC 58.908 55.000 0.00 0.00 0.00 4.16
2900 3226 0.817229 TGTTCATGCACGTCCAAGCA 60.817 50.000 0.39 0.39 45.92 3.91
3164 3490 4.271049 CAGAAATTCCGCATGTCTCGTATT 59.729 41.667 0.00 0.00 24.61 1.89
3231 3557 5.169295 AGAAAGCGTCTTGGTAGATGTTAC 58.831 41.667 0.00 0.00 39.24 2.50
3235 3561 3.119245 GCGTCTTGGTAGATGTTACCAGA 60.119 47.826 6.21 4.46 46.93 3.86
3445 3771 8.084590 AGATTCTGTTGTTTAAGGTTTCTACG 57.915 34.615 0.00 0.00 0.00 3.51
3661 4053 5.649557 TGGAAACAGAAAACAGATGTGTTG 58.350 37.500 9.27 0.00 40.17 3.33
3672 4065 6.538945 AACAGATGTGTTGGGTTTTTAGTT 57.461 33.333 7.55 0.00 45.58 2.24
3740 4133 1.259609 TTCAAATGCCTTCAGCCCTG 58.740 50.000 0.00 0.00 42.71 4.45
3742 4135 0.971386 CAAATGCCTTCAGCCCTGTT 59.029 50.000 0.00 0.00 42.71 3.16
3756 4149 1.203174 CCCTGTTCCTTTGGATTGGGT 60.203 52.381 9.42 0.00 33.93 4.51
3772 4165 1.758280 TGGGTTGACGACTGTAGTGTT 59.242 47.619 0.00 0.00 0.00 3.32
3773 4166 2.223876 TGGGTTGACGACTGTAGTGTTC 60.224 50.000 0.00 0.00 0.00 3.18
4002 4420 1.681793 CTACTACCCCGTGGAGATGTG 59.318 57.143 0.00 0.00 34.81 3.21
4007 4425 0.037590 CCCCGTGGAGATGTGGAAAA 59.962 55.000 0.00 0.00 0.00 2.29
4022 4440 4.220382 TGTGGAAAATTGTAATCAGCCTGG 59.780 41.667 0.00 0.00 0.00 4.45
4052 4470 1.098712 GTTTTGGCTCCGTGGTGACA 61.099 55.000 0.00 0.00 38.70 3.58
4082 4500 1.562008 TGGAAACGCAGGATATTCCCA 59.438 47.619 0.00 0.00 40.49 4.37
4161 4579 4.286032 TGCTGTATCTAGTTTGGTGGTTCT 59.714 41.667 0.00 0.00 0.00 3.01
4225 4647 4.856115 AACTTTTGAATTGTTGCCAACG 57.144 36.364 2.68 0.00 32.26 4.10
4268 4690 0.108424 CTGCTTCCTTCGTCTCAGGG 60.108 60.000 0.00 0.00 31.50 4.45
4277 4699 1.847328 TCGTCTCAGGGACATAAGCA 58.153 50.000 0.15 0.00 44.70 3.91
4281 4703 3.617531 CGTCTCAGGGACATAAGCACTTT 60.618 47.826 0.15 0.00 44.70 2.66
4312 4734 3.382048 GAGTTTACCTCGTCAACCTGT 57.618 47.619 0.00 0.00 0.00 4.00
4313 4735 3.725490 GAGTTTACCTCGTCAACCTGTT 58.275 45.455 0.00 0.00 0.00 3.16
4318 4740 3.832615 ACCTCGTCAACCTGTTTTAGT 57.167 42.857 0.00 0.00 0.00 2.24
4319 4741 4.146745 ACCTCGTCAACCTGTTTTAGTT 57.853 40.909 0.00 0.00 0.00 2.24
4321 4743 4.141779 ACCTCGTCAACCTGTTTTAGTTCT 60.142 41.667 0.00 0.00 0.00 3.01
4324 4746 3.311322 CGTCAACCTGTTTTAGTTCTGCA 59.689 43.478 0.00 0.00 0.00 4.41
4325 4747 4.201871 CGTCAACCTGTTTTAGTTCTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
4326 4748 5.646606 GTCAACCTGTTTTAGTTCTGCAAA 58.353 37.500 0.00 0.00 0.00 3.68
4327 4749 6.273071 GTCAACCTGTTTTAGTTCTGCAAAT 58.727 36.000 0.00 0.00 0.00 2.32
4328 4750 7.422399 GTCAACCTGTTTTAGTTCTGCAAATA 58.578 34.615 0.00 0.00 0.00 1.40
4332 4754 8.177119 ACCTGTTTTAGTTCTGCAAATAATCA 57.823 30.769 0.00 0.00 0.00 2.57
4333 4755 8.806146 ACCTGTTTTAGTTCTGCAAATAATCAT 58.194 29.630 0.00 0.00 0.00 2.45
4334 4756 9.079833 CCTGTTTTAGTTCTGCAAATAATCATG 57.920 33.333 0.00 0.00 0.00 3.07
4335 4757 8.984891 TGTTTTAGTTCTGCAAATAATCATGG 57.015 30.769 0.00 0.00 0.00 3.66
4336 4758 8.034215 TGTTTTAGTTCTGCAAATAATCATGGG 58.966 33.333 0.00 0.00 0.00 4.00
4337 4759 7.716799 TTTAGTTCTGCAAATAATCATGGGT 57.283 32.000 0.00 0.00 0.00 4.51
4339 4761 5.513233 AGTTCTGCAAATAATCATGGGTCT 58.487 37.500 0.00 0.00 0.00 3.85
4340 4762 5.954150 AGTTCTGCAAATAATCATGGGTCTT 59.046 36.000 0.00 0.00 0.00 3.01
4341 4763 6.096001 AGTTCTGCAAATAATCATGGGTCTTC 59.904 38.462 0.00 0.00 0.00 2.87
4342 4764 5.759059 TCTGCAAATAATCATGGGTCTTCT 58.241 37.500 0.00 0.00 0.00 2.85
4343 4765 5.824624 TCTGCAAATAATCATGGGTCTTCTC 59.175 40.000 0.00 0.00 0.00 2.87
4345 4767 5.136105 GCAAATAATCATGGGTCTTCTCCT 58.864 41.667 0.00 0.00 0.00 3.69
4346 4768 5.240403 GCAAATAATCATGGGTCTTCTCCTC 59.760 44.000 0.00 0.00 0.00 3.71
4347 4769 5.574970 AATAATCATGGGTCTTCTCCTCC 57.425 43.478 0.00 0.00 0.00 4.30
4348 4770 2.575921 ATCATGGGTCTTCTCCTCCA 57.424 50.000 0.00 0.00 0.00 3.86
4349 4771 2.575921 TCATGGGTCTTCTCCTCCAT 57.424 50.000 0.00 0.00 40.30 3.41
4351 4773 1.069823 CATGGGTCTTCTCCTCCATCG 59.930 57.143 0.00 0.00 37.86 3.84
4352 4774 1.330655 TGGGTCTTCTCCTCCATCGC 61.331 60.000 0.00 0.00 0.00 4.58
4354 6044 0.387565 GGTCTTCTCCTCCATCGCTC 59.612 60.000 0.00 0.00 0.00 5.03
4357 6047 2.081425 CTTCTCCTCCATCGCTCGGG 62.081 65.000 0.00 0.00 0.00 5.14
4361 6051 2.587194 CTCCATCGCTCGGGCTTG 60.587 66.667 5.36 2.42 36.09 4.01
4365 6055 3.127533 ATCGCTCGGGCTTGTTGC 61.128 61.111 5.36 0.00 41.94 4.17
4406 6108 2.688507 ACAGTCGAATGCACGAAGATT 58.311 42.857 13.64 0.00 43.75 2.40
4493 6206 5.655488 TGATCTCCGATCTTGTCTTTTCTC 58.345 41.667 5.55 0.00 0.00 2.87
4557 6270 7.824704 TCTAGAGTACGCTTATATTCCTACG 57.175 40.000 3.89 0.00 0.00 3.51
4575 6289 5.010719 TCCTACGGCGAGATATCTCAATTTT 59.989 40.000 27.97 12.91 43.00 1.82
4721 6440 2.101185 CTCGATCGCACACTCGCT 59.899 61.111 11.09 0.00 34.94 4.93
4763 6482 2.669364 TCGTTCCTTCTAGAAACGCAC 58.331 47.619 18.88 7.38 0.00 5.34
4764 6483 2.295349 TCGTTCCTTCTAGAAACGCACT 59.705 45.455 18.88 0.00 0.00 4.40
4774 6494 1.648467 GAAACGCACTGGAGGGCATC 61.648 60.000 1.07 0.00 0.00 3.91
4804 6524 2.737180 CTCGCACCTCACACCACT 59.263 61.111 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.440263 TGGAACAACCCAGTTTTGTCTGG 61.440 47.826 5.83 5.83 44.99 3.86
47 48 1.883275 CCACGTTTAGCCATTGGAACA 59.117 47.619 6.95 0.00 0.00 3.18
65 66 1.074727 TCGAATGAAAGCTTTCCCCCA 59.925 47.619 31.14 17.07 36.36 4.96
71 72 5.437289 TGTTGATGTCGAATGAAAGCTTT 57.563 34.783 12.53 12.53 0.00 3.51
72 73 5.633830 ATGTTGATGTCGAATGAAAGCTT 57.366 34.783 0.00 0.00 0.00 3.74
73 74 6.932356 ATATGTTGATGTCGAATGAAAGCT 57.068 33.333 0.00 0.00 0.00 3.74
74 75 8.715998 AGATATATGTTGATGTCGAATGAAAGC 58.284 33.333 0.00 0.00 0.00 3.51
129 131 6.715264 CCCCAAACTCTAATGTAGACTTTTGT 59.285 38.462 10.72 0.00 34.19 2.83
156 158 1.377202 CTAGCCTTGCTCGCCCAAA 60.377 57.895 0.00 0.00 40.44 3.28
269 271 5.869649 AACATTTGTCTAAAGCCAACCTT 57.130 34.783 0.00 0.00 34.51 3.50
273 275 6.373216 AGCGTATAACATTTGTCTAAAGCCAA 59.627 34.615 0.00 0.00 0.00 4.52
296 298 5.121105 TCCCTCCGCTACTTTTTAATTAGC 58.879 41.667 0.00 0.00 35.80 3.09
297 299 6.346896 ACTCCCTCCGCTACTTTTTAATTAG 58.653 40.000 0.00 0.00 0.00 1.73
298 300 6.303903 ACTCCCTCCGCTACTTTTTAATTA 57.696 37.500 0.00 0.00 0.00 1.40
299 301 5.175388 ACTCCCTCCGCTACTTTTTAATT 57.825 39.130 0.00 0.00 0.00 1.40
300 302 4.838904 ACTCCCTCCGCTACTTTTTAAT 57.161 40.909 0.00 0.00 0.00 1.40
301 303 4.774200 AGTACTCCCTCCGCTACTTTTTAA 59.226 41.667 0.00 0.00 0.00 1.52
302 304 4.347607 AGTACTCCCTCCGCTACTTTTTA 58.652 43.478 0.00 0.00 0.00 1.52
303 305 3.171528 AGTACTCCCTCCGCTACTTTTT 58.828 45.455 0.00 0.00 0.00 1.94
304 306 2.817665 AGTACTCCCTCCGCTACTTTT 58.182 47.619 0.00 0.00 0.00 2.27
305 307 2.528673 AGTACTCCCTCCGCTACTTT 57.471 50.000 0.00 0.00 0.00 2.66
306 308 2.496470 CAAAGTACTCCCTCCGCTACTT 59.504 50.000 0.00 0.00 32.03 2.24
307 309 2.100989 CAAAGTACTCCCTCCGCTACT 58.899 52.381 0.00 0.00 0.00 2.57
308 310 1.823610 ACAAAGTACTCCCTCCGCTAC 59.176 52.381 0.00 0.00 0.00 3.58
309 311 2.226962 ACAAAGTACTCCCTCCGCTA 57.773 50.000 0.00 0.00 0.00 4.26
310 312 1.349067 AACAAAGTACTCCCTCCGCT 58.651 50.000 0.00 0.00 0.00 5.52
311 313 2.180432 AAACAAAGTACTCCCTCCGC 57.820 50.000 0.00 0.00 0.00 5.54
312 314 4.868734 GTCATAAACAAAGTACTCCCTCCG 59.131 45.833 0.00 0.00 0.00 4.63
313 315 6.051179 AGTCATAAACAAAGTACTCCCTCC 57.949 41.667 0.00 0.00 0.00 4.30
314 316 9.668497 ATTAAGTCATAAACAAAGTACTCCCTC 57.332 33.333 0.00 0.00 0.00 4.30
346 348 9.496873 CCATCGGTATAAATTAAGTCATTGGTA 57.503 33.333 0.00 0.00 0.00 3.25
347 349 7.040686 GCCATCGGTATAAATTAAGTCATTGGT 60.041 37.037 0.00 0.00 0.00 3.67
348 350 7.305474 GCCATCGGTATAAATTAAGTCATTGG 58.695 38.462 0.00 0.00 0.00 3.16
349 351 7.174946 AGGCCATCGGTATAAATTAAGTCATTG 59.825 37.037 5.01 0.00 0.00 2.82
350 352 7.231467 AGGCCATCGGTATAAATTAAGTCATT 58.769 34.615 5.01 0.00 0.00 2.57
351 353 6.779860 AGGCCATCGGTATAAATTAAGTCAT 58.220 36.000 5.01 0.00 0.00 3.06
352 354 6.182507 AGGCCATCGGTATAAATTAAGTCA 57.817 37.500 5.01 0.00 0.00 3.41
353 355 8.665685 CATTAGGCCATCGGTATAAATTAAGTC 58.334 37.037 5.01 0.00 0.00 3.01
354 356 8.380099 TCATTAGGCCATCGGTATAAATTAAGT 58.620 33.333 5.01 0.00 0.00 2.24
355 357 8.786826 TCATTAGGCCATCGGTATAAATTAAG 57.213 34.615 5.01 0.00 0.00 1.85
356 358 7.335924 GCTCATTAGGCCATCGGTATAAATTAA 59.664 37.037 5.01 0.00 0.00 1.40
357 359 6.821665 GCTCATTAGGCCATCGGTATAAATTA 59.178 38.462 5.01 0.00 0.00 1.40
358 360 5.648092 GCTCATTAGGCCATCGGTATAAATT 59.352 40.000 5.01 0.00 0.00 1.82
359 361 5.186198 GCTCATTAGGCCATCGGTATAAAT 58.814 41.667 5.01 0.00 0.00 1.40
360 362 4.041075 TGCTCATTAGGCCATCGGTATAAA 59.959 41.667 5.01 0.00 0.00 1.40
361 363 3.580895 TGCTCATTAGGCCATCGGTATAA 59.419 43.478 5.01 0.00 0.00 0.98
362 364 3.056107 GTGCTCATTAGGCCATCGGTATA 60.056 47.826 5.01 0.00 0.00 1.47
363 365 1.977854 TGCTCATTAGGCCATCGGTAT 59.022 47.619 5.01 0.00 0.00 2.73
364 366 1.070134 GTGCTCATTAGGCCATCGGTA 59.930 52.381 5.01 0.00 0.00 4.02
365 367 0.179045 GTGCTCATTAGGCCATCGGT 60.179 55.000 5.01 0.00 0.00 4.69
366 368 1.224069 CGTGCTCATTAGGCCATCGG 61.224 60.000 5.01 0.00 0.00 4.18
367 369 0.530650 ACGTGCTCATTAGGCCATCG 60.531 55.000 5.01 0.00 0.00 3.84
368 370 1.668419 AACGTGCTCATTAGGCCATC 58.332 50.000 5.01 0.00 0.00 3.51
369 371 2.128771 AAACGTGCTCATTAGGCCAT 57.871 45.000 5.01 0.00 0.00 4.40
370 372 1.539388 CAAAACGTGCTCATTAGGCCA 59.461 47.619 5.01 0.00 0.00 5.36
371 373 1.539827 ACAAAACGTGCTCATTAGGCC 59.460 47.619 0.00 0.00 0.00 5.19
372 374 2.584791 CACAAAACGTGCTCATTAGGC 58.415 47.619 0.00 0.00 39.19 3.93
383 385 6.680874 TTAAGTCATTGGTACACAAAACGT 57.319 33.333 0.00 0.00 43.46 3.99
384 386 8.568732 AAATTAAGTCATTGGTACACAAAACG 57.431 30.769 0.00 0.00 43.46 3.60
418 420 9.846248 CGGAGAGAGAATTTTGAATGTAAAAAT 57.154 29.630 0.00 0.00 38.54 1.82
419 421 8.846211 ACGGAGAGAGAATTTTGAATGTAAAAA 58.154 29.630 0.00 0.00 33.67 1.94
420 422 8.391075 ACGGAGAGAGAATTTTGAATGTAAAA 57.609 30.769 0.00 0.00 34.39 1.52
421 423 7.979444 ACGGAGAGAGAATTTTGAATGTAAA 57.021 32.000 0.00 0.00 0.00 2.01
422 424 7.659799 TGAACGGAGAGAGAATTTTGAATGTAA 59.340 33.333 0.00 0.00 0.00 2.41
423 425 7.158697 TGAACGGAGAGAGAATTTTGAATGTA 58.841 34.615 0.00 0.00 0.00 2.29
424 426 5.997746 TGAACGGAGAGAGAATTTTGAATGT 59.002 36.000 0.00 0.00 0.00 2.71
425 427 6.486253 TGAACGGAGAGAGAATTTTGAATG 57.514 37.500 0.00 0.00 0.00 2.67
426 428 8.792830 TTATGAACGGAGAGAGAATTTTGAAT 57.207 30.769 0.00 0.00 0.00 2.57
427 429 7.878127 ACTTATGAACGGAGAGAGAATTTTGAA 59.122 33.333 0.00 0.00 0.00 2.69
428 430 7.386851 ACTTATGAACGGAGAGAGAATTTTGA 58.613 34.615 0.00 0.00 0.00 2.69
429 431 7.602517 ACTTATGAACGGAGAGAGAATTTTG 57.397 36.000 0.00 0.00 0.00 2.44
430 432 9.892130 AATACTTATGAACGGAGAGAGAATTTT 57.108 29.630 0.00 0.00 0.00 1.82
484 486 9.936759 TTGTTCACTCATTTCACTACATATGTA 57.063 29.630 14.75 14.75 0.00 2.29
485 487 8.846943 TTGTTCACTCATTTCACTACATATGT 57.153 30.769 13.93 13.93 0.00 2.29
486 488 9.546909 GTTTGTTCACTCATTTCACTACATATG 57.453 33.333 0.00 0.00 0.00 1.78
487 489 9.283768 TGTTTGTTCACTCATTTCACTACATAT 57.716 29.630 0.00 0.00 0.00 1.78
488 490 8.556194 GTGTTTGTTCACTCATTTCACTACATA 58.444 33.333 0.00 0.00 35.68 2.29
489 491 7.066887 TGTGTTTGTTCACTCATTTCACTACAT 59.933 33.333 0.00 0.00 38.90 2.29
490 492 6.372937 TGTGTTTGTTCACTCATTTCACTACA 59.627 34.615 0.00 0.00 38.90 2.74
491 493 6.687105 GTGTGTTTGTTCACTCATTTCACTAC 59.313 38.462 0.00 0.00 38.90 2.73
492 494 6.597672 AGTGTGTTTGTTCACTCATTTCACTA 59.402 34.615 0.00 0.00 40.28 2.74
493 495 5.415701 AGTGTGTTTGTTCACTCATTTCACT 59.584 36.000 0.00 0.00 40.28 3.41
494 496 5.640732 AGTGTGTTTGTTCACTCATTTCAC 58.359 37.500 0.00 0.00 40.28 3.18
495 497 5.895636 AGTGTGTTTGTTCACTCATTTCA 57.104 34.783 0.00 0.00 40.28 2.69
496 498 8.682128 TTTTAGTGTGTTTGTTCACTCATTTC 57.318 30.769 1.08 0.00 42.77 2.17
497 499 9.651913 ATTTTTAGTGTGTTTGTTCACTCATTT 57.348 25.926 1.08 0.00 42.77 2.32
498 500 9.086336 CATTTTTAGTGTGTTTGTTCACTCATT 57.914 29.630 1.08 0.00 42.77 2.57
499 501 8.465999 TCATTTTTAGTGTGTTTGTTCACTCAT 58.534 29.630 1.08 0.00 42.77 2.90
500 502 7.821652 TCATTTTTAGTGTGTTTGTTCACTCA 58.178 30.769 1.08 0.00 42.77 3.41
501 503 7.968405 ACTCATTTTTAGTGTGTTTGTTCACTC 59.032 33.333 1.08 0.00 42.77 3.51
502 504 7.826690 ACTCATTTTTAGTGTGTTTGTTCACT 58.173 30.769 0.00 0.00 45.21 3.41
503 505 8.460831 AACTCATTTTTAGTGTGTTTGTTCAC 57.539 30.769 0.00 0.00 38.63 3.18
511 513 9.609346 ACTGTAGTTAACTCATTTTTAGTGTGT 57.391 29.630 12.39 0.00 0.00 3.72
530 532 9.826574 CTGAAAGTATCTCTCTACTACTGTAGT 57.173 37.037 22.72 22.72 44.74 2.73
550 552 4.944317 GGGAATGGTCTAGGAAACTGAAAG 59.056 45.833 0.00 0.00 43.88 2.62
572 574 2.622436 GGTCTTCCTGTGAGAATTCGG 58.378 52.381 0.00 0.00 0.00 4.30
585 587 2.029964 TTGTCGCACCGGTCTTCC 59.970 61.111 2.59 0.00 0.00 3.46
596 599 0.027586 AGTTTTGACGCTGTTGTCGC 59.972 50.000 0.00 0.00 41.87 5.19
597 600 1.326245 TCAGTTTTGACGCTGTTGTCG 59.674 47.619 0.00 0.00 41.87 4.35
663 666 4.665833 TCAGTAGCGCCAAGTATTATGT 57.334 40.909 2.29 0.00 0.00 2.29
669 672 1.890489 TGACTTCAGTAGCGCCAAGTA 59.110 47.619 2.29 0.00 0.00 2.24
670 673 0.679505 TGACTTCAGTAGCGCCAAGT 59.320 50.000 2.29 4.81 0.00 3.16
924 930 1.229984 AGGTTGGAGAGGGGAAGGG 60.230 63.158 0.00 0.00 0.00 3.95
1605 1617 2.722201 CCAGTAGGACGGGCAGGAC 61.722 68.421 0.00 0.00 36.89 3.85
1699 1711 8.820933 CACAATTCACGATATCAAGTATCAAGT 58.179 33.333 3.12 0.00 39.36 3.16
1700 1712 9.034544 TCACAATTCACGATATCAAGTATCAAG 57.965 33.333 3.12 0.00 39.36 3.02
1701 1713 8.940768 TCACAATTCACGATATCAAGTATCAA 57.059 30.769 3.12 0.00 39.36 2.57
1702 1714 8.981647 CATCACAATTCACGATATCAAGTATCA 58.018 33.333 3.12 0.00 39.36 2.15
1703 1715 9.196552 TCATCACAATTCACGATATCAAGTATC 57.803 33.333 3.12 0.00 36.61 2.24
1704 1716 9.716531 ATCATCACAATTCACGATATCAAGTAT 57.283 29.630 3.12 0.00 0.00 2.12
1706 1718 9.716531 ATATCATCACAATTCACGATATCAAGT 57.283 29.630 3.12 0.00 0.00 3.16
1758 1771 7.809546 TGTCATTCAGTAATCGAGTAGATCT 57.190 36.000 0.00 0.00 38.98 2.75
1791 1804 1.887854 CAGCATGACACACCAATCCAA 59.112 47.619 0.00 0.00 39.69 3.53
1793 1806 1.200716 CACAGCATGACACACCAATCC 59.799 52.381 0.00 0.00 39.69 3.01
1795 1808 2.275134 TCACAGCATGACACACCAAT 57.725 45.000 0.00 0.00 39.69 3.16
1816 1838 4.263068 CCCTCAGTATCATCCCATAACCAC 60.263 50.000 0.00 0.00 0.00 4.16
1825 1847 3.933861 AAACCACCCTCAGTATCATCC 57.066 47.619 0.00 0.00 0.00 3.51
1834 1856 1.906574 AGCGAGATAAAACCACCCTCA 59.093 47.619 0.00 0.00 0.00 3.86
1835 1857 2.693267 AGCGAGATAAAACCACCCTC 57.307 50.000 0.00 0.00 0.00 4.30
1864 1887 1.737793 GCACTTAGTTGCACGCCTAAT 59.262 47.619 0.00 0.00 42.49 1.73
1865 1888 1.153353 GCACTTAGTTGCACGCCTAA 58.847 50.000 0.00 0.00 42.49 2.69
1866 1889 1.011968 CGCACTTAGTTGCACGCCTA 61.012 55.000 0.00 0.00 43.15 3.93
1867 1890 2.317609 CGCACTTAGTTGCACGCCT 61.318 57.895 0.00 0.00 43.15 5.52
1870 1893 2.099633 AAAACGCACTTAGTTGCACG 57.900 45.000 0.00 0.00 43.15 5.34
1902 1928 1.266718 GCCACATCAGAAAAGCGAACA 59.733 47.619 0.00 0.00 0.00 3.18
1910 1936 5.670485 AGTAATACATCGCCACATCAGAAA 58.330 37.500 0.00 0.00 0.00 2.52
1911 1937 5.276461 AGTAATACATCGCCACATCAGAA 57.724 39.130 0.00 0.00 0.00 3.02
1924 1950 7.238486 TGCAAAAATGGACCAAGTAATACAT 57.762 32.000 0.00 0.00 0.00 2.29
1927 1953 7.901029 TCATTGCAAAAATGGACCAAGTAATA 58.099 30.769 1.71 0.00 0.00 0.98
1932 1958 5.239351 TGATCATTGCAAAAATGGACCAAG 58.761 37.500 1.71 0.00 0.00 3.61
1960 2256 3.526534 CAGGGAGCTAGCAAAGAAGTAC 58.473 50.000 18.83 0.00 0.00 2.73
2033 2329 6.708054 CCCTAAACTGTATAGGCATTCTTCAG 59.292 42.308 0.00 0.00 38.90 3.02
2040 2336 3.327439 AGGCCCTAAACTGTATAGGCAT 58.673 45.455 0.00 3.64 38.90 4.40
2051 2347 1.348036 ACAGTCACTGAGGCCCTAAAC 59.652 52.381 13.14 0.00 35.18 2.01
2052 2348 1.729586 ACAGTCACTGAGGCCCTAAA 58.270 50.000 13.14 0.00 35.18 1.85
2060 2356 8.070171 CCAAAAAGTATACAAACAGTCACTGAG 58.930 37.037 13.14 3.40 35.18 3.35
2068 2364 8.141268 ACATGAACCCAAAAAGTATACAAACAG 58.859 33.333 5.50 0.00 0.00 3.16
2079 2375 6.164876 TCATTGCATACATGAACCCAAAAAG 58.835 36.000 0.00 0.00 0.00 2.27
2089 2385 5.313712 AGCAGATGATCATTGCATACATGA 58.686 37.500 28.60 2.16 40.22 3.07
2093 2389 6.798315 AAGTAGCAGATGATCATTGCATAC 57.202 37.500 28.60 25.41 40.22 2.39
2121 2417 2.359967 GCTTCACCGGGGAGCTAGT 61.360 63.158 17.65 0.00 0.00 2.57
2151 2447 1.551883 AGCCATTCTTCCACCAAATGC 59.448 47.619 0.00 0.00 0.00 3.56
2163 2459 5.893255 TGCCTTAAAATGTATCAGCCATTCT 59.107 36.000 0.00 0.00 31.49 2.40
2164 2460 6.147864 TGCCTTAAAATGTATCAGCCATTC 57.852 37.500 0.00 0.00 31.49 2.67
2165 2461 6.324512 TCATGCCTTAAAATGTATCAGCCATT 59.675 34.615 0.00 0.00 34.07 3.16
2166 2462 5.834742 TCATGCCTTAAAATGTATCAGCCAT 59.165 36.000 0.00 0.00 0.00 4.40
2167 2463 5.199723 TCATGCCTTAAAATGTATCAGCCA 58.800 37.500 0.00 0.00 0.00 4.75
2168 2464 5.300286 ACTCATGCCTTAAAATGTATCAGCC 59.700 40.000 0.00 0.00 0.00 4.85
2211 2532 0.955178 ATCAGCCGACGACCAGATAG 59.045 55.000 0.00 0.00 0.00 2.08
2221 2542 2.749621 ACTTCCAAATCAATCAGCCGAC 59.250 45.455 0.00 0.00 0.00 4.79
2223 2544 3.191162 TCAACTTCCAAATCAATCAGCCG 59.809 43.478 0.00 0.00 0.00 5.52
2252 2573 9.388506 ACTACAAACTCATGATTATTTCCAGAG 57.611 33.333 0.00 0.00 33.06 3.35
2253 2574 9.739276 AACTACAAACTCATGATTATTTCCAGA 57.261 29.630 0.00 0.00 0.00 3.86
2306 2627 8.601546 AGAATCAGACTAAGGAAAAAGACTCAT 58.398 33.333 0.00 0.00 0.00 2.90
2560 2881 3.814906 TGGGTGGGTGGGTGTGTG 61.815 66.667 0.00 0.00 0.00 3.82
2561 2882 3.816090 GTGGGTGGGTGGGTGTGT 61.816 66.667 0.00 0.00 0.00 3.72
2562 2883 4.596585 GGTGGGTGGGTGGGTGTG 62.597 72.222 0.00 0.00 0.00 3.82
2563 2884 3.429685 TAGGTGGGTGGGTGGGTGT 62.430 63.158 0.00 0.00 0.00 4.16
2564 2885 2.530661 TAGGTGGGTGGGTGGGTG 60.531 66.667 0.00 0.00 0.00 4.61
2565 2886 2.204090 CTAGGTGGGTGGGTGGGT 60.204 66.667 0.00 0.00 0.00 4.51
2566 2887 1.995626 CTCTAGGTGGGTGGGTGGG 60.996 68.421 0.00 0.00 0.00 4.61
2567 2888 0.042131 TACTCTAGGTGGGTGGGTGG 59.958 60.000 0.00 0.00 0.00 4.61
2568 2889 1.486211 CTACTCTAGGTGGGTGGGTG 58.514 60.000 0.00 0.00 0.00 4.61
2569 2890 0.325390 GCTACTCTAGGTGGGTGGGT 60.325 60.000 0.00 0.00 0.00 4.51
2570 2891 1.049289 GGCTACTCTAGGTGGGTGGG 61.049 65.000 0.00 0.00 0.00 4.61
2571 2892 0.032017 AGGCTACTCTAGGTGGGTGG 60.032 60.000 0.00 0.00 0.00 4.61
2572 2893 1.115467 CAGGCTACTCTAGGTGGGTG 58.885 60.000 0.00 0.00 0.00 4.61
2573 2894 0.711184 ACAGGCTACTCTAGGTGGGT 59.289 55.000 0.00 0.00 0.00 4.51
2574 2895 1.867363 AACAGGCTACTCTAGGTGGG 58.133 55.000 0.00 0.00 0.00 4.61
2575 2896 3.100671 AGAAACAGGCTACTCTAGGTGG 58.899 50.000 0.00 0.00 0.00 4.61
2576 2897 4.220821 TCAAGAAACAGGCTACTCTAGGTG 59.779 45.833 0.00 0.00 0.00 4.00
2577 2898 4.221041 GTCAAGAAACAGGCTACTCTAGGT 59.779 45.833 0.00 0.00 0.00 3.08
2578 2899 4.675671 CGTCAAGAAACAGGCTACTCTAGG 60.676 50.000 0.00 0.00 0.00 3.02
2579 2900 4.156190 TCGTCAAGAAACAGGCTACTCTAG 59.844 45.833 0.00 0.00 0.00 2.43
2580 2901 4.077108 TCGTCAAGAAACAGGCTACTCTA 58.923 43.478 0.00 0.00 0.00 2.43
2581 2902 2.891580 TCGTCAAGAAACAGGCTACTCT 59.108 45.455 0.00 0.00 0.00 3.24
2582 2903 3.246619 CTCGTCAAGAAACAGGCTACTC 58.753 50.000 0.00 0.00 0.00 2.59
2592 2913 2.859165 ATCAAGGCCTCGTCAAGAAA 57.141 45.000 5.23 0.00 0.00 2.52
2627 2948 3.801114 AAAAGAGAAGCCACCACAAAC 57.199 42.857 0.00 0.00 0.00 2.93
2639 2960 7.124573 TGGCATGCTCTATACTAAAAGAGAA 57.875 36.000 18.92 0.00 41.51 2.87
2647 2968 4.483950 AGGAACTGGCATGCTCTATACTA 58.516 43.478 18.92 0.00 37.18 1.82
2662 2983 5.418840 ACCATAATTTGCTGGTAAGGAACTG 59.581 40.000 5.50 0.00 43.91 3.16
2820 3146 2.679349 GCTTGCTGGGTTTTGGTTTCAA 60.679 45.455 0.00 0.00 0.00 2.69
2828 3154 2.041153 CGGAAGCTTGCTGGGTTTT 58.959 52.632 16.42 0.00 0.00 2.43
3231 3557 4.911390 AGTTCTTTGTTCTACCCATCTGG 58.089 43.478 0.00 0.00 41.37 3.86
3235 3561 5.485708 AGAGCTAGTTCTTTGTTCTACCCAT 59.514 40.000 2.81 0.00 0.00 4.00
3445 3771 2.157738 ACTGAATCAAACAGCCAGCTC 58.842 47.619 0.00 0.00 38.74 4.09
3650 4042 5.420739 ACAACTAAAAACCCAACACATCTGT 59.579 36.000 0.00 0.00 0.00 3.41
3659 4051 6.347859 AGTGACAAACAACTAAAAACCCAA 57.652 33.333 0.00 0.00 0.00 4.12
3661 4053 6.090223 CACAAGTGACAAACAACTAAAAACCC 59.910 38.462 0.00 0.00 0.00 4.11
3672 4065 1.543358 TGCTTGCACAAGTGACAAACA 59.457 42.857 11.77 6.83 40.45 2.83
3740 4133 2.030274 CGTCAACCCAATCCAAAGGAAC 60.030 50.000 0.00 0.00 34.34 3.62
3742 4135 1.422024 TCGTCAACCCAATCCAAAGGA 59.578 47.619 0.00 0.00 35.55 3.36
3756 4149 2.874086 TCTCGAACACTACAGTCGTCAA 59.126 45.455 0.00 0.00 0.00 3.18
3772 4165 6.262496 AGGACGAATGTGTTTATATCTCTCGA 59.738 38.462 0.00 0.00 0.00 4.04
3773 4166 6.439599 AGGACGAATGTGTTTATATCTCTCG 58.560 40.000 0.00 0.00 0.00 4.04
3923 4341 2.125106 ATCTGCTTCGCCGGGTTC 60.125 61.111 2.18 0.00 0.00 3.62
4002 4420 3.195396 TGCCAGGCTGATTACAATTTTCC 59.805 43.478 17.94 0.00 0.00 3.13
4007 4425 3.133362 CCAAATGCCAGGCTGATTACAAT 59.867 43.478 17.94 0.00 0.00 2.71
4022 4440 2.290367 GGAGCCAAAACAAACCAAATGC 59.710 45.455 0.00 0.00 0.00 3.56
4052 4470 2.495669 CCTGCGTTTCCACCCATTATTT 59.504 45.455 0.00 0.00 0.00 1.40
4102 4520 7.624360 AAATCTGGTAGCAATTATTCACGAA 57.376 32.000 0.00 0.00 0.00 3.85
4103 4521 7.624360 AAAATCTGGTAGCAATTATTCACGA 57.376 32.000 0.00 0.00 0.00 4.35
4161 4579 4.635765 GGACATCAAAAGATGATCAACGGA 59.364 41.667 12.02 0.00 45.91 4.69
4225 4647 5.229423 ACAACACATATGCAACATCCAAAC 58.771 37.500 1.58 0.00 0.00 2.93
4277 4699 6.957911 GAGGTAAACTCGGTAACACTGAAAGT 60.958 42.308 0.00 0.00 42.54 2.66
4281 4703 4.510038 GAGGTAAACTCGGTAACACTGA 57.490 45.455 0.00 0.00 36.29 3.41
4306 4728 8.637986 TGATTATTTGCAGAACTAAAACAGGTT 58.362 29.630 0.00 0.00 0.00 3.50
4307 4729 8.177119 TGATTATTTGCAGAACTAAAACAGGT 57.823 30.769 0.00 0.00 0.00 4.00
4309 4731 9.079833 CCATGATTATTTGCAGAACTAAAACAG 57.920 33.333 0.00 0.00 0.00 3.16
4310 4732 8.034215 CCCATGATTATTTGCAGAACTAAAACA 58.966 33.333 0.00 0.00 0.00 2.83
4311 4733 8.034804 ACCCATGATTATTTGCAGAACTAAAAC 58.965 33.333 0.00 0.00 0.00 2.43
4312 4734 8.133024 ACCCATGATTATTTGCAGAACTAAAA 57.867 30.769 0.00 0.00 0.00 1.52
4313 4735 7.615365 AGACCCATGATTATTTGCAGAACTAAA 59.385 33.333 0.00 0.00 0.00 1.85
4318 4740 6.189859 AGAAGACCCATGATTATTTGCAGAA 58.810 36.000 0.00 0.00 0.00 3.02
4319 4741 5.759059 AGAAGACCCATGATTATTTGCAGA 58.241 37.500 0.00 0.00 0.00 4.26
4321 4743 4.889409 GGAGAAGACCCATGATTATTTGCA 59.111 41.667 0.00 0.00 0.00 4.08
4324 4746 5.433051 TGGAGGAGAAGACCCATGATTATTT 59.567 40.000 0.00 0.00 0.00 1.40
4325 4747 4.977739 TGGAGGAGAAGACCCATGATTATT 59.022 41.667 0.00 0.00 0.00 1.40
4326 4748 4.570926 TGGAGGAGAAGACCCATGATTAT 58.429 43.478 0.00 0.00 0.00 1.28
4327 4749 4.007581 TGGAGGAGAAGACCCATGATTA 57.992 45.455 0.00 0.00 0.00 1.75
4328 4750 2.850833 TGGAGGAGAAGACCCATGATT 58.149 47.619 0.00 0.00 0.00 2.57
4332 4754 1.418334 CGATGGAGGAGAAGACCCAT 58.582 55.000 0.00 0.00 41.70 4.00
4333 4755 1.330655 GCGATGGAGGAGAAGACCCA 61.331 60.000 0.00 0.00 0.00 4.51
4334 4756 1.045911 AGCGATGGAGGAGAAGACCC 61.046 60.000 0.00 0.00 0.00 4.46
4335 4757 0.387565 GAGCGATGGAGGAGAAGACC 59.612 60.000 0.00 0.00 0.00 3.85
4336 4758 0.030101 CGAGCGATGGAGGAGAAGAC 59.970 60.000 0.00 0.00 0.00 3.01
4337 4759 1.103987 CCGAGCGATGGAGGAGAAGA 61.104 60.000 0.00 0.00 0.00 2.87
4339 4761 2.127869 CCCGAGCGATGGAGGAGAA 61.128 63.158 0.00 0.00 0.00 2.87
4340 4762 2.519541 CCCGAGCGATGGAGGAGA 60.520 66.667 0.00 0.00 0.00 3.71
4341 4763 4.292178 GCCCGAGCGATGGAGGAG 62.292 72.222 0.00 0.00 0.00 3.69
4342 4764 4.841617 AGCCCGAGCGATGGAGGA 62.842 66.667 0.00 0.00 46.67 3.71
4343 4765 3.854669 AAGCCCGAGCGATGGAGG 61.855 66.667 0.00 0.00 46.67 4.30
4345 4767 2.954684 AACAAGCCCGAGCGATGGA 61.955 57.895 3.17 0.00 46.67 3.41
4346 4768 2.436646 AACAAGCCCGAGCGATGG 60.437 61.111 3.17 0.00 46.67 3.51
4347 4769 2.787249 CAACAAGCCCGAGCGATG 59.213 61.111 0.00 0.00 46.67 3.84
4348 4770 3.127533 GCAACAAGCCCGAGCGAT 61.128 61.111 0.00 0.00 46.67 4.58
4357 6047 1.779683 GTCTACGTCGGCAACAAGC 59.220 57.895 0.00 0.00 44.65 4.01
4361 6051 0.110056 TCTTCGTCTACGTCGGCAAC 60.110 55.000 0.00 0.00 40.80 4.17
4365 6055 1.081892 TTCCTCTTCGTCTACGTCGG 58.918 55.000 0.00 0.11 40.80 4.79
4366 6056 2.888513 TTTCCTCTTCGTCTACGTCG 57.111 50.000 0.00 0.00 40.80 5.12
4368 6058 3.317430 ACTGTTTTCCTCTTCGTCTACGT 59.683 43.478 2.02 0.00 40.80 3.57
4386 6076 2.370281 ATCTTCGTGCATTCGACTGT 57.630 45.000 4.58 0.00 39.58 3.55
4438 6151 2.017049 ACGTCGCTAGGTATTTACGGT 58.983 47.619 0.00 0.00 34.81 4.83
4493 6206 2.958986 CGACAAGATCGTATTCGTCTCG 59.041 50.000 4.36 0.00 46.25 4.04
4557 6270 4.985409 AGTCGAAAATTGAGATATCTCGCC 59.015 41.667 24.27 5.69 45.72 5.54
4575 6289 3.192844 GGTAGAGTGGTGAAATGAGTCGA 59.807 47.826 0.00 0.00 0.00 4.20
4721 6440 2.027285 TGTGGCTAGCTTATCTTGTGCA 60.027 45.455 15.72 0.00 0.00 4.57
4763 6482 0.179048 TGTAATGCGATGCCCTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
4764 6483 0.463654 GTGTAATGCGATGCCCTCCA 60.464 55.000 0.00 0.00 0.00 3.86
4774 6494 1.739929 TGCGAGGGTGTGTAATGCG 60.740 57.895 0.00 0.00 0.00 4.73
4804 6524 1.549950 GGCAAAAAGGTGGATGGAGGA 60.550 52.381 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.