Multiple sequence alignment - TraesCS1B01G119500

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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 TraesCS1B01G119500 chr1B 100.000 3293 0 0 1 3293 141733238 141729946 0.000000e+00 6082
1 TraesCS1B01G119500 chr1B 94.994 1598 60 8 1712 3292 637633731 637632137 0.000000e+00 2490
2 TraesCS1B01G119500 chr1B 94.239 1597 70 12 1712 3292 591153938 591155528 0.000000e+00 2420
3 TraesCS1B01G119500 chr5B 97.312 2716 66 5 581 3292 14353437 14356149 0.000000e+00 4604
4 TraesCS1B01G119500 chr5B 96.364 1595 45 4 1712 3293 455289744 455288150 0.000000e+00 2612
5 TraesCS1B01G119500 chr5B 96.833 221 7 0 1486 1706 455290129 455289909 1.440000e-98 370
6 TraesCS1B01G119500 chr3B 96.489 1595 43 4 1712 3293 3762215 3760621 0.000000e+00 2623
7 TraesCS1B01G119500 chr3B 96.113 1595 49 4 1712 3293 4662688 4661094 0.000000e+00 2590
8 TraesCS1B01G119500 chr3B 95.928 221 9 0 1486 1706 3762565 3762345 3.120000e-95 359
9 TraesCS1B01G119500 chr3B 95.475 221 10 0 1486 1706 4663038 4662818 1.450000e-93 353
10 TraesCS1B01G119500 chrUn 94.668 1594 47 10 1712 3293 8807557 8805990 0.000000e+00 2438
11 TraesCS1B01G119500 chr7B 94.605 1594 47 10 1712 3293 714530355 714528789 0.000000e+00 2431
12 TraesCS1B01G119500 chr7B 94.354 1594 51 10 1712 3293 714451721 714450155 0.000000e+00 2409
13 TraesCS1B01G119500 chr7B 95.475 221 10 0 1486 1706 714530705 714530485 1.450000e-93 353
14 TraesCS1B01G119500 chr5A 94.605 1594 47 10 1712 3293 44278202 44276636 0.000000e+00 2431
15 TraesCS1B01G119500 chr5A 90.242 1117 91 8 578 1693 633045668 633044569 0.000000e+00 1443
16 TraesCS1B01G119500 chr5A 88.468 1136 95 14 579 1714 562130732 562131831 0.000000e+00 1339
17 TraesCS1B01G119500 chr6A 94.448 1585 49 10 1712 3293 223587258 223585710 0.000000e+00 2403
18 TraesCS1B01G119500 chr6A 89.737 1140 85 11 576 1714 508298177 508299285 0.000000e+00 1428
19 TraesCS1B01G119500 chr7D 93.469 1623 59 16 1712 3292 530866217 530864600 0.000000e+00 2366
20 TraesCS1B01G119500 chr7D 93.403 1622 61 15 1712 3292 70679851 70678235 0.000000e+00 2361
21 TraesCS1B01G119500 chr7D 93.284 1623 64 15 1712 3292 596121850 596120231 0.000000e+00 2351
22 TraesCS1B01G119500 chr7D 90.989 1143 83 10 574 1716 592400966 592402088 0.000000e+00 1522
23 TraesCS1B01G119500 chr7D 90.741 1134 71 11 581 1714 11642234 11643333 0.000000e+00 1482
24 TraesCS1B01G119500 chr6B 92.468 1155 54 10 581 1715 650726693 650727834 0.000000e+00 1620
25 TraesCS1B01G119500 chr6B 91.993 1149 48 18 2179 3290 650755239 650756380 0.000000e+00 1572
26 TraesCS1B01G119500 chr6B 92.644 435 23 2 2868 3293 449459800 449459366 4.670000e-173 617
27 TraesCS1B01G119500 chr5D 91.901 1136 73 10 581 1716 443521254 443522370 0.000000e+00 1570
28 TraesCS1B01G119500 chr4D 91.813 1136 75 9 581 1716 440465454 440464337 0.000000e+00 1567
29 TraesCS1B01G119500 chr2A 91.093 1134 83 8 581 1714 458970802 458969687 0.000000e+00 1519
30 TraesCS1B01G119500 chr2A 90.761 1104 85 7 587 1690 514763732 514764818 0.000000e+00 1458
31 TraesCS1B01G119500 chr1D 88.034 585 48 11 1 576 87778927 87778356 0.000000e+00 673
32 TraesCS1B01G119500 chr1A 86.147 462 46 10 1 454 84025000 84024549 1.780000e-132 483


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 TraesCS1B01G119500 chr1B 141729946 141733238 3292 True 6082.0 6082 100.0000 1 3293 1 chr1B.!!$R1 3292
1 TraesCS1B01G119500 chr1B 637632137 637633731 1594 True 2490.0 2490 94.9940 1712 3292 1 chr1B.!!$R2 1580
2 TraesCS1B01G119500 chr1B 591153938 591155528 1590 False 2420.0 2420 94.2390 1712 3292 1 chr1B.!!$F1 1580
3 TraesCS1B01G119500 chr5B 14353437 14356149 2712 False 4604.0 4604 97.3120 581 3292 1 chr5B.!!$F1 2711
4 TraesCS1B01G119500 chr5B 455288150 455290129 1979 True 1491.0 2612 96.5985 1486 3293 2 chr5B.!!$R1 1807
5 TraesCS1B01G119500 chr3B 3760621 3762565 1944 True 1491.0 2623 96.2085 1486 3293 2 chr3B.!!$R1 1807
6 TraesCS1B01G119500 chr3B 4661094 4663038 1944 True 1471.5 2590 95.7940 1486 3293 2 chr3B.!!$R2 1807
7 TraesCS1B01G119500 chrUn 8805990 8807557 1567 True 2438.0 2438 94.6680 1712 3293 1 chrUn.!!$R1 1581
8 TraesCS1B01G119500 chr7B 714450155 714451721 1566 True 2409.0 2409 94.3540 1712 3293 1 chr7B.!!$R1 1581
9 TraesCS1B01G119500 chr7B 714528789 714530705 1916 True 1392.0 2431 95.0400 1486 3293 2 chr7B.!!$R2 1807
10 TraesCS1B01G119500 chr5A 44276636 44278202 1566 True 2431.0 2431 94.6050 1712 3293 1 chr5A.!!$R1 1581
11 TraesCS1B01G119500 chr5A 633044569 633045668 1099 True 1443.0 1443 90.2420 578 1693 1 chr5A.!!$R2 1115
12 TraesCS1B01G119500 chr5A 562130732 562131831 1099 False 1339.0 1339 88.4680 579 1714 1 chr5A.!!$F1 1135
13 TraesCS1B01G119500 chr6A 223585710 223587258 1548 True 2403.0 2403 94.4480 1712 3293 1 chr6A.!!$R1 1581
14 TraesCS1B01G119500 chr6A 508298177 508299285 1108 False 1428.0 1428 89.7370 576 1714 1 chr6A.!!$F1 1138
15 TraesCS1B01G119500 chr7D 530864600 530866217 1617 True 2366.0 2366 93.4690 1712 3292 1 chr7D.!!$R2 1580
16 TraesCS1B01G119500 chr7D 70678235 70679851 1616 True 2361.0 2361 93.4030 1712 3292 1 chr7D.!!$R1 1580
17 TraesCS1B01G119500 chr7D 596120231 596121850 1619 True 2351.0 2351 93.2840 1712 3292 1 chr7D.!!$R3 1580
18 TraesCS1B01G119500 chr7D 592400966 592402088 1122 False 1522.0 1522 90.9890 574 1716 1 chr7D.!!$F2 1142
19 TraesCS1B01G119500 chr7D 11642234 11643333 1099 False 1482.0 1482 90.7410 581 1714 1 chr7D.!!$F1 1133
20 TraesCS1B01G119500 chr6B 650726693 650727834 1141 False 1620.0 1620 92.4680 581 1715 1 chr6B.!!$F1 1134
21 TraesCS1B01G119500 chr6B 650755239 650756380 1141 False 1572.0 1572 91.9930 2179 3290 1 chr6B.!!$F2 1111
22 TraesCS1B01G119500 chr5D 443521254 443522370 1116 False 1570.0 1570 91.9010 581 1716 1 chr5D.!!$F1 1135
23 TraesCS1B01G119500 chr4D 440464337 440465454 1117 True 1567.0 1567 91.8130 581 1716 1 chr4D.!!$R1 1135
24 TraesCS1B01G119500 chr2A 458969687 458970802 1115 True 1519.0 1519 91.0930 581 1714 1 chr2A.!!$R1 1133
25 TraesCS1B01G119500 chr2A 514763732 514764818 1086 False 1458.0 1458 90.7610 587 1690 1 chr2A.!!$F1 1103
26 TraesCS1B01G119500 chr1D 87778356 87778927 571 True 673.0 673 88.0340 1 576 1 chr1D.!!$R1 575

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
551 554 0.109458 ACTAGTCGCACGAATCGCAA 60.109 50.0 1.15 0.0 0.0 4.85 F
558 561 0.660005 GCACGAATCGCAAAGCACAA 60.660 50.0 1.15 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2488 2.204090 GTCCCTGTCCCCCTCCAA 60.204 66.667 0.00 0.0 0.00 3.53 R
2345 2669 3.696051 ACCTAACATGCATGACATTCCAC 59.304 43.478 32.75 0.0 36.64 4.02 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
58 59 1.640428 CTCTTGGCGCGAGTATTTCA 58.360 50.000 12.10 0.00 0.00 2.69
63 64 4.632251 TCTTGGCGCGAGTATTTCAAATAA 59.368 37.500 12.10 0.00 0.00 1.40
67 68 7.197071 TGGCGCGAGTATTTCAAATAAATAT 57.803 32.000 12.10 0.00 0.00 1.28
68 69 7.295201 TGGCGCGAGTATTTCAAATAAATATC 58.705 34.615 12.10 0.00 0.00 1.63
153 155 0.755686 TGCATGGGGTTTGGTTTCAC 59.244 50.000 0.00 0.00 0.00 3.18
156 158 1.269448 CATGGGGTTTGGTTTCACGAG 59.731 52.381 0.00 0.00 0.00 4.18
194 196 2.479566 TGCCACTCTCTCACCATTTC 57.520 50.000 0.00 0.00 0.00 2.17
196 198 2.373169 TGCCACTCTCTCACCATTTCTT 59.627 45.455 0.00 0.00 0.00 2.52
220 222 6.401477 CTTTTGACAAAAAGTACTTACGCG 57.599 37.500 8.92 3.53 44.84 6.01
228 230 6.018016 ACAAAAAGTACTTACGCGTGGTATTT 60.018 34.615 24.59 21.75 0.00 1.40
261 264 7.658525 ACATATGCAAAAGATTTACCCATCA 57.341 32.000 1.58 0.00 0.00 3.07
302 305 9.444600 AAAGAATTGCCTAGTTATTTAACGAGA 57.555 29.630 10.90 0.00 40.08 4.04
303 306 9.444600 AAGAATTGCCTAGTTATTTAACGAGAA 57.555 29.630 10.90 1.42 40.08 2.87
304 307 9.444600 AGAATTGCCTAGTTATTTAACGAGAAA 57.555 29.630 10.90 6.63 40.08 2.52
305 308 9.704098 GAATTGCCTAGTTATTTAACGAGAAAG 57.296 33.333 10.90 0.00 40.08 2.62
306 309 9.444600 AATTGCCTAGTTATTTAACGAGAAAGA 57.555 29.630 10.90 0.00 40.08 2.52
307 310 9.614792 ATTGCCTAGTTATTTAACGAGAAAGAT 57.385 29.630 10.90 0.36 40.08 2.40
344 347 8.704668 ACATATATTTCACATGTGGACTACTCA 58.295 33.333 25.16 0.78 31.83 3.41
345 348 8.982685 CATATATTTCACATGTGGACTACTCAC 58.017 37.037 25.16 0.00 35.82 3.51
347 350 4.681074 TTCACATGTGGACTACTCACAA 57.319 40.909 25.16 5.64 46.41 3.33
348 351 4.681074 TCACATGTGGACTACTCACAAA 57.319 40.909 25.16 0.00 46.41 2.83
349 352 4.631131 TCACATGTGGACTACTCACAAAG 58.369 43.478 25.16 0.00 46.41 2.77
350 353 3.187227 CACATGTGGACTACTCACAAAGC 59.813 47.826 18.51 0.00 46.41 3.51
351 354 3.181455 ACATGTGGACTACTCACAAAGCA 60.181 43.478 0.00 0.00 46.41 3.91
352 355 3.769739 TGTGGACTACTCACAAAGCAT 57.230 42.857 0.00 0.00 41.50 3.79
353 356 4.882842 TGTGGACTACTCACAAAGCATA 57.117 40.909 0.00 0.00 41.50 3.14
354 357 5.222079 TGTGGACTACTCACAAAGCATAA 57.778 39.130 0.00 0.00 41.50 1.90
355 358 5.616270 TGTGGACTACTCACAAAGCATAAA 58.384 37.500 0.00 0.00 41.50 1.40
356 359 6.058833 TGTGGACTACTCACAAAGCATAAAA 58.941 36.000 0.00 0.00 41.50 1.52
357 360 6.017440 TGTGGACTACTCACAAAGCATAAAAC 60.017 38.462 0.00 0.00 41.50 2.43
358 361 6.204882 GTGGACTACTCACAAAGCATAAAACT 59.795 38.462 0.00 0.00 35.39 2.66
359 362 6.426937 TGGACTACTCACAAAGCATAAAACTC 59.573 38.462 0.00 0.00 0.00 3.01
360 363 6.128254 GGACTACTCACAAAGCATAAAACTCC 60.128 42.308 0.00 0.00 0.00 3.85
361 364 6.296026 ACTACTCACAAAGCATAAAACTCCA 58.704 36.000 0.00 0.00 0.00 3.86
362 365 6.942576 ACTACTCACAAAGCATAAAACTCCAT 59.057 34.615 0.00 0.00 0.00 3.41
363 366 6.017400 ACTCACAAAGCATAAAACTCCATG 57.983 37.500 0.00 0.00 0.00 3.66
364 367 5.769662 ACTCACAAAGCATAAAACTCCATGA 59.230 36.000 0.00 0.00 0.00 3.07
365 368 6.012658 TCACAAAGCATAAAACTCCATGAC 57.987 37.500 0.00 0.00 0.00 3.06
366 369 5.048083 TCACAAAGCATAAAACTCCATGACC 60.048 40.000 0.00 0.00 0.00 4.02
367 370 4.832266 ACAAAGCATAAAACTCCATGACCA 59.168 37.500 0.00 0.00 0.00 4.02
368 371 5.163513 CAAAGCATAAAACTCCATGACCAC 58.836 41.667 0.00 0.00 0.00 4.16
369 372 4.032960 AGCATAAAACTCCATGACCACA 57.967 40.909 0.00 0.00 0.00 4.17
370 373 4.603131 AGCATAAAACTCCATGACCACAT 58.397 39.130 0.00 0.00 37.19 3.21
386 389 4.237349 CCACATGGTTAACCTGACAAAC 57.763 45.455 24.78 0.00 36.82 2.93
387 390 3.634448 CCACATGGTTAACCTGACAAACA 59.366 43.478 24.78 2.79 36.82 2.83
388 391 4.280677 CCACATGGTTAACCTGACAAACAT 59.719 41.667 24.78 5.17 32.29 2.71
389 392 5.221422 CCACATGGTTAACCTGACAAACATT 60.221 40.000 24.78 1.08 29.63 2.71
390 393 6.279882 CACATGGTTAACCTGACAAACATTT 58.720 36.000 24.78 0.00 29.63 2.32
391 394 6.420604 CACATGGTTAACCTGACAAACATTTC 59.579 38.462 24.78 0.00 29.63 2.17
392 395 5.523438 TGGTTAACCTGACAAACATTTCC 57.477 39.130 24.78 0.00 36.82 3.13
393 396 4.956700 TGGTTAACCTGACAAACATTTCCA 59.043 37.500 24.78 0.00 36.82 3.53
394 397 5.422331 TGGTTAACCTGACAAACATTTCCAA 59.578 36.000 24.78 0.00 36.82 3.53
395 398 6.070767 TGGTTAACCTGACAAACATTTCCAAA 60.071 34.615 24.78 0.00 36.82 3.28
396 399 6.989759 GGTTAACCTGACAAACATTTCCAAAT 59.010 34.615 17.83 0.00 0.00 2.32
397 400 7.497579 GGTTAACCTGACAAACATTTCCAAATT 59.502 33.333 17.83 0.00 0.00 1.82
398 401 6.923928 AACCTGACAAACATTTCCAAATTG 57.076 33.333 0.00 0.00 0.00 2.32
399 402 4.815846 ACCTGACAAACATTTCCAAATTGC 59.184 37.500 0.00 0.00 0.00 3.56
400 403 4.815308 CCTGACAAACATTTCCAAATTGCA 59.185 37.500 0.00 0.00 0.00 4.08
401 404 5.296283 CCTGACAAACATTTCCAAATTGCAA 59.704 36.000 0.00 0.00 0.00 4.08
402 405 6.116680 TGACAAACATTTCCAAATTGCAAC 57.883 33.333 0.00 0.00 0.00 4.17
403 406 5.645067 TGACAAACATTTCCAAATTGCAACA 59.355 32.000 0.00 0.00 0.00 3.33
404 407 6.149973 TGACAAACATTTCCAAATTGCAACAA 59.850 30.769 0.00 0.00 0.00 2.83
405 408 7.098074 ACAAACATTTCCAAATTGCAACAAT 57.902 28.000 0.00 0.00 0.00 2.71
406 409 7.194962 ACAAACATTTCCAAATTGCAACAATC 58.805 30.769 0.00 0.00 0.00 2.67
407 410 6.939132 AACATTTCCAAATTGCAACAATCA 57.061 29.167 0.00 0.00 0.00 2.57
408 411 7.513371 AACATTTCCAAATTGCAACAATCAT 57.487 28.000 0.00 0.00 0.00 2.45
409 412 6.904498 ACATTTCCAAATTGCAACAATCATG 58.096 32.000 0.00 1.44 0.00 3.07
410 413 6.487331 ACATTTCCAAATTGCAACAATCATGT 59.513 30.769 0.00 2.09 43.14 3.21
411 414 6.542574 TTTCCAAATTGCAACAATCATGTC 57.457 33.333 0.00 0.00 39.40 3.06
412 415 4.236147 TCCAAATTGCAACAATCATGTCG 58.764 39.130 0.00 0.00 39.40 4.35
413 416 4.022503 TCCAAATTGCAACAATCATGTCGA 60.023 37.500 0.00 0.00 39.40 4.20
414 417 4.090354 CCAAATTGCAACAATCATGTCGAC 59.910 41.667 9.11 9.11 39.40 4.20
415 418 4.502171 AATTGCAACAATCATGTCGACA 57.498 36.364 22.48 22.48 39.40 4.35
416 419 2.967459 TGCAACAATCATGTCGACAC 57.033 45.000 22.71 5.17 39.40 3.67
417 420 2.493035 TGCAACAATCATGTCGACACT 58.507 42.857 22.71 7.55 39.40 3.55
418 421 2.877786 TGCAACAATCATGTCGACACTT 59.122 40.909 22.71 12.00 39.40 3.16
419 422 3.058983 TGCAACAATCATGTCGACACTTC 60.059 43.478 22.71 3.99 39.40 3.01
420 423 3.187227 GCAACAATCATGTCGACACTTCT 59.813 43.478 22.71 1.02 39.40 2.85
421 424 4.388773 GCAACAATCATGTCGACACTTCTA 59.611 41.667 22.71 4.98 39.40 2.10
422 425 5.445142 GCAACAATCATGTCGACACTTCTAG 60.445 44.000 22.71 11.87 39.40 2.43
423 426 5.644977 ACAATCATGTCGACACTTCTAGA 57.355 39.130 22.71 12.11 33.41 2.43
424 427 6.214191 ACAATCATGTCGACACTTCTAGAT 57.786 37.500 22.71 13.77 33.41 1.98
425 428 6.269315 ACAATCATGTCGACACTTCTAGATC 58.731 40.000 22.71 0.00 33.41 2.75
426 429 6.127619 ACAATCATGTCGACACTTCTAGATCA 60.128 38.462 22.71 0.00 33.41 2.92
427 430 5.236655 TCATGTCGACACTTCTAGATCAC 57.763 43.478 22.71 0.00 0.00 3.06
428 431 4.944317 TCATGTCGACACTTCTAGATCACT 59.056 41.667 22.71 0.00 0.00 3.41
429 432 6.113411 TCATGTCGACACTTCTAGATCACTA 58.887 40.000 22.71 0.00 0.00 2.74
430 433 6.598064 TCATGTCGACACTTCTAGATCACTAA 59.402 38.462 22.71 0.00 0.00 2.24
431 434 6.424176 TGTCGACACTTCTAGATCACTAAG 57.576 41.667 15.76 0.00 0.00 2.18
432 435 5.354513 TGTCGACACTTCTAGATCACTAAGG 59.645 44.000 15.76 0.00 0.00 2.69
433 436 5.585445 GTCGACACTTCTAGATCACTAAGGA 59.415 44.000 11.55 0.00 0.00 3.36
434 437 6.093771 GTCGACACTTCTAGATCACTAAGGAA 59.906 42.308 11.55 0.00 0.00 3.36
435 438 6.093771 TCGACACTTCTAGATCACTAAGGAAC 59.906 42.308 0.00 0.00 0.00 3.62
436 439 6.532988 ACACTTCTAGATCACTAAGGAACC 57.467 41.667 0.00 0.00 0.00 3.62
437 440 5.422650 ACACTTCTAGATCACTAAGGAACCC 59.577 44.000 0.00 0.00 0.00 4.11
438 441 4.963628 ACTTCTAGATCACTAAGGAACCCC 59.036 45.833 0.00 0.00 0.00 4.95
439 442 3.924922 TCTAGATCACTAAGGAACCCCC 58.075 50.000 0.00 0.00 0.00 5.40
440 443 1.497161 AGATCACTAAGGAACCCCCG 58.503 55.000 0.00 0.00 40.87 5.73
441 444 1.007963 AGATCACTAAGGAACCCCCGA 59.992 52.381 0.00 0.00 40.87 5.14
442 445 2.047830 GATCACTAAGGAACCCCCGAT 58.952 52.381 0.00 0.00 40.87 4.18
443 446 1.200519 TCACTAAGGAACCCCCGATG 58.799 55.000 0.00 0.00 40.87 3.84
444 447 1.200519 CACTAAGGAACCCCCGATGA 58.799 55.000 0.00 0.00 40.87 2.92
445 448 1.139058 CACTAAGGAACCCCCGATGAG 59.861 57.143 0.00 0.00 40.87 2.90
446 449 1.007963 ACTAAGGAACCCCCGATGAGA 59.992 52.381 0.00 0.00 40.87 3.27
447 450 2.116238 CTAAGGAACCCCCGATGAGAA 58.884 52.381 0.00 0.00 40.87 2.87
448 451 0.618981 AAGGAACCCCCGATGAGAAC 59.381 55.000 0.00 0.00 40.87 3.01
449 452 0.546747 AGGAACCCCCGATGAGAACA 60.547 55.000 0.00 0.00 40.87 3.18
450 453 0.392595 GGAACCCCCGATGAGAACAC 60.393 60.000 0.00 0.00 0.00 3.32
451 454 0.392595 GAACCCCCGATGAGAACACC 60.393 60.000 0.00 0.00 0.00 4.16
452 455 0.840722 AACCCCCGATGAGAACACCT 60.841 55.000 0.00 0.00 0.00 4.00
453 456 1.265454 ACCCCCGATGAGAACACCTC 61.265 60.000 0.00 0.00 42.30 3.85
463 466 4.527509 TGAGAACACCTCATCAGAAGAC 57.472 45.455 0.00 0.00 46.38 3.01
464 467 3.897505 TGAGAACACCTCATCAGAAGACA 59.102 43.478 0.00 0.00 46.38 3.41
465 468 4.344968 TGAGAACACCTCATCAGAAGACAA 59.655 41.667 0.00 0.00 46.38 3.18
466 469 5.012458 TGAGAACACCTCATCAGAAGACAAT 59.988 40.000 0.00 0.00 46.38 2.71
467 470 5.243981 AGAACACCTCATCAGAAGACAATG 58.756 41.667 0.00 0.00 0.00 2.82
468 471 3.947868 ACACCTCATCAGAAGACAATGG 58.052 45.455 0.00 0.00 0.00 3.16
469 472 3.584406 ACACCTCATCAGAAGACAATGGA 59.416 43.478 0.00 0.00 0.00 3.41
470 473 4.226846 ACACCTCATCAGAAGACAATGGAT 59.773 41.667 0.00 0.00 0.00 3.41
471 474 5.426509 ACACCTCATCAGAAGACAATGGATA 59.573 40.000 0.00 0.00 0.00 2.59
472 475 5.757320 CACCTCATCAGAAGACAATGGATAC 59.243 44.000 0.00 0.00 0.00 2.24
473 476 5.163258 ACCTCATCAGAAGACAATGGATACC 60.163 44.000 0.00 0.00 0.00 2.73
474 477 5.163269 CCTCATCAGAAGACAATGGATACCA 60.163 44.000 0.00 0.00 38.19 3.25
475 478 5.674525 TCATCAGAAGACAATGGATACCAC 58.325 41.667 0.00 0.00 35.80 4.16
476 479 5.189539 TCATCAGAAGACAATGGATACCACA 59.810 40.000 0.00 0.00 35.80 4.17
477 480 5.497464 TCAGAAGACAATGGATACCACAA 57.503 39.130 0.00 0.00 35.80 3.33
478 481 5.491070 TCAGAAGACAATGGATACCACAAG 58.509 41.667 0.00 0.00 35.80 3.16
479 482 4.637534 CAGAAGACAATGGATACCACAAGG 59.362 45.833 0.00 0.00 35.80 3.61
498 501 9.319143 CCACAAGGTATTTTTGTTTGTATTTGA 57.681 29.630 0.00 0.00 36.67 2.69
509 512 9.681062 TTTTGTTTGTATTTGAAATTAACCCCA 57.319 25.926 0.00 0.00 0.00 4.96
510 513 9.681062 TTTGTTTGTATTTGAAATTAACCCCAA 57.319 25.926 0.00 0.00 0.00 4.12
511 514 8.664211 TGTTTGTATTTGAAATTAACCCCAAC 57.336 30.769 0.00 0.00 0.00 3.77
512 515 8.265055 TGTTTGTATTTGAAATTAACCCCAACA 58.735 29.630 0.00 0.00 0.00 3.33
513 516 9.278978 GTTTGTATTTGAAATTAACCCCAACAT 57.721 29.630 0.00 0.00 0.00 2.71
514 517 8.839310 TTGTATTTGAAATTAACCCCAACATG 57.161 30.769 0.00 0.00 0.00 3.21
515 518 7.967908 TGTATTTGAAATTAACCCCAACATGT 58.032 30.769 0.00 0.00 0.00 3.21
516 519 9.090103 TGTATTTGAAATTAACCCCAACATGTA 57.910 29.630 0.00 0.00 0.00 2.29
519 522 8.839310 TTTGAAATTAACCCCAACATGTATTG 57.161 30.769 0.00 0.00 0.00 1.90
520 523 7.546250 TGAAATTAACCCCAACATGTATTGT 57.454 32.000 0.00 0.00 41.53 2.71
521 524 8.651589 TGAAATTAACCCCAACATGTATTGTA 57.348 30.769 0.00 0.00 37.68 2.41
522 525 9.090103 TGAAATTAACCCCAACATGTATTGTAA 57.910 29.630 0.00 0.00 37.68 2.41
523 526 9.930693 GAAATTAACCCCAACATGTATTGTAAA 57.069 29.630 0.00 0.00 37.68 2.01
527 530 7.412853 AACCCCAACATGTATTGTAAATACC 57.587 36.000 0.00 0.00 37.68 2.73
528 531 6.494952 ACCCCAACATGTATTGTAAATACCA 58.505 36.000 0.00 0.00 37.68 3.25
529 532 7.129425 ACCCCAACATGTATTGTAAATACCAT 58.871 34.615 0.00 0.56 37.68 3.55
530 533 7.069331 ACCCCAACATGTATTGTAAATACCATG 59.931 37.037 0.00 11.61 37.68 3.66
531 534 6.922957 CCCAACATGTATTGTAAATACCATGC 59.077 38.462 0.00 0.00 37.68 4.06
532 535 7.417229 CCCAACATGTATTGTAAATACCATGCA 60.417 37.037 0.00 0.00 37.68 3.96
533 536 7.434897 CCAACATGTATTGTAAATACCATGCAC 59.565 37.037 0.00 0.00 37.68 4.57
534 537 7.880160 ACATGTATTGTAAATACCATGCACT 57.120 32.000 0.00 0.00 36.57 4.40
535 538 8.972458 ACATGTATTGTAAATACCATGCACTA 57.028 30.769 0.00 0.00 36.57 2.74
536 539 9.056005 ACATGTATTGTAAATACCATGCACTAG 57.944 33.333 0.00 0.00 36.57 2.57
537 540 9.056005 CATGTATTGTAAATACCATGCACTAGT 57.944 33.333 7.48 0.00 29.58 2.57
538 541 8.657074 TGTATTGTAAATACCATGCACTAGTC 57.343 34.615 0.00 0.00 0.00 2.59
539 542 6.844696 ATTGTAAATACCATGCACTAGTCG 57.155 37.500 0.00 0.00 0.00 4.18
540 543 4.116961 TGTAAATACCATGCACTAGTCGC 58.883 43.478 9.52 9.52 0.00 5.19
541 544 2.979814 AATACCATGCACTAGTCGCA 57.020 45.000 18.15 18.15 44.94 5.10
542 545 2.225068 ATACCATGCACTAGTCGCAC 57.775 50.000 18.19 0.00 43.35 5.34
543 546 0.179148 TACCATGCACTAGTCGCACG 60.179 55.000 18.19 12.36 43.35 5.34
544 547 1.153842 CCATGCACTAGTCGCACGA 60.154 57.895 18.19 0.00 43.35 4.35
545 548 0.735978 CCATGCACTAGTCGCACGAA 60.736 55.000 18.19 1.29 43.35 3.85
546 549 1.280982 CATGCACTAGTCGCACGAAT 58.719 50.000 18.19 0.00 43.35 3.34
547 550 1.256376 CATGCACTAGTCGCACGAATC 59.744 52.381 18.19 0.00 43.35 2.52
548 551 0.796870 TGCACTAGTCGCACGAATCG 60.797 55.000 13.71 0.00 33.55 3.34
549 552 1.910880 CACTAGTCGCACGAATCGC 59.089 57.895 1.15 0.00 0.00 4.58
550 553 0.796870 CACTAGTCGCACGAATCGCA 60.797 55.000 1.15 0.00 0.00 5.10
551 554 0.109458 ACTAGTCGCACGAATCGCAA 60.109 50.000 1.15 0.00 0.00 4.85
552 555 0.989164 CTAGTCGCACGAATCGCAAA 59.011 50.000 1.15 0.00 0.00 3.68
553 556 0.989164 TAGTCGCACGAATCGCAAAG 59.011 50.000 1.15 0.00 0.00 2.77
554 557 1.859135 GTCGCACGAATCGCAAAGC 60.859 57.895 1.15 1.07 0.00 3.51
555 558 2.173141 CGCACGAATCGCAAAGCA 59.827 55.556 1.15 0.00 0.00 3.91
556 559 2.139811 CGCACGAATCGCAAAGCAC 61.140 57.895 1.15 0.00 0.00 4.40
557 560 1.082169 GCACGAATCGCAAAGCACA 60.082 52.632 1.15 0.00 0.00 4.57
558 561 0.660005 GCACGAATCGCAAAGCACAA 60.660 50.000 1.15 0.00 0.00 3.33
559 562 1.752753 CACGAATCGCAAAGCACAAA 58.247 45.000 1.15 0.00 0.00 2.83
560 563 2.318578 CACGAATCGCAAAGCACAAAT 58.681 42.857 1.15 0.00 0.00 2.32
561 564 2.089427 CACGAATCGCAAAGCACAAATG 59.911 45.455 1.15 0.00 0.00 2.32
562 565 2.031245 ACGAATCGCAAAGCACAAATGA 60.031 40.909 1.15 0.00 0.00 2.57
563 566 2.979151 CGAATCGCAAAGCACAAATGAA 59.021 40.909 0.00 0.00 0.00 2.57
564 567 3.424861 CGAATCGCAAAGCACAAATGAAA 59.575 39.130 0.00 0.00 0.00 2.69
565 568 4.431986 CGAATCGCAAAGCACAAATGAAAG 60.432 41.667 0.00 0.00 0.00 2.62
566 569 2.741612 TCGCAAAGCACAAATGAAAGG 58.258 42.857 0.00 0.00 0.00 3.11
567 570 1.794116 CGCAAAGCACAAATGAAAGGG 59.206 47.619 0.00 0.00 0.00 3.95
568 571 2.145536 GCAAAGCACAAATGAAAGGGG 58.854 47.619 0.00 0.00 0.00 4.79
569 572 2.145536 CAAAGCACAAATGAAAGGGGC 58.854 47.619 0.00 0.00 0.00 5.80
570 573 1.422531 AAGCACAAATGAAAGGGGCA 58.577 45.000 0.00 0.00 0.00 5.36
571 574 1.648116 AGCACAAATGAAAGGGGCAT 58.352 45.000 0.00 0.00 0.00 4.40
572 575 1.980036 AGCACAAATGAAAGGGGCATT 59.020 42.857 0.00 0.00 37.56 3.56
686 705 4.329462 TTGGACTAAACCATGGCAAAAC 57.671 40.909 13.04 0.00 39.82 2.43
699 718 1.944709 GGCAAAACACTACCAACTCGT 59.055 47.619 0.00 0.00 0.00 4.18
705 724 6.262601 CAAAACACTACCAACTCGTGAAATT 58.737 36.000 0.00 0.00 33.13 1.82
1230 1250 4.323104 GGTTCTTACACTGAATCTGAGCCT 60.323 45.833 0.00 0.00 0.00 4.58
1320 1341 1.367346 TCCTGGGTTGTCCTATGCAA 58.633 50.000 0.00 0.00 36.20 4.08
1460 1481 7.655328 GCAGAGATGTGTGCTATAGTTTAGAAT 59.345 37.037 4.56 0.00 39.89 2.40
2133 2457 4.558226 TCTTCAAAGCCAAGCAGAGATA 57.442 40.909 0.00 0.00 0.00 1.98
2164 2488 1.133976 CGAGGAAGGCCATGAAGGAAT 60.134 52.381 5.01 0.00 41.22 3.01
2345 2669 4.090090 AGGCCTATATATATAGCTGGCCG 58.910 47.826 28.30 15.68 41.73 6.13
2511 2843 9.619316 CTATGCTAAGTACTCATGCTAAGTTAG 57.381 37.037 5.47 5.47 0.00 2.34
3113 3532 3.126225 GGCTCGTCGTCGGAGAGT 61.126 66.667 15.58 0.00 36.95 3.24
3133 3552 2.233305 ACGACTACCTCATCCACCTT 57.767 50.000 0.00 0.00 0.00 3.50
3236 3676 1.754234 GACCCATGGATTGCGCCTT 60.754 57.895 15.22 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 120 6.171921 CCCCATGCATTTTATTTTCTTGTGA 58.828 36.000 0.00 0.00 0.00 3.58
153 155 5.515982 GCATGCATACTCATAGATTCTCTCG 59.484 44.000 14.21 0.00 0.00 4.04
156 158 5.350914 GTGGCATGCATACTCATAGATTCTC 59.649 44.000 21.36 0.00 0.00 2.87
164 166 2.704596 AGAGAGTGGCATGCATACTCAT 59.295 45.455 35.54 26.94 42.44 2.90
194 196 7.097570 CGCGTAAGTACTTTTTGTCAAAAGAAG 60.098 37.037 14.49 9.02 45.12 2.85
196 198 6.183360 ACGCGTAAGTACTTTTTGTCAAAAGA 60.183 34.615 11.67 2.72 45.12 2.52
228 230 8.600449 AAATCTTTTGCATATGTTTCGGAAAA 57.400 26.923 4.46 0.00 0.00 2.29
233 235 7.032580 TGGGTAAATCTTTTGCATATGTTTCG 58.967 34.615 4.29 0.00 0.00 3.46
277 280 9.444600 TTCTCGTTAAATAACTAGGCAATTCTT 57.555 29.630 0.00 0.00 34.12 2.52
278 281 9.444600 TTTCTCGTTAAATAACTAGGCAATTCT 57.555 29.630 0.00 0.00 34.12 2.40
318 321 8.704668 TGAGTAGTCCACATGTGAAATATATGT 58.295 33.333 27.46 3.02 41.20 2.29
319 322 8.982685 GTGAGTAGTCCACATGTGAAATATATG 58.017 37.037 27.46 7.74 34.81 1.78
320 323 8.704668 TGTGAGTAGTCCACATGTGAAATATAT 58.295 33.333 27.46 3.65 39.36 0.86
321 324 8.073467 TGTGAGTAGTCCACATGTGAAATATA 57.927 34.615 27.46 9.35 39.36 0.86
322 325 6.946340 TGTGAGTAGTCCACATGTGAAATAT 58.054 36.000 27.46 10.30 39.36 1.28
323 326 6.353404 TGTGAGTAGTCCACATGTGAAATA 57.647 37.500 27.46 7.95 39.36 1.40
324 327 5.227569 TGTGAGTAGTCCACATGTGAAAT 57.772 39.130 27.46 9.19 39.36 2.17
325 328 4.681074 TGTGAGTAGTCCACATGTGAAA 57.319 40.909 27.46 11.91 39.36 2.69
326 329 4.681074 TTGTGAGTAGTCCACATGTGAA 57.319 40.909 27.46 3.21 43.17 3.18
327 330 4.631131 CTTTGTGAGTAGTCCACATGTGA 58.369 43.478 27.46 10.46 43.17 3.58
328 331 3.187227 GCTTTGTGAGTAGTCCACATGTG 59.813 47.826 19.31 19.31 43.17 3.21
329 332 3.181455 TGCTTTGTGAGTAGTCCACATGT 60.181 43.478 0.00 0.00 43.17 3.21
330 333 3.402110 TGCTTTGTGAGTAGTCCACATG 58.598 45.455 0.00 0.00 43.17 3.21
331 334 3.769739 TGCTTTGTGAGTAGTCCACAT 57.230 42.857 0.00 0.00 43.17 3.21
332 335 3.769739 ATGCTTTGTGAGTAGTCCACA 57.230 42.857 0.00 0.00 42.16 4.17
333 336 6.204882 AGTTTTATGCTTTGTGAGTAGTCCAC 59.795 38.462 0.00 0.00 35.23 4.02
334 337 6.296026 AGTTTTATGCTTTGTGAGTAGTCCA 58.704 36.000 0.00 0.00 0.00 4.02
335 338 6.128254 GGAGTTTTATGCTTTGTGAGTAGTCC 60.128 42.308 0.00 0.00 0.00 3.85
336 339 6.426937 TGGAGTTTTATGCTTTGTGAGTAGTC 59.573 38.462 0.00 0.00 0.00 2.59
337 340 6.296026 TGGAGTTTTATGCTTTGTGAGTAGT 58.704 36.000 0.00 0.00 0.00 2.73
338 341 6.801539 TGGAGTTTTATGCTTTGTGAGTAG 57.198 37.500 0.00 0.00 0.00 2.57
339 342 6.939730 TCATGGAGTTTTATGCTTTGTGAGTA 59.060 34.615 0.00 0.00 0.00 2.59
340 343 5.769662 TCATGGAGTTTTATGCTTTGTGAGT 59.230 36.000 0.00 0.00 0.00 3.41
341 344 6.088824 GTCATGGAGTTTTATGCTTTGTGAG 58.911 40.000 0.00 0.00 0.00 3.51
342 345 5.048083 GGTCATGGAGTTTTATGCTTTGTGA 60.048 40.000 0.00 0.00 0.00 3.58
343 346 5.163513 GGTCATGGAGTTTTATGCTTTGTG 58.836 41.667 0.00 0.00 0.00 3.33
344 347 4.832266 TGGTCATGGAGTTTTATGCTTTGT 59.168 37.500 0.00 0.00 0.00 2.83
345 348 5.163513 GTGGTCATGGAGTTTTATGCTTTG 58.836 41.667 0.00 0.00 0.00 2.77
346 349 4.832266 TGTGGTCATGGAGTTTTATGCTTT 59.168 37.500 0.00 0.00 0.00 3.51
347 350 4.406456 TGTGGTCATGGAGTTTTATGCTT 58.594 39.130 0.00 0.00 0.00 3.91
348 351 4.032960 TGTGGTCATGGAGTTTTATGCT 57.967 40.909 0.00 0.00 0.00 3.79
349 352 4.675510 CATGTGGTCATGGAGTTTTATGC 58.324 43.478 0.00 0.00 45.30 3.14
365 368 3.634448 TGTTTGTCAGGTTAACCATGTGG 59.366 43.478 26.26 10.12 38.89 4.17
366 369 4.909696 TGTTTGTCAGGTTAACCATGTG 57.090 40.909 26.26 15.74 38.89 3.21
367 370 6.462347 GGAAATGTTTGTCAGGTTAACCATGT 60.462 38.462 26.26 2.99 38.89 3.21
368 371 5.925969 GGAAATGTTTGTCAGGTTAACCATG 59.074 40.000 26.26 19.51 38.89 3.66
369 372 5.600484 TGGAAATGTTTGTCAGGTTAACCAT 59.400 36.000 26.26 8.95 38.89 3.55
370 373 4.956700 TGGAAATGTTTGTCAGGTTAACCA 59.043 37.500 26.26 3.80 38.89 3.67
371 374 5.523438 TGGAAATGTTTGTCAGGTTAACC 57.477 39.130 17.41 17.41 0.00 2.85
372 375 8.334632 CAATTTGGAAATGTTTGTCAGGTTAAC 58.665 33.333 0.00 0.00 0.00 2.01
373 376 7.011857 GCAATTTGGAAATGTTTGTCAGGTTAA 59.988 33.333 0.00 0.00 0.00 2.01
374 377 6.481644 GCAATTTGGAAATGTTTGTCAGGTTA 59.518 34.615 0.00 0.00 0.00 2.85
375 378 5.296531 GCAATTTGGAAATGTTTGTCAGGTT 59.703 36.000 0.00 0.00 0.00 3.50
376 379 4.815846 GCAATTTGGAAATGTTTGTCAGGT 59.184 37.500 0.00 0.00 0.00 4.00
377 380 4.815308 TGCAATTTGGAAATGTTTGTCAGG 59.185 37.500 0.00 0.00 0.00 3.86
378 381 5.987777 TGCAATTTGGAAATGTTTGTCAG 57.012 34.783 0.00 0.00 0.00 3.51
379 382 5.645067 TGTTGCAATTTGGAAATGTTTGTCA 59.355 32.000 0.59 0.00 26.96 3.58
380 383 6.116680 TGTTGCAATTTGGAAATGTTTGTC 57.883 33.333 0.59 0.00 26.96 3.18
381 384 6.506500 TTGTTGCAATTTGGAAATGTTTGT 57.493 29.167 0.59 0.00 26.96 2.83
382 385 7.194278 TGATTGTTGCAATTTGGAAATGTTTG 58.806 30.769 0.59 0.00 26.96 2.93
383 386 7.330900 TGATTGTTGCAATTTGGAAATGTTT 57.669 28.000 0.59 0.00 26.96 2.83
384 387 6.939132 TGATTGTTGCAATTTGGAAATGTT 57.061 29.167 0.59 0.00 26.96 2.71
385 388 6.487331 ACATGATTGTTGCAATTTGGAAATGT 59.513 30.769 0.59 8.18 29.55 2.71
386 389 6.904498 ACATGATTGTTGCAATTTGGAAATG 58.096 32.000 0.59 7.60 29.55 2.32
387 390 6.128499 CGACATGATTGTTGCAATTTGGAAAT 60.128 34.615 0.59 0.00 35.79 2.17
388 391 5.177142 CGACATGATTGTTGCAATTTGGAAA 59.823 36.000 0.59 0.00 35.79 3.13
389 392 4.685165 CGACATGATTGTTGCAATTTGGAA 59.315 37.500 0.59 0.00 35.79 3.53
390 393 4.022503 TCGACATGATTGTTGCAATTTGGA 60.023 37.500 0.59 0.00 37.20 3.53
391 394 4.090354 GTCGACATGATTGTTGCAATTTGG 59.910 41.667 11.55 0.00 37.20 3.28
392 395 4.680567 TGTCGACATGATTGTTGCAATTTG 59.319 37.500 15.76 0.00 37.20 2.32
393 396 4.681025 GTGTCGACATGATTGTTGCAATTT 59.319 37.500 23.12 0.00 37.20 1.82
394 397 4.022935 AGTGTCGACATGATTGTTGCAATT 60.023 37.500 23.12 0.00 37.20 2.32
395 398 3.503363 AGTGTCGACATGATTGTTGCAAT 59.497 39.130 23.12 0.00 37.20 3.56
396 399 2.877786 AGTGTCGACATGATTGTTGCAA 59.122 40.909 23.12 0.00 37.20 4.08
397 400 2.493035 AGTGTCGACATGATTGTTGCA 58.507 42.857 23.12 0.00 37.20 4.08
398 401 3.187227 AGAAGTGTCGACATGATTGTTGC 59.813 43.478 23.12 5.17 37.20 4.17
399 402 4.997905 AGAAGTGTCGACATGATTGTTG 57.002 40.909 23.12 0.00 38.43 3.33
400 403 6.025749 TCTAGAAGTGTCGACATGATTGTT 57.974 37.500 23.12 8.54 35.79 2.83
401 404 5.644977 TCTAGAAGTGTCGACATGATTGT 57.355 39.130 23.12 16.75 39.32 2.71
402 405 6.198029 GTGATCTAGAAGTGTCGACATGATTG 59.802 42.308 23.12 10.78 0.00 2.67
403 406 6.096141 AGTGATCTAGAAGTGTCGACATGATT 59.904 38.462 23.12 16.51 0.00 2.57
404 407 5.592282 AGTGATCTAGAAGTGTCGACATGAT 59.408 40.000 23.12 16.63 0.00 2.45
405 408 4.944317 AGTGATCTAGAAGTGTCGACATGA 59.056 41.667 23.12 12.95 0.00 3.07
406 409 5.242069 AGTGATCTAGAAGTGTCGACATG 57.758 43.478 23.12 8.20 0.00 3.21
407 410 6.038825 CCTTAGTGATCTAGAAGTGTCGACAT 59.961 42.308 23.12 6.42 0.00 3.06
408 411 5.354513 CCTTAGTGATCTAGAAGTGTCGACA 59.645 44.000 15.76 15.76 0.00 4.35
409 412 5.585445 TCCTTAGTGATCTAGAAGTGTCGAC 59.415 44.000 9.11 9.11 0.00 4.20
410 413 5.742063 TCCTTAGTGATCTAGAAGTGTCGA 58.258 41.667 0.00 0.00 0.00 4.20
411 414 6.259638 GTTCCTTAGTGATCTAGAAGTGTCG 58.740 44.000 0.00 0.00 0.00 4.35
412 415 6.406065 GGGTTCCTTAGTGATCTAGAAGTGTC 60.406 46.154 0.00 0.00 0.00 3.67
413 416 5.422650 GGGTTCCTTAGTGATCTAGAAGTGT 59.577 44.000 0.00 0.00 0.00 3.55
414 417 5.163395 GGGGTTCCTTAGTGATCTAGAAGTG 60.163 48.000 0.00 0.00 0.00 3.16
415 418 4.963628 GGGGTTCCTTAGTGATCTAGAAGT 59.036 45.833 0.00 0.00 0.00 3.01
416 419 4.345547 GGGGGTTCCTTAGTGATCTAGAAG 59.654 50.000 0.00 0.00 0.00 2.85
417 420 4.296056 GGGGGTTCCTTAGTGATCTAGAA 58.704 47.826 0.00 0.00 0.00 2.10
418 421 3.690438 CGGGGGTTCCTTAGTGATCTAGA 60.690 52.174 0.00 0.00 0.00 2.43
419 422 2.628657 CGGGGGTTCCTTAGTGATCTAG 59.371 54.545 0.00 0.00 0.00 2.43
420 423 2.245546 TCGGGGGTTCCTTAGTGATCTA 59.754 50.000 0.00 0.00 0.00 1.98
421 424 1.007963 TCGGGGGTTCCTTAGTGATCT 59.992 52.381 0.00 0.00 0.00 2.75
422 425 1.492764 TCGGGGGTTCCTTAGTGATC 58.507 55.000 0.00 0.00 0.00 2.92
423 426 1.768870 CATCGGGGGTTCCTTAGTGAT 59.231 52.381 0.00 0.00 0.00 3.06
424 427 1.200519 CATCGGGGGTTCCTTAGTGA 58.799 55.000 0.00 0.00 0.00 3.41
425 428 1.139058 CTCATCGGGGGTTCCTTAGTG 59.861 57.143 0.00 0.00 0.00 2.74
426 429 1.007963 TCTCATCGGGGGTTCCTTAGT 59.992 52.381 0.00 0.00 0.00 2.24
427 430 1.789523 TCTCATCGGGGGTTCCTTAG 58.210 55.000 0.00 0.00 0.00 2.18
428 431 1.835531 GTTCTCATCGGGGGTTCCTTA 59.164 52.381 0.00 0.00 0.00 2.69
429 432 0.618981 GTTCTCATCGGGGGTTCCTT 59.381 55.000 0.00 0.00 0.00 3.36
430 433 0.546747 TGTTCTCATCGGGGGTTCCT 60.547 55.000 0.00 0.00 0.00 3.36
431 434 0.392595 GTGTTCTCATCGGGGGTTCC 60.393 60.000 0.00 0.00 0.00 3.62
432 435 0.392595 GGTGTTCTCATCGGGGGTTC 60.393 60.000 0.00 0.00 0.00 3.62
433 436 0.840722 AGGTGTTCTCATCGGGGGTT 60.841 55.000 0.00 0.00 0.00 4.11
434 437 1.229529 AGGTGTTCTCATCGGGGGT 60.230 57.895 0.00 0.00 0.00 4.95
435 438 1.264749 TGAGGTGTTCTCATCGGGGG 61.265 60.000 0.00 0.00 46.71 5.40
436 439 2.286826 TGAGGTGTTCTCATCGGGG 58.713 57.895 0.00 0.00 46.71 5.73
443 446 4.527509 TGTCTTCTGATGAGGTGTTCTC 57.472 45.455 0.00 0.00 42.74 2.87
444 447 4.963318 TTGTCTTCTGATGAGGTGTTCT 57.037 40.909 0.00 0.00 0.00 3.01
445 448 4.394300 CCATTGTCTTCTGATGAGGTGTTC 59.606 45.833 0.00 0.00 0.00 3.18
446 449 4.042062 TCCATTGTCTTCTGATGAGGTGTT 59.958 41.667 0.00 0.00 0.00 3.32
447 450 3.584406 TCCATTGTCTTCTGATGAGGTGT 59.416 43.478 0.00 0.00 0.00 4.16
448 451 4.212143 TCCATTGTCTTCTGATGAGGTG 57.788 45.455 0.00 0.00 0.00 4.00
449 452 5.163258 GGTATCCATTGTCTTCTGATGAGGT 60.163 44.000 0.00 0.00 0.00 3.85
450 453 5.163269 TGGTATCCATTGTCTTCTGATGAGG 60.163 44.000 0.00 0.00 0.00 3.86
451 454 5.757320 GTGGTATCCATTGTCTTCTGATGAG 59.243 44.000 0.00 0.00 35.28 2.90
452 455 5.189539 TGTGGTATCCATTGTCTTCTGATGA 59.810 40.000 0.00 0.00 35.28 2.92
453 456 5.430886 TGTGGTATCCATTGTCTTCTGATG 58.569 41.667 0.00 0.00 35.28 3.07
454 457 5.698741 TGTGGTATCCATTGTCTTCTGAT 57.301 39.130 0.00 0.00 35.28 2.90
455 458 5.491070 CTTGTGGTATCCATTGTCTTCTGA 58.509 41.667 0.00 0.00 35.28 3.27
456 459 4.637534 CCTTGTGGTATCCATTGTCTTCTG 59.362 45.833 0.00 0.00 35.28 3.02
457 460 4.289672 ACCTTGTGGTATCCATTGTCTTCT 59.710 41.667 0.00 0.00 46.43 2.85
458 461 4.589908 ACCTTGTGGTATCCATTGTCTTC 58.410 43.478 0.00 0.00 46.43 2.87
459 462 4.657814 ACCTTGTGGTATCCATTGTCTT 57.342 40.909 0.00 0.00 46.43 3.01
472 475 9.319143 TCAAATACAAACAAAAATACCTTGTGG 57.681 29.630 0.00 0.00 37.10 4.17
483 486 9.681062 TGGGGTTAATTTCAAATACAAACAAAA 57.319 25.926 5.67 0.00 0.00 2.44
484 487 9.681062 TTGGGGTTAATTTCAAATACAAACAAA 57.319 25.926 5.67 0.00 0.00 2.83
485 488 9.110502 GTTGGGGTTAATTTCAAATACAAACAA 57.889 29.630 5.67 0.00 0.00 2.83
486 489 8.265055 TGTTGGGGTTAATTTCAAATACAAACA 58.735 29.630 5.67 0.00 0.00 2.83
487 490 8.664211 TGTTGGGGTTAATTTCAAATACAAAC 57.336 30.769 0.00 0.00 0.00 2.93
488 491 9.277783 CATGTTGGGGTTAATTTCAAATACAAA 57.722 29.630 0.00 0.00 0.00 2.83
489 492 8.432805 ACATGTTGGGGTTAATTTCAAATACAA 58.567 29.630 0.00 0.00 0.00 2.41
490 493 7.967908 ACATGTTGGGGTTAATTTCAAATACA 58.032 30.769 0.00 0.00 0.00 2.29
493 496 9.447157 CAATACATGTTGGGGTTAATTTCAAAT 57.553 29.630 2.30 0.00 0.00 2.32
494 497 8.432805 ACAATACATGTTGGGGTTAATTTCAAA 58.567 29.630 2.30 0.00 40.06 2.69
495 498 7.967908 ACAATACATGTTGGGGTTAATTTCAA 58.032 30.769 2.30 0.00 40.06 2.69
496 499 7.546250 ACAATACATGTTGGGGTTAATTTCA 57.454 32.000 2.30 0.00 40.06 2.69
497 500 9.930693 TTTACAATACATGTTGGGGTTAATTTC 57.069 29.630 2.30 0.00 43.63 2.17
501 504 8.968969 GGTATTTACAATACATGTTGGGGTTAA 58.031 33.333 2.30 0.00 43.63 2.01
502 505 8.114102 TGGTATTTACAATACATGTTGGGGTTA 58.886 33.333 2.30 0.00 43.63 2.85
503 506 6.954684 TGGTATTTACAATACATGTTGGGGTT 59.045 34.615 2.30 0.00 43.63 4.11
504 507 6.494952 TGGTATTTACAATACATGTTGGGGT 58.505 36.000 2.30 0.35 43.63 4.95
505 508 7.432869 CATGGTATTTACAATACATGTTGGGG 58.567 38.462 2.30 0.00 43.63 4.96
506 509 6.922957 GCATGGTATTTACAATACATGTTGGG 59.077 38.462 2.30 0.00 43.63 4.12
507 510 7.434897 GTGCATGGTATTTACAATACATGTTGG 59.565 37.037 2.30 0.00 43.63 3.77
508 511 8.190122 AGTGCATGGTATTTACAATACATGTTG 58.810 33.333 2.30 0.00 43.63 3.33
509 512 8.292444 AGTGCATGGTATTTACAATACATGTT 57.708 30.769 2.30 0.00 43.63 2.71
510 513 7.880160 AGTGCATGGTATTTACAATACATGT 57.120 32.000 2.69 2.69 46.36 3.21
511 514 9.056005 ACTAGTGCATGGTATTTACAATACATG 57.944 33.333 0.00 10.04 0.00 3.21
512 515 9.273016 GACTAGTGCATGGTATTTACAATACAT 57.727 33.333 0.00 0.00 0.00 2.29
513 516 7.436970 CGACTAGTGCATGGTATTTACAATACA 59.563 37.037 0.00 0.00 0.00 2.29
514 517 7.568861 GCGACTAGTGCATGGTATTTACAATAC 60.569 40.741 0.00 0.00 0.00 1.89
515 518 6.422701 GCGACTAGTGCATGGTATTTACAATA 59.577 38.462 0.00 0.00 0.00 1.90
516 519 5.236478 GCGACTAGTGCATGGTATTTACAAT 59.764 40.000 0.00 0.00 0.00 2.71
517 520 4.569162 GCGACTAGTGCATGGTATTTACAA 59.431 41.667 0.00 0.00 0.00 2.41
518 521 4.116961 GCGACTAGTGCATGGTATTTACA 58.883 43.478 0.00 0.00 0.00 2.41
519 522 4.025979 GTGCGACTAGTGCATGGTATTTAC 60.026 45.833 18.61 4.14 45.34 2.01
520 523 4.116961 GTGCGACTAGTGCATGGTATTTA 58.883 43.478 18.61 0.00 45.34 1.40
521 524 2.936498 GTGCGACTAGTGCATGGTATTT 59.064 45.455 18.61 0.00 45.34 1.40
522 525 2.550978 GTGCGACTAGTGCATGGTATT 58.449 47.619 18.61 0.00 45.34 1.89
523 526 1.536072 CGTGCGACTAGTGCATGGTAT 60.536 52.381 21.88 0.00 45.34 2.73
524 527 0.179148 CGTGCGACTAGTGCATGGTA 60.179 55.000 21.88 2.51 45.34 3.25
525 528 1.446099 CGTGCGACTAGTGCATGGT 60.446 57.895 21.88 0.00 45.34 3.55
526 529 0.735978 TTCGTGCGACTAGTGCATGG 60.736 55.000 25.73 18.62 46.74 3.66
528 531 1.560923 GATTCGTGCGACTAGTGCAT 58.439 50.000 18.61 6.94 45.34 3.96
529 532 0.796870 CGATTCGTGCGACTAGTGCA 60.797 55.000 13.71 13.71 40.70 4.57
530 533 1.910880 CGATTCGTGCGACTAGTGC 59.089 57.895 0.00 5.18 0.00 4.40
531 534 0.796870 TGCGATTCGTGCGACTAGTG 60.797 55.000 0.00 0.00 34.24 2.74
532 535 0.109458 TTGCGATTCGTGCGACTAGT 60.109 50.000 8.03 0.00 34.24 2.57
533 536 0.989164 TTTGCGATTCGTGCGACTAG 59.011 50.000 8.03 0.00 34.24 2.57
534 537 0.989164 CTTTGCGATTCGTGCGACTA 59.011 50.000 8.03 0.00 34.24 2.59
535 538 1.781555 CTTTGCGATTCGTGCGACT 59.218 52.632 8.03 0.00 34.24 4.18
536 539 1.859135 GCTTTGCGATTCGTGCGAC 60.859 57.895 8.03 0.00 34.24 5.19
537 540 2.313909 TGCTTTGCGATTCGTGCGA 61.314 52.632 8.03 0.00 34.24 5.10
538 541 2.139811 GTGCTTTGCGATTCGTGCG 61.140 57.895 8.03 0.00 34.24 5.34
539 542 0.660005 TTGTGCTTTGCGATTCGTGC 60.660 50.000 8.03 7.98 0.00 5.34
540 543 1.752753 TTTGTGCTTTGCGATTCGTG 58.247 45.000 8.03 0.00 0.00 4.35
541 544 2.031245 TCATTTGTGCTTTGCGATTCGT 60.031 40.909 8.03 0.00 0.00 3.85
542 545 2.583739 TCATTTGTGCTTTGCGATTCG 58.416 42.857 0.62 0.62 0.00 3.34
543 546 4.143263 CCTTTCATTTGTGCTTTGCGATTC 60.143 41.667 0.00 0.00 0.00 2.52
544 547 3.742369 CCTTTCATTTGTGCTTTGCGATT 59.258 39.130 0.00 0.00 0.00 3.34
545 548 3.319755 CCTTTCATTTGTGCTTTGCGAT 58.680 40.909 0.00 0.00 0.00 4.58
546 549 2.545532 CCCTTTCATTTGTGCTTTGCGA 60.546 45.455 0.00 0.00 0.00 5.10
547 550 1.794116 CCCTTTCATTTGTGCTTTGCG 59.206 47.619 0.00 0.00 0.00 4.85
548 551 2.145536 CCCCTTTCATTTGTGCTTTGC 58.854 47.619 0.00 0.00 0.00 3.68
549 552 2.145536 GCCCCTTTCATTTGTGCTTTG 58.854 47.619 0.00 0.00 0.00 2.77
550 553 1.767681 TGCCCCTTTCATTTGTGCTTT 59.232 42.857 0.00 0.00 0.00 3.51
551 554 1.422531 TGCCCCTTTCATTTGTGCTT 58.577 45.000 0.00 0.00 0.00 3.91
552 555 1.648116 ATGCCCCTTTCATTTGTGCT 58.352 45.000 0.00 0.00 0.00 4.40
553 556 2.477845 AATGCCCCTTTCATTTGTGC 57.522 45.000 0.00 0.00 30.60 4.57
554 557 5.065235 AGAAAAATGCCCCTTTCATTTGTG 58.935 37.500 2.26 0.00 41.66 3.33
555 558 5.308014 GAGAAAAATGCCCCTTTCATTTGT 58.692 37.500 2.26 0.00 41.66 2.83
556 559 4.696877 GGAGAAAAATGCCCCTTTCATTTG 59.303 41.667 2.26 0.00 41.66 2.32
557 560 4.563374 CGGAGAAAAATGCCCCTTTCATTT 60.563 41.667 4.83 0.00 43.61 2.32
558 561 3.055891 CGGAGAAAAATGCCCCTTTCATT 60.056 43.478 4.83 0.00 34.60 2.57
559 562 2.497273 CGGAGAAAAATGCCCCTTTCAT 59.503 45.455 4.83 0.00 34.60 2.57
560 563 1.892474 CGGAGAAAAATGCCCCTTTCA 59.108 47.619 4.83 0.00 34.60 2.69
561 564 2.164422 CTCGGAGAAAAATGCCCCTTTC 59.836 50.000 0.00 0.00 34.09 2.62
562 565 2.171003 CTCGGAGAAAAATGCCCCTTT 58.829 47.619 0.00 0.00 34.09 3.11
563 566 1.075536 ACTCGGAGAAAAATGCCCCTT 59.924 47.619 12.86 0.00 34.09 3.95
564 567 0.698818 ACTCGGAGAAAAATGCCCCT 59.301 50.000 12.86 0.00 34.09 4.79
565 568 2.413310 TACTCGGAGAAAAATGCCCC 57.587 50.000 12.86 0.00 34.09 5.80
566 569 4.983671 AAATACTCGGAGAAAAATGCCC 57.016 40.909 12.86 0.00 34.09 5.36
567 570 6.127842 TGGTTAAATACTCGGAGAAAAATGCC 60.128 38.462 12.86 6.91 34.09 4.40
568 571 6.848451 TGGTTAAATACTCGGAGAAAAATGC 58.152 36.000 12.86 0.00 34.09 3.56
569 572 9.685828 TTTTGGTTAAATACTCGGAGAAAAATG 57.314 29.630 12.86 0.00 34.09 2.32
571 574 9.518906 GTTTTTGGTTAAATACTCGGAGAAAAA 57.481 29.630 12.86 7.85 34.09 1.94
572 575 8.905850 AGTTTTTGGTTAAATACTCGGAGAAAA 58.094 29.630 12.86 2.00 34.37 2.29
686 705 3.498397 AGCAATTTCACGAGTTGGTAGTG 59.502 43.478 0.00 0.00 37.24 2.74
721 740 0.822164 CGGTCAGATTCGGGGTTAGT 59.178 55.000 0.00 0.00 0.00 2.24
1320 1341 7.822822 AGTTAGCGTTCAAGATTTAATACCTGT 59.177 33.333 0.00 0.00 0.00 4.00
1418 1439 4.019174 TCTCTGCACATCACACATCTCTA 58.981 43.478 0.00 0.00 0.00 2.43
1460 1481 9.421806 CATATTTATGGCACTTTCAAGTTTCAA 57.578 29.630 0.00 0.00 37.08 2.69
1538 1559 4.850680 TGTTTGTAGGTGTTCTCAGGTTT 58.149 39.130 0.00 0.00 0.00 3.27
1611 1652 9.321562 CTTTTTCAGTTAACACCTACTCTGTTA 57.678 33.333 8.61 0.00 33.79 2.41
2061 2385 9.733556 TTCAGCTTTTCCATACTTAACTCAATA 57.266 29.630 0.00 0.00 0.00 1.90
2133 2457 2.427506 GCCTTCCTCGTGTTCTGAATT 58.572 47.619 0.00 0.00 0.00 2.17
2164 2488 2.204090 GTCCCTGTCCCCCTCCAA 60.204 66.667 0.00 0.00 0.00 3.53
2345 2669 3.696051 ACCTAACATGCATGACATTCCAC 59.304 43.478 32.75 0.00 36.64 4.02
3113 3532 3.021695 CAAGGTGGATGAGGTAGTCGTA 58.978 50.000 0.00 0.00 0.00 3.43
3133 3552 2.282251 ACGAGCCCTCTGACGACA 60.282 61.111 0.00 0.00 0.00 4.35
3236 3676 0.759959 TCAACAACGCCTACTGGGAA 59.240 50.000 0.00 0.00 37.23 3.97


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

AutoCloner maintained by Alex Coulton.