Multiple sequence alignment - TraesCS2A01G440100

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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 TraesCS2A01G440100 chr2A 100.000 6318 0 0 1 6318 690930093 690936410 0.000000e+00 11668.0
1 TraesCS2A01G440100 chr2A 95.156 867 35 5 5458 6318 49769479 49768614 0.000000e+00 1362.0
2 TraesCS2A01G440100 chr2B 91.819 2567 123 39 394 2892 655009600 655007053 0.000000e+00 3496.0
3 TraesCS2A01G440100 chr2B 92.324 1889 109 15 2978 4832 655006828 655004942 0.000000e+00 2652.0
4 TraesCS2A01G440100 chr2B 94.328 670 28 4 4796 5458 655005014 655004348 0.000000e+00 1018.0
5 TraesCS2A01G440100 chr2B 86.810 326 33 6 7 326 655009936 655009615 7.790000e-94 355.0
6 TraesCS2A01G440100 chr2B 97.561 41 0 1 4829 4868 655005018 655004978 1.140000e-07 69.4
7 TraesCS2A01G440100 chr2D 93.785 1448 68 7 3401 4832 548076791 548075350 0.000000e+00 2156.0
8 TraesCS2A01G440100 chr2D 90.876 1655 79 29 394 2018 548079977 548078365 0.000000e+00 2154.0
9 TraesCS2A01G440100 chr2D 95.904 879 33 3 2015 2892 548078273 548077397 0.000000e+00 1421.0
10 TraesCS2A01G440100 chr2D 96.096 666 22 3 4796 5458 548075422 548074758 0.000000e+00 1083.0
11 TraesCS2A01G440100 chr2D 88.488 443 32 9 2972 3401 548077310 548076874 9.390000e-143 518.0
12 TraesCS2A01G440100 chr2D 90.854 164 10 2 80 243 548080145 548079987 1.380000e-51 215.0
13 TraesCS2A01G440100 chr2D 97.561 41 0 1 4829 4868 548075426 548075386 1.140000e-07 69.4
14 TraesCS2A01G440100 chr3A 96.756 863 24 4 5458 6318 699683029 699682169 0.000000e+00 1435.0
15 TraesCS2A01G440100 chr3A 96.194 867 27 4 5454 6318 699669474 699668612 0.000000e+00 1413.0
16 TraesCS2A01G440100 chr3A 95.963 867 32 3 5454 6318 699676255 699675390 0.000000e+00 1404.0
17 TraesCS2A01G440100 chr3A 95.470 861 39 0 5458 6318 584043117 584043977 0.000000e+00 1375.0
18 TraesCS2A01G440100 chr3A 95.035 866 42 1 5454 6318 572821706 572822571 0.000000e+00 1360.0
19 TraesCS2A01G440100 chr4A 95.397 869 35 5 5454 6318 126875772 126876639 0.000000e+00 1378.0
20 TraesCS2A01G440100 chr5A 95.167 869 36 5 5454 6318 588034086 588034952 0.000000e+00 1367.0
21 TraesCS2A01G440100 chr5A 95.255 864 38 3 5457 6318 588028345 588029207 0.000000e+00 1365.0
22 TraesCS2A01G440100 chr6A 76.471 374 44 27 6 362 53504297 53503951 5.070000e-36 163.0
23 TraesCS2A01G440100 chr6B 76.786 280 32 22 97 362 103664963 103665223 6.650000e-25 126.0


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 TraesCS2A01G440100 chr2A 690930093 690936410 6317 False 11668.000000 11668 100.000000 1 6318 1 chr2A.!!$F1 6317
1 TraesCS2A01G440100 chr2A 49768614 49769479 865 True 1362.000000 1362 95.156000 5458 6318 1 chr2A.!!$R1 860
2 TraesCS2A01G440100 chr2B 655004348 655009936 5588 True 1518.080000 3496 92.568400 7 5458 5 chr2B.!!$R1 5451
3 TraesCS2A01G440100 chr2D 548074758 548080145 5387 True 1088.057143 2156 93.366286 80 5458 7 chr2D.!!$R1 5378
4 TraesCS2A01G440100 chr3A 699682169 699683029 860 True 1435.000000 1435 96.756000 5458 6318 1 chr3A.!!$R3 860
5 TraesCS2A01G440100 chr3A 699668612 699669474 862 True 1413.000000 1413 96.194000 5454 6318 1 chr3A.!!$R1 864
6 TraesCS2A01G440100 chr3A 699675390 699676255 865 True 1404.000000 1404 95.963000 5454 6318 1 chr3A.!!$R2 864
7 TraesCS2A01G440100 chr3A 584043117 584043977 860 False 1375.000000 1375 95.470000 5458 6318 1 chr3A.!!$F2 860
8 TraesCS2A01G440100 chr3A 572821706 572822571 865 False 1360.000000 1360 95.035000 5454 6318 1 chr3A.!!$F1 864
9 TraesCS2A01G440100 chr4A 126875772 126876639 867 False 1378.000000 1378 95.397000 5454 6318 1 chr4A.!!$F1 864
10 TraesCS2A01G440100 chr5A 588034086 588034952 866 False 1367.000000 1367 95.167000 5454 6318 1 chr5A.!!$F2 864
11 TraesCS2A01G440100 chr5A 588028345 588029207 862 False 1365.000000 1365 95.255000 5457 6318 1 chr5A.!!$F1 861

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
383 390 0.039708 GTCTTGTGCCAAGCTGAAGC 60.040 55.0 9.35 0.0 42.49 3.86 F
745 763 0.175989 GTTCCTCTTCCTGCCTACCG 59.824 60.0 0.00 0.0 0.00 4.02 F
1646 1742 0.309302 CCGACGAGGAGTGATAGCTG 59.691 60.0 0.00 0.0 45.00 4.24 F
2465 2658 0.739112 CTGTGAGAGAGAAAGCGGCC 60.739 60.0 0.00 0.0 0.00 6.13 F
2974 3201 0.036164 CCCAACTCACACGGGATGAA 59.964 55.0 0.00 0.0 43.21 2.57 F
4647 5084 0.179062 CTCATTTCCTCCTCGCCCTG 60.179 60.0 0.00 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2397 0.099436 GAATGTCATCAACTGCCCGC 59.901 55.000 0.00 0.00 0.00 6.13 R
2465 2658 1.202604 ACCCACTTGTCACGGTTACTG 60.203 52.381 0.00 0.00 0.00 2.74 R
2746 2940 1.026718 AGATTTGCGCCTGCCAGTAC 61.027 55.000 4.18 0.00 41.78 2.73 R
4408 4845 0.244721 GGCACCAAAATCAGAGGCAC 59.755 55.000 0.00 0.00 0.00 5.01 R
4779 5217 0.389757 GTTGGCTAGATCCTCCGGTC 59.610 60.000 0.00 0.00 0.00 4.79 R
5455 5898 0.179233 GAAAATCCGGTCGCGACAAC 60.179 55.000 37.26 21.73 0.00 3.32 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
38 41 6.441093 TTCTTATGAACAATGCATGGTCTC 57.559 37.500 7.31 8.13 46.51 3.36
45 48 4.100707 ACAATGCATGGTCTCAAAATCG 57.899 40.909 0.00 0.00 0.00 3.34
53 56 1.136336 GGTCTCAAAATCGTGTGTCGC 60.136 52.381 0.00 0.00 39.67 5.19
64 67 2.159558 TCGTGTGTCGCTTGAGAGTATC 60.160 50.000 0.00 0.00 39.67 2.24
65 68 4.420639 TCGTGTGTCGCTTGAGAGTATCT 61.421 47.826 0.00 0.00 44.44 1.98
113 120 4.681744 TGTTGCTTTTGATGTTTCCTGTC 58.318 39.130 0.00 0.00 0.00 3.51
119 126 3.469008 TTGATGTTTCCTGTCGACTGT 57.531 42.857 17.92 0.00 0.00 3.55
181 188 4.679373 TTTGGTTGCCTTCTTTATGCAA 57.321 36.364 0.00 0.00 42.28 4.08
193 200 1.544724 TTATGCAACCTGAAGCCACC 58.455 50.000 0.00 0.00 0.00 4.61
194 201 0.403655 TATGCAACCTGAAGCCACCA 59.596 50.000 0.00 0.00 0.00 4.17
218 225 8.188139 CCACACCACTATTTTACCATGTTATTC 58.812 37.037 0.00 0.00 0.00 1.75
250 257 3.462021 GTCATACATGGACCTGCTTCTC 58.538 50.000 0.00 0.00 0.00 2.87
251 258 3.133721 GTCATACATGGACCTGCTTCTCT 59.866 47.826 0.00 0.00 0.00 3.10
261 268 1.471684 CCTGCTTCTCTGCAATGGAAC 59.528 52.381 0.00 0.00 42.83 3.62
268 275 1.538512 CTCTGCAATGGAACCTGTGTG 59.461 52.381 0.00 0.00 0.00 3.82
273 280 2.031157 GCAATGGAACCTGTGTGTGTAC 60.031 50.000 0.00 0.00 0.00 2.90
288 295 2.567169 TGTGTACTCCCACTGAATCCAG 59.433 50.000 0.00 0.00 45.76 3.86
305 312 3.955471 TCCAGACCTAGCAAAATTGGAG 58.045 45.455 0.00 0.00 0.00 3.86
309 316 2.424956 GACCTAGCAAAATTGGAGCAGG 59.575 50.000 0.00 0.00 34.73 4.85
337 344 4.008074 CCTTCAGGTTAGATGTGTGTGT 57.992 45.455 0.00 0.00 0.00 3.72
338 345 3.997021 CCTTCAGGTTAGATGTGTGTGTC 59.003 47.826 0.00 0.00 0.00 3.67
340 347 4.257267 TCAGGTTAGATGTGTGTGTCAG 57.743 45.455 0.00 0.00 0.00 3.51
341 348 2.738846 CAGGTTAGATGTGTGTGTCAGC 59.261 50.000 0.00 0.00 0.00 4.26
342 349 2.634940 AGGTTAGATGTGTGTGTCAGCT 59.365 45.455 0.00 0.00 35.67 4.24
343 350 3.071602 AGGTTAGATGTGTGTGTCAGCTT 59.928 43.478 0.00 0.00 33.55 3.74
344 351 3.433615 GGTTAGATGTGTGTGTCAGCTTC 59.566 47.826 0.00 0.00 33.55 3.86
345 352 2.916702 AGATGTGTGTGTCAGCTTCA 57.083 45.000 0.00 0.00 0.00 3.02
346 353 2.763933 AGATGTGTGTGTCAGCTTCAG 58.236 47.619 0.00 0.00 0.00 3.02
347 354 2.366590 AGATGTGTGTGTCAGCTTCAGA 59.633 45.455 0.00 0.00 0.00 3.27
348 355 2.916702 TGTGTGTGTCAGCTTCAGAT 57.083 45.000 0.00 0.00 0.00 2.90
349 356 2.486918 TGTGTGTGTCAGCTTCAGATG 58.513 47.619 0.00 0.00 0.00 2.90
350 357 2.158914 TGTGTGTGTCAGCTTCAGATGT 60.159 45.455 0.00 0.00 32.47 3.06
351 358 2.874701 GTGTGTGTCAGCTTCAGATGTT 59.125 45.455 0.00 0.00 32.47 2.71
352 359 2.874086 TGTGTGTCAGCTTCAGATGTTG 59.126 45.455 0.00 0.00 32.47 3.33
353 360 2.225019 GTGTGTCAGCTTCAGATGTTGG 59.775 50.000 1.03 0.00 32.47 3.77
354 361 2.104622 TGTGTCAGCTTCAGATGTTGGA 59.895 45.455 1.03 0.00 32.47 3.53
355 362 2.740981 GTGTCAGCTTCAGATGTTGGAG 59.259 50.000 1.03 0.00 35.29 3.86
356 363 2.289882 TGTCAGCTTCAGATGTTGGAGG 60.290 50.000 1.03 0.00 32.52 4.30
357 364 2.027745 GTCAGCTTCAGATGTTGGAGGA 60.028 50.000 1.03 0.00 32.52 3.71
358 365 2.027745 TCAGCTTCAGATGTTGGAGGAC 60.028 50.000 1.03 0.00 32.52 3.85
359 366 1.280421 AGCTTCAGATGTTGGAGGACC 59.720 52.381 0.00 0.00 32.52 4.46
360 367 1.280421 GCTTCAGATGTTGGAGGACCT 59.720 52.381 0.00 0.00 32.52 3.85
361 368 2.938756 GCTTCAGATGTTGGAGGACCTG 60.939 54.545 0.00 0.00 32.52 4.00
362 369 0.615331 TCAGATGTTGGAGGACCTGC 59.385 55.000 5.96 5.96 37.04 4.85
363 370 0.617413 CAGATGTTGGAGGACCTGCT 59.383 55.000 14.77 0.00 37.04 4.24
364 371 0.617413 AGATGTTGGAGGACCTGCTG 59.383 55.000 14.77 0.00 37.04 4.41
365 372 0.326264 GATGTTGGAGGACCTGCTGT 59.674 55.000 14.77 0.00 37.04 4.40
366 373 0.326264 ATGTTGGAGGACCTGCTGTC 59.674 55.000 14.77 5.31 43.67 3.51
367 374 0.764369 TGTTGGAGGACCTGCTGTCT 60.764 55.000 14.77 0.00 43.89 3.41
368 375 0.398318 GTTGGAGGACCTGCTGTCTT 59.602 55.000 14.77 0.00 43.89 3.01
369 376 0.397941 TTGGAGGACCTGCTGTCTTG 59.602 55.000 14.77 0.00 43.89 3.02
370 377 0.764369 TGGAGGACCTGCTGTCTTGT 60.764 55.000 14.77 0.00 43.89 3.16
371 378 0.321122 GGAGGACCTGCTGTCTTGTG 60.321 60.000 5.61 0.00 43.89 3.33
372 379 0.952984 GAGGACCTGCTGTCTTGTGC 60.953 60.000 0.00 0.00 43.89 4.57
373 380 1.968540 GGACCTGCTGTCTTGTGCC 60.969 63.158 6.86 0.00 43.89 5.01
374 381 1.227943 GACCTGCTGTCTTGTGCCA 60.228 57.895 0.40 0.00 41.03 4.92
375 382 0.819259 GACCTGCTGTCTTGTGCCAA 60.819 55.000 0.40 0.00 41.03 4.52
376 383 0.820891 ACCTGCTGTCTTGTGCCAAG 60.821 55.000 8.22 8.22 0.00 3.61
377 384 1.285023 CTGCTGTCTTGTGCCAAGC 59.715 57.895 9.35 6.35 0.00 4.01
378 385 1.152902 TGCTGTCTTGTGCCAAGCT 60.153 52.632 9.35 0.00 0.00 3.74
379 386 1.285023 GCTGTCTTGTGCCAAGCTG 59.715 57.895 9.35 9.41 0.00 4.24
380 387 1.168407 GCTGTCTTGTGCCAAGCTGA 61.168 55.000 9.35 0.00 0.00 4.26
381 388 1.311859 CTGTCTTGTGCCAAGCTGAA 58.688 50.000 9.35 0.00 0.00 3.02
382 389 1.266175 CTGTCTTGTGCCAAGCTGAAG 59.734 52.381 9.35 0.00 0.00 3.02
383 390 0.039708 GTCTTGTGCCAAGCTGAAGC 60.040 55.000 9.35 0.00 42.49 3.86
384 391 1.174712 TCTTGTGCCAAGCTGAAGCC 61.175 55.000 9.35 0.00 43.38 4.35
385 392 1.455402 TTGTGCCAAGCTGAAGCCA 60.455 52.632 0.00 0.00 43.38 4.75
386 393 1.042003 TTGTGCCAAGCTGAAGCCAA 61.042 50.000 0.00 0.00 43.38 4.52
387 394 1.042003 TGTGCCAAGCTGAAGCCAAA 61.042 50.000 0.00 0.00 43.38 3.28
388 395 0.319297 GTGCCAAGCTGAAGCCAAAG 60.319 55.000 0.00 0.00 43.38 2.77
389 396 0.467844 TGCCAAGCTGAAGCCAAAGA 60.468 50.000 0.00 0.00 43.38 2.52
390 397 0.675633 GCCAAGCTGAAGCCAAAGAA 59.324 50.000 0.00 0.00 43.38 2.52
391 398 1.069049 GCCAAGCTGAAGCCAAAGAAA 59.931 47.619 0.00 0.00 43.38 2.52
392 399 2.289257 GCCAAGCTGAAGCCAAAGAAAT 60.289 45.455 0.00 0.00 43.38 2.17
420 427 5.185056 GCAAACCATATGTTTACCCTCTTGT 59.815 40.000 1.24 0.00 45.35 3.16
421 428 6.295067 GCAAACCATATGTTTACCCTCTTGTT 60.295 38.462 1.24 0.00 45.35 2.83
425 432 6.884836 ACCATATGTTTACCCTCTTGTTCTTC 59.115 38.462 1.24 0.00 0.00 2.87
512 528 2.159517 GCCGATCAGATCACAACCAAAC 60.160 50.000 11.12 0.00 0.00 2.93
513 529 3.073678 CCGATCAGATCACAACCAAACA 58.926 45.455 11.12 0.00 0.00 2.83
514 530 3.501828 CCGATCAGATCACAACCAAACAA 59.498 43.478 11.12 0.00 0.00 2.83
515 531 4.378770 CCGATCAGATCACAACCAAACAAG 60.379 45.833 11.12 0.00 0.00 3.16
551 567 0.544223 TTAGCAGCGCCTTAATCCCA 59.456 50.000 2.29 0.00 0.00 4.37
552 568 0.764890 TAGCAGCGCCTTAATCCCAT 59.235 50.000 2.29 0.00 0.00 4.00
553 569 0.820891 AGCAGCGCCTTAATCCCATG 60.821 55.000 2.29 0.00 0.00 3.66
586 602 7.839680 ACCAGTGAAATTTACCATTTCTTCT 57.160 32.000 8.40 4.98 38.47 2.85
587 603 8.250143 ACCAGTGAAATTTACCATTTCTTCTT 57.750 30.769 8.40 0.00 38.47 2.52
604 620 4.272504 TCTTCTTCAACCAAAAGTAGCACG 59.727 41.667 0.00 0.00 0.00 5.34
615 631 6.711645 ACCAAAAGTAGCACGGTAAAAGATTA 59.288 34.615 0.00 0.00 0.00 1.75
698 714 1.474478 TCAGATCTCGCCAGAGTTGAC 59.526 52.381 0.00 0.00 44.65 3.18
709 725 2.847234 AGTTGACCCTGGCCGTCA 60.847 61.111 7.77 7.77 38.46 4.35
737 755 1.271597 GCACACATGGTTCCTCTTCCT 60.272 52.381 0.00 0.00 0.00 3.36
745 763 0.175989 GTTCCTCTTCCTGCCTACCG 59.824 60.000 0.00 0.00 0.00 4.02
787 827 1.394151 CCCACTTCCTCTCCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
969 1034 4.888325 AGAGCCCAGATCCCCCGG 62.888 72.222 0.00 0.00 0.00 5.73
1139 1208 3.333029 TGCTGAATTTGATCCGTGAGA 57.667 42.857 0.00 0.00 0.00 3.27
1140 1209 3.264947 TGCTGAATTTGATCCGTGAGAG 58.735 45.455 0.00 0.00 0.00 3.20
1254 1324 1.408822 GGTTTGGATCTCGCCCAGATT 60.409 52.381 0.00 0.00 42.48 2.40
1266 1336 2.373224 GCCCAGATTTTAGCTCTGCTT 58.627 47.619 0.00 0.00 40.44 3.91
1276 1346 7.880195 AGATTTTAGCTCTGCTTCTCTGTAAAA 59.120 33.333 0.00 0.00 40.44 1.52
1278 1348 7.602517 TTTAGCTCTGCTTCTCTGTAAAATC 57.397 36.000 0.00 0.00 40.44 2.17
1291 1361 5.305585 TCTGTAAAATCGTTTCCTCTTGCT 58.694 37.500 0.00 0.00 0.00 3.91
1296 1366 2.743636 TCGTTTCCTCTTGCTGGTAG 57.256 50.000 0.00 0.00 0.00 3.18
1339 1409 2.050144 AGTTCATGTGGTGGAGACTGT 58.950 47.619 0.00 0.00 0.00 3.55
1384 1471 2.426522 TGCTTGCTTGTGATACCACTC 58.573 47.619 0.00 0.00 43.55 3.51
1397 1484 5.047943 GTGATACCACTCTTGTCTGTACACT 60.048 44.000 0.00 0.00 40.10 3.55
1398 1485 5.183331 TGATACCACTCTTGTCTGTACACTC 59.817 44.000 0.00 0.00 34.61 3.51
1400 1487 2.628178 CCACTCTTGTCTGTACACTCCA 59.372 50.000 0.00 0.00 34.61 3.86
1401 1488 3.553096 CCACTCTTGTCTGTACACTCCAC 60.553 52.174 0.00 0.00 34.61 4.02
1402 1489 2.293677 ACTCTTGTCTGTACACTCCACG 59.706 50.000 0.00 0.00 34.61 4.94
1420 1513 3.120304 CCACGCTAGTGCTTTAAGGAAAC 60.120 47.826 2.40 0.00 46.62 2.78
1501 1597 1.276421 ACTCTGCGCTGATGGTTTAGT 59.724 47.619 17.78 7.31 0.00 2.24
1631 1727 5.251601 ACATTTAGAGCTAGAAGTCCGAC 57.748 43.478 0.00 0.00 0.00 4.79
1635 1731 0.658897 GAGCTAGAAGTCCGACGAGG 59.341 60.000 0.00 0.00 42.97 4.63
1646 1742 0.309302 CCGACGAGGAGTGATAGCTG 59.691 60.000 0.00 0.00 45.00 4.24
1659 1755 4.642885 AGTGATAGCTGACAAGACTAGTCC 59.357 45.833 19.38 4.63 35.15 3.85
1663 1759 4.529109 AGCTGACAAGACTAGTCCTTTC 57.471 45.455 19.38 9.79 35.15 2.62
1751 1847 1.388093 CTTGACGCGACAAGTGATGAG 59.612 52.381 33.14 14.69 41.32 2.90
1766 1862 3.090765 GAGCCTTGGGGTCCACAT 58.909 61.111 0.00 0.00 43.62 3.21
1859 1955 4.104897 GCTATCCCACCTCCCTTTTTATCT 59.895 45.833 0.00 0.00 0.00 1.98
1984 2080 5.560183 GCGTCATGTGTATAAGGTTATTGCC 60.560 44.000 0.00 0.00 0.00 4.52
2097 2289 2.292292 CAGTAACCACCAAAGGGAAACG 59.708 50.000 0.00 0.00 38.05 3.60
2132 2324 5.016985 CGTGCAAATTTTTATGAGCAATGC 58.983 37.500 0.00 0.00 33.37 3.56
2159 2352 9.941325 ATTCACTAATTAAAATTTGTGGATGCA 57.059 25.926 21.51 0.00 43.70 3.96
2204 2397 4.437239 ACTTGATAGCGAATGGTTCTGAG 58.563 43.478 0.00 0.00 0.00 3.35
2246 2439 9.993454 ATTCTCGATCATTATTCAAAGATCTCA 57.007 29.630 0.00 0.00 36.94 3.27
2296 2489 7.299246 ACAACTCTTTCTAGTTAAGGCTACA 57.701 36.000 0.00 0.00 37.61 2.74
2417 2610 1.518367 AAGTGGAAACTCTGGTGGGA 58.482 50.000 0.00 0.00 33.70 4.37
2465 2658 0.739112 CTGTGAGAGAGAAAGCGGCC 60.739 60.000 0.00 0.00 0.00 6.13
2491 2684 0.813610 CGTGACAAGTGGGTTCTGCA 60.814 55.000 0.00 0.00 0.00 4.41
2746 2940 7.715686 AGAACCTGTTAAAACCTCTTCAAGTAG 59.284 37.037 0.00 0.00 0.00 2.57
2761 2955 1.079405 GTAGTACTGGCAGGCGCAA 60.079 57.895 20.34 0.00 41.24 4.85
2821 3015 7.834181 TGATAGAAGGTATTTTAAGGCTGCTTT 59.166 33.333 1.74 1.74 0.00 3.51
2822 3016 9.338622 GATAGAAGGTATTTTAAGGCTGCTTTA 57.661 33.333 0.00 0.00 0.00 1.85
2824 3018 7.175797 AGAAGGTATTTTAAGGCTGCTTTACT 58.824 34.615 3.50 0.00 0.00 2.24
2861 3055 1.761449 TGACTGCTGCTGGTTTTCAA 58.239 45.000 11.29 0.00 0.00 2.69
2916 3143 4.584325 CAGTGGGATATGGTGGGTTAATTG 59.416 45.833 0.00 0.00 0.00 2.32
2933 3160 6.602009 GGTTAATTGTAGGTAGCATTCTTGGT 59.398 38.462 0.00 0.00 37.36 3.67
2948 3175 2.821378 TCTTGGTTGCATGATTGGTGAG 59.179 45.455 0.00 0.00 0.00 3.51
2953 3180 3.129287 GGTTGCATGATTGGTGAGTTAGG 59.871 47.826 0.00 0.00 0.00 2.69
2954 3181 3.719268 TGCATGATTGGTGAGTTAGGT 57.281 42.857 0.00 0.00 0.00 3.08
2956 3183 2.945668 GCATGATTGGTGAGTTAGGTCC 59.054 50.000 0.00 0.00 0.00 4.46
2958 3185 2.626785 TGATTGGTGAGTTAGGTCCCA 58.373 47.619 0.00 0.00 0.00 4.37
2959 3186 2.983192 TGATTGGTGAGTTAGGTCCCAA 59.017 45.455 0.00 0.00 39.35 4.12
2960 3187 2.943036 TTGGTGAGTTAGGTCCCAAC 57.057 50.000 0.00 0.00 30.51 3.77
2961 3188 2.112279 TGGTGAGTTAGGTCCCAACT 57.888 50.000 1.92 1.92 38.92 3.16
2969 3196 1.189524 TAGGTCCCAACTCACACGGG 61.190 60.000 0.00 0.00 41.76 5.28
2971 3198 4.225860 TCCCAACTCACACGGGAT 57.774 55.556 0.00 0.00 44.28 3.85
2972 3199 1.676968 TCCCAACTCACACGGGATG 59.323 57.895 0.00 0.00 44.28 3.51
2974 3201 0.036164 CCCAACTCACACGGGATGAA 59.964 55.000 0.00 0.00 43.21 2.57
2975 3202 1.442769 CCAACTCACACGGGATGAAG 58.557 55.000 0.00 0.00 0.00 3.02
3015 3348 9.331106 GCTATTGAAACAGAGTTAGTTTAAAGC 57.669 33.333 0.00 0.00 39.15 3.51
3018 3363 4.744136 AACAGAGTTAGTTTAAAGCGGC 57.256 40.909 0.00 0.00 0.00 6.53
3043 3388 4.265856 TGCCTATTAGAAGAGGTCCTCA 57.734 45.455 21.26 0.00 39.58 3.86
3046 3391 4.591072 GCCTATTAGAAGAGGTCCTCATGT 59.409 45.833 21.26 10.29 39.58 3.21
3085 3430 9.533253 AGTATGGTAAATGCAGCAATATTTTTC 57.467 29.630 0.00 0.00 0.00 2.29
3090 3435 8.720562 GGTAAATGCAGCAATATTTTTCAAAGT 58.279 29.630 0.00 0.00 0.00 2.66
3091 3436 9.532697 GTAAATGCAGCAATATTTTTCAAAGTG 57.467 29.630 0.00 0.00 0.00 3.16
3093 3438 7.966246 ATGCAGCAATATTTTTCAAAGTGAA 57.034 28.000 0.00 0.00 34.03 3.18
3114 3459 0.740868 TGCAGCAGTATCAGTTCGGC 60.741 55.000 0.00 0.00 0.00 5.54
3118 3463 2.359214 CAGCAGTATCAGTTCGGCTCTA 59.641 50.000 0.00 0.00 33.38 2.43
3123 3468 5.737635 GCAGTATCAGTTCGGCTCTAGATTT 60.738 44.000 0.00 0.00 0.00 2.17
3180 3525 5.818136 TTCACTCCTTCACTGAAGTTTTG 57.182 39.130 16.10 10.05 37.92 2.44
3188 3533 5.334105 CCTTCACTGAAGTTTTGTATCCACG 60.334 44.000 16.10 0.00 37.92 4.94
3216 3561 1.829222 TCGAAGTCCCCATCTAACACC 59.171 52.381 0.00 0.00 0.00 4.16
3237 3582 4.161001 ACCAAAGGCAATGAGGATGAATTC 59.839 41.667 0.00 0.00 0.00 2.17
3270 3615 2.233922 TCCTCGTGGATCTTCCTCAAAC 59.766 50.000 1.10 0.00 37.46 2.93
3307 3652 6.759497 AATGTATTTTCCTGGTTCTGCTAC 57.241 37.500 0.00 0.00 0.00 3.58
3361 3706 4.521639 ACTGAATGCATGTTCATGTCTTGT 59.478 37.500 0.00 0.00 37.47 3.16
3369 3714 6.025896 GCATGTTCATGTCTTGTCATGTAAG 58.974 40.000 13.24 0.00 43.70 2.34
3378 3723 9.586435 CATGTCTTGTCATGTAAGTCTGTTATA 57.414 33.333 10.68 0.00 39.93 0.98
3408 3836 9.944663 TGTAATGTTTTGACAAATAGTTCACTC 57.055 29.630 0.50 0.00 0.00 3.51
3413 3841 8.397906 TGTTTTGACAAATAGTTCACTCTTCAG 58.602 33.333 0.50 0.00 0.00 3.02
3430 3863 5.656480 TCTTCAGTTTGCATGTACGCTATA 58.344 37.500 0.00 0.00 0.00 1.31
3444 3877 9.909644 CATGTACGCTATAACTAGATTACCTTT 57.090 33.333 0.00 0.00 0.00 3.11
3519 3953 4.410492 AGATGAACGTCAATTCAAGTGC 57.590 40.909 0.00 0.00 41.78 4.40
3524 3958 4.275689 TGAACGTCAATTCAAGTGCTCAAT 59.724 37.500 0.00 0.00 35.65 2.57
3525 3959 4.410492 ACGTCAATTCAAGTGCTCAATC 57.590 40.909 0.00 0.00 0.00 2.67
3544 3978 8.523658 GCTCAATCAGTTTTTACTAAAAGGGAT 58.476 33.333 0.00 0.00 34.08 3.85
3580 4014 1.118838 GAGACTGGGAGTGCTATGCT 58.881 55.000 0.00 0.00 0.00 3.79
3583 4017 2.307098 AGACTGGGAGTGCTATGCTTTT 59.693 45.455 0.00 0.00 0.00 2.27
3632 4066 6.579666 TGGATTTGGAAACTCAAAGAGATG 57.420 37.500 0.31 0.00 39.59 2.90
3634 4068 6.207417 TGGATTTGGAAACTCAAAGAGATGAC 59.793 38.462 0.31 0.00 39.59 3.06
3683 4117 3.311048 GCTAATACAAAGACTGCTGAGGC 59.689 47.826 0.00 0.00 39.26 4.70
3702 4136 1.767759 CGGATCTTCTTGGCCCAAAT 58.232 50.000 0.00 0.00 0.00 2.32
3722 4156 6.540914 CCAAATTTGATGGATGATTTCCTTGG 59.459 38.462 19.86 0.00 45.68 3.61
3729 4163 0.753111 ATGATTTCCTTGGCGAGCCC 60.753 55.000 12.05 0.00 34.56 5.19
3748 4182 2.623915 GCAGCCACTCCAGCAACAG 61.624 63.158 0.00 0.00 0.00 3.16
3758 4192 0.318445 CCAGCAACAGAAAGTGCTGC 60.318 55.000 17.94 2.83 46.89 5.25
3767 4201 0.877743 GAAAGTGCTGCAGAACCTCC 59.122 55.000 21.83 6.70 0.00 4.30
3823 4257 0.609131 AATCCCAGGTGCCGAAACAG 60.609 55.000 0.00 0.00 0.00 3.16
3855 4292 2.299013 GGATGTCCAGGTTTGGTTTTCC 59.701 50.000 0.00 0.00 45.26 3.13
3861 4298 2.887152 CCAGGTTTGGTTTTCCTCTCTG 59.113 50.000 0.00 0.00 39.79 3.35
3863 4300 4.445735 CCAGGTTTGGTTTTCCTCTCTGTA 60.446 45.833 0.00 0.00 39.79 2.74
3890 4327 7.700322 TCGAAGCTGCTAAATATGTTAGAAG 57.300 36.000 0.90 7.90 32.04 2.85
3934 4371 2.554032 ACTGCCAGTATTGTGCTTTGAC 59.446 45.455 0.00 0.00 0.00 3.18
3936 4373 3.156293 TGCCAGTATTGTGCTTTGACAT 58.844 40.909 0.00 0.00 0.00 3.06
4268 4705 3.261580 CACTGGAAATATCAGCACGTCA 58.738 45.455 0.00 0.00 35.78 4.35
4394 4831 1.952367 GCAGATGTAGCACCTTTGGCT 60.952 52.381 0.00 0.00 45.18 4.75
4408 4845 1.114722 TTGGCTGCTCCCAAAACTGG 61.115 55.000 0.00 0.00 41.69 4.00
4412 4849 1.809567 CTGCTCCCAAAACTGGTGCC 61.810 60.000 0.00 0.00 40.73 5.01
4452 4889 3.425577 TTGCAAACACTCAAGAAGCAG 57.574 42.857 0.00 0.00 0.00 4.24
4592 5029 1.734465 GACTCTTTGAGCCGTGGATTG 59.266 52.381 0.00 0.00 32.04 2.67
4647 5084 0.179062 CTCATTTCCTCCTCGCCCTG 60.179 60.000 0.00 0.00 0.00 4.45
4678 5116 7.338800 ACTTGATTTCAGAAGTGTTGATGTT 57.661 32.000 0.00 0.00 31.09 2.71
4731 5169 0.696501 ACTTAGCCGATGTTGGGGTT 59.303 50.000 0.00 0.00 36.51 4.11
4734 5172 0.402504 TAGCCGATGTTGGGGTTGTT 59.597 50.000 0.00 0.00 36.51 2.83
4771 5209 1.429463 GTTCGACGACAAGGCTCAAT 58.571 50.000 0.00 0.00 0.00 2.57
4775 5213 1.646189 GACGACAAGGCTCAATCCTC 58.354 55.000 0.00 0.00 34.82 3.71
4776 5214 0.976641 ACGACAAGGCTCAATCCTCA 59.023 50.000 0.00 0.00 34.82 3.86
4777 5215 1.556911 ACGACAAGGCTCAATCCTCAT 59.443 47.619 0.00 0.00 34.82 2.90
4778 5216 1.938577 CGACAAGGCTCAATCCTCATG 59.061 52.381 0.00 0.00 34.82 3.07
4779 5217 2.295885 GACAAGGCTCAATCCTCATGG 58.704 52.381 0.00 0.00 34.82 3.66
4781 5219 2.295885 CAAGGCTCAATCCTCATGGAC 58.704 52.381 0.00 0.00 46.51 4.02
4782 5220 0.842635 AGGCTCAATCCTCATGGACC 59.157 55.000 0.00 0.00 46.51 4.46
4783 5221 0.533755 GGCTCAATCCTCATGGACCG 60.534 60.000 0.00 0.00 46.51 4.79
4784 5222 0.533755 GCTCAATCCTCATGGACCGG 60.534 60.000 0.00 0.00 46.51 5.28
4785 5223 1.123077 CTCAATCCTCATGGACCGGA 58.877 55.000 9.46 0.00 46.51 5.14
4786 5224 1.069823 CTCAATCCTCATGGACCGGAG 59.930 57.143 9.46 6.10 46.51 4.63
4800 5238 1.749033 CGGAGGATCTAGCCAACCC 59.251 63.158 0.00 0.00 33.73 4.11
4801 5239 0.760945 CGGAGGATCTAGCCAACCCT 60.761 60.000 0.00 0.00 33.73 4.34
5068 5508 0.934496 TCACCTCGCTTTTGTTGACG 59.066 50.000 0.00 0.00 0.00 4.35
5081 5521 1.333308 TGTTGACGGTCACATTGCTTG 59.667 47.619 10.97 0.00 0.00 4.01
5129 5569 3.013921 GGTCTTTGTCCAGTGTTGTCAA 58.986 45.455 0.00 0.00 0.00 3.18
5156 5596 0.888619 TTGTGTTTGTCGGGTTTGCA 59.111 45.000 0.00 0.00 0.00 4.08
5202 5642 9.281371 ACATCATGATTCGATTCAATCTTATGT 57.719 29.630 13.51 13.88 34.35 2.29
5310 5753 7.162761 TGAAATACTACTTCGGAAACCATCAA 58.837 34.615 0.00 0.00 0.00 2.57
5382 5825 0.934496 TCAAAAGCGTCCGAACACTG 59.066 50.000 0.00 0.00 0.00 3.66
5386 5829 0.670546 AAGCGTCCGAACACTGATGG 60.671 55.000 0.00 0.00 0.00 3.51
5397 5840 0.030235 CACTGATGGCATGGCATTCG 59.970 55.000 32.59 26.48 0.00 3.34
5403 5846 1.761449 TGGCATGGCATTCGTGTTAT 58.239 45.000 19.43 0.00 34.91 1.89
5451 5894 6.778821 TGACATTCTACCCTTGATTTTCTCA 58.221 36.000 0.00 0.00 0.00 3.27
5452 5895 6.881065 TGACATTCTACCCTTGATTTTCTCAG 59.119 38.462 0.00 0.00 34.68 3.35
5454 5897 7.461749 ACATTCTACCCTTGATTTTCTCAGAA 58.538 34.615 0.00 0.00 34.68 3.02
5455 5898 7.609532 ACATTCTACCCTTGATTTTCTCAGAAG 59.390 37.037 0.00 0.00 34.68 2.85
5469 5913 2.049802 GAAGTTGTCGCGACCGGA 60.050 61.111 34.34 18.62 34.56 5.14
5473 5917 0.601841 AGTTGTCGCGACCGGATTTT 60.602 50.000 34.34 11.60 34.56 1.82
5517 5961 2.113986 GTTGTGCTCACCAGCCCT 59.886 61.111 0.00 0.00 46.26 5.19
5616 6063 3.133003 CCATTCGGGTCTGAGAGTACAAT 59.867 47.826 0.00 0.00 0.00 2.71
5640 6087 2.253610 TGGTTTCTAGTGGTCGATGGT 58.746 47.619 0.00 0.00 0.00 3.55
6073 6521 1.372499 GCGTCTTAGCGACACCACA 60.372 57.895 0.00 0.00 42.98 4.17
6155 6603 3.817647 GCCACATAAAGGGCTTATGAGAG 59.182 47.826 12.01 3.48 46.88 3.20
6228 6678 6.475596 AAGGGCTTATGAGAAAATGGAATG 57.524 37.500 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.669427 AGACCATGCATTGTTCATAAGAAAAA 58.331 30.769 4.71 0.00 35.52 1.94
17 18 5.823209 TGAGACCATGCATTGTTCATAAG 57.177 39.130 4.71 0.00 0.00 1.73
22 23 4.560035 CGATTTTGAGACCATGCATTGTTC 59.440 41.667 4.71 5.70 0.00 3.18
32 35 2.131972 CGACACACGATTTTGAGACCA 58.868 47.619 0.00 0.00 45.77 4.02
33 36 1.136336 GCGACACACGATTTTGAGACC 60.136 52.381 0.00 0.00 45.77 3.85
45 48 3.175152 CAGATACTCTCAAGCGACACAC 58.825 50.000 0.00 0.00 0.00 3.82
53 56 6.344500 AGGCAACAATACAGATACTCTCAAG 58.656 40.000 0.00 0.00 41.41 3.02
64 67 7.820648 AGAATAGTTTTGAGGCAACAATACAG 58.179 34.615 15.38 0.00 35.38 2.74
65 68 7.759489 AGAATAGTTTTGAGGCAACAATACA 57.241 32.000 15.38 6.67 35.38 2.29
67 70 8.637986 ACAAAGAATAGTTTTGAGGCAACAATA 58.362 29.630 4.87 0.00 38.55 1.90
113 120 2.101125 CGTCAACAGCAAAAACAGTCG 58.899 47.619 0.00 0.00 0.00 4.18
119 126 1.202245 GCCTCACGTCAACAGCAAAAA 60.202 47.619 0.00 0.00 0.00 1.94
181 188 2.382770 TGGTGTGGTGGCTTCAGGT 61.383 57.895 0.00 0.00 0.00 4.00
183 190 0.396435 TAGTGGTGTGGTGGCTTCAG 59.604 55.000 0.00 0.00 0.00 3.02
193 200 8.956426 AGAATAACATGGTAAAATAGTGGTGTG 58.044 33.333 0.00 0.00 0.00 3.82
194 201 9.528489 AAGAATAACATGGTAAAATAGTGGTGT 57.472 29.630 0.00 0.00 0.00 4.16
218 225 3.384789 TCCATGTATGACCCGAGAAGAAG 59.615 47.826 0.00 0.00 0.00 2.85
250 257 1.001048 CACACACAGGTTCCATTGCAG 60.001 52.381 0.00 0.00 0.00 4.41
251 258 1.031235 CACACACAGGTTCCATTGCA 58.969 50.000 0.00 0.00 0.00 4.08
268 275 2.832129 TCTGGATTCAGTGGGAGTACAC 59.168 50.000 0.00 0.00 41.59 2.90
273 280 1.577736 AGGTCTGGATTCAGTGGGAG 58.422 55.000 0.00 0.00 41.59 4.30
288 295 2.424956 CCTGCTCCAATTTTGCTAGGTC 59.575 50.000 0.00 0.00 0.00 3.85
326 333 2.366590 TCTGAAGCTGACACACACATCT 59.633 45.455 0.00 0.00 0.00 2.90
327 334 2.759191 TCTGAAGCTGACACACACATC 58.241 47.619 0.00 0.00 0.00 3.06
328 335 2.916702 TCTGAAGCTGACACACACAT 57.083 45.000 0.00 0.00 0.00 3.21
329 336 2.158914 ACATCTGAAGCTGACACACACA 60.159 45.455 0.00 0.00 0.00 3.72
330 337 2.487934 ACATCTGAAGCTGACACACAC 58.512 47.619 0.00 0.00 0.00 3.82
331 338 2.874086 CAACATCTGAAGCTGACACACA 59.126 45.455 0.00 0.00 0.00 3.72
333 340 2.104622 TCCAACATCTGAAGCTGACACA 59.895 45.455 0.00 0.00 0.00 3.72
334 341 2.740981 CTCCAACATCTGAAGCTGACAC 59.259 50.000 0.00 0.00 0.00 3.67
336 343 2.027745 TCCTCCAACATCTGAAGCTGAC 60.028 50.000 0.00 0.00 0.00 3.51
337 344 2.027745 GTCCTCCAACATCTGAAGCTGA 60.028 50.000 0.00 0.00 0.00 4.26
338 345 2.354259 GTCCTCCAACATCTGAAGCTG 58.646 52.381 0.00 0.00 0.00 4.24
340 347 1.280421 AGGTCCTCCAACATCTGAAGC 59.720 52.381 0.00 0.00 35.89 3.86
341 348 2.938756 GCAGGTCCTCCAACATCTGAAG 60.939 54.545 0.00 0.00 35.89 3.02
342 349 1.003580 GCAGGTCCTCCAACATCTGAA 59.996 52.381 0.00 0.00 35.89 3.02
343 350 0.615331 GCAGGTCCTCCAACATCTGA 59.385 55.000 0.00 0.00 35.89 3.27
344 351 0.617413 AGCAGGTCCTCCAACATCTG 59.383 55.000 0.00 0.00 35.89 2.90
345 352 0.617413 CAGCAGGTCCTCCAACATCT 59.383 55.000 0.00 0.00 35.89 2.90
346 353 0.326264 ACAGCAGGTCCTCCAACATC 59.674 55.000 0.00 0.00 35.89 3.06
347 354 0.326264 GACAGCAGGTCCTCCAACAT 59.674 55.000 0.00 0.00 40.83 2.71
348 355 1.754745 GACAGCAGGTCCTCCAACA 59.245 57.895 0.00 0.00 40.83 3.33
349 356 4.703703 GACAGCAGGTCCTCCAAC 57.296 61.111 0.00 0.00 40.83 3.77
357 364 2.918248 TGGCACAAGACAGCAGGT 59.082 55.556 0.00 0.00 31.92 4.00
364 371 3.341291 GGCTTCAGCTTGGCACAAGAC 62.341 57.143 16.28 9.12 40.37 3.01
365 372 1.174712 GGCTTCAGCTTGGCACAAGA 61.175 55.000 16.28 0.00 40.37 3.02
366 373 1.288127 GGCTTCAGCTTGGCACAAG 59.712 57.895 9.75 9.75 40.37 3.16
367 374 1.042003 TTGGCTTCAGCTTGGCACAA 61.042 50.000 6.84 5.08 40.37 3.33
368 375 1.042003 TTTGGCTTCAGCTTGGCACA 61.042 50.000 6.84 0.00 41.70 4.57
369 376 0.319297 CTTTGGCTTCAGCTTGGCAC 60.319 55.000 6.84 0.00 41.70 5.01
370 377 0.467844 TCTTTGGCTTCAGCTTGGCA 60.468 50.000 0.00 3.73 41.70 4.92
371 378 0.675633 TTCTTTGGCTTCAGCTTGGC 59.324 50.000 0.00 0.00 41.70 4.52
372 379 3.243975 ACATTTCTTTGGCTTCAGCTTGG 60.244 43.478 0.00 0.00 41.70 3.61
373 380 3.739300 CACATTTCTTTGGCTTCAGCTTG 59.261 43.478 0.00 0.00 41.70 4.01
374 381 3.243975 CCACATTTCTTTGGCTTCAGCTT 60.244 43.478 0.00 0.00 41.70 3.74
375 382 2.298163 CCACATTTCTTTGGCTTCAGCT 59.702 45.455 0.00 0.00 41.70 4.24
376 383 2.680577 CCACATTTCTTTGGCTTCAGC 58.319 47.619 0.00 0.00 41.14 4.26
383 390 3.191078 TGGTTTGCCACATTTCTTTGG 57.809 42.857 0.00 0.00 40.46 3.28
408 415 6.659824 ACTGAAAGAAGAACAAGAGGGTAAA 58.340 36.000 0.00 0.00 37.43 2.01
425 432 6.444633 AGATGCACATTTCTTTGACTGAAAG 58.555 36.000 0.00 0.00 42.33 2.62
512 528 5.051907 GCTAATCTGATTTTGCGAATGCTTG 60.052 40.000 8.38 0.00 43.34 4.01
513 529 5.039333 GCTAATCTGATTTTGCGAATGCTT 58.961 37.500 8.38 0.00 43.34 3.91
514 530 4.096833 TGCTAATCTGATTTTGCGAATGCT 59.903 37.500 8.38 0.00 43.34 3.79
515 531 4.353737 TGCTAATCTGATTTTGCGAATGC 58.646 39.130 8.38 2.40 43.20 3.56
551 567 9.125026 GGTAAATTTCACTGGTAATCTCATCAT 57.875 33.333 0.00 0.00 0.00 2.45
552 568 8.106462 TGGTAAATTTCACTGGTAATCTCATCA 58.894 33.333 0.00 0.00 0.00 3.07
553 569 8.506168 TGGTAAATTTCACTGGTAATCTCATC 57.494 34.615 0.00 0.00 0.00 2.92
584 600 2.875933 CCGTGCTACTTTTGGTTGAAGA 59.124 45.455 0.00 0.00 0.00 2.87
585 601 2.616842 ACCGTGCTACTTTTGGTTGAAG 59.383 45.455 0.00 0.00 0.00 3.02
586 602 2.645802 ACCGTGCTACTTTTGGTTGAA 58.354 42.857 0.00 0.00 0.00 2.69
587 603 2.335316 ACCGTGCTACTTTTGGTTGA 57.665 45.000 0.00 0.00 0.00 3.18
604 620 4.095782 TCAATGCACCGCTAATCTTTTACC 59.904 41.667 0.00 0.00 0.00 2.85
615 631 1.071299 TCTGTGTCAATGCACCGCT 59.929 52.632 0.00 0.00 38.52 5.52
618 634 0.884704 ACGGTCTGTGTCAATGCACC 60.885 55.000 0.00 0.00 38.52 5.01
698 714 0.748005 CTACCATTTGACGGCCAGGG 60.748 60.000 2.24 0.00 0.00 4.45
709 725 2.825532 GGAACCATGTGTGCTACCATTT 59.174 45.455 0.00 0.00 0.00 2.32
745 763 4.796495 GGTGGGTGATGGCCGGTC 62.796 72.222 0.00 0.00 0.00 4.79
949 1014 2.146061 GGGGGATCTGGGCTCTCAG 61.146 68.421 0.00 0.00 36.17 3.35
950 1015 2.040464 GGGGGATCTGGGCTCTCA 60.040 66.667 0.00 0.00 0.00 3.27
969 1034 1.742268 GTCGCCGGGGACTCTATATAC 59.258 57.143 36.72 14.00 34.09 1.47
1089 1154 0.725117 CCTTGTAAAACGGCTAGCGG 59.275 55.000 19.74 19.74 0.00 5.52
1139 1208 1.216678 ACGGATCAGGATCTCACTCCT 59.783 52.381 9.01 0.00 46.92 3.69
1140 1209 1.698506 ACGGATCAGGATCTCACTCC 58.301 55.000 9.01 0.00 37.92 3.85
1183 1253 3.370315 CCTTGAGATTGACCTCCCTCTTG 60.370 52.174 0.00 0.00 32.32 3.02
1254 1324 6.311445 CGATTTTACAGAGAAGCAGAGCTAAA 59.689 38.462 0.00 0.00 38.25 1.85
1266 1336 5.408604 GCAAGAGGAAACGATTTTACAGAGA 59.591 40.000 0.00 0.00 0.00 3.10
1276 1346 2.567615 ACTACCAGCAAGAGGAAACGAT 59.432 45.455 0.00 0.00 0.00 3.73
1278 1348 2.069273 CACTACCAGCAAGAGGAAACG 58.931 52.381 0.00 0.00 0.00 3.60
1291 1361 4.441495 CGATAATTCACAGCTCCACTACCA 60.441 45.833 0.00 0.00 0.00 3.25
1296 1366 3.179443 TCCGATAATTCACAGCTCCAC 57.821 47.619 0.00 0.00 0.00 4.02
1339 1409 5.332743 AGGCAAAATTCAAGTTCCATCCTA 58.667 37.500 0.00 0.00 0.00 2.94
1384 1471 1.000163 AGCGTGGAGTGTACAGACAAG 60.000 52.381 0.00 0.00 37.31 3.16
1402 1489 7.611213 TTATCAGTTTCCTTAAAGCACTAGC 57.389 36.000 0.00 0.00 42.56 3.42
1482 1577 2.015736 ACTAAACCATCAGCGCAGAG 57.984 50.000 11.47 0.00 0.00 3.35
1531 1627 4.506654 GTGCATTCGGTAGTGTATTTCGAT 59.493 41.667 0.00 0.00 0.00 3.59
1631 1727 2.685388 TCTTGTCAGCTATCACTCCTCG 59.315 50.000 0.00 0.00 0.00 4.63
1635 1731 5.220970 GGACTAGTCTTGTCAGCTATCACTC 60.221 48.000 21.88 0.00 36.26 3.51
1646 1742 5.355910 AGAGATCGAAAGGACTAGTCTTGTC 59.644 44.000 21.88 17.70 0.00 3.18
1663 1759 8.680707 ACGAAATATGATACAATGAGAGATCG 57.319 34.615 0.00 0.00 0.00 3.69
1751 1847 2.362889 CCATGTGGACCCCAAGGC 60.363 66.667 0.00 0.00 34.18 4.35
1859 1955 5.439721 AGTTATAGGCATCATTTCAGCACA 58.560 37.500 0.00 0.00 0.00 4.57
1984 2080 6.694445 AGGATGGTCATTAGGGAATAAGAG 57.306 41.667 0.00 0.00 0.00 2.85
2033 2225 6.398918 TGTAGAAGTGATTCCTAACAAGCTC 58.601 40.000 0.00 0.00 0.00 4.09
2097 2289 4.434713 AATTTGCACGATACAAAGGTCC 57.565 40.909 0.00 0.00 40.14 4.46
2159 2352 3.055819 ACTCAATAATCGTCAGTGCCTGT 60.056 43.478 2.68 0.00 32.61 4.00
2204 2397 0.099436 GAATGTCATCAACTGCCCGC 59.901 55.000 0.00 0.00 0.00 6.13
2246 2439 4.640201 ACAAAAGCACAGACAACACATACT 59.360 37.500 0.00 0.00 0.00 2.12
2296 2489 7.957484 CGACAAGAAAATGTTTAATCACTCGAT 59.043 33.333 0.00 0.00 32.57 3.59
2465 2658 1.202604 ACCCACTTGTCACGGTTACTG 60.203 52.381 0.00 0.00 0.00 2.74
2746 2940 1.026718 AGATTTGCGCCTGCCAGTAC 61.027 55.000 4.18 0.00 41.78 2.73
2761 2955 4.643784 CCTTTCTTATCTTGCTGCCAGATT 59.356 41.667 19.68 6.30 0.00 2.40
2834 3028 4.286297 ACCAGCAGCAGTCATTTAACTA 57.714 40.909 0.00 0.00 0.00 2.24
2835 3029 3.146104 ACCAGCAGCAGTCATTTAACT 57.854 42.857 0.00 0.00 0.00 2.24
2843 3037 2.869233 TTTGAAAACCAGCAGCAGTC 57.131 45.000 0.00 0.00 0.00 3.51
2916 3143 3.343617 TGCAACCAAGAATGCTACCTAC 58.656 45.455 0.00 0.00 42.97 3.18
2933 3160 4.009675 GACCTAACTCACCAATCATGCAA 58.990 43.478 0.00 0.00 0.00 4.08
2948 3175 1.607251 CCGTGTGAGTTGGGACCTAAC 60.607 57.143 12.62 12.62 0.00 2.34
2953 3180 3.144285 TCCCGTGTGAGTTGGGAC 58.856 61.111 0.00 0.00 46.96 4.46
2956 3183 1.270839 ACTTCATCCCGTGTGAGTTGG 60.271 52.381 0.00 0.00 0.00 3.77
2958 3185 2.897969 ACTACTTCATCCCGTGTGAGTT 59.102 45.455 0.00 0.00 31.33 3.01
2959 3186 2.526432 ACTACTTCATCCCGTGTGAGT 58.474 47.619 0.00 0.00 32.74 3.41
2960 3187 4.580995 AGATACTACTTCATCCCGTGTGAG 59.419 45.833 0.00 0.00 0.00 3.51
2961 3188 4.533815 AGATACTACTTCATCCCGTGTGA 58.466 43.478 0.00 0.00 0.00 3.58
2963 3190 7.598759 AATTAGATACTACTTCATCCCGTGT 57.401 36.000 0.00 0.00 0.00 4.49
2964 3191 7.095607 GCAAATTAGATACTACTTCATCCCGTG 60.096 40.741 0.00 0.00 0.00 4.94
2965 3192 6.929606 GCAAATTAGATACTACTTCATCCCGT 59.070 38.462 0.00 0.00 0.00 5.28
2999 3332 6.478588 CAATAGCCGCTTTAAACTAACTCTG 58.521 40.000 0.00 0.00 0.00 3.35
3000 3333 5.064834 GCAATAGCCGCTTTAAACTAACTCT 59.935 40.000 0.00 0.00 33.58 3.24
3002 3335 5.231265 GCAATAGCCGCTTTAAACTAACT 57.769 39.130 0.00 0.00 33.58 2.24
3018 3363 6.495181 TGAGGACCTCTTCTAATAGGCAATAG 59.505 42.308 22.14 0.00 36.24 1.73
3033 3378 4.288105 ACAAGATTCAACATGAGGACCTCT 59.712 41.667 22.14 5.41 0.00 3.69
3085 3430 5.050644 TGATACTGCTGCATTTCACTTTG 57.949 39.130 1.31 0.00 0.00 2.77
3090 3435 3.371898 CGAACTGATACTGCTGCATTTCA 59.628 43.478 1.31 6.00 0.00 2.69
3091 3436 3.242543 CCGAACTGATACTGCTGCATTTC 60.243 47.826 1.31 1.19 0.00 2.17
3093 3438 2.283298 CCGAACTGATACTGCTGCATT 58.717 47.619 1.31 0.00 0.00 3.56
3114 3459 3.996480 CCCCGAGGCTAAAAATCTAGAG 58.004 50.000 0.00 0.00 0.00 2.43
3129 3474 3.617284 ACAATAAAAGGTAAGCCCCGAG 58.383 45.455 0.00 0.00 34.57 4.63
3130 3475 3.724732 ACAATAAAAGGTAAGCCCCGA 57.275 42.857 0.00 0.00 34.57 5.14
3132 3477 7.885009 TGTATAACAATAAAAGGTAAGCCCC 57.115 36.000 0.00 0.00 34.57 5.80
3180 3525 1.299468 CGAGGAGCTGCGTGGATAC 60.299 63.158 0.00 0.00 0.00 2.24
3188 3533 2.185608 GGGACTTCGAGGAGCTGC 59.814 66.667 0.00 0.00 0.00 5.25
3216 3561 4.096833 TCGAATTCATCCTCATTGCCTTTG 59.903 41.667 6.22 0.00 0.00 2.77
3285 3630 6.067217 AGTAGCAGAACCAGGAAAATACAT 57.933 37.500 0.00 0.00 0.00 2.29
3286 3631 5.499004 AGTAGCAGAACCAGGAAAATACA 57.501 39.130 0.00 0.00 0.00 2.29
3287 3632 5.354513 GGAAGTAGCAGAACCAGGAAAATAC 59.645 44.000 0.00 0.00 0.00 1.89
3289 3634 4.202567 TGGAAGTAGCAGAACCAGGAAAAT 60.203 41.667 0.00 0.00 0.00 1.82
3301 3646 2.408271 TCCTTGCATGGAAGTAGCAG 57.592 50.000 23.38 9.57 39.72 4.24
3396 3741 6.942532 TGCAAACTGAAGAGTGAACTATTT 57.057 33.333 0.00 0.00 30.61 1.40
3408 3836 4.864916 ATAGCGTACATGCAAACTGAAG 57.135 40.909 0.00 0.00 37.31 3.02
3413 3841 7.639162 ATCTAGTTATAGCGTACATGCAAAC 57.361 36.000 0.00 0.00 37.31 2.93
3430 3863 7.620880 TGTGCTACATGAAAGGTAATCTAGTT 58.379 34.615 0.00 0.00 30.07 2.24
3498 3931 4.067896 AGCACTTGAATTGACGTTCATCT 58.932 39.130 0.00 0.00 37.88 2.90
3499 3932 4.083855 TGAGCACTTGAATTGACGTTCATC 60.084 41.667 0.00 0.00 37.88 2.92
3519 3953 9.846248 CATCCCTTTTAGTAAAAACTGATTGAG 57.154 33.333 9.28 0.00 31.37 3.02
3524 3958 7.447238 CAGGTCATCCCTTTTAGTAAAAACTGA 59.553 37.037 9.28 6.57 42.73 3.41
3525 3959 7.447238 TCAGGTCATCCCTTTTAGTAAAAACTG 59.553 37.037 9.28 5.03 42.73 3.16
3544 3978 5.511373 CCAGTCTCAACAAACTATCAGGTCA 60.511 44.000 0.00 0.00 0.00 4.02
3554 3988 1.604278 GCACTCCCAGTCTCAACAAAC 59.396 52.381 0.00 0.00 0.00 2.93
3600 4034 8.885494 TTGAGTTTCCAAATCCAACAAATTAG 57.115 30.769 0.00 0.00 0.00 1.73
3601 4035 9.323985 CTTTGAGTTTCCAAATCCAACAAATTA 57.676 29.630 0.00 0.00 35.72 1.40
3632 4066 9.522804 CACCTGTAGAACAAGATAGAAATAGTC 57.477 37.037 0.00 0.00 0.00 2.59
3634 4068 7.981789 TGCACCTGTAGAACAAGATAGAAATAG 59.018 37.037 0.00 0.00 0.00 1.73
3678 4112 1.221840 GCCAAGAAGATCCGCCTCA 59.778 57.895 0.00 0.00 0.00 3.86
3683 4117 1.767759 ATTTGGGCCAAGAAGATCCG 58.232 50.000 19.90 0.00 0.00 4.18
3729 4163 3.730761 GTTGCTGGAGTGGCTGCG 61.731 66.667 0.00 0.00 0.00 5.18
3745 4179 1.133976 AGGTTCTGCAGCACTTTCTGT 60.134 47.619 16.13 0.00 36.49 3.41
3748 4182 0.877743 GGAGGTTCTGCAGCACTTTC 59.122 55.000 16.13 13.19 0.00 2.62
3767 4201 2.730090 GCATCAGCAAACAGATCAACCG 60.730 50.000 0.00 0.00 41.58 4.44
3855 4292 4.764679 AGCAGCTTCGATATACAGAGAG 57.235 45.455 0.00 0.00 0.00 3.20
3863 4300 9.929180 TTCTAACATATTTAGCAGCTTCGATAT 57.071 29.630 0.00 0.00 0.00 1.63
3887 4324 4.507710 TGGCACTGTGTCAGATAATCTTC 58.492 43.478 11.65 0.00 35.18 2.87
4212 4649 1.481056 GGTGGTGGTGCACTAGAGGT 61.481 60.000 17.98 0.00 34.40 3.85
4214 4651 0.320771 GTGGTGGTGGTGCACTAGAG 60.321 60.000 17.98 0.00 34.40 2.43
4268 4705 1.544314 GCTGCCTCAAGGTTCTGACTT 60.544 52.381 0.00 0.00 37.57 3.01
4408 4845 0.244721 GGCACCAAAATCAGAGGCAC 59.755 55.000 0.00 0.00 0.00 5.01
4412 4849 2.154462 ACGAAGGCACCAAAATCAGAG 58.846 47.619 0.00 0.00 0.00 3.35
4443 4880 2.087646 GGGGTCTTTAGCTGCTTCTTG 58.912 52.381 7.79 0.00 0.00 3.02
4444 4881 1.988846 AGGGGTCTTTAGCTGCTTCTT 59.011 47.619 7.79 0.00 0.00 2.52
4452 4889 5.257262 AGAAAGATCAAAGGGGTCTTTAGC 58.743 41.667 2.80 0.00 41.01 3.09
4592 5029 5.812642 ACGTCCAGTTATGTTCAGATCAATC 59.187 40.000 0.00 0.00 0.00 2.67
4626 5063 0.541863 GGGCGAGGAGGAAATGAGAA 59.458 55.000 0.00 0.00 0.00 2.87
4647 5084 6.564328 ACACTTCTGAAATCAAGTTTCCAAC 58.436 36.000 0.00 0.00 44.53 3.77
4662 5100 6.258727 GTGAAGAGAAACATCAACACTTCTGA 59.741 38.462 0.00 0.00 35.05 3.27
4731 5169 0.676466 CATCACTAAGGCCGCCAACA 60.676 55.000 13.15 0.00 0.00 3.33
4734 5172 2.589540 CCATCACTAAGGCCGCCA 59.410 61.111 13.15 0.00 0.00 5.69
4743 5181 1.536940 TGTCGTCGAACCCATCACTA 58.463 50.000 0.00 0.00 0.00 2.74
4775 5213 0.605589 GCTAGATCCTCCGGTCCATG 59.394 60.000 0.00 0.00 0.00 3.66
4776 5214 0.543174 GGCTAGATCCTCCGGTCCAT 60.543 60.000 0.00 0.00 0.00 3.41
4777 5215 1.152525 GGCTAGATCCTCCGGTCCA 60.153 63.158 0.00 0.00 0.00 4.02
4778 5216 0.759436 TTGGCTAGATCCTCCGGTCC 60.759 60.000 0.00 0.00 0.00 4.46
4779 5217 0.389757 GTTGGCTAGATCCTCCGGTC 59.610 60.000 0.00 0.00 0.00 4.79
4780 5218 1.049289 GGTTGGCTAGATCCTCCGGT 61.049 60.000 0.00 0.00 0.00 5.28
4781 5219 1.749033 GGTTGGCTAGATCCTCCGG 59.251 63.158 0.00 0.00 0.00 5.14
4782 5220 0.760945 AGGGTTGGCTAGATCCTCCG 60.761 60.000 0.00 0.00 0.00 4.63
4783 5221 1.052617 GAGGGTTGGCTAGATCCTCC 58.947 60.000 0.00 0.00 38.36 4.30
4784 5222 1.794714 TGAGGGTTGGCTAGATCCTC 58.205 55.000 2.82 2.82 43.06 3.71
4785 5223 2.053244 CATGAGGGTTGGCTAGATCCT 58.947 52.381 0.00 0.00 0.00 3.24
4786 5224 1.072965 CCATGAGGGTTGGCTAGATCC 59.927 57.143 0.00 0.00 0.00 3.36
4787 5225 2.050144 TCCATGAGGGTTGGCTAGATC 58.950 52.381 0.00 0.00 38.11 2.75
4788 5226 2.173569 GTTCCATGAGGGTTGGCTAGAT 59.826 50.000 0.00 0.00 38.11 1.98
4789 5227 1.559682 GTTCCATGAGGGTTGGCTAGA 59.440 52.381 0.00 0.00 38.11 2.43
4790 5228 1.281867 TGTTCCATGAGGGTTGGCTAG 59.718 52.381 0.00 0.00 38.11 3.42
4791 5229 1.367346 TGTTCCATGAGGGTTGGCTA 58.633 50.000 0.00 0.00 38.11 3.93
4792 5230 0.706433 ATGTTCCATGAGGGTTGGCT 59.294 50.000 0.00 0.00 38.11 4.75
4793 5231 0.819582 CATGTTCCATGAGGGTTGGC 59.180 55.000 0.00 0.00 38.11 4.52
4794 5232 1.477553 CCATGTTCCATGAGGGTTGG 58.522 55.000 5.80 0.00 38.11 3.77
4795 5233 1.477553 CCCATGTTCCATGAGGGTTG 58.522 55.000 5.80 0.00 38.11 3.77
4798 5236 1.039233 GCACCCATGTTCCATGAGGG 61.039 60.000 5.80 0.00 45.20 4.30
4799 5237 1.039233 GGCACCCATGTTCCATGAGG 61.039 60.000 5.80 7.71 0.00 3.86
4800 5238 1.378882 CGGCACCCATGTTCCATGAG 61.379 60.000 5.80 0.00 0.00 2.90
4801 5239 1.378382 CGGCACCCATGTTCCATGA 60.378 57.895 5.80 0.00 0.00 3.07
4818 5256 2.190578 GGTTGGCCAGATCCTCCG 59.809 66.667 5.11 0.00 34.09 4.63
4821 5259 0.625683 ATGAGGGTTGGCCAGATCCT 60.626 55.000 19.45 19.45 36.17 3.24
5052 5492 0.234884 GACCGTCAACAAAAGCGAGG 59.765 55.000 0.00 0.00 0.00 4.63
5068 5508 3.922240 CAGCAATTACAAGCAATGTGACC 59.078 43.478 5.51 0.00 43.77 4.02
5081 5521 7.065894 CGATACTTGAATACTGCAGCAATTAC 58.934 38.462 15.27 8.74 0.00 1.89
5129 5569 1.065401 CCGACAAACACAACACATGCT 59.935 47.619 0.00 0.00 0.00 3.79
5156 5596 0.108138 GACACAAGGGCAGCGTATCT 60.108 55.000 0.00 0.00 0.00 1.98
5202 5642 9.853555 CAATTTACAGAAGGTGCACATATTAAA 57.146 29.630 20.43 12.88 0.00 1.52
5310 5753 7.106439 TCCAAAACAGTGTTCAATGTAATGT 57.894 32.000 9.40 0.00 0.00 2.71
5363 5806 0.934496 CAGTGTTCGGACGCTTTTGA 59.066 50.000 7.32 0.00 43.89 2.69
5382 5825 0.457035 AACACGAATGCCATGCCATC 59.543 50.000 0.00 0.00 0.00 3.51
5386 5829 4.681025 CCAATTATAACACGAATGCCATGC 59.319 41.667 0.00 0.00 0.00 4.06
5451 5894 1.874345 ATCCGGTCGCGACAACTTCT 61.874 55.000 37.26 15.73 0.00 2.85
5452 5895 1.012486 AATCCGGTCGCGACAACTTC 61.012 55.000 37.26 20.29 0.00 3.01
5454 5897 0.601841 AAAATCCGGTCGCGACAACT 60.602 50.000 37.26 17.82 0.00 3.16
5455 5898 0.179233 GAAAATCCGGTCGCGACAAC 60.179 55.000 37.26 21.73 0.00 3.32
5517 5961 5.011125 GCCTCATCAGCTAACAGTAATCCTA 59.989 44.000 0.00 0.00 0.00 2.94
5607 6054 8.603304 ACCACTAGAAACCAATTATTGTACTCT 58.397 33.333 4.15 5.03 0.00 3.24
5616 6063 5.046159 ACCATCGACCACTAGAAACCAATTA 60.046 40.000 0.00 0.00 0.00 1.40
5640 6087 0.394488 TGAACCACAAACCGCTTCCA 60.394 50.000 0.00 0.00 0.00 3.53
6110 6558 4.357947 TCAGACGCCCGACTGTGC 62.358 66.667 16.85 0.00 38.61 4.57
6155 6603 7.092716 ACTGAGGCATGTTTGTTATTTCATTC 58.907 34.615 0.00 0.00 0.00 2.67
6228 6678 0.238289 CCGACTGTGGCATGTTTGTC 59.762 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.