Multiple sequence alignment - TraesCS7B01G065100

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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 TraesCS7B01G065100 chr7B 100.000 2756 0 0 1 2756 70522217 70519462 0.000000e+00 5090.0
1 TraesCS7B01G065100 chr7B 93.182 44 3 0 2707 2750 70489934 70489891 6.370000e-07 65.8
2 TraesCS7B01G065100 chr7A 84.232 1725 146 62 353 2026 116125509 116123860 0.000000e+00 1563.0
3 TraesCS7B01G065100 chr7A 85.603 257 12 8 2101 2342 116123828 116123582 2.120000e-61 246.0
4 TraesCS7B01G065100 chr7A 94.000 150 9 0 2391 2540 116123578 116123429 7.680000e-56 228.0
5 TraesCS7B01G065100 chr7A 91.892 148 11 1 3 150 116125840 116125694 3.600000e-49 206.0
6 TraesCS7B01G065100 chr7A 85.833 120 1 3 2632 2746 116123014 116122906 2.240000e-21 113.0
7 TraesCS7B01G065100 chr7D 84.844 1280 112 44 733 1960 111059673 111058424 0.000000e+00 1214.0
8 TraesCS7B01G065100 chr7D 85.714 357 11 15 2072 2417 111058293 111057966 9.450000e-90 340.0
9 TraesCS7B01G065100 chr7D 92.683 123 3 3 2634 2750 111057873 111057751 3.650000e-39 172.0
10 TraesCS7B01G065100 chr7D 78.431 255 47 5 352 604 111061620 111061372 2.840000e-35 159.0
11 TraesCS7B01G065100 chr7D 90.722 97 9 0 2385 2481 111057961 111057865 2.230000e-26 130.0
12 TraesCS7B01G065100 chr6B 78.125 160 33 2 347 505 15882083 15882241 1.750000e-17 100.0
13 TraesCS7B01G065100 chr2D 80.952 84 15 1 354 436 268900411 268900328 6.370000e-07 65.8


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 TraesCS7B01G065100 chr7B 70519462 70522217 2755 True 5090.0 5090 100.0000 1 2756 1 chr7B.!!$R2 2755
1 TraesCS7B01G065100 chr7A 116122906 116125840 2934 True 471.2 1563 88.3120 3 2746 5 chr7A.!!$R1 2743
2 TraesCS7B01G065100 chr7D 111057751 111061620 3869 True 403.0 1214 86.4788 352 2750 5 chr7D.!!$R1 2398

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
313 351 0.041663 ATAAACGCACACGCACACAC 60.042 50.0 0.0 0.0 45.53 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 3884 0.104855 TAGGTGAGGCACATCATCGC 59.895 55.0 0.0 0.0 35.37 4.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 0.172803 ACGATCCCTAACTGACGTGC 59.827 55.000 0.00 0.00 32.93 5.34
78 79 2.002586 CCACAAAGACTCGGCTATGTG 58.997 52.381 0.00 0.00 38.25 3.21
81 82 0.613260 AAAGACTCGGCTATGTGGCA 59.387 50.000 0.00 0.00 41.89 4.92
91 92 1.917273 CTATGTGGCATGCAACAAGC 58.083 50.000 30.83 7.23 45.96 4.01
92 93 1.475280 CTATGTGGCATGCAACAAGCT 59.525 47.619 30.83 17.61 45.94 3.74
93 94 0.682852 ATGTGGCATGCAACAAGCTT 59.317 45.000 30.83 12.61 45.94 3.74
99 100 4.213906 GTGGCATGCAACAAGCTTTTTAAT 59.786 37.500 20.70 0.00 45.94 1.40
106 107 4.984161 GCAACAAGCTTTTTAATCAGCTCA 59.016 37.500 8.89 0.00 46.01 4.26
113 114 6.567959 AGCTTTTTAATCAGCTCAAATAGGC 58.432 36.000 3.56 0.00 43.12 3.93
140 141 1.538950 CCTTGCAACAGAGCTCTTTCC 59.461 52.381 15.27 3.54 34.99 3.13
174 212 2.469736 GCTCAATGATGGGCGACTAGC 61.470 57.143 0.00 0.00 44.59 3.42
186 224 0.392998 CGACTAGCAGGTTTGGGCAT 60.393 55.000 0.00 0.00 0.00 4.40
190 228 1.490490 CTAGCAGGTTTGGGCATAGGA 59.510 52.381 0.00 0.00 0.00 2.94
195 233 2.231716 GGTTTGGGCATAGGAACCTT 57.768 50.000 0.00 0.00 38.74 3.50
200 238 0.831307 GGGCATAGGAACCTTCGAGT 59.169 55.000 0.00 0.00 0.00 4.18
210 248 3.244112 GGAACCTTCGAGTTCTCTTGGAA 60.244 47.826 14.87 1.22 44.56 3.53
214 252 4.223923 ACCTTCGAGTTCTCTTGGAATGAT 59.776 41.667 8.62 0.00 36.24 2.45
218 256 3.118629 CGAGTTCTCTTGGAATGATCCCA 60.119 47.826 0.00 0.00 45.95 4.37
225 263 5.039920 TCTTGGAATGATCCCATGTACAG 57.960 43.478 0.33 0.00 45.95 2.74
226 264 4.474651 TCTTGGAATGATCCCATGTACAGT 59.525 41.667 0.33 0.00 45.95 3.55
259 297 9.653067 TTTGTTTGTTTTATCACAGTACATACG 57.347 29.630 0.00 0.00 0.00 3.06
260 298 7.292292 TGTTTGTTTTATCACAGTACATACGC 58.708 34.615 0.00 0.00 0.00 4.42
264 302 7.039270 TGTTTTATCACAGTACATACGCAGAT 58.961 34.615 0.00 0.00 0.00 2.90
266 304 4.655762 ATCACAGTACATACGCAGATGT 57.344 40.909 5.83 5.83 42.68 3.06
277 315 6.512297 ACATACGCAGATGTTCATACATACA 58.488 36.000 0.00 0.00 44.90 2.29
278 316 6.983890 ACATACGCAGATGTTCATACATACAA 59.016 34.615 0.00 0.00 44.90 2.41
279 317 7.494298 ACATACGCAGATGTTCATACATACAAA 59.506 33.333 0.00 0.00 44.90 2.83
280 318 6.925610 ACGCAGATGTTCATACATACAAAT 57.074 33.333 0.00 0.00 44.90 2.32
283 321 9.705290 ACGCAGATGTTCATACATACAAATATA 57.295 29.630 0.00 0.00 44.90 0.86
284 322 9.958285 CGCAGATGTTCATACATACAAATATAC 57.042 33.333 0.00 0.00 44.90 1.47
304 342 9.767228 AATATACACTAACCATATAAACGCACA 57.233 29.630 0.00 0.00 0.00 4.57
305 343 5.789710 ACACTAACCATATAAACGCACAC 57.210 39.130 0.00 0.00 0.00 3.82
307 345 2.817538 AACCATATAAACGCACACGC 57.182 45.000 0.00 0.00 45.53 5.34
308 346 1.728068 ACCATATAAACGCACACGCA 58.272 45.000 0.00 0.00 45.53 5.24
309 347 1.395608 ACCATATAAACGCACACGCAC 59.604 47.619 0.00 0.00 45.53 5.34
310 348 1.395262 CCATATAAACGCACACGCACA 59.605 47.619 0.00 0.00 45.53 4.57
311 349 2.427169 CATATAAACGCACACGCACAC 58.573 47.619 0.00 0.00 45.53 3.82
312 350 1.499049 TATAAACGCACACGCACACA 58.501 45.000 0.00 0.00 45.53 3.72
313 351 0.041663 ATAAACGCACACGCACACAC 60.042 50.000 0.00 0.00 45.53 3.82
314 352 1.359459 TAAACGCACACGCACACACA 61.359 50.000 0.00 0.00 45.53 3.72
315 353 2.842588 AAACGCACACGCACACACAC 62.843 55.000 0.00 0.00 45.53 3.82
316 354 3.858989 CGCACACGCACACACACA 61.859 61.111 0.00 0.00 38.40 3.72
317 355 2.277247 GCACACGCACACACACAC 60.277 61.111 0.00 0.00 38.36 3.82
318 356 3.033166 GCACACGCACACACACACA 62.033 57.895 0.00 0.00 38.36 3.72
319 357 1.225991 CACACGCACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
320 358 1.669437 ACACGCACACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
321 359 1.225991 CACGCACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
322 360 1.669437 ACGCACACACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
323 361 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
324 362 1.872468 GCACACACACACACACACA 59.128 52.632 0.00 0.00 0.00 3.72
325 363 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
326 364 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
327 365 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
328 366 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
329 367 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
330 368 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
331 369 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
332 370 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
333 371 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
334 372 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
335 373 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
336 374 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
337 375 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
338 376 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
339 377 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
340 378 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
341 379 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
342 380 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
343 381 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
344 382 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
345 383 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
346 384 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
347 385 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
348 386 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
349 387 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
350 388 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
358 396 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
362 400 2.739379 CACACACACACACACACACTAA 59.261 45.455 0.00 0.00 0.00 2.24
366 404 1.305201 CACACACACACACTAACCCC 58.695 55.000 0.00 0.00 0.00 4.95
377 415 0.620556 ACTAACCCCATGAGCACCTG 59.379 55.000 0.00 0.00 0.00 4.00
393 431 0.103208 CCTGCGAGAGATAAAGCCGT 59.897 55.000 0.00 0.00 0.00 5.68
411 449 4.100035 AGCCGTCACATCATCTTGAGATTA 59.900 41.667 0.00 0.00 31.21 1.75
413 451 5.468072 GCCGTCACATCATCTTGAGATTAAT 59.532 40.000 0.00 0.00 31.21 1.40
433 471 0.107654 GAAGTCACCATAGGCGCCTT 60.108 55.000 37.74 19.80 0.00 4.35
437 475 2.173669 CACCATAGGCGCCTTCGTG 61.174 63.158 37.74 30.42 38.14 4.35
482 520 1.153353 GAACGAGCATCACCCGAAAA 58.847 50.000 0.00 0.00 33.17 2.29
489 527 1.818674 GCATCACCCGAAAACCTGAAT 59.181 47.619 0.00 0.00 0.00 2.57
509 547 7.545265 CCTGAATTAAATCCAGAAAAATGCGAA 59.455 33.333 0.00 0.00 0.00 4.70
513 551 4.853924 AATCCAGAAAAATGCGAACAGT 57.146 36.364 0.00 0.00 0.00 3.55
519 557 5.920273 CCAGAAAAATGCGAACAGTAATGTT 59.080 36.000 8.54 8.54 34.29 2.71
525 563 3.403968 TGCGAACAGTAATGTTAAGCCA 58.596 40.909 23.79 14.21 35.85 4.75
531 569 4.332828 ACAGTAATGTTAAGCCAAGGACC 58.667 43.478 0.00 0.00 0.00 4.46
540 578 3.612795 AAGCCAAGGACCTAAACCTTT 57.387 42.857 0.00 0.00 44.13 3.11
543 581 2.755208 GCCAAGGACCTAAACCTTTGGT 60.755 50.000 7.75 0.00 44.13 3.67
545 583 2.890945 CAAGGACCTAAACCTTTGGTGG 59.109 50.000 0.00 0.00 44.13 4.61
548 586 2.423803 GGACCTAAACCTTTGGTGGTGT 60.424 50.000 2.54 0.00 40.73 4.16
550 588 1.339929 CCTAAACCTTTGGTGGTGTGC 59.660 52.381 0.00 0.00 40.73 4.57
552 590 2.445682 AAACCTTTGGTGGTGTGCTA 57.554 45.000 0.00 0.00 40.73 3.49
553 591 1.981256 AACCTTTGGTGGTGTGCTAG 58.019 50.000 0.00 0.00 40.73 3.42
554 592 0.843984 ACCTTTGGTGGTGTGCTAGT 59.156 50.000 0.00 0.00 39.17 2.57
555 593 1.214424 ACCTTTGGTGGTGTGCTAGTT 59.786 47.619 0.00 0.00 39.17 2.24
556 594 2.306847 CCTTTGGTGGTGTGCTAGTTT 58.693 47.619 0.00 0.00 0.00 2.66
557 595 2.293399 CCTTTGGTGGTGTGCTAGTTTC 59.707 50.000 0.00 0.00 0.00 2.78
558 596 1.588674 TTGGTGGTGTGCTAGTTTCG 58.411 50.000 0.00 0.00 0.00 3.46
559 597 0.466543 TGGTGGTGTGCTAGTTTCGT 59.533 50.000 0.00 0.00 0.00 3.85
601 640 1.355066 GCTAGGCTCAGTTCGCACAC 61.355 60.000 0.00 0.00 0.00 3.82
615 654 4.624336 TCGCACACTGTAATTTGTTTGT 57.376 36.364 0.00 0.00 0.00 2.83
621 660 7.108005 GCACACTGTAATTTGTTTGTTAAACG 58.892 34.615 0.00 0.00 44.28 3.60
642 681 6.707599 ACGAACATGAGCTAGTTCTTTAAC 57.292 37.500 18.38 0.00 41.40 2.01
648 687 8.220755 ACATGAGCTAGTTCTTTAACAAAACA 57.779 30.769 8.15 0.00 38.12 2.83
715 2347 2.551032 CACGTAGCATATACCTCCACGA 59.449 50.000 0.00 0.00 0.00 4.35
717 2349 3.072211 CGTAGCATATACCTCCACGAGA 58.928 50.000 0.00 0.00 0.00 4.04
720 2352 2.158445 AGCATATACCTCCACGAGACCT 60.158 50.000 0.00 0.00 0.00 3.85
721 2353 2.628657 GCATATACCTCCACGAGACCTT 59.371 50.000 0.00 0.00 0.00 3.50
722 2354 3.305471 GCATATACCTCCACGAGACCTTC 60.305 52.174 0.00 0.00 0.00 3.46
723 2355 2.526888 ATACCTCCACGAGACCTTCA 57.473 50.000 0.00 0.00 0.00 3.02
724 2356 2.297698 TACCTCCACGAGACCTTCAA 57.702 50.000 0.00 0.00 0.00 2.69
725 2357 0.969894 ACCTCCACGAGACCTTCAAG 59.030 55.000 0.00 0.00 0.00 3.02
726 2358 0.247736 CCTCCACGAGACCTTCAAGG 59.752 60.000 0.22 0.22 42.49 3.61
727 2359 0.247736 CTCCACGAGACCTTCAAGGG 59.752 60.000 8.75 0.00 40.58 3.95
728 2360 0.178944 TCCACGAGACCTTCAAGGGA 60.179 55.000 8.75 0.00 40.58 4.20
729 2361 0.247736 CCACGAGACCTTCAAGGGAG 59.752 60.000 8.75 0.00 40.58 4.30
730 2362 0.247736 CACGAGACCTTCAAGGGAGG 59.752 60.000 8.75 0.00 40.58 4.30
731 2363 1.219393 CGAGACCTTCAAGGGAGGC 59.781 63.158 8.75 0.00 40.58 4.70
732 2364 1.604915 GAGACCTTCAAGGGAGGCC 59.395 63.158 8.75 0.00 40.58 5.19
733 2365 1.916206 GAGACCTTCAAGGGAGGCCC 61.916 65.000 8.75 0.00 45.90 5.80
1019 2665 2.047465 CCAGACGCAAGCAGAGCT 60.047 61.111 0.00 0.00 42.56 4.09
1021 2667 1.373873 CAGACGCAAGCAGAGCTGA 60.374 57.895 0.85 0.00 39.62 4.26
1234 2903 1.138047 GCCGTCGTCCACTGTTATCG 61.138 60.000 0.00 0.00 0.00 2.92
1308 2983 1.652012 GGAGACGGAGAGATCGCTG 59.348 63.158 2.76 0.00 0.00 5.18
1330 3005 0.030638 GAGCTGGAGATCGTCTGAGC 59.969 60.000 0.00 0.00 33.22 4.26
1519 3203 1.553690 CGAATGGGAGGTGGTGAGGT 61.554 60.000 0.00 0.00 0.00 3.85
1521 3205 0.475632 AATGGGAGGTGGTGAGGTCA 60.476 55.000 0.00 0.00 0.00 4.02
1526 3210 2.032681 GGTGGTGAGGTCACTGCC 59.967 66.667 9.90 8.48 45.73 4.85
1527 3211 2.520536 GGTGGTGAGGTCACTGCCT 61.521 63.158 9.90 0.00 45.73 4.75
1546 3236 3.964221 CTCGCGGCGACAACTGCTA 62.964 63.158 22.69 0.00 39.92 3.49
1547 3237 3.838795 CGCGGCGACAACTGCTAC 61.839 66.667 19.16 0.00 39.92 3.58
1549 3239 3.179265 CGGCGACAACTGCTACGG 61.179 66.667 0.00 0.00 0.00 4.02
1550 3240 2.813908 GGCGACAACTGCTACGGG 60.814 66.667 0.00 0.00 0.00 5.28
1551 3241 2.260434 GCGACAACTGCTACGGGA 59.740 61.111 0.00 0.00 0.00 5.14
1552 3242 1.373748 GCGACAACTGCTACGGGAA 60.374 57.895 0.00 0.00 0.00 3.97
1553 3243 1.623973 GCGACAACTGCTACGGGAAC 61.624 60.000 0.00 0.00 0.00 3.62
1565 3255 2.030862 GGGAACGTGGCGGTACAA 59.969 61.111 0.00 0.00 0.00 2.41
1609 3299 4.720902 TGGTGCGGCTGTGGGATG 62.721 66.667 0.00 0.00 0.00 3.51
1695 3388 2.525055 GTGTCGAGCTTCTGATCACTC 58.475 52.381 0.00 0.00 0.00 3.51
1696 3389 2.095008 GTGTCGAGCTTCTGATCACTCA 60.095 50.000 10.62 0.00 0.00 3.41
1698 3391 3.005791 TGTCGAGCTTCTGATCACTCAAA 59.994 43.478 10.62 0.00 0.00 2.69
1699 3392 3.611986 GTCGAGCTTCTGATCACTCAAAG 59.388 47.826 10.62 5.36 0.00 2.77
1701 3394 2.677337 GAGCTTCTGATCACTCAAAGCC 59.323 50.000 17.34 9.80 41.41 4.35
1710 3403 1.416030 TCACTCAAAGCCACTGTAGCA 59.584 47.619 0.29 0.00 0.00 3.49
1711 3404 2.038952 TCACTCAAAGCCACTGTAGCAT 59.961 45.455 0.29 0.00 0.00 3.79
1712 3405 2.816087 CACTCAAAGCCACTGTAGCATT 59.184 45.455 0.29 0.00 0.00 3.56
1713 3406 2.816087 ACTCAAAGCCACTGTAGCATTG 59.184 45.455 9.36 9.36 39.60 2.82
1715 3408 3.221771 TCAAAGCCACTGTAGCATTGTT 58.778 40.909 13.96 0.00 39.34 2.83
1716 3409 3.636300 TCAAAGCCACTGTAGCATTGTTT 59.364 39.130 13.96 0.00 39.34 2.83
1718 3411 3.146104 AGCCACTGTAGCATTGTTTCT 57.854 42.857 0.29 0.00 0.00 2.52
1719 3412 3.490348 AGCCACTGTAGCATTGTTTCTT 58.510 40.909 0.29 0.00 0.00 2.52
1722 3415 4.022849 GCCACTGTAGCATTGTTTCTTTCT 60.023 41.667 0.00 0.00 0.00 2.52
1726 3419 8.134895 CCACTGTAGCATTGTTTCTTTCTTTTA 58.865 33.333 0.00 0.00 0.00 1.52
1754 3447 7.818930 TCTGGAAGAATGAAATTGGCAATAAAC 59.181 33.333 14.05 8.48 42.31 2.01
1821 3524 1.270839 GCCGATGTACCCTGCACATAT 60.271 52.381 0.00 0.00 36.76 1.78
1836 3539 7.143340 CCTGCACATATAATGTTTTCATCCAG 58.857 38.462 0.00 0.00 42.70 3.86
1837 3540 7.201848 CCTGCACATATAATGTTTTCATCCAGT 60.202 37.037 0.00 0.00 42.70 4.00
1840 3543 7.859377 GCACATATAATGTTTTCATCCAGTCAG 59.141 37.037 0.00 0.00 42.70 3.51
1862 3565 4.397417 AGATCAGTTATTGCTTGCAACTCC 59.603 41.667 10.37 1.61 30.20 3.85
1865 3573 3.254166 CAGTTATTGCTTGCAACTCCAGT 59.746 43.478 10.37 0.00 30.20 4.00
1878 3586 4.709840 CCAGTTCCTCTGCTGGTG 57.290 61.111 2.66 0.00 45.28 4.17
1879 3587 1.673665 CCAGTTCCTCTGCTGGTGC 60.674 63.158 2.66 0.00 45.28 5.01
1881 3589 0.954449 CAGTTCCTCTGCTGGTGCTG 60.954 60.000 0.00 0.00 40.48 4.41
1884 3592 1.203441 TTCCTCTGCTGGTGCTGGAT 61.203 55.000 0.00 0.00 40.48 3.41
1886 3594 2.045634 TCTGCTGGTGCTGGATGC 60.046 61.111 0.00 0.00 40.48 3.91
1887 3595 3.138798 CTGCTGGTGCTGGATGCC 61.139 66.667 0.00 0.00 42.00 4.40
1888 3596 4.746309 TGCTGGTGCTGGATGCCC 62.746 66.667 0.00 0.00 42.00 5.36
1889 3597 4.746309 GCTGGTGCTGGATGCCCA 62.746 66.667 0.00 0.00 42.00 5.36
1890 3598 2.036098 CTGGTGCTGGATGCCCAA 59.964 61.111 0.00 0.00 42.98 4.12
1891 3599 2.283101 TGGTGCTGGATGCCCAAC 60.283 61.111 0.00 0.00 42.98 3.77
1892 3600 3.443045 GGTGCTGGATGCCCAACG 61.443 66.667 0.00 0.00 42.98 4.10
1893 3601 2.359850 GTGCTGGATGCCCAACGA 60.360 61.111 0.00 0.00 42.98 3.85
1894 3602 2.359850 TGCTGGATGCCCAACGAC 60.360 61.111 0.00 0.00 42.98 4.34
1904 3617 2.972505 CCAACGACACGCCTTGCT 60.973 61.111 0.00 0.00 0.00 3.91
1907 3620 0.370273 CAACGACACGCCTTGCTATC 59.630 55.000 0.00 0.00 0.00 2.08
1909 3622 0.458543 ACGACACGCCTTGCTATCTG 60.459 55.000 0.00 0.00 0.00 2.90
1910 3623 0.458543 CGACACGCCTTGCTATCTGT 60.459 55.000 0.00 0.00 0.00 3.41
1911 3624 1.002366 GACACGCCTTGCTATCTGTG 58.998 55.000 0.00 0.00 0.00 3.66
1922 3635 2.632512 TGCTATCTGTGACACCTGTTGA 59.367 45.455 2.45 0.00 0.00 3.18
1923 3636 3.261643 TGCTATCTGTGACACCTGTTGAT 59.738 43.478 2.45 2.46 0.00 2.57
1940 3656 6.529125 CCTGTTGATTTGCAAATGCTAGTTAG 59.471 38.462 28.67 15.49 42.66 2.34
1941 3657 6.389091 TGTTGATTTGCAAATGCTAGTTAGG 58.611 36.000 28.67 0.00 42.66 2.69
1963 3679 2.947652 CCATTGGCAGTAACAGAGATGG 59.052 50.000 0.00 0.00 0.00 3.51
1973 3692 2.238084 ACAGAGATGGCTACCAGTGA 57.762 50.000 0.00 0.00 36.75 3.41
1996 3750 3.797039 GCCAAAAGCTTATTTCCCCATC 58.203 45.455 0.00 0.00 38.99 3.51
1997 3751 3.197549 GCCAAAAGCTTATTTCCCCATCA 59.802 43.478 0.00 0.00 38.99 3.07
2006 3760 0.112995 TTTCCCCATCACTGCAGCTT 59.887 50.000 15.27 0.00 0.00 3.74
2010 3764 2.777114 TCCCCATCACTGCAGCTTATTA 59.223 45.455 15.27 0.00 0.00 0.98
2012 3766 3.434167 CCCCATCACTGCAGCTTATTACT 60.434 47.826 15.27 0.00 0.00 2.24
2021 3775 5.180117 ACTGCAGCTTATTACTTGTTGACAG 59.820 40.000 15.27 0.00 0.00 3.51
2026 3780 6.744537 CAGCTTATTACTTGTTGACAGAATGC 59.255 38.462 0.00 0.00 42.53 3.56
2028 3782 6.963805 GCTTATTACTTGTTGACAGAATGCTC 59.036 38.462 0.00 0.00 42.53 4.26
2029 3783 7.361201 GCTTATTACTTGTTGACAGAATGCTCA 60.361 37.037 0.00 0.00 42.53 4.26
2031 3785 2.551459 ACTTGTTGACAGAATGCTCAGC 59.449 45.455 0.00 0.00 42.53 4.26
2032 3786 2.556144 TGTTGACAGAATGCTCAGCT 57.444 45.000 0.00 0.00 42.53 4.24
2033 3787 2.854963 TGTTGACAGAATGCTCAGCTT 58.145 42.857 0.00 0.00 42.53 3.74
2034 3788 4.006780 TGTTGACAGAATGCTCAGCTTA 57.993 40.909 0.00 0.00 42.53 3.09
2035 3789 4.582869 TGTTGACAGAATGCTCAGCTTAT 58.417 39.130 0.00 0.00 42.53 1.73
2036 3790 5.005740 TGTTGACAGAATGCTCAGCTTATT 58.994 37.500 0.00 0.00 42.53 1.40
2039 3793 5.118990 TGACAGAATGCTCAGCTTATTACC 58.881 41.667 0.00 0.00 42.53 2.85
2049 3803 4.501071 TCAGCTTATTACCTGACGTTTCC 58.499 43.478 0.00 0.00 33.44 3.13
2053 3807 4.504858 CTTATTACCTGACGTTTCCTGCT 58.495 43.478 0.00 0.00 0.00 4.24
2055 3809 3.587797 TTACCTGACGTTTCCTGCTAG 57.412 47.619 0.00 0.00 0.00 3.42
2056 3810 0.037232 ACCTGACGTTTCCTGCTAGC 60.037 55.000 8.10 8.10 0.00 3.42
2057 3811 0.247736 CCTGACGTTTCCTGCTAGCT 59.752 55.000 17.23 0.00 0.00 3.32
2059 3813 2.094182 CCTGACGTTTCCTGCTAGCTAA 60.094 50.000 17.23 4.98 0.00 3.09
2062 3816 3.194755 TGACGTTTCCTGCTAGCTAATCA 59.805 43.478 17.23 6.10 0.00 2.57
2063 3817 3.522553 ACGTTTCCTGCTAGCTAATCAC 58.477 45.455 17.23 6.57 0.00 3.06
2064 3818 3.056107 ACGTTTCCTGCTAGCTAATCACA 60.056 43.478 17.23 0.00 0.00 3.58
2065 3819 3.307242 CGTTTCCTGCTAGCTAATCACAC 59.693 47.826 17.23 3.43 0.00 3.82
2066 3820 4.253685 GTTTCCTGCTAGCTAATCACACA 58.746 43.478 17.23 0.00 0.00 3.72
2067 3821 4.760530 TTCCTGCTAGCTAATCACACAT 57.239 40.909 17.23 0.00 0.00 3.21
2068 3822 4.760530 TCCTGCTAGCTAATCACACATT 57.239 40.909 17.23 0.00 0.00 2.71
2069 3823 4.697514 TCCTGCTAGCTAATCACACATTC 58.302 43.478 17.23 0.00 0.00 2.67
2070 3824 4.162131 TCCTGCTAGCTAATCACACATTCA 59.838 41.667 17.23 0.00 0.00 2.57
2071 3825 4.272018 CCTGCTAGCTAATCACACATTCAC 59.728 45.833 17.23 0.00 0.00 3.18
2072 3826 4.831107 TGCTAGCTAATCACACATTCACA 58.169 39.130 17.23 0.00 0.00 3.58
2073 3827 4.631377 TGCTAGCTAATCACACATTCACAC 59.369 41.667 17.23 0.00 0.00 3.82
2074 3828 4.872691 GCTAGCTAATCACACATTCACACT 59.127 41.667 7.70 0.00 0.00 3.55
2075 3829 5.220548 GCTAGCTAATCACACATTCACACTG 60.221 44.000 7.70 0.00 0.00 3.66
2076 3830 4.005650 AGCTAATCACACATTCACACTGG 58.994 43.478 0.00 0.00 0.00 4.00
2077 3831 4.002982 GCTAATCACACATTCACACTGGA 58.997 43.478 0.00 0.00 0.00 3.86
2078 3832 4.455533 GCTAATCACACATTCACACTGGAA 59.544 41.667 0.00 0.00 0.00 3.53
2079 3833 4.836125 AATCACACATTCACACTGGAAC 57.164 40.909 0.00 0.00 0.00 3.62
2284 4058 3.243367 CCAACAAATTCACCACACGACAT 60.243 43.478 0.00 0.00 0.00 3.06
2302 4076 2.172483 ATCGTGCCAGGACAGGACAC 62.172 60.000 8.01 0.00 37.28 3.67
2319 4093 3.433748 CGACTCCGTGAACGAACG 58.566 61.111 4.03 0.00 43.02 3.95
2327 4101 1.827315 CGTGAACGAACGCCACATGT 61.827 55.000 15.88 0.00 43.02 3.21
2332 4106 1.733041 CGAACGCCACATGTCTCGT 60.733 57.895 14.11 14.11 36.67 4.18
2385 4196 2.664916 GTAACCGTACGTCAAGCTGAA 58.335 47.619 15.21 0.00 0.00 3.02
2387 4198 0.672342 ACCGTACGTCAAGCTGAAGT 59.328 50.000 15.21 8.99 41.68 3.01
2498 4309 0.881118 CCTGCAGTTAACGTTGCCAT 59.119 50.000 13.81 0.00 39.54 4.40
2508 4319 2.049248 GTTGCCATGGTTGGTGCG 60.049 61.111 14.67 0.00 45.57 5.34
2540 4351 1.295357 TTGGGTGCGACATTACTGCG 61.295 55.000 0.00 0.00 0.00 5.18
2541 4352 1.740296 GGGTGCGACATTACTGCGT 60.740 57.895 0.00 0.00 0.00 5.24
2544 4355 1.625616 GTGCGACATTACTGCGTACT 58.374 50.000 0.00 0.00 35.94 2.73
2545 4356 2.478370 GGTGCGACATTACTGCGTACTA 60.478 50.000 13.69 0.00 37.52 1.82
2546 4357 2.529090 GTGCGACATTACTGCGTACTAC 59.471 50.000 0.00 0.00 35.94 2.73
2547 4358 1.771848 GCGACATTACTGCGTACTACG 59.228 52.381 4.12 4.12 45.88 3.51
2548 4359 2.789092 GCGACATTACTGCGTACTACGT 60.789 50.000 10.23 0.00 44.73 3.57
2549 4360 3.544048 GCGACATTACTGCGTACTACGTA 60.544 47.826 10.23 4.91 44.73 3.57
2550 4361 3.956305 CGACATTACTGCGTACTACGTAC 59.044 47.826 10.23 0.00 44.73 3.67
2559 4370 2.619013 GTACTACGTACGTGTGCCTT 57.381 50.000 30.25 10.24 29.20 4.35
2561 4372 1.774639 ACTACGTACGTGTGCCTTTG 58.225 50.000 30.25 11.75 0.00 2.77
2563 4374 1.276820 TACGTACGTGTGCCTTTGCG 61.277 55.000 30.25 0.00 41.78 4.85
2564 4375 2.554272 GTACGTGTGCCTTTGCGG 59.446 61.111 0.00 0.00 41.78 5.69
2565 4376 2.666862 TACGTGTGCCTTTGCGGG 60.667 61.111 0.00 0.00 41.78 6.13
2588 4707 2.433318 GCGGCTCGAGCTTGAAGT 60.433 61.111 34.46 0.00 41.70 3.01
2592 4711 0.739112 GGCTCGAGCTTGAAGTGAGG 60.739 60.000 34.46 0.00 41.70 3.86
2593 4712 0.739112 GCTCGAGCTTGAAGTGAGGG 60.739 60.000 29.88 0.00 38.21 4.30
2597 4716 1.433534 GAGCTTGAAGTGAGGGTTCG 58.566 55.000 0.00 0.00 0.00 3.95
2624 4743 4.657824 CCGCTTGACACCGACGGT 62.658 66.667 15.37 15.37 39.05 4.83
2751 4890 4.112341 CAGGACGGACGGACGGAC 62.112 72.222 6.00 0.00 38.39 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.031571 TGGTGCCGCCATCTTCATTC 61.032 55.000 0.00 0.00 43.61 2.67
1 2 1.001020 TGGTGCCGCCATCTTCATT 60.001 52.632 0.00 0.00 43.61 2.57
48 49 1.014352 GTCTTTGTGGCACGTCAGTT 58.986 50.000 13.77 0.00 0.00 3.16
53 54 1.594293 CCGAGTCTTTGTGGCACGT 60.594 57.895 13.77 0.00 32.68 4.49
58 59 2.002586 CACATAGCCGAGTCTTTGTGG 58.997 52.381 11.76 0.00 40.19 4.17
78 79 4.451774 TGATTAAAAAGCTTGTTGCATGCC 59.548 37.500 16.68 0.28 45.94 4.40
81 82 5.851047 GCTGATTAAAAAGCTTGTTGCAT 57.149 34.783 12.37 4.00 45.94 3.96
91 92 6.474751 GCTGCCTATTTGAGCTGATTAAAAAG 59.525 38.462 0.00 0.00 0.00 2.27
92 93 6.071447 TGCTGCCTATTTGAGCTGATTAAAAA 60.071 34.615 0.00 0.00 33.66 1.94
93 94 5.418524 TGCTGCCTATTTGAGCTGATTAAAA 59.581 36.000 0.00 0.00 33.66 1.52
99 100 2.723322 ATGCTGCCTATTTGAGCTGA 57.277 45.000 0.00 0.00 33.66 4.26
151 189 0.179062 GTCGCCCATCATTGAGCTCT 60.179 55.000 16.19 0.00 0.00 4.09
156 194 0.829990 TGCTAGTCGCCCATCATTGA 59.170 50.000 0.00 0.00 38.05 2.57
174 212 1.474330 GGTTCCTATGCCCAAACCTG 58.526 55.000 0.00 0.00 38.48 4.00
186 224 3.510360 CCAAGAGAACTCGAAGGTTCCTA 59.490 47.826 12.48 0.00 44.56 2.94
190 228 4.040461 TCATTCCAAGAGAACTCGAAGGTT 59.960 41.667 0.00 0.00 37.29 3.50
195 233 3.133003 GGGATCATTCCAAGAGAACTCGA 59.867 47.826 0.00 0.00 44.60 4.04
200 238 4.868172 ACATGGGATCATTCCAAGAGAA 57.132 40.909 0.00 0.00 44.60 2.87
210 248 9.288576 CAAATTACATACTGTACATGGGATCAT 57.711 33.333 0.00 0.00 31.69 2.45
214 252 8.735315 CAAACAAATTACATACTGTACATGGGA 58.265 33.333 0.00 0.00 31.69 4.37
246 284 4.082463 TGAACATCTGCGTATGTACTGTGA 60.082 41.667 4.35 0.00 39.16 3.58
251 289 7.593644 TGTATGTATGAACATCTGCGTATGTAC 59.406 37.037 4.35 0.87 42.92 2.90
252 290 7.653647 TGTATGTATGAACATCTGCGTATGTA 58.346 34.615 4.35 0.00 42.92 2.29
253 291 6.512297 TGTATGTATGAACATCTGCGTATGT 58.488 36.000 0.00 0.00 42.92 2.29
254 292 7.406799 TTGTATGTATGAACATCTGCGTATG 57.593 36.000 0.00 0.00 42.92 2.39
255 293 8.607441 ATTTGTATGTATGAACATCTGCGTAT 57.393 30.769 0.00 0.00 42.92 3.06
256 294 9.705290 ATATTTGTATGTATGAACATCTGCGTA 57.295 29.630 0.00 0.00 42.92 4.42
257 295 6.925610 ATTTGTATGTATGAACATCTGCGT 57.074 33.333 0.00 0.00 42.92 5.24
258 296 9.958285 GTATATTTGTATGTATGAACATCTGCG 57.042 33.333 0.00 0.00 42.92 5.18
278 316 9.767228 TGTGCGTTTATATGGTTAGTGTATATT 57.233 29.630 0.00 0.00 0.00 1.28
279 317 9.199982 GTGTGCGTTTATATGGTTAGTGTATAT 57.800 33.333 0.00 0.00 0.00 0.86
280 318 7.379262 CGTGTGCGTTTATATGGTTAGTGTATA 59.621 37.037 0.00 0.00 0.00 1.47
283 321 4.327898 CGTGTGCGTTTATATGGTTAGTGT 59.672 41.667 0.00 0.00 0.00 3.55
284 322 4.780946 GCGTGTGCGTTTATATGGTTAGTG 60.781 45.833 0.00 0.00 40.81 2.74
287 325 3.929417 GCGTGTGCGTTTATATGGTTA 57.071 42.857 0.00 0.00 40.81 2.85
288 326 2.817538 GCGTGTGCGTTTATATGGTT 57.182 45.000 0.00 0.00 40.81 3.67
300 338 2.277247 GTGTGTGTGTGCGTGTGC 60.277 61.111 0.00 0.00 43.20 4.57
301 339 1.225991 GTGTGTGTGTGTGCGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
302 340 1.669437 TGTGTGTGTGTGTGCGTGT 60.669 52.632 0.00 0.00 0.00 4.49
303 341 1.225991 GTGTGTGTGTGTGTGCGTG 60.226 57.895 0.00 0.00 0.00 5.34
304 342 1.669437 TGTGTGTGTGTGTGTGCGT 60.669 52.632 0.00 0.00 0.00 5.24
305 343 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
306 344 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
307 345 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
308 346 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
309 347 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
310 348 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
311 349 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
312 350 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
313 351 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
314 352 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
315 353 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
316 354 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
317 355 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
318 356 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
319 357 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
320 358 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
321 359 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
322 360 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
323 361 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
324 362 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
325 363 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
326 364 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
327 365 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
328 366 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
329 367 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
330 368 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
331 369 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
332 370 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
333 371 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
334 372 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
335 373 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
336 374 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
337 375 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
338 376 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
339 377 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
340 378 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
341 379 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
342 380 2.739913 GTTAGTGTGTGTGTGTGTGTGT 59.260 45.455 0.00 0.00 0.00 3.72
343 381 2.095213 GGTTAGTGTGTGTGTGTGTGTG 59.905 50.000 0.00 0.00 0.00 3.82
344 382 2.352388 GGTTAGTGTGTGTGTGTGTGT 58.648 47.619 0.00 0.00 0.00 3.72
345 383 1.668751 GGGTTAGTGTGTGTGTGTGTG 59.331 52.381 0.00 0.00 0.00 3.82
346 384 1.407712 GGGGTTAGTGTGTGTGTGTGT 60.408 52.381 0.00 0.00 0.00 3.72
347 385 1.305201 GGGGTTAGTGTGTGTGTGTG 58.695 55.000 0.00 0.00 0.00 3.82
348 386 0.913205 TGGGGTTAGTGTGTGTGTGT 59.087 50.000 0.00 0.00 0.00 3.72
349 387 1.879380 CATGGGGTTAGTGTGTGTGTG 59.121 52.381 0.00 0.00 0.00 3.82
350 388 1.771854 TCATGGGGTTAGTGTGTGTGT 59.228 47.619 0.00 0.00 0.00 3.72
358 396 0.620556 CAGGTGCTCATGGGGTTAGT 59.379 55.000 0.00 0.00 0.00 2.24
362 400 4.415150 CGCAGGTGCTCATGGGGT 62.415 66.667 9.32 0.00 39.32 4.95
366 404 0.104487 ATCTCTCGCAGGTGCTCATG 59.896 55.000 0.00 0.00 39.32 3.07
377 415 1.201343 GTGACGGCTTTATCTCTCGC 58.799 55.000 0.00 0.00 0.00 5.03
385 423 4.081697 TCTCAAGATGATGTGACGGCTTTA 60.082 41.667 0.00 0.00 0.00 1.85
386 424 3.005554 CTCAAGATGATGTGACGGCTTT 58.994 45.455 0.00 0.00 0.00 3.51
393 431 9.322773 GACTTCATTAATCTCAAGATGATGTGA 57.677 33.333 8.00 5.59 37.16 3.58
411 449 1.668419 GCGCCTATGGTGACTTCATT 58.332 50.000 0.00 0.00 34.74 2.57
413 451 1.220749 GGCGCCTATGGTGACTTCA 59.779 57.895 22.15 0.00 38.38 3.02
437 475 2.808321 GAGACGTTTCGGTCGGCC 60.808 66.667 0.00 0.00 41.81 6.13
482 520 6.813152 CGCATTTTTCTGGATTTAATTCAGGT 59.187 34.615 12.80 0.00 0.00 4.00
489 527 6.744112 ACTGTTCGCATTTTTCTGGATTTAA 58.256 32.000 0.00 0.00 0.00 1.52
509 547 4.042934 AGGTCCTTGGCTTAACATTACTGT 59.957 41.667 0.00 0.00 37.12 3.55
513 551 5.947566 GGTTTAGGTCCTTGGCTTAACATTA 59.052 40.000 0.00 0.00 0.00 1.90
519 557 4.403734 CAAAGGTTTAGGTCCTTGGCTTA 58.596 43.478 0.00 0.00 43.50 3.09
525 563 2.516702 ACCACCAAAGGTTTAGGTCCTT 59.483 45.455 0.00 0.00 45.84 3.36
531 569 2.306847 AGCACACCACCAAAGGTTTAG 58.693 47.619 0.00 0.00 40.77 1.85
540 578 0.466543 ACGAAACTAGCACACCACCA 59.533 50.000 0.00 0.00 0.00 4.17
543 581 2.831685 ATGACGAAACTAGCACACCA 57.168 45.000 0.00 0.00 0.00 4.17
615 654 7.724305 AAAGAACTAGCTCATGTTCGTTTAA 57.276 32.000 16.32 0.00 44.95 1.52
621 660 9.170584 GTTTTGTTAAAGAACTAGCTCATGTTC 57.829 33.333 15.19 15.19 41.84 3.18
715 2347 1.925972 GGGCCTCCCTTGAAGGTCT 60.926 63.158 10.82 0.00 41.34 3.85
717 2349 2.121506 TGGGCCTCCCTTGAAGGT 60.122 61.111 10.82 0.00 45.70 3.50
720 2352 3.264845 GGGTGGGCCTCCCTTGAA 61.265 66.667 31.99 0.00 45.70 2.69
731 2363 4.232061 TTGCAAGGTGGGGGTGGG 62.232 66.667 0.00 0.00 0.00 4.61
732 2364 2.917227 GTTGCAAGGTGGGGGTGG 60.917 66.667 0.00 0.00 0.00 4.61
733 2365 2.198426 AGTTGCAAGGTGGGGGTG 59.802 61.111 0.00 0.00 0.00 4.61
734 2366 2.198426 CAGTTGCAAGGTGGGGGT 59.802 61.111 0.00 0.00 0.00 4.95
938 2573 4.660771 CAGAGGGAGGTATTTAATGGAGGT 59.339 45.833 0.00 0.00 0.00 3.85
941 2576 4.307259 AGCAGAGGGAGGTATTTAATGGA 58.693 43.478 0.00 0.00 0.00 3.41
990 2625 2.444895 GTCTGGGGGAGGAGCGAT 60.445 66.667 0.00 0.00 0.00 4.58
1012 2658 0.319040 TCACTTCGTGTCAGCTCTGC 60.319 55.000 0.00 0.00 34.79 4.26
1019 2665 0.033504 GGCTTCCTCACTTCGTGTCA 59.966 55.000 0.00 0.00 34.79 3.58
1021 2667 0.468226 TTGGCTTCCTCACTTCGTGT 59.532 50.000 0.00 0.00 34.79 4.49
1032 2678 2.561373 CGGCGTTTCTTGGCTTCC 59.439 61.111 0.00 0.00 0.00 3.46
1058 2704 1.487976 GCTCCAGGATGTCCATCTTGA 59.512 52.381 17.92 7.16 44.69 3.02
1059 2705 1.211212 TGCTCCAGGATGTCCATCTTG 59.789 52.381 11.31 11.31 42.47 3.02
1234 2903 1.592939 GCTTCGAGGATCCTTCGGC 60.593 63.158 24.19 19.00 0.00 5.54
1245 2914 1.023513 CCAGCTCCAAAGGCTTCGAG 61.024 60.000 16.19 16.19 38.03 4.04
1284 2959 2.559922 ATCTCTCCGTCTCCGCTGGT 62.560 60.000 0.00 0.00 0.00 4.00
1308 2983 1.456705 AGACGATCTCCAGCTCCCC 60.457 63.158 0.00 0.00 0.00 4.81
1365 3040 2.893398 GCCGTGTACCTCTCCCTG 59.107 66.667 0.00 0.00 0.00 4.45
1455 3136 0.179171 ACACGCCGTAGTCATCTTCG 60.179 55.000 0.00 0.00 34.95 3.79
1499 3183 1.221840 CTCACCACCTCCCATTCGG 59.778 63.158 0.00 0.00 0.00 4.30
1526 3210 3.175240 CAGTTGTCGCCGCGAGAG 61.175 66.667 17.42 0.00 36.23 3.20
1529 3213 4.045771 TAGCAGTTGTCGCCGCGA 62.046 61.111 12.39 12.39 0.00 5.87
1530 3214 3.838795 GTAGCAGTTGTCGCCGCG 61.839 66.667 6.39 6.39 0.00 6.46
1531 3215 3.838795 CGTAGCAGTTGTCGCCGC 61.839 66.667 0.00 0.00 0.00 6.53
1547 3237 3.862394 TTGTACCGCCACGTTCCCG 62.862 63.158 0.00 0.00 40.83 5.14
1549 3239 1.005867 TCTTGTACCGCCACGTTCC 60.006 57.895 0.00 0.00 0.00 3.62
1550 3240 1.623973 GCTCTTGTACCGCCACGTTC 61.624 60.000 0.00 0.00 0.00 3.95
1551 3241 1.666872 GCTCTTGTACCGCCACGTT 60.667 57.895 0.00 0.00 0.00 3.99
1552 3242 2.048503 GCTCTTGTACCGCCACGT 60.049 61.111 0.00 0.00 0.00 4.49
1553 3243 2.813908 GGCTCTTGTACCGCCACG 60.814 66.667 7.46 0.00 43.25 4.94
1554 3244 2.436115 GGGCTCTTGTACCGCCAC 60.436 66.667 12.62 1.99 45.53 5.01
1555 3245 4.077184 CGGGCTCTTGTACCGCCA 62.077 66.667 12.62 0.00 45.53 5.69
1556 3246 3.718210 CTCGGGCTCTTGTACCGCC 62.718 68.421 0.00 4.54 46.78 6.13
1557 3247 2.202756 CTCGGGCTCTTGTACCGC 60.203 66.667 0.00 0.00 46.78 5.68
1672 3365 1.142778 GATCAGAAGCTCGACACGGC 61.143 60.000 0.00 0.00 0.00 5.68
1677 3370 2.929531 TGAGTGATCAGAAGCTCGAC 57.070 50.000 0.00 0.00 0.00 4.20
1695 3388 3.648339 AACAATGCTACAGTGGCTTTG 57.352 42.857 26.46 26.46 44.70 2.77
1696 3389 3.891366 AGAAACAATGCTACAGTGGCTTT 59.109 39.130 10.64 7.32 33.50 3.51
1698 3391 3.146104 AGAAACAATGCTACAGTGGCT 57.854 42.857 10.64 0.00 33.50 4.75
1699 3392 3.923017 AAGAAACAATGCTACAGTGGC 57.077 42.857 0.99 0.99 33.50 5.01
1701 3394 7.992180 AAAAGAAAGAAACAATGCTACAGTG 57.008 32.000 0.00 0.00 35.46 3.66
1722 3415 8.373981 TGCCAATTTCATTCTTCCAGAATAAAA 58.626 29.630 0.00 0.00 42.67 1.52
1726 3419 6.363167 TTGCCAATTTCATTCTTCCAGAAT 57.637 33.333 0.00 0.00 45.23 2.40
1728 3421 7.479352 TTATTGCCAATTTCATTCTTCCAGA 57.521 32.000 0.00 0.00 0.00 3.86
1729 3422 7.820872 AGTTTATTGCCAATTTCATTCTTCCAG 59.179 33.333 0.00 0.00 0.00 3.86
1730 3423 7.603404 CAGTTTATTGCCAATTTCATTCTTCCA 59.397 33.333 0.00 0.00 0.00 3.53
1731 3424 7.603784 ACAGTTTATTGCCAATTTCATTCTTCC 59.396 33.333 0.00 0.00 0.00 3.46
1754 3447 6.817765 TTTTGCTTCCACCTAAGATTACAG 57.182 37.500 0.00 0.00 0.00 2.74
1789 3485 5.047235 AGGGTACATCGGCTATCTAATTCAC 60.047 44.000 0.00 0.00 0.00 3.18
1791 3487 5.411781 CAGGGTACATCGGCTATCTAATTC 58.588 45.833 0.00 0.00 0.00 2.17
1821 3524 7.397221 ACTGATCTGACTGGATGAAAACATTA 58.603 34.615 6.60 0.00 0.00 1.90
1836 3539 4.952262 TGCAAGCAATAACTGATCTGAC 57.048 40.909 6.60 0.00 0.00 3.51
1837 3540 5.005740 AGTTGCAAGCAATAACTGATCTGA 58.994 37.500 11.00 0.00 38.28 3.27
1840 3543 4.156556 TGGAGTTGCAAGCAATAACTGATC 59.843 41.667 11.00 0.00 38.28 2.92
1865 3573 1.203441 ATCCAGCACCAGCAGAGGAA 61.203 55.000 0.00 0.00 45.49 3.36
1878 3586 2.359850 TGTCGTTGGGCATCCAGC 60.360 61.111 0.00 0.00 45.04 4.85
1879 3587 2.390599 CGTGTCGTTGGGCATCCAG 61.391 63.158 0.00 0.00 45.04 3.86
1881 3589 3.799755 GCGTGTCGTTGGGCATCC 61.800 66.667 0.00 0.00 0.00 3.51
1884 3592 4.555709 AAGGCGTGTCGTTGGGCA 62.556 61.111 0.00 0.00 0.00 5.36
1886 3594 4.025401 GCAAGGCGTGTCGTTGGG 62.025 66.667 1.69 0.00 40.04 4.12
1887 3595 1.019278 ATAGCAAGGCGTGTCGTTGG 61.019 55.000 1.69 0.00 40.04 3.77
1888 3596 0.370273 GATAGCAAGGCGTGTCGTTG 59.630 55.000 1.69 0.00 41.95 4.10
1889 3597 0.246635 AGATAGCAAGGCGTGTCGTT 59.753 50.000 1.69 0.00 0.00 3.85
1890 3598 0.458543 CAGATAGCAAGGCGTGTCGT 60.459 55.000 1.69 0.00 0.00 4.34
1891 3599 0.458543 ACAGATAGCAAGGCGTGTCG 60.459 55.000 1.69 0.00 0.00 4.35
1892 3600 1.002366 CACAGATAGCAAGGCGTGTC 58.998 55.000 1.69 0.00 0.00 3.67
1893 3601 0.608130 TCACAGATAGCAAGGCGTGT 59.392 50.000 1.69 0.00 0.00 4.49
1894 3602 1.002366 GTCACAGATAGCAAGGCGTG 58.998 55.000 0.00 0.00 0.00 5.34
1904 3617 4.455533 GCAAATCAACAGGTGTCACAGATA 59.544 41.667 5.12 0.00 0.00 1.98
1907 3620 2.358582 TGCAAATCAACAGGTGTCACAG 59.641 45.455 5.12 0.00 0.00 3.66
1909 3622 3.435105 TTGCAAATCAACAGGTGTCAC 57.565 42.857 0.00 0.00 0.00 3.67
1910 3623 4.370049 CATTTGCAAATCAACAGGTGTCA 58.630 39.130 21.70 0.00 33.73 3.58
1911 3624 3.184986 GCATTTGCAAATCAACAGGTGTC 59.815 43.478 21.70 3.38 41.59 3.67
1922 3635 3.768757 TGGCCTAACTAGCATTTGCAAAT 59.231 39.130 18.99 18.99 45.16 2.32
1923 3636 3.161067 TGGCCTAACTAGCATTTGCAAA 58.839 40.909 15.44 15.44 45.16 3.68
1963 3679 1.068264 GCTTTTGGCTTCACTGGTAGC 60.068 52.381 0.00 0.00 36.77 3.58
1991 3745 3.813443 AGTAATAAGCTGCAGTGATGGG 58.187 45.455 16.64 0.00 0.00 4.00
1996 3750 5.049474 TGTCAACAAGTAATAAGCTGCAGTG 60.049 40.000 16.64 4.57 0.00 3.66
1997 3751 5.063204 TGTCAACAAGTAATAAGCTGCAGT 58.937 37.500 16.64 0.00 0.00 4.40
2006 3760 6.092670 GCTGAGCATTCTGTCAACAAGTAATA 59.907 38.462 0.00 0.00 0.00 0.98
2010 3764 2.551459 GCTGAGCATTCTGTCAACAAGT 59.449 45.455 0.00 0.00 0.00 3.16
2012 3766 2.854963 AGCTGAGCATTCTGTCAACAA 58.145 42.857 7.39 0.00 0.00 2.83
2029 3783 4.504858 CAGGAAACGTCAGGTAATAAGCT 58.495 43.478 0.00 0.00 0.00 3.74
2031 3785 4.504858 AGCAGGAAACGTCAGGTAATAAG 58.495 43.478 0.00 0.00 0.00 1.73
2032 3786 4.546829 AGCAGGAAACGTCAGGTAATAA 57.453 40.909 0.00 0.00 0.00 1.40
2033 3787 4.441079 GCTAGCAGGAAACGTCAGGTAATA 60.441 45.833 10.63 0.00 0.00 0.98
2034 3788 3.679083 GCTAGCAGGAAACGTCAGGTAAT 60.679 47.826 10.63 0.00 0.00 1.89
2035 3789 2.353406 GCTAGCAGGAAACGTCAGGTAA 60.353 50.000 10.63 0.00 0.00 2.85
2036 3790 1.203994 GCTAGCAGGAAACGTCAGGTA 59.796 52.381 10.63 0.00 0.00 3.08
2039 3793 2.941453 TAGCTAGCAGGAAACGTCAG 57.059 50.000 18.83 0.00 0.00 3.51
2049 3803 4.872124 TGTGAATGTGTGATTAGCTAGCAG 59.128 41.667 18.83 0.00 0.00 4.24
2053 3807 5.046663 TCCAGTGTGAATGTGTGATTAGCTA 60.047 40.000 0.00 0.00 0.00 3.32
2055 3809 4.002982 TCCAGTGTGAATGTGTGATTAGC 58.997 43.478 0.00 0.00 0.00 3.09
2056 3810 5.469760 TGTTCCAGTGTGAATGTGTGATTAG 59.530 40.000 0.00 0.00 0.00 1.73
2057 3811 5.238432 GTGTTCCAGTGTGAATGTGTGATTA 59.762 40.000 0.00 0.00 0.00 1.75
2059 3813 3.565482 GTGTTCCAGTGTGAATGTGTGAT 59.435 43.478 0.00 0.00 0.00 3.06
2062 3816 2.945008 CTGTGTTCCAGTGTGAATGTGT 59.055 45.455 0.00 0.00 36.37 3.72
2063 3817 2.291465 CCTGTGTTCCAGTGTGAATGTG 59.709 50.000 0.00 0.00 39.74 3.21
2064 3818 2.172505 TCCTGTGTTCCAGTGTGAATGT 59.827 45.455 0.00 0.00 39.74 2.71
2065 3819 2.849942 TCCTGTGTTCCAGTGTGAATG 58.150 47.619 0.00 0.00 39.74 2.67
2066 3820 3.328931 AGATCCTGTGTTCCAGTGTGAAT 59.671 43.478 0.00 0.00 39.74 2.57
2067 3821 2.705658 AGATCCTGTGTTCCAGTGTGAA 59.294 45.455 0.00 0.00 39.74 3.18
2068 3822 2.300152 GAGATCCTGTGTTCCAGTGTGA 59.700 50.000 0.00 0.00 39.74 3.58
2069 3823 2.301296 AGAGATCCTGTGTTCCAGTGTG 59.699 50.000 0.00 0.00 39.74 3.82
2070 3824 2.301296 CAGAGATCCTGTGTTCCAGTGT 59.699 50.000 3.72 0.00 39.74 3.55
2071 3825 2.354503 CCAGAGATCCTGTGTTCCAGTG 60.355 54.545 9.47 0.00 41.33 3.66
2072 3826 1.905215 CCAGAGATCCTGTGTTCCAGT 59.095 52.381 9.47 0.00 41.33 4.00
2073 3827 1.406614 GCCAGAGATCCTGTGTTCCAG 60.407 57.143 9.47 0.00 41.33 3.86
2074 3828 0.615331 GCCAGAGATCCTGTGTTCCA 59.385 55.000 9.47 0.00 41.33 3.53
2075 3829 0.908198 AGCCAGAGATCCTGTGTTCC 59.092 55.000 9.47 0.00 41.33 3.62
2076 3830 1.552337 TGAGCCAGAGATCCTGTGTTC 59.448 52.381 9.47 8.76 41.33 3.18
2077 3831 1.554160 CTGAGCCAGAGATCCTGTGTT 59.446 52.381 9.47 1.62 41.33 3.32
2078 3832 1.193323 CTGAGCCAGAGATCCTGTGT 58.807 55.000 9.47 0.00 41.33 3.72
2079 3833 0.179078 GCTGAGCCAGAGATCCTGTG 60.179 60.000 6.40 0.00 41.33 3.66
2126 3880 0.178533 TGAGGCACATCATCGCATGA 59.821 50.000 0.00 2.05 44.55 3.07
2127 3881 0.306840 GTGAGGCACATCATCGCATG 59.693 55.000 0.00 0.00 36.15 4.06
2128 3882 0.816825 GGTGAGGCACATCATCGCAT 60.817 55.000 0.00 0.00 37.70 4.73
2129 3883 1.450134 GGTGAGGCACATCATCGCA 60.450 57.895 0.00 0.00 37.70 5.10
2130 3884 0.104855 TAGGTGAGGCACATCATCGC 59.895 55.000 0.00 0.00 35.37 4.58
2131 3885 1.539065 GGTAGGTGAGGCACATCATCG 60.539 57.143 0.00 0.00 35.37 3.84
2173 3928 1.606601 AAGAAAGAAAGGGCCGGCC 60.607 57.895 38.57 38.57 0.00 6.13
2174 3929 1.586541 CAAGAAAGAAAGGGCCGGC 59.413 57.895 21.18 21.18 0.00 6.13
2175 3930 1.877576 GCCAAGAAAGAAAGGGCCGG 61.878 60.000 0.00 0.00 38.70 6.13
2176 3931 1.178534 TGCCAAGAAAGAAAGGGCCG 61.179 55.000 0.00 0.00 43.96 6.13
2284 4058 2.523168 TGTCCTGTCCTGGCACGA 60.523 61.111 0.00 0.00 0.00 4.35
2302 4076 2.704193 GCGTTCGTTCACGGAGTCG 61.704 63.158 0.00 0.00 41.61 4.18
2319 4093 2.755929 GGAGAACGAGACATGTGGC 58.244 57.895 1.15 0.00 0.00 5.01
2385 4196 4.885907 CCATTACCATCATCAGCTTCAACT 59.114 41.667 0.00 0.00 0.00 3.16
2387 4198 3.633525 GCCATTACCATCATCAGCTTCAA 59.366 43.478 0.00 0.00 0.00 2.69
2399 4210 1.972872 GCTACTGCTGCCATTACCAT 58.027 50.000 0.00 0.00 36.03 3.55
2443 4254 2.415843 CGGACATACGGACCGCAT 59.584 61.111 15.39 3.05 40.19 4.73
2457 4268 4.728102 CGCGGTAGGTGCAACGGA 62.728 66.667 0.00 0.00 38.12 4.69
2516 4327 1.828461 TAATGTCGCACCCAACCGGA 61.828 55.000 9.46 0.00 34.64 5.14
2541 4352 2.921912 GCAAAGGCACACGTACGTAGTA 60.922 50.000 22.34 0.00 40.72 1.82
2544 4355 1.276820 CGCAAAGGCACACGTACGTA 61.277 55.000 22.34 0.00 41.24 3.57
2545 4356 2.591311 CGCAAAGGCACACGTACGT 61.591 57.895 16.72 16.72 41.24 3.57
2546 4357 2.170036 CGCAAAGGCACACGTACG 59.830 61.111 15.01 15.01 41.24 3.67
2547 4358 2.554272 CCGCAAAGGCACACGTAC 59.446 61.111 0.00 0.00 41.24 3.67
2548 4359 2.666862 CCCGCAAAGGCACACGTA 60.667 61.111 0.00 0.00 41.24 3.57
2570 4381 3.549150 CTTCAAGCTCGAGCCGCG 61.549 66.667 32.94 21.19 43.38 6.46
2571 4382 2.433318 ACTTCAAGCTCGAGCCGC 60.433 61.111 32.94 10.72 43.38 6.53
2572 4383 1.075425 CTCACTTCAAGCTCGAGCCG 61.075 60.000 32.94 24.09 43.38 5.52
2573 4384 0.739112 CCTCACTTCAAGCTCGAGCC 60.739 60.000 32.94 15.76 43.38 4.70
2574 4385 0.739112 CCCTCACTTCAAGCTCGAGC 60.739 60.000 30.01 30.01 42.49 5.03
2578 4697 1.433534 CGAACCCTCACTTCAAGCTC 58.566 55.000 0.00 0.00 0.00 4.09
2588 4707 3.307906 CCCGTGACCGAACCCTCA 61.308 66.667 0.00 0.00 35.63 3.86


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

AutoCloner maintained by Alex Coulton.