Multiple sequence alignment - TraesCS5B01G284900

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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 TraesCS5B01G284900 chr5B 100.000 5445 0 0 1 5445 470434919 470440363 0.000000e+00 10056.0
1 TraesCS5B01G284900 chr5B 86.199 1268 90 47 850 2045 470511840 470513094 0.000000e+00 1293.0
2 TraesCS5B01G284900 chr5B 80.303 528 82 17 1098 1620 469125060 469124550 3.980000e-101 379.0
3 TraesCS5B01G284900 chr5B 78.399 537 85 24 1097 1628 469300606 469300096 2.450000e-83 320.0
4 TraesCS5B01G284900 chr5B 81.356 354 38 16 1293 1642 470604048 470604377 4.180000e-66 263.0
5 TraesCS5B01G284900 chr5B 91.156 147 11 2 1097 1242 470603903 470604048 1.200000e-46 198.0
6 TraesCS5B01G284900 chr5A 91.608 4719 268 60 787 5445 493661860 493666510 0.000000e+00 6403.0
7 TraesCS5B01G284900 chr5A 87.533 1139 74 41 964 2045 493779210 493780337 0.000000e+00 1254.0
8 TraesCS5B01G284900 chr5A 83.128 895 133 14 3148 4029 493781817 493782706 0.000000e+00 800.0
9 TraesCS5B01G284900 chr5A 80.140 997 123 48 1094 2041 493817929 493816959 0.000000e+00 675.0
10 TraesCS5B01G284900 chr5A 87.179 117 10 4 841 953 493776449 493776564 1.590000e-25 128.0
11 TraesCS5B01G284900 chr5A 81.301 123 18 4 525 643 489907526 489907405 1.610000e-15 95.3
12 TraesCS5B01G284900 chr5D 94.975 2448 96 13 3014 5445 390373362 390375798 0.000000e+00 3814.0
13 TraesCS5B01G284900 chr5D 90.795 1510 80 28 850 2348 390371256 390372717 0.000000e+00 1964.0
14 TraesCS5B01G284900 chr5D 86.425 1267 89 39 850 2045 390417584 390418838 0.000000e+00 1310.0
15 TraesCS5B01G284900 chr5D 88.045 619 53 15 2345 2954 390372753 390373359 0.000000e+00 713.0
16 TraesCS5B01G284900 chr5D 94.000 450 27 0 4996 5445 102504361 102504810 0.000000e+00 682.0
17 TraesCS5B01G284900 chr5D 83.420 772 81 25 1097 1846 390504139 390504885 0.000000e+00 673.0
18 TraesCS5B01G284900 chr5D 88.213 526 50 7 1 518 390369492 390370013 7.750000e-173 617.0
19 TraesCS5B01G284900 chr5D 79.735 528 85 19 1098 1620 389461605 389461095 4.010000e-96 363.0
20 TraesCS5B01G284900 chr5D 83.770 191 29 2 4424 4613 390443551 390443740 4.330000e-41 180.0
21 TraesCS5B01G284900 chr4D 94.631 447 24 0 4999 5445 483367124 483366678 0.000000e+00 693.0
22 TraesCS5B01G284900 chr4D 94.183 447 26 0 4999 5445 480330449 480330895 0.000000e+00 682.0
23 TraesCS5B01G284900 chr4D 92.157 153 10 1 4627 4777 34661679 34661527 1.190000e-51 215.0
24 TraesCS5B01G284900 chr6B 94.420 448 25 0 4996 5443 277636633 277637080 0.000000e+00 689.0
25 TraesCS5B01G284900 chr6B 88.690 168 17 2 4614 4779 36133669 36133502 2.570000e-48 204.0
26 TraesCS5B01G284900 chr2B 94.420 448 23 2 4999 5445 760852433 760851987 0.000000e+00 688.0
27 TraesCS5B01G284900 chr2B 90.184 163 12 3 4618 4777 608226886 608226725 5.530000e-50 209.0
28 TraesCS5B01G284900 chr2B 90.000 160 16 0 4618 4777 368413414 368413573 1.990000e-49 207.0
29 TraesCS5B01G284900 chr1D 94.407 447 25 0 4999 5445 476504155 476504601 0.000000e+00 688.0
30 TraesCS5B01G284900 chr1D 94.183 447 26 0 4999 5445 338104618 338105064 0.000000e+00 682.0
31 TraesCS5B01G284900 chr3D 82.947 604 70 22 1096 1692 564806674 564807251 1.050000e-141 514.0
32 TraesCS5B01G284900 chr3B 87.097 279 32 4 1096 1372 752293164 752292888 4.090000e-81 313.0
33 TraesCS5B01G284900 chr3B 84.791 263 35 5 1435 1692 752301609 752301871 5.410000e-65 259.0
34 TraesCS5B01G284900 chr7D 90.533 169 11 4 4616 4780 119897334 119897167 9.180000e-53 219.0
35 TraesCS5B01G284900 chr7D 82.550 149 26 0 1449 1597 235397084 235396936 1.230000e-26 132.0
36 TraesCS5B01G284900 chr3A 86.154 195 20 6 4593 4780 199695689 199695495 2.570000e-48 204.0
37 TraesCS5B01G284900 chr2A 88.690 168 17 1 4613 4778 324614920 324615087 2.570000e-48 204.0
38 TraesCS5B01G284900 chr2A 83.465 127 15 4 525 647 535219730 535219854 4.460000e-21 113.0
39 TraesCS5B01G284900 chr4A 76.123 423 65 27 2534 2930 170804945 170805357 7.200000e-44 189.0
40 TraesCS5B01G284900 chrUn 81.879 149 27 0 1449 1597 86054520 86054372 5.730000e-25 126.0
41 TraesCS5B01G284900 chr6D 83.740 123 15 3 525 643 305742944 305743065 1.600000e-20 111.0
42 TraesCS5B01G284900 chr2D 87.097 62 7 1 4790 4850 50101936 50101997 9.790000e-08 69.4
43 TraesCS5B01G284900 chr7B 100.000 29 0 0 2611 2639 429216192 429216164 3.000000e-03 54.7


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 TraesCS5B01G284900 chr5B 470434919 470440363 5444 False 10056.000000 10056 100.000000 1 5445 1 chr5B.!!$F1 5444
1 TraesCS5B01G284900 chr5B 470511840 470513094 1254 False 1293.000000 1293 86.199000 850 2045 1 chr5B.!!$F2 1195
2 TraesCS5B01G284900 chr5B 469124550 469125060 510 True 379.000000 379 80.303000 1098 1620 1 chr5B.!!$R1 522
3 TraesCS5B01G284900 chr5B 469300096 469300606 510 True 320.000000 320 78.399000 1097 1628 1 chr5B.!!$R2 531
4 TraesCS5B01G284900 chr5A 493661860 493666510 4650 False 6403.000000 6403 91.608000 787 5445 1 chr5A.!!$F1 4658
5 TraesCS5B01G284900 chr5A 493776449 493782706 6257 False 727.333333 1254 85.946667 841 4029 3 chr5A.!!$F2 3188
6 TraesCS5B01G284900 chr5A 493816959 493817929 970 True 675.000000 675 80.140000 1094 2041 1 chr5A.!!$R2 947
7 TraesCS5B01G284900 chr5D 390369492 390375798 6306 False 1777.000000 3814 90.507000 1 5445 4 chr5D.!!$F5 5444
8 TraesCS5B01G284900 chr5D 390417584 390418838 1254 False 1310.000000 1310 86.425000 850 2045 1 chr5D.!!$F2 1195
9 TraesCS5B01G284900 chr5D 390504139 390504885 746 False 673.000000 673 83.420000 1097 1846 1 chr5D.!!$F4 749
10 TraesCS5B01G284900 chr5D 389461095 389461605 510 True 363.000000 363 79.735000 1098 1620 1 chr5D.!!$R1 522
11 TraesCS5B01G284900 chr3D 564806674 564807251 577 False 514.000000 514 82.947000 1096 1692 1 chr3D.!!$F1 596

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
123 124 0.103390 GAAGAGTTAGGAGGCTCGGC 59.897 60.0 8.69 0.00 36.88 5.54 F
142 143 0.176680 CGAGATGGTGGACAGAAGGG 59.823 60.0 0.00 0.00 0.00 3.95 F
1861 5666 0.319555 GGTTCGACACAGCAGCTGTA 60.320 55.0 27.80 9.82 43.43 2.74 F
2930 7533 0.036010 CGTGCCACAAATCCTCTCCT 60.036 55.0 0.00 0.00 0.00 3.69 F
3002 7605 0.986019 AGGGTGACGGGGCATATCAA 60.986 55.0 0.00 0.00 0.00 2.57 F
4156 8783 0.322456 CCATTCGCCTTCCTTGGACA 60.322 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 6115 0.170339 TGTACGGCAGTGTGATCGAG 59.830 55.000 0.00 0.0 0.00 4.04 R
2180 6195 5.215160 CGAAAAGCATGACAAGTTTAGCTT 58.785 37.500 0.00 0.0 43.43 3.74 R
3547 8161 0.036732 TGCAGCCTACCAACAGGAAG 59.963 55.000 0.00 0.0 38.00 3.46 R
3775 8401 0.742505 CGTGCCGACTATTACCCTGA 59.257 55.000 0.00 0.0 0.00 3.86 R
4172 8799 1.225855 GCGATAATGGCAATGGTCGA 58.774 50.000 13.88 0.0 0.00 4.20 R
4975 9616 2.751259 AGCCACATGAACAATAGCACAG 59.249 45.455 0.00 0.0 0.00 3.66 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
45 46 5.339695 GGATTGGTTAAACCCTGTGGATCTA 60.340 44.000 0.00 0.00 37.50 1.98
46 47 4.837093 TGGTTAAACCCTGTGGATCTAG 57.163 45.455 0.00 0.00 37.50 2.43
71 72 3.918294 AATGGATTGGGAGGCAAAATG 57.082 42.857 0.00 0.00 0.00 2.32
110 111 9.660180 GATTGAATAGTAAAAGAGGTGAAGAGT 57.340 33.333 0.00 0.00 0.00 3.24
122 123 1.135333 GTGAAGAGTTAGGAGGCTCGG 59.865 57.143 8.69 0.00 36.88 4.63
123 124 0.103390 GAAGAGTTAGGAGGCTCGGC 59.897 60.000 8.69 0.00 36.88 5.54
133 134 4.899239 GGCTCGGCGAGATGGTGG 62.899 72.222 38.56 13.43 0.00 4.61
136 137 2.678580 TCGGCGAGATGGTGGACA 60.679 61.111 4.99 0.00 0.00 4.02
142 143 0.176680 CGAGATGGTGGACAGAAGGG 59.823 60.000 0.00 0.00 0.00 3.95
151 152 1.376553 GACAGAAGGGGCTGCACTC 60.377 63.158 0.21 0.00 39.51 3.51
174 175 6.739112 TCTACATCGACTGTATTGATCTTGG 58.261 40.000 7.76 0.00 39.58 3.61
183 184 5.163258 ACTGTATTGATCTTGGGATGGAGAC 60.163 44.000 0.00 0.00 31.46 3.36
256 257 7.905493 GCTCATGAGTTAGCTAAATGTTGTTAC 59.095 37.037 23.38 0.00 35.80 2.50
280 281 8.234136 ACGAGAACCATATATCTTGTACTTGA 57.766 34.615 0.00 0.00 38.29 3.02
298 299 3.757947 TGAGTAGATGTTCCTCCCTCA 57.242 47.619 0.00 0.00 0.00 3.86
307 308 4.021102 TGTTCCTCCCTCATTTGTTCTC 57.979 45.455 0.00 0.00 0.00 2.87
309 310 1.555075 TCCTCCCTCATTTGTTCTCGG 59.445 52.381 0.00 0.00 0.00 4.63
314 315 3.133003 TCCCTCATTTGTTCTCGGATCTC 59.867 47.826 0.00 0.00 0.00 2.75
316 317 4.367450 CCTCATTTGTTCTCGGATCTCTC 58.633 47.826 0.00 0.00 0.00 3.20
317 318 4.367450 CTCATTTGTTCTCGGATCTCTCC 58.633 47.826 0.00 0.00 38.29 3.71
337 338 7.277981 TCTCTCCTAAACGATGTAAGCATTTTC 59.722 37.037 0.00 0.00 35.07 2.29
338 339 7.103641 TCTCCTAAACGATGTAAGCATTTTCT 58.896 34.615 0.00 0.00 35.07 2.52
339 340 7.606456 TCTCCTAAACGATGTAAGCATTTTCTT 59.394 33.333 0.00 0.00 35.07 2.52
340 341 7.748847 TCCTAAACGATGTAAGCATTTTCTTC 58.251 34.615 0.00 0.00 35.07 2.87
341 342 7.389330 TCCTAAACGATGTAAGCATTTTCTTCA 59.611 33.333 0.00 0.00 35.07 3.02
342 343 8.020819 CCTAAACGATGTAAGCATTTTCTTCAA 58.979 33.333 0.00 0.00 35.07 2.69
344 345 8.641499 AAACGATGTAAGCATTTTCTTCAAAA 57.359 26.923 0.00 0.00 35.07 2.44
345 346 8.641499 AACGATGTAAGCATTTTCTTCAAAAA 57.359 26.923 0.00 0.00 35.10 1.94
393 398 4.010349 GAGTTGCACTACCTTAAGGCAAT 58.990 43.478 21.92 4.83 45.03 3.56
397 402 1.670811 CACTACCTTAAGGCAATGGCG 59.329 52.381 21.92 0.00 42.47 5.69
398 403 0.663153 CTACCTTAAGGCAATGGCGC 59.337 55.000 21.92 0.00 42.47 6.53
399 404 1.092921 TACCTTAAGGCAATGGCGCG 61.093 55.000 21.92 0.00 42.47 6.86
401 406 3.050166 CTTAAGGCAATGGCGCGCA 62.050 57.895 34.42 19.50 42.47 6.09
415 422 4.147449 CGCACTGCCTCCATCCGA 62.147 66.667 0.00 0.00 0.00 4.55
423 430 1.837439 TGCCTCCATCCGAGTTTGTAT 59.163 47.619 0.00 0.00 36.82 2.29
427 434 3.118775 CCTCCATCCGAGTTTGTATGTCA 60.119 47.826 0.00 0.00 36.82 3.58
431 438 1.621317 TCCGAGTTTGTATGTCAGGCA 59.379 47.619 0.00 0.00 0.00 4.75
466 473 8.062065 TGGTGTTCAGTTTGACTAAAGAAAAT 57.938 30.769 0.00 0.00 0.00 1.82
495 502 8.567285 ACAATTCTTGAAATAGGACGAAGAAT 57.433 30.769 0.00 0.00 42.46 2.40
500 507 9.534565 TTCTTGAAATAGGACGAAGAATCATAG 57.465 33.333 0.00 0.00 29.75 2.23
546 553 9.726438 ATTATAAGTATTGCACATCTAAGTCCC 57.274 33.333 0.00 0.00 0.00 4.46
547 554 5.435686 AAGTATTGCACATCTAAGTCCCA 57.564 39.130 0.00 0.00 0.00 4.37
548 555 5.636903 AGTATTGCACATCTAAGTCCCAT 57.363 39.130 0.00 0.00 0.00 4.00
549 556 6.747414 AGTATTGCACATCTAAGTCCCATA 57.253 37.500 0.00 0.00 0.00 2.74
550 557 7.321717 AGTATTGCACATCTAAGTCCCATAT 57.678 36.000 0.00 0.00 0.00 1.78
551 558 7.390027 AGTATTGCACATCTAAGTCCCATATC 58.610 38.462 0.00 0.00 0.00 1.63
552 559 5.628797 TTGCACATCTAAGTCCCATATCA 57.371 39.130 0.00 0.00 0.00 2.15
553 560 5.830799 TGCACATCTAAGTCCCATATCAT 57.169 39.130 0.00 0.00 0.00 2.45
554 561 6.191657 TGCACATCTAAGTCCCATATCATT 57.808 37.500 0.00 0.00 0.00 2.57
555 562 5.999600 TGCACATCTAAGTCCCATATCATTG 59.000 40.000 0.00 0.00 0.00 2.82
556 563 6.183361 TGCACATCTAAGTCCCATATCATTGA 60.183 38.462 0.00 0.00 0.00 2.57
557 564 6.883217 GCACATCTAAGTCCCATATCATTGAT 59.117 38.462 4.28 4.28 0.00 2.57
558 565 7.065563 GCACATCTAAGTCCCATATCATTGATC 59.934 40.741 1.55 0.00 0.00 2.92
559 566 8.319881 CACATCTAAGTCCCATATCATTGATCT 58.680 37.037 1.55 0.00 0.00 2.75
560 567 8.888419 ACATCTAAGTCCCATATCATTGATCTT 58.112 33.333 1.55 2.28 0.00 2.40
563 570 8.523658 TCTAAGTCCCATATCATTGATCTTACG 58.476 37.037 1.55 0.00 0.00 3.18
564 571 6.042638 AGTCCCATATCATTGATCTTACGG 57.957 41.667 1.55 0.00 0.00 4.02
565 572 5.046304 AGTCCCATATCATTGATCTTACGGG 60.046 44.000 1.55 7.30 0.00 5.28
566 573 4.225042 TCCCATATCATTGATCTTACGGGG 59.775 45.833 1.55 6.64 0.00 5.73
567 574 4.225042 CCCATATCATTGATCTTACGGGGA 59.775 45.833 1.55 0.00 32.36 4.81
568 575 5.423015 CCATATCATTGATCTTACGGGGAG 58.577 45.833 1.55 0.00 0.00 4.30
569 576 5.187772 CCATATCATTGATCTTACGGGGAGA 59.812 44.000 1.55 0.00 0.00 3.71
570 577 6.126940 CCATATCATTGATCTTACGGGGAGAT 60.127 42.308 1.55 0.00 36.60 2.75
571 578 5.832539 ATCATTGATCTTACGGGGAGATT 57.167 39.130 0.00 0.00 34.13 2.40
572 579 5.215252 TCATTGATCTTACGGGGAGATTC 57.785 43.478 0.00 0.00 34.13 2.52
573 580 3.728076 TTGATCTTACGGGGAGATTCG 57.272 47.619 0.00 0.00 34.13 3.34
574 581 2.662866 TGATCTTACGGGGAGATTCGT 58.337 47.619 0.00 0.00 42.55 3.85
575 582 2.361119 TGATCTTACGGGGAGATTCGTG 59.639 50.000 0.00 0.00 40.05 4.35
576 583 1.843368 TCTTACGGGGAGATTCGTGT 58.157 50.000 0.00 0.00 40.05 4.49
577 584 3.003394 TCTTACGGGGAGATTCGTGTA 57.997 47.619 0.00 0.00 40.05 2.90
578 585 2.947652 TCTTACGGGGAGATTCGTGTAG 59.052 50.000 0.00 0.00 40.05 2.74
579 586 1.683943 TACGGGGAGATTCGTGTAGG 58.316 55.000 0.00 0.00 40.05 3.18
580 587 0.324091 ACGGGGAGATTCGTGTAGGT 60.324 55.000 0.00 0.00 38.25 3.08
581 588 1.064463 ACGGGGAGATTCGTGTAGGTA 60.064 52.381 0.00 0.00 38.25 3.08
582 589 2.236766 CGGGGAGATTCGTGTAGGTAT 58.763 52.381 0.00 0.00 0.00 2.73
583 590 2.626743 CGGGGAGATTCGTGTAGGTATT 59.373 50.000 0.00 0.00 0.00 1.89
584 591 3.069158 CGGGGAGATTCGTGTAGGTATTT 59.931 47.826 0.00 0.00 0.00 1.40
585 592 4.442472 CGGGGAGATTCGTGTAGGTATTTT 60.442 45.833 0.00 0.00 0.00 1.82
586 593 5.055144 GGGGAGATTCGTGTAGGTATTTTC 58.945 45.833 0.00 0.00 0.00 2.29
587 594 5.163332 GGGGAGATTCGTGTAGGTATTTTCT 60.163 44.000 0.00 0.00 0.00 2.52
588 595 6.346896 GGGAGATTCGTGTAGGTATTTTCTT 58.653 40.000 0.00 0.00 0.00 2.52
589 596 6.822170 GGGAGATTCGTGTAGGTATTTTCTTT 59.178 38.462 0.00 0.00 0.00 2.52
590 597 7.336176 GGGAGATTCGTGTAGGTATTTTCTTTT 59.664 37.037 0.00 0.00 0.00 2.27
591 598 8.727910 GGAGATTCGTGTAGGTATTTTCTTTTT 58.272 33.333 0.00 0.00 0.00 1.94
634 641 7.919690 TGCTTGATTAAGTCACTTATATGTGC 58.080 34.615 12.71 8.76 36.32 4.57
635 642 7.552330 TGCTTGATTAAGTCACTTATATGTGCA 59.448 33.333 12.71 4.79 36.32 4.57
636 643 8.397906 GCTTGATTAAGTCACTTATATGTGCAA 58.602 33.333 12.71 8.81 36.32 4.08
647 654 9.489084 TCACTTATATGTGCAATAACTATGACC 57.511 33.333 12.71 0.00 37.81 4.02
648 655 8.721478 CACTTATATGTGCAATAACTATGACCC 58.279 37.037 5.88 0.00 0.00 4.46
649 656 7.883311 ACTTATATGTGCAATAACTATGACCCC 59.117 37.037 0.00 0.00 0.00 4.95
650 657 4.796110 ATGTGCAATAACTATGACCCCT 57.204 40.909 0.00 0.00 0.00 4.79
651 658 5.904984 ATGTGCAATAACTATGACCCCTA 57.095 39.130 0.00 0.00 0.00 3.53
652 659 5.290493 TGTGCAATAACTATGACCCCTAG 57.710 43.478 0.00 0.00 0.00 3.02
653 660 4.966168 TGTGCAATAACTATGACCCCTAGA 59.034 41.667 0.00 0.00 0.00 2.43
654 661 5.163343 TGTGCAATAACTATGACCCCTAGAC 60.163 44.000 0.00 0.00 0.00 2.59
655 662 4.966168 TGCAATAACTATGACCCCTAGACA 59.034 41.667 0.00 0.00 0.00 3.41
682 689 9.277565 CAGTGCTGACATTGTATTTATGTTAAC 57.722 33.333 0.00 0.00 36.41 2.01
740 747 2.997315 CCAGTGAGTGGCCGGAGA 60.997 66.667 5.05 0.00 40.39 3.71
763 1118 4.240096 ACTAATTGTACTGAAACGACCCG 58.760 43.478 0.00 0.00 0.00 5.28
779 1134 3.056536 CGACCCGGTGATCATCATATTCT 60.057 47.826 6.80 0.00 0.00 2.40
780 1135 4.157840 CGACCCGGTGATCATCATATTCTA 59.842 45.833 6.80 0.00 0.00 2.10
781 1136 5.655488 GACCCGGTGATCATCATATTCTAG 58.345 45.833 6.80 0.00 0.00 2.43
782 1137 5.087323 ACCCGGTGATCATCATATTCTAGT 58.913 41.667 6.80 0.00 0.00 2.57
783 1138 5.047021 ACCCGGTGATCATCATATTCTAGTG 60.047 44.000 6.80 0.00 0.00 2.74
784 1139 5.047021 CCCGGTGATCATCATATTCTAGTGT 60.047 44.000 6.80 0.00 0.00 3.55
785 1140 6.096036 CCGGTGATCATCATATTCTAGTGTC 58.904 44.000 6.80 0.00 0.00 3.67
812 1167 4.714308 TGTCCCTGTTTGAAGGAAAACAAT 59.286 37.500 4.28 0.00 46.43 2.71
1053 4774 2.905415 TCCTCGGTACCTAGACCAAA 57.095 50.000 14.89 0.00 39.72 3.28
1054 4775 2.731572 TCCTCGGTACCTAGACCAAAG 58.268 52.381 14.89 0.00 39.72 2.77
1073 4794 0.814010 GAGCACCAAACCACGAGTGT 60.814 55.000 2.36 0.00 32.75 3.55
1282 5006 0.673644 CCTTCGACTTCAACGCCCAT 60.674 55.000 0.00 0.00 0.00 4.00
1858 5663 1.301244 CAGGTTCGACACAGCAGCT 60.301 57.895 0.00 0.00 0.00 4.24
1859 5664 1.301244 AGGTTCGACACAGCAGCTG 60.301 57.895 21.54 21.54 37.52 4.24
1860 5665 1.595382 GGTTCGACACAGCAGCTGT 60.595 57.895 23.11 23.11 46.51 4.40
1861 5666 0.319555 GGTTCGACACAGCAGCTGTA 60.320 55.000 27.80 9.82 43.43 2.74
1862 5667 1.063806 GTTCGACACAGCAGCTGTAG 58.936 55.000 27.80 22.08 43.43 2.74
1863 5668 0.667487 TTCGACACAGCAGCTGTAGC 60.667 55.000 27.80 19.91 43.43 3.58
1923 5748 8.521176 AGCATTTTCTGATTAATATCCATCTGC 58.479 33.333 0.00 0.00 0.00 4.26
1924 5749 8.521176 GCATTTTCTGATTAATATCCATCTGCT 58.479 33.333 0.00 0.00 0.00 4.24
1941 5770 3.120234 TCTGCTACGTGTTTGCAATGATG 60.120 43.478 0.00 0.00 36.22 3.07
2084 6080 1.196911 TTGGTACCCACATCCTACGG 58.803 55.000 10.07 0.00 30.78 4.02
2110 6115 1.165270 GTCATGGTAGTGTTGGGTGC 58.835 55.000 0.00 0.00 0.00 5.01
2140 6148 0.824109 TGCCGTACATTCTCTCCCTG 59.176 55.000 0.00 0.00 0.00 4.45
2164 6179 2.636644 TCATGACCCATGAGCCCAT 58.363 52.632 5.61 0.00 44.60 4.00
2179 6194 7.068593 CCATGAGCCCATAGAAACATCTTTTTA 59.931 37.037 0.00 0.00 0.00 1.52
2180 6195 8.469200 CATGAGCCCATAGAAACATCTTTTTAA 58.531 33.333 0.00 0.00 0.00 1.52
2202 6217 8.574196 TTAAAGCTAAACTTGTCATGCTTTTC 57.426 30.769 14.41 0.00 44.83 2.29
2250 6387 1.550072 GCCATGAGCTTAGGCCAAAAA 59.450 47.619 5.01 0.00 42.58 1.94
2270 6407 2.049156 GGCGCAAGACCAAAAGGC 60.049 61.111 10.83 0.00 42.36 4.35
2272 6409 2.650778 CGCAAGACCAAAAGGCCC 59.349 61.111 0.00 0.00 43.02 5.80
2273 6410 2.650778 GCAAGACCAAAAGGCCCG 59.349 61.111 0.00 0.00 0.00 6.13
2276 6413 0.313987 CAAGACCAAAAGGCCCGAAC 59.686 55.000 0.00 0.00 0.00 3.95
2292 6429 3.257624 CCCGAACTGACTAACCAACTAGT 59.742 47.826 0.00 0.00 34.76 2.57
2321 6458 5.715753 ACTACTCCCTTCGATCCATATTACC 59.284 44.000 0.00 0.00 0.00 2.85
2333 6470 6.292168 CGATCCATATTACCTGTCGTTCAAAC 60.292 42.308 0.00 0.00 0.00 2.93
2353 6529 6.038825 TCAAACGGGTGTATTTAGCAATATGG 59.961 38.462 0.00 0.00 0.00 2.74
2371 6547 3.225177 TGGATCGGAGGGAGTACTTAG 57.775 52.381 0.00 0.00 0.00 2.18
2459 6635 2.549064 TAGCAGCTGAACTTGCTTCA 57.451 45.000 20.43 0.00 38.92 3.02
2460 6636 0.950116 AGCAGCTGAACTTGCTTCAC 59.050 50.000 20.43 0.00 38.92 3.18
2466 6642 5.522456 CAGCTGAACTTGCTTCACAAAATA 58.478 37.500 8.42 0.00 38.92 1.40
2470 6646 8.359642 AGCTGAACTTGCTTCACAAAATATTAA 58.640 29.630 0.00 0.00 37.96 1.40
2475 6651 8.673626 ACTTGCTTCACAAAATATTAACATCG 57.326 30.769 0.00 0.00 37.96 3.84
2547 6723 1.375396 CACCCGATTGCCTCACGAA 60.375 57.895 0.00 0.00 0.00 3.85
2549 6725 2.452813 CCCGATTGCCTCACGAACG 61.453 63.158 0.00 0.00 0.00 3.95
2577 6756 5.774498 AGTTGGATCTCACAAAGGAAAAC 57.226 39.130 0.00 0.00 0.00 2.43
2639 6818 5.618640 GCATCTGAAACTTGCGATTTTCTCT 60.619 40.000 15.52 1.17 33.61 3.10
2658 6837 8.752766 TTTCTCTATCGTTCGTATCAAGTTTT 57.247 30.769 0.00 0.00 0.00 2.43
2664 6843 9.882856 CTATCGTTCGTATCAAGTTTTAAAGTC 57.117 33.333 0.00 0.00 0.00 3.01
2714 7313 1.393603 TTGTGATTTTGTGGGTCGCA 58.606 45.000 0.00 0.00 0.00 5.10
2930 7533 0.036010 CGTGCCACAAATCCTCTCCT 60.036 55.000 0.00 0.00 0.00 3.69
3002 7605 0.986019 AGGGTGACGGGGCATATCAA 60.986 55.000 0.00 0.00 0.00 2.57
3009 7612 4.154195 GTGACGGGGCATATCAAATCATAC 59.846 45.833 0.00 0.00 0.00 2.39
3012 7615 4.263905 ACGGGGCATATCAAATCATACCAT 60.264 41.667 0.00 0.00 0.00 3.55
3231 7840 9.355215 TCAAAACAGTATAGATCGAAGAGAAAC 57.645 33.333 0.00 0.00 43.63 2.78
3239 7848 9.654417 GTATAGATCGAAGAGAAACTAAGTGAC 57.346 37.037 0.00 0.00 43.63 3.67
3241 7850 7.222000 AGATCGAAGAGAAACTAAGTGACTT 57.778 36.000 2.37 2.37 43.63 3.01
3325 7936 4.643387 GTGTGCCGGCCTGGACTT 62.643 66.667 26.77 0.00 42.00 3.01
3439 8050 3.439129 GTGTTGCCATCTTACAGGTAACC 59.561 47.826 9.37 0.00 46.05 2.85
3543 8157 7.448420 CATCCAGATCAATGGTAGTAACTCAT 58.552 38.462 0.00 0.00 41.43 2.90
3547 8161 8.616076 CCAGATCAATGGTAGTAACTCATTTTC 58.384 37.037 0.00 0.00 35.47 2.29
3676 8290 2.671396 GTGACCGTGTCATGGTGATTAC 59.329 50.000 21.77 10.74 44.63 1.89
3705 8319 6.117911 TCCATTAACTGTTTGTGCATATCG 57.882 37.500 0.00 0.00 0.00 2.92
3720 8334 4.332543 TGCATATCGACCACATTGTTCTTC 59.667 41.667 0.00 0.00 0.00 2.87
3766 8381 7.067859 TCGTAAGCTATAACTGCTCTTTCCTTA 59.932 37.037 0.00 0.00 40.22 2.69
3905 8531 4.202111 GGGATTTGTTATGTATGTGTGCCC 60.202 45.833 0.00 0.00 0.00 5.36
4060 8687 6.198591 CCGCAAGTGTATCTAGTAAAAGCTAC 59.801 42.308 0.00 0.00 0.00 3.58
4102 8729 6.341316 TGATCCAACTACAAGAATCACTAGC 58.659 40.000 0.00 0.00 0.00 3.42
4111 8738 8.251721 ACTACAAGAATCACTAGCGATAAAACT 58.748 33.333 0.00 0.00 0.00 2.66
4156 8783 0.322456 CCATTCGCCTTCCTTGGACA 60.322 55.000 0.00 0.00 0.00 4.02
4172 8799 3.411446 TGGACAAATGCTCAAAGTCGAT 58.589 40.909 0.00 0.00 0.00 3.59
4180 8807 2.271800 GCTCAAAGTCGATCGACCATT 58.728 47.619 37.45 29.99 45.59 3.16
4184 8811 0.249120 AAGTCGATCGACCATTGCCA 59.751 50.000 37.45 3.85 45.59 4.92
4185 8812 0.465705 AGTCGATCGACCATTGCCAT 59.534 50.000 37.45 18.70 45.59 4.40
4303 8939 3.366679 CCTGAACTGCATCGCTTTGAATT 60.367 43.478 0.00 0.00 0.00 2.17
4334 8970 1.012086 CATCAAGCGGTGTCTCATGG 58.988 55.000 0.00 0.00 0.00 3.66
4365 9001 6.454848 GCTTCTATCATTGACACACTCGAAAG 60.455 42.308 0.00 0.00 0.00 2.62
4392 9028 2.312722 AAAACTTGCATGCAACAGCA 57.687 40.000 28.80 9.03 43.41 4.41
4430 9066 7.122501 TGACATTCATGTTATATGTGCCACTTT 59.877 33.333 0.00 0.00 41.95 2.66
4463 9099 9.747898 ACAATAAACCAATGGAGTACTAATTGA 57.252 29.630 23.21 10.43 33.96 2.57
4545 9181 2.290832 TGATATCCCACAAGTTGCTGCA 60.291 45.455 1.81 0.00 0.00 4.41
4568 9204 5.009010 CAGGAACTTTGTTTAGACACATGCT 59.991 40.000 0.00 0.00 34.60 3.79
4865 9504 9.889128 AAAGGAGAAATTGTTTTCAGATTGAAA 57.111 25.926 0.36 0.36 43.84 2.69
4980 9621 6.554334 TTTTAACTTATGACTGACCTGTGC 57.446 37.500 0.00 0.00 0.00 4.57
4997 9638 3.940852 CTGTGCTATTGTTCATGTGGCTA 59.059 43.478 0.00 0.00 0.00 3.93
5016 9657 5.074377 TGGCTATTGGAAATATGCCCTAGAA 59.926 40.000 13.29 0.00 39.60 2.10
5228 9869 6.122277 AGTTGTCATTTGATAACGGGATCAT 58.878 36.000 12.58 0.00 46.44 2.45
5254 9895 7.199167 TCATTAGGAGAATGATGTGAAGGAA 57.801 36.000 0.00 0.00 32.21 3.36
5261 9902 5.634118 AGAATGATGTGAAGGAAAAGACCA 58.366 37.500 0.00 0.00 0.00 4.02
5306 9947 8.367911 AGGATCGTATCAAGTTTATTGCTATCA 58.632 33.333 0.00 0.00 0.00 2.15
5408 10049 4.231753 CGTCGCAACGTAACTGGA 57.768 55.556 0.00 0.00 43.94 3.86
5410 10051 1.898938 CGTCGCAACGTAACTGGATA 58.101 50.000 0.00 0.00 43.94 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.938698 TTAACCAATCCTACTTGTCTGGTA 57.061 37.500 0.00 0.00 36.15 3.25
12 13 5.312443 AGGGTTTAACCAATCCTACTTGTCT 59.688 40.000 16.58 0.00 41.02 3.41
17 18 4.263771 CCACAGGGTTTAACCAATCCTACT 60.264 45.833 16.58 0.00 41.02 2.57
45 46 1.133668 GCCTCCCAATCCATTACAGCT 60.134 52.381 0.00 0.00 0.00 4.24
46 47 1.322442 GCCTCCCAATCCATTACAGC 58.678 55.000 0.00 0.00 0.00 4.40
97 98 2.835156 GCCTCCTAACTCTTCACCTCTT 59.165 50.000 0.00 0.00 0.00 2.85
99 100 2.429250 GAGCCTCCTAACTCTTCACCTC 59.571 54.545 0.00 0.00 0.00 3.85
107 108 2.065906 CTCGCCGAGCCTCCTAACTC 62.066 65.000 0.00 0.00 0.00 3.01
110 111 1.152735 ATCTCGCCGAGCCTCCTAA 60.153 57.895 9.77 0.00 0.00 2.69
122 123 0.460987 CCTTCTGTCCACCATCTCGC 60.461 60.000 0.00 0.00 0.00 5.03
123 124 0.176680 CCCTTCTGTCCACCATCTCG 59.823 60.000 0.00 0.00 0.00 4.04
133 134 1.376553 GAGTGCAGCCCCTTCTGTC 60.377 63.158 0.00 0.00 36.49 3.51
136 137 0.545309 TGTAGAGTGCAGCCCCTTCT 60.545 55.000 0.00 0.00 0.00 2.85
142 143 0.457851 AGTCGATGTAGAGTGCAGCC 59.542 55.000 0.00 0.00 0.00 4.85
174 175 4.378774 CTGAACATCATCAGTCTCCATCC 58.621 47.826 0.00 0.00 41.54 3.51
256 257 8.353684 ACTCAAGTACAAGATATATGGTTCTCG 58.646 37.037 0.00 0.00 0.00 4.04
280 281 4.785376 ACAAATGAGGGAGGAACATCTACT 59.215 41.667 0.00 0.00 0.00 2.57
284 285 4.593956 AGAACAAATGAGGGAGGAACATC 58.406 43.478 0.00 0.00 0.00 3.06
298 299 6.342111 GTTTAGGAGAGATCCGAGAACAAAT 58.658 40.000 0.00 0.00 34.28 2.32
307 308 3.992260 ACATCGTTTAGGAGAGATCCG 57.008 47.619 0.00 0.00 34.28 4.18
309 310 5.833082 TGCTTACATCGTTTAGGAGAGATC 58.167 41.667 0.00 0.00 0.00 2.75
314 315 7.308782 AGAAAATGCTTACATCGTTTAGGAG 57.691 36.000 0.00 0.00 34.62 3.69
316 317 7.526608 TGAAGAAAATGCTTACATCGTTTAGG 58.473 34.615 0.00 0.00 34.62 2.69
317 318 8.948853 TTGAAGAAAATGCTTACATCGTTTAG 57.051 30.769 0.00 0.00 34.62 1.85
366 371 6.089517 GCCTTAAGGTAGTGCAACTCTTCAT 61.090 44.000 22.55 0.00 39.82 2.57
373 378 3.119495 CCATTGCCTTAAGGTAGTGCAAC 60.119 47.826 24.01 7.00 43.84 4.17
398 403 4.147449 TCGGATGGAGGCAGTGCG 62.147 66.667 9.45 0.00 0.00 5.34
399 404 2.202987 CTCGGATGGAGGCAGTGC 60.203 66.667 6.55 6.55 39.22 4.40
407 412 3.118775 CCTGACATACAAACTCGGATGGA 60.119 47.826 0.00 0.00 0.00 3.41
408 413 3.198068 CCTGACATACAAACTCGGATGG 58.802 50.000 0.00 0.00 0.00 3.51
409 414 2.609459 GCCTGACATACAAACTCGGATG 59.391 50.000 0.00 0.00 0.00 3.51
415 422 6.594788 AAATCATTGCCTGACATACAAACT 57.405 33.333 0.00 0.00 36.48 2.66
441 448 7.455641 TTTTCTTTAGTCAAACTGAACACCA 57.544 32.000 0.00 0.00 0.00 4.17
520 527 9.726438 GGGACTTAGATGTGCAATACTTATAAT 57.274 33.333 0.00 0.00 0.00 1.28
521 528 8.710239 TGGGACTTAGATGTGCAATACTTATAA 58.290 33.333 0.00 0.00 0.00 0.98
522 529 8.257602 TGGGACTTAGATGTGCAATACTTATA 57.742 34.615 0.00 0.00 0.00 0.98
523 530 7.136822 TGGGACTTAGATGTGCAATACTTAT 57.863 36.000 0.00 0.00 0.00 1.73
524 531 6.553953 TGGGACTTAGATGTGCAATACTTA 57.446 37.500 0.00 0.00 0.00 2.24
525 532 5.435686 TGGGACTTAGATGTGCAATACTT 57.564 39.130 0.00 0.00 0.00 2.24
526 533 5.636903 ATGGGACTTAGATGTGCAATACT 57.363 39.130 0.00 0.00 0.00 2.12
527 534 7.161404 TGATATGGGACTTAGATGTGCAATAC 58.839 38.462 0.00 0.00 29.17 1.89
528 535 7.315066 TGATATGGGACTTAGATGTGCAATA 57.685 36.000 0.00 0.00 30.63 1.90
529 536 6.191657 TGATATGGGACTTAGATGTGCAAT 57.808 37.500 0.00 0.00 0.00 3.56
530 537 5.628797 TGATATGGGACTTAGATGTGCAA 57.371 39.130 0.00 0.00 0.00 4.08
531 538 5.830799 ATGATATGGGACTTAGATGTGCA 57.169 39.130 0.00 0.00 0.00 4.57
532 539 6.233434 TCAATGATATGGGACTTAGATGTGC 58.767 40.000 0.00 0.00 0.00 4.57
533 540 8.319881 AGATCAATGATATGGGACTTAGATGTG 58.680 37.037 0.00 0.00 0.00 3.21
534 541 8.446714 AGATCAATGATATGGGACTTAGATGT 57.553 34.615 0.00 0.00 0.00 3.06
537 544 8.523658 CGTAAGATCAATGATATGGGACTTAGA 58.476 37.037 0.00 0.00 43.02 2.10
538 545 7.761704 CCGTAAGATCAATGATATGGGACTTAG 59.238 40.741 0.00 0.00 43.02 2.18
539 546 7.310423 CCCGTAAGATCAATGATATGGGACTTA 60.310 40.741 13.97 6.00 44.19 2.24
540 547 6.467677 CCGTAAGATCAATGATATGGGACTT 58.532 40.000 0.00 0.00 43.02 3.01
541 548 5.046304 CCCGTAAGATCAATGATATGGGACT 60.046 44.000 13.97 0.00 44.19 3.85
542 549 5.178797 CCCGTAAGATCAATGATATGGGAC 58.821 45.833 13.97 2.83 44.19 4.46
543 550 4.225042 CCCCGTAAGATCAATGATATGGGA 59.775 45.833 18.80 0.00 44.19 4.37
544 551 4.225042 TCCCCGTAAGATCAATGATATGGG 59.775 45.833 12.72 12.72 42.08 4.00
545 552 5.187772 TCTCCCCGTAAGATCAATGATATGG 59.812 44.000 0.00 0.00 43.02 2.74
546 553 6.286240 TCTCCCCGTAAGATCAATGATATG 57.714 41.667 0.00 0.00 43.02 1.78
547 554 7.502060 AATCTCCCCGTAAGATCAATGATAT 57.498 36.000 0.00 0.00 43.02 1.63
548 555 6.350194 CGAATCTCCCCGTAAGATCAATGATA 60.350 42.308 0.00 0.00 43.02 2.15
549 556 5.567623 CGAATCTCCCCGTAAGATCAATGAT 60.568 44.000 0.00 0.00 43.02 2.45
550 557 4.262036 CGAATCTCCCCGTAAGATCAATGA 60.262 45.833 0.00 0.00 43.02 2.57
551 558 3.990469 CGAATCTCCCCGTAAGATCAATG 59.010 47.826 0.00 0.00 43.02 2.82
552 559 3.641906 ACGAATCTCCCCGTAAGATCAAT 59.358 43.478 0.00 0.00 37.23 2.57
553 560 3.028850 ACGAATCTCCCCGTAAGATCAA 58.971 45.455 0.00 0.00 37.23 2.57
554 561 2.361119 CACGAATCTCCCCGTAAGATCA 59.639 50.000 0.00 0.00 37.23 2.92
555 562 2.361438 ACACGAATCTCCCCGTAAGATC 59.639 50.000 0.00 0.00 37.23 2.75
556 563 2.385803 ACACGAATCTCCCCGTAAGAT 58.614 47.619 0.00 0.00 37.23 2.40
557 564 1.843368 ACACGAATCTCCCCGTAAGA 58.157 50.000 0.00 0.00 37.23 2.10
558 565 2.034305 CCTACACGAATCTCCCCGTAAG 59.966 54.545 0.00 0.00 37.23 2.34
559 566 2.026641 CCTACACGAATCTCCCCGTAA 58.973 52.381 0.00 0.00 37.23 3.18
560 567 1.064463 ACCTACACGAATCTCCCCGTA 60.064 52.381 0.00 0.00 37.23 4.02
561 568 0.324091 ACCTACACGAATCTCCCCGT 60.324 55.000 0.00 0.00 39.88 5.28
562 569 1.683943 TACCTACACGAATCTCCCCG 58.316 55.000 0.00 0.00 0.00 5.73
563 570 4.684484 AAATACCTACACGAATCTCCCC 57.316 45.455 0.00 0.00 0.00 4.81
564 571 5.915175 AGAAAATACCTACACGAATCTCCC 58.085 41.667 0.00 0.00 0.00 4.30
565 572 7.845066 AAAGAAAATACCTACACGAATCTCC 57.155 36.000 0.00 0.00 0.00 3.71
608 615 8.562892 GCACATATAAGTGACTTAATCAAGCAT 58.437 33.333 12.15 0.00 42.05 3.79
609 616 7.552330 TGCACATATAAGTGACTTAATCAAGCA 59.448 33.333 12.15 13.45 42.05 3.91
610 617 7.919690 TGCACATATAAGTGACTTAATCAAGC 58.080 34.615 12.15 11.26 42.05 4.01
621 628 9.489084 GGTCATAGTTATTGCACATATAAGTGA 57.511 33.333 12.15 0.00 42.05 3.41
622 629 8.721478 GGGTCATAGTTATTGCACATATAAGTG 58.279 37.037 3.71 3.71 42.37 3.16
623 630 7.883311 GGGGTCATAGTTATTGCACATATAAGT 59.117 37.037 0.00 0.00 0.00 2.24
624 631 8.103305 AGGGGTCATAGTTATTGCACATATAAG 58.897 37.037 0.00 0.00 0.00 1.73
625 632 7.984475 AGGGGTCATAGTTATTGCACATATAA 58.016 34.615 0.00 0.00 0.00 0.98
626 633 7.568128 AGGGGTCATAGTTATTGCACATATA 57.432 36.000 0.00 0.00 0.00 0.86
627 634 6.454223 AGGGGTCATAGTTATTGCACATAT 57.546 37.500 0.00 0.00 0.00 1.78
628 635 5.904984 AGGGGTCATAGTTATTGCACATA 57.095 39.130 0.00 0.00 0.00 2.29
629 636 4.796110 AGGGGTCATAGTTATTGCACAT 57.204 40.909 0.00 0.00 0.00 3.21
630 637 4.966168 TCTAGGGGTCATAGTTATTGCACA 59.034 41.667 0.00 0.00 0.00 4.57
631 638 5.163343 TGTCTAGGGGTCATAGTTATTGCAC 60.163 44.000 0.00 0.00 0.00 4.57
632 639 4.966168 TGTCTAGGGGTCATAGTTATTGCA 59.034 41.667 0.00 0.00 0.00 4.08
633 640 5.163343 TGTGTCTAGGGGTCATAGTTATTGC 60.163 44.000 0.00 0.00 0.00 3.56
634 641 6.098409 ACTGTGTCTAGGGGTCATAGTTATTG 59.902 42.308 0.00 0.00 31.49 1.90
635 642 6.098409 CACTGTGTCTAGGGGTCATAGTTATT 59.902 42.308 0.00 0.00 32.81 1.40
636 643 5.598830 CACTGTGTCTAGGGGTCATAGTTAT 59.401 44.000 0.00 0.00 32.81 1.89
637 644 4.954202 CACTGTGTCTAGGGGTCATAGTTA 59.046 45.833 0.00 0.00 32.81 2.24
638 645 3.769844 CACTGTGTCTAGGGGTCATAGTT 59.230 47.826 0.00 0.00 32.81 2.24
639 646 3.366396 CACTGTGTCTAGGGGTCATAGT 58.634 50.000 0.00 0.00 34.77 2.12
640 647 2.101582 GCACTGTGTCTAGGGGTCATAG 59.898 54.545 9.86 0.00 0.00 2.23
641 648 2.108168 GCACTGTGTCTAGGGGTCATA 58.892 52.381 9.86 0.00 0.00 2.15
642 649 0.905357 GCACTGTGTCTAGGGGTCAT 59.095 55.000 9.86 0.00 0.00 3.06
643 650 0.178932 AGCACTGTGTCTAGGGGTCA 60.179 55.000 9.86 0.00 0.00 4.02
644 651 0.247736 CAGCACTGTGTCTAGGGGTC 59.752 60.000 9.86 0.00 27.24 4.46
645 652 0.178932 TCAGCACTGTGTCTAGGGGT 60.179 55.000 9.86 0.00 30.58 4.95
646 653 0.247736 GTCAGCACTGTGTCTAGGGG 59.752 60.000 9.86 0.00 0.00 4.79
647 654 0.969149 TGTCAGCACTGTGTCTAGGG 59.031 55.000 9.86 0.00 0.00 3.53
648 655 2.998670 CAATGTCAGCACTGTGTCTAGG 59.001 50.000 9.86 0.00 0.00 3.02
649 656 3.657634 ACAATGTCAGCACTGTGTCTAG 58.342 45.455 9.86 3.38 33.45 2.43
650 657 3.751479 ACAATGTCAGCACTGTGTCTA 57.249 42.857 9.86 0.00 33.45 2.59
651 658 2.627515 ACAATGTCAGCACTGTGTCT 57.372 45.000 9.86 4.39 33.45 3.41
652 659 5.362556 AAATACAATGTCAGCACTGTGTC 57.637 39.130 9.86 2.00 35.69 3.67
653 660 6.430925 ACATAAATACAATGTCAGCACTGTGT 59.569 34.615 9.86 0.00 35.69 3.72
654 661 6.845302 ACATAAATACAATGTCAGCACTGTG 58.155 36.000 2.76 2.76 35.69 3.66
655 662 7.452880 AACATAAATACAATGTCAGCACTGT 57.547 32.000 0.00 0.00 38.67 3.55
718 725 1.513158 CGGCCACTCACTGGTAGAG 59.487 63.158 2.24 0.00 42.99 2.43
720 727 1.949847 CTCCGGCCACTCACTGGTAG 61.950 65.000 2.24 0.00 42.99 3.18
725 732 0.251653 TAGTTCTCCGGCCACTCACT 60.252 55.000 2.24 0.00 0.00 3.41
737 744 6.090493 GGGTCGTTTCAGTACAATTAGTTCTC 59.910 42.308 0.00 0.00 0.00 2.87
740 747 4.687483 CGGGTCGTTTCAGTACAATTAGTT 59.313 41.667 0.00 0.00 0.00 2.24
763 1118 9.019656 ACTAGACACTAGAATATGATGATCACC 57.980 37.037 11.94 0.00 0.00 4.02
779 1134 4.476297 TCAAACAGGGACACTAGACACTA 58.524 43.478 0.00 0.00 0.00 2.74
780 1135 3.305720 TCAAACAGGGACACTAGACACT 58.694 45.455 0.00 0.00 0.00 3.55
781 1136 3.746045 TCAAACAGGGACACTAGACAC 57.254 47.619 0.00 0.00 0.00 3.67
782 1137 3.071023 CCTTCAAACAGGGACACTAGACA 59.929 47.826 0.00 0.00 0.00 3.41
783 1138 3.323979 TCCTTCAAACAGGGACACTAGAC 59.676 47.826 0.00 0.00 34.24 2.59
784 1139 3.583228 TCCTTCAAACAGGGACACTAGA 58.417 45.455 0.00 0.00 34.24 2.43
785 1140 4.351874 TTCCTTCAAACAGGGACACTAG 57.648 45.455 0.00 0.00 34.24 2.57
812 1167 6.701841 GTCTCGGTCAGAAATATCAAGCAATA 59.298 38.462 0.00 0.00 30.72 1.90
827 1182 0.534412 AGCCAGATTGTCTCGGTCAG 59.466 55.000 0.00 0.00 0.00 3.51
831 1186 2.969628 AGTTAGCCAGATTGTCTCGG 57.030 50.000 0.00 0.00 0.00 4.63
886 1950 9.987272 TTCATACCAACATCAATAGTGATAGAG 57.013 33.333 5.17 0.00 42.88 2.43
946 2013 8.635765 TTCATTTAACTAGCAGGAATTCAACT 57.364 30.769 7.93 3.71 0.00 3.16
1053 4774 0.532862 CACTCGTGGTTTGGTGCTCT 60.533 55.000 0.00 0.00 0.00 4.09
1054 4775 0.814010 ACACTCGTGGTTTGGTGCTC 60.814 55.000 1.77 0.00 33.53 4.26
1360 5084 3.687102 CAGTACGCGACCCACCCA 61.687 66.667 15.93 0.00 0.00 4.51
1381 5105 3.585990 CGGATCCAATGCCGCCAC 61.586 66.667 13.41 0.00 41.17 5.01
1598 5355 3.041940 CGCCTCGAACACCACCAC 61.042 66.667 0.00 0.00 0.00 4.16
1858 5663 4.168922 TCGTGAGAGAAAAATCGCTACA 57.831 40.909 0.00 0.00 34.84 2.74
1922 5747 2.910482 CACATCATTGCAAACACGTAGC 59.090 45.455 1.71 0.00 0.00 3.58
1923 5748 4.145876 ACACATCATTGCAAACACGTAG 57.854 40.909 1.71 0.00 0.00 3.51
1924 5749 4.153296 CCTACACATCATTGCAAACACGTA 59.847 41.667 1.71 0.16 0.00 3.57
1967 5796 6.025749 TCGAAATCGAGCCATCTATAATGT 57.974 37.500 0.58 0.00 44.22 2.71
2084 6080 3.304659 CCAACACTACCATGACAAGTTGC 60.305 47.826 1.81 0.00 34.98 4.17
2110 6115 0.170339 TGTACGGCAGTGTGATCGAG 59.830 55.000 0.00 0.00 0.00 4.04
2180 6195 5.215160 CGAAAAGCATGACAAGTTTAGCTT 58.785 37.500 0.00 0.00 43.43 3.74
2202 6217 2.529151 GCCAAAATATGAGTTGCCACG 58.471 47.619 0.00 0.00 0.00 4.94
2250 6387 1.455383 CCTTTTGGTCTTGCGCCACT 61.455 55.000 4.18 0.00 35.46 4.00
2256 6393 1.460273 TTCGGGCCTTTTGGTCTTGC 61.460 55.000 0.84 0.00 45.37 4.01
2268 6405 0.035739 TTGGTTAGTCAGTTCGGGCC 59.964 55.000 0.00 0.00 0.00 5.80
2270 6407 2.833631 AGTTGGTTAGTCAGTTCGGG 57.166 50.000 0.00 0.00 0.00 5.14
2272 6409 5.287226 ACAACTAGTTGGTTAGTCAGTTCG 58.713 41.667 33.11 9.01 44.45 3.95
2273 6410 7.924947 AGTAACAACTAGTTGGTTAGTCAGTTC 59.075 37.037 33.11 16.71 44.45 3.01
2276 6413 8.574737 AGTAGTAACAACTAGTTGGTTAGTCAG 58.425 37.037 33.11 10.73 44.45 3.51
2292 6429 4.346730 TGGATCGAAGGGAGTAGTAACAA 58.653 43.478 0.00 0.00 0.00 2.83
2333 6470 5.063438 CGATCCATATTGCTAAATACACCCG 59.937 44.000 0.00 0.00 31.07 5.28
2336 6473 6.313905 CCTCCGATCCATATTGCTAAATACAC 59.686 42.308 0.00 0.00 31.07 2.90
2342 6479 3.515502 CTCCCTCCGATCCATATTGCTAA 59.484 47.826 0.00 0.00 0.00 3.09
2353 6529 5.318630 AGAATCTAAGTACTCCCTCCGATC 58.681 45.833 0.00 0.00 0.00 3.69
2438 6614 2.745821 TGAAGCAAGTTCAGCTGCTATG 59.254 45.455 9.47 6.55 42.53 2.23
2440 6616 2.146342 GTGAAGCAAGTTCAGCTGCTA 58.854 47.619 9.47 0.00 46.18 3.49
2442 6618 0.664761 TGTGAAGCAAGTTCAGCTGC 59.335 50.000 9.47 0.00 46.18 5.25
2459 6635 7.995289 TGGATTCTGCGATGTTAATATTTTGT 58.005 30.769 0.00 0.00 0.00 2.83
2460 6636 8.908678 CATGGATTCTGCGATGTTAATATTTTG 58.091 33.333 0.00 0.00 0.00 2.44
2466 6642 4.494350 GCATGGATTCTGCGATGTTAAT 57.506 40.909 0.00 0.00 0.00 1.40
2475 6651 2.785477 CGAATTTTCGCATGGATTCTGC 59.215 45.455 0.00 0.00 44.26 4.26
2547 6723 2.299013 TGTGAGATCCAACTACTTGCGT 59.701 45.455 0.00 0.00 0.00 5.24
2549 6725 4.154918 CCTTTGTGAGATCCAACTACTTGC 59.845 45.833 0.00 0.00 0.00 4.01
2593 6772 9.460906 GATGCAAAATCCTTAGATTCAAAGATC 57.539 33.333 0.00 0.00 42.03 2.75
2603 6782 7.596494 CAAGTTTCAGATGCAAAATCCTTAGA 58.404 34.615 0.00 0.00 0.00 2.10
2639 6818 8.577939 CGACTTTAAAACTTGATACGAACGATA 58.422 33.333 0.14 0.00 0.00 2.92
2768 7371 6.813649 TCTTGACGATGACCTTCAAATAAGAG 59.186 38.462 0.00 0.00 0.00 2.85
2958 7561 3.442625 TCAGCTGCATCATCCTTTTGAAG 59.557 43.478 9.47 0.00 0.00 3.02
2971 7574 2.267006 CACCCTCGTCAGCTGCAT 59.733 61.111 9.47 0.00 0.00 3.96
2974 7577 2.126307 CGTCACCCTCGTCAGCTG 60.126 66.667 7.63 7.63 0.00 4.24
3109 7712 4.220163 ACTTTGGCCACTACTAGTGTACTC 59.780 45.833 3.88 0.00 44.50 2.59
3110 7713 4.158015 ACTTTGGCCACTACTAGTGTACT 58.842 43.478 3.88 0.00 44.50 2.73
3111 7714 4.532314 ACTTTGGCCACTACTAGTGTAC 57.468 45.455 3.88 7.65 44.50 2.90
3112 7715 4.020839 GGAACTTTGGCCACTACTAGTGTA 60.021 45.833 3.88 0.00 44.50 2.90
3113 7716 3.244457 GGAACTTTGGCCACTACTAGTGT 60.244 47.826 3.88 0.00 44.50 3.55
3114 7717 3.244422 TGGAACTTTGGCCACTACTAGTG 60.244 47.826 3.88 9.02 45.53 2.74
3115 7718 2.976882 TGGAACTTTGGCCACTACTAGT 59.023 45.455 3.88 0.00 0.00 2.57
3231 7840 7.741027 ATGCCATTCATGATAAGTCACTTAG 57.259 36.000 3.12 0.00 37.14 2.18
3239 7848 5.220796 CGCCAGATATGCCATTCATGATAAG 60.221 44.000 0.00 0.00 36.63 1.73
3241 7850 4.193865 CGCCAGATATGCCATTCATGATA 58.806 43.478 0.00 0.00 36.63 2.15
3439 8050 6.035327 GCCTGTAACCTGTAAACTTATGTACG 59.965 42.308 0.00 0.00 0.00 3.67
3543 8157 3.486383 CAGCCTACCAACAGGAAGAAAA 58.514 45.455 0.00 0.00 38.00 2.29
3547 8161 0.036732 TGCAGCCTACCAACAGGAAG 59.963 55.000 0.00 0.00 38.00 3.46
3676 8290 4.320494 GCACAAACAGTTAATGGAGGACTG 60.320 45.833 1.51 1.51 44.77 3.51
3705 8319 3.040147 TCGGAGAAGAACAATGTGGTC 57.960 47.619 0.00 0.00 33.32 4.02
3720 8334 4.036971 ACGATGTTATCTTCCTCTTCGGAG 59.963 45.833 0.00 0.00 44.28 4.63
3774 8400 1.135527 CGTGCCGACTATTACCCTGAA 59.864 52.381 0.00 0.00 0.00 3.02
3775 8401 0.742505 CGTGCCGACTATTACCCTGA 59.257 55.000 0.00 0.00 0.00 3.86
3905 8531 7.387673 TGAGAAGTTGGTACATCTTGTATTGTG 59.612 37.037 0.00 0.00 46.88 3.33
4060 8687 6.794374 TGGATCAATGAATCATTAAACCACG 58.206 36.000 8.29 0.00 32.35 4.94
4111 8738 6.055588 GCCTCACATAAGATAGCTTGGTTTA 58.944 40.000 2.82 0.00 35.56 2.01
4156 8783 2.673368 GGTCGATCGACTTTGAGCATTT 59.327 45.455 38.48 0.00 44.04 2.32
4172 8799 1.225855 GCGATAATGGCAATGGTCGA 58.774 50.000 13.88 0.00 0.00 4.20
4239 8866 4.469657 AGTGGTTGAGACCTATTTTGCAA 58.530 39.130 0.00 0.00 46.66 4.08
4247 8874 2.642171 ATGGGAGTGGTTGAGACCTA 57.358 50.000 0.00 0.00 46.66 3.08
4303 8939 3.447586 ACCGCTTGATGCTAGAGAACTAA 59.552 43.478 0.00 0.00 40.11 2.24
4334 8970 4.096833 TGTGTCAATGATAGAAGCAATGGC 59.903 41.667 0.00 0.00 41.61 4.40
4365 9001 5.634439 TGTTGCATGCAAGTTTTACATCATC 59.366 36.000 32.64 16.25 36.52 2.92
4400 9036 7.449086 TGGCACATATAACATGAATGTCATCAT 59.551 33.333 0.00 0.00 40.80 2.45
4430 9066 8.962679 GTACTCCATTGGTTTATTGTTATTCCA 58.037 33.333 1.86 0.00 0.00 3.53
4459 9095 4.040339 GGTGTGGAATTTGTTCCCTTCAAT 59.960 41.667 4.86 0.00 40.39 2.57
4463 9099 2.325484 GGGTGTGGAATTTGTTCCCTT 58.675 47.619 4.86 0.00 40.39 3.95
4545 9181 5.133221 AGCATGTGTCTAAACAAAGTTCCT 58.867 37.500 0.00 0.00 37.08 3.36
4729 9368 7.560796 AGTCTTTCTAGAGATTCCAAAAGGA 57.439 36.000 0.00 0.00 0.00 3.36
4804 9443 8.518151 TTTTGTCACATGCTTAATATGTTGTG 57.482 30.769 0.00 0.00 36.67 3.33
4975 9616 2.751259 AGCCACATGAACAATAGCACAG 59.249 45.455 0.00 0.00 0.00 3.66
4980 9621 6.698008 TTCCAATAGCCACATGAACAATAG 57.302 37.500 0.00 0.00 0.00 1.73
4997 9638 5.065613 TGCTTCTAGGGCATATTTCCAAT 57.934 39.130 7.11 0.00 34.56 3.16
5228 9869 8.496534 TCCTTCACATCATTCTCCTAATGATA 57.503 34.615 11.71 0.00 43.38 2.15
5250 9891 6.002082 ACGCTTATAGTTTTGGTCTTTTCCT 58.998 36.000 0.00 0.00 0.00 3.36
5254 9895 5.935789 TGCTACGCTTATAGTTTTGGTCTTT 59.064 36.000 0.00 0.00 0.00 2.52
5261 9902 6.807230 CGATCCTATGCTACGCTTATAGTTTT 59.193 38.462 0.00 0.00 0.00 2.43
5281 9922 8.534333 TGATAGCAATAAACTTGATACGATCC 57.466 34.615 0.00 0.00 0.00 3.36
5306 9947 7.362401 GGAACAGATACTTGACATGCAGAAAAT 60.362 37.037 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.