Multiple sequence alignment - TraesCS1D01G223900

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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 TraesCS1D01G223900 chr1D 100.000 6389 0 0 1 6389 311695183 311688795 0.000000e+00 11799.0
1 TraesCS1D01G223900 chr1D 86.748 981 73 23 3502 4448 345380679 345381636 0.000000e+00 1038.0
2 TraesCS1D01G223900 chr1D 92.659 613 41 2 4475 5087 345382648 345383256 0.000000e+00 880.0
3 TraesCS1D01G223900 chr1A 95.663 2928 98 17 588 3502 391851432 391848521 0.000000e+00 4676.0
4 TraesCS1D01G223900 chr1A 96.252 1254 45 2 4470 5722 391847445 391846193 0.000000e+00 2054.0
5 TraesCS1D01G223900 chr1A 92.068 706 25 6 3502 4177 391848450 391847746 0.000000e+00 965.0
6 TraesCS1D01G223900 chr1A 85.205 953 90 26 4567 5518 391739395 391738493 0.000000e+00 931.0
7 TraesCS1D01G223900 chr1A 85.567 679 65 15 3723 4376 391752770 391752100 0.000000e+00 680.0
8 TraesCS1D01G223900 chr1A 85.420 679 66 15 3723 4376 391841341 391840671 0.000000e+00 675.0
9 TraesCS1D01G223900 chr1A 89.163 526 43 13 5774 6291 391846193 391845674 1.500000e-180 643.0
10 TraesCS1D01G223900 chr1A 97.034 236 7 0 4223 4458 391847746 391847511 1.290000e-106 398.0
11 TraesCS1D01G223900 chr1A 91.176 238 19 2 4 240 391852541 391852305 7.990000e-84 322.0
12 TraesCS1D01G223900 chr1A 84.568 162 11 4 6057 6204 391737301 391737140 1.440000e-31 148.0
13 TraesCS1D01G223900 chr1A 84.568 162 11 4 6057 6204 391827493 391827332 1.440000e-31 148.0
14 TraesCS1D01G223900 chr1A 87.379 103 12 1 238 340 391852067 391851966 4.050000e-22 117.0
15 TraesCS1D01G223900 chr1A 100.000 32 0 0 6351 6382 391845678 391845647 6.920000e-05 60.2
16 TraesCS1D01G223900 chr1B 96.078 2677 84 12 642 3313 421543771 421541111 0.000000e+00 4342.0
17 TraesCS1D01G223900 chr1B 96.364 1265 42 3 4457 5718 421539927 421538664 0.000000e+00 2078.0
18 TraesCS1D01G223900 chr1B 91.239 993 29 11 3502 4458 421540928 421539958 0.000000e+00 1299.0
19 TraesCS1D01G223900 chr1B 90.824 643 24 6 5774 6389 421538660 421538026 0.000000e+00 828.0
20 TraesCS1D01G223900 chr1B 85.477 241 30 4 1 240 421587976 421587740 4.950000e-61 246.0
21 TraesCS1D01G223900 chr1B 97.222 108 3 0 3395 3502 421541107 421541000 3.930000e-42 183.0
22 TraesCS1D01G223900 chr1B 82.609 138 23 1 238 375 421587502 421587366 3.130000e-23 121.0
23 TraesCS1D01G223900 chr7B 94.087 1150 62 4 1992 3139 312025363 312024218 0.000000e+00 1742.0
24 TraesCS1D01G223900 chr7B 93.663 1152 64 6 1992 3139 311928691 311927545 0.000000e+00 1714.0
25 TraesCS1D01G223900 chrUn 84.555 1023 97 28 4567 5579 915041 916012 0.000000e+00 959.0
26 TraesCS1D01G223900 chrUn 84.568 162 11 4 6057 6204 916455 916616 1.440000e-31 148.0
27 TraesCS1D01G223900 chr4A 97.500 80 2 0 6264 6343 626981493 626981572 3.110000e-28 137.0
28 TraesCS1D01G223900 chr3D 94.872 78 4 0 6264 6341 565374415 565374338 8.700000e-24 122.0
29 TraesCS1D01G223900 chr3A 93.827 81 5 0 6261 6341 434000892 434000972 8.700000e-24 122.0
30 TraesCS1D01G223900 chr7D 94.805 77 3 1 6264 6340 119165944 119166019 1.130000e-22 119.0
31 TraesCS1D01G223900 chr7D 93.590 78 5 0 6264 6341 195654031 195654108 4.050000e-22 117.0
32 TraesCS1D01G223900 chr7D 93.671 79 4 1 6264 6341 204247273 204247195 4.050000e-22 117.0
33 TraesCS1D01G223900 chr5A 92.683 82 4 2 6260 6341 613017655 613017734 4.050000e-22 117.0
34 TraesCS1D01G223900 chr3B 92.771 83 3 2 6264 6343 672774741 672774659 4.050000e-22 117.0


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 TraesCS1D01G223900 chr1D 311688795 311695183 6388 True 11799.0 11799 100.000000 1 6389 1 chr1D.!!$R1 6388
1 TraesCS1D01G223900 chr1D 345380679 345383256 2577 False 959.0 1038 89.703500 3502 5087 2 chr1D.!!$F1 1585
2 TraesCS1D01G223900 chr1A 391845647 391852541 6894 True 1154.4 4676 93.591875 4 6382 8 chr1A.!!$R5 6378
3 TraesCS1D01G223900 chr1A 391752100 391752770 670 True 680.0 680 85.567000 3723 4376 1 chr1A.!!$R1 653
4 TraesCS1D01G223900 chr1A 391840671 391841341 670 True 675.0 675 85.420000 3723 4376 1 chr1A.!!$R3 653
5 TraesCS1D01G223900 chr1A 391737140 391739395 2255 True 539.5 931 84.886500 4567 6204 2 chr1A.!!$R4 1637
6 TraesCS1D01G223900 chr1B 421538026 421543771 5745 True 1746.0 4342 94.345400 642 6389 5 chr1B.!!$R1 5747
7 TraesCS1D01G223900 chr7B 312024218 312025363 1145 True 1742.0 1742 94.087000 1992 3139 1 chr7B.!!$R2 1147
8 TraesCS1D01G223900 chr7B 311927545 311928691 1146 True 1714.0 1714 93.663000 1992 3139 1 chr7B.!!$R1 1147
9 TraesCS1D01G223900 chrUn 915041 916616 1575 False 553.5 959 84.561500 4567 6204 2 chrUn.!!$F1 1637

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
411 653 0.038251 TCGCAGTAGAGCAACACAGG 60.038 55.0 0.00 0.00 0.00 4.00 F
460 702 0.531532 CAAGGCATGCGGGAGAGTAG 60.532 60.0 12.44 0.00 0.00 2.57 F
704 1289 0.662619 TGCTTCTCAGGCAAACAACG 59.337 50.0 0.00 0.00 36.71 4.10 F
2395 2988 0.108472 TCCACGAGATTCAGCTGCAG 60.108 55.0 10.11 10.11 0.00 4.41 F
4208 4951 1.017177 TTACCACCGAGCACGCAATC 61.017 55.0 0.00 0.00 38.29 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2514 1.486310 TCCAAGAACGGCAGCATAGAT 59.514 47.619 0.00 0.0 0.00 1.98 R
2208 2801 1.571955 TGAGCTTATCCTGCCAGTCA 58.428 50.000 0.00 0.0 0.00 3.41 R
2600 3193 0.248289 ATGCAGGGCAATTGTTGAGC 59.752 50.000 7.40 7.6 43.62 4.26 R
4306 5051 0.042131 AATCCCCTCCACTGTACGGA 59.958 55.000 9.17 0.0 0.00 4.69 R
5773 8196 0.036577 CCTCTCTCAACCAGCACAGG 60.037 60.000 0.00 0.0 0.00 4.00 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
46 47 2.534019 CGACAGTGTTGCAAGCGGT 61.534 57.895 0.00 2.61 0.00 5.68
49 50 2.124320 AGTGTTGCAAGCGGTGGT 60.124 55.556 0.00 0.00 0.00 4.16
71 72 1.100510 TGGTTCTACGAGATCACCGG 58.899 55.000 0.00 0.00 29.64 5.28
73 74 0.591741 GTTCTACGAGATCACCGGCG 60.592 60.000 0.00 0.00 0.00 6.46
74 75 1.721664 TTCTACGAGATCACCGGCGG 61.722 60.000 27.06 27.06 0.00 6.13
75 76 3.195591 CTACGAGATCACCGGCGGG 62.196 68.421 31.78 19.08 40.11 6.13
99 100 1.515521 GAGGGGGTGTTGCGAACTTG 61.516 60.000 0.00 0.00 0.00 3.16
127 128 2.217112 GCTACAAGCGCGGTGATAG 58.783 57.895 13.41 17.38 0.00 2.08
149 150 0.179163 CGATGCGAGTGTGTAGCAGA 60.179 55.000 0.00 0.00 44.55 4.26
151 152 1.133216 GATGCGAGTGTGTAGCAGAGA 59.867 52.381 0.00 0.00 44.55 3.10
152 153 0.241213 TGCGAGTGTGTAGCAGAGAC 59.759 55.000 0.00 0.00 35.81 3.36
162 163 0.448197 TAGCAGAGACACTTCGAGCG 59.552 55.000 0.00 0.00 0.00 5.03
217 218 3.423154 GAGTGGCGAACAAGGGCG 61.423 66.667 0.00 0.00 0.00 6.13
262 504 2.202743 GCTATGACCAGCGACGCA 60.203 61.111 23.70 0.00 0.00 5.24
310 552 0.107897 ACGAAGTGCAAGGTGTGACA 60.108 50.000 0.00 0.00 42.51 3.58
311 553 0.583438 CGAAGTGCAAGGTGTGACAG 59.417 55.000 0.00 0.00 0.00 3.51
314 556 1.823470 GTGCAAGGTGTGACAGCCA 60.823 57.895 11.60 0.00 31.60 4.75
315 557 1.526686 TGCAAGGTGTGACAGCCAG 60.527 57.895 11.60 5.45 31.60 4.85
322 564 1.374631 TGTGACAGCCAGCGATGTC 60.375 57.895 0.00 3.39 44.88 3.06
342 584 4.301027 GACCCCTAGCCGGCGATG 62.301 72.222 23.20 13.32 0.00 3.84
345 587 4.976925 CCCTAGCCGGCGATGCTG 62.977 72.222 23.20 3.32 39.91 4.41
352 594 3.864686 CGGCGATGCTGGAAACGG 61.865 66.667 0.00 0.00 40.79 4.44
353 595 2.746277 GGCGATGCTGGAAACGGT 60.746 61.111 0.00 0.00 39.64 4.83
354 596 2.750888 GGCGATGCTGGAAACGGTC 61.751 63.158 0.00 0.00 39.64 4.79
355 597 2.032634 GCGATGCTGGAAACGGTCA 61.033 57.895 0.00 0.00 39.64 4.02
356 598 1.573829 GCGATGCTGGAAACGGTCAA 61.574 55.000 0.00 0.00 39.64 3.18
357 599 0.165944 CGATGCTGGAAACGGTCAAC 59.834 55.000 0.00 0.00 39.64 3.18
368 610 0.796312 ACGGTCAACGATGATGTTGC 59.204 50.000 0.00 0.00 46.85 4.17
369 611 0.795698 CGGTCAACGATGATGTTGCA 59.204 50.000 0.00 0.00 46.85 4.08
370 612 1.196581 CGGTCAACGATGATGTTGCAA 59.803 47.619 0.00 0.00 46.85 4.08
371 613 2.350293 CGGTCAACGATGATGTTGCAAA 60.350 45.455 0.00 0.00 46.85 3.68
372 614 3.236816 GGTCAACGATGATGTTGCAAAG 58.763 45.455 0.00 0.00 46.85 2.77
373 615 2.658325 GTCAACGATGATGTTGCAAAGC 59.342 45.455 0.00 0.00 46.85 3.51
374 616 2.553602 TCAACGATGATGTTGCAAAGCT 59.446 40.909 0.00 0.00 46.85 3.74
375 617 2.907910 ACGATGATGTTGCAAAGCTC 57.092 45.000 0.00 0.00 0.00 4.09
376 618 1.129251 ACGATGATGTTGCAAAGCTCG 59.871 47.619 0.00 8.52 0.00 5.03
377 619 1.394572 CGATGATGTTGCAAAGCTCGA 59.605 47.619 0.00 0.00 0.00 4.04
378 620 2.031314 CGATGATGTTGCAAAGCTCGAT 59.969 45.455 0.00 0.00 0.00 3.59
379 621 2.905959 TGATGTTGCAAAGCTCGATG 57.094 45.000 0.00 0.00 0.00 3.84
380 622 2.153645 TGATGTTGCAAAGCTCGATGT 58.846 42.857 0.00 0.00 0.00 3.06
381 623 2.553602 TGATGTTGCAAAGCTCGATGTT 59.446 40.909 0.00 0.00 0.00 2.71
382 624 3.750652 TGATGTTGCAAAGCTCGATGTTA 59.249 39.130 0.00 0.00 0.00 2.41
383 625 4.215185 TGATGTTGCAAAGCTCGATGTTAA 59.785 37.500 0.00 0.00 0.00 2.01
384 626 3.884169 TGTTGCAAAGCTCGATGTTAAC 58.116 40.909 0.00 0.00 0.00 2.01
385 627 3.234386 GTTGCAAAGCTCGATGTTAACC 58.766 45.455 0.00 0.00 0.00 2.85
386 628 1.810151 TGCAAAGCTCGATGTTAACCC 59.190 47.619 2.48 0.00 0.00 4.11
387 629 1.810151 GCAAAGCTCGATGTTAACCCA 59.190 47.619 2.48 0.00 0.00 4.51
388 630 2.227865 GCAAAGCTCGATGTTAACCCAA 59.772 45.455 2.48 0.00 0.00 4.12
389 631 3.821841 CAAAGCTCGATGTTAACCCAAC 58.178 45.455 2.48 0.00 37.67 3.77
390 632 2.109425 AGCTCGATGTTAACCCAACC 57.891 50.000 2.48 0.00 36.20 3.77
391 633 0.725117 GCTCGATGTTAACCCAACCG 59.275 55.000 2.48 0.05 36.20 4.44
392 634 1.942586 GCTCGATGTTAACCCAACCGT 60.943 52.381 2.48 0.00 36.20 4.83
393 635 1.997606 CTCGATGTTAACCCAACCGTC 59.002 52.381 2.48 0.00 36.20 4.79
394 636 0.717224 CGATGTTAACCCAACCGTCG 59.283 55.000 2.48 0.00 37.68 5.12
395 637 0.445043 GATGTTAACCCAACCGTCGC 59.555 55.000 2.48 0.00 36.20 5.19
396 638 0.250381 ATGTTAACCCAACCGTCGCA 60.250 50.000 2.48 0.00 36.20 5.10
397 639 0.881159 TGTTAACCCAACCGTCGCAG 60.881 55.000 2.48 0.00 36.20 5.18
398 640 0.881600 GTTAACCCAACCGTCGCAGT 60.882 55.000 0.00 0.00 0.00 4.40
399 641 0.678395 TTAACCCAACCGTCGCAGTA 59.322 50.000 0.00 0.00 0.00 2.74
410 652 1.063806 GTCGCAGTAGAGCAACACAG 58.936 55.000 0.00 0.00 0.00 3.66
411 653 0.038251 TCGCAGTAGAGCAACACAGG 60.038 55.000 0.00 0.00 0.00 4.00
412 654 1.016130 CGCAGTAGAGCAACACAGGG 61.016 60.000 0.00 0.00 0.00 4.45
422 664 1.686115 GCAACACAGGGGCCTTATGAT 60.686 52.381 0.00 0.00 0.00 2.45
442 684 5.789521 TGATTCCTTACATCTTCGACAACA 58.210 37.500 0.00 0.00 0.00 3.33
460 702 0.531532 CAAGGCATGCGGGAGAGTAG 60.532 60.000 12.44 0.00 0.00 2.57
474 716 0.985549 GAGTAGAGACGCGTGCAAAG 59.014 55.000 20.70 0.00 0.00 2.77
488 730 0.955919 GCAAAGTGAGAGGGGAACGG 60.956 60.000 0.00 0.00 0.00 4.44
491 733 4.452733 GTGAGAGGGGAACGGGCG 62.453 72.222 0.00 0.00 0.00 6.13
507 749 1.146041 GCGCCCACTGATCCACATA 59.854 57.895 0.00 0.00 0.00 2.29
510 752 2.549992 GCGCCCACTGATCCACATATTA 60.550 50.000 0.00 0.00 0.00 0.98
520 762 5.072055 TGATCCACATATTACATGCAAGGG 58.928 41.667 0.00 0.00 0.00 3.95
522 764 2.030893 CCACATATTACATGCAAGGGCG 60.031 50.000 0.00 0.00 45.35 6.13
527 769 0.813610 TTACATGCAAGGGCGATCGG 60.814 55.000 18.30 0.01 45.35 4.18
529 771 1.598962 CATGCAAGGGCGATCGGAT 60.599 57.895 18.30 0.00 45.35 4.18
535 777 3.928779 GGGCGATCGGATGGCTGA 61.929 66.667 21.65 0.00 34.17 4.26
536 778 2.663188 GGCGATCGGATGGCTGAC 60.663 66.667 21.65 4.74 34.17 3.51
539 781 1.006805 CGATCGGATGGCTGACTCC 60.007 63.158 7.38 0.00 30.79 3.85
561 803 2.125106 GCGACCGATCCCTTGCTT 60.125 61.111 0.00 0.00 0.00 3.91
562 804 2.174319 GCGACCGATCCCTTGCTTC 61.174 63.158 0.00 0.00 0.00 3.86
566 808 1.521681 CCGATCCCTTGCTTCCGTC 60.522 63.158 0.00 0.00 0.00 4.79
570 812 2.240162 ATCCCTTGCTTCCGTCGGTC 62.240 60.000 11.88 2.69 0.00 4.79
614 1198 8.732746 TCCTTAATAAACAAGGATTAGACAGC 57.267 34.615 0.00 0.00 45.25 4.40
671 1255 2.891191 TGGGGTGATTAAACTGGGAC 57.109 50.000 0.00 0.00 0.00 4.46
695 1280 1.675415 GGCTCAGTCTTGCTTCTCAGG 60.675 57.143 0.00 0.00 0.00 3.86
704 1289 0.662619 TGCTTCTCAGGCAAACAACG 59.337 50.000 0.00 0.00 36.71 4.10
735 1320 4.280819 TCACCCAAATCTCCAAATGATCC 58.719 43.478 0.00 0.00 0.00 3.36
868 1457 2.693017 GAGGAGGGGAGGAGCTCA 59.307 66.667 17.19 0.00 31.08 4.26
917 1509 2.629137 TCGTACTAGTTGCCAAGTCCAA 59.371 45.455 0.00 0.00 0.00 3.53
959 1552 3.649073 GACAATAACTTTTGGTGGGCAC 58.351 45.455 0.00 0.00 0.00 5.01
1475 2068 2.223180 GCGTCAAGGTTCGTTTTCTTGT 60.223 45.455 0.00 0.00 38.99 3.16
1501 2094 1.376609 GCATGGTCTTACCGGCCTTG 61.377 60.000 0.00 3.83 42.58 3.61
1758 2351 2.376518 TGGGGTTCTGATTTCTGAAGCT 59.623 45.455 21.01 0.00 45.43 3.74
1781 2374 7.819900 AGCTATACAGTACTTGGTGAAAGAAAG 59.180 37.037 0.00 0.00 39.38 2.62
2193 2786 6.874134 CCTACTACAGGTATGATGCAATTACC 59.126 42.308 12.74 12.74 39.91 2.85
2208 2801 1.546589 TTACCGTGGGTGGCGATCTT 61.547 55.000 0.00 0.00 36.19 2.40
2303 2896 5.074746 ACATGGAAGGTAACCCTCTTTTT 57.925 39.130 0.00 0.00 41.56 1.94
2335 2928 4.224370 GTCCCCCGCAATATCTCCTTAATA 59.776 45.833 0.00 0.00 0.00 0.98
2395 2988 0.108472 TCCACGAGATTCAGCTGCAG 60.108 55.000 10.11 10.11 0.00 4.41
2565 3158 3.067601 TGTCTGTACTCTGCTTCGAAACA 59.932 43.478 0.00 0.00 0.00 2.83
2566 3159 3.425858 GTCTGTACTCTGCTTCGAAACAC 59.574 47.826 0.00 0.00 0.00 3.32
2702 3302 6.639686 GCTGGCTATACAACATTGATTGAATG 59.360 38.462 0.00 0.00 46.20 2.67
2743 3343 6.886459 AGATCAGCCTTTCTAACTATTTTGCA 59.114 34.615 0.00 0.00 0.00 4.08
2937 3539 5.717178 TGCTAACACTCTCCTAAGTTCTGAT 59.283 40.000 0.00 0.00 0.00 2.90
3009 3611 4.864247 CGTTGAAAAATCATGGGATGTTCC 59.136 41.667 0.00 0.00 29.38 3.62
3085 3687 7.603180 TCTCCAGTGATTATTACTGTAGCAT 57.397 36.000 14.55 0.00 43.05 3.79
3201 3803 5.443283 AGGCATGTCATATGATGTTGAAGT 58.557 37.500 9.02 0.00 0.00 3.01
3202 3804 5.298527 AGGCATGTCATATGATGTTGAAGTG 59.701 40.000 9.02 1.42 0.00 3.16
3203 3805 4.974275 GCATGTCATATGATGTTGAAGTGC 59.026 41.667 9.02 7.14 31.64 4.40
3232 3835 2.197465 ACCTCTAACCCCAGGAATGAC 58.803 52.381 0.00 0.00 33.52 3.06
3318 3922 8.053963 TCTAGTAGTAGTTCCTAAGTGCTCATT 58.946 37.037 4.51 0.00 0.00 2.57
3319 3923 9.339850 CTAGTAGTAGTTCCTAAGTGCTCATTA 57.660 37.037 0.00 0.00 0.00 1.90
3346 3951 4.252971 TCTACTTGTTCAGCAGGTGTAC 57.747 45.455 2.57 2.57 37.96 2.90
3567 4245 1.203376 TCCTCCAGGGTCATGGTTACA 60.203 52.381 1.47 0.00 41.43 2.41
3591 4269 3.833070 GGTCTCCTCTGAAGGTCTACAAA 59.167 47.826 0.00 0.00 43.82 2.83
3681 4376 7.933577 TCCTGATGGATCATGTCTTTTACATAC 59.066 37.037 0.00 0.00 41.29 2.39
3720 4415 8.816640 ACACCTTGACACAAAATGATTAAATC 57.183 30.769 0.00 0.00 0.00 2.17
3777 4472 7.814587 GGTTTGAATTGAAATTTCCTACCTGAG 59.185 37.037 15.48 0.00 0.00 3.35
3890 4585 3.818180 TGTTTGAAAAATGCCATTGCCT 58.182 36.364 0.00 0.00 36.33 4.75
3891 4586 3.564644 TGTTTGAAAAATGCCATTGCCTG 59.435 39.130 0.00 0.00 36.33 4.85
3915 4610 2.562298 CCCACCTCTAAAAATTGCTGCA 59.438 45.455 0.00 0.00 0.00 4.41
4111 4829 8.555361 CATTTCTTATGCTAGAACTAGAAAGGC 58.445 37.037 12.33 0.00 35.73 4.35
4113 4831 5.360144 TCTTATGCTAGAACTAGAAAGGCGT 59.640 40.000 12.33 2.44 35.21 5.68
4114 4832 6.544931 TCTTATGCTAGAACTAGAAAGGCGTA 59.455 38.462 12.33 1.61 35.21 4.42
4115 4833 4.367386 TGCTAGAACTAGAAAGGCGTAC 57.633 45.455 12.33 0.00 35.21 3.67
4192 4932 6.204882 ACTTGTGCTTCCTTTATGTGTCTTAC 59.795 38.462 0.00 0.00 0.00 2.34
4208 4951 1.017177 TTACCACCGAGCACGCAATC 61.017 55.000 0.00 0.00 38.29 2.67
4306 5051 6.040166 GGTTGATGCATAGTTTCAAGGATGAT 59.960 38.462 0.00 0.00 34.96 2.45
4460 5234 9.727627 GAAAATATCTTCCAACTGATCATTCAC 57.272 33.333 0.00 0.00 0.00 3.18
4461 5235 9.471702 AAAATATCTTCCAACTGATCATTCACT 57.528 29.630 0.00 0.00 0.00 3.41
4462 5236 9.471702 AAATATCTTCCAACTGATCATTCACTT 57.528 29.630 0.00 0.00 0.00 3.16
4463 5237 6.998968 ATCTTCCAACTGATCATTCACTTC 57.001 37.500 0.00 0.00 0.00 3.01
4465 5239 5.702670 TCTTCCAACTGATCATTCACTTCAC 59.297 40.000 0.00 0.00 0.00 3.18
4692 6426 5.671463 ACTCTGATCTAGGATTGTCCCTA 57.329 43.478 0.00 0.00 37.19 3.53
4748 6482 5.627182 ATTCTCATTGCAGAGGACATAGT 57.373 39.130 3.36 0.00 36.30 2.12
4890 6624 1.202336 GCCAGCTACACATTGATTGGC 60.202 52.381 0.00 0.00 42.25 4.52
4935 6669 6.640499 TGAAAACTAGTGGCAAAATCAATTCG 59.360 34.615 0.00 0.00 0.00 3.34
5210 6944 4.437930 GGAGAAGTTGATTGCGGATTCAAG 60.438 45.833 13.54 0.00 0.00 3.02
5256 6990 1.934463 CGTCGCAACTGTTGAAGCT 59.066 52.632 23.81 0.00 0.00 3.74
5283 7017 1.694696 GTGTCAGACCTCCAAGTTCCT 59.305 52.381 0.00 0.00 0.00 3.36
5367 7101 4.322499 GGACTCGAGGAATGTCCAAAGTTA 60.322 45.833 18.41 0.00 46.79 2.24
5461 7195 9.494055 TTCCATTACCATATTTCATTTTACCCA 57.506 29.630 0.00 0.00 0.00 4.51
5473 7207 6.152638 TCATTTTACCCAGAAGGAAGGAAT 57.847 37.500 0.00 0.00 39.89 3.01
5683 8106 1.198759 GCAGGGTAGGTGTTGAGGGA 61.199 60.000 0.00 0.00 0.00 4.20
5712 8135 3.153629 AAATGGGGTTGGTGGCGGA 62.154 57.895 0.00 0.00 0.00 5.54
5722 8145 0.911769 TGGTGGCGGATCTGAAATCT 59.088 50.000 5.48 0.00 0.00 2.40
5723 8146 1.281867 TGGTGGCGGATCTGAAATCTT 59.718 47.619 5.48 0.00 0.00 2.40
5724 8147 1.672881 GGTGGCGGATCTGAAATCTTG 59.327 52.381 5.48 0.00 0.00 3.02
5725 8148 2.632377 GTGGCGGATCTGAAATCTTGA 58.368 47.619 5.48 0.00 0.00 3.02
5726 8149 2.611292 GTGGCGGATCTGAAATCTTGAG 59.389 50.000 5.48 0.00 0.00 3.02
5727 8150 1.601430 GGCGGATCTGAAATCTTGAGC 59.399 52.381 5.48 0.00 0.00 4.26
5728 8151 1.601430 GCGGATCTGAAATCTTGAGCC 59.399 52.381 5.48 0.00 33.41 4.70
5729 8152 2.216898 CGGATCTGAAATCTTGAGCCC 58.783 52.381 0.00 0.00 33.18 5.19
5730 8153 2.420547 CGGATCTGAAATCTTGAGCCCA 60.421 50.000 0.00 0.00 33.18 5.36
5731 8154 3.212685 GGATCTGAAATCTTGAGCCCAG 58.787 50.000 0.00 0.00 30.80 4.45
5732 8155 3.118112 GGATCTGAAATCTTGAGCCCAGA 60.118 47.826 0.00 0.00 35.48 3.86
5733 8156 4.521146 GATCTGAAATCTTGAGCCCAGAA 58.479 43.478 0.00 0.00 34.80 3.02
5734 8157 3.679389 TCTGAAATCTTGAGCCCAGAAC 58.321 45.455 0.00 0.00 0.00 3.01
5735 8158 2.417933 CTGAAATCTTGAGCCCAGAACG 59.582 50.000 0.00 0.00 0.00 3.95
5736 8159 2.038426 TGAAATCTTGAGCCCAGAACGA 59.962 45.455 0.00 0.00 0.00 3.85
5737 8160 2.100605 AATCTTGAGCCCAGAACGAC 57.899 50.000 0.00 0.00 0.00 4.34
5738 8161 1.270907 ATCTTGAGCCCAGAACGACT 58.729 50.000 0.00 0.00 0.00 4.18
5739 8162 0.603569 TCTTGAGCCCAGAACGACTC 59.396 55.000 0.00 0.00 0.00 3.36
5740 8163 0.390472 CTTGAGCCCAGAACGACTCC 60.390 60.000 0.00 0.00 0.00 3.85
5741 8164 1.827399 TTGAGCCCAGAACGACTCCC 61.827 60.000 0.00 0.00 0.00 4.30
5742 8165 3.003763 AGCCCAGAACGACTCCCC 61.004 66.667 0.00 0.00 0.00 4.81
5743 8166 3.319198 GCCCAGAACGACTCCCCA 61.319 66.667 0.00 0.00 0.00 4.96
5744 8167 2.982130 CCCAGAACGACTCCCCAG 59.018 66.667 0.00 0.00 0.00 4.45
5745 8168 2.266055 CCAGAACGACTCCCCAGC 59.734 66.667 0.00 0.00 0.00 4.85
5746 8169 2.583441 CCAGAACGACTCCCCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
5747 8170 1.079543 CAGAACGACTCCCCAGCAG 60.080 63.158 0.00 0.00 0.00 4.24
5748 8171 1.228894 AGAACGACTCCCCAGCAGA 60.229 57.895 0.00 0.00 0.00 4.26
5749 8172 1.216710 GAACGACTCCCCAGCAGAG 59.783 63.158 0.00 0.00 37.39 3.35
5750 8173 2.844072 GAACGACTCCCCAGCAGAGC 62.844 65.000 0.00 0.00 34.56 4.09
5751 8174 3.385384 CGACTCCCCAGCAGAGCA 61.385 66.667 0.00 0.00 34.56 4.26
5752 8175 2.583520 GACTCCCCAGCAGAGCAG 59.416 66.667 0.00 0.00 34.56 4.24
5753 8176 1.986757 GACTCCCCAGCAGAGCAGA 60.987 63.158 0.00 0.00 34.56 4.26
5754 8177 1.306825 ACTCCCCAGCAGAGCAGAT 60.307 57.895 0.00 0.00 34.56 2.90
5755 8178 1.146485 CTCCCCAGCAGAGCAGATG 59.854 63.158 0.00 0.00 0.00 2.90
5756 8179 2.192443 CCCCAGCAGAGCAGATGG 59.808 66.667 1.62 1.62 44.51 3.51
5757 8180 2.677289 CCCCAGCAGAGCAGATGGT 61.677 63.158 7.23 0.00 43.42 3.55
5758 8181 1.153208 CCCAGCAGAGCAGATGGTC 60.153 63.158 3.85 3.85 43.42 4.02
5759 8182 1.600638 CCAGCAGAGCAGATGGTCA 59.399 57.895 13.95 0.00 44.42 4.02
5760 8183 0.462225 CCAGCAGAGCAGATGGTCAG 60.462 60.000 13.95 7.36 44.42 3.51
5761 8184 0.535797 CAGCAGAGCAGATGGTCAGA 59.464 55.000 13.95 0.00 44.42 3.27
5762 8185 0.825410 AGCAGAGCAGATGGTCAGAG 59.175 55.000 13.95 5.11 44.42 3.35
5763 8186 0.822811 GCAGAGCAGATGGTCAGAGA 59.177 55.000 13.95 0.00 44.42 3.10
5764 8187 1.202440 GCAGAGCAGATGGTCAGAGAG 60.202 57.143 13.95 0.79 44.42 3.20
5765 8188 1.409790 CAGAGCAGATGGTCAGAGAGG 59.590 57.143 13.95 0.00 44.42 3.69
5766 8189 1.287442 AGAGCAGATGGTCAGAGAGGA 59.713 52.381 13.95 0.00 44.42 3.71
5767 8190 2.106566 GAGCAGATGGTCAGAGAGGAA 58.893 52.381 7.14 0.00 41.81 3.36
5768 8191 2.699846 GAGCAGATGGTCAGAGAGGAAT 59.300 50.000 7.14 0.00 41.81 3.01
5769 8192 3.113824 AGCAGATGGTCAGAGAGGAATT 58.886 45.455 0.00 0.00 0.00 2.17
5770 8193 3.134442 AGCAGATGGTCAGAGAGGAATTC 59.866 47.826 0.00 0.00 0.00 2.17
5771 8194 3.118482 GCAGATGGTCAGAGAGGAATTCA 60.118 47.826 7.93 0.00 0.00 2.57
5772 8195 4.695396 CAGATGGTCAGAGAGGAATTCAG 58.305 47.826 7.93 0.00 0.00 3.02
5773 8196 3.134442 AGATGGTCAGAGAGGAATTCAGC 59.866 47.826 7.93 0.00 0.00 4.26
5794 8217 1.376553 GTGCTGGTTGAGAGAGGCC 60.377 63.158 0.00 0.00 0.00 5.19
5829 8252 1.136329 AGCTCCCTCCAAAGCCTGAA 61.136 55.000 0.00 0.00 39.39 3.02
5864 8287 1.794116 CCAATTTGCAGCGGTTTCAAG 59.206 47.619 0.00 0.00 0.00 3.02
5870 8293 0.109597 GCAGCGGTTTCAAGTGGATG 60.110 55.000 0.00 0.00 0.00 3.51
5878 8301 3.496870 GGTTTCAAGTGGATGTGGAGACT 60.497 47.826 0.00 0.00 0.00 3.24
5891 8314 1.277273 TGGAGACTGGAAGCATCTGTG 59.723 52.381 0.00 0.00 37.60 3.66
5898 8321 4.210331 ACTGGAAGCATCTGTGTTCTTTT 58.790 39.130 0.00 0.00 37.60 2.27
5937 8360 6.468333 TTGATATCCATCCAAACAACATGG 57.532 37.500 0.00 0.00 38.83 3.66
5968 8391 6.114221 CGAGGCCGTTTCTAATTTTTCATA 57.886 37.500 0.00 0.00 0.00 2.15
5997 8675 4.027437 AGAAACCCAAAACTTAGCCACAA 58.973 39.130 0.00 0.00 0.00 3.33
6382 9174 4.752146 AGTAAACTCCGCTGTTGGTATAC 58.248 43.478 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.267351 CCATGACCACCGCTTGCAA 61.267 57.895 0.00 0.00 0.00 4.08
39 40 0.606401 AGAACCATGACCACCGCTTG 60.606 55.000 0.00 0.00 0.00 4.01
46 47 3.130516 GTGATCTCGTAGAACCATGACCA 59.869 47.826 0.00 0.00 34.09 4.02
49 50 2.357952 CGGTGATCTCGTAGAACCATGA 59.642 50.000 0.00 0.00 34.09 3.07
74 75 4.366684 CAACACCCCCTCTGCCCC 62.367 72.222 0.00 0.00 0.00 5.80
99 100 4.241999 CTTGTAGCGCATGCCGGC 62.242 66.667 22.73 22.73 44.31 6.13
118 119 3.044305 GCATCGCCCTATCACCGC 61.044 66.667 0.00 0.00 0.00 5.68
119 120 2.734723 CGCATCGCCCTATCACCG 60.735 66.667 0.00 0.00 0.00 4.94
125 126 1.033202 TACACACTCGCATCGCCCTA 61.033 55.000 0.00 0.00 0.00 3.53
127 128 1.878522 CTACACACTCGCATCGCCC 60.879 63.158 0.00 0.00 0.00 6.13
149 150 0.730265 CTAGCTCGCTCGAAGTGTCT 59.270 55.000 0.00 0.00 0.00 3.41
151 152 1.137825 GCTAGCTCGCTCGAAGTGT 59.862 57.895 7.70 0.00 0.00 3.55
152 153 0.865218 CTGCTAGCTCGCTCGAAGTG 60.865 60.000 17.23 0.00 0.00 3.16
177 178 3.357079 GCCTTGTCACTGCACCCG 61.357 66.667 0.00 0.00 0.00 5.28
181 182 1.071299 ACATCGCCTTGTCACTGCA 59.929 52.632 0.00 0.00 0.00 4.41
292 534 0.583438 CTGTCACACCTTGCACTTCG 59.417 55.000 0.00 0.00 0.00 3.79
300 542 2.116983 ATCGCTGGCTGTCACACCTT 62.117 55.000 0.00 0.00 0.00 3.50
306 548 2.125952 CGACATCGCTGGCTGTCA 60.126 61.111 12.91 0.00 41.46 3.58
331 573 3.025189 TTTCCAGCATCGCCGGCTA 62.025 57.895 26.68 15.56 40.23 3.93
337 579 1.573829 TTGACCGTTTCCAGCATCGC 61.574 55.000 0.00 0.00 0.00 4.58
340 582 0.250124 TCGTTGACCGTTTCCAGCAT 60.250 50.000 0.00 0.00 37.94 3.79
341 583 0.250124 ATCGTTGACCGTTTCCAGCA 60.250 50.000 0.00 0.00 37.94 4.41
342 584 0.165944 CATCGTTGACCGTTTCCAGC 59.834 55.000 0.00 0.00 37.94 4.85
343 585 1.790755 TCATCGTTGACCGTTTCCAG 58.209 50.000 0.00 0.00 37.94 3.86
344 586 2.073056 CATCATCGTTGACCGTTTCCA 58.927 47.619 0.00 0.00 37.94 3.53
345 587 2.073816 ACATCATCGTTGACCGTTTCC 58.926 47.619 0.00 0.00 37.94 3.13
346 588 3.806316 AACATCATCGTTGACCGTTTC 57.194 42.857 0.00 0.00 37.94 2.78
355 597 2.413239 CGAGCTTTGCAACATCATCGTT 60.413 45.455 0.00 0.00 0.00 3.85
356 598 1.129251 CGAGCTTTGCAACATCATCGT 59.871 47.619 0.00 0.00 0.00 3.73
357 599 1.394572 TCGAGCTTTGCAACATCATCG 59.605 47.619 0.00 5.53 0.00 3.84
358 600 3.181503 ACATCGAGCTTTGCAACATCATC 60.182 43.478 0.00 0.00 0.00 2.92
359 601 2.751259 ACATCGAGCTTTGCAACATCAT 59.249 40.909 0.00 0.00 0.00 2.45
360 602 2.153645 ACATCGAGCTTTGCAACATCA 58.846 42.857 0.00 0.00 0.00 3.07
361 603 2.907910 ACATCGAGCTTTGCAACATC 57.092 45.000 0.00 0.00 0.00 3.06
362 604 4.475944 GTTAACATCGAGCTTTGCAACAT 58.524 39.130 0.00 0.00 0.00 2.71
363 605 3.304391 GGTTAACATCGAGCTTTGCAACA 60.304 43.478 8.10 0.00 0.00 3.33
364 606 3.234386 GGTTAACATCGAGCTTTGCAAC 58.766 45.455 8.10 0.00 0.00 4.17
365 607 2.227865 GGGTTAACATCGAGCTTTGCAA 59.772 45.455 8.10 0.00 0.00 4.08
366 608 1.810151 GGGTTAACATCGAGCTTTGCA 59.190 47.619 8.10 0.00 0.00 4.08
367 609 1.810151 TGGGTTAACATCGAGCTTTGC 59.190 47.619 8.10 0.00 0.00 3.68
368 610 3.365969 GGTTGGGTTAACATCGAGCTTTG 60.366 47.826 8.10 0.00 41.18 2.77
369 611 2.817844 GGTTGGGTTAACATCGAGCTTT 59.182 45.455 8.10 0.00 41.18 3.51
370 612 2.433436 GGTTGGGTTAACATCGAGCTT 58.567 47.619 8.10 0.00 41.18 3.74
371 613 1.674817 CGGTTGGGTTAACATCGAGCT 60.675 52.381 8.10 0.00 41.18 4.09
372 614 0.725117 CGGTTGGGTTAACATCGAGC 59.275 55.000 8.10 7.58 41.18 5.03
373 615 1.997606 GACGGTTGGGTTAACATCGAG 59.002 52.381 8.10 0.00 41.18 4.04
374 616 1.669502 CGACGGTTGGGTTAACATCGA 60.670 52.381 8.10 0.00 45.12 3.59
375 617 0.717224 CGACGGTTGGGTTAACATCG 59.283 55.000 8.10 1.62 41.18 3.84
376 618 0.445043 GCGACGGTTGGGTTAACATC 59.555 55.000 8.10 0.00 41.18 3.06
377 619 0.250381 TGCGACGGTTGGGTTAACAT 60.250 50.000 8.10 0.00 41.18 2.71
378 620 0.881159 CTGCGACGGTTGGGTTAACA 60.881 55.000 8.10 0.00 41.18 2.41
379 621 0.881600 ACTGCGACGGTTGGGTTAAC 60.882 55.000 0.00 0.00 38.60 2.01
380 622 0.678395 TACTGCGACGGTTGGGTTAA 59.322 50.000 0.00 0.00 0.00 2.01
381 623 0.244450 CTACTGCGACGGTTGGGTTA 59.756 55.000 0.00 0.00 0.00 2.85
382 624 1.005394 CTACTGCGACGGTTGGGTT 60.005 57.895 0.00 0.00 0.00 4.11
383 625 1.874345 CTCTACTGCGACGGTTGGGT 61.874 60.000 0.00 0.00 0.00 4.51
384 626 1.153823 CTCTACTGCGACGGTTGGG 60.154 63.158 0.00 0.00 0.00 4.12
385 627 1.805945 GCTCTACTGCGACGGTTGG 60.806 63.158 0.00 0.00 0.00 3.77
386 628 0.666274 TTGCTCTACTGCGACGGTTG 60.666 55.000 0.00 0.00 35.36 3.77
387 629 0.666577 GTTGCTCTACTGCGACGGTT 60.667 55.000 0.00 0.00 37.56 4.44
388 630 1.080705 GTTGCTCTACTGCGACGGT 60.081 57.895 0.00 0.00 37.56 4.83
389 631 3.768632 GTTGCTCTACTGCGACGG 58.231 61.111 0.00 0.00 37.56 4.79
391 633 1.063806 CTGTGTTGCTCTACTGCGAC 58.936 55.000 0.00 0.00 45.09 5.19
392 634 0.038251 CCTGTGTTGCTCTACTGCGA 60.038 55.000 0.00 0.00 35.36 5.10
393 635 1.016130 CCCTGTGTTGCTCTACTGCG 61.016 60.000 0.00 0.00 35.36 5.18
394 636 0.674895 CCCCTGTGTTGCTCTACTGC 60.675 60.000 0.00 0.00 0.00 4.40
395 637 0.674895 GCCCCTGTGTTGCTCTACTG 60.675 60.000 0.00 0.00 0.00 2.74
396 638 1.679898 GCCCCTGTGTTGCTCTACT 59.320 57.895 0.00 0.00 0.00 2.57
397 639 1.377333 GGCCCCTGTGTTGCTCTAC 60.377 63.158 0.00 0.00 0.00 2.59
398 640 1.133809 AAGGCCCCTGTGTTGCTCTA 61.134 55.000 0.00 0.00 0.00 2.43
399 641 1.133809 TAAGGCCCCTGTGTTGCTCT 61.134 55.000 0.00 0.00 0.00 4.09
410 652 3.876309 TGTAAGGAATCATAAGGCCCC 57.124 47.619 0.00 0.00 0.00 5.80
411 653 5.248380 AGATGTAAGGAATCATAAGGCCC 57.752 43.478 0.00 0.00 0.00 5.80
412 654 5.409826 CGAAGATGTAAGGAATCATAAGGCC 59.590 44.000 0.00 0.00 0.00 5.19
422 664 4.994852 CCTTGTTGTCGAAGATGTAAGGAA 59.005 41.667 8.07 0.00 40.67 3.36
442 684 0.687757 TCTACTCTCCCGCATGCCTT 60.688 55.000 13.15 0.00 0.00 4.35
460 702 0.939577 TCTCACTTTGCACGCGTCTC 60.940 55.000 9.86 4.66 0.00 3.36
474 716 4.452733 CGCCCGTTCCCCTCTCAC 62.453 72.222 0.00 0.00 0.00 3.51
488 730 2.324014 TATGTGGATCAGTGGGCGCC 62.324 60.000 21.18 21.18 0.00 6.53
491 733 4.085357 TGTAATATGTGGATCAGTGGGC 57.915 45.455 0.00 0.00 0.00 5.36
507 749 1.229428 CGATCGCCCTTGCATGTAAT 58.771 50.000 0.26 0.00 37.32 1.89
510 752 2.329539 ATCCGATCGCCCTTGCATGT 62.330 55.000 10.32 0.00 37.32 3.21
520 762 1.663074 GAGTCAGCCATCCGATCGC 60.663 63.158 10.32 0.00 0.00 4.58
522 764 1.369321 GGGAGTCAGCCATCCGATC 59.631 63.158 0.00 0.00 36.38 3.69
527 769 1.372087 CGCTTTGGGAGTCAGCCATC 61.372 60.000 0.00 0.00 0.00 3.51
529 771 2.032528 CGCTTTGGGAGTCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
535 777 1.218316 GATCGGTCGCTTTGGGAGT 59.782 57.895 0.00 0.00 0.00 3.85
536 778 1.521681 GGATCGGTCGCTTTGGGAG 60.522 63.158 0.00 0.00 0.00 4.30
539 781 2.584608 AGGGATCGGTCGCTTTGG 59.415 61.111 9.85 0.00 44.38 3.28
596 838 7.064134 CACGTTATGCTGTCTAATCCTTGTTTA 59.936 37.037 0.00 0.00 0.00 2.01
597 839 5.938125 ACGTTATGCTGTCTAATCCTTGTTT 59.062 36.000 0.00 0.00 0.00 2.83
598 840 5.351465 CACGTTATGCTGTCTAATCCTTGTT 59.649 40.000 0.00 0.00 0.00 2.83
671 1255 1.155042 GAAGCAAGACTGAGCCACTG 58.845 55.000 0.00 0.00 0.00 3.66
735 1320 8.522178 AAGACTGACGAAGAACTAAAATAGTG 57.478 34.615 0.00 0.00 39.39 2.74
782 1367 1.778334 TGCTAGTTGCTACACACACG 58.222 50.000 0.13 0.00 43.37 4.49
917 1509 2.017049 GGTCAATACGCAATTCAGCCT 58.983 47.619 0.00 0.00 0.00 4.58
1501 2094 2.225467 AGTCAAGAAGCAAGCAGGAAC 58.775 47.619 0.00 0.00 0.00 3.62
1730 2323 8.434589 TTCAGAAATCAGAACCCCAAATTAAT 57.565 30.769 0.00 0.00 0.00 1.40
1758 2351 8.197592 TCCTTTCTTTCACCAAGTACTGTATA 57.802 34.615 0.00 0.00 33.66 1.47
1794 2387 3.880168 TGCATGGGGATCATATTGTGA 57.120 42.857 0.00 0.00 42.06 3.58
1921 2514 1.486310 TCCAAGAACGGCAGCATAGAT 59.514 47.619 0.00 0.00 0.00 1.98
2193 2786 2.100631 GTCAAGATCGCCACCCACG 61.101 63.158 0.00 0.00 0.00 4.94
2208 2801 1.571955 TGAGCTTATCCTGCCAGTCA 58.428 50.000 0.00 0.00 0.00 3.41
2395 2988 2.167398 TACTTCCGGTCACCAGCAGC 62.167 60.000 0.00 0.00 0.00 5.25
2565 3158 9.392259 GAATACCTTACTAATTTAGTTGCCAGT 57.608 33.333 14.00 8.04 40.14 4.00
2566 3159 9.614792 AGAATACCTTACTAATTTAGTTGCCAG 57.385 33.333 14.00 6.21 40.14 4.85
2600 3193 0.248289 ATGCAGGGCAATTGTTGAGC 59.752 50.000 7.40 7.60 43.62 4.26
2651 3251 6.264832 TGTTTTACAACACTTGAGCATTCAG 58.735 36.000 0.00 0.00 38.03 3.02
2937 3539 8.387813 ACTGGGTGAATACTTCCAAAAAGTATA 58.612 33.333 10.05 0.00 41.24 1.47
2948 3550 6.346096 TGCACTATTACTGGGTGAATACTTC 58.654 40.000 0.00 0.00 33.32 3.01
3009 3611 2.579207 TCGTTTTGGATAGCTCCGAG 57.421 50.000 0.00 0.00 45.37 4.63
3098 3700 8.916628 TGCAGCCAGTATAATTGATAACAATA 57.083 30.769 0.00 0.00 44.67 1.90
3107 3709 4.877823 TGACTTCTGCAGCCAGTATAATTG 59.122 41.667 16.01 0.00 40.09 2.32
3119 3721 4.820897 TGGTTATGTACTGACTTCTGCAG 58.179 43.478 7.63 7.63 39.26 4.41
3164 3766 3.136763 ACATGCCTAAGATGCAGATTCG 58.863 45.455 0.00 0.00 42.92 3.34
3201 3803 4.146564 GGGGTTAGAGGTTTTGTAAAGCA 58.853 43.478 4.44 0.00 0.00 3.91
3202 3804 4.146564 TGGGGTTAGAGGTTTTGTAAAGC 58.853 43.478 0.00 0.00 0.00 3.51
3203 3805 4.765339 CCTGGGGTTAGAGGTTTTGTAAAG 59.235 45.833 0.00 0.00 0.00 1.85
3232 3835 3.667726 CAGCATCGAGAATCACTGTATCG 59.332 47.826 0.00 0.00 33.17 2.92
3284 3887 8.517062 TTAGGAACTACTACTAGAACATGGAC 57.483 38.462 0.00 0.00 42.67 4.02
3318 3922 6.595326 CACCTGCTGAACAAGTAGATTGAATA 59.405 38.462 0.00 0.00 40.88 1.75
3319 3923 5.413833 CACCTGCTGAACAAGTAGATTGAAT 59.586 40.000 0.00 0.00 40.88 2.57
3567 4245 3.076182 TGTAGACCTTCAGAGGAGACCTT 59.924 47.826 0.00 0.00 46.74 3.50
3591 4269 3.117745 TGTTCCATGGATCACCTGAGAT 58.882 45.455 19.59 0.00 37.04 2.75
3681 4376 4.449068 GTCAAGGTGTAGAGTGTGAACATG 59.551 45.833 0.00 0.00 0.00 3.21
3777 4472 8.834465 AGAAGTGCTAAATGATCAATGTATCAC 58.166 33.333 0.00 4.74 38.65 3.06
3890 4585 2.298729 GCAATTTTTAGAGGTGGGCACA 59.701 45.455 0.00 0.00 0.00 4.57
3891 4586 2.562738 AGCAATTTTTAGAGGTGGGCAC 59.437 45.455 0.00 0.00 0.00 5.01
3915 4610 3.891366 CAGGATGGGTTGACAAAGAAGTT 59.109 43.478 0.00 0.00 0.00 2.66
4111 4829 2.095919 GCTTGCCCAACAAAGTAGTACG 60.096 50.000 0.00 0.00 37.96 3.67
4113 4831 3.146066 CTGCTTGCCCAACAAAGTAGTA 58.854 45.455 0.00 0.00 37.96 1.82
4114 4832 1.956477 CTGCTTGCCCAACAAAGTAGT 59.044 47.619 0.00 0.00 37.96 2.73
4115 4833 2.030805 GTCTGCTTGCCCAACAAAGTAG 60.031 50.000 0.00 0.00 37.96 2.57
4192 4932 1.577328 AAAGATTGCGTGCTCGGTGG 61.577 55.000 10.52 0.00 37.56 4.61
4242 4985 7.669722 TCATAAATTGGAAAAGGCTGTAGAAGT 59.330 33.333 0.00 0.00 0.00 3.01
4306 5051 0.042131 AATCCCCTCCACTGTACGGA 59.958 55.000 9.17 0.00 0.00 4.69
4458 5232 3.131709 AGTGTGATTGGGAGTGAAGTG 57.868 47.619 0.00 0.00 0.00 3.16
4460 5234 3.997021 GTGTAGTGTGATTGGGAGTGAAG 59.003 47.826 0.00 0.00 0.00 3.02
4461 5235 3.389656 TGTGTAGTGTGATTGGGAGTGAA 59.610 43.478 0.00 0.00 0.00 3.18
4462 5236 2.969262 TGTGTAGTGTGATTGGGAGTGA 59.031 45.455 0.00 0.00 0.00 3.41
4463 5237 3.401033 TGTGTAGTGTGATTGGGAGTG 57.599 47.619 0.00 0.00 0.00 3.51
4465 5239 4.761739 ACATTTGTGTAGTGTGATTGGGAG 59.238 41.667 0.00 0.00 0.00 4.30
4692 6426 5.694995 TCCTTGTTTCTGGATGAAAAGTCT 58.305 37.500 0.00 0.00 45.10 3.24
4748 6482 6.054941 TGCTGTTTCTTTCTACTGAATGTCA 58.945 36.000 0.00 0.00 31.56 3.58
4890 6624 2.071540 AGTGTGCAGACGATGTTGATG 58.928 47.619 8.52 0.00 0.00 3.07
4899 6633 3.060272 CACTAGTTTTCAGTGTGCAGACG 60.060 47.826 8.52 4.02 38.86 4.18
4935 6669 3.946558 AGCTTTCATCTTCATCTGCTTCC 59.053 43.478 0.00 0.00 0.00 3.46
5210 6944 2.261215 CTTCTGGAAGCCTTGGCAC 58.739 57.895 14.54 7.29 0.00 5.01
5238 6972 0.304705 AAGCTTCAACAGTTGCGACG 59.695 50.000 8.58 0.00 0.00 5.12
5256 6990 4.593206 ACTTGGAGGTCTGACACATAGAAA 59.407 41.667 10.38 0.00 0.00 2.52
5283 7017 1.351076 TCAGGCTGGTGACTTCATCA 58.649 50.000 15.73 0.00 35.38 3.07
5367 7101 4.215109 ACTACTCAACTGGCACCAAAAAT 58.785 39.130 0.00 0.00 0.00 1.82
5473 7207 6.824704 ACCAACCCGATCGATTTATTTCTTTA 59.175 34.615 18.66 0.00 0.00 1.85
5584 8007 9.645296 GGTTTCTCCACAAGCTAAATAAGCACC 62.645 44.444 0.00 0.00 44.34 5.01
5609 8032 8.977505 CCACATTTTCTAAACATTAAACACAGG 58.022 33.333 0.00 0.00 0.00 4.00
5683 8106 0.712380 ACCCCATTTGCTCCTGGATT 59.288 50.000 0.00 0.00 34.24 3.01
5712 8135 4.268359 GTTCTGGGCTCAAGATTTCAGAT 58.732 43.478 0.00 0.00 32.33 2.90
5722 8145 1.671742 GGAGTCGTTCTGGGCTCAA 59.328 57.895 0.00 0.00 0.00 3.02
5723 8146 2.283529 GGGAGTCGTTCTGGGCTCA 61.284 63.158 0.00 0.00 0.00 4.26
5724 8147 2.579738 GGGAGTCGTTCTGGGCTC 59.420 66.667 0.00 0.00 0.00 4.70
5725 8148 3.003763 GGGGAGTCGTTCTGGGCT 61.004 66.667 0.00 0.00 0.00 5.19
5726 8149 3.316573 CTGGGGAGTCGTTCTGGGC 62.317 68.421 0.00 0.00 0.00 5.36
5727 8150 2.982130 CTGGGGAGTCGTTCTGGG 59.018 66.667 0.00 0.00 0.00 4.45
5728 8151 2.266055 GCTGGGGAGTCGTTCTGG 59.734 66.667 0.00 0.00 0.00 3.86
5729 8152 1.079543 CTGCTGGGGAGTCGTTCTG 60.080 63.158 0.00 0.00 0.00 3.02
5730 8153 1.228894 TCTGCTGGGGAGTCGTTCT 60.229 57.895 0.00 0.00 0.00 3.01
5731 8154 1.216710 CTCTGCTGGGGAGTCGTTC 59.783 63.158 0.00 0.00 0.00 3.95
5732 8155 2.948720 GCTCTGCTGGGGAGTCGTT 61.949 63.158 0.00 0.00 33.73 3.85
5733 8156 3.386237 GCTCTGCTGGGGAGTCGT 61.386 66.667 0.00 0.00 33.73 4.34
5734 8157 3.368190 CTGCTCTGCTGGGGAGTCG 62.368 68.421 3.67 0.00 33.73 4.18
5735 8158 1.336632 ATCTGCTCTGCTGGGGAGTC 61.337 60.000 11.69 0.00 33.73 3.36
5736 8159 1.306825 ATCTGCTCTGCTGGGGAGT 60.307 57.895 11.69 0.00 33.73 3.85
5737 8160 1.146485 CATCTGCTCTGCTGGGGAG 59.854 63.158 5.58 5.58 0.00 4.30
5738 8161 2.372890 CCATCTGCTCTGCTGGGGA 61.373 63.158 0.00 0.00 0.00 4.81
5739 8162 2.192443 CCATCTGCTCTGCTGGGG 59.808 66.667 0.00 0.00 0.00 4.96
5740 8163 1.153208 GACCATCTGCTCTGCTGGG 60.153 63.158 0.00 0.00 32.89 4.45
5741 8164 0.462225 CTGACCATCTGCTCTGCTGG 60.462 60.000 0.00 0.00 34.84 4.85
5742 8165 0.535797 TCTGACCATCTGCTCTGCTG 59.464 55.000 0.00 0.00 0.00 4.41
5743 8166 0.825410 CTCTGACCATCTGCTCTGCT 59.175 55.000 0.00 0.00 0.00 4.24
5744 8167 0.822811 TCTCTGACCATCTGCTCTGC 59.177 55.000 0.00 0.00 0.00 4.26
5745 8168 1.409790 CCTCTCTGACCATCTGCTCTG 59.590 57.143 0.00 0.00 0.00 3.35
5746 8169 1.287442 TCCTCTCTGACCATCTGCTCT 59.713 52.381 0.00 0.00 0.00 4.09
5747 8170 1.774110 TCCTCTCTGACCATCTGCTC 58.226 55.000 0.00 0.00 0.00 4.26
5748 8171 2.244486 TTCCTCTCTGACCATCTGCT 57.756 50.000 0.00 0.00 0.00 4.24
5749 8172 3.118482 TGAATTCCTCTCTGACCATCTGC 60.118 47.826 2.27 0.00 0.00 4.26
5750 8173 4.695396 CTGAATTCCTCTCTGACCATCTG 58.305 47.826 2.27 0.00 0.00 2.90
5751 8174 3.134442 GCTGAATTCCTCTCTGACCATCT 59.866 47.826 2.27 0.00 0.00 2.90
5752 8175 3.465871 GCTGAATTCCTCTCTGACCATC 58.534 50.000 2.27 0.00 0.00 3.51
5753 8176 2.172293 GGCTGAATTCCTCTCTGACCAT 59.828 50.000 2.27 0.00 0.00 3.55
5754 8177 1.556911 GGCTGAATTCCTCTCTGACCA 59.443 52.381 2.27 0.00 0.00 4.02
5755 8178 1.836802 AGGCTGAATTCCTCTCTGACC 59.163 52.381 2.27 0.00 0.00 4.02
5756 8179 2.235898 ACAGGCTGAATTCCTCTCTGAC 59.764 50.000 23.66 0.00 0.00 3.51
5757 8180 2.235650 CACAGGCTGAATTCCTCTCTGA 59.764 50.000 23.66 0.00 0.00 3.27
5758 8181 2.630158 CACAGGCTGAATTCCTCTCTG 58.370 52.381 23.66 8.06 0.00 3.35
5759 8182 1.065564 GCACAGGCTGAATTCCTCTCT 60.066 52.381 23.66 0.00 36.96 3.10
5760 8183 1.377536 GCACAGGCTGAATTCCTCTC 58.622 55.000 23.66 0.00 36.96 3.20
5761 8184 3.566130 GCACAGGCTGAATTCCTCT 57.434 52.632 23.66 0.00 36.96 3.69
5772 8195 0.673022 CTCTCTCAACCAGCACAGGC 60.673 60.000 0.00 0.00 41.61 4.85
5773 8196 0.036577 CCTCTCTCAACCAGCACAGG 60.037 60.000 0.00 0.00 0.00 4.00
5794 8217 3.467776 GCTGGAGGCTCTAAACCTG 57.532 57.895 15.23 3.11 37.77 4.00
5829 8252 3.393426 AATTGGATTGGAGTGATGCCT 57.607 42.857 0.00 0.00 0.00 4.75
5841 8264 2.036992 TGAAACCGCTGCAAATTGGATT 59.963 40.909 0.00 0.00 0.00 3.01
5864 8287 1.677217 GCTTCCAGTCTCCACATCCAC 60.677 57.143 0.00 0.00 0.00 4.02
5870 8293 1.277557 ACAGATGCTTCCAGTCTCCAC 59.722 52.381 0.00 0.00 0.00 4.02
5878 8301 4.216257 GCTAAAAGAACACAGATGCTTCCA 59.784 41.667 0.00 0.00 0.00 3.53
5891 8314 2.293399 CAGGTGTGGTGGCTAAAAGAAC 59.707 50.000 0.00 0.00 0.00 3.01
5898 8321 0.840617 TCAAACAGGTGTGGTGGCTA 59.159 50.000 0.00 0.00 0.00 3.93
5968 8391 6.295292 GGCTAAGTTTTGGGTTTCTGATGAAT 60.295 38.462 0.00 0.00 31.56 2.57
5997 8675 4.603131 ACACTGGGCATTGATTATGAACT 58.397 39.130 0.00 0.00 36.26 3.01
6079 8830 7.693952 TCTTTGATTGTGTAGTTGTTGTTCTC 58.306 34.615 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.