Multiple sequence alignment - TraesCS5D01G043700

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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 TraesCS5D01G043700 chr5D 100.000 3130 0 0 1 3130 43047723 43050852 0.000000e+00 5781.0
1 TraesCS5D01G043700 chr5D 92.526 776 49 4 2355 3130 529079178 529078412 0.000000e+00 1103.0
2 TraesCS5D01G043700 chr5D 77.419 341 73 4 1358 1696 423474601 423474939 1.900000e-47 200.0
3 TraesCS5D01G043700 chr4D 95.078 772 38 0 2359 3130 1717715 1718486 0.000000e+00 1216.0
4 TraesCS5D01G043700 chr4D 92.139 776 56 3 2355 3130 441583353 441584123 0.000000e+00 1090.0
5 TraesCS5D01G043700 chr4D 81.495 281 33 8 466 733 263312513 263312239 2.450000e-51 213.0
6 TraesCS5D01G043700 chr5A 88.082 1074 48 16 731 1746 32146837 32147888 0.000000e+00 1201.0
7 TraesCS5D01G043700 chr5A 92.994 785 33 6 980 1746 30689463 30688683 0.000000e+00 1125.0
8 TraesCS5D01G043700 chr5A 79.862 581 89 20 1167 1727 31094028 31093456 1.750000e-107 399.0
9 TraesCS5D01G043700 chr5A 90.152 264 20 5 27 287 30690204 30689944 3.870000e-89 339.0
10 TraesCS5D01G043700 chr5A 88.448 277 23 3 2086 2358 32152603 32152874 3.010000e-85 326.0
11 TraesCS5D01G043700 chr5A 88.087 277 24 3 2086 2358 30688158 30687887 1.400000e-83 320.0
12 TraesCS5D01G043700 chr5A 93.038 158 10 1 314 470 30689951 30689794 2.430000e-56 230.0
13 TraesCS5D01G043700 chr5A 83.032 277 22 8 2088 2358 32136550 32136807 8.730000e-56 228.0
14 TraesCS5D01G043700 chr5A 78.363 342 68 6 1358 1696 536970922 536971260 1.890000e-52 217.0
15 TraesCS5D01G043700 chr5A 86.275 204 15 6 1890 2087 32136320 32136516 3.160000e-50 209.0
16 TraesCS5D01G043700 chr5A 85.897 156 7 1 731 871 30689799 30689644 5.410000e-33 152.0
17 TraesCS5D01G043700 chr5A 87.705 122 8 1 1896 2010 31093249 31093128 5.450000e-28 135.0
18 TraesCS5D01G043700 chr5A 86.458 96 7 4 1896 1986 32144306 32144400 1.990000e-17 100.0
19 TraesCS5D01G043700 chr5A 83.333 96 10 3 1896 1986 30705365 30705271 2.000000e-12 84.2
20 TraesCS5D01G043700 chr5A 91.837 49 1 1 1083 1128 31094098 31094050 7.250000e-07 65.8
21 TraesCS5D01G043700 chr5A 100.000 30 0 0 770 799 30127887 30127916 4.360000e-04 56.5
22 TraesCS5D01G043700 chr6D 94.330 776 43 1 2355 3130 7080849 7080075 0.000000e+00 1188.0
23 TraesCS5D01G043700 chr6D 93.299 776 43 3 2357 3128 6141841 6142611 0.000000e+00 1136.0
24 TraesCS5D01G043700 chr3D 94.430 772 43 0 2359 3130 21485880 21485109 0.000000e+00 1188.0
25 TraesCS5D01G043700 chr3D 93.694 777 41 4 2355 3129 595827530 595828300 0.000000e+00 1157.0
26 TraesCS5D01G043700 chr3D 92.051 780 53 3 2355 3130 1464762 1465536 0.000000e+00 1088.0
27 TraesCS5D01G043700 chr3D 87.500 216 21 5 467 679 253590835 253591047 8.670000e-61 244.0
28 TraesCS5D01G043700 chr7D 92.526 776 53 2 2355 3130 41232359 41233129 0.000000e+00 1107.0
29 TraesCS5D01G043700 chr7D 88.339 283 23 2 465 737 605758696 605758414 6.470000e-87 331.0
30 TraesCS5D01G043700 chr5B 92.599 581 19 9 780 1345 38679835 38680406 0.000000e+00 813.0
31 TraesCS5D01G043700 chr5B 94.678 357 19 0 1377 1733 38680400 38680756 3.530000e-154 555.0
32 TraesCS5D01G043700 chr5B 81.463 410 43 19 1971 2358 38640957 38641355 3.920000e-79 305.0
33 TraesCS5D01G043700 chr5B 88.745 231 22 4 57 287 38653040 38653266 2.380000e-71 279.0
34 TraesCS5D01G043700 chr5B 85.768 267 32 5 466 731 538593616 538593877 8.550000e-71 278.0
35 TraesCS5D01G043700 chr5B 84.937 239 24 7 2133 2359 38702881 38703119 6.750000e-57 231.0
36 TraesCS5D01G043700 chr5B 90.260 154 5 1 314 467 38653259 38653402 3.190000e-45 193.0
37 TraesCS5D01G043700 chr5B 85.455 165 12 4 2086 2244 38681112 38681270 8.980000e-36 161.0
38 TraesCS5D01G043700 chr5B 95.652 46 1 1 1941 1986 38644578 38644622 4.330000e-09 73.1
39 TraesCS5D01G043700 chr5B 87.500 56 6 1 1931 1986 37625323 37625269 2.610000e-06 63.9
40 TraesCS5D01G043700 chr1D 80.884 701 75 34 1087 1745 411514843 411514160 6.030000e-137 497.0
41 TraesCS5D01G043700 chr1D 84.158 101 6 5 1896 1986 411508647 411508547 4.300000e-14 89.8
42 TraesCS5D01G043700 chr1B 80.682 704 78 31 1087 1745 554695160 554694470 7.800000e-136 494.0
43 TraesCS5D01G043700 chr7B 88.112 286 23 4 464 739 505255221 505255505 2.330000e-86 329.0
44 TraesCS5D01G043700 chr7B 86.667 255 34 0 468 722 570329698 570329444 1.840000e-72 283.0
45 TraesCS5D01G043700 chr7A 87.726 277 24 2 464 730 533624030 533624306 6.520000e-82 315.0
46 TraesCS5D01G043700 chr2B 87.179 273 30 4 467 737 511768257 511767988 3.920000e-79 305.0
47 TraesCS5D01G043700 chr1A 86.245 269 29 7 466 730 553880687 553880951 5.110000e-73 285.0
48 TraesCS5D01G043700 chr2D 83.438 320 37 11 1429 1734 118854240 118853923 1.840000e-72 283.0
49 TraesCS5D01G043700 chr6A 82.072 251 26 9 469 702 50269554 50269306 2.460000e-46 196.0


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 TraesCS5D01G043700 chr5D 43047723 43050852 3129 False 5781.000000 5781 100.000000 1 3130 1 chr5D.!!$F1 3129
1 TraesCS5D01G043700 chr5D 529078412 529079178 766 True 1103.000000 1103 92.526000 2355 3130 1 chr5D.!!$R1 775
2 TraesCS5D01G043700 chr4D 1717715 1718486 771 False 1216.000000 1216 95.078000 2359 3130 1 chr4D.!!$F1 771
3 TraesCS5D01G043700 chr4D 441583353 441584123 770 False 1090.000000 1090 92.139000 2355 3130 1 chr4D.!!$F2 775
4 TraesCS5D01G043700 chr5A 32144306 32147888 3582 False 650.500000 1201 87.270000 731 1986 2 chr5A.!!$F5 1255
5 TraesCS5D01G043700 chr5A 30687887 30690204 2317 True 433.200000 1125 90.033600 27 2358 5 chr5A.!!$R2 2331
6 TraesCS5D01G043700 chr6D 7080075 7080849 774 True 1188.000000 1188 94.330000 2355 3130 1 chr6D.!!$R1 775
7 TraesCS5D01G043700 chr6D 6141841 6142611 770 False 1136.000000 1136 93.299000 2357 3128 1 chr6D.!!$F1 771
8 TraesCS5D01G043700 chr3D 21485109 21485880 771 True 1188.000000 1188 94.430000 2359 3130 1 chr3D.!!$R1 771
9 TraesCS5D01G043700 chr3D 595827530 595828300 770 False 1157.000000 1157 93.694000 2355 3129 1 chr3D.!!$F3 774
10 TraesCS5D01G043700 chr3D 1464762 1465536 774 False 1088.000000 1088 92.051000 2355 3130 1 chr3D.!!$F1 775
11 TraesCS5D01G043700 chr7D 41232359 41233129 770 False 1107.000000 1107 92.526000 2355 3130 1 chr7D.!!$F1 775
12 TraesCS5D01G043700 chr5B 38679835 38681270 1435 False 509.666667 813 90.910667 780 2244 3 chr5B.!!$F5 1464
13 TraesCS5D01G043700 chr1D 411514160 411514843 683 True 497.000000 497 80.884000 1087 1745 1 chr1D.!!$R2 658
14 TraesCS5D01G043700 chr1B 554694470 554695160 690 True 494.000000 494 80.682000 1087 1745 1 chr1B.!!$R1 658

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
972 2884 0.030603 GAGTCCATCCCCTCCTCCTT 60.031 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 4780 0.033504 CCTACCAACGGAGCGCATAT 59.966 55.0 11.47 0.0 0.0 1.78 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
22 23 5.324832 TCCCATCACTTTCTTCCTTCTTT 57.675 39.130 0.00 0.00 0.00 2.52
23 24 5.072741 TCCCATCACTTTCTTCCTTCTTTG 58.927 41.667 0.00 0.00 0.00 2.77
25 26 5.072741 CCATCACTTTCTTCCTTCTTTGGA 58.927 41.667 0.00 0.00 0.00 3.53
46 47 5.758296 TGGACACACTTTTCAAGTAGATGAC 59.242 40.000 0.00 0.00 40.46 3.06
76 77 1.475280 CATGACCATGCAGACCTTTGG 59.525 52.381 0.11 0.11 35.31 3.28
79 80 0.773644 ACCATGCAGACCTTTGGAGT 59.226 50.000 8.74 0.00 33.36 3.85
102 105 3.577848 CCCACCATCCATTCTCAACAAAA 59.422 43.478 0.00 0.00 0.00 2.44
185 188 4.749245 ACTCAAAGTTAAGGTTGCATCG 57.251 40.909 0.00 0.00 0.00 3.84
191 194 3.681593 AGTTAAGGTTGCATCGGCTAAA 58.318 40.909 0.00 0.00 41.91 1.85
201 204 2.682856 GCATCGGCTAAAGACATCCAAA 59.317 45.455 0.00 0.00 36.96 3.28
214 217 8.712285 AAAGACATCCAAATCATGCATAAAAG 57.288 30.769 0.00 0.00 0.00 2.27
216 219 8.070034 AGACATCCAAATCATGCATAAAAGAA 57.930 30.769 0.00 0.00 0.00 2.52
221 224 8.765488 TCCAAATCATGCATAAAAGAAGGATA 57.235 30.769 0.00 0.00 0.00 2.59
222 225 9.370930 TCCAAATCATGCATAAAAGAAGGATAT 57.629 29.630 0.00 0.00 0.00 1.63
277 280 8.526147 TGTCGTAGAACCTAGCTTACTAAAATT 58.474 33.333 0.00 0.00 39.69 1.82
287 290 9.237846 CCTAGCTTACTAAAATTATTGCTTTGC 57.762 33.333 0.00 0.00 0.00 3.68
294 297 8.895932 ACTAAAATTATTGCTTTGCTTACTCG 57.104 30.769 0.00 0.00 0.00 4.18
296 299 4.963276 ATTATTGCTTTGCTTACTCGCA 57.037 36.364 0.00 0.00 38.31 5.10
340 343 1.623973 GCACCCGTCGTTAAGAGTGC 61.624 60.000 0.00 0.00 39.98 4.40
353 356 5.572126 CGTTAAGAGTGCTGTTACTAGGAAC 59.428 44.000 11.20 11.20 0.00 3.62
359 362 4.161754 AGTGCTGTTACTAGGAACCATACC 59.838 45.833 15.42 0.03 0.00 2.73
464 467 0.970640 TTTGTGCATCTGCCAGCAAT 59.029 45.000 0.00 0.00 43.20 3.56
465 468 0.970640 TTGTGCATCTGCCAGCAATT 59.029 45.000 0.00 0.00 43.20 2.32
466 469 1.836802 TGTGCATCTGCCAGCAATTA 58.163 45.000 0.00 0.00 43.20 1.40
467 470 1.746787 TGTGCATCTGCCAGCAATTAG 59.253 47.619 0.00 0.00 43.20 1.73
480 483 4.989279 AGCAATTAGGCTGGTTGTAATG 57.011 40.909 13.04 0.00 43.89 1.90
481 484 3.701040 AGCAATTAGGCTGGTTGTAATGG 59.299 43.478 13.04 0.00 43.89 3.16
483 486 4.642885 GCAATTAGGCTGGTTGTAATGGTA 59.357 41.667 13.04 0.00 0.00 3.25
484 487 5.221048 GCAATTAGGCTGGTTGTAATGGTAG 60.221 44.000 13.04 0.00 0.00 3.18
485 488 5.710409 ATTAGGCTGGTTGTAATGGTAGT 57.290 39.130 0.00 0.00 0.00 2.73
486 489 6.818281 ATTAGGCTGGTTGTAATGGTAGTA 57.182 37.500 0.00 0.00 0.00 1.82
487 490 6.818281 TTAGGCTGGTTGTAATGGTAGTAT 57.182 37.500 0.00 0.00 0.00 2.12
488 491 5.291905 AGGCTGGTTGTAATGGTAGTATC 57.708 43.478 0.00 0.00 0.00 2.24
489 492 4.719773 AGGCTGGTTGTAATGGTAGTATCA 59.280 41.667 0.00 0.00 0.00 2.15
491 494 6.557253 AGGCTGGTTGTAATGGTAGTATCATA 59.443 38.462 0.00 0.00 0.00 2.15
492 495 6.874134 GGCTGGTTGTAATGGTAGTATCATAG 59.126 42.308 0.00 0.00 0.00 2.23
493 496 7.442656 GCTGGTTGTAATGGTAGTATCATAGT 58.557 38.462 0.00 0.00 0.00 2.12
494 497 7.931948 GCTGGTTGTAATGGTAGTATCATAGTT 59.068 37.037 0.00 0.00 0.00 2.24
531 534 7.440523 GTCAACTAGACAATTTTGATGAGGT 57.559 36.000 0.00 0.00 46.77 3.85
532 535 7.301054 GTCAACTAGACAATTTTGATGAGGTG 58.699 38.462 0.00 0.62 46.77 4.00
533 536 6.998074 TCAACTAGACAATTTTGATGAGGTGT 59.002 34.615 0.00 0.00 0.00 4.16
534 537 7.173218 TCAACTAGACAATTTTGATGAGGTGTC 59.827 37.037 0.00 0.00 36.48 3.67
535 538 6.533730 ACTAGACAATTTTGATGAGGTGTCA 58.466 36.000 0.00 0.00 38.24 3.58
536 539 7.170965 ACTAGACAATTTTGATGAGGTGTCAT 58.829 34.615 0.00 0.00 46.75 3.06
537 540 8.321353 ACTAGACAATTTTGATGAGGTGTCATA 58.679 33.333 0.00 0.00 43.92 2.15
538 541 7.621428 AGACAATTTTGATGAGGTGTCATAG 57.379 36.000 4.60 0.00 43.92 2.23
539 542 7.397221 AGACAATTTTGATGAGGTGTCATAGA 58.603 34.615 4.60 0.00 43.92 1.98
540 543 7.884877 AGACAATTTTGATGAGGTGTCATAGAA 59.115 33.333 4.60 0.00 43.92 2.10
541 544 8.585471 ACAATTTTGATGAGGTGTCATAGAAT 57.415 30.769 0.00 0.00 43.92 2.40
542 545 9.028284 ACAATTTTGATGAGGTGTCATAGAATT 57.972 29.630 0.00 0.00 43.92 2.17
552 555 9.958180 TGAGGTGTCATAGAATTAAATGAAGAA 57.042 29.630 4.25 0.00 34.06 2.52
567 570 7.684937 AAATGAAGAAAGAGAGGATTGAGTG 57.315 36.000 0.00 0.00 0.00 3.51
568 571 5.815233 TGAAGAAAGAGAGGATTGAGTGT 57.185 39.130 0.00 0.00 0.00 3.55
569 572 5.788450 TGAAGAAAGAGAGGATTGAGTGTC 58.212 41.667 0.00 0.00 0.00 3.67
570 573 5.305386 TGAAGAAAGAGAGGATTGAGTGTCA 59.695 40.000 0.00 0.00 0.00 3.58
571 574 6.013898 TGAAGAAAGAGAGGATTGAGTGTCAT 60.014 38.462 0.00 0.00 0.00 3.06
572 575 7.179160 TGAAGAAAGAGAGGATTGAGTGTCATA 59.821 37.037 0.00 0.00 0.00 2.15
574 577 7.725251 AGAAAGAGAGGATTGAGTGTCATATC 58.275 38.462 0.00 0.00 0.00 1.63
576 579 7.615039 AAGAGAGGATTGAGTGTCATATCAT 57.385 36.000 0.00 0.00 0.00 2.45
578 581 6.781507 AGAGAGGATTGAGTGTCATATCATGA 59.218 38.462 0.00 0.00 36.84 3.07
579 582 7.455323 AGAGAGGATTGAGTGTCATATCATGAT 59.545 37.037 13.81 13.81 42.04 2.45
580 583 8.661752 AGAGGATTGAGTGTCATATCATGATA 57.338 34.615 17.56 17.56 42.04 2.15
601 604 8.196802 TGATACCGTATCATAATAAATGCTGC 57.803 34.615 15.89 0.00 40.09 5.25
602 605 5.530519 ACCGTATCATAATAAATGCTGCG 57.469 39.130 0.00 0.00 0.00 5.18
603 606 4.994852 ACCGTATCATAATAAATGCTGCGT 59.005 37.500 0.00 0.00 0.00 5.24
604 607 5.120208 ACCGTATCATAATAAATGCTGCGTC 59.880 40.000 0.00 0.00 0.00 5.19
606 609 6.183360 CCGTATCATAATAAATGCTGCGTCAT 60.183 38.462 0.00 0.00 0.00 3.06
607 610 6.679919 CGTATCATAATAAATGCTGCGTCATG 59.320 38.462 0.00 0.00 0.00 3.07
618 621 3.942796 GCGTCATGCATGGCAATAA 57.057 47.368 29.36 5.74 43.62 1.40
621 624 3.899734 GCGTCATGCATGGCAATAAATA 58.100 40.909 29.36 3.43 43.62 1.40
622 625 4.297510 GCGTCATGCATGGCAATAAATAA 58.702 39.130 29.36 2.67 43.62 1.40
625 628 5.978919 CGTCATGCATGGCAATAAATAAAGT 59.021 36.000 29.36 0.00 43.62 2.66
626 629 7.138081 CGTCATGCATGGCAATAAATAAAGTA 58.862 34.615 29.36 0.78 43.62 2.24
627 630 7.809331 CGTCATGCATGGCAATAAATAAAGTAT 59.191 33.333 29.36 0.00 43.62 2.12
726 729 9.707957 AATTTATGATACTTCCCATTACAACCA 57.292 29.630 0.00 0.00 0.00 3.67
727 730 8.746052 TTTATGATACTTCCCATTACAACCAG 57.254 34.615 0.00 0.00 0.00 4.00
728 731 4.523083 TGATACTTCCCATTACAACCAGC 58.477 43.478 0.00 0.00 0.00 4.85
729 732 2.215942 ACTTCCCATTACAACCAGCC 57.784 50.000 0.00 0.00 0.00 4.85
927 2839 2.254152 ACAGGAGTAGGGAAGCATCA 57.746 50.000 0.00 0.00 0.00 3.07
947 2859 0.179100 CCCACATCATTCGACGAGCT 60.179 55.000 0.00 0.00 0.00 4.09
972 2884 0.030603 GAGTCCATCCCCTCCTCCTT 60.031 60.000 0.00 0.00 0.00 3.36
985 2897 1.308326 CTCCTTCGTCTCCCCCTCT 59.692 63.158 0.00 0.00 0.00 3.69
1137 3065 2.258591 GACGGCAGCGAGAAGACA 59.741 61.111 0.00 0.00 0.00 3.41
1422 3435 3.984193 ATGCGGAGGAAGCTGTGGC 62.984 63.158 0.00 0.00 39.06 5.01
1746 3776 1.376543 CAAGCAGCGGATCATGTCTT 58.623 50.000 0.00 0.00 0.00 3.01
1774 3822 5.301551 AGGTACTGATGATGAGTGACTGATC 59.698 44.000 5.04 5.04 37.18 2.92
1775 3823 4.304537 ACTGATGATGAGTGACTGATCG 57.695 45.455 7.51 0.00 26.81 3.69
1777 3825 4.036616 ACTGATGATGAGTGACTGATCGAG 59.963 45.833 7.51 5.93 26.81 4.04
1778 3826 3.950395 TGATGATGAGTGACTGATCGAGT 59.050 43.478 7.51 0.00 37.76 4.18
1779 3827 3.772060 TGATGAGTGACTGATCGAGTG 57.228 47.619 7.51 0.00 33.83 3.51
1780 3828 2.159324 TGATGAGTGACTGATCGAGTGC 60.159 50.000 7.51 0.00 33.83 4.40
1782 3830 0.169230 GAGTGACTGATCGAGTGCGT 59.831 55.000 0.00 0.00 38.98 5.24
1790 3846 1.325640 TGATCGAGTGCGTACGTAGAC 59.674 52.381 17.90 11.18 38.98 2.59
1792 3848 2.278026 TCGAGTGCGTACGTAGACTA 57.722 50.000 17.90 0.48 38.98 2.59
1796 3852 1.004185 AGTGCGTACGTAGACTATGCG 60.004 52.381 17.90 0.00 43.38 4.73
1809 3865 7.384124 CGTAGACTATGCGTGAATAATTATGC 58.616 38.462 0.00 0.00 31.68 3.14
1810 3866 7.273598 CGTAGACTATGCGTGAATAATTATGCT 59.726 37.037 5.03 0.00 31.68 3.79
1811 3867 9.569167 GTAGACTATGCGTGAATAATTATGCTA 57.431 33.333 5.03 0.00 0.00 3.49
1847 4050 3.632145 CCCTGCCCTATGTGTGAATTTAC 59.368 47.826 0.00 0.00 0.00 2.01
1854 4057 6.037172 GCCCTATGTGTGAATTTACTAGTGTG 59.963 42.308 5.39 0.00 0.00 3.82
1859 4062 4.452455 GTGTGAATTTACTAGTGTGCTGCT 59.548 41.667 5.39 0.00 0.00 4.24
1860 4063 5.637810 GTGTGAATTTACTAGTGTGCTGCTA 59.362 40.000 5.39 0.00 0.00 3.49
1861 4064 5.869344 TGTGAATTTACTAGTGTGCTGCTAG 59.131 40.000 5.39 7.78 41.11 3.42
1863 4066 7.033791 GTGAATTTACTAGTGTGCTGCTAGTA 58.966 38.462 5.39 14.25 44.98 1.82
1865 4068 4.634184 TTACTAGTGTGCTGCTAGTAGC 57.366 45.455 24.26 24.26 46.39 3.58
1866 4069 1.751924 ACTAGTGTGCTGCTAGTAGCC 59.248 52.381 27.20 19.07 44.98 3.93
1868 4071 2.145397 AGTGTGCTGCTAGTAGCCTA 57.855 50.000 27.20 14.83 41.51 3.93
1869 4072 2.028130 AGTGTGCTGCTAGTAGCCTAG 58.972 52.381 27.20 11.90 41.51 3.02
1870 4073 1.751924 GTGTGCTGCTAGTAGCCTAGT 59.248 52.381 27.20 0.00 41.51 2.57
1871 4074 2.950309 GTGTGCTGCTAGTAGCCTAGTA 59.050 50.000 27.20 7.96 41.51 1.82
1872 4075 2.950309 TGTGCTGCTAGTAGCCTAGTAC 59.050 50.000 27.20 18.89 41.51 2.73
1875 4078 2.293955 GCTGCTAGTAGCCTAGTACACC 59.706 54.545 21.02 0.00 41.51 4.16
1876 4079 2.548904 CTGCTAGTAGCCTAGTACACCG 59.451 54.545 19.41 0.00 41.51 4.94
1877 4080 2.092753 TGCTAGTAGCCTAGTACACCGT 60.093 50.000 19.41 0.00 41.51 4.83
1878 4081 3.134623 TGCTAGTAGCCTAGTACACCGTA 59.865 47.826 19.41 0.00 41.51 4.02
1879 4082 3.496507 GCTAGTAGCCTAGTACACCGTAC 59.503 52.174 11.33 0.00 42.35 3.67
1880 4083 3.922171 AGTAGCCTAGTACACCGTACT 57.078 47.619 11.28 11.28 0.00 2.73
1881 4084 3.539604 AGTAGCCTAGTACACCGTACTG 58.460 50.000 15.37 6.83 0.00 2.74
1882 4085 1.101331 AGCCTAGTACACCGTACTGC 58.899 55.000 15.37 11.42 0.00 4.40
1883 4086 0.101939 GCCTAGTACACCGTACTGCC 59.898 60.000 15.37 2.19 0.00 4.85
1884 4087 0.743097 CCTAGTACACCGTACTGCCC 59.257 60.000 15.37 0.00 0.00 5.36
1885 4088 1.684248 CCTAGTACACCGTACTGCCCT 60.684 57.143 15.37 0.00 0.00 5.19
1886 4089 2.421952 CCTAGTACACCGTACTGCCCTA 60.422 54.545 15.37 0.00 0.00 3.53
1887 4090 2.449137 AGTACACCGTACTGCCCTAT 57.551 50.000 6.02 0.00 0.00 2.57
1888 4091 3.582998 AGTACACCGTACTGCCCTATA 57.417 47.619 6.02 0.00 0.00 1.31
1889 4092 4.109877 AGTACACCGTACTGCCCTATAT 57.890 45.455 6.02 0.00 0.00 0.86
1890 4093 5.246981 AGTACACCGTACTGCCCTATATA 57.753 43.478 6.02 0.00 0.00 0.86
1891 4094 5.824421 AGTACACCGTACTGCCCTATATAT 58.176 41.667 6.02 0.00 0.00 0.86
1892 4095 5.651139 AGTACACCGTACTGCCCTATATATG 59.349 44.000 6.02 0.00 0.00 1.78
1893 4096 4.413760 ACACCGTACTGCCCTATATATGT 58.586 43.478 0.00 0.00 0.00 2.29
1894 4097 4.219944 ACACCGTACTGCCCTATATATGTG 59.780 45.833 0.00 0.00 0.00 3.21
1901 4104 7.602644 CGTACTGCCCTATATATGTGTGAATTT 59.397 37.037 0.00 0.00 0.00 1.82
1916 4119 5.399301 GTGTGAATTTTGGTCGTCTTTGATG 59.601 40.000 0.00 0.00 0.00 3.07
1928 4131 6.237861 GGTCGTCTTTGATGCAGTAGTATTTC 60.238 42.308 0.00 0.00 0.00 2.17
1929 4132 5.810587 TCGTCTTTGATGCAGTAGTATTTCC 59.189 40.000 0.00 0.00 0.00 3.13
1930 4133 5.812642 CGTCTTTGATGCAGTAGTATTTCCT 59.187 40.000 0.00 0.00 0.00 3.36
1933 4136 7.010923 GTCTTTGATGCAGTAGTATTTCCTCTG 59.989 40.741 0.00 0.00 0.00 3.35
1935 4138 7.418337 TTGATGCAGTAGTATTTCCTCTGTA 57.582 36.000 0.00 0.00 0.00 2.74
1995 4204 5.527582 AGCTTCCGTATAATTGATGTTGGTC 59.472 40.000 0.00 0.00 0.00 4.02
1999 4208 6.645306 TCCGTATAATTGATGTTGGTCAGAA 58.355 36.000 0.00 0.00 0.00 3.02
2010 4219 2.174363 TGGTCAGAATGTCACTGCAG 57.826 50.000 13.48 13.48 37.40 4.41
2083 4298 1.303091 AAACCGCTGGCGTAATCCAC 61.303 55.000 13.84 0.00 37.81 4.02
2104 4356 2.305927 CTGGAGATTGTTGGGGTACAGT 59.694 50.000 0.00 0.00 0.00 3.55
2170 4426 7.756722 AGAATAATTTCAGTTATGCTTGTGTGC 59.243 33.333 0.00 0.00 34.08 4.57
2218 4480 8.097038 TGCATAATTAGCTTATCTTGGGTCTAG 58.903 37.037 0.00 0.00 0.00 2.43
2219 4481 7.065204 GCATAATTAGCTTATCTTGGGTCTAGC 59.935 40.741 0.00 0.00 0.00 3.42
2220 4482 6.755542 AATTAGCTTATCTTGGGTCTAGCT 57.244 37.500 0.00 0.00 41.44 3.32
2221 4483 7.857404 AATTAGCTTATCTTGGGTCTAGCTA 57.143 36.000 0.00 0.00 39.48 3.32
2225 4487 6.764379 AGCTTATCTTGGGTCTAGCTAATTC 58.236 40.000 0.00 0.00 37.21 2.17
2244 4506 7.275560 GCTAATTCATGTTGGTGAAATTGGTAC 59.724 37.037 0.00 0.00 41.09 3.34
2249 4511 3.067461 TGTTGGTGAAATTGGTACTGCAC 59.933 43.478 0.00 0.00 0.00 4.57
2257 4519 8.466798 GGTGAAATTGGTACTGCACTTTATATT 58.533 33.333 0.00 0.00 0.00 1.28
2258 4520 9.289303 GTGAAATTGGTACTGCACTTTATATTG 57.711 33.333 0.00 0.00 0.00 1.90
2284 4546 4.114073 CACACATGCATGTTGTTTCAACT 58.886 39.130 29.48 1.09 39.39 3.16
2287 4549 5.978919 ACACATGCATGTTGTTTCAACTTAG 59.021 36.000 29.48 15.31 39.39 2.18
2297 4559 7.114095 TGTTGTTTCAACTTAGGTTCCTAGTT 58.886 34.615 12.66 4.04 32.73 2.24
2305 4567 7.497909 TCAACTTAGGTTCCTAGTTTCAACTTG 59.502 37.037 0.00 0.00 35.60 3.16
2316 4578 2.975410 TTCAACTTGCTTGCTGATCG 57.025 45.000 0.00 0.00 0.00 3.69
2335 4597 4.585955 TCGAGCAGTTTTCTAGAGTTGT 57.414 40.909 0.00 0.00 0.00 3.32
2432 4695 5.644644 GATGACAATTGGAAGTGGTTCATC 58.355 41.667 10.83 12.01 32.96 2.92
2475 4738 7.455641 AGTATTCTTCGTTCGGATCTATGAT 57.544 36.000 0.00 0.00 0.00 2.45
2481 4744 3.889538 TCGTTCGGATCTATGATCTGGTT 59.110 43.478 14.20 0.00 0.00 3.67
2517 4780 4.256920 GCTATTTCCTCTTGAAGTGCTCA 58.743 43.478 0.00 0.00 33.63 4.26
2553 4816 2.665603 GAGCTTCTCCCGCACCTT 59.334 61.111 0.00 0.00 0.00 3.50
2651 4914 4.203226 TGTGAATAGTGTTCTGGCAAACA 58.797 39.130 9.98 9.98 36.82 2.83
2874 5147 8.481314 AGTACTACTTAATTACTTACCTTGGGC 58.519 37.037 0.00 0.00 0.00 5.36
2877 5150 1.758936 AATTACTTACCTTGGGCCGC 58.241 50.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.219288 CCAAAGAAGGAAGAAAGTGATGGG 59.781 45.833 0.00 0.00 0.00 4.00
2 3 5.048434 GTCCAAAGAAGGAAGAAAGTGATGG 60.048 44.000 0.00 0.00 39.92 3.51
3 4 5.532406 TGTCCAAAGAAGGAAGAAAGTGATG 59.468 40.000 0.00 0.00 39.92 3.07
4 5 5.532779 GTGTCCAAAGAAGGAAGAAAGTGAT 59.467 40.000 0.00 0.00 39.92 3.06
6 7 4.640201 TGTGTCCAAAGAAGGAAGAAAGTG 59.360 41.667 0.00 0.00 39.92 3.16
7 8 4.640647 GTGTGTCCAAAGAAGGAAGAAAGT 59.359 41.667 0.00 0.00 39.92 2.66
8 9 4.884164 AGTGTGTCCAAAGAAGGAAGAAAG 59.116 41.667 0.00 0.00 39.92 2.62
9 10 4.855340 AGTGTGTCCAAAGAAGGAAGAAA 58.145 39.130 0.00 0.00 39.92 2.52
11 12 4.503714 AAGTGTGTCCAAAGAAGGAAGA 57.496 40.909 0.00 0.00 39.92 2.87
12 13 5.125417 TGAAAAGTGTGTCCAAAGAAGGAAG 59.875 40.000 0.00 0.00 39.92 3.46
14 15 4.594970 TGAAAAGTGTGTCCAAAGAAGGA 58.405 39.130 0.00 0.00 34.64 3.36
15 16 4.981806 TGAAAAGTGTGTCCAAAGAAGG 57.018 40.909 0.00 0.00 0.00 3.46
65 66 0.606673 GTGGGACTCCAAAGGTCTGC 60.607 60.000 0.00 0.00 46.04 4.26
66 67 0.036875 GGTGGGACTCCAAAGGTCTG 59.963 60.000 0.00 0.00 46.04 3.51
76 77 1.839994 TGAGAATGGATGGTGGGACTC 59.160 52.381 0.00 0.00 0.00 3.36
79 80 1.991813 TGTTGAGAATGGATGGTGGGA 59.008 47.619 0.00 0.00 0.00 4.37
115 118 3.947834 GGGTTTTCCACGAGATCATTCAT 59.052 43.478 0.00 0.00 42.91 2.57
116 119 3.244735 TGGGTTTTCCACGAGATCATTCA 60.245 43.478 0.00 0.00 41.46 2.57
126 129 1.234615 ATGACGCTGGGTTTTCCACG 61.235 55.000 0.00 0.00 41.46 4.94
127 130 0.240945 CATGACGCTGGGTTTTCCAC 59.759 55.000 0.00 0.00 41.46 4.02
168 171 2.514803 AGCCGATGCAACCTTAACTTT 58.485 42.857 0.00 0.00 41.13 2.66
185 188 4.098349 TGCATGATTTGGATGTCTTTAGCC 59.902 41.667 0.00 0.00 0.00 3.93
191 194 7.649533 TCTTTTATGCATGATTTGGATGTCT 57.350 32.000 10.16 0.00 36.96 3.41
221 224 9.703892 TGACCGAATCATTTCATTGTTTTTAAT 57.296 25.926 0.00 0.00 29.99 1.40
222 225 9.534565 TTGACCGAATCATTTCATTGTTTTTAA 57.465 25.926 0.00 0.00 37.11 1.52
298 301 6.148948 GCCAAAGCAAACTCTTTTTGTTTTT 58.851 32.000 8.33 3.42 39.59 1.94
300 303 5.295431 GCCAAAGCAAACTCTTTTTGTTT 57.705 34.783 0.00 0.00 39.53 2.83
315 318 1.508808 TTAACGACGGGTGCCAAAGC 61.509 55.000 0.00 0.00 40.48 3.51
316 319 0.515564 CTTAACGACGGGTGCCAAAG 59.484 55.000 0.00 0.00 0.00 2.77
318 321 0.320073 CTCTTAACGACGGGTGCCAA 60.320 55.000 0.00 0.00 0.00 4.52
340 343 5.934402 ACTGGTATGGTTCCTAGTAACAG 57.066 43.478 0.28 0.43 37.76 3.16
353 356 3.427503 GCGGTCATTTTCAACTGGTATGG 60.428 47.826 0.00 0.00 0.00 2.74
359 362 1.059657 CGCGCGGTCATTTTCAACTG 61.060 55.000 24.84 0.00 0.00 3.16
410 413 0.109458 CAGCACACACATGACATGCC 60.109 55.000 15.49 0.00 36.96 4.40
441 444 1.269936 GCTGGCAGATGCACAAAAGTT 60.270 47.619 20.86 0.00 44.36 2.66
443 446 0.315886 TGCTGGCAGATGCACAAAAG 59.684 50.000 20.86 0.00 44.36 2.27
464 467 6.384595 TGATACTACCATTACAACCAGCCTAA 59.615 38.462 0.00 0.00 0.00 2.69
465 468 5.900699 TGATACTACCATTACAACCAGCCTA 59.099 40.000 0.00 0.00 0.00 3.93
466 469 4.719773 TGATACTACCATTACAACCAGCCT 59.280 41.667 0.00 0.00 0.00 4.58
467 470 5.031066 TGATACTACCATTACAACCAGCC 57.969 43.478 0.00 0.00 0.00 4.85
491 494 9.751542 GTCTAGTTGACATGCATAATACTAACT 57.248 33.333 0.00 7.41 44.73 2.24
507 510 7.041098 ACACCTCATCAAAATTGTCTAGTTGAC 60.041 37.037 0.00 0.00 45.54 3.18
508 511 6.998074 ACACCTCATCAAAATTGTCTAGTTGA 59.002 34.615 0.00 0.00 34.68 3.18
509 512 7.041167 TGACACCTCATCAAAATTGTCTAGTTG 60.041 37.037 0.00 0.00 35.45 3.16
510 513 6.998074 TGACACCTCATCAAAATTGTCTAGTT 59.002 34.615 0.00 0.00 35.45 2.24
511 514 6.533730 TGACACCTCATCAAAATTGTCTAGT 58.466 36.000 0.00 0.00 35.45 2.57
513 516 8.539544 TCTATGACACCTCATCAAAATTGTCTA 58.460 33.333 0.00 0.00 38.21 2.59
514 517 7.397221 TCTATGACACCTCATCAAAATTGTCT 58.603 34.615 0.00 0.00 38.21 3.41
515 518 7.615582 TCTATGACACCTCATCAAAATTGTC 57.384 36.000 0.00 0.00 38.21 3.18
516 519 8.585471 ATTCTATGACACCTCATCAAAATTGT 57.415 30.769 0.00 0.00 38.21 2.71
522 525 9.904198 TCATTTAATTCTATGACACCTCATCAA 57.096 29.630 0.00 0.00 38.21 2.57
523 526 9.904198 TTCATTTAATTCTATGACACCTCATCA 57.096 29.630 2.75 0.00 38.21 3.07
526 529 9.958180 TTCTTCATTTAATTCTATGACACCTCA 57.042 29.630 2.75 0.00 30.89 3.86
540 543 9.972106 ACTCAATCCTCTCTTTCTTCATTTAAT 57.028 29.630 0.00 0.00 0.00 1.40
541 544 9.224267 CACTCAATCCTCTCTTTCTTCATTTAA 57.776 33.333 0.00 0.00 0.00 1.52
542 545 8.378565 ACACTCAATCCTCTCTTTCTTCATTTA 58.621 33.333 0.00 0.00 0.00 1.40
543 546 7.230027 ACACTCAATCCTCTCTTTCTTCATTT 58.770 34.615 0.00 0.00 0.00 2.32
544 547 6.777782 ACACTCAATCCTCTCTTTCTTCATT 58.222 36.000 0.00 0.00 0.00 2.57
545 548 6.013898 TGACACTCAATCCTCTCTTTCTTCAT 60.014 38.462 0.00 0.00 0.00 2.57
546 549 5.305386 TGACACTCAATCCTCTCTTTCTTCA 59.695 40.000 0.00 0.00 0.00 3.02
547 550 5.788450 TGACACTCAATCCTCTCTTTCTTC 58.212 41.667 0.00 0.00 0.00 2.87
550 553 7.495901 TGATATGACACTCAATCCTCTCTTTC 58.504 38.462 0.00 0.00 0.00 2.62
552 555 7.289549 TCATGATATGACACTCAATCCTCTCTT 59.710 37.037 0.00 0.00 33.59 2.85
553 556 6.781507 TCATGATATGACACTCAATCCTCTCT 59.218 38.462 0.00 0.00 33.59 3.10
554 557 6.990798 TCATGATATGACACTCAATCCTCTC 58.009 40.000 0.00 0.00 33.59 3.20
555 558 6.990908 TCATGATATGACACTCAATCCTCT 57.009 37.500 0.00 0.00 33.59 3.69
556 559 7.763528 GGTATCATGATATGACACTCAATCCTC 59.236 40.741 18.18 0.24 43.01 3.71
557 560 7.578380 CGGTATCATGATATGACACTCAATCCT 60.578 40.741 18.18 0.00 43.01 3.24
559 562 7.093354 ACGGTATCATGATATGACACTCAATC 58.907 38.462 18.18 1.44 43.01 2.67
562 565 7.393234 TGATACGGTATCATGATATGACACTCA 59.607 37.037 23.35 13.40 43.01 3.41
563 566 7.762382 TGATACGGTATCATGATATGACACTC 58.238 38.462 23.35 11.37 43.01 3.51
564 567 7.703058 TGATACGGTATCATGATATGACACT 57.297 36.000 23.35 3.07 43.01 3.55
578 581 6.816640 ACGCAGCATTTATTATGATACGGTAT 59.183 34.615 0.00 0.00 0.00 2.73
579 582 6.160684 ACGCAGCATTTATTATGATACGGTA 58.839 36.000 0.00 0.00 0.00 4.02
580 583 4.994852 ACGCAGCATTTATTATGATACGGT 59.005 37.500 0.00 0.00 0.00 4.83
582 585 6.151975 TGACGCAGCATTTATTATGATACG 57.848 37.500 0.00 0.00 0.00 3.06
583 586 6.467047 GCATGACGCAGCATTTATTATGATAC 59.533 38.462 0.00 0.00 41.79 2.24
584 587 6.545508 GCATGACGCAGCATTTATTATGATA 58.454 36.000 0.00 0.00 41.79 2.15
585 588 5.396484 GCATGACGCAGCATTTATTATGAT 58.604 37.500 0.00 0.00 41.79 2.45
600 603 2.206815 TTTATTGCCATGCATGACGC 57.793 45.000 28.31 22.48 38.76 5.19
601 604 5.978919 ACTTTATTTATTGCCATGCATGACG 59.021 36.000 28.31 13.23 38.76 4.35
602 605 9.480053 AATACTTTATTTATTGCCATGCATGAC 57.520 29.630 28.31 17.77 38.76 3.06
700 703 9.707957 TGGTTGTAATGGGAAGTATCATAAATT 57.292 29.630 0.00 0.00 0.00 1.82
701 704 9.354673 CTGGTTGTAATGGGAAGTATCATAAAT 57.645 33.333 0.00 0.00 0.00 1.40
702 705 7.284489 GCTGGTTGTAATGGGAAGTATCATAAA 59.716 37.037 0.00 0.00 0.00 1.40
703 706 6.770785 GCTGGTTGTAATGGGAAGTATCATAA 59.229 38.462 0.00 0.00 0.00 1.90
704 707 6.296026 GCTGGTTGTAATGGGAAGTATCATA 58.704 40.000 0.00 0.00 0.00 2.15
708 711 3.527665 AGGCTGGTTGTAATGGGAAGTAT 59.472 43.478 0.00 0.00 0.00 2.12
709 712 2.916934 AGGCTGGTTGTAATGGGAAGTA 59.083 45.455 0.00 0.00 0.00 2.24
710 713 1.710809 AGGCTGGTTGTAATGGGAAGT 59.289 47.619 0.00 0.00 0.00 3.01
711 714 2.514458 AGGCTGGTTGTAATGGGAAG 57.486 50.000 0.00 0.00 0.00 3.46
713 716 3.876156 GCTTAAGGCTGGTTGTAATGGGA 60.876 47.826 4.29 0.00 38.06 4.37
715 718 3.088532 TGCTTAAGGCTGGTTGTAATGG 58.911 45.455 4.29 0.00 42.39 3.16
716 719 4.202050 GGATGCTTAAGGCTGGTTGTAATG 60.202 45.833 4.29 0.00 42.39 1.90
717 720 3.954258 GGATGCTTAAGGCTGGTTGTAAT 59.046 43.478 4.29 0.00 42.39 1.89
718 721 3.352648 GGATGCTTAAGGCTGGTTGTAA 58.647 45.455 4.29 0.00 42.39 2.41
719 722 2.356741 GGGATGCTTAAGGCTGGTTGTA 60.357 50.000 4.29 0.00 42.39 2.41
721 724 1.106285 GGGATGCTTAAGGCTGGTTG 58.894 55.000 4.29 0.00 42.39 3.77
722 725 0.704076 TGGGATGCTTAAGGCTGGTT 59.296 50.000 4.29 0.00 42.39 3.67
724 727 1.684983 CAATGGGATGCTTAAGGCTGG 59.315 52.381 4.29 0.00 42.39 4.85
725 728 1.068127 GCAATGGGATGCTTAAGGCTG 59.932 52.381 4.29 0.00 43.06 4.85
726 729 1.342275 TGCAATGGGATGCTTAAGGCT 60.342 47.619 4.29 0.00 46.54 4.58
727 730 1.113788 TGCAATGGGATGCTTAAGGC 58.886 50.000 4.29 0.00 46.54 4.35
728 731 3.724374 CAATGCAATGGGATGCTTAAGG 58.276 45.455 4.29 0.00 46.54 2.69
729 732 3.128349 GCAATGCAATGGGATGCTTAAG 58.872 45.455 3.49 0.00 46.54 1.85
927 2839 0.460284 GCTCGTCGAATGATGTGGGT 60.460 55.000 0.00 0.00 32.69 4.51
947 2859 3.399181 GGGGATGGACTCACCGCA 61.399 66.667 0.00 0.00 37.81 5.69
972 2884 1.306970 GAGGAAGAGGGGGAGACGA 59.693 63.158 0.00 0.00 0.00 4.20
985 2897 0.908180 GGAACGGGGAGAAGGAGGAA 60.908 60.000 0.00 0.00 0.00 3.36
1033 2945 6.015940 GGACAAGTGGACAAGAAAAAGATGAT 60.016 38.462 0.00 0.00 0.00 2.45
1041 2953 5.367945 AGTTAGGACAAGTGGACAAGAAA 57.632 39.130 0.00 0.00 0.00 2.52
1137 3065 0.540923 GCAGCAGATGAGGAAGAGGT 59.459 55.000 0.00 0.00 0.00 3.85
1164 3092 3.056328 GGCGTCTTCTTGGCCACC 61.056 66.667 3.88 0.00 46.13 4.61
1405 3418 4.704833 GCCACAGCTTCCTCCGCA 62.705 66.667 0.00 0.00 35.50 5.69
1706 3729 1.045911 CCTGCTCCCCAGTCCTACTC 61.046 65.000 0.00 0.00 40.06 2.59
1707 3730 1.002274 CCTGCTCCCCAGTCCTACT 59.998 63.158 0.00 0.00 40.06 2.57
1708 3731 2.066999 CCCTGCTCCCCAGTCCTAC 61.067 68.421 0.00 0.00 40.06 3.18
1746 3776 4.158579 GTCACTCATCATCAGTACCTCACA 59.841 45.833 0.00 0.00 0.00 3.58
1774 3822 2.888951 CATAGTCTACGTACGCACTCG 58.111 52.381 16.72 6.40 42.43 4.18
1775 3823 2.637595 GCATAGTCTACGTACGCACTC 58.362 52.381 16.72 4.11 0.00 3.51
1777 3825 1.267732 ACGCATAGTCTACGTACGCAC 60.268 52.381 16.72 9.80 38.45 5.34
1778 3826 1.009078 ACGCATAGTCTACGTACGCA 58.991 50.000 16.72 0.23 38.45 5.24
1779 3827 1.004610 TCACGCATAGTCTACGTACGC 60.005 52.381 16.72 0.00 38.09 4.42
1780 3828 3.308820 TTCACGCATAGTCTACGTACG 57.691 47.619 15.01 15.01 38.09 3.67
1782 3830 9.550811 CATAATTATTCACGCATAGTCTACGTA 57.449 33.333 0.00 0.00 38.09 3.57
1790 3846 7.531280 AGCTAGCATAATTATTCACGCATAG 57.469 36.000 18.83 7.46 0.00 2.23
1792 3848 7.531280 CTAGCTAGCATAATTATTCACGCAT 57.469 36.000 18.83 0.00 0.00 4.73
1809 3865 2.354072 GGCGTCGCAGCTAGCTAG 60.354 66.667 18.86 16.84 42.61 3.42
1810 3866 3.900892 GGGCGTCGCAGCTAGCTA 61.901 66.667 18.86 0.00 42.61 3.32
1825 3881 2.442236 AATTCACACATAGGGCAGGG 57.558 50.000 0.00 0.00 0.00 4.45
1826 3882 4.526970 AGTAAATTCACACATAGGGCAGG 58.473 43.478 0.00 0.00 0.00 4.85
1847 4050 2.028130 AGGCTACTAGCAGCACACTAG 58.972 52.381 16.76 6.23 44.75 2.57
1859 4062 4.697514 CAGTACGGTGTACTAGGCTACTA 58.302 47.826 9.13 0.00 0.00 1.82
1860 4063 3.539604 CAGTACGGTGTACTAGGCTACT 58.460 50.000 9.13 0.00 0.00 2.57
1861 4064 2.032675 GCAGTACGGTGTACTAGGCTAC 59.967 54.545 9.13 0.00 0.00 3.58
1862 4065 2.292267 GCAGTACGGTGTACTAGGCTA 58.708 52.381 9.13 0.00 0.00 3.93
1863 4066 1.101331 GCAGTACGGTGTACTAGGCT 58.899 55.000 9.13 0.00 0.00 4.58
1865 4068 0.743097 GGGCAGTACGGTGTACTAGG 59.257 60.000 9.13 0.57 0.00 3.02
1866 4069 1.760192 AGGGCAGTACGGTGTACTAG 58.240 55.000 9.13 5.94 0.00 2.57
1868 4071 2.449137 ATAGGGCAGTACGGTGTACT 57.551 50.000 3.85 3.85 0.00 2.73
1869 4072 5.416952 ACATATATAGGGCAGTACGGTGTAC 59.583 44.000 0.00 0.00 0.00 2.90
1870 4073 5.416639 CACATATATAGGGCAGTACGGTGTA 59.583 44.000 0.00 0.00 0.00 2.90
1871 4074 4.219944 CACATATATAGGGCAGTACGGTGT 59.780 45.833 0.00 0.00 0.00 4.16
1872 4075 4.219944 ACACATATATAGGGCAGTACGGTG 59.780 45.833 0.00 0.00 0.00 4.94
1875 4078 5.638596 TCACACATATATAGGGCAGTACG 57.361 43.478 0.00 0.00 0.00 3.67
1876 4079 8.848474 AAATTCACACATATATAGGGCAGTAC 57.152 34.615 0.00 0.00 0.00 2.73
1877 4080 9.283768 CAAAATTCACACATATATAGGGCAGTA 57.716 33.333 0.00 0.00 0.00 2.74
1878 4081 7.231317 CCAAAATTCACACATATATAGGGCAGT 59.769 37.037 0.00 0.00 0.00 4.40
1879 4082 7.231317 ACCAAAATTCACACATATATAGGGCAG 59.769 37.037 0.00 0.00 0.00 4.85
1880 4083 7.066142 ACCAAAATTCACACATATATAGGGCA 58.934 34.615 0.00 0.00 0.00 5.36
1881 4084 7.524717 ACCAAAATTCACACATATATAGGGC 57.475 36.000 0.00 0.00 0.00 5.19
1882 4085 7.444183 ACGACCAAAATTCACACATATATAGGG 59.556 37.037 0.00 0.00 0.00 3.53
1883 4086 8.378172 ACGACCAAAATTCACACATATATAGG 57.622 34.615 0.00 0.00 0.00 2.57
1884 4087 9.261180 AGACGACCAAAATTCACACATATATAG 57.739 33.333 0.00 0.00 0.00 1.31
1885 4088 9.607988 AAGACGACCAAAATTCACACATATATA 57.392 29.630 0.00 0.00 0.00 0.86
1886 4089 8.506168 AAGACGACCAAAATTCACACATATAT 57.494 30.769 0.00 0.00 0.00 0.86
1887 4090 7.915293 AAGACGACCAAAATTCACACATATA 57.085 32.000 0.00 0.00 0.00 0.86
1888 4091 6.817765 AAGACGACCAAAATTCACACATAT 57.182 33.333 0.00 0.00 0.00 1.78
1889 4092 6.261158 TCAAAGACGACCAAAATTCACACATA 59.739 34.615 0.00 0.00 0.00 2.29
1890 4093 5.067153 TCAAAGACGACCAAAATTCACACAT 59.933 36.000 0.00 0.00 0.00 3.21
1891 4094 4.396478 TCAAAGACGACCAAAATTCACACA 59.604 37.500 0.00 0.00 0.00 3.72
1892 4095 4.915704 TCAAAGACGACCAAAATTCACAC 58.084 39.130 0.00 0.00 0.00 3.82
1893 4096 5.518812 CATCAAAGACGACCAAAATTCACA 58.481 37.500 0.00 0.00 0.00 3.58
1894 4097 4.382754 GCATCAAAGACGACCAAAATTCAC 59.617 41.667 0.00 0.00 0.00 3.18
1901 4104 2.254546 ACTGCATCAAAGACGACCAA 57.745 45.000 0.00 0.00 0.00 3.67
1916 4119 8.167605 TCATACTACAGAGGAAATACTACTGC 57.832 38.462 0.00 0.00 32.67 4.40
1928 4131 6.890979 TGATGTCTGATCATACTACAGAGG 57.109 41.667 11.98 0.00 40.55 3.69
1977 4186 7.919690 ACATTCTGACCAACATCAATTATACG 58.080 34.615 0.00 0.00 0.00 3.06
1986 4195 3.120060 GCAGTGACATTCTGACCAACATC 60.120 47.826 0.00 0.00 35.20 3.06
2034 4249 9.227777 GAAAAACAGTGGTTAACATATAGGAGT 57.772 33.333 8.10 0.00 35.82 3.85
2035 4250 9.226606 TGAAAAACAGTGGTTAACATATAGGAG 57.773 33.333 8.10 0.00 35.82 3.69
2036 4251 9.747898 ATGAAAAACAGTGGTTAACATATAGGA 57.252 29.630 8.10 0.00 35.82 2.94
2037 4252 9.787532 CATGAAAAACAGTGGTTAACATATAGG 57.212 33.333 8.10 0.00 35.82 2.57
2052 4267 3.052036 CCAGCGGTTTCATGAAAAACAG 58.948 45.455 22.07 13.27 40.22 3.16
2064 4279 1.003112 TGGATTACGCCAGCGGTTT 60.003 52.632 17.33 0.00 44.69 3.27
2083 4298 2.305927 ACTGTACCCCAACAATCTCCAG 59.694 50.000 0.00 0.00 0.00 3.86
2167 4423 6.739112 TGTGAGTCACTCAGTATATATGCAC 58.261 40.000 23.29 0.00 41.46 4.57
2170 4426 7.373493 TGCATGTGAGTCACTCAGTATATATG 58.627 38.462 23.29 15.30 41.46 1.78
2180 4442 5.757320 AGCTAATTATGCATGTGAGTCACTC 59.243 40.000 23.29 12.94 35.11 3.51
2218 4480 6.165577 ACCAATTTCACCAACATGAATTAGC 58.834 36.000 0.00 0.00 38.37 3.09
2219 4481 8.522830 AGTACCAATTTCACCAACATGAATTAG 58.477 33.333 0.00 0.00 38.37 1.73
2220 4482 8.303156 CAGTACCAATTTCACCAACATGAATTA 58.697 33.333 0.00 0.00 38.37 1.40
2221 4483 7.153985 CAGTACCAATTTCACCAACATGAATT 58.846 34.615 0.00 0.00 38.37 2.17
2225 4487 4.236935 GCAGTACCAATTTCACCAACATG 58.763 43.478 0.00 0.00 0.00 3.21
2244 4506 7.588854 GCATGTGTGTATCAATATAAAGTGCAG 59.411 37.037 0.00 0.00 0.00 4.41
2249 4511 9.955208 AACATGCATGTGTGTATCAATATAAAG 57.045 29.630 31.98 0.00 41.61 1.85
2257 4519 5.009410 TGAAACAACATGCATGTGTGTATCA 59.991 36.000 31.98 25.68 41.61 2.15
2258 4520 5.459768 TGAAACAACATGCATGTGTGTATC 58.540 37.500 31.98 23.77 41.61 2.24
2284 4546 5.937111 AGCAAGTTGAAACTAGGAACCTAA 58.063 37.500 7.16 0.00 38.57 2.69
2287 4549 4.793028 GCAAGCAAGTTGAAACTAGGAACC 60.793 45.833 7.16 0.00 38.57 3.62
2297 4559 2.481568 CTCGATCAGCAAGCAAGTTGAA 59.518 45.455 7.16 0.00 38.60 2.69
2316 4578 4.632153 TCCACAACTCTAGAAAACTGCTC 58.368 43.478 0.00 0.00 0.00 4.26
2321 4583 6.072112 TGCATTTCCACAACTCTAGAAAAC 57.928 37.500 0.00 0.00 32.41 2.43
2475 4738 1.885887 CGGGATTTTTGCTCAACCAGA 59.114 47.619 0.00 0.00 0.00 3.86
2481 4744 3.130340 GGAAATAGCGGGATTTTTGCTCA 59.870 43.478 0.00 0.00 40.06 4.26
2517 4780 0.033504 CCTACCAACGGAGCGCATAT 59.966 55.000 11.47 0.00 0.00 1.78
2651 4914 7.619050 CAAATCTGATAGACAGCTATGGGTAT 58.381 38.462 0.00 0.00 45.38 2.73
2874 5147 2.723124 AAAAGCTGTATTGGTTGCGG 57.277 45.000 0.00 0.00 0.00 5.69
3051 5326 1.141053 GCCATCGTGAAGGGGATAGTT 59.859 52.381 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.