Multiple sequence alignment - TraesCS2A01G533900

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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 TraesCS2A01G533900 chr2A 100.000 5782 0 0 1 5782 749835592 749841373 0.000000e+00 10678.0
1 TraesCS2A01G533900 chr2A 100.000 1645 0 0 6465 8109 749842056 749843700 0.000000e+00 3038.0
2 TraesCS2A01G533900 chr2D 95.162 4795 134 34 702 5435 618821986 618826743 0.000000e+00 7480.0
3 TraesCS2A01G533900 chr2D 94.416 788 18 8 6777 7540 618826739 618827524 0.000000e+00 1188.0
4 TraesCS2A01G533900 chr2D 94.729 683 29 4 1 681 618819314 618819991 0.000000e+00 1055.0
5 TraesCS2A01G533900 chr2D 94.764 573 29 1 7538 8109 618827558 618828130 0.000000e+00 891.0
6 TraesCS2A01G533900 chr2D 91.100 618 55 0 4045 4662 585030990 585031607 0.000000e+00 837.0
7 TraesCS2A01G533900 chr2D 89.073 302 25 4 6465 6758 306070085 306070386 1.290000e-97 368.0
8 TraesCS2A01G533900 chr2D 88.079 302 17 8 6465 6758 626591087 626590797 2.800000e-89 340.0
9 TraesCS2A01G533900 chr2D 89.804 255 17 3 6518 6763 585717347 585717093 1.310000e-82 318.0
10 TraesCS2A01G533900 chr2D 83.117 77 7 3 7691 7767 634655119 634655049 1.890000e-06 65.8
11 TraesCS2A01G533900 chr2B 83.499 1412 100 38 2650 4048 756104219 756105510 0.000000e+00 1194.0
12 TraesCS2A01G533900 chr2B 92.335 848 31 16 6759 7603 756106370 756107186 0.000000e+00 1175.0
13 TraesCS2A01G533900 chr2B 90.551 889 37 21 4664 5514 756105500 756106379 0.000000e+00 1133.0
14 TraesCS2A01G533900 chr2B 95.428 678 22 5 864 1540 756100768 756101437 0.000000e+00 1072.0
15 TraesCS2A01G533900 chr2B 92.035 452 30 5 1 450 756092404 756092851 1.490000e-176 630.0
16 TraesCS2A01G533900 chr2B 88.636 396 21 5 1825 2219 756102193 756102565 2.060000e-125 460.0
17 TraesCS2A01G533900 chr2B 90.759 303 27 1 1531 1833 756101854 756102155 3.520000e-108 403.0
18 TraesCS2A01G533900 chr2B 92.825 223 15 1 2257 2478 756102550 756102772 1.020000e-83 322.0
19 TraesCS2A01G533900 chr2B 92.929 99 7 0 766 864 756098832 756098930 2.360000e-30 145.0
20 TraesCS2A01G533900 chr2B 96.104 77 3 0 502 578 756098344 756098420 8.540000e-25 126.0
21 TraesCS2A01G533900 chr5B 91.276 619 53 1 4045 4662 529722948 529722330 0.000000e+00 843.0
22 TraesCS2A01G533900 chr5B 90.777 618 57 0 4045 4662 662263458 662264075 0.000000e+00 826.0
23 TraesCS2A01G533900 chr5B 98.361 61 0 1 5433 5492 659095226 659095166 1.110000e-18 106.0
24 TraesCS2A01G533900 chr5B 92.188 64 3 2 5427 5489 710758561 710758623 1.120000e-13 89.8
25 TraesCS2A01G533900 chr5B 85.185 81 3 6 5434 5514 462886728 462886799 3.140000e-09 75.0
26 TraesCS2A01G533900 chr5B 96.970 33 0 1 6756 6787 600322595 600322563 4.000000e-03 54.7
27 TraesCS2A01G533900 chr3D 91.115 619 55 0 4044 4662 41275026 41275644 0.000000e+00 839.0
28 TraesCS2A01G533900 chr3D 91.100 618 54 1 4045 4662 41368753 41369369 0.000000e+00 835.0
29 TraesCS2A01G533900 chr3D 88.254 315 18 5 6465 6770 21459836 21460140 7.740000e-95 359.0
30 TraesCS2A01G533900 chr7D 90.953 619 55 1 4044 4662 242800055 242800672 0.000000e+00 832.0
31 TraesCS2A01G533900 chr7D 86.900 771 59 18 6780 7533 634592744 634591999 0.000000e+00 826.0
32 TraesCS2A01G533900 chr7D 88.285 589 42 8 862 1441 634594947 634594377 0.000000e+00 680.0
33 TraesCS2A01G533900 chr7D 90.402 448 39 4 4664 5111 634593521 634593078 3.260000e-163 586.0
34 TraesCS2A01G533900 chr7D 79.536 689 104 28 4759 5426 480902345 480901673 2.670000e-124 457.0
35 TraesCS2A01G533900 chr7D 94.677 263 13 1 5512 5773 192449994 192450256 2.720000e-109 407.0
36 TraesCS2A01G533900 chr7D 87.042 355 24 6 1874 2217 634594365 634594022 1.650000e-101 381.0
37 TraesCS2A01G533900 chr7D 90.769 260 16 1 6515 6766 192450247 192449988 2.800000e-89 340.0
38 TraesCS2A01G533900 chr7D 83.815 346 19 9 5099 5435 634593060 634592743 2.210000e-75 294.0
39 TraesCS2A01G533900 chr7D 78.920 389 51 18 1047 1415 480904317 480903940 1.360000e-57 235.0
40 TraesCS2A01G533900 chr7D 85.714 56 6 2 2220 2274 634341390 634341336 3.160000e-04 58.4
41 TraesCS2A01G533900 chr6B 90.836 622 53 1 4045 4662 333707354 333706733 0.000000e+00 830.0
42 TraesCS2A01G533900 chr6B 100.000 28 0 0 6761 6788 332420781 332420754 1.500000e-02 52.8
43 TraesCS2A01G533900 chr4D 90.590 627 56 2 4038 4662 491554199 491554824 0.000000e+00 828.0
44 TraesCS2A01G533900 chr4D 93.103 261 17 1 5513 5772 346207173 346207433 1.650000e-101 381.0
45 TraesCS2A01G533900 chr4D 92.395 263 19 1 5512 5773 46613729 46613467 2.760000e-99 374.0
46 TraesCS2A01G533900 chr4D 90.706 269 24 1 5506 5773 46605922 46606190 2.780000e-94 357.0
47 TraesCS2A01G533900 chr4D 91.235 251 14 4 6516 6758 346207424 346207174 1.300000e-87 335.0
48 TraesCS2A01G533900 chr4D 89.098 266 20 5 6510 6766 46613470 46613735 1.020000e-83 322.0
49 TraesCS2A01G533900 chr5D 90.728 302 20 4 6465 6758 384770354 384770053 5.900000e-106 396.0
50 TraesCS2A01G533900 chr5D 94.422 251 13 1 5513 5762 384770052 384770302 1.280000e-102 385.0
51 TraesCS2A01G533900 chr5D 87.748 302 19 2 6465 6758 2276975 2276684 3.630000e-88 337.0
52 TraesCS2A01G533900 chr5D 91.593 226 10 2 6544 6760 384770388 384770613 3.680000e-78 303.0
53 TraesCS2A01G533900 chr5D 88.983 236 17 3 6544 6770 9946063 9946298 4.790000e-72 283.0
54 TraesCS2A01G533900 chr5D 87.838 222 16 2 6465 6686 530418279 530418489 4.860000e-62 250.0
55 TraesCS2A01G533900 chr5D 95.082 61 3 0 5432 5492 206601349 206601289 6.700000e-16 97.1
56 TraesCS2A01G533900 chr5D 95.000 60 2 1 5434 5492 473354391 473354332 8.670000e-15 93.5
57 TraesCS2A01G533900 chr5D 100.000 28 0 0 6761 6788 384468941 384468968 1.500000e-02 52.8
58 TraesCS2A01G533900 chr1D 90.066 302 22 2 6465 6758 105132839 105132538 1.280000e-102 385.0
59 TraesCS2A01G533900 chr1D 92.490 253 18 1 5513 5764 105132537 105132789 2.150000e-95 361.0
60 TraesCS2A01G533900 chr1D 90.805 261 23 1 5514 5773 422072811 422073071 1.670000e-91 348.0
61 TraesCS2A01G533900 chr1D 88.235 255 22 4 6515 6761 422073062 422072808 1.710000e-76 298.0
62 TraesCS2A01G533900 chr1D 96.429 56 2 0 5434 5489 291791958 291792013 8.670000e-15 93.5
63 TraesCS2A01G533900 chr1D 90.196 51 3 2 2224 2274 346843390 346843342 1.890000e-06 65.8
64 TraesCS2A01G533900 chr1D 90.476 42 2 2 6748 6789 407873388 407873427 4.000000e-03 54.7
65 TraesCS2A01G533900 chr4A 91.912 272 21 1 5512 5782 721947969 721948240 5.940000e-101 379.0
66 TraesCS2A01G533900 chr4A 90.873 252 15 2 6515 6758 721948222 721947971 1.690000e-86 331.0
67 TraesCS2A01G533900 chr4A 91.304 46 3 1 2229 2274 63799859 63799903 2.440000e-05 62.1
68 TraesCS2A01G533900 chr4A 100.000 28 0 0 6761 6788 69316846 69316819 1.500000e-02 52.8
69 TraesCS2A01G533900 chr1A 91.852 270 19 2 5514 5782 543186476 543186743 2.760000e-99 374.0
70 TraesCS2A01G533900 chr1A 86.667 315 24 9 1292 1598 253305195 253305499 4.690000e-87 333.0
71 TraesCS2A01G533900 chr1A 86.093 302 23 4 6465 6758 580089170 580089460 2.840000e-79 307.0
72 TraesCS2A01G533900 chr1A 84.488 303 27 6 6465 6759 297875324 297875034 1.720000e-71 281.0
73 TraesCS2A01G533900 chr1A 76.429 420 60 22 7589 7995 255276626 255276233 2.990000e-44 191.0
74 TraesCS2A01G533900 chr3B 87.213 305 21 3 6465 6761 284567562 284567268 1.690000e-86 331.0
75 TraesCS2A01G533900 chr5A 86.774 310 23 4 6465 6766 510277685 510277386 6.070000e-86 329.0
76 TraesCS2A01G533900 chr5A 86.184 304 22 5 6465 6760 11233964 11233673 2.200000e-80 311.0
77 TraesCS2A01G533900 chr5A 83.444 151 14 7 6629 6769 11310250 11310101 6.600000e-26 130.0
78 TraesCS2A01G533900 chr7A 87.171 304 20 4 6465 6760 676423690 676423398 2.180000e-85 327.0
79 TraesCS2A01G533900 chr7A 85.032 314 30 7 1292 1598 104130182 104129879 3.680000e-78 303.0
80 TraesCS2A01G533900 chr7A 74.377 843 119 60 1056 1823 548052670 548051850 3.730000e-68 270.0
81 TraesCS2A01G533900 chr6A 86.424 302 23 3 6465 6758 603562364 603562073 1.700000e-81 315.0
82 TraesCS2A01G533900 chr7B 73.623 853 137 55 1034 1822 506563752 506562924 1.750000e-61 248.0
83 TraesCS2A01G533900 chr7B 96.721 61 2 0 5432 5492 99367491 99367431 1.440000e-17 102.0
84 TraesCS2A01G533900 chr7B 97.222 36 1 0 2229 2264 609204715 609204680 2.440000e-05 62.1
85 TraesCS2A01G533900 chr4B 96.491 57 2 0 5433 5489 201334264 201334320 2.410000e-15 95.3
86 TraesCS2A01G533900 chr1B 92.308 65 4 1 5429 5492 450463249 450463313 3.120000e-14 91.6
87 TraesCS2A01G533900 chr6D 100.000 28 0 0 6761 6788 230786340 230786313 1.500000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G533900 chr2A 749835592 749843700 8108 False 6858.0 10678 100.000000 1 8109 2 chr2A.!!$F1 8108
1 TraesCS2A01G533900 chr2D 618819314 618828130 8816 False 2653.5 7480 94.767750 1 8109 4 chr2D.!!$F3 8108
2 TraesCS2A01G533900 chr2D 585030990 585031607 617 False 837.0 837 91.100000 4045 4662 1 chr2D.!!$F2 617
3 TraesCS2A01G533900 chr2B 756098344 756107186 8842 False 670.0 1194 91.451778 502 7603 9 chr2B.!!$F2 7101
4 TraesCS2A01G533900 chr5B 529722330 529722948 618 True 843.0 843 91.276000 4045 4662 1 chr5B.!!$R1 617
5 TraesCS2A01G533900 chr5B 662263458 662264075 617 False 826.0 826 90.777000 4045 4662 1 chr5B.!!$F2 617
6 TraesCS2A01G533900 chr3D 41275026 41275644 618 False 839.0 839 91.115000 4044 4662 1 chr3D.!!$F2 618
7 TraesCS2A01G533900 chr3D 41368753 41369369 616 False 835.0 835 91.100000 4045 4662 1 chr3D.!!$F3 617
8 TraesCS2A01G533900 chr7D 242800055 242800672 617 False 832.0 832 90.953000 4044 4662 1 chr7D.!!$F2 618
9 TraesCS2A01G533900 chr7D 634591999 634594947 2948 True 553.4 826 87.288800 862 7533 5 chr7D.!!$R4 6671
10 TraesCS2A01G533900 chr7D 480901673 480904317 2644 True 346.0 457 79.228000 1047 5426 2 chr7D.!!$R3 4379
11 TraesCS2A01G533900 chr6B 333706733 333707354 621 True 830.0 830 90.836000 4045 4662 1 chr6B.!!$R2 617
12 TraesCS2A01G533900 chr4D 491554199 491554824 625 False 828.0 828 90.590000 4038 4662 1 chr4D.!!$F4 624
13 TraesCS2A01G533900 chr5D 384770052 384770613 561 False 344.0 385 93.007500 5513 6760 2 chr5D.!!$F4 1247
14 TraesCS2A01G533900 chr7A 548051850 548052670 820 True 270.0 270 74.377000 1056 1823 1 chr7A.!!$R2 767
15 TraesCS2A01G533900 chr7B 506562924 506563752 828 True 248.0 248 73.623000 1034 1822 1 chr7B.!!$R2 788

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
313 316 0.179056 TGCTATACCGCTCCTTTGCC 60.179 55.000 0.00 0.00 0.00 4.52 F
696 699 0.740737 AAAACTGGAGTGCACTGTGC 59.259 50.000 27.27 25.15 45.29 4.57 F
867 5009 0.743701 GTGCTCCTCCATGTGCTCAG 60.744 60.000 0.00 0.00 0.00 3.35 F
2258 7097 1.054978 AAGAGGATTACCCCGGCCTC 61.055 60.000 13.92 13.92 45.70 4.70 F
3769 9943 0.249868 TTCGAAGTGTGGTGCTGAGG 60.250 55.000 0.00 0.00 0.00 3.86 F
4190 10366 2.230508 AGTTAAACGAGCCGATCTCACA 59.769 45.455 1.50 0.00 41.98 3.58 F
5646 11917 0.942884 GTCTCGAAACCGGTCGCTTT 60.943 55.000 8.04 0.00 40.88 3.51 F
6501 12772 0.173255 GGACCGGCCATTTGATGTTG 59.827 55.000 0.00 0.00 36.34 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 5456 0.460459 GGTTAGGCTCCAGCTCGTTC 60.460 60.000 0.00 0.0 41.70 3.95 R
2579 8737 0.174845 CCGTGTCCTATTTGCCGAGA 59.825 55.000 0.00 0.0 0.00 4.04 R
2633 8791 2.484889 GCCGAGTTCTGGGCTTTATAG 58.515 52.381 16.51 0.0 45.93 1.31 R
3988 10162 0.320073 TTCCAGTTCCAACTACGGCG 60.320 55.000 4.80 4.8 37.08 6.46 R
5623 11894 0.039798 CGACCGGTTTCGAGACTTGA 60.040 55.000 9.42 0.0 41.78 3.02 R
5658 11929 1.525995 CGGCTGGTCAGTTTGGTGT 60.526 57.895 0.00 0.0 0.00 4.16 R
6637 12908 0.037975 TACCAAGTCTCGAAACCGGC 60.038 55.000 0.00 0.0 0.00 6.13 R
7932 14278 0.457851 AAGGCGATGAGAGGAGAACG 59.542 55.000 0.00 0.0 0.00 3.95 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
63 64 4.836125 TTCGAGCTGAAGAAAAATGCTT 57.164 36.364 0.00 0.00 33.83 3.91
67 68 5.412594 TCGAGCTGAAGAAAAATGCTTATGT 59.587 36.000 0.00 0.00 33.83 2.29
93 94 4.690748 CCACATACATTCGTTGAAGTCACT 59.309 41.667 0.00 0.00 0.00 3.41
94 95 5.389830 CCACATACATTCGTTGAAGTCACTG 60.390 44.000 0.00 0.00 0.00 3.66
111 112 3.713248 TCACTGATCATGAGCCAAGGTAT 59.287 43.478 8.78 0.00 0.00 2.73
250 251 6.072452 GGATAGTGACATCGATGTATCTCACA 60.072 42.308 32.44 23.15 41.95 3.58
294 296 6.371595 TTCAATGCCTTATCCCAAAACAAT 57.628 33.333 0.00 0.00 0.00 2.71
313 316 0.179056 TGCTATACCGCTCCTTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
352 355 6.266558 ACAATACAATGTTTAAGTCCAAGCCA 59.733 34.615 0.00 0.00 0.00 4.75
353 356 4.853924 ACAATGTTTAAGTCCAAGCCAG 57.146 40.909 0.00 0.00 0.00 4.85
374 377 6.410540 CCAGCATCTAAGGTTCTTAACTCTT 58.589 40.000 0.00 0.00 0.00 2.85
410 413 7.062138 TGTCGTGTTACCGATAAAAACACTATC 59.938 37.037 13.70 6.38 46.82 2.08
411 414 7.062138 GTCGTGTTACCGATAAAAACACTATCA 59.938 37.037 13.70 0.00 46.82 2.15
412 415 7.274033 TCGTGTTACCGATAAAAACACTATCAG 59.726 37.037 13.70 1.18 46.82 2.90
427 430 4.148871 CACTATCAGCGAATGGTATTCACG 59.851 45.833 2.86 0.00 0.00 4.35
453 456 3.274288 AGGCATACAAGCAAGTTCTAGC 58.726 45.455 0.00 0.00 35.83 3.42
454 457 3.054802 AGGCATACAAGCAAGTTCTAGCT 60.055 43.478 0.00 0.00 44.31 3.32
455 458 4.162320 AGGCATACAAGCAAGTTCTAGCTA 59.838 41.667 0.00 0.00 40.90 3.32
456 459 4.509600 GGCATACAAGCAAGTTCTAGCTAG 59.490 45.833 15.01 15.01 40.90 3.42
498 501 2.252714 ACCTCTCCAAGAGTTCTCCAC 58.747 52.381 3.47 0.00 40.72 4.02
570 573 1.017387 GGTGGAACGCTGATGGATTC 58.983 55.000 0.00 0.00 38.12 2.52
586 589 5.733226 TGGATTCAAATACAGTATGCGTG 57.267 39.130 0.00 0.00 42.53 5.34
672 675 1.002250 GCGATACGTGTAGATGCGGG 61.002 60.000 0.00 0.00 0.00 6.13
681 684 3.001939 CGTGTAGATGCGGGGATTAAAAC 59.998 47.826 0.00 0.00 0.00 2.43
692 695 3.421844 GGGATTAAAACTGGAGTGCACT 58.578 45.455 21.88 21.88 0.00 4.40
693 696 3.191371 GGGATTAAAACTGGAGTGCACTG 59.809 47.826 27.27 12.98 0.00 3.66
696 699 0.740737 AAAACTGGAGTGCACTGTGC 59.259 50.000 27.27 25.15 45.29 4.57
713 2690 5.921976 CACTGTGCATTGTGATACAAATTGT 59.078 36.000 14.37 3.43 41.96 2.71
745 2722 1.740585 CACCGTGGAAAAACACTGTCA 59.259 47.619 0.00 0.00 36.80 3.58
799 3103 9.282569 AGATGTTAAATCTAATGGCTGAGAATC 57.717 33.333 0.00 0.00 0.00 2.52
817 3121 5.923204 AGAATCGCCAAAGTCTTATCTGAT 58.077 37.500 0.00 0.00 0.00 2.90
867 5009 0.743701 GTGCTCCTCCATGTGCTCAG 60.744 60.000 0.00 0.00 0.00 3.35
892 5034 3.744719 CGTCGACTCGCCTTCCCA 61.745 66.667 14.70 0.00 0.00 4.37
995 5143 1.140407 CTTTCGCCATCGTCGACTCC 61.140 60.000 14.70 0.00 35.51 3.85
996 5144 1.868987 TTTCGCCATCGTCGACTCCA 61.869 55.000 14.70 0.00 35.51 3.86
997 5145 1.663379 TTCGCCATCGTCGACTCCAT 61.663 55.000 14.70 0.00 35.51 3.41
998 5146 1.946156 CGCCATCGTCGACTCCATG 60.946 63.158 14.70 12.17 0.00 3.66
1036 5184 2.685380 CCCTTGCCTCCTCTCCGT 60.685 66.667 0.00 0.00 0.00 4.69
1086 5234 4.254709 AACAGCAGCGGCCTGTCA 62.255 61.111 11.46 0.00 42.56 3.58
1290 5456 1.374758 GCTTGAGGGACCGTCACTG 60.375 63.158 16.37 12.87 24.24 3.66
1447 5636 6.603095 GTCTGGTTTTGTGTAATTAGCTCTG 58.397 40.000 0.00 0.00 0.00 3.35
1726 6398 4.143305 GCGGATGCTTTCGAGATAATACAC 60.143 45.833 4.14 0.00 38.39 2.90
2069 6899 5.798125 TGGAACTGGTGCATTTTTATTCA 57.202 34.783 0.00 0.00 0.00 2.57
2114 6944 5.175491 GTGGTGTATTTGTTTGCTTCACATG 59.825 40.000 0.00 0.00 0.00 3.21
2151 6985 4.407945 TGCTATAGTGGGTTTTCCTCTACC 59.592 45.833 0.84 0.00 42.40 3.18
2258 7097 1.054978 AAGAGGATTACCCCGGCCTC 61.055 60.000 13.92 13.92 45.70 4.70
2407 7247 1.695597 AGGGCTAGATGGCTGGCTT 60.696 57.895 2.00 0.00 46.68 4.35
2509 8667 1.910671 ACTACCGGATTTGGCACCTTA 59.089 47.619 9.46 0.00 0.00 2.69
2529 8687 5.520649 CCTTAGCCGAGTATCAAAAAGACTC 59.479 44.000 0.00 0.00 36.95 3.36
2579 8737 4.668289 CAAAAACTTTGCCGACTGTTACT 58.332 39.130 0.00 0.00 0.00 2.24
2633 8791 3.120649 CGACAAAGAACATTTCCCGAGTC 60.121 47.826 0.00 0.00 0.00 3.36
2728 8886 1.432251 CGGTCGACGCTAATGGAGT 59.568 57.895 9.92 0.00 34.82 3.85
2763 8922 8.565896 ACATCATATTTGCTGAGTGTTTAAGA 57.434 30.769 0.00 0.00 0.00 2.10
2781 8940 4.992381 AAGACGATACACTGCAAAGTTC 57.008 40.909 0.00 0.00 0.00 3.01
2783 8942 3.064207 GACGATACACTGCAAAGTTCCA 58.936 45.455 0.00 0.00 0.00 3.53
2784 8943 3.472652 ACGATACACTGCAAAGTTCCAA 58.527 40.909 0.00 0.00 0.00 3.53
2805 8964 5.925969 CCAAAAGATTGCCGAGTGTATTTTT 59.074 36.000 0.00 0.00 35.10 1.94
2937 9096 5.123344 GGACTATTTGCCGAGTGTATTTTGT 59.877 40.000 0.00 0.00 0.00 2.83
2942 9101 4.902443 TGCCGAGTGTATTTTGTGAAAA 57.098 36.364 0.00 0.00 34.41 2.29
2996 9157 0.904394 ATTGCCGGCCTGACCATTTT 60.904 50.000 26.77 0.00 39.03 1.82
3331 9499 6.824196 TCCATCAAACACAAGTACTACACAAA 59.176 34.615 0.00 0.00 0.00 2.83
3430 9601 9.341899 CAAGTTATAGAATTTTACAAGTGTGCC 57.658 33.333 0.00 0.00 0.00 5.01
3709 9883 2.095567 CCACAAGCATGAGTAGCACAAC 60.096 50.000 0.00 0.00 0.00 3.32
3746 9920 0.614979 GGAGTCACAGTGCCCTCCTA 60.615 60.000 22.69 0.00 40.30 2.94
3749 9923 3.031736 GAGTCACAGTGCCCTCCTAATA 58.968 50.000 0.00 0.00 0.00 0.98
3769 9943 0.249868 TTCGAAGTGTGGTGCTGAGG 60.250 55.000 0.00 0.00 0.00 3.86
3961 10135 4.151157 GCTGCAAGAAAATTTACCAAGCTG 59.849 41.667 0.00 0.00 34.07 4.24
3988 10162 5.392487 GCTAAAAGGAGCAAGATGAGGAAAC 60.392 44.000 0.00 0.00 42.36 2.78
4047 10223 8.450964 GCATGTACTTTGTTTATTCTGCTTAGA 58.549 33.333 0.00 0.00 0.00 2.10
4110 10286 4.169508 CTCGTGACTCAACTCGAATCAAT 58.830 43.478 0.00 0.00 35.86 2.57
4113 10289 4.385748 CGTGACTCAACTCGAATCAATTCA 59.614 41.667 3.81 0.00 36.61 2.57
4190 10366 2.230508 AGTTAAACGAGCCGATCTCACA 59.769 45.455 1.50 0.00 41.98 3.58
4232 10408 2.349886 GGCTCAGTACAAAAGATCAGCG 59.650 50.000 0.00 0.00 0.00 5.18
4587 10768 2.356535 AGCCAATCTTGGATTCGAGCTT 60.357 45.455 13.14 0.00 46.48 3.74
5184 11438 7.365741 TCTCAATCTTCTTGTTTTGCTGATTC 58.634 34.615 0.00 0.00 0.00 2.52
5445 11712 4.444876 CCATTGATGAATACTCCCTCCGTT 60.445 45.833 0.00 0.00 0.00 4.44
5460 11727 6.906848 TCCCTCCGTTCCAAAATATAAGAAT 58.093 36.000 0.00 0.00 0.00 2.40
5461 11728 6.770785 TCCCTCCGTTCCAAAATATAAGAATG 59.229 38.462 0.00 0.00 0.00 2.67
5545 11815 5.768317 ACCAAAAACTATCACATTTCACGG 58.232 37.500 0.00 0.00 0.00 4.94
5571 11842 5.850614 ACGTGACAGAAACTACCACTTTAT 58.149 37.500 0.00 0.00 0.00 1.40
5594 11865 3.423996 TTTTGTGCGGAAAACTACCAC 57.576 42.857 0.00 0.00 0.00 4.16
5646 11917 0.942884 GTCTCGAAACCGGTCGCTTT 60.943 55.000 8.04 0.00 40.88 3.51
5658 11929 4.096558 CGCTTTGCCCGCGCTAAA 62.097 61.111 5.56 0.17 44.33 1.85
5703 11974 0.827507 GTTTCAGGTGCCATGGTGGT 60.828 55.000 14.67 0.00 40.46 4.16
5773 12044 4.922026 AAACGGCGGCTGTCGGTT 62.922 61.111 25.36 22.31 43.33 4.44
5774 12045 4.922026 AACGGCGGCTGTCGGTTT 62.922 61.111 25.36 7.07 43.33 3.27
5779 12050 3.645975 CGGCTGTCGGTTTGCGTT 61.646 61.111 0.00 0.00 34.75 4.84
5780 12051 2.251371 GGCTGTCGGTTTGCGTTC 59.749 61.111 0.00 0.00 0.00 3.95
5781 12052 2.539338 GGCTGTCGGTTTGCGTTCA 61.539 57.895 0.00 0.00 0.00 3.18
6494 12765 4.733542 CCGTGGGACCGGCCATTT 62.734 66.667 15.49 0.00 41.78 2.32
6495 12766 3.439540 CGTGGGACCGGCCATTTG 61.440 66.667 15.49 1.44 38.95 2.32
6496 12767 2.034999 GTGGGACCGGCCATTTGA 59.965 61.111 15.49 0.00 38.95 2.69
6497 12768 1.379843 GTGGGACCGGCCATTTGAT 60.380 57.895 15.49 0.00 38.95 2.57
6498 12769 1.379710 TGGGACCGGCCATTTGATG 60.380 57.895 15.49 0.00 38.95 3.07
6499 12770 1.379843 GGGACCGGCCATTTGATGT 60.380 57.895 15.49 0.00 38.95 3.06
6500 12771 0.970427 GGGACCGGCCATTTGATGTT 60.970 55.000 15.49 0.00 38.95 2.71
6501 12772 0.173255 GGACCGGCCATTTGATGTTG 59.827 55.000 0.00 0.00 36.34 3.33
6502 12773 1.173043 GACCGGCCATTTGATGTTGA 58.827 50.000 0.00 0.00 0.00 3.18
6503 12774 1.750778 GACCGGCCATTTGATGTTGAT 59.249 47.619 0.00 0.00 0.00 2.57
6504 12775 1.750778 ACCGGCCATTTGATGTTGATC 59.249 47.619 0.00 0.00 0.00 2.92
6505 12776 1.067516 CCGGCCATTTGATGTTGATCC 59.932 52.381 2.24 0.00 0.00 3.36
6506 12777 2.026641 CGGCCATTTGATGTTGATCCT 58.973 47.619 2.24 0.00 0.00 3.24
6507 12778 2.033801 CGGCCATTTGATGTTGATCCTC 59.966 50.000 2.24 0.00 0.00 3.71
6508 12779 3.294214 GGCCATTTGATGTTGATCCTCT 58.706 45.455 0.00 0.00 0.00 3.69
6509 12780 3.067742 GGCCATTTGATGTTGATCCTCTG 59.932 47.826 0.00 0.00 0.00 3.35
6510 12781 3.949754 GCCATTTGATGTTGATCCTCTGA 59.050 43.478 0.00 0.00 0.00 3.27
6511 12782 4.201990 GCCATTTGATGTTGATCCTCTGAC 60.202 45.833 0.00 0.00 0.00 3.51
6512 12783 4.034858 CCATTTGATGTTGATCCTCTGACG 59.965 45.833 0.00 0.00 0.00 4.35
6513 12784 4.535526 TTTGATGTTGATCCTCTGACGA 57.464 40.909 0.00 0.00 0.00 4.20
6594 12865 1.525995 CACCGTGGCACCTGAAACT 60.526 57.895 12.86 0.00 0.00 2.66
6602 12873 1.515521 GCACCTGAAACTTGGGACCG 61.516 60.000 0.00 0.00 0.00 4.79
6943 13222 5.373222 TGCTTCTGTAAGTCCAAAAGCTTA 58.627 37.500 0.00 0.00 39.76 3.09
6958 13237 5.948992 AAAGCTTAGATTTCGTGCTCTTT 57.051 34.783 0.00 0.00 33.10 2.52
6983 13265 3.176728 TTTTTGCCCGTGTGTCTCA 57.823 47.368 0.00 0.00 0.00 3.27
7011 13293 5.221441 TGTCTTAACCCGATCACATCTATGG 60.221 44.000 0.00 0.00 0.00 2.74
7170 13452 5.300969 TGTATCATTTTCTTGTCAGCTGC 57.699 39.130 9.47 4.92 0.00 5.25
7171 13453 5.005740 TGTATCATTTTCTTGTCAGCTGCT 58.994 37.500 9.47 0.00 0.00 4.24
7340 13648 9.099454 CCACTCTCTTAATAAAATACCACTGTC 57.901 37.037 0.00 0.00 0.00 3.51
7345 13653 8.176814 TCTTAATAAAATACCACTGTCGTTCG 57.823 34.615 0.00 0.00 0.00 3.95
7352 13660 1.362717 CACTGTCGTTCGTCCACCT 59.637 57.895 0.00 0.00 0.00 4.00
7596 13942 2.151202 CAAATGTGTAGCTGTCCCGTT 58.849 47.619 0.00 0.00 0.00 4.44
7606 13952 2.203437 GTCCCGTTGCCCCAGTTT 60.203 61.111 0.00 0.00 0.00 2.66
7626 13972 0.179468 TCAGGTATAGCCGGTTTGCC 59.821 55.000 1.90 1.00 43.70 4.52
7653 13999 0.532862 CATCGCTACCCCACACATCC 60.533 60.000 0.00 0.00 0.00 3.51
7700 14046 3.160269 CTCCAACATTTTCTTCCTGCCT 58.840 45.455 0.00 0.00 0.00 4.75
7756 14102 3.083349 CGGCCATCTCCTCCACCA 61.083 66.667 2.24 0.00 0.00 4.17
7770 14116 1.600636 CACCACCGCATCACCTTGT 60.601 57.895 0.00 0.00 0.00 3.16
7791 14137 4.320456 CGCCCCCATCCAGATCCG 62.320 72.222 0.00 0.00 0.00 4.18
7796 14142 1.356124 CCCCATCCAGATCCGATTCT 58.644 55.000 0.00 0.00 0.00 2.40
7820 14166 3.734902 GCAACATTCGGGGCTATCTTTTG 60.735 47.826 0.00 0.00 0.00 2.44
7894 14240 2.037620 CTGCCTCCGATTCTCCCCAG 62.038 65.000 0.00 0.00 0.00 4.45
7925 14271 2.840572 TCCCGCCGCCATTAGCTA 60.841 61.111 0.00 0.00 40.39 3.32
7942 14288 0.101399 CTACATGCGCGTTCTCCTCT 59.899 55.000 8.43 0.00 0.00 3.69
7956 14302 1.608590 CTCCTCTCATCGCCTTCTCTC 59.391 57.143 0.00 0.00 0.00 3.20
8028 14375 4.373116 GTGGTCGGCGGCTGAGAA 62.373 66.667 12.68 0.01 0.00 2.87
8075 14422 2.211806 CTCTTATCTTCCTGCTGCAGC 58.788 52.381 31.89 31.89 42.50 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.427161 AGATGGCAAATTTTAGCGAGC 57.573 42.857 0.00 0.00 0.00 5.03
10 11 6.124088 AGTAAGATGGCAAATTTTAGCGAG 57.876 37.500 0.00 0.00 0.00 5.03
11 12 6.509418 AAGTAAGATGGCAAATTTTAGCGA 57.491 33.333 0.00 0.00 0.00 4.93
12 13 7.008628 CAGAAAGTAAGATGGCAAATTTTAGCG 59.991 37.037 0.00 0.00 0.00 4.26
13 14 8.028938 TCAGAAAGTAAGATGGCAAATTTTAGC 58.971 33.333 0.00 0.00 0.00 3.09
67 68 3.818210 ACTTCAACGAATGTATGTGGCAA 59.182 39.130 0.00 0.00 0.00 4.52
93 94 2.854963 GCATACCTTGGCTCATGATCA 58.145 47.619 0.00 0.00 0.00 2.92
111 112 3.426615 AGGATTAAACCGAATGTTGGCA 58.573 40.909 0.00 0.00 37.23 4.92
263 264 9.972106 TTTGGGATAAGGCATTGAAATAAAAAT 57.028 25.926 0.00 0.00 0.00 1.82
294 296 0.179056 GGCAAAGGAGCGGTATAGCA 60.179 55.000 2.37 0.00 40.15 3.49
352 355 7.037945 AGGAAAGAGTTAAGAACCTTAGATGCT 60.038 37.037 0.00 0.00 0.00 3.79
353 356 7.106890 AGGAAAGAGTTAAGAACCTTAGATGC 58.893 38.462 0.00 0.00 0.00 3.91
410 413 1.006086 TGCGTGAATACCATTCGCTG 58.994 50.000 9.91 5.75 45.69 5.18
411 414 1.006832 GTGCGTGAATACCATTCGCT 58.993 50.000 9.91 0.00 45.69 4.93
412 415 0.724549 TGTGCGTGAATACCATTCGC 59.275 50.000 0.00 0.00 45.70 4.70
427 430 1.270550 ACTTGCTTGTATGCCTTGTGC 59.729 47.619 0.00 0.00 41.77 4.57
453 456 1.457009 GCAGCCCTAGACGGTCCTAG 61.457 65.000 4.14 6.16 36.70 3.02
454 457 1.455217 GCAGCCCTAGACGGTCCTA 60.455 63.158 4.14 0.00 0.00 2.94
455 458 2.760385 GCAGCCCTAGACGGTCCT 60.760 66.667 4.14 0.00 0.00 3.85
456 459 3.851128 GGCAGCCCTAGACGGTCC 61.851 72.222 0.00 0.00 0.00 4.46
570 573 9.031360 GGTATATATCCACGCATACTGTATTTG 57.969 37.037 0.00 0.00 0.00 2.32
586 589 2.381911 TCCCTTCGCCGGTATATATCC 58.618 52.381 1.90 0.00 0.00 2.59
611 614 4.072131 TCCTTGTTCGAAGGATTGAAAGG 58.928 43.478 0.00 4.09 41.27 3.11
616 619 5.163713 GGATTTCTCCTTGTTCGAAGGATTG 60.164 44.000 4.81 0.00 44.75 2.67
653 656 1.002250 CCCGCATCTACACGTATCGC 61.002 60.000 0.00 0.00 0.00 4.58
660 663 4.035208 CAGTTTTAATCCCCGCATCTACAC 59.965 45.833 0.00 0.00 0.00 2.90
672 675 3.821033 ACAGTGCACTCCAGTTTTAATCC 59.179 43.478 18.64 0.00 0.00 3.01
692 695 7.213216 AGTACAATTTGTATCACAATGCACA 57.787 32.000 12.16 0.00 38.00 4.57
693 696 7.429340 GCTAGTACAATTTGTATCACAATGCAC 59.571 37.037 12.16 0.00 38.00 4.57
696 699 9.838975 TTTGCTAGTACAATTTGTATCACAATG 57.161 29.630 12.16 1.89 38.00 2.82
745 2722 4.200874 TCACGGGAACAAAACAGTACAAT 58.799 39.130 0.00 0.00 0.00 2.71
799 3103 4.795278 GCAAAATCAGATAAGACTTTGGCG 59.205 41.667 0.00 0.00 35.81 5.69
867 5009 2.370393 GCGAGTCGACGTTGGAACC 61.370 63.158 18.61 0.00 35.59 3.62
892 5034 1.221840 CTTGGGTATCGTGCCAGCT 59.778 57.895 0.00 0.00 0.00 4.24
1036 5184 3.637998 GGAAACGGAGATAGATACGCA 57.362 47.619 0.00 0.00 0.00 5.24
1290 5456 0.460459 GGTTAGGCTCCAGCTCGTTC 60.460 60.000 0.00 0.00 41.70 3.95
1462 5651 1.544825 GCCACACACTAGAGGAGGCA 61.545 60.000 12.48 0.00 40.29 4.75
1726 6398 4.920927 CCTGGTTTTACAACAAATTAGGCG 59.079 41.667 0.00 0.00 34.15 5.52
2069 6899 5.163488 CCACATCCATATCACAAGCAAATGT 60.163 40.000 0.00 0.00 0.00 2.71
2114 6944 5.853282 CCACTATAGCAATACGTACCGTTAC 59.147 44.000 0.00 0.00 41.54 2.50
2151 6985 1.342174 AGCTTCCAACATGTTTGCCAG 59.658 47.619 8.77 6.37 0.00 4.85
2233 7072 2.093341 CCGGGGTAATCCTCTTTTTCGA 60.093 50.000 0.00 0.00 35.33 3.71
2240 7079 1.459730 GAGGCCGGGGTAATCCTCT 60.460 63.158 14.36 0.00 41.35 3.69
2298 7137 3.196939 TGCAAAAAGGCATTGAAAGCT 57.803 38.095 0.00 0.00 39.25 3.74
2529 8687 7.480542 CGAGTTTTATTTTGGGTTTACAGATCG 59.519 37.037 0.00 0.00 0.00 3.69
2531 8689 7.599171 CCGAGTTTTATTTTGGGTTTACAGAT 58.401 34.615 0.00 0.00 0.00 2.90
2572 8730 4.113354 GTCCTATTTGCCGAGAGTAACAG 58.887 47.826 0.00 0.00 0.00 3.16
2579 8737 0.174845 CCGTGTCCTATTTGCCGAGA 59.825 55.000 0.00 0.00 0.00 4.04
2633 8791 2.484889 GCCGAGTTCTGGGCTTTATAG 58.515 52.381 16.51 0.00 45.93 1.31
2728 8886 3.003585 GCAAATATGATGTCACGATGGCA 59.996 43.478 0.00 0.00 35.91 4.92
2763 8922 3.120321 TGGAACTTTGCAGTGTATCGT 57.880 42.857 0.00 0.00 31.60 3.73
2772 8931 3.465871 GGCAATCTTTTGGAACTTTGCA 58.534 40.909 7.62 0.00 40.81 4.08
2781 8940 4.701956 AATACACTCGGCAATCTTTTGG 57.298 40.909 0.00 0.00 33.22 3.28
2783 8942 6.744112 TCAAAAATACACTCGGCAATCTTTT 58.256 32.000 0.00 0.00 0.00 2.27
2784 8943 6.325919 TCAAAAATACACTCGGCAATCTTT 57.674 33.333 0.00 0.00 0.00 2.52
2832 8991 7.228507 TGTGTTTTCTGTAATACACTCAGCAAT 59.771 33.333 11.34 0.00 43.71 3.56
2904 9063 0.733150 GCAAATAGTCCAGAACCGCC 59.267 55.000 0.00 0.00 0.00 6.13
2996 9157 3.385384 CTGGGCGCCTCTCTGACA 61.385 66.667 28.56 12.95 0.00 3.58
3274 9442 6.005823 TCTTCATGTTTCATGGACAAGTGAT 58.994 36.000 9.39 0.00 0.00 3.06
3430 9601 2.558359 GGAACTTGTGGAAATCAGGTGG 59.442 50.000 0.00 0.00 0.00 4.61
3490 9661 7.901874 TTAACTTGTACGAATTTCAACTTGC 57.098 32.000 0.00 0.00 0.00 4.01
3709 9883 0.457851 CCAGGCGAGTTCTCCTAGTG 59.542 60.000 0.00 0.00 28.38 2.74
3746 9920 3.935203 CTCAGCACCACACTTCGAATATT 59.065 43.478 0.00 0.00 0.00 1.28
3749 9923 1.609061 CCTCAGCACCACACTTCGAAT 60.609 52.381 0.00 0.00 0.00 3.34
3769 9943 2.615262 CTACGGTTCTCAGCCTCCGC 62.615 65.000 0.00 0.00 45.76 5.54
3961 10135 3.876320 CTCATCTTGCTCCTTTTAGCTCC 59.124 47.826 0.00 0.00 43.19 4.70
3988 10162 0.320073 TTCCAGTTCCAACTACGGCG 60.320 55.000 4.80 4.80 37.08 6.46
4066 10242 2.720688 CTCGTTTAGTTCGCGAGCA 58.279 52.632 24.99 8.28 44.03 4.26
4098 10274 6.423905 TCTTCGAGTTTGAATTGATTCGAGTT 59.576 34.615 0.00 0.00 39.62 3.01
4137 10313 6.385649 AAACGATCTTAAACCAAAGCTTGA 57.614 33.333 0.00 0.00 0.00 3.02
4190 10366 5.418209 AGCCTAACGAGTTACATGAGTACTT 59.582 40.000 0.00 0.00 0.00 2.24
4232 10408 4.329545 TGGGACGCAGGGTGCTTC 62.330 66.667 9.06 0.00 42.25 3.86
4325 10501 5.643379 ACCAATTGTACATGACCACAATC 57.357 39.130 18.51 0.00 42.93 2.67
4587 10768 4.211164 TCGACTCGACTCGTTACTAAAACA 59.789 41.667 13.05 0.00 35.10 2.83
5290 11555 6.370166 GGCCAGCTATAGAATGAATGTAGAAC 59.630 42.308 3.21 0.00 0.00 3.01
5472 11739 9.979578 ATTTTTGACATTTTTGACACTAGCATA 57.020 25.926 0.00 0.00 0.00 3.14
5474 11741 7.763528 ACATTTTTGACATTTTTGACACTAGCA 59.236 29.630 0.00 0.00 0.00 3.49
5475 11742 8.130307 ACATTTTTGACATTTTTGACACTAGC 57.870 30.769 0.00 0.00 0.00 3.42
5477 11744 9.868277 AGAACATTTTTGACATTTTTGACACTA 57.132 25.926 0.00 0.00 0.00 2.74
5545 11815 4.117685 AGTGGTAGTTTCTGTCACGTTTC 58.882 43.478 0.00 0.00 33.98 2.78
5571 11842 3.632604 TGGTAGTTTTCCGCACAAAATCA 59.367 39.130 0.00 0.00 0.00 2.57
5623 11894 0.039798 CGACCGGTTTCGAGACTTGA 60.040 55.000 9.42 0.00 41.78 3.02
5646 11917 4.627801 TGGTGTTTAGCGCGGGCA 62.628 61.111 27.20 9.82 43.41 5.36
5658 11929 1.525995 CGGCTGGTCAGTTTGGTGT 60.526 57.895 0.00 0.00 0.00 4.16
5683 11954 1.580942 CACCATGGCACCTGAAACG 59.419 57.895 13.04 0.00 0.00 3.60
5762 12033 3.573489 GAACGCAAACCGACAGCCG 62.573 63.158 0.00 0.00 41.02 5.52
5764 12035 3.018973 TGAACGCAAACCGACAGC 58.981 55.556 0.00 0.00 41.02 4.40
6464 12735 1.459455 CCCACGGTTTGGTGCATTGA 61.459 55.000 0.00 0.00 45.25 2.57
6465 12736 1.006337 CCCACGGTTTGGTGCATTG 60.006 57.895 0.00 0.00 45.25 2.82
6466 12737 1.152652 TCCCACGGTTTGGTGCATT 60.153 52.632 0.00 0.00 45.25 3.56
6467 12738 1.901464 GTCCCACGGTTTGGTGCAT 60.901 57.895 0.00 0.00 45.25 3.96
6468 12739 2.517402 GTCCCACGGTTTGGTGCA 60.517 61.111 0.00 0.00 45.25 4.57
6469 12740 3.292159 GGTCCCACGGTTTGGTGC 61.292 66.667 0.00 0.00 45.25 5.01
6470 12741 2.975799 CGGTCCCACGGTTTGGTG 60.976 66.667 0.00 0.00 45.25 4.17
6478 12749 3.439540 CAAATGGCCGGTCCCACG 61.440 66.667 2.12 0.00 37.79 4.94
6479 12750 1.379843 ATCAAATGGCCGGTCCCAC 60.380 57.895 2.12 0.00 37.79 4.61
6480 12751 1.379710 CATCAAATGGCCGGTCCCA 60.380 57.895 2.12 2.64 39.65 4.37
6481 12752 0.970427 AACATCAAATGGCCGGTCCC 60.970 55.000 2.12 0.00 33.60 4.46
6482 12753 0.173255 CAACATCAAATGGCCGGTCC 59.827 55.000 2.12 5.67 33.60 4.46
6483 12754 1.173043 TCAACATCAAATGGCCGGTC 58.827 50.000 0.00 0.00 33.60 4.79
6484 12755 1.750778 GATCAACATCAAATGGCCGGT 59.249 47.619 1.90 0.00 33.60 5.28
6485 12756 1.067516 GGATCAACATCAAATGGCCGG 59.932 52.381 0.00 0.00 33.60 6.13
6486 12757 2.026641 AGGATCAACATCAAATGGCCG 58.973 47.619 0.00 0.00 33.60 6.13
6487 12758 3.067742 CAGAGGATCAACATCAAATGGCC 59.932 47.826 0.00 0.00 37.82 5.36
6488 12759 3.949754 TCAGAGGATCAACATCAAATGGC 59.050 43.478 0.00 0.00 37.82 4.40
6489 12760 4.034858 CGTCAGAGGATCAACATCAAATGG 59.965 45.833 0.00 0.00 37.82 3.16
6490 12761 4.872124 TCGTCAGAGGATCAACATCAAATG 59.128 41.667 0.00 0.00 37.82 2.32
6491 12762 4.872691 GTCGTCAGAGGATCAACATCAAAT 59.127 41.667 0.00 0.00 37.82 2.32
6492 12763 4.245660 GTCGTCAGAGGATCAACATCAAA 58.754 43.478 0.00 0.00 37.82 2.69
6493 12764 3.673323 CGTCGTCAGAGGATCAACATCAA 60.673 47.826 0.00 0.00 37.82 2.57
6494 12765 2.159379 CGTCGTCAGAGGATCAACATCA 60.159 50.000 0.00 0.00 37.82 3.07
6495 12766 2.455032 CGTCGTCAGAGGATCAACATC 58.545 52.381 0.00 0.00 37.82 3.06
6496 12767 1.469940 GCGTCGTCAGAGGATCAACAT 60.470 52.381 0.00 0.00 37.82 2.71
6497 12768 0.109272 GCGTCGTCAGAGGATCAACA 60.109 55.000 0.00 0.00 37.82 3.33
6498 12769 0.802607 GGCGTCGTCAGAGGATCAAC 60.803 60.000 0.00 0.00 37.82 3.18
6499 12770 1.511305 GGCGTCGTCAGAGGATCAA 59.489 57.895 0.00 0.00 37.82 2.57
6500 12771 2.761195 CGGCGTCGTCAGAGGATCA 61.761 63.158 0.00 0.00 37.82 2.92
6501 12772 2.024871 CGGCGTCGTCAGAGGATC 59.975 66.667 0.00 0.00 34.40 3.36
6602 12873 1.251251 AAGCATCAAACTGACCAGCC 58.749 50.000 0.00 0.00 0.00 4.85
6631 12902 3.488090 CTCGAAACCGGCCGCTTC 61.488 66.667 22.85 22.25 0.00 3.86
6637 12908 0.037975 TACCAAGTCTCGAAACCGGC 60.038 55.000 0.00 0.00 0.00 6.13
6666 12937 4.785417 CGGCACTTTTGTTTTAATCCGTA 58.215 39.130 0.00 0.00 0.00 4.02
6675 12946 2.086054 TTTGTGCGGCACTTTTGTTT 57.914 40.000 30.81 0.00 35.11 2.83
6676 12947 2.086054 TTTTGTGCGGCACTTTTGTT 57.914 40.000 30.81 0.00 35.11 2.83
6760 13039 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
6761 13040 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
6762 13041 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
6763 13042 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
6764 13043 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
6765 13044 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
6766 13045 1.718280 AATGATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
6767 13046 4.502777 GGTTAAATGATACTCCCTCCGTCC 60.503 50.000 0.00 0.00 0.00 4.79
6768 13047 4.344390 AGGTTAAATGATACTCCCTCCGTC 59.656 45.833 0.00 0.00 0.00 4.79
6967 13249 4.134623 GTGAGACACACGGGCAAA 57.865 55.556 0.00 0.00 39.78 3.68
6983 13265 2.631062 TGTGATCGGGTTAAGACACTGT 59.369 45.455 0.00 0.00 0.00 3.55
7011 13293 3.775654 CCCGGGTCCAGCTCTGAC 61.776 72.222 14.18 4.62 0.00 3.51
7170 13452 2.225963 GTGGTACTACGATCCGATCCAG 59.774 54.545 2.69 3.43 0.00 3.86
7171 13453 2.224606 GTGGTACTACGATCCGATCCA 58.775 52.381 2.69 0.00 0.00 3.41
7340 13648 2.719426 AGACTAAAGGTGGACGAACG 57.281 50.000 0.00 0.00 0.00 3.95
7596 13942 2.356741 GCTATACCTGAAAACTGGGGCA 60.357 50.000 0.00 0.00 0.00 5.36
7606 13952 1.407712 GGCAAACCGGCTATACCTGAA 60.408 52.381 0.00 0.00 37.17 3.02
7636 13982 2.363975 GGGATGTGTGGGGTAGCGA 61.364 63.158 0.00 0.00 0.00 4.93
7639 13985 1.993391 ACGGGGATGTGTGGGGTAG 60.993 63.158 0.00 0.00 0.00 3.18
7641 13987 3.646715 CACGGGGATGTGTGGGGT 61.647 66.667 0.00 0.00 35.12 4.95
7645 13991 0.955428 CTGGTTCACGGGGATGTGTG 60.955 60.000 0.00 0.00 40.74 3.82
7653 13999 0.528470 GAGAGAGACTGGTTCACGGG 59.472 60.000 0.00 0.00 0.00 5.28
7700 14046 4.074526 GCAGCGGGCAGAGACTCA 62.075 66.667 5.02 0.00 43.97 3.41
7756 14102 2.742372 GCGACAAGGTGATGCGGT 60.742 61.111 0.00 0.00 0.00 5.68
7784 14130 4.149571 CGAATGTTGCTAGAATCGGATCTG 59.850 45.833 0.00 0.00 0.00 2.90
7791 14137 1.604278 GCCCCGAATGTTGCTAGAATC 59.396 52.381 0.00 0.00 0.00 2.52
7796 14142 2.047061 AGATAGCCCCGAATGTTGCTA 58.953 47.619 0.00 0.00 40.30 3.49
7827 14173 2.813908 GCGTCGGCTCGATTGGTT 60.814 61.111 0.67 0.00 38.42 3.67
7847 14193 1.743394 GTTCAATCCTAGGGTTTGCGG 59.257 52.381 3.90 0.00 33.73 5.69
7925 14271 1.153745 GAGAGGAGAACGCGCATGT 60.154 57.895 5.73 0.00 0.00 3.21
7932 14278 0.457851 AAGGCGATGAGAGGAGAACG 59.542 55.000 0.00 0.00 0.00 3.95
7942 14288 1.819229 GCTGGAGAGAAGGCGATGA 59.181 57.895 0.00 0.00 0.00 2.92
7956 14302 4.988598 AAGGGACACGCACGCTGG 62.989 66.667 0.00 0.00 0.00 4.85
7982 14328 2.653115 CTGACCAGAGTCGCAGCA 59.347 61.111 0.00 0.00 46.74 4.41
8028 14375 4.698651 CCGCGCGCACCACAAAAT 62.699 61.111 32.61 0.00 0.00 1.82
8084 14431 2.280389 CATAGCGATGGCGGCAGT 60.280 61.111 19.29 5.66 46.35 4.40


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

AutoCloner maintained by Alex Coulton.