Multiple sequence alignment - TraesCS1D01G233600

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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 TraesCS1D01G233600 chr1D 100.000 4177 0 0 1 4177 322030843 322035019 0.000000e+00 7714.0
1 TraesCS1D01G233600 chr1D 90.942 828 39 17 3365 4177 422284535 422283729 0.000000e+00 1081.0
2 TraesCS1D01G233600 chr1D 79.724 1376 221 24 1057 2413 322130510 322131846 0.000000e+00 942.0
3 TraesCS1D01G233600 chr1D 77.483 453 81 15 1 440 389330623 389331067 6.930000e-63 252.0
4 TraesCS1D01G233600 chr1D 92.857 98 4 2 2573 2670 295184690 295184596 5.630000e-29 139.0
5 TraesCS1D01G233600 chr1D 83.226 155 20 5 1135 1286 293915208 293915057 2.030000e-28 137.0
6 TraesCS1D01G233600 chr1B 91.845 2428 160 21 1 2419 434658689 434661087 0.000000e+00 3352.0
7 TraesCS1D01G233600 chr1B 91.892 703 40 6 2676 3364 434661411 434662110 0.000000e+00 966.0
8 TraesCS1D01G233600 chr1B 91.250 160 11 2 2418 2574 434661248 434661407 9.100000e-52 215.0
9 TraesCS1D01G233600 chr1B 74.393 453 94 15 1 441 668508518 668508076 1.540000e-39 174.0
10 TraesCS1D01G233600 chr1B 90.179 112 7 2 2573 2683 448296396 448296504 4.350000e-30 143.0
11 TraesCS1D01G233600 chr1B 83.226 155 20 5 1135 1286 395260143 395259992 2.030000e-28 137.0
12 TraesCS1D01G233600 chr1A 94.396 803 25 11 1015 1803 405791970 405792766 0.000000e+00 1216.0
13 TraesCS1D01G233600 chr1A 91.530 791 29 12 1799 2574 405798052 405798819 0.000000e+00 1055.0
14 TraesCS1D01G233600 chr1A 93.391 696 39 3 2676 3364 405798823 405799518 0.000000e+00 1024.0
15 TraesCS1D01G233600 chr1A 78.236 1553 257 44 1057 2574 405819338 405820844 0.000000e+00 920.0
16 TraesCS1D01G233600 chr1A 78.876 516 96 10 85 589 405787211 405787724 1.860000e-88 337.0
17 TraesCS1D01G233600 chr5D 89.987 799 34 22 3397 4177 332410516 332411286 0.000000e+00 990.0
18 TraesCS1D01G233600 chr5D 98.234 453 8 0 3725 4177 41243298 41242846 0.000000e+00 793.0
19 TraesCS1D01G233600 chr5D 84.783 322 19 16 3365 3664 419287572 419287259 3.160000e-76 296.0
20 TraesCS1D01G233600 chr5D 80.286 350 64 4 1 346 441401834 441401486 4.140000e-65 259.0
21 TraesCS1D01G233600 chr5D 85.644 202 14 8 3450 3651 41243528 41243342 9.160000e-47 198.0
22 TraesCS1D01G233600 chr5D 93.204 103 2 3 2569 2670 205794746 205794648 3.370000e-31 147.0
23 TraesCS1D01G233600 chr5D 100.000 33 0 0 1882 1914 432782622 432782654 1.250000e-05 62.1
24 TraesCS1D01G233600 chr5D 100.000 31 0 0 1881 1911 432787988 432788018 1.620000e-04 58.4
25 TraesCS1D01G233600 chr6D 89.012 810 51 27 3389 4174 457011863 457012658 0.000000e+00 968.0
26 TraesCS1D01G233600 chr6D 78.027 446 92 5 1 440 382344044 382343599 4.110000e-70 276.0
27 TraesCS1D01G233600 chr6D 77.951 449 85 8 1 439 121158537 121158981 6.880000e-68 268.0
28 TraesCS1D01G233600 chr6D 93.878 98 3 2 2573 2670 238502913 238503007 1.210000e-30 145.0
29 TraesCS1D01G233600 chr7D 90.713 743 37 21 3439 4177 603191319 603192033 0.000000e+00 961.0
30 TraesCS1D01G233600 chr7D 97.130 453 13 0 3725 4177 39251637 39251185 0.000000e+00 765.0
31 TraesCS1D01G233600 chr7D 96.689 453 11 1 3725 4177 54722410 54722858 0.000000e+00 750.0
32 TraesCS1D01G233600 chr7D 88.851 296 17 4 3364 3651 54722079 54722366 2.390000e-92 350.0
33 TraesCS1D01G233600 chr7D 88.750 240 10 4 3422 3651 39251913 39251681 1.140000e-70 278.0
34 TraesCS1D01G233600 chr7D 76.837 449 92 7 1 440 610839777 610839332 4.170000e-60 243.0
35 TraesCS1D01G233600 chr5A 88.917 803 47 16 3392 4177 451389333 451388556 0.000000e+00 952.0
36 TraesCS1D01G233600 chr5A 79.083 349 70 2 1 346 443586919 443586571 1.940000e-58 237.0
37 TraesCS1D01G233600 chr3D 87.758 825 40 24 3364 4177 528011743 528010969 0.000000e+00 907.0
38 TraesCS1D01G233600 chr3D 97.351 453 12 0 3725 4177 180467645 180467193 0.000000e+00 771.0
39 TraesCS1D01G233600 chr3D 85.199 804 53 38 3397 4177 2322737 2323497 0.000000e+00 765.0
40 TraesCS1D01G233600 chr3D 89.153 295 16 7 3365 3651 180467975 180467689 1.850000e-93 353.0
41 TraesCS1D01G233600 chr3D 94.059 101 3 1 2570 2670 138076237 138076334 2.600000e-32 150.0
42 TraesCS1D01G233600 chr6B 86.430 818 61 20 3384 4177 519735494 519736285 0.000000e+00 850.0
43 TraesCS1D01G233600 chr6B 86.230 305 31 7 3364 3664 195836887 195837184 1.870000e-83 320.0
44 TraesCS1D01G233600 chr6B 91.743 109 4 3 2563 2669 203686574 203686469 3.370000e-31 147.0
45 TraesCS1D01G233600 chr6B 86.275 51 7 0 411 461 665316191 665316141 5.830000e-04 56.5
46 TraesCS1D01G233600 chr3A 89.808 677 48 15 3516 4177 657613215 657612545 0.000000e+00 848.0
47 TraesCS1D01G233600 chr3A 88.732 284 15 5 3376 3651 80608110 80607836 8.660000e-87 331.0
48 TraesCS1D01G233600 chr3A 95.050 101 0 3 2571 2670 269394413 269394317 2.010000e-33 154.0
49 TraesCS1D01G233600 chr3A 94.059 101 3 1 2570 2670 156231981 156232078 2.600000e-32 150.0
50 TraesCS1D01G233600 chr4A 85.413 569 38 22 3524 4075 655663638 655663098 2.200000e-152 549.0
51 TraesCS1D01G233600 chr5B 89.179 268 18 9 3397 3663 655265823 655266080 1.450000e-84 324.0
52 TraesCS1D01G233600 chr5B 100.000 33 0 0 1882 1914 525448439 525448471 1.250000e-05 62.1
53 TraesCS1D01G233600 chr5B 97.143 35 1 0 1877 1911 525453528 525453562 4.510000e-05 60.2
54 TraesCS1D01G233600 chr4D 77.728 449 86 9 1 440 357507715 357507272 3.200000e-66 263.0
55 TraesCS1D01G233600 chr4D 79.755 163 26 4 1 159 43051865 43051706 1.230000e-20 111.0
56 TraesCS1D01G233600 chr2A 76.818 440 81 17 15 441 761285516 761285947 1.170000e-55 228.0
57 TraesCS1D01G233600 chr2A 81.421 183 34 0 1135 1317 715967123 715966941 2.600000e-32 150.0
58 TraesCS1D01G233600 chr2B 75.221 452 86 17 12 441 794000202 793999755 1.530000e-44 191.0
59 TraesCS1D01G233600 chr2B 82.682 179 27 3 1135 1310 695439833 695439656 5.590000e-34 156.0
60 TraesCS1D01G233600 chr2B 81.356 177 31 2 1135 1310 695414251 695414076 4.350000e-30 143.0
61 TraesCS1D01G233600 chr2B 73.742 457 79 28 1 444 458070313 458069885 1.570000e-29 141.0
62 TraesCS1D01G233600 chr7B 94.059 101 3 3 2573 2670 701335265 701335165 2.600000e-32 150.0
63 TraesCS1D01G233600 chr7B 92.308 65 5 0 377 441 12839489 12839553 4.450000e-15 93.5
64 TraesCS1D01G233600 chr3B 87.952 83 8 2 3365 3445 57392077 57391995 3.440000e-16 97.1
65 TraesCS1D01G233600 chr2D 95.556 45 2 0 1877 1921 12661762 12661806 5.790000e-09 73.1


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 TraesCS1D01G233600 chr1D 322030843 322035019 4176 False 7714.0 7714 100.000000 1 4177 1 chr1D.!!$F1 4176
1 TraesCS1D01G233600 chr1D 422283729 422284535 806 True 1081.0 1081 90.942000 3365 4177 1 chr1D.!!$R3 812
2 TraesCS1D01G233600 chr1D 322130510 322131846 1336 False 942.0 942 79.724000 1057 2413 1 chr1D.!!$F2 1356
3 TraesCS1D01G233600 chr1B 434658689 434662110 3421 False 1511.0 3352 91.662333 1 3364 3 chr1B.!!$F2 3363
4 TraesCS1D01G233600 chr1A 405791970 405792766 796 False 1216.0 1216 94.396000 1015 1803 1 chr1A.!!$F2 788
5 TraesCS1D01G233600 chr1A 405798052 405799518 1466 False 1039.5 1055 92.460500 1799 3364 2 chr1A.!!$F4 1565
6 TraesCS1D01G233600 chr1A 405819338 405820844 1506 False 920.0 920 78.236000 1057 2574 1 chr1A.!!$F3 1517
7 TraesCS1D01G233600 chr1A 405787211 405787724 513 False 337.0 337 78.876000 85 589 1 chr1A.!!$F1 504
8 TraesCS1D01G233600 chr5D 332410516 332411286 770 False 990.0 990 89.987000 3397 4177 1 chr5D.!!$F1 780
9 TraesCS1D01G233600 chr5D 41242846 41243528 682 True 495.5 793 91.939000 3450 4177 2 chr5D.!!$R4 727
10 TraesCS1D01G233600 chr6D 457011863 457012658 795 False 968.0 968 89.012000 3389 4174 1 chr6D.!!$F3 785
11 TraesCS1D01G233600 chr7D 603191319 603192033 714 False 961.0 961 90.713000 3439 4177 1 chr7D.!!$F1 738
12 TraesCS1D01G233600 chr7D 54722079 54722858 779 False 550.0 750 92.770000 3364 4177 2 chr7D.!!$F2 813
13 TraesCS1D01G233600 chr7D 39251185 39251913 728 True 521.5 765 92.940000 3422 4177 2 chr7D.!!$R2 755
14 TraesCS1D01G233600 chr5A 451388556 451389333 777 True 952.0 952 88.917000 3392 4177 1 chr5A.!!$R2 785
15 TraesCS1D01G233600 chr3D 528010969 528011743 774 True 907.0 907 87.758000 3364 4177 1 chr3D.!!$R1 813
16 TraesCS1D01G233600 chr3D 2322737 2323497 760 False 765.0 765 85.199000 3397 4177 1 chr3D.!!$F1 780
17 TraesCS1D01G233600 chr3D 180467193 180467975 782 True 562.0 771 93.252000 3365 4177 2 chr3D.!!$R2 812
18 TraesCS1D01G233600 chr6B 519735494 519736285 791 False 850.0 850 86.430000 3384 4177 1 chr6B.!!$F2 793
19 TraesCS1D01G233600 chr3A 657612545 657613215 670 True 848.0 848 89.808000 3516 4177 1 chr3A.!!$R3 661
20 TraesCS1D01G233600 chr4A 655663098 655663638 540 True 549.0 549 85.413000 3524 4075 1 chr4A.!!$R1 551

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
979 993 0.031994 GTTTGCAAATGCCACGTCCT 59.968 50.0 16.21 0.00 41.18 3.85 F
2210 2256 0.391661 ACATGCCGAATTCGCTGTCT 60.392 50.0 22.36 1.21 38.18 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2879 3122 0.182775 AAACTTCTTCCGTGCCCACT 59.817 50.0 0.00 0.0 0.00 4.00 R
3291 3543 0.386113 GACAGAGGAGGTACCGATGC 59.614 60.0 6.18 0.0 44.74 3.91 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
43 44 2.415090 CCTTGTTGTAGTAGACCGTCGG 60.415 54.545 10.48 10.48 0.00 4.79
44 45 1.167851 TGTTGTAGTAGACCGTCGGG 58.832 55.000 17.28 0.00 40.11 5.14
52 53 0.606401 TAGACCGTCGGGAACTCGTT 60.606 55.000 17.28 0.00 36.97 3.85
81 82 1.207791 CCCAATAGGACCAGAGCACT 58.792 55.000 0.00 0.00 38.24 4.40
83 84 2.366916 CCCAATAGGACCAGAGCACTAG 59.633 54.545 0.00 0.00 38.24 2.57
107 108 2.668550 AACCGCCGTTGAGGAAGC 60.669 61.111 0.00 0.00 45.00 3.86
108 109 3.469863 AACCGCCGTTGAGGAAGCA 62.470 57.895 0.00 0.00 45.00 3.91
218 219 1.007271 CCGAATCCCACGAGATCCG 60.007 63.158 0.00 2.55 45.44 4.18
318 321 3.056821 TCAACTGTAGGGAGTCATTGTCG 60.057 47.826 0.00 0.00 0.00 4.35
331 334 2.095212 TCATTGTCGTCTCGTCTTCCTG 60.095 50.000 0.00 0.00 0.00 3.86
347 350 3.144657 TCCTGAGCATGACACAAACAT 57.855 42.857 0.00 0.00 0.00 2.71
348 351 2.815503 TCCTGAGCATGACACAAACATG 59.184 45.455 0.00 0.00 45.19 3.21
408 417 0.379669 GCAAGTGCCAAGATCCATCG 59.620 55.000 0.00 0.00 34.31 3.84
484 493 0.250234 TGAGGCGTGAAATCCCTCTG 59.750 55.000 7.36 0.00 44.32 3.35
523 532 2.629617 AGAGACGAAGGGGTACGAAAAA 59.370 45.455 0.00 0.00 0.00 1.94
585 595 3.347216 GAGGCTCATGACCTTGCTAAAA 58.653 45.455 10.25 0.00 37.77 1.52
590 600 6.036470 GGCTCATGACCTTGCTAAAAATTAC 58.964 40.000 4.84 0.00 0.00 1.89
602 612 8.620116 TTGCTAAAAATTACGTTACCCTTACT 57.380 30.769 0.00 0.00 0.00 2.24
612 622 2.761160 CCCTTACTTTGGGGCGGT 59.239 61.111 0.00 0.00 40.97 5.68
623 633 2.414785 GGGGCGGTATTTGTGGCTG 61.415 63.158 0.00 0.00 0.00 4.85
631 641 3.560068 CGGTATTTGTGGCTGTTAGATCC 59.440 47.826 0.00 0.00 0.00 3.36
634 644 1.367346 TTGTGGCTGTTAGATCCCCA 58.633 50.000 0.00 0.00 0.00 4.96
636 646 1.922447 TGTGGCTGTTAGATCCCCAAT 59.078 47.619 0.00 0.00 0.00 3.16
683 693 5.804473 CCTAATTTTATTTGCATGTCACGCA 59.196 36.000 0.00 0.00 37.68 5.24
820 830 1.522580 GCGAGGGAGAATCTGCCAC 60.523 63.158 22.75 15.42 44.71 5.01
845 855 0.249238 CCTCTAGCTGGCACACGATC 60.249 60.000 0.00 0.00 0.00 3.69
889 899 8.696410 TTTGGATGACTTTTTCACACTAAAAC 57.304 30.769 0.00 0.00 36.92 2.43
890 900 7.397892 TGGATGACTTTTTCACACTAAAACA 57.602 32.000 0.00 0.00 36.92 2.83
940 954 2.093235 CCACCCAGGTTTTCAAAAAGCA 60.093 45.455 16.94 0.00 45.95 3.91
943 957 2.093235 CCCAGGTTTTCAAAAAGCACCA 60.093 45.455 16.94 0.00 45.95 4.17
945 959 4.006319 CCAGGTTTTCAAAAAGCACCAAA 58.994 39.130 16.94 0.00 45.95 3.28
979 993 0.031994 GTTTGCAAATGCCACGTCCT 59.968 50.000 16.21 0.00 41.18 3.85
1333 1358 4.161295 TCATCCCTTCCGCCAGCG 62.161 66.667 4.75 4.75 39.44 5.18
1500 1528 1.565759 AGCCCACTGAATATTGGAGCA 59.434 47.619 0.00 0.00 34.46 4.26
1537 1565 1.630878 CCCTGGATATCTACCCCAAGC 59.369 57.143 2.05 0.00 0.00 4.01
1689 1717 1.276138 TCATCTCACGCCATGAAGTGT 59.724 47.619 16.37 2.08 36.69 3.55
1701 1729 3.539604 CATGAAGTGTCAGATCTTCCCC 58.460 50.000 12.69 0.00 39.19 4.81
1735 1763 4.299547 TGCTTGAGCGCGACAGGT 62.300 61.111 12.10 0.00 45.83 4.00
1746 1774 2.444624 CGACAGGTGCACGATTCGG 61.445 63.158 19.33 6.98 0.00 4.30
1756 1784 0.721718 CACGATTCGGAAGCTTGTCC 59.278 55.000 2.10 0.00 0.00 4.02
1872 1903 4.552674 TGAGAGGGCCATACACATACTTA 58.447 43.478 6.18 0.00 0.00 2.24
1921 1964 3.318275 TGGGAAGCTCTGTATCGTACATC 59.682 47.826 0.00 0.00 38.15 3.06
2110 2153 2.902705 TGTGTACCTGTCTGTTGTCC 57.097 50.000 0.00 0.00 0.00 4.02
2114 2157 2.038426 TGTACCTGTCTGTTGTCCATGG 59.962 50.000 4.97 4.97 0.00 3.66
2134 2180 2.225467 GCAGGGGTATGCAATCTTCTC 58.775 52.381 0.00 0.00 45.77 2.87
2199 2245 2.226437 GCTCTTTGAGAAAACATGCCGA 59.774 45.455 0.00 0.00 0.00 5.54
2204 2250 3.469899 TGAGAAAACATGCCGAATTCG 57.530 42.857 20.92 20.92 39.44 3.34
2208 2254 0.881118 AAACATGCCGAATTCGCTGT 59.119 45.000 22.36 19.57 38.18 4.40
2210 2256 0.391661 ACATGCCGAATTCGCTGTCT 60.392 50.000 22.36 1.21 38.18 3.41
2285 2331 6.763135 GTGAGTCCATGCTTATGTATGAAGAA 59.237 38.462 8.06 0.00 38.33 2.52
2288 2334 8.162878 AGTCCATGCTTATGTATGAAGAATTG 57.837 34.615 8.06 0.00 38.33 2.32
2289 2335 7.994911 AGTCCATGCTTATGTATGAAGAATTGA 59.005 33.333 8.06 0.00 38.33 2.57
2290 2336 8.623903 GTCCATGCTTATGTATGAAGAATTGAA 58.376 33.333 8.06 0.00 38.33 2.69
2291 2337 9.187996 TCCATGCTTATGTATGAAGAATTGAAA 57.812 29.630 8.06 0.00 38.33 2.69
2292 2338 9.806203 CCATGCTTATGTATGAAGAATTGAAAA 57.194 29.630 8.06 0.00 38.33 2.29
2321 2391 4.749245 AAAGTTTCCTTGTATGTGAGCG 57.251 40.909 0.00 0.00 0.00 5.03
2357 2427 5.714333 TGTGAGCATTGGGTTATTGTATTGT 59.286 36.000 0.00 0.00 0.00 2.71
2370 2440 9.906660 GGTTATTGTATTGTTGTGAAAATCAGA 57.093 29.630 0.00 0.00 0.00 3.27
2441 2673 9.545611 GTTATGATGCAATGTTTTCAATTTTCC 57.454 29.630 0.00 0.00 0.00 3.13
2550 2792 1.925255 TGCAAATCTTCCTCCCCTGAT 59.075 47.619 0.00 0.00 0.00 2.90
2578 2821 8.530804 TCTCCTTACACTTACTTTATACTCCC 57.469 38.462 0.00 0.00 0.00 4.30
2579 2822 8.342270 TCTCCTTACACTTACTTTATACTCCCT 58.658 37.037 0.00 0.00 0.00 4.20
2580 2823 8.530804 TCCTTACACTTACTTTATACTCCCTC 57.469 38.462 0.00 0.00 0.00 4.30
2581 2824 8.342270 TCCTTACACTTACTTTATACTCCCTCT 58.658 37.037 0.00 0.00 0.00 3.69
2582 2825 8.414778 CCTTACACTTACTTTATACTCCCTCTG 58.585 40.741 0.00 0.00 0.00 3.35
2583 2826 8.890410 TTACACTTACTTTATACTCCCTCTGT 57.110 34.615 0.00 0.00 0.00 3.41
2584 2827 7.407393 ACACTTACTTTATACTCCCTCTGTC 57.593 40.000 0.00 0.00 0.00 3.51
2585 2828 6.380560 ACACTTACTTTATACTCCCTCTGTCC 59.619 42.308 0.00 0.00 0.00 4.02
2586 2829 5.898397 ACTTACTTTATACTCCCTCTGTCCC 59.102 44.000 0.00 0.00 0.00 4.46
2587 2830 4.348020 ACTTTATACTCCCTCTGTCCCA 57.652 45.455 0.00 0.00 0.00 4.37
2588 2831 4.695606 ACTTTATACTCCCTCTGTCCCAA 58.304 43.478 0.00 0.00 0.00 4.12
2589 2832 5.098663 ACTTTATACTCCCTCTGTCCCAAA 58.901 41.667 0.00 0.00 0.00 3.28
2590 2833 5.550403 ACTTTATACTCCCTCTGTCCCAAAA 59.450 40.000 0.00 0.00 0.00 2.44
2591 2834 6.217693 ACTTTATACTCCCTCTGTCCCAAAAT 59.782 38.462 0.00 0.00 0.00 1.82
2592 2835 7.404980 ACTTTATACTCCCTCTGTCCCAAAATA 59.595 37.037 0.00 0.00 0.00 1.40
2593 2836 7.758820 TTATACTCCCTCTGTCCCAAAATAA 57.241 36.000 0.00 0.00 0.00 1.40
2594 2837 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
2595 2838 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
2596 2839 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
2597 2840 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
2598 2841 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
2599 2842 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
2600 2843 4.938226 CCTCTGTCCCAAAATAAGTGTCTC 59.062 45.833 0.00 0.00 0.00 3.36
2601 2844 5.513094 CCTCTGTCCCAAAATAAGTGTCTCA 60.513 44.000 0.00 0.00 0.00 3.27
2602 2845 5.935945 TCTGTCCCAAAATAAGTGTCTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2603 2846 5.763204 TCTGTCCCAAAATAAGTGTCTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
2604 2847 5.690865 TGTCCCAAAATAAGTGTCTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
2605 2848 5.763204 TGTCCCAAAATAAGTGTCTCAACTC 59.237 40.000 0.00 0.00 0.00 3.01
2606 2849 5.998363 GTCCCAAAATAAGTGTCTCAACTCT 59.002 40.000 0.00 0.00 0.00 3.24
2607 2850 7.159372 GTCCCAAAATAAGTGTCTCAACTCTA 58.841 38.462 0.00 0.00 0.00 2.43
2608 2851 7.332182 GTCCCAAAATAAGTGTCTCAACTCTAG 59.668 40.741 0.00 0.00 0.00 2.43
2609 2852 7.016268 TCCCAAAATAAGTGTCTCAACTCTAGT 59.984 37.037 0.00 0.00 0.00 2.57
2610 2853 8.311836 CCCAAAATAAGTGTCTCAACTCTAGTA 58.688 37.037 0.00 0.00 0.00 1.82
2611 2854 9.141400 CCAAAATAAGTGTCTCAACTCTAGTAC 57.859 37.037 0.00 0.00 0.00 2.73
2612 2855 9.692749 CAAAATAAGTGTCTCAACTCTAGTACA 57.307 33.333 0.00 0.00 0.00 2.90
2614 2857 9.694137 AAATAAGTGTCTCAACTCTAGTACAAC 57.306 33.333 0.00 0.00 0.00 3.32
2615 2858 6.963083 AAGTGTCTCAACTCTAGTACAACT 57.037 37.500 0.00 0.00 0.00 3.16
2616 2859 6.963083 AGTGTCTCAACTCTAGTACAACTT 57.037 37.500 0.00 0.00 0.00 2.66
2617 2860 7.349412 AGTGTCTCAACTCTAGTACAACTTT 57.651 36.000 0.00 0.00 0.00 2.66
2618 2861 7.203910 AGTGTCTCAACTCTAGTACAACTTTG 58.796 38.462 0.00 0.00 0.00 2.77
2619 2862 6.979238 GTGTCTCAACTCTAGTACAACTTTGT 59.021 38.462 0.00 0.00 44.86 2.83
2620 2863 8.133627 GTGTCTCAACTCTAGTACAACTTTGTA 58.866 37.037 0.00 0.00 42.35 2.41
2649 2892 8.868635 AAGTTAGTAGTACAAAGTTGAGACAC 57.131 34.615 2.52 0.00 0.00 3.67
2650 2893 8.235359 AGTTAGTAGTACAAAGTTGAGACACT 57.765 34.615 2.52 5.19 0.00 3.55
2651 2894 8.693625 AGTTAGTAGTACAAAGTTGAGACACTT 58.306 33.333 2.52 0.00 38.74 3.16
2652 2895 9.956720 GTTAGTAGTACAAAGTTGAGACACTTA 57.043 33.333 2.52 0.00 35.87 2.24
2653 2896 9.956720 TTAGTAGTACAAAGTTGAGACACTTAC 57.043 33.333 2.52 0.00 35.87 2.34
2654 2897 8.235359 AGTAGTACAAAGTTGAGACACTTACT 57.765 34.615 2.52 0.00 35.87 2.24
2655 2898 8.693625 AGTAGTACAAAGTTGAGACACTTACTT 58.306 33.333 2.52 0.00 35.87 2.24
2656 2899 9.310716 GTAGTACAAAGTTGAGACACTTACTTT 57.689 33.333 0.00 0.00 40.42 2.66
2659 2902 5.821204 CAAAGTTGAGACACTTACTTTGGG 58.179 41.667 20.03 7.37 46.83 4.12
2660 2903 5.367945 AAGTTGAGACACTTACTTTGGGA 57.632 39.130 0.00 0.00 35.10 4.37
2661 2904 4.704965 AGTTGAGACACTTACTTTGGGAC 58.295 43.478 0.00 0.00 0.00 4.46
2662 2905 3.380479 TGAGACACTTACTTTGGGACG 57.620 47.619 0.00 0.00 0.00 4.79
2663 2906 2.036733 TGAGACACTTACTTTGGGACGG 59.963 50.000 0.00 0.00 0.00 4.79
2664 2907 2.298163 GAGACACTTACTTTGGGACGGA 59.702 50.000 0.00 0.00 0.00 4.69
2665 2908 2.299297 AGACACTTACTTTGGGACGGAG 59.701 50.000 0.00 0.00 0.00 4.63
2666 2909 1.346722 ACACTTACTTTGGGACGGAGG 59.653 52.381 0.00 0.00 0.00 4.30
2667 2910 0.981943 ACTTACTTTGGGACGGAGGG 59.018 55.000 0.00 0.00 0.00 4.30
2668 2911 1.272807 CTTACTTTGGGACGGAGGGA 58.727 55.000 0.00 0.00 0.00 4.20
2669 2912 1.207329 CTTACTTTGGGACGGAGGGAG 59.793 57.143 0.00 0.00 0.00 4.30
2670 2913 0.616679 TACTTTGGGACGGAGGGAGG 60.617 60.000 0.00 0.00 0.00 4.30
2671 2914 1.612442 CTTTGGGACGGAGGGAGGA 60.612 63.158 0.00 0.00 0.00 3.71
2672 2915 1.151987 TTTGGGACGGAGGGAGGAA 60.152 57.895 0.00 0.00 0.00 3.36
2673 2916 1.486145 TTTGGGACGGAGGGAGGAAC 61.486 60.000 0.00 0.00 0.00 3.62
2674 2917 2.284405 GGGACGGAGGGAGGAACA 60.284 66.667 0.00 0.00 0.00 3.18
2690 2933 6.461788 GGGAGGAACACTAATCACTATGAGAC 60.462 46.154 0.00 0.00 0.00 3.36
2696 2939 2.898729 AATCACTATGAGACGGCAGG 57.101 50.000 0.00 0.00 0.00 4.85
2703 2946 0.907704 ATGAGACGGCAGGGGTGTAA 60.908 55.000 0.00 0.00 0.00 2.41
2731 2974 8.887717 AGTATCTTCACTTTCATTGCTTATGTC 58.112 33.333 0.00 0.00 35.64 3.06
2737 2980 7.715657 TCACTTTCATTGCTTATGTCAAAACT 58.284 30.769 0.00 0.00 35.64 2.66
2782 3025 4.655963 AGAATGTACTGTCCTGCACAAAT 58.344 39.130 0.00 0.00 33.31 2.32
2788 3031 2.033299 ACTGTCCTGCACAAATTTGTCG 59.967 45.455 20.85 16.32 39.91 4.35
2823 3066 9.702494 CTCTTACATGCATGAATACTCTAATGA 57.298 33.333 32.75 14.80 0.00 2.57
2873 3116 1.339151 GGGGACACTGTTGGAGATGAC 60.339 57.143 0.00 0.00 0.00 3.06
2879 3122 0.608130 CTGTTGGAGATGACGGTCCA 59.392 55.000 5.55 0.00 41.29 4.02
2896 3139 1.071471 CAGTGGGCACGGAAGAAGT 59.929 57.895 0.00 0.00 36.20 3.01
2966 3209 5.825905 TTGATGATGACAACGCAAAATTG 57.174 34.783 0.00 0.00 0.00 2.32
2988 3231 3.495806 GGTGGAGATGGATGCCTTCTTAG 60.496 52.174 3.73 0.00 38.01 2.18
3102 3348 2.969950 TCCAATATCTACGTGGAAGGGG 59.030 50.000 5.46 5.86 38.50 4.79
3141 3387 0.176449 GGAAATGTGCAAGGGGATGC 59.824 55.000 0.00 0.00 46.58 3.91
3237 3489 8.699749 GTTGAAATGCATTGGTAGTTTAGTTTC 58.300 33.333 13.82 3.23 0.00 2.78
3282 3534 7.555306 TGTGCTAGTTGACTACTATGTCTAG 57.445 40.000 0.00 0.00 38.63 2.43
3291 3543 8.605746 GTTGACTACTATGTCTAGTGAGTGTAG 58.394 40.741 0.00 0.00 38.65 2.74
3296 3552 4.560136 ATGTCTAGTGAGTGTAGCATCG 57.440 45.455 0.00 0.00 0.00 3.84
3308 3564 1.609555 GTAGCATCGGTACCTCCTCTG 59.390 57.143 10.90 1.33 31.28 3.35
3323 3579 4.081198 CCTCCTCTGTCTAGTTTGCAAGAT 60.081 45.833 0.00 0.00 0.00 2.40
3430 3693 0.981183 TAGGGCGGTCATTTCACACT 59.019 50.000 0.00 0.00 0.00 3.55
3448 3711 5.105392 TCACACTCCGTATTAAAATACCCGT 60.105 40.000 7.16 0.74 38.38 5.28
3676 3980 3.607777 AAAAACTGCGCGTTCGAAA 57.392 42.105 15.84 0.00 38.10 3.46
3677 3981 1.897641 AAAAACTGCGCGTTCGAAAA 58.102 40.000 15.84 0.00 38.10 2.29
3678 3982 1.185189 AAAACTGCGCGTTCGAAAAC 58.815 45.000 15.84 0.00 38.10 2.43
3679 3983 0.097325 AAACTGCGCGTTCGAAAACA 59.903 45.000 15.84 0.00 38.10 2.83
3680 3984 0.097325 AACTGCGCGTTCGAAAACAA 59.903 45.000 8.43 0.00 38.10 2.83
3681 3985 0.097325 ACTGCGCGTTCGAAAACAAA 59.903 45.000 8.43 0.00 38.10 2.83
3682 3986 1.184349 CTGCGCGTTCGAAAACAAAA 58.816 45.000 8.43 0.00 38.10 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.992427 GTCTACTACAACAAGGTTTCCCG 59.008 47.826 0.00 0.00 35.12 5.14
16 17 4.321718 GGTCTACTACAACAAGGTTTCCC 58.678 47.826 0.00 0.00 0.00 3.97
43 44 1.971695 CCTTGGCCCAACGAGTTCC 60.972 63.158 0.00 0.00 0.00 3.62
44 45 2.626780 GCCTTGGCCCAACGAGTTC 61.627 63.158 0.00 0.00 0.00 3.01
73 74 2.476619 CGGTTGTTGTTCTAGTGCTCTG 59.523 50.000 0.00 0.00 0.00 3.35
81 82 0.938713 CAACGGCGGTTGTTGTTCTA 59.061 50.000 24.55 0.00 46.69 2.10
83 84 4.295381 CAACGGCGGTTGTTGTTC 57.705 55.556 24.55 0.00 46.69 3.18
101 102 1.476891 TCGATCTACGCTTTGCTTCCT 59.523 47.619 0.00 0.00 42.26 3.36
102 103 1.922570 TCGATCTACGCTTTGCTTCC 58.077 50.000 0.00 0.00 42.26 3.46
107 108 3.491267 GGATCCTTTCGATCTACGCTTTG 59.509 47.826 3.84 0.00 45.90 2.77
108 109 3.132289 TGGATCCTTTCGATCTACGCTTT 59.868 43.478 14.23 0.00 45.90 3.51
218 219 3.448686 CATGTGGAGGTATGTCTTCGAC 58.551 50.000 0.00 0.00 33.05 4.20
220 221 2.205074 GCATGTGGAGGTATGTCTTCG 58.795 52.381 0.00 0.00 0.00 3.79
228 229 2.063979 CGGAGGGCATGTGGAGGTA 61.064 63.158 0.00 0.00 0.00 3.08
238 239 2.364973 TAGCACCATCGGAGGGCA 60.365 61.111 8.91 0.00 0.00 5.36
318 321 1.474478 TCATGCTCAGGAAGACGAGAC 59.526 52.381 0.00 0.00 0.00 3.36
347 350 5.407407 TCCTTTTTAGGTGTTTTTGTGCA 57.593 34.783 0.00 0.00 0.00 4.57
348 351 5.220586 GCTTCCTTTTTAGGTGTTTTTGTGC 60.221 40.000 0.00 0.00 0.00 4.57
465 474 0.250234 CAGAGGGATTTCACGCCTCA 59.750 55.000 0.00 0.00 33.12 3.86
523 532 4.341235 TCATGATCGAAAGTACCTTCGGAT 59.659 41.667 22.76 15.64 46.44 4.18
585 595 5.255687 CCCCAAAGTAAGGGTAACGTAATT 58.744 41.667 0.00 0.00 45.28 1.40
590 600 1.456296 GCCCCAAAGTAAGGGTAACG 58.544 55.000 0.00 0.00 45.95 3.18
602 612 1.536943 GCCACAAATACCGCCCCAAA 61.537 55.000 0.00 0.00 0.00 3.28
611 621 3.883489 GGGGATCTAACAGCCACAAATAC 59.117 47.826 0.00 0.00 0.00 1.89
612 622 3.525609 TGGGGATCTAACAGCCACAAATA 59.474 43.478 0.00 0.00 30.80 1.40
649 659 8.156822 TGCAAATAAAATTAGGGGGATCTTTT 57.843 30.769 0.00 0.00 0.00 2.27
650 660 7.747809 TGCAAATAAAATTAGGGGGATCTTT 57.252 32.000 0.00 0.00 0.00 2.52
802 812 1.522580 GTGGCAGATTCTCCCTCGC 60.523 63.158 0.00 0.00 0.00 5.03
814 824 2.363795 TAGAGGGGTCGGTGGCAG 60.364 66.667 0.00 0.00 0.00 4.85
820 830 3.541713 GCCAGCTAGAGGGGTCGG 61.542 72.222 0.00 0.00 0.00 4.79
845 855 0.606401 AACTGCACCGTTGGATCCAG 60.606 55.000 15.53 6.22 0.00 3.86
889 899 3.564644 TGCAAAACTTCCATGGCATTTTG 59.435 39.130 27.06 27.06 41.19 2.44
890 900 3.818180 TGCAAAACTTCCATGGCATTTT 58.182 36.364 6.96 10.39 0.00 1.82
940 954 1.021968 GTTCGCCTCACAGTTTTGGT 58.978 50.000 0.00 0.00 0.00 3.67
943 957 1.375551 AACGTTCGCCTCACAGTTTT 58.624 45.000 0.00 0.00 0.00 2.43
945 959 0.655733 CAAACGTTCGCCTCACAGTT 59.344 50.000 0.00 0.00 0.00 3.16
1198 1223 4.115199 GAAGGGGCGGCAGGTGAT 62.115 66.667 12.47 0.00 0.00 3.06
1279 1304 0.827368 GTGAGAAAGAGGGCGAGGAT 59.173 55.000 0.00 0.00 0.00 3.24
1510 1538 1.544825 TAGATATCCAGGGCCTGCGC 61.545 60.000 28.51 13.66 0.00 6.09
1511 1539 0.247736 GTAGATATCCAGGGCCTGCG 59.752 60.000 28.51 20.32 0.00 5.18
1512 1540 0.615850 GGTAGATATCCAGGGCCTGC 59.384 60.000 28.51 13.90 0.00 4.85
1513 1541 1.280457 GGGTAGATATCCAGGGCCTG 58.720 60.000 27.04 27.04 0.00 4.85
1552 1580 4.838486 CTCGAGCCAGGCGTCGAC 62.838 72.222 23.92 5.18 40.19 4.20
1689 1717 0.335019 TGGACTCGGGGAAGATCTGA 59.665 55.000 0.00 0.00 0.00 3.27
1701 1729 3.322466 AGCAACCCCCTGGACTCG 61.322 66.667 0.00 0.00 34.81 4.18
1735 1763 0.602638 ACAAGCTTCCGAATCGTGCA 60.603 50.000 12.99 0.00 0.00 4.57
1746 1774 0.804989 CGAACCCATGGACAAGCTTC 59.195 55.000 15.22 3.09 0.00 3.86
1756 1784 0.606401 AACCAGCAGACGAACCCATG 60.606 55.000 0.00 0.00 0.00 3.66
1921 1964 1.808945 AGAAAGCGTGAATTCCTGCAG 59.191 47.619 17.94 6.78 0.00 4.41
2110 2153 0.963962 GATTGCATACCCCTGCCATG 59.036 55.000 0.00 0.00 41.58 3.66
2114 2157 2.225467 GAGAAGATTGCATACCCCTGC 58.775 52.381 0.00 0.00 42.62 4.85
2134 2180 2.755103 GGCAAAAGGATAGGAACCACTG 59.245 50.000 0.00 0.00 0.00 3.66
2199 2245 3.411446 TGGATCAACAAGACAGCGAATT 58.589 40.909 0.00 0.00 0.00 2.17
2204 2250 4.877823 TGATGTATGGATCAACAAGACAGC 59.122 41.667 0.00 0.00 31.36 4.40
2285 2331 7.066307 AGGAAACTTTACCAGCATTTTCAAT 57.934 32.000 0.00 0.00 37.44 2.57
2321 2391 4.418392 CAATGCTCACAAGTAAGGCAATC 58.582 43.478 0.00 0.00 36.49 2.67
2370 2440 8.268850 ACTGCATGAAAACTAAAAGTCGATAT 57.731 30.769 0.00 0.00 0.00 1.63
2441 2673 8.970859 ATATCCTTGAGTTTAAACCTGATGAG 57.029 34.615 14.72 5.09 0.00 2.90
2499 2733 0.734309 CGGCAATGCAGCACATCTTA 59.266 50.000 7.79 0.00 38.34 2.10
2504 2746 0.887247 AATAACGGCAATGCAGCACA 59.113 45.000 7.79 0.00 35.83 4.57
2574 2817 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
2576 2819 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
2577 2820 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
2578 2821 5.551233 TGAGACACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
2579 2822 5.560722 TGAGACACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
2580 2823 5.765182 AGTTGAGACACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
2581 2824 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
2582 2825 5.998363 AGAGTTGAGACACTTATTTTGGGAC 59.002 40.000 0.00 0.00 0.00 4.46
2583 2826 6.187727 AGAGTTGAGACACTTATTTTGGGA 57.812 37.500 0.00 0.00 0.00 4.37
2584 2827 7.162082 ACTAGAGTTGAGACACTTATTTTGGG 58.838 38.462 0.00 0.00 0.00 4.12
2585 2828 9.141400 GTACTAGAGTTGAGACACTTATTTTGG 57.859 37.037 0.00 0.00 0.00 3.28
2586 2829 9.692749 TGTACTAGAGTTGAGACACTTATTTTG 57.307 33.333 0.00 0.00 0.00 2.44
2588 2831 9.694137 GTTGTACTAGAGTTGAGACACTTATTT 57.306 33.333 0.00 0.00 0.00 1.40
2589 2832 9.080097 AGTTGTACTAGAGTTGAGACACTTATT 57.920 33.333 0.00 0.00 0.00 1.40
2590 2833 8.638629 AGTTGTACTAGAGTTGAGACACTTAT 57.361 34.615 0.00 0.00 0.00 1.73
2591 2834 8.461249 AAGTTGTACTAGAGTTGAGACACTTA 57.539 34.615 0.00 0.00 0.00 2.24
2592 2835 6.963083 AGTTGTACTAGAGTTGAGACACTT 57.037 37.500 0.00 0.00 0.00 3.16
2593 2836 6.963083 AAGTTGTACTAGAGTTGAGACACT 57.037 37.500 0.00 0.00 0.00 3.55
2594 2837 6.979238 ACAAAGTTGTACTAGAGTTGAGACAC 59.021 38.462 0.00 0.00 40.16 3.67
2595 2838 7.108841 ACAAAGTTGTACTAGAGTTGAGACA 57.891 36.000 0.00 0.00 40.16 3.41
2623 2866 9.310716 GTGTCTCAACTTTGTACTACTAACTTT 57.689 33.333 0.00 0.00 0.00 2.66
2624 2867 8.693625 AGTGTCTCAACTTTGTACTACTAACTT 58.306 33.333 0.00 0.00 0.00 2.66
2625 2868 8.235359 AGTGTCTCAACTTTGTACTACTAACT 57.765 34.615 0.00 0.00 0.00 2.24
2626 2869 8.868635 AAGTGTCTCAACTTTGTACTACTAAC 57.131 34.615 0.00 0.00 37.05 2.34
2627 2870 9.956720 GTAAGTGTCTCAACTTTGTACTACTAA 57.043 33.333 0.00 0.00 40.77 2.24
2628 2871 9.347240 AGTAAGTGTCTCAACTTTGTACTACTA 57.653 33.333 0.00 0.00 40.77 1.82
2629 2872 8.235359 AGTAAGTGTCTCAACTTTGTACTACT 57.765 34.615 0.00 0.00 40.77 2.57
2630 2873 8.868635 AAGTAAGTGTCTCAACTTTGTACTAC 57.131 34.615 0.00 0.00 40.77 2.73
2631 2874 9.309516 CAAAGTAAGTGTCTCAACTTTGTACTA 57.690 33.333 15.26 0.00 46.99 1.82
2632 2875 8.197988 CAAAGTAAGTGTCTCAACTTTGTACT 57.802 34.615 15.26 1.78 46.99 2.73
2637 2880 5.589050 GTCCCAAAGTAAGTGTCTCAACTTT 59.411 40.000 0.00 0.00 41.56 2.66
2638 2881 5.123936 GTCCCAAAGTAAGTGTCTCAACTT 58.876 41.667 0.00 0.00 42.89 2.66
2639 2882 4.704965 GTCCCAAAGTAAGTGTCTCAACT 58.295 43.478 0.00 0.00 0.00 3.16
2640 2883 3.493503 CGTCCCAAAGTAAGTGTCTCAAC 59.506 47.826 0.00 0.00 0.00 3.18
2641 2884 3.493699 CCGTCCCAAAGTAAGTGTCTCAA 60.494 47.826 0.00 0.00 0.00 3.02
2642 2885 2.036733 CCGTCCCAAAGTAAGTGTCTCA 59.963 50.000 0.00 0.00 0.00 3.27
2643 2886 2.298163 TCCGTCCCAAAGTAAGTGTCTC 59.702 50.000 0.00 0.00 0.00 3.36
2644 2887 2.299297 CTCCGTCCCAAAGTAAGTGTCT 59.701 50.000 0.00 0.00 0.00 3.41
2645 2888 2.612221 CCTCCGTCCCAAAGTAAGTGTC 60.612 54.545 0.00 0.00 0.00 3.67
2646 2889 1.346722 CCTCCGTCCCAAAGTAAGTGT 59.653 52.381 0.00 0.00 0.00 3.55
2647 2890 1.338769 CCCTCCGTCCCAAAGTAAGTG 60.339 57.143 0.00 0.00 0.00 3.16
2648 2891 0.981943 CCCTCCGTCCCAAAGTAAGT 59.018 55.000 0.00 0.00 0.00 2.24
2649 2892 1.207329 CTCCCTCCGTCCCAAAGTAAG 59.793 57.143 0.00 0.00 0.00 2.34
2650 2893 1.272807 CTCCCTCCGTCCCAAAGTAA 58.727 55.000 0.00 0.00 0.00 2.24
2651 2894 0.616679 CCTCCCTCCGTCCCAAAGTA 60.617 60.000 0.00 0.00 0.00 2.24
2652 2895 1.918800 CCTCCCTCCGTCCCAAAGT 60.919 63.158 0.00 0.00 0.00 2.66
2653 2896 1.198759 TTCCTCCCTCCGTCCCAAAG 61.199 60.000 0.00 0.00 0.00 2.77
2654 2897 1.151987 TTCCTCCCTCCGTCCCAAA 60.152 57.895 0.00 0.00 0.00 3.28
2655 2898 1.916777 GTTCCTCCCTCCGTCCCAA 60.917 63.158 0.00 0.00 0.00 4.12
2656 2899 2.284405 GTTCCTCCCTCCGTCCCA 60.284 66.667 0.00 0.00 0.00 4.37
2657 2900 2.284405 TGTTCCTCCCTCCGTCCC 60.284 66.667 0.00 0.00 0.00 4.46
2658 2901 0.324091 TAGTGTTCCTCCCTCCGTCC 60.324 60.000 0.00 0.00 0.00 4.79
2659 2902 1.553706 TTAGTGTTCCTCCCTCCGTC 58.446 55.000 0.00 0.00 0.00 4.79
2660 2903 2.108970 GATTAGTGTTCCTCCCTCCGT 58.891 52.381 0.00 0.00 0.00 4.69
2661 2904 2.108168 TGATTAGTGTTCCTCCCTCCG 58.892 52.381 0.00 0.00 0.00 4.63
2662 2905 3.108376 AGTGATTAGTGTTCCTCCCTCC 58.892 50.000 0.00 0.00 0.00 4.30
2663 2906 5.598830 TCATAGTGATTAGTGTTCCTCCCTC 59.401 44.000 0.00 0.00 0.00 4.30
2664 2907 5.529289 TCATAGTGATTAGTGTTCCTCCCT 58.471 41.667 0.00 0.00 0.00 4.20
2665 2908 5.598830 TCTCATAGTGATTAGTGTTCCTCCC 59.401 44.000 0.00 0.00 0.00 4.30
2666 2909 6.508777 GTCTCATAGTGATTAGTGTTCCTCC 58.491 44.000 0.00 0.00 0.00 4.30
2667 2910 6.202937 CGTCTCATAGTGATTAGTGTTCCTC 58.797 44.000 0.00 0.00 0.00 3.71
2668 2911 5.067936 CCGTCTCATAGTGATTAGTGTTCCT 59.932 44.000 0.00 0.00 0.00 3.36
2669 2912 5.282510 CCGTCTCATAGTGATTAGTGTTCC 58.717 45.833 0.00 0.00 0.00 3.62
2670 2913 4.740695 GCCGTCTCATAGTGATTAGTGTTC 59.259 45.833 0.00 0.00 0.00 3.18
2671 2914 4.159693 TGCCGTCTCATAGTGATTAGTGTT 59.840 41.667 0.00 0.00 0.00 3.32
2672 2915 3.699538 TGCCGTCTCATAGTGATTAGTGT 59.300 43.478 0.00 0.00 0.00 3.55
2673 2916 4.294232 CTGCCGTCTCATAGTGATTAGTG 58.706 47.826 0.00 0.00 0.00 2.74
2674 2917 3.319405 CCTGCCGTCTCATAGTGATTAGT 59.681 47.826 0.00 0.00 0.00 2.24
2690 2933 0.539986 ATACTGTTACACCCCTGCCG 59.460 55.000 0.00 0.00 0.00 5.69
2696 2939 6.228258 TGAAAGTGAAGATACTGTTACACCC 58.772 40.000 0.00 0.00 0.00 4.61
2703 2946 8.671921 CATAAGCAATGAAAGTGAAGATACTGT 58.328 33.333 0.00 0.00 37.86 3.55
2751 2994 7.147742 TGCAGGACAGTACATTCTAATGATACA 60.148 37.037 9.60 0.00 39.67 2.29
2765 3008 4.537015 GACAAATTTGTGCAGGACAGTAC 58.463 43.478 27.85 5.59 42.43 2.73
2768 3011 2.290367 TCGACAAATTTGTGCAGGACAG 59.710 45.455 27.85 9.06 42.43 3.51
2782 3025 5.050644 TGTAAGAGCGTTCTATCGACAAA 57.949 39.130 0.90 0.00 31.96 2.83
2788 3031 4.984785 TCATGCATGTAAGAGCGTTCTATC 59.015 41.667 25.43 0.00 31.96 2.08
2796 3039 7.953158 TTAGAGTATTCATGCATGTAAGAGC 57.047 36.000 25.43 12.62 0.00 4.09
2823 3066 2.065799 AGTTTCTGAATCCCCCTGTGT 58.934 47.619 0.00 0.00 0.00 3.72
2852 3095 0.692476 CATCTCCAACAGTGTCCCCA 59.308 55.000 0.00 0.00 0.00 4.96
2853 3096 0.984230 TCATCTCCAACAGTGTCCCC 59.016 55.000 0.00 0.00 0.00 4.81
2879 3122 0.182775 AAACTTCTTCCGTGCCCACT 59.817 50.000 0.00 0.00 0.00 4.00
2896 3139 0.685097 CGTGAAGAGGACAGGGGAAA 59.315 55.000 0.00 0.00 0.00 3.13
2966 3209 0.842635 AGAAGGCATCCATCTCCACC 59.157 55.000 0.00 0.00 22.99 4.61
2988 3231 5.226194 AGGGAGCTAATCTCATCATCAAC 57.774 43.478 0.00 0.00 43.70 3.18
3102 3348 1.545651 CCACCAACTCCTCCTTTCCAC 60.546 57.143 0.00 0.00 0.00 4.02
3141 3387 1.003696 GTGGGAAGAAACTCTCCCCAG 59.996 57.143 0.07 0.00 46.72 4.45
3282 3534 1.749634 AGGTACCGATGCTACACTCAC 59.250 52.381 6.18 0.00 0.00 3.51
3291 3543 0.386113 GACAGAGGAGGTACCGATGC 59.614 60.000 6.18 0.00 44.74 3.91
3296 3552 3.119065 GCAAACTAGACAGAGGAGGTACC 60.119 52.174 2.73 2.73 39.35 3.34
3308 3564 8.480643 ACATACAAGTATCTTGCAAACTAGAC 57.519 34.615 0.00 0.00 30.28 2.59
3323 3579 8.094548 AGTCTCTGCATGTTTAACATACAAGTA 58.905 33.333 10.46 0.00 36.53 2.24
3335 3596 2.936919 TGGTCAGTCTCTGCATGTTT 57.063 45.000 0.00 0.00 0.00 2.83
3389 3650 3.181430 ACCCTTTATACGTTTTGTGGGGT 60.181 43.478 16.33 13.53 39.55 4.95
3430 3693 3.798548 GCGGACGGGTATTTTAATACGGA 60.799 47.826 6.55 0.00 41.66 4.69
3664 3968 0.908505 GTTTTGTTTTCGAACGCGCA 59.091 45.000 5.73 0.00 37.46 6.09
3665 3969 1.185189 AGTTTTGTTTTCGAACGCGC 58.815 45.000 5.73 0.00 37.46 6.86
3666 3970 2.391706 CGTAGTTTTGTTTTCGAACGCG 59.608 45.455 3.53 3.53 39.35 6.01
3667 3971 2.148016 GCGTAGTTTTGTTTTCGAACGC 59.852 45.455 7.99 7.99 31.44 4.84
3668 3972 2.391706 CGCGTAGTTTTGTTTTCGAACG 59.608 45.455 0.00 0.00 0.00 3.95
3669 3973 3.344852 ACGCGTAGTTTTGTTTTCGAAC 58.655 40.909 11.67 0.00 0.00 3.95
3670 3974 3.654952 ACGCGTAGTTTTGTTTTCGAA 57.345 38.095 11.67 0.00 0.00 3.71
3671 3975 3.181522 ACAACGCGTAGTTTTGTTTTCGA 60.182 39.130 14.46 0.00 42.02 3.71
3672 3976 3.063029 CACAACGCGTAGTTTTGTTTTCG 60.063 43.478 14.46 0.00 42.02 3.46
3673 3977 3.300691 GCACAACGCGTAGTTTTGTTTTC 60.301 43.478 14.46 0.68 41.31 2.29
3674 3978 2.595095 GCACAACGCGTAGTTTTGTTTT 59.405 40.909 14.46 0.00 41.31 2.43
3675 3979 2.178783 GCACAACGCGTAGTTTTGTTT 58.821 42.857 14.46 0.00 41.31 2.83
3676 3980 1.817609 GCACAACGCGTAGTTTTGTT 58.182 45.000 14.46 0.00 41.31 2.83
3677 3981 3.519774 GCACAACGCGTAGTTTTGT 57.480 47.368 14.46 10.44 41.31 2.83
3959 4337 8.141268 TCAGCATCAATCTATACACGTTCATAA 58.859 33.333 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.