Multiple sequence alignment - TraesCS3A01G488100

Loading Multiple Alignment...

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 TraesCS3A01G488100 chr3A 100.000 5382 0 0 1 5382 716066152 716071533 0.000000e+00 9939.0
1 TraesCS3A01G488100 chr3A 84.979 699 79 13 2415 3104 465662894 465662213 0.000000e+00 686.0
2 TraesCS3A01G488100 chr3A 84.857 700 82 13 2415 3104 128478011 128477326 0.000000e+00 684.0
3 TraesCS3A01G488100 chr3A 90.066 151 9 1 4274 4424 715804799 715804943 1.980000e-44 191.0
4 TraesCS3A01G488100 chr3D 93.904 2477 112 19 1630 4085 580539618 580542076 0.000000e+00 3701.0
5 TraesCS3A01G488100 chr3D 88.465 1205 69 33 4210 5382 580542075 580543241 0.000000e+00 1391.0
6 TraesCS3A01G488100 chr3D 84.918 789 49 23 2 730 47021174 47021952 0.000000e+00 734.0
7 TraesCS3A01G488100 chr3D 84.934 677 53 28 2 647 416984407 416985065 1.630000e-179 640.0
8 TraesCS3A01G488100 chr3D 91.768 413 24 6 2 405 589562798 589563209 2.810000e-157 566.0
9 TraesCS3A01G488100 chr3D 91.304 414 21 8 2 405 22759530 22759122 7.880000e-153 551.0
10 TraesCS3A01G488100 chr3D 93.151 365 23 2 802 1165 580538809 580539172 7.930000e-148 534.0
11 TraesCS3A01G488100 chr3D 88.471 399 36 7 1166 1558 580539223 580539617 1.750000e-129 473.0
12 TraesCS3A01G488100 chr3D 82.593 270 22 5 486 731 7682249 7682517 1.170000e-51 215.0
13 TraesCS3A01G488100 chr3D 92.308 65 5 0 730 794 580538689 580538753 5.740000e-15 93.5
14 TraesCS3A01G488100 chr3B 92.877 2485 133 19 1166 3639 775825578 775828029 0.000000e+00 3568.0
15 TraesCS3A01G488100 chr3B 84.789 1065 85 40 4210 5209 775830364 775831416 0.000000e+00 998.0
16 TraesCS3A01G488100 chr3B 94.713 435 21 1 3651 4085 775829933 775830365 0.000000e+00 675.0
17 TraesCS3A01G488100 chr3B 82.075 636 54 35 4797 5381 775830992 775831618 6.270000e-134 488.0
18 TraesCS3A01G488100 chr3B 94.388 196 10 1 968 1162 775825323 775825518 3.150000e-77 300.0
19 TraesCS3A01G488100 chr3B 94.040 151 9 0 4274 4424 775660898 775661048 4.190000e-56 230.0
20 TraesCS3A01G488100 chr3B 98.450 129 2 0 4083 4211 42702341 42702213 1.510000e-55 228.0
21 TraesCS3A01G488100 chr3B 79.714 350 42 8 408 730 809392391 809392738 5.420000e-55 226.0
22 TraesCS3A01G488100 chr3B 90.769 130 12 0 1315 1444 594457528 594457399 1.990000e-39 174.0
23 TraesCS3A01G488100 chr3B 90.000 130 13 0 1315 1444 422331799 422331670 9.270000e-38 169.0
24 TraesCS3A01G488100 chr6A 86.289 1838 197 34 2159 3979 616816992 616818791 0.000000e+00 1947.0
25 TraesCS3A01G488100 chr6A 85.137 693 77 13 2415 3098 101388562 101389237 0.000000e+00 686.0
26 TraesCS3A01G488100 chr6A 82.618 489 56 19 1655 2132 616816413 616816883 6.490000e-109 405.0
27 TraesCS3A01G488100 chr6A 83.954 349 40 12 309 647 54449355 54449013 2.420000e-83 320.0
28 TraesCS3A01G488100 chr6A 81.159 207 25 10 1340 1533 616816066 616816271 2.600000e-33 154.0
29 TraesCS3A01G488100 chr6D 84.820 1726 185 39 2266 3961 473085051 473083373 0.000000e+00 1664.0
30 TraesCS3A01G488100 chr6D 89.583 432 39 5 1632 2062 329077203 329076777 1.320000e-150 544.0
31 TraesCS3A01G488100 chr6D 78.979 666 78 28 1343 1991 473086094 473085474 1.090000e-106 398.0
32 TraesCS3A01G488100 chr6D 86.450 369 39 5 1628 1992 470411104 470411465 1.410000e-105 394.0
33 TraesCS3A01G488100 chr6D 91.339 127 11 0 1315 1441 329077332 329077206 1.990000e-39 174.0
34 TraesCS3A01G488100 chr6D 100.000 34 0 0 1959 1992 470411464 470411497 4.500000e-06 63.9
35 TraesCS3A01G488100 chr6B 85.461 1128 106 20 2884 3989 718384553 718383462 0.000000e+00 1122.0
36 TraesCS3A01G488100 chr6B 86.761 710 72 20 2159 2857 718385361 718384663 0.000000e+00 771.0
37 TraesCS3A01G488100 chr6B 80.320 813 91 39 1343 2126 718386250 718385478 7.880000e-153 551.0
38 TraesCS3A01G488100 chr7D 87.887 776 47 17 2 731 25015816 25015042 0.000000e+00 869.0
39 TraesCS3A01G488100 chr7D 83.949 785 56 33 4 732 114140672 114141442 0.000000e+00 688.0
40 TraesCS3A01G488100 chr7D 87.500 424 41 6 1631 2046 587180167 587180586 3.770000e-131 479.0
41 TraesCS3A01G488100 chr7D 86.612 366 38 6 1631 1992 598005994 598005636 1.410000e-105 394.0
42 TraesCS3A01G488100 chr7D 91.903 247 16 4 403 647 142073695 142073451 5.160000e-90 342.0
43 TraesCS3A01G488100 chr7D 96.992 133 3 1 4084 4216 270998670 270998539 7.020000e-54 222.0
44 TraesCS3A01G488100 chr4A 87.816 673 53 14 2 647 371939128 371939798 0.000000e+00 761.0
45 TraesCS3A01G488100 chr4A 94.928 138 7 0 4079 4216 292414845 292414708 3.260000e-52 217.0
46 TraesCS3A01G488100 chr4B 85.313 783 56 25 2 730 329115428 329114651 0.000000e+00 754.0
47 TraesCS3A01G488100 chr4D 87.761 670 35 22 2 629 506210486 506209822 0.000000e+00 739.0
48 TraesCS3A01G488100 chr4D 89.791 431 39 5 1632 2062 433631509 433631934 1.020000e-151 547.0
49 TraesCS3A01G488100 chr4D 90.551 127 12 0 1315 1441 433631380 433631506 9.270000e-38 169.0
50 TraesCS3A01G488100 chr5D 86.765 680 46 23 2 647 42605348 42606017 0.000000e+00 717.0
51 TraesCS3A01G488100 chr5D 98.450 129 2 0 4083 4211 269087869 269087741 1.510000e-55 228.0
52 TraesCS3A01G488100 chr5D 82.353 272 23 4 486 732 38347360 38347631 4.220000e-51 213.0
53 TraesCS3A01G488100 chr5D 81.004 279 24 11 486 740 48015286 48015559 1.530000e-45 195.0
54 TraesCS3A01G488100 chr5D 89.655 87 4 2 649 730 399067133 399067047 7.370000e-19 106.0
55 TraesCS3A01G488100 chr1A 85.859 693 75 12 2415 3098 389948707 389949385 0.000000e+00 715.0
56 TraesCS3A01G488100 chr1A 84.704 693 80 13 2415 3098 115543947 115543272 0.000000e+00 669.0
57 TraesCS3A01G488100 chr2A 84.692 699 81 14 2415 3104 37891942 37891261 0.000000e+00 675.0
58 TraesCS3A01G488100 chr2A 77.791 824 100 43 1343 2132 579835411 579834637 1.070000e-116 431.0
59 TraesCS3A01G488100 chrUn 83.727 719 59 27 2 674 96750293 96749587 1.270000e-175 627.0
60 TraesCS3A01G488100 chrUn 97.037 135 4 0 4081 4215 263461946 263461812 1.510000e-55 228.0
61 TraesCS3A01G488100 chr5A 90.049 412 37 3 1632 2042 610087522 610087114 1.030000e-146 531.0
62 TraesCS3A01G488100 chr5A 89.773 88 4 2 649 731 652683639 652683552 2.050000e-19 108.0
63 TraesCS3A01G488100 chr1D 90.465 409 25 7 2 405 335536597 335536198 1.330000e-145 527.0
64 TraesCS3A01G488100 chr1D 86.158 354 21 6 403 730 335536169 335535818 1.840000e-94 357.0
65 TraesCS3A01G488100 chr2D 79.042 668 73 32 124 732 30349492 30350151 3.910000e-106 396.0
66 TraesCS3A01G488100 chr2D 86.612 366 38 6 1631 1992 587153246 587152888 1.410000e-105 394.0
67 TraesCS3A01G488100 chr2D 85.559 367 42 6 1628 1990 362642502 362642861 1.830000e-99 374.0
68 TraesCS3A01G488100 chr2D 96.970 132 4 0 4083 4214 286778364 286778233 7.020000e-54 222.0
69 TraesCS3A01G488100 chr2D 96.241 133 5 0 4084 4216 451958898 451959030 9.080000e-53 219.0
70 TraesCS3A01G488100 chr2D 88.636 88 10 0 1959 2046 587152889 587152802 2.050000e-19 108.0
71 TraesCS3A01G488100 chr2D 88.506 87 10 0 1960 2046 362642862 362642948 7.370000e-19 106.0
72 TraesCS3A01G488100 chr7A 82.826 460 35 20 309 729 306317745 306318199 6.580000e-99 372.0
73 TraesCS3A01G488100 chr7B 92.213 244 19 0 404 647 709742976 709743219 3.990000e-91 346.0
74 TraesCS3A01G488100 chr7B 96.324 136 4 1 4084 4219 692157187 692157321 7.020000e-54 222.0
75 TraesCS3A01G488100 chr7B 87.500 96 6 5 649 738 667143456 667143551 7.370000e-19 106.0
76 TraesCS3A01G488100 chr7B 86.000 100 10 3 1959 2056 49583878 49583781 2.650000e-18 104.0
77 TraesCS3A01G488100 chr1B 82.353 323 31 7 437 734 291157800 291158121 1.920000e-64 257.0
78 TraesCS3A01G488100 chr5B 97.710 131 3 0 4084 4214 67434365 67434235 5.420000e-55 226.0


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 TraesCS3A01G488100 chr3A 716066152 716071533 5381 False 9939.000000 9939 100.000000 1 5382 1 chr3A.!!$F2 5381
1 TraesCS3A01G488100 chr3A 465662213 465662894 681 True 686.000000 686 84.979000 2415 3104 1 chr3A.!!$R2 689
2 TraesCS3A01G488100 chr3A 128477326 128478011 685 True 684.000000 684 84.857000 2415 3104 1 chr3A.!!$R1 689
3 TraesCS3A01G488100 chr3D 580538689 580543241 4552 False 1238.500000 3701 91.259800 730 5382 5 chr3D.!!$F5 4652
4 TraesCS3A01G488100 chr3D 47021174 47021952 778 False 734.000000 734 84.918000 2 730 1 chr3D.!!$F2 728
5 TraesCS3A01G488100 chr3D 416984407 416985065 658 False 640.000000 640 84.934000 2 647 1 chr3D.!!$F3 645
6 TraesCS3A01G488100 chr3B 775825323 775831618 6295 False 1205.800000 3568 89.768400 968 5381 5 chr3B.!!$F3 4413
7 TraesCS3A01G488100 chr6A 616816066 616818791 2725 False 835.333333 1947 83.355333 1340 3979 3 chr6A.!!$F2 2639
8 TraesCS3A01G488100 chr6A 101388562 101389237 675 False 686.000000 686 85.137000 2415 3098 1 chr6A.!!$F1 683
9 TraesCS3A01G488100 chr6D 473083373 473086094 2721 True 1031.000000 1664 81.899500 1343 3961 2 chr6D.!!$R2 2618
10 TraesCS3A01G488100 chr6D 329076777 329077332 555 True 359.000000 544 90.461000 1315 2062 2 chr6D.!!$R1 747
11 TraesCS3A01G488100 chr6B 718383462 718386250 2788 True 814.666667 1122 84.180667 1343 3989 3 chr6B.!!$R1 2646
12 TraesCS3A01G488100 chr7D 25015042 25015816 774 True 869.000000 869 87.887000 2 731 1 chr7D.!!$R1 729
13 TraesCS3A01G488100 chr7D 114140672 114141442 770 False 688.000000 688 83.949000 4 732 1 chr7D.!!$F1 728
14 TraesCS3A01G488100 chr4A 371939128 371939798 670 False 761.000000 761 87.816000 2 647 1 chr4A.!!$F1 645
15 TraesCS3A01G488100 chr4B 329114651 329115428 777 True 754.000000 754 85.313000 2 730 1 chr4B.!!$R1 728
16 TraesCS3A01G488100 chr4D 506209822 506210486 664 True 739.000000 739 87.761000 2 629 1 chr4D.!!$R1 627
17 TraesCS3A01G488100 chr4D 433631380 433631934 554 False 358.000000 547 90.171000 1315 2062 2 chr4D.!!$F1 747
18 TraesCS3A01G488100 chr5D 42605348 42606017 669 False 717.000000 717 86.765000 2 647 1 chr5D.!!$F2 645
19 TraesCS3A01G488100 chr1A 389948707 389949385 678 False 715.000000 715 85.859000 2415 3098 1 chr1A.!!$F1 683
20 TraesCS3A01G488100 chr1A 115543272 115543947 675 True 669.000000 669 84.704000 2415 3098 1 chr1A.!!$R1 683
21 TraesCS3A01G488100 chr2A 37891261 37891942 681 True 675.000000 675 84.692000 2415 3104 1 chr2A.!!$R1 689
22 TraesCS3A01G488100 chr2A 579834637 579835411 774 True 431.000000 431 77.791000 1343 2132 1 chr2A.!!$R2 789
23 TraesCS3A01G488100 chrUn 96749587 96750293 706 True 627.000000 627 83.727000 2 674 1 chrUn.!!$R1 672
24 TraesCS3A01G488100 chr1D 335535818 335536597 779 True 442.000000 527 88.311500 2 730 2 chr1D.!!$R1 728
25 TraesCS3A01G488100 chr2D 30349492 30350151 659 False 396.000000 396 79.042000 124 732 1 chr2D.!!$F1 608

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
647 783 0.534203 AGTGGCGGTTCGTGTTGAAT 60.534 50.000 0.00 0.0 39.21 2.57 F
1209 1479 0.036294 GCGGCTCTTTTCTACCCAGT 60.036 55.000 0.00 0.0 0.00 4.00 F
1425 1696 0.524862 TCCTCAAGTACGCTTCGTCC 59.475 55.000 0.00 0.0 41.54 4.79 F
1510 1792 2.488153 CTCTGTCGATGACACCTGTGTA 59.512 50.000 2.35 0.0 45.05 2.90 F
1678 2038 2.622064 AGAACACACTTCCTCACCAC 57.378 50.000 0.00 0.0 0.00 4.16 F
2295 2857 4.082787 CCTTGAGAAAACCGTGTAATGCAT 60.083 41.667 0.00 0.0 0.00 3.96 F
3649 6236 1.339631 TGAGATTTACCTTGTGCCCCG 60.340 52.381 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 3176 1.963515 CCAAGGCCCATTTATAGTGGC 59.036 52.381 0.00 0.0 43.26 5.01 R
2780 3347 1.280457 AGTCGAAGAAATCTGGGGCT 58.720 50.000 0.00 0.0 39.69 5.19 R
3158 3830 1.341080 CTTTGGGCCACTTTGGTGAT 58.659 50.000 5.23 0.0 45.61 3.06 R
3467 4143 3.737266 CACAAGTGTTAAATGCCAGCAAG 59.263 43.478 0.00 0.0 0.00 4.01 R
3649 6236 1.066858 TCGGAGTTCCAGTCAATCTGC 60.067 52.381 0.00 0.0 42.38 4.26 R
4193 6786 0.113776 ACTACTCCCTCCGTTCCACA 59.886 55.000 0.00 0.0 0.00 4.17 R
4679 7281 2.660206 CGGTTCCCCATCGACACA 59.340 61.111 0.00 0.0 0.00 3.72 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
21 26 2.744760 AGAGCAGCAGGAGTGATTAGA 58.255 47.619 0.00 0.00 0.00 2.10
57 64 6.948886 TCTTAGTACTTTGTCCTCTCATGTCT 59.051 38.462 0.00 0.00 0.00 3.41
91 104 7.792032 TGTCCCGAACTTAATCTATCTCAAAT 58.208 34.615 0.00 0.00 0.00 2.32
169 184 6.997655 TCGATGATATCTTTGCTTCTGGTAT 58.002 36.000 3.98 0.00 0.00 2.73
173 188 9.160496 GATGATATCTTTGCTTCTGGTATAAGG 57.840 37.037 3.98 0.00 0.00 2.69
174 189 8.262601 TGATATCTTTGCTTCTGGTATAAGGA 57.737 34.615 3.98 0.00 0.00 3.36
275 322 5.874810 TGATGATTACCTAGAGTGTTGTTGC 59.125 40.000 0.00 0.00 0.00 4.17
284 333 5.521735 CCTAGAGTGTTGTTGCTGATGATAC 59.478 44.000 0.00 0.00 0.00 2.24
647 783 0.534203 AGTGGCGGTTCGTGTTGAAT 60.534 50.000 0.00 0.00 39.21 2.57
657 817 5.176958 CGGTTCGTGTTGAATCTTTAGTTCT 59.823 40.000 0.00 0.00 39.21 3.01
660 820 7.095187 GGTTCGTGTTGAATCTTTAGTTCTCAT 60.095 37.037 0.00 0.00 39.21 2.90
701 866 1.080974 CGACACGGCCTTACGAACT 60.081 57.895 0.00 0.00 37.61 3.01
761 926 0.900421 TCACTCGAGAGGGTCGACTA 59.100 55.000 21.68 0.00 46.10 2.59
769 934 1.766496 AGAGGGTCGACTAGGAGAGAG 59.234 57.143 16.46 0.00 0.00 3.20
774 939 1.937899 GTCGACTAGGAGAGAGCTCAC 59.062 57.143 17.77 10.21 43.14 3.51
775 940 1.555533 TCGACTAGGAGAGAGCTCACA 59.444 52.381 17.77 0.00 43.14 3.58
777 942 3.388350 TCGACTAGGAGAGAGCTCACATA 59.612 47.826 17.77 7.98 43.14 2.29
794 959 4.938832 TCACATAATACGGTCCAACCAAAG 59.061 41.667 0.00 0.00 38.47 2.77
795 960 4.698304 CACATAATACGGTCCAACCAAAGT 59.302 41.667 0.00 0.00 38.47 2.66
796 961 5.182380 CACATAATACGGTCCAACCAAAGTT 59.818 40.000 0.00 0.00 38.47 2.66
797 962 5.771165 ACATAATACGGTCCAACCAAAGTTT 59.229 36.000 0.00 0.00 38.47 2.66
798 963 4.841443 AATACGGTCCAACCAAAGTTTC 57.159 40.909 0.00 0.00 38.47 2.78
799 964 2.131776 ACGGTCCAACCAAAGTTTCA 57.868 45.000 0.00 0.00 38.47 2.69
800 965 2.448453 ACGGTCCAACCAAAGTTTCAA 58.552 42.857 0.00 0.00 38.47 2.69
826 1039 2.551912 GCCCCAACGAAGTGTGGTG 61.552 63.158 0.00 0.00 45.00 4.17
849 1062 3.551454 CCAGTTCGTCGACCTAGTTTCAA 60.551 47.826 10.58 0.00 0.00 2.69
850 1063 4.046462 CAGTTCGTCGACCTAGTTTCAAA 58.954 43.478 10.58 0.00 0.00 2.69
894 1107 3.264947 CATGTGAAATCCTTCTCGCAGA 58.735 45.455 0.00 0.00 35.66 4.26
895 1108 3.401033 TGTGAAATCCTTCTCGCAGAA 57.599 42.857 0.00 0.00 34.09 3.02
979 1192 3.764466 CTGCTCTTCCTCCGCCGT 61.764 66.667 0.00 0.00 0.00 5.68
980 1193 3.302347 CTGCTCTTCCTCCGCCGTT 62.302 63.158 0.00 0.00 0.00 4.44
1021 1234 1.156034 GGCTCATAACCCGCGTTACC 61.156 60.000 4.92 0.00 37.28 2.85
1026 1239 2.019897 ATAACCCGCGTTACCTCCGG 62.020 60.000 4.92 0.00 37.28 5.14
1108 1322 0.612229 CCTTTGCTCTGCTCTCTCCA 59.388 55.000 0.00 0.00 0.00 3.86
1209 1479 0.036294 GCGGCTCTTTTCTACCCAGT 60.036 55.000 0.00 0.00 0.00 4.00
1210 1480 2.007547 GCGGCTCTTTTCTACCCAGTC 61.008 57.143 0.00 0.00 0.00 3.51
1211 1481 1.405661 CGGCTCTTTTCTACCCAGTCC 60.406 57.143 0.00 0.00 0.00 3.85
1217 1487 4.489737 TCTTTTCTACCCAGTCCTCTCAA 58.510 43.478 0.00 0.00 0.00 3.02
1421 1692 5.833082 TGAATCTATCCTCAAGTACGCTTC 58.167 41.667 0.00 0.00 31.49 3.86
1425 1696 0.524862 TCCTCAAGTACGCTTCGTCC 59.475 55.000 0.00 0.00 41.54 4.79
1510 1792 2.488153 CTCTGTCGATGACACCTGTGTA 59.512 50.000 2.35 0.00 45.05 2.90
1518 1803 8.512138 TGTCGATGACACCTGTGTATTATATAG 58.488 37.037 2.35 0.00 45.05 1.31
1545 1843 5.534207 TCAAATTGCAATCTTGTCACCTT 57.466 34.783 13.38 0.00 0.00 3.50
1549 1847 6.655078 AATTGCAATCTTGTCACCTTACTT 57.345 33.333 13.38 0.00 0.00 2.24
1561 1859 6.350103 TGTCACCTTACTTGTCATACAACAA 58.650 36.000 0.00 0.00 37.56 2.83
1562 1860 6.824196 TGTCACCTTACTTGTCATACAACAAA 59.176 34.615 0.00 0.00 38.60 2.83
1563 1861 7.130269 GTCACCTTACTTGTCATACAACAAAC 58.870 38.462 0.00 0.00 38.60 2.93
1564 1862 6.824196 TCACCTTACTTGTCATACAACAAACA 59.176 34.615 0.00 0.00 38.60 2.83
1606 1958 7.793036 AGACCATTACTCCCTAATCTGTTTAC 58.207 38.462 0.00 0.00 0.00 2.01
1646 2000 6.801539 TTACTTCCATGTAGCTTCAGTTTG 57.198 37.500 0.00 0.00 0.00 2.93
1647 2001 4.718961 ACTTCCATGTAGCTTCAGTTTGT 58.281 39.130 0.00 0.00 0.00 2.83
1648 2002 4.516698 ACTTCCATGTAGCTTCAGTTTGTG 59.483 41.667 0.00 0.00 0.00 3.33
1649 2003 4.085357 TCCATGTAGCTTCAGTTTGTGT 57.915 40.909 0.00 0.00 0.00 3.72
1673 2029 6.200475 GTGTACTTTGTAGAACACACTTCCTC 59.800 42.308 0.00 0.00 41.43 3.71
1678 2038 2.622064 AGAACACACTTCCTCACCAC 57.378 50.000 0.00 0.00 0.00 4.16
1807 2173 6.814146 GTCTCTTTAAGTGTGTGGAAGGATAG 59.186 42.308 0.00 0.00 0.00 2.08
1939 2405 4.645535 TCTATGCTCAATTGCCTCATACC 58.354 43.478 0.00 0.00 0.00 2.73
2154 2625 5.567915 GCGTATTGCCAGTTTTAACTTCTTC 59.432 40.000 0.00 0.00 37.08 2.87
2175 2735 6.823689 TCTTCAGGAGATTATTTTGGTACTGC 59.176 38.462 0.00 0.00 0.00 4.40
2295 2857 4.082787 CCTTGAGAAAACCGTGTAATGCAT 60.083 41.667 0.00 0.00 0.00 3.96
2403 2966 7.663905 CAGTACTTCTCTAGACATACAGGCTAT 59.336 40.741 0.00 0.00 37.18 2.97
3065 3736 5.006746 CGCATTGATAGGGAAAGTTACTCAC 59.993 44.000 0.00 0.00 0.00 3.51
3091 3763 7.578310 ATTGTAGATAATGCATTGCAGAAGT 57.422 32.000 22.27 4.99 43.65 3.01
3158 3830 4.263462 ACAAAGTCAACATGGATGGAGCTA 60.263 41.667 0.00 0.00 0.00 3.32
3217 3889 5.637387 GCCTACTGATTCTTAGATTAGCAGC 59.363 44.000 0.00 0.00 0.00 5.25
3384 4058 6.179906 AGCATGTATGTTGGCTACTCTATT 57.820 37.500 0.01 0.00 34.25 1.73
3586 4269 7.754851 ATAATGCTCATGTATGCAATCTTCA 57.245 32.000 12.82 0.00 42.74 3.02
3641 6219 5.048434 GCTCTTTGTTGCTGAGATTTACCTT 60.048 40.000 0.00 0.00 0.00 3.50
3642 6220 6.317789 TCTTTGTTGCTGAGATTTACCTTG 57.682 37.500 0.00 0.00 0.00 3.61
3643 6221 5.827797 TCTTTGTTGCTGAGATTTACCTTGT 59.172 36.000 0.00 0.00 0.00 3.16
3644 6222 5.437289 TTGTTGCTGAGATTTACCTTGTG 57.563 39.130 0.00 0.00 0.00 3.33
3649 6236 1.339631 TGAGATTTACCTTGTGCCCCG 60.340 52.381 0.00 0.00 0.00 5.73
3707 6297 5.357257 TCACGGAGGTAAGATTTAATCTGC 58.643 41.667 8.34 4.95 40.13 4.26
3741 6331 8.160106 AGAGAAAGTTGATGTTTCCATAAGAGT 58.840 33.333 0.00 0.00 34.93 3.24
3742 6332 8.103948 AGAAAGTTGATGTTTCCATAAGAGTG 57.896 34.615 0.00 0.00 34.93 3.51
3823 6415 1.796151 CTAATGCCACACCTGTGCG 59.204 57.895 0.00 0.00 44.34 5.34
3891 6483 7.228108 ACGTAAGGATTCAGTATAACGATCAGA 59.772 37.037 0.00 0.00 46.39 3.27
3956 6548 1.835494 GGAAGGTTCCCTTGCTAACC 58.165 55.000 7.22 0.00 46.30 2.85
3968 6560 6.019748 TCCCTTGCTAACCCAATTTAATTCA 58.980 36.000 0.00 0.00 0.00 2.57
4034 6626 7.093333 TGAGTGGTGATTCTTTGCTCTATTAGA 60.093 37.037 0.00 0.00 0.00 2.10
4038 6630 9.295825 TGGTGATTCTTTGCTCTATTAGAAAAA 57.704 29.630 0.00 0.00 31.99 1.94
4083 6676 6.407202 AGAAATGCGTAAGAACCTGAGTAAT 58.593 36.000 0.00 0.00 43.02 1.89
4084 6677 7.553334 AGAAATGCGTAAGAACCTGAGTAATA 58.447 34.615 0.00 0.00 43.02 0.98
4085 6678 7.491696 AGAAATGCGTAAGAACCTGAGTAATAC 59.508 37.037 0.00 0.00 43.02 1.89
4086 6679 5.909621 TGCGTAAGAACCTGAGTAATACT 57.090 39.130 0.00 0.00 43.02 2.12
4087 6680 5.888105 TGCGTAAGAACCTGAGTAATACTC 58.112 41.667 13.20 13.20 42.85 2.59
4088 6681 5.163581 TGCGTAAGAACCTGAGTAATACTCC 60.164 44.000 16.89 2.20 42.15 3.85
4089 6682 5.735638 GCGTAAGAACCTGAGTAATACTCCC 60.736 48.000 16.89 2.74 42.15 4.30
4090 6683 5.593502 CGTAAGAACCTGAGTAATACTCCCT 59.406 44.000 16.89 4.73 42.15 4.20
4091 6684 6.238703 CGTAAGAACCTGAGTAATACTCCCTC 60.239 46.154 16.89 8.49 42.15 4.30
4092 6685 4.548669 AGAACCTGAGTAATACTCCCTCC 58.451 47.826 16.89 3.98 44.44 4.30
4093 6686 2.946785 ACCTGAGTAATACTCCCTCCG 58.053 52.381 16.89 3.54 44.44 4.63
4094 6687 2.244252 ACCTGAGTAATACTCCCTCCGT 59.756 50.000 16.89 4.09 44.44 4.69
4095 6688 3.297736 CCTGAGTAATACTCCCTCCGTT 58.702 50.000 16.89 0.00 44.44 4.44
4096 6689 3.318557 CCTGAGTAATACTCCCTCCGTTC 59.681 52.174 16.89 0.00 44.44 3.95
4097 6690 3.294214 TGAGTAATACTCCCTCCGTTCC 58.706 50.000 16.89 0.00 44.44 3.62
4098 6691 3.294214 GAGTAATACTCCCTCCGTTCCA 58.706 50.000 9.19 0.00 39.28 3.53
4099 6692 3.703052 GAGTAATACTCCCTCCGTTCCAA 59.297 47.826 9.19 0.00 39.28 3.53
4100 6693 4.098894 AGTAATACTCCCTCCGTTCCAAA 58.901 43.478 0.00 0.00 0.00 3.28
4101 6694 4.533311 AGTAATACTCCCTCCGTTCCAAAA 59.467 41.667 0.00 0.00 0.00 2.44
4102 6695 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
4103 6696 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
4104 6697 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
4105 6698 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
4106 6699 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
4107 6700 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
4108 6701 3.328343 TCCCTCCGTTCCAAAATACTTGA 59.672 43.478 0.00 0.00 0.00 3.02
4109 6702 3.439129 CCCTCCGTTCCAAAATACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
4110 6703 4.324267 CCTCCGTTCCAAAATACTTGACT 58.676 43.478 0.00 0.00 0.00 3.41
4111 6704 4.760204 CCTCCGTTCCAAAATACTTGACTT 59.240 41.667 0.00 0.00 0.00 3.01
4112 6705 5.106673 CCTCCGTTCCAAAATACTTGACTTC 60.107 44.000 0.00 0.00 0.00 3.01
4113 6706 4.758165 TCCGTTCCAAAATACTTGACTTCC 59.242 41.667 0.00 0.00 0.00 3.46
4114 6707 4.517453 CCGTTCCAAAATACTTGACTTCCA 59.483 41.667 0.00 0.00 0.00 3.53
4115 6708 5.183140 CCGTTCCAAAATACTTGACTTCCAT 59.817 40.000 0.00 0.00 0.00 3.41
4116 6709 6.294508 CCGTTCCAAAATACTTGACTTCCATT 60.295 38.462 0.00 0.00 0.00 3.16
4117 6710 7.145323 CGTTCCAAAATACTTGACTTCCATTT 58.855 34.615 0.00 0.00 0.00 2.32
4118 6711 7.114811 CGTTCCAAAATACTTGACTTCCATTTG 59.885 37.037 0.00 0.00 0.00 2.32
4119 6712 7.595819 TCCAAAATACTTGACTTCCATTTGT 57.404 32.000 0.00 0.00 0.00 2.83
4120 6713 7.657336 TCCAAAATACTTGACTTCCATTTGTC 58.343 34.615 0.00 0.00 0.00 3.18
4121 6714 6.868339 CCAAAATACTTGACTTCCATTTGTCC 59.132 38.462 0.00 0.00 32.67 4.02
4122 6715 7.432869 CAAAATACTTGACTTCCATTTGTCCA 58.567 34.615 0.00 0.00 32.67 4.02
4123 6716 7.595819 AAATACTTGACTTCCATTTGTCCAA 57.404 32.000 0.00 0.00 32.67 3.53
4124 6717 7.595819 AATACTTGACTTCCATTTGTCCAAA 57.404 32.000 0.00 0.00 32.67 3.28
4125 6718 5.930837 ACTTGACTTCCATTTGTCCAAAA 57.069 34.783 0.00 0.00 33.56 2.44
4126 6719 6.293004 ACTTGACTTCCATTTGTCCAAAAA 57.707 33.333 0.00 0.00 33.56 1.94
4127 6720 6.888105 ACTTGACTTCCATTTGTCCAAAAAT 58.112 32.000 0.00 0.00 33.56 1.82
4128 6721 6.762661 ACTTGACTTCCATTTGTCCAAAAATG 59.237 34.615 0.00 3.25 43.94 2.32
4136 6729 6.966435 CATTTGTCCAAAAATGGATGTACC 57.034 37.500 0.19 0.00 41.71 3.34
4137 6730 6.700352 CATTTGTCCAAAAATGGATGTACCT 58.300 36.000 0.19 0.00 41.71 3.08
4138 6731 7.835822 CATTTGTCCAAAAATGGATGTACCTA 58.164 34.615 0.19 0.00 41.71 3.08
4139 6732 8.477256 CATTTGTCCAAAAATGGATGTACCTAT 58.523 33.333 0.19 0.00 41.71 2.57
4140 6733 9.707957 ATTTGTCCAAAAATGGATGTACCTATA 57.292 29.630 0.19 0.00 40.51 1.31
4141 6734 9.707957 TTTGTCCAAAAATGGATGTACCTATAT 57.292 29.630 0.19 0.00 40.51 0.86
4143 6736 9.787435 TGTCCAAAAATGGATGTACCTATATAC 57.213 33.333 0.19 0.00 40.51 1.47
4192 6785 5.999205 TTTGATAAATGGAAGGCATGTGT 57.001 34.783 0.00 0.00 0.00 3.72
4193 6786 5.999205 TTGATAAATGGAAGGCATGTGTT 57.001 34.783 0.00 0.00 0.00 3.32
4194 6787 5.327616 TGATAAATGGAAGGCATGTGTTG 57.672 39.130 0.00 0.00 0.00 3.33
4195 6788 4.771577 TGATAAATGGAAGGCATGTGTTGT 59.228 37.500 0.00 0.00 0.00 3.32
4196 6789 3.389925 AAATGGAAGGCATGTGTTGTG 57.610 42.857 0.00 0.00 0.00 3.33
4197 6790 1.259609 ATGGAAGGCATGTGTTGTGG 58.740 50.000 0.00 0.00 0.00 4.17
4198 6791 0.184692 TGGAAGGCATGTGTTGTGGA 59.815 50.000 0.00 0.00 0.00 4.02
4199 6792 1.327303 GGAAGGCATGTGTTGTGGAA 58.673 50.000 0.00 0.00 0.00 3.53
4200 6793 1.000274 GGAAGGCATGTGTTGTGGAAC 60.000 52.381 0.00 0.00 37.35 3.62
4201 6794 0.667993 AAGGCATGTGTTGTGGAACG 59.332 50.000 0.00 0.00 42.39 3.95
4202 6795 1.172180 AGGCATGTGTTGTGGAACGG 61.172 55.000 0.00 0.00 42.39 4.44
4203 6796 1.169661 GGCATGTGTTGTGGAACGGA 61.170 55.000 0.00 0.00 42.39 4.69
4204 6797 0.238289 GCATGTGTTGTGGAACGGAG 59.762 55.000 0.00 0.00 42.39 4.63
4205 6798 0.874390 CATGTGTTGTGGAACGGAGG 59.126 55.000 0.00 0.00 42.39 4.30
4206 6799 0.250727 ATGTGTTGTGGAACGGAGGG 60.251 55.000 0.00 0.00 42.39 4.30
4207 6800 1.338890 TGTGTTGTGGAACGGAGGGA 61.339 55.000 0.00 0.00 42.39 4.20
4208 6801 0.602905 GTGTTGTGGAACGGAGGGAG 60.603 60.000 0.00 0.00 42.39 4.30
4218 6811 3.135530 GGAACGGAGGGAGTAGTAGTCTA 59.864 52.174 4.99 0.00 0.00 2.59
4319 6912 0.524816 CGTGGTGGTCTTCCGATACG 60.525 60.000 0.00 0.00 36.30 3.06
4468 7070 9.367444 CGTTACTGAGGTAATTAATTGTTCTCT 57.633 33.333 11.05 1.47 39.67 3.10
4551 7153 2.159014 GGCATCATAGGGACGTTGTACA 60.159 50.000 0.00 0.00 0.00 2.90
4593 7195 8.458843 ACATGTCAGCAATGTAAAGTATTAACC 58.541 33.333 0.00 0.00 0.00 2.85
4643 7245 3.390175 ACAGTGATACCTGGAGCTACT 57.610 47.619 0.00 0.00 36.75 2.57
4674 7276 2.087462 TATGAGCTCATCACGGGGCG 62.087 60.000 31.92 0.00 41.91 6.13
4733 7343 2.281484 GTGCTGGACTGGGCGAAA 60.281 61.111 0.00 0.00 0.00 3.46
4761 7371 5.250235 TCGTCTAGGTGTTGATCTGAATC 57.750 43.478 0.00 0.00 0.00 2.52
4767 7415 5.779241 AGGTGTTGATCTGAATCCCTTTA 57.221 39.130 0.00 0.00 0.00 1.85
4772 7420 7.976175 GGTGTTGATCTGAATCCCTTTATTTTC 59.024 37.037 0.00 0.00 0.00 2.29
4773 7421 8.743714 GTGTTGATCTGAATCCCTTTATTTTCT 58.256 33.333 0.00 0.00 0.00 2.52
4801 7449 4.927267 ATACCTGAATCCTGGTTGAACA 57.073 40.909 0.00 0.00 43.30 3.18
4861 7509 2.558359 CCACCCAAAAGAATGACAGTCC 59.442 50.000 0.00 0.00 0.00 3.85
5160 7836 8.585471 TGCCATGAAGATTTTCTAGAGAAATT 57.415 30.769 5.57 2.73 42.83 1.82
5261 7965 3.182173 GCATGAACATTTTGTGAACGTGG 59.818 43.478 0.00 0.00 0.00 4.94
5262 7966 4.605968 CATGAACATTTTGTGAACGTGGA 58.394 39.130 0.00 0.00 0.00 4.02
5263 7967 4.703645 TGAACATTTTGTGAACGTGGAA 57.296 36.364 0.00 0.00 0.00 3.53
5264 7968 5.255710 TGAACATTTTGTGAACGTGGAAT 57.744 34.783 0.00 0.00 0.00 3.01
5265 7969 5.039984 TGAACATTTTGTGAACGTGGAATG 58.960 37.500 0.00 0.00 0.00 2.67
5266 7970 4.909696 ACATTTTGTGAACGTGGAATGA 57.090 36.364 0.00 0.00 0.00 2.57
5269 7973 4.703645 TTTTGTGAACGTGGAATGAACA 57.296 36.364 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.102972 TCTAATCACTCCTGCTGCTCTT 58.897 45.455 0.00 0.00 0.00 2.85
21 26 7.363968 GGACAAAGTACTAAGAGCAGGAACTAT 60.364 40.741 0.00 0.00 36.02 2.12
57 64 7.391620 AGATTAAGTTCGGGACAAAGAACATA 58.608 34.615 10.37 1.03 0.00 2.29
91 104 7.048629 TCATAAGACCACAAAAGCAAATCAA 57.951 32.000 0.00 0.00 0.00 2.57
134 147 7.254556 GCAAAGATATCATCGAGTTCAACATGA 60.255 37.037 5.32 0.00 0.00 3.07
173 188 9.952188 AACACTAGCTTAAAGAAGAAACATTTC 57.048 29.630 0.00 0.00 34.25 2.17
174 189 9.736023 CAACACTAGCTTAAAGAAGAAACATTT 57.264 29.630 0.00 0.00 34.25 2.32
275 322 5.980698 AAACTCTTGCATCGTATCATCAG 57.019 39.130 0.00 0.00 0.00 2.90
539 673 6.608002 ACACCAACCAATACTAAAAGGTTTGA 59.392 34.615 0.00 0.00 42.15 2.69
555 691 3.088789 ACTGGTTTGTAACACCAACCA 57.911 42.857 13.50 13.50 43.96 3.67
647 783 6.407202 GGCACTAAAGGATGAGAACTAAAGA 58.593 40.000 0.00 0.00 0.00 2.52
657 817 2.568062 TGTAACCGGCACTAAAGGATGA 59.432 45.455 0.00 0.00 0.00 2.92
660 820 2.250031 TCTGTAACCGGCACTAAAGGA 58.750 47.619 0.00 0.00 0.00 3.36
701 866 0.689745 AGAACCGGGCTATAGCACCA 60.690 55.000 25.53 0.00 42.67 4.17
761 926 3.823873 CCGTATTATGTGAGCTCTCTCCT 59.176 47.826 16.19 3.61 38.58 3.69
769 934 2.870411 GGTTGGACCGTATTATGTGAGC 59.130 50.000 0.00 0.00 0.00 4.26
774 939 5.890424 AACTTTGGTTGGACCGTATTATG 57.110 39.130 0.00 0.00 42.58 1.90
775 940 6.005198 TGAAACTTTGGTTGGACCGTATTAT 58.995 36.000 0.00 0.00 42.58 1.28
777 942 4.208746 TGAAACTTTGGTTGGACCGTATT 58.791 39.130 0.00 0.00 42.58 1.89
794 959 2.261361 GGGCCCGCATGTTGAAAC 59.739 61.111 5.69 0.00 0.00 2.78
795 960 2.994417 GGGGCCCGCATGTTGAAA 60.994 61.111 17.79 0.00 0.00 2.69
796 961 3.817210 TTGGGGCCCGCATGTTGAA 62.817 57.895 19.83 0.00 0.00 2.69
797 962 4.292145 TTGGGGCCCGCATGTTGA 62.292 61.111 19.83 0.00 0.00 3.18
798 963 4.067913 GTTGGGGCCCGCATGTTG 62.068 66.667 19.83 0.00 0.00 3.33
826 1039 0.243095 AACTAGGTCGACGAACTGGC 59.757 55.000 25.37 0.00 30.78 4.85
849 1062 6.058833 GGAAATTACACAAAAACCCCACATT 58.941 36.000 0.00 0.00 0.00 2.71
850 1063 5.131142 TGGAAATTACACAAAAACCCCACAT 59.869 36.000 0.00 0.00 0.00 3.21
905 1118 1.895131 ACTGCTTTGCCTTACAATGGG 59.105 47.619 0.00 0.00 38.31 4.00
915 1128 1.403679 TGTAACACACACTGCTTTGCC 59.596 47.619 0.00 0.00 30.04 4.52
1026 1239 4.959596 GCGATGAGGAGGAGGCGC 62.960 72.222 0.00 0.00 37.60 6.53
1052 1265 2.158900 ACTTGGATGTAGATGAAGGCCG 60.159 50.000 0.00 0.00 0.00 6.13
1145 1359 0.468400 GTAGAGGCGGTCAGATCCCT 60.468 60.000 0.00 0.00 0.00 4.20
1176 1446 1.166531 AGCCGCACCTGAACAGAAAC 61.167 55.000 3.19 0.00 0.00 2.78
1209 1479 2.035155 TCCGGCGTCTTGAGAGGA 59.965 61.111 6.01 0.00 32.08 3.71
1210 1480 2.182030 GTCCGGCGTCTTGAGAGG 59.818 66.667 6.01 0.00 0.00 3.69
1211 1481 2.202492 CGTCCGGCGTCTTGAGAG 60.202 66.667 6.01 0.00 35.54 3.20
1234 1504 1.080093 CTTACTGCTTCCGCGTGGA 60.080 57.895 15.21 15.21 44.61 4.02
1237 1507 2.434359 GGCTTACTGCTTCCGCGT 60.434 61.111 4.92 0.00 42.39 6.01
1260 1530 1.063942 TGAGCCTGATACGGAGAGGAA 60.064 52.381 0.00 0.00 0.00 3.36
1421 1692 2.084546 GAAAACAGAGGAATGGGGACG 58.915 52.381 0.00 0.00 0.00 4.79
1425 1696 4.953940 TTTTGGAAAACAGAGGAATGGG 57.046 40.909 0.00 0.00 0.00 4.00
1492 1774 3.953712 AATACACAGGTGTCATCGACA 57.046 42.857 8.56 0.00 43.74 4.35
1518 1803 6.128472 GGTGACAAGATTGCAATTTGATTTCC 60.128 38.462 26.73 20.50 0.00 3.13
1545 1843 8.846943 ATGAGATGTTTGTTGTATGACAAGTA 57.153 30.769 0.00 0.00 39.00 2.24
1549 1847 8.100164 TCCTTATGAGATGTTTGTTGTATGACA 58.900 33.333 0.00 0.00 0.00 3.58
1561 1859 7.918076 TGGTCTAAGTTTCCTTATGAGATGTT 58.082 34.615 0.00 0.00 32.82 2.71
1562 1860 7.496346 TGGTCTAAGTTTCCTTATGAGATGT 57.504 36.000 0.00 0.00 32.82 3.06
1563 1861 8.970859 AATGGTCTAAGTTTCCTTATGAGATG 57.029 34.615 0.00 0.00 32.82 2.90
1606 1958 5.163612 GGAAGTAAAAGGAGCAAATAGGCTG 60.164 44.000 0.00 0.00 45.99 4.85
1649 2003 6.127281 TGAGGAAGTGTGTTCTACAAAGTACA 60.127 38.462 0.00 0.00 41.89 2.90
1678 2038 4.520179 TGGAAGAGTCATTGTCCATCATG 58.480 43.478 0.00 0.00 35.22 3.07
1691 2051 4.081420 TGCTTTCTGATACCTGGAAGAGTC 60.081 45.833 0.00 0.00 34.07 3.36
1726 2086 6.327386 ACCTGTGATATAAACAGTGGGAAT 57.673 37.500 14.05 0.00 42.90 3.01
1807 2173 6.202570 TGCAATTGGAAGAAGCAATGTAAAAC 59.797 34.615 7.72 0.00 31.42 2.43
1939 2405 4.634883 AGAAGCAGAGCATGTTCTGTTATG 59.365 41.667 31.99 14.49 45.07 1.90
2048 2514 8.804912 TTGCAGGCCAAATTATCAATTTTATT 57.195 26.923 5.01 0.00 38.97 1.40
2054 2520 5.667466 CTTCTTGCAGGCCAAATTATCAAT 58.333 37.500 5.01 0.00 31.94 2.57
2055 2521 4.621274 GCTTCTTGCAGGCCAAATTATCAA 60.621 41.667 5.01 0.00 42.31 2.57
2056 2522 3.119029 GCTTCTTGCAGGCCAAATTATCA 60.119 43.478 5.01 0.00 42.31 2.15
2057 2523 3.131755 AGCTTCTTGCAGGCCAAATTATC 59.868 43.478 5.01 0.00 45.94 1.75
2059 2525 2.231964 CAGCTTCTTGCAGGCCAAATTA 59.768 45.455 5.01 0.00 45.94 1.40
2154 2625 5.116180 TCGCAGTACCAAAATAATCTCCTG 58.884 41.667 0.00 0.00 0.00 3.86
2175 2735 5.587388 TCCACCTACATAACCTACTTTCG 57.413 43.478 0.00 0.00 0.00 3.46
2295 2857 4.285790 AGCCCCACCCCTTCTCCA 62.286 66.667 0.00 0.00 0.00 3.86
2391 2954 5.039920 TCATTTGCTCATAGCCTGTATGT 57.960 39.130 0.00 0.00 41.51 2.29
2403 2966 6.072008 TGCTAGCTAAACAAATCATTTGCTCA 60.072 34.615 17.23 0.00 44.39 4.26
2497 3061 6.438741 TCTTGTAATATGCAATGTTTTCCCCA 59.561 34.615 0.00 0.00 0.00 4.96
2593 3158 5.513233 AGTGGCCTGAATTGAGAAACATAT 58.487 37.500 3.32 0.00 0.00 1.78
2594 3159 4.922206 AGTGGCCTGAATTGAGAAACATA 58.078 39.130 3.32 0.00 0.00 2.29
2611 3176 1.963515 CCAAGGCCCATTTATAGTGGC 59.036 52.381 0.00 0.00 43.26 5.01
2658 3223 4.141914 ACCTTCCAGAATGATTACTCGACC 60.142 45.833 0.00 0.00 39.69 4.79
2780 3347 1.280457 AGTCGAAGAAATCTGGGGCT 58.720 50.000 0.00 0.00 39.69 5.19
2807 3374 2.426522 TCAAGTAATTTCGCTGCAGCT 58.573 42.857 34.22 19.06 39.32 4.24
2863 3514 3.985019 AATCAATTGCCTTTGCCATCA 57.015 38.095 0.00 0.00 36.33 3.07
3065 3736 8.781196 ACTTCTGCAATGCATTATCTACAATAG 58.219 33.333 12.53 7.88 38.13 1.73
3091 3763 5.636543 GGAAAGAAGTCCGAACGATAAAGAA 59.363 40.000 0.00 0.00 0.00 2.52
3158 3830 1.341080 CTTTGGGCCACTTTGGTGAT 58.659 50.000 5.23 0.00 45.61 3.06
3445 4120 4.889832 CCAGAGTCAATGGCTCAAATAC 57.110 45.455 17.77 0.00 35.55 1.89
3467 4143 3.737266 CACAAGTGTTAAATGCCAGCAAG 59.263 43.478 0.00 0.00 0.00 4.01
3564 4240 6.650427 ATGAAGATTGCATACATGAGCATT 57.350 33.333 0.00 3.29 40.94 3.56
3641 6219 2.359850 GTCAATCTGCGGGGCACA 60.360 61.111 0.00 0.00 33.79 4.57
3642 6220 2.045926 AGTCAATCTGCGGGGCAC 60.046 61.111 0.00 0.00 33.79 5.01
3643 6221 2.046023 CAGTCAATCTGCGGGGCA 60.046 61.111 0.00 0.00 37.36 5.36
3644 6222 2.819984 TTCCAGTCAATCTGCGGGGC 62.820 60.000 0.00 0.00 42.38 5.80
3649 6236 1.066858 TCGGAGTTCCAGTCAATCTGC 60.067 52.381 0.00 0.00 42.38 4.26
3707 6297 5.404466 ACATCAACTTTCTCTCTGAGGAG 57.596 43.478 4.59 1.68 40.73 3.69
3741 6331 3.550820 ACCAACACAAGCATTAGACACA 58.449 40.909 0.00 0.00 0.00 3.72
3742 6332 5.008217 TGTTACCAACACAAGCATTAGACAC 59.992 40.000 0.00 0.00 36.25 3.67
3823 6415 4.201950 CCTTCAACAAATCATCGGATCCAC 60.202 45.833 13.41 0.00 31.88 4.02
3891 6483 1.140407 GCTACACGCTCGAAATCGCT 61.140 55.000 0.00 0.00 39.60 4.93
3968 6560 7.552687 TGCCATACTTGAGAACGAAAGATAAAT 59.447 33.333 0.00 0.00 0.00 1.40
3974 6566 4.452455 ACTTGCCATACTTGAGAACGAAAG 59.548 41.667 0.00 0.00 0.00 2.62
4059 6652 4.273148 ACTCAGGTTCTTACGCATTTCT 57.727 40.909 0.00 0.00 0.00 2.52
4083 6676 4.098894 AGTATTTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
4084 6677 2.910977 AGTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4085 6678 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
4086 6679 3.328343 TCAAGTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
4087 6680 3.439129 GTCAAGTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
4088 6681 4.324267 AGTCAAGTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
4089 6682 5.106673 GGAAGTCAAGTATTTTGGAACGGAG 60.107 44.000 0.00 0.00 0.00 4.63
4090 6683 4.758165 GGAAGTCAAGTATTTTGGAACGGA 59.242 41.667 0.00 0.00 0.00 4.69
4091 6684 4.517453 TGGAAGTCAAGTATTTTGGAACGG 59.483 41.667 0.00 0.00 0.00 4.44
4092 6685 5.682943 TGGAAGTCAAGTATTTTGGAACG 57.317 39.130 0.00 0.00 0.00 3.95
4093 6686 7.926018 ACAAATGGAAGTCAAGTATTTTGGAAC 59.074 33.333 0.00 0.00 29.41 3.62
4094 6687 8.017418 ACAAATGGAAGTCAAGTATTTTGGAA 57.983 30.769 0.00 0.00 29.41 3.53
4095 6688 7.255801 GGACAAATGGAAGTCAAGTATTTTGGA 60.256 37.037 0.00 0.00 36.50 3.53
4096 6689 6.868339 GGACAAATGGAAGTCAAGTATTTTGG 59.132 38.462 0.00 0.00 36.50 3.28
4097 6690 7.432869 TGGACAAATGGAAGTCAAGTATTTTG 58.567 34.615 0.00 0.00 36.50 2.44
4098 6691 7.595819 TGGACAAATGGAAGTCAAGTATTTT 57.404 32.000 0.00 0.00 36.50 1.82
4099 6692 7.595819 TTGGACAAATGGAAGTCAAGTATTT 57.404 32.000 0.00 0.00 36.50 1.40
4100 6693 7.595819 TTTGGACAAATGGAAGTCAAGTATT 57.404 32.000 0.00 0.00 36.50 1.89
4101 6694 7.595819 TTTTGGACAAATGGAAGTCAAGTAT 57.404 32.000 0.00 0.00 36.50 2.12
4102 6695 7.411486 TTTTTGGACAAATGGAAGTCAAGTA 57.589 32.000 0.00 0.00 36.50 2.24
4103 6696 5.930837 TTTTGGACAAATGGAAGTCAAGT 57.069 34.783 0.00 0.00 36.50 3.16
4104 6697 7.181143 CATTTTTGGACAAATGGAAGTCAAG 57.819 36.000 0.00 0.00 39.53 3.02
4113 6706 6.700352 AGGTACATCCATTTTTGGACAAATG 58.300 36.000 0.00 0.04 41.33 2.32
4114 6707 6.933514 AGGTACATCCATTTTTGGACAAAT 57.066 33.333 0.00 0.00 41.33 2.32
4115 6708 9.707957 ATATAGGTACATCCATTTTTGGACAAA 57.292 29.630 0.00 0.00 41.33 2.83
4117 6710 9.787435 GTATATAGGTACATCCATTTTTGGACA 57.213 33.333 0.00 0.00 41.33 4.02
4166 6759 8.707449 ACACATGCCTTCCATTTATCAAAATAT 58.293 29.630 0.00 0.00 33.45 1.28
4167 6760 8.076910 ACACATGCCTTCCATTTATCAAAATA 57.923 30.769 0.00 0.00 33.45 1.40
4168 6761 6.949715 ACACATGCCTTCCATTTATCAAAAT 58.050 32.000 0.00 0.00 35.65 1.82
4169 6762 6.357579 ACACATGCCTTCCATTTATCAAAA 57.642 33.333 0.00 0.00 29.71 2.44
4170 6763 5.999205 ACACATGCCTTCCATTTATCAAA 57.001 34.783 0.00 0.00 29.71 2.69
4171 6764 5.245751 ACAACACATGCCTTCCATTTATCAA 59.754 36.000 0.00 0.00 29.71 2.57
4172 6765 4.771577 ACAACACATGCCTTCCATTTATCA 59.228 37.500 0.00 0.00 29.71 2.15
4173 6766 5.104374 CACAACACATGCCTTCCATTTATC 58.896 41.667 0.00 0.00 29.71 1.75
4174 6767 4.081531 CCACAACACATGCCTTCCATTTAT 60.082 41.667 0.00 0.00 29.71 1.40
4175 6768 3.257873 CCACAACACATGCCTTCCATTTA 59.742 43.478 0.00 0.00 29.71 1.40
4176 6769 2.037511 CCACAACACATGCCTTCCATTT 59.962 45.455 0.00 0.00 29.71 2.32
4177 6770 1.619827 CCACAACACATGCCTTCCATT 59.380 47.619 0.00 0.00 29.71 3.16
4178 6771 1.203038 TCCACAACACATGCCTTCCAT 60.203 47.619 0.00 0.00 33.39 3.41
4179 6772 0.184692 TCCACAACACATGCCTTCCA 59.815 50.000 0.00 0.00 0.00 3.53
4180 6773 1.000274 GTTCCACAACACATGCCTTCC 60.000 52.381 0.00 0.00 32.14 3.46
4181 6774 1.334960 CGTTCCACAACACATGCCTTC 60.335 52.381 0.00 0.00 32.14 3.46
4182 6775 0.667993 CGTTCCACAACACATGCCTT 59.332 50.000 0.00 0.00 32.14 4.35
4183 6776 1.172180 CCGTTCCACAACACATGCCT 61.172 55.000 0.00 0.00 32.14 4.75
4184 6777 1.169661 TCCGTTCCACAACACATGCC 61.170 55.000 0.00 0.00 32.14 4.40
4185 6778 0.238289 CTCCGTTCCACAACACATGC 59.762 55.000 0.00 0.00 32.14 4.06
4186 6779 0.874390 CCTCCGTTCCACAACACATG 59.126 55.000 0.00 0.00 32.14 3.21
4187 6780 0.250727 CCCTCCGTTCCACAACACAT 60.251 55.000 0.00 0.00 32.14 3.21
4188 6781 1.147376 CCCTCCGTTCCACAACACA 59.853 57.895 0.00 0.00 32.14 3.72
4189 6782 0.602905 CTCCCTCCGTTCCACAACAC 60.603 60.000 0.00 0.00 32.14 3.32
4190 6783 1.052124 ACTCCCTCCGTTCCACAACA 61.052 55.000 0.00 0.00 32.14 3.33
4191 6784 0.971386 TACTCCCTCCGTTCCACAAC 59.029 55.000 0.00 0.00 0.00 3.32
4192 6785 1.263356 CTACTCCCTCCGTTCCACAA 58.737 55.000 0.00 0.00 0.00 3.33
4193 6786 0.113776 ACTACTCCCTCCGTTCCACA 59.886 55.000 0.00 0.00 0.00 4.17
4194 6787 2.022934 CTACTACTCCCTCCGTTCCAC 58.977 57.143 0.00 0.00 0.00 4.02
4195 6788 1.637553 ACTACTACTCCCTCCGTTCCA 59.362 52.381 0.00 0.00 0.00 3.53
4196 6789 2.092484 AGACTACTACTCCCTCCGTTCC 60.092 54.545 0.00 0.00 0.00 3.62
4197 6790 3.280197 AGACTACTACTCCCTCCGTTC 57.720 52.381 0.00 0.00 0.00 3.95
4198 6791 3.118075 GGTAGACTACTACTCCCTCCGTT 60.118 52.174 12.31 0.00 45.70 4.44
4199 6792 2.437651 GGTAGACTACTACTCCCTCCGT 59.562 54.545 12.31 0.00 45.70 4.69
4200 6793 2.547642 CGGTAGACTACTACTCCCTCCG 60.548 59.091 12.31 0.73 45.70 4.63
4201 6794 2.224499 CCGGTAGACTACTACTCCCTCC 60.224 59.091 12.31 0.00 45.70 4.30
4202 6795 2.437651 ACCGGTAGACTACTACTCCCTC 59.562 54.545 4.49 0.00 45.70 4.30
4203 6796 2.172293 CACCGGTAGACTACTACTCCCT 59.828 54.545 6.87 0.00 45.70 4.20
4204 6797 2.570135 CACCGGTAGACTACTACTCCC 58.430 57.143 6.87 0.00 45.70 4.30
4205 6798 1.946081 GCACCGGTAGACTACTACTCC 59.054 57.143 6.87 0.00 45.70 3.85
4206 6799 2.636830 TGCACCGGTAGACTACTACTC 58.363 52.381 6.87 0.00 45.70 2.59
4207 6800 2.795231 TGCACCGGTAGACTACTACT 57.205 50.000 6.87 0.00 45.70 2.57
4208 6801 3.855689 TTTGCACCGGTAGACTACTAC 57.144 47.619 6.87 0.00 45.70 2.73
4218 6811 2.682836 GCAATAATGTTTTGCACCGGT 58.317 42.857 0.00 0.00 46.78 5.28
4319 6912 2.553079 ATTCGTCTTCGACTGCTCTC 57.447 50.000 0.00 0.00 46.03 3.20
4551 7153 7.555195 TGCTGACATGTATCTGAAAATCTGAAT 59.445 33.333 0.00 0.00 0.00 2.57
4643 7245 4.821177 CTCATAGAGCAGCACGCA 57.179 55.556 0.00 0.00 46.13 5.24
4679 7281 2.660206 CGGTTCCCCATCGACACA 59.340 61.111 0.00 0.00 0.00 3.72
4733 7343 5.010112 CAGATCAACACCTAGACGATATGGT 59.990 44.000 0.00 0.00 0.00 3.55
4772 7420 7.233553 TCAACCAGGATTCAGGTATAGATGTAG 59.766 40.741 0.00 0.00 37.07 2.74
4773 7421 7.073208 TCAACCAGGATTCAGGTATAGATGTA 58.927 38.462 0.00 0.00 37.07 2.29
4790 7438 8.421784 ACATATACTAGTGTATGTTCAACCAGG 58.578 37.037 29.43 10.59 42.62 4.45
4791 7439 9.249457 CACATATACTAGTGTATGTTCAACCAG 57.751 37.037 31.40 19.61 42.62 4.00
4792 7440 7.709182 GCACATATACTAGTGTATGTTCAACCA 59.291 37.037 31.40 0.00 42.62 3.67
4793 7441 7.926555 AGCACATATACTAGTGTATGTTCAACC 59.073 37.037 31.40 20.39 42.62 3.77
4801 7449 6.978674 ACACCAGCACATATACTAGTGTAT 57.021 37.500 5.39 5.93 37.06 2.29
5115 7790 8.533965 CATGGCATGTTCAAAAATATTTCTACG 58.466 33.333 19.32 0.00 0.00 3.51
5223 7927 7.036996 TGTTCATGCAGTGTTAGAAAAATGA 57.963 32.000 0.00 0.00 0.00 2.57
5357 8071 6.884832 TCTTTCTTTTCCTTTTTCCTTTCCC 58.115 36.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.