Multiple sequence alignment - TraesCS2D01G252800

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 TraesCS2D01G252800 chr2D 100.000 5320 0 0 489 5808 304963025 304968344 0.000000e+00 9825.0
1 TraesCS2D01G252800 chr2D 100.000 210 0 0 1 210 304962537 304962746 7.060000e-104 388.0
2 TraesCS2D01G252800 chr2D 95.425 153 7 0 5656 5808 393072270 393072422 1.620000e-60 244.0
3 TraesCS2D01G252800 chr2D 87.440 207 24 1 4 210 536478260 536478464 2.710000e-58 237.0
4 TraesCS2D01G252800 chr2D 93.548 155 9 1 5655 5808 36032828 36032674 4.530000e-56 230.0
5 TraesCS2D01G252800 chr2D 87.692 130 15 1 516 644 536478618 536478747 3.630000e-32 150.0
6 TraesCS2D01G252800 chr2B 95.206 3880 124 24 1489 5334 373477269 373481120 0.000000e+00 6078.0
7 TraesCS2D01G252800 chr2B 94.828 870 26 10 598 1450 373476276 373477143 0.000000e+00 1339.0
8 TraesCS2D01G252800 chr2B 89.778 225 16 3 5380 5599 373481121 373481343 1.230000e-71 281.0
9 TraesCS2D01G252800 chr2B 91.667 48 4 0 5335 5382 274029649 274029602 3.760000e-07 67.6
10 TraesCS2D01G252800 chr2B 91.667 48 4 0 5335 5382 799577774 799577821 3.760000e-07 67.6
11 TraesCS2D01G252800 chr3A 87.798 1721 143 23 2621 4282 11893982 11892270 0.000000e+00 1953.0
12 TraesCS2D01G252800 chr3A 90.728 453 38 1 4369 4817 11892184 11891732 8.330000e-168 601.0
13 TraesCS2D01G252800 chr3A 83.564 578 52 23 928 1477 11895242 11894680 8.690000e-138 501.0
14 TraesCS2D01G252800 chr3A 93.464 153 10 0 5656 5808 645094630 645094478 1.630000e-55 228.0
15 TraesCS2D01G252800 chr2A 83.983 1667 237 20 2623 4284 383598823 383600464 0.000000e+00 1572.0
16 TraesCS2D01G252800 chr2A 94.219 640 32 5 675 1311 383596752 383597389 0.000000e+00 972.0
17 TraesCS2D01G252800 chr2A 82.486 177 17 5 1947 2110 383598140 383598315 6.070000e-30 143.0
18 TraesCS2D01G252800 chr3D 86.410 883 91 14 3414 4282 9096543 9097410 0.000000e+00 939.0
19 TraesCS2D01G252800 chr3D 89.280 653 49 10 2588 3223 9095898 9096546 0.000000e+00 798.0
20 TraesCS2D01G252800 chr3D 88.377 499 48 4 4371 4859 9097493 9097991 5.010000e-165 592.0
21 TraesCS2D01G252800 chr3D 83.188 690 63 32 814 1477 9093999 9094661 3.020000e-162 582.0
22 TraesCS2D01G252800 chr7D 90.594 202 17 1 9 210 124629292 124629491 3.450000e-67 267.0
23 TraesCS2D01G252800 chr7D 95.425 153 7 0 5656 5808 448510473 448510625 1.620000e-60 244.0
24 TraesCS2D01G252800 chr7D 93.506 154 10 0 5655 5808 105360818 105360665 4.530000e-56 230.0
25 TraesCS2D01G252800 chr7D 86.538 208 23 3 5 210 613398160 613397956 2.110000e-54 224.0
26 TraesCS2D01G252800 chr1A 89.048 210 20 1 1 210 578936857 578936651 2.080000e-64 257.0
27 TraesCS2D01G252800 chr1A 86.224 196 24 2 1 195 136962270 136962463 5.900000e-50 209.0
28 TraesCS2D01G252800 chr7A 91.444 187 14 1 4 190 127037634 127037818 7.470000e-64 255.0
29 TraesCS2D01G252800 chr7A 87.560 209 21 3 4 210 704780594 704780389 2.710000e-58 237.0
30 TraesCS2D01G252800 chr7A 94.444 90 5 0 519 608 127038170 127038259 7.850000e-29 139.0
31 TraesCS2D01G252800 chr5B 89.655 203 18 3 1 202 282008349 282008149 7.470000e-64 255.0
32 TraesCS2D01G252800 chr5B 93.464 153 10 0 5656 5808 295166489 295166337 1.630000e-55 228.0
33 TraesCS2D01G252800 chr6B 87.981 208 17 5 4 210 619496605 619496405 7.520000e-59 239.0
34 TraesCS2D01G252800 chr6B 88.325 197 20 3 5 201 711416353 711416546 3.500000e-57 233.0
35 TraesCS2D01G252800 chr6B 87.701 187 19 3 1 185 632284593 632284777 1.270000e-51 215.0
36 TraesCS2D01G252800 chr6B 89.313 131 14 0 516 646 710895118 710894988 1.290000e-36 165.0
37 TraesCS2D01G252800 chr6B 87.786 131 16 0 516 646 710945500 710945630 2.800000e-33 154.0
38 TraesCS2D01G252800 chr6B 86.260 131 18 0 516 646 710931820 710931950 6.070000e-30 143.0
39 TraesCS2D01G252800 chr4A 94.805 154 7 1 5656 5808 203955210 203955363 7.520000e-59 239.0
40 TraesCS2D01G252800 chr4A 93.548 155 10 0 5653 5807 63748038 63748192 1.260000e-56 231.0
41 TraesCS2D01G252800 chr6A 93.506 154 8 2 5656 5808 297778539 297778691 1.630000e-55 228.0
42 TraesCS2D01G252800 chr6A 94.444 54 2 1 515 567 60656943 60656890 1.340000e-11 82.4
43 TraesCS2D01G252800 chr6A 92.000 50 4 0 5333 5382 169203397 169203348 2.900000e-08 71.3
44 TraesCS2D01G252800 chr4B 88.083 193 20 3 10 202 27119314 27119125 5.860000e-55 226.0
45 TraesCS2D01G252800 chr4B 85.714 196 25 3 11 206 509031774 509031966 2.740000e-48 204.0
46 TraesCS2D01G252800 chr4B 84.211 133 21 0 516 648 509032316 509032448 4.720000e-26 130.0
47 TraesCS2D01G252800 chr5D 90.964 166 13 1 5 170 111957296 111957459 7.580000e-54 222.0
48 TraesCS2D01G252800 chr5D 92.481 133 9 1 516 648 111957909 111958040 7.680000e-44 189.0
49 TraesCS2D01G252800 chr5D 86.154 130 17 1 516 644 249067546 249067417 7.850000e-29 139.0
50 TraesCS2D01G252800 chr3B 87.831 189 21 2 1 188 424117814 424118001 2.720000e-53 220.0
51 TraesCS2D01G252800 chr3B 91.667 48 4 0 5335 5382 156913569 156913522 3.760000e-07 67.6
52 TraesCS2D01G252800 chr3B 91.667 48 4 0 5335 5382 801314215 801314262 3.760000e-07 67.6
53 TraesCS2D01G252800 chr4D 91.946 149 11 1 5 152 504228075 504227927 2.120000e-49 207.0
54 TraesCS2D01G252800 chr4D 90.840 131 11 1 516 646 504227811 504227682 2.150000e-39 174.0
55 TraesCS2D01G252800 chr4D 86.466 133 18 0 516 648 442746708 442746840 4.690000e-31 147.0
56 TraesCS2D01G252800 chr5A 83.575 207 25 8 8 210 331859451 331859250 9.940000e-43 185.0
57 TraesCS2D01G252800 chr5A 91.667 48 4 0 5335 5382 670269929 670269976 3.760000e-07 67.6
58 TraesCS2D01G252800 chr7B 92.000 50 4 0 5333 5382 131183320 131183271 2.900000e-08 71.3
59 TraesCS2D01G252800 chr7B 91.667 48 4 0 5335 5382 673616987 673617034 3.760000e-07 67.6
60 TraesCS2D01G252800 chr1D 95.349 43 2 0 5333 5375 387532942 387532984 1.040000e-07 69.4


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 TraesCS2D01G252800 chr2D 304962537 304968344 5807 False 5106.500000 9825 100.000000 1 5808 2 chr2D.!!$F2 5807
1 TraesCS2D01G252800 chr2B 373476276 373481343 5067 False 2566.000000 6078 93.270667 598 5599 3 chr2B.!!$F2 5001
2 TraesCS2D01G252800 chr3A 11891732 11895242 3510 True 1018.333333 1953 87.363333 928 4817 3 chr3A.!!$R2 3889
3 TraesCS2D01G252800 chr2A 383596752 383600464 3712 False 895.666667 1572 86.896000 675 4284 3 chr2A.!!$F1 3609
4 TraesCS2D01G252800 chr3D 9093999 9097991 3992 False 727.750000 939 86.813750 814 4859 4 chr3D.!!$F1 4045
5 TraesCS2D01G252800 chr5D 111957296 111958040 744 False 205.500000 222 91.722500 5 648 2 chr5D.!!$F1 643

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
166 167 0.305313 TTTTTCTTTCGACACCGGCG 59.695 50.000 0.00 0.0 36.24 6.46 F
1388 1571 0.042448 GTCTGTGCGTTTCCGTGTTC 60.042 55.000 0.00 0.0 36.15 3.18 F
2256 3058 1.141254 TCGGCTCCAAAAAGTGTACCA 59.859 47.619 0.00 0.0 0.00 3.25 F
3201 4064 0.240411 AGGTCGACACGCTTGAGTAC 59.760 55.000 18.91 0.0 0.00 2.73 F
3833 4696 0.796312 ATTGTTACGACGCTTGGCAG 59.204 50.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2112 0.239347 ACGCATTGCTCTTGCTTGTC 59.761 50.000 7.12 0.0 40.48 3.18 R
3118 3981 0.108585 GTGCCCTCAGGTCTGTTTGA 59.891 55.000 0.00 0.0 34.57 2.69 R
3525 4388 1.279271 GGCAGCTTCTCCCTCAGTTTA 59.721 52.381 0.00 0.0 0.00 2.01 R
4310 5234 0.171007 ATGCCTATTTGCGCACACAC 59.829 50.000 11.12 0.0 37.93 3.82 R
5676 6625 0.033781 AAAACTACGTGCACGCCCTA 59.966 50.000 37.35 21.7 44.43 3.53 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
154 155 3.575805 TGTCATCCCCAAGCTTTTTCTT 58.424 40.909 0.00 0.00 0.00 2.52
155 156 3.966665 TGTCATCCCCAAGCTTTTTCTTT 59.033 39.130 0.00 0.00 0.00 2.52
156 157 4.039124 TGTCATCCCCAAGCTTTTTCTTTC 59.961 41.667 0.00 0.00 0.00 2.62
157 158 3.255642 TCATCCCCAAGCTTTTTCTTTCG 59.744 43.478 0.00 0.00 0.00 3.46
160 161 2.360801 CCCCAAGCTTTTTCTTTCGACA 59.639 45.455 0.00 0.00 0.00 4.35
161 162 3.372060 CCCAAGCTTTTTCTTTCGACAC 58.628 45.455 0.00 0.00 0.00 3.67
162 163 3.372060 CCAAGCTTTTTCTTTCGACACC 58.628 45.455 0.00 0.00 0.00 4.16
163 164 3.035942 CAAGCTTTTTCTTTCGACACCG 58.964 45.455 0.00 0.00 37.07 4.94
164 165 1.602377 AGCTTTTTCTTTCGACACCGG 59.398 47.619 0.00 0.00 36.24 5.28
165 166 1.924629 GCTTTTTCTTTCGACACCGGC 60.925 52.381 0.00 0.00 36.24 6.13
166 167 0.305313 TTTTTCTTTCGACACCGGCG 59.695 50.000 0.00 0.00 36.24 6.46
184 185 3.361977 GCGGCGTGTGGATGGTTT 61.362 61.111 9.37 0.00 0.00 3.27
185 186 2.867472 CGGCGTGTGGATGGTTTC 59.133 61.111 0.00 0.00 0.00 2.78
186 187 2.686816 CGGCGTGTGGATGGTTTCC 61.687 63.158 0.00 0.00 45.69 3.13
204 205 2.851104 GGTGACGAAAAGCCGACG 59.149 61.111 0.00 0.00 0.00 5.12
205 206 2.170273 GTGACGAAAAGCCGACGC 59.830 61.111 0.00 0.00 0.00 5.19
520 521 4.759205 GGGTTGGCGGCAGGGAAT 62.759 66.667 12.87 0.00 0.00 3.01
567 670 7.387119 ACTCCATTAACGTTTTTAAGGGATC 57.613 36.000 14.17 0.00 41.93 3.36
568 671 6.943718 ACTCCATTAACGTTTTTAAGGGATCA 59.056 34.615 14.17 0.00 41.93 2.92
595 698 3.007290 GGTCCGTTGTAAGGGAGTAAACT 59.993 47.826 6.31 0.00 43.02 2.66
649 752 6.538263 AGGATCAGTTAGAAATGCCCTTATC 58.462 40.000 0.00 0.00 0.00 1.75
654 757 6.759827 TCAGTTAGAAATGCCCTTATCGTTAC 59.240 38.462 0.00 0.00 0.00 2.50
664 767 3.195661 CCTTATCGTTACACAAGAGGCC 58.804 50.000 0.00 0.00 0.00 5.19
666 769 2.094762 ATCGTTACACAAGAGGCCAC 57.905 50.000 5.01 0.00 0.00 5.01
668 771 1.289109 CGTTACACAAGAGGCCACGG 61.289 60.000 5.01 0.00 0.00 4.94
671 774 1.541310 TACACAAGAGGCCACGGAGG 61.541 60.000 5.01 0.00 41.84 4.30
705 812 4.439253 AAAGGGGAAGGGATTCGAATAG 57.561 45.455 11.38 0.00 0.00 1.73
720 827 6.747659 TTCGAATAGTTGAAAAGCAAAAGC 57.252 33.333 0.00 0.00 38.44 3.51
770 877 2.447714 GCTGATCTCCCTGGTCCCC 61.448 68.421 0.00 0.00 0.00 4.81
775 882 4.024984 CTCCCTGGTCCCCTCCCA 62.025 72.222 0.00 0.00 0.00 4.37
892 1003 2.121645 CATCCAATGCTTGCCCCTC 58.878 57.895 0.00 0.00 0.00 4.30
895 1006 2.037687 CAATGCTTGCCCCTCCCA 59.962 61.111 0.00 0.00 0.00 4.37
896 1007 2.037847 AATGCTTGCCCCTCCCAC 59.962 61.111 0.00 0.00 0.00 4.61
900 1011 3.350163 CTTGCCCCTCCCACCCAT 61.350 66.667 0.00 0.00 0.00 4.00
902 1013 1.545173 TTGCCCCTCCCACCCATTA 60.545 57.895 0.00 0.00 0.00 1.90
903 1014 1.869824 TTGCCCCTCCCACCCATTAC 61.870 60.000 0.00 0.00 0.00 1.89
904 1015 2.006991 GCCCCTCCCACCCATTACT 61.007 63.158 0.00 0.00 0.00 2.24
905 1016 1.922821 CCCCTCCCACCCATTACTG 59.077 63.158 0.00 0.00 0.00 2.74
913 1026 2.489073 CCCACCCATTACTGCCCTAATC 60.489 54.545 0.00 0.00 0.00 1.75
1042 1158 0.733223 GTCGCTTCTGACGTCCTTCC 60.733 60.000 14.12 0.00 0.00 3.46
1388 1571 0.042448 GTCTGTGCGTTTCCGTGTTC 60.042 55.000 0.00 0.00 36.15 3.18
1393 1576 1.843753 GTGCGTTTCCGTGTTCTTTTG 59.156 47.619 0.00 0.00 36.15 2.44
1483 1733 9.872721 GATTCTCTGATGAATCTGCTATATTCA 57.127 33.333 16.08 10.10 45.18 2.57
1484 1734 9.878667 ATTCTCTGATGAATCTGCTATATTCAG 57.121 33.333 12.32 0.00 44.27 3.02
1485 1735 8.419922 TCTCTGATGAATCTGCTATATTCAGT 57.580 34.615 12.32 4.27 44.27 3.41
1518 1946 5.659440 AAAAATGGTGCCATGTTAGTAGG 57.341 39.130 7.03 0.00 33.11 3.18
1526 1954 4.571176 GTGCCATGTTAGTAGGAAGTTAGC 59.429 45.833 0.00 0.00 0.00 3.09
1528 1956 4.811557 GCCATGTTAGTAGGAAGTTAGCTG 59.188 45.833 0.00 0.00 0.00 4.24
1546 1974 8.090214 AGTTAGCTGCATGTTTGATTGTTTTAT 58.910 29.630 1.02 0.00 0.00 1.40
1582 2011 7.171508 TCAACATGAAGATAAGCCGATTGTATC 59.828 37.037 0.00 0.00 0.00 2.24
1639 2071 8.669243 ACTGCTGCTATCAGTTTACTTTAAATC 58.331 33.333 0.00 0.00 41.61 2.17
1668 2112 2.095718 GCTGCGAAGAAAAAGGTGTAGG 60.096 50.000 0.00 0.00 0.00 3.18
1681 2365 1.270839 GGTGTAGGACAAGCAAGAGCA 60.271 52.381 0.00 0.00 45.49 4.26
1718 2402 1.486211 AGAGGAGTTATCACCACCCG 58.514 55.000 0.00 0.00 0.00 5.28
1728 2466 2.122547 ACCACCCGTCCTGAAGGT 60.123 61.111 0.00 0.00 36.34 3.50
1730 2468 2.663196 CACCCGTCCTGAAGGTCC 59.337 66.667 0.00 0.00 36.34 4.46
1763 2501 7.164122 ACGAGATAAAACTATCATGCATGGAT 58.836 34.615 25.97 18.83 0.00 3.41
1790 2528 6.925610 TGCTGGAAGTATGTAATTTAGCAG 57.074 37.500 0.00 0.00 32.79 4.24
1791 2529 5.296780 TGCTGGAAGTATGTAATTTAGCAGC 59.703 40.000 0.00 0.00 32.79 5.25
1792 2530 5.296780 GCTGGAAGTATGTAATTTAGCAGCA 59.703 40.000 0.00 0.00 35.30 4.41
1816 2555 9.099454 GCATGTTAAACTGCTTAGTCTATAGTT 57.901 33.333 0.00 0.00 35.49 2.24
1854 2597 1.384222 GGCTAGGATGCGTTTTGGGG 61.384 60.000 0.00 0.00 0.00 4.96
1866 2609 3.139077 CGTTTTGGGGTCAGATATAGGC 58.861 50.000 0.00 0.00 0.00 3.93
1927 2698 2.925578 TCATGCAGATTTTTCGCCAG 57.074 45.000 0.00 0.00 0.00 4.85
2224 3022 4.832266 TGCTTGATCCGCCCATTTAATAAT 59.168 37.500 2.13 0.00 0.00 1.28
2256 3058 1.141254 TCGGCTCCAAAAAGTGTACCA 59.859 47.619 0.00 0.00 0.00 3.25
2337 3139 3.067320 TCAGAATGGCAGTATCTGTCTCG 59.933 47.826 20.37 3.04 41.04 4.04
2420 3222 2.802816 CTGCTGCGTGATAAGTATTCCC 59.197 50.000 0.00 0.00 0.00 3.97
2546 3363 9.844790 TGAAAATAGTGATATTGAAAACTGCAG 57.155 29.630 13.48 13.48 0.00 4.41
2810 3640 2.875933 CGTTAAACCAGAGGAGTTTGCA 59.124 45.455 0.00 0.00 37.93 4.08
2969 3807 3.838903 TCAGAGGTTCTTTAGGGGAGTTC 59.161 47.826 0.00 0.00 0.00 3.01
3071 3934 4.277515 TCCAAGAGATTGAAGGTCACAG 57.722 45.455 0.00 0.00 0.00 3.66
3111 3974 3.451526 TGAAGCTGTCTATGCAGAATCG 58.548 45.455 0.00 0.00 38.70 3.34
3118 3981 5.220739 GCTGTCTATGCAGAATCGAAAACAT 60.221 40.000 0.00 0.00 38.70 2.71
3201 4064 0.240411 AGGTCGACACGCTTGAGTAC 59.760 55.000 18.91 0.00 0.00 2.73
3525 4388 1.001974 TCTGCTGTTACAACGCTGGAT 59.998 47.619 12.16 0.00 32.72 3.41
3612 4475 2.224867 ACAAGCTTACCTGCCACAGATT 60.225 45.455 0.00 0.00 32.44 2.40
3693 4556 2.087646 GGAATTCCTTCACAGAGCCAC 58.912 52.381 17.73 0.00 32.70 5.01
3833 4696 0.796312 ATTGTTACGACGCTTGGCAG 59.204 50.000 0.00 0.00 0.00 4.85
3916 4793 5.120674 TGTCTCATTTATGCACTTTCTGTCG 59.879 40.000 0.00 0.00 0.00 4.35
3929 4824 1.905637 TCTGTCGTGAGCTTCCACTA 58.094 50.000 4.26 0.00 35.02 2.74
4295 5219 7.822334 ACGAAAATGTATGTTGATCAGTCCTAA 59.178 33.333 0.00 0.00 0.00 2.69
4310 5234 5.877012 TCAGTCCTAAGCATAGCTCTTTTTG 59.123 40.000 0.00 0.00 38.25 2.44
4403 5337 4.425180 TTCACAAGTGGCTTACCTTACA 57.575 40.909 0.00 0.00 36.63 2.41
4544 5478 1.544093 CCATGCTTGGTATCATCGGCT 60.544 52.381 10.48 0.00 38.30 5.52
4565 5499 6.254589 CGGCTTGAAGAAGTTCTACTATTCTG 59.745 42.308 5.65 0.00 33.67 3.02
4711 5645 0.958382 TGAGCACCATTTACACCGCC 60.958 55.000 0.00 0.00 0.00 6.13
4762 5696 2.926838 GCTCGAAGATGTGGAAGTCTTC 59.073 50.000 3.80 3.80 44.27 2.87
4818 5757 6.255237 GCTCCGTCCTTTTAATGTAAGTAGTC 59.745 42.308 0.00 0.00 0.00 2.59
4859 5803 4.443978 ACCATTAGAATCACAGGGATGG 57.556 45.455 0.00 0.00 36.02 3.51
4860 5804 4.047166 ACCATTAGAATCACAGGGATGGA 58.953 43.478 6.48 0.00 36.02 3.41
4881 5826 4.987912 GGAATTGCCGTCAAATTTCTGAAA 59.012 37.500 5.15 5.15 35.56 2.69
4942 5887 9.947433 AATTTGAATTTGAATTTCTGCAGGATA 57.053 25.926 15.13 0.00 0.00 2.59
5001 5946 1.956170 CGACCACGCTGTGAAGCTT 60.956 57.895 0.00 0.00 35.23 3.74
5071 6016 3.191162 GGCTGTTGCATGATGAACACTTA 59.809 43.478 0.00 0.00 41.91 2.24
5078 6023 7.595875 TGTTGCATGATGAACACTTATTGAAAG 59.404 33.333 0.00 0.00 0.00 2.62
5083 6028 7.117241 TGATGAACACTTATTGAAAGACGTC 57.883 36.000 7.70 7.70 0.00 4.34
5288 6233 6.489700 TGTCCATGCTTGTATTCAGAAAAAGA 59.510 34.615 7.47 0.00 0.00 2.52
5314 6259 1.609072 GTTTGTGCCTCCTGAAGAACC 59.391 52.381 0.00 0.00 0.00 3.62
5317 6262 0.250338 GTGCCTCCTGAAGAACCGTT 60.250 55.000 0.00 0.00 0.00 4.44
5334 6279 0.323957 GTTCCAGCTCTTTACGGGGT 59.676 55.000 0.00 0.00 0.00 4.95
5335 6280 1.551883 GTTCCAGCTCTTTACGGGGTA 59.448 52.381 0.00 0.00 0.00 3.69
5336 6281 1.188863 TCCAGCTCTTTACGGGGTAC 58.811 55.000 0.00 0.00 0.00 3.34
5337 6282 1.192428 CCAGCTCTTTACGGGGTACT 58.808 55.000 0.00 0.00 0.00 2.73
5338 6283 1.553704 CCAGCTCTTTACGGGGTACTT 59.446 52.381 0.00 0.00 0.00 2.24
5339 6284 2.418334 CCAGCTCTTTACGGGGTACTTC 60.418 54.545 0.00 0.00 0.00 3.01
5340 6285 1.829849 AGCTCTTTACGGGGTACTTCC 59.170 52.381 0.00 0.00 0.00 3.46
5341 6286 1.829849 GCTCTTTACGGGGTACTTCCT 59.170 52.381 0.00 0.00 36.25 3.36
5342 6287 2.159128 GCTCTTTACGGGGTACTTCCTC 60.159 54.545 0.00 0.00 36.25 3.71
5343 6288 2.429971 CTCTTTACGGGGTACTTCCTCC 59.570 54.545 0.00 0.00 36.25 4.30
5346 6291 3.204418 CGGGGTACTTCCTCCGTC 58.796 66.667 0.00 0.00 41.66 4.79
5347 6292 1.379576 CGGGGTACTTCCTCCGTCT 60.380 63.158 0.00 0.00 41.66 4.18
5348 6293 1.382692 CGGGGTACTTCCTCCGTCTC 61.383 65.000 0.00 0.00 41.66 3.36
5349 6294 0.324091 GGGGTACTTCCTCCGTCTCA 60.324 60.000 0.00 0.00 36.25 3.27
5350 6295 1.688627 GGGGTACTTCCTCCGTCTCAT 60.689 57.143 0.00 0.00 36.25 2.90
5351 6296 2.423947 GGGGTACTTCCTCCGTCTCATA 60.424 54.545 0.00 0.00 36.25 2.15
5352 6297 3.294214 GGGTACTTCCTCCGTCTCATAA 58.706 50.000 0.00 0.00 36.25 1.90
5353 6298 3.896272 GGGTACTTCCTCCGTCTCATAAT 59.104 47.826 0.00 0.00 36.25 1.28
5354 6299 4.262079 GGGTACTTCCTCCGTCTCATAATG 60.262 50.000 0.00 0.00 36.25 1.90
5355 6300 4.341520 GGTACTTCCTCCGTCTCATAATGT 59.658 45.833 0.00 0.00 0.00 2.71
5356 6301 5.533903 GGTACTTCCTCCGTCTCATAATGTA 59.466 44.000 0.00 0.00 0.00 2.29
5357 6302 6.040166 GGTACTTCCTCCGTCTCATAATGTAA 59.960 42.308 0.00 0.00 0.00 2.41
5358 6303 6.150396 ACTTCCTCCGTCTCATAATGTAAG 57.850 41.667 0.00 0.00 0.00 2.34
5359 6304 5.892119 ACTTCCTCCGTCTCATAATGTAAGA 59.108 40.000 0.00 0.00 0.00 2.10
5360 6305 5.769484 TCCTCCGTCTCATAATGTAAGAC 57.231 43.478 0.00 0.00 36.82 3.01
5441 6390 5.733620 TTCGGGTCATATCCTACATAACC 57.266 43.478 0.00 0.00 0.00 2.85
5518 6467 6.939730 TCAACATGTAACTATGCAGGAGAAAA 59.060 34.615 0.00 0.00 0.00 2.29
5566 6515 8.546083 TGTATATGGGAAAATGCATACCTTTT 57.454 30.769 0.00 0.00 0.00 2.27
5661 6610 6.935167 ACAAAATTCCATGTTTCATACTCCC 58.065 36.000 0.00 0.00 0.00 4.30
5662 6611 6.725834 ACAAAATTCCATGTTTCATACTCCCT 59.274 34.615 0.00 0.00 0.00 4.20
5663 6612 7.093771 ACAAAATTCCATGTTTCATACTCCCTC 60.094 37.037 0.00 0.00 0.00 4.30
5664 6613 5.983333 ATTCCATGTTTCATACTCCCTCT 57.017 39.130 0.00 0.00 0.00 3.69
5665 6614 4.760530 TCCATGTTTCATACTCCCTCTG 57.239 45.455 0.00 0.00 0.00 3.35
5666 6615 4.104086 TCCATGTTTCATACTCCCTCTGT 58.896 43.478 0.00 0.00 0.00 3.41
5667 6616 4.162320 TCCATGTTTCATACTCCCTCTGTC 59.838 45.833 0.00 0.00 0.00 3.51
5668 6617 4.163078 CCATGTTTCATACTCCCTCTGTCT 59.837 45.833 0.00 0.00 0.00 3.41
5669 6618 5.355596 CATGTTTCATACTCCCTCTGTCTC 58.644 45.833 0.00 0.00 0.00 3.36
5670 6619 3.444034 TGTTTCATACTCCCTCTGTCTCG 59.556 47.826 0.00 0.00 0.00 4.04
5671 6620 2.350057 TCATACTCCCTCTGTCTCGG 57.650 55.000 0.00 0.00 0.00 4.63
5672 6621 1.564818 TCATACTCCCTCTGTCTCGGT 59.435 52.381 0.00 0.00 0.00 4.69
5673 6622 2.025226 TCATACTCCCTCTGTCTCGGTT 60.025 50.000 0.00 0.00 0.00 4.44
5674 6623 2.599408 TACTCCCTCTGTCTCGGTTT 57.401 50.000 0.00 0.00 0.00 3.27
5675 6624 2.599408 ACTCCCTCTGTCTCGGTTTA 57.401 50.000 0.00 0.00 0.00 2.01
5676 6625 3.103080 ACTCCCTCTGTCTCGGTTTAT 57.897 47.619 0.00 0.00 0.00 1.40
5677 6626 4.246712 ACTCCCTCTGTCTCGGTTTATA 57.753 45.455 0.00 0.00 0.00 0.98
5678 6627 4.208746 ACTCCCTCTGTCTCGGTTTATAG 58.791 47.826 0.00 0.00 0.00 1.31
5679 6628 3.563223 TCCCTCTGTCTCGGTTTATAGG 58.437 50.000 0.00 0.00 0.00 2.57
5680 6629 2.628657 CCCTCTGTCTCGGTTTATAGGG 59.371 54.545 0.00 0.00 36.73 3.53
5681 6630 2.036089 CCTCTGTCTCGGTTTATAGGGC 59.964 54.545 0.00 0.00 0.00 5.19
5682 6631 1.679680 TCTGTCTCGGTTTATAGGGCG 59.320 52.381 0.00 0.00 0.00 6.13
5683 6632 1.407979 CTGTCTCGGTTTATAGGGCGT 59.592 52.381 0.00 0.00 0.00 5.68
5684 6633 1.135527 TGTCTCGGTTTATAGGGCGTG 59.864 52.381 0.00 0.00 0.00 5.34
5685 6634 0.103572 TCTCGGTTTATAGGGCGTGC 59.896 55.000 0.00 0.00 0.00 5.34
5686 6635 0.179094 CTCGGTTTATAGGGCGTGCA 60.179 55.000 0.00 0.00 0.00 4.57
5687 6636 0.460635 TCGGTTTATAGGGCGTGCAC 60.461 55.000 6.82 6.82 0.00 4.57
5688 6637 1.758319 CGGTTTATAGGGCGTGCACG 61.758 60.000 34.01 34.01 43.27 5.34
5689 6638 0.741927 GGTTTATAGGGCGTGCACGT 60.742 55.000 36.80 22.06 42.22 4.49
5690 6639 1.471327 GGTTTATAGGGCGTGCACGTA 60.471 52.381 36.80 23.46 42.22 3.57
5691 6640 1.856597 GTTTATAGGGCGTGCACGTAG 59.143 52.381 36.80 13.39 42.22 3.51
5693 6642 1.105457 TATAGGGCGTGCACGTAGTT 58.895 50.000 36.80 22.82 41.61 2.24
5694 6643 0.248289 ATAGGGCGTGCACGTAGTTT 59.752 50.000 36.80 21.23 41.61 2.66
5695 6644 0.033781 TAGGGCGTGCACGTAGTTTT 59.966 50.000 36.80 19.97 41.61 2.43
5696 6645 0.033781 AGGGCGTGCACGTAGTTTTA 59.966 50.000 36.80 0.00 41.61 1.52
5697 6646 0.441145 GGGCGTGCACGTAGTTTTAG 59.559 55.000 36.80 9.58 41.61 1.85
5698 6647 1.421382 GGCGTGCACGTAGTTTTAGA 58.579 50.000 36.80 0.00 41.61 2.10
5699 6648 1.997606 GGCGTGCACGTAGTTTTAGAT 59.002 47.619 36.80 0.00 41.61 1.98
5700 6649 2.414138 GGCGTGCACGTAGTTTTAGATT 59.586 45.455 36.80 0.00 41.61 2.40
5701 6650 3.613737 GGCGTGCACGTAGTTTTAGATTA 59.386 43.478 36.80 0.00 41.61 1.75
5702 6651 4.269363 GGCGTGCACGTAGTTTTAGATTAT 59.731 41.667 36.80 0.00 41.61 1.28
5703 6652 5.421203 GCGTGCACGTAGTTTTAGATTATC 58.579 41.667 36.80 13.22 41.61 1.75
5704 6653 5.555818 GCGTGCACGTAGTTTTAGATTATCC 60.556 44.000 36.80 12.84 41.61 2.59
5705 6654 5.517411 CGTGCACGTAGTTTTAGATTATCCA 59.483 40.000 30.50 0.00 41.61 3.41
5706 6655 6.200286 CGTGCACGTAGTTTTAGATTATCCAT 59.800 38.462 30.50 0.00 41.61 3.41
5707 6656 7.254319 CGTGCACGTAGTTTTAGATTATCCATT 60.254 37.037 30.50 0.00 41.61 3.16
5708 6657 8.395633 GTGCACGTAGTTTTAGATTATCCATTT 58.604 33.333 0.00 0.00 41.61 2.32
5709 6658 8.394877 TGCACGTAGTTTTAGATTATCCATTTG 58.605 33.333 0.00 0.00 41.61 2.32
5710 6659 8.609176 GCACGTAGTTTTAGATTATCCATTTGA 58.391 33.333 0.00 0.00 41.61 2.69
5711 6660 9.916397 CACGTAGTTTTAGATTATCCATTTGAC 57.084 33.333 0.00 0.00 41.61 3.18
5712 6661 9.886132 ACGTAGTTTTAGATTATCCATTTGACT 57.114 29.630 0.00 0.00 37.78 3.41
5766 6715 9.778741 AAGTATATCATTGAATTCTTAAGCGGA 57.221 29.630 7.05 0.00 0.00 5.54
5767 6716 9.950496 AGTATATCATTGAATTCTTAAGCGGAT 57.050 29.630 7.05 3.46 0.00 4.18
5768 6717 9.979270 GTATATCATTGAATTCTTAAGCGGATG 57.021 33.333 7.05 0.00 0.00 3.51
5769 6718 6.949352 ATCATTGAATTCTTAAGCGGATGT 57.051 33.333 7.05 0.00 0.00 3.06
5770 6719 9.725019 ATATCATTGAATTCTTAAGCGGATGTA 57.275 29.630 7.05 0.00 0.00 2.29
5771 6720 7.482654 TCATTGAATTCTTAAGCGGATGTAG 57.517 36.000 7.05 0.00 0.00 2.74
5772 6721 7.047891 TCATTGAATTCTTAAGCGGATGTAGT 58.952 34.615 7.05 0.00 0.00 2.73
5773 6722 7.552687 TCATTGAATTCTTAAGCGGATGTAGTT 59.447 33.333 7.05 0.00 0.00 2.24
5774 6723 7.681939 TTGAATTCTTAAGCGGATGTAGTTT 57.318 32.000 7.05 0.00 0.00 2.66
5775 6724 7.681939 TGAATTCTTAAGCGGATGTAGTTTT 57.318 32.000 7.05 0.00 0.00 2.43
5776 6725 8.106247 TGAATTCTTAAGCGGATGTAGTTTTT 57.894 30.769 7.05 0.00 0.00 1.94
5777 6726 9.221933 TGAATTCTTAAGCGGATGTAGTTTTTA 57.778 29.630 7.05 0.00 0.00 1.52
5780 6729 9.836076 ATTCTTAAGCGGATGTAGTTTTTAAAC 57.164 29.630 0.00 0.00 39.17 2.01
5781 6730 8.380743 TCTTAAGCGGATGTAGTTTTTAAACA 57.619 30.769 7.97 0.00 41.30 2.83
5782 6731 9.005777 TCTTAAGCGGATGTAGTTTTTAAACAT 57.994 29.630 7.97 0.00 41.30 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 4.394712 AAGCTCCGCCTCCAACCG 62.395 66.667 0.00 0.00 0.00 4.44
109 110 2.046892 CACCAGGTCCAAGCTCCG 60.047 66.667 0.00 0.00 0.00 4.63
122 123 1.203001 GGGGATGACAAAGAACCACCA 60.203 52.381 0.00 0.00 0.00 4.17
168 169 2.867472 GAAACCATCCACACGCCG 59.133 61.111 0.00 0.00 0.00 6.46
176 177 0.320946 TTCGTCACCGGAAACCATCC 60.321 55.000 9.46 0.00 45.57 3.51
177 178 1.515081 TTTCGTCACCGGAAACCATC 58.485 50.000 9.46 0.00 33.95 3.51
178 179 1.877443 CTTTTCGTCACCGGAAACCAT 59.123 47.619 9.46 0.00 36.65 3.55
179 180 1.301423 CTTTTCGTCACCGGAAACCA 58.699 50.000 9.46 0.00 36.65 3.67
180 181 0.040692 GCTTTTCGTCACCGGAAACC 60.041 55.000 9.46 0.00 36.65 3.27
181 182 0.040692 GGCTTTTCGTCACCGGAAAC 60.041 55.000 9.46 4.43 36.65 2.78
182 183 1.500512 CGGCTTTTCGTCACCGGAAA 61.501 55.000 9.46 0.00 41.95 3.13
183 184 1.957186 CGGCTTTTCGTCACCGGAA 60.957 57.895 9.46 0.00 41.95 4.30
184 185 2.356553 CGGCTTTTCGTCACCGGA 60.357 61.111 9.46 0.00 41.95 5.14
185 186 2.356553 TCGGCTTTTCGTCACCGG 60.357 61.111 0.00 0.00 45.65 5.28
186 187 2.851104 GTCGGCTTTTCGTCACCG 59.149 61.111 0.00 0.00 46.97 4.94
187 188 2.851104 CGTCGGCTTTTCGTCACC 59.149 61.111 0.00 0.00 0.00 4.02
188 189 2.170273 GCGTCGGCTTTTCGTCAC 59.830 61.111 0.00 0.00 35.83 3.67
503 504 3.352990 TATTCCCTGCCGCCAACCC 62.353 63.158 0.00 0.00 0.00 4.11
504 505 1.823899 CTATTCCCTGCCGCCAACC 60.824 63.158 0.00 0.00 0.00 3.77
505 506 1.823899 CCTATTCCCTGCCGCCAAC 60.824 63.158 0.00 0.00 0.00 3.77
506 507 2.595095 CCTATTCCCTGCCGCCAA 59.405 61.111 0.00 0.00 0.00 4.52
507 508 3.488569 CCCTATTCCCTGCCGCCA 61.489 66.667 0.00 0.00 0.00 5.69
508 509 3.168528 TCCCTATTCCCTGCCGCC 61.169 66.667 0.00 0.00 0.00 6.13
509 510 1.984288 AACTCCCTATTCCCTGCCGC 61.984 60.000 0.00 0.00 0.00 6.53
510 511 0.179045 CAACTCCCTATTCCCTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
511 512 0.183731 CCAACTCCCTATTCCCTGCC 59.816 60.000 0.00 0.00 0.00 4.85
512 513 1.141858 CTCCAACTCCCTATTCCCTGC 59.858 57.143 0.00 0.00 0.00 4.85
513 514 2.482494 ACTCCAACTCCCTATTCCCTG 58.518 52.381 0.00 0.00 0.00 4.45
514 515 2.972153 ACTCCAACTCCCTATTCCCT 57.028 50.000 0.00 0.00 0.00 4.20
515 516 5.446260 TTTTACTCCAACTCCCTATTCCC 57.554 43.478 0.00 0.00 0.00 3.97
516 517 7.956328 AATTTTTACTCCAACTCCCTATTCC 57.044 36.000 0.00 0.00 0.00 3.01
561 664 0.032017 AACGGACCTAGCTGATCCCT 60.032 55.000 0.00 0.00 0.00 4.20
567 670 1.134788 CCCTTACAACGGACCTAGCTG 60.135 57.143 0.00 0.00 0.00 4.24
568 671 1.192428 CCCTTACAACGGACCTAGCT 58.808 55.000 0.00 0.00 0.00 3.32
608 711 8.267620 ACTGATCCTCAATATGGTCATAAAGA 57.732 34.615 0.00 0.00 0.00 2.52
616 719 7.446625 GCATTTCTAACTGATCCTCAATATGGT 59.553 37.037 0.00 0.00 0.00 3.55
649 752 1.289109 CCGTGGCCTCTTGTGTAACG 61.289 60.000 3.32 1.24 42.39 3.18
654 757 2.046892 CCTCCGTGGCCTCTTGTG 60.047 66.667 3.32 0.00 0.00 3.33
664 767 2.923035 ACCACCCTCACCTCCGTG 60.923 66.667 0.00 0.00 41.72 4.94
666 769 1.764571 TTTGACCACCCTCACCTCCG 61.765 60.000 0.00 0.00 0.00 4.63
668 771 1.545651 CCTTTTGACCACCCTCACCTC 60.546 57.143 0.00 0.00 0.00 3.85
671 774 0.539669 CCCCTTTTGACCACCCTCAC 60.540 60.000 0.00 0.00 0.00 3.51
675 778 0.541998 CCTTCCCCTTTTGACCACCC 60.542 60.000 0.00 0.00 0.00 4.61
676 779 0.541998 CCCTTCCCCTTTTGACCACC 60.542 60.000 0.00 0.00 0.00 4.61
678 781 1.466858 ATCCCTTCCCCTTTTGACCA 58.533 50.000 0.00 0.00 0.00 4.02
705 812 2.217429 TCCGGCTTTTGCTTTTCAAC 57.783 45.000 0.00 0.00 46.54 3.18
720 827 1.926426 ATGCCCCTTTCCTCTTCCGG 61.926 60.000 0.00 0.00 0.00 5.14
770 877 2.437651 GGGAGAAGAAGAGGAATGGGAG 59.562 54.545 0.00 0.00 0.00 4.30
775 882 1.843206 GGCAGGGAGAAGAAGAGGAAT 59.157 52.381 0.00 0.00 0.00 3.01
886 997 2.006991 AGTAATGGGTGGGAGGGGC 61.007 63.158 0.00 0.00 0.00 5.80
892 1003 0.923358 TTAGGGCAGTAATGGGTGGG 59.077 55.000 0.00 0.00 0.00 4.61
895 1006 1.780919 GGGATTAGGGCAGTAATGGGT 59.219 52.381 0.00 0.00 0.00 4.51
896 1007 1.075536 GGGGATTAGGGCAGTAATGGG 59.924 57.143 0.00 0.00 0.00 4.00
899 1010 2.349445 GGAGGGGATTAGGGCAGTAAT 58.651 52.381 0.00 0.00 0.00 1.89
900 1011 1.815757 GGAGGGGATTAGGGCAGTAA 58.184 55.000 0.00 0.00 0.00 2.24
902 1013 1.766461 CGGAGGGGATTAGGGCAGT 60.766 63.158 0.00 0.00 0.00 4.40
903 1014 3.151906 CGGAGGGGATTAGGGCAG 58.848 66.667 0.00 0.00 0.00 4.85
904 1015 2.320830 TAGCGGAGGGGATTAGGGCA 62.321 60.000 0.00 0.00 0.00 5.36
905 1016 1.125711 TTAGCGGAGGGGATTAGGGC 61.126 60.000 0.00 0.00 0.00 5.19
913 1026 1.749033 GGAGTGATTAGCGGAGGGG 59.251 63.158 0.00 0.00 0.00 4.79
1042 1158 2.169789 CCAGCACGGCGAAGATGAG 61.170 63.158 16.62 5.29 0.00 2.90
1388 1571 8.110002 GCACGAAATATTATTTGGAAGCAAAAG 58.890 33.333 15.45 0.74 0.00 2.27
1393 1576 6.033341 TGTGCACGAAATATTATTTGGAAGC 58.967 36.000 13.13 16.57 0.00 3.86
1518 1946 5.464168 ACAATCAAACATGCAGCTAACTTC 58.536 37.500 0.00 0.00 0.00 3.01
1526 1954 9.719279 ACAAAAATAAAACAATCAAACATGCAG 57.281 25.926 0.00 0.00 0.00 4.41
1528 1956 9.500864 ACACAAAAATAAAACAATCAAACATGC 57.499 25.926 0.00 0.00 0.00 4.06
1546 1974 9.624697 GCTTATCTTCATGTTGATACACAAAAA 57.375 29.630 8.96 0.00 40.36 1.94
1556 1984 5.185454 ACAATCGGCTTATCTTCATGTTGA 58.815 37.500 0.00 0.00 0.00 3.18
1614 2043 8.668353 TGATTTAAAGTAAACTGATAGCAGCAG 58.332 33.333 8.16 0.00 46.26 4.24
1639 2071 6.415867 CACCTTTTTCTTCGCAGCATTATATG 59.584 38.462 0.00 0.00 0.00 1.78
1644 2076 2.362077 ACACCTTTTTCTTCGCAGCATT 59.638 40.909 0.00 0.00 0.00 3.56
1652 2096 4.578928 TGCTTGTCCTACACCTTTTTCTTC 59.421 41.667 0.00 0.00 0.00 2.87
1668 2112 0.239347 ACGCATTGCTCTTGCTTGTC 59.761 50.000 7.12 0.00 40.48 3.18
1681 2365 4.336993 TCCTCTTAACAAAACACACGCATT 59.663 37.500 0.00 0.00 0.00 3.56
1718 2402 4.097361 GGGCCGGACCTTCAGGAC 62.097 72.222 23.07 0.00 39.19 3.85
1728 2466 0.614294 TTTATCTCGTTTGGGCCGGA 59.386 50.000 5.05 0.00 0.00 5.14
1730 2468 2.081462 AGTTTTATCTCGTTTGGGCCG 58.919 47.619 0.00 0.00 0.00 6.13
1763 2501 7.555914 TGCTAAATTACATACTTCCAGCAATCA 59.444 33.333 0.00 0.00 33.86 2.57
1790 2528 8.649973 ACTATAGACTAAGCAGTTTAACATGC 57.350 34.615 6.78 10.12 42.87 4.06
1816 2555 2.288763 GCCTTTTCATCGCCCTTTTTGA 60.289 45.455 0.00 0.00 0.00 2.69
1854 2597 9.800572 TGATATATCTACCTGCCTATATCTGAC 57.199 37.037 13.79 0.00 35.78 3.51
1866 2609 6.041511 GCACTCTGCATGATATATCTACCTG 58.958 44.000 13.79 7.34 44.26 4.00
1945 2719 1.878102 GCCAACACTGGAACACGAGAT 60.878 52.381 0.00 0.00 46.92 2.75
1949 2723 0.667993 ATTGCCAACACTGGAACACG 59.332 50.000 0.00 0.00 46.92 4.49
1983 2757 2.549754 AGAACTGGAAGCAACACAATCG 59.450 45.455 0.00 0.00 37.60 3.34
2224 3022 1.402896 GGAGCCGATCATCCACCTGA 61.403 60.000 4.19 0.00 35.54 3.86
2337 3139 5.810080 ATGGCTCCTAATAGGACAGTAAC 57.190 43.478 4.61 0.00 40.06 2.50
2435 3237 9.828852 CAACAACTGTTAAACTGTAAACACTTA 57.171 29.630 4.95 0.00 36.32 2.24
2436 3238 7.327518 GCAACAACTGTTAAACTGTAAACACTT 59.672 33.333 4.95 1.67 36.32 3.16
2437 3239 6.804783 GCAACAACTGTTAAACTGTAAACACT 59.195 34.615 4.95 0.00 36.32 3.55
2438 3240 6.804783 AGCAACAACTGTTAAACTGTAAACAC 59.195 34.615 4.95 0.00 36.32 3.32
2530 3347 5.586243 TCCAGCTACTGCAGTTTTCAATATC 59.414 40.000 27.06 0.00 42.74 1.63
2546 3363 6.001460 TTCTATAGAGAAGAGCTCCAGCTAC 58.999 44.000 10.93 0.00 43.39 3.58
2810 3640 4.202503 ACAGGAACATCTCTCACCAACATT 60.203 41.667 0.00 0.00 0.00 2.71
2969 3807 5.025826 GTCACGAATAATAAACAAAGGGCG 58.974 41.667 0.00 0.00 0.00 6.13
3043 3906 7.383300 GTGACCTTCAATCTCTTGGAAAATTTG 59.617 37.037 0.00 0.00 32.95 2.32
3071 3934 3.904571 TCAGCATGAGCAATTTTGTGTC 58.095 40.909 0.00 0.00 42.56 3.67
3111 3974 4.022849 CCCTCAGGTCTGTTTGATGTTTTC 60.023 45.833 0.00 0.00 0.00 2.29
3118 3981 0.108585 GTGCCCTCAGGTCTGTTTGA 59.891 55.000 0.00 0.00 34.57 2.69
3156 4019 1.421646 CCGATAAGGCCAAGGAATCCT 59.578 52.381 5.01 0.00 33.87 3.24
3201 4064 9.118300 AGCAATTCCTTAATCTTCTCATTACAG 57.882 33.333 0.00 0.00 0.00 2.74
3525 4388 1.279271 GGCAGCTTCTCCCTCAGTTTA 59.721 52.381 0.00 0.00 0.00 2.01
3612 4475 1.344114 GCAAGGAAAACAATGAGGGCA 59.656 47.619 0.00 0.00 0.00 5.36
3693 4556 2.628178 TCCTGATGATGCCCTTACTACG 59.372 50.000 0.00 0.00 0.00 3.51
3916 4793 4.759782 ACATGTGTATAGTGGAAGCTCAC 58.240 43.478 0.00 0.00 37.89 3.51
3929 4824 6.003326 TGTGGTGAAATTCAGACATGTGTAT 58.997 36.000 1.15 0.00 0.00 2.29
4286 5198 5.683876 AAAAGAGCTATGCTTAGGACTGA 57.316 39.130 8.57 0.00 39.88 3.41
4295 5219 3.304928 GCACACACAAAAAGAGCTATGCT 60.305 43.478 0.00 0.00 43.88 3.79
4310 5234 0.171007 ATGCCTATTTGCGCACACAC 59.829 50.000 11.12 0.00 37.93 3.82
4367 5297 6.152323 CCACTTGTGAAATCCATTCTCTTCAT 59.848 38.462 1.89 0.00 38.92 2.57
4377 5307 3.153919 GGTAAGCCACTTGTGAAATCCA 58.846 45.455 1.89 0.00 34.09 3.41
4565 5499 0.399233 AGGAGTGGGGTGAGGATAGC 60.399 60.000 0.00 0.00 0.00 2.97
4711 5645 1.500474 TGAGGCAAGGAGGGATGTAG 58.500 55.000 0.00 0.00 0.00 2.74
4762 5696 2.429351 GCGTGACTGAGCGTCTTCG 61.429 63.158 0.00 0.00 43.25 3.79
4818 5757 8.835467 AATGGTTACGTATTTTGATTGATTCG 57.165 30.769 0.00 0.00 0.00 3.34
4833 5777 4.468510 TCCCTGTGATTCTAATGGTTACGT 59.531 41.667 0.00 0.00 0.00 3.57
4848 5792 0.394216 CGGCAATTCCATCCCTGTGA 60.394 55.000 0.00 0.00 34.01 3.58
4859 5803 6.527957 CATTTCAGAAATTTGACGGCAATTC 58.472 36.000 3.50 6.91 33.25 2.17
4860 5804 5.106987 GCATTTCAGAAATTTGACGGCAATT 60.107 36.000 3.50 0.00 33.25 2.32
4881 5826 2.971330 TGGGTCATCCTTTTGTTTGCAT 59.029 40.909 0.00 0.00 36.20 3.96
4915 5860 8.314143 TCCTGCAGAAATTCAAATTCAAATTC 57.686 30.769 17.39 0.00 0.00 2.17
4916 5861 8.857694 ATCCTGCAGAAATTCAAATTCAAATT 57.142 26.923 17.39 0.00 0.00 1.82
4918 5863 9.373603 CATATCCTGCAGAAATTCAAATTCAAA 57.626 29.630 17.39 0.00 0.00 2.69
4919 5864 8.533657 ACATATCCTGCAGAAATTCAAATTCAA 58.466 29.630 17.39 0.00 0.00 2.69
4920 5865 7.977293 CACATATCCTGCAGAAATTCAAATTCA 59.023 33.333 17.39 0.00 0.00 2.57
4921 5866 8.192774 TCACATATCCTGCAGAAATTCAAATTC 58.807 33.333 17.39 0.00 0.00 2.17
4922 5867 8.070034 TCACATATCCTGCAGAAATTCAAATT 57.930 30.769 17.39 0.00 0.00 1.82
4923 5868 7.649533 TCACATATCCTGCAGAAATTCAAAT 57.350 32.000 17.39 0.00 0.00 2.32
4924 5869 7.339976 TCATCACATATCCTGCAGAAATTCAAA 59.660 33.333 17.39 0.00 0.00 2.69
4925 5870 6.829811 TCATCACATATCCTGCAGAAATTCAA 59.170 34.615 17.39 0.00 0.00 2.69
4926 5871 6.358991 TCATCACATATCCTGCAGAAATTCA 58.641 36.000 17.39 0.00 0.00 2.57
4942 5887 1.739466 GCACGTGGACATTCATCACAT 59.261 47.619 18.88 0.00 0.00 3.21
5049 5994 1.542915 AGTGTTCATCATGCAACAGCC 59.457 47.619 0.00 0.00 33.16 4.85
5078 6023 6.261118 ACAACCTAACATATAAGACGACGTC 58.739 40.000 20.25 20.25 0.00 4.34
5083 6028 6.312918 ACAGCAACAACCTAACATATAAGACG 59.687 38.462 0.00 0.00 0.00 4.18
5149 6094 2.416747 GCAGCAGATTGTCTACACACA 58.583 47.619 0.00 0.00 29.76 3.72
5288 6233 4.405358 TCTTCAGGAGGCACAAACATTTTT 59.595 37.500 0.00 0.00 0.00 1.94
5314 6259 0.739813 CCCCGTAAAGAGCTGGAACG 60.740 60.000 0.00 0.00 0.00 3.95
5317 6262 1.188863 GTACCCCGTAAAGAGCTGGA 58.811 55.000 0.00 0.00 0.00 3.86
5334 6279 7.013083 GTCTTACATTATGAGACGGAGGAAGTA 59.987 40.741 0.00 0.00 34.53 2.24
5335 6280 5.892119 TCTTACATTATGAGACGGAGGAAGT 59.108 40.000 0.00 0.00 0.00 3.01
5336 6281 6.210078 GTCTTACATTATGAGACGGAGGAAG 58.790 44.000 0.00 0.00 34.53 3.46
5337 6282 6.145338 GTCTTACATTATGAGACGGAGGAA 57.855 41.667 0.00 0.00 34.53 3.36
5338 6283 5.769484 GTCTTACATTATGAGACGGAGGA 57.231 43.478 0.00 0.00 34.53 3.71
5363 6308 1.407258 GTACTGCACCAGTGGCAAAAA 59.593 47.619 9.78 0.00 45.01 1.94
5364 6309 1.028905 GTACTGCACCAGTGGCAAAA 58.971 50.000 9.78 0.00 45.01 2.44
5365 6310 0.182537 AGTACTGCACCAGTGGCAAA 59.817 50.000 9.78 0.00 45.01 3.68
5366 6311 0.182537 AAGTACTGCACCAGTGGCAA 59.817 50.000 9.78 0.00 45.01 4.52
5367 6312 0.182537 AAAGTACTGCACCAGTGGCA 59.817 50.000 9.78 0.87 45.01 4.92
5368 6313 1.318576 AAAAGTACTGCACCAGTGGC 58.681 50.000 9.78 0.00 45.01 5.01
5369 6314 4.024048 CACTAAAAAGTACTGCACCAGTGG 60.024 45.833 7.91 7.91 45.01 4.00
5370 6315 4.024048 CCACTAAAAAGTACTGCACCAGTG 60.024 45.833 8.06 13.77 45.01 3.66
5372 6317 4.213482 GTCCACTAAAAAGTACTGCACCAG 59.787 45.833 0.00 0.00 37.52 4.00
5373 6318 4.131596 GTCCACTAAAAAGTACTGCACCA 58.868 43.478 0.00 0.00 0.00 4.17
5374 6319 4.131596 TGTCCACTAAAAAGTACTGCACC 58.868 43.478 0.00 0.00 0.00 5.01
5375 6320 5.296035 AGTTGTCCACTAAAAAGTACTGCAC 59.704 40.000 0.00 0.00 31.97 4.57
5376 6321 5.433526 AGTTGTCCACTAAAAAGTACTGCA 58.566 37.500 0.00 0.00 31.97 4.41
5377 6322 7.148457 GGATAGTTGTCCACTAAAAAGTACTGC 60.148 40.741 0.00 0.00 41.56 4.40
5378 6323 7.876068 TGGATAGTTGTCCACTAAAAAGTACTG 59.124 37.037 0.00 0.00 43.20 2.74
5419 6364 5.399991 AGGTTATGTAGGATATGACCCGAA 58.600 41.667 0.00 0.00 35.44 4.30
5518 6467 7.441017 ACATGGTTGCATATTGTAGTGTTTTT 58.559 30.769 0.00 0.00 0.00 1.94
5522 6471 9.002600 CATATACATGGTTGCATATTGTAGTGT 57.997 33.333 0.00 0.00 0.00 3.55
5523 6472 8.453320 CCATATACATGGTTGCATATTGTAGTG 58.547 37.037 0.00 0.00 45.92 2.74
5524 6473 8.565896 CCATATACATGGTTGCATATTGTAGT 57.434 34.615 0.00 0.00 45.92 2.73
5635 6584 8.527810 GGGAGTATGAAACATGGAATTTTGTAA 58.472 33.333 0.00 0.00 0.00 2.41
5636 6585 7.893302 AGGGAGTATGAAACATGGAATTTTGTA 59.107 33.333 0.00 0.00 0.00 2.41
5637 6586 6.725834 AGGGAGTATGAAACATGGAATTTTGT 59.274 34.615 0.00 0.00 0.00 2.83
5638 6587 7.123247 AGAGGGAGTATGAAACATGGAATTTTG 59.877 37.037 0.00 0.00 0.00 2.44
5639 6588 7.123247 CAGAGGGAGTATGAAACATGGAATTTT 59.877 37.037 0.00 0.00 0.00 1.82
5640 6589 6.604795 CAGAGGGAGTATGAAACATGGAATTT 59.395 38.462 0.00 0.00 0.00 1.82
5641 6590 6.125029 CAGAGGGAGTATGAAACATGGAATT 58.875 40.000 0.00 0.00 0.00 2.17
5642 6591 5.192522 ACAGAGGGAGTATGAAACATGGAAT 59.807 40.000 0.00 0.00 0.00 3.01
5643 6592 4.536090 ACAGAGGGAGTATGAAACATGGAA 59.464 41.667 0.00 0.00 0.00 3.53
5644 6593 4.104086 ACAGAGGGAGTATGAAACATGGA 58.896 43.478 0.00 0.00 0.00 3.41
5645 6594 4.163078 AGACAGAGGGAGTATGAAACATGG 59.837 45.833 0.00 0.00 0.00 3.66
5646 6595 5.350504 AGACAGAGGGAGTATGAAACATG 57.649 43.478 0.00 0.00 0.00 3.21
5647 6596 4.098654 CGAGACAGAGGGAGTATGAAACAT 59.901 45.833 0.00 0.00 0.00 2.71
5648 6597 3.444034 CGAGACAGAGGGAGTATGAAACA 59.556 47.826 0.00 0.00 0.00 2.83
5649 6598 3.181485 CCGAGACAGAGGGAGTATGAAAC 60.181 52.174 0.00 0.00 0.00 2.78
5650 6599 3.024547 CCGAGACAGAGGGAGTATGAAA 58.975 50.000 0.00 0.00 0.00 2.69
5651 6600 2.025226 ACCGAGACAGAGGGAGTATGAA 60.025 50.000 0.00 0.00 0.00 2.57
5652 6601 1.564818 ACCGAGACAGAGGGAGTATGA 59.435 52.381 0.00 0.00 0.00 2.15
5653 6602 2.060050 ACCGAGACAGAGGGAGTATG 57.940 55.000 0.00 0.00 0.00 2.39
5654 6603 2.830651 AACCGAGACAGAGGGAGTAT 57.169 50.000 0.00 0.00 0.00 2.12
5655 6604 2.599408 AAACCGAGACAGAGGGAGTA 57.401 50.000 0.00 0.00 0.00 2.59
5656 6605 2.599408 TAAACCGAGACAGAGGGAGT 57.401 50.000 0.00 0.00 0.00 3.85
5657 6606 3.570550 CCTATAAACCGAGACAGAGGGAG 59.429 52.174 0.00 0.00 0.00 4.30
5658 6607 3.563223 CCTATAAACCGAGACAGAGGGA 58.437 50.000 0.00 0.00 0.00 4.20
5659 6608 2.628657 CCCTATAAACCGAGACAGAGGG 59.371 54.545 0.00 0.00 36.68 4.30
5660 6609 2.036089 GCCCTATAAACCGAGACAGAGG 59.964 54.545 0.00 0.00 0.00 3.69
5661 6610 2.287668 CGCCCTATAAACCGAGACAGAG 60.288 54.545 0.00 0.00 0.00 3.35
5662 6611 1.679680 CGCCCTATAAACCGAGACAGA 59.320 52.381 0.00 0.00 0.00 3.41
5663 6612 1.407979 ACGCCCTATAAACCGAGACAG 59.592 52.381 0.00 0.00 0.00 3.51
5664 6613 1.135527 CACGCCCTATAAACCGAGACA 59.864 52.381 0.00 0.00 0.00 3.41
5665 6614 1.849097 CACGCCCTATAAACCGAGAC 58.151 55.000 0.00 0.00 0.00 3.36
5666 6615 0.103572 GCACGCCCTATAAACCGAGA 59.896 55.000 0.00 0.00 0.00 4.04
5667 6616 0.179094 TGCACGCCCTATAAACCGAG 60.179 55.000 0.00 0.00 0.00 4.63
5668 6617 0.460635 GTGCACGCCCTATAAACCGA 60.461 55.000 0.00 0.00 0.00 4.69
5669 6618 1.758319 CGTGCACGCCCTATAAACCG 61.758 60.000 28.16 0.00 0.00 4.44
5670 6619 0.741927 ACGTGCACGCCCTATAAACC 60.742 55.000 37.35 0.00 44.43 3.27
5671 6620 1.856597 CTACGTGCACGCCCTATAAAC 59.143 52.381 37.35 0.00 44.43 2.01
5672 6621 1.477700 ACTACGTGCACGCCCTATAAA 59.522 47.619 37.35 12.57 44.43 1.40
5673 6622 1.105457 ACTACGTGCACGCCCTATAA 58.895 50.000 37.35 13.91 44.43 0.98
5674 6623 1.105457 AACTACGTGCACGCCCTATA 58.895 50.000 37.35 20.98 44.43 1.31
5675 6624 0.248289 AAACTACGTGCACGCCCTAT 59.752 50.000 37.35 20.98 44.43 2.57
5676 6625 0.033781 AAAACTACGTGCACGCCCTA 59.966 50.000 37.35 21.70 44.43 3.53
5677 6626 0.033781 TAAAACTACGTGCACGCCCT 59.966 50.000 37.35 21.75 44.43 5.19
5678 6627 0.441145 CTAAAACTACGTGCACGCCC 59.559 55.000 37.35 0.00 44.43 6.13
5679 6628 1.421382 TCTAAAACTACGTGCACGCC 58.579 50.000 37.35 0.00 44.43 5.68
5680 6629 3.717350 AATCTAAAACTACGTGCACGC 57.283 42.857 37.35 0.72 44.43 5.34
5681 6630 5.517411 TGGATAATCTAAAACTACGTGCACG 59.483 40.000 35.99 35.99 46.33 5.34
5682 6631 6.897259 TGGATAATCTAAAACTACGTGCAC 57.103 37.500 6.82 6.82 0.00 4.57
5683 6632 8.394877 CAAATGGATAATCTAAAACTACGTGCA 58.605 33.333 0.00 0.00 0.00 4.57
5684 6633 8.609176 TCAAATGGATAATCTAAAACTACGTGC 58.391 33.333 0.00 0.00 0.00 5.34
5685 6634 9.916397 GTCAAATGGATAATCTAAAACTACGTG 57.084 33.333 0.00 0.00 0.00 4.49
5686 6635 9.886132 AGTCAAATGGATAATCTAAAACTACGT 57.114 29.630 0.00 0.00 0.00 3.57
5740 6689 9.778741 TCCGCTTAAGAATTCAATGATATACTT 57.221 29.630 6.67 0.00 0.00 2.24
5741 6690 9.950496 ATCCGCTTAAGAATTCAATGATATACT 57.050 29.630 6.67 0.00 0.00 2.12
5742 6691 9.979270 CATCCGCTTAAGAATTCAATGATATAC 57.021 33.333 6.67 0.00 0.00 1.47
5743 6692 9.725019 ACATCCGCTTAAGAATTCAATGATATA 57.275 29.630 6.67 0.00 0.00 0.86
5744 6693 8.627208 ACATCCGCTTAAGAATTCAATGATAT 57.373 30.769 6.67 0.00 0.00 1.63
5745 6694 9.208022 CTACATCCGCTTAAGAATTCAATGATA 57.792 33.333 6.67 0.00 0.00 2.15
5746 6695 6.949352 ACATCCGCTTAAGAATTCAATGAT 57.051 33.333 6.67 0.00 0.00 2.45
5747 6696 7.047891 ACTACATCCGCTTAAGAATTCAATGA 58.952 34.615 6.67 0.00 0.00 2.57
5748 6697 7.251704 ACTACATCCGCTTAAGAATTCAATG 57.748 36.000 6.67 3.37 0.00 2.82
5749 6698 7.865706 AACTACATCCGCTTAAGAATTCAAT 57.134 32.000 6.67 0.00 0.00 2.57
5750 6699 7.681939 AAACTACATCCGCTTAAGAATTCAA 57.318 32.000 6.67 0.00 0.00 2.69
5751 6700 7.681939 AAAACTACATCCGCTTAAGAATTCA 57.318 32.000 6.67 0.00 0.00 2.57
5754 6703 9.836076 GTTTAAAAACTACATCCGCTTAAGAAT 57.164 29.630 6.67 0.00 36.03 2.40
5755 6704 8.838365 TGTTTAAAAACTACATCCGCTTAAGAA 58.162 29.630 6.67 0.00 39.59 2.52
5756 6705 8.380743 TGTTTAAAAACTACATCCGCTTAAGA 57.619 30.769 6.67 0.00 39.59 2.10


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

AutoCloner maintained by Alex Coulton.