Multiple sequence alignment - TraesCS4D01G311400

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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 TraesCS4D01G311400 chr4D 100.000 3017 0 0 1 3017 477903481 477900465 0.000000e+00 5572
1 TraesCS4D01G311400 chr4B 92.805 1515 83 12 915 2416 604058950 604057449 0.000000e+00 2170
2 TraesCS4D01G311400 chr4B 87.728 383 38 3 6 388 550614989 550614616 3.570000e-119 438
3 TraesCS4D01G311400 chr4B 92.623 122 8 1 2769 2889 604057208 604057087 1.110000e-39 174
4 TraesCS4D01G311400 chr4B 90.840 131 6 4 2412 2541 604057418 604057293 1.440000e-38 171
5 TraesCS4D01G311400 chr4B 96.512 86 3 0 2626 2711 604057291 604057206 3.140000e-30 143
6 TraesCS4D01G311400 chr4A 90.944 1557 105 21 881 2416 684607251 684605710 0.000000e+00 2061
7 TraesCS4D01G311400 chr4A 89.313 131 8 4 2412 2541 684605679 684605554 3.110000e-35 159
8 TraesCS4D01G311400 chr4A 89.524 105 10 1 2786 2889 684605034 684604930 6.790000e-27 132
9 TraesCS4D01G311400 chr4A 90.816 98 5 1 2626 2723 684605552 684605459 8.780000e-26 128
10 TraesCS4D01G311400 chr2D 96.659 868 21 5 3 863 84919806 84918940 0.000000e+00 1435
11 TraesCS4D01G311400 chr2D 92.537 134 9 1 2884 3017 53792365 53792233 1.100000e-44 191
12 TraesCS4D01G311400 chr5D 96.096 871 27 4 1 865 168229403 168228534 0.000000e+00 1413
13 TraesCS4D01G311400 chr1D 95.857 869 18 6 1 864 188988928 188989783 0.000000e+00 1389
14 TraesCS4D01G311400 chr7D 94.023 870 45 4 1 864 269700171 269699303 0.000000e+00 1312
15 TraesCS4D01G311400 chr7D 93.023 129 9 0 2889 3017 425099371 425099243 3.970000e-44 189
16 TraesCS4D01G311400 chr7D 86.667 165 18 1 708 868 6881526 6881362 2.390000e-41 180
17 TraesCS4D01G311400 chr5A 94.269 698 33 4 175 866 635477684 635478380 0.000000e+00 1061
18 TraesCS4D01G311400 chr5A 95.000 180 8 1 1 180 635476589 635476767 6.370000e-72 281
19 TraesCS4D01G311400 chr2A 91.169 419 30 4 164 579 161264580 161264166 2.030000e-156 562
20 TraesCS4D01G311400 chr2A 89.109 303 26 4 572 868 161263628 161263327 1.320000e-98 370
21 TraesCS4D01G311400 chr7B 84.383 397 37 10 6 380 183004701 183004308 1.710000e-97 366
22 TraesCS4D01G311400 chr7B 89.706 272 23 2 598 864 183004285 183004014 2.880000e-90 342
23 TraesCS4D01G311400 chr5B 85.660 265 27 6 1828 2083 586801797 586801535 4.960000e-68 268
24 TraesCS4D01G311400 chr6D 93.750 128 8 0 2890 3017 14616166 14616039 3.070000e-45 193
25 TraesCS4D01G311400 chr6D 93.750 128 7 1 2890 3017 42407387 42407513 1.100000e-44 191
26 TraesCS4D01G311400 chr6D 93.077 130 9 0 2888 3017 464466002 464465873 1.100000e-44 191
27 TraesCS4D01G311400 chrUn 93.077 130 9 0 2888 3017 83928411 83928540 1.100000e-44 191
28 TraesCS4D01G311400 chr6B 92.537 134 9 1 2884 3017 43235666 43235798 1.100000e-44 191
29 TraesCS4D01G311400 chr3D 93.077 130 9 0 2888 3017 5039880 5040009 1.100000e-44 191
30 TraesCS4D01G311400 chr3A 91.729 133 11 0 2885 3017 716636766 716636898 5.140000e-43 185
31 TraesCS4D01G311400 chr1B 87.578 161 16 1 709 865 174594917 174594757 1.850000e-42 183


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 TraesCS4D01G311400 chr4D 477900465 477903481 3016 True 5572.0 5572 100.00000 1 3017 1 chr4D.!!$R1 3016
1 TraesCS4D01G311400 chr4B 604057087 604058950 1863 True 664.5 2170 93.19500 915 2889 4 chr4B.!!$R2 1974
2 TraesCS4D01G311400 chr4A 684604930 684607251 2321 True 620.0 2061 90.14925 881 2889 4 chr4A.!!$R1 2008
3 TraesCS4D01G311400 chr2D 84918940 84919806 866 True 1435.0 1435 96.65900 3 863 1 chr2D.!!$R2 860
4 TraesCS4D01G311400 chr5D 168228534 168229403 869 True 1413.0 1413 96.09600 1 865 1 chr5D.!!$R1 864
5 TraesCS4D01G311400 chr1D 188988928 188989783 855 False 1389.0 1389 95.85700 1 864 1 chr1D.!!$F1 863
6 TraesCS4D01G311400 chr7D 269699303 269700171 868 True 1312.0 1312 94.02300 1 864 1 chr7D.!!$R2 863
7 TraesCS4D01G311400 chr5A 635476589 635478380 1791 False 671.0 1061 94.63450 1 866 2 chr5A.!!$F1 865
8 TraesCS4D01G311400 chr2A 161263327 161264580 1253 True 466.0 562 90.13900 164 868 2 chr2A.!!$R1 704
9 TraesCS4D01G311400 chr7B 183004014 183004701 687 True 354.0 366 87.04450 6 864 2 chr7B.!!$R1 858

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
198 1150 0.331616 GAACCCCCAGCCTTGTACAT 59.668 55.0 0.0 0.0 0.00 2.29 F
1557 3071 0.250234 CTGCCAACGAGAAGGATGGA 59.750 55.0 0.0 0.0 34.13 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 3386 0.246635 CCCAGTTACCAGTGTCCTCG 59.753 60.0 0.0 0.0 0.0 4.63 R
2608 4172 0.036294 GGTCCTCCCTCCGTTTCAAG 60.036 60.0 0.0 0.0 0.0 3.02 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
96 126 7.504238 TCAAGCTCTTTTCATTTACCCTGTTAA 59.496 33.333 0.00 0.00 0.00 2.01
122 152 2.187599 AATCAAGCTGCACGTTCCGC 62.188 55.000 1.02 0.00 0.00 5.54
198 1150 0.331616 GAACCCCCAGCCTTGTACAT 59.668 55.000 0.00 0.00 0.00 2.29
222 1176 2.033424 GCATGGCCTCGTTTCTATTTCC 59.967 50.000 3.32 0.00 0.00 3.13
300 1254 2.472029 AGACAGGGCTGCTTAGTATGT 58.528 47.619 0.00 0.00 0.00 2.29
616 2117 6.151691 TGACGGTTGTTATAAGTGTACACTC 58.848 40.000 28.04 15.74 41.58 3.51
868 2376 5.865552 CCACCAATGCATTTTACTCTTTCAG 59.134 40.000 9.83 0.00 0.00 3.02
869 2377 6.449698 CACCAATGCATTTTACTCTTTCAGT 58.550 36.000 9.83 0.00 39.41 3.41
870 2378 7.309133 CCACCAATGCATTTTACTCTTTCAGTA 60.309 37.037 9.83 0.00 36.43 2.74
871 2379 8.081633 CACCAATGCATTTTACTCTTTCAGTAA 58.918 33.333 9.83 0.00 44.52 2.24
872 2380 8.806146 ACCAATGCATTTTACTCTTTCAGTAAT 58.194 29.630 9.83 0.00 45.34 1.89
873 2381 9.079833 CCAATGCATTTTACTCTTTCAGTAATG 57.920 33.333 9.83 0.00 45.34 1.90
874 2382 9.844790 CAATGCATTTTACTCTTTCAGTAATGA 57.155 29.630 9.83 0.00 45.34 2.57
876 2384 8.621532 TGCATTTTACTCTTTCAGTAATGAGT 57.378 30.769 10.37 10.37 45.34 3.41
877 2385 8.721478 TGCATTTTACTCTTTCAGTAATGAGTC 58.279 33.333 9.21 0.00 45.34 3.36
878 2386 8.940952 GCATTTTACTCTTTCAGTAATGAGTCT 58.059 33.333 9.21 0.00 45.34 3.24
892 2400 8.994429 AGTAATGAGTCTGTTTACTGATTCAG 57.006 34.615 12.17 12.17 41.26 3.02
893 2401 8.807118 AGTAATGAGTCTGTTTACTGATTCAGA 58.193 33.333 20.33 1.49 41.26 3.27
894 2402 9.081997 GTAATGAGTCTGTTTACTGATTCAGAG 57.918 37.037 20.33 6.81 41.26 3.35
911 2422 2.098842 GAGCCAAGTCGCATCGCATC 62.099 60.000 0.00 0.00 0.00 3.91
919 2430 3.289834 GCATCGCATCCCCGCATT 61.290 61.111 0.00 0.00 0.00 3.56
945 2456 2.046314 GCAGCCAAACCTAGCCGA 60.046 61.111 0.00 0.00 0.00 5.54
947 2458 1.648467 GCAGCCAAACCTAGCCGAAG 61.648 60.000 0.00 0.00 0.00 3.79
948 2459 1.377333 AGCCAAACCTAGCCGAAGC 60.377 57.895 0.00 0.00 40.32 3.86
950 2461 1.648467 GCCAAACCTAGCCGAAGCAG 61.648 60.000 0.00 0.00 43.56 4.24
952 2463 1.741770 AAACCTAGCCGAAGCAGCG 60.742 57.895 0.00 0.00 43.56 5.18
953 2464 4.821589 ACCTAGCCGAAGCAGCGC 62.822 66.667 0.00 0.00 43.56 5.92
1557 3071 0.250234 CTGCCAACGAGAAGGATGGA 59.750 55.000 0.00 0.00 34.13 3.41
1650 3164 2.927477 CAAGTTAAGAGATTGCCGCGTA 59.073 45.455 4.92 0.00 0.00 4.42
1652 3166 4.579454 AGTTAAGAGATTGCCGCGTATA 57.421 40.909 4.92 0.00 0.00 1.47
1696 3210 3.494048 GGTGCTCATAGAGGATGTTGAGG 60.494 52.174 0.00 0.00 36.85 3.86
1734 3248 1.013005 CGGCGCATCAGATCAGGATC 61.013 60.000 10.83 0.95 38.09 3.36
1872 3386 3.334054 AGGGACTCTGGGCTTGCC 61.334 66.667 2.49 2.49 0.00 4.52
2000 3514 4.376413 CGACATTTCAGAAGTTCAGGAACG 60.376 45.833 5.50 5.01 45.50 3.95
2034 3548 1.893919 GAGCTGCTCGGGAGGTTTCT 61.894 60.000 14.68 0.00 0.00 2.52
2035 3549 1.003233 GCTGCTCGGGAGGTTTCTT 60.003 57.895 0.00 0.00 0.00 2.52
2111 3625 3.057876 TGGTGATTACATGTTCCGTTTGC 60.058 43.478 2.30 0.00 0.00 3.68
2113 3627 4.158384 GTGATTACATGTTCCGTTTGCTG 58.842 43.478 2.30 0.00 0.00 4.41
2147 3661 1.524355 CATTGTATCTTGAGCTCGCCG 59.476 52.381 9.64 0.00 0.00 6.46
2158 3672 0.824759 AGCTCGCCGAACTAAGGATT 59.175 50.000 0.00 0.00 0.00 3.01
2159 3673 0.931005 GCTCGCCGAACTAAGGATTG 59.069 55.000 0.00 0.00 0.00 2.67
2160 3674 1.571919 CTCGCCGAACTAAGGATTGG 58.428 55.000 0.00 0.00 0.00 3.16
2161 3675 1.136305 CTCGCCGAACTAAGGATTGGA 59.864 52.381 0.00 0.00 0.00 3.53
2162 3676 1.551430 TCGCCGAACTAAGGATTGGAA 59.449 47.619 0.00 0.00 0.00 3.53
2165 3685 2.939640 GCCGAACTAAGGATTGGAAGCA 60.940 50.000 0.00 0.00 0.00 3.91
2171 3691 4.775236 ACTAAGGATTGGAAGCATGAGAC 58.225 43.478 0.00 0.00 0.00 3.36
2172 3692 2.725221 AGGATTGGAAGCATGAGACC 57.275 50.000 0.00 0.00 0.00 3.85
2176 3696 2.496899 TTGGAAGCATGAGACCCTTC 57.503 50.000 0.00 0.00 35.42 3.46
2179 3699 2.087646 GGAAGCATGAGACCCTTCAAC 58.912 52.381 0.00 0.00 37.34 3.18
2186 3706 1.282930 GAGACCCTTCAACGCGTGTC 61.283 60.000 14.98 15.04 0.00 3.67
2195 3715 2.251642 AACGCGTGTCCAGAAAGGC 61.252 57.895 14.98 0.00 37.29 4.35
2264 3791 5.241403 TCTGGGAAGAAGCATACTTTGAA 57.759 39.130 0.00 0.00 35.82 2.69
2272 3799 7.329471 GGAAGAAGCATACTTTGAATTTTGGTC 59.671 37.037 0.00 0.00 35.82 4.02
2276 3803 7.624360 AGCATACTTTGAATTTTGGTCGATA 57.376 32.000 0.00 0.00 0.00 2.92
2278 3805 6.414987 GCATACTTTGAATTTTGGTCGATAGC 59.585 38.462 0.00 0.00 0.00 2.97
2279 3806 5.957842 ACTTTGAATTTTGGTCGATAGCA 57.042 34.783 0.00 0.00 0.00 3.49
2280 3807 6.515272 ACTTTGAATTTTGGTCGATAGCAT 57.485 33.333 0.00 0.00 32.06 3.79
2282 3809 6.808212 ACTTTGAATTTTGGTCGATAGCATTG 59.192 34.615 0.00 0.00 32.06 2.82
2283 3810 5.247507 TGAATTTTGGTCGATAGCATTGG 57.752 39.130 0.00 0.00 32.06 3.16
2284 3811 4.946772 TGAATTTTGGTCGATAGCATTGGA 59.053 37.500 0.00 0.00 32.06 3.53
2286 3813 6.096705 TGAATTTTGGTCGATAGCATTGGAAT 59.903 34.615 0.00 0.00 32.06 3.01
2289 3816 4.681074 TGGTCGATAGCATTGGAATACA 57.319 40.909 0.00 0.00 0.00 2.29
2290 3817 5.227569 TGGTCGATAGCATTGGAATACAT 57.772 39.130 0.00 0.00 0.00 2.29
2303 3831 7.358600 GCATTGGAATACATGCATGTTTATTCG 60.359 37.037 35.45 23.31 41.97 3.34
2305 3833 5.592282 TGGAATACATGCATGTTTATTCGGT 59.408 36.000 35.45 13.05 41.97 4.69
2313 3841 6.260870 TGCATGTTTATTCGGTTGTACAAT 57.739 33.333 12.26 0.00 0.00 2.71
2328 3856 9.887406 CGGTTGTACAATTATATTGGTTTATCC 57.113 33.333 12.26 1.36 0.00 2.59
2343 3871 5.476599 TGGTTTATCCAATTCTGTGACCTTG 59.523 40.000 0.00 0.00 44.12 3.61
2353 3881 1.002888 CTGTGACCTTGAGTGCTCCAT 59.997 52.381 0.00 0.00 0.00 3.41
2354 3882 2.234661 CTGTGACCTTGAGTGCTCCATA 59.765 50.000 0.00 0.00 0.00 2.74
2389 3917 6.482898 TTATAATTTGGCAGGAATGCATGT 57.517 33.333 0.00 0.00 36.33 3.21
2474 4038 3.181469 ACCTTGCCCATACAGTATACACG 60.181 47.826 5.50 0.00 0.00 4.49
2486 4050 6.396829 ACAGTATACACGGAGTATTAACCC 57.603 41.667 5.50 0.00 41.61 4.11
2510 4074 4.405680 ACACCTCTGCAGCACTATGTATTA 59.594 41.667 9.47 0.00 0.00 0.98
2511 4075 5.070981 ACACCTCTGCAGCACTATGTATTAT 59.929 40.000 9.47 0.00 0.00 1.28
2512 4076 5.994054 CACCTCTGCAGCACTATGTATTATT 59.006 40.000 9.47 0.00 0.00 1.40
2523 4087 6.715280 CACTATGTATTATTCCCTGCTGGAT 58.285 40.000 11.88 0.00 44.66 3.41
2529 4093 5.848286 ATTATTCCCTGCTGGATGTGATA 57.152 39.130 11.88 0.00 44.66 2.15
2530 4094 5.848286 TTATTCCCTGCTGGATGTGATAT 57.152 39.130 11.88 0.00 44.66 1.63
2541 4105 8.722480 TGCTGGATGTGATATGCTTTATATAC 57.278 34.615 0.00 0.00 32.09 1.47
2542 4106 8.320617 TGCTGGATGTGATATGCTTTATATACA 58.679 33.333 0.00 0.00 32.09 2.29
2543 4107 9.334947 GCTGGATGTGATATGCTTTATATACAT 57.665 33.333 0.00 0.00 33.53 2.29
2562 4126 7.914427 ATACATATCCCTCTGTAACAGAACA 57.086 36.000 0.00 0.00 40.18 3.18
2563 4127 6.814954 ACATATCCCTCTGTAACAGAACAT 57.185 37.500 0.00 0.00 40.18 2.71
2564 4128 7.914427 ACATATCCCTCTGTAACAGAACATA 57.086 36.000 0.00 0.00 40.18 2.29
2565 4129 8.497910 ACATATCCCTCTGTAACAGAACATAT 57.502 34.615 0.00 0.00 40.18 1.78
2566 4130 8.370940 ACATATCCCTCTGTAACAGAACATATG 58.629 37.037 0.00 0.00 40.18 1.78
2567 4131 8.588472 CATATCCCTCTGTAACAGAACATATGA 58.412 37.037 10.38 0.00 40.18 2.15
2568 4132 6.222038 TCCCTCTGTAACAGAACATATGAC 57.778 41.667 10.38 3.20 40.18 3.06
2569 4133 5.043903 CCCTCTGTAACAGAACATATGACG 58.956 45.833 10.38 0.00 40.18 4.35
2570 4134 5.394224 CCCTCTGTAACAGAACATATGACGT 60.394 44.000 10.38 0.00 40.18 4.34
2571 4135 6.100004 CCTCTGTAACAGAACATATGACGTT 58.900 40.000 10.38 8.96 40.18 3.99
2572 4136 6.590292 CCTCTGTAACAGAACATATGACGTTT 59.410 38.462 10.38 0.00 40.18 3.60
2573 4137 7.117812 CCTCTGTAACAGAACATATGACGTTTT 59.882 37.037 10.38 0.00 40.18 2.43
2574 4138 8.373048 TCTGTAACAGAACATATGACGTTTTT 57.627 30.769 10.38 0.00 37.57 1.94
2616 4180 9.708222 CCAAGAAACATCTTATATCTTGAAACG 57.292 33.333 13.71 0.00 46.16 3.60
2617 4181 9.708222 CAAGAAACATCTTATATCTTGAAACGG 57.292 33.333 7.82 0.00 46.16 4.44
2618 4182 9.667107 AAGAAACATCTTATATCTTGAAACGGA 57.333 29.630 0.00 0.00 0.00 4.69
2619 4183 9.319143 AGAAACATCTTATATCTTGAAACGGAG 57.681 33.333 0.00 0.00 0.00 4.63
2620 4184 8.438676 AAACATCTTATATCTTGAAACGGAGG 57.561 34.615 0.00 0.00 0.00 4.30
2621 4185 6.525629 ACATCTTATATCTTGAAACGGAGGG 58.474 40.000 0.00 0.00 0.00 4.30
2622 4186 6.326583 ACATCTTATATCTTGAAACGGAGGGA 59.673 38.462 0.00 0.00 0.00 4.20
2623 4187 6.406692 TCTTATATCTTGAAACGGAGGGAG 57.593 41.667 0.00 0.00 0.00 4.30
2624 4188 5.304614 TCTTATATCTTGAAACGGAGGGAGG 59.695 44.000 0.00 0.00 0.00 4.30
2658 4222 3.063510 TGAGAATGGCAAGTTCAGAGG 57.936 47.619 3.86 0.00 0.00 3.69
2668 4232 1.931635 AGTTCAGAGGGGACAGTCTC 58.068 55.000 0.00 0.00 0.00 3.36
2723 4287 1.072331 GCAGTGACAAGAAGAGGGGAA 59.928 52.381 0.00 0.00 0.00 3.97
2724 4288 2.873649 GCAGTGACAAGAAGAGGGGAAG 60.874 54.545 0.00 0.00 0.00 3.46
2725 4289 1.349357 AGTGACAAGAAGAGGGGAAGC 59.651 52.381 0.00 0.00 0.00 3.86
2726 4290 0.693049 TGACAAGAAGAGGGGAAGCC 59.307 55.000 0.00 0.00 0.00 4.35
2741 4704 3.645687 GGGAAGCCATATTGCCCAATTTA 59.354 43.478 0.00 0.00 38.68 1.40
2751 4714 8.614346 CCATATTGCCCAATTTAAAGTGATTTG 58.386 33.333 16.81 7.59 32.50 2.32
2752 4715 9.381033 CATATTGCCCAATTTAAAGTGATTTGA 57.619 29.630 16.81 0.14 32.50 2.69
2753 4716 7.910441 ATTGCCCAATTTAAAGTGATTTGAG 57.090 32.000 16.81 0.00 0.00 3.02
2754 4717 6.662865 TGCCCAATTTAAAGTGATTTGAGA 57.337 33.333 16.81 0.00 0.00 3.27
2755 4718 7.243604 TGCCCAATTTAAAGTGATTTGAGAT 57.756 32.000 16.81 0.00 0.00 2.75
2756 4719 8.359875 TGCCCAATTTAAAGTGATTTGAGATA 57.640 30.769 16.81 0.00 0.00 1.98
2757 4720 8.250332 TGCCCAATTTAAAGTGATTTGAGATAC 58.750 33.333 16.81 0.00 0.00 2.24
2758 4721 8.470002 GCCCAATTTAAAGTGATTTGAGATACT 58.530 33.333 16.81 0.00 0.00 2.12
2767 4730 8.924511 AAGTGATTTGAGATACTTTTCCAAGA 57.075 30.769 0.00 0.00 33.72 3.02
2768 4731 8.558973 AGTGATTTGAGATACTTTTCCAAGAG 57.441 34.615 0.00 0.00 33.72 2.85
2769 4732 8.378565 AGTGATTTGAGATACTTTTCCAAGAGA 58.621 33.333 0.00 0.00 33.72 3.10
2770 4733 8.447053 GTGATTTGAGATACTTTTCCAAGAGAC 58.553 37.037 0.00 0.00 33.72 3.36
2771 4734 8.378565 TGATTTGAGATACTTTTCCAAGAGACT 58.621 33.333 0.00 0.00 33.72 3.24
2772 4735 7.969536 TTTGAGATACTTTTCCAAGAGACTG 57.030 36.000 0.00 0.00 33.72 3.51
2773 4736 6.672266 TGAGATACTTTTCCAAGAGACTGT 57.328 37.500 0.00 0.00 33.72 3.55
2774 4737 7.067496 TGAGATACTTTTCCAAGAGACTGTT 57.933 36.000 0.00 0.00 33.72 3.16
2775 4738 7.509546 TGAGATACTTTTCCAAGAGACTGTTT 58.490 34.615 0.00 0.00 33.72 2.83
2776 4739 7.657761 TGAGATACTTTTCCAAGAGACTGTTTC 59.342 37.037 0.00 0.00 33.72 2.78
2777 4740 7.740805 AGATACTTTTCCAAGAGACTGTTTCT 58.259 34.615 0.00 0.00 37.23 2.52
2778 4741 8.214364 AGATACTTTTCCAAGAGACTGTTTCTT 58.786 33.333 7.69 7.69 33.22 2.52
2779 4742 6.685527 ACTTTTCCAAGAGACTGTTTCTTC 57.314 37.500 10.33 0.00 33.22 2.87
2780 4743 6.418946 ACTTTTCCAAGAGACTGTTTCTTCT 58.581 36.000 10.33 0.00 33.22 2.85
2781 4744 7.565680 ACTTTTCCAAGAGACTGTTTCTTCTA 58.434 34.615 10.33 0.19 33.22 2.10
2782 4745 8.047310 ACTTTTCCAAGAGACTGTTTCTTCTAA 58.953 33.333 10.33 5.78 33.22 2.10
2783 4746 7.787725 TTTCCAAGAGACTGTTTCTTCTAAC 57.212 36.000 10.33 0.00 33.22 2.34
2784 4747 6.732896 TCCAAGAGACTGTTTCTTCTAACT 57.267 37.500 10.33 0.00 33.22 2.24
2785 4748 7.125792 TCCAAGAGACTGTTTCTTCTAACTT 57.874 36.000 10.33 0.00 33.22 2.66
2786 4749 7.565680 TCCAAGAGACTGTTTCTTCTAACTTT 58.434 34.615 10.33 0.00 33.22 2.66
2787 4750 8.047310 TCCAAGAGACTGTTTCTTCTAACTTTT 58.953 33.333 10.33 0.00 33.22 2.27
2799 4762 3.896122 TCTAACTTTTTGCAACATCGCC 58.104 40.909 0.00 0.00 0.00 5.54
2832 4795 1.141234 GGAGCCGGAGAAGGTTACG 59.859 63.158 5.05 0.00 0.00 3.18
2842 4805 2.231721 GAGAAGGTTACGAGCTGTTCCT 59.768 50.000 0.00 0.00 35.95 3.36
2889 4853 5.906073 AGGCGAAATTTAAGCAGCATATTT 58.094 33.333 16.71 0.00 0.00 1.40
2890 4854 6.340522 AGGCGAAATTTAAGCAGCATATTTT 58.659 32.000 16.71 0.00 0.00 1.82
2891 4855 6.818142 AGGCGAAATTTAAGCAGCATATTTTT 59.182 30.769 16.71 0.00 0.00 1.94
2929 4893 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
2930 4894 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
2932 4896 8.631480 TCCAATCTATTCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
2933 4897 7.176165 TCCAATCTATTCATCTTCAATCATGGC 59.824 37.037 0.00 0.00 0.00 4.40
2934 4898 7.039993 CCAATCTATTCATCTTCAATCATGGCA 60.040 37.037 0.00 0.00 0.00 4.92
2935 4899 7.689446 ATCTATTCATCTTCAATCATGGCAG 57.311 36.000 0.00 0.00 0.00 4.85
2936 4900 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
2937 4901 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
2938 4902 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
2939 4903 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
2940 4904 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
2941 4905 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
2942 4906 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
2943 4907 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
2944 4908 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
2945 4909 3.435327 TCAATCATGGCAGTACAACGAAC 59.565 43.478 0.00 0.00 0.00 3.95
2946 4910 2.535012 TCATGGCAGTACAACGAACA 57.465 45.000 0.00 0.00 0.00 3.18
2947 4911 2.139917 TCATGGCAGTACAACGAACAC 58.860 47.619 0.00 0.00 0.00 3.32
2948 4912 1.870402 CATGGCAGTACAACGAACACA 59.130 47.619 0.00 0.00 0.00 3.72
2949 4913 2.025589 TGGCAGTACAACGAACACAA 57.974 45.000 0.00 0.00 0.00 3.33
2950 4914 1.937223 TGGCAGTACAACGAACACAAG 59.063 47.619 0.00 0.00 0.00 3.16
2951 4915 2.206750 GGCAGTACAACGAACACAAGA 58.793 47.619 0.00 0.00 0.00 3.02
2952 4916 2.610374 GGCAGTACAACGAACACAAGAA 59.390 45.455 0.00 0.00 0.00 2.52
2953 4917 3.064271 GGCAGTACAACGAACACAAGAAA 59.936 43.478 0.00 0.00 0.00 2.52
2954 4918 4.261031 GGCAGTACAACGAACACAAGAAAT 60.261 41.667 0.00 0.00 0.00 2.17
2955 4919 5.049954 GGCAGTACAACGAACACAAGAAATA 60.050 40.000 0.00 0.00 0.00 1.40
2956 4920 6.423862 GCAGTACAACGAACACAAGAAATAA 58.576 36.000 0.00 0.00 0.00 1.40
2957 4921 6.908284 GCAGTACAACGAACACAAGAAATAAA 59.092 34.615 0.00 0.00 0.00 1.40
2958 4922 7.429920 GCAGTACAACGAACACAAGAAATAAAA 59.570 33.333 0.00 0.00 0.00 1.52
2959 4923 9.279904 CAGTACAACGAACACAAGAAATAAAAA 57.720 29.630 0.00 0.00 0.00 1.94
2980 4944 7.823745 AAAATTACATCCACATCCATAGACC 57.176 36.000 0.00 0.00 0.00 3.85
2981 4945 6.514012 AATTACATCCACATCCATAGACCA 57.486 37.500 0.00 0.00 0.00 4.02
2982 4946 3.845781 ACATCCACATCCATAGACCAC 57.154 47.619 0.00 0.00 0.00 4.16
2983 4947 3.114606 ACATCCACATCCATAGACCACA 58.885 45.455 0.00 0.00 0.00 4.17
2984 4948 3.718434 ACATCCACATCCATAGACCACAT 59.282 43.478 0.00 0.00 0.00 3.21
2985 4949 4.907269 ACATCCACATCCATAGACCACATA 59.093 41.667 0.00 0.00 0.00 2.29
2986 4950 5.012458 ACATCCACATCCATAGACCACATAG 59.988 44.000 0.00 0.00 0.00 2.23
2987 4951 3.903714 TCCACATCCATAGACCACATAGG 59.096 47.826 0.00 0.00 45.67 2.57
2988 4952 3.008375 CCACATCCATAGACCACATAGGG 59.992 52.174 0.00 0.00 43.89 3.53
2989 4953 3.903714 CACATCCATAGACCACATAGGGA 59.096 47.826 0.00 0.00 43.89 4.20
2990 4954 3.904339 ACATCCATAGACCACATAGGGAC 59.096 47.826 0.00 0.00 43.89 4.46
2991 4955 2.594131 TCCATAGACCACATAGGGACG 58.406 52.381 0.00 0.00 43.89 4.79
2992 4956 2.176148 TCCATAGACCACATAGGGACGA 59.824 50.000 0.00 0.00 43.89 4.20
2993 4957 2.296471 CCATAGACCACATAGGGACGAC 59.704 54.545 0.00 0.00 43.89 4.34
2994 4958 3.223435 CATAGACCACATAGGGACGACT 58.777 50.000 0.00 0.00 43.89 4.18
2995 4959 4.395625 CATAGACCACATAGGGACGACTA 58.604 47.826 0.00 0.00 43.89 2.59
2996 4960 2.652590 AGACCACATAGGGACGACTAC 58.347 52.381 0.00 0.00 43.89 2.73
2997 4961 2.025605 AGACCACATAGGGACGACTACA 60.026 50.000 0.00 0.00 43.89 2.74
2998 4962 2.756760 GACCACATAGGGACGACTACAA 59.243 50.000 0.00 0.00 43.89 2.41
2999 4963 2.758979 ACCACATAGGGACGACTACAAG 59.241 50.000 0.00 0.00 43.89 3.16
3000 4964 2.481449 CCACATAGGGACGACTACAAGC 60.481 54.545 0.00 0.00 0.00 4.01
3001 4965 2.165641 CACATAGGGACGACTACAAGCA 59.834 50.000 0.00 0.00 0.00 3.91
3002 4966 2.165845 ACATAGGGACGACTACAAGCAC 59.834 50.000 0.00 0.00 0.00 4.40
3003 4967 2.211250 TAGGGACGACTACAAGCACT 57.789 50.000 0.00 0.00 0.00 4.40
3004 4968 0.603569 AGGGACGACTACAAGCACTG 59.396 55.000 0.00 0.00 0.00 3.66
3005 4969 0.601558 GGGACGACTACAAGCACTGA 59.398 55.000 0.00 0.00 0.00 3.41
3006 4970 1.402984 GGGACGACTACAAGCACTGAG 60.403 57.143 0.00 0.00 0.00 3.35
3007 4971 1.402984 GGACGACTACAAGCACTGAGG 60.403 57.143 0.00 0.00 0.00 3.86
3008 4972 0.038159 ACGACTACAAGCACTGAGGC 60.038 55.000 0.00 0.00 0.00 4.70
3009 4973 1.073216 CGACTACAAGCACTGAGGCG 61.073 60.000 0.00 0.00 39.27 5.52
3010 4974 0.243907 GACTACAAGCACTGAGGCGA 59.756 55.000 0.00 0.00 39.27 5.54
3011 4975 0.244994 ACTACAAGCACTGAGGCGAG 59.755 55.000 0.00 0.00 39.27 5.03
3012 4976 1.079819 TACAAGCACTGAGGCGAGC 60.080 57.895 0.00 0.00 39.27 5.03
3013 4977 2.507110 TACAAGCACTGAGGCGAGCC 62.507 60.000 5.89 5.89 39.27 4.70
3014 4978 4.749310 AAGCACTGAGGCGAGCCG 62.749 66.667 8.63 0.00 41.95 5.52
3016 4980 4.742201 GCACTGAGGCGAGCCGAA 62.742 66.667 8.63 0.05 41.95 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 126 3.338249 ACGTGCAGCTTGATTAACAGAT 58.662 40.909 0.00 0.00 0.00 2.90
198 1150 3.769739 ATAGAAACGAGGCCATGCATA 57.230 42.857 5.01 0.00 0.00 3.14
222 1176 1.796982 CGGCGAGCTAGCTATATGCAG 60.797 57.143 19.38 15.57 45.94 4.41
300 1254 7.319646 GCCATTCAACATGTACTTTCCAATTA 58.680 34.615 0.00 0.00 0.00 1.40
616 2117 2.084546 GTGGGGATTCGAACCTCAAAG 58.915 52.381 17.41 0.00 39.78 2.77
868 2376 8.988064 TCTGAATCAGTAAACAGACTCATTAC 57.012 34.615 10.36 0.55 35.01 1.89
869 2377 7.761704 GCTCTGAATCAGTAAACAGACTCATTA 59.238 37.037 10.36 0.00 35.85 1.90
870 2378 6.593382 GCTCTGAATCAGTAAACAGACTCATT 59.407 38.462 10.36 0.00 35.85 2.57
871 2379 6.105333 GCTCTGAATCAGTAAACAGACTCAT 58.895 40.000 10.36 0.00 35.85 2.90
872 2380 5.473931 GCTCTGAATCAGTAAACAGACTCA 58.526 41.667 10.36 0.00 35.85 3.41
873 2381 4.867608 GGCTCTGAATCAGTAAACAGACTC 59.132 45.833 10.36 0.00 35.85 3.36
874 2382 4.284490 TGGCTCTGAATCAGTAAACAGACT 59.716 41.667 10.36 0.00 35.85 3.24
875 2383 4.569943 TGGCTCTGAATCAGTAAACAGAC 58.430 43.478 10.36 2.50 35.85 3.51
876 2384 4.890158 TGGCTCTGAATCAGTAAACAGA 57.110 40.909 10.36 0.00 37.71 3.41
877 2385 4.999950 ACTTGGCTCTGAATCAGTAAACAG 59.000 41.667 10.36 0.92 32.61 3.16
878 2386 4.973168 ACTTGGCTCTGAATCAGTAAACA 58.027 39.130 10.36 3.27 32.61 2.83
879 2387 4.092091 CGACTTGGCTCTGAATCAGTAAAC 59.908 45.833 10.36 0.74 32.61 2.01
890 2398 2.806856 GCGATGCGACTTGGCTCTG 61.807 63.158 0.00 0.00 0.00 3.35
891 2399 2.510238 GCGATGCGACTTGGCTCT 60.510 61.111 0.00 0.00 0.00 4.09
892 2400 2.098842 GATGCGATGCGACTTGGCTC 62.099 60.000 0.00 0.00 0.00 4.70
893 2401 2.124983 ATGCGATGCGACTTGGCT 60.125 55.556 0.00 0.00 0.00 4.75
894 2402 2.325857 GATGCGATGCGACTTGGC 59.674 61.111 0.00 0.00 0.00 4.52
911 2422 2.824041 CTTCCGGTCAATGCGGGG 60.824 66.667 0.00 0.00 0.00 5.73
919 2430 1.896660 GTTTGGCTGCTTCCGGTCA 60.897 57.895 0.00 0.00 0.00 4.02
1012 2526 2.946762 GGCTTTGGTGCTGTCGAC 59.053 61.111 9.11 9.11 0.00 4.20
1557 3071 2.676839 CAGATCAGCAAGCGTGAAATCT 59.323 45.455 2.99 5.05 0.00 2.40
1650 3164 2.099405 CCGAAAACAGGGCCAATGTAT 58.901 47.619 12.78 5.89 0.00 2.29
1652 3166 1.815817 GCCGAAAACAGGGCCAATGT 61.816 55.000 6.18 5.95 43.64 2.71
1696 3210 1.202177 CGCCATCACAAATGTACAGCC 60.202 52.381 0.33 0.00 0.00 4.85
1734 3248 1.291877 CTGTTTCCCTCGCTTCGTGG 61.292 60.000 0.82 0.82 39.77 4.94
1872 3386 0.246635 CCCAGTTACCAGTGTCCTCG 59.753 60.000 0.00 0.00 0.00 4.63
2000 3514 2.911484 CAGCTCACTTACAATCCTCCC 58.089 52.381 0.00 0.00 0.00 4.30
2034 3548 0.825840 CCAAAACTGGGGCCGAGAAA 60.826 55.000 23.31 0.00 0.00 2.52
2035 3549 1.228429 CCAAAACTGGGGCCGAGAA 60.228 57.895 23.31 0.00 0.00 2.87
2063 3577 3.698040 GCATCAAGATTCAACCAGTCCAT 59.302 43.478 0.00 0.00 0.00 3.41
2137 3651 0.963856 TCCTTAGTTCGGCGAGCTCA 60.964 55.000 29.21 17.99 0.00 4.26
2147 3661 5.295540 GTCTCATGCTTCCAATCCTTAGTTC 59.704 44.000 0.00 0.00 0.00 3.01
2158 3672 1.361204 TGAAGGGTCTCATGCTTCCA 58.639 50.000 7.33 0.00 0.00 3.53
2159 3673 2.087646 GTTGAAGGGTCTCATGCTTCC 58.912 52.381 7.33 0.79 0.00 3.46
2160 3674 1.734465 CGTTGAAGGGTCTCATGCTTC 59.266 52.381 3.78 3.78 0.00 3.86
2161 3675 1.813513 CGTTGAAGGGTCTCATGCTT 58.186 50.000 0.00 0.00 0.00 3.91
2162 3676 0.674895 GCGTTGAAGGGTCTCATGCT 60.675 55.000 0.00 0.00 0.00 3.79
2165 3685 0.670546 CACGCGTTGAAGGGTCTCAT 60.671 55.000 10.22 0.00 34.98 2.90
2171 3691 2.280524 TGGACACGCGTTGAAGGG 60.281 61.111 10.22 0.00 0.00 3.95
2172 3692 0.878523 TTCTGGACACGCGTTGAAGG 60.879 55.000 10.22 0.00 0.00 3.46
2176 3696 1.569493 CCTTTCTGGACACGCGTTG 59.431 57.895 10.22 8.21 38.35 4.10
2179 3699 3.777925 CGCCTTTCTGGACACGCG 61.778 66.667 3.53 3.53 38.35 6.01
2186 3706 5.309323 TGAAATAATCAACGCCTTTCTGG 57.691 39.130 0.00 0.00 34.30 3.86
2232 3752 3.366781 GCTTCTTCCCAGAAAACTGCATC 60.367 47.826 0.00 0.00 38.63 3.91
2246 3766 7.154656 ACCAAAATTCAAAGTATGCTTCTTCC 58.845 34.615 0.00 0.00 33.01 3.46
2264 3791 6.545666 TGTATTCCAATGCTATCGACCAAAAT 59.454 34.615 0.00 0.00 0.00 1.82
2272 3799 5.106436 ACATGCATGTATTCCAATGCTATCG 60.106 40.000 30.50 0.00 39.68 2.92
2276 3803 5.347620 AAACATGCATGTATTCCAATGCT 57.652 34.783 31.55 10.05 40.80 3.79
2278 3805 7.115236 CCGAATAAACATGCATGTATTCCAATG 59.885 37.037 31.25 22.86 40.80 2.82
2279 3806 7.147312 CCGAATAAACATGCATGTATTCCAAT 58.853 34.615 31.25 17.08 40.80 3.16
2280 3807 6.096141 ACCGAATAAACATGCATGTATTCCAA 59.904 34.615 31.25 17.84 40.80 3.53
2282 3809 6.072112 ACCGAATAAACATGCATGTATTCC 57.928 37.500 31.25 21.05 40.80 3.01
2283 3810 6.972328 ACAACCGAATAAACATGCATGTATTC 59.028 34.615 29.50 29.50 40.80 1.75
2284 3811 6.862209 ACAACCGAATAAACATGCATGTATT 58.138 32.000 31.55 26.25 40.80 1.89
2286 3813 5.888691 ACAACCGAATAAACATGCATGTA 57.111 34.783 31.55 18.32 40.80 2.29
2289 3816 5.888691 TGTACAACCGAATAAACATGCAT 57.111 34.783 0.00 0.00 0.00 3.96
2290 3817 5.690997 TTGTACAACCGAATAAACATGCA 57.309 34.783 3.59 0.00 0.00 3.96
2328 3856 3.144506 AGCACTCAAGGTCACAGAATTG 58.855 45.455 0.00 0.00 0.00 2.32
2343 3871 3.895232 TCCTCAACTTATGGAGCACTC 57.105 47.619 0.00 0.00 0.00 3.51
2354 3882 8.260114 CCTGCCAAATTATAAATTCCTCAACTT 58.740 33.333 0.00 0.00 0.00 2.66
2389 3917 6.711645 GGAACTATGTACCAGTACCACAAAAA 59.288 38.462 5.53 0.00 35.26 1.94
2474 4038 3.681874 GCAGAGGTGTGGGTTAATACTCC 60.682 52.174 0.00 0.00 0.00 3.85
2486 4050 1.338484 ACATAGTGCTGCAGAGGTGTG 60.338 52.381 20.43 12.21 0.00 3.82
2541 4105 8.588472 TCATATGTTCTGTTACAGAGGGATATG 58.412 37.037 25.15 25.15 41.75 1.78
2542 4106 8.589338 GTCATATGTTCTGTTACAGAGGGATAT 58.411 37.037 14.99 13.67 41.75 1.63
2543 4107 7.255486 CGTCATATGTTCTGTTACAGAGGGATA 60.255 40.741 14.99 12.23 41.75 2.59
2544 4108 6.461648 CGTCATATGTTCTGTTACAGAGGGAT 60.462 42.308 14.99 10.63 41.75 3.85
2545 4109 5.163550 CGTCATATGTTCTGTTACAGAGGGA 60.164 44.000 14.99 4.10 41.75 4.20
2546 4110 5.043903 CGTCATATGTTCTGTTACAGAGGG 58.956 45.833 14.99 3.53 41.75 4.30
2547 4111 5.651530 ACGTCATATGTTCTGTTACAGAGG 58.348 41.667 14.99 0.77 41.75 3.69
2548 4112 7.582435 AAACGTCATATGTTCTGTTACAGAG 57.418 36.000 14.99 3.14 41.75 3.35
2549 4113 7.956420 AAAACGTCATATGTTCTGTTACAGA 57.044 32.000 11.42 11.42 38.87 3.41
2590 4154 9.708222 CGTTTCAAGATATAAGATGTTTCTTGG 57.292 33.333 12.88 0.00 42.25 3.61
2591 4155 9.708222 CCGTTTCAAGATATAAGATGTTTCTTG 57.292 33.333 8.51 8.51 42.25 3.02
2592 4156 9.667107 TCCGTTTCAAGATATAAGATGTTTCTT 57.333 29.630 0.00 0.00 44.44 2.52
2593 4157 9.319143 CTCCGTTTCAAGATATAAGATGTTTCT 57.681 33.333 0.00 0.00 0.00 2.52
2594 4158 8.552034 CCTCCGTTTCAAGATATAAGATGTTTC 58.448 37.037 0.00 0.00 0.00 2.78
2595 4159 7.499232 CCCTCCGTTTCAAGATATAAGATGTTT 59.501 37.037 0.00 0.00 0.00 2.83
2596 4160 6.992715 CCCTCCGTTTCAAGATATAAGATGTT 59.007 38.462 0.00 0.00 0.00 2.71
2597 4161 6.326583 TCCCTCCGTTTCAAGATATAAGATGT 59.673 38.462 0.00 0.00 0.00 3.06
2598 4162 6.759272 TCCCTCCGTTTCAAGATATAAGATG 58.241 40.000 0.00 0.00 0.00 2.90
2599 4163 6.014156 CCTCCCTCCGTTTCAAGATATAAGAT 60.014 42.308 0.00 0.00 0.00 2.40
2600 4164 5.304614 CCTCCCTCCGTTTCAAGATATAAGA 59.695 44.000 0.00 0.00 0.00 2.10
2601 4165 5.304614 TCCTCCCTCCGTTTCAAGATATAAG 59.695 44.000 0.00 0.00 0.00 1.73
2602 4166 5.070047 GTCCTCCCTCCGTTTCAAGATATAA 59.930 44.000 0.00 0.00 0.00 0.98
2603 4167 4.587684 GTCCTCCCTCCGTTTCAAGATATA 59.412 45.833 0.00 0.00 0.00 0.86
2604 4168 3.388350 GTCCTCCCTCCGTTTCAAGATAT 59.612 47.826 0.00 0.00 0.00 1.63
2605 4169 2.764572 GTCCTCCCTCCGTTTCAAGATA 59.235 50.000 0.00 0.00 0.00 1.98
2606 4170 1.555533 GTCCTCCCTCCGTTTCAAGAT 59.444 52.381 0.00 0.00 0.00 2.40
2607 4171 0.974383 GTCCTCCCTCCGTTTCAAGA 59.026 55.000 0.00 0.00 0.00 3.02
2608 4172 0.036294 GGTCCTCCCTCCGTTTCAAG 60.036 60.000 0.00 0.00 0.00 3.02
2609 4173 0.473117 AGGTCCTCCCTCCGTTTCAA 60.473 55.000 0.00 0.00 40.71 2.69
2610 4174 1.157751 AGGTCCTCCCTCCGTTTCA 59.842 57.895 0.00 0.00 40.71 2.69
2611 4175 0.903454 TCAGGTCCTCCCTCCGTTTC 60.903 60.000 0.00 0.00 43.86 2.78
2612 4176 0.252742 ATCAGGTCCTCCCTCCGTTT 60.253 55.000 0.00 0.00 43.86 3.60
2613 4177 0.635009 TATCAGGTCCTCCCTCCGTT 59.365 55.000 0.00 0.00 43.86 4.44
2614 4178 0.186386 CTATCAGGTCCTCCCTCCGT 59.814 60.000 0.00 0.00 43.86 4.69
2615 4179 0.186386 ACTATCAGGTCCTCCCTCCG 59.814 60.000 0.00 0.00 43.86 4.63
2616 4180 1.710816 CACTATCAGGTCCTCCCTCC 58.289 60.000 0.00 0.00 43.86 4.30
2617 4181 1.218196 TCCACTATCAGGTCCTCCCTC 59.782 57.143 0.00 0.00 43.86 4.30
2619 4183 1.974236 CATCCACTATCAGGTCCTCCC 59.026 57.143 0.00 0.00 0.00 4.30
2620 4184 2.896685 CTCATCCACTATCAGGTCCTCC 59.103 54.545 0.00 0.00 0.00 4.30
2621 4185 3.838565 TCTCATCCACTATCAGGTCCTC 58.161 50.000 0.00 0.00 0.00 3.71
2622 4186 3.981516 TCTCATCCACTATCAGGTCCT 57.018 47.619 0.00 0.00 0.00 3.85
2623 4187 4.262808 CCATTCTCATCCACTATCAGGTCC 60.263 50.000 0.00 0.00 0.00 4.46
2624 4188 4.802248 GCCATTCTCATCCACTATCAGGTC 60.802 50.000 0.00 0.00 0.00 3.85
2658 4222 1.680249 GCCATTTCTGGAGACTGTCCC 60.680 57.143 3.76 6.30 46.31 4.46
2723 4287 5.424895 TCACTTTAAATTGGGCAATATGGCT 59.575 36.000 1.19 0.00 43.20 4.75
2724 4288 5.669477 TCACTTTAAATTGGGCAATATGGC 58.331 37.500 5.79 0.00 42.88 4.40
2725 4289 8.614346 CAAATCACTTTAAATTGGGCAATATGG 58.386 33.333 5.79 0.00 0.00 2.74
2726 4290 9.381033 TCAAATCACTTTAAATTGGGCAATATG 57.619 29.630 5.79 0.00 0.00 1.78
2741 4704 9.354673 TCTTGGAAAAGTATCTCAAATCACTTT 57.645 29.630 0.00 0.00 41.67 2.66
2751 4714 7.875554 AGAAACAGTCTCTTGGAAAAGTATCTC 59.124 37.037 0.00 0.00 0.00 2.75
2752 4715 7.740805 AGAAACAGTCTCTTGGAAAAGTATCT 58.259 34.615 0.00 0.00 0.00 1.98
2753 4716 7.971183 AGAAACAGTCTCTTGGAAAAGTATC 57.029 36.000 0.00 0.00 0.00 2.24
2754 4717 8.214364 AGAAGAAACAGTCTCTTGGAAAAGTAT 58.786 33.333 0.00 0.00 34.56 2.12
2755 4718 7.565680 AGAAGAAACAGTCTCTTGGAAAAGTA 58.434 34.615 0.00 0.00 34.56 2.24
2756 4719 6.418946 AGAAGAAACAGTCTCTTGGAAAAGT 58.581 36.000 0.00 0.00 34.56 2.66
2757 4720 6.934048 AGAAGAAACAGTCTCTTGGAAAAG 57.066 37.500 0.00 0.00 34.56 2.27
2758 4721 8.047310 AGTTAGAAGAAACAGTCTCTTGGAAAA 58.953 33.333 0.00 0.00 34.56 2.29
2759 4722 7.565680 AGTTAGAAGAAACAGTCTCTTGGAAA 58.434 34.615 0.00 0.00 34.56 3.13
2760 4723 7.125792 AGTTAGAAGAAACAGTCTCTTGGAA 57.874 36.000 0.00 0.00 34.56 3.53
2761 4724 6.732896 AGTTAGAAGAAACAGTCTCTTGGA 57.267 37.500 0.00 0.00 34.56 3.53
2762 4725 7.793927 AAAGTTAGAAGAAACAGTCTCTTGG 57.206 36.000 0.00 0.00 34.56 3.61
2763 4726 9.495754 CAAAAAGTTAGAAGAAACAGTCTCTTG 57.504 33.333 0.00 0.00 34.56 3.02
2764 4727 8.184848 GCAAAAAGTTAGAAGAAACAGTCTCTT 58.815 33.333 0.00 0.00 34.56 2.85
2765 4728 7.336931 TGCAAAAAGTTAGAAGAAACAGTCTCT 59.663 33.333 0.00 0.00 34.56 3.10
2766 4729 7.472543 TGCAAAAAGTTAGAAGAAACAGTCTC 58.527 34.615 0.00 0.00 34.56 3.36
2767 4730 7.391148 TGCAAAAAGTTAGAAGAAACAGTCT 57.609 32.000 0.00 0.00 38.69 3.24
2768 4731 7.540745 TGTTGCAAAAAGTTAGAAGAAACAGTC 59.459 33.333 0.00 0.00 0.00 3.51
2769 4732 7.375053 TGTTGCAAAAAGTTAGAAGAAACAGT 58.625 30.769 0.00 0.00 0.00 3.55
2770 4733 7.810766 TGTTGCAAAAAGTTAGAAGAAACAG 57.189 32.000 0.00 0.00 0.00 3.16
2771 4734 7.219917 CGATGTTGCAAAAAGTTAGAAGAAACA 59.780 33.333 0.00 0.00 0.00 2.83
2772 4735 7.547119 CGATGTTGCAAAAAGTTAGAAGAAAC 58.453 34.615 0.00 0.00 0.00 2.78
2773 4736 6.198216 GCGATGTTGCAAAAAGTTAGAAGAAA 59.802 34.615 0.00 0.00 34.15 2.52
2774 4737 5.685511 GCGATGTTGCAAAAAGTTAGAAGAA 59.314 36.000 0.00 0.00 34.15 2.52
2775 4738 5.212194 GCGATGTTGCAAAAAGTTAGAAGA 58.788 37.500 0.00 0.00 34.15 2.87
2776 4739 4.382754 GGCGATGTTGCAAAAAGTTAGAAG 59.617 41.667 0.00 0.00 36.28 2.85
2777 4740 4.295051 GGCGATGTTGCAAAAAGTTAGAA 58.705 39.130 0.00 0.00 36.28 2.10
2778 4741 3.608241 CGGCGATGTTGCAAAAAGTTAGA 60.608 43.478 0.00 0.00 36.28 2.10
2779 4742 2.656422 CGGCGATGTTGCAAAAAGTTAG 59.344 45.455 0.00 0.00 36.28 2.34
2780 4743 2.033550 ACGGCGATGTTGCAAAAAGTTA 59.966 40.909 16.62 0.00 36.28 2.24
2781 4744 1.202359 ACGGCGATGTTGCAAAAAGTT 60.202 42.857 16.62 0.00 36.28 2.66
2782 4745 0.383949 ACGGCGATGTTGCAAAAAGT 59.616 45.000 16.62 0.00 36.28 2.66
2783 4746 1.052287 GACGGCGATGTTGCAAAAAG 58.948 50.000 16.62 0.00 36.28 2.27
2784 4747 0.658829 CGACGGCGATGTTGCAAAAA 60.659 50.000 16.62 0.00 40.82 1.94
2785 4748 1.082431 CGACGGCGATGTTGCAAAA 60.082 52.632 16.62 0.00 40.82 2.44
2786 4749 2.553770 CGACGGCGATGTTGCAAA 59.446 55.556 16.62 0.00 40.82 3.68
2787 4750 3.418913 CCGACGGCGATGTTGCAA 61.419 61.111 15.16 0.00 40.82 4.08
2832 4795 0.673022 CAGCAGGTCAGGAACAGCTC 60.673 60.000 0.84 0.00 38.32 4.09
2842 4805 1.347378 TGCAACTATGTCAGCAGGTCA 59.653 47.619 0.00 0.00 32.48 4.02
2903 4867 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
2904 4868 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
2906 4870 9.074576 CCATGATTGAAGATGAATAGATTGGAA 57.925 33.333 0.00 0.00 0.00 3.53
2907 4871 7.176165 GCCATGATTGAAGATGAATAGATTGGA 59.824 37.037 0.00 0.00 0.00 3.53
2908 4872 7.039993 TGCCATGATTGAAGATGAATAGATTGG 60.040 37.037 0.00 0.00 0.00 3.16
2909 4873 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
2910 4874 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
2911 4875 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
2912 4876 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
2913 4877 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
2914 4878 7.281841 TGTACTGCCATGATTGAAGATGAATA 58.718 34.615 0.00 0.00 0.00 1.75
2915 4879 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
2916 4880 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
2917 4881 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
2918 4882 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
2919 4883 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
2920 4884 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
2921 4885 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
2922 4886 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
2923 4887 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
2924 4888 3.188254 TGTTCGTTGTACTGCCATGATTG 59.812 43.478 0.00 0.00 0.00 2.67
2925 4889 3.188460 GTGTTCGTTGTACTGCCATGATT 59.812 43.478 0.00 0.00 0.00 2.57
2926 4890 2.742053 GTGTTCGTTGTACTGCCATGAT 59.258 45.455 0.00 0.00 0.00 2.45
2927 4891 2.139917 GTGTTCGTTGTACTGCCATGA 58.860 47.619 0.00 0.00 0.00 3.07
2928 4892 1.870402 TGTGTTCGTTGTACTGCCATG 59.130 47.619 0.00 0.00 0.00 3.66
2929 4893 2.248280 TGTGTTCGTTGTACTGCCAT 57.752 45.000 0.00 0.00 0.00 4.40
2930 4894 1.937223 CTTGTGTTCGTTGTACTGCCA 59.063 47.619 0.00 0.00 0.00 4.92
2931 4895 2.206750 TCTTGTGTTCGTTGTACTGCC 58.793 47.619 0.00 0.00 0.00 4.85
2932 4896 3.936902 TTCTTGTGTTCGTTGTACTGC 57.063 42.857 0.00 0.00 0.00 4.40
2933 4897 8.829514 TTTTATTTCTTGTGTTCGTTGTACTG 57.170 30.769 0.00 0.00 0.00 2.74
2954 4918 9.349713 GGTCTATGGATGTGGATGTAATTTTTA 57.650 33.333 0.00 0.00 0.00 1.52
2955 4919 7.838696 TGGTCTATGGATGTGGATGTAATTTTT 59.161 33.333 0.00 0.00 0.00 1.94
2956 4920 7.285401 GTGGTCTATGGATGTGGATGTAATTTT 59.715 37.037 0.00 0.00 0.00 1.82
2957 4921 6.772716 GTGGTCTATGGATGTGGATGTAATTT 59.227 38.462 0.00 0.00 0.00 1.82
2958 4922 6.126507 TGTGGTCTATGGATGTGGATGTAATT 60.127 38.462 0.00 0.00 0.00 1.40
2959 4923 5.369404 TGTGGTCTATGGATGTGGATGTAAT 59.631 40.000 0.00 0.00 0.00 1.89
2960 4924 4.719273 TGTGGTCTATGGATGTGGATGTAA 59.281 41.667 0.00 0.00 0.00 2.41
2961 4925 4.294347 TGTGGTCTATGGATGTGGATGTA 58.706 43.478 0.00 0.00 0.00 2.29
2962 4926 3.114606 TGTGGTCTATGGATGTGGATGT 58.885 45.455 0.00 0.00 0.00 3.06
2963 4927 3.843893 TGTGGTCTATGGATGTGGATG 57.156 47.619 0.00 0.00 0.00 3.51
2964 4928 4.533707 CCTATGTGGTCTATGGATGTGGAT 59.466 45.833 0.00 0.00 0.00 3.41
2965 4929 3.903714 CCTATGTGGTCTATGGATGTGGA 59.096 47.826 0.00 0.00 0.00 4.02
2966 4930 3.008375 CCCTATGTGGTCTATGGATGTGG 59.992 52.174 0.00 0.00 0.00 4.17
2967 4931 3.903714 TCCCTATGTGGTCTATGGATGTG 59.096 47.826 0.00 0.00 0.00 3.21
2968 4932 3.904339 GTCCCTATGTGGTCTATGGATGT 59.096 47.826 0.00 0.00 0.00 3.06
2969 4933 3.056536 CGTCCCTATGTGGTCTATGGATG 60.057 52.174 0.00 0.00 0.00 3.51
2970 4934 3.165875 CGTCCCTATGTGGTCTATGGAT 58.834 50.000 0.00 0.00 0.00 3.41
2971 4935 2.176148 TCGTCCCTATGTGGTCTATGGA 59.824 50.000 0.00 0.00 0.00 3.41
2972 4936 2.296471 GTCGTCCCTATGTGGTCTATGG 59.704 54.545 0.00 0.00 0.00 2.74
2973 4937 3.223435 AGTCGTCCCTATGTGGTCTATG 58.777 50.000 0.00 0.00 0.00 2.23
2974 4938 3.596940 AGTCGTCCCTATGTGGTCTAT 57.403 47.619 0.00 0.00 0.00 1.98
2975 4939 3.200605 TGTAGTCGTCCCTATGTGGTCTA 59.799 47.826 0.00 0.00 0.00 2.59
2976 4940 2.025605 TGTAGTCGTCCCTATGTGGTCT 60.026 50.000 0.00 0.00 0.00 3.85
2977 4941 2.372264 TGTAGTCGTCCCTATGTGGTC 58.628 52.381 0.00 0.00 0.00 4.02
2978 4942 2.519771 TGTAGTCGTCCCTATGTGGT 57.480 50.000 0.00 0.00 0.00 4.16
2979 4943 2.481449 GCTTGTAGTCGTCCCTATGTGG 60.481 54.545 0.00 0.00 0.00 4.17
2980 4944 2.165641 TGCTTGTAGTCGTCCCTATGTG 59.834 50.000 0.00 0.00 0.00 3.21
2981 4945 2.165845 GTGCTTGTAGTCGTCCCTATGT 59.834 50.000 0.00 0.00 0.00 2.29
2982 4946 2.427453 AGTGCTTGTAGTCGTCCCTATG 59.573 50.000 0.00 0.00 0.00 2.23
2983 4947 2.427453 CAGTGCTTGTAGTCGTCCCTAT 59.573 50.000 0.00 0.00 0.00 2.57
2984 4948 1.816835 CAGTGCTTGTAGTCGTCCCTA 59.183 52.381 0.00 0.00 0.00 3.53
2985 4949 0.603569 CAGTGCTTGTAGTCGTCCCT 59.396 55.000 0.00 0.00 0.00 4.20
2986 4950 0.601558 TCAGTGCTTGTAGTCGTCCC 59.398 55.000 0.00 0.00 0.00 4.46
2987 4951 1.402984 CCTCAGTGCTTGTAGTCGTCC 60.403 57.143 0.00 0.00 0.00 4.79
2988 4952 1.983972 CCTCAGTGCTTGTAGTCGTC 58.016 55.000 0.00 0.00 0.00 4.20
2989 4953 0.038159 GCCTCAGTGCTTGTAGTCGT 60.038 55.000 0.00 0.00 0.00 4.34
2990 4954 1.073216 CGCCTCAGTGCTTGTAGTCG 61.073 60.000 0.00 0.00 0.00 4.18
2991 4955 0.243907 TCGCCTCAGTGCTTGTAGTC 59.756 55.000 0.00 0.00 0.00 2.59
2992 4956 0.244994 CTCGCCTCAGTGCTTGTAGT 59.755 55.000 0.00 0.00 0.00 2.73
2993 4957 1.080995 GCTCGCCTCAGTGCTTGTAG 61.081 60.000 0.00 0.00 0.00 2.74
2994 4958 1.079819 GCTCGCCTCAGTGCTTGTA 60.080 57.895 0.00 0.00 0.00 2.41
2995 4959 2.358003 GCTCGCCTCAGTGCTTGT 60.358 61.111 0.00 0.00 0.00 3.16
2996 4960 3.123620 GGCTCGCCTCAGTGCTTG 61.124 66.667 0.00 0.00 0.00 4.01
2997 4961 4.749310 CGGCTCGCCTCAGTGCTT 62.749 66.667 6.35 0.00 0.00 3.91
2999 4963 4.742201 TTCGGCTCGCCTCAGTGC 62.742 66.667 6.35 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.