Multiple sequence alignment - TraesCS5B01G367700

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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 TraesCS5B01G367700 chr5B 100.000 5192 0 0 1 5192 546118480 546113289 0.000000e+00 9588.0
1 TraesCS5B01G367700 chr5B 96.406 2393 81 3 1 2391 545874894 545872505 0.000000e+00 3938.0
2 TraesCS5B01G367700 chr5B 95.738 2393 85 4 1 2391 545897462 545895085 0.000000e+00 3838.0
3 TraesCS5B01G367700 chr5B 79.049 2229 392 53 464 2656 546319956 546317767 0.000000e+00 1459.0
4 TraesCS5B01G367700 chr5B 94.673 413 15 2 4787 5192 545870442 545870030 7.330000e-178 634.0
5 TraesCS5B01G367700 chr5B 94.431 413 16 2 4787 5192 545893021 545892609 3.410000e-176 628.0
6 TraesCS5B01G367700 chr5B 93.484 353 18 3 3726 4074 654900625 654900976 2.140000e-143 520.0
7 TraesCS5B01G367700 chr5B 96.154 286 8 1 3792 4074 595143106 595143391 1.020000e-126 464.0
8 TraesCS5B01G367700 chr5B 94.527 201 5 1 4998 5192 73350121 73349921 6.530000e-79 305.0
9 TraesCS5B01G367700 chr5B 93.532 201 7 1 4998 5192 486730332 486730132 1.410000e-75 294.0
10 TraesCS5B01G367700 chr5B 86.939 245 28 4 2663 2905 595141916 595142158 6.620000e-69 272.0
11 TraesCS5B01G367700 chr5B 97.727 44 0 1 4181 4224 545870477 545870435 2.010000e-09 75.0
12 TraesCS5B01G367700 chr5B 97.727 44 0 1 4181 4224 545893056 545893014 2.010000e-09 75.0
13 TraesCS5B01G367700 chr5D 96.925 2667 74 5 1 2661 447426781 447424117 0.000000e+00 4464.0
14 TraesCS5B01G367700 chr5D 84.870 1117 152 12 1549 2661 447502490 447501387 0.000000e+00 1110.0
15 TraesCS5B01G367700 chr5D 86.055 545 55 8 4391 4924 447423734 447423200 2.710000e-157 566.0
16 TraesCS5B01G367700 chr5D 92.945 326 10 3 4075 4398 447424125 447423811 3.660000e-126 462.0
17 TraesCS5B01G367700 chr5D 80.980 347 46 12 3351 3696 228256474 228256801 1.860000e-64 257.0
18 TraesCS5B01G367700 chr4B 77.518 2184 417 50 482 2630 3781918 3784062 0.000000e+00 1245.0
19 TraesCS5B01G367700 chr4B 94.527 201 5 1 4998 5192 391151694 391151894 6.530000e-79 305.0
20 TraesCS5B01G367700 chr3D 76.444 2182 432 56 482 2613 587048476 587046327 0.000000e+00 1107.0
21 TraesCS5B01G367700 chr3D 86.957 115 15 0 2971 3085 58538691 58538577 4.220000e-26 130.0
22 TraesCS5B01G367700 chr3D 85.185 81 7 1 3274 3349 132927015 132926935 1.550000e-10 78.7
23 TraesCS5B01G367700 chr3D 100.000 28 0 0 2923 2950 143952923 143952950 9.000000e-03 52.8
24 TraesCS5B01G367700 chr2B 84.127 945 138 10 1680 2617 775359771 775360710 0.000000e+00 904.0
25 TraesCS5B01G367700 chr5A 83.540 966 153 6 1651 2613 565659831 565660793 0.000000e+00 898.0
26 TraesCS5B01G367700 chr5A 94.085 355 16 3 3726 4077 659434432 659434080 7.650000e-148 534.0
27 TraesCS5B01G367700 chr5A 93.208 265 18 0 2663 2927 659435256 659434992 1.750000e-104 390.0
28 TraesCS5B01G367700 chr5A 94.527 201 5 1 4998 5192 585741218 585741418 6.530000e-79 305.0
29 TraesCS5B01G367700 chr5A 88.608 79 7 2 3401 3477 53303728 53303650 1.540000e-15 95.3
30 TraesCS5B01G367700 chr3B 80.405 1184 216 14 1435 2613 783619426 783618254 0.000000e+00 887.0
31 TraesCS5B01G367700 chr3B 85.441 261 28 8 2652 2905 819780994 819780737 3.990000e-66 263.0
32 TraesCS5B01G367700 chr3B 79.121 182 36 2 482 662 783620403 783620223 1.960000e-24 124.0
33 TraesCS5B01G367700 chr3B 87.654 81 5 1 3274 3349 189415440 189415360 7.160000e-14 89.8
34 TraesCS5B01G367700 chr4A 86.189 572 50 12 3196 3739 599941251 599941821 4.480000e-165 592.0
35 TraesCS5B01G367700 chr4A 92.068 353 23 3 3726 4074 645335259 645334908 4.670000e-135 492.0
36 TraesCS5B01G367700 chr4A 91.286 241 21 0 2946 3186 660437378 660437618 3.880000e-86 329.0
37 TraesCS5B01G367700 chr4A 89.286 252 24 2 2663 2913 645339935 645339686 3.900000e-81 313.0
38 TraesCS5B01G367700 chr4A 91.509 212 16 2 2716 2927 594368486 594368695 1.830000e-74 291.0
39 TraesCS5B01G367700 chr2D 95.467 353 11 3 3726 4075 528515734 528516084 4.540000e-155 558.0
40 TraesCS5B01G367700 chr2D 94.007 267 13 2 2663 2927 528515096 528515361 8.100000e-108 401.0
41 TraesCS5B01G367700 chr2D 100.000 28 0 0 2923 2950 92834956 92834929 9.000000e-03 52.8
42 TraesCS5B01G367700 chr3A 94.302 351 15 3 3726 4073 671007375 671007723 2.750000e-147 532.0
43 TraesCS5B01G367700 chr3A 95.876 291 6 4 3792 4077 713658996 713659285 2.830000e-127 466.0
44 TraesCS5B01G367700 chr3A 94.253 261 15 0 2661 2921 713657656 713657916 2.910000e-107 399.0
45 TraesCS5B01G367700 chr3A 91.985 262 13 1 2925 3186 711480455 711480708 1.370000e-95 361.0
46 TraesCS5B01G367700 chr3A 87.952 83 1 4 3274 3349 146609344 146609264 7.160000e-14 89.8
47 TraesCS5B01G367700 chr6B 92.135 356 22 4 3726 4077 720530129 720529776 1.000000e-136 497.0
48 TraesCS5B01G367700 chr6B 90.476 252 20 3 2663 2913 720530840 720530592 3.880000e-86 329.0
49 TraesCS5B01G367700 chr6B 93.532 201 7 1 4998 5192 471626806 471626606 1.410000e-75 294.0
50 TraesCS5B01G367700 chr6B 83.453 278 43 3 3421 3696 281258443 281258719 6.670000e-64 255.0
51 TraesCS5B01G367700 chr7A 91.785 353 23 4 3726 4074 595998768 595999118 2.170000e-133 486.0
52 TraesCS5B01G367700 chr7A 90.598 234 20 2 2953 3186 9201527 9201296 5.050000e-80 309.0
53 TraesCS5B01G367700 chr7A 87.121 264 20 5 2923 3186 9201285 9201036 2.370000e-73 287.0
54 TraesCS5B01G367700 chr7A 88.066 243 25 3 2663 2904 595997762 595998001 8.510000e-73 285.0
55 TraesCS5B01G367700 chr2A 91.667 264 14 4 2923 3186 262331785 262332040 4.940000e-95 359.0
56 TraesCS5B01G367700 chr2A 93.532 201 7 1 4998 5192 530670426 530670626 1.410000e-75 294.0
57 TraesCS5B01G367700 chr7B 83.333 408 47 9 3331 3736 747375444 747375832 1.780000e-94 357.0
58 TraesCS5B01G367700 chr7B 91.503 153 13 0 2946 3098 704313366 704313214 1.460000e-50 211.0
59 TraesCS5B01G367700 chr1A 92.000 200 11 5 4998 5192 328844167 328844366 5.120000e-70 276.0
60 TraesCS5B01G367700 chr1A 96.154 78 3 0 2923 3000 559835995 559835918 1.520000e-25 128.0
61 TraesCS5B01G367700 chr1A 100.000 28 0 0 2923 2950 559835530 559835503 9.000000e-03 52.8
62 TraesCS5B01G367700 chr7D 91.500 200 11 1 4998 5191 454076369 454076170 2.380000e-68 270.0
63 TraesCS5B01G367700 chr6A 85.985 264 23 5 2923 3186 617677385 617677634 2.380000e-68 270.0
64 TraesCS5B01G367700 chr6A 87.815 238 17 6 2950 3186 617677148 617677374 8.570000e-68 268.0
65 TraesCS5B01G367700 chr4D 93.671 158 7 2 3029 3186 305963514 305963360 3.130000e-57 233.0
66 TraesCS5B01G367700 chr4D 100.000 28 0 0 2923 2950 305963349 305963322 9.000000e-03 52.8
67 TraesCS5B01G367700 chr1B 83.036 112 19 0 3366 3477 684302187 684302298 9.200000e-18 102.0


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 TraesCS5B01G367700 chr5B 546113289 546118480 5191 True 9588.000000 9588 100.000000 1 5192 1 chr5B.!!$R3 5191
1 TraesCS5B01G367700 chr5B 545870030 545874894 4864 True 1549.000000 3938 96.268667 1 5192 3 chr5B.!!$R5 5191
2 TraesCS5B01G367700 chr5B 545892609 545897462 4853 True 1513.666667 3838 95.965333 1 5192 3 chr5B.!!$R6 5191
3 TraesCS5B01G367700 chr5B 546317767 546319956 2189 True 1459.000000 1459 79.049000 464 2656 1 chr5B.!!$R4 2192
4 TraesCS5B01G367700 chr5B 595141916 595143391 1475 False 368.000000 464 91.546500 2663 4074 2 chr5B.!!$F2 1411
5 TraesCS5B01G367700 chr5D 447423200 447426781 3581 True 1830.666667 4464 91.975000 1 4924 3 chr5D.!!$R2 4923
6 TraesCS5B01G367700 chr5D 447501387 447502490 1103 True 1110.000000 1110 84.870000 1549 2661 1 chr5D.!!$R1 1112
7 TraesCS5B01G367700 chr4B 3781918 3784062 2144 False 1245.000000 1245 77.518000 482 2630 1 chr4B.!!$F1 2148
8 TraesCS5B01G367700 chr3D 587046327 587048476 2149 True 1107.000000 1107 76.444000 482 2613 1 chr3D.!!$R3 2131
9 TraesCS5B01G367700 chr2B 775359771 775360710 939 False 904.000000 904 84.127000 1680 2617 1 chr2B.!!$F1 937
10 TraesCS5B01G367700 chr5A 565659831 565660793 962 False 898.000000 898 83.540000 1651 2613 1 chr5A.!!$F1 962
11 TraesCS5B01G367700 chr5A 659434080 659435256 1176 True 462.000000 534 93.646500 2663 4077 2 chr5A.!!$R2 1414
12 TraesCS5B01G367700 chr3B 783618254 783620403 2149 True 505.500000 887 79.763000 482 2613 2 chr3B.!!$R3 2131
13 TraesCS5B01G367700 chr4A 599941251 599941821 570 False 592.000000 592 86.189000 3196 3739 1 chr4A.!!$F2 543
14 TraesCS5B01G367700 chr2D 528515096 528516084 988 False 479.500000 558 94.737000 2663 4075 2 chr2D.!!$F1 1412
15 TraesCS5B01G367700 chr3A 713657656 713659285 1629 False 432.500000 466 95.064500 2661 4077 2 chr3A.!!$F3 1416
16 TraesCS5B01G367700 chr6B 720529776 720530840 1064 True 413.000000 497 91.305500 2663 4077 2 chr6B.!!$R2 1414
17 TraesCS5B01G367700 chr7A 595997762 595999118 1356 False 385.500000 486 89.925500 2663 4074 2 chr7A.!!$F1 1411

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
649 656 1.523711 CTCCACAACAGCACCGTGT 60.524 57.895 0.00 0.0 0.00 4.49 F
1045 1076 0.670162 GGCATTGCCGCATTCATACT 59.330 50.000 12.82 0.0 39.62 2.12 F
2930 4814 0.033504 GGTCACACACACGTCCAGAT 59.966 55.000 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 1954 2.284190 CGCACCATGTTTTTGGGTTTT 58.716 42.857 0.00 0.00 41.35 2.43 R
2938 4822 0.250081 GAGAGGCAATGACCCGATCC 60.250 60.000 0.00 0.00 0.00 3.36 R
4761 8104 0.167470 GTTCGACGGTGACTGATCGA 59.833 55.000 12.66 12.66 41.55 3.59 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
57 58 3.688694 ACGTGCCCACTACATAAAAGA 57.311 42.857 0.00 0.00 0.00 2.52
282 288 2.266279 AGAGAAAATCCCACCTCGGAA 58.734 47.619 0.00 0.00 36.56 4.30
356 362 7.867909 GGGATTAATGCTTTTGTATTAGCCTTC 59.132 37.037 6.93 0.00 38.04 3.46
363 369 5.066634 GCTTTTGTATTAGCCTTCTCCTTCC 59.933 44.000 0.00 0.00 0.00 3.46
365 371 6.388619 TTTGTATTAGCCTTCTCCTTCCTT 57.611 37.500 0.00 0.00 0.00 3.36
436 442 8.204836 ACATAGAGTAGGGAAACATATTGTCAC 58.795 37.037 0.00 0.00 0.00 3.67
554 561 2.105006 CACAAGTGCTATCTGCCAGT 57.895 50.000 0.00 0.00 42.00 4.00
649 656 1.523711 CTCCACAACAGCACCGTGT 60.524 57.895 0.00 0.00 0.00 4.49
696 703 1.831652 GCATCTATGGCGGGGTAGCT 61.832 60.000 0.00 0.00 37.29 3.32
758 768 3.967987 ACTAGGCCCTTCTCGTTATCAAT 59.032 43.478 0.00 0.00 0.00 2.57
990 1021 2.742856 CGGCATGCCTAGTGAATTCTGA 60.743 50.000 33.07 0.00 0.00 3.27
1045 1076 0.670162 GGCATTGCCGCATTCATACT 59.330 50.000 12.82 0.00 39.62 2.12
1240 1280 1.295101 CAGTATGCCGTGTGTCCCA 59.705 57.895 0.00 0.00 0.00 4.37
1395 1435 5.341462 CACATATGCGAGCTTAATTTGCATC 59.659 40.000 14.73 0.00 43.02 3.91
1647 1712 4.051237 GTTTCTGCTTGGGTTGTTGATTC 58.949 43.478 0.00 0.00 0.00 2.52
1728 1793 2.916716 CACGGACAATTATTGCAACAGC 59.083 45.455 0.00 0.00 0.00 4.40
1744 1809 2.795329 ACAGCTTGTATCCCAAAGTGG 58.205 47.619 0.00 0.00 37.25 4.00
1755 1820 1.967066 CCCAAAGTGGTGGTATTGCAA 59.033 47.619 0.00 0.00 36.90 4.08
1792 1857 3.245803 ACCTTGGAAGAGCTAGAGAAGGA 60.246 47.826 14.72 0.00 33.97 3.36
1889 1954 6.404184 CGAACCAACATATTGTAGCCATCAAA 60.404 38.462 0.00 0.00 33.60 2.69
2254 2319 6.959639 TTTTGGAGCTTCAAAGTACATTCT 57.040 33.333 19.36 0.00 37.82 2.40
2632 4504 0.898789 ACACGTGTGTCTAGGGAGGG 60.899 60.000 22.71 0.00 40.24 4.30
2839 4713 0.320073 CCGTTTTCTGCCTACGTGGA 60.320 55.000 0.00 0.00 38.35 4.02
2921 4805 2.279186 CGAGCACGGTCACACACA 60.279 61.111 0.00 0.00 35.72 3.72
2927 4811 2.105328 CGGTCACACACACGTCCA 59.895 61.111 0.00 0.00 0.00 4.02
2928 4812 1.949133 CGGTCACACACACGTCCAG 60.949 63.158 0.00 0.00 0.00 3.86
2929 4813 1.440060 GGTCACACACACGTCCAGA 59.560 57.895 0.00 0.00 0.00 3.86
2930 4814 0.033504 GGTCACACACACGTCCAGAT 59.966 55.000 0.00 0.00 0.00 2.90
2931 4815 1.419374 GTCACACACACGTCCAGATC 58.581 55.000 0.00 0.00 0.00 2.75
2932 4816 0.317160 TCACACACACGTCCAGATCC 59.683 55.000 0.00 0.00 0.00 3.36
2933 4817 0.670546 CACACACACGTCCAGATCCC 60.671 60.000 0.00 0.00 0.00 3.85
2934 4818 1.446099 CACACACGTCCAGATCCCG 60.446 63.158 0.00 0.00 0.00 5.14
2935 4819 1.906824 ACACACGTCCAGATCCCGT 60.907 57.895 0.00 0.00 34.71 5.28
2936 4820 1.153823 CACACGTCCAGATCCCGTC 60.154 63.158 0.00 0.00 31.46 4.79
2937 4821 2.102357 CACGTCCAGATCCCGTCG 59.898 66.667 0.00 0.00 31.46 5.12
2938 4822 3.138798 ACGTCCAGATCCCGTCGG 61.139 66.667 3.60 3.60 0.00 4.79
2939 4823 3.900892 CGTCCAGATCCCGTCGGG 61.901 72.222 25.31 25.31 46.11 5.14
2950 4834 2.792947 CCGTCGGGATCGGGTCATT 61.793 63.158 2.34 0.00 43.68 2.57
2954 4838 2.919043 GGGATCGGGTCATTGCCT 59.081 61.111 0.00 0.00 0.00 4.75
2956 4840 1.700042 GGGATCGGGTCATTGCCTCT 61.700 60.000 0.00 0.00 0.00 3.69
2961 4845 1.225704 GGGTCATTGCCTCTCCCAG 59.774 63.158 0.00 0.00 38.15 4.45
2962 4846 1.225704 GGTCATTGCCTCTCCCAGG 59.774 63.158 0.00 0.00 46.82 4.45
2989 4873 2.358615 GCCGTGGTCTGCATCACA 60.359 61.111 13.06 0.00 33.83 3.58
2990 4874 2.680913 GCCGTGGTCTGCATCACAC 61.681 63.158 13.06 9.34 33.83 3.82
2992 4876 0.246360 CCGTGGTCTGCATCACACTA 59.754 55.000 13.06 0.00 33.83 2.74
2993 4877 1.633561 CGTGGTCTGCATCACACTAG 58.366 55.000 13.06 0.00 33.83 2.57
2994 4878 1.737029 CGTGGTCTGCATCACACTAGG 60.737 57.143 13.06 0.00 33.83 3.02
2995 4879 0.250234 TGGTCTGCATCACACTAGGC 59.750 55.000 0.00 0.00 0.00 3.93
2996 4880 0.539051 GGTCTGCATCACACTAGGCT 59.461 55.000 0.00 0.00 0.00 4.58
2997 4881 1.649664 GTCTGCATCACACTAGGCTG 58.350 55.000 0.00 0.00 0.00 4.85
2998 4882 0.538584 TCTGCATCACACTAGGCTGG 59.461 55.000 0.00 0.00 0.00 4.85
2999 4883 0.538584 CTGCATCACACTAGGCTGGA 59.461 55.000 4.33 0.00 0.00 3.86
3000 4884 0.538584 TGCATCACACTAGGCTGGAG 59.461 55.000 4.33 0.00 0.00 3.86
3001 4885 0.813210 GCATCACACTAGGCTGGAGC 60.813 60.000 4.33 0.00 41.14 4.70
3002 4886 0.529337 CATCACACTAGGCTGGAGCG 60.529 60.000 4.33 0.00 43.26 5.03
3003 4887 2.303549 ATCACACTAGGCTGGAGCGC 62.304 60.000 4.33 0.00 43.26 5.92
3004 4888 2.681778 ACACTAGGCTGGAGCGCT 60.682 61.111 11.27 11.27 43.26 5.92
3005 4889 2.202851 CACTAGGCTGGAGCGCTG 60.203 66.667 18.48 0.22 43.26 5.18
3006 4890 4.154347 ACTAGGCTGGAGCGCTGC 62.154 66.667 23.36 23.36 43.26 5.25
3007 4891 4.906792 CTAGGCTGGAGCGCTGCC 62.907 72.222 26.87 26.10 46.42 4.85
3020 4904 2.821366 CTGCCGTGGTCAGCATCC 60.821 66.667 0.00 0.00 38.56 3.51
3021 4905 4.408821 TGCCGTGGTCAGCATCCC 62.409 66.667 0.00 0.00 33.08 3.85
3023 4907 4.489771 CCGTGGTCAGCATCCCCC 62.490 72.222 0.00 0.00 0.00 5.40
3024 4908 3.402681 CGTGGTCAGCATCCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
3124 5008 4.087892 CCTCCCGACCAGCCACTG 62.088 72.222 0.00 0.00 0.00 3.66
3125 5009 2.997315 CTCCCGACCAGCCACTGA 60.997 66.667 0.00 0.00 32.44 3.41
3126 5010 3.302347 CTCCCGACCAGCCACTGAC 62.302 68.421 0.00 0.00 32.44 3.51
3127 5011 4.742201 CCCGACCAGCCACTGACG 62.742 72.222 0.00 2.23 32.44 4.35
3129 5013 4.363990 CGACCAGCCACTGACGCT 62.364 66.667 0.00 0.00 36.91 5.07
3134 5018 4.385405 AGCCACTGACGCTGGAGC 62.385 66.667 0.00 0.00 34.56 4.70
3135 5019 4.385405 GCCACTGACGCTGGAGCT 62.385 66.667 0.00 0.00 39.32 4.09
3136 5020 2.345244 CCACTGACGCTGGAGCTT 59.655 61.111 0.00 0.00 39.32 3.74
3137 5021 2.031516 CCACTGACGCTGGAGCTTG 61.032 63.158 0.00 0.00 39.32 4.01
3138 5022 2.358003 ACTGACGCTGGAGCTTGC 60.358 61.111 0.00 0.00 39.32 4.01
3139 5023 3.123620 CTGACGCTGGAGCTTGCC 61.124 66.667 0.00 0.00 39.32 4.52
3141 5025 4.742201 GACGCTGGAGCTTGCCGA 62.742 66.667 0.00 0.00 39.32 5.54
3165 5049 4.697756 CCCGCCGCACCTTCTCAA 62.698 66.667 0.00 0.00 0.00 3.02
3166 5050 3.423154 CCGCCGCACCTTCTCAAC 61.423 66.667 0.00 0.00 0.00 3.18
3167 5051 3.777925 CGCCGCACCTTCTCAACG 61.778 66.667 0.00 0.00 0.00 4.10
3168 5052 2.665185 GCCGCACCTTCTCAACGT 60.665 61.111 0.00 0.00 0.00 3.99
3169 5053 2.668280 GCCGCACCTTCTCAACGTC 61.668 63.158 0.00 0.00 0.00 4.34
3170 5054 1.300620 CCGCACCTTCTCAACGTCA 60.301 57.895 0.00 0.00 0.00 4.35
3171 5055 1.284982 CCGCACCTTCTCAACGTCAG 61.285 60.000 0.00 0.00 0.00 3.51
3172 5056 1.284982 CGCACCTTCTCAACGTCAGG 61.285 60.000 0.00 0.00 0.00 3.86
3173 5057 0.033504 GCACCTTCTCAACGTCAGGA 59.966 55.000 0.00 0.00 0.00 3.86
3174 5058 1.540363 GCACCTTCTCAACGTCAGGAA 60.540 52.381 0.00 0.00 0.00 3.36
3175 5059 2.135933 CACCTTCTCAACGTCAGGAAC 58.864 52.381 0.00 0.00 0.00 3.62
3176 5060 1.070289 ACCTTCTCAACGTCAGGAACC 59.930 52.381 0.00 0.00 0.00 3.62
3177 5061 1.419374 CTTCTCAACGTCAGGAACCG 58.581 55.000 0.00 0.00 0.00 4.44
3178 5062 0.599204 TTCTCAACGTCAGGAACCGC 60.599 55.000 0.00 0.00 0.00 5.68
3179 5063 2.027625 CTCAACGTCAGGAACCGCC 61.028 63.158 0.00 0.00 0.00 6.13
3181 5065 2.027625 CAACGTCAGGAACCGCCTC 61.028 63.158 0.00 0.00 46.97 4.70
3182 5066 3.569049 AACGTCAGGAACCGCCTCG 62.569 63.158 0.00 0.00 46.97 4.63
3200 5084 4.944372 CCGGACGGCTACGATGGC 62.944 72.222 0.00 0.00 44.60 4.40
3220 5104 4.690719 CGGGGCAACACACGGCTA 62.691 66.667 0.00 0.00 44.36 3.93
3222 5106 2.281208 GGGCAACACACGGCTACA 60.281 61.111 0.00 0.00 39.74 2.74
3224 5108 1.241315 GGGCAACACACGGCTACAAT 61.241 55.000 0.00 0.00 39.74 2.71
3228 5112 0.874390 AACACACGGCTACAATGCTG 59.126 50.000 0.00 0.00 44.34 4.41
3229 5113 1.135315 CACACGGCTACAATGCTGC 59.865 57.895 0.00 0.00 42.69 5.25
3233 5117 1.746615 CGGCTACAATGCTGCAGGT 60.747 57.895 17.12 11.47 32.21 4.00
3236 5120 0.883833 GCTACAATGCTGCAGGTTGT 59.116 50.000 21.17 21.17 39.26 3.32
3244 5128 1.310933 GCTGCAGGTTGTCCCTCATG 61.311 60.000 17.12 0.00 43.86 3.07
3247 5131 1.021390 GCAGGTTGTCCCTCATGTCG 61.021 60.000 0.00 0.00 43.86 4.35
3269 5153 2.743928 CTCTGCACAAGGTCCCGC 60.744 66.667 0.00 0.00 0.00 6.13
3329 5213 3.535962 CGCTCTCCTGCCTCCTCC 61.536 72.222 0.00 0.00 0.00 4.30
3419 5629 0.606401 CTGCCTCCACGGTGTTCAAT 60.606 55.000 7.45 0.00 34.25 2.57
3462 5759 2.651361 CTCGTGTCGGCCTTGTCT 59.349 61.111 0.00 0.00 0.00 3.41
3483 5902 0.813610 CTGTGCTCGACCCAACAACA 60.814 55.000 0.00 0.00 0.00 3.33
3491 5917 0.387565 GACCCAACAACAACGCCAAT 59.612 50.000 0.00 0.00 0.00 3.16
3647 6137 0.666577 GGGACGGACGACAACTTCTG 60.667 60.000 0.00 0.00 0.00 3.02
3659 6149 1.990160 AACTTCTGGGCCGGTGAACA 61.990 55.000 13.14 0.00 0.00 3.18
3721 6211 1.516386 CGTGAACCAGCGCTCGTAT 60.516 57.895 7.13 0.00 0.00 3.06
3950 7203 5.248477 TCATAAACTCACTTAACTGAGCCCT 59.752 40.000 10.90 1.17 41.38 5.19
4002 7255 5.768164 AGATTACCGAAGACATGGTGTTTTT 59.232 36.000 0.00 0.00 39.30 1.94
4077 7332 4.346418 TGGTTTTGTGCAATTTACTCCCAT 59.654 37.500 0.00 0.00 0.00 4.00
4078 7333 4.929211 GGTTTTGTGCAATTTACTCCCATC 59.071 41.667 0.00 0.00 0.00 3.51
4079 7334 4.799564 TTTGTGCAATTTACTCCCATCC 57.200 40.909 0.00 0.00 0.00 3.51
4080 7335 3.448093 TGTGCAATTTACTCCCATCCA 57.552 42.857 0.00 0.00 0.00 3.41
4081 7336 3.088532 TGTGCAATTTACTCCCATCCAC 58.911 45.455 0.00 0.00 0.00 4.02
4082 7337 3.088532 GTGCAATTTACTCCCATCCACA 58.911 45.455 0.00 0.00 0.00 4.17
4083 7338 3.129287 GTGCAATTTACTCCCATCCACAG 59.871 47.826 0.00 0.00 0.00 3.66
4171 7426 3.600388 CAGAGCACCCTCGATAGTTTTT 58.400 45.455 0.00 0.00 43.05 1.94
4176 7431 5.930135 AGCACCCTCGATAGTTTTTCATAT 58.070 37.500 0.00 0.00 37.40 1.78
4177 7432 6.357367 AGCACCCTCGATAGTTTTTCATATT 58.643 36.000 0.00 0.00 37.40 1.28
4178 7433 6.828785 AGCACCCTCGATAGTTTTTCATATTT 59.171 34.615 0.00 0.00 37.40 1.40
4179 7434 6.912591 GCACCCTCGATAGTTTTTCATATTTG 59.087 38.462 0.00 0.00 37.40 2.32
4180 7435 7.201696 GCACCCTCGATAGTTTTTCATATTTGA 60.202 37.037 0.00 0.00 37.40 2.69
4181 7436 8.673711 CACCCTCGATAGTTTTTCATATTTGAA 58.326 33.333 0.00 0.00 37.46 2.69
4182 7437 8.893727 ACCCTCGATAGTTTTTCATATTTGAAG 58.106 33.333 0.00 0.00 39.25 3.02
4183 7438 9.109393 CCCTCGATAGTTTTTCATATTTGAAGA 57.891 33.333 0.00 0.00 39.25 2.87
4299 7554 5.181748 AGTGCAAACTAGCTCTTATTCTGG 58.818 41.667 0.00 0.00 34.99 3.86
4305 7560 6.613153 AACTAGCTCTTATTCTGGAACACT 57.387 37.500 0.00 0.00 0.00 3.55
4311 7566 5.567623 GCTCTTATTCTGGAACACTCACTGA 60.568 44.000 0.00 0.00 0.00 3.41
4354 7611 9.606631 AAAATATGTAGCCTCACTTCTTCTAAG 57.393 33.333 0.00 0.00 0.00 2.18
4392 7649 5.478679 TGTTTATACCATGTTTTGTCCTGGG 59.521 40.000 0.00 0.00 32.89 4.45
4398 7738 5.151454 ACCATGTTTTGTCCTGGGAAATAA 58.849 37.500 0.00 0.00 32.89 1.40
4410 7750 6.551227 GTCCTGGGAAATAATTATCAAAGCCT 59.449 38.462 0.00 0.00 0.00 4.58
4423 7763 4.399004 TCAAAGCCTCTCTCTCTTATGC 57.601 45.455 0.00 0.00 0.00 3.14
4424 7764 4.029520 TCAAAGCCTCTCTCTCTTATGCT 58.970 43.478 0.00 0.00 0.00 3.79
4425 7765 4.469227 TCAAAGCCTCTCTCTCTTATGCTT 59.531 41.667 0.00 0.00 39.09 3.91
4426 7766 4.670896 AAGCCTCTCTCTCTTATGCTTC 57.329 45.455 0.00 0.00 32.53 3.86
4427 7767 2.622942 AGCCTCTCTCTCTTATGCTTCG 59.377 50.000 0.00 0.00 0.00 3.79
4467 7809 2.073252 ACTATCGATCCAGGTCAGCA 57.927 50.000 0.00 0.00 0.00 4.41
4469 7811 2.766263 ACTATCGATCCAGGTCAGCAAA 59.234 45.455 0.00 0.00 0.00 3.68
4484 7826 2.235650 CAGCAAACTCTCCTCTGATCCA 59.764 50.000 0.00 0.00 0.00 3.41
4515 7857 2.408050 ACATCAGTCGTCTGTTTGCTC 58.592 47.619 9.48 0.00 41.91 4.26
4525 7867 1.205655 TCTGTTTGCTCTGATCGAGGG 59.794 52.381 13.84 3.00 40.25 4.30
4533 7875 4.812476 TGATCGAGGGCGCGTTGG 62.812 66.667 8.43 0.00 37.46 3.77
4587 7929 5.705441 TCAATCGGAATTTCAAACTACTGCT 59.295 36.000 0.00 0.00 0.00 4.24
4588 7930 6.876789 TCAATCGGAATTTCAAACTACTGCTA 59.123 34.615 0.00 0.00 0.00 3.49
4618 7960 0.187606 AGGGGTTTCCAGTTTGGTCC 59.812 55.000 0.00 0.00 39.03 4.46
4626 7968 2.574450 TCCAGTTTGGTCCGGTTAAAC 58.426 47.619 17.24 17.24 39.03 2.01
4627 7969 2.092538 TCCAGTTTGGTCCGGTTAAACA 60.093 45.455 22.87 4.78 39.03 2.83
4635 7977 0.106335 TCCGGTTAAACAAGGCACGA 59.894 50.000 0.00 0.00 0.00 4.35
4649 7991 3.858247 AGGCACGAAAGTCCATACTTAC 58.142 45.455 0.00 0.00 45.37 2.34
4651 7993 3.370061 GGCACGAAAGTCCATACTTACAC 59.630 47.826 0.00 0.00 45.37 2.90
4652 7994 3.370061 GCACGAAAGTCCATACTTACACC 59.630 47.826 0.00 0.00 45.37 4.16
4653 7995 3.611113 CACGAAAGTCCATACTTACACCG 59.389 47.826 0.00 0.00 45.37 4.94
4654 7996 3.256631 ACGAAAGTCCATACTTACACCGT 59.743 43.478 0.00 0.00 45.37 4.83
4655 7997 4.240096 CGAAAGTCCATACTTACACCGTT 58.760 43.478 0.00 0.00 45.37 4.44
4656 7998 5.048083 ACGAAAGTCCATACTTACACCGTTA 60.048 40.000 0.00 0.00 45.37 3.18
4657 7999 5.287035 CGAAAGTCCATACTTACACCGTTAC 59.713 44.000 0.00 0.00 45.37 2.50
4658 8000 5.726980 AAGTCCATACTTACACCGTTACA 57.273 39.130 0.00 0.00 44.26 2.41
4659 8001 5.064441 AGTCCATACTTACACCGTTACAC 57.936 43.478 0.00 0.00 29.00 2.90
4660 8002 3.853671 GTCCATACTTACACCGTTACACG 59.146 47.826 0.00 0.00 42.11 4.49
4661 8003 3.505680 TCCATACTTACACCGTTACACGT 59.494 43.478 0.00 0.00 40.58 4.49
4705 8048 7.073725 AGAGGATATAAGCCCCATAAAAACAGA 59.926 37.037 0.00 0.00 0.00 3.41
4706 8049 7.234355 AGGATATAAGCCCCATAAAAACAGAG 58.766 38.462 0.00 0.00 0.00 3.35
4709 8052 2.171003 AGCCCCATAAAAACAGAGCAC 58.829 47.619 0.00 0.00 0.00 4.40
4713 8056 3.119849 CCCCATAAAAACAGAGCACTTCG 60.120 47.826 0.00 0.00 0.00 3.79
4730 8073 5.694006 GCACTTCGCTCTACATATCTGAAAT 59.306 40.000 0.00 0.00 37.77 2.17
4731 8074 6.201806 GCACTTCGCTCTACATATCTGAAATT 59.798 38.462 0.00 0.00 37.77 1.82
4734 8077 9.817809 ACTTCGCTCTACATATCTGAAATTTAA 57.182 29.630 0.00 0.00 0.00 1.52
4761 8104 2.949826 GAGAGGTATCCCGCTCGAT 58.050 57.895 0.00 0.00 45.90 3.59
4762 8105 0.806241 GAGAGGTATCCCGCTCGATC 59.194 60.000 0.00 0.00 45.90 3.69
4763 8106 0.956410 AGAGGTATCCCGCTCGATCG 60.956 60.000 9.36 9.36 35.80 3.69
4776 8119 0.656259 TCGATCGATCAGTCACCGTC 59.344 55.000 24.40 0.00 0.00 4.79
4897 8248 2.021068 GCCGTAGCAGCCTGAGATCA 62.021 60.000 0.00 0.00 39.53 2.92
4988 8339 0.038892 GACAGGCAACCATTGTGCAG 60.039 55.000 0.00 0.00 37.17 4.41
5049 8406 1.950007 CTAGATCGGATGACGGCGT 59.050 57.895 14.65 14.65 44.45 5.68
5108 8465 0.319125 GAGGCCTCGACGATGGATTC 60.319 60.000 19.06 8.68 0.00 2.52
5109 8466 0.757188 AGGCCTCGACGATGGATTCT 60.757 55.000 0.00 7.55 0.00 2.40
5114 8471 2.294512 CCTCGACGATGGATTCTGATGA 59.705 50.000 0.00 0.00 0.00 2.92
5140 8497 1.675641 GGTTGCTGGCGGATCTTGT 60.676 57.895 0.00 0.00 0.00 3.16
5158 8515 2.279186 GTTTGTGTTGGTGCCGGC 60.279 61.111 22.73 22.73 0.00 6.13
5159 8516 3.893763 TTTGTGTTGGTGCCGGCG 61.894 61.111 23.90 0.00 0.00 6.46
5186 8543 9.424319 GGTTTCTGTTTTCTTTCTTTTCTTTCT 57.576 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
327 333 8.802267 GGCTAATACAAAAGCATTAATCCCATA 58.198 33.333 0.00 0.00 40.61 2.74
372 378 9.524496 TCAAAAGTATTCTACCTGTACAGAGTA 57.476 33.333 24.68 20.43 0.00 2.59
436 442 2.487762 TGCCGCATTAGTTTTTGAGGAG 59.512 45.455 0.00 0.00 35.07 3.69
554 561 1.557371 TGTCACAGGTGAGGTTGAACA 59.443 47.619 1.66 0.00 40.75 3.18
649 656 3.130633 CTCGGTTGTTGTTGATGACTCA 58.869 45.455 0.00 0.00 0.00 3.41
696 703 9.621629 ATCCCAAAATCGATAACATTAACACTA 57.378 29.630 0.00 0.00 0.00 2.74
739 749 3.741388 CGAATTGATAACGAGAAGGGCCT 60.741 47.826 0.00 0.00 0.00 5.19
740 750 2.544267 CGAATTGATAACGAGAAGGGCC 59.456 50.000 0.00 0.00 0.00 5.80
746 756 4.025730 GCTCATTGCGAATTGATAACGAGA 60.026 41.667 0.00 0.00 0.00 4.04
758 768 5.334319 CAATGACAATAAGCTCATTGCGAA 58.666 37.500 9.65 0.00 44.07 4.70
808 818 2.760159 CCCGGTTATTGCCAGCACG 61.760 63.158 0.00 0.00 0.00 5.34
1045 1076 1.280133 CCCTTCCTCTGCAATGAGTGA 59.720 52.381 2.63 0.00 32.50 3.41
1231 1271 1.406069 CCTACAGATGCTGGGACACAC 60.406 57.143 0.00 0.00 35.51 3.82
1240 1280 4.502950 GCTATTCTTGCTCCTACAGATGCT 60.503 45.833 0.00 0.00 0.00 3.79
1471 1533 4.647424 TGCTCACCTTTAAACTGTTTGG 57.353 40.909 15.69 10.72 0.00 3.28
1647 1712 6.036191 GCCCTCTCGTATTTTAGTTTCTTCAG 59.964 42.308 0.00 0.00 0.00 3.02
1728 1793 3.154827 ACCACCACTTTGGGATACAAG 57.845 47.619 0.00 0.00 43.37 3.16
1744 1809 5.964758 TGATCATCCTTTTTGCAATACCAC 58.035 37.500 0.00 0.00 0.00 4.16
1755 1820 7.413446 TCTTCCAAGGTTATGATCATCCTTTT 58.587 34.615 20.76 7.51 38.09 2.27
1889 1954 2.284190 CGCACCATGTTTTTGGGTTTT 58.716 42.857 0.00 0.00 41.35 2.43
2254 2319 5.487488 GTGGTAACCCCAGATATATCCATCA 59.513 44.000 9.18 0.00 46.45 3.07
2632 4504 4.132336 TGGAGATGCATTATCTGAAGTGC 58.868 43.478 0.00 5.63 46.12 4.40
2770 4644 0.530744 GCCATATCCGCCGATCAGTA 59.469 55.000 0.00 0.00 0.00 2.74
2839 4713 9.968870 TTTTCGCATTAAACCTAAACAGTTATT 57.031 25.926 0.00 0.00 0.00 1.40
2907 4783 2.867091 GACGTGTGTGTGACCGTGC 61.867 63.158 0.00 0.00 33.36 5.34
2913 4795 0.317160 GGATCTGGACGTGTGTGTGA 59.683 55.000 0.00 0.00 0.00 3.58
2921 4805 3.138798 CCGACGGGATCTGGACGT 61.139 66.667 5.81 0.00 44.35 4.34
2933 4817 1.591594 CAATGACCCGATCCCGACG 60.592 63.158 0.00 0.00 38.22 5.12
2934 4818 1.887707 GCAATGACCCGATCCCGAC 60.888 63.158 0.00 0.00 38.22 4.79
2935 4819 2.504032 GCAATGACCCGATCCCGA 59.496 61.111 0.00 0.00 38.22 5.14
2936 4820 2.591715 GGCAATGACCCGATCCCG 60.592 66.667 0.00 0.00 0.00 5.14
2937 4821 1.227973 GAGGCAATGACCCGATCCC 60.228 63.158 0.00 0.00 0.00 3.85
2938 4822 0.250081 GAGAGGCAATGACCCGATCC 60.250 60.000 0.00 0.00 0.00 3.36
2939 4823 0.250081 GGAGAGGCAATGACCCGATC 60.250 60.000 0.00 0.00 0.00 3.69
2940 4824 1.700042 GGGAGAGGCAATGACCCGAT 61.700 60.000 0.00 0.00 0.00 4.18
2941 4825 2.367202 GGGAGAGGCAATGACCCGA 61.367 63.158 0.00 0.00 0.00 5.14
2942 4826 2.190578 GGGAGAGGCAATGACCCG 59.809 66.667 0.00 0.00 0.00 5.28
2943 4827 1.225704 CTGGGAGAGGCAATGACCC 59.774 63.158 0.00 0.00 40.79 4.46
2944 4828 1.225704 CCTGGGAGAGGCAATGACC 59.774 63.158 0.00 0.00 34.01 4.02
2945 4829 4.972875 CCTGGGAGAGGCAATGAC 57.027 61.111 0.00 0.00 34.01 3.06
2970 4854 4.758251 TGATGCAGACCACGGCGG 62.758 66.667 13.24 0.00 39.90 6.13
2971 4855 3.490759 GTGATGCAGACCACGGCG 61.491 66.667 4.80 4.80 39.90 6.46
2974 4858 1.633561 CTAGTGTGATGCAGACCACG 58.366 55.000 10.69 0.00 36.15 4.94
2976 4860 0.250234 GCCTAGTGTGATGCAGACCA 59.750 55.000 0.00 0.00 0.00 4.02
2979 4863 0.538584 CCAGCCTAGTGTGATGCAGA 59.461 55.000 0.00 0.00 0.00 4.26
2981 4865 0.538584 CTCCAGCCTAGTGTGATGCA 59.461 55.000 0.00 0.00 0.00 3.96
2982 4866 0.813210 GCTCCAGCCTAGTGTGATGC 60.813 60.000 0.00 0.00 34.31 3.91
2984 4868 1.819229 CGCTCCAGCCTAGTGTGAT 59.181 57.895 0.00 0.00 37.91 3.06
2989 4873 4.154347 GCAGCGCTCCAGCCTAGT 62.154 66.667 7.13 0.00 37.91 2.57
2990 4874 4.906792 GGCAGCGCTCCAGCCTAG 62.907 72.222 25.52 6.38 44.92 3.02
3006 4890 4.489771 GGGGGATGCTGACCACGG 62.490 72.222 0.00 0.00 0.00 4.94
3007 4891 3.391665 GAGGGGGATGCTGACCACG 62.392 68.421 0.00 0.00 34.59 4.94
3008 4892 2.592308 GAGGGGGATGCTGACCAC 59.408 66.667 0.00 0.00 0.00 4.16
3009 4893 3.083349 CGAGGGGGATGCTGACCA 61.083 66.667 0.00 0.00 0.00 4.02
3010 4894 3.866582 CCGAGGGGGATGCTGACC 61.867 72.222 0.00 0.00 38.47 4.02
3011 4895 4.554036 GCCGAGGGGGATGCTGAC 62.554 72.222 0.00 0.00 38.47 3.51
3013 4897 4.864334 GTGCCGAGGGGGATGCTG 62.864 72.222 0.00 0.00 38.47 4.41
3039 4923 1.504275 AAGGGGATGCAGAGCTTGGT 61.504 55.000 0.00 0.00 0.00 3.67
3110 4994 4.742201 CGTCAGTGGCTGGTCGGG 62.742 72.222 0.00 0.00 31.51 5.14
3112 4996 4.363990 AGCGTCAGTGGCTGGTCG 62.364 66.667 0.00 3.92 39.77 4.79
3117 5001 4.385405 GCTCCAGCGTCAGTGGCT 62.385 66.667 0.00 0.00 42.61 4.75
3148 5032 4.697756 TTGAGAAGGTGCGGCGGG 62.698 66.667 9.78 0.00 0.00 6.13
3149 5033 3.423154 GTTGAGAAGGTGCGGCGG 61.423 66.667 9.78 0.00 0.00 6.13
3150 5034 3.777925 CGTTGAGAAGGTGCGGCG 61.778 66.667 0.51 0.51 0.00 6.46
3151 5035 2.665185 ACGTTGAGAAGGTGCGGC 60.665 61.111 0.00 0.00 0.00 6.53
3152 5036 1.284982 CTGACGTTGAGAAGGTGCGG 61.285 60.000 0.00 0.00 0.00 5.69
3153 5037 1.284982 CCTGACGTTGAGAAGGTGCG 61.285 60.000 0.00 0.00 0.00 5.34
3154 5038 0.033504 TCCTGACGTTGAGAAGGTGC 59.966 55.000 0.00 0.00 0.00 5.01
3155 5039 2.135933 GTTCCTGACGTTGAGAAGGTG 58.864 52.381 0.00 0.00 0.00 4.00
3156 5040 1.070289 GGTTCCTGACGTTGAGAAGGT 59.930 52.381 0.00 0.00 0.00 3.50
3157 5041 1.797025 GGTTCCTGACGTTGAGAAGG 58.203 55.000 0.00 0.00 0.00 3.46
3158 5042 1.419374 CGGTTCCTGACGTTGAGAAG 58.581 55.000 0.00 0.00 0.00 2.85
3159 5043 0.599204 GCGGTTCCTGACGTTGAGAA 60.599 55.000 0.00 0.00 0.00 2.87
3160 5044 1.006571 GCGGTTCCTGACGTTGAGA 60.007 57.895 0.00 0.00 0.00 3.27
3161 5045 2.027625 GGCGGTTCCTGACGTTGAG 61.028 63.158 0.00 0.00 0.00 3.02
3162 5046 2.029964 GGCGGTTCCTGACGTTGA 59.970 61.111 0.00 0.00 0.00 3.18
3163 5047 2.030562 AGGCGGTTCCTGACGTTG 59.969 61.111 0.00 0.00 45.54 4.10
3183 5067 4.944372 GCCATCGTAGCCGTCCGG 62.944 72.222 0.24 0.24 38.57 5.14
3185 5069 4.944372 CCGCCATCGTAGCCGTCC 62.944 72.222 0.00 0.00 35.01 4.79
3203 5087 4.690719 TAGCCGTGTGTTGCCCCG 62.691 66.667 0.00 0.00 0.00 5.73
3210 5094 1.577328 GCAGCATTGTAGCCGTGTGT 61.577 55.000 0.00 0.00 34.23 3.72
3220 5104 1.181098 GGGACAACCTGCAGCATTGT 61.181 55.000 25.96 25.96 39.23 2.71
3222 5106 4.102113 GGGACAACCTGCAGCATT 57.898 55.556 8.66 1.38 35.85 3.56
3236 5120 2.362503 AGCGTCCGACATGAGGGA 60.363 61.111 0.00 2.08 0.00 4.20
3244 5128 2.355837 TTGTGCAGAGCGTCCGAC 60.356 61.111 0.00 0.00 0.00 4.79
3247 5131 2.029844 GACCTTGTGCAGAGCGTCC 61.030 63.158 0.00 0.00 0.00 4.79
3410 5620 2.746277 AGCGCGGGATTGAACACC 60.746 61.111 8.83 0.00 0.00 4.16
3449 5746 2.031012 CAGCAGACAAGGCCGACA 59.969 61.111 0.00 0.00 0.00 4.35
3457 5754 1.300931 GGTCGAGCACAGCAGACAA 60.301 57.895 10.30 0.00 39.11 3.18
3458 5755 2.340078 GGTCGAGCACAGCAGACA 59.660 61.111 10.30 0.00 39.11 3.41
3462 5759 2.280797 GTTGGGTCGAGCACAGCA 60.281 61.111 17.59 1.79 31.55 4.41
3491 5917 4.028490 CCGGTAAGGGTGCTGCCA 62.028 66.667 0.00 0.00 39.65 4.92
3496 5922 2.108362 CGGATCCGGTAAGGGTGC 59.892 66.667 26.95 0.00 41.52 5.01
3596 6086 2.342650 CGCATTGGTCACCCTTGGG 61.343 63.158 3.77 3.77 0.00 4.12
3636 6126 2.742372 CCGGCCCAGAAGTTGTCG 60.742 66.667 0.00 0.00 0.00 4.35
3950 7203 1.399714 AAGACACTGATCGGCGGATA 58.600 50.000 7.21 0.00 31.51 2.59
4014 7268 5.754778 GTTTGCGAAAACCACTACAATACT 58.245 37.500 7.88 0.00 0.00 2.12
4171 7426 9.895138 TGATCTTCAACTCATCTTCAAATATGA 57.105 29.630 0.00 0.00 0.00 2.15
4176 7431 7.219322 TCACTGATCTTCAACTCATCTTCAAA 58.781 34.615 0.00 0.00 0.00 2.69
4177 7432 6.762333 TCACTGATCTTCAACTCATCTTCAA 58.238 36.000 0.00 0.00 0.00 2.69
4178 7433 6.350629 TCACTGATCTTCAACTCATCTTCA 57.649 37.500 0.00 0.00 0.00 3.02
4179 7434 7.846644 AATCACTGATCTTCAACTCATCTTC 57.153 36.000 0.00 0.00 0.00 2.87
4180 7435 7.336427 GGAAATCACTGATCTTCAACTCATCTT 59.664 37.037 12.26 0.00 0.00 2.40
4181 7436 6.822676 GGAAATCACTGATCTTCAACTCATCT 59.177 38.462 12.26 0.00 0.00 2.90
4182 7437 6.822676 AGGAAATCACTGATCTTCAACTCATC 59.177 38.462 12.26 0.00 0.00 2.92
4183 7438 6.719301 AGGAAATCACTGATCTTCAACTCAT 58.281 36.000 12.26 0.00 0.00 2.90
4184 7439 6.119240 AGGAAATCACTGATCTTCAACTCA 57.881 37.500 12.26 0.00 0.00 3.41
4185 7440 6.622462 GCAAGGAAATCACTGATCTTCAACTC 60.622 42.308 12.26 0.00 0.00 3.01
4186 7441 5.182760 GCAAGGAAATCACTGATCTTCAACT 59.817 40.000 12.26 3.65 0.00 3.16
4187 7442 5.048504 TGCAAGGAAATCACTGATCTTCAAC 60.049 40.000 12.26 0.00 0.00 3.18
4299 7554 9.046296 TCTTTATTTCTTCTTCAGTGAGTGTTC 57.954 33.333 0.00 0.00 0.00 3.18
4352 7609 7.081976 GGTATAAACAAACATTGAAGCGACTT 58.918 34.615 0.00 0.00 0.00 3.01
4354 7611 6.375377 TGGTATAAACAAACATTGAAGCGAC 58.625 36.000 0.00 0.00 0.00 5.19
4392 7649 9.777297 AGAGAGAGAGGCTTTGATAATTATTTC 57.223 33.333 0.00 0.00 0.00 2.17
4398 7738 7.016465 AGCATAAGAGAGAGAGGCTTTGATAAT 59.984 37.037 0.00 0.00 0.00 1.28
4410 7750 4.944317 TGTCTTCGAAGCATAAGAGAGAGA 59.056 41.667 20.56 0.00 32.56 3.10
4419 7759 2.279741 GGCACATGTCTTCGAAGCATA 58.720 47.619 24.70 13.81 0.00 3.14
4420 7760 1.089920 GGCACATGTCTTCGAAGCAT 58.910 50.000 20.56 21.22 0.00 3.79
4422 7762 0.445436 CTGGCACATGTCTTCGAAGC 59.555 55.000 20.56 15.24 38.20 3.86
4423 7763 1.728971 GACTGGCACATGTCTTCGAAG 59.271 52.381 19.35 19.35 38.20 3.79
4424 7764 1.069978 TGACTGGCACATGTCTTCGAA 59.930 47.619 0.00 0.00 38.20 3.71
4425 7765 0.678950 TGACTGGCACATGTCTTCGA 59.321 50.000 0.00 0.00 38.20 3.71
4426 7766 1.662629 GATGACTGGCACATGTCTTCG 59.337 52.381 0.00 0.00 38.20 3.79
4427 7767 2.703416 TGATGACTGGCACATGTCTTC 58.297 47.619 0.00 11.83 39.07 2.87
4467 7809 2.500910 CTGCTGGATCAGAGGAGAGTTT 59.499 50.000 6.65 0.00 36.19 2.66
4469 7811 1.688942 CCTGCTGGATCAGAGGAGAGT 60.689 57.143 2.92 0.00 36.19 3.24
4484 7826 1.747709 GACTGATGTTGATGCCTGCT 58.252 50.000 0.00 0.00 0.00 4.24
4515 7857 3.257561 CAACGCGCCCTCGATCAG 61.258 66.667 5.73 0.00 38.10 2.90
4533 7875 5.493133 TGTTACATCAAAATATGGACCGC 57.507 39.130 0.00 0.00 0.00 5.68
4576 7918 6.128007 CCTGTTGGGTTTATAGCAGTAGTTTG 60.128 42.308 0.00 0.00 0.00 2.93
4605 7947 2.950975 GTTTAACCGGACCAAACTGGAA 59.049 45.455 9.46 0.00 40.96 3.53
4610 7952 2.544277 GCCTTGTTTAACCGGACCAAAC 60.544 50.000 9.46 15.14 33.70 2.93
4618 7960 2.032426 ACTTTCGTGCCTTGTTTAACCG 59.968 45.455 0.00 0.00 0.00 4.44
4626 7968 2.699954 AGTATGGACTTTCGTGCCTTG 58.300 47.619 0.00 0.00 28.61 3.61
4627 7969 3.418684 AAGTATGGACTTTCGTGCCTT 57.581 42.857 0.00 0.00 43.70 4.35
4635 7977 5.928264 GTGTAACGGTGTAAGTATGGACTTT 59.072 40.000 0.00 0.00 43.70 2.66
4653 7995 8.770850 TTTCTACAAGCAATTTTACGTGTAAC 57.229 30.769 0.00 0.00 31.85 2.50
4654 7996 9.440784 CTTTTCTACAAGCAATTTTACGTGTAA 57.559 29.630 0.00 0.00 31.85 2.41
4655 7997 8.828644 TCTTTTCTACAAGCAATTTTACGTGTA 58.171 29.630 0.00 0.00 31.02 2.90
4656 7998 7.699566 TCTTTTCTACAAGCAATTTTACGTGT 58.300 30.769 0.00 0.00 33.13 4.49
4657 7999 7.323656 CCTCTTTTCTACAAGCAATTTTACGTG 59.676 37.037 0.00 0.00 0.00 4.49
4658 8000 7.227910 TCCTCTTTTCTACAAGCAATTTTACGT 59.772 33.333 0.00 0.00 0.00 3.57
4659 8001 7.581476 TCCTCTTTTCTACAAGCAATTTTACG 58.419 34.615 0.00 0.00 0.00 3.18
4689 8032 2.171003 GTGCTCTGTTTTTATGGGGCT 58.829 47.619 0.00 0.00 0.00 5.19
4706 8049 4.230314 TCAGATATGTAGAGCGAAGTGC 57.770 45.455 0.00 0.00 46.98 4.40
4761 8104 0.167470 GTTCGACGGTGACTGATCGA 59.833 55.000 12.66 12.66 41.55 3.59
4762 8105 0.797249 GGTTCGACGGTGACTGATCG 60.797 60.000 0.00 4.28 35.91 3.69
4763 8106 0.242825 TGGTTCGACGGTGACTGATC 59.757 55.000 0.00 0.00 0.00 2.92
4788 8131 4.156556 GCAAACTCAAGAGCCACATTATCA 59.843 41.667 0.00 0.00 0.00 2.15
4791 8134 3.485394 TGCAAACTCAAGAGCCACATTA 58.515 40.909 0.00 0.00 0.00 1.90
4897 8248 3.300711 GCCAAAGATACGGCGGTAT 57.699 52.632 16.03 16.03 42.01 2.73
4988 8339 1.830477 AGACCTCAGCCAGAAGACATC 59.170 52.381 0.00 0.00 0.00 3.06
5049 8406 4.527038 AGAAGGAAGTGGTATCGAGAACAA 59.473 41.667 0.00 0.00 0.00 2.83
5108 8465 3.982213 CAACCGTGCACATCATCAG 57.018 52.632 18.64 0.00 0.00 2.90
5140 8497 3.069980 GCCGGCACCAACACAAACA 62.070 57.895 24.80 0.00 0.00 2.83
5158 8515 6.330278 AGAAAAGAAAGAAAACAGAAACCCG 58.670 36.000 0.00 0.00 0.00 5.28
5159 8516 8.547967 AAAGAAAAGAAAGAAAACAGAAACCC 57.452 30.769 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.