Multiple sequence alignment - TraesCS4A01G468000

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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 TraesCS4A01G468000 chr4A 100.000 5736 0 0 1 5736 729859110 729864845 0.000000e+00 10593.0
1 TraesCS4A01G468000 chr4A 98.833 4797 48 5 1 4796 728432426 728427637 0.000000e+00 8541.0
2 TraesCS4A01G468000 chr4A 90.739 2516 195 22 3 2508 729532778 729530291 0.000000e+00 3321.0
3 TraesCS4A01G468000 chr4A 89.637 2451 232 15 1 2442 718930312 718927875 0.000000e+00 3099.0
4 TraesCS4A01G468000 chr4A 83.104 3338 472 64 1333 4617 729744666 729747964 0.000000e+00 2955.0
5 TraesCS4A01G468000 chr4A 89.141 2072 198 13 2586 4645 729530122 729528066 0.000000e+00 2555.0
6 TraesCS4A01G468000 chr4A 87.994 2124 216 22 2689 4795 729685198 729687299 0.000000e+00 2473.0
7 TraesCS4A01G468000 chr4A 87.765 2027 192 22 463 2474 729682930 729684915 0.000000e+00 2318.0
8 TraesCS4A01G468000 chr4A 88.136 1964 203 18 2699 4646 718927552 718925603 0.000000e+00 2309.0
9 TraesCS4A01G468000 chr4A 88.372 1935 192 17 2733 4646 728831351 728833273 0.000000e+00 2296.0
10 TraesCS4A01G468000 chr4A 87.023 1965 231 14 2698 4646 729080568 729078612 0.000000e+00 2194.0
11 TraesCS4A01G468000 chr4A 91.241 1233 82 13 666 1892 729048580 729047368 0.000000e+00 1655.0
12 TraesCS4A01G468000 chr4A 92.667 941 61 5 2051 2986 729047370 729046433 0.000000e+00 1349.0
13 TraesCS4A01G468000 chr4A 86.260 1179 153 7 1170 2346 729084742 729083571 0.000000e+00 1271.0
14 TraesCS4A01G468000 chr4A 88.379 1067 106 10 3218 4278 730067382 730066328 0.000000e+00 1267.0
15 TraesCS4A01G468000 chr4A 95.265 718 30 4 1 717 729815041 729815755 0.000000e+00 1134.0
16 TraesCS4A01G468000 chr4A 93.473 383 20 3 168 548 728456446 728456067 1.080000e-156 564.0
17 TraesCS4A01G468000 chr4A 90.633 395 20 10 4793 5187 728427602 728427225 5.130000e-140 508.0
18 TraesCS4A01G468000 chr4A 85.812 437 38 11 1 435 729049350 729048936 5.270000e-120 442.0
19 TraesCS4A01G468000 chr4A 86.783 401 40 8 3 399 729682520 729682911 8.830000e-118 435.0
20 TraesCS4A01G468000 chr4A 81.042 480 79 7 1 477 729743869 729744339 7.020000e-99 372.0
21 TraesCS4A01G468000 chr4A 83.155 374 35 6 4809 5176 729687366 729687717 3.340000e-82 316.0
22 TraesCS4A01G468000 chr4A 91.038 212 12 5 426 635 729048789 729048583 4.380000e-71 279.0
23 TraesCS4A01G468000 chr4A 91.534 189 12 2 5028 5216 729687785 729687969 2.050000e-64 257.0
24 TraesCS4A01G468000 chr4A 80.938 341 41 13 4897 5233 730065833 730065513 1.230000e-61 248.0
25 TraesCS4A01G468000 chr4A 88.636 176 15 3 5042 5216 728426062 728425891 5.820000e-50 209.0
26 TraesCS4A01G468000 chr4A 84.848 198 14 7 5536 5731 729077654 729077471 9.810000e-43 185.0
27 TraesCS4A01G468000 chr4A 81.364 220 22 14 4795 5000 729078285 729078071 1.650000e-35 161.0
28 TraesCS4A01G468000 chr4A 81.579 114 8 8 5497 5597 729525906 729525793 1.320000e-11 82.4
29 TraesCS4A01G468000 chr4A 82.000 100 12 4 4674 4770 728833280 728833376 4.760000e-11 80.5
30 TraesCS4A01G468000 chr7D 91.497 3493 272 21 1148 4631 10480945 10477469 0.000000e+00 4782.0
31 TraesCS4A01G468000 chr7D 82.929 3503 465 70 1334 4770 10472532 10469097 0.000000e+00 3033.0
32 TraesCS4A01G468000 chr7D 85.118 2251 286 33 1333 3550 10037243 10039477 0.000000e+00 2255.0
33 TraesCS4A01G468000 chr7D 90.941 1148 86 14 1 1139 10482062 10480924 0.000000e+00 1528.0
34 TraesCS4A01G468000 chr7D 81.066 1051 164 22 1 1043 10036481 10037504 0.000000e+00 806.0
35 TraesCS4A01G468000 chr7D 85.714 189 26 1 5312 5499 588690873 588691061 1.260000e-46 198.0
36 TraesCS4A01G468000 chr7D 82.011 189 16 8 4795 4971 10468985 10468803 1.670000e-30 145.0
37 TraesCS4A01G468000 chr7D 85.507 69 10 0 4881 4949 10090538 10090470 7.970000e-09 73.1
38 TraesCS4A01G468000 chr7A 93.561 1258 77 4 3 1258 9330046 9331301 0.000000e+00 1871.0
39 TraesCS4A01G468000 chr7A 88.165 1166 131 5 2689 3853 9332783 9333942 0.000000e+00 1382.0
40 TraesCS4A01G468000 chr7A 86.772 1202 132 20 1286 2474 9331302 9332489 0.000000e+00 1314.0
41 TraesCS4A01G468000 chr7A 84.359 959 121 15 3840 4795 9334612 9335544 0.000000e+00 913.0
42 TraesCS4A01G468000 chr7A 82.258 186 18 7 4788 4965 9335580 9335758 4.630000e-31 147.0
43 TraesCS4A01G468000 chrUn 73.114 822 185 28 1530 2331 8846013 8845208 1.590000e-65 261.0
44 TraesCS4A01G468000 chr1A 73.198 791 178 26 1534 2303 586334103 586333326 7.380000e-64 255.0
45 TraesCS4A01G468000 chr1A 86.070 201 22 5 5302 5500 508140404 508140600 1.620000e-50 211.0
46 TraesCS4A01G468000 chr1D 91.908 173 9 2 4793 4965 302076445 302076278 2.670000e-58 237.0
47 TraesCS4A01G468000 chr6D 87.647 170 19 2 5331 5499 181729567 181729735 4.530000e-46 196.0
48 TraesCS4A01G468000 chr5A 86.628 172 21 2 5330 5500 536118578 536118408 7.590000e-44 189.0
49 TraesCS4A01G468000 chr3B 85.876 177 22 3 5323 5497 637619778 637619603 9.810000e-43 185.0
50 TraesCS4A01G468000 chr5D 86.471 170 20 3 5332 5499 133249691 133249859 3.530000e-42 183.0
51 TraesCS4A01G468000 chr5D 86.228 167 22 1 5332 5497 7616444 7616610 4.570000e-41 180.0
52 TraesCS4A01G468000 chr2D 84.127 189 28 2 5312 5499 618178657 618178844 1.270000e-41 182.0
53 TraesCS4A01G468000 chr3D 84.270 178 27 1 5318 5495 25341028 25340852 7.640000e-39 172.0


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 TraesCS4A01G468000 chr4A 729859110 729864845 5735 False 10593.000000 10593 100.000000 1 5736 1 chr4A.!!$F2 5735
1 TraesCS4A01G468000 chr4A 728425891 728432426 6535 True 3086.000000 8541 92.700667 1 5216 3 chr4A.!!$R3 5215
2 TraesCS4A01G468000 chr4A 718925603 718930312 4709 True 2704.000000 3099 88.886500 1 4646 2 chr4A.!!$R2 4645
3 TraesCS4A01G468000 chr4A 729525793 729532778 6985 True 1986.133333 3321 87.153000 3 5597 3 chr4A.!!$R6 5594
4 TraesCS4A01G468000 chr4A 729743869 729747964 4095 False 1663.500000 2955 82.073000 1 4617 2 chr4A.!!$F5 4616
5 TraesCS4A01G468000 chr4A 728831351 728833376 2025 False 1188.250000 2296 85.186000 2733 4770 2 chr4A.!!$F3 2037
6 TraesCS4A01G468000 chr4A 729682520 729687969 5449 False 1159.800000 2473 87.446200 3 5216 5 chr4A.!!$F4 5213
7 TraesCS4A01G468000 chr4A 729815041 729815755 714 False 1134.000000 1134 95.265000 1 717 1 chr4A.!!$F1 716
8 TraesCS4A01G468000 chr4A 729077471 729084742 7271 True 952.750000 2194 84.873750 1170 5731 4 chr4A.!!$R5 4561
9 TraesCS4A01G468000 chr4A 729046433 729049350 2917 True 931.250000 1655 90.189500 1 2986 4 chr4A.!!$R4 2985
10 TraesCS4A01G468000 chr4A 730065513 730067382 1869 True 757.500000 1267 84.658500 3218 5233 2 chr4A.!!$R7 2015
11 TraesCS4A01G468000 chr7D 10477469 10482062 4593 True 3155.000000 4782 91.219000 1 4631 2 chr7D.!!$R3 4630
12 TraesCS4A01G468000 chr7D 10468803 10472532 3729 True 1589.000000 3033 82.470000 1334 4971 2 chr7D.!!$R2 3637
13 TraesCS4A01G468000 chr7D 10036481 10039477 2996 False 1530.500000 2255 83.092000 1 3550 2 chr7D.!!$F2 3549
14 TraesCS4A01G468000 chr7A 9330046 9335758 5712 False 1125.400000 1871 87.023000 3 4965 5 chr7A.!!$F1 4962
15 TraesCS4A01G468000 chrUn 8845208 8846013 805 True 261.000000 261 73.114000 1530 2331 1 chrUn.!!$R1 801
16 TraesCS4A01G468000 chr1A 586333326 586334103 777 True 255.000000 255 73.198000 1534 2303 1 chr1A.!!$R1 769

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
805 1003 3.194116 AGTGATGTGTCATGGCCATTTTC 59.806 43.478 17.92 9.97 36.60 2.29 F
1293 1506 0.696143 TGTTGAGAACCCTGGGTGGA 60.696 55.000 21.38 0.28 35.34 4.02 F
1587 1808 1.854743 CCATCAGCGACGAGTACAATG 59.145 52.381 0.00 0.00 0.00 2.82 F
3390 6551 0.776810 TTGGAGGATGTTGGCAGGAA 59.223 50.000 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 5758 5.229921 TCATTGTCATTTAGCCGCTTTAC 57.770 39.130 0.00 0.0 0.00 2.01 R
3390 6551 8.492673 TCTGTTGACGAGCTCATTAAAATAAT 57.507 30.769 15.40 0.0 0.00 1.28 R
3848 7054 2.847327 ATGTCCAGTGTCTCCAAGTG 57.153 50.000 0.00 0.0 0.00 3.16 R
5488 12456 0.109723 TTCTTGCGGTTAGGCCTTGT 59.890 50.000 12.58 0.0 34.25 3.16 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
800 997 3.431673 TTTAGTGATGTGTCATGGCCA 57.568 42.857 8.56 8.56 36.60 5.36
805 1003 3.194116 AGTGATGTGTCATGGCCATTTTC 59.806 43.478 17.92 9.97 36.60 2.29
1293 1506 0.696143 TGTTGAGAACCCTGGGTGGA 60.696 55.000 21.38 0.28 35.34 4.02
1587 1808 1.854743 CCATCAGCGACGAGTACAATG 59.145 52.381 0.00 0.00 0.00 2.82
2411 5227 4.755411 TCTCGATACATGTGGGAAGTTTC 58.245 43.478 9.11 0.00 0.00 2.78
2608 5758 1.940613 GGTGGCTAGAAATTACAGGCG 59.059 52.381 0.00 0.00 37.66 5.52
3390 6551 0.776810 TTGGAGGATGTTGGCAGGAA 59.223 50.000 0.00 0.00 0.00 3.36
3848 7054 5.639931 CCTACTAAACTTGGAGAGCTTGTTC 59.360 44.000 0.00 0.00 0.00 3.18
3916 7805 7.072454 AGCATCCCCTCAGACATAGTTAATTTA 59.928 37.037 0.00 0.00 0.00 1.40
4421 8316 0.685458 AGCATGTGAAATCCCTGGGC 60.685 55.000 8.22 0.00 0.00 5.36
4501 8396 5.191426 TCTAGGAAAGACACTACAGCGTAT 58.809 41.667 0.00 0.00 0.00 3.06
4573 8468 3.099841 TCCAACTGGGGTGGCACA 61.100 61.111 20.82 0.00 37.22 4.57
4746 8645 5.282510 ACGTACTTCATAGCAGAGCATAAC 58.717 41.667 0.00 0.00 0.00 1.89
4767 8666 4.462133 ACTCCTACTACATGCATCGTACT 58.538 43.478 0.00 0.00 0.00 2.73
4768 8667 5.618236 ACTCCTACTACATGCATCGTACTA 58.382 41.667 0.00 0.00 0.00 1.82
4769 8668 6.239396 ACTCCTACTACATGCATCGTACTAT 58.761 40.000 0.00 0.00 0.00 2.12
4770 8669 7.392418 ACTCCTACTACATGCATCGTACTATA 58.608 38.462 0.00 0.00 0.00 1.31
4801 8764 0.326595 TTCATAGCCCTGCCACGAAA 59.673 50.000 0.00 0.00 0.00 3.46
4867 9002 4.789481 GCTGAATCTTTGTTTTCGACAGCA 60.789 41.667 0.00 0.00 44.65 4.41
4878 9017 1.686355 TCGACAGCAAATGGTGGTTT 58.314 45.000 16.12 0.00 46.90 3.27
4888 9027 4.317488 CAAATGGTGGTTTTGGATCAAGG 58.683 43.478 0.00 0.00 31.82 3.61
4965 9120 4.842531 TGAATTAGTGAATGCTCCTCCA 57.157 40.909 0.00 0.00 0.00 3.86
5015 9598 0.729116 CATGCTGCGTTTGGTCTAGG 59.271 55.000 0.00 0.00 0.00 3.02
5017 9600 0.037326 TGCTGCGTTTGGTCTAGGAG 60.037 55.000 0.00 0.00 0.00 3.69
5137 10785 0.889186 CGGGAACTGGACAACCTTGG 60.889 60.000 0.00 0.00 37.04 3.61
5205 12162 6.166984 AGACAGAAGAATCTTGTCAAGTGA 57.833 37.500 15.11 0.00 36.76 3.41
5233 12190 9.699410 AATATTGTCCAATCTATTTGTTCCTGA 57.301 29.630 0.00 0.00 33.15 3.86
5234 12191 7.636150 ATTGTCCAATCTATTTGTTCCTGAG 57.364 36.000 0.00 0.00 33.15 3.35
5239 12196 5.124457 CCAATCTATTTGTTCCTGAGTGTGG 59.876 44.000 0.00 0.00 33.15 4.17
5240 12197 4.286297 TCTATTTGTTCCTGAGTGTGGG 57.714 45.455 0.00 0.00 0.00 4.61
5245 12202 4.546829 TTGTTCCTGAGTGTGGGTATAC 57.453 45.455 0.00 0.00 0.00 1.47
5247 12204 3.904965 TGTTCCTGAGTGTGGGTATACAA 59.095 43.478 5.01 0.00 31.36 2.41
5248 12205 4.251268 GTTCCTGAGTGTGGGTATACAAC 58.749 47.826 5.01 3.22 31.36 3.32
5264 12232 0.515564 CAACCTTTTGTAGCGTCGGG 59.484 55.000 0.00 0.00 0.00 5.14
5270 12238 2.243602 TTTGTAGCGTCGGGAAAAGT 57.756 45.000 0.00 0.00 0.00 2.66
5288 12256 3.582714 AGTTTTGCCTTATTCTGCAGC 57.417 42.857 9.47 0.00 38.95 5.25
5307 12275 4.515191 GCAGCGTTAATAATGGGAAGATGA 59.485 41.667 0.00 0.00 0.00 2.92
5311 12279 5.527582 GCGTTAATAATGGGAAGATGACAGT 59.472 40.000 0.00 0.00 0.00 3.55
5312 12280 6.704493 GCGTTAATAATGGGAAGATGACAGTA 59.296 38.462 0.00 0.00 0.00 2.74
5313 12281 7.225931 GCGTTAATAATGGGAAGATGACAGTAA 59.774 37.037 0.00 0.00 0.00 2.24
5314 12282 8.765219 CGTTAATAATGGGAAGATGACAGTAAG 58.235 37.037 0.00 0.00 0.00 2.34
5315 12283 9.057089 GTTAATAATGGGAAGATGACAGTAAGG 57.943 37.037 0.00 0.00 0.00 2.69
5316 12284 4.510167 AATGGGAAGATGACAGTAAGGG 57.490 45.455 0.00 0.00 0.00 3.95
5317 12285 1.559682 TGGGAAGATGACAGTAAGGGC 59.440 52.381 0.00 0.00 0.00 5.19
5318 12286 1.840635 GGGAAGATGACAGTAAGGGCT 59.159 52.381 0.00 0.00 0.00 5.19
5319 12287 2.239907 GGGAAGATGACAGTAAGGGCTT 59.760 50.000 0.00 0.00 0.00 4.35
5320 12288 3.274288 GGAAGATGACAGTAAGGGCTTG 58.726 50.000 0.00 0.00 0.00 4.01
5321 12289 3.307762 GGAAGATGACAGTAAGGGCTTGT 60.308 47.826 0.00 0.00 0.00 3.16
5322 12290 4.081087 GGAAGATGACAGTAAGGGCTTGTA 60.081 45.833 0.00 0.00 0.00 2.41
5323 12291 4.473477 AGATGACAGTAAGGGCTTGTAC 57.527 45.455 0.00 0.00 0.00 2.90
5324 12292 3.838317 AGATGACAGTAAGGGCTTGTACA 59.162 43.478 0.00 0.00 0.00 2.90
5325 12293 4.286032 AGATGACAGTAAGGGCTTGTACAA 59.714 41.667 8.28 8.28 0.00 2.41
5326 12294 4.634012 TGACAGTAAGGGCTTGTACAAT 57.366 40.909 9.13 0.00 0.00 2.71
5327 12295 4.323417 TGACAGTAAGGGCTTGTACAATG 58.677 43.478 9.13 4.44 0.00 2.82
5328 12296 3.081804 ACAGTAAGGGCTTGTACAATGC 58.918 45.455 9.13 13.99 0.00 3.56
5329 12297 3.081061 CAGTAAGGGCTTGTACAATGCA 58.919 45.455 22.76 0.00 0.00 3.96
5330 12298 3.505680 CAGTAAGGGCTTGTACAATGCAA 59.494 43.478 22.76 9.34 0.00 4.08
5331 12299 3.758554 AGTAAGGGCTTGTACAATGCAAG 59.241 43.478 22.76 9.09 44.34 4.01
5332 12300 1.549203 AGGGCTTGTACAATGCAAGG 58.451 50.000 22.76 8.55 42.44 3.61
5333 12301 1.203050 AGGGCTTGTACAATGCAAGGT 60.203 47.619 22.76 0.00 42.44 3.50
5334 12302 1.067635 GGGCTTGTACAATGCAAGGTG 60.068 52.381 22.76 7.37 42.44 4.00
5335 12303 1.669795 GGCTTGTACAATGCAAGGTGC 60.670 52.381 22.76 14.72 45.29 5.01
5336 12304 1.270550 GCTTGTACAATGCAAGGTGCT 59.729 47.619 18.96 0.00 45.31 4.40
5337 12305 2.288395 GCTTGTACAATGCAAGGTGCTT 60.288 45.455 18.96 0.00 45.31 3.91
5338 12306 3.057596 GCTTGTACAATGCAAGGTGCTTA 60.058 43.478 18.96 0.00 45.31 3.09
5339 12307 4.726416 CTTGTACAATGCAAGGTGCTTAG 58.274 43.478 9.13 4.87 45.31 2.18
5340 12308 4.014569 TGTACAATGCAAGGTGCTTAGA 57.985 40.909 9.81 0.00 45.31 2.10
5341 12309 4.002982 TGTACAATGCAAGGTGCTTAGAG 58.997 43.478 9.81 0.00 45.31 2.43
5342 12310 3.423539 ACAATGCAAGGTGCTTAGAGA 57.576 42.857 0.00 0.00 45.31 3.10
5343 12311 3.754965 ACAATGCAAGGTGCTTAGAGAA 58.245 40.909 0.00 0.00 45.31 2.87
5344 12312 4.144297 ACAATGCAAGGTGCTTAGAGAAA 58.856 39.130 0.00 0.00 45.31 2.52
5345 12313 4.768968 ACAATGCAAGGTGCTTAGAGAAAT 59.231 37.500 0.00 0.00 45.31 2.17
5346 12314 5.945784 ACAATGCAAGGTGCTTAGAGAAATA 59.054 36.000 0.00 0.00 45.31 1.40
5347 12315 6.434028 ACAATGCAAGGTGCTTAGAGAAATAA 59.566 34.615 0.00 0.00 45.31 1.40
5348 12316 7.039784 ACAATGCAAGGTGCTTAGAGAAATAAA 60.040 33.333 0.00 0.00 45.31 1.40
5349 12317 7.651027 ATGCAAGGTGCTTAGAGAAATAAAT 57.349 32.000 0.00 0.00 45.31 1.40
5350 12318 7.088589 TGCAAGGTGCTTAGAGAAATAAATC 57.911 36.000 1.43 0.00 45.31 2.17
5351 12319 6.658816 TGCAAGGTGCTTAGAGAAATAAATCA 59.341 34.615 1.43 0.00 45.31 2.57
5352 12320 7.148188 TGCAAGGTGCTTAGAGAAATAAATCAG 60.148 37.037 1.43 0.00 45.31 2.90
5353 12321 7.148171 GCAAGGTGCTTAGAGAAATAAATCAGT 60.148 37.037 0.00 0.00 40.96 3.41
5354 12322 8.394121 CAAGGTGCTTAGAGAAATAAATCAGTC 58.606 37.037 0.00 0.00 0.00 3.51
5355 12323 7.856415 AGGTGCTTAGAGAAATAAATCAGTCT 58.144 34.615 0.00 0.00 0.00 3.24
5356 12324 8.325046 AGGTGCTTAGAGAAATAAATCAGTCTT 58.675 33.333 0.00 0.00 0.00 3.01
5357 12325 8.951243 GGTGCTTAGAGAAATAAATCAGTCTTT 58.049 33.333 0.00 0.00 0.00 2.52
5366 12334 9.884465 AGAAATAAATCAGTCTTTTCTCAAACG 57.116 29.630 0.00 0.00 32.66 3.60
5367 12335 8.507470 AAATAAATCAGTCTTTTCTCAAACGC 57.493 30.769 0.00 0.00 0.00 4.84
5368 12336 4.489679 AATCAGTCTTTTCTCAAACGCC 57.510 40.909 0.00 0.00 0.00 5.68
5369 12337 1.864711 TCAGTCTTTTCTCAAACGCCG 59.135 47.619 0.00 0.00 0.00 6.46
5370 12338 1.864711 CAGTCTTTTCTCAAACGCCGA 59.135 47.619 0.00 0.00 0.00 5.54
5371 12339 2.480419 CAGTCTTTTCTCAAACGCCGAT 59.520 45.455 0.00 0.00 0.00 4.18
5372 12340 2.480419 AGTCTTTTCTCAAACGCCGATG 59.520 45.455 0.00 0.00 0.00 3.84
5373 12341 1.196808 TCTTTTCTCAAACGCCGATGC 59.803 47.619 0.00 0.00 0.00 3.91
5374 12342 1.197721 CTTTTCTCAAACGCCGATGCT 59.802 47.619 0.00 0.00 34.43 3.79
5375 12343 1.234821 TTTCTCAAACGCCGATGCTT 58.765 45.000 0.00 0.00 34.43 3.91
5376 12344 2.087501 TTCTCAAACGCCGATGCTTA 57.912 45.000 0.00 0.00 34.43 3.09
5377 12345 2.309528 TCTCAAACGCCGATGCTTAT 57.690 45.000 0.00 0.00 34.43 1.73
5378 12346 2.627945 TCTCAAACGCCGATGCTTATT 58.372 42.857 0.00 0.00 34.43 1.40
5379 12347 3.006940 TCTCAAACGCCGATGCTTATTT 58.993 40.909 0.00 0.00 34.43 1.40
5380 12348 3.100817 CTCAAACGCCGATGCTTATTTG 58.899 45.455 0.00 0.00 35.50 2.32
5381 12349 2.486203 TCAAACGCCGATGCTTATTTGT 59.514 40.909 0.00 0.00 35.59 2.83
5382 12350 3.685272 TCAAACGCCGATGCTTATTTGTA 59.315 39.130 0.00 0.00 35.59 2.41
5383 12351 4.154375 TCAAACGCCGATGCTTATTTGTAA 59.846 37.500 0.00 0.00 35.59 2.41
5384 12352 4.688511 AACGCCGATGCTTATTTGTAAA 57.311 36.364 0.00 0.00 34.43 2.01
5385 12353 4.273005 ACGCCGATGCTTATTTGTAAAG 57.727 40.909 0.00 0.00 34.43 1.85
5386 12354 3.064820 ACGCCGATGCTTATTTGTAAAGG 59.935 43.478 0.00 0.00 34.43 3.11
5387 12355 3.311322 CGCCGATGCTTATTTGTAAAGGA 59.689 43.478 0.00 0.00 34.43 3.36
5388 12356 4.552767 CGCCGATGCTTATTTGTAAAGGAG 60.553 45.833 0.00 0.00 34.43 3.69
5389 12357 4.574828 GCCGATGCTTATTTGTAAAGGAGA 59.425 41.667 0.00 0.00 33.53 3.71
5390 12358 5.277538 GCCGATGCTTATTTGTAAAGGAGAG 60.278 44.000 0.00 0.00 33.53 3.20
5391 12359 6.049149 CCGATGCTTATTTGTAAAGGAGAGA 58.951 40.000 0.00 0.00 0.00 3.10
5392 12360 6.018669 CCGATGCTTATTTGTAAAGGAGAGAC 60.019 42.308 0.00 0.00 0.00 3.36
5393 12361 6.291849 CGATGCTTATTTGTAAAGGAGAGACG 60.292 42.308 0.00 0.00 0.00 4.18
5394 12362 4.630069 TGCTTATTTGTAAAGGAGAGACGC 59.370 41.667 0.00 0.00 0.00 5.19
5395 12363 4.034163 GCTTATTTGTAAAGGAGAGACGCC 59.966 45.833 0.00 0.00 0.00 5.68
5396 12364 3.983044 ATTTGTAAAGGAGAGACGCCT 57.017 42.857 0.00 0.00 34.48 5.52
5397 12365 6.534475 TTATTTGTAAAGGAGAGACGCCTA 57.466 37.500 0.00 0.00 31.02 3.93
5398 12366 4.877378 TTTGTAAAGGAGAGACGCCTAA 57.123 40.909 0.00 0.00 31.02 2.69
5399 12367 5.416271 TTTGTAAAGGAGAGACGCCTAAT 57.584 39.130 0.00 0.00 31.02 1.73
5400 12368 5.416271 TTGTAAAGGAGAGACGCCTAATT 57.584 39.130 0.00 0.00 31.02 1.40
5401 12369 6.534475 TTGTAAAGGAGAGACGCCTAATTA 57.466 37.500 0.00 0.00 31.02 1.40
5402 12370 6.534475 TGTAAAGGAGAGACGCCTAATTAA 57.466 37.500 0.00 0.00 31.02 1.40
5403 12371 6.570692 TGTAAAGGAGAGACGCCTAATTAAG 58.429 40.000 0.00 0.00 31.02 1.85
5404 12372 3.737032 AGGAGAGACGCCTAATTAAGC 57.263 47.619 0.00 0.00 30.33 3.09
5413 12381 3.747854 GCCTAATTAAGCGTCTACCCT 57.252 47.619 0.00 0.00 0.00 4.34
5414 12382 3.391049 GCCTAATTAAGCGTCTACCCTG 58.609 50.000 0.00 0.00 0.00 4.45
5415 12383 3.181468 GCCTAATTAAGCGTCTACCCTGT 60.181 47.826 0.00 0.00 0.00 4.00
5416 12384 4.038402 GCCTAATTAAGCGTCTACCCTGTA 59.962 45.833 0.00 0.00 0.00 2.74
5417 12385 5.527033 CCTAATTAAGCGTCTACCCTGTAC 58.473 45.833 0.00 0.00 0.00 2.90
5418 12386 5.068198 CCTAATTAAGCGTCTACCCTGTACA 59.932 44.000 0.00 0.00 0.00 2.90
5419 12387 5.410355 AATTAAGCGTCTACCCTGTACAA 57.590 39.130 0.00 0.00 0.00 2.41
5420 12388 4.870123 TTAAGCGTCTACCCTGTACAAA 57.130 40.909 0.00 0.00 0.00 2.83
5421 12389 3.975168 AAGCGTCTACCCTGTACAAAT 57.025 42.857 0.00 0.00 0.00 2.32
5422 12390 6.528537 TTAAGCGTCTACCCTGTACAAATA 57.471 37.500 0.00 0.00 0.00 1.40
5423 12391 5.410355 AAGCGTCTACCCTGTACAAATAA 57.590 39.130 0.00 0.00 0.00 1.40
5424 12392 5.410355 AGCGTCTACCCTGTACAAATAAA 57.590 39.130 0.00 0.00 0.00 1.40
5425 12393 5.173664 AGCGTCTACCCTGTACAAATAAAC 58.826 41.667 0.00 0.00 0.00 2.01
5426 12394 4.931002 GCGTCTACCCTGTACAAATAAACA 59.069 41.667 0.00 0.00 0.00 2.83
5427 12395 5.163923 GCGTCTACCCTGTACAAATAAACAC 60.164 44.000 0.00 0.00 0.00 3.32
5428 12396 5.349543 CGTCTACCCTGTACAAATAAACACC 59.650 44.000 0.00 0.00 0.00 4.16
5429 12397 5.349543 GTCTACCCTGTACAAATAAACACCG 59.650 44.000 0.00 0.00 0.00 4.94
5430 12398 3.414269 ACCCTGTACAAATAAACACCGG 58.586 45.455 0.00 0.00 0.00 5.28
5431 12399 3.181441 ACCCTGTACAAATAAACACCGGT 60.181 43.478 0.00 0.00 0.00 5.28
5432 12400 3.189702 CCCTGTACAAATAAACACCGGTG 59.810 47.826 32.83 32.83 0.00 4.94
5433 12401 3.365565 CCTGTACAAATAAACACCGGTGC 60.366 47.826 34.26 14.11 0.00 5.01
5434 12402 3.478509 TGTACAAATAAACACCGGTGCT 58.521 40.909 34.26 20.93 0.00 4.40
5435 12403 3.884091 TGTACAAATAAACACCGGTGCTT 59.116 39.130 34.26 29.48 0.00 3.91
5436 12404 5.061853 TGTACAAATAAACACCGGTGCTTA 58.938 37.500 34.26 30.62 0.00 3.09
5437 12405 5.530171 TGTACAAATAAACACCGGTGCTTAA 59.470 36.000 34.26 17.52 0.00 1.85
5438 12406 5.517322 ACAAATAAACACCGGTGCTTAAA 57.483 34.783 34.26 14.92 0.00 1.52
5439 12407 5.903810 ACAAATAAACACCGGTGCTTAAAA 58.096 33.333 34.26 14.15 0.00 1.52
5440 12408 6.338937 ACAAATAAACACCGGTGCTTAAAAA 58.661 32.000 34.26 13.77 0.00 1.94
5461 12429 7.849322 AAAAAGGCCTGGTTTATTTCTCTAA 57.151 32.000 5.69 0.00 0.00 2.10
5462 12430 8.435931 AAAAAGGCCTGGTTTATTTCTCTAAT 57.564 30.769 5.69 0.00 0.00 1.73
5463 12431 9.541884 AAAAAGGCCTGGTTTATTTCTCTAATA 57.458 29.630 5.69 0.00 0.00 0.98
5464 12432 9.541884 AAAAGGCCTGGTTTATTTCTCTAATAA 57.458 29.630 5.69 0.00 37.01 1.40
5465 12433 8.521170 AAGGCCTGGTTTATTTCTCTAATAAC 57.479 34.615 5.69 0.00 38.19 1.89
5466 12434 7.061054 AGGCCTGGTTTATTTCTCTAATAACC 58.939 38.462 3.11 0.00 38.19 2.85
5467 12435 7.061054 GGCCTGGTTTATTTCTCTAATAACCT 58.939 38.462 0.00 0.00 38.19 3.50
5468 12436 7.228906 GGCCTGGTTTATTTCTCTAATAACCTC 59.771 40.741 0.00 0.00 38.19 3.85
5469 12437 7.228906 GCCTGGTTTATTTCTCTAATAACCTCC 59.771 40.741 0.00 0.00 38.19 4.30
5470 12438 8.495260 CCTGGTTTATTTCTCTAATAACCTCCT 58.505 37.037 0.00 0.00 38.19 3.69
5471 12439 9.907229 CTGGTTTATTTCTCTAATAACCTCCTT 57.093 33.333 0.00 0.00 38.19 3.36
5477 12445 8.966069 ATTTCTCTAATAACCTCCTTAAGCAC 57.034 34.615 0.00 0.00 0.00 4.40
5478 12446 6.481434 TCTCTAATAACCTCCTTAAGCACC 57.519 41.667 0.00 0.00 0.00 5.01
5479 12447 6.203072 TCTCTAATAACCTCCTTAAGCACCT 58.797 40.000 0.00 0.00 0.00 4.00
5480 12448 7.359849 TCTCTAATAACCTCCTTAAGCACCTA 58.640 38.462 0.00 0.00 0.00 3.08
5481 12449 7.506261 TCTCTAATAACCTCCTTAAGCACCTAG 59.494 40.741 0.00 0.00 0.00 3.02
5482 12450 4.691326 ATAACCTCCTTAAGCACCTAGC 57.309 45.455 0.00 0.00 46.19 3.42
5513 12481 2.161012 GGCCTAACCGCAAGAAACTAAC 59.839 50.000 0.00 0.00 43.02 2.34
5518 12486 1.069668 ACCGCAAGAAACTAACCGACT 59.930 47.619 0.00 0.00 43.02 4.18
5522 12490 2.157863 GCAAGAAACTAACCGACTCTGC 59.842 50.000 0.00 0.00 0.00 4.26
5523 12491 3.390135 CAAGAAACTAACCGACTCTGCA 58.610 45.455 0.00 0.00 0.00 4.41
5524 12492 3.746045 AGAAACTAACCGACTCTGCAA 57.254 42.857 0.00 0.00 0.00 4.08
5526 12494 3.808174 AGAAACTAACCGACTCTGCAAAC 59.192 43.478 0.00 0.00 0.00 2.93
5527 12495 3.470645 AACTAACCGACTCTGCAAACT 57.529 42.857 0.00 0.00 0.00 2.66
5528 12496 3.027974 ACTAACCGACTCTGCAAACTC 57.972 47.619 0.00 0.00 0.00 3.01
5530 12498 3.825014 ACTAACCGACTCTGCAAACTCTA 59.175 43.478 0.00 0.00 0.00 2.43
5534 12511 1.272490 CGACTCTGCAAACTCTACCCA 59.728 52.381 0.00 0.00 0.00 4.51
5577 12556 9.485206 TTTGTATTACTGTCTCTGAACCTTAAC 57.515 33.333 0.00 0.00 0.00 2.01
5589 12570 7.226720 TCTCTGAACCTTAACTGTCATTTGTTC 59.773 37.037 0.00 0.00 33.32 3.18
5659 12640 2.935849 CACCTCCTTGTTTTGTTTTGGC 59.064 45.455 0.00 0.00 0.00 4.52
5677 12658 0.324285 GCTGGCCATCATCCTAGAGG 59.676 60.000 5.51 0.00 0.00 3.69
5678 12659 1.727062 CTGGCCATCATCCTAGAGGT 58.273 55.000 5.51 0.00 36.34 3.85
5680 12661 0.689623 GGCCATCATCCTAGAGGTGG 59.310 60.000 0.00 5.12 36.34 4.61
5681 12662 1.722034 GCCATCATCCTAGAGGTGGA 58.278 55.000 11.77 1.69 38.06 4.02
5682 12663 2.264455 GCCATCATCCTAGAGGTGGAT 58.736 52.381 11.77 3.73 44.44 3.41
5683 12664 2.235898 GCCATCATCCTAGAGGTGGATC 59.764 54.545 11.77 0.00 41.94 3.36
5684 12665 2.495270 CCATCATCCTAGAGGTGGATCG 59.505 54.545 3.75 0.00 41.94 3.69
5685 12666 2.294449 TCATCCTAGAGGTGGATCGG 57.706 55.000 0.00 0.00 41.94 4.18
5686 12667 0.605589 CATCCTAGAGGTGGATCGGC 59.394 60.000 0.00 0.00 41.94 5.54
5687 12668 0.188587 ATCCTAGAGGTGGATCGGCA 59.811 55.000 0.00 0.00 39.96 5.69
5688 12669 0.468214 TCCTAGAGGTGGATCGGCAG 60.468 60.000 0.00 0.00 36.34 4.85
5689 12670 1.365633 CTAGAGGTGGATCGGCAGC 59.634 63.158 0.00 0.00 0.00 5.25
5690 12671 1.381191 TAGAGGTGGATCGGCAGCA 60.381 57.895 0.00 0.00 0.00 4.41
5694 12675 2.512515 GTGGATCGGCAGCAGACC 60.513 66.667 0.00 2.48 0.00 3.85
5704 12685 1.077212 CAGCAGACCCCTCCCATTG 60.077 63.158 0.00 0.00 0.00 2.82
5731 12712 5.048154 GCAGAAGCTCCTTTGAGAAAAGAAT 60.048 40.000 0.00 0.00 41.42 2.40
5732 12713 6.516360 GCAGAAGCTCCTTTGAGAAAAGAATT 60.516 38.462 0.00 0.00 41.42 2.17
5733 12714 6.862090 CAGAAGCTCCTTTGAGAAAAGAATTG 59.138 38.462 0.00 0.00 41.42 2.32
5734 12715 6.774656 AGAAGCTCCTTTGAGAAAAGAATTGA 59.225 34.615 0.00 0.00 41.42 2.57
5735 12716 6.324561 AGCTCCTTTGAGAAAAGAATTGAC 57.675 37.500 0.00 0.00 41.42 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
800 997 7.846644 TGTCTGCAACAAAAATGAAGAAAAT 57.153 28.000 0.00 0.00 34.25 1.82
805 1003 4.567558 TGCTTGTCTGCAACAAAAATGAAG 59.432 37.500 13.10 4.18 46.95 3.02
1293 1506 3.367292 CGCCAATGAATGTGGTAAGCTTT 60.367 43.478 3.20 0.00 38.50 3.51
1587 1808 0.320771 TTCCTCACCTCTTTGCGCTC 60.321 55.000 9.73 0.00 0.00 5.03
2411 5227 9.866936 CACAAATGAACAAACAGGAAAATAATG 57.133 29.630 0.00 0.00 0.00 1.90
2608 5758 5.229921 TCATTGTCATTTAGCCGCTTTAC 57.770 39.130 0.00 0.00 0.00 2.01
3390 6551 8.492673 TCTGTTGACGAGCTCATTAAAATAAT 57.507 30.769 15.40 0.00 0.00 1.28
3848 7054 2.847327 ATGTCCAGTGTCTCCAAGTG 57.153 50.000 0.00 0.00 0.00 3.16
3916 7805 0.912486 GCAGATAGGACAAGTGGGGT 59.088 55.000 0.00 0.00 0.00 4.95
4421 8316 2.609459 CCGTGCCTAACATAGCTCTTTG 59.391 50.000 0.00 0.00 0.00 2.77
4501 8396 3.393970 CCTGCCTCGAAGCCCAGA 61.394 66.667 3.02 0.00 0.00 3.86
4573 8468 1.961180 GCTCCATGCCGACTGGTACT 61.961 60.000 0.00 0.00 37.67 2.73
4746 8645 6.745159 ATAGTACGATGCATGTAGTAGGAG 57.255 41.667 2.46 0.00 32.76 3.69
4768 8667 8.428063 GCAGGGCTATGAAAGATAGACATATAT 58.572 37.037 0.00 0.00 31.28 0.86
4769 8668 7.147655 GGCAGGGCTATGAAAGATAGACATATA 60.148 40.741 0.00 0.00 31.28 0.86
4770 8669 6.352565 GGCAGGGCTATGAAAGATAGACATAT 60.353 42.308 0.00 0.00 31.28 1.78
4801 8764 6.365520 ACCACATCAGGAAAAGTTAAAGACT 58.634 36.000 0.00 0.00 41.47 3.24
4867 9002 3.973305 ACCTTGATCCAAAACCACCATTT 59.027 39.130 0.00 0.00 0.00 2.32
4878 9017 7.505585 ACAAGAAAAATACAGACCTTGATCCAA 59.494 33.333 0.00 0.00 36.03 3.53
4888 9027 8.045176 AGGCAGATTACAAGAAAAATACAGAC 57.955 34.615 0.00 0.00 0.00 3.51
5015 9598 3.166489 AGTAAGCAAGCACGATACCTC 57.834 47.619 0.00 0.00 0.00 3.85
5017 9600 4.033702 GGTTAAGTAAGCAAGCACGATACC 59.966 45.833 0.00 0.00 34.08 2.73
5239 12196 4.032104 CGACGCTACAAAAGGTTGTATACC 59.968 45.833 0.00 0.00 46.57 2.73
5240 12197 4.032104 CCGACGCTACAAAAGGTTGTATAC 59.968 45.833 0.00 0.00 46.57 1.47
5245 12202 0.515564 CCCGACGCTACAAAAGGTTG 59.484 55.000 0.00 0.00 40.84 3.77
5247 12204 0.393820 TTCCCGACGCTACAAAAGGT 59.606 50.000 0.00 0.00 0.00 3.50
5248 12205 1.515081 TTTCCCGACGCTACAAAAGG 58.485 50.000 0.00 0.00 0.00 3.11
5249 12206 2.546789 ACTTTTCCCGACGCTACAAAAG 59.453 45.455 13.04 13.04 39.13 2.27
5255 12223 1.264826 GCAAAACTTTTCCCGACGCTA 59.735 47.619 0.00 0.00 0.00 4.26
5260 12228 4.830600 AGAATAAGGCAAAACTTTTCCCGA 59.169 37.500 0.00 0.00 32.02 5.14
5261 12229 4.923281 CAGAATAAGGCAAAACTTTTCCCG 59.077 41.667 0.00 0.00 32.02 5.14
5264 12232 5.107337 GCTGCAGAATAAGGCAAAACTTTTC 60.107 40.000 20.43 0.00 39.93 2.29
5270 12238 1.885887 ACGCTGCAGAATAAGGCAAAA 59.114 42.857 20.43 0.00 39.93 2.44
5288 12256 8.657074 TTACTGTCATCTTCCCATTATTAACG 57.343 34.615 0.00 0.00 0.00 3.18
5307 12275 3.081804 GCATTGTACAAGCCCTTACTGT 58.918 45.455 14.65 0.00 0.00 3.55
5311 12279 3.088532 CCTTGCATTGTACAAGCCCTTA 58.911 45.455 14.65 0.09 42.57 2.69
5312 12280 1.895131 CCTTGCATTGTACAAGCCCTT 59.105 47.619 14.65 0.00 42.57 3.95
5313 12281 1.203050 ACCTTGCATTGTACAAGCCCT 60.203 47.619 14.65 0.00 42.57 5.19
5314 12282 1.067635 CACCTTGCATTGTACAAGCCC 60.068 52.381 14.65 5.35 42.57 5.19
5315 12283 1.669795 GCACCTTGCATTGTACAAGCC 60.670 52.381 14.65 7.78 44.26 4.35
5316 12284 1.701704 GCACCTTGCATTGTACAAGC 58.298 50.000 14.65 16.52 44.26 4.01
5327 12295 7.088589 TGATTTATTTCTCTAAGCACCTTGC 57.911 36.000 0.00 0.00 45.46 4.01
5328 12296 8.273780 ACTGATTTATTTCTCTAAGCACCTTG 57.726 34.615 0.00 0.00 0.00 3.61
5329 12297 8.325046 AGACTGATTTATTTCTCTAAGCACCTT 58.675 33.333 0.00 0.00 0.00 3.50
5330 12298 7.856415 AGACTGATTTATTTCTCTAAGCACCT 58.144 34.615 0.00 0.00 0.00 4.00
5331 12299 8.499403 AAGACTGATTTATTTCTCTAAGCACC 57.501 34.615 0.00 0.00 0.00 5.01
5340 12308 9.884465 CGTTTGAGAAAAGACTGATTTATTTCT 57.116 29.630 0.00 0.00 41.60 2.52
5341 12309 8.630840 GCGTTTGAGAAAAGACTGATTTATTTC 58.369 33.333 0.00 0.00 0.00 2.17
5342 12310 7.595130 GGCGTTTGAGAAAAGACTGATTTATTT 59.405 33.333 0.00 0.00 0.00 1.40
5343 12311 7.084486 GGCGTTTGAGAAAAGACTGATTTATT 58.916 34.615 0.00 0.00 0.00 1.40
5344 12312 6.612306 GGCGTTTGAGAAAAGACTGATTTAT 58.388 36.000 0.00 0.00 0.00 1.40
5345 12313 5.333798 CGGCGTTTGAGAAAAGACTGATTTA 60.334 40.000 0.00 0.00 0.00 1.40
5346 12314 4.554723 CGGCGTTTGAGAAAAGACTGATTT 60.555 41.667 0.00 0.00 0.00 2.17
5347 12315 3.058914 CGGCGTTTGAGAAAAGACTGATT 60.059 43.478 0.00 0.00 0.00 2.57
5348 12316 2.480419 CGGCGTTTGAGAAAAGACTGAT 59.520 45.455 0.00 0.00 0.00 2.90
5349 12317 1.864711 CGGCGTTTGAGAAAAGACTGA 59.135 47.619 0.00 0.00 0.00 3.41
5350 12318 1.864711 TCGGCGTTTGAGAAAAGACTG 59.135 47.619 6.85 0.00 0.00 3.51
5351 12319 2.234300 TCGGCGTTTGAGAAAAGACT 57.766 45.000 6.85 0.00 0.00 3.24
5352 12320 2.839474 CATCGGCGTTTGAGAAAAGAC 58.161 47.619 6.85 0.00 0.00 3.01
5353 12321 1.196808 GCATCGGCGTTTGAGAAAAGA 59.803 47.619 6.85 0.00 0.00 2.52
5354 12322 1.606606 GCATCGGCGTTTGAGAAAAG 58.393 50.000 6.85 0.00 0.00 2.27
5355 12323 3.765349 GCATCGGCGTTTGAGAAAA 57.235 47.368 6.85 0.00 0.00 2.29
5366 12334 4.574828 TCTCCTTTACAAATAAGCATCGGC 59.425 41.667 0.00 0.00 41.61 5.54
5367 12335 6.018669 GTCTCTCCTTTACAAATAAGCATCGG 60.019 42.308 0.00 0.00 0.00 4.18
5368 12336 6.291849 CGTCTCTCCTTTACAAATAAGCATCG 60.292 42.308 0.00 0.00 0.00 3.84
5369 12337 6.510317 GCGTCTCTCCTTTACAAATAAGCATC 60.510 42.308 0.00 0.00 0.00 3.91
5370 12338 5.294552 GCGTCTCTCCTTTACAAATAAGCAT 59.705 40.000 0.00 0.00 0.00 3.79
5371 12339 4.630069 GCGTCTCTCCTTTACAAATAAGCA 59.370 41.667 0.00 0.00 0.00 3.91
5372 12340 4.034163 GGCGTCTCTCCTTTACAAATAAGC 59.966 45.833 0.00 0.00 0.00 3.09
5373 12341 5.420409 AGGCGTCTCTCCTTTACAAATAAG 58.580 41.667 0.00 0.00 0.00 1.73
5374 12342 5.416271 AGGCGTCTCTCCTTTACAAATAA 57.584 39.130 0.00 0.00 0.00 1.40
5375 12343 6.534475 TTAGGCGTCTCTCCTTTACAAATA 57.466 37.500 0.00 0.00 35.21 1.40
5376 12344 3.983044 AGGCGTCTCTCCTTTACAAAT 57.017 42.857 0.00 0.00 0.00 2.32
5377 12345 4.877378 TTAGGCGTCTCTCCTTTACAAA 57.123 40.909 0.00 0.00 35.21 2.83
5378 12346 5.416271 AATTAGGCGTCTCTCCTTTACAA 57.584 39.130 0.00 0.00 35.21 2.41
5379 12347 6.534475 TTAATTAGGCGTCTCTCCTTTACA 57.466 37.500 0.00 0.00 35.21 2.41
5380 12348 5.462729 GCTTAATTAGGCGTCTCTCCTTTAC 59.537 44.000 3.59 0.00 35.21 2.01
5381 12349 5.598769 GCTTAATTAGGCGTCTCTCCTTTA 58.401 41.667 3.59 0.00 35.21 1.85
5382 12350 4.443621 GCTTAATTAGGCGTCTCTCCTTT 58.556 43.478 3.59 0.00 35.21 3.11
5383 12351 3.491104 CGCTTAATTAGGCGTCTCTCCTT 60.491 47.826 28.00 0.00 45.15 3.36
5384 12352 2.034812 CGCTTAATTAGGCGTCTCTCCT 59.965 50.000 28.00 0.00 45.15 3.69
5385 12353 2.395654 CGCTTAATTAGGCGTCTCTCC 58.604 52.381 28.00 0.00 45.15 3.71
5393 12361 3.181468 ACAGGGTAGACGCTTAATTAGGC 60.181 47.826 9.43 9.43 37.00 3.93
5394 12362 4.667519 ACAGGGTAGACGCTTAATTAGG 57.332 45.455 0.00 0.00 37.00 2.69
5395 12363 6.140303 TGTACAGGGTAGACGCTTAATTAG 57.860 41.667 0.00 0.00 37.00 1.73
5396 12364 6.528537 TTGTACAGGGTAGACGCTTAATTA 57.471 37.500 0.00 0.00 37.00 1.40
5397 12365 5.410355 TTGTACAGGGTAGACGCTTAATT 57.590 39.130 0.00 0.00 37.00 1.40
5398 12366 5.410355 TTTGTACAGGGTAGACGCTTAAT 57.590 39.130 0.00 0.00 37.00 1.40
5399 12367 4.870123 TTTGTACAGGGTAGACGCTTAA 57.130 40.909 0.00 0.00 37.00 1.85
5400 12368 6.528537 TTATTTGTACAGGGTAGACGCTTA 57.471 37.500 0.00 0.00 37.00 3.09
5401 12369 3.975168 ATTTGTACAGGGTAGACGCTT 57.025 42.857 0.00 0.00 37.00 4.68
5402 12370 5.173664 GTTTATTTGTACAGGGTAGACGCT 58.826 41.667 0.00 0.00 39.95 5.07
5403 12371 4.931002 TGTTTATTTGTACAGGGTAGACGC 59.069 41.667 0.00 0.00 0.00 5.19
5404 12372 5.349543 GGTGTTTATTTGTACAGGGTAGACG 59.650 44.000 0.00 0.00 0.00 4.18
5405 12373 5.349543 CGGTGTTTATTTGTACAGGGTAGAC 59.650 44.000 0.00 0.00 0.00 2.59
5406 12374 5.481105 CGGTGTTTATTTGTACAGGGTAGA 58.519 41.667 0.00 0.00 0.00 2.59
5407 12375 4.632688 CCGGTGTTTATTTGTACAGGGTAG 59.367 45.833 0.00 0.00 0.00 3.18
5408 12376 4.041444 ACCGGTGTTTATTTGTACAGGGTA 59.959 41.667 6.12 0.00 0.00 3.69
5409 12377 3.181441 ACCGGTGTTTATTTGTACAGGGT 60.181 43.478 6.12 0.00 0.00 4.34
5410 12378 3.189702 CACCGGTGTTTATTTGTACAGGG 59.810 47.826 26.95 0.00 0.00 4.45
5411 12379 3.365565 GCACCGGTGTTTATTTGTACAGG 60.366 47.826 33.92 4.71 0.00 4.00
5412 12380 3.500680 AGCACCGGTGTTTATTTGTACAG 59.499 43.478 33.92 5.41 0.00 2.74
5413 12381 3.478509 AGCACCGGTGTTTATTTGTACA 58.521 40.909 33.92 0.00 0.00 2.90
5414 12382 4.492791 AAGCACCGGTGTTTATTTGTAC 57.507 40.909 32.15 13.53 32.21 2.90
5415 12383 6.630444 TTTAAGCACCGGTGTTTATTTGTA 57.370 33.333 35.01 21.92 36.43 2.41
5416 12384 5.517322 TTTAAGCACCGGTGTTTATTTGT 57.483 34.783 35.01 18.18 36.43 2.83
5417 12385 6.830114 TTTTTAAGCACCGGTGTTTATTTG 57.170 33.333 35.01 11.91 36.43 2.32
5437 12405 7.849322 TTAGAGAAATAAACCAGGCCTTTTT 57.151 32.000 0.00 8.57 0.00 1.94
5438 12406 9.541884 TTATTAGAGAAATAAACCAGGCCTTTT 57.458 29.630 0.00 4.83 37.15 2.27
5439 12407 8.967918 GTTATTAGAGAAATAAACCAGGCCTTT 58.032 33.333 0.00 0.00 40.80 3.11
5440 12408 7.560262 GGTTATTAGAGAAATAAACCAGGCCTT 59.440 37.037 0.00 0.00 40.49 4.35
5441 12409 7.061054 GGTTATTAGAGAAATAAACCAGGCCT 58.939 38.462 0.00 0.00 40.49 5.19
5442 12410 7.061054 AGGTTATTAGAGAAATAAACCAGGCC 58.939 38.462 0.00 0.00 45.33 5.19
5443 12411 7.228906 GGAGGTTATTAGAGAAATAAACCAGGC 59.771 40.741 4.99 0.00 45.33 4.85
5444 12412 8.495260 AGGAGGTTATTAGAGAAATAAACCAGG 58.505 37.037 4.99 0.00 45.33 4.45
5445 12413 9.907229 AAGGAGGTTATTAGAGAAATAAACCAG 57.093 33.333 4.99 0.00 45.33 4.00
5452 12420 7.993758 GGTGCTTAAGGAGGTTATTAGAGAAAT 59.006 37.037 4.29 0.00 0.00 2.17
5453 12421 7.182206 AGGTGCTTAAGGAGGTTATTAGAGAAA 59.818 37.037 4.29 0.00 0.00 2.52
5454 12422 6.672657 AGGTGCTTAAGGAGGTTATTAGAGAA 59.327 38.462 4.29 0.00 0.00 2.87
5455 12423 6.203072 AGGTGCTTAAGGAGGTTATTAGAGA 58.797 40.000 4.29 0.00 0.00 3.10
5456 12424 6.487299 AGGTGCTTAAGGAGGTTATTAGAG 57.513 41.667 4.29 0.00 0.00 2.43
5457 12425 6.041751 GCTAGGTGCTTAAGGAGGTTATTAGA 59.958 42.308 4.29 0.00 38.95 2.10
5458 12426 6.183360 TGCTAGGTGCTTAAGGAGGTTATTAG 60.183 42.308 4.29 0.00 43.37 1.73
5459 12427 5.664006 TGCTAGGTGCTTAAGGAGGTTATTA 59.336 40.000 4.29 0.00 43.37 0.98
5460 12428 4.473559 TGCTAGGTGCTTAAGGAGGTTATT 59.526 41.667 4.29 0.00 43.37 1.40
5461 12429 4.037927 TGCTAGGTGCTTAAGGAGGTTAT 58.962 43.478 4.29 0.00 43.37 1.89
5462 12430 3.446968 TGCTAGGTGCTTAAGGAGGTTA 58.553 45.455 4.29 0.00 43.37 2.85
5463 12431 2.266279 TGCTAGGTGCTTAAGGAGGTT 58.734 47.619 4.29 0.00 43.37 3.50
5464 12432 1.952621 TGCTAGGTGCTTAAGGAGGT 58.047 50.000 4.29 0.00 43.37 3.85
5465 12433 3.209410 CAATGCTAGGTGCTTAAGGAGG 58.791 50.000 4.29 0.00 43.37 4.30
5466 12434 3.878778 ACAATGCTAGGTGCTTAAGGAG 58.121 45.455 4.29 0.00 43.37 3.69
5467 12435 4.224147 TGTACAATGCTAGGTGCTTAAGGA 59.776 41.667 4.29 0.00 43.37 3.36
5468 12436 4.513442 TGTACAATGCTAGGTGCTTAAGG 58.487 43.478 4.29 0.00 43.37 2.69
5469 12437 5.065218 CCTTGTACAATGCTAGGTGCTTAAG 59.935 44.000 9.13 0.00 43.37 1.85
5470 12438 4.941263 CCTTGTACAATGCTAGGTGCTTAA 59.059 41.667 9.13 0.00 43.37 1.85
5471 12439 4.513442 CCTTGTACAATGCTAGGTGCTTA 58.487 43.478 9.13 0.00 43.37 3.09
5472 12440 3.347216 CCTTGTACAATGCTAGGTGCTT 58.653 45.455 9.13 0.00 43.37 3.91
5473 12441 2.941415 GCCTTGTACAATGCTAGGTGCT 60.941 50.000 23.62 0.00 43.37 4.40
5474 12442 1.401905 GCCTTGTACAATGCTAGGTGC 59.598 52.381 23.62 7.87 43.25 5.01
5475 12443 2.017049 GGCCTTGTACAATGCTAGGTG 58.983 52.381 27.69 7.79 33.37 4.00
5476 12444 1.916181 AGGCCTTGTACAATGCTAGGT 59.084 47.619 27.69 12.79 33.37 3.08
5477 12445 2.717639 AGGCCTTGTACAATGCTAGG 57.282 50.000 27.69 18.10 33.37 3.02
5478 12446 3.877508 GGTTAGGCCTTGTACAATGCTAG 59.122 47.826 27.69 9.68 33.37 3.42
5479 12447 3.680475 CGGTTAGGCCTTGTACAATGCTA 60.680 47.826 27.69 17.89 33.37 3.49
5480 12448 2.723273 GGTTAGGCCTTGTACAATGCT 58.277 47.619 27.69 18.67 33.37 3.79
5481 12449 1.400494 CGGTTAGGCCTTGTACAATGC 59.600 52.381 23.06 23.06 34.25 3.56
5482 12450 1.400494 GCGGTTAGGCCTTGTACAATG 59.600 52.381 12.58 7.68 34.25 2.82
5483 12451 1.003812 TGCGGTTAGGCCTTGTACAAT 59.996 47.619 12.58 0.00 34.25 2.71
5484 12452 0.397187 TGCGGTTAGGCCTTGTACAA 59.603 50.000 12.58 8.28 34.25 2.41
5485 12453 0.397187 TTGCGGTTAGGCCTTGTACA 59.603 50.000 12.58 0.00 34.25 2.90
5486 12454 1.084289 CTTGCGGTTAGGCCTTGTAC 58.916 55.000 12.58 7.23 34.25 2.90
5487 12455 0.978151 TCTTGCGGTTAGGCCTTGTA 59.022 50.000 12.58 0.00 34.25 2.41
5488 12456 0.109723 TTCTTGCGGTTAGGCCTTGT 59.890 50.000 12.58 0.00 34.25 3.16
5489 12457 1.068541 GTTTCTTGCGGTTAGGCCTTG 60.069 52.381 12.58 0.00 34.25 3.61
5490 12458 1.202891 AGTTTCTTGCGGTTAGGCCTT 60.203 47.619 12.58 0.00 34.25 4.35
5491 12459 0.400594 AGTTTCTTGCGGTTAGGCCT 59.599 50.000 11.78 11.78 34.25 5.19
5492 12460 2.103537 TAGTTTCTTGCGGTTAGGCC 57.896 50.000 0.00 0.00 0.00 5.19
5493 12461 2.161012 GGTTAGTTTCTTGCGGTTAGGC 59.839 50.000 0.00 0.00 0.00 3.93
5494 12462 2.414138 CGGTTAGTTTCTTGCGGTTAGG 59.586 50.000 0.00 0.00 0.00 2.69
5495 12463 3.122445 GTCGGTTAGTTTCTTGCGGTTAG 59.878 47.826 0.00 0.00 0.00 2.34
5500 12468 2.408704 CAGAGTCGGTTAGTTTCTTGCG 59.591 50.000 0.00 0.00 0.00 4.85
5513 12481 1.404315 GGGTAGAGTTTGCAGAGTCGG 60.404 57.143 6.44 0.00 0.00 4.79
5518 12486 3.307691 CCAAGATGGGTAGAGTTTGCAGA 60.308 47.826 0.00 0.00 32.67 4.26
5522 12490 5.102953 TCATCCAAGATGGGTAGAGTTTG 57.897 43.478 4.83 0.00 38.32 2.93
5523 12491 5.779241 TTCATCCAAGATGGGTAGAGTTT 57.221 39.130 4.83 0.00 38.32 2.66
5524 12492 5.014123 TGTTTCATCCAAGATGGGTAGAGTT 59.986 40.000 4.83 0.00 38.32 3.01
5526 12494 4.878397 GTGTTTCATCCAAGATGGGTAGAG 59.122 45.833 4.83 0.00 38.32 2.43
5527 12495 4.536090 AGTGTTTCATCCAAGATGGGTAGA 59.464 41.667 4.83 0.00 38.32 2.59
5528 12496 4.848357 AGTGTTTCATCCAAGATGGGTAG 58.152 43.478 4.83 0.00 38.32 3.18
5530 12498 3.814504 AGTGTTTCATCCAAGATGGGT 57.185 42.857 4.83 0.00 38.32 4.51
5589 12570 1.586154 GCCATGGACTGGGTTGTTCG 61.586 60.000 18.40 0.00 46.06 3.95
5608 12589 0.394192 TGCATGGGAGATAGCCTTCG 59.606 55.000 0.00 0.00 0.00 3.79
5622 12603 2.046023 TGCCTTCTCCCGTGCATG 60.046 61.111 0.00 0.00 0.00 4.06
5624 12605 4.329545 GGTGCCTTCTCCCGTGCA 62.330 66.667 0.00 0.00 0.00 4.57
5645 12626 1.003580 TGGCCAGCCAAAACAAAACAA 59.996 42.857 9.42 0.00 44.12 2.83
5646 12627 0.615331 TGGCCAGCCAAAACAAAACA 59.385 45.000 9.42 0.00 44.12 2.83
5647 12628 3.467776 TGGCCAGCCAAAACAAAAC 57.532 47.368 9.42 0.00 44.12 2.43
5659 12640 1.347050 CACCTCTAGGATGATGGCCAG 59.653 57.143 13.05 0.00 38.94 4.85
5677 12658 2.512515 GGTCTGCTGCCGATCCAC 60.513 66.667 0.00 0.00 0.00 4.02
5678 12659 3.785859 GGGTCTGCTGCCGATCCA 61.786 66.667 17.24 0.00 31.80 3.41
5680 12661 3.453070 GAGGGGTCTGCTGCCGATC 62.453 68.421 0.00 0.00 0.00 3.69
5681 12662 3.474570 GAGGGGTCTGCTGCCGAT 61.475 66.667 0.00 0.00 0.00 4.18
5685 12666 2.988839 AATGGGAGGGGTCTGCTGC 61.989 63.158 0.00 0.00 0.00 5.25
5686 12667 1.077212 CAATGGGAGGGGTCTGCTG 60.077 63.158 0.00 0.00 0.00 4.41
5687 12668 0.253160 TACAATGGGAGGGGTCTGCT 60.253 55.000 0.00 0.00 0.00 4.24
5688 12669 0.181350 CTACAATGGGAGGGGTCTGC 59.819 60.000 0.00 0.00 0.00 4.26
5689 12670 0.181350 GCTACAATGGGAGGGGTCTG 59.819 60.000 0.00 0.00 0.00 3.51
5690 12671 0.253160 TGCTACAATGGGAGGGGTCT 60.253 55.000 0.00 0.00 0.00 3.85
5694 12675 1.748591 GCTTCTGCTACAATGGGAGGG 60.749 57.143 0.00 0.00 36.03 4.30


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

AutoCloner maintained by Alex Coulton.