Multiple sequence alignment - TraesCS5B01G469800

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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 TraesCS5B01G469800 chr5B 100.000 4273 0 0 1 4273 643304754 643309026 0.000000e+00 7891.0
1 TraesCS5B01G469800 chr5B 92.779 734 45 3 3472 4198 448224083 448224815 0.000000e+00 1055.0
2 TraesCS5B01G469800 chr5B 89.567 623 58 7 398 1014 319314734 319315355 0.000000e+00 784.0
3 TraesCS5B01G469800 chr5B 82.210 371 39 23 3476 3829 124641980 124641620 1.160000e-75 294.0
4 TraesCS5B01G469800 chr5B 88.083 193 22 1 1300 1492 643426427 643426618 1.200000e-55 228.0
5 TraesCS5B01G469800 chr5B 99.083 109 1 0 4165 4273 448224815 448224923 3.370000e-46 196.0
6 TraesCS5B01G469800 chr5B 86.842 152 13 2 3873 4018 41821448 41821598 3.420000e-36 163.0
7 TraesCS5B01G469800 chr5B 96.296 81 3 0 1490 1570 643437138 643437218 2.680000e-27 134.0
8 TraesCS5B01G469800 chr5B 93.617 47 2 1 1014 1060 643426384 643426429 7.670000e-08 69.4
9 TraesCS5B01G469800 chr5D 93.069 1688 94 18 1804 3477 512303858 512305536 0.000000e+00 2447.0
10 TraesCS5B01G469800 chr5D 90.193 622 55 6 398 1013 87164163 87163542 0.000000e+00 806.0
11 TraesCS5B01G469800 chr5D 86.357 711 54 18 1014 1710 512303113 512303794 0.000000e+00 736.0
12 TraesCS5B01G469800 chr5D 89.196 398 36 3 1 397 87168505 87168114 1.380000e-134 490.0
13 TraesCS5B01G469800 chr4A 90.048 623 56 6 398 1014 34862493 34861871 0.000000e+00 802.0
14 TraesCS5B01G469800 chr4A 85.256 312 33 10 3476 3780 711905307 711905002 4.150000e-80 309.0
15 TraesCS5B01G469800 chr4A 87.302 63 7 1 4143 4204 551494916 551494854 2.130000e-08 71.3
16 TraesCS5B01G469800 chr6A 89.888 623 52 4 398 1014 34970411 34971028 0.000000e+00 791.0
17 TraesCS5B01G469800 chr6A 89.103 624 62 3 398 1015 1951672 1951049 0.000000e+00 771.0
18 TraesCS5B01G469800 chr2A 89.711 622 57 7 398 1013 84142810 84143430 0.000000e+00 787.0
19 TraesCS5B01G469800 chr1B 89.567 623 59 6 398 1014 466928199 466928821 0.000000e+00 785.0
20 TraesCS5B01G469800 chr1B 89.698 398 37 4 1 397 551727693 551728087 4.930000e-139 505.0
21 TraesCS5B01G469800 chr1B 86.462 325 29 13 3476 3793 66201330 66201646 4.090000e-90 342.0
22 TraesCS5B01G469800 chr1B 88.028 284 25 8 3475 3753 434763495 434763774 1.150000e-85 327.0
23 TraesCS5B01G469800 chr7B 89.137 626 59 9 397 1014 355672614 355673238 0.000000e+00 771.0
24 TraesCS5B01G469800 chr7B 86.154 325 31 12 3476 3793 638449624 638449941 5.290000e-89 339.0
25 TraesCS5B01G469800 chr7B 89.552 67 6 1 4143 4208 721203255 721203189 2.740000e-12 84.2
26 TraesCS5B01G469800 chr7A 89.228 622 60 4 398 1013 218241947 218241327 0.000000e+00 771.0
27 TraesCS5B01G469800 chr7A 90.132 152 8 2 3873 4018 150722063 150722213 1.570000e-44 191.0
28 TraesCS5B01G469800 chr7A 88.060 67 7 1 4143 4208 719570164 719570098 1.270000e-10 78.7
29 TraesCS5B01G469800 chr5A 91.055 559 37 8 1014 1572 640681606 640682151 0.000000e+00 743.0
30 TraesCS5B01G469800 chr5A 84.885 741 66 22 2474 3198 640683066 640683776 0.000000e+00 706.0
31 TraesCS5B01G469800 chr5A 79.681 502 68 19 1884 2362 640682171 640682661 8.860000e-87 331.0
32 TraesCS5B01G469800 chr5A 84.940 332 31 11 2301 2615 640682658 640682987 6.890000e-83 318.0
33 TraesCS5B01G469800 chr7D 91.206 398 34 1 1 397 171332535 171332138 1.350000e-149 540.0
34 TraesCS5B01G469800 chr7D 91.206 398 34 1 1 397 171339330 171338933 1.350000e-149 540.0
35 TraesCS5B01G469800 chr7D 89.474 133 12 2 4143 4273 564893453 564893321 2.640000e-37 167.0
36 TraesCS5B01G469800 chr7D 89.552 67 6 1 4143 4208 623537957 623537891 2.740000e-12 84.2
37 TraesCS5B01G469800 chr1D 90.680 397 36 1 1 397 288100120 288099725 1.050000e-145 527.0
38 TraesCS5B01G469800 chr6D 90.428 397 38 0 1 397 6236884 6237280 1.360000e-144 523.0
39 TraesCS5B01G469800 chr6D 89.421 397 42 0 1 397 50998397 50998793 6.380000e-138 501.0
40 TraesCS5B01G469800 chr6D 88.477 243 17 4 3796 4027 408208886 408208644 2.520000e-72 283.0
41 TraesCS5B01G469800 chr6D 93.182 132 8 1 4143 4273 408208653 408208522 4.360000e-45 193.0
42 TraesCS5B01G469800 chr4D 90.201 398 36 3 1 397 373808065 373807670 2.280000e-142 516.0
43 TraesCS5B01G469800 chr2B 89.196 398 39 4 1 397 727589650 727590044 1.070000e-135 494.0
44 TraesCS5B01G469800 chr2B 87.500 152 12 3 3873 4018 83352581 83352731 7.350000e-38 169.0
45 TraesCS5B01G469800 chr2B 87.500 152 12 4 3873 4018 83397405 83397555 7.350000e-38 169.0
46 TraesCS5B01G469800 chr2B 95.455 44 2 0 2091 2134 23315020 23314977 2.130000e-08 71.3
47 TraesCS5B01G469800 chr6B 87.302 315 26 12 3474 3780 717082500 717082192 8.790000e-92 348.0
48 TraesCS5B01G469800 chr3B 85.849 318 32 11 3471 3780 784687159 784686847 4.120000e-85 326.0
49 TraesCS5B01G469800 chr3B 80.882 408 48 24 3476 3867 824981664 824982057 1.160000e-75 294.0
50 TraesCS5B01G469800 chr3D 78.285 548 69 37 3508 4018 517881511 517880977 1.490000e-79 307.0
51 TraesCS5B01G469800 chr3A 88.079 151 11 2 3874 4018 710054120 710054269 5.680000e-39 172.0
52 TraesCS5B01G469800 chrUn 88.806 134 11 4 4143 4273 92583693 92583561 1.230000e-35 161.0


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 TraesCS5B01G469800 chr5B 643304754 643309026 4272 False 7891.0 7891 100.00000 1 4273 1 chr5B.!!$F3 4272
1 TraesCS5B01G469800 chr5B 319314734 319315355 621 False 784.0 784 89.56700 398 1014 1 chr5B.!!$F2 616
2 TraesCS5B01G469800 chr5B 448224083 448224923 840 False 625.5 1055 95.93100 3472 4273 2 chr5B.!!$F5 801
3 TraesCS5B01G469800 chr5D 512303113 512305536 2423 False 1591.5 2447 89.71300 1014 3477 2 chr5D.!!$F1 2463
4 TraesCS5B01G469800 chr5D 87163542 87168505 4963 True 648.0 806 89.69450 1 1013 2 chr5D.!!$R1 1012
5 TraesCS5B01G469800 chr4A 34861871 34862493 622 True 802.0 802 90.04800 398 1014 1 chr4A.!!$R1 616
6 TraesCS5B01G469800 chr6A 34970411 34971028 617 False 791.0 791 89.88800 398 1014 1 chr6A.!!$F1 616
7 TraesCS5B01G469800 chr6A 1951049 1951672 623 True 771.0 771 89.10300 398 1015 1 chr6A.!!$R1 617
8 TraesCS5B01G469800 chr2A 84142810 84143430 620 False 787.0 787 89.71100 398 1013 1 chr2A.!!$F1 615
9 TraesCS5B01G469800 chr1B 466928199 466928821 622 False 785.0 785 89.56700 398 1014 1 chr1B.!!$F3 616
10 TraesCS5B01G469800 chr7B 355672614 355673238 624 False 771.0 771 89.13700 397 1014 1 chr7B.!!$F1 617
11 TraesCS5B01G469800 chr7A 218241327 218241947 620 True 771.0 771 89.22800 398 1013 1 chr7A.!!$R1 615
12 TraesCS5B01G469800 chr5A 640681606 640683776 2170 False 524.5 743 85.14025 1014 3198 4 chr5A.!!$F1 2184
13 TraesCS5B01G469800 chr3D 517880977 517881511 534 True 307.0 307 78.28500 3508 4018 1 chr3D.!!$R1 510

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
267 268 0.391597 ACTGGGTACGTCAACTGTGG 59.608 55.0 0.00 0.00 0.00 4.17 F
1066 5025 0.028770 CGATCCGTCTCAGCTCAGAC 59.971 60.0 7.85 7.85 39.68 3.51 F
1667 5637 0.322366 TCATCTTGCAACGCATGGGA 60.322 50.0 17.76 0.00 38.76 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 5218 0.179113 GCCAATTTATGCGTGGGGTG 60.179 55.0 0.0 0.0 32.71 4.61 R
2814 7164 0.988832 TTGTATGTTCCGGGGAAGCT 59.011 50.0 0.0 0.0 34.49 3.74 R
3546 7900 0.304098 GCTCAGATCACATCAAGCGC 59.696 55.0 0.0 0.0 32.97 5.92 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
26 27 1.880601 GCTGCCGCATTCGATCTACG 61.881 60.000 0.00 0.00 38.10 3.51
81 82 2.819608 GGCAGGATTTTCTACAAGTGCA 59.180 45.455 0.00 0.00 0.00 4.57
97 98 3.084039 AGTGCACCAATCACCATGTAAG 58.916 45.455 14.63 0.00 35.14 2.34
100 101 4.158394 GTGCACCAATCACCATGTAAGATT 59.842 41.667 5.22 0.00 32.53 2.40
103 104 5.577945 GCACCAATCACCATGTAAGATTTTG 59.422 40.000 0.00 0.35 30.04 2.44
112 113 6.582295 CACCATGTAAGATTTTGTACAAGTGC 59.418 38.462 8.56 2.30 34.53 4.40
113 114 6.092748 CCATGTAAGATTTTGTACAAGTGCC 58.907 40.000 8.56 0.40 34.08 5.01
114 115 5.699097 TGTAAGATTTTGTACAAGTGCCC 57.301 39.130 8.56 0.00 0.00 5.36
115 116 4.521256 TGTAAGATTTTGTACAAGTGCCCC 59.479 41.667 8.56 0.00 0.00 5.80
116 117 3.237268 AGATTTTGTACAAGTGCCCCA 57.763 42.857 8.56 0.00 0.00 4.96
149 150 4.249661 TGTTTCTGTGTTTCTTTTTGGCC 58.750 39.130 0.00 0.00 0.00 5.36
157 158 5.163814 TGTGTTTCTTTTTGGCCGAATTTTG 60.164 36.000 6.16 0.00 0.00 2.44
163 164 6.342111 TCTTTTTGGCCGAATTTTGTTACTT 58.658 32.000 6.16 0.00 0.00 2.24
166 167 8.488651 TTTTTGGCCGAATTTTGTTACTTAAA 57.511 26.923 6.16 0.00 0.00 1.52
169 170 9.760077 TTTGGCCGAATTTTGTTACTTAAATTA 57.240 25.926 0.00 0.00 34.91 1.40
189 190 7.959658 AATTATGTCAGATTCCACCAAATCA 57.040 32.000 0.00 0.00 37.98 2.57
205 206 7.011295 CCACCAAATCATTGCCAACATTATTAC 59.989 37.037 0.00 0.00 35.10 1.89
229 230 3.118592 GGGAAGATGGACCAGACAACTAG 60.119 52.174 0.00 0.00 0.00 2.57
233 234 5.568620 AGATGGACCAGACAACTAGTTTT 57.431 39.130 5.07 0.00 0.00 2.43
261 262 1.202557 GGTGACAACTGGGTACGTCAA 60.203 52.381 0.00 0.00 39.90 3.18
262 263 1.862827 GTGACAACTGGGTACGTCAAC 59.137 52.381 0.00 0.00 39.90 3.18
263 264 1.758280 TGACAACTGGGTACGTCAACT 59.242 47.619 0.00 0.00 35.54 3.16
264 265 2.132762 GACAACTGGGTACGTCAACTG 58.867 52.381 0.00 0.00 0.00 3.16
267 268 0.391597 ACTGGGTACGTCAACTGTGG 59.608 55.000 0.00 0.00 0.00 4.17
274 275 1.512926 ACGTCAACTGTGGATTGAGC 58.487 50.000 0.00 0.00 36.76 4.26
276 277 2.079158 CGTCAACTGTGGATTGAGCAT 58.921 47.619 0.00 0.00 36.76 3.79
282 283 4.261578 ACTGTGGATTGAGCATTTTTGG 57.738 40.909 0.00 0.00 0.00 3.28
284 285 4.240096 CTGTGGATTGAGCATTTTTGGTC 58.760 43.478 0.00 0.00 36.89 4.02
286 287 3.006752 GTGGATTGAGCATTTTTGGTCCA 59.993 43.478 3.04 0.00 35.63 4.02
287 288 3.258872 TGGATTGAGCATTTTTGGTCCAG 59.741 43.478 3.04 0.00 35.63 3.86
297 298 0.465460 TTTGGTCCAGCTGGTGTCAC 60.465 55.000 31.58 21.67 36.34 3.67
376 377 2.833943 TGAGACTGTGGTGTATGCAGAT 59.166 45.455 0.00 0.00 34.60 2.90
378 379 2.568956 AGACTGTGGTGTATGCAGATGT 59.431 45.455 0.00 0.00 34.60 3.06
379 380 2.932614 GACTGTGGTGTATGCAGATGTC 59.067 50.000 0.00 0.00 34.60 3.06
380 381 2.283298 CTGTGGTGTATGCAGATGTCC 58.717 52.381 0.00 0.00 32.39 4.02
381 382 1.627834 TGTGGTGTATGCAGATGTCCA 59.372 47.619 0.00 0.00 0.00 4.02
382 383 2.039613 TGTGGTGTATGCAGATGTCCAA 59.960 45.455 0.00 0.00 0.00 3.53
383 384 3.081061 GTGGTGTATGCAGATGTCCAAA 58.919 45.455 0.00 0.00 0.00 3.28
385 386 3.758023 TGGTGTATGCAGATGTCCAAAAG 59.242 43.478 0.00 0.00 0.00 2.27
422 4373 2.159142 ACTTTCCCATCGACATACGTCC 60.159 50.000 0.00 0.00 43.13 4.79
429 4380 1.944032 TCGACATACGTCCTCGATCA 58.056 50.000 7.77 0.00 43.13 2.92
437 4388 1.066143 ACGTCCTCGATCAGCCAAATT 60.066 47.619 0.00 0.00 40.62 1.82
496 4447 1.717077 ACCTCCTCTTGTGGTCCTAGA 59.283 52.381 0.00 0.00 36.02 2.43
499 4450 4.016479 ACCTCCTCTTGTGGTCCTAGATAA 60.016 45.833 0.00 0.00 36.02 1.75
509 4460 4.344390 GTGGTCCTAGATAACGAGGGATTT 59.656 45.833 0.00 0.00 39.00 2.17
526 4477 7.931948 CGAGGGATTTAGTCAAATACTACCATT 59.068 37.037 0.00 0.00 40.48 3.16
587 4538 2.102438 GTTAGGGTTACGGGCACGC 61.102 63.158 9.12 0.00 46.04 5.34
592 4543 2.262292 GTTACGGGCACGCCACTA 59.738 61.111 9.12 0.00 46.04 2.74
693 4649 0.842030 ATGGCCACCTCTTCTCACCA 60.842 55.000 8.16 0.00 0.00 4.17
721 4678 0.953471 CGTTGATCGCCCCTGTTTCA 60.953 55.000 0.00 0.00 0.00 2.69
725 4682 0.394352 GATCGCCCCTGTTTCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
734 4691 3.265791 CCTGTTTCACCATAGCAGAGAC 58.734 50.000 0.00 0.00 0.00 3.36
746 4703 1.484444 GCAGAGACAGGTGGGGAAGT 61.484 60.000 0.00 0.00 0.00 3.01
811 4769 1.926510 GCTCTTTTGCAAAAACGCACT 59.073 42.857 27.07 0.00 42.87 4.40
900 4859 2.473457 GGCGGTCAGGCGAAATTAA 58.527 52.632 0.00 0.00 35.04 1.40
921 4880 2.129607 GACCTCGCGTGAACAACTTAA 58.870 47.619 10.21 0.00 0.00 1.85
928 4887 5.260140 TCGCGTGAACAACTTAAAAAGAAG 58.740 37.500 5.77 0.00 0.00 2.85
950 4909 5.625150 AGTAGGACCCAGATATGCATTTTC 58.375 41.667 3.54 2.57 0.00 2.29
954 4913 5.721000 AGGACCCAGATATGCATTTTCAAAA 59.279 36.000 3.54 0.00 0.00 2.44
1000 4959 4.138290 TGAAAAAGAATTAGGACCGTGCA 58.862 39.130 0.00 0.00 0.00 4.57
1029 4988 0.637195 CTCTCCCCTCTTCCCCTGTA 59.363 60.000 0.00 0.00 0.00 2.74
1060 5019 1.663074 GATGCCGATCCGTCTCAGC 60.663 63.158 0.00 0.00 0.00 4.26
1061 5020 2.081425 GATGCCGATCCGTCTCAGCT 62.081 60.000 0.00 0.00 0.00 4.24
1063 5022 2.775856 GCCGATCCGTCTCAGCTCA 61.776 63.158 0.00 0.00 0.00 4.26
1065 5024 1.098129 CCGATCCGTCTCAGCTCAGA 61.098 60.000 0.00 0.00 0.00 3.27
1066 5025 0.028770 CGATCCGTCTCAGCTCAGAC 59.971 60.000 7.85 7.85 39.68 3.51
1067 5026 1.388547 GATCCGTCTCAGCTCAGACT 58.611 55.000 16.23 0.00 40.75 3.24
1068 5027 1.748493 GATCCGTCTCAGCTCAGACTT 59.252 52.381 16.23 0.26 40.75 3.01
1069 5028 1.169577 TCCGTCTCAGCTCAGACTTC 58.830 55.000 16.23 0.00 40.75 3.01
1107 5066 3.394836 GCCGCCTCCACTTCCTCT 61.395 66.667 0.00 0.00 0.00 3.69
1248 5207 2.277404 GAGTCGCCTCCTCCTCCT 59.723 66.667 0.00 0.00 0.00 3.69
1250 5209 2.835895 GTCGCCTCCTCCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
1251 5210 3.024356 TCGCCTCCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
1252 5211 2.042435 CGCCTCCTCCTCCTCCTT 60.042 66.667 0.00 0.00 0.00 3.36
1253 5212 2.131067 CGCCTCCTCCTCCTCCTTC 61.131 68.421 0.00 0.00 0.00 3.46
1295 5256 2.317609 GCCGCGAACTGAGCTTCAA 61.318 57.895 8.23 0.00 0.00 2.69
1383 5344 3.061697 GGTTTCTATTGTGTTCGTAGGCG 59.938 47.826 0.00 0.00 39.92 5.52
1424 5385 0.761802 GGGGCAGAGGATTCCTGTAG 59.238 60.000 10.74 2.66 31.76 2.74
1425 5386 1.501582 GGGCAGAGGATTCCTGTAGT 58.498 55.000 10.74 0.00 31.76 2.73
1426 5387 1.139853 GGGCAGAGGATTCCTGTAGTG 59.860 57.143 10.74 3.47 31.76 2.74
1523 5484 1.443194 CATTGTGGCGAGCAAGCAC 60.443 57.895 5.80 0.00 39.27 4.40
1529 5490 2.317609 GGCGAGCAAGCACGAAGAA 61.318 57.895 15.67 0.00 39.27 2.52
1539 5500 1.134220 AGCACGAAGAACCTTTGTCCA 60.134 47.619 0.00 0.00 0.00 4.02
1540 5501 1.673920 GCACGAAGAACCTTTGTCCAA 59.326 47.619 0.00 0.00 0.00 3.53
1592 5556 3.392882 CCCATTTTGTTGCTTCTCCAAC 58.607 45.455 0.00 0.00 44.07 3.77
1609 5579 2.571212 CAACAGCAGGTGGTTTGTCTA 58.429 47.619 4.26 0.00 0.00 2.59
1621 5591 6.267496 GTGGTTTGTCTAGCACCATTTTAT 57.733 37.500 6.30 0.00 42.59 1.40
1623 5593 7.822658 GTGGTTTGTCTAGCACCATTTTATAA 58.177 34.615 6.30 0.00 42.59 0.98
1624 5594 8.301002 GTGGTTTGTCTAGCACCATTTTATAAA 58.699 33.333 0.00 0.00 42.59 1.40
1626 5596 8.520351 GGTTTGTCTAGCACCATTTTATAAACT 58.480 33.333 0.00 0.00 0.00 2.66
1630 5600 9.906660 TGTCTAGCACCATTTTATAAACTTTTG 57.093 29.630 0.00 0.00 0.00 2.44
1634 5604 6.586082 AGCACCATTTTATAAACTTTTGCTCG 59.414 34.615 13.83 0.00 30.98 5.03
1653 5623 4.808364 GCTCGCTTCAACTTCTTATCATCT 59.192 41.667 0.00 0.00 0.00 2.90
1666 5636 0.742505 ATCATCTTGCAACGCATGGG 59.257 50.000 8.44 8.44 38.76 4.00
1667 5637 0.322366 TCATCTTGCAACGCATGGGA 60.322 50.000 17.76 0.00 38.76 4.37
1686 5660 2.158957 GGACGAGAGAACATGCCCATTA 60.159 50.000 0.00 0.00 0.00 1.90
1691 5665 4.576053 CGAGAGAACATGCCCATTAAATCA 59.424 41.667 0.00 0.00 0.00 2.57
1693 5667 6.427853 CGAGAGAACATGCCCATTAAATCATA 59.572 38.462 0.00 0.00 0.00 2.15
1700 5674 7.121382 ACATGCCCATTAAATCATATAGGGAG 58.879 38.462 0.00 0.00 36.96 4.30
1702 5676 7.341885 TGCCCATTAAATCATATAGGGAGAA 57.658 36.000 0.00 0.00 36.96 2.87
1703 5677 7.405292 TGCCCATTAAATCATATAGGGAGAAG 58.595 38.462 0.00 0.00 36.96 2.85
1704 5678 7.018550 TGCCCATTAAATCATATAGGGAGAAGT 59.981 37.037 0.00 0.00 36.96 3.01
1705 5679 7.554476 GCCCATTAAATCATATAGGGAGAAGTC 59.446 40.741 0.00 0.00 36.96 3.01
1706 5680 8.605947 CCCATTAAATCATATAGGGAGAAGTCA 58.394 37.037 0.00 0.00 36.96 3.41
1731 5705 4.882842 TTTTGTAAATGAAAGAGGGGCC 57.117 40.909 0.00 0.00 0.00 5.80
1732 5706 3.825908 TTGTAAATGAAAGAGGGGCCT 57.174 42.857 0.84 0.00 0.00 5.19
1733 5707 3.366052 TGTAAATGAAAGAGGGGCCTC 57.634 47.619 0.84 0.00 43.03 4.70
1734 5708 2.025321 TGTAAATGAAAGAGGGGCCTCC 60.025 50.000 0.00 0.00 43.70 4.30
1745 5719 3.097162 GGCCTCCCCCTCCGATTT 61.097 66.667 0.00 0.00 0.00 2.17
1746 5720 2.511403 GCCTCCCCCTCCGATTTC 59.489 66.667 0.00 0.00 0.00 2.17
1747 5721 2.073101 GCCTCCCCCTCCGATTTCT 61.073 63.158 0.00 0.00 0.00 2.52
1748 5722 0.763223 GCCTCCCCCTCCGATTTCTA 60.763 60.000 0.00 0.00 0.00 2.10
1749 5723 2.031495 CCTCCCCCTCCGATTTCTAT 57.969 55.000 0.00 0.00 0.00 1.98
1750 5724 2.339769 CCTCCCCCTCCGATTTCTATT 58.660 52.381 0.00 0.00 0.00 1.73
1751 5725 3.517612 CCTCCCCCTCCGATTTCTATTA 58.482 50.000 0.00 0.00 0.00 0.98
1752 5726 3.908103 CCTCCCCCTCCGATTTCTATTAA 59.092 47.826 0.00 0.00 0.00 1.40
1753 5727 4.349930 CCTCCCCCTCCGATTTCTATTAAA 59.650 45.833 0.00 0.00 0.00 1.52
1754 5728 5.014228 CCTCCCCCTCCGATTTCTATTAAAT 59.986 44.000 0.00 0.00 0.00 1.40
1755 5729 6.214819 CCTCCCCCTCCGATTTCTATTAAATA 59.785 42.308 0.00 0.00 0.00 1.40
1756 5730 7.256908 CCTCCCCCTCCGATTTCTATTAAATAA 60.257 40.741 0.00 0.00 0.00 1.40
1757 5731 8.048016 TCCCCCTCCGATTTCTATTAAATAAA 57.952 34.615 0.00 0.00 0.00 1.40
1758 5732 7.940688 TCCCCCTCCGATTTCTATTAAATAAAC 59.059 37.037 0.00 0.00 0.00 2.01
1759 5733 7.722285 CCCCCTCCGATTTCTATTAAATAAACA 59.278 37.037 0.00 0.00 0.00 2.83
1760 5734 9.127277 CCCCTCCGATTTCTATTAAATAAACAA 57.873 33.333 0.00 0.00 0.00 2.83
1788 5762 3.955471 TCAGGGAGAAGGCATTTGTAAG 58.045 45.455 0.00 0.00 0.00 2.34
1792 5766 5.011023 CAGGGAGAAGGCATTTGTAAGTTTT 59.989 40.000 0.00 0.00 0.00 2.43
1793 5767 5.011023 AGGGAGAAGGCATTTGTAAGTTTTG 59.989 40.000 0.00 0.00 0.00 2.44
1795 5769 6.280643 GGAGAAGGCATTTGTAAGTTTTGTT 58.719 36.000 0.00 0.00 0.00 2.83
1796 5770 6.420903 GGAGAAGGCATTTGTAAGTTTTGTTC 59.579 38.462 0.00 0.00 0.00 3.18
1797 5771 5.977129 AGAAGGCATTTGTAAGTTTTGTTCG 59.023 36.000 0.00 0.00 0.00 3.95
1798 5772 5.257082 AGGCATTTGTAAGTTTTGTTCGT 57.743 34.783 0.00 0.00 0.00 3.85
1800 5774 5.746721 AGGCATTTGTAAGTTTTGTTCGTTC 59.253 36.000 0.00 0.00 0.00 3.95
1812 5830 1.264020 TGTTCGTTCATTGTGCTGCTC 59.736 47.619 0.00 0.00 0.00 4.26
1836 5854 0.606096 GCAAAATTGGTTAGGCCCGT 59.394 50.000 0.00 0.00 36.04 5.28
1849 5871 2.112029 GCCCGTGCCCGAATTATTT 58.888 52.632 0.00 0.00 35.63 1.40
1852 5874 3.075884 GCCCGTGCCCGAATTATTTATA 58.924 45.455 0.00 0.00 35.63 0.98
1856 5878 5.064707 CCCGTGCCCGAATTATTTATATCTG 59.935 44.000 0.00 0.00 35.63 2.90
1858 5880 6.402118 CCGTGCCCGAATTATTTATATCTGTG 60.402 42.308 0.00 0.00 35.63 3.66
1869 5891 8.500753 TTATTTATATCTGTGCCGTTTTCTGT 57.499 30.769 0.00 0.00 0.00 3.41
1876 5898 2.097791 TGTGCCGTTTTCTGTTGGTTAC 59.902 45.455 0.00 0.00 0.00 2.50
1877 5899 2.356695 GTGCCGTTTTCTGTTGGTTACT 59.643 45.455 0.00 0.00 0.00 2.24
1880 5902 2.601266 CCGTTTTCTGTTGGTTACTGCG 60.601 50.000 0.00 0.00 0.00 5.18
1906 5928 7.215719 TGAACTATATCTATGGACTTGACCG 57.784 40.000 0.00 0.00 0.00 4.79
2014 6039 3.927758 TGCTTTCGATGGCAAATCATTTG 59.072 39.130 5.68 5.68 43.44 2.32
2143 6185 6.391227 AAAACTTGTTCAAGTATGAGTGGG 57.609 37.500 16.84 0.00 36.78 4.61
2146 6188 2.778299 TGTTCAAGTATGAGTGGGTGC 58.222 47.619 0.00 0.00 36.78 5.01
2173 6215 9.331282 GGGTATTGATCTCACTTATATTATGGC 57.669 37.037 0.00 0.00 0.00 4.40
2193 6235 1.126296 CGCAGATATCTTGCAGATGCG 59.874 52.381 15.77 15.77 41.51 4.73
2254 6296 9.296400 GTATTGTGTTCATTTGTTGTACTGTTT 57.704 29.630 0.00 0.00 0.00 2.83
2295 6338 9.430838 CAGCTTTAGAATTAATTTCAGATGTCG 57.569 33.333 1.43 0.00 36.75 4.35
2357 6458 0.826715 TCAGAGGATACAGCCAGTGC 59.173 55.000 0.00 0.00 41.41 4.40
2394 6495 2.888594 CAGCGAAAGTATCTCCGGAAA 58.111 47.619 5.23 0.00 0.00 3.13
2454 6555 1.411612 GCCCTTACGCAGGTATAGTGT 59.588 52.381 0.75 0.00 42.02 3.55
2460 6561 1.747355 ACGCAGGTATAGTGTTACGCT 59.253 47.619 3.31 3.31 0.00 5.07
2461 6562 2.117137 CGCAGGTATAGTGTTACGCTG 58.883 52.381 8.86 0.00 0.00 5.18
2507 6842 5.503683 GCTCAGCAGAACTATATTTGCACTG 60.504 44.000 0.00 0.00 38.97 3.66
2588 6936 8.898761 CCAACTGGTGCTTATTTGTAATGTATA 58.101 33.333 0.00 0.00 0.00 1.47
2733 7083 7.611855 AGAAATTATCTTCCACAGGACGAAAAT 59.388 33.333 0.00 0.00 33.75 1.82
2814 7164 1.383456 AACTGCACGCCTCAAAGCAA 61.383 50.000 0.00 0.00 36.44 3.91
2883 7233 1.612442 TGCTAGGCCGTTCCTCCTT 60.612 57.895 0.00 0.00 43.20 3.36
2994 7344 3.077556 AAGGAGTCCGCCTCGCAT 61.078 61.111 2.76 0.00 41.46 4.73
2998 7348 1.141019 GAGTCCGCCTCGCATGTAA 59.859 57.895 0.00 0.00 0.00 2.41
3057 7407 2.163815 CGAGGACCACTACTTGTACCTG 59.836 54.545 0.00 0.00 0.00 4.00
3078 7428 6.150140 ACCTGTTAAATGAAGAGACAGATTGC 59.850 38.462 3.56 0.00 39.97 3.56
3101 7451 0.249868 GGCGGTGTGATATAGCTGCA 60.250 55.000 1.02 0.00 0.00 4.41
3142 7494 1.269726 GCTGGTGTTGTGTTTCCATGG 60.270 52.381 4.97 4.97 0.00 3.66
3147 7499 3.004315 GGTGTTGTGTTTCCATGGTGTAG 59.996 47.826 12.58 0.00 0.00 2.74
3148 7500 3.630312 GTGTTGTGTTTCCATGGTGTAGT 59.370 43.478 12.58 0.00 0.00 2.73
3149 7501 3.629855 TGTTGTGTTTCCATGGTGTAGTG 59.370 43.478 12.58 0.00 0.00 2.74
3150 7502 3.569194 TGTGTTTCCATGGTGTAGTGT 57.431 42.857 12.58 0.00 0.00 3.55
3151 7503 4.691326 TGTGTTTCCATGGTGTAGTGTA 57.309 40.909 12.58 0.00 0.00 2.90
3152 7504 4.637276 TGTGTTTCCATGGTGTAGTGTAG 58.363 43.478 12.58 0.00 0.00 2.74
3164 7516 2.745821 TGTAGTGTAGCTGTAGGTCACG 59.254 50.000 0.00 0.00 34.71 4.35
3167 7519 1.135460 GTGTAGCTGTAGGTCACGGAC 60.135 57.143 0.00 0.00 35.28 4.79
3171 7523 0.525668 GCTGTAGGTCACGGACATCG 60.526 60.000 6.41 0.00 45.88 3.84
3243 7595 5.312079 AGCTGCTCCATTTTATGATACTCC 58.688 41.667 0.00 0.00 0.00 3.85
3264 7616 8.090788 ACTCCCTGTGAACTGTAATATATGTT 57.909 34.615 0.00 0.00 0.00 2.71
3269 7621 8.397906 CCTGTGAACTGTAATATATGTTGGTTG 58.602 37.037 0.00 0.00 0.00 3.77
3272 7624 7.696453 GTGAACTGTAATATATGTTGGTTGTGC 59.304 37.037 0.00 0.00 0.00 4.57
3274 7626 7.695480 ACTGTAATATATGTTGGTTGTGCAA 57.305 32.000 0.00 0.00 0.00 4.08
3370 7722 7.864379 CCTAATATGAGCAAAAATAGCACTTGG 59.136 37.037 0.00 0.00 0.00 3.61
3373 7725 6.588719 ATGAGCAAAAATAGCACTTGGTAA 57.411 33.333 0.00 0.00 31.31 2.85
3396 7750 5.788450 ACATCACTTCTACAAACAGAGGAG 58.212 41.667 0.00 0.00 0.00 3.69
3428 7782 6.991938 CCAACAAGAAAATGGGTCATCTTTA 58.008 36.000 0.00 0.00 30.01 1.85
3454 7808 4.764823 TGTGAAACACAGAAGGTTGTTCTT 59.235 37.500 0.25 0.00 45.67 2.52
3491 7845 6.532365 AGCGAAAATCGAGAAATAAGGATC 57.468 37.500 3.61 0.00 43.74 3.36
3493 7847 5.236478 GCGAAAATCGAGAAATAAGGATCCA 59.764 40.000 15.82 0.00 43.74 3.41
3495 7849 6.701841 CGAAAATCGAGAAATAAGGATCCAGA 59.298 38.462 15.82 0.48 43.74 3.86
3496 7850 7.306866 CGAAAATCGAGAAATAAGGATCCAGAC 60.307 40.741 15.82 0.00 43.74 3.51
3497 7851 4.569761 TCGAGAAATAAGGATCCAGACG 57.430 45.455 15.82 7.94 0.00 4.18
3533 7887 1.678970 GCGATTTGGGCTTCCTGGT 60.679 57.895 0.00 0.00 0.00 4.00
3537 7891 0.112412 ATTTGGGCTTCCTGGTCGTT 59.888 50.000 0.00 0.00 0.00 3.85
3545 7899 0.036388 TTCCTGGTCGTTGGATCTGC 60.036 55.000 0.00 0.00 31.76 4.26
3546 7900 1.811266 CCTGGTCGTTGGATCTGCG 60.811 63.158 0.00 0.00 0.00 5.18
3547 7901 2.434185 TGGTCGTTGGATCTGCGC 60.434 61.111 0.00 0.00 0.00 6.09
3556 7910 2.176273 GGATCTGCGCGCTTGATGT 61.176 57.895 32.52 18.46 0.00 3.06
3563 7917 1.423721 GCGCGCTTGATGTGATCTGA 61.424 55.000 26.67 0.00 0.00 3.27
3742 8097 1.885163 CGCCCGTGGAGAAACCTAGT 61.885 60.000 0.00 0.00 39.86 2.57
4100 8511 1.590259 GGCTTCTCATCGTCTCCGC 60.590 63.158 0.00 0.00 0.00 5.54
4137 8548 2.490217 CTCATCGTCTCCGCCGTT 59.510 61.111 0.00 0.00 0.00 4.44
4163 8607 0.937231 GCGCTGCTCCTAATCGTCTC 60.937 60.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.151689 TCCGATTTTGACACAAGACGAATC 59.848 41.667 0.00 0.00 0.00 2.52
81 82 6.916360 ACAAAATCTTACATGGTGATTGGT 57.084 33.333 0.00 4.09 31.70 3.67
97 98 4.494484 GATTGGGGCACTTGTACAAAATC 58.506 43.478 10.03 9.91 0.00 2.17
100 101 1.883275 CGATTGGGGCACTTGTACAAA 59.117 47.619 10.03 0.00 0.00 2.83
103 104 2.038387 ATCGATTGGGGCACTTGTAC 57.962 50.000 0.00 0.00 0.00 2.90
112 113 4.158394 ACAGAAACATCAAATCGATTGGGG 59.842 41.667 12.25 7.43 39.62 4.96
113 114 5.097529 CACAGAAACATCAAATCGATTGGG 58.902 41.667 12.25 7.56 39.62 4.12
114 115 5.702865 ACACAGAAACATCAAATCGATTGG 58.297 37.500 12.25 9.09 39.62 3.16
115 116 7.592533 AGAAACACAGAAACATCAAATCGATTG 59.407 33.333 12.25 1.97 40.58 2.67
116 117 7.651808 AGAAACACAGAAACATCAAATCGATT 58.348 30.769 4.39 4.39 29.21 3.34
163 164 9.473007 TGATTTGGTGGAATCTGACATAATTTA 57.527 29.630 0.00 0.00 37.04 1.40
166 167 8.418662 CAATGATTTGGTGGAATCTGACATAAT 58.581 33.333 0.00 0.00 37.04 1.28
169 170 5.394883 GCAATGATTTGGTGGAATCTGACAT 60.395 40.000 0.00 0.00 37.04 3.06
189 190 6.194235 TCTTCCCAGTAATAATGTTGGCAAT 58.806 36.000 1.92 0.00 0.00 3.56
205 206 1.279496 TGTCTGGTCCATCTTCCCAG 58.721 55.000 0.00 0.00 45.81 4.45
246 247 1.864711 CACAGTTGACGTACCCAGTTG 59.135 52.381 0.00 0.00 0.00 3.16
248 249 0.391597 CCACAGTTGACGTACCCAGT 59.608 55.000 0.00 0.00 0.00 4.00
249 250 0.677288 TCCACAGTTGACGTACCCAG 59.323 55.000 0.00 0.00 0.00 4.45
261 262 3.642848 ACCAAAAATGCTCAATCCACAGT 59.357 39.130 0.00 0.00 0.00 3.55
262 263 4.240096 GACCAAAAATGCTCAATCCACAG 58.760 43.478 0.00 0.00 0.00 3.66
263 264 3.006752 GGACCAAAAATGCTCAATCCACA 59.993 43.478 0.00 0.00 0.00 4.17
264 265 3.006752 TGGACCAAAAATGCTCAATCCAC 59.993 43.478 0.00 0.00 30.08 4.02
267 268 3.056322 AGCTGGACCAAAAATGCTCAATC 60.056 43.478 0.00 0.00 0.00 2.67
274 275 1.688197 ACACCAGCTGGACCAAAAATG 59.312 47.619 39.19 24.68 38.94 2.32
276 277 1.341482 TGACACCAGCTGGACCAAAAA 60.341 47.619 39.19 14.16 38.94 1.94
282 283 1.963338 GCAGTGACACCAGCTGGAC 60.963 63.158 39.19 25.37 38.94 4.02
284 285 1.512996 CTTGCAGTGACACCAGCTGG 61.513 60.000 31.60 31.60 42.17 4.85
286 287 1.528824 ACTTGCAGTGACACCAGCT 59.471 52.632 18.09 0.00 0.00 4.24
287 288 4.147701 ACTTGCAGTGACACCAGC 57.852 55.556 12.36 12.36 0.00 4.85
297 298 3.003068 CACCTCTGTTTCTTCACTTGCAG 59.997 47.826 0.00 0.00 0.00 4.41
342 343 1.123077 AGTCTCAACAGTGGTCTGCA 58.877 50.000 0.00 0.00 44.77 4.41
376 377 5.535783 TGCTTCATTCATCTTCTTTTGGACA 59.464 36.000 0.00 0.00 0.00 4.02
378 379 6.266103 AGTTGCTTCATTCATCTTCTTTTGGA 59.734 34.615 0.00 0.00 0.00 3.53
379 380 6.453092 AGTTGCTTCATTCATCTTCTTTTGG 58.547 36.000 0.00 0.00 0.00 3.28
380 381 7.941795 AAGTTGCTTCATTCATCTTCTTTTG 57.058 32.000 0.00 0.00 0.00 2.44
381 382 7.654923 GGAAAGTTGCTTCATTCATCTTCTTTT 59.345 33.333 0.00 0.00 0.00 2.27
382 383 7.150640 GGAAAGTTGCTTCATTCATCTTCTTT 58.849 34.615 0.00 0.00 0.00 2.52
383 384 6.294955 GGGAAAGTTGCTTCATTCATCTTCTT 60.295 38.462 0.00 0.00 0.00 2.52
385 386 5.047802 TGGGAAAGTTGCTTCATTCATCTTC 60.048 40.000 0.00 0.00 0.00 2.87
422 4373 1.004185 CTGCGAATTTGGCTGATCGAG 60.004 52.381 4.99 0.00 37.48 4.04
429 4380 3.006752 TGGATTTTTCTGCGAATTTGGCT 59.993 39.130 4.99 0.00 0.00 4.75
437 4388 3.609853 ACTATGCTGGATTTTTCTGCGA 58.390 40.909 0.00 0.00 32.79 5.10
496 4447 9.978044 GTAGTATTTGACTAAATCCCTCGTTAT 57.022 33.333 0.00 0.00 42.43 1.89
499 4450 6.381994 TGGTAGTATTTGACTAAATCCCTCGT 59.618 38.462 0.00 0.00 42.43 4.18
509 4460 7.652105 GCTCGAATCAATGGTAGTATTTGACTA 59.348 37.037 0.00 0.00 39.81 2.59
526 4477 4.307432 GGATTCCGATTTAGCTCGAATCA 58.693 43.478 17.82 4.50 41.12 2.57
550 4501 6.249192 CCTAACCCTCAATCCTCTTTTTCTT 58.751 40.000 0.00 0.00 0.00 2.52
586 4537 3.609258 CGCGATACGGTTAGTGGC 58.391 61.111 0.00 0.00 38.44 5.01
710 4667 0.323360 TGCTATGGTGAAACAGGGGC 60.323 55.000 0.00 0.00 39.98 5.80
721 4678 1.198713 CCACCTGTCTCTGCTATGGT 58.801 55.000 0.00 0.00 0.00 3.55
725 4682 0.116342 TTCCCCACCTGTCTCTGCTA 59.884 55.000 0.00 0.00 0.00 3.49
734 4691 1.557269 CCTCTCCACTTCCCCACCTG 61.557 65.000 0.00 0.00 0.00 4.00
746 4703 2.176889 CCGTAGTCCTTTTCCTCTCCA 58.823 52.381 0.00 0.00 0.00 3.86
800 4757 0.929824 CGACCAGCAGTGCGTTTTTG 60.930 55.000 10.00 1.53 0.00 2.44
900 4859 0.104304 AAGTTGTTCACGCGAGGTCT 59.896 50.000 15.93 0.00 0.00 3.85
908 4867 7.849515 GTCCTACTTCTTTTTAAGTTGTTCACG 59.150 37.037 0.00 0.00 40.20 4.35
921 4880 5.191722 TGCATATCTGGGTCCTACTTCTTTT 59.808 40.000 0.00 0.00 0.00 2.27
928 4887 5.376625 TGAAAATGCATATCTGGGTCCTAC 58.623 41.667 0.00 0.00 0.00 3.18
954 4913 9.667107 TCAAAAGTATCGATTGAGTCCTAATTT 57.333 29.630 1.71 0.00 0.00 1.82
972 4931 8.347035 CACGGTCCTAATTCTTTTTCAAAAGTA 58.653 33.333 11.01 3.36 44.37 2.24
1000 4959 4.385754 GGAAGAGGGGAGAGTAAAATGCAT 60.386 45.833 0.00 0.00 0.00 3.96
1069 5028 1.820906 CCGCCATGTCCATGTCTGG 60.821 63.158 6.53 1.85 44.64 3.86
1259 5218 0.179113 GCCAATTTATGCGTGGGGTG 60.179 55.000 0.00 0.00 32.71 4.61
1270 5231 1.083489 CTCAGTTCGCGGCCAATTTA 58.917 50.000 6.13 0.00 0.00 1.40
1271 5232 1.875963 CTCAGTTCGCGGCCAATTT 59.124 52.632 6.13 0.00 0.00 1.82
1295 5256 7.979444 TTCGAGAACAAAAATAATCTGGAGT 57.021 32.000 0.00 0.00 30.13 3.85
1354 5315 4.630069 CGAACACAATAGAAACCTACAGGG 59.370 45.833 0.00 0.00 40.27 4.45
1355 5316 5.235516 ACGAACACAATAGAAACCTACAGG 58.764 41.667 0.00 0.00 42.17 4.00
1383 5344 2.747855 CCCCAGTTTCCGCAGAGC 60.748 66.667 0.00 0.00 0.00 4.09
1390 5351 1.535444 CCCCAAACCCCCAGTTTCC 60.535 63.158 0.00 0.00 45.85 3.13
1398 5359 2.168272 AATCCTCTGCCCCAAACCCC 62.168 60.000 0.00 0.00 0.00 4.95
1438 5399 0.861837 CAGCACAGTCGGTCAGAAAC 59.138 55.000 0.00 0.00 0.00 2.78
1472 5433 3.617263 GGGTTATGCACTCGTAACAGAAG 59.383 47.826 9.50 0.00 43.26 2.85
1523 5484 3.563808 TCACATTGGACAAAGGTTCTTCG 59.436 43.478 0.00 0.00 28.05 3.79
1529 5490 3.244181 GGCATTTCACATTGGACAAAGGT 60.244 43.478 0.00 0.00 31.58 3.50
1539 5500 1.003464 GCAAAGGGGGCATTTCACATT 59.997 47.619 0.00 0.00 0.00 2.71
1540 5501 0.614812 GCAAAGGGGGCATTTCACAT 59.385 50.000 0.00 0.00 0.00 3.21
1592 5556 1.160137 GCTAGACAAACCACCTGCTG 58.840 55.000 0.00 0.00 0.00 4.41
1594 5558 0.875059 GTGCTAGACAAACCACCTGC 59.125 55.000 0.00 0.00 0.00 4.85
1595 5559 1.202758 TGGTGCTAGACAAACCACCTG 60.203 52.381 13.85 0.00 46.08 4.00
1596 5560 1.136828 TGGTGCTAGACAAACCACCT 58.863 50.000 13.85 0.00 46.08 4.00
1597 5561 2.200373 ATGGTGCTAGACAAACCACC 57.800 50.000 8.62 8.18 46.34 4.61
1609 5579 6.586082 CGAGCAAAAGTTTATAAAATGGTGCT 59.414 34.615 24.73 24.73 38.66 4.40
1615 5585 8.699749 GTTGAAGCGAGCAAAAGTTTATAAAAT 58.300 29.630 0.00 0.00 0.00 1.82
1621 5591 4.893424 AGTTGAAGCGAGCAAAAGTTTA 57.107 36.364 0.00 0.00 0.00 2.01
1623 5593 3.378427 AGAAGTTGAAGCGAGCAAAAGTT 59.622 39.130 0.00 0.00 0.00 2.66
1624 5594 2.945668 AGAAGTTGAAGCGAGCAAAAGT 59.054 40.909 0.00 0.00 0.00 2.66
1626 5596 5.238432 TGATAAGAAGTTGAAGCGAGCAAAA 59.762 36.000 0.00 0.00 0.00 2.44
1630 5600 4.808364 AGATGATAAGAAGTTGAAGCGAGC 59.192 41.667 0.00 0.00 0.00 5.03
1634 5604 6.187125 TGCAAGATGATAAGAAGTTGAAGC 57.813 37.500 0.00 0.00 0.00 3.86
1653 5623 2.281139 TCGTCCCATGCGTTGCAA 60.281 55.556 0.00 0.00 43.62 4.08
1666 5636 2.029838 AATGGGCATGTTCTCTCGTC 57.970 50.000 0.00 0.00 0.00 4.20
1667 5637 3.627395 TTAATGGGCATGTTCTCTCGT 57.373 42.857 0.00 0.00 0.00 4.18
1709 5683 4.904853 AGGCCCCTCTTTCATTTACAAAAA 59.095 37.500 0.00 0.00 0.00 1.94
1710 5684 4.488770 AGGCCCCTCTTTCATTTACAAAA 58.511 39.130 0.00 0.00 0.00 2.44
1711 5685 4.086457 GAGGCCCCTCTTTCATTTACAAA 58.914 43.478 0.00 0.00 39.80 2.83
1712 5686 3.563479 GGAGGCCCCTCTTTCATTTACAA 60.563 47.826 13.65 0.00 42.38 2.41
1713 5687 2.025321 GGAGGCCCCTCTTTCATTTACA 60.025 50.000 13.65 0.00 42.38 2.41
1714 5688 2.656002 GGAGGCCCCTCTTTCATTTAC 58.344 52.381 13.65 0.00 42.38 2.01
1728 5702 3.097162 AAATCGGAGGGGGAGGCC 61.097 66.667 0.00 0.00 0.00 5.19
1729 5703 0.763223 TAGAAATCGGAGGGGGAGGC 60.763 60.000 0.00 0.00 0.00 4.70
1730 5704 2.031495 ATAGAAATCGGAGGGGGAGG 57.969 55.000 0.00 0.00 0.00 4.30
1731 5705 5.562298 TTTAATAGAAATCGGAGGGGGAG 57.438 43.478 0.00 0.00 0.00 4.30
1732 5706 7.636036 TTATTTAATAGAAATCGGAGGGGGA 57.364 36.000 0.00 0.00 0.00 4.81
1733 5707 7.722285 TGTTTATTTAATAGAAATCGGAGGGGG 59.278 37.037 0.00 0.00 0.00 5.40
1734 5708 8.685838 TGTTTATTTAATAGAAATCGGAGGGG 57.314 34.615 0.00 0.00 0.00 4.79
1749 5723 9.983024 TCTCCCTGAACCATATTGTTTATTTAA 57.017 29.630 0.00 0.00 0.00 1.52
1750 5724 9.983024 TTCTCCCTGAACCATATTGTTTATTTA 57.017 29.630 0.00 0.00 0.00 1.40
1751 5725 8.893563 TTCTCCCTGAACCATATTGTTTATTT 57.106 30.769 0.00 0.00 0.00 1.40
1752 5726 7.561356 CCTTCTCCCTGAACCATATTGTTTATT 59.439 37.037 0.00 0.00 0.00 1.40
1753 5727 7.062957 CCTTCTCCCTGAACCATATTGTTTAT 58.937 38.462 0.00 0.00 0.00 1.40
1754 5728 6.423182 CCTTCTCCCTGAACCATATTGTTTA 58.577 40.000 0.00 0.00 0.00 2.01
1755 5729 5.264395 CCTTCTCCCTGAACCATATTGTTT 58.736 41.667 0.00 0.00 0.00 2.83
1756 5730 4.860022 CCTTCTCCCTGAACCATATTGTT 58.140 43.478 0.00 0.00 0.00 2.83
1757 5731 3.372025 GCCTTCTCCCTGAACCATATTGT 60.372 47.826 0.00 0.00 0.00 2.71
1758 5732 3.217626 GCCTTCTCCCTGAACCATATTG 58.782 50.000 0.00 0.00 0.00 1.90
1759 5733 2.852449 TGCCTTCTCCCTGAACCATATT 59.148 45.455 0.00 0.00 0.00 1.28
1760 5734 2.492025 TGCCTTCTCCCTGAACCATAT 58.508 47.619 0.00 0.00 0.00 1.78
1761 5735 1.965414 TGCCTTCTCCCTGAACCATA 58.035 50.000 0.00 0.00 0.00 2.74
1762 5736 1.302907 ATGCCTTCTCCCTGAACCAT 58.697 50.000 0.00 0.00 0.00 3.55
1763 5737 1.075601 AATGCCTTCTCCCTGAACCA 58.924 50.000 0.00 0.00 0.00 3.67
1764 5738 1.821136 CAAATGCCTTCTCCCTGAACC 59.179 52.381 0.00 0.00 0.00 3.62
1765 5739 2.519013 ACAAATGCCTTCTCCCTGAAC 58.481 47.619 0.00 0.00 0.00 3.18
1766 5740 2.978156 ACAAATGCCTTCTCCCTGAA 57.022 45.000 0.00 0.00 0.00 3.02
1767 5741 3.330701 ACTTACAAATGCCTTCTCCCTGA 59.669 43.478 0.00 0.00 0.00 3.86
1768 5742 3.690460 ACTTACAAATGCCTTCTCCCTG 58.310 45.455 0.00 0.00 0.00 4.45
1769 5743 4.388577 AACTTACAAATGCCTTCTCCCT 57.611 40.909 0.00 0.00 0.00 4.20
1770 5744 5.221441 ACAAAACTTACAAATGCCTTCTCCC 60.221 40.000 0.00 0.00 0.00 4.30
1771 5745 5.842907 ACAAAACTTACAAATGCCTTCTCC 58.157 37.500 0.00 0.00 0.00 3.71
1772 5746 6.142320 CGAACAAAACTTACAAATGCCTTCTC 59.858 38.462 0.00 0.00 0.00 2.87
1773 5747 5.977129 CGAACAAAACTTACAAATGCCTTCT 59.023 36.000 0.00 0.00 0.00 2.85
1774 5748 5.746721 ACGAACAAAACTTACAAATGCCTTC 59.253 36.000 0.00 0.00 0.00 3.46
1788 5762 3.301771 GCAGCACAATGAACGAACAAAAC 60.302 43.478 0.00 0.00 0.00 2.43
1792 5766 1.264020 GAGCAGCACAATGAACGAACA 59.736 47.619 0.00 0.00 0.00 3.18
1793 5767 1.264020 TGAGCAGCACAATGAACGAAC 59.736 47.619 0.00 0.00 0.00 3.95
1795 5769 1.150827 CTGAGCAGCACAATGAACGA 58.849 50.000 0.00 0.00 0.00 3.85
1796 5770 1.150827 TCTGAGCAGCACAATGAACG 58.849 50.000 0.00 0.00 0.00 3.95
1797 5771 3.198863 CTTCTGAGCAGCACAATGAAC 57.801 47.619 0.00 0.00 0.00 3.18
1812 5830 3.588955 GGCCTAACCAATTTTGCTTCTG 58.411 45.455 0.00 0.00 38.86 3.02
1836 5854 5.414454 GGCACAGATATAAATAATTCGGGCA 59.586 40.000 0.00 0.00 0.00 5.36
1849 5871 4.634004 CCAACAGAAAACGGCACAGATATA 59.366 41.667 0.00 0.00 0.00 0.86
1852 5874 1.608590 CCAACAGAAAACGGCACAGAT 59.391 47.619 0.00 0.00 0.00 2.90
1856 5878 2.356695 AGTAACCAACAGAAAACGGCAC 59.643 45.455 0.00 0.00 0.00 5.01
1858 5880 2.857104 GCAGTAACCAACAGAAAACGGC 60.857 50.000 0.00 0.00 0.00 5.68
1869 5891 7.050970 AGATATAGTTCATCGCAGTAACCAA 57.949 36.000 0.00 0.00 0.00 3.67
1876 5898 7.094508 AGTCCATAGATATAGTTCATCGCAG 57.905 40.000 0.00 0.00 0.00 5.18
1877 5899 7.176690 TCAAGTCCATAGATATAGTTCATCGCA 59.823 37.037 0.00 0.00 0.00 5.10
1880 5902 7.971168 CGGTCAAGTCCATAGATATAGTTCATC 59.029 40.741 0.00 0.00 0.00 2.92
1906 5928 3.282021 TGTCTCAGGCAAAGCAATATCC 58.718 45.455 0.00 0.00 0.00 2.59
2014 6039 1.221466 TGCTCTATGTAATGCCGCGC 61.221 55.000 0.00 0.00 0.00 6.86
2143 6185 2.604046 AGTGAGATCAATACCCGCAC 57.396 50.000 0.00 0.00 0.00 5.34
2146 6188 9.534565 CCATAATATAAGTGAGATCAATACCCG 57.465 37.037 0.00 0.00 0.00 5.28
2193 6235 4.177026 AGAACTGTGATATCAACTCGTGC 58.823 43.478 7.07 1.32 0.00 5.34
2254 6296 7.050970 TCTAAAGCTGTGAACAGAGAAGTAA 57.949 36.000 14.58 0.00 46.59 2.24
2295 6338 7.871853 TCAGTGTTAGAAAAACAAGGCTTATC 58.128 34.615 0.00 0.00 31.20 1.75
2300 6343 5.831997 ACATCAGTGTTAGAAAAACAAGGC 58.168 37.500 0.00 0.00 34.01 4.35
2394 6495 3.634910 ACCAAGTTTCAAGCCATACGTTT 59.365 39.130 0.00 0.00 0.00 3.60
2460 6561 5.584649 GCTACAGAATAATGGTGTTGCTACA 59.415 40.000 0.00 0.00 39.09 2.74
2461 6562 5.817816 AGCTACAGAATAATGGTGTTGCTAC 59.182 40.000 8.54 0.00 46.68 3.58
2494 6829 5.528690 AGTGTACATGGCAGTGCAAATATAG 59.471 40.000 18.61 1.58 35.90 1.31
2507 6842 1.202382 GGTCGACCTAGTGTACATGGC 60.202 57.143 27.64 0.00 0.00 4.40
2608 6958 6.239402 CCTGATTCCTTTTGTCTTTGACCATT 60.239 38.462 0.00 0.00 0.00 3.16
2617 6967 3.795688 TCAGCCTGATTCCTTTTGTCT 57.204 42.857 0.00 0.00 0.00 3.41
2733 7083 2.093869 GTGGTAAACTATGGCCTCGACA 60.094 50.000 3.32 0.00 0.00 4.35
2748 7098 1.195442 TCAGGCCGTGGATGTGGTAA 61.195 55.000 0.00 0.00 0.00 2.85
2814 7164 0.988832 TTGTATGTTCCGGGGAAGCT 59.011 50.000 0.00 0.00 34.49 3.74
2883 7233 3.509137 GAACCGTGCTGTCCGTCCA 62.509 63.158 0.00 0.00 0.00 4.02
2994 7344 1.336887 GCGTCCTGCTCTCTTGTTACA 60.337 52.381 0.00 0.00 41.73 2.41
2998 7348 2.259818 CGCGTCCTGCTCTCTTGT 59.740 61.111 0.00 0.00 43.27 3.16
3057 7407 6.170675 ACGCAATCTGTCTCTTCATTTAAC 57.829 37.500 0.00 0.00 0.00 2.01
3078 7428 0.859232 GCTATATCACACCGCCAACG 59.141 55.000 0.00 0.00 39.67 4.10
3115 7467 0.530650 ACACAACACCAGCAGAGTCG 60.531 55.000 0.00 0.00 0.00 4.18
3118 7470 1.334869 GGAAACACAACACCAGCAGAG 59.665 52.381 0.00 0.00 0.00 3.35
3142 7494 3.425892 CGTGACCTACAGCTACACTACAC 60.426 52.174 0.00 0.00 0.00 2.90
3147 7499 1.135460 GTCCGTGACCTACAGCTACAC 60.135 57.143 0.00 0.00 0.00 2.90
3148 7500 1.171308 GTCCGTGACCTACAGCTACA 58.829 55.000 0.00 0.00 0.00 2.74
3149 7501 1.171308 TGTCCGTGACCTACAGCTAC 58.829 55.000 0.00 0.00 0.00 3.58
3150 7502 2.022195 GATGTCCGTGACCTACAGCTA 58.978 52.381 0.00 0.00 0.00 3.32
3151 7503 0.818296 GATGTCCGTGACCTACAGCT 59.182 55.000 2.23 0.00 0.00 4.24
3152 7504 0.525668 CGATGTCCGTGACCTACAGC 60.526 60.000 2.23 0.00 0.00 4.40
3243 7595 8.397906 CAACCAACATATATTACAGTTCACAGG 58.602 37.037 0.00 0.00 0.00 4.00
3303 7655 9.528489 AGGTGAAACAATGGTTATTACTAACAT 57.472 29.630 5.46 0.00 37.87 2.71
3355 7707 7.370383 AGTGATGTTACCAAGTGCTATTTTTG 58.630 34.615 0.00 0.00 0.00 2.44
3370 7722 7.152645 TCCTCTGTTTGTAGAAGTGATGTTAC 58.847 38.462 0.00 0.00 0.00 2.50
3373 7725 5.788450 CTCCTCTGTTTGTAGAAGTGATGT 58.212 41.667 0.00 0.00 0.00 3.06
3396 7750 2.818130 TTTTCTTGTTGGGCAGATGC 57.182 45.000 0.00 0.00 41.14 3.91
3420 7774 7.041167 CCTTCTGTGTTTCACATGTAAAGATGA 60.041 37.037 0.00 0.00 43.71 2.92
3425 7779 6.151985 ACAACCTTCTGTGTTTCACATGTAAA 59.848 34.615 0.00 0.00 43.71 2.01
3428 7782 4.016444 ACAACCTTCTGTGTTTCACATGT 58.984 39.130 0.00 0.00 43.71 3.21
3504 7858 2.176273 CAAATCGCTGAGGAGCCGG 61.176 63.158 0.00 0.00 42.91 6.13
3533 7887 3.932580 AAGCGCGCAGATCCAACGA 62.933 57.895 35.10 0.00 0.00 3.85
3537 7891 2.175621 CATCAAGCGCGCAGATCCA 61.176 57.895 35.10 10.84 0.00 3.41
3545 7899 0.575859 CTCAGATCACATCAAGCGCG 59.424 55.000 0.00 0.00 0.00 6.86
3546 7900 0.304098 GCTCAGATCACATCAAGCGC 59.696 55.000 0.00 0.00 32.97 5.92
3547 7901 0.935898 GGCTCAGATCACATCAAGCG 59.064 55.000 0.00 0.00 39.68 4.68
3556 7910 1.786049 CGATCCGACGGCTCAGATCA 61.786 60.000 17.26 0.00 35.85 2.92
3942 8347 2.736826 CGCCTTCCTCCTTCCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
4111 8522 0.388659 GAGACGATGAGGAGCAGCAT 59.611 55.000 0.00 0.00 30.64 3.79
4112 8523 1.670949 GGAGACGATGAGGAGCAGCA 61.671 60.000 0.00 0.00 30.64 4.41
4146 8557 3.579066 GGAGACGATTAGGAGCAGC 57.421 57.895 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.