Multiple sequence alignment - TraesCS1B01G439200

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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 TraesCS1B01G439200 chr1B 100.000 6024 0 0 1 6024 660967150 660961127 0.000000e+00 11125.0
1 TraesCS1B01G439200 chr1B 92.201 3539 214 15 1447 4949 660531803 660528291 0.000000e+00 4950.0
2 TraesCS1B01G439200 chr1B 91.071 2184 170 20 2834 5006 660684377 660682208 0.000000e+00 2929.0
3 TraesCS1B01G439200 chr1B 89.604 1895 171 19 2744 4620 660746686 660744800 0.000000e+00 2385.0
4 TraesCS1B01G439200 chr1B 85.626 2268 294 24 2806 5055 661055413 661053160 0.000000e+00 2353.0
5 TraesCS1B01G439200 chr1B 86.403 2096 263 14 2969 5055 660950481 660948399 0.000000e+00 2272.0
6 TraesCS1B01G439200 chr1B 86.725 1710 169 34 2946 4619 660723343 660721656 0.000000e+00 1847.0
7 TraesCS1B01G439200 chr1B 88.114 1506 165 11 3554 5055 660914419 660912924 0.000000e+00 1777.0
8 TraesCS1B01G439200 chr1B 83.191 1642 246 17 2994 4619 660997285 660995658 0.000000e+00 1476.0
9 TraesCS1B01G439200 chr1B 89.752 1171 77 23 996 2136 660726065 660724908 0.000000e+00 1458.0
10 TraesCS1B01G439200 chr1B 88.742 1208 95 22 1001 2187 660652937 660651750 0.000000e+00 1439.0
11 TraesCS1B01G439200 chr1B 90.872 986 72 7 996 1970 660749488 660748510 0.000000e+00 1306.0
12 TraesCS1B01G439200 chr1B 89.514 906 81 5 4160 5055 660798351 660797450 0.000000e+00 1134.0
13 TraesCS1B01G439200 chr1B 84.096 962 106 20 1001 1931 661061803 661060858 0.000000e+00 885.0
14 TraesCS1B01G439200 chr1B 90.087 686 34 15 1447 2106 660686611 660685934 0.000000e+00 859.0
15 TraesCS1B01G439200 chr1B 89.919 615 52 5 796 1408 660916970 660916364 0.000000e+00 784.0
16 TraesCS1B01G439200 chr1B 83.555 827 114 12 1001 1820 660882095 660881284 0.000000e+00 754.0
17 TraesCS1B01G439200 chr1B 89.509 448 32 8 308 748 660687090 660686651 2.450000e-153 553.0
18 TraesCS1B01G439200 chr1B 89.448 417 40 2 993 1408 660532353 660531940 1.920000e-144 523.0
19 TraesCS1B01G439200 chr1B 84.118 510 38 15 5087 5574 660797043 660796555 2.560000e-123 453.0
20 TraesCS1B01G439200 chr1B 92.903 310 16 4 1 309 660570966 660570662 4.280000e-121 446.0
21 TraesCS1B01G439200 chr1B 92.332 313 12 8 1 309 660687448 660687144 9.270000e-118 435.0
22 TraesCS1B01G439200 chr1B 92.411 224 16 1 5336 5558 660681853 660681630 9.740000e-83 318.0
23 TraesCS1B01G439200 chr1B 89.669 242 18 3 308 548 660570608 660570373 9.810000e-78 302.0
24 TraesCS1B01G439200 chr1B 88.362 232 13 7 5626 5857 660796424 660796207 3.580000e-67 267.0
25 TraesCS1B01G439200 chr1B 82.392 301 47 5 4664 4961 660995577 660995280 2.150000e-64 257.0
26 TraesCS1B01G439200 chr1B 87.719 228 15 8 5630 5857 661052258 661052044 2.790000e-63 254.0
27 TraesCS1B01G439200 chr1B 88.945 199 14 5 5098 5295 661052749 661052558 7.800000e-59 239.0
28 TraesCS1B01G439200 chr1B 78.289 456 37 20 2350 2765 660651316 660650883 2.810000e-58 237.0
29 TraesCS1B01G439200 chr1B 87.560 209 13 9 546 742 660532793 660532586 4.700000e-56 230.0
30 TraesCS1B01G439200 chr1B 85.408 233 20 6 5626 5857 660681486 660681267 4.700000e-56 230.0
31 TraesCS1B01G439200 chr1B 98.400 125 2 0 5900 6024 660951369 660951245 2.830000e-53 220.0
32 TraesCS1B01G439200 chr1B 83.262 233 24 9 5626 5857 660462887 660462669 3.680000e-47 200.0
33 TraesCS1B01G439200 chr1B 89.726 146 10 2 5158 5299 660912537 660912393 1.330000e-41 182.0
34 TraesCS1B01G439200 chr1B 90.476 126 8 4 5056 5178 660682062 660681938 4.830000e-36 163.0
35 TraesCS1B01G439200 chr1B 95.146 103 5 0 5755 5857 660912340 660912238 4.830000e-36 163.0
36 TraesCS1B01G439200 chr1B 80.328 244 23 8 5408 5630 661052538 661052299 1.740000e-35 161.0
37 TraesCS1B01G439200 chr1B 90.722 97 9 0 5199 5295 660681948 660681852 4.900000e-26 130.0
38 TraesCS1B01G439200 chr1B 94.048 84 5 0 521 604 660918064 660917981 1.760000e-25 128.0
39 TraesCS1B01G439200 chr1B 76.577 222 39 10 39 255 633289493 633289706 6.380000e-20 110.0
40 TraesCS1B01G439200 chr1B 88.172 93 6 1 5742 5834 660908056 660907969 8.260000e-19 106.0
41 TraesCS1B01G439200 chr1B 93.651 63 4 0 5053 5115 660527475 660527413 1.790000e-15 95.3
42 TraesCS1B01G439200 chr1B 97.959 49 1 0 5851 5899 660998118 660998070 1.080000e-12 86.1
43 TraesCS1B01G439200 chr1B 92.683 41 3 0 5062 5102 660944968 660944928 6.520000e-05 60.2
44 TraesCS1B01G439200 chr1B 94.595 37 2 0 5062 5098 677304283 677304319 2.350000e-04 58.4
45 TraesCS1B01G439200 chr1D 89.798 2274 208 21 2791 5055 475178633 475176375 0.000000e+00 2892.0
46 TraesCS1B01G439200 chr1D 83.091 1650 240 25 2994 4619 475196141 475194507 0.000000e+00 1465.0
47 TraesCS1B01G439200 chr1D 84.699 830 118 7 996 1820 475197440 475196615 0.000000e+00 821.0
48 TraesCS1B01G439200 chr1D 90.019 521 31 11 5053 5558 475176000 475175486 0.000000e+00 654.0
49 TraesCS1B01G439200 chr1D 77.863 262 35 20 39 290 302342977 302342729 2.260000e-29 141.0
50 TraesCS1B01G439200 chr1D 88.172 93 6 1 5742 5834 475207805 475207718 8.260000e-19 106.0
51 TraesCS1B01G439200 chr1A 88.771 2271 215 26 2806 5055 570862395 570860144 0.000000e+00 2745.0
52 TraesCS1B01G439200 chr1A 90.753 1168 71 17 994 2136 570864958 570863803 0.000000e+00 1524.0
53 TraesCS1B01G439200 chr1A 82.821 1106 162 22 3876 4969 570877587 570876498 0.000000e+00 965.0
54 TraesCS1B01G439200 chr1A 88.675 415 42 5 996 1408 570880725 570880314 9.010000e-138 501.0
55 TraesCS1B01G439200 chr1A 83.848 421 28 22 5139 5558 570859676 570859295 1.230000e-96 364.0
56 TraesCS1B01G439200 chr1A 84.848 231 21 6 5626 5855 570859151 570858934 2.830000e-53 220.0
57 TraesCS1B01G439200 chr1A 87.288 118 9 1 380 497 570865118 570865007 4.900000e-26 130.0
58 TraesCS1B01G439200 chr1A 92.308 78 6 0 5553 5630 570859265 570859188 1.770000e-20 111.0
59 TraesCS1B01G439200 chr1A 94.643 56 3 0 5054 5109 570859725 570859670 2.990000e-13 87.9
60 TraesCS1B01G439200 chr1A 100.000 30 0 0 5069 5098 583989206 583989235 8.430000e-04 56.5
61 TraesCS1B01G439200 chr5B 78.372 823 138 24 1000 1813 18711302 18710511 1.170000e-136 497.0
62 TraesCS1B01G439200 chr4B 97.600 125 3 0 5900 6024 483086265 483086141 1.310000e-51 215.0
63 TraesCS1B01G439200 chr4B 96.800 125 4 0 5900 6024 483091209 483091085 6.120000e-50 209.0
64 TraesCS1B01G439200 chr3B 96.800 125 4 0 5900 6024 811145521 811145645 6.120000e-50 209.0
65 TraesCS1B01G439200 chr3B 96.000 125 5 0 5900 6024 811150489 811150613 2.850000e-48 204.0
66 TraesCS1B01G439200 chr6B 95.200 125 6 0 5900 6024 641891404 641891528 1.320000e-46 198.0
67 TraesCS1B01G439200 chr6B 92.857 126 9 0 5899 6024 712612476 712612351 3.710000e-42 183.0
68 TraesCS1B01G439200 chr2A 95.200 125 6 0 5900 6024 36188033 36187909 1.320000e-46 198.0
69 TraesCS1B01G439200 chr2A 80.995 221 34 8 48 264 743547848 743547632 1.040000e-37 169.0
70 TraesCS1B01G439200 chr7D 92.857 126 9 0 5899 6024 208647933 208647808 3.710000e-42 183.0
71 TraesCS1B01G439200 chr2B 84.699 183 22 5 40 219 584481818 584481997 1.730000e-40 178.0
72 TraesCS1B01G439200 chr2D 81.818 187 30 4 48 233 548599866 548600049 2.910000e-33 154.0
73 TraesCS1B01G439200 chr5A 79.612 206 31 9 74 276 77792946 77792749 2.930000e-28 137.0
74 TraesCS1B01G439200 chr3D 78.974 195 33 7 44 237 505555214 505555401 6.340000e-25 126.0


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 TraesCS1B01G439200 chr1B 660961127 660967150 6023 True 11125.000000 11125 100.000000 1 6024 1 chr1B.!!$R4 6023
1 TraesCS1B01G439200 chr1B 660744800 660749488 4688 True 1845.500000 2385 90.238000 996 4620 2 chr1B.!!$R11 3624
2 TraesCS1B01G439200 chr1B 660721656 660726065 4409 True 1652.500000 1847 88.238500 996 4619 2 chr1B.!!$R10 3623
3 TraesCS1B01G439200 chr1B 660527413 660532793 5380 True 1449.575000 4950 90.715000 546 5115 4 chr1B.!!$R6 4569
4 TraesCS1B01G439200 chr1B 661060858 661061803 945 True 885.000000 885 84.096000 1001 1931 1 chr1B.!!$R5 930
5 TraesCS1B01G439200 chr1B 660944928 660951369 6441 True 850.733333 2272 92.495333 2969 6024 3 chr1B.!!$R14 3055
6 TraesCS1B01G439200 chr1B 660650883 660652937 2054 True 838.000000 1439 83.515500 1001 2765 2 chr1B.!!$R8 1764
7 TraesCS1B01G439200 chr1B 660881284 660882095 811 True 754.000000 754 83.555000 1001 1820 1 chr1B.!!$R2 819
8 TraesCS1B01G439200 chr1B 661052044 661055413 3369 True 751.750000 2353 85.654500 2806 5857 4 chr1B.!!$R16 3051
9 TraesCS1B01G439200 chr1B 660681267 660687448 6181 True 702.125000 2929 90.252000 1 5857 8 chr1B.!!$R9 5856
10 TraesCS1B01G439200 chr1B 660796207 660798351 2144 True 618.000000 1134 87.331333 4160 5857 3 chr1B.!!$R12 1697
11 TraesCS1B01G439200 chr1B 660912238 660918064 5826 True 606.800000 1777 91.390600 521 5857 5 chr1B.!!$R13 5336
12 TraesCS1B01G439200 chr1B 660995280 660998118 2838 True 606.366667 1476 87.847333 2994 5899 3 chr1B.!!$R15 2905
13 TraesCS1B01G439200 chr1B 660570373 660570966 593 True 374.000000 446 91.286000 1 548 2 chr1B.!!$R7 547
14 TraesCS1B01G439200 chr1D 475175486 475178633 3147 True 1773.000000 2892 89.908500 2791 5558 2 chr1D.!!$R3 2767
15 TraesCS1B01G439200 chr1D 475194507 475197440 2933 True 1143.000000 1465 83.895000 996 4619 2 chr1D.!!$R4 3623
16 TraesCS1B01G439200 chr1A 570858934 570865118 6184 True 740.271429 2745 88.922714 380 5855 7 chr1A.!!$R1 5475
17 TraesCS1B01G439200 chr1A 570876498 570880725 4227 True 733.000000 965 85.748000 996 4969 2 chr1A.!!$R2 3973
18 TraesCS1B01G439200 chr5B 18710511 18711302 791 True 497.000000 497 78.372000 1000 1813 1 chr5B.!!$R1 813

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
882 1839 0.034477 CACCAACCATACCACCTCCC 60.034 60.0 0.00 0.00 0.00 4.30 F
883 1840 0.178843 ACCAACCATACCACCTCCCT 60.179 55.0 0.00 0.00 0.00 4.20 F
2604 5306 0.035317 GTCTGGATGGCTGTGTGTCA 59.965 55.0 0.00 0.00 33.36 3.58 F
2606 5308 0.035881 CTGGATGGCTGTGTGTCAGT 59.964 55.0 0.00 0.00 45.23 3.41 F
4154 9011 0.396435 AAGACTGCCATCAACGGTGA 59.604 50.0 5.17 5.17 38.41 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2603 5305 4.332637 GCCGCCTTGCACACACTG 62.333 66.667 0.0 0.0 0.00 3.66 R
2714 5515 4.436718 GCACCAAAAACACAAACATCAACC 60.437 41.667 0.0 0.0 0.00 3.77 R
4364 9239 0.744057 CACGGGTATGTGCAGCATGA 60.744 55.000 0.0 0.0 39.69 3.07 R
4458 9354 3.014623 TCCGTGACCTGTATGAGTAGTG 58.985 50.000 0.0 0.0 0.00 2.74 R
5928 13848 0.110823 CTTGTGCGCGAAACCTGTAC 60.111 55.000 12.1 0.0 0.00 2.90 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
201 204 1.082756 CGAAGCGGCAGTGTTTCAC 60.083 57.895 1.45 0.00 34.10 3.18
238 241 3.603965 TTTGGGTGTAACATTCTGGGT 57.396 42.857 0.00 0.00 39.98 4.51
239 242 4.726035 TTTGGGTGTAACATTCTGGGTA 57.274 40.909 0.00 0.00 39.98 3.69
242 245 3.394940 TGGGTGTAACATTCTGGGTAACA 59.605 43.478 0.00 0.00 39.98 2.41
246 249 6.386654 GGTGTAACATTCTGGGTAACAATTG 58.613 40.000 3.24 3.24 39.98 2.32
247 250 6.207810 GGTGTAACATTCTGGGTAACAATTGA 59.792 38.462 13.59 0.00 39.98 2.57
250 253 6.916360 AACATTCTGGGTAACAATTGATGT 57.084 33.333 13.59 5.17 46.82 3.06
366 426 5.651139 AGTCATGTTTTCTCCCATGAATCAG 59.349 40.000 4.07 0.00 46.46 2.90
377 437 5.601662 TCCCATGAATCAGACGATCTAAAC 58.398 41.667 0.00 0.00 0.00 2.01
414 474 7.890127 TCAAATCCACATACTCCATTTCTTCTT 59.110 33.333 0.00 0.00 0.00 2.52
431 491 9.683069 ATTTCTTCTTTGTAAAGTGCTATTGTG 57.317 29.630 4.45 0.00 37.31 3.33
432 492 8.445275 TTCTTCTTTGTAAAGTGCTATTGTGA 57.555 30.769 4.45 0.00 37.31 3.58
433 493 8.087982 TCTTCTTTGTAAAGTGCTATTGTGAG 57.912 34.615 4.45 0.00 37.31 3.51
434 494 6.241207 TCTTTGTAAAGTGCTATTGTGAGC 57.759 37.500 4.45 0.00 37.59 4.26
435 495 5.181245 TCTTTGTAAAGTGCTATTGTGAGCC 59.819 40.000 4.45 0.00 36.91 4.70
436 496 3.343617 TGTAAAGTGCTATTGTGAGCCC 58.656 45.455 0.00 0.00 42.11 5.19
479 539 8.167345 TGATAATTTTTACACGCATGCAAATTG 58.833 29.630 23.76 15.48 31.05 2.32
509 569 5.475273 AGAATCGCATTTGTAGATGTGTG 57.525 39.130 0.00 0.00 38.39 3.82
511 571 2.355197 TCGCATTTGTAGATGTGTGGG 58.645 47.619 0.00 0.00 38.39 4.61
578 641 1.423845 GTCGGTGCGCGAAATCAAT 59.576 52.632 12.10 0.00 0.00 2.57
596 659 2.509336 GACCCACTCATCACGCGG 60.509 66.667 12.47 0.00 0.00 6.46
700 1590 1.076332 GAATTCACCACCTTCGTCCG 58.924 55.000 0.00 0.00 0.00 4.79
751 1645 2.938869 GCAGCTAGCTTTTGACAAAGG 58.061 47.619 16.46 5.71 40.03 3.11
789 1694 1.421268 AGCAAAGACAGTGTCCCATCA 59.579 47.619 19.71 0.00 32.18 3.07
790 1695 1.808945 GCAAAGACAGTGTCCCATCAG 59.191 52.381 19.71 5.65 32.18 2.90
791 1696 2.811873 GCAAAGACAGTGTCCCATCAGT 60.812 50.000 19.71 0.00 32.18 3.41
792 1697 3.070018 CAAAGACAGTGTCCCATCAGTC 58.930 50.000 19.71 0.00 32.18 3.51
793 1698 2.015456 AGACAGTGTCCCATCAGTCA 57.985 50.000 19.71 0.00 32.18 3.41
794 1699 1.620819 AGACAGTGTCCCATCAGTCAC 59.379 52.381 19.71 0.00 32.18 3.67
825 1782 2.726821 AGTGTGCTCCATTATTGGTGG 58.273 47.619 3.65 0.00 44.06 4.61
881 1838 0.696501 ACACCAACCATACCACCTCC 59.303 55.000 0.00 0.00 0.00 4.30
882 1839 0.034477 CACCAACCATACCACCTCCC 60.034 60.000 0.00 0.00 0.00 4.30
883 1840 0.178843 ACCAACCATACCACCTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
884 1841 0.255890 CCAACCATACCACCTCCCTG 59.744 60.000 0.00 0.00 0.00 4.45
885 1842 0.394352 CAACCATACCACCTCCCTGC 60.394 60.000 0.00 0.00 0.00 4.85
918 1875 7.628794 GCTTCTTCGTCTCTTCCTAATCAGTTA 60.629 40.741 0.00 0.00 0.00 2.24
932 1889 6.263168 CCTAATCAGTTAATTAGCCCACCTTG 59.737 42.308 0.00 0.00 37.73 3.61
951 1908 2.510615 GTTCATCAAAGAACGAGGCG 57.489 50.000 0.00 0.00 38.58 5.52
952 1909 1.798813 GTTCATCAAAGAACGAGGCGT 59.201 47.619 0.00 0.00 43.97 5.68
1089 2063 3.301116 GCGACGAGTACAATCTTCTCAAC 59.699 47.826 0.00 0.00 0.00 3.18
1161 2135 3.251509 TTGCTGGAGAGGCTGGCA 61.252 61.111 3.38 0.00 0.00 4.92
1307 2281 3.403038 CAAAGTTCATGAAGAGGACGGT 58.597 45.455 8.80 0.00 0.00 4.83
1367 2341 2.738000 CGACCCAGATCAAAGAGCTCAG 60.738 54.545 17.77 5.46 0.00 3.35
1430 2511 4.985538 AGCTTACTACGTACTCTTGCAT 57.014 40.909 0.00 0.00 0.00 3.96
1431 2512 4.673441 AGCTTACTACGTACTCTTGCATG 58.327 43.478 0.00 0.00 0.00 4.06
1432 2513 3.243177 GCTTACTACGTACTCTTGCATGC 59.757 47.826 11.82 11.82 0.00 4.06
1433 2514 4.421058 CTTACTACGTACTCTTGCATGCA 58.579 43.478 18.46 18.46 0.00 3.96
1434 2515 2.881074 ACTACGTACTCTTGCATGCAG 58.119 47.619 21.50 14.85 0.00 4.41
1435 2516 2.231478 ACTACGTACTCTTGCATGCAGT 59.769 45.455 21.50 17.59 0.00 4.40
1441 2529 4.493057 CGTACTCTTGCATGCAGTTGTATG 60.493 45.833 21.50 21.81 40.44 2.39
1644 2789 3.726607 CCTTGCTGATGGATGAGAGTAC 58.273 50.000 0.00 0.00 0.00 2.73
2033 3341 5.374921 CAGGCTAGATCAAATGGTCATCTT 58.625 41.667 0.00 0.00 0.00 2.40
2034 3342 5.826737 CAGGCTAGATCAAATGGTCATCTTT 59.173 40.000 0.00 0.00 0.00 2.52
2035 3343 6.994496 CAGGCTAGATCAAATGGTCATCTTTA 59.006 38.462 0.00 0.00 0.00 1.85
2146 3465 6.128445 ACAAACACTCATTCATCTTAGCTTCG 60.128 38.462 0.00 0.00 0.00 3.79
2603 5305 1.016130 CGTCTGGATGGCTGTGTGTC 61.016 60.000 0.00 0.00 0.00 3.67
2604 5306 0.035317 GTCTGGATGGCTGTGTGTCA 59.965 55.000 0.00 0.00 33.36 3.58
2606 5308 0.035881 CTGGATGGCTGTGTGTCAGT 59.964 55.000 0.00 0.00 45.23 3.41
2662 5409 5.300286 CAGGACAGAGAACAAAGGACAAAAT 59.700 40.000 0.00 0.00 0.00 1.82
2714 5515 8.192110 TCACATGAATCATTATGGTTGTCAATG 58.808 33.333 0.00 0.00 0.00 2.82
2733 5535 6.960431 GTCAATGGTTGATGTTTGTGTTTTTG 59.040 34.615 0.00 0.00 42.47 2.44
2748 6390 6.535540 TGTGTTTTTGGTGCTAGTATTAGGA 58.464 36.000 0.00 0.00 0.00 2.94
2804 6447 8.718734 GTTTAGTGGGTCAAGTAGACTTATTTG 58.281 37.037 0.00 0.00 46.72 2.32
2878 6521 2.747446 CTGTTTTCACTTACCATCGGGG 59.253 50.000 0.00 0.00 44.81 5.73
2929 6628 6.647334 TGATTGATGCAAGAAAAGGTTACA 57.353 33.333 0.00 0.00 0.00 2.41
3085 7610 7.452880 TGTATGGAAAGAACAAGATTGGAAG 57.547 36.000 0.00 0.00 0.00 3.46
3149 7674 6.948353 AGAATAATTGCTACTACACGCATTG 58.052 36.000 0.00 0.00 35.85 2.82
3196 7721 3.589988 CATATCCGATGAGCAACCCTAC 58.410 50.000 0.00 0.00 0.00 3.18
3242 7767 7.576236 TGTTGATTCTCGAAGATTGTTCTTTC 58.424 34.615 0.00 0.00 42.34 2.62
3253 7778 8.899776 CGAAGATTGTTCTTTCAGAGAATTTTG 58.100 33.333 0.00 0.00 45.66 2.44
3547 8088 8.791749 TGTATATATCCAGAGGACTCCATGATA 58.208 37.037 0.00 1.53 32.98 2.15
3673 8420 8.725148 GTTAATAGAAATATGATCCAGCCAGTG 58.275 37.037 0.00 0.00 0.00 3.66
3870 8617 0.532115 GGTGCAGTTGGGGCAATTAG 59.468 55.000 0.00 0.00 43.91 1.73
3883 8630 4.133078 GGGCAATTAGAGAGACCAAGATG 58.867 47.826 0.00 0.00 0.00 2.90
3981 8830 5.440610 GGTGTTGGATCTTGGAGATTGTAT 58.559 41.667 0.00 0.00 34.53 2.29
4030 8879 3.762288 ACATAGGAAGTTCACGTCAGCTA 59.238 43.478 5.01 0.00 0.00 3.32
4115 8964 2.670414 CACTTGGAGACTCTCGATTTGC 59.330 50.000 1.74 0.00 0.00 3.68
4124 8973 6.205076 GGAGACTCTCGATTTGCTATACTGTA 59.795 42.308 1.74 0.00 0.00 2.74
4150 9007 1.466167 CTTCCAAGACTGCCATCAACG 59.534 52.381 0.00 0.00 0.00 4.10
4154 9011 0.396435 AAGACTGCCATCAACGGTGA 59.604 50.000 5.17 5.17 38.41 4.02
4280 9149 2.368875 ACTGACGACCCAGTGAGATTTT 59.631 45.455 8.55 0.00 44.93 1.82
4320 9189 0.733909 GGCAAATGCAACCTTCGCTC 60.734 55.000 7.80 0.00 44.36 5.03
4333 9208 1.469308 CTTCGCTCTCTTCGTACTGGT 59.531 52.381 0.00 0.00 0.00 4.00
4364 9239 1.068472 CCGAGCGTCTGTTCTGTAACT 60.068 52.381 0.00 0.00 36.51 2.24
4405 9280 5.920840 GTGCCTCCAAGTTCTTAAAATTCAC 59.079 40.000 0.00 0.00 0.00 3.18
4458 9354 2.295909 CCTCCCTCGAGAATCTCATGAC 59.704 54.545 15.71 0.00 38.52 3.06
4464 9360 4.578516 CCTCGAGAATCTCATGACACTACT 59.421 45.833 15.71 0.00 0.00 2.57
4570 9466 5.532155 AGAAGAGGGGCCATTAATGAAAAT 58.468 37.500 17.23 0.00 0.00 1.82
4629 9531 0.461339 TTCCGCTTCCGCTATTCACC 60.461 55.000 0.00 0.00 0.00 4.02
4633 9535 1.017387 GCTTCCGCTATTCACCCTTG 58.983 55.000 0.00 0.00 0.00 3.61
4641 9543 0.981183 TATTCACCCTTGCGTCCTGT 59.019 50.000 0.00 0.00 0.00 4.00
4743 9681 2.577606 TTGAACCCAATGTGGATCGT 57.422 45.000 0.00 0.00 40.96 3.73
4910 9848 2.290450 TGCAGAATCCATGTCAGCAGAA 60.290 45.455 0.00 0.00 33.19 3.02
4919 9857 3.318839 CCATGTCAGCAGAACCTTTGAAA 59.681 43.478 0.00 0.00 0.00 2.69
4977 9916 2.069273 CGTCGCAAAAGAATCTCTGGT 58.931 47.619 0.00 0.00 0.00 4.00
4980 9919 3.124297 GTCGCAAAAGAATCTCTGGTGAG 59.876 47.826 0.00 0.00 41.51 3.51
4991 9930 1.203523 CTCTGGTGAGGAAAGGAGACG 59.796 57.143 0.00 0.00 36.70 4.18
5030 9969 1.073923 CCACCAAGAACTAGCCACCTT 59.926 52.381 0.00 0.00 0.00 3.50
5031 9970 2.304761 CCACCAAGAACTAGCCACCTTA 59.695 50.000 0.00 0.00 0.00 2.69
5032 9971 3.244770 CCACCAAGAACTAGCCACCTTAA 60.245 47.826 0.00 0.00 0.00 1.85
5034 9973 4.636206 CACCAAGAACTAGCCACCTTAATC 59.364 45.833 0.00 0.00 0.00 1.75
5035 9974 4.200092 CCAAGAACTAGCCACCTTAATCC 58.800 47.826 0.00 0.00 0.00 3.01
5036 9975 4.324254 CCAAGAACTAGCCACCTTAATCCA 60.324 45.833 0.00 0.00 0.00 3.41
5037 9976 4.762289 AGAACTAGCCACCTTAATCCAG 57.238 45.455 0.00 0.00 0.00 3.86
5102 10951 3.327757 TGGGACTGAACATGCTACTCTTT 59.672 43.478 0.00 0.00 0.00 2.52
5115 10964 5.620206 TGCTACTCTTTTCCACTGATTTGA 58.380 37.500 0.00 0.00 0.00 2.69
5116 10965 6.240894 TGCTACTCTTTTCCACTGATTTGAT 58.759 36.000 0.00 0.00 0.00 2.57
5127 10978 4.393680 CCACTGATTTGATGCCATTTTTGG 59.606 41.667 0.00 0.00 0.00 3.28
5284 11420 1.269448 GCATGTCGCAAAAAGGAAGGA 59.731 47.619 0.00 0.00 41.79 3.36
5285 11421 2.288152 GCATGTCGCAAAAAGGAAGGAA 60.288 45.455 0.00 0.00 41.79 3.36
5299 11435 5.333566 AGGAAGGAAGGTTGGTTATTCAA 57.666 39.130 0.00 0.00 0.00 2.69
5360 11502 9.167311 CTAAACTATCAATCTTGTGGTAAGCTT 57.833 33.333 3.48 3.48 0.00 3.74
5362 11504 6.711277 ACTATCAATCTTGTGGTAAGCTTGA 58.289 36.000 9.86 7.96 36.99 3.02
5383 11525 7.148689 GCTTGATGGCTCTGTCAAAAATAAAAG 60.149 37.037 0.00 0.00 34.26 2.27
5405 11578 3.855950 GCAGACACTAATGCTGATTTTGC 59.144 43.478 0.00 0.00 39.38 3.68
5448 13265 3.593442 TTTCAACTGAATCTGGGTGGT 57.407 42.857 0.00 0.00 33.54 4.16
5494 13336 3.614870 GCTTTTCAGCCATACACCCAAAG 60.615 47.826 0.00 0.00 40.61 2.77
5525 13367 3.708403 TGTCATCTGTTCAGAGGCAAT 57.292 42.857 9.23 0.00 0.00 3.56
5539 13381 1.180029 GGCAATCAACATCAGGCACT 58.820 50.000 0.00 0.00 43.88 4.40
5580 13458 2.499693 TCCATCTCCATTACAGCACGAA 59.500 45.455 0.00 0.00 0.00 3.85
5618 13496 5.986135 GGCAGGAAGTACAGACACATAATAG 59.014 44.000 0.00 0.00 0.00 1.73
5628 13547 9.803315 GTACAGACACATAATAGAATTCTGTCA 57.197 33.333 18.47 0.00 40.95 3.58
5663 13582 6.151648 TGAGCTTTTACTGATTTCCAGGAATG 59.848 38.462 1.58 0.00 44.77 2.67
5669 13588 4.832590 CTGATTTCCAGGAATGCATCTC 57.167 45.455 1.58 0.00 39.23 2.75
5680 13599 2.581216 ATGCATCTCCATCACCATCC 57.419 50.000 0.00 0.00 0.00 3.51
5687 13606 0.621280 TCCATCACCATCCTCTGCCA 60.621 55.000 0.00 0.00 0.00 4.92
5795 13715 1.084289 GGAAATTGAGTTCGTCCCCG 58.916 55.000 0.00 0.00 0.00 5.73
5847 13767 1.000717 TGATCAGCTTTCGTGACGACA 60.001 47.619 7.39 0.00 34.89 4.35
5858 13778 3.422655 TCGTGACGACAAATACATCGAG 58.577 45.455 2.39 0.00 40.86 4.04
5859 13779 3.125658 TCGTGACGACAAATACATCGAGA 59.874 43.478 2.39 0.00 40.86 4.04
5860 13780 4.035684 CGTGACGACAAATACATCGAGAT 58.964 43.478 0.00 0.00 40.86 2.75
5861 13781 4.499399 CGTGACGACAAATACATCGAGATT 59.501 41.667 0.00 0.00 40.86 2.40
5862 13782 5.552656 CGTGACGACAAATACATCGAGATTG 60.553 44.000 0.00 0.00 40.86 2.67
5863 13783 5.515270 GTGACGACAAATACATCGAGATTGA 59.485 40.000 0.00 0.00 40.86 2.57
5865 13785 7.378728 GTGACGACAAATACATCGAGATTGATA 59.621 37.037 0.00 0.00 40.86 2.15
5866 13786 7.591426 TGACGACAAATACATCGAGATTGATAG 59.409 37.037 0.00 0.00 40.86 2.08
5867 13787 7.649057 ACGACAAATACATCGAGATTGATAGA 58.351 34.615 0.00 0.00 40.86 1.98
5868 13788 7.805542 ACGACAAATACATCGAGATTGATAGAG 59.194 37.037 0.00 0.00 40.86 2.43
5869 13789 7.805542 CGACAAATACATCGAGATTGATAGAGT 59.194 37.037 0.00 0.00 40.86 3.24
5870 13790 9.469807 GACAAATACATCGAGATTGATAGAGTT 57.530 33.333 0.00 0.00 0.00 3.01
5905 13825 7.826918 AAAAATGGTGCTAGGTACTGTTAAA 57.173 32.000 0.00 0.00 41.52 1.52
5906 13826 6.812879 AAATGGTGCTAGGTACTGTTAAAC 57.187 37.500 0.00 0.00 41.52 2.01
5907 13827 4.959560 TGGTGCTAGGTACTGTTAAACA 57.040 40.909 0.00 0.00 41.52 2.83
5909 13829 4.101274 TGGTGCTAGGTACTGTTAAACACA 59.899 41.667 0.00 0.00 41.52 3.72
5910 13830 5.221762 TGGTGCTAGGTACTGTTAAACACAT 60.222 40.000 0.00 0.00 41.52 3.21
5912 13832 7.046033 GGTGCTAGGTACTGTTAAACACATAT 58.954 38.462 0.00 0.00 41.52 1.78
5913 13833 7.551617 GGTGCTAGGTACTGTTAAACACATATT 59.448 37.037 0.00 0.00 41.52 1.28
5915 13835 8.315482 TGCTAGGTACTGTTAAACACATATTCA 58.685 33.333 0.00 0.00 41.52 2.57
5916 13836 9.326413 GCTAGGTACTGTTAAACACATATTCAT 57.674 33.333 0.00 0.00 41.52 2.57
5919 13839 9.162764 AGGTACTGTTAAACACATATTCATGTC 57.837 33.333 0.00 0.00 39.86 3.06
5920 13840 8.941977 GGTACTGTTAAACACATATTCATGTCA 58.058 33.333 0.00 0.00 43.73 3.58
5921 13841 9.755064 GTACTGTTAAACACATATTCATGTCAC 57.245 33.333 0.00 0.00 43.73 3.67
5922 13842 7.518161 ACTGTTAAACACATATTCATGTCACG 58.482 34.615 0.00 0.00 43.73 4.35
5924 13844 7.866729 TGTTAAACACATATTCATGTCACGTT 58.133 30.769 0.00 0.00 43.73 3.99
5925 13845 7.800847 TGTTAAACACATATTCATGTCACGTTG 59.199 33.333 0.00 0.00 43.73 4.10
5926 13846 4.944962 ACACATATTCATGTCACGTTGG 57.055 40.909 0.00 0.00 43.73 3.77
5927 13847 4.574892 ACACATATTCATGTCACGTTGGA 58.425 39.130 0.00 0.00 43.73 3.53
5928 13848 4.631377 ACACATATTCATGTCACGTTGGAG 59.369 41.667 0.00 0.00 43.73 3.86
5931 13851 5.810587 ACATATTCATGTCACGTTGGAGTAC 59.189 40.000 0.00 0.00 41.75 2.73
5932 13852 3.737032 TTCATGTCACGTTGGAGTACA 57.263 42.857 0.00 0.00 0.00 2.90
5933 13853 3.297830 TCATGTCACGTTGGAGTACAG 57.702 47.619 0.00 0.00 0.00 2.74
5935 13855 1.405872 TGTCACGTTGGAGTACAGGT 58.594 50.000 0.00 0.00 0.00 4.00
5936 13856 1.758280 TGTCACGTTGGAGTACAGGTT 59.242 47.619 0.00 0.00 0.00 3.50
5937 13857 2.168936 TGTCACGTTGGAGTACAGGTTT 59.831 45.455 0.00 0.00 0.00 3.27
5939 13859 1.790623 CACGTTGGAGTACAGGTTTCG 59.209 52.381 0.00 0.00 0.00 3.46
5941 13861 0.788391 GTTGGAGTACAGGTTTCGCG 59.212 55.000 0.00 0.00 0.00 5.87
5942 13862 0.947180 TTGGAGTACAGGTTTCGCGC 60.947 55.000 0.00 0.00 0.00 6.86
5943 13863 1.373748 GGAGTACAGGTTTCGCGCA 60.374 57.895 8.75 0.00 0.00 6.09
5944 13864 1.623973 GGAGTACAGGTTTCGCGCAC 61.624 60.000 8.75 0.00 0.00 5.34
5947 13867 0.110823 GTACAGGTTTCGCGCACAAG 60.111 55.000 8.75 0.00 0.00 3.16
5948 13868 1.225376 TACAGGTTTCGCGCACAAGG 61.225 55.000 8.75 0.00 0.00 3.61
5949 13869 2.110213 AGGTTTCGCGCACAAGGA 59.890 55.556 8.75 0.00 0.00 3.36
5952 13872 1.204312 GTTTCGCGCACAAGGAGAC 59.796 57.895 8.75 0.00 0.00 3.36
5953 13873 2.307309 TTTCGCGCACAAGGAGACG 61.307 57.895 8.75 0.00 0.00 4.18
5954 13874 2.964438 TTTCGCGCACAAGGAGACGT 62.964 55.000 8.75 0.00 0.00 4.34
5955 13875 3.470567 CGCGCACAAGGAGACGTC 61.471 66.667 7.70 7.70 0.00 4.34
5956 13876 3.112709 GCGCACAAGGAGACGTCC 61.113 66.667 13.01 3.55 44.33 4.79
5957 13877 2.338620 CGCACAAGGAGACGTCCA 59.661 61.111 13.01 0.00 46.80 4.02
5959 13879 1.374758 GCACAAGGAGACGTCCAGG 60.375 63.158 13.01 0.18 46.80 4.45
5960 13880 1.816863 GCACAAGGAGACGTCCAGGA 61.817 60.000 13.01 0.00 46.80 3.86
5961 13881 0.244994 CACAAGGAGACGTCCAGGAG 59.755 60.000 13.01 2.54 46.80 3.69
5962 13882 0.112606 ACAAGGAGACGTCCAGGAGA 59.887 55.000 13.01 0.00 46.80 3.71
5964 13884 2.025226 ACAAGGAGACGTCCAGGAGATA 60.025 50.000 13.01 0.00 46.80 1.98
5966 13886 2.128535 AGGAGACGTCCAGGAGATAGA 58.871 52.381 13.01 0.00 46.80 1.98
5967 13887 2.158726 AGGAGACGTCCAGGAGATAGAC 60.159 54.545 13.01 0.00 46.80 2.59
5968 13888 2.158726 GGAGACGTCCAGGAGATAGACT 60.159 54.545 13.01 0.00 43.31 3.24
5969 13889 3.071312 GGAGACGTCCAGGAGATAGACTA 59.929 52.174 13.01 0.00 43.31 2.59
5970 13890 4.312443 GAGACGTCCAGGAGATAGACTAG 58.688 52.174 13.01 0.00 0.00 2.57
5972 13892 2.778850 ACGTCCAGGAGATAGACTAGGT 59.221 50.000 0.00 0.00 0.00 3.08
5974 13894 3.566322 CGTCCAGGAGATAGACTAGGTTG 59.434 52.174 0.00 0.00 0.00 3.77
5975 13895 4.538738 GTCCAGGAGATAGACTAGGTTGT 58.461 47.826 0.00 0.00 0.00 3.32
5976 13896 4.957327 GTCCAGGAGATAGACTAGGTTGTT 59.043 45.833 0.00 0.00 0.00 2.83
5979 13899 6.159928 TCCAGGAGATAGACTAGGTTGTTAGA 59.840 42.308 0.00 0.00 0.00 2.10
5980 13900 6.263617 CCAGGAGATAGACTAGGTTGTTAGAC 59.736 46.154 0.00 0.00 0.00 2.59
5981 13901 6.829298 CAGGAGATAGACTAGGTTGTTAGACA 59.171 42.308 0.00 0.00 0.00 3.41
5982 13902 7.339721 CAGGAGATAGACTAGGTTGTTAGACAA 59.660 40.741 0.00 0.00 35.42 3.18
5983 13903 7.558444 AGGAGATAGACTAGGTTGTTAGACAAG 59.442 40.741 0.00 0.00 39.00 3.16
5984 13904 7.339976 GGAGATAGACTAGGTTGTTAGACAAGT 59.660 40.741 0.00 0.00 39.00 3.16
5985 13905 9.393512 GAGATAGACTAGGTTGTTAGACAAGTA 57.606 37.037 0.00 0.00 39.00 2.24
5986 13906 9.398538 AGATAGACTAGGTTGTTAGACAAGTAG 57.601 37.037 0.00 2.13 39.00 2.57
5988 13908 7.836479 AGACTAGGTTGTTAGACAAGTAGTT 57.164 36.000 13.10 5.51 39.00 2.24
5989 13909 7.884257 AGACTAGGTTGTTAGACAAGTAGTTC 58.116 38.462 13.10 8.98 39.00 3.01
5990 13910 7.504911 AGACTAGGTTGTTAGACAAGTAGTTCA 59.495 37.037 13.10 0.00 39.00 3.18
5991 13911 8.015185 ACTAGGTTGTTAGACAAGTAGTTCAA 57.985 34.615 0.00 0.00 39.00 2.69
5992 13912 8.648693 ACTAGGTTGTTAGACAAGTAGTTCAAT 58.351 33.333 0.00 0.00 39.00 2.57
5995 13915 9.654663 AGGTTGTTAGACAAGTAGTTCAATATC 57.345 33.333 0.00 0.00 39.00 1.63
5996 13916 9.654663 GGTTGTTAGACAAGTAGTTCAATATCT 57.345 33.333 0.00 0.00 39.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 192 1.234821 TTCATCGGTGAAACACTGCC 58.765 50.000 9.09 0.00 41.22 4.85
366 426 6.570692 TGAATCCTAGTTGGTTTAGATCGTC 58.429 40.000 0.00 0.00 37.07 4.20
414 474 3.756434 GGGCTCACAATAGCACTTTACAA 59.244 43.478 0.00 0.00 42.89 2.41
509 569 6.868339 CGGAGCATCAATTTTATTATTTCCCC 59.132 38.462 0.00 0.00 36.25 4.81
511 571 8.567948 TCTCGGAGCATCAATTTTATTATTTCC 58.432 33.333 0.00 0.00 36.25 3.13
578 641 2.261361 CGCGTGATGAGTGGGTCA 59.739 61.111 0.00 0.00 40.38 4.02
639 1522 2.029828 GCATCTCGAGAATACCGATGGT 60.030 50.000 20.91 0.00 40.16 3.55
640 1523 2.600731 GCATCTCGAGAATACCGATGG 58.399 52.381 20.91 2.13 35.35 3.51
682 1565 0.682852 TCGGACGAAGGTGGTGAATT 59.317 50.000 0.00 0.00 0.00 2.17
700 1590 1.498865 CTGTTGCTGTGTGGACGGTC 61.499 60.000 0.00 0.00 0.00 4.79
782 1676 3.381983 AGCGCGTGACTGATGGGA 61.382 61.111 8.43 0.00 0.00 4.37
789 1694 3.341043 CTTGTGCAGCGCGTGACT 61.341 61.111 8.43 0.00 0.00 3.41
790 1695 3.640000 ACTTGTGCAGCGCGTGAC 61.640 61.111 8.43 0.00 0.00 3.67
791 1696 3.639008 CACTTGTGCAGCGCGTGA 61.639 61.111 8.43 0.00 0.00 4.35
792 1697 3.940640 ACACTTGTGCAGCGCGTG 61.941 61.111 8.43 11.23 0.00 5.34
793 1698 3.940640 CACACTTGTGCAGCGCGT 61.941 61.111 8.43 0.00 39.39 6.01
838 1795 0.041833 TGGTGGAGGAAGAGGAGGAG 59.958 60.000 0.00 0.00 0.00 3.69
839 1796 0.252284 GTGGTGGAGGAAGAGGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
840 1797 1.268283 GGTGGTGGAGGAAGAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
882 1839 0.320247 ACGAAGAAGCCTGTGAGCAG 60.320 55.000 0.00 0.00 42.22 4.24
883 1840 0.319900 GACGAAGAAGCCTGTGAGCA 60.320 55.000 0.00 0.00 34.23 4.26
884 1841 0.037790 AGACGAAGAAGCCTGTGAGC 60.038 55.000 0.00 0.00 0.00 4.26
885 1842 1.543802 AGAGACGAAGAAGCCTGTGAG 59.456 52.381 0.00 0.00 0.00 3.51
918 1875 4.046286 TGATGAACAAGGTGGGCTAATT 57.954 40.909 0.00 0.00 0.00 1.40
932 1889 1.798813 ACGCCTCGTTCTTTGATGAAC 59.201 47.619 0.00 0.00 36.35 3.18
946 1903 1.064952 GTTCTCTCTAGCTCACGCCTC 59.935 57.143 0.00 0.00 36.60 4.70
947 1904 1.099689 GTTCTCTCTAGCTCACGCCT 58.900 55.000 0.00 0.00 36.60 5.52
948 1905 0.248296 CGTTCTCTCTAGCTCACGCC 60.248 60.000 0.00 0.00 36.60 5.68
951 1908 0.101579 GGGCGTTCTCTCTAGCTCAC 59.898 60.000 0.00 0.00 0.00 3.51
952 1909 0.033991 AGGGCGTTCTCTCTAGCTCA 60.034 55.000 0.00 0.00 31.38 4.26
1089 2063 3.447025 GATCTCCTTGCGGACCCGG 62.447 68.421 10.70 0.00 40.19 5.73
1161 2135 2.808919 TCGAGTTTCTCCTCCATGTCT 58.191 47.619 0.00 0.00 0.00 3.41
1307 2281 4.742201 GAGTCTTGAGCCGGCGCA 62.742 66.667 30.00 30.00 37.52 6.09
1367 2341 2.279120 CCTCCATGACGCGAGCTC 60.279 66.667 15.93 2.73 0.00 4.09
1430 2511 2.290197 TGCATCCAGACATACAACTGCA 60.290 45.455 0.00 0.00 36.15 4.41
1431 2512 2.358957 TGCATCCAGACATACAACTGC 58.641 47.619 0.00 0.00 33.40 4.40
1432 2513 3.181517 CGTTGCATCCAGACATACAACTG 60.182 47.826 0.00 0.00 36.21 3.16
1433 2514 3.002791 CGTTGCATCCAGACATACAACT 58.997 45.455 0.00 0.00 36.21 3.16
1434 2515 2.742053 ACGTTGCATCCAGACATACAAC 59.258 45.455 0.00 0.00 35.28 3.32
1435 2516 2.741517 CACGTTGCATCCAGACATACAA 59.258 45.455 0.00 0.00 0.00 2.41
1441 2529 2.015736 ATCTCACGTTGCATCCAGAC 57.984 50.000 0.00 0.00 0.00 3.51
1644 2789 0.588252 CGGCACCACTTTCAACTCTG 59.412 55.000 0.00 0.00 0.00 3.35
2035 3343 9.765795 GGAACTAAACATACTCAATACAGCTAT 57.234 33.333 0.00 0.00 0.00 2.97
2251 4344 7.653713 CACCAATCGAGCTATTAGTAAGAACAT 59.346 37.037 0.00 0.00 0.00 2.71
2253 4346 7.201145 TCACCAATCGAGCTATTAGTAAGAAC 58.799 38.462 0.00 0.00 0.00 3.01
2254 4347 7.342769 TCACCAATCGAGCTATTAGTAAGAA 57.657 36.000 0.00 0.00 0.00 2.52
2255 4348 6.954487 TCACCAATCGAGCTATTAGTAAGA 57.046 37.500 0.00 0.00 0.00 2.10
2508 5210 4.794248 TCGATTTATTGCATCACCTTCG 57.206 40.909 0.00 0.00 0.00 3.79
2603 5305 4.332637 GCCGCCTTGCACACACTG 62.333 66.667 0.00 0.00 0.00 3.66
2604 5306 4.873810 TGCCGCCTTGCACACACT 62.874 61.111 0.00 0.00 36.04 3.55
2714 5515 4.436718 GCACCAAAAACACAAACATCAACC 60.437 41.667 0.00 0.00 0.00 3.77
2733 5535 5.961396 TCTCGAATCCTAATACTAGCACC 57.039 43.478 0.00 0.00 0.00 5.01
2748 6390 7.012327 TGTCAAGTTTGAGTTTCAATCTCGAAT 59.988 33.333 2.08 0.00 35.90 3.34
3085 7610 1.337167 GGAAATGCTGCCTTGACCAAC 60.337 52.381 0.00 0.00 0.00 3.77
3149 7674 2.140717 ACATAAATTAGCTACGCCGGC 58.859 47.619 19.07 19.07 0.00 6.13
3196 7721 3.565764 TCATCTAGAGGTGCCATTTGG 57.434 47.619 4.02 0.00 38.53 3.28
3253 7778 7.550551 TCAGAAGGACATGAATCATTTGAGTAC 59.449 37.037 0.00 0.00 0.00 2.73
3319 7844 9.279778 AATGTAATTATAGCCAGTGGCAGTCCT 62.280 40.741 34.94 17.17 43.63 3.85
3562 8302 5.595542 TCCTTCTGCTATCCATTTCCATTTG 59.404 40.000 0.00 0.00 0.00 2.32
3673 8420 6.982141 TCACCGAACTGTCATAATTACCATAC 59.018 38.462 0.00 0.00 0.00 2.39
3870 8617 3.431572 GCGAATATGCATCTTGGTCTCTC 59.568 47.826 0.19 0.00 34.15 3.20
3883 8630 3.310774 ACACAGTCAATGAGCGAATATGC 59.689 43.478 0.00 0.00 0.00 3.14
3981 8830 4.213564 ACATGCTTGTTTTCCAACCAAA 57.786 36.364 0.00 0.00 29.55 3.28
4007 8856 2.924290 GCTGACGTGAACTTCCTATGTC 59.076 50.000 0.00 0.00 0.00 3.06
4030 8879 2.175202 TGGCCAATTCGCAAATACCTT 58.825 42.857 0.61 0.00 0.00 3.50
4115 8964 9.307121 CAGTCTTGGAAGTGAATTACAGTATAG 57.693 37.037 0.00 0.00 31.72 1.31
4124 8973 3.228188 TGGCAGTCTTGGAAGTGAATT 57.772 42.857 0.00 0.00 0.00 2.17
4280 9149 2.426024 CCGACTCATTTACTTCCTCCGA 59.574 50.000 0.00 0.00 0.00 4.55
4320 9189 2.712709 TCTCTCCACCAGTACGAAGAG 58.287 52.381 0.00 0.00 0.00 2.85
4333 9208 1.152943 ACGCTCGGCTATCTCTCCA 60.153 57.895 0.00 0.00 0.00 3.86
4364 9239 0.744057 CACGGGTATGTGCAGCATGA 60.744 55.000 0.00 0.00 39.69 3.07
4458 9354 3.014623 TCCGTGACCTGTATGAGTAGTG 58.985 50.000 0.00 0.00 0.00 2.74
4464 9360 4.545208 TCAAATTCCGTGACCTGTATGA 57.455 40.909 0.00 0.00 0.00 2.15
4570 9466 3.832527 TCCATCACTACCGATGATCAGA 58.167 45.455 0.09 0.00 44.67 3.27
4629 9531 1.002468 CTTCAACAACAGGACGCAAGG 60.002 52.381 0.00 0.00 46.39 3.61
4633 9535 1.295792 TCACTTCAACAACAGGACGC 58.704 50.000 0.00 0.00 0.00 5.19
4641 9543 2.164624 CCCGTTGGTTTCACTTCAACAA 59.835 45.455 0.00 0.00 40.31 2.83
4919 9857 8.877864 TCCTTGTCATCCTTAAACATGTAATT 57.122 30.769 0.00 0.00 0.00 1.40
4977 9916 3.156288 TCTTCTCGTCTCCTTTCCTCA 57.844 47.619 0.00 0.00 0.00 3.86
4980 9919 4.158764 TCTCATTCTTCTCGTCTCCTTTCC 59.841 45.833 0.00 0.00 0.00 3.13
4991 9930 4.381505 GGTGGTCACTCTCTCATTCTTCTC 60.382 50.000 0.93 0.00 0.00 2.87
5030 9969 6.061022 TCATTTGAGTTACCAGCTGGATTA 57.939 37.500 39.19 19.30 38.94 1.75
5031 9970 4.922206 TCATTTGAGTTACCAGCTGGATT 58.078 39.130 39.19 20.47 38.94 3.01
5032 9971 4.574674 TCATTTGAGTTACCAGCTGGAT 57.425 40.909 39.19 24.04 38.94 3.41
5034 9973 6.949352 ATTATCATTTGAGTTACCAGCTGG 57.051 37.500 31.60 31.60 42.17 4.85
5035 9974 7.988737 TCAATTATCATTTGAGTTACCAGCTG 58.011 34.615 6.78 6.78 0.00 4.24
5036 9975 8.579850 TTCAATTATCATTTGAGTTACCAGCT 57.420 30.769 0.00 0.00 34.76 4.24
5037 9976 8.462016 ACTTCAATTATCATTTGAGTTACCAGC 58.538 33.333 0.00 0.00 34.76 4.85
5102 10951 5.486735 AAAATGGCATCAAATCAGTGGAA 57.513 34.783 0.00 0.00 0.00 3.53
5115 10964 5.100344 TGCATTCATACCAAAAATGGCAT 57.900 34.783 0.00 0.00 32.31 4.40
5116 10965 4.020396 ACTGCATTCATACCAAAAATGGCA 60.020 37.500 0.00 0.00 32.31 4.92
5233 11366 7.290248 AGGTTATACAGCCATACATTACTGACT 59.710 37.037 0.00 0.00 34.25 3.41
5284 11420 4.772100 CACCCTGATTGAATAACCAACCTT 59.228 41.667 0.00 0.00 0.00 3.50
5285 11421 4.344104 CACCCTGATTGAATAACCAACCT 58.656 43.478 0.00 0.00 0.00 3.50
5299 11435 0.687757 TAGGCTTCGAGCACCCTGAT 60.688 55.000 0.00 0.00 44.75 2.90
5360 11502 6.158598 GCTTTTATTTTTGACAGAGCCATCA 58.841 36.000 0.00 0.00 0.00 3.07
5362 11504 6.015180 TCTGCTTTTATTTTTGACAGAGCCAT 60.015 34.615 0.00 0.00 0.00 4.40
5383 11525 3.855950 GCAAAATCAGCATTAGTGTCTGC 59.144 43.478 5.27 0.00 38.69 4.26
5414 13231 6.882610 TCAGTTGAAATTACAAGAGCATGT 57.117 33.333 0.00 0.00 37.32 3.21
5448 13265 6.312918 GCTTGAACGTTACTATGGAATCTTGA 59.687 38.462 0.00 0.00 0.00 3.02
5539 13381 6.219417 TGGAAAGAAAGCAGAATTTCAACA 57.781 33.333 0.00 0.00 40.86 3.33
5580 13458 1.899814 TCCTGCCGTCAGTGTTAAGAT 59.100 47.619 0.00 0.00 38.66 2.40
5618 13496 4.005650 TCATCTTGGCTGTGACAGAATTC 58.994 43.478 18.18 0.00 32.44 2.17
5628 13547 3.755378 CAGTAAAAGCTCATCTTGGCTGT 59.245 43.478 0.00 0.00 38.91 4.40
5663 13582 1.698532 AGAGGATGGTGATGGAGATGC 59.301 52.381 0.00 0.00 0.00 3.91
5669 13588 0.179026 CTGGCAGAGGATGGTGATGG 60.179 60.000 9.42 0.00 0.00 3.51
5680 13599 0.809385 CATGCAAACTCCTGGCAGAG 59.191 55.000 17.94 13.67 41.40 3.35
5687 13606 2.641305 GAGATGAGCATGCAAACTCCT 58.359 47.619 21.98 8.67 31.65 3.69
5722 13641 7.897575 AAGAAAGTCTGCAGTCAGTATAAAG 57.102 36.000 14.67 0.00 41.10 1.85
5723 13642 9.587772 GATAAGAAAGTCTGCAGTCAGTATAAA 57.412 33.333 14.67 0.00 41.10 1.40
5725 13644 7.342026 TGGATAAGAAAGTCTGCAGTCAGTATA 59.658 37.037 14.67 1.27 41.10 1.47
5727 13646 5.480422 TGGATAAGAAAGTCTGCAGTCAGTA 59.520 40.000 14.67 1.26 41.10 2.74
5728 13647 4.284490 TGGATAAGAAAGTCTGCAGTCAGT 59.716 41.667 14.67 0.00 41.10 3.41
5729 13648 4.825422 TGGATAAGAAAGTCTGCAGTCAG 58.175 43.478 14.67 0.00 41.67 3.51
5795 13715 6.929606 AGGTTGGCGATATATAGTTTCTTGAC 59.070 38.462 0.00 0.00 0.00 3.18
5882 13802 6.773685 TGTTTAACAGTACCTAGCACCATTTT 59.226 34.615 0.00 0.00 0.00 1.82
5883 13803 6.206048 GTGTTTAACAGTACCTAGCACCATTT 59.794 38.462 0.00 0.00 0.00 2.32
5885 13805 5.221762 TGTGTTTAACAGTACCTAGCACCAT 60.222 40.000 0.00 0.00 33.78 3.55
5886 13806 4.101274 TGTGTTTAACAGTACCTAGCACCA 59.899 41.667 0.00 0.00 33.78 4.17
5887 13807 4.634199 TGTGTTTAACAGTACCTAGCACC 58.366 43.478 0.00 0.00 33.78 5.01
5889 13809 8.315482 TGAATATGTGTTTAACAGTACCTAGCA 58.685 33.333 0.00 0.00 43.64 3.49
5890 13810 8.712285 TGAATATGTGTTTAACAGTACCTAGC 57.288 34.615 0.00 0.00 43.64 3.42
5909 13829 5.972935 TGTACTCCAACGTGACATGAATAT 58.027 37.500 0.00 0.00 0.00 1.28
5910 13830 5.394224 TGTACTCCAACGTGACATGAATA 57.606 39.130 0.00 0.00 0.00 1.75
5912 13832 3.554129 CCTGTACTCCAACGTGACATGAA 60.554 47.826 0.00 0.00 0.00 2.57
5913 13833 2.029380 CCTGTACTCCAACGTGACATGA 60.029 50.000 0.00 0.00 0.00 3.07
5915 13835 1.968493 ACCTGTACTCCAACGTGACAT 59.032 47.619 0.00 0.00 0.00 3.06
5916 13836 1.405872 ACCTGTACTCCAACGTGACA 58.594 50.000 0.00 0.00 0.00 3.58
5917 13837 2.521105 AACCTGTACTCCAACGTGAC 57.479 50.000 0.00 0.00 0.00 3.67
5919 13839 1.790623 CGAAACCTGTACTCCAACGTG 59.209 52.381 0.00 0.00 0.00 4.49
5920 13840 1.870993 GCGAAACCTGTACTCCAACGT 60.871 52.381 0.00 0.00 0.00 3.99
5921 13841 0.788391 GCGAAACCTGTACTCCAACG 59.212 55.000 0.00 0.00 0.00 4.10
5922 13842 0.788391 CGCGAAACCTGTACTCCAAC 59.212 55.000 0.00 0.00 0.00 3.77
5924 13844 1.373748 GCGCGAAACCTGTACTCCA 60.374 57.895 12.10 0.00 0.00 3.86
5925 13845 1.373748 TGCGCGAAACCTGTACTCC 60.374 57.895 12.10 0.00 0.00 3.85
5926 13846 0.942410 TGTGCGCGAAACCTGTACTC 60.942 55.000 12.10 0.00 0.00 2.59
5927 13847 0.531090 TTGTGCGCGAAACCTGTACT 60.531 50.000 12.10 0.00 0.00 2.73
5928 13848 0.110823 CTTGTGCGCGAAACCTGTAC 60.111 55.000 12.10 0.00 0.00 2.90
5931 13851 2.175184 CTCCTTGTGCGCGAAACCTG 62.175 60.000 12.10 2.62 0.00 4.00
5932 13852 1.961277 CTCCTTGTGCGCGAAACCT 60.961 57.895 12.10 0.00 0.00 3.50
5933 13853 1.959226 TCTCCTTGTGCGCGAAACC 60.959 57.895 12.10 0.00 0.00 3.27
5935 13855 2.307309 CGTCTCCTTGTGCGCGAAA 61.307 57.895 12.10 0.00 0.00 3.46
5936 13856 2.733218 CGTCTCCTTGTGCGCGAA 60.733 61.111 12.10 0.00 0.00 4.70
5937 13857 3.891586 GACGTCTCCTTGTGCGCGA 62.892 63.158 12.10 0.00 0.00 5.87
5939 13859 3.112709 GGACGTCTCCTTGTGCGC 61.113 66.667 16.46 0.00 33.07 6.09
5941 13861 1.374758 CCTGGACGTCTCCTTGTGC 60.375 63.158 16.46 0.00 37.48 4.57
5942 13862 0.244994 CTCCTGGACGTCTCCTTGTG 59.755 60.000 16.46 0.00 37.48 3.33
5943 13863 0.112606 TCTCCTGGACGTCTCCTTGT 59.887 55.000 16.46 0.00 37.48 3.16
5944 13864 1.479709 ATCTCCTGGACGTCTCCTTG 58.520 55.000 16.46 3.96 37.48 3.61
5947 13867 2.158726 AGTCTATCTCCTGGACGTCTCC 60.159 54.545 16.46 0.00 40.14 3.71
5948 13868 3.202829 AGTCTATCTCCTGGACGTCTC 57.797 52.381 16.46 6.30 40.14 3.36
5949 13869 3.071892 CCTAGTCTATCTCCTGGACGTCT 59.928 52.174 16.46 0.00 40.14 4.18
5952 13872 3.495434 ACCTAGTCTATCTCCTGGACG 57.505 52.381 0.00 0.00 40.14 4.79
5953 13873 4.538738 ACAACCTAGTCTATCTCCTGGAC 58.461 47.826 0.00 0.00 35.67 4.02
5954 13874 4.883021 ACAACCTAGTCTATCTCCTGGA 57.117 45.455 0.00 0.00 0.00 3.86
5955 13875 6.263617 GTCTAACAACCTAGTCTATCTCCTGG 59.736 46.154 0.00 0.00 0.00 4.45
5956 13876 6.829298 TGTCTAACAACCTAGTCTATCTCCTG 59.171 42.308 0.00 0.00 0.00 3.86
5957 13877 6.971340 TGTCTAACAACCTAGTCTATCTCCT 58.029 40.000 0.00 0.00 0.00 3.69
5959 13879 8.283699 ACTTGTCTAACAACCTAGTCTATCTC 57.716 38.462 0.00 0.00 33.96 2.75
5960 13880 9.398538 CTACTTGTCTAACAACCTAGTCTATCT 57.601 37.037 0.00 0.00 33.96 1.98
5961 13881 9.176460 ACTACTTGTCTAACAACCTAGTCTATC 57.824 37.037 0.00 0.00 33.96 2.08
5962 13882 9.531158 AACTACTTGTCTAACAACCTAGTCTAT 57.469 33.333 6.15 0.00 33.96 1.98
5964 13884 7.504911 TGAACTACTTGTCTAACAACCTAGTCT 59.495 37.037 6.15 0.00 33.96 3.24
5966 13886 7.592885 TGAACTACTTGTCTAACAACCTAGT 57.407 36.000 0.00 0.00 33.96 2.57
5969 13889 9.654663 GATATTGAACTACTTGTCTAACAACCT 57.345 33.333 0.00 0.00 33.96 3.50
5970 13890 9.654663 AGATATTGAACTACTTGTCTAACAACC 57.345 33.333 0.00 0.00 33.96 3.77


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

AutoCloner maintained by Alex Coulton.