Multiple sequence alignment - TraesCS4A01G238000

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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 TraesCS4A01G238000 chr4A 100.000 2486 0 0 538 3023 547199963 547202448 0.000000e+00 4591.0
1 TraesCS4A01G238000 chr4A 100.000 314 0 0 1 314 547199426 547199739 5.620000e-162 580.0
2 TraesCS4A01G238000 chr4A 99.510 204 1 0 2323 2526 547201546 547201749 3.680000e-99 372.0
3 TraesCS4A01G238000 chr4A 99.510 204 1 0 2121 2324 547201748 547201951 3.680000e-99 372.0
4 TraesCS4A01G238000 chr4B 92.904 1818 91 10 538 2327 73474200 73472393 0.000000e+00 2608.0
5 TraesCS4A01G238000 chr4B 90.240 707 59 6 2323 3020 73472602 73471897 0.000000e+00 915.0
6 TraesCS4A01G238000 chr4B 89.823 226 13 5 91 314 73474447 73474230 6.380000e-72 281.0
7 TraesCS4A01G238000 chr4D 90.296 1824 92 21 540 2327 49893897 49892123 0.000000e+00 2309.0
8 TraesCS4A01G238000 chr4D 90.268 709 58 8 2323 3022 49892332 49891626 0.000000e+00 917.0
9 TraesCS4A01G238000 chr4D 95.528 246 5 4 71 314 49894171 49893930 3.650000e-104 388.0
10 TraesCS4A01G238000 chr4D 94.444 180 7 1 49 228 49909461 49909285 1.070000e-69 274.0
11 TraesCS4A01G238000 chr4D 93.989 183 7 2 49 231 49913377 49913199 1.070000e-69 274.0
12 TraesCS4A01G238000 chr4D 93.443 183 8 2 49 231 49916687 49916509 4.970000e-68 268.0
13 TraesCS4A01G238000 chr4D 95.294 170 3 2 49 218 49911245 49911081 6.430000e-67 265.0
14 TraesCS4A01G238000 chr4D 100.000 32 0 0 49 80 49908103 49908072 3.250000e-05 60.2


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 TraesCS4A01G238000 chr4A 547199426 547202448 3022 False 1478.750000 4591 99.755000 1 3023 4 chr4A.!!$F1 3022
1 TraesCS4A01G238000 chr4B 73471897 73474447 2550 True 1268.000000 2608 90.989000 91 3020 3 chr4B.!!$R1 2929
2 TraesCS4A01G238000 chr4D 49891626 49894171 2545 True 1204.666667 2309 92.030667 71 3022 3 chr4D.!!$R1 2951
3 TraesCS4A01G238000 chr4D 49908072 49916687 8615 True 228.240000 274 95.434000 49 231 5 chr4D.!!$R2 182

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
169 5611 0.249699 CCTCCCAAAACCGGCAAAAC 60.250 55.0 0.0 0.0 0.00 2.43 F
1365 8901 0.597637 CATCGGTAGGCGATGGTGAC 60.598 60.0 0.0 0.0 39.41 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 9095 0.034756 CGTCCATCACACCACCTTCA 59.965 55.0 0.00 0.0 0.0 3.02 R
2474 10028 0.109597 GAATTGCTGCAACCTGGACG 60.110 55.0 18.51 0.0 0.0 4.79 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
18 19 4.704103 TCCTGCCCGAGGACTGCT 62.704 66.667 0.00 0.00 46.96 4.24
19 20 4.154347 CCTGCCCGAGGACTGCTC 62.154 72.222 0.00 0.00 46.33 4.26
20 21 3.073735 CTGCCCGAGGACTGCTCT 61.074 66.667 0.00 0.00 0.00 4.09
21 22 1.754621 CTGCCCGAGGACTGCTCTA 60.755 63.158 0.00 0.00 0.00 2.43
22 23 2.010582 CTGCCCGAGGACTGCTCTAC 62.011 65.000 0.00 0.00 0.00 2.59
23 24 2.787567 GCCCGAGGACTGCTCTACC 61.788 68.421 0.00 0.00 0.00 3.18
24 25 1.379977 CCCGAGGACTGCTCTACCA 60.380 63.158 0.00 0.00 0.00 3.25
25 26 1.388065 CCCGAGGACTGCTCTACCAG 61.388 65.000 0.00 0.00 38.78 4.00
35 36 2.770164 GCTCTACCAGCTGGAAAAGA 57.230 50.000 39.19 30.60 45.83 2.52
36 37 3.059352 GCTCTACCAGCTGGAAAAGAA 57.941 47.619 39.19 18.58 45.83 2.52
37 38 3.412386 GCTCTACCAGCTGGAAAAGAAA 58.588 45.455 39.19 15.58 45.83 2.52
38 39 3.821033 GCTCTACCAGCTGGAAAAGAAAA 59.179 43.478 39.19 14.95 45.83 2.29
39 40 4.083057 GCTCTACCAGCTGGAAAAGAAAAG 60.083 45.833 39.19 22.77 45.83 2.27
40 41 4.398319 TCTACCAGCTGGAAAAGAAAAGG 58.602 43.478 39.19 8.37 38.94 3.11
41 42 3.312736 ACCAGCTGGAAAAGAAAAGGA 57.687 42.857 39.19 0.00 38.94 3.36
42 43 3.642141 ACCAGCTGGAAAAGAAAAGGAA 58.358 40.909 39.19 0.00 38.94 3.36
43 44 4.030216 ACCAGCTGGAAAAGAAAAGGAAA 58.970 39.130 39.19 0.00 38.94 3.13
44 45 4.469586 ACCAGCTGGAAAAGAAAAGGAAAA 59.530 37.500 39.19 0.00 38.94 2.29
45 46 5.052481 CCAGCTGGAAAAGAAAAGGAAAAG 58.948 41.667 29.88 0.00 37.39 2.27
46 47 5.163416 CCAGCTGGAAAAGAAAAGGAAAAGA 60.163 40.000 29.88 0.00 37.39 2.52
47 48 5.981915 CAGCTGGAAAAGAAAAGGAAAAGAG 59.018 40.000 5.57 0.00 0.00 2.85
63 64 0.678048 AGAGGAAAAGCACCATCGCC 60.678 55.000 0.00 0.00 0.00 5.54
167 5609 1.834822 CCCTCCCAAAACCGGCAAA 60.835 57.895 0.00 0.00 0.00 3.68
168 5610 1.403687 CCCTCCCAAAACCGGCAAAA 61.404 55.000 0.00 0.00 0.00 2.44
169 5611 0.249699 CCTCCCAAAACCGGCAAAAC 60.250 55.000 0.00 0.00 0.00 2.43
291 7521 3.365265 CACCGCCCAAGAACCTGC 61.365 66.667 0.00 0.00 0.00 4.85
597 8083 1.202557 TCCGCTCCGTGTAAAAGTTGT 60.203 47.619 0.00 0.00 0.00 3.32
598 8084 1.600485 CCGCTCCGTGTAAAAGTTGTT 59.400 47.619 0.00 0.00 0.00 2.83
599 8085 2.601266 CCGCTCCGTGTAAAAGTTGTTG 60.601 50.000 0.00 0.00 0.00 3.33
663 8149 6.248433 TGGATCAAGTTTGAATTCTTAGGCT 58.752 36.000 7.05 0.00 41.13 4.58
803 8304 1.738099 CAGCGGAACAGAGGAACCG 60.738 63.158 0.00 0.00 46.74 4.44
824 8325 2.028112 GGGGTTTCTGGCAATCTTTTCC 60.028 50.000 0.00 0.00 0.00 3.13
844 8345 0.954452 GCCCATTCCGCAAGATAAGG 59.046 55.000 0.00 0.00 43.02 2.69
860 8361 7.459486 CAAGATAAGGTCGAATTGAGTTTCAG 58.541 38.462 0.00 0.00 0.00 3.02
942 8463 1.463674 CCTTTTACAAGCCGCCATCT 58.536 50.000 0.00 0.00 0.00 2.90
948 8469 1.098050 ACAAGCCGCCATCTGATTTC 58.902 50.000 0.00 0.00 0.00 2.17
1122 8643 2.903547 GAGCCGGCGCAAGAAACAA 61.904 57.895 26.33 0.00 43.02 2.83
1132 8653 2.604174 AAGAAACAACCGAGCGGCG 61.604 57.895 9.14 0.51 39.32 6.46
1335 8871 3.494378 CGCAGGAAGATGGCTGTG 58.506 61.111 0.00 0.00 0.00 3.66
1336 8872 2.110967 CGCAGGAAGATGGCTGTGG 61.111 63.158 0.00 0.00 0.00 4.17
1337 8873 1.300963 GCAGGAAGATGGCTGTGGA 59.699 57.895 0.00 0.00 0.00 4.02
1338 8874 0.747283 GCAGGAAGATGGCTGTGGAG 60.747 60.000 0.00 0.00 0.00 3.86
1339 8875 0.747283 CAGGAAGATGGCTGTGGAGC 60.747 60.000 0.00 0.00 45.40 4.70
1365 8901 0.597637 CATCGGTAGGCGATGGTGAC 60.598 60.000 0.00 0.00 39.41 3.67
1373 8909 0.960364 GGCGATGGTGACCACAATGT 60.960 55.000 6.40 0.00 35.80 2.71
1380 8916 2.224523 TGGTGACCACAATGTTCCTCTC 60.225 50.000 0.00 0.00 0.00 3.20
1392 8928 1.318886 TTCCTCTCTCTGCTGCTCCG 61.319 60.000 0.00 0.00 0.00 4.63
1545 9095 3.144506 CTCAGCTTCTGTTGATTGTGGT 58.855 45.455 0.00 0.00 33.10 4.16
1618 9168 1.558756 CAGAGATGGGGCTGAGTTCTT 59.441 52.381 0.00 0.00 34.06 2.52
1632 9182 5.684291 GCTGAGTTCTTCTGATCATCATGGA 60.684 44.000 0.00 0.00 0.00 3.41
1633 9183 5.915175 TGAGTTCTTCTGATCATCATGGAG 58.085 41.667 0.00 0.00 0.00 3.86
1634 9184 5.659971 TGAGTTCTTCTGATCATCATGGAGA 59.340 40.000 0.00 0.00 0.00 3.71
1635 9185 6.326843 TGAGTTCTTCTGATCATCATGGAGAT 59.673 38.462 0.00 0.00 37.48 2.75
1680 9230 0.041833 TGGAGCCAGAGCCTTCTAGT 59.958 55.000 0.00 0.00 41.25 2.57
1681 9231 1.288037 TGGAGCCAGAGCCTTCTAGTA 59.712 52.381 0.00 0.00 41.25 1.82
1682 9232 1.960689 GGAGCCAGAGCCTTCTAGTAG 59.039 57.143 0.00 0.00 41.25 2.57
1771 9321 0.868406 GCTTTGTGGACAGGTCTTCG 59.132 55.000 0.00 0.00 0.00 3.79
1839 9389 4.383552 GCTGATCATGGTAGAGTTCCAACT 60.384 45.833 0.00 0.00 43.16 3.16
1853 9403 3.874383 TCCAACTGTTCCCAAATCTGA 57.126 42.857 0.00 0.00 0.00 3.27
1863 9413 2.005451 CCCAAATCTGAAGCGACTCAG 58.995 52.381 7.65 7.65 43.62 3.35
1866 9416 0.901124 AATCTGAAGCGACTCAGCCT 59.099 50.000 8.83 0.00 42.25 4.58
1971 9521 1.533625 CAAAGCCTGAACCGAATCCA 58.466 50.000 0.00 0.00 0.00 3.41
1979 9529 0.521735 GAACCGAATCCACTGTTGGC 59.478 55.000 0.00 0.00 43.56 4.52
2136 9686 7.917597 TCTCTGTAGTCTGTACAATCGTTATC 58.082 38.462 0.00 0.00 0.00 1.75
2166 9716 3.030291 TGTCTTTTGGATTTGGCAGTGT 58.970 40.909 0.00 0.00 0.00 3.55
2191 9741 5.300539 TCTTACATGTTGCACTGCCTTTTTA 59.699 36.000 2.30 0.00 0.00 1.52
2248 9798 3.817647 CAGGGCATTAGTTCTAGATTGGC 59.182 47.826 0.00 0.00 0.00 4.52
2258 9808 8.974292 TTAGTTCTAGATTGGCTATTCCCTAT 57.026 34.615 0.00 0.00 0.00 2.57
2269 9823 4.775253 GGCTATTCCCTATTAGAGAGCAGT 59.225 45.833 0.00 0.00 0.00 4.40
2297 9851 3.434299 CCAGGTTGCAGCAATTCAATTTC 59.566 43.478 11.96 0.00 0.00 2.17
2299 9853 4.693566 CAGGTTGCAGCAATTCAATTTCAT 59.306 37.500 11.96 0.00 0.00 2.57
2304 9858 8.074972 GGTTGCAGCAATTCAATTTCATTTTTA 58.925 29.630 11.96 0.00 0.00 1.52
2305 9859 9.615295 GTTGCAGCAATTCAATTTCATTTTTAT 57.385 25.926 11.96 0.00 0.00 1.40
2328 9882 5.479124 TTTTTGTCCCCTAGACTCTGTAC 57.521 43.478 0.00 0.00 46.46 2.90
2329 9883 3.820195 TTGTCCCCTAGACTCTGTACA 57.180 47.619 0.00 0.00 46.46 2.90
2330 9884 3.820195 TGTCCCCTAGACTCTGTACAA 57.180 47.619 0.00 0.00 46.46 2.41
2331 9885 4.332683 TGTCCCCTAGACTCTGTACAAT 57.667 45.455 0.00 0.00 46.46 2.71
2332 9886 4.279145 TGTCCCCTAGACTCTGTACAATC 58.721 47.826 0.00 0.00 46.46 2.67
2333 9887 3.315749 GTCCCCTAGACTCTGTACAATCG 59.684 52.174 0.00 0.00 42.69 3.34
2334 9888 3.053842 TCCCCTAGACTCTGTACAATCGT 60.054 47.826 0.00 0.00 0.00 3.73
2335 9889 3.700038 CCCCTAGACTCTGTACAATCGTT 59.300 47.826 0.00 0.00 0.00 3.85
2336 9890 4.885907 CCCCTAGACTCTGTACAATCGTTA 59.114 45.833 0.00 0.00 0.00 3.18
2337 9891 5.535406 CCCCTAGACTCTGTACAATCGTTAT 59.465 44.000 0.00 0.00 0.00 1.89
2338 9892 6.294065 CCCCTAGACTCTGTACAATCGTTATC 60.294 46.154 0.00 0.00 0.00 1.75
2339 9893 6.364261 CCTAGACTCTGTACAATCGTTATCG 58.636 44.000 0.00 0.00 38.55 2.92
2362 9916 5.520376 ACAACTCTGTCTTTTGGATTTGG 57.480 39.130 0.00 0.00 0.00 3.28
2363 9917 4.202151 ACAACTCTGTCTTTTGGATTTGGC 60.202 41.667 0.00 0.00 0.00 4.52
2364 9918 3.565307 ACTCTGTCTTTTGGATTTGGCA 58.435 40.909 0.00 0.00 0.00 4.92
2365 9919 3.571401 ACTCTGTCTTTTGGATTTGGCAG 59.429 43.478 0.00 0.00 0.00 4.85
2366 9920 3.565307 TCTGTCTTTTGGATTTGGCAGT 58.435 40.909 0.00 0.00 0.00 4.40
2367 9921 3.318839 TCTGTCTTTTGGATTTGGCAGTG 59.681 43.478 0.00 0.00 0.00 3.66
2368 9922 3.030291 TGTCTTTTGGATTTGGCAGTGT 58.970 40.909 0.00 0.00 0.00 3.55
2369 9923 3.450457 TGTCTTTTGGATTTGGCAGTGTT 59.550 39.130 0.00 0.00 0.00 3.32
2370 9924 4.051237 GTCTTTTGGATTTGGCAGTGTTC 58.949 43.478 0.00 0.00 0.00 3.18
2371 9925 3.960102 TCTTTTGGATTTGGCAGTGTTCT 59.040 39.130 0.00 0.00 0.00 3.01
2372 9926 4.405358 TCTTTTGGATTTGGCAGTGTTCTT 59.595 37.500 0.00 0.00 0.00 2.52
2373 9927 5.596361 TCTTTTGGATTTGGCAGTGTTCTTA 59.404 36.000 0.00 0.00 0.00 2.10
2374 9928 4.846779 TTGGATTTGGCAGTGTTCTTAC 57.153 40.909 0.00 0.00 0.00 2.34
2375 9929 3.826524 TGGATTTGGCAGTGTTCTTACA 58.173 40.909 0.00 0.00 0.00 2.41
2376 9930 4.406456 TGGATTTGGCAGTGTTCTTACAT 58.594 39.130 0.00 0.00 36.50 2.29
2377 9931 4.218200 TGGATTTGGCAGTGTTCTTACATG 59.782 41.667 0.00 0.00 36.50 3.21
2378 9932 4.218417 GGATTTGGCAGTGTTCTTACATGT 59.782 41.667 2.69 2.69 36.50 3.21
2379 9933 5.278957 GGATTTGGCAGTGTTCTTACATGTT 60.279 40.000 2.30 0.00 36.50 2.71
2380 9934 4.566545 TTGGCAGTGTTCTTACATGTTG 57.433 40.909 2.30 0.00 36.50 3.33
2381 9935 2.293122 TGGCAGTGTTCTTACATGTTGC 59.707 45.455 2.30 4.86 37.81 4.17
2382 9936 2.293122 GGCAGTGTTCTTACATGTTGCA 59.707 45.455 14.78 0.00 39.07 4.08
2383 9937 3.300009 GCAGTGTTCTTACATGTTGCAC 58.700 45.455 2.30 6.74 38.12 4.57
2384 9938 3.003689 GCAGTGTTCTTACATGTTGCACT 59.996 43.478 2.30 8.89 38.12 4.40
2385 9939 4.530388 CAGTGTTCTTACATGTTGCACTG 58.470 43.478 21.55 21.55 43.71 3.66
2386 9940 3.003689 AGTGTTCTTACATGTTGCACTGC 59.996 43.478 2.30 0.00 36.50 4.40
2387 9941 2.293122 TGTTCTTACATGTTGCACTGCC 59.707 45.455 2.30 0.00 0.00 4.85
2388 9942 2.554032 GTTCTTACATGTTGCACTGCCT 59.446 45.455 2.30 0.00 0.00 4.75
2389 9943 2.862541 TCTTACATGTTGCACTGCCTT 58.137 42.857 2.30 0.00 0.00 4.35
2390 9944 3.221771 TCTTACATGTTGCACTGCCTTT 58.778 40.909 2.30 0.00 0.00 3.11
2391 9945 3.636300 TCTTACATGTTGCACTGCCTTTT 59.364 39.130 2.30 0.00 0.00 2.27
2392 9946 2.985957 ACATGTTGCACTGCCTTTTT 57.014 40.000 0.00 0.00 0.00 1.94
2393 9947 5.300539 TCTTACATGTTGCACTGCCTTTTTA 59.699 36.000 2.30 0.00 0.00 1.52
2394 9948 3.981211 ACATGTTGCACTGCCTTTTTAG 58.019 40.909 0.00 0.00 0.00 1.85
2395 9949 3.243839 ACATGTTGCACTGCCTTTTTAGG 60.244 43.478 0.00 0.00 0.00 2.69
2396 9950 2.383855 TGTTGCACTGCCTTTTTAGGT 58.616 42.857 0.00 0.00 0.00 3.08
2397 9951 2.763448 TGTTGCACTGCCTTTTTAGGTT 59.237 40.909 0.00 0.00 0.00 3.50
2398 9952 3.181480 TGTTGCACTGCCTTTTTAGGTTC 60.181 43.478 0.00 0.00 0.00 3.62
2399 9953 1.960689 TGCACTGCCTTTTTAGGTTCC 59.039 47.619 0.00 0.00 0.00 3.62
2400 9954 1.272490 GCACTGCCTTTTTAGGTTCCC 59.728 52.381 0.00 0.00 0.00 3.97
2401 9955 2.593026 CACTGCCTTTTTAGGTTCCCA 58.407 47.619 0.00 0.00 0.00 4.37
2402 9956 2.962421 CACTGCCTTTTTAGGTTCCCAA 59.038 45.455 0.00 0.00 0.00 4.12
2403 9957 3.386402 CACTGCCTTTTTAGGTTCCCAAA 59.614 43.478 0.00 0.00 0.00 3.28
2404 9958 3.386726 ACTGCCTTTTTAGGTTCCCAAAC 59.613 43.478 0.00 0.00 34.46 2.93
2405 9959 3.375699 TGCCTTTTTAGGTTCCCAAACA 58.624 40.909 0.00 0.00 37.10 2.83
2406 9960 3.970640 TGCCTTTTTAGGTTCCCAAACAT 59.029 39.130 0.00 0.00 37.10 2.71
2407 9961 4.410555 TGCCTTTTTAGGTTCCCAAACATT 59.589 37.500 0.00 0.00 37.10 2.71
2408 9962 4.754618 GCCTTTTTAGGTTCCCAAACATTG 59.245 41.667 0.00 0.00 37.10 2.82
2409 9963 5.454045 GCCTTTTTAGGTTCCCAAACATTGA 60.454 40.000 0.00 0.00 37.10 2.57
2410 9964 6.587273 CCTTTTTAGGTTCCCAAACATTGAA 58.413 36.000 0.00 0.00 37.10 2.69
2411 9965 7.051000 CCTTTTTAGGTTCCCAAACATTGAAA 58.949 34.615 0.00 0.00 37.10 2.69
2412 9966 7.719193 CCTTTTTAGGTTCCCAAACATTGAAAT 59.281 33.333 0.00 0.00 37.10 2.17
2413 9967 8.443953 TTTTTAGGTTCCCAAACATTGAAATG 57.556 30.769 1.45 1.45 42.10 2.32
2428 9982 7.524294 CATTGAAATGTACCCATTAACAAGC 57.476 36.000 0.00 0.00 40.42 4.01
2429 9983 6.656632 TTGAAATGTACCCATTAACAAGCA 57.343 33.333 0.00 0.00 40.42 3.91
2430 9984 6.266168 TGAAATGTACCCATTAACAAGCAG 57.734 37.500 0.00 0.00 40.42 4.24
2431 9985 5.184864 TGAAATGTACCCATTAACAAGCAGG 59.815 40.000 0.00 0.00 40.42 4.85
2432 9986 3.080300 TGTACCCATTAACAAGCAGGG 57.920 47.619 0.00 0.00 45.20 4.45
2433 9987 1.749063 GTACCCATTAACAAGCAGGGC 59.251 52.381 0.00 0.00 43.47 5.19
2434 9988 0.114168 ACCCATTAACAAGCAGGGCA 59.886 50.000 0.00 0.00 43.47 5.36
2435 9989 1.273211 ACCCATTAACAAGCAGGGCAT 60.273 47.619 0.00 0.00 43.47 4.40
2436 9990 1.832998 CCCATTAACAAGCAGGGCATT 59.167 47.619 0.00 0.00 31.81 3.56
2437 9991 3.030291 CCCATTAACAAGCAGGGCATTA 58.970 45.455 0.00 0.00 31.81 1.90
2438 9992 3.068590 CCCATTAACAAGCAGGGCATTAG 59.931 47.826 0.00 0.00 31.81 1.73
2439 9993 3.701040 CCATTAACAAGCAGGGCATTAGT 59.299 43.478 0.00 0.00 0.00 2.24
2440 9994 4.160252 CCATTAACAAGCAGGGCATTAGTT 59.840 41.667 0.00 0.00 0.00 2.24
2441 9995 5.343249 CATTAACAAGCAGGGCATTAGTTC 58.657 41.667 0.00 0.00 0.00 3.01
2442 9996 2.887151 ACAAGCAGGGCATTAGTTCT 57.113 45.000 0.00 0.00 0.00 3.01
2443 9997 4.301072 AACAAGCAGGGCATTAGTTCTA 57.699 40.909 0.00 0.00 0.00 2.10
2444 9998 4.301072 ACAAGCAGGGCATTAGTTCTAA 57.699 40.909 0.00 0.00 0.00 2.10
2445 9999 4.662278 ACAAGCAGGGCATTAGTTCTAAA 58.338 39.130 0.00 0.00 0.00 1.85
2446 10000 5.264395 ACAAGCAGGGCATTAGTTCTAAAT 58.736 37.500 0.00 0.00 0.00 1.40
2447 10001 5.716703 ACAAGCAGGGCATTAGTTCTAAATT 59.283 36.000 0.00 0.00 0.00 1.82
2448 10002 5.841957 AGCAGGGCATTAGTTCTAAATTG 57.158 39.130 0.00 0.00 0.00 2.32
2449 10003 4.646492 AGCAGGGCATTAGTTCTAAATTGG 59.354 41.667 0.00 0.00 0.00 3.16
2450 10004 4.737649 GCAGGGCATTAGTTCTAAATTGGC 60.738 45.833 9.65 9.65 0.00 4.52
2451 10005 4.646492 CAGGGCATTAGTTCTAAATTGGCT 59.354 41.667 14.63 4.27 0.00 4.75
2452 10006 5.827797 CAGGGCATTAGTTCTAAATTGGCTA 59.172 40.000 14.63 0.00 0.00 3.93
2453 10007 6.491403 CAGGGCATTAGTTCTAAATTGGCTAT 59.509 38.462 14.63 6.20 0.00 2.97
2454 10008 7.014615 CAGGGCATTAGTTCTAAATTGGCTATT 59.985 37.037 14.63 0.00 0.00 1.73
2455 10009 7.231519 AGGGCATTAGTTCTAAATTGGCTATTC 59.768 37.037 14.63 4.15 0.00 1.75
2456 10010 7.371159 GGCATTAGTTCTAAATTGGCTATTCC 58.629 38.462 10.43 0.00 0.00 3.01
2457 10011 7.371159 GCATTAGTTCTAAATTGGCTATTCCC 58.629 38.462 0.00 0.00 0.00 3.97
2458 10012 7.231519 GCATTAGTTCTAAATTGGCTATTCCCT 59.768 37.037 0.00 0.00 0.00 4.20
2459 10013 9.793259 CATTAGTTCTAAATTGGCTATTCCCTA 57.207 33.333 0.00 0.00 0.00 3.53
2466 10020 9.615660 TCTAAATTGGCTATTCCCTATTAGAGA 57.384 33.333 0.00 0.00 32.27 3.10
2467 10021 9.883142 CTAAATTGGCTATTCCCTATTAGAGAG 57.117 37.037 0.00 0.00 31.54 3.20
2468 10022 5.746990 TTGGCTATTCCCTATTAGAGAGC 57.253 43.478 0.00 0.00 0.00 4.09
2469 10023 4.752063 TGGCTATTCCCTATTAGAGAGCA 58.248 43.478 0.00 0.00 0.00 4.26
2470 10024 4.774726 TGGCTATTCCCTATTAGAGAGCAG 59.225 45.833 0.00 0.00 0.00 4.24
2471 10025 4.775253 GGCTATTCCCTATTAGAGAGCAGT 59.225 45.833 0.00 0.00 0.00 4.40
2472 10026 5.337169 GGCTATTCCCTATTAGAGAGCAGTG 60.337 48.000 0.00 0.00 0.00 3.66
2473 10027 5.245075 GCTATTCCCTATTAGAGAGCAGTGT 59.755 44.000 0.00 0.00 0.00 3.55
2474 10028 5.799827 ATTCCCTATTAGAGAGCAGTGTC 57.200 43.478 0.00 0.00 0.00 3.67
2475 10029 3.215151 TCCCTATTAGAGAGCAGTGTCG 58.785 50.000 0.00 0.00 0.00 4.35
2476 10030 2.952978 CCCTATTAGAGAGCAGTGTCGT 59.047 50.000 0.00 0.00 0.00 4.34
2477 10031 3.003897 CCCTATTAGAGAGCAGTGTCGTC 59.996 52.174 0.00 0.00 0.00 4.20
2478 10032 3.003897 CCTATTAGAGAGCAGTGTCGTCC 59.996 52.174 0.00 0.00 0.00 4.79
2479 10033 1.905637 TTAGAGAGCAGTGTCGTCCA 58.094 50.000 0.00 0.00 0.00 4.02
2480 10034 1.454201 TAGAGAGCAGTGTCGTCCAG 58.546 55.000 0.00 0.00 0.00 3.86
2481 10035 1.214062 GAGAGCAGTGTCGTCCAGG 59.786 63.158 0.00 0.00 0.00 4.45
2482 10036 1.528292 GAGAGCAGTGTCGTCCAGGT 61.528 60.000 0.00 0.00 0.00 4.00
2483 10037 1.115930 AGAGCAGTGTCGTCCAGGTT 61.116 55.000 0.00 0.00 0.00 3.50
2484 10038 0.946221 GAGCAGTGTCGTCCAGGTTG 60.946 60.000 0.00 0.00 0.00 3.77
2485 10039 2.607892 GCAGTGTCGTCCAGGTTGC 61.608 63.158 0.00 0.00 0.00 4.17
2486 10040 1.227527 CAGTGTCGTCCAGGTTGCA 60.228 57.895 0.00 0.00 0.00 4.08
2487 10041 1.069765 AGTGTCGTCCAGGTTGCAG 59.930 57.895 0.00 0.00 0.00 4.41
2488 10042 2.280797 TGTCGTCCAGGTTGCAGC 60.281 61.111 0.00 0.00 0.00 5.25
2489 10043 2.280797 GTCGTCCAGGTTGCAGCA 60.281 61.111 2.05 0.00 0.00 4.41
2490 10044 1.891919 GTCGTCCAGGTTGCAGCAA 60.892 57.895 2.83 2.83 0.00 3.91
2491 10045 1.073025 TCGTCCAGGTTGCAGCAAT 59.927 52.632 11.96 0.00 0.00 3.56
2492 10046 0.537143 TCGTCCAGGTTGCAGCAATT 60.537 50.000 11.96 0.00 0.00 2.32
2493 10047 0.109597 CGTCCAGGTTGCAGCAATTC 60.110 55.000 11.96 7.20 0.00 2.17
2494 10048 0.961019 GTCCAGGTTGCAGCAATTCA 59.039 50.000 11.96 0.00 0.00 2.57
2495 10049 1.340889 GTCCAGGTTGCAGCAATTCAA 59.659 47.619 11.96 0.00 0.00 2.69
2496 10050 2.028748 GTCCAGGTTGCAGCAATTCAAT 60.029 45.455 11.96 0.00 0.00 2.57
2497 10051 2.633967 TCCAGGTTGCAGCAATTCAATT 59.366 40.909 11.96 0.00 0.00 2.32
2498 10052 3.071312 TCCAGGTTGCAGCAATTCAATTT 59.929 39.130 11.96 0.00 0.00 1.82
2499 10053 3.434299 CCAGGTTGCAGCAATTCAATTTC 59.566 43.478 11.96 0.00 0.00 2.17
2500 10054 4.059511 CAGGTTGCAGCAATTCAATTTCA 58.940 39.130 11.96 0.00 0.00 2.69
2501 10055 4.693566 CAGGTTGCAGCAATTCAATTTCAT 59.306 37.500 11.96 0.00 0.00 2.57
2502 10056 5.180492 CAGGTTGCAGCAATTCAATTTCATT 59.820 36.000 11.96 0.00 0.00 2.57
2503 10057 5.766174 AGGTTGCAGCAATTCAATTTCATTT 59.234 32.000 11.96 0.00 0.00 2.32
2504 10058 6.263617 AGGTTGCAGCAATTCAATTTCATTTT 59.736 30.769 11.96 0.00 0.00 1.82
2505 10059 6.919115 GGTTGCAGCAATTCAATTTCATTTTT 59.081 30.769 11.96 0.00 0.00 1.94
2506 10060 8.074972 GGTTGCAGCAATTCAATTTCATTTTTA 58.925 29.630 11.96 0.00 0.00 1.52
2507 10061 9.615295 GTTGCAGCAATTCAATTTCATTTTTAT 57.385 25.926 11.96 0.00 0.00 1.40
2534 10088 1.265454 CCCCTAGACTCGGGCAACTT 61.265 60.000 6.54 0.00 40.54 2.66
2575 10129 7.377766 TGTTCAGCTCATTGTAATTTCCTAC 57.622 36.000 0.00 0.00 0.00 3.18
2579 10133 8.635765 TCAGCTCATTGTAATTTCCTACTTTT 57.364 30.769 0.00 0.00 0.00 2.27
2581 10135 7.274250 CAGCTCATTGTAATTTCCTACTTTTGC 59.726 37.037 0.00 0.00 0.00 3.68
2590 10144 2.151202 TCCTACTTTTGCTTTGGCTCG 58.849 47.619 0.00 0.00 39.59 5.03
2617 10172 5.022122 TGATATGGCTTCCAAATTGGTTCA 58.978 37.500 12.28 6.82 39.03 3.18
2635 10190 4.527564 GTTCACCTGATCGTGTTTCAAAG 58.472 43.478 1.38 0.00 35.18 2.77
2699 10254 5.121105 TCATATGTGGCTGTGAAGATTCAG 58.879 41.667 1.90 0.00 37.98 3.02
2716 10271 1.490490 TCAGTGCTTCAGTTTCCTGGT 59.510 47.619 0.00 0.00 39.31 4.00
2748 10303 6.266168 TGTGTTTTGATCTTTCTTGTGTGT 57.734 33.333 0.00 0.00 0.00 3.72
2750 10305 6.806249 TGTGTTTTGATCTTTCTTGTGTGTTC 59.194 34.615 0.00 0.00 0.00 3.18
2758 10313 6.609237 TCTTTCTTGTGTGTTCTCTTCATG 57.391 37.500 0.00 0.00 0.00 3.07
2759 10314 6.115446 TCTTTCTTGTGTGTTCTCTTCATGT 58.885 36.000 0.00 0.00 0.00 3.21
2770 10325 6.751425 GTGTTCTCTTCATGTCAGACTGATAG 59.249 42.308 8.73 2.12 0.00 2.08
2779 10334 5.139435 TGTCAGACTGATAGTTTCCACAG 57.861 43.478 8.73 0.00 36.58 3.66
2783 10338 4.221703 CAGACTGATAGTTTCCACAGGACT 59.778 45.833 0.00 0.00 35.08 3.85
2795 10350 3.636300 TCCACAGGACTGAAACCAAATTG 59.364 43.478 6.29 0.00 0.00 2.32
2803 10358 5.759763 GGACTGAAACCAAATTGCAGAAATT 59.240 36.000 1.56 0.00 40.32 1.82
2866 10423 7.934855 ATCAATGATTTGTAGTCTGCTCTTT 57.065 32.000 0.00 0.00 34.32 2.52
2874 10431 6.852420 TTGTAGTCTGCTCTTTATACCAGT 57.148 37.500 0.00 0.00 0.00 4.00
2890 10447 1.876156 CCAGTCAGCACCTTTCTGTTC 59.124 52.381 0.00 0.00 33.48 3.18
2905 10462 8.352942 ACCTTTCTGTTCAAATGATTTGTAGTC 58.647 33.333 16.62 7.37 41.36 2.59
2914 10471 9.567776 TTCAAATGATTTGTAGTCTGTTCCTTA 57.432 29.630 16.62 0.00 41.36 2.69
2926 10483 3.062763 CTGTTCCTTATATCCAGCAGCG 58.937 50.000 0.00 0.00 0.00 5.18
2940 10497 0.179179 GCAGCGCCTTTCTGATGAAC 60.179 55.000 2.29 0.00 33.54 3.18
2948 10505 5.276270 CGCCTTTCTGATGAACAAATATGG 58.724 41.667 0.00 0.00 31.02 2.74
2969 10526 5.637127 TGGTCAATGGATCATGCAGATAAT 58.363 37.500 0.00 0.00 37.00 1.28
2991 10548 3.005367 TGCTTTCCGATATCGTATCAGCA 59.995 43.478 23.67 23.67 35.42 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.154347 GAGCAGTCCTCGGGCAGG 62.154 72.222 0.00 0.00 45.15 4.85
3 4 1.754621 TAGAGCAGTCCTCGGGCAG 60.755 63.158 0.00 0.00 45.54 4.85
4 5 2.052690 GTAGAGCAGTCCTCGGGCA 61.053 63.158 0.00 0.00 45.54 5.36
5 6 2.787567 GGTAGAGCAGTCCTCGGGC 61.788 68.421 0.00 0.00 45.54 6.13
6 7 1.379977 TGGTAGAGCAGTCCTCGGG 60.380 63.158 0.00 0.00 45.54 5.14
7 8 2.111162 CTGGTAGAGCAGTCCTCGG 58.889 63.158 0.45 0.00 45.54 4.63
17 18 4.457257 CCTTTTCTTTTCCAGCTGGTAGAG 59.543 45.833 31.58 25.39 36.34 2.43
18 19 4.104102 TCCTTTTCTTTTCCAGCTGGTAGA 59.896 41.667 31.58 26.14 36.34 2.59
19 20 4.398319 TCCTTTTCTTTTCCAGCTGGTAG 58.602 43.478 31.58 24.52 36.34 3.18
20 21 4.447138 TCCTTTTCTTTTCCAGCTGGTA 57.553 40.909 31.58 20.93 36.34 3.25
21 22 3.312736 TCCTTTTCTTTTCCAGCTGGT 57.687 42.857 31.58 0.00 36.34 4.00
22 23 4.670896 TTTCCTTTTCTTTTCCAGCTGG 57.329 40.909 27.87 27.87 0.00 4.85
23 24 5.906073 TCTTTTCCTTTTCTTTTCCAGCTG 58.094 37.500 6.78 6.78 0.00 4.24
24 25 5.069648 CCTCTTTTCCTTTTCTTTTCCAGCT 59.930 40.000 0.00 0.00 0.00 4.24
25 26 5.069119 TCCTCTTTTCCTTTTCTTTTCCAGC 59.931 40.000 0.00 0.00 0.00 4.85
26 27 6.715347 TCCTCTTTTCCTTTTCTTTTCCAG 57.285 37.500 0.00 0.00 0.00 3.86
27 28 7.489239 TTTCCTCTTTTCCTTTTCTTTTCCA 57.511 32.000 0.00 0.00 0.00 3.53
28 29 7.011482 GCTTTTCCTCTTTTCCTTTTCTTTTCC 59.989 37.037 0.00 0.00 0.00 3.13
29 30 7.549134 TGCTTTTCCTCTTTTCCTTTTCTTTTC 59.451 33.333 0.00 0.00 0.00 2.29
30 31 7.334421 GTGCTTTTCCTCTTTTCCTTTTCTTTT 59.666 33.333 0.00 0.00 0.00 2.27
31 32 6.818644 GTGCTTTTCCTCTTTTCCTTTTCTTT 59.181 34.615 0.00 0.00 0.00 2.52
32 33 6.341316 GTGCTTTTCCTCTTTTCCTTTTCTT 58.659 36.000 0.00 0.00 0.00 2.52
33 34 5.163405 GGTGCTTTTCCTCTTTTCCTTTTCT 60.163 40.000 0.00 0.00 0.00 2.52
34 35 5.050490 GGTGCTTTTCCTCTTTTCCTTTTC 58.950 41.667 0.00 0.00 0.00 2.29
35 36 4.469586 TGGTGCTTTTCCTCTTTTCCTTTT 59.530 37.500 0.00 0.00 0.00 2.27
36 37 4.030216 TGGTGCTTTTCCTCTTTTCCTTT 58.970 39.130 0.00 0.00 0.00 3.11
37 38 3.642141 TGGTGCTTTTCCTCTTTTCCTT 58.358 40.909 0.00 0.00 0.00 3.36
38 39 3.312736 TGGTGCTTTTCCTCTTTTCCT 57.687 42.857 0.00 0.00 0.00 3.36
39 40 3.366374 CGATGGTGCTTTTCCTCTTTTCC 60.366 47.826 0.00 0.00 0.00 3.13
40 41 3.826466 CGATGGTGCTTTTCCTCTTTTC 58.174 45.455 0.00 0.00 0.00 2.29
41 42 2.029918 GCGATGGTGCTTTTCCTCTTTT 60.030 45.455 0.00 0.00 0.00 2.27
42 43 1.541588 GCGATGGTGCTTTTCCTCTTT 59.458 47.619 0.00 0.00 0.00 2.52
43 44 1.168714 GCGATGGTGCTTTTCCTCTT 58.831 50.000 0.00 0.00 0.00 2.85
44 45 0.678048 GGCGATGGTGCTTTTCCTCT 60.678 55.000 0.00 0.00 34.52 3.69
45 46 1.657751 GGGCGATGGTGCTTTTCCTC 61.658 60.000 0.00 0.00 34.52 3.71
46 47 1.678970 GGGCGATGGTGCTTTTCCT 60.679 57.895 0.00 0.00 34.52 3.36
47 48 2.710902 GGGGCGATGGTGCTTTTCC 61.711 63.158 0.00 0.00 34.52 3.13
63 64 4.825679 GGTGGGAGGAGGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
167 5609 1.269621 CGGTGTTCTTCCTGACGAGTT 60.270 52.381 0.00 0.00 0.00 3.01
168 5610 0.314302 CGGTGTTCTTCCTGACGAGT 59.686 55.000 0.00 0.00 0.00 4.18
169 5611 1.009389 GCGGTGTTCTTCCTGACGAG 61.009 60.000 0.00 0.00 0.00 4.18
291 7521 2.105477 CCACCTCTGGTATCCTGGATTG 59.895 54.545 15.55 4.19 32.11 2.67
597 8083 2.426522 CAGATTCTTGACGGAAGCCAA 58.573 47.619 0.00 0.00 32.74 4.52
598 8084 1.339055 CCAGATTCTTGACGGAAGCCA 60.339 52.381 0.00 0.00 32.74 4.75
599 8085 1.373570 CCAGATTCTTGACGGAAGCC 58.626 55.000 0.00 0.00 32.74 4.35
681 8167 3.647771 GTTTGGGAGGGGCGGAGT 61.648 66.667 0.00 0.00 0.00 3.85
803 8304 2.028112 GGAAAAGATTGCCAGAAACCCC 60.028 50.000 0.00 0.00 0.00 4.95
824 8325 0.588252 CTTATCTTGCGGAATGGGCG 59.412 55.000 0.00 0.00 0.00 6.13
844 8345 2.412089 CCGTCCTGAAACTCAATTCGAC 59.588 50.000 0.00 0.00 31.80 4.20
860 8361 1.991121 AAACCCTTTCCTTTCCGTCC 58.009 50.000 0.00 0.00 0.00 4.79
887 8388 0.591659 GCGGAAACAGAAGTTGGGAC 59.408 55.000 0.00 0.00 38.17 4.46
999 8520 0.461870 GCGGCATGTCTGGACACATA 60.462 55.000 5.52 0.00 45.05 2.29
1047 8568 0.327591 AAGGGAAGCTCCTCTTGCAG 59.672 55.000 0.00 0.00 43.96 4.41
1212 8733 4.124351 GCCCACCGATCGTCGTCA 62.124 66.667 15.09 0.00 38.40 4.35
1332 8868 2.352422 GATGCCTGGTGCTCCACA 59.648 61.111 2.64 1.76 42.00 4.17
1333 8869 2.821366 CGATGCCTGGTGCTCCAC 60.821 66.667 2.64 0.00 42.00 4.02
1334 8870 4.100084 CCGATGCCTGGTGCTCCA 62.100 66.667 7.39 7.39 42.00 3.86
1335 8871 2.650813 CTACCGATGCCTGGTGCTCC 62.651 65.000 0.00 0.00 40.73 4.70
1336 8872 1.227380 CTACCGATGCCTGGTGCTC 60.227 63.158 0.00 0.00 40.73 4.26
1337 8873 2.735772 CCTACCGATGCCTGGTGCT 61.736 63.158 0.00 0.00 40.73 4.40
1338 8874 2.203070 CCTACCGATGCCTGGTGC 60.203 66.667 0.00 0.00 40.73 5.01
1339 8875 2.203070 GCCTACCGATGCCTGGTG 60.203 66.667 0.00 0.00 40.73 4.17
1340 8876 3.849951 CGCCTACCGATGCCTGGT 61.850 66.667 0.00 0.00 43.62 4.00
1341 8877 3.536917 TCGCCTACCGATGCCTGG 61.537 66.667 0.00 0.00 41.89 4.45
1365 8901 2.027377 AGCAGAGAGAGGAACATTGTGG 60.027 50.000 0.00 0.00 0.00 4.17
1373 8909 1.318886 CGGAGCAGCAGAGAGAGGAA 61.319 60.000 0.00 0.00 0.00 3.36
1380 8916 1.521010 CATCACCGGAGCAGCAGAG 60.521 63.158 9.46 0.00 0.00 3.35
1392 8928 2.159170 CGACCTCTTCCTCTTCATCACC 60.159 54.545 0.00 0.00 0.00 4.02
1545 9095 0.034756 CGTCCATCACACCACCTTCA 59.965 55.000 0.00 0.00 0.00 3.02
1632 9182 6.610830 ACTCATTATCTCCAACTCTGTCATCT 59.389 38.462 0.00 0.00 0.00 2.90
1633 9183 6.815089 ACTCATTATCTCCAACTCTGTCATC 58.185 40.000 0.00 0.00 0.00 2.92
1634 9184 6.805016 ACTCATTATCTCCAACTCTGTCAT 57.195 37.500 0.00 0.00 0.00 3.06
1635 9185 6.211384 TCAACTCATTATCTCCAACTCTGTCA 59.789 38.462 0.00 0.00 0.00 3.58
1636 9186 6.634805 TCAACTCATTATCTCCAACTCTGTC 58.365 40.000 0.00 0.00 0.00 3.51
1637 9187 6.611613 TCAACTCATTATCTCCAACTCTGT 57.388 37.500 0.00 0.00 0.00 3.41
1638 9188 6.482641 CCATCAACTCATTATCTCCAACTCTG 59.517 42.308 0.00 0.00 0.00 3.35
1639 9189 6.385176 TCCATCAACTCATTATCTCCAACTCT 59.615 38.462 0.00 0.00 0.00 3.24
1640 9190 6.586344 TCCATCAACTCATTATCTCCAACTC 58.414 40.000 0.00 0.00 0.00 3.01
1680 9230 4.884961 ACTTCCCTTCCTCATAAGAGCTA 58.115 43.478 0.00 0.00 40.68 3.32
1681 9231 3.730269 ACTTCCCTTCCTCATAAGAGCT 58.270 45.455 0.00 0.00 40.68 4.09
1682 9232 4.495690 AACTTCCCTTCCTCATAAGAGC 57.504 45.455 0.00 0.00 40.68 4.09
1727 9277 1.486726 ACTCATAGGTAGCTGTTGCCC 59.513 52.381 4.27 0.00 40.80 5.36
1739 9289 2.163010 CCACAAAGCTTGCACTCATAGG 59.837 50.000 0.00 0.00 0.00 2.57
1771 9321 1.450312 CCAATCCCTGACCAGACGC 60.450 63.158 0.00 0.00 0.00 5.19
1839 9389 2.151202 GTCGCTTCAGATTTGGGAACA 58.849 47.619 0.00 0.00 39.83 3.18
1853 9403 0.106708 TTCACAAGGCTGAGTCGCTT 59.893 50.000 6.86 0.00 0.00 4.68
1863 9413 2.638744 AAGCAGCTCTTCACAAGGC 58.361 52.632 0.00 0.00 0.00 4.35
1903 9453 0.249826 GGAGCTGGTATGCTGAGAGC 60.250 60.000 0.00 0.00 44.17 4.09
1912 9462 1.632409 CCATATGCTGGGAGCTGGTAT 59.368 52.381 0.00 0.00 42.97 2.73
1971 9521 3.289834 CTGCTTGCGGCCAACAGT 61.290 61.111 2.24 0.00 40.92 3.55
1979 9529 4.060038 CCCAAAGGCTGCTTGCGG 62.060 66.667 0.00 0.00 44.05 5.69
2166 9716 2.862541 AGGCAGTGCAACATGTAAGAA 58.137 42.857 18.61 0.00 41.43 2.52
2225 9775 3.817647 CCAATCTAGAACTAATGCCCTGC 59.182 47.826 0.00 0.00 0.00 4.85
2248 9798 6.348950 CGACACTGCTCTCTAATAGGGAATAG 60.349 46.154 0.00 0.00 0.00 1.73
2258 9808 1.813178 CTGGACGACACTGCTCTCTAA 59.187 52.381 0.00 0.00 0.00 2.10
2269 9823 2.280797 GCTGCAACCTGGACGACA 60.281 61.111 0.00 0.00 0.00 4.35
2314 9868 4.985538 AACGATTGTACAGAGTCTAGGG 57.014 45.455 0.00 0.00 0.00 3.53
2340 9894 4.202151 GCCAAATCCAAAAGACAGAGTTGT 60.202 41.667 0.00 0.00 41.18 3.32
2341 9895 4.202141 TGCCAAATCCAAAAGACAGAGTTG 60.202 41.667 0.00 0.00 35.85 3.16
2342 9896 3.960102 TGCCAAATCCAAAAGACAGAGTT 59.040 39.130 0.00 0.00 0.00 3.01
2343 9897 3.565307 TGCCAAATCCAAAAGACAGAGT 58.435 40.909 0.00 0.00 0.00 3.24
2344 9898 3.571401 ACTGCCAAATCCAAAAGACAGAG 59.429 43.478 0.00 0.00 0.00 3.35
2345 9899 3.318839 CACTGCCAAATCCAAAAGACAGA 59.681 43.478 0.00 0.00 0.00 3.41
2346 9900 3.068590 ACACTGCCAAATCCAAAAGACAG 59.931 43.478 0.00 0.00 0.00 3.51
2347 9901 3.030291 ACACTGCCAAATCCAAAAGACA 58.970 40.909 0.00 0.00 0.00 3.41
2348 9902 3.733443 ACACTGCCAAATCCAAAAGAC 57.267 42.857 0.00 0.00 0.00 3.01
2349 9903 3.960102 AGAACACTGCCAAATCCAAAAGA 59.040 39.130 0.00 0.00 0.00 2.52
2350 9904 4.326504 AGAACACTGCCAAATCCAAAAG 57.673 40.909 0.00 0.00 0.00 2.27
2351 9905 4.751767 AAGAACACTGCCAAATCCAAAA 57.248 36.364 0.00 0.00 0.00 2.44
2352 9906 4.646945 TGTAAGAACACTGCCAAATCCAAA 59.353 37.500 0.00 0.00 0.00 3.28
2353 9907 4.211125 TGTAAGAACACTGCCAAATCCAA 58.789 39.130 0.00 0.00 0.00 3.53
2354 9908 3.826524 TGTAAGAACACTGCCAAATCCA 58.173 40.909 0.00 0.00 0.00 3.41
2355 9909 4.218417 ACATGTAAGAACACTGCCAAATCC 59.782 41.667 0.00 0.00 38.78 3.01
2356 9910 5.376854 ACATGTAAGAACACTGCCAAATC 57.623 39.130 0.00 0.00 38.78 2.17
2357 9911 5.531634 CAACATGTAAGAACACTGCCAAAT 58.468 37.500 0.00 0.00 38.78 2.32
2358 9912 4.736168 GCAACATGTAAGAACACTGCCAAA 60.736 41.667 0.00 0.00 38.78 3.28
2359 9913 3.243367 GCAACATGTAAGAACACTGCCAA 60.243 43.478 0.00 0.00 38.78 4.52
2360 9914 2.293122 GCAACATGTAAGAACACTGCCA 59.707 45.455 0.00 0.00 38.78 4.92
2361 9915 2.293122 TGCAACATGTAAGAACACTGCC 59.707 45.455 11.28 0.00 38.78 4.85
2362 9916 3.003689 AGTGCAACATGTAAGAACACTGC 59.996 43.478 14.55 11.52 41.43 4.40
2363 9917 4.530388 CAGTGCAACATGTAAGAACACTG 58.470 43.478 21.65 21.65 45.04 3.66
2364 9918 3.003689 GCAGTGCAACATGTAAGAACACT 59.996 43.478 11.09 6.08 41.43 3.55
2365 9919 3.300009 GCAGTGCAACATGTAAGAACAC 58.700 45.455 11.09 3.74 41.43 3.32
2366 9920 2.293122 GGCAGTGCAACATGTAAGAACA 59.707 45.455 18.61 0.00 41.43 3.18
2367 9921 2.554032 AGGCAGTGCAACATGTAAGAAC 59.446 45.455 18.61 0.00 41.43 3.01
2368 9922 2.862541 AGGCAGTGCAACATGTAAGAA 58.137 42.857 18.61 0.00 41.43 2.52
2369 9923 2.566833 AGGCAGTGCAACATGTAAGA 57.433 45.000 18.61 0.00 41.43 2.10
2370 9924 3.648339 AAAGGCAGTGCAACATGTAAG 57.352 42.857 18.61 0.00 41.43 2.34
2371 9925 4.399004 AAAAAGGCAGTGCAACATGTAA 57.601 36.364 18.61 0.00 41.43 2.41
2372 9926 4.022416 CCTAAAAAGGCAGTGCAACATGTA 60.022 41.667 18.61 0.71 41.43 2.29
2373 9927 2.985957 AAAAAGGCAGTGCAACATGT 57.014 40.000 18.61 0.00 41.43 3.21
2374 9928 3.243839 ACCTAAAAAGGCAGTGCAACATG 60.244 43.478 18.61 0.00 41.43 3.21
2375 9929 2.965147 ACCTAAAAAGGCAGTGCAACAT 59.035 40.909 18.61 1.12 41.43 2.71
2376 9930 2.383855 ACCTAAAAAGGCAGTGCAACA 58.616 42.857 18.61 0.00 41.43 3.33
2377 9931 3.381045 GAACCTAAAAAGGCAGTGCAAC 58.619 45.455 18.61 0.00 0.00 4.17
2378 9932 2.364002 GGAACCTAAAAAGGCAGTGCAA 59.636 45.455 18.61 0.00 0.00 4.08
2379 9933 1.960689 GGAACCTAAAAAGGCAGTGCA 59.039 47.619 18.61 0.00 0.00 4.57
2380 9934 2.724977 GGAACCTAAAAAGGCAGTGC 57.275 50.000 6.55 6.55 0.00 4.40
2395 9949 5.221541 TGGGTACATTTCAATGTTTGGGAAC 60.222 40.000 10.38 2.15 46.95 3.62
2396 9950 4.901849 TGGGTACATTTCAATGTTTGGGAA 59.098 37.500 10.38 0.00 46.95 3.97
2397 9951 4.483950 TGGGTACATTTCAATGTTTGGGA 58.516 39.130 10.38 0.00 46.95 4.37
2398 9952 4.881019 TGGGTACATTTCAATGTTTGGG 57.119 40.909 10.38 0.00 46.95 4.12
2399 9953 7.875041 TGTTAATGGGTACATTTCAATGTTTGG 59.125 33.333 10.38 0.00 46.95 3.28
2400 9954 8.824159 TGTTAATGGGTACATTTCAATGTTTG 57.176 30.769 10.38 0.00 46.95 2.93
2401 9955 9.487790 CTTGTTAATGGGTACATTTCAATGTTT 57.512 29.630 10.38 1.88 46.95 2.83
2402 9956 7.602265 GCTTGTTAATGGGTACATTTCAATGTT 59.398 33.333 10.38 0.00 46.95 2.71
2404 9958 7.095910 TGCTTGTTAATGGGTACATTTCAATG 58.904 34.615 0.00 0.00 44.69 2.82
2405 9959 7.238486 TGCTTGTTAATGGGTACATTTCAAT 57.762 32.000 0.00 0.00 44.69 2.57
2406 9960 6.295011 CCTGCTTGTTAATGGGTACATTTCAA 60.295 38.462 0.00 4.96 44.69 2.69
2407 9961 5.184864 CCTGCTTGTTAATGGGTACATTTCA 59.815 40.000 0.00 0.00 44.69 2.69
2408 9962 5.394115 CCCTGCTTGTTAATGGGTACATTTC 60.394 44.000 0.00 0.00 44.69 2.17
2409 9963 4.466015 CCCTGCTTGTTAATGGGTACATTT 59.534 41.667 0.00 0.00 44.69 2.32
2411 9965 3.631250 CCCTGCTTGTTAATGGGTACAT 58.369 45.455 0.00 0.00 39.54 2.29
2412 9966 2.882229 GCCCTGCTTGTTAATGGGTACA 60.882 50.000 0.00 0.00 39.97 2.90
2413 9967 1.749063 GCCCTGCTTGTTAATGGGTAC 59.251 52.381 0.00 0.00 39.97 3.34
2414 9968 1.356059 TGCCCTGCTTGTTAATGGGTA 59.644 47.619 0.00 0.00 39.97 3.69
2415 9969 0.114168 TGCCCTGCTTGTTAATGGGT 59.886 50.000 0.00 0.00 39.97 4.51
2416 9970 1.488390 ATGCCCTGCTTGTTAATGGG 58.512 50.000 0.00 0.00 40.74 4.00
2417 9971 3.701040 ACTAATGCCCTGCTTGTTAATGG 59.299 43.478 0.00 0.00 0.00 3.16
2418 9972 4.989279 ACTAATGCCCTGCTTGTTAATG 57.011 40.909 0.00 0.00 0.00 1.90
2419 9973 5.264395 AGAACTAATGCCCTGCTTGTTAAT 58.736 37.500 0.00 0.00 0.00 1.40
2420 9974 4.662278 AGAACTAATGCCCTGCTTGTTAA 58.338 39.130 0.00 0.00 0.00 2.01
2421 9975 4.301072 AGAACTAATGCCCTGCTTGTTA 57.699 40.909 0.00 0.00 0.00 2.41
2422 9976 3.160679 AGAACTAATGCCCTGCTTGTT 57.839 42.857 0.00 0.00 0.00 2.83
2423 9977 2.887151 AGAACTAATGCCCTGCTTGT 57.113 45.000 0.00 0.00 0.00 3.16
2424 9978 5.841957 ATTTAGAACTAATGCCCTGCTTG 57.158 39.130 0.00 0.00 0.00 4.01
2425 9979 5.127682 CCAATTTAGAACTAATGCCCTGCTT 59.872 40.000 0.00 0.00 0.00 3.91
2426 9980 4.646492 CCAATTTAGAACTAATGCCCTGCT 59.354 41.667 0.00 0.00 0.00 4.24
2427 9981 4.737649 GCCAATTTAGAACTAATGCCCTGC 60.738 45.833 0.00 0.00 0.00 4.85
2428 9982 4.646492 AGCCAATTTAGAACTAATGCCCTG 59.354 41.667 0.00 0.00 0.00 4.45
2429 9983 4.871822 AGCCAATTTAGAACTAATGCCCT 58.128 39.130 0.00 0.00 0.00 5.19
2430 9984 6.901081 ATAGCCAATTTAGAACTAATGCCC 57.099 37.500 0.00 0.00 0.00 5.36
2431 9985 7.371159 GGAATAGCCAATTTAGAACTAATGCC 58.629 38.462 0.00 0.00 36.34 4.40
2432 9986 7.231519 AGGGAATAGCCAATTTAGAACTAATGC 59.768 37.037 0.00 0.00 38.95 3.56
2433 9987 8.697507 AGGGAATAGCCAATTTAGAACTAATG 57.302 34.615 0.00 0.00 38.95 1.90
2440 9994 9.615660 TCTCTAATAGGGAATAGCCAATTTAGA 57.384 33.333 0.00 0.00 38.95 2.10
2441 9995 9.883142 CTCTCTAATAGGGAATAGCCAATTTAG 57.117 37.037 0.00 0.00 38.95 1.85
2442 9996 8.322091 GCTCTCTAATAGGGAATAGCCAATTTA 58.678 37.037 0.00 0.00 38.95 1.40
2443 9997 7.171653 GCTCTCTAATAGGGAATAGCCAATTT 58.828 38.462 0.00 0.00 38.95 1.82
2444 9998 6.273260 TGCTCTCTAATAGGGAATAGCCAATT 59.727 38.462 0.00 0.00 38.95 2.32
2445 9999 5.787494 TGCTCTCTAATAGGGAATAGCCAAT 59.213 40.000 0.00 0.00 38.95 3.16
2446 10000 5.155161 TGCTCTCTAATAGGGAATAGCCAA 58.845 41.667 0.00 0.00 38.95 4.52
2447 10001 4.752063 TGCTCTCTAATAGGGAATAGCCA 58.248 43.478 0.00 0.00 38.95 4.75
2448 10002 4.775253 ACTGCTCTCTAATAGGGAATAGCC 59.225 45.833 0.00 0.00 0.00 3.93
2449 10003 5.245075 ACACTGCTCTCTAATAGGGAATAGC 59.755 44.000 0.00 0.00 0.00 2.97
2450 10004 6.348950 CGACACTGCTCTCTAATAGGGAATAG 60.349 46.154 0.00 0.00 0.00 1.73
2451 10005 5.473846 CGACACTGCTCTCTAATAGGGAATA 59.526 44.000 0.00 0.00 0.00 1.75
2452 10006 4.279671 CGACACTGCTCTCTAATAGGGAAT 59.720 45.833 0.00 0.00 0.00 3.01
2453 10007 3.632604 CGACACTGCTCTCTAATAGGGAA 59.367 47.826 0.00 0.00 0.00 3.97
2454 10008 3.215151 CGACACTGCTCTCTAATAGGGA 58.785 50.000 0.00 0.00 0.00 4.20
2455 10009 2.952978 ACGACACTGCTCTCTAATAGGG 59.047 50.000 0.00 0.00 0.00 3.53
2456 10010 3.003897 GGACGACACTGCTCTCTAATAGG 59.996 52.174 0.00 0.00 0.00 2.57
2457 10011 3.628032 TGGACGACACTGCTCTCTAATAG 59.372 47.826 0.00 0.00 0.00 1.73
2458 10012 3.617284 TGGACGACACTGCTCTCTAATA 58.383 45.455 0.00 0.00 0.00 0.98
2459 10013 2.425312 CTGGACGACACTGCTCTCTAAT 59.575 50.000 0.00 0.00 0.00 1.73
2460 10014 1.813178 CTGGACGACACTGCTCTCTAA 59.187 52.381 0.00 0.00 0.00 2.10
2461 10015 1.454201 CTGGACGACACTGCTCTCTA 58.546 55.000 0.00 0.00 0.00 2.43
2462 10016 1.247419 CCTGGACGACACTGCTCTCT 61.247 60.000 0.00 0.00 0.00 3.10
2463 10017 1.214062 CCTGGACGACACTGCTCTC 59.786 63.158 0.00 0.00 0.00 3.20
2464 10018 1.115930 AACCTGGACGACACTGCTCT 61.116 55.000 0.00 0.00 0.00 4.09
2465 10019 0.946221 CAACCTGGACGACACTGCTC 60.946 60.000 0.00 0.00 0.00 4.26
2466 10020 1.069765 CAACCTGGACGACACTGCT 59.930 57.895 0.00 0.00 0.00 4.24
2467 10021 2.607892 GCAACCTGGACGACACTGC 61.608 63.158 0.00 0.00 0.00 4.40
2468 10022 1.224069 CTGCAACCTGGACGACACTG 61.224 60.000 0.00 0.00 0.00 3.66
2469 10023 1.069765 CTGCAACCTGGACGACACT 59.930 57.895 0.00 0.00 0.00 3.55
2470 10024 2.607892 GCTGCAACCTGGACGACAC 61.608 63.158 0.00 0.00 0.00 3.67
2471 10025 2.280797 GCTGCAACCTGGACGACA 60.281 61.111 0.00 0.00 0.00 4.35
2472 10026 1.237285 ATTGCTGCAACCTGGACGAC 61.237 55.000 18.51 0.00 0.00 4.34
2473 10027 0.537143 AATTGCTGCAACCTGGACGA 60.537 50.000 18.51 0.00 0.00 4.20
2474 10028 0.109597 GAATTGCTGCAACCTGGACG 60.110 55.000 18.51 0.00 0.00 4.79
2475 10029 0.961019 TGAATTGCTGCAACCTGGAC 59.039 50.000 18.51 6.33 0.00 4.02
2476 10030 1.702182 TTGAATTGCTGCAACCTGGA 58.298 45.000 18.51 0.25 0.00 3.86
2477 10031 2.754946 ATTGAATTGCTGCAACCTGG 57.245 45.000 18.51 0.00 0.00 4.45
2478 10032 4.059511 TGAAATTGAATTGCTGCAACCTG 58.940 39.130 18.51 0.00 0.00 4.00
2479 10033 4.339872 TGAAATTGAATTGCTGCAACCT 57.660 36.364 18.51 7.91 0.00 3.50
2480 10034 5.616488 AATGAAATTGAATTGCTGCAACC 57.384 34.783 18.51 12.88 33.44 3.77
2481 10035 7.917720 AAAAATGAAATTGAATTGCTGCAAC 57.082 28.000 18.51 6.63 36.10 4.17
2517 10071 2.474410 AAAAGTTGCCCGAGTCTAGG 57.526 50.000 0.00 0.00 0.00 3.02
2518 10072 4.755411 TCATAAAAGTTGCCCGAGTCTAG 58.245 43.478 0.00 0.00 0.00 2.43
2519 10073 4.811969 TCATAAAAGTTGCCCGAGTCTA 57.188 40.909 0.00 0.00 0.00 2.59
2520 10074 3.695830 TCATAAAAGTTGCCCGAGTCT 57.304 42.857 0.00 0.00 0.00 3.24
2521 10075 4.192317 AGATCATAAAAGTTGCCCGAGTC 58.808 43.478 0.00 0.00 0.00 3.36
2522 10076 4.192317 GAGATCATAAAAGTTGCCCGAGT 58.808 43.478 0.00 0.00 0.00 4.18
2523 10077 3.561725 GGAGATCATAAAAGTTGCCCGAG 59.438 47.826 0.00 0.00 0.00 4.63
2524 10078 3.054728 TGGAGATCATAAAAGTTGCCCGA 60.055 43.478 0.00 0.00 0.00 5.14
2525 10079 3.278574 TGGAGATCATAAAAGTTGCCCG 58.721 45.455 0.00 0.00 0.00 6.13
2526 10080 5.659440 TTTGGAGATCATAAAAGTTGCCC 57.341 39.130 0.00 0.00 0.00 5.36
2534 10088 8.125978 AGCTGAACAAATTTGGAGATCATAAA 57.874 30.769 21.74 0.00 0.00 1.40
2575 10129 4.250080 GCCGAGCCAAAGCAAAAG 57.750 55.556 0.00 0.00 43.56 2.27
2593 10147 5.127519 TGAACCAATTTGGAAGCCATATCAG 59.872 40.000 22.19 0.00 40.96 2.90
2595 10149 5.351458 GTGAACCAATTTGGAAGCCATATC 58.649 41.667 22.19 7.19 40.96 1.63
2596 10150 4.162131 GGTGAACCAATTTGGAAGCCATAT 59.838 41.667 22.19 0.00 40.96 1.78
2597 10151 3.513515 GGTGAACCAATTTGGAAGCCATA 59.486 43.478 22.19 0.00 40.96 2.74
2598 10152 2.302733 GGTGAACCAATTTGGAAGCCAT 59.697 45.455 22.19 0.00 40.96 4.40
2617 10172 2.549754 CTGCTTTGAAACACGATCAGGT 59.450 45.455 0.00 0.00 0.00 4.00
2649 10204 8.186178 ACTACATACTGATCAAAGCTAAAACG 57.814 34.615 0.00 0.00 0.00 3.60
2748 10303 7.473735 AACTATCAGTCTGACATGAAGAGAA 57.526 36.000 10.88 0.00 0.00 2.87
2750 10305 6.756074 GGAAACTATCAGTCTGACATGAAGAG 59.244 42.308 10.88 13.04 0.00 2.85
2758 10313 4.220821 TCCTGTGGAAACTATCAGTCTGAC 59.779 45.833 4.21 0.00 0.00 3.51
2759 10314 4.220821 GTCCTGTGGAAACTATCAGTCTGA 59.779 45.833 4.68 4.68 31.38 3.27
2770 10325 2.650322 TGGTTTCAGTCCTGTGGAAAC 58.350 47.619 7.71 7.71 45.91 2.78
2779 10334 4.320608 TTCTGCAATTTGGTTTCAGTCC 57.679 40.909 0.00 0.00 0.00 3.85
2783 10338 7.640852 CATGAAATTTCTGCAATTTGGTTTCA 58.359 30.769 18.64 11.49 43.89 2.69
2795 10350 4.094294 ACAATGCATGCATGAAATTTCTGC 59.906 37.500 32.79 24.03 36.68 4.26
2813 10368 6.215121 TGAACTGGTTTTATCTGCAACAATG 58.785 36.000 0.00 0.00 0.00 2.82
2822 10377 6.839124 TGATTGCATGAACTGGTTTTATCT 57.161 33.333 0.00 0.00 0.00 1.98
2866 10423 3.838317 ACAGAAAGGTGCTGACTGGTATA 59.162 43.478 0.00 0.00 36.86 1.47
2874 10431 4.206375 TCATTTGAACAGAAAGGTGCTGA 58.794 39.130 0.00 0.00 36.86 4.26
2905 10462 3.062763 CGCTGCTGGATATAAGGAACAG 58.937 50.000 0.00 0.00 0.00 3.16
2914 10471 0.471617 AGAAAGGCGCTGCTGGATAT 59.528 50.000 7.64 0.00 0.00 1.63
2926 10483 6.127647 TGACCATATTTGTTCATCAGAAAGGC 60.128 38.462 0.00 0.00 35.08 4.35
2940 10497 6.015772 TCTGCATGATCCATTGACCATATTTG 60.016 38.462 0.00 0.00 0.00 2.32
2969 10526 3.005367 TGCTGATACGATATCGGAAAGCA 59.995 43.478 31.79 31.79 46.65 3.91
2976 10533 5.573146 TGCTCTAATGCTGATACGATATCG 58.427 41.667 23.18 23.18 46.33 2.92
2985 10542 4.101274 ACATGAGACTGCTCTAATGCTGAT 59.899 41.667 0.00 0.00 41.84 2.90
2991 10548 6.939163 ACTTTGAAACATGAGACTGCTCTAAT 59.061 34.615 0.00 0.00 41.84 1.73


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

AutoCloner maintained by Alex Coulton.