Multiple sequence alignment - TraesCS5D01G031900

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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 TraesCS5D01G031900 chr5D 100.000 4927 0 0 1 4927 29171334 29166408 0.000000e+00 9099.0
1 TraesCS5D01G031900 chr5D 98.659 3506 26 4 1434 4927 29604317 29600821 0.000000e+00 6194.0
2 TraesCS5D01G031900 chr5D 96.648 358 3 2 1088 1437 29604857 29604501 1.980000e-163 586.0
3 TraesCS5D01G031900 chr5D 92.500 40 2 1 3780 3818 29167500 29167461 6.890000e-04 56.5
4 TraesCS5D01G031900 chr5D 92.500 40 2 1 3835 3874 29167555 29167517 6.890000e-04 56.5
5 TraesCS5D01G031900 chr5D 92.500 40 2 1 3780 3818 29601912 29601873 6.890000e-04 56.5
6 TraesCS5D01G031900 chr5D 92.500 40 2 1 3835 3874 29601967 29601929 6.890000e-04 56.5
7 TraesCS5D01G031900 chr5A 92.601 1811 81 18 3130 4927 19981226 19979456 0.000000e+00 2553.0
8 TraesCS5D01G031900 chr5A 96.415 1283 28 8 1748 3026 19982493 19981225 0.000000e+00 2098.0
9 TraesCS5D01G031900 chr5A 94.310 826 27 10 1 825 19984359 19983553 0.000000e+00 1247.0
10 TraesCS5D01G031900 chr5A 90.084 595 48 7 1 587 19985726 19985135 0.000000e+00 761.0
11 TraesCS5D01G031900 chr5A 91.549 426 11 7 1027 1437 19983522 19983107 9.260000e-157 564.0
12 TraesCS5D01G031900 chr5A 90.462 346 17 6 1421 1753 19982926 19982584 4.530000e-120 442.0
13 TraesCS5D01G031900 chr5A 97.458 118 2 1 3015 3132 363850907 363850791 3.010000e-47 200.0
14 TraesCS5D01G031900 chr5A 94.400 125 6 1 3008 3132 503040139 503040016 1.810000e-44 191.0
15 TraesCS5D01G031900 chr5A 92.500 40 2 1 3835 3874 19980585 19980547 6.890000e-04 56.5
16 TraesCS5D01G031900 chr5B 95.683 695 20 4 2212 2906 21533203 21533887 0.000000e+00 1109.0
17 TraesCS5D01G031900 chr5B 87.140 972 63 26 3979 4927 21534734 21535666 0.000000e+00 1046.0
18 TraesCS5D01G031900 chr5B 93.036 560 31 4 3130 3681 21533920 21534479 0.000000e+00 811.0
19 TraesCS5D01G031900 chr5B 88.448 580 36 7 1434 1988 21532557 21533130 0.000000e+00 671.0
20 TraesCS5D01G031900 chr5B 90.930 441 15 11 1021 1437 21531935 21532374 1.990000e-158 569.0
21 TraesCS5D01G031900 chrUn 100.000 416 0 0 3671 4086 477220471 477220886 0.000000e+00 769.0
22 TraesCS5D01G031900 chrUn 92.500 40 2 1 3832 3871 477220577 477220615 6.890000e-04 56.5
23 TraesCS5D01G031900 chrUn 92.500 40 2 1 3777 3815 477220632 477220671 6.890000e-04 56.5
24 TraesCS5D01G031900 chr3A 79.362 596 79 20 1 579 102437206 102437774 3.600000e-101 379.0
25 TraesCS5D01G031900 chr3A 79.362 596 79 22 1 579 102492156 102492724 3.600000e-101 379.0
26 TraesCS5D01G031900 chr3A 78.830 581 76 23 19 579 102389745 102390298 1.020000e-91 348.0
27 TraesCS5D01G031900 chr3B 79.125 594 81 18 1 579 135770092 135770657 2.170000e-98 370.0
28 TraesCS5D01G031900 chr3B 78.824 595 81 21 1 579 135815077 135815642 4.690000e-95 359.0
29 TraesCS5D01G031900 chr3D 79.027 596 77 21 1 579 85828283 85828847 1.010000e-96 364.0
30 TraesCS5D01G031900 chr4A 98.246 114 2 0 3022 3135 381221436 381221323 3.010000e-47 200.0
31 TraesCS5D01G031900 chr1B 98.246 114 2 0 3018 3131 687253936 687254049 3.010000e-47 200.0
32 TraesCS5D01G031900 chr7A 98.246 114 1 1 3019 3132 381253918 381254030 1.080000e-46 198.0
33 TraesCS5D01G031900 chr2A 97.414 116 2 1 3020 3135 16796698 16796584 3.890000e-46 196.0
34 TraesCS5D01G031900 chr2A 85.470 117 11 4 144 255 120046338 120046453 3.120000e-22 117.0
35 TraesCS5D01G031900 chr1A 96.610 118 4 0 3017 3134 436435028 436435145 3.890000e-46 196.0
36 TraesCS5D01G031900 chr7D 93.701 127 7 1 3005 3131 615266735 615266610 6.510000e-44 189.0
37 TraesCS5D01G031900 chr2B 81.967 122 9 8 144 252 169859056 169859177 1.890000e-14 91.6
38 TraesCS5D01G031900 chr2B 91.228 57 5 0 196 252 169858686 169858742 1.470000e-10 78.7


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 TraesCS5D01G031900 chr5D 29166408 29171334 4926 True 3070.666667 9099 95.000000 1 4927 3 chr5D.!!$R1 4926
1 TraesCS5D01G031900 chr5D 29600821 29604857 4036 True 1723.250000 6194 95.076750 1088 4927 4 chr5D.!!$R2 3839
2 TraesCS5D01G031900 chr5A 19979456 19985726 6270 True 1103.071429 2553 92.560143 1 4927 7 chr5A.!!$R3 4926
3 TraesCS5D01G031900 chr5B 21531935 21535666 3731 False 841.200000 1109 91.047400 1021 4927 5 chr5B.!!$F1 3906
4 TraesCS5D01G031900 chr3A 102437206 102437774 568 False 379.000000 379 79.362000 1 579 1 chr3A.!!$F2 578
5 TraesCS5D01G031900 chr3A 102492156 102492724 568 False 379.000000 379 79.362000 1 579 1 chr3A.!!$F3 578
6 TraesCS5D01G031900 chr3A 102389745 102390298 553 False 348.000000 348 78.830000 19 579 1 chr3A.!!$F1 560
7 TraesCS5D01G031900 chr3B 135770092 135770657 565 False 370.000000 370 79.125000 1 579 1 chr3B.!!$F1 578
8 TraesCS5D01G031900 chr3B 135815077 135815642 565 False 359.000000 359 78.824000 1 579 1 chr3B.!!$F2 578
9 TraesCS5D01G031900 chr3D 85828283 85828847 564 False 364.000000 364 79.027000 1 579 1 chr3D.!!$F1 578

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
851 2220 0.107703 GAATCGTCATGCCCAGGACA 60.108 55.000 12.71 1.86 41.73 4.02 F
854 2223 0.327924 TCGTCATGCCCAGGACAATT 59.672 50.000 12.71 0.00 41.73 2.32 F
857 2226 0.703488 TCATGCCCAGGACAATTCCA 59.297 50.000 0.00 0.00 45.72 3.53 F
1036 2405 0.823460 CCCACCCATTTCATTTCCCG 59.177 55.000 0.00 0.00 0.00 5.14 F
2569 4324 1.615392 GCAATGTCCTTTTCAGGCTGT 59.385 47.619 15.27 0.00 40.58 4.40 F
3505 5273 0.882927 TTCCTTTCACGCCCTTGTCG 60.883 55.000 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 3654 6.692849 ATGACAGCATGATATTAGGGAGAA 57.307 37.500 0.00 0.00 39.69 2.87 R
3031 4791 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69 R
3049 4809 8.311395 AGTTCTAGATACATCCATTTCTGTGA 57.689 34.615 0.00 0.00 0.00 3.58 R
3505 5273 0.321298 TCTTCCTTTGCGCCCTACAC 60.321 55.000 4.18 0.00 0.00 2.90 R
3543 5311 0.527565 GCCAGTTGATTCAACCGCAT 59.472 50.000 22.70 4.77 44.49 4.73 R
4372 6206 2.758009 GCAGAGCATCCTTGAGAGATC 58.242 52.381 0.00 0.00 33.66 2.75 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
45 46 1.205417 CATGTTGATGTGGCCCCTTTC 59.795 52.381 0.00 0.00 0.00 2.62
59 65 2.159014 CCCCTTTCACATGCATCAATGG 60.159 50.000 0.00 2.13 31.46 3.16
79 87 1.594862 GATGTTGACGTGGCATAGCTC 59.405 52.381 0.00 0.00 0.00 4.09
100 108 3.196685 TCCACGTTATCATGTCCATCACA 59.803 43.478 0.00 0.00 40.18 3.58
300 308 8.682936 AGACTTGAAATATATCCACAACATCC 57.317 34.615 0.00 0.00 0.00 3.51
330 338 1.066303 GCGGACACGATTGATCTCTCT 59.934 52.381 0.00 0.00 44.60 3.10
334 342 5.340803 CGGACACGATTGATCTCTCTAAAA 58.659 41.667 0.00 0.00 44.60 1.52
376 399 6.239402 CCACTCCCTCATTCAAAAATGTCTTT 60.239 38.462 0.00 0.00 42.46 2.52
379 402 7.177392 ACTCCCTCATTCAAAAATGTCTTTAGG 59.823 37.037 0.00 0.00 42.46 2.69
431 454 8.024145 TGGAGGCCTAAAGAAAAACAATTAAA 57.976 30.769 4.42 0.00 0.00 1.52
432 455 8.655901 TGGAGGCCTAAAGAAAAACAATTAAAT 58.344 29.630 4.42 0.00 0.00 1.40
480 503 4.923281 GTGGTGAAAAATAATGTGGACTGC 59.077 41.667 0.00 0.00 0.00 4.40
482 505 3.608073 GTGAAAAATAATGTGGACTGCGC 59.392 43.478 0.00 0.00 0.00 6.09
521 544 5.109500 TGTCAAGCATACCATGATTACCA 57.891 39.130 0.00 0.00 36.64 3.25
553 576 5.874810 GCGATCTTATATGGCCATCTTGTTA 59.125 40.000 24.80 3.19 0.00 2.41
556 579 8.446273 CGATCTTATATGGCCATCTTGTTAAAG 58.554 37.037 24.80 12.42 34.45 1.85
560 583 4.701956 ATGGCCATCTTGTTAAAGTTCG 57.298 40.909 14.09 0.00 34.78 3.95
582 605 5.045869 TCGGTTCAGTGATTAAAATCCTCCT 60.046 40.000 0.00 0.00 34.50 3.69
587 610 7.502060 TCAGTGATTAAAATCCTCCTTCTCT 57.498 36.000 0.41 0.00 34.50 3.10
588 611 7.560368 TCAGTGATTAAAATCCTCCTTCTCTC 58.440 38.462 0.41 0.00 34.50 3.20
600 1968 2.564553 CTTCTCTCGGGGTGAAGGCG 62.565 65.000 11.03 0.00 40.10 5.52
616 1984 4.020928 TGAAGGCGTTAACTTCTATGGACA 60.021 41.667 3.71 0.00 43.59 4.02
635 2003 4.262249 GGACACATGTATCTCTTAGGAGCC 60.262 50.000 3.76 0.00 39.31 4.70
684 2052 1.246056 TGAGGTTCGTACGGTCCAGG 61.246 60.000 23.60 0.00 0.00 4.45
771 2140 3.089284 AGCTTAACAAACAGGCCCATAC 58.911 45.455 0.00 0.00 0.00 2.39
776 2145 0.251916 CAAACAGGCCCATACGAGGA 59.748 55.000 0.00 0.00 0.00 3.71
783 2152 3.261897 CAGGCCCATACGAGGAATATCTT 59.738 47.826 0.00 0.00 0.00 2.40
825 2194 5.071384 TGAGGTGATGCATTGATATCTCTGT 59.929 40.000 0.00 0.00 0.00 3.41
827 2196 5.071384 AGGTGATGCATTGATATCTCTGTGA 59.929 40.000 0.00 0.00 0.00 3.58
828 2197 5.408909 GGTGATGCATTGATATCTCTGTGAG 59.591 44.000 0.00 0.00 0.00 3.51
831 2200 4.773013 TGCATTGATATCTCTGTGAGCAA 58.227 39.130 3.98 0.00 0.00 3.91
832 2201 4.814771 TGCATTGATATCTCTGTGAGCAAG 59.185 41.667 3.98 0.00 0.00 4.01
833 2202 5.055144 GCATTGATATCTCTGTGAGCAAGA 58.945 41.667 3.98 0.00 0.00 3.02
834 2203 5.526479 GCATTGATATCTCTGTGAGCAAGAA 59.474 40.000 3.98 0.00 0.00 2.52
836 2205 7.571613 GCATTGATATCTCTGTGAGCAAGAATC 60.572 40.741 3.98 0.00 0.00 2.52
838 2207 3.883830 ATCTCTGTGAGCAAGAATCGT 57.116 42.857 0.00 0.00 0.00 3.73
840 2209 2.558359 TCTCTGTGAGCAAGAATCGTCA 59.442 45.455 0.00 0.00 0.00 4.35
841 2210 3.194329 TCTCTGTGAGCAAGAATCGTCAT 59.806 43.478 0.00 0.00 0.00 3.06
842 2211 3.256558 TCTGTGAGCAAGAATCGTCATG 58.743 45.455 0.00 0.00 0.00 3.07
843 2212 1.733912 TGTGAGCAAGAATCGTCATGC 59.266 47.619 0.00 0.00 46.52 4.06
846 2215 2.481212 GCAAGAATCGTCATGCCCA 58.519 52.632 0.00 0.00 41.58 5.36
849 2218 0.911769 AAGAATCGTCATGCCCAGGA 59.088 50.000 0.00 0.00 0.00 3.86
850 2219 0.179000 AGAATCGTCATGCCCAGGAC 59.821 55.000 3.18 3.18 38.61 3.85
851 2220 0.107703 GAATCGTCATGCCCAGGACA 60.108 55.000 12.71 1.86 41.73 4.02
853 2222 0.548031 ATCGTCATGCCCAGGACAAT 59.452 50.000 12.71 0.00 41.73 2.71
854 2223 0.327924 TCGTCATGCCCAGGACAATT 59.672 50.000 12.71 0.00 41.73 2.32
855 2224 0.734889 CGTCATGCCCAGGACAATTC 59.265 55.000 12.71 0.00 41.73 2.17
856 2225 1.106285 GTCATGCCCAGGACAATTCC 58.894 55.000 8.07 0.00 41.33 3.01
857 2226 0.703488 TCATGCCCAGGACAATTCCA 59.297 50.000 0.00 0.00 45.72 3.53
858 2227 1.288633 TCATGCCCAGGACAATTCCAT 59.711 47.619 0.00 0.00 45.72 3.41
859 2228 1.411246 CATGCCCAGGACAATTCCATG 59.589 52.381 0.00 0.00 45.72 3.66
860 2229 0.971959 TGCCCAGGACAATTCCATGC 60.972 55.000 0.00 0.00 45.72 4.06
861 2230 0.971959 GCCCAGGACAATTCCATGCA 60.972 55.000 0.00 0.00 45.72 3.96
862 2231 1.559368 CCCAGGACAATTCCATGCAA 58.441 50.000 0.00 0.00 45.72 4.08
863 2232 2.112998 CCCAGGACAATTCCATGCAAT 58.887 47.619 0.00 0.00 45.72 3.56
864 2233 2.159014 CCCAGGACAATTCCATGCAATG 60.159 50.000 0.00 0.00 45.72 2.82
865 2234 2.546778 CAGGACAATTCCATGCAATGC 58.453 47.619 0.00 0.00 44.97 3.56
866 2235 2.167693 CAGGACAATTCCATGCAATGCT 59.832 45.455 6.82 0.00 44.97 3.79
867 2236 2.835764 AGGACAATTCCATGCAATGCTT 59.164 40.909 6.82 0.00 44.97 3.91
868 2237 3.262405 AGGACAATTCCATGCAATGCTTT 59.738 39.130 6.82 0.00 44.97 3.51
869 2238 4.004982 GGACAATTCCATGCAATGCTTTT 58.995 39.130 6.82 0.00 44.97 2.27
870 2239 4.142773 GGACAATTCCATGCAATGCTTTTG 60.143 41.667 6.82 4.40 44.97 2.44
871 2240 4.643463 ACAATTCCATGCAATGCTTTTGA 58.357 34.783 6.82 0.00 44.97 2.69
872 2241 4.453136 ACAATTCCATGCAATGCTTTTGAC 59.547 37.500 6.82 0.00 44.97 3.18
873 2242 2.747396 TCCATGCAATGCTTTTGACC 57.253 45.000 6.82 0.00 44.97 4.02
874 2243 1.969208 TCCATGCAATGCTTTTGACCA 59.031 42.857 6.82 0.00 44.97 4.02
875 2244 2.568062 TCCATGCAATGCTTTTGACCAT 59.432 40.909 6.82 0.00 44.97 3.55
876 2245 2.675844 CCATGCAATGCTTTTGACCATG 59.324 45.455 6.82 0.00 44.97 3.66
877 2246 3.331150 CATGCAATGCTTTTGACCATGT 58.669 40.909 6.82 0.00 37.62 3.21
878 2247 4.496360 CATGCAATGCTTTTGACCATGTA 58.504 39.130 6.82 0.00 37.62 2.29
879 2248 4.597404 TGCAATGCTTTTGACCATGTAA 57.403 36.364 6.82 0.00 0.00 2.41
880 2249 5.149973 TGCAATGCTTTTGACCATGTAAT 57.850 34.783 6.82 0.00 0.00 1.89
881 2250 5.549347 TGCAATGCTTTTGACCATGTAATT 58.451 33.333 6.82 0.00 0.00 1.40
882 2251 5.996513 TGCAATGCTTTTGACCATGTAATTT 59.003 32.000 6.82 0.00 0.00 1.82
883 2252 6.073167 TGCAATGCTTTTGACCATGTAATTTG 60.073 34.615 6.82 0.00 0.00 2.32
884 2253 6.308675 CAATGCTTTTGACCATGTAATTTGC 58.691 36.000 0.00 0.00 0.00 3.68
885 2254 5.212532 TGCTTTTGACCATGTAATTTGCT 57.787 34.783 0.00 0.00 0.00 3.91
886 2255 6.338214 TGCTTTTGACCATGTAATTTGCTA 57.662 33.333 0.00 0.00 0.00 3.49
887 2256 6.753180 TGCTTTTGACCATGTAATTTGCTAA 58.247 32.000 0.00 0.00 0.00 3.09
888 2257 7.212976 TGCTTTTGACCATGTAATTTGCTAAA 58.787 30.769 0.00 0.00 0.00 1.85
889 2258 7.712639 TGCTTTTGACCATGTAATTTGCTAAAA 59.287 29.630 0.00 0.00 0.00 1.52
890 2259 8.555361 GCTTTTGACCATGTAATTTGCTAAAAA 58.445 29.630 0.00 0.00 0.00 1.94
947 2316 9.840427 AAGTATTTTTATGTTGAAACGGATGAG 57.160 29.630 0.00 0.00 0.00 2.90
948 2317 9.226606 AGTATTTTTATGTTGAAACGGATGAGA 57.773 29.630 0.00 0.00 0.00 3.27
949 2318 9.274065 GTATTTTTATGTTGAAACGGATGAGAC 57.726 33.333 0.00 0.00 0.00 3.36
950 2319 6.869315 TTTTATGTTGAAACGGATGAGACA 57.131 33.333 0.00 0.00 0.00 3.41
951 2320 6.480524 TTTATGTTGAAACGGATGAGACAG 57.519 37.500 0.00 0.00 0.00 3.51
952 2321 3.744238 TGTTGAAACGGATGAGACAGA 57.256 42.857 0.00 0.00 0.00 3.41
953 2322 4.066646 TGTTGAAACGGATGAGACAGAA 57.933 40.909 0.00 0.00 0.00 3.02
954 2323 4.447290 TGTTGAAACGGATGAGACAGAAA 58.553 39.130 0.00 0.00 0.00 2.52
955 2324 5.063204 TGTTGAAACGGATGAGACAGAAAT 58.937 37.500 0.00 0.00 0.00 2.17
956 2325 5.530915 TGTTGAAACGGATGAGACAGAAATT 59.469 36.000 0.00 0.00 0.00 1.82
957 2326 6.708502 TGTTGAAACGGATGAGACAGAAATTA 59.291 34.615 0.00 0.00 0.00 1.40
958 2327 6.968131 TGAAACGGATGAGACAGAAATTAG 57.032 37.500 0.00 0.00 0.00 1.73
959 2328 6.697395 TGAAACGGATGAGACAGAAATTAGA 58.303 36.000 0.00 0.00 0.00 2.10
960 2329 6.590292 TGAAACGGATGAGACAGAAATTAGAC 59.410 38.462 0.00 0.00 0.00 2.59
961 2330 5.661056 ACGGATGAGACAGAAATTAGACA 57.339 39.130 0.00 0.00 0.00 3.41
962 2331 5.655488 ACGGATGAGACAGAAATTAGACAG 58.345 41.667 0.00 0.00 0.00 3.51
963 2332 5.046529 CGGATGAGACAGAAATTAGACAGG 58.953 45.833 0.00 0.00 0.00 4.00
964 2333 4.813697 GGATGAGACAGAAATTAGACAGGC 59.186 45.833 0.00 0.00 0.00 4.85
965 2334 4.207891 TGAGACAGAAATTAGACAGGCC 57.792 45.455 0.00 0.00 0.00 5.19
966 2335 3.840666 TGAGACAGAAATTAGACAGGCCT 59.159 43.478 0.00 0.00 0.00 5.19
967 2336 5.023452 TGAGACAGAAATTAGACAGGCCTA 58.977 41.667 3.98 0.00 0.00 3.93
968 2337 5.663106 TGAGACAGAAATTAGACAGGCCTAT 59.337 40.000 3.98 0.00 0.00 2.57
969 2338 6.839134 TGAGACAGAAATTAGACAGGCCTATA 59.161 38.462 3.98 0.00 0.00 1.31
970 2339 7.510685 TGAGACAGAAATTAGACAGGCCTATAT 59.489 37.037 3.98 0.00 0.00 0.86
971 2340 8.958060 AGACAGAAATTAGACAGGCCTATATA 57.042 34.615 3.98 0.00 0.00 0.86
972 2341 9.030452 AGACAGAAATTAGACAGGCCTATATAG 57.970 37.037 3.98 2.46 0.00 1.31
973 2342 8.728596 ACAGAAATTAGACAGGCCTATATAGT 57.271 34.615 3.98 0.00 0.00 2.12
974 2343 8.589338 ACAGAAATTAGACAGGCCTATATAGTG 58.411 37.037 3.98 0.00 0.00 2.74
975 2344 8.589338 CAGAAATTAGACAGGCCTATATAGTGT 58.411 37.037 3.98 0.00 0.00 3.55
976 2345 9.160412 AGAAATTAGACAGGCCTATATAGTGTT 57.840 33.333 3.98 0.00 0.00 3.32
977 2346 9.209175 GAAATTAGACAGGCCTATATAGTGTTG 57.791 37.037 3.98 6.14 0.00 3.33
978 2347 6.665992 TTAGACAGGCCTATATAGTGTTGG 57.334 41.667 3.98 0.00 0.00 3.77
979 2348 3.904339 AGACAGGCCTATATAGTGTTGGG 59.096 47.826 3.98 0.00 0.00 4.12
980 2349 2.372172 ACAGGCCTATATAGTGTTGGGC 59.628 50.000 3.98 6.25 42.68 5.36
983 2352 3.790089 GCCTATATAGTGTTGGGCCTT 57.210 47.619 4.53 0.00 34.19 4.35
984 2353 3.412386 GCCTATATAGTGTTGGGCCTTG 58.588 50.000 4.53 0.00 34.19 3.61
985 2354 3.412386 CCTATATAGTGTTGGGCCTTGC 58.588 50.000 4.53 0.00 0.00 4.01
986 2355 3.181445 CCTATATAGTGTTGGGCCTTGCA 60.181 47.826 4.53 0.00 0.00 4.08
987 2356 3.600448 ATATAGTGTTGGGCCTTGCAT 57.400 42.857 4.53 0.00 0.00 3.96
988 2357 2.236489 ATAGTGTTGGGCCTTGCATT 57.764 45.000 4.53 0.45 0.00 3.56
989 2358 1.544724 TAGTGTTGGGCCTTGCATTC 58.455 50.000 4.53 0.00 0.00 2.67
990 2359 1.080569 GTGTTGGGCCTTGCATTCG 60.081 57.895 4.53 0.00 0.00 3.34
991 2360 2.274645 TGTTGGGCCTTGCATTCGG 61.275 57.895 4.53 0.00 0.00 4.30
992 2361 2.679642 TTGGGCCTTGCATTCGGG 60.680 61.111 4.53 0.00 0.00 5.14
993 2362 3.216985 TTGGGCCTTGCATTCGGGA 62.217 57.895 4.53 0.00 0.00 5.14
994 2363 3.140814 GGGCCTTGCATTCGGGAC 61.141 66.667 0.84 0.00 0.00 4.46
995 2364 2.361104 GGCCTTGCATTCGGGACA 60.361 61.111 0.00 0.00 0.00 4.02
996 2365 2.409870 GGCCTTGCATTCGGGACAG 61.410 63.158 0.00 0.00 0.00 3.51
997 2366 2.409870 GCCTTGCATTCGGGACAGG 61.410 63.158 0.00 0.00 0.00 4.00
998 2367 2.409870 CCTTGCATTCGGGACAGGC 61.410 63.158 0.00 0.00 0.00 4.85
999 2368 2.361104 TTGCATTCGGGACAGGCC 60.361 61.111 0.00 0.00 0.00 5.19
1000 2369 4.776322 TGCATTCGGGACAGGCCG 62.776 66.667 0.00 0.00 37.63 6.13
1001 2370 4.778143 GCATTCGGGACAGGCCGT 62.778 66.667 0.00 0.00 37.63 5.68
1002 2371 2.819595 CATTCGGGACAGGCCGTG 60.820 66.667 4.94 2.95 37.63 4.94
1003 2372 3.000819 ATTCGGGACAGGCCGTGA 61.001 61.111 4.94 0.00 37.63 4.35
1004 2373 2.589157 ATTCGGGACAGGCCGTGAA 61.589 57.895 4.94 1.22 36.52 3.18
1005 2374 1.910580 ATTCGGGACAGGCCGTGAAT 61.911 55.000 5.71 5.71 37.50 2.57
1006 2375 2.511600 CGGGACAGGCCGTGAATC 60.512 66.667 4.94 0.00 37.63 2.52
1007 2376 2.124695 GGGACAGGCCGTGAATCC 60.125 66.667 4.94 5.25 37.63 3.01
1008 2377 2.124695 GGACAGGCCGTGAATCCC 60.125 66.667 4.94 0.00 0.00 3.85
1009 2378 2.670148 GGACAGGCCGTGAATCCCT 61.670 63.158 4.94 0.00 0.00 4.20
1010 2379 1.153349 GACAGGCCGTGAATCCCTC 60.153 63.158 4.94 0.00 0.00 4.30
1011 2380 2.202932 CAGGCCGTGAATCCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
1015 2384 3.833645 CCGTGAATCCCTCGGCGA 61.834 66.667 10.14 10.14 43.70 5.54
1016 2385 2.278857 CGTGAATCCCTCGGCGAG 60.279 66.667 29.16 29.16 0.00 5.03
1017 2386 2.586357 GTGAATCCCTCGGCGAGC 60.586 66.667 30.55 17.04 0.00 5.03
1018 2387 3.849951 TGAATCCCTCGGCGAGCC 61.850 66.667 30.55 15.89 0.00 4.70
1019 2388 4.610714 GAATCCCTCGGCGAGCCC 62.611 72.222 30.55 12.91 0.00 5.19
1036 2405 0.823460 CCCACCCATTTCATTTCCCG 59.177 55.000 0.00 0.00 0.00 5.14
1062 2431 2.478894 TCCGCACTGAAAATTCGAACTC 59.521 45.455 0.00 0.00 0.00 3.01
1063 2432 2.486128 CGCACTGAAAATTCGAACTCG 58.514 47.619 0.00 0.00 41.45 4.18
1064 2433 2.234187 GCACTGAAAATTCGAACTCGC 58.766 47.619 0.00 0.00 39.60 5.03
1066 2435 2.223144 CACTGAAAATTCGAACTCGCCA 59.777 45.455 0.00 0.00 39.60 5.69
1083 2469 2.275318 GCCACAGAAAGAGAGGAATCG 58.725 52.381 0.00 0.00 0.00 3.34
1101 2487 1.622752 GTCCCCAATTCCCCCTCCT 60.623 63.158 0.00 0.00 0.00 3.69
1105 2491 2.124151 CAATTCCCCCTCCTGCCG 60.124 66.667 0.00 0.00 0.00 5.69
1498 3108 3.017581 GGCTGAGGGTCATGGGGT 61.018 66.667 0.00 0.00 0.00 4.95
1511 3122 1.895131 CATGGGGTTTCTCTTGTTGGG 59.105 52.381 0.00 0.00 0.00 4.12
1535 3146 2.352032 GGTGGAGGACGAGGTGGAG 61.352 68.421 0.00 0.00 0.00 3.86
1804 3539 2.916716 GGTTTACAATTGCAGCATCGTG 59.083 45.455 5.05 0.00 0.00 4.35
2569 4324 1.615392 GCAATGTCCTTTTCAGGCTGT 59.385 47.619 15.27 0.00 40.58 4.40
2570 4325 2.036346 GCAATGTCCTTTTCAGGCTGTT 59.964 45.455 15.27 0.00 40.58 3.16
2571 4326 3.858503 GCAATGTCCTTTTCAGGCTGTTC 60.859 47.826 15.27 0.00 40.58 3.18
2572 4327 3.515602 ATGTCCTTTTCAGGCTGTTCT 57.484 42.857 15.27 0.00 40.58 3.01
2573 4328 3.297134 TGTCCTTTTCAGGCTGTTCTT 57.703 42.857 15.27 0.00 40.58 2.52
3031 4791 9.275572 TGTTACTGGAATTAATTACTACTCCCT 57.724 33.333 11.70 0.00 0.00 4.20
3049 4809 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
3050 4810 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
3051 4811 3.581755 CTCCGTTCCAAATTACTCGTCA 58.418 45.455 0.00 0.00 0.00 4.35
3052 4812 3.319755 TCCGTTCCAAATTACTCGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3053 4813 3.061322 CCGTTCCAAATTACTCGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3054 4814 3.122948 CCGTTCCAAATTACTCGTCACAG 59.877 47.826 0.00 0.00 0.00 3.66
3055 4815 3.985279 CGTTCCAAATTACTCGTCACAGA 59.015 43.478 0.00 0.00 0.00 3.41
3056 4816 4.446385 CGTTCCAAATTACTCGTCACAGAA 59.554 41.667 0.00 0.00 0.00 3.02
3505 5273 0.882927 TTCCTTTCACGCCCTTGTCG 60.883 55.000 0.00 0.00 0.00 4.35
3543 5311 7.125792 GGAAGATCCTACTTGTTGATCCTTA 57.874 40.000 0.00 0.00 36.41 2.69
4303 6137 2.435586 GGATGCAGCAGCGACAGT 60.436 61.111 3.51 0.00 46.23 3.55
4366 6200 3.099905 GTGAGATGGATCCCGGATCATA 58.900 50.000 25.68 15.75 40.50 2.15
4372 6206 7.398332 TGAGATGGATCCCGGATCATATATATG 59.602 40.741 25.68 15.47 40.50 1.78
4664 6504 4.492085 GGCGAAAGTAAACTTATCAGCGAC 60.492 45.833 0.00 0.00 34.61 5.19
4803 6643 2.037136 CGGCAGAAAGGAGCTGTGG 61.037 63.158 0.00 0.00 35.81 4.17
4839 6683 3.630892 AGTCTAGTACGGAGAGAAGCA 57.369 47.619 1.18 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.635324 CACATCAACATGCTACCATACACA 59.365 41.667 0.00 0.00 32.57 3.72
14 15 4.035558 CCACATCAACATGCTACCATACAC 59.964 45.833 0.00 0.00 32.57 2.90
17 18 3.213506 GCCACATCAACATGCTACCATA 58.786 45.455 0.00 0.00 32.57 2.74
59 65 1.594862 GAGCTATGCCACGTCAACATC 59.405 52.381 0.00 0.00 0.00 3.06
79 87 3.530535 TGTGATGGACATGATAACGTGG 58.469 45.455 0.00 0.00 37.35 4.94
82 90 5.525012 ACAAGATGTGATGGACATGATAACG 59.475 40.000 0.00 0.00 45.90 3.18
212 220 7.603784 AGTTTGGTGGCATCTTTTTCATTTATC 59.396 33.333 0.00 0.00 0.00 1.75
300 308 2.230940 CGTGTCCGCTAATGCTCCG 61.231 63.158 0.00 0.00 36.97 4.63
334 342 1.684450 GTGGGTTCGGTTGACCATTTT 59.316 47.619 0.51 0.00 38.98 1.82
347 368 2.879103 TTGAATGAGGGAGTGGGTTC 57.121 50.000 0.00 0.00 0.00 3.62
376 399 5.417580 GTGGATAACACCATCAAAAAGCCTA 59.582 40.000 0.00 0.00 44.49 3.93
480 503 5.647589 TGACATAGTAAAGAAGGTACAGCG 58.352 41.667 0.00 0.00 0.00 5.18
482 505 7.097192 TGCTTGACATAGTAAAGAAGGTACAG 58.903 38.462 0.00 0.00 0.00 2.74
521 544 5.711506 TGGCCATATAAGATCGCATTTGATT 59.288 36.000 0.00 0.00 0.00 2.57
553 576 7.230712 AGGATTTTAATCACTGAACCGAACTTT 59.769 33.333 4.97 0.00 37.15 2.66
556 579 6.403309 GGAGGATTTTAATCACTGAACCGAAC 60.403 42.308 4.97 0.00 37.15 3.95
560 583 6.887002 AGAAGGAGGATTTTAATCACTGAACC 59.113 38.462 4.97 0.00 37.15 3.62
582 605 2.646175 CGCCTTCACCCCGAGAGAA 61.646 63.158 0.00 0.00 0.00 2.87
587 610 1.004679 GTTAACGCCTTCACCCCGA 60.005 57.895 0.00 0.00 0.00 5.14
588 611 0.604511 AAGTTAACGCCTTCACCCCG 60.605 55.000 0.00 0.00 0.00 5.73
600 1968 9.250624 GAGATACATGTGTCCATAGAAGTTAAC 57.749 37.037 17.94 0.00 0.00 2.01
616 1984 3.833732 TCGGCTCCTAAGAGATACATGT 58.166 45.455 2.69 2.69 43.39 3.21
635 2003 6.446781 TGTTGGGTCTAGTTTACTCTATCG 57.553 41.667 0.00 0.00 0.00 2.92
684 2052 4.479619 GTTGTCTGGACTGCATTTGATTC 58.520 43.478 2.38 0.00 0.00 2.52
745 2113 2.491693 GGCCTGTTTGTTAAGCTGCATA 59.508 45.455 1.02 0.00 0.00 3.14
771 2140 1.543429 GGGTGCCCAAGATATTCCTCG 60.543 57.143 1.66 0.00 35.81 4.63
802 2171 5.408909 CACAGAGATATCAATGCATCACCTC 59.591 44.000 0.00 1.81 0.00 3.85
803 2172 5.071384 TCACAGAGATATCAATGCATCACCT 59.929 40.000 0.00 0.00 0.00 4.00
831 2200 0.179000 GTCCTGGGCATGACGATTCT 59.821 55.000 0.00 0.00 0.00 2.40
832 2201 0.107703 TGTCCTGGGCATGACGATTC 60.108 55.000 0.00 0.00 34.18 2.52
833 2202 0.327924 TTGTCCTGGGCATGACGATT 59.672 50.000 0.00 0.00 34.18 3.34
834 2203 0.548031 ATTGTCCTGGGCATGACGAT 59.452 50.000 0.00 0.00 34.18 3.73
836 2205 0.734889 GAATTGTCCTGGGCATGACG 59.265 55.000 0.00 0.00 34.18 4.35
838 2207 0.703488 TGGAATTGTCCTGGGCATGA 59.297 50.000 0.00 0.00 45.22 3.07
840 2209 1.784358 CATGGAATTGTCCTGGGCAT 58.216 50.000 0.00 0.00 45.22 4.40
841 2210 0.971959 GCATGGAATTGTCCTGGGCA 60.972 55.000 0.00 0.00 45.22 5.36
842 2211 0.971959 TGCATGGAATTGTCCTGGGC 60.972 55.000 0.00 0.00 45.22 5.36
843 2212 1.559368 TTGCATGGAATTGTCCTGGG 58.441 50.000 0.00 0.00 45.22 4.45
844 2213 2.740580 GCATTGCATGGAATTGTCCTGG 60.741 50.000 10.07 0.00 45.22 4.45
845 2214 2.167693 AGCATTGCATGGAATTGTCCTG 59.832 45.455 10.07 0.56 45.22 3.86
846 2215 2.463752 AGCATTGCATGGAATTGTCCT 58.536 42.857 10.07 2.01 45.22 3.85
849 2218 4.453136 GTCAAAAGCATTGCATGGAATTGT 59.547 37.500 10.07 0.00 0.00 2.71
850 2219 4.142773 GGTCAAAAGCATTGCATGGAATTG 60.143 41.667 10.07 6.79 0.00 2.32
851 2220 4.004982 GGTCAAAAGCATTGCATGGAATT 58.995 39.130 10.07 0.00 0.00 2.17
853 2222 2.367894 TGGTCAAAAGCATTGCATGGAA 59.632 40.909 11.91 0.79 0.00 3.53
854 2223 1.969208 TGGTCAAAAGCATTGCATGGA 59.031 42.857 11.91 0.00 0.00 3.41
855 2224 2.459060 TGGTCAAAAGCATTGCATGG 57.541 45.000 11.91 0.00 0.00 3.66
856 2225 3.331150 ACATGGTCAAAAGCATTGCATG 58.669 40.909 11.91 15.07 41.59 4.06
857 2226 3.688694 ACATGGTCAAAAGCATTGCAT 57.311 38.095 11.91 0.00 41.59 3.96
858 2227 4.597404 TTACATGGTCAAAAGCATTGCA 57.403 36.364 11.91 0.00 41.59 4.08
859 2228 6.308675 CAAATTACATGGTCAAAAGCATTGC 58.691 36.000 0.00 0.00 41.59 3.56
860 2229 6.148150 AGCAAATTACATGGTCAAAAGCATTG 59.852 34.615 0.00 0.00 41.59 2.82
861 2230 6.232692 AGCAAATTACATGGTCAAAAGCATT 58.767 32.000 0.00 0.00 41.59 3.56
862 2231 5.797051 AGCAAATTACATGGTCAAAAGCAT 58.203 33.333 0.00 0.00 44.28 3.79
863 2232 5.212532 AGCAAATTACATGGTCAAAAGCA 57.787 34.783 0.00 0.00 37.29 3.91
864 2233 7.650834 TTTAGCAAATTACATGGTCAAAAGC 57.349 32.000 0.00 0.00 0.00 3.51
921 2290 9.840427 CTCATCCGTTTCAACATAAAAATACTT 57.160 29.630 0.00 0.00 0.00 2.24
922 2291 9.226606 TCTCATCCGTTTCAACATAAAAATACT 57.773 29.630 0.00 0.00 0.00 2.12
923 2292 9.274065 GTCTCATCCGTTTCAACATAAAAATAC 57.726 33.333 0.00 0.00 0.00 1.89
924 2293 9.004717 TGTCTCATCCGTTTCAACATAAAAATA 57.995 29.630 0.00 0.00 0.00 1.40
925 2294 7.881142 TGTCTCATCCGTTTCAACATAAAAAT 58.119 30.769 0.00 0.00 0.00 1.82
926 2295 7.227711 TCTGTCTCATCCGTTTCAACATAAAAA 59.772 33.333 0.00 0.00 0.00 1.94
927 2296 6.708502 TCTGTCTCATCCGTTTCAACATAAAA 59.291 34.615 0.00 0.00 0.00 1.52
928 2297 6.227522 TCTGTCTCATCCGTTTCAACATAAA 58.772 36.000 0.00 0.00 0.00 1.40
929 2298 5.789521 TCTGTCTCATCCGTTTCAACATAA 58.210 37.500 0.00 0.00 0.00 1.90
930 2299 5.400066 TCTGTCTCATCCGTTTCAACATA 57.600 39.130 0.00 0.00 0.00 2.29
931 2300 4.271696 TCTGTCTCATCCGTTTCAACAT 57.728 40.909 0.00 0.00 0.00 2.71
932 2301 3.744238 TCTGTCTCATCCGTTTCAACA 57.256 42.857 0.00 0.00 0.00 3.33
933 2302 5.613358 ATTTCTGTCTCATCCGTTTCAAC 57.387 39.130 0.00 0.00 0.00 3.18
934 2303 7.117812 GTCTAATTTCTGTCTCATCCGTTTCAA 59.882 37.037 0.00 0.00 0.00 2.69
935 2304 6.590292 GTCTAATTTCTGTCTCATCCGTTTCA 59.410 38.462 0.00 0.00 0.00 2.69
936 2305 6.590292 TGTCTAATTTCTGTCTCATCCGTTTC 59.410 38.462 0.00 0.00 0.00 2.78
937 2306 6.464222 TGTCTAATTTCTGTCTCATCCGTTT 58.536 36.000 0.00 0.00 0.00 3.60
938 2307 6.037786 TGTCTAATTTCTGTCTCATCCGTT 57.962 37.500 0.00 0.00 0.00 4.44
939 2308 5.394663 CCTGTCTAATTTCTGTCTCATCCGT 60.395 44.000 0.00 0.00 0.00 4.69
940 2309 5.046529 CCTGTCTAATTTCTGTCTCATCCG 58.953 45.833 0.00 0.00 0.00 4.18
941 2310 4.813697 GCCTGTCTAATTTCTGTCTCATCC 59.186 45.833 0.00 0.00 0.00 3.51
942 2311 4.813697 GGCCTGTCTAATTTCTGTCTCATC 59.186 45.833 0.00 0.00 0.00 2.92
943 2312 4.472833 AGGCCTGTCTAATTTCTGTCTCAT 59.527 41.667 3.11 0.00 0.00 2.90
944 2313 3.840666 AGGCCTGTCTAATTTCTGTCTCA 59.159 43.478 3.11 0.00 0.00 3.27
945 2314 4.479786 AGGCCTGTCTAATTTCTGTCTC 57.520 45.455 3.11 0.00 0.00 3.36
946 2315 7.863901 ATATAGGCCTGTCTAATTTCTGTCT 57.136 36.000 17.99 0.00 0.00 3.41
947 2316 8.808092 ACTATATAGGCCTGTCTAATTTCTGTC 58.192 37.037 17.99 0.00 0.00 3.51
948 2317 8.589338 CACTATATAGGCCTGTCTAATTTCTGT 58.411 37.037 17.99 0.00 0.00 3.41
949 2318 8.589338 ACACTATATAGGCCTGTCTAATTTCTG 58.411 37.037 17.99 0.66 0.00 3.02
950 2319 8.728596 ACACTATATAGGCCTGTCTAATTTCT 57.271 34.615 17.99 0.00 0.00 2.52
951 2320 9.209175 CAACACTATATAGGCCTGTCTAATTTC 57.791 37.037 17.99 0.00 0.00 2.17
952 2321 8.157476 CCAACACTATATAGGCCTGTCTAATTT 58.843 37.037 17.99 0.00 0.00 1.82
953 2322 7.256691 CCCAACACTATATAGGCCTGTCTAATT 60.257 40.741 17.99 0.00 0.00 1.40
954 2323 6.213600 CCCAACACTATATAGGCCTGTCTAAT 59.786 42.308 17.99 2.18 0.00 1.73
955 2324 5.542635 CCCAACACTATATAGGCCTGTCTAA 59.457 44.000 17.99 0.00 0.00 2.10
956 2325 5.084519 CCCAACACTATATAGGCCTGTCTA 58.915 45.833 17.99 4.80 0.00 2.59
957 2326 3.904339 CCCAACACTATATAGGCCTGTCT 59.096 47.826 17.99 3.59 0.00 3.41
958 2327 3.557264 GCCCAACACTATATAGGCCTGTC 60.557 52.174 17.99 0.00 34.23 3.51
959 2328 2.372172 GCCCAACACTATATAGGCCTGT 59.628 50.000 17.99 12.48 34.23 4.00
960 2329 3.059352 GCCCAACACTATATAGGCCTG 57.941 52.381 17.99 0.00 34.23 4.85
963 2332 3.412386 CAAGGCCCAACACTATATAGGC 58.588 50.000 14.25 7.23 39.73 3.93
964 2333 3.181445 TGCAAGGCCCAACACTATATAGG 60.181 47.826 14.25 5.81 0.00 2.57
965 2334 4.085357 TGCAAGGCCCAACACTATATAG 57.915 45.455 8.27 8.27 0.00 1.31
966 2335 4.722526 ATGCAAGGCCCAACACTATATA 57.277 40.909 0.00 0.00 0.00 0.86
967 2336 3.600448 ATGCAAGGCCCAACACTATAT 57.400 42.857 0.00 0.00 0.00 0.86
968 2337 3.287222 GAATGCAAGGCCCAACACTATA 58.713 45.455 0.00 0.00 0.00 1.31
969 2338 2.102578 GAATGCAAGGCCCAACACTAT 58.897 47.619 0.00 0.00 0.00 2.12
970 2339 1.544724 GAATGCAAGGCCCAACACTA 58.455 50.000 0.00 0.00 0.00 2.74
971 2340 1.526575 CGAATGCAAGGCCCAACACT 61.527 55.000 0.00 0.00 0.00 3.55
972 2341 1.080569 CGAATGCAAGGCCCAACAC 60.081 57.895 0.00 0.00 0.00 3.32
973 2342 2.274645 CCGAATGCAAGGCCCAACA 61.275 57.895 0.00 0.00 0.00 3.33
974 2343 2.573340 CCGAATGCAAGGCCCAAC 59.427 61.111 0.00 0.00 0.00 3.77
975 2344 2.679642 CCCGAATGCAAGGCCCAA 60.680 61.111 0.00 0.00 0.00 4.12
976 2345 3.656280 TCCCGAATGCAAGGCCCA 61.656 61.111 0.00 0.00 0.00 5.36
977 2346 3.140814 GTCCCGAATGCAAGGCCC 61.141 66.667 0.00 0.00 0.00 5.80
978 2347 2.361104 TGTCCCGAATGCAAGGCC 60.361 61.111 0.00 0.00 0.00 5.19
979 2348 2.409870 CCTGTCCCGAATGCAAGGC 61.410 63.158 0.00 0.00 0.00 4.35
980 2349 2.409870 GCCTGTCCCGAATGCAAGG 61.410 63.158 0.00 0.00 0.00 3.61
981 2350 2.409870 GGCCTGTCCCGAATGCAAG 61.410 63.158 0.00 0.00 0.00 4.01
982 2351 2.361104 GGCCTGTCCCGAATGCAA 60.361 61.111 0.00 0.00 0.00 4.08
990 2359 2.124695 GGATTCACGGCCTGTCCC 60.125 66.667 0.00 0.00 0.00 4.46
991 2360 2.124695 GGGATTCACGGCCTGTCC 60.125 66.667 0.00 2.49 0.00 4.02
992 2361 1.153349 GAGGGATTCACGGCCTGTC 60.153 63.158 0.00 0.00 0.00 3.51
993 2362 2.990479 GAGGGATTCACGGCCTGT 59.010 61.111 0.00 0.00 0.00 4.00
994 2363 2.202932 CGAGGGATTCACGGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
995 2364 3.470888 CCGAGGGATTCACGGCCT 61.471 66.667 0.00 0.00 40.19 5.19
999 2368 2.278857 CTCGCCGAGGGATTCACG 60.279 66.667 6.13 0.00 0.00 4.35
1000 2369 2.586357 GCTCGCCGAGGGATTCAC 60.586 66.667 16.95 0.00 0.00 3.18
1001 2370 3.849951 GGCTCGCCGAGGGATTCA 61.850 66.667 16.95 0.00 0.00 2.57
1002 2371 4.610714 GGGCTCGCCGAGGGATTC 62.611 72.222 16.95 0.00 36.85 2.52
1011 2380 3.140814 GAAATGGGTGGGCTCGCC 61.141 66.667 7.98 7.98 42.66 5.54
1012 2381 1.322538 AATGAAATGGGTGGGCTCGC 61.323 55.000 0.00 0.00 0.00 5.03
1013 2382 1.134946 GAAATGAAATGGGTGGGCTCG 59.865 52.381 0.00 0.00 0.00 5.03
1014 2383 1.482182 GGAAATGAAATGGGTGGGCTC 59.518 52.381 0.00 0.00 0.00 4.70
1015 2384 1.571955 GGAAATGAAATGGGTGGGCT 58.428 50.000 0.00 0.00 0.00 5.19
1016 2385 0.541392 GGGAAATGAAATGGGTGGGC 59.459 55.000 0.00 0.00 0.00 5.36
1017 2386 0.823460 CGGGAAATGAAATGGGTGGG 59.177 55.000 0.00 0.00 0.00 4.61
1018 2387 0.823460 CCGGGAAATGAAATGGGTGG 59.177 55.000 0.00 0.00 0.00 4.61
1019 2388 0.175531 GCCGGGAAATGAAATGGGTG 59.824 55.000 2.18 0.00 0.00 4.61
1036 2405 1.862602 AATTTTCAGTGCGGACGGCC 61.863 55.000 0.00 0.00 42.61 6.13
1062 2431 2.275318 GATTCCTCTCTTTCTGTGGCG 58.725 52.381 0.00 0.00 0.00 5.69
1063 2432 2.275318 CGATTCCTCTCTTTCTGTGGC 58.725 52.381 0.00 0.00 0.00 5.01
1064 2433 3.516615 GACGATTCCTCTCTTTCTGTGG 58.483 50.000 0.00 0.00 0.00 4.17
1066 2435 2.498078 GGGACGATTCCTCTCTTTCTGT 59.502 50.000 0.00 0.00 42.38 3.41
1083 2469 1.622752 AGGAGGGGGAATTGGGGAC 60.623 63.158 0.00 0.00 0.00 4.46
1207 2604 4.176851 GGAGGAGTCGTCGGCGTC 62.177 72.222 10.18 3.14 39.49 5.19
1498 3108 1.202927 CCTCTGCCCCAACAAGAGAAA 60.203 52.381 0.54 0.00 0.00 2.52
1511 3122 2.680352 TCGTCCTCCACCTCTGCC 60.680 66.667 0.00 0.00 0.00 4.85
1535 3146 1.303643 CCCCAAGTCTGCACCTTCC 60.304 63.158 0.00 0.00 0.00 3.46
1916 3654 6.692849 ATGACAGCATGATATTAGGGAGAA 57.307 37.500 0.00 0.00 39.69 2.87
3031 4791 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69
3049 4809 8.311395 AGTTCTAGATACATCCATTTCTGTGA 57.689 34.615 0.00 0.00 0.00 3.58
3505 5273 0.321298 TCTTCCTTTGCGCCCTACAC 60.321 55.000 4.18 0.00 0.00 2.90
3543 5311 0.527565 GCCAGTTGATTCAACCGCAT 59.472 50.000 22.70 4.77 44.49 4.73
4366 6200 7.418139 GCAGAGCATCCTTGAGAGATCATATAT 60.418 40.741 0.00 0.00 33.66 0.86
4372 6206 2.758009 GCAGAGCATCCTTGAGAGATC 58.242 52.381 0.00 0.00 33.66 2.75
4664 6504 7.094463 ACCTCAAAGCTCAAACAATTATCTCAG 60.094 37.037 0.00 0.00 0.00 3.35
4803 6643 6.210287 ACTAGACTACTGGTAACTTGATGC 57.790 41.667 0.00 0.00 36.11 3.91
4839 6683 4.242475 CACTTGCATCACAGCATTTTCAT 58.758 39.130 0.00 0.00 45.19 2.57


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

AutoCloner maintained by Alex Coulton.