Multiple sequence alignment - TraesCS3D01G147800

Loading Multiple Alignment...

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 TraesCS3D01G147800 chr3D 100.000 2543 0 0 1 2543 112331964 112334506 0.000000e+00 4697
1 TraesCS3D01G147800 chr3D 91.880 234 17 2 2312 2543 427209021 427208788 2.440000e-85 326
2 TraesCS3D01G147800 chr3B 87.491 1383 83 47 259 1594 163152856 163154195 0.000000e+00 1513
3 TraesCS3D01G147800 chr3B 90.772 596 25 16 1636 2222 163154191 163154765 0.000000e+00 769
4 TraesCS3D01G147800 chr3B 88.519 270 17 5 1 260 163150154 163150419 5.280000e-82 315
5 TraesCS3D01G147800 chr3A 85.309 1409 104 52 381 1737 107974626 107975983 0.000000e+00 1360
6 TraesCS3D01G147800 chr3A 86.039 308 22 8 1883 2175 107976123 107976424 6.830000e-81 311
7 TraesCS3D01G147800 chr3A 82.086 374 28 17 1 347 107974267 107974628 1.490000e-72 283
8 TraesCS3D01G147800 chr3A 88.776 98 9 2 2215 2312 583580771 583580676 4.440000e-23 119
9 TraesCS3D01G147800 chr2A 92.623 244 17 1 2301 2543 504105102 504105345 1.450000e-92 350
10 TraesCS3D01G147800 chr2A 93.590 234 11 3 2313 2543 615300126 615300358 1.870000e-91 346
11 TraesCS3D01G147800 chr5A 93.220 236 14 2 2310 2543 135532647 135532882 1.870000e-91 346
12 TraesCS3D01G147800 chr5A 88.776 98 10 1 2215 2312 123979521 123979617 4.440000e-23 119
13 TraesCS3D01G147800 chr5A 86.813 91 11 1 2222 2312 565538414 565538325 1.610000e-17 100
14 TraesCS3D01G147800 chr2B 93.191 235 14 2 2311 2543 712747582 712747348 6.740000e-91 344
15 TraesCS3D01G147800 chr2B 92.275 233 15 3 2313 2543 278838396 278838627 6.780000e-86 327
16 TraesCS3D01G147800 chr2B 86.957 92 9 2 2222 2312 400607525 400607614 1.610000e-17 100
17 TraesCS3D01G147800 chr4A 92.704 233 15 2 2313 2543 414629831 414630063 4.050000e-88 335
18 TraesCS3D01G147800 chr4A 92.704 233 15 2 2313 2543 542951649 542951881 4.050000e-88 335
19 TraesCS3D01G147800 chr5B 92.672 232 15 2 2312 2543 548396752 548396981 1.460000e-87 333
20 TraesCS3D01G147800 chr6A 88.776 98 10 1 2215 2312 350839689 350839593 4.440000e-23 119
21 TraesCS3D01G147800 chr2D 89.362 94 9 1 2217 2310 16324842 16324934 1.600000e-22 117
22 TraesCS3D01G147800 chr1D 89.247 93 8 2 2220 2312 318557275 318557365 5.750000e-22 115
23 TraesCS3D01G147800 chr7A 86.957 92 9 3 2222 2312 113489777 113489688 1.610000e-17 100
24 TraesCS3D01G147800 chr7A 86.022 93 12 1 2220 2312 149308605 149308696 5.790000e-17 99


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 TraesCS3D01G147800 chr3D 112331964 112334506 2542 False 4697.000000 4697 100.000000 1 2543 1 chr3D.!!$F1 2542
1 TraesCS3D01G147800 chr3B 163150154 163154765 4611 False 865.666667 1513 88.927333 1 2222 3 chr3B.!!$F1 2221
2 TraesCS3D01G147800 chr3A 107974267 107976424 2157 False 651.333333 1360 84.478000 1 2175 3 chr3A.!!$F1 2174

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 3417 0.031178 AACCTTTGCTTGCTTGCTCG 59.969 50.0 3.47 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 5038 0.400213 CCACCTTGCCTTGTACTCCA 59.6 55.0 0.0 0.0 0.0 3.86 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
78 89 2.693267 AACGGAGTAATGAGGAAGCC 57.307 50.000 0.00 0.00 45.00 4.35
157 168 1.064758 TCCAGCACCGGCATAATTCTT 60.065 47.619 0.00 0.00 44.61 2.52
189 207 1.791555 CGTCGTACGTCCGCAAGTAAT 60.792 52.381 16.05 0.00 36.74 1.89
221 239 8.685257 ACTTATTCCTCCATCATATATGGACA 57.315 34.615 12.78 0.00 42.81 4.02
233 251 8.886719 CATCATATATGGACATAATTCAAGCGT 58.113 33.333 12.78 0.00 0.00 5.07
262 282 1.640428 CTCCAAGCGACGCATTAAGA 58.360 50.000 23.70 9.94 0.00 2.10
307 2765 5.667175 GCAAAGGAGCGAAATAATAGTACG 58.333 41.667 0.00 0.00 0.00 3.67
316 2782 5.657499 CGAAATAATAGTACGAGCAAGCAC 58.343 41.667 0.00 0.00 0.00 4.40
325 2791 1.565156 CGAGCAAGCACAGCCGTTTA 61.565 55.000 0.00 0.00 0.00 2.01
362 2833 2.511600 GGGAGCCATTGACGGACG 60.512 66.667 0.00 0.00 0.00 4.79
367 2838 2.867472 CCATTGACGGACGGCAAC 59.133 61.111 15.94 0.00 46.90 4.17
368 2839 1.963855 CCATTGACGGACGGCAACA 60.964 57.895 15.94 0.00 46.90 3.33
369 2840 1.206578 CATTGACGGACGGCAACAC 59.793 57.895 15.94 0.00 46.90 3.32
370 2841 2.314647 ATTGACGGACGGCAACACG 61.315 57.895 15.94 0.00 46.90 4.49
371 2842 2.981977 ATTGACGGACGGCAACACGT 62.982 55.000 15.94 0.00 46.90 4.49
494 2967 4.641645 CGGGGGAGCACAGCAACA 62.642 66.667 0.00 0.00 0.00 3.33
552 3029 1.906824 TTCGTGCGTCCCTTCCTCT 60.907 57.895 0.00 0.00 0.00 3.69
555 3032 1.374758 GTGCGTCCCTTCCTCTGTG 60.375 63.158 0.00 0.00 0.00 3.66
630 3127 0.605319 GTGCGGACAGATGGAAACCA 60.605 55.000 0.63 0.00 38.19 3.67
634 3131 1.676014 CGGACAGATGGAAACCAGTCC 60.676 57.143 13.96 13.96 40.68 3.85
636 3133 0.324943 ACAGATGGAAACCAGTCCCG 59.675 55.000 0.00 0.00 36.75 5.14
762 3283 1.073964 CACTGATCACCTCTGCGTTG 58.926 55.000 0.00 0.00 0.00 4.10
763 3284 0.671781 ACTGATCACCTCTGCGTTGC 60.672 55.000 0.00 0.00 0.00 4.17
764 3285 1.690283 CTGATCACCTCTGCGTTGCG 61.690 60.000 0.00 0.00 0.00 4.85
765 3286 1.738099 GATCACCTCTGCGTTGCGT 60.738 57.895 0.00 0.00 0.00 5.24
812 3337 1.589803 CCCTTTAAATACGGCCTCGG 58.410 55.000 0.00 0.00 41.39 4.63
882 3417 0.031178 AACCTTTGCTTGCTTGCTCG 59.969 50.000 3.47 0.00 0.00 5.03
905 3440 3.655211 CCAAGCCCCTCCACAGCT 61.655 66.667 0.00 0.00 38.88 4.24
906 3441 2.045536 CAAGCCCCTCCACAGCTC 60.046 66.667 0.00 0.00 35.30 4.09
907 3442 3.710722 AAGCCCCTCCACAGCTCG 61.711 66.667 0.00 0.00 35.30 5.03
910 3445 4.020617 CCCCTCCACAGCTCGCAA 62.021 66.667 0.00 0.00 0.00 4.85
911 3446 2.743928 CCCTCCACAGCTCGCAAC 60.744 66.667 0.00 0.00 0.00 4.17
912 3447 2.031012 CCTCCACAGCTCGCAACA 59.969 61.111 0.00 0.00 0.00 3.33
913 3448 2.031516 CCTCCACAGCTCGCAACAG 61.032 63.158 0.00 0.00 0.00 3.16
914 3449 1.301244 CTCCACAGCTCGCAACAGT 60.301 57.895 0.00 0.00 0.00 3.55
915 3450 1.563435 CTCCACAGCTCGCAACAGTG 61.563 60.000 0.00 0.00 0.00 3.66
924 3459 2.806929 GCAACAGTGCCAGCAACA 59.193 55.556 0.00 0.00 45.68 3.33
927 3477 0.173029 CAACAGTGCCAGCAACACAA 59.827 50.000 0.00 0.00 40.59 3.33
962 3512 4.060038 GCCGGTTCCGAGTTCCGA 62.060 66.667 13.08 0.00 46.05 4.55
1514 4079 4.357947 GGCCACAGCGACGACAGA 62.358 66.667 0.00 0.00 41.24 3.41
1594 4165 2.719376 GGCACAAGGCTGAACTGAA 58.281 52.632 0.00 0.00 44.01 3.02
1604 4175 1.148310 CTGAACTGAACCGCACGATT 58.852 50.000 0.00 0.00 0.00 3.34
1619 4190 4.119862 GCACGATTGGAGAATAGCTAACA 58.880 43.478 0.00 0.00 0.00 2.41
1649 4224 1.070710 CGGTCGACTAGCTAGCTAACG 60.071 57.143 29.13 29.13 33.31 3.18
1696 4272 5.577945 TCGAGGTGATTTATTTGGTTCGTAC 59.422 40.000 0.00 0.00 0.00 3.67
1742 4325 9.603298 TGTGACGTCGATTGTATTATTACTATC 57.397 33.333 11.62 8.34 37.28 2.08
1837 4436 1.333619 GCAACACATCTTGTCGTTGGT 59.666 47.619 16.89 0.00 37.51 3.67
1856 4455 2.242452 GGTAAGCCTCCCCATTTTCTCT 59.758 50.000 0.00 0.00 0.00 3.10
1868 4467 1.512156 TTTTCTCTTTGTCCCGCGGC 61.512 55.000 22.85 7.92 0.00 6.53
1929 4533 3.470567 CGCTCTCGGTTGACACGC 61.471 66.667 0.00 0.00 0.00 5.34
1930 4534 3.470567 GCTCTCGGTTGACACGCG 61.471 66.667 3.53 3.53 0.00 6.01
1931 4535 3.470567 CTCTCGGTTGACACGCGC 61.471 66.667 5.73 0.00 0.00 6.86
1932 4536 4.273257 TCTCGGTTGACACGCGCA 62.273 61.111 5.73 0.00 0.00 6.09
1933 4537 3.112075 CTCGGTTGACACGCGCAT 61.112 61.111 5.73 0.00 0.00 4.73
1934 4538 3.353114 CTCGGTTGACACGCGCATG 62.353 63.158 5.73 4.48 0.00 4.06
1936 4540 4.759096 GGTTGACACGCGCATGCC 62.759 66.667 13.15 3.98 38.08 4.40
1937 4541 4.024143 GTTGACACGCGCATGCCA 62.024 61.111 13.15 0.00 38.08 4.92
1938 4542 3.725459 TTGACACGCGCATGCCAG 61.725 61.111 13.15 8.88 38.08 4.85
2047 4672 1.021968 ACTTCGCTGCGTTTTCCTTT 58.978 45.000 22.48 0.00 0.00 3.11
2048 4673 1.002792 ACTTCGCTGCGTTTTCCTTTC 60.003 47.619 22.48 0.00 0.00 2.62
2049 4674 0.309612 TTCGCTGCGTTTTCCTTTCC 59.690 50.000 22.48 0.00 0.00 3.13
2050 4675 0.534203 TCGCTGCGTTTTCCTTTCCT 60.534 50.000 22.48 0.00 0.00 3.36
2051 4676 0.310854 CGCTGCGTTTTCCTTTCCTT 59.689 50.000 14.93 0.00 0.00 3.36
2164 4804 2.471749 CCGTTTCGCATTCGTCTGTAAC 60.472 50.000 0.00 0.00 36.96 2.50
2165 4805 2.407361 CGTTTCGCATTCGTCTGTAACT 59.593 45.455 0.00 0.00 36.96 2.24
2167 4807 4.141680 GTTTCGCATTCGTCTGTAACTTG 58.858 43.478 0.00 0.00 36.96 3.16
2168 4808 3.021269 TCGCATTCGTCTGTAACTTGT 57.979 42.857 0.00 0.00 36.96 3.16
2169 4809 2.984471 TCGCATTCGTCTGTAACTTGTC 59.016 45.455 0.00 0.00 36.96 3.18
2218 4859 0.674534 GTAGACCCCGACAGCCATAG 59.325 60.000 0.00 0.00 0.00 2.23
2222 4863 1.068741 GACCCCGACAGCCATAGTAAG 59.931 57.143 0.00 0.00 0.00 2.34
2223 4864 0.393077 CCCCGACAGCCATAGTAAGG 59.607 60.000 0.00 0.00 0.00 2.69
2224 4865 0.393077 CCCGACAGCCATAGTAAGGG 59.607 60.000 0.00 0.00 32.90 3.95
2234 4875 4.713792 CCATAGTAAGGGCTCCTTTGAT 57.286 45.455 11.15 1.91 41.69 2.57
2235 4876 5.053978 CCATAGTAAGGGCTCCTTTGATT 57.946 43.478 11.15 0.00 41.69 2.57
2236 4877 5.066593 CCATAGTAAGGGCTCCTTTGATTC 58.933 45.833 11.15 0.54 41.69 2.52
2237 4878 5.397899 CCATAGTAAGGGCTCCTTTGATTCA 60.398 44.000 11.15 0.00 41.69 2.57
2238 4879 4.657814 AGTAAGGGCTCCTTTGATTCAA 57.342 40.909 11.15 0.00 41.69 2.69
2239 4880 4.998051 AGTAAGGGCTCCTTTGATTCAAA 58.002 39.130 11.19 11.19 41.69 2.69
2302 4943 3.810310 TTTTTCCTGCATTGGTCGTTT 57.190 38.095 0.00 0.00 0.00 3.60
2303 4944 2.791383 TTTCCTGCATTGGTCGTTTG 57.209 45.000 0.00 0.00 0.00 2.93
2304 4945 1.974265 TTCCTGCATTGGTCGTTTGA 58.026 45.000 0.00 0.00 0.00 2.69
2305 4946 2.198827 TCCTGCATTGGTCGTTTGAT 57.801 45.000 0.00 0.00 0.00 2.57
2306 4947 2.513753 TCCTGCATTGGTCGTTTGATT 58.486 42.857 0.00 0.00 0.00 2.57
2307 4948 2.487762 TCCTGCATTGGTCGTTTGATTC 59.512 45.455 0.00 0.00 0.00 2.52
2308 4949 2.228582 CCTGCATTGGTCGTTTGATTCA 59.771 45.455 0.00 0.00 0.00 2.57
2309 4950 3.119388 CCTGCATTGGTCGTTTGATTCAT 60.119 43.478 0.00 0.00 0.00 2.57
2310 4951 4.096231 CCTGCATTGGTCGTTTGATTCATA 59.904 41.667 0.00 0.00 0.00 2.15
2311 4952 5.233957 TGCATTGGTCGTTTGATTCATAG 57.766 39.130 0.00 0.00 0.00 2.23
2312 4953 4.699735 TGCATTGGTCGTTTGATTCATAGT 59.300 37.500 0.00 0.00 0.00 2.12
2313 4954 5.030295 GCATTGGTCGTTTGATTCATAGTG 58.970 41.667 0.00 0.00 0.00 2.74
2314 4955 5.391950 GCATTGGTCGTTTGATTCATAGTGT 60.392 40.000 0.00 0.00 0.00 3.55
2315 4956 6.611381 CATTGGTCGTTTGATTCATAGTGTT 58.389 36.000 0.00 0.00 0.00 3.32
2316 4957 7.625395 GCATTGGTCGTTTGATTCATAGTGTTA 60.625 37.037 0.00 0.00 0.00 2.41
2317 4958 6.961359 TGGTCGTTTGATTCATAGTGTTAG 57.039 37.500 0.00 0.00 0.00 2.34
2318 4959 6.693466 TGGTCGTTTGATTCATAGTGTTAGA 58.307 36.000 0.00 0.00 0.00 2.10
2319 4960 7.156000 TGGTCGTTTGATTCATAGTGTTAGAA 58.844 34.615 0.00 0.00 0.00 2.10
2320 4961 7.330946 TGGTCGTTTGATTCATAGTGTTAGAAG 59.669 37.037 0.00 0.00 0.00 2.85
2321 4962 7.201530 GGTCGTTTGATTCATAGTGTTAGAAGG 60.202 40.741 0.00 0.00 0.00 3.46
2322 4963 6.816640 TCGTTTGATTCATAGTGTTAGAAGGG 59.183 38.462 0.00 0.00 0.00 3.95
2323 4964 6.816640 CGTTTGATTCATAGTGTTAGAAGGGA 59.183 38.462 0.00 0.00 0.00 4.20
2324 4965 7.010552 CGTTTGATTCATAGTGTTAGAAGGGAG 59.989 40.741 0.00 0.00 0.00 4.30
2325 4966 7.733773 TTGATTCATAGTGTTAGAAGGGAGA 57.266 36.000 0.00 0.00 0.00 3.71
2326 4967 7.353414 TGATTCATAGTGTTAGAAGGGAGAG 57.647 40.000 0.00 0.00 0.00 3.20
2327 4968 7.126061 TGATTCATAGTGTTAGAAGGGAGAGA 58.874 38.462 0.00 0.00 0.00 3.10
2328 4969 7.286546 TGATTCATAGTGTTAGAAGGGAGAGAG 59.713 40.741 0.00 0.00 0.00 3.20
2329 4970 6.328782 TCATAGTGTTAGAAGGGAGAGAGA 57.671 41.667 0.00 0.00 0.00 3.10
2330 4971 6.361433 TCATAGTGTTAGAAGGGAGAGAGAG 58.639 44.000 0.00 0.00 0.00 3.20
2331 4972 4.938575 AGTGTTAGAAGGGAGAGAGAGA 57.061 45.455 0.00 0.00 0.00 3.10
2332 4973 5.466127 AGTGTTAGAAGGGAGAGAGAGAT 57.534 43.478 0.00 0.00 0.00 2.75
2333 4974 5.837829 AGTGTTAGAAGGGAGAGAGAGATT 58.162 41.667 0.00 0.00 0.00 2.40
2334 4975 5.656416 AGTGTTAGAAGGGAGAGAGAGATTG 59.344 44.000 0.00 0.00 0.00 2.67
2335 4976 5.654650 GTGTTAGAAGGGAGAGAGAGATTGA 59.345 44.000 0.00 0.00 0.00 2.57
2336 4977 6.323739 GTGTTAGAAGGGAGAGAGAGATTGAT 59.676 42.308 0.00 0.00 0.00 2.57
2337 4978 6.323482 TGTTAGAAGGGAGAGAGAGATTGATG 59.677 42.308 0.00 0.00 0.00 3.07
2338 4979 4.225573 AGAAGGGAGAGAGAGATTGATGG 58.774 47.826 0.00 0.00 0.00 3.51
2339 4980 3.989600 AGGGAGAGAGAGATTGATGGA 57.010 47.619 0.00 0.00 0.00 3.41
2340 4981 4.277788 AGGGAGAGAGAGATTGATGGAA 57.722 45.455 0.00 0.00 0.00 3.53
2341 4982 4.830138 AGGGAGAGAGAGATTGATGGAAT 58.170 43.478 0.00 0.00 0.00 3.01
2342 4983 5.975113 AGGGAGAGAGAGATTGATGGAATA 58.025 41.667 0.00 0.00 0.00 1.75
2343 4984 6.018469 AGGGAGAGAGAGATTGATGGAATAG 58.982 44.000 0.00 0.00 0.00 1.73
2344 4985 5.779771 GGGAGAGAGAGATTGATGGAATAGT 59.220 44.000 0.00 0.00 0.00 2.12
2345 4986 6.269769 GGGAGAGAGAGATTGATGGAATAGTT 59.730 42.308 0.00 0.00 0.00 2.24
2346 4987 7.153985 GGAGAGAGAGATTGATGGAATAGTTG 58.846 42.308 0.00 0.00 0.00 3.16
2347 4988 7.201992 GGAGAGAGAGATTGATGGAATAGTTGT 60.202 40.741 0.00 0.00 0.00 3.32
2348 4989 8.088463 AGAGAGAGATTGATGGAATAGTTGTT 57.912 34.615 0.00 0.00 0.00 2.83
2349 4990 7.986320 AGAGAGAGATTGATGGAATAGTTGTTG 59.014 37.037 0.00 0.00 0.00 3.33
2350 4991 7.628234 AGAGAGATTGATGGAATAGTTGTTGT 58.372 34.615 0.00 0.00 0.00 3.32
2351 4992 8.762645 AGAGAGATTGATGGAATAGTTGTTGTA 58.237 33.333 0.00 0.00 0.00 2.41
2352 4993 9.553064 GAGAGATTGATGGAATAGTTGTTGTAT 57.447 33.333 0.00 0.00 0.00 2.29
2353 4994 9.911788 AGAGATTGATGGAATAGTTGTTGTATT 57.088 29.630 0.00 0.00 0.00 1.89
2354 4995 9.941664 GAGATTGATGGAATAGTTGTTGTATTG 57.058 33.333 0.00 0.00 0.00 1.90
2355 4996 8.408601 AGATTGATGGAATAGTTGTTGTATTGC 58.591 33.333 0.00 0.00 0.00 3.56
2356 4997 7.701539 TTGATGGAATAGTTGTTGTATTGCT 57.298 32.000 0.00 0.00 31.43 3.91
2357 4998 7.701539 TGATGGAATAGTTGTTGTATTGCTT 57.298 32.000 0.00 0.00 31.43 3.91
2358 4999 7.537715 TGATGGAATAGTTGTTGTATTGCTTG 58.462 34.615 0.00 0.00 31.43 4.01
2359 5000 7.392953 TGATGGAATAGTTGTTGTATTGCTTGA 59.607 33.333 0.00 0.00 31.43 3.02
2360 5001 7.144722 TGGAATAGTTGTTGTATTGCTTGAG 57.855 36.000 0.00 0.00 31.43 3.02
2361 5002 6.030228 GGAATAGTTGTTGTATTGCTTGAGC 58.970 40.000 0.00 0.00 42.50 4.26
2362 5003 3.923017 AGTTGTTGTATTGCTTGAGCC 57.077 42.857 0.00 0.00 41.18 4.70
2363 5004 3.490348 AGTTGTTGTATTGCTTGAGCCT 58.510 40.909 0.00 0.00 41.18 4.58
2364 5005 3.503748 AGTTGTTGTATTGCTTGAGCCTC 59.496 43.478 0.00 0.00 41.18 4.70
2365 5006 3.138884 TGTTGTATTGCTTGAGCCTCA 57.861 42.857 0.00 0.00 41.18 3.86
2366 5007 3.689347 TGTTGTATTGCTTGAGCCTCAT 58.311 40.909 0.00 0.00 41.18 2.90
2367 5008 3.441222 TGTTGTATTGCTTGAGCCTCATG 59.559 43.478 0.00 0.00 41.18 3.07
2368 5009 2.646930 TGTATTGCTTGAGCCTCATGG 58.353 47.619 9.39 0.96 41.18 3.66
2369 5010 2.239402 TGTATTGCTTGAGCCTCATGGA 59.761 45.455 9.39 3.84 41.18 3.41
2370 5011 1.760192 ATTGCTTGAGCCTCATGGAC 58.240 50.000 9.39 0.00 41.18 4.02
2371 5012 0.401356 TTGCTTGAGCCTCATGGACA 59.599 50.000 9.39 0.00 41.18 4.02
2372 5013 0.622136 TGCTTGAGCCTCATGGACAT 59.378 50.000 9.39 0.00 41.18 3.06
2373 5014 1.839354 TGCTTGAGCCTCATGGACATA 59.161 47.619 9.39 0.00 41.18 2.29
2374 5015 2.440627 TGCTTGAGCCTCATGGACATAT 59.559 45.455 9.39 0.00 41.18 1.78
2375 5016 3.647590 TGCTTGAGCCTCATGGACATATA 59.352 43.478 9.39 0.00 41.18 0.86
2376 5017 4.287845 TGCTTGAGCCTCATGGACATATAT 59.712 41.667 9.39 0.00 41.18 0.86
2377 5018 5.484998 TGCTTGAGCCTCATGGACATATATA 59.515 40.000 9.39 0.00 41.18 0.86
2378 5019 6.157471 TGCTTGAGCCTCATGGACATATATAT 59.843 38.462 9.39 0.00 41.18 0.86
2379 5020 7.345392 TGCTTGAGCCTCATGGACATATATATA 59.655 37.037 9.39 0.00 41.18 0.86
2380 5021 7.871973 GCTTGAGCCTCATGGACATATATATAG 59.128 40.741 9.39 0.00 34.57 1.31
2381 5022 7.846101 TGAGCCTCATGGACATATATATAGG 57.154 40.000 2.88 2.88 34.57 2.57
2382 5023 7.595488 TGAGCCTCATGGACATATATATAGGA 58.405 38.462 11.22 0.00 34.57 2.94
2383 5024 7.727634 TGAGCCTCATGGACATATATATAGGAG 59.272 40.741 11.22 4.46 34.57 3.69
2384 5025 7.600093 AGCCTCATGGACATATATATAGGAGT 58.400 38.462 11.22 3.60 34.57 3.85
2385 5026 8.737633 AGCCTCATGGACATATATATAGGAGTA 58.262 37.037 11.22 0.00 34.57 2.59
2386 5027 8.798402 GCCTCATGGACATATATATAGGAGTAC 58.202 40.741 11.22 5.04 34.57 2.73
2387 5028 9.868160 CCTCATGGACATATATATAGGAGTACA 57.132 37.037 11.22 9.95 34.57 2.90
2415 5056 2.270352 TTGGAGTACAAGGCAAGGTG 57.730 50.000 0.00 0.00 33.18 4.00
2416 5057 0.400213 TGGAGTACAAGGCAAGGTGG 59.600 55.000 0.00 0.00 0.00 4.61
2417 5058 0.690762 GGAGTACAAGGCAAGGTGGA 59.309 55.000 0.00 0.00 0.00 4.02
2418 5059 1.073284 GGAGTACAAGGCAAGGTGGAA 59.927 52.381 0.00 0.00 0.00 3.53
2419 5060 2.290960 GGAGTACAAGGCAAGGTGGAAT 60.291 50.000 0.00 0.00 0.00 3.01
2420 5061 3.054655 GGAGTACAAGGCAAGGTGGAATA 60.055 47.826 0.00 0.00 0.00 1.75
2421 5062 4.566907 GGAGTACAAGGCAAGGTGGAATAA 60.567 45.833 0.00 0.00 0.00 1.40
2422 5063 4.993028 AGTACAAGGCAAGGTGGAATAAA 58.007 39.130 0.00 0.00 0.00 1.40
2423 5064 5.580022 AGTACAAGGCAAGGTGGAATAAAT 58.420 37.500 0.00 0.00 0.00 1.40
2424 5065 5.652452 AGTACAAGGCAAGGTGGAATAAATC 59.348 40.000 0.00 0.00 0.00 2.17
2445 5086 7.931015 AATCCTACACTATCCTATGTTTCCA 57.069 36.000 0.00 0.00 0.00 3.53
2446 5087 8.511748 AATCCTACACTATCCTATGTTTCCAT 57.488 34.615 0.00 0.00 34.97 3.41
2447 5088 9.615660 AATCCTACACTATCCTATGTTTCCATA 57.384 33.333 0.00 0.00 32.29 2.74
2448 5089 9.615660 ATCCTACACTATCCTATGTTTCCATAA 57.384 33.333 0.00 0.00 33.23 1.90
2449 5090 9.615660 TCCTACACTATCCTATGTTTCCATAAT 57.384 33.333 0.00 0.00 33.23 1.28
2472 5113 5.738619 AACAAAAATACTCAACATCCCCC 57.261 39.130 0.00 0.00 0.00 5.40
2487 5128 4.619227 CCCCGCAGTCACAACGGT 62.619 66.667 7.64 0.00 45.49 4.83
2488 5129 2.340809 CCCGCAGTCACAACGGTA 59.659 61.111 7.64 0.00 45.49 4.02
2489 5130 1.736645 CCCGCAGTCACAACGGTAG 60.737 63.158 7.64 0.00 45.49 3.18
2490 5131 2.380410 CCGCAGTCACAACGGTAGC 61.380 63.158 0.43 0.00 42.01 3.58
2491 5132 2.716828 CGCAGTCACAACGGTAGCG 61.717 63.158 13.69 13.69 37.68 4.26
2492 5133 1.372499 GCAGTCACAACGGTAGCGA 60.372 57.895 22.88 0.00 0.00 4.93
2493 5134 1.615107 GCAGTCACAACGGTAGCGAC 61.615 60.000 22.88 8.20 0.00 5.19
2494 5135 1.081641 AGTCACAACGGTAGCGACG 60.082 57.895 22.88 13.36 37.36 5.12
2495 5136 2.429571 TCACAACGGTAGCGACGC 60.430 61.111 22.88 13.03 34.00 5.19
2496 5137 2.731721 CACAACGGTAGCGACGCA 60.732 61.111 23.70 5.17 34.00 5.24
2497 5138 2.430244 ACAACGGTAGCGACGCAG 60.430 61.111 23.70 12.40 34.00 5.18
2498 5139 2.126618 CAACGGTAGCGACGCAGA 60.127 61.111 23.70 6.47 34.00 4.26
2499 5140 2.126580 AACGGTAGCGACGCAGAC 60.127 61.111 23.70 18.49 34.00 3.51
2506 5147 4.400109 GCGACGCAGACGGTGAGA 62.400 66.667 16.42 0.00 46.96 3.27
2507 5148 2.502080 CGACGCAGACGGTGAGAC 60.502 66.667 0.00 0.00 46.04 3.36
2508 5149 2.955402 GACGCAGACGGTGAGACT 59.045 61.111 0.00 0.00 46.04 3.24
2509 5150 1.442857 GACGCAGACGGTGAGACTG 60.443 63.158 0.00 0.00 46.04 3.51
2510 5151 1.853114 GACGCAGACGGTGAGACTGA 61.853 60.000 0.00 0.00 43.62 3.41
2511 5152 1.285950 CGCAGACGGTGAGACTGAA 59.714 57.895 0.00 0.00 43.62 3.02
2512 5153 0.730834 CGCAGACGGTGAGACTGAAG 60.731 60.000 0.00 0.00 43.62 3.02
2513 5154 0.598562 GCAGACGGTGAGACTGAAGA 59.401 55.000 0.00 0.00 43.62 2.87
2514 5155 1.000163 GCAGACGGTGAGACTGAAGAA 60.000 52.381 0.00 0.00 43.62 2.52
2515 5156 2.924454 GCAGACGGTGAGACTGAAGAAG 60.924 54.545 0.00 0.00 43.62 2.85
2516 5157 2.554462 CAGACGGTGAGACTGAAGAAGA 59.446 50.000 0.00 0.00 43.62 2.87
2517 5158 3.004839 CAGACGGTGAGACTGAAGAAGAA 59.995 47.826 0.00 0.00 43.62 2.52
2518 5159 3.829601 AGACGGTGAGACTGAAGAAGAAT 59.170 43.478 0.00 0.00 0.00 2.40
2519 5160 4.082463 AGACGGTGAGACTGAAGAAGAATC 60.082 45.833 0.00 0.00 0.00 2.52
2520 5161 3.829601 ACGGTGAGACTGAAGAAGAATCT 59.170 43.478 0.00 0.00 37.57 2.40
2521 5162 4.172505 CGGTGAGACTGAAGAAGAATCTG 58.827 47.826 0.00 0.00 35.59 2.90
2522 5163 4.082517 CGGTGAGACTGAAGAAGAATCTGA 60.083 45.833 0.00 0.00 35.59 3.27
2523 5164 5.565637 CGGTGAGACTGAAGAAGAATCTGAA 60.566 44.000 0.00 0.00 35.59 3.02
2524 5165 5.868801 GGTGAGACTGAAGAAGAATCTGAAG 59.131 44.000 0.00 0.00 35.59 3.02
2525 5166 5.868801 GTGAGACTGAAGAAGAATCTGAAGG 59.131 44.000 0.00 0.00 35.59 3.46
2526 5167 4.831107 AGACTGAAGAAGAATCTGAAGGC 58.169 43.478 0.00 0.00 35.59 4.35
2527 5168 4.285517 AGACTGAAGAAGAATCTGAAGGCA 59.714 41.667 0.00 0.00 35.59 4.75
2528 5169 4.978099 ACTGAAGAAGAATCTGAAGGCAA 58.022 39.130 0.00 0.00 35.59 4.52
2529 5170 5.002516 ACTGAAGAAGAATCTGAAGGCAAG 58.997 41.667 0.00 0.00 35.59 4.01
2530 5171 3.755378 TGAAGAAGAATCTGAAGGCAAGC 59.245 43.478 0.00 0.00 35.59 4.01
2531 5172 2.720915 AGAAGAATCTGAAGGCAAGCC 58.279 47.619 2.02 2.02 33.59 4.35
2532 5173 1.399791 GAAGAATCTGAAGGCAAGCCG 59.600 52.381 5.28 0.00 41.95 5.52
2533 5174 0.615331 AGAATCTGAAGGCAAGCCGA 59.385 50.000 5.28 0.00 41.95 5.54
2534 5175 1.211457 AGAATCTGAAGGCAAGCCGAT 59.789 47.619 5.28 0.00 41.95 4.18
2535 5176 1.332997 GAATCTGAAGGCAAGCCGATG 59.667 52.381 5.28 0.00 41.95 3.84
2536 5177 0.465097 ATCTGAAGGCAAGCCGATGG 60.465 55.000 5.28 0.00 41.95 3.51
2537 5178 1.078214 CTGAAGGCAAGCCGATGGA 60.078 57.895 5.28 0.00 41.95 3.41
2538 5179 1.372087 CTGAAGGCAAGCCGATGGAC 61.372 60.000 5.28 0.00 41.95 4.02
2539 5180 1.377202 GAAGGCAAGCCGATGGACA 60.377 57.895 5.28 0.00 41.95 4.02
2540 5181 1.648467 GAAGGCAAGCCGATGGACAC 61.648 60.000 5.28 0.00 41.95 3.67
2541 5182 3.134127 GGCAAGCCGATGGACACC 61.134 66.667 0.00 0.00 0.00 4.16
2542 5183 3.134127 GCAAGCCGATGGACACCC 61.134 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 207 6.566079 ATGATGGAGGAATAAGTTCAGTGA 57.434 37.500 0.00 0.00 36.01 3.41
221 239 5.133221 AGCATTAAGGGACGCTTGAATTAT 58.867 37.500 14.61 0.00 0.00 1.28
233 251 0.908910 TCGCTTGGAGCATTAAGGGA 59.091 50.000 8.73 8.73 42.58 4.20
262 282 1.128188 AAGCAAGAGGGACCCGACTT 61.128 55.000 16.64 16.64 0.00 3.01
303 2761 2.730672 CGGCTGTGCTTGCTCGTAC 61.731 63.158 0.00 0.00 0.00 3.67
306 2764 1.565156 TAAACGGCTGTGCTTGCTCG 61.565 55.000 0.00 0.00 0.00 5.03
307 2765 0.166814 CTAAACGGCTGTGCTTGCTC 59.833 55.000 0.00 0.00 0.00 4.26
325 2791 4.021925 GGCCTCACCTTCACCGCT 62.022 66.667 0.00 0.00 34.51 5.52
351 2817 1.206578 GTGTTGCCGTCCGTCAATG 59.793 57.895 0.00 0.00 0.00 2.82
370 2841 6.144854 GGAAAGTTTTTACCATCCGTGTAAC 58.855 40.000 0.00 0.00 0.00 2.50
371 2842 5.826737 TGGAAAGTTTTTACCATCCGTGTAA 59.173 36.000 0.00 0.00 0.00 2.41
372 2843 5.374921 TGGAAAGTTTTTACCATCCGTGTA 58.625 37.500 0.00 0.00 0.00 2.90
402 2873 0.902531 CAGGCCGACTAGAAAGGGAA 59.097 55.000 0.00 0.00 0.00 3.97
403 2874 0.976073 CCAGGCCGACTAGAAAGGGA 60.976 60.000 0.00 0.00 0.00 4.20
404 2875 0.976073 TCCAGGCCGACTAGAAAGGG 60.976 60.000 0.00 0.00 0.00 3.95
490 2963 2.086869 GACCACCAGATCCATGTGTTG 58.913 52.381 6.23 0.00 0.00 3.33
494 2967 0.537188 GTCGACCACCAGATCCATGT 59.463 55.000 3.51 0.00 0.00 3.21
552 3029 2.224090 TGAAAAGGGACGACGATTCACA 60.224 45.455 0.00 0.00 0.00 3.58
555 3032 1.730612 GGTGAAAAGGGACGACGATTC 59.269 52.381 0.00 0.00 0.00 2.52
630 3127 0.179018 GCCCAGATATTTGCGGGACT 60.179 55.000 0.00 0.00 41.62 3.85
636 3133 1.263217 CGTAACCGCCCAGATATTTGC 59.737 52.381 0.00 0.00 0.00 3.68
762 3283 2.005537 CTTCAGCACAACGCAACGC 61.006 57.895 0.00 0.00 46.13 4.84
763 3284 2.005537 GCTTCAGCACAACGCAACG 61.006 57.895 0.00 0.00 46.13 4.10
764 3285 1.658409 GGCTTCAGCACAACGCAAC 60.658 57.895 0.30 0.00 46.13 4.17
765 3286 2.721231 GGCTTCAGCACAACGCAA 59.279 55.556 0.30 0.00 46.13 4.85
889 3424 2.045536 GAGCTGTGGAGGGGCTTG 60.046 66.667 0.00 0.00 36.37 4.01
890 3425 3.710722 CGAGCTGTGGAGGGGCTT 61.711 66.667 0.00 0.00 36.37 4.35
898 3433 2.941333 CACTGTTGCGAGCTGTGG 59.059 61.111 0.00 0.00 33.87 4.17
899 3434 2.250485 GCACTGTTGCGAGCTGTG 59.750 61.111 0.00 0.00 39.50 3.66
908 3443 0.173029 TTGTGTTGCTGGCACTGTTG 59.827 50.000 0.00 0.00 37.70 3.33
909 3444 0.173255 GTTGTGTTGCTGGCACTGTT 59.827 50.000 0.00 0.00 37.70 3.16
910 3445 0.680921 AGTTGTGTTGCTGGCACTGT 60.681 50.000 0.00 0.00 37.70 3.55
911 3446 0.248743 CAGTTGTGTTGCTGGCACTG 60.249 55.000 0.00 0.00 37.70 3.66
912 3447 1.386525 CCAGTTGTGTTGCTGGCACT 61.387 55.000 0.00 0.00 44.65 4.40
913 3448 1.066257 CCAGTTGTGTTGCTGGCAC 59.934 57.895 0.00 0.00 44.65 5.01
914 3449 3.524014 CCAGTTGTGTTGCTGGCA 58.476 55.556 0.00 0.00 44.65 4.92
923 3458 2.333938 GCAGCTGCACCAGTTGTG 59.666 61.111 33.36 0.00 43.05 3.33
924 3459 3.282157 CGCAGCTGCACCAGTTGT 61.282 61.111 36.03 0.00 43.05 3.32
947 3497 2.503375 CGTCGGAACTCGGAACCG 60.503 66.667 6.94 6.94 46.71 4.44
974 3524 3.957435 ATGGCCTCTCGGTCGACCA 62.957 63.158 32.80 19.01 37.90 4.02
1501 4066 2.556792 CGTCTCTGTCGTCGCTGT 59.443 61.111 0.00 0.00 0.00 4.40
1502 4067 2.202362 CCGTCTCTGTCGTCGCTG 60.202 66.667 0.00 0.00 0.00 5.18
1503 4068 4.104417 GCCGTCTCTGTCGTCGCT 62.104 66.667 0.00 0.00 0.00 4.93
1580 4151 1.165907 TGCGGTTCAGTTCAGCCTTG 61.166 55.000 0.00 0.00 0.00 3.61
1594 4165 1.806623 GCTATTCTCCAATCGTGCGGT 60.807 52.381 0.00 0.00 0.00 5.68
1604 4175 5.016831 TCACTCACTGTTAGCTATTCTCCA 58.983 41.667 0.00 0.00 0.00 3.86
1619 4190 2.281517 CTAGTCGACCGATCACTCACT 58.718 52.381 13.01 0.00 0.00 3.41
1649 4224 6.202570 CGATTAGGCCTCTATATACGTCCTAC 59.797 46.154 9.68 0.00 0.00 3.18
1742 4325 6.078202 TCGCCTAGAATAGAAGTGAGAATG 57.922 41.667 0.00 0.00 42.77 2.67
1812 4411 1.661178 CGACAAGATGTGTTGCAGCAC 60.661 52.381 25.01 25.01 41.96 4.40
1837 4436 4.202673 ACAAAGAGAAAATGGGGAGGCTTA 60.203 41.667 0.00 0.00 0.00 3.09
1868 4467 2.158959 CAGAAACGCTAGTCCGCCG 61.159 63.158 0.00 0.00 0.00 6.46
2164 4804 1.000163 AGTACACCAGCACTCGACAAG 60.000 52.381 0.00 0.00 0.00 3.16
2165 4805 1.000607 GAGTACACCAGCACTCGACAA 60.001 52.381 0.00 0.00 32.49 3.18
2167 4807 0.882474 AGAGTACACCAGCACTCGAC 59.118 55.000 0.00 0.00 44.77 4.20
2168 4808 2.357075 CTAGAGTACACCAGCACTCGA 58.643 52.381 0.00 0.00 44.77 4.04
2169 4809 1.202200 GCTAGAGTACACCAGCACTCG 60.202 57.143 5.90 0.00 44.77 4.18
2218 4859 5.316327 CTTTGAATCAAAGGAGCCCTTAC 57.684 43.478 23.96 0.00 43.92 2.34
2282 4923 3.131223 TCAAACGACCAATGCAGGAAAAA 59.869 39.130 0.00 0.00 0.00 1.94
2283 4924 2.690497 TCAAACGACCAATGCAGGAAAA 59.310 40.909 0.00 0.00 0.00 2.29
2284 4925 2.302260 TCAAACGACCAATGCAGGAAA 58.698 42.857 0.00 0.00 0.00 3.13
2285 4926 1.974265 TCAAACGACCAATGCAGGAA 58.026 45.000 0.00 0.00 0.00 3.36
2286 4927 2.198827 ATCAAACGACCAATGCAGGA 57.801 45.000 0.00 0.00 0.00 3.86
2287 4928 2.228582 TGAATCAAACGACCAATGCAGG 59.771 45.455 0.00 0.00 0.00 4.85
2288 4929 3.557577 TGAATCAAACGACCAATGCAG 57.442 42.857 0.00 0.00 0.00 4.41
2289 4930 4.699735 ACTATGAATCAAACGACCAATGCA 59.300 37.500 0.00 0.00 0.00 3.96
2290 4931 5.030295 CACTATGAATCAAACGACCAATGC 58.970 41.667 0.00 0.00 0.00 3.56
2291 4932 6.182039 ACACTATGAATCAAACGACCAATG 57.818 37.500 0.00 0.00 0.00 2.82
2292 4933 6.817765 AACACTATGAATCAAACGACCAAT 57.182 33.333 0.00 0.00 0.00 3.16
2293 4934 7.156000 TCTAACACTATGAATCAAACGACCAA 58.844 34.615 0.00 0.00 0.00 3.67
2294 4935 6.693466 TCTAACACTATGAATCAAACGACCA 58.307 36.000 0.00 0.00 0.00 4.02
2295 4936 7.201530 CCTTCTAACACTATGAATCAAACGACC 60.202 40.741 0.00 0.00 0.00 4.79
2296 4937 7.201530 CCCTTCTAACACTATGAATCAAACGAC 60.202 40.741 0.00 0.00 0.00 4.34
2297 4938 6.816640 CCCTTCTAACACTATGAATCAAACGA 59.183 38.462 0.00 0.00 0.00 3.85
2298 4939 6.816640 TCCCTTCTAACACTATGAATCAAACG 59.183 38.462 0.00 0.00 0.00 3.60
2299 4940 8.041323 TCTCCCTTCTAACACTATGAATCAAAC 58.959 37.037 0.00 0.00 0.00 2.93
2300 4941 8.146053 TCTCCCTTCTAACACTATGAATCAAA 57.854 34.615 0.00 0.00 0.00 2.69
2301 4942 7.619698 TCTCTCCCTTCTAACACTATGAATCAA 59.380 37.037 0.00 0.00 0.00 2.57
2302 4943 7.126061 TCTCTCCCTTCTAACACTATGAATCA 58.874 38.462 0.00 0.00 0.00 2.57
2303 4944 7.504238 TCTCTCTCCCTTCTAACACTATGAATC 59.496 40.741 0.00 0.00 0.00 2.52
2304 4945 7.358263 TCTCTCTCCCTTCTAACACTATGAAT 58.642 38.462 0.00 0.00 0.00 2.57
2305 4946 6.732487 TCTCTCTCCCTTCTAACACTATGAA 58.268 40.000 0.00 0.00 0.00 2.57
2306 4947 6.158871 TCTCTCTCTCCCTTCTAACACTATGA 59.841 42.308 0.00 0.00 0.00 2.15
2307 4948 6.361433 TCTCTCTCTCCCTTCTAACACTATG 58.639 44.000 0.00 0.00 0.00 2.23
2308 4949 6.584471 TCTCTCTCTCCCTTCTAACACTAT 57.416 41.667 0.00 0.00 0.00 2.12
2309 4950 6.584471 ATCTCTCTCTCCCTTCTAACACTA 57.416 41.667 0.00 0.00 0.00 2.74
2310 4951 4.938575 TCTCTCTCTCCCTTCTAACACT 57.061 45.455 0.00 0.00 0.00 3.55
2311 4952 5.654650 TCAATCTCTCTCTCCCTTCTAACAC 59.345 44.000 0.00 0.00 0.00 3.32
2312 4953 5.832221 TCAATCTCTCTCTCCCTTCTAACA 58.168 41.667 0.00 0.00 0.00 2.41
2313 4954 6.239289 CCATCAATCTCTCTCTCCCTTCTAAC 60.239 46.154 0.00 0.00 0.00 2.34
2314 4955 5.837979 CCATCAATCTCTCTCTCCCTTCTAA 59.162 44.000 0.00 0.00 0.00 2.10
2315 4956 5.135191 TCCATCAATCTCTCTCTCCCTTCTA 59.865 44.000 0.00 0.00 0.00 2.10
2316 4957 4.078688 TCCATCAATCTCTCTCTCCCTTCT 60.079 45.833 0.00 0.00 0.00 2.85
2317 4958 4.222336 TCCATCAATCTCTCTCTCCCTTC 58.778 47.826 0.00 0.00 0.00 3.46
2318 4959 4.277788 TCCATCAATCTCTCTCTCCCTT 57.722 45.455 0.00 0.00 0.00 3.95
2319 4960 3.989600 TCCATCAATCTCTCTCTCCCT 57.010 47.619 0.00 0.00 0.00 4.20
2320 4961 5.779771 ACTATTCCATCAATCTCTCTCTCCC 59.220 44.000 0.00 0.00 0.00 4.30
2321 4962 6.916360 ACTATTCCATCAATCTCTCTCTCC 57.084 41.667 0.00 0.00 0.00 3.71
2322 4963 7.725251 ACAACTATTCCATCAATCTCTCTCTC 58.275 38.462 0.00 0.00 0.00 3.20
2323 4964 7.673641 ACAACTATTCCATCAATCTCTCTCT 57.326 36.000 0.00 0.00 0.00 3.10
2324 4965 7.768120 ACAACAACTATTCCATCAATCTCTCTC 59.232 37.037 0.00 0.00 0.00 3.20
2325 4966 7.628234 ACAACAACTATTCCATCAATCTCTCT 58.372 34.615 0.00 0.00 0.00 3.10
2326 4967 7.856145 ACAACAACTATTCCATCAATCTCTC 57.144 36.000 0.00 0.00 0.00 3.20
2327 4968 9.911788 AATACAACAACTATTCCATCAATCTCT 57.088 29.630 0.00 0.00 0.00 3.10
2328 4969 9.941664 CAATACAACAACTATTCCATCAATCTC 57.058 33.333 0.00 0.00 0.00 2.75
2329 4970 8.408601 GCAATACAACAACTATTCCATCAATCT 58.591 33.333 0.00 0.00 0.00 2.40
2330 4971 8.408601 AGCAATACAACAACTATTCCATCAATC 58.591 33.333 0.00 0.00 0.00 2.67
2331 4972 8.297470 AGCAATACAACAACTATTCCATCAAT 57.703 30.769 0.00 0.00 0.00 2.57
2332 4973 7.701539 AGCAATACAACAACTATTCCATCAA 57.298 32.000 0.00 0.00 0.00 2.57
2333 4974 7.392953 TCAAGCAATACAACAACTATTCCATCA 59.607 33.333 0.00 0.00 0.00 3.07
2334 4975 7.761409 TCAAGCAATACAACAACTATTCCATC 58.239 34.615 0.00 0.00 0.00 3.51
2335 4976 7.629222 GCTCAAGCAATACAACAACTATTCCAT 60.629 37.037 0.00 0.00 41.59 3.41
2336 4977 6.349280 GCTCAAGCAATACAACAACTATTCCA 60.349 38.462 0.00 0.00 41.59 3.53
2337 4978 6.030228 GCTCAAGCAATACAACAACTATTCC 58.970 40.000 0.00 0.00 41.59 3.01
2338 4979 6.030228 GGCTCAAGCAATACAACAACTATTC 58.970 40.000 4.13 0.00 44.36 1.75
2339 4980 5.711976 AGGCTCAAGCAATACAACAACTATT 59.288 36.000 4.13 0.00 44.36 1.73
2340 4981 5.256474 AGGCTCAAGCAATACAACAACTAT 58.744 37.500 4.13 0.00 44.36 2.12
2341 4982 4.651778 AGGCTCAAGCAATACAACAACTA 58.348 39.130 4.13 0.00 44.36 2.24
2342 4983 3.490348 AGGCTCAAGCAATACAACAACT 58.510 40.909 4.13 0.00 44.36 3.16
2343 4984 3.253188 TGAGGCTCAAGCAATACAACAAC 59.747 43.478 16.28 0.00 44.36 3.32
2344 4985 3.485394 TGAGGCTCAAGCAATACAACAA 58.515 40.909 16.28 0.00 44.36 2.83
2345 4986 3.138884 TGAGGCTCAAGCAATACAACA 57.861 42.857 16.28 0.00 44.36 3.33
2346 4987 3.181493 CCATGAGGCTCAAGCAATACAAC 60.181 47.826 22.84 0.00 44.36 3.32
2347 4988 3.018856 CCATGAGGCTCAAGCAATACAA 58.981 45.455 22.84 0.00 44.36 2.41
2348 4989 2.239402 TCCATGAGGCTCAAGCAATACA 59.761 45.455 22.84 0.00 44.36 2.29
2349 4990 2.615912 GTCCATGAGGCTCAAGCAATAC 59.384 50.000 22.84 10.17 44.36 1.89
2350 4991 2.239402 TGTCCATGAGGCTCAAGCAATA 59.761 45.455 22.84 3.65 44.36 1.90
2351 4992 1.005097 TGTCCATGAGGCTCAAGCAAT 59.995 47.619 22.84 0.66 44.36 3.56
2352 4993 0.401356 TGTCCATGAGGCTCAAGCAA 59.599 50.000 22.84 5.13 44.36 3.91
2353 4994 0.622136 ATGTCCATGAGGCTCAAGCA 59.378 50.000 22.84 16.94 44.36 3.91
2354 4995 2.627515 TATGTCCATGAGGCTCAAGC 57.372 50.000 22.84 11.97 41.14 4.01
2355 4996 8.366401 CCTATATATATGTCCATGAGGCTCAAG 58.634 40.741 22.84 17.42 33.74 3.02
2356 4997 8.067488 TCCTATATATATGTCCATGAGGCTCAA 58.933 37.037 22.84 4.57 33.74 3.02
2357 4998 7.595488 TCCTATATATATGTCCATGAGGCTCA 58.405 38.462 21.19 21.19 33.74 4.26
2358 4999 7.728083 ACTCCTATATATATGTCCATGAGGCTC 59.272 40.741 7.79 7.79 33.74 4.70
2359 5000 7.600093 ACTCCTATATATATGTCCATGAGGCT 58.400 38.462 5.44 0.00 33.74 4.58
2360 5001 7.847711 ACTCCTATATATATGTCCATGAGGC 57.152 40.000 5.44 0.00 33.74 4.70
2361 5002 9.868160 TGTACTCCTATATATATGTCCATGAGG 57.132 37.037 5.44 2.71 0.00 3.86
2396 5037 1.202879 CCACCTTGCCTTGTACTCCAA 60.203 52.381 0.00 0.00 0.00 3.53
2397 5038 0.400213 CCACCTTGCCTTGTACTCCA 59.600 55.000 0.00 0.00 0.00 3.86
2398 5039 0.690762 TCCACCTTGCCTTGTACTCC 59.309 55.000 0.00 0.00 0.00 3.85
2399 5040 2.561478 TTCCACCTTGCCTTGTACTC 57.439 50.000 0.00 0.00 0.00 2.59
2400 5041 4.650972 TTATTCCACCTTGCCTTGTACT 57.349 40.909 0.00 0.00 0.00 2.73
2401 5042 5.163550 GGATTTATTCCACCTTGCCTTGTAC 60.164 44.000 0.00 0.00 44.74 2.90
2402 5043 4.953579 GGATTTATTCCACCTTGCCTTGTA 59.046 41.667 0.00 0.00 44.74 2.41
2403 5044 3.769300 GGATTTATTCCACCTTGCCTTGT 59.231 43.478 0.00 0.00 44.74 3.16
2404 5045 4.391405 GGATTTATTCCACCTTGCCTTG 57.609 45.455 0.00 0.00 44.74 3.61
2419 5060 9.442062 TGGAAACATAGGATAGTGTAGGATTTA 57.558 33.333 0.00 0.00 33.40 1.40
2420 5061 8.331931 TGGAAACATAGGATAGTGTAGGATTT 57.668 34.615 0.00 0.00 33.40 2.17
2421 5062 7.931015 TGGAAACATAGGATAGTGTAGGATT 57.069 36.000 0.00 0.00 33.40 3.01
2446 5087 8.973182 GGGGGATGTTGAGTATTTTTGTTATTA 58.027 33.333 0.00 0.00 0.00 0.98
2447 5088 7.847096 GGGGGATGTTGAGTATTTTTGTTATT 58.153 34.615 0.00 0.00 0.00 1.40
2448 5089 7.418337 GGGGGATGTTGAGTATTTTTGTTAT 57.582 36.000 0.00 0.00 0.00 1.89
2449 5090 6.844097 GGGGGATGTTGAGTATTTTTGTTA 57.156 37.500 0.00 0.00 0.00 2.41
2450 5091 5.738619 GGGGGATGTTGAGTATTTTTGTT 57.261 39.130 0.00 0.00 0.00 2.83
2473 5114 2.716828 CGCTACCGTTGTGACTGCG 61.717 63.158 0.00 0.00 36.19 5.18
2474 5115 1.372499 TCGCTACCGTTGTGACTGC 60.372 57.895 0.00 0.00 35.54 4.40
2475 5116 1.334992 CGTCGCTACCGTTGTGACTG 61.335 60.000 19.68 12.04 41.26 3.51
2476 5117 1.081641 CGTCGCTACCGTTGTGACT 60.082 57.895 19.68 0.00 41.26 3.41
2477 5118 2.713894 GCGTCGCTACCGTTGTGAC 61.714 63.158 10.68 14.36 40.38 3.67
2478 5119 2.429571 GCGTCGCTACCGTTGTGA 60.430 61.111 10.68 0.00 35.54 3.58
2479 5120 2.716828 CTGCGTCGCTACCGTTGTG 61.717 63.158 19.50 0.00 35.54 3.33
2480 5121 2.430244 CTGCGTCGCTACCGTTGT 60.430 61.111 19.50 0.00 35.54 3.32
2481 5122 2.126618 TCTGCGTCGCTACCGTTG 60.127 61.111 19.50 0.42 35.54 4.10
2482 5123 2.126580 GTCTGCGTCGCTACCGTT 60.127 61.111 19.50 0.00 35.54 4.44
2483 5124 4.456253 CGTCTGCGTCGCTACCGT 62.456 66.667 19.50 0.00 35.54 4.83
2485 5126 4.112341 ACCGTCTGCGTCGCTACC 62.112 66.667 19.50 4.72 36.15 3.18
2486 5127 2.874780 CACCGTCTGCGTCGCTAC 60.875 66.667 19.50 15.00 36.15 3.58
2487 5128 3.035576 CTCACCGTCTGCGTCGCTA 62.036 63.158 19.50 3.59 36.15 4.26
2488 5129 4.406173 CTCACCGTCTGCGTCGCT 62.406 66.667 19.50 0.00 36.15 4.93
2489 5130 4.400109 TCTCACCGTCTGCGTCGC 62.400 66.667 11.10 11.10 36.15 5.19
2490 5131 2.502080 GTCTCACCGTCTGCGTCG 60.502 66.667 0.00 0.00 36.15 5.12
2491 5132 1.442857 CAGTCTCACCGTCTGCGTC 60.443 63.158 0.00 0.00 36.15 5.19
2492 5133 1.452953 TTCAGTCTCACCGTCTGCGT 61.453 55.000 0.00 0.00 36.15 5.24
2493 5134 0.730834 CTTCAGTCTCACCGTCTGCG 60.731 60.000 0.00 0.00 37.95 5.18
2494 5135 0.598562 TCTTCAGTCTCACCGTCTGC 59.401 55.000 0.00 0.00 0.00 4.26
2495 5136 2.554462 TCTTCTTCAGTCTCACCGTCTG 59.446 50.000 0.00 0.00 0.00 3.51
2496 5137 2.865079 TCTTCTTCAGTCTCACCGTCT 58.135 47.619 0.00 0.00 0.00 4.18
2497 5138 3.644884 TTCTTCTTCAGTCTCACCGTC 57.355 47.619 0.00 0.00 0.00 4.79
2498 5139 3.829601 AGATTCTTCTTCAGTCTCACCGT 59.170 43.478 0.00 0.00 0.00 4.83
2499 5140 4.082517 TCAGATTCTTCTTCAGTCTCACCG 60.083 45.833 0.00 0.00 0.00 4.94
2500 5141 5.398603 TCAGATTCTTCTTCAGTCTCACC 57.601 43.478 0.00 0.00 0.00 4.02
2501 5142 5.868801 CCTTCAGATTCTTCTTCAGTCTCAC 59.131 44.000 0.00 0.00 0.00 3.51
2502 5143 5.568423 GCCTTCAGATTCTTCTTCAGTCTCA 60.568 44.000 0.00 0.00 0.00 3.27
2503 5144 4.869861 GCCTTCAGATTCTTCTTCAGTCTC 59.130 45.833 0.00 0.00 0.00 3.36
2504 5145 4.285517 TGCCTTCAGATTCTTCTTCAGTCT 59.714 41.667 0.00 0.00 0.00 3.24
2505 5146 4.573900 TGCCTTCAGATTCTTCTTCAGTC 58.426 43.478 0.00 0.00 0.00 3.51
2506 5147 4.630644 TGCCTTCAGATTCTTCTTCAGT 57.369 40.909 0.00 0.00 0.00 3.41
2507 5148 4.142643 GCTTGCCTTCAGATTCTTCTTCAG 60.143 45.833 0.00 0.00 0.00 3.02
2508 5149 3.755378 GCTTGCCTTCAGATTCTTCTTCA 59.245 43.478 0.00 0.00 0.00 3.02
2509 5150 3.128415 GGCTTGCCTTCAGATTCTTCTTC 59.872 47.826 4.11 0.00 0.00 2.87
2510 5151 3.087781 GGCTTGCCTTCAGATTCTTCTT 58.912 45.455 4.11 0.00 0.00 2.52
2511 5152 2.720915 GGCTTGCCTTCAGATTCTTCT 58.279 47.619 4.11 0.00 0.00 2.85
2512 5153 1.399791 CGGCTTGCCTTCAGATTCTTC 59.600 52.381 10.12 0.00 0.00 2.87
2513 5154 1.003580 TCGGCTTGCCTTCAGATTCTT 59.996 47.619 10.12 0.00 0.00 2.52
2514 5155 0.615331 TCGGCTTGCCTTCAGATTCT 59.385 50.000 10.12 0.00 0.00 2.40
2515 5156 1.332997 CATCGGCTTGCCTTCAGATTC 59.667 52.381 10.12 0.00 0.00 2.52
2516 5157 1.386533 CATCGGCTTGCCTTCAGATT 58.613 50.000 10.12 0.00 0.00 2.40
2517 5158 0.465097 CCATCGGCTTGCCTTCAGAT 60.465 55.000 10.12 2.33 0.00 2.90
2518 5159 1.078214 CCATCGGCTTGCCTTCAGA 60.078 57.895 10.12 0.00 0.00 3.27
2519 5160 1.078214 TCCATCGGCTTGCCTTCAG 60.078 57.895 10.12 0.00 0.00 3.02
2520 5161 1.377202 GTCCATCGGCTTGCCTTCA 60.377 57.895 10.12 0.00 0.00 3.02
2521 5162 1.377202 TGTCCATCGGCTTGCCTTC 60.377 57.895 10.12 0.00 0.00 3.46
2522 5163 1.675641 GTGTCCATCGGCTTGCCTT 60.676 57.895 10.12 0.00 0.00 4.35
2523 5164 2.045926 GTGTCCATCGGCTTGCCT 60.046 61.111 10.12 0.00 0.00 4.75
2524 5165 3.134127 GGTGTCCATCGGCTTGCC 61.134 66.667 0.75 0.75 0.00 4.52
2525 5166 3.134127 GGGTGTCCATCGGCTTGC 61.134 66.667 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.