Multiple sequence alignment - TraesCS5D01G418800

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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 TraesCS5D01G418800 chr5D 100.000 4132 0 0 1 4132 480363294 480367425 0.000000e+00 7631.0
1 TraesCS5D01G418800 chr5A 93.191 2908 109 36 1 2873 598863451 598866304 0.000000e+00 4191.0
2 TraesCS5D01G418800 chr5A 92.070 454 24 7 2871 3314 598866330 598866781 2.710000e-176 628.0
3 TraesCS5D01G418800 chr5A 85.965 399 32 15 3332 3709 598866765 598867160 4.970000e-109 405.0
4 TraesCS5D01G418800 chr5B 84.657 2783 251 87 1 2707 588512375 588515057 0.000000e+00 2612.0
5 TraesCS5D01G418800 chr5B 79.961 509 26 22 3450 3916 588515854 588516328 5.190000e-79 305.0
6 TraesCS5D01G418800 chr5B 81.301 369 46 10 2871 3216 588515297 588515665 1.130000e-70 278.0
7 TraesCS5D01G418800 chr5B 94.845 97 4 1 2777 2873 588515166 588515261 2.570000e-32 150.0
8 TraesCS5D01G418800 chr5B 90.909 44 4 0 3988 4031 588517467 588517510 4.460000e-05 60.2
9 TraesCS5D01G418800 chr2D 80.889 450 68 13 1646 2087 63381502 63381063 5.120000e-89 339.0
10 TraesCS5D01G418800 chr2D 83.333 258 34 7 1838 2087 649858761 649858505 3.210000e-56 230.0
11 TraesCS5D01G418800 chr3D 80.444 450 70 13 1646 2087 564093716 564094155 1.110000e-85 327.0
12 TraesCS5D01G418800 chr7B 79.556 450 74 13 1646 2087 615632698 615632259 5.190000e-79 305.0
13 TraesCS5D01G418800 chr7B 86.567 268 20 11 1034 1297 116070685 116070940 8.750000e-72 281.0
14 TraesCS5D01G418800 chr4D 79.111 450 76 13 1646 2087 435252864 435253303 1.120000e-75 294.0
15 TraesCS5D01G418800 chr4D 82.687 335 33 13 1035 1356 435252279 435252601 1.460000e-69 274.0
16 TraesCS5D01G418800 chr4D 82.524 206 20 8 1096 1297 361189209 361189402 2.550000e-37 167.0
17 TraesCS5D01G418800 chr6A 83.631 336 30 13 1034 1356 29401758 29402081 4.040000e-75 292.0
18 TraesCS5D01G418800 chr6A 83.721 258 33 7 1838 2087 32066659 32066915 6.910000e-58 235.0
19 TraesCS5D01G418800 chr2A 78.634 454 71 15 1646 2087 123336217 123335778 1.130000e-70 278.0
20 TraesCS5D01G418800 chr6B 85.821 268 22 11 1034 1297 720151232 720150977 1.890000e-68 270.0
21 TraesCS5D01G418800 chr3B 85.448 268 23 10 1034 1297 711740561 711740306 8.810000e-67 265.0
22 TraesCS5D01G418800 chr7A 83.582 268 28 8 1034 1297 440950393 440950648 1.920000e-58 237.0
23 TraesCS5D01G418800 chr7A 80.000 125 7 6 3560 3680 208523818 208523928 4.430000e-10 76.8


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 TraesCS5D01G418800 chr5D 480363294 480367425 4131 False 7631.000000 7631 100.000000 1 4132 1 chr5D.!!$F1 4131
1 TraesCS5D01G418800 chr5A 598863451 598867160 3709 False 1741.333333 4191 90.408667 1 3709 3 chr5A.!!$F1 3708
2 TraesCS5D01G418800 chr5B 588512375 588517510 5135 False 681.040000 2612 86.334600 1 4031 5 chr5B.!!$F1 4030
3 TraesCS5D01G418800 chr4D 435252279 435253303 1024 False 284.000000 294 80.899000 1035 2087 2 chr4D.!!$F2 1052

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
928 946 0.675208 TCTTGTCGCGCTCTCTCTCT 60.675 55.0 5.56 0.0 0.00 3.10 F
1856 2029 0.096628 CTGCGAGCTTCAGAATGCAC 59.903 55.0 10.40 1.4 34.76 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2159 0.465460 TGCAAGGTGTGAACAGGGAC 60.465 55.0 0.00 0.00 0.0 4.46 R
3750 4116 0.167908 GTTTTGATCGACATGGCGCA 59.832 50.0 18.42 6.63 0.0 6.09 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
75 76 2.764128 TCCATCCTCCCCAGACGC 60.764 66.667 0.00 0.00 0.00 5.19
192 193 2.831685 ACATGTTGAGCACCGAGTTA 57.168 45.000 0.00 0.00 0.00 2.24
198 199 1.292223 GAGCACCGAGTTAGCCACA 59.708 57.895 0.00 0.00 0.00 4.17
229 230 4.069232 CCAGGCCGAGCTTGACGA 62.069 66.667 1.22 0.00 37.87 4.20
790 806 2.785258 GCATGTCGCGGGAAAGTC 59.215 61.111 6.13 0.00 0.00 3.01
798 815 4.394712 CGGGAAAGTCAGCGGGCT 62.395 66.667 0.00 0.00 0.00 5.19
799 816 2.436824 GGGAAAGTCAGCGGGCTC 60.437 66.667 0.00 0.00 0.00 4.70
800 817 2.436824 GGAAAGTCAGCGGGCTCC 60.437 66.667 0.00 0.00 0.00 4.70
801 818 2.436824 GAAAGTCAGCGGGCTCCC 60.437 66.667 0.00 0.00 0.00 4.30
918 936 1.070577 CAGTTTTGTCCTCTTGTCGCG 60.071 52.381 0.00 0.00 0.00 5.87
928 946 0.675208 TCTTGTCGCGCTCTCTCTCT 60.675 55.000 5.56 0.00 0.00 3.10
995 1014 4.089757 CGAGGAGGGGGAAGGGGA 62.090 72.222 0.00 0.00 0.00 4.81
1146 1178 3.558829 ACTCGGTTTCCTCTTTCGTTTTC 59.441 43.478 0.00 0.00 0.00 2.29
1181 1232 0.608035 TTGGATTGGCTTCACCGACC 60.608 55.000 0.00 0.00 43.94 4.79
1205 1259 0.329596 GGGAGCTGACTGATTTGGGT 59.670 55.000 0.00 0.00 0.00 4.51
1355 1424 3.911661 AGAATGTGCTGCTCAAGTTTC 57.088 42.857 8.59 8.19 0.00 2.78
1417 1497 1.288335 CTGGGACTAGGAGGTGGTAGT 59.712 57.143 0.00 0.00 31.97 2.73
1422 1502 3.952967 GGACTAGGAGGTGGTAGTACTTG 59.047 52.174 0.00 0.00 28.68 3.16
1435 1515 5.933463 TGGTAGTACTTGGTGTTAATTTCCG 59.067 40.000 0.00 0.00 0.00 4.30
1492 1622 2.272146 CACCCGTTCCCCCATCAG 59.728 66.667 0.00 0.00 0.00 2.90
1527 1657 3.446442 AGAAGCCAGAATCATTGTGGT 57.554 42.857 14.84 0.00 45.35 4.16
1735 1902 4.143535 GCGCTCACTGCTTTTATCAAAAAC 60.144 41.667 0.00 0.00 40.11 2.43
1808 1978 2.954318 CCCATTAGGTTGCTCATCCTTG 59.046 50.000 4.96 0.00 35.51 3.61
1856 2029 0.096628 CTGCGAGCTTCAGAATGCAC 59.903 55.000 10.40 1.40 34.76 4.57
1863 2036 4.435253 CGAGCTTCAGAATGCACTTACTTG 60.435 45.833 0.00 0.00 34.76 3.16
1890 2073 3.610040 ACGAAGCATCCTCATTGTACA 57.390 42.857 0.00 0.00 0.00 2.90
1891 2074 3.525537 ACGAAGCATCCTCATTGTACAG 58.474 45.455 0.00 0.00 0.00 2.74
1892 2075 3.055819 ACGAAGCATCCTCATTGTACAGT 60.056 43.478 0.00 0.00 0.00 3.55
1893 2076 4.159693 ACGAAGCATCCTCATTGTACAGTA 59.840 41.667 0.00 0.00 0.00 2.74
1894 2077 4.742167 CGAAGCATCCTCATTGTACAGTAG 59.258 45.833 0.00 0.00 0.00 2.57
1909 2094 6.293698 TGTACAGTAGAGTACAGTCTGTTCA 58.706 40.000 11.54 13.21 46.77 3.18
1938 2123 3.456280 TCTGTTTTGGTTTCATGCAAGC 58.544 40.909 0.00 0.00 0.00 4.01
1947 2132 3.562505 GTTTCATGCAAGCAGTCAAGAG 58.437 45.455 0.00 0.00 0.00 2.85
1951 2136 2.090400 TGCAAGCAGTCAAGAGCTAG 57.910 50.000 0.00 0.00 40.90 3.42
1974 2159 2.604139 TCCTGCTTAAACTTTTGGGGG 58.396 47.619 0.00 0.00 0.00 5.40
1977 2162 2.299013 CTGCTTAAACTTTTGGGGGTCC 59.701 50.000 0.00 0.00 0.00 4.46
1991 2176 0.537371 GGGTCCCTGTTCACACCTTG 60.537 60.000 0.00 0.00 0.00 3.61
2138 2324 8.103305 GCATGTTTCTATATGGATCCCTTTCTA 58.897 37.037 9.90 0.00 0.00 2.10
2162 2348 9.712305 CTATATTCATCGGGTTCTGATTAAGTT 57.288 33.333 0.00 0.00 0.00 2.66
2272 2458 7.760131 ACATGCATGTTCAATTTAGCAATAC 57.240 32.000 26.61 0.00 37.90 1.89
2326 2512 3.751479 TGGGATAGATGGAATGTCACG 57.249 47.619 0.00 0.00 0.00 4.35
2328 2514 3.069586 TGGGATAGATGGAATGTCACGAC 59.930 47.826 0.00 0.00 0.00 4.34
2392 2582 3.378112 ACTTGCCACACATATACACATGC 59.622 43.478 0.00 0.00 0.00 4.06
2482 2672 6.798476 CACTGTAAATTGTGTGCATGTAGAAG 59.202 38.462 0.00 0.00 0.00 2.85
2721 2937 4.813750 AAGAAAATGCCCCTCTTTCATG 57.186 40.909 0.00 0.00 32.59 3.07
2731 2947 5.103982 TGCCCCTCTTTCATGATGATTCTTA 60.104 40.000 0.00 0.00 0.00 2.10
2733 2949 6.072064 GCCCCTCTTTCATGATGATTCTTATG 60.072 42.308 0.00 0.00 0.00 1.90
2856 3093 4.584743 TCAGGTGCGTAAGATGACAGATAT 59.415 41.667 0.00 0.00 43.02 1.63
2880 3155 6.737720 TCTAACTCATGGCTAACTCATCAT 57.262 37.500 0.00 0.00 0.00 2.45
2881 3156 6.519382 TCTAACTCATGGCTAACTCATCATG 58.481 40.000 0.00 0.00 38.54 3.07
2895 3170 4.018960 ACTCATCATGGGGCAGTATTATCC 60.019 45.833 0.00 0.00 0.00 2.59
2914 3189 4.630894 TCCGTGAAAATATCCAATGCAC 57.369 40.909 0.00 0.00 0.00 4.57
2963 3238 0.110644 CAAAACGAGAACGGCAGCTC 60.111 55.000 0.00 0.00 44.46 4.09
2997 3280 4.320023 TGCGTTTGAACAGTGGTATGTAT 58.680 39.130 0.00 0.00 31.70 2.29
3189 3483 6.408869 ACAGCAATAATAAGCAGGCATTTTT 58.591 32.000 0.00 0.00 0.00 1.94
3216 3514 4.374689 TTTGCCCAATACTGTACCTGAA 57.625 40.909 0.00 0.00 0.00 3.02
3217 3515 4.374689 TTGCCCAATACTGTACCTGAAA 57.625 40.909 0.00 0.00 0.00 2.69
3229 3528 5.701290 ACTGTACCTGAAATTCGAGAAAAGG 59.299 40.000 0.00 0.00 0.00 3.11
3237 3536 7.254590 CCTGAAATTCGAGAAAAGGCACTATAG 60.255 40.741 0.00 0.00 38.49 1.31
3263 3562 5.104374 GGTCATGTATGTGCCATTCTTTTG 58.896 41.667 0.00 0.00 0.00 2.44
3270 3569 4.582701 TGTGCCATTCTTTTGTGTTAGG 57.417 40.909 0.00 0.00 0.00 2.69
3275 3574 5.009210 TGCCATTCTTTTGTGTTAGGTGTAC 59.991 40.000 0.00 0.00 0.00 2.90
3279 3578 3.805422 TCTTTTGTGTTAGGTGTACGCTG 59.195 43.478 6.35 0.00 0.00 5.18
3297 3596 2.634940 GCTGCTACTCCCTGGAATATCA 59.365 50.000 0.00 0.00 0.00 2.15
3305 3604 2.444388 TCCCTGGAATATCAGCAATGCT 59.556 45.455 0.00 0.00 40.77 3.79
3306 3605 3.117398 TCCCTGGAATATCAGCAATGCTT 60.117 43.478 4.36 0.00 36.40 3.91
3307 3606 3.640029 CCCTGGAATATCAGCAATGCTTT 59.360 43.478 4.36 0.00 36.40 3.51
3308 3607 4.100498 CCCTGGAATATCAGCAATGCTTTT 59.900 41.667 4.36 0.00 36.40 2.27
3309 3608 5.395990 CCCTGGAATATCAGCAATGCTTTTT 60.396 40.000 4.36 0.00 36.40 1.94
3310 3609 5.751990 CCTGGAATATCAGCAATGCTTTTTC 59.248 40.000 4.36 6.36 36.40 2.29
3311 3610 6.406624 CCTGGAATATCAGCAATGCTTTTTCT 60.407 38.462 4.36 0.00 36.40 2.52
3312 3611 6.938507 TGGAATATCAGCAATGCTTTTTCTT 58.061 32.000 4.36 0.00 36.40 2.52
3313 3612 7.037438 TGGAATATCAGCAATGCTTTTTCTTC 58.963 34.615 4.36 5.48 36.40 2.87
3314 3613 7.093640 TGGAATATCAGCAATGCTTTTTCTTCT 60.094 33.333 4.36 0.00 36.40 2.85
3315 3614 7.763071 GGAATATCAGCAATGCTTTTTCTTCTT 59.237 33.333 4.36 0.00 36.40 2.52
3316 3615 9.148104 GAATATCAGCAATGCTTTTTCTTCTTT 57.852 29.630 4.36 0.00 36.40 2.52
3317 3616 8.699283 ATATCAGCAATGCTTTTTCTTCTTTC 57.301 30.769 4.36 0.00 36.40 2.62
3318 3617 5.291971 TCAGCAATGCTTTTTCTTCTTTCC 58.708 37.500 4.36 0.00 36.40 3.13
3319 3618 4.450080 CAGCAATGCTTTTTCTTCTTTCCC 59.550 41.667 4.36 0.00 36.40 3.97
3320 3619 3.429881 GCAATGCTTTTTCTTCTTTCCCG 59.570 43.478 0.00 0.00 0.00 5.14
3321 3620 2.793278 TGCTTTTTCTTCTTTCCCGC 57.207 45.000 0.00 0.00 0.00 6.13
3322 3621 1.339929 TGCTTTTTCTTCTTTCCCGCC 59.660 47.619 0.00 0.00 0.00 6.13
3323 3622 1.339929 GCTTTTTCTTCTTTCCCGCCA 59.660 47.619 0.00 0.00 0.00 5.69
3324 3623 2.223947 GCTTTTTCTTCTTTCCCGCCAA 60.224 45.455 0.00 0.00 0.00 4.52
3325 3624 3.739830 GCTTTTTCTTCTTTCCCGCCAAA 60.740 43.478 0.00 0.00 0.00 3.28
3326 3625 4.438148 CTTTTTCTTCTTTCCCGCCAAAA 58.562 39.130 0.00 0.00 0.00 2.44
3327 3626 4.473477 TTTTCTTCTTTCCCGCCAAAAA 57.527 36.364 0.00 0.00 0.00 1.94
3387 3698 4.018324 GTCCTTCAAAGTAGGAGGGGAATT 60.018 45.833 0.00 0.00 42.31 2.17
3427 3742 8.607713 TGATTTGGTCCTATTTTACTGGTTCTA 58.392 33.333 0.00 0.00 0.00 2.10
3514 3833 2.740826 TTAAGTCGTGCCTGCCGC 60.741 61.111 0.00 0.00 38.31 6.53
3570 3892 6.036953 CCTTATCTGCTGTCATGTTTCTCTTC 59.963 42.308 0.00 0.00 0.00 2.87
3672 4022 4.618489 CGATGTCAAAATGAGGCAAAGTTC 59.382 41.667 0.00 0.00 0.00 3.01
3709 4075 1.006922 GGCTTTGCTTGCTGTCCAC 60.007 57.895 0.00 0.00 0.00 4.02
3726 4092 3.879295 GTCCACATGTTGTATATGCAGCT 59.121 43.478 8.93 0.00 0.00 4.24
3727 4093 4.024556 GTCCACATGTTGTATATGCAGCTC 60.025 45.833 8.93 0.00 0.00 4.09
3728 4094 4.132336 CCACATGTTGTATATGCAGCTCT 58.868 43.478 8.93 0.00 0.00 4.09
3729 4095 4.024302 CCACATGTTGTATATGCAGCTCTG 60.024 45.833 8.93 8.60 0.00 3.35
3730 4096 4.573607 CACATGTTGTATATGCAGCTCTGT 59.426 41.667 8.93 9.12 0.00 3.41
3731 4097 4.813161 ACATGTTGTATATGCAGCTCTGTC 59.187 41.667 8.93 0.00 0.00 3.51
3732 4098 3.797039 TGTTGTATATGCAGCTCTGTCC 58.203 45.455 8.93 0.00 0.00 4.02
3734 4100 4.080919 TGTTGTATATGCAGCTCTGTCCTT 60.081 41.667 8.93 0.00 0.00 3.36
3735 4101 4.327982 TGTATATGCAGCTCTGTCCTTC 57.672 45.455 0.00 0.00 0.00 3.46
3736 4102 2.926778 ATATGCAGCTCTGTCCTTCC 57.073 50.000 0.00 0.00 0.00 3.46
3737 4103 0.461548 TATGCAGCTCTGTCCTTCCG 59.538 55.000 0.00 0.00 0.00 4.30
3738 4104 1.260538 ATGCAGCTCTGTCCTTCCGA 61.261 55.000 0.00 0.00 0.00 4.55
3741 4107 0.820226 CAGCTCTGTCCTTCCGATGA 59.180 55.000 0.00 0.00 0.00 2.92
3742 4108 1.205655 CAGCTCTGTCCTTCCGATGAA 59.794 52.381 0.00 0.00 0.00 2.57
3744 4110 2.503356 AGCTCTGTCCTTCCGATGAATT 59.497 45.455 0.00 0.00 0.00 2.17
3746 4112 3.691609 GCTCTGTCCTTCCGATGAATTTT 59.308 43.478 0.00 0.00 0.00 1.82
3747 4113 4.437930 GCTCTGTCCTTCCGATGAATTTTG 60.438 45.833 0.00 0.00 0.00 2.44
3748 4114 4.651778 TCTGTCCTTCCGATGAATTTTGT 58.348 39.130 0.00 0.00 0.00 2.83
3750 4116 4.651778 TGTCCTTCCGATGAATTTTGTCT 58.348 39.130 0.00 0.00 0.00 3.41
3752 4118 3.440173 TCCTTCCGATGAATTTTGTCTGC 59.560 43.478 0.00 0.00 0.00 4.26
3753 4119 3.419915 CTTCCGATGAATTTTGTCTGCG 58.580 45.455 0.00 0.00 0.00 5.18
3754 4120 1.130373 TCCGATGAATTTTGTCTGCGC 59.870 47.619 0.00 0.00 0.00 6.09
3755 4121 1.538276 CGATGAATTTTGTCTGCGCC 58.462 50.000 4.18 0.00 0.00 6.53
3757 4123 2.478370 CGATGAATTTTGTCTGCGCCAT 60.478 45.455 4.18 0.00 0.00 4.40
3759 4125 1.612950 TGAATTTTGTCTGCGCCATGT 59.387 42.857 4.18 0.00 0.00 3.21
3760 4126 2.253603 GAATTTTGTCTGCGCCATGTC 58.746 47.619 4.18 0.00 0.00 3.06
3761 4127 0.168788 ATTTTGTCTGCGCCATGTCG 59.831 50.000 4.18 0.00 0.00 4.35
3762 4128 0.882484 TTTTGTCTGCGCCATGTCGA 60.882 50.000 4.18 0.00 0.00 4.20
3763 4129 0.673333 TTTGTCTGCGCCATGTCGAT 60.673 50.000 4.18 0.00 0.00 3.59
3764 4130 1.083806 TTGTCTGCGCCATGTCGATC 61.084 55.000 4.18 0.00 0.00 3.69
3765 4131 1.519234 GTCTGCGCCATGTCGATCA 60.519 57.895 4.18 0.00 0.00 2.92
3766 4132 1.083806 GTCTGCGCCATGTCGATCAA 61.084 55.000 4.18 0.00 0.00 2.57
3799 4165 4.142687 CGGATGTTTTATCACCTGTGAACC 60.143 45.833 3.79 0.00 43.58 3.62
3822 4188 2.625375 GGAACTTGTCCCCGTTGAC 58.375 57.895 0.00 0.00 41.10 3.18
3823 4189 0.887836 GGAACTTGTCCCCGTTGACC 60.888 60.000 0.00 0.00 41.10 4.02
3825 4191 2.033602 CTTGTCCCCGTTGACCCC 59.966 66.667 0.00 0.00 34.25 4.95
3826 4192 3.562732 CTTGTCCCCGTTGACCCCC 62.563 68.421 0.00 0.00 34.25 5.40
3859 4225 4.135153 CACGACGAGCCCCTCTGG 62.135 72.222 0.00 0.00 37.09 3.86
3866 4232 3.635268 GAGCCCCTCTGGTTGCCTG 62.635 68.421 0.00 0.00 36.04 4.85
3871 4237 1.687612 CCTCTGGTTGCCTGATGGT 59.312 57.895 0.00 0.00 31.33 3.55
3877 4243 2.564062 CTGGTTGCCTGATGGTTTGAAT 59.436 45.455 0.00 0.00 35.27 2.57
3916 4288 1.274798 GGTTGCGTGCGATTTGGTTG 61.275 55.000 0.00 0.00 0.00 3.77
3917 4289 1.659954 TTGCGTGCGATTTGGTTGC 60.660 52.632 0.00 0.00 37.76 4.17
3918 4290 2.050533 GCGTGCGATTTGGTTGCA 60.051 55.556 0.00 0.00 45.03 4.08
3942 5242 2.289382 ACATGGTGTATTGTGCTCGACA 60.289 45.455 0.00 0.00 0.00 4.35
3953 5253 2.355126 CTCGACAGCGTGTGCACT 60.355 61.111 19.41 0.00 46.23 4.40
3971 5272 2.363680 CACTCCAGAATAGCAGTCGGAT 59.636 50.000 0.00 0.00 0.00 4.18
3973 5274 1.069204 TCCAGAATAGCAGTCGGATGC 59.931 52.381 4.80 4.80 46.88 3.91
3986 5287 2.315246 GGATGCAATCTGCTCCGTC 58.685 57.895 0.00 0.00 45.31 4.79
4036 5475 7.121974 ACTCACGAGTTCAAACAAGATAATG 57.878 36.000 0.00 0.00 38.83 1.90
4037 5476 6.147821 ACTCACGAGTTCAAACAAGATAATGG 59.852 38.462 0.00 0.00 38.83 3.16
4038 5477 6.227522 TCACGAGTTCAAACAAGATAATGGA 58.772 36.000 0.00 0.00 0.00 3.41
4039 5478 6.708502 TCACGAGTTCAAACAAGATAATGGAA 59.291 34.615 0.00 0.00 0.00 3.53
4040 5479 7.390440 TCACGAGTTCAAACAAGATAATGGAAT 59.610 33.333 0.00 0.00 0.00 3.01
4041 5480 7.482743 CACGAGTTCAAACAAGATAATGGAATG 59.517 37.037 0.00 0.00 0.00 2.67
4042 5481 7.390440 ACGAGTTCAAACAAGATAATGGAATGA 59.610 33.333 0.00 0.00 0.00 2.57
4043 5482 8.236586 CGAGTTCAAACAAGATAATGGAATGAA 58.763 33.333 0.00 0.00 0.00 2.57
4045 5484 9.865321 AGTTCAAACAAGATAATGGAATGAATG 57.135 29.630 0.00 0.00 0.00 2.67
4046 5485 9.090692 GTTCAAACAAGATAATGGAATGAATGG 57.909 33.333 0.00 0.00 0.00 3.16
4047 5486 8.365060 TCAAACAAGATAATGGAATGAATGGT 57.635 30.769 0.00 0.00 0.00 3.55
4048 5487 8.469200 TCAAACAAGATAATGGAATGAATGGTC 58.531 33.333 0.00 0.00 0.00 4.02
4049 5488 6.966534 ACAAGATAATGGAATGAATGGTCC 57.033 37.500 0.00 0.00 0.00 4.46
4050 5489 6.676558 ACAAGATAATGGAATGAATGGTCCT 58.323 36.000 0.00 0.00 34.77 3.85
4051 5490 7.815383 ACAAGATAATGGAATGAATGGTCCTA 58.185 34.615 0.00 0.00 34.77 2.94
4052 5491 8.451245 ACAAGATAATGGAATGAATGGTCCTAT 58.549 33.333 0.00 0.00 34.77 2.57
4053 5492 9.964354 CAAGATAATGGAATGAATGGTCCTATA 57.036 33.333 0.00 0.00 34.77 1.31
4054 5493 9.965902 AAGATAATGGAATGAATGGTCCTATAC 57.034 33.333 0.00 0.00 34.77 1.47
4065 5504 3.336138 GGTCCTATACCTATGCCTTGC 57.664 52.381 0.00 0.00 45.75 4.01
4066 5505 2.907042 GGTCCTATACCTATGCCTTGCT 59.093 50.000 0.00 0.00 45.75 3.91
4067 5506 3.328050 GGTCCTATACCTATGCCTTGCTT 59.672 47.826 0.00 0.00 45.75 3.91
4068 5507 4.319177 GTCCTATACCTATGCCTTGCTTG 58.681 47.826 0.00 0.00 0.00 4.01
4069 5508 3.973973 TCCTATACCTATGCCTTGCTTGT 59.026 43.478 0.00 0.00 0.00 3.16
4070 5509 5.011738 GTCCTATACCTATGCCTTGCTTGTA 59.988 44.000 0.00 0.00 0.00 2.41
4071 5510 5.011738 TCCTATACCTATGCCTTGCTTGTAC 59.988 44.000 0.00 0.00 0.00 2.90
4072 5511 5.012148 CCTATACCTATGCCTTGCTTGTACT 59.988 44.000 0.00 0.00 0.00 2.73
4073 5512 3.721087 ACCTATGCCTTGCTTGTACTT 57.279 42.857 0.00 0.00 0.00 2.24
4074 5513 4.034285 ACCTATGCCTTGCTTGTACTTT 57.966 40.909 0.00 0.00 0.00 2.66
4075 5514 4.010349 ACCTATGCCTTGCTTGTACTTTC 58.990 43.478 0.00 0.00 0.00 2.62
4076 5515 4.263506 ACCTATGCCTTGCTTGTACTTTCT 60.264 41.667 0.00 0.00 0.00 2.52
4077 5516 4.333926 CCTATGCCTTGCTTGTACTTTCTC 59.666 45.833 0.00 0.00 0.00 2.87
4078 5517 2.504367 TGCCTTGCTTGTACTTTCTCC 58.496 47.619 0.00 0.00 0.00 3.71
4079 5518 1.464997 GCCTTGCTTGTACTTTCTCCG 59.535 52.381 0.00 0.00 0.00 4.63
4080 5519 2.767505 CCTTGCTTGTACTTTCTCCGT 58.232 47.619 0.00 0.00 0.00 4.69
4081 5520 3.139077 CCTTGCTTGTACTTTCTCCGTT 58.861 45.455 0.00 0.00 0.00 4.44
4082 5521 3.564225 CCTTGCTTGTACTTTCTCCGTTT 59.436 43.478 0.00 0.00 0.00 3.60
4083 5522 4.319549 CCTTGCTTGTACTTTCTCCGTTTC 60.320 45.833 0.00 0.00 0.00 2.78
4084 5523 3.799366 TGCTTGTACTTTCTCCGTTTCA 58.201 40.909 0.00 0.00 0.00 2.69
4085 5524 4.193090 TGCTTGTACTTTCTCCGTTTCAA 58.807 39.130 0.00 0.00 0.00 2.69
4086 5525 4.272504 TGCTTGTACTTTCTCCGTTTCAAG 59.727 41.667 0.00 0.00 35.59 3.02
4087 5526 4.510340 GCTTGTACTTTCTCCGTTTCAAGA 59.490 41.667 0.00 0.00 34.79 3.02
4088 5527 5.179555 GCTTGTACTTTCTCCGTTTCAAGAT 59.820 40.000 0.00 0.00 34.79 2.40
4089 5528 6.539649 TTGTACTTTCTCCGTTTCAAGATG 57.460 37.500 0.00 0.00 0.00 2.90
4090 5529 5.607477 TGTACTTTCTCCGTTTCAAGATGT 58.393 37.500 0.00 0.00 0.00 3.06
4091 5530 6.053005 TGTACTTTCTCCGTTTCAAGATGTT 58.947 36.000 0.00 0.00 0.00 2.71
4092 5531 6.540914 TGTACTTTCTCCGTTTCAAGATGTTT 59.459 34.615 0.00 0.00 0.00 2.83
4093 5532 5.821204 ACTTTCTCCGTTTCAAGATGTTTG 58.179 37.500 0.00 0.00 0.00 2.93
4094 5533 5.588648 ACTTTCTCCGTTTCAAGATGTTTGA 59.411 36.000 0.00 0.00 0.00 2.69
4095 5534 6.094881 ACTTTCTCCGTTTCAAGATGTTTGAA 59.905 34.615 0.00 0.00 36.71 2.69
4096 5535 5.673337 TCTCCGTTTCAAGATGTTTGAAG 57.327 39.130 3.00 0.00 39.30 3.02
4097 5536 5.123227 TCTCCGTTTCAAGATGTTTGAAGT 58.877 37.500 3.00 0.00 39.30 3.01
4098 5537 5.588648 TCTCCGTTTCAAGATGTTTGAAGTT 59.411 36.000 3.00 0.00 39.30 2.66
4099 5538 5.816919 TCCGTTTCAAGATGTTTGAAGTTC 58.183 37.500 0.00 0.00 39.30 3.01
4100 5539 5.588648 TCCGTTTCAAGATGTTTGAAGTTCT 59.411 36.000 4.17 0.00 39.30 3.01
4101 5540 6.764085 TCCGTTTCAAGATGTTTGAAGTTCTA 59.236 34.615 4.17 0.00 39.30 2.10
4102 5541 7.444183 TCCGTTTCAAGATGTTTGAAGTTCTAT 59.556 33.333 4.17 0.00 39.30 1.98
4103 5542 7.535258 CCGTTTCAAGATGTTTGAAGTTCTATG 59.465 37.037 4.17 0.00 39.30 2.23
4104 5543 8.070171 CGTTTCAAGATGTTTGAAGTTCTATGT 58.930 33.333 4.17 0.00 39.30 2.29
4105 5544 9.736023 GTTTCAAGATGTTTGAAGTTCTATGTT 57.264 29.630 4.17 0.00 39.30 2.71
4107 5546 9.734620 TTCAAGATGTTTGAAGTTCTATGTTTG 57.265 29.630 4.17 1.61 33.90 2.93
4108 5547 8.902806 TCAAGATGTTTGAAGTTCTATGTTTGT 58.097 29.630 4.17 0.00 0.00 2.83
4109 5548 8.961092 CAAGATGTTTGAAGTTCTATGTTTGTG 58.039 33.333 4.17 0.00 0.00 3.33
4110 5549 7.141363 AGATGTTTGAAGTTCTATGTTTGTGC 58.859 34.615 4.17 0.00 0.00 4.57
4111 5550 6.449635 TGTTTGAAGTTCTATGTTTGTGCT 57.550 33.333 4.17 0.00 0.00 4.40
4112 5551 7.561021 TGTTTGAAGTTCTATGTTTGTGCTA 57.439 32.000 4.17 0.00 0.00 3.49
4113 5552 7.990917 TGTTTGAAGTTCTATGTTTGTGCTAA 58.009 30.769 4.17 0.00 0.00 3.09
4114 5553 8.128582 TGTTTGAAGTTCTATGTTTGTGCTAAG 58.871 33.333 4.17 0.00 0.00 2.18
4115 5554 6.241207 TGAAGTTCTATGTTTGTGCTAAGC 57.759 37.500 4.17 0.00 0.00 3.09
4116 5555 5.181245 TGAAGTTCTATGTTTGTGCTAAGCC 59.819 40.000 4.17 0.00 0.00 4.35
4117 5556 4.651778 AGTTCTATGTTTGTGCTAAGCCA 58.348 39.130 0.00 0.00 0.00 4.75
4118 5557 5.070001 AGTTCTATGTTTGTGCTAAGCCAA 58.930 37.500 0.00 0.00 0.00 4.52
4119 5558 5.534654 AGTTCTATGTTTGTGCTAAGCCAAA 59.465 36.000 0.00 0.00 0.00 3.28
4120 5559 5.371115 TCTATGTTTGTGCTAAGCCAAAC 57.629 39.130 17.14 17.14 43.24 2.93
4121 5560 5.070001 TCTATGTTTGTGCTAAGCCAAACT 58.930 37.500 21.42 13.80 43.29 2.66
4122 5561 4.670896 ATGTTTGTGCTAAGCCAAACTT 57.329 36.364 21.42 15.95 43.29 2.66
4123 5562 4.040445 TGTTTGTGCTAAGCCAAACTTC 57.960 40.909 21.42 5.65 43.29 3.01
4124 5563 3.699038 TGTTTGTGCTAAGCCAAACTTCT 59.301 39.130 21.42 0.00 43.29 2.85
4125 5564 4.159506 TGTTTGTGCTAAGCCAAACTTCTT 59.840 37.500 21.42 0.00 43.29 2.52
4126 5565 5.109210 GTTTGTGCTAAGCCAAACTTCTTT 58.891 37.500 16.88 0.00 41.60 2.52
4127 5566 6.127591 TGTTTGTGCTAAGCCAAACTTCTTTA 60.128 34.615 21.42 6.42 43.29 1.85
4128 5567 6.458232 TTGTGCTAAGCCAAACTTCTTTAA 57.542 33.333 0.00 0.00 39.97 1.52
4129 5568 6.072112 TGTGCTAAGCCAAACTTCTTTAAG 57.928 37.500 0.00 0.00 39.97 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 2.029964 GAGGGCCGTGTTCGAACA 59.970 61.111 26.53 26.53 39.71 3.18
128 129 3.110178 CGAGGGCCGTGTTCGAAC 61.110 66.667 21.42 21.42 39.71 3.95
229 230 3.060866 GAGGGTGCACTCCTTCGT 58.939 61.111 22.78 6.64 34.21 3.85
918 936 1.166531 GGCCGAGAGAGAGAGAGAGC 61.167 65.000 0.00 0.00 0.00 4.09
980 998 3.711782 CCTCCCCTTCCCCCTCCT 61.712 72.222 0.00 0.00 0.00 3.69
986 1004 1.403687 CGTCATCTCCTCCCCTTCCC 61.404 65.000 0.00 0.00 0.00 3.97
989 1007 0.978146 CACCGTCATCTCCTCCCCTT 60.978 60.000 0.00 0.00 0.00 3.95
990 1008 1.381872 CACCGTCATCTCCTCCCCT 60.382 63.158 0.00 0.00 0.00 4.79
995 1014 1.050988 CATCCCCACCGTCATCTCCT 61.051 60.000 0.00 0.00 0.00 3.69
1181 1232 1.949847 AATCAGTCAGCTCCCCGTCG 61.950 60.000 0.00 0.00 0.00 5.12
1190 1244 1.237285 ACGCACCCAAATCAGTCAGC 61.237 55.000 0.00 0.00 0.00 4.26
1205 1259 2.813474 GCACCGTATCTGCACGCA 60.813 61.111 0.00 0.00 40.59 5.24
1302 1363 2.046023 TGGATGTGGCCGAGCTTG 60.046 61.111 0.00 0.00 0.00 4.01
1391 1468 1.764054 CTCCTAGTCCCAGCCCCTG 60.764 68.421 0.00 0.00 0.00 4.45
1422 1502 9.030301 CATTGGAAATTATCGGAAATTAACACC 57.970 33.333 0.00 0.00 0.00 4.16
1435 1515 9.455847 GAGTAGCAATGAACATTGGAAATTATC 57.544 33.333 23.05 8.71 46.14 1.75
1478 1585 4.506255 GGGCTGATGGGGGAACGG 62.506 72.222 0.00 0.00 0.00 4.44
1480 1587 2.573893 GAAGGGGCTGATGGGGGAAC 62.574 65.000 0.00 0.00 0.00 3.62
1482 1589 2.696125 GAAGGGGCTGATGGGGGA 60.696 66.667 0.00 0.00 0.00 4.81
1487 1594 3.648067 TCTAATACTGGAAGGGGCTGATG 59.352 47.826 0.00 0.00 39.30 3.07
1492 1622 2.487445 GGCTTCTAATACTGGAAGGGGC 60.487 54.545 0.00 0.00 39.81 5.80
1527 1657 5.470777 CGGGTTCTACATTTCCACTACAAAA 59.529 40.000 0.00 0.00 0.00 2.44
1623 1764 8.703743 AGAAAGGATCATATATGGTAGCTCATC 58.296 37.037 12.78 6.37 0.00 2.92
1626 1767 7.147983 ACGAGAAAGGATCATATATGGTAGCTC 60.148 40.741 12.78 7.62 0.00 4.09
1791 1961 9.944376 GATAATATACAAGGATGAGCAACCTAA 57.056 33.333 0.00 0.00 35.25 2.69
1856 2029 3.690422 TGCTTCGTTTGCAACAAGTAAG 58.310 40.909 0.00 0.31 37.51 2.34
1863 2036 1.266718 TGAGGATGCTTCGTTTGCAAC 59.733 47.619 0.00 0.00 44.01 4.17
1890 2073 7.997773 TTGTATGAACAGACTGTACTCTACT 57.002 36.000 8.91 0.00 36.83 2.57
1891 2074 9.640963 ATTTTGTATGAACAGACTGTACTCTAC 57.359 33.333 8.91 9.05 36.83 2.59
1892 2075 9.856488 GATTTTGTATGAACAGACTGTACTCTA 57.144 33.333 8.91 0.00 36.83 2.43
1893 2076 8.589338 AGATTTTGTATGAACAGACTGTACTCT 58.411 33.333 8.91 0.00 36.83 3.24
1894 2077 8.651588 CAGATTTTGTATGAACAGACTGTACTC 58.348 37.037 8.91 4.38 36.83 2.59
1926 2111 3.562505 CTCTTGACTGCTTGCATGAAAC 58.437 45.455 3.33 0.00 0.00 2.78
1929 2114 1.162698 GCTCTTGACTGCTTGCATGA 58.837 50.000 3.33 0.00 0.00 3.07
1938 2123 2.823984 CAGGATGCTAGCTCTTGACTG 58.176 52.381 17.23 11.30 0.00 3.51
1974 2159 0.465460 TGCAAGGTGTGAACAGGGAC 60.465 55.000 0.00 0.00 0.00 4.46
1977 2162 2.746269 CAATTGCAAGGTGTGAACAGG 58.254 47.619 4.94 0.00 0.00 4.00
1991 2176 3.368739 AAGGTTATCCTGCAAGCAATTGC 60.369 43.478 23.05 23.05 44.35 3.56
2272 2458 6.292596 CGAACAGAGACAGAGGAAAAGAAAAG 60.293 42.308 0.00 0.00 0.00 2.27
2392 2582 4.085363 TGTTTACGAATTTGCAAACATGCG 60.085 37.500 15.41 12.78 36.31 4.73
2856 3093 6.544928 TGATGAGTTAGCCATGAGTTAGAA 57.455 37.500 0.00 0.00 0.00 2.10
2880 3155 1.796017 TCACGGATAATACTGCCCCA 58.204 50.000 0.00 0.00 0.00 4.96
2881 3156 2.922740 TTCACGGATAATACTGCCCC 57.077 50.000 0.00 0.00 0.00 5.80
2895 3170 3.490761 GGGGTGCATTGGATATTTTCACG 60.491 47.826 0.00 0.00 0.00 4.35
2914 3189 3.506067 CAGCAGGTACAAAGTAAAAGGGG 59.494 47.826 0.00 0.00 0.00 4.79
2977 3252 5.444087 CGTCATACATACCACTGTTCAAACG 60.444 44.000 0.00 0.00 0.00 3.60
2997 3280 4.513318 TGTCAATTCAGCATGTTAACGTCA 59.487 37.500 0.00 0.00 37.40 4.35
3189 3483 4.038162 GGTACAGTATTGGGCAAAACACAA 59.962 41.667 0.00 0.00 0.00 3.33
3216 3514 5.525378 CAGCTATAGTGCCTTTTCTCGAATT 59.475 40.000 0.84 0.00 0.00 2.17
3217 3515 5.053145 CAGCTATAGTGCCTTTTCTCGAAT 58.947 41.667 0.84 0.00 0.00 3.34
3229 3528 4.687948 CACATACATGACCAGCTATAGTGC 59.312 45.833 0.00 0.00 0.00 4.40
3237 3536 3.173540 TGGCACATACATGACCAGC 57.826 52.632 0.00 0.00 34.37 4.85
3263 3562 2.094854 AGTAGCAGCGTACACCTAACAC 60.095 50.000 0.00 0.00 0.00 3.32
3270 3569 0.179134 CAGGGAGTAGCAGCGTACAC 60.179 60.000 0.00 0.00 0.00 2.90
3275 3574 1.040646 TATTCCAGGGAGTAGCAGCG 58.959 55.000 0.00 0.00 0.00 5.18
3279 3578 2.634940 TGCTGATATTCCAGGGAGTAGC 59.365 50.000 0.00 0.00 34.82 3.58
3297 3596 4.635223 GGGAAAGAAGAAAAAGCATTGCT 58.365 39.130 5.03 5.03 42.56 3.91
3305 3604 4.473477 TTTTGGCGGGAAAGAAGAAAAA 57.527 36.364 0.00 0.00 0.00 1.94
3306 3605 4.473477 TTTTTGGCGGGAAAGAAGAAAA 57.527 36.364 0.00 0.00 0.00 2.29
3355 3654 5.964477 TCCTACTTTGAAGGACTGGTCATAT 59.036 40.000 3.10 0.00 38.24 1.78
3387 3698 3.132160 CCAAATCATGCTGCAACAAACA 58.868 40.909 6.36 0.00 0.00 2.83
3471 3786 4.917415 GCACATCACATTCCACTTGTAAAC 59.083 41.667 0.00 0.00 0.00 2.01
3514 3833 8.186178 ACTAATCAGTAATCACAACTAAAGCG 57.814 34.615 0.00 0.00 31.45 4.68
3599 3931 2.286523 ACACGGCTCCCCTTCTCAG 61.287 63.158 0.00 0.00 0.00 3.35
3650 3999 5.632347 CAGAACTTTGCCTCATTTTGACATC 59.368 40.000 0.00 0.00 0.00 3.06
3672 4022 2.285602 GCCGCACACGTTATTACATCAG 60.286 50.000 0.00 0.00 37.70 2.90
3709 4075 4.212847 GGACAGAGCTGCATATACAACATG 59.787 45.833 1.02 0.00 0.00 3.21
3726 4092 4.651778 ACAAAATTCATCGGAAGGACAGA 58.348 39.130 0.00 0.00 36.25 3.41
3727 4093 4.697352 AGACAAAATTCATCGGAAGGACAG 59.303 41.667 0.00 0.00 36.25 3.51
3728 4094 4.455533 CAGACAAAATTCATCGGAAGGACA 59.544 41.667 0.00 0.00 36.25 4.02
3729 4095 4.672801 GCAGACAAAATTCATCGGAAGGAC 60.673 45.833 0.00 0.00 36.25 3.85
3730 4096 3.440173 GCAGACAAAATTCATCGGAAGGA 59.560 43.478 0.00 0.00 36.25 3.36
3731 4097 3.728864 CGCAGACAAAATTCATCGGAAGG 60.729 47.826 0.00 0.00 36.25 3.46
3732 4098 3.419915 CGCAGACAAAATTCATCGGAAG 58.580 45.455 0.00 0.00 36.25 3.46
3734 4100 1.130373 GCGCAGACAAAATTCATCGGA 59.870 47.619 0.30 0.00 0.00 4.55
3735 4101 1.538276 GCGCAGACAAAATTCATCGG 58.462 50.000 0.30 0.00 0.00 4.18
3736 4102 1.538276 GGCGCAGACAAAATTCATCG 58.462 50.000 10.83 0.00 31.66 3.84
3747 4113 1.083806 TTGATCGACATGGCGCAGAC 61.084 55.000 18.42 7.79 0.00 3.51
3748 4114 0.390998 TTTGATCGACATGGCGCAGA 60.391 50.000 18.42 1.24 0.00 4.26
3750 4116 0.167908 GTTTTGATCGACATGGCGCA 59.832 50.000 18.42 6.63 0.00 6.09
3752 4118 2.443387 CATGTTTTGATCGACATGGCG 58.557 47.619 16.88 16.88 45.81 5.69
3757 4123 2.993220 CCGAGTCATGTTTTGATCGACA 59.007 45.455 0.00 0.00 37.46 4.35
3759 4125 3.586100 TCCGAGTCATGTTTTGATCGA 57.414 42.857 0.00 0.00 37.46 3.59
3760 4126 3.618594 ACATCCGAGTCATGTTTTGATCG 59.381 43.478 0.00 0.00 36.54 3.69
3761 4127 5.551760 AACATCCGAGTCATGTTTTGATC 57.448 39.130 3.58 0.00 40.83 2.92
3799 4165 1.375523 CGGGGACAAGTTCCTTCCG 60.376 63.158 0.00 0.00 45.09 4.30
3892 4259 2.170260 AAATCGCACGCAACCTGTCG 62.170 55.000 0.00 0.00 0.00 4.35
3919 4291 1.398041 CGAGCACAATACACCATGTGG 59.602 52.381 7.87 0.00 45.46 4.17
3921 4293 2.289382 TGTCGAGCACAATACACCATGT 60.289 45.455 0.00 0.00 29.30 3.21
3922 4294 2.345876 TGTCGAGCACAATACACCATG 58.654 47.619 0.00 0.00 29.30 3.66
3925 4297 0.721718 GCTGTCGAGCACAATACACC 59.278 55.000 0.00 0.00 45.46 4.16
3926 4298 0.366871 CGCTGTCGAGCACAATACAC 59.633 55.000 0.00 0.00 46.62 2.90
3927 4299 0.038618 ACGCTGTCGAGCACAATACA 60.039 50.000 0.00 0.00 46.62 2.29
3928 4300 0.366871 CACGCTGTCGAGCACAATAC 59.633 55.000 0.00 0.00 46.62 1.89
3930 4302 1.300931 ACACGCTGTCGAGCACAAT 60.301 52.632 0.00 0.00 46.62 2.71
3938 5238 3.406361 GGAGTGCACACGCTGTCG 61.406 66.667 21.04 0.00 36.56 4.35
3942 5242 0.608130 TATTCTGGAGTGCACACGCT 59.392 50.000 21.04 0.00 40.06 5.07
3953 5253 1.069204 GCATCCGACTGCTATTCTGGA 59.931 52.381 2.37 0.00 39.12 3.86
3973 5274 4.691860 AAATGAAAGACGGAGCAGATTG 57.308 40.909 0.00 0.00 0.00 2.67
3975 5276 3.119708 GCAAAATGAAAGACGGAGCAGAT 60.120 43.478 0.00 0.00 0.00 2.90
3979 5280 2.982470 CAAGCAAAATGAAAGACGGAGC 59.018 45.455 0.00 0.00 0.00 4.70
3980 5281 2.982470 GCAAGCAAAATGAAAGACGGAG 59.018 45.455 0.00 0.00 0.00 4.63
3982 5283 1.715519 CGCAAGCAAAATGAAAGACGG 59.284 47.619 0.00 0.00 0.00 4.79
3986 5287 1.715519 CGTCCGCAAGCAAAATGAAAG 59.284 47.619 0.00 0.00 0.00 2.62
4015 5454 6.480524 TCCATTATCTTGTTTGAACTCGTG 57.519 37.500 0.00 0.00 0.00 4.35
4017 5456 7.751732 TCATTCCATTATCTTGTTTGAACTCG 58.248 34.615 0.00 0.00 0.00 4.18
4025 5464 7.128077 AGGACCATTCATTCCATTATCTTGTT 58.872 34.615 0.00 0.00 33.92 2.83
4046 5485 4.202367 ACAAGCAAGGCATAGGTATAGGAC 60.202 45.833 0.00 0.00 0.00 3.85
4047 5486 3.973973 ACAAGCAAGGCATAGGTATAGGA 59.026 43.478 0.00 0.00 0.00 2.94
4048 5487 4.357918 ACAAGCAAGGCATAGGTATAGG 57.642 45.455 0.00 0.00 0.00 2.57
4049 5488 6.102897 AGTACAAGCAAGGCATAGGTATAG 57.897 41.667 0.00 0.00 0.00 1.31
4050 5489 6.494666 AAGTACAAGCAAGGCATAGGTATA 57.505 37.500 0.00 0.00 0.00 1.47
4051 5490 5.373812 AAGTACAAGCAAGGCATAGGTAT 57.626 39.130 0.00 0.00 0.00 2.73
4052 5491 4.837093 AAGTACAAGCAAGGCATAGGTA 57.163 40.909 0.00 0.00 0.00 3.08
4053 5492 3.721087 AAGTACAAGCAAGGCATAGGT 57.279 42.857 0.00 0.00 0.00 3.08
4054 5493 4.265073 AGAAAGTACAAGCAAGGCATAGG 58.735 43.478 0.00 0.00 0.00 2.57
4055 5494 4.333926 GGAGAAAGTACAAGCAAGGCATAG 59.666 45.833 0.00 0.00 0.00 2.23
4056 5495 4.261801 GGAGAAAGTACAAGCAAGGCATA 58.738 43.478 0.00 0.00 0.00 3.14
4057 5496 3.084786 GGAGAAAGTACAAGCAAGGCAT 58.915 45.455 0.00 0.00 0.00 4.40
4058 5497 2.504367 GGAGAAAGTACAAGCAAGGCA 58.496 47.619 0.00 0.00 0.00 4.75
4059 5498 1.464997 CGGAGAAAGTACAAGCAAGGC 59.535 52.381 0.00 0.00 0.00 4.35
4060 5499 2.767505 ACGGAGAAAGTACAAGCAAGG 58.232 47.619 0.00 0.00 0.00 3.61
4061 5500 4.272504 TGAAACGGAGAAAGTACAAGCAAG 59.727 41.667 0.00 0.00 0.00 4.01
4062 5501 4.193090 TGAAACGGAGAAAGTACAAGCAA 58.807 39.130 0.00 0.00 0.00 3.91
4063 5502 3.799366 TGAAACGGAGAAAGTACAAGCA 58.201 40.909 0.00 0.00 0.00 3.91
4064 5503 4.510340 TCTTGAAACGGAGAAAGTACAAGC 59.490 41.667 0.00 0.00 36.76 4.01
4065 5504 6.202954 ACATCTTGAAACGGAGAAAGTACAAG 59.797 38.462 0.00 0.00 37.41 3.16
4066 5505 6.053005 ACATCTTGAAACGGAGAAAGTACAA 58.947 36.000 0.00 0.00 0.00 2.41
4067 5506 5.607477 ACATCTTGAAACGGAGAAAGTACA 58.393 37.500 0.00 0.00 0.00 2.90
4068 5507 6.541111 AACATCTTGAAACGGAGAAAGTAC 57.459 37.500 0.00 0.00 0.00 2.73
4069 5508 6.764085 TCAAACATCTTGAAACGGAGAAAGTA 59.236 34.615 0.00 0.00 0.00 2.24
4070 5509 5.588648 TCAAACATCTTGAAACGGAGAAAGT 59.411 36.000 0.00 0.00 0.00 2.66
4071 5510 6.060028 TCAAACATCTTGAAACGGAGAAAG 57.940 37.500 0.00 0.00 0.00 2.62
4072 5511 6.094881 ACTTCAAACATCTTGAAACGGAGAAA 59.905 34.615 1.94 0.00 37.89 2.52
4073 5512 5.588648 ACTTCAAACATCTTGAAACGGAGAA 59.411 36.000 1.94 0.00 37.89 2.87
4074 5513 5.123227 ACTTCAAACATCTTGAAACGGAGA 58.877 37.500 1.94 0.00 37.89 3.71
4075 5514 5.424121 ACTTCAAACATCTTGAAACGGAG 57.576 39.130 1.94 0.00 37.89 4.63
4076 5515 5.588648 AGAACTTCAAACATCTTGAAACGGA 59.411 36.000 1.94 0.00 37.89 4.69
4077 5516 5.821204 AGAACTTCAAACATCTTGAAACGG 58.179 37.500 1.94 0.00 37.89 4.44
4078 5517 8.070171 ACATAGAACTTCAAACATCTTGAAACG 58.930 33.333 1.94 0.00 37.89 3.60
4079 5518 9.736023 AACATAGAACTTCAAACATCTTGAAAC 57.264 29.630 1.94 0.00 37.89 2.78
4081 5520 9.734620 CAAACATAGAACTTCAAACATCTTGAA 57.265 29.630 0.43 0.43 36.98 2.69
4082 5521 8.902806 ACAAACATAGAACTTCAAACATCTTGA 58.097 29.630 0.00 0.00 0.00 3.02
4083 5522 8.961092 CACAAACATAGAACTTCAAACATCTTG 58.039 33.333 0.00 0.00 0.00 3.02
4084 5523 7.649306 GCACAAACATAGAACTTCAAACATCTT 59.351 33.333 0.00 0.00 0.00 2.40
4085 5524 7.013655 AGCACAAACATAGAACTTCAAACATCT 59.986 33.333 0.00 0.00 0.00 2.90
4086 5525 7.141363 AGCACAAACATAGAACTTCAAACATC 58.859 34.615 0.00 0.00 0.00 3.06
4087 5526 7.042797 AGCACAAACATAGAACTTCAAACAT 57.957 32.000 0.00 0.00 0.00 2.71
4088 5527 6.449635 AGCACAAACATAGAACTTCAAACA 57.550 33.333 0.00 0.00 0.00 2.83
4089 5528 7.113544 GCTTAGCACAAACATAGAACTTCAAAC 59.886 37.037 0.00 0.00 0.00 2.93
4090 5529 7.138736 GCTTAGCACAAACATAGAACTTCAAA 58.861 34.615 0.00 0.00 0.00 2.69
4091 5530 6.293955 GGCTTAGCACAAACATAGAACTTCAA 60.294 38.462 6.53 0.00 0.00 2.69
4092 5531 5.181245 GGCTTAGCACAAACATAGAACTTCA 59.819 40.000 6.53 0.00 0.00 3.02
4093 5532 5.181245 TGGCTTAGCACAAACATAGAACTTC 59.819 40.000 6.53 0.00 0.00 3.01
4094 5533 5.070001 TGGCTTAGCACAAACATAGAACTT 58.930 37.500 6.53 0.00 0.00 2.66
4095 5534 4.651778 TGGCTTAGCACAAACATAGAACT 58.348 39.130 6.53 0.00 0.00 3.01
4096 5535 5.371115 TTGGCTTAGCACAAACATAGAAC 57.629 39.130 6.53 0.00 0.00 3.01
4104 5543 5.337578 AAAGAAGTTTGGCTTAGCACAAA 57.662 34.783 6.53 11.15 37.59 2.83
4105 5544 6.096282 ACTTAAAGAAGTTTGGCTTAGCACAA 59.904 34.615 6.53 5.30 43.70 3.33
4106 5545 5.592688 ACTTAAAGAAGTTTGGCTTAGCACA 59.407 36.000 6.53 0.00 43.70 4.57
4107 5546 6.073327 ACTTAAAGAAGTTTGGCTTAGCAC 57.927 37.500 6.53 0.00 43.70 4.40


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

AutoCloner maintained by Alex Coulton.