Multiple sequence alignment - TraesCS5B01G184700

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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 TraesCS5B01G184700 chr5B 100.000 7422 0 0 1 7422 335941372 335948793 0.000000e+00 13706.0
1 TraesCS5B01G184700 chr5A 93.080 6893 308 67 609 7422 387399078 387405880 0.000000e+00 9930.0
2 TraesCS5B01G184700 chr5A 91.786 280 21 2 291 570 387398288 387398565 9.030000e-104 388.0
3 TraesCS5B01G184700 chr5A 87.255 204 16 5 11 206 387396991 387397192 2.690000e-54 224.0
4 TraesCS5B01G184700 chr5D 94.249 6051 223 57 803 6829 294418481 294424430 0.000000e+00 9130.0
5 TraesCS5B01G184700 chr5D 91.024 635 17 10 6827 7422 294424470 294425103 0.000000e+00 821.0
6 TraesCS5B01G184700 chr5D 89.863 365 26 5 244 600 294417532 294417893 6.790000e-125 459.0
7 TraesCS5B01G184700 chr5D 86.122 245 19 6 1 237 294417251 294417488 4.450000e-62 250.0
8 TraesCS5B01G184700 chr5D 91.463 82 5 1 609 688 294418353 294418434 2.190000e-20 111.0
9 TraesCS5B01G184700 chr7A 87.037 54 4 3 747 797 6060764 6060711 2.890000e-04 58.4
10 TraesCS5B01G184700 chr6A 81.013 79 9 6 714 789 449801930 449801855 2.890000e-04 58.4
11 TraesCS5B01G184700 chr1B 100.000 28 0 0 747 774 328416452 328416425 1.300000e-02 52.8


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 TraesCS5B01G184700 chr5B 335941372 335948793 7421 False 13706.0 13706 100.0000 1 7422 1 chr5B.!!$F1 7421
1 TraesCS5B01G184700 chr5A 387396991 387405880 8889 False 3514.0 9930 90.7070 11 7422 3 chr5A.!!$F1 7411
2 TraesCS5B01G184700 chr5D 294417251 294425103 7852 False 2154.2 9130 90.5442 1 7422 5 chr5D.!!$F1 7421

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
704 2225 0.179009 TCCCATCCTAGTCGTACCCG 60.179 60.0 0.00 0.00 0.00 5.28 F
1022 2565 0.033011 TCTTCTCCCTCCCTCTTCGG 60.033 60.0 0.00 0.00 0.00 4.30 F
1983 3552 0.609131 CATTTGGGAGCGTTGGAGGT 60.609 55.0 0.00 0.00 0.00 3.85 F
2728 4299 0.033504 GAGCACAAAGTCAGGGTCGA 59.966 55.0 0.00 0.00 0.00 4.20 F
3597 5170 0.321671 TCCAGGAAGCTGAGAAACGG 59.678 55.0 0.00 0.00 0.00 4.44 F
3712 5285 0.537188 AGGAACCAGAGTATGCACCG 59.463 55.0 0.00 0.00 0.00 4.94 F
5006 6580 1.319947 TACAGGTGGGGATCCTCTCT 58.680 55.0 14.22 7.72 32.37 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 3260 0.387239 GCAGGTAAAAAGGTGCAGCG 60.387 55.000 10.78 0.00 35.91 5.18 R
1992 3561 1.219664 CGGTACAAAGATCCCGCCA 59.780 57.895 0.00 0.00 33.20 5.69 R
3905 5478 0.727398 GGAATGCTAGCCACACGAAC 59.273 55.000 13.29 0.00 0.00 3.95 R
3993 5566 1.407258 AGCTGGAGTTAGATGCGTCTC 59.593 52.381 12.83 0.00 35.87 3.36 R
4909 6483 1.002251 CGATCCGTGAAGAGAGGTAGC 60.002 57.143 0.00 0.00 0.00 3.58 R
5611 7190 0.955428 ACATCATCGCAAACGTGGCT 60.955 50.000 10.30 0.00 41.18 4.75 R
6900 8538 0.177141 CCATGCATTGCCTCCTTTGG 59.823 55.000 6.12 0.46 0.00 3.28 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
43 51 3.181426 TGTCGATATCCCTGGCTACCTAA 60.181 47.826 0.00 0.00 0.00 2.69
59 67 1.610624 CCTAAGTTTCCTCGCAAGCCA 60.611 52.381 0.00 0.00 37.18 4.75
60 68 1.734465 CTAAGTTTCCTCGCAAGCCAG 59.266 52.381 0.00 0.00 37.18 4.85
61 69 1.518903 AAGTTTCCTCGCAAGCCAGC 61.519 55.000 0.00 0.00 37.18 4.85
62 70 2.672996 TTTCCTCGCAAGCCAGCC 60.673 61.111 0.00 0.00 37.18 4.85
63 71 3.196207 TTTCCTCGCAAGCCAGCCT 62.196 57.895 0.00 0.00 37.18 4.58
116 131 5.192927 CCAAGCACATGGATTTTCCTAGTA 58.807 41.667 0.00 0.00 43.54 1.82
123 138 5.357032 ACATGGATTTTCCTAGTAAAAGCGG 59.643 40.000 3.16 0.00 35.98 5.52
130 145 2.300723 TCCTAGTAAAAGCGGCAGACAA 59.699 45.455 1.45 0.00 0.00 3.18
137 152 3.396260 AAAGCGGCAGACAAACTACTA 57.604 42.857 1.45 0.00 0.00 1.82
152 167 5.514500 AACTACTATCCAGCCAAAAAGGA 57.486 39.130 0.00 0.00 41.22 3.36
162 177 3.992427 CAGCCAAAAAGGAAGAGCAAATC 59.008 43.478 0.00 0.00 41.22 2.17
198 213 0.943835 AAACAAAGGAAATGCGCGCC 60.944 50.000 30.77 13.14 0.00 6.53
232 265 4.026475 CGTTGTTGTTGTTGTTGTTGTTGT 60.026 37.500 0.00 0.00 0.00 3.32
237 270 4.887748 TGTTGTTGTTGTTGTTGTTCCAT 58.112 34.783 0.00 0.00 0.00 3.41
238 271 5.300752 TGTTGTTGTTGTTGTTGTTCCATT 58.699 33.333 0.00 0.00 0.00 3.16
239 272 6.455647 TGTTGTTGTTGTTGTTGTTCCATTA 58.544 32.000 0.00 0.00 0.00 1.90
240 273 6.587990 TGTTGTTGTTGTTGTTGTTCCATTAG 59.412 34.615 0.00 0.00 0.00 1.73
241 274 6.274157 TGTTGTTGTTGTTGTTCCATTAGT 57.726 33.333 0.00 0.00 0.00 2.24
242 275 7.392494 TGTTGTTGTTGTTGTTCCATTAGTA 57.608 32.000 0.00 0.00 0.00 1.82
272 425 5.441500 TGTGGATTTTAACACTCTTGTCCA 58.558 37.500 0.00 0.00 38.39 4.02
320 1346 1.589630 CGTCGGTGTCTCCAATGGA 59.410 57.895 0.48 0.48 35.57 3.41
350 1376 1.552719 GGACAAGGAGGTGGTCTAGGT 60.553 57.143 0.00 0.00 0.00 3.08
359 1385 1.023502 GTGGTCTAGGTAGGAGCGAC 58.976 60.000 0.00 0.00 34.38 5.19
395 1421 0.179100 CATGTGGACGCGATCTCCTT 60.179 55.000 15.93 0.00 0.00 3.36
412 1438 6.645790 TCTCCTTCTTTACTTTACACGTCT 57.354 37.500 0.00 0.00 0.00 4.18
543 1575 0.403271 AGCTGCACCCTCTGACATTT 59.597 50.000 1.02 0.00 0.00 2.32
558 1590 6.834876 TCTGACATTTCATCGTTTCTCATTG 58.165 36.000 0.00 0.00 0.00 2.82
571 1603 6.908284 TCGTTTCTCATTGGTTTTTCTTTACG 59.092 34.615 0.00 0.00 0.00 3.18
573 1605 7.429920 CGTTTCTCATTGGTTTTTCTTTACGAA 59.570 33.333 0.00 0.00 0.00 3.85
655 2174 2.178912 TCTCCTTTGTTTACCCTGCG 57.821 50.000 0.00 0.00 0.00 5.18
667 2188 1.166531 ACCCTGCGAAAGAACTGCAC 61.167 55.000 0.00 0.00 34.42 4.57
689 2210 1.548081 TTTACTCGTCCGTGATCCCA 58.452 50.000 0.00 0.00 0.00 4.37
692 2213 1.364171 CTCGTCCGTGATCCCATCC 59.636 63.158 0.00 0.00 0.00 3.51
693 2214 1.076265 TCGTCCGTGATCCCATCCT 60.076 57.895 0.00 0.00 0.00 3.24
698 2219 0.598562 CCGTGATCCCATCCTAGTCG 59.401 60.000 0.00 0.00 0.00 4.18
701 2222 2.225963 CGTGATCCCATCCTAGTCGTAC 59.774 54.545 0.00 0.00 0.00 3.67
702 2223 2.557490 GTGATCCCATCCTAGTCGTACC 59.443 54.545 0.00 0.00 0.00 3.34
704 2225 0.179009 TCCCATCCTAGTCGTACCCG 60.179 60.000 0.00 0.00 0.00 5.28
709 2230 3.490419 CCATCCTAGTCGTACCCGAAAAG 60.490 52.174 0.00 0.00 46.26 2.27
712 2233 4.019174 TCCTAGTCGTACCCGAAAAGAAT 58.981 43.478 0.00 0.00 46.26 2.40
715 2236 5.745769 CCTAGTCGTACCCGAAAAGAATTAC 59.254 44.000 0.00 0.00 46.26 1.89
718 2239 4.564372 GTCGTACCCGAAAAGAATTACTCC 59.436 45.833 0.00 0.00 46.26 3.85
722 2243 3.054582 ACCCGAAAAGAATTACTCCCTCC 60.055 47.826 0.00 0.00 0.00 4.30
726 2247 4.329256 CGAAAAGAATTACTCCCTCCGTTC 59.671 45.833 0.00 0.00 0.00 3.95
733 2254 2.667473 ACTCCCTCCGTTCGTAAATG 57.333 50.000 0.00 0.00 0.00 2.32
736 2257 1.276989 TCCCTCCGTTCGTAAATGCTT 59.723 47.619 0.00 0.00 0.00 3.91
737 2258 1.396996 CCCTCCGTTCGTAAATGCTTG 59.603 52.381 0.00 0.00 0.00 4.01
739 2260 2.482721 CCTCCGTTCGTAAATGCTTGTT 59.517 45.455 0.00 0.00 0.00 2.83
740 2261 3.680937 CCTCCGTTCGTAAATGCTTGTTA 59.319 43.478 0.00 0.00 0.00 2.41
741 2262 4.201685 CCTCCGTTCGTAAATGCTTGTTAG 60.202 45.833 0.00 0.00 0.00 2.34
743 2264 4.386652 TCCGTTCGTAAATGCTTGTTAGAC 59.613 41.667 0.00 0.00 0.00 2.59
744 2265 4.312403 CGTTCGTAAATGCTTGTTAGACG 58.688 43.478 0.00 0.00 0.00 4.18
745 2266 3.984018 TCGTAAATGCTTGTTAGACGC 57.016 42.857 0.00 0.00 0.00 5.19
749 2270 5.577554 TCGTAAATGCTTGTTAGACGCAATA 59.422 36.000 0.00 0.00 37.20 1.90
753 2274 7.510428 AAATGCTTGTTAGACGCAATAAATG 57.490 32.000 0.00 0.00 37.20 2.32
757 2278 7.757526 TGCTTGTTAGACGCAATAAATGTATT 58.242 30.769 0.00 0.00 0.00 1.89
816 2338 9.781834 TTTATTTCTGTGATAAGTAATTTGCGG 57.218 29.630 0.00 0.00 0.00 5.69
817 2339 7.624360 ATTTCTGTGATAAGTAATTTGCGGA 57.376 32.000 0.00 0.00 0.00 5.54
818 2340 6.417191 TTCTGTGATAAGTAATTTGCGGAC 57.583 37.500 0.00 0.00 0.00 4.79
819 2341 4.873827 TCTGTGATAAGTAATTTGCGGACC 59.126 41.667 0.00 0.00 0.00 4.46
824 2365 2.871096 AGTAATTTGCGGACCAAGGA 57.129 45.000 0.00 0.00 34.34 3.36
829 2370 2.642154 TTTGCGGACCAAGGAAGTAA 57.358 45.000 0.00 0.00 34.34 2.24
831 2372 2.396590 TGCGGACCAAGGAAGTAATC 57.603 50.000 0.00 0.00 0.00 1.75
836 2377 4.683832 CGGACCAAGGAAGTAATCTACAG 58.316 47.826 0.00 0.00 0.00 2.74
837 2378 4.401519 CGGACCAAGGAAGTAATCTACAGA 59.598 45.833 0.00 0.00 0.00 3.41
838 2379 5.105473 CGGACCAAGGAAGTAATCTACAGAA 60.105 44.000 0.00 0.00 0.00 3.02
851 2392 6.651975 AATCTACAGAACTATACTTCCCGG 57.348 41.667 0.00 0.00 0.00 5.73
868 2409 1.134491 CCGGATCCAGGTTTCCTACAC 60.134 57.143 13.41 0.00 29.64 2.90
873 2414 2.253610 TCCAGGTTTCCTACACGTGAT 58.746 47.619 25.01 9.25 32.80 3.06
879 2420 3.678548 GGTTTCCTACACGTGATTCTCAC 59.321 47.826 25.01 11.37 43.65 3.51
881 2422 5.336213 GGTTTCCTACACGTGATTCTCACTA 60.336 44.000 25.01 0.00 44.85 2.74
888 2429 6.287107 ACACGTGATTCTCACTAAAAAGTG 57.713 37.500 25.01 7.24 44.85 3.16
984 2527 1.505353 CCGAGTTCGTTCGTAGCCT 59.495 57.895 0.48 0.00 38.88 4.58
1019 2562 1.719378 TGTCTCTTCTCCCTCCCTCTT 59.281 52.381 0.00 0.00 0.00 2.85
1020 2563 2.291930 TGTCTCTTCTCCCTCCCTCTTC 60.292 54.545 0.00 0.00 0.00 2.87
1021 2564 1.064314 TCTCTTCTCCCTCCCTCTTCG 60.064 57.143 0.00 0.00 0.00 3.79
1022 2565 0.033011 TCTTCTCCCTCCCTCTTCGG 60.033 60.000 0.00 0.00 0.00 4.30
1038 2582 3.467226 GGTCTCCGCCGAATCCCA 61.467 66.667 0.00 0.00 0.00 4.37
1090 2634 4.436998 CGGCGAGTTTCCTCCGCT 62.437 66.667 0.00 0.00 37.38 5.52
1109 2653 2.092323 CTTCCTTTCCCAATCCGAACC 58.908 52.381 0.00 0.00 0.00 3.62
1261 2805 3.123050 GCAAACAAGGCGTTTCAATTCT 58.877 40.909 0.00 0.00 44.78 2.40
1262 2806 3.060339 GCAAACAAGGCGTTTCAATTCTG 60.060 43.478 0.00 0.00 44.78 3.02
1280 2824 2.902486 TCTGTGATTTCTCAGGCTCAGT 59.098 45.455 9.14 0.00 37.87 3.41
1310 2854 6.183360 CCTCCAGCTCTGATTATCTTCTTCTT 60.183 42.308 0.00 0.00 0.00 2.52
1316 2860 9.737844 AGCTCTGATTATCTTCTTCTTTCTTTT 57.262 29.630 0.00 0.00 0.00 2.27
1317 2861 9.771915 GCTCTGATTATCTTCTTCTTTCTTTTG 57.228 33.333 0.00 0.00 0.00 2.44
1558 3113 2.424601 CAATTTCATGTGGCAGACCGAT 59.575 45.455 0.00 0.00 39.70 4.18
1643 3198 2.222445 TCTTTAACCAGCGCGTCTTTTC 59.778 45.455 8.43 0.00 0.00 2.29
1698 3260 8.239998 GCTATTTTATTAGCCATGAGATGAACC 58.760 37.037 0.00 0.00 38.93 3.62
1719 3281 1.341209 GCTGCACCTTTTTACCTGCTT 59.659 47.619 0.00 0.00 0.00 3.91
1763 3325 1.747355 CCATGCATGAGGGAACTGAAC 59.253 52.381 28.31 0.00 44.43 3.18
1777 3339 8.533569 AGGGAACTGAACTTTCTTGATTTAAA 57.466 30.769 0.00 0.00 41.13 1.52
1818 3380 7.400599 TCAAACTCCATACTACGTACATCTT 57.599 36.000 0.00 0.00 0.00 2.40
1855 3424 9.482175 ACTTTTTCAGTATATCTCTGTACCTCT 57.518 33.333 7.43 0.00 31.97 3.69
1864 3433 9.453325 GTATATCTCTGTACCTCTTCTTTTTCG 57.547 37.037 0.00 0.00 0.00 3.46
1865 3434 5.135508 TCTCTGTACCTCTTCTTTTTCGG 57.864 43.478 0.00 0.00 0.00 4.30
1908 3477 3.620488 GATTTTCTGGATGTGGTAGCCA 58.380 45.455 0.00 0.00 44.07 4.75
1914 3483 1.212688 TGGATGTGGTAGCCAATGGAG 59.787 52.381 2.05 0.00 43.12 3.86
1917 3486 2.969821 TGTGGTAGCCAATGGAGTTT 57.030 45.000 2.05 0.00 34.18 2.66
1977 3546 2.677003 CGCGTCATTTGGGAGCGTT 61.677 57.895 0.00 0.00 44.96 4.84
1980 3549 0.953471 CGTCATTTGGGAGCGTTGGA 60.953 55.000 0.00 0.00 0.00 3.53
1983 3552 0.609131 CATTTGGGAGCGTTGGAGGT 60.609 55.000 0.00 0.00 0.00 3.85
1992 3561 1.153046 CGTTGGAGGTGTTGGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
2007 3576 0.035820 GTGGTGGCGGGATCTTTGTA 60.036 55.000 0.00 0.00 0.00 2.41
2031 3600 4.478843 GATGTTGACATTGATCATCGGG 57.521 45.455 0.00 0.00 36.57 5.14
2187 3756 2.739913 GTTCAGTATGCGGTGCTGTAAA 59.260 45.455 6.84 0.00 40.91 2.01
2217 3786 3.057386 TCATGTGTGCATTAGTTTGCCTG 60.057 43.478 0.00 0.00 42.06 4.85
2263 3832 6.791867 AAGTATGAGGTGCTGTACTGATTA 57.208 37.500 3.61 0.00 0.00 1.75
2316 3885 2.912956 AGGGATCTTGCTTGTCCTGTTA 59.087 45.455 0.00 0.00 32.55 2.41
2371 3940 7.571025 TGGGAATTAGAGTATTTAAGTGTCCC 58.429 38.462 0.00 0.00 0.00 4.46
2418 3987 7.280652 TCTGTTTTGTTTGTGTTAGGTAGGTAC 59.719 37.037 0.00 0.00 0.00 3.34
2468 4037 5.523552 TCATGTGTATCAGATTACGCCTTTG 59.476 40.000 0.00 0.00 32.76 2.77
2494 4063 4.380531 CTTTGTCTGGCTCACTTACTCAA 58.619 43.478 0.00 0.00 0.00 3.02
2540 4111 7.277174 ACTTGTTTCCATGAAAAGAAGTAGG 57.723 36.000 16.72 0.00 45.51 3.18
2554 4125 5.211174 AGAAGTAGGTACAAAGGTGTGAC 57.789 43.478 0.00 0.00 38.82 3.67
2610 4181 9.350357 CAAATCTGAAATATTGAAGTTCAGTGG 57.650 33.333 10.90 1.54 45.50 4.00
2699 4270 3.062763 GACCAGCAATATCGTCTCCATG 58.937 50.000 0.00 0.00 0.00 3.66
2727 4298 0.249868 TGAGCACAAAGTCAGGGTCG 60.250 55.000 0.00 0.00 0.00 4.79
2728 4299 0.033504 GAGCACAAAGTCAGGGTCGA 59.966 55.000 0.00 0.00 0.00 4.20
2730 4301 0.531974 GCACAAAGTCAGGGTCGACA 60.532 55.000 18.91 0.00 38.43 4.35
2762 4333 2.635915 TGGTTTGGAACTCGTGACCTAT 59.364 45.455 0.00 0.00 0.00 2.57
2775 4346 0.839946 GACCTATCCCTGCACCATGT 59.160 55.000 0.00 0.00 0.00 3.21
2786 4357 4.269523 ACCATGTGCCAGCACCGT 62.270 61.111 19.47 10.28 45.63 4.83
2820 4391 7.397192 ACCTTATAACAATGCACCTTCATTTCT 59.603 33.333 0.00 0.00 34.68 2.52
2834 4405 9.393512 CACCTTCATTTCTCAGATATTCTTTCT 57.606 33.333 0.00 0.00 0.00 2.52
2835 4406 9.393512 ACCTTCATTTCTCAGATATTCTTTCTG 57.606 33.333 0.00 0.00 41.61 3.02
2889 4460 6.776116 TCTTTATCGTCAGTATACATCCCTGT 59.224 38.462 5.50 0.00 39.49 4.00
2999 4570 9.717942 ATAGTACAATTCATAGAAATCTCTGGC 57.282 33.333 0.00 0.00 32.70 4.85
3015 4586 5.389520 TCTCTGGCTGCTGACTTACTATAT 58.610 41.667 0.00 0.00 0.00 0.86
3083 4654 4.679197 GCAAATACAATGTTTGTTCAGCGA 59.321 37.500 0.00 0.00 42.22 4.93
3096 4667 9.123709 TGTTTGTTCAGCGATTTTAATTGATAC 57.876 29.630 0.00 0.00 0.00 2.24
3101 4672 9.341899 GTTCAGCGATTTTAATTGATACTTTGT 57.658 29.630 0.00 0.00 0.00 2.83
3136 4707 1.938577 GTATGATCACTGGTGCAGCTG 59.061 52.381 19.67 19.67 34.37 4.24
3346 4917 1.839424 ACCCCTAAACTGCTGCATTC 58.161 50.000 1.31 0.00 0.00 2.67
3502 5074 6.577103 TCTTCCACAGTTATCTCATCATGTC 58.423 40.000 0.00 0.00 0.00 3.06
3544 5116 3.312736 TCTCCCCTTCTTTTGTTTGCT 57.687 42.857 0.00 0.00 0.00 3.91
3597 5170 0.321671 TCCAGGAAGCTGAGAAACGG 59.678 55.000 0.00 0.00 0.00 4.44
3635 5208 6.929606 AGTAAGAATGCTAGAAAACGAAGTGT 59.070 34.615 0.00 0.00 45.00 3.55
3712 5285 0.537188 AGGAACCAGAGTATGCACCG 59.463 55.000 0.00 0.00 0.00 4.94
3735 5308 3.000819 TACAGGACCAGGTGCCGG 61.001 66.667 7.64 0.00 0.00 6.13
3905 5478 2.821991 AGGAGTTTGGTCTTCTCACG 57.178 50.000 0.00 0.00 0.00 4.35
4006 5579 7.636359 GTCATAAAAATGTGAGACGCATCTAAC 59.364 37.037 0.00 0.00 36.89 2.34
4048 5621 9.635404 AGTCACTATTAGCTGTCTTATAACTCT 57.365 33.333 0.00 0.00 0.00 3.24
4051 5624 7.596995 CACTATTAGCTGTCTTATAACTCTGCC 59.403 40.741 0.00 0.00 0.00 4.85
4178 5751 8.627208 ATGTTTCTTTCATGTAGTCTCACAAT 57.373 30.769 0.00 0.00 30.84 2.71
4179 5752 9.725019 ATGTTTCTTTCATGTAGTCTCACAATA 57.275 29.630 0.00 0.00 30.84 1.90
4180 5753 9.725019 TGTTTCTTTCATGTAGTCTCACAATAT 57.275 29.630 0.00 0.00 30.84 1.28
4266 5839 6.946340 TCAATATGTACAGCCGATCCATTAT 58.054 36.000 0.33 0.00 0.00 1.28
4293 5866 8.567948 GTCAGTTTTCATAAGATGTTTCAGGAA 58.432 33.333 0.00 0.00 0.00 3.36
4684 6258 5.707764 ACTCAAACTTAGAGATTCAAAGCCC 59.292 40.000 0.00 0.00 36.91 5.19
4739 6313 1.960689 GACTCCTCTATCTGGCCAGAC 59.039 57.143 37.39 17.49 40.75 3.51
4847 6421 7.015389 ACCATTACTAGCTTATGTAGGGACTTC 59.985 40.741 0.00 0.00 41.75 3.01
4952 6526 3.982058 CCGTGACTCTGTAAACTCTTGTC 59.018 47.826 0.00 0.00 0.00 3.18
4973 6547 4.785453 CTGGTCCTTGGGCCGCTC 62.785 72.222 5.77 0.00 0.00 5.03
5006 6580 1.319947 TACAGGTGGGGATCCTCTCT 58.680 55.000 14.22 7.72 32.37 3.10
5189 6766 6.555315 CCAATTTTCACTATTGGTCTACTGC 58.445 40.000 6.47 0.00 44.51 4.40
5199 6777 8.421784 CACTATTGGTCTACTGCCTAATTTCTA 58.578 37.037 0.00 0.00 0.00 2.10
5403 6981 8.631480 TGAAATTTCATCAGCTCTGCATATAT 57.369 30.769 16.91 0.00 31.01 0.86
5576 7155 5.207354 TGATTTGGCCATAAAGAATGCCTA 58.793 37.500 6.09 0.00 34.62 3.93
5589 7168 7.817418 AAAGAATGCCTACTTAACTGAAACA 57.183 32.000 0.00 0.00 0.00 2.83
5611 7190 6.237901 ACAATCATAGGTTTCAAGTGCTACA 58.762 36.000 0.00 0.00 0.00 2.74
5632 7211 1.665735 GCCACGTTTGCGATGATGTTT 60.666 47.619 0.00 0.00 42.00 2.83
5666 7245 1.336125 CCGTCGTGGAATACTACCTCC 59.664 57.143 0.00 0.00 42.00 4.30
5750 7330 0.749454 GGGCTGGGCATGTACTGAAG 60.749 60.000 0.00 0.00 0.00 3.02
5978 7558 6.422400 TCCACTGTTTTTGAACTTTGAACAAC 59.578 34.615 0.00 0.00 30.72 3.32
5984 7570 8.267367 TGTTTTTGAACTTTGAACAACGTTAAC 58.733 29.630 0.00 9.81 33.70 2.01
5985 7571 7.925703 TTTTGAACTTTGAACAACGTTAACA 57.074 28.000 0.00 0.00 33.70 2.41
5986 7572 7.555639 TTTGAACTTTGAACAACGTTAACAG 57.444 32.000 0.00 1.29 33.70 3.16
5987 7573 6.483385 TGAACTTTGAACAACGTTAACAGA 57.517 33.333 0.00 0.00 33.70 3.41
5988 7574 6.900189 TGAACTTTGAACAACGTTAACAGAA 58.100 32.000 0.00 0.00 33.70 3.02
5989 7575 6.797995 TGAACTTTGAACAACGTTAACAGAAC 59.202 34.615 0.00 0.00 33.70 3.01
6050 7636 2.941064 ACATGATTCACAAGATGGAGCG 59.059 45.455 0.00 0.00 0.00 5.03
6410 7998 4.655649 TGCAGAATATCACCCTAGATGTGT 59.344 41.667 10.84 3.74 35.25 3.72
6465 8053 2.169352 CCCTGCAGATAGTTGTGTAGCT 59.831 50.000 17.39 0.00 29.04 3.32
6471 8059 6.639563 TGCAGATAGTTGTGTAGCTCATTAA 58.360 36.000 0.00 0.00 0.00 1.40
6472 8060 6.535150 TGCAGATAGTTGTGTAGCTCATTAAC 59.465 38.462 0.00 0.00 0.00 2.01
6473 8061 6.535150 GCAGATAGTTGTGTAGCTCATTAACA 59.465 38.462 0.00 0.00 32.39 2.41
6474 8062 7.225538 GCAGATAGTTGTGTAGCTCATTAACAT 59.774 37.037 0.00 0.00 32.39 2.71
6475 8063 8.546244 CAGATAGTTGTGTAGCTCATTAACATG 58.454 37.037 0.00 0.00 32.39 3.21
6476 8064 8.478066 AGATAGTTGTGTAGCTCATTAACATGA 58.522 33.333 0.00 0.00 37.05 3.07
6477 8065 9.265901 GATAGTTGTGTAGCTCATTAACATGAT 57.734 33.333 0.00 0.00 38.81 2.45
6479 8067 8.425577 AGTTGTGTAGCTCATTAACATGATAC 57.574 34.615 0.00 0.00 38.81 2.24
6480 8068 8.260818 AGTTGTGTAGCTCATTAACATGATACT 58.739 33.333 0.00 0.00 38.81 2.12
6481 8069 8.543774 GTTGTGTAGCTCATTAACATGATACTC 58.456 37.037 0.00 0.00 38.81 2.59
6482 8070 6.918022 TGTGTAGCTCATTAACATGATACTCG 59.082 38.462 0.00 0.00 38.81 4.18
6483 8071 6.363626 GTGTAGCTCATTAACATGATACTCGG 59.636 42.308 0.00 0.00 38.81 4.63
6484 8072 5.791336 AGCTCATTAACATGATACTCGGA 57.209 39.130 0.00 0.00 38.81 4.55
6485 8073 6.161855 AGCTCATTAACATGATACTCGGAA 57.838 37.500 0.00 0.00 38.81 4.30
6486 8074 6.219473 AGCTCATTAACATGATACTCGGAAG 58.781 40.000 0.00 0.00 38.81 3.46
6487 8075 5.986135 GCTCATTAACATGATACTCGGAAGT 59.014 40.000 0.00 0.00 38.81 3.01
6488 8076 7.014326 AGCTCATTAACATGATACTCGGAAGTA 59.986 37.037 0.00 0.00 42.10 2.24
6489 8077 7.327275 GCTCATTAACATGATACTCGGAAGTAG 59.673 40.741 0.00 0.00 41.22 2.57
6490 8078 8.459911 TCATTAACATGATACTCGGAAGTAGA 57.540 34.615 0.00 0.00 41.22 2.59
6491 8079 8.350722 TCATTAACATGATACTCGGAAGTAGAC 58.649 37.037 0.00 0.00 41.22 2.59
6550 8138 4.044065 TGTTTCTGGATGTCCTACCCATTT 59.956 41.667 0.09 0.00 36.82 2.32
6633 8221 4.572389 CAGACAAAGATTATAGCGCCACTT 59.428 41.667 2.29 0.00 0.00 3.16
6676 8264 2.173782 TGAAAACACTGGGCCTCTGTAA 59.826 45.455 4.53 0.00 0.00 2.41
6679 8267 2.789409 ACACTGGGCCTCTGTAATTC 57.211 50.000 4.53 0.00 0.00 2.17
6687 8275 4.651503 TGGGCCTCTGTAATTCTCTCTTAG 59.348 45.833 4.53 0.00 0.00 2.18
6766 8360 1.508632 CTGGGGAACACAACAGTACG 58.491 55.000 0.00 0.00 0.00 3.67
6768 8362 1.202557 TGGGGAACACAACAGTACGAC 60.203 52.381 0.00 0.00 0.00 4.34
6815 8409 4.401519 CCTTCCAGAACATTTCAGCATCAT 59.598 41.667 0.00 0.00 0.00 2.45
6860 8496 0.931005 CTGCCGCCGTAAGATCTTTC 59.069 55.000 14.36 7.71 43.02 2.62
6900 8538 5.075858 TCACATTCCTCAATTTGCATTCC 57.924 39.130 0.00 0.00 0.00 3.01
7052 8712 2.490328 ACAAAACATCAACGCACCAG 57.510 45.000 0.00 0.00 0.00 4.00
7073 8733 5.875359 CCAGTCTGAAGTTTCTAACCCATAC 59.125 44.000 0.00 0.00 0.00 2.39
7087 8750 7.495055 TCTAACCCATACCGAAGATTTCTAAC 58.505 38.462 0.00 0.00 0.00 2.34
7244 8922 4.883585 TCATTAATCAACCATGCTCCTGTC 59.116 41.667 0.00 0.00 0.00 3.51
7266 8944 0.535780 CAGGACACTTGAGCAAGGCA 60.536 55.000 14.14 0.00 42.53 4.75
7402 9080 6.350110 GGCAGTTCATATTTAGCACCTGAAAA 60.350 38.462 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.913951 AATCCAGCCATCGGTGAGCA 61.914 55.000 11.02 0.00 40.02 4.26
9 10 2.438868 TATCGACAATCCAGCCATCG 57.561 50.000 0.00 0.00 0.00 3.84
61 69 1.721664 CTGTCGCCATGCATCCAAGG 61.722 60.000 0.00 0.00 33.00 3.61
62 70 1.028330 ACTGTCGCCATGCATCCAAG 61.028 55.000 0.00 0.00 0.00 3.61
63 71 0.251634 TACTGTCGCCATGCATCCAA 59.748 50.000 0.00 0.00 0.00 3.53
66 75 3.559655 TGTTATTACTGTCGCCATGCATC 59.440 43.478 0.00 0.00 0.00 3.91
81 90 5.536538 TCCATGTGCTTGGTTGTTGTTATTA 59.463 36.000 4.39 0.00 38.01 0.98
116 131 2.572290 AGTAGTTTGTCTGCCGCTTTT 58.428 42.857 0.00 0.00 0.00 2.27
123 138 3.198872 GGCTGGATAGTAGTTTGTCTGC 58.801 50.000 0.00 0.00 0.00 4.26
130 145 5.514500 TCCTTTTTGGCTGGATAGTAGTT 57.486 39.130 0.00 0.00 35.26 2.24
137 152 2.174360 GCTCTTCCTTTTTGGCTGGAT 58.826 47.619 0.00 0.00 35.26 3.41
198 213 2.590575 AACAACGCCTCGTGTGGG 60.591 61.111 0.00 0.00 39.99 4.61
210 225 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
232 265 8.877864 AAATCCACAAAGACATACTAATGGAA 57.122 30.769 0.00 0.00 37.47 3.53
238 271 9.787435 AGTGTTAAAATCCACAAAGACATACTA 57.213 29.630 0.00 0.00 33.99 1.82
239 272 8.691661 AGTGTTAAAATCCACAAAGACATACT 57.308 30.769 0.00 0.00 33.99 2.12
240 273 8.784043 AGAGTGTTAAAATCCACAAAGACATAC 58.216 33.333 0.00 0.00 33.99 2.39
241 274 8.918202 AGAGTGTTAAAATCCACAAAGACATA 57.082 30.769 0.00 0.00 33.99 2.29
242 275 7.823745 AGAGTGTTAAAATCCACAAAGACAT 57.176 32.000 0.00 0.00 33.99 3.06
320 1346 1.005215 CCTCCTTGTCCTTGGCTGAAT 59.995 52.381 0.00 0.00 0.00 2.57
350 1376 1.758936 TCATTCTTCCGTCGCTCCTA 58.241 50.000 0.00 0.00 0.00 2.94
359 1385 3.005554 ACATGACAGCTTCATTCTTCCG 58.994 45.455 0.00 1.48 42.87 4.30
395 1421 7.502120 ACTACTGAGACGTGTAAAGTAAAGA 57.498 36.000 0.00 0.00 0.00 2.52
465 1491 6.278363 AGTTGGTGCTGGTTTATACTATACG 58.722 40.000 0.00 0.00 0.00 3.06
466 1492 7.466860 GCAAGTTGGTGCTGGTTTATACTATAC 60.467 40.741 4.75 0.00 41.51 1.47
481 1513 2.050077 GAAGGCGCAAGTTGGTGC 60.050 61.111 10.83 3.85 43.38 5.01
543 1575 6.633500 AGAAAAACCAATGAGAAACGATGA 57.367 33.333 0.00 0.00 0.00 2.92
604 1636 8.391106 GCCTGTGAAACACTAAGAAACTATATG 58.609 37.037 0.00 0.00 45.67 1.78
655 2174 5.807344 ACGAGTAAAAAGTGCAGTTCTTTC 58.193 37.500 7.36 0.00 34.59 2.62
667 2188 2.928116 GGGATCACGGACGAGTAAAAAG 59.072 50.000 0.00 0.00 0.00 2.27
698 2219 5.095145 AGGGAGTAATTCTTTTCGGGTAC 57.905 43.478 0.00 0.00 0.00 3.34
701 2222 3.542648 GGAGGGAGTAATTCTTTTCGGG 58.457 50.000 0.00 0.00 0.00 5.14
702 2223 3.195661 CGGAGGGAGTAATTCTTTTCGG 58.804 50.000 0.00 0.00 0.00 4.30
704 2225 4.329256 CGAACGGAGGGAGTAATTCTTTTC 59.671 45.833 0.00 0.00 0.00 2.29
709 2230 2.955477 ACGAACGGAGGGAGTAATTC 57.045 50.000 0.00 0.00 0.00 2.17
712 2233 3.676873 GCATTTACGAACGGAGGGAGTAA 60.677 47.826 0.00 0.00 0.00 2.24
715 2236 1.134788 AGCATTTACGAACGGAGGGAG 60.135 52.381 0.00 0.00 0.00 4.30
718 2239 2.073816 ACAAGCATTTACGAACGGAGG 58.926 47.619 0.00 0.00 0.00 4.30
722 2243 4.312403 CGTCTAACAAGCATTTACGAACG 58.688 43.478 0.00 0.00 0.00 3.95
726 2247 3.715618 TGCGTCTAACAAGCATTTACG 57.284 42.857 0.00 0.00 35.81 3.18
733 2254 8.614994 AAATACATTTATTGCGTCTAACAAGC 57.385 30.769 0.00 0.00 0.00 4.01
792 2314 8.609176 GTCCGCAAATTACTTATCACAGAAATA 58.391 33.333 0.00 0.00 0.00 1.40
799 2321 5.448632 CCTTGGTCCGCAAATTACTTATCAC 60.449 44.000 0.00 0.00 0.00 3.06
800 2322 4.638421 CCTTGGTCCGCAAATTACTTATCA 59.362 41.667 0.00 0.00 0.00 2.15
812 2334 1.906574 AGATTACTTCCTTGGTCCGCA 59.093 47.619 0.00 0.00 0.00 5.69
813 2335 2.693267 AGATTACTTCCTTGGTCCGC 57.307 50.000 0.00 0.00 0.00 5.54
814 2336 4.401519 TCTGTAGATTACTTCCTTGGTCCG 59.598 45.833 0.00 0.00 0.00 4.79
816 2338 6.937392 AGTTCTGTAGATTACTTCCTTGGTC 58.063 40.000 0.00 0.00 0.00 4.02
817 2339 6.936968 AGTTCTGTAGATTACTTCCTTGGT 57.063 37.500 0.00 0.00 0.00 3.67
818 2340 9.968870 GTATAGTTCTGTAGATTACTTCCTTGG 57.031 37.037 0.00 0.00 0.00 3.61
824 2365 8.848182 CGGGAAGTATAGTTCTGTAGATTACTT 58.152 37.037 17.74 0.00 0.00 2.24
829 2370 5.950023 TCCGGGAAGTATAGTTCTGTAGAT 58.050 41.667 17.74 0.00 0.00 1.98
831 2372 5.183522 GGATCCGGGAAGTATAGTTCTGTAG 59.816 48.000 17.74 8.39 0.00 2.74
836 2377 3.258622 CCTGGATCCGGGAAGTATAGTTC 59.741 52.174 33.38 11.29 45.10 3.01
837 2378 3.240302 CCTGGATCCGGGAAGTATAGTT 58.760 50.000 33.38 0.00 45.10 2.24
838 2379 2.179424 ACCTGGATCCGGGAAGTATAGT 59.821 50.000 41.12 17.22 45.10 2.12
846 2387 0.340558 TAGGAAACCTGGATCCGGGA 59.659 55.000 41.12 18.72 45.10 5.14
849 2390 1.470979 CGTGTAGGAAACCTGGATCCG 60.471 57.143 7.39 1.76 40.78 4.18
851 2392 2.232941 TCACGTGTAGGAAACCTGGATC 59.767 50.000 16.51 0.00 34.61 3.36
873 2414 4.573201 CCCGTTGACACTTTTTAGTGAGAA 59.427 41.667 11.90 1.97 42.02 2.87
879 2420 1.069500 CGGCCCGTTGACACTTTTTAG 60.069 52.381 0.00 0.00 0.00 1.85
881 2422 1.731093 CGGCCCGTTGACACTTTTT 59.269 52.632 0.00 0.00 0.00 1.94
888 2429 3.919973 TACGAAGCGGCCCGTTGAC 62.920 63.158 20.04 0.00 39.86 3.18
984 2527 0.471211 AGACACGTGAGAAGGGGGAA 60.471 55.000 25.01 0.00 0.00 3.97
1021 2564 3.447025 CTGGGATTCGGCGGAGACC 62.447 68.421 7.21 5.39 0.00 3.85
1022 2565 2.107141 CTGGGATTCGGCGGAGAC 59.893 66.667 7.21 0.00 0.00 3.36
1090 2634 1.612199 CGGTTCGGATTGGGAAAGGAA 60.612 52.381 0.00 0.00 0.00 3.36
1261 2805 2.902486 AGACTGAGCCTGAGAAATCACA 59.098 45.455 0.00 0.00 0.00 3.58
1262 2806 3.260740 CAGACTGAGCCTGAGAAATCAC 58.739 50.000 0.00 0.00 33.65 3.06
1280 2824 0.619832 AATCAGAGCTGGAGGGCAGA 60.620 55.000 0.00 0.00 34.17 4.26
1558 3113 2.453521 ACATGCTGGTACGAGTTCCTA 58.546 47.619 6.75 0.00 0.00 2.94
1643 3198 7.090953 AGCAAACTACAGTAGAAGCTAGTAG 57.909 40.000 14.94 0.00 38.43 2.57
1698 3260 0.387239 GCAGGTAAAAAGGTGCAGCG 60.387 55.000 10.78 0.00 35.91 5.18
1719 3281 4.026744 TCAAACTGAATTCCCACAAACCA 58.973 39.130 2.27 0.00 0.00 3.67
1804 3366 6.316440 TCACACACAAAGATGTACGTAGTA 57.684 37.500 0.00 0.00 45.11 1.82
1809 3371 6.706055 AAGTATCACACACAAAGATGTACG 57.294 37.500 0.00 0.00 37.82 3.67
1848 3417 4.995487 ACACATCCGAAAAAGAAGAGGTAC 59.005 41.667 0.00 0.00 0.00 3.34
1849 3418 4.994852 CACACATCCGAAAAAGAAGAGGTA 59.005 41.667 0.00 0.00 0.00 3.08
1850 3419 3.815401 CACACATCCGAAAAAGAAGAGGT 59.185 43.478 0.00 0.00 0.00 3.85
1851 3420 3.189287 CCACACATCCGAAAAAGAAGAGG 59.811 47.826 0.00 0.00 0.00 3.69
1852 3421 3.815401 ACCACACATCCGAAAAAGAAGAG 59.185 43.478 0.00 0.00 0.00 2.85
1853 3422 3.563808 CACCACACATCCGAAAAAGAAGA 59.436 43.478 0.00 0.00 0.00 2.87
1854 3423 3.853307 GCACCACACATCCGAAAAAGAAG 60.853 47.826 0.00 0.00 0.00 2.85
1855 3424 2.034053 GCACCACACATCCGAAAAAGAA 59.966 45.455 0.00 0.00 0.00 2.52
1863 3432 2.159393 CCAAATTAGCACCACACATCCG 60.159 50.000 0.00 0.00 0.00 4.18
1864 3433 2.825532 ACCAAATTAGCACCACACATCC 59.174 45.455 0.00 0.00 0.00 3.51
1865 3434 3.367292 CCACCAAATTAGCACCACACATC 60.367 47.826 0.00 0.00 0.00 3.06
1908 3477 4.845796 ACCATTTTCCATCCAAACTCCATT 59.154 37.500 0.00 0.00 0.00 3.16
1914 3483 3.328505 CAGCACCATTTTCCATCCAAAC 58.671 45.455 0.00 0.00 0.00 2.93
1917 3486 1.559368 CCAGCACCATTTTCCATCCA 58.441 50.000 0.00 0.00 0.00 3.41
1977 3546 2.923035 CCACCACCAACACCTCCA 59.077 61.111 0.00 0.00 0.00 3.86
1980 3549 4.579384 CCGCCACCACCAACACCT 62.579 66.667 0.00 0.00 0.00 4.00
1983 3552 3.561120 GATCCCGCCACCACCAACA 62.561 63.158 0.00 0.00 0.00 3.33
1992 3561 1.219664 CGGTACAAAGATCCCGCCA 59.780 57.895 0.00 0.00 33.20 5.69
2031 3600 4.978580 GCAGTTGAAGACTTTGGATCAAAC 59.021 41.667 0.00 0.00 36.10 2.93
2187 3756 5.503927 ACTAATGCACACATGAAGGAATCT 58.496 37.500 0.00 0.00 36.36 2.40
2263 3832 7.394359 AGAGGTAAACTAATGCACACATGAATT 59.606 33.333 0.00 0.00 37.82 2.17
2316 3885 2.863809 CCAGCCTAACTTTCCAACAGT 58.136 47.619 0.00 0.00 0.00 3.55
2371 3940 1.388547 TAGCGCTAATTGCCCCTTTG 58.611 50.000 16.33 0.00 38.78 2.77
2385 3954 4.041723 ACACAAACAAAACAGAATAGCGC 58.958 39.130 0.00 0.00 0.00 5.92
2540 4111 2.443887 TAGCCGTCACACCTTTGTAC 57.556 50.000 0.00 0.00 33.30 2.90
2654 4225 7.223387 GTCGTACCGTTTAATGGAATAGAATGT 59.777 37.037 10.55 0.00 0.00 2.71
2655 4226 7.306983 GGTCGTACCGTTTAATGGAATAGAATG 60.307 40.741 10.55 0.00 0.00 2.67
2683 4254 2.987149 CGGTACATGGAGACGATATTGC 59.013 50.000 0.00 0.00 0.00 3.56
2699 4270 2.475487 GACTTTGTGCTCAGTTCGGTAC 59.525 50.000 0.00 0.00 0.00 3.34
2727 4298 2.099098 CCAAACCAAATAGCCGGATGTC 59.901 50.000 5.05 0.00 0.00 3.06
2728 4299 2.099405 CCAAACCAAATAGCCGGATGT 58.901 47.619 5.05 0.00 0.00 3.06
2730 4301 2.758423 GTTCCAAACCAAATAGCCGGAT 59.242 45.455 5.05 0.00 0.00 4.18
2775 4346 2.034048 TTGTAGACACGGTGCTGGCA 62.034 55.000 8.30 7.56 0.00 4.92
2786 4357 6.373216 GGTGCATTGTTATAAGGTTGTAGACA 59.627 38.462 0.00 0.00 0.00 3.41
2837 4408 9.256477 CGCAAACCAGATAATTAGTATTACAGA 57.744 33.333 0.00 0.00 0.00 3.41
2842 4413 8.732746 AAGACGCAAACCAGATAATTAGTATT 57.267 30.769 0.00 0.00 0.00 1.89
2862 4433 6.072618 AGGGATGTATACTGACGATAAAGACG 60.073 42.308 4.17 0.00 0.00 4.18
2928 4499 7.732025 TGTCAACCAACAATTCTAAGTAGAGA 58.268 34.615 0.00 0.00 33.21 3.10
2973 4544 9.717942 GCCAGAGATTTCTATGAATTGTACTAT 57.282 33.333 3.83 0.00 37.37 2.12
2999 4570 6.640499 GCAAGACTCATATAGTAAGTCAGCAG 59.360 42.308 16.07 0.00 41.49 4.24
3055 4626 7.462109 TGAACAAACATTGTATTTGCAACTC 57.538 32.000 0.00 0.00 44.59 3.01
3060 4631 4.679197 TCGCTGAACAAACATTGTATTTGC 59.321 37.500 0.00 0.00 44.59 3.68
3096 4667 8.279970 TCATACCTGTCCAAATGAATACAAAG 57.720 34.615 0.00 0.00 0.00 2.77
3101 4672 7.716560 CAGTGATCATACCTGTCCAAATGAATA 59.283 37.037 0.00 0.00 32.47 1.75
3136 4707 6.678878 TGAGATTGTAGTACACAGTTGAGAC 58.321 40.000 1.43 0.00 38.72 3.36
3544 5116 8.593945 AAAAGATCCATTAGCATACAAAAGGA 57.406 30.769 0.00 0.00 0.00 3.36
3597 5170 4.798574 CATTCTTACTGGTTTGCTCCAAC 58.201 43.478 0.00 0.00 37.01 3.77
3635 5208 3.753815 TGATTTGGTGACAGATGAGCAA 58.246 40.909 0.00 0.00 44.54 3.91
3712 5285 0.820871 CACCTGGTCCTGTAGAGAGC 59.179 60.000 0.00 0.00 0.00 4.09
3735 5308 4.016444 TGAATGGGGTTTTACATCAGCTC 58.984 43.478 0.00 0.00 0.00 4.09
3794 5367 3.760684 AGATCTCCAACAAATGCAAGGAC 59.239 43.478 0.00 0.00 0.00 3.85
3905 5478 0.727398 GGAATGCTAGCCACACGAAC 59.273 55.000 13.29 0.00 0.00 3.95
3993 5566 1.407258 AGCTGGAGTTAGATGCGTCTC 59.593 52.381 12.83 0.00 35.87 3.36
4006 5579 3.007398 AGTGACTTGGTAAGAAGCTGGAG 59.993 47.826 0.00 0.00 0.00 3.86
4048 5621 4.696479 AATAACCAAACAAATGTGGGCA 57.304 36.364 4.85 0.00 39.39 5.36
4051 5624 7.784633 AACAGAAATAACCAAACAAATGTGG 57.215 32.000 0.00 0.00 41.00 4.17
4178 5751 9.309516 GGATGTTCGTTTACTATCACAAAGATA 57.690 33.333 0.00 0.00 38.19 1.98
4179 5752 8.041323 AGGATGTTCGTTTACTATCACAAAGAT 58.959 33.333 0.00 0.00 40.86 2.40
4180 5753 7.383687 AGGATGTTCGTTTACTATCACAAAGA 58.616 34.615 0.00 0.00 0.00 2.52
4181 5754 7.596749 AGGATGTTCGTTTACTATCACAAAG 57.403 36.000 0.00 0.00 0.00 2.77
4197 5770 8.469200 TGAATGAATTGGTCATAAAGGATGTTC 58.531 33.333 0.00 0.00 46.80 3.18
4266 5839 7.719193 TCCTGAAACATCTTATGAAAACTGACA 59.281 33.333 0.00 0.00 0.00 3.58
4283 5856 3.845781 AGAGCAGAAGTTCCTGAAACA 57.154 42.857 0.00 0.00 40.56 2.83
4293 5866 8.225603 TCAAATTAACTGAAAAGAGCAGAAGT 57.774 30.769 0.00 0.00 36.86 3.01
4707 6281 2.048127 GGAGTCGAGGTGCACCAC 60.048 66.667 36.39 29.23 38.89 4.16
4739 6313 4.785301 TCCAAAGAATAGGCAGAAGGATG 58.215 43.478 0.00 0.00 0.00 3.51
4847 6421 2.656560 ACCGAAGAGTCCAAAGATCG 57.343 50.000 0.00 0.00 0.00 3.69
4909 6483 1.002251 CGATCCGTGAAGAGAGGTAGC 60.002 57.143 0.00 0.00 0.00 3.58
4952 6526 2.282462 GGCCCAAGGACCAGTGTG 60.282 66.667 0.00 0.00 0.00 3.82
4973 6547 6.384015 TCCCCACCTGTATATATATTGCTCAG 59.616 42.308 0.00 5.53 0.00 3.35
5006 6580 1.659022 TTTGAGTAATCACCGGGGGA 58.341 50.000 2.42 0.00 0.00 4.81
5034 6608 6.126940 ACAGATCTAGTGACAATGTATGGCTT 60.127 38.462 0.00 0.00 38.19 4.35
5035 6609 5.365025 ACAGATCTAGTGACAATGTATGGCT 59.635 40.000 0.00 0.00 38.19 4.75
5036 6610 5.464722 CACAGATCTAGTGACAATGTATGGC 59.535 44.000 15.93 0.00 39.30 4.40
5037 6611 6.809869 TCACAGATCTAGTGACAATGTATGG 58.190 40.000 18.29 0.00 40.80 2.74
5099 6675 6.442513 AGAGAAAATTGGGAGCTTAAATCG 57.557 37.500 0.00 0.00 0.00 3.34
5262 6840 4.973168 TCTGCACCAAATGAGTAGAAAGT 58.027 39.130 0.00 0.00 0.00 2.66
5403 6981 2.289382 TGCAGTGATACCGAAGAAGCAA 60.289 45.455 0.00 0.00 0.00 3.91
5416 6994 1.376424 CAACGAGCCCTGCAGTGAT 60.376 57.895 13.81 0.00 0.00 3.06
5589 7168 5.355350 GCTGTAGCACTTGAAACCTATGATT 59.645 40.000 0.00 0.00 41.59 2.57
5611 7190 0.955428 ACATCATCGCAAACGTGGCT 60.955 50.000 10.30 0.00 41.18 4.75
5632 7211 1.816835 ACGACGGACATAGAAGCAGAA 59.183 47.619 0.00 0.00 0.00 3.02
5750 7330 4.379652 TGAAGAAAAGGCCAAGAAATTGC 58.620 39.130 5.01 0.00 0.00 3.56
5978 7558 4.813296 AAAGAAGCAGGTTCTGTTAACG 57.187 40.909 15.65 0.00 45.44 3.18
5984 7570 5.702349 AGATTGAAAAGAAGCAGGTTCTG 57.298 39.130 15.65 0.00 45.44 3.02
5986 7572 6.076981 TGAAGATTGAAAAGAAGCAGGTTC 57.923 37.500 4.00 4.00 35.08 3.62
5987 7573 5.010415 CCTGAAGATTGAAAAGAAGCAGGTT 59.990 40.000 0.00 0.00 33.87 3.50
5988 7574 4.522022 CCTGAAGATTGAAAAGAAGCAGGT 59.478 41.667 0.00 0.00 33.87 4.00
5989 7575 4.522022 ACCTGAAGATTGAAAAGAAGCAGG 59.478 41.667 0.00 0.00 40.02 4.85
6050 7636 3.941483 CTCAAACCCCATGTACTCATGTC 59.059 47.826 7.30 0.00 46.99 3.06
6174 7760 5.154222 GCTAAAGATTTGAAACCTGAACCG 58.846 41.667 0.00 0.00 0.00 4.44
6287 7874 9.082313 ACTGAAAATTCATAAATCAGTTCCAGT 57.918 29.630 1.13 0.00 46.22 4.00
6315 7902 1.895131 AGGCACGGATGAATTTGCTTT 59.105 42.857 0.00 0.00 35.24 3.51
6318 7905 2.880890 AGATAGGCACGGATGAATTTGC 59.119 45.455 0.00 0.00 0.00 3.68
6319 7906 4.129380 TGAGATAGGCACGGATGAATTTG 58.871 43.478 0.00 0.00 0.00 2.32
6320 7907 4.422073 TGAGATAGGCACGGATGAATTT 57.578 40.909 0.00 0.00 0.00 1.82
6321 7908 4.630644 ATGAGATAGGCACGGATGAATT 57.369 40.909 0.00 0.00 0.00 2.17
6323 7910 3.134623 ACAATGAGATAGGCACGGATGAA 59.865 43.478 0.00 0.00 0.00 2.57
6325 7912 3.117491 ACAATGAGATAGGCACGGATG 57.883 47.619 0.00 0.00 0.00 3.51
6326 7913 3.006967 GGTACAATGAGATAGGCACGGAT 59.993 47.826 0.00 0.00 0.00 4.18
6327 7914 2.364324 GGTACAATGAGATAGGCACGGA 59.636 50.000 0.00 0.00 0.00 4.69
6410 7998 9.299963 CAGTGAACAATTTCTGACAACAAAATA 57.700 29.630 0.00 0.00 32.36 1.40
6456 8044 7.435192 CGAGTATCATGTTAATGAGCTACACAA 59.565 37.037 0.00 0.00 45.88 3.33
6457 8045 6.918022 CGAGTATCATGTTAATGAGCTACACA 59.082 38.462 0.00 0.00 45.88 3.72
6465 8053 8.350722 GTCTACTTCCGAGTATCATGTTAATGA 58.649 37.037 0.00 0.00 40.90 2.57
6471 8059 5.437946 TGAGTCTACTTCCGAGTATCATGT 58.562 41.667 0.00 0.00 37.71 3.21
6472 8060 6.378710 TTGAGTCTACTTCCGAGTATCATG 57.621 41.667 0.00 0.00 37.71 3.07
6473 8061 6.458478 CGTTTGAGTCTACTTCCGAGTATCAT 60.458 42.308 0.00 0.00 37.71 2.45
6474 8062 5.163784 CGTTTGAGTCTACTTCCGAGTATCA 60.164 44.000 0.00 0.00 37.71 2.15
6475 8063 5.264712 CGTTTGAGTCTACTTCCGAGTATC 58.735 45.833 0.00 0.00 37.71 2.24
6476 8064 4.438472 GCGTTTGAGTCTACTTCCGAGTAT 60.438 45.833 0.00 0.00 37.71 2.12
6477 8065 3.120060 GCGTTTGAGTCTACTTCCGAGTA 60.120 47.826 0.00 0.00 37.33 2.59
6478 8066 2.351544 GCGTTTGAGTCTACTTCCGAGT 60.352 50.000 0.00 0.00 39.97 4.18
6479 8067 2.095161 AGCGTTTGAGTCTACTTCCGAG 60.095 50.000 0.00 0.00 0.00 4.63
6480 8068 1.884579 AGCGTTTGAGTCTACTTCCGA 59.115 47.619 0.00 0.00 0.00 4.55
6481 8069 2.251893 GAGCGTTTGAGTCTACTTCCG 58.748 52.381 0.00 0.00 0.00 4.30
6482 8070 2.095364 TCGAGCGTTTGAGTCTACTTCC 60.095 50.000 0.00 0.00 0.00 3.46
6483 8071 3.198863 TCGAGCGTTTGAGTCTACTTC 57.801 47.619 0.00 0.00 0.00 3.01
6484 8072 3.502920 CATCGAGCGTTTGAGTCTACTT 58.497 45.455 0.00 0.00 0.00 2.24
6485 8073 2.732597 GCATCGAGCGTTTGAGTCTACT 60.733 50.000 0.00 0.00 0.00 2.57
6486 8074 1.584308 GCATCGAGCGTTTGAGTCTAC 59.416 52.381 0.00 0.00 0.00 2.59
6487 8075 1.909376 GCATCGAGCGTTTGAGTCTA 58.091 50.000 0.00 0.00 0.00 2.59
6488 8076 2.743195 GCATCGAGCGTTTGAGTCT 58.257 52.632 0.00 0.00 0.00 3.24
6550 8138 7.921787 TCTGAAGAAACGTGCTATTTTTGTTA 58.078 30.769 0.00 0.00 0.00 2.41
6633 8221 2.807967 GCAGCACTGATTATTGGCGATA 59.192 45.455 0.81 0.00 0.00 2.92
6665 8253 4.651962 ACTAAGAGAGAATTACAGAGGCCC 59.348 45.833 0.00 0.00 0.00 5.80
6676 8264 7.939039 TGATGTTGGTTCAAACTAAGAGAGAAT 59.061 33.333 0.00 0.00 29.69 2.40
6679 8267 6.931281 TCTGATGTTGGTTCAAACTAAGAGAG 59.069 38.462 0.00 0.00 29.69 3.20
6687 8275 6.258230 TCATGATCTGATGTTGGTTCAAAC 57.742 37.500 0.00 0.00 0.00 2.93
6748 8342 1.121378 TCGTACTGTTGTGTTCCCCA 58.879 50.000 0.00 0.00 0.00 4.96
6758 8352 4.015084 ACCATGCTACTAGTCGTACTGTT 58.985 43.478 0.00 0.00 0.00 3.16
6759 8353 3.618351 ACCATGCTACTAGTCGTACTGT 58.382 45.455 0.00 0.00 0.00 3.55
6860 8496 7.360691 GGAATGTGATGTAGGAAATCATGATCG 60.361 40.741 9.06 0.00 36.49 3.69
6900 8538 0.177141 CCATGCATTGCCTCCTTTGG 59.823 55.000 6.12 0.46 0.00 3.28
6987 8647 9.294030 GTATGGCAATACATTTCAGAAAGAAAG 57.706 33.333 6.35 0.00 38.77 2.62
6990 8650 8.579850 AAGTATGGCAATACATTTCAGAAAGA 57.420 30.769 13.79 0.00 41.09 2.52
7052 8712 4.868734 CGGTATGGGTTAGAAACTTCAGAC 59.131 45.833 0.00 0.00 0.00 3.51
7073 8733 3.334691 TGGTGCTGTTAGAAATCTTCGG 58.665 45.455 0.00 0.00 34.02 4.30
7087 8750 1.410153 GCATCCCCTAAATTGGTGCTG 59.590 52.381 0.00 0.00 0.00 4.41
7244 8922 1.233019 CTTGCTCAAGTGTCCTGGTG 58.767 55.000 1.61 0.00 33.87 4.17
7256 8934 3.069300 TGCTAAAAACAATGCCTTGCTCA 59.931 39.130 1.19 0.00 35.69 4.26
7266 8944 5.627499 TCGCTTCAGATGCTAAAAACAAT 57.373 34.783 6.72 0.00 0.00 2.71
7310 8988 0.888285 GGGCAGCTGCACTATGATCC 60.888 60.000 37.63 23.51 42.27 3.36


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

AutoCloner maintained by Alex Coulton.