Multiple sequence alignment - TraesCS1A01G168100

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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 TraesCS1A01G168100 chr1A 100.000 5228 0 0 1 5228 300861073 300855846 0.000000e+00 9655.0
1 TraesCS1A01G168100 chr1A 76.847 704 114 38 1248 1935 520122816 520123486 8.330000e-93 351.0
2 TraesCS1A01G168100 chr1B 91.369 2746 155 51 2003 4685 331145926 331143200 0.000000e+00 3683.0
3 TraesCS1A01G168100 chr1B 89.662 2012 157 26 1 1979 331147913 331145920 0.000000e+00 2516.0
4 TraesCS1A01G168100 chr1B 76.836 708 125 28 1248 1935 573215957 573216645 3.850000e-96 363.0
5 TraesCS1A01G168100 chr1B 75.849 265 57 6 335 592 10980774 10981038 1.530000e-25 128.0
6 TraesCS1A01G168100 chr1D 91.295 2757 130 50 2003 4696 246937881 246940590 0.000000e+00 3661.0
7 TraesCS1A01G168100 chr1D 94.133 1176 55 5 815 1981 246936717 246937887 0.000000e+00 1777.0
8 TraesCS1A01G168100 chr1D 85.904 830 98 12 1 825 246865796 246866611 0.000000e+00 867.0
9 TraesCS1A01G168100 chr1D 93.972 282 17 0 4703 4984 246941111 246941392 1.350000e-115 427.0
10 TraesCS1A01G168100 chr1D 77.195 706 125 26 1247 1935 423764013 423764699 3.820000e-101 379.0
11 TraesCS1A01G168100 chr1D 89.950 199 11 6 4997 5187 246941371 246941568 1.120000e-61 248.0
12 TraesCS1A01G168100 chr1D 88.889 81 4 4 5046 5122 246942810 246942889 1.550000e-15 95.3
13 TraesCS1A01G168100 chr2D 77.811 338 71 4 261 595 572048600 572048264 6.860000e-49 206.0
14 TraesCS1A01G168100 chr2D 73.248 471 85 28 177 640 563137747 563138183 3.280000e-27 134.0
15 TraesCS1A01G168100 chr6A 77.429 319 47 21 1251 1547 39180926 39180611 3.240000e-37 167.0
16 TraesCS1A01G168100 chr6A 92.754 69 5 0 2043 2111 39180116 39180048 3.330000e-17 100.0
17 TraesCS1A01G168100 chr6D 90.678 118 9 1 1251 1368 34999787 34999672 7.010000e-34 156.0
18 TraesCS1A01G168100 chr6D 76.384 271 52 10 363 627 443751438 443751702 9.130000e-28 135.0
19 TraesCS1A01G168100 chr6D 87.611 113 14 0 1435 1547 34999576 34999464 1.180000e-26 132.0
20 TraesCS1A01G168100 chr6D 87.629 97 9 1 5119 5212 329484146 329484050 5.540000e-20 110.0
21 TraesCS1A01G168100 chr6D 86.408 103 4 8 2024 2121 34998997 34998900 2.580000e-18 104.0
22 TraesCS1A01G168100 chr6B 88.800 125 11 2 1251 1374 72379515 72379393 3.260000e-32 150.0
23 TraesCS1A01G168100 chr6B 76.952 269 58 4 344 610 720948807 720949073 3.260000e-32 150.0
24 TraesCS1A01G168100 chr6B 85.841 113 16 0 1435 1547 72379300 72379188 2.560000e-23 121.0
25 TraesCS1A01G168100 chr6B 88.350 103 6 4 2024 2121 72378499 72378398 9.200000e-23 119.0
26 TraesCS1A01G168100 chr6B 81.308 107 17 3 4553 4658 41022533 41022429 3.350000e-12 84.2
27 TraesCS1A01G168100 chr6B 81.609 87 10 3 4572 4658 41130178 41130098 3.380000e-07 67.6
28 TraesCS1A01G168100 chr7A 77.689 251 50 5 394 640 127570112 127570360 1.170000e-31 148.0
29 TraesCS1A01G168100 chr3D 77.510 249 52 4 395 640 19286287 19286040 4.220000e-31 147.0
30 TraesCS1A01G168100 chr3D 72.581 434 108 9 215 640 140781493 140781063 1.180000e-26 132.0
31 TraesCS1A01G168100 chr7B 73.708 445 85 29 178 615 562393824 562393405 1.520000e-30 145.0
32 TraesCS1A01G168100 chr7D 73.191 470 89 30 179 640 153772051 153771611 9.130000e-28 135.0
33 TraesCS1A01G168100 chr7D 84.694 98 12 2 5119 5213 254706381 254706284 1.550000e-15 95.3
34 TraesCS1A01G168100 chr3B 73.198 444 89 28 178 615 32504658 32505077 3.280000e-27 134.0
35 TraesCS1A01G168100 chr3B 73.198 444 89 28 178 615 32555389 32555808 3.280000e-27 134.0
36 TraesCS1A01G168100 chr5D 86.598 97 10 1 5119 5212 125912721 125912625 2.580000e-18 104.0
37 TraesCS1A01G168100 chr5D 84.536 97 12 2 5119 5212 261770135 261770231 5.570000e-15 93.5
38 TraesCS1A01G168100 chr2A 72.182 417 86 22 179 588 55941857 55942250 3.330000e-17 100.0
39 TraesCS1A01G168100 chr2B 84.466 103 12 3 5113 5212 19847641 19847742 1.200000e-16 99.0
40 TraesCS1A01G168100 chr5A 83.505 97 8 3 5119 5212 338417646 338417737 3.350000e-12 84.2
41 TraesCS1A01G168100 chr3A 81.538 65 11 1 291 354 585035598 585035534 9.000000e-03 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 TraesCS1A01G168100 chr1A 300855846 300861073 5227 True 9655.00 9655 100.0000 1 5228 1 chr1A.!!$R1 5227
1 TraesCS1A01G168100 chr1A 520122816 520123486 670 False 351.00 351 76.8470 1248 1935 1 chr1A.!!$F1 687
2 TraesCS1A01G168100 chr1B 331143200 331147913 4713 True 3099.50 3683 90.5155 1 4685 2 chr1B.!!$R1 4684
3 TraesCS1A01G168100 chr1B 573215957 573216645 688 False 363.00 363 76.8360 1248 1935 1 chr1B.!!$F2 687
4 TraesCS1A01G168100 chr1D 246936717 246942889 6172 False 1241.66 3661 91.6478 815 5187 5 chr1D.!!$F3 4372
5 TraesCS1A01G168100 chr1D 246865796 246866611 815 False 867.00 867 85.9040 1 825 1 chr1D.!!$F1 824
6 TraesCS1A01G168100 chr1D 423764013 423764699 686 False 379.00 379 77.1950 1247 1935 1 chr1D.!!$F2 688

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
486 490 0.110056 GCACGACGACTTTCCGACTA 60.110 55.0 0.0 0.0 0.0 2.59 F
1375 1408 0.105964 TCCATCTTCCTCCCCTCTCG 60.106 60.0 0.0 0.0 0.0 4.04 F
2748 2814 0.181350 GATGTGATGTCCCTGTCCCC 59.819 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2049 0.035458 TCCACACACACACACACACA 59.965 50.0 0.0 0.00 0.00 3.72 R
2901 2967 0.240945 CAGCCCACAAACCATCGTTC 59.759 55.0 0.0 0.00 0.00 3.95 R
4728 5420 0.450583 GCGATGGACGACAGTACTGA 59.549 55.0 29.3 5.99 45.77 3.41 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
19 20 1.070786 GAGTCTGGCCCGAAACACA 59.929 57.895 0.00 0.00 0.00 3.72
70 71 2.790791 CCACCTTTTGTTGGCGCCA 61.791 57.895 29.03 29.03 0.00 5.69
96 97 1.880675 GGTCTGTCTCGTCTTCTGTGA 59.119 52.381 0.00 0.00 0.00 3.58
111 112 3.443052 TCTGTGATTTTGGGCCATGAAT 58.557 40.909 7.26 11.36 0.00 2.57
114 115 4.092279 TGTGATTTTGGGCCATGAATGTA 58.908 39.130 17.34 6.52 0.00 2.29
136 137 3.407967 GGATCCCGTCCCTTGCCA 61.408 66.667 0.00 0.00 41.50 4.92
137 138 2.674754 GATCCCGTCCCTTGCCAA 59.325 61.111 0.00 0.00 0.00 4.52
144 145 1.675219 GTCCCTTGCCAACGGTAGA 59.325 57.895 0.00 0.00 0.00 2.59
154 155 1.482593 CCAACGGTAGAGCTCCTGATT 59.517 52.381 10.93 0.00 0.00 2.57
155 156 2.482142 CCAACGGTAGAGCTCCTGATTC 60.482 54.545 10.93 0.00 0.00 2.52
194 197 6.388619 AATTATCTAGGGTTTGTGTCCTGT 57.611 37.500 0.00 0.00 34.75 4.00
213 216 3.458163 CAGGAAGGCGAGGCGGTA 61.458 66.667 0.00 0.00 0.00 4.02
246 249 7.340232 CACTGAAAATGGAATAAGATTCTCCCA 59.660 37.037 0.00 0.00 0.00 4.37
254 257 1.885049 AAGATTCTCCCAGCCTAGCA 58.115 50.000 0.00 0.00 0.00 3.49
289 292 4.337763 CGTCTAGCATCATTGAAAAGTGC 58.662 43.478 2.42 2.42 34.24 4.40
295 298 3.674138 GCATCATTGAAAAGTGCGTGGAT 60.674 43.478 0.00 0.00 0.00 3.41
305 308 0.944386 GTGCGTGGATGTGTGTCTTT 59.056 50.000 0.00 0.00 0.00 2.52
315 318 3.576078 TGTGTGTCTTTGGTGGATCTT 57.424 42.857 0.00 0.00 0.00 2.40
316 319 3.213506 TGTGTGTCTTTGGTGGATCTTG 58.786 45.455 0.00 0.00 0.00 3.02
317 320 3.214328 GTGTGTCTTTGGTGGATCTTGT 58.786 45.455 0.00 0.00 0.00 3.16
322 325 2.649312 TCTTTGGTGGATCTTGTGGGAT 59.351 45.455 0.00 0.00 0.00 3.85
324 327 4.290985 TCTTTGGTGGATCTTGTGGGATTA 59.709 41.667 0.00 0.00 0.00 1.75
341 345 5.835819 TGGGATTAATTGGTGTTTGTCTTCA 59.164 36.000 0.00 0.00 0.00 3.02
356 360 3.071457 TGTCTTCAGTGGATCTGCTTTGA 59.929 43.478 0.00 0.00 43.32 2.69
366 370 6.095160 AGTGGATCTGCTTTGATCTGATTTTC 59.905 38.462 12.22 0.00 41.72 2.29
371 375 5.469760 TCTGCTTTGATCTGATTTTCGTTCA 59.530 36.000 0.00 0.00 0.00 3.18
374 378 5.450385 GCTTTGATCTGATTTTCGTTCATCG 59.550 40.000 0.00 0.00 41.41 3.84
380 384 3.191669 TGATTTTCGTTCATCGGCGTAT 58.808 40.909 6.85 0.00 40.32 3.06
486 490 0.110056 GCACGACGACTTTCCGACTA 60.110 55.000 0.00 0.00 0.00 2.59
505 509 9.023962 TCCGACTATCTACTAAAACAAGGTTTA 57.976 33.333 0.00 0.00 0.00 2.01
510 514 6.173427 TCTACTAAAACAAGGTTTACCCGT 57.827 37.500 0.00 0.00 38.74 5.28
532 536 3.736227 TCCAATAAGGGAGGGGTGATA 57.264 47.619 0.00 0.00 38.24 2.15
600 604 7.309805 CGATAGGTGGTCTATGGACATAAATGA 60.310 40.741 11.67 0.00 43.77 2.57
601 605 6.770286 AGGTGGTCTATGGACATAAATGAT 57.230 37.500 11.67 0.00 43.77 2.45
656 660 5.518847 GCCATGATGTTTGATGAATTGACAG 59.481 40.000 0.00 0.00 0.00 3.51
659 663 6.880942 TGATGTTTGATGAATTGACAGACA 57.119 33.333 0.00 0.00 34.28 3.41
712 716 4.895297 AGCAGAATGGAAGTTTTCTCCAAA 59.105 37.500 0.00 0.00 37.07 3.28
859 875 2.032894 CGTCGATATTCCATGCAACACC 60.033 50.000 0.00 0.00 0.00 4.16
883 905 4.525874 GGGTTGTCTATACGGCTATACCTT 59.474 45.833 0.00 0.00 35.61 3.50
987 1009 0.954452 CTCAGAAACCACAAGCCACC 59.046 55.000 0.00 0.00 0.00 4.61
994 1016 4.954970 CACAAGCCACCCGCCAGT 62.955 66.667 0.00 0.00 38.78 4.00
1148 1170 1.335324 CGAAGTCCGACCAAGTAACGT 60.335 52.381 0.00 0.00 41.76 3.99
1155 1177 2.344500 CCAAGTAACGTCCCGCCA 59.656 61.111 0.00 0.00 0.00 5.69
1219 1243 0.396435 TGGCTGGTCATCTTTCACGT 59.604 50.000 0.00 0.00 0.00 4.49
1235 1259 6.422100 TCTTTCACGTGAGAATTCTTCTGAAG 59.578 38.462 19.11 14.00 40.87 3.02
1375 1408 0.105964 TCCATCTTCCTCCCCTCTCG 60.106 60.000 0.00 0.00 0.00 4.04
1430 1478 6.484643 GCAAGAGCTAATCATATTGGTCTTCA 59.515 38.462 0.00 0.00 42.80 3.02
1505 1553 1.738099 CGTCAACCTGAAGCCTCGG 60.738 63.158 0.00 0.00 0.00 4.63
1568 1616 1.301087 CCTACCACAAACCGCGACA 60.301 57.895 8.23 0.00 0.00 4.35
1569 1617 1.562575 CCTACCACAAACCGCGACAC 61.563 60.000 8.23 0.00 0.00 3.67
1570 1618 1.562575 CTACCACAAACCGCGACACC 61.563 60.000 8.23 0.00 0.00 4.16
1946 2004 1.573829 TTCACGGTGAGCAAATCGGC 61.574 55.000 11.14 0.00 0.00 5.54
1972 2030 2.352915 GGAGAGCGCACGATCGAG 60.353 66.667 24.34 16.03 35.44 4.04
1973 2031 2.405594 GAGAGCGCACGATCGAGT 59.594 61.111 24.34 0.00 35.44 4.18
1974 2032 1.936880 GAGAGCGCACGATCGAGTG 60.937 63.158 24.34 21.75 44.47 3.51
1975 2033 2.202492 GAGCGCACGATCGAGTGT 60.202 61.111 24.34 11.14 43.61 3.55
1978 2036 3.064178 CGCACGATCGAGTGTGTG 58.936 61.111 24.34 12.33 44.83 3.82
1979 2037 1.729484 CGCACGATCGAGTGTGTGT 60.729 57.895 24.34 0.00 44.83 3.72
1980 2038 1.775344 GCACGATCGAGTGTGTGTG 59.225 57.895 24.34 7.96 43.61 3.82
1981 2039 0.939577 GCACGATCGAGTGTGTGTGT 60.940 55.000 24.34 0.00 43.61 3.72
1982 2040 0.778223 CACGATCGAGTGTGTGTGTG 59.222 55.000 24.34 0.90 37.35 3.82
1983 2041 0.384309 ACGATCGAGTGTGTGTGTGT 59.616 50.000 24.34 0.00 0.00 3.72
1984 2042 0.778223 CGATCGAGTGTGTGTGTGTG 59.222 55.000 10.26 0.00 0.00 3.82
1985 2043 1.852942 GATCGAGTGTGTGTGTGTGT 58.147 50.000 0.00 0.00 0.00 3.72
1986 2044 1.522676 GATCGAGTGTGTGTGTGTGTG 59.477 52.381 0.00 0.00 0.00 3.82
1987 2045 0.245266 TCGAGTGTGTGTGTGTGTGT 59.755 50.000 0.00 0.00 0.00 3.72
1988 2046 0.369931 CGAGTGTGTGTGTGTGTGTG 59.630 55.000 0.00 0.00 0.00 3.82
1989 2047 1.438651 GAGTGTGTGTGTGTGTGTGT 58.561 50.000 0.00 0.00 0.00 3.72
1990 2048 1.128507 GAGTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1991 2049 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1992 2050 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1993 2051 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1994 2052 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1995 2053 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1996 2054 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1997 2055 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1998 2056 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1999 2057 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2000 2058 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2001 2059 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2040 2099 4.157472 TGCTGATTTAATTTGATCGGTGCA 59.843 37.500 9.83 9.65 32.45 4.57
2150 2209 4.093556 CACCGTCCTCTTAAATTTCTCAGC 59.906 45.833 0.00 0.00 0.00 4.26
2152 2211 4.568760 CCGTCCTCTTAAATTTCTCAGCTC 59.431 45.833 0.00 0.00 0.00 4.09
2153 2212 5.171476 CGTCCTCTTAAATTTCTCAGCTCA 58.829 41.667 0.00 0.00 0.00 4.26
2154 2213 5.290643 CGTCCTCTTAAATTTCTCAGCTCAG 59.709 44.000 0.00 0.00 0.00 3.35
2155 2214 6.169800 GTCCTCTTAAATTTCTCAGCTCAGT 58.830 40.000 0.00 0.00 0.00 3.41
2156 2215 6.652900 GTCCTCTTAAATTTCTCAGCTCAGTT 59.347 38.462 0.00 0.00 0.00 3.16
2191 2250 1.302993 CCCGGGGCTTTCTTTTCGA 60.303 57.895 14.71 0.00 0.00 3.71
2193 2252 0.521735 CCGGGGCTTTCTTTTCGAAG 59.478 55.000 0.00 0.00 32.21 3.79
2229 2294 3.647649 CTCTCCGGTCACATGCGCA 62.648 63.158 14.96 14.96 0.00 6.09
2448 2514 6.594788 ATTTGCAGGACATGTACAATTTCT 57.405 33.333 11.55 0.00 0.00 2.52
2748 2814 0.181350 GATGTGATGTCCCTGTCCCC 59.819 60.000 0.00 0.00 0.00 4.81
2752 2818 1.303282 GATGTCCCTGTCCCCAACC 59.697 63.158 0.00 0.00 0.00 3.77
2856 2922 4.241555 AGCGCGGGATCCCATGAC 62.242 66.667 30.42 15.89 35.37 3.06
2901 2967 4.561213 TGTTAAACTGTACTGATCGATGCG 59.439 41.667 0.54 0.00 0.00 4.73
2922 2988 0.889186 ACGATGGTTTGTGGGCTGTC 60.889 55.000 0.00 0.00 0.00 3.51
2943 3009 6.993079 TGTCACTGATTTACTCTCTGCTTTA 58.007 36.000 0.00 0.00 0.00 1.85
3018 3084 0.106519 ATAATGGCCAGGTGAGGTGC 60.107 55.000 13.05 0.00 0.00 5.01
3152 3230 7.422465 ACACATTTGGAATGCCATAATAAGT 57.578 32.000 0.00 0.00 45.46 2.24
3292 3387 1.866063 GCAACCGCGATTAGGAGAGAG 60.866 57.143 8.23 0.00 0.00 3.20
3296 3392 2.758979 ACCGCGATTAGGAGAGAGAAAA 59.241 45.455 8.23 0.00 0.00 2.29
3305 3401 7.701078 CGATTAGGAGAGAGAAAATCGTGTTAA 59.299 37.037 7.41 0.00 42.27 2.01
3341 3437 2.098443 GGCTGTTGTTCAGAAAAACCGA 59.902 45.455 12.90 0.00 46.27 4.69
3471 3570 6.901081 AGTGAAAACTTATCTTTTCCCAGG 57.099 37.500 2.75 0.00 38.76 4.45
3500 3599 2.159226 GGTCGGAACAGATCGTCAGATT 60.159 50.000 0.00 0.00 37.19 2.40
3517 3616 2.364647 AGATTCTCAGATCGCATCAGCA 59.635 45.455 0.00 0.00 42.27 4.41
3558 3657 3.993736 CGTCTCACATGTACATGGTCAAA 59.006 43.478 33.32 15.84 42.91 2.69
3575 3677 4.438744 GGTCAAAACAGTGGAGTGAAACAG 60.439 45.833 0.00 0.00 41.43 3.16
3576 3678 4.394920 GTCAAAACAGTGGAGTGAAACAGA 59.605 41.667 0.00 0.00 41.43 3.41
3589 3691 3.251004 GTGAAACAGACCACTTTAGCTGG 59.749 47.826 0.00 0.00 36.32 4.85
3759 3892 6.299141 TCAGACTGAGCTTAGTGGAATTTTT 58.701 36.000 16.95 0.00 0.00 1.94
3848 4015 2.622942 TGGGTGCAAAAGCTCAAGTAAG 59.377 45.455 0.00 0.00 0.00 2.34
3868 4035 0.322906 CAAGCCTTTCTCCCTGACCC 60.323 60.000 0.00 0.00 0.00 4.46
3889 4056 4.082354 CCCTTTTCTCCAGATTCTTGCAAG 60.082 45.833 20.81 20.81 0.00 4.01
3904 4071 2.346803 TGCAAGATTTAGACGCCACTC 58.653 47.619 0.00 0.00 0.00 3.51
3920 4087 3.426292 GCCACTCGTGCCTCTAAAAATTC 60.426 47.826 0.00 0.00 0.00 2.17
3921 4088 3.751175 CCACTCGTGCCTCTAAAAATTCA 59.249 43.478 0.00 0.00 0.00 2.57
3922 4089 4.396166 CCACTCGTGCCTCTAAAAATTCAT 59.604 41.667 0.00 0.00 0.00 2.57
4020 4190 1.118965 TCACCAAGGCCTTCGTCAGA 61.119 55.000 17.29 7.13 0.00 3.27
4059 4229 3.214250 CTACTGGATCCTCGGCGCC 62.214 68.421 19.07 19.07 0.00 6.53
4182 4352 3.818787 GCCGACCAGCCTTGCATG 61.819 66.667 0.00 0.00 0.00 4.06
4229 4399 1.382420 AGTCTCCAGCCAGCTAGGG 60.382 63.158 0.00 0.00 38.09 3.53
4401 4578 7.787935 CGTTTTATTCTCCGAATAAAGATGACG 59.212 37.037 18.88 18.88 34.67 4.35
4411 4588 6.202954 CCGAATAAAGATGACGCCTTTTAGAT 59.797 38.462 0.00 0.00 35.65 1.98
4506 4683 7.768582 TCAAACATCTCACACGATGGTATAAAT 59.231 33.333 5.85 0.00 40.30 1.40
4584 4761 1.199624 GACACCAAAAAGCTGTTGCG 58.800 50.000 5.11 2.03 45.42 4.85
4591 4768 3.000825 CCAAAAAGCTGTTGCGGTAAAAC 59.999 43.478 5.11 0.00 45.42 2.43
4592 4769 3.512033 AAAAGCTGTTGCGGTAAAACA 57.488 38.095 0.00 0.00 45.42 2.83
4606 4784 4.698575 GGTAAAACATGAGGCACCAAAAA 58.301 39.130 0.00 0.00 0.00 1.94
4622 4800 5.236263 CACCAAAAAGTGAATTTTAGGGCAC 59.764 40.000 8.14 0.00 40.27 5.01
4659 4837 2.630580 TCCAACAACTGCCCCAAAATAC 59.369 45.455 0.00 0.00 0.00 1.89
4678 4856 1.135915 ACGGCACTTCAAACATGCAAA 59.864 42.857 0.00 0.00 41.27 3.68
4679 4857 2.224018 ACGGCACTTCAAACATGCAAAT 60.224 40.909 0.00 0.00 41.27 2.32
4680 4858 2.156117 CGGCACTTCAAACATGCAAATG 59.844 45.455 0.00 0.00 41.27 2.32
4685 4863 6.075280 GCACTTCAAACATGCAAATGATTTC 58.925 36.000 0.00 0.00 39.23 2.17
4696 4874 8.286800 ACATGCAAATGATTTCTTTTGAACATG 58.713 29.630 21.56 21.56 41.09 3.21
4697 4875 7.192148 TGCAAATGATTTCTTTTGAACATGG 57.808 32.000 18.02 0.00 41.01 3.66
4698 4876 6.081693 GCAAATGATTTCTTTTGAACATGGC 58.918 36.000 18.02 0.00 41.01 4.40
4701 4879 7.989416 AATGATTTCTTTTGAACATGGCAAT 57.011 28.000 0.00 0.00 38.30 3.56
4710 5402 1.949525 GAACATGGCAATATGTCCGCT 59.050 47.619 0.00 0.00 40.24 5.52
4767 5459 1.213094 ACTGAAACACGACGCCGAAG 61.213 55.000 0.00 0.00 39.50 3.79
4769 5461 2.586635 AAACACGACGCCGAAGCA 60.587 55.556 0.00 0.00 39.83 3.91
4803 5495 1.440060 CCGAACGCCATAGTAGCCA 59.560 57.895 0.00 0.00 0.00 4.75
4876 5568 2.112297 GCGAAAGTGGGGTGGTGA 59.888 61.111 0.00 0.00 0.00 4.02
4897 5589 1.084370 GGTGCGGTCGATTGGAAGAG 61.084 60.000 0.00 0.00 0.00 2.85
4898 5590 0.108804 GTGCGGTCGATTGGAAGAGA 60.109 55.000 0.00 0.00 0.00 3.10
4914 5606 1.074926 AGAGGCGGTGGATCCAGAT 60.075 57.895 16.81 0.00 35.57 2.90
4952 5644 2.439156 GCAGTGGTGGCCAGATCC 60.439 66.667 5.11 4.34 32.34 3.36
4953 5645 3.080641 CAGTGGTGGCCAGATCCA 58.919 61.111 5.11 7.81 32.34 3.41
4990 5682 3.771160 CGGCAGCGTAGGAGGGTT 61.771 66.667 0.00 0.00 0.00 4.11
4991 5683 2.669240 GGCAGCGTAGGAGGGTTT 59.331 61.111 0.00 0.00 0.00 3.27
4992 5684 1.745489 GGCAGCGTAGGAGGGTTTG 60.745 63.158 0.00 0.00 0.00 2.93
4993 5685 2.399356 GCAGCGTAGGAGGGTTTGC 61.399 63.158 0.00 0.00 0.00 3.68
4994 5686 1.003839 CAGCGTAGGAGGGTTTGCA 60.004 57.895 0.00 0.00 0.00 4.08
4995 5687 1.021390 CAGCGTAGGAGGGTTTGCAG 61.021 60.000 0.00 0.00 0.00 4.41
4996 5688 2.399356 GCGTAGGAGGGTTTGCAGC 61.399 63.158 0.00 0.00 0.00 5.25
4997 5689 2.100631 CGTAGGAGGGTTTGCAGCG 61.101 63.158 0.00 0.00 0.00 5.18
4998 5690 1.745489 GTAGGAGGGTTTGCAGCGG 60.745 63.158 0.00 0.00 0.00 5.52
4999 5691 2.221299 TAGGAGGGTTTGCAGCGGT 61.221 57.895 0.00 0.00 0.00 5.68
5000 5692 2.463589 TAGGAGGGTTTGCAGCGGTG 62.464 60.000 10.98 10.98 0.00 4.94
5001 5693 3.365265 GAGGGTTTGCAGCGGTGG 61.365 66.667 17.54 0.00 0.00 4.61
5002 5694 4.974721 AGGGTTTGCAGCGGTGGG 62.975 66.667 17.54 0.00 0.00 4.61
5003 5695 4.966787 GGGTTTGCAGCGGTGGGA 62.967 66.667 17.54 0.00 0.00 4.37
5004 5696 3.365265 GGTTTGCAGCGGTGGGAG 61.365 66.667 17.54 0.00 0.00 4.30
5005 5697 3.365265 GTTTGCAGCGGTGGGAGG 61.365 66.667 17.54 0.00 0.00 4.30
5018 5710 2.265904 GGGAGGCCGCGAAAGTTTT 61.266 57.895 8.23 0.00 0.00 2.43
5070 5766 8.966868 CCTTCCCAGCTTTTGTATAGAAATTAA 58.033 33.333 0.00 0.00 0.00 1.40
5172 5868 2.203394 GCGGATGACATGGGCCAT 60.203 61.111 14.78 14.78 0.00 4.40
5173 5869 1.073025 GCGGATGACATGGGCCATA 59.927 57.895 20.73 3.91 0.00 2.74
5191 5887 4.564782 CATATCCCATATGGCAGTGACT 57.435 45.455 16.97 2.06 39.11 3.41
5192 5888 2.945080 ATCCCATATGGCAGTGACTG 57.055 50.000 16.97 8.52 34.12 3.51
5194 5890 2.758130 TCCCATATGGCAGTGACTGTA 58.242 47.619 16.97 4.32 33.43 2.74
5196 5892 2.435805 CCCATATGGCAGTGACTGTACT 59.564 50.000 16.97 1.58 33.43 2.73
5202 5898 2.814410 CAGTGACTGTACTGCACCG 58.186 57.895 4.01 8.79 41.31 4.94
5203 5899 0.032130 CAGTGACTGTACTGCACCGT 59.968 55.000 4.01 0.00 41.31 4.83
5204 5900 1.268625 CAGTGACTGTACTGCACCGTA 59.731 52.381 4.01 0.00 41.31 4.02
5205 5901 1.268899 AGTGACTGTACTGCACCGTAC 59.731 52.381 17.28 8.85 40.06 3.67
5221 7131 2.889678 CCGTACAGTACTATCTTCCCCC 59.110 54.545 9.10 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.814954 ATTGGAACCACTCTAGTACATGAT 57.185 37.500 0.00 0.00 0.00 2.45
70 71 0.678366 AGACGAGACAGACCAGCGAT 60.678 55.000 0.00 0.00 0.00 4.58
75 76 1.609072 CACAGAAGACGAGACAGACCA 59.391 52.381 0.00 0.00 0.00 4.02
77 78 3.840890 ATCACAGAAGACGAGACAGAC 57.159 47.619 0.00 0.00 0.00 3.51
96 97 4.693042 CCATACATTCATGGCCCAAAAT 57.307 40.909 0.00 0.00 39.18 1.82
136 137 2.741145 AGAATCAGGAGCTCTACCGTT 58.259 47.619 14.64 2.79 0.00 4.44
137 138 2.445682 AGAATCAGGAGCTCTACCGT 57.554 50.000 14.64 0.00 0.00 4.83
168 169 7.728532 ACAGGACACAAACCCTAGATAATTTTT 59.271 33.333 0.00 0.00 0.00 1.94
169 170 7.238710 ACAGGACACAAACCCTAGATAATTTT 58.761 34.615 0.00 0.00 0.00 1.82
170 171 6.790319 ACAGGACACAAACCCTAGATAATTT 58.210 36.000 0.00 0.00 0.00 1.82
171 172 6.388619 ACAGGACACAAACCCTAGATAATT 57.611 37.500 0.00 0.00 0.00 1.40
194 197 4.082523 CCGCCTCGCCTTCCTGAA 62.083 66.667 0.00 0.00 0.00 3.02
213 216 0.036732 TCCATTTTCAGTGAGCCGCT 59.963 50.000 0.00 0.00 0.00 5.52
246 249 0.106469 TCCATCGAGACTGCTAGGCT 60.106 55.000 0.00 0.00 35.22 4.58
254 257 1.588674 CTAGACGCTCCATCGAGACT 58.411 55.000 0.00 0.00 38.52 3.24
280 283 1.333308 CACACATCCACGCACTTTTCA 59.667 47.619 0.00 0.00 0.00 2.69
282 285 1.333619 GACACACATCCACGCACTTTT 59.666 47.619 0.00 0.00 0.00 2.27
289 292 1.264020 CACCAAAGACACACATCCACG 59.736 52.381 0.00 0.00 0.00 4.94
295 298 3.213506 CAAGATCCACCAAAGACACACA 58.786 45.455 0.00 0.00 0.00 3.72
305 308 4.879295 ATTAATCCCACAAGATCCACCA 57.121 40.909 0.00 0.00 0.00 4.17
315 318 5.144100 AGACAAACACCAATTAATCCCACA 58.856 37.500 0.00 0.00 0.00 4.17
316 319 5.722021 AGACAAACACCAATTAATCCCAC 57.278 39.130 0.00 0.00 0.00 4.61
317 320 5.835819 TGAAGACAAACACCAATTAATCCCA 59.164 36.000 0.00 0.00 0.00 4.37
322 325 5.888724 TCCACTGAAGACAAACACCAATTAA 59.111 36.000 0.00 0.00 0.00 1.40
324 327 4.277476 TCCACTGAAGACAAACACCAATT 58.723 39.130 0.00 0.00 0.00 2.32
341 345 4.774660 ATCAGATCAAAGCAGATCCACT 57.225 40.909 9.37 0.00 44.32 4.00
356 360 2.285220 CGCCGATGAACGAAAATCAGAT 59.715 45.455 0.00 0.00 45.77 2.90
366 370 1.392168 ACACAAATACGCCGATGAACG 59.608 47.619 0.00 0.00 42.18 3.95
371 375 5.779922 ACATATAGACACAAATACGCCGAT 58.220 37.500 0.00 0.00 0.00 4.18
374 378 7.241663 TCAAACATATAGACACAAATACGCC 57.758 36.000 0.00 0.00 0.00 5.68
411 415 8.343168 ACAACCATCACCGATAAAAAGAAATA 57.657 30.769 0.00 0.00 0.00 1.40
412 416 7.227049 ACAACCATCACCGATAAAAAGAAAT 57.773 32.000 0.00 0.00 0.00 2.17
413 417 6.642707 ACAACCATCACCGATAAAAAGAAA 57.357 33.333 0.00 0.00 0.00 2.52
418 422 5.533154 AGAACAACAACCATCACCGATAAAA 59.467 36.000 0.00 0.00 0.00 1.52
421 425 4.280436 AGAACAACAACCATCACCGATA 57.720 40.909 0.00 0.00 0.00 2.92
429 433 1.535462 GCGCACTAGAACAACAACCAT 59.465 47.619 0.30 0.00 0.00 3.55
430 434 0.941542 GCGCACTAGAACAACAACCA 59.058 50.000 0.30 0.00 0.00 3.67
486 490 6.772605 ACGGGTAAACCTTGTTTTAGTAGAT 58.227 36.000 0.00 0.00 36.97 1.98
505 509 3.724001 TCCCTTATTGGAGACGGGT 57.276 52.632 0.00 0.00 38.35 5.28
685 689 5.010012 GGAGAAAACTTCCATTCTGCTCAAA 59.990 40.000 0.00 0.00 39.88 2.69
691 695 6.639632 TCTTTGGAGAAAACTTCCATTCTG 57.360 37.500 0.00 0.00 43.87 3.02
841 857 1.264020 CCGGTGTTGCATGGAATATCG 59.736 52.381 19.88 19.88 0.00 2.92
859 875 3.119708 GGTATAGCCGTATAGACAACCCG 60.120 52.174 0.00 0.00 0.00 5.28
987 1009 0.893270 TGTCCATTTCCAACTGGCGG 60.893 55.000 0.00 0.00 34.44 6.13
993 1015 1.335872 CCGTGCTTGTCCATTTCCAAC 60.336 52.381 0.00 0.00 0.00 3.77
994 1016 0.958091 CCGTGCTTGTCCATTTCCAA 59.042 50.000 0.00 0.00 0.00 3.53
1235 1259 2.175322 GCAGCGCAGAAACAGAGC 59.825 61.111 11.47 0.00 0.00 4.09
1349 1379 1.481871 GGAGGAAGATGGACCGTACA 58.518 55.000 0.00 0.00 0.00 2.90
1430 1478 2.835431 CCCGACGCTCCCTGAGAT 60.835 66.667 0.00 0.00 0.00 2.75
1505 1553 2.355837 TGCAGCCACGTCGAGTTC 60.356 61.111 0.00 0.00 0.00 3.01
1568 1616 0.615261 GGAAGAAGACGAGGGAGGGT 60.615 60.000 0.00 0.00 0.00 4.34
1569 1617 0.324830 AGGAAGAAGACGAGGGAGGG 60.325 60.000 0.00 0.00 0.00 4.30
1570 1618 1.107945 GAGGAAGAAGACGAGGGAGG 58.892 60.000 0.00 0.00 0.00 4.30
1608 1660 0.753867 TACTCGGTTGGTGTTGCAGA 59.246 50.000 0.00 0.00 0.00 4.26
1615 1673 2.025418 GCACGGTACTCGGTTGGTG 61.025 63.158 8.31 0.00 44.45 4.17
1659 1717 1.952990 TCAACGTAACTGTACCCGACA 59.047 47.619 0.00 0.00 36.35 4.35
1692 1750 2.041976 CCAGTCAGTCGTCACCAGT 58.958 57.895 0.00 0.00 0.00 4.00
1837 1895 4.821589 GGCCCTTGCGACGGAGAG 62.822 72.222 0.00 0.00 38.85 3.20
1972 2030 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1973 2031 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1974 2032 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1975 2033 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1976 2034 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1977 2035 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1978 2036 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1979 2037 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1980 2038 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1981 2039 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1982 2040 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1983 2041 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1984 2042 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1985 2043 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1986 2044 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1987 2045 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1988 2046 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1989 2047 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1990 2048 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
1991 2049 0.035458 TCCACACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
1992 2050 1.135803 GTTCCACACACACACACACAC 60.136 52.381 0.00 0.00 0.00 3.82
1993 2051 1.160989 GTTCCACACACACACACACA 58.839 50.000 0.00 0.00 0.00 3.72
1994 2052 0.450184 GGTTCCACACACACACACAC 59.550 55.000 0.00 0.00 0.00 3.82
1995 2053 1.021920 CGGTTCCACACACACACACA 61.022 55.000 0.00 0.00 0.00 3.72
1996 2054 0.741574 TCGGTTCCACACACACACAC 60.742 55.000 0.00 0.00 0.00 3.82
1997 2055 0.179234 ATCGGTTCCACACACACACA 59.821 50.000 0.00 0.00 0.00 3.72
1998 2056 1.002900 CAATCGGTTCCACACACACAC 60.003 52.381 0.00 0.00 0.00 3.82
1999 2057 1.304254 CAATCGGTTCCACACACACA 58.696 50.000 0.00 0.00 0.00 3.72
2000 2058 0.040425 GCAATCGGTTCCACACACAC 60.040 55.000 0.00 0.00 0.00 3.82
2001 2059 0.179032 AGCAATCGGTTCCACACACA 60.179 50.000 0.00 0.00 0.00 3.72
2205 2264 3.071479 GCATGTGACCGGAGAGTTTTAA 58.929 45.455 9.46 0.00 0.00 1.52
2207 2266 1.523758 GCATGTGACCGGAGAGTTTT 58.476 50.000 9.46 0.00 0.00 2.43
2229 2294 2.031919 TGAGGCCACAATTCGCGT 59.968 55.556 5.01 0.00 0.00 6.01
2361 2426 1.876156 GCACAAGGGTCAAAGAGTCAG 59.124 52.381 0.00 0.00 0.00 3.51
2521 2587 0.247301 GTACTTCATCACTTGCGCGC 60.247 55.000 27.26 27.26 0.00 6.86
2736 2802 2.153401 CAGGTTGGGGACAGGGACA 61.153 63.158 0.00 0.00 44.54 4.02
2856 2922 5.597182 ACATTTTGAAGATCCATCCATCCTG 59.403 40.000 0.00 0.00 0.00 3.86
2901 2967 0.240945 CAGCCCACAAACCATCGTTC 59.759 55.000 0.00 0.00 0.00 3.95
2910 2976 2.363306 AATCAGTGACAGCCCACAAA 57.637 45.000 0.00 0.00 39.42 2.83
2922 2988 6.713520 GCATAAAGCAGAGAGTAAATCAGTG 58.286 40.000 0.00 0.00 44.79 3.66
2943 3009 1.764723 TCGACCTGGATGATCAAGCAT 59.235 47.619 0.00 0.00 0.00 3.79
2982 3048 5.107607 GCCATTATAAACCGTGACATCTACG 60.108 44.000 0.00 0.00 40.98 3.51
3152 3230 3.511934 ACTTGTGCCAAACAACCAGTAAA 59.488 39.130 0.00 0.00 43.96 2.01
3196 3274 3.988976 AGTAAGCATGAGTGGATGTGT 57.011 42.857 0.00 0.00 0.00 3.72
3305 3401 4.796231 GCCTGTCCGCGTCGTCAT 62.796 66.667 4.92 0.00 0.00 3.06
3341 3437 1.619332 GGAAGGTTCTCTCAAGGACGT 59.381 52.381 0.00 0.00 30.92 4.34
3453 3549 8.585018 CAATACAACCTGGGAAAAGATAAGTTT 58.415 33.333 0.00 0.00 0.00 2.66
3458 3554 6.147437 ACCAATACAACCTGGGAAAAGATA 57.853 37.500 0.00 0.00 37.00 1.98
3459 3555 5.010708 ACCAATACAACCTGGGAAAAGAT 57.989 39.130 0.00 0.00 37.00 2.40
3471 3570 3.306166 CGATCTGTTCCGACCAATACAAC 59.694 47.826 0.00 0.00 0.00 3.32
3500 3599 2.904697 ATTGCTGATGCGATCTGAGA 57.095 45.000 0.00 0.00 38.92 3.27
3558 3657 2.238646 TGGTCTGTTTCACTCCACTGTT 59.761 45.455 0.00 0.00 0.00 3.16
3575 3677 1.798813 CACGTTCCAGCTAAAGTGGTC 59.201 52.381 7.24 0.00 35.86 4.02
3576 3678 1.878953 CACGTTCCAGCTAAAGTGGT 58.121 50.000 7.24 0.00 35.86 4.16
3763 3896 7.627340 TCGCAAAGAGTACAAGTAAAGAAAAG 58.373 34.615 0.00 0.00 0.00 2.27
3764 3897 7.542534 TCGCAAAGAGTACAAGTAAAGAAAA 57.457 32.000 0.00 0.00 0.00 2.29
3765 3898 7.542534 TTCGCAAAGAGTACAAGTAAAGAAA 57.457 32.000 0.00 0.00 0.00 2.52
3766 3899 6.292703 GCTTCGCAAAGAGTACAAGTAAAGAA 60.293 38.462 0.00 0.00 34.14 2.52
3767 3900 5.176958 GCTTCGCAAAGAGTACAAGTAAAGA 59.823 40.000 0.00 0.00 34.14 2.52
3768 3901 5.177696 AGCTTCGCAAAGAGTACAAGTAAAG 59.822 40.000 0.00 0.00 34.14 1.85
3776 3909 2.080286 TCCAGCTTCGCAAAGAGTAC 57.920 50.000 0.00 0.00 34.14 2.73
3848 4015 0.962855 GGTCAGGGAGAAAGGCTTGC 60.963 60.000 0.00 0.00 0.00 4.01
3868 4035 5.954296 TCTTGCAAGAATCTGGAGAAAAG 57.046 39.130 26.61 0.00 30.73 2.27
3904 4071 5.551760 AGACATGAATTTTTAGAGGCACG 57.448 39.130 0.00 0.00 0.00 5.34
3920 4087 5.530171 CCATCCCATCTGAAAAGTAGACATG 59.470 44.000 0.00 0.00 0.00 3.21
3921 4088 5.398353 CCCATCCCATCTGAAAAGTAGACAT 60.398 44.000 0.00 0.00 0.00 3.06
3922 4089 4.080356 CCCATCCCATCTGAAAAGTAGACA 60.080 45.833 0.00 0.00 0.00 3.41
4020 4190 5.184892 AGAAATGCAGGTTCTTGTAGGAT 57.815 39.130 9.15 0.00 31.10 3.24
4059 4229 3.763319 CGACTTACGAAGTGGCCG 58.237 61.111 0.00 0.00 45.73 6.13
4182 4352 1.523258 AGCGATCATGCTCAGTGCC 60.523 57.895 0.00 0.00 42.95 5.01
4185 4355 1.523258 GCCAGCGATCATGCTCAGT 60.523 57.895 0.00 0.00 45.23 3.41
4229 4399 4.779733 TGCTCCGGGTCCTCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
4401 4578 6.809630 ACTGTGAAAGAAGATCTAAAAGGC 57.190 37.500 0.00 0.00 0.00 4.35
4495 4672 5.869649 ACCTTTTGGCCATTTATACCATC 57.130 39.130 6.09 0.00 45.59 3.51
4497 4674 8.840200 TTTATACCTTTTGGCCATTTATACCA 57.160 30.769 6.09 0.00 45.59 3.25
4506 4683 7.609532 CCATTTTGATTTTATACCTTTTGGCCA 59.390 33.333 0.00 0.00 45.59 5.36
4584 4761 4.329462 TTTTGGTGCCTCATGTTTTACC 57.671 40.909 0.00 0.00 0.00 2.85
4591 4768 3.731652 TTCACTTTTTGGTGCCTCATG 57.268 42.857 0.00 0.00 37.16 3.07
4592 4769 4.961438 AATTCACTTTTTGGTGCCTCAT 57.039 36.364 0.00 0.00 37.16 2.90
4606 4784 6.670695 ATTTTGAGTGCCCTAAAATTCACT 57.329 33.333 0.00 0.00 41.90 3.41
4622 4800 7.168637 CAGTTGTTGGAGATGAACAATTTTGAG 59.831 37.037 0.00 0.00 43.34 3.02
4659 4837 1.850377 TTTGCATGTTTGAAGTGCCG 58.150 45.000 0.00 0.00 38.06 5.69
4678 4856 9.104965 CATATTGCCATGTTCAAAAGAAATCAT 57.895 29.630 2.37 0.00 0.00 2.45
4679 4857 8.095792 ACATATTGCCATGTTCAAAAGAAATCA 58.904 29.630 2.37 0.00 35.60 2.57
4680 4858 8.483307 ACATATTGCCATGTTCAAAAGAAATC 57.517 30.769 2.37 0.00 35.60 2.17
4685 4863 4.799949 CGGACATATTGCCATGTTCAAAAG 59.200 41.667 2.37 0.00 39.25 2.27
4696 4874 1.221414 GAGACAGCGGACATATTGCC 58.779 55.000 0.00 0.00 0.00 4.52
4697 4875 0.855349 CGAGACAGCGGACATATTGC 59.145 55.000 0.00 0.00 0.00 3.56
4698 4876 2.492019 TCGAGACAGCGGACATATTG 57.508 50.000 0.00 0.00 0.00 1.90
4701 4879 0.738975 CCTTCGAGACAGCGGACATA 59.261 55.000 0.00 0.00 0.00 2.29
4727 5419 1.794437 GCGATGGACGACAGTACTGAC 60.794 57.143 29.30 21.49 45.77 3.51
4728 5420 0.450583 GCGATGGACGACAGTACTGA 59.549 55.000 29.30 5.99 45.77 3.41
4767 5459 2.395690 CCGCGACGATTCAGTTGC 59.604 61.111 8.23 9.46 45.57 4.17
4769 5461 2.813908 GGCCGCGACGATTCAGTT 60.814 61.111 8.23 0.00 0.00 3.16
4803 5495 2.056906 AAAGCACGAAGGGCCAGTCT 62.057 55.000 6.18 0.00 0.00 3.24
4862 5554 2.380285 ACCGTCACCACCCCACTTT 61.380 57.895 0.00 0.00 0.00 2.66
4876 5568 3.229156 TTCCAATCGACCGCACCGT 62.229 57.895 0.00 0.00 0.00 4.83
4897 5589 1.070445 CATCTGGATCCACCGCCTC 59.930 63.158 11.44 0.00 42.61 4.70
4898 5590 2.446848 CCATCTGGATCCACCGCCT 61.447 63.158 11.44 0.00 42.61 5.52
4914 5606 3.799286 TTGTTGCACCATCCCGCCA 62.799 57.895 0.00 0.00 0.00 5.69
4952 5644 1.450312 GTCCCACCGAATCCAGCTG 60.450 63.158 6.78 6.78 0.00 4.24
4953 5645 2.990479 GTCCCACCGAATCCAGCT 59.010 61.111 0.00 0.00 0.00 4.24
4956 5648 4.090588 GCCGTCCCACCGAATCCA 62.091 66.667 0.00 0.00 0.00 3.41
4974 5666 1.745489 CAAACCCTCCTACGCTGCC 60.745 63.158 0.00 0.00 0.00 4.85
4984 5676 3.365265 CCACCGCTGCAAACCCTC 61.365 66.667 0.00 0.00 0.00 4.30
4985 5677 4.974721 CCCACCGCTGCAAACCCT 62.975 66.667 0.00 0.00 0.00 4.34
4986 5678 4.966787 TCCCACCGCTGCAAACCC 62.967 66.667 0.00 0.00 0.00 4.11
4987 5679 3.365265 CTCCCACCGCTGCAAACC 61.365 66.667 0.00 0.00 0.00 3.27
4988 5680 3.365265 CCTCCCACCGCTGCAAAC 61.365 66.667 0.00 0.00 0.00 2.93
4998 5690 4.699522 ACTTTCGCGGCCTCCCAC 62.700 66.667 6.13 0.00 0.00 4.61
4999 5691 2.969300 AAAACTTTCGCGGCCTCCCA 62.969 55.000 6.13 0.00 0.00 4.37
5000 5692 2.196382 GAAAACTTTCGCGGCCTCCC 62.196 60.000 6.13 0.00 0.00 4.30
5001 5693 1.209383 GAAAACTTTCGCGGCCTCC 59.791 57.895 6.13 0.00 0.00 4.30
5002 5694 4.841029 GAAAACTTTCGCGGCCTC 57.159 55.556 6.13 0.00 0.00 4.70
5010 5702 3.840468 ACCACCACAAACGAAAACTTTC 58.160 40.909 0.00 0.00 0.00 2.62
5011 5703 3.256136 TGACCACCACAAACGAAAACTTT 59.744 39.130 0.00 0.00 0.00 2.66
5012 5704 2.820787 TGACCACCACAAACGAAAACTT 59.179 40.909 0.00 0.00 0.00 2.66
5013 5705 2.438411 TGACCACCACAAACGAAAACT 58.562 42.857 0.00 0.00 0.00 2.66
5014 5706 2.923605 TGACCACCACAAACGAAAAC 57.076 45.000 0.00 0.00 0.00 2.43
5018 5710 1.588674 GACATGACCACCACAAACGA 58.411 50.000 0.00 0.00 0.00 3.85
5028 5720 1.347707 GAAGGTGTCTGGACATGACCA 59.652 52.381 16.16 16.16 43.97 4.02
5148 5844 1.575244 CCATGTCATCCGCACTACAG 58.425 55.000 0.00 0.00 0.00 2.74
5172 5868 3.317406 ACAGTCACTGCCATATGGGATA 58.683 45.455 23.30 6.45 38.95 2.59
5173 5869 2.130193 ACAGTCACTGCCATATGGGAT 58.870 47.619 23.30 7.99 38.95 3.85
5196 5892 3.379372 GGAAGATAGTACTGTACGGTGCA 59.621 47.826 22.75 10.68 0.00 4.57
5197 5893 3.243334 GGGAAGATAGTACTGTACGGTGC 60.243 52.174 17.87 16.12 0.00 5.01
5200 5896 2.889678 GGGGGAAGATAGTACTGTACGG 59.110 54.545 11.97 0.00 0.00 4.02
5201 5897 3.559069 TGGGGGAAGATAGTACTGTACG 58.441 50.000 11.97 0.00 0.00 3.67
5202 5898 3.321396 GCTGGGGGAAGATAGTACTGTAC 59.679 52.174 9.93 9.93 0.00 2.90
5203 5899 3.206866 AGCTGGGGGAAGATAGTACTGTA 59.793 47.826 5.39 0.00 0.00 2.74
5204 5900 2.022918 AGCTGGGGGAAGATAGTACTGT 60.023 50.000 5.39 0.00 0.00 3.55
5205 5901 2.683768 AGCTGGGGGAAGATAGTACTG 58.316 52.381 5.39 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.