Multiple sequence alignment - TraesCS6D01G116400

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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 TraesCS6D01G116400 chr6D 100.000 2738 0 0 1 2738 82695089 82697826 0.000000e+00 5057.0
1 TraesCS6D01G116400 chr6D 94.590 647 28 5 1 641 222499606 222500251 0.000000e+00 994.0
2 TraesCS6D01G116400 chr6D 94.427 646 29 6 1 641 62806208 62805565 0.000000e+00 987.0
3 TraesCS6D01G116400 chr6D 85.714 392 41 11 1963 2343 278603889 278603502 1.530000e-107 399.0
4 TraesCS6D01G116400 chr6D 86.705 173 18 2 655 826 262233592 262233424 1.290000e-43 187.0
5 TraesCS6D01G116400 chr6D 85.632 174 20 2 655 828 462491434 462491266 7.790000e-41 178.0
6 TraesCS6D01G116400 chr6D 83.511 188 29 2 2507 2693 348607386 348607200 1.010000e-39 174.0
7 TraesCS6D01G116400 chr6A 88.337 1329 110 18 647 1964 99503551 99504845 0.000000e+00 1554.0
8 TraesCS6D01G116400 chr6A 83.508 952 90 35 1057 1965 54201733 54200806 0.000000e+00 826.0
9 TraesCS6D01G116400 chr6A 88.221 399 44 3 2342 2738 99504847 99505244 8.870000e-130 473.0
10 TraesCS6D01G116400 chr6A 87.733 375 43 3 2337 2708 54200810 54200436 4.190000e-118 435.0
11 TraesCS6D01G116400 chr6A 85.311 177 20 4 655 830 556975991 556976162 7.790000e-41 178.0
12 TraesCS6D01G116400 chr6B 88.961 1241 126 7 729 1965 9760289 9759056 0.000000e+00 1522.0
13 TraesCS6D01G116400 chr6B 81.170 701 100 13 1236 1928 101703013 101703689 4.010000e-148 534.0
14 TraesCS6D01G116400 chr6B 90.231 389 32 2 2351 2738 9759047 9758664 1.130000e-138 503.0
15 TraesCS6D01G116400 chr6B 88.830 188 21 0 824 1011 101702538 101702725 5.900000e-57 231.0
16 TraesCS6D01G116400 chr6B 83.550 231 22 7 1066 1292 101702725 101702943 4.620000e-48 202.0
17 TraesCS6D01G116400 chr7D 94.470 651 25 5 1 641 572048973 572048324 0.000000e+00 992.0
18 TraesCS6D01G116400 chr7D 94.565 644 26 7 1 639 410157840 410157201 0.000000e+00 987.0
19 TraesCS6D01G116400 chr7D 84.844 640 82 6 958 1594 565671569 565670942 4.980000e-177 630.0
20 TraesCS6D01G116400 chr7D 87.425 167 15 3 655 821 282878221 282878381 1.290000e-43 187.0
21 TraesCS6D01G116400 chr7D 94.000 50 3 0 911 960 565681894 565681845 2.920000e-10 76.8
22 TraesCS6D01G116400 chr2D 94.453 649 27 7 1 641 261198212 261198859 0.000000e+00 990.0
23 TraesCS6D01G116400 chr2D 94.427 646 31 4 1 641 301735256 301735901 0.000000e+00 989.0
24 TraesCS6D01G116400 chr2D 94.419 645 30 5 2 641 315296927 315297570 0.000000e+00 987.0
25 TraesCS6D01G116400 chr2D 94.316 651 25 10 1 642 331636402 331637049 0.000000e+00 987.0
26 TraesCS6D01G116400 chr2D 84.596 396 50 9 1952 2342 20687642 20687253 1.540000e-102 383.0
27 TraesCS6D01G116400 chr2D 85.523 373 47 5 1976 2342 512920942 512920571 1.540000e-102 383.0
28 TraesCS6D01G116400 chr2D 77.698 278 46 15 1082 1352 115149947 115149679 3.650000e-34 156.0
29 TraesCS6D01G116400 chr5D 94.272 646 32 4 1 641 187457301 187456656 0.000000e+00 983.0
30 TraesCS6D01G116400 chr5D 87.371 388 33 8 1964 2342 260675584 260675964 5.420000e-117 431.0
31 TraesCS6D01G116400 chr5D 85.450 378 45 7 1964 2336 482604524 482604896 4.280000e-103 385.0
32 TraesCS6D01G116400 chrUn 82.340 889 84 35 1114 1966 70140739 70141590 0.000000e+00 704.0
33 TraesCS6D01G116400 chrUn 88.250 400 37 6 2348 2738 70145316 70145714 1.150000e-128 470.0
34 TraesCS6D01G116400 chrUn 83.696 184 28 2 2507 2689 260027730 260027548 3.620000e-39 172.0
35 TraesCS6D01G116400 chrUn 83.784 185 27 3 2507 2689 397613453 397613270 3.620000e-39 172.0
36 TraesCS6D01G116400 chrUn 86.897 145 19 0 867 1011 70140570 70140714 2.180000e-36 163.0
37 TraesCS6D01G116400 chr4D 81.989 744 80 21 824 1551 486812621 486811916 1.410000e-162 582.0
38 TraesCS6D01G116400 chr4D 85.632 174 20 2 653 826 506325902 506326070 7.790000e-41 178.0
39 TraesCS6D01G116400 chr2A 86.684 383 40 5 1964 2341 1221076 1220700 5.450000e-112 414.0
40 TraesCS6D01G116400 chr2A 79.476 458 54 25 1374 1808 5405117 5404677 3.450000e-74 289.0
41 TraesCS6D01G116400 chr2A 92.405 158 12 0 1114 1271 5405328 5405171 2.740000e-55 226.0
42 TraesCS6D01G116400 chr2A 100.000 31 0 0 824 854 5407039 5407009 1.060000e-04 58.4
43 TraesCS6D01G116400 chr5A 85.678 391 40 11 1964 2342 631755008 631754622 5.490000e-107 398.0
44 TraesCS6D01G116400 chr5B 84.715 386 48 7 1965 2346 55034987 55034609 2.570000e-100 375.0
45 TraesCS6D01G116400 chr5B 85.714 175 18 4 655 828 592082493 592082661 7.790000e-41 178.0
46 TraesCS6D01G116400 chr1B 84.635 384 45 10 1965 2342 53267926 53268301 1.200000e-98 370.0
47 TraesCS6D01G116400 chr1B 78.061 196 25 13 503 684 408032091 408031900 1.040000e-19 108.0
48 TraesCS6D01G116400 chr3D 85.326 184 22 2 653 836 169450359 169450181 4.660000e-43 185.0
49 TraesCS6D01G116400 chr2B 88.742 151 10 5 824 967 2335520 2335670 7.790000e-41 178.0
50 TraesCS6D01G116400 chr2B 82.500 160 15 9 1030 1188 2335678 2335825 7.960000e-26 128.0
51 TraesCS6D01G116400 chr3B 84.746 177 23 1 655 831 511628787 511628959 1.010000e-39 174.0
52 TraesCS6D01G116400 chr1D 83.511 188 29 2 2507 2693 458763408 458763222 1.010000e-39 174.0
53 TraesCS6D01G116400 chr1D 83.784 185 28 2 2507 2690 471759077 471759260 1.010000e-39 174.0


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 TraesCS6D01G116400 chr6D 82695089 82697826 2737 False 5057.000000 5057 100.000000 1 2738 1 chr6D.!!$F1 2737
1 TraesCS6D01G116400 chr6D 222499606 222500251 645 False 994.000000 994 94.590000 1 641 1 chr6D.!!$F2 640
2 TraesCS6D01G116400 chr6D 62805565 62806208 643 True 987.000000 987 94.427000 1 641 1 chr6D.!!$R1 640
3 TraesCS6D01G116400 chr6A 99503551 99505244 1693 False 1013.500000 1554 88.279000 647 2738 2 chr6A.!!$F2 2091
4 TraesCS6D01G116400 chr6A 54200436 54201733 1297 True 630.500000 826 85.620500 1057 2708 2 chr6A.!!$R1 1651
5 TraesCS6D01G116400 chr6B 9758664 9760289 1625 True 1012.500000 1522 89.596000 729 2738 2 chr6B.!!$R1 2009
6 TraesCS6D01G116400 chr6B 101702538 101703689 1151 False 322.333333 534 84.516667 824 1928 3 chr6B.!!$F1 1104
7 TraesCS6D01G116400 chr7D 572048324 572048973 649 True 992.000000 992 94.470000 1 641 1 chr7D.!!$R4 640
8 TraesCS6D01G116400 chr7D 410157201 410157840 639 True 987.000000 987 94.565000 1 639 1 chr7D.!!$R1 638
9 TraesCS6D01G116400 chr7D 565670942 565671569 627 True 630.000000 630 84.844000 958 1594 1 chr7D.!!$R2 636
10 TraesCS6D01G116400 chr2D 261198212 261198859 647 False 990.000000 990 94.453000 1 641 1 chr2D.!!$F1 640
11 TraesCS6D01G116400 chr2D 301735256 301735901 645 False 989.000000 989 94.427000 1 641 1 chr2D.!!$F2 640
12 TraesCS6D01G116400 chr2D 315296927 315297570 643 False 987.000000 987 94.419000 2 641 1 chr2D.!!$F3 639
13 TraesCS6D01G116400 chr2D 331636402 331637049 647 False 987.000000 987 94.316000 1 642 1 chr2D.!!$F4 641
14 TraesCS6D01G116400 chr5D 187456656 187457301 645 True 983.000000 983 94.272000 1 641 1 chr5D.!!$R1 640
15 TraesCS6D01G116400 chrUn 70140570 70145714 5144 False 445.666667 704 85.829000 867 2738 3 chrUn.!!$F1 1871
16 TraesCS6D01G116400 chr4D 486811916 486812621 705 True 582.000000 582 81.989000 824 1551 1 chr4D.!!$R1 727

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
468 483 1.001068 TCGTGGCATTTGGACTTCGTA 59.999 47.619 0.0 0.0 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2552 0.170339 GGCGACCAACAAACTATGCC 59.83 55.0 0.0 0.0 0.0 4.4 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
90 97 2.687425 TGAGAATTCAGCGAGAGAGAGG 59.313 50.000 8.44 0.00 0.00 3.69
163 170 1.676746 CATCATTGGAGAGGCACCAG 58.323 55.000 0.00 0.00 38.70 4.00
257 264 2.101917 TGAATATTTCGTCGACTCCCCC 59.898 50.000 14.70 0.00 0.00 5.40
291 299 5.715279 GGATTTTGGGGGTATTTATAGAGCC 59.285 44.000 0.00 0.00 32.36 4.70
298 306 4.597940 GGGGTATTTATAGAGCCAAGAGGT 59.402 45.833 0.00 0.00 34.83 3.85
468 483 1.001068 TCGTGGCATTTGGACTTCGTA 59.999 47.619 0.00 0.00 0.00 3.43
667 690 6.398234 TGCTAGTGTTAAGAGATGATCTCC 57.602 41.667 18.29 4.33 44.42 3.71
680 703 6.597153 GAGATGATCTCCCAGCACAATATGC 61.597 48.000 11.36 0.00 45.17 3.14
681 704 8.915601 GAGATGATCTCCCAGCACAATATGCA 62.916 46.154 11.36 0.00 46.25 3.96
692 715 4.282950 CACAATATGCATGTCTCACCAC 57.717 45.455 10.16 0.00 0.00 4.16
693 716 3.690628 CACAATATGCATGTCTCACCACA 59.309 43.478 10.16 0.00 0.00 4.17
706 729 8.906867 CATGTCTCACCACATTTTTAGGAATAT 58.093 33.333 0.00 0.00 34.60 1.28
707 730 8.506168 TGTCTCACCACATTTTTAGGAATATC 57.494 34.615 0.00 0.00 0.00 1.63
765 788 5.893687 TGTAGGCATGCTTTTATTGTCATG 58.106 37.500 18.92 0.00 39.29 3.07
796 819 7.651027 ACAAATGCAAGGCTTAAGATAAGAT 57.349 32.000 6.67 0.00 0.00 2.40
803 826 7.148188 TGCAAGGCTTAAGATAAGATTGTCTTG 60.148 37.037 6.67 1.21 38.76 3.02
821 844 5.178797 GTCTTGTCAACCACTATACATGCT 58.821 41.667 0.00 0.00 0.00 3.79
856 879 2.543777 ACTGCCTGTGTCAATTACGT 57.456 45.000 0.00 0.00 0.00 3.57
871 894 8.077386 TGTCAATTACGTGGTTAATTTTCTTCC 58.923 33.333 0.00 0.00 0.00 3.46
890 913 4.545823 TCCGAAAATAGCCGCTTATTTG 57.454 40.909 0.00 0.00 34.39 2.32
893 916 3.960002 CGAAAATAGCCGCTTATTTGTCG 59.040 43.478 0.00 3.60 34.39 4.35
1174 1251 7.122055 AGTTTTGTGGTCACTTACATTTCTTCA 59.878 33.333 2.66 0.00 0.00 3.02
1212 1289 1.079490 AGACATGGGAGTCCTCAAGGA 59.921 52.381 9.58 0.00 43.08 3.36
1271 1481 3.077359 CTCTTGGCTCCTGGTAAGTTTG 58.923 50.000 0.00 0.00 0.00 2.93
1334 1544 6.732531 TGCATCATCTATACATTTGCTAGC 57.267 37.500 8.10 8.10 0.00 3.42
1352 1562 8.640063 TTGCTAGCCATATGTGAAATTCATAT 57.360 30.769 13.29 10.01 38.52 1.78
1353 1563 8.047413 TGCTAGCCATATGTGAAATTCATATG 57.953 34.615 13.29 11.27 46.84 1.78
1357 1567 5.097529 CCATATGTGAAATTCATATGCCGC 58.902 41.667 14.25 0.00 46.38 6.53
1360 1570 0.041400 TGAAATTCATATGCCGCGCG 60.041 50.000 25.67 25.67 0.00 6.86
1373 1583 1.193650 GCCGCGCGTCATAAATTATCA 59.806 47.619 29.95 0.00 0.00 2.15
1472 1688 1.073897 GACTTGCAGGAAGGCCAGT 59.926 57.895 5.01 0.00 41.87 4.00
1499 1718 4.054671 GCTATACCAGAGATTGCAGTGAC 58.945 47.826 0.00 0.00 0.00 3.67
1640 1885 2.161410 TGTTGAAACTACCGCATGATGC 59.839 45.455 7.49 7.49 40.69 3.91
1731 1981 5.314923 TCTGCAAGATATTCCTGTTTTGC 57.685 39.130 0.00 0.43 38.67 3.68
1735 1985 4.427312 CAAGATATTCCTGTTTTGCCAGC 58.573 43.478 0.00 0.00 0.00 4.85
1760 2010 8.445493 GCAATTAAATTTCAAGGAGAACATTGG 58.555 33.333 0.00 0.00 38.19 3.16
1833 2083 5.047306 TCACCTTGATCTCACATACGAGTTT 60.047 40.000 0.00 0.00 34.46 2.66
1841 2091 5.227908 TCTCACATACGAGTTTTTCTCACC 58.772 41.667 0.00 0.00 42.88 4.02
1842 2092 4.951254 TCACATACGAGTTTTTCTCACCA 58.049 39.130 0.00 0.00 42.88 4.17
1863 2113 5.071250 ACCAACAGGAGTACTACACAATTCA 59.929 40.000 8.10 0.00 0.00 2.57
1884 2134 6.358974 TCACATGTTCTTGAGTCCTATTCA 57.641 37.500 0.00 0.00 0.00 2.57
1930 2187 0.911769 TGGTCTACCTGGCTCATTGG 59.088 55.000 0.02 0.00 36.82 3.16
1941 2198 1.674962 GGCTCATTGGTCATTGCTCTC 59.325 52.381 0.00 0.00 0.00 3.20
1965 2222 7.648142 TCACAATGACACCTGATTTCTTTTAC 58.352 34.615 0.00 0.00 0.00 2.01
1966 2223 7.502226 TCACAATGACACCTGATTTCTTTTACT 59.498 33.333 0.00 0.00 0.00 2.24
1967 2224 8.783093 CACAATGACACCTGATTTCTTTTACTA 58.217 33.333 0.00 0.00 0.00 1.82
1968 2225 9.003658 ACAATGACACCTGATTTCTTTTACTAG 57.996 33.333 0.00 0.00 0.00 2.57
1969 2226 9.003658 CAATGACACCTGATTTCTTTTACTAGT 57.996 33.333 0.00 0.00 0.00 2.57
1970 2227 7.962964 TGACACCTGATTTCTTTTACTAGTG 57.037 36.000 5.39 0.00 0.00 2.74
1971 2228 7.506114 TGACACCTGATTTCTTTTACTAGTGT 58.494 34.615 5.39 0.00 37.43 3.55
1972 2229 7.990886 TGACACCTGATTTCTTTTACTAGTGTT 59.009 33.333 5.39 0.00 35.06 3.32
1973 2230 8.747538 ACACCTGATTTCTTTTACTAGTGTTT 57.252 30.769 5.39 0.00 31.06 2.83
1974 2231 8.621286 ACACCTGATTTCTTTTACTAGTGTTTG 58.379 33.333 5.39 0.00 31.06 2.93
1975 2232 8.076178 CACCTGATTTCTTTTACTAGTGTTTGG 58.924 37.037 5.39 0.00 0.00 3.28
1976 2233 7.230712 ACCTGATTTCTTTTACTAGTGTTTGGG 59.769 37.037 5.39 0.00 0.00 4.12
1977 2234 7.309194 CCTGATTTCTTTTACTAGTGTTTGGGG 60.309 40.741 5.39 0.00 0.00 4.96
1978 2235 5.777850 TTTCTTTTACTAGTGTTTGGGGC 57.222 39.130 5.39 0.00 0.00 5.80
1979 2236 3.404899 TCTTTTACTAGTGTTTGGGGCG 58.595 45.455 5.39 0.00 0.00 6.13
1980 2237 1.525941 TTTACTAGTGTTTGGGGCGC 58.474 50.000 5.39 0.00 0.00 6.53
1981 2238 0.321830 TTACTAGTGTTTGGGGCGCC 60.322 55.000 21.18 21.18 0.00 6.53
1982 2239 1.481901 TACTAGTGTTTGGGGCGCCA 61.482 55.000 30.85 20.22 0.00 5.69
1983 2240 2.281900 TAGTGTTTGGGGCGCCAC 60.282 61.111 30.85 28.40 0.00 5.01
1984 2241 3.853698 TAGTGTTTGGGGCGCCACC 62.854 63.158 29.43 25.52 37.93 4.61
2001 2258 3.726517 CCTGTGGCGCCGTTTGAG 61.727 66.667 23.90 12.16 0.00 3.02
2002 2259 2.664851 CTGTGGCGCCGTTTGAGA 60.665 61.111 23.90 0.26 0.00 3.27
2003 2260 2.664851 TGTGGCGCCGTTTGAGAG 60.665 61.111 23.90 0.00 0.00 3.20
2004 2261 3.423154 GTGGCGCCGTTTGAGAGG 61.423 66.667 23.90 0.00 0.00 3.69
2005 2262 3.621805 TGGCGCCGTTTGAGAGGA 61.622 61.111 23.90 0.00 0.00 3.71
2006 2263 2.358247 GGCGCCGTTTGAGAGGAA 60.358 61.111 12.58 0.00 0.00 3.36
2007 2264 2.391389 GGCGCCGTTTGAGAGGAAG 61.391 63.158 12.58 0.00 0.00 3.46
2008 2265 3.028366 GCGCCGTTTGAGAGGAAGC 62.028 63.158 0.00 0.00 0.00 3.86
2009 2266 1.374758 CGCCGTTTGAGAGGAAGCT 60.375 57.895 0.00 0.00 0.00 3.74
2010 2267 1.630244 CGCCGTTTGAGAGGAAGCTG 61.630 60.000 0.00 0.00 0.00 4.24
2011 2268 0.603975 GCCGTTTGAGAGGAAGCTGT 60.604 55.000 0.00 0.00 0.00 4.40
2012 2269 1.151668 CCGTTTGAGAGGAAGCTGTG 58.848 55.000 0.00 0.00 0.00 3.66
2013 2270 1.541233 CCGTTTGAGAGGAAGCTGTGT 60.541 52.381 0.00 0.00 0.00 3.72
2014 2271 1.528586 CGTTTGAGAGGAAGCTGTGTG 59.471 52.381 0.00 0.00 0.00 3.82
2015 2272 1.265365 GTTTGAGAGGAAGCTGTGTGC 59.735 52.381 0.00 0.00 43.29 4.57
2016 2273 0.469494 TTGAGAGGAAGCTGTGTGCA 59.531 50.000 0.00 0.00 45.94 4.57
2017 2274 0.689055 TGAGAGGAAGCTGTGTGCAT 59.311 50.000 0.00 0.00 45.94 3.96
2018 2275 1.085091 GAGAGGAAGCTGTGTGCATG 58.915 55.000 0.00 0.00 45.94 4.06
2019 2276 0.399454 AGAGGAAGCTGTGTGCATGT 59.601 50.000 0.00 0.00 45.94 3.21
2020 2277 1.202855 AGAGGAAGCTGTGTGCATGTT 60.203 47.619 0.00 0.00 45.94 2.71
2021 2278 1.610522 GAGGAAGCTGTGTGCATGTTT 59.389 47.619 0.00 0.00 45.94 2.83
2022 2279 2.034124 AGGAAGCTGTGTGCATGTTTT 58.966 42.857 0.00 0.00 45.94 2.43
2023 2280 2.431782 AGGAAGCTGTGTGCATGTTTTT 59.568 40.909 0.00 0.00 45.94 1.94
2024 2281 3.636300 AGGAAGCTGTGTGCATGTTTTTA 59.364 39.130 0.00 0.00 45.94 1.52
2025 2282 4.281688 AGGAAGCTGTGTGCATGTTTTTAT 59.718 37.500 0.00 0.00 45.94 1.40
2026 2283 4.990426 GGAAGCTGTGTGCATGTTTTTATT 59.010 37.500 0.00 0.00 45.94 1.40
2027 2284 6.015519 AGGAAGCTGTGTGCATGTTTTTATTA 60.016 34.615 0.00 0.00 45.94 0.98
2028 2285 6.644592 GGAAGCTGTGTGCATGTTTTTATTAA 59.355 34.615 0.00 0.00 45.94 1.40
2029 2286 7.170658 GGAAGCTGTGTGCATGTTTTTATTAAA 59.829 33.333 0.00 0.00 45.94 1.52
2030 2287 8.430801 AAGCTGTGTGCATGTTTTTATTAAAA 57.569 26.923 0.00 0.00 45.94 1.52
2031 2288 8.430801 AGCTGTGTGCATGTTTTTATTAAAAA 57.569 26.923 9.69 9.69 45.94 1.94
2051 2308 2.693267 AACATAAAGTCCTCGCCTCC 57.307 50.000 0.00 0.00 0.00 4.30
2052 2309 1.867363 ACATAAAGTCCTCGCCTCCT 58.133 50.000 0.00 0.00 0.00 3.69
2053 2310 2.188817 ACATAAAGTCCTCGCCTCCTT 58.811 47.619 0.00 0.00 0.00 3.36
2054 2311 2.168728 ACATAAAGTCCTCGCCTCCTTC 59.831 50.000 0.00 0.00 0.00 3.46
2055 2312 2.233305 TAAAGTCCTCGCCTCCTTCT 57.767 50.000 0.00 0.00 0.00 2.85
2056 2313 2.233305 AAAGTCCTCGCCTCCTTCTA 57.767 50.000 0.00 0.00 0.00 2.10
2057 2314 2.233305 AAGTCCTCGCCTCCTTCTAA 57.767 50.000 0.00 0.00 0.00 2.10
2058 2315 2.233305 AGTCCTCGCCTCCTTCTAAA 57.767 50.000 0.00 0.00 0.00 1.85
2059 2316 2.537143 AGTCCTCGCCTCCTTCTAAAA 58.463 47.619 0.00 0.00 0.00 1.52
2060 2317 2.904434 AGTCCTCGCCTCCTTCTAAAAA 59.096 45.455 0.00 0.00 0.00 1.94
2141 2398 5.794726 AAAAATTACCACCACAACCTACC 57.205 39.130 0.00 0.00 0.00 3.18
2142 2399 4.456662 AAATTACCACCACAACCTACCA 57.543 40.909 0.00 0.00 0.00 3.25
2143 2400 3.713826 ATTACCACCACAACCTACCAG 57.286 47.619 0.00 0.00 0.00 4.00
2144 2401 0.688487 TACCACCACAACCTACCAGC 59.312 55.000 0.00 0.00 0.00 4.85
2145 2402 1.671054 CCACCACAACCTACCAGCG 60.671 63.158 0.00 0.00 0.00 5.18
2146 2403 1.369692 CACCACAACCTACCAGCGA 59.630 57.895 0.00 0.00 0.00 4.93
2147 2404 0.670546 CACCACAACCTACCAGCGAG 60.671 60.000 0.00 0.00 0.00 5.03
2148 2405 1.119574 ACCACAACCTACCAGCGAGT 61.120 55.000 0.00 0.00 0.00 4.18
2149 2406 0.670546 CCACAACCTACCAGCGAGTG 60.671 60.000 0.00 0.00 0.00 3.51
2150 2407 1.004918 ACAACCTACCAGCGAGTGC 60.005 57.895 0.00 0.00 43.24 4.40
2151 2408 1.741770 CAACCTACCAGCGAGTGCC 60.742 63.158 0.00 0.00 44.31 5.01
2152 2409 2.214216 AACCTACCAGCGAGTGCCA 61.214 57.895 0.00 0.00 44.31 4.92
2153 2410 2.125512 CCTACCAGCGAGTGCCAC 60.126 66.667 0.00 0.00 44.31 5.01
2154 2411 2.650116 CCTACCAGCGAGTGCCACT 61.650 63.158 0.00 0.00 44.31 4.00
2155 2412 1.293498 CTACCAGCGAGTGCCACTT 59.707 57.895 0.00 0.00 44.31 3.16
2156 2413 0.320771 CTACCAGCGAGTGCCACTTT 60.321 55.000 0.00 0.00 44.31 2.66
2157 2414 0.602638 TACCAGCGAGTGCCACTTTG 60.603 55.000 0.00 0.00 44.31 2.77
2158 2415 2.253452 CAGCGAGTGCCACTTTGC 59.747 61.111 13.31 13.31 44.31 3.68
2159 2416 2.203195 AGCGAGTGCCACTTTGCA 60.203 55.556 20.52 0.41 44.31 4.08
2160 2417 1.823470 AGCGAGTGCCACTTTGCAA 60.823 52.632 20.52 0.00 44.11 4.08
2161 2418 1.658409 GCGAGTGCCACTTTGCAAC 60.658 57.895 15.52 0.00 44.11 4.17
2162 2419 1.008538 CGAGTGCCACTTTGCAACC 60.009 57.895 0.00 0.00 44.11 3.77
2163 2420 1.363807 GAGTGCCACTTTGCAACCC 59.636 57.895 0.00 0.00 44.11 4.11
2164 2421 1.076044 AGTGCCACTTTGCAACCCT 60.076 52.632 0.00 0.00 44.11 4.34
2165 2422 1.109323 AGTGCCACTTTGCAACCCTC 61.109 55.000 0.00 0.00 44.11 4.30
2166 2423 1.832167 TGCCACTTTGCAACCCTCC 60.832 57.895 0.00 0.00 38.56 4.30
2167 2424 1.832167 GCCACTTTGCAACCCTCCA 60.832 57.895 0.00 0.00 0.00 3.86
2168 2425 1.187567 GCCACTTTGCAACCCTCCAT 61.188 55.000 0.00 0.00 0.00 3.41
2169 2426 1.341080 CCACTTTGCAACCCTCCATT 58.659 50.000 0.00 0.00 0.00 3.16
2170 2427 1.693606 CCACTTTGCAACCCTCCATTT 59.306 47.619 0.00 0.00 0.00 2.32
2171 2428 2.896685 CCACTTTGCAACCCTCCATTTA 59.103 45.455 0.00 0.00 0.00 1.40
2172 2429 3.323403 CCACTTTGCAACCCTCCATTTAA 59.677 43.478 0.00 0.00 0.00 1.52
2173 2430 4.202305 CCACTTTGCAACCCTCCATTTAAA 60.202 41.667 0.00 0.00 0.00 1.52
2174 2431 5.363939 CACTTTGCAACCCTCCATTTAAAA 58.636 37.500 0.00 0.00 0.00 1.52
2175 2432 5.819901 CACTTTGCAACCCTCCATTTAAAAA 59.180 36.000 0.00 0.00 0.00 1.94
2193 2450 4.302559 AAAAATACCAGAGGTCCTCACC 57.697 45.455 21.26 0.00 44.19 4.02
2206 2463 5.386958 GGTCCTCACCTCCATTTAAAAAC 57.613 43.478 0.00 0.00 40.00 2.43
2207 2464 4.830600 GGTCCTCACCTCCATTTAAAAACA 59.169 41.667 0.00 0.00 40.00 2.83
2208 2465 5.303333 GGTCCTCACCTCCATTTAAAAACAA 59.697 40.000 0.00 0.00 40.00 2.83
2209 2466 6.183360 GGTCCTCACCTCCATTTAAAAACAAA 60.183 38.462 0.00 0.00 40.00 2.83
2210 2467 7.269316 GTCCTCACCTCCATTTAAAAACAAAA 58.731 34.615 0.00 0.00 0.00 2.44
2211 2468 7.766738 GTCCTCACCTCCATTTAAAAACAAAAA 59.233 33.333 0.00 0.00 0.00 1.94
2273 2530 8.614994 AATTTTATAAAAGATTTCTCACCGCG 57.385 30.769 15.45 0.00 0.00 6.46
2274 2531 5.728351 TTATAAAAGATTTCTCACCGCGG 57.272 39.130 26.86 26.86 0.00 6.46
2275 2532 1.892209 AAAAGATTTCTCACCGCGGT 58.108 45.000 28.70 28.70 0.00 5.68
2276 2533 1.439679 AAAGATTTCTCACCGCGGTC 58.560 50.000 31.80 15.93 0.00 4.79
2277 2534 0.320374 AAGATTTCTCACCGCGGTCA 59.680 50.000 31.80 17.39 0.00 4.02
2278 2535 0.320374 AGATTTCTCACCGCGGTCAA 59.680 50.000 31.80 18.73 0.00 3.18
2279 2536 0.442699 GATTTCTCACCGCGGTCAAC 59.557 55.000 31.80 11.82 0.00 3.18
2280 2537 0.953960 ATTTCTCACCGCGGTCAACC 60.954 55.000 31.80 0.00 0.00 3.77
2281 2538 2.313051 TTTCTCACCGCGGTCAACCA 62.313 55.000 31.80 10.15 35.14 3.67
2282 2539 2.709125 TTCTCACCGCGGTCAACCAG 62.709 60.000 31.80 16.95 35.14 4.00
2283 2540 4.980805 TCACCGCGGTCAACCAGC 62.981 66.667 31.80 3.32 35.14 4.85
2284 2541 4.988598 CACCGCGGTCAACCAGCT 62.989 66.667 31.80 0.00 34.81 4.24
2285 2542 4.250305 ACCGCGGTCAACCAGCTT 62.250 61.111 28.70 0.00 34.81 3.74
2286 2543 3.726517 CCGCGGTCAACCAGCTTG 61.727 66.667 19.50 0.00 34.81 4.01
2287 2544 2.972505 CGCGGTCAACCAGCTTGT 60.973 61.111 0.00 0.00 34.81 3.16
2288 2545 2.639286 GCGGTCAACCAGCTTGTG 59.361 61.111 0.00 0.00 34.38 3.33
2289 2546 2.639286 CGGTCAACCAGCTTGTGC 59.361 61.111 0.00 0.00 40.05 4.57
2290 2547 2.908073 CGGTCAACCAGCTTGTGCC 61.908 63.158 0.00 0.00 40.80 5.01
2291 2548 1.827789 GGTCAACCAGCTTGTGCCA 60.828 57.895 0.00 0.00 40.80 4.92
2292 2549 1.360192 GTCAACCAGCTTGTGCCAC 59.640 57.895 0.00 0.00 40.80 5.01
2293 2550 2.186160 TCAACCAGCTTGTGCCACG 61.186 57.895 0.00 0.00 40.80 4.94
2294 2551 2.124320 AACCAGCTTGTGCCACGT 60.124 55.556 0.00 0.00 40.80 4.49
2295 2552 2.480610 AACCAGCTTGTGCCACGTG 61.481 57.895 9.08 9.08 40.80 4.49
2296 2553 3.663176 CCAGCTTGTGCCACGTGG 61.663 66.667 30.66 30.66 40.80 4.94
2308 2565 2.330231 CCACGTGGCATAGTTTGTTG 57.670 50.000 24.02 0.00 0.00 3.33
2309 2566 1.068610 CCACGTGGCATAGTTTGTTGG 60.069 52.381 24.02 0.00 0.00 3.77
2310 2567 1.606668 CACGTGGCATAGTTTGTTGGT 59.393 47.619 7.95 0.00 0.00 3.67
2311 2568 1.877443 ACGTGGCATAGTTTGTTGGTC 59.123 47.619 0.00 0.00 0.00 4.02
2312 2569 1.136085 CGTGGCATAGTTTGTTGGTCG 60.136 52.381 0.00 0.00 0.00 4.79
2313 2570 0.878416 TGGCATAGTTTGTTGGTCGC 59.122 50.000 0.00 0.00 0.00 5.19
2314 2571 0.170339 GGCATAGTTTGTTGGTCGCC 59.830 55.000 0.00 0.00 0.00 5.54
2315 2572 0.170339 GCATAGTTTGTTGGTCGCCC 59.830 55.000 0.00 0.00 0.00 6.13
2316 2573 1.821216 CATAGTTTGTTGGTCGCCCT 58.179 50.000 0.00 0.00 0.00 5.19
2317 2574 2.159382 CATAGTTTGTTGGTCGCCCTT 58.841 47.619 0.00 0.00 0.00 3.95
2318 2575 1.886886 TAGTTTGTTGGTCGCCCTTC 58.113 50.000 0.00 0.00 0.00 3.46
2319 2576 0.106918 AGTTTGTTGGTCGCCCTTCA 60.107 50.000 0.00 0.00 0.00 3.02
2320 2577 0.030235 GTTTGTTGGTCGCCCTTCAC 59.970 55.000 0.00 0.00 0.00 3.18
2321 2578 1.440938 TTTGTTGGTCGCCCTTCACG 61.441 55.000 0.00 0.00 0.00 4.35
2322 2579 3.723348 GTTGGTCGCCCTTCACGC 61.723 66.667 0.00 0.00 0.00 5.34
2323 2580 4.243008 TTGGTCGCCCTTCACGCA 62.243 61.111 0.00 0.00 0.00 5.24
2324 2581 3.545124 TTGGTCGCCCTTCACGCAT 62.545 57.895 0.00 0.00 0.00 4.73
2325 2582 2.173758 TTGGTCGCCCTTCACGCATA 62.174 55.000 0.00 0.00 0.00 3.14
2326 2583 1.883084 GGTCGCCCTTCACGCATAG 60.883 63.158 0.00 0.00 0.00 2.23
2327 2584 2.202878 TCGCCCTTCACGCATAGC 60.203 61.111 0.00 0.00 0.00 2.97
2328 2585 2.202932 CGCCCTTCACGCATAGCT 60.203 61.111 0.00 0.00 0.00 3.32
2329 2586 1.815421 CGCCCTTCACGCATAGCTT 60.815 57.895 0.00 0.00 0.00 3.74
2330 2587 0.529773 CGCCCTTCACGCATAGCTTA 60.530 55.000 0.00 0.00 0.00 3.09
2331 2588 1.663695 GCCCTTCACGCATAGCTTAA 58.336 50.000 0.00 0.00 0.00 1.85
2332 2589 2.222027 GCCCTTCACGCATAGCTTAAT 58.778 47.619 0.00 0.00 0.00 1.40
2333 2590 2.031682 GCCCTTCACGCATAGCTTAATG 60.032 50.000 0.00 0.00 0.00 1.90
2334 2591 2.549754 CCCTTCACGCATAGCTTAATGG 59.450 50.000 0.00 0.00 0.00 3.16
2335 2592 2.549754 CCTTCACGCATAGCTTAATGGG 59.450 50.000 11.00 11.00 43.43 4.00
2343 2600 5.460646 CGCATAGCTTAATGGGTTTAATGG 58.539 41.667 0.00 0.00 35.64 3.16
2349 2606 4.464597 GCTTAATGGGTTTAATGGTCCACA 59.535 41.667 0.00 0.00 31.48 4.17
2403 6380 1.004560 CTCTGTGTCCACACCGCAT 60.005 57.895 7.38 0.00 45.88 4.73
2422 6400 6.318648 ACCGCATTGTTGATACTTTACATGAT 59.681 34.615 0.00 0.00 0.00 2.45
2477 6455 9.914131 TCTCACCATTATCTGACTAATTATTCG 57.086 33.333 0.00 0.00 0.00 3.34
2492 6470 5.705609 ATTATTCGGTTGTTGCTTGTTCT 57.294 34.783 0.00 0.00 0.00 3.01
2525 6503 1.203063 TGTGTGGCTAGGTCTCAGTCT 60.203 52.381 0.00 0.00 0.00 3.24
2670 6650 0.822532 ACCAAGTCTCGGTCGACTGT 60.823 55.000 23.27 1.57 43.14 3.55
2724 6710 6.757478 TGTGGTGTATGTACAATATTGGTACG 59.243 38.462 19.37 0.00 43.10 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 97 5.335035 CCGTAGTTAGTAGCTAGATGGCTTC 60.335 48.000 0.00 0.00 42.97 3.86
163 170 2.434774 GGGGTTCACCACCTCCAC 59.565 66.667 0.00 0.00 46.38 4.02
257 264 1.560505 CCCAAAATCCCAGAACCCTG 58.439 55.000 0.00 0.00 40.09 4.45
274 282 4.019231 CCTCTTGGCTCTATAAATACCCCC 60.019 50.000 0.00 0.00 0.00 5.40
291 299 3.717294 CCCCCGGACCACCTCTTG 61.717 72.222 0.73 0.00 0.00 3.02
468 483 7.984422 TTACATCGCAGGAAATCAATATCAT 57.016 32.000 0.00 0.00 0.00 2.45
625 648 3.699538 AGCATAGTGATACGTCTCCAACA 59.300 43.478 0.00 0.00 0.00 3.33
642 665 7.177568 GGGAGATCATCTCTTAACACTAGCATA 59.822 40.741 14.54 0.00 42.95 3.14
643 666 6.014669 GGGAGATCATCTCTTAACACTAGCAT 60.015 42.308 14.54 0.00 42.95 3.79
644 667 5.303078 GGGAGATCATCTCTTAACACTAGCA 59.697 44.000 14.54 0.00 42.95 3.49
645 668 5.303078 TGGGAGATCATCTCTTAACACTAGC 59.697 44.000 14.54 0.00 42.95 3.42
680 703 6.573664 TTCCTAAAAATGTGGTGAGACATG 57.426 37.500 0.00 0.00 36.66 3.21
681 704 9.125026 GATATTCCTAAAAATGTGGTGAGACAT 57.875 33.333 0.00 0.00 38.23 3.06
682 705 8.328758 AGATATTCCTAAAAATGTGGTGAGACA 58.671 33.333 0.00 0.00 0.00 3.41
683 706 8.738645 AGATATTCCTAAAAATGTGGTGAGAC 57.261 34.615 0.00 0.00 0.00 3.36
724 747 5.552178 CCTACAATGGGTTATCTCTTAGCC 58.448 45.833 0.00 0.00 0.00 3.93
765 788 7.145323 TCTTAAGCCTTGCATTTGTTTTAGAC 58.855 34.615 0.00 0.00 0.00 2.59
796 819 5.411361 GCATGTATAGTGGTTGACAAGACAA 59.589 40.000 0.00 0.00 0.00 3.18
803 826 6.986817 ACATAAGAGCATGTATAGTGGTTGAC 59.013 38.462 0.00 0.00 37.37 3.18
821 844 6.316140 CACAGGCAGTTATTAAGCACATAAGA 59.684 38.462 0.00 0.00 0.00 2.10
871 894 3.960002 CGACAAATAAGCGGCTATTTTCG 59.040 43.478 1.35 9.68 30.67 3.46
890 913 2.332362 CTGAGCCAATGCATGCCGAC 62.332 60.000 16.68 0.00 41.13 4.79
893 916 0.533491 TTTCTGAGCCAATGCATGCC 59.467 50.000 16.68 0.00 41.13 4.40
969 1013 4.033358 GTCCTGATTCATAAGCGACACTTG 59.967 45.833 0.00 0.00 39.58 3.16
1084 1139 8.781196 CATGGATGATGTAGTCTAATGGAAAAG 58.219 37.037 0.00 0.00 0.00 2.27
1098 1153 7.147602 CCATCTCTTATAGCCATGGATGATGTA 60.148 40.741 18.40 0.00 36.84 2.29
1174 1251 5.268118 TGTCTCAGCGATTATCAAGACAT 57.732 39.130 10.56 0.00 38.47 3.06
1352 1562 1.193650 GATAATTTATGACGCGCGGCA 59.806 47.619 43.18 43.18 37.65 5.69
1353 1563 1.193650 TGATAATTTATGACGCGCGGC 59.806 47.619 35.22 34.04 0.00 6.53
1414 1626 6.613233 ACAAAACAAAGAACACAATACGACA 58.387 32.000 0.00 0.00 0.00 4.35
1472 1688 5.835819 ACTGCAATCTCTGGTATAGCTCTTA 59.164 40.000 3.20 0.00 0.00 2.10
1499 1718 0.744414 AGGCCGAAACACATGGATCG 60.744 55.000 0.00 1.22 35.19 3.69
1678 1923 5.633830 TTTTCAATTGCTCATCTCCAGTC 57.366 39.130 0.00 0.00 0.00 3.51
1706 1951 3.920231 ACAGGAATATCTTGCAGAGCA 57.080 42.857 0.00 0.00 36.47 4.26
1725 1970 6.857451 CCTTGAAATTTAATTGCTGGCAAAAC 59.143 34.615 12.06 0.11 39.55 2.43
1731 1981 7.153985 TGTTCTCCTTGAAATTTAATTGCTGG 58.846 34.615 0.00 0.55 36.30 4.85
1735 1985 9.492973 ACCAATGTTCTCCTTGAAATTTAATTG 57.507 29.630 0.00 0.00 36.30 2.32
1778 2028 5.357742 TGTAGCACATGGACATGAGTTAT 57.642 39.130 18.38 4.84 41.20 1.89
1833 2083 4.897076 TGTAGTACTCCTGTTGGTGAGAAA 59.103 41.667 0.00 0.00 32.84 2.52
1841 2091 5.989168 TGTGAATTGTGTAGTACTCCTGTTG 59.011 40.000 0.00 0.00 0.00 3.33
1842 2092 6.169557 TGTGAATTGTGTAGTACTCCTGTT 57.830 37.500 0.00 0.00 0.00 3.16
1908 2158 1.958288 ATGAGCCAGGTAGACCAAGT 58.042 50.000 0.66 0.00 38.89 3.16
1910 2160 1.281867 CCAATGAGCCAGGTAGACCAA 59.718 52.381 0.66 0.00 38.89 3.67
1918 2168 0.458669 GCAATGACCAATGAGCCAGG 59.541 55.000 0.00 0.00 0.00 4.45
1941 2198 7.651808 AGTAAAAGAAATCAGGTGTCATTGTG 58.348 34.615 0.00 0.00 0.00 3.33
1965 2222 2.033448 TGGCGCCCCAAACACTAG 59.967 61.111 26.77 0.00 38.46 2.57
1966 2223 2.281900 GTGGCGCCCCAAACACTA 60.282 61.111 26.77 0.00 44.33 2.74
1984 2241 3.726517 CTCAAACGGCGCCACAGG 61.727 66.667 28.98 12.87 0.00 4.00
1985 2242 2.664851 TCTCAAACGGCGCCACAG 60.665 61.111 28.98 13.29 0.00 3.66
1986 2243 2.664851 CTCTCAAACGGCGCCACA 60.665 61.111 28.98 3.21 0.00 4.17
1987 2244 3.423154 CCTCTCAAACGGCGCCAC 61.423 66.667 28.98 0.00 0.00 5.01
1988 2245 3.171828 TTCCTCTCAAACGGCGCCA 62.172 57.895 28.98 4.99 0.00 5.69
1989 2246 2.358247 TTCCTCTCAAACGGCGCC 60.358 61.111 19.07 19.07 0.00 6.53
1990 2247 3.028366 GCTTCCTCTCAAACGGCGC 62.028 63.158 6.90 0.00 0.00 6.53
1991 2248 1.374758 AGCTTCCTCTCAAACGGCG 60.375 57.895 4.80 4.80 0.00 6.46
1992 2249 0.603975 ACAGCTTCCTCTCAAACGGC 60.604 55.000 0.00 0.00 0.00 5.68
1993 2250 1.151668 CACAGCTTCCTCTCAAACGG 58.848 55.000 0.00 0.00 0.00 4.44
1994 2251 1.528586 CACACAGCTTCCTCTCAAACG 59.471 52.381 0.00 0.00 0.00 3.60
1995 2252 1.265365 GCACACAGCTTCCTCTCAAAC 59.735 52.381 0.00 0.00 41.15 2.93
1996 2253 1.134128 TGCACACAGCTTCCTCTCAAA 60.134 47.619 0.00 0.00 45.94 2.69
1997 2254 0.469494 TGCACACAGCTTCCTCTCAA 59.531 50.000 0.00 0.00 45.94 3.02
1998 2255 0.689055 ATGCACACAGCTTCCTCTCA 59.311 50.000 0.00 0.00 45.94 3.27
1999 2256 1.085091 CATGCACACAGCTTCCTCTC 58.915 55.000 0.00 0.00 45.94 3.20
2000 2257 0.399454 ACATGCACACAGCTTCCTCT 59.601 50.000 0.00 0.00 45.94 3.69
2001 2258 1.242076 AACATGCACACAGCTTCCTC 58.758 50.000 0.00 0.00 45.94 3.71
2002 2259 1.696063 AAACATGCACACAGCTTCCT 58.304 45.000 0.00 0.00 45.94 3.36
2003 2260 2.514205 AAAACATGCACACAGCTTCC 57.486 45.000 0.00 0.00 45.94 3.46
2004 2261 7.636259 TTAATAAAAACATGCACACAGCTTC 57.364 32.000 0.00 0.00 45.94 3.86
2005 2262 8.430801 TTTTAATAAAAACATGCACACAGCTT 57.569 26.923 0.00 0.00 35.41 3.74
2006 2263 8.430801 TTTTTAATAAAAACATGCACACAGCT 57.569 26.923 6.80 0.00 38.58 4.24
2029 2286 3.756963 GGAGGCGAGGACTTTATGTTTTT 59.243 43.478 0.00 0.00 0.00 1.94
2030 2287 3.009143 AGGAGGCGAGGACTTTATGTTTT 59.991 43.478 0.00 0.00 0.00 2.43
2031 2288 2.572104 AGGAGGCGAGGACTTTATGTTT 59.428 45.455 0.00 0.00 0.00 2.83
2032 2289 2.188817 AGGAGGCGAGGACTTTATGTT 58.811 47.619 0.00 0.00 0.00 2.71
2033 2290 1.867363 AGGAGGCGAGGACTTTATGT 58.133 50.000 0.00 0.00 0.00 2.29
2034 2291 2.432510 AGAAGGAGGCGAGGACTTTATG 59.567 50.000 0.00 0.00 0.00 1.90
2035 2292 2.753247 AGAAGGAGGCGAGGACTTTAT 58.247 47.619 0.00 0.00 0.00 1.40
2036 2293 2.233305 AGAAGGAGGCGAGGACTTTA 57.767 50.000 0.00 0.00 0.00 1.85
2037 2294 2.233305 TAGAAGGAGGCGAGGACTTT 57.767 50.000 0.00 0.00 0.00 2.66
2038 2295 2.233305 TTAGAAGGAGGCGAGGACTT 57.767 50.000 0.00 0.00 0.00 3.01
2039 2296 2.233305 TTTAGAAGGAGGCGAGGACT 57.767 50.000 0.00 0.00 0.00 3.85
2040 2297 3.329929 TTTTTAGAAGGAGGCGAGGAC 57.670 47.619 0.00 0.00 0.00 3.85
2119 2376 5.209659 TGGTAGGTTGTGGTGGTAATTTTT 58.790 37.500 0.00 0.00 0.00 1.94
2120 2377 4.805744 TGGTAGGTTGTGGTGGTAATTTT 58.194 39.130 0.00 0.00 0.00 1.82
2121 2378 4.403734 CTGGTAGGTTGTGGTGGTAATTT 58.596 43.478 0.00 0.00 0.00 1.82
2122 2379 3.812882 GCTGGTAGGTTGTGGTGGTAATT 60.813 47.826 0.00 0.00 0.00 1.40
2123 2380 2.290705 GCTGGTAGGTTGTGGTGGTAAT 60.291 50.000 0.00 0.00 0.00 1.89
2124 2381 1.072648 GCTGGTAGGTTGTGGTGGTAA 59.927 52.381 0.00 0.00 0.00 2.85
2125 2382 0.688487 GCTGGTAGGTTGTGGTGGTA 59.312 55.000 0.00 0.00 0.00 3.25
2126 2383 1.454539 GCTGGTAGGTTGTGGTGGT 59.545 57.895 0.00 0.00 0.00 4.16
2127 2384 1.671054 CGCTGGTAGGTTGTGGTGG 60.671 63.158 0.00 0.00 0.00 4.61
2128 2385 0.670546 CTCGCTGGTAGGTTGTGGTG 60.671 60.000 0.00 0.00 0.00 4.17
2129 2386 1.119574 ACTCGCTGGTAGGTTGTGGT 61.120 55.000 0.00 0.00 0.00 4.16
2130 2387 0.670546 CACTCGCTGGTAGGTTGTGG 60.671 60.000 0.00 0.00 0.00 4.17
2131 2388 1.291877 GCACTCGCTGGTAGGTTGTG 61.292 60.000 0.00 0.00 34.30 3.33
2132 2389 1.004918 GCACTCGCTGGTAGGTTGT 60.005 57.895 0.00 0.00 34.30 3.32
2133 2390 1.741770 GGCACTCGCTGGTAGGTTG 60.742 63.158 0.00 0.00 38.60 3.77
2134 2391 2.214216 TGGCACTCGCTGGTAGGTT 61.214 57.895 0.00 0.00 38.60 3.50
2135 2392 2.603473 TGGCACTCGCTGGTAGGT 60.603 61.111 0.00 0.00 38.60 3.08
2136 2393 2.125512 GTGGCACTCGCTGGTAGG 60.126 66.667 11.13 0.00 38.60 3.18
2137 2394 0.320771 AAAGTGGCACTCGCTGGTAG 60.321 55.000 22.31 0.00 38.60 3.18
2138 2395 0.602638 CAAAGTGGCACTCGCTGGTA 60.603 55.000 22.31 0.00 38.60 3.25
2139 2396 1.893808 CAAAGTGGCACTCGCTGGT 60.894 57.895 22.31 0.07 38.60 4.00
2140 2397 2.949106 CAAAGTGGCACTCGCTGG 59.051 61.111 22.31 0.00 38.60 4.85
2141 2398 2.062361 TTGCAAAGTGGCACTCGCTG 62.062 55.000 30.33 23.50 44.86 5.18
2142 2399 1.823470 TTGCAAAGTGGCACTCGCT 60.823 52.632 30.33 12.89 44.86 4.93
2143 2400 1.658409 GTTGCAAAGTGGCACTCGC 60.658 57.895 26.49 26.49 44.86 5.03
2144 2401 1.008538 GGTTGCAAAGTGGCACTCG 60.009 57.895 22.31 16.10 44.86 4.18
2145 2402 1.109323 AGGGTTGCAAAGTGGCACTC 61.109 55.000 22.31 9.33 44.86 3.51
2146 2403 1.076044 AGGGTTGCAAAGTGGCACT 60.076 52.632 15.88 15.88 44.86 4.40
2147 2404 1.363807 GAGGGTTGCAAAGTGGCAC 59.636 57.895 10.29 10.29 44.86 5.01
2148 2405 1.832167 GGAGGGTTGCAAAGTGGCA 60.832 57.895 0.00 0.00 43.19 4.92
2149 2406 1.187567 ATGGAGGGTTGCAAAGTGGC 61.188 55.000 0.00 0.00 0.00 5.01
2150 2407 1.341080 AATGGAGGGTTGCAAAGTGG 58.659 50.000 0.00 0.00 0.00 4.00
2151 2408 4.599047 TTAAATGGAGGGTTGCAAAGTG 57.401 40.909 0.00 0.00 0.00 3.16
2152 2409 5.622346 TTTTAAATGGAGGGTTGCAAAGT 57.378 34.783 0.00 0.00 0.00 2.66
2172 2429 4.302559 GGTGAGGACCTCTGGTATTTTT 57.697 45.455 22.14 0.00 39.47 1.94
2184 2441 4.830600 TGTTTTTAAATGGAGGTGAGGACC 59.169 41.667 0.00 0.00 43.52 4.46
2185 2442 6.399639 TTGTTTTTAAATGGAGGTGAGGAC 57.600 37.500 0.00 0.00 0.00 3.85
2186 2443 7.425224 TTTTGTTTTTAAATGGAGGTGAGGA 57.575 32.000 0.00 0.00 0.00 3.71
2247 2504 9.072294 CGCGGTGAGAAATCTTTTATAAAATTT 57.928 29.630 10.97 9.61 0.00 1.82
2248 2505 7.700656 CCGCGGTGAGAAATCTTTTATAAAATT 59.299 33.333 19.50 3.34 0.00 1.82
2249 2506 7.148137 ACCGCGGTGAGAAATCTTTTATAAAAT 60.148 33.333 33.75 0.00 0.00 1.82
2250 2507 6.149807 ACCGCGGTGAGAAATCTTTTATAAAA 59.850 34.615 33.75 10.16 0.00 1.52
2251 2508 5.644636 ACCGCGGTGAGAAATCTTTTATAAA 59.355 36.000 33.75 0.00 0.00 1.40
2252 2509 5.180271 ACCGCGGTGAGAAATCTTTTATAA 58.820 37.500 33.75 0.00 0.00 0.98
2253 2510 4.761975 ACCGCGGTGAGAAATCTTTTATA 58.238 39.130 33.75 0.00 0.00 0.98
2254 2511 3.606687 ACCGCGGTGAGAAATCTTTTAT 58.393 40.909 33.75 0.00 0.00 1.40
2255 2512 2.997986 GACCGCGGTGAGAAATCTTTTA 59.002 45.455 39.65 0.00 0.00 1.52
2256 2513 1.804748 GACCGCGGTGAGAAATCTTTT 59.195 47.619 39.65 5.39 0.00 2.27
2257 2514 1.270625 TGACCGCGGTGAGAAATCTTT 60.271 47.619 39.65 5.66 0.00 2.52
2258 2515 0.320374 TGACCGCGGTGAGAAATCTT 59.680 50.000 39.65 6.34 0.00 2.40
2259 2516 0.320374 TTGACCGCGGTGAGAAATCT 59.680 50.000 39.65 7.32 0.00 2.40
2260 2517 0.442699 GTTGACCGCGGTGAGAAATC 59.557 55.000 39.65 20.21 0.00 2.17
2261 2518 0.953960 GGTTGACCGCGGTGAGAAAT 60.954 55.000 39.65 9.27 0.00 2.17
2262 2519 1.595929 GGTTGACCGCGGTGAGAAA 60.596 57.895 39.65 21.06 0.00 2.52
2263 2520 2.029964 GGTTGACCGCGGTGAGAA 59.970 61.111 39.65 22.19 0.00 2.87
2264 2521 3.220999 CTGGTTGACCGCGGTGAGA 62.221 63.158 39.65 18.51 39.43 3.27
2265 2522 2.738521 CTGGTTGACCGCGGTGAG 60.739 66.667 39.65 18.58 39.43 3.51
2266 2523 4.980805 GCTGGTTGACCGCGGTGA 62.981 66.667 39.65 28.20 39.43 4.02
2267 2524 4.988598 AGCTGGTTGACCGCGGTG 62.989 66.667 39.65 21.66 39.38 4.94
2268 2525 4.250305 AAGCTGGTTGACCGCGGT 62.250 61.111 34.89 34.89 39.38 5.68
2269 2526 3.726517 CAAGCTGGTTGACCGCGG 61.727 66.667 26.86 26.86 38.60 6.46
2270 2527 2.972505 ACAAGCTGGTTGACCGCG 60.973 61.111 24.71 0.00 38.60 6.46
2271 2528 2.639286 CACAAGCTGGTTGACCGC 59.361 61.111 24.71 8.33 38.60 5.68
2272 2529 2.639286 GCACAAGCTGGTTGACCG 59.361 61.111 24.71 13.56 38.60 4.79
2273 2530 1.827789 TGGCACAAGCTGGTTGACC 60.828 57.895 24.71 22.64 38.60 4.02
2274 2531 1.360192 GTGGCACAAGCTGGTTGAC 59.640 57.895 24.71 15.58 44.16 3.18
2275 2532 2.186160 CGTGGCACAAGCTGGTTGA 61.186 57.895 24.71 0.62 44.16 3.18
2276 2533 2.332514 CGTGGCACAAGCTGGTTG 59.667 61.111 19.09 17.29 44.16 3.77
2277 2534 2.124320 ACGTGGCACAAGCTGGTT 60.124 55.556 19.09 0.00 44.16 3.67
2278 2535 2.901840 CACGTGGCACAAGCTGGT 60.902 61.111 19.09 2.91 44.16 4.00
2279 2536 3.663176 CCACGTGGCACAAGCTGG 61.663 66.667 24.02 11.77 44.16 4.85
2289 2546 1.068610 CCAACAAACTATGCCACGTGG 60.069 52.381 30.66 30.66 38.53 4.94
2290 2547 1.606668 ACCAACAAACTATGCCACGTG 59.393 47.619 9.08 9.08 0.00 4.49
2291 2548 1.877443 GACCAACAAACTATGCCACGT 59.123 47.619 0.00 0.00 0.00 4.49
2292 2549 1.136085 CGACCAACAAACTATGCCACG 60.136 52.381 0.00 0.00 0.00 4.94
2293 2550 1.401018 GCGACCAACAAACTATGCCAC 60.401 52.381 0.00 0.00 0.00 5.01
2294 2551 0.878416 GCGACCAACAAACTATGCCA 59.122 50.000 0.00 0.00 0.00 4.92
2295 2552 0.170339 GGCGACCAACAAACTATGCC 59.830 55.000 0.00 0.00 0.00 4.40
2296 2553 3.694889 GGCGACCAACAAACTATGC 57.305 52.632 0.00 0.00 0.00 3.14
2309 2566 2.526120 GCTATGCGTGAAGGGCGAC 61.526 63.158 0.00 0.00 0.00 5.19
2310 2567 2.202878 GCTATGCGTGAAGGGCGA 60.203 61.111 0.00 0.00 0.00 5.54
2311 2568 0.529773 TAAGCTATGCGTGAAGGGCG 60.530 55.000 0.00 0.00 0.00 6.13
2312 2569 1.663695 TTAAGCTATGCGTGAAGGGC 58.336 50.000 0.00 0.00 0.00 5.19
2313 2570 2.549754 CCATTAAGCTATGCGTGAAGGG 59.450 50.000 0.00 0.00 0.00 3.95
2314 2571 2.549754 CCCATTAAGCTATGCGTGAAGG 59.450 50.000 0.00 0.00 0.00 3.46
2315 2572 3.206150 ACCCATTAAGCTATGCGTGAAG 58.794 45.455 0.00 0.00 0.00 3.02
2316 2573 3.275617 ACCCATTAAGCTATGCGTGAA 57.724 42.857 0.00 0.00 0.00 3.18
2317 2574 3.275617 AACCCATTAAGCTATGCGTGA 57.724 42.857 0.00 0.00 0.00 4.35
2318 2575 5.493133 TTAAACCCATTAAGCTATGCGTG 57.507 39.130 0.00 0.00 0.00 5.34
2319 2576 5.009610 CCATTAAACCCATTAAGCTATGCGT 59.990 40.000 0.00 0.00 36.94 5.24
2320 2577 5.009610 ACCATTAAACCCATTAAGCTATGCG 59.990 40.000 0.00 0.00 36.94 4.73
2321 2578 6.405278 ACCATTAAACCCATTAAGCTATGC 57.595 37.500 0.00 0.00 36.94 3.14
2322 2579 6.549364 TGGACCATTAAACCCATTAAGCTATG 59.451 38.462 0.00 0.00 36.94 2.23
2323 2580 6.549736 GTGGACCATTAAACCCATTAAGCTAT 59.450 38.462 0.00 0.00 36.94 2.97
2324 2581 5.889289 GTGGACCATTAAACCCATTAAGCTA 59.111 40.000 0.00 0.00 36.94 3.32
2325 2582 4.709886 GTGGACCATTAAACCCATTAAGCT 59.290 41.667 0.00 0.00 36.94 3.74
2326 2583 4.464597 TGTGGACCATTAAACCCATTAAGC 59.535 41.667 0.00 0.00 36.94 3.09
2327 2584 5.714806 AGTGTGGACCATTAAACCCATTAAG 59.285 40.000 0.00 0.00 36.94 1.85
2328 2585 5.646215 AGTGTGGACCATTAAACCCATTAA 58.354 37.500 0.00 0.00 37.86 1.40
2329 2586 5.263872 AGTGTGGACCATTAAACCCATTA 57.736 39.130 0.00 0.00 0.00 1.90
2330 2587 4.126520 AGTGTGGACCATTAAACCCATT 57.873 40.909 0.00 0.00 0.00 3.16
2331 2588 3.825908 AGTGTGGACCATTAAACCCAT 57.174 42.857 0.00 0.00 0.00 4.00
2332 2589 3.653836 AGTAGTGTGGACCATTAAACCCA 59.346 43.478 0.00 0.00 0.00 4.51
2333 2590 4.296621 AGTAGTGTGGACCATTAAACCC 57.703 45.455 0.00 0.00 0.00 4.11
2334 2591 6.644248 AAAAGTAGTGTGGACCATTAAACC 57.356 37.500 0.00 0.00 0.00 3.27
2339 2596 8.755028 AGTTTTTAAAAAGTAGTGTGGACCATT 58.245 29.630 17.48 0.00 30.14 3.16
2340 2597 8.301252 AGTTTTTAAAAAGTAGTGTGGACCAT 57.699 30.769 17.48 0.00 30.14 3.55
2343 2600 8.975410 ACAAGTTTTTAAAAAGTAGTGTGGAC 57.025 30.769 18.90 3.28 31.62 4.02
2456 6434 9.273016 ACAACCGAATAATTAGTCAGATAATGG 57.727 33.333 12.94 6.50 0.00 3.16
2477 6455 5.831997 ACATAAAGAGAACAAGCAACAACC 58.168 37.500 0.00 0.00 0.00 3.77
2492 6470 5.705441 CCTAGCCACACAGAAAACATAAAGA 59.295 40.000 0.00 0.00 0.00 2.52
2525 6503 3.069079 AGACTTGGCTACGTCTCAGTA 57.931 47.619 3.20 0.00 35.72 2.74
2534 6512 3.669251 ACTTGAGTGAGACTTGGCTAC 57.331 47.619 0.00 0.00 0.00 3.58
2638 6618 2.906389 AGACTTGGTTATGTCTCAGGCA 59.094 45.455 0.00 0.00 36.84 4.75
2712 6698 7.930217 AGATTTCAACATCCGTACCAATATTG 58.070 34.615 8.58 8.58 0.00 1.90


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

AutoCloner maintained by Alex Coulton.