Multiple sequence alignment - TraesCS5A01G090500

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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 TraesCS5A01G090500 chr5A 100.000 5836 0 0 1 5836 122952910 122958745 0.000000e+00 10778.0
1 TraesCS5A01G090500 chr5A 88.006 717 45 15 846 1559 504720520 504719842 0.000000e+00 809.0
2 TraesCS5A01G090500 chr5A 88.636 220 21 2 5482 5701 632151202 632150987 1.250000e-66 265.0
3 TraesCS5A01G090500 chr5A 100.000 65 0 0 3256 3320 504719775 504719839 2.860000e-23 121.0
4 TraesCS5A01G090500 chr5A 92.593 54 4 0 5349 5402 122997115 122997168 1.740000e-10 78.7
5 TraesCS5A01G090500 chr5A 89.362 47 2 3 5154 5199 122958015 122958059 8.170000e-04 56.5
6 TraesCS5A01G090500 chr5A 89.362 47 2 3 5106 5150 122958063 122958108 8.170000e-04 56.5
7 TraesCS5A01G090500 chr5D 95.698 5184 166 30 1 5150 115946802 115951962 0.000000e+00 8285.0
8 TraesCS5A01G090500 chr5D 88.208 212 5 2 5141 5332 115951904 115952115 9.780000e-58 235.0
9 TraesCS5A01G090500 chr5D 97.500 40 1 0 5702 5741 115952297 115952336 1.050000e-07 69.4
10 TraesCS5A01G090500 chr5B 94.506 5060 138 44 223 5205 127501054 127506050 0.000000e+00 7675.0
11 TraesCS5A01G090500 chr5B 92.230 2677 160 18 943 3609 252302842 252300204 0.000000e+00 3747.0
12 TraesCS5A01G090500 chr5B 94.757 782 28 9 2832 3609 704278578 704277806 0.000000e+00 1205.0
13 TraesCS5A01G090500 chr5B 89.700 767 34 16 1260 2023 704279303 704278579 0.000000e+00 937.0
14 TraesCS5A01G090500 chr5B 90.096 313 13 3 1249 1559 678674092 678673796 1.970000e-104 390.0
15 TraesCS5A01G090500 chr5B 85.854 205 26 3 23 226 127500532 127500734 1.270000e-51 215.0
16 TraesCS5A01G090500 chr5B 90.476 126 10 2 5712 5836 127506383 127506507 1.300000e-36 165.0
17 TraesCS5A01G090500 chr4A 91.401 1477 91 18 1511 2979 321175704 321174256 0.000000e+00 1991.0
18 TraesCS5A01G090500 chr4A 93.365 633 42 0 2977 3609 321129404 321128772 0.000000e+00 937.0
19 TraesCS5A01G090500 chr4A 93.214 501 31 3 936 1434 321184579 321184080 0.000000e+00 734.0
20 TraesCS5A01G090500 chr4A 79.426 1011 194 13 3787 4793 721384825 721385825 0.000000e+00 702.0
21 TraesCS5A01G090500 chr4A 90.222 225 21 1 5482 5705 607232476 607232252 5.720000e-75 292.0
22 TraesCS5A01G090500 chr1B 91.509 954 49 8 1073 2023 332154903 332153979 0.000000e+00 1284.0
23 TraesCS5A01G090500 chr1B 93.606 782 44 5 2832 3609 332153978 332153199 0.000000e+00 1162.0
24 TraesCS5A01G090500 chr1B 94.426 610 24 5 2285 2886 122923476 122922869 0.000000e+00 929.0
25 TraesCS5A01G090500 chr1B 89.048 767 39 10 1260 2023 169942250 169941526 0.000000e+00 909.0
26 TraesCS5A01G090500 chr1B 96.667 510 11 3 3100 3609 169941321 169940818 0.000000e+00 843.0
27 TraesCS5A01G090500 chr1B 93.484 399 24 2 936 1333 122924252 122923855 5.040000e-165 592.0
28 TraesCS5A01G090500 chr1B 94.043 235 14 0 1073 1307 390429479 390429245 2.000000e-94 357.0
29 TraesCS5A01G090500 chr1B 90.141 213 15 5 2832 3040 169941525 169941315 7.450000e-69 272.0
30 TraesCS5A01G090500 chr1B 95.833 48 2 0 3562 3609 390429242 390429195 1.740000e-10 78.7
31 TraesCS5A01G090500 chr1A 88.598 1070 66 23 846 1911 483640780 483641797 0.000000e+00 1249.0
32 TraesCS5A01G090500 chr4B 94.246 782 33 8 2832 3609 564198136 564197363 0.000000e+00 1184.0
33 TraesCS5A01G090500 chr4B 93.990 782 35 8 2832 3609 175549171 175548398 0.000000e+00 1173.0
34 TraesCS5A01G090500 chr4B 89.048 767 39 9 1260 2023 175549896 175549172 0.000000e+00 909.0
35 TraesCS5A01G090500 chr4B 89.048 767 39 15 1260 2023 564198861 564198137 0.000000e+00 909.0
36 TraesCS5A01G090500 chr7B 92.977 598 35 3 2285 2876 623471067 623470471 0.000000e+00 865.0
37 TraesCS5A01G090500 chr7B 79.259 1080 194 27 3726 4793 451354362 451355423 0.000000e+00 726.0
38 TraesCS5A01G090500 chr7B 93.250 400 25 2 936 1333 623268373 623267974 6.510000e-164 588.0
39 TraesCS5A01G090500 chr7B 95.000 260 12 1 2285 2544 623266263 623266005 1.960000e-109 407.0
40 TraesCS5A01G090500 chr7B 88.235 221 19 4 5482 5701 733770551 733770765 2.090000e-64 257.0
41 TraesCS5A01G090500 chr7A 79.141 1117 201 30 3690 4793 484595862 484596959 0.000000e+00 743.0
42 TraesCS5A01G090500 chr7A 78.317 1010 207 11 3787 4793 14190524 14189524 4.930000e-180 641.0
43 TraesCS5A01G090500 chr7A 82.558 430 73 2 3120 3548 484595340 484595768 1.540000e-100 377.0
44 TraesCS5A01G090500 chr7A 88.372 215 18 5 3544 3754 474792404 474792615 9.710000e-63 252.0
45 TraesCS5A01G090500 chr7D 79.051 1117 202 29 3690 4793 434148763 434149860 0.000000e+00 737.0
46 TraesCS5A01G090500 chr7D 78.713 1010 203 10 3787 4793 14881448 14880448 0.000000e+00 664.0
47 TraesCS5A01G090500 chr7D 82.093 430 75 2 3120 3548 434148241 434148669 3.320000e-97 366.0
48 TraesCS5A01G090500 chr7D 90.909 231 17 2 3544 3771 413254752 413254981 2.040000e-79 307.0
49 TraesCS5A01G090500 chr7D 71.868 846 201 30 3876 4704 366451927 366452752 5.930000e-50 209.0
50 TraesCS5A01G090500 chr2B 88.789 223 22 3 5481 5702 777953954 777953734 2.680000e-68 270.0
51 TraesCS5A01G090500 chr2B 88.789 223 22 3 5481 5702 778009405 778009185 2.680000e-68 270.0
52 TraesCS5A01G090500 chr2B 87.611 226 21 6 5479 5701 785955156 785955377 7.500000e-64 255.0
53 TraesCS5A01G090500 chr2B 76.293 232 47 8 2336 2563 798320542 798320315 3.690000e-22 117.0
54 TraesCS5A01G090500 chrUn 88.341 223 23 3 5481 5702 369116358 369116138 1.250000e-66 265.0
55 TraesCS5A01G090500 chr6A 88.688 221 19 3 5482 5702 63128640 63128426 1.250000e-66 265.0
56 TraesCS5A01G090500 chr6A 86.864 236 20 3 5469 5703 384090296 384090071 2.700000e-63 254.0
57 TraesCS5A01G090500 chr6A 86.036 222 19 4 5470 5689 603095815 603095604 1.640000e-55 228.0
58 TraesCS5A01G090500 chr2A 88.636 220 20 3 5482 5701 137264339 137264125 4.480000e-66 263.0
59 TraesCS5A01G090500 chr2A 80.702 171 27 6 2396 2563 765039944 765040111 1.710000e-25 128.0
60 TraesCS5A01G090500 chr2D 77.059 170 35 4 2396 2563 639666671 639666838 1.730000e-15 95.3


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 TraesCS5A01G090500 chr5A 122952910 122958745 5835 False 3630.333333 10778 92.908000 1 5836 3 chr5A.!!$F3 5835
1 TraesCS5A01G090500 chr5A 504719842 504720520 678 True 809.000000 809 88.006000 846 1559 1 chr5A.!!$R1 713
2 TraesCS5A01G090500 chr5D 115946802 115952336 5534 False 2863.133333 8285 93.802000 1 5741 3 chr5D.!!$F1 5740
3 TraesCS5A01G090500 chr5B 252300204 252302842 2638 True 3747.000000 3747 92.230000 943 3609 1 chr5B.!!$R1 2666
4 TraesCS5A01G090500 chr5B 127500532 127506507 5975 False 2685.000000 7675 90.278667 23 5836 3 chr5B.!!$F1 5813
5 TraesCS5A01G090500 chr5B 704277806 704279303 1497 True 1071.000000 1205 92.228500 1260 3609 2 chr5B.!!$R3 2349
6 TraesCS5A01G090500 chr4A 321174256 321175704 1448 True 1991.000000 1991 91.401000 1511 2979 1 chr4A.!!$R2 1468
7 TraesCS5A01G090500 chr4A 321128772 321129404 632 True 937.000000 937 93.365000 2977 3609 1 chr4A.!!$R1 632
8 TraesCS5A01G090500 chr4A 721384825 721385825 1000 False 702.000000 702 79.426000 3787 4793 1 chr4A.!!$F1 1006
9 TraesCS5A01G090500 chr1B 332153199 332154903 1704 True 1223.000000 1284 92.557500 1073 3609 2 chr1B.!!$R3 2536
10 TraesCS5A01G090500 chr1B 122922869 122924252 1383 True 760.500000 929 93.955000 936 2886 2 chr1B.!!$R1 1950
11 TraesCS5A01G090500 chr1B 169940818 169942250 1432 True 674.666667 909 91.952000 1260 3609 3 chr1B.!!$R2 2349
12 TraesCS5A01G090500 chr1A 483640780 483641797 1017 False 1249.000000 1249 88.598000 846 1911 1 chr1A.!!$F1 1065
13 TraesCS5A01G090500 chr4B 564197363 564198861 1498 True 1046.500000 1184 91.647000 1260 3609 2 chr4B.!!$R2 2349
14 TraesCS5A01G090500 chr4B 175548398 175549896 1498 True 1041.000000 1173 91.519000 1260 3609 2 chr4B.!!$R1 2349
15 TraesCS5A01G090500 chr7B 623470471 623471067 596 True 865.000000 865 92.977000 2285 2876 1 chr7B.!!$R1 591
16 TraesCS5A01G090500 chr7B 451354362 451355423 1061 False 726.000000 726 79.259000 3726 4793 1 chr7B.!!$F1 1067
17 TraesCS5A01G090500 chr7B 623266005 623268373 2368 True 497.500000 588 94.125000 936 2544 2 chr7B.!!$R2 1608
18 TraesCS5A01G090500 chr7A 14189524 14190524 1000 True 641.000000 641 78.317000 3787 4793 1 chr7A.!!$R1 1006
19 TraesCS5A01G090500 chr7A 484595340 484596959 1619 False 560.000000 743 80.849500 3120 4793 2 chr7A.!!$F2 1673
20 TraesCS5A01G090500 chr7D 14880448 14881448 1000 True 664.000000 664 78.713000 3787 4793 1 chr7D.!!$R1 1006
21 TraesCS5A01G090500 chr7D 434148241 434149860 1619 False 551.500000 737 80.572000 3120 4793 2 chr7D.!!$F3 1673
22 TraesCS5A01G090500 chr7D 366451927 366452752 825 False 209.000000 209 71.868000 3876 4704 1 chr7D.!!$F1 828

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
826 1161 0.745845 CGCCCCACCTTCAGATTCTG 60.746 60.000 7.38 7.38 0.00 3.02 F
928 1265 0.887836 TGCTGCTGGTTCTTGAGCTG 60.888 55.000 0.00 0.00 36.11 4.24 F
2068 3026 0.239347 CGCTTGCAGCTGCTTAACTT 59.761 50.000 36.61 0.00 39.60 2.66 F
2494 4188 2.261671 GCGCTCCTCACCTTCGAA 59.738 61.111 0.00 0.00 0.00 3.71 F
3623 5348 2.403378 GGAGAGCGAGCACGAGTCT 61.403 63.158 8.01 8.16 42.66 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 3026 0.244994 GAGCAGAGGAAGAAGCGACA 59.755 55.000 0.00 0.00 0.00 4.35 R
2642 4336 0.252103 TACTCCCGCTTCACCTTCCT 60.252 55.000 0.00 0.00 0.00 3.36 R
3857 5588 1.062148 TCGTAGAAGCACGAGATCACG 59.938 52.381 11.16 11.16 45.45 4.35 R
4208 5939 2.182030 GTGAAGAGGGAGACGGCG 59.818 66.667 4.80 4.80 0.00 6.46 R
5591 7498 0.104197 AATCATCTCCCTCCCCCTCC 60.104 60.000 0.00 0.00 0.00 4.30 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
30 31 5.485662 TGATAGACGTGTCTGAGTATGTG 57.514 43.478 12.66 0.00 40.71 3.21
48 49 2.986290 CGTGCCTCCACATACCCA 59.014 61.111 0.00 0.00 42.17 4.51
52 53 2.456577 GTGCCTCCACATACCCATTTT 58.543 47.619 0.00 0.00 41.67 1.82
54 55 2.042297 TGCCTCCACATACCCATTTTGA 59.958 45.455 0.00 0.00 0.00 2.69
100 101 2.602878 GGTCAATTTAGACGACTGCGA 58.397 47.619 0.00 0.00 41.64 5.10
118 119 4.432712 TGCGATCGATTTGAAGAGATCAA 58.567 39.130 21.57 0.00 46.22 2.57
150 151 1.028905 TTTTGTGACCGGGCTTTGAG 58.971 50.000 9.82 0.00 0.00 3.02
183 184 3.056328 GCTCGGTCAGTTTGGGGC 61.056 66.667 0.00 0.00 0.00 5.80
249 574 5.064198 ACACACAACGATCGTAAATTATGGG 59.936 40.000 23.04 18.03 0.00 4.00
386 716 8.135382 AGTTACTAAGCTGGATAAGACAAAGA 57.865 34.615 0.00 0.00 0.00 2.52
431 765 3.071479 CCGTCGAAGGAAAGAAATGGAA 58.929 45.455 12.53 0.00 0.00 3.53
446 780 2.940994 TGGAAAACCCAATCACGAGA 57.059 45.000 0.00 0.00 43.29 4.04
456 790 2.283298 CAATCACGAGATCAACCCCAG 58.717 52.381 0.00 0.00 31.90 4.45
460 795 0.905357 ACGAGATCAACCCCAGGAAG 59.095 55.000 0.00 0.00 0.00 3.46
653 988 1.442857 CACGTCAGAGCCGACTCAC 60.443 63.158 0.35 0.00 46.09 3.51
655 990 1.442857 CGTCAGAGCCGACTCACAC 60.443 63.158 0.35 0.00 46.09 3.82
821 1156 3.636231 CACCGCCCCACCTTCAGA 61.636 66.667 0.00 0.00 0.00 3.27
825 1160 1.604378 CGCCCCACCTTCAGATTCT 59.396 57.895 0.00 0.00 0.00 2.40
826 1161 0.745845 CGCCCCACCTTCAGATTCTG 60.746 60.000 7.38 7.38 0.00 3.02
886 1223 4.873129 TGAGCGCGAGGAATCGGC 62.873 66.667 12.10 1.96 0.00 5.54
897 1234 1.435408 GGAATCGGCTTGAGCTGCTC 61.435 60.000 22.38 22.38 46.62 4.26
928 1265 0.887836 TGCTGCTGGTTCTTGAGCTG 60.888 55.000 0.00 0.00 36.11 4.24
929 1266 1.584380 GCTGCTGGTTCTTGAGCTGG 61.584 60.000 0.00 0.00 36.11 4.85
932 1269 1.377994 CTGGTTCTTGAGCTGGGCT 59.622 57.895 0.00 0.00 43.88 5.19
956 1293 1.952990 TGCTTCTTTGATCGTTTGGCA 59.047 42.857 0.00 0.00 0.00 4.92
988 1333 2.444895 GGAGGAGGCGGAGGTGAT 60.445 66.667 0.00 0.00 0.00 3.06
1068 1413 2.439701 TCGCCGACGAGAGGGAAT 60.440 61.111 0.00 0.00 45.12 3.01
1705 2608 0.887836 CCAGATGCCCATGACATCCG 60.888 60.000 19.25 12.48 44.08 4.18
1756 2659 3.005148 AAGATGCCCATGCCCAGCT 62.005 57.895 0.00 0.00 36.33 4.24
1761 2664 3.766691 CCCATGCCCAGCTGCAAC 61.767 66.667 8.66 0.00 45.84 4.17
2064 3022 3.256936 CACGCTTGCAGCTGCTTA 58.743 55.556 36.61 23.89 39.60 3.09
2068 3026 0.239347 CGCTTGCAGCTGCTTAACTT 59.761 50.000 36.61 0.00 39.60 2.66
2494 4188 2.261671 GCGCTCCTCACCTTCGAA 59.738 61.111 0.00 0.00 0.00 3.71
2824 4533 2.853542 TTGGCAGAGACTGGGGCA 60.854 61.111 0.00 0.00 35.11 5.36
2881 4590 4.643387 GGCACTTGGCTCACCGGT 62.643 66.667 0.00 0.00 44.01 5.28
2930 4639 2.429610 GCTGGCATCATTCAGGTGATTT 59.570 45.455 0.00 0.00 36.72 2.17
2936 4645 5.413833 GGCATCATTCAGGTGATTTATCGAT 59.586 40.000 2.16 2.16 36.72 3.59
2937 4646 6.402983 GGCATCATTCAGGTGATTTATCGATC 60.403 42.308 0.00 0.00 36.72 3.69
2938 4647 6.148315 GCATCATTCAGGTGATTTATCGATCA 59.852 38.462 0.00 0.00 36.72 2.92
2939 4648 7.308169 GCATCATTCAGGTGATTTATCGATCAA 60.308 37.037 0.00 0.00 37.75 2.57
2942 4651 8.777413 TCATTCAGGTGATTTATCGATCAAATC 58.223 33.333 21.17 21.17 40.99 2.17
2946 4655 8.374743 TCAGGTGATTTATCGATCAAATCCATA 58.625 33.333 23.05 12.00 40.25 2.74
2947 4656 8.446273 CAGGTGATTTATCGATCAAATCCATAC 58.554 37.037 23.05 18.12 40.25 2.39
3022 4743 8.985315 AAATGCTCATGTATCTTCTCCAATTA 57.015 30.769 0.00 0.00 0.00 1.40
3623 5348 2.403378 GGAGAGCGAGCACGAGTCT 61.403 63.158 8.01 8.16 42.66 3.24
4208 5939 2.184579 GTCTACTGCGTGCTCCCC 59.815 66.667 0.00 0.00 0.00 4.81
4840 6574 0.320374 TTCAGCTTCCCGTAGTGGTG 59.680 55.000 0.00 0.00 35.15 4.17
4910 6646 6.939730 TGCTTCATGGAGTTCAGTTATTGTTA 59.060 34.615 2.16 0.00 0.00 2.41
4936 6672 3.629398 GCTGTTTGATGGTGGATTCCTAG 59.371 47.826 3.95 0.00 0.00 3.02
4938 6674 3.591527 TGTTTGATGGTGGATTCCTAGGT 59.408 43.478 9.08 0.00 0.00 3.08
4957 6693 1.067283 GTAGCTGAGCTCAACTGCTGA 60.067 52.381 29.43 15.93 44.17 4.26
4959 6695 1.003349 AGCTGAGCTCAACTGCTGATT 59.997 47.619 23.72 4.48 44.17 2.57
4962 6698 3.626670 GCTGAGCTCAACTGCTGATTTAT 59.373 43.478 18.85 0.00 44.17 1.40
5084 6835 5.983540 AGCTAGAAATACTTGGAGTTCAGG 58.016 41.667 0.00 0.00 0.00 3.86
5118 6887 7.865706 ACCATAATACTCTTGTCACATTTCC 57.134 36.000 0.00 0.00 0.00 3.13
5139 6916 2.715046 GGTGATTCAGAGCCATTGTGA 58.285 47.619 0.00 0.00 0.00 3.58
5218 7012 2.356125 GGCCAAGCGGATATGACCATAT 60.356 50.000 0.00 2.40 36.75 1.78
5222 7016 4.393062 CCAAGCGGATATGACCATATTCAC 59.607 45.833 8.55 0.07 34.36 3.18
5368 7188 7.116233 GTCACAAAACCAAATTGCTCGAATATT 59.884 33.333 0.00 0.00 0.00 1.28
5369 7189 7.655328 TCACAAAACCAAATTGCTCGAATATTT 59.345 29.630 0.00 0.00 0.00 1.40
5370 7190 8.920665 CACAAAACCAAATTGCTCGAATATTTA 58.079 29.630 0.00 0.00 0.00 1.40
5412 7286 5.741982 AGCAACTTTCACACGAACAATTTAC 59.258 36.000 0.00 0.00 0.00 2.01
5421 7328 7.569297 TCACACGAACAATTTACTATGTTGAC 58.431 34.615 0.00 0.00 39.73 3.18
5430 7337 8.372459 ACAATTTACTATGTTGACCAGTCAGTA 58.628 33.333 0.09 0.00 41.13 2.74
5449 7356 4.588899 AGTAATTTACTGCCATGCTGTGA 58.411 39.130 8.27 0.00 40.67 3.58
5469 7376 7.412346 GCTGTGATGTTGTTGTCTAATACAGAG 60.412 40.741 0.00 0.00 39.87 3.35
5478 7385 2.432510 GTCTAATACAGAGCTGCCACCT 59.567 50.000 0.00 0.00 32.51 4.00
5479 7386 3.637229 GTCTAATACAGAGCTGCCACCTA 59.363 47.826 0.00 0.00 32.51 3.08
5480 7387 3.891977 TCTAATACAGAGCTGCCACCTAG 59.108 47.826 0.00 0.00 0.00 3.02
5481 7388 1.418334 ATACAGAGCTGCCACCTAGG 58.582 55.000 7.41 7.41 41.84 3.02
5482 7389 0.687757 TACAGAGCTGCCACCTAGGG 60.688 60.000 14.81 1.73 38.09 3.53
5483 7390 1.687146 CAGAGCTGCCACCTAGGGA 60.687 63.158 14.81 0.00 38.09 4.20
5484 7391 1.687493 AGAGCTGCCACCTAGGGAC 60.687 63.158 14.81 2.12 38.09 4.46
5485 7392 3.077556 AGCTGCCACCTAGGGACG 61.078 66.667 14.81 0.54 38.09 4.79
5486 7393 3.075005 GCTGCCACCTAGGGACGA 61.075 66.667 14.81 0.00 38.09 4.20
5487 7394 3.082579 GCTGCCACCTAGGGACGAG 62.083 68.421 14.81 4.80 38.09 4.18
5488 7395 1.379977 CTGCCACCTAGGGACGAGA 60.380 63.158 14.81 0.00 38.09 4.04
5489 7396 1.668101 CTGCCACCTAGGGACGAGAC 61.668 65.000 14.81 0.00 38.09 3.36
5490 7397 1.380112 GCCACCTAGGGACGAGACT 60.380 63.158 14.81 0.00 38.09 3.24
5491 7398 0.971447 GCCACCTAGGGACGAGACTT 60.971 60.000 14.81 0.00 38.09 3.01
5492 7399 0.818296 CCACCTAGGGACGAGACTTG 59.182 60.000 14.81 0.00 30.78 3.16
5493 7400 0.173708 CACCTAGGGACGAGACTTGC 59.826 60.000 14.81 0.00 30.78 4.01
5494 7401 0.971447 ACCTAGGGACGAGACTTGCC 60.971 60.000 14.81 0.00 30.78 4.52
5495 7402 0.684805 CCTAGGGACGAGACTTGCCT 60.685 60.000 0.00 0.00 38.55 4.75
5496 7403 0.457851 CTAGGGACGAGACTTGCCTG 59.542 60.000 0.00 0.00 35.22 4.85
5497 7404 1.605058 TAGGGACGAGACTTGCCTGC 61.605 60.000 0.00 0.00 35.22 4.85
5498 7405 2.659610 GGACGAGACTTGCCTGCT 59.340 61.111 0.00 0.00 0.00 4.24
5499 7406 1.446966 GGACGAGACTTGCCTGCTC 60.447 63.158 0.00 0.00 0.00 4.26
5500 7407 1.446966 GACGAGACTTGCCTGCTCC 60.447 63.158 0.00 0.00 0.00 4.70
5501 7408 2.125350 CGAGACTTGCCTGCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
5502 7409 2.270527 GAGACTTGCCTGCTCCCC 59.729 66.667 0.00 0.00 0.00 4.81
5503 7410 3.334054 AGACTTGCCTGCTCCCCC 61.334 66.667 0.00 0.00 0.00 5.40
5504 7411 4.785453 GACTTGCCTGCTCCCCCG 62.785 72.222 0.00 0.00 0.00 5.73
5522 7429 4.107051 GCGTGTGCCCATCTGTGC 62.107 66.667 0.00 0.00 33.98 4.57
5523 7430 2.359107 CGTGTGCCCATCTGTGCT 60.359 61.111 0.00 0.00 0.00 4.40
5524 7431 2.393768 CGTGTGCCCATCTGTGCTC 61.394 63.158 0.00 0.00 0.00 4.26
5525 7432 2.042831 GTGTGCCCATCTGTGCTCC 61.043 63.158 0.00 0.00 0.00 4.70
5526 7433 2.439156 GTGCCCATCTGTGCTCCC 60.439 66.667 0.00 0.00 0.00 4.30
5527 7434 2.934932 TGCCCATCTGTGCTCCCA 60.935 61.111 0.00 0.00 0.00 4.37
5528 7435 2.439156 GCCCATCTGTGCTCCCAC 60.439 66.667 0.00 0.00 42.40 4.61
5529 7436 2.124983 CCCATCTGTGCTCCCACG 60.125 66.667 0.00 0.00 45.04 4.94
5530 7437 2.665000 CCATCTGTGCTCCCACGT 59.335 61.111 0.00 0.00 45.04 4.49
5531 7438 1.613317 CCCATCTGTGCTCCCACGTA 61.613 60.000 0.00 0.00 45.04 3.57
5532 7439 0.460284 CCATCTGTGCTCCCACGTAC 60.460 60.000 0.00 0.00 45.04 3.67
5533 7440 0.802222 CATCTGTGCTCCCACGTACG 60.802 60.000 15.01 15.01 45.04 3.67
5534 7441 1.248785 ATCTGTGCTCCCACGTACGT 61.249 55.000 16.72 16.72 45.04 3.57
5535 7442 1.733041 CTGTGCTCCCACGTACGTG 60.733 63.158 35.57 35.57 45.04 4.49
5547 7454 4.593597 CACGTACGTGGCTTGATTTAAT 57.406 40.909 35.09 0.00 42.00 1.40
5548 7455 4.965062 CACGTACGTGGCTTGATTTAATT 58.035 39.130 35.09 0.00 42.00 1.40
5549 7456 4.786068 CACGTACGTGGCTTGATTTAATTG 59.214 41.667 35.09 8.58 42.00 2.32
5550 7457 4.142773 ACGTACGTGGCTTGATTTAATTGG 60.143 41.667 22.14 0.00 0.00 3.16
5551 7458 4.093703 CGTACGTGGCTTGATTTAATTGGA 59.906 41.667 7.22 0.00 0.00 3.53
5552 7459 5.391097 CGTACGTGGCTTGATTTAATTGGAA 60.391 40.000 7.22 0.00 0.00 3.53
5553 7460 5.659440 ACGTGGCTTGATTTAATTGGAAT 57.341 34.783 0.00 0.00 0.00 3.01
5554 7461 6.767524 ACGTGGCTTGATTTAATTGGAATA 57.232 33.333 0.00 0.00 0.00 1.75
5555 7462 7.164230 ACGTGGCTTGATTTAATTGGAATAA 57.836 32.000 0.00 0.00 0.00 1.40
5556 7463 7.607250 ACGTGGCTTGATTTAATTGGAATAAA 58.393 30.769 0.00 0.00 0.00 1.40
5557 7464 8.091449 ACGTGGCTTGATTTAATTGGAATAAAA 58.909 29.630 0.00 0.00 0.00 1.52
5558 7465 9.097257 CGTGGCTTGATTTAATTGGAATAAAAT 57.903 29.630 0.00 0.00 0.00 1.82
5568 7475 8.826293 TTAATTGGAATAAAATAAGACCCGGT 57.174 30.769 0.00 0.00 0.00 5.28
5569 7476 6.954487 ATTGGAATAAAATAAGACCCGGTC 57.046 37.500 9.81 9.81 0.00 4.79
5570 7477 4.784177 TGGAATAAAATAAGACCCGGTCC 58.216 43.478 14.32 0.00 32.18 4.46
5571 7478 4.139786 GGAATAAAATAAGACCCGGTCCC 58.860 47.826 14.32 0.35 32.18 4.46
5572 7479 4.385532 GGAATAAAATAAGACCCGGTCCCA 60.386 45.833 14.32 2.49 32.18 4.37
5573 7480 2.502142 AAAATAAGACCCGGTCCCAC 57.498 50.000 14.32 0.00 32.18 4.61
5574 7481 0.622136 AAATAAGACCCGGTCCCACC 59.378 55.000 14.32 0.00 32.18 4.61
5575 7482 1.276859 AATAAGACCCGGTCCCACCC 61.277 60.000 14.32 0.00 33.75 4.61
5576 7483 3.929723 TAAGACCCGGTCCCACCCC 62.930 68.421 14.32 0.00 33.75 4.95
5580 7487 4.745013 CCCGGTCCCACCCCCTTA 62.745 72.222 0.00 0.00 33.75 2.69
5581 7488 2.611486 CCGGTCCCACCCCCTTAA 60.611 66.667 0.00 0.00 33.75 1.85
5582 7489 2.232836 CCGGTCCCACCCCCTTAAA 61.233 63.158 0.00 0.00 33.75 1.52
5583 7490 1.769006 CGGTCCCACCCCCTTAAAA 59.231 57.895 0.00 0.00 33.75 1.52
5584 7491 0.333652 CGGTCCCACCCCCTTAAAAT 59.666 55.000 0.00 0.00 33.75 1.82
5585 7492 1.683938 CGGTCCCACCCCCTTAAAATC 60.684 57.143 0.00 0.00 33.75 2.17
5586 7493 1.359818 GGTCCCACCCCCTTAAAATCA 59.640 52.381 0.00 0.00 30.04 2.57
5587 7494 2.623239 GGTCCCACCCCCTTAAAATCAG 60.623 54.545 0.00 0.00 30.04 2.90
5588 7495 1.643811 TCCCACCCCCTTAAAATCAGG 59.356 52.381 0.00 0.00 0.00 3.86
5606 7513 3.462501 GGGGAGGGGGAGGGAGAT 61.463 72.222 0.00 0.00 0.00 2.75
5607 7514 2.122189 GGGAGGGGGAGGGAGATG 60.122 72.222 0.00 0.00 0.00 2.90
5608 7515 2.727071 GGGAGGGGGAGGGAGATGA 61.727 68.421 0.00 0.00 0.00 2.92
5609 7516 1.556561 GGAGGGGGAGGGAGATGAT 59.443 63.158 0.00 0.00 0.00 2.45
5610 7517 0.104197 GGAGGGGGAGGGAGATGATT 60.104 60.000 0.00 0.00 0.00 2.57
5611 7518 1.152271 GGAGGGGGAGGGAGATGATTA 59.848 57.143 0.00 0.00 0.00 1.75
5612 7519 2.545810 GAGGGGGAGGGAGATGATTAG 58.454 57.143 0.00 0.00 0.00 1.73
5613 7520 2.112691 GAGGGGGAGGGAGATGATTAGA 59.887 54.545 0.00 0.00 0.00 2.10
5614 7521 2.738186 AGGGGGAGGGAGATGATTAGAT 59.262 50.000 0.00 0.00 0.00 1.98
5615 7522 3.147615 AGGGGGAGGGAGATGATTAGATT 59.852 47.826 0.00 0.00 0.00 2.40
5616 7523 3.521531 GGGGGAGGGAGATGATTAGATTC 59.478 52.174 0.00 0.00 0.00 2.52
5617 7524 3.196685 GGGGAGGGAGATGATTAGATTCG 59.803 52.174 0.00 0.00 0.00 3.34
5618 7525 4.090090 GGGAGGGAGATGATTAGATTCGA 58.910 47.826 0.00 0.00 0.00 3.71
5619 7526 4.528596 GGGAGGGAGATGATTAGATTCGAA 59.471 45.833 0.00 0.00 0.00 3.71
5620 7527 5.012148 GGGAGGGAGATGATTAGATTCGAAA 59.988 44.000 0.00 0.00 0.00 3.46
5621 7528 6.162777 GGAGGGAGATGATTAGATTCGAAAG 58.837 44.000 0.00 0.00 0.00 2.62
5622 7529 6.107901 AGGGAGATGATTAGATTCGAAAGG 57.892 41.667 0.00 0.00 0.00 3.11
5623 7530 5.841237 AGGGAGATGATTAGATTCGAAAGGA 59.159 40.000 0.00 0.00 0.00 3.36
5624 7531 6.327626 AGGGAGATGATTAGATTCGAAAGGAA 59.672 38.462 0.00 0.00 39.42 3.36
5625 7532 6.992715 GGGAGATGATTAGATTCGAAAGGAAA 59.007 38.462 0.00 0.00 38.36 3.13
5626 7533 7.172361 GGGAGATGATTAGATTCGAAAGGAAAG 59.828 40.741 0.00 0.00 38.36 2.62
5627 7534 7.928706 GGAGATGATTAGATTCGAAAGGAAAGA 59.071 37.037 0.00 0.00 38.36 2.52
5628 7535 9.319143 GAGATGATTAGATTCGAAAGGAAAGAA 57.681 33.333 0.00 0.00 38.36 2.52
5629 7536 9.323985 AGATGATTAGATTCGAAAGGAAAGAAG 57.676 33.333 0.00 0.00 38.36 2.85
5630 7537 9.319143 GATGATTAGATTCGAAAGGAAAGAAGA 57.681 33.333 0.00 0.00 38.36 2.87
5631 7538 9.672673 ATGATTAGATTCGAAAGGAAAGAAGAA 57.327 29.630 0.00 0.00 38.36 2.52
5632 7539 9.502091 TGATTAGATTCGAAAGGAAAGAAGAAA 57.498 29.630 0.00 0.00 38.36 2.52
5660 7567 3.669354 CGTAGGATGAAGTGGGAGC 57.331 57.895 0.00 0.00 0.00 4.70
5661 7568 0.824109 CGTAGGATGAAGTGGGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
5662 7569 1.471676 CGTAGGATGAAGTGGGAGCAC 60.472 57.143 0.00 0.00 0.00 4.40
5663 7570 0.824109 TAGGATGAAGTGGGAGCACG 59.176 55.000 0.00 0.00 0.00 5.34
5664 7571 1.450312 GGATGAAGTGGGAGCACGG 60.450 63.158 0.00 0.00 0.00 4.94
5665 7572 1.596934 GATGAAGTGGGAGCACGGA 59.403 57.895 0.00 0.00 0.00 4.69
5666 7573 0.179000 GATGAAGTGGGAGCACGGAT 59.821 55.000 0.00 0.00 0.00 4.18
5667 7574 1.412710 GATGAAGTGGGAGCACGGATA 59.587 52.381 0.00 0.00 0.00 2.59
5668 7575 0.824109 TGAAGTGGGAGCACGGATAG 59.176 55.000 0.00 0.00 0.00 2.08
5669 7576 0.105039 GAAGTGGGAGCACGGATAGG 59.895 60.000 0.00 0.00 0.00 2.57
5670 7577 0.325296 AAGTGGGAGCACGGATAGGA 60.325 55.000 0.00 0.00 0.00 2.94
5671 7578 0.757188 AGTGGGAGCACGGATAGGAG 60.757 60.000 0.00 0.00 0.00 3.69
5672 7579 2.134287 TGGGAGCACGGATAGGAGC 61.134 63.158 0.00 0.00 0.00 4.70
5673 7580 2.134287 GGGAGCACGGATAGGAGCA 61.134 63.158 0.00 0.00 0.00 4.26
5674 7581 1.476007 GGGAGCACGGATAGGAGCAT 61.476 60.000 0.00 0.00 0.00 3.79
5675 7582 0.320247 GGAGCACGGATAGGAGCATG 60.320 60.000 0.00 0.00 0.00 4.06
5676 7583 0.676184 GAGCACGGATAGGAGCATGA 59.324 55.000 0.00 0.00 0.00 3.07
5677 7584 1.069204 GAGCACGGATAGGAGCATGAA 59.931 52.381 0.00 0.00 0.00 2.57
5678 7585 1.486310 AGCACGGATAGGAGCATGAAA 59.514 47.619 0.00 0.00 0.00 2.69
5679 7586 2.092968 AGCACGGATAGGAGCATGAAAA 60.093 45.455 0.00 0.00 0.00 2.29
5680 7587 2.289002 GCACGGATAGGAGCATGAAAAG 59.711 50.000 0.00 0.00 0.00 2.27
5681 7588 2.874701 CACGGATAGGAGCATGAAAAGG 59.125 50.000 0.00 0.00 0.00 3.11
5682 7589 2.158755 ACGGATAGGAGCATGAAAAGGG 60.159 50.000 0.00 0.00 0.00 3.95
5683 7590 2.104792 CGGATAGGAGCATGAAAAGGGA 59.895 50.000 0.00 0.00 0.00 4.20
5684 7591 3.749226 GGATAGGAGCATGAAAAGGGAG 58.251 50.000 0.00 0.00 0.00 4.30
5685 7592 2.717639 TAGGAGCATGAAAAGGGAGC 57.282 50.000 0.00 0.00 0.00 4.70
5686 7593 0.700564 AGGAGCATGAAAAGGGAGCA 59.299 50.000 0.00 0.00 0.00 4.26
5687 7594 1.101331 GGAGCATGAAAAGGGAGCAG 58.899 55.000 0.00 0.00 0.00 4.24
5688 7595 1.101331 GAGCATGAAAAGGGAGCAGG 58.899 55.000 0.00 0.00 0.00 4.85
5689 7596 0.969409 AGCATGAAAAGGGAGCAGGC 60.969 55.000 0.00 0.00 39.38 4.85
5690 7597 1.252904 GCATGAAAAGGGAGCAGGCA 61.253 55.000 0.00 0.00 38.97 4.75
5691 7598 1.259609 CATGAAAAGGGAGCAGGCAA 58.740 50.000 0.00 0.00 0.00 4.52
5692 7599 1.203994 CATGAAAAGGGAGCAGGCAAG 59.796 52.381 0.00 0.00 0.00 4.01
5693 7600 1.181098 TGAAAAGGGAGCAGGCAAGC 61.181 55.000 0.00 0.00 0.00 4.01
5694 7601 1.881903 GAAAAGGGAGCAGGCAAGCC 61.882 60.000 2.02 2.02 34.23 4.35
5695 7602 4.729918 AAGGGAGCAGGCAAGCCG 62.730 66.667 5.28 2.12 41.95 5.52
5698 7605 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
5699 7606 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
5700 7607 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
5757 7664 2.238144 CAGAGTGTCCTGAATGTGGGAT 59.762 50.000 0.00 0.00 36.29 3.85
5763 7670 3.165071 GTCCTGAATGTGGGATTTTGGT 58.835 45.455 0.00 0.00 33.89 3.67
5768 7675 4.594970 TGAATGTGGGATTTTGGTCGTAT 58.405 39.130 0.00 0.00 0.00 3.06
5769 7676 4.638421 TGAATGTGGGATTTTGGTCGTATC 59.362 41.667 0.00 0.00 0.00 2.24
5785 7692 1.138464 GTATCGGTGACCTTTCTCCCC 59.862 57.143 0.00 0.00 32.49 4.81
5815 7723 2.153247 CGTACAACTCTTGTCGCAACTC 59.847 50.000 0.00 0.00 44.12 3.01
5830 7738 2.863704 GCAACTCGATTTTGCCTGCTTT 60.864 45.455 17.19 0.00 43.02 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.201920 GCACATACTCAGACACGTCTATCA 60.202 45.833 0.00 0.00 37.98 2.15
9 10 4.283678 GCACATACTCAGACACGTCTATC 58.716 47.826 0.00 0.00 37.98 2.08
15 16 0.984829 CACGCACATACTCAGACACG 59.015 55.000 0.00 0.00 0.00 4.49
17 18 0.389817 GGCACGCACATACTCAGACA 60.390 55.000 0.00 0.00 0.00 3.41
19 20 0.173481 GAGGCACGCACATACTCAGA 59.827 55.000 0.00 0.00 0.00 3.27
21 22 1.218047 GGAGGCACGCACATACTCA 59.782 57.895 0.00 0.00 0.00 3.41
27 28 1.375396 GTATGTGGAGGCACGCACA 60.375 57.895 8.19 8.19 35.44 4.57
30 31 2.513897 GGGTATGTGGAGGCACGC 60.514 66.667 0.00 0.00 0.00 5.34
48 49 6.936335 CCTCAAACCAAGCCTAAATTCAAAAT 59.064 34.615 0.00 0.00 0.00 1.82
52 53 3.831911 CCCTCAAACCAAGCCTAAATTCA 59.168 43.478 0.00 0.00 0.00 2.57
54 55 3.173151 CCCCTCAAACCAAGCCTAAATT 58.827 45.455 0.00 0.00 0.00 1.82
118 119 5.123820 CCGGTCACAAAATCATGATACAGTT 59.876 40.000 9.04 0.00 0.00 3.16
183 184 2.048877 ACGAACTACAACCCCGCG 60.049 61.111 0.00 0.00 0.00 6.46
249 574 0.172578 ATGTCACATGTGCATGCTGC 59.827 50.000 25.16 12.29 45.29 5.25
362 690 8.773404 TTCTTTGTCTTATCCAGCTTAGTAAC 57.227 34.615 0.00 0.00 0.00 2.50
363 691 9.787435 TTTTCTTTGTCTTATCCAGCTTAGTAA 57.213 29.630 0.00 0.00 0.00 2.24
431 765 3.081804 GGTTGATCTCGTGATTGGGTTT 58.918 45.455 0.87 0.00 32.19 3.27
446 780 2.677228 CGGCTTCCTGGGGTTGAT 59.323 61.111 0.00 0.00 0.00 2.57
554 889 1.089920 CTGAGGTTTGATTCGGCTGG 58.910 55.000 0.00 0.00 0.00 4.85
821 1156 7.753132 GTCGAAATTATAGCGAGATCTCAGAAT 59.247 37.037 22.31 13.28 34.41 2.40
825 1160 5.240844 TGGTCGAAATTATAGCGAGATCTCA 59.759 40.000 22.31 3.55 34.41 3.27
826 1161 5.569823 GTGGTCGAAATTATAGCGAGATCTC 59.430 44.000 13.05 13.05 34.41 2.75
932 1269 3.253188 CCAAACGATCAAAGAAGCAGGAA 59.747 43.478 0.00 0.00 0.00 3.36
956 1293 4.021916 CCTCCTCCAAATCAGCTCAAAAT 58.978 43.478 0.00 0.00 0.00 1.82
988 1333 3.014085 GCGACATCCCTCCACCGAA 62.014 63.158 0.00 0.00 0.00 4.30
1482 1976 1.448893 GTTGAGGAACGCCGGCATA 60.449 57.895 28.98 0.00 39.96 3.14
1593 2087 4.096003 TACGCCTCCTTGCAGCCC 62.096 66.667 0.00 0.00 0.00 5.19
1705 2608 0.674895 ATGGAGAAGCGCTTGGACAC 60.675 55.000 30.47 12.92 0.00 3.67
1845 2748 0.815615 GCTCGTTCTTGGGCCATAGG 60.816 60.000 7.26 0.58 0.00 2.57
1887 2793 3.310860 GACGAATCCGGTGGTGGCT 62.311 63.158 0.00 0.00 40.78 4.75
2064 3022 2.760374 CAGAGGAAGAAGCGACAAGTT 58.240 47.619 0.00 0.00 0.00 2.66
2068 3026 0.244994 GAGCAGAGGAAGAAGCGACA 59.755 55.000 0.00 0.00 0.00 4.35
2401 4094 2.507471 GAGGATGGAGAGGATGGTGTTT 59.493 50.000 0.00 0.00 0.00 2.83
2642 4336 0.252103 TACTCCCGCTTCACCTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
2824 4533 0.615331 ACATCCATGTCGCCTTCACT 59.385 50.000 0.00 0.00 35.87 3.41
2930 4639 6.765512 TGCAACAAGTATGGATTTGATCGATA 59.234 34.615 0.00 0.00 0.00 2.92
2936 4645 4.081406 AGCTGCAACAAGTATGGATTTGA 58.919 39.130 1.02 0.00 0.00 2.69
2937 4646 4.082625 TCAGCTGCAACAAGTATGGATTTG 60.083 41.667 9.47 0.00 0.00 2.32
2938 4647 4.081406 TCAGCTGCAACAAGTATGGATTT 58.919 39.130 9.47 0.00 0.00 2.17
2939 4648 3.441572 GTCAGCTGCAACAAGTATGGATT 59.558 43.478 9.47 0.00 0.00 3.01
2942 4651 2.095567 GTGTCAGCTGCAACAAGTATGG 60.096 50.000 9.47 0.00 0.00 2.74
2946 4655 1.462616 TTGTGTCAGCTGCAACAAGT 58.537 45.000 22.57 0.00 0.00 3.16
2947 4656 2.565210 TTTGTGTCAGCTGCAACAAG 57.435 45.000 24.07 0.00 0.00 3.16
3022 4743 1.137404 GCCTGCGCGTTCATCAATT 59.863 52.632 8.43 0.00 0.00 2.32
3857 5588 1.062148 TCGTAGAAGCACGAGATCACG 59.938 52.381 11.16 11.16 45.45 4.35
4013 5744 3.379865 GAGGTTGATGGGCGCGGTA 62.380 63.158 8.83 0.00 0.00 4.02
4208 5939 2.182030 GTGAAGAGGGAGACGGCG 59.818 66.667 4.80 4.80 0.00 6.46
4721 6455 3.036026 CCAGACGAAGACGATGGTG 57.964 57.895 0.00 0.00 41.28 4.17
4840 6574 3.674997 TCAGATGAACTTGGTAACTGCC 58.325 45.455 0.00 0.00 37.61 4.85
4882 6618 2.157738 ACTGAACTCCATGAAGCAAGC 58.842 47.619 0.00 0.00 0.00 4.01
4910 6646 4.265073 GAATCCACCATCAAACAGCTACT 58.735 43.478 0.00 0.00 0.00 2.57
4936 6672 0.248843 AGCAGTTGAGCTCAGCTACC 59.751 55.000 29.63 22.66 42.18 3.18
4938 6674 1.260544 TCAGCAGTTGAGCTCAGCTA 58.739 50.000 29.63 13.98 44.54 3.32
5098 6849 5.872617 CACCGGAAATGTGACAAGAGTATTA 59.127 40.000 9.46 0.00 35.74 0.98
5099 6850 4.695455 CACCGGAAATGTGACAAGAGTATT 59.305 41.667 9.46 0.00 35.74 1.89
5100 6851 4.020573 TCACCGGAAATGTGACAAGAGTAT 60.021 41.667 9.46 0.00 37.80 2.12
5101 6852 3.322541 TCACCGGAAATGTGACAAGAGTA 59.677 43.478 9.46 0.00 37.80 2.59
5118 6887 1.399440 CACAATGGCTCTGAATCACCG 59.601 52.381 0.00 0.00 0.00 4.94
5139 6916 5.659440 ATTCACAAGTGACCAAAGTTGTT 57.341 34.783 1.73 0.00 40.85 2.83
5332 7129 3.278574 TGGTTTTGTGACACCTTCTGAG 58.721 45.455 2.45 0.00 33.76 3.35
5339 7136 3.530535 AGCAATTTGGTTTTGTGACACC 58.469 40.909 2.45 0.00 0.00 4.16
5340 7137 3.242712 CGAGCAATTTGGTTTTGTGACAC 59.757 43.478 2.14 0.00 0.00 3.67
5430 7337 3.765511 ACATCACAGCATGGCAGTAAATT 59.234 39.130 0.00 0.00 43.62 1.82
5449 7356 5.352569 GCAGCTCTGTATTAGACAACAACAT 59.647 40.000 0.00 0.00 37.70 2.71
5469 7376 3.075005 TCGTCCCTAGGTGGCAGC 61.075 66.667 9.02 9.02 0.00 5.25
5478 7385 1.605058 GCAGGCAAGTCTCGTCCCTA 61.605 60.000 0.00 0.00 0.00 3.53
5479 7386 2.948720 GCAGGCAAGTCTCGTCCCT 61.949 63.158 0.00 0.00 0.00 4.20
5480 7387 2.435059 GCAGGCAAGTCTCGTCCC 60.435 66.667 0.00 0.00 0.00 4.46
5481 7388 1.446966 GAGCAGGCAAGTCTCGTCC 60.447 63.158 0.00 0.00 0.00 4.79
5482 7389 1.446966 GGAGCAGGCAAGTCTCGTC 60.447 63.158 0.00 0.00 0.00 4.20
5483 7390 2.659610 GGAGCAGGCAAGTCTCGT 59.340 61.111 0.00 0.00 0.00 4.18
5484 7391 2.125350 GGGAGCAGGCAAGTCTCG 60.125 66.667 0.00 0.00 0.00 4.04
5485 7392 2.270527 GGGGAGCAGGCAAGTCTC 59.729 66.667 0.00 0.00 0.00 3.36
5486 7393 3.334054 GGGGGAGCAGGCAAGTCT 61.334 66.667 0.00 0.00 0.00 3.24
5487 7394 4.785453 CGGGGGAGCAGGCAAGTC 62.785 72.222 0.00 0.00 0.00 3.01
5505 7412 4.107051 GCACAGATGGGCACACGC 62.107 66.667 1.27 0.00 45.57 5.34
5511 7418 2.439156 GTGGGAGCACAGATGGGC 60.439 66.667 0.00 0.00 46.94 5.36
5512 7419 1.613317 TACGTGGGAGCACAGATGGG 61.613 60.000 0.00 0.00 0.00 4.00
5513 7420 0.460284 GTACGTGGGAGCACAGATGG 60.460 60.000 0.00 0.00 0.00 3.51
5514 7421 0.802222 CGTACGTGGGAGCACAGATG 60.802 60.000 7.22 0.00 0.00 2.90
5515 7422 1.248785 ACGTACGTGGGAGCACAGAT 61.249 55.000 22.14 0.00 0.00 2.90
5516 7423 1.900016 ACGTACGTGGGAGCACAGA 60.900 57.895 22.14 0.00 0.00 3.41
5517 7424 1.733041 CACGTACGTGGGAGCACAG 60.733 63.158 35.09 11.03 42.00 3.66
5518 7425 2.337170 CACGTACGTGGGAGCACA 59.663 61.111 35.09 0.00 42.00 4.57
5526 7433 4.593597 ATTAAATCAAGCCACGTACGTG 57.406 40.909 35.57 35.57 45.02 4.49
5527 7434 4.142773 CCAATTAAATCAAGCCACGTACGT 60.143 41.667 16.72 16.72 0.00 3.57
5528 7435 4.093703 TCCAATTAAATCAAGCCACGTACG 59.906 41.667 15.01 15.01 0.00 3.67
5529 7436 5.554822 TCCAATTAAATCAAGCCACGTAC 57.445 39.130 0.00 0.00 0.00 3.67
5530 7437 6.767524 ATTCCAATTAAATCAAGCCACGTA 57.232 33.333 0.00 0.00 0.00 3.57
5531 7438 5.659440 ATTCCAATTAAATCAAGCCACGT 57.341 34.783 0.00 0.00 0.00 4.49
5532 7439 8.472683 TTTTATTCCAATTAAATCAAGCCACG 57.527 30.769 0.00 0.00 0.00 4.94
5542 7449 9.257428 ACCGGGTCTTATTTTATTCCAATTAAA 57.743 29.630 6.32 0.00 0.00 1.52
5543 7450 8.826293 ACCGGGTCTTATTTTATTCCAATTAA 57.174 30.769 6.32 0.00 0.00 1.40
5544 7451 7.503230 GGACCGGGTCTTATTTTATTCCAATTA 59.497 37.037 25.39 0.00 32.47 1.40
5545 7452 6.322969 GGACCGGGTCTTATTTTATTCCAATT 59.677 38.462 25.39 0.00 32.47 2.32
5546 7453 5.831525 GGACCGGGTCTTATTTTATTCCAAT 59.168 40.000 25.39 0.00 32.47 3.16
5547 7454 5.195185 GGACCGGGTCTTATTTTATTCCAA 58.805 41.667 25.39 0.00 32.47 3.53
5548 7455 4.385532 GGGACCGGGTCTTATTTTATTCCA 60.386 45.833 25.39 0.00 32.47 3.53
5549 7456 4.139786 GGGACCGGGTCTTATTTTATTCC 58.860 47.826 25.39 11.00 32.47 3.01
5550 7457 4.577693 GTGGGACCGGGTCTTATTTTATTC 59.422 45.833 25.39 5.74 32.47 1.75
5551 7458 4.529897 GTGGGACCGGGTCTTATTTTATT 58.470 43.478 25.39 0.00 32.47 1.40
5552 7459 3.117776 GGTGGGACCGGGTCTTATTTTAT 60.118 47.826 25.39 0.00 32.47 1.40
5553 7460 2.239402 GGTGGGACCGGGTCTTATTTTA 59.761 50.000 25.39 3.32 32.47 1.52
5554 7461 1.005097 GGTGGGACCGGGTCTTATTTT 59.995 52.381 25.39 0.00 32.47 1.82
5555 7462 0.622136 GGTGGGACCGGGTCTTATTT 59.378 55.000 25.39 0.00 32.47 1.40
5556 7463 1.276859 GGGTGGGACCGGGTCTTATT 61.277 60.000 25.39 0.00 39.83 1.40
5557 7464 1.691689 GGGTGGGACCGGGTCTTAT 60.692 63.158 25.39 0.00 39.83 1.73
5558 7465 2.284847 GGGTGGGACCGGGTCTTA 60.285 66.667 25.39 12.68 39.83 2.10
5563 7470 4.745013 TAAGGGGGTGGGACCGGG 62.745 72.222 6.32 0.00 39.83 5.73
5564 7471 1.791695 TTTTAAGGGGGTGGGACCGG 61.792 60.000 0.00 0.00 39.83 5.28
5565 7472 0.333652 ATTTTAAGGGGGTGGGACCG 59.666 55.000 0.00 0.00 39.83 4.79
5566 7473 1.359818 TGATTTTAAGGGGGTGGGACC 59.640 52.381 0.00 0.00 37.60 4.46
5567 7474 2.623239 CCTGATTTTAAGGGGGTGGGAC 60.623 54.545 0.00 0.00 0.00 4.46
5568 7475 1.643811 CCTGATTTTAAGGGGGTGGGA 59.356 52.381 0.00 0.00 0.00 4.37
5569 7476 2.159179 CCTGATTTTAAGGGGGTGGG 57.841 55.000 0.00 0.00 0.00 4.61
5589 7496 3.462501 ATCTCCCTCCCCCTCCCC 61.463 72.222 0.00 0.00 0.00 4.81
5590 7497 2.054834 ATCATCTCCCTCCCCCTCCC 62.055 65.000 0.00 0.00 0.00 4.30
5591 7498 0.104197 AATCATCTCCCTCCCCCTCC 60.104 60.000 0.00 0.00 0.00 4.30
5592 7499 2.112691 TCTAATCATCTCCCTCCCCCTC 59.887 54.545 0.00 0.00 0.00 4.30
5593 7500 2.165112 TCTAATCATCTCCCTCCCCCT 58.835 52.381 0.00 0.00 0.00 4.79
5594 7501 2.723530 TCTAATCATCTCCCTCCCCC 57.276 55.000 0.00 0.00 0.00 5.40
5595 7502 3.196685 CGAATCTAATCATCTCCCTCCCC 59.803 52.174 0.00 0.00 0.00 4.81
5596 7503 4.090090 TCGAATCTAATCATCTCCCTCCC 58.910 47.826 0.00 0.00 0.00 4.30
5597 7504 5.730296 TTCGAATCTAATCATCTCCCTCC 57.270 43.478 0.00 0.00 0.00 4.30
5598 7505 6.015010 TCCTTTCGAATCTAATCATCTCCCTC 60.015 42.308 0.00 0.00 0.00 4.30
5599 7506 5.841237 TCCTTTCGAATCTAATCATCTCCCT 59.159 40.000 0.00 0.00 0.00 4.20
5600 7507 6.102897 TCCTTTCGAATCTAATCATCTCCC 57.897 41.667 0.00 0.00 0.00 4.30
5601 7508 7.928706 TCTTTCCTTTCGAATCTAATCATCTCC 59.071 37.037 0.00 0.00 0.00 3.71
5602 7509 8.879342 TCTTTCCTTTCGAATCTAATCATCTC 57.121 34.615 0.00 0.00 0.00 2.75
5603 7510 9.323985 CTTCTTTCCTTTCGAATCTAATCATCT 57.676 33.333 0.00 0.00 0.00 2.90
5604 7511 9.319143 TCTTCTTTCCTTTCGAATCTAATCATC 57.681 33.333 0.00 0.00 0.00 2.92
5605 7512 9.672673 TTCTTCTTTCCTTTCGAATCTAATCAT 57.327 29.630 0.00 0.00 0.00 2.45
5606 7513 9.502091 TTTCTTCTTTCCTTTCGAATCTAATCA 57.498 29.630 0.00 0.00 0.00 2.57
5631 7538 5.238650 CACTTCATCCTACGGTTGTCTTTTT 59.761 40.000 0.00 0.00 0.00 1.94
5632 7539 4.755123 CACTTCATCCTACGGTTGTCTTTT 59.245 41.667 0.00 0.00 0.00 2.27
5633 7540 4.315803 CACTTCATCCTACGGTTGTCTTT 58.684 43.478 0.00 0.00 0.00 2.52
5634 7541 3.306780 CCACTTCATCCTACGGTTGTCTT 60.307 47.826 0.00 0.00 0.00 3.01
5635 7542 2.233922 CCACTTCATCCTACGGTTGTCT 59.766 50.000 0.00 0.00 0.00 3.41
5636 7543 2.618053 CCACTTCATCCTACGGTTGTC 58.382 52.381 0.00 0.00 0.00 3.18
5637 7544 1.278127 CCCACTTCATCCTACGGTTGT 59.722 52.381 0.00 0.00 0.00 3.32
5638 7545 1.553248 TCCCACTTCATCCTACGGTTG 59.447 52.381 0.00 0.00 0.00 3.77
5639 7546 1.831736 CTCCCACTTCATCCTACGGTT 59.168 52.381 0.00 0.00 0.00 4.44
5640 7547 1.486211 CTCCCACTTCATCCTACGGT 58.514 55.000 0.00 0.00 0.00 4.83
5641 7548 0.105039 GCTCCCACTTCATCCTACGG 59.895 60.000 0.00 0.00 0.00 4.02
5642 7549 0.824109 TGCTCCCACTTCATCCTACG 59.176 55.000 0.00 0.00 0.00 3.51
5643 7550 1.471676 CGTGCTCCCACTTCATCCTAC 60.472 57.143 0.00 0.00 39.86 3.18
5644 7551 0.824109 CGTGCTCCCACTTCATCCTA 59.176 55.000 0.00 0.00 39.86 2.94
5645 7552 1.599047 CGTGCTCCCACTTCATCCT 59.401 57.895 0.00 0.00 39.86 3.24
5646 7553 1.450312 CCGTGCTCCCACTTCATCC 60.450 63.158 0.00 0.00 39.86 3.51
5647 7554 0.179000 ATCCGTGCTCCCACTTCATC 59.821 55.000 0.00 0.00 39.86 2.92
5648 7555 1.414181 CTATCCGTGCTCCCACTTCAT 59.586 52.381 0.00 0.00 39.86 2.57
5649 7556 0.824109 CTATCCGTGCTCCCACTTCA 59.176 55.000 0.00 0.00 39.86 3.02
5650 7557 0.105039 CCTATCCGTGCTCCCACTTC 59.895 60.000 0.00 0.00 39.86 3.01
5651 7558 0.325296 TCCTATCCGTGCTCCCACTT 60.325 55.000 0.00 0.00 39.86 3.16
5652 7559 0.757188 CTCCTATCCGTGCTCCCACT 60.757 60.000 0.00 0.00 39.86 4.00
5653 7560 1.742768 CTCCTATCCGTGCTCCCAC 59.257 63.158 0.00 0.00 38.62 4.61
5654 7561 2.134287 GCTCCTATCCGTGCTCCCA 61.134 63.158 0.00 0.00 0.00 4.37
5655 7562 1.476007 ATGCTCCTATCCGTGCTCCC 61.476 60.000 0.00 0.00 0.00 4.30
5656 7563 0.320247 CATGCTCCTATCCGTGCTCC 60.320 60.000 0.00 0.00 0.00 4.70
5657 7564 0.676184 TCATGCTCCTATCCGTGCTC 59.324 55.000 0.00 0.00 0.00 4.26
5658 7565 1.123077 TTCATGCTCCTATCCGTGCT 58.877 50.000 0.00 0.00 0.00 4.40
5659 7566 1.953559 TTTCATGCTCCTATCCGTGC 58.046 50.000 0.00 0.00 0.00 5.34
5660 7567 2.874701 CCTTTTCATGCTCCTATCCGTG 59.125 50.000 0.00 0.00 0.00 4.94
5661 7568 2.158755 CCCTTTTCATGCTCCTATCCGT 60.159 50.000 0.00 0.00 0.00 4.69
5662 7569 2.104792 TCCCTTTTCATGCTCCTATCCG 59.895 50.000 0.00 0.00 0.00 4.18
5663 7570 3.749226 CTCCCTTTTCATGCTCCTATCC 58.251 50.000 0.00 0.00 0.00 2.59
5664 7571 3.145286 GCTCCCTTTTCATGCTCCTATC 58.855 50.000 0.00 0.00 0.00 2.08
5665 7572 2.511218 TGCTCCCTTTTCATGCTCCTAT 59.489 45.455 0.00 0.00 0.00 2.57
5666 7573 1.915489 TGCTCCCTTTTCATGCTCCTA 59.085 47.619 0.00 0.00 0.00 2.94
5667 7574 0.700564 TGCTCCCTTTTCATGCTCCT 59.299 50.000 0.00 0.00 0.00 3.69
5668 7575 1.101331 CTGCTCCCTTTTCATGCTCC 58.899 55.000 0.00 0.00 0.00 4.70
5669 7576 1.101331 CCTGCTCCCTTTTCATGCTC 58.899 55.000 0.00 0.00 0.00 4.26
5670 7577 0.969409 GCCTGCTCCCTTTTCATGCT 60.969 55.000 0.00 0.00 0.00 3.79
5671 7578 1.252904 TGCCTGCTCCCTTTTCATGC 61.253 55.000 0.00 0.00 0.00 4.06
5672 7579 1.203994 CTTGCCTGCTCCCTTTTCATG 59.796 52.381 0.00 0.00 0.00 3.07
5673 7580 1.553706 CTTGCCTGCTCCCTTTTCAT 58.446 50.000 0.00 0.00 0.00 2.57
5674 7581 1.181098 GCTTGCCTGCTCCCTTTTCA 61.181 55.000 0.00 0.00 0.00 2.69
5675 7582 1.588597 GCTTGCCTGCTCCCTTTTC 59.411 57.895 0.00 0.00 0.00 2.29
5676 7583 1.910276 GGCTTGCCTGCTCCCTTTT 60.910 57.895 4.11 0.00 0.00 2.27
5677 7584 2.283460 GGCTTGCCTGCTCCCTTT 60.283 61.111 4.11 0.00 0.00 3.11
5678 7585 4.729918 CGGCTTGCCTGCTCCCTT 62.730 66.667 10.12 0.00 0.00 3.95
5681 7588 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
5682 7589 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
5683 7590 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
5693 7600 3.616721 CCTAGGTGGCGGATCCGG 61.617 72.222 33.98 16.02 40.19 5.14
5694 7601 2.520982 TCCTAGGTGGCGGATCCG 60.521 66.667 30.03 30.03 43.09 4.18
5695 7602 2.508751 GGTCCTAGGTGGCGGATCC 61.509 68.421 9.08 0.00 35.26 3.36
5696 7603 0.178970 TAGGTCCTAGGTGGCGGATC 60.179 60.000 9.08 0.00 35.26 3.36
5697 7604 0.178958 CTAGGTCCTAGGTGGCGGAT 60.179 60.000 17.24 0.00 35.26 4.18
5698 7605 1.229359 CTAGGTCCTAGGTGGCGGA 59.771 63.158 17.24 0.00 35.26 5.54
5699 7606 1.833049 CCTAGGTCCTAGGTGGCGG 60.833 68.421 30.49 10.48 46.15 6.13
5700 7607 3.857764 CCTAGGTCCTAGGTGGCG 58.142 66.667 30.49 10.16 46.15 5.69
5763 7670 1.747355 GGAGAAAGGTCACCGATACGA 59.253 52.381 0.00 0.00 0.00 3.43
5768 7675 3.801620 GGGGAGAAAGGTCACCGA 58.198 61.111 0.00 0.00 35.46 4.69
5779 7686 1.683025 TACGCCATTCACGGGGAGA 60.683 57.895 0.56 0.00 41.43 3.71
5785 7692 1.710013 AGAGTTGTACGCCATTCACG 58.290 50.000 0.00 0.00 0.00 4.35
5811 7719 3.383761 CAAAAGCAGGCAAAATCGAGTT 58.616 40.909 0.00 0.00 0.00 3.01
5812 7720 2.863704 GCAAAAGCAGGCAAAATCGAGT 60.864 45.455 0.00 0.00 0.00 4.18
5815 7723 0.435769 CGCAAAAGCAGGCAAAATCG 59.564 50.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.