Multiple sequence alignment - TraesCS7B01G247800

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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 TraesCS7B01G247800 chr7B 100.000 3446 0 0 1 3446 458113115 458116560 0.000000e+00 6364
1 TraesCS7B01G247800 chr7D 87.331 2960 186 82 75 2939 440211252 440214117 0.000000e+00 3214
2 TraesCS7B01G247800 chr7D 88.517 418 21 12 3041 3446 440214155 440214557 6.690000e-132 481
3 TraesCS7B01G247800 chr7A 87.266 1547 138 35 820 2339 491973601 491975115 0.000000e+00 1711
4 TraesCS7B01G247800 chr7A 82.411 506 28 28 2959 3446 491975653 491976115 5.390000e-103 385
5 TraesCS7B01G247800 chr7A 81.858 452 51 23 2508 2939 491975228 491975668 5.470000e-93 351
6 TraesCS7B01G247800 chr7A 77.812 329 46 15 152 463 491972923 491973241 9.830000e-41 178
7 TraesCS7B01G247800 chr6D 93.158 190 7 1 1404 1587 78490701 78490512 1.220000e-69 274
8 TraesCS7B01G247800 chr1D 95.541 157 7 0 1303 1459 388962940 388963096 5.710000e-63 252
9 TraesCS7B01G247800 chr1D 74.876 402 80 13 1373 1771 450462587 450462204 2.750000e-36 163


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 TraesCS7B01G247800 chr7B 458113115 458116560 3445 False 6364.00 6364 100.00000 1 3446 1 chr7B.!!$F1 3445
1 TraesCS7B01G247800 chr7D 440211252 440214557 3305 False 1847.50 3214 87.92400 75 3446 2 chr7D.!!$F1 3371
2 TraesCS7B01G247800 chr7A 491972923 491976115 3192 False 656.25 1711 82.33675 152 3446 4 chr7A.!!$F1 3294

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
64 65 0.029834 GGGTGCTATTGCGATTGCTG 59.970 55.0 19.16 0.0 43.34 4.41 F
757 858 0.034670 AAGCATCCAACCTCCTGCTC 60.035 55.0 0.00 0.0 43.82 4.26 F
1826 1958 0.036010 AATTCCGTGCCAGGAGTCAG 60.036 55.0 0.00 0.0 41.98 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2037 1.436336 CGTAGGATCGGTGGTGTCC 59.564 63.158 0.0 0.0 0.0 4.02 R
2390 2538 0.248012 TAATGGCGAGGCGAGAAACA 59.752 50.000 0.0 0.0 0.0 2.83 R
3087 3280 0.107703 CATGGTATGGTGGTCGCAGT 60.108 55.000 0.0 0.0 0.0 4.40 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
17 18 3.886340 CTGGCACTAGCAGCACAG 58.114 61.111 9.64 9.81 44.61 3.66
18 19 1.004080 CTGGCACTAGCAGCACAGT 60.004 57.895 9.64 0.00 44.61 3.55
19 20 0.604780 CTGGCACTAGCAGCACAGTT 60.605 55.000 9.64 0.00 44.61 3.16
20 21 0.179020 TGGCACTAGCAGCACAGTTT 60.179 50.000 9.64 0.00 44.61 2.66
21 22 1.071542 TGGCACTAGCAGCACAGTTTA 59.928 47.619 9.64 0.00 44.61 2.01
22 23 1.734465 GGCACTAGCAGCACAGTTTAG 59.266 52.381 9.64 0.00 44.61 1.85
23 24 1.734465 GCACTAGCAGCACAGTTTAGG 59.266 52.381 0.00 0.00 41.58 2.69
24 25 2.350522 CACTAGCAGCACAGTTTAGGG 58.649 52.381 0.00 0.00 0.00 3.53
25 26 1.978580 ACTAGCAGCACAGTTTAGGGT 59.021 47.619 0.00 0.00 0.00 4.34
26 27 2.289694 ACTAGCAGCACAGTTTAGGGTG 60.290 50.000 0.00 0.00 38.05 4.61
27 28 0.250901 AGCAGCACAGTTTAGGGTGG 60.251 55.000 0.00 0.00 35.58 4.61
28 29 0.250727 GCAGCACAGTTTAGGGTGGA 60.251 55.000 0.00 0.00 35.58 4.02
29 30 1.523758 CAGCACAGTTTAGGGTGGAC 58.476 55.000 0.00 0.00 35.58 4.02
30 31 1.136828 AGCACAGTTTAGGGTGGACA 58.863 50.000 0.00 0.00 35.58 4.02
31 32 1.072331 AGCACAGTTTAGGGTGGACAG 59.928 52.381 0.00 0.00 35.58 3.51
32 33 1.882352 GCACAGTTTAGGGTGGACAGG 60.882 57.143 0.00 0.00 35.58 4.00
33 34 1.420138 CACAGTTTAGGGTGGACAGGT 59.580 52.381 0.00 0.00 0.00 4.00
34 35 1.697982 ACAGTTTAGGGTGGACAGGTC 59.302 52.381 0.00 0.00 0.00 3.85
35 36 1.697432 CAGTTTAGGGTGGACAGGTCA 59.303 52.381 1.41 0.00 0.00 4.02
36 37 1.978580 AGTTTAGGGTGGACAGGTCAG 59.021 52.381 1.41 0.00 0.00 3.51
37 38 0.690762 TTTAGGGTGGACAGGTCAGC 59.309 55.000 1.41 0.00 0.00 4.26
38 39 0.178903 TTAGGGTGGACAGGTCAGCT 60.179 55.000 1.41 0.00 33.61 4.24
39 40 0.614979 TAGGGTGGACAGGTCAGCTC 60.615 60.000 1.41 0.00 33.61 4.09
40 41 2.217038 GGGTGGACAGGTCAGCTCA 61.217 63.158 1.41 0.00 33.61 4.26
41 42 1.294780 GGTGGACAGGTCAGCTCAG 59.705 63.158 1.41 0.00 0.00 3.35
42 43 1.188219 GGTGGACAGGTCAGCTCAGA 61.188 60.000 1.41 0.00 0.00 3.27
43 44 0.246086 GTGGACAGGTCAGCTCAGAG 59.754 60.000 1.41 0.00 0.00 3.35
44 45 0.902048 TGGACAGGTCAGCTCAGAGG 60.902 60.000 0.00 0.00 0.00 3.69
45 46 1.612395 GGACAGGTCAGCTCAGAGGG 61.612 65.000 0.00 0.00 0.00 4.30
46 47 1.611851 ACAGGTCAGCTCAGAGGGG 60.612 63.158 0.00 0.00 0.00 4.79
47 48 2.040278 AGGTCAGCTCAGAGGGGG 59.960 66.667 0.00 0.00 0.00 5.40
48 49 2.284995 GGTCAGCTCAGAGGGGGT 60.285 66.667 0.00 0.00 0.00 4.95
49 50 2.664081 GGTCAGCTCAGAGGGGGTG 61.664 68.421 0.00 0.00 0.00 4.61
50 51 3.005539 TCAGCTCAGAGGGGGTGC 61.006 66.667 0.00 0.00 0.00 5.01
51 52 3.007920 CAGCTCAGAGGGGGTGCT 61.008 66.667 0.00 0.00 0.00 4.40
52 53 1.687146 CAGCTCAGAGGGGGTGCTA 60.687 63.158 0.00 0.00 32.29 3.49
53 54 1.053264 CAGCTCAGAGGGGGTGCTAT 61.053 60.000 0.00 0.00 32.29 2.97
54 55 0.327000 AGCTCAGAGGGGGTGCTATT 60.327 55.000 0.00 0.00 31.71 1.73
55 56 0.179034 GCTCAGAGGGGGTGCTATTG 60.179 60.000 0.00 0.00 0.00 1.90
56 57 0.179034 CTCAGAGGGGGTGCTATTGC 60.179 60.000 0.00 0.00 40.20 3.56
57 58 1.524621 CAGAGGGGGTGCTATTGCG 60.525 63.158 0.00 0.00 43.34 4.85
58 59 1.689233 AGAGGGGGTGCTATTGCGA 60.689 57.895 0.00 0.00 43.34 5.10
59 60 1.056700 AGAGGGGGTGCTATTGCGAT 61.057 55.000 0.00 0.00 43.34 4.58
60 61 0.179018 GAGGGGGTGCTATTGCGATT 60.179 55.000 0.00 0.00 43.34 3.34
61 62 0.466189 AGGGGGTGCTATTGCGATTG 60.466 55.000 0.00 0.00 43.34 2.67
62 63 1.360192 GGGGTGCTATTGCGATTGC 59.640 57.895 12.84 12.84 43.34 3.56
63 64 1.103398 GGGGTGCTATTGCGATTGCT 61.103 55.000 19.16 0.00 43.34 3.91
64 65 0.029834 GGGTGCTATTGCGATTGCTG 59.970 55.000 19.16 0.00 43.34 4.41
65 66 1.016627 GGTGCTATTGCGATTGCTGA 58.983 50.000 19.16 0.00 43.34 4.26
66 67 1.605710 GGTGCTATTGCGATTGCTGAT 59.394 47.619 19.16 3.25 43.34 2.90
67 68 2.033801 GGTGCTATTGCGATTGCTGATT 59.966 45.455 19.16 0.00 43.34 2.57
68 69 3.040795 GTGCTATTGCGATTGCTGATTG 58.959 45.455 19.16 3.20 43.34 2.67
69 70 2.944349 TGCTATTGCGATTGCTGATTGA 59.056 40.909 19.16 0.00 43.34 2.57
70 71 3.002965 TGCTATTGCGATTGCTGATTGAG 59.997 43.478 19.16 0.00 43.34 3.02
71 72 3.608707 GCTATTGCGATTGCTGATTGAGG 60.609 47.826 12.51 0.00 43.34 3.86
72 73 0.452987 TTGCGATTGCTGATTGAGGC 59.547 50.000 6.47 0.00 43.34 4.70
73 74 1.358046 GCGATTGCTGATTGAGGCC 59.642 57.895 0.00 0.00 38.39 5.19
80 81 1.213678 TGCTGATTGAGGCCTTATGCT 59.786 47.619 6.77 0.00 40.92 3.79
90 91 5.342017 TGAGGCCTTATGCTATACTGGTAT 58.658 41.667 6.77 0.00 40.92 2.73
91 92 6.499436 TGAGGCCTTATGCTATACTGGTATA 58.501 40.000 6.77 1.28 40.92 1.47
108 109 7.498443 ACTGGTATAGTATTTTACTGCCTGTC 58.502 38.462 0.00 0.00 39.81 3.51
112 113 7.868415 GGTATAGTATTTTACTGCCTGTCTCTG 59.132 40.741 0.00 0.00 39.81 3.35
139 140 0.700564 AGCTGATGAAGGAAAGGGCA 59.299 50.000 0.00 0.00 0.00 5.36
142 143 2.686118 GCTGATGAAGGAAAGGGCATCT 60.686 50.000 0.00 0.00 38.31 2.90
144 145 2.216898 GATGAAGGAAAGGGCATCTCG 58.783 52.381 0.00 0.00 35.46 4.04
146 147 0.464554 GAAGGAAAGGGCATCTCGGG 60.465 60.000 0.00 0.00 0.00 5.14
172 173 4.084223 GCAAAACAGAGCAATGTTCCATTG 60.084 41.667 11.62 11.62 42.49 2.82
189 190 0.602562 TTGCCCGATTTGCTTGGAAG 59.397 50.000 0.00 0.00 0.00 3.46
193 194 1.474077 CCCGATTTGCTTGGAAGAAGG 59.526 52.381 0.00 0.00 0.00 3.46
195 196 2.436417 CGATTTGCTTGGAAGAAGGGA 58.564 47.619 0.00 0.00 0.00 4.20
201 202 1.475682 GCTTGGAAGAAGGGAATGCAG 59.524 52.381 0.00 0.00 0.00 4.41
203 204 3.629087 CTTGGAAGAAGGGAATGCAGAT 58.371 45.455 0.00 0.00 0.00 2.90
207 208 5.769835 TGGAAGAAGGGAATGCAGATTAAT 58.230 37.500 0.00 0.00 0.00 1.40
222 223 7.692172 TGCAGATTAATATGAGAATCCCATCA 58.308 34.615 14.18 0.00 33.34 3.07
267 273 6.152661 ACCAAGAGATCCGAAATTGCAAATTA 59.847 34.615 1.71 0.00 0.00 1.40
391 412 2.597340 CATTCCCCACGAGGCCAT 59.403 61.111 5.01 0.00 0.00 4.40
393 414 3.060614 ATTCCCCACGAGGCCATGG 62.061 63.158 7.63 7.63 35.59 3.66
447 469 1.080705 CTCCCGACGACAAGTGTCC 60.081 63.158 5.88 0.00 41.86 4.02
448 470 2.048503 CCCGACGACAAGTGTCCC 60.049 66.667 5.88 0.00 41.86 4.46
449 471 2.048503 CCGACGACAAGTGTCCCC 60.049 66.667 5.88 0.00 41.86 4.81
450 472 2.571216 CCGACGACAAGTGTCCCCT 61.571 63.158 5.88 0.00 41.86 4.79
451 473 1.366366 CGACGACAAGTGTCCCCTT 59.634 57.895 5.88 0.00 41.86 3.95
452 474 0.666577 CGACGACAAGTGTCCCCTTC 60.667 60.000 5.88 0.00 41.86 3.46
453 475 0.320508 GACGACAAGTGTCCCCTTCC 60.321 60.000 5.88 0.00 41.86 3.46
454 476 0.763223 ACGACAAGTGTCCCCTTCCT 60.763 55.000 5.88 0.00 41.86 3.36
469 491 3.056080 CCTTCCTCCCTCCCATGATTAA 58.944 50.000 0.00 0.00 0.00 1.40
472 494 1.776667 CCTCCCTCCCATGATTAAGCA 59.223 52.381 0.00 0.00 0.00 3.91
483 505 2.237643 TGATTAAGCAGCACCAGCAAA 58.762 42.857 0.00 0.00 45.49 3.68
532 567 0.814010 CCCATTGTACTACCGCCAGC 60.814 60.000 0.00 0.00 0.00 4.85
534 569 1.520787 ATTGTACTACCGCCAGCGC 60.521 57.895 6.50 0.00 38.24 5.92
535 570 2.918230 ATTGTACTACCGCCAGCGCC 62.918 60.000 2.29 0.00 38.24 6.53
536 571 4.137872 GTACTACCGCCAGCGCCA 62.138 66.667 2.29 0.00 38.24 5.69
571 617 7.090173 CGCCAAGATAAATGGAGAAAGAAAAA 58.910 34.615 0.00 0.00 39.81 1.94
612 682 1.005156 CGCCAAAACCCCACCAATG 60.005 57.895 0.00 0.00 0.00 2.82
613 683 1.753368 CGCCAAAACCCCACCAATGT 61.753 55.000 0.00 0.00 0.00 2.71
614 684 0.250252 GCCAAAACCCCACCAATGTG 60.250 55.000 0.00 0.00 42.39 3.21
615 685 1.127343 CCAAAACCCCACCAATGTGT 58.873 50.000 0.00 0.00 41.09 3.72
619 689 1.406860 AACCCCACCAATGTGTTGCC 61.407 55.000 0.00 0.00 41.09 4.52
620 690 2.582493 CCCCACCAATGTGTTGCCC 61.582 63.158 0.00 0.00 41.09 5.36
621 691 2.650196 CCACCAATGTGTTGCCCG 59.350 61.111 0.00 0.00 41.09 6.13
622 692 2.049248 CACCAATGTGTTGCCCGC 60.049 61.111 0.00 0.00 37.72 6.13
623 693 3.669344 ACCAATGTGTTGCCCGCG 61.669 61.111 0.00 0.00 33.90 6.46
624 694 3.669344 CCAATGTGTTGCCCGCGT 61.669 61.111 4.92 0.00 33.90 6.01
625 695 2.126888 CAATGTGTTGCCCGCGTC 60.127 61.111 4.92 0.00 0.00 5.19
626 696 3.722295 AATGTGTTGCCCGCGTCG 61.722 61.111 4.92 0.00 0.00 5.12
721 822 2.352715 GCTTTGGACAGCCCACAATTAC 60.353 50.000 0.00 0.00 46.62 1.89
748 849 0.169009 GCTCGTCCAAAGCATCCAAC 59.831 55.000 0.00 0.00 39.61 3.77
750 851 0.400213 TCGTCCAAAGCATCCAACCT 59.600 50.000 0.00 0.00 0.00 3.50
751 852 0.804989 CGTCCAAAGCATCCAACCTC 59.195 55.000 0.00 0.00 0.00 3.85
752 853 1.177401 GTCCAAAGCATCCAACCTCC 58.823 55.000 0.00 0.00 0.00 4.30
753 854 1.075601 TCCAAAGCATCCAACCTCCT 58.924 50.000 0.00 0.00 0.00 3.69
754 855 1.180029 CCAAAGCATCCAACCTCCTG 58.820 55.000 0.00 0.00 0.00 3.86
756 857 0.407139 AAAGCATCCAACCTCCTGCT 59.593 50.000 0.00 0.00 46.41 4.24
757 858 0.034670 AAGCATCCAACCTCCTGCTC 60.035 55.000 0.00 0.00 43.82 4.26
758 859 1.452833 GCATCCAACCTCCTGCTCC 60.453 63.158 0.00 0.00 0.00 4.70
759 860 1.919600 GCATCCAACCTCCTGCTCCT 61.920 60.000 0.00 0.00 0.00 3.69
760 861 0.179936 CATCCAACCTCCTGCTCCTC 59.820 60.000 0.00 0.00 0.00 3.71
761 862 0.985490 ATCCAACCTCCTGCTCCTCC 60.985 60.000 0.00 0.00 0.00 4.30
762 863 1.614824 CCAACCTCCTGCTCCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
763 864 1.621672 CCAACCTCCTGCTCCTCCTC 61.622 65.000 0.00 0.00 0.00 3.71
764 865 1.306568 AACCTCCTGCTCCTCCTCC 60.307 63.158 0.00 0.00 0.00 4.30
765 866 1.820866 AACCTCCTGCTCCTCCTCCT 61.821 60.000 0.00 0.00 0.00 3.69
766 867 1.457455 CCTCCTGCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
767 868 1.457455 CTCCTGCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
768 869 1.938596 TCCTGCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
769 870 1.457455 CCTGCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
770 871 1.457455 CTGCTCCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
771 872 1.938596 TGCTCCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
834 940 1.404843 CTAGCCAGGACCAGGACTAC 58.595 60.000 7.20 0.00 0.00 2.73
835 941 1.008403 TAGCCAGGACCAGGACTACT 58.992 55.000 7.20 0.00 0.00 2.57
836 942 0.324830 AGCCAGGACCAGGACTACTC 60.325 60.000 7.20 0.00 0.00 2.59
837 943 1.331399 GCCAGGACCAGGACTACTCC 61.331 65.000 7.20 0.00 36.71 3.85
838 944 0.041238 CCAGGACCAGGACTACTCCA 59.959 60.000 0.00 0.00 39.39 3.86
855 962 8.191534 ACTACTCCAGTATATAAACATCCCAC 57.808 38.462 0.00 0.00 34.98 4.61
897 1004 0.108585 CAAGGTGTGGTGGTGCTACT 59.891 55.000 0.00 0.00 0.00 2.57
953 1060 0.584876 GGAGTCGGAAACAACAACCG 59.415 55.000 0.00 0.00 46.71 4.44
1010 1133 2.745884 TGCAAGAATGGGCGTCGG 60.746 61.111 0.00 0.00 0.00 4.79
1050 1173 4.488911 ATCGGCAGGGGCTCCTCT 62.489 66.667 0.00 0.00 42.67 3.69
1166 1289 4.899239 CATCCTCCGCGGCCTCAC 62.899 72.222 23.51 0.00 0.00 3.51
1205 1328 3.151022 CCTGGAGGCCGAGGTCTC 61.151 72.222 14.98 14.98 45.35 3.36
1215 1338 4.477975 GAGGTCTCCGCGTCCGTG 62.478 72.222 4.92 0.00 0.00 4.94
1287 1413 4.148825 GAGATCAGGCGGTGCGGT 62.149 66.667 0.00 0.00 0.00 5.68
1724 1856 4.007644 CCTGGCGAGGTGTCTGCA 62.008 66.667 6.60 0.00 34.16 4.41
1821 1953 1.002624 GTCCAATTCCGTGCCAGGA 60.003 57.895 0.00 0.00 38.79 3.86
1826 1958 0.036010 AATTCCGTGCCAGGAGTCAG 60.036 55.000 0.00 0.00 41.98 3.51
1845 1977 1.663702 CGAGAAGGCCACGTTCGTT 60.664 57.895 5.01 0.00 34.07 3.85
1866 1998 2.100603 CCGAAGAGCGTCCTCGAC 59.899 66.667 7.34 0.00 43.05 4.20
1995 2133 1.826024 GAGCTGGATCACGGTCCAT 59.174 57.895 0.00 0.00 46.67 3.41
2038 2182 4.722700 AAGAGCCCGCAATGCCGT 62.723 61.111 0.00 0.00 0.00 5.68
2076 2223 2.178521 GACACCGACAGCGACGAT 59.821 61.111 0.00 0.00 40.82 3.73
2086 2233 3.186047 GCGACGATTCACCCGTGG 61.186 66.667 0.00 0.00 40.67 4.94
2087 2234 2.508439 CGACGATTCACCCGTGGG 60.508 66.667 2.58 2.58 40.67 4.61
2088 2235 2.818274 GACGATTCACCCGTGGGC 60.818 66.667 4.41 0.00 40.67 5.36
2089 2236 4.752879 ACGATTCACCCGTGGGCG 62.753 66.667 4.41 2.46 38.97 6.13
2090 2237 4.444838 CGATTCACCCGTGGGCGA 62.445 66.667 4.41 0.00 41.33 5.54
2091 2238 2.818274 GATTCACCCGTGGGCGAC 60.818 66.667 4.41 0.00 41.33 5.19
2196 2343 2.438434 GGCACGGGCAGCTGTAAT 60.438 61.111 13.89 0.00 43.71 1.89
2198 2345 2.040544 GCACGGGCAGCTGTAATGT 61.041 57.895 16.64 6.40 40.72 2.71
2208 2355 1.078759 GCTGTAATGTCGAGCGCAGT 61.079 55.000 11.47 0.00 0.00 4.40
2235 2382 1.922545 GGTAATCACGTGGTTAGCGAC 59.077 52.381 28.86 17.16 0.00 5.19
2283 2430 5.440610 AGCAATGGATTCTTTTCCGATACT 58.559 37.500 0.00 0.00 38.74 2.12
2295 2442 4.789012 TTCCGATACTACGTCCTGTTTT 57.211 40.909 0.00 0.00 0.00 2.43
2307 2454 1.064017 TCCTGTTTTGCTTGTCCCAGT 60.064 47.619 0.00 0.00 0.00 4.00
2309 2456 1.002468 CTGTTTTGCTTGTCCCAGTCG 60.002 52.381 0.00 0.00 0.00 4.18
2345 2493 1.187567 ACCGGCCCGTTTACAGTACT 61.188 55.000 0.00 0.00 0.00 2.73
2346 2494 0.817013 CCGGCCCGTTTACAGTACTA 59.183 55.000 0.85 0.00 0.00 1.82
2365 2513 5.161943 ACTACTGTACCACATTTCTTCCC 57.838 43.478 0.00 0.00 0.00 3.97
2381 2529 3.668386 CCCCCGCTGTTGTTCTTC 58.332 61.111 0.00 0.00 0.00 2.87
2390 2538 3.003689 CGCTGTTGTTCTTCCTGTCATTT 59.996 43.478 0.00 0.00 0.00 2.32
2392 2540 4.202050 GCTGTTGTTCTTCCTGTCATTTGT 60.202 41.667 0.00 0.00 0.00 2.83
2396 2544 6.152661 TGTTGTTCTTCCTGTCATTTGTTTCT 59.847 34.615 0.00 0.00 0.00 2.52
2475 2627 4.424711 GAATGCCAGCCCGGGTGA 62.425 66.667 24.63 4.69 32.22 4.02
2493 2646 0.966875 GATCACCACTTGGCATGGCA 60.967 55.000 19.43 19.43 41.31 4.92
2510 2663 1.760527 CACACATGGTGGGGTGAGA 59.239 57.895 0.00 0.00 44.04 3.27
2512 2665 0.850100 ACACATGGTGGGGTGAGAAA 59.150 50.000 0.00 0.00 37.94 2.52
2539 2692 1.641677 CATCGATCGGGCGGTTTTC 59.358 57.895 16.41 0.00 0.00 2.29
2546 2702 2.962569 GGGCGGTTTTCTTCTGGC 59.037 61.111 0.00 0.00 36.26 4.85
2661 2823 1.741770 GTCGGGTGTGAGTGGCATC 60.742 63.158 0.00 0.00 0.00 3.91
2795 2978 0.108615 CCTGACAGGGACGCTTGTAG 60.109 60.000 14.26 0.00 0.00 2.74
2796 2979 0.603569 CTGACAGGGACGCTTGTAGT 59.396 55.000 0.00 0.00 0.00 2.73
2873 3058 2.506438 CCGTCGGTCTCGCTTTCC 60.506 66.667 2.08 0.00 36.13 3.13
2909 3094 3.797546 GCGAGCAGGCAGAGCAAC 61.798 66.667 0.00 0.00 0.00 4.17
2914 3105 2.974148 CAGGCAGAGCAACGCACA 60.974 61.111 0.00 0.00 0.00 4.57
2921 3112 1.958205 GAGCAACGCACAGCAGAGT 60.958 57.895 0.00 0.00 0.00 3.24
2931 3122 3.486375 CGCACAGCAGAGTATGGATTTTG 60.486 47.826 0.00 0.00 0.00 2.44
2932 3123 3.441572 GCACAGCAGAGTATGGATTTTGT 59.558 43.478 0.00 0.00 0.00 2.83
2933 3124 4.673580 GCACAGCAGAGTATGGATTTTGTG 60.674 45.833 0.00 0.00 37.16 3.33
2934 3125 4.456911 CACAGCAGAGTATGGATTTTGTGT 59.543 41.667 0.00 0.00 31.37 3.72
2935 3126 4.697352 ACAGCAGAGTATGGATTTTGTGTC 59.303 41.667 0.00 0.00 0.00 3.67
2936 3127 3.935203 AGCAGAGTATGGATTTTGTGTCG 59.065 43.478 0.00 0.00 0.00 4.35
2937 3128 3.684788 GCAGAGTATGGATTTTGTGTCGT 59.315 43.478 0.00 0.00 0.00 4.34
2938 3129 4.154195 GCAGAGTATGGATTTTGTGTCGTT 59.846 41.667 0.00 0.00 0.00 3.85
2939 3130 5.334879 GCAGAGTATGGATTTTGTGTCGTTT 60.335 40.000 0.00 0.00 0.00 3.60
2940 3131 6.668323 CAGAGTATGGATTTTGTGTCGTTTT 58.332 36.000 0.00 0.00 0.00 2.43
2941 3132 7.138736 CAGAGTATGGATTTTGTGTCGTTTTT 58.861 34.615 0.00 0.00 0.00 1.94
2964 3155 7.784633 TTTTTCTTTCTTGCGAAATGGATTT 57.215 28.000 0.00 0.00 38.39 2.17
2965 3156 7.784633 TTTTCTTTCTTGCGAAATGGATTTT 57.215 28.000 0.00 0.00 38.39 1.82
2966 3157 6.768029 TTCTTTCTTGCGAAATGGATTTTG 57.232 33.333 0.00 0.00 38.39 2.44
2970 3161 4.545610 TCTTGCGAAATGGATTTTGTGTC 58.454 39.130 0.00 0.00 34.39 3.67
3019 3210 1.372997 CGTCCTCCGACTTGTGGTG 60.373 63.158 0.00 0.00 39.56 4.17
3028 3219 3.803082 CTTGTGGTGATGGCGCGG 61.803 66.667 8.83 0.00 0.00 6.46
3029 3220 4.634703 TTGTGGTGATGGCGCGGT 62.635 61.111 8.83 0.00 0.00 5.68
3032 3223 4.634703 TGGTGATGGCGCGGTGTT 62.635 61.111 8.83 0.00 0.00 3.32
3034 3225 2.175811 GTGATGGCGCGGTGTTTC 59.824 61.111 8.83 0.00 0.00 2.78
3076 3269 3.968265 ACCACCACCAATTTAGGATCTG 58.032 45.455 0.00 0.00 0.00 2.90
3077 3270 2.689983 CCACCACCAATTTAGGATCTGC 59.310 50.000 0.00 0.00 0.00 4.26
3078 3271 2.355756 CACCACCAATTTAGGATCTGCG 59.644 50.000 0.00 0.00 0.00 5.18
3079 3272 2.026262 ACCACCAATTTAGGATCTGCGT 60.026 45.455 0.00 0.00 0.00 5.24
3087 3280 1.540435 TAGGATCTGCGTGTGTGGCA 61.540 55.000 0.00 0.00 38.92 4.92
3121 3317 1.381928 CCATGGGAGCACAGCACATC 61.382 60.000 2.85 0.00 0.00 3.06
3125 3321 2.103042 GGAGCACAGCACATCGGAC 61.103 63.158 0.00 0.00 0.00 4.79
3144 3340 2.917343 GACCTGTACGTTTACGGTAAGC 59.083 50.000 7.24 4.83 44.95 3.09
3145 3341 2.295909 ACCTGTACGTTTACGGTAAGCA 59.704 45.455 13.89 4.17 44.95 3.91
3146 3342 2.919229 CCTGTACGTTTACGGTAAGCAG 59.081 50.000 13.89 11.27 44.95 4.24
3157 3365 4.025015 ACGGTAAGCAGTAATAGTGACG 57.975 45.455 0.00 0.00 0.00 4.35
3194 3402 1.709147 GATGCATGTGGACCAGCGTC 61.709 60.000 2.46 9.85 38.38 5.19
3195 3403 2.046892 GCATGTGGACCAGCGTCT 60.047 61.111 0.00 0.00 39.15 4.18
3281 3502 4.329545 GTTGGGCAGGCCTGACGA 62.330 66.667 37.21 29.64 40.25 4.20
3282 3503 4.329545 TTGGGCAGGCCTGACGAC 62.330 66.667 37.21 22.27 40.25 4.34
3306 3528 2.186076 CGAGAGGACGAGATTTTTCCG 58.814 52.381 0.00 0.00 34.31 4.30
3365 3587 2.050077 GCTTGGGTTGCTTCACGC 60.050 61.111 0.00 0.00 39.77 5.34
3413 3635 0.798771 CCAGCTTCTGACGACGTAGC 60.799 60.000 11.61 11.61 32.44 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.604780 AACTGTGCTGCTAGTGCCAG 60.605 55.000 17.49 17.49 38.71 4.85
1 2 0.179020 AAACTGTGCTGCTAGTGCCA 60.179 50.000 10.10 4.85 38.71 4.92
2 3 1.734465 CTAAACTGTGCTGCTAGTGCC 59.266 52.381 10.10 1.22 38.71 5.01
3 4 1.734465 CCTAAACTGTGCTGCTAGTGC 59.266 52.381 10.10 3.44 40.20 4.40
4 5 2.289694 ACCCTAAACTGTGCTGCTAGTG 60.290 50.000 10.10 2.09 0.00 2.74
5 6 1.978580 ACCCTAAACTGTGCTGCTAGT 59.021 47.619 0.00 2.66 0.00 2.57
6 7 2.350522 CACCCTAAACTGTGCTGCTAG 58.649 52.381 0.00 1.97 0.00 3.42
7 8 1.003118 CCACCCTAAACTGTGCTGCTA 59.997 52.381 0.00 0.00 0.00 3.49
8 9 0.250901 CCACCCTAAACTGTGCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
9 10 0.250727 TCCACCCTAAACTGTGCTGC 60.251 55.000 0.00 0.00 0.00 5.25
10 11 1.202758 TGTCCACCCTAAACTGTGCTG 60.203 52.381 0.00 0.00 0.00 4.41
11 12 1.072331 CTGTCCACCCTAAACTGTGCT 59.928 52.381 0.00 0.00 0.00 4.40
12 13 1.523758 CTGTCCACCCTAAACTGTGC 58.476 55.000 0.00 0.00 0.00 4.57
13 14 1.420138 ACCTGTCCACCCTAAACTGTG 59.580 52.381 0.00 0.00 0.00 3.66
14 15 1.697982 GACCTGTCCACCCTAAACTGT 59.302 52.381 0.00 0.00 0.00 3.55
15 16 1.697432 TGACCTGTCCACCCTAAACTG 59.303 52.381 0.00 0.00 0.00 3.16
16 17 1.978580 CTGACCTGTCCACCCTAAACT 59.021 52.381 0.00 0.00 0.00 2.66
17 18 1.610886 GCTGACCTGTCCACCCTAAAC 60.611 57.143 0.00 0.00 0.00 2.01
18 19 0.690762 GCTGACCTGTCCACCCTAAA 59.309 55.000 0.00 0.00 0.00 1.85
19 20 0.178903 AGCTGACCTGTCCACCCTAA 60.179 55.000 0.00 0.00 0.00 2.69
20 21 0.614979 GAGCTGACCTGTCCACCCTA 60.615 60.000 0.00 0.00 0.00 3.53
21 22 1.915769 GAGCTGACCTGTCCACCCT 60.916 63.158 0.00 0.00 0.00 4.34
22 23 2.177594 CTGAGCTGACCTGTCCACCC 62.178 65.000 0.00 0.00 0.00 4.61
23 24 1.188219 TCTGAGCTGACCTGTCCACC 61.188 60.000 0.00 0.00 0.00 4.61
24 25 0.246086 CTCTGAGCTGACCTGTCCAC 59.754 60.000 0.00 0.00 0.00 4.02
25 26 0.902048 CCTCTGAGCTGACCTGTCCA 60.902 60.000 0.00 0.00 0.00 4.02
26 27 1.612395 CCCTCTGAGCTGACCTGTCC 61.612 65.000 0.00 0.00 0.00 4.02
27 28 1.612395 CCCCTCTGAGCTGACCTGTC 61.612 65.000 0.00 0.00 0.00 3.51
28 29 1.611851 CCCCTCTGAGCTGACCTGT 60.612 63.158 0.00 0.00 0.00 4.00
29 30 2.365586 CCCCCTCTGAGCTGACCTG 61.366 68.421 0.00 0.00 0.00 4.00
30 31 2.040278 CCCCCTCTGAGCTGACCT 59.960 66.667 0.00 0.00 0.00 3.85
31 32 2.284995 ACCCCCTCTGAGCTGACC 60.285 66.667 0.00 0.00 0.00 4.02
32 33 2.985456 CACCCCCTCTGAGCTGAC 59.015 66.667 0.00 0.00 0.00 3.51
33 34 2.168272 TAGCACCCCCTCTGAGCTGA 62.168 60.000 0.00 0.00 36.80 4.26
34 35 1.053264 ATAGCACCCCCTCTGAGCTG 61.053 60.000 0.00 0.00 36.80 4.24
35 36 0.327000 AATAGCACCCCCTCTGAGCT 60.327 55.000 0.00 0.00 39.22 4.09
36 37 0.179034 CAATAGCACCCCCTCTGAGC 60.179 60.000 0.00 0.00 0.00 4.26
37 38 0.179034 GCAATAGCACCCCCTCTGAG 60.179 60.000 0.00 0.00 41.58 3.35
38 39 1.915228 GCAATAGCACCCCCTCTGA 59.085 57.895 0.00 0.00 41.58 3.27
39 40 1.524621 CGCAATAGCACCCCCTCTG 60.525 63.158 0.00 0.00 42.27 3.35
40 41 1.056700 ATCGCAATAGCACCCCCTCT 61.057 55.000 0.00 0.00 42.27 3.69
41 42 0.179018 AATCGCAATAGCACCCCCTC 60.179 55.000 0.00 0.00 42.27 4.30
42 43 0.466189 CAATCGCAATAGCACCCCCT 60.466 55.000 0.00 0.00 42.27 4.79
43 44 2.032981 CAATCGCAATAGCACCCCC 58.967 57.895 0.00 0.00 42.27 5.40
44 45 1.103398 AGCAATCGCAATAGCACCCC 61.103 55.000 0.00 0.00 42.27 4.95
45 46 0.029834 CAGCAATCGCAATAGCACCC 59.970 55.000 0.00 0.00 42.27 4.61
46 47 1.016627 TCAGCAATCGCAATAGCACC 58.983 50.000 0.00 0.00 42.27 5.01
47 48 3.040795 CAATCAGCAATCGCAATAGCAC 58.959 45.455 0.00 0.00 42.27 4.40
48 49 2.944349 TCAATCAGCAATCGCAATAGCA 59.056 40.909 0.00 0.00 42.27 3.49
49 50 3.552541 CTCAATCAGCAATCGCAATAGC 58.447 45.455 0.00 0.00 42.27 2.97
50 51 3.608707 GCCTCAATCAGCAATCGCAATAG 60.609 47.826 0.00 0.00 42.27 1.73
51 52 2.291465 GCCTCAATCAGCAATCGCAATA 59.709 45.455 0.00 0.00 42.27 1.90
52 53 1.066605 GCCTCAATCAGCAATCGCAAT 59.933 47.619 0.00 0.00 42.27 3.56
53 54 0.452987 GCCTCAATCAGCAATCGCAA 59.547 50.000 0.00 0.00 42.27 4.85
54 55 1.378882 GGCCTCAATCAGCAATCGCA 61.379 55.000 0.00 0.00 42.27 5.10
55 56 1.099879 AGGCCTCAATCAGCAATCGC 61.100 55.000 0.00 0.00 38.99 4.58
56 57 1.386533 AAGGCCTCAATCAGCAATCG 58.613 50.000 5.23 0.00 0.00 3.34
57 58 3.305199 GCATAAGGCCTCAATCAGCAATC 60.305 47.826 5.23 0.00 36.11 2.67
58 59 2.626743 GCATAAGGCCTCAATCAGCAAT 59.373 45.455 5.23 0.00 36.11 3.56
59 60 2.026641 GCATAAGGCCTCAATCAGCAA 58.973 47.619 5.23 0.00 36.11 3.91
60 61 1.213678 AGCATAAGGCCTCAATCAGCA 59.786 47.619 5.23 0.00 46.50 4.41
61 62 1.978454 AGCATAAGGCCTCAATCAGC 58.022 50.000 5.23 5.01 46.50 4.26
62 63 5.873712 CAGTATAGCATAAGGCCTCAATCAG 59.126 44.000 5.23 0.00 46.50 2.90
63 64 5.280164 CCAGTATAGCATAAGGCCTCAATCA 60.280 44.000 5.23 0.00 46.50 2.57
64 65 5.181748 CCAGTATAGCATAAGGCCTCAATC 58.818 45.833 5.23 0.00 46.50 2.67
65 66 4.599241 ACCAGTATAGCATAAGGCCTCAAT 59.401 41.667 5.23 0.00 46.50 2.57
66 67 3.973973 ACCAGTATAGCATAAGGCCTCAA 59.026 43.478 5.23 0.00 46.50 3.02
67 68 3.587498 ACCAGTATAGCATAAGGCCTCA 58.413 45.455 5.23 0.00 46.50 3.86
68 69 5.941555 ATACCAGTATAGCATAAGGCCTC 57.058 43.478 5.23 0.00 46.50 4.70
69 70 6.503944 ACTATACCAGTATAGCATAAGGCCT 58.496 40.000 19.99 0.00 45.48 5.19
70 71 6.793505 ACTATACCAGTATAGCATAAGGCC 57.206 41.667 19.99 0.00 45.48 5.19
90 91 5.720041 ACCAGAGACAGGCAGTAAAATACTA 59.280 40.000 0.00 0.00 37.23 1.82
91 92 4.532521 ACCAGAGACAGGCAGTAAAATACT 59.467 41.667 0.00 0.00 40.28 2.12
104 105 2.141517 CAGCTTCACAACCAGAGACAG 58.858 52.381 0.00 0.00 0.00 3.51
108 109 3.049708 TCATCAGCTTCACAACCAGAG 57.950 47.619 0.00 0.00 0.00 3.35
112 113 2.783135 TCCTTCATCAGCTTCACAACC 58.217 47.619 0.00 0.00 0.00 3.77
139 140 2.154462 CTCTGTTTTGCAACCCGAGAT 58.846 47.619 0.00 0.00 34.01 2.75
142 143 0.749818 TGCTCTGTTTTGCAACCCGA 60.750 50.000 0.00 0.00 36.15 5.14
172 173 0.887933 TTCTTCCAAGCAAATCGGGC 59.112 50.000 0.00 0.00 0.00 6.13
189 190 8.627208 TTCTCATATTAATCTGCATTCCCTTC 57.373 34.615 0.00 0.00 0.00 3.46
193 194 7.613022 TGGGATTCTCATATTAATCTGCATTCC 59.387 37.037 0.00 0.00 33.50 3.01
195 196 9.186837 GATGGGATTCTCATATTAATCTGCATT 57.813 33.333 0.00 0.00 33.50 3.56
201 202 9.852091 GCTTTTGATGGGATTCTCATATTAATC 57.148 33.333 0.00 0.00 0.00 1.75
203 204 8.765488 TGCTTTTGATGGGATTCTCATATTAA 57.235 30.769 0.00 0.00 0.00 1.40
207 208 4.581824 GCTGCTTTTGATGGGATTCTCATA 59.418 41.667 0.00 0.00 0.00 2.15
222 223 1.082366 CGTAAACGCCGCTGCTTTT 60.082 52.632 9.41 9.41 41.31 2.27
267 273 7.875971 AGTTTCTTGCTCGAATTGTAATCTTT 58.124 30.769 0.00 0.00 0.00 2.52
281 287 2.218603 TGTCGGGAAAGTTTCTTGCTC 58.781 47.619 15.05 0.00 0.00 4.26
360 373 2.629617 GGGGAATGGAATATTGCACTGG 59.370 50.000 12.23 0.00 0.00 4.00
394 415 2.733593 GCACAGCAAGCAAGCAGC 60.734 61.111 3.19 0.00 46.19 5.25
395 416 1.371758 CAGCACAGCAAGCAAGCAG 60.372 57.895 3.19 0.00 36.85 4.24
398 419 1.081376 GCTCAGCACAGCAAGCAAG 60.081 57.895 10.30 0.00 38.72 4.01
399 420 0.250424 TAGCTCAGCACAGCAAGCAA 60.250 50.000 15.48 0.00 42.40 3.91
400 421 0.672711 CTAGCTCAGCACAGCAAGCA 60.673 55.000 15.48 4.69 42.40 3.91
447 469 0.402566 ATCATGGGAGGGAGGAAGGG 60.403 60.000 0.00 0.00 0.00 3.95
448 470 1.527457 AATCATGGGAGGGAGGAAGG 58.473 55.000 0.00 0.00 0.00 3.46
449 471 3.497584 GCTTAATCATGGGAGGGAGGAAG 60.498 52.174 0.00 0.00 0.00 3.46
450 472 2.443255 GCTTAATCATGGGAGGGAGGAA 59.557 50.000 0.00 0.00 0.00 3.36
451 473 2.057922 GCTTAATCATGGGAGGGAGGA 58.942 52.381 0.00 0.00 0.00 3.71
452 474 1.776667 TGCTTAATCATGGGAGGGAGG 59.223 52.381 0.00 0.00 0.00 4.30
453 475 2.813354 GCTGCTTAATCATGGGAGGGAG 60.813 54.545 0.00 0.00 0.00 4.30
454 476 1.143684 GCTGCTTAATCATGGGAGGGA 59.856 52.381 0.00 0.00 0.00 4.20
469 491 2.501602 GGGTTTTGCTGGTGCTGCT 61.502 57.895 0.00 0.00 40.48 4.24
472 494 0.825010 CTCAGGGTTTTGCTGGTGCT 60.825 55.000 0.00 0.00 40.48 4.40
515 545 1.762222 GCGCTGGCGGTAGTACAATG 61.762 60.000 16.61 0.00 40.19 2.82
534 569 3.391665 CTTGGCGGTAGGAGGCTGG 62.392 68.421 0.00 0.00 35.01 4.85
535 570 1.690219 ATCTTGGCGGTAGGAGGCTG 61.690 60.000 0.00 0.00 35.01 4.85
536 571 0.105658 TATCTTGGCGGTAGGAGGCT 60.106 55.000 0.00 0.00 35.01 4.58
544 590 3.644966 TTCTCCATTTATCTTGGCGGT 57.355 42.857 0.00 0.00 34.06 5.68
576 622 2.224305 GGCGTGCCTTCCTATTCTATGT 60.224 50.000 2.98 0.00 0.00 2.29
684 779 4.090057 GCAAAGCCAGCGTCCGAC 62.090 66.667 0.00 0.00 0.00 4.79
721 822 3.234630 TTTGGACGAGCGAGGTGGG 62.235 63.158 0.00 0.00 0.00 4.61
748 849 1.457455 GAGGAGGAGGAGCAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
750 851 1.938596 AGGAGGAGGAGGAGCAGGA 60.939 63.158 0.00 0.00 0.00 3.86
751 852 1.457455 GAGGAGGAGGAGGAGCAGG 60.457 68.421 0.00 0.00 0.00 4.85
752 853 1.457455 GGAGGAGGAGGAGGAGCAG 60.457 68.421 0.00 0.00 0.00 4.24
753 854 1.938596 AGGAGGAGGAGGAGGAGCA 60.939 63.158 0.00 0.00 0.00 4.26
754 855 1.152546 GAGGAGGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
756 857 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
757 858 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
758 859 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
759 860 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
760 861 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
761 862 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
762 863 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
763 864 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
764 865 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
765 866 0.556380 AAGGAGGAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
766 867 0.398381 CAAGGAGGAGGAGGAGGAGG 60.398 65.000 0.00 0.00 0.00 4.30
767 868 0.338120 ACAAGGAGGAGGAGGAGGAG 59.662 60.000 0.00 0.00 0.00 3.69
768 869 1.571457 CTACAAGGAGGAGGAGGAGGA 59.429 57.143 0.00 0.00 0.00 3.71
769 870 1.289530 ACTACAAGGAGGAGGAGGAGG 59.710 57.143 0.00 0.00 0.00 4.30
770 871 2.763448 CAACTACAAGGAGGAGGAGGAG 59.237 54.545 0.00 0.00 0.00 3.69
771 872 2.821437 CAACTACAAGGAGGAGGAGGA 58.179 52.381 0.00 0.00 0.00 3.71
817 918 0.324830 GAGTAGTCCTGGTCCTGGCT 60.325 60.000 9.96 12.13 0.00 4.75
818 919 1.331399 GGAGTAGTCCTGGTCCTGGC 61.331 65.000 9.55 5.65 40.17 4.85
834 940 6.183361 TGTGGTGGGATGTTTATATACTGGAG 60.183 42.308 0.00 0.00 0.00 3.86
835 941 5.668080 TGTGGTGGGATGTTTATATACTGGA 59.332 40.000 0.00 0.00 0.00 3.86
836 942 5.935945 TGTGGTGGGATGTTTATATACTGG 58.064 41.667 0.00 0.00 0.00 4.00
837 943 6.262273 GGTTGTGGTGGGATGTTTATATACTG 59.738 42.308 0.00 0.00 0.00 2.74
838 944 6.362248 GGTTGTGGTGGGATGTTTATATACT 58.638 40.000 0.00 0.00 0.00 2.12
855 962 1.340889 CTTTGGTGTGATGGGTTGTGG 59.659 52.381 0.00 0.00 0.00 4.17
888 995 4.082523 GGGCGAGCAGTAGCACCA 62.083 66.667 0.00 0.00 45.49 4.17
953 1060 2.665185 GTGGCGTGTGGTCTGTCC 60.665 66.667 0.00 0.00 0.00 4.02
1215 1338 4.778143 ATGTCAAGGCCGCCGTCC 62.778 66.667 3.05 0.00 0.00 4.79
1216 1339 3.499737 CATGTCAAGGCCGCCGTC 61.500 66.667 3.05 0.00 0.00 4.79
1227 1353 1.471501 GCGTACTCCATGAGCATGTCA 60.472 52.381 9.39 0.00 40.38 3.58
1261 1387 2.892640 CCTGATCTCGTCGGCCAA 59.107 61.111 2.24 0.00 31.43 4.52
1326 1452 3.474570 AGCCCGAGCAGGATGTCC 61.475 66.667 0.00 0.00 45.00 4.02
1821 1953 2.659610 GTGGCCTTCTCGCTGACT 59.340 61.111 3.32 0.00 0.00 3.41
1826 1958 3.479269 CGAACGTGGCCTTCTCGC 61.479 66.667 3.32 0.00 35.98 5.03
1845 1977 2.283676 AGGACGCTCTTCGGGGAA 60.284 61.111 0.00 0.00 43.86 3.97
1899 2037 1.436336 CGTAGGATCGGTGGTGTCC 59.564 63.158 0.00 0.00 0.00 4.02
1959 2097 3.311110 GCGTCCCAGGTCCAGTCA 61.311 66.667 0.00 0.00 0.00 3.41
2028 2172 3.869272 GGCTCTGACGGCATTGCG 61.869 66.667 9.11 0.85 0.00 4.85
2071 2218 2.818274 GCCCACGGGTGAATCGTC 60.818 66.667 3.54 0.00 38.94 4.20
2164 2311 0.870307 GTGCCATCGTAACGATCGCT 60.870 55.000 16.60 5.43 47.00 4.93
2196 2343 0.803380 CATCATCACTGCGCTCGACA 60.803 55.000 9.73 0.00 0.00 4.35
2198 2345 1.227060 CCATCATCACTGCGCTCGA 60.227 57.895 9.73 2.20 0.00 4.04
2208 2355 3.904800 ACCACGTGATTACCATCATCA 57.095 42.857 19.30 0.00 41.64 3.07
2235 2382 4.266976 GTGATTGGAACGGTACTACAATCG 59.733 45.833 11.78 0.85 46.27 3.34
2236 2383 5.172934 TGTGATTGGAACGGTACTACAATC 58.827 41.667 10.30 10.30 44.57 2.67
2237 2384 5.155278 TGTGATTGGAACGGTACTACAAT 57.845 39.130 0.00 0.00 34.73 2.71
2283 2430 2.215196 GGACAAGCAAAACAGGACGTA 58.785 47.619 0.00 0.00 0.00 3.57
2295 2442 2.031012 CTGCGACTGGGACAAGCA 59.969 61.111 0.00 0.00 40.00 3.91
2326 2474 1.187567 AGTACTGTAAACGGGCCGGT 61.188 55.000 31.78 24.00 0.00 5.28
2345 2493 3.264964 GGGGGAAGAAATGTGGTACAGTA 59.735 47.826 0.00 0.00 41.80 2.74
2346 2494 2.041216 GGGGGAAGAAATGTGGTACAGT 59.959 50.000 0.00 0.00 41.80 3.55
2365 2513 1.073199 AGGAAGAACAACAGCGGGG 59.927 57.895 0.00 0.00 0.00 5.73
2381 2529 2.154462 AGGCGAGAAACAAATGACAGG 58.846 47.619 0.00 0.00 0.00 4.00
2390 2538 0.248012 TAATGGCGAGGCGAGAAACA 59.752 50.000 0.00 0.00 0.00 2.83
2392 2540 2.325583 AATAATGGCGAGGCGAGAAA 57.674 45.000 0.00 0.00 0.00 2.52
2396 2544 0.391228 TGCTAATAATGGCGAGGCGA 59.609 50.000 0.00 0.00 35.46 5.54
2435 2587 2.412089 CGCTAGCTGTGTTAAGTTGGAC 59.588 50.000 13.93 0.00 0.00 4.02
2473 2625 0.966875 GCCATGCCAAGTGGTGATCA 60.967 55.000 0.00 0.00 39.01 2.92
2474 2626 0.966875 TGCCATGCCAAGTGGTGATC 60.967 55.000 0.00 0.00 39.01 2.92
2475 2627 1.077086 TGCCATGCCAAGTGGTGAT 59.923 52.632 0.00 0.00 39.01 3.06
2478 2631 2.198150 TGTGCCATGCCAAGTGGT 59.802 55.556 0.00 0.00 39.01 4.16
2482 2635 4.902308 CATGTGTGCCATGCCAAG 57.098 55.556 0.00 0.00 44.21 3.61
2493 2646 0.850100 TTTCTCACCCCACCATGTGT 59.150 50.000 0.00 0.00 34.14 3.72
2499 2652 1.839424 CATTCCTTTCTCACCCCACC 58.161 55.000 0.00 0.00 0.00 4.61
2503 2656 0.960364 TGCGCATTCCTTTCTCACCC 60.960 55.000 5.66 0.00 0.00 4.61
2504 2657 1.064654 GATGCGCATTCCTTTCTCACC 59.935 52.381 26.12 2.67 0.00 4.02
2505 2658 1.267732 CGATGCGCATTCCTTTCTCAC 60.268 52.381 26.12 6.33 0.00 3.51
2506 2659 1.009078 CGATGCGCATTCCTTTCTCA 58.991 50.000 26.12 0.00 0.00 3.27
2510 2663 0.583438 CGATCGATGCGCATTCCTTT 59.417 50.000 26.12 8.12 0.00 3.11
2512 2665 1.665916 CCGATCGATGCGCATTCCT 60.666 57.895 26.12 11.76 0.00 3.36
2534 2687 1.200020 CATGACCGGCCAGAAGAAAAC 59.800 52.381 0.00 0.00 0.00 2.43
2539 2692 1.138859 TGATACATGACCGGCCAGAAG 59.861 52.381 0.00 0.00 0.00 2.85
2546 2702 1.226859 ACGCGTGATACATGACCGG 60.227 57.895 12.93 0.00 0.00 5.28
2795 2978 1.405821 AGGTACTCTGCGTGCTCATAC 59.594 52.381 0.00 0.00 0.00 2.39
2796 2979 1.763968 AGGTACTCTGCGTGCTCATA 58.236 50.000 0.00 0.00 0.00 2.15
2892 3077 3.797546 GTTGCTCTGCCTGCTCGC 61.798 66.667 0.00 0.00 0.00 5.03
2893 3078 3.485431 CGTTGCTCTGCCTGCTCG 61.485 66.667 0.00 0.00 0.00 5.03
2895 3080 4.631247 TGCGTTGCTCTGCCTGCT 62.631 61.111 0.00 0.00 0.00 4.24
2898 3083 2.667536 CTGTGCGTTGCTCTGCCT 60.668 61.111 0.00 0.00 0.00 4.75
2908 3093 0.826715 ATCCATACTCTGCTGTGCGT 59.173 50.000 0.00 0.00 0.00 5.24
2909 3094 1.945387 AATCCATACTCTGCTGTGCG 58.055 50.000 0.00 0.00 0.00 5.34
2914 3105 3.935203 CGACACAAAATCCATACTCTGCT 59.065 43.478 0.00 0.00 0.00 4.24
2949 3140 4.549458 AGACACAAAATCCATTTCGCAAG 58.451 39.130 0.00 0.00 0.00 4.01
2950 3141 4.545610 GAGACACAAAATCCATTTCGCAA 58.454 39.130 0.00 0.00 0.00 4.85
2951 3142 3.364864 CGAGACACAAAATCCATTTCGCA 60.365 43.478 0.00 0.00 0.00 5.10
2952 3143 3.163594 CGAGACACAAAATCCATTTCGC 58.836 45.455 0.00 0.00 0.00 4.70
2953 3144 4.404507 ACGAGACACAAAATCCATTTCG 57.595 40.909 0.00 0.00 0.00 3.46
2954 3145 5.625311 GTCAACGAGACACAAAATCCATTTC 59.375 40.000 7.67 0.00 46.77 2.17
2955 3146 5.519722 GTCAACGAGACACAAAATCCATTT 58.480 37.500 7.67 0.00 46.77 2.32
2956 3147 5.108385 GTCAACGAGACACAAAATCCATT 57.892 39.130 7.67 0.00 46.77 3.16
2957 3148 4.749245 GTCAACGAGACACAAAATCCAT 57.251 40.909 7.67 0.00 46.77 3.41
3005 3196 1.021390 GCCATCACCACAAGTCGGAG 61.021 60.000 0.00 0.00 0.00 4.63
3006 3197 1.003839 GCCATCACCACAAGTCGGA 60.004 57.895 0.00 0.00 0.00 4.55
3019 3210 2.480555 CAGAAACACCGCGCCATC 59.519 61.111 0.00 0.00 0.00 3.51
3028 3219 0.947180 TTACCTCGCGGCAGAAACAC 60.947 55.000 6.13 0.00 0.00 3.32
3029 3220 0.947180 GTTACCTCGCGGCAGAAACA 60.947 55.000 6.13 0.00 0.00 2.83
3032 3223 0.739462 CATGTTACCTCGCGGCAGAA 60.739 55.000 6.13 0.00 0.00 3.02
3034 3225 2.813179 GCATGTTACCTCGCGGCAG 61.813 63.158 6.13 0.00 0.00 4.85
3079 3272 4.168291 TGGTCGCAGTGCCACACA 62.168 61.111 14.98 7.47 36.74 3.72
3087 3280 0.107703 CATGGTATGGTGGTCGCAGT 60.108 55.000 0.00 0.00 0.00 4.40
3121 3317 0.240945 ACCGTAAACGTACAGGTCCG 59.759 55.000 1.41 0.00 34.23 4.79
3125 3321 2.919229 CTGCTTACCGTAAACGTACAGG 59.081 50.000 1.41 0.00 37.74 4.00
3144 3340 4.142578 ACTCTCACAGCGTCACTATTACTG 60.143 45.833 0.00 0.00 0.00 2.74
3145 3341 4.011023 ACTCTCACAGCGTCACTATTACT 58.989 43.478 0.00 0.00 0.00 2.24
3146 3342 4.099120 CACTCTCACAGCGTCACTATTAC 58.901 47.826 0.00 0.00 0.00 1.89
3157 3365 2.423926 TCTTTCGTCACTCTCACAGC 57.576 50.000 0.00 0.00 0.00 4.40
3283 3504 0.175989 AAAATCTCGTCCTCTCGGGC 59.824 55.000 0.00 0.00 34.39 6.13
3365 3587 3.895102 TACCCGGAACAACGTCGCG 62.895 63.158 0.73 0.00 0.00 5.87
3413 3635 5.550981 GTTTCGCATCAATGTAGTACAGTG 58.449 41.667 21.75 21.75 44.66 3.66


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

AutoCloner maintained by Alex Coulton.