Multiple sequence alignment - TraesCS4A01G209400

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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 TraesCS4A01G209400 chr4A 100.000 6653 0 0 1 6653 502900041 502906693 0.000000e+00 12286.0
1 TraesCS4A01G209400 chr4A 92.308 143 11 0 2544 2686 680587802 680587660 3.150000e-48 204.0
2 TraesCS4A01G209400 chr4D 96.712 2190 53 5 3003 5173 90990522 90992711 0.000000e+00 3627.0
3 TraesCS4A01G209400 chr4D 95.825 1485 52 7 1017 2497 90988371 90989849 0.000000e+00 2390.0
4 TraesCS4A01G209400 chr4D 93.342 1532 59 18 5145 6653 90992722 90994233 0.000000e+00 2224.0
5 TraesCS4A01G209400 chr4D 96.269 268 9 1 2739 3005 90989834 90990101 7.920000e-119 438.0
6 TraesCS4A01G209400 chr4D 94.815 135 6 1 2551 2685 30403333 30403466 6.760000e-50 209.0
7 TraesCS4A01G209400 chr4D 96.970 33 1 0 5888 5920 1405935 1405903 1.000000e-03 56.5
8 TraesCS4A01G209400 chr4D 100.000 28 0 0 5893 5920 81986955 81986928 1.200000e-02 52.8
9 TraesCS4A01G209400 chr4B 94.633 1565 63 14 4002 5561 127102570 127104118 0.000000e+00 2405.0
10 TraesCS4A01G209400 chr4B 93.796 1354 69 8 2675 4018 127094254 127095602 0.000000e+00 2021.0
11 TraesCS4A01G209400 chr4B 92.672 655 41 6 5959 6607 127105036 127105689 0.000000e+00 937.0
12 TraesCS4A01G209400 chr4B 92.780 651 37 2 1538 2188 127093521 127094161 0.000000e+00 933.0
13 TraesCS4A01G209400 chr4B 93.705 556 33 2 989 1543 127092579 127093133 0.000000e+00 832.0
14 TraesCS4A01G209400 chr4B 95.050 101 4 1 2453 2552 127094156 127094256 2.480000e-34 158.0
15 TraesCS4A01G209400 chr4B 83.784 111 16 2 424 533 167384660 167384551 3.280000e-18 104.0
16 TraesCS4A01G209400 chr6D 89.679 872 62 9 1 871 168288263 168287419 0.000000e+00 1086.0
17 TraesCS4A01G209400 chr6D 95.420 131 6 0 2550 2680 295604311 295604181 6.760000e-50 209.0
18 TraesCS4A01G209400 chr6D 100.000 28 0 0 5893 5920 110873580 110873553 1.200000e-02 52.8
19 TraesCS4A01G209400 chr5A 88.787 874 78 14 1 874 269849446 269848593 0.000000e+00 1053.0
20 TraesCS4A01G209400 chr5A 88.060 67 7 1 5740 5806 678574989 678574924 1.990000e-10 78.7
21 TraesCS4A01G209400 chr5A 78.761 113 19 4 5739 5848 346350856 346350746 3.330000e-08 71.3
22 TraesCS4A01G209400 chr3B 91.032 591 44 7 178 760 659452280 659451691 0.000000e+00 789.0
23 TraesCS4A01G209400 chr3B 87.097 372 37 7 2182 2552 472912448 472912809 1.730000e-110 411.0
24 TraesCS4A01G209400 chr3B 84.112 214 27 7 1 211 739685984 739685775 4.070000e-47 200.0
25 TraesCS4A01G209400 chr3B 86.364 88 8 2 5739 5826 732904954 732904871 7.100000e-15 93.5
26 TraesCS4A01G209400 chr3B 85.542 83 11 1 2792 2874 564044016 564044097 1.190000e-12 86.1
27 TraesCS4A01G209400 chr3B 85.185 81 11 1 2792 2872 85351606 85351685 1.540000e-11 82.4
28 TraesCS4A01G209400 chr3B 86.957 69 8 1 807 875 764119362 764119429 7.150000e-10 76.8
29 TraesCS4A01G209400 chr3D 86.828 372 38 8 2182 2552 363124088 363124449 8.030000e-109 405.0
30 TraesCS4A01G209400 chr3D 85.542 83 11 1 2792 2874 431840050 431840131 1.190000e-12 86.1
31 TraesCS4A01G209400 chr3D 95.455 44 2 0 831 874 369457574 369457617 3.330000e-08 71.3
32 TraesCS4A01G209400 chr7D 92.748 262 19 0 1 262 400476365 400476104 4.870000e-101 379.0
33 TraesCS4A01G209400 chr7D 84.192 291 13 8 576 866 400476106 400475849 1.110000e-62 252.0
34 TraesCS4A01G209400 chr7D 96.850 127 4 0 2551 2677 567712580 567712454 5.230000e-51 213.0
35 TraesCS4A01G209400 chr3A 85.753 372 33 9 2182 2552 483483581 483483933 6.300000e-100 375.0
36 TraesCS4A01G209400 chr3A 79.570 186 28 6 421 598 639643370 639643553 2.520000e-24 124.0
37 TraesCS4A01G209400 chr3A 85.542 83 11 1 2792 2874 569236543 569236624 1.190000e-12 86.1
38 TraesCS4A01G209400 chr1D 90.000 300 16 9 576 874 88755968 88755682 6.300000e-100 375.0
39 TraesCS4A01G209400 chr1D 90.840 262 24 0 1 262 88756227 88755966 1.060000e-92 351.0
40 TraesCS4A01G209400 chr1D 96.154 130 5 0 2551 2680 90518861 90518732 5.230000e-51 213.0
41 TraesCS4A01G209400 chr5D 89.632 299 13 12 576 874 199730171 199730451 1.360000e-96 364.0
42 TraesCS4A01G209400 chr5D 91.221 262 23 0 1 262 199729912 199730173 2.280000e-94 357.0
43 TraesCS4A01G209400 chr5D 96.212 132 5 0 2551 2682 241844078 241844209 4.040000e-52 217.0
44 TraesCS4A01G209400 chr5D 95.455 132 6 0 2551 2682 115924648 115924517 1.880000e-50 211.0
45 TraesCS4A01G209400 chr1A 90.840 262 24 0 1 262 517801077 517800816 1.060000e-92 351.0
46 TraesCS4A01G209400 chr1A 91.165 249 13 7 576 824 517801816 517801577 4.970000e-86 329.0
47 TraesCS4A01G209400 chr1A 88.043 276 18 7 576 851 517800818 517800558 5.010000e-81 313.0
48 TraesCS4A01G209400 chr1A 76.518 247 35 11 424 653 13488345 13488105 5.450000e-21 113.0
49 TraesCS4A01G209400 chr1B 95.420 131 6 0 2551 2681 643155994 643156124 6.760000e-50 209.0
50 TraesCS4A01G209400 chr1B 97.143 35 0 1 5893 5927 322736061 322736028 2.590000e-04 58.4
51 TraesCS4A01G209400 chr2D 93.007 143 7 3 2550 2689 351287924 351287782 8.750000e-49 206.0
52 TraesCS4A01G209400 chr2D 97.500 40 1 0 835 874 487613554 487613593 1.200000e-07 69.4
53 TraesCS4A01G209400 chr2D 100.000 29 0 0 5892 5920 78690659 78690687 3.000000e-03 54.7
54 TraesCS4A01G209400 chr7B 84.821 112 17 0 424 535 572508193 572508082 5.450000e-21 113.0
55 TraesCS4A01G209400 chr5B 76.518 247 35 11 424 653 141158900 141158660 5.450000e-21 113.0
56 TraesCS4A01G209400 chr6B 83.784 111 16 2 424 533 45731055 45730946 3.280000e-18 104.0
57 TraesCS4A01G209400 chr6B 85.915 71 8 1 5895 5963 641047832 641047902 2.570000e-09 75.0
58 TraesCS4A01G209400 chr7A 96.875 32 1 0 5930 5961 542627618 542627649 3.000000e-03 54.7
59 TraesCS4A01G209400 chr2B 100.000 29 0 0 5894 5922 118318770 118318742 3.000000e-03 54.7
60 TraesCS4A01G209400 chr2B 100.000 29 0 0 5892 5920 153898092 153898064 3.000000e-03 54.7


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 TraesCS4A01G209400 chr4A 502900041 502906693 6652 False 12286.00 12286 100.00000 1 6653 1 chr4A.!!$F1 6652
1 TraesCS4A01G209400 chr4D 90988371 90994233 5862 False 2169.75 3627 95.53700 1017 6653 4 chr4D.!!$F2 5636
2 TraesCS4A01G209400 chr4B 127102570 127105689 3119 False 1671.00 2405 93.65250 4002 6607 2 chr4B.!!$F2 2605
3 TraesCS4A01G209400 chr4B 127092579 127095602 3023 False 986.00 2021 93.83275 989 4018 4 chr4B.!!$F1 3029
4 TraesCS4A01G209400 chr6D 168287419 168288263 844 True 1086.00 1086 89.67900 1 871 1 chr6D.!!$R2 870
5 TraesCS4A01G209400 chr5A 269848593 269849446 853 True 1053.00 1053 88.78700 1 874 1 chr5A.!!$R1 873
6 TraesCS4A01G209400 chr3B 659451691 659452280 589 True 789.00 789 91.03200 178 760 1 chr3B.!!$R1 582
7 TraesCS4A01G209400 chr7D 400475849 400476365 516 True 315.50 379 88.47000 1 866 2 chr7D.!!$R2 865
8 TraesCS4A01G209400 chr1D 88755682 88756227 545 True 363.00 375 90.42000 1 874 2 chr1D.!!$R2 873
9 TraesCS4A01G209400 chr5D 199729912 199730451 539 False 360.50 364 90.42650 1 874 2 chr5D.!!$F2 873
10 TraesCS4A01G209400 chr1A 517800558 517801816 1258 True 331.00 351 90.01600 1 851 3 chr1A.!!$R2 850

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
820 1894 0.038892 GACACATCGTACGTGGTGGT 60.039 55.0 30.38 21.42 38.74 4.16 F
821 1895 0.319211 ACACATCGTACGTGGTGGTG 60.319 55.0 30.38 24.41 38.74 4.17 F
2307 3778 0.253160 TGGGTGTATGAGGCCTCCTT 60.253 55.0 29.95 19.25 31.76 3.36 F
2564 4036 0.259938 TAAGGTACTCCCTCCGTCCC 59.740 60.0 0.00 0.00 45.47 4.46 F
3418 5313 0.815615 GCACCAAGAATCTAGCGGGG 60.816 60.0 0.00 0.00 0.00 5.73 F
3979 5883 1.191535 TGACGTTCCAGGGATAGGTG 58.808 55.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 3764 0.105039 CCGTCAAGGAGGCCTCATAC 59.895 60.000 33.29 21.14 45.00 2.39 R
2352 3823 0.322277 AGCGACGTCCTAGAGGTCAA 60.322 55.000 10.58 0.00 44.50 3.18 R
4013 5917 0.396417 AGACAGGTAGCTCGCAGGAT 60.396 55.000 0.00 0.00 0.00 3.24 R
4211 6117 1.064685 GGGATCAACGGGTTCCTCATT 60.065 52.381 0.00 0.00 35.94 2.57 R
5407 7370 2.604914 CGTGCACAGTTCTTAGCTATGG 59.395 50.000 18.64 0.00 0.00 2.74 R
5947 8594 1.006758 TCCACAATACTCCCTCCGTCT 59.993 52.381 0.00 0.00 0.00 4.18 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
28 768 6.106673 AGATCAACTATTGGGTAACTGAACG 58.893 40.000 0.00 0.00 0.00 3.95
72 812 4.753662 TAGCCTGACCGCCGGAGT 62.754 66.667 11.71 0.00 0.00 3.85
96 836 1.483827 AGCATGTGTGATCATCCGACT 59.516 47.619 0.00 0.00 0.00 4.18
112 852 0.686769 GACTCCCCCGTGTCATACCT 60.687 60.000 0.00 0.00 33.57 3.08
149 889 3.723235 CTAGCACTCGCCGCACCAT 62.723 63.158 0.00 0.00 39.83 3.55
237 978 0.958382 GGCCAGCATACGGAACAACA 60.958 55.000 0.00 0.00 0.00 3.33
242 983 3.733727 CCAGCATACGGAACAACAAAAAC 59.266 43.478 0.00 0.00 0.00 2.43
254 995 1.007387 CAAAAACCGAGCAGCACCC 60.007 57.895 0.00 0.00 0.00 4.61
267 1329 3.941188 CACCCGCACACCACTCCT 61.941 66.667 0.00 0.00 0.00 3.69
273 1335 2.294078 GCACACCACTCCTAGGCCT 61.294 63.158 11.78 11.78 0.00 5.19
312 1374 2.102420 CGACATACCATTGGACAGCCTA 59.898 50.000 10.37 0.00 34.31 3.93
321 1383 4.321304 CCATTGGACAGCCTATAGTACGAG 60.321 50.000 0.00 0.00 34.31 4.18
331 1393 2.578586 ATAGTACGAGCACCCCCGGT 62.579 60.000 0.00 0.00 35.62 5.28
360 1422 2.881513 ACAAATGCGTCATACACCAACA 59.118 40.909 0.00 0.00 0.00 3.33
364 1426 2.289565 TGCGTCATACACCAACAACAA 58.710 42.857 0.00 0.00 0.00 2.83
376 1438 0.865769 AACAACAACGTCGATCTGGC 59.134 50.000 0.00 0.00 0.00 4.85
386 1448 3.129502 GATCTGGCGCTGCTGCAA 61.130 61.111 16.29 6.18 39.64 4.08
460 1522 1.168407 CGCCAATCTCGCCAATGGAT 61.168 55.000 2.05 0.00 34.82 3.41
481 1543 2.094700 TGAACGTGATCTAGAGTGGTGC 60.095 50.000 0.00 0.00 0.00 5.01
624 1686 4.166888 GAGGCGGCATCTGGAGCA 62.167 66.667 13.08 0.00 0.00 4.26
676 1744 3.930012 GGATCGGGAGCGAAGGGG 61.930 72.222 0.00 0.00 0.00 4.79
677 1745 3.155167 GATCGGGAGCGAAGGGGT 61.155 66.667 0.00 0.00 0.00 4.95
678 1746 1.831286 GATCGGGAGCGAAGGGGTA 60.831 63.158 0.00 0.00 0.00 3.69
679 1747 1.807495 GATCGGGAGCGAAGGGGTAG 61.807 65.000 0.00 0.00 0.00 3.18
680 1748 3.537874 CGGGAGCGAAGGGGTAGG 61.538 72.222 0.00 0.00 0.00 3.18
681 1749 3.162154 GGGAGCGAAGGGGTAGGG 61.162 72.222 0.00 0.00 0.00 3.53
707 1775 1.686110 GATGAGGAGGACGGGTGGT 60.686 63.158 0.00 0.00 0.00 4.16
747 1816 3.326880 TGGGTAGTGGGTCTCTTTTCTTC 59.673 47.826 0.00 0.00 0.00 2.87
756 1825 6.975197 GTGGGTCTCTTTTCTTCTTCTTTTTG 59.025 38.462 0.00 0.00 0.00 2.44
798 1872 0.759436 GATAGGAGAAGCGGGGGTGA 60.759 60.000 0.00 0.00 0.00 4.02
819 1893 0.734942 GGACACATCGTACGTGGTGG 60.735 60.000 30.38 19.42 38.74 4.61
820 1894 0.038892 GACACATCGTACGTGGTGGT 60.039 55.000 30.38 21.42 38.74 4.16
821 1895 0.319211 ACACATCGTACGTGGTGGTG 60.319 55.000 30.38 24.41 38.74 4.17
846 1920 0.466963 GGGGGTCGAACCATTACGAT 59.533 55.000 23.64 0.00 41.02 3.73
854 1928 4.266976 GTCGAACCATTACGATGTTCGATT 59.733 41.667 23.78 0.00 45.67 3.34
874 1948 8.722622 TCGATTCCCCTTTAATAGTAGAGATT 57.277 34.615 0.00 0.00 0.00 2.40
875 1949 8.585881 TCGATTCCCCTTTAATAGTAGAGATTG 58.414 37.037 0.00 0.00 0.00 2.67
876 1950 8.368668 CGATTCCCCTTTAATAGTAGAGATTGT 58.631 37.037 0.00 0.00 0.00 2.71
879 1953 9.496710 TTCCCCTTTAATAGTAGAGATTGTACA 57.503 33.333 0.00 0.00 0.00 2.90
880 1954 9.670442 TCCCCTTTAATAGTAGAGATTGTACAT 57.330 33.333 0.00 0.00 0.00 2.29
881 1955 9.712305 CCCCTTTAATAGTAGAGATTGTACATG 57.288 37.037 0.00 0.00 0.00 3.21
882 1956 9.209175 CCCTTTAATAGTAGAGATTGTACATGC 57.791 37.037 0.00 0.00 0.00 4.06
883 1957 9.209175 CCTTTAATAGTAGAGATTGTACATGCC 57.791 37.037 0.00 0.00 0.00 4.40
884 1958 9.209175 CTTTAATAGTAGAGATTGTACATGCCC 57.791 37.037 0.00 0.00 0.00 5.36
885 1959 8.492415 TTAATAGTAGAGATTGTACATGCCCT 57.508 34.615 0.00 0.00 0.00 5.19
886 1960 9.596308 TTAATAGTAGAGATTGTACATGCCCTA 57.404 33.333 0.00 0.00 0.00 3.53
887 1961 7.710676 ATAGTAGAGATTGTACATGCCCTAG 57.289 40.000 0.00 0.00 0.00 3.02
888 1962 4.835615 AGTAGAGATTGTACATGCCCTAGG 59.164 45.833 0.06 0.06 0.00 3.02
889 1963 2.975489 AGAGATTGTACATGCCCTAGGG 59.025 50.000 24.89 24.89 38.57 3.53
899 1973 4.530857 CCCTAGGGCGCCGAACAG 62.531 72.222 22.54 13.90 0.00 3.16
900 1974 4.530857 CCTAGGGCGCCGAACAGG 62.531 72.222 22.54 19.02 44.97 4.00
901 1975 3.458163 CTAGGGCGCCGAACAGGA 61.458 66.667 22.54 0.00 45.00 3.86
902 1976 3.432051 CTAGGGCGCCGAACAGGAG 62.432 68.421 22.54 5.41 45.00 3.69
908 1982 2.185608 GCCGAACAGGAGCTCCTC 59.814 66.667 33.06 20.44 46.65 3.71
909 1983 2.492090 CCGAACAGGAGCTCCTCG 59.508 66.667 33.06 29.77 46.65 4.63
910 1984 2.046864 CCGAACAGGAGCTCCTCGA 61.047 63.158 32.96 0.00 46.65 4.04
911 1985 1.388065 CCGAACAGGAGCTCCTCGAT 61.388 60.000 32.96 22.86 46.65 3.59
912 1986 0.457851 CGAACAGGAGCTCCTCGATT 59.542 55.000 33.06 24.95 46.65 3.34
913 1987 1.134965 CGAACAGGAGCTCCTCGATTT 60.135 52.381 33.06 21.47 46.65 2.17
914 1988 2.545731 GAACAGGAGCTCCTCGATTTC 58.454 52.381 33.06 24.81 46.65 2.17
915 1989 1.859302 ACAGGAGCTCCTCGATTTCT 58.141 50.000 33.06 6.69 46.65 2.52
916 1990 1.754226 ACAGGAGCTCCTCGATTTCTC 59.246 52.381 33.06 1.32 46.65 2.87
917 1991 1.753649 CAGGAGCTCCTCGATTTCTCA 59.246 52.381 33.06 0.00 46.65 3.27
918 1992 2.167281 CAGGAGCTCCTCGATTTCTCAA 59.833 50.000 33.06 0.00 46.65 3.02
919 1993 3.037549 AGGAGCTCCTCGATTTCTCAAT 58.962 45.455 30.40 2.58 44.77 2.57
920 1994 3.129871 GGAGCTCCTCGATTTCTCAATG 58.870 50.000 26.25 0.00 0.00 2.82
921 1995 3.431486 GGAGCTCCTCGATTTCTCAATGT 60.431 47.826 26.25 0.00 0.00 2.71
922 1996 3.791245 AGCTCCTCGATTTCTCAATGTC 58.209 45.455 0.00 0.00 0.00 3.06
923 1997 3.450457 AGCTCCTCGATTTCTCAATGTCT 59.550 43.478 0.00 0.00 0.00 3.41
924 1998 4.646945 AGCTCCTCGATTTCTCAATGTCTA 59.353 41.667 0.00 0.00 0.00 2.59
925 1999 5.127845 AGCTCCTCGATTTCTCAATGTCTAA 59.872 40.000 0.00 0.00 0.00 2.10
926 2000 5.812642 GCTCCTCGATTTCTCAATGTCTAAA 59.187 40.000 0.00 0.00 0.00 1.85
927 2001 6.313905 GCTCCTCGATTTCTCAATGTCTAAAA 59.686 38.462 0.00 0.00 0.00 1.52
928 2002 7.148407 GCTCCTCGATTTCTCAATGTCTAAAAA 60.148 37.037 0.00 0.00 0.00 1.94
1009 2083 3.174987 CTCACCCACCCACCCACA 61.175 66.667 0.00 0.00 0.00 4.17
1015 2089 4.596585 CACCCACCCACACCCCAC 62.597 72.222 0.00 0.00 0.00 4.61
1187 2263 2.856864 TGTGGGTACTCCTCCATCTCTA 59.143 50.000 0.00 0.00 35.28 2.43
1462 2539 0.543749 GGGTAGATTGTGAGCTGCCT 59.456 55.000 0.00 0.00 42.82 4.75
1491 2568 3.582120 CGTGCGTGTGGGCAGTTT 61.582 61.111 0.00 0.00 44.93 2.66
1507 2584 1.610522 AGTTTGATGCTTGCTTTCGCT 59.389 42.857 0.00 0.00 36.97 4.93
1742 3212 6.443832 AGTCCATCCCCAAAAGCTAAATATT 58.556 36.000 0.00 0.00 0.00 1.28
1794 3264 6.239217 TCAGTTTATCACTCATATGGCACT 57.761 37.500 2.13 0.00 30.92 4.40
1890 3361 2.167487 GGGAGAGGCACTTCTCAGTAAG 59.833 54.545 11.36 0.00 41.55 2.34
2064 3535 1.879380 CAGCGGTGAATTTTGTCTCCA 59.121 47.619 9.50 0.00 31.81 3.86
2241 3712 1.308998 CCTCCAACTTCAACTTGCGT 58.691 50.000 0.00 0.00 0.00 5.24
2292 3763 0.905337 GACACCTCAGCCTACTGGGT 60.905 60.000 0.00 0.00 43.50 4.51
2307 3778 0.253160 TGGGTGTATGAGGCCTCCTT 60.253 55.000 29.95 19.25 31.76 3.36
2328 3799 2.029964 GGCGTCCTTTCGTGTCCA 59.970 61.111 0.00 0.00 0.00 4.02
2352 3823 2.280552 CCCACATTGCTTGCAGCCT 61.281 57.895 5.82 0.00 41.51 4.58
2419 3890 2.363406 AGCTCCTTTGCCATGGCC 60.363 61.111 33.44 16.18 41.09 5.36
2435 3906 2.851071 GCCCGTGCTCTCGATAGCT 61.851 63.158 21.63 0.00 43.19 3.32
2442 3913 0.515564 GCTCTCGATAGCTCCGACTC 59.484 60.000 15.01 0.00 39.50 3.36
2517 3989 6.348950 CCATGTTGGATTTCGCTAGTTGTTTA 60.349 38.462 0.00 0.00 40.96 2.01
2545 4017 3.009473 AGTGGACAGGTTCTGCATACAAT 59.991 43.478 0.00 0.00 34.37 2.71
2549 4021 4.576463 GGACAGGTTCTGCATACAATAAGG 59.424 45.833 0.00 0.00 34.37 2.69
2550 4022 5.179452 ACAGGTTCTGCATACAATAAGGT 57.821 39.130 0.00 0.00 34.37 3.50
2551 4023 6.308015 ACAGGTTCTGCATACAATAAGGTA 57.692 37.500 0.00 0.00 34.37 3.08
2552 4024 6.113411 ACAGGTTCTGCATACAATAAGGTAC 58.887 40.000 0.00 0.00 34.37 3.34
2553 4025 6.070194 ACAGGTTCTGCATACAATAAGGTACT 60.070 38.462 0.00 0.00 35.49 2.73
2554 4026 6.480320 CAGGTTCTGCATACAATAAGGTACTC 59.520 42.308 0.00 0.00 38.49 2.59
2555 4027 5.758784 GGTTCTGCATACAATAAGGTACTCC 59.241 44.000 0.00 0.00 38.49 3.85
2556 4028 5.546621 TCTGCATACAATAAGGTACTCCC 57.453 43.478 0.00 0.00 38.49 4.30
2558 4030 5.304614 TCTGCATACAATAAGGTACTCCCTC 59.695 44.000 0.00 0.00 45.47 4.30
2559 4031 4.347000 TGCATACAATAAGGTACTCCCTCC 59.653 45.833 0.00 0.00 45.47 4.30
2560 4032 4.560919 GCATACAATAAGGTACTCCCTCCG 60.561 50.000 0.00 0.00 45.47 4.63
2561 4033 3.111741 ACAATAAGGTACTCCCTCCGT 57.888 47.619 0.00 0.00 45.47 4.69
2562 4034 3.029570 ACAATAAGGTACTCCCTCCGTC 58.970 50.000 0.00 0.00 45.47 4.79
2563 4035 2.364647 CAATAAGGTACTCCCTCCGTCC 59.635 54.545 0.00 0.00 45.47 4.79
2564 4036 0.259938 TAAGGTACTCCCTCCGTCCC 59.740 60.000 0.00 0.00 45.47 4.46
2565 4037 1.807771 AAGGTACTCCCTCCGTCCCA 61.808 60.000 0.00 0.00 45.47 4.37
2566 4038 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
2567 4039 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
2568 4040 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2569 4041 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2570 4042 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2571 4043 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2572 4044 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2573 4045 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2574 4046 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2575 4047 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2576 4048 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2577 4049 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2578 4050 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2579 4051 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2580 4052 5.566469 TCCGTCCCAAAATTCTTGTCTTAT 58.434 37.500 0.00 0.00 0.00 1.73
2581 4053 6.713276 TCCGTCCCAAAATTCTTGTCTTATA 58.287 36.000 0.00 0.00 0.00 0.98
2582 4054 7.343357 TCCGTCCCAAAATTCTTGTCTTATAT 58.657 34.615 0.00 0.00 0.00 0.86
2583 4055 7.832187 TCCGTCCCAAAATTCTTGTCTTATATT 59.168 33.333 0.00 0.00 0.00 1.28
2584 4056 8.466798 CCGTCCCAAAATTCTTGTCTTATATTT 58.533 33.333 0.00 0.00 0.00 1.40
2631 4103 9.578439 AGTTACGTTTTAGTGTTAGATACATCC 57.422 33.333 0.00 0.00 39.39 3.51
2632 4104 8.526681 GTTACGTTTTAGTGTTAGATACATCCG 58.473 37.037 0.00 0.00 39.39 4.18
2633 4105 6.624423 ACGTTTTAGTGTTAGATACATCCGT 58.376 36.000 0.00 0.00 39.39 4.69
2634 4106 7.761409 ACGTTTTAGTGTTAGATACATCCGTA 58.239 34.615 0.00 0.00 39.39 4.02
2635 4107 8.408601 ACGTTTTAGTGTTAGATACATCCGTAT 58.591 33.333 0.00 0.00 41.16 3.06
2651 4123 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2652 4124 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2653 4125 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2654 4126 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2655 4127 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2656 4128 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2664 4136 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2665 4137 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2666 4138 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2667 4139 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2668 4140 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2669 4141 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2670 4142 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2671 4143 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2672 4144 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2673 4145 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2688 4160 6.318396 GGACGGAGGGAGTATATATGAACTAC 59.682 46.154 0.00 0.00 0.00 2.73
2690 4162 7.236529 ACGGAGGGAGTATATATGAACTACAA 58.763 38.462 0.00 0.00 0.00 2.41
2710 4182 9.252635 ACTACAATTAAACAGTACTAGTAGCCT 57.747 33.333 1.87 0.00 31.98 4.58
2740 4212 6.542821 TCACAAGAAACAGGGAAGATATGTT 58.457 36.000 0.00 0.00 38.76 2.71
2765 4237 7.461182 AAGTCGTCCATGAATTTTGGAATTA 57.539 32.000 11.46 0.56 44.62 1.40
2997 4469 1.209747 GGGGGTGGACTAGATGAACAC 59.790 57.143 0.00 0.00 0.00 3.32
3000 4472 3.244770 GGGGTGGACTAGATGAACACAAA 60.245 47.826 0.00 0.00 33.91 2.83
3208 5103 6.923478 AGGGATAGGTAGGAGGATATGATACT 59.077 42.308 0.00 0.00 0.00 2.12
3389 5284 5.957771 ATTGGAACTAGATTGAGGTAGCA 57.042 39.130 0.00 0.00 0.00 3.49
3418 5313 0.815615 GCACCAAGAATCTAGCGGGG 60.816 60.000 0.00 0.00 0.00 5.73
3450 5345 1.557099 TGAATAGTGTCTCGTGGGCT 58.443 50.000 0.00 0.00 0.00 5.19
3561 5457 7.941431 AGTACTACACAGCTAAGATAACTGT 57.059 36.000 0.00 0.00 45.25 3.55
3591 5487 1.702401 TGGACAGTTTCTGGCATGGTA 59.298 47.619 4.97 0.00 42.18 3.25
3764 5660 3.476295 ACTAGTGCATTGCAATTCACG 57.524 42.857 28.41 20.48 41.47 4.35
3840 5736 2.525368 AGGGTTAAGGTGCATTTGACC 58.475 47.619 15.33 15.33 34.44 4.02
3855 5751 4.301072 TTTGACCTGAACCCCATCTTAG 57.699 45.455 0.00 0.00 0.00 2.18
3868 5764 3.373001 CCCATCTTAGCTGGAATTGGGAA 60.373 47.826 18.01 0.00 44.15 3.97
3869 5765 4.280819 CCATCTTAGCTGGAATTGGGAAA 58.719 43.478 0.00 0.00 35.70 3.13
3979 5883 1.191535 TGACGTTCCAGGGATAGGTG 58.808 55.000 0.00 0.00 0.00 4.00
4011 5915 8.682936 AATAACCAGCCTAGAATAGAACAATG 57.317 34.615 0.00 0.00 42.77 2.82
4013 5917 6.808321 ACCAGCCTAGAATAGAACAATGTA 57.192 37.500 0.00 0.00 42.77 2.29
4068 5974 2.381911 TCCCGTCCGTAGCTCTTTATT 58.618 47.619 0.00 0.00 0.00 1.40
4121 6027 3.838565 TGGTTTTCATACCAGAAAGGCA 58.161 40.909 0.00 0.00 43.14 4.75
4151 6057 6.219417 TGCACCATTCATAAAAGGTTATGG 57.781 37.500 6.62 0.00 44.62 2.74
4179 6085 7.014038 ACAGTCAATTTCATTCTCTCAGCTTTT 59.986 33.333 0.00 0.00 0.00 2.27
4211 6117 3.410631 TGTTGTTTTATCTCAGGGCGA 57.589 42.857 0.00 0.00 0.00 5.54
4336 6246 7.708998 TGTTGTAACACCCTCTTAATTTTGAC 58.291 34.615 0.00 0.00 33.17 3.18
4374 6284 6.018262 TGCGACAATACTGCTATTTCCATTAC 60.018 38.462 0.00 0.00 0.00 1.89
4377 6287 5.763204 ACAATACTGCTATTTCCATTACGGG 59.237 40.000 0.00 0.00 34.36 5.28
4459 6369 3.105937 GTGAAAGTTTTTCCGCTGTGAC 58.894 45.455 0.00 0.00 0.00 3.67
4688 6611 5.554822 TTCCAAAACACAGTATATTCGGC 57.445 39.130 0.00 0.00 0.00 5.54
4780 6703 8.827832 TGAAAACCATTTAGATCTCCATTGAT 57.172 30.769 0.00 0.00 0.00 2.57
5152 7076 1.351153 GGCGCTACTTTCAGTGAGTC 58.649 55.000 7.64 0.00 0.00 3.36
5215 7178 1.464997 GTCGAGTCTGCAAATTGTCCC 59.535 52.381 0.00 0.00 0.00 4.46
5368 7331 7.623630 TCTGGTACTGATCATTTTTCTCATCA 58.376 34.615 0.00 0.00 0.00 3.07
5407 7370 6.421405 GCAAATTGACAAGATTTCAACAACC 58.579 36.000 0.00 0.00 35.82 3.77
5437 7400 0.533978 AACTGTGCACGCACCATGTA 60.534 50.000 18.91 0.00 45.63 2.29
5574 7539 7.772292 ACTATGTGATCATGCTTACAGATGTTT 59.228 33.333 0.00 0.00 35.70 2.83
5615 7580 5.077564 AGGGTGGAAACATAGTCTTTTTCC 58.922 41.667 11.06 11.06 45.85 3.13
5692 8095 9.295825 CCCTCTGTGCCAAAATATAATGTATTA 57.704 33.333 0.00 0.00 0.00 0.98
5727 8130 8.232913 ACAAGTCAATGTTTACTATGTTTGGT 57.767 30.769 0.00 0.00 0.00 3.67
5820 8223 9.790297 ATGGATCTAATGGTACTAATCTGGTAT 57.210 33.333 0.00 0.00 0.00 2.73
5917 8547 7.024345 TGTACTCCCTCCGTCTCATAATATA 57.976 40.000 0.00 0.00 0.00 0.86
5919 8549 7.610692 TGTACTCCCTCCGTCTCATAATATAAG 59.389 40.741 0.00 0.00 0.00 1.73
5920 8550 6.553857 ACTCCCTCCGTCTCATAATATAAGT 58.446 40.000 0.00 0.00 0.00 2.24
5922 8552 5.715279 TCCCTCCGTCTCATAATATAAGTGG 59.285 44.000 0.00 0.00 0.00 4.00
5923 8553 5.480772 CCCTCCGTCTCATAATATAAGTGGT 59.519 44.000 0.00 0.00 0.00 4.16
5924 8554 6.390721 CCTCCGTCTCATAATATAAGTGGTG 58.609 44.000 0.00 0.00 0.00 4.17
5927 8557 8.467963 TCCGTCTCATAATATAAGTGGTGTTA 57.532 34.615 0.00 0.00 0.00 2.41
5928 8558 8.573885 TCCGTCTCATAATATAAGTGGTGTTAG 58.426 37.037 0.00 0.00 0.00 2.34
6021 8668 6.744418 CAAGAATTGCAACATTGTTGTATCG 58.256 36.000 25.88 5.58 40.39 2.92
6056 8703 9.522804 GTAGACTCAAATCATACAAGGTAGAAG 57.477 37.037 0.00 0.00 0.00 2.85
6061 8708 7.103641 TCAAATCATACAAGGTAGAAGTCCAC 58.896 38.462 0.00 0.00 0.00 4.02
6177 8826 5.784906 TCACCATGGATCAACTATAGGCATA 59.215 40.000 21.47 0.00 0.00 3.14
6276 8925 9.991906 ATGATTTCATCAATCTTGAAACTTTGT 57.008 25.926 1.32 0.00 43.65 2.83
6375 9026 9.533253 AAGAAACTCTTAATTGTTGATGGTTTG 57.467 29.630 0.00 0.00 34.42 2.93
6376 9027 8.912988 AGAAACTCTTAATTGTTGATGGTTTGA 58.087 29.630 0.00 0.00 0.00 2.69
6377 9028 8.871686 AAACTCTTAATTGTTGATGGTTTGAC 57.128 30.769 0.00 0.00 0.00 3.18
6378 9029 7.581213 ACTCTTAATTGTTGATGGTTTGACA 57.419 32.000 0.00 0.00 0.00 3.58
6448 9111 5.348451 CGGATTGATCGTGTGCATTCATATA 59.652 40.000 0.00 0.00 0.00 0.86
6546 9210 4.904241 ACTCAACATTCTTCTCCTTGAGG 58.096 43.478 9.78 0.00 41.38 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.093640 ACGTTCAGTTACCCAATAGTTGATCTA 60.094 37.037 0.00 0.00 0.00 1.98
28 768 3.663105 GTCGTGTTCTACTTCTTCGTCAC 59.337 47.826 0.00 0.00 0.00 3.67
69 809 4.749099 GGATGATCACACATGCTTCTACTC 59.251 45.833 0.00 0.00 36.08 2.59
72 812 3.384467 TCGGATGATCACACATGCTTCTA 59.616 43.478 0.00 0.00 36.67 2.10
96 836 2.363975 GCAGGTATGACACGGGGGA 61.364 63.158 0.00 0.00 0.00 4.81
158 898 2.678934 TAGGTGCGACGGAAGGCT 60.679 61.111 0.00 0.00 36.51 4.58
237 978 2.551912 CGGGTGCTGCTCGGTTTTT 61.552 57.895 0.00 0.00 37.44 1.94
254 995 2.125512 GCCTAGGAGTGGTGTGCG 60.126 66.667 14.75 0.00 0.00 5.34
267 1329 0.107456 CGGAGGACGTACTAGGCCTA 59.893 60.000 13.09 13.09 37.93 3.93
295 1357 5.185249 CGTACTATAGGCTGTCCAATGGTAT 59.815 44.000 4.43 0.00 33.74 2.73
312 1374 1.831286 CCGGGGGTGCTCGTACTAT 60.831 63.158 0.00 0.00 0.00 2.12
344 1406 1.954927 TGTTGTTGGTGTATGACGCA 58.045 45.000 0.00 0.00 0.00 5.24
350 1412 2.823984 TCGACGTTGTTGTTGGTGTAT 58.176 42.857 1.96 0.00 0.00 2.29
360 1422 2.380410 GCGCCAGATCGACGTTGTT 61.380 57.895 0.00 0.00 0.00 2.83
376 1438 1.268386 CCTATGTGAATTGCAGCAGCG 60.268 52.381 0.00 0.00 46.23 5.18
386 1448 4.876107 CGGTTCTTTACAGCCTATGTGAAT 59.124 41.667 0.00 0.00 43.80 2.57
460 1522 2.094700 GCACCACTCTAGATCACGTTCA 60.095 50.000 0.00 0.00 0.00 3.18
481 1543 3.320610 TCCACTCCTCCCTCTTATCTG 57.679 52.381 0.00 0.00 0.00 2.90
676 1744 0.755686 CCTCATCTCCTGCACCCTAC 59.244 60.000 0.00 0.00 0.00 3.18
677 1745 0.636647 TCCTCATCTCCTGCACCCTA 59.363 55.000 0.00 0.00 0.00 3.53
678 1746 0.690411 CTCCTCATCTCCTGCACCCT 60.690 60.000 0.00 0.00 0.00 4.34
679 1747 1.694133 CCTCCTCATCTCCTGCACCC 61.694 65.000 0.00 0.00 0.00 4.61
680 1748 0.689080 TCCTCCTCATCTCCTGCACC 60.689 60.000 0.00 0.00 0.00 5.01
681 1749 0.463620 GTCCTCCTCATCTCCTGCAC 59.536 60.000 0.00 0.00 0.00 4.57
707 1775 2.962786 CGAACGCACGTCCCACAA 60.963 61.111 0.00 0.00 0.00 3.33
798 1872 0.896940 ACCACGTACGATGTGTCCCT 60.897 55.000 24.41 0.00 33.37 4.20
805 1879 1.011968 CACCACCACCACGTACGATG 61.012 60.000 24.41 15.70 0.00 3.84
829 1903 2.304751 ACATCGTAATGGTTCGACCC 57.695 50.000 0.00 0.00 37.50 4.46
846 1920 7.562454 TCTCTACTATTAAAGGGGAATCGAACA 59.438 37.037 0.00 0.00 0.00 3.18
854 1928 9.670442 ATGTACAATCTCTACTATTAAAGGGGA 57.330 33.333 0.00 0.00 0.00 4.81
882 1956 4.530857 CTGTTCGGCGCCCTAGGG 62.531 72.222 24.89 24.89 38.57 3.53
883 1957 4.530857 CCTGTTCGGCGCCCTAGG 62.531 72.222 23.46 18.73 0.00 3.02
884 1958 3.432051 CTCCTGTTCGGCGCCCTAG 62.432 68.421 23.46 13.56 0.00 3.02
885 1959 3.458163 CTCCTGTTCGGCGCCCTA 61.458 66.667 23.46 6.42 0.00 3.53
890 1964 3.764466 AGGAGCTCCTGTTCGGCG 61.764 66.667 34.74 0.00 46.55 6.46
899 1973 2.969628 TTGAGAAATCGAGGAGCTCC 57.030 50.000 26.22 26.22 0.00 4.70
900 1974 3.791245 ACATTGAGAAATCGAGGAGCTC 58.209 45.455 4.71 4.71 0.00 4.09
901 1975 3.450457 AGACATTGAGAAATCGAGGAGCT 59.550 43.478 0.00 0.00 0.00 4.09
902 1976 3.791245 AGACATTGAGAAATCGAGGAGC 58.209 45.455 0.00 0.00 0.00 4.70
903 1977 7.834068 TTTTAGACATTGAGAAATCGAGGAG 57.166 36.000 0.00 0.00 0.00 3.69
974 2048 9.733556 GTGGGTGAGGGATTTTATTTTATTTTT 57.266 29.630 0.00 0.00 0.00 1.94
975 2049 8.325787 GGTGGGTGAGGGATTTTATTTTATTTT 58.674 33.333 0.00 0.00 0.00 1.82
976 2050 7.092623 GGGTGGGTGAGGGATTTTATTTTATTT 60.093 37.037 0.00 0.00 0.00 1.40
977 2051 6.385759 GGGTGGGTGAGGGATTTTATTTTATT 59.614 38.462 0.00 0.00 0.00 1.40
978 2052 5.903010 GGGTGGGTGAGGGATTTTATTTTAT 59.097 40.000 0.00 0.00 0.00 1.40
979 2053 5.222568 TGGGTGGGTGAGGGATTTTATTTTA 60.223 40.000 0.00 0.00 0.00 1.52
980 2054 4.101114 GGGTGGGTGAGGGATTTTATTTT 58.899 43.478 0.00 0.00 0.00 1.82
981 2055 3.078305 TGGGTGGGTGAGGGATTTTATTT 59.922 43.478 0.00 0.00 0.00 1.40
982 2056 2.657459 TGGGTGGGTGAGGGATTTTATT 59.343 45.455 0.00 0.00 0.00 1.40
983 2057 2.024369 GTGGGTGGGTGAGGGATTTTAT 60.024 50.000 0.00 0.00 0.00 1.40
984 2058 1.356398 GTGGGTGGGTGAGGGATTTTA 59.644 52.381 0.00 0.00 0.00 1.52
985 2059 0.114364 GTGGGTGGGTGAGGGATTTT 59.886 55.000 0.00 0.00 0.00 1.82
986 2060 1.774300 GTGGGTGGGTGAGGGATTT 59.226 57.895 0.00 0.00 0.00 2.17
987 2061 2.238701 GGTGGGTGGGTGAGGGATT 61.239 63.158 0.00 0.00 0.00 3.01
988 2062 2.614013 GGTGGGTGGGTGAGGGAT 60.614 66.667 0.00 0.00 0.00 3.85
989 2063 4.995058 GGGTGGGTGGGTGAGGGA 62.995 72.222 0.00 0.00 0.00 4.20
991 2065 3.966543 GTGGGTGGGTGGGTGAGG 61.967 72.222 0.00 0.00 0.00 3.86
1187 2263 1.211456 CTGGAAGGAGATGAGGGCTT 58.789 55.000 0.00 0.00 0.00 4.35
1394 2470 3.271755 TCCCCATTCCAGATCATTTCCAA 59.728 43.478 0.00 0.00 0.00 3.53
1462 2539 3.283684 CGCACGGAAAGGCACCAA 61.284 61.111 0.00 0.00 0.00 3.67
1507 2584 1.544246 TCGAGCTCACGATTCTCCAAA 59.456 47.619 15.40 0.00 37.37 3.28
1562 3032 6.127083 TGCATACACATTTCCATCAGTAGAGA 60.127 38.462 0.00 0.00 0.00 3.10
1563 3033 6.051074 TGCATACACATTTCCATCAGTAGAG 58.949 40.000 0.00 0.00 0.00 2.43
1794 3264 3.311028 GGGGATTAAAGGAAATGGGGGAA 60.311 47.826 0.00 0.00 0.00 3.97
1818 3289 5.419239 TGGGGGATGAAAAGCTATTTTTG 57.581 39.130 0.00 0.00 39.06 2.44
1890 3361 3.385577 GGTCGAGCAGTATTCCTCATTC 58.614 50.000 10.30 0.00 0.00 2.67
1967 3438 0.546122 CCATTTCCCTGGTCATCGGA 59.454 55.000 0.00 0.00 0.00 4.55
1995 3466 1.670406 CTGGAGGTGCAGCACAGAC 60.670 63.158 26.78 15.45 35.86 3.51
2045 3516 1.880027 GTGGAGACAAAATTCACCGCT 59.120 47.619 0.00 0.00 46.06 5.52
2047 3518 1.196808 CCGTGGAGACAAAATTCACCG 59.803 52.381 0.00 0.00 46.06 4.94
2081 3552 2.252072 TAGTCCTCCACGGCAATGGC 62.252 60.000 0.00 0.00 39.85 4.40
2091 3562 1.549170 GGCGAAGAAAGTAGTCCTCCA 59.451 52.381 0.00 0.00 0.00 3.86
2241 3712 0.108804 CCGCGTCAAAGAAGGAGCTA 60.109 55.000 4.92 0.00 0.00 3.32
2248 3719 1.959226 GCTGGACCGCGTCAAAGAA 60.959 57.895 4.92 0.00 33.68 2.52
2292 3763 0.824109 CGTCAAGGAGGCCTCATACA 59.176 55.000 33.29 14.38 30.89 2.29
2293 3764 0.105039 CCGTCAAGGAGGCCTCATAC 59.895 60.000 33.29 21.14 45.00 2.39
2295 3766 3.313874 CCGTCAAGGAGGCCTCAT 58.686 61.111 33.29 25.66 45.00 2.90
2307 3778 2.355363 CACGAAAGGACGCCGTCA 60.355 61.111 20.08 0.00 33.96 4.35
2316 3787 1.966451 GCACCCTGGACACGAAAGG 60.966 63.158 0.00 0.00 0.00 3.11
2352 3823 0.322277 AGCGACGTCCTAGAGGTCAA 60.322 55.000 10.58 0.00 44.50 3.18
2419 3890 1.284408 GGAGCTATCGAGAGCACGG 59.716 63.158 31.59 0.00 45.43 4.94
2517 3989 2.887152 GCAGAACCTGTCCACTGAAATT 59.113 45.455 0.00 0.00 33.43 1.82
2549 4021 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2550 4022 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2551 4023 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2552 4024 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2553 4025 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2554 4026 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2555 4027 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2556 4028 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2557 4029 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2558 4030 5.897377 ATAAGACAAGAATTTTGGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
2605 4077 9.578439 GGATGTATCTAACACTAAAACGTAACT 57.422 33.333 0.00 0.00 42.09 2.24
2606 4078 8.526681 CGGATGTATCTAACACTAAAACGTAAC 58.473 37.037 0.00 0.00 42.09 2.50
2607 4079 8.243426 ACGGATGTATCTAACACTAAAACGTAA 58.757 33.333 0.00 0.00 42.09 3.18
2608 4080 7.761409 ACGGATGTATCTAACACTAAAACGTA 58.239 34.615 0.00 0.00 42.09 3.57
2609 4081 6.624423 ACGGATGTATCTAACACTAAAACGT 58.376 36.000 0.00 0.00 42.09 3.99
2610 4082 8.792831 ATACGGATGTATCTAACACTAAAACG 57.207 34.615 0.00 0.00 42.09 3.60
2625 4097 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2626 4098 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2627 4099 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2628 4100 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2629 4101 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2630 4102 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2638 4110 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2639 4111 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2640 4112 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2641 4113 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2642 4114 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2643 4115 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2644 4116 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2645 4117 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2646 4118 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2647 4119 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2648 4120 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2649 4121 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2650 4122 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2651 4123 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2652 4124 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2653 4125 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2654 4126 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2655 4127 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2656 4128 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2657 4129 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2658 4130 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2659 4131 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2660 4132 4.044952 TCATATATACTCCCTCCGTCCCAA 59.955 45.833 0.00 0.00 0.00 4.12
2661 4133 3.594685 TCATATATACTCCCTCCGTCCCA 59.405 47.826 0.00 0.00 0.00 4.37
2662 4134 4.246712 TCATATATACTCCCTCCGTCCC 57.753 50.000 0.00 0.00 0.00 4.46
2663 4135 5.262804 AGTTCATATATACTCCCTCCGTCC 58.737 45.833 0.00 0.00 0.00 4.79
2664 4136 6.883217 TGTAGTTCATATATACTCCCTCCGTC 59.117 42.308 0.00 0.00 0.00 4.79
2665 4137 6.787170 TGTAGTTCATATATACTCCCTCCGT 58.213 40.000 0.00 0.00 0.00 4.69
2666 4138 7.698506 TTGTAGTTCATATATACTCCCTCCG 57.301 40.000 0.00 0.00 0.00 4.63
2688 4160 9.088512 CAAGAGGCTACTAGTACTGTTTAATTG 57.911 37.037 5.39 0.00 0.00 2.32
2690 4162 8.591114 TCAAGAGGCTACTAGTACTGTTTAAT 57.409 34.615 5.39 0.00 0.00 1.40
2740 4212 7.461182 AATTCCAAAATTCATGGACGACTTA 57.539 32.000 11.42 0.00 46.37 2.24
2765 4237 5.220710 TCTAGCTCAAGAAGTGCTCTTTT 57.779 39.130 2.00 0.00 45.25 2.27
3283 5178 4.265073 AGCTAGCCATGTAAAACAGAAGG 58.735 43.478 12.13 0.00 0.00 3.46
3319 5214 8.669243 GCTACTGACATACTGCTTTAATCTTTT 58.331 33.333 0.00 0.00 0.00 2.27
3389 5284 4.521146 AGATTCTTGGTGCGAAATCTGAT 58.479 39.130 0.00 0.00 0.00 2.90
3418 5313 8.444715 CGAGACACTATTCATCCTATACACTAC 58.555 40.741 0.00 0.00 0.00 2.73
3450 5345 4.097551 TGATTTGAATCTGTGACCCACA 57.902 40.909 5.42 0.00 42.42 4.17
3561 5457 5.163405 GCCAGAAACTGTCCATCTATCTACA 60.163 44.000 0.00 0.00 0.00 2.74
3591 5487 6.840780 AGTAAAATAAACATCAAGCTGCCT 57.159 33.333 0.00 0.00 0.00 4.75
3840 5736 1.839994 TCCAGCTAAGATGGGGTTCAG 59.160 52.381 1.98 0.00 38.44 3.02
3855 5751 4.949856 TGACTAGAATTTCCCAATTCCAGC 59.050 41.667 0.00 0.00 46.80 4.85
3979 5883 4.772886 TCTAGGCTGGTTATTTTCTCCC 57.227 45.455 0.00 0.00 0.00 4.30
4011 5915 1.001158 GACAGGTAGCTCGCAGGATAC 60.001 57.143 0.00 0.00 0.00 2.24
4013 5917 0.396417 AGACAGGTAGCTCGCAGGAT 60.396 55.000 0.00 0.00 0.00 3.24
4121 6027 5.933463 CCTTTTATGAATGGTGCAACACATT 59.067 36.000 6.58 9.54 39.37 2.71
4151 6057 6.149142 AGCTGAGAGAATGAAATTGACTGTTC 59.851 38.462 0.00 0.00 36.07 3.18
4211 6117 1.064685 GGGATCAACGGGTTCCTCATT 60.065 52.381 0.00 0.00 35.94 2.57
4336 6246 4.654091 ATTGTCGCATTAAATTCCCCAG 57.346 40.909 0.00 0.00 0.00 4.45
4374 6284 2.921754 GTGTCATTTCTCGTAACTCCCG 59.078 50.000 0.00 0.00 0.00 5.14
4377 6287 6.128795 CCAAAGAGTGTCATTTCTCGTAACTC 60.129 42.308 0.00 0.00 36.03 3.01
4459 6369 9.590451 AGCTTCAATACAAAAATACCATGAATG 57.410 29.630 0.00 0.00 0.00 2.67
4500 6410 6.183360 GGATGTGAAGGGTGATATTTGAACTG 60.183 42.308 0.00 0.00 0.00 3.16
4610 6532 3.438087 CCTTCACAGTGCAACCAATCTAG 59.562 47.826 0.00 0.00 37.80 2.43
5215 7178 3.852471 TGAAATCGAAACACAGTCACG 57.148 42.857 0.00 0.00 0.00 4.35
5333 7296 6.850752 TGATCAGTACCAGAACTGTAATCA 57.149 37.500 0.00 4.60 45.78 2.57
5368 7331 6.095300 TGTCAATTTGCGTTGGATATGATCTT 59.905 34.615 0.00 0.00 0.00 2.40
5407 7370 2.604914 CGTGCACAGTTCTTAGCTATGG 59.395 50.000 18.64 0.00 0.00 2.74
5593 7558 5.386958 GGAAAAAGACTATGTTTCCACCC 57.613 43.478 15.46 0.00 46.37 4.61
5712 8115 7.604927 TCCTACACATGACCAAACATAGTAAAC 59.395 37.037 0.00 0.00 0.00 2.01
5716 8119 5.755409 TCCTACACATGACCAAACATAGT 57.245 39.130 0.00 0.00 0.00 2.12
5855 8258 8.781067 TTCAAAAGTGAAATGTTTCTACATCG 57.219 30.769 6.99 0.00 44.14 3.84
5932 8579 8.197592 TCCCTCCGTCTTATAATATAAAAGCA 57.802 34.615 0.00 0.00 0.00 3.91
5944 8591 3.641906 CCACAATACTCCCTCCGTCTTAT 59.358 47.826 0.00 0.00 0.00 1.73
5946 8593 1.831736 CCACAATACTCCCTCCGTCTT 59.168 52.381 0.00 0.00 0.00 3.01
5947 8594 1.006758 TCCACAATACTCCCTCCGTCT 59.993 52.381 0.00 0.00 0.00 4.18
5963 8610 4.718961 AGCACATATTCCCTATGTTCCAC 58.281 43.478 0.00 0.00 46.71 4.02
6021 8668 6.560253 ATGATTTGAGTCTACCAACACAAC 57.440 37.500 0.00 0.00 30.95 3.32
6056 8703 8.665685 AGAAAACTCACATTTTATATCGTGGAC 58.334 33.333 0.00 0.00 31.90 4.02
6374 9025 7.064134 GTCCATTTGTACTTGACGATAATGTCA 59.936 37.037 0.00 0.00 46.63 3.58
6375 9026 7.064134 TGTCCATTTGTACTTGACGATAATGTC 59.936 37.037 0.00 0.00 39.37 3.06
6376 9027 6.876789 TGTCCATTTGTACTTGACGATAATGT 59.123 34.615 0.00 0.00 0.00 2.71
6377 9028 7.302350 TGTCCATTTGTACTTGACGATAATG 57.698 36.000 0.00 0.00 0.00 1.90
6378 9029 7.148306 GGTTGTCCATTTGTACTTGACGATAAT 60.148 37.037 0.00 0.00 0.00 1.28
6448 9111 8.934023 TCCAACAAATAGACAAGGACTTATTT 57.066 30.769 0.00 0.00 0.00 1.40
6470 9133 5.365605 TCTCCAACAAGTTAAAGTCTCTCCA 59.634 40.000 0.00 0.00 0.00 3.86
6528 9192 3.795688 TGCCTCAAGGAGAAGAATGTT 57.204 42.857 0.00 0.00 37.39 2.71
6546 9210 0.733909 GGGCAAGCTCGTGAAATTGC 60.734 55.000 11.61 11.61 45.64 3.56


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

AutoCloner maintained by Alex Coulton.