Multiple sequence alignment - TraesCS3A01G382900

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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 TraesCS3A01G382900 chr3A 100.000 3832 0 0 1 3832 632424041 632427872 0.000000e+00 7077.0
1 TraesCS3A01G382900 chr3A 78.601 715 144 6 2105 2815 632732234 632732943 7.500000e-127 464.0
2 TraesCS3A01G382900 chr3A 85.217 230 32 2 1202 1430 632736273 632736501 6.400000e-58 235.0
3 TraesCS3A01G382900 chr3A 76.804 388 70 17 1050 1430 632395244 632395618 2.330000e-47 200.0
4 TraesCS3A01G382900 chr3A 75.410 366 90 0 2389 2754 632040851 632041216 1.090000e-40 178.0
5 TraesCS3A01G382900 chr3A 77.778 279 50 7 1627 1899 632288663 632288935 1.100000e-35 161.0
6 TraesCS3A01G382900 chr3A 76.412 301 67 4 1626 1924 632039989 632040287 3.960000e-35 159.0
7 TraesCS3A01G382900 chr3D 93.599 2234 86 25 802 2999 488575581 488573369 0.000000e+00 3280.0
8 TraesCS3A01G382900 chr3D 86.750 717 53 22 3114 3828 488573359 488572683 0.000000e+00 760.0
9 TraesCS3A01G382900 chr3D 79.716 705 138 5 2113 2815 489619568 489620269 4.420000e-139 505.0
10 TraesCS3A01G382900 chr3D 76.546 388 71 17 1050 1430 488584210 488583836 1.090000e-45 195.0
11 TraesCS3A01G382900 chr3D 77.409 301 64 4 1626 1924 488951344 488951046 3.930000e-40 176.0
12 TraesCS3A01G382900 chr3D 77.978 277 47 10 1630 1899 488904214 488903945 1.100000e-35 161.0
13 TraesCS3A01G382900 chr6A 97.344 753 14 1 1 753 396385447 396386193 0.000000e+00 1275.0
14 TraesCS3A01G382900 chr6A 96.448 366 13 0 200 565 306727857 306728222 4.230000e-169 604.0
15 TraesCS3A01G382900 chr6A 95.050 202 10 0 1 202 306727496 306727697 6.180000e-83 318.0
16 TraesCS3A01G382900 chr2A 97.297 740 14 1 1 740 773001739 773002472 0.000000e+00 1251.0
17 TraesCS3A01G382900 chr2A 81.967 122 18 4 1311 1430 765105744 765105863 2.440000e-17 100.0
18 TraesCS3A01G382900 chr2D 96.896 741 16 2 1 740 647481408 647480674 0.000000e+00 1234.0
19 TraesCS3A01G382900 chr2D 77.578 223 44 6 1211 1430 639680199 639679980 3.110000e-26 130.0
20 TraesCS3A01G382900 chr2D 93.056 72 4 1 3010 3081 204417175 204417105 1.880000e-18 104.0
21 TraesCS3A01G382900 chr6D 97.328 711 19 0 1 711 36069211 36069921 0.000000e+00 1208.0
22 TraesCS3A01G382900 chr2B 94.834 755 28 5 1 753 483131836 483132581 0.000000e+00 1168.0
23 TraesCS3A01G382900 chr2B 77.451 204 42 4 1230 1431 798732716 798732515 6.720000e-23 119.0
24 TraesCS3A01G382900 chr2B 94.203 69 3 1 3013 3081 193209394 193209327 1.880000e-18 104.0
25 TraesCS3A01G382900 chr7A 93.758 753 14 4 1 753 61803358 61804077 0.000000e+00 1099.0
26 TraesCS3A01G382900 chr6B 93.201 706 43 3 1 706 661060143 661059443 0.000000e+00 1033.0
27 TraesCS3A01G382900 chr6B 91.781 73 5 1 3009 3081 62536730 62536801 2.440000e-17 100.0
28 TraesCS3A01G382900 chr3B 92.146 713 54 2 1 711 728262852 728263564 0.000000e+00 1005.0
29 TraesCS3A01G382900 chr3B 79.261 704 143 3 2113 2815 652289753 652290454 4.450000e-134 488.0
30 TraesCS3A01G382900 chr3B 76.744 301 66 4 1626 1924 651425996 651426294 8.520000e-37 165.0
31 TraesCS3A01G382900 chr3B 95.522 67 2 1 3015 3081 467226386 467226451 5.240000e-19 106.0
32 TraesCS3A01G382900 chrUn 95.484 155 7 0 557 711 326493151 326493305 8.220000e-62 248.0
33 TraesCS3A01G382900 chr1D 79.359 281 52 6 1647 1924 365083467 365083190 3.910000e-45 193.0
34 TraesCS3A01G382900 chr1D 71.710 661 170 14 2112 2762 365082856 365082203 6.580000e-38 169.0
35 TraesCS3A01G382900 chr1B 79.286 280 54 4 1647 1924 488475160 488474883 3.910000e-45 193.0
36 TraesCS3A01G382900 chr1B 80.269 223 40 4 1211 1431 488482274 488482054 8.520000e-37 165.0
37 TraesCS3A01G382900 chr1A 79.924 264 47 6 1647 1907 463959858 463959598 5.050000e-44 189.0
38 TraesCS3A01G382900 chr1A 71.837 664 164 17 2112 2762 463959264 463958611 6.580000e-38 169.0
39 TraesCS3A01G382900 chr4A 93.151 73 4 1 3009 3081 712733802 712733731 5.240000e-19 106.0
40 TraesCS3A01G382900 chr7D 94.203 69 3 1 3013 3081 47416060 47416127 1.880000e-18 104.0
41 TraesCS3A01G382900 chr7B 95.455 66 2 1 3016 3081 66196620 66196684 1.880000e-18 104.0
42 TraesCS3A01G382900 chr7B 87.500 64 6 2 1821 1883 116047846 116047784 5.310000e-09 73.1
43 TraesCS3A01G382900 chr5D 95.455 66 2 1 3016 3081 504793016 504792952 1.880000e-18 104.0
44 TraesCS3A01G382900 chr5A 95.455 66 2 1 3016 3081 207681915 207681851 1.880000e-18 104.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G382900 chr3A 632424041 632427872 3831 False 7077.0 7077 100.0000 1 3832 1 chr3A.!!$F3 3831
1 TraesCS3A01G382900 chr3A 632732234 632736501 4267 False 349.5 464 81.9090 1202 2815 2 chr3A.!!$F5 1613
2 TraesCS3A01G382900 chr3D 488572683 488575581 2898 True 2020.0 3280 90.1745 802 3828 2 chr3D.!!$R4 3026
3 TraesCS3A01G382900 chr3D 489619568 489620269 701 False 505.0 505 79.7160 2113 2815 1 chr3D.!!$F1 702
4 TraesCS3A01G382900 chr6A 396385447 396386193 746 False 1275.0 1275 97.3440 1 753 1 chr6A.!!$F1 752
5 TraesCS3A01G382900 chr6A 306727496 306728222 726 False 461.0 604 95.7490 1 565 2 chr6A.!!$F2 564
6 TraesCS3A01G382900 chr2A 773001739 773002472 733 False 1251.0 1251 97.2970 1 740 1 chr2A.!!$F2 739
7 TraesCS3A01G382900 chr2D 647480674 647481408 734 True 1234.0 1234 96.8960 1 740 1 chr2D.!!$R3 739
8 TraesCS3A01G382900 chr6D 36069211 36069921 710 False 1208.0 1208 97.3280 1 711 1 chr6D.!!$F1 710
9 TraesCS3A01G382900 chr2B 483131836 483132581 745 False 1168.0 1168 94.8340 1 753 1 chr2B.!!$F1 752
10 TraesCS3A01G382900 chr7A 61803358 61804077 719 False 1099.0 1099 93.7580 1 753 1 chr7A.!!$F1 752
11 TraesCS3A01G382900 chr6B 661059443 661060143 700 True 1033.0 1033 93.2010 1 706 1 chr6B.!!$R1 705
12 TraesCS3A01G382900 chr3B 728262852 728263564 712 False 1005.0 1005 92.1460 1 711 1 chr3B.!!$F4 710
13 TraesCS3A01G382900 chr3B 652289753 652290454 701 False 488.0 488 79.2610 2113 2815 1 chr3B.!!$F3 702

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
758 926 0.033228 ATCATGGCTAGTCTCGCTGC 59.967 55.0 0.0 0.0 0.00 5.25 F
1199 1390 0.178926 TGAGGTTCTTCCGGGGTGTA 60.179 55.0 0.0 0.0 41.99 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 2105 0.323957 GGAAGCGGTAGGTCTTGGTT 59.676 55.0 0.00 0.0 0.0 3.67 R
2944 3157 0.536006 CCCCTCCTAGTACCGTACCG 60.536 65.0 5.02 0.0 0.0 4.02 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
101 103 8.300286 CAGACTTAGATGTGAGTAAAGACTTGA 58.700 37.037 0.00 0.00 35.45 3.02
711 879 5.220815 GCAAATCTGCTGAGTTGGAATCTAG 60.221 44.000 27.53 7.32 45.19 2.43
712 880 4.686191 ATCTGCTGAGTTGGAATCTAGG 57.314 45.455 0.00 0.00 0.00 3.02
713 881 3.713003 TCTGCTGAGTTGGAATCTAGGA 58.287 45.455 0.00 0.00 0.00 2.94
714 882 3.703556 TCTGCTGAGTTGGAATCTAGGAG 59.296 47.826 0.00 0.00 0.00 3.69
715 883 3.445008 TGCTGAGTTGGAATCTAGGAGT 58.555 45.455 0.00 0.00 0.00 3.85
716 884 4.610333 TGCTGAGTTGGAATCTAGGAGTA 58.390 43.478 0.00 0.00 0.00 2.59
723 891 7.069578 TGAGTTGGAATCTAGGAGTATGTTACC 59.930 40.741 0.00 0.00 0.00 2.85
733 901 6.973460 AGGAGTATGTTACCGCTAAGTTAT 57.027 37.500 0.00 0.00 0.00 1.89
740 908 6.237887 TGTTACCGCTAAGTTATTACCCAT 57.762 37.500 0.00 0.00 0.00 4.00
741 909 6.282930 TGTTACCGCTAAGTTATTACCCATC 58.717 40.000 0.00 0.00 0.00 3.51
753 921 4.899352 ATTACCCATCATGGCTAGTCTC 57.101 45.455 0.00 0.00 35.79 3.36
754 922 1.043816 ACCCATCATGGCTAGTCTCG 58.956 55.000 0.00 0.00 35.79 4.04
755 923 0.320247 CCCATCATGGCTAGTCTCGC 60.320 60.000 0.00 0.00 35.79 5.03
756 924 0.678395 CCATCATGGCTAGTCTCGCT 59.322 55.000 0.00 0.00 0.00 4.93
757 925 1.604947 CCATCATGGCTAGTCTCGCTG 60.605 57.143 0.00 0.00 0.00 5.18
758 926 0.033228 ATCATGGCTAGTCTCGCTGC 59.967 55.000 0.00 0.00 0.00 5.25
759 927 1.039785 TCATGGCTAGTCTCGCTGCT 61.040 55.000 0.00 0.00 0.00 4.24
760 928 0.179089 CATGGCTAGTCTCGCTGCTT 60.179 55.000 0.00 0.00 0.00 3.91
761 929 0.179089 ATGGCTAGTCTCGCTGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
762 930 2.170434 GGCTAGTCTCGCTGCTTGC 61.170 63.158 0.00 0.00 38.57 4.01
763 931 2.170434 GCTAGTCTCGCTGCTTGCC 61.170 63.158 0.00 0.00 38.78 4.52
764 932 1.875813 CTAGTCTCGCTGCTTGCCG 60.876 63.158 0.00 0.00 38.78 5.69
765 933 2.549611 CTAGTCTCGCTGCTTGCCGT 62.550 60.000 0.00 0.00 38.78 5.68
766 934 2.819117 TAGTCTCGCTGCTTGCCGTG 62.819 60.000 0.00 0.00 38.78 4.94
772 940 2.281761 CTGCTTGCCGTGGAGGTT 60.282 61.111 0.00 0.00 43.70 3.50
773 941 2.281484 TGCTTGCCGTGGAGGTTC 60.281 61.111 0.00 0.00 43.70 3.62
774 942 2.281484 GCTTGCCGTGGAGGTTCA 60.281 61.111 0.00 0.00 43.70 3.18
775 943 2.617274 GCTTGCCGTGGAGGTTCAC 61.617 63.158 0.00 0.00 43.70 3.18
776 944 1.227823 CTTGCCGTGGAGGTTCACA 60.228 57.895 0.00 0.00 43.70 3.58
777 945 1.227823 TTGCCGTGGAGGTTCACAG 60.228 57.895 0.00 0.00 43.70 3.66
778 946 2.358737 GCCGTGGAGGTTCACAGG 60.359 66.667 0.00 0.00 43.70 4.00
779 947 2.347490 CCGTGGAGGTTCACAGGG 59.653 66.667 0.00 0.00 37.50 4.45
780 948 2.347490 CGTGGAGGTTCACAGGGG 59.653 66.667 0.00 0.00 37.50 4.79
781 949 2.034221 GTGGAGGTTCACAGGGGC 59.966 66.667 0.00 0.00 37.57 5.80
782 950 3.636231 TGGAGGTTCACAGGGGCG 61.636 66.667 0.00 0.00 0.00 6.13
795 963 3.766691 GGGCGCCGTTCAGAGGTA 61.767 66.667 22.54 0.00 0.00 3.08
796 964 2.202756 GGCGCCGTTCAGAGGTAG 60.203 66.667 12.58 0.00 0.00 3.18
797 965 2.707849 GGCGCCGTTCAGAGGTAGA 61.708 63.158 12.58 0.00 0.00 2.59
798 966 1.214589 GCGCCGTTCAGAGGTAGAA 59.785 57.895 0.00 0.00 0.00 2.10
799 967 0.802607 GCGCCGTTCAGAGGTAGAAG 60.803 60.000 0.00 0.00 0.00 2.85
800 968 0.526662 CGCCGTTCAGAGGTAGAAGT 59.473 55.000 0.00 0.00 0.00 3.01
816 984 4.107127 AGAAGTAGGATCTGCCGTATCT 57.893 45.455 0.00 0.00 43.43 1.98
861 1029 1.061729 CGCTGTGCACGTTTTGTCA 59.938 52.632 13.13 0.00 0.00 3.58
911 1079 9.479549 ACTATATGTTTTTGGAATCTTGGATGT 57.520 29.630 0.00 0.00 0.00 3.06
915 1083 5.365025 TGTTTTTGGAATCTTGGATGTTGGA 59.635 36.000 0.00 0.00 0.00 3.53
967 1144 4.216257 GCAGTTGGCAGAGTAGAAAATTGA 59.784 41.667 0.00 0.00 43.97 2.57
972 1149 3.376546 GGCAGAGTAGAAAATTGAGCAGG 59.623 47.826 0.00 0.00 0.00 4.85
1159 1337 3.818210 AGAGACATACTAGCACATCCTCG 59.182 47.826 0.00 0.00 0.00 4.63
1160 1338 2.294791 AGACATACTAGCACATCCTCGC 59.705 50.000 0.00 0.00 0.00 5.03
1178 1356 2.826128 TCGCCTTATCTGTGTCTGAAGT 59.174 45.455 0.00 0.00 0.00 3.01
1179 1357 3.119459 TCGCCTTATCTGTGTCTGAAGTC 60.119 47.826 0.00 0.00 0.00 3.01
1182 1373 4.081972 GCCTTATCTGTGTCTGAAGTCTGA 60.082 45.833 0.00 0.00 0.00 3.27
1194 1385 0.977395 AAGTCTGAGGTTCTTCCGGG 59.023 55.000 0.00 0.00 41.99 5.73
1196 1387 1.157751 TCTGAGGTTCTTCCGGGGT 59.842 57.895 0.00 0.00 41.99 4.95
1198 1389 1.460689 TGAGGTTCTTCCGGGGTGT 60.461 57.895 0.00 0.00 41.99 4.16
1199 1390 0.178926 TGAGGTTCTTCCGGGGTGTA 60.179 55.000 0.00 0.00 41.99 2.90
1200 1391 0.978907 GAGGTTCTTCCGGGGTGTAA 59.021 55.000 0.00 0.00 41.99 2.41
1201 1392 0.689055 AGGTTCTTCCGGGGTGTAAC 59.311 55.000 0.00 0.00 41.99 2.50
1431 1622 2.599677 CCTCCTCTACATCCTGGTACC 58.400 57.143 4.43 4.43 0.00 3.34
1501 1695 1.950828 CACCATCATCAGTCTGGCTC 58.049 55.000 0.00 0.00 33.12 4.70
1541 1739 1.960040 TAGCCATGCTCACCCTGTCG 61.960 60.000 0.00 0.00 40.44 4.35
1736 1934 4.125695 GACGAGAACGACCCCGGG 62.126 72.222 15.80 15.80 42.66 5.73
1869 2067 4.802051 GCTTCGCCATCCCCTGCA 62.802 66.667 0.00 0.00 0.00 4.41
1907 2105 3.760035 GCCGTCTTCTGCCTCGGA 61.760 66.667 6.63 0.00 44.86 4.55
1931 2129 1.067582 GACCTACCGCTTCCATCCG 59.932 63.158 0.00 0.00 0.00 4.18
1936 2134 0.461135 TACCGCTTCCATCCGTTACC 59.539 55.000 0.00 0.00 0.00 2.85
1953 2151 5.236911 CCGTTACCAAGTGCTAACAAGTAAA 59.763 40.000 0.00 0.00 0.00 2.01
1954 2152 6.238429 CCGTTACCAAGTGCTAACAAGTAAAA 60.238 38.462 0.00 0.00 0.00 1.52
1956 2154 7.532884 CGTTACCAAGTGCTAACAAGTAAAATC 59.467 37.037 0.00 0.00 0.00 2.17
1957 2155 6.327279 ACCAAGTGCTAACAAGTAAAATCC 57.673 37.500 0.00 0.00 0.00 3.01
1959 2157 5.390613 CAAGTGCTAACAAGTAAAATCCCG 58.609 41.667 0.00 0.00 0.00 5.14
1960 2158 4.648651 AGTGCTAACAAGTAAAATCCCGT 58.351 39.130 0.00 0.00 0.00 5.28
1985 2183 5.306937 TGATTCTGAAGACCTCCTGTTGTTA 59.693 40.000 0.00 0.00 0.00 2.41
1987 2185 5.623956 TCTGAAGACCTCCTGTTGTTAAA 57.376 39.130 0.00 0.00 0.00 1.52
2022 2220 8.296713 TCTGAAACTGAAACCTTATTTGCATAC 58.703 33.333 0.00 0.00 0.00 2.39
2172 2379 0.034059 CCTCTCGCAGTGGTTCACTT 59.966 55.000 0.00 0.00 42.59 3.16
2573 2780 0.251653 TCTTCTACGACCAGGTGCCT 60.252 55.000 0.00 0.00 0.00 4.75
2713 2920 2.650322 GTTCTCCAACAACCTGAACCA 58.350 47.619 0.00 0.00 33.16 3.67
2795 3002 1.134487 CATGTACTTTGCGCGGGTG 59.866 57.895 8.83 0.00 0.00 4.61
2810 3017 2.550978 CGGGTGTATGTGCCTAAGAAG 58.449 52.381 0.00 0.00 0.00 2.85
2821 3034 3.889538 GTGCCTAAGAAGAAGGGTGTTTT 59.110 43.478 0.00 0.00 34.46 2.43
2822 3035 3.888930 TGCCTAAGAAGAAGGGTGTTTTG 59.111 43.478 0.00 0.00 34.46 2.44
2860 3073 6.663953 TCTGCCCTATAATAACTGGCTACTAG 59.336 42.308 0.00 0.00 42.62 2.57
2865 3078 8.524487 CCCTATAATAACTGGCTACTAGTCTTG 58.476 40.741 0.00 0.00 0.00 3.02
2878 3091 0.681175 AGTCTTGCATTTTGGTGGCC 59.319 50.000 0.00 0.00 0.00 5.36
2882 3095 3.699038 GTCTTGCATTTTGGTGGCCTATA 59.301 43.478 3.32 0.00 0.00 1.31
2942 3155 9.908152 TTTATACATAACGATGATGTAGGACAG 57.092 33.333 12.09 0.00 41.74 3.51
2944 3157 2.604046 AACGATGATGTAGGACAGGC 57.396 50.000 0.00 0.00 0.00 4.85
2946 3159 0.319040 CGATGATGTAGGACAGGCGG 60.319 60.000 0.00 0.00 0.00 6.13
2947 3160 0.753262 GATGATGTAGGACAGGCGGT 59.247 55.000 0.00 0.00 0.00 5.68
2968 3181 0.743097 CGGTACTAGGAGGGGTTTCG 59.257 60.000 0.00 0.00 0.00 3.46
2980 3193 2.040412 AGGGGTTTCGCTCTCAGAAAAT 59.960 45.455 0.00 0.00 39.03 1.82
2990 3203 4.676924 CGCTCTCAGAAAATGGAAAACAAC 59.323 41.667 0.00 0.00 0.00 3.32
2993 3206 7.425606 GCTCTCAGAAAATGGAAAACAACTTA 58.574 34.615 0.00 0.00 0.00 2.24
2994 3207 8.084684 GCTCTCAGAAAATGGAAAACAACTTAT 58.915 33.333 0.00 0.00 0.00 1.73
2997 3210 9.626045 CTCAGAAAATGGAAAACAACTTATACC 57.374 33.333 0.00 0.00 0.00 2.73
2998 3211 8.293867 TCAGAAAATGGAAAACAACTTATACCG 58.706 33.333 0.00 0.00 0.00 4.02
3000 3213 4.976224 ATGGAAAACAACTTATACCGGC 57.024 40.909 0.00 0.00 0.00 6.13
3025 3238 4.189639 CCGCATAGGTAATACTCCTTCC 57.810 50.000 0.00 0.00 36.60 3.46
3026 3239 3.367087 CCGCATAGGTAATACTCCTTCCG 60.367 52.174 0.00 0.00 36.60 4.30
3028 3241 4.615452 CGCATAGGTAATACTCCTTCCGTC 60.615 50.000 0.00 0.00 36.60 4.79
3029 3242 4.321824 GCATAGGTAATACTCCTTCCGTCC 60.322 50.000 0.00 0.00 36.60 4.79
3030 3243 2.675583 AGGTAATACTCCTTCCGTCCC 58.324 52.381 0.00 0.00 30.18 4.46
3031 3244 2.023695 AGGTAATACTCCTTCCGTCCCA 60.024 50.000 0.00 0.00 30.18 4.37
3032 3245 2.970640 GGTAATACTCCTTCCGTCCCAT 59.029 50.000 0.00 0.00 0.00 4.00
3033 3246 4.140853 AGGTAATACTCCTTCCGTCCCATA 60.141 45.833 0.00 0.00 30.18 2.74
3034 3247 4.590222 GGTAATACTCCTTCCGTCCCATAA 59.410 45.833 0.00 0.00 0.00 1.90
3035 3248 5.247792 GGTAATACTCCTTCCGTCCCATAAT 59.752 44.000 0.00 0.00 0.00 1.28
3036 3249 4.891992 ATACTCCTTCCGTCCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
3037 3250 2.478292 ACTCCTTCCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
3038 3251 3.649843 ACTCCTTCCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
3039 3252 4.035112 ACTCCTTCCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
3040 3253 4.472108 ACTCCTTCCGTCCCATAATGTAAA 59.528 41.667 0.00 0.00 0.00 2.01
3041 3254 5.031066 TCCTTCCGTCCCATAATGTAAAG 57.969 43.478 0.00 0.00 0.00 1.85
3042 3255 4.717778 TCCTTCCGTCCCATAATGTAAAGA 59.282 41.667 0.00 0.00 0.00 2.52
3043 3256 4.814771 CCTTCCGTCCCATAATGTAAAGAC 59.185 45.833 0.00 0.00 0.00 3.01
3044 3257 4.049546 TCCGTCCCATAATGTAAAGACG 57.950 45.455 3.52 3.52 44.88 4.18
3045 3258 3.448301 TCCGTCCCATAATGTAAAGACGT 59.552 43.478 9.20 0.00 44.06 4.34
3046 3259 4.081531 TCCGTCCCATAATGTAAAGACGTT 60.082 41.667 9.20 0.00 44.06 3.99
3047 3260 4.632688 CCGTCCCATAATGTAAAGACGTTT 59.367 41.667 9.20 0.00 44.06 3.60
3048 3261 5.122711 CCGTCCCATAATGTAAAGACGTTTT 59.877 40.000 9.20 0.00 44.06 2.43
3049 3262 6.313411 CCGTCCCATAATGTAAAGACGTTTTA 59.687 38.462 9.20 0.00 44.06 1.52
3050 3263 7.011669 CCGTCCCATAATGTAAAGACGTTTTAT 59.988 37.037 9.20 0.00 44.06 1.40
3051 3264 7.849026 CGTCCCATAATGTAAAGACGTTTTATG 59.151 37.037 0.00 0.00 41.48 1.90
3052 3265 8.885722 GTCCCATAATGTAAAGACGTTTTATGA 58.114 33.333 0.00 0.00 36.22 2.15
3053 3266 8.885722 TCCCATAATGTAAAGACGTTTTATGAC 58.114 33.333 0.00 0.00 36.22 3.06
3054 3267 8.670135 CCCATAATGTAAAGACGTTTTATGACA 58.330 33.333 0.00 0.00 36.22 3.58
3055 3268 9.485591 CCATAATGTAAAGACGTTTTATGACAC 57.514 33.333 0.00 0.00 36.22 3.67
3059 3272 8.821147 ATGTAAAGACGTTTTATGACACTACA 57.179 30.769 0.00 0.00 0.00 2.74
3060 3273 8.064447 TGTAAAGACGTTTTATGACACTACAC 57.936 34.615 0.00 0.00 0.00 2.90
3061 3274 7.922278 TGTAAAGACGTTTTATGACACTACACT 59.078 33.333 0.00 0.00 0.00 3.55
3062 3275 9.398170 GTAAAGACGTTTTATGACACTACACTA 57.602 33.333 0.00 0.00 0.00 2.74
3063 3276 8.516811 AAAGACGTTTTATGACACTACACTAG 57.483 34.615 0.00 0.00 0.00 2.57
3064 3277 7.211966 AGACGTTTTATGACACTACACTAGT 57.788 36.000 0.00 0.00 40.28 2.57
3092 3305 6.842081 AAAAACGTCTTAGTGTCAAAAACG 57.158 33.333 0.00 0.00 35.00 3.60
3093 3306 5.535043 AAACGTCTTAGTGTCAAAAACGT 57.465 34.783 0.00 0.00 42.95 3.99
3094 3307 4.766969 ACGTCTTAGTGTCAAAAACGTC 57.233 40.909 0.00 0.00 37.30 4.34
3095 3308 4.427312 ACGTCTTAGTGTCAAAAACGTCT 58.573 39.130 0.00 0.00 37.30 4.18
3096 3309 4.866486 ACGTCTTAGTGTCAAAAACGTCTT 59.134 37.500 0.00 0.00 37.30 3.01
3097 3310 6.035843 ACGTCTTAGTGTCAAAAACGTCTTA 58.964 36.000 0.00 0.00 37.30 2.10
3098 3311 6.020360 ACGTCTTAGTGTCAAAAACGTCTTAC 60.020 38.462 0.00 0.00 37.30 2.34
3099 3312 6.020440 CGTCTTAGTGTCAAAAACGTCTTACA 60.020 38.462 0.00 0.00 0.00 2.41
3100 3313 7.306399 CGTCTTAGTGTCAAAAACGTCTTACAT 60.306 37.037 0.00 0.00 0.00 2.29
3101 3314 8.333186 GTCTTAGTGTCAAAAACGTCTTACATT 58.667 33.333 0.00 0.00 0.00 2.71
3102 3315 9.531942 TCTTAGTGTCAAAAACGTCTTACATTA 57.468 29.630 0.00 0.00 0.00 1.90
3103 3316 9.577003 CTTAGTGTCAAAAACGTCTTACATTAC 57.423 33.333 0.00 0.00 0.00 1.89
3104 3317 6.642917 AGTGTCAAAAACGTCTTACATTACG 58.357 36.000 0.00 0.00 44.47 3.18
3105 3318 6.476380 AGTGTCAAAAACGTCTTACATTACGA 59.524 34.615 1.45 0.00 41.55 3.43
3106 3319 6.784227 GTGTCAAAAACGTCTTACATTACGAG 59.216 38.462 1.45 0.00 41.55 4.18
3107 3320 6.696583 TGTCAAAAACGTCTTACATTACGAGA 59.303 34.615 1.45 0.00 41.55 4.04
3108 3321 7.000200 GTCAAAAACGTCTTACATTACGAGAC 59.000 38.462 1.45 0.00 41.55 3.36
3112 3325 3.075866 GTCTTACATTACGAGACGGGG 57.924 52.381 0.00 0.00 31.54 5.73
3124 3337 2.414481 CGAGACGGGGTACTATATGTCG 59.586 54.545 0.00 0.00 0.00 4.35
3275 3488 6.319911 TGTTCACACATTCTTCATGTAAACCA 59.680 34.615 0.00 0.00 45.06 3.67
3285 3498 2.107366 CATGTAAACCATGGAACCCCC 58.893 52.381 21.47 1.31 46.03 5.40
3294 3507 1.377229 TGGAACCCCCAACGCTAAG 59.623 57.895 0.00 0.00 43.29 2.18
3316 3529 1.153628 AACGAGTCGCCACATAGCC 60.154 57.895 13.59 0.00 0.00 3.93
3322 3535 0.601311 GTCGCCACATAGCCCTGATC 60.601 60.000 0.00 0.00 0.00 2.92
3323 3536 1.048160 TCGCCACATAGCCCTGATCA 61.048 55.000 0.00 0.00 0.00 2.92
3331 3544 4.395231 CACATAGCCCTGATCAGCATAATG 59.605 45.833 17.76 17.71 0.00 1.90
3374 3587 1.407437 CCGAAAAGGCCACTCTAGCAT 60.407 52.381 5.01 0.00 0.00 3.79
3378 3591 3.550437 AAAGGCCACTCTAGCATAGTG 57.450 47.619 5.01 3.60 43.26 2.74
3438 4647 2.820197 TCATCTACAGCACGTGAGACTT 59.180 45.455 22.23 0.00 0.00 3.01
3483 5126 3.395273 TGATATGAAGGGCACATCATCCA 59.605 43.478 10.48 7.46 35.58 3.41
3500 5883 1.815003 CACCAATCGCTCGCATGGA 60.815 57.895 16.20 0.00 36.75 3.41
3517 5900 4.401925 CATGGAAGGGAAGTTTCAACTCT 58.598 43.478 0.00 0.00 38.57 3.24
3518 5901 4.519906 TGGAAGGGAAGTTTCAACTCTT 57.480 40.909 0.00 0.00 38.57 2.85
3519 5902 4.867086 TGGAAGGGAAGTTTCAACTCTTT 58.133 39.130 0.00 0.00 38.57 2.52
3520 5903 4.887655 TGGAAGGGAAGTTTCAACTCTTTC 59.112 41.667 0.00 0.00 38.57 2.62
3527 5910 5.699001 GGAAGTTTCAACTCTTTCTCTCTCC 59.301 44.000 0.00 0.00 38.57 3.71
3538 5921 3.260269 TTCTCTCTCCTTGTCTTCCCA 57.740 47.619 0.00 0.00 0.00 4.37
3541 5924 2.170187 CTCTCTCCTTGTCTTCCCATGG 59.830 54.545 4.14 4.14 0.00 3.66
3559 5942 2.752807 GGGCCCATTTCCTCGCCTA 61.753 63.158 19.95 0.00 41.35 3.93
3594 6376 2.164624 GAGTAGAAGACGTCATGGCACT 59.835 50.000 19.50 13.23 0.00 4.40
3643 6425 4.969196 CGTGCCGACTGCCTGTGT 62.969 66.667 0.00 0.00 40.16 3.72
3644 6426 3.044305 GTGCCGACTGCCTGTGTC 61.044 66.667 0.00 0.00 40.16 3.67
3646 6428 4.314440 GCCGACTGCCTGTGTCCA 62.314 66.667 0.00 0.00 0.00 4.02
3647 6429 2.665000 CCGACTGCCTGTGTCCAT 59.335 61.111 0.00 0.00 0.00 3.41
3648 6430 1.448540 CCGACTGCCTGTGTCCATC 60.449 63.158 0.00 0.00 0.00 3.51
3649 6431 1.293179 CGACTGCCTGTGTCCATCA 59.707 57.895 0.00 0.00 0.00 3.07
3650 6432 0.320683 CGACTGCCTGTGTCCATCAA 60.321 55.000 0.00 0.00 0.00 2.57
3651 6433 1.160137 GACTGCCTGTGTCCATCAAC 58.840 55.000 0.00 0.00 0.00 3.18
3652 6434 0.603707 ACTGCCTGTGTCCATCAACG 60.604 55.000 0.00 0.00 0.00 4.10
3653 6435 1.915614 CTGCCTGTGTCCATCAACGC 61.916 60.000 0.00 0.00 0.00 4.84
3655 6437 1.302431 CCTGTGTCCATCAACGCCA 60.302 57.895 0.00 0.00 0.00 5.69
3656 6438 1.577328 CCTGTGTCCATCAACGCCAC 61.577 60.000 0.00 0.00 0.00 5.01
3657 6439 1.900585 CTGTGTCCATCAACGCCACG 61.901 60.000 0.00 0.00 0.00 4.94
3658 6440 1.959226 GTGTCCATCAACGCCACGT 60.959 57.895 0.00 0.00 43.97 4.49
3670 6452 2.113139 CCACGTTTCCCACTGCCT 59.887 61.111 0.00 0.00 0.00 4.75
3676 6458 3.210012 TTTCCCACTGCCTGCTCCC 62.210 63.158 0.00 0.00 0.00 4.30
3677 6459 4.664267 TCCCACTGCCTGCTCCCT 62.664 66.667 0.00 0.00 0.00 4.20
3732 6514 4.225942 TGGTCAAATATCTCACAAGCTCCT 59.774 41.667 0.00 0.00 0.00 3.69
3769 6760 0.838122 CACACCCTCCACTTCCCTCT 60.838 60.000 0.00 0.00 0.00 3.69
3774 6765 0.041833 CCTCCACTTCCCTCTCCTCA 59.958 60.000 0.00 0.00 0.00 3.86
3790 6781 1.227943 TCATAGCCATGCCGCTTCC 60.228 57.895 1.62 0.00 40.39 3.46
3828 6819 0.699399 TCCACTCTCGAAGGAGGAGT 59.301 55.000 6.63 2.86 40.85 3.85
3829 6820 1.075698 TCCACTCTCGAAGGAGGAGTT 59.924 52.381 6.63 0.00 40.85 3.01
3830 6821 1.203523 CCACTCTCGAAGGAGGAGTTG 59.796 57.143 6.63 0.00 40.85 3.16
3831 6822 2.163509 CACTCTCGAAGGAGGAGTTGA 58.836 52.381 6.63 0.00 40.85 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 5.825593 TCTTCAGGGAATTTCTGTACTGT 57.174 39.130 8.83 0.00 34.15 3.55
711 879 7.596621 GGTAATAACTTAGCGGTAACATACTCC 59.403 40.741 2.26 0.00 0.00 3.85
712 880 7.596621 GGGTAATAACTTAGCGGTAACATACTC 59.403 40.741 2.26 0.00 36.42 2.59
713 881 7.069826 TGGGTAATAACTTAGCGGTAACATACT 59.930 37.037 2.26 0.00 36.42 2.12
714 882 7.209475 TGGGTAATAACTTAGCGGTAACATAC 58.791 38.462 2.26 3.11 36.42 2.39
715 883 7.358770 TGGGTAATAACTTAGCGGTAACATA 57.641 36.000 2.26 0.22 36.42 2.29
716 884 6.237887 TGGGTAATAACTTAGCGGTAACAT 57.762 37.500 2.26 0.00 36.42 2.71
723 891 4.154195 GCCATGATGGGTAATAACTTAGCG 59.846 45.833 14.26 0.00 38.19 4.26
740 908 1.039785 AGCAGCGAGACTAGCCATGA 61.040 55.000 3.70 0.00 34.64 3.07
741 909 0.179089 AAGCAGCGAGACTAGCCATG 60.179 55.000 3.70 0.00 34.64 3.66
755 923 2.281761 AACCTCCACGGCAAGCAG 60.282 61.111 0.00 0.00 35.61 4.24
756 924 2.281484 GAACCTCCACGGCAAGCA 60.281 61.111 0.00 0.00 35.61 3.91
757 925 2.281484 TGAACCTCCACGGCAAGC 60.281 61.111 0.00 0.00 35.61 4.01
758 926 1.227823 TGTGAACCTCCACGGCAAG 60.228 57.895 0.00 0.00 39.80 4.01
759 927 1.227823 CTGTGAACCTCCACGGCAA 60.228 57.895 0.00 0.00 39.80 4.52
760 928 2.425592 CTGTGAACCTCCACGGCA 59.574 61.111 0.00 0.00 39.80 5.69
761 929 2.358737 CCTGTGAACCTCCACGGC 60.359 66.667 0.00 0.00 41.01 5.68
762 930 2.347490 CCCTGTGAACCTCCACGG 59.653 66.667 0.00 0.00 41.78 4.94
763 931 2.347490 CCCCTGTGAACCTCCACG 59.653 66.667 0.00 0.00 39.80 4.94
764 932 2.034221 GCCCCTGTGAACCTCCAC 59.966 66.667 0.00 0.00 37.55 4.02
765 933 3.636231 CGCCCCTGTGAACCTCCA 61.636 66.667 0.00 0.00 0.00 3.86
778 946 3.718210 CTACCTCTGAACGGCGCCC 62.718 68.421 23.46 7.69 0.00 6.13
779 947 2.202756 CTACCTCTGAACGGCGCC 60.203 66.667 19.07 19.07 0.00 6.53
780 948 0.802607 CTTCTACCTCTGAACGGCGC 60.803 60.000 6.90 0.00 0.00 6.53
781 949 0.526662 ACTTCTACCTCTGAACGGCG 59.473 55.000 4.80 4.80 0.00 6.46
782 950 2.099427 CCTACTTCTACCTCTGAACGGC 59.901 54.545 0.00 0.00 0.00 5.68
783 951 3.618351 TCCTACTTCTACCTCTGAACGG 58.382 50.000 0.00 0.00 0.00 4.44
784 952 5.008217 CAGATCCTACTTCTACCTCTGAACG 59.992 48.000 0.00 0.00 32.36 3.95
785 953 5.221165 GCAGATCCTACTTCTACCTCTGAAC 60.221 48.000 0.00 0.00 32.36 3.18
786 954 4.890581 GCAGATCCTACTTCTACCTCTGAA 59.109 45.833 0.00 0.00 32.36 3.02
787 955 4.465886 GCAGATCCTACTTCTACCTCTGA 58.534 47.826 0.00 0.00 32.36 3.27
788 956 3.572255 GGCAGATCCTACTTCTACCTCTG 59.428 52.174 0.00 0.00 33.49 3.35
789 957 3.749310 CGGCAGATCCTACTTCTACCTCT 60.749 52.174 0.00 0.00 0.00 3.69
790 958 2.554893 CGGCAGATCCTACTTCTACCTC 59.445 54.545 0.00 0.00 0.00 3.85
791 959 2.091775 ACGGCAGATCCTACTTCTACCT 60.092 50.000 0.00 0.00 0.00 3.08
792 960 2.308690 ACGGCAGATCCTACTTCTACC 58.691 52.381 0.00 0.00 0.00 3.18
793 961 5.005094 AGATACGGCAGATCCTACTTCTAC 58.995 45.833 0.00 0.00 0.00 2.59
794 962 5.244189 AGATACGGCAGATCCTACTTCTA 57.756 43.478 0.00 0.00 0.00 2.10
795 963 4.107127 AGATACGGCAGATCCTACTTCT 57.893 45.455 0.00 0.00 0.00 2.85
796 964 4.321378 GGAAGATACGGCAGATCCTACTTC 60.321 50.000 0.00 0.00 0.00 3.01
797 965 3.574826 GGAAGATACGGCAGATCCTACTT 59.425 47.826 0.00 0.00 0.00 2.24
798 966 3.158676 GGAAGATACGGCAGATCCTACT 58.841 50.000 0.00 0.00 0.00 2.57
799 967 3.057174 CAGGAAGATACGGCAGATCCTAC 60.057 52.174 0.00 0.00 35.59 3.18
800 968 3.157881 CAGGAAGATACGGCAGATCCTA 58.842 50.000 0.00 0.00 35.59 2.94
816 984 3.636231 CGGTGGGTCAGCCAGGAA 61.636 66.667 0.00 0.00 36.17 3.36
847 1015 5.212194 ACATTATCTTGACAAAACGTGCAC 58.788 37.500 6.82 6.82 0.00 4.57
888 1056 8.042515 CCAACATCCAAGATTCCAAAAACATAT 58.957 33.333 0.00 0.00 0.00 1.78
889 1057 7.234371 TCCAACATCCAAGATTCCAAAAACATA 59.766 33.333 0.00 0.00 0.00 2.29
890 1058 6.043012 TCCAACATCCAAGATTCCAAAAACAT 59.957 34.615 0.00 0.00 0.00 2.71
891 1059 5.365025 TCCAACATCCAAGATTCCAAAAACA 59.635 36.000 0.00 0.00 0.00 2.83
892 1060 5.852827 TCCAACATCCAAGATTCCAAAAAC 58.147 37.500 0.00 0.00 0.00 2.43
893 1061 5.602145 ACTCCAACATCCAAGATTCCAAAAA 59.398 36.000 0.00 0.00 0.00 1.94
894 1062 5.147032 ACTCCAACATCCAAGATTCCAAAA 58.853 37.500 0.00 0.00 0.00 2.44
895 1063 4.739793 ACTCCAACATCCAAGATTCCAAA 58.260 39.130 0.00 0.00 0.00 3.28
896 1064 4.387026 ACTCCAACATCCAAGATTCCAA 57.613 40.909 0.00 0.00 0.00 3.53
897 1065 4.626287 GCTACTCCAACATCCAAGATTCCA 60.626 45.833 0.00 0.00 0.00 3.53
898 1066 3.879892 GCTACTCCAACATCCAAGATTCC 59.120 47.826 0.00 0.00 0.00 3.01
899 1067 3.879892 GGCTACTCCAACATCCAAGATTC 59.120 47.826 0.00 0.00 34.01 2.52
900 1068 3.266772 TGGCTACTCCAACATCCAAGATT 59.733 43.478 0.00 0.00 43.21 2.40
901 1069 2.846206 TGGCTACTCCAACATCCAAGAT 59.154 45.455 0.00 0.00 43.21 2.40
902 1070 2.265367 TGGCTACTCCAACATCCAAGA 58.735 47.619 0.00 0.00 43.21 3.02
903 1071 2.787473 TGGCTACTCCAACATCCAAG 57.213 50.000 0.00 0.00 43.21 3.61
954 1131 4.837972 ACCTCCTGCTCAATTTTCTACTC 58.162 43.478 0.00 0.00 0.00 2.59
964 1141 0.615331 CTTGCCTACCTCCTGCTCAA 59.385 55.000 0.00 0.00 0.00 3.02
967 1144 1.997874 CCCTTGCCTACCTCCTGCT 60.998 63.158 0.00 0.00 0.00 4.24
972 1149 0.256177 CCTTTCCCCTTGCCTACCTC 59.744 60.000 0.00 0.00 0.00 3.85
1104 1281 2.936570 GATGATGAAGAGCGCGGCG 61.937 63.158 19.62 19.62 0.00 6.46
1145 1322 1.776662 TAAGGCGAGGATGTGCTAGT 58.223 50.000 0.00 0.00 0.00 2.57
1146 1323 2.560542 AGATAAGGCGAGGATGTGCTAG 59.439 50.000 0.00 0.00 0.00 3.42
1159 1337 4.081972 TCAGACTTCAGACACAGATAAGGC 60.082 45.833 0.00 0.00 0.00 4.35
1160 1338 5.394005 CCTCAGACTTCAGACACAGATAAGG 60.394 48.000 0.00 0.00 0.00 2.69
1178 1356 1.157751 ACCCCGGAAGAACCTCAGA 59.842 57.895 0.73 0.00 36.31 3.27
1179 1357 1.296715 CACCCCGGAAGAACCTCAG 59.703 63.158 0.73 0.00 36.31 3.35
1182 1373 0.689055 GTTACACCCCGGAAGAACCT 59.311 55.000 0.73 0.00 36.31 3.50
1194 1385 1.608801 CCACCCCTACGTTGTTACACC 60.609 57.143 0.00 0.00 0.00 4.16
1196 1387 1.619827 CTCCACCCCTACGTTGTTACA 59.380 52.381 0.00 0.00 0.00 2.41
1198 1389 1.269012 CCTCCACCCCTACGTTGTTA 58.731 55.000 0.00 0.00 0.00 2.41
1199 1390 0.765519 ACCTCCACCCCTACGTTGTT 60.766 55.000 0.00 0.00 0.00 2.83
1200 1391 1.152183 ACCTCCACCCCTACGTTGT 60.152 57.895 0.00 0.00 0.00 3.32
1201 1392 1.595357 GACCTCCACCCCTACGTTG 59.405 63.158 0.00 0.00 0.00 4.10
1486 1680 2.170187 GTTGAGGAGCCAGACTGATGAT 59.830 50.000 3.32 0.00 0.00 2.45
1487 1681 1.552337 GTTGAGGAGCCAGACTGATGA 59.448 52.381 3.32 0.00 0.00 2.92
1501 1695 1.002868 CCCTGCAGGACAGTTGAGG 60.003 63.158 34.91 10.00 45.68 3.86
1634 1832 3.383505 GGTAGAGGGAGAAGAAGAAGAGC 59.616 52.174 0.00 0.00 0.00 4.09
1679 1877 4.641645 TGGACGCAGGGCTTGTGG 62.642 66.667 14.90 1.85 41.69 4.17
1755 1953 3.314693 AGTACCACCAGTTGAAGAAGGA 58.685 45.455 0.00 0.00 0.00 3.36
1859 2057 4.511246 ATGGCGGTGCAGGGGATG 62.511 66.667 0.00 0.00 0.00 3.51
1886 2084 2.676822 AGGCAGAAGACGGCGAGA 60.677 61.111 16.62 0.00 38.05 4.04
1907 2105 0.323957 GGAAGCGGTAGGTCTTGGTT 59.676 55.000 0.00 0.00 0.00 3.67
1936 2134 5.048991 ACGGGATTTTACTTGTTAGCACTTG 60.049 40.000 0.00 0.00 0.00 3.16
1954 2152 2.840651 AGGTCTTCAGAATCAACGGGAT 59.159 45.455 0.00 0.00 38.05 3.85
1956 2154 2.622436 GAGGTCTTCAGAATCAACGGG 58.378 52.381 0.00 0.00 0.00 5.28
1957 2155 2.234908 AGGAGGTCTTCAGAATCAACGG 59.765 50.000 0.00 0.00 0.00 4.44
1959 2157 4.278975 ACAGGAGGTCTTCAGAATCAAC 57.721 45.455 0.00 0.00 0.00 3.18
1960 2158 4.103153 ACAACAGGAGGTCTTCAGAATCAA 59.897 41.667 0.00 0.00 0.00 2.57
1985 2183 5.873179 TTCAGTTTCAGAAGAACACGTTT 57.127 34.783 0.00 0.00 32.39 3.60
1987 2185 4.094442 GGTTTCAGTTTCAGAAGAACACGT 59.906 41.667 0.00 0.00 32.39 4.49
2022 2220 2.097036 TCTGCATGCCAAGAAAGATGG 58.903 47.619 16.68 0.00 41.08 3.51
2082 2283 2.517919 GGTGGCTCCATGATCCCC 59.482 66.667 0.00 0.00 35.97 4.81
2172 2379 1.321474 CTTGCCTGCTTGGTGAAGAA 58.679 50.000 0.00 0.00 38.35 2.52
2383 2590 1.028330 AGCAGCAACGACCATCATGG 61.028 55.000 0.54 0.54 45.02 3.66
2573 2780 4.299547 AAGCTGCGCAGACCGTCA 62.300 61.111 40.21 0.00 39.71 4.35
2713 2920 5.357032 CAGTAAAAATAATCGAGGTGCCCTT 59.643 40.000 0.00 0.00 31.76 3.95
2795 3002 4.192317 CACCCTTCTTCTTAGGCACATAC 58.808 47.826 0.00 0.00 0.00 2.39
2810 3017 1.111277 ACTGCACCAAAACACCCTTC 58.889 50.000 0.00 0.00 0.00 3.46
2860 3073 0.681175 AGGCCACCAAAATGCAAGAC 59.319 50.000 5.01 0.00 0.00 3.01
2865 3078 5.049828 GTGATTTATAGGCCACCAAAATGC 58.950 41.667 5.01 1.49 0.00 3.56
2878 3091 8.978564 AGCAGACTTCGATATGTGATTTATAG 57.021 34.615 0.00 0.00 0.00 1.31
2882 3095 8.554528 CAATTAGCAGACTTCGATATGTGATTT 58.445 33.333 0.00 0.00 0.00 2.17
2942 3155 1.169034 CCTCCTAGTACCGTACCGCC 61.169 65.000 5.02 0.00 0.00 6.13
2944 3157 0.536006 CCCCTCCTAGTACCGTACCG 60.536 65.000 5.02 0.00 0.00 4.02
2946 3159 2.443958 AACCCCTCCTAGTACCGTAC 57.556 55.000 0.00 0.00 0.00 3.67
2947 3160 2.683742 CGAAACCCCTCCTAGTACCGTA 60.684 54.545 0.00 0.00 0.00 4.02
2968 3181 5.836347 AGTTGTTTTCCATTTTCTGAGAGC 58.164 37.500 0.00 0.00 0.00 4.09
2980 3193 3.752665 TGCCGGTATAAGTTGTTTTCCA 58.247 40.909 1.90 0.00 0.00 3.53
3007 3220 4.220163 GGGACGGAAGGAGTATTACCTATG 59.780 50.000 0.00 0.00 36.67 2.23
3016 3229 3.649843 ACATTATGGGACGGAAGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
3017 3230 2.478292 ACATTATGGGACGGAAGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
3019 3232 4.717778 TCTTTACATTATGGGACGGAAGGA 59.282 41.667 0.00 0.00 0.00 3.36
3021 3234 4.506654 CGTCTTTACATTATGGGACGGAAG 59.493 45.833 17.16 5.41 41.50 3.46
3022 3235 4.081531 ACGTCTTTACATTATGGGACGGAA 60.082 41.667 23.35 2.60 46.80 4.30
3024 3237 3.788937 ACGTCTTTACATTATGGGACGG 58.211 45.455 23.35 13.20 46.80 4.79
3026 3239 8.885722 TCATAAAACGTCTTTACATTATGGGAC 58.114 33.333 0.00 0.00 32.53 4.46
3028 3241 8.670135 TGTCATAAAACGTCTTTACATTATGGG 58.330 33.333 0.00 0.00 32.53 4.00
3029 3242 9.485591 GTGTCATAAAACGTCTTTACATTATGG 57.514 33.333 0.00 0.00 32.53 2.74
3033 3246 9.263538 TGTAGTGTCATAAAACGTCTTTACATT 57.736 29.630 0.00 0.00 0.00 2.71
3034 3247 8.706035 GTGTAGTGTCATAAAACGTCTTTACAT 58.294 33.333 0.00 0.00 0.00 2.29
3035 3248 7.922278 AGTGTAGTGTCATAAAACGTCTTTACA 59.078 33.333 0.00 0.00 0.00 2.41
3036 3249 8.290663 AGTGTAGTGTCATAAAACGTCTTTAC 57.709 34.615 0.00 0.00 0.00 2.01
3037 3250 9.616634 CTAGTGTAGTGTCATAAAACGTCTTTA 57.383 33.333 0.00 0.00 0.00 1.85
3038 3251 8.139989 ACTAGTGTAGTGTCATAAAACGTCTTT 58.860 33.333 0.00 0.00 37.69 2.52
3039 3252 7.655490 ACTAGTGTAGTGTCATAAAACGTCTT 58.345 34.615 0.00 0.00 37.69 3.01
3040 3253 7.211966 ACTAGTGTAGTGTCATAAAACGTCT 57.788 36.000 0.00 0.00 37.69 4.18
3069 3282 6.372981 ACGTTTTTGACACTAAGACGTTTTT 58.627 32.000 0.00 0.00 38.91 1.94
3070 3283 5.930405 ACGTTTTTGACACTAAGACGTTTT 58.070 33.333 3.50 0.00 38.91 2.43
3071 3284 5.349543 AGACGTTTTTGACACTAAGACGTTT 59.650 36.000 9.21 2.80 41.60 3.60
3072 3285 4.866486 AGACGTTTTTGACACTAAGACGTT 59.134 37.500 9.21 0.22 41.60 3.99
3073 3286 4.427312 AGACGTTTTTGACACTAAGACGT 58.573 39.130 7.96 7.96 43.82 4.34
3074 3287 5.385396 AAGACGTTTTTGACACTAAGACG 57.615 39.130 0.00 0.00 35.39 4.18
3075 3288 7.225523 TGTAAGACGTTTTTGACACTAAGAC 57.774 36.000 0.00 0.00 0.00 3.01
3076 3289 8.428186 AATGTAAGACGTTTTTGACACTAAGA 57.572 30.769 0.00 0.00 0.00 2.10
3077 3290 9.577003 GTAATGTAAGACGTTTTTGACACTAAG 57.423 33.333 0.00 0.00 0.00 2.18
3078 3291 8.268052 CGTAATGTAAGACGTTTTTGACACTAA 58.732 33.333 0.00 0.00 34.39 2.24
3079 3292 7.647318 TCGTAATGTAAGACGTTTTTGACACTA 59.353 33.333 0.00 0.00 40.00 2.74
3080 3293 6.476380 TCGTAATGTAAGACGTTTTTGACACT 59.524 34.615 0.00 0.00 40.00 3.55
3081 3294 6.639212 TCGTAATGTAAGACGTTTTTGACAC 58.361 36.000 0.00 0.00 40.00 3.67
3082 3295 6.696583 TCTCGTAATGTAAGACGTTTTTGACA 59.303 34.615 0.00 0.00 40.00 3.58
3083 3296 7.000200 GTCTCGTAATGTAAGACGTTTTTGAC 59.000 38.462 0.00 0.00 40.00 3.18
3084 3297 7.097342 GTCTCGTAATGTAAGACGTTTTTGA 57.903 36.000 0.00 0.00 40.00 2.69
3092 3305 2.424956 ACCCCGTCTCGTAATGTAAGAC 59.575 50.000 0.00 0.00 36.82 3.01
3093 3306 2.726821 ACCCCGTCTCGTAATGTAAGA 58.273 47.619 0.00 0.00 0.00 2.10
3094 3307 3.629398 AGTACCCCGTCTCGTAATGTAAG 59.371 47.826 0.00 0.00 0.00 2.34
3095 3308 3.620488 AGTACCCCGTCTCGTAATGTAA 58.380 45.455 0.00 0.00 0.00 2.41
3096 3309 3.281727 AGTACCCCGTCTCGTAATGTA 57.718 47.619 0.00 0.00 0.00 2.29
3097 3310 2.134789 AGTACCCCGTCTCGTAATGT 57.865 50.000 0.00 0.00 0.00 2.71
3098 3311 5.413833 ACATATAGTACCCCGTCTCGTAATG 59.586 44.000 0.00 0.00 0.00 1.90
3099 3312 5.564550 ACATATAGTACCCCGTCTCGTAAT 58.435 41.667 0.00 0.00 0.00 1.89
3100 3313 4.973168 ACATATAGTACCCCGTCTCGTAA 58.027 43.478 0.00 0.00 0.00 3.18
3101 3314 4.569943 GACATATAGTACCCCGTCTCGTA 58.430 47.826 0.00 0.00 0.00 3.43
3102 3315 3.406764 GACATATAGTACCCCGTCTCGT 58.593 50.000 0.00 0.00 0.00 4.18
3103 3316 2.414481 CGACATATAGTACCCCGTCTCG 59.586 54.545 0.00 0.00 0.00 4.04
3104 3317 3.668447 TCGACATATAGTACCCCGTCTC 58.332 50.000 0.00 0.00 0.00 3.36
3105 3318 3.777106 TCGACATATAGTACCCCGTCT 57.223 47.619 0.00 0.00 0.00 4.18
3106 3319 6.238593 GGAATATCGACATATAGTACCCCGTC 60.239 46.154 0.00 0.00 0.00 4.79
3107 3320 5.591877 GGAATATCGACATATAGTACCCCGT 59.408 44.000 0.00 0.00 0.00 5.28
3108 3321 5.009410 GGGAATATCGACATATAGTACCCCG 59.991 48.000 0.00 0.00 26.14 5.73
3109 3322 6.134754 AGGGAATATCGACATATAGTACCCC 58.865 44.000 0.00 0.00 31.85 4.95
3110 3323 8.757982 TTAGGGAATATCGACATATAGTACCC 57.242 38.462 0.00 0.00 31.85 3.69
3138 3351 9.099454 GCTTTAAGTTGTAGACATATAGTGCTT 57.901 33.333 0.00 0.00 0.00 3.91
3140 3353 8.649973 AGCTTTAAGTTGTAGACATATAGTGC 57.350 34.615 0.00 0.00 0.00 4.40
3275 3488 0.034477 CTTAGCGTTGGGGGTTCCAT 60.034 55.000 0.00 0.00 46.52 3.41
3289 3502 1.416434 GCGACTCGTTGCACTTAGC 59.584 57.895 4.44 0.00 45.96 3.09
3294 3507 1.011968 TATGTGGCGACTCGTTGCAC 61.012 55.000 11.12 7.88 41.74 4.57
3316 3529 3.062763 GACGGTCATTATGCTGATCAGG 58.937 50.000 23.89 6.47 0.00 3.86
3322 3535 4.378770 GCCATATTGACGGTCATTATGCTG 60.379 45.833 29.90 23.02 38.45 4.41
3323 3536 3.753272 GCCATATTGACGGTCATTATGCT 59.247 43.478 29.90 11.07 38.45 3.79
3331 3544 3.548014 CCAAAATCGCCATATTGACGGTC 60.548 47.826 0.00 0.00 0.00 4.79
3374 3587 0.902984 ACTGTGTCGGATGGCCACTA 60.903 55.000 8.16 0.00 0.00 2.74
3407 3620 1.211818 CTGTAGATGAAGCGCGCTCC 61.212 60.000 36.57 25.39 0.00 4.70
3438 4647 2.817258 CGCCCAAAGACTCCAAATACAA 59.183 45.455 0.00 0.00 0.00 2.41
3483 5126 1.078497 TTCCATGCGAGCGATTGGT 60.078 52.632 10.08 0.00 0.00 3.67
3500 5883 6.007485 AGAGAAAGAGTTGAAACTTCCCTT 57.993 37.500 0.00 0.00 39.88 3.95
3517 5900 3.587498 TGGGAAGACAAGGAGAGAGAAA 58.413 45.455 0.00 0.00 0.00 2.52
3518 5901 3.260269 TGGGAAGACAAGGAGAGAGAA 57.740 47.619 0.00 0.00 0.00 2.87
3519 5902 3.102972 CATGGGAAGACAAGGAGAGAGA 58.897 50.000 0.00 0.00 0.00 3.10
3520 5903 2.170187 CCATGGGAAGACAAGGAGAGAG 59.830 54.545 2.85 0.00 31.02 3.20
3541 5924 2.069165 ATAGGCGAGGAAATGGGCCC 62.069 60.000 17.59 17.59 46.75 5.80
3559 5942 4.223700 TCTTCTACTCACTGTGCCATTGAT 59.776 41.667 2.12 0.00 0.00 2.57
3576 6358 2.688446 CCTAGTGCCATGACGTCTTCTA 59.312 50.000 17.92 7.18 0.00 2.10
3594 6376 1.601903 CATTAATTGGCGCGCTTCCTA 59.398 47.619 32.29 14.67 0.00 2.94
3633 6415 0.603707 CGTTGATGGACACAGGCAGT 60.604 55.000 0.00 0.00 0.00 4.40
3635 6417 1.965930 GCGTTGATGGACACAGGCA 60.966 57.895 0.00 0.00 0.00 4.75
3650 6432 2.590575 CAGTGGGAAACGTGGCGT 60.591 61.111 0.00 0.00 43.97 5.68
3651 6433 4.025401 GCAGTGGGAAACGTGGCG 62.025 66.667 0.00 0.00 0.00 5.69
3652 6434 3.670377 GGCAGTGGGAAACGTGGC 61.670 66.667 0.00 0.00 0.00 5.01
3653 6435 2.113139 AGGCAGTGGGAAACGTGG 59.887 61.111 0.00 0.00 0.00 4.94
3655 6437 2.594592 GCAGGCAGTGGGAAACGT 60.595 61.111 0.00 0.00 0.00 3.99
3656 6438 2.281761 AGCAGGCAGTGGGAAACG 60.282 61.111 0.00 0.00 0.00 3.60
3657 6439 1.973812 GGAGCAGGCAGTGGGAAAC 60.974 63.158 0.00 0.00 0.00 2.78
3658 6440 2.436109 GGAGCAGGCAGTGGGAAA 59.564 61.111 0.00 0.00 0.00 3.13
3659 6441 3.650950 GGGAGCAGGCAGTGGGAA 61.651 66.667 0.00 0.00 0.00 3.97
3660 6442 4.664267 AGGGAGCAGGCAGTGGGA 62.664 66.667 0.00 0.00 0.00 4.37
3663 6445 4.106925 GGGAGGGAGCAGGCAGTG 62.107 72.222 0.00 0.00 0.00 3.66
3676 6458 3.662759 TTTTTATAGCCACTGGGGGAG 57.337 47.619 0.00 0.00 37.04 4.30
3702 6484 5.185454 TGTGAGATATTTGACCATGGTGAC 58.815 41.667 25.52 9.69 0.00 3.67
3732 6514 4.271533 GGTGTGAGTAATCGTGTTTGAACA 59.728 41.667 0.00 0.00 36.38 3.18
3769 6760 1.699054 AAGCGGCATGGCTATGAGGA 61.699 55.000 15.09 0.00 43.93 3.71
3774 6765 2.113986 GGGAAGCGGCATGGCTAT 59.886 61.111 18.09 2.24 43.93 2.97
3799 6790 1.761174 GAGAGTGGAACCCAGCCAA 59.239 57.895 0.00 0.00 37.80 4.52
3802 6793 0.390472 CTTCGAGAGTGGAACCCAGC 60.390 60.000 0.00 0.00 37.80 4.85


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

AutoCloner maintained by Alex Coulton.