Multiple sequence alignment - TraesCS5A01G374500

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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 TraesCS5A01G374500 chr5A 100.000 5248 0 0 1 5248 572836706 572841953 0.000000e+00 9692.0
1 TraesCS5A01G374500 chr5A 93.571 840 51 2 1 840 510499389 510498553 0.000000e+00 1249.0
2 TraesCS5A01G374500 chr5A 92.943 836 56 2 1 835 11912054 11911221 0.000000e+00 1214.0
3 TraesCS5A01G374500 chr5A 93.292 805 44 7 1 805 567293809 567294603 0.000000e+00 1179.0
4 TraesCS5A01G374500 chr5A 83.858 985 155 4 3081 4063 28105099 28104117 0.000000e+00 935.0
5 TraesCS5A01G374500 chr5D 89.803 2442 145 41 2163 4553 453814690 453817078 0.000000e+00 3035.0
6 TraesCS5A01G374500 chr5D 90.687 1267 70 22 856 2079 453813430 453814691 0.000000e+00 1642.0
7 TraesCS5A01G374500 chr5D 93.669 695 37 2 4556 5248 453817049 453817738 0.000000e+00 1033.0
8 TraesCS5A01G374500 chr5D 83.418 983 159 4 3081 4061 40092727 40091747 0.000000e+00 909.0
9 TraesCS5A01G374500 chr5B 91.555 2084 130 22 2021 4075 554512767 554514833 0.000000e+00 2832.0
10 TraesCS5A01G374500 chr5B 90.810 914 50 17 1145 2028 554511671 554512580 0.000000e+00 1192.0
11 TraesCS5A01G374500 chr5B 94.413 698 34 2 4556 5248 554515284 554515981 0.000000e+00 1068.0
12 TraesCS5A01G374500 chr5B 84.130 983 152 4 3081 4061 33627692 33628672 0.000000e+00 948.0
13 TraesCS5A01G374500 chr5B 89.974 379 17 4 3991 4350 554514834 554515210 2.210000e-128 470.0
14 TraesCS5A01G374500 chr5B 90.370 270 13 6 857 1121 554511213 554511474 5.030000e-90 342.0
15 TraesCS5A01G374500 chr5B 91.579 95 5 3 4460 4553 554515221 554515313 1.530000e-25 128.0
16 TraesCS5A01G374500 chr4A 93.279 863 49 3 1 854 41031822 41030960 0.000000e+00 1264.0
17 TraesCS5A01G374500 chr7A 94.507 801 39 5 1 800 499740767 499741563 0.000000e+00 1230.0
18 TraesCS5A01G374500 chr7A 93.612 454 29 0 353 806 427806712 427806259 0.000000e+00 678.0
19 TraesCS5A01G374500 chr7A 86.528 193 15 6 1231 1418 735050119 735049933 8.910000e-48 202.0
20 TraesCS5A01G374500 chr7A 98.039 51 1 0 1629 1679 477221408 477221358 7.240000e-14 89.8
21 TraesCS5A01G374500 chr1A 92.388 867 45 12 1 851 583508286 583509147 0.000000e+00 1216.0
22 TraesCS5A01G374500 chr1A 93.071 736 38 2 29 761 20185337 20186062 0.000000e+00 1064.0
23 TraesCS5A01G374500 chr3A 93.324 749 41 5 118 858 686705964 686705217 0.000000e+00 1098.0
24 TraesCS5A01G374500 chr7D 86.534 453 56 4 1 453 83381235 83380788 1.310000e-135 494.0
25 TraesCS5A01G374500 chr4B 86.029 408 32 15 1029 1418 609768007 609767607 1.050000e-111 414.0
26 TraesCS5A01G374500 chr7B 98.039 51 1 0 1629 1679 429187073 429187023 7.240000e-14 89.8


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 TraesCS5A01G374500 chr5A 572836706 572841953 5247 False 9692.000000 9692 100.000000 1 5248 1 chr5A.!!$F2 5247
1 TraesCS5A01G374500 chr5A 510498553 510499389 836 True 1249.000000 1249 93.571000 1 840 1 chr5A.!!$R3 839
2 TraesCS5A01G374500 chr5A 11911221 11912054 833 True 1214.000000 1214 92.943000 1 835 1 chr5A.!!$R1 834
3 TraesCS5A01G374500 chr5A 567293809 567294603 794 False 1179.000000 1179 93.292000 1 805 1 chr5A.!!$F1 804
4 TraesCS5A01G374500 chr5A 28104117 28105099 982 True 935.000000 935 83.858000 3081 4063 1 chr5A.!!$R2 982
5 TraesCS5A01G374500 chr5D 453813430 453817738 4308 False 1903.333333 3035 91.386333 856 5248 3 chr5D.!!$F1 4392
6 TraesCS5A01G374500 chr5D 40091747 40092727 980 True 909.000000 909 83.418000 3081 4061 1 chr5D.!!$R1 980
7 TraesCS5A01G374500 chr5B 554511213 554515981 4768 False 1005.333333 2832 91.450167 857 5248 6 chr5B.!!$F2 4391
8 TraesCS5A01G374500 chr5B 33627692 33628672 980 False 948.000000 948 84.130000 3081 4061 1 chr5B.!!$F1 980
9 TraesCS5A01G374500 chr4A 41030960 41031822 862 True 1264.000000 1264 93.279000 1 854 1 chr4A.!!$R1 853
10 TraesCS5A01G374500 chr7A 499740767 499741563 796 False 1230.000000 1230 94.507000 1 800 1 chr7A.!!$F1 799
11 TraesCS5A01G374500 chr1A 583508286 583509147 861 False 1216.000000 1216 92.388000 1 851 1 chr1A.!!$F2 850
12 TraesCS5A01G374500 chr1A 20185337 20186062 725 False 1064.000000 1064 93.071000 29 761 1 chr1A.!!$F1 732
13 TraesCS5A01G374500 chr3A 686705217 686705964 747 True 1098.000000 1098 93.324000 118 858 1 chr3A.!!$R1 740

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
750 776 0.323999 GCCGGGTTAGGAAATGGGTT 60.324 55.0 2.18 0.0 0.0 4.11 F
1106 1147 0.615544 CCCACCTGCATTCCACCAAT 60.616 55.0 0.00 0.0 0.0 3.16 F
1987 2234 0.684805 TGGGGTTTTGGAAAGCGTGT 60.685 50.0 0.00 0.0 0.0 4.49 F
2884 3353 0.035152 CCAGCTGACTATTGGCCACA 60.035 55.0 17.39 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 1932 0.808755 CGAATCCGTTTTCCCCAAGG 59.191 55.0 0.0 0.00 0.00 3.61 R
2849 3318 0.611896 CTGGTTCCACCCAACCCATC 60.612 60.0 0.0 0.00 44.82 3.51 R
3264 3734 0.036388 TGCCGGTGAATGAGTTCTCC 60.036 55.0 1.9 0.42 42.10 3.71 R
4331 4904 0.036732 TGAGACCTCAACCATGTGGC 59.963 55.0 0.0 0.00 42.72 5.01 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
392 394 2.282251 AGCACCTCCTCGTCGTCA 60.282 61.111 0.00 0.00 0.00 4.35
650 658 2.221055 GCGAATCAGTGTGACTTTTCGT 59.779 45.455 14.93 0.00 40.51 3.85
750 776 0.323999 GCCGGGTTAGGAAATGGGTT 60.324 55.000 2.18 0.00 0.00 4.11
854 889 1.542108 GCGGCTGGAGATGCTCTTATT 60.542 52.381 0.00 0.00 0.00 1.40
855 890 2.289072 GCGGCTGGAGATGCTCTTATTA 60.289 50.000 0.00 0.00 0.00 0.98
857 892 4.573900 CGGCTGGAGATGCTCTTATTATT 58.426 43.478 0.00 0.00 0.00 1.40
858 893 5.724328 CGGCTGGAGATGCTCTTATTATTA 58.276 41.667 0.00 0.00 0.00 0.98
859 894 5.578727 CGGCTGGAGATGCTCTTATTATTAC 59.421 44.000 0.00 0.00 0.00 1.89
860 895 5.578727 GGCTGGAGATGCTCTTATTATTACG 59.421 44.000 0.00 0.00 0.00 3.18
861 896 5.062809 GCTGGAGATGCTCTTATTATTACGC 59.937 44.000 0.00 0.00 0.00 4.42
862 897 6.096673 TGGAGATGCTCTTATTATTACGCA 57.903 37.500 0.00 0.00 0.00 5.24
863 898 6.159293 TGGAGATGCTCTTATTATTACGCAG 58.841 40.000 0.00 0.00 0.00 5.18
864 899 6.015434 TGGAGATGCTCTTATTATTACGCAGA 60.015 38.462 0.00 0.00 0.00 4.26
865 900 6.868864 GGAGATGCTCTTATTATTACGCAGAA 59.131 38.462 0.00 0.00 0.00 3.02
866 901 7.062839 GGAGATGCTCTTATTATTACGCAGAAG 59.937 40.741 0.00 0.00 0.00 2.85
949 984 3.041211 TGAGATCAAATCCGTCCATCCT 58.959 45.455 0.00 0.00 0.00 3.24
950 985 3.070159 TGAGATCAAATCCGTCCATCCTC 59.930 47.826 0.00 0.00 0.00 3.71
952 987 1.578897 TCAAATCCGTCCATCCTCCA 58.421 50.000 0.00 0.00 0.00 3.86
953 988 1.486310 TCAAATCCGTCCATCCTCCAG 59.514 52.381 0.00 0.00 0.00 3.86
1018 1054 1.000771 TCGGTGTCTCCTCTCCCTG 60.001 63.158 0.00 0.00 0.00 4.45
1024 1065 2.445654 CTCCTCTCCCTGCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
1038 1079 3.976490 CTCCCTAGTCCACCCCGCA 62.976 68.421 0.00 0.00 0.00 5.69
1106 1147 0.615544 CCCACCTGCATTCCACCAAT 60.616 55.000 0.00 0.00 0.00 3.16
1112 1153 1.750778 CTGCATTCCACCAATACCCAC 59.249 52.381 0.00 0.00 0.00 4.61
1117 1158 2.274104 CACCAATACCCACCCCCG 59.726 66.667 0.00 0.00 0.00 5.73
1157 1371 1.151777 GCACGCATACACGCCACTAT 61.152 55.000 0.00 0.00 36.19 2.12
1195 1413 3.227276 CCCCCAGATCTCGACCCG 61.227 72.222 0.00 0.00 0.00 5.28
1196 1414 2.123854 CCCCAGATCTCGACCCGA 60.124 66.667 0.00 0.00 0.00 5.14
1297 1516 1.278238 CAAATCCGCGTCAGGTAGTC 58.722 55.000 4.92 0.00 0.00 2.59
1298 1517 0.892755 AAATCCGCGTCAGGTAGTCA 59.107 50.000 4.92 0.00 0.00 3.41
1495 1717 5.248020 TCTGCTCTGAGAATCTTTTCCTTCT 59.752 40.000 9.28 0.00 34.92 2.85
1497 1719 5.936956 TGCTCTGAGAATCTTTTCCTTCTTC 59.063 40.000 9.28 0.00 34.92 2.87
1498 1720 6.172630 GCTCTGAGAATCTTTTCCTTCTTCT 58.827 40.000 9.28 0.00 34.92 2.85
1506 1750 3.136443 TCTTTTCCTTCTTCTCTGGTGCA 59.864 43.478 0.00 0.00 0.00 4.57
1528 1772 3.997021 ACTGGACTGTTCGCTTAATCTTG 59.003 43.478 0.00 0.00 0.00 3.02
1530 1774 4.385825 TGGACTGTTCGCTTAATCTTGTT 58.614 39.130 0.00 0.00 0.00 2.83
1535 1779 5.295787 ACTGTTCGCTTAATCTTGTTTGTGA 59.704 36.000 0.00 0.00 0.00 3.58
1609 1853 6.038997 GTCTGAAGGGTAAGACTGTAACAT 57.961 41.667 0.00 0.00 39.79 2.71
1677 1922 4.042934 TGCTCATGATGAATCAGGATCCAT 59.957 41.667 15.82 0.00 45.17 3.41
1687 1932 5.357878 TGAATCAGGATCCATGCAAAACTAC 59.642 40.000 15.82 0.00 0.00 2.73
1754 1999 4.159321 TGTTCATCTCTCAGGAGCTAACAG 59.841 45.833 0.00 0.00 39.31 3.16
1835 2080 1.895798 TGGCTACACTCCAGTTCAGAG 59.104 52.381 0.00 0.00 37.39 3.35
1842 2087 3.181461 ACACTCCAGTTCAGAGTTCCAAG 60.181 47.826 0.00 0.00 41.87 3.61
1852 2097 5.013568 TCAGAGTTCCAAGTTTGTTACGA 57.986 39.130 0.00 0.00 0.00 3.43
1870 2117 8.118893 TGTTACGACTTGTAGTTTTTAGTGTC 57.881 34.615 0.00 0.00 33.75 3.67
1872 2119 8.758715 GTTACGACTTGTAGTTTTTAGTGTCAT 58.241 33.333 0.00 0.00 33.75 3.06
1943 2190 3.772572 AGTGGTGGGCTGTTTAAACTTTT 59.227 39.130 18.72 0.00 0.00 2.27
1944 2191 4.957327 AGTGGTGGGCTGTTTAAACTTTTA 59.043 37.500 18.72 0.00 0.00 1.52
1959 2206 9.589461 TTTAAACTTTTAATATGACCCCTGTCA 57.411 29.630 0.00 0.00 42.26 3.58
1987 2234 0.684805 TGGGGTTTTGGAAAGCGTGT 60.685 50.000 0.00 0.00 0.00 4.49
2010 2257 3.997681 GGTGAAGCTTCTCTACCTTTGAC 59.002 47.826 26.09 12.03 0.00 3.18
2018 2265 5.506649 GCTTCTCTACCTTTGACTAGGATCG 60.507 48.000 0.00 0.00 38.73 3.69
2060 2502 9.243105 TCTTTATAAAATCAGGAGAAAAGGGTG 57.757 33.333 0.00 0.00 0.00 4.61
2076 2518 8.170730 AGAAAAGGGTGTCATAAGGTTCTTAAT 58.829 33.333 0.00 0.00 0.00 1.40
2077 2519 9.457436 GAAAAGGGTGTCATAAGGTTCTTAATA 57.543 33.333 0.00 0.00 0.00 0.98
2079 2521 9.990868 AAAGGGTGTCATAAGGTTCTTAATAAT 57.009 29.630 0.00 0.00 0.00 1.28
2122 2565 5.385396 ACGTAGTCAAAGTTGAAAGTTCG 57.615 39.130 0.00 0.82 29.74 3.95
2124 2567 6.035843 ACGTAGTCAAAGTTGAAAGTTCGTA 58.964 36.000 0.00 0.00 29.74 3.43
2142 2585 6.210185 AGTTCGTATACAGTAAGGACCAAAGT 59.790 38.462 3.32 0.00 0.00 2.66
2145 2588 8.297470 TCGTATACAGTAAGGACCAAAGTTAT 57.703 34.615 3.32 0.00 0.00 1.89
2149 2592 5.727434 ACAGTAAGGACCAAAGTTATACCG 58.273 41.667 0.00 0.00 0.00 4.02
2150 2593 5.246883 ACAGTAAGGACCAAAGTTATACCGT 59.753 40.000 0.00 0.00 0.00 4.83
2199 2642 1.210478 GCTTGAGGGCTTGAGTGGATA 59.790 52.381 0.00 0.00 0.00 2.59
2202 2645 1.770658 TGAGGGCTTGAGTGGATATGG 59.229 52.381 0.00 0.00 0.00 2.74
2209 2652 3.314635 GCTTGAGTGGATATGGCTTGAAG 59.685 47.826 0.00 0.00 0.00 3.02
2210 2653 2.923121 TGAGTGGATATGGCTTGAAGC 58.077 47.619 9.04 9.04 41.46 3.86
2221 2664 2.573941 GCTTGAAGCCACATGATTCC 57.426 50.000 5.74 0.00 34.48 3.01
2245 2688 6.631636 CCGCAGTCAGTTAAGTTTCTTTTTAC 59.368 38.462 0.00 0.00 0.00 2.01
2260 2703 9.118236 GTTTCTTTTTACTGATGGAAAAGATCG 57.882 33.333 10.25 0.00 44.30 3.69
2270 2713 3.934068 TGGAAAAGATCGTAGGACCAAC 58.066 45.455 0.00 0.00 0.00 3.77
2272 2715 3.933332 GGAAAAGATCGTAGGACCAACTG 59.067 47.826 0.00 0.00 0.00 3.16
2278 2721 2.463752 TCGTAGGACCAACTGCCTAAT 58.536 47.619 0.00 0.00 38.42 1.73
2279 2722 3.634504 TCGTAGGACCAACTGCCTAATA 58.365 45.455 0.00 0.00 38.42 0.98
2280 2723 3.382546 TCGTAGGACCAACTGCCTAATAC 59.617 47.826 0.00 0.00 38.42 1.89
2281 2724 3.131577 CGTAGGACCAACTGCCTAATACA 59.868 47.826 0.00 0.00 38.42 2.29
2282 2725 3.914426 AGGACCAACTGCCTAATACAG 57.086 47.619 0.00 0.00 41.08 2.74
2300 2743 6.924913 ATACAGTAGATGATATGCACCTGT 57.075 37.500 0.00 0.00 0.00 4.00
2329 2780 6.995511 TGGTGGACAGCATACTTTAATAAC 57.004 37.500 0.00 0.00 33.39 1.89
2345 2796 9.536510 ACTTTAATAACCCTAATAGCAAACCAA 57.463 29.630 0.00 0.00 0.00 3.67
2370 2821 0.771127 AGTTGGCAAGTGGCTAGGAA 59.229 50.000 6.80 0.00 44.01 3.36
2375 2826 1.160137 GCAAGTGGCTAGGAACACAG 58.840 55.000 0.00 0.00 39.99 3.66
2426 2877 2.287970 TGCTTCAGTGAATTGCAAGCTG 60.288 45.455 15.30 10.50 40.18 4.24
2435 2886 3.056393 TGAATTGCAAGCTGAGATTTGGG 60.056 43.478 4.94 0.00 0.00 4.12
2440 2891 2.680339 GCAAGCTGAGATTTGGGACTAC 59.320 50.000 0.00 0.00 0.00 2.73
2477 2929 5.689514 TGGTTATTTTGACAAAGACAATGCG 59.310 36.000 0.10 0.00 0.00 4.73
2478 2930 5.388371 GGTTATTTTGACAAAGACAATGCGC 60.388 40.000 0.00 0.00 0.00 6.09
2480 2932 0.940833 TTGACAAAGACAATGCGCGA 59.059 45.000 12.10 0.00 0.00 5.87
2507 2959 5.239525 ACTTGTTGCTTCTTTGCCTACTTAG 59.760 40.000 0.00 0.00 0.00 2.18
2511 2963 6.768861 TGTTGCTTCTTTGCCTACTTAGTAAA 59.231 34.615 0.00 0.00 0.00 2.01
2582 3048 6.085573 TGACATCATTGTGATTTGTTAAGCG 58.914 36.000 0.00 0.00 34.28 4.68
2655 3122 9.686683 ATTTTACTATTTGTTGATAGGCAGAGT 57.313 29.630 0.00 0.00 34.58 3.24
2681 3150 1.944709 GTCAACACAAACCCGTAGCTT 59.055 47.619 0.00 0.00 0.00 3.74
2701 3170 4.340381 GCTTGGGAATATCATGCAAACTCT 59.660 41.667 0.00 0.00 35.97 3.24
2702 3171 5.506982 GCTTGGGAATATCATGCAAACTCTC 60.507 44.000 0.00 0.00 35.97 3.20
2705 3174 5.163353 TGGGAATATCATGCAAACTCTCGTA 60.163 40.000 0.00 0.00 0.00 3.43
2739 3208 4.294347 TGGTGGGATCTGTCATATGTACA 58.706 43.478 0.00 0.00 0.00 2.90
2743 3212 5.012046 GTGGGATCTGTCATATGTACATCCA 59.988 44.000 12.68 6.56 30.70 3.41
2744 3213 5.012046 TGGGATCTGTCATATGTACATCCAC 59.988 44.000 12.68 8.09 30.70 4.02
2746 3215 4.955811 TCTGTCATATGTACATCCACCC 57.044 45.455 12.68 0.00 0.00 4.61
2794 3263 7.772332 AAATTCAGTAGAATGCTTACTACCG 57.228 36.000 0.00 0.00 43.52 4.02
2795 3264 4.913335 TCAGTAGAATGCTTACTACCGG 57.087 45.455 0.00 0.00 39.53 5.28
2796 3265 4.529897 TCAGTAGAATGCTTACTACCGGA 58.470 43.478 9.46 0.00 39.53 5.14
2816 3285 4.734266 GGAAGGGAATATGATGCCTCTTT 58.266 43.478 0.00 0.00 40.73 2.52
2820 3289 3.823304 GGGAATATGATGCCTCTTTGACC 59.177 47.826 0.00 0.00 0.00 4.02
2836 3305 1.720533 TGACCTACCTGAGTTACCCCT 59.279 52.381 0.00 0.00 0.00 4.79
2848 3317 6.781014 CCTGAGTTACCCCTGTGTAAGATATA 59.219 42.308 0.00 0.00 31.66 0.86
2849 3318 7.039644 CCTGAGTTACCCCTGTGTAAGATATAG 60.040 44.444 0.00 0.00 31.66 1.31
2884 3353 0.035152 CCAGCTGACTATTGGCCACA 60.035 55.000 17.39 0.00 0.00 4.17
2888 3357 3.947196 CAGCTGACTATTGGCCACATTTA 59.053 43.478 8.42 0.00 0.00 1.40
2919 3388 2.890602 GCCTTTCTACTCTCCCCTCTGT 60.891 54.545 0.00 0.00 0.00 3.41
2953 3423 8.950208 TTAAACTGGGTTTGGTCTTTAAAATG 57.050 30.769 5.99 0.00 36.37 2.32
2954 3424 6.553953 AACTGGGTTTGGTCTTTAAAATGT 57.446 33.333 0.00 0.00 0.00 2.71
2959 3429 7.493367 TGGGTTTGGTCTTTAAAATGTAACTG 58.507 34.615 0.00 0.00 0.00 3.16
2963 3433 6.952773 TGGTCTTTAAAATGTAACTGTGCT 57.047 33.333 0.00 0.00 0.00 4.40
3020 3490 9.941991 CAATAAACGAAGATTTTACTGCATTTG 57.058 29.630 0.00 0.00 0.00 2.32
3023 3493 8.452989 AAACGAAGATTTTACTGCATTTGATC 57.547 30.769 0.00 0.00 0.00 2.92
3051 3521 8.599055 TCATGAATATGACTTCTTGTATGCTC 57.401 34.615 0.00 0.00 38.37 4.26
3070 3540 3.869912 GCTCAAGTGCAAGTCCCTGATTA 60.870 47.826 0.00 0.00 0.00 1.75
3108 3578 3.051081 AGTCATGAGGTCTTGCTGTTC 57.949 47.619 0.00 0.00 0.00 3.18
3258 3728 2.268298 CTTCGGGTTCTTGATACACCG 58.732 52.381 0.00 0.00 42.45 4.94
3264 3734 2.030457 GGTTCTTGATACACCGATTGCG 59.970 50.000 0.00 0.00 37.24 4.85
3300 3770 1.751927 CATGGGAGTTGGAGCAGGC 60.752 63.158 0.00 0.00 0.00 4.85
3405 3875 3.614092 CATGCTTCATTACACCTCTGGT 58.386 45.455 0.00 0.00 35.62 4.00
3433 3903 5.934043 CAGTTCAAGATACCACTTGTGATCA 59.066 40.000 1.89 0.00 44.96 2.92
3456 3926 2.978010 CCTGGTGGTGTTGGTCGC 60.978 66.667 0.00 0.00 0.00 5.19
3504 3974 4.416620 GTCTTGAGTCATACTTCCAGTCG 58.583 47.826 0.00 0.00 0.00 4.18
3702 4172 1.002868 GCCTGGTGAGCATGTGACT 60.003 57.895 0.00 0.00 0.00 3.41
3792 4262 3.960755 ACGATCCTGAGGTGATTGACATA 59.039 43.478 0.00 0.00 0.00 2.29
4044 4599 2.480555 CAGATTGTTGCCGCCGTC 59.519 61.111 0.00 0.00 0.00 4.79
4087 4642 4.340263 CATCATCTGTTTCAGCATCGTTG 58.660 43.478 0.00 0.00 0.00 4.10
4232 4805 2.224161 GCTGAATGCTACTAGGGTCTGG 60.224 54.545 0.00 0.00 38.95 3.86
4261 4834 7.396055 TCGGGTTTATTGGAAGAAATCTTTGAT 59.604 33.333 0.00 0.00 36.11 2.57
4292 4865 5.323371 GCAAGGTATAGCCATTTGTTTGA 57.677 39.130 0.00 0.00 40.61 2.69
4293 4866 5.906073 GCAAGGTATAGCCATTTGTTTGAT 58.094 37.500 0.00 0.00 40.61 2.57
4295 4868 7.488322 GCAAGGTATAGCCATTTGTTTGATTA 58.512 34.615 0.00 0.00 40.61 1.75
4296 4869 8.143835 GCAAGGTATAGCCATTTGTTTGATTAT 58.856 33.333 0.00 0.00 40.61 1.28
4297 4870 9.683069 CAAGGTATAGCCATTTGTTTGATTATC 57.317 33.333 0.00 0.00 40.61 1.75
4298 4871 9.646522 AAGGTATAGCCATTTGTTTGATTATCT 57.353 29.630 0.00 0.00 40.61 1.98
4311 4884 8.364129 TGTTTGATTATCTTTGTTTTGCCTTC 57.636 30.769 0.00 0.00 0.00 3.46
4323 4896 9.317936 CTTTGTTTTGCCTTCTAAAGAAAGATT 57.682 29.630 12.63 0.00 43.67 2.40
4324 4897 8.647143 TTGTTTTGCCTTCTAAAGAAAGATTG 57.353 30.769 0.00 0.00 33.07 2.67
4328 4901 7.440523 TTGCCTTCTAAAGAAAGATTGTCTC 57.559 36.000 0.00 0.00 33.07 3.36
4331 4904 5.582665 CCTTCTAAAGAAAGATTGTCTCGGG 59.417 44.000 0.00 0.00 33.07 5.14
4332 4905 4.504858 TCTAAAGAAAGATTGTCTCGGGC 58.495 43.478 0.00 0.00 0.00 6.13
4344 4917 1.746615 CTCGGGCCACATGGTTGAG 60.747 63.158 4.39 0.00 37.57 3.02
4364 4937 5.971763 TGAGGTCTCAAGAAAGCTTAGATC 58.028 41.667 0.00 0.00 36.53 2.75
4365 4938 5.481824 TGAGGTCTCAAGAAAGCTTAGATCA 59.518 40.000 0.00 0.00 36.53 2.92
4366 4939 6.155910 TGAGGTCTCAAGAAAGCTTAGATCAT 59.844 38.462 0.00 0.00 36.53 2.45
4367 4940 6.347696 AGGTCTCAAGAAAGCTTAGATCATG 58.652 40.000 0.00 0.00 31.81 3.07
4368 4941 6.155910 AGGTCTCAAGAAAGCTTAGATCATGA 59.844 38.462 0.00 0.00 31.81 3.07
4369 4942 6.257630 GGTCTCAAGAAAGCTTAGATCATGAC 59.742 42.308 0.00 3.79 31.81 3.06
4370 4943 6.815641 GTCTCAAGAAAGCTTAGATCATGACA 59.184 38.462 0.00 0.00 31.81 3.58
4371 4944 7.495279 GTCTCAAGAAAGCTTAGATCATGACAT 59.505 37.037 0.00 0.00 31.81 3.06
4372 4945 7.710044 TCTCAAGAAAGCTTAGATCATGACATC 59.290 37.037 0.00 0.00 31.81 3.06
4373 4946 6.765036 TCAAGAAAGCTTAGATCATGACATCC 59.235 38.462 0.00 0.00 31.81 3.51
4374 4947 6.244552 AGAAAGCTTAGATCATGACATCCA 57.755 37.500 0.00 0.00 0.00 3.41
4375 4948 6.289834 AGAAAGCTTAGATCATGACATCCAG 58.710 40.000 0.00 0.00 0.00 3.86
4376 4949 5.883685 AAGCTTAGATCATGACATCCAGA 57.116 39.130 0.00 0.00 0.00 3.86
4377 4950 5.883685 AGCTTAGATCATGACATCCAGAA 57.116 39.130 0.00 0.00 0.00 3.02
4413 4986 0.319813 GCCTCACCACCAATTGCAAC 60.320 55.000 0.00 0.00 0.00 4.17
4414 4987 1.039068 CCTCACCACCAATTGCAACA 58.961 50.000 0.00 0.00 0.00 3.33
4415 4988 1.619827 CCTCACCACCAATTGCAACAT 59.380 47.619 0.00 0.00 0.00 2.71
4421 4994 4.334759 CACCACCAATTGCAACATTGAAAA 59.665 37.500 13.20 0.00 0.00 2.29
4435 5008 7.515684 GCAACATTGAAAAGAAGATCACAACAC 60.516 37.037 0.00 0.00 0.00 3.32
4437 5010 5.514274 TTGAAAAGAAGATCACAACACCC 57.486 39.130 0.00 0.00 0.00 4.61
4455 5028 1.305381 CCTTCTCCAGGGGACGAGT 60.305 63.158 0.00 0.00 39.39 4.18
4462 5035 4.070552 AGGGGACGAGTCGCTTGC 62.071 66.667 13.59 0.00 41.61 4.01
4517 5092 6.227298 ACCATACTTACAGAGATTGTCCAG 57.773 41.667 0.00 0.00 41.29 3.86
4520 5095 6.462207 CCATACTTACAGAGATTGTCCAGGAG 60.462 46.154 0.00 0.00 41.29 3.69
4527 5102 0.107459 GATTGTCCAGGAGTCCAGGC 60.107 60.000 15.79 11.19 29.61 4.85
4528 5103 0.548682 ATTGTCCAGGAGTCCAGGCT 60.549 55.000 15.79 0.00 29.61 4.58
4529 5104 0.116342 TTGTCCAGGAGTCCAGGCTA 59.884 55.000 15.79 4.27 29.61 3.93
4530 5105 0.116342 TGTCCAGGAGTCCAGGCTAA 59.884 55.000 15.79 0.96 29.61 3.09
4531 5106 0.827368 GTCCAGGAGTCCAGGCTAAG 59.173 60.000 15.79 0.00 29.61 2.18
4532 5107 0.978146 TCCAGGAGTCCAGGCTAAGC 60.978 60.000 15.79 0.00 29.61 3.09
4533 5108 0.980231 CCAGGAGTCCAGGCTAAGCT 60.980 60.000 12.86 0.00 0.00 3.74
4534 5109 1.689575 CCAGGAGTCCAGGCTAAGCTA 60.690 57.143 12.86 0.00 0.00 3.32
4535 5110 1.410882 CAGGAGTCCAGGCTAAGCTAC 59.589 57.143 12.86 0.00 0.00 3.58
4536 5111 1.007238 AGGAGTCCAGGCTAAGCTACA 59.993 52.381 12.86 0.00 0.00 2.74
4537 5112 1.137282 GGAGTCCAGGCTAAGCTACAC 59.863 57.143 3.60 0.00 0.00 2.90
4538 5113 2.104170 GAGTCCAGGCTAAGCTACACT 58.896 52.381 0.00 0.00 0.00 3.55
4539 5114 3.288964 GAGTCCAGGCTAAGCTACACTA 58.711 50.000 0.00 0.00 0.00 2.74
4540 5115 3.292460 AGTCCAGGCTAAGCTACACTAG 58.708 50.000 0.00 0.00 0.00 2.57
4554 5129 5.559427 CTACACTAGCTAGATGATCGCAT 57.441 43.478 27.45 7.27 37.47 4.73
4605 5180 2.673368 CGGCTTACATTCTCACAGAACC 59.327 50.000 0.00 0.00 37.00 3.62
4613 5188 3.836365 TTCTCACAGAACCACACATGA 57.164 42.857 0.00 0.00 0.00 3.07
4631 5206 3.144657 TGACATCACAGCTGGAACAAT 57.855 42.857 19.93 0.71 38.70 2.71
4646 5221 3.428045 GGAACAATACCATCAGCAACAGC 60.428 47.826 0.00 0.00 0.00 4.40
4656 5231 1.072159 AGCAACAGCAGGAGGTGAC 59.928 57.895 1.32 0.00 45.95 3.67
4657 5232 1.227943 GCAACAGCAGGAGGTGACA 60.228 57.895 1.32 0.00 45.95 3.58
4685 5260 0.187361 CCAACCTCCCTTCAAACCCA 59.813 55.000 0.00 0.00 0.00 4.51
4808 5383 0.960364 GCATCTTGCCGGACCTGAAA 60.960 55.000 5.05 0.00 37.42 2.69
5087 5665 2.604174 CGACGGATTAATGGCGGCC 61.604 63.158 13.32 13.32 0.00 6.13
5091 5669 1.086696 CGGATTAATGGCGGCCATAG 58.913 55.000 33.13 16.55 44.40 2.23
5136 5716 7.821359 CCATGAAGAGTAACCATGACCTATATG 59.179 40.741 0.00 0.00 39.86 1.78
5146 5726 4.931601 CCATGACCTATATGTGTTCCATCG 59.068 45.833 0.00 0.00 34.86 3.84
5151 5731 5.601662 ACCTATATGTGTTCCATCGACTTG 58.398 41.667 0.00 0.00 34.86 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
650 658 2.603473 CGGGTCCCCACTGTCAGA 60.603 66.667 6.91 0.00 35.37 3.27
738 764 1.133915 GCCGGATCAACCCATTTCCTA 60.134 52.381 5.05 0.00 34.64 2.94
741 767 1.724582 CCGCCGGATCAACCCATTTC 61.725 60.000 5.05 0.00 34.64 2.17
818 844 3.839432 GCGCCCTCTAGACCGCTT 61.839 66.667 16.22 0.00 42.83 4.68
854 889 8.583810 AATTATTTAGCGTCTTCTGCGTAATA 57.416 30.769 0.00 0.00 37.44 0.98
855 890 7.307219 GGAATTATTTAGCGTCTTCTGCGTAAT 60.307 37.037 0.00 0.00 37.44 1.89
857 892 5.461078 GGAATTATTTAGCGTCTTCTGCGTA 59.539 40.000 0.00 0.00 37.44 4.42
858 893 4.270325 GGAATTATTTAGCGTCTTCTGCGT 59.730 41.667 0.00 0.00 37.44 5.24
859 894 4.270084 TGGAATTATTTAGCGTCTTCTGCG 59.730 41.667 0.00 0.00 37.44 5.18
860 895 5.734855 TGGAATTATTTAGCGTCTTCTGC 57.265 39.130 0.00 0.00 0.00 4.26
861 896 6.183360 TGCTTGGAATTATTTAGCGTCTTCTG 60.183 38.462 0.00 0.00 34.65 3.02
862 897 5.880332 TGCTTGGAATTATTTAGCGTCTTCT 59.120 36.000 0.00 0.00 34.65 2.85
863 898 6.119144 TGCTTGGAATTATTTAGCGTCTTC 57.881 37.500 0.00 0.00 34.65 2.87
864 899 6.699575 ATGCTTGGAATTATTTAGCGTCTT 57.300 33.333 0.00 0.00 34.65 3.01
865 900 6.498304 CAATGCTTGGAATTATTTAGCGTCT 58.502 36.000 0.00 0.00 34.65 4.18
866 901 6.738352 CAATGCTTGGAATTATTTAGCGTC 57.262 37.500 0.00 0.00 34.65 5.19
897 932 7.315247 TGATTTCGTTTCTGACTCTTTGAAA 57.685 32.000 0.00 0.00 0.00 2.69
949 984 2.811514 GCCGATGGAGATGGCTGGA 61.812 63.158 0.00 0.00 45.40 3.86
950 985 2.281345 GCCGATGGAGATGGCTGG 60.281 66.667 0.00 0.00 45.40 4.85
1018 1054 2.768769 GGGGTGGACTAGGGAGGC 60.769 72.222 0.00 0.00 0.00 4.70
1024 1065 2.683933 AGGTGCGGGGTGGACTAG 60.684 66.667 0.00 0.00 39.22 2.57
1038 1079 4.052229 CGGCGGAGTGAACGAGGT 62.052 66.667 0.00 0.00 0.00 3.85
1061 1102 2.768344 GGCGGAGGAATGGAGGGA 60.768 66.667 0.00 0.00 0.00 4.20
1064 1105 2.190578 GGTGGCGGAGGAATGGAG 59.809 66.667 0.00 0.00 0.00 3.86
1112 1153 3.073356 TGTTTATTTATAGAGGGCGGGGG 59.927 47.826 0.00 0.00 0.00 5.40
1117 1158 3.363673 GCGCGTGTTTATTTATAGAGGGC 60.364 47.826 8.43 0.00 0.00 5.19
1195 1413 1.105759 GCCATTGCAGATGGGAGGTC 61.106 60.000 21.74 7.80 39.53 3.85
1196 1414 1.076485 GCCATTGCAGATGGGAGGT 60.076 57.895 21.74 0.00 39.53 3.85
1495 1717 0.394192 CAGTCCAGTGCACCAGAGAA 59.606 55.000 14.63 0.00 0.00 2.87
1497 1719 0.107456 AACAGTCCAGTGCACCAGAG 59.893 55.000 14.63 2.47 0.00 3.35
1498 1720 0.106708 GAACAGTCCAGTGCACCAGA 59.893 55.000 14.63 7.87 0.00 3.86
1506 1750 3.963428 AGATTAAGCGAACAGTCCAGT 57.037 42.857 0.00 0.00 0.00 4.00
1528 1772 3.035942 GTCTGCACACGAAATCACAAAC 58.964 45.455 0.00 0.00 0.00 2.93
1530 1774 1.601903 GGTCTGCACACGAAATCACAA 59.398 47.619 0.00 0.00 0.00 3.33
1535 1779 1.238439 CCTTGGTCTGCACACGAAAT 58.762 50.000 0.00 0.00 0.00 2.17
1580 1824 4.223923 CAGTCTTACCCTTCAGACTTGGAT 59.776 45.833 0.00 0.00 46.31 3.41
1609 1853 2.343758 GCAGGCGAGGAAGTGTGA 59.656 61.111 0.00 0.00 0.00 3.58
1677 1922 2.757894 TTCCCCAAGGTAGTTTTGCA 57.242 45.000 0.00 0.00 0.00 4.08
1687 1932 0.808755 CGAATCCGTTTTCCCCAAGG 59.191 55.000 0.00 0.00 0.00 3.61
1842 2087 9.202545 CACTAAAAACTACAAGTCGTAACAAAC 57.797 33.333 0.00 0.00 0.00 2.93
1852 2097 7.551262 TGACACATGACACTAAAAACTACAAGT 59.449 33.333 0.00 0.00 0.00 3.16
1870 2117 5.414360 AGCAGACAACTATAGTGACACATG 58.586 41.667 6.06 2.26 0.00 3.21
1872 2119 6.208797 ACTTAGCAGACAACTATAGTGACACA 59.791 38.462 6.06 0.00 0.00 3.72
1959 2206 4.576330 TTCCAAAACCCCATGTGTTTTT 57.424 36.364 16.40 0.00 42.38 1.94
1987 2234 3.646162 TCAAAGGTAGAGAAGCTTCACCA 59.354 43.478 27.28 11.70 45.11 4.17
2076 2518 9.542462 CGTCCTTCCTCTGTTTATGAAATATTA 57.458 33.333 0.00 0.00 0.00 0.98
2077 2519 8.047310 ACGTCCTTCCTCTGTTTATGAAATATT 58.953 33.333 0.00 0.00 0.00 1.28
2079 2521 6.942976 ACGTCCTTCCTCTGTTTATGAAATA 58.057 36.000 0.00 0.00 0.00 1.40
2085 2528 5.014858 TGACTACGTCCTTCCTCTGTTTAT 58.985 41.667 0.00 0.00 0.00 1.40
2108 2551 8.985805 CCTTACTGTATACGAACTTTCAACTTT 58.014 33.333 0.00 0.00 0.00 2.66
2122 2565 9.755804 GGTATAACTTTGGTCCTTACTGTATAC 57.244 37.037 0.00 0.00 0.00 1.47
2124 2567 7.124750 ACGGTATAACTTTGGTCCTTACTGTAT 59.875 37.037 0.00 0.00 29.73 2.29
2142 2585 5.876460 GGCTTTCTGTCCTAAAACGGTATAA 59.124 40.000 0.00 0.00 0.00 0.98
2145 2588 3.071312 TGGCTTTCTGTCCTAAAACGGTA 59.929 43.478 0.00 0.00 0.00 4.02
2149 2592 4.822350 AGAACTGGCTTTCTGTCCTAAAAC 59.178 41.667 1.71 0.00 34.40 2.43
2150 2593 4.821805 CAGAACTGGCTTTCTGTCCTAAAA 59.178 41.667 16.70 0.00 45.12 1.52
2202 2645 1.202222 CGGAATCATGTGGCTTCAAGC 60.202 52.381 0.00 0.00 41.46 4.01
2209 2652 1.026182 TGACTGCGGAATCATGTGGC 61.026 55.000 0.00 0.00 0.00 5.01
2210 2653 1.012086 CTGACTGCGGAATCATGTGG 58.988 55.000 0.00 0.00 0.00 4.17
2220 2663 4.813296 AAAGAAACTTAACTGACTGCGG 57.187 40.909 0.00 0.00 0.00 5.69
2221 2664 7.373441 CAGTAAAAAGAAACTTAACTGACTGCG 59.627 37.037 12.15 0.00 0.00 5.18
2245 2688 4.141937 TGGTCCTACGATCTTTTCCATCAG 60.142 45.833 0.00 0.00 0.00 2.90
2260 2703 4.161754 ACTGTATTAGGCAGTTGGTCCTAC 59.838 45.833 0.00 0.00 43.87 3.18
2270 2713 7.490725 GTGCATATCATCTACTGTATTAGGCAG 59.509 40.741 0.00 0.00 39.67 4.85
2272 2715 6.758886 GGTGCATATCATCTACTGTATTAGGC 59.241 42.308 0.00 0.00 0.00 3.93
2278 2721 6.551227 AGAACAGGTGCATATCATCTACTGTA 59.449 38.462 0.00 0.00 36.98 2.74
2279 2722 5.365025 AGAACAGGTGCATATCATCTACTGT 59.635 40.000 0.00 0.00 39.38 3.55
2280 2723 5.851720 AGAACAGGTGCATATCATCTACTG 58.148 41.667 0.00 0.00 33.48 2.74
2281 2724 6.326064 AGAAGAACAGGTGCATATCATCTACT 59.674 38.462 0.00 0.00 33.48 2.57
2282 2725 6.423302 CAGAAGAACAGGTGCATATCATCTAC 59.577 42.308 0.00 0.00 33.48 2.59
2300 2743 2.906389 AGTATGCTGTCCACCAGAAGAA 59.094 45.455 0.00 0.00 44.49 2.52
2310 2753 8.919777 ATTAGGGTTATTAAAGTATGCTGTCC 57.080 34.615 0.00 0.00 0.00 4.02
2329 2780 8.621286 CAACTACTTATTGGTTTGCTATTAGGG 58.379 37.037 0.00 0.00 0.00 3.53
2345 2796 3.721087 AGCCACTTGCCAACTACTTAT 57.279 42.857 0.00 0.00 42.71 1.73
2356 2807 1.160137 CTGTGTTCCTAGCCACTTGC 58.840 55.000 6.88 0.00 41.71 4.01
2370 2821 6.077993 TCCCTAGATATACTGCAATCTGTGT 58.922 40.000 8.58 0.00 34.36 3.72
2375 2826 7.093727 TGCTTACTCCCTAGATATACTGCAATC 60.094 40.741 0.00 0.00 0.00 2.67
2459 2910 2.115595 CGCGCATTGTCTTTGTCAAAA 58.884 42.857 8.75 0.00 0.00 2.44
2460 2911 1.332065 TCGCGCATTGTCTTTGTCAAA 59.668 42.857 8.75 0.00 0.00 2.69
2470 2922 0.874390 AACAAGTCATCGCGCATTGT 59.126 45.000 8.75 4.82 35.70 2.71
2477 2929 2.975851 CAAAGAAGCAACAAGTCATCGC 59.024 45.455 0.00 0.00 0.00 4.58
2478 2930 2.975851 GCAAAGAAGCAACAAGTCATCG 59.024 45.455 0.00 0.00 0.00 3.84
2480 2932 2.961062 AGGCAAAGAAGCAACAAGTCAT 59.039 40.909 0.00 0.00 35.83 3.06
2516 2968 9.905713 TGGAAATAGAGTAAATACAGCTTCAAT 57.094 29.630 0.00 0.00 0.00 2.57
2544 3010 9.467258 CACAATGATGTCAGTTTTTACTGAAAT 57.533 29.630 10.03 10.03 46.81 2.17
2550 3016 9.248291 ACAAATCACAATGATGTCAGTTTTTAC 57.752 29.630 0.00 0.00 37.15 2.01
2564 3030 6.926280 TTAAGCGCTTAACAAATCACAATG 57.074 33.333 33.05 0.00 30.78 2.82
2611 3078 2.917713 ATATTGTGCCAAACCCAGGA 57.082 45.000 0.00 0.00 0.00 3.86
2645 3112 7.182817 TGTGTTGACTTAATACTCTGCCTAT 57.817 36.000 0.00 0.00 32.23 2.57
2647 3114 5.483685 TGTGTTGACTTAATACTCTGCCT 57.516 39.130 0.00 0.00 32.23 4.75
2650 3117 6.347402 CGGGTTTGTGTTGACTTAATACTCTG 60.347 42.308 0.00 0.00 32.23 3.35
2655 3122 5.409214 GCTACGGGTTTGTGTTGACTTAATA 59.591 40.000 0.00 0.00 0.00 0.98
2656 3123 4.214758 GCTACGGGTTTGTGTTGACTTAAT 59.785 41.667 0.00 0.00 0.00 1.40
2658 3125 3.132925 GCTACGGGTTTGTGTTGACTTA 58.867 45.455 0.00 0.00 0.00 2.24
2681 3150 4.129380 CGAGAGTTTGCATGATATTCCCA 58.871 43.478 0.00 0.00 0.00 4.37
2686 3155 7.212976 AGTTCATACGAGAGTTTGCATGATAT 58.787 34.615 0.00 0.00 46.40 1.63
2701 3170 3.556213 CCCACCAACTGAAGTTCATACGA 60.556 47.826 5.91 0.00 35.83 3.43
2702 3171 2.742053 CCCACCAACTGAAGTTCATACG 59.258 50.000 5.91 0.00 35.83 3.06
2705 3174 3.331889 AGATCCCACCAACTGAAGTTCAT 59.668 43.478 5.91 0.00 35.83 2.57
2743 3212 7.511028 TGGAAAATAAATCCAGTTTACTTGGGT 59.489 33.333 0.00 0.00 41.98 4.51
2744 3213 7.902087 TGGAAAATAAATCCAGTTTACTTGGG 58.098 34.615 0.00 0.00 41.98 4.12
2780 3249 2.433239 TCCCTTCCGGTAGTAAGCATTC 59.567 50.000 7.37 0.00 0.00 2.67
2781 3250 2.474112 TCCCTTCCGGTAGTAAGCATT 58.526 47.619 7.37 0.00 0.00 3.56
2794 3263 4.379302 AAGAGGCATCATATTCCCTTCC 57.621 45.455 0.00 0.00 0.00 3.46
2795 3264 5.240403 GTCAAAGAGGCATCATATTCCCTTC 59.760 44.000 0.00 0.00 0.00 3.46
2796 3265 5.136105 GTCAAAGAGGCATCATATTCCCTT 58.864 41.667 0.00 0.00 0.00 3.95
2801 3270 5.370880 AGGTAGGTCAAAGAGGCATCATATT 59.629 40.000 0.00 0.00 0.00 1.28
2805 3274 2.237143 CAGGTAGGTCAAAGAGGCATCA 59.763 50.000 0.00 0.00 0.00 3.07
2816 3285 1.720533 AGGGGTAACTCAGGTAGGTCA 59.279 52.381 0.00 0.00 42.85 4.02
2820 3289 2.537143 ACACAGGGGTAACTCAGGTAG 58.463 52.381 0.00 0.00 42.85 3.18
2836 3305 5.908831 ACCCAACCCATCTATATCTTACACA 59.091 40.000 0.00 0.00 0.00 3.72
2848 3317 1.071314 TGGTTCCACCCAACCCATCT 61.071 55.000 0.00 0.00 44.82 2.90
2849 3318 0.611896 CTGGTTCCACCCAACCCATC 60.612 60.000 0.00 0.00 44.82 3.51
2905 3374 2.091775 GCTTCCTACAGAGGGGAGAGTA 60.092 54.545 0.00 0.00 43.94 2.59
2919 3388 4.830600 CCAAACCCAGTTTAAAGCTTCCTA 59.169 41.667 0.00 0.00 33.70 2.94
2953 3423 4.993029 ATGGAGAGAGTAGCACAGTTAC 57.007 45.455 0.00 0.00 0.00 2.50
2954 3424 5.265191 AGAATGGAGAGAGTAGCACAGTTA 58.735 41.667 0.00 0.00 0.00 2.24
2959 3429 6.648879 ATAGAAGAATGGAGAGAGTAGCAC 57.351 41.667 0.00 0.00 0.00 4.40
3002 3472 9.630098 TGAAAGATCAAATGCAGTAAAATCTTC 57.370 29.630 14.84 10.79 32.41 2.87
3023 3493 9.661187 GCATACAAGAAGTCATATTCATGAAAG 57.339 33.333 13.09 5.93 42.79 2.62
3051 3521 4.012374 ACATAATCAGGGACTTGCACTTG 58.988 43.478 0.00 0.00 34.60 3.16
3084 3554 3.517100 ACAGCAAGACCTCATGACTACAT 59.483 43.478 0.00 0.00 37.19 2.29
3108 3578 4.560856 CCCTCGCGAAGAGCCTCG 62.561 72.222 11.33 0.00 45.54 4.63
3258 3728 2.352960 GGTGAATGAGTTCTCCGCAATC 59.647 50.000 0.00 0.00 38.00 2.67
3264 3734 0.036388 TGCCGGTGAATGAGTTCTCC 60.036 55.000 1.90 0.42 42.10 3.71
3405 3875 1.985159 AGTGGTATCTTGAACTGGCCA 59.015 47.619 4.71 4.71 0.00 5.36
3433 3903 1.418908 CCAACACCACCAGGACCTCT 61.419 60.000 0.00 0.00 38.69 3.69
3456 3926 1.248785 AATGCTCTGCACCAAGCTGG 61.249 55.000 11.15 0.00 43.04 4.85
3792 4262 1.156736 CGAATGGCTTCAACGACCTT 58.843 50.000 0.00 0.00 0.00 3.50
3978 4448 2.667199 GTTGCGGCGTAGGGTGTT 60.667 61.111 9.37 0.00 0.00 3.32
4087 4642 2.355010 AGCCAGGGCAGATACAAATC 57.645 50.000 13.63 0.00 44.88 2.17
4232 4805 5.880887 AGATTTCTTCCAATAAACCCGAGTC 59.119 40.000 0.00 0.00 0.00 3.36
4282 4855 9.384682 GGCAAAACAAAGATAATCAAACAAATG 57.615 29.630 0.00 0.00 0.00 2.32
4285 4858 8.729805 AAGGCAAAACAAAGATAATCAAACAA 57.270 26.923 0.00 0.00 0.00 2.83
4295 4868 8.695456 TCTTTCTTTAGAAGGCAAAACAAAGAT 58.305 29.630 0.00 0.00 33.42 2.40
4296 4869 8.062065 TCTTTCTTTAGAAGGCAAAACAAAGA 57.938 30.769 0.00 0.00 35.21 2.52
4297 4870 8.877808 ATCTTTCTTTAGAAGGCAAAACAAAG 57.122 30.769 0.00 0.00 35.21 2.77
4298 4871 9.097257 CAATCTTTCTTTAGAAGGCAAAACAAA 57.903 29.630 0.00 0.00 35.21 2.83
4301 4874 8.138074 AGACAATCTTTCTTTAGAAGGCAAAAC 58.862 33.333 0.00 0.00 35.21 2.43
4302 4875 8.237811 AGACAATCTTTCTTTAGAAGGCAAAA 57.762 30.769 0.00 0.00 35.21 2.44
4311 4884 3.623510 GGCCCGAGACAATCTTTCTTTAG 59.376 47.826 0.00 0.00 0.00 1.85
4323 4896 2.525124 AACCATGTGGCCCGAGACA 61.525 57.895 0.00 0.00 39.32 3.41
4324 4897 2.040544 CAACCATGTGGCCCGAGAC 61.041 63.158 0.00 0.00 39.32 3.36
4328 4901 2.751436 CCTCAACCATGTGGCCCG 60.751 66.667 0.00 0.00 39.32 6.13
4331 4904 0.036732 TGAGACCTCAACCATGTGGC 59.963 55.000 0.00 0.00 42.72 5.01
4332 4905 2.038952 TCTTGAGACCTCAACCATGTGG 59.961 50.000 8.27 0.00 43.90 4.17
4344 4917 6.257630 GTCATGATCTAAGCTTTCTTGAGACC 59.742 42.308 3.20 0.00 33.85 3.85
4367 4940 2.676839 CTGCTGACATGTTCTGGATGTC 59.323 50.000 0.00 0.00 46.72 3.06
4368 4941 2.708051 CTGCTGACATGTTCTGGATGT 58.292 47.619 0.00 0.00 36.73 3.06
4369 4942 1.400846 GCTGCTGACATGTTCTGGATG 59.599 52.381 0.00 0.00 0.00 3.51
4370 4943 1.681166 GGCTGCTGACATGTTCTGGAT 60.681 52.381 0.00 0.00 0.00 3.41
4371 4944 0.321919 GGCTGCTGACATGTTCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
4372 4945 0.607217 TGGCTGCTGACATGTTCTGG 60.607 55.000 0.00 0.00 0.00 3.86
4373 4946 1.460504 ATGGCTGCTGACATGTTCTG 58.539 50.000 11.68 0.00 41.12 3.02
4374 4947 3.972368 ATGGCTGCTGACATGTTCT 57.028 47.368 11.68 0.00 41.12 3.01
4413 4986 5.922544 GGGTGTTGTGATCTTCTTTTCAATG 59.077 40.000 0.00 0.00 0.00 2.82
4414 4987 5.011023 GGGGTGTTGTGATCTTCTTTTCAAT 59.989 40.000 0.00 0.00 0.00 2.57
4415 4988 4.340950 GGGGTGTTGTGATCTTCTTTTCAA 59.659 41.667 0.00 0.00 0.00 2.69
4421 4994 2.982488 AGAAGGGGTGTTGTGATCTTCT 59.018 45.455 0.00 0.00 36.94 2.85
4437 5010 1.305381 ACTCGTCCCCTGGAGAAGG 60.305 63.158 0.00 0.00 46.94 3.46
4462 5035 4.380233 CCTTAAGTTGCTTGGCTGATCAAG 60.380 45.833 0.97 0.00 44.97 3.02
4517 5092 1.137282 GTGTAGCTTAGCCTGGACTCC 59.863 57.143 0.00 0.00 0.00 3.85
4520 5095 3.719173 CTAGTGTAGCTTAGCCTGGAC 57.281 52.381 0.00 0.00 0.00 4.02
4531 5106 5.955005 GATGCGATCATCTAGCTAGTGTAGC 60.955 48.000 20.10 19.63 46.49 3.58
4532 5107 5.559427 ATGCGATCATCTAGCTAGTGTAG 57.441 43.478 20.10 8.95 0.00 2.74
4533 5108 5.553290 GATGCGATCATCTAGCTAGTGTA 57.447 43.478 20.10 7.31 44.38 2.90
4534 5109 4.433186 GATGCGATCATCTAGCTAGTGT 57.567 45.455 20.10 7.99 44.38 3.55
4545 5120 4.279420 TGTAGCTTAGACTGATGCGATCAT 59.721 41.667 0.00 0.00 38.85 2.45
4546 5121 3.632145 TGTAGCTTAGACTGATGCGATCA 59.368 43.478 0.00 0.00 37.76 2.92
4547 5122 3.978217 GTGTAGCTTAGACTGATGCGATC 59.022 47.826 0.00 0.00 0.00 3.69
4548 5123 3.634448 AGTGTAGCTTAGACTGATGCGAT 59.366 43.478 0.00 0.00 30.27 4.58
4549 5124 3.017442 AGTGTAGCTTAGACTGATGCGA 58.983 45.455 0.00 0.00 30.27 5.10
4550 5125 3.428746 AGTGTAGCTTAGACTGATGCG 57.571 47.619 0.00 0.00 30.27 4.73
4605 5180 1.467342 CCAGCTGTGATGTCATGTGTG 59.533 52.381 13.81 0.00 0.00 3.82
4613 5188 3.244875 TGGTATTGTTCCAGCTGTGATGT 60.245 43.478 13.81 0.00 0.00 3.06
4631 5206 0.983467 TCCTGCTGTTGCTGATGGTA 59.017 50.000 0.00 0.00 40.01 3.25
4646 5221 1.004080 CTGGCTGTGTCACCTCCTG 60.004 63.158 0.00 2.25 0.00 3.86
4656 5231 2.674380 GAGGTTGGGCTGGCTGTG 60.674 66.667 0.00 0.00 0.00 3.66
4657 5232 3.971702 GGAGGTTGGGCTGGCTGT 61.972 66.667 0.00 0.00 0.00 4.40
4701 5276 3.771160 GAGGGAAAGGGCGAGCGA 61.771 66.667 0.00 0.00 0.00 4.93
4808 5383 1.333636 CCTTCTCCATCCGGCTGACT 61.334 60.000 6.92 0.00 0.00 3.41
5087 5665 3.564644 CCTCTTGCAATGGCTCTTCTATG 59.435 47.826 0.00 0.00 41.91 2.23
5091 5669 0.455005 GCCTCTTGCAATGGCTCTTC 59.545 55.000 26.62 6.82 43.05 2.87


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

AutoCloner maintained by Alex Coulton.