Multiple sequence alignment - TraesCS3A01G053200

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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 TraesCS3A01G053200 chr3A 100.000 2345 0 0 1 2345 29723499 29725843 0.000000e+00 4331
1 TraesCS3A01G053200 chr3A 91.013 612 47 1 995 1598 29529892 29530503 0.000000e+00 819
2 TraesCS3A01G053200 chr3A 92.915 494 33 2 1599 2092 29534257 29534748 0.000000e+00 717
3 TraesCS3A01G053200 chr3A 91.736 121 10 0 2090 2210 29549266 29549386 4.010000e-38 169
4 TraesCS3A01G053200 chr6A 96.486 683 23 1 1 683 599307339 599306658 0.000000e+00 1127
5 TraesCS3A01G053200 chr6A 96.774 310 10 0 678 987 599306366 599306057 3.450000e-143 518
6 TraesCS3A01G053200 chr4B 92.805 681 49 0 3 683 648836862 648836182 0.000000e+00 987
7 TraesCS3A01G053200 chr7B 89.751 683 70 0 1 683 136324820 136324138 0.000000e+00 874
8 TraesCS3A01G053200 chr7B 85.526 684 96 3 1 683 585497154 585497835 0.000000e+00 712
9 TraesCS3A01G053200 chr7B 90.291 309 29 1 678 985 136323846 136323538 1.010000e-108 403
10 TraesCS3A01G053200 chr7B 84.244 311 45 3 679 987 585498128 585498436 1.360000e-77 300
11 TraesCS3A01G053200 chr2A 88.596 684 76 2 1 683 751730851 751731533 0.000000e+00 830
12 TraesCS3A01G053200 chr2A 89.355 310 30 1 678 987 751731825 751732131 1.020000e-103 387
13 TraesCS3A01G053200 chr2B 85.234 684 99 2 1 683 36847594 36848276 0.000000e+00 702
14 TraesCS3A01G053200 chr6B 84.964 685 99 4 1 683 33456185 33455503 0.000000e+00 691
15 TraesCS3A01G053200 chrUn 81.337 643 98 13 988 1611 316645388 316646027 9.670000e-139 503
16 TraesCS3A01G053200 chrUn 77.153 569 100 23 1000 1554 43664828 43665380 1.050000e-78 303
17 TraesCS3A01G053200 chrUn 83.013 312 47 5 677 987 436997647 436997953 6.380000e-71 278
18 TraesCS3A01G053200 chr3B 81.337 643 98 13 988 1611 35037692 35038331 9.670000e-139 503
19 TraesCS3A01G053200 chr3B 81.337 643 98 13 988 1611 35119158 35119797 9.670000e-139 503
20 TraesCS3A01G053200 chr2D 79.094 684 141 2 1 683 383340847 383340165 9.810000e-129 470
21 TraesCS3A01G053200 chr2D 78.331 683 143 2 1 683 637045483 637046160 9.950000e-119 436
22 TraesCS3A01G053200 chr3D 80.727 633 84 11 988 1584 21328958 21328328 2.120000e-125 459
23 TraesCS3A01G053200 chr3D 91.241 137 12 0 2209 2345 387025983 387025847 1.110000e-43 187
24 TraesCS3A01G053200 chr5B 92.308 312 21 3 678 987 31105601 31105291 7.690000e-120 440
25 TraesCS3A01G053200 chr1D 85.443 316 39 6 678 992 81782621 81782930 2.910000e-84 322
26 TraesCS3A01G053200 chr1D 85.484 310 39 4 678 987 318712581 318712884 3.760000e-83 318
27 TraesCS3A01G053200 chr1B 81.073 317 50 9 678 991 419393996 419393687 6.470000e-61 244
28 TraesCS3A01G053200 chr1B 92.701 137 8 2 2209 2345 596255484 596255350 1.840000e-46 196
29 TraesCS3A01G053200 chr1B 91.304 138 10 2 2209 2345 628674076 628673940 1.110000e-43 187
30 TraesCS3A01G053200 chr1A 94.203 138 8 0 2208 2345 248034527 248034390 6.570000e-51 211
31 TraesCS3A01G053200 chr1A 92.701 137 10 0 2209 2345 10743775 10743911 5.110000e-47 198
32 TraesCS3A01G053200 chr7D 91.971 137 11 0 2209 2345 611134694 611134558 2.380000e-45 193
33 TraesCS3A01G053200 chr7A 91.971 137 11 0 2209 2345 208520883 208520747 2.380000e-45 193
34 TraesCS3A01G053200 chr4D 91.852 135 11 0 2209 2343 224036069 224035935 3.080000e-44 189
35 TraesCS3A01G053200 chr4D 91.241 137 12 0 2209 2345 314399111 314399247 1.110000e-43 187


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 TraesCS3A01G053200 chr3A 29723499 29725843 2344 False 4331.0 4331 100.0000 1 2345 1 chr3A.!!$F2 2344
1 TraesCS3A01G053200 chr3A 29529892 29534748 4856 False 768.0 819 91.9640 995 2092 2 chr3A.!!$F3 1097
2 TraesCS3A01G053200 chr6A 599306057 599307339 1282 True 822.5 1127 96.6300 1 987 2 chr6A.!!$R1 986
3 TraesCS3A01G053200 chr4B 648836182 648836862 680 True 987.0 987 92.8050 3 683 1 chr4B.!!$R1 680
4 TraesCS3A01G053200 chr7B 136323538 136324820 1282 True 638.5 874 90.0210 1 985 2 chr7B.!!$R1 984
5 TraesCS3A01G053200 chr7B 585497154 585498436 1282 False 506.0 712 84.8850 1 987 2 chr7B.!!$F1 986
6 TraesCS3A01G053200 chr2A 751730851 751732131 1280 False 608.5 830 88.9755 1 987 2 chr2A.!!$F1 986
7 TraesCS3A01G053200 chr2B 36847594 36848276 682 False 702.0 702 85.2340 1 683 1 chr2B.!!$F1 682
8 TraesCS3A01G053200 chr6B 33455503 33456185 682 True 691.0 691 84.9640 1 683 1 chr6B.!!$R1 682
9 TraesCS3A01G053200 chrUn 316645388 316646027 639 False 503.0 503 81.3370 988 1611 1 chrUn.!!$F2 623
10 TraesCS3A01G053200 chrUn 43664828 43665380 552 False 303.0 303 77.1530 1000 1554 1 chrUn.!!$F1 554
11 TraesCS3A01G053200 chr3B 35037692 35038331 639 False 503.0 503 81.3370 988 1611 1 chr3B.!!$F1 623
12 TraesCS3A01G053200 chr3B 35119158 35119797 639 False 503.0 503 81.3370 988 1611 1 chr3B.!!$F2 623
13 TraesCS3A01G053200 chr2D 383340165 383340847 682 True 470.0 470 79.0940 1 683 1 chr2D.!!$R1 682
14 TraesCS3A01G053200 chr2D 637045483 637046160 677 False 436.0 436 78.3310 1 683 1 chr2D.!!$F1 682
15 TraesCS3A01G053200 chr3D 21328328 21328958 630 True 459.0 459 80.7270 988 1584 1 chr3D.!!$R1 596

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
484 485 0.107459 AGCTCTGGGAAATTCTCGGC 60.107 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 6421 0.330941 TCTTGCATGCATGTGGGGTA 59.669 50.0 26.79 8.63 0.0 3.69 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
175 176 2.205074 CGACTTGCAGTCAGTCAAAGT 58.795 47.619 15.46 0.00 45.30 2.66
305 306 1.198759 TTGACCTAGCAGTGGACCCC 61.199 60.000 0.00 0.00 0.00 4.95
484 485 0.107459 AGCTCTGGGAAATTCTCGGC 60.107 55.000 0.00 0.00 0.00 5.54
700 998 0.108424 GCTGAGATGCTCAAGACCGT 60.108 55.000 0.00 0.00 40.18 4.83
857 1156 1.374252 TCGCGCCTGGACTTCTTTC 60.374 57.895 0.00 0.00 0.00 2.62
865 1164 2.164624 CCTGGACTTCTTTCGTCGATCT 59.835 50.000 0.00 0.00 32.24 2.75
939 1238 1.005037 CTACGCTGCCTGTTGTGGA 60.005 57.895 0.00 0.00 0.00 4.02
962 1261 7.067251 TGGATTTATTAATTTAAAGCCGGACGT 59.933 33.333 5.05 0.00 46.04 4.34
1073 1380 1.303888 TCCTTGTAGCCTCCGACGT 60.304 57.895 0.00 0.00 0.00 4.34
1189 1496 1.526225 GTTAGGAGATTGGCCGGCC 60.526 63.158 39.40 39.40 0.00 6.13
1190 1497 1.998438 TTAGGAGATTGGCCGGCCA 60.998 57.895 44.23 44.23 45.63 5.36
1257 1564 4.966787 GCTGCCGGTGGGGTCAAA 62.967 66.667 1.90 0.00 38.44 2.69
1333 1640 1.134431 TCAGCTCAACTGTGAACTGCA 60.134 47.619 2.88 0.00 44.37 4.41
1342 1649 6.233434 TCAACTGTGAACTGCAATAAGATCT 58.767 36.000 0.00 0.00 0.00 2.75
1365 1672 2.384391 GATCGATTGCTTGCCGCCAG 62.384 60.000 0.00 0.00 38.05 4.85
1404 1711 1.335182 CACCGATCGATGCTGAGTACT 59.665 52.381 18.66 0.00 0.00 2.73
1416 1723 3.901844 TGCTGAGTACTTTGAGGTTACCT 59.098 43.478 2.34 2.34 36.03 3.08
1481 1813 4.757019 TGTGAGAGAGAGGACTACGTAT 57.243 45.455 0.00 0.00 0.00 3.06
1558 1906 4.504858 TCGCTCCCTTTGAGAAGATAAAC 58.495 43.478 0.00 0.00 44.42 2.01
1643 5744 4.364860 AGCATGCGTCGTTATTACATGTA 58.635 39.130 13.01 0.08 40.15 2.29
1667 5768 9.139174 GTACATAACTGGGAAAACATTTCATTG 57.861 33.333 5.32 0.00 0.00 2.82
1693 5794 3.070015 CCATTTTCTTGCTCCAACCAACT 59.930 43.478 0.00 0.00 0.00 3.16
1719 5820 1.686236 AGGAATGGACTCCACCCAAT 58.314 50.000 16.73 0.00 38.02 3.16
1730 5831 3.009143 ACTCCACCCAATTCACTAGAACC 59.991 47.826 0.00 0.00 36.39 3.62
1731 5832 2.027561 TCCACCCAATTCACTAGAACCG 60.028 50.000 0.00 0.00 36.39 4.44
1770 5871 6.656693 CACTCTCTATTTGGTTCCTCAAACAT 59.343 38.462 0.00 0.00 39.13 2.71
1772 5873 8.043710 ACTCTCTATTTGGTTCCTCAAACATAG 58.956 37.037 0.00 0.00 39.13 2.23
1779 5880 5.253330 TGGTTCCTCAAACATAGCCTAAAG 58.747 41.667 0.00 0.00 39.81 1.85
1782 5883 2.952310 CCTCAAACATAGCCTAAAGCCC 59.048 50.000 0.00 0.00 45.47 5.19
1793 5894 3.116939 AGCCTAAAGCCCTGAGAGATAGA 60.117 47.826 0.00 0.00 45.47 1.98
1847 5948 4.081862 CGACCACCAATAAGAAGTCCTACA 60.082 45.833 0.00 0.00 0.00 2.74
1848 5949 5.568023 CGACCACCAATAAGAAGTCCTACAA 60.568 44.000 0.00 0.00 0.00 2.41
1962 6063 9.933723 AATTATGGAAAAAGTCAGAAAATCAGG 57.066 29.630 0.00 0.00 0.00 3.86
1963 6064 5.789643 TGGAAAAAGTCAGAAAATCAGGG 57.210 39.130 0.00 0.00 0.00 4.45
1967 6068 6.040955 GGAAAAAGTCAGAAAATCAGGGAACT 59.959 38.462 0.00 0.00 46.44 3.01
1968 6069 7.417911 GGAAAAAGTCAGAAAATCAGGGAACTT 60.418 37.037 0.00 0.00 40.21 2.66
2074 6175 8.216453 CGAAAATGTCCTTCATTGAAAAATGTC 58.784 33.333 0.01 0.00 44.85 3.06
2092 6193 2.643933 TCGTGCTGACAGAGATGAAG 57.356 50.000 6.65 0.00 0.00 3.02
2093 6194 1.203287 TCGTGCTGACAGAGATGAAGG 59.797 52.381 6.65 0.00 0.00 3.46
2094 6195 1.067283 CGTGCTGACAGAGATGAAGGT 60.067 52.381 6.65 0.00 0.00 3.50
2095 6196 2.615869 GTGCTGACAGAGATGAAGGTC 58.384 52.381 6.65 0.00 0.00 3.85
2096 6197 2.028658 GTGCTGACAGAGATGAAGGTCA 60.029 50.000 6.65 0.00 37.89 4.02
2099 6200 1.552337 TGACAGAGATGAAGGTCAGCC 59.448 52.381 0.00 0.00 35.51 4.85
2101 6202 1.830477 ACAGAGATGAAGGTCAGCCTC 59.170 52.381 0.00 0.00 46.33 4.70
2102 6203 1.138661 CAGAGATGAAGGTCAGCCTCC 59.861 57.143 6.75 0.00 46.33 4.30
2103 6204 1.008206 AGAGATGAAGGTCAGCCTCCT 59.992 52.381 6.75 0.00 46.33 3.69
2104 6205 2.246067 AGAGATGAAGGTCAGCCTCCTA 59.754 50.000 6.75 0.00 46.33 2.94
2105 6206 3.034635 GAGATGAAGGTCAGCCTCCTAA 58.965 50.000 0.00 0.00 46.33 2.69
2106 6207 3.037549 AGATGAAGGTCAGCCTCCTAAG 58.962 50.000 0.00 0.00 46.33 2.18
2107 6208 2.623418 TGAAGGTCAGCCTCCTAAGA 57.377 50.000 0.00 0.00 46.33 2.10
2108 6209 2.461695 TGAAGGTCAGCCTCCTAAGAG 58.538 52.381 0.00 0.00 46.33 2.85
2109 6210 2.225394 TGAAGGTCAGCCTCCTAAGAGT 60.225 50.000 0.00 0.00 46.33 3.24
2110 6211 3.011369 TGAAGGTCAGCCTCCTAAGAGTA 59.989 47.826 0.00 0.00 46.33 2.59
2111 6212 3.983533 AGGTCAGCCTCCTAAGAGTAT 57.016 47.619 0.00 0.00 42.67 2.12
2112 6213 3.839778 AGGTCAGCCTCCTAAGAGTATC 58.160 50.000 0.00 0.00 42.67 2.24
2113 6214 2.554893 GGTCAGCCTCCTAAGAGTATCG 59.445 54.545 0.00 0.00 42.67 2.92
2114 6215 3.215975 GTCAGCCTCCTAAGAGTATCGT 58.784 50.000 0.00 0.00 42.67 3.73
2115 6216 3.003897 GTCAGCCTCCTAAGAGTATCGTG 59.996 52.174 0.00 0.00 42.67 4.35
2116 6217 2.952978 CAGCCTCCTAAGAGTATCGTGT 59.047 50.000 0.00 0.00 42.67 4.49
2117 6218 4.135306 CAGCCTCCTAAGAGTATCGTGTA 58.865 47.826 0.00 0.00 42.67 2.90
2118 6219 4.579340 CAGCCTCCTAAGAGTATCGTGTAA 59.421 45.833 0.00 0.00 42.67 2.41
2119 6220 5.241949 CAGCCTCCTAAGAGTATCGTGTAAT 59.758 44.000 0.00 0.00 42.67 1.89
2120 6221 5.834204 AGCCTCCTAAGAGTATCGTGTAATT 59.166 40.000 0.00 0.00 42.67 1.40
2121 6222 7.002879 AGCCTCCTAAGAGTATCGTGTAATTA 58.997 38.462 0.00 0.00 42.67 1.40
2122 6223 7.504911 AGCCTCCTAAGAGTATCGTGTAATTAA 59.495 37.037 0.00 0.00 42.67 1.40
2123 6224 8.139989 GCCTCCTAAGAGTATCGTGTAATTAAA 58.860 37.037 0.00 0.00 42.67 1.52
2162 6263 9.674068 AGACTCTTTCCATTTAGGTAGAAATTC 57.326 33.333 0.00 0.00 39.02 2.17
2163 6264 8.494016 ACTCTTTCCATTTAGGTAGAAATTCG 57.506 34.615 0.00 0.00 39.02 3.34
2164 6265 7.553044 ACTCTTTCCATTTAGGTAGAAATTCGG 59.447 37.037 0.00 0.00 39.02 4.30
2165 6266 7.626390 TCTTTCCATTTAGGTAGAAATTCGGA 58.374 34.615 0.00 0.00 39.02 4.55
2166 6267 8.104566 TCTTTCCATTTAGGTAGAAATTCGGAA 58.895 33.333 0.00 0.00 39.02 4.30
2167 6268 8.817092 TTTCCATTTAGGTAGAAATTCGGAAT 57.183 30.769 0.00 0.00 33.89 3.01
2168 6269 9.908747 TTTCCATTTAGGTAGAAATTCGGAATA 57.091 29.630 3.22 0.00 33.89 1.75
2169 6270 8.897872 TCCATTTAGGTAGAAATTCGGAATAC 57.102 34.615 3.22 2.09 39.02 1.89
2170 6271 8.487848 TCCATTTAGGTAGAAATTCGGAATACA 58.512 33.333 3.22 0.00 39.02 2.29
2171 6272 9.116067 CCATTTAGGTAGAAATTCGGAATACAA 57.884 33.333 3.22 0.00 0.00 2.41
2176 6277 7.996385 AGGTAGAAATTCGGAATACAAATTGG 58.004 34.615 3.22 0.00 0.00 3.16
2177 6278 7.614192 AGGTAGAAATTCGGAATACAAATTGGT 59.386 33.333 3.22 0.00 0.00 3.67
2178 6279 8.895737 GGTAGAAATTCGGAATACAAATTGGTA 58.104 33.333 3.22 0.00 0.00 3.25
2179 6280 9.712359 GTAGAAATTCGGAATACAAATTGGTAC 57.288 33.333 3.22 0.00 0.00 3.34
2180 6281 7.768240 AGAAATTCGGAATACAAATTGGTACC 58.232 34.615 4.43 4.43 0.00 3.34
2181 6282 7.614192 AGAAATTCGGAATACAAATTGGTACCT 59.386 33.333 14.36 0.00 0.00 3.08
2182 6283 6.693315 ATTCGGAATACAAATTGGTACCTG 57.307 37.500 14.36 5.33 0.00 4.00
2183 6284 5.423704 TCGGAATACAAATTGGTACCTGA 57.576 39.130 14.36 1.90 0.00 3.86
2184 6285 5.806818 TCGGAATACAAATTGGTACCTGAA 58.193 37.500 14.36 0.00 0.00 3.02
2185 6286 6.419791 TCGGAATACAAATTGGTACCTGAAT 58.580 36.000 14.36 2.26 0.00 2.57
2186 6287 6.887545 TCGGAATACAAATTGGTACCTGAATT 59.112 34.615 14.36 8.86 0.00 2.17
2187 6288 7.394923 TCGGAATACAAATTGGTACCTGAATTT 59.605 33.333 14.36 14.32 33.07 1.82
2188 6289 8.679100 CGGAATACAAATTGGTACCTGAATTTA 58.321 33.333 17.90 8.30 31.92 1.40
2199 6300 8.625786 TGGTACCTGAATTTAGTTAACTTTCC 57.374 34.615 14.49 0.43 0.00 3.13
2200 6301 8.219178 TGGTACCTGAATTTAGTTAACTTTCCA 58.781 33.333 14.49 3.12 0.00 3.53
2201 6302 9.070179 GGTACCTGAATTTAGTTAACTTTCCAA 57.930 33.333 14.49 0.00 0.00 3.53
2202 6303 9.888878 GTACCTGAATTTAGTTAACTTTCCAAC 57.111 33.333 14.49 4.28 0.00 3.77
2203 6304 8.762481 ACCTGAATTTAGTTAACTTTCCAACT 57.238 30.769 14.49 0.00 38.50 3.16
2204 6305 9.197306 ACCTGAATTTAGTTAACTTTCCAACTT 57.803 29.630 14.49 2.47 36.44 2.66
2205 6306 9.678941 CCTGAATTTAGTTAACTTTCCAACTTC 57.321 33.333 14.49 11.61 36.44 3.01
2206 6307 9.382244 CTGAATTTAGTTAACTTTCCAACTTCG 57.618 33.333 14.49 5.34 36.44 3.79
2207 6308 8.347035 TGAATTTAGTTAACTTTCCAACTTCGG 58.653 33.333 14.49 0.00 36.44 4.30
2208 6309 7.812690 ATTTAGTTAACTTTCCAACTTCGGT 57.187 32.000 14.49 0.00 36.44 4.69
2209 6310 8.907222 ATTTAGTTAACTTTCCAACTTCGGTA 57.093 30.769 14.49 0.00 36.44 4.02
2210 6311 7.713764 TTAGTTAACTTTCCAACTTCGGTAC 57.286 36.000 14.49 0.00 36.44 3.34
2211 6312 5.922053 AGTTAACTTTCCAACTTCGGTACT 58.078 37.500 1.12 0.00 30.89 2.73
2212 6313 5.987953 AGTTAACTTTCCAACTTCGGTACTC 59.012 40.000 1.12 0.00 30.89 2.59
2213 6314 3.397849 ACTTTCCAACTTCGGTACTCC 57.602 47.619 0.00 0.00 0.00 3.85
2214 6315 2.038164 ACTTTCCAACTTCGGTACTCCC 59.962 50.000 0.00 0.00 0.00 4.30
2215 6316 2.019807 TTCCAACTTCGGTACTCCCT 57.980 50.000 0.00 0.00 0.00 4.20
2216 6317 2.019807 TCCAACTTCGGTACTCCCTT 57.980 50.000 0.00 0.00 0.00 3.95
2217 6318 1.897802 TCCAACTTCGGTACTCCCTTC 59.102 52.381 0.00 0.00 0.00 3.46
2218 6319 1.621814 CCAACTTCGGTACTCCCTTCA 59.378 52.381 0.00 0.00 0.00 3.02
2219 6320 2.236395 CCAACTTCGGTACTCCCTTCAT 59.764 50.000 0.00 0.00 0.00 2.57
2220 6321 3.307480 CCAACTTCGGTACTCCCTTCATT 60.307 47.826 0.00 0.00 0.00 2.57
2221 6322 4.324267 CAACTTCGGTACTCCCTTCATTT 58.676 43.478 0.00 0.00 0.00 2.32
2222 6323 4.635699 ACTTCGGTACTCCCTTCATTTT 57.364 40.909 0.00 0.00 0.00 1.82
2223 6324 4.981812 ACTTCGGTACTCCCTTCATTTTT 58.018 39.130 0.00 0.00 0.00 1.94
2224 6325 6.117975 ACTTCGGTACTCCCTTCATTTTTA 57.882 37.500 0.00 0.00 0.00 1.52
2225 6326 6.718294 ACTTCGGTACTCCCTTCATTTTTAT 58.282 36.000 0.00 0.00 0.00 1.40
2226 6327 7.854337 ACTTCGGTACTCCCTTCATTTTTATA 58.146 34.615 0.00 0.00 0.00 0.98
2227 6328 8.491958 ACTTCGGTACTCCCTTCATTTTTATAT 58.508 33.333 0.00 0.00 0.00 0.86
2228 6329 9.991906 CTTCGGTACTCCCTTCATTTTTATATA 57.008 33.333 0.00 0.00 0.00 0.86
2229 6330 9.768662 TTCGGTACTCCCTTCATTTTTATATAC 57.231 33.333 0.00 0.00 0.00 1.47
2230 6331 8.926374 TCGGTACTCCCTTCATTTTTATATACA 58.074 33.333 0.00 0.00 0.00 2.29
2231 6332 9.550406 CGGTACTCCCTTCATTTTTATATACAA 57.450 33.333 0.00 0.00 0.00 2.41
2234 6335 8.465273 ACTCCCTTCATTTTTATATACAAGGC 57.535 34.615 0.00 0.00 0.00 4.35
2235 6336 7.505923 ACTCCCTTCATTTTTATATACAAGGCC 59.494 37.037 0.00 0.00 0.00 5.19
2236 6337 7.358263 TCCCTTCATTTTTATATACAAGGCCA 58.642 34.615 5.01 0.00 0.00 5.36
2237 6338 7.286775 TCCCTTCATTTTTATATACAAGGCCAC 59.713 37.037 5.01 0.00 0.00 5.01
2238 6339 7.069331 CCCTTCATTTTTATATACAAGGCCACA 59.931 37.037 5.01 0.00 0.00 4.17
2239 6340 8.474025 CCTTCATTTTTATATACAAGGCCACAA 58.526 33.333 5.01 0.00 0.00 3.33
2240 6341 9.868277 CTTCATTTTTATATACAAGGCCACAAA 57.132 29.630 5.01 0.00 0.00 2.83
2241 6342 9.646427 TTCATTTTTATATACAAGGCCACAAAC 57.354 29.630 5.01 0.00 0.00 2.93
2242 6343 9.030452 TCATTTTTATATACAAGGCCACAAACT 57.970 29.630 5.01 0.00 0.00 2.66
2243 6344 9.301153 CATTTTTATATACAAGGCCACAAACTC 57.699 33.333 5.01 0.00 0.00 3.01
2244 6345 8.410673 TTTTTATATACAAGGCCACAAACTCA 57.589 30.769 5.01 0.00 0.00 3.41
2245 6346 8.410673 TTTTATATACAAGGCCACAAACTCAA 57.589 30.769 5.01 0.00 0.00 3.02
2246 6347 8.410673 TTTATATACAAGGCCACAAACTCAAA 57.589 30.769 5.01 0.00 0.00 2.69
2247 6348 8.588290 TTATATACAAGGCCACAAACTCAAAT 57.412 30.769 5.01 0.00 0.00 2.32
2248 6349 5.806654 ATACAAGGCCACAAACTCAAATT 57.193 34.783 5.01 0.00 0.00 1.82
2249 6350 6.909550 ATACAAGGCCACAAACTCAAATTA 57.090 33.333 5.01 0.00 0.00 1.40
2250 6351 4.944048 ACAAGGCCACAAACTCAAATTAC 58.056 39.130 5.01 0.00 0.00 1.89
2251 6352 4.404073 ACAAGGCCACAAACTCAAATTACA 59.596 37.500 5.01 0.00 0.00 2.41
2252 6353 4.853924 AGGCCACAAACTCAAATTACAG 57.146 40.909 5.01 0.00 0.00 2.74
2253 6354 3.573967 AGGCCACAAACTCAAATTACAGG 59.426 43.478 5.01 0.00 0.00 4.00
2254 6355 3.317150 GCCACAAACTCAAATTACAGGC 58.683 45.455 0.00 0.00 0.00 4.85
2255 6356 3.243704 GCCACAAACTCAAATTACAGGCA 60.244 43.478 0.00 0.00 38.27 4.75
2256 6357 4.298332 CCACAAACTCAAATTACAGGCAC 58.702 43.478 0.00 0.00 0.00 5.01
2257 6358 4.298332 CACAAACTCAAATTACAGGCACC 58.702 43.478 0.00 0.00 0.00 5.01
2258 6359 3.957497 ACAAACTCAAATTACAGGCACCA 59.043 39.130 0.00 0.00 0.00 4.17
2259 6360 4.404073 ACAAACTCAAATTACAGGCACCAA 59.596 37.500 0.00 0.00 0.00 3.67
2260 6361 5.070313 ACAAACTCAAATTACAGGCACCAAT 59.930 36.000 0.00 0.00 0.00 3.16
2261 6362 6.266558 ACAAACTCAAATTACAGGCACCAATA 59.733 34.615 0.00 0.00 0.00 1.90
2262 6363 7.039082 ACAAACTCAAATTACAGGCACCAATAT 60.039 33.333 0.00 0.00 0.00 1.28
2263 6364 8.465999 CAAACTCAAATTACAGGCACCAATATA 58.534 33.333 0.00 0.00 0.00 0.86
2264 6365 8.588290 AACTCAAATTACAGGCACCAATATAA 57.412 30.769 0.00 0.00 0.00 0.98
2265 6366 8.588290 ACTCAAATTACAGGCACCAATATAAA 57.412 30.769 0.00 0.00 0.00 1.40
2266 6367 9.030452 ACTCAAATTACAGGCACCAATATAAAA 57.970 29.630 0.00 0.00 0.00 1.52
2275 6376 9.816354 ACAGGCACCAATATAAAATTTAATGTC 57.184 29.630 0.00 0.00 0.00 3.06
2278 6379 9.816354 GGCACCAATATAAAATTTAATGTCTGT 57.184 29.630 0.00 0.00 0.00 3.41
2289 6390 8.729805 AAATTTAATGTCTGTTTTGAAAGCCA 57.270 26.923 0.00 0.00 0.00 4.75
2290 6391 8.907222 AATTTAATGTCTGTTTTGAAAGCCAT 57.093 26.923 0.00 0.00 0.00 4.40
2291 6392 7.712264 TTTAATGTCTGTTTTGAAAGCCATG 57.288 32.000 0.00 0.00 0.00 3.66
2292 6393 4.942761 ATGTCTGTTTTGAAAGCCATGT 57.057 36.364 0.00 0.00 0.00 3.21
2293 6394 4.734398 TGTCTGTTTTGAAAGCCATGTT 57.266 36.364 0.00 0.00 0.00 2.71
2294 6395 5.083533 TGTCTGTTTTGAAAGCCATGTTT 57.916 34.783 0.00 0.00 0.00 2.83
2295 6396 5.486526 TGTCTGTTTTGAAAGCCATGTTTT 58.513 33.333 0.00 0.00 0.00 2.43
2296 6397 5.580297 TGTCTGTTTTGAAAGCCATGTTTTC 59.420 36.000 11.15 11.15 34.24 2.29
2297 6398 5.812127 GTCTGTTTTGAAAGCCATGTTTTCT 59.188 36.000 16.33 0.00 34.63 2.52
2298 6399 6.978080 GTCTGTTTTGAAAGCCATGTTTTCTA 59.022 34.615 16.33 9.44 34.63 2.10
2299 6400 7.653311 GTCTGTTTTGAAAGCCATGTTTTCTAT 59.347 33.333 16.33 0.00 34.63 1.98
2300 6401 7.867403 TCTGTTTTGAAAGCCATGTTTTCTATC 59.133 33.333 16.33 9.06 34.63 2.08
2301 6402 6.928492 TGTTTTGAAAGCCATGTTTTCTATCC 59.072 34.615 16.33 7.25 34.63 2.59
2302 6403 4.963276 TGAAAGCCATGTTTTCTATCCG 57.037 40.909 16.33 0.00 34.63 4.18
2303 6404 4.331968 TGAAAGCCATGTTTTCTATCCGT 58.668 39.130 16.33 0.00 34.63 4.69
2304 6405 4.764823 TGAAAGCCATGTTTTCTATCCGTT 59.235 37.500 16.33 0.00 34.63 4.44
2305 6406 5.242838 TGAAAGCCATGTTTTCTATCCGTTT 59.757 36.000 16.33 0.00 34.63 3.60
2306 6407 6.431543 TGAAAGCCATGTTTTCTATCCGTTTA 59.568 34.615 16.33 0.00 34.63 2.01
2307 6408 5.813080 AGCCATGTTTTCTATCCGTTTAC 57.187 39.130 0.00 0.00 0.00 2.01
2308 6409 5.497474 AGCCATGTTTTCTATCCGTTTACT 58.503 37.500 0.00 0.00 0.00 2.24
2309 6410 5.354234 AGCCATGTTTTCTATCCGTTTACTG 59.646 40.000 0.00 0.00 0.00 2.74
2310 6411 5.448632 GCCATGTTTTCTATCCGTTTACTGG 60.449 44.000 0.00 0.00 0.00 4.00
2311 6412 5.065988 CCATGTTTTCTATCCGTTTACTGGG 59.934 44.000 0.00 0.00 0.00 4.45
2312 6413 5.486735 TGTTTTCTATCCGTTTACTGGGA 57.513 39.130 0.00 0.00 36.61 4.37
2313 6414 6.057321 TGTTTTCTATCCGTTTACTGGGAT 57.943 37.500 0.00 0.00 44.92 3.85
2314 6415 6.110707 TGTTTTCTATCCGTTTACTGGGATC 58.889 40.000 0.00 0.00 42.01 3.36
2315 6416 5.943349 TTTCTATCCGTTTACTGGGATCA 57.057 39.130 0.00 0.00 42.01 2.92
2316 6417 4.931661 TCTATCCGTTTACTGGGATCAC 57.068 45.455 0.00 0.00 42.01 3.06
2317 6418 4.543689 TCTATCCGTTTACTGGGATCACT 58.456 43.478 0.00 0.00 42.01 3.41
2318 6419 5.698104 TCTATCCGTTTACTGGGATCACTA 58.302 41.667 0.00 0.00 42.01 2.74
2319 6420 6.131264 TCTATCCGTTTACTGGGATCACTAA 58.869 40.000 0.00 0.00 42.01 2.24
2320 6421 5.888982 ATCCGTTTACTGGGATCACTAAT 57.111 39.130 0.00 0.00 38.70 1.73
2321 6422 6.989155 ATCCGTTTACTGGGATCACTAATA 57.011 37.500 0.00 0.00 38.70 0.98
2322 6423 6.152932 TCCGTTTACTGGGATCACTAATAC 57.847 41.667 0.00 0.00 0.00 1.89
2323 6424 5.069516 TCCGTTTACTGGGATCACTAATACC 59.930 44.000 0.00 0.00 39.12 2.73
2324 6425 5.295152 CGTTTACTGGGATCACTAATACCC 58.705 45.833 0.00 0.00 37.61 3.69
2325 6426 5.618236 GTTTACTGGGATCACTAATACCCC 58.382 45.833 0.00 0.00 37.61 4.95
2326 6427 3.431411 ACTGGGATCACTAATACCCCA 57.569 47.619 0.00 0.00 44.21 4.96
2327 6428 3.046374 ACTGGGATCACTAATACCCCAC 58.954 50.000 0.00 0.00 41.78 4.61
2328 6429 3.045634 CTGGGATCACTAATACCCCACA 58.954 50.000 0.00 0.00 41.78 4.17
2329 6430 3.652869 CTGGGATCACTAATACCCCACAT 59.347 47.826 0.00 0.00 41.78 3.21
2330 6431 3.394274 TGGGATCACTAATACCCCACATG 59.606 47.826 0.00 0.00 41.78 3.21
2331 6432 3.412386 GGATCACTAATACCCCACATGC 58.588 50.000 0.00 0.00 0.00 4.06
2332 6433 3.181445 GGATCACTAATACCCCACATGCA 60.181 47.826 0.00 0.00 0.00 3.96
2333 6434 4.507335 GGATCACTAATACCCCACATGCAT 60.507 45.833 0.00 0.00 0.00 3.96
2334 6435 3.819368 TCACTAATACCCCACATGCATG 58.181 45.455 25.09 25.09 0.00 4.06
2335 6436 2.294233 CACTAATACCCCACATGCATGC 59.706 50.000 26.53 11.82 0.00 4.06
2336 6437 2.091939 ACTAATACCCCACATGCATGCA 60.092 45.455 26.53 25.04 0.00 3.96
2337 6438 1.863325 AATACCCCACATGCATGCAA 58.137 45.000 26.68 8.49 0.00 4.08
2338 6439 1.405872 ATACCCCACATGCATGCAAG 58.594 50.000 26.68 23.45 0.00 4.01
2339 6440 0.330941 TACCCCACATGCATGCAAGA 59.669 50.000 28.20 4.03 0.00 3.02
2340 6441 0.542467 ACCCCACATGCATGCAAGAA 60.542 50.000 28.20 3.61 0.00 2.52
2341 6442 0.609151 CCCCACATGCATGCAAGAAA 59.391 50.000 28.20 3.18 0.00 2.52
2342 6443 1.002201 CCCCACATGCATGCAAGAAAA 59.998 47.619 28.20 2.35 0.00 2.29
2343 6444 2.070783 CCCACATGCATGCAAGAAAAC 58.929 47.619 28.20 0.00 0.00 2.43
2344 6445 2.289195 CCCACATGCATGCAAGAAAACT 60.289 45.455 28.20 5.86 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 306 3.626680 ATCCGCCACCGATATCGCG 62.627 63.158 19.78 16.32 44.08 5.87
464 465 1.139058 GCCGAGAATTTCCCAGAGCTA 59.861 52.381 0.00 0.00 0.00 3.32
700 998 1.872952 CTTGCATCAGACGTTGTTGGA 59.127 47.619 0.00 0.00 0.00 3.53
857 1156 1.591248 CCAACGCAAAAAGATCGACG 58.409 50.000 0.00 0.00 0.00 5.12
865 1164 1.227002 GTTCCGGCCAACGCAAAAA 60.227 52.632 2.24 0.00 42.52 1.94
962 1261 4.707030 TTTAGAACGAAGACGCCAGATA 57.293 40.909 0.00 0.00 43.96 1.98
1117 1424 2.709475 GCCGCGTGCATAGGAAAG 59.291 61.111 13.61 0.00 40.77 2.62
1196 1503 2.377628 TTTCTTGTCAGCGGCGGTCT 62.378 55.000 9.40 0.00 0.00 3.85
1275 1582 4.410400 CGGCACTTGGAGGGGGTC 62.410 72.222 0.00 0.00 0.00 4.46
1333 1640 7.117523 GCAAGCAATCGATCACTAGATCTTATT 59.882 37.037 0.00 1.90 46.84 1.40
1342 1649 1.570813 CGGCAAGCAATCGATCACTA 58.429 50.000 0.00 0.00 0.00 2.74
1365 1672 2.670414 GTGGAGCTATAATCTGCGATGC 59.330 50.000 0.00 0.00 0.00 3.91
1372 1679 3.687125 TCGATCGGTGGAGCTATAATCT 58.313 45.455 16.41 0.00 0.00 2.40
1481 1813 0.607217 CATGCAGAGTTGGCTCCACA 60.607 55.000 0.00 0.00 42.59 4.17
1624 5725 7.650504 AGTTATGTACATGTAATAACGACGCAT 59.349 33.333 25.24 17.31 40.25 4.73
1643 5744 7.961351 TCAATGAAATGTTTTCCCAGTTATGT 58.039 30.769 0.00 0.00 0.00 2.29
1667 5768 4.021192 TGGTTGGAGCAAGAAAATGGAATC 60.021 41.667 0.00 0.00 0.00 2.52
1681 5782 2.740447 CCTACGTTTAGTTGGTTGGAGC 59.260 50.000 0.00 0.00 40.23 4.70
1693 5794 3.196254 GGTGGAGTCCATTCCTACGTTTA 59.804 47.826 16.67 0.00 38.12 2.01
1719 5820 3.576982 AGTCATGGTTCGGTTCTAGTGAA 59.423 43.478 0.00 0.00 0.00 3.18
1730 5831 2.146342 AGAGTGCAAAGTCATGGTTCG 58.854 47.619 0.00 0.00 0.00 3.95
1731 5832 3.406764 AGAGAGTGCAAAGTCATGGTTC 58.593 45.455 0.00 0.00 0.00 3.62
1770 5871 2.848678 TCTCTCAGGGCTTTAGGCTA 57.151 50.000 3.20 0.00 41.46 3.93
1772 5873 3.235200 TCTATCTCTCAGGGCTTTAGGC 58.765 50.000 0.00 0.00 40.90 3.93
1779 5880 3.511146 CCTTCATCTCTATCTCTCAGGGC 59.489 52.174 0.00 0.00 0.00 5.19
1782 5883 5.827267 TGTGACCTTCATCTCTATCTCTCAG 59.173 44.000 0.00 0.00 0.00 3.35
1793 5894 7.173907 CACTAAATTTCTGTGTGACCTTCATCT 59.826 37.037 13.11 0.00 0.00 2.90
1942 6043 6.040955 AGTTCCCTGATTTTCTGACTTTTTCC 59.959 38.462 0.00 0.00 0.00 3.13
2007 6108 7.867403 TGAGCTTTTAGTTTTTGACATCCAATC 59.133 33.333 0.00 0.00 34.23 2.67
2074 6175 1.067283 ACCTTCATCTCTGTCAGCACG 60.067 52.381 0.00 0.00 0.00 5.34
2092 6193 2.554893 CGATACTCTTAGGAGGCTGACC 59.445 54.545 6.82 0.00 43.46 4.02
2093 6194 3.003897 CACGATACTCTTAGGAGGCTGAC 59.996 52.174 6.82 0.00 43.46 3.51
2094 6195 3.215151 CACGATACTCTTAGGAGGCTGA 58.785 50.000 6.82 0.00 43.46 4.26
2095 6196 2.952978 ACACGATACTCTTAGGAGGCTG 59.047 50.000 6.82 0.00 43.46 4.85
2096 6197 3.300239 ACACGATACTCTTAGGAGGCT 57.700 47.619 6.82 0.00 43.46 4.58
2097 6198 5.708877 ATTACACGATACTCTTAGGAGGC 57.291 43.478 6.82 0.00 43.46 4.70
2136 6237 9.674068 GAATTTCTACCTAAATGGAAAGAGTCT 57.326 33.333 0.00 0.00 39.71 3.24
2137 6238 8.604890 CGAATTTCTACCTAAATGGAAAGAGTC 58.395 37.037 0.00 0.00 39.71 3.36
2138 6239 7.553044 CCGAATTTCTACCTAAATGGAAAGAGT 59.447 37.037 0.00 0.00 39.71 3.24
2139 6240 7.769044 TCCGAATTTCTACCTAAATGGAAAGAG 59.231 37.037 0.00 0.00 39.71 2.85
2140 6241 7.626390 TCCGAATTTCTACCTAAATGGAAAGA 58.374 34.615 0.00 0.00 39.71 2.52
2141 6242 7.859325 TCCGAATTTCTACCTAAATGGAAAG 57.141 36.000 0.00 0.00 39.71 2.62
2142 6243 8.817092 ATTCCGAATTTCTACCTAAATGGAAA 57.183 30.769 0.00 0.00 35.87 3.13
2143 6244 9.333724 GTATTCCGAATTTCTACCTAAATGGAA 57.666 33.333 0.00 0.00 36.31 3.53
2144 6245 8.487848 TGTATTCCGAATTTCTACCTAAATGGA 58.512 33.333 0.00 0.00 39.71 3.41
2145 6246 8.671384 TGTATTCCGAATTTCTACCTAAATGG 57.329 34.615 0.00 0.00 42.93 3.16
2150 6251 9.116067 CCAATTTGTATTCCGAATTTCTACCTA 57.884 33.333 0.00 0.00 35.36 3.08
2151 6252 7.614192 ACCAATTTGTATTCCGAATTTCTACCT 59.386 33.333 0.00 0.00 35.36 3.08
2152 6253 7.768240 ACCAATTTGTATTCCGAATTTCTACC 58.232 34.615 0.00 0.00 35.36 3.18
2153 6254 9.712359 GTACCAATTTGTATTCCGAATTTCTAC 57.288 33.333 0.00 0.00 35.36 2.59
2154 6255 8.895737 GGTACCAATTTGTATTCCGAATTTCTA 58.104 33.333 7.15 0.00 35.36 2.10
2155 6256 7.614192 AGGTACCAATTTGTATTCCGAATTTCT 59.386 33.333 15.94 0.00 35.36 2.52
2156 6257 7.700656 CAGGTACCAATTTGTATTCCGAATTTC 59.299 37.037 15.94 0.00 35.36 2.17
2157 6258 7.394923 TCAGGTACCAATTTGTATTCCGAATTT 59.605 33.333 15.94 0.00 35.36 1.82
2158 6259 6.887545 TCAGGTACCAATTTGTATTCCGAATT 59.112 34.615 15.94 0.00 37.59 2.17
2159 6260 6.419791 TCAGGTACCAATTTGTATTCCGAAT 58.580 36.000 15.94 0.00 0.00 3.34
2160 6261 5.806818 TCAGGTACCAATTTGTATTCCGAA 58.193 37.500 15.94 0.00 0.00 4.30
2161 6262 5.423704 TCAGGTACCAATTTGTATTCCGA 57.576 39.130 15.94 0.00 0.00 4.55
2162 6263 6.693315 ATTCAGGTACCAATTTGTATTCCG 57.307 37.500 15.94 0.00 0.00 4.30
2173 6274 9.070179 GGAAAGTTAACTAAATTCAGGTACCAA 57.930 33.333 15.94 0.02 0.00 3.67
2174 6275 8.219178 TGGAAAGTTAACTAAATTCAGGTACCA 58.781 33.333 15.94 0.08 0.00 3.25
2175 6276 8.625786 TGGAAAGTTAACTAAATTCAGGTACC 57.374 34.615 8.92 2.73 0.00 3.34
2176 6277 9.888878 GTTGGAAAGTTAACTAAATTCAGGTAC 57.111 33.333 8.92 3.11 0.00 3.34
2177 6278 9.856162 AGTTGGAAAGTTAACTAAATTCAGGTA 57.144 29.630 8.92 0.00 35.50 3.08
2178 6279 8.762481 AGTTGGAAAGTTAACTAAATTCAGGT 57.238 30.769 8.92 0.00 35.50 4.00
2179 6280 9.678941 GAAGTTGGAAAGTTAACTAAATTCAGG 57.321 33.333 17.68 0.00 40.14 3.86
2180 6281 9.382244 CGAAGTTGGAAAGTTAACTAAATTCAG 57.618 33.333 20.39 13.26 40.14 3.02
2181 6282 8.347035 CCGAAGTTGGAAAGTTAACTAAATTCA 58.653 33.333 20.39 9.91 40.14 2.57
2182 6283 8.347771 ACCGAAGTTGGAAAGTTAACTAAATTC 58.652 33.333 8.92 12.60 40.14 2.17
2183 6284 8.229253 ACCGAAGTTGGAAAGTTAACTAAATT 57.771 30.769 8.92 4.93 40.14 1.82
2184 6285 7.812690 ACCGAAGTTGGAAAGTTAACTAAAT 57.187 32.000 8.92 0.00 40.14 1.40
2185 6286 7.986889 AGTACCGAAGTTGGAAAGTTAACTAAA 59.013 33.333 8.92 0.00 40.14 1.85
2186 6287 7.500141 AGTACCGAAGTTGGAAAGTTAACTAA 58.500 34.615 8.92 0.00 40.14 2.24
2187 6288 7.054491 AGTACCGAAGTTGGAAAGTTAACTA 57.946 36.000 8.92 0.00 40.14 2.24
2188 6289 5.922053 AGTACCGAAGTTGGAAAGTTAACT 58.078 37.500 1.12 1.12 40.14 2.24
2189 6290 5.178252 GGAGTACCGAAGTTGGAAAGTTAAC 59.822 44.000 0.00 0.00 40.14 2.01
2190 6291 5.299949 GGAGTACCGAAGTTGGAAAGTTAA 58.700 41.667 0.00 0.00 40.14 2.01
2191 6292 4.262592 GGGAGTACCGAAGTTGGAAAGTTA 60.263 45.833 0.00 0.00 40.14 2.24
2192 6293 3.495629 GGGAGTACCGAAGTTGGAAAGTT 60.496 47.826 0.00 0.00 43.41 2.66
2193 6294 2.038164 GGGAGTACCGAAGTTGGAAAGT 59.962 50.000 0.00 0.00 36.97 2.66
2194 6295 2.302157 AGGGAGTACCGAAGTTGGAAAG 59.698 50.000 0.00 0.00 46.96 2.62
2195 6296 2.332117 AGGGAGTACCGAAGTTGGAAA 58.668 47.619 0.00 0.00 46.96 3.13
2196 6297 2.019807 AGGGAGTACCGAAGTTGGAA 57.980 50.000 0.00 0.00 46.96 3.53
2197 6298 1.897802 GAAGGGAGTACCGAAGTTGGA 59.102 52.381 0.00 0.00 46.96 3.53
2198 6299 1.621814 TGAAGGGAGTACCGAAGTTGG 59.378 52.381 0.00 0.00 46.96 3.77
2199 6300 3.611766 ATGAAGGGAGTACCGAAGTTG 57.388 47.619 0.00 0.00 46.96 3.16
2200 6301 4.635699 AAATGAAGGGAGTACCGAAGTT 57.364 40.909 0.00 0.00 46.96 2.66
2201 6302 4.635699 AAAATGAAGGGAGTACCGAAGT 57.364 40.909 0.00 0.00 46.96 3.01
2202 6303 8.904099 ATATAAAAATGAAGGGAGTACCGAAG 57.096 34.615 0.00 0.00 46.96 3.79
2203 6304 9.768662 GTATATAAAAATGAAGGGAGTACCGAA 57.231 33.333 0.00 0.00 46.96 4.30
2204 6305 8.926374 TGTATATAAAAATGAAGGGAGTACCGA 58.074 33.333 0.00 0.00 46.96 4.69
2205 6306 9.550406 TTGTATATAAAAATGAAGGGAGTACCG 57.450 33.333 0.00 0.00 46.96 4.02
2208 6309 9.569122 GCCTTGTATATAAAAATGAAGGGAGTA 57.431 33.333 0.00 0.00 31.03 2.59
2209 6310 7.505923 GGCCTTGTATATAAAAATGAAGGGAGT 59.494 37.037 0.00 0.00 31.03 3.85
2210 6311 7.505585 TGGCCTTGTATATAAAAATGAAGGGAG 59.494 37.037 3.32 0.00 31.03 4.30
2211 6312 7.286775 GTGGCCTTGTATATAAAAATGAAGGGA 59.713 37.037 3.32 0.00 31.03 4.20
2212 6313 7.069331 TGTGGCCTTGTATATAAAAATGAAGGG 59.931 37.037 3.32 0.00 31.03 3.95
2213 6314 8.006298 TGTGGCCTTGTATATAAAAATGAAGG 57.994 34.615 3.32 0.00 33.10 3.46
2214 6315 9.868277 TTTGTGGCCTTGTATATAAAAATGAAG 57.132 29.630 3.32 0.00 0.00 3.02
2215 6316 9.646427 GTTTGTGGCCTTGTATATAAAAATGAA 57.354 29.630 3.32 0.00 0.00 2.57
2216 6317 9.030452 AGTTTGTGGCCTTGTATATAAAAATGA 57.970 29.630 3.32 0.00 0.00 2.57
2217 6318 9.301153 GAGTTTGTGGCCTTGTATATAAAAATG 57.699 33.333 3.32 0.00 0.00 2.32
2218 6319 9.030452 TGAGTTTGTGGCCTTGTATATAAAAAT 57.970 29.630 3.32 0.00 0.00 1.82
2219 6320 8.410673 TGAGTTTGTGGCCTTGTATATAAAAA 57.589 30.769 3.32 0.00 0.00 1.94
2220 6321 8.410673 TTGAGTTTGTGGCCTTGTATATAAAA 57.589 30.769 3.32 0.00 0.00 1.52
2221 6322 8.410673 TTTGAGTTTGTGGCCTTGTATATAAA 57.589 30.769 3.32 0.00 0.00 1.40
2222 6323 8.588290 ATTTGAGTTTGTGGCCTTGTATATAA 57.412 30.769 3.32 0.00 0.00 0.98
2223 6324 8.588290 AATTTGAGTTTGTGGCCTTGTATATA 57.412 30.769 3.32 0.00 0.00 0.86
2224 6325 7.480760 AATTTGAGTTTGTGGCCTTGTATAT 57.519 32.000 3.32 0.00 0.00 0.86
2225 6326 6.909550 AATTTGAGTTTGTGGCCTTGTATA 57.090 33.333 3.32 0.00 0.00 1.47
2226 6327 5.806654 AATTTGAGTTTGTGGCCTTGTAT 57.193 34.783 3.32 0.00 0.00 2.29
2227 6328 5.594725 TGTAATTTGAGTTTGTGGCCTTGTA 59.405 36.000 3.32 0.00 0.00 2.41
2228 6329 4.404073 TGTAATTTGAGTTTGTGGCCTTGT 59.596 37.500 3.32 0.00 0.00 3.16
2229 6330 4.942852 TGTAATTTGAGTTTGTGGCCTTG 58.057 39.130 3.32 0.00 0.00 3.61
2230 6331 4.039124 CCTGTAATTTGAGTTTGTGGCCTT 59.961 41.667 3.32 0.00 0.00 4.35
2231 6332 3.573967 CCTGTAATTTGAGTTTGTGGCCT 59.426 43.478 3.32 0.00 0.00 5.19
2232 6333 3.860754 GCCTGTAATTTGAGTTTGTGGCC 60.861 47.826 0.00 0.00 0.00 5.36
2233 6334 3.243704 TGCCTGTAATTTGAGTTTGTGGC 60.244 43.478 0.00 0.00 37.38 5.01
2234 6335 4.298332 GTGCCTGTAATTTGAGTTTGTGG 58.702 43.478 0.00 0.00 0.00 4.17
2235 6336 4.202101 TGGTGCCTGTAATTTGAGTTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
2236 6337 3.957497 TGGTGCCTGTAATTTGAGTTTGT 59.043 39.130 0.00 0.00 0.00 2.83
2237 6338 4.582701 TGGTGCCTGTAATTTGAGTTTG 57.417 40.909 0.00 0.00 0.00 2.93
2238 6339 5.806654 ATTGGTGCCTGTAATTTGAGTTT 57.193 34.783 0.00 0.00 0.00 2.66
2239 6340 8.588290 TTATATTGGTGCCTGTAATTTGAGTT 57.412 30.769 0.00 0.00 0.00 3.01
2240 6341 8.588290 TTTATATTGGTGCCTGTAATTTGAGT 57.412 30.769 0.00 0.00 0.00 3.41
2249 6350 9.816354 GACATTAAATTTTATATTGGTGCCTGT 57.184 29.630 0.00 0.00 0.00 4.00
2252 6353 9.816354 ACAGACATTAAATTTTATATTGGTGCC 57.184 29.630 0.00 0.00 0.00 5.01
2263 6364 9.171877 TGGCTTTCAAAACAGACATTAAATTTT 57.828 25.926 0.00 0.00 0.00 1.82
2264 6365 8.729805 TGGCTTTCAAAACAGACATTAAATTT 57.270 26.923 0.00 0.00 0.00 1.82
2265 6366 8.776470 CATGGCTTTCAAAACAGACATTAAATT 58.224 29.630 0.00 0.00 36.55 1.82
2266 6367 7.933033 ACATGGCTTTCAAAACAGACATTAAAT 59.067 29.630 0.00 0.00 36.55 1.40
2267 6368 7.271511 ACATGGCTTTCAAAACAGACATTAAA 58.728 30.769 0.00 0.00 36.55 1.52
2268 6369 6.815089 ACATGGCTTTCAAAACAGACATTAA 58.185 32.000 0.00 0.00 36.55 1.40
2269 6370 6.403866 ACATGGCTTTCAAAACAGACATTA 57.596 33.333 0.00 0.00 36.55 1.90
2270 6371 5.280654 ACATGGCTTTCAAAACAGACATT 57.719 34.783 0.00 0.00 36.55 2.71
2271 6372 4.942761 ACATGGCTTTCAAAACAGACAT 57.057 36.364 0.00 0.00 39.55 3.06
2272 6373 4.734398 AACATGGCTTTCAAAACAGACA 57.266 36.364 0.00 0.00 30.65 3.41
2273 6374 5.812127 AGAAAACATGGCTTTCAAAACAGAC 59.188 36.000 19.06 0.00 35.62 3.51
2274 6375 5.976458 AGAAAACATGGCTTTCAAAACAGA 58.024 33.333 19.06 0.00 35.62 3.41
2275 6376 7.116805 GGATAGAAAACATGGCTTTCAAAACAG 59.883 37.037 19.06 0.00 35.62 3.16
2276 6377 6.928492 GGATAGAAAACATGGCTTTCAAAACA 59.072 34.615 19.06 5.11 35.62 2.83
2277 6378 6.089417 CGGATAGAAAACATGGCTTTCAAAAC 59.911 38.462 19.06 9.34 35.62 2.43
2278 6379 6.155827 CGGATAGAAAACATGGCTTTCAAAA 58.844 36.000 19.06 8.84 35.62 2.44
2279 6380 5.242838 ACGGATAGAAAACATGGCTTTCAAA 59.757 36.000 19.06 10.62 35.62 2.69
2280 6381 4.764823 ACGGATAGAAAACATGGCTTTCAA 59.235 37.500 19.06 0.00 35.62 2.69
2281 6382 4.331968 ACGGATAGAAAACATGGCTTTCA 58.668 39.130 19.06 9.59 35.62 2.69
2282 6383 4.965119 ACGGATAGAAAACATGGCTTTC 57.035 40.909 12.35 12.35 33.75 2.62
2283 6384 5.722021 AAACGGATAGAAAACATGGCTTT 57.278 34.783 0.00 0.00 0.00 3.51
2284 6385 5.944007 AGTAAACGGATAGAAAACATGGCTT 59.056 36.000 0.00 0.00 0.00 4.35
2285 6386 5.354234 CAGTAAACGGATAGAAAACATGGCT 59.646 40.000 0.00 0.00 0.00 4.75
2286 6387 5.448632 CCAGTAAACGGATAGAAAACATGGC 60.449 44.000 0.00 0.00 0.00 4.40
2287 6388 5.065988 CCCAGTAAACGGATAGAAAACATGG 59.934 44.000 0.00 0.00 0.00 3.66
2288 6389 5.878116 TCCCAGTAAACGGATAGAAAACATG 59.122 40.000 0.00 0.00 0.00 3.21
2289 6390 6.057321 TCCCAGTAAACGGATAGAAAACAT 57.943 37.500 0.00 0.00 0.00 2.71
2290 6391 5.486735 TCCCAGTAAACGGATAGAAAACA 57.513 39.130 0.00 0.00 0.00 2.83
2291 6392 6.036844 GTGATCCCAGTAAACGGATAGAAAAC 59.963 42.308 0.00 0.00 39.04 2.43
2292 6393 6.070424 AGTGATCCCAGTAAACGGATAGAAAA 60.070 38.462 0.00 0.00 39.04 2.29
2293 6394 5.424252 AGTGATCCCAGTAAACGGATAGAAA 59.576 40.000 0.00 0.00 39.04 2.52
2294 6395 4.960469 AGTGATCCCAGTAAACGGATAGAA 59.040 41.667 0.00 0.00 39.04 2.10
2295 6396 4.543689 AGTGATCCCAGTAAACGGATAGA 58.456 43.478 0.00 0.00 39.04 1.98
2296 6397 4.939052 AGTGATCCCAGTAAACGGATAG 57.061 45.455 0.00 0.00 39.04 2.08
2297 6398 6.989155 ATTAGTGATCCCAGTAAACGGATA 57.011 37.500 0.00 0.00 40.44 2.59
2298 6399 5.888982 ATTAGTGATCCCAGTAAACGGAT 57.111 39.130 0.00 0.00 40.44 4.18
2299 6400 5.069516 GGTATTAGTGATCCCAGTAAACGGA 59.930 44.000 0.00 0.00 40.44 4.69
2300 6401 5.295152 GGTATTAGTGATCCCAGTAAACGG 58.705 45.833 0.00 0.00 40.44 4.44
2301 6402 5.295152 GGGTATTAGTGATCCCAGTAAACG 58.705 45.833 0.00 0.00 40.44 3.60
2302 6403 5.131475 TGGGGTATTAGTGATCCCAGTAAAC 59.869 44.000 0.00 0.00 42.21 2.01
2303 6404 5.290335 TGGGGTATTAGTGATCCCAGTAAA 58.710 41.667 0.00 0.00 42.21 2.01
2304 6405 4.898268 TGGGGTATTAGTGATCCCAGTAA 58.102 43.478 0.00 0.00 42.21 2.24
2305 6406 4.562934 TGGGGTATTAGTGATCCCAGTA 57.437 45.455 0.00 0.00 42.21 2.74
2306 6407 3.431411 TGGGGTATTAGTGATCCCAGT 57.569 47.619 0.00 0.00 42.21 4.00
2308 6409 3.138123 TGTGGGGTATTAGTGATCCCA 57.862 47.619 0.00 0.00 44.59 4.37
2309 6410 3.810743 GCATGTGGGGTATTAGTGATCCC 60.811 52.174 0.00 0.00 39.22 3.85
2310 6411 3.181445 TGCATGTGGGGTATTAGTGATCC 60.181 47.826 0.00 0.00 0.00 3.36
2311 6412 4.085357 TGCATGTGGGGTATTAGTGATC 57.915 45.455 0.00 0.00 0.00 2.92
2312 6413 4.401022 CATGCATGTGGGGTATTAGTGAT 58.599 43.478 18.91 0.00 0.00 3.06
2313 6414 3.819368 CATGCATGTGGGGTATTAGTGA 58.181 45.455 18.91 0.00 0.00 3.41
2314 6415 2.294233 GCATGCATGTGGGGTATTAGTG 59.706 50.000 26.79 0.00 0.00 2.74
2315 6416 2.091939 TGCATGCATGTGGGGTATTAGT 60.092 45.455 26.79 0.00 0.00 2.24
2316 6417 2.585330 TGCATGCATGTGGGGTATTAG 58.415 47.619 26.79 0.00 0.00 1.73
2317 6418 2.744352 TGCATGCATGTGGGGTATTA 57.256 45.000 26.79 1.42 0.00 0.98
2318 6419 1.758280 CTTGCATGCATGTGGGGTATT 59.242 47.619 26.79 0.00 0.00 1.89
2319 6420 1.063792 TCTTGCATGCATGTGGGGTAT 60.064 47.619 26.79 0.00 0.00 2.73
2320 6421 0.330941 TCTTGCATGCATGTGGGGTA 59.669 50.000 26.79 8.63 0.00 3.69
2321 6422 0.542467 TTCTTGCATGCATGTGGGGT 60.542 50.000 26.79 0.00 0.00 4.95
2322 6423 0.609151 TTTCTTGCATGCATGTGGGG 59.391 50.000 26.79 14.73 0.00 4.96
2323 6424 2.070783 GTTTTCTTGCATGCATGTGGG 58.929 47.619 26.79 16.34 0.00 4.61
2324 6425 3.034721 AGTTTTCTTGCATGCATGTGG 57.965 42.857 26.79 16.66 0.00 4.17


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

AutoCloner maintained by Alex Coulton.