Multiple sequence alignment - TraesCS1A01G063400

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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 TraesCS1A01G063400 chr1A 100.000 3252 0 0 1 3252 44371833 44368582 0.000000e+00 6006.0
1 TraesCS1A01G063400 chr1A 88.535 157 17 1 357 512 32875567 32875411 4.280000e-44 189.0
2 TraesCS1A01G063400 chr1B 90.750 1654 131 12 837 2481 63935594 63933954 0.000000e+00 2187.0
3 TraesCS1A01G063400 chr1B 91.271 653 41 5 837 1485 63957072 63956432 0.000000e+00 876.0
4 TraesCS1A01G063400 chr1B 90.812 653 41 6 837 1485 63950082 63949445 0.000000e+00 856.0
5 TraesCS1A01G063400 chr1B 90.658 653 42 6 837 1485 63943092 63942455 0.000000e+00 850.0
6 TraesCS1A01G063400 chr1B 92.188 256 15 3 515 766 63957322 63957068 1.110000e-94 357.0
7 TraesCS1A01G063400 chr1B 91.406 256 17 3 515 766 63943342 63943088 2.400000e-91 346.0
8 TraesCS1A01G063400 chr1B 91.406 256 17 3 515 766 63950332 63950078 2.400000e-91 346.0
9 TraesCS1A01G063400 chr1B 92.308 234 10 1 1480 1713 63944584 63944359 3.130000e-85 326.0
10 TraesCS1A01G063400 chr1B 92.308 234 10 1 1480 1713 63951574 63951349 3.130000e-85 326.0
11 TraesCS1A01G063400 chr1B 92.308 234 9 2 1480 1713 63937038 63936814 1.130000e-84 324.0
12 TraesCS1A01G063400 chr1B 88.583 254 17 3 515 766 63935833 63935590 6.820000e-77 298.0
13 TraesCS1A01G063400 chr1B 90.476 168 15 1 2953 3120 63933862 63933696 1.520000e-53 220.0
14 TraesCS1A01G063400 chr1B 91.667 48 4 0 3187 3234 63933064 63933017 2.090000e-07 67.6
15 TraesCS1A01G063400 chr1D 87.833 863 85 10 1622 2477 44637900 44637051 0.000000e+00 994.0
16 TraesCS1A01G063400 chr1D 84.603 643 71 22 2485 3117 44637000 44636376 5.960000e-172 614.0
17 TraesCS1A01G063400 chr1D 87.138 552 36 16 1050 1601 44638408 44637892 7.770000e-166 593.0
18 TraesCS1A01G063400 chr1D 80.000 270 29 15 515 771 44638879 44638622 3.330000e-40 176.0
19 TraesCS1A01G063400 chr7A 99.071 323 3 0 1 323 158417587 158417265 6.050000e-162 580.0
20 TraesCS1A01G063400 chr7A 98.452 323 4 1 1 323 34765926 34766247 4.710000e-158 568.0
21 TraesCS1A01G063400 chr7A 98.142 323 5 1 1 323 34785235 34785556 2.190000e-156 562.0
22 TraesCS1A01G063400 chr7A 94.444 180 8 2 334 511 158416800 158416621 3.200000e-70 276.0
23 TraesCS1A01G063400 chr7A 91.720 157 12 1 355 511 34786228 34786383 1.960000e-52 217.0
24 TraesCS1A01G063400 chr3A 98.762 323 4 0 1 323 524321963 524322285 2.810000e-160 575.0
25 TraesCS1A01G063400 chr3A 97.833 323 7 0 1 323 600068979 600068657 2.830000e-155 558.0
26 TraesCS1A01G063400 chr3A 92.350 183 8 3 336 518 524322781 524322957 4.160000e-64 255.0
27 TraesCS1A01G063400 chr3A 91.954 174 12 2 337 509 600068162 600067990 3.240000e-60 243.0
28 TraesCS1A01G063400 chr5A 98.452 323 4 1 1 323 465635657 465635978 4.710000e-158 568.0
29 TraesCS1A01G063400 chr5A 92.179 179 9 2 334 512 465636805 465636978 6.970000e-62 248.0
30 TraesCS1A01G063400 chr5A 88.571 175 15 4 336 510 402642389 402642220 1.180000e-49 207.0
31 TraesCS1A01G063400 chr3D 97.523 323 6 2 1 323 465468519 465468199 4.740000e-153 551.0
32 TraesCS1A01G063400 chr3D 90.503 179 11 3 335 513 465467713 465467541 7.020000e-57 231.0
33 TraesCS1A01G063400 chr6A 95.666 323 10 3 1 323 98911861 98912179 1.730000e-142 516.0
34 TraesCS1A01G063400 chr4D 95.666 323 10 3 1 323 490638835 490639153 1.730000e-142 516.0
35 TraesCS1A01G063400 chrUn 92.369 249 12 4 837 1081 352527370 352527615 6.680000e-92 348.0
36 TraesCS1A01G063400 chrUn 91.120 259 18 3 512 766 352527117 352527374 2.400000e-91 346.0
37 TraesCS1A01G063400 chrUn 92.308 234 10 1 1480 1713 339391155 339391380 3.130000e-85 326.0
38 TraesCS1A01G063400 chrUn 92.308 234 10 1 1480 1713 352525878 352526103 3.130000e-85 326.0
39 TraesCS1A01G063400 chrUn 92.308 234 10 1 1480 1713 403970375 403970600 3.130000e-85 326.0
40 TraesCS1A01G063400 chrUn 81.818 154 22 3 1093 1240 313568318 313568165 1.230000e-24 124.0
41 TraesCS1A01G063400 chrUn 81.818 154 22 3 1093 1240 313572077 313571924 1.230000e-24 124.0
42 TraesCS1A01G063400 chrUn 81.818 154 22 3 1093 1240 313605898 313605745 1.230000e-24 124.0
43 TraesCS1A01G063400 chrUn 81.529 157 23 3 1090 1240 465333322 465333478 1.230000e-24 124.0
44 TraesCS1A01G063400 chr2D 93.631 157 9 1 356 512 46164476 46164631 1.950000e-57 233.0


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 TraesCS1A01G063400 chr1A 44368582 44371833 3251 True 6006.000000 6006 100.000000 1 3252 1 chr1A.!!$R2 3251
1 TraesCS1A01G063400 chr1B 63933017 63937038 4021 True 619.320000 2187 90.756800 515 3234 5 chr1B.!!$R1 2719
2 TraesCS1A01G063400 chr1B 63956432 63957322 890 True 616.500000 876 91.729500 515 1485 2 chr1B.!!$R4 970
3 TraesCS1A01G063400 chr1B 63949445 63951574 2129 True 509.333333 856 91.508667 515 1713 3 chr1B.!!$R3 1198
4 TraesCS1A01G063400 chr1B 63942455 63944584 2129 True 507.333333 850 91.457333 515 1713 3 chr1B.!!$R2 1198
5 TraesCS1A01G063400 chr1D 44636376 44638879 2503 True 594.250000 994 84.893500 515 3117 4 chr1D.!!$R1 2602
6 TraesCS1A01G063400 chr7A 158416621 158417587 966 True 428.000000 580 96.757500 1 511 2 chr7A.!!$R1 510
7 TraesCS1A01G063400 chr7A 34785235 34786383 1148 False 389.500000 562 94.931000 1 511 2 chr7A.!!$F2 510
8 TraesCS1A01G063400 chr3A 524321963 524322957 994 False 415.000000 575 95.556000 1 518 2 chr3A.!!$F1 517
9 TraesCS1A01G063400 chr3A 600067990 600068979 989 True 400.500000 558 94.893500 1 509 2 chr3A.!!$R1 508
10 TraesCS1A01G063400 chr5A 465635657 465636978 1321 False 408.000000 568 95.315500 1 512 2 chr5A.!!$F1 511
11 TraesCS1A01G063400 chr3D 465467541 465468519 978 True 391.000000 551 94.013000 1 513 2 chr3D.!!$R1 512
12 TraesCS1A01G063400 chrUn 352525878 352527615 1737 False 340.000000 348 91.932333 512 1713 3 chrUn.!!$F4 1201

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
987 2168 0.038526 AGAAACCTGATCGCGAACGT 60.039 50.0 15.24 1.3 41.18 3.99 F
1248 2429 0.250166 CCAGGTTCCTCGACCGTTTT 60.250 55.0 0.00 0.0 44.62 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 3200 1.377856 GAGGAGGCAGCCCAAGAAC 60.378 63.158 8.22 0.0 0.00 3.01 R
3160 4399 0.970427 TGTCGATGCCTACTCCAGCA 60.970 55.000 0.00 0.0 44.45 4.41 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
283 284 1.693799 ATCCCCACACCAAACCCTAT 58.306 50.000 0.00 0.00 0.00 2.57
323 324 5.934043 CGGCAGAAATCATCATAGGATAACA 59.066 40.000 0.00 0.00 30.87 2.41
325 326 7.413767 CGGCAGAAATCATCATAGGATAACATG 60.414 40.741 0.00 0.00 30.87 3.21
326 327 7.249147 GCAGAAATCATCATAGGATAACATGC 58.751 38.462 0.00 0.00 30.87 4.06
327 328 7.094506 GCAGAAATCATCATAGGATAACATGCA 60.095 37.037 0.00 0.00 30.87 3.96
328 329 8.451748 CAGAAATCATCATAGGATAACATGCAG 58.548 37.037 0.00 0.00 30.87 4.41
329 330 6.754702 AATCATCATAGGATAACATGCAGC 57.245 37.500 0.00 0.00 30.87 5.25
330 331 4.248058 TCATCATAGGATAACATGCAGCG 58.752 43.478 0.00 0.00 30.87 5.18
331 332 3.044235 TCATAGGATAACATGCAGCGG 57.956 47.619 0.00 0.00 0.00 5.52
463 1508 1.613317 AATCGACGGCATCCAGGTGA 61.613 55.000 0.00 0.00 0.00 4.02
465 1510 1.153369 CGACGGCATCCAGGTGATT 60.153 57.895 0.00 0.00 0.00 2.57
513 1559 5.571357 GGTGTGCCAAATACATTTTTCGTAG 59.429 40.000 0.00 0.00 34.09 3.51
527 1573 2.579207 TCGTAGAAAGATTGCCTCGG 57.421 50.000 0.00 0.00 0.00 4.63
624 1678 1.267121 ACATGAACACGGCCTACTCT 58.733 50.000 0.00 0.00 0.00 3.24
710 1771 6.458342 GCGTCCTTCCTTGGTCAAATTATTAG 60.458 42.308 0.00 0.00 0.00 1.73
747 1808 6.774170 TGGTAGTACTTATGACATACGATGGT 59.226 38.462 0.00 0.00 33.60 3.55
765 1826 5.051039 CGATGGTTTCGTATACACATGGAAG 60.051 44.000 3.32 0.00 43.01 3.46
766 1827 4.509616 TGGTTTCGTATACACATGGAAGG 58.490 43.478 3.32 0.00 0.00 3.46
767 1828 4.223255 TGGTTTCGTATACACATGGAAGGA 59.777 41.667 3.32 0.00 0.00 3.36
768 1829 4.809426 GGTTTCGTATACACATGGAAGGAG 59.191 45.833 3.32 0.00 0.00 3.69
769 1830 4.665833 TTCGTATACACATGGAAGGAGG 57.334 45.455 3.32 0.00 0.00 4.30
770 1831 2.963101 TCGTATACACATGGAAGGAGGG 59.037 50.000 3.32 0.00 0.00 4.30
771 1832 2.037251 CGTATACACATGGAAGGAGGGG 59.963 54.545 3.32 0.00 0.00 4.79
772 1833 1.522900 ATACACATGGAAGGAGGGGG 58.477 55.000 0.00 0.00 0.00 5.40
773 1834 0.120377 TACACATGGAAGGAGGGGGT 59.880 55.000 0.00 0.00 0.00 4.95
774 1835 0.120377 ACACATGGAAGGAGGGGGTA 59.880 55.000 0.00 0.00 0.00 3.69
775 1836 1.275002 ACACATGGAAGGAGGGGGTAT 60.275 52.381 0.00 0.00 0.00 2.73
776 1837 1.421646 CACATGGAAGGAGGGGGTATC 59.578 57.143 0.00 0.00 0.00 2.24
777 1838 1.010793 ACATGGAAGGAGGGGGTATCA 59.989 52.381 0.00 0.00 0.00 2.15
778 1839 2.135189 CATGGAAGGAGGGGGTATCAA 58.865 52.381 0.00 0.00 0.00 2.57
779 1840 2.605825 TGGAAGGAGGGGGTATCAAT 57.394 50.000 0.00 0.00 0.00 2.57
780 1841 2.871796 TGGAAGGAGGGGGTATCAATT 58.128 47.619 0.00 0.00 0.00 2.32
781 1842 3.206464 TGGAAGGAGGGGGTATCAATTT 58.794 45.455 0.00 0.00 0.00 1.82
782 1843 3.600617 TGGAAGGAGGGGGTATCAATTTT 59.399 43.478 0.00 0.00 0.00 1.82
783 1844 4.796816 TGGAAGGAGGGGGTATCAATTTTA 59.203 41.667 0.00 0.00 0.00 1.52
784 1845 5.103686 TGGAAGGAGGGGGTATCAATTTTAG 60.104 44.000 0.00 0.00 0.00 1.85
785 1846 4.455070 AGGAGGGGGTATCAATTTTAGC 57.545 45.455 0.00 0.00 0.00 3.09
786 1847 3.140332 AGGAGGGGGTATCAATTTTAGCC 59.860 47.826 5.26 5.26 36.66 3.93
787 1848 3.117284 GGAGGGGGTATCAATTTTAGCCA 60.117 47.826 12.95 0.00 38.66 4.75
788 1849 3.889538 GAGGGGGTATCAATTTTAGCCAC 59.110 47.826 12.95 10.30 40.26 5.01
789 1850 2.621526 GGGGGTATCAATTTTAGCCACG 59.378 50.000 12.95 0.00 38.66 4.94
790 1851 3.284617 GGGGTATCAATTTTAGCCACGT 58.715 45.455 12.95 0.00 38.66 4.49
791 1852 3.066203 GGGGTATCAATTTTAGCCACGTG 59.934 47.826 9.08 9.08 38.66 4.49
792 1853 3.066203 GGGTATCAATTTTAGCCACGTGG 59.934 47.826 30.66 30.66 37.22 4.94
803 1864 2.669229 CACGTGGCACTGGCATGA 60.669 61.111 26.93 0.00 46.06 3.07
804 1865 2.359107 ACGTGGCACTGGCATGAG 60.359 61.111 26.93 15.34 46.06 2.90
805 1866 3.129502 CGTGGCACTGGCATGAGG 61.130 66.667 17.89 1.02 46.06 3.86
806 1867 2.753043 GTGGCACTGGCATGAGGG 60.753 66.667 11.13 0.00 43.71 4.30
807 1868 4.746309 TGGCACTGGCATGAGGGC 62.746 66.667 0.07 0.00 42.11 5.19
808 1869 4.437587 GGCACTGGCATGAGGGCT 62.438 66.667 8.42 0.00 42.49 5.19
809 1870 2.362120 GCACTGGCATGAGGGCTT 60.362 61.111 0.00 0.00 39.48 4.35
810 1871 2.413142 GCACTGGCATGAGGGCTTC 61.413 63.158 0.00 0.00 39.48 3.86
811 1872 1.001764 CACTGGCATGAGGGCTTCA 60.002 57.895 0.39 0.39 43.83 3.02
812 1873 1.001641 ACTGGCATGAGGGCTTCAC 60.002 57.895 0.00 0.00 43.83 3.18
813 1874 2.046023 TGGCATGAGGGCTTCACG 60.046 61.111 0.00 0.00 43.83 4.35
814 1875 2.045926 GGCATGAGGGCTTCACGT 60.046 61.111 0.00 0.00 38.99 4.49
815 1876 1.675641 GGCATGAGGGCTTCACGTT 60.676 57.895 0.00 0.00 38.99 3.99
816 1877 1.244019 GGCATGAGGGCTTCACGTTT 61.244 55.000 0.00 0.00 38.99 3.60
817 1878 1.448985 GCATGAGGGCTTCACGTTTA 58.551 50.000 0.00 0.00 38.99 2.01
818 1879 1.810151 GCATGAGGGCTTCACGTTTAA 59.190 47.619 0.00 0.00 38.99 1.52
819 1880 2.423538 GCATGAGGGCTTCACGTTTAAT 59.576 45.455 0.00 0.00 38.99 1.40
820 1881 3.119495 GCATGAGGGCTTCACGTTTAATT 60.119 43.478 0.00 0.00 38.99 1.40
821 1882 4.662145 CATGAGGGCTTCACGTTTAATTC 58.338 43.478 0.00 0.00 38.99 2.17
822 1883 3.745799 TGAGGGCTTCACGTTTAATTCA 58.254 40.909 0.00 0.00 0.00 2.57
823 1884 4.331968 TGAGGGCTTCACGTTTAATTCAT 58.668 39.130 0.00 0.00 0.00 2.57
824 1885 4.155826 TGAGGGCTTCACGTTTAATTCATG 59.844 41.667 0.00 0.00 0.00 3.07
825 1886 3.119495 AGGGCTTCACGTTTAATTCATGC 60.119 43.478 0.00 0.00 0.00 4.06
826 1887 2.845967 GGCTTCACGTTTAATTCATGCG 59.154 45.455 0.00 0.00 0.00 4.73
827 1888 3.488489 GCTTCACGTTTAATTCATGCGT 58.512 40.909 0.00 0.00 36.13 5.24
831 1892 2.338228 CACGTTTAATTCATGCGTGTGC 59.662 45.455 5.68 0.00 45.07 4.57
865 2042 3.671716 ACCAGGAAAGTTACACCGATTC 58.328 45.455 0.00 0.00 0.00 2.52
907 2084 3.328505 TCCAAAAGAATCGTCGGGTTAC 58.671 45.455 0.00 0.00 0.00 2.50
920 2097 4.038402 CGTCGGGTTACTATATTCCTGGTT 59.962 45.833 0.00 0.00 0.00 3.67
921 2098 5.452356 CGTCGGGTTACTATATTCCTGGTTT 60.452 44.000 0.00 0.00 0.00 3.27
978 2159 1.153549 GCCTCGCGAGAAACCTGAT 60.154 57.895 36.59 0.00 41.32 2.90
979 2160 1.148759 GCCTCGCGAGAAACCTGATC 61.149 60.000 36.59 9.99 41.32 2.92
980 2161 0.867753 CCTCGCGAGAAACCTGATCG 60.868 60.000 36.59 12.33 41.32 3.69
984 2165 3.030209 CGAGAAACCTGATCGCGAA 57.970 52.632 15.24 0.00 41.70 4.70
985 2166 0.640768 CGAGAAACCTGATCGCGAAC 59.359 55.000 15.24 12.18 41.70 3.95
986 2167 0.640768 GAGAAACCTGATCGCGAACG 59.359 55.000 15.24 7.08 42.01 3.95
987 2168 0.038526 AGAAACCTGATCGCGAACGT 60.039 50.000 15.24 1.30 41.18 3.99
1015 2196 0.317103 GTCCATGTCGTCTCGATCCG 60.317 60.000 0.00 0.00 38.42 4.18
1204 2385 2.659016 CCTCCGCAGTCTGCAAGA 59.341 61.111 24.13 17.88 45.36 3.02
1248 2429 0.250166 CCAGGTTCCTCGACCGTTTT 60.250 55.000 0.00 0.00 44.62 2.43
1293 2474 2.275318 CTCCTTGGATTCTTCGAGTGC 58.725 52.381 0.00 0.00 0.00 4.40
1339 2520 1.766461 CCTCCCTACCGCATCCCTT 60.766 63.158 0.00 0.00 0.00 3.95
1342 2523 0.759436 TCCCTACCGCATCCCTTCTC 60.759 60.000 0.00 0.00 0.00 2.87
1419 2600 0.531090 GTGGCCGCCAATACGATGTA 60.531 55.000 15.39 0.00 34.18 2.29
1535 2716 3.146066 CCGTTCCTCCATTGTTCAAGAA 58.854 45.455 0.00 0.00 0.00 2.52
1592 2773 2.203294 AACAAGGGCCACGTCCAC 60.203 61.111 6.18 0.00 0.00 4.02
1682 2863 2.074576 GCCTTTGTTTACTCCTCGGAC 58.925 52.381 0.00 0.00 0.00 4.79
1698 2879 1.682849 GACACTGGTGTATGGGGCA 59.317 57.895 6.35 0.00 45.05 5.36
1721 2902 6.367422 GCAATCTTATCTCAATAGAGGTTCCG 59.633 42.308 0.00 0.00 42.34 4.30
1789 2970 5.512473 TGCGTTTTATTGGTTGTTGTCTAC 58.488 37.500 0.00 0.00 0.00 2.59
1790 2971 5.066117 TGCGTTTTATTGGTTGTTGTCTACA 59.934 36.000 0.00 0.00 34.12 2.74
1814 2995 4.694339 AGGATGGCATACTTAAGTTCGAC 58.306 43.478 14.49 8.12 0.00 4.20
1829 3010 4.579869 AGTTCGACTTGGATATGCAAAGT 58.420 39.130 11.06 10.63 36.87 2.66
1836 3017 5.749462 ACTTGGATATGCAAAGTCTAGCTT 58.251 37.500 11.06 0.00 39.52 3.74
1853 3034 1.680338 CTTTGATTAAGGGGCCTCCG 58.320 55.000 0.00 0.00 41.52 4.63
1939 3120 5.630121 CCTTGCCATATTGTATTACCCTCA 58.370 41.667 0.00 0.00 0.00 3.86
1957 3138 3.244353 CCTCACCTCGAAATATGGCAGAT 60.244 47.826 0.00 0.00 0.00 2.90
1959 3140 2.810274 CACCTCGAAATATGGCAGATGG 59.190 50.000 0.00 0.00 0.00 3.51
1982 3163 2.884012 TGTCGATTTTCATGGTGTTGCT 59.116 40.909 0.00 0.00 0.00 3.91
2007 3188 2.215196 GGTTGTTGCAGAAGACCGTTA 58.785 47.619 0.00 0.00 0.00 3.18
2019 3200 4.687483 AGAAGACCGTTAAAATGTGTACCG 59.313 41.667 0.00 0.00 0.00 4.02
2063 3244 0.698818 AGGAAGGAGGGACGCAAAAT 59.301 50.000 0.00 0.00 0.00 1.82
2129 3311 7.011950 ACGTGAACACCAATGTATATATGGTTG 59.988 37.037 4.09 3.87 44.92 3.77
2165 3347 5.775686 TGCAATCCAAAAGACTTCATGAAG 58.224 37.500 29.74 29.74 43.79 3.02
2166 3348 5.166398 GCAATCCAAAAGACTTCATGAAGG 58.834 41.667 33.11 18.28 42.53 3.46
2167 3349 5.166398 CAATCCAAAAGACTTCATGAAGGC 58.834 41.667 33.11 31.95 46.75 4.35
2201 3383 3.870633 ACTACCATCCTTTCACGAGTC 57.129 47.619 0.00 0.00 0.00 3.36
2206 3388 4.282496 ACCATCCTTTCACGAGTCTCTAT 58.718 43.478 0.00 0.00 0.00 1.98
2226 3408 8.445588 TCTCTATACACCAGGTGATTACTCATA 58.554 37.037 27.39 5.66 36.96 2.15
2250 3432 7.719871 ACTTAGTCTTTATCTTGCAGGAGTA 57.280 36.000 4.35 0.00 0.00 2.59
2261 3443 3.517296 TGCAGGAGTAACCCAATTTGA 57.483 42.857 0.00 0.00 40.05 2.69
2263 3445 4.415596 TGCAGGAGTAACCCAATTTGATT 58.584 39.130 0.00 0.00 40.05 2.57
2264 3446 5.575157 TGCAGGAGTAACCCAATTTGATTA 58.425 37.500 0.00 0.00 40.05 1.75
2277 3459 6.819649 CCCAATTTGATTATGTTCTGCACATT 59.180 34.615 0.00 0.00 44.40 2.71
2370 3555 7.521585 CGGTAAAAGGAAGCAGTTAGACATTTT 60.522 37.037 0.00 0.00 0.00 1.82
2380 3566 6.660949 AGCAGTTAGACATTTTCCTTTGCTAT 59.339 34.615 0.00 0.00 36.51 2.97
2381 3567 6.969473 GCAGTTAGACATTTTCCTTTGCTATC 59.031 38.462 0.00 0.00 0.00 2.08
2384 3570 8.103305 AGTTAGACATTTTCCTTTGCTATCTGA 58.897 33.333 0.00 0.00 0.00 3.27
2404 3590 8.738645 ATCTGAAGTAGTTGTCTTTTGTCTTT 57.261 30.769 0.00 0.00 0.00 2.52
2410 3596 7.975750 AGTAGTTGTCTTTTGTCTTTGAGAAC 58.024 34.615 0.00 0.00 34.34 3.01
2478 3664 8.172352 TGCAACCTCAAAGCTAGTTTTATTAA 57.828 30.769 4.08 0.00 0.00 1.40
2515 3747 7.093771 ACAACTTCCATTGAATCCATACTTTCC 60.094 37.037 0.00 0.00 33.57 3.13
2522 3754 9.533253 CCATTGAATCCATACTTTCCAAAATAC 57.467 33.333 0.00 0.00 0.00 1.89
2548 3780 7.225145 CCAGTGTTTTTGTCATTTGTTCATGAT 59.775 33.333 0.00 0.00 35.60 2.45
2578 3810 7.881142 TCTACAGGTGATTGGTTTATTTTGTG 58.119 34.615 0.00 0.00 0.00 3.33
2583 3815 4.149747 GTGATTGGTTTATTTTGTGGCACG 59.850 41.667 13.77 0.00 0.00 5.34
2584 3816 2.141535 TGGTTTATTTTGTGGCACGC 57.858 45.000 13.77 0.00 40.62 5.34
2600 3832 4.397730 TGGCACGCATATGTAAAACTGAAT 59.602 37.500 4.29 0.00 0.00 2.57
2602 3834 5.804979 GGCACGCATATGTAAAACTGAATTT 59.195 36.000 4.29 0.00 0.00 1.82
2614 3846 5.535753 AAACTGAATTTCTTGTCTTGGGG 57.464 39.130 0.00 0.00 0.00 4.96
2616 3848 4.145052 ACTGAATTTCTTGTCTTGGGGTC 58.855 43.478 0.00 0.00 0.00 4.46
2648 3880 4.322057 AGGCAAAATACCCAAGATCACT 57.678 40.909 0.00 0.00 0.00 3.41
2650 3882 5.086621 AGGCAAAATACCCAAGATCACTTT 58.913 37.500 0.00 0.00 33.70 2.66
2651 3883 5.047092 AGGCAAAATACCCAAGATCACTTTG 60.047 40.000 0.00 0.00 33.70 2.77
2656 3888 8.356657 CAAAATACCCAAGATCACTTTGTGTTA 58.643 33.333 0.00 0.00 34.79 2.41
2657 3889 7.448748 AATACCCAAGATCACTTTGTGTTAC 57.551 36.000 0.00 0.00 34.79 2.50
2662 3894 7.106239 CCCAAGATCACTTTGTGTTACTAGAT 58.894 38.462 0.00 0.00 34.79 1.98
2663 3895 7.278868 CCCAAGATCACTTTGTGTTACTAGATC 59.721 40.741 0.00 0.00 34.79 2.75
2711 3943 7.938140 TTTTCTCCTATTAACATGTCCAAGG 57.062 36.000 0.00 4.51 0.00 3.61
2715 3947 6.615316 TCTCCTATTAACATGTCCAAGGATGA 59.385 38.462 15.54 12.87 31.56 2.92
2716 3948 7.127186 TCTCCTATTAACATGTCCAAGGATGAA 59.873 37.037 15.54 6.19 31.56 2.57
2723 3955 7.722949 AACATGTCCAAGGATGAATTTACAT 57.277 32.000 0.00 0.00 0.00 2.29
2732 3966 9.880157 CCAAGGATGAATTTACATGAGAAAAAT 57.120 29.630 0.00 0.00 0.00 1.82
2825 4064 8.752187 AGTGTTAATGAATATTTCTTGCATGGT 58.248 29.630 0.00 0.00 0.00 3.55
2826 4065 9.023967 GTGTTAATGAATATTTCTTGCATGGTC 57.976 33.333 0.00 0.00 0.00 4.02
2832 4071 7.669427 TGAATATTTCTTGCATGGTCTTGTTT 58.331 30.769 0.00 0.00 0.00 2.83
2833 4072 8.801299 TGAATATTTCTTGCATGGTCTTGTTTA 58.199 29.630 0.00 0.00 0.00 2.01
2834 4073 9.807649 GAATATTTCTTGCATGGTCTTGTTTAT 57.192 29.630 0.00 0.00 0.00 1.40
2835 4074 9.807649 AATATTTCTTGCATGGTCTTGTTTATC 57.192 29.630 0.00 0.00 0.00 1.75
2841 4080 6.135290 TGCATGGTCTTGTTTATCTATTGC 57.865 37.500 0.00 0.00 0.00 3.56
2863 4102 9.703892 ATTGCTAGCATAAAGAGTGAGTTATAG 57.296 33.333 20.13 0.00 0.00 1.31
2918 4157 8.983724 GTAGCTATATTTGTCAGTCCATCTTTC 58.016 37.037 0.00 0.00 0.00 2.62
2930 4169 7.064016 GTCAGTCCATCTTTCTAATTGTCTCAC 59.936 40.741 0.00 0.00 0.00 3.51
2939 4178 7.766278 TCTTTCTAATTGTCTCACTATTGCCTC 59.234 37.037 0.00 0.00 0.00 4.70
2946 4185 4.646945 TGTCTCACTATTGCCTCCTCTTAG 59.353 45.833 0.00 0.00 0.00 2.18
2954 4193 8.153550 CACTATTGCCTCCTCTTAGTCATTTAT 58.846 37.037 0.00 0.00 0.00 1.40
2956 4195 6.814954 TTGCCTCCTCTTAGTCATTTATCT 57.185 37.500 0.00 0.00 0.00 1.98
2959 4198 8.319057 TGCCTCCTCTTAGTCATTTATCTTTA 57.681 34.615 0.00 0.00 0.00 1.85
2960 4199 8.938883 TGCCTCCTCTTAGTCATTTATCTTTAT 58.061 33.333 0.00 0.00 0.00 1.40
3000 4239 9.809096 CTGTTCTTAATGCTCTGACTTCTTATA 57.191 33.333 0.00 0.00 0.00 0.98
3118 4357 7.880160 TCTGGTTCAATGGGTAAGAATATTG 57.120 36.000 0.00 0.00 33.09 1.90
3119 4358 7.410174 TCTGGTTCAATGGGTAAGAATATTGT 58.590 34.615 0.00 0.00 33.46 2.71
3120 4359 7.556275 TCTGGTTCAATGGGTAAGAATATTGTC 59.444 37.037 0.00 0.00 33.46 3.18
3121 4360 7.410174 TGGTTCAATGGGTAAGAATATTGTCT 58.590 34.615 0.00 0.00 33.46 3.41
3122 4361 7.556275 TGGTTCAATGGGTAAGAATATTGTCTC 59.444 37.037 0.00 0.00 33.46 3.36
3123 4362 7.556275 GGTTCAATGGGTAAGAATATTGTCTCA 59.444 37.037 0.00 0.00 33.46 3.27
3124 4363 8.956426 GTTCAATGGGTAAGAATATTGTCTCAA 58.044 33.333 0.00 0.00 33.46 3.02
3125 4364 9.699410 TTCAATGGGTAAGAATATTGTCTCAAT 57.301 29.630 0.00 0.80 33.46 2.57
3150 4389 6.449635 TGTAGTTTGAGAGTTTTTGCATGT 57.550 33.333 0.00 0.00 0.00 3.21
3151 4390 6.264832 TGTAGTTTGAGAGTTTTTGCATGTG 58.735 36.000 0.00 0.00 0.00 3.21
3160 4399 6.913170 AGAGTTTTTGCATGTGAAATATCGT 58.087 32.000 0.00 0.00 0.00 3.73
3176 4422 1.589993 CGTGCTGGAGTAGGCATCG 60.590 63.158 0.00 0.00 40.66 3.84
3180 4426 0.390860 GCTGGAGTAGGCATCGACAT 59.609 55.000 0.00 0.00 0.00 3.06
3184 4430 4.072839 CTGGAGTAGGCATCGACATACTA 58.927 47.826 0.95 0.00 37.28 1.82
3185 4431 3.819337 TGGAGTAGGCATCGACATACTAC 59.181 47.826 3.75 3.75 37.28 2.73
3188 4434 4.462133 AGTAGGCATCGACATACTACTGT 58.538 43.478 15.75 0.00 41.83 3.55
3189 4435 3.717400 AGGCATCGACATACTACTGTG 57.283 47.619 0.00 0.00 0.00 3.66
3190 4436 3.024547 AGGCATCGACATACTACTGTGT 58.975 45.455 0.00 0.00 0.00 3.72
3192 4438 4.036498 AGGCATCGACATACTACTGTGTAC 59.964 45.833 0.00 0.00 0.00 2.90
3193 4439 4.288531 GCATCGACATACTACTGTGTACC 58.711 47.826 0.00 0.00 0.00 3.34
3197 5014 7.680350 GCATCGACATACTACTGTGTACCTTAA 60.680 40.741 0.00 0.00 0.00 1.85
3201 5018 9.049523 CGACATACTACTGTGTACCTTAATCTA 57.950 37.037 0.00 0.00 0.00 1.98
3205 5022 6.736123 ACTACTGTGTACCTTAATCTATGCG 58.264 40.000 0.00 0.00 0.00 4.73
3242 5059 9.448294 GTAATAAGATGTTTCTGAGTACCTACG 57.552 37.037 0.00 0.00 30.65 3.51
3243 5060 7.876936 ATAAGATGTTTCTGAGTACCTACGA 57.123 36.000 0.00 0.00 30.72 3.43
3244 5061 6.777213 AAGATGTTTCTGAGTACCTACGAT 57.223 37.500 0.00 0.00 30.72 3.73
3245 5062 7.876936 AAGATGTTTCTGAGTACCTACGATA 57.123 36.000 0.00 0.00 30.72 2.92
3246 5063 8.466617 AAGATGTTTCTGAGTACCTACGATAT 57.533 34.615 0.00 0.00 30.72 1.63
3247 5064 9.570468 AAGATGTTTCTGAGTACCTACGATATA 57.430 33.333 0.00 0.00 30.72 0.86
3248 5065 9.742144 AGATGTTTCTGAGTACCTACGATATAT 57.258 33.333 0.00 0.00 0.00 0.86
3249 5066 9.776158 GATGTTTCTGAGTACCTACGATATATG 57.224 37.037 0.00 0.00 0.00 1.78
3250 5067 8.687292 TGTTTCTGAGTACCTACGATATATGT 57.313 34.615 0.00 0.00 0.00 2.29
3251 5068 9.128404 TGTTTCTGAGTACCTACGATATATGTT 57.872 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
283 284 1.637478 GCCGTTATTTTGGTCGCCGA 61.637 55.000 0.00 0.00 0.00 5.54
340 1385 3.041627 GCTCGCTCGAACCGTCTCT 62.042 63.158 5.24 0.00 0.00 3.10
463 1508 3.465871 ACAGATTGCAAAAACGCCAAAT 58.534 36.364 1.71 0.00 0.00 2.32
465 1510 2.159184 TGACAGATTGCAAAAACGCCAA 60.159 40.909 1.71 0.00 0.00 4.52
513 1559 4.082787 TGAAATTGACCGAGGCAATCTTTC 60.083 41.667 5.58 7.99 35.06 2.62
527 1573 8.559536 TCTGTTATTCACTCAGTTGAAATTGAC 58.440 33.333 0.00 0.00 38.95 3.18
576 1627 1.966451 GTTCTGTGCCCCCGTCTTG 60.966 63.158 0.00 0.00 0.00 3.02
747 1808 4.141801 CCCTCCTTCCATGTGTATACGAAA 60.142 45.833 0.00 0.00 0.00 3.46
758 1819 1.819753 TGATACCCCCTCCTTCCATG 58.180 55.000 0.00 0.00 0.00 3.66
760 1821 2.605825 ATTGATACCCCCTCCTTCCA 57.394 50.000 0.00 0.00 0.00 3.53
765 1826 3.117284 TGGCTAAAATTGATACCCCCTCC 60.117 47.826 0.00 0.00 0.00 4.30
766 1827 3.889538 GTGGCTAAAATTGATACCCCCTC 59.110 47.826 0.00 0.00 0.00 4.30
767 1828 3.687264 CGTGGCTAAAATTGATACCCCCT 60.687 47.826 0.00 0.00 0.00 4.79
768 1829 2.621526 CGTGGCTAAAATTGATACCCCC 59.378 50.000 0.00 0.00 0.00 5.40
769 1830 3.066203 CACGTGGCTAAAATTGATACCCC 59.934 47.826 7.95 0.00 0.00 4.95
770 1831 3.066203 CCACGTGGCTAAAATTGATACCC 59.934 47.826 24.02 0.00 0.00 3.69
771 1832 4.287238 CCACGTGGCTAAAATTGATACC 57.713 45.455 24.02 0.00 0.00 2.73
785 1846 3.740397 CATGCCAGTGCCACGTGG 61.740 66.667 30.66 30.66 36.33 4.94
786 1847 2.669229 TCATGCCAGTGCCACGTG 60.669 61.111 9.08 9.08 36.33 4.49
787 1848 2.359107 CTCATGCCAGTGCCACGT 60.359 61.111 0.00 0.00 36.33 4.49
788 1849 3.129502 CCTCATGCCAGTGCCACG 61.130 66.667 0.00 0.00 36.33 4.94
789 1850 2.753043 CCCTCATGCCAGTGCCAC 60.753 66.667 0.00 0.00 36.33 5.01
790 1851 4.746309 GCCCTCATGCCAGTGCCA 62.746 66.667 0.00 0.00 36.33 4.92
791 1852 3.951769 AAGCCCTCATGCCAGTGCC 62.952 63.158 0.00 0.00 36.33 5.01
792 1853 2.362120 AAGCCCTCATGCCAGTGC 60.362 61.111 0.00 0.00 38.26 4.40
793 1854 1.001764 TGAAGCCCTCATGCCAGTG 60.002 57.895 0.00 0.00 0.00 3.66
794 1855 1.001641 GTGAAGCCCTCATGCCAGT 60.002 57.895 0.00 0.00 36.14 4.00
795 1856 2.110967 CGTGAAGCCCTCATGCCAG 61.111 63.158 0.00 0.00 36.14 4.85
796 1857 2.046023 CGTGAAGCCCTCATGCCA 60.046 61.111 0.00 0.00 36.14 4.92
797 1858 1.244019 AAACGTGAAGCCCTCATGCC 61.244 55.000 5.70 0.00 43.87 4.40
798 1859 1.448985 TAAACGTGAAGCCCTCATGC 58.551 50.000 5.70 0.00 43.87 4.06
799 1860 4.155826 TGAATTAAACGTGAAGCCCTCATG 59.844 41.667 0.00 4.46 45.31 3.07
800 1861 4.331968 TGAATTAAACGTGAAGCCCTCAT 58.668 39.130 0.00 0.00 36.14 2.90
801 1862 3.745799 TGAATTAAACGTGAAGCCCTCA 58.254 40.909 0.00 0.00 0.00 3.86
802 1863 4.662145 CATGAATTAAACGTGAAGCCCTC 58.338 43.478 0.00 0.00 0.00 4.30
803 1864 3.119495 GCATGAATTAAACGTGAAGCCCT 60.119 43.478 0.00 0.00 0.00 5.19
804 1865 3.179048 GCATGAATTAAACGTGAAGCCC 58.821 45.455 0.00 0.00 0.00 5.19
805 1866 2.845967 CGCATGAATTAAACGTGAAGCC 59.154 45.455 0.00 0.00 0.00 4.35
806 1867 3.488489 ACGCATGAATTAAACGTGAAGC 58.512 40.909 0.00 0.00 35.33 3.86
811 1872 2.580589 GCACACGCATGAATTAAACGT 58.419 42.857 0.00 0.00 38.36 3.99
812 1873 1.572717 CGCACACGCATGAATTAAACG 59.427 47.619 0.00 0.00 38.40 3.60
826 1887 0.383860 GTTAACTTCCGTGCGCACAC 60.384 55.000 37.03 22.20 43.76 3.82
827 1888 1.500512 GGTTAACTTCCGTGCGCACA 61.501 55.000 37.03 18.84 0.00 4.57
828 1889 1.205820 GGTTAACTTCCGTGCGCAC 59.794 57.895 30.42 30.42 0.00 5.34
829 1890 1.225376 CTGGTTAACTTCCGTGCGCA 61.225 55.000 5.66 5.66 0.00 6.09
830 1891 1.495951 CTGGTTAACTTCCGTGCGC 59.504 57.895 0.00 0.00 0.00 6.09
831 1892 0.320073 TCCTGGTTAACTTCCGTGCG 60.320 55.000 5.42 0.00 0.00 5.34
832 1893 1.886886 TTCCTGGTTAACTTCCGTGC 58.113 50.000 5.42 0.00 0.00 5.34
833 1894 3.473625 ACTTTCCTGGTTAACTTCCGTG 58.526 45.455 5.42 0.00 0.00 4.94
834 1895 3.851458 ACTTTCCTGGTTAACTTCCGT 57.149 42.857 5.42 0.00 0.00 4.69
835 1896 5.049886 GTGTAACTTTCCTGGTTAACTTCCG 60.050 44.000 5.42 0.00 32.06 4.30
836 1897 5.240183 GGTGTAACTTTCCTGGTTAACTTCC 59.760 44.000 5.42 0.00 36.74 3.46
837 1898 5.049886 CGGTGTAACTTTCCTGGTTAACTTC 60.050 44.000 5.42 0.00 36.74 3.01
838 1899 4.818005 CGGTGTAACTTTCCTGGTTAACTT 59.182 41.667 5.42 0.00 36.74 2.66
839 1900 4.101430 TCGGTGTAACTTTCCTGGTTAACT 59.899 41.667 5.42 0.00 36.74 2.24
907 2084 6.543465 TGCAGATGTGAAAACCAGGAATATAG 59.457 38.462 0.00 0.00 0.00 1.31
920 2097 1.872952 CTTCCGTGTGCAGATGTGAAA 59.127 47.619 1.99 0.00 0.00 2.69
921 2098 1.202639 ACTTCCGTGTGCAGATGTGAA 60.203 47.619 1.99 4.88 0.00 3.18
950 2131 0.586319 CTCGCGAGGCAAAAAGAACA 59.414 50.000 28.40 0.00 0.00 3.18
978 2159 3.116055 CGAAAAACAACGTTCGCGA 57.884 47.368 3.71 3.71 44.71 5.87
982 2163 3.687200 ACATGGACGAAAAACAACGTTC 58.313 40.909 0.00 0.00 42.74 3.95
984 2165 2.285950 CGACATGGACGAAAAACAACGT 60.286 45.455 8.49 0.00 45.32 3.99
985 2166 2.285950 ACGACATGGACGAAAAACAACG 60.286 45.455 18.41 0.00 34.70 4.10
986 2167 3.001939 AGACGACATGGACGAAAAACAAC 59.998 43.478 18.41 3.30 34.70 3.32
987 2168 3.199677 AGACGACATGGACGAAAAACAA 58.800 40.909 18.41 0.00 34.70 2.83
1248 2429 4.858680 TTCCGGTGGTGCGCACAA 62.859 61.111 38.60 28.88 0.00 3.33
1419 2600 4.790962 CCATGGCGGCAGCTGAGT 62.791 66.667 20.43 0.00 44.37 3.41
1510 2691 0.893727 AACAATGGAGGAACGGCCAC 60.894 55.000 2.24 0.00 40.13 5.01
1535 2716 2.960688 GCCCCGTTGAGGAAGCTCT 61.961 63.158 0.00 0.00 45.00 4.09
1563 2744 1.648720 CCTTGTTGGTGCAGTCGTG 59.351 57.895 0.00 0.00 0.00 4.35
1564 2745 1.525995 CCCTTGTTGGTGCAGTCGT 60.526 57.895 0.00 0.00 0.00 4.34
1565 2746 2.908073 GCCCTTGTTGGTGCAGTCG 61.908 63.158 0.00 0.00 33.85 4.18
1566 2747 2.564721 GGCCCTTGTTGGTGCAGTC 61.565 63.158 0.00 0.00 34.87 3.51
1567 2748 2.521708 GGCCCTTGTTGGTGCAGT 60.522 61.111 0.00 0.00 34.87 4.40
1592 2773 3.052082 CTGAACTGGCAGGCACCG 61.052 66.667 20.34 2.29 32.26 4.94
1682 2863 1.064463 AGATTGCCCCATACACCAGTG 60.064 52.381 0.00 0.00 0.00 3.66
1698 2879 7.507616 AGACGGAACCTCTATTGAGATAAGATT 59.492 37.037 5.68 0.00 42.73 2.40
1721 2902 2.797156 GCATGTGTCACGGATATGAGAC 59.203 50.000 5.44 0.00 41.93 3.36
1789 2970 5.584649 TCGAACTTAAGTATGCCATCCTTTG 59.415 40.000 8.92 0.00 0.00 2.77
1790 2971 5.585047 GTCGAACTTAAGTATGCCATCCTTT 59.415 40.000 8.92 0.00 0.00 3.11
1792 2973 4.406003 AGTCGAACTTAAGTATGCCATCCT 59.594 41.667 8.92 0.00 0.00 3.24
1814 2995 6.690194 AAAGCTAGACTTTGCATATCCAAG 57.310 37.500 10.21 0.00 47.00 3.61
1829 3010 3.123273 AGGCCCCTTAATCAAAGCTAGA 58.877 45.455 0.00 0.00 33.49 2.43
1836 3017 1.919771 CCGGAGGCCCCTTAATCAA 59.080 57.895 0.00 0.00 46.14 2.57
1939 3120 2.705658 TCCATCTGCCATATTTCGAGGT 59.294 45.455 0.00 0.00 0.00 3.85
1957 3138 3.684908 ACACCATGAAAATCGACATCCA 58.315 40.909 0.00 0.00 0.00 3.41
1959 3140 3.853671 GCAACACCATGAAAATCGACATC 59.146 43.478 0.00 0.00 0.00 3.06
1982 3163 3.146066 GGTCTTCTGCAACAACCATGTA 58.854 45.455 0.00 0.00 39.40 2.29
2007 3188 2.295070 GCCCAAGAACGGTACACATTTT 59.705 45.455 0.00 0.00 0.00 1.82
2019 3200 1.377856 GAGGAGGCAGCCCAAGAAC 60.378 63.158 8.22 0.00 0.00 3.01
2047 3228 4.398319 CCATATATTTTGCGTCCCTCCTT 58.602 43.478 0.00 0.00 0.00 3.36
2063 3244 8.193953 TCAATGTCTTCAGAGTATGCCATATA 57.806 34.615 0.00 0.00 0.00 0.86
2122 3304 7.517614 TTGCATCAACTTAAGTTCAACCATA 57.482 32.000 18.00 0.00 35.83 2.74
2129 3311 7.867403 TCTTTTGGATTGCATCAACTTAAGTTC 59.133 33.333 18.00 7.75 35.83 3.01
2139 3321 5.477637 TCATGAAGTCTTTTGGATTGCATCA 59.522 36.000 0.00 0.00 28.76 3.07
2165 3347 6.543831 GGATGGTAGTTATTGATATGATGGCC 59.456 42.308 0.00 0.00 0.00 5.36
2166 3348 7.341805 AGGATGGTAGTTATTGATATGATGGC 58.658 38.462 0.00 0.00 0.00 4.40
2167 3349 9.745018 AAAGGATGGTAGTTATTGATATGATGG 57.255 33.333 0.00 0.00 0.00 3.51
2201 3383 6.961360 TGAGTAATCACCTGGTGTATAGAG 57.039 41.667 25.15 0.00 34.79 2.43
2206 3388 7.837689 ACTAAGTATGAGTAATCACCTGGTGTA 59.162 37.037 25.15 13.17 34.79 2.90
2226 3408 6.613153 ACTCCTGCAAGATAAAGACTAAGT 57.387 37.500 0.00 0.00 34.07 2.24
2239 3421 3.826157 TCAAATTGGGTTACTCCTGCAAG 59.174 43.478 0.00 0.00 36.25 4.01
2243 3425 7.645058 ACATAATCAAATTGGGTTACTCCTG 57.355 36.000 0.00 0.00 36.25 3.86
2250 3432 6.165577 GTGCAGAACATAATCAAATTGGGTT 58.834 36.000 0.00 0.00 0.00 4.11
2356 3540 5.126396 AGCAAAGGAAAATGTCTAACTGC 57.874 39.130 0.00 0.00 0.00 4.40
2357 3541 8.180267 CAGATAGCAAAGGAAAATGTCTAACTG 58.820 37.037 0.00 0.00 0.00 3.16
2370 3555 6.211584 AGACAACTACTTCAGATAGCAAAGGA 59.788 38.462 0.00 0.00 0.00 3.36
2380 3566 7.822334 TCAAAGACAAAAGACAACTACTTCAGA 59.178 33.333 0.00 0.00 0.00 3.27
2381 3567 7.974675 TCAAAGACAAAAGACAACTACTTCAG 58.025 34.615 0.00 0.00 0.00 3.02
2384 3570 8.451748 GTTCTCAAAGACAAAAGACAACTACTT 58.548 33.333 0.00 0.00 0.00 2.24
2447 3633 7.938140 AACTAGCTTTGAGGTTGCAAATATA 57.062 32.000 0.00 0.00 37.16 0.86
2450 3636 5.535753 AAACTAGCTTTGAGGTTGCAAAT 57.464 34.783 0.00 0.00 37.16 2.32
2481 3667 7.877097 TGGATTCAATGGAAGTTGTTTTTATGG 59.123 33.333 0.00 0.00 36.25 2.74
2482 3668 8.830201 TGGATTCAATGGAAGTTGTTTTTATG 57.170 30.769 0.00 0.00 36.25 1.90
2498 3730 9.265862 TGGTATTTTGGAAAGTATGGATTCAAT 57.734 29.630 0.00 0.00 0.00 2.57
2515 3747 8.663911 ACAAATGACAAAAACACTGGTATTTTG 58.336 29.630 15.74 15.74 45.14 2.44
2522 3754 6.534436 TCATGAACAAATGACAAAAACACTGG 59.466 34.615 0.00 0.00 31.58 4.00
2565 3797 1.409064 TGCGTGCCACAAAATAAACCA 59.591 42.857 0.00 0.00 0.00 3.67
2567 3799 4.862018 ACATATGCGTGCCACAAAATAAAC 59.138 37.500 1.58 0.00 0.00 2.01
2568 3800 5.065704 ACATATGCGTGCCACAAAATAAA 57.934 34.783 1.58 0.00 0.00 1.40
2569 3801 4.710423 ACATATGCGTGCCACAAAATAA 57.290 36.364 1.58 0.00 0.00 1.40
2570 3802 5.819825 TTACATATGCGTGCCACAAAATA 57.180 34.783 1.58 0.00 0.00 1.40
2578 3810 4.349663 TTCAGTTTTACATATGCGTGCC 57.650 40.909 1.58 0.00 0.00 5.01
2583 3815 9.846248 AGACAAGAAATTCAGTTTTACATATGC 57.154 29.630 1.58 0.00 0.00 3.14
2588 3820 7.417342 CCCCAAGACAAGAAATTCAGTTTTACA 60.417 37.037 0.00 0.00 0.00 2.41
2589 3821 6.923508 CCCCAAGACAAGAAATTCAGTTTTAC 59.076 38.462 0.00 0.00 0.00 2.01
2592 3824 4.962362 ACCCCAAGACAAGAAATTCAGTTT 59.038 37.500 0.00 0.00 0.00 2.66
2594 3826 4.145052 GACCCCAAGACAAGAAATTCAGT 58.855 43.478 0.00 0.00 0.00 3.41
2595 3827 3.507622 GGACCCCAAGACAAGAAATTCAG 59.492 47.826 0.00 0.00 0.00 3.02
2600 3832 3.611025 AATGGACCCCAAGACAAGAAA 57.389 42.857 0.00 0.00 36.95 2.52
2602 3834 4.946160 ATAAATGGACCCCAAGACAAGA 57.054 40.909 0.00 0.00 36.95 3.02
2610 3842 4.338795 TGCCTTAAATAAATGGACCCCA 57.661 40.909 0.00 0.00 38.19 4.96
2611 3843 5.685520 TTTGCCTTAAATAAATGGACCCC 57.314 39.130 0.00 0.00 0.00 4.95
2614 3846 8.261522 TGGGTATTTTGCCTTAAATAAATGGAC 58.738 33.333 0.00 0.00 33.18 4.02
2616 3848 9.108284 CTTGGGTATTTTGCCTTAAATAAATGG 57.892 33.333 0.00 0.00 33.18 3.16
2685 3917 8.971073 CCTTGGACATGTTAATAGGAGAAAATT 58.029 33.333 0.00 0.00 0.00 1.82
2793 4027 9.210426 CAAGAAATATTCATTAACACTACGCAC 57.790 33.333 0.00 0.00 0.00 5.34
2795 4029 7.908082 TGCAAGAAATATTCATTAACACTACGC 59.092 33.333 0.00 0.00 0.00 4.42
2796 4030 9.935682 ATGCAAGAAATATTCATTAACACTACG 57.064 29.630 0.00 0.00 0.00 3.51
2800 4034 8.931385 ACCATGCAAGAAATATTCATTAACAC 57.069 30.769 0.00 0.00 0.00 3.32
2802 4036 9.807649 AAGACCATGCAAGAAATATTCATTAAC 57.192 29.630 0.00 0.00 0.00 2.01
2815 4054 7.415541 GCAATAGATAAACAAGACCATGCAAGA 60.416 37.037 0.00 0.00 0.00 3.02
2832 4071 9.083422 ACTCACTCTTTATGCTAGCAATAGATA 57.917 33.333 23.54 6.16 0.00 1.98
2833 4072 7.961351 ACTCACTCTTTATGCTAGCAATAGAT 58.039 34.615 23.54 7.31 0.00 1.98
2834 4073 7.353414 ACTCACTCTTTATGCTAGCAATAGA 57.647 36.000 23.54 20.93 0.00 1.98
2835 4074 9.703892 ATAACTCACTCTTTATGCTAGCAATAG 57.296 33.333 23.54 18.01 0.00 1.73
2909 4148 9.605275 CAATAGTGAGACAATTAGAAAGATGGA 57.395 33.333 0.00 0.00 0.00 3.41
2918 4157 5.923204 AGGAGGCAATAGTGAGACAATTAG 58.077 41.667 0.00 0.00 0.00 1.73
2924 4163 4.647399 ACTAAGAGGAGGCAATAGTGAGAC 59.353 45.833 0.00 0.00 0.00 3.36
2930 4169 8.592809 AGATAAATGACTAAGAGGAGGCAATAG 58.407 37.037 0.00 0.00 38.21 1.73
2946 4185 6.851330 CCGAGCGGAAAATAAAGATAAATGAC 59.149 38.462 2.00 0.00 37.50 3.06
2964 4203 2.074547 TTAAGAACAGTTCCGAGCGG 57.925 50.000 9.85 1.74 0.00 5.52
2966 4205 3.003480 AGCATTAAGAACAGTTCCGAGC 58.997 45.455 9.85 7.53 0.00 5.03
3017 4256 5.416271 AGTTCCACTACAAACATCGGTAT 57.584 39.130 0.00 0.00 0.00 2.73
3040 4279 6.996879 AGCATCTATGTATCTTGCAACATCTT 59.003 34.615 5.04 0.00 37.50 2.40
3121 4360 8.845227 TGCAAAAACTCTCAAACTACATATTGA 58.155 29.630 0.00 0.00 34.57 2.57
3122 4361 9.630098 ATGCAAAAACTCTCAAACTACATATTG 57.370 29.630 0.00 0.00 0.00 1.90
3123 4362 9.630098 CATGCAAAAACTCTCAAACTACATATT 57.370 29.630 0.00 0.00 0.00 1.28
3124 4363 8.796475 ACATGCAAAAACTCTCAAACTACATAT 58.204 29.630 0.00 0.00 0.00 1.78
3125 4364 8.075574 CACATGCAAAAACTCTCAAACTACATA 58.924 33.333 0.00 0.00 0.00 2.29
3126 4365 6.919662 CACATGCAAAAACTCTCAAACTACAT 59.080 34.615 0.00 0.00 0.00 2.29
3127 4366 6.094742 TCACATGCAAAAACTCTCAAACTACA 59.905 34.615 0.00 0.00 0.00 2.74
3128 4367 6.494842 TCACATGCAAAAACTCTCAAACTAC 58.505 36.000 0.00 0.00 0.00 2.73
3129 4368 6.691754 TCACATGCAAAAACTCTCAAACTA 57.308 33.333 0.00 0.00 0.00 2.24
3130 4369 5.581126 TCACATGCAAAAACTCTCAAACT 57.419 34.783 0.00 0.00 0.00 2.66
3139 4378 5.345741 AGCACGATATTTCACATGCAAAAAC 59.654 36.000 0.00 0.00 35.51 2.43
3146 4385 3.873361 ACTCCAGCACGATATTTCACATG 59.127 43.478 0.00 0.00 0.00 3.21
3150 4389 3.492656 GCCTACTCCAGCACGATATTTCA 60.493 47.826 0.00 0.00 0.00 2.69
3151 4390 3.060602 GCCTACTCCAGCACGATATTTC 58.939 50.000 0.00 0.00 0.00 2.17
3160 4399 0.970427 TGTCGATGCCTACTCCAGCA 60.970 55.000 0.00 0.00 44.45 4.41
3180 4426 7.716560 TCGCATAGATTAAGGTACACAGTAGTA 59.283 37.037 0.00 0.00 0.00 1.82
3184 4430 5.360144 ACTCGCATAGATTAAGGTACACAGT 59.640 40.000 0.00 0.00 0.00 3.55
3185 4431 5.833082 ACTCGCATAGATTAAGGTACACAG 58.167 41.667 0.00 0.00 0.00 3.66
3188 4434 9.656040 TTTAAAACTCGCATAGATTAAGGTACA 57.344 29.630 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.