Multiple sequence alignment - TraesCS7A01G128200

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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 TraesCS7A01G128200 chr7A 100.000 2441 0 0 1 2441 82175466 82177906 0.000000e+00 4508.0
1 TraesCS7A01G128200 chr7A 93.333 45 1 2 2333 2375 75674043 75674087 5.630000e-07 65.8
2 TraesCS7A01G128200 chr7D 89.710 1584 65 40 366 1877 79521627 79523184 0.000000e+00 1932.0
3 TraesCS7A01G128200 chr7D 88.923 325 18 12 64 372 79521115 79521437 3.810000e-103 385.0
4 TraesCS7A01G128200 chr7D 93.243 74 5 0 1962 2035 477857628 477857555 2.570000e-20 110.0
5 TraesCS7A01G128200 chr7D 80.469 128 15 4 1912 2039 420089906 420090023 3.340000e-14 89.8
6 TraesCS7A01G128200 chr7B 86.097 1194 70 51 714 1836 26691154 26692322 0.000000e+00 1197.0
7 TraesCS7A01G128200 chr7B 89.831 413 34 5 2034 2441 26692398 26692807 7.730000e-145 523.0
8 TraesCS7A01G128200 chr7B 90.263 380 19 6 366 729 26690768 26691145 4.720000e-132 481.0
9 TraesCS7A01G128200 chr7B 84.765 361 26 18 24 366 26690339 26690688 3.890000e-88 335.0
10 TraesCS7A01G128200 chr7B 97.674 43 1 0 1835 1877 26692357 26692399 9.360000e-10 75.0
11 TraesCS7A01G128200 chr7B 82.418 91 9 6 1879 1963 693317306 693317395 3.370000e-09 73.1
12 TraesCS7A01G128200 chr5B 91.743 109 9 0 2049 2157 272997612 272997720 4.200000e-33 152.0
13 TraesCS7A01G128200 chr5B 91.743 109 9 0 2049 2157 557738356 557738248 4.200000e-33 152.0
14 TraesCS7A01G128200 chr5B 90.826 109 10 0 2049 2157 253036994 253037102 1.960000e-31 147.0
15 TraesCS7A01G128200 chr5B 90.826 109 10 0 2049 2157 335976348 335976456 1.960000e-31 147.0
16 TraesCS7A01G128200 chr5B 78.889 180 26 11 1868 2039 491710543 491710368 7.130000e-21 111.0
17 TraesCS7A01G128200 chr5B 75.824 182 32 12 1869 2040 307879655 307879834 5.590000e-12 82.4
18 TraesCS7A01G128200 chr5B 93.182 44 1 2 1864 1907 704299426 704299385 2.030000e-06 63.9
19 TraesCS7A01G128200 chr3B 91.743 109 9 0 2049 2157 89816652 89816544 4.200000e-33 152.0
20 TraesCS7A01G128200 chr3B 91.743 109 9 0 2049 2157 220472503 220472611 4.200000e-33 152.0
21 TraesCS7A01G128200 chr3B 95.238 42 1 1 2335 2375 754207128 754207087 5.630000e-07 65.8
22 TraesCS7A01G128200 chr3B 88.679 53 6 0 1911 1963 801134515 801134463 5.630000e-07 65.8
23 TraesCS7A01G128200 chr2B 91.743 109 9 0 2049 2157 545923281 545923173 4.200000e-33 152.0
24 TraesCS7A01G128200 chr2B 93.243 74 5 0 1962 2035 368413487 368413414 2.570000e-20 110.0
25 TraesCS7A01G128200 chr2B 84.259 108 16 1 2335 2441 404204165 404204272 1.190000e-18 104.0
26 TraesCS7A01G128200 chr2B 75.135 185 31 14 1863 2036 756557004 756556824 3.370000e-09 73.1
27 TraesCS7A01G128200 chr6A 90.826 109 10 0 2049 2157 596281219 596281111 1.960000e-31 147.0
28 TraesCS7A01G128200 chr6A 78.261 161 20 9 1877 2037 400120828 400120683 3.340000e-14 89.8
29 TraesCS7A01G128200 chr3D 80.000 170 22 11 1875 2035 612268615 612268449 5.520000e-22 115.0
30 TraesCS7A01G128200 chr3D 82.258 124 12 2 1907 2030 583473350 583473237 5.550000e-17 99.0
31 TraesCS7A01G128200 chr2A 83.721 129 11 3 1907 2035 342647517 342647399 1.980000e-21 113.0
32 TraesCS7A01G128200 chr2A 95.122 41 1 1 2337 2376 72393530 72393570 2.030000e-06 63.9
33 TraesCS7A01G128200 chr2D 80.000 165 22 10 1879 2035 291992054 291991893 7.130000e-21 111.0
34 TraesCS7A01G128200 chr2D 92.105 76 5 1 1962 2037 53197245 53197319 3.320000e-19 106.0
35 TraesCS7A01G128200 chr2D 92.000 75 6 0 1962 2036 586930853 586930927 3.320000e-19 106.0
36 TraesCS7A01G128200 chr4A 93.243 74 5 0 1962 2035 729053690 729053763 2.570000e-20 110.0
37 TraesCS7A01G128200 chr4A 77.011 174 28 10 1869 2034 727265113 727264944 3.340000e-14 89.8
38 TraesCS7A01G128200 chr4B 82.222 135 13 5 1912 2045 506925051 506924927 3.320000e-19 106.0
39 TraesCS7A01G128200 chr3A 79.290 169 20 13 1879 2037 28077268 28077431 1.190000e-18 104.0
40 TraesCS7A01G128200 chr3A 81.452 124 13 2 1912 2035 459048378 459048491 2.580000e-15 93.5
41 TraesCS7A01G128200 chr3A 95.238 42 1 1 2336 2376 721225112 721225071 5.630000e-07 65.8
42 TraesCS7A01G128200 chr6B 77.419 186 29 12 1861 2036 17806052 17806234 5.550000e-17 99.0
43 TraesCS7A01G128200 chr6B 79.091 110 13 2 1917 2026 568047957 568048056 1.570000e-07 67.6
44 TraesCS7A01G128200 chr6B 77.778 126 17 4 1912 2036 701379994 701380109 1.570000e-07 67.6
45 TraesCS7A01G128200 chr4D 95.238 42 1 1 2336 2376 98521584 98521543 5.630000e-07 65.8
46 TraesCS7A01G128200 chr4D 95.122 41 1 1 2338 2377 139073471 139073431 2.030000e-06 63.9
47 TraesCS7A01G128200 chr1A 95.122 41 1 1 2336 2375 513704947 513704907 2.030000e-06 63.9
48 TraesCS7A01G128200 chr1A 81.081 74 13 1 2369 2441 328822845 328822918 9.430000e-05 58.4
49 TraesCS7A01G128200 chr1D 81.081 74 13 1 2369 2441 256110029 256110102 9.430000e-05 58.4


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 TraesCS7A01G128200 chr7A 82175466 82177906 2440 False 4508.0 4508 100.0000 1 2441 1 chr7A.!!$F2 2440
1 TraesCS7A01G128200 chr7D 79521115 79523184 2069 False 1158.5 1932 89.3165 64 1877 2 chr7D.!!$F2 1813
2 TraesCS7A01G128200 chr7B 26690339 26692807 2468 False 522.2 1197 89.7260 24 2441 5 chr7B.!!$F2 2417

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
330 353 0.036105 TTGGCTGCTCGATCACACAT 60.036 50.0 0.0 0.0 0.0 3.21 F
1305 1619 0.040058 AGCCATCCCTGTGCAATGAA 59.960 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1701 0.110104 CCATCATCCTCCTCCTTGGC 59.890 60.0 0.0 0.0 35.26 4.52 R
2299 2694 0.540923 GCAGAGCATGGAACTCCTCT 59.459 55.0 0.0 0.0 34.56 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
48 49 1.002868 GCAGTGGCAGTGGTCTGAT 60.003 57.895 22.98 0.00 43.76 2.90
49 50 0.250234 GCAGTGGCAGTGGTCTGATA 59.750 55.000 22.98 0.00 43.76 2.15
50 51 1.134280 GCAGTGGCAGTGGTCTGATAT 60.134 52.381 22.98 0.00 43.76 1.63
51 52 2.558378 CAGTGGCAGTGGTCTGATATG 58.442 52.381 14.66 0.00 43.76 1.78
52 53 1.134280 AGTGGCAGTGGTCTGATATGC 60.134 52.381 0.00 0.00 43.76 3.14
53 54 1.134280 GTGGCAGTGGTCTGATATGCT 60.134 52.381 0.00 0.00 43.76 3.79
54 55 1.139654 TGGCAGTGGTCTGATATGCTC 59.860 52.381 0.00 0.00 43.76 4.26
55 56 1.415659 GGCAGTGGTCTGATATGCTCT 59.584 52.381 0.00 0.00 43.76 4.09
57 58 3.553922 GGCAGTGGTCTGATATGCTCTAC 60.554 52.174 0.00 0.00 43.76 2.59
58 59 3.320541 GCAGTGGTCTGATATGCTCTACT 59.679 47.826 0.00 0.00 43.76 2.57
59 60 4.520874 GCAGTGGTCTGATATGCTCTACTA 59.479 45.833 0.00 0.00 43.76 1.82
60 61 5.563867 GCAGTGGTCTGATATGCTCTACTAC 60.564 48.000 0.00 0.00 43.76 2.73
61 62 5.532779 CAGTGGTCTGATATGCTCTACTACA 59.467 44.000 0.00 0.00 43.76 2.74
62 63 5.533154 AGTGGTCTGATATGCTCTACTACAC 59.467 44.000 0.00 0.00 30.06 2.90
63 64 5.299531 GTGGTCTGATATGCTCTACTACACA 59.700 44.000 0.00 0.00 0.00 3.72
64 65 6.015856 GTGGTCTGATATGCTCTACTACACAT 60.016 42.308 0.00 0.00 0.00 3.21
65 66 6.551227 TGGTCTGATATGCTCTACTACACATT 59.449 38.462 0.00 0.00 0.00 2.71
124 130 1.282738 TGCATATCGATCCCCATGCAT 59.717 47.619 23.27 0.00 46.46 3.96
146 153 1.138859 CACATGAATACGGCAGGGAGA 59.861 52.381 0.00 0.00 0.00 3.71
148 155 0.394565 ATGAATACGGCAGGGAGAGC 59.605 55.000 0.00 0.00 0.00 4.09
151 158 1.739338 AATACGGCAGGGAGAGCGAG 61.739 60.000 0.00 0.00 0.00 5.03
152 159 2.626255 ATACGGCAGGGAGAGCGAGA 62.626 60.000 0.00 0.00 0.00 4.04
177 186 2.653890 CCATTGTTTGACGTGAGCTTG 58.346 47.619 0.00 0.00 0.00 4.01
201 210 3.439293 AGCGAGTCGTTTGATGAGTATG 58.561 45.455 15.08 0.00 0.00 2.39
252 261 1.622811 TGGTTTGCCCATTTCCATGTC 59.377 47.619 0.00 0.00 38.72 3.06
293 306 2.229543 GAGTGGCTGTTTCATTCATGCA 59.770 45.455 0.00 0.00 0.00 3.96
294 307 2.829720 AGTGGCTGTTTCATTCATGCAT 59.170 40.909 0.00 0.00 0.00 3.96
297 310 2.418197 GGCTGTTTCATTCATGCATGCT 60.418 45.455 22.25 8.75 0.00 3.79
298 311 3.181484 GGCTGTTTCATTCATGCATGCTA 60.181 43.478 22.25 12.43 0.00 3.49
299 312 4.042398 GCTGTTTCATTCATGCATGCTAG 58.958 43.478 22.25 12.98 0.00 3.42
300 313 4.036567 TGTTTCATTCATGCATGCTAGC 57.963 40.909 22.25 8.10 0.00 3.42
315 328 0.873743 CTAGCAGAGTAGCGCTTGGC 60.874 60.000 18.68 12.74 39.70 4.52
325 338 2.510012 CGCTTGGCTGCTCGATCA 60.510 61.111 0.00 0.00 0.00 2.92
326 339 2.806856 CGCTTGGCTGCTCGATCAC 61.807 63.158 0.00 0.00 0.00 3.06
327 340 1.742880 GCTTGGCTGCTCGATCACA 60.743 57.895 0.00 0.00 0.00 3.58
330 353 0.036105 TTGGCTGCTCGATCACACAT 60.036 50.000 0.00 0.00 0.00 3.21
384 606 8.474577 GCAAGAAATATATGCAGTCAAATTTCG 58.525 33.333 12.91 5.79 39.81 3.46
442 670 0.809241 CATGCTTGGAGAGAGACCGC 60.809 60.000 0.00 0.00 0.00 5.68
443 675 2.202676 GCTTGGAGAGAGACCGCG 60.203 66.667 0.00 0.00 0.00 6.46
469 701 0.463204 GCTGCTAGATGCTGGACTGA 59.537 55.000 0.00 0.00 43.37 3.41
669 909 3.009115 TACAGTGGCCTCCCCTGC 61.009 66.667 3.32 0.00 34.58 4.85
693 933 2.347322 GCCAGGACTCTGTCGCTCT 61.347 63.158 0.00 0.00 39.31 4.09
694 934 1.806568 CCAGGACTCTGTCGCTCTC 59.193 63.158 0.00 0.00 39.31 3.20
695 935 0.679640 CCAGGACTCTGTCGCTCTCT 60.680 60.000 0.00 0.00 39.31 3.10
696 936 0.732571 CAGGACTCTGTCGCTCTCTC 59.267 60.000 0.00 0.00 36.30 3.20
697 937 0.393808 AGGACTCTGTCGCTCTCTCC 60.394 60.000 0.00 0.00 32.65 3.71
698 938 0.678366 GGACTCTGTCGCTCTCTCCA 60.678 60.000 0.00 0.00 32.65 3.86
701 941 0.307453 CTCTGTCGCTCTCTCCATCG 59.693 60.000 0.00 0.00 0.00 3.84
702 942 1.299014 CTGTCGCTCTCTCCATCGC 60.299 63.158 0.00 0.00 0.00 4.58
703 943 2.026879 GTCGCTCTCTCCATCGCC 59.973 66.667 0.00 0.00 0.00 5.54
721 963 1.218585 CTGTGCTGCCAGAGAGAGG 59.781 63.158 11.25 0.00 34.44 3.69
729 971 1.109323 GCCAGAGAGAGGGAGAGAGC 61.109 65.000 0.00 0.00 0.00 4.09
730 972 0.552848 CCAGAGAGAGGGAGAGAGCT 59.447 60.000 0.00 0.00 0.00 4.09
731 973 1.063717 CCAGAGAGAGGGAGAGAGCTT 60.064 57.143 0.00 0.00 0.00 3.74
744 1018 4.036734 GGAGAGAGCTTGACTGAGAGTATG 59.963 50.000 0.00 0.00 0.00 2.39
751 1025 4.677584 CTTGACTGAGAGTATGTGGCTAC 58.322 47.826 0.00 0.00 0.00 3.58
762 1036 0.327924 TGTGGCTACCCAAGTCCATG 59.672 55.000 0.00 0.00 44.33 3.66
802 1086 1.421646 GGGGAGAGAGAGAGAGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
806 1094 3.244249 GGAGAGAGAGAGAGAGAGGCTAC 60.244 56.522 0.00 0.00 0.00 3.58
901 1190 2.004733 GTCGCCAGTACAAATACCCAC 58.995 52.381 0.00 0.00 30.88 4.61
923 1212 1.597854 CGCTTCACTCCACTTGCCA 60.598 57.895 0.00 0.00 0.00 4.92
963 1252 1.755380 GCCCTCTTCTACCTTCGCTAA 59.245 52.381 0.00 0.00 0.00 3.09
1239 1547 4.880537 CCTAGACGGGCAGCAGCG 62.881 72.222 0.00 0.00 43.41 5.18
1282 1590 0.186386 CTATCCTCCTCCTCCACCGT 59.814 60.000 0.00 0.00 0.00 4.83
1298 1612 2.821366 GTCGCAGCCATCCCTGTG 60.821 66.667 0.00 0.00 43.03 3.66
1305 1619 0.040058 AGCCATCCCTGTGCAATGAA 59.960 50.000 0.00 0.00 0.00 2.57
1307 1621 1.843368 CCATCCCTGTGCAATGAACT 58.157 50.000 0.00 0.00 0.00 3.01
1316 1630 0.317160 TGCAATGAACTCTCGTCGGT 59.683 50.000 0.00 0.00 0.00 4.69
1343 1657 2.125106 GAGCACAGGGGCGTTAGG 60.125 66.667 0.00 0.00 39.27 2.69
1460 1774 4.997565 TGATCGATCGAGCATATGCATAA 58.002 39.130 30.45 13.63 45.16 1.90
1486 1803 9.635404 ACATTCTCTAGTCTAGCTAATTACTGT 57.365 33.333 11.47 0.00 0.00 3.55
1527 1868 6.056884 TCTCTAGTTAGTTCTAGCAGTAGCC 58.943 44.000 0.00 0.00 43.56 3.93
1576 1917 3.317711 TGAATTGGTGTTTGCTTCATCGT 59.682 39.130 0.00 0.00 0.00 3.73
1577 1918 3.559238 ATTGGTGTTTGCTTCATCGTC 57.441 42.857 0.00 0.00 0.00 4.20
1584 1925 4.024893 GTGTTTGCTTCATCGTCTCTTCAA 60.025 41.667 0.00 0.00 0.00 2.69
1590 1931 6.108687 TGCTTCATCGTCTCTTCAATGTATT 58.891 36.000 0.00 0.00 0.00 1.89
1612 1953 9.783256 GTATTATTAGTTCGGCTTTGATGTTTT 57.217 29.630 0.00 0.00 0.00 2.43
1641 1988 4.894114 AGCTAGGTATCTATGGTCGTGTTT 59.106 41.667 0.00 0.00 0.00 2.83
1650 1997 9.017669 GTATCTATGGTCGTGTTTACTGTTTAG 57.982 37.037 0.00 0.00 0.00 1.85
1651 1998 7.218228 TCTATGGTCGTGTTTACTGTTTAGA 57.782 36.000 0.00 0.00 0.00 2.10
1663 2014 4.910458 ACTGTTTAGAATGGTACTGCCT 57.090 40.909 0.00 0.00 38.35 4.75
1732 2084 1.399714 TGTCTCTCTCACGTGGTGTT 58.600 50.000 17.00 0.00 34.79 3.32
1808 2164 2.094752 ACGCAGACATATTGCCCAAAAC 60.095 45.455 0.00 0.00 38.31 2.43
1830 2186 7.722949 AACGGGATCGGGAAACTATATTATA 57.277 36.000 0.00 0.00 41.39 0.98
1877 2272 7.501225 AGCCCCAACACTACAATACATAAATAC 59.499 37.037 0.00 0.00 0.00 1.89
1878 2273 7.501225 GCCCCAACACTACAATACATAAATACT 59.499 37.037 0.00 0.00 0.00 2.12
1888 2283 7.893658 ACAATACATAAATACTACTCCCTCCG 58.106 38.462 0.00 0.00 0.00 4.63
1889 2284 7.508296 ACAATACATAAATACTACTCCCTCCGT 59.492 37.037 0.00 0.00 0.00 4.69
1890 2285 8.365647 CAATACATAAATACTACTCCCTCCGTT 58.634 37.037 0.00 0.00 0.00 4.44
1891 2286 6.402456 ACATAAATACTACTCCCTCCGTTC 57.598 41.667 0.00 0.00 0.00 3.95
1892 2287 5.303845 ACATAAATACTACTCCCTCCGTTCC 59.696 44.000 0.00 0.00 0.00 3.62
1893 2288 3.684408 AATACTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
1894 2289 4.803329 AATACTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
1895 2290 4.803329 ATACTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
1896 2291 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1897 2292 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1898 2293 3.705072 ACTACTCCCTCCGTTCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
1899 2294 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
1900 2295 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
1901 2296 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
1902 2297 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
1903 2298 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
1904 2299 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
1905 2300 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
1906 2301 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1907 2302 6.127253 CCCTCCGTTCCTAAATGTAAGTCTTA 60.127 42.308 0.00 0.00 0.00 2.10
1908 2303 7.418712 CCCTCCGTTCCTAAATGTAAGTCTTAT 60.419 40.741 0.00 0.00 0.00 1.73
1909 2304 7.438459 CCTCCGTTCCTAAATGTAAGTCTTATG 59.562 40.741 0.00 0.00 0.00 1.90
1910 2305 8.070034 TCCGTTCCTAAATGTAAGTCTTATGA 57.930 34.615 0.00 0.00 0.00 2.15
1911 2306 8.533657 TCCGTTCCTAAATGTAAGTCTTATGAA 58.466 33.333 0.00 0.00 0.00 2.57
1912 2307 8.601476 CCGTTCCTAAATGTAAGTCTTATGAAC 58.399 37.037 0.00 0.00 31.90 3.18
1913 2308 9.367444 CGTTCCTAAATGTAAGTCTTATGAACT 57.633 33.333 0.00 0.00 32.51 3.01
1968 2363 9.809096 GAGTATAGATTCACTCATTTTCACTCA 57.191 33.333 0.00 0.00 40.74 3.41
1974 2369 9.688592 AGATTCACTCATTTTCACTCATTTTTC 57.311 29.630 0.00 0.00 0.00 2.29
1975 2370 9.688592 GATTCACTCATTTTCACTCATTTTTCT 57.311 29.630 0.00 0.00 0.00 2.52
1977 2372 9.520204 TTCACTCATTTTCACTCATTTTTCTTC 57.480 29.630 0.00 0.00 0.00 2.87
1978 2373 7.857389 TCACTCATTTTCACTCATTTTTCTTCG 59.143 33.333 0.00 0.00 0.00 3.79
1979 2374 7.645340 CACTCATTTTCACTCATTTTTCTTCGT 59.355 33.333 0.00 0.00 0.00 3.85
1980 2375 8.836413 ACTCATTTTCACTCATTTTTCTTCGTA 58.164 29.630 0.00 0.00 0.00 3.43
1981 2376 9.107367 CTCATTTTCACTCATTTTTCTTCGTAC 57.893 33.333 0.00 0.00 0.00 3.67
1982 2377 7.796660 TCATTTTCACTCATTTTTCTTCGTACG 59.203 33.333 9.53 9.53 0.00 3.67
1983 2378 6.592798 TTTCACTCATTTTTCTTCGTACGT 57.407 33.333 16.05 0.00 0.00 3.57
1984 2379 7.697352 TTTCACTCATTTTTCTTCGTACGTA 57.303 32.000 16.05 4.53 0.00 3.57
1985 2380 6.922980 TCACTCATTTTTCTTCGTACGTAG 57.077 37.500 16.05 15.48 0.00 3.51
1987 2382 6.580041 TCACTCATTTTTCTTCGTACGTAGTC 59.420 38.462 19.49 0.00 43.93 2.59
1988 2383 5.860716 ACTCATTTTTCTTCGTACGTAGTCC 59.139 40.000 19.49 0.00 43.93 3.85
1989 2384 5.771469 TCATTTTTCTTCGTACGTAGTCCA 58.229 37.500 19.49 4.81 43.93 4.02
1990 2385 6.392354 TCATTTTTCTTCGTACGTAGTCCAT 58.608 36.000 19.49 7.14 43.93 3.41
1991 2386 7.537715 TCATTTTTCTTCGTACGTAGTCCATA 58.462 34.615 19.49 0.00 43.93 2.74
1992 2387 8.192774 TCATTTTTCTTCGTACGTAGTCCATAT 58.807 33.333 19.49 7.37 43.93 1.78
1993 2388 8.814235 CATTTTTCTTCGTACGTAGTCCATATT 58.186 33.333 19.49 0.71 43.93 1.28
1994 2389 7.745022 TTTTCTTCGTACGTAGTCCATATTG 57.255 36.000 19.49 0.00 43.93 1.90
1995 2390 4.852138 TCTTCGTACGTAGTCCATATTGC 58.148 43.478 19.49 0.00 43.93 3.56
1996 2391 4.336153 TCTTCGTACGTAGTCCATATTGCA 59.664 41.667 19.49 0.00 43.93 4.08
1997 2392 4.635833 TCGTACGTAGTCCATATTGCAA 57.364 40.909 16.05 0.00 43.93 4.08
1998 2393 5.190992 TCGTACGTAGTCCATATTGCAAT 57.809 39.130 17.56 17.56 43.93 3.56
1999 2394 5.217393 TCGTACGTAGTCCATATTGCAATC 58.783 41.667 16.86 0.52 43.93 2.67
2000 2395 5.009310 TCGTACGTAGTCCATATTGCAATCT 59.991 40.000 16.86 8.98 43.93 2.40
2001 2396 5.690409 CGTACGTAGTCCATATTGCAATCTT 59.310 40.000 16.86 1.71 43.93 2.40
2002 2397 6.200286 CGTACGTAGTCCATATTGCAATCTTT 59.800 38.462 16.86 0.00 43.93 2.52
2003 2398 7.380333 CGTACGTAGTCCATATTGCAATCTTTA 59.620 37.037 16.86 0.00 43.93 1.85
2004 2399 9.037737 GTACGTAGTCCATATTGCAATCTTTAA 57.962 33.333 16.86 0.00 43.93 1.52
2005 2400 8.500753 ACGTAGTCCATATTGCAATCTTTAAA 57.499 30.769 16.86 0.00 29.74 1.52
2006 2401 8.952278 ACGTAGTCCATATTGCAATCTTTAAAA 58.048 29.630 16.86 0.00 29.74 1.52
2007 2402 9.781834 CGTAGTCCATATTGCAATCTTTAAAAA 57.218 29.630 16.86 0.00 0.00 1.94
2010 2405 9.860898 AGTCCATATTGCAATCTTTAAAAAGAC 57.139 29.630 16.86 10.52 46.80 3.01
2011 2406 9.860898 GTCCATATTGCAATCTTTAAAAAGACT 57.139 29.630 16.86 0.00 46.80 3.24
2028 2423 8.515695 AAAAAGACTTATATTTAGGAACGGGG 57.484 34.615 0.00 0.00 0.00 5.73
2029 2424 5.820404 AGACTTATATTTAGGAACGGGGG 57.180 43.478 0.00 0.00 0.00 5.40
2053 2448 9.416284 GGGGAGTATAAAATTTCCAATGACTAA 57.584 33.333 0.00 0.00 0.00 2.24
2104 2499 1.216990 AATGGCGAGGGAGGAAATCT 58.783 50.000 0.00 0.00 0.00 2.40
2106 2501 0.909610 TGGCGAGGGAGGAAATCTGT 60.910 55.000 0.00 0.00 0.00 3.41
2107 2502 0.253327 GGCGAGGGAGGAAATCTGTT 59.747 55.000 0.00 0.00 0.00 3.16
2129 2524 8.768957 TGTTTGACAAATGTTGAAGAAAATGA 57.231 26.923 3.49 0.00 0.00 2.57
2130 2525 8.655092 TGTTTGACAAATGTTGAAGAAAATGAC 58.345 29.630 3.49 0.00 0.00 3.06
2136 2531 6.753897 AATGTTGAAGAAAATGACGAAAGC 57.246 33.333 0.00 0.00 0.00 3.51
2154 2549 1.919340 CACAGTTTGCTTTGTGCGC 59.081 52.632 0.00 0.00 46.63 6.09
2155 2550 0.801451 CACAGTTTGCTTTGTGCGCA 60.801 50.000 5.66 5.66 46.63 6.09
2162 2557 2.352229 CTTTGTGCGCACACCACG 60.352 61.111 40.84 24.38 46.86 4.94
2169 2564 2.355837 CGCACACCACGTAGCTGT 60.356 61.111 0.00 0.00 0.00 4.40
2170 2565 2.657757 CGCACACCACGTAGCTGTG 61.658 63.158 12.74 12.74 38.68 3.66
2231 2626 9.477484 AAGTTAGACAGAAAACTATAGTGTGTG 57.523 33.333 6.06 9.00 34.91 3.82
2233 2628 6.420913 AGACAGAAAACTATAGTGTGTGGT 57.579 37.500 6.06 2.95 0.00 4.16
2298 2693 5.132502 TGTTGGACATGTCAGATTTGAACT 58.867 37.500 26.47 0.00 34.49 3.01
2299 2694 6.295249 TGTTGGACATGTCAGATTTGAACTA 58.705 36.000 26.47 1.01 34.49 2.24
2303 2698 5.814705 GGACATGTCAGATTTGAACTAGAGG 59.185 44.000 26.47 0.00 34.49 3.69
2341 2737 7.093354 TGCTAAGAGTGATTGTTAAGAGAGTG 58.907 38.462 0.00 0.00 0.00 3.51
2342 2738 6.533367 GCTAAGAGTGATTGTTAAGAGAGTGG 59.467 42.308 0.00 0.00 0.00 4.00
2353 2749 5.309543 TGTTAAGAGAGTGGATTTTCTCCCA 59.690 40.000 0.00 0.00 44.23 4.37
2413 2812 2.390225 TTGGTTTAACCCCTGCATGT 57.610 45.000 12.02 0.00 37.50 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.044966 GCACGTAGTAAATTAACATGATGCAAC 60.045 37.037 0.00 0.00 41.61 4.17
2 3 6.092807 TGCACGTAGTAAATTAACATGATGCA 59.907 34.615 0.00 0.00 41.61 3.96
3 4 6.482835 TGCACGTAGTAAATTAACATGATGC 58.517 36.000 0.00 0.00 41.61 3.91
4 5 7.161900 CGTTGCACGTAGTAAATTAACATGATG 59.838 37.037 0.00 0.00 41.61 3.07
5 6 7.177407 CGTTGCACGTAGTAAATTAACATGAT 58.823 34.615 0.00 0.00 41.61 2.45
6 7 6.527089 CGTTGCACGTAGTAAATTAACATGA 58.473 36.000 0.00 0.00 41.61 3.07
7 8 5.224313 GCGTTGCACGTAGTAAATTAACATG 59.776 40.000 9.76 0.00 44.73 3.21
8 9 5.107026 TGCGTTGCACGTAGTAAATTAACAT 60.107 36.000 9.76 0.00 44.73 2.71
9 10 4.210746 TGCGTTGCACGTAGTAAATTAACA 59.789 37.500 9.76 0.00 44.73 2.41
10 11 4.700332 TGCGTTGCACGTAGTAAATTAAC 58.300 39.130 9.76 0.00 44.73 2.01
11 12 4.948588 CTGCGTTGCACGTAGTAAATTAA 58.051 39.130 14.95 0.00 46.68 1.40
12 13 4.571375 CTGCGTTGCACGTAGTAAATTA 57.429 40.909 14.95 0.00 46.68 1.40
13 14 3.449322 CTGCGTTGCACGTAGTAAATT 57.551 42.857 14.95 0.00 46.68 1.82
20 21 3.342627 GCCACTGCGTTGCACGTA 61.343 61.111 9.76 5.24 44.73 3.57
22 23 4.671549 CTGCCACTGCGTTGCACG 62.672 66.667 3.93 4.61 45.88 5.34
48 49 7.726216 AGCATGTAAATGTGTAGTAGAGCATA 58.274 34.615 0.00 0.00 0.00 3.14
49 50 6.586344 AGCATGTAAATGTGTAGTAGAGCAT 58.414 36.000 0.00 0.00 0.00 3.79
50 51 5.977635 AGCATGTAAATGTGTAGTAGAGCA 58.022 37.500 0.00 0.00 0.00 4.26
51 52 5.463724 GGAGCATGTAAATGTGTAGTAGAGC 59.536 44.000 0.00 0.00 0.00 4.09
52 53 6.699204 CAGGAGCATGTAAATGTGTAGTAGAG 59.301 42.308 0.00 0.00 0.00 2.43
53 54 6.573434 CAGGAGCATGTAAATGTGTAGTAGA 58.427 40.000 0.00 0.00 0.00 2.59
54 55 5.235186 GCAGGAGCATGTAAATGTGTAGTAG 59.765 44.000 0.00 0.00 41.58 2.57
55 56 5.104941 AGCAGGAGCATGTAAATGTGTAGTA 60.105 40.000 0.00 0.00 45.49 1.82
57 58 4.034858 CAGCAGGAGCATGTAAATGTGTAG 59.965 45.833 0.00 0.00 45.49 2.74
58 59 3.940852 CAGCAGGAGCATGTAAATGTGTA 59.059 43.478 0.00 0.00 45.49 2.90
59 60 2.751259 CAGCAGGAGCATGTAAATGTGT 59.249 45.455 0.00 0.00 45.49 3.72
60 61 2.479049 GCAGCAGGAGCATGTAAATGTG 60.479 50.000 0.00 0.00 45.49 3.21
61 62 1.747355 GCAGCAGGAGCATGTAAATGT 59.253 47.619 0.00 0.00 45.49 2.71
62 63 1.066605 GGCAGCAGGAGCATGTAAATG 59.933 52.381 0.00 0.00 45.49 2.32
63 64 1.341285 TGGCAGCAGGAGCATGTAAAT 60.341 47.619 0.00 0.00 45.49 1.40
64 65 0.038021 TGGCAGCAGGAGCATGTAAA 59.962 50.000 0.00 0.00 45.49 2.01
65 66 0.393402 CTGGCAGCAGGAGCATGTAA 60.393 55.000 0.00 0.00 45.49 2.41
124 130 0.747644 CCCTGCCGTATTCATGTGCA 60.748 55.000 0.00 0.00 0.00 4.57
146 153 2.748058 AAACAATGGCCGGTCTCGCT 62.748 55.000 7.97 0.00 34.56 4.93
148 155 0.953471 TCAAACAATGGCCGGTCTCG 60.953 55.000 7.97 0.00 0.00 4.04
151 158 1.209127 CGTCAAACAATGGCCGGTC 59.791 57.895 0.00 0.00 0.00 4.79
152 159 1.527380 ACGTCAAACAATGGCCGGT 60.527 52.632 1.90 0.00 0.00 5.28
177 186 1.656095 CTCATCAAACGACTCGCTTCC 59.344 52.381 0.00 0.00 0.00 3.46
201 210 0.822532 CTGCCTCATTCTCCCATGCC 60.823 60.000 0.00 0.00 0.00 4.40
252 261 5.509927 CTCGAGTGGAGAGGTACAAACCG 62.510 56.522 3.62 0.00 46.23 4.44
283 296 3.139077 CTCTGCTAGCATGCATGAATGA 58.861 45.455 30.64 15.65 42.48 2.57
293 306 0.749649 AAGCGCTACTCTGCTAGCAT 59.250 50.000 19.72 6.17 41.46 3.79
294 307 0.179127 CAAGCGCTACTCTGCTAGCA 60.179 55.000 18.22 18.22 41.46 3.49
297 310 1.141881 GCCAAGCGCTACTCTGCTA 59.858 57.895 12.05 0.00 41.46 3.49
298 311 2.125350 GCCAAGCGCTACTCTGCT 60.125 61.111 12.05 0.00 44.97 4.24
309 322 1.742880 TGTGATCGAGCAGCCAAGC 60.743 57.895 2.20 0.00 0.00 4.01
315 328 0.651031 CTGCATGTGTGATCGAGCAG 59.349 55.000 2.20 3.87 42.69 4.24
321 334 7.279536 TCTCTTAATTTCTCTGCATGTGTGATC 59.720 37.037 0.00 0.00 0.00 2.92
322 335 7.108194 TCTCTTAATTTCTCTGCATGTGTGAT 58.892 34.615 0.00 0.00 0.00 3.06
323 336 6.466812 TCTCTTAATTTCTCTGCATGTGTGA 58.533 36.000 0.00 0.00 0.00 3.58
325 338 5.879223 CCTCTCTTAATTTCTCTGCATGTGT 59.121 40.000 0.00 0.00 0.00 3.72
326 339 5.220815 GCCTCTCTTAATTTCTCTGCATGTG 60.221 44.000 0.00 0.00 0.00 3.21
327 340 4.880696 GCCTCTCTTAATTTCTCTGCATGT 59.119 41.667 0.00 0.00 0.00 3.21
330 353 4.558226 TGCCTCTCTTAATTTCTCTGCA 57.442 40.909 0.00 0.00 0.00 4.41
442 670 0.247974 GCATCTAGCAGCTTTGCACG 60.248 55.000 15.95 0.00 44.79 5.34
443 675 3.618774 GCATCTAGCAGCTTTGCAC 57.381 52.632 15.95 0.00 44.79 4.57
456 688 0.035630 GCCACTTCAGTCCAGCATCT 60.036 55.000 0.00 0.00 0.00 2.90
469 701 1.319614 AACAAACCGCAGTGCCACTT 61.320 50.000 10.11 0.00 0.00 3.16
669 909 3.465403 CAGAGTCCTGGCCGGGAG 61.465 72.222 34.74 18.43 36.77 4.30
701 941 2.436292 CTCTCTGGCAGCACAGGC 60.436 66.667 10.34 0.00 38.98 4.85
702 942 1.218585 CTCTCTCTGGCAGCACAGG 59.781 63.158 10.34 0.00 38.98 4.00
703 943 1.218585 CCTCTCTCTGGCAGCACAG 59.781 63.158 10.34 2.07 39.84 3.66
721 963 2.446435 ACTCTCAGTCAAGCTCTCTCC 58.554 52.381 0.00 0.00 0.00 3.71
729 971 3.883830 AGCCACATACTCTCAGTCAAG 57.116 47.619 0.00 0.00 0.00 3.02
730 972 3.447586 GGTAGCCACATACTCTCAGTCAA 59.552 47.826 0.00 0.00 0.00 3.18
731 973 3.024547 GGTAGCCACATACTCTCAGTCA 58.975 50.000 0.00 0.00 0.00 3.41
744 1018 0.394352 CCATGGACTTGGGTAGCCAC 60.394 60.000 14.60 2.40 34.37 5.01
751 1025 0.105862 ATCATGGCCATGGACTTGGG 60.106 55.000 38.81 16.50 39.24 4.12
762 1036 3.755434 GGCAGTGCTATCATGGCC 58.245 61.111 16.11 0.00 37.20 5.36
802 1086 1.406069 CCCAGTCCATCACACAGTAGC 60.406 57.143 0.00 0.00 0.00 3.58
806 1094 0.686789 TGTCCCAGTCCATCACACAG 59.313 55.000 0.00 0.00 0.00 3.66
856 1144 1.678970 CAGGTAAGCTTGGTGGCCC 60.679 63.158 9.86 0.00 0.00 5.80
857 1145 0.960861 GACAGGTAAGCTTGGTGGCC 60.961 60.000 9.86 0.00 0.00 5.36
858 1146 0.960861 GGACAGGTAAGCTTGGTGGC 60.961 60.000 9.86 5.51 0.00 5.01
859 1147 0.693049 AGGACAGGTAAGCTTGGTGG 59.307 55.000 9.86 0.00 0.00 4.61
862 1150 1.072331 ACACAGGACAGGTAAGCTTGG 59.928 52.381 9.86 0.00 0.00 3.61
901 1190 1.302033 AAGTGGAGTGAAGCGGCAG 60.302 57.895 1.45 0.00 0.00 4.85
923 1212 1.422781 CTGGCTGGATGTATGGGTCAT 59.577 52.381 0.00 0.00 0.00 3.06
963 1252 1.064946 CAGAAGTAGCTAGCGCGCT 59.935 57.895 38.01 38.01 43.83 5.92
966 1255 2.733517 CCTTACAGAAGTAGCTAGCGC 58.266 52.381 9.55 0.00 0.00 5.92
967 1256 2.359531 AGCCTTACAGAAGTAGCTAGCG 59.640 50.000 9.55 0.00 32.02 4.26
968 1257 3.549221 CGAGCCTTACAGAAGTAGCTAGC 60.549 52.174 6.62 6.62 33.42 3.42
969 1258 3.878103 TCGAGCCTTACAGAAGTAGCTAG 59.122 47.826 0.00 0.00 33.42 3.42
1179 1469 3.649652 AAGCTGAGGAGGGGGAGGG 62.650 68.421 0.00 0.00 0.00 4.30
1185 1475 2.438075 GCAGCAAGCTGAGGAGGG 60.438 66.667 25.03 0.00 46.30 4.30
1239 1547 4.189580 TTGGGGATAGCTGCCGCC 62.190 66.667 17.84 15.89 37.54 6.13
1242 1550 1.149401 GAGGTTGGGGATAGCTGCC 59.851 63.158 0.00 0.00 0.00 4.85
1282 1590 4.783621 GCACAGGGATGGCTGCGA 62.784 66.667 0.00 0.00 0.00 5.10
1328 1642 3.562732 AACCCTAACGCCCCTGTGC 62.563 63.158 0.00 0.00 0.00 4.57
1387 1701 0.110104 CCATCATCCTCCTCCTTGGC 59.890 60.000 0.00 0.00 35.26 4.52
1398 1712 3.806507 GCTCAAGATCCAGACCATCATCC 60.807 52.174 0.00 0.00 0.00 3.51
1460 1774 9.635404 ACAGTAATTAGCTAGACTAGAGAATGT 57.365 33.333 13.91 4.80 30.79 2.71
1482 1799 4.838986 AGAACCAACCTAGTGATGTACAGT 59.161 41.667 0.33 0.00 36.09 3.55
1483 1800 5.186021 AGAGAACCAACCTAGTGATGTACAG 59.814 44.000 0.33 0.00 0.00 2.74
1484 1801 5.084519 AGAGAACCAACCTAGTGATGTACA 58.915 41.667 0.00 0.00 0.00 2.90
1485 1802 5.662674 AGAGAACCAACCTAGTGATGTAC 57.337 43.478 0.00 0.00 0.00 2.90
1486 1803 6.491383 ACTAGAGAACCAACCTAGTGATGTA 58.509 40.000 0.00 0.00 40.89 2.29
1576 1917 8.421784 AGCCGAACTAATAATACATTGAAGAGA 58.578 33.333 0.00 0.00 0.00 3.10
1577 1918 8.594881 AGCCGAACTAATAATACATTGAAGAG 57.405 34.615 0.00 0.00 0.00 2.85
1584 1925 8.677148 ACATCAAAGCCGAACTAATAATACAT 57.323 30.769 0.00 0.00 0.00 2.29
1590 1931 7.966204 GCTTAAAACATCAAAGCCGAACTAATA 59.034 33.333 0.00 0.00 39.74 0.98
1612 1953 6.114089 CGACCATAGATACCTAGCTAGCTTA 58.886 44.000 24.88 10.01 0.00 3.09
1613 1954 4.944930 CGACCATAGATACCTAGCTAGCTT 59.055 45.833 24.88 7.70 0.00 3.74
1641 1988 6.097839 CCTAGGCAGTACCATTCTAAACAGTA 59.902 42.308 0.00 0.00 43.14 2.74
1650 1997 2.116238 TCACCCTAGGCAGTACCATTC 58.884 52.381 2.05 0.00 43.14 2.67
1651 1998 1.838077 GTCACCCTAGGCAGTACCATT 59.162 52.381 2.05 0.00 43.14 3.16
1663 2014 3.459828 TCAAAGATCATGGGTCACCCTA 58.540 45.455 16.04 0.05 45.70 3.53
1685 2036 8.845227 TGCTGAGAAAACAACAGTAAAATGATA 58.155 29.630 0.00 0.00 34.60 2.15
1701 2052 4.993584 GTGAGAGAGACAATGCTGAGAAAA 59.006 41.667 0.00 0.00 0.00 2.29
1705 2056 2.094803 ACGTGAGAGAGACAATGCTGAG 60.095 50.000 0.00 0.00 0.00 3.35
1808 2164 7.549839 TGTTATAATATAGTTTCCCGATCCCG 58.450 38.462 0.00 0.00 0.00 5.14
1830 2186 7.158697 GGGCTTGATTTTACCAAGTTTATGTT 58.841 34.615 0.00 0.00 42.11 2.71
1877 2272 3.705072 ACATTTAGGAACGGAGGGAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
1878 2273 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
1879 2274 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
1880 2275 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1881 2276 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1882 2277 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
1883 2278 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1884 2279 8.195436 TCATAAGACTTACATTTAGGAACGGAG 58.805 37.037 0.00 0.00 0.00 4.63
1885 2280 8.070034 TCATAAGACTTACATTTAGGAACGGA 57.930 34.615 0.00 0.00 0.00 4.69
1886 2281 8.601476 GTTCATAAGACTTACATTTAGGAACGG 58.399 37.037 0.00 0.00 37.91 4.44
1887 2282 9.367444 AGTTCATAAGACTTACATTTAGGAACG 57.633 33.333 12.39 0.00 45.39 3.95
1942 2337 9.809096 TGAGTGAAAATGAGTGAATCTATACTC 57.191 33.333 0.00 0.00 42.77 2.59
1948 2343 9.688592 GAAAAATGAGTGAAAATGAGTGAATCT 57.311 29.630 0.00 0.00 0.00 2.40
1949 2344 9.688592 AGAAAAATGAGTGAAAATGAGTGAATC 57.311 29.630 0.00 0.00 0.00 2.52
1951 2346 9.520204 GAAGAAAAATGAGTGAAAATGAGTGAA 57.480 29.630 0.00 0.00 0.00 3.18
1952 2347 7.857389 CGAAGAAAAATGAGTGAAAATGAGTGA 59.143 33.333 0.00 0.00 0.00 3.41
1953 2348 7.645340 ACGAAGAAAAATGAGTGAAAATGAGTG 59.355 33.333 0.00 0.00 0.00 3.51
1954 2349 7.707104 ACGAAGAAAAATGAGTGAAAATGAGT 58.293 30.769 0.00 0.00 0.00 3.41
1955 2350 9.107367 GTACGAAGAAAAATGAGTGAAAATGAG 57.893 33.333 0.00 0.00 0.00 2.90
1956 2351 7.796660 CGTACGAAGAAAAATGAGTGAAAATGA 59.203 33.333 10.44 0.00 0.00 2.57
1957 2352 7.586300 ACGTACGAAGAAAAATGAGTGAAAATG 59.414 33.333 24.41 0.00 0.00 2.32
1958 2353 7.636326 ACGTACGAAGAAAAATGAGTGAAAAT 58.364 30.769 24.41 0.00 0.00 1.82
1959 2354 7.007313 ACGTACGAAGAAAAATGAGTGAAAA 57.993 32.000 24.41 0.00 0.00 2.29
1960 2355 6.592798 ACGTACGAAGAAAAATGAGTGAAA 57.407 33.333 24.41 0.00 0.00 2.69
1961 2356 6.919662 ACTACGTACGAAGAAAAATGAGTGAA 59.080 34.615 24.41 0.00 0.00 3.18
1962 2357 6.441274 ACTACGTACGAAGAAAAATGAGTGA 58.559 36.000 24.41 0.00 0.00 3.41
1963 2358 6.183359 GGACTACGTACGAAGAAAAATGAGTG 60.183 42.308 24.41 0.00 0.00 3.51
1964 2359 5.860716 GGACTACGTACGAAGAAAAATGAGT 59.139 40.000 24.41 8.26 0.00 3.41
1965 2360 5.860182 TGGACTACGTACGAAGAAAAATGAG 59.140 40.000 24.41 5.34 0.00 2.90
1966 2361 5.771469 TGGACTACGTACGAAGAAAAATGA 58.229 37.500 24.41 0.00 0.00 2.57
1967 2362 6.642683 ATGGACTACGTACGAAGAAAAATG 57.357 37.500 24.41 3.37 0.00 2.32
1968 2363 8.814235 CAATATGGACTACGTACGAAGAAAAAT 58.186 33.333 24.41 9.38 0.00 1.82
1969 2364 7.201461 GCAATATGGACTACGTACGAAGAAAAA 60.201 37.037 24.41 1.93 0.00 1.94
1970 2365 6.254157 GCAATATGGACTACGTACGAAGAAAA 59.746 38.462 24.41 3.54 0.00 2.29
1971 2366 5.745294 GCAATATGGACTACGTACGAAGAAA 59.255 40.000 24.41 2.98 0.00 2.52
1972 2367 5.163632 TGCAATATGGACTACGTACGAAGAA 60.164 40.000 24.41 3.26 0.00 2.52
1973 2368 4.336153 TGCAATATGGACTACGTACGAAGA 59.664 41.667 24.41 5.68 0.00 2.87
1974 2369 4.603985 TGCAATATGGACTACGTACGAAG 58.396 43.478 24.41 0.00 0.00 3.79
1975 2370 4.635833 TGCAATATGGACTACGTACGAA 57.364 40.909 24.41 0.13 0.00 3.85
1976 2371 4.635833 TTGCAATATGGACTACGTACGA 57.364 40.909 24.41 4.69 0.00 3.43
1977 2372 5.220381 AGATTGCAATATGGACTACGTACG 58.780 41.667 12.97 15.01 0.00 3.67
1978 2373 7.478520 AAAGATTGCAATATGGACTACGTAC 57.521 36.000 12.97 0.00 0.00 3.67
1979 2374 9.602568 TTTAAAGATTGCAATATGGACTACGTA 57.397 29.630 12.97 0.00 0.00 3.57
1980 2375 8.500753 TTTAAAGATTGCAATATGGACTACGT 57.499 30.769 12.97 0.00 0.00 3.57
1981 2376 9.781834 TTTTTAAAGATTGCAATATGGACTACG 57.218 29.630 12.97 0.00 0.00 3.51
1984 2379 9.860898 GTCTTTTTAAAGATTGCAATATGGACT 57.139 29.630 12.97 1.46 45.83 3.85
1985 2380 9.860898 AGTCTTTTTAAAGATTGCAATATGGAC 57.139 29.630 12.97 10.07 45.83 4.02
2002 2397 9.617523 CCCCGTTCCTAAATATAAGTCTTTTTA 57.382 33.333 0.00 0.00 0.00 1.52
2003 2398 7.558807 CCCCCGTTCCTAAATATAAGTCTTTTT 59.441 37.037 0.00 0.00 0.00 1.94
2004 2399 7.058525 CCCCCGTTCCTAAATATAAGTCTTTT 58.941 38.462 0.00 0.00 0.00 2.27
2005 2400 6.598503 CCCCCGTTCCTAAATATAAGTCTTT 58.401 40.000 0.00 0.00 0.00 2.52
2006 2401 6.183810 CCCCCGTTCCTAAATATAAGTCTT 57.816 41.667 0.00 0.00 0.00 3.01
2007 2402 5.820404 CCCCCGTTCCTAAATATAAGTCT 57.180 43.478 0.00 0.00 0.00 3.24
2026 2421 6.839134 AGTCATTGGAAATTTTATACTCCCCC 59.161 38.462 0.00 0.00 0.00 5.40
2027 2422 7.898014 AGTCATTGGAAATTTTATACTCCCC 57.102 36.000 0.00 0.00 0.00 4.81
2082 2477 0.695924 TTTCCTCCCTCGCCATTTCA 59.304 50.000 0.00 0.00 0.00 2.69
2090 2485 3.003480 GTCAAACAGATTTCCTCCCTCG 58.997 50.000 0.00 0.00 0.00 4.63
2104 2499 8.655092 GTCATTTTCTTCAACATTTGTCAAACA 58.345 29.630 0.00 0.00 0.00 2.83
2106 2501 7.757173 TCGTCATTTTCTTCAACATTTGTCAAA 59.243 29.630 0.00 0.00 0.00 2.69
2107 2502 7.254137 TCGTCATTTTCTTCAACATTTGTCAA 58.746 30.769 0.00 0.00 0.00 3.18
2136 2531 0.801451 TGCGCACAAAGCAAACTGTG 60.801 50.000 5.66 0.00 46.13 3.66
2213 2608 4.754618 TGCACCACACACTATAGTTTTCTG 59.245 41.667 1.56 0.00 0.00 3.02
2215 2610 5.682943 TTGCACCACACACTATAGTTTTC 57.317 39.130 1.56 0.00 0.00 2.29
2228 2623 1.203523 GTGTTCAACCTTTGCACCACA 59.796 47.619 0.00 0.00 0.00 4.17
2231 2626 3.659850 GGTGTTCAACCTTTGCACC 57.340 52.632 0.00 0.00 46.55 5.01
2271 2666 6.871844 TCAAATCTGACATGTCCAACAAAAA 58.128 32.000 22.85 0.71 0.00 1.94
2272 2667 6.462552 TCAAATCTGACATGTCCAACAAAA 57.537 33.333 22.85 1.47 0.00 2.44
2284 2679 6.672266 AACTCCTCTAGTTCAAATCTGACA 57.328 37.500 0.00 0.00 45.64 3.58
2298 2693 1.759445 GCAGAGCATGGAACTCCTCTA 59.241 52.381 0.00 0.00 33.60 2.43
2299 2694 0.540923 GCAGAGCATGGAACTCCTCT 59.459 55.000 0.00 0.00 34.56 3.69
2303 2698 3.456280 CTCTTAGCAGAGCATGGAACTC 58.544 50.000 0.00 0.00 40.39 3.01
2398 2797 6.183361 ACCAAAAATTACATGCAGGGGTTAAA 60.183 34.615 2.31 0.00 0.00 1.52
2401 2800 3.650461 ACCAAAAATTACATGCAGGGGTT 59.350 39.130 2.31 0.00 0.00 4.11
2413 2812 5.893255 AGCATGCCATCTCTACCAAAAATTA 59.107 36.000 15.66 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.