Multiple sequence alignment - TraesCS2A01G102000

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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 TraesCS2A01G102000 chr2A 100.000 3671 0 0 1 3671 54956519 54952849 0.000000e+00 6780.0
1 TraesCS2A01G102000 chr2A 84.067 1726 139 71 1002 2673 54882345 54883988 0.000000e+00 1539.0
2 TraesCS2A01G102000 chr2A 85.976 164 13 7 750 910 54882141 54882297 2.270000e-37 167.0
3 TraesCS2A01G102000 chr2D 89.514 2899 156 73 100 2926 54488905 54486083 0.000000e+00 3533.0
4 TraesCS2A01G102000 chr2D 83.213 1936 171 87 818 2675 54317309 54319168 0.000000e+00 1633.0
5 TraesCS2A01G102000 chr2D 85.484 682 82 10 2994 3669 54485758 54485088 0.000000e+00 695.0
6 TraesCS2A01G102000 chr2B 83.661 2136 178 83 648 2675 85073601 85075673 0.000000e+00 1853.0
7 TraesCS2A01G102000 chr2B 92.669 1023 45 15 1975 2990 85176921 85175922 0.000000e+00 1447.0
8 TraesCS2A01G102000 chr2B 83.648 1535 123 79 515 1986 85178415 85176946 0.000000e+00 1327.0
9 TraesCS2A01G102000 chr2B 87.778 360 38 4 2994 3353 85175096 85174743 2.040000e-112 416.0
10 TraesCS2A01G102000 chr2B 88.043 92 8 2 376 464 85073192 85073283 5.010000e-19 106.0
11 TraesCS2A01G102000 chr4B 85.449 323 42 5 1267 1588 380653769 380654087 7.600000e-87 331.0
12 TraesCS2A01G102000 chr4B 89.933 149 15 0 1042 1190 380653478 380653626 3.740000e-45 193.0
13 TraesCS2A01G102000 chr4B 100.000 32 0 0 70 101 12501355 12501386 3.960000e-05 60.2
14 TraesCS2A01G102000 chr4D 85.139 323 43 5 1267 1588 304690478 304690796 3.540000e-85 326.0
15 TraesCS2A01G102000 chr4D 89.933 149 15 0 1042 1190 304690191 304690339 3.740000e-45 193.0
16 TraesCS2A01G102000 chr4D 89.091 55 6 0 48 102 473982011 473981957 6.580000e-08 69.4
17 TraesCS2A01G102000 chr4A 85.809 303 40 3 1286 1588 174157172 174156873 5.920000e-83 318.0
18 TraesCS2A01G102000 chr4A 89.262 149 16 0 1042 1190 174157472 174157324 1.740000e-43 187.0
19 TraesCS2A01G102000 chr5A 77.686 484 87 18 1055 1523 317248159 317247682 3.610000e-70 276.0
20 TraesCS2A01G102000 chr3A 75.926 486 84 23 1043 1520 650056199 650056659 6.170000e-53 219.0
21 TraesCS2A01G102000 chr1D 94.828 58 1 1 46 103 354720759 354720814 5.050000e-14 89.8
22 TraesCS2A01G102000 chr1D 100.000 32 0 0 71 102 19408013 19407982 3.960000e-05 60.2
23 TraesCS2A01G102000 chr5B 91.803 61 2 2 48 105 21150813 21150873 8.450000e-12 82.4
24 TraesCS2A01G102000 chr5B 100.000 33 0 0 70 102 37056759 37056791 1.100000e-05 62.1
25 TraesCS2A01G102000 chr3D 97.222 36 1 0 70 105 478530091 478530056 1.100000e-05 62.1
26 TraesCS2A01G102000 chr3B 97.143 35 1 0 70 104 617997266 617997232 3.960000e-05 60.2
27 TraesCS2A01G102000 chr1A 86.538 52 6 1 61 111 203818658 203818709 5.120000e-04 56.5
28 TraesCS2A01G102000 chr7B 100.000 28 0 0 40 67 639796191 639796218 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G102000 chr2A 54952849 54956519 3670 True 6780.000000 6780 100.000000 1 3671 1 chr2A.!!$R1 3670
1 TraesCS2A01G102000 chr2A 54882141 54883988 1847 False 853.000000 1539 85.021500 750 2673 2 chr2A.!!$F1 1923
2 TraesCS2A01G102000 chr2D 54485088 54488905 3817 True 2114.000000 3533 87.499000 100 3669 2 chr2D.!!$R1 3569
3 TraesCS2A01G102000 chr2D 54317309 54319168 1859 False 1633.000000 1633 83.213000 818 2675 1 chr2D.!!$F1 1857
4 TraesCS2A01G102000 chr2B 85174743 85178415 3672 True 1063.333333 1447 88.031667 515 3353 3 chr2B.!!$R1 2838
5 TraesCS2A01G102000 chr2B 85073192 85075673 2481 False 979.500000 1853 85.852000 376 2675 2 chr2B.!!$F1 2299
6 TraesCS2A01G102000 chr4B 380653478 380654087 609 False 262.000000 331 87.691000 1042 1588 2 chr4B.!!$F2 546
7 TraesCS2A01G102000 chr4D 304690191 304690796 605 False 259.500000 326 87.536000 1042 1588 2 chr4D.!!$F1 546
8 TraesCS2A01G102000 chr4A 174156873 174157472 599 True 252.500000 318 87.535500 1042 1588 2 chr4A.!!$R1 546

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
601 797 0.244178 GCTAGCCGGCTATGACCTAC 59.756 60.0 35.29 15.2 0.00 3.18 F
843 1062 0.394938 ACCATATAATCGCACGCCCA 59.605 50.0 0.00 0.0 0.00 5.36 F
1512 1894 0.597637 GGATCATGCACGAGTACCGG 60.598 60.0 0.00 0.0 43.93 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2802 0.036105 TGCGTGATCATGGTTCTGCT 60.036 50.0 16.59 0.0 0.0 4.24 R
2272 2805 0.036105 TGCTGCGTGATCATGGTTCT 60.036 50.0 16.59 0.0 0.0 3.01 R
3354 4885 0.661020 CGAATGGACAATAACCGGGC 59.339 55.0 6.32 0.0 0.0 6.13 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
18 19 3.713902 CCGCTGCCAGAAATCCTAT 57.286 52.632 0.00 0.00 0.00 2.57
19 20 1.972872 CCGCTGCCAGAAATCCTATT 58.027 50.000 0.00 0.00 0.00 1.73
20 21 1.876156 CCGCTGCCAGAAATCCTATTC 59.124 52.381 0.00 0.00 0.00 1.75
21 22 2.486191 CCGCTGCCAGAAATCCTATTCT 60.486 50.000 0.00 0.00 40.23 2.40
22 23 3.209410 CGCTGCCAGAAATCCTATTCTT 58.791 45.455 0.00 0.00 37.56 2.52
23 24 4.380531 CGCTGCCAGAAATCCTATTCTTA 58.619 43.478 0.00 0.00 37.56 2.10
24 25 4.999950 CGCTGCCAGAAATCCTATTCTTAT 59.000 41.667 0.00 0.00 37.56 1.73
25 26 5.106791 CGCTGCCAGAAATCCTATTCTTATG 60.107 44.000 0.00 0.00 37.56 1.90
26 27 5.767168 GCTGCCAGAAATCCTATTCTTATGT 59.233 40.000 0.00 0.00 37.56 2.29
27 28 6.293845 GCTGCCAGAAATCCTATTCTTATGTG 60.294 42.308 0.00 0.00 37.56 3.21
28 29 5.532406 TGCCAGAAATCCTATTCTTATGTGC 59.468 40.000 0.00 0.00 37.56 4.57
29 30 5.767168 GCCAGAAATCCTATTCTTATGTGCT 59.233 40.000 0.00 0.00 37.56 4.40
30 31 6.072783 GCCAGAAATCCTATTCTTATGTGCTC 60.073 42.308 0.00 0.00 37.56 4.26
31 32 6.994496 CCAGAAATCCTATTCTTATGTGCTCA 59.006 38.462 0.00 0.00 37.56 4.26
32 33 7.664731 CCAGAAATCCTATTCTTATGTGCTCAT 59.335 37.037 6.50 6.50 37.56 2.90
33 34 9.064706 CAGAAATCCTATTCTTATGTGCTCATT 57.935 33.333 6.57 0.00 37.56 2.57
34 35 9.638176 AGAAATCCTATTCTTATGTGCTCATTT 57.362 29.630 6.57 0.00 36.23 2.32
35 36 9.674824 GAAATCCTATTCTTATGTGCTCATTTG 57.325 33.333 6.57 0.97 35.70 2.32
36 37 6.624352 TCCTATTCTTATGTGCTCATTTGC 57.376 37.500 6.57 0.00 35.70 3.68
37 38 6.359804 TCCTATTCTTATGTGCTCATTTGCT 58.640 36.000 6.57 0.00 35.70 3.91
38 39 6.830324 TCCTATTCTTATGTGCTCATTTGCTT 59.170 34.615 6.57 0.00 35.70 3.91
39 40 7.340232 TCCTATTCTTATGTGCTCATTTGCTTT 59.660 33.333 6.57 0.00 35.70 3.51
40 41 7.977853 CCTATTCTTATGTGCTCATTTGCTTTT 59.022 33.333 6.57 0.00 35.70 2.27
43 44 9.880157 ATTCTTATGTGCTCATTTGCTTTTAAT 57.120 25.926 6.57 0.00 35.70 1.40
52 53 9.801873 TGCTCATTTGCTTTTAATAAATACTCC 57.198 29.630 0.00 0.00 0.00 3.85
53 54 9.249457 GCTCATTTGCTTTTAATAAATACTCCC 57.751 33.333 0.00 0.00 0.00 4.30
56 57 9.750125 CATTTGCTTTTAATAAATACTCCCTCC 57.250 33.333 0.00 0.00 0.00 4.30
57 58 7.562454 TTGCTTTTAATAAATACTCCCTCCG 57.438 36.000 0.00 0.00 0.00 4.63
58 59 6.655930 TGCTTTTAATAAATACTCCCTCCGT 58.344 36.000 0.00 0.00 0.00 4.69
59 60 7.794041 TGCTTTTAATAAATACTCCCTCCGTA 58.206 34.615 0.00 0.00 0.00 4.02
60 61 8.266473 TGCTTTTAATAAATACTCCCTCCGTAA 58.734 33.333 0.00 0.00 0.00 3.18
61 62 9.112725 GCTTTTAATAAATACTCCCTCCGTAAA 57.887 33.333 0.00 0.00 0.00 2.01
67 68 8.904099 ATAAATACTCCCTCCGTAAAGAAATG 57.096 34.615 0.00 0.00 0.00 2.32
68 69 2.987232 ACTCCCTCCGTAAAGAAATGC 58.013 47.619 0.00 0.00 0.00 3.56
69 70 2.304761 ACTCCCTCCGTAAAGAAATGCA 59.695 45.455 0.00 0.00 0.00 3.96
70 71 3.244770 ACTCCCTCCGTAAAGAAATGCAA 60.245 43.478 0.00 0.00 0.00 4.08
71 72 3.756434 CTCCCTCCGTAAAGAAATGCAAA 59.244 43.478 0.00 0.00 0.00 3.68
72 73 3.504520 TCCCTCCGTAAAGAAATGCAAAC 59.495 43.478 0.00 0.00 0.00 2.93
73 74 3.488489 CCTCCGTAAAGAAATGCAAACG 58.512 45.455 0.00 0.00 0.00 3.60
74 75 2.908626 CTCCGTAAAGAAATGCAAACGC 59.091 45.455 0.00 0.00 0.00 4.84
75 76 2.550606 TCCGTAAAGAAATGCAAACGCT 59.449 40.909 0.00 0.00 0.00 5.07
76 77 2.908626 CCGTAAAGAAATGCAAACGCTC 59.091 45.455 0.00 0.00 0.00 5.03
77 78 3.364964 CCGTAAAGAAATGCAAACGCTCT 60.365 43.478 0.00 0.00 0.00 4.09
78 79 4.219033 CGTAAAGAAATGCAAACGCTCTT 58.781 39.130 0.00 0.00 0.00 2.85
79 80 5.379003 CGTAAAGAAATGCAAACGCTCTTA 58.621 37.500 0.00 0.00 0.00 2.10
80 81 6.021596 CGTAAAGAAATGCAAACGCTCTTAT 58.978 36.000 0.00 0.00 0.00 1.73
81 82 7.177407 CGTAAAGAAATGCAAACGCTCTTATA 58.823 34.615 0.00 0.00 0.00 0.98
82 83 7.850982 CGTAAAGAAATGCAAACGCTCTTATAT 59.149 33.333 0.00 0.00 0.00 0.86
83 84 9.503427 GTAAAGAAATGCAAACGCTCTTATATT 57.497 29.630 0.00 0.00 0.00 1.28
84 85 8.986477 AAAGAAATGCAAACGCTCTTATATTT 57.014 26.923 0.00 0.00 0.00 1.40
85 86 8.620533 AAGAAATGCAAACGCTCTTATATTTC 57.379 30.769 0.00 0.00 34.94 2.17
86 87 7.989826 AGAAATGCAAACGCTCTTATATTTCT 58.010 30.769 0.00 0.00 38.24 2.52
87 88 8.462016 AGAAATGCAAACGCTCTTATATTTCTT 58.538 29.630 0.00 0.00 39.33 2.52
88 89 8.620533 AAATGCAAACGCTCTTATATTTCTTC 57.379 30.769 0.00 0.00 0.00 2.87
89 90 6.735678 TGCAAACGCTCTTATATTTCTTCA 57.264 33.333 0.00 0.00 0.00 3.02
90 91 6.542852 TGCAAACGCTCTTATATTTCTTCAC 58.457 36.000 0.00 0.00 0.00 3.18
91 92 6.148645 TGCAAACGCTCTTATATTTCTTCACA 59.851 34.615 0.00 0.00 0.00 3.58
92 93 6.684555 GCAAACGCTCTTATATTTCTTCACAG 59.315 38.462 0.00 0.00 0.00 3.66
93 94 7.413000 GCAAACGCTCTTATATTTCTTCACAGA 60.413 37.037 0.00 0.00 0.00 3.41
94 95 7.763172 AACGCTCTTATATTTCTTCACAGAG 57.237 36.000 0.00 0.00 0.00 3.35
95 96 6.276847 ACGCTCTTATATTTCTTCACAGAGG 58.723 40.000 0.00 0.00 0.00 3.69
96 97 5.694006 CGCTCTTATATTTCTTCACAGAGGG 59.306 44.000 0.00 0.00 34.68 4.30
97 98 6.461648 CGCTCTTATATTTCTTCACAGAGGGA 60.462 42.308 4.76 0.00 40.49 4.20
98 99 6.928492 GCTCTTATATTTCTTCACAGAGGGAG 59.072 42.308 0.00 0.00 0.00 4.30
114 115 4.162509 AGAGGGAGTACATAGAGCAAAACC 59.837 45.833 0.00 0.00 0.00 3.27
119 120 5.410439 GGAGTACATAGAGCAAAACCGAAAA 59.590 40.000 0.00 0.00 0.00 2.29
178 184 9.578439 ACGTAATTACCTTAGACACTAATCAAC 57.422 33.333 10.01 0.00 0.00 3.18
181 187 4.838904 ACCTTAGACACTAATCAACCCC 57.161 45.455 0.00 0.00 0.00 4.95
222 229 0.331278 CCATGCCCCCAACTAGTGAA 59.669 55.000 0.00 0.00 0.00 3.18
223 230 1.272425 CCATGCCCCCAACTAGTGAAA 60.272 52.381 0.00 0.00 0.00 2.69
234 241 7.988028 CCCCCAACTAGTGAAAAATTAAAAACA 59.012 33.333 0.00 0.00 0.00 2.83
251 258 4.546829 AAACAGCCAAATCAGCAATCAT 57.453 36.364 0.00 0.00 0.00 2.45
320 327 7.524698 GCAAAACATGGGAATAACTACCTTCAA 60.525 37.037 0.00 0.00 0.00 2.69
402 411 1.668101 GGAAACCCAACCAACGCACA 61.668 55.000 0.00 0.00 0.00 4.57
575 771 1.276622 GTGAGCAAGTTAGGAGGGGA 58.723 55.000 0.00 0.00 0.00 4.81
601 797 0.244178 GCTAGCCGGCTATGACCTAC 59.756 60.000 35.29 15.20 0.00 3.18
835 1054 7.834068 CAAGATACCTTGGACCATATAATCG 57.166 40.000 0.00 0.00 44.58 3.34
843 1062 0.394938 ACCATATAATCGCACGCCCA 59.605 50.000 0.00 0.00 0.00 5.36
871 1090 1.672356 CCCATCCGCCATTCGATCC 60.672 63.158 0.00 0.00 41.67 3.36
910 1141 1.045407 GGTCTGGTCCAGTGTGTGTA 58.955 55.000 18.65 0.00 32.61 2.90
1098 1360 1.484240 GAGCTCATCCTGCACTACCTT 59.516 52.381 9.40 0.00 0.00 3.50
1170 1432 4.294416 AGACATCTACAAGTTCGATCCG 57.706 45.455 0.00 0.00 0.00 4.18
1204 1482 6.294176 CCCTTGTAAGTTCTCAACCAATCAAG 60.294 42.308 0.00 0.00 0.00 3.02
1205 1483 6.263168 CCTTGTAAGTTCTCAACCAATCAAGT 59.737 38.462 0.00 0.00 31.23 3.16
1237 1529 1.577736 ATGTAGTCCCTGCTCTGCTT 58.422 50.000 0.00 0.00 0.00 3.91
1250 1542 0.981183 TCTGCTTACCATGGTTCGGT 59.019 50.000 25.38 0.00 40.73 4.69
1257 1549 4.682320 GCTTACCATGGTTCGGTTCTGATA 60.682 45.833 25.38 0.00 37.99 2.15
1411 1792 1.745489 GACAAGCCCATCCACGACC 60.745 63.158 0.00 0.00 0.00 4.79
1512 1894 0.597637 GGATCATGCACGAGTACCGG 60.598 60.000 0.00 0.00 43.93 5.28
1605 1998 2.535485 TACGCCCATCCCACTTGCTG 62.535 60.000 0.00 0.00 0.00 4.41
1606 1999 2.036256 GCCCATCCCACTTGCTGT 59.964 61.111 0.00 0.00 0.00 4.40
1630 2026 5.301805 TGATTAGTTAGTCGATCAGGCATGA 59.698 40.000 2.36 2.36 40.50 3.07
1639 2035 1.086067 ATCAGGCATGAACTGTCGCG 61.086 55.000 4.62 0.00 39.39 5.87
1718 2117 3.329814 TGGCATGCATTCTATCCTGATCT 59.670 43.478 21.36 0.00 0.00 2.75
1803 2216 5.482163 TGATCGGTTATGCATCCATCTTA 57.518 39.130 0.19 0.00 32.85 2.10
1804 2217 5.863965 TGATCGGTTATGCATCCATCTTAA 58.136 37.500 0.19 0.00 32.85 1.85
1805 2218 5.934043 TGATCGGTTATGCATCCATCTTAAG 59.066 40.000 0.19 0.00 32.85 1.85
1806 2219 5.290493 TCGGTTATGCATCCATCTTAAGT 57.710 39.130 0.19 0.00 32.85 2.24
1811 2224 8.017373 CGGTTATGCATCCATCTTAAGTTATTG 58.983 37.037 0.19 0.00 32.85 1.90
1818 2231 8.844244 GCATCCATCTTAAGTTATTGATTGACT 58.156 33.333 1.63 0.00 0.00 3.41
1840 2261 5.724854 ACTAAATTGCCCTCTAACCTGAGTA 59.275 40.000 0.00 0.00 32.50 2.59
1841 2262 4.489306 AATTGCCCTCTAACCTGAGTAC 57.511 45.455 0.00 0.00 32.50 2.73
1844 2265 2.832129 TGCCCTCTAACCTGAGTACTTG 59.168 50.000 0.00 0.00 32.50 3.16
1845 2283 2.418884 GCCCTCTAACCTGAGTACTTGC 60.419 54.545 0.00 0.00 32.50 4.01
1849 2287 5.394333 CCCTCTAACCTGAGTACTTGCTAAC 60.394 48.000 0.00 0.00 32.50 2.34
1866 2320 5.247862 TGCTAACATCACATCACATCAAGT 58.752 37.500 0.00 0.00 0.00 3.16
1867 2321 6.405538 TGCTAACATCACATCACATCAAGTA 58.594 36.000 0.00 0.00 0.00 2.24
1872 2326 6.036470 ACATCACATCACATCAAGTAGTACG 58.964 40.000 0.00 0.00 0.00 3.67
1874 2328 5.399013 TCACATCACATCAAGTAGTACGTG 58.601 41.667 9.67 9.67 0.00 4.49
1875 2329 5.182380 TCACATCACATCAAGTAGTACGTGA 59.818 40.000 19.16 19.16 40.61 4.35
1880 2334 6.863275 TCACATCAAGTAGTACGTGAATGAT 58.137 36.000 20.44 11.26 39.82 2.45
1881 2335 7.992008 TCACATCAAGTAGTACGTGAATGATA 58.008 34.615 20.44 10.89 39.82 2.15
1882 2336 7.913821 TCACATCAAGTAGTACGTGAATGATAC 59.086 37.037 20.44 0.00 39.82 2.24
1883 2337 7.915923 CACATCAAGTAGTACGTGAATGATACT 59.084 37.037 20.44 2.33 39.82 2.12
1884 2338 7.915923 ACATCAAGTAGTACGTGAATGATACTG 59.084 37.037 20.44 14.78 39.82 2.74
1885 2339 7.387119 TCAAGTAGTACGTGAATGATACTGT 57.613 36.000 15.39 0.00 33.84 3.55
1886 2340 8.496707 TCAAGTAGTACGTGAATGATACTGTA 57.503 34.615 15.39 0.00 33.84 2.74
1888 2342 7.256756 AGTAGTACGTGAATGATACTGTACC 57.743 40.000 0.00 0.00 33.10 3.34
1892 2346 4.181578 ACGTGAATGATACTGTACCTTGC 58.818 43.478 0.00 0.00 0.00 4.01
1894 2348 4.629634 CGTGAATGATACTGTACCTTGCAA 59.370 41.667 0.00 0.00 0.00 4.08
1895 2349 5.220472 CGTGAATGATACTGTACCTTGCAAG 60.220 44.000 19.93 19.93 0.00 4.01
1896 2350 5.643777 GTGAATGATACTGTACCTTGCAAGT 59.356 40.000 24.35 14.80 0.00 3.16
1899 2353 7.880713 TGAATGATACTGTACCTTGCAAGTAAA 59.119 33.333 24.35 11.22 0.00 2.01
1919 2374 8.547967 AGTAAAACGAGAGATGCTTAATTTGA 57.452 30.769 0.00 0.00 0.00 2.69
1921 2376 9.214953 GTAAAACGAGAGATGCTTAATTTGATG 57.785 33.333 0.00 0.00 0.00 3.07
1924 2379 6.344500 ACGAGAGATGCTTAATTTGATGTCT 58.656 36.000 0.00 0.00 0.00 3.41
1925 2380 7.492524 ACGAGAGATGCTTAATTTGATGTCTA 58.507 34.615 0.00 0.00 0.00 2.59
1964 2419 5.277538 GGAGAAATTAGCTTCGCGATTGATT 60.278 40.000 10.88 4.85 0.00 2.57
1965 2420 5.742446 AGAAATTAGCTTCGCGATTGATTC 58.258 37.500 10.88 8.80 0.00 2.52
2066 2583 7.201470 GGCACATCTACGTGTATGATATTGATG 60.201 40.741 16.17 0.00 39.19 3.07
2070 2600 8.642020 CATCTACGTGTATGATATTGATGTGTG 58.358 37.037 0.00 0.00 0.00 3.82
2076 2606 7.409697 GTGTATGATATTGATGTGTGGTTCAC 58.590 38.462 0.00 0.00 46.31 3.18
2109 2642 1.278985 CAGTTGGATGACTGGGTGCTA 59.721 52.381 0.00 0.00 42.58 3.49
2294 2827 2.713770 CATGATCACGCAGCAGCC 59.286 61.111 0.00 0.00 37.52 4.85
2463 2996 2.429571 GACAACGCGCACGGAGTA 60.430 61.111 5.73 0.00 41.61 2.59
2770 3319 8.261492 AGAAGCATGAAACAATCTTGTACTAG 57.739 34.615 0.00 0.00 41.31 2.57
2771 3320 7.880195 AGAAGCATGAAACAATCTTGTACTAGT 59.120 33.333 0.00 0.00 41.31 2.57
2772 3321 9.151471 GAAGCATGAAACAATCTTGTACTAGTA 57.849 33.333 0.00 0.00 41.31 1.82
2778 3327 7.333423 TGAAACAATCTTGTACTAGTACATGCC 59.667 37.037 31.05 19.23 44.54 4.40
2861 3410 8.785329 TTATTGAACAAGCAGACATGTACATA 57.215 30.769 8.32 0.00 0.00 2.29
2948 3501 1.303643 AAGGAGAGGGCGGCAAAAG 60.304 57.895 12.47 0.00 0.00 2.27
2959 3512 3.000082 GCGGCAAAAGCCTATGTTATC 58.000 47.619 4.85 0.00 0.00 1.75
3016 4547 5.121611 GTGAAACTTTGTTGGTCCCTTTTTG 59.878 40.000 0.00 0.00 0.00 2.44
3017 4548 3.904800 ACTTTGTTGGTCCCTTTTTGG 57.095 42.857 0.00 0.00 0.00 3.28
3018 4549 3.178046 ACTTTGTTGGTCCCTTTTTGGT 58.822 40.909 0.00 0.00 0.00 3.67
3019 4550 3.585289 ACTTTGTTGGTCCCTTTTTGGTT 59.415 39.130 0.00 0.00 0.00 3.67
3020 4551 4.042311 ACTTTGTTGGTCCCTTTTTGGTTT 59.958 37.500 0.00 0.00 0.00 3.27
3021 4552 5.248705 ACTTTGTTGGTCCCTTTTTGGTTTA 59.751 36.000 0.00 0.00 0.00 2.01
3022 4553 5.959583 TTGTTGGTCCCTTTTTGGTTTAT 57.040 34.783 0.00 0.00 0.00 1.40
3025 4556 3.930035 TGGTCCCTTTTTGGTTTATGGT 58.070 40.909 0.00 0.00 0.00 3.55
3038 4569 5.295950 TGGTTTATGGTTTCAATGCAAGTG 58.704 37.500 0.00 0.00 0.00 3.16
3051 4582 6.344500 TCAATGCAAGTGTTGTTTATGGTTT 58.656 32.000 0.00 0.00 31.21 3.27
3052 4583 6.478344 TCAATGCAAGTGTTGTTTATGGTTTC 59.522 34.615 0.00 0.00 31.21 2.78
3053 4584 5.590530 TGCAAGTGTTGTTTATGGTTTCT 57.409 34.783 0.00 0.00 0.00 2.52
3112 4643 1.668751 GGGCGTCGCAAATGATAGAAA 59.331 47.619 20.50 0.00 0.00 2.52
3124 4655 4.736611 ATGATAGAAATCACATGGCCCT 57.263 40.909 0.00 0.00 44.79 5.19
3142 4673 1.136891 CCTGTCCATATGCAGACGTGA 59.863 52.381 10.84 0.00 35.71 4.35
3149 4680 2.757686 TATGCAGACGTGACGATCTC 57.242 50.000 13.70 0.00 0.00 2.75
3209 4740 3.143807 TGTTGCCGTCAAGAAAACAAG 57.856 42.857 0.00 0.00 31.93 3.16
3227 4758 1.168853 AGAGGGTAGGGGGTATCTCC 58.831 60.000 0.00 0.00 0.00 3.71
3230 4761 0.566679 GGGTAGGGGGTATCTCCTGT 59.433 60.000 4.01 0.00 34.75 4.00
3231 4762 1.061579 GGGTAGGGGGTATCTCCTGTT 60.062 57.143 4.01 0.00 34.75 3.16
3240 4771 4.407945 GGGGTATCTCCTGTTTAGTGCTTA 59.592 45.833 0.00 0.00 36.25 3.09
3264 4795 4.398358 CGAGATGAAGTTAGTGGAGGTGTA 59.602 45.833 0.00 0.00 0.00 2.90
3272 4803 2.889522 AGTGGAGGTGTATATGGGGT 57.110 50.000 0.00 0.00 0.00 4.95
3273 4804 5.102956 AGTTAGTGGAGGTGTATATGGGGTA 60.103 44.000 0.00 0.00 0.00 3.69
3328 4859 5.586155 TTCAAGTAGGTTTGATTACCCCA 57.414 39.130 0.00 0.00 39.08 4.96
3339 4870 0.694444 ATTACCCCAGGGAGCACGAT 60.694 55.000 7.25 0.00 38.96 3.73
3340 4871 0.031917 TTACCCCAGGGAGCACGATA 60.032 55.000 7.25 0.00 38.96 2.92
3354 4885 2.481449 GCACGATATAATCCTAGCCCCG 60.481 54.545 0.00 0.00 0.00 5.73
3356 4887 1.068741 CGATATAATCCTAGCCCCGCC 59.931 57.143 0.00 0.00 0.00 6.13
3358 4889 0.974010 TATAATCCTAGCCCCGCCCG 60.974 60.000 0.00 0.00 0.00 6.13
3372 4908 0.661020 CGCCCGGTTATTGTCCATTC 59.339 55.000 0.00 0.00 0.00 2.67
3382 4918 5.995282 GGTTATTGTCCATTCGGATACATCA 59.005 40.000 0.00 0.00 45.33 3.07
3384 4920 3.469008 TGTCCATTCGGATACATCACC 57.531 47.619 0.00 0.00 45.33 4.02
3386 4922 3.434155 GTCCATTCGGATACATCACCGC 61.434 54.545 0.00 0.00 45.33 5.68
3387 4923 5.660710 GTCCATTCGGATACATCACCGCT 62.661 52.174 0.00 0.00 45.33 5.52
3389 4925 3.630204 CGGATACATCACCGCTGC 58.370 61.111 0.00 0.00 42.55 5.25
3409 4945 3.791586 GCTCTGAGGCTCCCCCAC 61.792 72.222 12.86 0.00 35.39 4.61
3433 4969 1.284841 CCTGCCTTTCCCTCCATCCT 61.285 60.000 0.00 0.00 0.00 3.24
3442 4978 1.704007 CCCTCCATCCTGCCTCTTCC 61.704 65.000 0.00 0.00 0.00 3.46
3467 5003 3.493350 CGATTGGAACCAGCATAGCTAGT 60.493 47.826 0.00 0.00 36.40 2.57
3469 5005 2.187958 TGGAACCAGCATAGCTAGTGT 58.812 47.619 0.00 0.00 36.40 3.55
3471 5007 2.093447 GGAACCAGCATAGCTAGTGTGT 60.093 50.000 0.00 0.00 36.40 3.72
3499 5035 2.888863 CTCGTGAGGTGAGGCTCC 59.111 66.667 12.86 3.14 0.00 4.70
3500 5036 2.680352 TCGTGAGGTGAGGCTCCC 60.680 66.667 12.86 12.67 0.00 4.30
3501 5037 2.997315 CGTGAGGTGAGGCTCCCA 60.997 66.667 19.85 7.98 0.00 4.37
3505 5041 1.559682 GTGAGGTGAGGCTCCCATTTA 59.440 52.381 19.85 0.00 0.00 1.40
3506 5042 2.026262 GTGAGGTGAGGCTCCCATTTAA 60.026 50.000 19.85 0.00 0.00 1.52
3526 5062 2.284625 TGTGGGGATGGCTCGAGT 60.285 61.111 15.13 0.00 0.00 4.18
3551 5087 0.865362 ACGGGGGACACCTATAGGAT 59.135 55.000 26.01 12.66 40.03 3.24
3595 5132 4.839706 CCCCGGGGATGCCCTTTG 62.840 72.222 38.41 8.49 44.66 2.77
3606 5143 2.444696 CCCTTTGGGTGGATGCCA 59.555 61.111 0.00 0.00 38.25 4.92
3613 5150 2.763215 GGTGGATGCCAAGGGTGA 59.237 61.111 0.00 0.00 34.18 4.02
3614 5151 1.678970 GGTGGATGCCAAGGGTGAC 60.679 63.158 0.00 0.00 34.18 3.67
3639 5176 1.448540 AGCGAGGACCTCATTTGCG 60.449 57.895 21.49 7.93 0.00 4.85
3642 5179 1.298157 CGAGGACCTCATTTGCGCAA 61.298 55.000 21.02 21.02 0.00 4.85
3646 5183 0.874390 GACCTCATTTGCGCAAGTGA 59.126 50.000 36.05 36.05 36.01 3.41
3649 5186 2.297033 ACCTCATTTGCGCAAGTGATTT 59.703 40.909 37.75 27.44 36.64 2.17
3650 5187 2.664568 CCTCATTTGCGCAAGTGATTTG 59.335 45.455 37.75 28.33 36.64 2.32
3653 5190 3.490155 TCATTTGCGCAAGTGATTTGTTG 59.510 39.130 35.53 14.90 39.08 3.33
3654 5191 1.850377 TTGCGCAAGTGATTTGTTGG 58.150 45.000 21.02 0.00 39.08 3.77
3659 5196 2.340337 GCAAGTGATTTGTTGGGATGC 58.660 47.619 0.00 0.00 39.08 3.91
3664 5201 1.083489 GATTTGTTGGGATGCGACGA 58.917 50.000 0.00 0.00 0.00 4.20
3669 5206 3.350909 TTGGGATGCGACGACGGAG 62.351 63.158 9.67 0.00 43.81 4.63
3670 5207 3.515286 GGGATGCGACGACGGAGA 61.515 66.667 9.67 0.00 43.81 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.876156 GAATAGGATTTCTGGCAGCGG 59.124 52.381 10.34 0.00 0.00 5.52
1 2 2.843701 AGAATAGGATTTCTGGCAGCG 58.156 47.619 10.34 0.00 34.68 5.18
2 3 5.767168 ACATAAGAATAGGATTTCTGGCAGC 59.233 40.000 10.34 0.00 36.12 5.25
3 4 6.293845 GCACATAAGAATAGGATTTCTGGCAG 60.294 42.308 8.58 8.58 36.12 4.85
4 5 5.532406 GCACATAAGAATAGGATTTCTGGCA 59.468 40.000 0.00 0.00 36.12 4.92
5 6 5.767168 AGCACATAAGAATAGGATTTCTGGC 59.233 40.000 0.00 0.00 36.12 4.85
6 7 6.994496 TGAGCACATAAGAATAGGATTTCTGG 59.006 38.462 0.00 0.00 36.12 3.86
7 8 8.618702 ATGAGCACATAAGAATAGGATTTCTG 57.381 34.615 0.00 0.00 36.12 3.02
8 9 9.638176 AAATGAGCACATAAGAATAGGATTTCT 57.362 29.630 0.00 0.00 35.18 2.52
9 10 9.674824 CAAATGAGCACATAAGAATAGGATTTC 57.325 33.333 0.00 0.00 35.50 2.17
10 11 8.139989 GCAAATGAGCACATAAGAATAGGATTT 58.860 33.333 0.00 0.00 35.50 2.17
11 12 7.504911 AGCAAATGAGCACATAAGAATAGGATT 59.495 33.333 0.00 0.00 35.50 3.01
12 13 7.002879 AGCAAATGAGCACATAAGAATAGGAT 58.997 34.615 0.00 0.00 35.50 3.24
13 14 6.359804 AGCAAATGAGCACATAAGAATAGGA 58.640 36.000 0.00 0.00 35.50 2.94
14 15 6.630444 AGCAAATGAGCACATAAGAATAGG 57.370 37.500 0.00 0.00 35.50 2.57
15 16 8.922058 AAAAGCAAATGAGCACATAAGAATAG 57.078 30.769 0.00 0.00 35.50 1.73
17 18 9.880157 ATTAAAAGCAAATGAGCACATAAGAAT 57.120 25.926 0.00 0.00 35.50 2.40
26 27 9.801873 GGAGTATTTATTAAAAGCAAATGAGCA 57.198 29.630 0.00 0.00 36.85 4.26
27 28 9.249457 GGGAGTATTTATTAAAAGCAAATGAGC 57.751 33.333 0.00 0.00 0.00 4.26
30 31 9.750125 GGAGGGAGTATTTATTAAAAGCAAATG 57.250 33.333 0.00 0.00 0.00 2.32
31 32 8.630037 CGGAGGGAGTATTTATTAAAAGCAAAT 58.370 33.333 0.00 0.00 0.00 2.32
32 33 7.612633 ACGGAGGGAGTATTTATTAAAAGCAAA 59.387 33.333 0.00 0.00 0.00 3.68
33 34 7.114095 ACGGAGGGAGTATTTATTAAAAGCAA 58.886 34.615 0.00 0.00 0.00 3.91
34 35 6.655930 ACGGAGGGAGTATTTATTAAAAGCA 58.344 36.000 0.00 0.00 0.00 3.91
35 36 8.667076 TTACGGAGGGAGTATTTATTAAAAGC 57.333 34.615 0.00 0.00 0.00 3.51
41 42 9.338622 CATTTCTTTACGGAGGGAGTATTTATT 57.661 33.333 0.00 0.00 0.00 1.40
42 43 7.444487 GCATTTCTTTACGGAGGGAGTATTTAT 59.556 37.037 0.00 0.00 0.00 1.40
43 44 6.764560 GCATTTCTTTACGGAGGGAGTATTTA 59.235 38.462 0.00 0.00 0.00 1.40
44 45 5.589050 GCATTTCTTTACGGAGGGAGTATTT 59.411 40.000 0.00 0.00 0.00 1.40
45 46 5.123936 GCATTTCTTTACGGAGGGAGTATT 58.876 41.667 0.00 0.00 0.00 1.89
46 47 4.163458 TGCATTTCTTTACGGAGGGAGTAT 59.837 41.667 0.00 0.00 0.00 2.12
47 48 3.516300 TGCATTTCTTTACGGAGGGAGTA 59.484 43.478 0.00 0.00 0.00 2.59
48 49 2.304761 TGCATTTCTTTACGGAGGGAGT 59.695 45.455 0.00 0.00 0.00 3.85
49 50 2.985896 TGCATTTCTTTACGGAGGGAG 58.014 47.619 0.00 0.00 0.00 4.30
50 51 3.426787 TTGCATTTCTTTACGGAGGGA 57.573 42.857 0.00 0.00 0.00 4.20
51 52 3.669557 CGTTTGCATTTCTTTACGGAGGG 60.670 47.826 0.00 0.00 0.00 4.30
52 53 3.488489 CGTTTGCATTTCTTTACGGAGG 58.512 45.455 0.00 0.00 0.00 4.30
53 54 2.908626 GCGTTTGCATTTCTTTACGGAG 59.091 45.455 0.00 0.00 42.15 4.63
54 55 2.550606 AGCGTTTGCATTTCTTTACGGA 59.449 40.909 0.00 0.00 46.23 4.69
55 56 2.908626 GAGCGTTTGCATTTCTTTACGG 59.091 45.455 0.00 0.00 46.23 4.02
56 57 3.810373 AGAGCGTTTGCATTTCTTTACG 58.190 40.909 0.00 0.00 46.23 3.18
57 58 9.503427 AATATAAGAGCGTTTGCATTTCTTTAC 57.497 29.630 0.00 0.00 46.23 2.01
59 60 8.986477 AAATATAAGAGCGTTTGCATTTCTTT 57.014 26.923 0.00 0.00 46.23 2.52
60 61 8.462016 AGAAATATAAGAGCGTTTGCATTTCTT 58.538 29.630 14.16 0.00 46.23 2.52
61 62 7.989826 AGAAATATAAGAGCGTTTGCATTTCT 58.010 30.769 14.16 14.16 46.23 2.52
62 63 8.620533 AAGAAATATAAGAGCGTTTGCATTTC 57.379 30.769 0.00 0.00 46.23 2.17
63 64 8.243426 TGAAGAAATATAAGAGCGTTTGCATTT 58.757 29.630 0.00 0.00 46.23 2.32
64 65 7.698130 GTGAAGAAATATAAGAGCGTTTGCATT 59.302 33.333 0.00 0.00 46.23 3.56
65 66 7.148255 TGTGAAGAAATATAAGAGCGTTTGCAT 60.148 33.333 0.00 0.00 46.23 3.96
66 67 6.148645 TGTGAAGAAATATAAGAGCGTTTGCA 59.851 34.615 0.00 0.00 46.23 4.08
67 68 6.542852 TGTGAAGAAATATAAGAGCGTTTGC 58.457 36.000 0.00 0.00 43.24 3.68
68 69 7.963981 TCTGTGAAGAAATATAAGAGCGTTTG 58.036 34.615 0.00 0.00 0.00 2.93
69 70 7.278868 CCTCTGTGAAGAAATATAAGAGCGTTT 59.721 37.037 0.00 0.00 0.00 3.60
70 71 6.758886 CCTCTGTGAAGAAATATAAGAGCGTT 59.241 38.462 0.00 0.00 0.00 4.84
71 72 6.276847 CCTCTGTGAAGAAATATAAGAGCGT 58.723 40.000 0.00 0.00 0.00 5.07
72 73 5.694006 CCCTCTGTGAAGAAATATAAGAGCG 59.306 44.000 0.00 0.00 0.00 5.03
73 74 6.821388 TCCCTCTGTGAAGAAATATAAGAGC 58.179 40.000 0.00 0.00 0.00 4.09
74 75 8.017418 ACTCCCTCTGTGAAGAAATATAAGAG 57.983 38.462 0.00 0.00 0.00 2.85
75 76 7.979786 ACTCCCTCTGTGAAGAAATATAAGA 57.020 36.000 0.00 0.00 0.00 2.10
76 77 8.696374 TGTACTCCCTCTGTGAAGAAATATAAG 58.304 37.037 0.00 0.00 0.00 1.73
77 78 8.603898 TGTACTCCCTCTGTGAAGAAATATAA 57.396 34.615 0.00 0.00 0.00 0.98
78 79 8.783660 ATGTACTCCCTCTGTGAAGAAATATA 57.216 34.615 0.00 0.00 0.00 0.86
79 80 7.682787 ATGTACTCCCTCTGTGAAGAAATAT 57.317 36.000 0.00 0.00 0.00 1.28
80 81 8.059461 TCTATGTACTCCCTCTGTGAAGAAATA 58.941 37.037 0.00 0.00 0.00 1.40
81 82 6.897966 TCTATGTACTCCCTCTGTGAAGAAAT 59.102 38.462 0.00 0.00 0.00 2.17
82 83 6.253758 TCTATGTACTCCCTCTGTGAAGAAA 58.746 40.000 0.00 0.00 0.00 2.52
83 84 5.827756 TCTATGTACTCCCTCTGTGAAGAA 58.172 41.667 0.00 0.00 0.00 2.52
84 85 5.441500 CTCTATGTACTCCCTCTGTGAAGA 58.558 45.833 0.00 0.00 0.00 2.87
85 86 4.037446 GCTCTATGTACTCCCTCTGTGAAG 59.963 50.000 0.00 0.00 0.00 3.02
86 87 3.954904 GCTCTATGTACTCCCTCTGTGAA 59.045 47.826 0.00 0.00 0.00 3.18
87 88 3.053619 TGCTCTATGTACTCCCTCTGTGA 60.054 47.826 0.00 0.00 0.00 3.58
88 89 3.291584 TGCTCTATGTACTCCCTCTGTG 58.708 50.000 0.00 0.00 0.00 3.66
89 90 3.671740 TGCTCTATGTACTCCCTCTGT 57.328 47.619 0.00 0.00 0.00 3.41
90 91 5.112686 GTTTTGCTCTATGTACTCCCTCTG 58.887 45.833 0.00 0.00 0.00 3.35
91 92 4.162509 GGTTTTGCTCTATGTACTCCCTCT 59.837 45.833 0.00 0.00 0.00 3.69
92 93 4.443621 GGTTTTGCTCTATGTACTCCCTC 58.556 47.826 0.00 0.00 0.00 4.30
93 94 3.118738 CGGTTTTGCTCTATGTACTCCCT 60.119 47.826 0.00 0.00 0.00 4.20
94 95 3.118884 TCGGTTTTGCTCTATGTACTCCC 60.119 47.826 0.00 0.00 0.00 4.30
95 96 4.119442 TCGGTTTTGCTCTATGTACTCC 57.881 45.455 0.00 0.00 0.00 3.85
96 97 6.476243 TTTTCGGTTTTGCTCTATGTACTC 57.524 37.500 0.00 0.00 0.00 2.59
97 98 6.870971 TTTTTCGGTTTTGCTCTATGTACT 57.129 33.333 0.00 0.00 0.00 2.73
98 99 6.033513 GCATTTTTCGGTTTTGCTCTATGTAC 59.966 38.462 0.00 0.00 0.00 2.90
114 115 1.463056 TCGCAGGTGTAGCATTTTTCG 59.537 47.619 0.00 0.00 0.00 3.46
119 120 1.442769 CTGTTCGCAGGTGTAGCATT 58.557 50.000 0.00 0.00 41.40 3.56
205 212 2.990740 TTTTCACTAGTTGGGGGCAT 57.009 45.000 0.00 0.00 0.00 4.40
222 229 7.565323 TGCTGATTTGGCTGTTTTTAATTTT 57.435 28.000 0.00 0.00 0.00 1.82
223 230 7.565323 TTGCTGATTTGGCTGTTTTTAATTT 57.435 28.000 0.00 0.00 0.00 1.82
234 241 2.596904 GCATGATTGCTGATTTGGCT 57.403 45.000 0.00 0.00 45.77 4.75
251 258 1.066430 GGGATTCTCACGTACCTTGCA 60.066 52.381 0.00 0.00 0.00 4.08
253 260 3.488721 CGTAGGGATTCTCACGTACCTTG 60.489 52.174 0.00 0.00 0.00 3.61
333 340 8.222433 CGTATTACCAGTTACGAAAATTCAACA 58.778 33.333 0.00 0.00 42.83 3.33
345 352 9.688592 ATGCTATTCTTACGTATTACCAGTTAC 57.311 33.333 0.00 0.00 0.00 2.50
402 411 1.078214 CCGGATGAGGTGTGCATGT 60.078 57.895 0.00 0.00 0.00 3.21
495 528 7.645340 GCATGCATTCTCTTATTTCGTGTAAAT 59.355 33.333 14.21 0.00 40.87 1.40
496 529 6.966632 GCATGCATTCTCTTATTTCGTGTAAA 59.033 34.615 14.21 0.00 0.00 2.01
497 530 6.316140 AGCATGCATTCTCTTATTTCGTGTAA 59.684 34.615 21.98 0.00 0.00 2.41
498 531 5.817296 AGCATGCATTCTCTTATTTCGTGTA 59.183 36.000 21.98 0.00 0.00 2.90
499 532 4.637534 AGCATGCATTCTCTTATTTCGTGT 59.362 37.500 21.98 0.00 0.00 4.49
500 533 4.968181 CAGCATGCATTCTCTTATTTCGTG 59.032 41.667 21.98 0.00 0.00 4.35
501 534 4.036027 CCAGCATGCATTCTCTTATTTCGT 59.964 41.667 21.98 0.00 31.97 3.85
502 535 4.274214 TCCAGCATGCATTCTCTTATTTCG 59.726 41.667 21.98 0.00 31.97 3.46
503 536 5.762825 TCCAGCATGCATTCTCTTATTTC 57.237 39.130 21.98 0.00 31.97 2.17
504 537 6.322969 TGAATCCAGCATGCATTCTCTTATTT 59.677 34.615 21.98 0.00 31.97 1.40
505 538 5.831525 TGAATCCAGCATGCATTCTCTTATT 59.168 36.000 21.98 7.49 31.97 1.40
506 539 5.382616 TGAATCCAGCATGCATTCTCTTAT 58.617 37.500 21.98 0.00 31.97 1.73
507 540 4.784177 TGAATCCAGCATGCATTCTCTTA 58.216 39.130 21.98 2.03 31.97 2.10
508 541 3.628008 TGAATCCAGCATGCATTCTCTT 58.372 40.909 21.98 5.22 31.97 2.85
586 782 1.286260 CTCGTAGGTCATAGCCGGC 59.714 63.158 21.89 21.89 0.00 6.13
587 783 0.311165 CACTCGTAGGTCATAGCCGG 59.689 60.000 0.00 0.00 0.00 6.13
588 784 0.317938 GCACTCGTAGGTCATAGCCG 60.318 60.000 0.00 0.00 0.00 5.52
589 785 1.033574 AGCACTCGTAGGTCATAGCC 58.966 55.000 0.00 0.00 0.00 3.93
590 786 1.866063 GCAGCACTCGTAGGTCATAGC 60.866 57.143 0.00 0.00 0.00 2.97
591 787 1.678627 AGCAGCACTCGTAGGTCATAG 59.321 52.381 0.00 0.00 0.00 2.23
592 788 1.763968 AGCAGCACTCGTAGGTCATA 58.236 50.000 0.00 0.00 0.00 2.15
593 789 1.405821 GTAGCAGCACTCGTAGGTCAT 59.594 52.381 0.00 0.00 0.00 3.06
594 790 0.809385 GTAGCAGCACTCGTAGGTCA 59.191 55.000 0.00 0.00 0.00 4.02
595 791 1.096416 AGTAGCAGCACTCGTAGGTC 58.904 55.000 0.00 0.00 0.00 3.85
596 792 2.093075 TCTAGTAGCAGCACTCGTAGGT 60.093 50.000 0.00 0.00 0.00 3.08
597 793 2.562635 TCTAGTAGCAGCACTCGTAGG 58.437 52.381 0.00 0.00 0.00 3.18
601 797 2.096169 CCGTATCTAGTAGCAGCACTCG 60.096 54.545 0.00 0.00 0.00 4.18
799 1018 1.852895 GGTATCTTGTCAGTTAGCGCG 59.147 52.381 0.00 0.00 0.00 6.86
843 1062 3.161450 CGGATGGGATGGACGGGT 61.161 66.667 0.00 0.00 0.00 5.28
871 1090 2.499289 CCAGAATCTATCTCGGGGATGG 59.501 54.545 0.00 0.00 35.73 3.51
910 1141 3.118811 CGATCAGAAGAAGGGAGAAGCTT 60.119 47.826 0.00 0.00 0.00 3.74
1204 1482 3.372954 GACTACATACAGCGGTGATCAC 58.627 50.000 23.44 17.91 0.00 3.06
1205 1483 2.361119 GGACTACATACAGCGGTGATCA 59.639 50.000 23.44 6.19 0.00 2.92
1237 1529 5.129650 TCATTATCAGAACCGAACCATGGTA 59.870 40.000 20.12 0.00 39.29 3.25
1250 1542 5.066893 GCTGCAGTTCCATTCATTATCAGAA 59.933 40.000 16.64 0.00 0.00 3.02
1257 1549 1.188863 GGGCTGCAGTTCCATTCATT 58.811 50.000 16.64 0.00 0.00 2.57
1323 1704 2.344500 CCGTTGGGGTACTTGCGA 59.656 61.111 0.00 0.00 0.00 5.10
1531 1913 4.922026 GGTGTTGACGGCGGTGGT 62.922 66.667 13.24 0.00 0.00 4.16
1534 1916 2.030490 TTGTAGGTGTTGACGGCGGT 62.030 55.000 13.24 0.00 0.00 5.68
1605 1998 4.933330 TGCCTGATCGACTAACTAATCAC 58.067 43.478 0.00 0.00 0.00 3.06
1606 1999 5.301805 TCATGCCTGATCGACTAACTAATCA 59.698 40.000 0.00 0.00 0.00 2.57
1612 2005 3.553511 CAGTTCATGCCTGATCGACTAAC 59.446 47.826 6.40 0.00 31.38 2.34
1639 2035 2.114825 CCGGTAACTAAACGATCGAGC 58.885 52.381 24.34 5.96 0.00 5.03
1671 2070 1.087202 GTGACACTGTTGCACACGGA 61.087 55.000 12.81 0.00 35.45 4.69
1706 2105 2.520069 GGGCGAGAAGATCAGGATAGA 58.480 52.381 0.00 0.00 0.00 1.98
1803 2216 8.366359 AGGGCAATTTAGTCAATCAATAACTT 57.634 30.769 0.00 0.00 0.00 2.66
1804 2217 7.836183 AGAGGGCAATTTAGTCAATCAATAACT 59.164 33.333 0.00 0.00 0.00 2.24
1805 2218 8.000780 AGAGGGCAATTTAGTCAATCAATAAC 57.999 34.615 0.00 0.00 0.00 1.89
1806 2219 9.693739 TTAGAGGGCAATTTAGTCAATCAATAA 57.306 29.630 0.00 0.00 0.00 1.40
1811 2224 6.038714 CAGGTTAGAGGGCAATTTAGTCAATC 59.961 42.308 0.00 0.00 0.00 2.67
1813 2226 5.013704 TCAGGTTAGAGGGCAATTTAGTCAA 59.986 40.000 0.00 0.00 0.00 3.18
1818 2231 5.724854 AGTACTCAGGTTAGAGGGCAATTTA 59.275 40.000 0.00 0.00 39.97 1.40
1840 2261 5.247862 TGATGTGATGTGATGTTAGCAAGT 58.752 37.500 0.00 0.00 0.00 3.16
1841 2262 5.806366 TGATGTGATGTGATGTTAGCAAG 57.194 39.130 0.00 0.00 0.00 4.01
1844 2265 5.808042 ACTTGATGTGATGTGATGTTAGC 57.192 39.130 0.00 0.00 0.00 3.09
1845 2283 9.025020 GTACTACTTGATGTGATGTGATGTTAG 57.975 37.037 0.00 0.00 0.00 2.34
1849 2287 6.020360 CACGTACTACTTGATGTGATGTGATG 60.020 42.308 0.00 0.00 31.48 3.07
1866 2320 7.680350 GCAAGGTACAGTATCATTCACGTACTA 60.680 40.741 0.00 0.00 32.04 1.82
1867 2321 6.561614 CAAGGTACAGTATCATTCACGTACT 58.438 40.000 0.00 0.00 32.04 2.73
1872 2326 5.643777 ACTTGCAAGGTACAGTATCATTCAC 59.356 40.000 29.18 0.00 0.00 3.18
1874 2328 7.843490 TTACTTGCAAGGTACAGTATCATTC 57.157 36.000 29.18 0.00 0.00 2.67
1875 2329 8.512138 GTTTTACTTGCAAGGTACAGTATCATT 58.488 33.333 29.18 6.97 0.00 2.57
1880 2334 5.599732 TCGTTTTACTTGCAAGGTACAGTA 58.400 37.500 29.18 10.36 0.00 2.74
1881 2335 4.444536 TCGTTTTACTTGCAAGGTACAGT 58.555 39.130 29.18 11.42 0.00 3.55
1882 2336 4.748102 TCTCGTTTTACTTGCAAGGTACAG 59.252 41.667 29.18 15.64 0.00 2.74
1883 2337 4.695396 TCTCGTTTTACTTGCAAGGTACA 58.305 39.130 29.18 9.54 0.00 2.90
1884 2338 4.986659 TCTCTCGTTTTACTTGCAAGGTAC 59.013 41.667 29.18 18.53 0.00 3.34
1885 2339 5.204409 TCTCTCGTTTTACTTGCAAGGTA 57.796 39.130 29.18 16.17 0.00 3.08
1886 2340 4.067972 TCTCTCGTTTTACTTGCAAGGT 57.932 40.909 29.18 17.13 0.00 3.50
1888 2342 4.153117 AGCATCTCTCGTTTTACTTGCAAG 59.847 41.667 24.84 24.84 0.00 4.01
1892 2346 9.055248 CAAATTAAGCATCTCTCGTTTTACTTG 57.945 33.333 0.00 0.00 0.00 3.16
1894 2348 8.547967 TCAAATTAAGCATCTCTCGTTTTACT 57.452 30.769 0.00 0.00 0.00 2.24
1895 2349 9.214953 CATCAAATTAAGCATCTCTCGTTTTAC 57.785 33.333 0.00 0.00 0.00 2.01
1896 2350 8.946085 ACATCAAATTAAGCATCTCTCGTTTTA 58.054 29.630 0.00 0.00 0.00 1.52
1899 2353 6.820656 AGACATCAAATTAAGCATCTCTCGTT 59.179 34.615 0.00 0.00 0.00 3.85
1919 2374 4.225942 TCCTCCAATCAAAGCAGTAGACAT 59.774 41.667 0.00 0.00 0.00 3.06
1921 2376 4.081420 TCTCCTCCAATCAAAGCAGTAGAC 60.081 45.833 0.00 0.00 0.00 2.59
1924 2379 4.908601 TTCTCCTCCAATCAAAGCAGTA 57.091 40.909 0.00 0.00 0.00 2.74
1925 2380 3.795688 TTCTCCTCCAATCAAAGCAGT 57.204 42.857 0.00 0.00 0.00 4.40
1970 2425 1.227497 GGCTGCCACTAGCTAGCTG 60.227 63.158 27.68 18.34 42.07 4.24
2045 2562 7.814587 CCACACATCAATATCATACACGTAGAT 59.185 37.037 0.00 0.00 0.00 1.98
2046 2563 7.145323 CCACACATCAATATCATACACGTAGA 58.855 38.462 0.00 0.00 0.00 2.59
2047 2564 6.923508 ACCACACATCAATATCATACACGTAG 59.076 38.462 0.00 0.00 0.00 3.51
2109 2642 2.103263 GGTCTTCTTGTAGATCCGGCAT 59.897 50.000 0.00 0.00 0.00 4.40
2269 2802 0.036105 TGCGTGATCATGGTTCTGCT 60.036 50.000 16.59 0.00 0.00 4.24
2272 2805 0.036105 TGCTGCGTGATCATGGTTCT 60.036 50.000 16.59 0.00 0.00 3.01
2308 2841 3.537874 CGGGATCGTGGGGAGTCC 61.538 72.222 0.00 0.00 0.00 3.85
2463 2996 2.482374 GCGTAGTACGACGGCTGT 59.518 61.111 26.29 0.00 46.05 4.40
2535 3068 4.856607 GACTCTTCCGGGCTCGCG 62.857 72.222 0.00 0.00 34.56 5.87
2568 3116 3.353600 TCGAAGCACGACCCGTTA 58.646 55.556 2.09 0.00 46.45 3.18
2644 3192 2.170187 ACTGAGGAAGCATCTGATGACC 59.830 50.000 21.30 18.01 0.00 4.02
2646 3194 3.773667 AGAACTGAGGAAGCATCTGATGA 59.226 43.478 21.30 0.00 0.00 2.92
2749 3298 8.251750 TGTACTAGTACAAGATTGTTTCATGC 57.748 34.615 29.20 1.32 42.49 4.06
2927 3480 2.469465 TTTGCCGCCCTCTCCTTCAG 62.469 60.000 0.00 0.00 0.00 3.02
2972 3526 9.982291 GTTTCACAACATACAATCATTATACGT 57.018 29.630 0.00 0.00 32.54 3.57
2989 3543 3.194755 AGGGACCAACAAAGTTTCACAAC 59.805 43.478 0.00 0.00 0.00 3.32
2990 3544 3.436243 AGGGACCAACAAAGTTTCACAA 58.564 40.909 0.00 0.00 0.00 3.33
2992 3546 4.465632 AAAGGGACCAACAAAGTTTCAC 57.534 40.909 0.00 0.00 0.00 3.18
2997 4528 3.178046 ACCAAAAAGGGACCAACAAAGT 58.822 40.909 0.00 0.00 43.89 2.66
3016 4547 5.296748 ACACTTGCATTGAAACCATAAACC 58.703 37.500 2.94 0.00 0.00 3.27
3017 4548 6.257630 ACAACACTTGCATTGAAACCATAAAC 59.742 34.615 4.82 0.00 0.00 2.01
3018 4549 6.344500 ACAACACTTGCATTGAAACCATAAA 58.656 32.000 4.82 0.00 0.00 1.40
3019 4550 5.911752 ACAACACTTGCATTGAAACCATAA 58.088 33.333 4.82 0.00 0.00 1.90
3020 4551 5.528043 ACAACACTTGCATTGAAACCATA 57.472 34.783 4.82 0.00 0.00 2.74
3021 4552 4.405116 ACAACACTTGCATTGAAACCAT 57.595 36.364 4.82 0.00 0.00 3.55
3022 4553 3.883830 ACAACACTTGCATTGAAACCA 57.116 38.095 4.82 0.00 0.00 3.67
3025 4556 6.344500 ACCATAAACAACACTTGCATTGAAA 58.656 32.000 4.82 0.00 0.00 2.69
3092 4623 1.295792 TTCTATCATTTGCGACGCCC 58.704 50.000 18.69 0.00 0.00 6.13
3095 4626 5.142635 TGTGATTTCTATCATTTGCGACG 57.857 39.130 0.00 0.00 42.49 5.12
3112 4643 2.324879 ATGGACAGGGCCATGTGAT 58.675 52.632 30.62 16.58 46.62 3.06
3124 4655 1.469079 CGTCACGTCTGCATATGGACA 60.469 52.381 4.56 0.00 33.19 4.02
3142 4673 1.211969 CCGTGTCAACCGAGATCGT 59.788 57.895 1.09 0.00 37.74 3.73
3149 4680 1.067846 TCTTCTCATCCGTGTCAACCG 60.068 52.381 0.00 0.00 0.00 4.44
3209 4740 1.168853 AGGAGATACCCCCTACCCTC 58.831 60.000 0.00 0.00 40.05 4.30
3227 4758 5.864474 ACTTCATCTCGTAAGCACTAAACAG 59.136 40.000 0.00 0.00 37.18 3.16
3230 4761 7.541091 CACTAACTTCATCTCGTAAGCACTAAA 59.459 37.037 0.00 0.00 37.18 1.85
3231 4762 7.027760 CACTAACTTCATCTCGTAAGCACTAA 58.972 38.462 0.00 0.00 37.18 2.24
3240 4771 3.193691 CACCTCCACTAACTTCATCTCGT 59.806 47.826 0.00 0.00 0.00 4.18
3328 4859 3.702045 GCTAGGATTATATCGTGCTCCCT 59.298 47.826 0.00 0.00 0.00 4.20
3339 4870 0.974010 CGGGCGGGGCTAGGATTATA 60.974 60.000 0.00 0.00 0.00 0.98
3340 4871 2.291043 CGGGCGGGGCTAGGATTAT 61.291 63.158 0.00 0.00 0.00 1.28
3354 4885 0.661020 CGAATGGACAATAACCGGGC 59.339 55.000 6.32 0.00 0.00 6.13
3356 4887 2.319136 TCCGAATGGACAATAACCGG 57.681 50.000 0.00 0.00 40.17 5.28
3409 4945 1.631071 GGAGGGAAAGGCAGGAGAGG 61.631 65.000 0.00 0.00 0.00 3.69
3433 4969 1.078214 CCAATCGCAGGAAGAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
3442 4978 1.600957 CTATGCTGGTTCCAATCGCAG 59.399 52.381 9.44 0.00 33.72 5.18
3467 5003 1.302431 CGAGCCCATTCCACACACA 60.302 57.895 0.00 0.00 0.00 3.72
3469 5005 1.302431 CACGAGCCCATTCCACACA 60.302 57.895 0.00 0.00 0.00 3.72
3471 5007 1.296392 CTCACGAGCCCATTCCACA 59.704 57.895 0.00 0.00 0.00 4.17
3499 5035 2.168313 GCCATCCCCACAGTTTAAATGG 59.832 50.000 0.00 0.07 36.19 3.16
3500 5036 3.099141 AGCCATCCCCACAGTTTAAATG 58.901 45.455 0.00 0.00 0.00 2.32
3501 5037 3.365472 GAGCCATCCCCACAGTTTAAAT 58.635 45.455 0.00 0.00 0.00 1.40
3505 5041 1.002134 CGAGCCATCCCCACAGTTT 60.002 57.895 0.00 0.00 0.00 2.66
3506 5042 1.903877 CTCGAGCCATCCCCACAGTT 61.904 60.000 0.00 0.00 0.00 3.16
3534 5070 2.715763 TCATCCTATAGGTGTCCCCC 57.284 55.000 18.51 0.00 36.34 5.40
3539 5075 7.676043 ACTGCTACATTATCATCCTATAGGTGT 59.324 37.037 18.51 14.87 36.34 4.16
3541 5077 8.671987 AACTGCTACATTATCATCCTATAGGT 57.328 34.615 18.51 3.47 36.34 3.08
3551 5087 4.180817 CCACGTGAACTGCTACATTATCA 58.819 43.478 19.30 0.00 0.00 2.15
3594 5131 2.863484 ACCCTTGGCATCCACCCA 60.863 61.111 0.00 0.00 30.78 4.51
3595 5132 2.362889 CACCCTTGGCATCCACCC 60.363 66.667 0.00 0.00 30.78 4.61
3606 5143 2.594592 GCTGCAACGGTCACCCTT 60.595 61.111 0.00 0.00 0.00 3.95
3613 5150 4.681978 GGTCCTCGCTGCAACGGT 62.682 66.667 9.99 0.00 0.00 4.83
3614 5151 4.379243 AGGTCCTCGCTGCAACGG 62.379 66.667 9.99 0.37 0.00 4.44
3616 5153 0.674895 AATGAGGTCCTCGCTGCAAC 60.675 55.000 14.34 0.00 32.35 4.17
3639 5176 2.340337 GCATCCCAACAAATCACTTGC 58.660 47.619 0.00 0.00 38.75 4.01
3642 5179 1.812571 GTCGCATCCCAACAAATCACT 59.187 47.619 0.00 0.00 0.00 3.41
3646 5183 0.802494 GTCGTCGCATCCCAACAAAT 59.198 50.000 0.00 0.00 0.00 2.32
3649 5186 2.431771 CGTCGTCGCATCCCAACA 60.432 61.111 0.00 0.00 0.00 3.33
3650 5187 3.186047 CCGTCGTCGCATCCCAAC 61.186 66.667 0.00 0.00 35.54 3.77
3653 5190 3.515286 TCTCCGTCGTCGCATCCC 61.515 66.667 0.00 0.00 35.54 3.85


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

AutoCloner maintained by Alex Coulton.