Multiple sequence alignment - TraesCS2D01G474600

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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 TraesCS2D01G474600 chr2D 100.000 2720 0 0 1 2720 577546526 577549245 0.000000e+00 5024.0
1 TraesCS2D01G474600 chr2D 90.141 71 6 1 2091 2161 10888584 10888653 1.040000e-14 91.6
2 TraesCS2D01G474600 chr2D 84.000 75 9 3 525 597 598231877 598231804 4.860000e-08 69.4
3 TraesCS2D01G474600 chr2B 91.515 1921 139 10 4 1908 695117475 695115563 0.000000e+00 2623.0
4 TraesCS2D01G474600 chr2B 91.622 1504 88 18 585 2073 695113201 695111721 0.000000e+00 2045.0
5 TraesCS2D01G474600 chr2B 91.045 67 6 0 2099 2165 31581558 31581492 1.040000e-14 91.6
6 TraesCS2D01G474600 chr2A 90.662 1103 87 12 810 1907 715908264 715907173 0.000000e+00 1452.0
7 TraesCS2D01G474600 chr2A 91.493 670 44 10 1146 1815 715903371 715902715 0.000000e+00 909.0
8 TraesCS2D01G474600 chr2A 84.499 729 90 11 4 714 715909231 715908508 0.000000e+00 699.0
9 TraesCS2D01G474600 chr2A 86.804 485 38 12 585 1069 715882807 715882349 4.010000e-143 518.0
10 TraesCS2D01G474600 chr2A 86.626 486 37 14 585 1069 715904617 715904159 1.870000e-141 512.0
11 TraesCS2D01G474600 chr2A 86.744 347 39 5 2376 2719 715900117 715899775 1.980000e-101 379.0
12 TraesCS2D01G474600 chr2A 94.737 114 6 0 700 813 715908493 715908380 7.740000e-41 178.0
13 TraesCS2D01G474600 chrUn 80.376 744 120 14 998 1734 108608262 108608986 2.380000e-150 542.0
14 TraesCS2D01G474600 chrUn 82.033 551 79 15 1151 1697 108604202 108604736 4.130000e-123 451.0
15 TraesCS2D01G474600 chrUn 91.026 234 21 0 2482 2715 20430369 20430136 1.570000e-82 316.0
16 TraesCS2D01G474600 chr4B 80.376 744 120 15 998 1734 665435726 665436450 2.380000e-150 542.0
17 TraesCS2D01G474600 chr4B 80.194 722 120 16 1019 1734 665381955 665381251 1.120000e-143 520.0
18 TraesCS2D01G474600 chr4B 79.363 722 126 12 1019 1734 665383285 665382581 1.130000e-133 486.0
19 TraesCS2D01G474600 chr4B 79.224 722 127 15 1019 1734 665384615 665383911 5.270000e-132 481.0
20 TraesCS2D01G474600 chr4B 77.915 566 92 17 1140 1702 665391165 665390630 3.380000e-84 322.0
21 TraesCS2D01G474600 chr4B 92.537 67 3 2 2099 2165 387790056 387790120 8.020000e-16 95.3
22 TraesCS2D01G474600 chr6A 90.717 237 22 0 2479 2715 107701010 107701246 1.570000e-82 316.0
23 TraesCS2D01G474600 chr6A 89.873 237 24 0 2479 2715 107692491 107692727 3.400000e-79 305.0
24 TraesCS2D01G474600 chr6A 92.537 67 5 0 2099 2165 139516386 139516320 2.230000e-16 97.1
25 TraesCS2D01G474600 chr5D 90.558 233 22 0 2483 2715 92465403 92465635 2.630000e-80 309.0
26 TraesCS2D01G474600 chr5D 95.161 62 3 0 2104 2165 466574186 466574247 6.200000e-17 99.0
27 TraesCS2D01G474600 chr6D 89.958 239 23 1 2479 2716 89329664 89329902 9.460000e-80 307.0
28 TraesCS2D01G474600 chr6D 80.769 156 22 8 435 586 9059539 9059690 6.150000e-22 115.0
29 TraesCS2D01G474600 chr7D 90.171 234 23 0 2479 2712 562148956 562149189 3.400000e-79 305.0
30 TraesCS2D01G474600 chr7D 86.585 82 8 3 2082 2161 46411868 46411948 1.340000e-13 87.9
31 TraesCS2D01G474600 chr6B 89.873 237 24 0 2479 2715 171728230 171728466 3.400000e-79 305.0
32 TraesCS2D01G474600 chr5B 89.300 243 24 1 2467 2709 98518969 98519209 1.220000e-78 303.0
33 TraesCS2D01G474600 chr5B 77.143 175 32 8 413 583 28269981 28270151 8.020000e-16 95.3
34 TraesCS2D01G474600 chr3B 79.695 197 34 5 394 587 637652826 637653019 1.310000e-28 137.0
35 TraesCS2D01G474600 chr3B 91.304 69 5 1 2101 2169 772893528 772893595 2.880000e-15 93.5
36 TraesCS2D01G474600 chr3D 81.250 160 22 6 435 592 511717370 511717217 3.680000e-24 122.0
37 TraesCS2D01G474600 chr3D 80.328 122 23 1 435 555 105245564 105245443 1.040000e-14 91.6
38 TraesCS2D01G474600 chr3D 80.328 122 23 1 435 555 105272310 105272189 1.040000e-14 91.6
39 TraesCS2D01G474600 chr1B 80.667 150 27 2 435 583 161987934 161988082 6.150000e-22 115.0
40 TraesCS2D01G474600 chr4D 93.548 62 4 0 2104 2165 310377665 310377726 2.880000e-15 93.5
41 TraesCS2D01G474600 chr1A 94.828 58 3 0 2104 2161 518772205 518772148 1.040000e-14 91.6
42 TraesCS2D01G474600 chr3A 77.215 158 31 5 407 562 749867682 749867528 1.340000e-13 87.9


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 TraesCS2D01G474600 chr2D 577546526 577549245 2719 False 5024.000000 5024 100.000000 1 2720 1 chr2D.!!$F2 2719
1 TraesCS2D01G474600 chr2B 695111721 695117475 5754 True 2334.000000 2623 91.568500 4 2073 2 chr2B.!!$R2 2069
2 TraesCS2D01G474600 chr2A 715899775 715909231 9456 True 688.166667 1452 89.126833 4 2719 6 chr2A.!!$R2 2715
3 TraesCS2D01G474600 chrUn 108604202 108608986 4784 False 496.500000 542 81.204500 998 1734 2 chrUn.!!$F1 736
4 TraesCS2D01G474600 chr4B 665435726 665436450 724 False 542.000000 542 80.376000 998 1734 1 chr4B.!!$F2 736
5 TraesCS2D01G474600 chr4B 665381251 665384615 3364 True 495.666667 520 79.593667 1019 1734 3 chr4B.!!$R2 715
6 TraesCS2D01G474600 chr4B 665390630 665391165 535 True 322.000000 322 77.915000 1140 1702 1 chr4B.!!$R1 562

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
147 149 0.105039 GGTAGCAGATCCGGAACTGG 59.895 60.0 34.56 20.58 35.05 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 12205 1.197721 ACAAGAGCAATGCGTTGTAGC 59.802 47.619 21.75 5.96 38.27 3.58 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
29 30 2.440796 CCGGCATGCAAGGTGGAT 60.441 61.111 21.36 0.00 0.00 3.41
38 40 1.983224 CAAGGTGGATGACGGAGGT 59.017 57.895 0.00 0.00 0.00 3.85
52 54 1.596934 GAGGTGGCGTGGATTGAGA 59.403 57.895 0.00 0.00 0.00 3.27
53 55 0.741221 GAGGTGGCGTGGATTGAGAC 60.741 60.000 0.00 0.00 0.00 3.36
58 60 2.264480 CGTGGATTGAGACGCCCA 59.736 61.111 0.00 0.00 0.00 5.36
107 109 1.374947 GGCTCCGGCATAGGCATTA 59.625 57.895 9.99 0.00 43.71 1.90
130 132 2.113986 GTGGGCAAGCAGTGAGGT 59.886 61.111 0.00 0.00 0.00 3.85
147 149 0.105039 GGTAGCAGATCCGGAACTGG 59.895 60.000 34.56 20.58 35.05 4.00
151 153 2.285368 AGATCCGGAACTGGCCCA 60.285 61.111 14.25 0.00 0.00 5.36
188 194 1.439353 CCGCTCCATCACAATTCGGG 61.439 60.000 0.00 0.00 32.55 5.14
189 195 1.729881 GCTCCATCACAATTCGGGC 59.270 57.895 0.00 0.00 0.00 6.13
271 277 1.700042 GCCGGAGATGGGATTGGAGT 61.700 60.000 5.05 0.00 0.00 3.85
273 279 1.620819 CCGGAGATGGGATTGGAGTAG 59.379 57.143 0.00 0.00 0.00 2.57
278 284 3.243724 AGATGGGATTGGAGTAGCTACC 58.756 50.000 20.31 11.50 0.00 3.18
289 295 2.950309 GAGTAGCTACCAGACCGAATCA 59.050 50.000 20.31 0.00 0.00 2.57
302 308 1.559682 CCGAATCAAAGAAGGGGAGGA 59.440 52.381 0.00 0.00 0.00 3.71
319 325 0.741915 GGAGAAGAGACGAAGCGGAT 59.258 55.000 0.00 0.00 0.00 4.18
321 327 0.741915 AGAAGAGACGAAGCGGATCC 59.258 55.000 0.00 0.00 0.00 3.36
326 332 4.554363 ACGAAGCGGATCCGAGCG 62.554 66.667 37.64 32.64 42.83 5.03
407 430 2.476051 GTTGACATGGCAGACGCG 59.524 61.111 3.53 3.53 39.92 6.01
426 449 1.842381 GCCCTGGCCGCCTTATATCT 61.842 60.000 11.61 0.00 34.56 1.98
427 450 1.568504 CCCTGGCCGCCTTATATCTA 58.431 55.000 11.61 0.00 0.00 1.98
451 474 3.029483 TGCATTTGGGCTGGATATGAA 57.971 42.857 0.00 0.00 34.04 2.57
470 493 3.590824 GGCACCAGACAATTCGGG 58.409 61.111 0.00 0.00 42.54 5.14
498 521 3.814268 CGGTTTGAGGCGCCCATG 61.814 66.667 26.15 7.57 0.00 3.66
500 523 2.568090 GTTTGAGGCGCCCATGTG 59.432 61.111 26.15 0.00 0.00 3.21
501 524 1.971167 GTTTGAGGCGCCCATGTGA 60.971 57.895 26.15 2.70 0.00 3.58
503 526 2.410322 TTTGAGGCGCCCATGTGAGT 62.410 55.000 26.15 0.00 0.00 3.41
505 528 2.360350 AGGCGCCCATGTGAGTTG 60.360 61.111 26.15 0.00 0.00 3.16
506 529 4.120331 GGCGCCCATGTGAGTTGC 62.120 66.667 18.11 0.00 0.00 4.17
533 557 1.991121 TTACGGTCACTGACAGGTCT 58.009 50.000 13.09 0.00 33.68 3.85
543 567 3.314331 ACAGGTCTGTCTGCCCGG 61.314 66.667 0.00 0.00 40.24 5.73
583 607 3.748863 CGTCTGGCTGTAGATGCTT 57.251 52.632 0.00 0.00 0.00 3.91
635 659 9.703892 CATTAGAATTCCACCAACATTTTTGTA 57.296 29.630 0.65 0.00 0.00 2.41
691 715 6.746364 GTCATGAATGTTCTGCTTGATCTTTC 59.254 38.462 0.00 0.00 33.11 2.62
799 852 1.970114 CTGGTGCTGCAGGTTGGAG 60.970 63.158 17.12 0.00 38.97 3.86
876 1048 1.475751 GCTATAGCAGGCAGGAGCAAA 60.476 52.381 20.01 0.00 41.29 3.68
922 1100 3.561120 TTGCCACCGCCACCCTAAG 62.561 63.158 0.00 0.00 0.00 2.18
1003 1181 1.072173 CCACCCATAGATTCGCCATGA 59.928 52.381 0.00 0.00 0.00 3.07
1112 1290 1.067142 TGACCTTATCGTCCTGCACAC 60.067 52.381 0.00 0.00 31.35 3.82
1420 1601 3.043713 CGCTGGCAACGCTCAAGA 61.044 61.111 0.00 0.00 42.51 3.02
1747 10966 0.179189 GCATGCACGCTGGTTTAGAC 60.179 55.000 14.21 0.00 0.00 2.59
1852 11102 5.434408 TGAGCTTCAATATGTTCTGCTCAT 58.566 37.500 14.69 0.00 46.62 2.90
1859 11109 9.661187 CTTCAATATGTTCTGCTCATGAAATAC 57.339 33.333 0.00 0.00 0.00 1.89
1860 11110 7.854534 TCAATATGTTCTGCTCATGAAATACG 58.145 34.615 0.00 0.00 0.00 3.06
2009 11338 6.127730 CCGGCTTATTTGAATTTAGTCTTGGT 60.128 38.462 0.00 0.00 0.00 3.67
2011 11340 8.455682 CGGCTTATTTGAATTTAGTCTTGGTTA 58.544 33.333 0.00 0.00 0.00 2.85
2060 12182 1.269413 CCACTTTGCCTGTTCTTGCTG 60.269 52.381 0.00 0.00 0.00 4.41
2062 12184 0.319297 CTTTGCCTGTTCTTGCTGCC 60.319 55.000 0.00 0.00 0.00 4.85
2087 12209 3.793144 GCACTGGCGCACTGCTAC 61.793 66.667 10.83 0.00 45.43 3.58
2088 12210 2.357396 CACTGGCGCACTGCTACA 60.357 61.111 10.83 0.00 45.43 2.74
2089 12211 1.960763 CACTGGCGCACTGCTACAA 60.961 57.895 10.83 0.00 45.43 2.41
2090 12212 1.961277 ACTGGCGCACTGCTACAAC 60.961 57.895 10.83 0.00 45.43 3.32
2091 12213 3.015293 CTGGCGCACTGCTACAACG 62.015 63.158 10.83 0.00 45.43 4.10
2094 12216 3.168271 CGCACTGCTACAACGCAT 58.832 55.556 0.00 0.00 39.52 4.73
2095 12217 1.497278 CGCACTGCTACAACGCATT 59.503 52.632 0.00 0.00 39.52 3.56
2097 12219 3.005823 CACTGCTACAACGCATTGC 57.994 52.632 0.00 0.00 39.66 3.56
2098 12220 0.518636 CACTGCTACAACGCATTGCT 59.481 50.000 7.12 0.00 39.66 3.91
2099 12221 0.798776 ACTGCTACAACGCATTGCTC 59.201 50.000 7.12 0.00 39.66 4.26
2100 12222 1.081892 CTGCTACAACGCATTGCTCT 58.918 50.000 7.12 0.00 39.66 4.09
2103 12225 1.197721 GCTACAACGCATTGCTCTTGT 59.802 47.619 19.43 19.43 39.66 3.16
2105 12227 2.869233 ACAACGCATTGCTCTTGTTT 57.131 40.000 13.11 0.00 39.66 2.83
2106 12228 3.163630 ACAACGCATTGCTCTTGTTTT 57.836 38.095 13.11 0.00 39.66 2.43
2107 12229 3.115554 ACAACGCATTGCTCTTGTTTTC 58.884 40.909 13.11 0.00 39.66 2.29
2108 12230 2.036556 ACGCATTGCTCTTGTTTTCG 57.963 45.000 7.12 0.00 0.00 3.46
2110 12232 1.971962 CGCATTGCTCTTGTTTTCGAC 59.028 47.619 7.12 0.00 0.00 4.20
2111 12233 2.601979 CGCATTGCTCTTGTTTTCGACA 60.602 45.455 7.12 0.00 36.19 4.35
2112 12234 3.371168 GCATTGCTCTTGTTTTCGACAA 58.629 40.909 0.16 0.00 45.70 3.18
2113 12235 3.796178 GCATTGCTCTTGTTTTCGACAAA 59.204 39.130 0.16 0.00 46.99 2.83
2114 12236 4.085415 GCATTGCTCTTGTTTTCGACAAAG 60.085 41.667 0.16 0.00 46.99 2.77
2115 12237 4.955925 TTGCTCTTGTTTTCGACAAAGA 57.044 36.364 0.00 0.00 46.99 2.52
2116 12238 4.536364 TGCTCTTGTTTTCGACAAAGAG 57.464 40.909 15.93 15.93 46.99 2.85
2117 12239 3.938963 TGCTCTTGTTTTCGACAAAGAGT 59.061 39.130 19.02 0.00 46.99 3.24
2119 12241 4.034048 GCTCTTGTTTTCGACAAAGAGTGA 59.966 41.667 19.02 9.21 46.99 3.41
2120 12242 5.447279 GCTCTTGTTTTCGACAAAGAGTGAA 60.447 40.000 19.02 0.00 46.99 3.18
2121 12243 6.677781 TCTTGTTTTCGACAAAGAGTGAAT 57.322 33.333 0.00 0.00 46.99 2.57
2122 12244 7.083875 TCTTGTTTTCGACAAAGAGTGAATT 57.916 32.000 0.00 0.00 46.99 2.17
2124 12246 8.026607 TCTTGTTTTCGACAAAGAGTGAATTTT 58.973 29.630 0.00 0.00 46.99 1.82
2127 12249 9.796120 TGTTTTCGACAAAGAGTGAATTTTATT 57.204 25.926 0.00 0.00 34.69 1.40
2130 12252 9.445786 TTTCGACAAAGAGTGAATTTTATTGAC 57.554 29.630 0.00 0.00 0.00 3.18
2131 12253 8.378172 TCGACAAAGAGTGAATTTTATTGACT 57.622 30.769 0.00 0.00 0.00 3.41
2132 12254 8.495949 TCGACAAAGAGTGAATTTTATTGACTC 58.504 33.333 9.94 9.94 34.47 3.36
2134 12256 9.950680 GACAAAGAGTGAATTTTATTGACTCAA 57.049 29.630 17.22 0.00 36.34 3.02
2143 12265 9.761504 TGAATTTTATTGACTCAAAATGAAGCA 57.238 25.926 0.00 0.00 35.19 3.91
2147 12269 9.761504 TTTTATTGACTCAAAATGAAGCATCAA 57.238 25.926 0.00 0.00 39.49 2.57
2149 12271 4.801891 TGACTCAAAATGAAGCATCAAGC 58.198 39.130 0.00 0.00 46.19 4.01
2162 12284 4.952262 GCATCAAGCAGATACAAACAGA 57.048 40.909 0.00 0.00 44.79 3.41
2163 12285 5.300969 GCATCAAGCAGATACAAACAGAA 57.699 39.130 0.00 0.00 44.79 3.02
2164 12286 5.888105 GCATCAAGCAGATACAAACAGAAT 58.112 37.500 0.00 0.00 44.79 2.40
2165 12287 5.970023 GCATCAAGCAGATACAAACAGAATC 59.030 40.000 0.00 0.00 44.79 2.52
2166 12288 6.403964 GCATCAAGCAGATACAAACAGAATCA 60.404 38.462 0.00 0.00 44.79 2.57
2167 12289 7.532571 CATCAAGCAGATACAAACAGAATCAA 58.467 34.615 0.00 0.00 34.43 2.57
2172 12942 5.163581 GCAGATACAAACAGAATCAAGGCAT 60.164 40.000 0.00 0.00 0.00 4.40
2186 12956 3.312718 GCATGCCTTTGCCACCCA 61.313 61.111 6.36 0.00 36.60 4.51
2187 12957 2.662070 GCATGCCTTTGCCACCCAT 61.662 57.895 6.36 0.00 36.60 4.00
2188 12958 1.219664 CATGCCTTTGCCACCCATG 59.780 57.895 0.00 0.00 36.33 3.66
2189 12959 1.078891 ATGCCTTTGCCACCCATGA 59.921 52.632 0.00 0.00 36.33 3.07
2191 12961 0.544833 TGCCTTTGCCACCCATGAAT 60.545 50.000 0.00 0.00 36.33 2.57
2192 12962 0.176449 GCCTTTGCCACCCATGAATC 59.824 55.000 0.00 0.00 0.00 2.52
2194 12964 1.462616 CTTTGCCACCCATGAATCGA 58.537 50.000 0.00 0.00 0.00 3.59
2195 12965 1.133025 CTTTGCCACCCATGAATCGAC 59.867 52.381 0.00 0.00 0.00 4.20
2196 12966 0.327924 TTGCCACCCATGAATCGACT 59.672 50.000 0.00 0.00 0.00 4.18
2197 12967 0.107703 TGCCACCCATGAATCGACTC 60.108 55.000 0.00 0.00 0.00 3.36
2198 12968 1.154205 GCCACCCATGAATCGACTCG 61.154 60.000 0.00 0.00 0.00 4.18
2199 12969 0.530650 CCACCCATGAATCGACTCGG 60.531 60.000 0.00 0.00 0.00 4.63
2200 12970 0.175760 CACCCATGAATCGACTCGGT 59.824 55.000 0.00 0.00 0.00 4.69
2201 12971 0.902531 ACCCATGAATCGACTCGGTT 59.097 50.000 0.00 0.00 30.82 4.44
2202 12972 1.278127 ACCCATGAATCGACTCGGTTT 59.722 47.619 0.00 0.00 27.16 3.27
2203 12973 1.665679 CCCATGAATCGACTCGGTTTG 59.334 52.381 0.00 0.00 27.16 2.93
2204 12974 2.616960 CCATGAATCGACTCGGTTTGA 58.383 47.619 0.00 0.00 27.16 2.69
2205 12975 2.348666 CCATGAATCGACTCGGTTTGAC 59.651 50.000 0.00 0.00 27.16 3.18
2206 12976 3.254060 CATGAATCGACTCGGTTTGACT 58.746 45.455 0.00 0.00 27.16 3.41
2207 12977 4.421058 CATGAATCGACTCGGTTTGACTA 58.579 43.478 0.00 0.00 27.16 2.59
2208 12978 4.508461 TGAATCGACTCGGTTTGACTAA 57.492 40.909 0.00 0.00 27.16 2.24
2209 12979 4.482386 TGAATCGACTCGGTTTGACTAAG 58.518 43.478 0.00 0.00 27.16 2.18
2210 12980 4.022589 TGAATCGACTCGGTTTGACTAAGT 60.023 41.667 0.00 0.00 27.16 2.24
2211 12981 3.996150 TCGACTCGGTTTGACTAAGTT 57.004 42.857 0.00 0.00 0.00 2.66
2212 12982 4.311816 TCGACTCGGTTTGACTAAGTTT 57.688 40.909 0.00 0.00 0.00 2.66
2213 12983 4.293415 TCGACTCGGTTTGACTAAGTTTC 58.707 43.478 0.00 0.00 0.00 2.78
2214 12984 4.046462 CGACTCGGTTTGACTAAGTTTCA 58.954 43.478 0.00 0.00 0.00 2.69
2215 12985 4.505191 CGACTCGGTTTGACTAAGTTTCAA 59.495 41.667 0.00 0.00 0.00 2.69
2224 12994 8.558700 GGTTTGACTAAGTTTCAAATACGGTTA 58.441 33.333 6.11 0.00 43.16 2.85
2226 12996 8.891671 TTGACTAAGTTTCAAATACGGTTACT 57.108 30.769 0.00 0.00 29.89 2.24
2242 13012 3.258622 GGTTACTAATCATAGAGCCGCCT 59.741 47.826 0.00 0.00 33.15 5.52
2244 13014 3.393089 ACTAATCATAGAGCCGCCTTG 57.607 47.619 0.00 0.00 33.15 3.61
2257 13027 3.058160 CCTTGGCACCCGAAGCAG 61.058 66.667 0.00 0.00 0.00 4.24
2263 13033 1.748879 GCACCCGAAGCAGGCATTA 60.749 57.895 0.00 0.00 0.00 1.90
2287 13057 3.134442 ACAAGGCACAACAATTCCAACAT 59.866 39.130 0.00 0.00 0.00 2.71
2288 13058 4.343526 ACAAGGCACAACAATTCCAACATA 59.656 37.500 0.00 0.00 0.00 2.29
2289 13059 5.163364 ACAAGGCACAACAATTCCAACATAA 60.163 36.000 0.00 0.00 0.00 1.90
2292 13062 5.053145 GGCACAACAATTCCAACATAAACA 58.947 37.500 0.00 0.00 0.00 2.83
2301 13071 9.077885 ACAATTCCAACATAAACAGAACAGTAT 57.922 29.630 0.00 0.00 0.00 2.12
2302 13072 9.559958 CAATTCCAACATAAACAGAACAGTATC 57.440 33.333 0.00 0.00 0.00 2.24
2307 13097 7.538678 CCAACATAAACAGAACAGTATCAAAGC 59.461 37.037 0.00 0.00 0.00 3.51
2311 13101 8.905702 CATAAACAGAACAGTATCAAAGCAAAC 58.094 33.333 0.00 0.00 0.00 2.93
2312 13102 6.449635 AACAGAACAGTATCAAAGCAAACA 57.550 33.333 0.00 0.00 0.00 2.83
2349 13139 8.675705 AATTTTCCCTTAAACAAAATGACTGG 57.324 30.769 0.00 0.00 31.56 4.00
2350 13140 6.800072 TTTCCCTTAAACAAAATGACTGGT 57.200 33.333 0.00 0.00 0.00 4.00
2351 13141 6.800072 TTCCCTTAAACAAAATGACTGGTT 57.200 33.333 0.00 0.00 0.00 3.67
2353 13143 5.894393 TCCCTTAAACAAAATGACTGGTTCA 59.106 36.000 0.00 0.00 39.11 3.18
2355 13145 7.070571 TCCCTTAAACAAAATGACTGGTTCAAT 59.929 33.333 0.00 0.00 37.92 2.57
2358 13148 9.097257 CTTAAACAAAATGACTGGTTCAATGTT 57.903 29.630 0.00 0.00 39.43 2.71
2359 13149 7.538303 AAACAAAATGACTGGTTCAATGTTC 57.462 32.000 0.00 0.00 38.03 3.18
2360 13150 5.280945 ACAAAATGACTGGTTCAATGTTCG 58.719 37.500 0.00 0.00 37.92 3.95
2361 13151 5.067153 ACAAAATGACTGGTTCAATGTTCGA 59.933 36.000 0.00 0.00 37.92 3.71
2362 13152 4.749245 AATGACTGGTTCAATGTTCGAC 57.251 40.909 0.00 0.00 37.92 4.20
2363 13153 2.131972 TGACTGGTTCAATGTTCGACG 58.868 47.619 0.00 0.00 0.00 5.12
2364 13154 2.223852 TGACTGGTTCAATGTTCGACGA 60.224 45.455 0.00 0.00 0.00 4.20
2365 13155 2.132762 ACTGGTTCAATGTTCGACGAC 58.867 47.619 0.00 0.00 0.00 4.34
2366 13156 2.223971 ACTGGTTCAATGTTCGACGACT 60.224 45.455 0.00 0.00 0.00 4.18
2367 13157 2.131972 TGGTTCAATGTTCGACGACTG 58.868 47.619 0.00 0.00 0.00 3.51
2368 13158 2.223852 TGGTTCAATGTTCGACGACTGA 60.224 45.455 0.00 0.00 0.00 3.41
2369 13159 2.993899 GGTTCAATGTTCGACGACTGAT 59.006 45.455 0.00 0.00 0.00 2.90
2370 13160 3.432252 GGTTCAATGTTCGACGACTGATT 59.568 43.478 0.00 0.00 0.00 2.57
2371 13161 4.386230 GTTCAATGTTCGACGACTGATTG 58.614 43.478 0.00 6.68 0.00 2.67
2372 13162 3.908213 TCAATGTTCGACGACTGATTGA 58.092 40.909 16.01 16.01 0.00 2.57
2374 13164 4.385748 TCAATGTTCGACGACTGATTGAAG 59.614 41.667 16.99 0.38 29.23 3.02
2380 13664 3.749609 TCGACGACTGATTGAAGACACTA 59.250 43.478 0.00 0.00 0.00 2.74
2395 13679 9.781834 TTGAAGACACTACAAACAAACTAAATG 57.218 29.630 0.00 0.00 0.00 2.32
2399 13683 8.952278 AGACACTACAAACAAACTAAATGAACA 58.048 29.630 0.00 0.00 0.00 3.18
2405 13689 7.551585 ACAAACAAACTAAATGAACATCCACA 58.448 30.769 0.00 0.00 0.00 4.17
2413 13697 7.450074 ACTAAATGAACATCCACAACTACTCA 58.550 34.615 0.00 0.00 0.00 3.41
2449 13734 4.926244 ACTAAGATAGACGATGCACACAG 58.074 43.478 0.00 0.00 0.00 3.66
2460 13745 2.089017 GCACACAGCGCATCATGTA 58.911 52.632 11.47 0.00 0.00 2.29
2461 13746 0.027194 GCACACAGCGCATCATGTAG 59.973 55.000 11.47 2.53 0.00 2.74
2462 13747 0.027194 CACACAGCGCATCATGTAGC 59.973 55.000 11.47 0.00 0.00 3.58
2463 13748 0.391528 ACACAGCGCATCATGTAGCA 60.392 50.000 11.47 0.00 0.00 3.49
2469 13754 0.306840 CGCATCATGTAGCAAGCAGG 59.693 55.000 11.51 0.00 0.00 4.85
2471 13756 1.385528 CATCATGTAGCAAGCAGGCA 58.614 50.000 2.37 0.00 35.83 4.75
2481 13766 3.564345 AAGCAGGCAGGCTCACAGG 62.564 63.158 4.11 0.00 45.07 4.00
2514 13799 1.554583 GGAGGACAAGGTGGAGGGTC 61.555 65.000 0.00 0.00 0.00 4.46
2527 13812 0.323542 GAGGGTCGACTCCTTCTGGA 60.324 60.000 21.74 0.00 40.69 3.86
2546 13831 1.204941 GATGTTGTAGTCAGCGAGGGT 59.795 52.381 0.00 0.00 0.00 4.34
2571 13856 0.179702 CATCCTCTAGCTGCTTGCCA 59.820 55.000 7.79 0.00 44.23 4.92
2583 13868 0.172803 GCTTGCCAGCAAAGATCAGG 59.827 55.000 4.63 0.00 46.49 3.86
2586 13871 2.042831 GCCAGCAAAGATCAGGCGT 61.043 57.895 0.00 0.00 35.42 5.68
2634 13919 2.274542 TCCTGGATCTTGGCCTTAACA 58.725 47.619 3.32 0.00 0.00 2.41
2643 13928 5.092554 TCTTGGCCTTAACATTGTCGATA 57.907 39.130 3.32 0.00 0.00 2.92
2649 13934 5.109903 GCCTTAACATTGTCGATAGTGTCT 58.890 41.667 10.61 4.72 37.40 3.41
2652 13937 6.980978 CCTTAACATTGTCGATAGTGTCTGAT 59.019 38.462 10.61 0.00 37.40 2.90
2655 13940 5.344066 ACATTGTCGATAGTGTCTGATGAC 58.656 41.667 4.45 0.00 43.20 3.06
2664 13949 1.895798 GTGTCTGATGACTCCACCTCA 59.104 52.381 0.00 0.00 43.29 3.86
2667 13952 2.093764 GTCTGATGACTCCACCTCAAGG 60.094 54.545 0.00 0.00 39.94 3.61
2682 13967 2.237143 CTCAAGGGTGATAGTCTTGCCA 59.763 50.000 0.00 0.00 38.13 4.92
2687 13972 2.419297 GGGTGATAGTCTTGCCAGTCAG 60.419 54.545 0.00 0.00 0.00 3.51
2688 13973 2.419297 GGTGATAGTCTTGCCAGTCAGG 60.419 54.545 0.00 0.00 41.84 3.86
2694 13979 0.687354 TCTTGCCAGTCAGGGTCTTC 59.313 55.000 0.00 0.00 38.09 2.87
2712 13997 1.931906 TCACGAAGATCTGCATCTGC 58.068 50.000 0.51 0.00 38.55 4.26
2714 13999 5.678169 CTTCACGAAGATCTGCATCTGCAA 61.678 45.833 6.31 0.00 44.81 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.107508 CTCCGTCATCCACCTTGCAT 60.108 55.000 0.00 0.00 0.00 3.96
18 19 1.296392 CTCCGTCATCCACCTTGCA 59.704 57.895 0.00 0.00 0.00 4.08
20 21 0.391661 CACCTCCGTCATCCACCTTG 60.392 60.000 0.00 0.00 0.00 3.61
21 22 1.553690 CCACCTCCGTCATCCACCTT 61.554 60.000 0.00 0.00 0.00 3.50
58 60 3.848347 CTCGCACACAGCTCCACGT 62.848 63.158 0.00 0.00 42.61 4.49
112 114 2.124507 TACCTCACTGCTTGCCCACC 62.125 60.000 0.00 0.00 0.00 4.61
119 121 1.484240 GGATCTGCTACCTCACTGCTT 59.516 52.381 0.00 0.00 0.00 3.91
130 132 1.686325 GGCCAGTTCCGGATCTGCTA 61.686 60.000 29.62 1.88 0.00 3.49
165 171 1.369091 AATTGTGATGGAGCGGTCGC 61.369 55.000 8.77 7.32 42.33 5.19
166 172 0.652592 GAATTGTGATGGAGCGGTCG 59.347 55.000 8.77 0.00 0.00 4.79
167 173 0.652592 CGAATTGTGATGGAGCGGTC 59.347 55.000 5.93 5.93 0.00 4.79
189 195 4.101448 CAGGGAGGAGTTGGGCCG 62.101 72.222 0.00 0.00 0.00 6.13
204 210 1.078759 GACGGCTCCATCAACGACAG 61.079 60.000 0.00 0.00 0.00 3.51
271 277 4.021229 TCTTTGATTCGGTCTGGTAGCTA 58.979 43.478 0.00 0.00 0.00 3.32
273 279 3.247006 TCTTTGATTCGGTCTGGTAGC 57.753 47.619 0.00 0.00 0.00 3.58
278 284 2.027192 TCCCCTTCTTTGATTCGGTCTG 60.027 50.000 0.00 0.00 0.00 3.51
289 295 3.178046 GTCTCTTCTCCTCCCCTTCTTT 58.822 50.000 0.00 0.00 0.00 2.52
302 308 0.741915 GGATCCGCTTCGTCTCTTCT 59.258 55.000 0.00 0.00 0.00 2.85
326 332 1.079336 AGTAACTTCGCCCCGCTTC 60.079 57.895 0.00 0.00 0.00 3.86
379 402 2.840753 ATGTCAACCCGGCCCACTT 61.841 57.895 0.00 0.00 0.00 3.16
391 414 3.422303 GCGCGTCTGCCATGTCAA 61.422 61.111 8.43 0.00 38.08 3.18
407 430 1.377333 GATATAAGGCGGCCAGGGC 60.377 63.158 23.09 1.81 41.06 5.19
411 434 2.018355 TGGTAGATATAAGGCGGCCA 57.982 50.000 23.09 0.60 0.00 5.36
419 442 5.711506 CAGCCCAAATGCATGGTAGATATAA 59.288 40.000 0.00 0.00 38.91 0.98
420 443 5.255687 CAGCCCAAATGCATGGTAGATATA 58.744 41.667 0.00 0.00 38.91 0.86
426 449 0.334335 TCCAGCCCAAATGCATGGTA 59.666 50.000 0.00 0.00 38.91 3.25
427 450 0.325860 ATCCAGCCCAAATGCATGGT 60.326 50.000 0.00 0.00 38.91 3.55
451 474 1.002134 CCGAATTGTCTGGTGCCCT 60.002 57.895 0.00 0.00 0.00 5.19
464 487 2.750237 GGCCTCAAACGCCCGAAT 60.750 61.111 0.00 0.00 40.78 3.34
470 493 2.050442 CAAACCGGCCTCAAACGC 60.050 61.111 0.00 0.00 0.00 4.84
543 567 1.079888 CAAACCGGCCTCAAATGCC 60.080 57.895 0.00 0.00 45.70 4.40
546 570 1.250840 GCCTCAAACCGGCCTCAAAT 61.251 55.000 0.00 0.00 41.73 2.32
667 691 6.431852 TGAAAGATCAAGCAGAACATTCATGA 59.568 34.615 0.00 0.00 33.61 3.07
691 715 9.486857 GATTTGCTGAAATCATCGTATATCATG 57.513 33.333 4.97 0.00 44.81 3.07
752 805 3.941483 CGTGCTTCAATTCCAACCTCTAT 59.059 43.478 0.00 0.00 0.00 1.98
799 852 0.804989 GTGTGACTTACTGCCCATGC 59.195 55.000 0.00 0.00 38.26 4.06
876 1048 1.022982 CATCGCACTGCACACCTGAT 61.023 55.000 1.11 0.00 0.00 2.90
922 1100 9.680315 AACAACGAATGAAGTAGTCTATATAGC 57.320 33.333 4.75 0.92 0.00 2.97
943 1121 7.225538 TCTCTTCTCTTCAATGAACTGAACAAC 59.774 37.037 0.00 0.00 32.00 3.32
950 1128 6.522625 TCGATCTCTTCTCTTCAATGAACT 57.477 37.500 0.00 0.00 0.00 3.01
981 1159 1.600916 GGCGAATCTATGGGTGGGC 60.601 63.158 0.00 0.00 0.00 5.36
1003 1181 1.349357 GAGGAAGAGCAGAAAGGTGGT 59.651 52.381 0.00 0.00 0.00 4.16
1314 1495 3.451556 CTCGATCATGGCCTGCCGT 62.452 63.158 3.32 0.00 39.42 5.68
1420 1601 2.819115 CTGTGTCTCGCTTAGCATCAT 58.181 47.619 4.70 0.00 0.00 2.45
1512 1693 1.686325 CCCAGTGGTCGATGTAGGGG 61.686 65.000 8.74 0.00 0.00 4.79
1664 10883 1.598130 ACCTGCTCAAAGTCGGCAC 60.598 57.895 0.00 0.00 32.33 5.01
1734 10953 3.963428 ATCTGAAGTCTAAACCAGCGT 57.037 42.857 0.00 0.00 0.00 5.07
1735 10954 4.452455 ACAAATCTGAAGTCTAAACCAGCG 59.548 41.667 0.00 0.00 0.00 5.18
1736 10955 5.693814 CACAAATCTGAAGTCTAAACCAGC 58.306 41.667 0.00 0.00 0.00 4.85
1737 10956 5.471456 AGCACAAATCTGAAGTCTAAACCAG 59.529 40.000 0.00 0.00 0.00 4.00
1738 10957 5.376625 AGCACAAATCTGAAGTCTAAACCA 58.623 37.500 0.00 0.00 0.00 3.67
1739 10958 5.106515 GGAGCACAAATCTGAAGTCTAAACC 60.107 44.000 0.00 0.00 0.00 3.27
1740 10959 5.470098 TGGAGCACAAATCTGAAGTCTAAAC 59.530 40.000 0.00 0.00 0.00 2.01
1747 10966 3.309138 CGAGATGGAGCACAAATCTGAAG 59.691 47.826 3.81 0.00 30.83 3.02
1782 11001 9.405587 CACGAACATGGTTAATAAAAGAAACAT 57.594 29.630 0.00 0.00 33.18 2.71
1783 11002 8.407064 ACACGAACATGGTTAATAAAAGAAACA 58.593 29.630 0.00 0.00 0.00 2.83
2009 11338 7.545265 GGCAGCACAAAAATGTGAGATAATTAA 59.455 33.333 12.80 0.00 42.02 1.40
2011 11340 5.870978 GGCAGCACAAAAATGTGAGATAATT 59.129 36.000 12.80 0.00 42.02 1.40
2012 11341 5.186409 AGGCAGCACAAAAATGTGAGATAAT 59.814 36.000 12.80 0.00 42.02 1.28
2017 11346 2.400399 CAGGCAGCACAAAAATGTGAG 58.600 47.619 12.80 5.51 42.02 3.51
2050 12172 1.597854 CACCTCGGCAGCAAGAACA 60.598 57.895 0.00 0.00 0.00 3.18
2073 12195 2.863153 GTTGTAGCAGTGCGCCAG 59.137 61.111 10.00 0.00 44.04 4.85
2074 12196 3.041351 CGTTGTAGCAGTGCGCCA 61.041 61.111 10.00 7.59 44.04 5.69
2075 12197 4.445545 GCGTTGTAGCAGTGCGCC 62.446 66.667 10.00 4.73 44.04 6.53
2083 12205 1.197721 ACAAGAGCAATGCGTTGTAGC 59.802 47.619 21.75 5.96 38.27 3.58
2084 12206 3.542712 AACAAGAGCAATGCGTTGTAG 57.457 42.857 22.82 8.11 38.79 2.74
2085 12207 3.980646 AAACAAGAGCAATGCGTTGTA 57.019 38.095 22.82 0.00 38.79 2.41
2086 12208 2.869233 AAACAAGAGCAATGCGTTGT 57.131 40.000 19.49 18.84 40.45 3.32
2087 12209 2.151736 CGAAAACAAGAGCAATGCGTTG 59.848 45.455 14.54 14.54 38.39 4.10
2088 12210 2.032799 TCGAAAACAAGAGCAATGCGTT 59.967 40.909 0.00 0.00 0.00 4.84
2089 12211 1.601903 TCGAAAACAAGAGCAATGCGT 59.398 42.857 0.00 0.00 0.00 5.24
2090 12212 1.971962 GTCGAAAACAAGAGCAATGCG 59.028 47.619 0.00 0.00 0.00 4.73
2091 12213 2.998772 TGTCGAAAACAAGAGCAATGC 58.001 42.857 0.00 0.00 34.03 3.56
2100 12222 9.796120 ATAAAATTCACTCTTTGTCGAAAACAA 57.204 25.926 0.00 0.00 46.11 2.83
2105 12227 8.836413 AGTCAATAAAATTCACTCTTTGTCGAA 58.164 29.630 0.00 0.00 0.00 3.71
2106 12228 8.378172 AGTCAATAAAATTCACTCTTTGTCGA 57.622 30.769 0.00 0.00 0.00 4.20
2107 12229 8.282592 TGAGTCAATAAAATTCACTCTTTGTCG 58.717 33.333 5.47 0.00 35.50 4.35
2108 12230 9.950680 TTGAGTCAATAAAATTCACTCTTTGTC 57.049 29.630 0.08 0.00 35.50 3.18
2117 12239 9.761504 TGCTTCATTTTGAGTCAATAAAATTCA 57.238 25.926 6.36 0.00 35.07 2.57
2120 12242 9.932207 TGATGCTTCATTTTGAGTCAATAAAAT 57.068 25.926 6.36 0.85 37.06 1.82
2121 12243 9.761504 TTGATGCTTCATTTTGAGTCAATAAAA 57.238 25.926 6.36 0.00 0.00 1.52
2122 12244 9.414295 CTTGATGCTTCATTTTGAGTCAATAAA 57.586 29.630 6.36 0.00 0.00 1.40
2124 12246 7.031372 GCTTGATGCTTCATTTTGAGTCAATA 58.969 34.615 6.36 1.98 38.95 1.90
2127 12249 4.278919 TGCTTGATGCTTCATTTTGAGTCA 59.721 37.500 2.75 0.00 43.37 3.41
2128 12250 4.801891 TGCTTGATGCTTCATTTTGAGTC 58.198 39.130 2.75 0.00 43.37 3.36
2129 12251 4.521639 TCTGCTTGATGCTTCATTTTGAGT 59.478 37.500 2.75 0.00 43.37 3.41
2130 12252 5.055642 TCTGCTTGATGCTTCATTTTGAG 57.944 39.130 2.75 0.00 43.37 3.02
2131 12253 5.654603 ATCTGCTTGATGCTTCATTTTGA 57.345 34.783 2.75 1.59 43.37 2.69
2132 12254 6.327154 TGTATCTGCTTGATGCTTCATTTTG 58.673 36.000 2.75 0.00 43.37 2.44
2134 12256 6.519679 TTGTATCTGCTTGATGCTTCATTT 57.480 33.333 2.75 0.00 43.37 2.32
2135 12257 6.071784 TGTTTGTATCTGCTTGATGCTTCATT 60.072 34.615 2.75 0.00 43.37 2.57
2137 12259 4.761227 TGTTTGTATCTGCTTGATGCTTCA 59.239 37.500 0.00 0.00 43.37 3.02
2140 12262 4.582869 TCTGTTTGTATCTGCTTGATGCT 58.417 39.130 8.96 0.00 43.37 3.79
2142 12264 7.080353 TGATTCTGTTTGTATCTGCTTGATG 57.920 36.000 3.60 0.00 36.65 3.07
2143 12265 7.148120 CCTTGATTCTGTTTGTATCTGCTTGAT 60.148 37.037 0.00 0.00 39.11 2.57
2144 12266 6.149973 CCTTGATTCTGTTTGTATCTGCTTGA 59.850 38.462 0.00 0.00 0.00 3.02
2145 12267 6.320171 CCTTGATTCTGTTTGTATCTGCTTG 58.680 40.000 0.00 0.00 0.00 4.01
2147 12269 4.397417 GCCTTGATTCTGTTTGTATCTGCT 59.603 41.667 0.00 0.00 0.00 4.24
2149 12271 5.885230 TGCCTTGATTCTGTTTGTATCTG 57.115 39.130 0.00 0.00 0.00 2.90
2150 12272 5.163581 GCATGCCTTGATTCTGTTTGTATCT 60.164 40.000 6.36 0.00 0.00 1.98
2151 12273 5.039333 GCATGCCTTGATTCTGTTTGTATC 58.961 41.667 6.36 0.00 0.00 2.24
2152 12274 4.142093 GGCATGCCTTGATTCTGTTTGTAT 60.142 41.667 29.98 0.00 0.00 2.29
2153 12275 3.193267 GGCATGCCTTGATTCTGTTTGTA 59.807 43.478 29.98 0.00 0.00 2.41
2154 12276 2.028748 GGCATGCCTTGATTCTGTTTGT 60.029 45.455 29.98 0.00 0.00 2.83
2155 12277 2.232941 AGGCATGCCTTGATTCTGTTTG 59.767 45.455 34.07 0.00 45.70 2.93
2156 12278 2.532843 AGGCATGCCTTGATTCTGTTT 58.467 42.857 34.07 7.20 45.70 2.83
2157 12279 2.226962 AGGCATGCCTTGATTCTGTT 57.773 45.000 34.07 7.79 45.70 3.16
2158 12280 3.994165 AGGCATGCCTTGATTCTGT 57.006 47.368 34.07 8.64 45.70 3.41
2172 12942 0.544833 ATTCATGGGTGGCAAAGGCA 60.545 50.000 0.00 0.00 43.71 4.75
2185 12955 3.254060 AGTCAAACCGAGTCGATTCATG 58.746 45.455 15.64 0.00 0.00 3.07
2186 12956 3.594603 AGTCAAACCGAGTCGATTCAT 57.405 42.857 15.64 0.00 0.00 2.57
2187 12957 4.022589 ACTTAGTCAAACCGAGTCGATTCA 60.023 41.667 15.64 0.00 0.00 2.57
2188 12958 4.483311 ACTTAGTCAAACCGAGTCGATTC 58.517 43.478 15.64 0.00 0.00 2.52
2189 12959 4.516365 ACTTAGTCAAACCGAGTCGATT 57.484 40.909 15.64 0.00 0.00 3.34
2191 12961 3.996150 AACTTAGTCAAACCGAGTCGA 57.004 42.857 15.64 0.00 0.00 4.20
2192 12962 4.046462 TGAAACTTAGTCAAACCGAGTCG 58.954 43.478 5.29 5.29 0.00 4.18
2194 12964 6.937436 ATTTGAAACTTAGTCAAACCGAGT 57.063 33.333 1.94 0.00 45.19 4.18
2195 12965 7.007697 CGTATTTGAAACTTAGTCAAACCGAG 58.992 38.462 12.03 0.03 45.19 4.63
2196 12966 6.073657 CCGTATTTGAAACTTAGTCAAACCGA 60.074 38.462 16.18 0.65 45.19 4.69
2197 12967 6.075280 CCGTATTTGAAACTTAGTCAAACCG 58.925 40.000 1.94 7.49 45.19 4.44
2198 12968 6.962686 ACCGTATTTGAAACTTAGTCAAACC 58.037 36.000 1.94 0.00 45.19 3.27
2199 12969 9.373750 GTAACCGTATTTGAAACTTAGTCAAAC 57.626 33.333 1.94 0.00 45.19 2.93
2200 12970 9.328845 AGTAACCGTATTTGAAACTTAGTCAAA 57.671 29.630 2.37 2.37 46.12 2.69
2201 12971 8.891671 AGTAACCGTATTTGAAACTTAGTCAA 57.108 30.769 0.00 0.00 33.21 3.18
2202 12972 9.979578 TTAGTAACCGTATTTGAAACTTAGTCA 57.020 29.630 0.00 0.00 0.00 3.41
2211 12981 9.472361 GCTCTATGATTAGTAACCGTATTTGAA 57.528 33.333 0.00 0.00 0.00 2.69
2212 12982 8.086522 GGCTCTATGATTAGTAACCGTATTTGA 58.913 37.037 0.00 0.00 0.00 2.69
2213 12983 7.061905 CGGCTCTATGATTAGTAACCGTATTTG 59.938 40.741 0.00 0.00 34.51 2.32
2214 12984 7.088905 CGGCTCTATGATTAGTAACCGTATTT 58.911 38.462 0.00 0.00 34.51 1.40
2215 12985 6.618811 CGGCTCTATGATTAGTAACCGTATT 58.381 40.000 0.00 0.00 34.51 1.89
2224 12994 2.037772 CCAAGGCGGCTCTATGATTAGT 59.962 50.000 13.70 0.00 0.00 2.24
2226 12996 2.839486 CCAAGGCGGCTCTATGATTA 57.161 50.000 13.70 0.00 0.00 1.75
2248 13018 1.173043 TGTTTAATGCCTGCTTCGGG 58.827 50.000 0.00 0.00 0.00 5.14
2257 13027 3.104843 TGTTGTGCCTTGTTTAATGCC 57.895 42.857 0.00 0.00 0.00 4.40
2263 13033 3.902881 TGGAATTGTTGTGCCTTGTTT 57.097 38.095 0.00 0.00 0.00 2.83
2287 13057 7.990917 TGTTTGCTTTGATACTGTTCTGTTTA 58.009 30.769 0.00 0.00 0.00 2.01
2288 13058 6.862209 TGTTTGCTTTGATACTGTTCTGTTT 58.138 32.000 0.00 0.00 0.00 2.83
2289 13059 6.318648 TCTGTTTGCTTTGATACTGTTCTGTT 59.681 34.615 0.00 0.00 0.00 3.16
2292 13062 7.516198 AATCTGTTTGCTTTGATACTGTTCT 57.484 32.000 0.00 0.00 0.00 3.01
2327 13117 6.800072 ACCAGTCATTTTGTTTAAGGGAAA 57.200 33.333 0.00 0.00 0.00 3.13
2340 13130 4.319477 CGTCGAACATTGAACCAGTCATTT 60.319 41.667 0.00 0.00 35.70 2.32
2341 13131 3.186409 CGTCGAACATTGAACCAGTCATT 59.814 43.478 0.00 0.00 35.70 2.57
2342 13132 2.736721 CGTCGAACATTGAACCAGTCAT 59.263 45.455 0.00 0.00 35.70 3.06
2344 13134 2.155155 GTCGTCGAACATTGAACCAGTC 59.845 50.000 0.00 0.00 0.00 3.51
2346 13136 2.155732 CAGTCGTCGAACATTGAACCAG 59.844 50.000 0.00 0.00 0.00 4.00
2347 13137 2.131972 CAGTCGTCGAACATTGAACCA 58.868 47.619 0.00 0.00 0.00 3.67
2348 13138 2.400399 TCAGTCGTCGAACATTGAACC 58.600 47.619 0.00 0.00 0.00 3.62
2349 13139 4.149922 TCAATCAGTCGTCGAACATTGAAC 59.850 41.667 16.61 0.00 29.46 3.18
2350 13140 4.303282 TCAATCAGTCGTCGAACATTGAA 58.697 39.130 16.61 6.35 29.46 2.69
2351 13141 3.908213 TCAATCAGTCGTCGAACATTGA 58.092 40.909 15.62 15.62 0.00 2.57
2353 13143 4.386049 GTCTTCAATCAGTCGTCGAACATT 59.614 41.667 0.00 0.00 0.00 2.71
2355 13145 3.243267 TGTCTTCAATCAGTCGTCGAACA 60.243 43.478 0.00 0.00 0.00 3.18
2358 13148 2.552743 AGTGTCTTCAATCAGTCGTCGA 59.447 45.455 0.00 0.00 0.00 4.20
2359 13149 2.935042 AGTGTCTTCAATCAGTCGTCG 58.065 47.619 0.00 0.00 0.00 5.12
2360 13150 4.795268 TGTAGTGTCTTCAATCAGTCGTC 58.205 43.478 0.00 0.00 0.00 4.20
2361 13151 4.848562 TGTAGTGTCTTCAATCAGTCGT 57.151 40.909 0.00 0.00 0.00 4.34
2362 13152 5.462068 TGTTTGTAGTGTCTTCAATCAGTCG 59.538 40.000 0.00 0.00 0.00 4.18
2363 13153 6.844696 TGTTTGTAGTGTCTTCAATCAGTC 57.155 37.500 0.00 0.00 0.00 3.51
2364 13154 7.336931 AGTTTGTTTGTAGTGTCTTCAATCAGT 59.663 33.333 0.00 0.00 28.10 3.41
2365 13155 7.697691 AGTTTGTTTGTAGTGTCTTCAATCAG 58.302 34.615 0.00 0.00 28.10 2.90
2366 13156 7.624360 AGTTTGTTTGTAGTGTCTTCAATCA 57.376 32.000 0.00 0.00 0.00 2.57
2367 13157 9.997482 TTTAGTTTGTTTGTAGTGTCTTCAATC 57.003 29.630 0.00 0.00 0.00 2.67
2369 13159 9.781834 CATTTAGTTTGTTTGTAGTGTCTTCAA 57.218 29.630 0.00 0.00 0.00 2.69
2370 13160 9.168451 TCATTTAGTTTGTTTGTAGTGTCTTCA 57.832 29.630 0.00 0.00 0.00 3.02
2371 13161 9.997482 TTCATTTAGTTTGTTTGTAGTGTCTTC 57.003 29.630 0.00 0.00 0.00 2.87
2372 13162 9.783256 GTTCATTTAGTTTGTTTGTAGTGTCTT 57.217 29.630 0.00 0.00 0.00 3.01
2374 13164 9.730420 ATGTTCATTTAGTTTGTTTGTAGTGTC 57.270 29.630 0.00 0.00 0.00 3.67
2380 13664 7.551585 TGTGGATGTTCATTTAGTTTGTTTGT 58.448 30.769 0.00 0.00 0.00 2.83
2394 13678 5.290493 AGTTGAGTAGTTGTGGATGTTCA 57.710 39.130 0.00 0.00 0.00 3.18
2395 13679 5.758296 TGAAGTTGAGTAGTTGTGGATGTTC 59.242 40.000 0.00 0.00 0.00 3.18
2399 13683 5.680619 TGTTGAAGTTGAGTAGTTGTGGAT 58.319 37.500 0.00 0.00 0.00 3.41
2434 13718 1.805539 GCGCTGTGTGCATCGTCTA 60.806 57.895 0.00 0.00 43.06 2.59
2449 13734 0.316772 CTGCTTGCTACATGATGCGC 60.317 55.000 0.00 0.00 0.00 6.09
2452 13737 1.333931 CTGCCTGCTTGCTACATGATG 59.666 52.381 0.00 0.00 0.00 3.07
2453 13738 1.676746 CTGCCTGCTTGCTACATGAT 58.323 50.000 0.00 0.00 0.00 2.45
2454 13739 0.393402 CCTGCCTGCTTGCTACATGA 60.393 55.000 0.00 0.00 0.00 3.07
2455 13740 2.001361 GCCTGCCTGCTTGCTACATG 62.001 60.000 0.00 0.00 0.00 3.21
2456 13741 1.751927 GCCTGCCTGCTTGCTACAT 60.752 57.895 0.00 0.00 0.00 2.29
2457 13742 2.360350 GCCTGCCTGCTTGCTACA 60.360 61.111 0.00 0.00 0.00 2.74
2458 13743 2.045536 AGCCTGCCTGCTTGCTAC 60.046 61.111 4.53 0.00 38.85 3.58
2460 13745 3.962694 TGAGCCTGCCTGCTTGCT 61.963 61.111 5.82 5.82 42.95 3.91
2461 13746 3.745803 GTGAGCCTGCCTGCTTGC 61.746 66.667 0.00 0.00 42.95 4.01
2462 13747 2.281970 TGTGAGCCTGCCTGCTTG 60.282 61.111 0.00 0.00 42.95 4.01
2463 13748 2.033757 CTGTGAGCCTGCCTGCTT 59.966 61.111 0.00 0.00 42.95 3.91
2487 13772 3.382832 CTTGTCCTCCGCCTCCGT 61.383 66.667 0.00 0.00 0.00 4.69
2499 13784 1.186267 AGTCGACCCTCCACCTTGTC 61.186 60.000 13.01 0.00 0.00 3.18
2502 13787 4.115270 GAGTCGACCCTCCACCTT 57.885 61.111 13.01 0.00 0.00 3.50
2527 13812 1.066858 CACCCTCGCTGACTACAACAT 60.067 52.381 0.00 0.00 0.00 2.71
2546 13831 2.444706 AGCTAGAGGATGGCCGCA 60.445 61.111 0.00 0.00 39.96 5.69
2571 13856 1.878775 GCAACGCCTGATCTTTGCT 59.121 52.632 0.00 0.00 40.97 3.91
2573 13858 0.169672 CCAGCAACGCCTGATCTTTG 59.830 55.000 0.00 0.00 34.77 2.77
2574 13859 0.250901 ACCAGCAACGCCTGATCTTT 60.251 50.000 0.00 0.00 34.77 2.52
2586 13871 2.933287 ATCCCACCGGACCAGCAA 60.933 61.111 9.46 0.00 42.48 3.91
2649 13934 1.279496 CCCTTGAGGTGGAGTCATCA 58.721 55.000 0.00 0.00 0.00 3.07
2664 13949 2.237392 GACTGGCAAGACTATCACCCTT 59.763 50.000 0.00 0.00 0.00 3.95
2667 13952 2.419297 CCTGACTGGCAAGACTATCACC 60.419 54.545 0.00 0.00 0.00 4.02
2673 13958 0.472734 AGACCCTGACTGGCAAGACT 60.473 55.000 0.00 0.00 0.00 3.24
2682 13967 1.996798 TCTTCGTGAAGACCCTGACT 58.003 50.000 8.19 0.00 42.06 3.41


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

AutoCloner maintained by Alex Coulton.