Multiple sequence alignment - TraesCS3D01G507700

Loading Multiple Alignment...

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 TraesCS3D01G507700 chr3D 100.000 4405 0 0 798 5202 594184106 594179702 0.000000e+00 8135.0
1 TraesCS3D01G507700 chr3D 95.613 3100 84 19 1273 4336 594494651 594497734 0.000000e+00 4924.0
2 TraesCS3D01G507700 chr3D 97.696 2474 46 8 2516 4987 594363597 594366061 0.000000e+00 4242.0
3 TraesCS3D01G507700 chr3D 89.208 871 83 8 1265 2133 594362227 594363088 0.000000e+00 1077.0
4 TraesCS3D01G507700 chr3D 79.970 1313 197 36 3065 4342 594077812 594076531 0.000000e+00 907.0
5 TraesCS3D01G507700 chr3D 100.000 449 0 0 1 449 594184903 594184455 0.000000e+00 830.0
6 TraesCS3D01G507700 chr3D 85.396 404 33 11 2293 2675 594079819 594079421 3.780000e-106 396.0
7 TraesCS3D01G507700 chr3D 85.149 404 32 13 2293 2675 594078971 594078575 6.320000e-104 388.0
8 TraesCS3D01G507700 chr3D 86.817 311 34 2 2148 2458 594363160 594363463 1.790000e-89 340.0
9 TraesCS3D01G507700 chr3D 93.855 179 7 2 4990 5168 594366102 594366276 3.090000e-67 267.0
10 TraesCS3D01G507700 chr3D 91.925 161 13 0 1265 1425 594053643 594053483 5.240000e-55 226.0
11 TraesCS3D01G507700 chr3D 90.683 161 5 7 4990 5148 571465518 571465366 6.830000e-49 206.0
12 TraesCS3D01G507700 chr3D 90.683 161 5 7 4990 5148 579494802 579494954 6.830000e-49 206.0
13 TraesCS3D01G507700 chr3D 98.077 52 1 0 374 425 594184106 594184055 1.990000e-14 91.6
14 TraesCS3D01G507700 chr3B 94.921 3977 82 34 1273 5202 797224594 797220691 0.000000e+00 6115.0
15 TraesCS3D01G507700 chr3B 91.644 2214 119 28 2148 4336 798107629 798109801 0.000000e+00 3003.0
16 TraesCS3D01G507700 chr3B 82.121 2254 293 57 2148 4333 798122890 798125101 0.000000e+00 1829.0
17 TraesCS3D01G507700 chr3B 97.096 861 24 1 1273 2133 798106699 798107558 0.000000e+00 1450.0
18 TraesCS3D01G507700 chr3B 89.716 564 27 9 798 1331 797637724 797638286 0.000000e+00 691.0
19 TraesCS3D01G507700 chr3B 85.494 648 73 6 1498 2124 797638549 797639196 0.000000e+00 656.0
20 TraesCS3D01G507700 chr3B 82.824 425 37 14 1 389 797225747 797225323 1.070000e-91 348.0
21 TraesCS3D01G507700 chr3B 85.161 310 26 10 125 425 797637477 797637775 3.040000e-77 300.0
22 TraesCS3D01G507700 chr3B 94.737 38 2 0 4837 4874 169902153 169902190 5.630000e-05 60.2
23 TraesCS3D01G507700 chr3A 95.623 2079 64 8 798 2856 724947054 724949125 0.000000e+00 3310.0
24 TraesCS3D01G507700 chr3A 96.052 1697 51 7 2427 4111 725099851 725101543 0.000000e+00 2748.0
25 TraesCS3D01G507700 chr3A 82.936 1635 221 36 2736 4335 725119760 725121371 0.000000e+00 1421.0
26 TraesCS3D01G507700 chr3A 82.890 1543 214 32 2736 4246 725167876 725169400 0.000000e+00 1341.0
27 TraesCS3D01G507700 chr3A 90.270 555 27 10 798 1333 724945891 724946437 0.000000e+00 701.0
28 TraesCS3D01G507700 chr3A 90.072 554 28 10 799 1333 724937629 724938174 0.000000e+00 693.0
29 TraesCS3D01G507700 chr3A 89.910 555 30 9 798 1333 724935239 724935786 0.000000e+00 691.0
30 TraesCS3D01G507700 chr3A 89.730 555 31 8 798 1333 724941238 724941785 0.000000e+00 686.0
31 TraesCS3D01G507700 chr3A 89.550 555 32 8 798 1333 724940055 724940602 0.000000e+00 680.0
32 TraesCS3D01G507700 chr3A 89.369 555 33 7 798 1333 724944727 724945274 0.000000e+00 675.0
33 TraesCS3D01G507700 chr3A 89.189 555 34 8 798 1333 724942399 724942946 0.000000e+00 669.0
34 TraesCS3D01G507700 chr3A 85.100 651 76 6 1495 2124 724895217 724895867 0.000000e+00 645.0
35 TraesCS3D01G507700 chr3A 84.219 659 74 11 1502 2133 725119028 725119683 9.570000e-172 614.0
36 TraesCS3D01G507700 chr3A 86.799 553 38 10 799 1333 724938792 724939327 2.070000e-168 603.0
37 TraesCS3D01G507700 chr3A 84.420 629 75 10 1267 1875 724797954 724797329 9.640000e-167 597.0
38 TraesCS3D01G507700 chr3A 90.709 409 20 4 941 1331 724894549 724894957 3.570000e-146 529.0
39 TraesCS3D01G507700 chr3A 87.727 440 54 0 1685 2124 725098817 725099256 9.990000e-142 514.0
40 TraesCS3D01G507700 chr3A 87.273 440 36 11 1273 1697 725098252 725098686 7.830000e-133 484.0
41 TraesCS3D01G507700 chr3A 83.119 545 63 15 2148 2692 725099344 725099859 2.190000e-128 470.0
42 TraesCS3D01G507700 chr3A 87.113 388 33 12 75 448 724940930 724941314 1.730000e-114 424.0
43 TraesCS3D01G507700 chr3A 84.536 388 26 21 74 448 724938501 724938867 2.300000e-93 353.0
44 TraesCS3D01G507700 chr3A 84.238 387 27 20 75 448 724946765 724947130 3.860000e-91 346.0
45 TraesCS3D01G507700 chr3A 86.154 325 30 10 75 387 724939655 724939976 2.320000e-88 337.0
46 TraesCS3D01G507700 chr3A 83.679 386 29 21 76 448 724937340 724937704 3.000000e-87 333.0
47 TraesCS3D01G507700 chr3A 83.505 388 27 15 74 448 724936113 724936476 1.400000e-85 327.0
48 TraesCS3D01G507700 chr3A 83.247 388 31 20 74 448 724943274 724943640 5.020000e-85 326.0
49 TraesCS3D01G507700 chr3A 84.273 337 39 9 125 448 724893876 724894211 3.020000e-82 316.0
50 TraesCS3D01G507700 chr3A 82.597 385 30 15 74 445 724942112 724942472 6.540000e-79 305.0
51 TraesCS3D01G507700 chr3A 86.000 250 28 2 2209 2458 724949136 724949378 1.440000e-65 261.0
52 TraesCS3D01G507700 chr3A 90.714 140 10 3 312 448 724939992 724940131 3.200000e-42 183.0
53 TraesCS3D01G507700 chr3A 89.552 67 6 1 125 190 725097762 725097828 3.340000e-12 84.2
54 TraesCS3D01G507700 chr7A 81.498 2243 315 54 2148 4333 92363067 92360868 0.000000e+00 1751.0
55 TraesCS3D01G507700 chr7A 90.566 159 9 5 4990 5148 105168347 105168195 6.830000e-49 206.0
56 TraesCS3D01G507700 chrUn 82.890 1543 214 32 2736 4246 33329828 33331352 0.000000e+00 1341.0
57 TraesCS3D01G507700 chrUn 89.550 555 32 8 798 1333 341820590 341821137 0.000000e+00 680.0
58 TraesCS3D01G507700 chrUn 90.024 411 23 4 941 1333 341819452 341819862 2.780000e-142 516.0
59 TraesCS3D01G507700 chrUn 87.047 386 33 12 75 446 341821465 341821847 2.240000e-113 420.0
60 TraesCS3D01G507700 chrUn 86.154 325 30 10 75 387 341820190 341820511 2.320000e-88 337.0
61 TraesCS3D01G507700 chrUn 90.714 140 10 3 312 448 341820527 341820666 3.200000e-42 183.0
62 TraesCS3D01G507700 chr1D 90.506 158 9 5 4990 5147 37884055 37883904 2.460000e-48 204.0
63 TraesCS3D01G507700 chr1A 90.506 158 9 5 4990 5147 254348925 254349076 2.460000e-48 204.0
64 TraesCS3D01G507700 chr5D 89.091 165 12 3 4990 5154 296949509 296949351 3.180000e-47 200.0
65 TraesCS3D01G507700 chr2B 86.592 179 16 7 4990 5167 53410719 53410890 1.910000e-44 191.0
66 TraesCS3D01G507700 chr7B 85.714 63 7 2 2 62 673124978 673125040 1.210000e-06 65.8
67 TraesCS3D01G507700 chr5B 100.000 28 0 0 4847 4874 466429865 466429838 9.000000e-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 TraesCS3D01G507700 chr3D 594179702 594184903 5201 True 3018.866667 8135 99.359000 1 5202 3 chr3D.!!$R4 5201
1 TraesCS3D01G507700 chr3D 594494651 594497734 3083 False 4924.000000 4924 95.613000 1273 4336 1 chr3D.!!$F2 3063
2 TraesCS3D01G507700 chr3D 594362227 594366276 4049 False 1481.500000 4242 91.894000 1265 5168 4 chr3D.!!$F3 3903
3 TraesCS3D01G507700 chr3D 594076531 594079819 3288 True 563.666667 907 83.505000 2293 4342 3 chr3D.!!$R3 2049
4 TraesCS3D01G507700 chr3B 797220691 797225747 5056 True 3231.500000 6115 88.872500 1 5202 2 chr3B.!!$R1 5201
5 TraesCS3D01G507700 chr3B 798106699 798109801 3102 False 2226.500000 3003 94.370000 1273 4336 2 chr3B.!!$F4 3063
6 TraesCS3D01G507700 chr3B 798122890 798125101 2211 False 1829.000000 1829 82.121000 2148 4333 1 chr3B.!!$F2 2185
7 TraesCS3D01G507700 chr3B 797637477 797639196 1719 False 549.000000 691 86.790333 125 2124 3 chr3B.!!$F3 1999
8 TraesCS3D01G507700 chr3A 725167876 725169400 1524 False 1341.000000 1341 82.890000 2736 4246 1 chr3A.!!$F1 1510
9 TraesCS3D01G507700 chr3A 725119028 725121371 2343 False 1017.500000 1421 83.577500 1502 4335 2 chr3A.!!$F5 2833
10 TraesCS3D01G507700 chr3A 725097762 725101543 3781 False 860.040000 2748 88.744600 125 4111 5 chr3A.!!$F4 3986
11 TraesCS3D01G507700 chr3A 724935239 724949378 14139 False 626.473684 3310 87.489211 74 2856 19 chr3A.!!$F3 2782
12 TraesCS3D01G507700 chr3A 724797329 724797954 625 True 597.000000 597 84.420000 1267 1875 1 chr3A.!!$R1 608
13 TraesCS3D01G507700 chr3A 724893876 724895867 1991 False 496.666667 645 86.694000 125 2124 3 chr3A.!!$F2 1999
14 TraesCS3D01G507700 chr7A 92360868 92363067 2199 True 1751.000000 1751 81.498000 2148 4333 1 chr7A.!!$R1 2185
15 TraesCS3D01G507700 chrUn 33329828 33331352 1524 False 1341.000000 1341 82.890000 2736 4246 1 chrUn.!!$F1 1510
16 TraesCS3D01G507700 chrUn 341819452 341821847 2395 False 427.200000 680 88.697800 75 1333 5 chrUn.!!$F2 1258

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
824 5297 0.170561 CCACCTACCGTCTCGACAAG 59.829 60.0 0.00 0.0 0.00 3.16 F
1170 5953 0.032813 CCATCCAAGGGTGCCAAGAT 60.033 55.0 0.00 0.0 0.00 2.40 F
1248 6031 0.036294 AAAGCTACGGGCAGAACTCC 60.036 55.0 5.51 0.0 44.79 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 15198 1.301716 CAGCAGCCAGTGTTACCGT 60.302 57.895 0.00 0.00 0.00 4.83 R
2817 16397 2.232452 AGCGGTACTCATCATGATAGCC 59.768 50.000 8.15 5.63 0.00 3.93 R
4582 18572 3.056607 TCATCTGTCAAGTCGAGCATCAA 60.057 43.478 0.00 0.00 33.17 2.57 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
66 67 2.049802 GACGCTGTTTCGGACGGA 60.050 61.111 3.30 0.00 36.72 4.69
67 68 1.445582 GACGCTGTTTCGGACGGAT 60.446 57.895 3.30 0.00 36.72 4.18
87 4429 1.367471 CGCCGGCTGGATCTAATCA 59.633 57.895 26.68 0.00 37.49 2.57
100 4442 7.148440 GCTGGATCTAATCAGTTTATCATCTGC 60.148 40.741 0.00 0.00 33.81 4.26
109 4451 2.693250 TTATCATCTGCCGGACGCGG 62.693 60.000 12.47 0.00 46.15 6.46
152 4497 7.066645 TCCATTGAATTTGTGCTAGAGATGAAG 59.933 37.037 0.00 0.00 0.00 3.02
157 4503 9.269453 TGAATTTGTGCTAGAGATGAAGATATG 57.731 33.333 0.00 0.00 0.00 1.78
162 4508 4.082517 TGCTAGAGATGAAGATATGCCGTC 60.083 45.833 0.00 0.00 0.00 4.79
176 4523 1.695242 TGCCGTCTAGAAAACCCTTCA 59.305 47.619 0.00 0.00 0.00 3.02
179 4526 3.127030 GCCGTCTAGAAAACCCTTCAATG 59.873 47.826 0.00 0.00 0.00 2.82
183 4530 4.079253 TCTAGAAAACCCTTCAATGTGCC 58.921 43.478 0.00 0.00 0.00 5.01
194 4541 2.953020 TCAATGTGCCGCAAATTTACC 58.047 42.857 6.00 0.00 0.00 2.85
265 4622 1.036707 CTCCCTTCCATCTCTCGACC 58.963 60.000 0.00 0.00 0.00 4.79
346 4807 3.402681 CCGCCTCCCATCCACACT 61.403 66.667 0.00 0.00 0.00 3.55
349 4810 2.976490 GCCTCCCATCCACACTGCT 61.976 63.158 0.00 0.00 0.00 4.24
814 5287 2.893398 GTCCTCTGCCACCTACCG 59.107 66.667 0.00 0.00 0.00 4.02
815 5288 1.982938 GTCCTCTGCCACCTACCGT 60.983 63.158 0.00 0.00 0.00 4.83
816 5289 1.681327 TCCTCTGCCACCTACCGTC 60.681 63.158 0.00 0.00 0.00 4.79
817 5290 1.682684 CCTCTGCCACCTACCGTCT 60.683 63.158 0.00 0.00 0.00 4.18
818 5291 1.668101 CCTCTGCCACCTACCGTCTC 61.668 65.000 0.00 0.00 0.00 3.36
819 5292 1.994507 CTCTGCCACCTACCGTCTCG 61.995 65.000 0.00 0.00 0.00 4.04
820 5293 2.034532 TGCCACCTACCGTCTCGA 59.965 61.111 0.00 0.00 0.00 4.04
821 5294 2.267681 CTGCCACCTACCGTCTCGAC 62.268 65.000 0.00 0.00 0.00 4.20
822 5295 2.338015 GCCACCTACCGTCTCGACA 61.338 63.158 0.00 0.00 0.00 4.35
823 5296 1.870055 GCCACCTACCGTCTCGACAA 61.870 60.000 0.00 0.00 0.00 3.18
824 5297 0.170561 CCACCTACCGTCTCGACAAG 59.829 60.000 0.00 0.00 0.00 3.16
825 5298 0.879765 CACCTACCGTCTCGACAAGT 59.120 55.000 0.00 0.00 0.00 3.16
826 5299 1.268899 CACCTACCGTCTCGACAAGTT 59.731 52.381 0.00 0.00 0.00 2.66
827 5300 1.538950 ACCTACCGTCTCGACAAGTTC 59.461 52.381 0.00 0.00 0.00 3.01
828 5301 1.135460 CCTACCGTCTCGACAAGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
829 5302 1.811359 CTACCGTCTCGACAAGTTCCT 59.189 52.381 0.00 0.00 0.00 3.36
830 5303 1.901591 ACCGTCTCGACAAGTTCCTA 58.098 50.000 0.00 0.00 0.00 2.94
831 5304 1.811359 ACCGTCTCGACAAGTTCCTAG 59.189 52.381 0.00 0.00 0.00 3.02
832 5305 1.132643 CCGTCTCGACAAGTTCCTAGG 59.867 57.143 0.82 0.82 0.00 3.02
833 5306 1.132643 CGTCTCGACAAGTTCCTAGGG 59.867 57.143 9.46 0.00 0.00 3.53
834 5307 2.169330 GTCTCGACAAGTTCCTAGGGT 58.831 52.381 9.46 0.00 0.00 4.34
835 5308 2.561858 GTCTCGACAAGTTCCTAGGGTT 59.438 50.000 9.46 0.00 0.00 4.11
836 5309 3.006644 GTCTCGACAAGTTCCTAGGGTTT 59.993 47.826 9.46 0.00 0.00 3.27
837 5310 3.257624 TCTCGACAAGTTCCTAGGGTTTC 59.742 47.826 9.46 0.00 0.00 2.78
838 5311 2.967201 TCGACAAGTTCCTAGGGTTTCA 59.033 45.455 9.46 0.00 0.00 2.69
839 5312 3.064931 CGACAAGTTCCTAGGGTTTCAC 58.935 50.000 9.46 0.00 0.00 3.18
840 5313 3.064931 GACAAGTTCCTAGGGTTTCACG 58.935 50.000 9.46 0.00 0.00 4.35
841 5314 1.804748 CAAGTTCCTAGGGTTTCACGC 59.195 52.381 9.46 0.00 0.00 5.34
842 5315 0.323957 AGTTCCTAGGGTTTCACGCC 59.676 55.000 9.46 0.00 0.00 5.68
843 5316 1.017701 GTTCCTAGGGTTTCACGCCG 61.018 60.000 9.46 0.00 0.00 6.46
844 5317 2.791501 TTCCTAGGGTTTCACGCCGC 62.792 60.000 9.46 0.00 0.00 6.53
845 5318 2.818274 CTAGGGTTTCACGCCGCC 60.818 66.667 0.00 0.00 0.00 6.13
846 5319 4.745751 TAGGGTTTCACGCCGCCG 62.746 66.667 0.00 0.00 41.14 6.46
996 5764 1.002142 TCGCCGTCATATCGTTCGATT 60.002 47.619 12.77 0.00 32.54 3.34
1015 5792 3.005539 AGATGCTGCCCGTCCAGT 61.006 61.111 0.00 0.00 35.28 4.00
1149 5932 3.306902 TGGAGACATGGAGGAGGTC 57.693 57.895 0.00 0.00 35.49 3.85
1150 5933 0.413434 TGGAGACATGGAGGAGGTCA 59.587 55.000 0.00 0.00 37.87 4.02
1151 5934 0.827368 GGAGACATGGAGGAGGTCAC 59.173 60.000 0.00 0.00 37.87 3.67
1152 5935 0.827368 GAGACATGGAGGAGGTCACC 59.173 60.000 0.00 0.00 37.87 4.02
1153 5936 0.117140 AGACATGGAGGAGGTCACCA 59.883 55.000 0.00 0.00 37.87 4.17
1154 5937 1.207791 GACATGGAGGAGGTCACCAT 58.792 55.000 0.00 0.00 43.97 3.55
1155 5938 1.139853 GACATGGAGGAGGTCACCATC 59.860 57.143 0.00 0.00 41.68 3.51
1156 5939 0.471617 CATGGAGGAGGTCACCATCC 59.528 60.000 0.00 0.58 41.68 3.51
1157 5940 0.044702 ATGGAGGAGGTCACCATCCA 59.955 55.000 15.69 15.69 39.83 3.41
1158 5941 0.178876 TGGAGGAGGTCACCATCCAA 60.179 55.000 11.97 0.00 38.12 3.53
1159 5942 0.543749 GGAGGAGGTCACCATCCAAG 59.456 60.000 13.16 0.00 38.12 3.61
1160 5943 0.543749 GAGGAGGTCACCATCCAAGG 59.456 60.000 13.16 0.00 38.12 3.61
1161 5944 0.916358 AGGAGGTCACCATCCAAGGG 60.916 60.000 13.16 0.00 38.12 3.95
1162 5945 1.208165 GGAGGTCACCATCCAAGGGT 61.208 60.000 0.00 0.00 39.88 4.34
1167 5950 3.270944 ACCATCCAAGGGTGCCAA 58.729 55.556 0.00 0.00 37.23 4.52
1168 5951 1.077265 ACCATCCAAGGGTGCCAAG 59.923 57.895 0.00 0.00 37.23 3.61
1169 5952 1.383799 CCATCCAAGGGTGCCAAGA 59.616 57.895 0.00 0.00 0.00 3.02
1170 5953 0.032813 CCATCCAAGGGTGCCAAGAT 60.033 55.000 0.00 0.00 0.00 2.40
1173 5956 1.750399 CCAAGGGTGCCAAGATCCG 60.750 63.158 0.00 0.00 0.00 4.18
1185 5968 2.222678 CCAAGATCCGATTTCTCATGCG 59.777 50.000 0.00 0.00 0.00 4.73
1188 5971 2.101415 AGATCCGATTTCTCATGCGACA 59.899 45.455 0.00 0.00 0.00 4.35
1189 5972 1.926561 TCCGATTTCTCATGCGACAG 58.073 50.000 0.00 0.00 0.00 3.51
1190 5973 1.476488 TCCGATTTCTCATGCGACAGA 59.524 47.619 0.00 0.00 0.00 3.41
1191 5974 1.590238 CCGATTTCTCATGCGACAGAC 59.410 52.381 0.00 0.00 0.00 3.51
1192 5975 2.262211 CGATTTCTCATGCGACAGACA 58.738 47.619 0.00 0.00 0.00 3.41
1193 5976 2.862536 CGATTTCTCATGCGACAGACAT 59.137 45.455 0.00 0.00 0.00 3.06
1194 5977 3.302286 CGATTTCTCATGCGACAGACATG 60.302 47.826 0.00 0.00 45.08 3.21
1195 5978 2.014335 TTCTCATGCGACAGACATGG 57.986 50.000 0.00 0.00 44.09 3.66
1196 5979 1.185315 TCTCATGCGACAGACATGGA 58.815 50.000 0.00 0.00 44.09 3.41
1197 5980 1.135721 TCTCATGCGACAGACATGGAG 59.864 52.381 0.00 0.00 44.09 3.86
1198 5981 0.460811 TCATGCGACAGACATGGAGC 60.461 55.000 0.00 0.00 44.09 4.70
1199 5982 0.461516 CATGCGACAGACATGGAGCT 60.462 55.000 0.00 0.00 40.99 4.09
1200 5983 0.461516 ATGCGACAGACATGGAGCTG 60.462 55.000 0.00 9.94 38.10 4.24
1201 5984 2.459442 GCGACAGACATGGAGCTGC 61.459 63.158 0.00 0.00 35.57 5.25
1202 5985 1.217511 CGACAGACATGGAGCTGCT 59.782 57.895 6.82 0.00 35.57 4.24
1203 5986 1.082679 CGACAGACATGGAGCTGCTG 61.083 60.000 7.01 4.98 35.57 4.41
1204 5987 1.367599 GACAGACATGGAGCTGCTGC 61.368 60.000 14.73 14.73 35.57 5.25
1214 5997 4.689484 GCTGCTGCTCAGAACAGA 57.311 55.556 8.53 0.00 45.72 3.41
1215 5998 3.156157 GCTGCTGCTCAGAACAGAT 57.844 52.632 8.53 0.00 45.72 2.90
1216 5999 1.451067 GCTGCTGCTCAGAACAGATT 58.549 50.000 8.53 0.00 45.72 2.40
1217 6000 1.397692 GCTGCTGCTCAGAACAGATTC 59.602 52.381 8.53 0.00 45.72 2.52
1218 6001 1.659601 CTGCTGCTCAGAACAGATTCG 59.340 52.381 4.91 0.00 45.72 3.34
1219 6002 1.005340 GCTGCTCAGAACAGATTCGG 58.995 55.000 4.91 0.00 40.04 4.30
1220 6003 1.005340 CTGCTCAGAACAGATTCGGC 58.995 55.000 0.00 0.00 40.04 5.54
1221 6004 0.321346 TGCTCAGAACAGATTCGGCA 59.679 50.000 0.00 0.00 40.04 5.69
1222 6005 0.723981 GCTCAGAACAGATTCGGCAC 59.276 55.000 0.00 0.00 40.04 5.01
1223 6006 1.941209 GCTCAGAACAGATTCGGCACA 60.941 52.381 0.00 0.00 40.04 4.57
1224 6007 1.728971 CTCAGAACAGATTCGGCACAC 59.271 52.381 0.00 0.00 40.04 3.82
1225 6008 0.439985 CAGAACAGATTCGGCACACG 59.560 55.000 0.00 0.00 46.11 4.49
1237 6020 0.438830 GGCACACGAAGAAAGCTACG 59.561 55.000 0.00 0.00 0.00 3.51
1238 6021 0.438830 GCACACGAAGAAAGCTACGG 59.561 55.000 0.00 0.00 0.00 4.02
1239 6022 1.068474 CACACGAAGAAAGCTACGGG 58.932 55.000 0.00 0.00 35.22 5.28
1240 6023 0.669625 ACACGAAGAAAGCTACGGGC 60.670 55.000 0.00 0.00 42.19 6.13
1241 6024 0.669318 CACGAAGAAAGCTACGGGCA 60.669 55.000 5.51 0.00 44.79 5.36
1242 6025 0.389948 ACGAAGAAAGCTACGGGCAG 60.390 55.000 5.51 0.00 44.79 4.85
1243 6026 0.108804 CGAAGAAAGCTACGGGCAGA 60.109 55.000 5.51 0.00 44.79 4.26
1244 6027 1.671850 CGAAGAAAGCTACGGGCAGAA 60.672 52.381 5.51 0.00 44.79 3.02
1245 6028 1.732809 GAAGAAAGCTACGGGCAGAAC 59.267 52.381 5.51 0.00 44.79 3.01
1246 6029 0.977395 AGAAAGCTACGGGCAGAACT 59.023 50.000 5.51 0.00 44.79 3.01
1247 6030 1.066787 AGAAAGCTACGGGCAGAACTC 60.067 52.381 5.51 0.00 44.79 3.01
1248 6031 0.036294 AAAGCTACGGGCAGAACTCC 60.036 55.000 5.51 0.00 44.79 3.85
1249 6032 1.900545 AAGCTACGGGCAGAACTCCC 61.901 60.000 5.51 0.00 44.79 4.30
1250 6033 2.359967 GCTACGGGCAGAACTCCCT 61.360 63.158 0.00 0.00 41.69 4.20
1251 6034 1.900545 GCTACGGGCAGAACTCCCTT 61.901 60.000 0.00 0.00 41.69 3.95
1252 6035 1.481871 CTACGGGCAGAACTCCCTTA 58.518 55.000 0.00 0.00 41.69 2.69
1253 6036 2.040178 CTACGGGCAGAACTCCCTTAT 58.960 52.381 0.00 0.00 41.69 1.73
1254 6037 0.831307 ACGGGCAGAACTCCCTTATC 59.169 55.000 0.00 0.00 41.69 1.75
1255 6038 0.830648 CGGGCAGAACTCCCTTATCA 59.169 55.000 0.00 0.00 41.69 2.15
1256 6039 1.202580 CGGGCAGAACTCCCTTATCAG 60.203 57.143 0.00 0.00 41.69 2.90
1257 6040 1.475930 GGGCAGAACTCCCTTATCAGC 60.476 57.143 0.00 0.00 40.66 4.26
1258 6041 1.576356 GCAGAACTCCCTTATCAGCG 58.424 55.000 0.00 0.00 0.00 5.18
1259 6042 1.137086 GCAGAACTCCCTTATCAGCGA 59.863 52.381 0.00 0.00 0.00 4.93
1260 6043 2.801342 GCAGAACTCCCTTATCAGCGAG 60.801 54.545 0.00 0.00 0.00 5.03
1261 6044 2.035632 AGAACTCCCTTATCAGCGAGG 58.964 52.381 0.00 0.00 0.00 4.63
1262 6045 2.032620 GAACTCCCTTATCAGCGAGGA 58.967 52.381 0.00 0.00 34.91 3.71
1263 6046 2.160721 ACTCCCTTATCAGCGAGGAA 57.839 50.000 0.00 0.00 34.91 3.36
1264 6047 2.035632 ACTCCCTTATCAGCGAGGAAG 58.964 52.381 0.00 0.00 34.91 3.46
1265 6048 2.311463 CTCCCTTATCAGCGAGGAAGA 58.689 52.381 0.00 0.00 34.91 2.87
1275 6058 0.755686 GCGAGGAAGACCATGGAGAT 59.244 55.000 21.47 2.80 38.94 2.75
1291 13208 3.242867 GGAGATATGGAGGACACCATCA 58.757 50.000 4.52 0.00 46.24 3.07
1310 13227 0.322546 AAAGGGTGCCAAGATCCGAC 60.323 55.000 0.00 0.00 0.00 4.79
1701 13934 6.583427 GTGGTGATTTTATCCCGTGTTTTTAC 59.417 38.462 0.00 0.00 0.00 2.01
1739 13984 4.796231 ATCCGGAGTGCGCACGTC 62.796 66.667 32.94 27.40 36.20 4.34
1797 14045 4.678742 ACTTCTTAACGAGTCGTACTTTGC 59.321 41.667 20.23 0.00 39.99 3.68
2153 14471 3.459227 TGGTGATGATGATTGAGCCCTTA 59.541 43.478 0.00 0.00 0.00 2.69
2753 16333 1.851658 CACTTTTGTGCCTTTTCGGG 58.148 50.000 0.00 0.00 44.07 5.14
2817 16397 2.094338 GGTAGGAGTGGAAACCTGTACG 60.094 54.545 0.00 0.00 37.68 3.67
4350 18340 8.707938 ATTCTTGGCTCATGTTTTAAATTAGC 57.292 30.769 0.00 0.00 0.00 3.09
4582 18572 4.801891 CTTAGCAGTGCAAACATGATTGT 58.198 39.130 19.20 0.00 37.82 2.71
4635 18626 2.436646 CCAGCCAGGCAAGTACCG 60.437 66.667 15.80 0.00 33.69 4.02
4729 18720 2.227388 GTGAGCTTTGAACACTCCATGG 59.773 50.000 4.97 4.97 0.00 3.66
4742 18737 0.546122 TCCATGGCCGAGTAGCAAAT 59.454 50.000 6.96 0.00 0.00 2.32
4743 18738 1.765904 TCCATGGCCGAGTAGCAAATA 59.234 47.619 6.96 0.00 0.00 1.40
4744 18739 2.146342 CCATGGCCGAGTAGCAAATAG 58.854 52.381 0.00 0.00 0.00 1.73
4869 18867 7.548097 TGTGTTGTGGCTTTAGTTCAAATTTA 58.452 30.769 0.00 0.00 0.00 1.40
4873 18871 9.093970 GTTGTGGCTTTAGTTCAAATTTAAACT 57.906 29.630 11.45 11.45 39.07 2.66
4886 18884 6.536941 TCAAATTTAAACTTCCAAAAGCGCTT 59.463 30.769 18.98 18.98 35.81 4.68
4887 18885 6.525121 AATTTAAACTTCCAAAAGCGCTTC 57.475 33.333 25.24 0.00 35.81 3.86
4888 18886 4.640789 TTAAACTTCCAAAAGCGCTTCA 57.359 36.364 25.24 4.97 35.81 3.02
4983 18989 2.045561 TTGCGTTGGAACCTCAAGAA 57.954 45.000 0.00 0.00 0.00 2.52
4987 18993 2.616842 GCGTTGGAACCTCAAGAAGAAA 59.383 45.455 0.00 0.00 0.00 2.52
5045 19089 2.156098 GGACCACATACGGAGCAAAAA 58.844 47.619 0.00 0.00 0.00 1.94
5046 19090 2.752903 GGACCACATACGGAGCAAAAAT 59.247 45.455 0.00 0.00 0.00 1.82
5047 19091 3.427503 GGACCACATACGGAGCAAAAATG 60.428 47.826 0.00 0.00 0.00 2.32
5048 19092 3.417101 ACCACATACGGAGCAAAAATGA 58.583 40.909 0.00 0.00 0.00 2.57
5049 19093 3.440173 ACCACATACGGAGCAAAAATGAG 59.560 43.478 0.00 0.00 0.00 2.90
5050 19094 3.440173 CCACATACGGAGCAAAAATGAGT 59.560 43.478 0.00 0.00 0.00 3.41
5051 19095 4.406069 CACATACGGAGCAAAAATGAGTG 58.594 43.478 0.00 0.00 0.00 3.51
5052 19096 4.154015 CACATACGGAGCAAAAATGAGTGA 59.846 41.667 0.00 0.00 0.00 3.41
5053 19097 4.759693 ACATACGGAGCAAAAATGAGTGAA 59.240 37.500 0.00 0.00 0.00 3.18
5054 19098 5.415701 ACATACGGAGCAAAAATGAGTGAAT 59.584 36.000 0.00 0.00 0.00 2.57
5055 19099 6.597672 ACATACGGAGCAAAAATGAGTGAATA 59.402 34.615 0.00 0.00 0.00 1.75
5056 19100 5.296813 ACGGAGCAAAAATGAGTGAATAC 57.703 39.130 0.00 0.00 0.00 1.89
5057 19101 4.759693 ACGGAGCAAAAATGAGTGAATACA 59.240 37.500 0.00 0.00 0.00 2.29
5058 19102 5.415701 ACGGAGCAAAAATGAGTGAATACAT 59.584 36.000 0.00 0.00 0.00 2.29
5059 19103 5.740569 CGGAGCAAAAATGAGTGAATACATG 59.259 40.000 0.00 0.00 0.00 3.21
5060 19104 5.517770 GGAGCAAAAATGAGTGAATACATGC 59.482 40.000 0.00 0.00 0.00 4.06
5122 19181 8.253810 TCATAGTGGAATCTCTACAAAGACTTG 58.746 37.037 0.00 0.00 38.61 3.16
5134 19193 7.741785 TCTACAAAGACTTGGATTTAGGAACA 58.258 34.615 0.00 0.00 36.82 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.074412 GACCTTTGCAACAGCTAGCTTA 58.926 45.455 16.46 0.00 0.00 3.09
39 40 1.289109 AAACAGCGTCCGATCAACCG 61.289 55.000 0.00 0.00 0.00 4.44
66 67 1.194781 ATTAGATCCAGCCGGCGGAT 61.195 55.000 36.63 36.63 46.20 4.18
67 68 1.816863 GATTAGATCCAGCCGGCGGA 61.817 60.000 32.20 32.20 36.84 5.54
70 71 0.394565 ACTGATTAGATCCAGCCGGC 59.605 55.000 21.89 21.89 33.90 6.13
72 73 5.541845 TGATAAACTGATTAGATCCAGCCG 58.458 41.667 0.00 0.00 33.90 5.52
73 74 7.333921 CAGATGATAAACTGATTAGATCCAGCC 59.666 40.741 0.00 0.00 36.38 4.85
74 75 7.148440 GCAGATGATAAACTGATTAGATCCAGC 60.148 40.741 0.00 0.00 36.38 4.85
75 76 7.333921 GGCAGATGATAAACTGATTAGATCCAG 59.666 40.741 0.00 0.00 36.38 3.86
76 77 7.164122 GGCAGATGATAAACTGATTAGATCCA 58.836 38.462 0.00 0.00 36.38 3.41
77 78 6.312426 CGGCAGATGATAAACTGATTAGATCC 59.688 42.308 0.00 0.00 36.38 3.36
87 4429 1.806623 GCGTCCGGCAGATGATAAACT 60.807 52.381 0.00 0.00 42.87 2.66
109 4451 2.923121 TGGAATCTAATGGCAGTGCTC 58.077 47.619 16.11 5.84 0.00 4.26
119 4461 9.412460 TCTAGCACAAATTCAATGGAATCTAAT 57.588 29.630 0.00 0.00 42.87 1.73
152 4497 4.338379 AGGGTTTTCTAGACGGCATATC 57.662 45.455 0.00 0.00 0.00 1.63
157 4503 2.467566 TGAAGGGTTTTCTAGACGGC 57.532 50.000 0.00 0.00 0.00 5.68
162 4508 3.119849 CGGCACATTGAAGGGTTTTCTAG 60.120 47.826 0.00 0.00 0.00 2.43
176 4523 3.324993 CAAGGTAAATTTGCGGCACATT 58.675 40.909 8.48 8.48 0.00 2.71
179 4526 1.708822 CCAAGGTAAATTTGCGGCAC 58.291 50.000 0.05 0.00 0.00 5.01
183 4530 1.994916 CAGGCCAAGGTAAATTTGCG 58.005 50.000 5.01 0.00 0.00 4.85
217 4572 0.317854 GTGCGGGCTCTTGTTTGTTC 60.318 55.000 0.00 0.00 0.00 3.18
265 4622 1.906574 TGAAACCCTAGGTAGCCACTG 59.093 52.381 8.29 0.00 33.12 3.66
334 4795 2.352422 GCAGCAGTGTGGATGGGA 59.648 61.111 0.00 0.00 0.00 4.37
797 5270 1.946475 GACGGTAGGTGGCAGAGGAC 61.946 65.000 0.00 0.00 0.00 3.85
798 5271 1.681327 GACGGTAGGTGGCAGAGGA 60.681 63.158 0.00 0.00 0.00 3.71
799 5272 1.668101 GAGACGGTAGGTGGCAGAGG 61.668 65.000 0.00 0.00 0.00 3.69
800 5273 1.810532 GAGACGGTAGGTGGCAGAG 59.189 63.158 0.00 0.00 0.00 3.35
801 5274 2.044555 CGAGACGGTAGGTGGCAGA 61.045 63.158 0.00 0.00 0.00 4.26
802 5275 2.044555 TCGAGACGGTAGGTGGCAG 61.045 63.158 0.00 0.00 0.00 4.85
803 5276 2.034532 TCGAGACGGTAGGTGGCA 59.965 61.111 0.00 0.00 0.00 4.92
804 5277 1.870055 TTGTCGAGACGGTAGGTGGC 61.870 60.000 0.00 0.00 0.00 5.01
805 5278 0.170561 CTTGTCGAGACGGTAGGTGG 59.829 60.000 0.00 0.00 0.00 4.61
806 5279 0.879765 ACTTGTCGAGACGGTAGGTG 59.120 55.000 0.00 0.00 0.00 4.00
807 5280 1.538950 GAACTTGTCGAGACGGTAGGT 59.461 52.381 0.00 0.00 0.00 3.08
808 5281 1.135460 GGAACTTGTCGAGACGGTAGG 60.135 57.143 0.00 0.00 0.00 3.18
809 5282 1.811359 AGGAACTTGTCGAGACGGTAG 59.189 52.381 0.00 0.00 27.25 3.18
810 5283 1.901591 AGGAACTTGTCGAGACGGTA 58.098 50.000 0.00 0.00 27.25 4.02
811 5284 1.811359 CTAGGAACTTGTCGAGACGGT 59.189 52.381 0.00 0.00 41.75 4.83
812 5285 1.132643 CCTAGGAACTTGTCGAGACGG 59.867 57.143 1.05 0.00 41.75 4.79
813 5286 1.132643 CCCTAGGAACTTGTCGAGACG 59.867 57.143 11.48 0.00 41.75 4.18
814 5287 2.169330 ACCCTAGGAACTTGTCGAGAC 58.831 52.381 11.48 0.00 41.75 3.36
815 5288 2.599408 ACCCTAGGAACTTGTCGAGA 57.401 50.000 11.48 0.00 41.75 4.04
816 5289 3.006537 TGAAACCCTAGGAACTTGTCGAG 59.993 47.826 11.48 0.00 41.75 4.04
817 5290 2.967201 TGAAACCCTAGGAACTTGTCGA 59.033 45.455 11.48 0.00 41.75 4.20
818 5291 3.064931 GTGAAACCCTAGGAACTTGTCG 58.935 50.000 11.48 0.00 41.75 4.35
819 5292 3.064931 CGTGAAACCCTAGGAACTTGTC 58.935 50.000 11.48 0.00 41.75 3.18
820 5293 2.809299 GCGTGAAACCCTAGGAACTTGT 60.809 50.000 11.48 0.00 41.75 3.16
821 5294 1.804748 GCGTGAAACCCTAGGAACTTG 59.195 52.381 11.48 0.00 41.75 3.16
822 5295 1.271217 GGCGTGAAACCCTAGGAACTT 60.271 52.381 11.48 0.00 41.75 2.66
823 5296 0.323957 GGCGTGAAACCCTAGGAACT 59.676 55.000 11.48 0.00 46.37 3.01
824 5297 1.017701 CGGCGTGAAACCCTAGGAAC 61.018 60.000 11.48 0.00 0.00 3.62
825 5298 1.294138 CGGCGTGAAACCCTAGGAA 59.706 57.895 11.48 0.00 0.00 3.36
826 5299 2.975536 CGGCGTGAAACCCTAGGA 59.024 61.111 11.48 0.00 0.00 2.94
827 5300 2.818274 GCGGCGTGAAACCCTAGG 60.818 66.667 9.37 0.06 0.00 3.02
828 5301 2.818274 GGCGGCGTGAAACCCTAG 60.818 66.667 9.37 0.00 0.00 3.02
829 5302 4.745751 CGGCGGCGTGAAACCCTA 62.746 66.667 24.74 0.00 0.00 3.53
996 5764 3.002583 TGGACGGGCAGCATCTCA 61.003 61.111 0.00 0.00 0.00 3.27
1139 5922 0.178876 TTGGATGGTGACCTCCTCCA 60.179 55.000 17.18 15.82 42.06 3.86
1140 5923 0.543749 CTTGGATGGTGACCTCCTCC 59.456 60.000 17.18 13.88 32.47 4.30
1141 5924 0.543749 CCTTGGATGGTGACCTCCTC 59.456 60.000 17.18 6.34 32.47 3.71
1142 5925 0.916358 CCCTTGGATGGTGACCTCCT 60.916 60.000 17.18 0.00 32.47 3.69
1143 5926 1.208165 ACCCTTGGATGGTGACCTCC 61.208 60.000 2.11 8.13 33.94 4.30
1144 5927 2.387952 ACCCTTGGATGGTGACCTC 58.612 57.895 2.11 0.00 33.94 3.85
1145 5928 4.690153 ACCCTTGGATGGTGACCT 57.310 55.556 2.11 0.00 33.94 3.85
1150 5933 1.077265 CTTGGCACCCTTGGATGGT 59.923 57.895 0.00 0.00 36.21 3.55
1151 5934 0.032813 ATCTTGGCACCCTTGGATGG 60.033 55.000 0.00 0.00 0.00 3.51
1152 5935 1.396653 GATCTTGGCACCCTTGGATG 58.603 55.000 0.00 0.00 0.00 3.51
1153 5936 0.259938 GGATCTTGGCACCCTTGGAT 59.740 55.000 0.00 0.00 0.00 3.41
1154 5937 1.691219 GGATCTTGGCACCCTTGGA 59.309 57.895 0.00 0.00 0.00 3.53
1155 5938 1.750399 CGGATCTTGGCACCCTTGG 60.750 63.158 0.00 0.00 0.00 3.61
1156 5939 0.107017 ATCGGATCTTGGCACCCTTG 60.107 55.000 0.00 0.00 0.00 3.61
1157 5940 0.625849 AATCGGATCTTGGCACCCTT 59.374 50.000 0.00 0.00 0.00 3.95
1158 5941 0.625849 AAATCGGATCTTGGCACCCT 59.374 50.000 0.00 0.00 0.00 4.34
1159 5942 1.025041 GAAATCGGATCTTGGCACCC 58.975 55.000 0.00 0.00 0.00 4.61
1160 5943 1.943340 GAGAAATCGGATCTTGGCACC 59.057 52.381 0.00 0.00 0.00 5.01
1161 5944 2.632377 TGAGAAATCGGATCTTGGCAC 58.368 47.619 0.00 0.00 0.00 5.01
1162 5945 3.208594 CATGAGAAATCGGATCTTGGCA 58.791 45.455 0.00 0.00 0.00 4.92
1163 5946 2.031333 GCATGAGAAATCGGATCTTGGC 60.031 50.000 0.00 0.00 0.00 4.52
1164 5947 2.222678 CGCATGAGAAATCGGATCTTGG 59.777 50.000 0.00 0.00 0.00 3.61
1165 5948 3.060003 GTCGCATGAGAAATCGGATCTTG 60.060 47.826 0.00 0.00 0.00 3.02
1166 5949 3.126831 GTCGCATGAGAAATCGGATCTT 58.873 45.455 0.00 0.00 0.00 2.40
1167 5950 2.101415 TGTCGCATGAGAAATCGGATCT 59.899 45.455 0.00 0.00 0.00 2.75
1168 5951 2.473816 TGTCGCATGAGAAATCGGATC 58.526 47.619 0.00 0.00 0.00 3.36
1169 5952 2.101415 TCTGTCGCATGAGAAATCGGAT 59.899 45.455 0.00 0.00 0.00 4.18
1170 5953 1.476488 TCTGTCGCATGAGAAATCGGA 59.524 47.619 0.00 0.00 0.00 4.55
1173 5956 3.002042 CCATGTCTGTCGCATGAGAAATC 59.998 47.826 0.00 0.00 44.60 2.17
1185 5968 1.367599 GCAGCAGCTCCATGTCTGTC 61.368 60.000 0.00 2.75 37.91 3.51
1197 5980 1.397692 GAATCTGTTCTGAGCAGCAGC 59.602 52.381 15.68 0.00 44.52 5.25
1198 5981 1.659601 CGAATCTGTTCTGAGCAGCAG 59.340 52.381 15.68 5.67 46.31 4.24
1199 5982 1.673923 CCGAATCTGTTCTGAGCAGCA 60.674 52.381 15.68 6.42 34.21 4.41
1200 5983 1.005340 CCGAATCTGTTCTGAGCAGC 58.995 55.000 15.68 2.66 34.21 5.25
1201 5984 1.005340 GCCGAATCTGTTCTGAGCAG 58.995 55.000 14.52 14.52 35.43 4.24
1202 5985 0.321346 TGCCGAATCTGTTCTGAGCA 59.679 50.000 0.00 0.00 32.00 4.26
1203 5986 0.723981 GTGCCGAATCTGTTCTGAGC 59.276 55.000 0.00 0.00 32.00 4.26
1204 5987 1.728971 GTGTGCCGAATCTGTTCTGAG 59.271 52.381 0.00 0.00 32.00 3.35
1205 5988 1.795768 GTGTGCCGAATCTGTTCTGA 58.204 50.000 0.00 0.00 32.00 3.27
1206 5989 0.439985 CGTGTGCCGAATCTGTTCTG 59.560 55.000 0.00 0.00 39.56 3.02
1207 5990 0.317160 TCGTGTGCCGAATCTGTTCT 59.683 50.000 0.00 0.00 44.03 3.01
1208 5991 2.822306 TCGTGTGCCGAATCTGTTC 58.178 52.632 0.00 0.00 44.03 3.18
1216 5999 0.315886 TAGCTTTCTTCGTGTGCCGA 59.684 50.000 0.00 0.00 45.66 5.54
1217 6000 0.438830 GTAGCTTTCTTCGTGTGCCG 59.561 55.000 0.00 0.00 38.13 5.69
1218 6001 0.438830 CGTAGCTTTCTTCGTGTGCC 59.561 55.000 0.00 0.00 0.00 5.01
1219 6002 0.438830 CCGTAGCTTTCTTCGTGTGC 59.561 55.000 0.00 0.00 32.21 4.57
1220 6003 1.068474 CCCGTAGCTTTCTTCGTGTG 58.932 55.000 0.00 0.00 32.21 3.82
1221 6004 0.669625 GCCCGTAGCTTTCTTCGTGT 60.670 55.000 0.00 0.00 38.99 4.49
1222 6005 0.669318 TGCCCGTAGCTTTCTTCGTG 60.669 55.000 0.00 0.00 44.23 4.35
1223 6006 0.389948 CTGCCCGTAGCTTTCTTCGT 60.390 55.000 0.00 0.00 44.23 3.85
1224 6007 0.108804 TCTGCCCGTAGCTTTCTTCG 60.109 55.000 0.00 0.00 44.23 3.79
1225 6008 1.732809 GTTCTGCCCGTAGCTTTCTTC 59.267 52.381 0.00 0.00 44.23 2.87
1226 6009 1.348036 AGTTCTGCCCGTAGCTTTCTT 59.652 47.619 0.00 0.00 44.23 2.52
1227 6010 0.977395 AGTTCTGCCCGTAGCTTTCT 59.023 50.000 0.00 0.00 44.23 2.52
1228 6011 1.360820 GAGTTCTGCCCGTAGCTTTC 58.639 55.000 0.00 0.00 44.23 2.62
1229 6012 0.036294 GGAGTTCTGCCCGTAGCTTT 60.036 55.000 0.00 0.00 44.23 3.51
1230 6013 1.597461 GGAGTTCTGCCCGTAGCTT 59.403 57.895 0.00 0.00 44.23 3.74
1231 6014 2.359967 GGGAGTTCTGCCCGTAGCT 61.360 63.158 0.00 0.00 44.23 3.32
1232 6015 2.187163 GGGAGTTCTGCCCGTAGC 59.813 66.667 0.00 0.00 44.14 3.58
1237 6020 1.475930 GCTGATAAGGGAGTTCTGCCC 60.476 57.143 6.74 0.00 46.40 5.36
1238 6021 1.808133 CGCTGATAAGGGAGTTCTGCC 60.808 57.143 2.08 2.08 32.60 4.85
1239 6022 1.137086 TCGCTGATAAGGGAGTTCTGC 59.863 52.381 0.00 0.00 0.00 4.26
1240 6023 2.223923 CCTCGCTGATAAGGGAGTTCTG 60.224 54.545 20.03 4.05 44.30 3.02
1241 6024 2.035632 CCTCGCTGATAAGGGAGTTCT 58.964 52.381 20.03 0.00 44.30 3.01
1242 6025 2.032620 TCCTCGCTGATAAGGGAGTTC 58.967 52.381 20.03 0.00 44.30 3.01
1243 6026 2.160721 TCCTCGCTGATAAGGGAGTT 57.839 50.000 20.03 0.00 44.30 3.01
1244 6027 2.035632 CTTCCTCGCTGATAAGGGAGT 58.964 52.381 20.03 0.00 44.30 3.85
1245 6028 2.035321 GTCTTCCTCGCTGATAAGGGAG 59.965 54.545 15.87 15.87 45.05 4.30
1246 6029 2.032620 GTCTTCCTCGCTGATAAGGGA 58.967 52.381 0.00 0.00 33.21 4.20
1247 6030 1.069358 GGTCTTCCTCGCTGATAAGGG 59.931 57.143 0.00 0.00 33.21 3.95
1248 6031 1.757118 TGGTCTTCCTCGCTGATAAGG 59.243 52.381 0.00 0.00 34.23 2.69
1249 6032 3.388308 CATGGTCTTCCTCGCTGATAAG 58.612 50.000 0.00 0.00 34.23 1.73
1250 6033 2.103094 CCATGGTCTTCCTCGCTGATAA 59.897 50.000 2.57 0.00 34.23 1.75
1251 6034 1.688735 CCATGGTCTTCCTCGCTGATA 59.311 52.381 2.57 0.00 34.23 2.15
1252 6035 0.467384 CCATGGTCTTCCTCGCTGAT 59.533 55.000 2.57 0.00 34.23 2.90
1253 6036 0.614697 TCCATGGTCTTCCTCGCTGA 60.615 55.000 12.58 0.00 34.23 4.26
1254 6037 0.179089 CTCCATGGTCTTCCTCGCTG 60.179 60.000 12.58 0.00 34.23 5.18
1255 6038 0.324738 TCTCCATGGTCTTCCTCGCT 60.325 55.000 12.58 0.00 34.23 4.93
1256 6039 0.755686 ATCTCCATGGTCTTCCTCGC 59.244 55.000 12.58 0.00 34.23 5.03
1257 6040 3.056250 CCATATCTCCATGGTCTTCCTCG 60.056 52.174 12.58 0.00 40.62 4.63
1258 6041 4.163427 TCCATATCTCCATGGTCTTCCTC 58.837 47.826 12.58 0.00 44.98 3.71
1259 6042 4.166539 CTCCATATCTCCATGGTCTTCCT 58.833 47.826 12.58 0.00 44.98 3.36
1260 6043 3.262915 CCTCCATATCTCCATGGTCTTCC 59.737 52.174 12.58 0.00 44.98 3.46
1261 6044 4.020662 GTCCTCCATATCTCCATGGTCTTC 60.021 50.000 12.58 0.00 44.98 2.87
1262 6045 3.906846 GTCCTCCATATCTCCATGGTCTT 59.093 47.826 12.58 0.00 44.98 3.01
1263 6046 3.116590 TGTCCTCCATATCTCCATGGTCT 60.117 47.826 12.58 0.00 44.98 3.85
1264 6047 3.007398 GTGTCCTCCATATCTCCATGGTC 59.993 52.174 12.58 0.00 44.98 4.02
1265 6048 2.975489 GTGTCCTCCATATCTCCATGGT 59.025 50.000 12.58 0.00 44.98 3.55
1275 6058 2.509548 CCCTTTGATGGTGTCCTCCATA 59.490 50.000 1.08 0.00 46.72 2.74
1291 13208 0.322546 GTCGGATCTTGGCACCCTTT 60.323 55.000 0.00 0.00 0.00 3.11
1310 13227 3.340928 TCCATGTCTGTTGCATGAGAAG 58.659 45.455 0.00 0.00 44.60 2.85
1701 13934 5.760253 GGATTCACAACCTACACATAGATGG 59.240 44.000 0.00 0.00 0.00 3.51
1739 13984 2.847327 TCTTCTGGTTCCTTGAGCTG 57.153 50.000 0.00 0.00 0.00 4.24
1797 14045 3.134804 ACTTTCATCATCCTCTAACCCCG 59.865 47.826 0.00 0.00 0.00 5.73
1849 14097 8.511321 TGGTAGTCATTCAATTCAATGTTGTAC 58.489 33.333 1.76 3.19 35.56 2.90
2153 14471 3.614092 CATCCATCAGTAGCCACAAAGT 58.386 45.455 0.00 0.00 0.00 2.66
2514 15198 1.301716 CAGCAGCCAGTGTTACCGT 60.302 57.895 0.00 0.00 0.00 4.83
2753 16333 2.349886 GGACAAGAATCAGATGACACGC 59.650 50.000 0.00 0.00 0.00 5.34
2817 16397 2.232452 AGCGGTACTCATCATGATAGCC 59.768 50.000 8.15 5.63 0.00 3.93
4582 18572 3.056607 TCATCTGTCAAGTCGAGCATCAA 60.057 43.478 0.00 0.00 33.17 2.57
4635 18626 5.973565 CCGTTTAGATCAAGCATGGAATTTC 59.026 40.000 0.00 0.00 0.00 2.17
4729 18720 4.277921 AGGTACTACTATTTGCTACTCGGC 59.722 45.833 0.00 0.00 36.02 5.54
4742 18737 4.659115 TGCTGTGTTCAGAGGTACTACTA 58.341 43.478 0.00 0.00 41.55 1.82
4743 18738 3.497332 TGCTGTGTTCAGAGGTACTACT 58.503 45.455 0.00 0.00 41.55 2.57
4744 18739 3.936372 TGCTGTGTTCAGAGGTACTAC 57.064 47.619 0.00 0.00 41.55 2.73
4869 18867 3.068024 TGATGAAGCGCTTTTGGAAGTTT 59.932 39.130 25.84 0.00 35.25 2.66
4873 18871 2.819019 TGATGATGAAGCGCTTTTGGAA 59.181 40.909 25.84 9.89 0.00 3.53
4886 18884 1.066757 GTCGCTGAGCTCTGATGATGA 59.933 52.381 23.35 9.59 0.00 2.92
4887 18885 1.202382 TGTCGCTGAGCTCTGATGATG 60.202 52.381 23.35 7.62 0.00 3.07
4888 18886 1.067364 CTGTCGCTGAGCTCTGATGAT 59.933 52.381 23.35 0.00 0.00 2.45
5009 19053 6.222038 TGTGGTCCATAGTGAAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
5045 19089 7.283807 TGCATTTTAGAGCATGTATTCACTCAT 59.716 33.333 0.00 0.00 35.51 2.90
5046 19090 6.598850 TGCATTTTAGAGCATGTATTCACTCA 59.401 34.615 0.00 0.00 35.51 3.41
5047 19091 7.019774 TGCATTTTAGAGCATGTATTCACTC 57.980 36.000 0.00 0.00 35.51 3.51
5096 19155 7.962995 AGTCTTTGTAGAGATTCCACTATGA 57.037 36.000 0.00 0.00 0.00 2.15
5122 19181 3.385115 TCCCTCCTCTGTTCCTAAATCC 58.615 50.000 0.00 0.00 0.00 3.01
5134 19193 3.885976 TTCGATGATACTCCCTCCTCT 57.114 47.619 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.