Multiple sequence alignment - TraesCS5B01G530800

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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 TraesCS5B01G530800 chr5B 100.000 3835 0 0 1 3835 689226258 689222424 0.000000e+00 7083.0
1 TraesCS5B01G530800 chr5B 84.390 205 21 8 1204 1400 665208823 665208622 1.410000e-44 191.0
2 TraesCS5B01G530800 chr5B 90.476 63 4 2 2858 2919 599553929 599553868 8.830000e-12 82.4
3 TraesCS5B01G530800 chr5B 93.617 47 3 0 2875 2921 680309970 680310016 1.910000e-08 71.3
4 TraesCS5B01G530800 chr3B 94.365 976 19 9 2869 3835 753167208 753168156 0.000000e+00 1465.0
5 TraesCS5B01G530800 chr3B 83.405 693 79 11 3143 3832 460239666 460240325 9.110000e-171 610.0
6 TraesCS5B01G530800 chr3B 84.456 193 25 4 1215 1402 625202712 625202520 6.540000e-43 185.0
7 TraesCS5B01G530800 chr3B 79.310 232 33 12 2924 3147 460181560 460181784 8.580000e-32 148.0
8 TraesCS5B01G530800 chr3B 86.111 72 8 2 2871 2941 745239506 745239436 4.110000e-10 76.8
9 TraesCS5B01G530800 chr4A 88.314 1121 65 32 919 2010 623326438 623327521 0.000000e+00 1284.0
10 TraesCS5B01G530800 chr4A 92.810 612 27 6 2179 2775 623327745 623328354 0.000000e+00 870.0
11 TraesCS5B01G530800 chr4A 74.930 359 49 21 7 343 623324039 623324378 4.020000e-25 126.0
12 TraesCS5B01G530800 chr4A 90.625 64 6 0 2874 2937 654936117 654936180 6.830000e-13 86.1
13 TraesCS5B01G530800 chr5D 93.113 755 35 7 2073 2812 546076009 546075257 0.000000e+00 1090.0
14 TraesCS5B01G530800 chr5D 89.157 664 30 16 845 1484 546077376 546076731 0.000000e+00 789.0
15 TraesCS5B01G530800 chr5D 83.075 839 82 30 1 805 546078725 546077913 0.000000e+00 708.0
16 TraesCS5B01G530800 chr5D 85.811 296 20 11 1785 2073 546076462 546076182 1.040000e-75 294.0
17 TraesCS5B01G530800 chr5D 84.211 209 22 8 1204 1404 528401960 528402165 3.910000e-45 193.0
18 TraesCS5B01G530800 chr5D 85.915 71 10 0 2079 2149 546075902 546075832 4.110000e-10 76.8
19 TraesCS5B01G530800 chr3A 85.200 973 94 25 2874 3835 623361823 623360890 0.000000e+00 953.0
20 TraesCS5B01G530800 chr3A 85.263 95 13 1 2884 2978 24753226 24753133 3.150000e-16 97.1
21 TraesCS5B01G530800 chr6B 78.768 763 118 29 2874 3610 712322511 712321767 4.480000e-129 472.0
22 TraesCS5B01G530800 chr1D 83.590 390 64 0 2286 2675 6779195 6778806 2.180000e-97 366.0
23 TraesCS5B01G530800 chr1D 84.000 200 27 5 1179 1374 6780049 6779851 1.820000e-43 187.0
24 TraesCS5B01G530800 chr1D 89.062 64 7 0 2874 2937 355097074 355097137 3.180000e-11 80.5
25 TraesCS5B01G530800 chr1A 83.684 380 62 0 2286 2665 8264840 8264461 3.640000e-95 359.0
26 TraesCS5B01G530800 chr1A 74.411 594 101 25 2874 3435 397085492 397086066 1.400000e-49 207.0
27 TraesCS5B01G530800 chr1A 91.304 138 12 0 1244 1381 8266132 8265995 5.060000e-44 189.0
28 TraesCS5B01G530800 chr1B 83.978 362 58 0 2286 2647 8947882 8948243 7.890000e-92 348.0
29 TraesCS5B01G530800 chr1B 87.500 176 17 5 1207 1381 8946613 8946784 8.400000e-47 198.0
30 TraesCS5B01G530800 chr5A 87.356 174 18 3 1242 1412 656466910 656467082 3.020000e-46 196.0
31 TraesCS5B01G530800 chr2A 75.744 437 80 19 3008 3435 666317471 666317890 3.020000e-46 196.0
32 TraesCS5B01G530800 chr6D 74.297 498 82 31 2883 3348 222661374 222660891 6.590000e-38 169.0
33 TraesCS5B01G530800 chr2D 74.089 494 85 29 2885 3348 606699473 606698993 3.070000e-36 163.0
34 TraesCS5B01G530800 chr2D 89.394 66 5 2 2862 2927 629069203 629069266 8.830000e-12 82.4
35 TraesCS5B01G530800 chr7B 76.510 298 55 11 3145 3436 662898552 662898264 8.580000e-32 148.0
36 TraesCS5B01G530800 chr2B 84.615 78 9 3 2865 2941 534703928 534704003 1.480000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G530800 chr5B 689222424 689226258 3834 True 7083.00 7083 100.000000 1 3835 1 chr5B.!!$R3 3834
1 TraesCS5B01G530800 chr3B 753167208 753168156 948 False 1465.00 1465 94.365000 2869 3835 1 chr3B.!!$F3 966
2 TraesCS5B01G530800 chr3B 460239666 460240325 659 False 610.00 610 83.405000 3143 3832 1 chr3B.!!$F2 689
3 TraesCS5B01G530800 chr4A 623324039 623328354 4315 False 760.00 1284 85.351333 7 2775 3 chr4A.!!$F2 2768
4 TraesCS5B01G530800 chr5D 546075257 546078725 3468 True 591.56 1090 87.414200 1 2812 5 chr5D.!!$R1 2811
5 TraesCS5B01G530800 chr3A 623360890 623361823 933 True 953.00 953 85.200000 2874 3835 1 chr3A.!!$R2 961
6 TraesCS5B01G530800 chr6B 712321767 712322511 744 True 472.00 472 78.768000 2874 3610 1 chr6B.!!$R1 736
7 TraesCS5B01G530800 chr1D 6778806 6780049 1243 True 276.50 366 83.795000 1179 2675 2 chr1D.!!$R1 1496
8 TraesCS5B01G530800 chr1A 8264461 8266132 1671 True 274.00 359 87.494000 1244 2665 2 chr1A.!!$R1 1421
9 TraesCS5B01G530800 chr1A 397085492 397086066 574 False 207.00 207 74.411000 2874 3435 1 chr1A.!!$F1 561
10 TraesCS5B01G530800 chr1B 8946613 8948243 1630 False 273.00 348 85.739000 1207 2647 2 chr1B.!!$F1 1440

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
777 2236 0.036294 GAAAGTCCCCTTCCACTCCG 60.036 60.0 0.00 0.0 0.00 4.63 F
2017 4113 0.030235 CATCCGCACCTTGCATCATG 59.970 55.0 0.00 0.0 45.36 3.07 F
2789 5790 0.179076 CTAGCCGATGCATGTCACCA 60.179 55.0 2.46 0.0 41.13 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 5742 0.108615 CATCTCGAGGAAACGCTGGT 60.109 55.0 13.56 0.0 0.00 4.00 R
2827 5828 0.179004 TTTTGGTCGCAGGACATGGT 60.179 50.0 0.00 0.0 45.28 3.55 R
3730 6832 0.879090 CCGGTTCCAGCTTACCAAAC 59.121 55.0 9.43 0.0 33.94 2.93 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
26 27 9.639563 AATCTTTCCTTTCTTCTTCTTCTCTTT 57.360 29.630 0.00 0.00 0.00 2.52
28 29 9.114952 TCTTTCCTTTCTTCTTCTTCTCTTTTC 57.885 33.333 0.00 0.00 0.00 2.29
30 31 8.669946 TTCCTTTCTTCTTCTTCTCTTTTCTC 57.330 34.615 0.00 0.00 0.00 2.87
63 67 3.201045 TGCTAGGCATACCACCATTACAA 59.799 43.478 0.00 0.00 39.06 2.41
72 76 4.440826 ACCACCATTACAACAAGGTACA 57.559 40.909 0.00 0.00 32.01 2.90
73 77 4.139038 ACCACCATTACAACAAGGTACAC 58.861 43.478 0.00 0.00 32.01 2.90
81 88 7.552687 CCATTACAACAAGGTACACATATGTCT 59.447 37.037 5.07 0.00 40.48 3.41
89 96 4.820716 AGGTACACATATGTCTACGTCTCC 59.179 45.833 5.07 7.52 40.48 3.71
91 98 4.634184 ACACATATGTCTACGTCTCCAC 57.366 45.455 5.07 0.00 31.55 4.02
99 106 2.230508 GTCTACGTCTCCACACATTCCA 59.769 50.000 0.00 0.00 0.00 3.53
112 119 0.179020 CATTCCAATCCTAGCCGGCA 60.179 55.000 31.54 14.00 0.00 5.69
116 123 0.954452 CCAATCCTAGCCGGCAATTC 59.046 55.000 31.54 0.00 0.00 2.17
118 125 0.550914 AATCCTAGCCGGCAATTCCA 59.449 50.000 31.54 7.30 34.01 3.53
128 145 2.495669 CCGGCAATTCCAAAAGGTATGT 59.504 45.455 0.00 0.00 34.01 2.29
130 147 3.056891 CGGCAATTCCAAAAGGTATGTGT 60.057 43.478 0.00 0.00 34.01 3.72
169 186 7.693020 TGTGTATTGTACATTACATGACATGC 58.307 34.615 25.38 15.18 41.34 4.06
173 190 7.628769 ATTGTACATTACATGACATGCTTCA 57.371 32.000 15.49 3.27 38.68 3.02
187 204 4.487019 CATGCTTCATGTGTTGTAATGCA 58.513 39.130 0.00 0.00 37.12 3.96
188 205 4.163458 TGCTTCATGTGTTGTAATGCAG 57.837 40.909 0.00 0.00 0.00 4.41
189 206 3.057386 TGCTTCATGTGTTGTAATGCAGG 60.057 43.478 0.00 0.00 0.00 4.85
190 207 3.674138 GCTTCATGTGTTGTAATGCAGGG 60.674 47.826 0.00 0.00 0.00 4.45
191 208 1.818060 TCATGTGTTGTAATGCAGGGC 59.182 47.619 0.00 0.00 0.00 5.19
192 209 1.545136 CATGTGTTGTAATGCAGGGCA 59.455 47.619 0.00 0.00 44.86 5.36
212 229 4.178545 CATTCCTTGCTTTGTTGGGTAG 57.821 45.455 0.00 0.00 0.00 3.18
289 322 0.849417 GCTTGATTCCCATCCCCTCT 59.151 55.000 0.00 0.00 0.00 3.69
329 362 1.730064 CGTATGTTTCCACCCGACTTG 59.270 52.381 0.00 0.00 0.00 3.16
348 381 4.147449 TGATCGGCGCCTCCACTG 62.147 66.667 26.68 7.77 34.01 3.66
349 382 4.148825 GATCGGCGCCTCCACTGT 62.149 66.667 26.68 1.55 34.01 3.55
350 383 3.665675 GATCGGCGCCTCCACTGTT 62.666 63.158 26.68 2.03 34.01 3.16
351 384 3.958147 ATCGGCGCCTCCACTGTTG 62.958 63.158 26.68 5.22 34.01 3.33
354 387 2.980233 GCGCCTCCACTGTTGCTT 60.980 61.111 0.00 0.00 0.00 3.91
357 390 1.073897 GCCTCCACTGTTGCTTCCT 59.926 57.895 0.00 0.00 0.00 3.36
387 1048 0.725117 CGTTCGGCCCTTATGTTGTC 59.275 55.000 0.00 0.00 0.00 3.18
401 1062 1.680735 TGTTGTCCATTTTCGCAAGCT 59.319 42.857 0.00 0.00 37.18 3.74
403 1064 0.597568 TGTCCATTTTCGCAAGCTGG 59.402 50.000 0.00 0.00 37.18 4.85
405 1066 0.895100 TCCATTTTCGCAAGCTGGCT 60.895 50.000 12.26 0.00 37.18 4.75
406 1067 0.457337 CCATTTTCGCAAGCTGGCTC 60.457 55.000 12.26 0.00 37.18 4.70
407 1068 0.795735 CATTTTCGCAAGCTGGCTCG 60.796 55.000 12.26 0.00 37.18 5.03
408 1069 1.926511 ATTTTCGCAAGCTGGCTCGG 61.927 55.000 12.26 0.00 37.18 4.63
448 1109 3.015312 GCCCGCTTACTTCTCCCGT 62.015 63.158 0.00 0.00 0.00 5.28
467 1591 2.930012 TTCGATCGACCGCATCCACG 62.930 60.000 19.26 0.00 0.00 4.94
506 1930 0.810031 CGGTTACTCAAGATGGCGGG 60.810 60.000 0.00 0.00 0.00 6.13
533 1957 0.179089 CTCCACAGGCTTCTCGGATG 60.179 60.000 0.00 0.00 0.00 3.51
559 1983 4.503007 CCGATTGACTGTGTACCTATTTCG 59.497 45.833 0.00 0.00 0.00 3.46
563 1987 3.056393 TGACTGTGTACCTATTTCGTGGG 60.056 47.826 0.00 0.00 33.95 4.61
571 1995 4.023726 ACCTATTTCGTGGGCAACTTAA 57.976 40.909 0.00 0.00 29.93 1.85
574 1998 5.048294 ACCTATTTCGTGGGCAACTTAAAAG 60.048 40.000 0.00 0.00 29.93 2.27
585 2009 7.811236 GTGGGCAACTTAAAAGTAGTTATTTCC 59.189 37.037 0.00 0.00 38.57 3.13
586 2010 7.506261 TGGGCAACTTAAAAGTAGTTATTTCCA 59.494 33.333 0.00 0.00 38.57 3.53
587 2011 8.027189 GGGCAACTTAAAAGTAGTTATTTCCAG 58.973 37.037 0.00 0.00 38.57 3.86
588 2012 8.027189 GGCAACTTAAAAGTAGTTATTTCCAGG 58.973 37.037 0.00 0.00 38.57 4.45
591 2015 9.856162 AACTTAAAAGTAGTTATTTCCAGGTCA 57.144 29.630 0.00 0.00 38.57 4.02
602 2059 4.519906 TTTCCAGGTCAAAGATATCCCC 57.480 45.455 0.00 0.00 0.00 4.81
603 2060 3.438131 TCCAGGTCAAAGATATCCCCT 57.562 47.619 0.00 0.00 0.00 4.79
604 2061 4.569676 TCCAGGTCAAAGATATCCCCTA 57.430 45.455 0.00 0.00 0.00 3.53
605 2062 4.232091 TCCAGGTCAAAGATATCCCCTAC 58.768 47.826 0.00 0.00 0.00 3.18
609 2066 3.599348 GTCAAAGATATCCCCTACCCCT 58.401 50.000 0.00 0.00 0.00 4.79
613 2070 2.652369 AGATATCCCCTACCCCTCGTA 58.348 52.381 0.00 0.00 0.00 3.43
635 2092 1.555533 ACGGAGTTCTTTCCATCCCTC 59.444 52.381 0.00 0.00 37.78 4.30
653 2110 4.040461 TCCCTCCGTATTTCATGAATCTCC 59.960 45.833 9.40 0.00 0.00 3.71
715 2174 9.610705 CTAATAGCTATTATTCTGCCATGTGAT 57.389 33.333 23.21 0.00 33.96 3.06
771 2230 0.978907 TACCGTGAAAGTCCCCTTCC 59.021 55.000 0.00 0.00 0.00 3.46
777 2236 0.036294 GAAAGTCCCCTTCCACTCCG 60.036 60.000 0.00 0.00 0.00 4.63
795 2254 3.944015 CTCCGGAGCTCATTTGAGAATTT 59.056 43.478 20.67 0.00 44.74 1.82
796 2255 3.691118 TCCGGAGCTCATTTGAGAATTTG 59.309 43.478 17.19 0.00 44.74 2.32
798 2257 3.432782 GGAGCTCATTTGAGAATTTGCG 58.567 45.455 17.19 0.00 44.74 4.85
805 2264 2.420628 TTGAGAATTTGCGGTGCTTG 57.579 45.000 0.00 0.00 0.00 4.01
806 2265 1.317613 TGAGAATTTGCGGTGCTTGT 58.682 45.000 0.00 0.00 0.00 3.16
807 2266 1.001487 TGAGAATTTGCGGTGCTTGTG 60.001 47.619 0.00 0.00 0.00 3.33
808 2267 0.314935 AGAATTTGCGGTGCTTGTGG 59.685 50.000 0.00 0.00 0.00 4.17
809 2268 0.313672 GAATTTGCGGTGCTTGTGGA 59.686 50.000 0.00 0.00 0.00 4.02
810 2269 0.968405 AATTTGCGGTGCTTGTGGAT 59.032 45.000 0.00 0.00 0.00 3.41
811 2270 0.527565 ATTTGCGGTGCTTGTGGATC 59.472 50.000 0.00 0.00 0.00 3.36
812 2271 1.851021 TTTGCGGTGCTTGTGGATCG 61.851 55.000 0.00 0.00 41.16 3.69
814 2273 3.853330 CGGTGCTTGTGGATCGCG 61.853 66.667 0.00 0.00 30.21 5.87
817 2276 1.638467 GTGCTTGTGGATCGCGATC 59.362 57.895 35.42 35.42 37.11 3.69
818 2277 1.083806 GTGCTTGTGGATCGCGATCA 61.084 55.000 40.62 27.48 39.54 2.92
819 2278 0.807275 TGCTTGTGGATCGCGATCAG 60.807 55.000 40.62 31.43 39.54 2.90
820 2279 0.807667 GCTTGTGGATCGCGATCAGT 60.808 55.000 40.62 15.71 39.54 3.41
823 2282 3.384668 CTTGTGGATCGCGATCAGTAAT 58.615 45.455 40.62 13.72 39.54 1.89
824 2283 3.452755 TGTGGATCGCGATCAGTAATT 57.547 42.857 40.62 12.92 39.54 1.40
826 2285 5.134202 TGTGGATCGCGATCAGTAATTAT 57.866 39.130 40.62 11.35 39.54 1.28
829 2288 5.405571 GTGGATCGCGATCAGTAATTATTGT 59.594 40.000 40.62 10.11 39.54 2.71
830 2289 5.989168 TGGATCGCGATCAGTAATTATTGTT 59.011 36.000 40.62 9.42 39.54 2.83
832 2291 7.817478 TGGATCGCGATCAGTAATTATTGTTAT 59.183 33.333 40.62 8.64 39.54 1.89
833 2292 8.656849 GGATCGCGATCAGTAATTATTGTTATT 58.343 33.333 40.62 8.30 39.54 1.40
836 2295 8.632551 TCGCGATCAGTAATTATTGTTATTACG 58.367 33.333 3.71 6.31 41.26 3.18
837 2296 7.418801 CGCGATCAGTAATTATTGTTATTACGC 59.581 37.037 0.00 13.27 41.26 4.42
861 2840 3.682292 GAGCTTGTAGGCCACCGGG 62.682 68.421 6.32 0.00 37.18 5.73
893 2875 2.238942 AGACAAAGTCACATCACGCA 57.761 45.000 0.00 0.00 34.60 5.24
931 2913 2.098831 GTTTCCGTAGCCGCACTCC 61.099 63.158 0.00 0.00 0.00 3.85
942 2924 1.444553 CGCACTCCGTCTGTCCTTC 60.445 63.158 0.00 0.00 0.00 3.46
987 2970 3.787001 GCCCTCCTTCCCAGACCG 61.787 72.222 0.00 0.00 0.00 4.79
992 2980 4.452733 CCTTCCCAGACCGTCGCC 62.453 72.222 0.00 0.00 0.00 5.54
1040 3028 4.031129 CAGCCAGCCAGCCAGTCT 62.031 66.667 0.00 0.00 0.00 3.24
1041 3029 3.715097 AGCCAGCCAGCCAGTCTC 61.715 66.667 0.00 0.00 0.00 3.36
1069 3062 2.042843 GGCGGGAGGGAAGAGAGA 60.043 66.667 0.00 0.00 0.00 3.10
1070 3063 2.131067 GGCGGGAGGGAAGAGAGAG 61.131 68.421 0.00 0.00 0.00 3.20
1071 3064 2.131067 GCGGGAGGGAAGAGAGAGG 61.131 68.421 0.00 0.00 0.00 3.69
1072 3065 1.456705 CGGGAGGGAAGAGAGAGGG 60.457 68.421 0.00 0.00 0.00 4.30
1188 3196 2.238701 TTGGAGGGAAGGGAAGGCC 61.239 63.158 0.00 0.00 0.00 5.19
1190 3198 3.798511 GAGGGAAGGGAAGGCCGG 61.799 72.222 0.00 0.00 33.83 6.13
1193 3201 3.798511 GGAAGGGAAGGCCGGGAG 61.799 72.222 2.18 0.00 33.83 4.30
1396 3410 4.394712 CCACACAGGTCCCTCCGC 62.395 72.222 0.00 0.00 41.99 5.54
1397 3411 4.394712 CACACAGGTCCCTCCGCC 62.395 72.222 0.00 0.00 41.99 6.13
1419 3433 4.095400 TCCCCTCCCCTGCTCTCC 62.095 72.222 0.00 0.00 0.00 3.71
1433 3452 0.552848 CTCTCCTCTCCTCTGCTCCT 59.447 60.000 0.00 0.00 0.00 3.69
1484 3503 3.987807 GATGCTTTCCATCGATCGATC 57.012 47.619 27.20 15.68 40.84 3.69
1514 3533 0.815734 TTCCTCGCAGCACTAGTACC 59.184 55.000 0.00 0.00 0.00 3.34
1525 3559 1.407258 CACTAGTACCAGCTCTGCTCC 59.593 57.143 0.00 0.00 36.40 4.70
1537 3571 1.209990 CTCTGCTCCTCTTGGCTGATT 59.790 52.381 0.00 0.00 36.24 2.57
1539 3573 3.044156 TCTGCTCCTCTTGGCTGATTAT 58.956 45.455 0.00 0.00 32.92 1.28
1543 3577 5.555017 TGCTCCTCTTGGCTGATTATAATC 58.445 41.667 17.09 17.09 35.97 1.75
1548 3582 6.488006 TCCTCTTGGCTGATTATAATCTTTGC 59.512 38.462 22.77 21.28 36.39 3.68
1557 3591 9.339492 GCTGATTATAATCTTTGCAAGCTATTC 57.661 33.333 22.77 0.00 36.39 1.75
1569 3603 2.200373 AGCTATTCGTGCCCTGTTTT 57.800 45.000 0.00 0.00 0.00 2.43
1581 3616 2.288213 GCCCTGTTTTTAGTGGTTCAGC 60.288 50.000 0.00 0.00 0.00 4.26
1607 3642 2.095263 CGTTTGGGTGCAGTTTATCCTG 60.095 50.000 0.00 0.00 35.49 3.86
1609 3644 2.198827 TGGGTGCAGTTTATCCTGTG 57.801 50.000 0.00 0.00 34.84 3.66
1614 3649 2.417933 GTGCAGTTTATCCTGTGAGCAG 59.582 50.000 0.00 0.00 42.22 4.24
1673 3715 0.107214 TCGGATGATGGAAACCCAGC 60.107 55.000 0.00 0.00 40.40 4.85
1692 3734 5.352293 CCCAGCAAATTTCTAAATTTCAGCC 59.648 40.000 9.83 1.70 44.38 4.85
1693 3735 5.062558 CCAGCAAATTTCTAAATTTCAGCCG 59.937 40.000 9.83 5.41 44.38 5.52
1722 3767 7.781056 TGGCTCAATTAATCCAAAAGGAATAC 58.219 34.615 0.00 0.00 0.00 1.89
1758 3803 6.091305 CGTGTGTTCAACAGAGTATGATGATT 59.909 38.462 0.00 0.00 40.07 2.57
1776 3821 4.462133 TGATTCTTTCAAACGGTTGGGTA 58.538 39.130 14.34 0.00 35.29 3.69
1777 3822 4.517453 TGATTCTTTCAAACGGTTGGGTAG 59.483 41.667 14.34 8.42 35.29 3.18
1822 3867 6.624423 CCAAATTCAGTTTCTACCCTGATTG 58.376 40.000 0.00 0.00 37.54 2.67
1828 3873 8.477419 TTCAGTTTCTACCCTGATTGAAATTT 57.523 30.769 0.00 0.00 37.54 1.82
1830 3875 7.039784 TCAGTTTCTACCCTGATTGAAATTTGG 60.040 37.037 0.00 0.00 32.93 3.28
1869 3914 5.996513 TGAAACCACCCAATCATGAATTTTG 59.003 36.000 0.00 0.00 0.00 2.44
1892 3937 9.820229 TTTGCTTTCGAATATAGTAACAAACTG 57.180 29.630 0.00 0.00 39.39 3.16
1936 3998 9.862371 GTTGACTATGTTATCCCTGTATATCAG 57.138 37.037 0.00 0.00 43.27 2.90
1938 4000 9.025041 TGACTATGTTATCCCTGTATATCAGTG 57.975 37.037 0.00 0.00 42.19 3.66
2014 4110 3.113745 CCATCCGCACCTTGCATC 58.886 61.111 0.00 0.00 45.36 3.91
2015 4111 1.750018 CCATCCGCACCTTGCATCA 60.750 57.895 0.00 0.00 45.36 3.07
2016 4112 1.105167 CCATCCGCACCTTGCATCAT 61.105 55.000 0.00 0.00 45.36 2.45
2017 4113 0.030235 CATCCGCACCTTGCATCATG 59.970 55.000 0.00 0.00 45.36 3.07
2018 4114 1.731433 ATCCGCACCTTGCATCATGC 61.731 55.000 1.35 1.35 45.36 4.06
2033 4393 5.032863 GCATCATGCATCAACAGAAACTAC 58.967 41.667 4.20 0.00 44.26 2.73
2042 4402 8.629158 TGCATCAACAGAAACTACAACTAAATT 58.371 29.630 0.00 0.00 0.00 1.82
2046 4406 8.962679 TCAACAGAAACTACAACTAAATTTGGT 58.037 29.630 0.65 0.65 0.00 3.67
2151 4995 5.902613 TGCTCACAAATATTCTCCAAAGG 57.097 39.130 0.00 0.00 0.00 3.11
2192 5036 5.925397 TGCACCTGCTTAAAATTTGTATGTG 59.075 36.000 0.00 0.00 42.66 3.21
2223 5073 8.777413 TCAGTTATCTAGCATCAACATTATTGC 58.223 33.333 0.00 0.00 35.34 3.56
2245 5222 4.180817 CCCGGTTTGCTCAAAAATATTCC 58.819 43.478 0.00 0.00 31.33 3.01
2246 5223 4.322349 CCCGGTTTGCTCAAAAATATTCCA 60.322 41.667 0.00 0.00 31.33 3.53
2249 5226 5.118510 CGGTTTGCTCAAAAATATTCCACAC 59.881 40.000 0.00 0.00 31.33 3.82
2251 5228 6.650390 GGTTTGCTCAAAAATATTCCACACAT 59.350 34.615 0.00 0.00 31.33 3.21
2254 5245 8.755696 TTGCTCAAAAATATTCCACACATAAC 57.244 30.769 0.00 0.00 0.00 1.89
2431 5432 2.935955 GCCACCTTCGACAACGTG 59.064 61.111 0.00 0.00 40.69 4.49
2650 5651 2.728817 GCCGAGATCTACCGGGTG 59.271 66.667 20.81 0.00 45.42 4.61
2722 5723 1.383803 AGAGGGGCAGTCCATCCTC 60.384 63.158 0.95 0.00 46.90 3.71
2752 5753 1.228154 AGAACCCACCAGCGTTTCC 60.228 57.895 0.00 0.00 0.00 3.13
2775 5776 2.482864 GAGATGCTGCTCTTTCTAGCC 58.517 52.381 0.00 0.00 42.05 3.93
2776 5777 1.202510 AGATGCTGCTCTTTCTAGCCG 60.203 52.381 0.00 0.00 42.05 5.52
2777 5778 0.826715 ATGCTGCTCTTTCTAGCCGA 59.173 50.000 0.00 0.00 42.05 5.54
2778 5779 0.826715 TGCTGCTCTTTCTAGCCGAT 59.173 50.000 0.00 0.00 42.05 4.18
2779 5780 1.216122 GCTGCTCTTTCTAGCCGATG 58.784 55.000 0.00 0.00 42.05 3.84
2780 5781 1.216122 CTGCTCTTTCTAGCCGATGC 58.784 55.000 0.00 0.00 42.05 3.91
2789 5790 0.179076 CTAGCCGATGCATGTCACCA 60.179 55.000 2.46 0.00 41.13 4.17
2813 5814 1.549203 AGCCATTTCGGTTGATTGCT 58.451 45.000 0.00 0.00 36.97 3.91
2814 5815 1.895131 AGCCATTTCGGTTGATTGCTT 59.105 42.857 0.00 0.00 36.97 3.91
2815 5816 3.088532 AGCCATTTCGGTTGATTGCTTA 58.911 40.909 0.00 0.00 36.97 3.09
2816 5817 3.509575 AGCCATTTCGGTTGATTGCTTAA 59.490 39.130 0.00 0.00 36.97 1.85
2817 5818 4.160252 AGCCATTTCGGTTGATTGCTTAAT 59.840 37.500 0.00 0.00 36.97 1.40
2818 5819 4.869861 GCCATTTCGGTTGATTGCTTAATT 59.130 37.500 0.00 0.00 36.97 1.40
2819 5820 6.039616 GCCATTTCGGTTGATTGCTTAATTA 58.960 36.000 0.00 0.00 36.97 1.40
2820 5821 6.533367 GCCATTTCGGTTGATTGCTTAATTAA 59.467 34.615 0.00 0.00 36.97 1.40
2821 5822 7.224557 GCCATTTCGGTTGATTGCTTAATTAAT 59.775 33.333 0.00 0.00 36.97 1.40
2822 5823 9.743057 CCATTTCGGTTGATTGCTTAATTAATA 57.257 29.630 0.00 0.00 0.00 0.98
2826 5827 9.729023 TTCGGTTGATTGCTTAATTAATATGTG 57.271 29.630 0.00 0.00 0.00 3.21
2827 5828 9.114952 TCGGTTGATTGCTTAATTAATATGTGA 57.885 29.630 0.00 0.00 0.00 3.58
2828 5829 9.169468 CGGTTGATTGCTTAATTAATATGTGAC 57.831 33.333 0.00 0.00 0.00 3.67
2829 5830 9.463443 GGTTGATTGCTTAATTAATATGTGACC 57.537 33.333 0.00 0.00 0.00 4.02
2835 5836 8.165239 TGCTTAATTAATATGTGACCATGTCC 57.835 34.615 0.00 0.00 32.29 4.02
2836 5837 7.998383 TGCTTAATTAATATGTGACCATGTCCT 59.002 33.333 0.00 0.00 32.29 3.85
2837 5838 8.292448 GCTTAATTAATATGTGACCATGTCCTG 58.708 37.037 0.00 0.00 32.29 3.86
2838 5839 6.639632 AATTAATATGTGACCATGTCCTGC 57.360 37.500 0.00 0.00 32.29 4.85
2839 5840 2.245159 ATATGTGACCATGTCCTGCG 57.755 50.000 0.00 0.00 32.29 5.18
2840 5841 1.190643 TATGTGACCATGTCCTGCGA 58.809 50.000 0.00 0.00 32.29 5.10
2841 5842 0.391661 ATGTGACCATGTCCTGCGAC 60.392 55.000 0.00 0.00 39.66 5.19
2842 5843 1.741770 GTGACCATGTCCTGCGACC 60.742 63.158 0.00 0.00 38.32 4.79
2843 5844 2.213513 TGACCATGTCCTGCGACCA 61.214 57.895 0.00 0.00 38.32 4.02
2844 5845 1.003839 GACCATGTCCTGCGACCAA 60.004 57.895 0.00 0.00 38.32 3.67
2845 5846 0.605319 GACCATGTCCTGCGACCAAA 60.605 55.000 0.00 0.00 38.32 3.28
2846 5847 0.179004 ACCATGTCCTGCGACCAAAA 60.179 50.000 0.00 0.00 38.32 2.44
2847 5848 1.176527 CCATGTCCTGCGACCAAAAT 58.823 50.000 0.00 0.00 38.32 1.82
2848 5849 2.290641 ACCATGTCCTGCGACCAAAATA 60.291 45.455 0.00 0.00 38.32 1.40
2849 5850 2.752354 CCATGTCCTGCGACCAAAATAA 59.248 45.455 0.00 0.00 38.32 1.40
2850 5851 3.192422 CCATGTCCTGCGACCAAAATAAA 59.808 43.478 0.00 0.00 38.32 1.40
2851 5852 4.142182 CCATGTCCTGCGACCAAAATAAAT 60.142 41.667 0.00 0.00 38.32 1.40
2852 5853 5.410067 CATGTCCTGCGACCAAAATAAATT 58.590 37.500 0.00 0.00 38.32 1.82
2853 5854 5.054390 TGTCCTGCGACCAAAATAAATTC 57.946 39.130 0.00 0.00 38.32 2.17
2854 5855 4.520874 TGTCCTGCGACCAAAATAAATTCA 59.479 37.500 0.00 0.00 38.32 2.57
2855 5856 5.095490 GTCCTGCGACCAAAATAAATTCAG 58.905 41.667 0.00 0.00 32.40 3.02
2856 5857 5.007034 TCCTGCGACCAAAATAAATTCAGA 58.993 37.500 0.00 0.00 0.00 3.27
2857 5858 5.475220 TCCTGCGACCAAAATAAATTCAGAA 59.525 36.000 0.00 0.00 0.00 3.02
2858 5859 5.801947 CCTGCGACCAAAATAAATTCAGAAG 59.198 40.000 0.00 0.00 0.00 2.85
2859 5860 5.708948 TGCGACCAAAATAAATTCAGAAGG 58.291 37.500 0.00 0.00 0.00 3.46
2860 5861 5.242838 TGCGACCAAAATAAATTCAGAAGGT 59.757 36.000 0.00 0.00 0.00 3.50
2861 5862 6.156519 GCGACCAAAATAAATTCAGAAGGTT 58.843 36.000 0.00 0.00 0.00 3.50
2862 5863 7.040340 TGCGACCAAAATAAATTCAGAAGGTTA 60.040 33.333 0.00 0.00 0.00 2.85
2863 5864 7.973944 GCGACCAAAATAAATTCAGAAGGTTAT 59.026 33.333 0.00 0.00 0.00 1.89
2864 5865 9.855021 CGACCAAAATAAATTCAGAAGGTTATT 57.145 29.630 8.08 8.08 0.00 1.40
2963 5971 6.787085 AACTCTTTTAACCGTCAGATTCTG 57.213 37.500 7.38 7.38 0.00 3.02
2964 5972 5.238583 ACTCTTTTAACCGTCAGATTCTGG 58.761 41.667 13.59 0.51 31.51 3.86
2965 5973 5.011738 ACTCTTTTAACCGTCAGATTCTGGA 59.988 40.000 13.59 0.00 31.51 3.86
2966 5974 5.235516 TCTTTTAACCGTCAGATTCTGGAC 58.764 41.667 13.59 9.35 31.51 4.02
2967 5975 4.610605 TTTAACCGTCAGATTCTGGACA 57.389 40.909 13.59 0.00 31.51 4.02
2968 5976 2.457366 AACCGTCAGATTCTGGACAC 57.543 50.000 13.59 4.13 31.51 3.67
2969 5977 1.633774 ACCGTCAGATTCTGGACACT 58.366 50.000 13.59 0.00 31.51 3.55
2971 5979 2.028930 ACCGTCAGATTCTGGACACTTC 60.029 50.000 13.59 0.00 31.51 3.01
3037 6071 0.895530 TGGAAGAGCTACTTGACCCG 59.104 55.000 3.55 0.00 39.13 5.28
3038 6072 0.460459 GGAAGAGCTACTTGACCCGC 60.460 60.000 3.55 0.00 39.13 6.13
3039 6073 0.460459 GAAGAGCTACTTGACCCGCC 60.460 60.000 3.55 0.00 39.13 6.13
3040 6074 2.202756 GAGCTACTTGACCCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
3041 6075 3.718210 GAGCTACTTGACCCGCCGG 62.718 68.421 0.00 0.00 0.00 6.13
3042 6076 3.766691 GCTACTTGACCCGCCGGA 61.767 66.667 5.05 0.00 0.00 5.14
3043 6077 3.090219 GCTACTTGACCCGCCGGAT 62.090 63.158 5.05 0.00 0.00 4.18
3044 6078 1.067582 CTACTTGACCCGCCGGATC 59.932 63.158 5.05 0.00 0.00 3.36
3045 6079 1.380785 TACTTGACCCGCCGGATCT 60.381 57.895 5.05 0.00 0.00 2.75
3046 6080 1.389609 TACTTGACCCGCCGGATCTC 61.390 60.000 5.05 0.00 0.00 2.75
3047 6081 3.447025 CTTGACCCGCCGGATCTCC 62.447 68.421 5.05 0.00 0.00 3.71
3128 6182 2.042762 CACCCTCCTCATCCCCCA 59.957 66.667 0.00 0.00 0.00 4.96
3303 6360 1.577328 CCGTTGGGTAGTTGCAGCAG 61.577 60.000 2.55 0.00 0.00 4.24
3730 6832 4.216687 TGAATAAAAAGCTACAACCGGTGG 59.783 41.667 8.52 8.06 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.762218 CCTAGCAATATCCCACTGAGAAAAG 59.238 44.000 0.00 0.00 0.00 2.27
26 27 3.071602 GCCTAGCAATATCCCACTGAGAA 59.928 47.826 0.00 0.00 0.00 2.87
28 29 2.369860 TGCCTAGCAATATCCCACTGAG 59.630 50.000 0.00 0.00 34.76 3.35
30 31 2.936919 TGCCTAGCAATATCCCACTG 57.063 50.000 0.00 0.00 34.76 3.66
63 67 5.651139 AGACGTAGACATATGTGTACCTTGT 59.349 40.000 28.07 22.21 40.45 3.16
72 76 4.014406 TGTGTGGAGACGTAGACATATGT 58.986 43.478 8.43 8.43 33.70 2.29
73 77 4.632538 TGTGTGGAGACGTAGACATATG 57.367 45.455 0.00 0.00 0.00 1.78
81 88 3.369052 GGATTGGAATGTGTGGAGACGTA 60.369 47.826 0.00 0.00 0.00 3.57
89 96 1.942657 CGGCTAGGATTGGAATGTGTG 59.057 52.381 0.00 0.00 0.00 3.82
91 98 1.597742 CCGGCTAGGATTGGAATGTG 58.402 55.000 0.00 0.00 45.00 3.21
99 106 0.550914 TGGAATTGCCGGCTAGGATT 59.449 50.000 29.70 20.69 45.00 3.01
118 125 4.283212 CCACCAATCCAACACATACCTTTT 59.717 41.667 0.00 0.00 0.00 2.27
128 145 2.956132 ACACATTCCACCAATCCAACA 58.044 42.857 0.00 0.00 0.00 3.33
130 147 5.083122 ACAATACACATTCCACCAATCCAA 58.917 37.500 0.00 0.00 0.00 3.53
169 186 3.674138 GCCCTGCATTACAACACATGAAG 60.674 47.826 0.00 0.00 0.00 3.02
173 190 1.921982 TGCCCTGCATTACAACACAT 58.078 45.000 0.00 0.00 31.71 3.21
191 208 3.573967 ACTACCCAACAAAGCAAGGAATG 59.426 43.478 0.00 0.00 0.00 2.67
192 209 3.844640 ACTACCCAACAAAGCAAGGAAT 58.155 40.909 0.00 0.00 0.00 3.01
193 210 3.306472 ACTACCCAACAAAGCAAGGAA 57.694 42.857 0.00 0.00 0.00 3.36
194 211 2.955660 CAACTACCCAACAAAGCAAGGA 59.044 45.455 0.00 0.00 0.00 3.36
195 212 2.693074 ACAACTACCCAACAAAGCAAGG 59.307 45.455 0.00 0.00 0.00 3.61
196 213 5.508200 TTACAACTACCCAACAAAGCAAG 57.492 39.130 0.00 0.00 0.00 4.01
212 229 1.154197 GCCGGTCCACTCTTTACAAC 58.846 55.000 1.90 0.00 0.00 3.32
240 262 7.283807 GGGCGGAAAAATAGAAAGAGGTAATAA 59.716 37.037 0.00 0.00 0.00 1.40
241 263 6.769341 GGGCGGAAAAATAGAAAGAGGTAATA 59.231 38.462 0.00 0.00 0.00 0.98
242 264 5.593095 GGGCGGAAAAATAGAAAGAGGTAAT 59.407 40.000 0.00 0.00 0.00 1.89
289 322 3.243234 ACGCATTCCGACAACATGAAAAA 60.243 39.130 0.00 0.00 41.02 1.94
344 377 1.239968 GCAGGGAGGAAGCAACAGTG 61.240 60.000 0.00 0.00 0.00 3.66
345 378 1.073897 GCAGGGAGGAAGCAACAGT 59.926 57.895 0.00 0.00 0.00 3.55
348 381 2.747855 CGGCAGGGAGGAAGCAAC 60.748 66.667 0.00 0.00 0.00 4.17
349 382 4.722700 GCGGCAGGGAGGAAGCAA 62.723 66.667 0.00 0.00 0.00 3.91
351 384 4.847444 GAGCGGCAGGGAGGAAGC 62.847 72.222 1.45 0.00 0.00 3.86
387 1048 0.457337 GAGCCAGCTTGCGAAAATGG 60.457 55.000 3.83 3.09 36.02 3.16
403 1064 3.936772 TTCATTGGTGCCCCCGAGC 62.937 63.158 0.00 0.00 35.15 5.03
405 1066 2.034999 GTTCATTGGTGCCCCCGA 59.965 61.111 0.00 0.00 35.15 5.14
406 1067 3.068064 GGTTCATTGGTGCCCCCG 61.068 66.667 0.00 0.00 35.15 5.73
407 1068 1.984026 CAGGTTCATTGGTGCCCCC 60.984 63.158 0.00 0.00 0.00 5.40
408 1069 0.831711 AACAGGTTCATTGGTGCCCC 60.832 55.000 0.00 0.00 0.00 5.80
409 1070 1.047801 AAACAGGTTCATTGGTGCCC 58.952 50.000 0.00 0.00 0.00 5.36
416 1077 1.815817 GCGGGCCAAACAGGTTCATT 61.816 55.000 4.39 0.00 40.61 2.57
448 1109 1.226859 GTGGATGCGGTCGATCGAA 60.227 57.895 24.71 13.29 0.00 3.71
519 1943 1.144936 GGACCATCCGAGAAGCCTG 59.855 63.158 0.00 0.00 0.00 4.85
545 1969 1.624312 TGCCCACGAAATAGGTACACA 59.376 47.619 0.00 0.00 0.00 3.72
559 1983 7.811236 GGAAATAACTACTTTTAAGTTGCCCAC 59.189 37.037 0.00 0.00 40.37 4.61
563 1987 8.573885 ACCTGGAAATAACTACTTTTAAGTTGC 58.426 33.333 0.00 0.00 40.37 4.17
574 1998 9.274206 GGATATCTTTGACCTGGAAATAACTAC 57.726 37.037 0.00 0.00 0.00 2.73
585 2009 3.328050 GGGTAGGGGATATCTTTGACCTG 59.672 52.174 2.05 0.00 0.00 4.00
586 2010 3.599348 GGGTAGGGGATATCTTTGACCT 58.401 50.000 2.05 5.83 0.00 3.85
587 2011 2.643304 GGGGTAGGGGATATCTTTGACC 59.357 54.545 2.05 5.88 0.00 4.02
588 2012 3.583526 GAGGGGTAGGGGATATCTTTGAC 59.416 52.174 2.05 0.00 0.00 3.18
590 2014 2.567615 CGAGGGGTAGGGGATATCTTTG 59.432 54.545 2.05 0.00 0.00 2.77
591 2015 2.181642 ACGAGGGGTAGGGGATATCTTT 59.818 50.000 2.05 0.00 0.00 2.52
603 2060 0.620556 AACTCCGTCTACGAGGGGTA 59.379 55.000 3.65 0.00 43.02 3.69
604 2061 0.679321 GAACTCCGTCTACGAGGGGT 60.679 60.000 3.65 0.00 43.02 4.95
605 2062 0.394080 AGAACTCCGTCTACGAGGGG 60.394 60.000 3.65 0.00 43.02 4.79
609 2066 2.507484 TGGAAAGAACTCCGTCTACGA 58.493 47.619 3.65 0.00 43.02 3.43
613 2070 1.555533 GGGATGGAAAGAACTCCGTCT 59.444 52.381 10.80 0.00 46.71 4.18
635 2092 8.607441 TTAAGATGGAGATTCATGAAATACGG 57.393 34.615 13.09 0.00 0.00 4.02
653 2110 8.276325 GCTAACAACCATTACGATCTTAAGATG 58.724 37.037 22.61 15.83 34.37 2.90
705 2164 9.237187 TGTTTTCTACTATTTTATCACATGGCA 57.763 29.630 0.00 0.00 0.00 4.92
740 2199 6.591062 GGACTTTCACGGTACATTGTATTACA 59.409 38.462 0.00 0.00 0.00 2.41
744 2203 4.510571 GGGACTTTCACGGTACATTGTAT 58.489 43.478 0.00 0.00 0.00 2.29
771 2230 1.205655 TCTCAAATGAGCTCCGGAGTG 59.794 52.381 31.43 20.47 41.80 3.51
777 2236 3.432782 CGCAAATTCTCAAATGAGCTCC 58.567 45.455 12.15 0.00 41.80 4.70
780 2239 2.919229 CACCGCAAATTCTCAAATGAGC 59.081 45.455 5.53 0.00 41.80 4.26
781 2240 2.919229 GCACCGCAAATTCTCAAATGAG 59.081 45.455 3.99 3.99 43.36 2.90
795 2254 2.741985 CGATCCACAAGCACCGCA 60.742 61.111 0.00 0.00 0.00 5.69
796 2255 4.166011 GCGATCCACAAGCACCGC 62.166 66.667 0.00 0.00 35.91 5.68
798 2257 1.766143 GATCGCGATCCACAAGCACC 61.766 60.000 33.80 9.44 31.76 5.01
805 2264 5.405571 ACAATAATTACTGATCGCGATCCAC 59.594 40.000 38.25 20.81 37.02 4.02
806 2265 5.538118 ACAATAATTACTGATCGCGATCCA 58.462 37.500 38.25 26.72 37.02 3.41
807 2266 6.467723 AACAATAATTACTGATCGCGATCC 57.532 37.500 38.25 24.08 37.02 3.36
810 2269 8.632551 CGTAATAACAATAATTACTGATCGCGA 58.367 33.333 13.09 13.09 37.56 5.87
811 2270 7.418801 GCGTAATAACAATAATTACTGATCGCG 59.581 37.037 0.00 0.00 37.56 5.87
812 2271 8.433126 AGCGTAATAACAATAATTACTGATCGC 58.567 33.333 0.04 0.95 37.56 4.58
837 2296 2.362717 GGTGGCCTACAAGCTCTAGTAG 59.637 54.545 3.32 11.83 37.92 2.57
839 2298 1.196012 GGTGGCCTACAAGCTCTAGT 58.804 55.000 3.32 0.00 0.00 2.57
840 2299 0.103208 CGGTGGCCTACAAGCTCTAG 59.897 60.000 3.32 0.00 0.00 2.43
841 2300 1.327690 CCGGTGGCCTACAAGCTCTA 61.328 60.000 3.32 0.00 0.00 2.43
843 2302 2.125106 CCGGTGGCCTACAAGCTC 60.125 66.667 3.32 0.00 0.00 4.09
861 2840 2.555757 ACTTTGTCTTCTTGGCTCATGC 59.444 45.455 0.00 0.00 38.76 4.06
864 2843 3.206150 GTGACTTTGTCTTCTTGGCTCA 58.794 45.455 0.00 0.00 33.15 4.26
893 2875 2.775032 AAATGCTACGTCCACGCGGT 62.775 55.000 12.47 0.00 44.43 5.68
905 2887 2.004017 CGGCTACGGAAACAAATGCTA 58.996 47.619 0.00 0.00 36.18 3.49
942 2924 4.338400 GGAGGGACTTGATTTTTATTCCGG 59.662 45.833 0.00 0.00 41.55 5.14
992 2980 1.372997 CTGCTTTGGCTGCTTGCTG 60.373 57.895 0.00 0.06 42.39 4.41
1038 3026 4.507916 CGCCCGAGGAGGAGGAGA 62.508 72.222 0.00 0.00 45.00 3.71
1158 3160 1.153289 CCTCCAACCGATCAGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
1402 3416 4.095400 GGAGAGCAGGGGAGGGGA 62.095 72.222 0.00 0.00 0.00 4.81
1413 3427 1.109323 GGAGCAGAGGAGAGGAGAGC 61.109 65.000 0.00 0.00 0.00 4.09
1419 3433 0.819259 CGAGGAGGAGCAGAGGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
1433 3452 2.277084 GCGAATTTAAGGAAGCGAGGA 58.723 47.619 0.00 0.00 0.00 3.71
1485 3504 1.612156 CTGCGAGGAATCGATCGATC 58.388 55.000 29.48 21.16 41.40 3.69
1486 3505 0.387878 GCTGCGAGGAATCGATCGAT 60.388 55.000 24.60 24.60 41.40 3.59
1487 3506 1.008424 GCTGCGAGGAATCGATCGA 60.008 57.895 21.86 21.86 41.40 3.59
1488 3507 1.299392 TGCTGCGAGGAATCGATCG 60.299 57.895 9.36 9.36 41.79 3.69
1489 3508 0.249238 AGTGCTGCGAGGAATCGATC 60.249 55.000 0.00 0.00 34.64 3.69
1490 3509 1.000827 CTAGTGCTGCGAGGAATCGAT 60.001 52.381 1.17 0.00 34.64 3.59
1491 3510 0.382158 CTAGTGCTGCGAGGAATCGA 59.618 55.000 1.17 0.00 34.64 3.59
1492 3511 0.101399 ACTAGTGCTGCGAGGAATCG 59.899 55.000 0.00 0.00 0.00 3.34
1500 3519 0.526524 GAGCTGGTACTAGTGCTGCG 60.527 60.000 9.95 1.15 35.76 5.18
1514 3533 1.449956 GCCAAGAGGAGCAGAGCTG 60.450 63.158 0.00 0.00 39.88 4.24
1525 3559 7.268199 TGCAAAGATTATAATCAGCCAAGAG 57.732 36.000 24.00 8.54 37.89 2.85
1537 3571 6.293407 GGCACGAATAGCTTGCAAAGATTATA 60.293 38.462 9.41 0.00 41.66 0.98
1539 3573 4.201910 GGCACGAATAGCTTGCAAAGATTA 60.202 41.667 9.41 0.00 41.66 1.75
1548 3582 1.453155 AACAGGGCACGAATAGCTTG 58.547 50.000 0.00 0.00 0.00 4.01
1557 3591 1.314730 ACCACTAAAAACAGGGCACG 58.685 50.000 0.00 0.00 0.00 5.34
1569 3603 1.629043 ACGAGAGGCTGAACCACTAA 58.371 50.000 0.00 0.00 39.81 2.24
1581 3616 0.535102 AACTGCACCCAAACGAGAGG 60.535 55.000 0.00 0.00 0.00 3.69
1624 3659 9.582431 TGTTCAAATAGTAACTAGTAGATGCAC 57.418 33.333 3.59 0.00 0.00 4.57
1673 3715 7.290118 CAAACCGGCTGAAATTTAGAAATTTG 58.710 34.615 15.79 5.80 45.70 2.32
1676 3718 5.478407 CCAAACCGGCTGAAATTTAGAAAT 58.522 37.500 0.00 0.00 0.00 2.17
1692 3734 4.448537 TTGGATTAATTGAGCCAAACCG 57.551 40.909 16.71 0.00 37.46 4.44
1693 3735 5.643348 CCTTTTGGATTAATTGAGCCAAACC 59.357 40.000 26.67 4.94 46.62 3.27
1722 3767 0.163788 GAACACACGCATCCAGTTCG 59.836 55.000 0.00 0.00 30.69 3.95
1758 3803 2.438763 TCCTACCCAACCGTTTGAAAGA 59.561 45.455 0.00 0.00 34.24 2.52
1822 3867 6.661805 TCAAGGGTATTCAGGTACCAAATTTC 59.338 38.462 15.94 9.64 44.84 2.17
1828 3873 4.263594 GGTTTCAAGGGTATTCAGGTACCA 60.264 45.833 15.94 0.00 44.84 3.25
1830 3875 4.698780 GTGGTTTCAAGGGTATTCAGGTAC 59.301 45.833 0.00 0.00 0.00 3.34
1869 3914 9.821662 AAACAGTTTGTTACTATATTCGAAAGC 57.178 29.630 0.00 0.00 40.14 3.51
1882 3927 8.974408 ACTTTGACAAAAGAAACAGTTTGTTAC 58.026 29.630 8.75 3.14 45.53 2.50
1883 3928 9.535878 AACTTTGACAAAAGAAACAGTTTGTTA 57.464 25.926 8.75 0.00 45.53 2.41
1884 3929 8.334632 CAACTTTGACAAAAGAAACAGTTTGTT 58.665 29.630 2.34 2.46 45.53 2.83
1886 3931 7.850501 ACAACTTTGACAAAAGAAACAGTTTG 58.149 30.769 2.34 0.00 44.81 2.93
1887 3932 8.334632 CAACAACTTTGACAAAAGAAACAGTTT 58.665 29.630 0.00 0.00 44.81 2.66
1888 3933 7.708752 TCAACAACTTTGACAAAAGAAACAGTT 59.291 29.630 1.62 0.00 44.81 3.16
1890 3935 7.501515 GTCAACAACTTTGACAAAAGAAACAG 58.498 34.615 11.39 0.00 44.81 3.16
1936 3998 4.681744 TGACAAAAAGAAACTGGCATCAC 58.318 39.130 0.00 0.00 0.00 3.06
1938 4000 5.984926 TCATTGACAAAAAGAAACTGGCATC 59.015 36.000 0.00 0.00 0.00 3.91
2011 4107 6.185852 TGTAGTTTCTGTTGATGCATGATG 57.814 37.500 2.46 0.00 0.00 3.07
2014 4110 6.005583 AGTTGTAGTTTCTGTTGATGCATG 57.994 37.500 2.46 0.00 0.00 4.06
2015 4111 7.744087 TTAGTTGTAGTTTCTGTTGATGCAT 57.256 32.000 0.00 0.00 0.00 3.96
2016 4112 7.561021 TTTAGTTGTAGTTTCTGTTGATGCA 57.439 32.000 0.00 0.00 0.00 3.96
2017 4113 9.463443 AAATTTAGTTGTAGTTTCTGTTGATGC 57.537 29.630 0.00 0.00 0.00 3.91
2019 4115 9.965824 CCAAATTTAGTTGTAGTTTCTGTTGAT 57.034 29.630 0.00 0.00 0.00 2.57
2021 4117 9.233232 GACCAAATTTAGTTGTAGTTTCTGTTG 57.767 33.333 0.00 0.00 0.00 3.33
2022 4118 8.126700 CGACCAAATTTAGTTGTAGTTTCTGTT 58.873 33.333 0.00 0.00 0.00 3.16
2033 4393 4.082787 ACAGCCATCGACCAAATTTAGTTG 60.083 41.667 0.00 0.00 0.00 3.16
2042 4402 3.886505 ACTTTAAAACAGCCATCGACCAA 59.113 39.130 0.00 0.00 0.00 3.67
2046 4406 2.227865 GGCACTTTAAAACAGCCATCGA 59.772 45.455 16.20 0.00 44.59 3.59
2151 4995 4.878397 AGGTGCAGCAATGTAATTAGAGAC 59.122 41.667 19.63 0.00 32.46 3.36
2161 5005 1.619654 TTAAGCAGGTGCAGCAATGT 58.380 45.000 19.63 3.05 45.16 2.71
2192 5036 6.283694 TGTTGATGCTAGATAACTGACATCC 58.716 40.000 11.84 2.65 38.17 3.51
2222 5072 2.734276 TATTTTTGAGCAAACCGGGC 57.266 45.000 6.32 0.00 0.00 6.13
2223 5073 4.180817 GGAATATTTTTGAGCAAACCGGG 58.819 43.478 6.32 0.00 0.00 5.73
2245 5222 5.740569 GCAGCAATGTGATTAGTTATGTGTG 59.259 40.000 0.00 0.00 0.00 3.82
2246 5223 5.415389 TGCAGCAATGTGATTAGTTATGTGT 59.585 36.000 0.00 0.00 0.00 3.72
2249 5226 6.252015 GTGTTGCAGCAATGTGATTAGTTATG 59.748 38.462 11.96 0.00 0.00 1.90
2251 5228 5.473162 AGTGTTGCAGCAATGTGATTAGTTA 59.527 36.000 11.96 0.00 0.00 2.24
2254 5245 4.430137 AGTGTTGCAGCAATGTGATTAG 57.570 40.909 11.96 0.00 0.00 1.73
2654 5655 3.793144 CGACAGCGCCTTCTTGCC 61.793 66.667 2.29 0.00 0.00 4.52
2704 5705 1.383803 GAGGATGGACTGCCCCTCT 60.384 63.158 0.00 0.00 38.74 3.69
2741 5742 0.108615 CATCTCGAGGAAACGCTGGT 60.109 55.000 13.56 0.00 0.00 4.00
2752 5753 2.582728 AGAAAGAGCAGCATCTCGAG 57.417 50.000 5.93 5.93 38.12 4.04
2789 5790 2.198827 TCAACCGAAATGGCTGACAT 57.801 45.000 0.00 0.00 37.92 3.06
2809 5810 8.629158 GGACATGGTCACATATTAATTAAGCAA 58.371 33.333 3.94 0.00 34.99 3.91
2811 5812 8.292448 CAGGACATGGTCACATATTAATTAAGC 58.708 37.037 3.94 0.00 34.99 3.09
2812 5813 8.292448 GCAGGACATGGTCACATATTAATTAAG 58.708 37.037 3.94 0.00 34.99 1.85
2813 5814 7.041440 CGCAGGACATGGTCACATATTAATTAA 60.041 37.037 0.00 0.00 34.99 1.40
2814 5815 6.426633 CGCAGGACATGGTCACATATTAATTA 59.573 38.462 0.00 0.00 34.99 1.40
2815 5816 5.239306 CGCAGGACATGGTCACATATTAATT 59.761 40.000 0.00 0.00 34.99 1.40
2816 5817 4.756642 CGCAGGACATGGTCACATATTAAT 59.243 41.667 0.00 0.00 34.99 1.40
2817 5818 4.126437 CGCAGGACATGGTCACATATTAA 58.874 43.478 0.00 0.00 34.99 1.40
2818 5819 3.386402 TCGCAGGACATGGTCACATATTA 59.614 43.478 0.00 0.00 34.99 0.98
2819 5820 2.170397 TCGCAGGACATGGTCACATATT 59.830 45.455 0.00 0.00 34.99 1.28
2820 5821 1.762370 TCGCAGGACATGGTCACATAT 59.238 47.619 0.00 0.00 34.99 1.78
2821 5822 1.134818 GTCGCAGGACATGGTCACATA 60.135 52.381 0.00 0.00 42.91 2.29
2822 5823 0.391661 GTCGCAGGACATGGTCACAT 60.392 55.000 0.00 0.00 42.91 3.21
2823 5824 1.005037 GTCGCAGGACATGGTCACA 60.005 57.895 0.00 0.00 42.91 3.58
2824 5825 1.741770 GGTCGCAGGACATGGTCAC 60.742 63.158 0.00 0.00 45.28 3.67
2825 5826 1.763546 TTGGTCGCAGGACATGGTCA 61.764 55.000 0.00 0.00 45.28 4.02
2826 5827 0.605319 TTTGGTCGCAGGACATGGTC 60.605 55.000 0.00 0.00 45.28 4.02
2827 5828 0.179004 TTTTGGTCGCAGGACATGGT 60.179 50.000 0.00 0.00 45.28 3.55
2828 5829 1.176527 ATTTTGGTCGCAGGACATGG 58.823 50.000 0.00 0.00 45.28 3.66
2829 5830 4.433186 TTTATTTTGGTCGCAGGACATG 57.567 40.909 0.00 0.00 45.28 3.21
2830 5831 5.184864 TGAATTTATTTTGGTCGCAGGACAT 59.815 36.000 0.00 0.00 45.28 3.06
2831 5832 4.520874 TGAATTTATTTTGGTCGCAGGACA 59.479 37.500 0.00 0.00 45.28 4.02
2832 5833 5.054390 TGAATTTATTTTGGTCGCAGGAC 57.946 39.130 0.00 0.00 42.66 3.85
2833 5834 5.007034 TCTGAATTTATTTTGGTCGCAGGA 58.993 37.500 0.00 0.00 0.00 3.86
2834 5835 5.309323 TCTGAATTTATTTTGGTCGCAGG 57.691 39.130 0.00 0.00 0.00 4.85
2835 5836 5.801947 CCTTCTGAATTTATTTTGGTCGCAG 59.198 40.000 0.00 0.00 0.00 5.18
2836 5837 5.242838 ACCTTCTGAATTTATTTTGGTCGCA 59.757 36.000 0.00 0.00 0.00 5.10
2837 5838 5.709966 ACCTTCTGAATTTATTTTGGTCGC 58.290 37.500 0.00 0.00 0.00 5.19
2838 5839 9.855021 AATAACCTTCTGAATTTATTTTGGTCG 57.145 29.630 9.62 0.00 0.00 4.79
2968 5976 2.183555 GCGTGGTAGGGACGGAAG 59.816 66.667 0.00 0.00 37.30 3.46
2969 5977 3.384532 GGCGTGGTAGGGACGGAA 61.385 66.667 0.00 0.00 37.30 4.30
2978 5986 1.089920 GAGTAGAGAACGGCGTGGTA 58.910 55.000 15.70 0.00 0.00 3.25
3022 6056 2.711922 CGGCGGGTCAAGTAGCTCT 61.712 63.158 0.00 0.00 0.00 4.09
3040 6074 2.646143 GACTAGCGGCGGAGATCC 59.354 66.667 9.78 0.00 0.00 3.36
3041 6075 2.252855 CGACTAGCGGCGGAGATC 59.747 66.667 9.78 0.00 36.03 2.75
3050 6084 1.655329 GGTGGAGATCCGACTAGCG 59.345 63.158 0.00 0.00 39.43 4.26
3128 6182 1.303317 GGGGTGGTGCTGAAACGAT 60.303 57.895 0.00 0.00 0.00 3.73
3287 6344 1.604604 GTTCTGCTGCAACTACCCAA 58.395 50.000 3.02 0.00 0.00 4.12
3730 6832 0.879090 CCGGTTCCAGCTTACCAAAC 59.121 55.000 9.43 0.00 33.94 2.93
3772 6875 6.753744 GCTTTGGTCCAAATAGATGTGATTTC 59.246 38.462 17.43 0.00 32.70 2.17


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

AutoCloner maintained by Alex Coulton.