Multiple sequence alignment - TraesCS4B01G298100

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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 TraesCS4B01G298100 chr4B 100.000 6845 0 0 1 6845 583474691 583481535 0.000000e+00 12641.0
1 TraesCS4B01G298100 chr4A 94.748 3389 114 16 3398 6754 4591310 4587954 0.000000e+00 5214.0
2 TraesCS4B01G298100 chr4A 92.625 2834 108 47 47 2855 4594521 4591764 0.000000e+00 3982.0
3 TraesCS4B01G298100 chr4A 97.233 253 7 0 2934 3186 4591647 4591395 4.910000e-116 429.0
4 TraesCS4B01G298100 chr4A 92.784 97 6 1 837 932 45361081 45361177 9.260000e-29 139.0
5 TraesCS4B01G298100 chr4A 91.667 96 2 3 6753 6845 4587926 4587834 2.000000e-25 128.0
6 TraesCS4B01G298100 chr4A 94.203 69 4 0 3211 3279 4591395 4591327 9.390000e-19 106.0
7 TraesCS4B01G298100 chr4A 94.340 53 3 0 696 748 5969053 5969105 1.580000e-11 82.4
8 TraesCS4B01G298100 chr4D 96.241 3059 99 9 3404 6450 466018828 466021882 0.000000e+00 4998.0
9 TraesCS4B01G298100 chr4D 94.261 3032 97 38 191 3186 466015761 466018751 0.000000e+00 4564.0
10 TraesCS4B01G298100 chr4D 95.146 309 9 1 6448 6756 466021911 466022213 3.710000e-132 483.0
11 TraesCS4B01G298100 chr4D 93.814 97 6 0 40 136 466015582 466015678 5.530000e-31 147.0
12 TraesCS4B01G298100 chr4D 94.624 93 5 0 6753 6845 466022239 466022331 1.990000e-30 145.0
13 TraesCS4B01G298100 chr5D 88.095 210 9 4 794 1000 217742113 217742309 1.150000e-57 235.0
14 TraesCS4B01G298100 chr5D 100.000 29 0 0 1028 1056 524485159 524485187 3.000000e-03 54.7
15 TraesCS4B01G298100 chr3D 91.018 167 13 1 797 961 330252911 330252745 2.480000e-54 224.0
16 TraesCS4B01G298100 chr1B 92.857 112 8 0 1374 1485 316642451 316642340 5.490000e-36 163.0
17 TraesCS4B01G298100 chr6D 77.695 269 55 5 3405 3670 353350357 353350623 7.110000e-35 159.0
18 TraesCS4B01G298100 chr6B 77.695 269 55 5 3405 3670 525114066 525113800 7.110000e-35 159.0
19 TraesCS4B01G298100 chr6B 90.110 91 7 2 3299 3388 48073209 48073298 4.340000e-22 117.0
20 TraesCS4B01G298100 chr6A 75.926 270 58 6 3405 3670 489228513 489228247 1.550000e-26 132.0
21 TraesCS4B01G298100 chr7D 87.200 125 2 3 946 1069 12550395 12550284 5.570000e-26 130.0
22 TraesCS4B01G298100 chr7D 96.970 33 1 0 1025 1057 12550017 12549985 1.000000e-03 56.5
23 TraesCS4B01G298100 chr7B 92.391 92 5 2 3299 3389 652987748 652987658 5.570000e-26 130.0
24 TraesCS4B01G298100 chr7B 93.103 87 4 2 3299 3384 706070956 706071041 7.210000e-25 126.0
25 TraesCS4B01G298100 chr7B 92.222 90 5 2 3299 3387 709759305 709759393 7.210000e-25 126.0
26 TraesCS4B01G298100 chr7B 96.226 53 2 0 696 748 423179207 423179259 3.400000e-13 87.9
27 TraesCS4B01G298100 chr7B 94.340 53 3 0 696 748 734276049 734276101 1.580000e-11 82.4
28 TraesCS4B01G298100 chr1A 93.258 89 5 1 849 936 314478186 314478274 5.570000e-26 130.0
29 TraesCS4B01G298100 chr1A 89.394 66 1 1 991 1056 540392240 540392181 2.050000e-10 78.7
30 TraesCS4B01G298100 chr3A 89.899 99 7 3 3299 3396 534992227 534992131 2.590000e-24 124.0
31 TraesCS4B01G298100 chr3A 92.308 52 4 0 696 747 690464177 690464228 2.650000e-09 75.0
32 TraesCS4B01G298100 chr3A 89.130 46 3 1 975 1020 555114837 555114880 1.000000e-03 56.5
33 TraesCS4B01G298100 chr5A 91.304 92 4 4 3299 3388 392031079 392030990 9.320000e-24 122.0
34 TraesCS4B01G298100 chr5A 91.304 92 4 4 3299 3388 392033071 392032982 9.320000e-24 122.0
35 TraesCS4B01G298100 chr5A 89.247 93 8 2 3299 3390 31115778 31115687 1.560000e-21 115.0
36 TraesCS4B01G298100 chr2A 90.110 91 7 2 3299 3388 763397778 763397867 4.340000e-22 117.0
37 TraesCS4B01G298100 chr5B 89.888 89 8 1 849 936 498069660 498069572 5.610000e-21 113.0
38 TraesCS4B01G298100 chr1D 94.643 56 3 0 693 748 488428251 488428196 3.400000e-13 87.9
39 TraesCS4B01G298100 chr2D 89.062 64 1 1 993 1056 102288528 102288585 2.650000e-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 TraesCS4B01G298100 chr4B 583474691 583481535 6844 False 12641.0 12641 100.0000 1 6845 1 chr4B.!!$F1 6844
1 TraesCS4B01G298100 chr4A 4587834 4594521 6687 True 1971.8 5214 94.0952 47 6845 5 chr4A.!!$R1 6798
2 TraesCS4B01G298100 chr4D 466015582 466022331 6749 False 2067.4 4998 94.8172 40 6845 5 chr4D.!!$F1 6805

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
186 191 0.106769 TTCACCAGAAAGTGCAGGCA 60.107 50.000 0.00 0.00 37.68 4.75 F
189 194 0.183492 ACCAGAAAGTGCAGGCAGAA 59.817 50.000 0.00 0.00 0.00 3.02 F
1503 1556 1.443872 GTACCTCGGTGAGCACACG 60.444 63.158 8.22 4.25 46.77 4.49 F
1929 1998 0.812412 ACGTGGTTGGGTTCAGAACG 60.812 55.000 7.22 0.00 33.79 3.95 F
3804 3946 0.034896 CGGGGTACAACAGCTTCACT 59.965 55.000 0.00 0.00 0.00 3.41 F
4149 4294 0.392998 GCATTCTCACCATGACGGGT 60.393 55.000 0.00 0.00 43.56 5.28 F
4425 4570 0.968901 CACTGATTGCCATGGCCTGT 60.969 55.000 33.44 23.07 41.09 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1734 1.000607 CTCACCTCCGTGTCGAAGAAA 60.001 52.381 0.00 0.00 39.69 2.52 R
1806 1875 1.076485 GGGAGGATGCAGCCATGTT 60.076 57.895 25.38 0.79 0.00 2.71 R
2459 2530 0.674895 ACAGAGAAAGTGATGGCGCC 60.675 55.000 22.73 22.73 0.00 6.53 R
3834 3976 1.038681 TGCCGCCATACCTCGACTTA 61.039 55.000 0.00 0.00 0.00 2.24 R
4629 4774 0.391130 TGCCCATGTACTGCGACTTC 60.391 55.000 0.00 0.00 0.00 3.01 R
4950 5095 1.080974 CGGGTACGCGAAGAACACT 60.081 57.895 26.40 0.00 0.00 3.55 R
6401 6574 1.337118 GGTGGCCAGTTCCAAATGAA 58.663 50.000 5.11 0.00 37.96 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
19 20 0.831307 AAGGAAGGGATACACGCTCC 59.169 55.000 0.00 0.00 40.92 4.70
20 21 0.325296 AGGAAGGGATACACGCTCCA 60.325 55.000 0.00 0.00 40.92 3.86
21 22 0.759346 GGAAGGGATACACGCTCCAT 59.241 55.000 0.00 0.00 40.92 3.41
22 23 1.270358 GGAAGGGATACACGCTCCATC 60.270 57.143 0.00 0.00 40.92 3.51
23 24 0.759346 AAGGGATACACGCTCCATCC 59.241 55.000 0.00 0.00 40.92 3.51
24 25 0.398522 AGGGATACACGCTCCATCCA 60.399 55.000 7.86 0.00 40.09 3.41
25 26 0.468226 GGGATACACGCTCCATCCAA 59.532 55.000 7.86 0.00 40.09 3.53
26 27 1.134220 GGGATACACGCTCCATCCAAA 60.134 52.381 7.86 0.00 40.09 3.28
27 28 2.213499 GGATACACGCTCCATCCAAAG 58.787 52.381 0.00 0.00 38.50 2.77
28 29 2.420129 GGATACACGCTCCATCCAAAGT 60.420 50.000 0.00 0.00 38.50 2.66
29 30 2.851263 TACACGCTCCATCCAAAGTT 57.149 45.000 0.00 0.00 0.00 2.66
30 31 1.523758 ACACGCTCCATCCAAAGTTC 58.476 50.000 0.00 0.00 0.00 3.01
31 32 0.804989 CACGCTCCATCCAAAGTTCC 59.195 55.000 0.00 0.00 0.00 3.62
32 33 0.400213 ACGCTCCATCCAAAGTTCCA 59.600 50.000 0.00 0.00 0.00 3.53
33 34 1.202879 ACGCTCCATCCAAAGTTCCAA 60.203 47.619 0.00 0.00 0.00 3.53
34 35 1.885887 CGCTCCATCCAAAGTTCCAAA 59.114 47.619 0.00 0.00 0.00 3.28
35 36 2.095059 CGCTCCATCCAAAGTTCCAAAG 60.095 50.000 0.00 0.00 0.00 2.77
36 37 2.893489 GCTCCATCCAAAGTTCCAAAGT 59.107 45.455 0.00 0.00 0.00 2.66
37 38 4.079253 GCTCCATCCAAAGTTCCAAAGTA 58.921 43.478 0.00 0.00 0.00 2.24
38 39 4.082733 GCTCCATCCAAAGTTCCAAAGTAC 60.083 45.833 0.00 0.00 0.00 2.73
44 45 4.038642 TCCAAAGTTCCAAAGTACCATTGC 59.961 41.667 3.96 0.00 0.00 3.56
58 59 0.818445 CATTGCCTGGAGCCTAGCAG 60.818 60.000 0.00 0.00 42.71 4.24
136 137 1.676014 GCACAGCTCGGACTTGGTAAT 60.676 52.381 0.00 0.00 0.00 1.89
138 139 1.623811 ACAGCTCGGACTTGGTAATGT 59.376 47.619 0.00 0.00 0.00 2.71
139 140 2.038557 ACAGCTCGGACTTGGTAATGTT 59.961 45.455 0.00 0.00 0.00 2.71
141 142 4.250464 CAGCTCGGACTTGGTAATGTTTA 58.750 43.478 0.00 0.00 0.00 2.01
142 143 4.876107 CAGCTCGGACTTGGTAATGTTTAT 59.124 41.667 0.00 0.00 0.00 1.40
147 152 7.168804 GCTCGGACTTGGTAATGTTTATAGTAC 59.831 40.741 0.00 0.00 0.00 2.73
168 173 8.915057 AGTACTATCATATGTACTACGGTGTT 57.085 34.615 1.90 0.00 44.97 3.32
169 174 8.997323 AGTACTATCATATGTACTACGGTGTTC 58.003 37.037 1.90 0.00 44.97 3.18
170 175 7.812690 ACTATCATATGTACTACGGTGTTCA 57.187 36.000 1.90 0.00 0.00 3.18
171 176 7.646314 ACTATCATATGTACTACGGTGTTCAC 58.354 38.462 1.90 0.00 0.00 3.18
172 177 5.252969 TCATATGTACTACGGTGTTCACC 57.747 43.478 11.53 11.53 0.00 4.02
174 179 3.587797 ATGTACTACGGTGTTCACCAG 57.412 47.619 19.90 13.42 0.00 4.00
178 183 3.107642 ACTACGGTGTTCACCAGAAAG 57.892 47.619 19.90 13.07 35.08 2.62
179 184 2.433239 ACTACGGTGTTCACCAGAAAGT 59.567 45.455 19.90 13.59 35.08 2.66
183 188 1.334869 GGTGTTCACCAGAAAGTGCAG 59.665 52.381 16.01 0.00 37.68 4.41
185 190 0.312102 GTTCACCAGAAAGTGCAGGC 59.688 55.000 0.00 0.00 37.68 4.85
186 191 0.106769 TTCACCAGAAAGTGCAGGCA 60.107 50.000 0.00 0.00 37.68 4.75
187 192 0.535780 TCACCAGAAAGTGCAGGCAG 60.536 55.000 0.00 0.00 37.68 4.85
188 193 0.535780 CACCAGAAAGTGCAGGCAGA 60.536 55.000 0.00 0.00 0.00 4.26
189 194 0.183492 ACCAGAAAGTGCAGGCAGAA 59.817 50.000 0.00 0.00 0.00 3.02
227 257 2.027073 GCGCATTCCTCACGTCACA 61.027 57.895 0.30 0.00 0.00 3.58
228 258 1.565156 GCGCATTCCTCACGTCACAA 61.565 55.000 0.30 0.00 0.00 3.33
252 282 2.878406 CACGAAACAGTCAAATCCCAGT 59.122 45.455 0.00 0.00 0.00 4.00
256 286 1.901591 ACAGTCAAATCCCAGTGCAG 58.098 50.000 0.00 0.00 0.00 4.41
260 298 3.624861 CAGTCAAATCCCAGTGCAGATAC 59.375 47.826 0.00 0.00 0.00 2.24
261 299 2.609459 GTCAAATCCCAGTGCAGATACG 59.391 50.000 0.00 0.00 0.00 3.06
297 335 1.853963 CTCAGGCACCTGGTAGTACT 58.146 55.000 16.52 0.00 43.75 2.73
298 336 2.949054 GCTCAGGCACCTGGTAGTACTA 60.949 54.545 16.52 0.00 43.75 1.82
299 337 2.688958 CTCAGGCACCTGGTAGTACTAC 59.311 54.545 22.53 22.53 43.75 2.73
304 342 4.348754 AGGCACCTGGTAGTACTACAAAAA 59.651 41.667 29.38 13.85 37.78 1.94
819 860 2.944557 CGCTCGTCGTCCATGTCG 60.945 66.667 0.00 0.00 0.00 4.35
1350 1403 1.522355 CATGATCAACGGCGGCTCT 60.522 57.895 13.24 0.00 0.00 4.09
1425 1478 2.667969 CGACAAGACGCAGATGATGAAA 59.332 45.455 0.00 0.00 0.00 2.69
1503 1556 1.443872 GTACCTCGGTGAGCACACG 60.444 63.158 8.22 4.25 46.77 4.49
1508 1561 2.738139 CGGTGAGCACACGCATGA 60.738 61.111 8.22 0.00 46.77 3.07
1547 1614 5.995897 TGTCATTCCTCATGCATGAATCTAG 59.004 40.000 28.39 16.80 36.18 2.43
1549 1616 7.157347 GTCATTCCTCATGCATGAATCTAGTA 58.843 38.462 28.39 10.31 36.18 1.82
1667 1734 3.842923 CTGCGGCAGGAGATCGGT 61.843 66.667 22.11 0.00 38.15 4.69
1767 1834 3.011369 GGGGGAGAAGGTAACCAAGATTT 59.989 47.826 0.00 0.00 37.17 2.17
1783 1852 7.951591 ACCAAGATTTACATTGCTTAAACACT 58.048 30.769 0.00 0.00 0.00 3.55
1790 1859 3.133721 ACATTGCTTAAACACTTTGCCCA 59.866 39.130 0.00 0.00 0.00 5.36
1795 1864 5.016173 TGCTTAAACACTTTGCCCATATCT 58.984 37.500 0.00 0.00 0.00 1.98
1798 1867 7.141363 GCTTAAACACTTTGCCCATATCTATG 58.859 38.462 0.00 0.00 0.00 2.23
1929 1998 0.812412 ACGTGGTTGGGTTCAGAACG 60.812 55.000 7.22 0.00 33.79 3.95
2038 2107 1.664151 CCGCCAACGAAGAGGTAATTC 59.336 52.381 0.00 0.00 43.93 2.17
2046 2115 4.824848 CGAAGAGGTAATTCGTGTCTTG 57.175 45.455 0.17 0.00 43.42 3.02
2048 2117 4.921515 CGAAGAGGTAATTCGTGTCTTGAA 59.078 41.667 0.17 0.00 43.42 2.69
2049 2118 5.164080 CGAAGAGGTAATTCGTGTCTTGAAC 60.164 44.000 0.17 0.00 43.42 3.18
2050 2119 5.209818 AGAGGTAATTCGTGTCTTGAACA 57.790 39.130 0.00 0.00 34.78 3.18
2051 2120 5.794894 AGAGGTAATTCGTGTCTTGAACAT 58.205 37.500 0.00 0.00 40.80 2.71
2052 2121 6.931838 AGAGGTAATTCGTGTCTTGAACATA 58.068 36.000 0.00 0.00 40.80 2.29
2053 2122 7.556844 AGAGGTAATTCGTGTCTTGAACATAT 58.443 34.615 0.00 0.00 40.80 1.78
2054 2123 8.692710 AGAGGTAATTCGTGTCTTGAACATATA 58.307 33.333 0.00 0.00 40.80 0.86
2055 2124 9.477484 GAGGTAATTCGTGTCTTGAACATATAT 57.523 33.333 0.00 0.00 40.80 0.86
2112 2181 4.671377 TGAACATTTGTGTTGCTTCTGAC 58.329 39.130 0.00 0.00 31.35 3.51
2113 2182 4.157472 TGAACATTTGTGTTGCTTCTGACA 59.843 37.500 0.00 0.00 31.35 3.58
2117 2186 5.068198 ACATTTGTGTTGCTTCTGACAATCT 59.932 36.000 0.00 0.00 0.00 2.40
2434 2505 1.743252 GGAGGAAGGCAAGCACGAG 60.743 63.158 0.00 0.00 0.00 4.18
2435 2506 2.359230 AGGAAGGCAAGCACGAGC 60.359 61.111 0.00 0.00 42.56 5.03
2436 2507 2.669569 GGAAGGCAAGCACGAGCA 60.670 61.111 7.77 0.00 45.49 4.26
2437 2508 2.684843 GGAAGGCAAGCACGAGCAG 61.685 63.158 7.77 0.00 45.49 4.24
2438 2509 3.319926 GAAGGCAAGCACGAGCAGC 62.320 63.158 7.77 10.52 45.49 5.25
2439 2510 4.631247 AGGCAAGCACGAGCAGCA 62.631 61.111 19.86 0.00 45.49 4.41
2440 2511 4.395583 GGCAAGCACGAGCAGCAC 62.396 66.667 19.86 8.93 45.49 4.40
2441 2512 4.395583 GCAAGCACGAGCAGCACC 62.396 66.667 15.14 0.00 45.49 5.01
2442 2513 2.667536 CAAGCACGAGCAGCACCT 60.668 61.111 7.77 0.00 45.49 4.00
2443 2514 2.111878 AAGCACGAGCAGCACCTT 59.888 55.556 7.77 0.00 45.49 3.50
2444 2515 2.256591 AAGCACGAGCAGCACCTTG 61.257 57.895 7.77 0.00 45.49 3.61
2445 2516 4.395583 GCACGAGCAGCACCTTGC 62.396 66.667 0.00 0.00 45.46 4.01
2855 2931 3.376078 GACCCCACGCGAGGTACA 61.376 66.667 21.30 0.00 36.17 2.90
2857 2933 2.202878 CCCCACGCGAGGTACATG 60.203 66.667 21.30 5.35 0.00 3.21
2858 2934 2.717044 CCCCACGCGAGGTACATGA 61.717 63.158 21.30 0.00 0.00 3.07
2859 2935 1.518572 CCCACGCGAGGTACATGAC 60.519 63.158 21.30 0.00 0.00 3.06
2860 2936 1.872234 CCACGCGAGGTACATGACG 60.872 63.158 15.93 0.00 0.00 4.35
2861 2937 1.872234 CACGCGAGGTACATGACGG 60.872 63.158 15.93 0.00 0.00 4.79
2862 2938 2.338015 ACGCGAGGTACATGACGGT 61.338 57.895 15.93 0.00 0.00 4.83
2863 2939 1.585521 CGCGAGGTACATGACGGTC 60.586 63.158 0.00 0.00 0.00 4.79
2864 2940 1.509463 GCGAGGTACATGACGGTCA 59.491 57.895 14.01 14.01 0.00 4.02
2866 2942 0.179145 CGAGGTACATGACGGTCACC 60.179 60.000 13.92 10.08 0.00 4.02
2900 2993 3.410516 CCGTTGCACGCACGATGA 61.411 61.111 10.87 0.00 40.91 2.92
2901 2994 2.739704 CCGTTGCACGCACGATGAT 61.740 57.895 10.87 0.00 40.91 2.45
2902 2995 1.578367 CGTTGCACGCACGATGATG 60.578 57.895 3.31 0.00 33.65 3.07
2904 2997 2.397754 TTGCACGCACGATGATGGG 61.398 57.895 0.00 0.00 38.44 4.00
2913 3006 3.930400 CGATGATGGGTCGTAACGA 57.070 52.632 0.00 0.00 34.56 3.85
2914 3007 2.197792 CGATGATGGGTCGTAACGAA 57.802 50.000 0.00 0.00 37.72 3.85
2915 3008 2.739292 CGATGATGGGTCGTAACGAAT 58.261 47.619 0.00 0.00 37.72 3.34
2916 3009 3.120792 CGATGATGGGTCGTAACGAATT 58.879 45.455 0.00 0.00 37.72 2.17
2918 3011 4.033587 CGATGATGGGTCGTAACGAATTTT 59.966 41.667 0.00 0.00 37.72 1.82
2919 3012 5.446741 CGATGATGGGTCGTAACGAATTTTT 60.447 40.000 0.00 0.00 37.72 1.94
2920 3013 5.037015 TGATGGGTCGTAACGAATTTTTG 57.963 39.130 0.00 0.00 37.72 2.44
2921 3014 4.515944 TGATGGGTCGTAACGAATTTTTGT 59.484 37.500 0.00 0.00 37.72 2.83
2923 3016 4.846509 TGGGTCGTAACGAATTTTTGTTC 58.153 39.130 0.00 0.00 37.72 3.18
2987 3124 1.572085 CGCTGAACCTCAAGTGGCTG 61.572 60.000 0.00 0.00 0.00 4.85
3161 3298 2.879907 GGCTACGACACGCAGGTA 59.120 61.111 0.00 0.00 0.00 3.08
3254 3394 2.823154 GCCTCACTAGTCTGTCTCTGTT 59.177 50.000 0.00 0.00 0.00 3.16
3255 3395 3.119637 GCCTCACTAGTCTGTCTCTGTTC 60.120 52.174 0.00 0.00 0.00 3.18
3269 3409 2.825836 GTTCATGGGCTCGCCAGG 60.826 66.667 10.51 0.00 37.98 4.45
3279 3419 0.316841 GCTCGCCAGGATCTCCTAAG 59.683 60.000 0.00 0.00 46.65 2.18
3280 3420 1.698506 CTCGCCAGGATCTCCTAAGT 58.301 55.000 0.00 0.00 46.65 2.24
3283 3423 3.223435 TCGCCAGGATCTCCTAAGTAAG 58.777 50.000 0.00 0.00 46.65 2.34
3284 3424 3.117625 TCGCCAGGATCTCCTAAGTAAGA 60.118 47.826 0.00 0.00 46.65 2.10
3285 3425 3.254657 CGCCAGGATCTCCTAAGTAAGAG 59.745 52.174 0.00 0.00 46.65 2.85
3286 3426 3.576550 GCCAGGATCTCCTAAGTAAGAGG 59.423 52.174 0.00 0.00 46.65 3.69
3287 3427 4.156477 CCAGGATCTCCTAAGTAAGAGGG 58.844 52.174 0.00 0.00 46.65 4.30
3289 3429 4.586841 CAGGATCTCCTAAGTAAGAGGGTG 59.413 50.000 0.00 0.00 46.65 4.61
3290 3430 4.233287 AGGATCTCCTAAGTAAGAGGGTGT 59.767 45.833 0.00 0.00 46.48 4.16
3294 3434 5.152934 TCTCCTAAGTAAGAGGGTGTTTGT 58.847 41.667 0.00 0.00 34.56 2.83
3295 3435 5.605488 TCTCCTAAGTAAGAGGGTGTTTGTT 59.395 40.000 0.00 0.00 34.56 2.83
3296 3436 6.100714 TCTCCTAAGTAAGAGGGTGTTTGTTT 59.899 38.462 0.00 0.00 34.56 2.83
3297 3437 6.665695 TCCTAAGTAAGAGGGTGTTTGTTTT 58.334 36.000 0.00 0.00 34.56 2.43
3298 3438 7.804147 TCCTAAGTAAGAGGGTGTTTGTTTTA 58.196 34.615 0.00 0.00 34.56 1.52
3299 3439 8.273605 TCCTAAGTAAGAGGGTGTTTGTTTTAA 58.726 33.333 0.00 0.00 34.56 1.52
3300 3440 8.347771 CCTAAGTAAGAGGGTGTTTGTTTTAAC 58.652 37.037 0.00 0.00 0.00 2.01
3301 3441 6.704289 AGTAAGAGGGTGTTTGTTTTAACC 57.296 37.500 0.00 0.00 0.00 2.85
3302 3442 6.189133 AGTAAGAGGGTGTTTGTTTTAACCA 58.811 36.000 0.00 0.00 34.18 3.67
3303 3443 6.664384 AGTAAGAGGGTGTTTGTTTTAACCAA 59.336 34.615 0.00 0.00 34.18 3.67
3304 3444 6.361768 AAGAGGGTGTTTGTTTTAACCAAA 57.638 33.333 0.00 0.00 34.18 3.28
3305 3445 5.726397 AGAGGGTGTTTGTTTTAACCAAAC 58.274 37.500 17.21 17.21 44.64 2.93
3315 3455 4.928601 GTTTTAACCAAACAGTCAGGGAC 58.071 43.478 0.00 0.00 43.93 4.46
3316 3456 4.513406 TTTAACCAAACAGTCAGGGACT 57.487 40.909 0.00 0.00 44.44 3.85
3317 3457 4.513406 TTAACCAAACAGTCAGGGACTT 57.487 40.909 0.00 0.00 41.37 3.01
3318 3458 3.382083 AACCAAACAGTCAGGGACTTT 57.618 42.857 0.00 0.00 41.37 2.66
3319 3459 3.382083 ACCAAACAGTCAGGGACTTTT 57.618 42.857 0.00 0.00 41.37 2.27
3320 3460 3.708451 ACCAAACAGTCAGGGACTTTTT 58.292 40.909 5.04 5.04 41.36 1.94
3321 3461 4.862371 ACCAAACAGTCAGGGACTTTTTA 58.138 39.130 9.43 0.00 39.53 1.52
3322 3462 4.887655 ACCAAACAGTCAGGGACTTTTTAG 59.112 41.667 9.43 6.18 39.53 1.85
3323 3463 4.278419 CCAAACAGTCAGGGACTTTTTAGG 59.722 45.833 9.43 9.60 39.53 2.69
3324 3464 3.790089 ACAGTCAGGGACTTTTTAGGG 57.210 47.619 0.00 0.00 41.37 3.53
3325 3465 3.323775 ACAGTCAGGGACTTTTTAGGGA 58.676 45.455 0.00 0.00 41.37 4.20
3326 3466 3.072622 ACAGTCAGGGACTTTTTAGGGAC 59.927 47.826 0.00 0.00 41.37 4.46
3327 3467 3.328050 CAGTCAGGGACTTTTTAGGGACT 59.672 47.826 0.00 0.00 41.37 3.85
3328 3468 3.981375 AGTCAGGGACTTTTTAGGGACTT 59.019 43.478 0.00 0.00 40.28 3.01
3329 3469 4.072839 GTCAGGGACTTTTTAGGGACTTG 58.927 47.826 0.00 0.00 36.39 3.16
3330 3470 3.720002 TCAGGGACTTTTTAGGGACTTGT 59.280 43.478 0.00 0.00 36.39 3.16
3331 3471 3.821033 CAGGGACTTTTTAGGGACTTGTG 59.179 47.826 0.00 0.00 36.39 3.33
3332 3472 3.720002 AGGGACTTTTTAGGGACTTGTGA 59.280 43.478 0.00 0.00 34.75 3.58
3333 3473 3.819337 GGGACTTTTTAGGGACTTGTGAC 59.181 47.826 0.00 0.00 41.75 3.67
3334 3474 4.445879 GGGACTTTTTAGGGACTTGTGACT 60.446 45.833 0.00 0.00 41.75 3.41
3335 3475 5.131067 GGACTTTTTAGGGACTTGTGACTT 58.869 41.667 0.00 0.00 41.75 3.01
3336 3476 6.293698 GGACTTTTTAGGGACTTGTGACTTA 58.706 40.000 0.00 0.00 41.75 2.24
3337 3477 6.204301 GGACTTTTTAGGGACTTGTGACTTAC 59.796 42.308 0.00 0.00 41.75 2.34
3338 3478 6.655930 ACTTTTTAGGGACTTGTGACTTACA 58.344 36.000 0.00 0.00 41.75 2.41
3339 3479 7.114095 ACTTTTTAGGGACTTGTGACTTACAA 58.886 34.615 0.00 0.00 46.62 2.41
3351 3491 7.925043 TTGTGACTTACAAGTTGGAACTAAA 57.075 32.000 7.96 0.00 44.07 1.85
3352 3492 7.925043 TGTGACTTACAAGTTGGAACTAAAA 57.075 32.000 7.96 0.00 39.88 1.52
3353 3493 8.338072 TGTGACTTACAAGTTGGAACTAAAAA 57.662 30.769 7.96 0.00 39.88 1.94
3379 3519 6.681729 AGTCTAGGACTTATGAACCAAACA 57.318 37.500 0.00 0.00 40.28 2.83
3380 3520 7.259088 AGTCTAGGACTTATGAACCAAACAT 57.741 36.000 0.00 0.00 40.28 2.71
3381 3521 7.106239 AGTCTAGGACTTATGAACCAAACATG 58.894 38.462 0.00 0.00 40.28 3.21
3382 3522 6.316390 GTCTAGGACTTATGAACCAAACATGG 59.684 42.308 0.00 0.00 0.00 3.66
3383 3523 3.763897 AGGACTTATGAACCAAACATGGC 59.236 43.478 0.00 0.00 0.00 4.40
3384 3524 3.119137 GGACTTATGAACCAAACATGGCC 60.119 47.826 0.00 0.00 0.00 5.36
3385 3525 3.763897 GACTTATGAACCAAACATGGCCT 59.236 43.478 3.32 0.00 0.00 5.19
3386 3526 4.929479 ACTTATGAACCAAACATGGCCTA 58.071 39.130 3.32 0.00 0.00 3.93
3387 3527 5.329399 ACTTATGAACCAAACATGGCCTAA 58.671 37.500 3.32 0.00 0.00 2.69
3388 3528 5.777732 ACTTATGAACCAAACATGGCCTAAA 59.222 36.000 3.32 0.00 0.00 1.85
3389 3529 6.440328 ACTTATGAACCAAACATGGCCTAAAT 59.560 34.615 3.32 0.00 0.00 1.40
3390 3530 7.617723 ACTTATGAACCAAACATGGCCTAAATA 59.382 33.333 3.32 0.00 0.00 1.40
3391 3531 8.546083 TTATGAACCAAACATGGCCTAAATAT 57.454 30.769 3.32 0.00 0.00 1.28
3392 3532 6.865834 TGAACCAAACATGGCCTAAATATT 57.134 33.333 3.32 0.00 0.00 1.28
3393 3533 6.872920 TGAACCAAACATGGCCTAAATATTC 58.127 36.000 3.32 0.00 0.00 1.75
3394 3534 6.667414 TGAACCAAACATGGCCTAAATATTCT 59.333 34.615 3.32 0.00 0.00 2.40
3395 3535 6.715347 ACCAAACATGGCCTAAATATTCTC 57.285 37.500 3.32 0.00 0.00 2.87
3396 3536 6.435164 ACCAAACATGGCCTAAATATTCTCT 58.565 36.000 3.32 0.00 0.00 3.10
3400 3540 9.090692 CAAACATGGCCTAAATATTCTCTTTTG 57.909 33.333 3.32 0.00 0.00 2.44
3726 3868 2.705821 CCTCGTCAAGCTCGCCTCT 61.706 63.158 0.00 0.00 0.00 3.69
3804 3946 0.034896 CGGGGTACAACAGCTTCACT 59.965 55.000 0.00 0.00 0.00 3.41
3846 3988 3.118482 TGTCGGTCTCTAAGTCGAGGTAT 60.118 47.826 0.00 0.00 32.09 2.73
3872 4014 1.735376 ATTCGCGCGATACAGGAGGT 61.735 55.000 35.21 8.22 0.00 3.85
3885 4030 3.474570 GAGGTGGAGGCGGATGCT 61.475 66.667 0.00 0.00 42.25 3.79
4029 4174 3.302347 CTCCGTCTTCCCGCTGCTT 62.302 63.158 0.00 0.00 0.00 3.91
4149 4294 0.392998 GCATTCTCACCATGACGGGT 60.393 55.000 0.00 0.00 43.56 5.28
4425 4570 0.968901 CACTGATTGCCATGGCCTGT 60.969 55.000 33.44 23.07 41.09 4.00
4893 5038 1.153901 GCCGACGATCAACGAGGAA 60.154 57.895 9.57 0.00 45.77 3.36
4950 5095 1.118965 TGGACGTGGAGCTGAGGAAA 61.119 55.000 0.00 0.00 0.00 3.13
4954 5099 0.034059 CGTGGAGCTGAGGAAAGTGT 59.966 55.000 0.00 0.00 0.00 3.55
5163 5308 0.471780 TGGACCTCAAGTGGCTCAGA 60.472 55.000 0.00 0.00 0.00 3.27
5211 5356 2.034221 GCCCTGTTCAGTGGGTCC 59.966 66.667 0.00 0.00 45.06 4.46
5383 5537 4.036734 TGCTCACAAATCTCAACTTCCAAC 59.963 41.667 0.00 0.00 0.00 3.77
5403 5557 5.174216 CCAACGCCAAACTTAACATTTGTAC 59.826 40.000 6.67 0.00 35.65 2.90
5409 5563 7.858879 CGCCAAACTTAACATTTGTACTTACTT 59.141 33.333 0.00 0.00 35.65 2.24
5535 5690 1.131638 AGCTGTCAGGTGGTCAGAAA 58.868 50.000 3.14 0.00 0.00 2.52
5775 5930 2.120718 AGCCACGAGACCCTCCTT 59.879 61.111 0.00 0.00 0.00 3.36
5778 5933 2.583441 CCACGAGACCCTCCTTGCA 61.583 63.158 0.00 0.00 0.00 4.08
5847 6002 3.064987 GCAGGCCTTCGCGTAGAGA 62.065 63.158 14.87 0.00 35.02 3.10
5858 6014 2.093310 TCGCGTAGAGAAGTACAGAACG 59.907 50.000 5.77 0.00 30.01 3.95
5860 6016 3.242349 CGCGTAGAGAAGTACAGAACGAT 60.242 47.826 0.00 0.00 0.00 3.73
5992 6156 5.284660 CACAAGATGAATAAACTTTGCGAGC 59.715 40.000 0.00 0.00 0.00 5.03
6163 6327 1.886777 GAGCTGCCCTTCGAGATGC 60.887 63.158 0.00 0.00 0.00 3.91
6399 6572 6.824305 AAATTGTGTACTGAAGATTCTGGG 57.176 37.500 0.00 0.00 0.00 4.45
6401 6574 3.248024 TGTGTACTGAAGATTCTGGGGT 58.752 45.455 0.00 0.00 0.00 4.95
6599 6804 0.834612 CAAATCATTGCTGCCCCCAT 59.165 50.000 0.00 0.00 0.00 4.00
6609 6814 3.921104 TGCTGCCCCCATATTATTTTGA 58.079 40.909 0.00 0.00 0.00 2.69
6629 6834 0.104304 GGCCGAGGAGCGAAAAGATA 59.896 55.000 0.00 0.00 44.57 1.98
6712 6917 7.807977 TCAAGCTTGGTTTCCATAATATCTC 57.192 36.000 25.73 0.00 31.53 2.75
6808 7045 5.186409 ACTTGCGGAAGTGTTCTTATAGGTA 59.814 40.000 22.32 0.00 41.12 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.831307 GGAGCGTGTATCCCTTCCTT 59.169 55.000 0.00 0.00 0.00 3.36
1 2 0.325296 TGGAGCGTGTATCCCTTCCT 60.325 55.000 0.00 0.00 35.86 3.36
2 3 0.759346 ATGGAGCGTGTATCCCTTCC 59.241 55.000 0.00 0.00 35.86 3.46
3 4 1.270358 GGATGGAGCGTGTATCCCTTC 60.270 57.143 0.00 0.00 35.43 3.46
4 5 0.759346 GGATGGAGCGTGTATCCCTT 59.241 55.000 0.00 0.00 35.43 3.95
5 6 0.398522 TGGATGGAGCGTGTATCCCT 60.399 55.000 0.00 0.00 39.68 4.20
6 7 0.468226 TTGGATGGAGCGTGTATCCC 59.532 55.000 0.00 0.00 39.68 3.85
7 8 2.213499 CTTTGGATGGAGCGTGTATCC 58.787 52.381 0.00 0.00 40.59 2.59
8 9 2.906354 ACTTTGGATGGAGCGTGTATC 58.094 47.619 0.00 0.00 0.00 2.24
9 10 3.270877 GAACTTTGGATGGAGCGTGTAT 58.729 45.455 0.00 0.00 0.00 2.29
10 11 2.614481 GGAACTTTGGATGGAGCGTGTA 60.614 50.000 0.00 0.00 0.00 2.90
11 12 1.523758 GAACTTTGGATGGAGCGTGT 58.476 50.000 0.00 0.00 0.00 4.49
12 13 0.804989 GGAACTTTGGATGGAGCGTG 59.195 55.000 0.00 0.00 0.00 5.34
13 14 0.400213 TGGAACTTTGGATGGAGCGT 59.600 50.000 0.00 0.00 0.00 5.07
14 15 1.533625 TTGGAACTTTGGATGGAGCG 58.466 50.000 0.00 0.00 0.00 5.03
15 16 2.893489 ACTTTGGAACTTTGGATGGAGC 59.107 45.455 0.00 0.00 0.00 4.70
16 17 4.459337 GGTACTTTGGAACTTTGGATGGAG 59.541 45.833 0.00 0.00 0.00 3.86
17 18 4.141135 TGGTACTTTGGAACTTTGGATGGA 60.141 41.667 0.00 0.00 0.00 3.41
18 19 4.148838 TGGTACTTTGGAACTTTGGATGG 58.851 43.478 0.00 0.00 0.00 3.51
19 20 5.982890 ATGGTACTTTGGAACTTTGGATG 57.017 39.130 0.00 0.00 0.00 3.51
20 21 5.279456 GCAATGGTACTTTGGAACTTTGGAT 60.279 40.000 9.94 0.00 0.00 3.41
21 22 4.038642 GCAATGGTACTTTGGAACTTTGGA 59.961 41.667 9.94 0.00 0.00 3.53
22 23 4.306600 GCAATGGTACTTTGGAACTTTGG 58.693 43.478 9.94 0.00 0.00 3.28
23 24 4.039124 AGGCAATGGTACTTTGGAACTTTG 59.961 41.667 9.94 0.00 0.00 2.77
24 25 4.039124 CAGGCAATGGTACTTTGGAACTTT 59.961 41.667 9.94 0.00 0.00 2.66
25 26 3.573967 CAGGCAATGGTACTTTGGAACTT 59.426 43.478 9.94 0.00 0.00 2.66
26 27 3.157087 CAGGCAATGGTACTTTGGAACT 58.843 45.455 9.94 0.00 0.00 3.01
27 28 2.231235 CCAGGCAATGGTACTTTGGAAC 59.769 50.000 9.94 0.00 44.91 3.62
28 29 2.524306 CCAGGCAATGGTACTTTGGAA 58.476 47.619 9.94 0.00 44.91 3.53
29 30 2.214376 CCAGGCAATGGTACTTTGGA 57.786 50.000 9.94 0.00 44.91 3.53
44 45 2.505006 CTGCTGCTAGGCTCCAGG 59.495 66.667 14.55 0.00 0.00 4.45
54 55 1.127343 GAGATAGGAACCCTGCTGCT 58.873 55.000 0.00 0.00 34.61 4.24
58 59 2.364002 GAGACAGAGATAGGAACCCTGC 59.636 54.545 0.00 0.00 34.61 4.85
147 152 7.082602 GGTGAACACCGTAGTACATATGATAG 58.917 42.308 10.38 0.00 42.29 2.08
164 169 1.334869 CCTGCACTTTCTGGTGAACAC 59.665 52.381 0.00 0.00 39.34 3.32
166 171 0.312102 GCCTGCACTTTCTGGTGAAC 59.688 55.000 0.00 0.00 39.34 3.18
168 173 0.535780 CTGCCTGCACTTTCTGGTGA 60.536 55.000 0.00 0.00 39.34 4.02
169 174 0.535780 TCTGCCTGCACTTTCTGGTG 60.536 55.000 0.00 0.00 39.91 4.17
170 175 0.183492 TTCTGCCTGCACTTTCTGGT 59.817 50.000 0.00 0.00 0.00 4.00
171 176 0.595095 GTTCTGCCTGCACTTTCTGG 59.405 55.000 0.00 0.00 0.00 3.86
172 177 1.266175 CTGTTCTGCCTGCACTTTCTG 59.734 52.381 0.00 0.00 0.00 3.02
174 179 1.597742 TCTGTTCTGCCTGCACTTTC 58.402 50.000 0.00 0.00 0.00 2.62
178 183 1.527034 TGATTCTGTTCTGCCTGCAC 58.473 50.000 0.00 0.00 0.00 4.57
179 184 2.089201 CATGATTCTGTTCTGCCTGCA 58.911 47.619 0.00 0.00 0.00 4.41
183 188 3.427233 GCTTGACATGATTCTGTTCTGCC 60.427 47.826 0.00 0.00 0.00 4.85
185 190 4.668431 CGTGCTTGACATGATTCTGTTCTG 60.668 45.833 0.00 0.00 37.49 3.02
186 191 3.434641 CGTGCTTGACATGATTCTGTTCT 59.565 43.478 0.00 0.00 37.49 3.01
187 192 3.425359 CCGTGCTTGACATGATTCTGTTC 60.425 47.826 0.00 0.00 37.49 3.18
188 193 2.485426 CCGTGCTTGACATGATTCTGTT 59.515 45.455 0.00 0.00 37.49 3.16
189 194 2.079158 CCGTGCTTGACATGATTCTGT 58.921 47.619 0.00 0.00 37.49 3.41
227 257 3.066203 GGGATTTGACTGTTTCGTGTGTT 59.934 43.478 0.00 0.00 0.00 3.32
228 258 2.616842 GGGATTTGACTGTTTCGTGTGT 59.383 45.455 0.00 0.00 0.00 3.72
261 299 3.512516 GCCAGGATCAGCAACGGC 61.513 66.667 0.00 0.00 41.61 5.68
1191 1244 3.057548 TCGAACTCGTAGCCGCCA 61.058 61.111 0.00 0.00 40.80 5.69
1350 1403 2.877975 GTACGAGTACCAGGGCAGA 58.122 57.895 2.13 0.00 0.00 4.26
1411 1464 2.263077 GACGTCTTTCATCATCTGCGT 58.737 47.619 8.70 0.00 0.00 5.24
1425 1478 1.515020 GCTGATCTGCCTGACGTCT 59.485 57.895 17.92 0.00 0.00 4.18
1503 1556 3.251729 ACATGTCAGAACAACAGTCATGC 59.748 43.478 0.00 0.00 39.30 4.06
1508 1561 4.516698 GGAATGACATGTCAGAACAACAGT 59.483 41.667 30.63 10.52 43.61 3.55
1547 1614 3.179830 CAACGCTCATCAGTACTGGTAC 58.820 50.000 22.48 7.85 36.35 3.34
1549 1616 1.066858 CCAACGCTCATCAGTACTGGT 60.067 52.381 22.48 13.58 0.00 4.00
1667 1734 1.000607 CTCACCTCCGTGTCGAAGAAA 60.001 52.381 0.00 0.00 39.69 2.52
1767 1834 4.342378 TGGGCAAAGTGTTTAAGCAATGTA 59.658 37.500 0.00 0.00 0.00 2.29
1806 1875 1.076485 GGGAGGATGCAGCCATGTT 60.076 57.895 25.38 0.79 0.00 2.71
1815 1884 3.859414 AGAGCGCTGGGAGGATGC 61.859 66.667 18.48 0.00 0.00 3.91
1816 1885 2.108566 CAGAGCGCTGGGAGGATG 59.891 66.667 18.48 0.00 38.51 3.51
2054 2123 8.462016 GCATGTTTGTTTTCCTTCAGTCTATAT 58.538 33.333 0.00 0.00 0.00 0.86
2055 2124 7.446931 TGCATGTTTGTTTTCCTTCAGTCTATA 59.553 33.333 0.00 0.00 0.00 1.31
2112 2181 4.360563 ACGACGCCTAGTTTGATAGATTG 58.639 43.478 0.00 0.00 0.00 2.67
2113 2182 4.650754 ACGACGCCTAGTTTGATAGATT 57.349 40.909 0.00 0.00 0.00 2.40
2117 2186 3.016031 TGGTACGACGCCTAGTTTGATA 58.984 45.455 0.00 0.00 0.00 2.15
2459 2530 0.674895 ACAGAGAAAGTGATGGCGCC 60.675 55.000 22.73 22.73 0.00 6.53
2670 2746 0.846427 TTGAACTCCATCCTGCCCCT 60.846 55.000 0.00 0.00 0.00 4.79
2900 2993 5.441709 AACAAAAATTCGTTACGACCCAT 57.558 34.783 7.06 0.00 34.89 4.00
2901 2994 4.552378 CGAACAAAAATTCGTTACGACCCA 60.552 41.667 7.06 0.00 45.07 4.51
2902 2995 3.901877 CGAACAAAAATTCGTTACGACCC 59.098 43.478 7.06 0.00 45.07 4.46
2913 3006 6.426025 GTCCCTAGTAGACACGAACAAAAATT 59.574 38.462 0.00 0.00 34.27 1.82
2914 3007 5.930569 GTCCCTAGTAGACACGAACAAAAAT 59.069 40.000 0.00 0.00 34.27 1.82
2915 3008 5.291971 GTCCCTAGTAGACACGAACAAAAA 58.708 41.667 0.00 0.00 34.27 1.94
2916 3009 4.557296 CGTCCCTAGTAGACACGAACAAAA 60.557 45.833 12.94 0.00 33.70 2.44
2918 3011 2.485426 CGTCCCTAGTAGACACGAACAA 59.515 50.000 12.94 0.00 33.70 2.83
2919 3012 2.079158 CGTCCCTAGTAGACACGAACA 58.921 52.381 12.94 0.00 33.70 3.18
2920 3013 2.350522 TCGTCCCTAGTAGACACGAAC 58.649 52.381 16.67 0.00 36.59 3.95
2921 3014 2.768253 TCGTCCCTAGTAGACACGAA 57.232 50.000 16.67 5.52 36.59 3.85
2923 3016 2.287373 GTGATCGTCCCTAGTAGACACG 59.713 54.545 12.32 12.32 33.70 4.49
2924 3017 2.287373 CGTGATCGTCCCTAGTAGACAC 59.713 54.545 0.00 0.00 33.70 3.67
2925 3018 2.558378 CGTGATCGTCCCTAGTAGACA 58.442 52.381 0.00 0.07 33.70 3.41
2926 3019 1.263752 GCGTGATCGTCCCTAGTAGAC 59.736 57.143 0.00 0.99 39.49 2.59
2927 3020 1.140452 AGCGTGATCGTCCCTAGTAGA 59.860 52.381 0.00 0.00 39.49 2.59
2930 3023 1.384989 CCAGCGTGATCGTCCCTAGT 61.385 60.000 0.00 0.00 39.49 2.57
2931 3024 1.101635 TCCAGCGTGATCGTCCCTAG 61.102 60.000 0.00 0.00 39.49 3.02
2932 3025 1.077285 TCCAGCGTGATCGTCCCTA 60.077 57.895 0.00 0.00 39.49 3.53
3191 3328 9.955208 CATCATCAGTTTGCTTAATGCTTATAA 57.045 29.630 0.00 0.00 43.37 0.98
3192 3329 8.077991 GCATCATCAGTTTGCTTAATGCTTATA 58.922 33.333 0.00 0.00 43.37 0.98
3193 3330 6.921857 GCATCATCAGTTTGCTTAATGCTTAT 59.078 34.615 0.00 0.00 43.37 1.73
3194 3331 6.267817 GCATCATCAGTTTGCTTAATGCTTA 58.732 36.000 0.00 0.00 43.37 3.09
3195 3332 5.107133 GCATCATCAGTTTGCTTAATGCTT 58.893 37.500 0.00 0.00 43.37 3.91
3196 3333 4.441079 GGCATCATCAGTTTGCTTAATGCT 60.441 41.667 0.00 0.00 43.37 3.79
3197 3334 3.800506 GGCATCATCAGTTTGCTTAATGC 59.199 43.478 0.00 0.00 43.25 3.56
3198 3335 4.039703 CGGCATCATCAGTTTGCTTAATG 58.960 43.478 0.00 0.00 36.62 1.90
3199 3336 3.947196 TCGGCATCATCAGTTTGCTTAAT 59.053 39.130 0.00 0.00 36.62 1.40
3200 3337 3.342719 TCGGCATCATCAGTTTGCTTAA 58.657 40.909 0.00 0.00 36.62 1.85
3201 3338 2.984562 TCGGCATCATCAGTTTGCTTA 58.015 42.857 0.00 0.00 36.62 3.09
3202 3339 1.825090 TCGGCATCATCAGTTTGCTT 58.175 45.000 0.00 0.00 36.62 3.91
3203 3340 1.674441 CATCGGCATCATCAGTTTGCT 59.326 47.619 0.00 0.00 36.62 3.91
3204 3341 1.862815 GCATCGGCATCATCAGTTTGC 60.863 52.381 0.00 0.00 40.72 3.68
3254 3394 2.769621 ATCCTGGCGAGCCCATGA 60.770 61.111 12.05 5.78 44.33 3.07
3255 3395 2.281345 GATCCTGGCGAGCCCATG 60.281 66.667 12.05 2.03 44.33 3.66
3269 3409 6.070710 ACAAACACCCTCTTACTTAGGAGATC 60.071 42.308 0.00 0.00 36.08 2.75
3279 3419 6.453926 TGGTTAAAACAAACACCCTCTTAC 57.546 37.500 0.00 0.00 0.00 2.34
3280 3420 7.477945 TTTGGTTAAAACAAACACCCTCTTA 57.522 32.000 0.00 0.00 33.26 2.10
3294 3434 4.862371 AGTCCCTGACTGTTTGGTTAAAA 58.138 39.130 0.00 0.00 41.76 1.52
3295 3435 4.513406 AGTCCCTGACTGTTTGGTTAAA 57.487 40.909 0.00 0.00 41.76 1.52
3296 3436 4.513406 AAGTCCCTGACTGTTTGGTTAA 57.487 40.909 0.00 0.00 42.59 2.01
3297 3437 4.513406 AAAGTCCCTGACTGTTTGGTTA 57.487 40.909 0.00 0.00 42.59 2.85
3298 3438 3.382083 AAAGTCCCTGACTGTTTGGTT 57.618 42.857 0.00 0.00 42.59 3.67
3299 3439 3.382083 AAAAGTCCCTGACTGTTTGGT 57.618 42.857 0.00 0.00 42.59 3.67
3300 3440 4.278419 CCTAAAAAGTCCCTGACTGTTTGG 59.722 45.833 18.30 15.80 45.98 3.28
3301 3441 4.278419 CCCTAAAAAGTCCCTGACTGTTTG 59.722 45.833 18.30 10.52 45.98 2.93
3303 3443 3.720002 TCCCTAAAAAGTCCCTGACTGTT 59.280 43.478 0.00 0.00 42.59 3.16
3304 3444 3.072622 GTCCCTAAAAAGTCCCTGACTGT 59.927 47.826 0.00 0.00 42.59 3.55
3305 3445 3.328050 AGTCCCTAAAAAGTCCCTGACTG 59.672 47.826 0.00 0.00 42.59 3.51
3306 3446 3.599348 AGTCCCTAAAAAGTCCCTGACT 58.401 45.455 0.00 0.00 45.64 3.41
3307 3447 4.072839 CAAGTCCCTAAAAAGTCCCTGAC 58.927 47.826 0.00 0.00 0.00 3.51
3308 3448 3.720002 ACAAGTCCCTAAAAAGTCCCTGA 59.280 43.478 0.00 0.00 0.00 3.86
3309 3449 3.821033 CACAAGTCCCTAAAAAGTCCCTG 59.179 47.826 0.00 0.00 0.00 4.45
3310 3450 3.720002 TCACAAGTCCCTAAAAAGTCCCT 59.280 43.478 0.00 0.00 0.00 4.20
3311 3451 3.819337 GTCACAAGTCCCTAAAAAGTCCC 59.181 47.826 0.00 0.00 0.00 4.46
3312 3452 4.715713 AGTCACAAGTCCCTAAAAAGTCC 58.284 43.478 0.00 0.00 0.00 3.85
3313 3453 6.764560 TGTAAGTCACAAGTCCCTAAAAAGTC 59.235 38.462 0.00 0.00 32.95 3.01
3314 3454 6.655930 TGTAAGTCACAAGTCCCTAAAAAGT 58.344 36.000 0.00 0.00 32.95 2.66
3315 3455 7.562454 TTGTAAGTCACAAGTCCCTAAAAAG 57.438 36.000 0.00 0.00 42.29 2.27
3327 3467 7.925043 TTTAGTTCCAACTTGTAAGTCACAA 57.075 32.000 0.00 0.00 44.97 3.33
3328 3468 7.925043 TTTTAGTTCCAACTTGTAAGTCACA 57.075 32.000 0.00 0.00 38.57 3.58
3356 3496 6.681729 TGTTTGGTTCATAAGTCCTAGACT 57.318 37.500 0.00 0.00 45.64 3.24
3357 3497 6.316390 CCATGTTTGGTTCATAAGTCCTAGAC 59.684 42.308 0.00 0.00 38.30 2.59
3358 3498 6.414732 CCATGTTTGGTTCATAAGTCCTAGA 58.585 40.000 0.00 0.00 38.30 2.43
3359 3499 5.066505 GCCATGTTTGGTTCATAAGTCCTAG 59.933 44.000 0.00 0.00 45.57 3.02
3360 3500 4.947388 GCCATGTTTGGTTCATAAGTCCTA 59.053 41.667 0.00 0.00 45.57 2.94
3361 3501 3.763897 GCCATGTTTGGTTCATAAGTCCT 59.236 43.478 0.00 0.00 45.57 3.85
3362 3502 3.119137 GGCCATGTTTGGTTCATAAGTCC 60.119 47.826 0.00 0.00 45.57 3.85
3363 3503 3.763897 AGGCCATGTTTGGTTCATAAGTC 59.236 43.478 5.01 0.00 45.57 3.01
3364 3504 3.778265 AGGCCATGTTTGGTTCATAAGT 58.222 40.909 5.01 0.00 45.57 2.24
3365 3505 5.913137 TTAGGCCATGTTTGGTTCATAAG 57.087 39.130 5.01 0.00 45.57 1.73
3366 3506 6.865834 ATTTAGGCCATGTTTGGTTCATAA 57.134 33.333 5.01 0.00 45.57 1.90
3367 3507 8.546083 AATATTTAGGCCATGTTTGGTTCATA 57.454 30.769 5.01 0.00 45.57 2.15
3368 3508 7.345392 AGAATATTTAGGCCATGTTTGGTTCAT 59.655 33.333 5.01 0.00 45.57 2.57
3369 3509 6.667414 AGAATATTTAGGCCATGTTTGGTTCA 59.333 34.615 5.01 0.00 45.57 3.18
3370 3510 7.068716 AGAGAATATTTAGGCCATGTTTGGTTC 59.931 37.037 5.01 0.00 45.57 3.62
3371 3511 6.897413 AGAGAATATTTAGGCCATGTTTGGTT 59.103 34.615 5.01 0.00 45.57 3.67
3372 3512 6.435164 AGAGAATATTTAGGCCATGTTTGGT 58.565 36.000 5.01 0.00 45.57 3.67
3373 3513 6.966534 AGAGAATATTTAGGCCATGTTTGG 57.033 37.500 5.01 0.00 46.66 3.28
3374 3514 9.090692 CAAAAGAGAATATTTAGGCCATGTTTG 57.909 33.333 5.01 0.00 0.00 2.93
3375 3515 8.815912 ACAAAAGAGAATATTTAGGCCATGTTT 58.184 29.630 5.01 0.00 0.00 2.83
3376 3516 8.366359 ACAAAAGAGAATATTTAGGCCATGTT 57.634 30.769 5.01 0.00 0.00 2.71
3377 3517 7.961326 ACAAAAGAGAATATTTAGGCCATGT 57.039 32.000 5.01 0.00 0.00 3.21
3380 3520 8.966868 CCTAAACAAAAGAGAATATTTAGGCCA 58.033 33.333 5.01 0.00 40.82 5.36
3381 3521 8.967918 ACCTAAACAAAAGAGAATATTTAGGCC 58.032 33.333 16.72 0.00 46.68 5.19
3386 3526 9.981114 CACCAACCTAAACAAAAGAGAATATTT 57.019 29.630 0.00 0.00 0.00 1.40
3387 3527 9.362151 TCACCAACCTAAACAAAAGAGAATATT 57.638 29.630 0.00 0.00 0.00 1.28
3388 3528 8.793592 GTCACCAACCTAAACAAAAGAGAATAT 58.206 33.333 0.00 0.00 0.00 1.28
3389 3529 7.229907 GGTCACCAACCTAAACAAAAGAGAATA 59.770 37.037 0.00 0.00 45.45 1.75
3390 3530 6.040504 GGTCACCAACCTAAACAAAAGAGAAT 59.959 38.462 0.00 0.00 45.45 2.40
3391 3531 5.358725 GGTCACCAACCTAAACAAAAGAGAA 59.641 40.000 0.00 0.00 45.45 2.87
3392 3532 4.885325 GGTCACCAACCTAAACAAAAGAGA 59.115 41.667 0.00 0.00 45.45 3.10
3393 3533 4.261031 CGGTCACCAACCTAAACAAAAGAG 60.261 45.833 0.00 0.00 46.87 2.85
3394 3534 3.628487 CGGTCACCAACCTAAACAAAAGA 59.372 43.478 0.00 0.00 46.87 2.52
3395 3535 3.794138 GCGGTCACCAACCTAAACAAAAG 60.794 47.826 0.00 0.00 46.87 2.27
3396 3536 2.099427 GCGGTCACCAACCTAAACAAAA 59.901 45.455 0.00 0.00 46.87 2.44
3400 3540 1.571215 CCGCGGTCACCAACCTAAAC 61.571 60.000 19.50 0.00 46.87 2.01
3804 3946 4.498346 TCGTACCCCGAGTTGTCA 57.502 55.556 0.00 0.00 41.60 3.58
3834 3976 1.038681 TGCCGCCATACCTCGACTTA 61.039 55.000 0.00 0.00 0.00 2.24
3872 4014 1.382557 TCCTTAGCATCCGCCTCCA 60.383 57.895 0.00 0.00 39.83 3.86
4005 4150 1.511768 CGGGAAGACGGAGAAGACC 59.488 63.158 0.00 0.00 0.00 3.85
4008 4153 1.153745 CAGCGGGAAGACGGAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
4017 4162 2.437359 CCCAGAAGCAGCGGGAAG 60.437 66.667 0.00 0.00 43.21 3.46
4404 4549 0.625316 AGGCCATGGCAATCAGTGTA 59.375 50.000 36.56 0.00 44.11 2.90
4425 4570 2.697761 GCCGAGCGTGAGTGGAGTA 61.698 63.158 0.00 0.00 0.00 2.59
4629 4774 0.391130 TGCCCATGTACTGCGACTTC 60.391 55.000 0.00 0.00 0.00 3.01
4809 4954 3.681835 GACGTGTCAGGGGCGAGT 61.682 66.667 0.00 0.00 0.00 4.18
4950 5095 1.080974 CGGGTACGCGAAGAACACT 60.081 57.895 26.40 0.00 0.00 3.55
4954 5099 2.176546 CGACGGGTACGCGAAGAA 59.823 61.111 35.08 0.00 46.04 2.52
5163 5308 3.797353 ACCATCGCGCATTCCCCT 61.797 61.111 8.75 0.00 0.00 4.79
5211 5356 4.379813 CCGAACCCAATGTTTTCTCTGATG 60.380 45.833 0.00 0.00 37.29 3.07
5383 5537 7.357303 AGTAAGTACAAATGTTAAGTTTGGCG 58.643 34.615 14.40 0.00 40.08 5.69
5477 5632 2.029380 ACCTGCCAAAAATAAGCGGTTC 60.029 45.455 1.59 0.00 32.21 3.62
5535 5690 4.427394 GCGATCGCAATCCTCTGT 57.573 55.556 33.89 0.00 41.49 3.41
5562 5717 1.407258 AGTATCCTCGACTGCTTCAGC 59.593 52.381 0.00 0.00 42.50 4.26
5775 5930 3.361158 CCATCGCGGTGGTTTGCA 61.361 61.111 30.46 0.00 34.46 4.08
5778 5933 4.344865 AGGCCATCGCGGTGGTTT 62.345 61.111 36.95 23.54 41.47 3.27
5847 6002 5.411781 GGATCAGTTCATCGTTCTGTACTT 58.588 41.667 0.00 0.00 0.00 2.24
5911 6067 5.211174 ACCTACTAAGAACTTGGTCACAC 57.789 43.478 6.82 0.00 35.81 3.82
5912 6068 6.073314 ACTACCTACTAAGAACTTGGTCACA 58.927 40.000 6.82 0.00 35.81 3.58
5992 6156 8.681486 TGGACATTTCATCTAATCCTTGTATG 57.319 34.615 0.00 0.00 0.00 2.39
6021 6185 3.074412 GGCCGGAGTTCATATATTGTGG 58.926 50.000 5.05 0.00 0.00 4.17
6107 6271 7.430502 CGAACAAGATTTCTCATCTTATTTGCC 59.569 37.037 0.00 0.00 36.68 4.52
6152 6316 3.475566 TTAATCCCAGCATCTCGAAGG 57.524 47.619 0.00 0.00 0.00 3.46
6156 6320 4.143030 CGCTTAATTAATCCCAGCATCTCG 60.143 45.833 11.82 0.00 0.00 4.04
6163 6327 6.207417 ACATCAATCCGCTTAATTAATCCCAG 59.793 38.462 0.00 0.00 0.00 4.45
6386 6559 4.159135 CCAAATGAACCCCAGAATCTTCAG 59.841 45.833 0.00 0.00 0.00 3.02
6401 6574 1.337118 GGTGGCCAGTTCCAAATGAA 58.663 50.000 5.11 0.00 37.96 2.57
6533 6738 6.613271 AGATACACATACATCCACTTCCTCTT 59.387 38.462 0.00 0.00 0.00 2.85
6534 6739 6.139671 AGATACACATACATCCACTTCCTCT 58.860 40.000 0.00 0.00 0.00 3.69
6535 6740 6.412362 AGATACACATACATCCACTTCCTC 57.588 41.667 0.00 0.00 0.00 3.71
6536 6741 6.267928 GGTAGATACACATACATCCACTTCCT 59.732 42.308 0.00 0.00 0.00 3.36
6537 6742 6.456501 GGTAGATACACATACATCCACTTCC 58.543 44.000 0.00 0.00 0.00 3.46
6538 6743 6.016527 TCGGTAGATACACATACATCCACTTC 60.017 42.308 0.00 0.00 0.00 3.01
6599 6804 3.740115 GCTCCTCGGCCTCAAAATAATA 58.260 45.455 0.00 0.00 0.00 0.98
6609 6814 1.617947 ATCTTTTCGCTCCTCGGCCT 61.618 55.000 0.00 0.00 39.05 5.19
6629 6834 9.268268 TGTAAAGAAAATGACAGTTTCGATACT 57.732 29.630 27.24 2.36 39.48 2.12
6712 6917 3.865329 CGATGCACCAACTATTTCATCG 58.135 45.455 7.81 7.81 44.29 3.84
6790 7027 9.984190 CTATTCCTTACCTATAAGAACACTTCC 57.016 37.037 0.00 0.00 40.38 3.46
6808 7045 7.633991 GCAGTAGCTAGGTTTCTTCTATTCCTT 60.634 40.741 0.00 0.00 37.91 3.36


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

AutoCloner maintained by Alex Coulton.