Multiple sequence alignment - TraesCS7B01G270300

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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 TraesCS7B01G270300 chr7B 100.000 6390 0 0 815 7204 495336635 495343024 0.000000e+00 11801.0
1 TraesCS7B01G270300 chr7B 100.000 539 0 0 1 539 495335821 495336359 0.000000e+00 996.0
2 TraesCS7B01G270300 chr7D 92.191 2971 136 37 825 3763 471555598 471558504 0.000000e+00 4113.0
3 TraesCS7B01G270300 chr7D 95.622 1142 26 12 6072 7204 471560763 471561889 0.000000e+00 1810.0
4 TraesCS7B01G270300 chr7D 91.651 1042 47 14 5004 6024 471559593 471560615 0.000000e+00 1406.0
5 TraesCS7B01G270300 chr7D 94.531 640 26 6 4144 4780 471558959 471559592 0.000000e+00 979.0
6 TraesCS7B01G270300 chr7D 85.610 549 52 13 1 539 471554980 471555511 1.060000e-152 551.0
7 TraesCS7B01G270300 chr7D 96.667 150 5 0 3764 3913 471558594 471558743 4.310000e-62 250.0
8 TraesCS7B01G270300 chr7D 89.941 169 16 1 3976 4143 471558759 471558927 4.380000e-52 217.0
9 TraesCS7B01G270300 chr7D 90.076 131 11 2 4958 5087 63561568 63561439 1.240000e-37 169.0
10 TraesCS7B01G270300 chr7D 89.844 128 13 0 4960 5087 160550559 160550432 1.610000e-36 165.0
11 TraesCS7B01G270300 chr7A 88.734 2015 132 38 818 2766 526133909 526131924 0.000000e+00 2375.0
12 TraesCS7B01G270300 chr7A 90.940 1170 72 17 6048 7204 526127973 526126825 0.000000e+00 1543.0
13 TraesCS7B01G270300 chr7A 94.540 641 27 4 4144 4781 526129828 526129193 0.000000e+00 983.0
14 TraesCS7B01G270300 chr7A 86.760 929 49 40 4931 5848 526129201 526128336 0.000000e+00 966.0
15 TraesCS7B01G270300 chr7A 85.176 823 63 20 3378 4143 526130678 526129858 0.000000e+00 789.0
16 TraesCS7B01G270300 chr7A 85.122 531 63 10 2819 3341 526131205 526130683 4.950000e-146 529.0
17 TraesCS7B01G270300 chr7A 94.030 335 16 3 1 331 526134570 526134236 8.340000e-139 505.0
18 TraesCS7B01G270300 chr7A 93.064 173 8 1 371 539 526134131 526133959 4.310000e-62 250.0
19 TraesCS7B01G270300 chr7A 93.750 128 6 2 4791 4917 83728728 83728602 2.650000e-44 191.0
20 TraesCS7B01G270300 chr7A 89.844 128 13 0 4960 5087 161689499 161689372 1.610000e-36 165.0
21 TraesCS7B01G270300 chr3B 85.153 229 32 2 2317 2544 102598543 102598316 4.350000e-57 233.0
22 TraesCS7B01G270300 chr3B 94.574 129 7 0 4791 4919 659784397 659784269 4.410000e-47 200.0
23 TraesCS7B01G270300 chr3B 89.610 154 14 2 4765 4917 115549490 115549642 2.050000e-45 195.0
24 TraesCS7B01G270300 chr3B 85.075 134 16 4 4957 5086 114150183 114150050 4.530000e-27 134.0
25 TraesCS7B01G270300 chr3D 84.914 232 27 4 2317 2544 63246511 63246284 2.020000e-55 228.0
26 TraesCS7B01G270300 chr3D 92.199 141 9 2 4778 4917 67064772 67064911 1.590000e-46 198.0
27 TraesCS7B01G270300 chr3A 84.716 229 33 2 2317 2544 72297487 72297260 2.020000e-55 228.0
28 TraesCS7B01G270300 chr3A 94.118 136 6 2 4783 4917 742879117 742879251 9.470000e-49 206.0
29 TraesCS7B01G270300 chr3A 84.247 146 21 1 4941 5086 79398339 79398482 2.710000e-29 141.0
30 TraesCS7B01G270300 chrUn 94.737 133 7 0 4787 4919 322720540 322720408 2.630000e-49 207.0
31 TraesCS7B01G270300 chrUn 82.292 96 15 2 2432 2526 106121202 106121296 1.670000e-11 82.4
32 TraesCS7B01G270300 chr5B 96.063 127 5 0 4791 4917 446414499 446414373 2.630000e-49 207.0
33 TraesCS7B01G270300 chr6B 94.697 132 7 0 4786 4917 644809028 644808897 9.470000e-49 206.0
34 TraesCS7B01G270300 chr1A 92.806 139 8 2 4788 4925 576149835 576149972 4.410000e-47 200.0
35 TraesCS7B01G270300 chr5D 92.424 132 10 0 4957 5088 256749945 256749814 9.540000e-44 189.0
36 TraesCS7B01G270300 chr5A 88.889 135 15 0 4954 5088 335291440 335291574 4.470000e-37 167.0
37 TraesCS7B01G270300 chr4B 89.313 131 14 0 4957 5087 78607762 78607632 1.610000e-36 165.0
38 TraesCS7B01G270300 chr4B 82.292 96 15 2 2432 2526 111702392 111702298 1.670000e-11 82.4
39 TraesCS7B01G270300 chr6A 89.147 129 12 2 4960 5087 599048873 599048746 7.480000e-35 159.0
40 TraesCS7B01G270300 chr1D 88.636 132 13 2 4954 5084 351254713 351254843 7.480000e-35 159.0
41 TraesCS7B01G270300 chr6D 75.000 212 40 10 2320 2526 389743594 389743797 1.290000e-12 86.1
42 TraesCS7B01G270300 chr4D 82.292 96 15 2 2432 2526 278001367 278001461 1.670000e-11 82.4
43 TraesCS7B01G270300 chr2A 85.714 63 3 6 4937 4997 113599328 113599386 2.170000e-05 62.1


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 TraesCS7B01G270300 chr7B 495335821 495343024 7203 False 6398.500000 11801 100.000000 1 7204 2 chr7B.!!$F1 7203
1 TraesCS7B01G270300 chr7D 471554980 471561889 6909 False 1332.285714 4113 92.316143 1 7204 7 chr7D.!!$F1 7203
2 TraesCS7B01G270300 chr7A 526126825 526134570 7745 True 992.500000 2375 89.795750 1 7204 8 chr7A.!!$R3 7203

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
867 1017 0.762461 CTCTCCTGTCTCCATCCCCC 60.762 65.0 0.00 0.00 0.00 5.40 F
1101 1259 0.389426 ACCGCAAGTACATGTCGGAC 60.389 55.0 28.07 9.26 40.23 4.79 F
2782 3055 0.179037 GTAGTTGGGGTATTCGGGCC 60.179 60.0 0.00 0.00 0.00 5.80 F
3317 4226 0.035915 GAGGAAGAGCAGGTGGGTTC 60.036 60.0 0.00 0.00 0.00 3.62 F
3341 4250 0.617249 AGCAAGGAGGTGGAGAGGAG 60.617 60.0 0.00 0.00 0.00 3.69 F
4112 5163 0.861837 GAACTGCTCGCATTATCGGG 59.138 55.0 0.00 0.00 0.00 5.14 F
4808 5893 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.00 44.66 3.13 F
4812 5897 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2406 0.035439 CGGTGGTGTAAGCCTTGGAT 60.035 55.000 0.00 0.00 0.00 3.41 R
3097 4001 0.105039 CCTCGGCACATCCCTCTTAC 59.895 60.000 0.00 0.00 0.00 2.34 R
4094 5142 0.178068 ACCCGATAATGCGAGCAGTT 59.822 50.000 2.72 1.21 0.00 3.16 R
4789 5874 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12 R
4793 5878 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
5180 6270 0.821517 TCCCACCTGCGTGTATACAG 59.178 55.000 5.62 2.03 38.41 2.74 R
6068 7381 1.908619 TGCAGAGATAAGGGAGTTGCA 59.091 47.619 0.00 0.00 37.70 4.08 R
6492 7894 3.063180 GCACTCAGATGAAACTTCCATCG 59.937 47.826 0.00 0.00 43.73 3.84 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
42 43 8.076910 TGCCCAAAATTGTGATTCATATTAGT 57.923 30.769 0.00 0.00 0.00 2.24
154 156 6.677076 AGACATACTACCCCTTTCCAGTTTAT 59.323 38.462 0.00 0.00 0.00 1.40
336 423 6.276847 AGATATGAGAAACGAGTAAGCCTTG 58.723 40.000 0.00 0.00 0.00 3.61
342 429 4.753610 AGAAACGAGTAAGCCTTGTAAACC 59.246 41.667 0.00 0.00 36.75 3.27
349 436 5.074804 AGTAAGCCTTGTAAACCGGAAAAT 58.925 37.500 9.46 0.00 0.00 1.82
352 439 4.913784 AGCCTTGTAAACCGGAAAATAGA 58.086 39.130 9.46 0.00 0.00 1.98
353 440 4.941873 AGCCTTGTAAACCGGAAAATAGAG 59.058 41.667 9.46 0.00 0.00 2.43
354 441 4.698780 GCCTTGTAAACCGGAAAATAGAGT 59.301 41.667 9.46 0.00 0.00 3.24
355 442 5.876460 GCCTTGTAAACCGGAAAATAGAGTA 59.124 40.000 9.46 0.00 0.00 2.59
356 443 6.541278 GCCTTGTAAACCGGAAAATAGAGTAT 59.459 38.462 9.46 0.00 0.00 2.12
375 476 7.913789 AGAGTATGTAGTATCTCTCTAGGTGG 58.086 42.308 0.00 0.00 32.72 4.61
439 546 1.681793 GGGACAGCTTGATCTAGCGTA 59.318 52.381 20.91 0.00 45.82 4.42
491 598 6.211785 GGAGAACCTTTTCCTTTCTCTCTCTA 59.788 42.308 9.72 0.00 43.24 2.43
492 599 7.093068 GGAGAACCTTTTCCTTTCTCTCTCTAT 60.093 40.741 9.72 0.00 43.24 1.98
493 600 7.847096 AGAACCTTTTCCTTTCTCTCTCTATC 58.153 38.462 0.00 0.00 31.28 2.08
494 601 7.678171 AGAACCTTTTCCTTTCTCTCTCTATCT 59.322 37.037 0.00 0.00 31.28 1.98
867 1017 0.762461 CTCTCCTGTCTCCATCCCCC 60.762 65.000 0.00 0.00 0.00 5.40
870 1020 1.768077 CCTGTCTCCATCCCCCTCC 60.768 68.421 0.00 0.00 0.00 4.30
1101 1259 0.389426 ACCGCAAGTACATGTCGGAC 60.389 55.000 28.07 9.26 40.23 4.79
1113 1271 2.673341 TCGGACTCGAGCTGCTGT 60.673 61.111 13.61 0.00 40.88 4.40
1158 1316 2.483714 CCAGAAGCTGGTACATACGCAT 60.484 50.000 5.31 0.00 45.82 4.73
1204 1362 6.877322 TCGGTTATGCTATAGGCTTTATTTCC 59.123 38.462 1.04 0.00 42.39 3.13
1215 1373 6.136541 AGGCTTTATTTCCGTTGATTCATC 57.863 37.500 0.00 0.00 0.00 2.92
1216 1374 5.652014 AGGCTTTATTTCCGTTGATTCATCA 59.348 36.000 0.00 0.00 34.44 3.07
1246 1411 2.276740 CAGGATTGGGTGGGGCTC 59.723 66.667 0.00 0.00 0.00 4.70
1311 1476 0.539051 CATCTGGAGGCGAAAGTCCT 59.461 55.000 0.00 0.00 39.72 3.85
1414 1579 1.809133 TCTGTTACACCCACCCAGAA 58.191 50.000 0.00 0.00 0.00 3.02
1563 1731 6.831353 TCAAAGTGTTTTCTTCTGTTGGGATA 59.169 34.615 0.00 0.00 0.00 2.59
1719 1907 3.696898 TCGTGTTTTGGGATTTGTTTCG 58.303 40.909 0.00 0.00 0.00 3.46
1720 1908 3.128938 TCGTGTTTTGGGATTTGTTTCGT 59.871 39.130 0.00 0.00 0.00 3.85
1721 1909 3.860536 CGTGTTTTGGGATTTGTTTCGTT 59.139 39.130 0.00 0.00 0.00 3.85
1722 1910 4.259610 CGTGTTTTGGGATTTGTTTCGTTG 60.260 41.667 0.00 0.00 0.00 4.10
1723 1911 3.619038 TGTTTTGGGATTTGTTTCGTTGC 59.381 39.130 0.00 0.00 0.00 4.17
1724 1912 3.526931 TTTGGGATTTGTTTCGTTGCA 57.473 38.095 0.00 0.00 0.00 4.08
1725 1913 3.742433 TTGGGATTTGTTTCGTTGCAT 57.258 38.095 0.00 0.00 0.00 3.96
1726 1914 3.742433 TGGGATTTGTTTCGTTGCATT 57.258 38.095 0.00 0.00 0.00 3.56
1727 1915 4.065321 TGGGATTTGTTTCGTTGCATTT 57.935 36.364 0.00 0.00 0.00 2.32
1728 1916 4.054671 TGGGATTTGTTTCGTTGCATTTC 58.945 39.130 0.00 0.00 0.00 2.17
1729 1917 3.431912 GGGATTTGTTTCGTTGCATTTCC 59.568 43.478 0.00 0.00 0.00 3.13
1730 1918 3.431912 GGATTTGTTTCGTTGCATTTCCC 59.568 43.478 0.00 0.00 0.00 3.97
1731 1919 2.517650 TTGTTTCGTTGCATTTCCCC 57.482 45.000 0.00 0.00 0.00 4.81
1732 1920 1.698506 TGTTTCGTTGCATTTCCCCT 58.301 45.000 0.00 0.00 0.00 4.79
1733 1921 1.611491 TGTTTCGTTGCATTTCCCCTC 59.389 47.619 0.00 0.00 0.00 4.30
1734 1922 1.611491 GTTTCGTTGCATTTCCCCTCA 59.389 47.619 0.00 0.00 0.00 3.86
1735 1923 1.988293 TTCGTTGCATTTCCCCTCAA 58.012 45.000 0.00 0.00 0.00 3.02
1736 1924 1.988293 TCGTTGCATTTCCCCTCAAA 58.012 45.000 0.00 0.00 0.00 2.69
1737 1925 2.311463 TCGTTGCATTTCCCCTCAAAA 58.689 42.857 0.00 0.00 0.00 2.44
1738 1926 2.695666 TCGTTGCATTTCCCCTCAAAAA 59.304 40.909 0.00 0.00 0.00 1.94
1767 1955 3.241322 GCATTTGAATACTTGATGCGCAC 59.759 43.478 14.90 7.75 34.50 5.34
1791 1981 9.888878 CACATCTCCATACACATGAAAAATATC 57.111 33.333 0.00 0.00 33.67 1.63
1813 2003 2.039879 ACTGGTAGATTTTCAAGGGCGT 59.960 45.455 0.00 0.00 0.00 5.68
2049 2278 7.012358 CACTGTCTATTTTCTCTCGCTTTTTC 58.988 38.462 0.00 0.00 0.00 2.29
2060 2289 6.852664 TCTCTCGCTTTTTCTTTTCAAAGTT 58.147 32.000 0.00 0.00 37.31 2.66
2073 2302 7.164803 TCTTTTCAAAGTTGTCCAACCAAAAT 58.835 30.769 6.55 0.00 42.06 1.82
2177 2406 2.429930 CACTTCTTCCACCGGCCA 59.570 61.111 0.00 0.00 0.00 5.36
2602 2834 4.680237 CAGGTCCGCCGTGCAGAA 62.680 66.667 0.00 0.00 40.50 3.02
2621 2853 2.203640 AGGAGGGTCGACAGTGCA 60.204 61.111 18.91 0.00 0.00 4.57
2654 2886 4.760047 GTGCGCATGACCCCGTCT 62.760 66.667 15.91 0.00 33.15 4.18
2773 3046 5.793034 TCTCTTCTAGTAGTAGTTGGGGT 57.207 43.478 4.51 0.00 0.00 4.95
2782 3055 0.179037 GTAGTTGGGGTATTCGGGCC 60.179 60.000 0.00 0.00 0.00 5.80
2891 3789 2.284151 GAGGGGGAGGGAGAGACC 59.716 72.222 0.00 0.00 38.08 3.85
2909 3807 2.691526 GACCGGGGGATCCAAAAATAAC 59.308 50.000 15.23 0.00 34.36 1.89
3097 4001 3.088532 CGATGGAGAGAGGAATAGGGAG 58.911 54.545 0.00 0.00 0.00 4.30
3112 4016 0.470341 GGGAGTAAGAGGGATGTGCC 59.530 60.000 0.00 0.00 0.00 5.01
3174 4082 2.593346 AGAGAACGATGATGACCAGC 57.407 50.000 0.00 0.00 0.00 4.85
3184 4092 2.819117 GATGACCAGCGCTGACGACA 62.819 60.000 38.06 26.38 43.93 4.35
3188 4096 3.250323 CAGCGCTGACGACATCCG 61.250 66.667 33.66 0.00 43.93 4.18
3216 4124 1.592223 GCTAGGGTCTCACTTGCGT 59.408 57.895 0.00 0.00 0.00 5.24
3245 4153 1.544917 ATGCCAACCCCTTCCCTCT 60.545 57.895 0.00 0.00 0.00 3.69
3249 4157 1.002857 CCAACCCCTTCCCTCTTGAT 58.997 55.000 0.00 0.00 0.00 2.57
3267 4175 2.953648 TGATGTCGCGGAACTTAGGATA 59.046 45.455 6.13 0.00 0.00 2.59
3317 4226 0.035915 GAGGAAGAGCAGGTGGGTTC 60.036 60.000 0.00 0.00 0.00 3.62
3318 4227 0.768221 AGGAAGAGCAGGTGGGTTCA 60.768 55.000 0.00 0.00 0.00 3.18
3341 4250 0.617249 AGCAAGGAGGTGGAGAGGAG 60.617 60.000 0.00 0.00 0.00 3.69
3345 4254 1.383803 GGAGGTGGAGAGGAGCCAT 60.384 63.158 0.00 0.00 37.81 4.40
3349 4258 1.061812 AGGTGGAGAGGAGCCATACAT 60.062 52.381 0.00 0.00 37.81 2.29
3355 4264 3.556004 GGAGAGGAGCCATACATTGTAGC 60.556 52.174 2.53 1.66 0.00 3.58
3375 4284 8.319143 TGTAGCCTAGTTTAAACATCAAAGAC 57.681 34.615 20.06 9.82 0.00 3.01
3457 4367 4.962995 TGGGAGATATATTGTAGCTAGGGC 59.037 45.833 0.00 0.00 39.06 5.19
3511 4422 4.111916 AGAGCAATGTCAAACCAAAAACG 58.888 39.130 0.00 0.00 0.00 3.60
3539 4450 6.849588 TCTGACATTCATCACGAATATTGG 57.150 37.500 0.00 0.00 42.70 3.16
3668 4590 1.770294 TTGTTTTGCTTCTCCGGGTT 58.230 45.000 0.00 0.00 0.00 4.11
3872 4891 5.391736 CCTGATGTGCAATCTTCAGAAACTC 60.392 44.000 17.05 0.00 40.02 3.01
3884 4903 4.408182 TCAGAAACTCAATAGCTAGCCC 57.592 45.455 12.13 0.00 0.00 5.19
3885 4904 4.033709 TCAGAAACTCAATAGCTAGCCCT 58.966 43.478 12.13 0.00 0.00 5.19
3917 4964 2.033550 CCTGGTAGACACGCTGTATCTC 59.966 54.545 0.00 0.00 0.00 2.75
3929 4976 5.624081 CACGCTGTATCTCGTACGATTTTAT 59.376 40.000 19.87 12.20 37.14 1.40
3933 4980 7.458071 CGCTGTATCTCGTACGATTTTATTACG 60.458 40.741 19.87 12.71 39.94 3.18
3946 4993 6.702723 CGATTTTATTACGACCTTACATGGGA 59.297 38.462 0.00 0.00 0.00 4.37
3952 4999 1.473434 CGACCTTACATGGGAGCCTTC 60.473 57.143 0.00 0.00 0.00 3.46
4007 5055 6.032094 CGGATTAAGCATCATATTGCAATCC 58.968 40.000 16.86 15.34 44.19 3.01
4010 5058 8.404000 GGATTAAGCATCATATTGCAATCCTAG 58.596 37.037 16.86 4.67 44.22 3.02
4027 5075 2.427453 CCTAGCCTCAAGTGTCGTATGT 59.573 50.000 0.00 0.00 0.00 2.29
4074 5122 7.504403 AGAGTATGTATGATTCCAACTTCCTG 58.496 38.462 0.00 0.00 0.00 3.86
4094 5142 4.325422 CCTGAGCCTACCTATATAGCCAGA 60.325 50.000 4.04 0.00 0.00 3.86
4096 5144 5.017490 TGAGCCTACCTATATAGCCAGAAC 58.983 45.833 4.04 0.58 0.00 3.01
4097 5145 5.222358 TGAGCCTACCTATATAGCCAGAACT 60.222 44.000 4.04 4.70 0.00 3.01
4098 5146 5.020132 AGCCTACCTATATAGCCAGAACTG 58.980 45.833 4.04 0.00 0.00 3.16
4112 5163 0.861837 GAACTGCTCGCATTATCGGG 59.138 55.000 0.00 0.00 0.00 5.14
4116 5167 0.874175 TGCTCGCATTATCGGGTTCG 60.874 55.000 0.00 0.00 37.82 3.95
4169 5251 3.519913 GGAGTTGGAAGGTATCTTGGAGT 59.480 47.826 0.00 0.00 32.52 3.85
4182 5264 3.496331 TCTTGGAGTTGAAATGTTCCCC 58.504 45.455 0.00 0.00 0.00 4.81
4195 5277 8.220755 TGAAATGTTCCCCTTTTCTATTATCG 57.779 34.615 0.00 0.00 37.82 2.92
4224 5306 7.902920 AATGTAGGTAGGAATTTGATGCAAT 57.097 32.000 0.00 0.00 0.00 3.56
4233 5315 7.193377 AGGAATTTGATGCAATGTTTTTGTC 57.807 32.000 0.00 0.00 0.00 3.18
4236 5318 7.254863 GGAATTTGATGCAATGTTTTTGTCTGT 60.255 33.333 0.00 0.00 0.00 3.41
4306 5388 8.186163 TCAGCACAATCTGATCAATGAATTAAC 58.814 33.333 9.17 0.00 38.11 2.01
4433 5515 9.747898 AAGGTTGAAGTAACACATATTTCCATA 57.252 29.630 0.00 0.00 41.18 2.74
4474 5556 7.879070 AGATGTAAGAAGACGTACACAAACTA 58.121 34.615 0.00 0.00 41.84 2.24
4518 5603 1.888215 AGTCCACAATCTGCACAGTG 58.112 50.000 0.00 0.00 0.00 3.66
4525 5610 3.978855 CACAATCTGCACAGTGTCAAATG 59.021 43.478 1.61 0.00 0.00 2.32
4799 5884 8.826293 AGTTATGCTTACTATATACTCCCTCC 57.174 38.462 0.00 0.00 0.00 4.30
4800 5885 7.556996 AGTTATGCTTACTATATACTCCCTCCG 59.443 40.741 0.00 0.00 0.00 4.63
4801 5886 5.252586 TGCTTACTATATACTCCCTCCGT 57.747 43.478 0.00 0.00 0.00 4.69
4802 5887 5.251764 TGCTTACTATATACTCCCTCCGTC 58.748 45.833 0.00 0.00 0.00 4.79
4803 5888 4.639755 GCTTACTATATACTCCCTCCGTCC 59.360 50.000 0.00 0.00 0.00 4.79
4804 5889 3.347077 ACTATATACTCCCTCCGTCCG 57.653 52.381 0.00 0.00 0.00 4.79
4805 5890 2.026449 ACTATATACTCCCTCCGTCCGG 60.026 54.545 0.00 0.00 0.00 5.14
4806 5891 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
4807 5892 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
4808 5893 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4809 5894 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4810 5895 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4811 5896 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4812 5897 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4813 5898 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4814 5899 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4815 5900 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4816 5901 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4817 5902 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4818 5903 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4819 5904 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4820 5905 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4821 5906 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4822 5907 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4823 5908 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4824 5909 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4825 5910 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4826 5911 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
4827 5912 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
4828 5913 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
4836 5921 9.492973 ACTTGTCATCAAAATGAATAAAAAGGG 57.507 29.630 0.00 0.00 43.42 3.95
4837 5922 9.709495 CTTGTCATCAAAATGAATAAAAAGGGA 57.291 29.630 0.00 0.00 43.42 4.20
4839 5924 9.656040 TGTCATCAAAATGAATAAAAAGGGATG 57.344 29.630 0.00 0.00 43.42 3.51
4840 5925 9.657419 GTCATCAAAATGAATAAAAAGGGATGT 57.343 29.630 0.00 0.00 43.42 3.06
4858 5943 9.830186 AAGGGATGTATCTAGATGTATTGTAGT 57.170 33.333 15.79 0.00 0.00 2.73
4859 5944 9.830186 AGGGATGTATCTAGATGTATTGTAGTT 57.170 33.333 15.79 0.00 0.00 2.24
4882 5967 9.793259 AGTTCTAGATACATTCCTTTTTGTTCA 57.207 29.630 0.00 0.00 0.00 3.18
4896 5981 9.883142 TCCTTTTTGTTCATTTTAATGACAAGT 57.117 25.926 4.70 0.00 44.54 3.16
4909 5994 9.491675 TTTTAATGACAAGTATTTACAGACGGA 57.508 29.630 0.00 0.00 0.00 4.69
4910 5995 8.697846 TTAATGACAAGTATTTACAGACGGAG 57.302 34.615 0.00 0.00 0.00 4.63
4911 5996 5.068234 TGACAAGTATTTACAGACGGAGG 57.932 43.478 0.00 0.00 0.00 4.30
4912 5997 4.081862 TGACAAGTATTTACAGACGGAGGG 60.082 45.833 0.00 0.00 0.00 4.30
4913 5998 4.091549 ACAAGTATTTACAGACGGAGGGA 58.908 43.478 0.00 0.00 0.00 4.20
4914 5999 4.159879 ACAAGTATTTACAGACGGAGGGAG 59.840 45.833 0.00 0.00 0.00 4.30
4915 6000 3.978610 AGTATTTACAGACGGAGGGAGT 58.021 45.455 0.00 0.00 0.00 3.85
4916 6001 5.121380 AGTATTTACAGACGGAGGGAGTA 57.879 43.478 0.00 0.00 0.00 2.59
4917 6002 4.886489 AGTATTTACAGACGGAGGGAGTAC 59.114 45.833 0.00 0.00 0.00 2.73
4918 6003 2.885135 TTACAGACGGAGGGAGTACA 57.115 50.000 0.00 0.00 0.00 2.90
4919 6004 2.414994 TACAGACGGAGGGAGTACAG 57.585 55.000 0.00 0.00 0.00 2.74
4920 6005 0.323542 ACAGACGGAGGGAGTACAGG 60.324 60.000 0.00 0.00 0.00 4.00
4921 6006 1.380112 AGACGGAGGGAGTACAGGC 60.380 63.158 0.00 0.00 0.00 4.85
4922 6007 2.363925 ACGGAGGGAGTACAGGCC 60.364 66.667 0.00 0.00 0.00 5.19
4923 6008 2.363795 CGGAGGGAGTACAGGCCA 60.364 66.667 5.01 0.00 0.00 5.36
4924 6009 1.987855 CGGAGGGAGTACAGGCCAA 60.988 63.158 5.01 0.00 0.00 4.52
4925 6010 1.338136 CGGAGGGAGTACAGGCCAAT 61.338 60.000 5.01 0.00 0.00 3.16
4926 6011 0.470341 GGAGGGAGTACAGGCCAATC 59.530 60.000 5.01 0.00 0.00 2.67
4927 6012 1.204146 GAGGGAGTACAGGCCAATCA 58.796 55.000 5.01 0.00 0.00 2.57
4928 6013 1.559682 GAGGGAGTACAGGCCAATCAA 59.440 52.381 5.01 0.00 0.00 2.57
4929 6014 1.282157 AGGGAGTACAGGCCAATCAAC 59.718 52.381 5.01 0.00 0.00 3.18
4930 6015 1.282157 GGGAGTACAGGCCAATCAACT 59.718 52.381 5.01 0.00 0.00 3.16
4931 6016 2.504175 GGGAGTACAGGCCAATCAACTA 59.496 50.000 5.01 0.00 0.00 2.24
4932 6017 3.054655 GGGAGTACAGGCCAATCAACTAA 60.055 47.826 5.01 0.00 0.00 2.24
4933 6018 4.192317 GGAGTACAGGCCAATCAACTAAG 58.808 47.826 5.01 0.00 0.00 2.18
4934 6019 4.323562 GGAGTACAGGCCAATCAACTAAGT 60.324 45.833 5.01 0.00 0.00 2.24
4935 6020 5.242795 AGTACAGGCCAATCAACTAAGTT 57.757 39.130 5.01 0.00 0.00 2.66
4936 6021 6.368779 AGTACAGGCCAATCAACTAAGTTA 57.631 37.500 5.01 0.00 0.00 2.24
4937 6022 6.958767 AGTACAGGCCAATCAACTAAGTTAT 58.041 36.000 5.01 0.00 0.00 1.89
4951 6036 7.767198 TCAACTAAGTTATGGTTACCATGTAGC 59.233 37.037 25.61 9.74 44.84 3.58
4955 6040 6.500589 AGTTATGGTTACCATGTAGCATCT 57.499 37.500 25.61 7.82 44.84 2.90
4956 6041 6.525629 AGTTATGGTTACCATGTAGCATCTC 58.474 40.000 25.61 6.36 44.84 2.75
5022 6107 9.589111 TCAGATGTATATAAACACGTTTTAGCA 57.411 29.630 0.00 0.00 34.23 3.49
5062 6147 8.827177 TTTCAGTCCGTATGTAATCCATATTC 57.173 34.615 0.00 0.00 38.29 1.75
5147 6237 3.363788 GTACGATTTGTACCGTGCAAG 57.636 47.619 2.19 0.00 46.39 4.01
5153 6243 3.738830 TTTGTACCGTGCAAGTACTCT 57.261 42.857 22.19 0.00 40.61 3.24
5251 6341 2.151307 TAGGGCTGACGAGGGAGTGT 62.151 60.000 0.00 0.00 0.00 3.55
5282 6372 1.744368 CAGCGCTTCACCATCAGCT 60.744 57.895 7.50 0.00 33.52 4.24
5286 6376 1.088340 CGCTTCACCATCAGCTCCAG 61.088 60.000 0.00 0.00 33.52 3.86
5298 6388 3.664495 CTCCAGCAGCACCAACAG 58.336 61.111 0.00 0.00 0.00 3.16
5322 6412 2.202743 CGGCATCACGTCGTGGAT 60.203 61.111 24.33 13.69 38.15 3.41
5356 6446 2.033602 GCCACCACCACCACTACC 59.966 66.667 0.00 0.00 0.00 3.18
5367 6457 3.006728 CACTACCCCGGCCTCCAA 61.007 66.667 0.00 0.00 0.00 3.53
5403 6493 4.287781 TCGACAGCGGCGTTCCAA 62.288 61.111 9.37 0.00 38.28 3.53
5433 6523 3.561120 GACGGACCCCATTGCCACA 62.561 63.158 0.00 0.00 0.00 4.17
5440 6530 0.819582 CCCCATTGCCACACTGATTC 59.180 55.000 0.00 0.00 0.00 2.52
5547 6647 1.686587 CACCAGCATTGATCCATGCAT 59.313 47.619 27.90 13.84 45.59 3.96
5719 6825 4.021981 GTGATCATGGGATGTACATCGAGA 60.022 45.833 25.65 20.05 38.69 4.04
5759 6865 7.283329 AGTAAGAAATCTCTCTCTCTCTCTCC 58.717 42.308 0.00 0.00 0.00 3.71
5769 6875 3.051803 TCTCTCTCTCTCCCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
5771 6877 3.051803 TCTCTCTCTCCCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
5772 6878 3.309296 TCTCTCTCCCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
5773 6879 3.051803 TCTCTCTCCCTCTCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
5774 6880 3.309296 TCTCTCCCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
5775 6881 3.041211 CTCTCCCTCTCTCTCTCTCTCA 58.959 54.545 0.00 0.00 0.00 3.27
5776 6882 2.771943 TCTCCCTCTCTCTCTCTCTCAC 59.228 54.545 0.00 0.00 0.00 3.51
5777 6883 2.505407 CTCCCTCTCTCTCTCTCTCACA 59.495 54.545 0.00 0.00 0.00 3.58
5816 6922 0.961019 TGCTGTTGAACATGGGAAGC 59.039 50.000 0.00 0.00 0.00 3.86
5822 6928 3.270877 GTTGAACATGGGAAGCTCGTAT 58.729 45.455 0.00 0.00 0.00 3.06
5860 6967 1.266989 GCGCACATATTTAGGGAAGCC 59.733 52.381 0.30 0.00 0.00 4.35
5890 6997 4.445453 TGTATCCAGTGCTGCTAGATTTG 58.555 43.478 0.00 0.00 0.00 2.32
5965 7210 9.236006 GGAATATTAGACCGGTACAACTAGATA 57.764 37.037 7.34 6.30 0.00 1.98
6038 7303 0.318360 TGTACGCCACTGTCTCAACG 60.318 55.000 0.00 0.00 0.00 4.10
6218 7615 1.541588 GGGTGAAAGAGCAACACATCC 59.458 52.381 0.00 0.00 36.42 3.51
6492 7894 4.830046 TCTCCCAATGTGTCTAGATAGAGC 59.170 45.833 0.00 0.00 32.01 4.09
6516 7918 3.141398 TGGAAGTTTCATCTGAGTGCAC 58.859 45.455 9.40 9.40 0.00 4.57
6654 8060 1.672356 GTCGGCTGTGGTTGCTCAT 60.672 57.895 0.00 0.00 0.00 2.90
6851 8259 3.120321 TGTCCGAGCAAAGAAGCTAAA 57.880 42.857 0.00 0.00 46.75 1.85
6898 8306 5.755849 ACCTTTGTAAAGCTGGTATATGCT 58.244 37.500 0.00 0.00 41.82 3.79
7013 8421 5.882557 ACTAAGATGGCAAAGTAAGGTGATG 59.117 40.000 0.00 0.00 0.00 3.07
7109 8519 6.017357 GCATGCATGAGAGAGAATCAATGTTA 60.017 38.462 30.64 0.00 37.82 2.41
7110 8520 7.308649 GCATGCATGAGAGAGAATCAATGTTAT 60.309 37.037 30.64 0.00 37.82 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.114952 CAGTTGATACTAGAGTGATACTCAAGA 57.885 37.037 11.17 0.00 39.05 3.02
154 156 2.868964 AGGAGTATGCCCAGGACTTA 57.131 50.000 0.00 0.00 0.00 2.24
349 436 9.038072 CCACCTAGAGAGATACTACATACTCTA 57.962 40.741 0.00 0.00 39.39 2.43
352 439 7.037873 CCTCCACCTAGAGAGATACTACATACT 60.038 44.444 0.00 0.00 35.82 2.12
353 440 7.107542 CCTCCACCTAGAGAGATACTACATAC 58.892 46.154 0.00 0.00 35.82 2.39
354 441 6.793482 ACCTCCACCTAGAGAGATACTACATA 59.207 42.308 0.00 0.00 35.82 2.29
355 442 5.613544 ACCTCCACCTAGAGAGATACTACAT 59.386 44.000 0.00 0.00 35.82 2.29
356 443 4.976442 ACCTCCACCTAGAGAGATACTACA 59.024 45.833 0.00 0.00 35.82 2.74
394 501 7.017651 CCTCCCTATAACTCCACCTATTTCATT 59.982 40.741 0.00 0.00 0.00 2.57
439 546 2.357637 CACACGAAACACCTTTGGACAT 59.642 45.455 0.00 0.00 0.00 3.06
491 598 5.598830 TCGCTTTAACTGAAGGGATAGAGAT 59.401 40.000 0.94 0.00 41.76 2.75
492 599 4.954202 TCGCTTTAACTGAAGGGATAGAGA 59.046 41.667 0.94 0.00 41.76 3.10
493 600 5.263968 TCGCTTTAACTGAAGGGATAGAG 57.736 43.478 0.94 0.00 41.76 2.43
816 931 2.593956 GGAAAGGGAGACACCGGCT 61.594 63.158 0.00 0.00 40.11 5.52
823 938 0.906066 GGTGGAGAGGAAAGGGAGAC 59.094 60.000 0.00 0.00 0.00 3.36
867 1017 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
870 1020 1.541672 GAGGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
933 1083 0.998928 TTGCCTGGCTATCTTCCCAA 59.001 50.000 21.03 0.00 0.00 4.12
1204 1362 8.658609 TGCATACATATACATGATGAATCAACG 58.341 33.333 0.00 0.00 40.69 4.10
1215 1373 6.094464 CACCCAATCCTGCATACATATACATG 59.906 42.308 0.00 0.00 38.21 3.21
1216 1374 6.182627 CACCCAATCCTGCATACATATACAT 58.817 40.000 0.00 0.00 0.00 2.29
1414 1579 8.879427 ACTATAGAAATTAACCTGGCAGTTTT 57.121 30.769 14.43 8.70 0.00 2.43
1450 1616 3.390175 AGCTAGAAGTTAGCCTCCAGA 57.610 47.619 0.00 0.00 41.25 3.86
1655 1824 6.963049 ATACACAATAAACTGACGAGAACC 57.037 37.500 0.00 0.00 0.00 3.62
1737 1925 8.284693 GCATCAAGTATTCAAATGCAACTTTTT 58.715 29.630 0.00 0.00 34.12 1.94
1738 1926 7.359431 CGCATCAAGTATTCAAATGCAACTTTT 60.359 33.333 0.00 0.00 33.61 2.27
1739 1927 6.089820 CGCATCAAGTATTCAAATGCAACTTT 59.910 34.615 0.00 0.00 33.61 2.66
1740 1928 5.574055 CGCATCAAGTATTCAAATGCAACTT 59.426 36.000 0.00 0.00 33.61 2.66
1767 1955 9.888878 GTGATATTTTTCATGTGTATGGAGATG 57.111 33.333 0.00 0.00 34.97 2.90
1791 1981 2.420022 CGCCCTTGAAAATCTACCAGTG 59.580 50.000 0.00 0.00 0.00 3.66
1813 2003 6.369629 TCCTTTTGTTCCAAGATTCCTACAA 58.630 36.000 0.00 0.00 0.00 2.41
2049 2278 6.793492 TTTTGGTTGGACAACTTTGAAAAG 57.207 33.333 14.14 1.22 40.94 2.27
2060 2289 5.630121 AGTCATGTCTATTTTGGTTGGACA 58.370 37.500 0.00 0.00 40.43 4.02
2073 2302 3.889538 CACCCGAGGAATAGTCATGTCTA 59.110 47.826 2.09 2.09 0.00 2.59
2177 2406 0.035439 CGGTGGTGTAAGCCTTGGAT 60.035 55.000 0.00 0.00 0.00 3.41
2423 2652 0.765510 AGTTGGTCTTCTCGGGCTTT 59.234 50.000 0.00 0.00 0.00 3.51
2598 2830 0.814457 CTGTCGACCCTCCTCTTCTG 59.186 60.000 14.12 0.00 0.00 3.02
2602 2834 1.979693 GCACTGTCGACCCTCCTCT 60.980 63.158 14.12 0.00 0.00 3.69
2654 2886 3.047280 GCGGCGTTGACCATGTCA 61.047 61.111 9.37 0.00 41.09 3.58
2689 2921 3.252974 CGAAGCTAAAGTCCTGGATGT 57.747 47.619 0.00 0.00 0.00 3.06
2843 3119 4.694339 AGAGTATGTTAGATTGAACGGCC 58.306 43.478 0.00 0.00 31.59 6.13
2891 3789 2.741145 TGGTTATTTTTGGATCCCCCG 58.259 47.619 9.90 0.00 37.93 5.73
2909 3807 4.096984 GTGCACTTTCCCTTGATATCTTGG 59.903 45.833 10.32 5.99 0.00 3.61
2927 3825 5.007626 TCACTCTAAGTTGTTCAATGTGCAC 59.992 40.000 10.75 10.75 0.00 4.57
3009 3907 5.104374 GGTTGCATGTAGATCCAAATTGTG 58.896 41.667 0.00 0.00 0.00 3.33
3097 4001 0.105039 CCTCGGCACATCCCTCTTAC 59.895 60.000 0.00 0.00 0.00 2.34
3112 4016 1.218316 CTCCCTTTTCCGTCCCTCG 59.782 63.158 0.00 0.00 39.52 4.63
3121 4025 2.158667 TCAACCTCCACACTCCCTTTTC 60.159 50.000 0.00 0.00 0.00 2.29
3216 4124 2.096248 GGGTTGGCATCATCCGTTTAA 58.904 47.619 0.00 0.00 34.38 1.52
3245 4153 1.546923 TCCTAAGTTCCGCGACATCAA 59.453 47.619 8.23 0.00 0.00 2.57
3249 4157 1.066605 GCTATCCTAAGTTCCGCGACA 59.933 52.381 8.23 0.00 0.00 4.35
3317 4226 0.035630 CTCCACCTCCTTGCTCCTTG 60.036 60.000 0.00 0.00 0.00 3.61
3318 4227 0.178891 TCTCCACCTCCTTGCTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
3341 4250 7.066525 TGTTTAAACTAGGCTACAATGTATGGC 59.933 37.037 18.72 1.30 0.00 4.40
3345 4254 9.727859 TTGATGTTTAAACTAGGCTACAATGTA 57.272 29.630 18.72 0.00 0.00 2.29
3349 4258 8.780249 GTCTTTGATGTTTAAACTAGGCTACAA 58.220 33.333 18.72 10.88 0.00 2.41
3355 4264 6.488683 TGTGGGTCTTTGATGTTTAAACTAGG 59.511 38.462 18.72 3.69 0.00 3.02
3375 4284 7.790823 AAACAATGATTTCTTTTCTTGTGGG 57.209 32.000 0.00 0.00 0.00 4.61
3457 4367 4.917415 GGTTTTGATTTTGTCATCCACTCG 59.083 41.667 0.00 0.00 36.54 4.18
3511 4422 1.524355 CGTGATGAATGTCAGATCGGC 59.476 52.381 0.00 0.00 0.00 5.54
3539 4450 3.365220 GTGCTCTTGTGTACTCGACAATC 59.635 47.826 0.00 0.00 40.66 2.67
3686 4608 8.519799 AGAAATCTTCTGAACCACAAACTTTA 57.480 30.769 0.00 0.00 38.91 1.85
3731 4654 3.573538 AGCAACACAAATAAGTCATGCCA 59.426 39.130 0.00 0.00 33.09 4.92
3872 4891 6.350612 GGACTATTAGTGAGGGCTAGCTATTG 60.351 46.154 15.72 0.50 0.00 1.90
3884 4903 5.007823 CGTGTCTACCAGGACTATTAGTGAG 59.992 48.000 0.00 0.00 37.16 3.51
3885 4904 4.880120 CGTGTCTACCAGGACTATTAGTGA 59.120 45.833 0.00 0.00 37.16 3.41
3917 4964 7.663630 TGTAAGGTCGTAATAAAATCGTACG 57.336 36.000 9.53 9.53 41.46 3.67
3929 4976 1.483415 GGCTCCCATGTAAGGTCGTAA 59.517 52.381 0.00 0.00 0.00 3.18
3933 4980 1.473434 CGAAGGCTCCCATGTAAGGTC 60.473 57.143 0.00 0.00 0.00 3.85
3946 4993 1.525535 GGCTGATGCATCGAAGGCT 60.526 57.895 24.87 0.00 41.91 4.58
3952 4999 1.065273 GCTTTGGGCTGATGCATCG 59.935 57.895 21.34 16.36 41.91 3.84
4007 5055 3.784701 ACATACGACACTTGAGGCTAG 57.215 47.619 0.00 0.00 0.00 3.42
4074 5122 5.126384 CAGTTCTGGCTATATAGGTAGGCTC 59.874 48.000 11.72 0.00 44.87 4.70
4094 5142 0.178068 ACCCGATAATGCGAGCAGTT 59.822 50.000 2.72 1.21 0.00 3.16
4096 5144 0.861837 GAACCCGATAATGCGAGCAG 59.138 55.000 3.58 0.00 0.00 4.24
4097 5145 0.874175 CGAACCCGATAATGCGAGCA 60.874 55.000 0.00 0.00 38.22 4.26
4098 5146 0.874607 ACGAACCCGATAATGCGAGC 60.875 55.000 0.00 0.00 39.50 5.03
4112 5163 7.336975 CAAATTGAAATGAAAAGGACACGAAC 58.663 34.615 0.00 0.00 0.00 3.95
4116 5167 7.571798 GCATCCAAATTGAAATGAAAAGGACAC 60.572 37.037 10.93 0.00 0.00 3.67
4169 5251 8.682710 CGATAATAGAAAAGGGGAACATTTCAA 58.317 33.333 0.00 0.00 44.79 2.69
4182 5264 9.245962 ACCTACATTTCGTCGATAATAGAAAAG 57.754 33.333 0.00 0.00 36.39 2.27
4195 5277 7.630924 CATCAAATTCCTACCTACATTTCGTC 58.369 38.462 0.00 0.00 0.00 4.20
4224 5306 3.192422 CACAACCCTCACAGACAAAAACA 59.808 43.478 0.00 0.00 0.00 2.83
4233 5315 1.073199 GACCCCACAACCCTCACAG 59.927 63.158 0.00 0.00 0.00 3.66
4236 5318 1.385347 AGTGACCCCACAACCCTCA 60.385 57.895 0.00 0.00 45.54 3.86
4306 5388 7.013655 CAGAATTTCCCTCACCTTACCATTATG 59.986 40.741 0.00 0.00 0.00 1.90
4474 5556 3.305199 GCGTGTAGAACTGACCTACAACT 60.305 47.826 12.66 0.00 45.38 3.16
4518 5603 5.343249 CCCTAATTAAGCACAGCATTTGAC 58.657 41.667 0.00 0.00 0.00 3.18
4525 5610 2.951642 TGATGCCCTAATTAAGCACAGC 59.048 45.455 11.03 6.01 39.77 4.40
4650 5735 9.396022 CAAATTTAGAAAGTAGGGCAAGAGATA 57.604 33.333 0.00 0.00 0.00 1.98
4651 5736 7.890655 ACAAATTTAGAAAGTAGGGCAAGAGAT 59.109 33.333 0.00 0.00 0.00 2.75
4660 5745 9.678941 GGAAAGTGAACAAATTTAGAAAGTAGG 57.321 33.333 0.00 0.00 0.00 3.18
4781 5866 4.874966 CGGACGGAGGGAGTATATAGTAAG 59.125 50.000 0.00 0.00 0.00 2.34
4782 5867 4.323792 CCGGACGGAGGGAGTATATAGTAA 60.324 50.000 4.40 0.00 37.50 2.24
4783 5868 3.198635 CCGGACGGAGGGAGTATATAGTA 59.801 52.174 4.40 0.00 37.50 1.82
4784 5869 2.026449 CCGGACGGAGGGAGTATATAGT 60.026 54.545 4.40 0.00 37.50 2.12
4785 5870 2.238144 TCCGGACGGAGGGAGTATATAG 59.762 54.545 9.76 0.00 39.76 1.31
4786 5871 2.269023 TCCGGACGGAGGGAGTATATA 58.731 52.381 9.76 0.00 39.76 0.86
4787 5872 1.070604 TCCGGACGGAGGGAGTATAT 58.929 55.000 9.76 0.00 39.76 0.86
4788 5873 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
4789 5874 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
4790 5875 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
4791 5876 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
4792 5877 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4793 5878 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4794 5879 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4795 5880 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4796 5881 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4797 5882 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4798 5883 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4799 5884 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4800 5885 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4801 5886 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
4802 5887 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
4803 5888 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
4810 5895 9.492973 CCCTTTTTATTCATTTTGATGACAAGT 57.507 29.630 0.00 0.00 37.32 3.16
4811 5896 9.709495 TCCCTTTTTATTCATTTTGATGACAAG 57.291 29.630 0.00 0.00 37.32 3.16
4813 5898 9.656040 CATCCCTTTTTATTCATTTTGATGACA 57.344 29.630 0.00 0.00 0.00 3.58
4814 5899 9.657419 ACATCCCTTTTTATTCATTTTGATGAC 57.343 29.630 0.00 0.00 32.39 3.06
4832 5917 9.830186 ACTACAATACATCTAGATACATCCCTT 57.170 33.333 4.54 0.00 0.00 3.95
4833 5918 9.830186 AACTACAATACATCTAGATACATCCCT 57.170 33.333 4.54 0.00 0.00 4.20
4856 5941 9.793259 TGAACAAAAAGGAATGTATCTAGAACT 57.207 29.630 0.00 0.00 0.00 3.01
4870 5955 9.883142 ACTTGTCATTAAAATGAACAAAAAGGA 57.117 25.926 6.95 0.00 46.13 3.36
4883 5968 9.491675 TCCGTCTGTAAATACTTGTCATTAAAA 57.508 29.630 0.00 0.00 0.00 1.52
4884 5969 9.146984 CTCCGTCTGTAAATACTTGTCATTAAA 57.853 33.333 0.00 0.00 0.00 1.52
4885 5970 7.762615 CCTCCGTCTGTAAATACTTGTCATTAA 59.237 37.037 0.00 0.00 0.00 1.40
4886 5971 7.262772 CCTCCGTCTGTAAATACTTGTCATTA 58.737 38.462 0.00 0.00 0.00 1.90
4887 5972 6.106673 CCTCCGTCTGTAAATACTTGTCATT 58.893 40.000 0.00 0.00 0.00 2.57
4888 5973 5.395324 CCCTCCGTCTGTAAATACTTGTCAT 60.395 44.000 0.00 0.00 0.00 3.06
4889 5974 4.081862 CCCTCCGTCTGTAAATACTTGTCA 60.082 45.833 0.00 0.00 0.00 3.58
4890 5975 4.159135 TCCCTCCGTCTGTAAATACTTGTC 59.841 45.833 0.00 0.00 0.00 3.18
4891 5976 4.091549 TCCCTCCGTCTGTAAATACTTGT 58.908 43.478 0.00 0.00 0.00 3.16
4892 5977 4.159879 ACTCCCTCCGTCTGTAAATACTTG 59.840 45.833 0.00 0.00 0.00 3.16
4893 5978 4.351127 ACTCCCTCCGTCTGTAAATACTT 58.649 43.478 0.00 0.00 0.00 2.24
4894 5979 3.978610 ACTCCCTCCGTCTGTAAATACT 58.021 45.455 0.00 0.00 0.00 2.12
4895 5980 4.641989 TGTACTCCCTCCGTCTGTAAATAC 59.358 45.833 0.00 0.00 0.00 1.89
4896 5981 4.858850 TGTACTCCCTCCGTCTGTAAATA 58.141 43.478 0.00 0.00 0.00 1.40
4897 5982 3.700038 CTGTACTCCCTCCGTCTGTAAAT 59.300 47.826 0.00 0.00 0.00 1.40
4898 5983 3.087031 CTGTACTCCCTCCGTCTGTAAA 58.913 50.000 0.00 0.00 0.00 2.01
4899 5984 2.619849 CCTGTACTCCCTCCGTCTGTAA 60.620 54.545 0.00 0.00 0.00 2.41
4900 5985 1.064906 CCTGTACTCCCTCCGTCTGTA 60.065 57.143 0.00 0.00 0.00 2.74
4901 5986 0.323542 CCTGTACTCCCTCCGTCTGT 60.324 60.000 0.00 0.00 0.00 3.41
4902 5987 1.668101 GCCTGTACTCCCTCCGTCTG 61.668 65.000 0.00 0.00 0.00 3.51
4903 5988 1.380112 GCCTGTACTCCCTCCGTCT 60.380 63.158 0.00 0.00 0.00 4.18
4904 5989 2.424733 GGCCTGTACTCCCTCCGTC 61.425 68.421 0.00 0.00 0.00 4.79
4905 5990 2.363925 GGCCTGTACTCCCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
4906 5991 1.338136 ATTGGCCTGTACTCCCTCCG 61.338 60.000 3.32 0.00 0.00 4.63
4907 5992 0.470341 GATTGGCCTGTACTCCCTCC 59.530 60.000 3.32 0.00 0.00 4.30
4908 5993 1.204146 TGATTGGCCTGTACTCCCTC 58.796 55.000 3.32 0.00 0.00 4.30
4909 5994 1.282157 GTTGATTGGCCTGTACTCCCT 59.718 52.381 3.32 0.00 0.00 4.20
4910 5995 1.282157 AGTTGATTGGCCTGTACTCCC 59.718 52.381 3.32 0.00 0.00 4.30
4911 5996 2.789409 AGTTGATTGGCCTGTACTCC 57.211 50.000 3.32 0.00 0.00 3.85
4912 5997 4.833390 ACTTAGTTGATTGGCCTGTACTC 58.167 43.478 3.32 0.00 0.00 2.59
4913 5998 4.910458 ACTTAGTTGATTGGCCTGTACT 57.090 40.909 3.32 3.09 0.00 2.73
4914 5999 6.038271 CCATAACTTAGTTGATTGGCCTGTAC 59.962 42.308 8.00 0.00 0.00 2.90
4915 6000 6.119536 CCATAACTTAGTTGATTGGCCTGTA 58.880 40.000 8.00 0.00 0.00 2.74
4916 6001 4.949856 CCATAACTTAGTTGATTGGCCTGT 59.050 41.667 8.00 0.00 0.00 4.00
4917 6002 4.949856 ACCATAACTTAGTTGATTGGCCTG 59.050 41.667 17.50 0.00 30.20 4.85
4918 6003 5.193099 ACCATAACTTAGTTGATTGGCCT 57.807 39.130 17.50 0.00 30.20 5.19
4919 6004 5.914898 AACCATAACTTAGTTGATTGGCC 57.085 39.130 17.50 0.00 30.20 5.36
4920 6005 6.376018 TGGTAACCATAACTTAGTTGATTGGC 59.624 38.462 17.50 7.31 30.20 4.52
4921 6006 7.931578 TGGTAACCATAACTTAGTTGATTGG 57.068 36.000 8.00 13.40 32.00 3.16
4922 6007 8.956426 ACATGGTAACCATAACTTAGTTGATTG 58.044 33.333 8.00 3.13 43.15 2.67
4924 6009 9.832445 CTACATGGTAACCATAACTTAGTTGAT 57.168 33.333 8.00 0.00 43.15 2.57
4925 6010 7.767198 GCTACATGGTAACCATAACTTAGTTGA 59.233 37.037 8.00 0.00 43.15 3.18
4926 6011 7.551262 TGCTACATGGTAACCATAACTTAGTTG 59.449 37.037 8.00 0.00 43.15 3.16
4927 6012 7.626390 TGCTACATGGTAACCATAACTTAGTT 58.374 34.615 2.32 2.32 43.15 2.24
4928 6013 7.190335 TGCTACATGGTAACCATAACTTAGT 57.810 36.000 0.00 0.00 43.15 2.24
4929 6014 8.150945 AGATGCTACATGGTAACCATAACTTAG 58.849 37.037 0.00 0.00 43.15 2.18
4930 6015 8.029782 AGATGCTACATGGTAACCATAACTTA 57.970 34.615 0.00 0.00 43.15 2.24
4931 6016 6.900194 AGATGCTACATGGTAACCATAACTT 58.100 36.000 0.00 0.00 43.15 2.66
4932 6017 6.327626 AGAGATGCTACATGGTAACCATAACT 59.672 38.462 0.00 0.00 43.15 2.24
4933 6018 6.525629 AGAGATGCTACATGGTAACCATAAC 58.474 40.000 0.00 0.00 43.15 1.89
4934 6019 6.239600 GGAGAGATGCTACATGGTAACCATAA 60.240 42.308 0.00 0.00 43.15 1.90
4935 6020 5.246203 GGAGAGATGCTACATGGTAACCATA 59.754 44.000 0.00 0.00 43.15 2.74
4936 6021 4.040952 GGAGAGATGCTACATGGTAACCAT 59.959 45.833 0.00 0.00 46.37 3.55
4937 6022 3.388024 GGAGAGATGCTACATGGTAACCA 59.612 47.826 0.00 0.00 38.19 3.67
4951 6036 8.715998 CATCTTATAATTTGGAACGGAGAGATG 58.284 37.037 0.00 0.00 32.54 2.90
4955 6040 8.265055 AGAACATCTTATAATTTGGAACGGAGA 58.735 33.333 0.00 0.00 0.00 3.71
4956 6041 8.438676 AGAACATCTTATAATTTGGAACGGAG 57.561 34.615 0.00 0.00 0.00 4.63
4991 6076 7.869016 ACGTGTTTATATACATCTGATTCGG 57.131 36.000 0.00 0.00 0.00 4.30
4996 6081 9.589111 TGCTAAAACGTGTTTATATACATCTGA 57.411 29.630 0.00 0.00 31.63 3.27
5022 6107 6.151691 CGGACTGAAATGAATGAACAAACAT 58.848 36.000 0.00 0.00 0.00 2.71
5180 6270 0.821517 TCCCACCTGCGTGTATACAG 59.178 55.000 5.62 2.03 38.41 2.74
5282 6372 2.595463 GCTGTTGGTGCTGCTGGA 60.595 61.111 0.00 0.00 0.00 3.86
5295 6385 4.710167 TGATGCCGCTGCTGCTGT 62.710 61.111 16.81 5.98 38.71 4.40
5306 6396 1.148157 CTCATCCACGACGTGATGCC 61.148 60.000 28.83 0.00 35.23 4.40
5322 6412 4.794439 CGCCGGTGATCGTGCTCA 62.794 66.667 10.20 0.00 37.11 4.26
5403 6493 1.288127 GTCCGTCGGTGTGCTTACT 59.712 57.895 11.88 0.00 0.00 2.24
5433 6523 1.553690 CCTGGTGGACCGGAATCAGT 61.554 60.000 9.46 0.00 45.36 3.41
5589 6693 6.322456 TGTCACAGATTAATCAAACCAAACCA 59.678 34.615 17.56 0.32 0.00 3.67
5719 6825 3.870559 TCTTACTCCTCCTTTGGACCTT 58.129 45.455 0.00 0.00 31.94 3.50
5759 6865 3.009723 GTGTGTGAGAGAGAGAGAGAGG 58.990 54.545 0.00 0.00 0.00 3.69
5769 6875 2.495669 TGTGAAGTGTGTGTGTGAGAGA 59.504 45.455 0.00 0.00 0.00 3.10
5771 6877 3.132824 AGATGTGAAGTGTGTGTGTGAGA 59.867 43.478 0.00 0.00 0.00 3.27
5772 6878 3.461061 AGATGTGAAGTGTGTGTGTGAG 58.539 45.455 0.00 0.00 0.00 3.51
5773 6879 3.541996 AGATGTGAAGTGTGTGTGTGA 57.458 42.857 0.00 0.00 0.00 3.58
5774 6880 4.621068 AAAGATGTGAAGTGTGTGTGTG 57.379 40.909 0.00 0.00 0.00 3.82
5775 6881 5.401550 CAAAAAGATGTGAAGTGTGTGTGT 58.598 37.500 0.00 0.00 0.00 3.72
5776 6882 4.266029 GCAAAAAGATGTGAAGTGTGTGTG 59.734 41.667 0.00 0.00 0.00 3.82
5777 6883 4.158394 AGCAAAAAGATGTGAAGTGTGTGT 59.842 37.500 0.00 0.00 0.00 3.72
5816 6922 7.431376 CGCCATTATTGGTACTATACATACGAG 59.569 40.741 5.58 0.00 45.57 4.18
5822 6928 4.992319 GTGCGCCATTATTGGTACTATACA 59.008 41.667 4.18 0.00 45.57 2.29
5872 6979 3.008375 AGAACAAATCTAGCAGCACTGGA 59.992 43.478 0.00 0.00 40.59 3.86
5890 6997 3.846383 GCACGACAAGCAAGAAGAAGAAC 60.846 47.826 0.00 0.00 0.00 3.01
5947 7054 6.786967 ACATTTATCTAGTTGTACCGGTCT 57.213 37.500 12.40 4.12 0.00 3.85
6061 7374 7.580302 GCAGAGATAAGGGAGTTGCATGATATA 60.580 40.741 0.00 0.00 0.00 0.86
6068 7381 1.908619 TGCAGAGATAAGGGAGTTGCA 59.091 47.619 0.00 0.00 37.70 4.08
6070 7383 3.686726 GTGTTGCAGAGATAAGGGAGTTG 59.313 47.826 0.00 0.00 0.00 3.16
6437 7839 3.502123 AATCTAGAGAGAGAGACGGGG 57.498 52.381 0.00 0.00 34.35 5.73
6439 7841 5.617252 AGGTAAATCTAGAGAGAGAGACGG 58.383 45.833 0.00 0.00 34.35 4.79
6440 7842 7.497909 AGAAAGGTAAATCTAGAGAGAGAGACG 59.502 40.741 0.00 0.00 34.35 4.18
6441 7843 8.747538 AGAAAGGTAAATCTAGAGAGAGAGAC 57.252 38.462 0.00 0.00 34.35 3.36
6442 7844 8.778059 AGAGAAAGGTAAATCTAGAGAGAGAGA 58.222 37.037 0.00 0.00 34.35 3.10
6446 7848 9.403583 GAGAAGAGAAAGGTAAATCTAGAGAGA 57.596 37.037 0.00 0.00 35.71 3.10
6492 7894 3.063180 GCACTCAGATGAAACTTCCATCG 59.937 47.826 0.00 0.00 43.73 3.84
6678 8084 4.755411 AGACCACGATAAACGATGATTGT 58.245 39.130 0.00 0.00 45.77 2.71
6755 8163 8.027771 AGCAATAGAATCAGAAAGCAAGAAAAG 58.972 33.333 0.00 0.00 0.00 2.27
6829 8237 4.465632 TTAGCTTCTTTGCTCGGACATA 57.534 40.909 0.00 0.00 42.97 2.29
6835 8243 4.622740 CCCAAATTTTAGCTTCTTTGCTCG 59.377 41.667 0.00 0.00 42.97 5.03
6851 8259 8.321353 GGTATCATTTCCTTCTTTTCCCAAATT 58.679 33.333 0.00 0.00 0.00 1.82
6898 8306 5.867903 AACAAATGGACCAATTCAACAGA 57.132 34.783 0.00 0.00 0.00 3.41
7110 8520 9.952030 TGTGACAGTATAACAAAAGAATATGGA 57.048 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.