Multiple sequence alignment - TraesCS4A01G016800

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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 TraesCS4A01G016800 chr4A 100.000 5368 0 0 1 5368 11359658 11365025 0.000000e+00 9913
1 TraesCS4A01G016800 chr4A 88.079 864 57 20 1 835 11326334 11327180 0.000000e+00 983
2 TraesCS4A01G016800 chr4B 94.852 2331 78 22 2072 4387 570738415 570736112 0.000000e+00 3602
3 TraesCS4A01G016800 chr4B 86.147 1783 128 54 1 1721 570741435 570739710 0.000000e+00 1814
4 TraesCS4A01G016800 chr4B 94.237 642 23 6 4430 5065 570736031 570735398 0.000000e+00 968
5 TraesCS4A01G016800 chr4B 92.135 267 20 1 5103 5368 570735390 570735124 5.080000e-100 375
6 TraesCS4A01G016800 chr4D 95.333 1607 58 10 2074 3666 456496387 456494784 0.000000e+00 2536
7 TraesCS4A01G016800 chr4D 86.551 2134 163 54 1 2074 456498506 456496437 0.000000e+00 2237
8 TraesCS4A01G016800 chr4D 94.356 939 43 6 4430 5362 456494027 456493093 0.000000e+00 1432
9 TraesCS4A01G016800 chr4D 96.215 687 26 0 3701 4387 456494797 456494111 0.000000e+00 1125


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 TraesCS4A01G016800 chr4A 11359658 11365025 5367 False 9913.00 9913 100.00000 1 5368 1 chr4A.!!$F2 5367
1 TraesCS4A01G016800 chr4A 11326334 11327180 846 False 983.00 983 88.07900 1 835 1 chr4A.!!$F1 834
2 TraesCS4A01G016800 chr4B 570735124 570741435 6311 True 1689.75 3602 91.84275 1 5368 4 chr4B.!!$R1 5367
3 TraesCS4A01G016800 chr4D 456493093 456498506 5413 True 1832.50 2536 93.11375 1 5362 4 chr4D.!!$R1 5361

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
288 289 0.107268 GGGTACACGTTGTGGAGGTT 59.893 55.000 1.64 0.0 37.94 3.50 F
1256 1316 0.038159 CAGTTGACCCGACTGACTCC 60.038 60.000 8.30 0.0 45.84 3.85 F
1880 2044 0.532573 ACTGAGAGGCGTACCATGTG 59.467 55.000 0.00 0.0 39.06 3.21 F
1983 2148 0.811616 GGTGCACCTTCGCCTCTATG 60.812 60.000 29.12 0.0 33.93 2.23 F
3213 4283 1.543802 GCAGCTCCAGAGTATATCGCT 59.456 52.381 0.00 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2023 0.532573 ACACATGGTACGCCTCTCAG 59.467 55.000 0.00 0.00 35.27 3.35 R
3126 4196 1.600916 AGTTGGACCAGCTTTCGCC 60.601 57.895 4.77 0.00 36.60 5.54 R
3298 4368 0.036010 AGAGCGAAGACCCAACATGG 60.036 55.000 0.00 0.00 37.25 3.66 R
3299 4369 1.081892 CAGAGCGAAGACCCAACATG 58.918 55.000 0.00 0.00 0.00 3.21 R
5084 6257 0.243636 GGGCATTGTACAACCAGTGC 59.756 55.000 19.14 19.14 44.58 4.40 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
156 157 2.498167 CCTTGTTCTTCCACTGACAGG 58.502 52.381 7.51 0.00 0.00 4.00
188 189 1.449601 GAGAAGGGCGGCGATCAAA 60.450 57.895 12.98 0.00 0.00 2.69
190 191 3.095898 GAAGGGCGGCGATCAAACG 62.096 63.158 12.98 0.00 0.00 3.60
191 192 3.599285 AAGGGCGGCGATCAAACGA 62.599 57.895 12.98 0.00 35.09 3.85
205 206 0.108615 AAACGACAGAGGAGATGCGG 60.109 55.000 0.00 0.00 0.00 5.69
228 229 3.181458 CGGCTAAGGAAATAGGTAAGGCA 60.181 47.826 0.00 0.00 0.00 4.75
243 244 1.889545 AGGCAGCACAGAGAAAGAAC 58.110 50.000 0.00 0.00 0.00 3.01
281 282 3.128852 TGCTTAATGGGTACACGTTGT 57.871 42.857 13.00 0.00 0.00 3.32
285 286 2.178912 AATGGGTACACGTTGTGGAG 57.821 50.000 0.60 0.00 37.94 3.86
288 289 0.107268 GGGTACACGTTGTGGAGGTT 59.893 55.000 1.64 0.00 37.94 3.50
318 347 8.819643 ACACTAGCAAGAGTACTTAGAAAAAG 57.180 34.615 0.00 0.00 34.70 2.27
375 409 5.125097 ACATTGCAAAACAAATCCAAAAGCA 59.875 32.000 1.71 0.00 42.86 3.91
376 410 4.879104 TGCAAAACAAATCCAAAAGCAG 57.121 36.364 0.00 0.00 0.00 4.24
388 422 2.602878 CAAAAGCAGAGCGCATCAAAT 58.397 42.857 11.47 0.00 46.13 2.32
405 439 4.438148 TCAAATTCGATTATGTGAGGCGA 58.562 39.130 0.00 0.00 0.00 5.54
427 461 0.462789 AAACCAACGGAGACTGACGT 59.537 50.000 0.00 0.00 46.48 4.34
454 488 3.704231 ATCCACCAGCCATGCGACC 62.704 63.158 0.00 0.00 0.00 4.79
456 490 2.438975 CACCAGCCATGCGACCAT 60.439 61.111 0.00 0.00 0.00 3.55
467 501 3.270027 CATGCGACCATGGTTTCTTCTA 58.730 45.455 20.85 2.20 44.07 2.10
488 522 2.125912 GGCTCGTGTGCGACTCAT 60.126 61.111 0.00 0.00 42.81 2.90
853 897 0.541863 AAGCCCCCTGTACAATCTCG 59.458 55.000 0.00 0.00 0.00 4.04
902 956 1.821061 CGTCTTCTCTGCACAGGGGT 61.821 60.000 0.00 0.00 0.00 4.95
909 963 2.038557 TCTCTGCACAGGGGTTAAAGAC 59.961 50.000 0.00 0.00 0.00 3.01
973 1027 2.352814 CCACCAACGTGTAGAAGAGAGG 60.353 54.545 0.00 0.00 38.41 3.69
998 1052 2.670148 GGCGGAAGATCCCACCACT 61.670 63.158 0.00 0.00 31.38 4.00
1079 1133 1.224965 CGACCTACTACTACCTCCGC 58.775 60.000 0.00 0.00 0.00 5.54
1083 1137 0.587285 CTACTACTACCTCCGCTGCG 59.413 60.000 16.34 16.34 0.00 5.18
1110 1164 1.001503 CAGCTCCTCCTCCCACTCT 59.998 63.158 0.00 0.00 0.00 3.24
1111 1165 1.001503 AGCTCCTCCTCCCACTCTG 59.998 63.158 0.00 0.00 0.00 3.35
1112 1166 2.730524 GCTCCTCCTCCCACTCTGC 61.731 68.421 0.00 0.00 0.00 4.26
1114 1168 3.465403 CCTCCTCCCACTCTGCCG 61.465 72.222 0.00 0.00 0.00 5.69
1201 1261 4.323477 CCCCGTGCGGTTCTTGGA 62.323 66.667 9.90 0.00 0.00 3.53
1203 1263 2.742372 CCGTGCGGTTCTTGGAGG 60.742 66.667 1.93 0.00 0.00 4.30
1209 1269 4.699522 GGTTCTTGGAGGCGGCGT 62.700 66.667 9.37 0.00 0.00 5.68
1256 1316 0.038159 CAGTTGACCCGACTGACTCC 60.038 60.000 8.30 0.00 45.84 3.85
1480 1550 2.429971 CTGCTCAGCTCAGTTATCCTCA 59.570 50.000 0.00 0.00 0.00 3.86
1504 1574 1.456518 TGCTCCTCCTGATCCCTCG 60.457 63.158 0.00 0.00 0.00 4.63
1512 1582 4.467084 TGATCCCTCGCGTTGCCC 62.467 66.667 5.77 0.00 0.00 5.36
1547 1621 0.676782 CTTTGCTGACTTACCCGGGG 60.677 60.000 27.92 12.73 0.00 5.73
1604 1678 4.581309 TCAGGAAAGGAAGCTCATTCAT 57.419 40.909 0.00 0.00 39.91 2.57
1605 1679 4.521146 TCAGGAAAGGAAGCTCATTCATC 58.479 43.478 0.00 0.00 39.91 2.92
1606 1680 3.631227 CAGGAAAGGAAGCTCATTCATCC 59.369 47.826 0.00 0.00 39.91 3.51
1607 1681 3.526841 AGGAAAGGAAGCTCATTCATCCT 59.473 43.478 0.00 0.00 44.08 3.24
1608 1682 3.882288 GGAAAGGAAGCTCATTCATCCTC 59.118 47.826 2.86 0.00 41.39 3.71
1609 1683 4.385088 GGAAAGGAAGCTCATTCATCCTCT 60.385 45.833 2.86 0.00 41.39 3.69
1625 1699 0.979665 CTCTTCCTGTCAGCTGGGAA 59.020 55.000 18.40 18.40 37.53 3.97
1721 1795 4.833380 TGTGAGTGCCTCTCTTACTACTTT 59.167 41.667 7.37 0.00 43.13 2.66
1722 1796 5.304614 TGTGAGTGCCTCTCTTACTACTTTT 59.695 40.000 7.37 0.00 43.13 2.27
1723 1797 6.492429 TGTGAGTGCCTCTCTTACTACTTTTA 59.508 38.462 7.37 0.00 43.13 1.52
1727 1801 4.468868 TGCCTCTCTTACTACTTTTACCCC 59.531 45.833 0.00 0.00 0.00 4.95
1728 1802 4.715792 GCCTCTCTTACTACTTTTACCCCT 59.284 45.833 0.00 0.00 0.00 4.79
1741 1902 9.908152 CTACTTTTACCCCTATTTTTCTTTGTG 57.092 33.333 0.00 0.00 0.00 3.33
1743 1904 8.418662 ACTTTTACCCCTATTTTTCTTTGTGTC 58.581 33.333 0.00 0.00 0.00 3.67
1754 1915 7.985634 TTTTTCTTTGTGTCTATTTGTCAGC 57.014 32.000 0.00 0.00 0.00 4.26
1758 1919 6.291377 TCTTTGTGTCTATTTGTCAGCTTCT 58.709 36.000 0.00 0.00 0.00 2.85
1759 1920 7.441836 TCTTTGTGTCTATTTGTCAGCTTCTA 58.558 34.615 0.00 0.00 0.00 2.10
1760 1921 7.600375 TCTTTGTGTCTATTTGTCAGCTTCTAG 59.400 37.037 0.00 0.00 0.00 2.43
1774 1935 2.159028 GCTTCTAGTACTTGCCTCCTGG 60.159 54.545 0.00 0.00 0.00 4.45
1825 1986 4.379082 GGCTGTTTTGGTTATTCGTACTGG 60.379 45.833 0.00 0.00 0.00 4.00
1826 1987 4.214758 GCTGTTTTGGTTATTCGTACTGGT 59.785 41.667 0.00 0.00 0.00 4.00
1827 1988 5.676532 TGTTTTGGTTATTCGTACTGGTG 57.323 39.130 0.00 0.00 0.00 4.17
1828 1989 4.515944 TGTTTTGGTTATTCGTACTGGTGG 59.484 41.667 0.00 0.00 0.00 4.61
1829 1990 4.354893 TTTGGTTATTCGTACTGGTGGT 57.645 40.909 0.00 0.00 0.00 4.16
1830 1991 5.480642 TTTGGTTATTCGTACTGGTGGTA 57.519 39.130 0.00 0.00 0.00 3.25
1862 2023 5.415221 TCTTGGATTTGGTTTGTGTTGAAC 58.585 37.500 0.00 0.00 0.00 3.18
1880 2044 0.532573 ACTGAGAGGCGTACCATGTG 59.467 55.000 0.00 0.00 39.06 3.21
1899 2064 3.260380 TGTGTGGGGCAAAATTTGGATAG 59.740 43.478 7.89 0.00 0.00 2.08
1906 2071 4.333372 GGGCAAAATTTGGATAGCATGTTG 59.667 41.667 7.89 0.00 0.00 3.33
1907 2072 4.937015 GGCAAAATTTGGATAGCATGTTGT 59.063 37.500 7.89 0.00 0.00 3.32
1908 2073 5.412286 GGCAAAATTTGGATAGCATGTTGTT 59.588 36.000 7.89 0.00 0.00 2.83
1926 2091 7.132694 TGTTGTTATGCATCTTACACTTCTG 57.867 36.000 0.19 0.00 0.00 3.02
1931 2096 4.990543 TGCATCTTACACTTCTGTTTCG 57.009 40.909 0.00 0.00 0.00 3.46
1934 2099 4.377431 GCATCTTACACTTCTGTTTCGGTG 60.377 45.833 0.00 0.00 35.99 4.94
1958 2123 8.554528 GTGACTAGTTTTTACCTACTTTGTTCC 58.445 37.037 0.00 0.00 0.00 3.62
1959 2124 8.488668 TGACTAGTTTTTACCTACTTTGTTCCT 58.511 33.333 0.00 0.00 0.00 3.36
1983 2148 0.811616 GGTGCACCTTCGCCTCTATG 60.812 60.000 29.12 0.00 33.93 2.23
1997 3016 3.053917 GCCTCTATGTTTGTCCCCCTTTA 60.054 47.826 0.00 0.00 0.00 1.85
2016 3035 8.507524 CCCTTTATTATTAGGGTAAGCATAGC 57.492 38.462 0.00 0.00 45.12 2.97
2017 3036 8.107095 CCCTTTATTATTAGGGTAAGCATAGCA 58.893 37.037 0.16 0.00 45.12 3.49
2018 3037 9.686683 CCTTTATTATTAGGGTAAGCATAGCAT 57.313 33.333 0.16 0.00 0.00 3.79
2043 3062 4.848000 TGCCATGGTGCATGAACT 57.152 50.000 14.67 0.00 43.81 3.01
2044 3063 2.268999 TGCCATGGTGCATGAACTG 58.731 52.632 14.67 0.00 43.81 3.16
2051 3070 2.161855 TGGTGCATGAACTGGAACATC 58.838 47.619 3.21 0.00 38.08 3.06
2121 3190 7.019418 CAGTTCACATGTTCAGTATCATTGTG 58.981 38.462 0.00 0.00 0.00 3.33
2136 3205 5.694231 TCATTGTGAACCTGAAGATGTTG 57.306 39.130 0.00 0.00 0.00 3.33
2179 3248 5.418676 ACACACATTTCCTTTGTTTCTTGG 58.581 37.500 0.00 0.00 0.00 3.61
2184 3253 3.390175 TTCCTTTGTTTCTTGGTGGGA 57.610 42.857 0.00 0.00 0.00 4.37
2566 3635 4.322574 GGTAGGTTCAAGACTCCTTACCAC 60.323 50.000 0.00 0.00 34.78 4.16
2585 3654 9.163899 CTTACCACTAATTTTCTACTTTCCTCC 57.836 37.037 0.00 0.00 0.00 4.30
2596 3666 4.715297 TCTACTTTCCTCCGGCTATTTTCT 59.285 41.667 0.00 0.00 0.00 2.52
2600 3670 3.261981 TCCTCCGGCTATTTTCTTGTC 57.738 47.619 0.00 0.00 0.00 3.18
2612 3682 6.183360 GCTATTTTCTTGTCTCCTGATGGTTC 60.183 42.308 0.00 0.00 34.23 3.62
2701 3771 3.609853 TGGTTATTGCTCAGATGGTGAC 58.390 45.455 0.00 0.00 0.00 3.67
2887 3957 5.487488 TCTTTTAGGAGGTGCTGATCCTTTA 59.513 40.000 9.05 0.00 43.62 1.85
2971 4041 9.669353 CATCATGCTGAAAACCAAGTTATATAC 57.331 33.333 0.00 0.00 0.00 1.47
3023 4093 6.761242 TCTTGACTCGGTATGGTTGAAATATG 59.239 38.462 0.00 0.00 0.00 1.78
3051 4121 3.935828 GACTCTGATTACAAGCCAACCTC 59.064 47.826 0.00 0.00 0.00 3.85
3168 4238 4.142469 GGGGATAAAACTCATGTTTCCACG 60.142 45.833 0.00 0.00 44.70 4.94
3213 4283 1.543802 GCAGCTCCAGAGTATATCGCT 59.456 52.381 0.00 0.00 0.00 4.93
3297 4367 7.559590 TTTGTTTCATGTTACAAAAATGGGG 57.440 32.000 18.86 0.00 40.26 4.96
3298 4368 5.059833 TGTTTCATGTTACAAAAATGGGGC 58.940 37.500 0.00 0.00 0.00 5.80
3299 4369 3.971245 TCATGTTACAAAAATGGGGCC 57.029 42.857 0.00 0.00 0.00 5.80
3313 4397 2.046285 GGGCCATGTTGGGTCTTCG 61.046 63.158 4.39 0.00 38.19 3.79
3368 4452 3.189606 TCCGGCCTAAATCATCCCATAT 58.810 45.455 0.00 0.00 0.00 1.78
3372 4456 5.072329 CCGGCCTAAATCATCCCATATCTAT 59.928 44.000 0.00 0.00 0.00 1.98
3373 4457 5.994054 CGGCCTAAATCATCCCATATCTATG 59.006 44.000 0.00 0.00 0.00 2.23
3374 4458 6.183361 CGGCCTAAATCATCCCATATCTATGA 60.183 42.308 0.00 0.00 35.75 2.15
3375 4459 6.995091 GGCCTAAATCATCCCATATCTATGAC 59.005 42.308 0.00 0.00 35.75 3.06
3376 4460 7.365921 GGCCTAAATCATCCCATATCTATGACA 60.366 40.741 0.00 0.00 35.75 3.58
3377 4461 7.714377 GCCTAAATCATCCCATATCTATGACAG 59.286 40.741 0.00 0.00 35.75 3.51
3378 4462 8.985922 CCTAAATCATCCCATATCTATGACAGA 58.014 37.037 0.00 0.00 35.75 3.41
3381 4465 9.902684 AAATCATCCCATATCTATGACAGAATC 57.097 33.333 0.00 0.00 36.67 2.52
3382 4466 8.619683 ATCATCCCATATCTATGACAGAATCA 57.380 34.615 0.00 0.00 43.13 2.57
3444 4539 4.220693 TGGTGTTCTCCAATCATGTAGG 57.779 45.455 0.00 0.00 34.24 3.18
3531 4626 5.021458 ACATTTCCTGATCCAGCAATTTCT 58.979 37.500 0.00 0.00 0.00 2.52
3537 4632 5.305128 TCCTGATCCAGCAATTTCTTTGTTT 59.695 36.000 0.00 0.00 37.65 2.83
3589 4684 2.876581 GGAAATGGTCCACTCCACTTT 58.123 47.619 14.58 1.86 46.97 2.66
3590 4685 4.028993 GGAAATGGTCCACTCCACTTTA 57.971 45.455 14.58 0.00 46.97 1.85
3665 4760 7.495135 TGGCAGTACATATGAACATGTATTG 57.505 36.000 10.38 12.00 45.11 1.90
3668 4763 9.435688 GGCAGTACATATGAACATGTATTGATA 57.564 33.333 17.66 0.00 45.13 2.15
3678 4773 9.830294 ATGAACATGTATTGATAATATTGTGCG 57.170 29.630 0.00 0.00 0.00 5.34
3744 4839 6.122277 TCTGGATAAACCCATTCTCATGTTC 58.878 40.000 0.00 0.00 38.00 3.18
3793 4888 0.969894 AGGCAGACGTCTACAGCTTT 59.030 50.000 19.57 7.78 0.00 3.51
3812 4907 2.564721 GGGGTGGTGTTGCTTGAGC 61.565 63.158 0.00 0.00 42.50 4.26
4102 5197 1.596934 GCAGGTTGACATCCGGAGA 59.403 57.895 11.34 0.00 0.00 3.71
4269 5364 1.241315 ACGGCTGTACATTTGGTGGC 61.241 55.000 0.00 0.00 0.00 5.01
4282 5377 0.036164 TGGTGGCGAGCTGTGTAATT 59.964 50.000 0.00 0.00 0.00 1.40
4319 5414 2.159324 GCTTCTTGCTCATTTGTAGGGC 60.159 50.000 0.00 0.00 38.95 5.19
4349 5444 2.802787 ATATGACTACGGCACTCTGC 57.197 50.000 0.00 0.00 44.08 4.26
4387 5482 4.020218 CACCAAATCTGAGAGGTGTTCCTA 60.020 45.833 10.32 0.00 45.24 2.94
4389 5484 5.073144 ACCAAATCTGAGAGGTGTTCCTAAA 59.927 40.000 0.00 0.00 45.24 1.85
4390 5485 5.412904 CCAAATCTGAGAGGTGTTCCTAAAC 59.587 44.000 0.00 0.00 45.24 2.01
4391 5486 4.828072 ATCTGAGAGGTGTTCCTAAACC 57.172 45.455 0.00 0.00 45.24 3.27
4392 5487 2.904434 TCTGAGAGGTGTTCCTAAACCC 59.096 50.000 0.00 0.00 45.24 4.11
4393 5488 2.907042 CTGAGAGGTGTTCCTAAACCCT 59.093 50.000 0.00 0.00 45.24 4.34
4394 5489 4.094476 CTGAGAGGTGTTCCTAAACCCTA 58.906 47.826 0.00 0.00 45.24 3.53
4395 5490 4.495565 TGAGAGGTGTTCCTAAACCCTAA 58.504 43.478 0.00 0.00 45.24 2.69
4396 5491 4.909088 TGAGAGGTGTTCCTAAACCCTAAA 59.091 41.667 0.00 0.00 45.24 1.85
4397 5492 5.221783 TGAGAGGTGTTCCTAAACCCTAAAC 60.222 44.000 0.00 0.00 45.24 2.01
4398 5493 4.042560 AGAGGTGTTCCTAAACCCTAAACC 59.957 45.833 0.00 0.00 45.24 3.27
4402 5509 3.008266 TGTTCCTAAACCCTAAACCCTCG 59.992 47.826 0.00 0.00 34.28 4.63
4409 5516 2.703798 CCTAAACCCTCGTCGCGGA 61.704 63.158 6.13 0.00 0.00 5.54
4470 5608 2.967270 GGAGCATTTCCAGGCTTGT 58.033 52.632 0.00 0.00 46.01 3.16
4471 5609 0.813821 GGAGCATTTCCAGGCTTGTC 59.186 55.000 0.00 0.00 46.01 3.18
4472 5610 1.538047 GAGCATTTCCAGGCTTGTCA 58.462 50.000 0.00 0.00 41.22 3.58
4473 5611 2.097825 GAGCATTTCCAGGCTTGTCAT 58.902 47.619 0.00 0.00 41.22 3.06
4476 5614 1.479323 CATTTCCAGGCTTGTCATGGG 59.521 52.381 0.00 0.00 46.22 4.00
4477 5615 0.899717 TTTCCAGGCTTGTCATGGGC 60.900 55.000 0.00 0.00 46.22 5.36
4514 5652 4.202050 GCCCAATTGTGCTCGATAAGAAAT 60.202 41.667 5.58 0.00 0.00 2.17
4517 5655 6.404623 CCCAATTGTGCTCGATAAGAAATTGA 60.405 38.462 16.15 0.00 35.72 2.57
4581 5719 3.568853 AGCTGCATATTTCTCAGGCAATC 59.431 43.478 1.02 0.00 33.58 2.67
4606 5744 5.509498 CAATTCCTTTGTCCAGATAGGGAA 58.491 41.667 0.00 0.00 39.05 3.97
4607 5745 5.796502 ATTCCTTTGTCCAGATAGGGAAA 57.203 39.130 0.00 0.00 39.05 3.13
4786 5930 2.053627 GAACAAAAACAGCAGCGATGG 58.946 47.619 1.46 0.00 0.00 3.51
4816 5960 1.308998 CTGCTAAGGCGGGTAAATGG 58.691 55.000 0.00 0.00 40.90 3.16
4974 6118 7.508636 AGATCCTACATCAGACAATCATACAGT 59.491 37.037 0.00 0.00 0.00 3.55
5065 6238 9.589461 CTTAACTAAATCTAGGGGAGTATCAGA 57.411 37.037 0.00 0.00 36.25 3.27
5066 6239 9.589461 TTAACTAAATCTAGGGGAGTATCAGAG 57.411 37.037 0.00 0.00 36.25 3.35
5067 6240 7.409408 ACTAAATCTAGGGGAGTATCAGAGA 57.591 40.000 0.00 0.00 36.25 3.10
5068 6241 7.827787 ACTAAATCTAGGGGAGTATCAGAGAA 58.172 38.462 0.00 0.00 36.25 2.87
5069 6242 6.987403 AAATCTAGGGGAGTATCAGAGAAC 57.013 41.667 0.00 0.00 36.25 3.01
5071 6244 5.313280 TCTAGGGGAGTATCAGAGAACTC 57.687 47.826 7.04 7.04 41.16 3.01
5072 6245 4.727332 TCTAGGGGAGTATCAGAGAACTCA 59.273 45.833 14.66 0.00 43.21 3.41
5073 6246 3.909732 AGGGGAGTATCAGAGAACTCAG 58.090 50.000 14.66 0.00 43.21 3.35
5074 6247 2.364002 GGGGAGTATCAGAGAACTCAGC 59.636 54.545 14.66 2.38 43.21 4.26
5075 6248 3.027412 GGGAGTATCAGAGAACTCAGCA 58.973 50.000 14.66 0.00 43.21 4.41
5076 6249 3.449018 GGGAGTATCAGAGAACTCAGCAA 59.551 47.826 14.66 0.00 43.21 3.91
5077 6250 4.081420 GGGAGTATCAGAGAACTCAGCAAA 60.081 45.833 14.66 0.00 43.21 3.68
5078 6251 5.482908 GGAGTATCAGAGAACTCAGCAAAA 58.517 41.667 14.66 0.00 43.21 2.44
5079 6252 5.934625 GGAGTATCAGAGAACTCAGCAAAAA 59.065 40.000 14.66 0.00 43.21 1.94
5080 6253 6.128418 GGAGTATCAGAGAACTCAGCAAAAAC 60.128 42.308 14.66 0.00 43.21 2.43
5081 6254 6.291377 AGTATCAGAGAACTCAGCAAAAACA 58.709 36.000 4.64 0.00 0.00 2.83
5082 6255 6.939163 AGTATCAGAGAACTCAGCAAAAACAT 59.061 34.615 4.64 0.00 0.00 2.71
5083 6256 6.645790 ATCAGAGAACTCAGCAAAAACATT 57.354 33.333 4.64 0.00 0.00 2.71
5084 6257 5.824429 TCAGAGAACTCAGCAAAAACATTG 58.176 37.500 4.64 0.00 0.00 2.82
5085 6258 4.443394 CAGAGAACTCAGCAAAAACATTGC 59.557 41.667 5.06 5.06 45.22 3.56
5093 6266 3.322230 GCAAAAACATTGCACTGGTTG 57.678 42.857 8.24 9.88 44.34 3.77
5094 6267 2.677337 GCAAAAACATTGCACTGGTTGT 59.323 40.909 8.24 0.00 44.34 3.32
5095 6268 3.868077 GCAAAAACATTGCACTGGTTGTA 59.132 39.130 8.24 0.00 44.34 2.41
5096 6269 4.260172 GCAAAAACATTGCACTGGTTGTAC 60.260 41.667 8.24 0.00 44.34 2.90
5097 6270 4.727507 AAAACATTGCACTGGTTGTACA 57.272 36.364 8.24 0.00 0.00 2.90
5098 6271 4.727507 AAACATTGCACTGGTTGTACAA 57.272 36.364 6.53 3.59 36.48 2.41
5099 6272 4.935352 AACATTGCACTGGTTGTACAAT 57.065 36.364 12.26 0.00 41.82 2.71
5101 6274 2.791383 TTGCACTGGTTGTACAATGC 57.209 45.000 20.09 20.09 27.77 3.56
5144 6317 6.338146 AGGTTTCCTTTTACTGCAAAACTTC 58.662 36.000 6.39 0.00 32.65 3.01
5145 6318 6.071051 AGGTTTCCTTTTACTGCAAAACTTCA 60.071 34.615 6.39 0.00 32.65 3.02
5151 6324 7.719633 TCCTTTTACTGCAAAACTTCATACTCT 59.280 33.333 0.00 0.00 32.65 3.24
5165 6338 7.453393 ACTTCATACTCTGTTGATTTCCAGAA 58.547 34.615 0.00 0.00 37.27 3.02
5192 6365 5.712152 ATGAGGTTTCATTTTCTGGTGAC 57.288 39.130 0.00 0.00 41.24 3.67
5196 6369 4.580580 AGGTTTCATTTTCTGGTGACACTC 59.419 41.667 5.39 0.00 35.60 3.51
5220 6393 2.586425 ACTGTGAATTCCCAGTGTTGG 58.414 47.619 20.88 0.00 40.30 3.77
5278 6452 2.200373 ACTGTGTAGGCATTGGAACC 57.800 50.000 0.00 0.00 0.00 3.62
5281 6455 0.035820 GTGTAGGCATTGGAACCGGA 60.036 55.000 9.46 0.00 0.00 5.14
5301 6475 6.376299 ACCGGAAAATTTCCTGTTAATCTACC 59.624 38.462 21.04 0.00 43.63 3.18
5306 6480 6.980051 AATTTCCTGTTAATCTACCGACAC 57.020 37.500 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.032071 CTTCCGGTGGTGGTGACC 59.968 66.667 0.00 0.00 43.48 4.02
55 56 0.105224 ATGTTGTCCGTTGTCCGTCA 59.895 50.000 0.00 0.00 33.66 4.35
66 67 4.392138 GCTTGTGGTAAGTCTATGTTGTCC 59.608 45.833 0.00 0.00 0.00 4.02
67 68 4.392138 GGCTTGTGGTAAGTCTATGTTGTC 59.608 45.833 0.00 0.00 0.00 3.18
68 69 4.324267 GGCTTGTGGTAAGTCTATGTTGT 58.676 43.478 0.00 0.00 0.00 3.32
69 70 3.689649 GGGCTTGTGGTAAGTCTATGTTG 59.310 47.826 0.00 0.00 0.00 3.33
139 140 0.108585 GCCCTGTCAGTGGAAGAACA 59.891 55.000 10.58 0.00 0.00 3.18
145 146 2.055689 CTGTTGGCCCTGTCAGTGGA 62.056 60.000 0.00 0.00 0.00 4.02
156 157 0.251634 CTTCTCCTCCTCTGTTGGCC 59.748 60.000 0.00 0.00 0.00 5.36
188 189 3.069980 GCCGCATCTCCTCTGTCGT 62.070 63.158 0.00 0.00 0.00 4.34
190 191 2.279120 CGCCGCATCTCCTCTGTC 60.279 66.667 0.00 0.00 0.00 3.51
191 192 3.842923 CCGCCGCATCTCCTCTGT 61.843 66.667 0.00 0.00 0.00 3.41
205 206 3.400255 CCTTACCTATTTCCTTAGCCGC 58.600 50.000 0.00 0.00 0.00 6.53
228 229 3.057174 CCTAGTCGTTCTTTCTCTGTGCT 60.057 47.826 0.00 0.00 0.00 4.40
281 282 5.081728 TCTTGCTAGTGTAAGTAACCTCCA 58.918 41.667 0.00 0.00 37.23 3.86
285 286 7.155655 AGTACTCTTGCTAGTGTAAGTAACC 57.844 40.000 10.85 0.19 37.23 2.85
288 289 9.730705 TTCTAAGTACTCTTGCTAGTGTAAGTA 57.269 33.333 10.85 1.84 37.23 2.24
375 409 4.512944 ACATAATCGAATTTGATGCGCTCT 59.487 37.500 9.73 0.00 0.00 4.09
376 410 4.610122 CACATAATCGAATTTGATGCGCTC 59.390 41.667 9.73 4.27 0.00 5.03
421 455 3.319122 TGGTGGATCATCTATCACGTCAG 59.681 47.826 0.00 0.00 36.20 3.51
422 456 3.295973 TGGTGGATCATCTATCACGTCA 58.704 45.455 0.00 0.00 36.20 4.35
425 459 2.611473 GGCTGGTGGATCATCTATCACG 60.611 54.545 0.00 0.00 36.20 4.35
427 461 2.693210 TGGCTGGTGGATCATCTATCA 58.307 47.619 0.00 0.00 36.20 2.15
454 488 3.372206 CGAGCCACTTAGAAGAAACCATG 59.628 47.826 0.00 0.00 0.00 3.66
456 490 2.367567 ACGAGCCACTTAGAAGAAACCA 59.632 45.455 0.00 0.00 0.00 3.67
488 522 7.744678 ACTTTTACTAGCTTACCCCTAATCA 57.255 36.000 0.00 0.00 0.00 2.57
549 583 9.956720 GAAATTTGGATATCGAGATCAAATTGT 57.043 29.630 25.87 20.07 32.74 2.71
853 897 0.472471 TGGTGGTGGAAGTGAACTCC 59.528 55.000 0.00 0.00 0.00 3.85
902 956 5.587043 ACATGTTTGAGTGTTCCGTCTTTAA 59.413 36.000 0.00 0.00 0.00 1.52
909 963 2.131972 TCGACATGTTTGAGTGTTCCG 58.868 47.619 0.00 0.00 0.00 4.30
973 1027 2.506472 GATCTTCCGCCCCTGTCC 59.494 66.667 0.00 0.00 0.00 4.02
1007 1061 2.464459 GGAACGGAGCTGCGAATGG 61.464 63.158 34.91 4.91 0.00 3.16
1061 1115 2.220313 CAGCGGAGGTAGTAGTAGGTC 58.780 57.143 0.00 0.00 35.08 3.85
1066 1120 3.510846 CGCAGCGGAGGTAGTAGT 58.489 61.111 7.00 0.00 35.08 2.73
1083 1137 4.173924 GAGGAGCTGCTGAGGGGC 62.174 72.222 14.48 0.00 0.00 5.80
1086 1140 2.433994 GGAGGAGGAGCTGCTGAGG 61.434 68.421 14.48 0.00 30.82 3.86
1088 1142 2.364842 GGGAGGAGGAGCTGCTGA 60.365 66.667 14.48 0.00 30.82 4.26
1089 1143 2.686470 TGGGAGGAGGAGCTGCTG 60.686 66.667 14.48 0.00 30.82 4.41
1090 1144 2.686835 GTGGGAGGAGGAGCTGCT 60.687 66.667 7.79 7.79 34.11 4.24
1091 1145 2.686835 AGTGGGAGGAGGAGCTGC 60.687 66.667 0.00 0.00 0.00 5.25
1093 1147 1.001503 CAGAGTGGGAGGAGGAGCT 59.998 63.158 0.00 0.00 0.00 4.09
1094 1148 2.730524 GCAGAGTGGGAGGAGGAGC 61.731 68.421 0.00 0.00 0.00 4.70
1096 1150 2.039624 GGCAGAGTGGGAGGAGGA 59.960 66.667 0.00 0.00 0.00 3.71
1097 1151 3.465403 CGGCAGAGTGGGAGGAGG 61.465 72.222 0.00 0.00 0.00 4.30
1098 1152 4.154347 GCGGCAGAGTGGGAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
1360 1429 2.303022 TGAGACTGGAGAAAAATCCGCT 59.697 45.455 0.00 0.00 42.77 5.52
1512 1582 2.741612 CAAAGCTAGAGAGAGATGGCG 58.258 52.381 0.00 0.00 0.00 5.69
1517 1590 3.696045 AGTCAGCAAAGCTAGAGAGAGA 58.304 45.455 0.00 0.00 36.40 3.10
1547 1621 1.153469 CTGCTCCTCTTTCCTCCGC 60.153 63.158 0.00 0.00 0.00 5.54
1604 1678 0.906756 CCCAGCTGACAGGAAGAGGA 60.907 60.000 17.39 0.00 0.00 3.71
1605 1679 0.906756 TCCCAGCTGACAGGAAGAGG 60.907 60.000 17.39 4.23 0.00 3.69
1606 1680 0.979665 TTCCCAGCTGACAGGAAGAG 59.020 55.000 17.39 0.00 34.75 2.85
1607 1681 3.164024 TTCCCAGCTGACAGGAAGA 57.836 52.632 17.39 0.00 34.75 2.87
1609 1683 1.902508 CTACTTCCCAGCTGACAGGAA 59.097 52.381 17.39 18.03 37.33 3.36
1625 1699 3.273618 AGTTCCCCATCTCTTCCTCTACT 59.726 47.826 0.00 0.00 0.00 2.57
1721 1795 9.816787 AATAGACACAAAGAAAAATAGGGGTAA 57.183 29.630 0.00 0.00 0.00 2.85
1722 1796 9.816787 AAATAGACACAAAGAAAAATAGGGGTA 57.183 29.630 0.00 0.00 0.00 3.69
1723 1797 8.585018 CAAATAGACACAAAGAAAAATAGGGGT 58.415 33.333 0.00 0.00 0.00 4.95
1728 1802 9.677567 GCTGACAAATAGACACAAAGAAAAATA 57.322 29.630 0.00 0.00 0.00 1.40
1735 1809 6.551385 AGAAGCTGACAAATAGACACAAAG 57.449 37.500 0.00 0.00 0.00 2.77
1741 1902 7.009723 GCAAGTACTAGAAGCTGACAAATAGAC 59.990 40.741 0.00 0.00 0.00 2.59
1743 1904 6.256757 GGCAAGTACTAGAAGCTGACAAATAG 59.743 42.308 0.00 0.00 0.00 1.73
1754 1915 3.100671 ACCAGGAGGCAAGTACTAGAAG 58.899 50.000 0.00 0.00 39.06 2.85
1758 1919 1.906574 CCAACCAGGAGGCAAGTACTA 59.093 52.381 0.00 0.00 41.22 1.82
1759 1920 0.693049 CCAACCAGGAGGCAAGTACT 59.307 55.000 0.00 0.00 41.22 2.73
1760 1921 3.249687 CCAACCAGGAGGCAAGTAC 57.750 57.895 0.00 0.00 41.22 2.73
1825 1986 6.817140 CCAAATCCAAGAACTACTACTACCAC 59.183 42.308 0.00 0.00 0.00 4.16
1826 1987 6.499350 ACCAAATCCAAGAACTACTACTACCA 59.501 38.462 0.00 0.00 0.00 3.25
1827 1988 6.944096 ACCAAATCCAAGAACTACTACTACC 58.056 40.000 0.00 0.00 0.00 3.18
1828 1989 8.718734 CAAACCAAATCCAAGAACTACTACTAC 58.281 37.037 0.00 0.00 0.00 2.73
1829 1990 8.434392 ACAAACCAAATCCAAGAACTACTACTA 58.566 33.333 0.00 0.00 0.00 1.82
1830 1991 7.228706 CACAAACCAAATCCAAGAACTACTACT 59.771 37.037 0.00 0.00 0.00 2.57
1862 2023 0.532573 ACACATGGTACGCCTCTCAG 59.467 55.000 0.00 0.00 35.27 3.35
1880 2044 2.235898 TGCTATCCAAATTTTGCCCCAC 59.764 45.455 3.50 0.00 0.00 4.61
1887 2051 8.200364 GCATAACAACATGCTATCCAAATTTT 57.800 30.769 0.00 0.00 46.35 1.82
1906 2071 6.955963 CGAAACAGAAGTGTAAGATGCATAAC 59.044 38.462 0.00 0.00 35.08 1.89
1907 2072 6.092122 CCGAAACAGAAGTGTAAGATGCATAA 59.908 38.462 0.00 0.00 35.08 1.90
1908 2073 5.580691 CCGAAACAGAAGTGTAAGATGCATA 59.419 40.000 0.00 0.00 35.08 3.14
1926 2091 6.925718 AGTAGGTAAAAACTAGTCACCGAAAC 59.074 38.462 0.00 4.06 34.36 2.78
1931 2096 8.442632 AACAAAGTAGGTAAAAACTAGTCACC 57.557 34.615 0.00 1.83 0.00 4.02
1934 2099 8.899427 AGGAACAAAGTAGGTAAAAACTAGTC 57.101 34.615 0.00 0.00 0.00 2.59
1958 2123 1.739562 GCGAAGGTGCACCAGAGAG 60.740 63.158 36.39 22.27 38.89 3.20
1959 2124 2.343758 GCGAAGGTGCACCAGAGA 59.656 61.111 36.39 0.00 38.89 3.10
2016 3035 2.559231 TGCACCATGGCATGCTAATATG 59.441 45.455 23.49 15.71 42.55 1.78
2017 3036 2.879154 TGCACCATGGCATGCTAATAT 58.121 42.857 23.49 4.64 42.55 1.28
2018 3037 2.361643 TGCACCATGGCATGCTAATA 57.638 45.000 23.49 5.20 42.55 0.98
2019 3038 3.210733 TGCACCATGGCATGCTAAT 57.789 47.368 23.49 9.12 42.55 1.73
2020 3039 4.759893 TGCACCATGGCATGCTAA 57.240 50.000 23.49 6.88 42.55 3.09
2033 3052 3.921119 TTGATGTTCCAGTTCATGCAC 57.079 42.857 0.00 0.00 0.00 4.57
2040 3059 7.725844 ACCTAAGAAGAAATTGATGTTCCAGTT 59.274 33.333 0.00 0.00 0.00 3.16
2042 3061 7.693969 ACCTAAGAAGAAATTGATGTTCCAG 57.306 36.000 0.00 0.00 0.00 3.86
2043 3062 8.359642 CAAACCTAAGAAGAAATTGATGTTCCA 58.640 33.333 0.00 0.00 0.00 3.53
2044 3063 8.576442 TCAAACCTAAGAAGAAATTGATGTTCC 58.424 33.333 0.00 0.00 0.00 3.62
2121 3190 4.044426 GCAACAACAACATCTTCAGGTTC 58.956 43.478 0.00 0.00 0.00 3.62
2179 3248 1.688735 TCGATGGATCTGATGTCCCAC 59.311 52.381 0.00 0.00 34.76 4.61
2184 3253 4.437239 GTCACTTTCGATGGATCTGATGT 58.563 43.478 0.00 0.00 0.00 3.06
2585 3654 3.861840 TCAGGAGACAAGAAAATAGCCG 58.138 45.455 0.00 0.00 0.00 5.52
2596 3666 4.766891 GGAAAATGAACCATCAGGAGACAA 59.233 41.667 0.00 0.00 39.39 3.18
2600 3670 3.129988 GCAGGAAAATGAACCATCAGGAG 59.870 47.826 0.00 0.00 39.39 3.69
2612 3682 2.005451 CTCCGTCTGAGCAGGAAAATG 58.995 52.381 0.00 0.00 33.47 2.32
2701 3771 4.887748 ACTCATACACCAGAAGTCTGTTG 58.112 43.478 7.51 5.98 41.44 3.33
2887 3957 4.420214 ACCTTAAGCCTTATTCCCCATGAT 59.580 41.667 0.00 0.00 0.00 2.45
2971 4041 3.244976 GTTTGATGCCTTGAAATCACGG 58.755 45.455 1.75 1.75 38.21 4.94
3023 4093 4.937620 TGGCTTGTAATCAGAGTCAACATC 59.062 41.667 0.00 0.00 0.00 3.06
3051 4121 6.954487 ACAAGTTAAGTTAAAAGACCCCAG 57.046 37.500 0.00 0.00 0.00 4.45
3126 4196 1.600916 AGTTGGACCAGCTTTCGCC 60.601 57.895 4.77 0.00 36.60 5.54
3183 4253 2.302157 CTCTGGAGCTGCATATCCATGA 59.698 50.000 17.71 15.34 44.45 3.07
3276 4346 4.454161 GGCCCCATTTTTGTAACATGAAAC 59.546 41.667 0.00 0.00 0.00 2.78
3278 4348 3.648067 TGGCCCCATTTTTGTAACATGAA 59.352 39.130 0.00 0.00 0.00 2.57
3280 4350 3.692257 TGGCCCCATTTTTGTAACATG 57.308 42.857 0.00 0.00 0.00 3.21
3281 4351 3.586618 ACATGGCCCCATTTTTGTAACAT 59.413 39.130 0.00 0.00 33.90 2.71
3282 4352 2.975489 ACATGGCCCCATTTTTGTAACA 59.025 40.909 0.00 0.00 33.90 2.41
3283 4353 3.694043 ACATGGCCCCATTTTTGTAAC 57.306 42.857 0.00 0.00 33.90 2.50
3285 4355 2.304180 CCAACATGGCCCCATTTTTGTA 59.696 45.455 0.00 0.00 33.90 2.41
3286 4356 1.073603 CCAACATGGCCCCATTTTTGT 59.926 47.619 0.00 2.73 33.90 2.83
3287 4357 1.613785 CCCAACATGGCCCCATTTTTG 60.614 52.381 0.00 4.57 35.79 2.44
3289 4359 0.475437 ACCCAACATGGCCCCATTTT 60.475 50.000 0.00 0.00 35.79 1.82
3291 4361 1.306056 GACCCAACATGGCCCCATT 60.306 57.895 0.00 0.00 35.79 3.16
3292 4362 1.814292 AAGACCCAACATGGCCCCAT 61.814 55.000 0.00 0.00 35.79 4.00
3293 4363 2.439553 GAAGACCCAACATGGCCCCA 62.440 60.000 0.00 0.00 35.79 4.96
3295 4365 2.046285 CGAAGACCCAACATGGCCC 61.046 63.158 0.00 0.00 35.79 5.80
3296 4366 2.700773 GCGAAGACCCAACATGGCC 61.701 63.158 0.00 0.00 35.79 5.36
3297 4367 1.648467 GAGCGAAGACCCAACATGGC 61.648 60.000 0.00 0.00 35.79 4.40
3298 4368 0.036010 AGAGCGAAGACCCAACATGG 60.036 55.000 0.00 0.00 37.25 3.66
3299 4369 1.081892 CAGAGCGAAGACCCAACATG 58.918 55.000 0.00 0.00 0.00 3.21
3313 4397 7.980099 TCAACTTAGGTTTAGCTAATACAGAGC 59.020 37.037 7.08 1.54 35.35 4.09
3368 4452 5.363101 GCTTCACCATGATTCTGTCATAGA 58.637 41.667 0.00 0.00 45.76 1.98
3372 4456 2.618816 GGGCTTCACCATGATTCTGTCA 60.619 50.000 0.00 0.00 42.05 3.58
3373 4457 2.019984 GGGCTTCACCATGATTCTGTC 58.980 52.381 0.00 0.00 42.05 3.51
3374 4458 1.637553 AGGGCTTCACCATGATTCTGT 59.362 47.619 0.00 0.00 42.05 3.41
3375 4459 2.431954 AGGGCTTCACCATGATTCTG 57.568 50.000 0.00 0.00 42.05 3.02
3376 4460 4.803329 AATAGGGCTTCACCATGATTCT 57.197 40.909 0.00 0.00 42.05 2.40
3377 4461 4.646492 ACAAATAGGGCTTCACCATGATTC 59.354 41.667 0.00 0.00 42.05 2.52
3378 4462 4.613437 ACAAATAGGGCTTCACCATGATT 58.387 39.130 0.00 0.00 42.05 2.57
3379 4463 4.255510 ACAAATAGGGCTTCACCATGAT 57.744 40.909 0.00 0.00 42.05 2.45
3380 4464 3.737559 ACAAATAGGGCTTCACCATGA 57.262 42.857 0.00 0.00 42.05 3.07
3381 4465 4.806640 AAACAAATAGGGCTTCACCATG 57.193 40.909 0.00 0.00 42.05 3.66
3382 4466 6.496911 ACTTTAAACAAATAGGGCTTCACCAT 59.503 34.615 0.00 0.00 42.05 3.55
3559 4654 6.661805 GGAGTGGACCATTTCCTACATTTAAA 59.338 38.462 16.81 0.00 46.10 1.52
3589 4684 9.871238 GCCAGTCTCGAATTTAATAGGAATATA 57.129 33.333 0.00 0.00 0.00 0.86
3590 4685 7.824779 GGCCAGTCTCGAATTTAATAGGAATAT 59.175 37.037 0.00 0.00 0.00 1.28
3609 4704 7.530426 AAATCCAAGAATAATATGGCCAGTC 57.470 36.000 13.05 1.31 34.13 3.51
3698 4793 9.268268 CCAGAAATAAGCAATGCATATTCATTT 57.732 29.630 14.84 2.89 32.44 2.32
3700 4795 8.185506 TCCAGAAATAAGCAATGCATATTCAT 57.814 30.769 14.84 5.50 32.44 2.57
3704 4799 9.918630 GTTTATCCAGAAATAAGCAATGCATAT 57.081 29.630 8.35 1.89 0.00 1.78
3705 4800 8.359642 GGTTTATCCAGAAATAAGCAATGCATA 58.640 33.333 8.35 0.00 35.97 3.14
3706 4801 7.212274 GGTTTATCCAGAAATAAGCAATGCAT 58.788 34.615 8.35 0.00 35.97 3.96
3707 4802 6.406849 GGGTTTATCCAGAAATAAGCAATGCA 60.407 38.462 8.35 0.00 38.11 3.96
3708 4803 5.985530 GGGTTTATCCAGAAATAAGCAATGC 59.014 40.000 0.00 0.00 38.11 3.56
3709 4804 7.111247 TGGGTTTATCCAGAAATAAGCAATG 57.889 36.000 0.00 0.00 38.11 2.82
3710 4805 7.919385 ATGGGTTTATCCAGAAATAAGCAAT 57.081 32.000 0.00 0.00 40.56 3.56
3711 4806 7.619302 AGAATGGGTTTATCCAGAAATAAGCAA 59.381 33.333 0.00 0.00 40.56 3.91
3712 4807 7.125391 AGAATGGGTTTATCCAGAAATAAGCA 58.875 34.615 0.00 0.00 40.56 3.91
3713 4808 7.285401 TGAGAATGGGTTTATCCAGAAATAAGC 59.715 37.037 0.00 0.00 40.56 3.09
3714 4809 8.752005 TGAGAATGGGTTTATCCAGAAATAAG 57.248 34.615 0.00 0.00 40.56 1.73
3744 4839 4.058817 GAGGCGACCTGTGAATATTAAGG 58.941 47.826 2.98 8.94 31.76 2.69
3793 4888 1.152777 CTCAAGCAACACCACCCCA 60.153 57.895 0.00 0.00 0.00 4.96
3812 4907 3.057547 CTCGTCTCCCGGTCAGCAG 62.058 68.421 0.00 0.00 37.11 4.24
3895 4990 2.432456 TACAGCCTGCGCTTGTCG 60.432 61.111 9.73 0.00 45.55 4.35
4015 5110 0.257328 AGACCTCTGAGATCTGCGGA 59.743 55.000 0.00 0.00 0.00 5.54
4102 5197 2.833957 GGGACGGTGTTGGAGGTT 59.166 61.111 0.00 0.00 0.00 3.50
4189 5284 1.847890 GCACTTGCGCGGTCCTAAAA 61.848 55.000 8.83 0.00 0.00 1.52
4269 5364 5.095691 AGAAACAACAATTACACAGCTCG 57.904 39.130 0.00 0.00 0.00 5.03
4282 5377 5.277974 GCAAGAAGCATCACTAGAAACAACA 60.278 40.000 0.00 0.00 44.79 3.33
4319 5414 2.124903 GTAGTCATATTCCGTGCCACG 58.875 52.381 10.95 10.95 42.11 4.94
4349 5444 7.381948 TCAGATTTGGTGAAAAACAATTCATCG 59.618 33.333 0.00 0.00 42.20 3.84
4383 5478 2.833943 GACGAGGGTTTAGGGTTTAGGA 59.166 50.000 0.00 0.00 0.00 2.94
4387 5482 0.321034 GCGACGAGGGTTTAGGGTTT 60.321 55.000 0.00 0.00 0.00 3.27
4389 5484 2.976356 GCGACGAGGGTTTAGGGT 59.024 61.111 0.00 0.00 0.00 4.34
4390 5485 2.202703 CGCGACGAGGGTTTAGGG 60.203 66.667 0.00 0.00 0.00 3.53
4391 5486 2.202703 CCGCGACGAGGGTTTAGG 60.203 66.667 8.23 0.00 0.00 2.69
4392 5487 1.226603 CTCCGCGACGAGGGTTTAG 60.227 63.158 17.93 3.73 0.00 1.85
4393 5488 2.879907 CTCCGCGACGAGGGTTTA 59.120 61.111 17.93 0.00 0.00 2.01
4394 5489 4.736896 GCTCCGCGACGAGGGTTT 62.737 66.667 17.93 0.00 0.00 3.27
4402 5509 3.728279 ATAAACCCGGCTCCGCGAC 62.728 63.158 8.23 0.00 38.24 5.19
4409 5516 0.546122 TGCAGATGATAAACCCGGCT 59.454 50.000 0.00 0.00 0.00 5.52
4422 5529 4.001652 CAGTTTCTGTCATGTCTGCAGAT 58.998 43.478 21.47 0.83 36.28 2.90
4469 5607 2.354821 GACGAATTTGGTAGCCCATGAC 59.645 50.000 0.00 0.00 41.49 3.06
4470 5608 2.639065 GACGAATTTGGTAGCCCATGA 58.361 47.619 0.00 0.00 41.49 3.07
4471 5609 1.330521 CGACGAATTTGGTAGCCCATG 59.669 52.381 0.00 0.00 41.49 3.66
4472 5610 1.663695 CGACGAATTTGGTAGCCCAT 58.336 50.000 0.00 0.00 41.49 4.00
4473 5611 1.022451 GCGACGAATTTGGTAGCCCA 61.022 55.000 0.00 0.00 39.65 5.36
4475 5613 1.719709 GGCGACGAATTTGGTAGCC 59.280 57.895 17.15 17.15 46.31 3.93
4476 5614 1.022451 TGGGCGACGAATTTGGTAGC 61.022 55.000 0.00 7.87 35.61 3.58
4477 5615 1.444836 TTGGGCGACGAATTTGGTAG 58.555 50.000 0.00 0.00 0.00 3.18
4514 5652 7.125659 TCAAGACCCTATCTGATAACATGTCAA 59.874 37.037 0.00 0.00 37.88 3.18
4517 5655 7.071698 ACATCAAGACCCTATCTGATAACATGT 59.928 37.037 0.00 0.00 37.88 3.21
4551 5689 4.761227 TGAGAAATATGCAGCTGTGACAAA 59.239 37.500 16.64 0.00 0.00 2.83
4552 5690 4.325972 TGAGAAATATGCAGCTGTGACAA 58.674 39.130 16.64 0.00 0.00 3.18
4553 5691 3.937079 CTGAGAAATATGCAGCTGTGACA 59.063 43.478 16.64 5.17 0.00 3.58
4581 5719 3.313526 CCTATCTGGACAAAGGAATTGCG 59.686 47.826 0.00 0.00 43.13 4.85
4607 5745 9.102453 GGAGTCCTTTCCAGTAGGTATATATTT 57.898 37.037 0.41 0.00 37.20 1.40
4615 5753 1.555058 GGGGAGTCCTTTCCAGTAGGT 60.555 57.143 9.58 0.00 39.09 3.08
4616 5754 1.205055 GGGGAGTCCTTTCCAGTAGG 58.795 60.000 9.58 0.00 39.09 3.18
4617 5755 2.255770 AGGGGAGTCCTTTCCAGTAG 57.744 55.000 9.58 0.00 45.47 2.57
4658 5799 8.377799 AGGCTCATTTTTCCATTTTATCTTGTT 58.622 29.630 0.00 0.00 0.00 2.83
4816 5960 2.594654 CGAGAAATGAGACACGCTGTAC 59.405 50.000 0.00 0.00 0.00 2.90
4822 5966 6.089551 AGTTTATTGTCGAGAAATGAGACACG 59.910 38.462 0.00 0.00 43.54 4.49
4974 6118 2.967201 TCTTGACCAACTTACTCCCGAA 59.033 45.455 0.00 0.00 0.00 4.30
5065 6238 4.114794 GTGCAATGTTTTTGCTGAGTTCT 58.885 39.130 11.18 0.00 45.13 3.01
5066 6239 4.026310 CAGTGCAATGTTTTTGCTGAGTTC 60.026 41.667 5.87 0.00 45.13 3.01
5067 6240 3.866910 CAGTGCAATGTTTTTGCTGAGTT 59.133 39.130 5.87 0.00 45.13 3.01
5068 6241 3.450578 CAGTGCAATGTTTTTGCTGAGT 58.549 40.909 5.87 0.00 45.13 3.41
5069 6242 2.798283 CCAGTGCAATGTTTTTGCTGAG 59.202 45.455 13.82 1.91 45.13 3.35
5071 6244 2.553086 ACCAGTGCAATGTTTTTGCTG 58.447 42.857 13.82 0.71 45.13 4.41
5072 6245 2.937799 CAACCAGTGCAATGTTTTTGCT 59.062 40.909 13.82 0.00 45.13 3.91
5073 6246 2.677337 ACAACCAGTGCAATGTTTTTGC 59.323 40.909 13.82 3.44 45.11 3.68
5074 6247 4.867047 TGTACAACCAGTGCAATGTTTTTG 59.133 37.500 13.82 14.53 40.01 2.44
5075 6248 5.078411 TGTACAACCAGTGCAATGTTTTT 57.922 34.783 13.82 0.42 40.01 1.94
5076 6249 4.727507 TGTACAACCAGTGCAATGTTTT 57.272 36.364 13.82 2.88 40.01 2.43
5077 6250 4.727507 TTGTACAACCAGTGCAATGTTT 57.272 36.364 13.82 1.46 45.95 2.83
5083 6256 0.958091 GGCATTGTACAACCAGTGCA 59.042 50.000 25.33 0.00 46.41 4.57
5084 6257 0.243636 GGGCATTGTACAACCAGTGC 59.756 55.000 19.14 19.14 44.58 4.40
5085 6258 0.887933 GGGGCATTGTACAACCAGTG 59.112 55.000 11.22 6.50 0.00 3.66
5086 6259 0.251608 GGGGGCATTGTACAACCAGT 60.252 55.000 11.22 0.00 0.00 4.00
5087 6260 2.578683 GGGGGCATTGTACAACCAG 58.421 57.895 11.22 5.34 0.00 4.00
5088 6261 4.854587 GGGGGCATTGTACAACCA 57.145 55.556 11.22 0.00 0.00 3.67
5135 6308 7.327032 GGAAATCAACAGAGTATGAAGTTTTGC 59.673 37.037 0.00 0.00 0.00 3.68
5144 6317 8.048534 ACAATTCTGGAAATCAACAGAGTATG 57.951 34.615 0.00 0.00 43.84 2.39
5145 6318 9.911788 ATACAATTCTGGAAATCAACAGAGTAT 57.088 29.630 0.00 0.00 43.84 2.12
5151 6324 6.947733 ACCTCATACAATTCTGGAAATCAACA 59.052 34.615 0.00 0.00 0.00 3.33
5165 6338 7.451255 TCACCAGAAAATGAAACCTCATACAAT 59.549 33.333 0.00 0.00 41.66 2.71
5192 6365 4.248859 CTGGGAATTCACAGTACAGAGTG 58.751 47.826 26.65 1.61 42.29 3.51
5281 6455 7.446013 TGTGTCGGTAGATTAACAGGAAATTTT 59.554 33.333 0.00 0.00 0.00 1.82
5301 6475 6.951256 TCTATTTCTGAATGACTTGTGTCG 57.049 37.500 0.00 0.00 45.70 4.35


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

AutoCloner maintained by Alex Coulton.