Multiple sequence alignment - TraesCS7A01G312500

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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 TraesCS7A01G312500 chr7A 100.000 4994 0 0 1 4994 443390531 443395524 0.000000e+00 9223.0
1 TraesCS7A01G312500 chr7A 100.000 74 0 0 2040 2113 443392498 443392571 2.420000e-28 137.0
2 TraesCS7A01G312500 chr7A 100.000 74 0 0 1968 2041 443392570 443392643 2.420000e-28 137.0
3 TraesCS7A01G312500 chr7D 95.187 2057 64 16 1 2041 391579325 391581362 0.000000e+00 3217.0
4 TraesCS7A01G312500 chr7D 96.402 1751 61 1 2040 3788 391581289 391583039 0.000000e+00 2883.0
5 TraesCS7A01G312500 chr7D 90.464 797 39 17 3790 4585 391583128 391583888 0.000000e+00 1016.0
6 TraesCS7A01G312500 chr7D 95.455 176 8 0 4819 4994 391583896 391584071 1.060000e-71 281.0
7 TraesCS7A01G312500 chr7B 95.268 1754 78 4 2040 3788 388170509 388172262 0.000000e+00 2774.0
8 TraesCS7A01G312500 chr7B 92.072 1955 95 26 123 2041 388168652 388170582 0.000000e+00 2697.0
9 TraesCS7A01G312500 chr7B 92.561 699 41 6 3790 4488 388172446 388173133 0.000000e+00 992.0
10 TraesCS7A01G312500 chr7B 93.491 169 11 0 4826 4994 388173172 388173340 8.300000e-63 252.0
11 TraesCS7A01G312500 chr7B 92.126 127 7 1 1 124 388168392 388168518 5.140000e-40 176.0
12 TraesCS7A01G312500 chr7B 92.373 118 9 0 4696 4813 642274133 642274016 8.600000e-38 169.0
13 TraesCS7A01G312500 chr4A 91.031 223 20 0 4595 4817 300464243 300464021 8.120000e-78 302.0
14 TraesCS7A01G312500 chr5B 95.122 41 2 0 4522 4562 5434858 5434898 1.160000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G312500 chr7A 443390531 443395524 4993 False 3165.666667 9223 100.0000 1 4994 3 chr7A.!!$F1 4993
1 TraesCS7A01G312500 chr7D 391579325 391584071 4746 False 1849.250000 3217 94.3770 1 4994 4 chr7D.!!$F1 4993
2 TraesCS7A01G312500 chr7B 388168392 388173340 4948 False 1378.200000 2774 93.1036 1 4994 5 chr7B.!!$F1 4993

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
989 1141 1.167781 AACCCTACGCACCAAAACCG 61.168 55.0 0.00 0.0 0.0 4.44 F
2375 2559 0.038709 GCGTGCATTGCCCTGTTTAA 60.039 50.0 6.12 0.0 0.0 1.52 F
2571 2756 2.237392 AGACCCTCCAAATCAGCAGTAC 59.763 50.0 0.00 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2495 2680 2.557490 TCACATGCATGCTGCTGTTTAA 59.443 40.909 26.53 4.00 45.31 1.52 R
3240 3426 0.475906 ACTGCAAAGGCTTCCAGTCT 59.524 50.000 21.04 6.48 41.91 3.24 R
4549 4917 0.117340 ACAAGCAGGTACTCCCTCCT 59.883 55.000 0.00 0.00 43.86 3.69 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
81 85 3.107601 TGAAACCCATCCAACCAACAAA 58.892 40.909 0.00 0.00 0.00 2.83
109 113 4.386312 GGATCCACTAACCAAATCATCCCA 60.386 45.833 6.95 0.00 0.00 4.37
341 480 3.738282 GCCATAAACGCAAAAATCACACA 59.262 39.130 0.00 0.00 0.00 3.72
343 482 4.143347 CCATAAACGCAAAAATCACACAGC 60.143 41.667 0.00 0.00 0.00 4.40
366 505 5.624491 GCTAAGATAACTGTCGACGGTAATC 59.376 44.000 29.37 18.79 34.49 1.75
446 586 1.717194 TTCCCTTCGAATCGAAACCG 58.283 50.000 18.99 7.75 45.23 4.44
551 691 3.200483 CGAAATAGGGTTAGGGTTTCGG 58.800 50.000 9.83 0.00 44.18 4.30
989 1141 1.167781 AACCCTACGCACCAAAACCG 61.168 55.000 0.00 0.00 0.00 4.44
1209 1363 7.090953 TGGACGCGATAAATCCTTTTAATTT 57.909 32.000 15.93 0.00 33.34 1.82
1358 1515 3.209410 GGGCTACATGACCAGATTTCTG 58.791 50.000 0.00 0.39 45.54 3.02
1398 1555 5.108517 TGCTGAACCTGTGTTTTGATTTTC 58.891 37.500 0.00 0.00 33.97 2.29
1407 1564 6.237915 CCTGTGTTTTGATTTTCTGCTGTTTC 60.238 38.462 0.00 0.00 0.00 2.78
1487 1644 1.672356 GAGGAAGCGCAAGGAAGCA 60.672 57.895 11.47 0.00 35.48 3.91
1553 1710 7.533426 GCTGTATTGAAGATTGACTGATTGTT 58.467 34.615 0.00 0.00 0.00 2.83
1705 1862 3.454447 TCACATATGGATCGGTTCAGGTT 59.546 43.478 7.80 0.00 0.00 3.50
1728 1885 2.821378 GCTGTTATGGCATGCATGGATA 59.179 45.455 27.34 6.92 0.00 2.59
1758 1915 9.790344 ATTTTTCATAATTGGGACATTCACAAA 57.210 25.926 0.00 0.00 43.81 2.83
1770 1927 7.232330 TGGGACATTCACAAATTACAAGATTCA 59.768 33.333 0.00 0.00 0.00 2.57
1784 1941 6.774354 ACAAGATTCACATTGCATTTGTTC 57.226 33.333 0.31 0.00 0.00 3.18
1841 2000 9.575868 TGTAGAAGGATAGAATGGAGTAACTAG 57.424 37.037 0.00 0.00 0.00 2.57
2019 2200 9.996554 TCATTACTTGTCTCATTTACTTTCTGA 57.003 29.630 0.00 0.00 0.00 3.27
2023 2204 8.682936 ACTTGTCTCATTTACTTTCTGAATGT 57.317 30.769 12.71 12.71 33.60 2.71
2024 2205 8.778358 ACTTGTCTCATTTACTTTCTGAATGTC 58.222 33.333 11.64 0.00 33.60 3.06
2025 2206 8.675705 TTGTCTCATTTACTTTCTGAATGTCA 57.324 30.769 11.64 0.00 33.60 3.58
2026 2207 8.315391 TGTCTCATTTACTTTCTGAATGTCAG 57.685 34.615 11.64 0.00 45.59 3.51
2027 2208 7.388776 TGTCTCATTTACTTTCTGAATGTCAGG 59.611 37.037 11.64 3.79 44.39 3.86
2028 2209 7.389053 GTCTCATTTACTTTCTGAATGTCAGGT 59.611 37.037 11.64 0.00 44.39 4.00
2029 2210 8.593679 TCTCATTTACTTTCTGAATGTCAGGTA 58.406 33.333 11.64 0.00 44.39 3.08
2030 2211 9.388506 CTCATTTACTTTCTGAATGTCAGGTAT 57.611 33.333 11.64 0.00 44.39 2.73
2031 2212 9.383519 TCATTTACTTTCTGAATGTCAGGTATC 57.616 33.333 11.64 0.00 44.39 2.24
2032 2213 9.166173 CATTTACTTTCTGAATGTCAGGTATCA 57.834 33.333 11.64 0.00 44.39 2.15
2033 2214 9.739276 ATTTACTTTCTGAATGTCAGGTATCAA 57.261 29.630 11.64 0.00 44.39 2.57
2034 2215 9.567776 TTTACTTTCTGAATGTCAGGTATCAAA 57.432 29.630 11.64 3.34 44.39 2.69
2035 2216 7.678947 ACTTTCTGAATGTCAGGTATCAAAG 57.321 36.000 5.46 9.27 44.39 2.77
2036 2217 6.656693 ACTTTCTGAATGTCAGGTATCAAAGG 59.343 38.462 15.26 3.54 44.39 3.11
2037 2218 6.373005 TTCTGAATGTCAGGTATCAAAGGA 57.627 37.500 5.46 0.00 44.39 3.36
2038 2219 6.566079 TCTGAATGTCAGGTATCAAAGGAT 57.434 37.500 5.46 0.00 44.39 3.24
2039 2220 7.675161 TCTGAATGTCAGGTATCAAAGGATA 57.325 36.000 5.46 0.00 44.39 2.59
2040 2221 8.267620 TCTGAATGTCAGGTATCAAAGGATAT 57.732 34.615 5.46 0.00 44.39 1.63
2041 2222 8.152898 TCTGAATGTCAGGTATCAAAGGATATG 58.847 37.037 5.46 0.00 44.39 1.78
2042 2223 7.805163 TGAATGTCAGGTATCAAAGGATATGT 58.195 34.615 0.00 0.00 38.24 2.29
2043 2224 8.274322 TGAATGTCAGGTATCAAAGGATATGTT 58.726 33.333 0.00 0.00 38.24 2.71
2044 2225 8.682936 AATGTCAGGTATCAAAGGATATGTTC 57.317 34.615 0.00 0.00 38.24 3.18
2045 2226 7.437713 TGTCAGGTATCAAAGGATATGTTCT 57.562 36.000 0.00 0.00 38.24 3.01
2046 2227 7.500992 TGTCAGGTATCAAAGGATATGTTCTC 58.499 38.462 0.00 0.00 38.24 2.87
2047 2228 6.931840 GTCAGGTATCAAAGGATATGTTCTCC 59.068 42.308 0.00 0.00 38.24 3.71
2048 2229 6.615316 TCAGGTATCAAAGGATATGTTCTCCA 59.385 38.462 0.00 0.00 38.24 3.86
2049 2230 6.708054 CAGGTATCAAAGGATATGTTCTCCAC 59.292 42.308 0.00 0.00 38.24 4.02
2050 2231 6.617371 AGGTATCAAAGGATATGTTCTCCACT 59.383 38.462 0.00 0.00 38.24 4.00
2051 2232 7.127955 AGGTATCAAAGGATATGTTCTCCACTT 59.872 37.037 0.00 0.00 38.24 3.16
2052 2233 8.429641 GGTATCAAAGGATATGTTCTCCACTTA 58.570 37.037 0.00 0.00 38.24 2.24
2053 2234 9.832445 GTATCAAAGGATATGTTCTCCACTTAA 57.168 33.333 0.00 0.00 38.24 1.85
2216 2399 6.858993 TCCTTTTTCCGTCGACATTATTTTTG 59.141 34.615 17.16 0.00 0.00 2.44
2240 2424 8.239038 TGTGGGTTCACTTAATTTTTGTGATA 57.761 30.769 8.11 0.45 43.94 2.15
2286 2470 9.699410 ATTCATTCTCTTTATTACCCATGAACA 57.301 29.630 0.00 0.00 33.43 3.18
2375 2559 0.038709 GCGTGCATTGCCCTGTTTAA 60.039 50.000 6.12 0.00 0.00 1.52
2394 2578 6.071952 TGTTTAATTCAGCCTTCTCCATGTTC 60.072 38.462 0.00 0.00 0.00 3.18
2495 2680 4.990426 GCACCAAGCACTTGTAATTTGAAT 59.010 37.500 9.41 0.00 44.79 2.57
2571 2756 2.237392 AGACCCTCCAAATCAGCAGTAC 59.763 50.000 0.00 0.00 0.00 2.73
2870 3056 4.844884 ACACCATCCTCCTAGTTAAAAGC 58.155 43.478 0.00 0.00 0.00 3.51
2926 3112 9.950680 TTCAATACTTCTCATTTTGTGTTCTTC 57.049 29.630 0.00 0.00 0.00 2.87
2954 3140 7.279981 GGTAATGTTTCCATTAAAATGCCCTTC 59.720 37.037 0.00 0.00 43.36 3.46
2972 3158 7.290061 TGCCCTTCTTAAGTATTGAATGCTAT 58.710 34.615 1.63 0.00 0.00 2.97
2990 3176 4.820173 TGCTATGAATTGCCTCTCTGAATG 59.180 41.667 0.00 0.00 0.00 2.67
2997 3183 3.325293 TGCCTCTCTGAATGTCTTCAC 57.675 47.619 0.00 0.00 36.46 3.18
3020 3206 4.093556 CCGAAGTCTTTGTCTAAATGCTCC 59.906 45.833 0.00 0.00 0.00 4.70
3389 3575 6.581542 GCCTATAGTTAGCACATTACTGTACG 59.418 42.308 0.00 0.00 33.14 3.67
3415 3601 0.030638 AACCATTGTTGTCTGCGTGC 59.969 50.000 0.00 0.00 32.13 5.34
3670 3856 7.323416 GCTTGTAGTTTTTATTTGCATTTTGGC 59.677 33.333 0.00 0.00 0.00 4.52
3686 3872 4.890158 TTTGGCTGACTATTCTGTCTGA 57.110 40.909 0.00 0.00 37.88 3.27
3791 4159 8.370266 ACCAGGTATAGTTAACATCAGTAACA 57.630 34.615 8.61 0.00 0.00 2.41
3825 4193 1.674359 AGCGTTCCATGTCAACAACA 58.326 45.000 5.80 0.00 43.51 3.33
3856 4224 5.163622 TGCATGCTGGCTAGATTAACTTTTC 60.164 40.000 20.33 0.00 34.04 2.29
3899 4267 6.175471 TCATCTAATGCTCACTTGTGATGTT 58.825 36.000 3.79 3.12 33.82 2.71
4008 4376 2.165845 CCGGTAAACAGTACTGGAGGAG 59.834 54.545 26.12 12.45 44.72 3.69
4179 4547 3.017442 GAGGTAGAGAATTTTGGGTGCC 58.983 50.000 0.00 0.00 0.00 5.01
4185 4553 2.037641 GAGAATTTTGGGTGCCTGCTTT 59.962 45.455 0.00 0.00 0.00 3.51
4253 4621 7.257003 TGGTGAACATATTTTGTGTGCATATC 58.743 34.615 0.00 0.00 37.46 1.63
4260 4628 1.581934 TTGTGTGCATATCTAGCGGC 58.418 50.000 0.00 0.00 33.85 6.53
4273 4641 3.897325 TCTAGCGGCGTAATGTATGAAG 58.103 45.455 9.37 0.00 0.00 3.02
4321 4689 4.383118 CGTATGAAGACTGATGGGTCCTTT 60.383 45.833 0.00 0.00 36.95 3.11
4351 4719 3.258372 TGTGCTTGTGGTTTGTTTTGGTA 59.742 39.130 0.00 0.00 0.00 3.25
4373 4741 1.165270 GTCGGCAAACATGGCTTACT 58.835 50.000 0.00 0.00 0.00 2.24
4375 4743 2.030274 GTCGGCAAACATGGCTTACTTT 60.030 45.455 0.00 0.00 0.00 2.66
4376 4744 2.030363 TCGGCAAACATGGCTTACTTTG 60.030 45.455 0.00 0.00 0.00 2.77
4377 4745 2.288152 CGGCAAACATGGCTTACTTTGT 60.288 45.455 0.00 0.00 0.00 2.83
4378 4746 3.057876 CGGCAAACATGGCTTACTTTGTA 60.058 43.478 0.00 0.00 0.00 2.41
4379 4747 4.380444 CGGCAAACATGGCTTACTTTGTAT 60.380 41.667 0.00 0.00 0.00 2.29
4392 4760 4.467198 ACTTTGTATTGTACTCCCTCCG 57.533 45.455 0.00 0.00 0.00 4.63
4399 4767 1.263356 TGTACTCCCTCCGTTCCAAG 58.737 55.000 0.00 0.00 0.00 3.61
4407 4775 3.073356 TCCCTCCGTTCCAAGTTAATTGT 59.927 43.478 0.00 0.00 37.17 2.71
4465 4833 5.817816 ACTTTGACCAAGTCTAGTGAAGTTG 59.182 40.000 0.00 0.00 42.62 3.16
4491 4859 4.816925 GGCTTGTCATAATTGAGTACTCCC 59.183 45.833 20.11 5.42 30.85 4.30
4494 4862 6.258947 GCTTGTCATAATTGAGTACTCCCTTC 59.741 42.308 20.11 0.00 30.85 3.46
4514 4882 6.591834 CCCTTCTGTTCCATAATATAAGAGCG 59.408 42.308 0.00 0.00 0.00 5.03
4516 4884 7.116948 CCTTCTGTTCCATAATATAAGAGCGTG 59.883 40.741 0.00 0.00 0.00 5.34
4518 4886 6.923508 TCTGTTCCATAATATAAGAGCGTGTG 59.076 38.462 0.00 0.00 0.00 3.82
4521 4889 5.538118 TCCATAATATAAGAGCGTGTGTGG 58.462 41.667 0.00 0.00 0.00 4.17
4522 4890 5.069914 TCCATAATATAAGAGCGTGTGTGGT 59.930 40.000 0.00 0.00 0.00 4.16
4523 4891 5.405571 CCATAATATAAGAGCGTGTGTGGTC 59.594 44.000 0.00 0.00 36.63 4.02
4525 4893 2.656560 ATAAGAGCGTGTGTGGTCTC 57.343 50.000 0.00 0.00 45.41 3.36
4526 4894 1.324383 TAAGAGCGTGTGTGGTCTCA 58.676 50.000 0.00 0.00 45.41 3.27
4528 4896 0.464036 AGAGCGTGTGTGGTCTCAAA 59.536 50.000 0.00 0.00 42.77 2.69
4529 4897 1.134521 AGAGCGTGTGTGGTCTCAAAA 60.135 47.619 0.00 0.00 42.77 2.44
4530 4898 1.668751 GAGCGTGTGTGGTCTCAAAAA 59.331 47.619 0.00 0.00 33.66 1.94
4531 4899 1.400494 AGCGTGTGTGGTCTCAAAAAC 59.600 47.619 0.00 0.00 0.00 2.43
4532 4900 1.854434 GCGTGTGTGGTCTCAAAAACG 60.854 52.381 0.00 0.00 0.00 3.60
4533 4901 1.822581 GTGTGTGGTCTCAAAAACGC 58.177 50.000 0.00 0.00 0.00 4.84
4535 4903 2.088423 TGTGTGGTCTCAAAAACGCTT 58.912 42.857 0.00 0.00 0.00 4.68
4540 4908 6.038382 TGTGTGGTCTCAAAAACGCTTTTATA 59.962 34.615 0.00 0.00 32.85 0.98
4541 4909 7.081976 GTGTGGTCTCAAAAACGCTTTTATAT 58.918 34.615 0.00 0.00 32.85 0.86
4542 4910 7.593644 GTGTGGTCTCAAAAACGCTTTTATATT 59.406 33.333 0.00 0.00 32.85 1.28
4544 4912 9.783256 GTGGTCTCAAAAACGCTTTTATATTAT 57.217 29.630 0.00 0.00 32.85 1.28
4545 4913 9.781834 TGGTCTCAAAAACGCTTTTATATTATG 57.218 29.630 0.00 0.00 32.85 1.90
4546 4914 9.233232 GGTCTCAAAAACGCTTTTATATTATGG 57.767 33.333 0.00 0.00 32.85 2.74
4547 4915 9.997482 GTCTCAAAAACGCTTTTATATTATGGA 57.003 29.630 0.00 0.00 32.85 3.41
4585 4953 1.153745 GTGGCAGCTAGTCTGGTCG 60.154 63.158 13.68 0.00 43.06 4.79
4588 4956 1.435515 GCAGCTAGTCTGGTCGAGG 59.564 63.158 13.68 0.00 43.06 4.63
4589 4957 1.316706 GCAGCTAGTCTGGTCGAGGT 61.317 60.000 13.68 0.00 43.06 3.85
4590 4958 1.178276 CAGCTAGTCTGGTCGAGGTT 58.822 55.000 6.34 0.00 39.15 3.50
4591 4959 1.135257 CAGCTAGTCTGGTCGAGGTTG 60.135 57.143 6.34 0.00 39.15 3.77
4592 4960 0.889306 GCTAGTCTGGTCGAGGTTGT 59.111 55.000 0.00 0.00 0.00 3.32
4593 4961 1.272769 GCTAGTCTGGTCGAGGTTGTT 59.727 52.381 0.00 0.00 0.00 2.83
4594 4962 2.288886 GCTAGTCTGGTCGAGGTTGTTT 60.289 50.000 0.00 0.00 0.00 2.83
4595 4963 2.240493 AGTCTGGTCGAGGTTGTTTG 57.760 50.000 0.00 0.00 0.00 2.93
4596 4964 1.202651 AGTCTGGTCGAGGTTGTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
4597 4965 0.834612 TCTGGTCGAGGTTGTTTGGT 59.165 50.000 0.00 0.00 0.00 3.67
4598 4966 1.210967 TCTGGTCGAGGTTGTTTGGTT 59.789 47.619 0.00 0.00 0.00 3.67
4599 4967 1.333619 CTGGTCGAGGTTGTTTGGTTG 59.666 52.381 0.00 0.00 0.00 3.77
4600 4968 1.065345 TGGTCGAGGTTGTTTGGTTGA 60.065 47.619 0.00 0.00 0.00 3.18
4601 4969 2.227194 GGTCGAGGTTGTTTGGTTGAT 58.773 47.619 0.00 0.00 0.00 2.57
4602 4970 2.031157 GGTCGAGGTTGTTTGGTTGATG 60.031 50.000 0.00 0.00 0.00 3.07
4603 4971 1.606668 TCGAGGTTGTTTGGTTGATGC 59.393 47.619 0.00 0.00 0.00 3.91
4604 4972 1.335872 CGAGGTTGTTTGGTTGATGCC 60.336 52.381 0.00 0.00 0.00 4.40
4605 4973 1.000843 GAGGTTGTTTGGTTGATGCCC 59.999 52.381 0.00 0.00 0.00 5.36
4606 4974 0.755686 GGTTGTTTGGTTGATGCCCA 59.244 50.000 0.00 0.00 0.00 5.36
4607 4975 1.540146 GGTTGTTTGGTTGATGCCCAC 60.540 52.381 0.00 0.00 0.00 4.61
4608 4976 1.137872 GTTGTTTGGTTGATGCCCACA 59.862 47.619 0.00 0.00 0.00 4.17
4609 4977 1.039068 TGTTTGGTTGATGCCCACAG 58.961 50.000 0.00 0.00 0.00 3.66
4610 4978 0.319813 GTTTGGTTGATGCCCACAGC 60.320 55.000 0.00 0.00 44.14 4.40
4627 4995 3.851955 CAGCCCTGCCAATCCATC 58.148 61.111 0.00 0.00 0.00 3.51
4628 4996 2.191513 CAGCCCTGCCAATCCATCG 61.192 63.158 0.00 0.00 0.00 3.84
4629 4997 2.908940 GCCCTGCCAATCCATCGG 60.909 66.667 0.00 0.00 0.00 4.18
4658 5026 4.385358 AAATATTGGTGACCGATTTGGC 57.615 40.909 10.13 0.00 43.94 4.52
4659 5027 1.757682 TATTGGTGACCGATTTGGCC 58.242 50.000 10.13 0.00 43.94 5.36
4660 5028 1.312371 ATTGGTGACCGATTTGGCCG 61.312 55.000 0.00 0.00 43.94 6.13
4661 5029 3.810896 GGTGACCGATTTGGCCGC 61.811 66.667 0.00 0.00 43.94 6.53
4662 5030 3.810896 GTGACCGATTTGGCCGCC 61.811 66.667 1.04 1.04 43.94 6.13
4663 5031 4.337177 TGACCGATTTGGCCGCCA 62.337 61.111 8.43 8.43 43.94 5.69
4664 5032 3.508840 GACCGATTTGGCCGCCAG 61.509 66.667 12.95 2.93 43.94 4.85
4667 5035 3.520862 CGATTTGGCCGCCAGCAT 61.521 61.111 12.95 9.00 46.50 3.79
4668 5036 2.414594 GATTTGGCCGCCAGCATC 59.585 61.111 12.95 14.06 46.50 3.91
4669 5037 2.043652 ATTTGGCCGCCAGCATCT 60.044 55.556 12.95 0.00 46.50 2.90
4670 5038 2.068277 GATTTGGCCGCCAGCATCTC 62.068 60.000 19.72 8.81 46.50 2.75
4679 5047 2.586245 CAGCATCTCGCCCTGGAA 59.414 61.111 0.00 0.00 44.04 3.53
4680 5048 1.147824 CAGCATCTCGCCCTGGAAT 59.852 57.895 0.00 0.00 44.04 3.01
4681 5049 0.465097 CAGCATCTCGCCCTGGAATT 60.465 55.000 0.00 0.00 44.04 2.17
4682 5050 0.465097 AGCATCTCGCCCTGGAATTG 60.465 55.000 0.00 0.00 44.04 2.32
4683 5051 1.450531 GCATCTCGCCCTGGAATTGG 61.451 60.000 0.00 0.00 32.94 3.16
4684 5052 1.152881 ATCTCGCCCTGGAATTGGC 60.153 57.895 0.00 0.00 44.41 4.52
4685 5053 1.639635 ATCTCGCCCTGGAATTGGCT 61.640 55.000 0.00 0.00 45.71 4.75
4686 5054 0.980754 TCTCGCCCTGGAATTGGCTA 60.981 55.000 0.00 0.00 45.71 3.93
4687 5055 0.109342 CTCGCCCTGGAATTGGCTAT 59.891 55.000 0.00 0.00 45.71 2.97
4688 5056 0.108585 TCGCCCTGGAATTGGCTATC 59.891 55.000 0.00 0.00 45.71 2.08
4689 5057 1.230635 CGCCCTGGAATTGGCTATCG 61.231 60.000 0.00 0.00 45.71 2.92
4690 5058 0.108585 GCCCTGGAATTGGCTATCGA 59.891 55.000 0.00 0.00 44.46 3.59
4691 5059 1.879796 GCCCTGGAATTGGCTATCGAG 60.880 57.143 0.00 0.00 44.46 4.04
4692 5060 1.417890 CCCTGGAATTGGCTATCGAGT 59.582 52.381 0.00 0.00 0.00 4.18
4693 5061 2.487934 CCTGGAATTGGCTATCGAGTG 58.512 52.381 0.00 0.00 0.00 3.51
4694 5062 2.103094 CCTGGAATTGGCTATCGAGTGA 59.897 50.000 0.00 0.00 0.00 3.41
4695 5063 3.432186 CCTGGAATTGGCTATCGAGTGAA 60.432 47.826 0.00 0.00 0.00 3.18
4696 5064 3.531538 TGGAATTGGCTATCGAGTGAAC 58.468 45.455 0.00 0.00 0.00 3.18
4697 5065 3.197766 TGGAATTGGCTATCGAGTGAACT 59.802 43.478 0.00 0.00 0.00 3.01
4698 5066 3.557595 GGAATTGGCTATCGAGTGAACTG 59.442 47.826 0.00 0.00 0.00 3.16
4699 5067 2.672961 TTGGCTATCGAGTGAACTGG 57.327 50.000 0.00 0.00 0.00 4.00
4700 5068 1.847328 TGGCTATCGAGTGAACTGGA 58.153 50.000 0.00 0.00 35.23 3.86
4701 5069 2.176045 TGGCTATCGAGTGAACTGGAA 58.824 47.619 0.00 0.00 34.44 3.53
4702 5070 2.565391 TGGCTATCGAGTGAACTGGAAA 59.435 45.455 0.00 0.00 34.44 3.13
4703 5071 3.190874 GGCTATCGAGTGAACTGGAAAG 58.809 50.000 0.00 0.00 34.44 2.62
4704 5072 2.605366 GCTATCGAGTGAACTGGAAAGC 59.395 50.000 0.00 0.00 34.44 3.51
4705 5073 1.714794 ATCGAGTGAACTGGAAAGCG 58.285 50.000 0.00 0.00 34.44 4.68
4706 5074 0.944311 TCGAGTGAACTGGAAAGCGC 60.944 55.000 0.00 0.00 0.00 5.92
4707 5075 1.869690 GAGTGAACTGGAAAGCGCC 59.130 57.895 2.29 0.00 0.00 6.53
4708 5076 0.884704 GAGTGAACTGGAAAGCGCCA 60.885 55.000 2.29 0.00 36.30 5.69
4709 5077 0.465460 AGTGAACTGGAAAGCGCCAA 60.465 50.000 2.29 0.00 37.52 4.52
4710 5078 0.598065 GTGAACTGGAAAGCGCCAAT 59.402 50.000 2.29 0.00 37.52 3.16
4711 5079 0.597568 TGAACTGGAAAGCGCCAATG 59.402 50.000 2.29 0.00 37.52 2.82
4712 5080 0.109132 GAACTGGAAAGCGCCAATGG 60.109 55.000 2.29 0.00 37.52 3.16
4713 5081 1.535204 AACTGGAAAGCGCCAATGGG 61.535 55.000 2.29 0.00 37.52 4.00
4745 5113 3.205784 CAAAAATTTGGAGCCCAACCA 57.794 42.857 6.19 0.00 43.82 3.67
4746 5114 2.877786 CAAAAATTTGGAGCCCAACCAC 59.122 45.455 6.19 0.00 43.82 4.16
4747 5115 1.799933 AAATTTGGAGCCCAACCACA 58.200 45.000 6.19 0.00 43.82 4.17
4748 5116 1.047801 AATTTGGAGCCCAACCACAC 58.952 50.000 6.19 0.00 43.82 3.82
4749 5117 1.178534 ATTTGGAGCCCAACCACACG 61.179 55.000 6.19 0.00 43.82 4.49
4750 5118 3.783362 TTGGAGCCCAACCACACGG 62.783 63.158 2.84 0.00 38.75 4.94
4751 5119 3.948719 GGAGCCCAACCACACGGA 61.949 66.667 0.00 0.00 35.59 4.69
4752 5120 2.351276 GAGCCCAACCACACGGAT 59.649 61.111 0.00 0.00 35.59 4.18
4753 5121 1.600107 GAGCCCAACCACACGGATA 59.400 57.895 0.00 0.00 35.59 2.59
4754 5122 0.743345 GAGCCCAACCACACGGATAC 60.743 60.000 0.00 0.00 35.59 2.24
4755 5123 1.747745 GCCCAACCACACGGATACC 60.748 63.158 0.00 0.00 35.59 2.73
4756 5124 1.680487 CCCAACCACACGGATACCA 59.320 57.895 0.00 0.00 35.59 3.25
4757 5125 0.037017 CCCAACCACACGGATACCAA 59.963 55.000 0.00 0.00 35.59 3.67
4758 5126 1.340600 CCCAACCACACGGATACCAAT 60.341 52.381 0.00 0.00 35.59 3.16
4759 5127 1.742831 CCAACCACACGGATACCAATG 59.257 52.381 0.00 0.00 35.59 2.82
4760 5128 1.132262 CAACCACACGGATACCAATGC 59.868 52.381 0.00 0.00 35.59 3.56
4761 5129 0.326595 ACCACACGGATACCAATGCA 59.673 50.000 0.00 0.00 35.59 3.96
4762 5130 1.016627 CCACACGGATACCAATGCAG 58.983 55.000 0.00 0.00 0.00 4.41
4763 5131 0.378257 CACACGGATACCAATGCAGC 59.622 55.000 0.00 0.00 0.00 5.25
4764 5132 1.089481 ACACGGATACCAATGCAGCG 61.089 55.000 0.00 0.00 0.00 5.18
4765 5133 1.523711 ACGGATACCAATGCAGCGG 60.524 57.895 2.66 2.66 0.00 5.52
4766 5134 1.523711 CGGATACCAATGCAGCGGT 60.524 57.895 13.86 13.86 39.41 5.68
4767 5135 1.498865 CGGATACCAATGCAGCGGTC 61.499 60.000 12.85 0.90 36.69 4.79
4768 5136 0.463654 GGATACCAATGCAGCGGTCA 60.464 55.000 12.85 1.95 36.69 4.02
4769 5137 1.378531 GATACCAATGCAGCGGTCAA 58.621 50.000 12.85 0.00 36.69 3.18
4770 5138 1.064060 GATACCAATGCAGCGGTCAAC 59.936 52.381 12.85 3.54 36.69 3.18
4801 5169 2.185350 CTGGGCAGCTCACGGTAG 59.815 66.667 0.00 0.00 0.00 3.18
4802 5170 4.082523 TGGGCAGCTCACGGTAGC 62.083 66.667 0.00 3.25 43.11 3.58
4808 5176 2.805546 GCTCACGGTAGCGATCCA 59.194 61.111 22.88 0.29 31.76 3.41
4809 5177 1.141019 GCTCACGGTAGCGATCCAA 59.859 57.895 22.88 0.29 31.76 3.53
4810 5178 0.459585 GCTCACGGTAGCGATCCAAA 60.460 55.000 22.88 0.00 31.76 3.28
4811 5179 1.278238 CTCACGGTAGCGATCCAAAC 58.722 55.000 22.88 0.00 0.00 2.93
4812 5180 0.604073 TCACGGTAGCGATCCAAACA 59.396 50.000 22.88 0.00 0.00 2.83
4813 5181 0.719465 CACGGTAGCGATCCAAACAC 59.281 55.000 22.88 0.00 0.00 3.32
4814 5182 0.319083 ACGGTAGCGATCCAAACACA 59.681 50.000 22.88 0.00 0.00 3.72
4815 5183 0.719465 CGGTAGCGATCCAAACACAC 59.281 55.000 9.07 0.00 0.00 3.82
4816 5184 1.084289 GGTAGCGATCCAAACACACC 58.916 55.000 0.00 0.00 0.00 4.16
4817 5185 0.719465 GTAGCGATCCAAACACACCG 59.281 55.000 0.00 0.00 0.00 4.94
4837 5205 2.260247 TGCAAAGCAGCACATCTCC 58.740 52.632 0.00 0.00 40.11 3.71
4843 5211 1.376543 AGCAGCACATCTCCAAATCG 58.623 50.000 0.00 0.00 0.00 3.34
4927 5295 3.430042 AACAGTCAATGTCCAGCATCT 57.570 42.857 0.00 0.00 43.00 2.90
4944 5312 4.929808 AGCATCTTTTGTGTAGGAGTAACG 59.070 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 85 4.478317 TGATTTGGTTAGTGGATCCCTGAT 59.522 41.667 9.90 0.00 0.00 2.90
109 113 9.620660 CTATTAAAATTCTAGTTTTTGCGGTGT 57.379 29.630 13.09 0.00 33.62 4.16
142 281 2.140717 CGAGAAGCCGGTAAGTTGTTT 58.859 47.619 1.90 0.00 0.00 2.83
341 480 3.015327 ACCGTCGACAGTTATCTTAGCT 58.985 45.455 17.16 0.00 0.00 3.32
343 482 6.141462 GGATTACCGTCGACAGTTATCTTAG 58.859 44.000 22.98 2.62 0.00 2.18
366 505 0.178068 ATTTCTGATCGGGGTGTCGG 59.822 55.000 0.62 0.00 0.00 4.79
446 586 3.375299 GGGACATATTCTGCGGCATAATC 59.625 47.826 15.69 4.29 0.00 1.75
533 673 2.849537 TCCCGAAACCCTAACCCTATT 58.150 47.619 0.00 0.00 0.00 1.73
551 691 2.737039 GCTTCAGGTGAGTCGATCTTCC 60.737 54.545 0.00 0.00 0.00 3.46
637 777 1.071371 CGTCGTCTCTCGTTATCTCGG 60.071 57.143 0.00 0.00 40.80 4.63
711 854 1.021202 GCATAATAACTGGCACCGCA 58.979 50.000 0.00 0.00 0.00 5.69
1209 1363 1.901464 GCCTTCAGTTCCCGGCAAA 60.901 57.895 0.00 0.00 42.06 3.68
1358 1515 5.801350 TCAGCAAGTGCACAATATTAGAC 57.199 39.130 21.04 0.00 45.16 2.59
1398 1555 3.997021 AGAATCTAACACCGAAACAGCAG 59.003 43.478 0.00 0.00 0.00 4.24
1407 1564 2.332063 ATGCCCAGAATCTAACACCG 57.668 50.000 0.00 0.00 0.00 4.94
1487 1644 2.091885 GTCCTCATCTCCTGTCTCCTCT 60.092 54.545 0.00 0.00 0.00 3.69
1553 1710 2.897780 GCGTGCAAGCCAAAATCAA 58.102 47.368 14.16 0.00 0.00 2.57
1705 1862 0.747852 CATGCATGCCATAACAGCCA 59.252 50.000 14.93 0.00 31.47 4.75
1728 1885 8.814931 TGAATGTCCCAATTATGAAAAATCAGT 58.185 29.630 0.00 0.00 0.00 3.41
1751 1908 7.924947 TGCAATGTGAATCTTGTAATTTGTGAA 59.075 29.630 0.00 0.00 0.00 3.18
1758 1915 8.836268 AACAAATGCAATGTGAATCTTGTAAT 57.164 26.923 9.03 0.00 34.28 1.89
2017 2198 7.805163 ACATATCCTTTGATACCTGACATTCA 58.195 34.615 0.00 0.00 36.32 2.57
2018 2199 8.682936 AACATATCCTTTGATACCTGACATTC 57.317 34.615 0.00 0.00 36.32 2.67
2019 2200 8.497745 AGAACATATCCTTTGATACCTGACATT 58.502 33.333 0.00 0.00 36.32 2.71
2020 2201 8.038862 AGAACATATCCTTTGATACCTGACAT 57.961 34.615 0.00 0.00 36.32 3.06
2021 2202 7.419057 GGAGAACATATCCTTTGATACCTGACA 60.419 40.741 0.00 0.00 36.32 3.58
2022 2203 6.931840 GGAGAACATATCCTTTGATACCTGAC 59.068 42.308 0.00 0.00 36.32 3.51
2023 2204 6.615316 TGGAGAACATATCCTTTGATACCTGA 59.385 38.462 0.00 0.00 36.32 3.86
2024 2205 6.708054 GTGGAGAACATATCCTTTGATACCTG 59.292 42.308 0.00 0.00 36.32 4.00
2025 2206 6.617371 AGTGGAGAACATATCCTTTGATACCT 59.383 38.462 0.00 0.00 36.32 3.08
2026 2207 6.831976 AGTGGAGAACATATCCTTTGATACC 58.168 40.000 0.00 0.00 36.32 2.73
2027 2208 9.832445 TTAAGTGGAGAACATATCCTTTGATAC 57.168 33.333 0.00 0.00 36.32 2.24
2065 2246 9.996554 TCAGAAAGTAAATGAGACAAGTAATGA 57.003 29.630 0.00 0.00 0.00 2.57
2069 2250 9.778741 ACATTCAGAAAGTAAATGAGACAAGTA 57.221 29.630 1.65 0.00 35.03 2.24
2070 2251 8.682936 ACATTCAGAAAGTAAATGAGACAAGT 57.317 30.769 1.65 0.00 35.03 3.16
2071 2252 8.777413 TGACATTCAGAAAGTAAATGAGACAAG 58.223 33.333 1.65 0.00 35.03 3.16
2072 2253 8.675705 TGACATTCAGAAAGTAAATGAGACAA 57.324 30.769 1.65 0.00 35.03 3.18
2188 2371 3.891056 ATGTCGACGGAAAAAGGAAAC 57.109 42.857 11.62 0.00 0.00 2.78
2196 2379 5.453648 CCACAAAAATAATGTCGACGGAAA 58.546 37.500 11.62 0.00 0.00 3.13
2216 2399 8.138712 TGTATCACAAAAATTAAGTGAACCCAC 58.861 33.333 10.38 0.00 44.47 4.61
2240 2424 6.219473 TGAATTTGCCATTTTCATAACGTGT 58.781 32.000 0.00 0.00 0.00 4.49
2285 2469 5.233050 GTCCAGTAACATTCTCATGACGATG 59.767 44.000 10.55 10.55 34.11 3.84
2286 2470 5.105351 TGTCCAGTAACATTCTCATGACGAT 60.105 40.000 0.00 0.00 34.11 3.73
2296 2480 9.612620 CTGAGTTAAAATTGTCCAGTAACATTC 57.387 33.333 0.00 0.00 0.00 2.67
2375 2559 3.726557 TGAACATGGAGAAGGCTGAAT 57.273 42.857 0.00 0.00 0.00 2.57
2394 2578 6.472163 GTCCTTGGTATCAAATTAAACGCATG 59.528 38.462 0.00 0.00 31.77 4.06
2495 2680 2.557490 TCACATGCATGCTGCTGTTTAA 59.443 40.909 26.53 4.00 45.31 1.52
2571 2756 3.671433 GCCATATTTATGCGCACATCCTG 60.671 47.826 14.90 6.47 37.74 3.86
2870 3056 7.168302 CAGACTTTTAGGCTAATACGACATCTG 59.832 40.741 7.96 10.23 26.27 2.90
2954 3140 9.403110 GGCAATTCATAGCATTCAATACTTAAG 57.597 33.333 0.00 0.00 0.00 1.85
2972 3158 4.564782 AGACATTCAGAGAGGCAATTCA 57.435 40.909 0.00 0.00 0.00 2.57
2990 3176 3.718815 AGACAAAGACTTCGGTGAAGAC 58.281 45.455 13.13 7.18 41.71 3.01
2997 3183 4.093556 GGAGCATTTAGACAAAGACTTCGG 59.906 45.833 0.00 0.00 0.00 4.30
3020 3206 3.303351 AAATTGGCCAGGGAGACATAG 57.697 47.619 5.11 0.00 0.00 2.23
3076 3262 2.227388 GGCACACAAGATGAGGAAAGTG 59.773 50.000 0.00 0.00 0.00 3.16
3078 3264 1.815003 GGGCACACAAGATGAGGAAAG 59.185 52.381 0.00 0.00 0.00 2.62
3192 3378 9.206870 CAAACAACCTGCAATATAACTGAAATT 57.793 29.630 0.00 0.00 0.00 1.82
3240 3426 0.475906 ACTGCAAAGGCTTCCAGTCT 59.524 50.000 21.04 6.48 41.91 3.24
3371 3557 4.240096 ACACCGTACAGTAATGTGCTAAC 58.760 43.478 5.98 0.00 0.00 2.34
3788 3974 2.680805 CGCTACCCTCCATGAACATGTT 60.681 50.000 11.78 11.78 37.11 2.71
3791 4159 1.204146 ACGCTACCCTCCATGAACAT 58.796 50.000 0.00 0.00 0.00 2.71
3827 4195 1.099295 TCTAGCCAGCATGCATGTGC 61.099 55.000 26.79 24.22 45.38 4.57
3828 4196 1.605753 ATCTAGCCAGCATGCATGTG 58.394 50.000 26.79 21.34 31.97 3.21
3856 4224 1.028330 ATGTGATGCAGCCAAGGACG 61.028 55.000 0.00 0.00 0.00 4.79
4008 4376 8.406297 CAAAGGTTTTCTAAGCCAGGATATAAC 58.594 37.037 0.00 0.00 32.14 1.89
4092 4460 3.193479 GTCTTGGCTTTTCCCTAATGTGG 59.807 47.826 0.00 0.00 0.00 4.17
4207 4575 1.804151 GTCATCGCCTTTTGCACAGTA 59.196 47.619 0.00 0.00 41.33 2.74
4226 4594 4.340666 TGCACACAAAATATGTTCACCAGT 59.659 37.500 0.00 0.00 41.46 4.00
4253 4621 3.639538 ACTTCATACATTACGCCGCTAG 58.360 45.455 0.00 0.00 0.00 3.42
4273 4641 9.869844 CGGATAAGAATCAGATATGTTTTCAAC 57.130 33.333 7.97 0.00 33.41 3.18
4351 4719 0.968405 AAGCCATGTTTGCCGACAAT 59.032 45.000 0.00 0.00 35.21 2.71
4373 4741 4.322953 GGAACGGAGGGAGTACAATACAAA 60.323 45.833 0.00 0.00 0.00 2.83
4375 4743 2.762327 GGAACGGAGGGAGTACAATACA 59.238 50.000 0.00 0.00 0.00 2.29
4376 4744 2.762327 TGGAACGGAGGGAGTACAATAC 59.238 50.000 0.00 0.00 0.00 1.89
4377 4745 3.104519 TGGAACGGAGGGAGTACAATA 57.895 47.619 0.00 0.00 0.00 1.90
4378 4746 1.946984 TGGAACGGAGGGAGTACAAT 58.053 50.000 0.00 0.00 0.00 2.71
4379 4747 1.621814 CTTGGAACGGAGGGAGTACAA 59.378 52.381 0.00 0.00 0.00 2.41
4392 4760 8.843885 ACCTAGAACTACAATTAACTTGGAAC 57.156 34.615 0.00 0.00 39.30 3.62
4457 4825 6.743575 ATTATGACAAGCCTACAACTTCAC 57.256 37.500 0.00 0.00 0.00 3.18
4465 4833 6.702282 GGAGTACTCAATTATGACAAGCCTAC 59.298 42.308 23.91 0.00 0.00 3.18
4491 4859 7.653713 ACACGCTCTTATATTATGGAACAGAAG 59.346 37.037 0.00 0.00 45.00 2.85
4514 4882 1.400494 AGCGTTTTTGAGACCACACAC 59.600 47.619 0.00 0.00 0.00 3.82
4516 4884 2.844122 AAGCGTTTTTGAGACCACAC 57.156 45.000 0.00 0.00 0.00 3.82
4518 4886 9.783256 ATAATATAAAAGCGTTTTTGAGACCAC 57.217 29.630 18.77 0.00 37.12 4.16
4521 4889 9.997482 TCCATAATATAAAAGCGTTTTTGAGAC 57.003 29.630 18.77 0.00 37.12 3.36
4528 4896 8.630037 CCTCCTTTCCATAATATAAAAGCGTTT 58.370 33.333 2.53 2.53 0.00 3.60
4529 4897 7.230712 CCCTCCTTTCCATAATATAAAAGCGTT 59.769 37.037 3.21 0.00 0.00 4.84
4530 4898 6.715264 CCCTCCTTTCCATAATATAAAAGCGT 59.285 38.462 3.21 0.00 0.00 5.07
4531 4899 6.940298 TCCCTCCTTTCCATAATATAAAAGCG 59.060 38.462 3.21 0.00 0.00 4.68
4532 4900 7.945109 ACTCCCTCCTTTCCATAATATAAAAGC 59.055 37.037 3.21 0.00 0.00 3.51
4535 4903 8.887393 GGTACTCCCTCCTTTCCATAATATAAA 58.113 37.037 0.00 0.00 0.00 1.40
4540 4908 4.660771 CAGGTACTCCCTCCTTTCCATAAT 59.339 45.833 0.00 0.00 43.86 1.28
4541 4909 4.037927 CAGGTACTCCCTCCTTTCCATAA 58.962 47.826 0.00 0.00 43.86 1.90
4542 4910 3.654273 CAGGTACTCCCTCCTTTCCATA 58.346 50.000 0.00 0.00 43.86 2.74
4544 4912 1.952621 CAGGTACTCCCTCCTTTCCA 58.047 55.000 0.00 0.00 43.86 3.53
4545 4913 0.542333 GCAGGTACTCCCTCCTTTCC 59.458 60.000 0.00 0.00 43.86 3.13
4546 4914 1.574263 AGCAGGTACTCCCTCCTTTC 58.426 55.000 0.00 0.00 43.86 2.62
4547 4915 1.630878 CAAGCAGGTACTCCCTCCTTT 59.369 52.381 0.00 0.00 38.22 3.11
4548 4916 1.280457 CAAGCAGGTACTCCCTCCTT 58.720 55.000 0.00 0.00 42.48 3.36
4549 4917 0.117340 ACAAGCAGGTACTCCCTCCT 59.883 55.000 0.00 0.00 43.86 3.69
4550 4918 0.250513 CACAAGCAGGTACTCCCTCC 59.749 60.000 0.00 0.00 43.86 4.30
4585 4953 1.000843 GGGCATCAACCAAACAACCTC 59.999 52.381 0.00 0.00 0.00 3.85
4588 4956 1.137872 TGTGGGCATCAACCAAACAAC 59.862 47.619 0.00 0.00 40.24 3.32
4589 4957 1.411977 CTGTGGGCATCAACCAAACAA 59.588 47.619 0.00 0.00 40.24 2.83
4590 4958 1.039068 CTGTGGGCATCAACCAAACA 58.961 50.000 0.00 0.00 40.24 2.83
4591 4959 0.319813 GCTGTGGGCATCAACCAAAC 60.320 55.000 0.00 0.00 40.24 2.93
4592 4960 2.048601 GCTGTGGGCATCAACCAAA 58.951 52.632 0.00 0.00 40.24 3.28
4593 4961 3.776158 GCTGTGGGCATCAACCAA 58.224 55.556 0.00 0.00 40.24 3.67
4610 4978 2.191513 CGATGGATTGGCAGGGCTG 61.192 63.158 0.00 0.00 0.00 4.85
4611 4979 2.194056 CGATGGATTGGCAGGGCT 59.806 61.111 0.00 0.00 0.00 5.19
4612 4980 2.908940 CCGATGGATTGGCAGGGC 60.909 66.667 0.00 0.00 0.00 5.19
4618 4986 3.585990 GGCGTGCCGATGGATTGG 61.586 66.667 0.00 0.00 0.00 3.16
4619 4987 1.932011 TTTGGCGTGCCGATGGATTG 61.932 55.000 6.37 0.00 39.42 2.67
4620 4988 1.247419 TTTTGGCGTGCCGATGGATT 61.247 50.000 6.37 0.00 39.42 3.01
4621 4989 1.037030 ATTTTGGCGTGCCGATGGAT 61.037 50.000 6.37 0.00 39.42 3.41
4622 4990 0.393132 TATTTTGGCGTGCCGATGGA 60.393 50.000 6.37 0.00 39.42 3.41
4623 4991 0.667993 ATATTTTGGCGTGCCGATGG 59.332 50.000 6.37 0.00 39.42 3.51
4624 4992 2.118683 CAATATTTTGGCGTGCCGATG 58.881 47.619 6.37 0.00 39.42 3.84
4625 4993 1.066908 CCAATATTTTGGCGTGCCGAT 59.933 47.619 6.37 3.19 45.71 4.18
4626 4994 0.453793 CCAATATTTTGGCGTGCCGA 59.546 50.000 6.37 0.60 45.71 5.54
4627 4995 2.956469 CCAATATTTTGGCGTGCCG 58.044 52.632 6.37 0.00 45.71 5.69
4635 5003 4.566360 GCCAAATCGGTCACCAATATTTTG 59.434 41.667 0.00 0.00 36.97 2.44
4636 5004 4.382577 GGCCAAATCGGTCACCAATATTTT 60.383 41.667 0.00 0.00 40.18 1.82
4637 5005 3.132111 GGCCAAATCGGTCACCAATATTT 59.868 43.478 0.00 0.00 40.18 1.40
4638 5006 2.693074 GGCCAAATCGGTCACCAATATT 59.307 45.455 0.00 0.00 40.18 1.28
4639 5007 2.306847 GGCCAAATCGGTCACCAATAT 58.693 47.619 0.00 0.00 40.18 1.28
4640 5008 1.757682 GGCCAAATCGGTCACCAATA 58.242 50.000 0.00 0.00 40.18 1.90
4641 5009 1.312371 CGGCCAAATCGGTCACCAAT 61.312 55.000 2.24 0.00 40.64 3.16
4642 5010 1.969064 CGGCCAAATCGGTCACCAA 60.969 57.895 2.24 0.00 40.64 3.67
4643 5011 2.359354 CGGCCAAATCGGTCACCA 60.359 61.111 2.24 0.00 40.64 4.17
4644 5012 3.810896 GCGGCCAAATCGGTCACC 61.811 66.667 2.24 0.00 40.64 4.02
4645 5013 3.810896 GGCGGCCAAATCGGTCAC 61.811 66.667 15.62 0.00 40.64 3.67
4646 5014 4.337177 TGGCGGCCAAATCGGTCA 62.337 61.111 21.55 0.00 40.64 4.02
4647 5015 3.508840 CTGGCGGCCAAATCGGTC 61.509 66.667 23.94 0.00 36.97 4.79
4650 5018 3.474230 GATGCTGGCGGCCAAATCG 62.474 63.158 23.94 12.39 40.92 3.34
4651 5019 2.068277 GAGATGCTGGCGGCCAAATC 62.068 60.000 25.91 25.91 40.92 2.17
4652 5020 2.043652 AGATGCTGGCGGCCAAAT 60.044 55.556 23.94 18.84 40.92 2.32
4653 5021 2.751436 GAGATGCTGGCGGCCAAA 60.751 61.111 23.94 14.68 40.92 3.28
4661 5029 2.335092 ATTCCAGGGCGAGATGCTGG 62.335 60.000 0.00 0.00 45.43 4.85
4662 5030 0.465097 AATTCCAGGGCGAGATGCTG 60.465 55.000 0.00 0.00 45.43 4.41
4663 5031 0.465097 CAATTCCAGGGCGAGATGCT 60.465 55.000 0.00 0.00 45.43 3.79
4664 5032 1.450531 CCAATTCCAGGGCGAGATGC 61.451 60.000 0.00 0.00 45.38 3.91
4665 5033 1.450531 GCCAATTCCAGGGCGAGATG 61.451 60.000 0.00 0.00 40.93 2.90
4666 5034 1.152881 GCCAATTCCAGGGCGAGAT 60.153 57.895 0.00 0.00 40.93 2.75
4667 5035 2.272146 GCCAATTCCAGGGCGAGA 59.728 61.111 0.00 0.00 40.93 4.04
4672 5040 1.417890 ACTCGATAGCCAATTCCAGGG 59.582 52.381 0.00 0.00 0.00 4.45
4673 5041 2.103094 TCACTCGATAGCCAATTCCAGG 59.897 50.000 0.00 0.00 0.00 4.45
4674 5042 3.459232 TCACTCGATAGCCAATTCCAG 57.541 47.619 0.00 0.00 0.00 3.86
4675 5043 3.197766 AGTTCACTCGATAGCCAATTCCA 59.802 43.478 0.00 0.00 0.00 3.53
4676 5044 3.557595 CAGTTCACTCGATAGCCAATTCC 59.442 47.826 0.00 0.00 0.00 3.01
4677 5045 3.557595 CCAGTTCACTCGATAGCCAATTC 59.442 47.826 0.00 0.00 0.00 2.17
4678 5046 3.197766 TCCAGTTCACTCGATAGCCAATT 59.802 43.478 0.00 0.00 0.00 2.32
4679 5047 2.766263 TCCAGTTCACTCGATAGCCAAT 59.234 45.455 0.00 0.00 0.00 3.16
4680 5048 2.176045 TCCAGTTCACTCGATAGCCAA 58.824 47.619 0.00 0.00 0.00 4.52
4681 5049 1.847328 TCCAGTTCACTCGATAGCCA 58.153 50.000 0.00 0.00 0.00 4.75
4682 5050 2.961526 TTCCAGTTCACTCGATAGCC 57.038 50.000 0.00 0.00 0.00 3.93
4683 5051 2.605366 GCTTTCCAGTTCACTCGATAGC 59.395 50.000 2.32 2.32 33.20 2.97
4684 5052 2.854777 CGCTTTCCAGTTCACTCGATAG 59.145 50.000 0.00 0.00 0.00 2.08
4685 5053 2.876091 CGCTTTCCAGTTCACTCGATA 58.124 47.619 0.00 0.00 0.00 2.92
4686 5054 1.714794 CGCTTTCCAGTTCACTCGAT 58.285 50.000 0.00 0.00 0.00 3.59
4687 5055 0.944311 GCGCTTTCCAGTTCACTCGA 60.944 55.000 0.00 0.00 0.00 4.04
4688 5056 1.493311 GCGCTTTCCAGTTCACTCG 59.507 57.895 0.00 0.00 0.00 4.18
4689 5057 0.884704 TGGCGCTTTCCAGTTCACTC 60.885 55.000 7.64 0.00 0.00 3.51
4690 5058 0.465460 TTGGCGCTTTCCAGTTCACT 60.465 50.000 7.64 0.00 37.44 3.41
4691 5059 0.598065 ATTGGCGCTTTCCAGTTCAC 59.402 50.000 7.64 0.00 37.44 3.18
4692 5060 0.597568 CATTGGCGCTTTCCAGTTCA 59.402 50.000 7.64 0.00 37.44 3.18
4693 5061 0.109132 CCATTGGCGCTTTCCAGTTC 60.109 55.000 7.64 0.00 37.44 3.01
4694 5062 1.535204 CCCATTGGCGCTTTCCAGTT 61.535 55.000 7.64 0.00 37.44 3.16
4695 5063 1.978617 CCCATTGGCGCTTTCCAGT 60.979 57.895 7.64 0.00 37.44 4.00
4696 5064 2.887360 CCCATTGGCGCTTTCCAG 59.113 61.111 7.64 0.00 37.44 3.86
4725 5093 2.877786 GTGGTTGGGCTCCAAATTTTTG 59.122 45.455 8.06 0.00 45.73 2.44
4726 5094 2.507471 TGTGGTTGGGCTCCAAATTTTT 59.493 40.909 8.06 0.00 45.73 1.94
4727 5095 2.122768 TGTGGTTGGGCTCCAAATTTT 58.877 42.857 8.06 0.00 45.73 1.82
4728 5096 1.416030 GTGTGGTTGGGCTCCAAATTT 59.584 47.619 8.06 0.00 45.73 1.82
4729 5097 1.047801 GTGTGGTTGGGCTCCAAATT 58.952 50.000 8.06 0.00 45.73 1.82
4730 5098 1.178534 CGTGTGGTTGGGCTCCAAAT 61.179 55.000 8.06 0.00 45.73 2.32
4731 5099 1.826054 CGTGTGGTTGGGCTCCAAA 60.826 57.895 8.06 0.00 45.73 3.28
4732 5100 2.203280 CGTGTGGTTGGGCTCCAA 60.203 61.111 2.84 2.84 41.69 3.53
4733 5101 4.263572 CCGTGTGGTTGGGCTCCA 62.264 66.667 0.00 0.00 0.00 3.86
4734 5102 1.906105 TATCCGTGTGGTTGGGCTCC 61.906 60.000 0.00 0.00 36.30 4.70
4735 5103 0.743345 GTATCCGTGTGGTTGGGCTC 60.743 60.000 0.00 0.00 36.30 4.70
4736 5104 1.298667 GTATCCGTGTGGTTGGGCT 59.701 57.895 0.00 0.00 36.30 5.19
4737 5105 1.747745 GGTATCCGTGTGGTTGGGC 60.748 63.158 0.00 0.00 36.30 5.36
4738 5106 0.037017 TTGGTATCCGTGTGGTTGGG 59.963 55.000 0.00 0.00 36.30 4.12
4739 5107 1.742831 CATTGGTATCCGTGTGGTTGG 59.257 52.381 0.00 0.00 36.30 3.77
4740 5108 1.132262 GCATTGGTATCCGTGTGGTTG 59.868 52.381 0.00 0.00 36.30 3.77
4741 5109 1.271652 TGCATTGGTATCCGTGTGGTT 60.272 47.619 0.00 0.00 36.30 3.67
4742 5110 0.326595 TGCATTGGTATCCGTGTGGT 59.673 50.000 0.00 0.00 36.30 4.16
4743 5111 1.016627 CTGCATTGGTATCCGTGTGG 58.983 55.000 0.00 0.00 0.00 4.17
4744 5112 0.378257 GCTGCATTGGTATCCGTGTG 59.622 55.000 0.00 0.00 0.00 3.82
4745 5113 1.089481 CGCTGCATTGGTATCCGTGT 61.089 55.000 0.00 0.00 0.00 4.49
4746 5114 1.643292 CGCTGCATTGGTATCCGTG 59.357 57.895 0.00 0.00 0.00 4.94
4747 5115 1.523711 CCGCTGCATTGGTATCCGT 60.524 57.895 0.00 0.00 0.00 4.69
4748 5116 1.498865 GACCGCTGCATTGGTATCCG 61.499 60.000 9.78 0.00 38.99 4.18
4749 5117 0.463654 TGACCGCTGCATTGGTATCC 60.464 55.000 9.78 0.00 38.99 2.59
4750 5118 1.064060 GTTGACCGCTGCATTGGTATC 59.936 52.381 9.78 0.52 38.99 2.24
4751 5119 1.094785 GTTGACCGCTGCATTGGTAT 58.905 50.000 9.78 0.00 38.99 2.73
4752 5120 1.295357 CGTTGACCGCTGCATTGGTA 61.295 55.000 9.78 0.00 38.99 3.25
4753 5121 2.616330 CGTTGACCGCTGCATTGGT 61.616 57.895 9.59 9.59 42.42 3.67
4754 5122 2.176546 CGTTGACCGCTGCATTGG 59.823 61.111 0.00 2.94 0.00 3.16
4784 5152 2.185350 CTACCGTGAGCTGCCCAG 59.815 66.667 0.00 0.00 0.00 4.45
4785 5153 4.082523 GCTACCGTGAGCTGCCCA 62.083 66.667 0.00 0.00 39.50 5.36
4787 5155 3.432051 ATCGCTACCGTGAGCTGCC 62.432 63.158 0.00 0.00 40.51 4.85
4788 5156 1.946650 GATCGCTACCGTGAGCTGC 60.947 63.158 0.00 0.00 40.51 5.25
4789 5157 1.299468 GGATCGCTACCGTGAGCTG 60.299 63.158 0.00 0.00 40.51 4.24
4790 5158 1.320344 TTGGATCGCTACCGTGAGCT 61.320 55.000 4.50 0.00 40.51 4.09
4791 5159 0.459585 TTTGGATCGCTACCGTGAGC 60.460 55.000 0.00 0.00 39.20 4.26
4792 5160 1.278238 GTTTGGATCGCTACCGTGAG 58.722 55.000 0.00 0.00 35.54 3.51
4793 5161 0.604073 TGTTTGGATCGCTACCGTGA 59.396 50.000 0.00 0.00 35.54 4.35
4794 5162 0.719465 GTGTTTGGATCGCTACCGTG 59.281 55.000 0.00 0.00 35.54 4.94
4795 5163 0.319083 TGTGTTTGGATCGCTACCGT 59.681 50.000 0.00 0.00 35.54 4.83
4796 5164 0.719465 GTGTGTTTGGATCGCTACCG 59.281 55.000 0.00 0.00 0.00 4.02
4797 5165 1.084289 GGTGTGTTTGGATCGCTACC 58.916 55.000 0.00 0.00 0.00 3.18
4798 5166 0.719465 CGGTGTGTTTGGATCGCTAC 59.281 55.000 0.00 0.00 0.00 3.58
4799 5167 0.390603 CCGGTGTGTTTGGATCGCTA 60.391 55.000 0.00 0.00 0.00 4.26
4800 5168 1.671054 CCGGTGTGTTTGGATCGCT 60.671 57.895 0.00 0.00 0.00 4.93
4801 5169 1.964373 ACCGGTGTGTTTGGATCGC 60.964 57.895 6.12 0.00 0.00 4.58
4802 5170 1.866237 CACCGGTGTGTTTGGATCG 59.134 57.895 26.95 0.00 37.72 3.69
4803 5171 1.169661 TGCACCGGTGTGTTTGGATC 61.170 55.000 33.92 15.44 44.65 3.36
4804 5172 0.753479 TTGCACCGGTGTGTTTGGAT 60.753 50.000 33.92 0.00 44.65 3.41
4805 5173 0.965866 TTTGCACCGGTGTGTTTGGA 60.966 50.000 33.92 7.06 44.65 3.53
4806 5174 0.527385 CTTTGCACCGGTGTGTTTGG 60.527 55.000 33.92 16.27 44.65 3.28
4807 5175 1.145162 GCTTTGCACCGGTGTGTTTG 61.145 55.000 33.92 20.84 44.65 2.93
4808 5176 1.140804 GCTTTGCACCGGTGTGTTT 59.859 52.632 33.92 0.00 44.65 2.83
4809 5177 2.003658 CTGCTTTGCACCGGTGTGTT 62.004 55.000 33.92 0.00 44.65 3.32
4810 5178 2.439338 TGCTTTGCACCGGTGTGT 60.439 55.556 33.92 0.00 44.65 3.72
4811 5179 2.332514 CTGCTTTGCACCGGTGTG 59.667 61.111 33.92 21.81 45.65 3.82
4812 5180 3.595758 GCTGCTTTGCACCGGTGT 61.596 61.111 33.92 0.00 33.79 4.16
4813 5181 3.594775 TGCTGCTTTGCACCGGTG 61.595 61.111 30.66 30.66 38.12 4.94
4837 5205 2.420628 TTTGTGCAGCTTCCGATTTG 57.579 45.000 0.00 0.00 0.00 2.32
4843 5211 2.422276 ACGAATTTTGTGCAGCTTCC 57.578 45.000 0.00 0.00 0.00 3.46
4927 5295 5.296531 GGAAAACCGTTACTCCTACACAAAA 59.703 40.000 5.43 0.00 0.00 2.44
4944 5312 1.197036 GTTAGTGAGCGCTGGAAAACC 59.803 52.381 18.48 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.