Multiple sequence alignment - TraesCS3D01G107900

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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 TraesCS3D01G107900 chr3D 100.000 5544 0 0 1 5544 61564400 61569943 0 10238
1 TraesCS3D01G107900 chr3A 91.703 2278 83 36 2579 4778 69640665 69642914 0 3062
2 TraesCS3D01G107900 chr3A 87.424 1805 87 59 3 1710 69638054 69639815 0 1947
3 TraesCS3D01G107900 chr3A 88.221 849 60 20 1707 2535 69639839 69640667 0 977
4 TraesCS3D01G107900 chr3A 92.183 678 25 7 4893 5544 69646597 69647272 0 933
5 TraesCS3D01G107900 chr3B 92.468 2111 61 43 2728 4785 97735778 97737843 0 2928
6 TraesCS3D01G107900 chr3B 86.667 2580 159 74 52 2535 97733242 97735732 0 2687
7 TraesCS3D01G107900 chr3B 93.124 669 26 8 4876 5544 97738122 97738770 0 963


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 TraesCS3D01G107900 chr3D 61564400 61569943 5543 False 10238.000000 10238 100.00000 1 5544 1 chr3D.!!$F1 5543
1 TraesCS3D01G107900 chr3A 69638054 69647272 9218 False 1729.750000 3062 89.88275 3 5544 4 chr3A.!!$F1 5541
2 TraesCS3D01G107900 chr3B 97733242 97738770 5528 False 2192.666667 2928 90.75300 52 5544 3 chr3B.!!$F1 5492

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
703 764 0.037697 TTTGGCGCGTGATGAGTAGT 60.038 50.0 8.43 0.0 0.00 2.73 F
705 766 0.380733 TGGCGCGTGATGAGTAGTAG 59.619 55.0 8.43 0.0 0.00 2.57 F
1940 2129 0.031857 CACACGCATGGCTCCAAAAA 59.968 50.0 0.00 0.0 0.00 1.94 F
1944 2133 0.531657 CGCATGGCTCCAAAAATCCA 59.468 50.0 0.00 0.0 0.00 3.41 F
2309 2516 0.755686 TTTGGTTGATGGTTGGGTGC 59.244 50.0 0.00 0.0 0.00 5.01 F
3223 3478 1.041437 CGATCTTGGGTAGGAGTCCC 58.959 60.0 5.25 0.0 44.81 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2058 0.036732 TGCTGAATTTCCTGACCGCT 59.963 50.0 0.00 0.0 0.00 5.52 R
1964 2153 0.322975 CTGTTCAGCCCAGCACTACT 59.677 55.0 0.00 0.0 0.00 2.57 R
2801 3032 0.036164 AGCCCACGCATACACAAAGA 59.964 50.0 0.00 0.0 37.52 2.52 R
3122 3373 0.107017 CCGGCAATTGGAGAGGATGT 60.107 55.0 7.72 0.0 0.00 3.06 R
3293 3554 0.313043 ACGTTCACCTGTCGTTCGAT 59.687 50.0 0.00 0.0 34.07 3.59 R
5194 9107 0.035439 TCAAAAGGCCCTCGGTGATC 60.035 55.0 0.00 0.0 0.00 2.92 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
39 40 2.095718 GGCAGAAGTAGAAAAACAGCGG 60.096 50.000 0.00 0.00 0.00 5.52
46 47 5.080969 AGTAGAAAAACAGCGGCAGTATA 57.919 39.130 1.45 0.00 0.00 1.47
141 144 5.633182 CCAAAGCACGCACAATAATTTAACT 59.367 36.000 0.00 0.00 0.00 2.24
167 170 8.741603 TGACAACAAATCATCAGTGATCATAT 57.258 30.769 1.56 0.00 44.20 1.78
170 173 9.617523 ACAACAAATCATCAGTGATCATATACA 57.382 29.630 1.56 0.00 44.20 2.29
307 318 5.237048 CCATCGGTCAACATTTGGAATTTT 58.763 37.500 0.00 0.00 0.00 1.82
308 319 5.700373 CCATCGGTCAACATTTGGAATTTTT 59.300 36.000 0.00 0.00 0.00 1.94
309 320 6.347563 CCATCGGTCAACATTTGGAATTTTTG 60.348 38.462 0.00 0.00 0.00 2.44
311 322 6.520272 TCGGTCAACATTTGGAATTTTTGAT 58.480 32.000 0.00 0.00 0.00 2.57
312 323 7.661968 TCGGTCAACATTTGGAATTTTTGATA 58.338 30.769 0.00 0.00 0.00 2.15
314 325 8.934825 CGGTCAACATTTGGAATTTTTGATAAT 58.065 29.630 0.00 0.00 0.00 1.28
358 374 9.148104 CTTAGGTTTCTTAAGTGTACCATGTAC 57.852 37.037 18.69 0.00 0.00 2.90
359 375 7.312415 AGGTTTCTTAAGTGTACCATGTACT 57.688 36.000 18.69 0.00 0.00 2.73
360 376 7.742767 AGGTTTCTTAAGTGTACCATGTACTT 58.257 34.615 18.69 1.69 38.19 2.24
367 383 3.009033 AGTGTACCATGTACTTGCACCAT 59.991 43.478 11.70 0.00 0.00 3.55
373 389 7.659799 TGTACCATGTACTTGCACCATATAATC 59.340 37.037 3.24 0.00 0.00 1.75
414 438 2.814097 GCACTGTAACCACCACCATTCT 60.814 50.000 0.00 0.00 0.00 2.40
415 439 3.074412 CACTGTAACCACCACCATTCTC 58.926 50.000 0.00 0.00 0.00 2.87
433 457 1.373246 CCCACCAAAGCACGCATTG 60.373 57.895 0.12 0.12 0.00 2.82
561 598 2.279741 TCAATGATCGGAAAAGCCTCG 58.720 47.619 0.00 0.00 0.00 4.63
595 632 3.069158 CCAATCATGGGGAGAGCAAAATC 59.931 47.826 0.00 0.00 43.51 2.17
596 633 3.958798 CAATCATGGGGAGAGCAAAATCT 59.041 43.478 0.00 0.00 0.00 2.40
638 688 1.730487 AAAAACGTGCATGTGCCGA 59.270 47.368 13.39 0.00 41.18 5.54
702 763 0.370273 GTTTGGCGCGTGATGAGTAG 59.630 55.000 8.43 0.00 0.00 2.57
703 764 0.037697 TTTGGCGCGTGATGAGTAGT 60.038 50.000 8.43 0.00 0.00 2.73
704 765 0.812549 TTGGCGCGTGATGAGTAGTA 59.187 50.000 8.43 0.00 0.00 1.82
705 766 0.380733 TGGCGCGTGATGAGTAGTAG 59.619 55.000 8.43 0.00 0.00 2.57
706 767 0.661552 GGCGCGTGATGAGTAGTAGA 59.338 55.000 8.43 0.00 0.00 2.59
707 768 1.334239 GGCGCGTGATGAGTAGTAGAG 60.334 57.143 8.43 0.00 0.00 2.43
784 886 1.153628 CCGTCCACGTCCAATCTCC 60.154 63.158 0.00 0.00 37.74 3.71
949 1069 2.658268 CACGCGCACAGACAGACA 60.658 61.111 5.73 0.00 0.00 3.41
950 1070 2.355126 ACGCGCACAGACAGACAG 60.355 61.111 5.73 0.00 0.00 3.51
951 1071 2.050077 CGCGCACAGACAGACAGA 60.050 61.111 8.75 0.00 0.00 3.41
952 1072 1.661509 CGCGCACAGACAGACAGAA 60.662 57.895 8.75 0.00 0.00 3.02
953 1073 1.612469 CGCGCACAGACAGACAGAAG 61.612 60.000 8.75 0.00 0.00 2.85
956 1076 0.598680 GCACAGACAGACAGAAGCGT 60.599 55.000 0.00 0.00 0.00 5.07
1365 1524 3.423154 CGCTGCCACTCCGTTTCC 61.423 66.667 0.00 0.00 0.00 3.13
1425 1585 9.257428 AGCTTAGTTTAACAGTCCTCTAATACT 57.743 33.333 0.00 0.00 0.00 2.12
1437 1597 6.938030 AGTCCTCTAATACTACAATCTCTCCG 59.062 42.308 0.00 0.00 0.00 4.63
1441 1601 8.077386 CCTCTAATACTACAATCTCTCCGTTTC 58.923 40.741 0.00 0.00 0.00 2.78
1457 1617 0.387565 TTTCCTTTCCAAAGCCGCAC 59.612 50.000 0.00 0.00 34.69 5.34
1474 1634 2.472488 CGCACTTTTTCCTGCACATTTC 59.528 45.455 0.00 0.00 32.57 2.17
1496 1656 4.020573 TCTCATACCAACACACGATTTCCT 60.021 41.667 0.00 0.00 0.00 3.36
1517 1677 4.152402 CCTCCGATTCTACAAACAACACAG 59.848 45.833 0.00 0.00 0.00 3.66
1536 1696 4.806247 CACAGGATTGACGATTTCTACCTC 59.194 45.833 0.00 0.00 0.00 3.85
1679 1841 1.953686 ACAAGCACGCTTTACCAATGT 59.046 42.857 0.44 0.00 33.42 2.71
1697 1859 3.940209 TGTGTCCAAATCTTGCAATCC 57.060 42.857 0.00 0.00 0.00 3.01
1704 1866 7.603784 GTGTCCAAATCTTGCAATCCTAAAAAT 59.396 33.333 0.00 0.00 0.00 1.82
1757 1946 6.144886 GCGTTGATGATGTATTACCATTACGA 59.855 38.462 16.44 0.00 34.05 3.43
1760 1949 6.153756 TGATGATGTATTACCATTACGACGG 58.846 40.000 0.00 0.00 0.00 4.79
1806 1995 1.576421 CTTGTGAACCGCAAGCCTC 59.424 57.895 7.23 0.00 43.37 4.70
1807 1996 0.886490 CTTGTGAACCGCAAGCCTCT 60.886 55.000 7.23 0.00 43.37 3.69
1808 1997 1.165907 TTGTGAACCGCAAGCCTCTG 61.166 55.000 0.00 0.00 30.10 3.35
1809 1998 1.598130 GTGAACCGCAAGCCTCTGT 60.598 57.895 0.00 0.00 0.00 3.41
1840 2029 2.344025 GTAGTTTACAACGCCTCAGGG 58.656 52.381 0.00 0.00 36.23 4.45
1866 2055 6.981559 TCAATACAAACCTTTTTGCCAAGTAC 59.018 34.615 0.00 0.00 45.32 2.73
1867 2056 3.776340 ACAAACCTTTTTGCCAAGTACG 58.224 40.909 0.00 0.00 45.32 3.67
1868 2057 3.193903 ACAAACCTTTTTGCCAAGTACGT 59.806 39.130 0.00 0.00 45.32 3.57
1869 2058 4.398673 ACAAACCTTTTTGCCAAGTACGTA 59.601 37.500 0.00 0.00 45.32 3.57
1893 2082 3.057315 CGGTCAGGAAATTCAGCATTTGT 60.057 43.478 0.00 0.00 35.02 2.83
1925 2114 0.596082 AATGGCTGCGTTAACCACAC 59.404 50.000 0.00 0.00 35.99 3.82
1926 2115 1.573829 ATGGCTGCGTTAACCACACG 61.574 55.000 0.00 0.00 40.75 4.49
1940 2129 0.031857 CACACGCATGGCTCCAAAAA 59.968 50.000 0.00 0.00 0.00 1.94
1941 2130 0.968405 ACACGCATGGCTCCAAAAAT 59.032 45.000 0.00 0.00 0.00 1.82
1943 2132 0.532115 ACGCATGGCTCCAAAAATCC 59.468 50.000 0.00 0.00 0.00 3.01
1944 2133 0.531657 CGCATGGCTCCAAAAATCCA 59.468 50.000 0.00 0.00 0.00 3.41
1945 2134 1.736696 CGCATGGCTCCAAAAATCCAC 60.737 52.381 0.00 0.00 0.00 4.02
1947 2136 2.093341 GCATGGCTCCAAAAATCCACAT 60.093 45.455 0.00 0.00 0.00 3.21
1948 2137 3.788937 CATGGCTCCAAAAATCCACATC 58.211 45.455 0.00 0.00 0.00 3.06
1949 2138 2.886913 TGGCTCCAAAAATCCACATCA 58.113 42.857 0.00 0.00 0.00 3.07
1950 2139 3.443052 TGGCTCCAAAAATCCACATCAT 58.557 40.909 0.00 0.00 0.00 2.45
1952 2141 5.022122 TGGCTCCAAAAATCCACATCATAA 58.978 37.500 0.00 0.00 0.00 1.90
1953 2142 5.662208 TGGCTCCAAAAATCCACATCATAAT 59.338 36.000 0.00 0.00 0.00 1.28
1955 2144 6.041296 GGCTCCAAAAATCCACATCATAATCT 59.959 38.462 0.00 0.00 0.00 2.40
1956 2145 7.231317 GGCTCCAAAAATCCACATCATAATCTA 59.769 37.037 0.00 0.00 0.00 1.98
1957 2146 8.295288 GCTCCAAAAATCCACATCATAATCTAG 58.705 37.037 0.00 0.00 0.00 2.43
1958 2147 9.347240 CTCCAAAAATCCACATCATAATCTAGT 57.653 33.333 0.00 0.00 0.00 2.57
1977 2166 2.242708 AGTAGAGTAGTAGTGCTGGGCT 59.757 50.000 0.00 0.00 0.00 5.19
1978 2167 1.479709 AGAGTAGTAGTGCTGGGCTG 58.520 55.000 0.00 0.00 0.00 4.85
2088 2277 5.379732 AGGTTTGAAACTGTGAAACGAAA 57.620 34.783 8.09 0.00 42.39 3.46
2090 2279 4.029750 GGTTTGAAACTGTGAAACGAAACG 59.970 41.667 8.09 0.00 42.39 3.60
2091 2280 4.665281 TTGAAACTGTGAAACGAAACGA 57.335 36.364 0.00 0.00 42.39 3.85
2148 2337 3.771216 CTCCTATTGGCCAGGCAATTAT 58.229 45.455 22.43 8.25 32.82 1.28
2174 2366 5.004922 TGACTTTTGGTTAGGCTTTTGTG 57.995 39.130 0.00 0.00 0.00 3.33
2207 2399 6.154706 AGCATAGCATGATCTATGACATGAGA 59.845 38.462 18.99 0.00 45.39 3.27
2242 2434 7.686438 TGACATTTATGCTTGAGTGTTATGT 57.314 32.000 0.00 0.00 0.00 2.29
2260 2455 8.223100 GTGTTATGTTTTAACAGTACTTACCGG 58.777 37.037 0.00 0.00 43.04 5.28
2262 2457 8.987890 GTTATGTTTTAACAGTACTTACCGGAA 58.012 33.333 9.46 0.00 43.04 4.30
2302 2509 4.895668 AAAGATGCATTTGGTTGATGGT 57.104 36.364 0.00 0.00 0.00 3.55
2306 2513 1.347050 TGCATTTGGTTGATGGTTGGG 59.653 47.619 0.00 0.00 0.00 4.12
2309 2516 0.755686 TTTGGTTGATGGTTGGGTGC 59.244 50.000 0.00 0.00 0.00 5.01
2467 2686 9.555727 GTTATAACAGTAATTAGGCAATCTCCA 57.444 33.333 10.81 0.00 0.00 3.86
2505 2724 6.618287 TTACAAGGACATGTTCTTGAAGTG 57.382 37.500 40.97 23.34 41.94 3.16
2535 2755 2.555227 GGGACTTTCAGCTCCAATGGAA 60.555 50.000 2.61 0.00 0.00 3.53
2536 2756 2.489722 GGACTTTCAGCTCCAATGGAAC 59.510 50.000 2.61 0.00 0.00 3.62
2552 2772 4.336889 TGGAACACAACAAAAACACCAA 57.663 36.364 0.00 0.00 0.00 3.67
2553 2773 4.703897 TGGAACACAACAAAAACACCAAA 58.296 34.783 0.00 0.00 0.00 3.28
2554 2774 5.308825 TGGAACACAACAAAAACACCAAAT 58.691 33.333 0.00 0.00 0.00 2.32
2555 2775 5.765182 TGGAACACAACAAAAACACCAAATT 59.235 32.000 0.00 0.00 0.00 1.82
2556 2776 6.934645 TGGAACACAACAAAAACACCAAATTA 59.065 30.769 0.00 0.00 0.00 1.40
2557 2777 7.118390 TGGAACACAACAAAAACACCAAATTAG 59.882 33.333 0.00 0.00 0.00 1.73
2558 2778 6.976636 ACACAACAAAAACACCAAATTAGG 57.023 33.333 0.00 0.00 0.00 2.69
2559 2779 6.702329 ACACAACAAAAACACCAAATTAGGA 58.298 32.000 0.00 0.00 0.00 2.94
2560 2780 7.162082 ACACAACAAAAACACCAAATTAGGAA 58.838 30.769 0.00 0.00 0.00 3.36
2561 2781 7.661847 ACACAACAAAAACACCAAATTAGGAAA 59.338 29.630 0.00 0.00 0.00 3.13
2562 2782 7.960195 CACAACAAAAACACCAAATTAGGAAAC 59.040 33.333 0.00 0.00 0.00 2.78
2563 2783 7.119992 ACAACAAAAACACCAAATTAGGAAACC 59.880 33.333 0.00 0.00 0.00 3.27
2564 2784 6.712276 ACAAAAACACCAAATTAGGAAACCA 58.288 32.000 0.00 0.00 0.00 3.67
2565 2785 7.168905 ACAAAAACACCAAATTAGGAAACCAA 58.831 30.769 0.00 0.00 0.00 3.67
2566 2786 7.665974 ACAAAAACACCAAATTAGGAAACCAAA 59.334 29.630 0.00 0.00 0.00 3.28
2567 2787 8.515414 CAAAAACACCAAATTAGGAAACCAAAA 58.485 29.630 0.00 0.00 0.00 2.44
2568 2788 7.857734 AAACACCAAATTAGGAAACCAAAAG 57.142 32.000 0.00 0.00 0.00 2.27
2569 2789 5.364778 ACACCAAATTAGGAAACCAAAAGC 58.635 37.500 0.00 0.00 0.00 3.51
2570 2790 5.104735 ACACCAAATTAGGAAACCAAAAGCA 60.105 36.000 0.00 0.00 0.00 3.91
2571 2791 5.997129 CACCAAATTAGGAAACCAAAAGCAT 59.003 36.000 0.00 0.00 0.00 3.79
2572 2792 7.158021 CACCAAATTAGGAAACCAAAAGCATA 58.842 34.615 0.00 0.00 0.00 3.14
2573 2793 7.823799 CACCAAATTAGGAAACCAAAAGCATAT 59.176 33.333 0.00 0.00 0.00 1.78
2574 2794 8.382405 ACCAAATTAGGAAACCAAAAGCATATT 58.618 29.630 0.00 0.00 0.00 1.28
2575 2795 8.882736 CCAAATTAGGAAACCAAAAGCATATTC 58.117 33.333 0.00 0.00 0.00 1.75
2576 2796 9.657419 CAAATTAGGAAACCAAAAGCATATTCT 57.343 29.630 0.00 0.00 0.00 2.40
2579 2799 8.519799 TTAGGAAACCAAAAGCATATTCTAGG 57.480 34.615 0.00 0.00 0.00 3.02
2580 2800 6.731467 AGGAAACCAAAAGCATATTCTAGGA 58.269 36.000 0.00 0.00 0.00 2.94
2586 2806 7.520798 ACCAAAAGCATATTCTAGGATCATCA 58.479 34.615 0.00 0.00 0.00 3.07
2645 2868 1.544314 GGAAGCTTGAGGAGTGCAAGT 60.544 52.381 2.10 0.00 43.50 3.16
2646 2869 2.289694 GGAAGCTTGAGGAGTGCAAGTA 60.290 50.000 2.10 0.00 43.50 2.24
2647 2870 2.758736 AGCTTGAGGAGTGCAAGTAG 57.241 50.000 0.00 0.00 43.50 2.57
2648 2871 1.974236 AGCTTGAGGAGTGCAAGTAGT 59.026 47.619 0.00 0.00 43.50 2.73
2649 2872 3.165875 AGCTTGAGGAGTGCAAGTAGTA 58.834 45.455 0.00 0.00 43.50 1.82
2652 2879 5.422331 AGCTTGAGGAGTGCAAGTAGTAATA 59.578 40.000 0.00 0.00 43.50 0.98
2655 2882 6.852420 TGAGGAGTGCAAGTAGTAATAACT 57.148 37.500 0.00 0.00 39.91 2.24
2684 2911 3.496331 GGAATTGTTGTTCCTTGAGGGA 58.504 45.455 0.00 0.00 43.49 4.20
2753 2984 2.739913 TGAAACTTACGGCGGAATCAAG 59.260 45.455 13.24 8.71 0.00 3.02
2759 2990 2.361104 GGCGGAATCAAGGGCACA 60.361 61.111 0.00 0.00 0.00 4.57
2790 3021 2.789409 TCTCTGCTTTCTTTAGGGGC 57.211 50.000 0.00 0.00 0.00 5.80
2797 3028 3.200385 TGCTTTCTTTAGGGGCCGTATTA 59.800 43.478 6.80 0.00 0.00 0.98
2798 3029 4.141344 TGCTTTCTTTAGGGGCCGTATTAT 60.141 41.667 6.80 0.00 0.00 1.28
2800 3031 5.048921 GCTTTCTTTAGGGGCCGTATTATTC 60.049 44.000 6.80 0.00 0.00 1.75
2801 3032 5.899631 TTCTTTAGGGGCCGTATTATTCT 57.100 39.130 6.80 0.00 0.00 2.40
2803 3034 5.152934 TCTTTAGGGGCCGTATTATTCTCT 58.847 41.667 6.80 0.00 0.00 3.10
2804 3035 5.605488 TCTTTAGGGGCCGTATTATTCTCTT 59.395 40.000 6.80 0.00 0.00 2.85
2830 3069 1.080569 GCGTGGGCTTTTGGTCATG 60.081 57.895 0.00 0.00 35.83 3.07
2863 3102 7.172361 GGCAAATCTCTAAGTAGAATAGCTTGG 59.828 40.741 0.00 0.00 0.00 3.61
3083 3334 4.393834 TGCTCTATGTAAGCAACCAAACA 58.606 39.130 0.00 0.00 46.29 2.83
3084 3335 5.009631 TGCTCTATGTAAGCAACCAAACAT 58.990 37.500 0.00 0.00 46.29 2.71
3085 3336 6.176896 TGCTCTATGTAAGCAACCAAACATA 58.823 36.000 0.00 0.00 46.29 2.29
3086 3337 6.828273 TGCTCTATGTAAGCAACCAAACATAT 59.172 34.615 0.00 0.00 46.29 1.78
3087 3338 7.990314 TGCTCTATGTAAGCAACCAAACATATA 59.010 33.333 0.00 0.00 46.29 0.86
3088 3339 8.283291 GCTCTATGTAAGCAACCAAACATATAC 58.717 37.037 0.00 0.00 39.61 1.47
3089 3340 9.325198 CTCTATGTAAGCAACCAAACATATACA 57.675 33.333 0.00 0.00 35.05 2.29
3090 3341 9.845740 TCTATGTAAGCAACCAAACATATACAT 57.154 29.630 0.00 0.00 35.05 2.29
3092 3343 7.328277 TGTAAGCAACCAAACATATACATCC 57.672 36.000 0.00 0.00 0.00 3.51
3093 3344 7.116075 TGTAAGCAACCAAACATATACATCCT 58.884 34.615 0.00 0.00 0.00 3.24
3097 3348 6.058183 GCAACCAAACATATACATCCTCTCT 58.942 40.000 0.00 0.00 0.00 3.10
3121 3372 3.932710 TCTCCTTTGATTACATCGCACAC 59.067 43.478 0.00 0.00 0.00 3.82
3122 3373 3.669536 TCCTTTGATTACATCGCACACA 58.330 40.909 0.00 0.00 0.00 3.72
3123 3374 3.435327 TCCTTTGATTACATCGCACACAC 59.565 43.478 0.00 0.00 0.00 3.82
3124 3375 3.188254 CCTTTGATTACATCGCACACACA 59.812 43.478 0.00 0.00 0.00 3.72
3138 3389 2.163010 CACACACATCCTCTCCAATTGC 59.837 50.000 0.00 0.00 0.00 3.56
3195 3450 5.278957 GGTTTCAGTATTTGTCATGCTGGTT 60.279 40.000 0.83 0.00 33.46 3.67
3196 3451 5.627499 TTCAGTATTTGTCATGCTGGTTC 57.373 39.130 0.83 0.00 33.46 3.62
3197 3452 4.650734 TCAGTATTTGTCATGCTGGTTCA 58.349 39.130 0.83 0.00 33.46 3.18
3198 3453 5.255687 TCAGTATTTGTCATGCTGGTTCAT 58.744 37.500 0.83 0.00 33.46 2.57
3199 3454 5.124297 TCAGTATTTGTCATGCTGGTTCATG 59.876 40.000 0.83 0.00 43.84 3.07
3200 3455 3.880047 ATTTGTCATGCTGGTTCATGG 57.120 42.857 4.21 0.00 42.96 3.66
3201 3456 2.291209 TTGTCATGCTGGTTCATGGT 57.709 45.000 4.21 0.00 42.96 3.55
3210 3465 2.941415 GCTGGTTCATGGTTCCGATCTT 60.941 50.000 0.00 0.00 0.00 2.40
3223 3478 1.041437 CGATCTTGGGTAGGAGTCCC 58.959 60.000 5.25 0.00 44.81 4.46
3263 3524 5.106442 CGTGTGTTCTGGCTTGTATATGTA 58.894 41.667 0.00 0.00 0.00 2.29
3265 3526 5.005394 GTGTGTTCTGGCTTGTATATGTACG 59.995 44.000 0.00 0.00 33.36 3.67
3275 3536 5.107453 GCTTGTATATGTACGTCAATGGAGC 60.107 44.000 0.00 0.00 33.36 4.70
3276 3537 5.784578 TGTATATGTACGTCAATGGAGCT 57.215 39.130 0.00 0.00 33.36 4.09
3277 3538 6.887626 TGTATATGTACGTCAATGGAGCTA 57.112 37.500 0.00 0.00 33.36 3.32
3280 3541 4.937201 ATGTACGTCAATGGAGCTATGA 57.063 40.909 0.00 0.00 0.00 2.15
3288 3549 5.050499 CGTCAATGGAGCTATGATTTCTGAC 60.050 44.000 0.00 0.00 0.00 3.51
3289 3550 6.054295 GTCAATGGAGCTATGATTTCTGACT 58.946 40.000 0.00 0.00 0.00 3.41
3290 3551 6.541641 GTCAATGGAGCTATGATTTCTGACTT 59.458 38.462 0.00 0.00 0.00 3.01
3291 3552 6.541278 TCAATGGAGCTATGATTTCTGACTTG 59.459 38.462 0.00 0.00 0.00 3.16
3293 3554 6.544928 TGGAGCTATGATTTCTGACTTGTA 57.455 37.500 0.00 0.00 0.00 2.41
3301 3576 5.705902 TGATTTCTGACTTGTATCGAACGA 58.294 37.500 0.00 0.00 0.00 3.85
3688 3963 4.019983 GAGTCGCTCTCCCAGGAA 57.980 61.111 0.00 0.00 37.22 3.36
3695 3970 2.001803 CTCTCCCAGGAAATGCCCA 58.998 57.895 0.00 0.00 37.37 5.36
3698 3973 0.259647 CTCCCAGGAAATGCCCATCA 59.740 55.000 0.00 0.00 37.37 3.07
3699 3974 0.709397 TCCCAGGAAATGCCCATCAA 59.291 50.000 0.00 0.00 37.37 2.57
3700 3975 1.078490 TCCCAGGAAATGCCCATCAAA 59.922 47.619 0.00 0.00 37.37 2.69
3701 3976 2.121129 CCCAGGAAATGCCCATCAAAT 58.879 47.619 0.00 0.00 37.37 2.32
3702 3977 2.158871 CCCAGGAAATGCCCATCAAATG 60.159 50.000 0.00 0.00 37.37 2.32
3703 3978 2.557317 CAGGAAATGCCCATCAAATGC 58.443 47.619 0.00 0.00 37.37 3.56
3704 3979 2.093394 CAGGAAATGCCCATCAAATGCA 60.093 45.455 0.00 0.00 39.68 3.96
3706 3981 2.875933 GGAAATGCCCATCAAATGCATG 59.124 45.455 0.00 0.00 44.49 4.06
3707 3982 2.631160 AATGCCCATCAAATGCATGG 57.369 45.000 0.00 0.00 44.49 3.66
3715 4002 2.715749 TCAAATGCATGGGAGACGAT 57.284 45.000 0.00 0.00 0.00 3.73
4231 4530 1.511464 CGACTGCTACCACGTCGTC 60.511 63.158 0.00 0.00 43.82 4.20
4644 4950 9.443283 GAATAGAAACATGAATGACAGCATTAC 57.557 33.333 0.00 0.00 44.47 1.89
4677 4987 6.375455 AGTTGCAGGATTTTTGGATAGTAGTG 59.625 38.462 0.00 0.00 0.00 2.74
4785 6488 1.880027 CTTGAGTGTTTGGGTAGGCAC 59.120 52.381 0.00 0.00 0.00 5.01
4786 6489 0.840617 TGAGTGTTTGGGTAGGCACA 59.159 50.000 0.00 0.00 34.59 4.57
4788 6491 0.843984 AGTGTTTGGGTAGGCACAGT 59.156 50.000 0.00 0.00 34.59 3.55
4839 8590 5.127682 TCAGTACACATACACTGAGATGCAT 59.872 40.000 0.00 0.00 44.70 3.96
4844 8595 5.814188 ACACATACACTGAGATGCATTAGTG 59.186 40.000 25.44 25.44 44.52 2.74
4863 8614 3.496130 AGTGCAACAAATTCTCAGTCGAG 59.504 43.478 0.00 0.00 41.43 4.04
4864 8615 3.494626 GTGCAACAAATTCTCAGTCGAGA 59.505 43.478 0.00 0.00 41.29 4.04
4865 8616 4.609336 GTGCAACAAATTCTCAGTCGAGAC 60.609 45.833 0.00 0.00 42.20 3.36
4866 8617 6.975713 GTGCAACAAATTCTCAGTCGAGACA 61.976 44.000 5.99 0.00 42.20 3.41
4867 8618 8.667295 GTGCAACAAATTCTCAGTCGAGACAG 62.667 46.154 5.99 0.00 42.20 3.51
4870 8621 3.579685 TCTCAGTCGAGACAGCGG 58.420 61.111 5.99 0.00 43.55 5.52
4871 8622 1.003718 TCTCAGTCGAGACAGCGGA 60.004 57.895 5.99 0.00 43.55 5.54
4872 8623 1.135731 CTCAGTCGAGACAGCGGAC 59.864 63.158 5.99 0.00 42.34 4.79
4874 8625 0.036671 TCAGTCGAGACAGCGGACTA 60.037 55.000 5.99 0.00 0.00 2.59
4886 8768 3.055385 ACAGCGGACTAGGATTTAGCAAA 60.055 43.478 0.00 0.00 0.00 3.68
4915 8820 1.821216 ACAAAATTCAGCCGTCCGAT 58.179 45.000 0.00 0.00 0.00 4.18
5011 8924 0.110295 TGCAAGCCAAGCAGACCTAA 59.890 50.000 0.00 0.00 37.02 2.69
5123 9036 4.272018 CGCTGCATTTCTAAGCTAATGTCT 59.728 41.667 8.37 0.00 34.88 3.41
5183 9096 1.270094 TGCCGTCACAAGTCTTGGTAG 60.270 52.381 16.85 6.58 34.12 3.18
5185 9098 2.547218 GCCGTCACAAGTCTTGGTAGAA 60.547 50.000 16.85 0.00 34.12 2.10
5194 9107 2.840651 AGTCTTGGTAGAATCACCCAGG 59.159 50.000 4.19 0.40 37.84 4.45
5247 9178 1.837499 CGGAGGGACCCTGGGTATC 60.837 68.421 20.90 16.55 35.25 2.24
5328 9259 2.695666 GGCTAGTATCTGGCTCTTGACA 59.304 50.000 5.23 0.00 38.07 3.58
5331 9262 4.382040 GCTAGTATCTGGCTCTTGACAACA 60.382 45.833 0.00 0.00 35.09 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.092091 CGCTGTTTTTCTACTTCTGCCTAG 59.908 45.833 0.00 0.00 0.00 3.02
141 144 6.880942 TGATCACTGATGATTTGTTGTCAA 57.119 33.333 0.00 0.00 46.01 3.18
167 170 7.523293 AAAACATGATTGTGATCCTGTTGTA 57.477 32.000 0.00 0.00 44.86 2.41
359 375 2.032117 CGCTTGCGATTATATGGTGCAA 60.032 45.455 9.60 0.00 42.68 4.08
360 376 1.530720 CGCTTGCGATTATATGGTGCA 59.469 47.619 9.60 0.00 0.00 4.57
367 383 2.989166 CTGCTGATCGCTTGCGATTATA 59.011 45.455 27.42 17.17 40.11 0.98
373 389 1.080435 TTCTCTGCTGATCGCTTGCG 61.080 55.000 8.87 8.87 40.11 4.85
387 407 2.047061 TGGTGGTTACAGTGCTTCTCT 58.953 47.619 0.00 0.00 0.00 3.10
414 438 1.530419 AATGCGTGCTTTGGTGGGA 60.530 52.632 0.00 0.00 0.00 4.37
415 439 1.373246 CAATGCGTGCTTTGGTGGG 60.373 57.895 11.43 0.00 0.00 4.61
433 457 3.069074 TCATGCTGAATTATTGTGCGC 57.931 42.857 0.00 0.00 0.00 6.09
521 558 0.033601 TGCTGTTGGTGGGAGTGTTT 60.034 50.000 0.00 0.00 0.00 2.83
561 598 5.187576 TCCCCATGATTGGTGATTTCTTTTC 59.812 40.000 0.00 0.00 41.91 2.29
702 763 1.728672 CGCCGAACTCCTCCTCTAC 59.271 63.158 0.00 0.00 0.00 2.59
703 764 2.119655 GCGCCGAACTCCTCCTCTA 61.120 63.158 0.00 0.00 0.00 2.43
704 765 3.453679 GCGCCGAACTCCTCCTCT 61.454 66.667 0.00 0.00 0.00 3.69
705 766 4.516195 GGCGCCGAACTCCTCCTC 62.516 72.222 12.58 0.00 0.00 3.71
849 954 2.167693 GTGGGGGTTGGCTTTTATTAGC 59.832 50.000 0.00 0.00 40.48 3.09
911 1020 4.806481 GCGAGCGAGCGTCGTACA 62.806 66.667 14.60 0.00 42.81 2.90
1365 1524 7.772292 TGATCTGATGGAGTAAAAATCAAGGAG 59.228 37.037 0.00 0.00 30.28 3.69
1425 1585 4.285003 TGGAAAGGAAACGGAGAGATTGTA 59.715 41.667 0.00 0.00 0.00 2.41
1426 1586 3.072476 TGGAAAGGAAACGGAGAGATTGT 59.928 43.478 0.00 0.00 0.00 2.71
1427 1587 3.674997 TGGAAAGGAAACGGAGAGATTG 58.325 45.455 0.00 0.00 0.00 2.67
1432 1592 2.227194 GCTTTGGAAAGGAAACGGAGA 58.773 47.619 1.45 0.00 36.53 3.71
1437 1597 0.387565 TGCGGCTTTGGAAAGGAAAC 59.612 50.000 0.00 0.00 36.53 2.78
1441 1601 0.389025 AAAGTGCGGCTTTGGAAAGG 59.611 50.000 0.00 0.00 45.00 3.11
1457 1617 6.095377 GGTATGAGAAATGTGCAGGAAAAAG 58.905 40.000 0.00 0.00 0.00 2.27
1474 1634 4.253685 AGGAAATCGTGTGTTGGTATGAG 58.746 43.478 0.00 0.00 0.00 2.90
1496 1656 4.062293 CCTGTGTTGTTTGTAGAATCGGA 58.938 43.478 0.00 0.00 0.00 4.55
1517 1677 3.804873 GCAGAGGTAGAAATCGTCAATCC 59.195 47.826 0.00 0.00 0.00 3.01
1536 1696 2.852413 CGTAGTGGTAAATCTGTCGCAG 59.148 50.000 1.02 1.02 0.00 5.18
1643 1805 5.163864 CGTGCTTGTTTATGACAGAGCATAA 60.164 40.000 16.11 0.00 45.30 1.90
1679 1841 6.662865 TTTTAGGATTGCAAGATTTGGACA 57.337 33.333 4.94 0.00 0.00 4.02
1704 1866 7.821652 TCATTGAGGAAAAATAATGCGTGTAA 58.178 30.769 0.00 0.00 32.14 2.41
1757 1946 2.440247 GCATTAGGCTTGCCCCGT 60.440 61.111 8.17 0.00 40.25 5.28
1760 1949 4.256090 CGCGCATTAGGCTTGCCC 62.256 66.667 8.75 0.00 41.67 5.36
1808 1997 5.868116 GTTGTAAACTACGGTCGTCGTCAC 61.868 50.000 9.48 3.19 46.62 3.67
1809 1998 3.848191 GTTGTAAACTACGGTCGTCGTCA 60.848 47.826 9.48 0.00 46.62 4.35
1840 2029 5.815222 ACTTGGCAAAAAGGTTTGTATTGAC 59.185 36.000 0.00 0.00 45.06 3.18
1866 2055 1.927174 CTGAATTTCCTGACCGCTACG 59.073 52.381 0.00 0.00 0.00 3.51
1867 2056 1.666189 GCTGAATTTCCTGACCGCTAC 59.334 52.381 0.00 0.00 0.00 3.58
1868 2057 1.277842 TGCTGAATTTCCTGACCGCTA 59.722 47.619 0.00 0.00 0.00 4.26
1869 2058 0.036732 TGCTGAATTTCCTGACCGCT 59.963 50.000 0.00 0.00 0.00 5.52
1893 2082 1.280133 CAGCCATTGACTTCTCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
1925 2114 0.531657 TGGATTTTTGGAGCCATGCG 59.468 50.000 0.00 0.00 0.00 4.73
1926 2115 1.275856 TGTGGATTTTTGGAGCCATGC 59.724 47.619 0.00 0.00 32.26 4.06
1927 2116 3.196039 TGATGTGGATTTTTGGAGCCATG 59.804 43.478 0.00 0.00 32.26 3.66
1928 2117 3.443052 TGATGTGGATTTTTGGAGCCAT 58.557 40.909 0.00 0.00 32.26 4.40
1947 2136 9.713713 CAGCACTACTACTCTACTAGATTATGA 57.286 37.037 0.00 0.00 0.00 2.15
1948 2137 8.941977 CCAGCACTACTACTCTACTAGATTATG 58.058 40.741 0.00 0.00 0.00 1.90
1949 2138 8.104566 CCCAGCACTACTACTCTACTAGATTAT 58.895 40.741 0.00 0.00 0.00 1.28
1950 2139 7.451732 CCCAGCACTACTACTCTACTAGATTA 58.548 42.308 0.00 0.00 0.00 1.75
1952 2141 5.746656 GCCCAGCACTACTACTCTACTAGAT 60.747 48.000 0.00 0.00 0.00 1.98
1953 2142 4.444591 GCCCAGCACTACTACTCTACTAGA 60.445 50.000 0.00 0.00 0.00 2.43
1955 2144 3.458857 AGCCCAGCACTACTACTCTACTA 59.541 47.826 0.00 0.00 0.00 1.82
1956 2145 2.242708 AGCCCAGCACTACTACTCTACT 59.757 50.000 0.00 0.00 0.00 2.57
1957 2146 2.359531 CAGCCCAGCACTACTACTCTAC 59.640 54.545 0.00 0.00 0.00 2.59
1958 2147 2.241430 TCAGCCCAGCACTACTACTCTA 59.759 50.000 0.00 0.00 0.00 2.43
1959 2148 1.006043 TCAGCCCAGCACTACTACTCT 59.994 52.381 0.00 0.00 0.00 3.24
1960 2149 1.475403 TCAGCCCAGCACTACTACTC 58.525 55.000 0.00 0.00 0.00 2.59
1964 2153 0.322975 CTGTTCAGCCCAGCACTACT 59.677 55.000 0.00 0.00 0.00 2.57
1965 2154 0.674895 CCTGTTCAGCCCAGCACTAC 60.675 60.000 0.00 0.00 0.00 2.73
1967 2156 1.708993 TTCCTGTTCAGCCCAGCACT 61.709 55.000 0.00 0.00 0.00 4.40
1969 2158 1.073722 CTTCCTGTTCAGCCCAGCA 59.926 57.895 0.00 0.00 0.00 4.41
1977 2166 1.000955 GAGGAGAACGCTTCCTGTTCA 59.999 52.381 7.60 0.00 46.34 3.18
1978 2167 1.273886 AGAGGAGAACGCTTCCTGTTC 59.726 52.381 7.60 0.00 44.72 3.18
2148 2337 5.669164 AAAGCCTAACCAAAAGTCAAACA 57.331 34.783 0.00 0.00 0.00 2.83
2174 2366 8.253810 TCATAGATCATGCTATGCTACCTAAAC 58.746 37.037 12.89 0.00 44.65 2.01
2207 2399 7.121611 TCAAGCATAAATGTCATGACTCAACAT 59.878 33.333 25.55 9.14 35.20 2.71
2242 2434 6.128580 GCGATTTCCGGTAAGTACTGTTAAAA 60.129 38.462 0.00 0.00 39.04 1.52
2260 2455 3.429061 AACGTACACGAAAGCGATTTC 57.571 42.857 15.97 15.97 43.02 2.17
2262 2457 4.681025 TCTTTAACGTACACGAAAGCGATT 59.319 37.500 9.04 0.00 43.02 3.34
2302 2509 2.049185 AACACAACGCAGCACCCAA 61.049 52.632 0.00 0.00 0.00 4.12
2306 2513 0.375454 TACACAACACAACGCAGCAC 59.625 50.000 0.00 0.00 0.00 4.40
2309 2516 3.878086 AAGATACACAACACAACGCAG 57.122 42.857 0.00 0.00 0.00 5.18
2489 2708 7.043192 CCAACATTTTCACTTCAAGAACATGTC 60.043 37.037 0.00 0.00 42.39 3.06
2494 2713 5.748630 GTCCCAACATTTTCACTTCAAGAAC 59.251 40.000 0.00 0.00 0.00 3.01
2505 2724 4.550422 GAGCTGAAAGTCCCAACATTTTC 58.450 43.478 0.00 0.00 35.30 2.29
2535 2755 6.702329 TCCTAATTTGGTGTTTTTGTTGTGT 58.298 32.000 5.81 0.00 0.00 3.72
2536 2756 7.602517 TTCCTAATTTGGTGTTTTTGTTGTG 57.397 32.000 5.81 0.00 0.00 3.33
2537 2757 7.119992 GGTTTCCTAATTTGGTGTTTTTGTTGT 59.880 33.333 5.81 0.00 0.00 3.32
2538 2758 7.119846 TGGTTTCCTAATTTGGTGTTTTTGTTG 59.880 33.333 5.81 0.00 0.00 3.33
2539 2759 7.168905 TGGTTTCCTAATTTGGTGTTTTTGTT 58.831 30.769 5.81 0.00 0.00 2.83
2540 2760 6.712276 TGGTTTCCTAATTTGGTGTTTTTGT 58.288 32.000 5.81 0.00 0.00 2.83
2541 2761 7.617041 TTGGTTTCCTAATTTGGTGTTTTTG 57.383 32.000 5.81 0.00 0.00 2.44
2542 2762 8.637196 TTTTGGTTTCCTAATTTGGTGTTTTT 57.363 26.923 5.81 0.00 0.00 1.94
2543 2763 7.148154 GCTTTTGGTTTCCTAATTTGGTGTTTT 60.148 33.333 5.81 0.00 0.00 2.43
2544 2764 6.317642 GCTTTTGGTTTCCTAATTTGGTGTTT 59.682 34.615 5.81 0.00 0.00 2.83
2545 2765 5.820423 GCTTTTGGTTTCCTAATTTGGTGTT 59.180 36.000 5.81 0.00 0.00 3.32
2546 2766 5.104735 TGCTTTTGGTTTCCTAATTTGGTGT 60.105 36.000 5.81 0.00 0.00 4.16
2547 2767 5.363939 TGCTTTTGGTTTCCTAATTTGGTG 58.636 37.500 5.81 0.00 0.00 4.17
2548 2768 5.622346 TGCTTTTGGTTTCCTAATTTGGT 57.378 34.783 5.81 0.00 0.00 3.67
2549 2769 8.791327 AATATGCTTTTGGTTTCCTAATTTGG 57.209 30.769 0.00 0.00 0.00 3.28
2550 2770 9.657419 AGAATATGCTTTTGGTTTCCTAATTTG 57.343 29.630 0.00 0.00 0.00 2.32
2553 2773 9.136323 CCTAGAATATGCTTTTGGTTTCCTAAT 57.864 33.333 0.00 0.00 0.00 1.73
2554 2774 8.333235 TCCTAGAATATGCTTTTGGTTTCCTAA 58.667 33.333 0.00 0.00 0.00 2.69
2555 2775 7.867921 TCCTAGAATATGCTTTTGGTTTCCTA 58.132 34.615 0.00 0.00 0.00 2.94
2556 2776 6.731467 TCCTAGAATATGCTTTTGGTTTCCT 58.269 36.000 0.00 0.00 0.00 3.36
2557 2777 7.285401 TGATCCTAGAATATGCTTTTGGTTTCC 59.715 37.037 0.00 0.00 0.00 3.13
2558 2778 8.225603 TGATCCTAGAATATGCTTTTGGTTTC 57.774 34.615 0.00 0.00 0.00 2.78
2559 2779 8.773033 ATGATCCTAGAATATGCTTTTGGTTT 57.227 30.769 0.00 0.00 0.00 3.27
2560 2780 8.000709 TGATGATCCTAGAATATGCTTTTGGTT 58.999 33.333 0.00 0.00 0.00 3.67
2561 2781 7.446625 GTGATGATCCTAGAATATGCTTTTGGT 59.553 37.037 0.00 0.00 0.00 3.67
2562 2782 7.446319 TGTGATGATCCTAGAATATGCTTTTGG 59.554 37.037 0.00 0.00 0.00 3.28
2563 2783 8.387190 TGTGATGATCCTAGAATATGCTTTTG 57.613 34.615 0.00 0.00 0.00 2.44
2564 2784 8.985315 TTGTGATGATCCTAGAATATGCTTTT 57.015 30.769 0.00 0.00 0.00 2.27
2565 2785 8.985315 TTTGTGATGATCCTAGAATATGCTTT 57.015 30.769 0.00 0.00 0.00 3.51
2566 2786 8.216423 ACTTTGTGATGATCCTAGAATATGCTT 58.784 33.333 0.00 0.00 0.00 3.91
2567 2787 7.743749 ACTTTGTGATGATCCTAGAATATGCT 58.256 34.615 0.00 0.00 0.00 3.79
2568 2788 7.976135 ACTTTGTGATGATCCTAGAATATGC 57.024 36.000 0.00 0.00 0.00 3.14
2569 2789 8.781196 CCAACTTTGTGATGATCCTAGAATATG 58.219 37.037 0.00 0.00 0.00 1.78
2570 2790 8.717717 TCCAACTTTGTGATGATCCTAGAATAT 58.282 33.333 0.00 0.00 0.00 1.28
2571 2791 8.089625 TCCAACTTTGTGATGATCCTAGAATA 57.910 34.615 0.00 0.00 0.00 1.75
2572 2792 6.962182 TCCAACTTTGTGATGATCCTAGAAT 58.038 36.000 0.00 0.00 0.00 2.40
2573 2793 6.373005 TCCAACTTTGTGATGATCCTAGAA 57.627 37.500 0.00 0.00 0.00 2.10
2574 2794 6.373005 TTCCAACTTTGTGATGATCCTAGA 57.627 37.500 0.00 0.00 0.00 2.43
2575 2795 6.656693 AGTTTCCAACTTTGTGATGATCCTAG 59.343 38.462 0.00 0.00 39.04 3.02
2576 2796 6.542821 AGTTTCCAACTTTGTGATGATCCTA 58.457 36.000 0.00 0.00 39.04 2.94
2577 2797 5.388654 AGTTTCCAACTTTGTGATGATCCT 58.611 37.500 0.00 0.00 39.04 3.24
2578 2798 5.712152 AGTTTCCAACTTTGTGATGATCC 57.288 39.130 0.00 0.00 39.04 3.36
2618 2838 1.188219 TCCTCAAGCTTCCTCTGCGT 61.188 55.000 0.00 0.00 35.28 5.24
2619 2839 0.459934 CTCCTCAAGCTTCCTCTGCG 60.460 60.000 0.00 0.00 35.28 5.18
2620 2840 0.612744 ACTCCTCAAGCTTCCTCTGC 59.387 55.000 0.00 0.00 0.00 4.26
2621 2841 1.675415 GCACTCCTCAAGCTTCCTCTG 60.675 57.143 0.00 0.00 0.00 3.35
2623 2843 0.322975 TGCACTCCTCAAGCTTCCTC 59.677 55.000 0.00 0.00 0.00 3.71
2624 2844 0.767375 TTGCACTCCTCAAGCTTCCT 59.233 50.000 0.00 0.00 0.00 3.36
2626 2846 1.889545 ACTTGCACTCCTCAAGCTTC 58.110 50.000 0.00 0.00 43.40 3.86
2628 2848 1.974236 ACTACTTGCACTCCTCAAGCT 59.026 47.619 2.97 0.00 43.40 3.74
2629 2849 2.464157 ACTACTTGCACTCCTCAAGC 57.536 50.000 2.97 0.00 43.40 4.01
2630 2850 7.324178 AGTTATTACTACTTGCACTCCTCAAG 58.676 38.462 0.00 1.63 44.71 3.02
2645 2868 5.987019 ATTCCCTGCCCAAGTTATTACTA 57.013 39.130 0.00 0.00 33.17 1.82
2646 2869 4.881157 ATTCCCTGCCCAAGTTATTACT 57.119 40.909 0.00 0.00 35.68 2.24
2647 2870 4.709886 ACAATTCCCTGCCCAAGTTATTAC 59.290 41.667 0.00 0.00 0.00 1.89
2648 2871 4.941713 ACAATTCCCTGCCCAAGTTATTA 58.058 39.130 0.00 0.00 0.00 0.98
2649 2872 3.790126 ACAATTCCCTGCCCAAGTTATT 58.210 40.909 0.00 0.00 0.00 1.40
2652 2879 1.693606 CAACAATTCCCTGCCCAAGTT 59.306 47.619 0.00 0.00 0.00 2.66
2655 2882 1.691434 GAACAACAATTCCCTGCCCAA 59.309 47.619 0.00 0.00 0.00 4.12
2684 2911 1.551883 GGCTGGCAAAAGGTTGATCAT 59.448 47.619 0.00 0.00 36.83 2.45
2723 2950 4.274069 CGCCGTAAGTTTCATGATTGATG 58.726 43.478 0.00 0.00 0.00 3.07
2726 2953 2.675844 TCCGCCGTAAGTTTCATGATTG 59.324 45.455 0.00 0.00 0.00 2.67
2753 2984 0.743097 GATGCCTTGATTCTGTGCCC 59.257 55.000 0.00 0.00 0.00 5.36
2759 2990 3.648507 AAGCAGAGATGCCTTGATTCT 57.351 42.857 0.00 0.00 34.90 2.40
2790 3021 6.200286 ACGCATACACAAAGAGAATAATACGG 59.800 38.462 0.00 0.00 0.00 4.02
2797 3028 3.009723 CCCACGCATACACAAAGAGAAT 58.990 45.455 0.00 0.00 0.00 2.40
2798 3029 2.422597 CCCACGCATACACAAAGAGAA 58.577 47.619 0.00 0.00 0.00 2.87
2800 3031 0.447801 GCCCACGCATACACAAAGAG 59.552 55.000 0.00 0.00 34.03 2.85
2801 3032 0.036164 AGCCCACGCATACACAAAGA 59.964 50.000 0.00 0.00 37.52 2.52
2803 3034 1.323412 AAAGCCCACGCATACACAAA 58.677 45.000 0.00 0.00 37.52 2.83
2804 3035 1.000827 CAAAAGCCCACGCATACACAA 60.001 47.619 0.00 0.00 37.52 3.33
2830 3069 2.092699 ACTTAGAGATTTGCCAGCTCCC 60.093 50.000 0.00 0.00 0.00 4.30
2863 3102 0.598065 GAATCCCTGCACCACAACAC 59.402 55.000 0.00 0.00 0.00 3.32
3082 3333 7.669304 TCAAAGGAGAGAGAGAGGATGTATATG 59.331 40.741 0.00 0.00 0.00 1.78
3083 3334 7.764617 TCAAAGGAGAGAGAGAGGATGTATAT 58.235 38.462 0.00 0.00 0.00 0.86
3084 3335 7.155442 TCAAAGGAGAGAGAGAGGATGTATA 57.845 40.000 0.00 0.00 0.00 1.47
3085 3336 6.024563 TCAAAGGAGAGAGAGAGGATGTAT 57.975 41.667 0.00 0.00 0.00 2.29
3086 3337 5.458451 TCAAAGGAGAGAGAGAGGATGTA 57.542 43.478 0.00 0.00 0.00 2.29
3087 3338 4.329638 TCAAAGGAGAGAGAGAGGATGT 57.670 45.455 0.00 0.00 0.00 3.06
3088 3339 5.874897 AATCAAAGGAGAGAGAGAGGATG 57.125 43.478 0.00 0.00 0.00 3.51
3089 3340 6.439487 TGTAATCAAAGGAGAGAGAGAGGAT 58.561 40.000 0.00 0.00 0.00 3.24
3090 3341 5.832221 TGTAATCAAAGGAGAGAGAGAGGA 58.168 41.667 0.00 0.00 0.00 3.71
3091 3342 6.514870 CGATGTAATCAAAGGAGAGAGAGAGG 60.515 46.154 0.00 0.00 45.97 3.69
3092 3343 6.437928 CGATGTAATCAAAGGAGAGAGAGAG 58.562 44.000 0.00 0.00 45.97 3.20
3093 3344 5.221145 GCGATGTAATCAAAGGAGAGAGAGA 60.221 44.000 0.00 0.00 45.97 3.10
3097 3348 4.081697 TGTGCGATGTAATCAAAGGAGAGA 60.082 41.667 0.00 0.00 45.97 3.10
3121 3372 1.019673 CGGCAATTGGAGAGGATGTG 58.980 55.000 7.72 0.00 0.00 3.21
3122 3373 0.107017 CCGGCAATTGGAGAGGATGT 60.107 55.000 7.72 0.00 0.00 3.06
3123 3374 1.450531 GCCGGCAATTGGAGAGGATG 61.451 60.000 24.80 0.00 0.00 3.51
3124 3375 1.152881 GCCGGCAATTGGAGAGGAT 60.153 57.895 24.80 0.00 0.00 3.24
3138 3389 4.142556 ACAAACTCGTAAATAATTGGCCGG 60.143 41.667 0.00 0.00 0.00 6.13
3182 3437 2.291209 ACCATGAACCAGCATGACAA 57.709 45.000 0.00 0.00 46.64 3.18
3195 3450 1.285280 ACCCAAGATCGGAACCATGA 58.715 50.000 0.00 0.00 0.00 3.07
3196 3451 2.485479 CCTACCCAAGATCGGAACCATG 60.485 54.545 0.00 0.00 0.00 3.66
3197 3452 1.768870 CCTACCCAAGATCGGAACCAT 59.231 52.381 0.00 0.00 0.00 3.55
3198 3453 1.200519 CCTACCCAAGATCGGAACCA 58.799 55.000 0.00 0.00 0.00 3.67
3199 3454 1.413077 CTCCTACCCAAGATCGGAACC 59.587 57.143 0.00 0.00 0.00 3.62
3200 3455 2.101082 GACTCCTACCCAAGATCGGAAC 59.899 54.545 0.00 0.00 0.00 3.62
3201 3456 2.385803 GACTCCTACCCAAGATCGGAA 58.614 52.381 0.00 0.00 0.00 4.30
3223 3478 0.537188 ACGGGAGCACAGTAGGATTG 59.463 55.000 0.00 0.00 0.00 2.67
3263 3524 4.813161 CAGAAATCATAGCTCCATTGACGT 59.187 41.667 0.00 0.00 0.00 4.34
3265 3526 6.054295 AGTCAGAAATCATAGCTCCATTGAC 58.946 40.000 0.00 0.00 33.33 3.18
3275 3536 7.644157 TCGTTCGATACAAGTCAGAAATCATAG 59.356 37.037 0.00 0.00 0.00 2.23
3276 3537 7.431376 GTCGTTCGATACAAGTCAGAAATCATA 59.569 37.037 0.00 0.00 0.00 2.15
3277 3538 6.253727 GTCGTTCGATACAAGTCAGAAATCAT 59.746 38.462 0.00 0.00 0.00 2.45
3280 3541 5.466819 TGTCGTTCGATACAAGTCAGAAAT 58.533 37.500 0.00 0.00 0.00 2.17
3288 3549 3.211803 TCACCTGTCGTTCGATACAAG 57.788 47.619 0.00 0.00 0.00 3.16
3289 3550 3.311106 GTTCACCTGTCGTTCGATACAA 58.689 45.455 0.00 0.00 0.00 2.41
3290 3551 2.666344 CGTTCACCTGTCGTTCGATACA 60.666 50.000 0.00 0.00 0.00 2.29
3291 3552 1.909532 CGTTCACCTGTCGTTCGATAC 59.090 52.381 0.00 0.00 0.00 2.24
3293 3554 0.313043 ACGTTCACCTGTCGTTCGAT 59.687 50.000 0.00 0.00 34.07 3.59
3301 3576 1.069765 CAGCTCCACGTTCACCTGT 59.930 57.895 0.00 0.00 0.00 4.00
3688 3963 2.631160 CCATGCATTTGATGGGCATT 57.369 45.000 0.00 0.00 45.34 3.56
3695 3970 2.715749 TCGTCTCCCATGCATTTGAT 57.284 45.000 0.00 0.00 0.00 2.57
3698 3973 2.715749 TCATCGTCTCCCATGCATTT 57.284 45.000 0.00 0.00 0.00 2.32
3699 3974 2.158711 ACATCATCGTCTCCCATGCATT 60.159 45.455 0.00 0.00 0.00 3.56
3700 3975 1.419012 ACATCATCGTCTCCCATGCAT 59.581 47.619 0.00 0.00 0.00 3.96
3701 3976 0.832626 ACATCATCGTCTCCCATGCA 59.167 50.000 0.00 0.00 0.00 3.96
3702 3977 1.069823 AGACATCATCGTCTCCCATGC 59.930 52.381 0.00 0.00 42.70 4.06
3703 3978 2.547430 CCAGACATCATCGTCTCCCATG 60.547 54.545 0.00 0.00 44.49 3.66
3704 3979 1.690893 CCAGACATCATCGTCTCCCAT 59.309 52.381 0.00 0.00 44.49 4.00
3705 3980 1.114627 CCAGACATCATCGTCTCCCA 58.885 55.000 0.00 0.00 44.49 4.37
3706 3981 0.390860 CCCAGACATCATCGTCTCCC 59.609 60.000 0.00 0.00 44.49 4.30
3707 3982 1.339610 CTCCCAGACATCATCGTCTCC 59.660 57.143 0.00 0.00 44.49 3.71
3709 3984 3.582210 CGTCTCCCAGACATCATCGTCT 61.582 54.545 4.60 0.00 45.30 4.18
3715 4002 2.885113 CGCGTCTCCCAGACATCA 59.115 61.111 0.00 0.00 45.30 3.07
4390 4689 3.604582 CAGGAACCTCTTGATGAACTCC 58.395 50.000 0.00 0.00 0.00 3.85
4659 4965 9.614792 ATTACACTCACTACTATCCAAAAATCC 57.385 33.333 0.00 0.00 0.00 3.01
4677 4987 3.906720 TTCCCTGTGCCTATTACACTC 57.093 47.619 0.00 0.00 38.86 3.51
4718 5028 5.658634 TCTCTGTCTGCCTAATTCACTGTAT 59.341 40.000 0.00 0.00 0.00 2.29
4719 5029 5.016831 TCTCTGTCTGCCTAATTCACTGTA 58.983 41.667 0.00 0.00 0.00 2.74
4785 6488 6.708054 ACATAAGAAAACTCAAGGACTCACTG 59.292 38.462 0.00 0.00 0.00 3.66
4786 6489 6.831976 ACATAAGAAAACTCAAGGACTCACT 58.168 36.000 0.00 0.00 0.00 3.41
4788 6491 9.793259 AATTACATAAGAAAACTCAAGGACTCA 57.207 29.630 0.00 0.00 0.00 3.41
4839 8590 5.053811 TCGACTGAGAATTTGTTGCACTAA 58.946 37.500 0.00 0.00 0.00 2.24
4854 8605 1.135731 GTCCGCTGTCTCGACTGAG 59.864 63.158 7.95 4.74 43.99 3.35
4856 8607 0.375454 CTAGTCCGCTGTCTCGACTG 59.625 60.000 0.00 0.00 0.00 3.51
4857 8608 0.745128 CCTAGTCCGCTGTCTCGACT 60.745 60.000 0.00 0.00 0.00 4.18
4858 8609 0.743701 TCCTAGTCCGCTGTCTCGAC 60.744 60.000 0.00 0.00 0.00 4.20
4859 8610 0.180642 ATCCTAGTCCGCTGTCTCGA 59.819 55.000 0.00 0.00 0.00 4.04
4860 8611 1.025812 AATCCTAGTCCGCTGTCTCG 58.974 55.000 0.00 0.00 0.00 4.04
4863 8614 2.100916 TGCTAAATCCTAGTCCGCTGTC 59.899 50.000 0.00 0.00 0.00 3.51
4864 8615 2.108168 TGCTAAATCCTAGTCCGCTGT 58.892 47.619 0.00 0.00 0.00 4.40
4865 8616 2.890808 TGCTAAATCCTAGTCCGCTG 57.109 50.000 0.00 0.00 0.00 5.18
4866 8617 3.906720 TTTGCTAAATCCTAGTCCGCT 57.093 42.857 0.00 0.00 0.00 5.52
4867 8618 3.064958 GGTTTTGCTAAATCCTAGTCCGC 59.935 47.826 0.00 0.00 0.00 5.54
4868 8619 3.308866 CGGTTTTGCTAAATCCTAGTCCG 59.691 47.826 0.00 0.00 0.00 4.79
4870 8621 5.874895 AACGGTTTTGCTAAATCCTAGTC 57.125 39.130 0.00 0.00 0.00 2.59
4871 8622 8.886719 GTTATAACGGTTTTGCTAAATCCTAGT 58.113 33.333 0.00 0.00 0.00 2.57
4872 8623 8.885722 TGTTATAACGGTTTTGCTAAATCCTAG 58.114 33.333 10.92 0.00 0.00 3.02
4874 8625 7.690952 TGTTATAACGGTTTTGCTAAATCCT 57.309 32.000 10.92 0.00 0.00 3.24
4886 8768 5.048573 ACGGCTGAATTTTGTTATAACGGTT 60.049 36.000 10.92 0.00 0.00 4.44
5123 9036 1.675801 CTCAACTCTCTGCCCTGCA 59.324 57.895 0.00 0.00 36.92 4.41
5183 9096 0.830648 TCGGTGATCCTGGGTGATTC 59.169 55.000 0.00 0.00 0.00 2.52
5185 9098 1.050988 CCTCGGTGATCCTGGGTGAT 61.051 60.000 0.00 0.00 0.00 3.06
5194 9107 0.035439 TCAAAAGGCCCTCGGTGATC 60.035 55.000 0.00 0.00 0.00 2.92
5307 9238 2.695666 TGTCAAGAGCCAGATACTAGCC 59.304 50.000 0.00 0.00 0.00 3.93
5328 9259 4.141287 AGATAGAGAGCTACATCGCTGTT 58.859 43.478 0.00 0.00 41.08 3.16
5331 9262 3.000041 CGAGATAGAGAGCTACATCGCT 59.000 50.000 0.00 0.00 44.33 4.93


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

AutoCloner maintained by Alex Coulton.