Multiple sequence alignment - TraesCS2B01G592600

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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 TraesCS2B01G592600 chr2B 100.000 2935 0 0 1 2935 777522939 777520005 0.000000e+00 5421.0
1 TraesCS2B01G592600 chr2B 82.326 1092 85 47 517 1553 777549974 777548936 0.000000e+00 848.0
2 TraesCS2B01G592600 chr2B 82.514 692 56 38 888 1553 777659053 777658401 5.530000e-152 547.0
3 TraesCS2B01G592600 chr2B 82.438 689 55 35 772 1437 777635407 777634762 2.570000e-150 542.0
4 TraesCS2B01G592600 chr2B 76.451 913 107 62 702 1553 777619230 777618365 2.120000e-106 396.0
5 TraesCS2B01G592600 chr2B 74.242 528 49 45 361 875 777607871 777607418 1.100000e-29 141.0
6 TraesCS2B01G592600 chr2B 88.889 108 7 2 32 139 777608285 777608183 8.540000e-26 128.0
7 TraesCS2B01G592600 chr2D 82.611 1639 112 73 3 1553 634483409 634481856 0.000000e+00 1288.0
8 TraesCS2B01G592600 chr2D 82.148 633 65 29 942 1552 634658871 634658265 1.570000e-137 499.0
9 TraesCS2B01G592600 chr2D 78.468 901 82 62 32 881 634557618 634556779 1.220000e-133 486.0
10 TraesCS2B01G592600 chr2D 91.168 351 23 6 1207 1553 634556369 634556023 1.230000e-128 470.0
11 TraesCS2B01G592600 chr2D 82.281 570 52 26 1015 1553 634575487 634574936 5.770000e-122 448.0
12 TraesCS2B01G592600 chr2D 80.184 434 32 19 1556 1954 634481784 634481370 2.880000e-70 276.0
13 TraesCS2B01G592600 chr2D 83.806 247 28 9 888 1133 634556654 634556419 1.060000e-54 224.0
14 TraesCS2B01G592600 chr2D 77.844 334 38 16 702 1018 634575828 634575514 1.080000e-39 174.0
15 TraesCS2B01G592600 chr2D 91.935 62 5 0 32 93 634659661 634659600 1.450000e-13 87.9
16 TraesCS2B01G592600 chr2D 83.696 92 4 6 1629 1709 634574794 634574703 3.140000e-10 76.8
17 TraesCS2B01G592600 chr2A 82.271 1647 121 78 3 1553 778913752 778915323 0.000000e+00 1266.0
18 TraesCS2B01G592600 chr2A 88.383 835 53 18 2129 2931 778915919 778916741 0.000000e+00 965.0
19 TraesCS2B01G592600 chr2A 79.019 1611 159 98 29 1553 778826339 778827856 0.000000e+00 937.0
20 TraesCS2B01G592600 chr2A 86.049 810 61 22 784 1553 778876136 778876933 0.000000e+00 822.0
21 TraesCS2B01G592600 chr2A 82.020 812 88 38 764 1553 778759802 778760577 3.190000e-179 638.0
22 TraesCS2B01G592600 chr2A 83.752 517 42 16 1548 2031 778915385 778915892 4.460000e-123 451.0
23 TraesCS2B01G592600 chr2A 80.263 228 24 8 211 429 778869836 778870051 5.070000e-33 152.0
24 TraesCS2B01G592600 chr2A 89.320 103 4 7 41 139 778813618 778813717 3.970000e-24 122.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G592600 chr2B 777520005 777522939 2934 True 5421.000000 5421 100.000000 1 2935 1 chr2B.!!$R1 2934
1 TraesCS2B01G592600 chr2B 777548936 777549974 1038 True 848.000000 848 82.326000 517 1553 1 chr2B.!!$R2 1036
2 TraesCS2B01G592600 chr2B 777658401 777659053 652 True 547.000000 547 82.514000 888 1553 1 chr2B.!!$R5 665
3 TraesCS2B01G592600 chr2B 777634762 777635407 645 True 542.000000 542 82.438000 772 1437 1 chr2B.!!$R4 665
4 TraesCS2B01G592600 chr2B 777618365 777619230 865 True 396.000000 396 76.451000 702 1553 1 chr2B.!!$R3 851
5 TraesCS2B01G592600 chr2D 634481370 634483409 2039 True 782.000000 1288 81.397500 3 1954 2 chr2D.!!$R1 1951
6 TraesCS2B01G592600 chr2D 634556023 634557618 1595 True 393.333333 486 84.480667 32 1553 3 chr2D.!!$R2 1521
7 TraesCS2B01G592600 chr2D 634658265 634659661 1396 True 293.450000 499 87.041500 32 1552 2 chr2D.!!$R4 1520
8 TraesCS2B01G592600 chr2D 634574703 634575828 1125 True 232.933333 448 81.273667 702 1709 3 chr2D.!!$R3 1007
9 TraesCS2B01G592600 chr2A 778826339 778827856 1517 False 937.000000 937 79.019000 29 1553 1 chr2A.!!$F3 1524
10 TraesCS2B01G592600 chr2A 778913752 778916741 2989 False 894.000000 1266 84.802000 3 2931 3 chr2A.!!$F6 2928
11 TraesCS2B01G592600 chr2A 778876136 778876933 797 False 822.000000 822 86.049000 784 1553 1 chr2A.!!$F5 769
12 TraesCS2B01G592600 chr2A 778759802 778760577 775 False 638.000000 638 82.020000 764 1553 1 chr2A.!!$F1 789

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
567 719 0.037326 ACCGTGCCACACAGACATAG 60.037 55.0 0.0 0.0 33.4 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2741 0.108424 GTCGATGCAAGCCTCTCTGT 60.108 55.0 0.0 0.0 0.0 3.41 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
17 18 2.684104 TCGTCCTCTCTCCCCAGG 59.316 66.667 0.00 0.00 0.00 4.45
18 19 1.929088 TCGTCCTCTCTCCCCAGGA 60.929 63.158 0.00 0.00 36.38 3.86
180 198 4.612412 GCCCCGACGACCAACACA 62.612 66.667 0.00 0.00 0.00 3.72
181 199 2.663852 CCCCGACGACCAACACAC 60.664 66.667 0.00 0.00 0.00 3.82
183 201 1.954146 CCCGACGACCAACACACTG 60.954 63.158 0.00 0.00 0.00 3.66
185 203 1.066752 CGACGACCAACACACTGGA 59.933 57.895 0.00 0.00 38.96 3.86
186 204 1.213094 CGACGACCAACACACTGGAC 61.213 60.000 0.00 0.00 38.96 4.02
187 205 0.104304 GACGACCAACACACTGGACT 59.896 55.000 0.00 0.00 38.96 3.85
188 206 0.539986 ACGACCAACACACTGGACTT 59.460 50.000 0.00 0.00 38.96 3.01
189 207 0.937304 CGACCAACACACTGGACTTG 59.063 55.000 0.00 0.00 38.96 3.16
190 208 1.742411 CGACCAACACACTGGACTTGT 60.742 52.381 0.00 0.00 38.96 3.16
192 210 1.308998 CCAACACACTGGACTTGTCC 58.691 55.000 12.54 12.54 38.96 4.02
196 214 0.600255 CACACTGGACTTGTCCGACC 60.600 60.000 14.24 0.00 0.00 4.79
197 215 0.759436 ACACTGGACTTGTCCGACCT 60.759 55.000 14.24 0.00 0.00 3.85
198 216 0.393077 CACTGGACTTGTCCGACCTT 59.607 55.000 14.24 0.00 0.00 3.50
200 218 0.388649 CTGGACTTGTCCGACCTTCG 60.389 60.000 14.24 0.00 40.07 3.79
202 220 1.737008 GACTTGTCCGACCTTCGCC 60.737 63.158 0.00 0.00 38.82 5.54
326 433 4.943591 GTGCCGCGCGTGCATATG 62.944 66.667 35.83 19.63 41.46 1.78
346 458 4.621269 AGTCTGGACTTGACCGGT 57.379 55.556 6.92 6.92 38.83 5.28
354 466 2.813908 CTTGACCGGTACCAGCGC 60.814 66.667 7.34 0.00 37.85 5.92
355 467 4.382320 TTGACCGGTACCAGCGCC 62.382 66.667 7.34 0.00 37.85 6.53
357 469 4.382320 GACCGGTACCAGCGCCAA 62.382 66.667 7.34 0.00 37.85 4.52
358 470 4.692475 ACCGGTACCAGCGCCAAC 62.692 66.667 4.49 0.00 37.85 3.77
359 471 4.388499 CCGGTACCAGCGCCAACT 62.388 66.667 13.54 0.00 37.85 3.16
363 475 0.676782 GGTACCAGCGCCAACTCAAT 60.677 55.000 7.15 0.00 0.00 2.57
387 499 5.571791 TGCAAGATTCCATCCATCTATCA 57.428 39.130 0.00 0.00 30.35 2.15
488 631 0.239347 ACTGAACGAACGGTCCTACG 59.761 55.000 9.71 0.00 40.31 3.51
510 653 3.305744 GCTCCTACTCCTGCTGCTAATAC 60.306 52.174 0.00 0.00 0.00 1.89
567 719 0.037326 ACCGTGCCACACAGACATAG 60.037 55.000 0.00 0.00 33.40 2.23
628 792 3.241530 ACGGTGGAGGAAGCTGCA 61.242 61.111 1.02 0.00 0.00 4.41
650 814 1.219124 GGACGCAAGGAGAGCATCA 59.781 57.895 0.00 0.00 46.39 3.07
678 842 4.805231 CCGTACGTCCATGCCGCA 62.805 66.667 15.21 0.00 0.00 5.69
726 897 3.261137 GGCTTCTATGTATAGGACACCCC 59.739 52.174 0.00 0.00 42.17 4.95
727 898 3.901844 GCTTCTATGTATAGGACACCCCA 59.098 47.826 0.00 0.00 42.17 4.96
856 1084 1.226046 CACTGACCGCTACGTCTCG 60.226 63.158 0.00 0.00 33.70 4.04
865 1093 1.090625 GCTACGTCTCGCTCTCTCCA 61.091 60.000 0.00 0.00 0.00 3.86
869 1097 1.791103 CGTCTCGCTCTCTCCATCCC 61.791 65.000 0.00 0.00 0.00 3.85
876 1123 1.999648 CTCTCTCCATCCCTCTCCTG 58.000 60.000 0.00 0.00 0.00 3.86
1075 1512 1.645704 CGCTGCTGAGCAAGAGCAAT 61.646 55.000 9.07 0.00 45.65 3.56
1117 1570 1.815613 GCTCACTGCTCACTCTGTCTA 59.184 52.381 0.00 0.00 38.95 2.59
1237 1736 4.020617 CCGAAGCTGGAGTGCCCA 62.021 66.667 0.00 0.00 44.25 5.36
1471 1988 4.020617 CCGGACCAGCAGGAGCAA 62.021 66.667 0.35 0.00 45.49 3.91
1513 2039 0.613853 TCTTCCCGTTCCTCACCGAT 60.614 55.000 0.00 0.00 0.00 4.18
1514 2040 0.460284 CTTCCCGTTCCTCACCGATG 60.460 60.000 0.00 0.00 0.00 3.84
1515 2041 1.895020 TTCCCGTTCCTCACCGATGG 61.895 60.000 0.00 0.00 0.00 3.51
1603 2213 4.083862 GAGGACTTCGGCGGCCTT 62.084 66.667 18.34 0.00 0.00 4.35
1668 2278 2.277949 ATCGGCGTCGTCATGTCG 60.278 61.111 10.18 5.98 38.03 4.35
1693 2322 2.202676 CGCTCGAGGCTCCTGTTC 60.203 66.667 15.58 0.00 39.13 3.18
1714 2347 2.483741 ATCATCGCAGCCTCGATCGG 62.484 60.000 16.41 5.93 46.22 4.18
1726 2359 0.100682 TCGATCGGTCAGCTAGTTGC 59.899 55.000 16.41 0.00 43.29 4.17
1780 2425 4.226113 CTGAGCTAGGAATGTACGTACC 57.774 50.000 22.43 7.54 0.00 3.34
1781 2426 3.623703 TGAGCTAGGAATGTACGTACCA 58.376 45.455 22.43 11.24 0.00 3.25
1782 2427 3.630769 TGAGCTAGGAATGTACGTACCAG 59.369 47.826 22.43 10.67 0.00 4.00
1783 2428 3.629087 AGCTAGGAATGTACGTACCAGT 58.371 45.455 22.43 10.13 0.00 4.00
1786 2431 4.497674 GCTAGGAATGTACGTACCAGTCTG 60.498 50.000 22.43 13.08 0.00 3.51
1789 2434 2.941453 ATGTACGTACCAGTCTGCAG 57.059 50.000 22.43 7.63 0.00 4.41
1790 2435 1.612676 TGTACGTACCAGTCTGCAGT 58.387 50.000 22.43 0.00 0.00 4.40
1800 2461 2.547211 CCAGTCTGCAGTGTTTCTTCTG 59.453 50.000 14.67 9.84 35.12 3.02
1829 2494 7.333423 GCTTAGGTATAAATGATGTGGCGATTA 59.667 37.037 0.00 0.00 0.00 1.75
1881 2546 1.879927 TAGCAGCAGGGAGGAGGACT 61.880 60.000 0.00 0.00 0.00 3.85
1882 2547 2.297129 GCAGCAGGGAGGAGGACTT 61.297 63.158 0.00 0.00 0.00 3.01
1883 2548 0.978146 GCAGCAGGGAGGAGGACTTA 60.978 60.000 0.00 0.00 0.00 2.24
1884 2549 1.573108 CAGCAGGGAGGAGGACTTAA 58.427 55.000 0.00 0.00 0.00 1.85
1885 2550 1.484240 CAGCAGGGAGGAGGACTTAAG 59.516 57.143 0.00 0.00 0.00 1.85
1886 2551 1.079658 AGCAGGGAGGAGGACTTAAGT 59.920 52.381 8.13 8.13 0.00 2.24
1887 2552 2.315155 AGCAGGGAGGAGGACTTAAGTA 59.685 50.000 8.42 0.00 0.00 2.24
1888 2553 3.051727 AGCAGGGAGGAGGACTTAAGTAT 60.052 47.826 8.42 0.00 0.00 2.12
1895 2560 6.040729 GGGAGGAGGACTTAAGTATGTAACTC 59.959 46.154 8.42 11.08 37.50 3.01
1904 2569 2.715046 AGTATGTAACTCGGTCCGTGA 58.285 47.619 19.68 0.00 30.33 4.35
1919 2584 7.663827 TCGGTCCGTGAAGTGATATAATATTT 58.336 34.615 11.88 0.00 0.00 1.40
1965 2630 5.127031 GGTTATATGGTGTGGTTGCTCAATT 59.873 40.000 0.00 0.00 0.00 2.32
2012 2677 5.729974 GTGGGGAACTACGAAATGTTATC 57.270 43.478 0.00 0.00 29.82 1.75
2015 2680 6.036844 GTGGGGAACTACGAAATGTTATCTTC 59.963 42.308 0.00 0.00 29.82 2.87
2031 2696 9.896645 ATGTTATCTTCATCATGAACTTACACT 57.103 29.630 0.00 0.00 32.21 3.55
2035 2700 7.718334 TCTTCATCATGAACTTACACTAGGA 57.282 36.000 0.00 0.00 32.21 2.94
2037 2702 8.593679 TCTTCATCATGAACTTACACTAGGAAA 58.406 33.333 0.00 0.00 32.21 3.13
2038 2703 8.777865 TTCATCATGAACTTACACTAGGAAAG 57.222 34.615 0.00 0.00 30.26 2.62
2039 2704 8.134202 TCATCATGAACTTACACTAGGAAAGA 57.866 34.615 0.00 0.00 0.00 2.52
2041 2706 8.660373 CATCATGAACTTACACTAGGAAAGAAC 58.340 37.037 0.00 3.26 0.00 3.01
2042 2707 7.732025 TCATGAACTTACACTAGGAAAGAACA 58.268 34.615 0.00 7.29 0.00 3.18
2044 2709 8.836413 CATGAACTTACACTAGGAAAGAACAAA 58.164 33.333 7.69 0.00 0.00 2.83
2057 2722 7.602753 AGGAAAGAACAAATAAATGTAGTGGC 58.397 34.615 0.00 0.00 32.02 5.01
2058 2723 7.451566 AGGAAAGAACAAATAAATGTAGTGGCT 59.548 33.333 0.00 0.00 32.02 4.75
2059 2724 7.542130 GGAAAGAACAAATAAATGTAGTGGCTG 59.458 37.037 0.00 0.00 32.02 4.85
2060 2725 5.954335 AGAACAAATAAATGTAGTGGCTGC 58.046 37.500 0.00 0.00 32.02 5.25
2061 2726 5.711976 AGAACAAATAAATGTAGTGGCTGCT 59.288 36.000 0.00 0.00 32.02 4.24
2062 2727 6.884295 AGAACAAATAAATGTAGTGGCTGCTA 59.116 34.615 0.00 0.00 32.02 3.49
2063 2728 7.557719 AGAACAAATAAATGTAGTGGCTGCTAT 59.442 33.333 0.00 0.00 32.02 2.97
2064 2729 8.746052 AACAAATAAATGTAGTGGCTGCTATA 57.254 30.769 0.00 0.00 32.02 1.31
2065 2730 8.746052 ACAAATAAATGTAGTGGCTGCTATAA 57.254 30.769 0.00 0.00 0.00 0.98
2066 2731 8.621286 ACAAATAAATGTAGTGGCTGCTATAAC 58.379 33.333 0.00 0.00 0.00 1.89
2067 2732 8.840321 CAAATAAATGTAGTGGCTGCTATAACT 58.160 33.333 0.00 1.61 0.00 2.24
2069 2734 9.490379 AATAAATGTAGTGGCTGCTATAACTAC 57.510 33.333 19.13 19.13 43.38 2.73
2071 2736 5.258456 TGTAGTGGCTGCTATAACTACAC 57.742 43.478 22.10 11.51 46.10 2.90
2072 2737 4.707934 TGTAGTGGCTGCTATAACTACACA 59.292 41.667 22.10 11.92 46.10 3.72
2073 2738 4.819105 AGTGGCTGCTATAACTACACAA 57.181 40.909 0.00 0.00 0.00 3.33
2074 2739 5.359194 AGTGGCTGCTATAACTACACAAT 57.641 39.130 0.00 0.00 0.00 2.71
2075 2740 5.745227 AGTGGCTGCTATAACTACACAATT 58.255 37.500 0.00 0.00 0.00 2.32
2076 2741 6.884832 AGTGGCTGCTATAACTACACAATTA 58.115 36.000 0.00 0.00 0.00 1.40
2077 2742 6.761714 AGTGGCTGCTATAACTACACAATTAC 59.238 38.462 0.00 0.00 0.00 1.89
2078 2743 6.537301 GTGGCTGCTATAACTACACAATTACA 59.463 38.462 0.00 0.00 0.00 2.41
2079 2744 6.761242 TGGCTGCTATAACTACACAATTACAG 59.239 38.462 0.00 0.00 0.00 2.74
2080 2745 6.984474 GGCTGCTATAACTACACAATTACAGA 59.016 38.462 0.00 0.00 0.00 3.41
2081 2746 7.169982 GGCTGCTATAACTACACAATTACAGAG 59.830 40.741 0.00 0.00 0.00 3.35
2082 2747 7.921214 GCTGCTATAACTACACAATTACAGAGA 59.079 37.037 0.00 0.00 0.00 3.10
2083 2748 9.457110 CTGCTATAACTACACAATTACAGAGAG 57.543 37.037 0.00 0.00 0.00 3.20
2084 2749 8.414003 TGCTATAACTACACAATTACAGAGAGG 58.586 37.037 0.00 0.00 0.00 3.69
2085 2750 7.382759 GCTATAACTACACAATTACAGAGAGGC 59.617 40.741 0.00 0.00 0.00 4.70
2086 2751 5.746990 AACTACACAATTACAGAGAGGCT 57.253 39.130 0.00 0.00 0.00 4.58
2087 2752 5.746990 ACTACACAATTACAGAGAGGCTT 57.253 39.130 0.00 0.00 0.00 4.35
2088 2753 5.482908 ACTACACAATTACAGAGAGGCTTG 58.517 41.667 0.00 0.00 0.00 4.01
2089 2754 3.077359 ACACAATTACAGAGAGGCTTGC 58.923 45.455 0.00 0.00 0.00 4.01
2090 2755 3.076621 CACAATTACAGAGAGGCTTGCA 58.923 45.455 0.00 0.00 0.00 4.08
2091 2756 3.693085 CACAATTACAGAGAGGCTTGCAT 59.307 43.478 0.00 0.00 0.00 3.96
2092 2757 3.944015 ACAATTACAGAGAGGCTTGCATC 59.056 43.478 0.00 0.00 0.00 3.91
2093 2758 2.299993 TTACAGAGAGGCTTGCATCG 57.700 50.000 1.60 0.00 0.00 3.84
2094 2759 1.474330 TACAGAGAGGCTTGCATCGA 58.526 50.000 1.60 0.00 0.00 3.59
2095 2760 0.108424 ACAGAGAGGCTTGCATCGAC 60.108 55.000 1.60 1.37 0.00 4.20
2096 2761 0.108472 CAGAGAGGCTTGCATCGACA 60.108 55.000 1.60 0.00 0.00 4.35
2097 2762 0.175302 AGAGAGGCTTGCATCGACAG 59.825 55.000 1.60 0.00 0.00 3.51
2098 2763 0.108424 GAGAGGCTTGCATCGACAGT 60.108 55.000 1.60 0.00 0.00 3.55
2099 2764 1.135139 GAGAGGCTTGCATCGACAGTA 59.865 52.381 1.60 0.00 0.00 2.74
2100 2765 1.135915 AGAGGCTTGCATCGACAGTAG 59.864 52.381 1.60 0.00 0.00 2.57
2101 2766 1.135139 GAGGCTTGCATCGACAGTAGA 59.865 52.381 0.00 0.00 0.00 2.59
2102 2767 1.550524 AGGCTTGCATCGACAGTAGAA 59.449 47.619 0.00 0.00 0.00 2.10
2103 2768 2.028112 AGGCTTGCATCGACAGTAGAAA 60.028 45.455 0.00 0.00 0.00 2.52
2104 2769 2.349886 GGCTTGCATCGACAGTAGAAAG 59.650 50.000 0.00 0.00 0.00 2.62
2105 2770 3.254060 GCTTGCATCGACAGTAGAAAGA 58.746 45.455 0.00 0.00 0.00 2.52
2106 2771 3.679980 GCTTGCATCGACAGTAGAAAGAA 59.320 43.478 0.00 0.00 0.00 2.52
2107 2772 4.434857 GCTTGCATCGACAGTAGAAAGAAC 60.435 45.833 0.00 0.00 0.00 3.01
2108 2773 3.242518 TGCATCGACAGTAGAAAGAACG 58.757 45.455 0.00 0.00 0.00 3.95
2109 2774 2.599082 GCATCGACAGTAGAAAGAACGG 59.401 50.000 0.00 0.00 0.00 4.44
2110 2775 3.834610 CATCGACAGTAGAAAGAACGGT 58.165 45.455 0.00 0.00 0.00 4.83
2111 2776 3.278367 TCGACAGTAGAAAGAACGGTG 57.722 47.619 0.00 0.00 0.00 4.94
2112 2777 2.620115 TCGACAGTAGAAAGAACGGTGT 59.380 45.455 0.00 0.00 0.00 4.16
2113 2778 2.724690 CGACAGTAGAAAGAACGGTGTG 59.275 50.000 0.00 0.00 0.00 3.82
2114 2779 3.057734 GACAGTAGAAAGAACGGTGTGG 58.942 50.000 0.00 0.00 0.00 4.17
2115 2780 2.433239 ACAGTAGAAAGAACGGTGTGGT 59.567 45.455 0.00 0.00 0.00 4.16
2116 2781 3.118519 ACAGTAGAAAGAACGGTGTGGTT 60.119 43.478 0.00 0.00 0.00 3.67
2117 2782 3.875134 CAGTAGAAAGAACGGTGTGGTTT 59.125 43.478 0.00 0.00 0.00 3.27
2118 2783 4.025145 CAGTAGAAAGAACGGTGTGGTTTC 60.025 45.833 0.00 0.00 0.00 2.78
2119 2784 1.937899 AGAAAGAACGGTGTGGTTTCG 59.062 47.619 0.00 0.00 33.29 3.46
2120 2785 1.003223 GAAAGAACGGTGTGGTTTCGG 60.003 52.381 0.00 0.00 0.00 4.30
2121 2786 0.816421 AAGAACGGTGTGGTTTCGGG 60.816 55.000 0.00 0.00 0.00 5.14
2122 2787 1.227615 GAACGGTGTGGTTTCGGGA 60.228 57.895 0.00 0.00 0.00 5.14
2123 2788 1.226030 GAACGGTGTGGTTTCGGGAG 61.226 60.000 0.00 0.00 0.00 4.30
2124 2789 1.974973 AACGGTGTGGTTTCGGGAGT 61.975 55.000 0.00 0.00 0.00 3.85
2125 2790 1.959226 CGGTGTGGTTTCGGGAGTG 60.959 63.158 0.00 0.00 0.00 3.51
2126 2791 1.448497 GGTGTGGTTTCGGGAGTGA 59.552 57.895 0.00 0.00 0.00 3.41
2127 2792 0.602905 GGTGTGGTTTCGGGAGTGAG 60.603 60.000 0.00 0.00 0.00 3.51
2151 2816 2.291741 CTCAAGGCACCAAAACAGAGAC 59.708 50.000 0.00 0.00 0.00 3.36
2177 2842 7.020914 ACTTTCAACAGAGTGATCTCAAAAC 57.979 36.000 0.00 0.00 42.66 2.43
2183 2848 6.166984 ACAGAGTGATCTCAAAACAGAGAA 57.833 37.500 0.00 0.00 46.81 2.87
2184 2849 6.586344 ACAGAGTGATCTCAAAACAGAGAAA 58.414 36.000 0.00 0.00 46.81 2.52
2187 2852 7.226325 CAGAGTGATCTCAAAACAGAGAAACTT 59.774 37.037 11.51 3.55 46.81 2.66
2214 2879 3.304123 CGGTCATTTTTCTACCACGCAAA 60.304 43.478 0.00 0.00 32.55 3.68
2221 2886 5.351233 TTTTCTACCACGCAAACTACATG 57.649 39.130 0.00 0.00 0.00 3.21
2222 2887 3.945981 TCTACCACGCAAACTACATGA 57.054 42.857 0.00 0.00 0.00 3.07
2238 2903 0.107456 ATGACATGCCTCGATCCACC 59.893 55.000 0.00 0.00 0.00 4.61
2251 2916 2.159707 CGATCCACCGTTGAATGTGTTC 60.160 50.000 0.00 0.00 34.85 3.18
2295 2960 5.883328 TTGCTGATATACGACGAAACATC 57.117 39.130 0.00 0.00 0.00 3.06
2311 2976 6.536582 ACGAAACATCAAGATACATCCTCAAG 59.463 38.462 0.00 0.00 0.00 3.02
2313 2978 5.363562 ACATCAAGATACATCCTCAAGCA 57.636 39.130 0.00 0.00 0.00 3.91
2314 2979 5.121811 ACATCAAGATACATCCTCAAGCAC 58.878 41.667 0.00 0.00 0.00 4.40
2317 2982 3.444703 AGATACATCCTCAAGCACGAC 57.555 47.619 0.00 0.00 0.00 4.34
2322 2987 1.126846 CATCCTCAAGCACGACGAAAC 59.873 52.381 0.00 0.00 0.00 2.78
2325 2990 0.878523 CTCAAGCACGACGAAACCCA 60.879 55.000 0.00 0.00 0.00 4.51
2338 3003 5.847515 CGACGAAACCCAATAAAAACTGTAC 59.152 40.000 0.00 0.00 0.00 2.90
2339 3004 6.075762 ACGAAACCCAATAAAAACTGTACC 57.924 37.500 0.00 0.00 0.00 3.34
2431 3105 9.486857 GAAGAAACCGCATAAAAGTAGATAAAC 57.513 33.333 0.00 0.00 0.00 2.01
2438 3112 8.276325 CCGCATAAAAGTAGATAAACATCTGAC 58.724 37.037 0.00 0.00 32.36 3.51
2445 3119 9.654663 AAAGTAGATAAACATCTGACAAGTACC 57.345 33.333 0.00 0.00 32.36 3.34
2450 3124 4.810191 AACATCTGACAAGTACCCTCTC 57.190 45.455 0.00 0.00 0.00 3.20
2461 3135 4.489306 AGTACCCTCTCATTTTACCTGC 57.511 45.455 0.00 0.00 0.00 4.85
2483 3157 7.309133 CCTGCACATAAAAGGACAGAAATGTTA 60.309 37.037 0.00 0.00 32.43 2.41
2561 3236 5.923684 TCTTTTAACAATCACGGCAAATTCC 59.076 36.000 0.00 0.00 0.00 3.01
2592 3267 5.398603 AAACGAACATGGAAATTGCCATA 57.601 34.783 18.17 0.00 46.70 2.74
2594 3269 4.743493 ACGAACATGGAAATTGCCATAAC 58.257 39.130 18.17 10.83 46.70 1.89
2595 3270 4.219507 ACGAACATGGAAATTGCCATAACA 59.780 37.500 18.17 0.00 46.70 2.41
2604 3279 5.994668 GGAAATTGCCATAACAAAAGGTTCA 59.005 36.000 0.00 0.00 40.96 3.18
2622 3297 6.527423 AGGTTCATTTGTCATGCTTGAAAAT 58.473 32.000 6.07 10.12 29.13 1.82
2623 3298 6.647895 AGGTTCATTTGTCATGCTTGAAAATC 59.352 34.615 6.07 0.00 29.13 2.17
2626 3301 6.160684 TCATTTGTCATGCTTGAAAATCTGG 58.839 36.000 6.07 4.09 29.13 3.86
2634 3309 1.743394 CTTGAAAATCTGGCGTACCCC 59.257 52.381 0.00 0.00 33.59 4.95
2635 3310 0.693622 TGAAAATCTGGCGTACCCCA 59.306 50.000 0.00 0.00 33.59 4.96
2636 3311 1.283613 TGAAAATCTGGCGTACCCCAT 59.716 47.619 0.00 0.00 33.64 4.00
2637 3312 1.947456 GAAAATCTGGCGTACCCCATC 59.053 52.381 0.00 0.00 33.64 3.51
2691 3366 9.300681 TCAAAGTCCTAAAAGAAACATCATGAT 57.699 29.630 1.18 1.18 0.00 2.45
2772 3447 9.967245 GACAAATTTTGACCAAACTAGAAAAAC 57.033 29.630 15.81 0.00 0.00 2.43
2773 3448 8.652463 ACAAATTTTGACCAAACTAGAAAAACG 58.348 29.630 15.81 0.00 0.00 3.60
2775 3450 9.857957 AAATTTTGACCAAACTAGAAAAACGTA 57.142 25.926 0.00 0.00 0.00 3.57
2801 3486 2.615747 GCTAACCAGTCCCCAGAACTTC 60.616 54.545 0.00 0.00 0.00 3.01
2809 3494 3.017442 GTCCCCAGAACTTCCAAATAGC 58.983 50.000 0.00 0.00 0.00 2.97
2875 3560 3.882888 CAGTAAAGAAACCAACAGCTCCA 59.117 43.478 0.00 0.00 0.00 3.86
2888 3573 3.037485 GCTCCACGCTCTTACACTC 57.963 57.895 0.00 0.00 35.14 3.51
2890 3575 0.803117 CTCCACGCTCTTACACTCGA 59.197 55.000 0.00 0.00 0.00 4.04
2891 3576 1.199327 CTCCACGCTCTTACACTCGAA 59.801 52.381 0.00 0.00 0.00 3.71
2931 3628 3.194542 AGGAACACTCTGATTTCTCCTCG 59.805 47.826 0.00 0.00 0.00 4.63
2932 3629 3.056465 GGAACACTCTGATTTCTCCTCGT 60.056 47.826 0.00 0.00 0.00 4.18
2933 3630 3.859411 ACACTCTGATTTCTCCTCGTC 57.141 47.619 0.00 0.00 0.00 4.20
2934 3631 2.494073 ACACTCTGATTTCTCCTCGTCC 59.506 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.506907 TTCCTGGGGAGAGAGGACGA 61.507 60.000 0.00 0.00 38.14 4.20
15 16 2.610859 AGGGGGCGTGTCATTCCT 60.611 61.111 0.00 0.00 0.00 3.36
17 18 2.511600 CGAGGGGGCGTGTCATTC 60.512 66.667 0.00 0.00 0.00 2.67
18 19 4.778143 GCGAGGGGGCGTGTCATT 62.778 66.667 0.00 0.00 0.00 2.57
96 102 4.253257 CTAGAGCCGGTCGGTCGC 62.253 72.222 11.25 5.53 44.07 5.19
97 103 4.253257 GCTAGAGCCGGTCGGTCG 62.253 72.222 11.25 0.00 44.07 4.79
142 148 1.219522 GATCGGCGTTAATGGGGACG 61.220 60.000 6.85 0.00 41.89 4.79
143 149 0.883370 GGATCGGCGTTAATGGGGAC 60.883 60.000 6.85 0.00 0.00 4.46
144 150 1.448497 GGATCGGCGTTAATGGGGA 59.552 57.895 6.85 0.00 0.00 4.81
145 151 1.959226 CGGATCGGCGTTAATGGGG 60.959 63.158 6.85 0.00 0.00 4.96
169 187 0.539986 AAGTCCAGTGTGTTGGTCGT 59.460 50.000 0.00 0.00 39.35 4.34
172 190 2.038387 GACAAGTCCAGTGTGTTGGT 57.962 50.000 0.00 0.00 39.35 3.67
183 201 1.737008 GCGAAGGTCGGACAAGTCC 60.737 63.158 10.76 9.22 46.18 3.85
185 203 2.342648 GGCGAAGGTCGGACAAGT 59.657 61.111 10.76 0.00 40.84 3.16
186 204 2.809601 CGGCGAAGGTCGGACAAG 60.810 66.667 10.76 0.00 40.84 3.16
240 317 1.957695 TCGCATCGGCATCAGCATC 60.958 57.895 0.00 0.00 44.61 3.91
241 318 2.109593 TCGCATCGGCATCAGCAT 59.890 55.556 0.00 0.00 44.61 3.79
242 319 2.891936 GTCGCATCGGCATCAGCA 60.892 61.111 0.00 0.00 44.61 4.41
243 320 3.993234 CGTCGCATCGGCATCAGC 61.993 66.667 0.00 0.00 41.24 4.26
244 321 1.662760 ATCGTCGCATCGGCATCAG 60.663 57.895 0.00 0.00 41.24 2.90
245 322 1.950630 CATCGTCGCATCGGCATCA 60.951 57.895 0.00 0.00 41.24 3.07
329 436 1.254954 GTACCGGTCAAGTCCAGACT 58.745 55.000 12.40 0.00 44.94 3.24
343 450 2.813908 GAGTTGGCGCTGGTACCG 60.814 66.667 7.64 3.32 0.00 4.02
346 458 1.539388 CAAATTGAGTTGGCGCTGGTA 59.461 47.619 7.64 0.00 0.00 3.25
354 466 4.885413 TGGAATCTTGCAAATTGAGTTGG 58.115 39.130 0.00 0.00 0.00 3.77
355 467 5.579511 GGATGGAATCTTGCAAATTGAGTTG 59.420 40.000 0.00 0.00 44.71 3.16
356 468 5.246656 TGGATGGAATCTTGCAAATTGAGTT 59.753 36.000 0.00 0.00 44.71 3.01
357 469 4.773674 TGGATGGAATCTTGCAAATTGAGT 59.226 37.500 0.00 0.00 44.71 3.41
358 470 5.333299 TGGATGGAATCTTGCAAATTGAG 57.667 39.130 0.00 0.00 44.71 3.02
359 471 5.659525 AGATGGATGGAATCTTGCAAATTGA 59.340 36.000 0.00 0.00 44.71 2.57
363 475 6.367161 TGATAGATGGATGGAATCTTGCAAA 58.633 36.000 0.00 0.00 44.71 3.68
447 572 2.622962 CCAAGGAAACCGAACGGCC 61.623 63.158 13.32 6.71 39.32 6.13
488 631 1.115467 TTAGCAGCAGGAGTAGGAGC 58.885 55.000 0.00 0.00 0.00 4.70
554 702 4.045104 GCGTTCTATCTATGTCTGTGTGG 58.955 47.826 0.00 0.00 0.00 4.17
555 703 3.726235 CGCGTTCTATCTATGTCTGTGTG 59.274 47.826 0.00 0.00 0.00 3.82
556 704 3.626217 TCGCGTTCTATCTATGTCTGTGT 59.374 43.478 5.77 0.00 0.00 3.72
557 705 3.969352 GTCGCGTTCTATCTATGTCTGTG 59.031 47.826 5.77 0.00 0.00 3.66
567 719 1.521749 CGTCAGCGTCGCGTTCTATC 61.522 60.000 12.30 0.00 0.00 2.08
606 770 2.425592 CTTCCTCCACCGTGCACA 59.574 61.111 18.64 0.00 0.00 4.57
628 792 1.153549 GCTCTCCTTGCGTCCGAAT 60.154 57.895 0.00 0.00 0.00 3.34
650 814 3.446570 CGTACGGCCGGAGAACCT 61.447 66.667 31.76 9.01 0.00 3.50
713 884 0.400594 GCCCATGGGGTGTCCTATAC 59.599 60.000 32.23 7.45 46.51 1.47
755 934 1.283029 TGGTCGTGGGCTACTAGTAGT 59.717 52.381 26.76 8.14 35.65 2.73
756 935 2.048444 TGGTCGTGGGCTACTAGTAG 57.952 55.000 23.25 23.25 36.29 2.57
757 936 2.094675 GTTGGTCGTGGGCTACTAGTA 58.905 52.381 1.89 1.89 0.00 1.82
856 1084 0.188342 AGGAGAGGGATGGAGAGAGC 59.812 60.000 0.00 0.00 0.00 4.09
865 1093 1.423161 GCAATTAGCCAGGAGAGGGAT 59.577 52.381 0.00 0.00 37.23 3.85
1075 1512 3.268965 GACTGACCTGCGCGAGTGA 62.269 63.158 12.10 0.00 0.00 3.41
1117 1570 0.036765 TACGTTGCTTGCCGGAGAAT 60.037 50.000 5.05 0.00 0.00 2.40
1524 2053 3.121030 CGAACTGCGGCAGGAAGG 61.121 66.667 31.38 15.04 35.51 3.46
1603 2213 3.640407 GGTGGCCAGGTGAGCTCA 61.640 66.667 13.74 13.74 0.00 4.26
1635 2245 1.153086 GATCATCAGTTGCCGGCCT 60.153 57.895 26.77 12.40 0.00 5.19
1678 2307 2.302260 TGATAGAACAGGAGCCTCGAG 58.698 52.381 5.13 5.13 0.00 4.04
1726 2359 5.050091 CACACTGCAGACTGGTAAAAGTAAG 60.050 44.000 23.35 0.00 0.00 2.34
1728 2361 4.141801 ACACACTGCAGACTGGTAAAAGTA 60.142 41.667 23.35 0.00 0.00 2.24
1729 2362 3.206150 CACACTGCAGACTGGTAAAAGT 58.794 45.455 23.35 0.00 0.00 2.66
1730 2363 3.206150 ACACACTGCAGACTGGTAAAAG 58.794 45.455 23.35 3.82 0.00 2.27
1776 2421 3.113260 AGAAACACTGCAGACTGGTAC 57.887 47.619 23.35 10.18 0.00 3.34
1777 2422 3.388024 AGAAGAAACACTGCAGACTGGTA 59.612 43.478 23.35 0.00 0.00 3.25
1779 2424 2.547211 CAGAAGAAACACTGCAGACTGG 59.453 50.000 23.35 9.22 0.00 4.00
1780 2425 3.461061 TCAGAAGAAACACTGCAGACTG 58.539 45.455 23.35 12.08 34.57 3.51
1781 2426 3.827008 TCAGAAGAAACACTGCAGACT 57.173 42.857 23.35 8.36 34.57 3.24
1782 2427 3.364764 GCATCAGAAGAAACACTGCAGAC 60.365 47.826 23.35 6.14 34.57 3.51
1783 2428 2.810274 GCATCAGAAGAAACACTGCAGA 59.190 45.455 23.35 0.00 34.57 4.26
1786 2431 3.911661 AAGCATCAGAAGAAACACTGC 57.088 42.857 0.00 0.00 34.57 4.40
1789 2434 8.718102 TTATACCTAAGCATCAGAAGAAACAC 57.282 34.615 0.00 0.00 0.00 3.32
1790 2435 9.905713 ATTTATACCTAAGCATCAGAAGAAACA 57.094 29.630 0.00 0.00 0.00 2.83
1800 2461 6.402550 CGCCACATCATTTATACCTAAGCATC 60.403 42.308 0.00 0.00 0.00 3.91
1829 2494 4.592351 TCATGGTCCATTGGTTCAAACAAT 59.408 37.500 0.00 0.00 39.00 2.71
1881 2546 4.699735 TCACGGACCGAGTTACATACTTAA 59.300 41.667 23.38 0.00 37.17 1.85
1882 2547 4.260985 TCACGGACCGAGTTACATACTTA 58.739 43.478 23.38 0.00 37.17 2.24
1883 2548 3.084039 TCACGGACCGAGTTACATACTT 58.916 45.455 23.38 0.00 37.17 2.24
1884 2549 2.715046 TCACGGACCGAGTTACATACT 58.285 47.619 23.38 0.00 40.71 2.12
1885 2550 3.119708 ACTTCACGGACCGAGTTACATAC 60.120 47.826 23.38 0.00 0.00 2.39
1886 2551 3.084039 ACTTCACGGACCGAGTTACATA 58.916 45.455 23.38 0.00 0.00 2.29
1887 2552 1.891150 ACTTCACGGACCGAGTTACAT 59.109 47.619 23.38 0.00 0.00 2.29
1888 2553 1.001048 CACTTCACGGACCGAGTTACA 60.001 52.381 23.38 0.00 0.00 2.41
1895 2560 7.884816 AAATATTATATCACTTCACGGACCG 57.115 36.000 13.61 13.61 0.00 4.79
1948 2613 3.257873 CCAATAATTGAGCAACCACACCA 59.742 43.478 0.00 0.00 0.00 4.17
1988 2653 3.053831 ACATTTCGTAGTTCCCCACTG 57.946 47.619 0.00 0.00 35.97 3.66
1999 2664 9.599866 AGTTCATGATGAAGATAACATTTCGTA 57.400 29.630 8.33 0.00 37.00 3.43
2012 2677 8.777865 TTTCCTAGTGTAAGTTCATGATGAAG 57.222 34.615 8.33 0.00 37.00 3.02
2015 2680 8.660373 GTTCTTTCCTAGTGTAAGTTCATGATG 58.340 37.037 0.00 0.00 0.00 3.07
2031 2696 8.736244 GCCACTACATTTATTTGTTCTTTCCTA 58.264 33.333 0.00 0.00 0.00 2.94
2034 2699 7.062255 GCAGCCACTACATTTATTTGTTCTTTC 59.938 37.037 0.00 0.00 0.00 2.62
2035 2700 6.868339 GCAGCCACTACATTTATTTGTTCTTT 59.132 34.615 0.00 0.00 0.00 2.52
2037 2702 5.711976 AGCAGCCACTACATTTATTTGTTCT 59.288 36.000 0.00 0.00 0.00 3.01
2038 2703 5.954335 AGCAGCCACTACATTTATTTGTTC 58.046 37.500 0.00 0.00 0.00 3.18
2039 2704 5.982890 AGCAGCCACTACATTTATTTGTT 57.017 34.783 0.00 0.00 0.00 2.83
2041 2706 8.840321 AGTTATAGCAGCCACTACATTTATTTG 58.160 33.333 0.00 0.00 0.00 2.32
2042 2707 8.980481 AGTTATAGCAGCCACTACATTTATTT 57.020 30.769 0.00 0.00 0.00 1.40
2044 2709 8.647796 TGTAGTTATAGCAGCCACTACATTTAT 58.352 33.333 15.63 0.00 44.21 1.40
2046 2711 6.884832 TGTAGTTATAGCAGCCACTACATTT 58.115 36.000 15.63 0.00 44.21 2.32
2047 2712 6.479972 TGTAGTTATAGCAGCCACTACATT 57.520 37.500 15.63 0.00 44.21 2.71
2050 2715 5.258456 TGTGTAGTTATAGCAGCCACTAC 57.742 43.478 12.08 12.08 41.33 2.73
2051 2716 5.925506 TTGTGTAGTTATAGCAGCCACTA 57.074 39.130 0.00 0.00 0.00 2.74
2052 2717 4.819105 TTGTGTAGTTATAGCAGCCACT 57.181 40.909 0.00 0.00 0.00 4.00
2055 2720 6.984474 TCTGTAATTGTGTAGTTATAGCAGCC 59.016 38.462 0.00 0.00 0.00 4.85
2056 2721 7.921214 TCTCTGTAATTGTGTAGTTATAGCAGC 59.079 37.037 0.00 0.00 0.00 5.25
2057 2722 9.457110 CTCTCTGTAATTGTGTAGTTATAGCAG 57.543 37.037 0.00 0.00 0.00 4.24
2058 2723 8.414003 CCTCTCTGTAATTGTGTAGTTATAGCA 58.586 37.037 0.00 0.00 0.00 3.49
2059 2724 7.382759 GCCTCTCTGTAATTGTGTAGTTATAGC 59.617 40.741 0.00 0.00 0.00 2.97
2060 2725 8.634444 AGCCTCTCTGTAATTGTGTAGTTATAG 58.366 37.037 0.00 0.00 0.00 1.31
2061 2726 8.534954 AGCCTCTCTGTAATTGTGTAGTTATA 57.465 34.615 0.00 0.00 0.00 0.98
2062 2727 7.425224 AGCCTCTCTGTAATTGTGTAGTTAT 57.575 36.000 0.00 0.00 0.00 1.89
2063 2728 6.852420 AGCCTCTCTGTAATTGTGTAGTTA 57.148 37.500 0.00 0.00 0.00 2.24
2064 2729 5.746990 AGCCTCTCTGTAATTGTGTAGTT 57.253 39.130 0.00 0.00 0.00 2.24
2065 2730 5.482908 CAAGCCTCTCTGTAATTGTGTAGT 58.517 41.667 0.00 0.00 0.00 2.73
2066 2731 4.331168 GCAAGCCTCTCTGTAATTGTGTAG 59.669 45.833 0.00 0.00 0.00 2.74
2067 2732 4.253685 GCAAGCCTCTCTGTAATTGTGTA 58.746 43.478 0.00 0.00 0.00 2.90
2068 2733 3.077359 GCAAGCCTCTCTGTAATTGTGT 58.923 45.455 0.00 0.00 0.00 3.72
2069 2734 3.076621 TGCAAGCCTCTCTGTAATTGTG 58.923 45.455 0.00 0.00 0.00 3.33
2070 2735 3.423539 TGCAAGCCTCTCTGTAATTGT 57.576 42.857 0.00 0.00 0.00 2.71
2071 2736 3.002042 CGATGCAAGCCTCTCTGTAATTG 59.998 47.826 0.00 0.00 0.00 2.32
2072 2737 3.118629 TCGATGCAAGCCTCTCTGTAATT 60.119 43.478 0.00 0.00 0.00 1.40
2073 2738 2.432146 TCGATGCAAGCCTCTCTGTAAT 59.568 45.455 0.00 0.00 0.00 1.89
2074 2739 1.824852 TCGATGCAAGCCTCTCTGTAA 59.175 47.619 0.00 0.00 0.00 2.41
2075 2740 1.135139 GTCGATGCAAGCCTCTCTGTA 59.865 52.381 0.00 0.00 0.00 2.74
2076 2741 0.108424 GTCGATGCAAGCCTCTCTGT 60.108 55.000 0.00 0.00 0.00 3.41
2077 2742 0.108472 TGTCGATGCAAGCCTCTCTG 60.108 55.000 0.00 0.00 0.00 3.35
2078 2743 0.175302 CTGTCGATGCAAGCCTCTCT 59.825 55.000 0.00 0.00 0.00 3.10
2079 2744 0.108424 ACTGTCGATGCAAGCCTCTC 60.108 55.000 0.00 0.00 0.00 3.20
2080 2745 1.135915 CTACTGTCGATGCAAGCCTCT 59.864 52.381 0.00 0.00 0.00 3.69
2081 2746 1.135139 TCTACTGTCGATGCAAGCCTC 59.865 52.381 0.00 0.00 0.00 4.70
2082 2747 1.186200 TCTACTGTCGATGCAAGCCT 58.814 50.000 0.00 0.00 0.00 4.58
2083 2748 2.010145 TTCTACTGTCGATGCAAGCC 57.990 50.000 0.00 0.00 0.00 4.35
2084 2749 3.254060 TCTTTCTACTGTCGATGCAAGC 58.746 45.455 0.00 0.00 0.00 4.01
2085 2750 4.201532 CGTTCTTTCTACTGTCGATGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
2086 2751 3.673338 CGTTCTTTCTACTGTCGATGCAA 59.327 43.478 0.00 0.00 0.00 4.08
2087 2752 3.242518 CGTTCTTTCTACTGTCGATGCA 58.757 45.455 0.00 0.00 0.00 3.96
2088 2753 2.599082 CCGTTCTTTCTACTGTCGATGC 59.401 50.000 0.00 0.00 0.00 3.91
2089 2754 3.608506 CACCGTTCTTTCTACTGTCGATG 59.391 47.826 0.00 0.00 0.00 3.84
2090 2755 3.255149 ACACCGTTCTTTCTACTGTCGAT 59.745 43.478 0.00 0.00 0.00 3.59
2091 2756 2.620115 ACACCGTTCTTTCTACTGTCGA 59.380 45.455 0.00 0.00 0.00 4.20
2092 2757 2.724690 CACACCGTTCTTTCTACTGTCG 59.275 50.000 0.00 0.00 0.00 4.35
2093 2758 3.057734 CCACACCGTTCTTTCTACTGTC 58.942 50.000 0.00 0.00 0.00 3.51
2094 2759 2.433239 ACCACACCGTTCTTTCTACTGT 59.567 45.455 0.00 0.00 0.00 3.55
2095 2760 3.107642 ACCACACCGTTCTTTCTACTG 57.892 47.619 0.00 0.00 0.00 2.74
2096 2761 3.832615 AACCACACCGTTCTTTCTACT 57.167 42.857 0.00 0.00 0.00 2.57
2097 2762 3.060070 CGAAACCACACCGTTCTTTCTAC 60.060 47.826 0.00 0.00 0.00 2.59
2098 2763 3.125316 CGAAACCACACCGTTCTTTCTA 58.875 45.455 0.00 0.00 0.00 2.10
2099 2764 1.937899 CGAAACCACACCGTTCTTTCT 59.062 47.619 0.00 0.00 0.00 2.52
2100 2765 1.003223 CCGAAACCACACCGTTCTTTC 60.003 52.381 0.00 0.00 0.00 2.62
2101 2766 1.018910 CCGAAACCACACCGTTCTTT 58.981 50.000 0.00 0.00 0.00 2.52
2102 2767 0.816421 CCCGAAACCACACCGTTCTT 60.816 55.000 0.00 0.00 0.00 2.52
2103 2768 1.227734 CCCGAAACCACACCGTTCT 60.228 57.895 0.00 0.00 0.00 3.01
2104 2769 1.226030 CTCCCGAAACCACACCGTTC 61.226 60.000 0.00 0.00 0.00 3.95
2105 2770 1.227734 CTCCCGAAACCACACCGTT 60.228 57.895 0.00 0.00 0.00 4.44
2106 2771 2.424302 CTCCCGAAACCACACCGT 59.576 61.111 0.00 0.00 0.00 4.83
2107 2772 1.959226 CACTCCCGAAACCACACCG 60.959 63.158 0.00 0.00 0.00 4.94
2108 2773 0.602905 CTCACTCCCGAAACCACACC 60.603 60.000 0.00 0.00 0.00 4.16
2109 2774 1.228657 GCTCACTCCCGAAACCACAC 61.229 60.000 0.00 0.00 0.00 3.82
2110 2775 1.070786 GCTCACTCCCGAAACCACA 59.929 57.895 0.00 0.00 0.00 4.17
2111 2776 0.670854 GAGCTCACTCCCGAAACCAC 60.671 60.000 9.40 0.00 36.90 4.16
2112 2777 0.832135 AGAGCTCACTCCCGAAACCA 60.832 55.000 17.77 0.00 44.65 3.67
2113 2778 0.108567 GAGAGCTCACTCCCGAAACC 60.109 60.000 17.77 0.00 44.65 3.27
2114 2779 0.603569 TGAGAGCTCACTCCCGAAAC 59.396 55.000 17.77 0.00 44.65 2.78
2115 2780 1.273606 CTTGAGAGCTCACTCCCGAAA 59.726 52.381 17.77 0.00 44.65 3.46
2116 2781 0.891373 CTTGAGAGCTCACTCCCGAA 59.109 55.000 17.77 0.00 44.65 4.30
2117 2782 0.967887 CCTTGAGAGCTCACTCCCGA 60.968 60.000 17.77 0.00 44.65 5.14
2118 2783 1.515020 CCTTGAGAGCTCACTCCCG 59.485 63.158 17.77 0.00 44.65 5.14
2119 2784 1.220477 GCCTTGAGAGCTCACTCCC 59.780 63.158 17.77 0.00 44.65 4.30
2120 2785 0.390998 GTGCCTTGAGAGCTCACTCC 60.391 60.000 17.77 2.51 44.65 3.85
2121 2786 0.390998 GGTGCCTTGAGAGCTCACTC 60.391 60.000 17.77 6.24 43.82 3.51
2122 2787 1.123861 TGGTGCCTTGAGAGCTCACT 61.124 55.000 17.77 0.00 39.66 3.41
2123 2788 0.250467 TTGGTGCCTTGAGAGCTCAC 60.250 55.000 17.77 10.80 39.66 3.51
2124 2789 0.473755 TTTGGTGCCTTGAGAGCTCA 59.526 50.000 17.77 0.00 37.91 4.26
2125 2790 1.268079 GTTTTGGTGCCTTGAGAGCTC 59.732 52.381 5.27 5.27 0.00 4.09
2126 2791 1.322442 GTTTTGGTGCCTTGAGAGCT 58.678 50.000 0.00 0.00 0.00 4.09
2127 2792 1.000938 CTGTTTTGGTGCCTTGAGAGC 60.001 52.381 0.00 0.00 0.00 4.09
2151 2816 6.609237 TTGAGATCACTCTGTTGAAAGTTG 57.391 37.500 0.00 0.00 42.99 3.16
2177 2842 5.424121 AATGACCGTTGAAAGTTTCTCTG 57.576 39.130 16.33 8.61 0.00 3.35
2183 2848 6.095720 TGGTAGAAAAATGACCGTTGAAAGTT 59.904 34.615 0.00 0.00 35.91 2.66
2184 2849 5.591067 TGGTAGAAAAATGACCGTTGAAAGT 59.409 36.000 0.00 0.00 35.91 2.66
2187 2852 4.024725 CGTGGTAGAAAAATGACCGTTGAA 60.025 41.667 0.00 0.00 35.91 2.69
2214 2879 2.036475 GGATCGAGGCATGTCATGTAGT 59.964 50.000 14.26 0.00 0.00 2.73
2221 2886 1.592669 CGGTGGATCGAGGCATGTC 60.593 63.158 0.00 0.00 0.00 3.06
2222 2887 1.899437 AACGGTGGATCGAGGCATGT 61.899 55.000 0.00 0.00 0.00 3.21
2238 2903 5.094429 TGAATCACTGAACACATTCAACG 57.906 39.130 0.00 0.00 44.28 4.10
2251 2916 1.452110 TTGGGACGCATGAATCACTG 58.548 50.000 0.00 0.00 0.00 3.66
2295 2960 3.553511 GTCGTGCTTGAGGATGTATCTTG 59.446 47.826 0.00 0.00 0.00 3.02
2311 2976 2.973419 TTTATTGGGTTTCGTCGTGC 57.027 45.000 0.00 0.00 0.00 5.34
2313 2978 4.336153 ACAGTTTTTATTGGGTTTCGTCGT 59.664 37.500 0.00 0.00 0.00 4.34
2314 2979 4.851010 ACAGTTTTTATTGGGTTTCGTCG 58.149 39.130 0.00 0.00 0.00 5.12
2317 2982 5.916320 GTGGTACAGTTTTTATTGGGTTTCG 59.084 40.000 0.00 0.00 41.80 3.46
2322 2987 9.765795 TTTTTATGTGGTACAGTTTTTATTGGG 57.234 29.630 0.00 0.00 41.80 4.12
2419 3093 9.654663 GGTACTTGTCAGATGTTTATCTACTTT 57.345 33.333 0.00 0.00 41.71 2.66
2431 3105 5.350504 AATGAGAGGGTACTTGTCAGATG 57.649 43.478 0.00 0.00 0.00 2.90
2438 3112 4.636206 GCAGGTAAAATGAGAGGGTACTTG 59.364 45.833 0.00 0.00 0.00 3.16
2445 3119 6.757897 TTTATGTGCAGGTAAAATGAGAGG 57.242 37.500 0.00 0.00 0.00 3.69
2450 3124 6.686630 TGTCCTTTTATGTGCAGGTAAAATG 58.313 36.000 13.56 11.75 31.56 2.32
2494 3168 1.952367 GCCATGCTTAGCCAGTGAACT 60.952 52.381 0.29 0.00 0.00 3.01
2531 3206 5.176590 TGCCGTGATTGTTAAAAGAAATTGC 59.823 36.000 0.00 0.00 0.00 3.56
2534 3209 7.961325 ATTTGCCGTGATTGTTAAAAGAAAT 57.039 28.000 0.00 0.00 0.00 2.17
2572 3247 4.219507 TGTTATGGCAATTTCCATGTTCGT 59.780 37.500 18.60 0.00 45.84 3.85
2573 3248 4.742417 TGTTATGGCAATTTCCATGTTCG 58.258 39.130 18.60 0.00 45.84 3.95
2585 3260 6.352516 ACAAATGAACCTTTTGTTATGGCAA 58.647 32.000 0.00 0.00 42.96 4.52
2592 3267 5.673514 AGCATGACAAATGAACCTTTTGTT 58.326 33.333 0.00 0.00 44.90 2.83
2594 3269 5.754406 TCAAGCATGACAAATGAACCTTTTG 59.246 36.000 0.00 0.00 39.43 2.44
2595 3270 5.916318 TCAAGCATGACAAATGAACCTTTT 58.084 33.333 0.00 0.00 0.00 2.27
2604 3279 4.933400 GCCAGATTTTCAAGCATGACAAAT 59.067 37.500 0.00 10.00 34.61 2.32
2609 3284 2.161855 ACGCCAGATTTTCAAGCATGA 58.838 42.857 0.00 0.00 0.00 3.07
2622 3297 0.693622 TTTTGATGGGGTACGCCAGA 59.306 50.000 32.09 20.48 42.25 3.86
2623 3298 1.201414 GTTTTTGATGGGGTACGCCAG 59.799 52.381 32.09 0.00 42.25 4.85
2626 3301 3.372660 TTTGTTTTTGATGGGGTACGC 57.627 42.857 0.29 0.29 43.69 4.42
2635 3310 5.634859 GGCGAACATCAGATTTGTTTTTGAT 59.365 36.000 0.00 0.00 37.43 2.57
2636 3311 4.981674 GGCGAACATCAGATTTGTTTTTGA 59.018 37.500 0.00 0.00 37.43 2.69
2637 3312 4.744137 TGGCGAACATCAGATTTGTTTTTG 59.256 37.500 0.00 0.00 37.43 2.44
2734 3409 8.908903 TGGTCAAAATTTGTCTTGTTACATAGT 58.091 29.630 5.56 0.00 0.00 2.12
2735 3410 9.743057 TTGGTCAAAATTTGTCTTGTTACATAG 57.257 29.630 5.56 0.00 0.00 2.23
2737 3412 8.878769 GTTTGGTCAAAATTTGTCTTGTTACAT 58.121 29.630 5.56 0.00 31.33 2.29
2738 3413 8.091449 AGTTTGGTCAAAATTTGTCTTGTTACA 58.909 29.630 5.56 0.00 31.33 2.41
2739 3414 8.474006 AGTTTGGTCAAAATTTGTCTTGTTAC 57.526 30.769 5.56 0.00 31.33 2.50
2772 3447 1.571919 GGACTGGTTAGCATGCTACG 58.428 55.000 26.87 16.72 0.00 3.51
2773 3448 1.475213 GGGGACTGGTTAGCATGCTAC 60.475 57.143 26.87 19.88 0.00 3.58
2775 3450 1.207488 TGGGGACTGGTTAGCATGCT 61.207 55.000 25.99 25.99 0.00 3.79
2801 3486 6.166984 TCACCTAGAATCTCAGCTATTTGG 57.833 41.667 0.00 0.00 0.00 3.28
2809 3494 4.464244 TCACCAGTTCACCTAGAATCTCAG 59.536 45.833 0.00 0.00 38.76 3.35
2847 3532 7.450903 AGCTGTTGGTTTCTTTACTGTATAGT 58.549 34.615 0.00 0.00 40.99 2.12
2851 3536 5.061179 GGAGCTGTTGGTTTCTTTACTGTA 58.939 41.667 0.00 0.00 0.00 2.74
2875 3560 2.358267 CCCTATTCGAGTGTAAGAGCGT 59.642 50.000 0.00 0.00 0.00 5.07
2888 3573 4.576463 CCTGAATTCTGGTTTCCCTATTCG 59.424 45.833 20.30 0.00 31.79 3.34
2890 3575 5.796502 TCCTGAATTCTGGTTTCCCTATT 57.203 39.130 25.50 0.00 36.48 1.73
2891 3576 5.015178 TGTTCCTGAATTCTGGTTTCCCTAT 59.985 40.000 25.50 0.00 36.48 2.57
2903 3600 6.093357 GGAGAAATCAGAGTGTTCCTGAATTC 59.907 42.308 11.07 11.07 44.67 2.17
2909 3606 3.194542 CGAGGAGAAATCAGAGTGTTCCT 59.805 47.826 3.68 3.68 36.34 3.36


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

AutoCloner maintained by Alex Coulton.