Multiple sequence alignment - TraesCS1D01G309100

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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 TraesCS1D01G309100 chr1D 100.000 3497 0 0 1 3497 405106904 405110400 0.000000e+00 6458.0
1 TraesCS1D01G309100 chr1B 87.716 1392 94 35 560 1923 544993758 544995100 0.000000e+00 1552.0
2 TraesCS1D01G309100 chr1B 89.649 570 31 12 2227 2772 544995323 544995888 0.000000e+00 701.0
3 TraesCS1D01G309100 chr1B 88.073 545 42 9 32 555 544993180 544993722 2.960000e-175 625.0
4 TraesCS1D01G309100 chr1B 82.955 352 22 20 2771 3097 544995928 544996266 2.050000e-72 283.0
5 TraesCS1D01G309100 chr1B 87.111 225 11 6 3273 3494 544996470 544996679 4.510000e-59 239.0
6 TraesCS1D01G309100 chr1A 83.384 993 69 44 561 1519 500559765 500560695 0.000000e+00 832.0
7 TraesCS1D01G309100 chr1A 85.426 446 28 14 24 447 500559243 500559673 2.490000e-116 429.0
8 TraesCS1D01G309100 chr1A 85.417 384 23 18 2401 2772 500561726 500562088 5.510000e-98 368.0
9 TraesCS1D01G309100 chr1A 90.148 203 8 6 2771 2968 500562128 500562323 1.610000e-63 254.0
10 TraesCS1D01G309100 chr1A 76.832 505 45 36 3000 3471 500562399 500562864 5.880000e-53 219.0
11 TraesCS1D01G309100 chr1A 93.220 59 4 0 497 555 500559674 500559732 1.730000e-13 87.9
12 TraesCS1D01G309100 chr3A 88.538 253 23 4 1116 1364 699576295 699576545 5.670000e-78 302.0
13 TraesCS1D01G309100 chr7D 87.705 244 26 3 1123 1362 617733792 617734035 7.390000e-72 281.0
14 TraesCS1D01G309100 chr2B 88.667 150 17 0 980 1129 71733224 71733075 2.140000e-42 183.0


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 TraesCS1D01G309100 chr1D 405106904 405110400 3496 False 6458.000000 6458 100.000000 1 3497 1 chr1D.!!$F1 3496
1 TraesCS1D01G309100 chr1B 544993180 544996679 3499 False 680.000000 1552 87.100800 32 3494 5 chr1B.!!$F1 3462
2 TraesCS1D01G309100 chr1A 500559243 500562864 3621 False 364.983333 832 85.737833 24 3471 6 chr1A.!!$F1 3447

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
558 589 0.176449 CGTGCATCCCATGAGACTCA 59.824 55.0 7.80 7.8 31.89 3.41 F
1536 1630 0.107312 ACTGGCAGTGCATGAGATCC 60.107 55.0 21.37 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2146 0.250234 TCAGTGCAGCCATACCAGTC 59.750 55.0 0.0 0.0 0.0 3.51 R
2974 3511 0.036765 CCAGCCAAGCTACAACCGTA 60.037 55.0 0.0 0.0 36.4 4.02 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
20 21 2.512692 TACCTAGTGGGAGCGTAACA 57.487 50.000 0.00 0.00 38.76 2.41
21 22 1.861982 ACCTAGTGGGAGCGTAACAT 58.138 50.000 0.00 0.00 38.76 2.71
22 23 2.185387 ACCTAGTGGGAGCGTAACATT 58.815 47.619 0.00 0.00 38.76 2.71
79 80 0.253347 AAATGGGGAGAGGAGCCTGA 60.253 55.000 0.00 0.00 0.00 3.86
108 109 3.016474 GAGGCACGTGAAAGCGAGC 62.016 63.158 22.23 0.00 45.14 5.03
143 144 0.958822 ACATTTGCGGTCCAAGGAAC 59.041 50.000 0.00 0.00 34.34 3.62
245 272 3.490759 CCTGTGATGCGTGCGTCC 61.491 66.667 11.29 4.05 0.00 4.79
260 287 2.548057 TGCGTCCACTCTTTCATTGAAC 59.452 45.455 0.00 0.00 0.00 3.18
284 311 2.290071 CCTTAAATCCGGCGGGTGATAT 60.290 50.000 27.98 8.90 33.83 1.63
295 322 1.666023 CGGGTGATATGTCGTCATCGG 60.666 57.143 0.00 0.00 37.69 4.18
485 513 0.458669 CACCTCAGCCAAATCCATGC 59.541 55.000 0.00 0.00 0.00 4.06
544 575 1.867865 TGCGTGATTCTTTTACGTGCA 59.132 42.857 0.00 0.00 39.79 4.57
547 578 3.670203 CGTGATTCTTTTACGTGCATCC 58.330 45.455 0.00 0.00 33.48 3.51
555 586 2.309528 TTACGTGCATCCCATGAGAC 57.690 50.000 0.00 0.00 34.47 3.36
558 589 0.176449 CGTGCATCCCATGAGACTCA 59.824 55.000 7.80 7.80 31.89 3.41
598 663 8.147642 TCTTCTCTTACTTGCAAGAAAAGAAG 57.852 34.615 31.76 31.76 38.21 2.85
744 819 4.754667 GTCCGTCGGCCTTGACCC 62.755 72.222 6.34 0.00 35.40 4.46
778 853 4.692228 CAGATAAAGAGGAGGAGCTTCAC 58.308 47.826 0.00 0.00 0.00 3.18
791 866 1.566018 GCTTCACAAAGGACGACCCG 61.566 60.000 0.00 0.00 40.87 5.28
843 918 3.041940 AACCGGTCGAGCAAAGCG 61.042 61.111 8.04 0.04 37.37 4.68
848 923 4.430423 GTCGAGCAAAGCGCACCG 62.430 66.667 11.47 3.38 46.13 4.94
864 939 1.064134 CCGCGTCACATCATCTCGA 59.936 57.895 4.92 0.00 0.00 4.04
867 942 1.535636 GCGTCACATCATCTCGAGCG 61.536 60.000 7.81 3.13 0.00 5.03
869 944 1.298638 TCACATCATCTCGAGCGCG 60.299 57.895 7.81 2.41 39.35 6.86
872 947 2.050533 ATCATCTCGAGCGCGCTC 60.051 61.111 43.32 43.32 39.55 5.03
873 948 2.551006 ATCATCTCGAGCGCGCTCT 61.551 57.895 46.19 31.82 40.69 4.09
1005 1087 4.508128 GACCGAGGCGCGATGGAA 62.508 66.667 12.10 0.00 44.57 3.53
1273 1361 2.684843 CCGTCCAAGAAGCAGCAGC 61.685 63.158 0.00 0.00 42.56 5.25
1274 1362 1.962822 CGTCCAAGAAGCAGCAGCA 60.963 57.895 3.17 0.00 45.49 4.41
1277 1371 2.567049 CAAGAAGCAGCAGCAGGC 59.433 61.111 3.17 0.00 45.49 4.85
1380 1474 2.135933 GTGCTGCTCAACTTCTACGTT 58.864 47.619 0.00 0.00 0.00 3.99
1503 1597 1.528309 CGGCAAAACCAGGTGAGGT 60.528 57.895 0.00 0.00 45.91 3.85
1536 1630 0.107312 ACTGGCAGTGCATGAGATCC 60.107 55.000 21.37 0.00 0.00 3.36
1539 1633 1.022735 GGCAGTGCATGAGATCCTTG 58.977 55.000 18.61 0.00 0.00 3.61
1559 1653 0.528017 TGCTTCTCGAGATTCGCACT 59.472 50.000 22.69 0.00 40.21 4.40
1590 1697 9.770097 ATACAATGATTAACATCTCGATTCACT 57.230 29.630 0.00 0.00 38.38 3.41
1592 1699 9.035607 ACAATGATTAACATCTCGATTCACTAC 57.964 33.333 0.00 0.00 38.38 2.73
1603 1710 6.379386 TCTCGATTCACTACATAATTAGCCG 58.621 40.000 0.00 0.00 0.00 5.52
1634 1741 1.138228 AGTCAGTTAACCCCACCCCC 61.138 60.000 0.88 0.00 0.00 5.40
1662 1780 7.772332 AAAGAGTATTACCAGTTGCTAATCG 57.228 36.000 0.00 0.00 0.00 3.34
1667 1785 2.094762 ACCAGTTGCTAATCGTGTCC 57.905 50.000 0.00 0.00 0.00 4.02
1669 1787 2.002586 CCAGTTGCTAATCGTGTCCAG 58.997 52.381 0.00 0.00 0.00 3.86
1670 1788 2.612972 CCAGTTGCTAATCGTGTCCAGT 60.613 50.000 0.00 0.00 0.00 4.00
1678 1796 6.170506 TGCTAATCGTGTCCAGTTATTTTCT 58.829 36.000 0.00 0.00 0.00 2.52
1679 1797 7.324935 TGCTAATCGTGTCCAGTTATTTTCTA 58.675 34.615 0.00 0.00 0.00 2.10
1680 1798 7.277098 TGCTAATCGTGTCCAGTTATTTTCTAC 59.723 37.037 0.00 0.00 0.00 2.59
1681 1799 6.642683 AATCGTGTCCAGTTATTTTCTACG 57.357 37.500 0.00 0.00 0.00 3.51
1682 1800 5.375417 TCGTGTCCAGTTATTTTCTACGA 57.625 39.130 0.00 0.00 35.94 3.43
1683 1801 5.396484 TCGTGTCCAGTTATTTTCTACGAG 58.604 41.667 0.00 0.00 33.75 4.18
1698 1816 3.564637 CGAGTAGTCGTGAGTGTCG 57.435 57.895 11.92 0.00 41.57 4.35
1711 1829 1.738350 GAGTGTCGTAGCAGCTGTAGA 59.262 52.381 16.64 7.00 0.00 2.59
1712 1830 1.740585 AGTGTCGTAGCAGCTGTAGAG 59.259 52.381 16.64 5.35 0.00 2.43
1722 1840 3.549299 CAGCTGTAGAGTTGCTTTTGG 57.451 47.619 5.25 0.00 34.51 3.28
1723 1841 1.882623 AGCTGTAGAGTTGCTTTTGGC 59.117 47.619 0.00 0.00 42.22 4.52
1726 1844 3.126000 GCTGTAGAGTTGCTTTTGGCTAG 59.874 47.826 0.00 0.00 42.39 3.42
1727 1845 3.074412 TGTAGAGTTGCTTTTGGCTAGC 58.926 45.455 6.04 6.04 42.39 3.42
1739 2146 3.876274 TTGGCTAGCTAGTGAAGTCTG 57.124 47.619 21.62 0.00 0.00 3.51
1750 2165 2.234908 AGTGAAGTCTGACTGGTATGGC 59.765 50.000 11.71 0.00 0.00 4.40
1763 2178 3.743521 TGGTATGGCTGCACTGAATATC 58.256 45.455 0.50 0.00 0.00 1.63
1765 2180 3.750130 GGTATGGCTGCACTGAATATCTG 59.250 47.826 0.50 0.00 0.00 2.90
1868 2295 3.835395 TCATTATTTCCAACCCCACAACC 59.165 43.478 0.00 0.00 0.00 3.77
1869 2296 3.330126 TTATTTCCAACCCCACAACCA 57.670 42.857 0.00 0.00 0.00 3.67
1870 2297 1.419381 ATTTCCAACCCCACAACCAC 58.581 50.000 0.00 0.00 0.00 4.16
1871 2298 0.041238 TTTCCAACCCCACAACCACA 59.959 50.000 0.00 0.00 0.00 4.17
1872 2299 0.041238 TTCCAACCCCACAACCACAA 59.959 50.000 0.00 0.00 0.00 3.33
1923 2350 4.221041 TCTTTCTCCAACAAACGGGTTTTT 59.779 37.500 0.00 0.00 0.00 1.94
1942 2369 2.955342 TTTAGGGTAACAAACGGGCT 57.045 45.000 0.00 0.00 39.74 5.19
1943 2370 2.955342 TTAGGGTAACAAACGGGCTT 57.045 45.000 0.00 0.00 39.74 4.35
1944 2371 2.955342 TAGGGTAACAAACGGGCTTT 57.045 45.000 0.00 0.00 39.74 3.51
1945 2372 2.955342 AGGGTAACAAACGGGCTTTA 57.045 45.000 0.00 0.00 39.74 1.85
1946 2373 3.444792 AGGGTAACAAACGGGCTTTAT 57.555 42.857 0.00 0.00 39.74 1.40
1947 2374 4.573021 AGGGTAACAAACGGGCTTTATA 57.427 40.909 0.00 0.00 39.74 0.98
1948 2375 4.920999 AGGGTAACAAACGGGCTTTATAA 58.079 39.130 0.00 0.00 39.74 0.98
1949 2376 5.512298 AGGGTAACAAACGGGCTTTATAAT 58.488 37.500 0.00 0.00 39.74 1.28
1950 2377 6.661777 AGGGTAACAAACGGGCTTTATAATA 58.338 36.000 0.00 0.00 39.74 0.98
1951 2378 7.118060 AGGGTAACAAACGGGCTTTATAATAA 58.882 34.615 0.00 0.00 39.74 1.40
1952 2379 7.614974 AGGGTAACAAACGGGCTTTATAATAAA 59.385 33.333 0.00 0.00 39.74 1.40
1953 2380 8.249638 GGGTAACAAACGGGCTTTATAATAAAA 58.750 33.333 0.00 0.00 39.74 1.52
1954 2381 9.806203 GGTAACAAACGGGCTTTATAATAAAAT 57.194 29.630 0.00 0.00 0.00 1.82
1978 2405 9.802039 AATAAAAGGACCAAACACTAATCACTA 57.198 29.630 0.00 0.00 0.00 2.74
2055 2489 5.525012 TGTATGCATTTTTCTCAGGATCTCG 59.475 40.000 3.54 0.00 0.00 4.04
2075 2510 3.004315 TCGGTTCTTTGACAATTCCAAGC 59.996 43.478 0.00 0.00 0.00 4.01
2079 2514 2.158325 TCTTTGACAATTCCAAGCCCCT 60.158 45.455 0.00 0.00 0.00 4.79
2080 2515 1.923356 TTGACAATTCCAAGCCCCTC 58.077 50.000 0.00 0.00 0.00 4.30
2081 2516 0.776810 TGACAATTCCAAGCCCCTCA 59.223 50.000 0.00 0.00 0.00 3.86
2082 2517 1.272092 TGACAATTCCAAGCCCCTCAG 60.272 52.381 0.00 0.00 0.00 3.35
2122 2557 7.657336 TGATTAAAGCTTTTGACTTTGGTAGG 58.343 34.615 18.47 0.00 37.86 3.18
2146 2597 1.699083 TGGAACAACTCATGAGCAGGA 59.301 47.619 22.83 0.00 31.92 3.86
2186 2639 2.279741 CCCGACAATGTGACCATAGTG 58.720 52.381 0.00 0.00 0.00 2.74
2187 2640 1.665679 CCGACAATGTGACCATAGTGC 59.334 52.381 0.00 0.00 0.00 4.40
2188 2641 2.345876 CGACAATGTGACCATAGTGCA 58.654 47.619 0.00 0.00 0.00 4.57
2189 2642 2.094258 CGACAATGTGACCATAGTGCAC 59.906 50.000 9.40 9.40 0.00 4.57
2190 2643 3.073678 GACAATGTGACCATAGTGCACA 58.926 45.455 21.04 5.47 45.40 4.57
2191 2644 3.076621 ACAATGTGACCATAGTGCACAG 58.923 45.455 21.04 8.31 44.66 3.66
2192 2645 2.408271 ATGTGACCATAGTGCACAGG 57.592 50.000 21.04 19.27 44.66 4.00
2196 2649 3.146066 GTGACCATAGTGCACAGGAAAA 58.854 45.455 24.19 10.09 32.96 2.29
2198 2651 3.568007 TGACCATAGTGCACAGGAAAAAC 59.432 43.478 24.19 12.57 0.00 2.43
2199 2652 3.561143 ACCATAGTGCACAGGAAAAACA 58.439 40.909 24.19 0.00 0.00 2.83
2200 2653 3.317993 ACCATAGTGCACAGGAAAAACAC 59.682 43.478 24.19 0.00 0.00 3.32
2201 2654 3.317711 CCATAGTGCACAGGAAAAACACA 59.682 43.478 21.04 0.00 33.69 3.72
2203 2656 2.722094 AGTGCACAGGAAAAACACAGA 58.278 42.857 21.04 0.00 33.69 3.41
2204 2657 3.290710 AGTGCACAGGAAAAACACAGAT 58.709 40.909 21.04 0.00 33.69 2.90
2205 2658 3.701040 AGTGCACAGGAAAAACACAGATT 59.299 39.130 21.04 0.00 33.69 2.40
2206 2659 4.887071 AGTGCACAGGAAAAACACAGATTA 59.113 37.500 21.04 0.00 33.69 1.75
2207 2660 4.976116 GTGCACAGGAAAAACACAGATTAC 59.024 41.667 13.17 0.00 0.00 1.89
2208 2661 4.642437 TGCACAGGAAAAACACAGATTACA 59.358 37.500 0.00 0.00 0.00 2.41
2209 2662 5.215160 GCACAGGAAAAACACAGATTACAG 58.785 41.667 0.00 0.00 0.00 2.74
2211 2664 6.294176 GCACAGGAAAAACACAGATTACAGAT 60.294 38.462 0.00 0.00 0.00 2.90
2213 2666 8.950210 CACAGGAAAAACACAGATTACAGATAT 58.050 33.333 0.00 0.00 0.00 1.63
2214 2667 9.167311 ACAGGAAAAACACAGATTACAGATATC 57.833 33.333 0.00 0.00 0.00 1.63
2215 2668 9.388506 CAGGAAAAACACAGATTACAGATATCT 57.611 33.333 0.00 0.00 32.66 1.98
2238 2691 8.129496 TCTATATGTTGTGAGTTAACCTGACA 57.871 34.615 0.88 0.00 35.34 3.58
2239 2692 8.590204 TCTATATGTTGTGAGTTAACCTGACAA 58.410 33.333 0.88 6.31 43.74 3.18
2240 2693 9.383519 CTATATGTTGTGAGTTAACCTGACAAT 57.616 33.333 14.36 5.96 46.68 2.71
2242 2695 9.905713 ATATGTTGTGAGTTAACCTGACAATAT 57.094 29.630 19.14 19.14 46.68 1.28
2243 2696 7.433708 TGTTGTGAGTTAACCTGACAATATG 57.566 36.000 14.36 0.00 46.68 1.78
2244 2697 7.220740 TGTTGTGAGTTAACCTGACAATATGA 58.779 34.615 14.36 2.28 46.68 2.15
2245 2698 7.172532 TGTTGTGAGTTAACCTGACAATATGAC 59.827 37.037 14.36 6.21 46.68 3.06
2246 2699 6.170506 TGTGAGTTAACCTGACAATATGACC 58.829 40.000 0.88 0.00 34.12 4.02
2247 2700 6.170506 GTGAGTTAACCTGACAATATGACCA 58.829 40.000 0.88 0.00 0.00 4.02
2248 2701 6.823689 GTGAGTTAACCTGACAATATGACCAT 59.176 38.462 0.88 0.00 0.00 3.55
2249 2702 6.823182 TGAGTTAACCTGACAATATGACCATG 59.177 38.462 0.88 0.00 0.00 3.66
2250 2703 6.122277 AGTTAACCTGACAATATGACCATGG 58.878 40.000 11.19 11.19 0.00 3.66
2251 2704 4.591321 AACCTGACAATATGACCATGGT 57.409 40.909 19.89 19.89 0.00 3.55
2320 2773 3.599343 TGACAATGTGTCCATAGTGCTC 58.401 45.455 5.96 0.00 46.40 4.26
2321 2774 2.939103 GACAATGTGTCCATAGTGCTCC 59.061 50.000 0.00 0.00 41.37 4.70
2344 2797 2.804647 AGCAAAACTGCGTTTTACACC 58.195 42.857 15.54 7.81 42.78 4.16
2346 2799 2.924290 GCAAAACTGCGTTTTACACCAA 59.076 40.909 15.54 0.00 42.78 3.67
2347 2800 3.368236 GCAAAACTGCGTTTTACACCAAA 59.632 39.130 15.54 0.00 42.78 3.28
2348 2801 4.033472 GCAAAACTGCGTTTTACACCAAAT 59.967 37.500 15.54 0.00 42.78 2.32
2349 2802 5.488458 CAAAACTGCGTTTTACACCAAATG 58.512 37.500 15.54 2.40 42.78 2.32
2377 2838 0.395686 AGATGACGATGGGCCATGAG 59.604 55.000 26.77 19.64 0.00 2.90
2392 2853 4.324267 GCCATGAGTGTACAAACCTAACT 58.676 43.478 0.00 0.00 0.00 2.24
2396 2857 6.370718 CCATGAGTGTACAAACCTAACTTACC 59.629 42.308 0.00 0.00 0.00 2.85
2402 2863 8.092687 AGTGTACAAACCTAACTTACCTATGTG 58.907 37.037 0.00 0.00 0.00 3.21
2615 3079 6.741992 TTCTGCTCACACCTGTAAATTATG 57.258 37.500 0.00 0.00 0.00 1.90
2616 3080 4.635765 TCTGCTCACACCTGTAAATTATGC 59.364 41.667 0.00 0.00 0.00 3.14
2639 3106 5.004061 GCTCTGTTTTTGTAAACGTGGTTTC 59.996 40.000 0.00 0.00 45.29 2.78
2642 3109 6.010294 TGTTTTTGTAAACGTGGTTTCTGA 57.990 33.333 0.00 0.00 45.29 3.27
2643 3110 6.087522 TGTTTTTGTAAACGTGGTTTCTGAG 58.912 36.000 0.00 0.00 45.29 3.35
2644 3111 5.883503 TTTTGTAAACGTGGTTTCTGAGT 57.116 34.783 0.00 0.00 37.01 3.41
2645 3112 5.883503 TTTGTAAACGTGGTTTCTGAGTT 57.116 34.783 0.00 0.00 37.01 3.01
2648 3115 2.413310 AACGTGGTTTCTGAGTTGGT 57.587 45.000 0.00 0.00 0.00 3.67
2649 3116 1.663695 ACGTGGTTTCTGAGTTGGTG 58.336 50.000 0.00 0.00 0.00 4.17
2651 3118 1.597663 CGTGGTTTCTGAGTTGGTGTC 59.402 52.381 0.00 0.00 0.00 3.67
2652 3119 2.741878 CGTGGTTTCTGAGTTGGTGTCT 60.742 50.000 0.00 0.00 0.00 3.41
2654 3121 3.694566 GTGGTTTCTGAGTTGGTGTCTTT 59.305 43.478 0.00 0.00 0.00 2.52
2655 3122 4.157840 GTGGTTTCTGAGTTGGTGTCTTTT 59.842 41.667 0.00 0.00 0.00 2.27
2656 3123 4.398044 TGGTTTCTGAGTTGGTGTCTTTTC 59.602 41.667 0.00 0.00 0.00 2.29
2673 3140 2.766970 TTCTTAAACTGCGTTGGTGC 57.233 45.000 0.00 0.00 0.00 5.01
2674 3141 1.961793 TCTTAAACTGCGTTGGTGCT 58.038 45.000 0.00 0.00 35.36 4.40
2676 3143 0.030101 TTAAACTGCGTTGGTGCTGC 59.970 50.000 0.00 0.00 37.32 5.25
2723 3209 2.738521 CACGGACGGGCTTGTCAG 60.739 66.667 11.44 9.91 40.72 3.51
2915 3444 0.179018 ATAAATCGAGGCTGGGTGGC 60.179 55.000 0.00 0.00 42.15 5.01
2916 3445 2.587322 TAAATCGAGGCTGGGTGGCG 62.587 60.000 0.00 0.00 46.88 5.69
2920 3449 4.767255 GAGGCTGGGTGGCGAGTG 62.767 72.222 0.00 0.00 46.88 3.51
2960 3497 4.726416 ACATGAAAACGATTGCTGTGATC 58.274 39.130 0.00 0.00 0.00 2.92
2968 3505 2.274437 GATTGCTGTGATCGAGCTGAA 58.726 47.619 15.44 5.31 37.35 3.02
2970 3507 1.931906 TGCTGTGATCGAGCTGAATC 58.068 50.000 15.44 0.00 37.35 2.52
2971 3508 1.479730 TGCTGTGATCGAGCTGAATCT 59.520 47.619 15.44 0.00 37.35 2.40
2973 3510 3.243334 TGCTGTGATCGAGCTGAATCTAG 60.243 47.826 15.44 0.00 37.35 2.43
2974 3511 3.243367 GCTGTGATCGAGCTGAATCTAGT 60.243 47.826 0.90 0.00 33.37 2.57
2975 3512 4.023622 GCTGTGATCGAGCTGAATCTAGTA 60.024 45.833 0.90 0.00 33.37 1.82
2976 3513 5.425577 TGTGATCGAGCTGAATCTAGTAC 57.574 43.478 0.90 0.00 0.00 2.73
2977 3514 4.024809 TGTGATCGAGCTGAATCTAGTACG 60.025 45.833 0.90 0.00 0.00 3.67
3005 3598 4.404654 GGCTGGTTTTCTGGCGCG 62.405 66.667 0.00 0.00 0.00 6.86
3050 3644 1.686587 CCAGATACGATACCACTGCCA 59.313 52.381 0.00 0.00 0.00 4.92
3051 3645 2.545952 CCAGATACGATACCACTGCCAC 60.546 54.545 0.00 0.00 0.00 5.01
3052 3646 2.362397 CAGATACGATACCACTGCCACT 59.638 50.000 0.00 0.00 0.00 4.00
3053 3647 2.362397 AGATACGATACCACTGCCACTG 59.638 50.000 0.00 0.00 0.00 3.66
3054 3648 0.174845 TACGATACCACTGCCACTGC 59.825 55.000 0.00 0.00 38.26 4.40
3055 3649 1.815421 CGATACCACTGCCACTGCC 60.815 63.158 0.00 0.00 36.33 4.85
3056 3650 1.299648 GATACCACTGCCACTGCCA 59.700 57.895 0.00 0.00 36.33 4.92
3073 3667 3.315949 AGTACCGGCCCGCTGAAA 61.316 61.111 0.00 0.00 0.00 2.69
3097 3691 5.700846 TCAAGACAAGAGACAACGAGATAC 58.299 41.667 0.00 0.00 0.00 2.24
3098 3692 5.473846 TCAAGACAAGAGACAACGAGATACT 59.526 40.000 0.00 0.00 0.00 2.12
3099 3693 5.303747 AGACAAGAGACAACGAGATACTG 57.696 43.478 0.00 0.00 0.00 2.74
3100 3694 3.839293 ACAAGAGACAACGAGATACTGC 58.161 45.455 0.00 0.00 0.00 4.40
3101 3695 3.508012 ACAAGAGACAACGAGATACTGCT 59.492 43.478 0.00 0.00 0.00 4.24
3102 3696 3.773860 AGAGACAACGAGATACTGCTG 57.226 47.619 0.00 0.00 0.00 4.41
3103 3697 3.348119 AGAGACAACGAGATACTGCTGA 58.652 45.455 0.00 0.00 0.00 4.26
3104 3698 3.759086 AGAGACAACGAGATACTGCTGAA 59.241 43.478 0.00 0.00 0.00 3.02
3105 3699 4.218635 AGAGACAACGAGATACTGCTGAAA 59.781 41.667 0.00 0.00 0.00 2.69
3106 3700 5.078411 AGACAACGAGATACTGCTGAAAT 57.922 39.130 0.00 0.00 0.00 2.17
3107 3701 5.105752 AGACAACGAGATACTGCTGAAATC 58.894 41.667 0.00 0.39 0.00 2.17
3108 3702 5.078411 ACAACGAGATACTGCTGAAATCT 57.922 39.130 11.07 11.07 32.70 2.40
3109 3703 5.105752 ACAACGAGATACTGCTGAAATCTC 58.894 41.667 20.32 20.32 41.38 2.75
3110 3704 4.991153 ACGAGATACTGCTGAAATCTCA 57.009 40.909 25.06 0.00 43.79 3.27
3111 3705 5.330455 ACGAGATACTGCTGAAATCTCAA 57.670 39.130 25.06 0.00 43.79 3.02
3112 3706 5.347342 ACGAGATACTGCTGAAATCTCAAG 58.653 41.667 25.06 17.83 43.79 3.02
3113 3707 5.105554 ACGAGATACTGCTGAAATCTCAAGT 60.106 40.000 25.06 18.22 43.79 3.16
3114 3708 5.458452 CGAGATACTGCTGAAATCTCAAGTC 59.542 44.000 25.06 10.93 43.79 3.01
3115 3709 6.291648 AGATACTGCTGAAATCTCAAGTCA 57.708 37.500 0.00 0.00 0.00 3.41
3116 3710 6.705302 AGATACTGCTGAAATCTCAAGTCAA 58.295 36.000 0.00 0.00 0.00 3.18
3117 3711 6.817641 AGATACTGCTGAAATCTCAAGTCAAG 59.182 38.462 0.00 0.00 0.00 3.02
3118 3712 4.712476 ACTGCTGAAATCTCAAGTCAAGT 58.288 39.130 0.00 0.00 0.00 3.16
3119 3713 4.514441 ACTGCTGAAATCTCAAGTCAAGTG 59.486 41.667 0.00 0.00 0.00 3.16
3120 3714 3.817084 TGCTGAAATCTCAAGTCAAGTGG 59.183 43.478 0.00 0.00 0.00 4.00
3126 3720 3.049708 TCTCAAGTCAAGTGGCAGATG 57.950 47.619 0.00 0.00 0.00 2.90
3170 3771 1.732941 TCATGGCACGTAACACATCC 58.267 50.000 0.00 0.00 0.00 3.51
3173 3809 0.946700 TGGCACGTAACACATCCACG 60.947 55.000 0.00 0.00 41.32 4.94
3234 3871 0.663153 GTGGTGGAGCACTTGACAAC 59.337 55.000 1.69 0.00 34.40 3.32
3274 3938 2.294233 TGTGAAGAAACAATGAGCCAGC 59.706 45.455 0.00 0.00 0.00 4.85
3281 3945 4.098960 AGAAACAATGAGCCAGCCATATTG 59.901 41.667 8.61 8.61 35.47 1.90
3303 3967 3.055747 GCAAACCTGCTACTAAGACCTCT 60.056 47.826 0.00 0.00 45.74 3.69
3311 3975 4.948621 TGCTACTAAGACCTCTAGTTCACC 59.051 45.833 0.00 0.00 0.00 4.02
3312 3976 4.035441 GCTACTAAGACCTCTAGTTCACCG 59.965 50.000 0.00 0.00 0.00 4.94
3313 3977 4.031636 ACTAAGACCTCTAGTTCACCGT 57.968 45.455 0.00 0.00 0.00 4.83
3314 3978 5.171339 ACTAAGACCTCTAGTTCACCGTA 57.829 43.478 0.00 0.00 0.00 4.02
3315 3979 5.564550 ACTAAGACCTCTAGTTCACCGTAA 58.435 41.667 0.00 0.00 0.00 3.18
3316 3980 4.780275 AAGACCTCTAGTTCACCGTAAC 57.220 45.455 0.00 0.00 0.00 2.50
3317 3981 2.746362 AGACCTCTAGTTCACCGTAACG 59.254 50.000 0.00 0.00 34.46 3.18
3318 3982 1.200948 ACCTCTAGTTCACCGTAACGC 59.799 52.381 0.00 0.00 34.46 4.84
3319 3983 1.200716 CCTCTAGTTCACCGTAACGCA 59.799 52.381 0.00 0.00 34.46 5.24
3320 3984 2.248487 CTCTAGTTCACCGTAACGCAC 58.752 52.381 0.00 0.00 34.46 5.34
3426 4105 1.640210 AAGCGCGAAACACACACACA 61.640 50.000 12.10 0.00 0.00 3.72
3427 4106 1.932564 GCGCGAAACACACACACAC 60.933 57.895 12.10 0.00 0.00 3.82
3428 4107 1.421877 CGCGAAACACACACACACA 59.578 52.632 0.00 0.00 0.00 3.72
3429 4108 0.855670 CGCGAAACACACACACACAC 60.856 55.000 0.00 0.00 0.00 3.82
3430 4109 0.167033 GCGAAACACACACACACACA 59.833 50.000 0.00 0.00 0.00 3.72
3431 4110 1.877101 CGAAACACACACACACACAC 58.123 50.000 0.00 0.00 0.00 3.82
3432 4111 1.463056 CGAAACACACACACACACACT 59.537 47.619 0.00 0.00 0.00 3.55
3433 4112 2.668945 CGAAACACACACACACACACTA 59.331 45.455 0.00 0.00 0.00 2.74
3434 4113 3.482923 CGAAACACACACACACACACTAC 60.483 47.826 0.00 0.00 0.00 2.73
3437 4116 4.041740 ACACACACACACACACTACTAG 57.958 45.455 0.00 0.00 0.00 2.57
3441 4120 4.227538 CACACACACACACTACTAGTAGC 58.772 47.826 26.54 0.00 36.66 3.58
3471 4150 0.480252 AGCCATCAGAAATAGCCCCC 59.520 55.000 0.00 0.00 0.00 5.40
3475 4154 1.417890 CATCAGAAATAGCCCCCGACT 59.582 52.381 0.00 0.00 0.00 4.18
3495 4174 4.489795 GCACGCACGCGATCACAG 62.490 66.667 19.66 0.00 42.83 3.66
3496 4175 2.804931 CACGCACGCGATCACAGA 60.805 61.111 19.66 0.00 42.83 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.806434 TGTTACGCTCCCACTAGGTAA 58.194 47.619 0.00 0.00 36.75 2.85
1 2 2.512692 TGTTACGCTCCCACTAGGTA 57.487 50.000 0.00 0.00 36.75 3.08
2 3 1.861982 ATGTTACGCTCCCACTAGGT 58.138 50.000 0.00 0.00 36.75 3.08
3 4 2.431057 AGAATGTTACGCTCCCACTAGG 59.569 50.000 0.00 0.00 0.00 3.02
4 5 3.802948 AGAATGTTACGCTCCCACTAG 57.197 47.619 0.00 0.00 0.00 2.57
5 6 4.275810 AGTAGAATGTTACGCTCCCACTA 58.724 43.478 0.00 0.00 0.00 2.74
6 7 3.097614 AGTAGAATGTTACGCTCCCACT 58.902 45.455 0.00 0.00 0.00 4.00
7 8 3.445857 GAGTAGAATGTTACGCTCCCAC 58.554 50.000 0.00 0.00 0.00 4.61
8 9 2.429610 GGAGTAGAATGTTACGCTCCCA 59.570 50.000 0.00 0.00 37.21 4.37
9 10 2.429610 TGGAGTAGAATGTTACGCTCCC 59.570 50.000 0.00 0.00 41.14 4.30
10 11 3.445857 GTGGAGTAGAATGTTACGCTCC 58.554 50.000 0.00 0.00 41.92 4.70
11 12 3.130693 AGGTGGAGTAGAATGTTACGCTC 59.869 47.826 0.00 0.00 0.00 5.03
12 13 3.097614 AGGTGGAGTAGAATGTTACGCT 58.902 45.455 0.00 0.00 0.00 5.07
13 14 3.521947 AGGTGGAGTAGAATGTTACGC 57.478 47.619 0.00 0.00 0.00 4.42
14 15 6.446781 TCTAAGGTGGAGTAGAATGTTACG 57.553 41.667 0.00 0.00 0.00 3.18
15 16 6.757478 GCTTCTAAGGTGGAGTAGAATGTTAC 59.243 42.308 0.00 0.00 36.13 2.50
16 17 6.127140 GGCTTCTAAGGTGGAGTAGAATGTTA 60.127 42.308 0.00 0.00 36.13 2.41
17 18 5.338463 GGCTTCTAAGGTGGAGTAGAATGTT 60.338 44.000 0.00 0.00 36.13 2.71
18 19 4.162509 GGCTTCTAAGGTGGAGTAGAATGT 59.837 45.833 0.00 0.00 36.13 2.71
19 20 4.407296 AGGCTTCTAAGGTGGAGTAGAATG 59.593 45.833 0.00 0.00 36.13 2.67
20 21 4.625963 AGGCTTCTAAGGTGGAGTAGAAT 58.374 43.478 0.00 0.00 36.13 2.40
21 22 4.062490 AGGCTTCTAAGGTGGAGTAGAA 57.938 45.455 0.00 0.00 35.54 2.10
22 23 3.759815 AGGCTTCTAAGGTGGAGTAGA 57.240 47.619 0.00 0.00 0.00 2.59
108 109 2.032860 ATGTCCCAGATTCTCCGCCG 62.033 60.000 0.00 0.00 0.00 6.46
114 115 1.004745 ACCGCAAATGTCCCAGATTCT 59.995 47.619 0.00 0.00 0.00 2.40
136 137 3.729862 GAGTATACCTCCCGTTCCTTG 57.270 52.381 0.00 0.00 33.79 3.61
211 229 6.729690 TCACAGGGTTTTCAATGAAAGAAT 57.270 33.333 8.51 0.00 32.93 2.40
245 272 3.160679 AGGGGGTTCAATGAAAGAGTG 57.839 47.619 0.00 0.00 0.00 3.51
485 513 6.055231 TCACGTCAAATTCCAGTTTACTTG 57.945 37.500 0.00 0.00 0.00 3.16
544 575 2.396608 CAGAGGTGAGTCTCATGGGAT 58.603 52.381 5.68 0.00 36.30 3.85
547 578 0.177604 GGCAGAGGTGAGTCTCATGG 59.822 60.000 5.68 0.00 36.30 3.66
555 586 1.554160 AGATTCTGTGGCAGAGGTGAG 59.446 52.381 12.15 0.00 41.75 3.51
558 589 2.235898 GAGAAGATTCTGTGGCAGAGGT 59.764 50.000 12.15 0.88 41.75 3.85
615 680 1.287730 CTGCTGAGTTGCGGTCACTC 61.288 60.000 0.00 0.00 34.82 3.51
616 681 1.301244 CTGCTGAGTTGCGGTCACT 60.301 57.895 0.00 0.00 34.82 3.41
618 683 0.179059 TTTCTGCTGAGTTGCGGTCA 60.179 50.000 0.00 0.00 40.06 4.02
619 684 0.944386 TTTTCTGCTGAGTTGCGGTC 59.056 50.000 0.00 0.00 40.06 4.79
620 685 0.947244 CTTTTCTGCTGAGTTGCGGT 59.053 50.000 0.00 0.00 40.06 5.68
621 686 1.229428 TCTTTTCTGCTGAGTTGCGG 58.771 50.000 0.00 0.00 40.46 5.69
623 688 2.606551 GGCTTCTTTTCTGCTGAGTTGC 60.607 50.000 0.00 0.00 0.00 4.17
624 689 2.883386 AGGCTTCTTTTCTGCTGAGTTG 59.117 45.455 0.00 0.00 0.00 3.16
625 690 3.145286 GAGGCTTCTTTTCTGCTGAGTT 58.855 45.455 0.00 0.00 0.00 3.01
626 691 2.777094 GAGGCTTCTTTTCTGCTGAGT 58.223 47.619 0.00 0.00 0.00 3.41
627 692 1.731160 CGAGGCTTCTTTTCTGCTGAG 59.269 52.381 0.00 0.00 0.00 3.35
628 693 1.800805 CGAGGCTTCTTTTCTGCTGA 58.199 50.000 0.00 0.00 0.00 4.26
629 694 0.167689 GCGAGGCTTCTTTTCTGCTG 59.832 55.000 0.00 0.00 0.00 4.41
717 792 1.134901 CCGACGGACAAGACGAGAG 59.865 63.158 8.64 0.00 34.93 3.20
718 793 2.974489 GCCGACGGACAAGACGAGA 61.974 63.158 20.50 0.00 34.93 4.04
744 819 2.159184 TCTTTATCTGCAGCTCAGTCCG 60.159 50.000 9.47 0.00 43.32 4.79
778 853 2.424705 TTCCGTCGGGTCGTCCTTTG 62.425 60.000 12.29 0.00 33.83 2.77
791 866 1.878953 TGGCTCTGTTTTCTTCCGTC 58.121 50.000 0.00 0.00 0.00 4.79
831 906 4.430423 CGGTGCGCTTTGCTCGAC 62.430 66.667 9.73 0.00 46.63 4.20
843 918 1.756375 GAGATGATGTGACGCGGTGC 61.756 60.000 12.47 0.00 0.00 5.01
848 923 1.535636 CGCTCGAGATGATGTGACGC 61.536 60.000 18.75 0.00 0.00 5.19
850 925 1.535636 CGCGCTCGAGATGATGTGAC 61.536 60.000 18.75 0.00 38.10 3.67
1255 1343 2.684843 GCTGCTGCTTCTTGGACGG 61.685 63.158 8.53 0.00 36.03 4.79
1257 1345 1.584380 CCTGCTGCTGCTTCTTGGAC 61.584 60.000 17.00 0.00 40.48 4.02
1258 1346 1.303074 CCTGCTGCTGCTTCTTGGA 60.303 57.895 17.00 0.00 40.48 3.53
1260 1348 2.567049 GCCTGCTGCTGCTTCTTG 59.433 61.111 17.00 2.17 40.48 3.02
1277 1371 3.075005 TCTTCTCCTTCCCCGCCG 61.075 66.667 0.00 0.00 0.00 6.46
1284 1378 0.177836 GCAGCCTCCTCTTCTCCTTC 59.822 60.000 0.00 0.00 0.00 3.46
1313 1407 4.680237 TGCCCCTGTTGTCGCTCG 62.680 66.667 0.00 0.00 0.00 5.03
1503 1597 2.951642 CTGCCAGTTGAGGACAGAAAAA 59.048 45.455 0.00 0.00 35.91 1.94
1536 1630 1.322936 GCGAATCTCGAGAAGCACAAG 59.677 52.381 25.76 13.48 43.74 3.16
1539 1633 0.642800 GTGCGAATCTCGAGAAGCAC 59.357 55.000 35.48 35.48 43.74 4.40
1590 1697 4.394439 TGACTGCACGGCTAATTATGTA 57.606 40.909 0.00 0.00 0.00 2.29
1591 1698 3.260475 TGACTGCACGGCTAATTATGT 57.740 42.857 0.00 0.00 0.00 2.29
1592 1699 4.142708 TGTTTGACTGCACGGCTAATTATG 60.143 41.667 0.00 0.00 0.00 1.90
1603 1710 4.495844 GGTTAACTGACTGTTTGACTGCAC 60.496 45.833 5.42 0.00 39.89 4.57
1634 1741 6.481954 AGCAACTGGTAATACTCTTTTTCG 57.518 37.500 0.00 0.00 0.00 3.46
1662 1780 7.311408 ACTACTCGTAGAAAATAACTGGACAC 58.689 38.462 10.83 0.00 36.97 3.67
1680 1798 0.788995 ACGACACTCACGACTACTCG 59.211 55.000 0.00 0.00 46.06 4.18
1681 1799 2.222774 GCTACGACACTCACGACTACTC 60.223 54.545 0.00 0.00 34.70 2.59
1682 1800 1.731160 GCTACGACACTCACGACTACT 59.269 52.381 0.00 0.00 34.70 2.57
1683 1801 1.462283 TGCTACGACACTCACGACTAC 59.538 52.381 0.00 0.00 34.70 2.73
1690 1808 1.468914 CTACAGCTGCTACGACACTCA 59.531 52.381 15.27 0.00 0.00 3.41
1694 1812 1.822506 ACTCTACAGCTGCTACGACA 58.177 50.000 15.27 0.00 0.00 4.35
1698 1816 2.663826 AGCAACTCTACAGCTGCTAC 57.336 50.000 15.27 0.00 43.17 3.58
1716 1834 4.629200 CAGACTTCACTAGCTAGCCAAAAG 59.371 45.833 20.91 18.49 0.00 2.27
1717 1835 4.283467 TCAGACTTCACTAGCTAGCCAAAA 59.717 41.667 20.91 8.75 0.00 2.44
1718 1836 3.832490 TCAGACTTCACTAGCTAGCCAAA 59.168 43.478 20.91 11.08 0.00 3.28
1720 1838 2.755655 GTCAGACTTCACTAGCTAGCCA 59.244 50.000 20.91 4.33 0.00 4.75
1721 1839 3.020984 AGTCAGACTTCACTAGCTAGCC 58.979 50.000 20.91 3.59 0.00 3.93
1722 1840 3.181491 CCAGTCAGACTTCACTAGCTAGC 60.181 52.174 20.91 6.62 0.00 3.42
1723 1841 4.013728 ACCAGTCAGACTTCACTAGCTAG 58.986 47.826 19.44 19.44 0.00 3.42
1726 1844 4.440802 CCATACCAGTCAGACTTCACTAGC 60.441 50.000 0.00 0.00 0.00 3.42
1727 1845 4.440802 GCCATACCAGTCAGACTTCACTAG 60.441 50.000 0.00 0.00 0.00 2.57
1739 2146 0.250234 TCAGTGCAGCCATACCAGTC 59.750 55.000 0.00 0.00 0.00 3.51
1765 2180 1.133790 AGAAAAATCCGATGCAGCTGC 59.866 47.619 31.89 31.89 42.50 5.25
1768 2183 2.919229 CACAAGAAAAATCCGATGCAGC 59.081 45.455 0.00 0.00 0.00 5.25
1872 2299 0.943673 GGCCACGCAATTTGCTTTTT 59.056 45.000 18.57 0.00 42.25 1.94
1923 2350 2.955342 AGCCCGTTTGTTACCCTAAA 57.045 45.000 0.00 0.00 0.00 1.85
1924 2351 2.955342 AAGCCCGTTTGTTACCCTAA 57.045 45.000 0.00 0.00 0.00 2.69
1925 2352 2.955342 AAAGCCCGTTTGTTACCCTA 57.045 45.000 0.00 0.00 0.00 3.53
1926 2353 2.955342 TAAAGCCCGTTTGTTACCCT 57.045 45.000 0.00 0.00 0.00 4.34
1927 2354 5.840243 ATTATAAAGCCCGTTTGTTACCC 57.160 39.130 0.00 0.00 0.00 3.69
1928 2355 9.806203 ATTTTATTATAAAGCCCGTTTGTTACC 57.194 29.630 0.00 0.00 0.00 2.85
1937 2364 9.687210 GGTCCTTTTATTTTATTATAAAGCCCG 57.313 33.333 0.00 0.00 33.03 6.13
1950 2377 9.758651 GTGATTAGTGTTTGGTCCTTTTATTTT 57.241 29.630 0.00 0.00 0.00 1.82
1951 2378 9.143155 AGTGATTAGTGTTTGGTCCTTTTATTT 57.857 29.630 0.00 0.00 0.00 1.40
1952 2379 8.706322 AGTGATTAGTGTTTGGTCCTTTTATT 57.294 30.769 0.00 0.00 0.00 1.40
1953 2380 9.227777 GTAGTGATTAGTGTTTGGTCCTTTTAT 57.772 33.333 0.00 0.00 0.00 1.40
1954 2381 8.212312 TGTAGTGATTAGTGTTTGGTCCTTTTA 58.788 33.333 0.00 0.00 0.00 1.52
2030 2458 6.292757 CGAGATCCTGAGAAAAATGCATACAG 60.293 42.308 0.00 3.62 0.00 2.74
2032 2460 5.049818 CCGAGATCCTGAGAAAAATGCATAC 60.050 44.000 0.00 0.00 0.00 2.39
2055 2489 3.554960 GGGCTTGGAATTGTCAAAGAACC 60.555 47.826 0.00 0.00 36.99 3.62
2075 2510 1.555533 GTGGTCTAAAGGACTGAGGGG 59.444 57.143 0.00 0.00 43.97 4.79
2079 2514 5.762179 AATCATGTGGTCTAAAGGACTGA 57.238 39.130 0.00 0.00 43.97 3.41
2080 2515 7.414540 GCTTTAATCATGTGGTCTAAAGGACTG 60.415 40.741 0.00 0.00 43.97 3.51
2081 2516 6.599638 GCTTTAATCATGTGGTCTAAAGGACT 59.400 38.462 0.00 0.00 43.97 3.85
2082 2517 6.599638 AGCTTTAATCATGTGGTCTAAAGGAC 59.400 38.462 0.00 0.00 43.79 3.85
2105 2540 5.010617 TCCATTTCCTACCAAAGTCAAAAGC 59.989 40.000 0.00 0.00 0.00 3.51
2122 2557 4.380233 CCTGCTCATGAGTTGTTCCATTTC 60.380 45.833 23.38 3.35 0.00 2.17
2141 2592 4.943705 TCACTGTTCCTTTCATATTCCTGC 59.056 41.667 0.00 0.00 0.00 4.85
2146 2597 4.700213 CGGGTTCACTGTTCCTTTCATATT 59.300 41.667 0.00 0.00 0.00 1.28
2186 2639 5.008613 TCTGTAATCTGTGTTTTTCCTGTGC 59.991 40.000 0.00 0.00 0.00 4.57
2187 2640 6.618287 TCTGTAATCTGTGTTTTTCCTGTG 57.382 37.500 0.00 0.00 0.00 3.66
2188 2641 9.167311 GATATCTGTAATCTGTGTTTTTCCTGT 57.833 33.333 0.00 0.00 0.00 4.00
2189 2642 9.388506 AGATATCTGTAATCTGTGTTTTTCCTG 57.611 33.333 3.89 0.00 32.44 3.86
2213 2666 8.129496 TGTCAGGTTAACTCACAACATATAGA 57.871 34.615 5.42 0.00 0.00 1.98
2214 2667 8.771920 TTGTCAGGTTAACTCACAACATATAG 57.228 34.615 5.42 0.00 0.00 1.31
2217 2670 9.161629 CATATTGTCAGGTTAACTCACAACATA 57.838 33.333 15.26 8.83 30.04 2.29
2218 2671 7.882791 TCATATTGTCAGGTTAACTCACAACAT 59.117 33.333 15.26 9.72 30.04 2.71
2219 2672 7.172532 GTCATATTGTCAGGTTAACTCACAACA 59.827 37.037 15.26 8.27 30.04 3.33
2220 2673 7.360946 GGTCATATTGTCAGGTTAACTCACAAC 60.361 40.741 15.26 7.19 30.04 3.32
2221 2674 6.653320 GGTCATATTGTCAGGTTAACTCACAA 59.347 38.462 15.28 15.28 0.00 3.33
2222 2675 6.170506 GGTCATATTGTCAGGTTAACTCACA 58.829 40.000 5.42 3.41 0.00 3.58
2223 2676 6.170506 TGGTCATATTGTCAGGTTAACTCAC 58.829 40.000 5.42 0.79 0.00 3.51
2224 2677 6.367374 TGGTCATATTGTCAGGTTAACTCA 57.633 37.500 5.42 0.00 0.00 3.41
2225 2678 6.260936 CCATGGTCATATTGTCAGGTTAACTC 59.739 42.308 2.57 0.00 0.00 3.01
2226 2679 6.122277 CCATGGTCATATTGTCAGGTTAACT 58.878 40.000 2.57 0.00 0.00 2.24
2227 2680 5.885912 ACCATGGTCATATTGTCAGGTTAAC 59.114 40.000 13.00 0.00 0.00 2.01
2228 2681 6.073447 ACCATGGTCATATTGTCAGGTTAA 57.927 37.500 13.00 0.00 0.00 2.01
2229 2682 5.708736 ACCATGGTCATATTGTCAGGTTA 57.291 39.130 13.00 0.00 0.00 2.85
2230 2683 4.591321 ACCATGGTCATATTGTCAGGTT 57.409 40.909 13.00 0.00 0.00 3.50
2231 2684 4.473196 TGTACCATGGTCATATTGTCAGGT 59.527 41.667 23.76 0.00 0.00 4.00
2232 2685 4.816385 GTGTACCATGGTCATATTGTCAGG 59.184 45.833 23.76 0.00 0.00 3.86
2233 2686 5.427378 TGTGTACCATGGTCATATTGTCAG 58.573 41.667 23.76 0.00 0.00 3.51
2234 2687 5.188751 TCTGTGTACCATGGTCATATTGTCA 59.811 40.000 23.76 10.83 0.00 3.58
2235 2688 5.670485 TCTGTGTACCATGGTCATATTGTC 58.330 41.667 23.76 6.98 0.00 3.18
2236 2689 5.692115 TCTGTGTACCATGGTCATATTGT 57.308 39.130 23.76 0.00 0.00 2.71
2237 2690 7.572523 ATTTCTGTGTACCATGGTCATATTG 57.427 36.000 23.76 8.91 0.00 1.90
2238 2691 7.441157 CGTATTTCTGTGTACCATGGTCATATT 59.559 37.037 23.76 0.00 0.00 1.28
2239 2692 6.929049 CGTATTTCTGTGTACCATGGTCATAT 59.071 38.462 23.76 9.56 0.00 1.78
2240 2693 6.277605 CGTATTTCTGTGTACCATGGTCATA 58.722 40.000 23.76 15.77 0.00 2.15
2241 2694 5.116180 CGTATTTCTGTGTACCATGGTCAT 58.884 41.667 23.76 0.00 0.00 3.06
2242 2695 4.500127 CGTATTTCTGTGTACCATGGTCA 58.500 43.478 23.76 16.33 0.00 4.02
2243 2696 3.308866 GCGTATTTCTGTGTACCATGGTC 59.691 47.826 23.76 13.76 0.00 4.02
2244 2697 3.267483 GCGTATTTCTGTGTACCATGGT 58.733 45.455 23.55 23.55 0.00 3.55
2245 2698 3.266636 TGCGTATTTCTGTGTACCATGG 58.733 45.455 11.19 11.19 0.00 3.66
2246 2699 4.180817 TCTGCGTATTTCTGTGTACCATG 58.819 43.478 0.00 0.00 0.00 3.66
2247 2700 4.465632 TCTGCGTATTTCTGTGTACCAT 57.534 40.909 0.00 0.00 0.00 3.55
2248 2701 3.945981 TCTGCGTATTTCTGTGTACCA 57.054 42.857 0.00 0.00 0.00 3.25
2249 2702 5.808540 TGTAATCTGCGTATTTCTGTGTACC 59.191 40.000 0.00 0.00 0.00 3.34
2250 2703 6.750501 TCTGTAATCTGCGTATTTCTGTGTAC 59.249 38.462 0.00 0.00 0.00 2.90
2251 2704 6.859017 TCTGTAATCTGCGTATTTCTGTGTA 58.141 36.000 0.00 0.00 0.00 2.90
2300 2753 2.939103 GGAGCACTATGGACACATTGTC 59.061 50.000 0.00 0.00 46.23 3.18
2344 2797 6.471198 CCATCGTCATCTGAAATGAACATTTG 59.529 38.462 15.92 4.81 40.77 2.32
2346 2799 5.066893 CCCATCGTCATCTGAAATGAACATT 59.933 40.000 5.73 0.00 0.00 2.71
2347 2800 4.577693 CCCATCGTCATCTGAAATGAACAT 59.422 41.667 5.73 0.00 0.00 2.71
2348 2801 3.940852 CCCATCGTCATCTGAAATGAACA 59.059 43.478 5.73 0.00 0.00 3.18
2349 2802 3.242870 GCCCATCGTCATCTGAAATGAAC 60.243 47.826 5.73 0.00 0.00 3.18
2377 2838 7.148523 GCACATAGGTAAGTTAGGTTTGTACAC 60.149 40.741 0.00 0.00 0.00 2.90
2392 2853 6.007076 TCCTGAAACATTTGCACATAGGTAA 58.993 36.000 0.00 0.00 0.00 2.85
2396 2857 4.802039 GCATCCTGAAACATTTGCACATAG 59.198 41.667 0.00 0.00 0.00 2.23
2402 2863 2.613691 CCTGCATCCTGAAACATTTGC 58.386 47.619 0.00 0.00 0.00 3.68
2593 3057 4.635765 GCATAATTTACAGGTGTGAGCAGA 59.364 41.667 0.00 0.00 0.00 4.26
2615 3079 4.023739 ACCACGTTTACAAAAACAGAGC 57.976 40.909 0.00 0.00 44.37 4.09
2616 3080 6.250527 CAGAAACCACGTTTACAAAAACAGAG 59.749 38.462 0.00 0.00 44.37 3.35
2639 3106 7.189512 CAGTTTAAGAAAAGACACCAACTCAG 58.810 38.462 0.00 0.00 0.00 3.35
2642 3109 5.448632 CGCAGTTTAAGAAAAGACACCAACT 60.449 40.000 0.00 0.00 0.00 3.16
2643 3110 4.733405 CGCAGTTTAAGAAAAGACACCAAC 59.267 41.667 0.00 0.00 0.00 3.77
2644 3111 4.396790 ACGCAGTTTAAGAAAAGACACCAA 59.603 37.500 0.00 0.00 37.78 3.67
2645 3112 3.942748 ACGCAGTTTAAGAAAAGACACCA 59.057 39.130 0.00 0.00 37.78 4.17
2673 3140 0.994995 CGAGAAAGATCACACGGCAG 59.005 55.000 0.00 0.00 0.00 4.85
2674 3141 0.601057 TCGAGAAAGATCACACGGCA 59.399 50.000 0.00 0.00 0.00 5.69
2723 3209 1.468914 GTGCCAAAGTAAGCCTACAGC 59.531 52.381 0.00 0.00 44.25 4.40
2740 3226 1.330521 TCTCGCAAAGTCACAAAGTGC 59.669 47.619 0.00 0.00 32.98 4.40
2818 3347 2.093711 GGTTGGTTCTGCCTTTTTGTGT 60.094 45.455 0.00 0.00 38.35 3.72
2915 3444 1.209128 GTGTCACCACTCAACACTCG 58.791 55.000 0.00 0.00 40.07 4.18
2916 3445 2.309528 TGTGTCACCACTCAACACTC 57.690 50.000 0.00 0.00 42.89 3.51
2917 3446 2.236146 TCTTGTGTCACCACTCAACACT 59.764 45.455 0.00 0.00 42.89 3.55
2918 3447 2.351726 GTCTTGTGTCACCACTCAACAC 59.648 50.000 0.00 0.00 42.34 3.32
2919 3448 2.027653 TGTCTTGTGTCACCACTCAACA 60.028 45.455 0.00 0.00 42.34 3.33
2920 3449 2.627945 TGTCTTGTGTCACCACTCAAC 58.372 47.619 0.00 0.00 42.34 3.18
2921 3450 3.118445 TCATGTCTTGTGTCACCACTCAA 60.118 43.478 0.00 0.00 42.34 3.02
2960 3497 3.181499 ACAACCGTACTAGATTCAGCTCG 60.181 47.826 0.00 0.00 0.00 5.03
2961 3498 4.373348 ACAACCGTACTAGATTCAGCTC 57.627 45.455 0.00 0.00 0.00 4.09
2968 3505 3.181478 GCCAAGCTACAACCGTACTAGAT 60.181 47.826 0.00 0.00 0.00 1.98
2970 3507 2.165845 AGCCAAGCTACAACCGTACTAG 59.834 50.000 0.00 0.00 36.99 2.57
2971 3508 2.094390 CAGCCAAGCTACAACCGTACTA 60.094 50.000 0.00 0.00 36.40 1.82
2973 3510 1.076332 CAGCCAAGCTACAACCGTAC 58.924 55.000 0.00 0.00 36.40 3.67
2974 3511 0.036765 CCAGCCAAGCTACAACCGTA 60.037 55.000 0.00 0.00 36.40 4.02
2975 3512 1.302511 CCAGCCAAGCTACAACCGT 60.303 57.895 0.00 0.00 36.40 4.83
2976 3513 0.889186 AACCAGCCAAGCTACAACCG 60.889 55.000 0.00 0.00 36.40 4.44
2977 3514 1.328279 AAACCAGCCAAGCTACAACC 58.672 50.000 0.00 0.00 36.40 3.77
3055 3649 2.869503 ATTTCAGCGGGCCGGTACTG 62.870 60.000 31.94 25.85 35.27 2.74
3056 3650 2.588856 GATTTCAGCGGGCCGGTACT 62.589 60.000 31.94 15.05 35.27 2.73
3073 3667 4.855715 TCTCGTTGTCTCTTGTCTTGAT 57.144 40.909 0.00 0.00 0.00 2.57
3097 3691 4.083431 CCACTTGACTTGAGATTTCAGCAG 60.083 45.833 0.00 0.00 34.15 4.24
3098 3692 3.817084 CCACTTGACTTGAGATTTCAGCA 59.183 43.478 0.00 0.00 34.15 4.41
3099 3693 3.365767 GCCACTTGACTTGAGATTTCAGC 60.366 47.826 0.00 0.00 34.15 4.26
3100 3694 3.817084 TGCCACTTGACTTGAGATTTCAG 59.183 43.478 0.00 0.00 34.15 3.02
3101 3695 3.817084 CTGCCACTTGACTTGAGATTTCA 59.183 43.478 0.00 0.00 0.00 2.69
3102 3696 4.067896 TCTGCCACTTGACTTGAGATTTC 58.932 43.478 0.00 0.00 0.00 2.17
3103 3697 4.090761 TCTGCCACTTGACTTGAGATTT 57.909 40.909 0.00 0.00 0.00 2.17
3104 3698 3.777106 TCTGCCACTTGACTTGAGATT 57.223 42.857 0.00 0.00 0.00 2.40
3105 3699 3.607741 CATCTGCCACTTGACTTGAGAT 58.392 45.455 0.00 0.00 0.00 2.75
3106 3700 2.289882 CCATCTGCCACTTGACTTGAGA 60.290 50.000 0.00 0.00 0.00 3.27
3107 3701 2.082231 CCATCTGCCACTTGACTTGAG 58.918 52.381 0.00 0.00 0.00 3.02
3108 3702 1.421268 ACCATCTGCCACTTGACTTGA 59.579 47.619 0.00 0.00 0.00 3.02
3109 3703 1.538512 CACCATCTGCCACTTGACTTG 59.461 52.381 0.00 0.00 0.00 3.16
3110 3704 1.143684 ACACCATCTGCCACTTGACTT 59.856 47.619 0.00 0.00 0.00 3.01
3111 3705 0.767375 ACACCATCTGCCACTTGACT 59.233 50.000 0.00 0.00 0.00 3.41
3112 3706 1.160137 GACACCATCTGCCACTTGAC 58.840 55.000 0.00 0.00 0.00 3.18
3113 3707 0.764271 TGACACCATCTGCCACTTGA 59.236 50.000 0.00 0.00 0.00 3.02
3114 3708 1.608055 TTGACACCATCTGCCACTTG 58.392 50.000 0.00 0.00 0.00 3.16
3115 3709 1.956477 GTTTGACACCATCTGCCACTT 59.044 47.619 0.00 0.00 0.00 3.16
3116 3710 1.609208 GTTTGACACCATCTGCCACT 58.391 50.000 0.00 0.00 0.00 4.00
3117 3711 0.238289 CGTTTGACACCATCTGCCAC 59.762 55.000 0.00 0.00 0.00 5.01
3118 3712 0.107643 TCGTTTGACACCATCTGCCA 59.892 50.000 0.00 0.00 0.00 4.92
3119 3713 1.131126 CATCGTTTGACACCATCTGCC 59.869 52.381 0.00 0.00 0.00 4.85
3120 3714 1.466360 GCATCGTTTGACACCATCTGC 60.466 52.381 0.00 0.00 0.00 4.26
3126 3720 0.949105 AGTCGGCATCGTTTGACACC 60.949 55.000 0.00 0.00 37.69 4.16
3199 3836 1.134098 ACCACCTCGAGGGCAATATTG 60.134 52.381 34.04 20.69 40.27 1.90
3201 3838 0.469917 CACCACCTCGAGGGCAATAT 59.530 55.000 34.04 10.46 40.27 1.28
3202 3839 1.622607 CCACCACCTCGAGGGCAATA 61.623 60.000 34.04 0.00 40.27 1.90
3203 3840 2.671070 CACCACCTCGAGGGCAAT 59.329 61.111 34.04 14.61 40.27 3.56
3265 3909 2.076207 TTGCAATATGGCTGGCTCAT 57.924 45.000 3.19 0.00 34.04 2.90
3266 3910 1.477700 GTTTGCAATATGGCTGGCTCA 59.522 47.619 0.00 0.00 34.04 4.26
3299 3963 1.200716 TGCGTTACGGTGAACTAGAGG 59.799 52.381 6.94 0.00 0.00 3.69
3317 3981 2.024022 TCAGTTTGTTGCGCGTGC 59.976 55.556 15.48 15.48 43.20 5.34
3318 3982 0.579630 TAGTCAGTTTGTTGCGCGTG 59.420 50.000 8.43 0.00 0.00 5.34
3319 3983 0.580104 GTAGTCAGTTTGTTGCGCGT 59.420 50.000 8.43 0.00 0.00 6.01
3320 3984 0.110823 GGTAGTCAGTTTGTTGCGCG 60.111 55.000 0.00 0.00 0.00 6.86
3321 3985 0.110823 CGGTAGTCAGTTTGTTGCGC 60.111 55.000 0.00 0.00 0.00 6.09
3322 3986 1.493772 TCGGTAGTCAGTTTGTTGCG 58.506 50.000 0.00 0.00 0.00 4.85
3323 3987 4.483476 AATTCGGTAGTCAGTTTGTTGC 57.517 40.909 0.00 0.00 0.00 4.17
3426 4105 3.572682 TGTTGCTGCTACTAGTAGTGTGT 59.427 43.478 26.76 0.00 35.65 3.72
3427 4106 4.174411 TGTTGCTGCTACTAGTAGTGTG 57.826 45.455 26.76 18.49 35.65 3.82
3428 4107 4.382040 CCATGTTGCTGCTACTAGTAGTGT 60.382 45.833 26.76 5.79 35.65 3.55
3429 4108 4.115516 CCATGTTGCTGCTACTAGTAGTG 58.884 47.826 26.76 20.79 35.65 2.74
3430 4109 4.023980 TCCATGTTGCTGCTACTAGTAGT 58.976 43.478 26.76 8.14 35.65 2.73
3431 4110 4.615949 CTCCATGTTGCTGCTACTAGTAG 58.384 47.826 23.25 23.25 36.29 2.57
3432 4111 3.181475 GCTCCATGTTGCTGCTACTAGTA 60.181 47.826 14.81 1.89 0.00 1.82
3433 4112 2.419297 GCTCCATGTTGCTGCTACTAGT 60.419 50.000 14.81 0.00 0.00 2.57
3434 4113 2.208431 GCTCCATGTTGCTGCTACTAG 58.792 52.381 14.81 7.46 0.00 2.57
3437 4116 0.677731 TGGCTCCATGTTGCTGCTAC 60.678 55.000 7.29 7.29 0.00 3.58
3441 4120 0.738975 CTGATGGCTCCATGTTGCTG 59.261 55.000 6.07 0.00 36.70 4.41
3475 4154 4.715892 TGATCGCGTGCGTGCTCA 62.716 61.111 14.47 12.34 40.74 4.26


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

AutoCloner maintained by Alex Coulton.