Multiple sequence alignment - TraesCS2D01G109800

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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 TraesCS2D01G109800 chr2D 100.000 5735 0 0 1 5735 60941633 60947367 0.000000e+00 10591.0
1 TraesCS2D01G109800 chr2D 91.542 201 8 4 1 195 60918869 60919066 9.470000e-68 268.0
2 TraesCS2D01G109800 chr2A 88.308 4841 294 128 913 5640 61464873 61469554 0.000000e+00 5553.0
3 TraesCS2D01G109800 chr2A 88.076 369 21 8 545 890 61464228 61464596 3.200000e-112 416.0
4 TraesCS2D01G109800 chr2A 89.865 296 22 3 195 489 61462415 61462703 1.950000e-99 374.0
5 TraesCS2D01G109800 chr2A 90.090 111 4 3 5579 5684 61469575 61469683 2.790000e-28 137.0
6 TraesCS2D01G109800 chr2A 93.243 74 4 1 26 98 61424630 61424703 2.190000e-19 108.0
7 TraesCS2D01G109800 chr2B 88.462 3666 227 83 2177 5735 95758832 95762408 0.000000e+00 4246.0
8 TraesCS2D01G109800 chr2B 91.709 1375 63 22 739 2097 95757453 95758792 0.000000e+00 1860.0
9 TraesCS2D01G109800 chr2B 86.842 456 24 9 1 447 95754865 95755293 1.450000e-130 477.0
10 TraesCS2D01G109800 chr2B 91.589 321 24 2 1696 2016 78083931 78084248 1.900000e-119 440.0
11 TraesCS2D01G109800 chr2B 89.820 167 15 2 1312 1477 78083285 78083450 4.500000e-51 213.0
12 TraesCS2D01G109800 chr2B 82.727 110 7 6 578 677 95755382 95755489 2.850000e-13 87.9
13 TraesCS2D01G109800 chr5B 77.021 631 130 14 4071 4696 54156901 54157521 1.180000e-91 348.0
14 TraesCS2D01G109800 chr6D 89.219 269 13 8 1639 1906 427974455 427974708 7.170000e-84 322.0
15 TraesCS2D01G109800 chr6D 92.308 208 15 1 1306 1512 427974683 427974890 1.560000e-75 294.0
16 TraesCS2D01G109800 chr6B 75.827 695 124 32 4035 4695 658552881 658553565 4.310000e-81 313.0
17 TraesCS2D01G109800 chr6B 76.307 287 64 4 4035 4319 658557751 658558035 3.580000e-32 150.0
18 TraesCS2D01G109800 chr1D 76.441 590 124 13 4084 4664 318851469 318850886 7.220000e-79 305.0
19 TraesCS2D01G109800 chr1D 96.970 33 0 1 492 524 436378183 436378214 3.000000e-03 54.7
20 TraesCS2D01G109800 chr1B 76.214 597 125 15 4084 4669 431404240 431403650 3.360000e-77 300.0
21 TraesCS2D01G109800 chr6A 74.820 695 131 37 4035 4695 582812822 582813506 2.040000e-69 274.0
22 TraesCS2D01G109800 chr3A 78.797 316 61 6 4053 4365 192817116 192816804 2.090000e-49 207.0
23 TraesCS2D01G109800 chr3A 74.632 272 65 4 1821 2090 570671256 570671525 3.630000e-22 117.0
24 TraesCS2D01G109800 chr3B 77.532 316 65 6 4053 4365 239247730 239247418 9.810000e-43 185.0
25 TraesCS2D01G109800 chr3D 77.215 316 66 6 4053 4365 162177188 162176876 4.570000e-41 180.0
26 TraesCS2D01G109800 chr7D 97.143 35 0 1 490 524 21276938 21276971 2.230000e-04 58.4
27 TraesCS2D01G109800 chr1A 97.059 34 0 1 491 524 58633400 58633368 8.030000e-04 56.5


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 TraesCS2D01G109800 chr2D 60941633 60947367 5734 False 10591.000 10591 100.00000 1 5735 1 chr2D.!!$F2 5734
1 TraesCS2D01G109800 chr2A 61462415 61469683 7268 False 1620.000 5553 89.08475 195 5684 4 chr2A.!!$F2 5489
2 TraesCS2D01G109800 chr2B 95754865 95762408 7543 False 1667.725 4246 87.43500 1 5735 4 chr2B.!!$F2 5734
3 TraesCS2D01G109800 chr2B 78083285 78084248 963 False 326.500 440 90.70450 1312 2016 2 chr2B.!!$F1 704
4 TraesCS2D01G109800 chr5B 54156901 54157521 620 False 348.000 348 77.02100 4071 4696 1 chr5B.!!$F1 625
5 TraesCS2D01G109800 chr6B 658552881 658553565 684 False 313.000 313 75.82700 4035 4695 1 chr6B.!!$F1 660
6 TraesCS2D01G109800 chr1D 318850886 318851469 583 True 305.000 305 76.44100 4084 4664 1 chr1D.!!$R1 580
7 TraesCS2D01G109800 chr1B 431403650 431404240 590 True 300.000 300 76.21400 4084 4669 1 chr1B.!!$R1 585
8 TraesCS2D01G109800 chr6A 582812822 582813506 684 False 274.000 274 74.82000 4035 4695 1 chr6A.!!$F1 660

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
146 153 0.108851 TGTCATGTGATCGACCACCG 60.109 55.0 7.64 0.0 36.26 4.94 F
416 425 0.179119 ATCGTTGGTGGCTACGCTAC 60.179 55.0 0.00 0.0 39.31 3.58 F
531 1891 0.249489 GCAGTGGCGATTCGGAGTAT 60.249 55.0 8.34 0.0 0.00 2.12 F
922 4586 0.266152 TCCTCCAATCTCCCTCCTCC 59.734 60.0 0.00 0.0 0.00 4.30 F
923 4587 0.267356 CCTCCAATCTCCCTCCTCCT 59.733 60.0 0.00 0.0 0.00 3.69 F
2470 6474 0.682209 GTACTAGGTGCAGGGACGGA 60.682 60.0 0.00 0.0 0.00 4.69 F
2995 7043 0.179076 ACAAGCAAACAAAGGGCAGC 60.179 50.0 0.00 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 4750 0.616111 GTGAGGAGCAGGAGGAGGAA 60.616 60.000 0.00 0.00 0.00 3.36 R
2174 6133 0.316772 CCGAACAGTACGCGATCGAT 60.317 55.000 21.57 8.54 39.41 3.59 R
2429 6433 0.178998 TACTGGTAGAGGGGCGCTAG 60.179 60.000 7.64 0.00 0.00 3.42 R
2434 6438 0.466922 TACGCTACTGGTAGAGGGGC 60.467 60.000 11.44 0.00 37.30 5.80 R
2786 6815 0.831307 CCCTCACCTACCAAGCCTAC 59.169 60.000 0.00 0.00 0.00 3.18 R
4449 8600 0.033405 TCCGGGAGTAGGTCTTCCAG 60.033 60.000 0.00 0.00 41.93 3.86 R
4815 8970 1.067516 ACGAACGGGAAGAAACGAGAA 59.932 47.619 0.00 0.00 0.00 2.87 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
61 68 3.653009 CCTGTGTGCAGCGTGTGG 61.653 66.667 0.00 0.00 41.26 4.17
146 153 0.108851 TGTCATGTGATCGACCACCG 60.109 55.000 7.64 0.00 36.26 4.94
156 163 4.083862 GACCACCGGAGCCAGGAC 62.084 72.222 9.46 0.00 0.00 3.85
215 222 3.125573 GAAGCTTTCCGGCCCGAC 61.126 66.667 3.71 0.00 0.00 4.79
319 327 0.395724 ATTCCGTTTCCTCCATGGCC 60.396 55.000 6.96 0.00 35.26 5.36
415 424 0.179121 CATCGTTGGTGGCTACGCTA 60.179 55.000 0.00 0.00 37.66 4.26
416 425 0.179119 ATCGTTGGTGGCTACGCTAC 60.179 55.000 0.00 0.00 39.31 3.58
417 426 2.156446 CGTTGGTGGCTACGCTACG 61.156 63.158 9.87 9.87 40.94 3.51
418 427 2.125832 TTGGTGGCTACGCTACGC 60.126 61.111 0.00 0.00 40.94 4.42
419 428 2.642254 TTGGTGGCTACGCTACGCT 61.642 57.895 0.00 0.00 40.94 5.07
471 498 4.430908 GGTCGTGTACCCTTCTATTGAAG 58.569 47.826 9.64 9.64 46.82 3.02
519 1879 9.561270 TTTTTAAAGTTTAAAAATTGCAGTGGC 57.439 25.926 29.54 0.00 34.90 5.01
521 1881 4.314740 AGTTTAAAAATTGCAGTGGCGA 57.685 36.364 0.00 0.00 45.35 5.54
522 1882 4.881920 AGTTTAAAAATTGCAGTGGCGAT 58.118 34.783 0.00 0.00 46.32 4.58
529 1889 2.125512 GCAGTGGCGATTCGGAGT 60.126 61.111 8.34 0.00 0.00 3.85
530 1890 1.141019 GCAGTGGCGATTCGGAGTA 59.859 57.895 8.34 0.00 0.00 2.59
531 1891 0.249489 GCAGTGGCGATTCGGAGTAT 60.249 55.000 8.34 0.00 0.00 2.12
532 1892 1.806623 GCAGTGGCGATTCGGAGTATT 60.807 52.381 8.34 0.00 0.00 1.89
533 1893 2.128035 CAGTGGCGATTCGGAGTATTC 58.872 52.381 8.34 0.00 0.00 1.75
534 1894 1.129326 GTGGCGATTCGGAGTATTCG 58.871 55.000 8.34 0.00 39.63 3.34
541 1901 2.876581 TCGGAGTATTCGAGTGGCA 58.123 52.632 0.00 0.00 44.37 4.92
542 1902 1.399714 TCGGAGTATTCGAGTGGCAT 58.600 50.000 0.00 0.00 44.37 4.40
543 1903 1.067060 TCGGAGTATTCGAGTGGCATG 59.933 52.381 0.00 0.00 44.37 4.06
544 1904 1.202417 CGGAGTATTCGAGTGGCATGT 60.202 52.381 0.00 0.00 42.19 3.21
545 1905 2.034179 CGGAGTATTCGAGTGGCATGTA 59.966 50.000 0.00 0.00 42.19 2.29
546 1906 3.305403 CGGAGTATTCGAGTGGCATGTAT 60.305 47.826 0.00 0.00 42.19 2.29
547 1907 4.238514 GGAGTATTCGAGTGGCATGTATC 58.761 47.826 0.00 0.00 0.00 2.24
556 2053 4.816385 CGAGTGGCATGTATCCAATTAACT 59.184 41.667 0.00 0.00 35.01 2.24
559 2056 7.136822 AGTGGCATGTATCCAATTAACTCTA 57.863 36.000 0.00 0.00 35.01 2.43
621 2126 0.829333 CAGCTCTGCCTATCAGTGGT 59.171 55.000 0.00 0.00 44.80 4.16
626 2140 1.139654 TCTGCCTATCAGTGGTCATGC 59.860 52.381 0.00 0.00 43.32 4.06
668 2183 2.938451 GTCGTCCATTCATGAATGCAGA 59.062 45.455 33.78 27.74 45.06 4.26
707 3248 3.611113 CAGAGCGATTTTGCCAAAGATTG 59.389 43.478 0.00 0.00 34.65 2.67
726 3267 3.678965 TGCTCCTTCCTCTCAGTCTAT 57.321 47.619 0.00 0.00 0.00 1.98
734 3275 7.644062 TCCTTCCTCTCAGTCTATAAGAAGAA 58.356 38.462 0.00 0.00 33.03 2.52
765 4189 0.687354 TTTGACTGGACCAGAGCTCC 59.313 55.000 28.56 11.17 35.18 4.70
808 4232 1.079543 ATGTCTGTCAGCTGGTCGC 60.080 57.895 15.13 2.80 39.57 5.19
913 4576 1.205893 GAAGTGACGCTCCTCCAATCT 59.794 52.381 0.00 0.00 0.00 2.40
914 4577 0.820871 AGTGACGCTCCTCCAATCTC 59.179 55.000 0.00 0.00 0.00 2.75
917 4581 1.002274 ACGCTCCTCCAATCTCCCT 59.998 57.895 0.00 0.00 0.00 4.20
922 4586 0.266152 TCCTCCAATCTCCCTCCTCC 59.734 60.000 0.00 0.00 0.00 4.30
923 4587 0.267356 CCTCCAATCTCCCTCCTCCT 59.733 60.000 0.00 0.00 0.00 3.69
1011 4698 2.350895 CACGGAATGCCACCTCCA 59.649 61.111 0.00 0.00 0.00 3.86
1057 4744 2.366167 CCAGGCTCCTCCTCCTCA 59.634 66.667 0.00 0.00 45.52 3.86
1063 4750 1.390125 CTCCTCCTCCTCACCACCT 59.610 63.158 0.00 0.00 0.00 4.00
1148 4835 4.617520 TGGTCACCACGCACGCAT 62.618 61.111 0.00 0.00 0.00 4.73
1431 5118 4.704833 TGCCAGGAGCTGTTCGGC 62.705 66.667 0.00 0.00 44.23 5.54
1440 5127 3.414700 CTGTTCGGCCACACGCTC 61.415 66.667 2.24 0.00 37.74 5.03
1632 5319 2.890474 GGCCGCATCTACCACGTG 60.890 66.667 9.08 9.08 0.00 4.49
1993 5948 2.747686 GGGCCGAGAAGACCAACA 59.252 61.111 0.00 0.00 0.00 3.33
2093 6048 1.299926 CCGCCACGCTAGGTATGTC 60.300 63.158 0.00 0.00 0.00 3.06
2134 6089 6.314784 GTGCAGACACAGTCAAATTATTACC 58.685 40.000 0.00 0.00 46.61 2.85
2137 6092 4.328983 AGACACAGTCAAATTATTACCGCG 59.671 41.667 0.00 0.00 34.60 6.46
2191 6150 1.035772 CGATCGATCGCGTACTGTTC 58.964 55.000 32.34 0.00 43.84 3.18
2273 6251 1.167781 TGAGTGACGCCGTACTGACA 61.168 55.000 0.00 0.00 0.00 3.58
2395 6399 1.239296 GGTAACAACGGGGAACAGGC 61.239 60.000 0.00 0.00 0.00 4.85
2435 6439 2.547299 TAGGAGACTAGGACTAGCGC 57.453 55.000 0.00 0.00 43.67 5.92
2437 6441 1.174078 GGAGACTAGGACTAGCGCCC 61.174 65.000 2.29 0.00 36.66 6.13
2468 6472 1.432251 CGTACTAGGTGCAGGGACG 59.568 63.158 0.00 0.00 0.00 4.79
2469 6473 1.814527 GTACTAGGTGCAGGGACGG 59.185 63.158 0.00 0.00 0.00 4.79
2470 6474 0.682209 GTACTAGGTGCAGGGACGGA 60.682 60.000 0.00 0.00 0.00 4.69
2471 6475 0.682209 TACTAGGTGCAGGGACGGAC 60.682 60.000 0.00 0.00 0.00 4.79
2515 6519 9.005777 GGTTGGACAAATAGTTACAGACAAATA 57.994 33.333 0.00 0.00 0.00 1.40
2557 6564 3.983344 GCCATTCGCATTTGGATTGTATC 59.017 43.478 0.23 0.00 37.47 2.24
2580 6587 2.645730 ACAGTTCATCACGAGCTCTC 57.354 50.000 12.85 0.00 31.92 3.20
2604 6615 1.142870 CCTGCCTCCGGATAAATGGAA 59.857 52.381 3.57 0.00 32.89 3.53
2649 6660 8.842358 TTTTTATCCACTTCTTCGACAAGTAT 57.158 30.769 8.32 3.70 32.61 2.12
2652 6663 6.969828 ATCCACTTCTTCGACAAGTATTTC 57.030 37.500 8.32 0.00 32.61 2.17
2653 6664 5.849510 TCCACTTCTTCGACAAGTATTTCA 58.150 37.500 8.32 0.00 32.61 2.69
2655 6666 5.926542 CCACTTCTTCGACAAGTATTTCAGA 59.073 40.000 8.32 0.00 32.61 3.27
2656 6667 6.128795 CCACTTCTTCGACAAGTATTTCAGAC 60.129 42.308 8.32 0.00 32.61 3.51
2692 6705 3.253230 TGATGCACTTACACACTCGATG 58.747 45.455 0.00 0.00 0.00 3.84
2712 6735 1.002251 GAGAGCTCACGGTTCGGATAG 60.002 57.143 17.77 0.00 0.00 2.08
2725 6748 2.984562 TCGGATAGTTTCTGCAATGCA 58.015 42.857 7.99 7.99 36.92 3.96
2771 6794 2.741092 GAGTTGTGGAGCACGGGA 59.259 61.111 0.00 0.00 37.14 5.14
2786 6815 3.728845 CACGGGAGTTAGTTATCATGGG 58.271 50.000 0.00 0.00 44.67 4.00
2852 6881 1.002659 AGCACGTATGGCAAACCTACA 59.997 47.619 0.00 0.00 36.63 2.74
2853 6882 1.129811 GCACGTATGGCAAACCTACAC 59.870 52.381 0.00 0.00 36.63 2.90
2854 6883 2.695359 CACGTATGGCAAACCTACACT 58.305 47.619 0.00 0.00 36.63 3.55
2855 6884 2.415168 CACGTATGGCAAACCTACACTG 59.585 50.000 0.00 0.00 36.63 3.66
2856 6885 2.300723 ACGTATGGCAAACCTACACTGA 59.699 45.455 0.00 0.00 36.63 3.41
2857 6886 2.671396 CGTATGGCAAACCTACACTGAC 59.329 50.000 0.00 0.00 36.63 3.51
2883 6918 1.736586 CTAGCTCTGCCGGTGTAGG 59.263 63.158 1.90 0.00 0.00 3.18
2919 6954 2.509336 CGACGGCAGGATGTGGTC 60.509 66.667 0.00 0.00 39.31 4.02
2938 6973 1.066430 TCCATGGTAGCAGAAACCGAC 60.066 52.381 12.58 0.00 40.08 4.79
2973 7021 1.135575 GCATTCAACAGCCACTACTGC 60.136 52.381 0.00 0.00 41.60 4.40
2975 7023 2.340210 TTCAACAGCCACTACTGCAA 57.660 45.000 0.00 0.00 41.60 4.08
2976 7024 2.340210 TCAACAGCCACTACTGCAAA 57.660 45.000 0.00 0.00 41.60 3.68
2977 7025 1.946768 TCAACAGCCACTACTGCAAAC 59.053 47.619 0.00 0.00 41.60 2.93
2978 7026 1.675483 CAACAGCCACTACTGCAAACA 59.325 47.619 0.00 0.00 41.60 2.83
2980 7028 1.949525 ACAGCCACTACTGCAAACAAG 59.050 47.619 0.00 0.00 41.60 3.16
2981 7029 0.954452 AGCCACTACTGCAAACAAGC 59.046 50.000 0.00 0.00 0.00 4.01
2982 7030 0.667993 GCCACTACTGCAAACAAGCA 59.332 50.000 0.00 0.00 43.35 3.91
2984 7032 2.481104 GCCACTACTGCAAACAAGCAAA 60.481 45.455 0.00 0.00 45.13 3.68
2985 7033 3.115554 CCACTACTGCAAACAAGCAAAC 58.884 45.455 0.00 0.00 45.13 2.93
2986 7034 3.428725 CCACTACTGCAAACAAGCAAACA 60.429 43.478 0.00 0.00 45.13 2.83
2987 7035 4.172505 CACTACTGCAAACAAGCAAACAA 58.827 39.130 0.00 0.00 45.13 2.83
2988 7036 4.624882 CACTACTGCAAACAAGCAAACAAA 59.375 37.500 0.00 0.00 45.13 2.83
2989 7037 4.864247 ACTACTGCAAACAAGCAAACAAAG 59.136 37.500 0.00 0.00 45.13 2.77
2993 7041 2.354259 CAAACAAGCAAACAAAGGGCA 58.646 42.857 0.00 0.00 0.00 5.36
2994 7042 2.314323 AACAAGCAAACAAAGGGCAG 57.686 45.000 0.00 0.00 0.00 4.85
2995 7043 0.179076 ACAAGCAAACAAAGGGCAGC 60.179 50.000 0.00 0.00 0.00 5.25
2996 7044 0.881600 CAAGCAAACAAAGGGCAGCC 60.882 55.000 1.26 1.26 0.00 4.85
3040 7093 0.460987 CTTTGGGCGCTTCGATCTCT 60.461 55.000 7.64 0.00 0.00 3.10
3041 7094 0.460284 TTTGGGCGCTTCGATCTCTC 60.460 55.000 7.64 0.00 0.00 3.20
3042 7095 1.323271 TTGGGCGCTTCGATCTCTCT 61.323 55.000 7.64 0.00 0.00 3.10
3043 7096 1.007849 GGGCGCTTCGATCTCTCTC 60.008 63.158 7.64 0.00 0.00 3.20
3058 7111 7.340743 TCGATCTCTCTCCTTTTACATTTCTCT 59.659 37.037 0.00 0.00 0.00 3.10
3060 7113 9.665719 GATCTCTCTCCTTTTACATTTCTCTTT 57.334 33.333 0.00 0.00 0.00 2.52
3126 7202 1.528542 CGATCGAGCTGGTCCCCTA 60.529 63.158 10.26 0.00 0.00 3.53
3127 7203 1.797211 CGATCGAGCTGGTCCCCTAC 61.797 65.000 10.26 0.00 0.00 3.18
3139 7215 2.201022 CCCCTACGATCGGAGTGGG 61.201 68.421 28.77 28.77 39.58 4.61
3149 7225 2.517919 GGAGTGGGGATGGATGGC 59.482 66.667 0.00 0.00 0.00 4.40
3166 7242 1.304282 GCCCAGCCTCAAATCCTCA 59.696 57.895 0.00 0.00 0.00 3.86
3207 7288 6.366315 ACACATAGATTCGTCTGAGTACTC 57.634 41.667 16.32 16.32 0.00 2.59
3222 7303 4.101898 TGAGTACTCTAGGTTGCCAAACAA 59.898 41.667 23.01 0.00 38.10 2.83
3267 7348 0.448990 CACTTAGCACATGCACGCAT 59.551 50.000 6.64 0.00 45.16 4.73
3298 7379 6.072948 TCACAACAGAAAGAAAGTCGTTTTGA 60.073 34.615 2.39 0.00 0.00 2.69
3310 7395 8.391106 AGAAAGTCGTTTTGATAATACTCATGC 58.609 33.333 0.00 0.00 0.00 4.06
3317 7405 8.554528 CGTTTTGATAATACTCATGCTCAAGAT 58.445 33.333 0.00 0.00 0.00 2.40
3357 7445 1.065199 TCTGATGCCACCTTAAGCCAG 60.065 52.381 0.00 0.00 0.00 4.85
3428 7516 0.535780 ACCGACATGCATGGCCTATG 60.536 55.000 29.41 16.40 39.88 2.23
3506 7594 1.249407 GTTGCCCCATCGGTACAAAA 58.751 50.000 0.00 0.00 0.00 2.44
3517 7605 2.355132 TCGGTACAAAACACACGCATTT 59.645 40.909 0.00 0.00 0.00 2.32
3519 7607 3.548268 CGGTACAAAACACACGCATTTTT 59.452 39.130 0.00 0.00 0.00 1.94
3520 7608 4.733887 CGGTACAAAACACACGCATTTTTA 59.266 37.500 0.00 0.00 0.00 1.52
3530 7624 5.049680 ACACACGCATTTTTAGTTAGGACAG 60.050 40.000 0.00 0.00 0.00 3.51
3533 7627 6.077838 CACGCATTTTTAGTTAGGACAGAAC 58.922 40.000 0.00 0.00 0.00 3.01
3606 7704 0.257039 GGCCCTCCACTGTGATGATT 59.743 55.000 9.86 0.00 0.00 2.57
3607 7705 1.490490 GGCCCTCCACTGTGATGATTA 59.510 52.381 9.86 0.00 0.00 1.75
3685 7785 4.400109 GCGCTGTCGTCGTCCAGA 62.400 66.667 15.57 0.00 38.14 3.86
3785 7887 4.864334 CTCGTCCATGGCCTGGGC 62.864 72.222 14.23 14.23 46.92 5.36
3788 7890 4.828296 GTCCATGGCCTGGGCTGG 62.828 72.222 23.59 23.59 46.85 4.85
3851 7961 2.245532 GCACACGACACGACTTGC 59.754 61.111 0.00 0.00 0.00 4.01
3864 7974 0.748005 GACTTGCACCACACCAGTGT 60.748 55.000 0.00 0.00 44.39 3.55
3977 8107 4.755123 AGTTTCAGTTTTGGTAGGTCGATG 59.245 41.667 0.00 0.00 0.00 3.84
3983 8113 2.168458 TTGGTAGGTCGATGGATGGA 57.832 50.000 0.00 0.00 0.00 3.41
3985 8115 1.970640 TGGTAGGTCGATGGATGGATG 59.029 52.381 0.00 0.00 0.00 3.51
3987 8117 0.976641 TAGGTCGATGGATGGATGGC 59.023 55.000 0.00 0.00 0.00 4.40
3988 8118 0.765903 AGGTCGATGGATGGATGGCT 60.766 55.000 0.00 0.00 0.00 4.75
3990 8120 0.683973 GTCGATGGATGGATGGCTCT 59.316 55.000 0.00 0.00 0.00 4.09
3998 8128 2.029828 GGATGGATGGCTCTGTACGTAG 60.030 54.545 0.00 0.00 0.00 3.51
4010 8140 1.131693 TGTACGTAGCTGACCGACATG 59.868 52.381 0.00 0.00 0.00 3.21
4023 8153 6.468956 GCTGACCGACATGTGTTAATTTAATG 59.531 38.462 1.15 0.00 0.00 1.90
4024 8154 7.625395 GCTGACCGACATGTGTTAATTTAATGA 60.625 37.037 1.15 0.00 0.00 2.57
4025 8155 8.100508 TGACCGACATGTGTTAATTTAATGAA 57.899 30.769 1.15 0.00 0.00 2.57
4026 8156 8.018520 TGACCGACATGTGTTAATTTAATGAAC 58.981 33.333 1.15 0.00 0.00 3.18
4027 8157 7.309920 ACCGACATGTGTTAATTTAATGAACC 58.690 34.615 1.15 0.00 0.00 3.62
4392 8522 2.124819 CAGGGCTGCAAGATCGCT 60.125 61.111 0.50 0.00 34.07 4.93
4741 8895 3.165875 CTGGGCCTCGGATAGAATAGAA 58.834 50.000 4.53 0.00 0.00 2.10
4759 8913 8.360390 AGAATAGAAATGAGTGGGTTTTTGAAC 58.640 33.333 0.00 0.00 0.00 3.18
4780 8935 2.160813 CGACAAAATAAGGGGTGGTTCG 59.839 50.000 0.00 0.00 0.00 3.95
4815 8970 4.967442 GTCAGGAAAGGGGTTATACTAGGT 59.033 45.833 0.00 0.00 0.00 3.08
4876 9034 1.328279 AAAACTGTTAGTGCCAGCCC 58.672 50.000 0.00 0.00 33.09 5.19
4999 9159 8.770828 TCTTTACAACAGAGGACGAAAATTAAG 58.229 33.333 0.00 0.00 0.00 1.85
5021 9181 3.535561 GATGTGTCATGGTTCTAGTGGG 58.464 50.000 0.00 0.00 0.00 4.61
5037 9197 1.273327 GTGGGCAAATGACAAGGGAAG 59.727 52.381 0.00 0.00 0.00 3.46
5093 9257 4.188462 TCTAACGCCACTTATTCACCATG 58.812 43.478 0.00 0.00 0.00 3.66
5110 9274 2.288457 CCATGCTATCTACCCGTGACTG 60.288 54.545 0.00 0.00 0.00 3.51
5111 9275 2.430248 TGCTATCTACCCGTGACTGA 57.570 50.000 0.00 0.00 0.00 3.41
5112 9276 2.945456 TGCTATCTACCCGTGACTGAT 58.055 47.619 0.00 0.00 0.00 2.90
5113 9277 3.296854 TGCTATCTACCCGTGACTGATT 58.703 45.455 0.00 0.00 0.00 2.57
5139 9305 4.081917 GTCCTTAACTGACCTTCTCCAGAG 60.082 50.000 0.00 0.00 34.65 3.35
5141 9307 0.980423 AACTGACCTTCTCCAGAGGC 59.020 55.000 0.00 0.00 34.65 4.70
5158 9324 1.303806 GCTTGCCGTCCCCCTTTTA 60.304 57.895 0.00 0.00 0.00 1.52
5159 9325 0.683179 GCTTGCCGTCCCCCTTTTAT 60.683 55.000 0.00 0.00 0.00 1.40
5161 9327 1.476488 CTTGCCGTCCCCCTTTTATTG 59.524 52.381 0.00 0.00 0.00 1.90
5162 9328 0.699399 TGCCGTCCCCCTTTTATTGA 59.301 50.000 0.00 0.00 0.00 2.57
5164 9330 2.291930 TGCCGTCCCCCTTTTATTGAAT 60.292 45.455 0.00 0.00 0.00 2.57
5165 9331 2.361119 GCCGTCCCCCTTTTATTGAATC 59.639 50.000 0.00 0.00 0.00 2.52
5166 9332 3.898482 CCGTCCCCCTTTTATTGAATCT 58.102 45.455 0.00 0.00 0.00 2.40
5167 9333 3.632145 CCGTCCCCCTTTTATTGAATCTG 59.368 47.826 0.00 0.00 0.00 2.90
5168 9334 3.632145 CGTCCCCCTTTTATTGAATCTGG 59.368 47.826 0.00 0.00 0.00 3.86
5169 9335 4.627741 CGTCCCCCTTTTATTGAATCTGGA 60.628 45.833 0.00 0.00 0.00 3.86
5170 9336 4.645136 GTCCCCCTTTTATTGAATCTGGAC 59.355 45.833 0.00 0.00 32.64 4.02
5171 9337 3.960755 CCCCCTTTTATTGAATCTGGACC 59.039 47.826 0.00 0.00 0.00 4.46
5172 9338 4.326132 CCCCCTTTTATTGAATCTGGACCT 60.326 45.833 0.00 0.00 0.00 3.85
5173 9339 4.889995 CCCCTTTTATTGAATCTGGACCTC 59.110 45.833 0.00 0.00 0.00 3.85
5174 9340 5.509498 CCCTTTTATTGAATCTGGACCTCA 58.491 41.667 0.00 0.00 0.00 3.86
5175 9341 6.131961 CCCTTTTATTGAATCTGGACCTCAT 58.868 40.000 0.00 0.00 0.00 2.90
5177 9343 6.017605 CCTTTTATTGAATCTGGACCTCATCG 60.018 42.308 0.00 0.00 0.00 3.84
5178 9344 5.614324 TTATTGAATCTGGACCTCATCGT 57.386 39.130 0.00 0.00 0.00 3.73
5179 9345 3.526931 TTGAATCTGGACCTCATCGTC 57.473 47.619 0.00 0.00 0.00 4.20
5180 9346 2.739943 TGAATCTGGACCTCATCGTCT 58.260 47.619 0.00 0.00 33.07 4.18
5192 9358 3.118956 CCTCATCGTCTTCTTACAGCCTT 60.119 47.826 0.00 0.00 0.00 4.35
5249 9415 1.596934 GACTTCATCAGGGCCGTCA 59.403 57.895 0.00 0.00 0.00 4.35
5312 9478 2.494918 GTGTCGGATGAGACCCCG 59.505 66.667 0.00 0.00 46.57 5.73
5445 9611 2.638480 TGAAGGTGCTAAAGTGCTGT 57.362 45.000 0.00 0.00 0.00 4.40
5452 9618 4.887655 AGGTGCTAAAGTGCTGTAACTTTT 59.112 37.500 13.31 0.00 45.84 2.27
5499 9665 0.613012 GCCTTCTTGTTCCCATGCCT 60.613 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 57 3.898509 GTTTGGCCACACGCTGCA 61.899 61.111 3.88 0.00 37.74 4.41
114 121 3.704231 ATGACATGCCCGGTGCTCC 62.704 63.158 14.76 0.00 42.00 4.70
115 122 2.124570 ATGACATGCCCGGTGCTC 60.125 61.111 14.76 6.20 42.00 4.26
116 123 2.438975 CATGACATGCCCGGTGCT 60.439 61.111 14.76 0.00 42.00 4.40
117 124 2.751436 ACATGACATGCCCGGTGC 60.751 61.111 15.49 4.04 41.77 5.01
118 125 0.749091 ATCACATGACATGCCCGGTG 60.749 55.000 15.49 6.04 0.00 4.94
119 126 0.464373 GATCACATGACATGCCCGGT 60.464 55.000 15.49 0.44 0.00 5.28
120 127 1.501337 CGATCACATGACATGCCCGG 61.501 60.000 15.49 0.00 0.00 5.73
121 128 0.530431 TCGATCACATGACATGCCCG 60.530 55.000 15.49 12.74 0.00 6.13
126 133 1.471501 CGGTGGTCGATCACATGACAT 60.472 52.381 28.86 0.00 42.43 3.06
127 134 0.108851 CGGTGGTCGATCACATGACA 60.109 55.000 28.86 0.00 42.43 3.58
129 136 0.968393 TCCGGTGGTCGATCACATGA 60.968 55.000 28.86 20.73 42.43 3.07
146 153 2.105128 CATCGTCGTCCTGGCTCC 59.895 66.667 0.00 0.00 0.00 4.70
154 161 3.330853 GATGCCGCCATCGTCGTC 61.331 66.667 0.00 0.00 38.59 4.20
192 199 2.126071 CCGGAAAGCTTCGCGAGA 60.126 61.111 9.59 0.00 39.20 4.04
247 255 1.005805 TGGCCACATTGCTAATCTGGT 59.994 47.619 0.00 0.00 30.46 4.00
319 327 2.401766 GGCATGGAGTGAGGTTGCG 61.402 63.158 0.00 0.00 34.17 4.85
374 383 0.457851 AGATTCTCGCGTCCCTTCTG 59.542 55.000 5.77 0.00 0.00 3.02
459 477 3.370315 AGCAGGAGCACTTCAATAGAAGG 60.370 47.826 9.72 1.04 46.12 3.46
496 1856 6.757010 TCGCCACTGCAATTTTTAAACTTTAA 59.243 30.769 0.00 0.00 37.32 1.52
497 1857 6.273825 TCGCCACTGCAATTTTTAAACTTTA 58.726 32.000 0.00 0.00 37.32 1.85
501 1861 5.590104 AATCGCCACTGCAATTTTTAAAC 57.410 34.783 0.00 0.00 37.32 2.01
505 1865 2.327568 CGAATCGCCACTGCAATTTTT 58.672 42.857 0.00 0.00 37.32 1.94
507 1867 0.171007 CCGAATCGCCACTGCAATTT 59.829 50.000 0.00 0.00 37.32 1.82
509 1869 1.078497 TCCGAATCGCCACTGCAAT 60.078 52.632 0.00 0.00 37.32 3.56
513 1873 2.128035 GAATACTCCGAATCGCCACTG 58.872 52.381 0.00 0.00 0.00 3.66
516 1876 1.001706 CTCGAATACTCCGAATCGCCA 60.002 52.381 0.00 0.00 35.48 5.69
518 1878 2.044860 CACTCGAATACTCCGAATCGC 58.955 52.381 0.00 0.00 35.48 4.58
519 1879 2.651701 CCACTCGAATACTCCGAATCG 58.348 52.381 0.00 0.00 35.48 3.34
521 1881 1.754803 TGCCACTCGAATACTCCGAAT 59.245 47.619 0.00 0.00 35.48 3.34
522 1882 1.179152 TGCCACTCGAATACTCCGAA 58.821 50.000 0.00 0.00 35.48 4.30
523 1883 1.067060 CATGCCACTCGAATACTCCGA 59.933 52.381 0.00 0.00 34.61 4.55
525 1885 2.604046 ACATGCCACTCGAATACTCC 57.396 50.000 0.00 0.00 0.00 3.85
556 2053 6.040247 CGGCTGTCACTACATTAACATTAGA 58.960 40.000 0.00 0.00 34.37 2.10
559 2056 4.575885 ACGGCTGTCACTACATTAACATT 58.424 39.130 0.00 0.00 34.37 2.71
616 2121 2.260869 GCAACCACGCATGACCACT 61.261 57.895 0.00 0.00 0.00 4.00
617 2122 2.255252 GCAACCACGCATGACCAC 59.745 61.111 0.00 0.00 0.00 4.16
619 2124 2.562912 CTGCAACCACGCATGACC 59.437 61.111 0.00 0.00 42.06 4.02
621 2126 1.898094 AAGCTGCAACCACGCATGA 60.898 52.632 1.02 0.00 42.06 3.07
626 2140 3.168628 CTTTCAAGCTGCAACCACG 57.831 52.632 1.02 0.00 0.00 4.94
668 2183 3.554934 CTCTGGAGTAGCACTGATCTCT 58.445 50.000 0.00 0.00 0.00 3.10
707 3248 5.381757 TCTTATAGACTGAGAGGAAGGAGC 58.618 45.833 0.00 0.00 0.00 4.70
726 3267 9.847224 AGTCAAACAAGGTTAATCTTCTTCTTA 57.153 29.630 0.00 0.00 0.00 2.10
734 3275 5.070685 GGTCCAGTCAAACAAGGTTAATCT 58.929 41.667 0.00 0.00 0.00 2.40
808 4232 1.651240 CTTGTGATTGCAGGAGGGCG 61.651 60.000 0.00 0.00 36.28 6.13
882 4306 3.522553 AGCGTCACTTCTTATAGCAACC 58.477 45.455 0.00 0.00 0.00 3.77
913 4576 2.359404 GTCGGTGAGGAGGAGGGA 59.641 66.667 0.00 0.00 0.00 4.20
914 4577 3.141488 CGTCGGTGAGGAGGAGGG 61.141 72.222 0.00 0.00 0.00 4.30
1011 4698 1.594331 GTCGCTTGGTTCTTGGAGTT 58.406 50.000 0.00 0.00 0.00 3.01
1057 4744 1.920835 GCAGGAGGAGGAAGGTGGT 60.921 63.158 0.00 0.00 0.00 4.16
1063 4750 0.616111 GTGAGGAGCAGGAGGAGGAA 60.616 60.000 0.00 0.00 0.00 3.36
1131 4818 4.617520 ATGCGTGCGTGGTGACCA 62.618 61.111 0.00 0.00 0.00 4.02
1132 4819 4.088762 CATGCGTGCGTGGTGACC 62.089 66.667 6.15 0.00 0.00 4.02
1133 4820 4.741781 GCATGCGTGCGTGGTGAC 62.742 66.667 16.43 0.00 42.28 3.67
1148 4835 2.125552 CATTGGCGTCGAGGAGCA 60.126 61.111 9.75 0.00 34.54 4.26
1632 5319 3.948719 TTGGACACGAGGTGGGCC 61.949 66.667 0.00 0.00 37.94 5.80
1702 5651 3.226429 TTCTTGTGGCTCTCGCGCT 62.226 57.895 5.56 0.00 36.88 5.92
1711 5660 1.576421 CCGCACTTCTTCTTGTGGC 59.424 57.895 0.00 0.00 36.62 5.01
2050 6005 2.028385 GGAAGGTGGTGTAGTTGTCGAT 60.028 50.000 0.00 0.00 0.00 3.59
2111 6066 5.121611 CGGTAATAATTTGACTGTGTCTGCA 59.878 40.000 0.00 0.00 33.15 4.41
2112 6067 5.560148 CGGTAATAATTTGACTGTGTCTGC 58.440 41.667 0.00 0.00 33.15 4.26
2134 6089 2.969238 CTAAGATGGGGCTGCGCG 60.969 66.667 10.72 0.00 0.00 6.86
2137 6092 0.811616 CGTGTCTAAGATGGGGCTGC 60.812 60.000 0.00 0.00 0.00 5.25
2143 6098 3.254060 CCACTGTTCGTGTCTAAGATGG 58.746 50.000 0.00 0.00 42.20 3.51
2145 6100 2.671351 CGCCACTGTTCGTGTCTAAGAT 60.671 50.000 0.00 0.00 42.20 2.40
2146 6101 1.335597 CGCCACTGTTCGTGTCTAAGA 60.336 52.381 0.00 0.00 42.20 2.10
2148 6103 0.942410 GCGCCACTGTTCGTGTCTAA 60.942 55.000 0.00 0.00 42.20 2.10
2149 6104 1.372499 GCGCCACTGTTCGTGTCTA 60.372 57.895 0.00 0.00 42.20 2.59
2150 6105 2.661866 GCGCCACTGTTCGTGTCT 60.662 61.111 0.00 0.00 42.20 3.41
2151 6106 2.661866 AGCGCCACTGTTCGTGTC 60.662 61.111 2.29 0.00 42.20 3.67
2174 6133 0.316772 CCGAACAGTACGCGATCGAT 60.317 55.000 21.57 8.54 39.41 3.59
2252 6230 1.443872 CAGTACGGCGTCACTCACC 60.444 63.158 19.21 0.00 0.00 4.02
2254 6232 1.167781 TGTCAGTACGGCGTCACTCA 61.168 55.000 19.21 10.73 0.00 3.41
2273 6251 1.167851 CACTTGCATTCCCACGATGT 58.832 50.000 0.00 0.00 0.00 3.06
2306 6310 3.361158 CGGCATCCCACGCAAACA 61.361 61.111 0.00 0.00 0.00 2.83
2395 6399 1.475682 GAAGAAGCAATGGAAGCAGGG 59.524 52.381 0.00 0.00 0.00 4.45
2426 6430 2.201708 GGTAGAGGGGCGCTAGTCC 61.202 68.421 7.64 0.00 42.75 3.85
2427 6431 1.455217 TGGTAGAGGGGCGCTAGTC 60.455 63.158 7.64 0.80 0.00 2.59
2429 6433 0.178998 TACTGGTAGAGGGGCGCTAG 60.179 60.000 7.64 0.00 0.00 3.42
2430 6434 0.178998 CTACTGGTAGAGGGGCGCTA 60.179 60.000 7.64 0.00 35.21 4.26
2432 6436 3.130227 CTACTGGTAGAGGGGCGC 58.870 66.667 0.00 0.00 35.21 6.53
2433 6437 2.846652 CGCTACTGGTAGAGGGGCG 61.847 68.421 11.44 4.77 39.26 6.13
2434 6438 0.466922 TACGCTACTGGTAGAGGGGC 60.467 60.000 11.44 0.00 37.30 5.80
2435 6439 1.133853 AGTACGCTACTGGTAGAGGGG 60.134 57.143 11.44 0.94 37.69 4.79
2437 6441 3.181456 ACCTAGTACGCTACTGGTAGAGG 60.181 52.174 11.44 9.73 39.81 3.69
2468 6472 2.049433 CACGACGTGGTCCAGTCC 60.049 66.667 20.26 0.00 34.10 3.85
2469 6473 1.371389 GTCACGACGTGGTCCAGTC 60.371 63.158 26.55 1.58 33.87 3.51
2470 6474 1.826921 AGTCACGACGTGGTCCAGT 60.827 57.895 26.55 8.43 33.87 4.00
2471 6475 1.371758 CAGTCACGACGTGGTCCAG 60.372 63.158 26.55 12.19 33.87 3.86
2515 6519 3.158676 GCACCCTAGCTAGCACTAGTAT 58.841 50.000 18.83 0.00 38.39 2.12
2557 6564 4.428209 AGAGCTCGTGATGAACTGTTATG 58.572 43.478 8.37 0.00 0.00 1.90
2634 6645 5.856986 TCGTCTGAAATACTTGTCGAAGAAG 59.143 40.000 4.30 4.30 39.69 2.85
2637 6648 6.072029 CTTCGTCTGAAATACTTGTCGAAG 57.928 41.667 8.98 8.98 43.71 3.79
2649 6660 6.277605 TCATTTGTACTCACTTCGTCTGAAA 58.722 36.000 0.00 0.00 32.66 2.69
2652 6663 5.445142 GCATCATTTGTACTCACTTCGTCTG 60.445 44.000 0.00 0.00 0.00 3.51
2653 6664 4.627467 GCATCATTTGTACTCACTTCGTCT 59.373 41.667 0.00 0.00 0.00 4.18
2655 6666 4.152402 GTGCATCATTTGTACTCACTTCGT 59.848 41.667 0.00 0.00 37.89 3.85
2656 6667 4.389992 AGTGCATCATTTGTACTCACTTCG 59.610 41.667 0.00 0.00 46.94 3.79
2671 6684 3.056891 TCATCGAGTGTGTAAGTGCATCA 60.057 43.478 0.00 0.00 0.00 3.07
2692 6705 1.002251 CTATCCGAACCGTGAGCTCTC 60.002 57.143 16.19 10.75 0.00 3.20
2725 6748 5.658634 TGCCAATGATCACTTACTCTAGTCT 59.341 40.000 0.00 0.00 0.00 3.24
2735 6758 4.091549 ACTCCAAATGCCAATGATCACTT 58.908 39.130 0.00 0.00 0.00 3.16
2737 6760 4.178540 CAACTCCAAATGCCAATGATCAC 58.821 43.478 0.00 0.00 0.00 3.06
2771 6794 5.163195 CCAAGCCTACCCATGATAACTAACT 60.163 44.000 0.00 0.00 0.00 2.24
2786 6815 0.831307 CCCTCACCTACCAAGCCTAC 59.169 60.000 0.00 0.00 0.00 3.18
2828 6857 3.173284 GGTTTGCCATACGTGCTCGTC 62.173 57.143 18.12 3.92 41.78 4.20
2838 6867 3.670625 GTGTCAGTGTAGGTTTGCCATA 58.329 45.455 0.00 0.00 37.19 2.74
2839 6868 2.504367 GTGTCAGTGTAGGTTTGCCAT 58.496 47.619 0.00 0.00 37.19 4.40
2840 6869 1.808512 CGTGTCAGTGTAGGTTTGCCA 60.809 52.381 0.00 0.00 37.19 4.92
2841 6870 0.865769 CGTGTCAGTGTAGGTTTGCC 59.134 55.000 0.00 0.00 0.00 4.52
2852 6881 2.179517 GCTAGCTCGCGTGTCAGT 59.820 61.111 7.70 0.00 0.00 3.41
2853 6882 1.585002 GAGCTAGCTCGCGTGTCAG 60.585 63.158 28.04 6.40 33.06 3.51
2854 6883 2.041115 AGAGCTAGCTCGCGTGTCA 61.041 57.895 33.31 0.00 46.90 3.58
2855 6884 1.585002 CAGAGCTAGCTCGCGTGTC 60.585 63.158 33.31 13.69 46.90 3.67
2856 6885 2.487428 CAGAGCTAGCTCGCGTGT 59.513 61.111 33.31 17.10 46.90 4.49
2857 6886 2.953824 GCAGAGCTAGCTCGCGTG 60.954 66.667 33.31 27.30 46.90 5.34
2883 6918 1.666888 CGCACTTCCAATTCCACAAGC 60.667 52.381 0.00 0.00 0.00 4.01
2915 6950 1.004277 GGTTTCTGCTACCATGGACCA 59.996 52.381 21.47 10.92 35.67 4.02
2919 6954 1.369625 GTCGGTTTCTGCTACCATGG 58.630 55.000 11.19 11.19 35.31 3.66
2920 6955 1.369625 GGTCGGTTTCTGCTACCATG 58.630 55.000 0.00 0.00 35.31 3.66
2938 6973 0.107508 AATGCGGTCAGATCACAGGG 60.108 55.000 0.00 0.00 0.00 4.45
2973 7021 2.352342 CTGCCCTTTGTTTGCTTGTTTG 59.648 45.455 0.00 0.00 0.00 2.93
2975 7023 1.743431 GCTGCCCTTTGTTTGCTTGTT 60.743 47.619 0.00 0.00 0.00 2.83
2976 7024 0.179076 GCTGCCCTTTGTTTGCTTGT 60.179 50.000 0.00 0.00 0.00 3.16
2977 7025 0.881600 GGCTGCCCTTTGTTTGCTTG 60.882 55.000 7.66 0.00 0.00 4.01
2978 7026 1.447217 GGCTGCCCTTTGTTTGCTT 59.553 52.632 7.66 0.00 0.00 3.91
2980 7028 2.031012 GGGCTGCCCTTTGTTTGC 59.969 61.111 30.42 0.00 41.34 3.68
2981 7029 0.397564 AATGGGCTGCCCTTTGTTTG 59.602 50.000 35.80 0.00 45.70 2.93
2982 7030 0.397564 CAATGGGCTGCCCTTTGTTT 59.602 50.000 38.66 23.26 46.97 2.83
2984 7032 3.795905 CAATGGGCTGCCCTTTGT 58.204 55.556 38.66 22.62 46.97 2.83
2986 7034 1.914764 CCACAATGGGCTGCCCTTT 60.915 57.895 35.80 31.64 45.70 3.11
2987 7035 2.284112 CCACAATGGGCTGCCCTT 60.284 61.111 35.80 28.00 45.70 3.95
2995 7043 1.378382 TCCATCGTGCCACAATGGG 60.378 57.895 14.64 0.45 40.34 4.00
2996 7044 1.996786 GCTCCATCGTGCCACAATGG 61.997 60.000 8.57 8.57 41.12 3.16
2998 7046 1.002257 TGCTCCATCGTGCCACAAT 60.002 52.632 0.00 0.00 0.00 2.71
2999 7047 1.965930 GTGCTCCATCGTGCCACAA 60.966 57.895 0.00 0.00 0.00 3.33
3003 7051 2.045926 AAGGTGCTCCATCGTGCC 60.046 61.111 7.70 0.00 35.89 5.01
3008 7056 1.467920 CCCAAAGAAGGTGCTCCATC 58.532 55.000 7.70 4.63 35.89 3.51
3069 7122 2.526304 TCACGTCCACTGAGAAAAGG 57.474 50.000 0.00 0.00 0.00 3.11
3070 7123 3.246226 CAGTTCACGTCCACTGAGAAAAG 59.754 47.826 15.74 0.00 42.74 2.27
3073 7126 1.068588 CCAGTTCACGTCCACTGAGAA 59.931 52.381 20.57 2.13 42.74 2.87
3074 7135 0.673985 CCAGTTCACGTCCACTGAGA 59.326 55.000 20.57 0.00 42.74 3.27
3126 7202 2.134287 CCATCCCCACTCCGATCGT 61.134 63.158 15.09 0.00 0.00 3.73
3127 7203 1.188219 ATCCATCCCCACTCCGATCG 61.188 60.000 8.51 8.51 0.00 3.69
3149 7225 2.091994 AGATTGAGGATTTGAGGCTGGG 60.092 50.000 0.00 0.00 0.00 4.45
3154 7230 4.267536 TGCAGAAGATTGAGGATTTGAGG 58.732 43.478 0.00 0.00 0.00 3.86
3155 7231 4.335874 CCTGCAGAAGATTGAGGATTTGAG 59.664 45.833 17.39 0.00 0.00 3.02
3156 7232 4.267536 CCTGCAGAAGATTGAGGATTTGA 58.732 43.478 17.39 0.00 0.00 2.69
3157 7233 3.181489 GCCTGCAGAAGATTGAGGATTTG 60.181 47.826 17.39 0.00 0.00 2.32
3158 7234 3.022406 GCCTGCAGAAGATTGAGGATTT 58.978 45.455 17.39 0.00 0.00 2.17
3159 7235 2.025605 TGCCTGCAGAAGATTGAGGATT 60.026 45.455 17.39 0.00 0.00 3.01
3160 7236 1.562942 TGCCTGCAGAAGATTGAGGAT 59.437 47.619 17.39 0.00 0.00 3.24
3161 7237 0.986527 TGCCTGCAGAAGATTGAGGA 59.013 50.000 17.39 0.00 0.00 3.71
3166 7242 0.674895 GTCGGTGCCTGCAGAAGATT 60.675 55.000 17.39 0.00 0.00 2.40
3207 7288 2.557924 TGCTCATTGTTTGGCAACCTAG 59.442 45.455 0.00 0.00 40.28 3.02
3310 7395 2.920524 AGCTGGATTGCTCATCTTGAG 58.079 47.619 0.08 0.08 46.90 3.02
3317 7405 0.833287 GGACCTAGCTGGATTGCTCA 59.167 55.000 0.00 0.00 42.97 4.26
3329 7417 0.755686 GGTGGCATCAGAGGACCTAG 59.244 60.000 0.00 0.00 0.00 3.02
3357 7445 2.256461 CGGCTTGCTCTTGTTGCC 59.744 61.111 0.00 0.00 40.14 4.52
3506 7594 4.817464 TGTCCTAACTAAAAATGCGTGTGT 59.183 37.500 0.00 0.00 0.00 3.72
3517 7605 6.349280 GCAATGCATGTTCTGTCCTAACTAAA 60.349 38.462 0.00 0.00 0.00 1.85
3519 7607 4.635765 GCAATGCATGTTCTGTCCTAACTA 59.364 41.667 0.00 0.00 0.00 2.24
3520 7608 3.441572 GCAATGCATGTTCTGTCCTAACT 59.558 43.478 0.00 0.00 0.00 2.24
3546 7640 1.135257 CCCTATCTATCTTGAGGCGCG 60.135 57.143 0.00 0.00 0.00 6.86
3599 7697 0.829990 TCCGCTGTGGCTAATCATCA 59.170 50.000 1.39 0.00 37.80 3.07
3606 7704 3.003173 AAGGCTCCGCTGTGGCTA 61.003 61.111 6.69 0.00 39.64 3.93
3607 7705 4.711949 CAAGGCTCCGCTGTGGCT 62.712 66.667 1.39 0.37 42.00 4.75
3684 7784 3.969802 ACCGACACCGTGGACGTC 61.970 66.667 7.13 7.13 37.74 4.34
3685 7785 4.274700 CACCGACACCGTGGACGT 62.275 66.667 15.43 0.00 37.74 4.34
3864 7974 1.455248 GTACTTATTGCCGGTTGCCA 58.545 50.000 1.90 0.00 40.16 4.92
3977 8107 0.753262 ACGTACAGAGCCATCCATCC 59.247 55.000 0.00 0.00 0.00 3.51
3983 8113 1.405821 GTCAGCTACGTACAGAGCCAT 59.594 52.381 11.40 0.00 39.65 4.40
3985 8115 0.100861 GGTCAGCTACGTACAGAGCC 59.899 60.000 11.40 0.00 39.65 4.70
3987 8117 1.062294 GTCGGTCAGCTACGTACAGAG 59.938 57.143 0.00 0.00 0.00 3.35
3988 8118 1.081892 GTCGGTCAGCTACGTACAGA 58.918 55.000 0.00 0.00 0.00 3.41
3990 8120 1.131693 CATGTCGGTCAGCTACGTACA 59.868 52.381 0.00 7.90 0.00 2.90
3998 8128 4.419522 AAATTAACACATGTCGGTCAGC 57.580 40.909 0.00 0.00 0.00 4.26
4023 8153 1.607148 ACCGCTGCAAAGTTAAGGTTC 59.393 47.619 0.00 0.00 0.00 3.62
4024 8154 1.336755 CACCGCTGCAAAGTTAAGGTT 59.663 47.619 0.00 0.00 0.00 3.50
4025 8155 0.951558 CACCGCTGCAAAGTTAAGGT 59.048 50.000 0.00 0.00 0.00 3.50
4026 8156 1.234821 TCACCGCTGCAAAGTTAAGG 58.765 50.000 0.00 0.00 0.00 2.69
4027 8157 2.474526 CGATCACCGCTGCAAAGTTAAG 60.475 50.000 0.00 0.00 0.00 1.85
4449 8600 0.033405 TCCGGGAGTAGGTCTTCCAG 60.033 60.000 0.00 0.00 41.93 3.86
4741 8895 3.697045 TGTCGTTCAAAAACCCACTCATT 59.303 39.130 0.00 0.00 31.27 2.57
4759 8913 2.160813 CGAACCACCCCTTATTTTGTCG 59.839 50.000 0.00 0.00 0.00 4.35
4780 8935 4.563786 CCCTTTCCTGACTAAACCTGAGAC 60.564 50.000 0.00 0.00 0.00 3.36
4815 8970 1.067516 ACGAACGGGAAGAAACGAGAA 59.932 47.619 0.00 0.00 0.00 2.87
4876 9034 2.223735 GGGCATTGCAGATCTGAACATG 60.224 50.000 27.04 21.67 0.00 3.21
4999 9159 3.535561 CCACTAGAACCATGACACATCC 58.464 50.000 0.00 0.00 0.00 3.51
5021 9181 0.881118 TCGCTTCCCTTGTCATTTGC 59.119 50.000 0.00 0.00 0.00 3.68
5037 9197 1.856265 CTCCCTGTTTGCCTTGTCGC 61.856 60.000 0.00 0.00 0.00 5.19
5093 9257 5.047943 ACATAATCAGTCACGGGTAGATAGC 60.048 44.000 0.00 0.00 0.00 2.97
5110 9274 6.987404 GGAGAAGGTCAGTTAAGGACATAATC 59.013 42.308 8.89 4.53 37.00 1.75
5111 9275 6.443849 TGGAGAAGGTCAGTTAAGGACATAAT 59.556 38.462 8.89 0.00 37.00 1.28
5112 9276 5.783360 TGGAGAAGGTCAGTTAAGGACATAA 59.217 40.000 8.89 0.00 37.00 1.90
5113 9277 5.338632 TGGAGAAGGTCAGTTAAGGACATA 58.661 41.667 8.89 0.00 37.00 2.29
5139 9305 2.774687 TAAAAGGGGGACGGCAAGCC 62.775 60.000 0.00 0.00 0.00 4.35
5141 9307 1.476488 CAATAAAAGGGGGACGGCAAG 59.524 52.381 0.00 0.00 0.00 4.01
5158 9324 3.708631 AGACGATGAGGTCCAGATTCAAT 59.291 43.478 0.00 0.00 37.66 2.57
5159 9325 3.099905 AGACGATGAGGTCCAGATTCAA 58.900 45.455 0.00 0.00 37.66 2.69
5161 9327 3.383185 AGAAGACGATGAGGTCCAGATTC 59.617 47.826 0.00 0.00 37.66 2.52
5162 9328 3.370104 AGAAGACGATGAGGTCCAGATT 58.630 45.455 0.00 0.00 37.66 2.40
5164 9330 2.516227 AGAAGACGATGAGGTCCAGA 57.484 50.000 0.00 0.00 37.66 3.86
5165 9331 3.444034 TGTAAGAAGACGATGAGGTCCAG 59.556 47.826 0.00 0.00 37.66 3.86
5166 9332 3.427573 TGTAAGAAGACGATGAGGTCCA 58.572 45.455 0.00 0.00 37.66 4.02
5167 9333 3.735514 GCTGTAAGAAGACGATGAGGTCC 60.736 52.174 0.00 0.00 34.67 4.46
5168 9334 3.440228 GCTGTAAGAAGACGATGAGGTC 58.560 50.000 0.00 0.00 34.07 3.85
5169 9335 2.166664 GGCTGTAAGAAGACGATGAGGT 59.833 50.000 0.00 0.00 34.07 3.85
5170 9336 2.428890 AGGCTGTAAGAAGACGATGAGG 59.571 50.000 0.00 0.00 34.07 3.86
5171 9337 3.791973 AGGCTGTAAGAAGACGATGAG 57.208 47.619 0.00 0.00 34.07 2.90
5172 9338 3.849911 CAAGGCTGTAAGAAGACGATGA 58.150 45.455 0.00 0.00 34.07 2.92
5173 9339 2.349886 GCAAGGCTGTAAGAAGACGATG 59.650 50.000 0.00 0.00 34.07 3.84
5174 9340 2.622436 GCAAGGCTGTAAGAAGACGAT 58.378 47.619 0.00 0.00 34.07 3.73
5175 9341 1.337823 GGCAAGGCTGTAAGAAGACGA 60.338 52.381 0.00 0.00 34.07 4.20
5177 9343 1.003696 AGGGCAAGGCTGTAAGAAGAC 59.996 52.381 0.00 0.00 34.07 3.01
5178 9344 1.362224 AGGGCAAGGCTGTAAGAAGA 58.638 50.000 0.00 0.00 34.07 2.87
5179 9345 2.206576 AAGGGCAAGGCTGTAAGAAG 57.793 50.000 0.00 0.00 34.07 2.85
5180 9346 2.238521 CAAAGGGCAAGGCTGTAAGAA 58.761 47.619 0.00 0.00 34.07 2.52
5315 9481 1.743995 AATACAAGTCCACGGCGCC 60.744 57.895 19.07 19.07 0.00 6.53
5445 9611 3.057174 CGCAATGGCCAAGGTAAAAGTTA 60.057 43.478 10.96 0.00 36.38 2.24
5452 9618 1.077787 CCTCGCAATGGCCAAGGTA 60.078 57.895 10.96 0.00 35.66 3.08


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

AutoCloner maintained by Alex Coulton.