Multiple sequence alignment - TraesCS3D01G127900

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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 TraesCS3D01G127900 chr3D 100.000 3059 0 0 1 3059 85826056 85829114 0.000000e+00 5650.0
1 TraesCS3D01G127900 chr3D 84.689 627 63 15 2192 2812 2398745 2398146 2.030000e-166 595.0
2 TraesCS3D01G127900 chr3D 98.438 256 3 1 2805 3059 85834463 85834718 1.670000e-122 449.0
3 TraesCS3D01G127900 chr3D 94.595 259 12 2 2803 3059 299674383 299674641 1.710000e-107 399.0
4 TraesCS3D01G127900 chr3D 89.950 199 20 0 1 199 597220165 597220363 1.090000e-64 257.0
5 TraesCS3D01G127900 chr3B 93.642 2375 95 19 473 2812 135768324 135770677 0.000000e+00 3498.0
6 TraesCS3D01G127900 chr3B 94.302 1948 67 14 473 2396 135710908 135712835 0.000000e+00 2942.0
7 TraesCS3D01G127900 chr3B 93.816 1795 74 14 1037 2812 135813886 135815662 0.000000e+00 2665.0
8 TraesCS3D01G127900 chr3B 94.291 578 19 4 473 1041 135807848 135808420 0.000000e+00 872.0
9 TraesCS3D01G127900 chr3B 91.048 458 21 2 1 438 135750026 135750483 4.360000e-168 601.0
10 TraesCS3D01G127900 chr3B 96.396 111 4 0 337 447 135710800 135710910 1.870000e-42 183.0
11 TraesCS3D01G127900 chr3B 95.495 111 5 0 337 447 135807740 135807850 8.720000e-41 178.0
12 TraesCS3D01G127900 chr3A 93.876 1094 51 6 1730 2812 102389230 102390318 0.000000e+00 1635.0
13 TraesCS3D01G127900 chr3A 91.494 917 33 13 838 1741 102435840 102436724 0.000000e+00 1219.0
14 TraesCS3D01G127900 chr3A 90.611 916 43 11 838 1741 102388565 102389449 0.000000e+00 1175.0
15 TraesCS3D01G127900 chr3A 96.319 652 19 2 2165 2812 102437144 102437794 0.000000e+00 1066.0
16 TraesCS3D01G127900 chr3A 96.319 652 19 2 2165 2812 102492094 102492744 0.000000e+00 1066.0
17 TraesCS3D01G127900 chr3A 94.923 453 18 2 1730 2177 102436500 102436952 0.000000e+00 704.0
18 TraesCS3D01G127900 chr3A 94.923 453 18 2 1730 2177 102491450 102491902 0.000000e+00 704.0
19 TraesCS3D01G127900 chr3A 93.634 377 12 5 1377 1741 102491298 102491674 1.240000e-153 553.0
20 TraesCS3D01G127900 chr3A 89.272 261 16 10 562 816 102435382 102435636 1.770000e-82 316.0
21 TraesCS3D01G127900 chr3A 94.472 199 11 0 1 199 746909373 746909571 1.070000e-79 307.0
22 TraesCS3D01G127900 chr3A 88.800 250 16 10 562 805 102490151 102490394 2.310000e-76 296.0
23 TraesCS3D01G127900 chr3A 90.278 144 4 5 672 814 102388350 102388484 2.420000e-41 180.0
24 TraesCS3D01G127900 chr2D 91.184 828 55 2 924 1739 393204783 393205604 0.000000e+00 1109.0
25 TraesCS3D01G127900 chr2D 90.588 765 54 2 987 1739 393069612 393070370 0.000000e+00 998.0
26 TraesCS3D01G127900 chr2D 87.735 799 72 10 923 1701 393215333 393216125 0.000000e+00 909.0
27 TraesCS3D01G127900 chr2D 95.312 256 11 1 2805 3059 476737572 476737827 3.670000e-109 405.0
28 TraesCS3D01G127900 chr2D 96.000 250 9 1 2811 3059 570966950 570966701 3.670000e-109 405.0
29 TraesCS3D01G127900 chr2D 90.306 196 19 0 1 196 412634356 412634551 1.090000e-64 257.0
30 TraesCS3D01G127900 chr1D 89.976 828 62 2 924 1739 113994937 113994119 0.000000e+00 1050.0
31 TraesCS3D01G127900 chr1D 96.000 250 9 1 2811 3059 188325572 188325323 3.670000e-109 405.0
32 TraesCS3D01G127900 chr1D 96.000 250 9 1 2811 3059 188331193 188330944 3.670000e-109 405.0
33 TraesCS3D01G127900 chr1B 89.531 831 69 5 921 1739 174252477 174251653 0.000000e+00 1037.0
34 TraesCS3D01G127900 chr1B 91.967 361 29 0 1730 2090 174251875 174251515 9.790000e-140 507.0
35 TraesCS3D01G127900 chr1B 92.929 198 14 0 1 198 26331350 26331547 3.860000e-74 289.0
36 TraesCS3D01G127900 chr1A 86.454 657 70 6 2164 2812 247806294 247805649 0.000000e+00 702.0
37 TraesCS3D01G127900 chr4A 90.625 448 41 1 196 643 252337148 252337594 7.300000e-166 593.0
38 TraesCS3D01G127900 chr4A 96.985 199 6 0 1 199 252336923 252337121 4.890000e-88 335.0
39 TraesCS3D01G127900 chr4A 86.111 180 15 5 639 809 255587222 255587400 5.210000e-43 185.0
40 TraesCS3D01G127900 chr2B 93.075 361 25 0 1730 2090 464879046 464879406 2.090000e-146 529.0
41 TraesCS3D01G127900 chr2B 92.244 361 28 0 1730 2090 464898636 464898996 2.100000e-141 512.0
42 TraesCS3D01G127900 chr2B 89.524 105 11 0 921 1025 464898004 464898108 1.910000e-27 134.0
43 TraesCS3D01G127900 chr7D 96.063 254 9 1 2807 3059 139853313 139853566 2.190000e-111 412.0
44 TraesCS3D01G127900 chr7D 96.000 250 9 1 2811 3059 29740343 29740094 3.670000e-109 405.0
45 TraesCS3D01G127900 chr5D 77.984 754 96 34 2088 2792 29171488 29170756 2.840000e-110 409.0
46 TraesCS3D01G127900 chr5D 95.312 256 11 1 2805 3059 506105555 506105810 3.670000e-109 405.0
47 TraesCS3D01G127900 chr5A 77.822 762 91 34 2089 2792 19985884 19985143 1.710000e-107 399.0
48 TraesCS3D01G127900 chr5A 76.463 752 92 38 2089 2791 19984514 19983799 2.270000e-86 329.0
49 TraesCS3D01G127900 chr7A 94.416 197 11 0 1 197 472130662 472130466 1.380000e-78 303.0
50 TraesCS3D01G127900 chr7A 92.929 198 14 0 1 198 681666535 681666338 3.860000e-74 289.0
51 TraesCS3D01G127900 chr7B 88.614 202 23 0 1 202 232267077 232267278 2.360000e-61 246.0
52 TraesCS3D01G127900 chr2A 97.297 37 1 0 2092 2128 4071664 4071700 2.550000e-06 63.9


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 TraesCS3D01G127900 chr3D 85826056 85829114 3058 False 5650.000000 5650 100.000000 1 3059 1 chr3D.!!$F1 3058
1 TraesCS3D01G127900 chr3D 2398146 2398745 599 True 595.000000 595 84.689000 2192 2812 1 chr3D.!!$R1 620
2 TraesCS3D01G127900 chr3B 135768324 135770677 2353 False 3498.000000 3498 93.642000 473 2812 1 chr3B.!!$F2 2339
3 TraesCS3D01G127900 chr3B 135813886 135815662 1776 False 2665.000000 2665 93.816000 1037 2812 1 chr3B.!!$F3 1775
4 TraesCS3D01G127900 chr3B 135710800 135712835 2035 False 1562.500000 2942 95.349000 337 2396 2 chr3B.!!$F4 2059
5 TraesCS3D01G127900 chr3B 135807740 135808420 680 False 525.000000 872 94.893000 337 1041 2 chr3B.!!$F5 704
6 TraesCS3D01G127900 chr3A 102388350 102390318 1968 False 996.666667 1635 91.588333 672 2812 3 chr3A.!!$F2 2140
7 TraesCS3D01G127900 chr3A 102435382 102437794 2412 False 826.250000 1219 93.002000 562 2812 4 chr3A.!!$F3 2250
8 TraesCS3D01G127900 chr3A 102490151 102492744 2593 False 654.750000 1066 93.419000 562 2812 4 chr3A.!!$F4 2250
9 TraesCS3D01G127900 chr2D 393204783 393205604 821 False 1109.000000 1109 91.184000 924 1739 1 chr2D.!!$F2 815
10 TraesCS3D01G127900 chr2D 393069612 393070370 758 False 998.000000 998 90.588000 987 1739 1 chr2D.!!$F1 752
11 TraesCS3D01G127900 chr2D 393215333 393216125 792 False 909.000000 909 87.735000 923 1701 1 chr2D.!!$F3 778
12 TraesCS3D01G127900 chr1D 113994119 113994937 818 True 1050.000000 1050 89.976000 924 1739 1 chr1D.!!$R1 815
13 TraesCS3D01G127900 chr1B 174251515 174252477 962 True 772.000000 1037 90.749000 921 2090 2 chr1B.!!$R1 1169
14 TraesCS3D01G127900 chr1A 247805649 247806294 645 True 702.000000 702 86.454000 2164 2812 1 chr1A.!!$R1 648
15 TraesCS3D01G127900 chr4A 252336923 252337594 671 False 464.000000 593 93.805000 1 643 2 chr4A.!!$F2 642
16 TraesCS3D01G127900 chr2B 464898004 464898996 992 False 323.000000 512 90.884000 921 2090 2 chr2B.!!$F2 1169
17 TraesCS3D01G127900 chr5D 29170756 29171488 732 True 409.000000 409 77.984000 2088 2792 1 chr5D.!!$R1 704
18 TraesCS3D01G127900 chr5A 19983799 19985884 2085 True 364.000000 399 77.142500 2089 2792 2 chr5A.!!$R1 703

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
451 482 0.107017 AAAGGATGCCGATGAGGTGG 60.107 55.0 0.0 0.0 43.7 4.61 F
455 486 0.249657 GATGCCGATGAGGTGGTCTC 60.250 60.0 0.0 0.0 43.7 3.36 F
1838 2235 0.317160 TTGTTGACGGCAGACTCGAT 59.683 50.0 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2215 0.103390 TCGAGTCTGCCGTCAACAAA 59.897 50.000 0.0 0.0 0.0 2.83 R
1846 2243 1.072331 AGTGGTGATCAAAGAAGCCGT 59.928 47.619 0.0 0.0 0.0 5.68 R
3029 5076 1.077993 AGAGACCCTGCTACAGTTCCT 59.922 52.381 0.0 0.0 0.0 3.36 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
110 111 0.949105 ACCTGCGCTTTAGTGGAACG 60.949 55.000 9.73 0.00 45.86 3.95
153 154 2.377628 TACGATCATTGCCGAGGCCC 62.378 60.000 12.05 0.00 41.09 5.80
210 241 4.148079 TCATGGCGCCCAATTTATAATCA 58.852 39.130 26.77 0.00 36.95 2.57
230 261 5.537300 TCATAGCCTCTTCCAACTGATAC 57.463 43.478 0.00 0.00 0.00 2.24
242 273 5.842907 TCCAACTGATACAGATTATCACCG 58.157 41.667 5.76 0.00 35.18 4.94
260 291 3.559024 CTGCAAGTGGAGCACGAG 58.441 61.111 0.00 0.00 39.64 4.18
264 295 1.560860 GCAAGTGGAGCACGAGTCAC 61.561 60.000 0.00 0.00 39.64 3.67
265 296 0.946221 CAAGTGGAGCACGAGTCACC 60.946 60.000 0.00 0.00 39.64 4.02
281 312 2.480419 GTCACCCTGTTCTTGAACATCG 59.520 50.000 15.35 11.08 31.47 3.84
299 330 1.631388 TCGTGGGGATTAAAAGCAGGA 59.369 47.619 0.00 0.00 0.00 3.86
313 344 3.764466 AGGAGCCTGAACGCGGAG 61.764 66.667 12.47 2.70 0.00 4.63
327 358 4.247380 GGAGCTGCATCCTCCCGG 62.247 72.222 18.31 0.00 42.46 5.73
334 365 2.423446 CATCCTCCCGGCTGTAGC 59.577 66.667 0.00 0.00 41.14 3.58
337 368 3.905678 CCTCCCGGCTGTAGCGAG 61.906 72.222 0.00 0.00 43.26 5.03
345 376 1.854227 GGCTGTAGCGAGGTCATTAC 58.146 55.000 0.00 0.00 43.26 1.89
379 410 1.672881 GAAATCAGGGCGAACTCCATG 59.327 52.381 0.00 0.00 39.13 3.66
450 481 1.019673 CAAAGGATGCCGATGAGGTG 58.980 55.000 0.00 0.00 43.70 4.00
451 482 0.107017 AAAGGATGCCGATGAGGTGG 60.107 55.000 0.00 0.00 43.70 4.61
455 486 0.249657 GATGCCGATGAGGTGGTCTC 60.250 60.000 0.00 0.00 43.70 3.36
578 609 6.293626 CCTTATCCGTATCAATGAAAGGCTTG 60.294 42.308 0.00 0.00 0.00 4.01
582 613 3.624861 CGTATCAATGAAAGGCTTGAGCT 59.375 43.478 0.00 0.00 41.70 4.09
682 713 4.124943 AGCAGCAGATGGCCAGGG 62.125 66.667 13.05 3.88 46.50 4.45
685 716 3.095163 AGCAGATGGCCAGGGAGG 61.095 66.667 13.05 0.00 46.50 4.30
687 718 2.072487 GCAGATGGCCAGGGAGGTA 61.072 63.158 13.05 0.00 40.61 3.08
688 719 1.832912 CAGATGGCCAGGGAGGTAC 59.167 63.158 13.05 0.00 40.61 3.34
895 1122 0.608130 GGGGCAAAGGTGAACCAATC 59.392 55.000 1.62 0.00 38.89 2.67
896 1123 1.337118 GGGCAAAGGTGAACCAATCA 58.663 50.000 1.62 0.00 38.89 2.57
897 1124 1.691434 GGGCAAAGGTGAACCAATCAA 59.309 47.619 1.62 0.00 40.50 2.57
898 1125 2.302733 GGGCAAAGGTGAACCAATCAAT 59.697 45.455 1.62 0.00 40.50 2.57
899 1126 3.513515 GGGCAAAGGTGAACCAATCAATA 59.486 43.478 1.62 0.00 40.50 1.90
900 1127 4.162131 GGGCAAAGGTGAACCAATCAATAT 59.838 41.667 1.62 0.00 40.50 1.28
901 1128 5.362430 GGGCAAAGGTGAACCAATCAATATA 59.638 40.000 1.62 0.00 40.50 0.86
911 1138 8.946085 GTGAACCAATCAATATAAAGTCAGACA 58.054 33.333 2.66 0.00 40.50 3.41
1021 1297 4.731612 CAGTCGACCAGCAGCGCT 62.732 66.667 13.01 2.64 40.77 5.92
1281 1557 1.257750 TGGACATGCTGCTCTACCGT 61.258 55.000 0.00 0.00 0.00 4.83
1320 1596 2.105528 AACGACCAGAACACGCGT 59.894 55.556 5.58 5.58 36.68 6.01
1350 1635 3.338126 CTACCTGTTCCGCGACGCT 62.338 63.158 19.02 0.00 0.00 5.07
1351 1636 3.620300 TACCTGTTCCGCGACGCTG 62.620 63.158 19.02 12.03 0.00 5.18
1613 2010 2.150424 CGTCGTCGCCTTTGTTGAT 58.850 52.632 0.00 0.00 0.00 2.57
1625 2022 2.768253 TTGTTGATGGCAGACTCGAT 57.232 45.000 0.00 0.00 0.00 3.59
1838 2235 0.317160 TTGTTGACGGCAGACTCGAT 59.683 50.000 0.00 0.00 0.00 3.59
1844 2241 2.425668 TGACGGCAGACTCGATAAATGA 59.574 45.455 0.00 0.00 0.00 2.57
1846 2243 2.165641 ACGGCAGACTCGATAAATGACA 59.834 45.455 0.00 0.00 0.00 3.58
2007 2404 1.498865 CGCAGGTCATAATCCACCGC 61.499 60.000 0.00 0.00 37.79 5.68
2111 2520 4.144297 ACTAGATAATACCCCGCACGTTA 58.856 43.478 0.00 0.00 0.00 3.18
2134 2545 9.988350 GTTATTGCGGGAATAGTTTGATATATG 57.012 33.333 2.20 0.00 0.00 1.78
2278 2938 2.294791 TGTTGTCGCCCTTTTTACATGG 59.705 45.455 0.00 0.00 0.00 3.66
2386 3054 4.319766 CCGATTTGAGATTTTATGCGGAGG 60.320 45.833 0.00 0.00 38.57 4.30
2389 3057 4.415881 TTGAGATTTTATGCGGAGGCTA 57.584 40.909 0.00 0.00 40.82 3.93
2530 3212 3.683365 TCAACAGCATTAGCAGACTCA 57.317 42.857 0.00 0.00 45.49 3.41
2608 3293 7.391554 CCTCATCCAAAAATGTCTTCAGACTTA 59.608 37.037 8.41 0.00 44.99 2.24
2697 4742 7.009448 CGTGATGAAAAATAATGTGGAATGTGG 59.991 37.037 0.00 0.00 0.00 4.17
2722 4767 7.097834 GTGTACCTTCTTTACTATGTCAAGCT 58.902 38.462 0.00 0.00 0.00 3.74
2812 4859 3.480470 CATTGTCTCCTGGTTGAACTGT 58.520 45.455 0.00 0.00 0.00 3.55
2813 4860 3.644966 TTGTCTCCTGGTTGAACTGTT 57.355 42.857 0.00 0.00 0.00 3.16
2814 4861 2.917933 TGTCTCCTGGTTGAACTGTTG 58.082 47.619 0.00 0.00 0.00 3.33
2815 4862 2.222027 GTCTCCTGGTTGAACTGTTGG 58.778 52.381 0.00 0.00 0.00 3.77
2816 4863 2.123589 TCTCCTGGTTGAACTGTTGGA 58.876 47.619 0.00 0.00 0.00 3.53
2817 4864 2.507886 TCTCCTGGTTGAACTGTTGGAA 59.492 45.455 0.00 0.00 0.00 3.53
2818 4865 3.053991 TCTCCTGGTTGAACTGTTGGAAA 60.054 43.478 0.00 0.00 0.00 3.13
2819 4866 3.891366 CTCCTGGTTGAACTGTTGGAAAT 59.109 43.478 0.00 0.00 0.00 2.17
2820 4867 5.055265 TCCTGGTTGAACTGTTGGAAATA 57.945 39.130 0.00 0.00 0.00 1.40
2821 4868 5.640147 TCCTGGTTGAACTGTTGGAAATAT 58.360 37.500 0.00 0.00 0.00 1.28
2822 4869 5.476599 TCCTGGTTGAACTGTTGGAAATATG 59.523 40.000 0.00 0.00 0.00 1.78
2823 4870 5.476599 CCTGGTTGAACTGTTGGAAATATGA 59.523 40.000 0.00 0.00 0.00 2.15
2824 4871 6.349611 CCTGGTTGAACTGTTGGAAATATGAG 60.350 42.308 0.00 0.00 0.00 2.90
2825 4872 5.048083 TGGTTGAACTGTTGGAAATATGAGC 60.048 40.000 0.00 0.00 0.00 4.26
2826 4873 5.048083 GGTTGAACTGTTGGAAATATGAGCA 60.048 40.000 0.00 0.00 0.00 4.26
2827 4874 6.446318 GTTGAACTGTTGGAAATATGAGCAA 58.554 36.000 0.00 0.00 0.00 3.91
2828 4875 6.839124 TGAACTGTTGGAAATATGAGCAAT 57.161 33.333 0.00 0.00 0.00 3.56
2829 4876 7.230849 TGAACTGTTGGAAATATGAGCAATT 57.769 32.000 0.00 0.00 0.00 2.32
2830 4877 7.669427 TGAACTGTTGGAAATATGAGCAATTT 58.331 30.769 0.00 0.00 0.00 1.82
2831 4878 8.801299 TGAACTGTTGGAAATATGAGCAATTTA 58.199 29.630 0.00 0.00 0.00 1.40
2832 4879 8.986477 AACTGTTGGAAATATGAGCAATTTAC 57.014 30.769 0.00 0.00 0.00 2.01
2833 4880 7.547227 ACTGTTGGAAATATGAGCAATTTACC 58.453 34.615 0.00 0.00 0.00 2.85
2834 4881 6.559810 TGTTGGAAATATGAGCAATTTACCG 58.440 36.000 0.00 0.00 0.00 4.02
2835 4882 6.375736 TGTTGGAAATATGAGCAATTTACCGA 59.624 34.615 0.00 0.00 0.00 4.69
2836 4883 7.094162 TGTTGGAAATATGAGCAATTTACCGAA 60.094 33.333 0.00 0.00 0.00 4.30
2837 4884 7.581213 TGGAAATATGAGCAATTTACCGAAT 57.419 32.000 0.00 0.00 0.00 3.34
2838 4885 7.424803 TGGAAATATGAGCAATTTACCGAATG 58.575 34.615 0.00 0.00 0.00 2.67
2839 4886 7.284261 TGGAAATATGAGCAATTTACCGAATGA 59.716 33.333 0.00 0.00 0.00 2.57
2840 4887 8.299570 GGAAATATGAGCAATTTACCGAATGAT 58.700 33.333 0.00 0.00 0.00 2.45
2841 4888 9.683069 GAAATATGAGCAATTTACCGAATGATT 57.317 29.630 0.00 0.00 0.00 2.57
2872 4919 8.894768 ACAGAAATACTAGATAAAGCATGACC 57.105 34.615 0.00 0.00 0.00 4.02
2873 4920 8.486210 ACAGAAATACTAGATAAAGCATGACCA 58.514 33.333 0.00 0.00 0.00 4.02
2874 4921 8.986847 CAGAAATACTAGATAAAGCATGACCAG 58.013 37.037 0.00 0.00 0.00 4.00
2875 4922 8.928448 AGAAATACTAGATAAAGCATGACCAGA 58.072 33.333 0.00 0.00 0.00 3.86
2876 4923 9.547753 GAAATACTAGATAAAGCATGACCAGAA 57.452 33.333 0.00 0.00 0.00 3.02
2880 4927 8.256356 ACTAGATAAAGCATGACCAGAATAGT 57.744 34.615 0.00 0.00 0.00 2.12
2881 4928 9.368416 ACTAGATAAAGCATGACCAGAATAGTA 57.632 33.333 0.00 0.00 0.00 1.82
2882 4929 9.853555 CTAGATAAAGCATGACCAGAATAGTAG 57.146 37.037 0.00 0.00 0.00 2.57
2883 4930 8.256356 AGATAAAGCATGACCAGAATAGTAGT 57.744 34.615 0.00 0.00 0.00 2.73
2884 4931 8.147058 AGATAAAGCATGACCAGAATAGTAGTG 58.853 37.037 0.00 0.00 0.00 2.74
2885 4932 5.939764 AAGCATGACCAGAATAGTAGTGA 57.060 39.130 0.00 0.00 0.00 3.41
2886 4933 6.491714 AAGCATGACCAGAATAGTAGTGAT 57.508 37.500 0.00 0.00 0.00 3.06
2887 4934 7.603180 AAGCATGACCAGAATAGTAGTGATA 57.397 36.000 0.00 0.00 0.00 2.15
2888 4935 7.603180 AGCATGACCAGAATAGTAGTGATAA 57.397 36.000 0.00 0.00 0.00 1.75
2889 4936 8.023021 AGCATGACCAGAATAGTAGTGATAAA 57.977 34.615 0.00 0.00 0.00 1.40
2890 4937 8.486210 AGCATGACCAGAATAGTAGTGATAAAA 58.514 33.333 0.00 0.00 0.00 1.52
2891 4938 8.552034 GCATGACCAGAATAGTAGTGATAAAAC 58.448 37.037 0.00 0.00 0.00 2.43
2892 4939 9.599866 CATGACCAGAATAGTAGTGATAAAACA 57.400 33.333 0.00 0.00 0.00 2.83
2894 4941 9.653287 TGACCAGAATAGTAGTGATAAAACAAG 57.347 33.333 0.00 0.00 0.00 3.16
2895 4942 8.494016 ACCAGAATAGTAGTGATAAAACAAGC 57.506 34.615 0.00 0.00 0.00 4.01
2896 4943 7.553044 ACCAGAATAGTAGTGATAAAACAAGCC 59.447 37.037 0.00 0.00 0.00 4.35
2897 4944 7.552687 CCAGAATAGTAGTGATAAAACAAGCCA 59.447 37.037 0.00 0.00 0.00 4.75
2898 4945 9.113838 CAGAATAGTAGTGATAAAACAAGCCAT 57.886 33.333 0.00 0.00 0.00 4.40
2899 4946 9.113838 AGAATAGTAGTGATAAAACAAGCCATG 57.886 33.333 0.00 0.00 0.00 3.66
2900 4947 5.567138 AGTAGTGATAAAACAAGCCATGC 57.433 39.130 0.00 0.00 0.00 4.06
2901 4948 3.492421 AGTGATAAAACAAGCCATGCG 57.508 42.857 0.00 0.00 0.00 4.73
2902 4949 3.081061 AGTGATAAAACAAGCCATGCGA 58.919 40.909 0.00 0.00 0.00 5.10
2903 4950 3.696051 AGTGATAAAACAAGCCATGCGAT 59.304 39.130 0.00 0.00 0.00 4.58
2904 4951 4.158394 AGTGATAAAACAAGCCATGCGATT 59.842 37.500 0.00 0.00 0.00 3.34
2905 4952 4.864247 GTGATAAAACAAGCCATGCGATTT 59.136 37.500 0.00 0.00 0.00 2.17
2906 4953 4.863689 TGATAAAACAAGCCATGCGATTTG 59.136 37.500 0.00 0.00 0.00 2.32
2907 4954 3.383620 AAAACAAGCCATGCGATTTGA 57.616 38.095 0.00 0.00 0.00 2.69
2908 4955 2.352503 AACAAGCCATGCGATTTGAC 57.647 45.000 0.00 0.00 0.00 3.18
2909 4956 1.246649 ACAAGCCATGCGATTTGACA 58.753 45.000 0.00 0.00 0.00 3.58
2910 4957 1.612950 ACAAGCCATGCGATTTGACAA 59.387 42.857 0.00 0.00 0.00 3.18
2911 4958 2.035704 ACAAGCCATGCGATTTGACAAA 59.964 40.909 2.48 2.48 0.00 2.83
2912 4959 2.642139 AGCCATGCGATTTGACAAAG 57.358 45.000 6.77 0.00 0.00 2.77
2913 4960 2.161855 AGCCATGCGATTTGACAAAGA 58.838 42.857 6.77 0.00 0.00 2.52
2914 4961 2.163010 AGCCATGCGATTTGACAAAGAG 59.837 45.455 6.77 4.17 0.00 2.85
2915 4962 2.162208 GCCATGCGATTTGACAAAGAGA 59.838 45.455 6.77 0.00 0.00 3.10
2916 4963 3.366273 GCCATGCGATTTGACAAAGAGAA 60.366 43.478 6.77 0.00 0.00 2.87
2917 4964 4.409570 CCATGCGATTTGACAAAGAGAAG 58.590 43.478 6.77 0.00 0.00 2.85
2918 4965 4.409570 CATGCGATTTGACAAAGAGAAGG 58.590 43.478 6.77 0.00 0.00 3.46
2919 4966 3.476552 TGCGATTTGACAAAGAGAAGGT 58.523 40.909 6.77 0.00 0.00 3.50
2920 4967 4.637276 TGCGATTTGACAAAGAGAAGGTA 58.363 39.130 6.77 0.00 0.00 3.08
2921 4968 5.060506 TGCGATTTGACAAAGAGAAGGTAA 58.939 37.500 6.77 0.00 0.00 2.85
2922 4969 5.529430 TGCGATTTGACAAAGAGAAGGTAAA 59.471 36.000 6.77 0.00 0.00 2.01
2923 4970 5.851703 GCGATTTGACAAAGAGAAGGTAAAC 59.148 40.000 6.77 0.00 0.00 2.01
2924 4971 6.512741 GCGATTTGACAAAGAGAAGGTAAACA 60.513 38.462 6.77 0.00 0.00 2.83
2925 4972 7.414436 CGATTTGACAAAGAGAAGGTAAACAA 58.586 34.615 6.77 0.00 0.00 2.83
2926 4973 7.376072 CGATTTGACAAAGAGAAGGTAAACAAC 59.624 37.037 6.77 0.00 0.00 3.32
2927 4974 7.696992 TTTGACAAAGAGAAGGTAAACAACT 57.303 32.000 0.00 0.00 0.00 3.16
2928 4975 7.696992 TTGACAAAGAGAAGGTAAACAACTT 57.303 32.000 0.00 0.00 0.00 2.66
2929 4976 7.316544 TGACAAAGAGAAGGTAAACAACTTC 57.683 36.000 0.00 0.00 42.56 3.01
2963 5010 9.862371 ATGAACTGTAACTAAACACATCTAGAG 57.138 33.333 0.00 0.00 0.00 2.43
2964 5011 7.813148 TGAACTGTAACTAAACACATCTAGAGC 59.187 37.037 0.00 0.00 0.00 4.09
2965 5012 7.228314 ACTGTAACTAAACACATCTAGAGCA 57.772 36.000 0.00 0.00 0.00 4.26
2966 5013 7.316640 ACTGTAACTAAACACATCTAGAGCAG 58.683 38.462 0.00 0.00 0.00 4.24
2967 5014 7.176865 ACTGTAACTAAACACATCTAGAGCAGA 59.823 37.037 0.00 0.00 37.79 4.26
2968 5015 8.067751 TGTAACTAAACACATCTAGAGCAGAT 57.932 34.615 0.00 0.00 45.35 2.90
2969 5016 9.185680 TGTAACTAAACACATCTAGAGCAGATA 57.814 33.333 0.00 0.00 42.40 1.98
2970 5017 9.672086 GTAACTAAACACATCTAGAGCAGATAG 57.328 37.037 0.00 0.00 42.40 2.08
2971 5018 7.889873 ACTAAACACATCTAGAGCAGATAGT 57.110 36.000 0.00 0.41 42.40 2.12
2972 5019 8.982091 ACTAAACACATCTAGAGCAGATAGTA 57.018 34.615 0.00 0.00 42.40 1.82
2973 5020 9.581289 ACTAAACACATCTAGAGCAGATAGTAT 57.419 33.333 0.00 0.00 42.40 2.12
2976 5023 7.624360 ACACATCTAGAGCAGATAGTATAGC 57.376 40.000 0.00 0.00 42.40 2.97
2977 5024 7.171653 ACACATCTAGAGCAGATAGTATAGCA 58.828 38.462 0.00 0.00 42.40 3.49
2978 5025 7.667635 ACACATCTAGAGCAGATAGTATAGCAA 59.332 37.037 0.00 0.00 42.40 3.91
2979 5026 8.183536 CACATCTAGAGCAGATAGTATAGCAAG 58.816 40.741 0.00 4.67 42.40 4.01
2980 5027 7.888021 ACATCTAGAGCAGATAGTATAGCAAGT 59.112 37.037 0.00 0.00 42.40 3.16
2981 5028 8.739039 CATCTAGAGCAGATAGTATAGCAAGTT 58.261 37.037 0.00 0.00 42.40 2.66
2982 5029 8.105097 TCTAGAGCAGATAGTATAGCAAGTTG 57.895 38.462 0.00 0.00 0.00 3.16
2983 5030 5.537188 AGAGCAGATAGTATAGCAAGTTGC 58.463 41.667 20.44 20.44 45.46 4.17
2995 5042 9.559732 AGTATAGCAAGTTGCATATATGAAACA 57.440 29.630 30.09 15.10 46.59 2.83
2996 5043 9.817365 GTATAGCAAGTTGCATATATGAAACAG 57.183 33.333 30.09 23.74 46.59 3.16
2997 5044 8.681486 ATAGCAAGTTGCATATATGAAACAGA 57.319 30.769 30.09 15.18 46.59 3.41
2998 5045 7.024340 AGCAAGTTGCATATATGAAACAGAG 57.976 36.000 30.09 21.57 46.59 3.35
2999 5046 6.600822 AGCAAGTTGCATATATGAAACAGAGT 59.399 34.615 30.09 13.05 46.59 3.24
3000 5047 6.909357 GCAAGTTGCATATATGAAACAGAGTC 59.091 38.462 30.09 15.06 46.59 3.36
3001 5048 7.201679 GCAAGTTGCATATATGAAACAGAGTCT 60.202 37.037 30.09 12.13 46.59 3.24
3002 5049 9.317936 CAAGTTGCATATATGAAACAGAGTCTA 57.682 33.333 30.09 0.00 46.59 2.59
3003 5050 9.890629 AAGTTGCATATATGAAACAGAGTCTAA 57.109 29.630 30.09 0.00 46.59 2.10
3004 5051 9.319143 AGTTGCATATATGAAACAGAGTCTAAC 57.681 33.333 30.09 7.77 46.59 2.34
3005 5052 9.098355 GTTGCATATATGAAACAGAGTCTAACA 57.902 33.333 25.77 4.24 44.17 2.41
3006 5053 9.836864 TTGCATATATGAAACAGAGTCTAACAT 57.163 29.630 17.10 0.00 0.00 2.71
3014 5061 8.239038 TGAAACAGAGTCTAACATATCTAGGG 57.761 38.462 0.00 0.00 0.00 3.53
3015 5062 6.658188 AACAGAGTCTAACATATCTAGGGC 57.342 41.667 0.00 0.00 0.00 5.19
3016 5063 5.706447 ACAGAGTCTAACATATCTAGGGCA 58.294 41.667 0.00 0.00 0.00 5.36
3017 5064 6.136857 ACAGAGTCTAACATATCTAGGGCAA 58.863 40.000 0.00 0.00 0.00 4.52
3018 5065 6.611642 ACAGAGTCTAACATATCTAGGGCAAA 59.388 38.462 0.00 0.00 0.00 3.68
3019 5066 6.926272 CAGAGTCTAACATATCTAGGGCAAAC 59.074 42.308 0.00 0.00 0.00 2.93
3020 5067 6.611642 AGAGTCTAACATATCTAGGGCAAACA 59.388 38.462 0.00 0.00 0.00 2.83
3021 5068 6.583562 AGTCTAACATATCTAGGGCAAACAC 58.416 40.000 0.00 0.00 0.00 3.32
3022 5069 6.384305 AGTCTAACATATCTAGGGCAAACACT 59.616 38.462 0.00 0.00 0.00 3.55
3023 5070 7.563924 AGTCTAACATATCTAGGGCAAACACTA 59.436 37.037 0.00 0.00 0.00 2.74
3024 5071 7.868415 GTCTAACATATCTAGGGCAAACACTAG 59.132 40.741 0.00 0.00 38.38 2.57
3025 5072 6.808321 AACATATCTAGGGCAAACACTAGA 57.192 37.500 7.46 7.46 46.80 2.43
3026 5073 6.808321 ACATATCTAGGGCAAACACTAGAA 57.192 37.500 8.98 0.68 46.12 2.10
3027 5074 6.583562 ACATATCTAGGGCAAACACTAGAAC 58.416 40.000 8.98 0.00 46.12 3.01
3028 5075 6.156256 ACATATCTAGGGCAAACACTAGAACA 59.844 38.462 8.98 1.65 46.12 3.18
3029 5076 4.967084 TCTAGGGCAAACACTAGAACAA 57.033 40.909 2.59 0.00 41.84 2.83
3030 5077 4.894784 TCTAGGGCAAACACTAGAACAAG 58.105 43.478 2.59 0.00 41.84 3.16
3031 5078 2.863809 AGGGCAAACACTAGAACAAGG 58.136 47.619 0.00 0.00 0.00 3.61
3032 5079 2.441750 AGGGCAAACACTAGAACAAGGA 59.558 45.455 0.00 0.00 0.00 3.36
3033 5080 3.117663 AGGGCAAACACTAGAACAAGGAA 60.118 43.478 0.00 0.00 0.00 3.36
3034 5081 3.004419 GGGCAAACACTAGAACAAGGAAC 59.996 47.826 0.00 0.00 0.00 3.62
3035 5082 9.791025 CTAGGGCAAACACTAGAACAAGGAACT 62.791 44.444 0.00 0.00 39.03 3.01
3036 5083 4.261197 GGCAAACACTAGAACAAGGAACTG 60.261 45.833 0.00 0.00 40.86 3.16
3037 5084 4.335594 GCAAACACTAGAACAAGGAACTGT 59.664 41.667 0.00 0.00 40.86 3.55
3038 5085 5.526111 GCAAACACTAGAACAAGGAACTGTA 59.474 40.000 0.00 0.00 40.86 2.74
3039 5086 6.292919 GCAAACACTAGAACAAGGAACTGTAG 60.293 42.308 0.00 0.00 40.86 2.74
3040 5087 4.884247 ACACTAGAACAAGGAACTGTAGC 58.116 43.478 0.00 0.00 40.86 3.58
3041 5088 4.344102 ACACTAGAACAAGGAACTGTAGCA 59.656 41.667 0.00 0.00 40.86 3.49
3042 5089 4.926238 CACTAGAACAAGGAACTGTAGCAG 59.074 45.833 0.00 0.00 40.86 4.24
3043 5090 3.409026 AGAACAAGGAACTGTAGCAGG 57.591 47.619 1.08 0.00 40.86 4.85
3044 5091 2.039084 AGAACAAGGAACTGTAGCAGGG 59.961 50.000 1.08 0.00 40.86 4.45
3045 5092 1.435256 ACAAGGAACTGTAGCAGGGT 58.565 50.000 1.08 0.00 40.86 4.34
3046 5093 1.348036 ACAAGGAACTGTAGCAGGGTC 59.652 52.381 1.08 0.00 40.86 4.46
3047 5094 1.625818 CAAGGAACTGTAGCAGGGTCT 59.374 52.381 1.08 0.00 40.86 3.85
3048 5095 1.562783 AGGAACTGTAGCAGGGTCTC 58.437 55.000 1.08 0.00 37.18 3.36
3049 5096 1.077993 AGGAACTGTAGCAGGGTCTCT 59.922 52.381 1.08 0.00 37.18 3.10
3050 5097 2.312140 AGGAACTGTAGCAGGGTCTCTA 59.688 50.000 1.08 0.00 37.18 2.43
3051 5098 3.097614 GGAACTGTAGCAGGGTCTCTAA 58.902 50.000 1.08 0.00 35.51 2.10
3052 5099 3.119065 GGAACTGTAGCAGGGTCTCTAAC 60.119 52.174 1.08 0.00 35.51 2.34
3053 5100 3.170991 ACTGTAGCAGGGTCTCTAACA 57.829 47.619 1.08 0.00 35.51 2.41
3054 5101 3.093057 ACTGTAGCAGGGTCTCTAACAG 58.907 50.000 7.26 7.26 36.65 3.16
3055 5102 3.245300 ACTGTAGCAGGGTCTCTAACAGA 60.245 47.826 13.36 0.00 35.36 3.41
3056 5103 3.764434 CTGTAGCAGGGTCTCTAACAGAA 59.236 47.826 3.89 0.00 34.48 3.02
3057 5104 4.157246 TGTAGCAGGGTCTCTAACAGAAA 58.843 43.478 0.00 0.00 30.72 2.52
3058 5105 3.971245 AGCAGGGTCTCTAACAGAAAG 57.029 47.619 0.00 0.00 30.72 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 9.847224 AGAAATTAAGTCTTCCAAAGTCTGTTA 57.153 29.630 0.00 0.00 0.00 2.41
55 56 8.383318 TCAGAAATTAAGTCTTCCAAAGTCTG 57.617 34.615 0.00 0.00 0.00 3.51
56 57 8.432805 TCTCAGAAATTAAGTCTTCCAAAGTCT 58.567 33.333 0.00 0.00 0.00 3.24
110 111 2.751806 CTCTTCTTGGCCAACTTGATCC 59.248 50.000 16.05 0.00 0.00 3.36
210 241 5.211973 TCTGTATCAGTTGGAAGAGGCTAT 58.788 41.667 0.00 0.00 32.61 2.97
230 261 2.031314 CACTTGCAGCGGTGATAATCTG 59.969 50.000 20.69 7.04 35.69 2.90
242 273 2.666190 TCGTGCTCCACTTGCAGC 60.666 61.111 0.00 0.00 41.41 5.25
281 312 1.751351 GCTCCTGCTTTTAATCCCCAC 59.249 52.381 0.00 0.00 36.03 4.61
299 330 4.749310 CAGCTCCGCGTTCAGGCT 62.749 66.667 4.92 4.00 0.00 4.58
321 352 3.905678 CCTCGCTACAGCCGGGAG 61.906 72.222 2.18 0.00 40.10 4.30
324 355 2.298158 AATGACCTCGCTACAGCCGG 62.298 60.000 0.00 0.00 37.91 6.13
327 358 2.860735 CAAGTAATGACCTCGCTACAGC 59.139 50.000 0.00 0.00 37.78 4.40
334 365 0.810031 CGCCCCAAGTAATGACCTCG 60.810 60.000 0.00 0.00 0.00 4.63
337 368 1.308998 CATCGCCCCAAGTAATGACC 58.691 55.000 0.00 0.00 0.00 4.02
345 376 1.076044 ATTTCCCCATCGCCCCAAG 60.076 57.895 0.00 0.00 0.00 3.61
379 410 1.521580 GCTGCTATGGATCCAAGCTC 58.478 55.000 31.32 23.86 37.16 4.09
451 482 0.324091 TAAGGAGGGTCCGTGGAGAC 60.324 60.000 0.00 0.00 42.75 3.36
455 486 1.134491 GTCAATAAGGAGGGTCCGTGG 60.134 57.143 0.00 0.00 42.75 4.94
578 609 6.387041 TCAATTCAAATCCATGATCAGCTC 57.613 37.500 0.09 0.00 0.00 4.09
582 613 5.889289 TCTGCTCAATTCAAATCCATGATCA 59.111 36.000 0.00 0.00 0.00 2.92
682 713 3.468770 TCTGCTCTGATCTACGTACCTC 58.531 50.000 0.00 0.00 0.00 3.85
685 716 4.025229 CAGTCTCTGCTCTGATCTACGTAC 60.025 50.000 0.00 0.00 34.02 3.67
687 718 2.942376 CAGTCTCTGCTCTGATCTACGT 59.058 50.000 0.00 0.00 34.02 3.57
688 719 2.290367 CCAGTCTCTGCTCTGATCTACG 59.710 54.545 0.00 0.00 34.02 3.51
895 1122 5.258622 GCGTTGCTGTCTGACTTTATATTG 58.741 41.667 9.51 0.00 0.00 1.90
896 1123 4.032900 CGCGTTGCTGTCTGACTTTATATT 59.967 41.667 9.51 0.00 0.00 1.28
897 1124 3.551890 CGCGTTGCTGTCTGACTTTATAT 59.448 43.478 9.51 0.00 0.00 0.86
898 1125 2.921121 CGCGTTGCTGTCTGACTTTATA 59.079 45.455 9.51 0.00 0.00 0.98
899 1126 1.726791 CGCGTTGCTGTCTGACTTTAT 59.273 47.619 9.51 0.00 0.00 1.40
900 1127 1.136690 CGCGTTGCTGTCTGACTTTA 58.863 50.000 9.51 0.00 0.00 1.85
901 1128 1.934463 CGCGTTGCTGTCTGACTTT 59.066 52.632 9.51 0.00 0.00 2.66
1021 1297 1.725641 CTAACCATCAGCTTCACGCA 58.274 50.000 0.00 0.00 42.61 5.24
1070 1346 3.900892 CGTACCTCGGCGGCTGAT 61.901 66.667 12.67 0.61 35.61 2.90
1167 1443 0.251832 TGGAGAAGTCGGAGAAGCCT 60.252 55.000 0.00 0.00 39.69 4.58
1320 1596 1.679977 CAGGTAGACCCGGAACCGA 60.680 63.158 15.07 0.00 42.83 4.69
1613 2010 3.521560 GTGTCATTTATCGAGTCTGCCA 58.478 45.455 0.00 0.00 0.00 4.92
1625 2022 5.000591 TGATCAAAGAAGCCGTGTCATTTA 58.999 37.500 0.00 0.00 0.00 1.40
1792 2189 4.685026 CGCTATCCGCCGTCCGAG 62.685 72.222 0.00 0.00 40.02 4.63
1818 2215 0.103390 TCGAGTCTGCCGTCAACAAA 59.897 50.000 0.00 0.00 0.00 2.83
1838 2235 5.000591 TGATCAAAGAAGCCGTGTCATTTA 58.999 37.500 0.00 0.00 0.00 1.40
1844 2241 1.202758 TGGTGATCAAAGAAGCCGTGT 60.203 47.619 0.00 0.00 0.00 4.49
1846 2243 1.072331 AGTGGTGATCAAAGAAGCCGT 59.928 47.619 0.00 0.00 0.00 5.68
1940 2337 1.819632 GCCTGGCACACCGGATTAG 60.820 63.158 15.17 0.00 46.41 1.73
2007 2404 2.265904 TACGAGGATGATCGCCGGG 61.266 63.158 2.18 0.00 46.60 5.73
2111 2520 8.635765 AACATATATCAAACTATTCCCGCAAT 57.364 30.769 0.00 0.00 0.00 3.56
2239 2899 4.766373 ACAACAACATGCTACCATCAATGA 59.234 37.500 0.00 0.00 0.00 2.57
2278 2938 3.426159 CCCACGTCAAACATGCACTTATC 60.426 47.826 0.00 0.00 0.00 1.75
2386 3054 4.201950 CCATGAATGCCAGTTTGTAGTAGC 60.202 45.833 0.00 0.00 0.00 3.58
2389 3057 2.493278 GCCATGAATGCCAGTTTGTAGT 59.507 45.455 0.00 0.00 0.00 2.73
2697 4742 7.097834 AGCTTGACATAGTAAAGAAGGTACAC 58.902 38.462 0.00 0.00 0.00 2.90
2812 4859 7.397892 TTCGGTAAATTGCTCATATTTCCAA 57.602 32.000 0.00 0.00 0.00 3.53
2813 4860 7.284261 TCATTCGGTAAATTGCTCATATTTCCA 59.716 33.333 0.00 0.00 0.00 3.53
2814 4861 7.648142 TCATTCGGTAAATTGCTCATATTTCC 58.352 34.615 0.00 0.00 0.00 3.13
2815 4862 9.683069 AATCATTCGGTAAATTGCTCATATTTC 57.317 29.630 0.00 0.00 0.00 2.17
2846 4893 9.331282 GGTCATGCTTTATCTAGTATTTCTGTT 57.669 33.333 0.00 0.00 0.00 3.16
2847 4894 8.486210 TGGTCATGCTTTATCTAGTATTTCTGT 58.514 33.333 0.00 0.00 0.00 3.41
2848 4895 8.893219 TGGTCATGCTTTATCTAGTATTTCTG 57.107 34.615 0.00 0.00 0.00 3.02
2849 4896 8.928448 TCTGGTCATGCTTTATCTAGTATTTCT 58.072 33.333 0.00 0.00 0.00 2.52
2850 4897 9.547753 TTCTGGTCATGCTTTATCTAGTATTTC 57.452 33.333 0.00 0.00 0.00 2.17
2854 4901 9.368416 ACTATTCTGGTCATGCTTTATCTAGTA 57.632 33.333 0.00 0.00 0.00 1.82
2855 4902 8.256356 ACTATTCTGGTCATGCTTTATCTAGT 57.744 34.615 0.00 0.00 0.00 2.57
2856 4903 9.853555 CTACTATTCTGGTCATGCTTTATCTAG 57.146 37.037 0.00 0.00 0.00 2.43
2857 4904 9.368416 ACTACTATTCTGGTCATGCTTTATCTA 57.632 33.333 0.00 0.00 0.00 1.98
2858 4905 8.147058 CACTACTATTCTGGTCATGCTTTATCT 58.853 37.037 0.00 0.00 0.00 1.98
2859 4906 8.144478 TCACTACTATTCTGGTCATGCTTTATC 58.856 37.037 0.00 0.00 0.00 1.75
2860 4907 8.023021 TCACTACTATTCTGGTCATGCTTTAT 57.977 34.615 0.00 0.00 0.00 1.40
2861 4908 7.418337 TCACTACTATTCTGGTCATGCTTTA 57.582 36.000 0.00 0.00 0.00 1.85
2862 4909 6.299805 TCACTACTATTCTGGTCATGCTTT 57.700 37.500 0.00 0.00 0.00 3.51
2863 4910 5.939764 TCACTACTATTCTGGTCATGCTT 57.060 39.130 0.00 0.00 0.00 3.91
2864 4911 7.603180 TTATCACTACTATTCTGGTCATGCT 57.397 36.000 0.00 0.00 0.00 3.79
2865 4912 8.552034 GTTTTATCACTACTATTCTGGTCATGC 58.448 37.037 0.00 0.00 0.00 4.06
2866 4913 9.599866 TGTTTTATCACTACTATTCTGGTCATG 57.400 33.333 0.00 0.00 0.00 3.07
2868 4915 9.653287 CTTGTTTTATCACTACTATTCTGGTCA 57.347 33.333 0.00 0.00 0.00 4.02
2869 4916 8.604890 GCTTGTTTTATCACTACTATTCTGGTC 58.395 37.037 0.00 0.00 0.00 4.02
2870 4917 7.553044 GGCTTGTTTTATCACTACTATTCTGGT 59.447 37.037 0.00 0.00 0.00 4.00
2871 4918 7.552687 TGGCTTGTTTTATCACTACTATTCTGG 59.447 37.037 0.00 0.00 0.00 3.86
2872 4919 8.492673 TGGCTTGTTTTATCACTACTATTCTG 57.507 34.615 0.00 0.00 0.00 3.02
2873 4920 9.113838 CATGGCTTGTTTTATCACTACTATTCT 57.886 33.333 0.00 0.00 0.00 2.40
2874 4921 7.857885 GCATGGCTTGTTTTATCACTACTATTC 59.142 37.037 2.12 0.00 0.00 1.75
2875 4922 7.467267 CGCATGGCTTGTTTTATCACTACTATT 60.467 37.037 2.12 0.00 0.00 1.73
2876 4923 6.017934 CGCATGGCTTGTTTTATCACTACTAT 60.018 38.462 2.12 0.00 0.00 2.12
2877 4924 5.293324 CGCATGGCTTGTTTTATCACTACTA 59.707 40.000 2.12 0.00 0.00 1.82
2878 4925 4.094887 CGCATGGCTTGTTTTATCACTACT 59.905 41.667 2.12 0.00 0.00 2.57
2879 4926 4.094294 TCGCATGGCTTGTTTTATCACTAC 59.906 41.667 2.12 0.00 0.00 2.73
2880 4927 4.257731 TCGCATGGCTTGTTTTATCACTA 58.742 39.130 2.12 0.00 0.00 2.74
2881 4928 3.081061 TCGCATGGCTTGTTTTATCACT 58.919 40.909 2.12 0.00 0.00 3.41
2882 4929 3.485947 TCGCATGGCTTGTTTTATCAC 57.514 42.857 2.12 0.00 0.00 3.06
2883 4930 4.717233 AATCGCATGGCTTGTTTTATCA 57.283 36.364 2.12 0.00 0.00 2.15
2884 4931 5.004726 GTCAAATCGCATGGCTTGTTTTATC 59.995 40.000 2.12 0.00 0.00 1.75
2885 4932 4.864247 GTCAAATCGCATGGCTTGTTTTAT 59.136 37.500 2.12 0.00 0.00 1.40
2886 4933 4.233789 GTCAAATCGCATGGCTTGTTTTA 58.766 39.130 2.12 0.00 0.00 1.52
2887 4934 3.059166 GTCAAATCGCATGGCTTGTTTT 58.941 40.909 2.12 0.00 0.00 2.43
2888 4935 2.035704 TGTCAAATCGCATGGCTTGTTT 59.964 40.909 2.12 0.00 0.00 2.83
2889 4936 1.612950 TGTCAAATCGCATGGCTTGTT 59.387 42.857 2.12 0.00 0.00 2.83
2890 4937 1.246649 TGTCAAATCGCATGGCTTGT 58.753 45.000 2.12 0.00 0.00 3.16
2891 4938 2.350899 TTGTCAAATCGCATGGCTTG 57.649 45.000 0.00 0.00 0.00 4.01
2892 4939 2.557924 TCTTTGTCAAATCGCATGGCTT 59.442 40.909 0.00 0.00 0.00 4.35
2893 4940 2.161855 TCTTTGTCAAATCGCATGGCT 58.838 42.857 0.00 0.00 0.00 4.75
2894 4941 2.162208 TCTCTTTGTCAAATCGCATGGC 59.838 45.455 0.00 0.00 0.00 4.40
2895 4942 4.409570 CTTCTCTTTGTCAAATCGCATGG 58.590 43.478 0.00 0.00 0.00 3.66
2896 4943 4.083110 ACCTTCTCTTTGTCAAATCGCATG 60.083 41.667 0.00 0.00 0.00 4.06
2897 4944 4.074970 ACCTTCTCTTTGTCAAATCGCAT 58.925 39.130 0.00 0.00 0.00 4.73
2898 4945 3.476552 ACCTTCTCTTTGTCAAATCGCA 58.523 40.909 0.00 0.00 0.00 5.10
2899 4946 5.607119 TTACCTTCTCTTTGTCAAATCGC 57.393 39.130 0.00 0.00 0.00 4.58
2900 4947 6.954944 TGTTTACCTTCTCTTTGTCAAATCG 58.045 36.000 0.00 0.00 0.00 3.34
2901 4948 8.406297 AGTTGTTTACCTTCTCTTTGTCAAATC 58.594 33.333 0.00 0.00 0.00 2.17
2902 4949 8.293699 AGTTGTTTACCTTCTCTTTGTCAAAT 57.706 30.769 0.00 0.00 0.00 2.32
2903 4950 7.696992 AGTTGTTTACCTTCTCTTTGTCAAA 57.303 32.000 0.00 0.00 0.00 2.69
2904 4951 7.610305 AGAAGTTGTTTACCTTCTCTTTGTCAA 59.390 33.333 0.00 0.00 31.32 3.18
2905 4952 7.110155 AGAAGTTGTTTACCTTCTCTTTGTCA 58.890 34.615 0.00 0.00 31.32 3.58
2906 4953 7.555306 AGAAGTTGTTTACCTTCTCTTTGTC 57.445 36.000 0.00 0.00 31.32 3.18
2907 4954 7.610305 TGAAGAAGTTGTTTACCTTCTCTTTGT 59.390 33.333 2.68 0.00 35.40 2.83
2908 4955 7.985476 TGAAGAAGTTGTTTACCTTCTCTTTG 58.015 34.615 2.68 0.00 35.40 2.77
2909 4956 8.753497 ATGAAGAAGTTGTTTACCTTCTCTTT 57.247 30.769 2.68 0.00 35.40 2.52
2937 4984 9.862371 CTCTAGATGTGTTTAGTTACAGTTCAT 57.138 33.333 0.00 0.00 0.00 2.57
2938 4985 7.813148 GCTCTAGATGTGTTTAGTTACAGTTCA 59.187 37.037 0.00 0.00 0.00 3.18
2939 4986 7.813148 TGCTCTAGATGTGTTTAGTTACAGTTC 59.187 37.037 0.00 0.00 0.00 3.01
2940 4987 7.667557 TGCTCTAGATGTGTTTAGTTACAGTT 58.332 34.615 0.00 0.00 0.00 3.16
2941 4988 7.176865 TCTGCTCTAGATGTGTTTAGTTACAGT 59.823 37.037 0.00 0.00 0.00 3.55
2942 4989 7.539436 TCTGCTCTAGATGTGTTTAGTTACAG 58.461 38.462 0.00 0.00 0.00 2.74
2943 4990 7.462571 TCTGCTCTAGATGTGTTTAGTTACA 57.537 36.000 0.00 0.00 0.00 2.41
2944 4991 9.672086 CTATCTGCTCTAGATGTGTTTAGTTAC 57.328 37.037 0.00 0.00 45.66 2.50
2945 4992 9.409918 ACTATCTGCTCTAGATGTGTTTAGTTA 57.590 33.333 0.00 0.00 45.66 2.24
2946 4993 8.299990 ACTATCTGCTCTAGATGTGTTTAGTT 57.700 34.615 0.00 0.00 45.66 2.24
2947 4994 7.889873 ACTATCTGCTCTAGATGTGTTTAGT 57.110 36.000 0.00 0.00 45.66 2.24
2950 4997 8.519526 GCTATACTATCTGCTCTAGATGTGTTT 58.480 37.037 0.00 0.00 45.66 2.83
2951 4998 7.667635 TGCTATACTATCTGCTCTAGATGTGTT 59.332 37.037 0.00 0.00 45.66 3.32
2952 4999 7.171653 TGCTATACTATCTGCTCTAGATGTGT 58.828 38.462 0.00 0.00 45.66 3.72
2953 5000 7.622893 TGCTATACTATCTGCTCTAGATGTG 57.377 40.000 0.00 0.00 45.66 3.21
2954 5001 7.888021 ACTTGCTATACTATCTGCTCTAGATGT 59.112 37.037 0.00 0.00 45.66 3.06
2955 5002 8.279970 ACTTGCTATACTATCTGCTCTAGATG 57.720 38.462 0.00 0.00 45.66 2.90
2957 5004 7.308891 GCAACTTGCTATACTATCTGCTCTAGA 60.309 40.741 6.50 0.00 40.96 2.43
2958 5005 6.806249 GCAACTTGCTATACTATCTGCTCTAG 59.194 42.308 6.50 0.00 40.96 2.43
2959 5006 6.265422 TGCAACTTGCTATACTATCTGCTCTA 59.735 38.462 14.78 0.00 45.31 2.43
2960 5007 5.069648 TGCAACTTGCTATACTATCTGCTCT 59.930 40.000 14.78 0.00 45.31 4.09
2961 5008 5.292765 TGCAACTTGCTATACTATCTGCTC 58.707 41.667 14.78 0.00 45.31 4.26
2962 5009 5.282055 TGCAACTTGCTATACTATCTGCT 57.718 39.130 14.78 0.00 45.31 4.24
2963 5010 7.840342 ATATGCAACTTGCTATACTATCTGC 57.160 36.000 14.78 0.00 45.31 4.26
2969 5016 9.559732 TGTTTCATATATGCAACTTGCTATACT 57.440 29.630 22.98 0.00 45.31 2.12
2970 5017 9.817365 CTGTTTCATATATGCAACTTGCTATAC 57.183 33.333 22.98 4.95 45.31 1.47
2971 5018 9.777297 TCTGTTTCATATATGCAACTTGCTATA 57.223 29.630 22.98 13.00 45.31 1.31
2972 5019 8.681486 TCTGTTTCATATATGCAACTTGCTAT 57.319 30.769 22.98 11.53 45.31 2.97
2973 5020 7.770433 ACTCTGTTTCATATATGCAACTTGCTA 59.230 33.333 22.98 7.21 45.31 3.49
2974 5021 6.600822 ACTCTGTTTCATATATGCAACTTGCT 59.399 34.615 22.98 6.54 45.31 3.91
2975 5022 6.789262 ACTCTGTTTCATATATGCAACTTGC 58.211 36.000 22.98 6.82 45.29 4.01
2976 5023 8.206325 AGACTCTGTTTCATATATGCAACTTG 57.794 34.615 22.98 17.05 35.44 3.16
2977 5024 9.890629 TTAGACTCTGTTTCATATATGCAACTT 57.109 29.630 22.98 9.60 35.44 2.66
2978 5025 9.319143 GTTAGACTCTGTTTCATATATGCAACT 57.681 33.333 22.98 8.16 35.44 3.16
2979 5026 9.098355 TGTTAGACTCTGTTTCATATATGCAAC 57.902 33.333 18.00 18.00 35.06 4.17
2980 5027 9.836864 ATGTTAGACTCTGTTTCATATATGCAA 57.163 29.630 7.92 0.34 0.00 4.08
2988 5035 8.865090 CCCTAGATATGTTAGACTCTGTTTCAT 58.135 37.037 0.00 0.00 0.00 2.57
2989 5036 7.201920 GCCCTAGATATGTTAGACTCTGTTTCA 60.202 40.741 0.00 0.00 0.00 2.69
2990 5037 7.149307 GCCCTAGATATGTTAGACTCTGTTTC 58.851 42.308 0.00 0.00 0.00 2.78
2991 5038 6.611642 TGCCCTAGATATGTTAGACTCTGTTT 59.388 38.462 0.00 0.00 0.00 2.83
2992 5039 6.136857 TGCCCTAGATATGTTAGACTCTGTT 58.863 40.000 0.00 0.00 0.00 3.16
2993 5040 5.706447 TGCCCTAGATATGTTAGACTCTGT 58.294 41.667 0.00 0.00 0.00 3.41
2994 5041 6.656632 TTGCCCTAGATATGTTAGACTCTG 57.343 41.667 0.00 0.00 0.00 3.35
2995 5042 6.611642 TGTTTGCCCTAGATATGTTAGACTCT 59.388 38.462 0.00 0.00 0.00 3.24
2996 5043 6.702282 GTGTTTGCCCTAGATATGTTAGACTC 59.298 42.308 0.00 0.00 0.00 3.36
2997 5044 6.384305 AGTGTTTGCCCTAGATATGTTAGACT 59.616 38.462 0.00 0.00 0.00 3.24
2998 5045 6.583562 AGTGTTTGCCCTAGATATGTTAGAC 58.416 40.000 0.00 0.00 0.00 2.59
2999 5046 6.808321 AGTGTTTGCCCTAGATATGTTAGA 57.192 37.500 0.00 0.00 0.00 2.10
3000 5047 7.952671 TCTAGTGTTTGCCCTAGATATGTTAG 58.047 38.462 0.00 0.00 35.82 2.34
3001 5048 7.907841 TCTAGTGTTTGCCCTAGATATGTTA 57.092 36.000 0.00 0.00 35.82 2.41
3002 5049 6.808321 TCTAGTGTTTGCCCTAGATATGTT 57.192 37.500 0.00 0.00 35.82 2.71
3003 5050 6.156256 TGTTCTAGTGTTTGCCCTAGATATGT 59.844 38.462 0.00 0.00 39.40 2.29
3004 5051 6.582636 TGTTCTAGTGTTTGCCCTAGATATG 58.417 40.000 0.00 0.00 39.40 1.78
3005 5052 6.808321 TGTTCTAGTGTTTGCCCTAGATAT 57.192 37.500 0.00 0.00 39.40 1.63
3006 5053 6.351881 CCTTGTTCTAGTGTTTGCCCTAGATA 60.352 42.308 0.00 0.00 39.40 1.98
3007 5054 5.491982 CTTGTTCTAGTGTTTGCCCTAGAT 58.508 41.667 0.00 0.00 39.40 1.98
3008 5055 4.262894 CCTTGTTCTAGTGTTTGCCCTAGA 60.263 45.833 0.00 0.00 38.26 2.43
3009 5056 4.003648 CCTTGTTCTAGTGTTTGCCCTAG 58.996 47.826 0.00 0.00 33.46 3.02
3010 5057 3.649023 TCCTTGTTCTAGTGTTTGCCCTA 59.351 43.478 0.00 0.00 0.00 3.53
3011 5058 2.441750 TCCTTGTTCTAGTGTTTGCCCT 59.558 45.455 0.00 0.00 0.00 5.19
3012 5059 2.858745 TCCTTGTTCTAGTGTTTGCCC 58.141 47.619 0.00 0.00 0.00 5.36
3013 5060 3.883489 AGTTCCTTGTTCTAGTGTTTGCC 59.117 43.478 0.00 0.00 0.00 4.52
3014 5061 4.335594 ACAGTTCCTTGTTCTAGTGTTTGC 59.664 41.667 0.00 0.00 0.00 3.68
3015 5062 6.292919 GCTACAGTTCCTTGTTCTAGTGTTTG 60.293 42.308 0.00 0.00 32.56 2.93
3016 5063 5.758784 GCTACAGTTCCTTGTTCTAGTGTTT 59.241 40.000 0.00 0.00 32.56 2.83
3017 5064 5.163343 TGCTACAGTTCCTTGTTCTAGTGTT 60.163 40.000 0.00 0.00 32.56 3.32
3018 5065 4.344102 TGCTACAGTTCCTTGTTCTAGTGT 59.656 41.667 0.00 0.00 32.56 3.55
3019 5066 4.883083 TGCTACAGTTCCTTGTTCTAGTG 58.117 43.478 0.00 0.00 32.56 2.74
3020 5067 4.021016 CCTGCTACAGTTCCTTGTTCTAGT 60.021 45.833 0.00 0.00 32.56 2.57
3021 5068 4.499183 CCTGCTACAGTTCCTTGTTCTAG 58.501 47.826 0.00 0.00 32.56 2.43
3022 5069 3.260884 CCCTGCTACAGTTCCTTGTTCTA 59.739 47.826 0.00 0.00 32.56 2.10
3023 5070 2.039084 CCCTGCTACAGTTCCTTGTTCT 59.961 50.000 0.00 0.00 32.56 3.01
3024 5071 2.224548 ACCCTGCTACAGTTCCTTGTTC 60.225 50.000 0.00 0.00 32.56 3.18
3025 5072 1.774856 ACCCTGCTACAGTTCCTTGTT 59.225 47.619 0.00 0.00 32.56 2.83
3026 5073 1.348036 GACCCTGCTACAGTTCCTTGT 59.652 52.381 0.00 0.00 35.09 3.16
3027 5074 1.625818 AGACCCTGCTACAGTTCCTTG 59.374 52.381 0.00 0.00 0.00 3.61
3028 5075 1.903183 GAGACCCTGCTACAGTTCCTT 59.097 52.381 0.00 0.00 0.00 3.36
3029 5076 1.077993 AGAGACCCTGCTACAGTTCCT 59.922 52.381 0.00 0.00 0.00 3.36
3030 5077 1.562783 AGAGACCCTGCTACAGTTCC 58.437 55.000 0.00 0.00 0.00 3.62
3031 5078 3.510360 TGTTAGAGACCCTGCTACAGTTC 59.490 47.826 0.00 0.00 0.00 3.01
3032 5079 3.507411 TGTTAGAGACCCTGCTACAGTT 58.493 45.455 0.00 0.00 0.00 3.16
3033 5080 3.093057 CTGTTAGAGACCCTGCTACAGT 58.907 50.000 0.00 0.00 31.38 3.55
3034 5081 3.357203 TCTGTTAGAGACCCTGCTACAG 58.643 50.000 0.00 0.00 34.37 2.74
3035 5082 3.451402 TCTGTTAGAGACCCTGCTACA 57.549 47.619 0.00 0.00 0.00 2.74
3036 5083 4.749976 CTTTCTGTTAGAGACCCTGCTAC 58.250 47.826 0.00 0.00 0.00 3.58
3038 5085 3.971245 CTTTCTGTTAGAGACCCTGCT 57.029 47.619 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.