Multiple sequence alignment - TraesCS7D01G146500

Loading Multiple Alignment...

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 TraesCS7D01G146500 chr7D 100.000 7198 0 0 1 7198 93778422 93785619 0.000000e+00 13293.0
1 TraesCS7D01G146500 chr7D 85.816 282 35 5 4 283 561885773 561885495 1.960000e-75 294.0
2 TraesCS7D01G146500 chr7A 93.365 1884 76 27 2305 4154 96556214 96558082 0.000000e+00 2741.0
3 TraesCS7D01G146500 chr7A 89.770 1740 109 31 1 1734 96553670 96555346 0.000000e+00 2163.0
4 TraesCS7D01G146500 chr7A 95.969 1017 34 6 5298 6311 96559283 96560295 0.000000e+00 1644.0
5 TraesCS7D01G146500 chr7A 96.407 668 15 3 4148 4811 96558157 96558819 0.000000e+00 1092.0
6 TraesCS7D01G146500 chr7A 95.011 441 20 2 4865 5304 96558819 96559258 0.000000e+00 691.0
7 TraesCS7D01G146500 chr7A 96.173 392 14 1 1916 2307 96555743 96556133 2.190000e-179 640.0
8 TraesCS7D01G146500 chr7A 93.243 148 6 1 1735 1878 96555466 96555613 1.570000e-51 215.0
9 TraesCS7D01G146500 chr7A 85.849 212 8 5 7005 7198 96562880 96563087 9.470000e-49 206.0
10 TraesCS7D01G146500 chr7A 89.922 129 9 4 6313 6440 96560499 96560624 5.780000e-36 163.0
11 TraesCS7D01G146500 chr7A 85.714 84 8 2 6850 6929 96562269 96562352 1.290000e-12 86.1
12 TraesCS7D01G146500 chr7B 93.732 1356 61 11 961 2307 46990856 46992196 0.000000e+00 2012.0
13 TraesCS7D01G146500 chr7B 90.210 1379 96 18 5561 6928 46995908 46997258 0.000000e+00 1762.0
14 TraesCS7D01G146500 chr7B 94.139 819 35 3 2305 3118 46992276 46993086 0.000000e+00 1234.0
15 TraesCS7D01G146500 chr7B 96.536 664 18 3 4148 4807 46994460 46995122 0.000000e+00 1094.0
16 TraesCS7D01G146500 chr7B 96.277 376 11 3 4930 5304 46995121 46995494 1.330000e-171 614.0
17 TraesCS7D01G146500 chr7B 95.038 262 12 1 5303 5563 46995524 46995785 1.870000e-110 411.0
18 TraesCS7D01G146500 chr7B 90.816 294 19 5 3867 4154 46994123 46994414 3.150000e-103 387.0
19 TraesCS7D01G146500 chr7B 85.434 357 20 14 3139 3492 46993150 46993477 6.910000e-90 342.0
20 TraesCS7D01G146500 chr7B 85.000 280 38 1 1 280 46989029 46989304 1.530000e-71 281.0
21 TraesCS7D01G146500 chr7B 89.394 198 5 4 7013 7198 46997440 46997633 1.210000e-57 235.0
22 TraesCS7D01G146500 chr7B 82.243 214 35 3 57 269 532146904 532147115 1.600000e-41 182.0
23 TraesCS7D01G146500 chr7B 94.286 70 4 0 5 74 417872971 417873040 2.750000e-19 108.0
24 TraesCS7D01G146500 chr4A 82.452 473 51 19 2674 3138 75431328 75431776 1.130000e-102 385.0
25 TraesCS7D01G146500 chr4B 81.607 473 54 17 2674 3138 483767161 483767608 1.910000e-95 361.0
26 TraesCS7D01G146500 chr2D 86.310 336 34 8 619 948 630636653 630636324 8.880000e-94 355.0
27 TraesCS7D01G146500 chr2D 80.567 247 43 5 443 686 626478685 626478929 1.230000e-42 185.0
28 TraesCS7D01G146500 chr2D 89.041 146 15 1 5159 5304 221650735 221650879 5.740000e-41 180.0
29 TraesCS7D01G146500 chr2D 88.514 148 13 2 4775 4918 17208515 17208662 7.420000e-40 176.0
30 TraesCS7D01G146500 chr5B 83.247 388 40 15 441 804 565494858 565495244 4.160000e-87 333.0
31 TraesCS7D01G146500 chr5B 79.221 308 44 14 665 955 484642244 484641940 5.700000e-46 196.0
32 TraesCS7D01G146500 chr5B 88.060 134 16 0 4778 4911 82212300 82212167 7.470000e-35 159.0
33 TraesCS7D01G146500 chr5B 96.552 58 2 0 2295 2352 462321266 462321209 5.940000e-16 97.1
34 TraesCS7D01G146500 chr5A 89.139 267 25 3 688 951 580514830 580515095 5.380000e-86 329.0
35 TraesCS7D01G146500 chr5D 87.952 249 27 1 441 686 379216887 379217135 2.540000e-74 291.0
36 TraesCS7D01G146500 chr5D 87.586 145 17 1 5161 5304 283009685 283009829 4.470000e-37 167.0
37 TraesCS7D01G146500 chr5D 95.556 45 2 0 2812 2856 356905929 356905973 1.000000e-08 73.1
38 TraesCS7D01G146500 chrUn 88.793 232 23 3 444 672 277779514 277779283 1.530000e-71 281.0
39 TraesCS7D01G146500 chr6D 85.145 276 37 4 1 275 134235522 134235794 5.500000e-71 279.0
40 TraesCS7D01G146500 chr6D 85.199 277 36 5 1 275 134673927 134674200 5.500000e-71 279.0
41 TraesCS7D01G146500 chr6D 89.231 130 14 0 4775 4904 7565198 7565327 5.780000e-36 163.0
42 TraesCS7D01G146500 chr2B 82.090 335 35 14 632 948 217419434 217419107 5.540000e-66 263.0
43 TraesCS7D01G146500 chr2B 79.943 349 48 13 440 782 73808135 73808467 3.360000e-58 237.0
44 TraesCS7D01G146500 chr2B 88.112 143 17 0 4770 4912 171995534 171995392 3.450000e-38 171.0
45 TraesCS7D01G146500 chr2B 86.755 151 20 0 5155 5305 243784817 243784667 1.240000e-37 169.0
46 TraesCS7D01G146500 chr2B 100.000 29 0 0 4033 4061 590926327 590926299 4.000000e-03 54.7
47 TraesCS7D01G146500 chr3D 89.848 197 19 1 1 197 429781728 429781923 1.200000e-62 252.0
48 TraesCS7D01G146500 chr3D 93.496 123 8 0 4782 4904 5616241 5616119 4.440000e-42 183.0
49 TraesCS7D01G146500 chr3D 91.935 124 7 2 4778 4898 383544161 383544038 3.450000e-38 171.0
50 TraesCS7D01G146500 chr3D 90.769 130 6 3 4775 4904 43024290 43024167 1.240000e-37 169.0
51 TraesCS7D01G146500 chr6A 82.971 276 44 3 1 275 175559595 175559868 5.580000e-61 246.0
52 TraesCS7D01G146500 chr2A 85.106 235 35 0 5 239 666979848 666979614 2.590000e-59 241.0
53 TraesCS7D01G146500 chr2A 91.406 128 8 1 4778 4905 445715002 445714878 9.600000e-39 172.0
54 TraesCS7D01G146500 chr4D 90.164 183 18 0 2674 2856 394150003 394150185 9.330000e-59 239.0
55 TraesCS7D01G146500 chr4D 89.349 169 18 0 441 609 418494054 418493886 5.660000e-51 213.0
56 TraesCS7D01G146500 chr1D 90.588 170 16 0 441 610 269822158 269821989 7.270000e-55 226.0
57 TraesCS7D01G146500 chr1D 89.781 137 14 0 5168 5304 314705612 314705748 7.420000e-40 176.0
58 TraesCS7D01G146500 chr1D 88.321 137 16 0 5168 5304 351254856 351254720 1.610000e-36 165.0
59 TraesCS7D01G146500 chr1A 89.759 166 15 2 445 609 79110106 79109942 2.030000e-50 211.0
60 TraesCS7D01G146500 chr1A 90.511 137 13 0 5168 5304 395177455 395177591 1.600000e-41 182.0
61 TraesCS7D01G146500 chr1A 88.321 137 16 0 5168 5304 452043806 452043670 1.610000e-36 165.0
62 TraesCS7D01G146500 chr3A 87.234 141 17 1 4775 4914 198296881 198297021 7.470000e-35 159.0
63 TraesCS7D01G146500 chr3B 80.303 132 23 1 3010 3138 55718227 55718096 5.940000e-16 97.1


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 TraesCS7D01G146500 chr7D 93778422 93785619 7197 False 13293.00 13293 100.0000 1 7198 1 chr7D.!!$F1 7197
1 TraesCS7D01G146500 chr7A 96553670 96563087 9417 False 964.11 2741 92.1423 1 7198 10 chr7A.!!$F1 7197
2 TraesCS7D01G146500 chr7B 46989029 46997633 8604 False 837.20 2012 91.6576 1 7198 10 chr7B.!!$F3 7197

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
540 1940 0.037232 AAGGAAGAAACTCGCCGGAG 60.037 55.000 5.05 0.0 46.13 4.63 F
2041 3673 0.252696 ACCTCCTACCCATGCACTGA 60.253 55.000 0.00 0.0 0.00 3.41 F
2395 4110 0.882927 TAGCGGTTGTGCAGTTGACC 60.883 55.000 0.00 0.0 37.31 4.02 F
3853 5851 1.439679 GCCGAAAGTACAACTGAGGG 58.560 55.000 0.00 0.0 0.00 4.30 F
5535 7706 1.066918 GCACATTGGCCAGCTATGC 59.933 57.895 14.60 14.8 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 4245 1.134521 TGAAACTGACAAGCGGACACT 60.135 47.619 0.00 0.00 0.00 3.55 R
3566 5396 0.179134 CGGAGGTCAACGATGTCTCC 60.179 60.000 19.54 19.54 40.88 3.71 R
3947 5997 1.226311 AAATGTCCCCAGATCTCCCC 58.774 55.000 0.00 0.00 0.00 4.81 R
5750 8047 1.133809 TCCTTGGGCTAGGCAAGTGT 61.134 55.000 19.14 0.00 35.15 3.55 R
6462 10124 0.107214 ATCCACCGTGGCAATACAGG 60.107 55.000 13.19 0.00 37.47 4.00 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
122 128 7.526608 TCTAGTTTTTACATCTCCAATTTGCG 58.473 34.615 0.00 0.00 0.00 4.85
293 299 5.204409 TGCTCAAAGTTTTGCATCATCTT 57.796 34.783 8.47 0.00 38.05 2.40
383 389 2.352342 CCCAAAACAGCAAGCAAAACAG 59.648 45.455 0.00 0.00 0.00 3.16
408 1807 2.631062 TGAAGTAAACTGAGCCCGAAGA 59.369 45.455 0.00 0.00 0.00 2.87
419 1818 1.599047 CCCGAAGACAGCCATCACT 59.401 57.895 0.00 0.00 0.00 3.41
485 1885 2.285083 TGAGTTTTCACAGTTGGGTCG 58.715 47.619 0.00 0.00 0.00 4.79
486 1886 1.602377 GAGTTTTCACAGTTGGGTCGG 59.398 52.381 0.00 0.00 0.00 4.79
488 1888 1.332686 GTTTTCACAGTTGGGTCGGTC 59.667 52.381 0.00 0.00 0.00 4.79
492 1892 0.320421 CACAGTTGGGTCGGTCGATT 60.320 55.000 0.00 0.00 0.00 3.34
498 1898 0.108963 TGGGTCGGTCGATTTTGGTT 59.891 50.000 0.00 0.00 0.00 3.67
516 1916 3.269381 TGGTTGAAGGGAGAAATAGCCAT 59.731 43.478 0.00 0.00 0.00 4.40
517 1917 4.476846 TGGTTGAAGGGAGAAATAGCCATA 59.523 41.667 0.00 0.00 0.00 2.74
518 1918 5.066593 GGTTGAAGGGAGAAATAGCCATAG 58.933 45.833 0.00 0.00 0.00 2.23
519 1919 4.982241 TGAAGGGAGAAATAGCCATAGG 57.018 45.455 0.00 0.00 0.00 2.57
520 1920 3.652869 TGAAGGGAGAAATAGCCATAGGG 59.347 47.826 0.00 0.00 37.18 3.53
521 1921 3.655972 AGGGAGAAATAGCCATAGGGA 57.344 47.619 0.00 0.00 35.59 4.20
522 1922 3.954662 AGGGAGAAATAGCCATAGGGAA 58.045 45.455 0.00 0.00 35.59 3.97
523 1923 3.913163 AGGGAGAAATAGCCATAGGGAAG 59.087 47.826 0.00 0.00 35.59 3.46
524 1924 3.009584 GGGAGAAATAGCCATAGGGAAGG 59.990 52.174 0.00 0.00 35.59 3.46
525 1925 3.910627 GGAGAAATAGCCATAGGGAAGGA 59.089 47.826 0.00 0.00 35.59 3.36
526 1926 4.351111 GGAGAAATAGCCATAGGGAAGGAA 59.649 45.833 0.00 0.00 35.59 3.36
527 1927 5.513962 GGAGAAATAGCCATAGGGAAGGAAG 60.514 48.000 0.00 0.00 35.59 3.46
528 1928 5.227593 AGAAATAGCCATAGGGAAGGAAGA 58.772 41.667 0.00 0.00 35.59 2.87
529 1929 5.672194 AGAAATAGCCATAGGGAAGGAAGAA 59.328 40.000 0.00 0.00 35.59 2.52
530 1930 5.994416 AATAGCCATAGGGAAGGAAGAAA 57.006 39.130 0.00 0.00 35.59 2.52
531 1931 3.653835 AGCCATAGGGAAGGAAGAAAC 57.346 47.619 0.00 0.00 35.59 2.78
532 1932 3.193782 AGCCATAGGGAAGGAAGAAACT 58.806 45.455 0.00 0.00 35.59 2.66
533 1933 3.201045 AGCCATAGGGAAGGAAGAAACTC 59.799 47.826 0.00 0.00 35.59 3.01
534 1934 3.798202 CCATAGGGAAGGAAGAAACTCG 58.202 50.000 0.00 0.00 35.59 4.18
535 1935 3.198872 CATAGGGAAGGAAGAAACTCGC 58.801 50.000 0.00 0.00 0.00 5.03
536 1936 0.325272 AGGGAAGGAAGAAACTCGCC 59.675 55.000 0.00 0.00 0.00 5.54
537 1937 1.019805 GGGAAGGAAGAAACTCGCCG 61.020 60.000 0.00 0.00 0.00 6.46
540 1940 0.037232 AAGGAAGAAACTCGCCGGAG 60.037 55.000 5.05 0.00 46.13 4.63
560 1960 0.391793 GGGAGGAAGAAGCTCGTTGG 60.392 60.000 0.00 0.00 0.00 3.77
569 1969 2.046314 GCTCGTTGGGCAGGCTAA 60.046 61.111 0.00 0.00 0.00 3.09
578 1978 2.746277 GCAGGCTAACCCGGTGTG 60.746 66.667 0.00 0.00 39.21 3.82
583 1983 0.538118 GGCTAACCCGGTGTGTATCA 59.462 55.000 0.00 0.00 0.00 2.15
600 2000 1.221635 TCATAGGGTTCATGGTGGGG 58.778 55.000 0.00 0.00 0.00 4.96
617 2017 4.295119 GCGGTGGTGGACGACAGT 62.295 66.667 0.00 0.00 0.00 3.55
619 2019 2.030562 GGTGGTGGACGACAGTGG 59.969 66.667 0.00 0.00 0.00 4.00
620 2020 2.803817 GGTGGTGGACGACAGTGGT 61.804 63.158 0.00 0.00 0.00 4.16
623 2023 2.030562 GTGGACGACAGTGGTGGG 59.969 66.667 0.00 0.00 0.00 4.61
624 2024 3.238497 TGGACGACAGTGGTGGGG 61.238 66.667 0.00 0.00 0.00 4.96
625 2025 4.016706 GGACGACAGTGGTGGGGG 62.017 72.222 0.00 0.00 0.00 5.40
681 2081 2.201490 CGGGGCCTAGAGGGATGA 59.799 66.667 0.84 0.00 37.23 2.92
682 2082 2.210711 CGGGGCCTAGAGGGATGAC 61.211 68.421 0.84 0.00 37.23 3.06
686 2086 2.873525 GCCTAGAGGGATGACCGGC 61.874 68.421 0.00 0.00 46.96 6.13
712 2126 2.931649 GGGTGGTTTCGGGGAGGA 60.932 66.667 0.00 0.00 0.00 3.71
715 2129 2.203669 TGGTTTCGGGGAGGACGA 60.204 61.111 0.00 0.00 38.78 4.20
718 2132 3.387947 TTTCGGGGAGGACGAGGC 61.388 66.667 0.00 0.00 41.81 4.70
812 2226 0.811281 GGTTGGAAGAAAGCATCGGG 59.189 55.000 0.00 0.00 0.00 5.14
827 2241 0.460284 TCGGGAGAAAGAAGATGCGC 60.460 55.000 0.00 0.00 34.75 6.09
841 2255 2.816087 AGATGCGCTGTGATCTGTTTTT 59.184 40.909 9.73 0.00 0.00 1.94
850 2264 6.511767 CGCTGTGATCTGTTTTTAGAAACTGT 60.512 38.462 9.96 1.85 44.33 3.55
853 2267 8.050778 TGTGATCTGTTTTTAGAAACTGTTGT 57.949 30.769 9.96 2.07 44.33 3.32
897 2311 4.039245 CCGTTAGATTAGAGATCAAGGGCA 59.961 45.833 0.00 0.00 0.00 5.36
941 2355 1.610624 GGGATTTTCAGTCGACTGGCA 60.611 52.381 37.82 25.27 43.91 4.92
948 2362 1.972223 AGTCGACTGGCACGTAGCT 60.972 57.895 19.30 0.00 44.79 3.32
954 2368 1.437986 CTGGCACGTAGCTAGTCCC 59.562 63.158 12.77 0.00 45.85 4.46
955 2369 2.017559 CTGGCACGTAGCTAGTCCCC 62.018 65.000 12.77 0.00 45.85 4.81
956 2370 1.757340 GGCACGTAGCTAGTCCCCT 60.757 63.158 0.00 0.00 44.79 4.79
957 2371 1.734748 GCACGTAGCTAGTCCCCTC 59.265 63.158 0.00 0.00 41.15 4.30
958 2372 1.736365 GCACGTAGCTAGTCCCCTCC 61.736 65.000 0.00 0.00 41.15 4.30
1201 2615 2.752238 CGCTCGACTCCCTCCAGT 60.752 66.667 0.00 0.00 0.00 4.00
1215 2629 2.294078 CCAGTTCCTCGCCTCCCTT 61.294 63.158 0.00 0.00 0.00 3.95
1467 2881 2.656069 GGACGTGCTGAAGGGGCTA 61.656 63.158 0.00 0.00 0.00 3.93
1730 3144 4.617959 TGCGATGAAGTTGCCTATACTAC 58.382 43.478 0.00 0.00 36.30 2.73
1731 3145 4.341235 TGCGATGAAGTTGCCTATACTACT 59.659 41.667 0.00 0.00 36.30 2.57
1734 3148 5.241949 CGATGAAGTTGCCTATACTACTCCT 59.758 44.000 0.00 0.00 0.00 3.69
1735 3149 6.430308 CGATGAAGTTGCCTATACTACTCCTA 59.570 42.308 0.00 0.00 0.00 2.94
1736 3150 7.121463 CGATGAAGTTGCCTATACTACTCCTAT 59.879 40.741 0.00 0.00 0.00 2.57
1737 3151 9.463902 GATGAAGTTGCCTATACTACTCCTATA 57.536 37.037 0.00 0.00 0.00 1.31
1768 3300 0.685097 TAGCCTTTGACGCAAGAGGT 59.315 50.000 15.07 9.58 43.62 3.85
2041 3673 0.252696 ACCTCCTACCCATGCACTGA 60.253 55.000 0.00 0.00 0.00 3.41
2074 3706 1.898574 CAAGGCACGGGCAAGAGTT 60.899 57.895 13.89 0.00 43.71 3.01
2180 3812 2.698855 AGCTACCCATGCACTGTAAG 57.301 50.000 0.00 0.00 42.29 2.34
2395 4110 0.882927 TAGCGGTTGTGCAGTTGACC 60.883 55.000 0.00 0.00 37.31 4.02
2525 4245 7.809331 GTCAGTTTATGCATTGTTCTTGATTGA 59.191 33.333 3.54 0.00 0.00 2.57
2532 4252 4.715896 CATTGTTCTTGATTGAGTGTCCG 58.284 43.478 0.00 0.00 0.00 4.79
2650 4377 3.933332 GGTATGCCTCAGTGACACTAAAC 59.067 47.826 8.02 0.00 0.00 2.01
2697 4424 4.815308 CCTCATGCTACTGATCTTTCTTGG 59.185 45.833 0.00 0.00 0.00 3.61
2876 4603 5.885230 TTGCCAACATTTCACATAGAGAG 57.115 39.130 0.00 0.00 0.00 3.20
2906 4633 5.807011 GTCATGGCATGGTCTTAAAAATCAC 59.193 40.000 26.15 9.20 0.00 3.06
2980 4710 8.159229 ACCCATAGTCCTAACTGAAGTTAAAT 57.841 34.615 4.57 0.00 39.70 1.40
3060 4790 3.981211 TGAGCAAATTCCAAAGCTTCAC 58.019 40.909 0.00 0.00 37.48 3.18
3075 4805 6.478512 AAGCTTCACTTATTTTTCCCACAA 57.521 33.333 0.00 0.00 36.62 3.33
3292 5068 3.573967 ACAATCTCCATTTCACACAACCC 59.426 43.478 0.00 0.00 0.00 4.11
3371 5147 2.676839 GCAATCACAGACACTGGATCAG 59.323 50.000 0.00 0.00 35.51 2.90
3380 5156 4.341520 CAGACACTGGATCAGAGATGATGA 59.658 45.833 1.59 0.00 35.18 2.92
3492 5268 3.667282 CGTGACGGTCGTGGAGGT 61.667 66.667 0.00 0.00 0.00 3.85
3493 5269 2.732658 GTGACGGTCGTGGAGGTT 59.267 61.111 0.00 0.00 0.00 3.50
3495 5271 2.048503 GACGGTCGTGGAGGTTGG 60.049 66.667 0.00 0.00 0.00 3.77
3499 5275 4.717313 GTCGTGGAGGTTGGGGGC 62.717 72.222 0.00 0.00 0.00 5.80
3502 5278 4.410400 GTGGAGGTTGGGGGCGAG 62.410 72.222 0.00 0.00 0.00 5.03
3641 5471 2.422945 GGACTCAGGTTGGGTTTGACTT 60.423 50.000 0.00 0.00 26.09 3.01
3653 5483 2.417719 GTTTGACTTGCGGAGATCACT 58.582 47.619 0.00 0.00 0.00 3.41
3729 5559 2.836981 AGCACCTAAGCTCACAGATCTT 59.163 45.455 0.00 0.00 42.18 2.40
3732 5728 3.055530 CACCTAAGCTCACAGATCTTGGT 60.056 47.826 0.00 0.00 0.00 3.67
3853 5851 1.439679 GCCGAAAGTACAACTGAGGG 58.560 55.000 0.00 0.00 0.00 4.30
3969 6019 2.565841 GGAGATCTGGGGACATTTTCG 58.434 52.381 0.00 0.00 41.51 3.46
4284 6417 3.837731 TGGAACTTTCATTTGGGATTCCC 59.162 43.478 15.40 15.40 45.71 3.97
4487 6621 1.467342 GAAGACCGAATTTCAACCCCG 59.533 52.381 0.00 0.00 0.00 5.73
4823 6960 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
4824 6961 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4825 6962 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4826 6963 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4827 6964 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4828 6965 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4841 6978 4.978083 ACGGATGTATCTAGACACGTTT 57.022 40.909 0.00 0.00 30.52 3.60
4842 6979 5.320549 ACGGATGTATCTAGACACGTTTT 57.679 39.130 0.00 0.00 30.52 2.43
4843 6980 6.441093 ACGGATGTATCTAGACACGTTTTA 57.559 37.500 0.00 0.00 30.52 1.52
4844 6981 6.855836 ACGGATGTATCTAGACACGTTTTAA 58.144 36.000 0.00 0.00 30.52 1.52
4845 6982 7.486647 ACGGATGTATCTAGACACGTTTTAAT 58.513 34.615 0.00 0.00 30.52 1.40
4846 6983 7.434307 ACGGATGTATCTAGACACGTTTTAATG 59.566 37.037 0.00 0.00 30.52 1.90
4847 6984 7.434307 CGGATGTATCTAGACACGTTTTAATGT 59.566 37.037 0.00 0.00 30.52 2.71
4848 6985 9.095065 GGATGTATCTAGACACGTTTTAATGTT 57.905 33.333 0.00 0.00 30.52 2.71
4855 6992 9.531942 TCTAGACACGTTTTAATGTTAGAAACA 57.468 29.630 0.00 0.00 46.94 2.83
4905 7042 8.314751 CAAGTAATATGAATCGGAGGGAGTATT 58.685 37.037 0.00 0.00 0.00 1.89
4916 7053 6.110707 TCGGAGGGAGTATTTGTTTTATGTC 58.889 40.000 0.00 0.00 0.00 3.06
4919 7056 7.120726 CGGAGGGAGTATTTGTTTTATGTCTTT 59.879 37.037 0.00 0.00 0.00 2.52
4921 7058 9.626045 GAGGGAGTATTTGTTTTATGTCTTTTG 57.374 33.333 0.00 0.00 0.00 2.44
4922 7059 9.362151 AGGGAGTATTTGTTTTATGTCTTTTGA 57.638 29.630 0.00 0.00 0.00 2.69
4923 7060 9.626045 GGGAGTATTTGTTTTATGTCTTTTGAG 57.374 33.333 0.00 0.00 0.00 3.02
5128 7267 1.674817 GCTACTTTTCACTGCCGCCTA 60.675 52.381 0.00 0.00 0.00 3.93
5145 7284 2.226674 GCCTACAGTTCTGTTGCTTTCC 59.773 50.000 10.74 0.00 0.00 3.13
5236 7375 1.847818 TGGACAGAAACGAGTGAACG 58.152 50.000 0.00 0.00 39.31 3.95
5535 7706 1.066918 GCACATTGGCCAGCTATGC 59.933 57.895 14.60 14.80 0.00 3.14
5553 7724 5.762218 GCTATGCACATCTCCAGAAGTAAAT 59.238 40.000 0.00 0.00 0.00 1.40
5609 7906 7.880713 GGAATTTTAGTGCTTTGGGGATTAAAA 59.119 33.333 0.00 0.00 39.91 1.52
5692 7989 6.994496 TGATAACTATGCTCAAAGGGATCTTG 59.006 38.462 0.00 0.00 32.75 3.02
5711 8008 1.425066 TGTTTGCAGTGGGAGGATTCT 59.575 47.619 0.00 0.00 0.00 2.40
5750 8047 6.298441 TCAAGATCACAATCACATAGACCA 57.702 37.500 0.00 0.00 34.07 4.02
5998 8295 1.137282 CCTTACCGCTTCTCCCTTCTC 59.863 57.143 0.00 0.00 0.00 2.87
6051 8348 7.976414 TGGAAGGATATTTTGATCCACAATT 57.024 32.000 5.29 0.00 46.94 2.32
6182 8481 3.519510 TGGACTTGAAGGATAAGTGGAGG 59.480 47.826 0.00 0.00 38.42 4.30
6190 8489 4.762289 AGGATAAGTGGAGGAACATGAC 57.238 45.455 0.00 0.00 0.00 3.06
6214 8513 6.038825 ACGAGATAGTGGAGAGACATACTTTG 59.961 42.308 0.00 0.00 0.00 2.77
6267 8566 3.767673 TCTTTTACCGATGGAGTAGCTGT 59.232 43.478 0.00 0.00 0.00 4.40
6321 8822 3.746940 AGAAGCTTACTAACGGGCAAAA 58.253 40.909 0.00 0.00 0.00 2.44
6354 8855 8.035984 GGATGCTATTATAGGTGTAAAGTCTCC 58.964 40.741 1.12 0.00 0.00 3.71
6361 8862 1.675116 GGTGTAAAGTCTCCCTTCGGC 60.675 57.143 0.00 0.00 31.27 5.54
6363 8864 1.275291 TGTAAAGTCTCCCTTCGGCAG 59.725 52.381 0.00 0.00 31.27 4.85
6404 8905 4.695217 TTCTGGTTGTTGTTGAAGTGTC 57.305 40.909 0.00 0.00 0.00 3.67
6407 8908 2.160615 TGGTTGTTGTTGAAGTGTCGTG 59.839 45.455 0.00 0.00 0.00 4.35
6462 10124 4.054780 TGTCCGAGCATATTACACCTTC 57.945 45.455 0.00 0.00 0.00 3.46
6474 10136 2.200373 ACACCTTCCTGTATTGCCAC 57.800 50.000 0.00 0.00 0.00 5.01
6487 10313 0.888736 TTGCCACGGTGGATGTTCTG 60.889 55.000 30.65 1.78 40.96 3.02
6509 10335 4.103153 TGAGATAACCTCATCCCAACCATC 59.897 45.833 0.00 0.00 46.38 3.51
6575 10555 6.643770 ACTGCTCACAAAATGATCATGTTTTC 59.356 34.615 9.46 0.00 36.48 2.29
6576 10556 5.927689 TGCTCACAAAATGATCATGTTTTCC 59.072 36.000 9.46 0.00 36.48 3.13
6617 10598 7.384932 TGTGTACACATTACATCTTGTTCTCAG 59.615 37.037 24.62 0.00 36.21 3.35
6625 10606 3.879295 ACATCTTGTTCTCAGTGGTGTTG 59.121 43.478 0.00 0.00 0.00 3.33
6628 10609 1.279840 GTTCTCAGTGGTGTTGCGC 59.720 57.895 0.00 0.00 0.00 6.09
6653 10634 3.465742 TTGTGCTCATCAGGCTCTATC 57.534 47.619 0.00 0.00 0.00 2.08
6662 10643 4.718774 TCATCAGGCTCTATCCAGTTCTTT 59.281 41.667 0.00 0.00 0.00 2.52
6665 10646 4.532126 TCAGGCTCTATCCAGTTCTTTTGA 59.468 41.667 0.00 0.00 0.00 2.69
6667 10648 4.780021 AGGCTCTATCCAGTTCTTTTGAGA 59.220 41.667 0.00 0.00 0.00 3.27
6672 10653 2.483876 TCCAGTTCTTTTGAGACTGCG 58.516 47.619 0.00 0.00 36.82 5.18
6677 10658 5.506317 CCAGTTCTTTTGAGACTGCGATTTT 60.506 40.000 0.00 0.00 36.82 1.82
6689 10670 2.780014 CTGCGATTTTCGTGCATCAATC 59.220 45.455 0.00 0.00 42.81 2.67
6691 10672 2.780014 GCGATTTTCGTGCATCAATCAG 59.220 45.455 0.00 0.00 42.81 2.90
6692 10673 3.357021 CGATTTTCGTGCATCAATCAGG 58.643 45.455 0.00 0.00 34.72 3.86
6693 10674 2.634982 TTTTCGTGCATCAATCAGGC 57.365 45.000 0.00 0.00 0.00 4.85
6694 10675 1.825090 TTTCGTGCATCAATCAGGCT 58.175 45.000 0.00 0.00 0.00 4.58
6695 10676 1.372582 TTCGTGCATCAATCAGGCTC 58.627 50.000 0.00 0.00 0.00 4.70
6696 10677 0.807275 TCGTGCATCAATCAGGCTCG 60.807 55.000 0.00 0.00 43.44 5.03
6703 10684 1.822613 CAATCAGGCTCGCAGGCAT 60.823 57.895 11.23 0.00 44.19 4.40
6734 10715 5.590259 TGTGTTTTTCTCCCTCTTCTTCTTG 59.410 40.000 0.00 0.00 0.00 3.02
6747 10731 3.550437 TCTTCTTGAGCTAGATTGCCC 57.450 47.619 0.00 0.00 0.00 5.36
6754 10738 2.170607 TGAGCTAGATTGCCCAGGTTAC 59.829 50.000 0.00 0.00 0.00 2.50
6757 10741 2.101917 GCTAGATTGCCCAGGTTACGTA 59.898 50.000 0.00 0.00 0.00 3.57
6758 10742 3.431207 GCTAGATTGCCCAGGTTACGTAA 60.431 47.826 3.29 3.29 0.00 3.18
6759 10743 3.926058 AGATTGCCCAGGTTACGTAAT 57.074 42.857 11.86 0.00 0.00 1.89
6760 10744 3.805207 AGATTGCCCAGGTTACGTAATC 58.195 45.455 11.86 11.26 0.00 1.75
6761 10745 2.406596 TTGCCCAGGTTACGTAATCC 57.593 50.000 14.91 15.04 0.00 3.01
6762 10746 0.542805 TGCCCAGGTTACGTAATCCC 59.457 55.000 14.91 10.58 0.00 3.85
6763 10747 0.835276 GCCCAGGTTACGTAATCCCT 59.165 55.000 14.91 12.69 0.00 4.20
6764 10748 1.474498 GCCCAGGTTACGTAATCCCTG 60.474 57.143 26.73 26.73 43.34 4.45
6765 10749 1.835531 CCCAGGTTACGTAATCCCTGT 59.164 52.381 29.12 7.90 42.39 4.00
6766 10750 2.237893 CCCAGGTTACGTAATCCCTGTT 59.762 50.000 29.12 7.59 42.39 3.16
6767 10751 3.267483 CCAGGTTACGTAATCCCTGTTG 58.733 50.000 29.12 18.40 42.39 3.33
6768 10752 3.307199 CCAGGTTACGTAATCCCTGTTGT 60.307 47.826 29.12 6.38 42.39 3.32
6769 10753 4.081531 CCAGGTTACGTAATCCCTGTTGTA 60.082 45.833 29.12 0.00 42.39 2.41
6792 10776 8.033038 TGTAACATGTACTTGAGACCTGATTAC 58.967 37.037 15.13 10.37 0.00 1.89
6828 10812 1.903404 CTTGTGCGCCTTCCCCTTT 60.903 57.895 4.18 0.00 0.00 3.11
6829 10813 1.456705 TTGTGCGCCTTCCCCTTTT 60.457 52.632 4.18 0.00 0.00 2.27
6830 10814 1.045911 TTGTGCGCCTTCCCCTTTTT 61.046 50.000 4.18 0.00 0.00 1.94
6831 10815 1.289066 GTGCGCCTTCCCCTTTTTC 59.711 57.895 4.18 0.00 0.00 2.29
6832 10816 1.152652 TGCGCCTTCCCCTTTTTCA 60.153 52.632 4.18 0.00 0.00 2.69
6833 10817 0.757188 TGCGCCTTCCCCTTTTTCAA 60.757 50.000 4.18 0.00 0.00 2.69
6834 10818 0.391228 GCGCCTTCCCCTTTTTCAAA 59.609 50.000 0.00 0.00 0.00 2.69
6835 10819 1.202592 GCGCCTTCCCCTTTTTCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
6836 10820 2.754472 CGCCTTCCCCTTTTTCAAAAG 58.246 47.619 5.21 5.21 43.82 2.27
6991 10982 1.873270 GCCCTTTTTGTAGGCGTGGG 61.873 60.000 0.00 0.00 36.84 4.61
7001 11113 0.251073 TAGGCGTGGGCTACTTTTCC 59.749 55.000 0.00 0.00 39.70 3.13
7103 11711 2.900546 CCCTATTCCTGCCGAGAATAGT 59.099 50.000 18.60 0.00 46.23 2.12
7146 11754 3.243002 CGTCCTTCTATCCGGAACAGTAC 60.243 52.174 9.01 0.20 0.00 2.73
7155 11768 3.116531 GAACAGTACCCGCCGCAC 61.117 66.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 315 8.885693 AGGTTTAATGAGAAGCCTCTATTTTT 57.114 30.769 0.00 0.00 35.27 1.94
360 366 0.463474 TTTGCTTGCTGTTTTGGGGC 60.463 50.000 0.00 0.00 0.00 5.80
370 376 3.445096 ACTTCAGTTCTGTTTTGCTTGCT 59.555 39.130 0.00 0.00 0.00 3.91
383 389 2.737252 CGGGCTCAGTTTACTTCAGTTC 59.263 50.000 0.00 0.00 0.00 3.01
408 1807 1.601171 GAGGAGCAGTGATGGCTGT 59.399 57.895 0.00 0.00 42.78 4.40
433 1832 1.596477 CAGCTATTGCGAGGGGAGC 60.596 63.158 0.00 0.00 45.42 4.70
459 1859 3.001330 CCAACTGTGAAAACTCAGTCGAC 59.999 47.826 7.70 7.70 0.00 4.20
461 1861 2.287915 CCCAACTGTGAAAACTCAGTCG 59.712 50.000 0.00 0.00 0.00 4.18
473 1873 0.320421 AATCGACCGACCCAACTGTG 60.320 55.000 0.00 0.00 0.00 3.66
485 1885 2.488153 CTCCCTTCAACCAAAATCGACC 59.512 50.000 0.00 0.00 0.00 4.79
486 1886 3.408634 TCTCCCTTCAACCAAAATCGAC 58.591 45.455 0.00 0.00 0.00 4.20
488 1888 4.846779 TTTCTCCCTTCAACCAAAATCG 57.153 40.909 0.00 0.00 0.00 3.34
492 1892 4.086457 GGCTATTTCTCCCTTCAACCAAA 58.914 43.478 0.00 0.00 0.00 3.28
498 1898 3.652869 CCCTATGGCTATTTCTCCCTTCA 59.347 47.826 0.00 0.00 0.00 3.02
516 1916 1.553704 GGCGAGTTTCTTCCTTCCCTA 59.446 52.381 0.00 0.00 0.00 3.53
517 1917 0.325272 GGCGAGTTTCTTCCTTCCCT 59.675 55.000 0.00 0.00 0.00 4.20
518 1918 1.019805 CGGCGAGTTTCTTCCTTCCC 61.020 60.000 0.00 0.00 0.00 3.97
519 1919 1.019805 CCGGCGAGTTTCTTCCTTCC 61.020 60.000 9.30 0.00 0.00 3.46
520 1920 0.037605 TCCGGCGAGTTTCTTCCTTC 60.038 55.000 9.30 0.00 0.00 3.46
521 1921 0.037232 CTCCGGCGAGTTTCTTCCTT 60.037 55.000 9.30 0.00 0.00 3.36
522 1922 1.592223 CTCCGGCGAGTTTCTTCCT 59.408 57.895 9.30 0.00 0.00 3.36
523 1923 1.448013 CCTCCGGCGAGTTTCTTCC 60.448 63.158 9.30 0.00 33.93 3.46
524 1924 1.448013 CCCTCCGGCGAGTTTCTTC 60.448 63.158 9.30 0.00 33.93 2.87
525 1925 2.663196 CCCTCCGGCGAGTTTCTT 59.337 61.111 9.30 0.00 33.93 2.52
526 1926 3.391382 CCCCTCCGGCGAGTTTCT 61.391 66.667 9.30 0.00 33.93 2.52
527 1927 3.372554 CTCCCCTCCGGCGAGTTTC 62.373 68.421 9.30 0.00 33.93 2.78
528 1928 3.391382 CTCCCCTCCGGCGAGTTT 61.391 66.667 9.30 0.00 33.93 2.66
534 1934 2.687566 TTCTTCCTCCCCTCCGGC 60.688 66.667 0.00 0.00 0.00 6.13
535 1935 2.736826 GCTTCTTCCTCCCCTCCGG 61.737 68.421 0.00 0.00 0.00 5.14
536 1936 1.681486 GAGCTTCTTCCTCCCCTCCG 61.681 65.000 0.00 0.00 0.00 4.63
537 1937 1.681486 CGAGCTTCTTCCTCCCCTCC 61.681 65.000 0.00 0.00 0.00 4.30
540 1940 0.391793 CAACGAGCTTCTTCCTCCCC 60.392 60.000 0.00 0.00 0.00 4.81
560 1960 4.029809 ACACCGGGTTAGCCTGCC 62.030 66.667 6.32 0.00 39.86 4.85
569 1969 1.343681 ACCCTATGATACACACCGGGT 60.344 52.381 6.32 0.00 44.44 5.28
573 1973 4.141482 ACCATGAACCCTATGATACACACC 60.141 45.833 0.00 0.00 0.00 4.16
578 1978 3.244911 CCCCACCATGAACCCTATGATAC 60.245 52.174 0.00 0.00 0.00 2.24
583 1983 1.930520 GCCCCACCATGAACCCTAT 59.069 57.895 0.00 0.00 0.00 2.57
600 2000 4.295119 ACTGTCGTCCACCACCGC 62.295 66.667 0.00 0.00 0.00 5.68
623 2023 4.815108 GAATCCCCACACCGCCCC 62.815 72.222 0.00 0.00 0.00 5.80
628 2028 3.615509 TTCGGCGAATCCCCACACC 62.616 63.158 19.83 0.00 0.00 4.16
629 2029 2.046700 TTCGGCGAATCCCCACAC 60.047 61.111 19.83 0.00 0.00 3.82
630 2030 1.832719 TTCTTCGGCGAATCCCCACA 61.833 55.000 23.96 0.00 0.00 4.17
631 2031 0.675522 TTTCTTCGGCGAATCCCCAC 60.676 55.000 23.96 0.00 0.00 4.61
632 2032 0.037017 TTTTCTTCGGCGAATCCCCA 59.963 50.000 23.96 3.71 0.00 4.96
792 2206 0.447801 CCGATGCTTTCTTCCAACCG 59.552 55.000 0.00 0.00 0.00 4.44
812 2226 2.341257 TCACAGCGCATCTTCTTTCTC 58.659 47.619 11.47 0.00 0.00 2.87
827 2241 8.184192 ACAACAGTTTCTAAAAACAGATCACAG 58.816 33.333 0.00 0.00 45.94 3.66
841 2255 6.269077 TCATCTTCCACCTACAACAGTTTCTA 59.731 38.462 0.00 0.00 0.00 2.10
850 2264 2.906389 AGCAGTCATCTTCCACCTACAA 59.094 45.455 0.00 0.00 0.00 2.41
853 2267 1.833630 CCAGCAGTCATCTTCCACCTA 59.166 52.381 0.00 0.00 0.00 3.08
897 2311 1.924731 TGGGTCAGTCGATGTTCTCT 58.075 50.000 0.00 0.00 0.00 3.10
925 2339 0.179094 ACGTGCCAGTCGACTGAAAA 60.179 50.000 40.21 24.44 46.59 2.29
941 2355 1.229643 GGGAGGGGACTAGCTACGT 59.770 63.158 0.00 0.00 44.43 3.57
965 2379 3.566016 TAGGGTTTGGGGGCGAGGA 62.566 63.158 0.00 0.00 0.00 3.71
1201 2615 2.687566 GGGAAGGGAGGCGAGGAA 60.688 66.667 0.00 0.00 0.00 3.36
1560 2974 3.288484 TCGCCAACGATCTGCTCT 58.712 55.556 0.00 0.00 45.12 4.09
1635 3049 6.153680 CCAGAACAGAAGAATACTCACCTAGT 59.846 42.308 0.00 0.00 42.62 2.57
1684 3098 4.796231 CGTCTCAGAACCCCGCCG 62.796 72.222 0.00 0.00 0.00 6.46
1735 3149 8.989980 GCGTCAAAGGCTAAAAGTATAAGATAT 58.010 33.333 0.00 0.00 0.00 1.63
1736 3150 7.982919 TGCGTCAAAGGCTAAAAGTATAAGATA 59.017 33.333 0.00 0.00 0.00 1.98
1737 3151 6.821665 TGCGTCAAAGGCTAAAAGTATAAGAT 59.178 34.615 0.00 0.00 0.00 2.40
1975 3606 7.397892 TGTGAACACCTCTATTTTTGTTTGA 57.602 32.000 2.46 0.00 32.34 2.69
2041 3673 4.631131 GTGCCTTGCCTGAAGTAAAATTT 58.369 39.130 0.00 0.00 0.00 1.82
2074 3706 1.902508 AGCTAGCTCAACTTGCCTGTA 59.097 47.619 12.68 0.00 46.85 2.74
2180 3812 1.234821 TTCAGACGTGCCATTGGAAC 58.765 50.000 6.95 5.07 0.00 3.62
2395 4110 8.622948 AAAGACTAGGTTTAGACAAAGATTGG 57.377 34.615 0.00 0.00 34.12 3.16
2525 4245 1.134521 TGAAACTGACAAGCGGACACT 60.135 47.619 0.00 0.00 0.00 3.55
2532 4252 7.491048 TGGTAAAAGAATTTGAAACTGACAAGC 59.509 33.333 0.00 0.00 39.02 4.01
2678 4405 6.552445 AGTACCAAGAAAGATCAGTAGCAT 57.448 37.500 0.00 0.00 0.00 3.79
2697 4424 6.554334 TGTCATTCTTACAAGCCAAAGTAC 57.446 37.500 0.00 0.00 0.00 2.73
2876 4603 2.936202 AGACCATGCCATGACATTACC 58.064 47.619 6.18 0.00 0.00 2.85
3060 4790 8.579863 AGAGTTGATTCTTGTGGGAAAAATAAG 58.420 33.333 0.00 0.00 0.00 1.73
3157 4930 9.540538 TGAAATCCATTTTCCTACAAATCCTAA 57.459 29.630 0.00 0.00 42.63 2.69
3158 4931 9.189156 CTGAAATCCATTTTCCTACAAATCCTA 57.811 33.333 0.00 0.00 42.63 2.94
3275 5051 4.078537 TGTATGGGTTGTGTGAAATGGAG 58.921 43.478 0.00 0.00 0.00 3.86
3292 5068 8.032952 TCTTCTGCTGAAAATTACAGTGTATG 57.967 34.615 3.28 0.00 37.64 2.39
3371 5147 8.386606 GTGTCTTGTGATTTACTTCATCATCTC 58.613 37.037 0.00 0.00 33.22 2.75
3380 5156 5.701290 GCCTACTGTGTCTTGTGATTTACTT 59.299 40.000 0.00 0.00 0.00 2.24
3504 5280 2.203126 CCTCCTCCATGGCTTCGC 60.203 66.667 6.96 0.00 35.26 4.70
3505 5281 1.445095 CTCCTCCTCCATGGCTTCG 59.555 63.158 6.96 0.00 35.26 3.79
3556 5386 1.313091 CGATGTCTCCCTCCACGTCA 61.313 60.000 0.00 0.00 0.00 4.35
3566 5396 0.179134 CGGAGGTCAACGATGTCTCC 60.179 60.000 19.54 19.54 40.88 3.71
3617 5447 2.176798 TCAAACCCAACCTGAGTCCATT 59.823 45.455 0.00 0.00 0.00 3.16
3641 5471 2.887783 GGAGAAGATAGTGATCTCCGCA 59.112 50.000 5.38 0.00 46.99 5.69
3729 5559 4.314440 GTGCGAGCCTGGACACCA 62.314 66.667 0.00 0.00 0.00 4.17
3808 5806 2.066340 CCTCAGCTGGTTACACCCA 58.934 57.895 15.13 0.00 37.50 4.51
3853 5851 2.747855 CTTGCCGGTGCCTTCCTC 60.748 66.667 1.90 0.00 36.33 3.71
3947 5997 1.226311 AAATGTCCCCAGATCTCCCC 58.774 55.000 0.00 0.00 0.00 4.81
3980 6030 5.893687 TCGCTCGGTCACTACAAATTATTA 58.106 37.500 0.00 0.00 0.00 0.98
3983 6033 3.853831 TCGCTCGGTCACTACAAATTA 57.146 42.857 0.00 0.00 0.00 1.40
4008 6059 7.433680 ACTTTTGGAATTTGCACTACCTTTAG 58.566 34.615 0.00 0.00 0.00 1.85
4009 6060 7.286775 AGACTTTTGGAATTTGCACTACCTTTA 59.713 33.333 0.00 0.00 0.00 1.85
4048 6099 5.408604 GCATGTAAAACATATACTCCCTCCG 59.591 44.000 0.00 0.00 36.53 4.63
4284 6417 2.178912 TAGAACAGGCCCAGAAAACG 57.821 50.000 0.00 0.00 0.00 3.60
4487 6621 6.925610 TCATGTATGACCTTATGAACTTGC 57.074 37.500 0.00 0.00 0.00 4.01
4643 6780 0.515127 CAACGCTACAATTCGCACCA 59.485 50.000 0.00 0.00 0.00 4.17
4645 6782 0.165944 AGCAACGCTACAATTCGCAC 59.834 50.000 0.00 0.00 36.99 5.34
4818 6955 6.630444 AAACGTGTCTAGATACATCCGTAT 57.370 37.500 18.39 1.44 41.16 3.06
4819 6956 6.441093 AAAACGTGTCTAGATACATCCGTA 57.559 37.500 18.39 0.00 32.82 4.02
4820 6957 4.978083 AAACGTGTCTAGATACATCCGT 57.022 40.909 18.39 8.45 34.68 4.69
4821 6958 7.434307 ACATTAAAACGTGTCTAGATACATCCG 59.566 37.037 18.39 7.85 0.00 4.18
4822 6959 8.644318 ACATTAAAACGTGTCTAGATACATCC 57.356 34.615 18.39 0.00 0.00 3.51
4829 6966 9.531942 TGTTTCTAACATTAAAACGTGTCTAGA 57.468 29.630 0.00 0.00 36.25 2.43
4845 6982 5.711506 TGTCTAGGTACGGATGTTTCTAACA 59.288 40.000 0.00 0.00 46.94 2.41
4846 6983 6.199937 TGTCTAGGTACGGATGTTTCTAAC 57.800 41.667 0.00 0.00 0.00 2.34
4847 6984 6.839124 TTGTCTAGGTACGGATGTTTCTAA 57.161 37.500 0.00 0.00 0.00 2.10
4848 6985 6.839124 TTTGTCTAGGTACGGATGTTTCTA 57.161 37.500 0.00 0.00 0.00 2.10
4849 6986 5.733620 TTTGTCTAGGTACGGATGTTTCT 57.266 39.130 0.00 0.00 0.00 2.52
4850 6987 6.338937 AGATTTGTCTAGGTACGGATGTTTC 58.661 40.000 0.00 0.00 0.00 2.78
4851 6988 6.295719 AGATTTGTCTAGGTACGGATGTTT 57.704 37.500 0.00 0.00 0.00 2.83
4852 6989 5.934402 AGATTTGTCTAGGTACGGATGTT 57.066 39.130 0.00 0.00 0.00 2.71
4853 6990 6.832384 TCTTAGATTTGTCTAGGTACGGATGT 59.168 38.462 0.00 0.00 0.00 3.06
4854 6991 7.140048 GTCTTAGATTTGTCTAGGTACGGATG 58.860 42.308 0.00 0.00 0.00 3.51
4855 6992 6.832384 TGTCTTAGATTTGTCTAGGTACGGAT 59.168 38.462 0.00 0.00 0.00 4.18
4856 6993 6.182627 TGTCTTAGATTTGTCTAGGTACGGA 58.817 40.000 0.00 0.00 0.00 4.69
4857 6994 6.446781 TGTCTTAGATTTGTCTAGGTACGG 57.553 41.667 0.00 0.00 0.00 4.02
4858 6995 7.536855 ACTTGTCTTAGATTTGTCTAGGTACG 58.463 38.462 0.00 0.00 0.00 3.67
4950 7087 7.861629 TGTCTCCATTTGATATAACTCCTTGT 58.138 34.615 0.00 0.00 0.00 3.16
5128 7267 6.093785 TTTCTCTGGAAAGCAACAGAACTGT 61.094 40.000 1.32 1.32 42.62 3.55
5217 7356 1.406180 TCGTTCACTCGTTTCTGTCCA 59.594 47.619 0.00 0.00 0.00 4.02
5227 7366 4.031991 TGTTTTAGTGTGTTCGTTCACTCG 59.968 41.667 12.11 0.00 42.77 4.18
5236 7375 8.941977 TGTATATGGACATGTTTTAGTGTGTTC 58.058 33.333 0.00 0.00 0.00 3.18
5350 7520 7.774134 TGCTGTATGTTCAAATGCTGATTTAT 58.226 30.769 0.00 0.00 32.78 1.40
5351 7521 7.155655 TGCTGTATGTTCAAATGCTGATTTA 57.844 32.000 0.00 0.00 32.78 1.40
5513 7684 1.669049 TAGCTGGCCAATGTGCATGC 61.669 55.000 16.24 11.82 0.00 4.06
5535 7706 9.334947 ACATCATAATTTACTTCTGGAGATGTG 57.665 33.333 0.00 0.00 40.32 3.21
5609 7906 9.668497 GGGTGTTCTACATATTAAGAAAAGACT 57.332 33.333 0.00 0.00 33.70 3.24
5621 7918 5.216622 TGCCTAGAAGGGTGTTCTACATAT 58.783 41.667 0.00 0.00 35.37 1.78
5629 7926 3.200165 GGACTTATGCCTAGAAGGGTGTT 59.800 47.826 0.00 0.00 35.37 3.32
5669 7966 6.904626 ACAAGATCCCTTTGAGCATAGTTAT 58.095 36.000 0.56 0.00 0.00 1.89
5692 7989 2.087646 GAGAATCCTCCCACTGCAAAC 58.912 52.381 0.00 0.00 33.30 2.93
5750 8047 1.133809 TCCTTGGGCTAGGCAAGTGT 61.134 55.000 19.14 0.00 35.15 3.55
5935 8232 2.401351 ACTACGGCTTCGAGACAAAAC 58.599 47.619 0.00 0.00 37.63 2.43
5998 8295 3.667960 GCTACCAAATCTTCACAACAGCG 60.668 47.826 0.00 0.00 0.00 5.18
6051 8348 5.492895 TGTTCTACCAATAAAAGCATCGGA 58.507 37.500 0.00 0.00 0.00 4.55
6151 8450 1.542915 CCTTCAAGTCCACCTGCAATG 59.457 52.381 0.00 0.00 0.00 2.82
6182 8481 4.576873 TCTCTCCACTATCTCGTCATGTTC 59.423 45.833 0.00 0.00 0.00 3.18
6190 8489 6.434596 CAAAGTATGTCTCTCCACTATCTCG 58.565 44.000 0.00 0.00 0.00 4.04
6214 8513 4.079958 AGTTTCACCATATAGAACCACCCC 60.080 45.833 0.00 0.00 0.00 4.95
6303 8602 2.163613 GCATTTTGCCCGTTAGTAAGCT 59.836 45.455 0.00 0.00 37.42 3.74
6327 8828 8.728596 AGACTTTACACCTATAATAGCATCCT 57.271 34.615 0.00 0.00 0.00 3.24
6328 8829 8.035984 GGAGACTTTACACCTATAATAGCATCC 58.964 40.741 0.00 0.00 0.00 3.51
6354 8855 4.321230 AAGCAATTCTTAAACTGCCGAAGG 60.321 41.667 0.00 0.00 42.30 3.46
6385 8886 2.418628 ACGACACTTCAACAACAACCAG 59.581 45.455 0.00 0.00 0.00 4.00
6404 8905 1.883021 GACAGAAAATGCCCCCACG 59.117 57.895 0.00 0.00 0.00 4.94
6407 8908 0.608035 TCACGACAGAAAATGCCCCC 60.608 55.000 0.00 0.00 0.00 5.40
6462 10124 0.107214 ATCCACCGTGGCAATACAGG 60.107 55.000 13.19 0.00 37.47 4.00
6474 10136 3.133003 AGGTTATCTCAGAACATCCACCG 59.867 47.826 0.00 0.00 0.00 4.94
6487 10313 4.349342 AGATGGTTGGGATGAGGTTATCTC 59.651 45.833 0.00 0.00 42.74 2.75
6575 10555 5.008613 GTGTACACATGCATAAACTATGGGG 59.991 44.000 21.14 0.00 36.68 4.96
6576 10556 5.588246 TGTGTACACATGCATAAACTATGGG 59.412 40.000 24.62 0.00 36.21 4.00
6604 10585 3.304257 GCAACACCACTGAGAACAAGATG 60.304 47.826 0.00 0.00 0.00 2.90
6628 10609 0.376152 GCCTGATGAGCACAATCGTG 59.624 55.000 0.00 0.00 46.56 4.35
6643 10624 4.836825 TCAAAAGAACTGGATAGAGCCTG 58.163 43.478 0.00 0.00 0.00 4.85
6653 10634 2.483876 TCGCAGTCTCAAAAGAACTGG 58.516 47.619 4.14 0.00 34.20 4.00
6662 10643 1.194547 GCACGAAAATCGCAGTCTCAA 59.805 47.619 0.00 0.00 45.12 3.02
6665 10646 1.394917 GATGCACGAAAATCGCAGTCT 59.605 47.619 0.00 0.00 45.12 3.24
6667 10648 1.155889 TGATGCACGAAAATCGCAGT 58.844 45.000 0.00 0.00 45.12 4.40
6672 10653 3.111098 GCCTGATTGATGCACGAAAATC 58.889 45.455 0.00 0.00 0.00 2.17
6677 10658 0.807275 CGAGCCTGATTGATGCACGA 60.807 55.000 0.00 0.00 40.69 4.35
6689 10670 1.144716 TAGAATGCCTGCGAGCCTG 59.855 57.895 0.00 0.00 0.00 4.85
6691 10672 0.462759 AAGTAGAATGCCTGCGAGCC 60.463 55.000 0.00 0.00 32.34 4.70
6692 10673 0.654683 CAAGTAGAATGCCTGCGAGC 59.345 55.000 0.00 0.00 32.34 5.03
6693 10674 1.662629 CACAAGTAGAATGCCTGCGAG 59.337 52.381 0.00 0.00 32.34 5.03
6694 10675 1.001974 ACACAAGTAGAATGCCTGCGA 59.998 47.619 0.00 0.00 32.34 5.10
6695 10676 1.442769 ACACAAGTAGAATGCCTGCG 58.557 50.000 0.00 0.00 32.34 5.18
6696 10677 3.923017 AAACACAAGTAGAATGCCTGC 57.077 42.857 0.00 0.00 0.00 4.85
6703 10684 6.248569 AGAGGGAGAAAAACACAAGTAGAA 57.751 37.500 0.00 0.00 0.00 2.10
6734 10715 2.803492 CGTAACCTGGGCAATCTAGCTC 60.803 54.545 0.00 0.00 34.90 4.09
6754 10738 6.103997 AGTACATGTTACAACAGGGATTACG 58.896 40.000 2.30 0.00 44.34 3.18
6757 10741 6.539173 TCAAGTACATGTTACAACAGGGATT 58.461 36.000 2.30 0.00 44.34 3.01
6758 10742 6.013725 TCTCAAGTACATGTTACAACAGGGAT 60.014 38.462 2.30 0.00 44.34 3.85
6759 10743 5.305902 TCTCAAGTACATGTTACAACAGGGA 59.694 40.000 2.30 0.00 44.34 4.20
6760 10744 5.408604 GTCTCAAGTACATGTTACAACAGGG 59.591 44.000 2.30 3.89 44.34 4.45
6761 10745 5.408604 GGTCTCAAGTACATGTTACAACAGG 59.591 44.000 2.30 5.28 45.43 4.00
6762 10746 6.146184 CAGGTCTCAAGTACATGTTACAACAG 59.854 42.308 2.30 0.00 43.04 3.16
6763 10747 5.989168 CAGGTCTCAAGTACATGTTACAACA 59.011 40.000 2.30 0.00 44.06 3.33
6764 10748 6.220930 TCAGGTCTCAAGTACATGTTACAAC 58.779 40.000 2.30 0.00 30.94 3.32
6765 10749 6.413783 TCAGGTCTCAAGTACATGTTACAA 57.586 37.500 2.30 0.00 30.94 2.41
6766 10750 6.605471 ATCAGGTCTCAAGTACATGTTACA 57.395 37.500 2.30 0.00 30.94 2.41
6767 10751 8.033038 TGTAATCAGGTCTCAAGTACATGTTAC 58.967 37.037 2.30 0.25 32.38 2.50
6768 10752 8.129496 TGTAATCAGGTCTCAAGTACATGTTA 57.871 34.615 2.30 0.00 30.94 2.41
6769 10753 7.004555 TGTAATCAGGTCTCAAGTACATGTT 57.995 36.000 2.30 0.00 30.94 2.71
6792 10776 3.125316 CAAGGCACCAACAACTTCATTG 58.875 45.455 0.00 0.00 44.60 2.82
6810 10794 1.463553 AAAAGGGGAAGGCGCACAAG 61.464 55.000 10.83 0.00 0.00 3.16
6930 10921 8.685838 ACTCACTATGCCAACTAGTTTAAAAA 57.314 30.769 5.07 0.00 0.00 1.94
6931 10922 8.685838 AACTCACTATGCCAACTAGTTTAAAA 57.314 30.769 5.07 0.00 0.00 1.52
6932 10923 8.685838 AAACTCACTATGCCAACTAGTTTAAA 57.314 30.769 5.07 0.00 34.79 1.52
6933 10924 9.431887 CTAAACTCACTATGCCAACTAGTTTAA 57.568 33.333 5.07 0.00 37.44 1.52
6934 10925 8.591072 ACTAAACTCACTATGCCAACTAGTTTA 58.409 33.333 5.07 0.00 37.07 2.01
6935 10926 7.450903 ACTAAACTCACTATGCCAACTAGTTT 58.549 34.615 5.07 0.00 38.71 2.66
6936 10927 7.005709 ACTAAACTCACTATGCCAACTAGTT 57.994 36.000 1.12 1.12 0.00 2.24
6937 10928 6.437793 AGACTAAACTCACTATGCCAACTAGT 59.562 38.462 0.00 0.00 0.00 2.57
6938 10929 6.868622 AGACTAAACTCACTATGCCAACTAG 58.131 40.000 0.00 0.00 0.00 2.57
6939 10930 6.852420 AGACTAAACTCACTATGCCAACTA 57.148 37.500 0.00 0.00 0.00 2.24
6940 10931 5.746990 AGACTAAACTCACTATGCCAACT 57.253 39.130 0.00 0.00 0.00 3.16
6941 10932 6.426937 TGAAAGACTAAACTCACTATGCCAAC 59.573 38.462 0.00 0.00 0.00 3.77
6942 10933 6.530120 TGAAAGACTAAACTCACTATGCCAA 58.470 36.000 0.00 0.00 0.00 4.52
6943 10934 6.109156 TGAAAGACTAAACTCACTATGCCA 57.891 37.500 0.00 0.00 0.00 4.92
6944 10935 6.037610 CCATGAAAGACTAAACTCACTATGCC 59.962 42.308 0.00 0.00 0.00 4.40
6945 10936 6.457528 GCCATGAAAGACTAAACTCACTATGC 60.458 42.308 0.00 0.00 0.00 3.14
6946 10937 6.037610 GGCCATGAAAGACTAAACTCACTATG 59.962 42.308 0.00 0.00 0.00 2.23
6947 10938 6.116126 GGCCATGAAAGACTAAACTCACTAT 58.884 40.000 0.00 0.00 0.00 2.12
6948 10939 5.488341 GGCCATGAAAGACTAAACTCACTA 58.512 41.667 0.00 0.00 0.00 2.74
6949 10940 4.327680 GGCCATGAAAGACTAAACTCACT 58.672 43.478 0.00 0.00 0.00 3.41
6991 10982 2.762745 TCCAAGACACGGAAAAGTAGC 58.237 47.619 0.00 0.00 0.00 3.58
7001 11113 0.321564 TGCCTGGAATCCAAGACACG 60.322 55.000 2.61 0.00 30.80 4.49
7067 11667 2.758852 TAGGGCCCACCGGAAAGAGT 62.759 60.000 27.56 0.00 46.96 3.24
7068 11668 1.345715 ATAGGGCCCACCGGAAAGAG 61.346 60.000 27.56 0.00 46.96 2.85
7069 11669 0.917333 AATAGGGCCCACCGGAAAGA 60.917 55.000 27.56 0.00 46.96 2.52
7070 11670 0.465642 GAATAGGGCCCACCGGAAAG 60.466 60.000 27.56 0.00 46.96 2.62
7155 11768 1.734137 CTACGGTCGTGGATGAGGG 59.266 63.158 6.25 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.