Multiple sequence alignment - TraesCS3B01G611500

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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 TraesCS3B01G611500 chr3B 100.000 3830 0 0 1 3830 829251291 829255120 0.000000e+00 7073
1 TraesCS3B01G611500 chr7B 88.584 2549 265 17 3 2543 13245331 13242801 0.000000e+00 3072
2 TraesCS3B01G611500 chr7B 88.725 204 21 2 2772 2975 13242517 13242316 8.220000e-62 248
3 TraesCS3B01G611500 chr2B 85.268 2335 289 29 225 2533 799537750 799535445 0.000000e+00 2355
4 TraesCS3B01G611500 chr2B 84.771 2029 269 22 65 2083 799548675 799546677 0.000000e+00 1999
5 TraesCS3B01G611500 chr2B 84.355 2039 252 39 60 2085 799608976 799606992 0.000000e+00 1936
6 TraesCS3B01G611500 chr2B 78.814 1029 182 26 920 1921 1520785 1521804 0.000000e+00 660
7 TraesCS3B01G611500 chr2B 81.918 365 46 13 2179 2533 799565870 799565516 1.350000e-74 291
8 TraesCS3B01G611500 chr2D 88.372 1849 190 14 225 2071 642216351 642218176 0.000000e+00 2200
9 TraesCS3B01G611500 chr2D 85.329 2038 238 38 60 2085 642208918 642210906 0.000000e+00 2050
10 TraesCS3B01G611500 chr2D 86.418 1097 127 12 121 1216 642124019 642122944 0.000000e+00 1181
11 TraesCS3B01G611500 chr2D 84.296 796 92 17 1214 2009 642121575 642120813 0.000000e+00 747
12 TraesCS3B01G611500 chr2D 87.629 291 32 3 2245 2533 642218605 642218893 6.130000e-88 335
13 TraesCS3B01G611500 chr2D 85.670 321 43 2 2199 2519 642337918 642337601 6.130000e-88 335
14 TraesCS3B01G611500 chr2D 85.128 195 23 5 3276 3469 537004936 537005125 1.090000e-45 195
15 TraesCS3B01G611500 chr2A 88.270 1850 190 15 225 2071 767024508 767026333 0.000000e+00 2189
16 TraesCS3B01G611500 chr2A 85.403 1973 236 28 55 2013 767032765 767034699 0.000000e+00 2001
17 TraesCS3B01G611500 chr2A 86.207 290 36 3 2245 2532 767026771 767027058 1.030000e-80 311
18 TraesCS3B01G611500 chr5A 86.316 1827 162 35 442 2217 659255824 659254035 0.000000e+00 1908
19 TraesCS3B01G611500 chr5A 87.464 694 60 4 937 1603 688929444 688930137 0.000000e+00 774
20 TraesCS3B01G611500 chr5A 84.545 440 28 11 44 445 659261422 659260985 2.140000e-107 399
21 TraesCS3B01G611500 chr4D 85.550 1308 148 19 229 1522 504255841 504257121 0.000000e+00 1330
22 TraesCS3B01G611500 chr5B 91.444 561 41 4 3276 3830 170633110 170633669 0.000000e+00 763
23 TraesCS3B01G611500 chr5B 92.245 245 17 2 3032 3275 170632290 170632533 2.830000e-91 346
24 TraesCS3B01G611500 chr5B 87.129 202 21 3 3634 3830 170633673 170633874 1.380000e-54 224
25 TraesCS3B01G611500 chr4B 79.032 868 138 31 1688 2524 650865425 650866279 4.320000e-154 555
26 TraesCS3B01G611500 chr4B 77.473 364 57 15 1596 1939 3626027 3625669 1.090000e-45 195
27 TraesCS3B01G611500 chr5D 85.770 513 47 16 3276 3773 458681984 458682485 1.580000e-143 520
28 TraesCS3B01G611500 chr3A 84.720 517 53 18 3275 3776 738429955 738429450 9.560000e-136 494
29 TraesCS3B01G611500 chr3A 84.720 517 53 18 3275 3776 738519205 738518700 9.560000e-136 494
30 TraesCS3B01G611500 chr3A 84.526 517 51 20 3275 3776 738617341 738616839 5.750000e-133 484
31 TraesCS3B01G611500 chrUn 84.526 517 51 20 3275 3776 340647184 340646682 5.750000e-133 484
32 TraesCS3B01G611500 chrUn 84.615 494 50 18 3298 3776 388840197 388839715 5.790000e-128 468
33 TraesCS3B01G611500 chr6B 84.436 514 52 17 3276 3773 705392111 705392612 7.440000e-132 481
34 TraesCS3B01G611500 chr6B 85.171 263 34 3 2247 2508 27910376 27910118 8.160000e-67 265
35 TraesCS3B01G611500 chr6D 84.496 258 31 8 2247 2501 16154532 16154281 2.960000e-61 246
36 TraesCS3B01G611500 chr1A 83.333 246 32 5 3032 3275 292527633 292527395 6.440000e-53 219


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 TraesCS3B01G611500 chr3B 829251291 829255120 3829 False 7073.000000 7073 100.000000 1 3830 1 chr3B.!!$F1 3829
1 TraesCS3B01G611500 chr7B 13242316 13245331 3015 True 1660.000000 3072 88.654500 3 2975 2 chr7B.!!$R1 2972
2 TraesCS3B01G611500 chr2B 799535445 799537750 2305 True 2355.000000 2355 85.268000 225 2533 1 chr2B.!!$R1 2308
3 TraesCS3B01G611500 chr2B 799546677 799548675 1998 True 1999.000000 1999 84.771000 65 2083 1 chr2B.!!$R2 2018
4 TraesCS3B01G611500 chr2B 799606992 799608976 1984 True 1936.000000 1936 84.355000 60 2085 1 chr2B.!!$R4 2025
5 TraesCS3B01G611500 chr2B 1520785 1521804 1019 False 660.000000 660 78.814000 920 1921 1 chr2B.!!$F1 1001
6 TraesCS3B01G611500 chr2D 642208918 642210906 1988 False 2050.000000 2050 85.329000 60 2085 1 chr2D.!!$F2 2025
7 TraesCS3B01G611500 chr2D 642216351 642218893 2542 False 1267.500000 2200 88.000500 225 2533 2 chr2D.!!$F3 2308
8 TraesCS3B01G611500 chr2D 642120813 642124019 3206 True 964.000000 1181 85.357000 121 2009 2 chr2D.!!$R2 1888
9 TraesCS3B01G611500 chr2A 767032765 767034699 1934 False 2001.000000 2001 85.403000 55 2013 1 chr2A.!!$F1 1958
10 TraesCS3B01G611500 chr2A 767024508 767027058 2550 False 1250.000000 2189 87.238500 225 2532 2 chr2A.!!$F2 2307
11 TraesCS3B01G611500 chr5A 659254035 659255824 1789 True 1908.000000 1908 86.316000 442 2217 1 chr5A.!!$R1 1775
12 TraesCS3B01G611500 chr5A 688929444 688930137 693 False 774.000000 774 87.464000 937 1603 1 chr5A.!!$F1 666
13 TraesCS3B01G611500 chr4D 504255841 504257121 1280 False 1330.000000 1330 85.550000 229 1522 1 chr4D.!!$F1 1293
14 TraesCS3B01G611500 chr5B 170632290 170633874 1584 False 444.333333 763 90.272667 3032 3830 3 chr5B.!!$F1 798
15 TraesCS3B01G611500 chr4B 650865425 650866279 854 False 555.000000 555 79.032000 1688 2524 1 chr4B.!!$F1 836
16 TraesCS3B01G611500 chr5D 458681984 458682485 501 False 520.000000 520 85.770000 3276 3773 1 chr5D.!!$F1 497
17 TraesCS3B01G611500 chr3A 738429450 738429955 505 True 494.000000 494 84.720000 3275 3776 1 chr3A.!!$R1 501
18 TraesCS3B01G611500 chr3A 738518700 738519205 505 True 494.000000 494 84.720000 3275 3776 1 chr3A.!!$R2 501
19 TraesCS3B01G611500 chr3A 738616839 738617341 502 True 484.000000 484 84.526000 3275 3776 1 chr3A.!!$R3 501
20 TraesCS3B01G611500 chrUn 340646682 340647184 502 True 484.000000 484 84.526000 3275 3776 1 chrUn.!!$R1 501
21 TraesCS3B01G611500 chr6B 705392111 705392612 501 False 481.000000 481 84.436000 3276 3773 1 chr6B.!!$F1 497

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
719 750 0.033920 GCCACCTGCTTTCTTTTGGG 59.966 55.0 0.00 0.0 36.87 4.12 F
897 928 0.244721 TGTCGACAGCAGACATCAGG 59.755 55.0 15.76 0.0 42.91 3.86 F
2570 4393 0.103390 TGGTTTCGAGACAACTGCGA 59.897 50.0 8.50 0.0 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 3492 0.106149 ACGTCCCTTCTTGTGTCCAC 59.894 55.0 0.00 0.0 0.0 4.02 R
2678 4501 0.314935 CAAAAACCATCCGCAGCTGT 59.685 50.0 16.64 0.0 0.0 4.40 R
3697 6198 5.361285 TGCTGTGGGTTTTACACTGTAAAAT 59.639 36.0 23.60 0.0 39.2 1.82 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
28 29 9.851686 ATGATTAGTTCTATTGTTGCTATGGAA 57.148 29.630 0.00 0.00 0.00 3.53
391 414 1.451028 GGTCACTGATGGCTGGAGC 60.451 63.158 0.00 0.00 41.14 4.70
475 498 1.661112 GTTCCTGCTCATGTTCGCTAC 59.339 52.381 0.00 0.00 0.00 3.58
499 522 3.195698 GCGGCGGAACATCTCCAC 61.196 66.667 9.78 0.00 45.74 4.02
504 527 1.516386 CGGAACATCTCCACCGTCG 60.516 63.158 0.00 0.00 45.74 5.12
515 546 3.239253 ACCGTCGCAAGGACCCTT 61.239 61.111 0.00 0.00 42.99 3.95
556 587 2.963101 TGGCAGACTACATAGCGGTATT 59.037 45.455 3.95 0.00 0.00 1.89
718 749 0.318955 CGCCACCTGCTTTCTTTTGG 60.319 55.000 0.00 0.00 38.05 3.28
719 750 0.033920 GCCACCTGCTTTCTTTTGGG 59.966 55.000 0.00 0.00 36.87 4.12
783 814 2.328099 GGCAGTTGGACCTTGCTCG 61.328 63.158 13.41 0.00 37.93 5.03
791 822 3.358076 GACCTTGCTCGTAGCCGCT 62.358 63.158 0.00 0.00 41.51 5.52
890 921 3.067601 TGAGTAAGTTTGTCGACAGCAGA 59.932 43.478 19.11 0.11 0.00 4.26
891 922 3.381949 AGTAAGTTTGTCGACAGCAGAC 58.618 45.455 19.11 15.14 38.98 3.51
893 924 2.533266 AGTTTGTCGACAGCAGACAT 57.467 45.000 19.11 0.00 46.44 3.06
894 925 2.408050 AGTTTGTCGACAGCAGACATC 58.592 47.619 19.11 2.12 46.44 3.06
895 926 2.135139 GTTTGTCGACAGCAGACATCA 58.865 47.619 19.11 0.00 46.44 3.07
896 927 2.070262 TTGTCGACAGCAGACATCAG 57.930 50.000 19.11 0.00 46.44 2.90
897 928 0.244721 TGTCGACAGCAGACATCAGG 59.755 55.000 15.76 0.00 42.91 3.86
898 929 0.528017 GTCGACAGCAGACATCAGGA 59.472 55.000 11.55 0.00 38.42 3.86
899 930 1.067565 GTCGACAGCAGACATCAGGAA 60.068 52.381 11.55 0.00 38.42 3.36
982 1019 2.769095 GAGGTTCTACAGGGAGCTCATT 59.231 50.000 17.19 0.00 37.73 2.57
990 1029 1.211457 CAGGGAGCTCATTACCTGCTT 59.789 52.381 19.74 0.00 43.41 3.91
1035 1074 3.069586 TGGACTATAAGTTCTGGCCATCG 59.930 47.826 5.51 0.00 0.00 3.84
1075 1114 6.209589 AGCCATAGAGCTATTCGATAACAAGA 59.790 38.462 0.00 0.00 42.70 3.02
1089 1128 5.220662 CGATAACAAGAGCCAAATGTTCGAT 60.221 40.000 0.00 0.00 38.22 3.59
1401 2822 3.043586 CAACATAGTCGTATCTGTCCGC 58.956 50.000 0.00 0.00 0.00 5.54
1543 3035 5.279156 GGATGCAAAGATTTGTGGAAGAAGT 60.279 40.000 7.12 0.00 40.24 3.01
1590 3082 8.515695 TTTCAGATGATACTAAGAAGTCGGTA 57.484 34.615 0.00 0.00 37.15 4.02
1605 3097 3.069729 AGTCGGTATTGGAAGAGGTATGC 59.930 47.826 0.00 0.00 0.00 3.14
1641 3133 5.244626 GGCATGTAAAGGCAATGAGGATATT 59.755 40.000 0.00 0.00 0.00 1.28
1664 3156 2.891580 TGAGGAGTTACAGTGGTCAGTC 59.108 50.000 0.00 0.00 0.00 3.51
1770 3262 5.106987 GCACTTTGCCACCAAAATATTCTTG 60.107 40.000 0.00 0.00 40.21 3.02
1807 3299 5.769662 TGTGTGGAAGAGCAAGATTATGTTT 59.230 36.000 0.00 0.00 0.00 2.83
1922 3414 6.712179 TGCCAATAATGAAGCAACATATGA 57.288 33.333 10.38 0.00 30.97 2.15
1924 3416 6.546772 TGCCAATAATGAAGCAACATATGAGA 59.453 34.615 10.38 0.00 30.97 3.27
1947 3442 6.937465 AGAGTCTTGATTTTTCTAAGGTGGAC 59.063 38.462 0.00 0.00 0.00 4.02
1996 3492 4.763793 ACAACAGAAGAAGAATGTGGGATG 59.236 41.667 0.00 0.00 0.00 3.51
2078 3586 3.116551 AGGGAGGAGCTGGACATACTAAT 60.117 47.826 0.00 0.00 0.00 1.73
2089 3810 2.303311 GACATACTAATGGAGGAGGGGC 59.697 54.545 0.00 0.00 37.43 5.80
2091 3812 1.119574 TACTAATGGAGGAGGGGCGC 61.120 60.000 0.00 0.00 0.00 6.53
2094 3815 2.889521 TAATGGAGGAGGGGCGCAGA 62.890 60.000 10.83 0.00 0.00 4.26
2096 3817 4.168291 GGAGGAGGGGCGCAGAAG 62.168 72.222 10.83 0.00 0.00 2.85
2097 3818 3.077556 GAGGAGGGGCGCAGAAGA 61.078 66.667 10.83 0.00 0.00 2.87
2098 3819 2.366167 AGGAGGGGCGCAGAAGAT 60.366 61.111 10.83 0.00 0.00 2.40
2099 3820 2.203126 GGAGGGGCGCAGAAGATG 60.203 66.667 10.83 0.00 0.00 2.90
2104 3876 2.586792 GGCGCAGAAGATGGGAGT 59.413 61.111 10.83 0.00 44.43 3.85
2107 3879 1.986575 GCGCAGAAGATGGGAGTTGC 61.987 60.000 0.30 0.00 44.43 4.17
2110 3882 1.081892 CAGAAGATGGGAGTTGCACG 58.918 55.000 0.00 0.00 0.00 5.34
2116 3888 3.535561 AGATGGGAGTTGCACGAAATAG 58.464 45.455 0.00 0.00 0.00 1.73
2183 3970 2.641815 AGAACCTGGAGAAGCTGAACAT 59.358 45.455 0.00 0.00 0.00 2.71
2189 3988 6.721318 ACCTGGAGAAGCTGAACATAATAAA 58.279 36.000 0.00 0.00 0.00 1.40
2190 3989 7.349598 ACCTGGAGAAGCTGAACATAATAAAT 58.650 34.615 0.00 0.00 0.00 1.40
2224 4023 1.005748 CTGGACAGAAGCAGCGTGA 60.006 57.895 0.00 0.00 0.00 4.35
2236 4035 2.631428 GCGTGAAGCTGCGTTTGA 59.369 55.556 7.30 0.00 44.04 2.69
2267 4066 2.928396 ACCTGCCTTAGCCCGTGT 60.928 61.111 0.00 0.00 38.69 4.49
2295 4094 0.329261 TTGCTGTTGGGCTGCTAGAT 59.671 50.000 0.00 0.00 41.79 1.98
2296 4095 1.203237 TGCTGTTGGGCTGCTAGATA 58.797 50.000 0.00 0.00 41.79 1.98
2297 4096 1.134401 TGCTGTTGGGCTGCTAGATAC 60.134 52.381 0.00 0.00 41.79 2.24
2307 4109 0.396556 TGCTAGATACGGTGGAGGCA 60.397 55.000 0.00 0.00 0.00 4.75
2370 4172 2.358957 GTGGAGATGTTGTGCTATGCA 58.641 47.619 0.00 0.00 35.60 3.96
2448 4250 1.825090 TTACCGTCGTCTGGCTTCTA 58.175 50.000 0.00 0.00 0.00 2.10
2460 4262 1.889545 GGCTTCTATCCACTGCCATC 58.110 55.000 0.00 0.00 42.79 3.51
2465 4267 4.378774 CTTCTATCCACTGCCATCTTCAG 58.621 47.826 0.00 0.00 37.56 3.02
2475 4277 1.342819 GCCATCTTCAGTCGCTCCTAT 59.657 52.381 0.00 0.00 0.00 2.57
2519 4321 1.420138 GGGTGTGGAGGAGTTCTTCAA 59.580 52.381 0.00 0.00 31.63 2.69
2524 4326 1.988107 TGGAGGAGTTCTTCAAGCCAT 59.012 47.619 0.00 0.00 0.00 4.40
2540 4363 1.753847 GCCATCATTCCATTTCCGGGA 60.754 52.381 0.00 0.00 0.00 5.14
2545 4368 0.395724 ATTCCATTTCCGGGACAGCC 60.396 55.000 0.00 0.00 33.18 4.85
2546 4369 2.813226 TTCCATTTCCGGGACAGCCG 62.813 60.000 0.00 0.00 33.18 5.52
2548 4371 2.046314 ATTTCCGGGACAGCCGTG 60.046 61.111 0.00 0.00 33.83 4.94
2552 4375 4.838152 CCGGGACAGCCGTGGATG 62.838 72.222 1.93 1.93 37.56 3.51
2556 4379 1.303317 GGACAGCCGTGGATGGTTT 60.303 57.895 9.23 0.00 35.60 3.27
2559 4382 1.375396 CAGCCGTGGATGGTTTCGA 60.375 57.895 0.00 0.00 0.00 3.71
2560 4383 1.079127 AGCCGTGGATGGTTTCGAG 60.079 57.895 0.00 0.00 0.00 4.04
2561 4384 1.079405 GCCGTGGATGGTTTCGAGA 60.079 57.895 0.00 0.00 0.00 4.04
2564 4387 1.606994 CCGTGGATGGTTTCGAGACAA 60.607 52.381 8.50 0.00 0.00 3.18
2569 4392 1.126846 GATGGTTTCGAGACAACTGCG 59.873 52.381 8.50 0.00 0.00 5.18
2570 4393 0.103390 TGGTTTCGAGACAACTGCGA 59.897 50.000 8.50 0.00 0.00 5.10
2571 4394 1.214367 GGTTTCGAGACAACTGCGAA 58.786 50.000 8.50 0.00 41.62 4.70
2580 4403 2.420022 AGACAACTGCGAATGGTTATGC 59.580 45.455 0.00 0.00 0.00 3.14
2581 4404 2.158559 ACAACTGCGAATGGTTATGCA 58.841 42.857 0.00 0.00 35.75 3.96
2586 4409 2.642427 TGCGAATGGTTATGCAGATGT 58.358 42.857 0.00 0.00 32.73 3.06
2588 4411 3.443329 TGCGAATGGTTATGCAGATGTTT 59.557 39.130 0.00 0.00 32.73 2.83
2590 4413 4.201950 GCGAATGGTTATGCAGATGTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
2602 4425 5.039480 CAGATGTTTCTGCGAATGTTTCT 57.961 39.130 0.00 0.00 42.79 2.52
2603 4426 4.849926 CAGATGTTTCTGCGAATGTTTCTG 59.150 41.667 0.00 0.00 42.79 3.02
2604 4427 2.998772 TGTTTCTGCGAATGTTTCTGC 58.001 42.857 0.00 0.00 0.00 4.26
2605 4428 2.357323 TGTTTCTGCGAATGTTTCTGCA 59.643 40.909 0.00 0.00 37.53 4.41
2610 4433 1.135603 TGCGAATGTTTCTGCAGATGC 60.136 47.619 19.04 13.72 42.50 3.91
2612 4435 2.782163 CGAATGTTTCTGCAGATGCTG 58.218 47.619 19.04 5.86 42.66 4.41
2621 4444 3.331319 CAGATGCTGCGGATGCTC 58.669 61.111 0.00 0.00 43.34 4.26
2622 4445 2.110627 AGATGCTGCGGATGCTCC 59.889 61.111 0.00 0.00 43.34 4.70
2623 4446 2.110627 GATGCTGCGGATGCTCCT 59.889 61.111 0.00 0.00 43.34 3.69
2643 4466 2.401766 GGACAGCTGCGGATGGTTG 61.402 63.158 16.45 0.00 32.48 3.77
2646 4469 3.058160 AGCTGCGGATGGTTGTGC 61.058 61.111 0.00 0.00 0.00 4.57
2648 4471 3.803082 CTGCGGATGGTTGTGCGG 61.803 66.667 0.00 0.00 33.26 5.69
2649 4472 4.321966 TGCGGATGGTTGTGCGGA 62.322 61.111 0.00 0.00 33.26 5.54
2650 4473 2.824041 GCGGATGGTTGTGCGGAT 60.824 61.111 0.00 0.00 33.26 4.18
2652 4475 2.472059 CGGATGGTTGTGCGGATGG 61.472 63.158 0.00 0.00 0.00 3.51
2653 4476 1.378514 GGATGGTTGTGCGGATGGT 60.379 57.895 0.00 0.00 0.00 3.55
2654 4477 0.965363 GGATGGTTGTGCGGATGGTT 60.965 55.000 0.00 0.00 0.00 3.67
2655 4478 0.171007 GATGGTTGTGCGGATGGTTG 59.829 55.000 0.00 0.00 0.00 3.77
2656 4479 0.539438 ATGGTTGTGCGGATGGTTGT 60.539 50.000 0.00 0.00 0.00 3.32
2657 4480 1.285641 GGTTGTGCGGATGGTTGTG 59.714 57.895 0.00 0.00 0.00 3.33
2658 4481 1.371635 GTTGTGCGGATGGTTGTGC 60.372 57.895 0.00 0.00 0.00 4.57
2659 4482 2.902419 TTGTGCGGATGGTTGTGCG 61.902 57.895 0.00 0.00 35.93 5.34
2660 4483 4.101790 GTGCGGATGGTTGTGCGG 62.102 66.667 0.00 0.00 33.26 5.69
2661 4484 4.321966 TGCGGATGGTTGTGCGGA 62.322 61.111 0.00 0.00 33.26 5.54
2662 4485 2.824041 GCGGATGGTTGTGCGGAT 60.824 61.111 0.00 0.00 33.26 4.18
2663 4486 2.406616 GCGGATGGTTGTGCGGATT 61.407 57.895 0.00 0.00 33.26 3.01
2664 4487 1.429021 CGGATGGTTGTGCGGATTG 59.571 57.895 0.00 0.00 0.00 2.67
2665 4488 1.305219 CGGATGGTTGTGCGGATTGT 61.305 55.000 0.00 0.00 0.00 2.71
2666 4489 0.171007 GGATGGTTGTGCGGATTGTG 59.829 55.000 0.00 0.00 0.00 3.33
2667 4490 0.456653 GATGGTTGTGCGGATTGTGC 60.457 55.000 0.00 0.00 0.00 4.57
2668 4491 2.126888 GGTTGTGCGGATTGTGCG 60.127 61.111 0.00 0.00 34.24 5.34
2669 4492 2.126888 GTTGTGCGGATTGTGCGG 60.127 61.111 0.00 0.00 34.24 5.69
2670 4493 2.281139 TTGTGCGGATTGTGCGGA 60.281 55.556 0.00 0.00 34.24 5.54
2671 4494 1.673993 TTGTGCGGATTGTGCGGAT 60.674 52.632 0.00 0.00 32.75 4.18
2672 4495 1.240641 TTGTGCGGATTGTGCGGATT 61.241 50.000 0.00 0.00 32.75 3.01
2673 4496 1.062525 GTGCGGATTGTGCGGATTC 59.937 57.895 0.00 0.00 32.75 2.52
2674 4497 2.112198 TGCGGATTGTGCGGATTCC 61.112 57.895 0.00 0.00 34.24 3.01
2684 4507 2.202932 CGGATTCCGGGACAGCTG 60.203 66.667 17.53 13.48 44.15 4.24
2685 4508 2.514824 GGATTCCGGGACAGCTGC 60.515 66.667 15.27 6.61 0.00 5.25
2686 4509 2.892425 GATTCCGGGACAGCTGCG 60.892 66.667 15.27 9.57 0.00 5.18
2687 4510 4.473520 ATTCCGGGACAGCTGCGG 62.474 66.667 21.16 21.16 0.00 5.69
2692 4515 4.101448 GGGACAGCTGCGGATGGT 62.101 66.667 16.45 0.26 32.48 3.55
2693 4516 2.045926 GGACAGCTGCGGATGGTT 60.046 61.111 16.45 0.00 32.48 3.67
2707 4530 2.288763 GGATGGTTTTTGGATTGTGCGT 60.289 45.455 0.00 0.00 0.00 5.24
2711 4534 3.249917 GGTTTTTGGATTGTGCGTATGG 58.750 45.455 0.00 0.00 0.00 2.74
2713 4536 4.082679 GGTTTTTGGATTGTGCGTATGGTA 60.083 41.667 0.00 0.00 0.00 3.25
2714 4537 4.688511 TTTTGGATTGTGCGTATGGTAC 57.311 40.909 0.00 0.00 0.00 3.34
2767 4677 3.615224 CCGTAGGCTACTTTACCCAAA 57.385 47.619 21.51 0.00 46.14 3.28
2770 4680 4.317488 CGTAGGCTACTTTACCCAAACAA 58.683 43.478 21.51 0.00 0.00 2.83
2827 4737 5.518865 AGGGGCTAATTCATTGTATTGTGT 58.481 37.500 0.00 0.00 0.00 3.72
2829 4739 6.772716 AGGGGCTAATTCATTGTATTGTGTAG 59.227 38.462 0.00 0.00 0.00 2.74
2830 4740 6.546034 GGGGCTAATTCATTGTATTGTGTAGT 59.454 38.462 0.00 0.00 0.00 2.73
2876 4786 3.726557 TTCCATGAGCCTTTGATGACT 57.273 42.857 0.00 0.00 0.00 3.41
2877 4787 2.995283 TCCATGAGCCTTTGATGACTG 58.005 47.619 0.00 0.00 0.00 3.51
2879 4789 2.089201 CATGAGCCTTTGATGACTGCA 58.911 47.619 0.00 0.00 0.00 4.41
2882 4792 0.251033 AGCCTTTGATGACTGCAGCA 60.251 50.000 15.27 13.46 38.92 4.41
2915 4825 8.289618 TCCGCTATAGCAATTTGTGATATTTTC 58.710 33.333 23.99 0.00 39.53 2.29
2930 4840 6.659242 GTGATATTTTCCCTTCTCAAAGACCA 59.341 38.462 0.00 0.00 34.14 4.02
2944 4854 5.063204 TCAAAGACCATTCACTTACCTGTG 58.937 41.667 0.00 0.00 39.15 3.66
2946 4856 2.639839 AGACCATTCACTTACCTGTGCT 59.360 45.455 0.00 0.00 37.81 4.40
2947 4857 3.003480 GACCATTCACTTACCTGTGCTC 58.997 50.000 0.00 0.00 37.81 4.26
2975 4885 0.816018 TGACCGCCGACATGTTTGTT 60.816 50.000 0.00 0.00 35.79 2.83
2976 4886 1.149987 GACCGCCGACATGTTTGTTA 58.850 50.000 0.00 0.00 35.79 2.41
2977 4887 1.735571 GACCGCCGACATGTTTGTTAT 59.264 47.619 0.00 0.00 35.79 1.89
2978 4888 2.931325 GACCGCCGACATGTTTGTTATA 59.069 45.455 0.00 0.00 35.79 0.98
2979 4889 2.674357 ACCGCCGACATGTTTGTTATAC 59.326 45.455 0.00 0.00 35.79 1.47
2980 4890 2.933906 CCGCCGACATGTTTGTTATACT 59.066 45.455 0.00 0.00 35.79 2.12
2981 4891 3.000925 CCGCCGACATGTTTGTTATACTC 59.999 47.826 0.00 0.00 35.79 2.59
2982 4892 3.863424 CGCCGACATGTTTGTTATACTCT 59.137 43.478 0.00 0.00 35.79 3.24
2983 4893 4.328983 CGCCGACATGTTTGTTATACTCTT 59.671 41.667 0.00 0.00 35.79 2.85
2984 4894 5.500290 CGCCGACATGTTTGTTATACTCTTC 60.500 44.000 0.00 0.00 35.79 2.87
2985 4895 5.581085 GCCGACATGTTTGTTATACTCTTCT 59.419 40.000 0.00 0.00 35.79 2.85
2986 4896 6.092259 GCCGACATGTTTGTTATACTCTTCTT 59.908 38.462 0.00 0.00 35.79 2.52
2987 4897 7.456253 CCGACATGTTTGTTATACTCTTCTTG 58.544 38.462 0.00 0.00 35.79 3.02
2988 4898 7.117812 CCGACATGTTTGTTATACTCTTCTTGT 59.882 37.037 0.00 0.00 35.79 3.16
2989 4899 8.162880 CGACATGTTTGTTATACTCTTCTTGTC 58.837 37.037 0.00 0.00 35.79 3.18
2990 4900 9.209175 GACATGTTTGTTATACTCTTCTTGTCT 57.791 33.333 0.00 0.00 35.79 3.41
3001 4911 8.774546 ATACTCTTCTTGTCTAATCTGATGGA 57.225 34.615 0.00 0.00 0.00 3.41
3002 4912 6.872920 ACTCTTCTTGTCTAATCTGATGGAC 58.127 40.000 13.58 13.58 0.00 4.02
3003 4913 6.438741 ACTCTTCTTGTCTAATCTGATGGACA 59.561 38.462 17.12 17.12 37.00 4.02
3004 4914 7.125507 ACTCTTCTTGTCTAATCTGATGGACAT 59.874 37.037 19.87 7.43 38.29 3.06
3005 4915 7.270779 TCTTCTTGTCTAATCTGATGGACATG 58.729 38.462 19.87 20.36 38.29 3.21
3006 4916 6.796785 TCTTGTCTAATCTGATGGACATGA 57.203 37.500 22.98 22.98 39.11 3.07
3007 4917 6.814043 TCTTGTCTAATCTGATGGACATGAG 58.186 40.000 22.98 18.44 37.68 2.90
3008 4918 5.541953 TGTCTAATCTGATGGACATGAGG 57.458 43.478 17.12 0.00 34.38 3.86
3009 4919 5.211201 TGTCTAATCTGATGGACATGAGGA 58.789 41.667 17.12 1.35 34.38 3.71
3010 4920 5.303845 TGTCTAATCTGATGGACATGAGGAG 59.696 44.000 17.12 0.00 34.38 3.69
3011 4921 5.304101 GTCTAATCTGATGGACATGAGGAGT 59.696 44.000 0.00 0.00 0.00 3.85
3012 4922 4.418973 AATCTGATGGACATGAGGAGTG 57.581 45.455 0.00 0.00 0.00 3.51
3013 4923 2.825223 TCTGATGGACATGAGGAGTGT 58.175 47.619 0.00 0.00 0.00 3.55
3014 4924 2.498885 TCTGATGGACATGAGGAGTGTG 59.501 50.000 0.00 0.00 0.00 3.82
3015 4925 2.235650 CTGATGGACATGAGGAGTGTGT 59.764 50.000 0.00 0.00 0.00 3.72
3016 4926 2.639347 TGATGGACATGAGGAGTGTGTT 59.361 45.455 0.00 0.00 0.00 3.32
3017 4927 3.072915 TGATGGACATGAGGAGTGTGTTT 59.927 43.478 0.00 0.00 0.00 2.83
3018 4928 4.285775 TGATGGACATGAGGAGTGTGTTTA 59.714 41.667 0.00 0.00 0.00 2.01
3019 4929 4.271696 TGGACATGAGGAGTGTGTTTAG 57.728 45.455 0.00 0.00 0.00 1.85
3020 4930 3.901222 TGGACATGAGGAGTGTGTTTAGA 59.099 43.478 0.00 0.00 0.00 2.10
3021 4931 4.532126 TGGACATGAGGAGTGTGTTTAGAT 59.468 41.667 0.00 0.00 0.00 1.98
3022 4932 5.013079 TGGACATGAGGAGTGTGTTTAGATT 59.987 40.000 0.00 0.00 0.00 2.40
3023 4933 5.940470 GGACATGAGGAGTGTGTTTAGATTT 59.060 40.000 0.00 0.00 0.00 2.17
3024 4934 7.103641 GGACATGAGGAGTGTGTTTAGATTTA 58.896 38.462 0.00 0.00 0.00 1.40
3025 4935 7.606456 GGACATGAGGAGTGTGTTTAGATTTAA 59.394 37.037 0.00 0.00 0.00 1.52
3026 4936 9.167311 GACATGAGGAGTGTGTTTAGATTTAAT 57.833 33.333 0.00 0.00 0.00 1.40
3027 4937 9.520515 ACATGAGGAGTGTGTTTAGATTTAATT 57.479 29.630 0.00 0.00 0.00 1.40
3063 4973 5.947503 TTTGACGCTTGAATGTTTTTCAG 57.052 34.783 0.00 0.00 0.00 3.02
3106 5016 4.336433 CCTGACAAATGACCATATGACACC 59.664 45.833 3.65 0.00 0.00 4.16
3117 5028 2.647529 TATGACACCTGTACTGCACG 57.352 50.000 0.00 0.00 0.00 5.34
3126 5037 2.221055 CCTGTACTGCACGAAAACAGAC 59.779 50.000 9.52 0.00 39.93 3.51
3129 5040 1.865865 ACTGCACGAAAACAGACGAT 58.134 45.000 0.00 0.00 37.35 3.73
3173 5084 4.524802 ATGGGTCAGGCAAGATATTTGA 57.475 40.909 0.00 0.00 0.00 2.69
3195 5106 1.232119 CGGTAACCCTGGTCAACAAC 58.768 55.000 0.00 0.00 0.00 3.32
3210 5121 4.099419 GTCAACAACCCACTCCAGAAAAAT 59.901 41.667 0.00 0.00 0.00 1.82
3211 5122 4.340950 TCAACAACCCACTCCAGAAAAATC 59.659 41.667 0.00 0.00 0.00 2.17
3243 5154 1.074926 TCTCTCCATCTCCAGGGCC 60.075 63.158 0.00 0.00 0.00 5.80
3268 5179 3.204505 CATGTGCCCAACTTGCAAG 57.795 52.632 24.84 24.84 41.06 4.01
3269 5180 0.320073 CATGTGCCCAACTTGCAAGG 60.320 55.000 29.18 14.35 41.06 3.61
3304 5791 5.447548 GCAGCAAGAAAGAAGATCATCAGAC 60.448 44.000 0.10 0.00 0.00 3.51
3339 5833 1.911357 TGATCCACAGGTCAGCATCTT 59.089 47.619 0.00 0.00 0.00 2.40
3393 5888 3.703052 GCATGAACAAATCAGGGAGGAAT 59.297 43.478 0.00 0.00 42.53 3.01
3450 5945 4.985538 TGCTGAACTTCTGGGAAATTACT 58.014 39.130 0.00 0.00 0.00 2.24
3487 5982 7.279750 TCAATTACATTGACATCATCATGGG 57.720 36.000 0.00 0.00 43.84 4.00
3498 5994 8.993404 TGACATCATCATGGGAAAATACATTA 57.007 30.769 0.00 0.00 33.82 1.90
3720 6425 4.904253 TTTACAGTGTAAAACCCACAGC 57.096 40.909 23.06 0.00 35.24 4.40
3726 6431 4.328712 CAGTGTAAAACCCACAGCAAAAAC 59.671 41.667 0.00 0.00 35.24 2.43
3730 6435 5.364157 TGTAAAACCCACAGCAAAAACCTAT 59.636 36.000 0.00 0.00 0.00 2.57
3791 6496 7.589958 TTTACATTGTAAAATCCCAGTGTGT 57.410 32.000 17.46 0.00 34.07 3.72
3795 6500 7.430441 ACATTGTAAAATCCCAGTGTGTAAAC 58.570 34.615 0.00 0.00 31.35 2.01
3796 6501 7.286775 ACATTGTAAAATCCCAGTGTGTAAACT 59.713 33.333 0.00 0.00 31.35 2.66
3798 6503 7.266922 TGTAAAATCCCAGTGTGTAAACTTC 57.733 36.000 0.00 0.00 0.00 3.01
3799 6504 6.829298 TGTAAAATCCCAGTGTGTAAACTTCA 59.171 34.615 0.00 0.00 0.00 3.02
3800 6505 6.391227 AAAATCCCAGTGTGTAAACTTCAG 57.609 37.500 0.00 0.00 0.00 3.02
3801 6506 4.706842 ATCCCAGTGTGTAAACTTCAGT 57.293 40.909 0.00 0.00 0.00 3.41
3802 6507 5.818678 ATCCCAGTGTGTAAACTTCAGTA 57.181 39.130 0.00 0.00 0.00 2.74
3803 6508 4.952460 TCCCAGTGTGTAAACTTCAGTAC 58.048 43.478 0.00 0.00 0.00 2.73
3804 6509 4.652421 TCCCAGTGTGTAAACTTCAGTACT 59.348 41.667 0.00 0.00 0.00 2.73
3805 6510 5.129815 TCCCAGTGTGTAAACTTCAGTACTT 59.870 40.000 0.00 0.00 0.00 2.24
3808 6517 7.186804 CCAGTGTGTAAACTTCAGTACTTTTG 58.813 38.462 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.060347 CCATAGCAACAATAGAACTAATCATGT 57.940 33.333 0.00 0.00 0.00 3.21
1 2 9.276590 TCCATAGCAACAATAGAACTAATCATG 57.723 33.333 0.00 0.00 0.00 3.07
9 10 8.292448 CCACATATTCCATAGCAACAATAGAAC 58.708 37.037 0.00 0.00 0.00 3.01
13 14 8.214364 TGTACCACATATTCCATAGCAACAATA 58.786 33.333 0.00 0.00 0.00 1.90
43 44 3.068732 CACCGTCCAGATGTAGACATGAT 59.931 47.826 0.00 0.00 36.57 2.45
44 45 2.427095 CACCGTCCAGATGTAGACATGA 59.573 50.000 0.00 0.00 36.57 3.07
45 46 2.166459 ACACCGTCCAGATGTAGACATG 59.834 50.000 0.00 0.00 36.57 3.21
46 47 2.457598 ACACCGTCCAGATGTAGACAT 58.542 47.619 0.00 0.00 39.70 3.06
47 48 1.919240 ACACCGTCCAGATGTAGACA 58.081 50.000 0.00 0.00 33.08 3.41
48 49 3.276857 TCTACACCGTCCAGATGTAGAC 58.723 50.000 8.82 0.00 46.33 2.59
50 51 6.316640 CCTATATCTACACCGTCCAGATGTAG 59.683 46.154 11.88 11.88 46.27 2.74
51 52 6.013119 TCCTATATCTACACCGTCCAGATGTA 60.013 42.308 0.00 0.00 31.60 2.29
52 53 5.010933 CCTATATCTACACCGTCCAGATGT 58.989 45.833 0.00 0.00 31.60 3.06
231 245 9.820229 CAGTCGAATTAAACTAGTAAAATTGCA 57.180 29.630 16.15 0.00 0.00 4.08
391 414 0.107214 ACCATTCCATAGGTGCACCG 60.107 55.000 29.68 15.92 42.08 4.94
449 472 2.936919 ACATGAGCAGGAACACTTGA 57.063 45.000 0.00 0.00 0.00 3.02
499 522 2.434359 GAAGGGTCCTTGCGACGG 60.434 66.667 7.03 0.00 42.99 4.79
504 527 1.377856 GCCAGAGAAGGGTCCTTGC 60.378 63.158 7.03 0.33 36.26 4.01
556 587 1.522092 GACATGTGGCCGAGGATGA 59.478 57.895 1.15 0.00 0.00 2.92
710 741 2.258013 CGTCTGCGCCCCAAAAGAA 61.258 57.895 4.18 0.00 0.00 2.52
783 814 1.871080 AATATCAGCACAGCGGCTAC 58.129 50.000 0.26 0.00 43.68 3.58
890 921 5.241662 GTTTAGCTTCACTCTTCCTGATGT 58.758 41.667 0.00 0.00 0.00 3.06
891 922 4.328440 CGTTTAGCTTCACTCTTCCTGATG 59.672 45.833 0.00 0.00 0.00 3.07
893 924 3.572682 TCGTTTAGCTTCACTCTTCCTGA 59.427 43.478 0.00 0.00 0.00 3.86
894 925 3.914312 TCGTTTAGCTTCACTCTTCCTG 58.086 45.455 0.00 0.00 0.00 3.86
895 926 3.827302 TCTCGTTTAGCTTCACTCTTCCT 59.173 43.478 0.00 0.00 0.00 3.36
896 927 4.175787 TCTCGTTTAGCTTCACTCTTCC 57.824 45.455 0.00 0.00 0.00 3.46
897 928 5.117897 CAGTTCTCGTTTAGCTTCACTCTTC 59.882 44.000 0.00 0.00 0.00 2.87
898 929 4.985409 CAGTTCTCGTTTAGCTTCACTCTT 59.015 41.667 0.00 0.00 0.00 2.85
899 930 4.551388 CAGTTCTCGTTTAGCTTCACTCT 58.449 43.478 0.00 0.00 0.00 3.24
943 980 4.841422 ACCTCTTCATGATCCAACTTCTG 58.159 43.478 0.00 0.00 0.00 3.02
982 1019 2.101783 CATGCAAATGGGAAGCAGGTA 58.898 47.619 0.00 0.00 42.14 3.08
990 1029 0.040058 ACTGAGCCATGCAAATGGGA 59.960 50.000 8.41 0.00 41.94 4.37
1035 1074 5.918608 TCTATGGCTTTACTCTGGAATGTC 58.081 41.667 0.00 0.00 0.00 3.06
1089 1128 2.430465 GAGAGCTGCATCTCAACCAAA 58.570 47.619 19.13 0.00 44.32 3.28
1401 2822 1.642037 CTGCAGCCTTGACACATCGG 61.642 60.000 0.00 0.00 0.00 4.18
1543 3035 1.071699 GACAGGTAAGGAGTGGCACAA 59.928 52.381 21.41 0.00 44.16 3.33
1590 3082 4.079558 ACCATTCTGCATACCTCTTCCAAT 60.080 41.667 0.00 0.00 0.00 3.16
1605 3097 0.258484 TACATGCCCCCACCATTCTG 59.742 55.000 0.00 0.00 0.00 3.02
1641 3133 4.673968 ACTGACCACTGTAACTCCTCATA 58.326 43.478 0.00 0.00 0.00 2.15
1664 3156 1.750018 TGCCATGGATTCAGTGCGG 60.750 57.895 18.40 0.00 0.00 5.69
1747 3239 5.990996 ACAAGAATATTTTGGTGGCAAAGTG 59.009 36.000 12.13 0.00 0.00 3.16
1807 3299 1.075601 ACTTCCCTGATTGCCTCCAA 58.924 50.000 0.00 0.00 35.01 3.53
1855 3347 1.737816 GCAGCATGTAGGGGCATTG 59.262 57.895 0.00 0.00 39.31 2.82
1922 3414 6.937465 GTCCACCTTAGAAAAATCAAGACTCT 59.063 38.462 0.00 0.00 0.00 3.24
1924 3416 6.004574 GGTCCACCTTAGAAAAATCAAGACT 58.995 40.000 0.00 0.00 0.00 3.24
1947 3442 1.526917 CCCCCTTCTGCTAATGCGG 60.527 63.158 0.00 0.00 46.48 5.69
1996 3492 0.106149 ACGTCCCTTCTTGTGTCCAC 59.894 55.000 0.00 0.00 0.00 4.02
2089 3810 0.674581 TGCAACTCCCATCTTCTGCG 60.675 55.000 0.00 0.00 32.45 5.18
2091 3812 1.081892 CGTGCAACTCCCATCTTCTG 58.918 55.000 0.00 0.00 31.75 3.02
2094 3815 2.270352 TTTCGTGCAACTCCCATCTT 57.730 45.000 0.00 0.00 31.75 2.40
2096 3817 2.614057 CCTATTTCGTGCAACTCCCATC 59.386 50.000 0.00 0.00 31.75 3.51
2097 3818 2.643551 CCTATTTCGTGCAACTCCCAT 58.356 47.619 0.00 0.00 31.75 4.00
2098 3819 1.339631 CCCTATTTCGTGCAACTCCCA 60.340 52.381 0.00 0.00 31.75 4.37
2099 3820 1.379527 CCCTATTTCGTGCAACTCCC 58.620 55.000 0.00 0.00 31.75 4.30
2104 3876 1.209504 CTCCTCCCCTATTTCGTGCAA 59.790 52.381 0.00 0.00 0.00 4.08
2107 3879 1.123928 AGCTCCTCCCCTATTTCGTG 58.876 55.000 0.00 0.00 0.00 4.35
2110 3882 3.933861 TTTCAGCTCCTCCCCTATTTC 57.066 47.619 0.00 0.00 0.00 2.17
2224 4023 1.230324 GAAGGTCTCAAACGCAGCTT 58.770 50.000 0.00 0.00 0.00 3.74
2233 4032 1.056660 GGTGGAGGTGAAGGTCTCAA 58.943 55.000 0.00 0.00 35.22 3.02
2236 4035 1.484444 GCAGGTGGAGGTGAAGGTCT 61.484 60.000 0.00 0.00 0.00 3.85
2267 4066 1.375908 CCAACAGCAAGCTCCGCTA 60.376 57.895 10.06 0.00 38.25 4.26
2370 4172 4.655647 CTGCTGCAGTGGTGGGCT 62.656 66.667 21.21 0.00 0.00 5.19
2385 4187 2.124570 CTGGCGTGGGAATCCCTG 60.125 66.667 20.55 13.01 45.70 4.45
2448 4250 1.134580 CGACTGAAGATGGCAGTGGAT 60.135 52.381 0.00 0.00 45.94 3.41
2460 4262 3.182967 GTCACAATAGGAGCGACTGAAG 58.817 50.000 0.00 0.00 0.00 3.02
2465 4267 2.094182 TCCTTGTCACAATAGGAGCGAC 60.094 50.000 0.00 0.00 33.23 5.19
2475 4277 6.040391 CCTTCTTAAACCAATCCTTGTCACAA 59.960 38.462 0.00 0.00 0.00 3.33
2502 4304 1.072331 GGCTTGAAGAACTCCTCCACA 59.928 52.381 0.00 0.00 0.00 4.17
2519 4321 1.696063 CCGGAAATGGAATGATGGCT 58.304 50.000 0.00 0.00 0.00 4.75
2524 4326 1.681780 GCTGTCCCGGAAATGGAATGA 60.682 52.381 0.73 0.00 32.59 2.57
2540 4363 1.671054 CGAAACCATCCACGGCTGT 60.671 57.895 0.00 0.00 0.00 4.40
2545 4368 1.459592 GTTGTCTCGAAACCATCCACG 59.540 52.381 0.00 0.00 0.00 4.94
2546 4369 2.480419 CAGTTGTCTCGAAACCATCCAC 59.520 50.000 0.00 0.00 0.00 4.02
2548 4371 1.464997 GCAGTTGTCTCGAAACCATCC 59.535 52.381 0.00 0.00 0.00 3.51
2550 4373 1.148310 CGCAGTTGTCTCGAAACCAT 58.852 50.000 0.00 0.00 0.00 3.55
2552 4375 1.214367 TTCGCAGTTGTCTCGAAACC 58.786 50.000 0.00 0.00 38.97 3.27
2556 4379 0.317160 ACCATTCGCAGTTGTCTCGA 59.683 50.000 0.00 0.00 0.00 4.04
2559 4382 2.420022 GCATAACCATTCGCAGTTGTCT 59.580 45.455 0.00 0.00 0.00 3.41
2560 4383 2.161410 TGCATAACCATTCGCAGTTGTC 59.839 45.455 0.00 0.00 0.00 3.18
2561 4384 2.158559 TGCATAACCATTCGCAGTTGT 58.841 42.857 0.00 0.00 0.00 3.32
2580 4403 4.849926 CAGAAACATTCGCAGAAACATCTG 59.150 41.667 1.50 1.50 45.90 2.90
2581 4404 4.614535 GCAGAAACATTCGCAGAAACATCT 60.615 41.667 0.00 0.00 45.90 2.90
2582 4405 3.605486 GCAGAAACATTCGCAGAAACATC 59.395 43.478 0.00 0.00 45.90 3.06
2583 4406 3.004629 TGCAGAAACATTCGCAGAAACAT 59.995 39.130 5.83 0.00 45.90 2.71
2584 4407 2.357323 TGCAGAAACATTCGCAGAAACA 59.643 40.909 5.83 0.00 45.90 2.83
2590 4413 1.135603 GCATCTGCAGAAACATTCGCA 60.136 47.619 22.50 0.00 41.59 5.10
2591 4414 1.131883 AGCATCTGCAGAAACATTCGC 59.868 47.619 22.50 13.89 45.16 4.70
2592 4415 2.782163 CAGCATCTGCAGAAACATTCG 58.218 47.619 22.50 4.63 45.16 3.34
2604 4427 3.331319 GAGCATCCGCAGCATCTG 58.669 61.111 0.00 0.00 42.27 2.90
2619 4442 4.463879 CCGCAGCTGTCCCAGGAG 62.464 72.222 16.64 0.00 31.21 3.69
2621 4444 3.790437 ATCCGCAGCTGTCCCAGG 61.790 66.667 16.64 11.20 31.21 4.45
2622 4445 2.513204 CATCCGCAGCTGTCCCAG 60.513 66.667 16.64 2.15 34.12 4.45
2623 4446 4.100084 CCATCCGCAGCTGTCCCA 62.100 66.667 16.64 0.00 0.00 4.37
2643 4466 4.101790 CCGCACAACCATCCGCAC 62.102 66.667 0.00 0.00 0.00 5.34
2646 4469 1.305219 ACAATCCGCACAACCATCCG 61.305 55.000 0.00 0.00 0.00 4.18
2648 4471 0.456653 GCACAATCCGCACAACCATC 60.457 55.000 0.00 0.00 0.00 3.51
2649 4472 1.586028 GCACAATCCGCACAACCAT 59.414 52.632 0.00 0.00 0.00 3.55
2650 4473 2.902419 CGCACAATCCGCACAACCA 61.902 57.895 0.00 0.00 0.00 3.67
2652 4475 1.922135 ATCCGCACAATCCGCACAAC 61.922 55.000 0.00 0.00 0.00 3.32
2653 4476 1.240641 AATCCGCACAATCCGCACAA 61.241 50.000 0.00 0.00 0.00 3.33
2654 4477 1.643868 GAATCCGCACAATCCGCACA 61.644 55.000 0.00 0.00 0.00 4.57
2655 4478 1.062525 GAATCCGCACAATCCGCAC 59.937 57.895 0.00 0.00 0.00 5.34
2656 4479 2.112198 GGAATCCGCACAATCCGCA 61.112 57.895 0.00 0.00 0.00 5.69
2657 4480 2.715624 GGAATCCGCACAATCCGC 59.284 61.111 0.00 0.00 0.00 5.54
2659 4482 2.186826 CCCGGAATCCGCACAATCC 61.187 63.158 17.50 0.00 46.86 3.01
2660 4483 1.153249 TCCCGGAATCCGCACAATC 60.153 57.895 17.50 0.00 46.86 2.67
2661 4484 1.451387 GTCCCGGAATCCGCACAAT 60.451 57.895 17.50 0.00 46.86 2.71
2662 4485 2.046700 GTCCCGGAATCCGCACAA 60.047 61.111 17.50 0.00 46.86 3.33
2663 4486 3.309436 CTGTCCCGGAATCCGCACA 62.309 63.158 17.50 18.58 46.86 4.57
2664 4487 2.511600 CTGTCCCGGAATCCGCAC 60.512 66.667 17.50 14.94 46.86 5.34
2665 4488 4.467084 GCTGTCCCGGAATCCGCA 62.467 66.667 17.50 8.25 46.86 5.69
2666 4489 4.162690 AGCTGTCCCGGAATCCGC 62.163 66.667 17.50 3.26 46.86 5.54
2668 4491 2.514824 GCAGCTGTCCCGGAATCC 60.515 66.667 16.64 0.00 0.00 3.01
2669 4492 2.892425 CGCAGCTGTCCCGGAATC 60.892 66.667 16.64 0.00 0.00 2.52
2670 4493 4.473520 CCGCAGCTGTCCCGGAAT 62.474 66.667 22.29 0.00 44.55 3.01
2675 4498 3.628646 AACCATCCGCAGCTGTCCC 62.629 63.158 16.64 0.00 0.00 4.46
2676 4499 1.244019 AAAACCATCCGCAGCTGTCC 61.244 55.000 16.64 0.00 0.00 4.02
2677 4500 0.598065 AAAAACCATCCGCAGCTGTC 59.402 50.000 16.64 6.83 0.00 3.51
2678 4501 0.314935 CAAAAACCATCCGCAGCTGT 59.685 50.000 16.64 0.00 0.00 4.40
2679 4502 0.388907 CCAAAAACCATCCGCAGCTG 60.389 55.000 10.11 10.11 0.00 4.24
2680 4503 0.539438 TCCAAAAACCATCCGCAGCT 60.539 50.000 0.00 0.00 0.00 4.24
2681 4504 0.532115 ATCCAAAAACCATCCGCAGC 59.468 50.000 0.00 0.00 0.00 5.25
2682 4505 2.029110 ACAATCCAAAAACCATCCGCAG 60.029 45.455 0.00 0.00 0.00 5.18
2683 4506 1.967066 ACAATCCAAAAACCATCCGCA 59.033 42.857 0.00 0.00 0.00 5.69
2684 4507 2.336667 CACAATCCAAAAACCATCCGC 58.663 47.619 0.00 0.00 0.00 5.54
2685 4508 2.336667 GCACAATCCAAAAACCATCCG 58.663 47.619 0.00 0.00 0.00 4.18
2686 4509 2.288763 ACGCACAATCCAAAAACCATCC 60.289 45.455 0.00 0.00 0.00 3.51
2687 4510 3.025287 ACGCACAATCCAAAAACCATC 57.975 42.857 0.00 0.00 0.00 3.51
2688 4511 4.493547 CATACGCACAATCCAAAAACCAT 58.506 39.130 0.00 0.00 0.00 3.55
2689 4512 3.305676 CCATACGCACAATCCAAAAACCA 60.306 43.478 0.00 0.00 0.00 3.67
2690 4513 3.249917 CCATACGCACAATCCAAAAACC 58.750 45.455 0.00 0.00 0.00 3.27
2691 4514 3.908213 ACCATACGCACAATCCAAAAAC 58.092 40.909 0.00 0.00 0.00 2.43
2692 4515 4.519350 TGTACCATACGCACAATCCAAAAA 59.481 37.500 0.00 0.00 0.00 1.94
2693 4516 4.072839 TGTACCATACGCACAATCCAAAA 58.927 39.130 0.00 0.00 0.00 2.44
2707 4530 0.392706 CCATCCGCAGCTGTACCATA 59.607 55.000 16.64 0.00 0.00 2.74
2711 4534 2.464459 GCACCATCCGCAGCTGTAC 61.464 63.158 16.64 0.00 0.00 2.90
2715 4538 3.094062 ATACGCACCATCCGCAGCT 62.094 57.895 0.00 0.00 0.00 4.24
2716 4539 2.588877 ATACGCACCATCCGCAGC 60.589 61.111 0.00 0.00 0.00 5.25
2717 4540 2.246739 CCATACGCACCATCCGCAG 61.247 63.158 0.00 0.00 0.00 5.18
2718 4541 1.677637 TACCATACGCACCATCCGCA 61.678 55.000 0.00 0.00 0.00 5.69
2719 4542 1.068417 TACCATACGCACCATCCGC 59.932 57.895 0.00 0.00 0.00 5.54
2720 4543 0.937699 CGTACCATACGCACCATCCG 60.938 60.000 0.00 0.00 45.81 4.18
2721 4544 2.895039 CGTACCATACGCACCATCC 58.105 57.895 0.00 0.00 45.81 3.51
2743 4566 2.102578 GGTAAAGTAGCCTACGGACCA 58.897 52.381 14.35 0.00 32.96 4.02
2744 4567 1.410517 GGGTAAAGTAGCCTACGGACC 59.589 57.143 12.03 12.03 42.93 4.46
2745 4568 2.102578 TGGGTAAAGTAGCCTACGGAC 58.897 52.381 5.20 0.00 46.32 4.79
2747 4570 3.264947 GTTTGGGTAAAGTAGCCTACGG 58.735 50.000 5.20 0.00 46.32 4.02
2750 4573 5.180271 CGATTGTTTGGGTAAAGTAGCCTA 58.820 41.667 5.20 0.00 46.32 3.93
2751 4574 4.007659 CGATTGTTTGGGTAAAGTAGCCT 58.992 43.478 5.20 0.00 46.32 4.58
2754 4577 3.754323 TGGCGATTGTTTGGGTAAAGTAG 59.246 43.478 0.00 0.00 0.00 2.57
2757 4580 2.671070 GCTGGCGATTGTTTGGGTAAAG 60.671 50.000 0.00 0.00 0.00 1.85
2759 4582 0.885196 GCTGGCGATTGTTTGGGTAA 59.115 50.000 0.00 0.00 0.00 2.85
2760 4583 1.302383 CGCTGGCGATTGTTTGGGTA 61.302 55.000 9.51 0.00 42.83 3.69
2761 4584 2.625823 CGCTGGCGATTGTTTGGGT 61.626 57.895 9.51 0.00 42.83 4.51
2762 4585 2.179018 CGCTGGCGATTGTTTGGG 59.821 61.111 9.51 0.00 42.83 4.12
2764 4587 2.179018 CCCGCTGGCGATTGTTTG 59.821 61.111 16.79 0.00 42.83 2.93
2784 4694 0.396811 CCTCAAACCCGAACCACTCT 59.603 55.000 0.00 0.00 0.00 3.24
2849 4759 9.453572 GTCATCAAAGGCTCATGGAAATATATA 57.546 33.333 0.00 0.00 0.00 0.86
2850 4760 8.168725 AGTCATCAAAGGCTCATGGAAATATAT 58.831 33.333 0.00 0.00 0.00 0.86
2854 4764 4.401519 CAGTCATCAAAGGCTCATGGAAAT 59.598 41.667 0.00 0.00 0.00 2.17
2858 4768 1.404391 GCAGTCATCAAAGGCTCATGG 59.596 52.381 0.00 0.00 0.00 3.66
2891 4801 7.538678 GGGAAAATATCACAAATTGCTATAGCG 59.461 37.037 19.55 7.56 45.83 4.26
2898 4808 7.322664 TGAGAAGGGAAAATATCACAAATTGC 58.677 34.615 0.00 0.00 32.04 3.56
2915 4825 4.026356 AGTGAATGGTCTTTGAGAAGGG 57.974 45.455 0.00 0.00 33.56 3.95
2920 4830 5.180117 CACAGGTAAGTGAATGGTCTTTGAG 59.820 44.000 0.00 0.00 42.05 3.02
2930 4840 1.676014 GCCGAGCACAGGTAAGTGAAT 60.676 52.381 0.00 0.00 42.05 2.57
2961 4871 5.581085 AGAAGAGTATAACAAACATGTCGGC 59.419 40.000 0.00 0.00 0.00 5.54
2975 4885 9.868160 TCCATCAGATTAGACAAGAAGAGTATA 57.132 33.333 0.00 0.00 0.00 1.47
2976 4886 8.637986 GTCCATCAGATTAGACAAGAAGAGTAT 58.362 37.037 5.71 0.00 0.00 2.12
2977 4887 7.615757 TGTCCATCAGATTAGACAAGAAGAGTA 59.384 37.037 9.68 0.00 36.36 2.59
2978 4888 6.438741 TGTCCATCAGATTAGACAAGAAGAGT 59.561 38.462 9.68 0.00 36.36 3.24
2979 4889 6.871844 TGTCCATCAGATTAGACAAGAAGAG 58.128 40.000 9.68 0.00 36.36 2.85
2980 4890 6.857437 TGTCCATCAGATTAGACAAGAAGA 57.143 37.500 9.68 0.00 36.36 2.87
2981 4891 7.270779 TCATGTCCATCAGATTAGACAAGAAG 58.729 38.462 14.38 7.59 42.14 2.85
2982 4892 7.186570 TCATGTCCATCAGATTAGACAAGAA 57.813 36.000 14.38 4.00 42.14 2.52
2983 4893 6.183360 CCTCATGTCCATCAGATTAGACAAGA 60.183 42.308 14.38 14.03 42.14 3.02
2984 4894 5.990386 CCTCATGTCCATCAGATTAGACAAG 59.010 44.000 14.38 11.28 42.14 3.16
2985 4895 5.662657 TCCTCATGTCCATCAGATTAGACAA 59.337 40.000 14.38 2.35 42.14 3.18
2986 4896 5.211201 TCCTCATGTCCATCAGATTAGACA 58.789 41.667 13.22 13.22 42.95 3.41
2987 4897 5.304101 ACTCCTCATGTCCATCAGATTAGAC 59.696 44.000 0.00 4.05 0.00 2.59
2988 4898 5.303845 CACTCCTCATGTCCATCAGATTAGA 59.696 44.000 0.00 0.00 0.00 2.10
2989 4899 5.070180 ACACTCCTCATGTCCATCAGATTAG 59.930 44.000 0.00 0.00 0.00 1.73
2990 4900 4.964897 ACACTCCTCATGTCCATCAGATTA 59.035 41.667 0.00 0.00 0.00 1.75
2991 4901 3.779183 ACACTCCTCATGTCCATCAGATT 59.221 43.478 0.00 0.00 0.00 2.40
2992 4902 3.134262 CACACTCCTCATGTCCATCAGAT 59.866 47.826 0.00 0.00 0.00 2.90
2993 4903 2.498885 CACACTCCTCATGTCCATCAGA 59.501 50.000 0.00 0.00 0.00 3.27
2994 4904 2.235650 ACACACTCCTCATGTCCATCAG 59.764 50.000 0.00 0.00 0.00 2.90
2995 4905 2.259917 ACACACTCCTCATGTCCATCA 58.740 47.619 0.00 0.00 0.00 3.07
2996 4906 3.340814 AACACACTCCTCATGTCCATC 57.659 47.619 0.00 0.00 0.00 3.51
2997 4907 3.795688 AAACACACTCCTCATGTCCAT 57.204 42.857 0.00 0.00 0.00 3.41
2998 4908 3.901222 TCTAAACACACTCCTCATGTCCA 59.099 43.478 0.00 0.00 0.00 4.02
2999 4909 4.537135 TCTAAACACACTCCTCATGTCC 57.463 45.455 0.00 0.00 0.00 4.02
3000 4910 8.547967 TTAAATCTAAACACACTCCTCATGTC 57.452 34.615 0.00 0.00 0.00 3.06
3001 4911 9.520515 AATTAAATCTAAACACACTCCTCATGT 57.479 29.630 0.00 0.00 0.00 3.21
3005 4915 9.543018 CGAAAATTAAATCTAAACACACTCCTC 57.457 33.333 0.00 0.00 0.00 3.71
3006 4916 8.512138 CCGAAAATTAAATCTAAACACACTCCT 58.488 33.333 0.00 0.00 0.00 3.69
3007 4917 8.508875 TCCGAAAATTAAATCTAAACACACTCC 58.491 33.333 0.00 0.00 0.00 3.85
3008 4918 9.326339 GTCCGAAAATTAAATCTAAACACACTC 57.674 33.333 0.00 0.00 0.00 3.51
3009 4919 9.063615 AGTCCGAAAATTAAATCTAAACACACT 57.936 29.630 0.00 0.00 0.00 3.55
3010 4920 9.113876 CAGTCCGAAAATTAAATCTAAACACAC 57.886 33.333 0.00 0.00 0.00 3.82
3011 4921 8.842280 ACAGTCCGAAAATTAAATCTAAACACA 58.158 29.630 0.00 0.00 0.00 3.72
3012 4922 9.326339 GACAGTCCGAAAATTAAATCTAAACAC 57.674 33.333 0.00 0.00 0.00 3.32
3013 4923 9.280174 AGACAGTCCGAAAATTAAATCTAAACA 57.720 29.630 0.00 0.00 0.00 2.83
3106 5016 2.097396 CGTCTGTTTTCGTGCAGTACAG 60.097 50.000 0.00 0.00 38.00 2.74
3117 5028 4.835199 TTTAGCGCTATCGTCTGTTTTC 57.165 40.909 19.60 0.00 38.14 2.29
3126 5037 0.503117 GCGTCCTTTTAGCGCTATCG 59.497 55.000 19.60 15.77 46.55 2.92
3152 5063 4.210331 GTCAAATATCTTGCCTGACCCAT 58.790 43.478 0.00 0.00 32.10 4.00
3153 5064 3.620488 GTCAAATATCTTGCCTGACCCA 58.380 45.455 0.00 0.00 32.10 4.51
3157 5068 2.421388 CCGGGTCAAATATCTTGCCTGA 60.421 50.000 0.00 0.00 0.00 3.86
3165 5076 3.473625 CAGGGTTACCGGGTCAAATATC 58.526 50.000 6.32 0.00 43.47 1.63
3195 5106 2.041620 TCCCTGATTTTTCTGGAGTGGG 59.958 50.000 0.00 0.00 0.00 4.61
3231 5142 1.077930 CTGTGTGGCCCTGGAGATG 60.078 63.158 0.00 0.00 0.00 2.90
3268 5179 4.724602 TGCTGCTCGTCTCGTGCC 62.725 66.667 12.27 1.11 44.12 5.01
3269 5180 2.724708 CTTGCTGCTCGTCTCGTGC 61.725 63.158 0.00 8.82 44.82 5.34
3304 5791 2.082231 GGATCATGATGCTGATTCCCG 58.918 52.381 19.05 0.00 36.01 5.14
3339 5833 3.898123 AGAGAGAAGTTGGTGAGCAGTTA 59.102 43.478 0.00 0.00 0.00 2.24
3498 5994 7.603404 TCCATTCGAATCATTTCAATGCTTTTT 59.397 29.630 7.92 0.00 36.36 1.94
3697 6198 5.361285 TGCTGTGGGTTTTACACTGTAAAAT 59.639 36.000 23.60 0.00 39.20 1.82
3773 6478 7.339721 TGAAGTTTACACACTGGGATTTTACAA 59.660 33.333 0.00 0.00 0.00 2.41
3795 6500 8.621286 ACACTGGAAATTACAAAAGTACTGAAG 58.379 33.333 0.00 0.00 0.00 3.02
3796 6501 8.514330 ACACTGGAAATTACAAAAGTACTGAA 57.486 30.769 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.