Multiple sequence alignment - TraesCS4A01G462500

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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 TraesCS4A01G462500 chr4A 100.000 3466 0 0 1 3466 726578442 726574977 0.000000e+00 6401
1 TraesCS4A01G462500 chr4A 84.848 198 25 5 200 396 252794705 252794898 9.820000e-46 195
2 TraesCS4A01G462500 chr4A 82.775 209 29 6 2 207 547998927 547998723 2.750000e-41 180
3 TraesCS4A01G462500 chr7A 93.246 1599 99 6 858 2451 10830392 10831986 0.000000e+00 2346
4 TraesCS4A01G462500 chr7A 90.268 1233 97 16 1242 2455 10380393 10381621 0.000000e+00 1591
5 TraesCS4A01G462500 chr7A 86.667 615 52 21 23 626 10803215 10803810 0.000000e+00 654
6 TraesCS4A01G462500 chr7A 85.973 221 17 11 2538 2749 10832156 10832371 1.250000e-54 224
7 TraesCS4A01G462500 chr7A 87.310 197 17 3 2471 2659 10831971 10832167 5.820000e-53 219
8 TraesCS4A01G462500 chr7D 91.579 1330 104 5 1131 2455 11260842 11262168 0.000000e+00 1829
9 TraesCS4A01G462500 chr7D 89.560 182 17 2 682 861 31996925 31996744 2.690000e-56 230
10 TraesCS4A01G462500 chr7D 86.730 211 15 10 2542 2744 11262337 11262542 4.500000e-54 222
11 TraesCS4A01G462500 chr7D 82.843 204 23 10 858 1056 11260522 11260718 4.600000e-39 172
12 TraesCS4A01G462500 chr2B 95.489 665 19 3 2802 3466 359530723 359530070 0.000000e+00 1051
13 TraesCS4A01G462500 chr2B 90.028 722 56 9 2750 3466 556485339 556486049 0.000000e+00 920
14 TraesCS4A01G462500 chr2B 89.598 721 60 9 2751 3466 394954629 394955339 0.000000e+00 902
15 TraesCS4A01G462500 chr2B 81.057 1135 179 20 1284 2393 547865673 547864550 0.000000e+00 872
16 TraesCS4A01G462500 chr2B 83.356 727 92 21 2751 3466 68604155 68603447 0.000000e+00 645
17 TraesCS4A01G462500 chr2B 77.604 1152 201 27 1284 2393 547430250 547429114 0.000000e+00 645
18 TraesCS4A01G462500 chr2B 78.022 1092 190 28 1282 2330 547441252 547440168 2.920000e-180 641
19 TraesCS4A01G462500 chr2B 77.993 1086 193 24 1282 2329 547097124 547096047 1.050000e-179 640
20 TraesCS4A01G462500 chr2B 88.267 375 25 10 2750 3121 796651755 796651397 6.870000e-117 431
21 TraesCS4A01G462500 chr2B 91.620 179 13 2 685 861 771215317 771215139 2.670000e-61 246
22 TraesCS4A01G462500 chr2B 81.481 189 28 3 2181 2362 655299629 655299441 7.750000e-32 148
23 TraesCS4A01G462500 chr6A 91.911 717 42 7 2752 3466 563144497 563143795 0.000000e+00 989
24 TraesCS4A01G462500 chr6A 85.279 197 24 5 200 395 384451678 384451486 7.590000e-47 198
25 TraesCS4A01G462500 chr3B 90.808 718 51 10 2750 3466 360084609 360083906 0.000000e+00 946
26 TraesCS4A01G462500 chr1A 90.707 721 46 10 2752 3466 6161626 6162331 0.000000e+00 941
27 TraesCS4A01G462500 chr1A 83.356 727 103 14 2746 3466 501044391 501045105 0.000000e+00 656
28 TraesCS4A01G462500 chr1A 74.220 609 133 13 1773 2363 97793262 97793864 2.080000e-57 233
29 TraesCS4A01G462500 chr1A 73.034 534 124 14 1836 2353 546503174 546502645 1.650000e-38 171
30 TraesCS4A01G462500 chr2D 78.910 1394 232 42 1284 2640 469227138 469225770 0.000000e+00 889
31 TraesCS4A01G462500 chr2D 78.062 743 131 19 1284 2001 468950456 468949721 1.140000e-119 440
32 TraesCS4A01G462500 chr2D 90.556 180 15 2 684 861 109696156 109695977 1.610000e-58 237
33 TraesCS4A01G462500 chr2D 82.775 209 28 8 2 207 619442343 619442546 2.750000e-41 180
34 TraesCS4A01G462500 chr2A 80.423 1134 179 23 1284 2393 610996222 610995108 0.000000e+00 824
35 TraesCS4A01G462500 chr2A 85.279 197 24 5 200 395 696848337 696848529 7.590000e-47 198
36 TraesCS4A01G462500 chr2A 82.036 167 18 6 2480 2640 610995022 610994862 7.810000e-27 132
37 TraesCS4A01G462500 chr2A 79.474 190 32 3 2181 2363 691415346 691415157 1.010000e-25 128
38 TraesCS4A01G462500 chr4D 86.963 721 76 14 2752 3466 449817662 449816954 0.000000e+00 795
39 TraesCS4A01G462500 chr4D 91.209 182 14 2 682 861 35722300 35722481 2.670000e-61 246
40 TraesCS4A01G462500 chr4D 90.556 180 16 1 683 861 419245229 419245408 1.610000e-58 237
41 TraesCS4A01G462500 chr4D 85.714 196 23 5 200 394 48053317 48053508 5.870000e-48 202
42 TraesCS4A01G462500 chr4D 82.775 209 29 6 2 207 77029914 77030118 2.750000e-41 180
43 TraesCS4A01G462500 chr4D 82.857 210 27 7 2 207 472499179 472499383 2.750000e-41 180
44 TraesCS4A01G462500 chr5D 85.853 721 83 13 2752 3466 443832583 443831876 0.000000e+00 749
45 TraesCS4A01G462500 chr5D 83.158 285 39 6 8 290 25299853 25299576 5.740000e-63 252
46 TraesCS4A01G462500 chr5D 77.748 373 53 19 43 395 493832175 493832537 5.870000e-48 202
47 TraesCS4A01G462500 chr5D 83.744 203 26 6 8 207 9104808 9104610 5.910000e-43 185
48 TraesCS4A01G462500 chr3A 84.844 706 85 17 2752 3454 22670562 22669876 0.000000e+00 691
49 TraesCS4A01G462500 chr5B 77.127 529 103 7 1840 2353 46746727 46746202 1.220000e-74 291
50 TraesCS4A01G462500 chr5B 88.889 189 20 1 674 861 99602923 99603111 7.480000e-57 231
51 TraesCS4A01G462500 chr1D 76.051 547 111 10 1773 2303 79116258 79116800 2.050000e-67 267
52 TraesCS4A01G462500 chr1D 74.172 604 140 10 1774 2363 451940716 451940115 1.610000e-58 237
53 TraesCS4A01G462500 chr7B 91.257 183 11 4 682 861 606591267 606591087 9.610000e-61 244
54 TraesCS4A01G462500 chr7B 75.670 485 93 16 1839 2303 691458744 691459223 5.820000e-53 219
55 TraesCS4A01G462500 chr3D 89.947 189 15 3 677 861 486691447 486691635 1.240000e-59 241
56 TraesCS4A01G462500 chr3D 90.556 180 16 1 683 861 533955696 533955517 1.610000e-58 237
57 TraesCS4A01G462500 chr3D 86.082 194 22 5 683 873 614670365 614670174 1.630000e-48 204
58 TraesCS4A01G462500 chr3D 77.865 384 45 22 43 395 527144384 527144758 5.870000e-48 202
59 TraesCS4A01G462500 chr1B 74.194 589 136 10 1779 2353 621947015 621946429 7.480000e-57 231
60 TraesCS4A01G462500 chr6D 85.787 197 23 5 200 395 333807119 333807311 1.630000e-48 204
61 TraesCS4A01G462500 chr6D 84.694 196 28 2 200 395 407917071 407917264 9.820000e-46 195
62 TraesCS4A01G462500 chr6D 83.173 208 27 7 2 207 456832151 456832352 2.120000e-42 183
63 TraesCS4A01G462500 chr6D 82.775 209 29 6 2 208 14600568 14600771 2.750000e-41 180


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 TraesCS4A01G462500 chr4A 726574977 726578442 3465 True 6401.000000 6401 100.000000 1 3466 1 chr4A.!!$R2 3465
1 TraesCS4A01G462500 chr7A 10380393 10381621 1228 False 1591.000000 1591 90.268000 1242 2455 1 chr7A.!!$F1 1213
2 TraesCS4A01G462500 chr7A 10830392 10832371 1979 False 929.666667 2346 88.843000 858 2749 3 chr7A.!!$F3 1891
3 TraesCS4A01G462500 chr7A 10803215 10803810 595 False 654.000000 654 86.667000 23 626 1 chr7A.!!$F2 603
4 TraesCS4A01G462500 chr7D 11260522 11262542 2020 False 741.000000 1829 87.050667 858 2744 3 chr7D.!!$F1 1886
5 TraesCS4A01G462500 chr2B 359530070 359530723 653 True 1051.000000 1051 95.489000 2802 3466 1 chr2B.!!$R2 664
6 TraesCS4A01G462500 chr2B 556485339 556486049 710 False 920.000000 920 90.028000 2750 3466 1 chr2B.!!$F2 716
7 TraesCS4A01G462500 chr2B 394954629 394955339 710 False 902.000000 902 89.598000 2751 3466 1 chr2B.!!$F1 715
8 TraesCS4A01G462500 chr2B 547864550 547865673 1123 True 872.000000 872 81.057000 1284 2393 1 chr2B.!!$R6 1109
9 TraesCS4A01G462500 chr2B 68603447 68604155 708 True 645.000000 645 83.356000 2751 3466 1 chr2B.!!$R1 715
10 TraesCS4A01G462500 chr2B 547429114 547430250 1136 True 645.000000 645 77.604000 1284 2393 1 chr2B.!!$R4 1109
11 TraesCS4A01G462500 chr2B 547440168 547441252 1084 True 641.000000 641 78.022000 1282 2330 1 chr2B.!!$R5 1048
12 TraesCS4A01G462500 chr2B 547096047 547097124 1077 True 640.000000 640 77.993000 1282 2329 1 chr2B.!!$R3 1047
13 TraesCS4A01G462500 chr6A 563143795 563144497 702 True 989.000000 989 91.911000 2752 3466 1 chr6A.!!$R2 714
14 TraesCS4A01G462500 chr3B 360083906 360084609 703 True 946.000000 946 90.808000 2750 3466 1 chr3B.!!$R1 716
15 TraesCS4A01G462500 chr1A 6161626 6162331 705 False 941.000000 941 90.707000 2752 3466 1 chr1A.!!$F1 714
16 TraesCS4A01G462500 chr1A 501044391 501045105 714 False 656.000000 656 83.356000 2746 3466 1 chr1A.!!$F3 720
17 TraesCS4A01G462500 chr1A 97793262 97793864 602 False 233.000000 233 74.220000 1773 2363 1 chr1A.!!$F2 590
18 TraesCS4A01G462500 chr2D 469225770 469227138 1368 True 889.000000 889 78.910000 1284 2640 1 chr2D.!!$R3 1356
19 TraesCS4A01G462500 chr2D 468949721 468950456 735 True 440.000000 440 78.062000 1284 2001 1 chr2D.!!$R2 717
20 TraesCS4A01G462500 chr2A 610994862 610996222 1360 True 478.000000 824 81.229500 1284 2640 2 chr2A.!!$R2 1356
21 TraesCS4A01G462500 chr4D 449816954 449817662 708 True 795.000000 795 86.963000 2752 3466 1 chr4D.!!$R1 714
22 TraesCS4A01G462500 chr5D 443831876 443832583 707 True 749.000000 749 85.853000 2752 3466 1 chr5D.!!$R3 714
23 TraesCS4A01G462500 chr3A 22669876 22670562 686 True 691.000000 691 84.844000 2752 3454 1 chr3A.!!$R1 702
24 TraesCS4A01G462500 chr5B 46746202 46746727 525 True 291.000000 291 77.127000 1840 2353 1 chr5B.!!$R1 513
25 TraesCS4A01G462500 chr1D 79116258 79116800 542 False 267.000000 267 76.051000 1773 2303 1 chr1D.!!$F1 530
26 TraesCS4A01G462500 chr1D 451940115 451940716 601 True 237.000000 237 74.172000 1774 2363 1 chr1D.!!$R1 589
27 TraesCS4A01G462500 chr1B 621946429 621947015 586 True 231.000000 231 74.194000 1779 2353 1 chr1B.!!$R1 574

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
641 657 0.028770 CTGAGACGCTCCTCGATCAC 59.971 60.0 0.0 0.0 41.67 3.06 F
1708 1820 0.037232 AGAACTCACCTTACCTGCGC 60.037 55.0 0.0 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2331 0.240411 CTTCTTTGAGCCTGCTGCAC 59.76 55.0 0.0 0.0 44.83 4.57 R
2662 2848 0.609662 TGCATCAGTACAGCAGCTCA 59.39 50.0 0.0 0.0 33.75 4.26 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
46 47 3.660865 TCTAAGAAGAGGCACGGTTTTC 58.339 45.455 0.00 0.00 0.00 2.29
78 79 4.347096 ACGGTTGTGATTTCGCGA 57.653 50.000 3.71 3.71 0.00 5.87
79 80 2.607457 ACGGTTGTGATTTCGCGAA 58.393 47.368 19.38 19.38 0.00 4.70
85 86 2.163818 TGTGATTTCGCGAAAGAGGT 57.836 45.000 34.38 20.98 33.32 3.85
112 113 2.418197 CGTGCCTCTATCGGAAAAGGAA 60.418 50.000 7.61 0.00 0.00 3.36
116 117 4.457949 TGCCTCTATCGGAAAAGGAAAAAC 59.542 41.667 7.61 0.00 0.00 2.43
117 118 4.142447 GCCTCTATCGGAAAAGGAAAAACC 60.142 45.833 7.61 0.00 39.35 3.27
211 214 9.793259 AAACATATCAATATGGAATCTAACGGT 57.207 29.630 13.18 0.00 43.38 4.83
310 313 6.422776 AAAACTATCAGGTTGCGATAACTG 57.577 37.500 0.00 0.00 0.00 3.16
321 324 1.276844 GATAACTGACGCGGCATGC 59.723 57.895 18.76 9.90 41.47 4.06
347 350 3.486708 GCGTCACTTGTCACAACATGAAA 60.487 43.478 0.00 0.00 39.72 2.69
357 360 4.972440 GTCACAACATGAAAAAGTGAGAGC 59.028 41.667 0.00 0.00 39.72 4.09
370 373 2.740981 AGTGAGAGCGATCTTTGCAAAG 59.259 45.455 29.53 29.53 37.36 2.77
410 413 1.507562 TTCGAAGTGAAAGATGCGCA 58.492 45.000 14.96 14.96 32.37 6.09
415 418 3.486584 GAAGTGAAAGATGCGCAAGAAG 58.513 45.455 17.11 0.00 43.02 2.85
416 419 2.498167 AGTGAAAGATGCGCAAGAAGT 58.502 42.857 17.11 0.00 43.02 3.01
426 429 2.095969 TGCGCAAGAAGTATTTCCAACG 60.096 45.455 8.16 0.00 43.02 4.10
432 435 4.203654 AGAAGTATTTCCAACGGAGTCC 57.796 45.455 0.00 0.00 34.47 3.85
474 477 2.760385 ACCCTCACCGCTAGAGCC 60.760 66.667 0.00 0.00 37.91 4.70
475 478 2.759973 CCCTCACCGCTAGAGCCA 60.760 66.667 0.00 0.00 37.91 4.75
477 480 2.055042 CCTCACCGCTAGAGCCAGT 61.055 63.158 0.00 0.00 37.91 4.00
479 482 2.510238 CACCGCTAGAGCCAGTGC 60.510 66.667 0.00 0.00 35.82 4.40
482 485 3.826754 CGCTAGAGCCAGTGCGGA 61.827 66.667 0.00 0.00 43.97 5.54
483 486 2.202810 GCTAGAGCCAGTGCGGAC 60.203 66.667 0.00 0.00 44.33 4.79
484 487 2.103143 CTAGAGCCAGTGCGGACG 59.897 66.667 0.00 0.00 44.33 4.79
485 488 3.417275 CTAGAGCCAGTGCGGACGG 62.417 68.421 12.24 12.24 44.33 4.79
491 494 4.135153 CAGTGCGGACGGGGAGAG 62.135 72.222 0.00 0.00 0.00 3.20
509 512 1.217779 GCTGGAGGCAGAGACAGAC 59.782 63.158 0.00 0.00 41.35 3.51
604 620 0.600057 ACCTACGTCCACGAAACCTC 59.400 55.000 6.03 0.00 43.02 3.85
635 651 4.200283 CCGGCTGAGACGCTCCTC 62.200 72.222 0.00 0.00 29.68 3.71
636 652 4.544689 CGGCTGAGACGCTCCTCG 62.545 72.222 0.00 3.08 45.38 4.63
637 653 3.134792 GGCTGAGACGCTCCTCGA 61.135 66.667 4.73 0.00 41.67 4.04
638 654 2.485795 GGCTGAGACGCTCCTCGAT 61.486 63.158 4.73 0.00 41.67 3.59
639 655 1.008995 GCTGAGACGCTCCTCGATC 60.009 63.158 4.73 0.00 41.67 3.69
640 656 1.719725 GCTGAGACGCTCCTCGATCA 61.720 60.000 0.00 0.00 41.67 2.92
641 657 0.028770 CTGAGACGCTCCTCGATCAC 59.971 60.000 0.00 0.00 41.67 3.06
642 658 0.676782 TGAGACGCTCCTCGATCACA 60.677 55.000 0.00 0.00 41.67 3.58
643 659 0.248296 GAGACGCTCCTCGATCACAC 60.248 60.000 0.00 0.00 41.67 3.82
644 660 1.226717 GACGCTCCTCGATCACACC 60.227 63.158 0.00 0.00 41.67 4.16
645 661 1.658686 GACGCTCCTCGATCACACCT 61.659 60.000 0.00 0.00 41.67 4.00
646 662 1.251527 ACGCTCCTCGATCACACCTT 61.252 55.000 0.00 0.00 41.67 3.50
647 663 0.526524 CGCTCCTCGATCACACCTTC 60.527 60.000 0.00 0.00 41.67 3.46
648 664 0.820871 GCTCCTCGATCACACCTTCT 59.179 55.000 0.00 0.00 0.00 2.85
649 665 1.202359 GCTCCTCGATCACACCTTCTC 60.202 57.143 0.00 0.00 0.00 2.87
650 666 1.064803 CTCCTCGATCACACCTTCTCG 59.935 57.143 0.00 0.00 0.00 4.04
651 667 1.095600 CCTCGATCACACCTTCTCGA 58.904 55.000 0.00 0.00 37.77 4.04
652 668 1.202200 CCTCGATCACACCTTCTCGAC 60.202 57.143 0.00 0.00 35.41 4.20
653 669 1.468914 CTCGATCACACCTTCTCGACA 59.531 52.381 0.00 0.00 35.41 4.35
654 670 1.883926 TCGATCACACCTTCTCGACAA 59.116 47.619 0.00 0.00 35.41 3.18
655 671 2.492088 TCGATCACACCTTCTCGACAAT 59.508 45.455 0.00 0.00 35.41 2.71
656 672 2.600420 CGATCACACCTTCTCGACAATG 59.400 50.000 0.00 0.00 33.07 2.82
657 673 3.589988 GATCACACCTTCTCGACAATGT 58.410 45.455 0.00 0.00 0.00 2.71
658 674 2.754472 TCACACCTTCTCGACAATGTG 58.246 47.619 7.17 7.17 39.00 3.21
659 675 1.195448 CACACCTTCTCGACAATGTGC 59.805 52.381 8.36 0.00 31.91 4.57
660 676 1.070758 ACACCTTCTCGACAATGTGCT 59.929 47.619 8.36 0.00 0.00 4.40
661 677 1.728971 CACCTTCTCGACAATGTGCTC 59.271 52.381 0.00 0.00 0.00 4.26
662 678 0.994995 CCTTCTCGACAATGTGCTCG 59.005 55.000 0.00 0.00 0.00 5.03
663 679 1.670087 CCTTCTCGACAATGTGCTCGT 60.670 52.381 0.00 0.00 0.00 4.18
664 680 1.651138 CTTCTCGACAATGTGCTCGTC 59.349 52.381 0.00 0.00 0.00 4.20
665 681 0.881796 TCTCGACAATGTGCTCGTCT 59.118 50.000 0.00 0.00 0.00 4.18
666 682 1.135660 TCTCGACAATGTGCTCGTCTC 60.136 52.381 0.00 0.00 0.00 3.36
667 683 0.454452 TCGACAATGTGCTCGTCTCG 60.454 55.000 0.00 0.00 0.00 4.04
668 684 0.454452 CGACAATGTGCTCGTCTCGA 60.454 55.000 0.00 0.00 0.00 4.04
669 685 1.698165 GACAATGTGCTCGTCTCGAA 58.302 50.000 0.00 0.00 34.74 3.71
670 686 1.651138 GACAATGTGCTCGTCTCGAAG 59.349 52.381 0.00 0.00 34.74 3.79
671 687 0.368227 CAATGTGCTCGTCTCGAAGC 59.632 55.000 0.00 0.00 34.74 3.86
672 688 0.737715 AATGTGCTCGTCTCGAAGCC 60.738 55.000 4.45 0.00 34.74 4.35
673 689 2.507324 GTGCTCGTCTCGAAGCCC 60.507 66.667 4.45 0.00 34.74 5.19
674 690 2.989253 TGCTCGTCTCGAAGCCCA 60.989 61.111 4.45 0.00 34.74 5.36
675 691 2.261671 GCTCGTCTCGAAGCCCAA 59.738 61.111 0.00 0.00 34.74 4.12
676 692 1.153549 GCTCGTCTCGAAGCCCAAT 60.154 57.895 0.00 0.00 34.74 3.16
677 693 0.741221 GCTCGTCTCGAAGCCCAATT 60.741 55.000 0.00 0.00 34.74 2.32
678 694 1.002366 CTCGTCTCGAAGCCCAATTG 58.998 55.000 0.00 0.00 34.74 2.32
679 695 0.320374 TCGTCTCGAAGCCCAATTGT 59.680 50.000 4.43 0.00 31.06 2.71
680 696 0.443869 CGTCTCGAAGCCCAATTGTG 59.556 55.000 4.43 0.00 0.00 3.33
681 697 1.808411 GTCTCGAAGCCCAATTGTGA 58.192 50.000 4.43 0.00 0.00 3.58
682 698 2.151202 GTCTCGAAGCCCAATTGTGAA 58.849 47.619 4.43 0.00 0.00 3.18
683 699 2.552315 GTCTCGAAGCCCAATTGTGAAA 59.448 45.455 4.43 0.00 0.00 2.69
684 700 2.813754 TCTCGAAGCCCAATTGTGAAAG 59.186 45.455 4.43 0.00 0.00 2.62
685 701 1.885887 TCGAAGCCCAATTGTGAAAGG 59.114 47.619 4.43 0.00 0.00 3.11
686 702 1.067635 CGAAGCCCAATTGTGAAAGGG 60.068 52.381 4.43 0.00 44.37 3.95
687 703 1.970640 GAAGCCCAATTGTGAAAGGGT 59.029 47.619 4.43 0.52 43.42 4.34
688 704 1.632589 AGCCCAATTGTGAAAGGGTC 58.367 50.000 4.43 0.00 43.42 4.46
689 705 1.147817 AGCCCAATTGTGAAAGGGTCT 59.852 47.619 4.43 0.00 43.42 3.85
690 706 2.378547 AGCCCAATTGTGAAAGGGTCTA 59.621 45.455 4.43 0.00 43.42 2.59
691 707 3.011708 AGCCCAATTGTGAAAGGGTCTAT 59.988 43.478 4.43 0.00 43.42 1.98
692 708 3.381590 GCCCAATTGTGAAAGGGTCTATC 59.618 47.826 4.43 0.00 43.42 2.08
693 709 4.860022 CCCAATTGTGAAAGGGTCTATCT 58.140 43.478 4.43 0.00 36.52 1.98
694 710 5.631481 GCCCAATTGTGAAAGGGTCTATCTA 60.631 44.000 4.43 0.00 43.42 1.98
695 711 6.423182 CCCAATTGTGAAAGGGTCTATCTAA 58.577 40.000 4.43 0.00 36.52 2.10
696 712 6.543831 CCCAATTGTGAAAGGGTCTATCTAAG 59.456 42.308 4.43 0.00 36.52 2.18
697 713 7.338710 CCAATTGTGAAAGGGTCTATCTAAGA 58.661 38.462 4.43 0.00 0.00 2.10
712 728 8.856153 TCTATCTAAGACCATCTAGATGTGAC 57.144 38.462 27.03 18.84 37.11 3.67
713 729 8.440771 TCTATCTAAGACCATCTAGATGTGACA 58.559 37.037 27.03 10.43 37.11 3.58
714 730 9.241919 CTATCTAAGACCATCTAGATGTGACAT 57.758 37.037 27.03 15.49 37.11 3.06
716 732 8.628630 TCTAAGACCATCTAGATGTGACATAG 57.371 38.462 27.03 21.67 37.11 2.23
717 733 8.221251 TCTAAGACCATCTAGATGTGACATAGT 58.779 37.037 27.03 17.31 37.11 2.12
718 734 7.667575 AAGACCATCTAGATGTGACATAGTT 57.332 36.000 27.03 9.32 37.11 2.24
719 735 8.768501 AAGACCATCTAGATGTGACATAGTTA 57.231 34.615 27.03 0.00 37.11 2.24
720 736 8.948401 AGACCATCTAGATGTGACATAGTTAT 57.052 34.615 27.03 9.39 37.11 1.89
721 737 8.801299 AGACCATCTAGATGTGACATAGTTATG 58.199 37.037 27.03 12.12 37.11 1.90
722 738 8.484214 ACCATCTAGATGTGACATAGTTATGT 57.516 34.615 27.03 12.67 41.88 2.29
723 739 8.580720 ACCATCTAGATGTGACATAGTTATGTC 58.419 37.037 27.03 20.26 45.93 3.06
752 768 8.771920 TCTAAACTGATGTACACACTATTTGG 57.228 34.615 0.00 0.00 0.00 3.28
753 769 6.817765 AAACTGATGTACACACTATTTGGG 57.182 37.500 0.00 0.00 33.17 4.12
754 770 4.843728 ACTGATGTACACACTATTTGGGG 58.156 43.478 0.00 0.00 29.81 4.96
755 771 4.288626 ACTGATGTACACACTATTTGGGGT 59.711 41.667 0.00 0.00 29.81 4.95
756 772 4.839121 TGATGTACACACTATTTGGGGTC 58.161 43.478 0.00 0.00 29.81 4.46
757 773 4.534500 TGATGTACACACTATTTGGGGTCT 59.466 41.667 0.00 0.00 29.81 3.85
758 774 5.722441 TGATGTACACACTATTTGGGGTCTA 59.278 40.000 0.00 0.00 29.81 2.59
759 775 6.385759 TGATGTACACACTATTTGGGGTCTAT 59.614 38.462 0.00 0.00 29.81 1.98
760 776 6.630203 TGTACACACTATTTGGGGTCTATT 57.370 37.500 0.00 0.00 29.81 1.73
761 777 7.023171 TGTACACACTATTTGGGGTCTATTT 57.977 36.000 0.00 0.00 29.81 1.40
762 778 7.463431 TGTACACACTATTTGGGGTCTATTTT 58.537 34.615 0.00 0.00 29.81 1.82
763 779 7.945664 TGTACACACTATTTGGGGTCTATTTTT 59.054 33.333 0.00 0.00 29.81 1.94
797 813 5.876612 TTTTTGTTTCTTGTTGCTGCATT 57.123 30.435 1.84 0.00 0.00 3.56
798 814 6.974932 TTTTTGTTTCTTGTTGCTGCATTA 57.025 29.167 1.84 0.00 0.00 1.90
799 815 7.551035 TTTTTGTTTCTTGTTGCTGCATTAT 57.449 28.000 1.84 0.00 0.00 1.28
800 816 8.654230 TTTTTGTTTCTTGTTGCTGCATTATA 57.346 26.923 1.84 0.00 0.00 0.98
801 817 8.830201 TTTTGTTTCTTGTTGCTGCATTATAT 57.170 26.923 1.84 0.00 0.00 0.86
802 818 9.920133 TTTTGTTTCTTGTTGCTGCATTATATA 57.080 25.926 1.84 0.00 0.00 0.86
808 824 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
809 825 8.136800 TCTTGTTGCTGCATTATATATTTGTGG 58.863 33.333 1.84 0.00 0.00 4.17
810 826 6.747125 TGTTGCTGCATTATATATTTGTGGG 58.253 36.000 1.84 0.00 0.00 4.61
811 827 6.548993 TGTTGCTGCATTATATATTTGTGGGA 59.451 34.615 1.84 0.00 0.00 4.37
812 828 6.822667 TGCTGCATTATATATTTGTGGGAG 57.177 37.500 0.00 0.00 0.00 4.30
813 829 6.306199 TGCTGCATTATATATTTGTGGGAGT 58.694 36.000 0.00 0.00 0.00 3.85
814 830 6.777091 TGCTGCATTATATATTTGTGGGAGTT 59.223 34.615 0.00 0.00 0.00 3.01
815 831 7.287466 TGCTGCATTATATATTTGTGGGAGTTT 59.713 33.333 0.00 0.00 0.00 2.66
816 832 8.792633 GCTGCATTATATATTTGTGGGAGTTTA 58.207 33.333 0.00 0.00 0.00 2.01
825 841 8.877864 ATATTTGTGGGAGTTTAGATTTGACA 57.122 30.769 0.00 0.00 0.00 3.58
826 842 7.781324 ATTTGTGGGAGTTTAGATTTGACAT 57.219 32.000 0.00 0.00 0.00 3.06
827 843 7.595819 TTTGTGGGAGTTTAGATTTGACATT 57.404 32.000 0.00 0.00 0.00 2.71
828 844 7.595819 TTGTGGGAGTTTAGATTTGACATTT 57.404 32.000 0.00 0.00 0.00 2.32
829 845 7.595819 TGTGGGAGTTTAGATTTGACATTTT 57.404 32.000 0.00 0.00 0.00 1.82
830 846 8.017418 TGTGGGAGTTTAGATTTGACATTTTT 57.983 30.769 0.00 0.00 0.00 1.94
831 847 9.137459 TGTGGGAGTTTAGATTTGACATTTTTA 57.863 29.630 0.00 0.00 0.00 1.52
832 848 9.974980 GTGGGAGTTTAGATTTGACATTTTTAA 57.025 29.630 0.00 0.00 0.00 1.52
865 881 8.956426 TCTAGATGTGAATTAAACAAACCCATC 58.044 33.333 0.00 0.00 0.00 3.51
904 921 3.498082 GGACATGTTGGACGCAAATAAC 58.502 45.455 0.00 0.00 0.00 1.89
911 928 4.563184 TGTTGGACGCAAATAACAAACAAC 59.437 37.500 0.00 0.00 36.97 3.32
917 934 7.115520 TGGACGCAAATAACAAACAACAATATG 59.884 33.333 0.00 0.00 0.00 1.78
920 937 9.464714 ACGCAAATAACAAACAACAATATGTTA 57.535 25.926 0.00 0.00 42.49 2.41
1031 1052 4.553678 ACTATCCTTTATCCGGAGTTCCA 58.446 43.478 11.34 0.00 33.29 3.53
1128 1200 4.699522 GCGGCCGTGGAGAGGTTT 62.700 66.667 28.70 0.00 0.00 3.27
1129 1201 2.032071 CGGCCGTGGAGAGGTTTT 59.968 61.111 19.50 0.00 0.00 2.43
1150 1222 4.388499 TTCGGCTCGCAACCCTCC 62.388 66.667 0.00 0.00 0.00 4.30
1210 1282 4.626081 GCCGCCCGCATACCATCT 62.626 66.667 0.00 0.00 37.47 2.90
1211 1283 2.666190 CCGCCCGCATACCATCTG 60.666 66.667 0.00 0.00 0.00 2.90
1233 1305 3.685214 CTCGTCGCTGTTCCCCTCG 62.685 68.421 0.00 0.00 0.00 4.63
1234 1306 3.744719 CGTCGCTGTTCCCCTCGA 61.745 66.667 0.00 0.00 0.00 4.04
1268 1340 0.759346 GCCCTTGATCTCCACCGTAT 59.241 55.000 0.00 0.00 0.00 3.06
1269 1341 1.968493 GCCCTTGATCTCCACCGTATA 59.032 52.381 0.00 0.00 0.00 1.47
1611 1705 2.097038 CCTGCTTGAAGTCGCCGAG 61.097 63.158 0.00 0.00 0.00 4.63
1624 1718 1.464429 CGCCGAGAGTGTTCGATTCG 61.464 60.000 0.00 0.00 43.03 3.34
1708 1820 0.037232 AGAACTCACCTTACCTGCGC 60.037 55.000 0.00 0.00 0.00 6.09
1753 1865 3.593096 TGATCTCAGTGTGATCAGCAAC 58.407 45.455 26.37 7.74 43.47 4.17
1762 1874 0.457853 TGATCAGCAACGTACCGCTC 60.458 55.000 4.23 0.00 35.96 5.03
1771 1883 0.874390 ACGTACCGCTCGTTGTAGAA 59.126 50.000 0.00 0.00 38.38 2.10
1828 1949 3.744942 CAGATAATCTCGGAACATGGCTG 59.255 47.826 0.00 0.00 0.00 4.85
1960 2081 1.146263 GATGGGAAATCGGACGGCT 59.854 57.895 0.00 0.00 0.00 5.52
2237 2371 6.322969 AGAAGCCTGCATTGAATTTATCATCA 59.677 34.615 0.00 0.00 38.03 3.07
2402 2577 6.013206 TGGATTAGTTGGCTTACCTTCACTTA 60.013 38.462 0.00 0.00 36.63 2.24
2406 2581 5.491982 AGTTGGCTTACCTTCACTTATCAG 58.508 41.667 0.00 0.00 36.63 2.90
2518 2693 5.355071 TGCTCATCTTGGATTCATGTGTTAC 59.645 40.000 0.00 0.00 0.00 2.50
2530 2705 4.839121 TCATGTGTTACCTTCCATGTACC 58.161 43.478 0.00 0.00 36.81 3.34
2564 2746 6.952938 ACATAGCCATCTGAGATGAATCTAGA 59.047 38.462 23.29 0.00 37.25 2.43
2578 2760 9.618890 AGATGAATCTAGACTATATCTGCTCTC 57.381 37.037 0.00 0.00 38.49 3.20
2747 3046 7.008021 AGGCTTTGAAATGTTTTCCATACAT 57.992 32.000 0.00 0.00 37.82 2.29
2853 3173 4.274459 CCAACAAAGTCTCAAAGTCTCCAG 59.726 45.833 0.00 0.00 0.00 3.86
2861 3182 8.602472 AAGTCTCAAAGTCTCCAGAAGTATAT 57.398 34.615 0.00 0.00 0.00 0.86
2947 3273 2.594303 CACAACCGGCTGGCTCAA 60.594 61.111 12.89 0.00 39.70 3.02
2948 3274 2.192861 CACAACCGGCTGGCTCAAA 61.193 57.895 12.89 0.00 39.70 2.69
2949 3275 1.454847 ACAACCGGCTGGCTCAAAA 60.455 52.632 12.89 0.00 39.70 2.44
2950 3276 0.827507 ACAACCGGCTGGCTCAAAAT 60.828 50.000 12.89 0.00 39.70 1.82
2951 3277 1.173043 CAACCGGCTGGCTCAAAATA 58.827 50.000 12.89 0.00 39.70 1.40
2952 3278 1.133025 CAACCGGCTGGCTCAAAATAG 59.867 52.381 12.89 0.00 39.70 1.73
3073 3404 1.774894 TAACCAAACGCTCCCTGGCT 61.775 55.000 0.00 0.00 33.19 4.75
3097 3428 0.607217 TCGGAGTGAGTAGCGACCAA 60.607 55.000 0.00 0.00 0.00 3.67
3304 3635 8.047310 ACTGAACTCGGTGGAGAAATATTAAAT 58.953 33.333 0.00 0.00 43.27 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.070685 GCCTCTTCTTAGAAGGACCAAAAA 58.929 41.667 20.29 0.00 0.00 1.94
15 16 4.104102 TGCCTCTTCTTAGAAGGACCAAAA 59.896 41.667 20.29 0.21 0.00 2.44
16 17 3.650942 TGCCTCTTCTTAGAAGGACCAAA 59.349 43.478 20.29 0.89 0.00 3.28
17 18 3.008049 GTGCCTCTTCTTAGAAGGACCAA 59.992 47.826 20.29 1.57 29.60 3.67
18 19 2.567615 GTGCCTCTTCTTAGAAGGACCA 59.432 50.000 20.29 12.13 29.60 4.02
19 20 2.417515 CGTGCCTCTTCTTAGAAGGACC 60.418 54.545 20.29 10.00 31.51 4.46
20 21 2.417515 CCGTGCCTCTTCTTAGAAGGAC 60.418 54.545 20.29 11.29 31.80 3.85
21 22 1.825474 CCGTGCCTCTTCTTAGAAGGA 59.175 52.381 20.29 7.79 0.00 3.36
22 23 1.550976 ACCGTGCCTCTTCTTAGAAGG 59.449 52.381 20.29 8.71 0.00 3.46
23 24 3.320673 AACCGTGCCTCTTCTTAGAAG 57.679 47.619 15.30 15.30 0.00 2.85
24 25 3.764237 AAACCGTGCCTCTTCTTAGAA 57.236 42.857 0.00 0.00 0.00 2.10
25 26 3.556423 GGAAAACCGTGCCTCTTCTTAGA 60.556 47.826 0.00 0.00 0.00 2.10
26 27 2.742589 GGAAAACCGTGCCTCTTCTTAG 59.257 50.000 0.00 0.00 0.00 2.18
27 28 2.370849 AGGAAAACCGTGCCTCTTCTTA 59.629 45.455 0.00 0.00 0.00 2.10
28 29 1.143073 AGGAAAACCGTGCCTCTTCTT 59.857 47.619 0.00 0.00 0.00 2.52
29 30 0.765510 AGGAAAACCGTGCCTCTTCT 59.234 50.000 0.00 0.00 0.00 2.85
30 31 1.535896 GAAGGAAAACCGTGCCTCTTC 59.464 52.381 0.00 0.00 0.00 2.87
31 32 1.605753 GAAGGAAAACCGTGCCTCTT 58.394 50.000 0.00 0.00 0.00 2.85
46 47 2.125912 CGTGCCTCTCGTGGAAGG 60.126 66.667 0.00 0.00 0.00 3.46
78 79 2.047560 GCACGGCCGTACCTCTTT 60.048 61.111 33.70 1.55 35.61 2.52
79 80 4.078516 GGCACGGCCGTACCTCTT 62.079 66.667 35.63 8.46 39.62 2.85
116 117 1.112916 AAACCAAACCGGGAGCAAGG 61.113 55.000 6.32 0.81 40.22 3.61
117 118 0.750249 AAAACCAAACCGGGAGCAAG 59.250 50.000 6.32 0.00 40.22 4.01
118 119 1.196012 AAAAACCAAACCGGGAGCAA 58.804 45.000 6.32 0.00 40.22 3.91
194 197 6.037830 CCGTTTTCACCGTTAGATTCCATATT 59.962 38.462 0.00 0.00 0.00 1.28
203 206 5.355596 TCTTAAACCGTTTTCACCGTTAGA 58.644 37.500 0.96 0.00 0.00 2.10
211 214 5.923684 GCATCCAAATCTTAAACCGTTTTCA 59.076 36.000 0.96 0.00 0.00 2.69
283 286 3.745799 TCGCAACCTGATAGTTTTTCCA 58.254 40.909 0.00 0.00 0.00 3.53
321 324 1.006086 TTGTGACAAGTGACGCACTG 58.994 50.000 12.22 9.41 44.62 3.66
327 330 6.092748 ACTTTTTCATGTTGTGACAAGTGAC 58.907 36.000 11.46 0.00 38.38 3.67
347 350 2.771089 TGCAAAGATCGCTCTCACTTT 58.229 42.857 0.00 0.00 33.69 2.66
357 360 4.499183 AGGAGTACTCTTTGCAAAGATCG 58.501 43.478 35.40 27.68 43.52 3.69
370 373 7.481642 TCGAAATCACTAATTGAGGAGTACTC 58.518 38.462 14.87 14.87 46.78 2.59
410 413 4.565028 GGGACTCCGTTGGAAATACTTCTT 60.565 45.833 0.00 0.00 0.00 2.52
426 429 2.124695 GCACCAATCCGGGACTCC 60.125 66.667 0.00 0.00 40.22 3.85
432 435 3.451894 GCCCAAGCACCAATCCGG 61.452 66.667 0.00 0.00 39.53 5.14
474 477 4.135153 CTCTCCCCGTCCGCACTG 62.135 72.222 0.00 0.00 0.00 3.66
481 484 3.151022 CCTCCAGCTCTCCCCGTC 61.151 72.222 0.00 0.00 0.00 4.79
484 487 3.478274 CTGCCTCCAGCTCTCCCC 61.478 72.222 0.00 0.00 44.23 4.81
485 488 2.364842 TCTGCCTCCAGCTCTCCC 60.365 66.667 0.00 0.00 44.23 4.30
486 489 1.381056 TCTCTGCCTCCAGCTCTCC 60.381 63.158 0.00 0.00 44.23 3.71
487 490 0.969917 TGTCTCTGCCTCCAGCTCTC 60.970 60.000 0.00 0.00 44.23 3.20
488 491 0.971959 CTGTCTCTGCCTCCAGCTCT 60.972 60.000 0.00 0.00 44.23 4.09
489 492 0.969917 TCTGTCTCTGCCTCCAGCTC 60.970 60.000 0.00 0.00 44.23 4.09
490 493 1.078166 TCTGTCTCTGCCTCCAGCT 59.922 57.895 0.00 0.00 44.23 4.24
491 494 1.217779 GTCTGTCTCTGCCTCCAGC 59.782 63.158 0.00 0.00 39.00 4.85
492 495 0.972134 TTGTCTGTCTCTGCCTCCAG 59.028 55.000 0.00 0.00 40.54 3.86
533 536 4.494484 GGCGCATTGAGGATTAAGTTTTT 58.506 39.130 10.83 0.00 0.00 1.94
538 541 1.528586 CTCGGCGCATTGAGGATTAAG 59.471 52.381 10.83 0.00 0.00 1.85
540 543 3.289128 CTCGGCGCATTGAGGATTA 57.711 52.632 10.83 0.00 0.00 1.75
541 544 4.131376 CTCGGCGCATTGAGGATT 57.869 55.556 10.83 0.00 0.00 3.01
583 599 0.668401 GGTTTCGTGGACGTAGGTGG 60.668 60.000 0.00 0.00 40.80 4.61
584 600 0.316204 AGGTTTCGTGGACGTAGGTG 59.684 55.000 0.00 0.00 40.80 4.00
585 601 0.600057 GAGGTTTCGTGGACGTAGGT 59.400 55.000 0.00 0.00 40.80 3.08
586 602 0.455633 CGAGGTTTCGTGGACGTAGG 60.456 60.000 0.00 0.00 41.84 3.18
587 603 0.518636 TCGAGGTTTCGTGGACGTAG 59.481 55.000 0.00 0.00 46.72 3.51
588 604 1.131126 GATCGAGGTTTCGTGGACGTA 59.869 52.381 0.00 0.00 46.72 3.57
626 642 1.226717 GGTGTGATCGAGGAGCGTC 60.227 63.158 0.00 0.00 41.80 5.19
627 643 1.251527 AAGGTGTGATCGAGGAGCGT 61.252 55.000 0.00 0.00 41.80 5.07
628 644 0.526524 GAAGGTGTGATCGAGGAGCG 60.527 60.000 0.00 0.00 42.69 5.03
629 645 0.820871 AGAAGGTGTGATCGAGGAGC 59.179 55.000 0.00 0.00 0.00 4.70
630 646 1.064803 CGAGAAGGTGTGATCGAGGAG 59.935 57.143 0.00 0.00 37.35 3.69
631 647 1.095600 CGAGAAGGTGTGATCGAGGA 58.904 55.000 0.00 0.00 37.35 3.71
632 648 1.095600 TCGAGAAGGTGTGATCGAGG 58.904 55.000 0.00 0.00 39.11 4.63
633 649 1.468914 TGTCGAGAAGGTGTGATCGAG 59.531 52.381 0.00 0.00 44.07 4.04
634 650 1.530323 TGTCGAGAAGGTGTGATCGA 58.470 50.000 0.00 0.00 41.51 3.59
635 651 2.347697 TTGTCGAGAAGGTGTGATCG 57.652 50.000 0.00 0.00 36.54 3.69
636 652 3.369147 CACATTGTCGAGAAGGTGTGATC 59.631 47.826 26.28 0.00 39.30 2.92
637 653 3.329386 CACATTGTCGAGAAGGTGTGAT 58.671 45.455 26.28 0.00 39.30 3.06
638 654 2.754472 CACATTGTCGAGAAGGTGTGA 58.246 47.619 26.28 0.00 39.30 3.58
639 655 1.195448 GCACATTGTCGAGAAGGTGTG 59.805 52.381 31.75 25.53 39.31 3.82
640 656 1.070758 AGCACATTGTCGAGAAGGTGT 59.929 47.619 31.75 20.08 39.31 4.16
641 657 1.728971 GAGCACATTGTCGAGAAGGTG 59.271 52.381 29.09 29.09 39.93 4.00
642 658 1.670087 CGAGCACATTGTCGAGAAGGT 60.670 52.381 6.80 6.80 38.50 3.50
643 659 0.994995 CGAGCACATTGTCGAGAAGG 59.005 55.000 5.32 5.32 38.50 3.46
644 660 1.651138 GACGAGCACATTGTCGAGAAG 59.349 52.381 0.22 0.00 39.53 2.85
645 661 1.269723 AGACGAGCACATTGTCGAGAA 59.730 47.619 0.00 0.00 45.76 2.87
646 662 0.881796 AGACGAGCACATTGTCGAGA 59.118 50.000 3.70 0.00 45.76 4.04
647 663 1.263776 GAGACGAGCACATTGTCGAG 58.736 55.000 3.70 0.00 45.76 4.04
648 664 0.454452 CGAGACGAGCACATTGTCGA 60.454 55.000 3.70 0.00 45.76 4.20
649 665 0.454452 TCGAGACGAGCACATTGTCG 60.454 55.000 0.00 0.00 45.76 4.35
650 666 1.651138 CTTCGAGACGAGCACATTGTC 59.349 52.381 0.00 0.00 42.03 3.18
651 667 1.702886 CTTCGAGACGAGCACATTGT 58.297 50.000 0.00 0.00 37.14 2.71
652 668 0.368227 GCTTCGAGACGAGCACATTG 59.632 55.000 1.96 0.00 37.14 2.82
653 669 0.737715 GGCTTCGAGACGAGCACATT 60.738 55.000 8.94 0.00 37.14 2.71
654 670 1.153745 GGCTTCGAGACGAGCACAT 60.154 57.895 8.94 0.00 37.14 3.21
655 671 2.258591 GGCTTCGAGACGAGCACA 59.741 61.111 8.94 0.00 37.14 4.57
656 672 2.507324 GGGCTTCGAGACGAGCAC 60.507 66.667 8.94 1.11 37.14 4.40
657 673 1.888436 ATTGGGCTTCGAGACGAGCA 61.888 55.000 8.94 0.00 37.14 4.26
658 674 0.741221 AATTGGGCTTCGAGACGAGC 60.741 55.000 0.00 0.00 37.14 5.03
659 675 1.002366 CAATTGGGCTTCGAGACGAG 58.998 55.000 0.00 0.00 37.14 4.18
660 676 0.320374 ACAATTGGGCTTCGAGACGA 59.680 50.000 10.83 0.00 0.00 4.20
661 677 0.443869 CACAATTGGGCTTCGAGACG 59.556 55.000 10.83 0.00 0.00 4.18
662 678 1.808411 TCACAATTGGGCTTCGAGAC 58.192 50.000 10.83 0.00 0.00 3.36
663 679 2.559698 TTCACAATTGGGCTTCGAGA 57.440 45.000 10.83 0.00 0.00 4.04
664 680 2.095059 CCTTTCACAATTGGGCTTCGAG 60.095 50.000 10.83 0.15 0.00 4.04
665 681 1.885887 CCTTTCACAATTGGGCTTCGA 59.114 47.619 10.83 0.00 0.00 3.71
666 682 1.067635 CCCTTTCACAATTGGGCTTCG 60.068 52.381 10.83 0.00 32.49 3.79
667 683 1.970640 ACCCTTTCACAATTGGGCTTC 59.029 47.619 10.83 0.00 43.25 3.86
668 684 1.970640 GACCCTTTCACAATTGGGCTT 59.029 47.619 10.83 0.00 43.25 4.35
669 685 1.147817 AGACCCTTTCACAATTGGGCT 59.852 47.619 10.83 0.00 43.25 5.19
670 686 1.632589 AGACCCTTTCACAATTGGGC 58.367 50.000 10.83 0.00 43.25 5.36
671 687 4.860022 AGATAGACCCTTTCACAATTGGG 58.140 43.478 10.83 5.72 44.89 4.12
672 688 7.281100 GTCTTAGATAGACCCTTTCACAATTGG 59.719 40.741 10.83 0.00 46.30 3.16
673 689 8.202745 GTCTTAGATAGACCCTTTCACAATTG 57.797 38.462 3.24 3.24 46.30 2.32
687 703 8.440771 TGTCACATCTAGATGGTCTTAGATAGA 58.559 37.037 31.19 12.99 42.91 1.98
688 704 8.628630 TGTCACATCTAGATGGTCTTAGATAG 57.371 38.462 31.19 7.13 42.91 2.08
690 706 9.241919 CTATGTCACATCTAGATGGTCTTAGAT 57.758 37.037 31.19 18.30 42.91 1.98
691 707 8.221251 ACTATGTCACATCTAGATGGTCTTAGA 58.779 37.037 31.19 17.61 42.91 2.10
692 708 8.402798 ACTATGTCACATCTAGATGGTCTTAG 57.597 38.462 31.19 26.97 42.91 2.18
693 709 8.768501 AACTATGTCACATCTAGATGGTCTTA 57.231 34.615 31.19 20.54 42.91 2.10
694 710 7.667575 AACTATGTCACATCTAGATGGTCTT 57.332 36.000 31.19 20.52 42.91 3.01
695 711 8.801299 CATAACTATGTCACATCTAGATGGTCT 58.199 37.037 31.19 12.34 42.91 3.85
696 712 8.580720 ACATAACTATGTCACATCTAGATGGTC 58.419 37.037 31.19 21.43 42.96 4.02
697 713 8.484214 ACATAACTATGTCACATCTAGATGGT 57.516 34.615 31.19 17.34 42.96 3.55
726 742 9.383519 CCAAATAGTGTGTACATCAGTTTAGAT 57.616 33.333 0.00 0.00 0.00 1.98
727 743 7.822334 CCCAAATAGTGTGTACATCAGTTTAGA 59.178 37.037 0.00 0.00 0.00 2.10
728 744 7.065803 CCCCAAATAGTGTGTACATCAGTTTAG 59.934 40.741 0.00 0.00 0.00 1.85
729 745 6.882140 CCCCAAATAGTGTGTACATCAGTTTA 59.118 38.462 0.00 0.00 0.00 2.01
730 746 5.710099 CCCCAAATAGTGTGTACATCAGTTT 59.290 40.000 0.00 0.00 0.00 2.66
731 747 5.222048 ACCCCAAATAGTGTGTACATCAGTT 60.222 40.000 0.00 0.00 0.00 3.16
732 748 4.288626 ACCCCAAATAGTGTGTACATCAGT 59.711 41.667 0.00 5.03 0.00 3.41
733 749 4.843728 ACCCCAAATAGTGTGTACATCAG 58.156 43.478 0.00 0.00 0.00 2.90
734 750 4.534500 AGACCCCAAATAGTGTGTACATCA 59.466 41.667 0.00 0.00 0.00 3.07
735 751 5.099042 AGACCCCAAATAGTGTGTACATC 57.901 43.478 0.00 0.00 0.00 3.06
736 752 6.824958 ATAGACCCCAAATAGTGTGTACAT 57.175 37.500 0.00 0.00 0.00 2.29
737 753 6.630203 AATAGACCCCAAATAGTGTGTACA 57.370 37.500 0.00 0.00 0.00 2.90
738 754 7.933215 AAAATAGACCCCAAATAGTGTGTAC 57.067 36.000 0.00 0.00 0.00 2.90
775 791 5.876612 AATGCAGCAACAAGAAACAAAAA 57.123 30.435 0.00 0.00 0.00 1.94
776 792 8.830201 ATATAATGCAGCAACAAGAAACAAAA 57.170 26.923 0.00 0.00 0.00 2.44
782 798 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
783 799 8.136800 CCACAAATATATAATGCAGCAACAAGA 58.863 33.333 0.00 0.00 0.00 3.02
784 800 7.383029 CCCACAAATATATAATGCAGCAACAAG 59.617 37.037 0.00 0.00 0.00 3.16
785 801 7.069208 TCCCACAAATATATAATGCAGCAACAA 59.931 33.333 0.00 0.00 0.00 2.83
786 802 6.548993 TCCCACAAATATATAATGCAGCAACA 59.451 34.615 0.00 0.00 0.00 3.33
787 803 6.980593 TCCCACAAATATATAATGCAGCAAC 58.019 36.000 0.00 0.00 0.00 4.17
788 804 6.777091 ACTCCCACAAATATATAATGCAGCAA 59.223 34.615 0.00 0.00 0.00 3.91
789 805 6.306199 ACTCCCACAAATATATAATGCAGCA 58.694 36.000 0.00 0.00 0.00 4.41
790 806 6.824305 ACTCCCACAAATATATAATGCAGC 57.176 37.500 0.00 0.00 0.00 5.25
799 815 9.967451 TGTCAAATCTAAACTCCCACAAATATA 57.033 29.630 0.00 0.00 0.00 0.86
800 816 8.877864 TGTCAAATCTAAACTCCCACAAATAT 57.122 30.769 0.00 0.00 0.00 1.28
801 817 8.877864 ATGTCAAATCTAAACTCCCACAAATA 57.122 30.769 0.00 0.00 0.00 1.40
802 818 7.781324 ATGTCAAATCTAAACTCCCACAAAT 57.219 32.000 0.00 0.00 0.00 2.32
803 819 7.595819 AATGTCAAATCTAAACTCCCACAAA 57.404 32.000 0.00 0.00 0.00 2.83
804 820 7.595819 AAATGTCAAATCTAAACTCCCACAA 57.404 32.000 0.00 0.00 0.00 3.33
805 821 7.595819 AAAATGTCAAATCTAAACTCCCACA 57.404 32.000 0.00 0.00 0.00 4.17
806 822 9.974980 TTAAAAATGTCAAATCTAAACTCCCAC 57.025 29.630 0.00 0.00 0.00 4.61
837 853 8.739039 TGGGTTTGTTTAATTCACATCTAGATG 58.261 33.333 27.63 27.63 44.15 2.90
838 854 8.877864 TGGGTTTGTTTAATTCACATCTAGAT 57.122 30.769 0.00 0.00 0.00 1.98
839 855 8.877864 ATGGGTTTGTTTAATTCACATCTAGA 57.122 30.769 0.00 0.00 0.00 2.43
840 856 7.910162 CGATGGGTTTGTTTAATTCACATCTAG 59.090 37.037 0.00 0.00 32.32 2.43
841 857 7.392113 ACGATGGGTTTGTTTAATTCACATCTA 59.608 33.333 0.00 0.00 32.32 1.98
842 858 6.208599 ACGATGGGTTTGTTTAATTCACATCT 59.791 34.615 0.00 0.00 32.32 2.90
843 859 6.307800 CACGATGGGTTTGTTTAATTCACATC 59.692 38.462 0.00 0.00 0.00 3.06
844 860 6.015856 TCACGATGGGTTTGTTTAATTCACAT 60.016 34.615 0.00 0.00 0.00 3.21
845 861 5.299531 TCACGATGGGTTTGTTTAATTCACA 59.700 36.000 0.00 0.00 0.00 3.58
846 862 5.764131 TCACGATGGGTTTGTTTAATTCAC 58.236 37.500 0.00 0.00 0.00 3.18
847 863 6.392625 TTCACGATGGGTTTGTTTAATTCA 57.607 33.333 0.00 0.00 0.00 2.57
848 864 6.128929 GCTTTCACGATGGGTTTGTTTAATTC 60.129 38.462 0.00 0.00 0.00 2.17
849 865 5.694458 GCTTTCACGATGGGTTTGTTTAATT 59.306 36.000 0.00 0.00 0.00 1.40
850 866 5.221342 TGCTTTCACGATGGGTTTGTTTAAT 60.221 36.000 0.00 0.00 0.00 1.40
851 867 4.098044 TGCTTTCACGATGGGTTTGTTTAA 59.902 37.500 0.00 0.00 0.00 1.52
852 868 3.632604 TGCTTTCACGATGGGTTTGTTTA 59.367 39.130 0.00 0.00 0.00 2.01
853 869 2.428890 TGCTTTCACGATGGGTTTGTTT 59.571 40.909 0.00 0.00 0.00 2.83
854 870 2.028130 TGCTTTCACGATGGGTTTGTT 58.972 42.857 0.00 0.00 0.00 2.83
855 871 1.686355 TGCTTTCACGATGGGTTTGT 58.314 45.000 0.00 0.00 0.00 2.83
856 872 2.030007 ACATGCTTTCACGATGGGTTTG 60.030 45.455 0.00 0.00 0.00 2.93
857 873 2.228822 GACATGCTTTCACGATGGGTTT 59.771 45.455 0.00 0.00 0.00 3.27
858 874 1.812571 GACATGCTTTCACGATGGGTT 59.187 47.619 0.00 0.00 0.00 4.11
859 875 1.453155 GACATGCTTTCACGATGGGT 58.547 50.000 0.00 0.00 0.00 4.51
860 876 0.374758 CGACATGCTTTCACGATGGG 59.625 55.000 0.00 0.00 0.00 4.00
861 877 0.247814 GCGACATGCTTTCACGATGG 60.248 55.000 0.00 0.00 41.73 3.51
862 878 3.209429 GCGACATGCTTTCACGATG 57.791 52.632 0.00 0.00 41.73 3.84
890 907 4.744570 TGTTGTTTGTTATTTGCGTCCAA 58.255 34.783 0.00 0.00 0.00 3.53
904 921 8.434661 GCCACTCAATTAACATATTGTTGTTTG 58.565 33.333 3.22 6.88 41.30 2.93
1031 1052 1.103398 GTGGCCTTTGCTGTGTGTCT 61.103 55.000 3.32 0.00 37.74 3.41
1116 1188 1.792949 CGAAGACAAAACCTCTCCACG 59.207 52.381 0.00 0.00 0.00 4.94
1118 1190 1.542547 GCCGAAGACAAAACCTCTCCA 60.543 52.381 0.00 0.00 0.00 3.86
1119 1191 1.157585 GCCGAAGACAAAACCTCTCC 58.842 55.000 0.00 0.00 0.00 3.71
1120 1192 2.070028 GAGCCGAAGACAAAACCTCTC 58.930 52.381 0.00 0.00 0.00 3.20
1122 1194 0.790814 CGAGCCGAAGACAAAACCTC 59.209 55.000 0.00 0.00 0.00 3.85
1123 1195 1.228657 GCGAGCCGAAGACAAAACCT 61.229 55.000 0.00 0.00 0.00 3.50
1126 1198 0.306533 GTTGCGAGCCGAAGACAAAA 59.693 50.000 0.00 0.00 0.00 2.44
1127 1199 1.503818 GGTTGCGAGCCGAAGACAAA 61.504 55.000 0.00 0.00 0.00 2.83
1128 1200 1.959226 GGTTGCGAGCCGAAGACAA 60.959 57.895 0.00 0.00 0.00 3.18
1129 1201 2.357034 GGTTGCGAGCCGAAGACA 60.357 61.111 0.00 0.00 0.00 3.41
1202 1274 0.955178 CGACGAGAGGCAGATGGTAT 59.045 55.000 0.00 0.00 41.50 2.73
1207 1279 1.599606 AACAGCGACGAGAGGCAGAT 61.600 55.000 0.00 0.00 41.50 2.90
1210 1282 2.258591 GAACAGCGACGAGAGGCA 59.741 61.111 0.00 0.00 41.50 4.75
1211 1283 2.507324 GGAACAGCGACGAGAGGC 60.507 66.667 0.00 0.00 0.00 4.70
1233 1305 1.067250 GGCGATGAGAGAGCTGGTC 59.933 63.158 0.00 0.00 0.00 4.02
1234 1306 2.430610 GGGCGATGAGAGAGCTGGT 61.431 63.158 0.00 0.00 0.00 4.00
1268 1340 1.806461 GCCATCGATCGTGGGAGCTA 61.806 60.000 26.93 5.32 37.22 3.32
1269 1341 3.133014 CCATCGATCGTGGGAGCT 58.867 61.111 21.74 0.00 32.98 4.09
1624 1718 5.622770 ATTTGTTCTTAATGGTGTCGACC 57.377 39.130 14.12 4.20 43.48 4.79
1708 1820 7.653311 TCACACTCAATTATAAGATGGTCATCG 59.347 37.037 5.43 0.00 42.48 3.84
1762 1874 1.855513 TGTCCACGGTTTCTACAACG 58.144 50.000 0.00 0.00 0.00 4.10
1767 1879 1.553248 CCTGGATGTCCACGGTTTCTA 59.447 52.381 0.00 0.00 42.01 2.10
1768 1880 0.324943 CCTGGATGTCCACGGTTTCT 59.675 55.000 0.00 0.00 42.01 2.52
1771 1883 1.374947 CACCTGGATGTCCACGGTT 59.625 57.895 15.90 4.67 42.00 4.44
1795 1916 4.442052 CCGAGATTATCTGCCAAGTCTGAA 60.442 45.833 0.00 0.00 0.00 3.02
1828 1949 3.471806 GCTTCCTCCCCCGTCTCC 61.472 72.222 0.00 0.00 0.00 3.71
1960 2081 2.756829 TCTTCCACGTTTATGTTGCGA 58.243 42.857 0.00 0.00 0.00 5.10
2197 2331 0.240411 CTTCTTTGAGCCTGCTGCAC 59.760 55.000 0.00 0.00 44.83 4.57
2237 2371 5.359009 CCACATCAGCCATTCTATTTGAAGT 59.641 40.000 0.00 0.00 38.18 3.01
2406 2581 8.856490 TGCAACTCAAAAAGATTTCTAGAAAC 57.144 30.769 19.94 13.40 32.51 2.78
2475 2650 9.717942 GATGAGCATACTAAGATTTCCAATACT 57.282 33.333 0.00 0.00 0.00 2.12
2476 2651 9.717942 AGATGAGCATACTAAGATTTCCAATAC 57.282 33.333 0.00 0.00 0.00 1.89
2478 2653 9.064706 CAAGATGAGCATACTAAGATTTCCAAT 57.935 33.333 0.00 0.00 0.00 3.16
2479 2654 7.500227 CCAAGATGAGCATACTAAGATTTCCAA 59.500 37.037 0.00 0.00 0.00 3.53
2480 2655 6.994496 CCAAGATGAGCATACTAAGATTTCCA 59.006 38.462 0.00 0.00 0.00 3.53
2481 2656 7.220030 TCCAAGATGAGCATACTAAGATTTCC 58.780 38.462 0.00 0.00 0.00 3.13
2482 2657 8.845413 ATCCAAGATGAGCATACTAAGATTTC 57.155 34.615 0.00 0.00 0.00 2.17
2483 2658 9.282569 GAATCCAAGATGAGCATACTAAGATTT 57.717 33.333 0.00 0.00 0.00 2.17
2484 2659 8.435187 TGAATCCAAGATGAGCATACTAAGATT 58.565 33.333 0.00 0.00 0.00 2.40
2487 2662 7.660617 ACATGAATCCAAGATGAGCATACTAAG 59.339 37.037 0.00 0.00 0.00 2.18
2518 2693 4.408921 TGTATCAAGGAGGTACATGGAAGG 59.591 45.833 0.00 0.00 0.00 3.46
2530 2705 5.479724 TCTCAGATGGCTATGTATCAAGGAG 59.520 44.000 0.00 0.00 0.00 3.69
2564 2746 8.367156 GGAGAAATCAAAGAGAGCAGATATAGT 58.633 37.037 0.00 0.00 0.00 2.12
2604 2790 1.213296 ATACGAAGGCTTCCCCACAT 58.787 50.000 20.97 5.01 35.39 3.21
2606 2792 1.664873 GAATACGAAGGCTTCCCCAC 58.335 55.000 20.97 6.09 35.39 4.61
2660 2846 1.598132 GCATCAGTACAGCAGCTCATG 59.402 52.381 0.00 0.00 0.00 3.07
2661 2847 1.208776 TGCATCAGTACAGCAGCTCAT 59.791 47.619 0.00 0.00 33.75 2.90
2662 2848 0.609662 TGCATCAGTACAGCAGCTCA 59.390 50.000 0.00 0.00 33.75 4.26
2716 3015 6.017934 GGAAAACATTTCAAAGCCTTTTCTCC 60.018 38.462 5.32 0.00 31.31 3.71
2869 3192 1.086696 TTCTGTGCGAGCCTTTATGC 58.913 50.000 0.00 0.00 0.00 3.14
2872 3195 3.226884 GGTTCTGTGCGAGCCTTTA 57.773 52.632 0.00 0.00 39.70 1.85
2881 3204 3.939066 TCTAGCCTTTTAGGTTCTGTGC 58.061 45.455 0.00 0.00 37.80 4.57
3073 3404 1.642037 CGCTACTCACTCCGACGGAA 61.642 60.000 18.93 1.89 0.00 4.30
3140 3471 9.758651 GGTTTTTAACAGGACAACAAATATTCT 57.241 29.630 0.00 0.00 0.00 2.40
3304 3635 2.195727 TGGAGGACAGTCCATATTGCA 58.804 47.619 22.31 9.43 41.99 4.08


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

AutoCloner maintained by Alex Coulton.