Multiple sequence alignment - TraesCS5B01G002000

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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 TraesCS5B01G002000 chr5B 100.000 3336 0 0 1 3336 2804457 2807792 0.000000e+00 6161.0
1 TraesCS5B01G002000 chr5B 81.202 1447 166 69 964 2349 2883411 2884812 0.000000e+00 1068.0
2 TraesCS5B01G002000 chr5B 82.514 1281 134 45 1124 2361 2614312 2613079 0.000000e+00 1042.0
3 TraesCS5B01G002000 chr5B 79.677 620 115 10 2719 3332 625121615 625122229 1.420000e-118 436.0
4 TraesCS5B01G002000 chr5B 80.793 328 50 10 570 896 509183344 509183659 9.250000e-61 244.0
5 TraesCS5B01G002000 chr5B 83.957 187 16 7 372 545 2883166 2883351 2.060000e-37 167.0
6 TraesCS5B01G002000 chr5A 89.269 2395 180 34 119 2455 1835882 1833507 0.000000e+00 2928.0
7 TraesCS5B01G002000 chr5A 83.461 1306 134 43 1092 2351 1759544 1758275 0.000000e+00 1140.0
8 TraesCS5B01G002000 chr5A 84.662 665 67 23 1144 1786 1714335 1713684 6.070000e-177 630.0
9 TraesCS5B01G002000 chr5A 93.103 377 23 2 2006 2382 1803140 1802767 1.750000e-152 549.0
10 TraesCS5B01G002000 chr5A 85.714 497 44 15 1865 2349 1713566 1713085 1.790000e-137 499.0
11 TraesCS5B01G002000 chr5A 84.716 229 15 13 1144 1356 1336426 1336650 9.380000e-51 211.0
12 TraesCS5B01G002000 chr5A 85.500 200 18 3 374 563 1803409 1803211 7.300000e-47 198.0
13 TraesCS5B01G002000 chr5A 82.143 224 29 8 632 846 36491738 36491959 7.350000e-42 182.0
14 TraesCS5B01G002000 chr5A 83.333 186 10 6 374 543 1760179 1759999 5.760000e-33 152.0
15 TraesCS5B01G002000 chr5A 94.366 71 4 0 2383 2453 1802688 1802618 3.520000e-20 110.0
16 TraesCS5B01G002000 chr5A 84.314 102 14 2 223 324 1760273 1760174 7.620000e-17 99.0
17 TraesCS5B01G002000 chr5A 84.536 97 5 5 2460 2556 1833193 1833107 1.650000e-13 87.9
18 TraesCS5B01G002000 chr5A 96.154 52 1 1 404 454 1714502 1714451 2.130000e-12 84.2
19 TraesCS5B01G002000 chr5A 97.436 39 1 0 971 1009 1759949 1759911 2.150000e-07 67.6
20 TraesCS5B01G002000 chr5D 91.446 1473 88 20 935 2398 2797125 2798568 0.000000e+00 1988.0
21 TraesCS5B01G002000 chr5D 82.197 1438 164 47 964 2349 3070461 3071858 0.000000e+00 1153.0
22 TraesCS5B01G002000 chr5D 83.765 1275 134 33 1124 2352 3012527 3013774 0.000000e+00 1140.0
23 TraesCS5B01G002000 chr5D 92.369 747 46 5 2592 3336 2842476 2843213 0.000000e+00 1053.0
24 TraesCS5B01G002000 chr5D 92.023 514 28 5 126 628 2796562 2797073 0.000000e+00 710.0
25 TraesCS5B01G002000 chr5D 79.885 348 45 18 569 896 496697449 496697791 7.200000e-57 231.0
26 TraesCS5B01G002000 chr5D 84.530 181 15 3 371 541 3070226 3070403 2.060000e-37 167.0
27 TraesCS5B01G002000 chr3B 81.041 749 126 14 2594 3336 595363069 595363807 1.720000e-162 582.0
28 TraesCS5B01G002000 chr3D 81.541 753 92 26 2593 3336 453137571 453138285 8.030000e-161 577.0
29 TraesCS5B01G002000 chr3D 79.806 723 128 12 2623 3336 98543393 98542680 8.260000e-141 510.0
30 TraesCS5B01G002000 chr3D 76.429 280 46 16 569 837 505555216 505555486 2.090000e-27 134.0
31 TraesCS5B01G002000 chr2A 82.115 643 107 5 2696 3336 756921290 756921926 8.140000e-151 544.0
32 TraesCS5B01G002000 chr2A 80.243 329 44 14 573 892 14852400 14852084 9.310000e-56 228.0
33 TraesCS5B01G002000 chr2A 100.000 28 0 0 1884 1911 9325963 9325990 6.000000e-03 52.8
34 TraesCS5B01G002000 chr4A 82.268 626 99 6 2720 3336 717418865 717419487 6.340000e-147 531.0
35 TraesCS5B01G002000 chr7A 79.548 753 136 15 2593 3336 693991429 693990686 3.810000e-144 521.0
36 TraesCS5B01G002000 chr7A 86.517 89 8 3 43 128 51173859 51173772 9.850000e-16 95.3
37 TraesCS5B01G002000 chr7A 86.517 89 8 3 43 128 51237842 51237755 9.850000e-16 95.3
38 TraesCS5B01G002000 chr7A 91.304 69 2 3 63 128 51101079 51101012 1.270000e-14 91.6
39 TraesCS5B01G002000 chr2D 79.370 698 131 11 2645 3336 628341185 628340495 2.330000e-131 479.0
40 TraesCS5B01G002000 chr2D 82.239 259 34 9 569 822 180244829 180245080 2.610000e-51 213.0
41 TraesCS5B01G002000 chr3A 82.675 329 40 10 569 888 66217856 66218176 3.280000e-70 276.0
42 TraesCS5B01G002000 chr6B 80.427 281 35 12 624 888 204054761 204055037 2.630000e-46 196.0
43 TraesCS5B01G002000 chr7D 77.901 362 47 15 569 899 597413205 597412846 9.440000e-46 195.0
44 TraesCS5B01G002000 chr7D 78.929 280 46 10 569 837 623821465 623821188 9.510000e-41 178.0
45 TraesCS5B01G002000 chr7D 85.577 104 14 1 2 105 618410291 618410393 1.270000e-19 108.0
46 TraesCS5B01G002000 chr7B 78.039 255 41 12 649 896 507944846 507944600 2.680000e-31 147.0
47 TraesCS5B01G002000 chr1A 82.143 112 17 3 12 122 551057913 551057804 3.540000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G002000 chr5B 2804457 2807792 3335 False 6161.000000 6161 100.000000 1 3336 1 chr5B.!!$F1 3335
1 TraesCS5B01G002000 chr5B 2613079 2614312 1233 True 1042.000000 1042 82.514000 1124 2361 1 chr5B.!!$R1 1237
2 TraesCS5B01G002000 chr5B 2883166 2884812 1646 False 617.500000 1068 82.579500 372 2349 2 chr5B.!!$F4 1977
3 TraesCS5B01G002000 chr5B 625121615 625122229 614 False 436.000000 436 79.677000 2719 3332 1 chr5B.!!$F3 613
4 TraesCS5B01G002000 chr5A 1833107 1835882 2775 True 1507.950000 2928 86.902500 119 2556 2 chr5A.!!$R4 2437
5 TraesCS5B01G002000 chr5A 1713085 1714502 1417 True 404.400000 630 88.843333 404 2349 3 chr5A.!!$R1 1945
6 TraesCS5B01G002000 chr5A 1758275 1760273 1998 True 364.650000 1140 87.136000 223 2351 4 chr5A.!!$R2 2128
7 TraesCS5B01G002000 chr5A 1802618 1803409 791 True 285.666667 549 90.989667 374 2453 3 chr5A.!!$R3 2079
8 TraesCS5B01G002000 chr5D 2796562 2798568 2006 False 1349.000000 1988 91.734500 126 2398 2 chr5D.!!$F4 2272
9 TraesCS5B01G002000 chr5D 3012527 3013774 1247 False 1140.000000 1140 83.765000 1124 2352 1 chr5D.!!$F2 1228
10 TraesCS5B01G002000 chr5D 2842476 2843213 737 False 1053.000000 1053 92.369000 2592 3336 1 chr5D.!!$F1 744
11 TraesCS5B01G002000 chr5D 3070226 3071858 1632 False 660.000000 1153 83.363500 371 2349 2 chr5D.!!$F5 1978
12 TraesCS5B01G002000 chr3B 595363069 595363807 738 False 582.000000 582 81.041000 2594 3336 1 chr3B.!!$F1 742
13 TraesCS5B01G002000 chr3D 453137571 453138285 714 False 577.000000 577 81.541000 2593 3336 1 chr3D.!!$F1 743
14 TraesCS5B01G002000 chr3D 98542680 98543393 713 True 510.000000 510 79.806000 2623 3336 1 chr3D.!!$R1 713
15 TraesCS5B01G002000 chr2A 756921290 756921926 636 False 544.000000 544 82.115000 2696 3336 1 chr2A.!!$F2 640
16 TraesCS5B01G002000 chr4A 717418865 717419487 622 False 531.000000 531 82.268000 2720 3336 1 chr4A.!!$F1 616
17 TraesCS5B01G002000 chr7A 693990686 693991429 743 True 521.000000 521 79.548000 2593 3336 1 chr7A.!!$R4 743
18 TraesCS5B01G002000 chr2D 628340495 628341185 690 True 479.000000 479 79.370000 2645 3336 1 chr2D.!!$R1 691

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
906 958 0.099613 TCGCGTGCAACACAAATTGT 59.9 45.0 5.77 0.0 41.74 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 2933 0.392998 AATTGGCGCCGATGAAGAGT 60.393 50.0 29.91 10.32 0.0 3.24 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
33 34 8.525290 ACTAATTTAGTGCCATAAATTCTGCT 57.475 30.769 15.42 0.56 41.91 4.24
34 35 9.627123 ACTAATTTAGTGCCATAAATTCTGCTA 57.373 29.630 15.42 2.76 41.91 3.49
35 36 9.884465 CTAATTTAGTGCCATAAATTCTGCTAC 57.116 33.333 15.42 0.00 41.91 3.58
36 37 8.525290 AATTTAGTGCCATAAATTCTGCTACT 57.475 30.769 9.16 0.00 39.87 2.57
37 38 7.938140 TTTAGTGCCATAAATTCTGCTACTT 57.062 32.000 0.00 0.00 0.00 2.24
38 39 7.938140 TTAGTGCCATAAATTCTGCTACTTT 57.062 32.000 0.00 0.00 0.00 2.66
39 40 6.840780 AGTGCCATAAATTCTGCTACTTTT 57.159 33.333 0.00 0.00 0.00 2.27
40 41 6.856895 AGTGCCATAAATTCTGCTACTTTTC 58.143 36.000 0.00 0.00 0.00 2.29
41 42 6.036470 GTGCCATAAATTCTGCTACTTTTCC 58.964 40.000 0.00 0.00 0.00 3.13
42 43 5.951747 TGCCATAAATTCTGCTACTTTTCCT 59.048 36.000 0.00 0.00 0.00 3.36
43 44 6.437162 TGCCATAAATTCTGCTACTTTTCCTT 59.563 34.615 0.00 0.00 0.00 3.36
44 45 7.613801 TGCCATAAATTCTGCTACTTTTCCTTA 59.386 33.333 0.00 0.00 0.00 2.69
45 46 8.633561 GCCATAAATTCTGCTACTTTTCCTTAT 58.366 33.333 0.00 0.00 0.00 1.73
53 54 8.561738 TCTGCTACTTTTCCTTATAAAGTTGG 57.438 34.615 6.33 2.81 41.69 3.77
54 55 8.161425 TCTGCTACTTTTCCTTATAAAGTTGGT 58.839 33.333 6.33 0.00 41.69 3.67
55 56 8.331730 TGCTACTTTTCCTTATAAAGTTGGTC 57.668 34.615 6.33 0.00 41.69 4.02
56 57 7.118680 TGCTACTTTTCCTTATAAAGTTGGTCG 59.881 37.037 6.33 0.00 41.69 4.79
57 58 7.332678 GCTACTTTTCCTTATAAAGTTGGTCGA 59.667 37.037 6.33 0.00 41.69 4.20
58 59 9.379791 CTACTTTTCCTTATAAAGTTGGTCGAT 57.620 33.333 6.33 0.00 41.69 3.59
59 60 8.040716 ACTTTTCCTTATAAAGTTGGTCGATG 57.959 34.615 0.00 0.00 41.69 3.84
60 61 7.664318 ACTTTTCCTTATAAAGTTGGTCGATGT 59.336 33.333 0.00 0.00 41.69 3.06
61 62 9.158233 CTTTTCCTTATAAAGTTGGTCGATGTA 57.842 33.333 0.00 0.00 0.00 2.29
62 63 9.675464 TTTTCCTTATAAAGTTGGTCGATGTAT 57.325 29.630 0.00 0.00 0.00 2.29
63 64 9.675464 TTTCCTTATAAAGTTGGTCGATGTATT 57.325 29.630 0.00 0.00 0.00 1.89
72 73 9.458374 AAAGTTGGTCGATGTATTAAAACTTTG 57.542 29.630 8.84 0.00 42.12 2.77
73 74 8.385898 AGTTGGTCGATGTATTAAAACTTTGA 57.614 30.769 0.00 0.00 0.00 2.69
74 75 8.287503 AGTTGGTCGATGTATTAAAACTTTGAC 58.712 33.333 0.00 0.00 37.27 3.18
75 76 7.972832 TGGTCGATGTATTAAAACTTTGACT 57.027 32.000 0.00 0.00 37.75 3.41
76 77 8.385898 TGGTCGATGTATTAAAACTTTGACTT 57.614 30.769 0.00 0.00 37.75 3.01
77 78 9.491675 TGGTCGATGTATTAAAACTTTGACTTA 57.508 29.630 0.00 0.27 37.75 2.24
78 79 9.968743 GGTCGATGTATTAAAACTTTGACTTAG 57.031 33.333 0.00 0.00 37.75 2.18
79 80 9.968743 GTCGATGTATTAAAACTTTGACTTAGG 57.031 33.333 0.00 0.00 36.06 2.69
80 81 9.932207 TCGATGTATTAAAACTTTGACTTAGGA 57.068 29.630 0.00 0.00 0.00 2.94
81 82 9.968743 CGATGTATTAAAACTTTGACTTAGGAC 57.031 33.333 0.00 0.00 0.00 3.85
108 109 6.408858 AAACTAGATGTGCACTTATTCACG 57.591 37.500 19.41 7.33 36.06 4.35
109 110 4.433615 ACTAGATGTGCACTTATTCACGG 58.566 43.478 19.41 6.68 36.06 4.94
110 111 3.610040 AGATGTGCACTTATTCACGGA 57.390 42.857 19.41 0.00 36.06 4.69
111 112 4.142609 AGATGTGCACTTATTCACGGAT 57.857 40.909 19.41 0.00 36.06 4.18
112 113 5.276461 AGATGTGCACTTATTCACGGATA 57.724 39.130 19.41 0.00 36.06 2.59
113 114 5.292765 AGATGTGCACTTATTCACGGATAG 58.707 41.667 19.41 0.00 36.06 2.08
114 115 4.729227 TGTGCACTTATTCACGGATAGA 57.271 40.909 19.41 0.00 36.06 1.98
115 116 4.682787 TGTGCACTTATTCACGGATAGAG 58.317 43.478 19.41 0.00 36.06 2.43
116 117 4.051922 GTGCACTTATTCACGGATAGAGG 58.948 47.826 10.32 0.00 0.00 3.69
117 118 3.958147 TGCACTTATTCACGGATAGAGGA 59.042 43.478 0.00 0.00 0.00 3.71
133 134 7.096551 GGATAGAGGAAGTAGGTAGTACTACG 58.903 46.154 23.40 0.00 46.14 3.51
163 164 5.234757 GCAAATGGGCATATATTGTGTGTTG 59.765 40.000 0.00 0.00 0.00 3.33
238 259 4.706842 TTAAGGAGTAATCCATCTGGCC 57.293 45.455 12.54 0.00 34.44 5.36
249 270 2.170166 CCATCTGGCCTAAACTTTGCA 58.830 47.619 3.32 0.00 0.00 4.08
329 350 3.256631 GGTGACTAGAAACCCAACTACGA 59.743 47.826 0.00 0.00 0.00 3.43
354 375 6.488006 ACACACTTGATGCTTGTTAGAAGAAT 59.512 34.615 0.00 0.00 0.00 2.40
387 409 5.104109 AGGATGCAACACCTAATAAAGCCTA 60.104 40.000 8.38 0.00 34.47 3.93
421 444 5.401531 TGCTAGTAAGTAGTGGAAACAGG 57.598 43.478 0.00 0.00 44.46 4.00
547 590 7.911651 AGAGAAGATGGAATGTACTTTCTTGA 58.088 34.615 17.99 6.28 0.00 3.02
567 610 6.425417 TCTTGATTTGCAAACGTACTACATCA 59.575 34.615 15.41 8.09 35.74 3.07
569 612 4.377911 TTTGCAAACGTACTACATCACG 57.622 40.909 8.05 0.00 43.63 4.35
581 624 0.179004 ACATCACGTTTTGGCTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
608 651 0.321564 TTGCTCCCGGATGAACAGTG 60.322 55.000 0.73 0.00 0.00 3.66
621 664 4.882671 TGAACAGTGACTCAAAAGAAGC 57.117 40.909 0.00 0.00 0.00 3.86
626 669 3.807622 CAGTGACTCAAAAGAAGCGGTAA 59.192 43.478 0.00 0.00 0.00 2.85
627 670 4.272504 CAGTGACTCAAAAGAAGCGGTAAA 59.727 41.667 0.00 0.00 0.00 2.01
630 673 6.708949 AGTGACTCAAAAGAAGCGGTAAAATA 59.291 34.615 0.00 0.00 0.00 1.40
631 674 7.390718 AGTGACTCAAAAGAAGCGGTAAAATAT 59.609 33.333 0.00 0.00 0.00 1.28
678 721 6.715344 TTATGAATGTTCGTGTTAGTGTCC 57.285 37.500 0.00 0.00 0.00 4.02
681 724 2.519377 TGTTCGTGTTAGTGTCCCAG 57.481 50.000 0.00 0.00 0.00 4.45
701 744 4.250464 CAGGCATGCTTGACAATTTTCAT 58.750 39.130 24.43 0.00 30.96 2.57
719 762 2.098607 TCATACGAAACGGAGCAGTAGG 59.901 50.000 0.00 0.00 0.00 3.18
725 768 1.053424 AACGGAGCAGTAGGGTTTCA 58.947 50.000 0.00 0.00 0.00 2.69
748 791 7.385267 TCATCAGTGAAAATACAAATTTGGGG 58.615 34.615 21.74 0.00 35.46 4.96
756 799 9.277783 TGAAAATACAAATTTGGGGTAACATTG 57.722 29.630 21.74 0.00 35.46 2.82
758 801 6.943899 ATACAAATTTGGGGTAACATTGGT 57.056 33.333 21.74 0.00 39.74 3.67
760 803 4.410555 ACAAATTTGGGGTAACATTGGTGT 59.589 37.500 21.74 0.00 41.28 4.16
763 806 6.749036 AATTTGGGGTAACATTGGTGTTTA 57.251 33.333 0.00 0.00 46.07 2.01
838 890 7.013655 GGTAGCATTTGGATGTGACTATGAATT 59.986 37.037 0.00 0.00 35.63 2.17
897 949 3.769009 AAATCATTTTTCGCGTGCAAC 57.231 38.095 5.77 0.00 0.00 4.17
898 950 2.414058 ATCATTTTTCGCGTGCAACA 57.586 40.000 5.77 0.00 35.74 3.33
906 958 0.099613 TCGCGTGCAACACAAATTGT 59.900 45.000 5.77 0.00 41.74 2.71
911 963 4.444468 GCGTGCAACACAAATTGTATTTG 58.556 39.130 12.67 12.67 37.51 2.32
912 964 4.608000 GCGTGCAACACAAATTGTATTTGG 60.608 41.667 16.56 7.65 37.51 3.28
913 965 4.742167 CGTGCAACACAAATTGTATTTGGA 59.258 37.500 16.56 12.95 37.51 3.53
914 966 5.332205 CGTGCAACACAAATTGTATTTGGAC 60.332 40.000 22.70 22.70 38.91 4.02
915 967 4.742167 TGCAACACAAATTGTATTTGGACG 59.258 37.500 16.56 6.89 37.51 4.79
916 968 4.149747 GCAACACAAATTGTATTTGGACGG 59.850 41.667 16.56 5.80 37.51 4.79
917 969 3.908213 ACACAAATTGTATTTGGACGGC 58.092 40.909 14.55 0.00 36.32 5.68
918 970 3.572255 ACACAAATTGTATTTGGACGGCT 59.428 39.130 14.55 0.00 36.32 5.52
919 971 3.919804 CACAAATTGTATTTGGACGGCTG 59.080 43.478 14.55 0.00 33.92 4.85
920 972 3.823873 ACAAATTGTATTTGGACGGCTGA 59.176 39.130 14.55 0.00 33.92 4.26
921 973 4.279671 ACAAATTGTATTTGGACGGCTGAA 59.720 37.500 14.55 0.00 33.92 3.02
923 975 5.461032 AATTGTATTTGGACGGCTGAAAA 57.539 34.783 0.00 0.00 0.00 2.29
924 976 4.497473 TTGTATTTGGACGGCTGAAAAG 57.503 40.909 0.00 0.00 0.00 2.27
925 977 2.817258 TGTATTTGGACGGCTGAAAAGG 59.183 45.455 0.00 0.00 0.00 3.11
926 978 1.995376 ATTTGGACGGCTGAAAAGGT 58.005 45.000 0.00 0.00 0.00 3.50
947 999 9.660180 AAAGGTCAATTAAAACTTGTTTAGCAA 57.340 25.926 0.00 0.00 35.50 3.91
1023 1402 1.212935 CAAATACCCTCTCACCCCCAG 59.787 57.143 0.00 0.00 0.00 4.45
1042 1424 0.318762 GTCACCACCTCACTCACTCC 59.681 60.000 0.00 0.00 0.00 3.85
1118 1503 3.832490 TCTTCACCGATCTTCTTCTTCCA 59.168 43.478 0.00 0.00 0.00 3.53
1145 1530 4.922719 GATCTTTCTGTAGATCGTTCCGT 58.077 43.478 0.00 0.00 40.67 4.69
1207 1595 2.179517 GTCGCTCCTCCTCACACG 59.820 66.667 0.00 0.00 0.00 4.49
1474 1880 2.680352 TCCCACCAGAGCGAGGAC 60.680 66.667 0.00 0.00 0.00 3.85
1518 1933 2.415090 CGGCATTGCAAGAAGAAGAAGG 60.415 50.000 11.39 0.00 0.00 3.46
1528 1961 3.188773 AGAAGAAGAAGGGCAGGAAGAT 58.811 45.455 0.00 0.00 0.00 2.40
1532 1965 2.160721 AGAAGGGCAGGAAGATACGA 57.839 50.000 0.00 0.00 0.00 3.43
1537 1970 1.437986 GCAGGAAGATACGACGGCT 59.562 57.895 0.00 0.00 0.00 5.52
1801 2312 0.038159 CTGTCCTCGACCACCAGAAC 60.038 60.000 0.00 0.00 0.00 3.01
1802 2313 0.757561 TGTCCTCGACCACCAGAACA 60.758 55.000 0.00 0.00 0.00 3.18
1912 2465 1.212934 AGGAGGACGAGGTGGAGGTA 61.213 60.000 0.00 0.00 0.00 3.08
1928 2481 1.032114 GGTAGTTGACAGGGGCATGC 61.032 60.000 9.90 9.90 0.00 4.06
2024 2580 2.260434 CGGTCACCACGGACGAAT 59.740 61.111 0.00 0.00 38.70 3.34
2029 2585 0.109458 TCACCACGGACGAATCGAAG 60.109 55.000 10.55 2.35 0.00 3.79
2074 2633 2.018544 CAGAGCTACCGAGGACGAG 58.981 63.158 0.00 0.00 42.66 4.18
2352 2932 5.300752 CGCCTGATCATTACTCCAAACTAT 58.699 41.667 0.00 0.00 0.00 2.12
2353 2933 6.455647 CGCCTGATCATTACTCCAAACTATA 58.544 40.000 0.00 0.00 0.00 1.31
2354 2934 6.366332 CGCCTGATCATTACTCCAAACTATAC 59.634 42.308 0.00 0.00 0.00 1.47
2364 2944 6.150396 ACTCCAAACTATACTCTTCATCGG 57.850 41.667 0.00 0.00 0.00 4.18
2377 2962 0.109365 TCATCGGCGCCAATTTTGTG 60.109 50.000 28.98 13.12 0.00 3.33
2380 2965 0.596083 TCGGCGCCAATTTTGTGTTG 60.596 50.000 28.98 5.10 0.00 3.33
2428 3086 2.238942 TGTTGATCGTCTTGCTGTGT 57.761 45.000 0.00 0.00 0.00 3.72
2482 3449 4.870426 ACCATAGAGTGCACTTTATTGACG 59.130 41.667 26.07 16.20 0.00 4.35
2484 3451 5.580691 CCATAGAGTGCACTTTATTGACGAA 59.419 40.000 23.46 1.26 0.00 3.85
2542 3509 5.070180 TCTCCAAATCATGTCTCTGATCTCC 59.930 44.000 0.00 0.00 34.79 3.71
2556 3523 7.554118 GTCTCTGATCTCCATGACCAAAAATTA 59.446 37.037 0.00 0.00 0.00 1.40
2557 3524 8.277197 TCTCTGATCTCCATGACCAAAAATTAT 58.723 33.333 0.00 0.00 0.00 1.28
2558 3525 8.455903 TCTGATCTCCATGACCAAAAATTATC 57.544 34.615 0.00 0.00 0.00 1.75
2559 3526 8.277197 TCTGATCTCCATGACCAAAAATTATCT 58.723 33.333 0.00 0.00 0.00 1.98
2560 3527 8.455903 TGATCTCCATGACCAAAAATTATCTC 57.544 34.615 0.00 0.00 0.00 2.75
2561 3528 8.277197 TGATCTCCATGACCAAAAATTATCTCT 58.723 33.333 0.00 0.00 0.00 3.10
2562 3529 7.870509 TCTCCATGACCAAAAATTATCTCTG 57.129 36.000 0.00 0.00 0.00 3.35
2563 3530 7.632861 TCTCCATGACCAAAAATTATCTCTGA 58.367 34.615 0.00 0.00 0.00 3.27
2564 3531 8.277197 TCTCCATGACCAAAAATTATCTCTGAT 58.723 33.333 0.00 0.00 0.00 2.90
2565 3532 8.455903 TCCATGACCAAAAATTATCTCTGATC 57.544 34.615 0.00 0.00 0.00 2.92
2566 3533 8.277197 TCCATGACCAAAAATTATCTCTGATCT 58.723 33.333 0.00 0.00 0.00 2.75
2567 3534 8.350722 CCATGACCAAAAATTATCTCTGATCTG 58.649 37.037 0.00 0.00 0.00 2.90
2568 3535 8.900781 CATGACCAAAAATTATCTCTGATCTGT 58.099 33.333 0.00 0.00 0.00 3.41
2569 3536 8.868522 TGACCAAAAATTATCTCTGATCTGTT 57.131 30.769 0.00 0.00 0.00 3.16
2570 3537 8.733458 TGACCAAAAATTATCTCTGATCTGTTG 58.267 33.333 0.00 0.00 0.00 3.33
2571 3538 7.542025 ACCAAAAATTATCTCTGATCTGTTGC 58.458 34.615 0.00 0.00 0.00 4.17
2572 3539 7.395489 ACCAAAAATTATCTCTGATCTGTTGCT 59.605 33.333 0.00 0.00 0.00 3.91
2573 3540 8.248945 CCAAAAATTATCTCTGATCTGTTGCTT 58.751 33.333 0.00 0.00 0.00 3.91
2576 3543 9.896645 AAAATTATCTCTGATCTGTTGCTTAGA 57.103 29.630 0.00 0.00 0.00 2.10
2577 3544 9.896645 AAATTATCTCTGATCTGTTGCTTAGAA 57.103 29.630 0.00 0.00 0.00 2.10
2578 3545 8.885494 ATTATCTCTGATCTGTTGCTTAGAAC 57.115 34.615 0.00 0.00 0.00 3.01
2579 3546 5.728637 TCTCTGATCTGTTGCTTAGAACA 57.271 39.130 0.00 0.00 34.64 3.18
2580 3547 5.473931 TCTCTGATCTGTTGCTTAGAACAC 58.526 41.667 0.00 0.00 32.39 3.32
2581 3548 4.569943 TCTGATCTGTTGCTTAGAACACC 58.430 43.478 0.00 0.00 32.39 4.16
2582 3549 4.284490 TCTGATCTGTTGCTTAGAACACCT 59.716 41.667 0.00 0.00 32.39 4.00
2583 3550 4.569943 TGATCTGTTGCTTAGAACACCTC 58.430 43.478 0.00 0.00 32.39 3.85
2584 3551 4.040339 TGATCTGTTGCTTAGAACACCTCA 59.960 41.667 0.00 0.00 32.39 3.86
2585 3552 3.728845 TCTGTTGCTTAGAACACCTCAC 58.271 45.455 0.00 0.00 32.39 3.51
2586 3553 3.388024 TCTGTTGCTTAGAACACCTCACT 59.612 43.478 0.00 0.00 32.39 3.41
2587 3554 4.587262 TCTGTTGCTTAGAACACCTCACTA 59.413 41.667 0.00 0.00 32.39 2.74
2588 3555 4.883083 TGTTGCTTAGAACACCTCACTAG 58.117 43.478 0.00 0.00 30.75 2.57
2589 3556 4.587262 TGTTGCTTAGAACACCTCACTAGA 59.413 41.667 0.00 0.00 30.75 2.43
2590 3557 5.246203 TGTTGCTTAGAACACCTCACTAGAT 59.754 40.000 0.00 0.00 30.75 1.98
2615 3582 1.705873 AGTCGATTCCTTATCCGCCT 58.294 50.000 0.00 0.00 0.00 5.52
2619 3586 3.739810 GTCGATTCCTTATCCGCCTTAAC 59.260 47.826 0.00 0.00 0.00 2.01
2628 3596 6.941436 TCCTTATCCGCCTTAACAAAGTAAAA 59.059 34.615 0.00 0.00 0.00 1.52
2650 3618 7.721409 AAATTTTACTCCGGGCCTAAAAATA 57.279 32.000 0.84 0.00 0.00 1.40
2694 3662 2.240230 CGGTTGAGTAAAAGCCGCA 58.760 52.632 0.00 0.00 35.90 5.69
2714 3686 4.101448 CCCCTTCACTGCCCTCCG 62.101 72.222 0.00 0.00 0.00 4.63
2819 3802 2.978824 GCCGCTGTCCTCTACCAA 59.021 61.111 0.00 0.00 0.00 3.67
2868 3851 1.084370 GGCGAAGAAGTGGTGGATCG 61.084 60.000 0.00 0.00 0.00 3.69
2872 3855 3.195698 GAAGTGGTGGATCGGCGC 61.196 66.667 0.00 0.00 0.00 6.53
2907 3893 1.203001 ACGGGATTTGGCTTTTCTGGA 60.203 47.619 0.00 0.00 0.00 3.86
2914 3900 1.971695 GGCTTTTCTGGACGGTGGG 60.972 63.158 0.00 0.00 0.00 4.61
2917 3903 3.501040 TTTTCTGGACGGTGGGGGC 62.501 63.158 0.00 0.00 0.00 5.80
2918 3904 4.974438 TTCTGGACGGTGGGGGCT 62.974 66.667 0.00 0.00 0.00 5.19
2921 3907 3.976490 CTGGACGGTGGGGGCTCTA 62.976 68.421 0.00 0.00 0.00 2.43
3039 4025 1.825474 TCTCCCATCGAAGGTTCACTC 59.175 52.381 5.87 0.00 0.00 3.51
3314 4312 8.581578 GTTTTGGTATTGGGAAGAAGAATACAA 58.418 33.333 0.00 0.00 35.24 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.627123 AGCAGAATTTATGGCACTAAATTAGTA 57.373 29.630 18.78 0.00 39.95 1.82
8 9 8.525290 AGCAGAATTTATGGCACTAAATTAGT 57.475 30.769 18.78 0.00 39.95 2.24
9 10 9.884465 GTAGCAGAATTTATGGCACTAAATTAG 57.116 33.333 18.78 16.32 39.95 1.73
10 11 9.627123 AGTAGCAGAATTTATGGCACTAAATTA 57.373 29.630 18.78 8.05 39.95 1.40
11 12 8.525290 AGTAGCAGAATTTATGGCACTAAATT 57.475 30.769 18.81 18.81 41.62 1.82
12 13 8.525290 AAGTAGCAGAATTTATGGCACTAAAT 57.475 30.769 0.00 0.00 33.72 1.40
13 14 7.938140 AAGTAGCAGAATTTATGGCACTAAA 57.062 32.000 0.00 0.00 0.00 1.85
14 15 7.938140 AAAGTAGCAGAATTTATGGCACTAA 57.062 32.000 0.00 0.00 0.00 2.24
15 16 7.067008 GGAAAAGTAGCAGAATTTATGGCACTA 59.933 37.037 0.00 0.00 0.00 2.74
16 17 6.127619 GGAAAAGTAGCAGAATTTATGGCACT 60.128 38.462 0.00 0.00 0.00 4.40
17 18 6.036470 GGAAAAGTAGCAGAATTTATGGCAC 58.964 40.000 0.00 0.00 0.00 5.01
18 19 5.951747 AGGAAAAGTAGCAGAATTTATGGCA 59.048 36.000 0.00 0.00 0.00 4.92
19 20 6.456795 AGGAAAAGTAGCAGAATTTATGGC 57.543 37.500 0.00 0.00 0.00 4.40
27 28 9.010029 CCAACTTTATAAGGAAAAGTAGCAGAA 57.990 33.333 0.98 0.00 44.35 3.02
28 29 8.161425 ACCAACTTTATAAGGAAAAGTAGCAGA 58.839 33.333 0.98 0.00 44.35 4.26
29 30 8.336801 ACCAACTTTATAAGGAAAAGTAGCAG 57.663 34.615 0.98 0.00 44.35 4.24
30 31 7.118680 CGACCAACTTTATAAGGAAAAGTAGCA 59.881 37.037 0.98 0.00 44.35 3.49
31 32 7.332678 TCGACCAACTTTATAAGGAAAAGTAGC 59.667 37.037 0.98 0.00 44.35 3.58
32 33 8.767478 TCGACCAACTTTATAAGGAAAAGTAG 57.233 34.615 0.98 0.81 44.35 2.57
33 34 9.158233 CATCGACCAACTTTATAAGGAAAAGTA 57.842 33.333 0.98 0.00 44.35 2.24
34 35 7.664318 ACATCGACCAACTTTATAAGGAAAAGT 59.336 33.333 0.98 0.00 46.45 2.66
35 36 8.040716 ACATCGACCAACTTTATAAGGAAAAG 57.959 34.615 0.98 0.00 39.38 2.27
36 37 7.989416 ACATCGACCAACTTTATAAGGAAAA 57.011 32.000 0.98 0.00 0.00 2.29
37 38 9.675464 AATACATCGACCAACTTTATAAGGAAA 57.325 29.630 0.98 0.00 0.00 3.13
46 47 9.458374 CAAAGTTTTAATACATCGACCAACTTT 57.542 29.630 0.00 0.00 41.58 2.66
47 48 8.842280 TCAAAGTTTTAATACATCGACCAACTT 58.158 29.630 0.00 0.00 35.29 2.66
48 49 8.287503 GTCAAAGTTTTAATACATCGACCAACT 58.712 33.333 0.00 0.00 0.00 3.16
49 50 8.287503 AGTCAAAGTTTTAATACATCGACCAAC 58.712 33.333 0.00 0.00 0.00 3.77
50 51 8.385898 AGTCAAAGTTTTAATACATCGACCAA 57.614 30.769 0.00 0.00 0.00 3.67
51 52 7.972832 AGTCAAAGTTTTAATACATCGACCA 57.027 32.000 0.00 0.00 0.00 4.02
52 53 9.968743 CTAAGTCAAAGTTTTAATACATCGACC 57.031 33.333 0.00 0.00 0.00 4.79
53 54 9.968743 CCTAAGTCAAAGTTTTAATACATCGAC 57.031 33.333 0.00 2.32 0.00 4.20
54 55 9.932207 TCCTAAGTCAAAGTTTTAATACATCGA 57.068 29.630 0.00 0.00 0.00 3.59
55 56 9.968743 GTCCTAAGTCAAAGTTTTAATACATCG 57.031 33.333 0.00 0.00 0.00 3.84
83 84 7.298122 CGTGAATAAGTGCACATCTAGTTTTT 58.702 34.615 21.04 4.70 34.78 1.94
84 85 6.128282 CCGTGAATAAGTGCACATCTAGTTTT 60.128 38.462 21.04 4.20 34.78 2.43
85 86 5.351465 CCGTGAATAAGTGCACATCTAGTTT 59.649 40.000 21.04 4.99 34.78 2.66
86 87 4.870426 CCGTGAATAAGTGCACATCTAGTT 59.130 41.667 21.04 5.77 34.78 2.24
87 88 4.159693 TCCGTGAATAAGTGCACATCTAGT 59.840 41.667 21.04 6.45 34.78 2.57
88 89 4.682787 TCCGTGAATAAGTGCACATCTAG 58.317 43.478 21.04 9.22 34.78 2.43
89 90 4.729227 TCCGTGAATAAGTGCACATCTA 57.271 40.909 21.04 7.69 34.78 1.98
90 91 3.610040 TCCGTGAATAAGTGCACATCT 57.390 42.857 21.04 5.44 34.78 2.90
91 92 5.289595 TCTATCCGTGAATAAGTGCACATC 58.710 41.667 21.04 11.83 34.78 3.06
92 93 5.276461 TCTATCCGTGAATAAGTGCACAT 57.724 39.130 21.04 10.23 34.78 3.21
93 94 4.441495 CCTCTATCCGTGAATAAGTGCACA 60.441 45.833 21.04 0.00 34.78 4.57
94 95 4.051922 CCTCTATCCGTGAATAAGTGCAC 58.948 47.826 9.40 9.40 0.00 4.57
95 96 3.958147 TCCTCTATCCGTGAATAAGTGCA 59.042 43.478 0.00 0.00 0.00 4.57
96 97 4.585955 TCCTCTATCCGTGAATAAGTGC 57.414 45.455 0.00 0.00 0.00 4.40
97 98 6.150396 ACTTCCTCTATCCGTGAATAAGTG 57.850 41.667 0.00 0.00 0.00 3.16
98 99 6.490721 CCTACTTCCTCTATCCGTGAATAAGT 59.509 42.308 0.00 0.00 0.00 2.24
99 100 6.490721 ACCTACTTCCTCTATCCGTGAATAAG 59.509 42.308 0.00 0.00 0.00 1.73
100 101 6.371278 ACCTACTTCCTCTATCCGTGAATAA 58.629 40.000 0.00 0.00 0.00 1.40
101 102 5.950023 ACCTACTTCCTCTATCCGTGAATA 58.050 41.667 0.00 0.00 0.00 1.75
102 103 4.805744 ACCTACTTCCTCTATCCGTGAAT 58.194 43.478 0.00 0.00 0.00 2.57
103 104 4.246712 ACCTACTTCCTCTATCCGTGAA 57.753 45.455 0.00 0.00 0.00 3.18
104 105 3.947612 ACCTACTTCCTCTATCCGTGA 57.052 47.619 0.00 0.00 0.00 4.35
105 106 4.716794 ACTACCTACTTCCTCTATCCGTG 58.283 47.826 0.00 0.00 0.00 4.94
106 107 5.606329 AGTACTACCTACTTCCTCTATCCGT 59.394 44.000 0.00 0.00 30.80 4.69
107 108 6.112927 AGTACTACCTACTTCCTCTATCCG 57.887 45.833 0.00 0.00 30.80 4.18
108 109 7.039363 TCGTAGTACTACCTACTTCCTCTATCC 60.039 44.444 24.06 0.00 36.95 2.59
109 110 7.891561 TCGTAGTACTACCTACTTCCTCTATC 58.108 42.308 24.06 0.00 36.95 2.08
110 111 7.508977 ACTCGTAGTACTACCTACTTCCTCTAT 59.491 40.741 24.06 0.00 36.95 1.98
111 112 6.836527 ACTCGTAGTACTACCTACTTCCTCTA 59.163 42.308 24.06 0.00 36.95 2.43
112 113 5.660864 ACTCGTAGTACTACCTACTTCCTCT 59.339 44.000 24.06 0.00 36.95 3.69
113 114 5.912892 ACTCGTAGTACTACCTACTTCCTC 58.087 45.833 24.06 0.00 36.95 3.71
114 115 5.948742 ACTCGTAGTACTACCTACTTCCT 57.051 43.478 24.06 0.00 36.95 3.36
115 116 6.676700 GCAAACTCGTAGTACTACCTACTTCC 60.677 46.154 24.06 7.52 36.95 3.46
116 117 6.128172 TGCAAACTCGTAGTACTACCTACTTC 60.128 42.308 24.06 10.76 36.95 3.01
117 118 5.707298 TGCAAACTCGTAGTACTACCTACTT 59.293 40.000 24.06 11.85 36.95 2.24
133 134 6.201425 CACAATATATGCCCATTTGCAAACTC 59.799 38.462 15.41 4.56 45.84 3.01
266 287 7.218204 CGGCAACTAGAAATATTTTGCACTTAC 59.782 37.037 18.63 5.17 43.54 2.34
277 298 6.885922 ACTACTTTCCGGCAACTAGAAATAT 58.114 36.000 0.00 0.00 36.36 1.28
329 350 5.368145 TCTTCTAACAAGCATCAAGTGTGT 58.632 37.500 0.00 0.00 0.00 3.72
354 375 5.435686 AGGTGTTGCATCCTCTACAATTA 57.564 39.130 0.00 0.00 0.00 1.40
421 444 5.003804 TCCCACTGTCTTCTGCTTTATTTC 58.996 41.667 0.00 0.00 0.00 2.17
547 590 4.953269 CGTGATGTAGTACGTTTGCAAAT 58.047 39.130 16.21 2.51 35.70 2.32
567 610 1.073199 CTCCTGGGAGCCAAAACGT 59.927 57.895 3.52 0.00 35.31 3.99
608 651 8.965986 AAATATTTTACCGCTTCTTTTGAGTC 57.034 30.769 0.00 0.00 0.00 3.36
678 721 2.754946 AAATTGTCAAGCATGCCTGG 57.245 45.000 15.66 4.10 0.00 4.45
681 724 4.266029 CGTATGAAAATTGTCAAGCATGCC 59.734 41.667 15.66 0.00 0.00 4.40
701 744 0.813184 CCCTACTGCTCCGTTTCGTA 59.187 55.000 0.00 0.00 0.00 3.43
725 768 7.315066 ACCCCAAATTTGTATTTTCACTGAT 57.685 32.000 16.73 0.00 31.63 2.90
736 779 5.602978 ACACCAATGTTACCCCAAATTTGTA 59.397 36.000 16.73 0.42 34.46 2.41
792 844 3.131400 ACCTGCGAAGTTTTAGGCAAAAA 59.869 39.130 0.00 0.00 35.46 1.94
805 857 1.737838 TCCAAATGCTACCTGCGAAG 58.262 50.000 0.00 0.00 46.63 3.79
808 860 1.064505 CACATCCAAATGCTACCTGCG 59.935 52.381 0.00 0.00 46.63 5.18
874 926 5.232202 TGTTGCACGCGAAAAATGATTTTTA 59.768 32.000 15.93 0.00 42.51 1.52
880 932 1.202188 TGTGTTGCACGCGAAAAATGA 60.202 42.857 15.93 0.00 37.14 2.57
884 936 1.914634 ATTTGTGTTGCACGCGAAAA 58.085 40.000 15.93 0.01 35.80 2.29
889 941 4.444468 CAAATACAATTTGTGTTGCACGC 58.556 39.130 12.30 0.00 41.98 5.34
890 942 4.742167 TCCAAATACAATTTGTGTTGCACG 59.258 37.500 12.30 4.83 41.98 5.34
892 944 4.742167 CGTCCAAATACAATTTGTGTTGCA 59.258 37.500 12.30 0.45 41.98 4.08
897 949 3.919804 CAGCCGTCCAAATACAATTTGTG 59.080 43.478 12.30 0.00 0.00 3.33
898 950 3.823873 TCAGCCGTCCAAATACAATTTGT 59.176 39.130 7.30 7.30 0.00 2.83
906 958 3.078837 GACCTTTTCAGCCGTCCAAATA 58.921 45.455 0.00 0.00 0.00 1.40
911 963 1.534729 ATTGACCTTTTCAGCCGTCC 58.465 50.000 0.00 0.00 34.94 4.79
912 964 4.759516 TTAATTGACCTTTTCAGCCGTC 57.240 40.909 0.00 0.00 34.94 4.79
913 965 5.068591 AGTTTTAATTGACCTTTTCAGCCGT 59.931 36.000 0.00 0.00 34.94 5.68
914 966 5.528870 AGTTTTAATTGACCTTTTCAGCCG 58.471 37.500 0.00 0.00 34.94 5.52
915 967 6.761242 ACAAGTTTTAATTGACCTTTTCAGCC 59.239 34.615 0.00 0.00 34.94 4.85
916 968 7.770801 ACAAGTTTTAATTGACCTTTTCAGC 57.229 32.000 0.00 0.00 34.94 4.26
920 972 9.660180 TGCTAAACAAGTTTTAATTGACCTTTT 57.340 25.926 3.25 0.00 34.23 2.27
921 973 9.660180 TTGCTAAACAAGTTTTAATTGACCTTT 57.340 25.926 3.25 0.00 33.24 3.11
923 975 7.709182 GGTTGCTAAACAAGTTTTAATTGACCT 59.291 33.333 3.25 0.00 39.50 3.85
924 976 7.492994 TGGTTGCTAAACAAGTTTTAATTGACC 59.507 33.333 3.25 6.22 39.50 4.02
925 977 8.413899 TGGTTGCTAAACAAGTTTTAATTGAC 57.586 30.769 3.25 0.00 39.50 3.18
926 978 9.436957 TTTGGTTGCTAAACAAGTTTTAATTGA 57.563 25.926 3.25 0.00 39.50 2.57
1023 1402 0.318762 GGAGTGAGTGAGGTGGTGAC 59.681 60.000 0.00 0.00 0.00 3.67
1042 1424 3.997021 GGTTGTGTAGTGAGATTGTGAGG 59.003 47.826 0.00 0.00 0.00 3.86
1143 1528 2.158959 GCCACCGTCATCTCGAACG 61.159 63.158 0.41 0.41 0.00 3.95
1144 1529 2.158959 CGCCACCGTCATCTCGAAC 61.159 63.158 0.00 0.00 0.00 3.95
1145 1530 2.180769 CGCCACCGTCATCTCGAA 59.819 61.111 0.00 0.00 0.00 3.71
1252 1640 1.153289 GATGGCGCTCCACATGTCT 60.153 57.895 7.64 0.00 46.92 3.41
1314 1717 3.214123 CCATCGGGTAGCCGACGA 61.214 66.667 36.19 16.92 45.06 4.20
1315 1718 4.944372 GCCATCGGGTAGCCGACG 62.944 72.222 36.19 28.99 45.06 5.12
1452 1858 3.374402 CGCTCTGGTGGGACGAGT 61.374 66.667 0.00 0.00 0.00 4.18
1453 1859 3.057547 CTCGCTCTGGTGGGACGAG 62.058 68.421 0.00 0.00 43.46 4.18
1474 1880 2.024163 TCATCATCGACGACGGCG 59.976 61.111 19.07 19.07 44.79 6.46
1482 1888 1.066422 GCCGCTGAGTCATCATCGA 59.934 57.895 3.31 0.00 45.55 3.59
1486 1892 1.371337 GCAATGCCGCTGAGTCATCA 61.371 55.000 0.00 0.00 0.00 3.07
1518 1933 1.591863 GCCGTCGTATCTTCCTGCC 60.592 63.158 0.00 0.00 0.00 4.85
1597 2036 1.433879 GCGAGACATAGACGGCAGT 59.566 57.895 0.00 0.00 0.00 4.40
1801 2312 0.596600 CTGGCTGTTGCTGTTGCTTG 60.597 55.000 0.00 0.00 40.48 4.01
1802 2313 0.752743 TCTGGCTGTTGCTGTTGCTT 60.753 50.000 0.00 0.00 40.48 3.91
1912 2465 1.303888 CAGCATGCCCCTGTCAACT 60.304 57.895 15.66 0.00 0.00 3.16
1928 2481 4.704833 CGCCACCACCTCCACCAG 62.705 72.222 0.00 0.00 0.00 4.00
1969 2522 5.762179 ACTTGTTGATGACTATCCTGGAA 57.238 39.130 0.00 0.00 32.09 3.53
2052 2608 1.754621 TCCTCGGTAGCTCTGCAGG 60.755 63.158 15.13 5.82 0.00 4.85
2352 2932 0.464036 ATTGGCGCCGATGAAGAGTA 59.536 50.000 28.77 0.00 0.00 2.59
2353 2933 0.392998 AATTGGCGCCGATGAAGAGT 60.393 50.000 29.91 10.32 0.00 3.24
2354 2934 0.734889 AAATTGGCGCCGATGAAGAG 59.265 50.000 29.91 0.00 0.00 2.85
2364 2944 1.929836 TCAACAACACAAAATTGGCGC 59.070 42.857 0.00 0.00 0.00 6.53
2377 2962 7.491048 ACAAACCATTGTCAAATACTCAACAAC 59.509 33.333 0.00 0.00 46.78 3.32
2458 3116 5.220472 CGTCAATAAAGTGCACTCTATGGTG 60.220 44.000 21.95 12.28 39.91 4.17
2496 3463 7.444487 GGAGACCATGGGAAAACATAAGTATAC 59.556 40.741 18.09 0.00 0.00 1.47
2498 3465 6.069088 TGGAGACCATGGGAAAACATAAGTAT 60.069 38.462 18.09 0.00 0.00 2.12
2500 3467 4.044065 TGGAGACCATGGGAAAACATAAGT 59.956 41.667 18.09 0.00 0.00 2.24
2502 3469 4.666412 TGGAGACCATGGGAAAACATAA 57.334 40.909 18.09 0.00 0.00 1.90
2504 3471 3.541242 TTGGAGACCATGGGAAAACAT 57.459 42.857 18.09 0.00 31.53 2.71
2505 3472 3.320610 TTTGGAGACCATGGGAAAACA 57.679 42.857 18.09 5.50 31.53 2.83
2506 3473 3.831911 TGATTTGGAGACCATGGGAAAAC 59.168 43.478 18.09 6.29 31.53 2.43
2507 3474 4.125124 TGATTTGGAGACCATGGGAAAA 57.875 40.909 18.09 9.10 31.53 2.29
2508 3475 3.824001 TGATTTGGAGACCATGGGAAA 57.176 42.857 18.09 7.10 31.53 3.13
2509 3476 3.011595 ACATGATTTGGAGACCATGGGAA 59.988 43.478 18.09 1.23 40.32 3.97
2510 3477 2.582172 ACATGATTTGGAGACCATGGGA 59.418 45.455 18.09 0.00 40.32 4.37
2511 3478 2.954318 GACATGATTTGGAGACCATGGG 59.046 50.000 18.09 0.00 40.32 4.00
2512 3479 3.881688 GAGACATGATTTGGAGACCATGG 59.118 47.826 11.19 11.19 40.32 3.66
2513 3480 4.575236 CAGAGACATGATTTGGAGACCATG 59.425 45.833 0.00 0.00 41.40 3.66
2542 3509 8.900781 ACAGATCAGAGATAATTTTTGGTCATG 58.099 33.333 0.00 0.00 0.00 3.07
2556 3523 6.105333 GTGTTCTAAGCAACAGATCAGAGAT 58.895 40.000 0.00 0.00 36.94 2.75
2557 3524 5.473931 GTGTTCTAAGCAACAGATCAGAGA 58.526 41.667 0.00 0.00 36.94 3.10
2558 3525 4.629200 GGTGTTCTAAGCAACAGATCAGAG 59.371 45.833 0.00 0.00 36.94 3.35
2559 3526 4.284490 AGGTGTTCTAAGCAACAGATCAGA 59.716 41.667 0.00 0.00 36.94 3.27
2560 3527 4.573900 AGGTGTTCTAAGCAACAGATCAG 58.426 43.478 0.00 0.00 36.94 2.90
2561 3528 4.040339 TGAGGTGTTCTAAGCAACAGATCA 59.960 41.667 0.00 0.00 36.94 2.92
2562 3529 4.390297 GTGAGGTGTTCTAAGCAACAGATC 59.610 45.833 0.00 0.00 36.94 2.75
2563 3530 4.040952 AGTGAGGTGTTCTAAGCAACAGAT 59.959 41.667 0.00 0.00 36.94 2.90
2564 3531 3.388024 AGTGAGGTGTTCTAAGCAACAGA 59.612 43.478 0.00 0.00 36.94 3.41
2565 3532 3.733337 AGTGAGGTGTTCTAAGCAACAG 58.267 45.455 0.00 0.00 36.94 3.16
2566 3533 3.838244 AGTGAGGTGTTCTAAGCAACA 57.162 42.857 0.00 0.00 33.75 3.33
2567 3534 5.135508 TCTAGTGAGGTGTTCTAAGCAAC 57.864 43.478 0.00 0.00 0.00 4.17
2568 3535 7.321153 GTTATCTAGTGAGGTGTTCTAAGCAA 58.679 38.462 0.00 0.00 0.00 3.91
2569 3536 6.127423 GGTTATCTAGTGAGGTGTTCTAAGCA 60.127 42.308 0.00 0.00 0.00 3.91
2570 3537 6.097129 AGGTTATCTAGTGAGGTGTTCTAAGC 59.903 42.308 0.00 0.00 0.00 3.09
2571 3538 7.648039 AGGTTATCTAGTGAGGTGTTCTAAG 57.352 40.000 0.00 0.00 0.00 2.18
2572 3539 8.749026 CTAGGTTATCTAGTGAGGTGTTCTAA 57.251 38.462 0.00 0.00 40.37 2.10
2585 3552 8.895737 GGATAAGGAATCGACTAGGTTATCTAG 58.104 40.741 0.00 0.00 41.95 2.43
2586 3553 7.551974 CGGATAAGGAATCGACTAGGTTATCTA 59.448 40.741 12.47 0.00 35.21 1.98
2587 3554 6.374894 CGGATAAGGAATCGACTAGGTTATCT 59.625 42.308 12.47 0.00 35.21 1.98
2588 3555 6.553524 CGGATAAGGAATCGACTAGGTTATC 58.446 44.000 0.00 0.00 35.21 1.75
2589 3556 5.105837 GCGGATAAGGAATCGACTAGGTTAT 60.106 44.000 0.00 0.00 35.21 1.89
2590 3557 4.217118 GCGGATAAGGAATCGACTAGGTTA 59.783 45.833 0.00 0.00 35.21 2.85
2598 3565 3.385433 TGTTAAGGCGGATAAGGAATCGA 59.615 43.478 0.00 0.00 35.21 3.59
2628 3596 7.064229 TGATATTTTTAGGCCCGGAGTAAAAT 58.936 34.615 0.73 9.99 0.00 1.82
2650 3618 5.103000 GCGCGATGGAGTAAGTATAATGAT 58.897 41.667 12.10 0.00 0.00 2.45
2694 3662 1.920835 GAGGGCAGTGAAGGGGAGT 60.921 63.158 0.00 0.00 0.00 3.85
2819 3802 3.359950 GAGGAGGAGGCACAAATCAAAT 58.640 45.455 0.00 0.00 0.00 2.32
2917 3903 0.107456 ATCCATGGCAAGGCGTAGAG 59.893 55.000 6.96 0.00 0.00 2.43
2918 3904 0.546122 AATCCATGGCAAGGCGTAGA 59.454 50.000 6.96 0.00 0.00 2.59
2921 3907 2.053865 CCAATCCATGGCAAGGCGT 61.054 57.895 6.96 0.00 43.80 5.68
3039 4025 2.398036 GTCGGGCGTGTATTTGCG 59.602 61.111 0.00 0.00 0.00 4.85
3314 4312 3.710326 TTCGTGCTAGCAATAGATCGT 57.290 42.857 21.29 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.