Multiple sequence alignment - TraesCS3B01G499800

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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 TraesCS3B01G499800 chr3B 100.000 4802 0 0 1 4802 744420861 744416060 0.000000e+00 8868.0
1 TraesCS3B01G499800 chr3B 96.249 3732 104 18 1 3701 747492035 747495761 0.000000e+00 6083.0
2 TraesCS3B01G499800 chr3B 86.315 1403 146 21 984 2379 745203414 745202051 0.000000e+00 1485.0
3 TraesCS3B01G499800 chr3B 85.524 1354 151 31 1027 2367 745474836 745473515 0.000000e+00 1373.0
4 TraesCS3B01G499800 chr3B 87.018 1063 130 6 945 2004 744590532 744591589 0.000000e+00 1192.0
5 TraesCS3B01G499800 chr3B 86.501 1089 139 6 945 2030 746856426 746855343 0.000000e+00 1190.0
6 TraesCS3B01G499800 chr3B 85.963 1090 127 18 951 2017 745450524 745449438 0.000000e+00 1142.0
7 TraesCS3B01G499800 chr3B 98.117 478 9 0 4325 4802 747496128 747496605 0.000000e+00 833.0
8 TraesCS3B01G499800 chr3B 84.872 509 67 9 2447 2949 744511373 744510869 5.550000e-139 505.0
9 TraesCS3B01G499800 chr3B 83.491 527 70 14 2469 2983 744545226 744544705 4.350000e-130 475.0
10 TraesCS3B01G499800 chr3B 91.509 212 13 4 2159 2367 744339656 744339447 2.190000e-73 287.0
11 TraesCS3B01G499800 chr3B 90.000 70 7 0 3510 3579 744216139 744216070 1.840000e-14 91.6
12 TraesCS3B01G499800 chr3B 96.970 33 0 1 4258 4290 747496113 747496082 2.000000e-03 54.7
13 TraesCS3B01G499800 chr3D 90.375 2691 174 38 841 3496 560235283 560232643 0.000000e+00 3456.0
14 TraesCS3B01G499800 chr3D 84.150 1388 173 33 957 2324 560551529 560552889 0.000000e+00 1301.0
15 TraesCS3B01G499800 chr3D 86.393 1073 122 18 1029 2082 560785843 560784776 0.000000e+00 1151.0
16 TraesCS3B01G499800 chr3D 83.588 524 70 13 2472 2983 560285223 560284704 1.210000e-130 477.0
17 TraesCS3B01G499800 chr3D 89.157 249 19 2 2126 2374 560784652 560784412 2.170000e-78 303.0
18 TraesCS3B01G499800 chr3D 85.340 191 28 0 3510 3700 560232597 560232407 1.050000e-46 198.0
19 TraesCS3B01G499800 chr3D 88.235 68 7 1 4101 4168 532939233 532939299 3.980000e-11 80.5
20 TraesCS3B01G499800 chr3A 91.842 2378 155 17 4 2368 696333942 696331591 0.000000e+00 3280.0
21 TraesCS3B01G499800 chr3A 91.600 2381 159 19 1 2366 629086018 629088372 0.000000e+00 3251.0
22 TraesCS3B01G499800 chr3A 90.806 1240 79 18 2417 3632 629088655 629089883 0.000000e+00 1626.0
23 TraesCS3B01G499800 chr3A 94.181 653 32 2 2417 3063 696331309 696330657 0.000000e+00 990.0
24 TraesCS3B01G499800 chr3A 83.525 522 71 13 2469 2977 629057931 629058450 1.560000e-129 473.0
25 TraesCS3B01G499800 chr3A 90.521 211 15 2 3698 3904 629090206 629090415 1.700000e-69 274.0
26 TraesCS3B01G499800 chr3A 90.521 211 15 2 3698 3904 696330632 696330423 1.700000e-69 274.0
27 TraesCS3B01G499800 chr3A 86.275 255 29 4 2115 2367 696638289 696638539 6.120000e-69 272.0
28 TraesCS3B01G499800 chr3A 77.204 465 55 30 3005 3426 696342334 696341878 1.740000e-54 224.0
29 TraesCS3B01G499800 chrUn 100.000 424 0 0 2515 2938 476666784 476666361 0.000000e+00 784.0
30 TraesCS3B01G499800 chrUn 85.938 192 24 2 59 247 182460738 182460547 8.150000e-48 202.0
31 TraesCS3B01G499800 chrUn 92.500 40 2 1 2388 2427 332808869 332808831 6.710000e-04 56.5
32 TraesCS3B01G499800 chrUn 92.500 40 2 1 2388 2427 342444008 342444046 6.710000e-04 56.5
33 TraesCS3B01G499800 chr7D 83.181 547 76 10 4268 4802 382942703 382942161 2.010000e-133 486.0
34 TraesCS3B01G499800 chr7D 86.979 192 22 2 59 247 44748002 44747811 3.760000e-51 213.0
35 TraesCS3B01G499800 chr7D 85.938 192 24 2 59 247 382044641 382044450 8.150000e-48 202.0
36 TraesCS3B01G499800 chr5D 85.333 375 47 6 4434 4802 173759856 173760228 9.750000e-102 381.0
37 TraesCS3B01G499800 chr5A 83.155 374 52 9 4434 4802 195640898 195641265 9.960000e-87 331.0
38 TraesCS3B01G499800 chr5A 92.857 42 2 1 4158 4199 318269123 318269083 5.190000e-05 60.2
39 TraesCS3B01G499800 chr2D 86.458 192 23 2 59 247 306134676 306134485 1.750000e-49 207.0
40 TraesCS3B01G499800 chr2D 97.059 34 1 0 4166 4199 496635992 496636025 1.870000e-04 58.4
41 TraesCS3B01G499800 chr6D 85.938 192 24 2 59 247 172753460 172753269 8.150000e-48 202.0
42 TraesCS3B01G499800 chr6D 94.286 35 2 0 4165 4199 157373750 157373784 2.000000e-03 54.7
43 TraesCS3B01G499800 chr1D 85.938 192 24 2 59 247 350957330 350957521 8.150000e-48 202.0
44 TraesCS3B01G499800 chr1D 77.436 195 22 11 3510 3700 385622393 385622569 3.960000e-16 97.1
45 TraesCS3B01G499800 chr6A 81.595 163 21 4 2884 3039 341646864 341647024 5.050000e-25 126.0
46 TraesCS3B01G499800 chr6A 92.308 39 3 0 4162 4200 39426713 39426751 6.710000e-04 56.5
47 TraesCS3B01G499800 chr4D 81.053 95 13 5 4076 4168 444258735 444258826 2.400000e-08 71.3
48 TraesCS3B01G499800 chr1B 95.349 43 2 0 2385 2427 629772898 629772940 8.620000e-08 69.4
49 TraesCS3B01G499800 chr1A 97.436 39 1 0 2388 2426 4722284 4722322 3.100000e-07 67.6
50 TraesCS3B01G499800 chr1A 86.207 58 4 2 4115 4168 508650341 508650398 5.190000e-05 60.2
51 TraesCS3B01G499800 chr4A 80.000 95 14 5 4076 4168 23562126 23562035 1.120000e-06 65.8
52 TraesCS3B01G499800 chr7A 95.000 40 2 0 4160 4199 699921354 699921393 4.010000e-06 63.9
53 TraesCS3B01G499800 chr7B 97.059 34 1 0 2388 2421 548471970 548472003 1.870000e-04 58.4
54 TraesCS3B01G499800 chr6B 97.059 34 1 0 4166 4199 674410798 674410831 1.870000e-04 58.4
55 TraesCS3B01G499800 chr6B 100.000 29 0 0 4164 4192 685150941 685150913 2.000000e-03 54.7
56 TraesCS3B01G499800 chr5B 92.105 38 3 0 4162 4199 686200448 686200411 2.000000e-03 54.7
57 TraesCS3B01G499800 chr2A 92.308 39 0 3 4162 4198 103374727 103374764 9.000000e-03 52.8


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 TraesCS3B01G499800 chr3B 744416060 744420861 4801 True 8868.000000 8868 100.000000 1 4802 1 chr3B.!!$R3 4801
1 TraesCS3B01G499800 chr3B 747492035 747496605 4570 False 3458.000000 6083 97.183000 1 4802 2 chr3B.!!$F2 4801
2 TraesCS3B01G499800 chr3B 745202051 745203414 1363 True 1485.000000 1485 86.315000 984 2379 1 chr3B.!!$R6 1395
3 TraesCS3B01G499800 chr3B 745473515 745474836 1321 True 1373.000000 1373 85.524000 1027 2367 1 chr3B.!!$R8 1340
4 TraesCS3B01G499800 chr3B 744590532 744591589 1057 False 1192.000000 1192 87.018000 945 2004 1 chr3B.!!$F1 1059
5 TraesCS3B01G499800 chr3B 746855343 746856426 1083 True 1190.000000 1190 86.501000 945 2030 1 chr3B.!!$R9 1085
6 TraesCS3B01G499800 chr3B 745449438 745450524 1086 True 1142.000000 1142 85.963000 951 2017 1 chr3B.!!$R7 1066
7 TraesCS3B01G499800 chr3B 744510869 744511373 504 True 505.000000 505 84.872000 2447 2949 1 chr3B.!!$R4 502
8 TraesCS3B01G499800 chr3B 744544705 744545226 521 True 475.000000 475 83.491000 2469 2983 1 chr3B.!!$R5 514
9 TraesCS3B01G499800 chr3D 560232407 560235283 2876 True 1827.000000 3456 87.857500 841 3700 2 chr3D.!!$R2 2859
10 TraesCS3B01G499800 chr3D 560551529 560552889 1360 False 1301.000000 1301 84.150000 957 2324 1 chr3D.!!$F2 1367
11 TraesCS3B01G499800 chr3D 560784412 560785843 1431 True 727.000000 1151 87.775000 1029 2374 2 chr3D.!!$R3 1345
12 TraesCS3B01G499800 chr3D 560284704 560285223 519 True 477.000000 477 83.588000 2472 2983 1 chr3D.!!$R1 511
13 TraesCS3B01G499800 chr3A 629086018 629090415 4397 False 1717.000000 3251 90.975667 1 3904 3 chr3A.!!$F3 3903
14 TraesCS3B01G499800 chr3A 696330423 696333942 3519 True 1514.666667 3280 92.181333 4 3904 3 chr3A.!!$R2 3900
15 TraesCS3B01G499800 chr3A 629057931 629058450 519 False 473.000000 473 83.525000 2469 2977 1 chr3A.!!$F1 508
16 TraesCS3B01G499800 chr7D 382942161 382942703 542 True 486.000000 486 83.181000 4268 4802 1 chr7D.!!$R3 534

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
83 84 0.106268 TGGGCCTGCTCAAGTTTTCA 60.106 50.000 4.53 0.0 0.0 2.69 F
367 370 1.089481 ACATAGCGTGCAACCCATCG 61.089 55.000 0.00 0.0 0.0 3.84 F
693 700 1.337703 GCATGTCTGTGTTGAAGCCAA 59.662 47.619 0.00 0.0 0.0 4.52 F
2250 2448 0.250510 TTGGTGTCCGCAATGCTGTA 60.251 50.000 2.94 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2099 1.079266 CCAGCTCTGTCTGTCCTGC 60.079 63.158 0.00 0.00 32.32 4.85 R
2250 2448 0.673985 GAAAGCCGGGCACTTTCTTT 59.326 50.000 23.09 11.58 46.14 2.52 R
2454 2911 1.825090 TGAGCAGGCCAACAGTTATG 58.175 50.000 5.01 0.00 0.00 1.90 R
3929 4918 0.040499 TGGTGTTGGCCTAAATCCCC 59.960 55.000 3.32 0.00 0.00 4.81 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
83 84 0.106268 TGGGCCTGCTCAAGTTTTCA 60.106 50.000 4.53 0.00 0.00 2.69
274 277 2.356227 CCTTAACCTTCCTCTTCCCTGC 60.356 54.545 0.00 0.00 0.00 4.85
310 313 8.129840 CGATAGTAACAAAGTACTGCTACTGAT 58.870 37.037 0.00 0.00 35.85 2.90
328 331 8.089597 GCTACTGATATAGATCATCATCCATGG 58.910 40.741 4.97 4.97 41.33 3.66
334 337 2.029560 AGATCATCATCCATGGTCGACG 60.030 50.000 12.58 2.16 46.24 5.12
367 370 1.089481 ACATAGCGTGCAACCCATCG 61.089 55.000 0.00 0.00 0.00 3.84
441 445 5.036117 TCTGGGATAAGTGAGCCATTAAC 57.964 43.478 0.00 0.00 34.10 2.01
651 655 1.804748 GATTGGTGGGAACAAGACGTC 59.195 52.381 7.70 7.70 46.06 4.34
693 700 1.337703 GCATGTCTGTGTTGAAGCCAA 59.662 47.619 0.00 0.00 0.00 4.52
735 743 6.514048 GCTCCACAATATTTTCTATGGTGAGC 60.514 42.308 2.06 0.00 32.02 4.26
750 758 3.756434 TGGTGAGCTGCAAAGTTAATACC 59.244 43.478 1.02 0.00 0.00 2.73
760 768 7.753580 GCTGCAAAGTTAATACCGAGTATTTTT 59.246 33.333 12.51 6.78 39.18 1.94
863 907 5.464965 TTGAAACTCTTTGTTGAGTCGAC 57.535 39.130 7.70 7.70 45.49 4.20
1390 1472 2.326897 CGCTCATCATTGGCGCTG 59.673 61.111 7.64 0.00 42.28 5.18
2011 2099 2.292267 GTGTGCTGGGATACATTCAGG 58.708 52.381 0.00 0.00 39.74 3.86
2250 2448 0.250510 TTGGTGTCCGCAATGCTGTA 60.251 50.000 2.94 0.00 0.00 2.74
2488 2945 5.188751 GGCCTGCTCATAGATAAGATACCTT 59.811 44.000 0.00 0.00 36.43 3.50
2511 2973 9.561069 CCTTAACTATGTATGCTACCATTTTCT 57.439 33.333 0.00 0.00 32.85 2.52
2935 3403 9.936759 AAAGAAGAAAGGATCTCTGTAAGTTAG 57.063 33.333 0.00 0.00 37.42 2.34
2936 3404 8.658840 AGAAGAAAGGATCTCTGTAAGTTAGT 57.341 34.615 0.00 0.00 37.42 2.24
2937 3405 9.095700 AGAAGAAAGGATCTCTGTAAGTTAGTT 57.904 33.333 0.00 0.00 37.42 2.24
3022 3505 1.074405 TCTCTTGGCATGCTTTCTGGT 59.926 47.619 18.92 0.00 0.00 4.00
3039 3522 4.724399 TCTGGTTGTGGTGTTACATGATT 58.276 39.130 0.00 0.00 0.00 2.57
3195 3706 6.494146 GGGCTATCTAGTAGTCTAATGTGGTT 59.506 42.308 0.00 0.00 35.31 3.67
3250 3761 7.618502 TGTGTTGTGAAGTTGTTGTAGTTAT 57.381 32.000 0.00 0.00 0.00 1.89
3263 3774 9.546909 GTTGTTGTAGTTATCATGAATCAACTG 57.453 33.333 21.75 0.00 36.13 3.16
3276 3788 5.754782 TGAATCAACTGGGTATGCATTAGT 58.245 37.500 3.54 2.07 0.00 2.24
3289 3801 3.305177 ATTAGTGGTCGGCGGCGTT 62.305 57.895 31.06 14.48 0.00 4.84
3302 3814 0.454285 CGGCGTTCATCGTTGCAAAT 60.454 50.000 0.00 0.00 42.13 2.32
3383 3914 7.469260 GTTTGTTTGTTAGACTGTCAGCTAAA 58.531 34.615 10.88 3.78 0.00 1.85
3387 3918 4.893608 TGTTAGACTGTCAGCTAAATGCA 58.106 39.130 10.88 0.00 45.94 3.96
3392 3923 2.751259 ACTGTCAGCTAAATGCACATGG 59.249 45.455 0.00 0.00 45.94 3.66
3398 3929 4.280425 TCAGCTAAATGCACATGGTGAAAA 59.720 37.500 0.00 0.00 45.94 2.29
3426 3957 2.268280 CTGTGCTGCCAGAGAGGG 59.732 66.667 11.25 0.00 34.44 4.30
3654 4219 2.187946 CTGCTTCGGCGGGATTCT 59.812 61.111 7.21 0.00 45.37 2.40
3655 4220 2.125147 TGCTTCGGCGGGATTCTG 60.125 61.111 7.21 0.00 45.37 3.02
3657 4222 1.143183 GCTTCGGCGGGATTCTGTA 59.857 57.895 7.21 0.00 0.00 2.74
3659 4224 0.174845 CTTCGGCGGGATTCTGTACA 59.825 55.000 7.21 0.00 0.00 2.90
3661 4226 0.387929 TCGGCGGGATTCTGTACATC 59.612 55.000 7.21 0.00 0.00 3.06
3663 4228 0.600255 GGCGGGATTCTGTACATCGG 60.600 60.000 0.00 0.00 0.00 4.18
3761 4746 2.358247 ACCTTACCCGTTGCAGCG 60.358 61.111 16.72 16.72 0.00 5.18
3782 4767 4.754667 GACGGCGTCCTTGTCCCC 62.755 72.222 28.72 0.73 0.00 4.81
3791 4776 1.227383 CCTTGTCCCCCATACTGCC 59.773 63.158 0.00 0.00 0.00 4.85
3830 4819 0.462047 GTCGTGCCGATCCCATTCTT 60.462 55.000 0.67 0.00 38.42 2.52
3836 4825 1.353103 CGATCCCATTCTTGCACGC 59.647 57.895 0.00 0.00 0.00 5.34
3838 4827 1.001020 ATCCCATTCTTGCACGCCA 60.001 52.632 0.00 0.00 0.00 5.69
3849 4838 4.624364 CACGCCACCTCCACAGCA 62.624 66.667 0.00 0.00 0.00 4.41
3880 4869 1.016130 AAGCGTCATCGGAAGTGCTG 61.016 55.000 4.17 0.00 37.56 4.41
3890 4879 1.034292 GGAAGTGCTGGATTCCTGCC 61.034 60.000 26.15 18.70 45.86 4.85
3897 4886 1.137675 GCTGGATTCCTGCCCATTTTC 59.862 52.381 20.66 0.00 41.62 2.29
3898 4887 1.406539 CTGGATTCCTGCCCATTTTCG 59.593 52.381 3.95 0.00 0.00 3.46
3915 4904 4.747218 GGGTGCCCGGAAACAATA 57.253 55.556 0.73 0.00 0.00 1.90
3916 4905 2.964343 GGGTGCCCGGAAACAATAA 58.036 52.632 0.73 0.00 0.00 1.40
3917 4906 0.815095 GGGTGCCCGGAAACAATAAG 59.185 55.000 0.73 0.00 0.00 1.73
3918 4907 0.815095 GGTGCCCGGAAACAATAAGG 59.185 55.000 0.73 0.00 0.00 2.69
3919 4908 1.541379 GTGCCCGGAAACAATAAGGT 58.459 50.000 0.73 0.00 0.00 3.50
3920 4909 1.201414 GTGCCCGGAAACAATAAGGTG 59.799 52.381 0.73 0.00 0.00 4.00
3921 4910 1.202952 TGCCCGGAAACAATAAGGTGT 60.203 47.619 0.73 0.00 0.00 4.16
3922 4911 1.201414 GCCCGGAAACAATAAGGTGTG 59.799 52.381 0.73 0.00 0.00 3.82
3923 4912 2.785562 CCCGGAAACAATAAGGTGTGA 58.214 47.619 0.73 0.00 0.00 3.58
3924 4913 2.747446 CCCGGAAACAATAAGGTGTGAG 59.253 50.000 0.73 0.00 0.00 3.51
3925 4914 2.747446 CCGGAAACAATAAGGTGTGAGG 59.253 50.000 0.00 0.00 0.00 3.86
3926 4915 3.558321 CCGGAAACAATAAGGTGTGAGGA 60.558 47.826 0.00 0.00 0.00 3.71
3927 4916 3.684788 CGGAAACAATAAGGTGTGAGGAG 59.315 47.826 0.00 0.00 0.00 3.69
3928 4917 4.010349 GGAAACAATAAGGTGTGAGGAGG 58.990 47.826 0.00 0.00 0.00 4.30
3929 4918 3.721087 AACAATAAGGTGTGAGGAGGG 57.279 47.619 0.00 0.00 0.00 4.30
3930 4919 1.916181 ACAATAAGGTGTGAGGAGGGG 59.084 52.381 0.00 0.00 0.00 4.79
3931 4920 1.212935 CAATAAGGTGTGAGGAGGGGG 59.787 57.143 0.00 0.00 0.00 5.40
3946 4935 2.896278 GGGGGATTTAGGCCAACAC 58.104 57.895 5.01 0.00 0.00 3.32
3947 4936 0.686441 GGGGGATTTAGGCCAACACC 60.686 60.000 5.01 1.01 0.00 4.16
3948 4937 0.040499 GGGGATTTAGGCCAACACCA 59.960 55.000 5.01 0.00 0.00 4.17
3949 4938 1.182667 GGGATTTAGGCCAACACCAC 58.817 55.000 5.01 0.00 0.00 4.16
3950 4939 1.182667 GGATTTAGGCCAACACCACC 58.817 55.000 5.01 0.00 0.00 4.61
3951 4940 0.808755 GATTTAGGCCAACACCACCG 59.191 55.000 5.01 0.00 0.00 4.94
3952 4941 0.111639 ATTTAGGCCAACACCACCGT 59.888 50.000 5.01 0.00 0.00 4.83
3953 4942 0.535553 TTTAGGCCAACACCACCGTC 60.536 55.000 5.01 0.00 0.00 4.79
3954 4943 2.400269 TTAGGCCAACACCACCGTCC 62.400 60.000 5.01 0.00 0.00 4.79
3956 4945 4.922026 GCCAACACCACCGTCCGT 62.922 66.667 0.00 0.00 0.00 4.69
3957 4946 2.203098 CCAACACCACCGTCCGTT 60.203 61.111 0.00 0.00 0.00 4.44
3958 4947 1.820481 CCAACACCACCGTCCGTTT 60.820 57.895 0.00 0.00 0.00 3.60
3959 4948 1.353804 CAACACCACCGTCCGTTTG 59.646 57.895 0.00 0.00 0.00 2.93
3960 4949 1.820481 AACACCACCGTCCGTTTGG 60.820 57.895 3.70 3.70 36.39 3.28
3961 4950 2.975799 CACCACCGTCCGTTTGGG 60.976 66.667 8.81 0.00 34.41 4.12
3962 4951 3.481999 ACCACCGTCCGTTTGGGT 61.482 61.111 8.81 0.00 37.00 4.51
3963 4952 2.667199 CCACCGTCCGTTTGGGTC 60.667 66.667 0.00 0.00 37.00 4.46
3964 4953 3.039588 CACCGTCCGTTTGGGTCG 61.040 66.667 0.00 0.00 45.31 4.79
3971 4960 4.157817 CGTTTGGGTCGACGGTAG 57.842 61.111 9.92 0.00 35.74 3.18
3972 4961 1.444895 CGTTTGGGTCGACGGTAGG 60.445 63.158 9.92 0.00 35.74 3.18
3973 4962 1.079612 GTTTGGGTCGACGGTAGGG 60.080 63.158 9.92 0.00 0.00 3.53
3974 4963 2.285024 TTTGGGTCGACGGTAGGGG 61.285 63.158 9.92 0.00 0.00 4.79
3998 4987 3.038352 CGTCCACGCAAATATTGTCAG 57.962 47.619 0.00 0.00 0.00 3.51
3999 4988 2.415168 CGTCCACGCAAATATTGTCAGT 59.585 45.455 0.00 0.00 0.00 3.41
4000 4989 3.724716 CGTCCACGCAAATATTGTCAGTG 60.725 47.826 0.00 0.00 34.75 3.66
4001 4990 2.161410 TCCACGCAAATATTGTCAGTGC 59.839 45.455 0.00 0.00 34.16 4.40
4004 4993 2.549633 GCAAATATTGTCAGTGCGCT 57.450 45.000 9.73 0.00 0.00 5.92
4005 4994 2.444351 GCAAATATTGTCAGTGCGCTC 58.556 47.619 9.73 4.74 0.00 5.03
4006 4995 2.159531 GCAAATATTGTCAGTGCGCTCA 60.160 45.455 9.73 0.00 0.00 4.26
4007 4996 3.670359 GCAAATATTGTCAGTGCGCTCAA 60.670 43.478 9.73 0.00 0.00 3.02
4008 4997 4.665212 CAAATATTGTCAGTGCGCTCAAT 58.335 39.130 15.87 15.87 35.24 2.57
4009 4998 4.542662 AATATTGTCAGTGCGCTCAATC 57.457 40.909 15.24 0.00 33.48 2.67
4010 4999 0.723414 ATTGTCAGTGCGCTCAATCG 59.277 50.000 9.73 0.00 0.00 3.34
4011 5000 0.319469 TTGTCAGTGCGCTCAATCGA 60.319 50.000 9.73 0.00 0.00 3.59
4012 5001 0.108662 TGTCAGTGCGCTCAATCGAT 60.109 50.000 9.73 0.00 0.00 3.59
4013 5002 0.574454 GTCAGTGCGCTCAATCGATC 59.426 55.000 9.73 0.00 0.00 3.69
4014 5003 0.528466 TCAGTGCGCTCAATCGATCC 60.528 55.000 9.73 0.00 0.00 3.36
4015 5004 0.807275 CAGTGCGCTCAATCGATCCA 60.807 55.000 9.73 0.00 0.00 3.41
4016 5005 0.105593 AGTGCGCTCAATCGATCCAT 59.894 50.000 9.73 0.00 0.00 3.41
4017 5006 0.510359 GTGCGCTCAATCGATCCATC 59.490 55.000 9.73 0.00 0.00 3.51
4018 5007 0.601046 TGCGCTCAATCGATCCATCC 60.601 55.000 9.73 0.00 0.00 3.51
4019 5008 0.601046 GCGCTCAATCGATCCATCCA 60.601 55.000 0.00 0.00 0.00 3.41
4020 5009 1.943046 GCGCTCAATCGATCCATCCAT 60.943 52.381 0.00 0.00 0.00 3.41
4021 5010 2.420642 CGCTCAATCGATCCATCCATT 58.579 47.619 0.00 0.00 0.00 3.16
4022 5011 2.810274 CGCTCAATCGATCCATCCATTT 59.190 45.455 0.00 0.00 0.00 2.32
4023 5012 3.364664 CGCTCAATCGATCCATCCATTTG 60.365 47.826 0.00 0.00 0.00 2.32
4024 5013 3.817084 GCTCAATCGATCCATCCATTTGA 59.183 43.478 0.00 0.00 0.00 2.69
4025 5014 4.458295 GCTCAATCGATCCATCCATTTGAT 59.542 41.667 0.00 0.00 0.00 2.57
4026 5015 5.048224 GCTCAATCGATCCATCCATTTGATT 60.048 40.000 0.00 0.00 0.00 2.57
4027 5016 6.516194 GCTCAATCGATCCATCCATTTGATTT 60.516 38.462 0.00 0.00 0.00 2.17
4028 5017 6.741109 TCAATCGATCCATCCATTTGATTTG 58.259 36.000 0.00 0.00 0.00 2.32
4029 5018 6.321945 TCAATCGATCCATCCATTTGATTTGT 59.678 34.615 0.00 0.00 0.00 2.83
4030 5019 5.756195 TCGATCCATCCATTTGATTTGTC 57.244 39.130 0.00 0.00 0.00 3.18
4031 5020 5.439721 TCGATCCATCCATTTGATTTGTCT 58.560 37.500 0.00 0.00 0.00 3.41
4032 5021 6.591001 TCGATCCATCCATTTGATTTGTCTA 58.409 36.000 0.00 0.00 0.00 2.59
4033 5022 6.707608 TCGATCCATCCATTTGATTTGTCTAG 59.292 38.462 0.00 0.00 0.00 2.43
4034 5023 6.707608 CGATCCATCCATTTGATTTGTCTAGA 59.292 38.462 0.00 0.00 0.00 2.43
4035 5024 7.307632 CGATCCATCCATTTGATTTGTCTAGAC 60.308 40.741 16.32 16.32 0.00 2.59
4036 5025 5.817296 TCCATCCATTTGATTTGTCTAGACG 59.183 40.000 17.85 0.38 0.00 4.18
4037 5026 5.008019 CCATCCATTTGATTTGTCTAGACGG 59.992 44.000 17.85 9.47 0.00 4.79
4038 5027 5.160607 TCCATTTGATTTGTCTAGACGGT 57.839 39.130 17.85 6.31 0.00 4.83
4039 5028 5.556915 TCCATTTGATTTGTCTAGACGGTT 58.443 37.500 17.85 4.78 0.00 4.44
4040 5029 6.001460 TCCATTTGATTTGTCTAGACGGTTT 58.999 36.000 17.85 2.98 0.00 3.27
4041 5030 6.488683 TCCATTTGATTTGTCTAGACGGTTTT 59.511 34.615 17.85 1.21 0.00 2.43
4042 5031 7.013846 TCCATTTGATTTGTCTAGACGGTTTTT 59.986 33.333 17.85 0.00 0.00 1.94
4043 5032 7.114811 CCATTTGATTTGTCTAGACGGTTTTTG 59.885 37.037 17.85 8.49 0.00 2.44
4044 5033 5.682943 TGATTTGTCTAGACGGTTTTTGG 57.317 39.130 17.85 0.00 0.00 3.28
4045 5034 5.127491 TGATTTGTCTAGACGGTTTTTGGT 58.873 37.500 17.85 0.00 0.00 3.67
4046 5035 5.237779 TGATTTGTCTAGACGGTTTTTGGTC 59.762 40.000 17.85 6.44 0.00 4.02
4047 5036 3.823281 TGTCTAGACGGTTTTTGGTCA 57.177 42.857 17.85 0.00 35.63 4.02
4048 5037 4.139859 TGTCTAGACGGTTTTTGGTCAA 57.860 40.909 17.85 0.00 35.63 3.18
4049 5038 4.710324 TGTCTAGACGGTTTTTGGTCAAT 58.290 39.130 17.85 0.00 35.63 2.57
4050 5039 5.127491 TGTCTAGACGGTTTTTGGTCAATT 58.873 37.500 17.85 0.00 35.63 2.32
4051 5040 5.591067 TGTCTAGACGGTTTTTGGTCAATTT 59.409 36.000 17.85 0.00 35.63 1.82
4052 5041 6.095720 TGTCTAGACGGTTTTTGGTCAATTTT 59.904 34.615 17.85 0.00 35.63 1.82
4053 5042 6.976349 GTCTAGACGGTTTTTGGTCAATTTTT 59.024 34.615 7.22 0.00 35.63 1.94
4054 5043 8.130469 GTCTAGACGGTTTTTGGTCAATTTTTA 58.870 33.333 7.22 0.00 35.63 1.52
4055 5044 8.130469 TCTAGACGGTTTTTGGTCAATTTTTAC 58.870 33.333 0.00 0.00 35.63 2.01
4056 5045 6.631962 AGACGGTTTTTGGTCAATTTTTACA 58.368 32.000 0.00 0.00 35.63 2.41
4057 5046 7.097834 AGACGGTTTTTGGTCAATTTTTACAA 58.902 30.769 0.00 0.00 35.63 2.41
4058 5047 7.766738 AGACGGTTTTTGGTCAATTTTTACAAT 59.233 29.630 0.00 0.00 35.63 2.71
4059 5048 8.270080 ACGGTTTTTGGTCAATTTTTACAATT 57.730 26.923 0.00 0.00 0.00 2.32
4060 5049 8.731605 ACGGTTTTTGGTCAATTTTTACAATTT 58.268 25.926 0.00 0.00 0.00 1.82
4074 5063 9.979578 ATTTTTACAATTTAGACATTCAGTGCA 57.020 25.926 0.00 0.00 0.00 4.57
4075 5064 9.979578 TTTTTACAATTTAGACATTCAGTGCAT 57.020 25.926 0.00 0.00 0.00 3.96
4086 5075 8.969260 AGACATTCAGTGCATATAAATCTGAA 57.031 30.769 13.90 13.90 45.03 3.02
4087 5076 9.399797 AGACATTCAGTGCATATAAATCTGAAA 57.600 29.630 15.09 2.98 44.44 2.69
4121 5110 8.970691 ATTGCACATAGTTCTTAAATCACAAC 57.029 30.769 0.00 0.00 0.00 3.32
4122 5111 7.503521 TGCACATAGTTCTTAAATCACAACA 57.496 32.000 0.00 0.00 0.00 3.33
4123 5112 7.935520 TGCACATAGTTCTTAAATCACAACAA 58.064 30.769 0.00 0.00 0.00 2.83
4124 5113 8.409371 TGCACATAGTTCTTAAATCACAACAAA 58.591 29.630 0.00 0.00 0.00 2.83
4125 5114 9.410556 GCACATAGTTCTTAAATCACAACAAAT 57.589 29.630 0.00 0.00 0.00 2.32
4139 5128 9.793252 AATCACAACAAATAAACATCTCATAGC 57.207 29.630 0.00 0.00 0.00 2.97
4140 5129 8.565896 TCACAACAAATAAACATCTCATAGCT 57.434 30.769 0.00 0.00 0.00 3.32
4141 5130 9.013229 TCACAACAAATAAACATCTCATAGCTT 57.987 29.630 0.00 0.00 0.00 3.74
4147 5136 9.722056 CAAATAAACATCTCATAGCTTACAACC 57.278 33.333 0.00 0.00 0.00 3.77
4148 5137 9.461312 AAATAAACATCTCATAGCTTACAACCA 57.539 29.630 0.00 0.00 0.00 3.67
4149 5138 9.461312 AATAAACATCTCATAGCTTACAACCAA 57.539 29.630 0.00 0.00 0.00 3.67
4150 5139 7.759489 AAACATCTCATAGCTTACAACCAAA 57.241 32.000 0.00 0.00 0.00 3.28
4151 5140 7.944729 AACATCTCATAGCTTACAACCAAAT 57.055 32.000 0.00 0.00 0.00 2.32
4152 5141 7.325660 ACATCTCATAGCTTACAACCAAATG 57.674 36.000 0.00 0.00 0.00 2.32
4153 5142 7.112122 ACATCTCATAGCTTACAACCAAATGA 58.888 34.615 0.00 0.00 0.00 2.57
4154 5143 7.611467 ACATCTCATAGCTTACAACCAAATGAA 59.389 33.333 0.00 0.00 0.00 2.57
4155 5144 8.627403 CATCTCATAGCTTACAACCAAATGAAT 58.373 33.333 0.00 0.00 0.00 2.57
4156 5145 8.579850 TCTCATAGCTTACAACCAAATGAATT 57.420 30.769 0.00 0.00 0.00 2.17
4157 5146 9.023962 TCTCATAGCTTACAACCAAATGAATTT 57.976 29.630 0.00 0.00 0.00 1.82
4171 5160 9.719355 ACCAAATGAATTTAAAATTGTACTCCC 57.281 29.630 0.00 0.00 0.00 4.30
4172 5161 9.942850 CCAAATGAATTTAAAATTGTACTCCCT 57.057 29.630 0.00 0.00 0.00 4.20
4175 5164 9.855021 AATGAATTTAAAATTGTACTCCCTTCG 57.145 29.630 0.00 0.00 0.00 3.79
4176 5165 8.398878 TGAATTTAAAATTGTACTCCCTTCGT 57.601 30.769 0.00 0.00 0.00 3.85
4177 5166 8.508875 TGAATTTAAAATTGTACTCCCTTCGTC 58.491 33.333 0.00 0.00 0.00 4.20
4178 5167 6.806388 TTTAAAATTGTACTCCCTTCGTCC 57.194 37.500 0.00 0.00 0.00 4.79
4179 5168 3.345508 AAATTGTACTCCCTTCGTCCC 57.654 47.619 0.00 0.00 0.00 4.46
4180 5169 1.946984 ATTGTACTCCCTTCGTCCCA 58.053 50.000 0.00 0.00 0.00 4.37
4181 5170 1.946984 TTGTACTCCCTTCGTCCCAT 58.053 50.000 0.00 0.00 0.00 4.00
4182 5171 2.832643 TGTACTCCCTTCGTCCCATA 57.167 50.000 0.00 0.00 0.00 2.74
4183 5172 3.104519 TGTACTCCCTTCGTCCCATAA 57.895 47.619 0.00 0.00 0.00 1.90
4184 5173 3.649843 TGTACTCCCTTCGTCCCATAAT 58.350 45.455 0.00 0.00 0.00 1.28
4185 5174 4.806892 TGTACTCCCTTCGTCCCATAATA 58.193 43.478 0.00 0.00 0.00 0.98
4186 5175 5.399991 TGTACTCCCTTCGTCCCATAATAT 58.600 41.667 0.00 0.00 0.00 1.28
4187 5176 6.554784 TGTACTCCCTTCGTCCCATAATATA 58.445 40.000 0.00 0.00 0.00 0.86
4188 5177 7.011994 TGTACTCCCTTCGTCCCATAATATAA 58.988 38.462 0.00 0.00 0.00 0.98
4189 5178 7.510001 TGTACTCCCTTCGTCCCATAATATAAA 59.490 37.037 0.00 0.00 0.00 1.40
4190 5179 7.383156 ACTCCCTTCGTCCCATAATATAAAA 57.617 36.000 0.00 0.00 0.00 1.52
4191 5180 7.450903 ACTCCCTTCGTCCCATAATATAAAAG 58.549 38.462 0.00 0.00 0.00 2.27
4192 5181 7.072076 ACTCCCTTCGTCCCATAATATAAAAGT 59.928 37.037 0.00 0.00 0.00 2.66
4193 5182 8.495160 TCCCTTCGTCCCATAATATAAAAGTA 57.505 34.615 0.00 0.00 0.00 2.24
4194 5183 9.108111 TCCCTTCGTCCCATAATATAAAAGTAT 57.892 33.333 0.00 0.00 0.00 2.12
4195 5184 9.734984 CCCTTCGTCCCATAATATAAAAGTATT 57.265 33.333 0.00 0.00 0.00 1.89
4238 5227 9.574516 AGAAAGAAAATACATGTACTGGTTTCT 57.425 29.630 19.81 19.81 36.73 2.52
4252 5241 3.764237 GGTTTCTTACCTGAGTCCACA 57.236 47.619 0.00 0.00 44.10 4.17
4253 5242 4.287766 GGTTTCTTACCTGAGTCCACAT 57.712 45.455 0.00 0.00 44.10 3.21
4254 5243 5.416271 GGTTTCTTACCTGAGTCCACATA 57.584 43.478 0.00 0.00 44.10 2.29
4255 5244 5.990668 GGTTTCTTACCTGAGTCCACATAT 58.009 41.667 0.00 0.00 44.10 1.78
4256 5245 5.817816 GGTTTCTTACCTGAGTCCACATATG 59.182 44.000 0.00 0.00 44.10 1.78
4257 5246 6.407202 GTTTCTTACCTGAGTCCACATATGT 58.593 40.000 1.41 1.41 0.00 2.29
4258 5247 6.620877 TTCTTACCTGAGTCCACATATGTT 57.379 37.500 5.37 0.00 0.00 2.71
4259 5248 6.620877 TCTTACCTGAGTCCACATATGTTT 57.379 37.500 5.37 0.00 0.00 2.83
4260 5249 7.727578 TCTTACCTGAGTCCACATATGTTTA 57.272 36.000 5.37 0.00 0.00 2.01
4261 5250 8.141298 TCTTACCTGAGTCCACATATGTTTAA 57.859 34.615 5.37 0.00 0.00 1.52
4262 5251 8.768397 TCTTACCTGAGTCCACATATGTTTAAT 58.232 33.333 5.37 0.00 0.00 1.40
4263 5252 8.958119 TTACCTGAGTCCACATATGTTTAATC 57.042 34.615 5.37 6.66 0.00 1.75
4264 5253 6.957631 ACCTGAGTCCACATATGTTTAATCA 58.042 36.000 5.37 10.79 0.00 2.57
4265 5254 7.402054 ACCTGAGTCCACATATGTTTAATCAA 58.598 34.615 5.37 0.00 0.00 2.57
4266 5255 7.888021 ACCTGAGTCCACATATGTTTAATCAAA 59.112 33.333 5.37 0.00 0.00 2.69
4290 5279 9.768662 AAATCATTTTAAAGCTGAATGTGAGTT 57.231 25.926 6.63 7.45 33.60 3.01
4293 5282 7.862372 TCATTTTAAAGCTGAATGTGAGTTGTC 59.138 33.333 10.35 0.00 33.60 3.18
4296 5285 2.775890 AGCTGAATGTGAGTTGTCCAG 58.224 47.619 0.00 0.00 0.00 3.86
4302 5291 3.661745 GTGAGTTGTCCAGTCACGT 57.338 52.632 0.00 0.00 44.30 4.49
4315 5304 5.637810 GTCCAGTCACGTATTTCTTGATGAA 59.362 40.000 0.00 0.00 0.00 2.57
4364 5362 1.508088 GCTCCACATTTTCGCCCTG 59.492 57.895 0.00 0.00 0.00 4.45
4396 5394 2.618709 CCTTGGTCAAAGAGGTTGTCAC 59.381 50.000 0.00 0.00 38.24 3.67
4622 5621 4.801330 TGTCTTCACAATAGTCGACCAT 57.199 40.909 13.01 0.00 0.00 3.55
4641 5640 7.565029 TCGACCATTGAGGATATATACCATCAT 59.435 37.037 0.00 0.00 41.22 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 6.796785 AATTTGACCCTTATTTAGCAGCAT 57.203 33.333 0.00 0.00 0.00 3.79
241 244 1.192428 GGTTAAGGCGAAGGAGAGGA 58.808 55.000 0.00 0.00 0.00 3.71
310 313 5.066505 CGTCGACCATGGATGATGATCTATA 59.933 44.000 21.47 0.00 33.31 1.31
328 331 4.580528 TGTTTTAAGTGCTTTTCGTCGAC 58.419 39.130 5.18 5.18 0.00 4.20
334 337 6.362632 CACGCTATGTTTTAAGTGCTTTTC 57.637 37.500 0.00 0.00 0.00 2.29
367 370 3.860930 TTTGAACGCTCAGGGCCCC 62.861 63.158 21.43 0.78 37.74 5.80
651 655 2.742053 CAATTGACTGTGGACGGGTAAG 59.258 50.000 0.00 0.00 0.00 2.34
701 708 6.491403 AGAAAATATTGTGGAGCAAGTGAAGT 59.509 34.615 0.00 0.00 40.86 3.01
735 743 9.274065 GAAAAATACTCGGTATTAACTTTGCAG 57.726 33.333 8.95 0.00 37.69 4.41
815 859 4.413760 TCTCGAGAGAAGTCCCCTAAAAA 58.586 43.478 12.08 0.00 41.32 1.94
816 860 4.043608 TCTCGAGAGAAGTCCCCTAAAA 57.956 45.455 12.08 0.00 41.32 1.52
817 861 3.733883 TCTCGAGAGAAGTCCCCTAAA 57.266 47.619 12.08 0.00 41.32 1.85
818 862 3.733883 TTCTCGAGAGAAGTCCCCTAA 57.266 47.619 15.94 0.00 42.06 2.69
828 872 8.307483 ACAAAGAGTTTCAATATTCTCGAGAGA 58.693 33.333 15.94 8.39 39.12 3.10
829 873 8.472683 ACAAAGAGTTTCAATATTCTCGAGAG 57.527 34.615 15.94 3.64 32.90 3.20
830 874 8.712363 CAACAAAGAGTTTCAATATTCTCGAGA 58.288 33.333 12.08 12.08 38.74 4.04
1224 1306 3.069980 GATGTCGCGGAGGAGCACT 62.070 63.158 6.13 0.00 36.85 4.40
2011 2099 1.079266 CCAGCTCTGTCTGTCCTGC 60.079 63.158 0.00 0.00 32.32 4.85
2092 2283 3.277715 TCAATTGACACAGCACAGTTCA 58.722 40.909 3.38 0.00 0.00 3.18
2093 2284 3.969117 TCAATTGACACAGCACAGTTC 57.031 42.857 3.38 0.00 0.00 3.01
2250 2448 0.673985 GAAAGCCGGGCACTTTCTTT 59.326 50.000 23.09 11.58 46.14 2.52
2454 2911 1.825090 TGAGCAGGCCAACAGTTATG 58.175 50.000 5.01 0.00 0.00 1.90
2488 2945 9.899661 ACAAGAAAATGGTAGCATACATAGTTA 57.100 29.630 8.04 0.00 45.43 2.24
2935 3403 3.811497 GGACGGCTTGGTGGTATTATAAC 59.189 47.826 0.00 0.00 0.00 1.89
2936 3404 3.181452 GGGACGGCTTGGTGGTATTATAA 60.181 47.826 0.00 0.00 0.00 0.98
2937 3405 2.369532 GGGACGGCTTGGTGGTATTATA 59.630 50.000 0.00 0.00 0.00 0.98
2938 3406 1.142262 GGGACGGCTTGGTGGTATTAT 59.858 52.381 0.00 0.00 0.00 1.28
3022 3505 6.065374 ACAACCTAATCATGTAACACCACAA 58.935 36.000 0.00 0.00 30.84 3.33
3133 3628 5.927115 ACTGCAAGGTAAAACGAAAAACAAA 59.073 32.000 0.00 0.00 39.30 2.83
3250 3761 4.233632 TGCATACCCAGTTGATTCATGA 57.766 40.909 0.00 0.00 0.00 3.07
3263 3774 1.878953 CCGACCACTAATGCATACCC 58.121 55.000 0.00 0.00 0.00 3.69
3289 3801 0.179192 GCGAGCATTTGCAACGATGA 60.179 50.000 20.08 0.00 45.16 2.92
3293 3805 2.430942 GCAGCGAGCATTTGCAACG 61.431 57.895 0.00 14.42 45.16 4.10
3318 3842 2.040412 CCCTCAAAGGCACTCCTAACTT 59.960 50.000 0.00 0.00 43.40 2.66
3332 3856 1.450669 GATAACGCCCGCCCTCAAA 60.451 57.895 0.00 0.00 0.00 2.69
3383 3914 4.877378 ACTCATTTTTCACCATGTGCAT 57.123 36.364 0.00 0.00 32.98 3.96
3387 3918 4.586001 AGCTGAACTCATTTTTCACCATGT 59.414 37.500 0.00 0.00 0.00 3.21
3392 3923 3.732721 GCACAGCTGAACTCATTTTTCAC 59.267 43.478 23.35 0.00 0.00 3.18
3426 3957 0.323360 TAAGCAACACCTCCATGCCC 60.323 55.000 0.00 0.00 40.93 5.36
3431 3962 3.561143 ACATTTGTAAGCAACACCTCCA 58.439 40.909 0.00 0.00 38.00 3.86
3433 3964 8.082242 AGAAAATACATTTGTAAGCAACACCTC 58.918 33.333 0.00 0.00 38.00 3.85
3481 4014 1.619332 TGGCAGCAGCAATCAATTTGA 59.381 42.857 2.65 0.75 44.61 2.69
3648 4213 3.393089 AGCATCCGATGTACAGAATCC 57.607 47.619 10.10 0.00 0.00 3.01
3654 4219 7.624360 AAAATTTAGAAGCATCCGATGTACA 57.376 32.000 10.10 0.00 0.00 2.90
3822 4811 2.568090 GTGGCGTGCAAGAATGGG 59.432 61.111 2.99 0.00 0.00 4.00
3830 4819 4.624364 CTGTGGAGGTGGCGTGCA 62.624 66.667 0.00 0.00 0.00 4.57
3836 4825 0.460284 GACGTATGCTGTGGAGGTGG 60.460 60.000 0.00 0.00 0.00 4.61
3838 4827 0.614979 AGGACGTATGCTGTGGAGGT 60.615 55.000 0.00 0.00 0.00 3.85
3849 4838 0.892755 TGACGCTTGGAAGGACGTAT 59.107 50.000 0.00 0.00 39.16 3.06
3880 4869 0.746659 CCGAAAATGGGCAGGAATCC 59.253 55.000 0.00 0.00 0.00 3.01
3904 4893 2.747446 CCTCACACCTTATTGTTTCCGG 59.253 50.000 0.00 0.00 0.00 5.14
3905 4894 3.670625 TCCTCACACCTTATTGTTTCCG 58.329 45.455 0.00 0.00 0.00 4.30
3906 4895 4.010349 CCTCCTCACACCTTATTGTTTCC 58.990 47.826 0.00 0.00 0.00 3.13
3907 4896 4.010349 CCCTCCTCACACCTTATTGTTTC 58.990 47.826 0.00 0.00 0.00 2.78
3908 4897 3.245264 CCCCTCCTCACACCTTATTGTTT 60.245 47.826 0.00 0.00 0.00 2.83
3909 4898 2.308866 CCCCTCCTCACACCTTATTGTT 59.691 50.000 0.00 0.00 0.00 2.83
3910 4899 1.916181 CCCCTCCTCACACCTTATTGT 59.084 52.381 0.00 0.00 0.00 2.71
3911 4900 1.212935 CCCCCTCCTCACACCTTATTG 59.787 57.143 0.00 0.00 0.00 1.90
3912 4901 1.596496 CCCCCTCCTCACACCTTATT 58.404 55.000 0.00 0.00 0.00 1.40
3913 4902 3.341833 CCCCCTCCTCACACCTTAT 57.658 57.895 0.00 0.00 0.00 1.73
3914 4903 4.910613 CCCCCTCCTCACACCTTA 57.089 61.111 0.00 0.00 0.00 2.69
3928 4917 0.686441 GGTGTTGGCCTAAATCCCCC 60.686 60.000 3.32 0.00 0.00 5.40
3929 4918 0.040499 TGGTGTTGGCCTAAATCCCC 59.960 55.000 3.32 0.00 0.00 4.81
3930 4919 1.182667 GTGGTGTTGGCCTAAATCCC 58.817 55.000 3.32 0.00 0.00 3.85
3931 4920 1.182667 GGTGGTGTTGGCCTAAATCC 58.817 55.000 3.32 0.27 0.00 3.01
3932 4921 0.808755 CGGTGGTGTTGGCCTAAATC 59.191 55.000 3.32 0.00 0.00 2.17
3933 4922 0.111639 ACGGTGGTGTTGGCCTAAAT 59.888 50.000 3.32 0.00 0.00 1.40
3934 4923 0.535553 GACGGTGGTGTTGGCCTAAA 60.536 55.000 3.32 0.00 0.00 1.85
3935 4924 1.071814 GACGGTGGTGTTGGCCTAA 59.928 57.895 3.32 0.00 0.00 2.69
3936 4925 2.745037 GACGGTGGTGTTGGCCTA 59.255 61.111 3.32 0.00 0.00 3.93
3937 4926 4.265056 GGACGGTGGTGTTGGCCT 62.265 66.667 3.32 0.00 0.00 5.19
3939 4928 4.922026 ACGGACGGTGGTGTTGGC 62.922 66.667 0.00 0.00 0.00 4.52
3940 4929 1.820481 AAACGGACGGTGGTGTTGG 60.820 57.895 0.00 0.00 0.00 3.77
3941 4930 1.353804 CAAACGGACGGTGGTGTTG 59.646 57.895 0.00 0.00 0.00 3.33
3942 4931 1.820481 CCAAACGGACGGTGGTGTT 60.820 57.895 8.11 0.00 0.00 3.32
3943 4932 2.203098 CCAAACGGACGGTGGTGT 60.203 61.111 8.11 0.00 0.00 4.16
3944 4933 2.975799 CCCAAACGGACGGTGGTG 60.976 66.667 13.34 0.00 0.00 4.17
3945 4934 3.465258 GACCCAAACGGACGGTGGT 62.465 63.158 13.34 4.09 34.64 4.16
3946 4935 2.667199 GACCCAAACGGACGGTGG 60.667 66.667 9.05 9.05 34.64 4.61
3947 4936 3.039588 CGACCCAAACGGACGGTG 61.040 66.667 0.00 0.00 44.72 4.94
3954 4943 1.444895 CCTACCGTCGACCCAAACG 60.445 63.158 10.58 0.00 38.58 3.60
3955 4944 1.079612 CCCTACCGTCGACCCAAAC 60.080 63.158 10.58 0.00 0.00 2.93
3956 4945 2.285024 CCCCTACCGTCGACCCAAA 61.285 63.158 10.58 0.00 0.00 3.28
3957 4946 2.681064 CCCCTACCGTCGACCCAA 60.681 66.667 10.58 0.00 0.00 4.12
3978 4967 2.415168 ACTGACAATATTTGCGTGGACG 59.585 45.455 0.00 0.00 43.27 4.79
3979 4968 3.747193 CACTGACAATATTTGCGTGGAC 58.253 45.455 0.00 0.00 0.00 4.02
3980 4969 2.161410 GCACTGACAATATTTGCGTGGA 59.839 45.455 0.00 0.00 0.00 4.02
3981 4970 2.518949 GCACTGACAATATTTGCGTGG 58.481 47.619 0.00 0.00 0.00 4.94
3985 4974 2.159531 TGAGCGCACTGACAATATTTGC 60.160 45.455 11.47 0.00 0.00 3.68
3986 4975 3.745332 TGAGCGCACTGACAATATTTG 57.255 42.857 11.47 0.00 0.00 2.32
3987 4976 4.494690 CGATTGAGCGCACTGACAATATTT 60.495 41.667 11.47 0.00 33.92 1.40
3988 4977 3.001634 CGATTGAGCGCACTGACAATATT 59.998 43.478 11.47 0.00 33.92 1.28
3989 4978 2.541346 CGATTGAGCGCACTGACAATAT 59.459 45.455 11.47 0.00 33.92 1.28
3990 4979 1.926510 CGATTGAGCGCACTGACAATA 59.073 47.619 11.47 0.00 33.92 1.90
3991 4980 0.723414 CGATTGAGCGCACTGACAAT 59.277 50.000 11.47 12.71 35.99 2.71
3992 4981 0.319469 TCGATTGAGCGCACTGACAA 60.319 50.000 11.47 8.25 0.00 3.18
3993 4982 0.108662 ATCGATTGAGCGCACTGACA 60.109 50.000 11.47 0.00 0.00 3.58
3994 4983 0.574454 GATCGATTGAGCGCACTGAC 59.426 55.000 11.47 0.00 0.00 3.51
3995 4984 0.528466 GGATCGATTGAGCGCACTGA 60.528 55.000 11.47 0.92 0.00 3.41
3996 4985 0.807275 TGGATCGATTGAGCGCACTG 60.807 55.000 11.47 0.00 0.00 3.66
3997 4986 0.105593 ATGGATCGATTGAGCGCACT 59.894 50.000 11.47 0.00 0.00 4.40
3998 4987 0.510359 GATGGATCGATTGAGCGCAC 59.490 55.000 11.47 3.13 0.00 5.34
3999 4988 0.601046 GGATGGATCGATTGAGCGCA 60.601 55.000 11.47 0.00 0.00 6.09
4000 4989 0.601046 TGGATGGATCGATTGAGCGC 60.601 55.000 0.00 0.00 0.00 5.92
4001 4990 2.090400 ATGGATGGATCGATTGAGCG 57.910 50.000 0.00 0.00 0.00 5.03
4002 4991 3.817084 TCAAATGGATGGATCGATTGAGC 59.183 43.478 0.00 0.00 35.76 4.26
4003 4992 6.570672 AATCAAATGGATGGATCGATTGAG 57.429 37.500 0.00 0.00 35.76 3.02
4004 4993 6.321945 ACAAATCAAATGGATGGATCGATTGA 59.678 34.615 0.00 0.00 35.76 2.57
4005 4994 6.509656 ACAAATCAAATGGATGGATCGATTG 58.490 36.000 0.00 0.00 35.76 2.67
4006 4995 6.548622 AGACAAATCAAATGGATGGATCGATT 59.451 34.615 0.00 0.00 36.90 3.34
4007 4996 6.066690 AGACAAATCAAATGGATGGATCGAT 58.933 36.000 0.00 0.00 36.02 3.59
4008 4997 5.439721 AGACAAATCAAATGGATGGATCGA 58.560 37.500 0.00 0.00 36.02 3.59
4009 4998 5.762825 AGACAAATCAAATGGATGGATCG 57.237 39.130 0.00 0.00 36.02 3.69
4010 4999 7.307632 CGTCTAGACAAATCAAATGGATGGATC 60.308 40.741 22.37 0.00 36.02 3.36
4011 5000 6.484643 CGTCTAGACAAATCAAATGGATGGAT 59.515 38.462 22.37 0.00 36.02 3.41
4012 5001 5.817296 CGTCTAGACAAATCAAATGGATGGA 59.183 40.000 22.37 0.00 36.02 3.41
4013 5002 5.008019 CCGTCTAGACAAATCAAATGGATGG 59.992 44.000 22.37 6.50 36.02 3.51
4014 5003 5.586243 ACCGTCTAGACAAATCAAATGGATG 59.414 40.000 22.37 1.13 36.02 3.51
4015 5004 5.745227 ACCGTCTAGACAAATCAAATGGAT 58.255 37.500 22.37 1.50 38.05 3.41
4016 5005 5.160607 ACCGTCTAGACAAATCAAATGGA 57.839 39.130 22.37 0.00 0.00 3.41
4017 5006 5.880054 AACCGTCTAGACAAATCAAATGG 57.120 39.130 22.37 13.63 0.00 3.16
4018 5007 7.114811 CCAAAAACCGTCTAGACAAATCAAATG 59.885 37.037 22.37 10.60 0.00 2.32
4019 5008 7.145323 CCAAAAACCGTCTAGACAAATCAAAT 58.855 34.615 22.37 0.00 0.00 2.32
4020 5009 6.095720 ACCAAAAACCGTCTAGACAAATCAAA 59.904 34.615 22.37 0.00 0.00 2.69
4021 5010 5.591067 ACCAAAAACCGTCTAGACAAATCAA 59.409 36.000 22.37 0.00 0.00 2.57
4022 5011 5.127491 ACCAAAAACCGTCTAGACAAATCA 58.873 37.500 22.37 0.00 0.00 2.57
4023 5012 5.237779 TGACCAAAAACCGTCTAGACAAATC 59.762 40.000 22.37 6.97 0.00 2.17
4024 5013 5.127491 TGACCAAAAACCGTCTAGACAAAT 58.873 37.500 22.37 4.28 0.00 2.32
4025 5014 4.515361 TGACCAAAAACCGTCTAGACAAA 58.485 39.130 22.37 0.00 0.00 2.83
4026 5015 4.139859 TGACCAAAAACCGTCTAGACAA 57.860 40.909 22.37 0.00 0.00 3.18
4027 5016 3.823281 TGACCAAAAACCGTCTAGACA 57.177 42.857 22.37 0.00 0.00 3.41
4028 5017 5.684550 AATTGACCAAAAACCGTCTAGAC 57.315 39.130 13.18 13.18 0.00 2.59
4029 5018 6.702716 AAAATTGACCAAAAACCGTCTAGA 57.297 33.333 0.00 0.00 0.00 2.43
4030 5019 7.916450 TGTAAAAATTGACCAAAAACCGTCTAG 59.084 33.333 0.00 0.00 0.00 2.43
4031 5020 7.769220 TGTAAAAATTGACCAAAAACCGTCTA 58.231 30.769 0.00 0.00 0.00 2.59
4032 5021 6.631962 TGTAAAAATTGACCAAAAACCGTCT 58.368 32.000 0.00 0.00 0.00 4.18
4033 5022 6.889019 TGTAAAAATTGACCAAAAACCGTC 57.111 33.333 0.00 0.00 0.00 4.79
4034 5023 7.851387 ATTGTAAAAATTGACCAAAAACCGT 57.149 28.000 0.00 0.00 0.00 4.83
4048 5037 9.979578 TGCACTGAATGTCTAAATTGTAAAAAT 57.020 25.926 0.00 0.00 0.00 1.82
4049 5038 9.979578 ATGCACTGAATGTCTAAATTGTAAAAA 57.020 25.926 0.00 0.00 0.00 1.94
4061 5050 8.969260 TTCAGATTTATATGCACTGAATGTCT 57.031 30.769 9.00 0.00 40.86 3.41
4096 5085 8.575589 TGTTGTGATTTAAGAACTATGTGCAAT 58.424 29.630 0.00 0.00 0.00 3.56
4097 5086 7.935520 TGTTGTGATTTAAGAACTATGTGCAA 58.064 30.769 0.00 0.00 0.00 4.08
4098 5087 7.503521 TGTTGTGATTTAAGAACTATGTGCA 57.496 32.000 0.00 0.00 0.00 4.57
4099 5088 8.795786 TTTGTTGTGATTTAAGAACTATGTGC 57.204 30.769 0.00 0.00 0.00 4.57
4113 5102 9.793252 GCTATGAGATGTTTATTTGTTGTGATT 57.207 29.630 0.00 0.00 0.00 2.57
4114 5103 9.182214 AGCTATGAGATGTTTATTTGTTGTGAT 57.818 29.630 0.00 0.00 0.00 3.06
4115 5104 8.565896 AGCTATGAGATGTTTATTTGTTGTGA 57.434 30.769 0.00 0.00 0.00 3.58
4121 5110 9.722056 GGTTGTAAGCTATGAGATGTTTATTTG 57.278 33.333 0.00 0.00 0.00 2.32
4122 5111 9.461312 TGGTTGTAAGCTATGAGATGTTTATTT 57.539 29.630 0.00 0.00 0.00 1.40
4123 5112 9.461312 TTGGTTGTAAGCTATGAGATGTTTATT 57.539 29.630 0.00 0.00 0.00 1.40
4124 5113 9.461312 TTTGGTTGTAAGCTATGAGATGTTTAT 57.539 29.630 0.00 0.00 0.00 1.40
4125 5114 8.856153 TTTGGTTGTAAGCTATGAGATGTTTA 57.144 30.769 0.00 0.00 0.00 2.01
4126 5115 7.759489 TTTGGTTGTAAGCTATGAGATGTTT 57.241 32.000 0.00 0.00 0.00 2.83
4127 5116 7.611467 TCATTTGGTTGTAAGCTATGAGATGTT 59.389 33.333 0.00 0.00 0.00 2.71
4128 5117 7.112122 TCATTTGGTTGTAAGCTATGAGATGT 58.888 34.615 0.00 0.00 0.00 3.06
4129 5118 7.558161 TCATTTGGTTGTAAGCTATGAGATG 57.442 36.000 0.00 0.00 0.00 2.90
4130 5119 8.757982 ATTCATTTGGTTGTAAGCTATGAGAT 57.242 30.769 0.00 6.72 33.35 2.75
4131 5120 8.579850 AATTCATTTGGTTGTAAGCTATGAGA 57.420 30.769 0.00 5.47 33.35 3.27
4145 5134 9.719355 GGGAGTACAATTTTAAATTCATTTGGT 57.281 29.630 0.00 0.00 0.00 3.67
4146 5135 9.942850 AGGGAGTACAATTTTAAATTCATTTGG 57.057 29.630 0.00 0.00 0.00 3.28
4149 5138 9.855021 CGAAGGGAGTACAATTTTAAATTCATT 57.145 29.630 0.00 0.00 0.00 2.57
4150 5139 9.020731 ACGAAGGGAGTACAATTTTAAATTCAT 57.979 29.630 0.00 0.00 0.00 2.57
4151 5140 8.398878 ACGAAGGGAGTACAATTTTAAATTCA 57.601 30.769 0.00 0.00 0.00 2.57
4152 5141 7.966753 GGACGAAGGGAGTACAATTTTAAATTC 59.033 37.037 0.00 0.00 0.00 2.17
4153 5142 7.094075 GGGACGAAGGGAGTACAATTTTAAATT 60.094 37.037 0.00 0.00 0.00 1.82
4154 5143 6.376299 GGGACGAAGGGAGTACAATTTTAAAT 59.624 38.462 0.00 0.00 0.00 1.40
4155 5144 5.706833 GGGACGAAGGGAGTACAATTTTAAA 59.293 40.000 0.00 0.00 0.00 1.52
4156 5145 5.221884 TGGGACGAAGGGAGTACAATTTTAA 60.222 40.000 0.00 0.00 0.00 1.52
4157 5146 4.286549 TGGGACGAAGGGAGTACAATTTTA 59.713 41.667 0.00 0.00 0.00 1.52
4158 5147 3.073356 TGGGACGAAGGGAGTACAATTTT 59.927 43.478 0.00 0.00 0.00 1.82
4159 5148 2.640826 TGGGACGAAGGGAGTACAATTT 59.359 45.455 0.00 0.00 0.00 1.82
4160 5149 2.262637 TGGGACGAAGGGAGTACAATT 58.737 47.619 0.00 0.00 0.00 2.32
4161 5150 1.946984 TGGGACGAAGGGAGTACAAT 58.053 50.000 0.00 0.00 0.00 2.71
4162 5151 1.946984 ATGGGACGAAGGGAGTACAA 58.053 50.000 0.00 0.00 0.00 2.41
4163 5152 2.832643 TATGGGACGAAGGGAGTACA 57.167 50.000 0.00 0.00 0.00 2.90
4164 5153 5.997384 ATATTATGGGACGAAGGGAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
4165 5154 8.495160 TTTTATATTATGGGACGAAGGGAGTA 57.505 34.615 0.00 0.00 0.00 2.59
4166 5155 7.072076 ACTTTTATATTATGGGACGAAGGGAGT 59.928 37.037 0.00 0.00 0.00 3.85
4167 5156 7.450903 ACTTTTATATTATGGGACGAAGGGAG 58.549 38.462 0.00 0.00 0.00 4.30
4168 5157 7.383156 ACTTTTATATTATGGGACGAAGGGA 57.617 36.000 0.00 0.00 0.00 4.20
4169 5158 9.734984 AATACTTTTATATTATGGGACGAAGGG 57.265 33.333 0.00 0.00 0.00 3.95
4212 5201 9.574516 AGAAACCAGTACATGTATTTTCTTTCT 57.425 29.630 19.10 17.36 31.46 2.52
4233 5222 6.407202 ACATATGTGGACTCAGGTAAGAAAC 58.593 40.000 7.78 0.00 0.00 2.78
4234 5223 6.620877 ACATATGTGGACTCAGGTAAGAAA 57.379 37.500 7.78 0.00 0.00 2.52
4235 5224 6.620877 AACATATGTGGACTCAGGTAAGAA 57.379 37.500 9.63 0.00 0.00 2.52
4236 5225 6.620877 AAACATATGTGGACTCAGGTAAGA 57.379 37.500 9.63 0.00 0.00 2.10
4237 5226 8.964476 ATTAAACATATGTGGACTCAGGTAAG 57.036 34.615 9.63 0.00 0.00 2.34
4238 5227 8.544622 TGATTAAACATATGTGGACTCAGGTAA 58.455 33.333 9.63 0.00 0.00 2.85
4239 5228 8.084985 TGATTAAACATATGTGGACTCAGGTA 57.915 34.615 9.63 0.00 0.00 3.08
4240 5229 6.957631 TGATTAAACATATGTGGACTCAGGT 58.042 36.000 9.63 0.00 0.00 4.00
4241 5230 7.864108 TTGATTAAACATATGTGGACTCAGG 57.136 36.000 9.63 0.00 0.00 3.86
4242 5231 9.941664 GATTTGATTAAACATATGTGGACTCAG 57.058 33.333 9.63 0.00 0.00 3.35
4243 5232 9.460019 TGATTTGATTAAACATATGTGGACTCA 57.540 29.630 9.63 7.54 0.00 3.41
4261 5250 9.932207 TCACATTCAGCTTTAAAATGATTTGAT 57.068 25.926 12.42 2.32 35.03 2.57
4262 5251 9.414295 CTCACATTCAGCTTTAAAATGATTTGA 57.586 29.630 12.42 10.92 35.03 2.69
4263 5252 9.199982 ACTCACATTCAGCTTTAAAATGATTTG 57.800 29.630 12.42 7.48 35.03 2.32
4264 5253 9.768662 AACTCACATTCAGCTTTAAAATGATTT 57.231 25.926 12.42 0.00 35.03 2.17
4265 5254 9.199982 CAACTCACATTCAGCTTTAAAATGATT 57.800 29.630 12.42 0.00 35.03 2.57
4266 5255 8.362639 ACAACTCACATTCAGCTTTAAAATGAT 58.637 29.630 12.42 0.00 35.03 2.45
4274 5263 3.554934 TGGACAACTCACATTCAGCTTT 58.445 40.909 0.00 0.00 0.00 3.51
4278 5267 3.496130 GTGACTGGACAACTCACATTCAG 59.504 47.826 5.39 0.00 35.39 3.02
4290 5279 4.594123 TCAAGAAATACGTGACTGGACA 57.406 40.909 0.00 0.00 32.59 4.02
4293 5282 6.480524 TTTCATCAAGAAATACGTGACTGG 57.519 37.500 0.00 0.00 41.17 4.00
4315 5304 0.598065 GCAGCAAACTTCACCCGATT 59.402 50.000 0.00 0.00 0.00 3.34
4318 5307 1.576421 GAGCAGCAAACTTCACCCG 59.424 57.895 0.00 0.00 0.00 5.28
4323 5312 3.413522 GCATGGAGCAGCAAACTTC 57.586 52.632 0.00 0.00 44.79 3.01
4364 5362 4.827284 TCTTTGACCAAGGGTGAGATTTTC 59.173 41.667 0.00 0.00 35.25 2.29
4396 5394 0.389391 ATCGTAGGGAATGAGCGTGG 59.611 55.000 0.00 0.00 0.00 4.94
4641 5640 6.408092 CCAATACAACAAGGATGCTACCTAGA 60.408 42.308 2.96 0.00 39.62 2.43


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

AutoCloner maintained by Alex Coulton.