Multiple sequence alignment - TraesCS5D01G323000

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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 TraesCS5D01G323000 chr5D 100.000 4272 0 0 1 4272 415260439 415264710 0.000000e+00 7890.0
1 TraesCS5D01G323000 chr5D 97.222 72 2 0 3444 3515 415263953 415263882 5.800000e-24 122.0
2 TraesCS5D01G323000 chr5A 93.162 2486 105 30 925 3365 527844504 527846969 0.000000e+00 3589.0
3 TraesCS5D01G323000 chr5A 90.495 747 48 13 3511 4254 527847010 527847736 0.000000e+00 965.0
4 TraesCS5D01G323000 chr5A 90.909 297 24 3 94 390 527844188 527844481 3.100000e-106 396.0
5 TraesCS5D01G323000 chr5A 96.262 107 4 0 1 107 527844058 527844164 4.390000e-40 176.0
6 TraesCS5D01G323000 chr5A 98.507 67 1 0 3381 3447 527846948 527847014 7.500000e-23 119.0
7 TraesCS5D01G323000 chr5B 92.969 1465 64 16 1913 3365 501238356 501239793 0.000000e+00 2098.0
8 TraesCS5D01G323000 chr5B 95.368 950 39 3 894 1840 501237406 501238353 0.000000e+00 1506.0
9 TraesCS5D01G323000 chr5B 95.761 519 21 1 3511 4028 501239834 501240352 0.000000e+00 835.0
10 TraesCS5D01G323000 chr5B 92.903 155 6 3 4048 4200 501240337 501240488 2.000000e-53 220.0
11 TraesCS5D01G323000 chr5B 93.269 104 7 0 1 104 501219295 501219398 2.060000e-33 154.0
12 TraesCS5D01G323000 chr5B 95.946 74 2 1 3440 3513 538723976 538724048 7.500000e-23 119.0
13 TraesCS5D01G323000 chr5B 77.596 183 35 5 722 901 681204401 681204580 5.840000e-19 106.0
14 TraesCS5D01G323000 chr5B 97.872 47 1 0 104 150 501219434 501219480 9.850000e-12 82.4
15 TraesCS5D01G323000 chr3D 79.853 1360 165 58 974 2290 519393225 519391932 0.000000e+00 893.0
16 TraesCS5D01G323000 chr3D 81.879 149 18 8 759 901 605701855 605702000 2.700000e-22 117.0
17 TraesCS5D01G323000 chr3B 88.347 738 60 12 974 1700 684112215 684111493 0.000000e+00 863.0
18 TraesCS5D01G323000 chr3B 83.559 961 104 27 974 1911 683790286 683789357 0.000000e+00 850.0
19 TraesCS5D01G323000 chr3A 88.244 689 46 14 974 1652 654404978 654404315 0.000000e+00 791.0
20 TraesCS5D01G323000 chr3A 88.168 262 30 1 641 901 49872755 49873016 1.150000e-80 311.0
21 TraesCS5D01G323000 chr3A 78.261 184 33 6 722 901 711061508 711061328 1.260000e-20 111.0
22 TraesCS5D01G323000 chr3A 90.476 42 4 0 3570 3611 654396458 654396417 5.970000e-04 56.5
23 TraesCS5D01G323000 chr7B 94.981 259 13 0 641 899 659622981 659622723 1.430000e-109 407.0
24 TraesCS5D01G323000 chr7B 92.093 215 16 1 428 641 659623297 659623083 6.940000e-78 302.0
25 TraesCS5D01G323000 chr6D 88.213 263 29 2 641 901 27729045 27729307 3.210000e-81 313.0
26 TraesCS5D01G323000 chr6D 95.890 73 3 0 3442 3514 377341668 377341740 7.500000e-23 119.0
27 TraesCS5D01G323000 chr1D 91.031 223 20 0 662 884 302917529 302917307 6.940000e-78 302.0
28 TraesCS5D01G323000 chr1D 82.143 252 45 0 651 902 78116561 78116812 2.590000e-52 217.0
29 TraesCS5D01G323000 chr1D 97.333 75 1 1 3442 3515 257365447 257365373 4.480000e-25 126.0
30 TraesCS5D01G323000 chr1D 97.260 73 1 1 3444 3515 257365373 257365445 5.800000e-24 122.0
31 TraesCS5D01G323000 chr7D 87.500 256 32 0 646 901 68916676 68916421 3.230000e-76 296.0
32 TraesCS5D01G323000 chr7D 94.872 39 1 1 37 74 166257970 166257932 4.610000e-05 60.2
33 TraesCS5D01G323000 chr1B 95.890 73 3 0 3442 3514 132296786 132296714 7.500000e-23 119.0
34 TraesCS5D01G323000 chr7A 94.667 75 2 1 3442 3516 69218956 69219028 9.710000e-22 115.0
35 TraesCS5D01G323000 chr7A 92.308 39 2 1 37 74 167827405 167827367 2.000000e-03 54.7
36 TraesCS5D01G323000 chr4A 90.110 91 5 2 3445 3532 274736256 274736167 9.710000e-22 115.0
37 TraesCS5D01G323000 chr1A 92.683 82 2 3 3445 3523 454330133 454330213 9.710000e-22 115.0


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 TraesCS5D01G323000 chr5D 415260439 415264710 4271 False 7890.00 7890 100.00000 1 4272 1 chr5D.!!$F1 4271
1 TraesCS5D01G323000 chr5A 527844058 527847736 3678 False 1049.00 3589 93.86700 1 4254 5 chr5A.!!$F1 4253
2 TraesCS5D01G323000 chr5B 501237406 501240488 3082 False 1164.75 2098 94.25025 894 4200 4 chr5B.!!$F4 3306
3 TraesCS5D01G323000 chr3D 519391932 519393225 1293 True 893.00 893 79.85300 974 2290 1 chr3D.!!$R1 1316
4 TraesCS5D01G323000 chr3B 684111493 684112215 722 True 863.00 863 88.34700 974 1700 1 chr3B.!!$R2 726
5 TraesCS5D01G323000 chr3B 683789357 683790286 929 True 850.00 850 83.55900 974 1911 1 chr3B.!!$R1 937
6 TraesCS5D01G323000 chr3A 654404315 654404978 663 True 791.00 791 88.24400 974 1652 1 chr3A.!!$R2 678
7 TraesCS5D01G323000 chr7B 659622723 659623297 574 True 354.50 407 93.53700 428 899 2 chr7B.!!$R1 471

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
676 815 0.178068 TAATGAAGGGCTCAGTCGGC 59.822 55.0 0.0 0.00 37.52 5.54 F
1007 1150 0.035915 TCCGATTTCGCCATGGACAA 60.036 50.0 18.4 3.46 38.18 3.18 F
1643 1822 0.390124 ACCGACGCTTTCAAGGTACA 59.610 50.0 0.0 0.00 32.76 2.90 F
2216 2431 1.846007 TGTGGTGCCAGTCTTTGTTT 58.154 45.0 0.0 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2641 0.255033 AATCAGGGCCGGGAGTTAAC 59.745 55.000 2.18 0.0 0.0 2.01 R
2451 2668 1.357420 ACACAGGCCCCATATTTCACA 59.643 47.619 0.00 0.0 0.0 3.58 R
3266 3525 2.504175 GGCTTGGGTCCTTATGTCAGTA 59.496 50.000 0.00 0.0 0.0 2.74 R
4145 4439 0.899019 GGCGCCTTTCCCCATTAAAA 59.101 50.000 22.15 0.0 0.0 1.52 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
26 27 2.553602 CCACTGCTGTAATGCACAAGAA 59.446 45.455 0.00 0.00 38.12 2.52
38 39 2.286950 TGCACAAGAACGAATCAACTGC 60.287 45.455 0.00 0.00 0.00 4.40
78 79 6.454795 TGAATACCAAGGAGCAAATTTGAAC 58.545 36.000 22.31 13.30 0.00 3.18
85 86 3.070015 AGGAGCAAATTTGAACACCTTGG 59.930 43.478 22.31 0.00 0.00 3.61
107 108 7.961325 TGGTTTCTTTAAATGAAATTGGAGC 57.039 32.000 12.72 4.79 36.10 4.70
108 109 7.504403 TGGTTTCTTTAAATGAAATTGGAGCA 58.496 30.769 12.72 6.52 36.10 4.26
109 110 7.989741 TGGTTTCTTTAAATGAAATTGGAGCAA 59.010 29.630 12.72 0.00 36.10 3.91
110 111 8.835439 GGTTTCTTTAAATGAAATTGGAGCAAA 58.165 29.630 12.72 0.00 36.10 3.68
142 178 2.413112 CGCAAGGTTAGTGTGACATCAG 59.587 50.000 0.00 0.00 0.00 2.90
153 189 2.893489 TGTGACATCAGTGCTAGTCTGT 59.107 45.455 13.72 0.66 34.86 3.41
168 204 6.877322 TGCTAGTCTGTTTATTAGTGGGAAAC 59.123 38.462 0.00 0.00 34.37 2.78
169 205 6.877322 GCTAGTCTGTTTATTAGTGGGAAACA 59.123 38.462 0.00 0.00 39.96 2.83
258 294 9.631639 GTTAAATTTTTGTGTGCAAATGTAGTC 57.368 29.630 0.00 0.00 43.26 2.59
280 316 2.945278 TGCTTTCAATGGTCGAAATGC 58.055 42.857 0.00 0.00 32.21 3.56
347 383 7.038587 TGAGTGGGCTACAGTTTATCTTAAAGA 60.039 37.037 3.15 0.00 31.34 2.52
348 384 7.862675 AGTGGGCTACAGTTTATCTTAAAGAT 58.137 34.615 3.15 0.00 38.70 2.40
349 385 7.770897 AGTGGGCTACAGTTTATCTTAAAGATG 59.229 37.037 3.15 0.00 35.37 2.90
350 386 7.769044 GTGGGCTACAGTTTATCTTAAAGATGA 59.231 37.037 0.00 0.00 35.37 2.92
351 387 7.987458 TGGGCTACAGTTTATCTTAAAGATGAG 59.013 37.037 0.00 0.00 35.37 2.90
413 449 2.577112 CGCGAGCTGACGTCGAAT 60.577 61.111 11.62 0.00 39.92 3.34
414 450 2.560151 CGCGAGCTGACGTCGAATC 61.560 63.158 11.62 7.31 39.92 2.52
415 451 2.560151 GCGAGCTGACGTCGAATCG 61.560 63.158 23.53 23.53 39.92 3.34
416 452 1.226046 CGAGCTGACGTCGAATCGT 60.226 57.895 21.05 0.15 46.88 3.73
417 453 1.456678 CGAGCTGACGTCGAATCGTG 61.457 60.000 21.05 0.00 44.21 4.35
418 454 0.179197 GAGCTGACGTCGAATCGTGA 60.179 55.000 11.62 0.00 44.21 4.35
419 455 0.240145 AGCTGACGTCGAATCGTGAA 59.760 50.000 11.62 0.00 44.21 3.18
420 456 0.635731 GCTGACGTCGAATCGTGAAG 59.364 55.000 11.62 4.95 44.21 3.02
421 457 1.260206 CTGACGTCGAATCGTGAAGG 58.740 55.000 11.62 0.00 44.21 3.46
422 458 0.731514 TGACGTCGAATCGTGAAGGC 60.732 55.000 11.62 0.00 44.21 4.35
423 459 1.411493 GACGTCGAATCGTGAAGGCC 61.411 60.000 5.75 0.00 44.21 5.19
449 485 4.481930 AGAAGAGCTATCAATCGTCTCG 57.518 45.455 0.00 0.00 29.83 4.04
469 505 1.002773 GGAGAAACCTGCTACCGGAAA 59.997 52.381 9.46 0.00 35.41 3.13
470 506 2.355818 GGAGAAACCTGCTACCGGAAAT 60.356 50.000 9.46 0.00 35.41 2.17
550 587 2.473530 AAATACATGTTGATGCCGCG 57.526 45.000 2.30 0.00 32.14 6.46
581 618 4.821589 GGGGCGGCTCGAGTTCTG 62.822 72.222 15.13 4.35 0.00 3.02
584 621 4.778415 GCGGCTCGAGTTCTGCGA 62.778 66.667 15.13 0.00 36.23 5.10
586 623 2.226896 CGGCTCGAGTTCTGCGATG 61.227 63.158 15.13 0.00 37.13 3.84
598 635 2.124570 GCGATGTGCAGGGATGGT 60.125 61.111 0.00 0.00 45.45 3.55
601 638 1.299541 CGATGTGCAGGGATGGTAAC 58.700 55.000 0.00 0.00 0.00 2.50
606 643 1.202099 TGCAGGGATGGTAACGGGAA 61.202 55.000 0.00 0.00 42.51 3.97
635 672 1.079819 AGCTCATCGTTGGTGGTCG 60.080 57.895 0.00 0.00 0.00 4.79
643 782 4.263572 TTGGTGGTCGTGGGGCAG 62.264 66.667 0.00 0.00 0.00 4.85
655 794 0.268869 TGGGGCAGGTCATAGGAGAT 59.731 55.000 0.00 0.00 0.00 2.75
671 810 7.344093 TCATAGGAGATATAATGAAGGGCTCAG 59.656 40.741 0.00 0.00 37.52 3.35
672 811 5.410602 AGGAGATATAATGAAGGGCTCAGT 58.589 41.667 0.00 0.00 37.52 3.41
675 814 2.918712 ATAATGAAGGGCTCAGTCGG 57.081 50.000 0.00 0.00 37.52 4.79
676 815 0.178068 TAATGAAGGGCTCAGTCGGC 59.822 55.000 0.00 0.00 37.52 5.54
716 855 3.111853 ACGAGATCAAACTGCAGTCAA 57.888 42.857 21.95 9.07 0.00 3.18
719 858 3.434641 CGAGATCAAACTGCAGTCAACAT 59.565 43.478 21.95 9.93 0.00 2.71
768 907 9.228949 TGAGAGTCGTAGAGTAAATTTAGAAGT 57.771 33.333 0.00 0.00 42.24 3.01
843 982 0.761802 GGCCAATCCCACAACCAAAA 59.238 50.000 0.00 0.00 0.00 2.44
892 1031 5.530915 TGATGAATAAAGCTTGGTATTCCCG 59.469 40.000 20.59 0.00 36.35 5.14
921 1060 4.739046 ACAGAAGAATTGCTGTTTCTCG 57.261 40.909 0.00 0.00 42.33 4.04
1007 1150 0.035915 TCCGATTTCGCCATGGACAA 60.036 50.000 18.40 3.46 38.18 3.18
1215 1379 3.589654 CTTCAGCTCCGCGTCCCAA 62.590 63.158 4.92 0.00 0.00 4.12
1444 1621 2.248248 TGGAGGTCGTCAAGTGAGATT 58.752 47.619 0.00 0.00 0.00 2.40
1453 1630 5.118817 GTCGTCAAGTGAGATTGTTTAGTCC 59.881 44.000 0.00 0.00 0.00 3.85
1475 1653 1.004560 CTCTTGCTCCGTTGCTCCA 60.005 57.895 0.00 0.00 0.00 3.86
1484 1662 1.164411 CCGTTGCTCCATTGCTGTTA 58.836 50.000 0.00 0.00 0.00 2.41
1489 1667 4.439153 CGTTGCTCCATTGCTGTTATTGAT 60.439 41.667 0.00 0.00 0.00 2.57
1629 1808 1.966451 CACCAAGGGCAAGACCGAC 60.966 63.158 0.00 0.00 40.62 4.79
1643 1822 0.390124 ACCGACGCTTTCAAGGTACA 59.610 50.000 0.00 0.00 32.76 2.90
1669 1848 8.637986 AGATGGCTTAAACTGTTGTTCAAAATA 58.362 29.630 0.00 0.00 34.96 1.40
1715 1894 7.056006 CCAAACATGCCCATAGATATATGCTA 58.944 38.462 1.61 0.00 0.00 3.49
1773 1958 2.435372 ACCAGTGAGAAAGTTTGCCA 57.565 45.000 0.00 0.00 0.00 4.92
1880 2078 7.505585 TGGTTATTTGATGAAGGGGATACATTC 59.494 37.037 0.00 0.00 39.74 2.67
1911 2109 3.243839 CCCTGTGAAAAGGAACCAACATG 60.244 47.826 0.00 0.00 40.02 3.21
1919 2117 2.519013 AGGAACCAACATGGAGCTTTC 58.481 47.619 2.85 0.00 40.96 2.62
1931 2129 4.882671 TGGAGCTTTCTTTATCGCATTC 57.117 40.909 0.00 0.00 0.00 2.67
1994 2193 7.833786 AGCAAATACATGTTGTCTTTCATGAT 58.166 30.769 2.30 0.00 42.52 2.45
1999 2198 8.991243 ATACATGTTGTCTTTCATGATTTTGG 57.009 30.769 2.30 0.00 42.52 3.28
2000 2199 6.225318 ACATGTTGTCTTTCATGATTTTGGG 58.775 36.000 11.27 0.00 42.52 4.12
2001 2200 5.867903 TGTTGTCTTTCATGATTTTGGGT 57.132 34.783 0.00 0.00 0.00 4.51
2002 2201 6.232581 TGTTGTCTTTCATGATTTTGGGTT 57.767 33.333 0.00 0.00 0.00 4.11
2003 2202 6.648192 TGTTGTCTTTCATGATTTTGGGTTT 58.352 32.000 0.00 0.00 0.00 3.27
2026 2225 9.382275 GTTTTGGCCTTCATTTATGTGATTTAT 57.618 29.630 3.32 0.00 0.00 1.40
2040 2239 4.397730 TGTGATTTATTTACACCGCAGCAT 59.602 37.500 0.00 0.00 34.18 3.79
2129 2334 4.369182 CCCATCAGTTGGTAACGATACTC 58.631 47.826 2.69 0.00 44.83 2.59
2216 2431 1.846007 TGTGGTGCCAGTCTTTGTTT 58.154 45.000 0.00 0.00 0.00 2.83
2309 2524 8.961634 GTATCCAGCATCTCTGTATCTGTATAA 58.038 37.037 0.00 0.00 41.25 0.98
2424 2641 3.193479 GCTTTTCCTGGTGTTATTCCCAG 59.807 47.826 0.00 0.00 46.43 4.45
2451 2668 4.141018 ACTCCCGGCCCTGATTTAATTTAT 60.141 41.667 0.00 0.00 0.00 1.40
2837 3057 5.066505 GGGACAGGAACAATGTGAATCATAC 59.933 44.000 0.00 0.00 35.48 2.39
2858 3078 9.132923 TCATACTTGACTACATTAGTAAGGAGG 57.867 37.037 0.75 0.00 39.59 4.30
2957 3177 6.512903 GCTTAAGTTGGTGAGACTAAAACCAC 60.513 42.308 4.02 0.00 43.55 4.16
2997 3225 5.705905 GGTTAGAATCTGCCACTTAAACACT 59.294 40.000 0.00 0.00 0.00 3.55
3001 3230 6.006449 AGAATCTGCCACTTAAACACTGATT 58.994 36.000 0.00 0.00 33.38 2.57
3266 3525 4.660168 AGATTCCAATGTGAAAGCTGAGT 58.340 39.130 0.00 0.00 0.00 3.41
3349 3608 2.121506 AGGAAGGCCCTGGGAACA 60.122 61.111 19.27 0.00 45.61 3.18
3350 3609 1.778383 AGGAAGGCCCTGGGAACAA 60.778 57.895 19.27 0.00 45.61 2.83
3351 3610 1.155155 GGAAGGCCCTGGGAACAAA 59.845 57.895 19.27 0.00 42.06 2.83
3352 3611 1.185618 GGAAGGCCCTGGGAACAAAC 61.186 60.000 19.27 0.00 42.06 2.93
3353 3612 0.469144 GAAGGCCCTGGGAACAAACA 60.469 55.000 19.27 0.00 42.06 2.83
3354 3613 0.031616 AAGGCCCTGGGAACAAACAA 60.032 50.000 19.27 0.00 42.06 2.83
3355 3614 0.759060 AGGCCCTGGGAACAAACAAC 60.759 55.000 19.27 0.00 42.06 3.32
3356 3615 0.759060 GGCCCTGGGAACAAACAACT 60.759 55.000 19.27 0.00 42.06 3.16
3357 3616 0.389025 GCCCTGGGAACAAACAACTG 59.611 55.000 19.27 0.00 42.06 3.16
3358 3617 2.026905 GCCCTGGGAACAAACAACTGA 61.027 52.381 19.27 0.00 42.06 3.41
3359 3618 2.597455 CCCTGGGAACAAACAACTGAT 58.403 47.619 7.01 0.00 42.06 2.90
3360 3619 3.761897 CCCTGGGAACAAACAACTGATA 58.238 45.455 7.01 0.00 42.06 2.15
3361 3620 3.506067 CCCTGGGAACAAACAACTGATAC 59.494 47.826 7.01 0.00 42.06 2.24
3362 3621 4.398319 CCTGGGAACAAACAACTGATACT 58.602 43.478 0.00 0.00 42.06 2.12
3363 3622 5.514136 CCCTGGGAACAAACAACTGATACTA 60.514 44.000 7.01 0.00 42.06 1.82
3364 3623 6.180472 CCTGGGAACAAACAACTGATACTAT 58.820 40.000 0.00 0.00 42.06 2.12
3365 3624 6.094048 CCTGGGAACAAACAACTGATACTATG 59.906 42.308 0.00 0.00 42.06 2.23
3366 3625 6.539173 TGGGAACAAACAACTGATACTATGT 58.461 36.000 0.00 0.00 37.44 2.29
3367 3626 6.429692 TGGGAACAAACAACTGATACTATGTG 59.570 38.462 0.00 0.00 37.44 3.21
3368 3627 6.430000 GGGAACAAACAACTGATACTATGTGT 59.570 38.462 0.00 0.00 0.00 3.72
3369 3628 7.040686 GGGAACAAACAACTGATACTATGTGTT 60.041 37.037 0.00 0.00 0.00 3.32
3370 3629 8.995220 GGAACAAACAACTGATACTATGTGTTA 58.005 33.333 0.00 0.00 0.00 2.41
3427 3686 0.948678 TTGTACGCACTGGCCTTTTC 59.051 50.000 3.32 0.00 36.38 2.29
3447 3706 8.485578 CTTTTCTAGGAGGGATCAATAGTACT 57.514 38.462 0.00 0.00 0.00 2.73
3448 3707 8.480133 TTTTCTAGGAGGGATCAATAGTACTC 57.520 38.462 0.00 0.00 0.00 2.59
3449 3708 6.142259 TCTAGGAGGGATCAATAGTACTCC 57.858 45.833 0.00 0.00 43.67 3.85
3450 3709 4.134933 AGGAGGGATCAATAGTACTCCC 57.865 50.000 0.00 2.62 46.56 4.30
3454 3713 2.826725 GGGATCAATAGTACTCCCTCCG 59.173 54.545 0.00 0.00 43.45 4.63
3455 3714 3.498334 GGATCAATAGTACTCCCTCCGT 58.502 50.000 0.00 0.00 0.00 4.69
3456 3715 4.508047 GGGATCAATAGTACTCCCTCCGTA 60.508 50.000 0.00 0.00 43.45 4.02
3457 3716 5.075493 GGATCAATAGTACTCCCTCCGTAA 58.925 45.833 0.00 0.00 0.00 3.18
3458 3717 5.537674 GGATCAATAGTACTCCCTCCGTAAA 59.462 44.000 0.00 0.00 0.00 2.01
3459 3718 6.294620 GGATCAATAGTACTCCCTCCGTAAAG 60.295 46.154 0.00 0.00 0.00 1.85
3460 3719 5.759059 TCAATAGTACTCCCTCCGTAAAGA 58.241 41.667 0.00 0.00 0.00 2.52
3461 3720 6.189859 TCAATAGTACTCCCTCCGTAAAGAA 58.810 40.000 0.00 0.00 0.00 2.52
3462 3721 6.664816 TCAATAGTACTCCCTCCGTAAAGAAA 59.335 38.462 0.00 0.00 0.00 2.52
3463 3722 7.343833 TCAATAGTACTCCCTCCGTAAAGAAAT 59.656 37.037 0.00 0.00 0.00 2.17
3464 3723 8.636213 CAATAGTACTCCCTCCGTAAAGAAATA 58.364 37.037 0.00 0.00 0.00 1.40
3465 3724 8.953223 ATAGTACTCCCTCCGTAAAGAAATAT 57.047 34.615 0.00 0.00 0.00 1.28
3467 3726 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
3468 3727 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
3469 3728 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3470 3729 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3471 3730 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3472 3731 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
3473 3732 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
3474 3733 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
3475 3734 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
3505 3764 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
3506 3765 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
3507 3766 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3508 3767 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
3509 3768 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3510 3769 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3511 3770 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3512 3771 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3513 3772 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3514 3773 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
3600 3860 3.092334 AGATTTGCCGTGTTTTTGTCC 57.908 42.857 0.00 0.00 0.00 4.02
3726 3986 2.031245 TCATCATCGTGTGTTGGTTTGC 60.031 45.455 0.00 0.00 0.00 3.68
3868 4131 6.473455 GGAGATATTTGGCTTTGTTTCGAATG 59.527 38.462 0.00 0.00 0.00 2.67
3891 4154 4.321675 GGTTTAACTGAAAATGGCCGTCAT 60.322 41.667 0.00 0.00 37.79 3.06
3898 4161 5.360714 ACTGAAAATGGCCGTCATTATGATT 59.639 36.000 0.00 0.00 44.68 2.57
3903 4166 8.458573 AAAATGGCCGTCATTATGATTAGTTA 57.541 30.769 0.00 0.00 44.68 2.24
3943 4206 5.339530 CCTTTTGGAGGTCATCTAGGTGAAT 60.340 44.000 7.42 0.00 44.07 2.57
3951 4214 7.202047 GGAGGTCATCTAGGTGAATTGATTAGT 60.202 40.741 7.42 0.00 0.00 2.24
3966 4229 5.359194 TGATTAGTGAGGGAACTTCCATC 57.641 43.478 14.47 14.47 46.80 3.51
4028 4319 8.967218 CACATTTGTTAACGACAATCTTTGATT 58.033 29.630 0.26 0.00 46.99 2.57
4029 4320 9.528018 ACATTTGTTAACGACAATCTTTGATTT 57.472 25.926 0.26 0.00 46.99 2.17
4145 4439 5.255397 TCTGGACATCACATACCCTTTTT 57.745 39.130 0.00 0.00 0.00 1.94
4182 4476 1.643880 CCCAAGGCGCAAAATTCATC 58.356 50.000 10.83 0.00 0.00 2.92
4183 4477 1.067000 CCCAAGGCGCAAAATTCATCA 60.067 47.619 10.83 0.00 0.00 3.07
4184 4478 2.419021 CCCAAGGCGCAAAATTCATCAT 60.419 45.455 10.83 0.00 0.00 2.45
4211 4505 5.777802 ACTCATAGATAGTGTACAGCATGC 58.222 41.667 10.51 10.51 42.53 4.06
4245 4539 8.445361 ACCCTGTAGATTTAAGGTAGAAAGAA 57.555 34.615 0.00 0.00 0.00 2.52
4258 4552 7.654022 AGGTAGAAAGAAGAGAGATTACAGG 57.346 40.000 0.00 0.00 0.00 4.00
4259 4553 6.609616 AGGTAGAAAGAAGAGAGATTACAGGG 59.390 42.308 0.00 0.00 0.00 4.45
4260 4554 5.948742 AGAAAGAAGAGAGATTACAGGGG 57.051 43.478 0.00 0.00 0.00 4.79
4261 4555 5.594777 AGAAAGAAGAGAGATTACAGGGGA 58.405 41.667 0.00 0.00 0.00 4.81
4262 4556 6.026186 AGAAAGAAGAGAGATTACAGGGGAA 58.974 40.000 0.00 0.00 0.00 3.97
4263 4557 5.948742 AAGAAGAGAGATTACAGGGGAAG 57.051 43.478 0.00 0.00 0.00 3.46
4264 4558 5.213868 AGAAGAGAGATTACAGGGGAAGA 57.786 43.478 0.00 0.00 0.00 2.87
4265 4559 4.959839 AGAAGAGAGATTACAGGGGAAGAC 59.040 45.833 0.00 0.00 0.00 3.01
4266 4560 4.338795 AGAGAGATTACAGGGGAAGACA 57.661 45.455 0.00 0.00 0.00 3.41
4267 4561 4.889780 AGAGAGATTACAGGGGAAGACAT 58.110 43.478 0.00 0.00 0.00 3.06
4268 4562 4.653341 AGAGAGATTACAGGGGAAGACATG 59.347 45.833 0.00 0.00 0.00 3.21
4269 4563 4.366267 AGAGATTACAGGGGAAGACATGT 58.634 43.478 0.00 0.00 0.00 3.21
4270 4564 4.785376 AGAGATTACAGGGGAAGACATGTT 59.215 41.667 0.00 0.00 0.00 2.71
4271 4565 5.104259 AGATTACAGGGGAAGACATGTTC 57.896 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.660887 AAAAACAAATTGCAGTTGATTCGT 57.339 29.167 16.58 0.00 0.00 3.85
78 79 8.558700 CCAATTTCATTTAAAGAAACCAAGGTG 58.441 33.333 12.17 0.00 37.76 4.00
142 178 5.974108 TCCCACTAATAAACAGACTAGCAC 58.026 41.667 0.00 0.00 0.00 4.40
185 221 7.165460 AGGGATAAAAGTCCGGTAAATTTTG 57.835 36.000 10.54 0.00 39.26 2.44
244 280 4.277921 TGAAAGCATGACTACATTTGCACA 59.722 37.500 0.00 0.00 35.31 4.57
258 294 3.305094 GCATTTCGACCATTGAAAGCATG 59.695 43.478 0.00 0.00 38.60 4.06
295 331 2.368875 GCACCTAAGCTCTATTGGGCTA 59.631 50.000 0.76 0.00 37.87 3.93
296 332 1.141858 GCACCTAAGCTCTATTGGGCT 59.858 52.381 0.00 0.00 40.85 5.19
302 338 1.115467 ACTGCGCACCTAAGCTCTAT 58.885 50.000 5.66 0.00 0.00 1.98
309 345 1.005037 CCACTCACTGCGCACCTAA 60.005 57.895 5.66 0.00 0.00 2.69
310 346 2.656646 CCACTCACTGCGCACCTA 59.343 61.111 5.66 0.00 0.00 3.08
347 383 2.614259 CTGGGCCTACAGTATCCTCAT 58.386 52.381 4.53 0.00 33.81 2.90
348 384 2.088104 CTGGGCCTACAGTATCCTCA 57.912 55.000 4.53 0.00 33.81 3.86
396 432 2.560151 GATTCGACGTCAGCTCGCG 61.560 63.158 17.16 0.00 34.07 5.87
397 433 2.560151 CGATTCGACGTCAGCTCGC 61.560 63.158 17.16 0.00 0.00 5.03
398 434 1.226046 ACGATTCGACGTCAGCTCG 60.226 57.895 21.72 21.72 43.02 5.03
399 435 0.179197 TCACGATTCGACGTCAGCTC 60.179 55.000 17.16 7.23 44.76 4.09
400 436 0.240145 TTCACGATTCGACGTCAGCT 59.760 50.000 17.16 0.00 44.76 4.24
401 437 0.635731 CTTCACGATTCGACGTCAGC 59.364 55.000 17.16 0.00 44.76 4.26
402 438 1.260206 CCTTCACGATTCGACGTCAG 58.740 55.000 17.16 8.67 44.76 3.51
403 439 0.731514 GCCTTCACGATTCGACGTCA 60.732 55.000 17.16 0.00 44.76 4.35
404 440 1.411493 GGCCTTCACGATTCGACGTC 61.411 60.000 13.95 5.18 44.76 4.34
406 442 0.099968 TAGGCCTTCACGATTCGACG 59.900 55.000 12.58 3.51 39.31 5.12
407 443 1.134560 AGTAGGCCTTCACGATTCGAC 59.865 52.381 12.58 0.00 0.00 4.20
408 444 1.471119 AGTAGGCCTTCACGATTCGA 58.529 50.000 12.58 0.00 0.00 3.71
409 445 2.617308 TCTAGTAGGCCTTCACGATTCG 59.383 50.000 12.58 4.14 0.00 3.34
410 446 4.338682 TCTTCTAGTAGGCCTTCACGATTC 59.661 45.833 12.58 0.00 0.00 2.52
411 447 4.279145 TCTTCTAGTAGGCCTTCACGATT 58.721 43.478 12.58 0.00 0.00 3.34
412 448 3.886505 CTCTTCTAGTAGGCCTTCACGAT 59.113 47.826 12.58 0.00 0.00 3.73
413 449 3.280295 CTCTTCTAGTAGGCCTTCACGA 58.720 50.000 12.58 3.24 0.00 4.35
414 450 2.223618 GCTCTTCTAGTAGGCCTTCACG 60.224 54.545 12.58 0.37 0.00 4.35
415 451 3.028130 AGCTCTTCTAGTAGGCCTTCAC 58.972 50.000 12.58 3.34 0.00 3.18
416 452 3.390175 AGCTCTTCTAGTAGGCCTTCA 57.610 47.619 12.58 0.00 0.00 3.02
417 453 5.074115 TGATAGCTCTTCTAGTAGGCCTTC 58.926 45.833 12.58 5.68 0.00 3.46
418 454 5.068215 TGATAGCTCTTCTAGTAGGCCTT 57.932 43.478 12.58 0.00 0.00 4.35
419 455 4.733077 TGATAGCTCTTCTAGTAGGCCT 57.267 45.455 11.78 11.78 0.00 5.19
420 456 5.392595 CGATTGATAGCTCTTCTAGTAGGCC 60.393 48.000 0.00 0.00 0.00 5.19
421 457 5.182380 ACGATTGATAGCTCTTCTAGTAGGC 59.818 44.000 0.00 0.00 0.00 3.93
422 458 6.653320 AGACGATTGATAGCTCTTCTAGTAGG 59.347 42.308 0.00 0.00 0.00 3.18
423 459 7.411480 CGAGACGATTGATAGCTCTTCTAGTAG 60.411 44.444 0.00 0.00 0.00 2.57
449 485 0.611714 TTCCGGTAGCAGGTTTCTCC 59.388 55.000 0.00 0.00 0.00 3.71
535 572 1.922135 GAACCGCGGCATCAACATGT 61.922 55.000 28.58 0.00 31.86 3.21
550 587 4.410400 CCCCTGCCCTGACGAACC 62.410 72.222 0.00 0.00 0.00 3.62
581 618 0.463654 TTACCATCCCTGCACATCGC 60.464 55.000 0.00 0.00 42.89 4.58
584 621 0.107214 CCGTTACCATCCCTGCACAT 60.107 55.000 0.00 0.00 0.00 3.21
586 623 1.451387 CCCGTTACCATCCCTGCAC 60.451 63.158 0.00 0.00 0.00 4.57
598 635 2.432444 CTGCCAATGAAGTTCCCGTTA 58.568 47.619 0.00 0.00 0.00 3.18
601 638 0.962356 AGCTGCCAATGAAGTTCCCG 60.962 55.000 0.00 0.00 0.00 5.14
606 643 1.339438 ACGATGAGCTGCCAATGAAGT 60.339 47.619 0.00 0.00 0.00 3.01
635 672 0.691078 TCTCCTATGACCTGCCCCAC 60.691 60.000 0.00 0.00 0.00 4.61
643 782 6.385467 AGCCCTTCATTATATCTCCTATGACC 59.615 42.308 0.00 0.00 0.00 4.02
655 794 2.037251 GCCGACTGAGCCCTTCATTATA 59.963 50.000 0.00 0.00 34.68 0.98
671 810 3.044305 GGCGCCATATCTGCCGAC 61.044 66.667 24.80 0.00 39.30 4.79
675 814 0.731417 GATGATGGCGCCATATCTGC 59.269 55.000 40.56 27.39 36.70 4.26
676 815 2.103537 TGATGATGGCGCCATATCTG 57.896 50.000 40.56 0.00 36.70 2.90
768 907 3.480470 GAATGCCTGGCTAAGCTATGAA 58.520 45.455 21.03 0.00 0.00 2.57
774 913 1.379642 AAGCGAATGCCTGGCTAAGC 61.380 55.000 21.03 18.45 44.31 3.09
939 1081 3.124636 CCTCCACGGTTCGATTTGTAAAG 59.875 47.826 0.00 0.00 0.00 1.85
1215 1379 4.787280 CGCTGGAGGAGGGGGAGT 62.787 72.222 0.00 0.00 0.00 3.85
1444 1621 1.968493 AGCAAGAGACGGGACTAAACA 59.032 47.619 0.00 0.00 0.00 2.83
1453 1630 2.383527 GCAACGGAGCAAGAGACGG 61.384 63.158 0.00 0.00 0.00 4.79
1475 1653 3.812053 GCGAGAGGATCAATAACAGCAAT 59.188 43.478 0.00 0.00 37.82 3.56
1484 1662 2.114616 AGTTCAGGCGAGAGGATCAAT 58.885 47.619 0.00 0.00 37.82 2.57
1489 1667 0.827925 ACACAGTTCAGGCGAGAGGA 60.828 55.000 0.00 0.00 0.00 3.71
1629 1808 1.398390 GCCATCTGTACCTTGAAAGCG 59.602 52.381 0.00 0.00 0.00 4.68
1643 1822 6.463995 TTTGAACAACAGTTTAAGCCATCT 57.536 33.333 0.00 0.00 0.00 2.90
1669 1848 4.461081 TGGTTAATAGCGAAACTTTGGCAT 59.539 37.500 10.68 0.87 36.79 4.40
1715 1894 6.070767 ACTGTACCATGCTACAAACTGTATCT 60.071 38.462 2.62 0.00 31.66 1.98
1773 1958 9.025041 CATCAAAAGTTCCCCTAAAAATAGACT 57.975 33.333 0.00 0.00 0.00 3.24
1846 2042 7.287466 CCCCTTCATCAAATAACCAATGTCATA 59.713 37.037 0.00 0.00 0.00 2.15
1865 2063 5.827797 GCATACAAAGAATGTATCCCCTTCA 59.172 40.000 0.00 0.00 43.63 3.02
1866 2064 5.241728 GGCATACAAAGAATGTATCCCCTTC 59.758 44.000 0.00 0.00 43.63 3.46
1867 2065 5.140454 GGCATACAAAGAATGTATCCCCTT 58.860 41.667 0.00 0.00 43.63 3.95
1880 2078 3.826157 TCCTTTTCACAGGGCATACAAAG 59.174 43.478 0.00 0.00 34.24 2.77
1911 2109 3.627577 TGGAATGCGATAAAGAAAGCTCC 59.372 43.478 0.00 0.00 0.00 4.70
1947 2146 1.750778 GATTTGTGGTTCGGATGCCAT 59.249 47.619 5.33 0.00 37.09 4.40
1956 2155 6.646240 ACATGTATTTGCTTGATTTGTGGTTC 59.354 34.615 0.00 0.00 0.00 3.62
1994 2193 3.941704 AATGAAGGCCAAAACCCAAAA 57.058 38.095 5.01 0.00 0.00 2.44
1997 2196 3.906846 ACATAAATGAAGGCCAAAACCCA 59.093 39.130 5.01 0.00 0.00 4.51
1998 2197 4.020662 TCACATAAATGAAGGCCAAAACCC 60.021 41.667 5.01 0.00 0.00 4.11
1999 2198 5.146010 TCACATAAATGAAGGCCAAAACC 57.854 39.130 5.01 0.00 0.00 3.27
2000 2199 7.671495 AAATCACATAAATGAAGGCCAAAAC 57.329 32.000 5.01 0.00 30.82 2.43
2001 2200 9.956640 AATAAATCACATAAATGAAGGCCAAAA 57.043 25.926 5.01 0.00 30.82 2.44
2002 2201 9.956640 AAATAAATCACATAAATGAAGGCCAAA 57.043 25.926 5.01 0.00 30.82 3.28
2026 2225 2.499197 TGAAAGATGCTGCGGTGTAAA 58.501 42.857 0.00 0.00 0.00 2.01
2101 2304 4.100479 CCAACTGATGGGCTGCAA 57.900 55.556 0.50 0.00 46.27 4.08
2129 2334 6.521151 ACAGGGAAAGCTTTGATAATGAAG 57.479 37.500 18.30 0.00 0.00 3.02
2216 2431 3.780294 ACAGGATTCTACATGGGCAGTAA 59.220 43.478 0.00 0.00 0.00 2.24
2309 2524 7.308348 CCTTACAGACAACGGTTCAATAAATGT 60.308 37.037 0.00 0.00 0.00 2.71
2321 2536 1.549170 AGTAGGCCTTACAGACAACGG 59.451 52.381 12.58 0.00 34.56 4.44
2424 2641 0.255033 AATCAGGGCCGGGAGTTAAC 59.745 55.000 2.18 0.00 0.00 2.01
2451 2668 1.357420 ACACAGGCCCCATATTTCACA 59.643 47.619 0.00 0.00 0.00 3.58
2837 3057 7.837863 TCAACCTCCTTACTAATGTAGTCAAG 58.162 38.462 0.00 0.00 40.14 3.02
2858 3078 6.534793 AGAAACATGAAACCACATTGTTCAAC 59.465 34.615 0.00 0.00 0.00 3.18
3266 3525 2.504175 GGCTTGGGTCCTTATGTCAGTA 59.496 50.000 0.00 0.00 0.00 2.74
3356 3615 9.035890 CCCTCCTATGAATAACACATAGTATCA 57.964 37.037 0.00 0.00 42.99 2.15
3357 3616 9.256228 TCCCTCCTATGAATAACACATAGTATC 57.744 37.037 0.00 0.00 42.99 2.24
3358 3617 9.615660 TTCCCTCCTATGAATAACACATAGTAT 57.384 33.333 0.00 0.00 42.99 2.12
3359 3618 8.867097 GTTCCCTCCTATGAATAACACATAGTA 58.133 37.037 0.00 0.00 42.99 1.82
3360 3619 7.347222 TGTTCCCTCCTATGAATAACACATAGT 59.653 37.037 0.00 0.00 42.99 2.12
3361 3620 7.735917 TGTTCCCTCCTATGAATAACACATAG 58.264 38.462 0.00 0.00 43.68 2.23
3362 3621 7.684317 TGTTCCCTCCTATGAATAACACATA 57.316 36.000 0.00 0.00 0.00 2.29
3363 3622 6.575244 TGTTCCCTCCTATGAATAACACAT 57.425 37.500 0.00 0.00 0.00 3.21
3364 3623 6.381498 TTGTTCCCTCCTATGAATAACACA 57.619 37.500 0.00 0.00 0.00 3.72
3365 3624 6.657541 TGTTTGTTCCCTCCTATGAATAACAC 59.342 38.462 0.00 0.00 30.16 3.32
3366 3625 6.785076 TGTTTGTTCCCTCCTATGAATAACA 58.215 36.000 0.00 0.00 31.43 2.41
3367 3626 7.393515 AGTTGTTTGTTCCCTCCTATGAATAAC 59.606 37.037 0.00 0.00 0.00 1.89
3368 3627 7.393234 CAGTTGTTTGTTCCCTCCTATGAATAA 59.607 37.037 0.00 0.00 0.00 1.40
3369 3628 6.884295 CAGTTGTTTGTTCCCTCCTATGAATA 59.116 38.462 0.00 0.00 0.00 1.75
3370 3629 5.711976 CAGTTGTTTGTTCCCTCCTATGAAT 59.288 40.000 0.00 0.00 0.00 2.57
3371 3630 5.070001 CAGTTGTTTGTTCCCTCCTATGAA 58.930 41.667 0.00 0.00 0.00 2.57
3372 3631 4.349636 TCAGTTGTTTGTTCCCTCCTATGA 59.650 41.667 0.00 0.00 0.00 2.15
3373 3632 4.651778 TCAGTTGTTTGTTCCCTCCTATG 58.348 43.478 0.00 0.00 0.00 2.23
3374 3633 4.993705 TCAGTTGTTTGTTCCCTCCTAT 57.006 40.909 0.00 0.00 0.00 2.57
3375 3634 4.993705 ATCAGTTGTTTGTTCCCTCCTA 57.006 40.909 0.00 0.00 0.00 2.94
3376 3635 3.884037 ATCAGTTGTTTGTTCCCTCCT 57.116 42.857 0.00 0.00 0.00 3.69
3377 3636 4.652822 AGTATCAGTTGTTTGTTCCCTCC 58.347 43.478 0.00 0.00 0.00 4.30
3427 3686 5.265989 GGGAGTACTATTGATCCCTCCTAG 58.734 50.000 8.10 0.00 46.72 3.02
3447 3706 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
3448 3707 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
3449 3708 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
3479 3738 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
3480 3739 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3481 3740 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3482 3741 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
3483 3742 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
3484 3743 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3485 3744 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3486 3745 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3487 3746 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3488 3747 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3489 3748 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
3490 3749 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
3491 3750 8.716674 ATGTACTCCCTCCGTAAAGAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
3492 3751 7.509659 AGATGTACTCCCTCCGTAAAGAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
3493 3752 6.837568 AGATGTACTCCCTCCGTAAAGAAATA 59.162 38.462 0.00 0.00 0.00 1.40
3494 3753 5.661759 AGATGTACTCCCTCCGTAAAGAAAT 59.338 40.000 0.00 0.00 0.00 2.17
3495 3754 5.021458 AGATGTACTCCCTCCGTAAAGAAA 58.979 41.667 0.00 0.00 0.00 2.52
3496 3755 4.401519 CAGATGTACTCCCTCCGTAAAGAA 59.598 45.833 0.00 0.00 0.00 2.52
3497 3756 3.952323 CAGATGTACTCCCTCCGTAAAGA 59.048 47.826 0.00 0.00 0.00 2.52
3498 3757 3.700038 ACAGATGTACTCCCTCCGTAAAG 59.300 47.826 0.00 0.00 0.00 1.85
3499 3758 3.705051 ACAGATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
3500 3759 3.377253 ACAGATGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 0.00 3.18
3501 3760 4.719026 ATACAGATGTACTCCCTCCGTA 57.281 45.455 0.00 0.00 32.72 4.02
3502 3761 3.596940 ATACAGATGTACTCCCTCCGT 57.403 47.619 0.00 0.00 32.72 4.69
3503 3762 7.339721 ACATAATATACAGATGTACTCCCTCCG 59.660 40.741 0.00 0.00 32.07 4.63
3504 3763 8.596781 ACATAATATACAGATGTACTCCCTCC 57.403 38.462 0.00 0.00 32.07 4.30
3505 3764 9.244292 TGACATAATATACAGATGTACTCCCTC 57.756 37.037 0.00 0.00 33.99 4.30
3506 3765 9.026121 GTGACATAATATACAGATGTACTCCCT 57.974 37.037 0.00 0.00 33.99 4.20
3507 3766 8.803235 TGTGACATAATATACAGATGTACTCCC 58.197 37.037 0.00 0.00 33.99 4.30
3544 3804 5.042463 TGACTACAACAAATGGGAAGTCA 57.958 39.130 0.00 0.00 41.29 3.41
3545 3805 6.381801 CATTGACTACAACAAATGGGAAGTC 58.618 40.000 0.00 0.00 38.90 3.01
3600 3860 4.190001 GGCTGATGATGGCTACATAGATG 58.810 47.826 0.00 0.00 37.47 2.90
3651 3911 3.066760 GCAAGTAGCACCATAACCCATTC 59.933 47.826 0.00 0.00 44.79 2.67
3726 3986 6.320672 GGCCCATGATGAGGAATGATTATTAG 59.679 42.308 0.00 0.00 0.00 1.73
3868 4131 3.004944 TGACGGCCATTTTCAGTTAAACC 59.995 43.478 2.24 0.00 0.00 3.27
3891 4154 9.693739 AATCAACCACCACATAACTAATCATAA 57.306 29.630 0.00 0.00 0.00 1.90
3898 4161 6.134535 AGGAAATCAACCACCACATAACTA 57.865 37.500 0.00 0.00 0.00 2.24
3903 4166 4.202346 CCAAAAGGAAATCAACCACCACAT 60.202 41.667 0.00 0.00 0.00 3.21
3943 4206 5.488919 AGATGGAAGTTCCCTCACTAATCAA 59.511 40.000 24.08 1.85 34.15 2.57
3951 4214 1.003580 GCACAGATGGAAGTTCCCTCA 59.996 52.381 24.08 6.44 34.15 3.86
3966 4229 3.490759 GACGACCGGCATGCACAG 61.491 66.667 21.36 9.68 0.00 3.66
4037 4328 9.611284 CATCAAAGATTGTCGTTCATCTAAAAA 57.389 29.630 0.00 0.00 0.00 1.94
4038 4329 8.998377 TCATCAAAGATTGTCGTTCATCTAAAA 58.002 29.630 0.00 0.00 0.00 1.52
4039 4330 8.546597 TCATCAAAGATTGTCGTTCATCTAAA 57.453 30.769 0.00 0.00 0.00 1.85
4040 4331 7.201556 GCTCATCAAAGATTGTCGTTCATCTAA 60.202 37.037 0.00 0.00 0.00 2.10
4041 4332 6.256539 GCTCATCAAAGATTGTCGTTCATCTA 59.743 38.462 0.00 0.00 0.00 1.98
4042 4333 5.064452 GCTCATCAAAGATTGTCGTTCATCT 59.936 40.000 0.00 0.00 0.00 2.90
4043 4334 5.261661 GCTCATCAAAGATTGTCGTTCATC 58.738 41.667 0.00 0.00 0.00 2.92
4044 4335 4.095483 GGCTCATCAAAGATTGTCGTTCAT 59.905 41.667 0.00 0.00 0.00 2.57
4045 4336 3.436704 GGCTCATCAAAGATTGTCGTTCA 59.563 43.478 0.00 0.00 0.00 3.18
4046 4337 3.181506 GGGCTCATCAAAGATTGTCGTTC 60.182 47.826 0.00 0.00 0.00 3.95
4047 4338 2.749621 GGGCTCATCAAAGATTGTCGTT 59.250 45.455 0.00 0.00 0.00 3.85
4048 4339 2.026822 AGGGCTCATCAAAGATTGTCGT 60.027 45.455 0.00 0.00 0.00 4.34
4049 4340 2.636830 AGGGCTCATCAAAGATTGTCG 58.363 47.619 0.00 0.00 0.00 4.35
4050 4341 4.012374 TCAAGGGCTCATCAAAGATTGTC 58.988 43.478 0.00 0.00 0.00 3.18
4051 4342 4.015084 CTCAAGGGCTCATCAAAGATTGT 58.985 43.478 0.00 0.00 0.00 2.71
4052 4343 4.267536 TCTCAAGGGCTCATCAAAGATTG 58.732 43.478 0.00 0.00 0.00 2.67
4053 4344 4.581309 TCTCAAGGGCTCATCAAAGATT 57.419 40.909 0.00 0.00 0.00 2.40
4054 4345 4.079901 ACATCTCAAGGGCTCATCAAAGAT 60.080 41.667 0.00 0.00 0.00 2.40
4055 4346 3.265221 ACATCTCAAGGGCTCATCAAAGA 59.735 43.478 0.00 0.00 0.00 2.52
4056 4347 3.377485 CACATCTCAAGGGCTCATCAAAG 59.623 47.826 0.00 0.00 0.00 2.77
4057 4348 3.245016 ACACATCTCAAGGGCTCATCAAA 60.245 43.478 0.00 0.00 0.00 2.69
4058 4349 2.306805 ACACATCTCAAGGGCTCATCAA 59.693 45.455 0.00 0.00 0.00 2.57
4059 4350 1.911357 ACACATCTCAAGGGCTCATCA 59.089 47.619 0.00 0.00 0.00 3.07
4060 4351 2.706339 ACACATCTCAAGGGCTCATC 57.294 50.000 0.00 0.00 0.00 2.92
4061 4352 3.110705 AGTACACATCTCAAGGGCTCAT 58.889 45.455 0.00 0.00 0.00 2.90
4062 4353 2.540383 AGTACACATCTCAAGGGCTCA 58.460 47.619 0.00 0.00 0.00 4.26
4145 4439 0.899019 GGCGCCTTTCCCCATTAAAA 59.101 50.000 22.15 0.00 0.00 1.52
4182 4476 7.922811 TGCTGTACACTATCTATGAGTTGAATG 59.077 37.037 0.00 0.00 0.00 2.67
4183 4477 8.011844 TGCTGTACACTATCTATGAGTTGAAT 57.988 34.615 0.00 0.00 0.00 2.57
4184 4478 7.404671 TGCTGTACACTATCTATGAGTTGAA 57.595 36.000 0.00 0.00 0.00 2.69
4245 4539 4.338795 TGTCTTCCCCTGTAATCTCTCT 57.661 45.455 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.