Multiple sequence alignment - TraesCS5B01G247800

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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 TraesCS5B01G247800 chr5B 100.000 6982 0 0 1 6982 429818492 429825473 0.000000e+00 12894.0
1 TraesCS5B01G247800 chr5B 93.586 2136 70 27 388 2480 429725837 429727948 0.000000e+00 3123.0
2 TraesCS5B01G247800 chr5B 89.913 1953 173 17 5045 6981 429887370 429889314 0.000000e+00 2494.0
3 TraesCS5B01G247800 chr5B 85.687 1586 122 45 3373 4946 429885877 429887369 0.000000e+00 1574.0
4 TraesCS5B01G247800 chr5B 88.030 1203 103 16 3782 4982 429729338 429730501 0.000000e+00 1386.0
5 TraesCS5B01G247800 chr5B 91.676 853 67 2 5260 6111 429730494 429731343 0.000000e+00 1179.0
6 TraesCS5B01G247800 chr5B 80.869 1704 144 86 280 1865 429881515 429883154 0.000000e+00 1173.0
7 TraesCS5B01G247800 chr5B 94.585 554 22 7 1896 2444 429883151 429883701 0.000000e+00 850.0
8 TraesCS5B01G247800 chr5B 86.964 606 51 13 3 581 429725234 429725838 0.000000e+00 656.0
9 TraesCS5B01G247800 chr5B 84.638 345 41 11 2448 2787 429884026 429884363 4.040000e-87 333.0
10 TraesCS5B01G247800 chr5A 92.103 6547 299 73 3 6448 464632639 464639068 0.000000e+00 9025.0
11 TraesCS5B01G247800 chr5D 91.463 2624 178 35 1642 4254 363975751 363978339 0.000000e+00 3563.0
12 TraesCS5B01G247800 chr5D 89.896 1633 85 27 3 1570 363974130 363975747 0.000000e+00 2028.0
13 TraesCS5B01G247800 chr5D 89.787 1645 80 26 3 1570 363338078 363339711 0.000000e+00 2026.0
14 TraesCS5B01G247800 chr5D 88.089 1612 134 32 3 1579 363175778 363177366 0.000000e+00 1860.0
15 TraesCS5B01G247800 chr5D 93.543 1115 32 17 1642 2736 363339715 363340809 0.000000e+00 1624.0
16 TraesCS5B01G247800 chr5D 93.617 1081 36 21 1639 2707 363177465 363178524 0.000000e+00 1583.0
17 TraesCS5B01G247800 chr5D 88.142 1324 146 9 5260 6579 363343195 363344511 0.000000e+00 1565.0
18 TraesCS5B01G247800 chr5D 90.212 1134 103 7 5260 6389 363181098 363182227 0.000000e+00 1472.0
19 TraesCS5B01G247800 chr5D 88.529 1203 99 11 3781 4982 363179941 363181105 0.000000e+00 1421.0
20 TraesCS5B01G247800 chr5D 89.732 1120 93 8 5264 6380 363979491 363980591 0.000000e+00 1411.0
21 TraesCS5B01G247800 chr5D 87.947 1203 101 11 3781 4982 363342043 363343202 0.000000e+00 1378.0
22 TraesCS5B01G247800 chr5D 83.454 689 85 18 4295 4960 363978766 363979448 1.290000e-171 614.0
23 TraesCS5B01G247800 chr5D 89.686 223 18 5 3565 3786 363341800 363342018 5.330000e-71 279.0
24 TraesCS5B01G247800 chr5D 88.987 227 17 7 3565 3786 363179693 363179916 2.480000e-69 274.0
25 TraesCS5B01G247800 chr5D 77.032 283 51 11 4985 5261 542373618 542373344 4.360000e-32 150.0
26 TraesCS5B01G247800 chr5D 79.487 195 28 4 6385 6579 363187370 363187552 2.040000e-25 128.0
27 TraesCS5B01G247800 chr5D 87.255 102 11 2 3433 3532 363179605 363179706 1.590000e-21 115.0
28 TraesCS5B01G247800 chr6B 81.933 476 80 5 1913 2385 179464122 179464594 1.410000e-106 398.0
29 TraesCS5B01G247800 chr6B 82.432 148 21 3 3122 3269 413272091 413271949 2.640000e-24 124.0
30 TraesCS5B01G247800 chr6A 81.851 281 40 10 4987 5259 605869025 605869302 7.050000e-55 226.0
31 TraesCS5B01G247800 chr6A 89.256 121 9 3 3152 3270 221545052 221544934 1.570000e-31 148.0
32 TraesCS5B01G247800 chr6A 86.923 130 15 2 4989 5116 578940628 578940499 2.030000e-30 145.0
33 TraesCS5B01G247800 chr1B 80.969 289 39 10 4985 5260 664074555 664074840 1.530000e-51 215.0
34 TraesCS5B01G247800 chr7A 80.851 282 40 10 4985 5264 705143291 705143560 7.100000e-50 209.0
35 TraesCS5B01G247800 chr6D 76.240 383 80 11 5495 5870 93528474 93528096 7.150000e-45 193.0
36 TraesCS5B01G247800 chr3A 78.671 286 55 6 4976 5259 20837776 20838057 1.200000e-42 185.0
37 TraesCS5B01G247800 chr3D 85.393 178 15 5 3107 3280 1111445 1111615 2.590000e-39 174.0
38 TraesCS5B01G247800 chr3D 78.814 118 23 2 5146 5262 390048584 390048700 2.090000e-10 78.7
39 TraesCS5B01G247800 chr3D 93.478 46 3 0 5213 5258 590329946 590329991 1.260000e-07 69.4
40 TraesCS5B01G247800 chr3D 80.000 75 15 0 2116 2190 355991369 355991443 1.000000e-03 56.5
41 TraesCS5B01G247800 chr3B 85.366 164 20 1 3107 3270 559885350 559885509 4.330000e-37 167.0
42 TraesCS5B01G247800 chr3B 79.121 91 18 1 2101 2190 457201239 457201329 2.100000e-05 62.1
43 TraesCS5B01G247800 chr4D 82.051 195 25 8 6208 6398 405453289 405453101 2.610000e-34 158.0
44 TraesCS5B01G247800 chr4B 81.707 164 26 1 3107 3270 672393 672234 4.390000e-27 134.0
45 TraesCS5B01G247800 chr4B 94.595 74 3 1 3868 3941 644707689 644707761 5.720000e-21 113.0
46 TraesCS5B01G247800 chr4A 79.275 193 36 4 4985 5174 626956131 626956322 1.580000e-26 132.0
47 TraesCS5B01G247800 chr2B 86.207 116 15 1 3155 3270 777552507 777552393 2.640000e-24 124.0
48 TraesCS5B01G247800 chr2D 84.874 119 18 0 3152 3270 271541095 271540977 3.420000e-23 121.0


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 TraesCS5B01G247800 chr5B 429818492 429825473 6981 False 12894.000000 12894 100.000000 1 6982 1 chr5B.!!$F1 6981
1 TraesCS5B01G247800 chr5B 429725234 429731343 6109 False 1586.000000 3123 90.064000 3 6111 4 chr5B.!!$F2 6108
2 TraesCS5B01G247800 chr5B 429881515 429889314 7799 False 1284.800000 2494 87.138400 280 6981 5 chr5B.!!$F3 6701
3 TraesCS5B01G247800 chr5A 464632639 464639068 6429 False 9025.000000 9025 92.103000 3 6448 1 chr5A.!!$F1 6445
4 TraesCS5B01G247800 chr5D 363974130 363980591 6461 False 1904.000000 3563 88.636250 3 6380 4 chr5D.!!$F4 6377
5 TraesCS5B01G247800 chr5D 363338078 363344511 6433 False 1374.400000 2026 89.821000 3 6579 5 chr5D.!!$F3 6576
6 TraesCS5B01G247800 chr5D 363175778 363182227 6449 False 1120.833333 1860 89.448167 3 6389 6 chr5D.!!$F2 6386

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
874 1221 0.033991 TAAGCAGTCTCGGGCTCTCT 60.034 55.000 0.00 0.00 40.01 3.10 F
887 1234 0.103208 GCTCTCTGTCCATACCACCG 59.897 60.000 0.00 0.00 0.00 4.94 F
925 1272 2.159787 CGACATCACGAGCAAAAGAAGG 60.160 50.000 0.00 0.00 35.09 3.46 F
2070 2536 2.367512 GAGATGGGGCTGGAGGGT 60.368 66.667 0.00 0.00 0.00 4.34 F
2964 4646 2.087857 TTTTCCAACCGGGCATCCCT 62.088 55.000 6.32 0.00 42.67 4.20 F
3920 7342 0.097150 GTCGCGGAGGAGAAAAATGC 59.903 55.000 6.13 0.00 0.00 3.56 F
4487 8339 1.005569 TGTGAGTAGTCCGGACTCCAT 59.994 52.381 39.49 25.71 42.29 3.41 F
5456 9625 0.318441 TGCAGAGGAGTTTCGACCAG 59.682 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 3327 0.385751 ACTAGGGTCGCGATCATGTG 59.614 55.000 22.78 13.93 0.00 3.21 R
2789 4419 3.025322 ACAATTCTGTTGTGGGTGGAA 57.975 42.857 0.00 0.00 28.57 3.53 R
2884 4566 3.638160 ACGGAGGGAACGCATAATTACTA 59.362 43.478 0.00 0.00 34.00 1.82 R
3177 4860 1.134610 GCAAGGATGGCAAATTCCAGG 60.135 52.381 8.26 1.17 39.89 4.45 R
4228 7671 1.083489 TTGATTGAACGGTGGCGATC 58.917 50.000 0.00 5.12 0.00 3.69 R
5387 9556 0.620556 GCACCAGGGAAATCAGGAGA 59.379 55.000 0.00 0.00 0.00 3.71 R
5717 9886 1.341080 CAGCCTGGTTGTTTGGGAAT 58.659 50.000 1.90 0.00 0.00 3.01 R
6513 10703 0.034337 ACTAATGTCGTGGGTTGCGT 59.966 50.000 0.00 0.00 0.00 5.24 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
30 31 0.179124 GACACCAGATCTCGCCACTC 60.179 60.000 0.00 0.00 0.00 3.51
50 51 3.346315 TCCACATGCATGACGAGAAATT 58.654 40.909 32.75 4.13 0.00 1.82
66 67 3.762823 AGAAATTCTAACCTCGTCGTCCT 59.237 43.478 0.00 0.00 0.00 3.85
174 175 1.091771 CGAAGATGAAGCGCCACCAT 61.092 55.000 2.29 4.95 0.00 3.55
181 182 0.599728 GAAGCGCCACCATTGCAAAA 60.600 50.000 1.71 0.00 0.00 2.44
191 192 5.055812 CCACCATTGCAAAAGCTAAAAAGA 58.944 37.500 1.71 0.00 0.00 2.52
276 289 2.696893 GCAGGTAGAGGGGAGGGA 59.303 66.667 0.00 0.00 0.00 4.20
312 352 5.380900 TGAAATTAATGTGGTGTCCAGTGA 58.619 37.500 0.00 0.00 32.34 3.41
474 553 2.031245 TGCAATTTGCTGTTGGTACGAG 60.031 45.455 21.19 0.00 45.31 4.18
548 821 9.825109 GAGTAATAATTTGCTCTAGAGAACCTT 57.175 33.333 24.24 11.03 40.32 3.50
592 865 9.098746 CACACAAACGTAATCATTTTAGTACAC 57.901 33.333 0.00 0.00 0.00 2.90
636 916 1.382522 ATTGCCTAATGGTGTCAGCG 58.617 50.000 0.00 0.00 35.27 5.18
726 1056 4.579340 CGTATACAGGCAGAAGGAACTAGA 59.421 45.833 3.32 0.00 38.49 2.43
730 1060 2.564947 CAGGCAGAAGGAACTAGACACT 59.435 50.000 0.00 0.00 38.49 3.55
767 1099 2.224378 CCAGCTCCTGTGTTCAAAGAGA 60.224 50.000 0.00 0.00 0.00 3.10
768 1100 3.065655 CAGCTCCTGTGTTCAAAGAGAG 58.934 50.000 0.00 0.00 0.00 3.20
791 1129 9.692325 AGAGGCATTCAAGAAAACTTAATCTAT 57.308 29.630 0.00 0.00 0.00 1.98
874 1221 0.033991 TAAGCAGTCTCGGGCTCTCT 60.034 55.000 0.00 0.00 40.01 3.10
876 1223 2.347322 GCAGTCTCGGGCTCTCTGT 61.347 63.158 0.00 0.00 0.00 3.41
887 1234 0.103208 GCTCTCTGTCCATACCACCG 59.897 60.000 0.00 0.00 0.00 4.94
925 1272 2.159787 CGACATCACGAGCAAAAGAAGG 60.160 50.000 0.00 0.00 35.09 3.46
1803 2266 2.483188 GGAACATCGGTAAGCCTAGTGG 60.483 54.545 0.00 0.00 0.00 4.00
2070 2536 2.367512 GAGATGGGGCTGGAGGGT 60.368 66.667 0.00 0.00 0.00 4.34
2367 2833 4.388499 GTCTTCTTCGGCCCCGCA 62.388 66.667 0.00 0.00 39.59 5.69
2454 3246 2.448926 ATACGTGCACAGTGCTGTTA 57.551 45.000 25.83 13.76 45.31 2.41
2465 3257 4.746115 CACAGTGCTGTTAATTGTTGCATT 59.254 37.500 1.57 0.00 42.83 3.56
2502 3327 3.619233 ATGTACGTGTTTGGACTTTGC 57.381 42.857 0.00 0.00 0.00 3.68
2592 3432 7.938140 TGATGTTTAGGGTTTGATCTTTAGG 57.062 36.000 0.00 0.00 0.00 2.69
2593 3433 7.466804 TGATGTTTAGGGTTTGATCTTTAGGT 58.533 34.615 0.00 0.00 0.00 3.08
2594 3434 7.393234 TGATGTTTAGGGTTTGATCTTTAGGTG 59.607 37.037 0.00 0.00 0.00 4.00
2595 3435 6.843752 TGTTTAGGGTTTGATCTTTAGGTGA 58.156 36.000 0.00 0.00 0.00 4.02
2596 3436 6.940298 TGTTTAGGGTTTGATCTTTAGGTGAG 59.060 38.462 0.00 0.00 0.00 3.51
2597 3437 6.945636 TTAGGGTTTGATCTTTAGGTGAGA 57.054 37.500 0.00 0.00 0.00 3.27
2666 3523 3.454858 ACCTATGGGGGTATATCTGCAG 58.545 50.000 7.63 7.63 37.90 4.41
2667 3524 3.181395 ACCTATGGGGGTATATCTGCAGT 60.181 47.826 14.67 3.75 37.90 4.40
2668 3525 3.452627 CCTATGGGGGTATATCTGCAGTC 59.547 52.174 14.67 0.76 0.00 3.51
2809 4439 2.746279 TCCACCCACAACAGAATTGT 57.254 45.000 0.00 0.00 39.87 2.71
2897 4579 3.698029 ACGACGGTAGTAATTATGCGT 57.302 42.857 0.00 0.00 0.00 5.24
2964 4646 2.087857 TTTTCCAACCGGGCATCCCT 62.088 55.000 6.32 0.00 42.67 4.20
2970 4652 2.828549 CCGGGCATCCCTTTTCCG 60.829 66.667 0.00 0.00 42.67 4.30
2983 4665 4.770010 TCCCTTTTCCGTTAATTGCTCAAT 59.230 37.500 0.00 0.00 0.00 2.57
2989 4671 9.405587 CTTTTCCGTTAATTGCTCAATAGAAAA 57.594 29.630 0.00 0.00 0.00 2.29
3129 4812 4.763793 ACTTCAGTTAGCAAGCATGACAAT 59.236 37.500 0.00 0.00 0.00 2.71
3140 4823 3.900941 AGCATGACAATTTTCGTGGTTC 58.099 40.909 11.73 0.00 39.65 3.62
3173 4856 5.396750 TTTTTGATAAAAACTTGCCGTGC 57.603 34.783 0.00 0.00 35.57 5.34
3174 4857 3.717400 TTGATAAAAACTTGCCGTGCA 57.283 38.095 0.00 0.00 36.47 4.57
3177 4860 2.715737 TAAAAACTTGCCGTGCATCC 57.284 45.000 0.00 0.00 38.76 3.51
3272 4956 6.426633 TGACGTGTGACACTTATCATTTGATT 59.573 34.615 14.42 0.00 32.61 2.57
3337 5120 0.253327 GCCCGGAGAACAAGAGGAAT 59.747 55.000 0.73 0.00 0.00 3.01
3371 5154 2.058798 AGAAGCAACATCACGTACGTG 58.941 47.619 36.46 36.46 46.64 4.49
3551 6653 7.363007 GGGAAGCTTACTCCCAAAAAGAATAAG 60.363 40.741 15.95 0.00 43.06 1.73
3656 6758 1.268437 GCGAAGATCTGCTTGCATTCC 60.268 52.381 0.00 0.00 36.83 3.01
3781 6890 4.052159 CGAAGCAAGTCTCCTGATACAT 57.948 45.455 0.00 0.00 0.00 2.29
3782 6891 5.188327 CGAAGCAAGTCTCCTGATACATA 57.812 43.478 0.00 0.00 0.00 2.29
3783 6892 4.979197 CGAAGCAAGTCTCCTGATACATAC 59.021 45.833 0.00 0.00 0.00 2.39
3784 6893 5.450550 CGAAGCAAGTCTCCTGATACATACA 60.451 44.000 0.00 0.00 0.00 2.29
3920 7342 0.097150 GTCGCGGAGGAGAAAAATGC 59.903 55.000 6.13 0.00 0.00 3.56
3924 7346 1.305219 CGGAGGAGAAAAATGCGCCA 61.305 55.000 4.18 0.00 30.73 5.69
4034 7473 5.355596 CATGTGTTCCTATCTTCCTCACTC 58.644 45.833 0.00 0.00 0.00 3.51
4057 7496 3.197983 GCTGGACCTGGATTACTACAGTT 59.802 47.826 0.00 0.00 32.90 3.16
4140 7583 5.697473 TGTTTGTGTGTTTCAGTTCTTCA 57.303 34.783 0.00 0.00 0.00 3.02
4228 7671 1.728971 GGACTTCGACAATGTGAGCAG 59.271 52.381 0.00 0.00 0.00 4.24
4270 7713 8.483758 TCAACAAGGACCTTAATTATCTACTCC 58.516 37.037 6.38 0.00 0.00 3.85
4271 7714 8.487028 CAACAAGGACCTTAATTATCTACTCCT 58.513 37.037 6.38 0.00 0.00 3.69
4333 8181 3.491964 CCATGCGCTCCATCAATTGATTT 60.492 43.478 18.41 0.00 31.21 2.17
4476 8324 1.239296 TACGCGGCACTGTGAGTAGT 61.239 55.000 12.47 8.13 0.00 2.73
4487 8339 1.005569 TGTGAGTAGTCCGGACTCCAT 59.994 52.381 39.49 25.71 42.29 3.41
4527 8379 5.437289 CAGTTGGAGTACTGAATTTTGCA 57.563 39.130 0.00 0.00 46.72 4.08
4531 8383 7.115378 CAGTTGGAGTACTGAATTTTGCAAATC 59.885 37.037 13.65 9.25 46.72 2.17
4541 8393 5.925397 TGAATTTTGCAAATCATAAGCGTGT 59.075 32.000 13.65 0.00 0.00 4.49
4542 8394 7.087007 TGAATTTTGCAAATCATAAGCGTGTA 58.913 30.769 13.65 0.00 0.00 2.90
4543 8395 6.869421 ATTTTGCAAATCATAAGCGTGTAC 57.131 33.333 13.65 0.00 0.00 2.90
4808 8672 3.545124 TAGTTGCCACCGCCACTGG 62.545 63.158 0.00 0.00 40.93 4.00
4817 8681 1.369692 CCGCCACTGGTCACTGTTA 59.630 57.895 0.00 0.00 0.00 2.41
4853 8726 1.477700 TGAATACTTTGCATGCAGGCC 59.522 47.619 22.16 2.73 0.00 5.19
4952 8825 4.398319 ACATGAAGGTGAAGTTTCCGATT 58.602 39.130 0.00 0.00 0.00 3.34
4961 8855 4.274950 GTGAAGTTTCCGATTGAGTTCCAA 59.725 41.667 0.00 0.00 39.41 3.53
4962 8856 4.515191 TGAAGTTTCCGATTGAGTTCCAAG 59.485 41.667 0.00 0.00 38.31 3.61
4967 8861 3.599343 TCCGATTGAGTTCCAAGTCATG 58.401 45.455 0.00 0.00 38.11 3.07
4974 8868 2.731976 GAGTTCCAAGTCATGTCACGTC 59.268 50.000 0.00 0.00 0.00 4.34
4975 8869 2.365617 AGTTCCAAGTCATGTCACGTCT 59.634 45.455 0.00 0.00 0.00 4.18
4976 8870 2.724977 TCCAAGTCATGTCACGTCTC 57.275 50.000 0.00 0.00 0.00 3.36
4977 8871 1.960689 TCCAAGTCATGTCACGTCTCA 59.039 47.619 0.00 0.00 0.00 3.27
4978 8872 2.562738 TCCAAGTCATGTCACGTCTCAT 59.437 45.455 0.00 0.00 0.00 2.90
4979 8873 2.669924 CCAAGTCATGTCACGTCTCATG 59.330 50.000 18.00 18.00 41.64 3.07
4980 8874 3.578688 CAAGTCATGTCACGTCTCATGA 58.421 45.455 20.97 20.97 45.07 3.07
4984 8878 4.660789 TCATGTCACGTCTCATGATGAT 57.339 40.909 20.97 0.00 43.29 2.45
4985 8879 4.365723 TCATGTCACGTCTCATGATGATG 58.634 43.478 20.97 4.48 43.29 3.07
4986 8880 3.169355 TGTCACGTCTCATGATGATGG 57.831 47.619 14.76 0.00 33.61 3.51
4987 8881 2.497273 TGTCACGTCTCATGATGATGGT 59.503 45.455 14.76 0.00 33.61 3.55
4988 8882 3.055891 TGTCACGTCTCATGATGATGGTT 60.056 43.478 14.76 0.00 33.61 3.67
4989 8883 3.935203 GTCACGTCTCATGATGATGGTTT 59.065 43.478 14.76 0.00 33.61 3.27
4990 8884 4.393062 GTCACGTCTCATGATGATGGTTTT 59.607 41.667 14.76 0.00 33.61 2.43
4991 8885 4.631377 TCACGTCTCATGATGATGGTTTTC 59.369 41.667 14.76 0.00 33.61 2.29
4992 8886 4.392754 CACGTCTCATGATGATGGTTTTCA 59.607 41.667 14.76 0.00 33.61 2.69
4993 8887 4.393062 ACGTCTCATGATGATGGTTTTCAC 59.607 41.667 14.76 0.00 33.61 3.18
4994 8888 4.633126 CGTCTCATGATGATGGTTTTCACT 59.367 41.667 0.00 0.00 0.00 3.41
4995 8889 5.122869 CGTCTCATGATGATGGTTTTCACTT 59.877 40.000 0.00 0.00 0.00 3.16
4996 8890 6.348786 CGTCTCATGATGATGGTTTTCACTTT 60.349 38.462 0.00 0.00 0.00 2.66
4997 8891 7.025963 GTCTCATGATGATGGTTTTCACTTTC 58.974 38.462 0.00 0.00 0.00 2.62
4998 8892 6.716173 TCTCATGATGATGGTTTTCACTTTCA 59.284 34.615 0.00 0.00 0.00 2.69
4999 8893 6.916440 TCATGATGATGGTTTTCACTTTCAG 58.084 36.000 0.00 0.00 0.00 3.02
5000 8894 6.491062 TCATGATGATGGTTTTCACTTTCAGT 59.509 34.615 0.00 0.00 0.00 3.41
5027 8921 7.529880 GATTTTGATGAAATCCGCTGAATTT 57.470 32.000 1.07 0.00 45.14 1.82
5028 8922 6.949578 TTTTGATGAAATCCGCTGAATTTC 57.050 33.333 7.83 7.83 44.73 2.17
5029 8923 5.641783 TTGATGAAATCCGCTGAATTTCA 57.358 34.783 15.73 15.73 44.73 2.69
5036 8930 9.603921 ATGAAATCCGCTGAATTTCATTAATTT 57.396 25.926 17.85 4.68 46.65 1.82
5037 8931 9.434420 TGAAATCCGCTGAATTTCATTAATTTT 57.566 25.926 11.62 0.00 38.79 1.82
5040 8934 7.985634 TCCGCTGAATTTCATTAATTTTAGC 57.014 32.000 0.00 4.93 40.08 3.09
5041 8935 7.542890 TCCGCTGAATTTCATTAATTTTAGCA 58.457 30.769 12.27 0.00 41.67 3.49
5042 8936 7.701924 TCCGCTGAATTTCATTAATTTTAGCAG 59.298 33.333 12.27 4.24 41.67 4.24
5043 8937 7.701924 CCGCTGAATTTCATTAATTTTAGCAGA 59.298 33.333 12.27 0.00 41.67 4.26
5069 8964 7.971722 ACACTAAAATATTTATGTTCCGCCAAC 59.028 33.333 0.01 0.00 35.28 3.77
5079 8974 4.223556 TGTTCCGCCAACATATTTAGGA 57.776 40.909 0.00 0.00 40.29 2.94
5085 8980 7.176589 TCCGCCAACATATTTAGGAAATTTT 57.823 32.000 0.00 0.00 32.38 1.82
5086 8981 7.038659 TCCGCCAACATATTTAGGAAATTTTG 58.961 34.615 0.00 0.00 32.38 2.44
5174 9069 7.411486 TTCAAATGAATATTTCGGCCCTTTA 57.589 32.000 0.00 0.00 34.34 1.85
5175 9070 7.595819 TCAAATGAATATTTCGGCCCTTTAT 57.404 32.000 0.00 0.00 34.34 1.40
5176 9071 8.017418 TCAAATGAATATTTCGGCCCTTTATT 57.983 30.769 0.00 0.00 34.34 1.40
5179 9074 5.369833 TGAATATTTCGGCCCTTTATTCGA 58.630 37.500 0.00 0.00 33.83 3.71
5187 9082 4.459685 TCGGCCCTTTATTCGAAATGAAAA 59.540 37.500 0.00 0.30 40.71 2.29
5189 9084 4.868171 GGCCCTTTATTCGAAATGAAAACC 59.132 41.667 0.00 0.00 40.71 3.27
5190 9085 5.474825 GCCCTTTATTCGAAATGAAAACCA 58.525 37.500 0.00 0.00 40.71 3.67
5209 9104 9.528018 GAAAACCAAAATCACTGAAATTGACTA 57.472 29.630 8.16 0.00 0.00 2.59
5226 9121 4.942852 TGACTAATTTTTGGTTGGTGCTG 58.057 39.130 0.00 0.00 0.00 4.41
5230 9125 6.591001 ACTAATTTTTGGTTGGTGCTGAAAT 58.409 32.000 0.00 0.00 0.00 2.17
5231 9126 7.053498 ACTAATTTTTGGTTGGTGCTGAAATT 58.947 30.769 0.00 0.00 0.00 1.82
5232 9127 6.772360 AATTTTTGGTTGGTGCTGAAATTT 57.228 29.167 0.00 0.00 0.00 1.82
5242 9137 8.282592 GGTTGGTGCTGAAATTTTTCTAAAATC 58.717 33.333 4.80 0.00 38.02 2.17
5243 9138 8.825745 GTTGGTGCTGAAATTTTTCTAAAATCA 58.174 29.630 4.80 0.00 38.02 2.57
5294 9463 7.358066 GTTGATCTGATGTGCTTTATGTATGG 58.642 38.462 0.00 0.00 0.00 2.74
5456 9625 0.318441 TGCAGAGGAGTTTCGACCAG 59.682 55.000 0.00 0.00 0.00 4.00
5642 9811 3.636231 CCCAAGCCGGTGTGGAGA 61.636 66.667 22.89 0.00 42.00 3.71
5717 9886 1.371183 CGAGTTCCTTGGCCTCACA 59.629 57.895 3.32 0.00 0.00 3.58
5773 9942 0.749649 ACTGGCGATGAGATCCTCAC 59.250 55.000 0.00 0.00 43.63 3.51
5906 10075 0.706433 AGGTGAAGCCCATGGTGAAT 59.294 50.000 11.73 0.00 38.26 2.57
5946 10115 4.002506 AGCCGTCGGTGCACATCA 62.003 61.111 20.43 0.00 0.00 3.07
5987 10156 0.682209 ATGGAGCAATGTGAGGCCAC 60.682 55.000 5.01 0.00 43.46 5.01
6006 10175 5.533903 GGCCACAGAGATCATCACAATTATT 59.466 40.000 0.00 0.00 0.00 1.40
6007 10176 6.040166 GGCCACAGAGATCATCACAATTATTT 59.960 38.462 0.00 0.00 0.00 1.40
6008 10177 7.137426 GCCACAGAGATCATCACAATTATTTC 58.863 38.462 0.00 0.00 0.00 2.17
6058 10241 1.663695 ACTGTAGTGTTGCAGCGTTT 58.336 45.000 0.00 0.00 40.30 3.60
6061 10244 1.740585 TGTAGTGTTGCAGCGTTTTGT 59.259 42.857 0.00 0.00 0.00 2.83
6075 10258 6.347079 GCAGCGTTTTGTAGTGTATGTAAAGA 60.347 38.462 0.00 0.00 0.00 2.52
6077 10260 6.702723 AGCGTTTTGTAGTGTATGTAAAGACA 59.297 34.615 0.00 0.00 40.72 3.41
6161 10346 4.952460 TGTAATTAGTTCATAGGCCGGTC 58.048 43.478 0.00 0.00 0.00 4.79
6175 10360 1.539827 GCCGGTCATAAGCAGTTTGTT 59.460 47.619 1.90 0.00 0.00 2.83
6287 10476 6.156949 AGTTCCTATTAAGGCATCAGTCTCAA 59.843 38.462 0.00 0.00 43.31 3.02
6314 10503 1.045407 TGACAGGTTTACGAGCACCT 58.955 50.000 0.00 0.00 44.88 4.00
6315 10504 1.000506 TGACAGGTTTACGAGCACCTC 59.999 52.381 0.00 0.00 41.86 3.85
6316 10505 1.272769 GACAGGTTTACGAGCACCTCT 59.727 52.381 0.00 0.00 41.86 3.69
6317 10506 2.490903 GACAGGTTTACGAGCACCTCTA 59.509 50.000 0.00 0.00 41.86 2.43
6319 10508 3.056749 ACAGGTTTACGAGCACCTCTAAG 60.057 47.826 0.00 0.00 41.86 2.18
6458 10648 4.904895 ACATATCTCCAGGGTCATCATG 57.095 45.455 0.00 0.00 0.00 3.07
6507 10697 2.083002 GCCTCTCCTTTTGCTGAAGAG 58.917 52.381 1.84 0.00 0.00 2.85
6510 10700 3.940221 CCTCTCCTTTTGCTGAAGAGATG 59.060 47.826 0.00 0.00 0.00 2.90
6513 10703 4.529769 TCTCCTTTTGCTGAAGAGATGAGA 59.470 41.667 1.84 0.00 0.00 3.27
6515 10705 3.370366 CCTTTTGCTGAAGAGATGAGACG 59.630 47.826 1.84 0.00 0.00 4.18
6524 10714 1.078759 GAGATGAGACGCAACCCACG 61.079 60.000 0.00 0.00 0.00 4.94
6555 10745 1.212934 ACCCGTCTGGAGACTCCCTA 61.213 60.000 19.11 3.88 42.66 3.53
6601 10791 1.067846 CGTCGAACTCAATGTCCTCCA 60.068 52.381 0.00 0.00 0.00 3.86
6604 10794 1.726791 CGAACTCAATGTCCTCCAACG 59.273 52.381 0.00 0.00 0.00 4.10
6605 10795 2.609491 CGAACTCAATGTCCTCCAACGA 60.609 50.000 0.00 0.00 0.00 3.85
6625 10815 0.812014 TGGCGATGACGTTGTTGTGT 60.812 50.000 0.00 0.00 41.98 3.72
6626 10816 0.110823 GGCGATGACGTTGTTGTGTC 60.111 55.000 0.00 0.00 41.98 3.67
6650 10840 4.309950 GGCGACGACCCTGGTTGT 62.310 66.667 8.99 8.99 44.68 3.32
6654 10844 1.530013 CGACGACCCTGGTTGTAGGT 61.530 60.000 9.21 0.00 42.31 3.08
6666 10856 1.695788 GTTGTAGGTGGTGTAGGGTGT 59.304 52.381 0.00 0.00 0.00 4.16
6682 10872 1.998438 TGTGGGCCACGGGATACAT 60.998 57.895 30.14 0.00 37.14 2.29
6684 10874 1.690985 TGGGCCACGGGATACATCA 60.691 57.895 0.00 0.00 39.74 3.07
6686 10876 0.110486 GGGCCACGGGATACATCATT 59.890 55.000 4.39 0.00 39.74 2.57
6697 10887 2.346766 TACATCATTGGCGGCAAGAT 57.653 45.000 28.83 24.82 0.00 2.40
6771 10961 1.671054 CGTCGTGGGTGGCAAAGAT 60.671 57.895 0.00 0.00 0.00 2.40
6787 10977 0.835941 AGATGCTAGAAGCTGGGTGG 59.164 55.000 0.00 0.00 42.97 4.61
6809 10999 2.816012 GGCTAGGGCGAAGAGGTC 59.184 66.667 0.00 0.00 39.81 3.85
6819 11009 2.362632 AAGAGGTCGGGGAGGTCG 60.363 66.667 0.00 0.00 0.00 4.79
6837 11027 1.063567 TCGAAATTAATGGGGTGGGGG 60.064 52.381 0.00 0.00 0.00 5.40
6838 11028 1.063567 CGAAATTAATGGGGTGGGGGA 60.064 52.381 0.00 0.00 0.00 4.81
6839 11029 2.624557 CGAAATTAATGGGGTGGGGGAA 60.625 50.000 0.00 0.00 0.00 3.97
6861 11051 5.667539 ATACTAGCTTGTATGCCATCGAT 57.332 39.130 18.26 0.00 32.51 3.59
6863 11053 2.916702 AGCTTGTATGCCATCGATGA 57.083 45.000 26.86 8.19 0.00 2.92
6865 11055 1.196354 GCTTGTATGCCATCGATGAGC 59.804 52.381 26.86 25.00 0.00 4.26
6880 11070 0.249398 TGAGCGAGCTAGGGGAAAAC 59.751 55.000 0.00 0.00 0.00 2.43
6889 11079 2.171003 CTAGGGGAAAACAAAGGCTGG 58.829 52.381 0.00 0.00 0.00 4.85
6894 11084 2.483013 GGGAAAACAAAGGCTGGACAAC 60.483 50.000 0.00 0.00 0.00 3.32
6897 11087 4.038642 GGAAAACAAAGGCTGGACAACATA 59.961 41.667 0.00 0.00 0.00 2.29
6898 11088 5.452636 GGAAAACAAAGGCTGGACAACATAA 60.453 40.000 0.00 0.00 0.00 1.90
6903 11093 2.102578 AGGCTGGACAACATAAATGCC 58.897 47.619 0.00 0.00 39.40 4.40
6904 11094 1.136891 GGCTGGACAACATAAATGCCC 59.863 52.381 0.00 0.00 33.66 5.36
6943 11133 5.124776 CGGACACAAATCTAGCCCAAATTTA 59.875 40.000 0.00 0.00 0.00 1.40
6949 11139 8.667463 CACAAATCTAGCCCAAATTTAAATTGG 58.333 33.333 14.04 15.48 45.62 3.16
6968 11158 1.643880 GAAATGGGCAAAAGCGGATG 58.356 50.000 0.00 0.00 0.00 3.51
6981 11171 1.283736 GCGGATGTCGGTTCGTTTAT 58.716 50.000 0.00 0.00 39.69 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.376234 AGAATTTCTCGTCATGCATGTGG 59.624 43.478 25.43 17.88 0.00 4.17
50 51 2.237143 TCCTTAGGACGACGAGGTTAGA 59.763 50.000 0.00 0.00 0.00 2.10
66 67 7.712639 GCAATGTAGATTCTTGTCATCTCCTTA 59.287 37.037 0.00 0.00 32.94 2.69
191 192 7.398332 TGGCTTTAGCTAGTAGTTTAGGTTAGT 59.602 37.037 1.26 0.00 41.70 2.24
257 270 2.446802 CCTCCCCTCTACCTGCCC 60.447 72.222 0.00 0.00 0.00 5.36
474 553 8.437742 CACTGGAAATGCACATTTAAAGAAATC 58.562 33.333 17.75 3.04 40.77 2.17
548 821 2.954989 TGTGCTTTCATTGCTTGGTACA 59.045 40.909 0.00 0.00 0.00 2.90
592 865 2.328099 GCCGAAGCAGTGGTTCTGG 61.328 63.158 27.39 27.24 43.78 3.86
726 1056 1.057851 TCAAAGGGGAACGGGAGTGT 61.058 55.000 0.00 0.00 46.69 3.55
730 1060 1.770927 TGGTCAAAGGGGAACGGGA 60.771 57.895 0.00 0.00 0.00 5.14
767 1099 9.247861 ACATAGATTAAGTTTTCTTGAATGCCT 57.752 29.630 0.00 0.00 40.70 4.75
768 1100 9.860898 AACATAGATTAAGTTTTCTTGAATGCC 57.139 29.630 0.00 0.00 40.70 4.40
874 1221 0.036765 GCAGAACGGTGGTATGGACA 60.037 55.000 0.00 0.00 0.00 4.02
876 1223 0.249120 CTGCAGAACGGTGGTATGGA 59.751 55.000 8.42 0.00 0.00 3.41
925 1272 0.034477 CTGGGTGGTGGTATGGGTTC 60.034 60.000 0.00 0.00 0.00 3.62
1803 2266 3.159472 TGAAATAGCCCATCCATGCATC 58.841 45.455 0.00 0.00 0.00 3.91
2465 3257 5.712217 GTACATACGATAGCAACAGCAAA 57.288 39.130 0.00 0.00 42.67 3.68
2502 3327 0.385751 ACTAGGGTCGCGATCATGTG 59.614 55.000 22.78 13.93 0.00 3.21
2666 3523 6.375945 AAATTTTGGCTGAAATGTTTGGAC 57.624 33.333 1.24 0.00 30.06 4.02
2667 3524 6.600822 TCAAAATTTTGGCTGAAATGTTTGGA 59.399 30.769 26.45 2.94 38.66 3.53
2668 3525 6.793349 TCAAAATTTTGGCTGAAATGTTTGG 58.207 32.000 26.45 0.07 38.66 3.28
2789 4419 3.025322 ACAATTCTGTTGTGGGTGGAA 57.975 42.857 0.00 0.00 28.57 3.53
2884 4566 3.638160 ACGGAGGGAACGCATAATTACTA 59.362 43.478 0.00 0.00 34.00 1.82
2964 4646 9.751542 TTTTTCTATTGAGCAATTAACGGAAAA 57.248 25.926 0.52 8.13 32.50 2.29
3158 4841 1.271102 GGGATGCACGGCAAGTTTTTA 59.729 47.619 2.68 0.00 43.62 1.52
3173 4856 1.690352 GGATGGCAAATTCCAGGGATG 59.310 52.381 0.70 0.00 39.89 3.51
3174 4857 1.577242 AGGATGGCAAATTCCAGGGAT 59.423 47.619 8.26 0.00 39.89 3.85
3177 4860 1.134610 GCAAGGATGGCAAATTCCAGG 60.135 52.381 8.26 1.17 39.89 4.45
3301 5084 3.000727 CGGGCGAACTCTAGTCATTTTT 58.999 45.455 0.00 0.00 0.00 1.94
3371 5154 1.728971 CGTGATCTGTCTTTCCACAGC 59.271 52.381 0.00 0.00 43.18 4.40
3430 6494 2.623502 GCTCCTAGTCCCTACCAGTGAA 60.624 54.545 0.00 0.00 0.00 3.18
3551 6653 2.384382 CAGCCAAACGTGTGTGATTTC 58.616 47.619 4.73 0.00 0.00 2.17
3904 7321 1.226407 GCGCATTTTTCTCCTCCGC 60.226 57.895 0.30 0.00 0.00 5.54
3945 7372 6.295719 ACCATTTCTTCAGTTATCTACCGT 57.704 37.500 0.00 0.00 0.00 4.83
3946 7373 8.765219 CAATACCATTTCTTCAGTTATCTACCG 58.235 37.037 0.00 0.00 0.00 4.02
3947 7374 8.560374 GCAATACCATTTCTTCAGTTATCTACC 58.440 37.037 0.00 0.00 0.00 3.18
3948 7375 9.331282 AGCAATACCATTTCTTCAGTTATCTAC 57.669 33.333 0.00 0.00 0.00 2.59
3999 7436 2.095059 GGAACACATGGCATGTCTGAAC 60.095 50.000 29.32 17.59 42.70 3.18
4034 7473 1.754803 TGTAGTAATCCAGGTCCAGCG 59.245 52.381 0.00 0.00 0.00 5.18
4125 7564 5.030936 GCTCAAAGTGAAGAACTGAAACAC 58.969 41.667 0.00 0.00 39.81 3.32
4140 7583 1.318576 CAAGGAAACCCGCTCAAAGT 58.681 50.000 0.00 0.00 0.00 2.66
4228 7671 1.083489 TTGATTGAACGGTGGCGATC 58.917 50.000 0.00 5.12 0.00 3.69
4268 7711 9.928618 CCAAGAGGACTTCAGATATATATAGGA 57.071 37.037 0.00 0.00 36.89 2.94
4269 7712 9.707957 ACCAAGAGGACTTCAGATATATATAGG 57.292 37.037 0.00 0.00 38.69 2.57
4274 7717 7.921041 TTCACCAAGAGGACTTCAGATATAT 57.079 36.000 0.00 0.00 38.69 0.86
4285 7728 4.957327 AGGAGTACTATTCACCAAGAGGAC 59.043 45.833 0.00 0.00 35.18 3.85
4288 7731 6.380274 TGGTTAGGAGTACTATTCACCAAGAG 59.620 42.308 12.07 0.00 37.22 2.85
4333 8181 1.769026 CCTTCCTCGATGTCCTGAGA 58.231 55.000 0.00 0.00 34.04 3.27
4392 8240 1.116536 TGTAGGAGACCACCAACGCA 61.117 55.000 0.00 0.00 0.00 5.24
4396 8244 3.256704 AGGATTTGTAGGAGACCACCAA 58.743 45.455 0.00 0.00 0.00 3.67
4476 8324 3.262151 TCAAAATGTACATGGAGTCCGGA 59.738 43.478 9.63 0.00 0.00 5.14
4527 8379 5.233476 CCACATACGTACACGCTTATGATTT 59.767 40.000 15.25 0.00 44.43 2.17
4531 8383 3.441163 ACCACATACGTACACGCTTATG 58.559 45.455 0.00 6.30 44.43 1.90
4541 8393 3.997681 CCACATGACAAACCACATACGTA 59.002 43.478 0.00 0.00 0.00 3.57
4542 8394 2.811431 CCACATGACAAACCACATACGT 59.189 45.455 0.00 0.00 0.00 3.57
4543 8395 2.811431 ACCACATGACAAACCACATACG 59.189 45.455 0.00 0.00 0.00 3.06
4808 8672 6.795098 TCACATGGTTAACATAACAGTGAC 57.205 37.500 8.10 0.00 37.84 3.67
4817 8681 9.859427 CAAAGTATTCAATCACATGGTTAACAT 57.141 29.630 8.10 0.00 41.57 2.71
4952 8825 2.102420 ACGTGACATGACTTGGAACTCA 59.898 45.455 0.00 0.00 0.00 3.41
4967 8861 3.170791 ACCATCATCATGAGACGTGAC 57.829 47.619 0.09 0.00 30.57 3.67
4974 8868 6.916440 TGAAAGTGAAAACCATCATCATGAG 58.084 36.000 0.09 0.00 30.57 2.90
4975 8869 6.897706 TGAAAGTGAAAACCATCATCATGA 57.102 33.333 0.00 0.00 30.57 3.07
5004 8898 7.098477 TGAAATTCAGCGGATTTCATCAAAAT 58.902 30.769 16.20 0.00 38.79 1.82
5005 8899 6.453943 TGAAATTCAGCGGATTTCATCAAAA 58.546 32.000 16.20 0.01 38.79 2.44
5006 8900 6.023357 TGAAATTCAGCGGATTTCATCAAA 57.977 33.333 16.20 0.53 38.79 2.69
5007 8901 5.641783 TGAAATTCAGCGGATTTCATCAA 57.358 34.783 16.20 0.80 38.79 2.57
5008 8902 5.840243 ATGAAATTCAGCGGATTTCATCA 57.160 34.783 21.81 12.24 46.14 3.07
5011 8905 9.434420 AAAATTAATGAAATTCAGCGGATTTCA 57.566 25.926 20.02 20.02 44.93 2.69
5014 8908 9.034544 GCTAAAATTAATGAAATTCAGCGGATT 57.965 29.630 1.10 0.00 36.76 3.01
5015 8909 8.196771 TGCTAAAATTAATGAAATTCAGCGGAT 58.803 29.630 1.10 0.00 42.71 4.18
5016 8910 7.542890 TGCTAAAATTAATGAAATTCAGCGGA 58.457 30.769 1.10 0.00 42.71 5.54
5017 8911 7.701924 TCTGCTAAAATTAATGAAATTCAGCGG 59.298 33.333 1.10 14.03 44.21 5.52
5018 8912 8.526681 GTCTGCTAAAATTAATGAAATTCAGCG 58.473 33.333 1.10 0.00 42.71 5.18
5019 8913 9.357652 TGTCTGCTAAAATTAATGAAATTCAGC 57.642 29.630 1.10 0.00 41.49 4.26
5038 8932 8.612619 CGGAACATAAATATTTTAGTGTCTGCT 58.387 33.333 5.91 0.00 0.00 4.24
5039 8933 7.376072 GCGGAACATAAATATTTTAGTGTCTGC 59.624 37.037 5.91 15.07 0.00 4.26
5040 8934 7.855904 GGCGGAACATAAATATTTTAGTGTCTG 59.144 37.037 5.91 10.73 0.00 3.51
5041 8935 7.554835 TGGCGGAACATAAATATTTTAGTGTCT 59.445 33.333 5.91 2.12 0.00 3.41
5042 8936 7.699566 TGGCGGAACATAAATATTTTAGTGTC 58.300 34.615 5.91 6.29 0.00 3.67
5043 8937 7.633193 TGGCGGAACATAAATATTTTAGTGT 57.367 32.000 5.91 6.84 0.00 3.55
5063 8958 6.816140 ACCAAAATTTCCTAAATATGTTGGCG 59.184 34.615 15.42 0.00 39.07 5.69
5155 9050 6.001460 TCGAATAAAGGGCCGAAATATTCAT 58.999 36.000 21.91 0.00 34.27 2.57
5174 9069 7.925483 TCAGTGATTTTGGTTTTCATTTCGAAT 59.075 29.630 0.00 0.00 32.32 3.34
5175 9070 7.261325 TCAGTGATTTTGGTTTTCATTTCGAA 58.739 30.769 0.00 0.00 0.00 3.71
5176 9071 6.800543 TCAGTGATTTTGGTTTTCATTTCGA 58.199 32.000 0.00 0.00 0.00 3.71
5205 9100 5.195001 TCAGCACCAACCAAAAATTAGTC 57.805 39.130 0.00 0.00 0.00 2.59
5209 9104 6.772360 AAATTTCAGCACCAACCAAAAATT 57.228 29.167 0.00 0.00 0.00 1.82
5214 9109 5.096443 AGAAAAATTTCAGCACCAACCAA 57.904 34.783 8.47 0.00 39.61 3.67
5215 9110 4.751767 AGAAAAATTTCAGCACCAACCA 57.248 36.364 8.47 0.00 39.61 3.67
5218 9113 8.954950 TGATTTTAGAAAAATTTCAGCACCAA 57.045 26.923 8.47 0.00 39.61 3.67
5242 9137 4.744137 TCGTGAGCATGGTTTTCAATTTTG 59.256 37.500 0.00 0.00 0.00 2.44
5243 9138 4.942852 TCGTGAGCATGGTTTTCAATTTT 58.057 34.783 0.00 0.00 0.00 1.82
5294 9463 2.223572 CCTTCCAAATATCTGCGTTGGC 60.224 50.000 0.00 0.00 41.38 4.52
5381 9550 3.718956 CCAGGGAAATCAGGAGAAGGTAT 59.281 47.826 0.00 0.00 0.00 2.73
5387 9556 0.620556 GCACCAGGGAAATCAGGAGA 59.379 55.000 0.00 0.00 0.00 3.71
5456 9625 1.352156 CCAGTGCGAAGTAGGCGAAC 61.352 60.000 0.00 0.00 37.57 3.95
5642 9811 2.565834 GGCGACATAGTACATGGGGTAT 59.434 50.000 0.00 0.00 33.76 2.73
5717 9886 1.341080 CAGCCTGGTTGTTTGGGAAT 58.659 50.000 1.90 0.00 0.00 3.01
5773 9942 1.949847 CTCCACCTGCCAGTAGTCCG 61.950 65.000 0.00 0.00 0.00 4.79
5906 10075 2.596851 GCTCCTGAACCTGAGCCCA 61.597 63.158 0.08 0.00 46.50 5.36
5946 10115 2.058675 CTTCAGAACCCTGGTCGGT 58.941 57.895 0.00 0.00 40.76 4.69
6006 10175 8.677148 AGCAACAATTCTCTACTAACAAAGAA 57.323 30.769 0.00 0.00 32.69 2.52
6007 10176 8.677148 AAGCAACAATTCTCTACTAACAAAGA 57.323 30.769 0.00 0.00 0.00 2.52
6022 10205 7.878127 ACACTACAGTACTCATAAGCAACAATT 59.122 33.333 0.00 0.00 0.00 2.32
6058 10241 8.439993 TTTTGCTGTCTTTACATACACTACAA 57.560 30.769 0.00 0.00 34.37 2.41
6161 10346 7.905126 TCGTGTATATCAACAAACTGCTTATG 58.095 34.615 0.00 0.00 0.00 1.90
6211 10400 5.928264 CAGAAAAATGAAAATCAGGGGTGAC 59.072 40.000 0.00 0.00 0.00 3.67
6212 10401 5.837979 TCAGAAAAATGAAAATCAGGGGTGA 59.162 36.000 0.00 0.00 0.00 4.02
6213 10402 6.100404 TCAGAAAAATGAAAATCAGGGGTG 57.900 37.500 0.00 0.00 0.00 4.61
6214 10403 6.745794 TTCAGAAAAATGAAAATCAGGGGT 57.254 33.333 0.00 0.00 36.28 4.95
6314 10503 5.802465 TGGTAGACGTCTCTTCTTCTTAGA 58.198 41.667 23.89 0.00 0.00 2.10
6315 10504 6.497785 TTGGTAGACGTCTCTTCTTCTTAG 57.502 41.667 23.89 0.00 0.00 2.18
6316 10505 5.106237 GCTTGGTAGACGTCTCTTCTTCTTA 60.106 44.000 23.89 0.00 0.00 2.10
6317 10506 4.321378 GCTTGGTAGACGTCTCTTCTTCTT 60.321 45.833 23.89 0.00 0.00 2.52
6319 10508 3.057456 TGCTTGGTAGACGTCTCTTCTTC 60.057 47.826 23.89 9.36 0.00 2.87
6413 10603 8.478877 TGTTGTTGTGGTTTTAGATAATGGTTT 58.521 29.630 0.00 0.00 0.00 3.27
6458 10648 1.471287 TGTGATGCTCAAGATTGCTGC 59.529 47.619 0.00 0.00 0.00 5.25
6507 10697 1.080093 TCGTGGGTTGCGTCTCATC 60.080 57.895 0.00 0.00 0.00 2.92
6510 10700 0.949105 AATGTCGTGGGTTGCGTCTC 60.949 55.000 0.00 0.00 0.00 3.36
6513 10703 0.034337 ACTAATGTCGTGGGTTGCGT 59.966 50.000 0.00 0.00 0.00 5.24
6524 10714 3.698040 TCCAGACGGGTAAGACTAATGTC 59.302 47.826 0.00 0.00 39.61 3.06
6585 10775 3.040147 TCGTTGGAGGACATTGAGTTC 57.960 47.619 0.00 0.00 0.00 3.01
6601 10791 0.669318 ACAACGTCATCGCCATCGTT 60.669 50.000 0.00 0.00 45.16 3.85
6604 10794 0.796312 ACAACAACGTCATCGCCATC 59.204 50.000 0.00 0.00 41.18 3.51
6605 10795 0.516877 CACAACAACGTCATCGCCAT 59.483 50.000 0.00 0.00 41.18 4.40
6611 10801 1.497991 CCTCGACACAACAACGTCAT 58.502 50.000 0.00 0.00 32.24 3.06
6638 10828 1.295423 CCACCTACAACCAGGGTCG 59.705 63.158 0.00 0.00 40.29 4.79
6645 10835 1.002773 CACCCTACACCACCTACAACC 59.997 57.143 0.00 0.00 0.00 3.77
6650 10840 0.545787 CCCACACCCTACACCACCTA 60.546 60.000 0.00 0.00 0.00 3.08
6654 10844 3.253838 GGCCCACACCCTACACCA 61.254 66.667 0.00 0.00 0.00 4.17
6666 10856 1.059584 ATGATGTATCCCGTGGCCCA 61.060 55.000 0.00 0.00 0.00 5.36
6677 10867 2.346766 TCTTGCCGCCAATGATGTAT 57.653 45.000 0.00 0.00 0.00 2.29
6682 10872 1.314534 CCACATCTTGCCGCCAATGA 61.315 55.000 4.32 0.00 0.00 2.57
6684 10874 0.611618 TTCCACATCTTGCCGCCAAT 60.612 50.000 0.00 0.00 0.00 3.16
6686 10876 1.228398 TTTCCACATCTTGCCGCCA 60.228 52.632 0.00 0.00 0.00 5.69
6697 10887 3.587933 GCCGGCGTTGTTTCCACA 61.588 61.111 12.58 0.00 0.00 4.17
6755 10945 1.971167 GCATCTTTGCCACCCACGA 60.971 57.895 0.00 0.00 43.38 4.35
6771 10961 1.679311 CACCACCCAGCTTCTAGCA 59.321 57.895 1.09 0.00 45.56 3.49
6773 10963 1.078143 GCCACCACCCAGCTTCTAG 60.078 63.158 0.00 0.00 0.00 2.43
6774 10964 2.954684 CGCCACCACCCAGCTTCTA 61.955 63.158 0.00 0.00 0.00 2.10
6809 10999 2.218603 CCATTAATTTCGACCTCCCCG 58.781 52.381 0.00 0.00 0.00 5.73
6819 11009 2.858787 TCCCCCACCCCATTAATTTC 57.141 50.000 0.00 0.00 0.00 2.17
6837 11027 5.470368 TCGATGGCATACAAGCTAGTATTC 58.530 41.667 0.00 0.00 32.56 1.75
6838 11028 5.468540 TCGATGGCATACAAGCTAGTATT 57.531 39.130 0.00 0.00 32.56 1.89
6839 11029 5.185828 TCATCGATGGCATACAAGCTAGTAT 59.814 40.000 24.61 0.00 35.14 2.12
6861 11051 0.249398 GTTTTCCCCTAGCTCGCTCA 59.751 55.000 0.00 0.00 0.00 4.26
6863 11053 0.690762 TTGTTTTCCCCTAGCTCGCT 59.309 50.000 0.00 0.00 0.00 4.93
6865 11055 2.084546 CCTTTGTTTTCCCCTAGCTCG 58.915 52.381 0.00 0.00 0.00 5.03
6873 11063 1.408969 TGTCCAGCCTTTGTTTTCCC 58.591 50.000 0.00 0.00 0.00 3.97
6880 11070 3.928375 GCATTTATGTTGTCCAGCCTTTG 59.072 43.478 0.00 0.00 0.00 2.77
6889 11079 2.559998 CCACGGGCATTTATGTTGTC 57.440 50.000 0.00 0.00 0.00 3.18
6928 11118 9.617523 CATTTCCAATTTAAATTTGGGCTAGAT 57.382 29.630 20.12 8.10 0.00 1.98
6943 11133 2.813172 CGCTTTTGCCCATTTCCAATTT 59.187 40.909 0.00 0.00 43.93 1.82
6949 11139 1.066929 ACATCCGCTTTTGCCCATTTC 60.067 47.619 0.00 0.00 43.93 2.17
6951 11141 0.532115 GACATCCGCTTTTGCCCATT 59.468 50.000 0.00 0.00 43.93 3.16
6957 11147 0.179225 CGAACCGACATCCGCTTTTG 60.179 55.000 0.00 0.00 36.84 2.44


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

AutoCloner maintained by Alex Coulton.