Multiple sequence alignment - TraesCS4B01G201200

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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 TraesCS4B01G201200 chr4B 100.000 7669 0 0 1 7669 429100523 429092855 0.000000e+00 14163.0
1 TraesCS4B01G201200 chr3B 96.720 3079 68 8 2359 5424 581334590 581337648 0.000000e+00 5096.0
2 TraesCS4B01G201200 chr3B 96.842 2248 64 5 5426 7669 581339090 581341334 0.000000e+00 3751.0
3 TraesCS4B01G201200 chr3B 95.122 1394 50 6 814 2195 581333152 581334539 0.000000e+00 2182.0
4 TraesCS4B01G201200 chr3B 83.850 452 67 4 2049 2496 597821510 597821061 7.110000e-115 425.0
5 TraesCS4B01G201200 chr3B 97.345 113 3 0 7018 7130 581344530 581344418 7.850000e-45 193.0
6 TraesCS4B01G201200 chr3B 90.278 72 7 0 610 681 79886313 79886242 2.280000e-15 95.3
7 TraesCS4B01G201200 chr3B 90.411 73 5 2 610 681 402977391 402977462 2.280000e-15 95.3
8 TraesCS4B01G201200 chr3B 90.141 71 7 0 611 681 168191019 168190949 8.190000e-15 93.5
9 TraesCS4B01G201200 chr4A 95.815 2891 86 14 2550 5424 115911573 115914444 0.000000e+00 4636.0
10 TraesCS4B01G201200 chr4A 95.947 1283 32 8 6185 7464 115916856 115918121 0.000000e+00 2063.0
11 TraesCS4B01G201200 chr4A 91.764 1202 61 15 814 1982 115910284 115911480 0.000000e+00 1637.0
12 TraesCS4B01G201200 chr4A 97.641 763 17 1 5426 6187 115915853 115916615 0.000000e+00 1308.0
13 TraesCS4B01G201200 chr4A 95.732 164 7 0 7506 7669 115918533 115918696 1.640000e-66 265.0
14 TraesCS4B01G201200 chr4D 95.202 2897 78 15 2544 5424 349014374 349011523 0.000000e+00 4523.0
15 TraesCS4B01G201200 chr4D 97.777 2249 37 7 5426 7669 349010081 349007841 0.000000e+00 3864.0
16 TraesCS4B01G201200 chr4D 92.794 1138 49 12 820 1929 349016895 349015763 0.000000e+00 1616.0
17 TraesCS4B01G201200 chr4D 86.300 854 60 23 1 823 349017755 349016928 0.000000e+00 876.0
18 TraesCS4B01G201200 chr4D 93.711 159 8 2 2359 2516 34816416 34816573 3.580000e-58 237.0
19 TraesCS4B01G201200 chr4D 92.857 112 7 1 1928 2038 349014508 349014397 2.210000e-35 161.0
20 TraesCS4B01G201200 chr6A 96.152 2573 68 13 2518 5083 466322691 466325239 0.000000e+00 4174.0
21 TraesCS4B01G201200 chr6A 94.937 1837 57 6 5866 7669 466328232 466330065 0.000000e+00 2844.0
22 TraesCS4B01G201200 chr6A 95.570 1264 44 7 4166 5424 466336981 466338237 0.000000e+00 2013.0
23 TraesCS4B01G201200 chr6A 95.686 1020 40 4 6653 7669 466343451 466344469 0.000000e+00 1637.0
24 TraesCS4B01G201200 chr6A 95.388 1019 39 5 6658 7669 466361478 466362495 0.000000e+00 1615.0
25 TraesCS4B01G201200 chr6A 95.976 994 36 2 5426 6415 466339681 466340674 0.000000e+00 1611.0
26 TraesCS4B01G201200 chr6A 93.452 1008 40 10 6663 7669 466348302 466349284 0.000000e+00 1472.0
27 TraesCS4B01G201200 chr6A 91.032 1037 37 26 6663 7669 466356665 466357675 0.000000e+00 1349.0
28 TraesCS4B01G201200 chr6A 89.147 645 49 14 1 630 466219703 466220341 0.000000e+00 784.0
29 TraesCS4B01G201200 chr6A 99.020 408 4 0 5426 5833 466327826 466328233 0.000000e+00 732.0
30 TraesCS4B01G201200 chr6A 96.865 319 9 1 5106 5424 466325645 466325962 4.070000e-147 532.0
31 TraesCS4B01G201200 chr6A 90.461 304 22 5 1738 2038 466322384 466322683 2.010000e-105 394.0
32 TraesCS4B01G201200 chr6A 90.947 243 14 3 840 1078 466295124 466295362 3.450000e-83 320.0
33 TraesCS4B01G201200 chr6A 92.169 166 11 2 2351 2515 454803435 454803271 4.630000e-57 233.0
34 TraesCS4B01G201200 chr6A 95.890 73 3 0 1074 1146 466322315 466322387 1.350000e-22 119.0
35 TraesCS4B01G201200 chr6A 88.608 79 7 2 611 689 11671900 11671976 2.280000e-15 95.3
36 TraesCS4B01G201200 chr7B 84.894 470 65 3 2051 2516 60569874 60569407 3.240000e-128 470.0
37 TraesCS4B01G201200 chr7B 90.526 190 14 4 2171 2360 186869003 186868818 1.650000e-61 248.0
38 TraesCS4B01G201200 chr2D 87.824 386 42 5 1 382 551339134 551339518 1.520000e-121 448.0
39 TraesCS4B01G201200 chr2D 89.333 75 7 1 619 693 204713356 204713283 8.190000e-15 93.5
40 TraesCS4B01G201200 chr3A 85.507 414 38 12 2074 2474 644664216 644663812 5.540000e-111 412.0
41 TraesCS4B01G201200 chr3A 92.547 161 11 1 2036 2195 313655328 313655168 5.990000e-56 230.0
42 TraesCS4B01G201200 chr7D 85.752 379 45 8 2132 2507 52710821 52710449 7.210000e-105 392.0
43 TraesCS4B01G201200 chr7D 91.713 181 12 3 2197 2375 618492607 618492428 1.650000e-61 248.0
44 TraesCS4B01G201200 chr7D 93.168 161 9 1 2037 2195 230275001 230275161 1.290000e-57 235.0
45 TraesCS4B01G201200 chr7D 92.593 162 10 1 2036 2195 386079039 386079200 1.660000e-56 231.0
46 TraesCS4B01G201200 chr6B 95.210 167 8 0 2196 2362 29400047 29399881 1.640000e-66 265.0
47 TraesCS4B01G201200 chr1B 95.181 166 8 0 2195 2360 639429630 639429465 5.900000e-66 263.0
48 TraesCS4B01G201200 chr1B 93.023 172 11 1 2192 2362 188456625 188456796 4.590000e-62 250.0
49 TraesCS4B01G201200 chr1B 90.141 71 7 0 611 681 63888178 63888248 8.190000e-15 93.5
50 TraesCS4B01G201200 chr6D 95.122 164 8 0 2197 2360 445766549 445766386 7.630000e-65 259.0
51 TraesCS4B01G201200 chr5A 88.889 198 22 0 2318 2515 611541371 611541174 2.140000e-60 244.0
52 TraesCS4B01G201200 chr5A 88.947 190 17 2 2033 2220 611541741 611541554 1.660000e-56 231.0
53 TraesCS4B01G201200 chr3D 92.638 163 10 2 2362 2523 442970029 442969868 4.630000e-57 233.0
54 TraesCS4B01G201200 chr3D 89.041 73 6 2 396 468 573320672 573320742 1.060000e-13 89.8
55 TraesCS4B01G201200 chr1D 92.547 161 10 1 2037 2195 344057705 344057865 5.990000e-56 230.0
56 TraesCS4B01G201200 chr1D 92.500 160 11 1 2036 2195 89716325 89716167 2.150000e-55 228.0
57 TraesCS4B01G201200 chr5B 85.714 203 21 7 2199 2397 663141301 663141103 2.800000e-49 207.0
58 TraesCS4B01G201200 chr2B 78.212 358 46 17 1 354 426099881 426100210 4.690000e-47 200.0
59 TraesCS4B01G201200 chr2B 90.411 73 7 0 610 682 721493841 721493769 6.330000e-16 97.1
60 TraesCS4B01G201200 chr2B 90.278 72 7 0 610 681 498445479 498445408 2.280000e-15 95.3
61 TraesCS4B01G201200 chrUn 80.455 220 36 3 165 384 48479647 48479859 2.210000e-35 161.0
62 TraesCS4B01G201200 chrUn 80.455 220 36 3 165 384 235121751 235121963 2.210000e-35 161.0
63 TraesCS4B01G201200 chrUn 80.455 220 36 3 165 384 306495347 306495135 2.210000e-35 161.0
64 TraesCS4B01G201200 chrUn 96.296 54 2 0 415 468 285039071 285039124 1.060000e-13 89.8
65 TraesCS4B01G201200 chr7A 87.500 80 10 0 612 691 673094053 673093974 8.190000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G201200 chr4B 429092855 429100523 7668 True 14163.000000 14163 100.000000 1 7669 1 chr4B.!!$R1 7668
1 TraesCS4B01G201200 chr3B 581333152 581341334 8182 False 3676.333333 5096 96.228000 814 7669 3 chr3B.!!$F2 6855
2 TraesCS4B01G201200 chr4A 115910284 115918696 8412 False 1981.800000 4636 95.379800 814 7669 5 chr4A.!!$F1 6855
3 TraesCS4B01G201200 chr4D 349007841 349017755 9914 True 2208.000000 4523 92.986000 1 7669 5 chr4D.!!$R1 7668
4 TraesCS4B01G201200 chr6A 466336981 466349284 12303 False 1683.250000 2013 95.171000 4166 7669 4 chr6A.!!$F5 3503
5 TraesCS4B01G201200 chr6A 466356665 466362495 5830 False 1482.000000 1615 93.210000 6658 7669 2 chr6A.!!$F6 1011
6 TraesCS4B01G201200 chr6A 466322315 466330065 7750 False 1465.833333 4174 95.554167 1074 7669 6 chr6A.!!$F4 6595
7 TraesCS4B01G201200 chr6A 466219703 466220341 638 False 784.000000 784 89.147000 1 630 1 chr6A.!!$F2 629
8 TraesCS4B01G201200 chr5A 611541174 611541741 567 True 237.500000 244 88.918000 2033 2515 2 chr5A.!!$R1 482

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
316 319 0.243907 ACTCCATGGTTGAGTCGTCG 59.756 55.000 12.58 0.0 38.71 5.12 F
843 911 0.377554 AATGTCGAGCGAGACGTAGG 59.622 55.000 9.21 0.0 43.70 3.18 F
1790 1891 0.249868 TCAGAGGTTTCGTGCACCAG 60.250 55.000 12.15 0.0 36.67 4.00 F
2047 3418 1.071385 CTGGGCATGTACTCCCTCATC 59.929 57.143 15.92 0.0 43.04 2.92 F
3153 4627 1.089920 ATGGTGCAGTCGATCAAAGC 58.910 50.000 0.00 0.0 0.00 3.51 F
3287 4761 1.186200 TCTCTTGGTCCTCCATGTCG 58.814 55.000 0.00 0.0 43.91 4.35 F
4656 6130 2.302445 AGCTCTCCATCAGATGCCATAC 59.698 50.000 4.68 0.0 0.00 2.39 F
5424 7288 1.154197 GCGGCGTTTTTCTCCTTACT 58.846 50.000 9.37 0.0 0.00 2.24 F
6055 9798 3.058293 CCGCTCAAACAATCTGCTAACAA 60.058 43.478 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1633 1.302832 CCACAGGTGGTTCTGCTCC 60.303 63.158 10.34 0.00 45.53 4.70 R
2344 3807 0.468648 CCATTACTCCCTCCGTTCCC 59.531 60.000 0.00 0.00 0.00 3.97 R
3153 4627 0.169672 CAAGTTCTTCAGCATGCCCG 59.830 55.000 15.66 6.18 34.76 6.13 R
3287 4761 0.535335 TATCGGCACTCACCAGGAAC 59.465 55.000 0.00 0.00 0.00 3.62 R
4965 6444 1.139226 GCACACACACTTGGTTTGCG 61.139 55.000 0.00 0.00 30.10 4.85 R
5083 6562 5.625311 GCACACGTAATTTCCTTTCTCTTTG 59.375 40.000 0.00 0.00 0.00 2.77 R
6055 9798 2.689785 CGCGTTGCCATGTGACCAT 61.690 57.895 0.00 0.00 0.00 3.55 R
6654 10647 3.260884 ACACCTGATTATGTGGACTTCGT 59.739 43.478 0.00 0.00 36.80 3.85 R
7552 19284 5.885230 TTAAATCTGCACTTGATGGTCTG 57.115 39.130 0.00 0.00 0.00 3.51 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
119 121 1.814394 TCCTTTGACATGTGCATGAGC 59.186 47.619 17.85 10.05 41.20 4.26
135 137 3.213206 TGAGCTTGTGTTGGTTCTCAT 57.787 42.857 0.00 0.00 0.00 2.90
159 162 7.011499 TGTAAGCACCCTGTAATTCTAAAGA 57.989 36.000 0.00 0.00 0.00 2.52
181 184 4.306767 TCGAGGTCGATCCAACGA 57.693 55.556 15.69 15.69 44.22 3.85
184 187 1.209275 CGAGGTCGATCCAACGATGC 61.209 60.000 13.52 0.00 43.93 3.91
219 222 0.401395 CCAATGGAGGCCCTACCCTA 60.401 60.000 0.00 0.00 40.58 3.53
238 241 5.131977 ACCCTACATTACCATCAGCACATAA 59.868 40.000 0.00 0.00 0.00 1.90
254 257 4.794655 GCACATAACTTGAAGGCCGAAAAA 60.795 41.667 0.00 0.00 0.00 1.94
313 316 3.143675 CCACTCCATGGTTGAGTCG 57.856 57.895 12.58 0.00 44.46 4.18
314 317 0.321671 CCACTCCATGGTTGAGTCGT 59.678 55.000 12.58 0.00 44.46 4.34
315 318 1.673033 CCACTCCATGGTTGAGTCGTC 60.673 57.143 12.58 0.00 44.46 4.20
316 319 0.243907 ACTCCATGGTTGAGTCGTCG 59.756 55.000 12.58 0.00 38.71 5.12
317 320 0.458543 CTCCATGGTTGAGTCGTCGG 60.459 60.000 12.58 0.00 0.00 4.79
318 321 1.447838 CCATGGTTGAGTCGTCGGG 60.448 63.158 2.57 0.00 0.00 5.14
319 322 2.100631 CATGGTTGAGTCGTCGGGC 61.101 63.158 0.00 0.00 0.00 6.13
320 323 2.579657 ATGGTTGAGTCGTCGGGCA 61.580 57.895 0.00 0.00 0.00 5.36
321 324 2.029964 GGTTGAGTCGTCGGGCAA 59.970 61.111 0.00 0.00 0.00 4.52
363 366 2.063979 ATCGGCCGGTCTGATTCCA 61.064 57.895 27.83 0.77 37.52 3.53
404 407 1.012486 GGACAACGGTAAGGACAGCG 61.012 60.000 0.00 0.00 44.63 5.18
407 410 1.909781 AACGGTAAGGACAGCGGGA 60.910 57.895 0.00 0.00 43.44 5.14
411 414 1.623542 GGTAAGGACAGCGGGATGGT 61.624 60.000 0.00 0.00 0.00 3.55
425 428 1.381872 ATGGTGACGGAGGAGGAGG 60.382 63.158 0.00 0.00 0.00 4.30
434 437 4.814041 AGGAGGAGGGGAGGCAGC 62.814 72.222 0.00 0.00 0.00 5.25
474 477 4.388499 GGAGAGGTGCCGCGGAAA 62.388 66.667 33.48 14.13 0.00 3.13
476 479 4.394712 AGAGGTGCCGCGGAAAGG 62.395 66.667 33.48 0.95 0.00 3.11
477 480 4.388499 GAGGTGCCGCGGAAAGGA 62.388 66.667 33.48 0.00 0.00 3.36
478 481 3.682292 GAGGTGCCGCGGAAAGGAT 62.682 63.158 33.48 8.75 0.00 3.24
479 482 3.508840 GGTGCCGCGGAAAGGATG 61.509 66.667 33.48 0.00 0.00 3.51
480 483 3.508840 GTGCCGCGGAAAGGATGG 61.509 66.667 33.48 0.00 0.00 3.51
481 484 4.028490 TGCCGCGGAAAGGATGGT 62.028 61.111 33.48 0.00 0.00 3.55
483 486 2.824041 CCGCGGAAAGGATGGTGG 60.824 66.667 24.07 0.00 0.00 4.61
484 487 2.824041 CGCGGAAAGGATGGTGGG 60.824 66.667 0.00 0.00 0.00 4.61
485 488 2.440247 GCGGAAAGGATGGTGGGG 60.440 66.667 0.00 0.00 0.00 4.96
486 489 2.440247 CGGAAAGGATGGTGGGGC 60.440 66.667 0.00 0.00 0.00 5.80
487 490 2.770130 GGAAAGGATGGTGGGGCA 59.230 61.111 0.00 0.00 0.00 5.36
488 491 1.380380 GGAAAGGATGGTGGGGCAG 60.380 63.158 0.00 0.00 0.00 4.85
489 492 1.380380 GAAAGGATGGTGGGGCAGG 60.380 63.158 0.00 0.00 0.00 4.85
490 493 1.856873 AAAGGATGGTGGGGCAGGA 60.857 57.895 0.00 0.00 0.00 3.86
491 494 1.224003 AAAGGATGGTGGGGCAGGAT 61.224 55.000 0.00 0.00 0.00 3.24
492 495 1.941403 AAGGATGGTGGGGCAGGATG 61.941 60.000 0.00 0.00 40.87 3.51
493 496 2.386100 GGATGGTGGGGCAGGATGA 61.386 63.158 0.00 0.00 39.69 2.92
508 525 1.683319 GGATGACTGGGCTTTCTTCCC 60.683 57.143 0.00 0.00 44.17 3.97
548 565 5.175859 CCTTCGCTGGTAATTTAAGACTCA 58.824 41.667 0.00 0.00 0.00 3.41
552 569 7.681939 TCGCTGGTAATTTAAGACTCAAAAT 57.318 32.000 0.00 0.00 0.00 1.82
561 578 6.963049 TTTAAGACTCAAAATAGAGCGACC 57.037 37.500 0.00 0.00 39.26 4.79
579 596 3.677148 CGACCACATGCAAGTCTAGATGT 60.677 47.826 0.00 0.00 0.00 3.06
640 658 3.189287 GTGGTTAGGTTGCATGTCAAGAG 59.811 47.826 3.27 0.00 34.91 2.85
654 672 8.260114 TGCATGTCAAGAGAAATAAGATAGTGA 58.740 33.333 0.00 0.00 0.00 3.41
655 673 8.763356 GCATGTCAAGAGAAATAAGATAGTGAG 58.237 37.037 0.00 0.00 0.00 3.51
710 734 1.789464 GAGGTATTCGAATGCAGAGCG 59.211 52.381 24.64 0.00 0.00 5.03
729 753 3.583276 GACGTGTCCGGGCACATCA 62.583 63.158 36.28 0.00 39.19 3.07
745 769 1.676006 CATCACGGACATTTTAGGGCC 59.324 52.381 0.00 0.00 0.00 5.80
787 819 0.930310 CGTGCCAACACCATCGATAG 59.070 55.000 0.00 0.00 44.40 2.08
815 883 9.469097 GTAGGAGATAGTAACATACATGGATCT 57.531 37.037 0.00 0.00 0.00 2.75
842 910 2.102633 GAAATGTCGAGCGAGACGTAG 58.897 52.381 9.21 0.00 43.70 3.51
843 911 0.377554 AATGTCGAGCGAGACGTAGG 59.622 55.000 9.21 0.00 43.70 3.18
933 1010 1.312815 GGCTTGCCATATCAGGTGTC 58.687 55.000 6.79 0.00 0.00 3.67
934 1011 1.312815 GCTTGCCATATCAGGTGTCC 58.687 55.000 0.00 0.00 0.00 4.02
935 1012 1.408683 GCTTGCCATATCAGGTGTCCA 60.409 52.381 0.00 0.00 0.00 4.02
977 1058 1.676529 TCCAGGAGAAAGAGCGTATCG 59.323 52.381 0.00 0.00 0.00 2.92
1164 1252 2.749044 CGGAGTCGTCGGAGGGAA 60.749 66.667 0.00 0.00 0.00 3.97
1424 1518 3.411351 CACCGCCGTGAAGGTTCG 61.411 66.667 0.00 0.00 43.14 3.95
1548 1642 1.372087 CGAAGGCCATGGAGCAGAAC 61.372 60.000 18.40 0.00 0.00 3.01
1584 1681 1.756367 GCCGAAGCGATGAGTACTAC 58.244 55.000 0.00 0.00 0.00 2.73
1626 1723 2.992114 AGAGACCGTGCCGCTCTT 60.992 61.111 0.00 0.00 35.59 2.85
1751 1851 1.416049 CGACCATGTTCAGTTCGCG 59.584 57.895 0.00 0.00 0.00 5.87
1785 1886 2.415512 GGTGTAATCAGAGGTTTCGTGC 59.584 50.000 0.00 0.00 0.00 5.34
1790 1891 0.249868 TCAGAGGTTTCGTGCACCAG 60.250 55.000 12.15 0.00 36.67 4.00
1896 2001 2.355126 CTCGATCGTCCGCATGGG 60.355 66.667 15.94 2.06 35.24 4.00
1897 2002 2.831284 TCGATCGTCCGCATGGGA 60.831 61.111 15.94 5.03 44.68 4.37
2047 3418 1.071385 CTGGGCATGTACTCCCTCATC 59.929 57.143 15.92 0.00 43.04 2.92
2107 3480 8.275187 TCCAATTTAAAGGGCTCATCTCTATA 57.725 34.615 4.24 0.00 0.00 1.31
2206 3579 2.649531 ACTCATCTCTACTCCCTCCG 57.350 55.000 0.00 0.00 0.00 4.63
2211 3584 1.296984 TCTCTACTCCCTCCGTTCCT 58.703 55.000 0.00 0.00 0.00 3.36
2217 3590 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2230 3687 8.827677 CCGTTCCTAAATATTTGTCTTTCTAGG 58.172 37.037 11.05 6.95 0.00 3.02
2231 3688 8.336080 CGTTCCTAAATATTTGTCTTTCTAGGC 58.664 37.037 11.05 0.00 0.00 3.93
2241 3698 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
2243 3700 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
2244 3701 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
2247 3704 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
2249 3706 4.895668 AGGCATTTCAAATGGACACAAT 57.104 36.364 12.14 0.00 0.00 2.71
2252 3709 7.658525 AGGCATTTCAAATGGACACAATATA 57.341 32.000 12.14 0.00 0.00 0.86
2253 3710 8.253867 AGGCATTTCAAATGGACACAATATAT 57.746 30.769 12.14 0.00 0.00 0.86
2255 3712 7.385752 GGCATTTCAAATGGACACAATATATGG 59.614 37.037 12.14 0.00 0.00 2.74
2259 3722 8.765488 TTCAAATGGACACAATATATGGATGT 57.235 30.769 0.00 0.00 0.00 3.06
2260 3723 9.859152 TTCAAATGGACACAATATATGGATGTA 57.141 29.630 0.00 0.00 0.00 2.29
2263 3726 9.812347 AAATGGACACAATATATGGATGTATGT 57.188 29.630 0.00 0.00 0.00 2.29
2266 3729 8.539544 TGGACACAATATATGGATGTATGTAGG 58.460 37.037 0.00 0.00 0.00 3.18
2267 3730 7.495934 GGACACAATATATGGATGTATGTAGGC 59.504 40.741 0.00 0.00 0.00 3.93
2286 3749 8.801882 TGTAGGCATATTTTAAAGTGTAGCTT 57.198 30.769 0.00 0.00 39.52 3.74
2297 3760 9.515020 TTTTAAAGTGTAGCTTCACTCATTTTG 57.485 29.630 24.10 0.00 46.25 2.44
2298 3761 4.756084 AGTGTAGCTTCACTCATTTTGC 57.244 40.909 19.22 0.00 44.07 3.68
2300 3763 4.823989 AGTGTAGCTTCACTCATTTTGCTT 59.176 37.500 19.22 0.00 44.07 3.91
2301 3764 5.049129 AGTGTAGCTTCACTCATTTTGCTTC 60.049 40.000 19.22 0.00 44.07 3.86
2302 3765 3.549299 AGCTTCACTCATTTTGCTTCG 57.451 42.857 0.00 0.00 0.00 3.79
2303 3766 2.880890 AGCTTCACTCATTTTGCTTCGT 59.119 40.909 0.00 0.00 0.00 3.85
2304 3767 4.065088 AGCTTCACTCATTTTGCTTCGTA 58.935 39.130 0.00 0.00 0.00 3.43
2308 3771 6.402118 GCTTCACTCATTTTGCTTCGTATGTA 60.402 38.462 0.00 0.00 0.00 2.29
2309 3772 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2310 3773 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2311 3774 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2312 3775 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2313 3776 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2315 3778 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2316 3779 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2324 3787 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
2329 3792 8.764524 ATGTAGTCACTTGTTGAAATCTCTAC 57.235 34.615 0.00 0.00 35.39 2.59
2336 3799 7.768582 TCACTTGTTGAAATCTCTACAAAGACA 59.231 33.333 0.00 0.00 43.56 3.41
2337 3800 8.397906 CACTTGTTGAAATCTCTACAAAGACAA 58.602 33.333 0.00 0.00 43.56 3.18
2360 3823 1.732117 TTTGGGAACGGAGGGAGTAA 58.268 50.000 0.00 0.00 0.00 2.24
2479 3942 6.855763 AAATGCCTTGGTTGATGAGATTTA 57.144 33.333 0.00 0.00 0.00 1.40
2481 3944 6.855763 ATGCCTTGGTTGATGAGATTTAAA 57.144 33.333 0.00 0.00 0.00 1.52
2600 4063 5.279384 ACAAACGTAAACACACAACAAACA 58.721 33.333 0.00 0.00 0.00 2.83
2601 4064 5.747197 ACAAACGTAAACACACAACAAACAA 59.253 32.000 0.00 0.00 0.00 2.83
2602 4065 6.255020 ACAAACGTAAACACACAACAAACAAA 59.745 30.769 0.00 0.00 0.00 2.83
2603 4066 5.809373 ACGTAAACACACAACAAACAAAC 57.191 34.783 0.00 0.00 0.00 2.93
2604 4067 5.279384 ACGTAAACACACAACAAACAAACA 58.721 33.333 0.00 0.00 0.00 2.83
2605 4068 5.747197 ACGTAAACACACAACAAACAAACAA 59.253 32.000 0.00 0.00 0.00 2.83
2606 4069 6.255020 ACGTAAACACACAACAAACAAACAAA 59.745 30.769 0.00 0.00 0.00 2.83
2607 4070 7.117454 CGTAAACACACAACAAACAAACAAAA 58.883 30.769 0.00 0.00 0.00 2.44
2608 4071 7.634817 CGTAAACACACAACAAACAAACAAAAA 59.365 29.630 0.00 0.00 0.00 1.94
2662 4125 3.396560 AGTCCAAAGTTACACTAACGGC 58.603 45.455 0.00 0.00 43.29 5.68
2735 4208 1.976474 GGAACATTGGCCTCCGCAA 60.976 57.895 3.32 0.00 36.38 4.85
2819 4292 4.239304 CCTTTACATATACATACGGCGCA 58.761 43.478 10.83 0.00 0.00 6.09
2822 4295 6.128391 CCTTTACATATACATACGGCGCAAAT 60.128 38.462 10.83 0.00 0.00 2.32
2824 4297 5.682943 ACATATACATACGGCGCAAATTT 57.317 34.783 10.83 0.00 0.00 1.82
2832 4305 3.833545 ACGGCGCAAATTTAACATACA 57.166 38.095 10.83 0.00 0.00 2.29
2994 4467 6.127647 GGTCACATGCCATAGAAAAATTCTCA 60.128 38.462 0.00 0.00 41.14 3.27
3093 4567 9.953697 CATTAGTCACTACTGGTATCTTAACTC 57.046 37.037 0.00 0.00 36.36 3.01
3153 4627 1.089920 ATGGTGCAGTCGATCAAAGC 58.910 50.000 0.00 0.00 0.00 3.51
3287 4761 1.186200 TCTCTTGGTCCTCCATGTCG 58.814 55.000 0.00 0.00 43.91 4.35
3426 4900 5.643379 TCTTATCATTGCCCTCAAAACAC 57.357 39.130 0.00 0.00 35.56 3.32
3528 5002 3.070018 CAGAGACATGTCAAAGGTCACC 58.930 50.000 27.02 0.00 34.04 4.02
3843 5317 5.103000 CCAAACTCGGACAGTCTACATAAG 58.897 45.833 0.00 0.00 32.30 1.73
4200 5674 3.631686 TGCATGGGAAAGAACGGAATATG 59.368 43.478 0.00 0.00 0.00 1.78
4242 5716 8.653036 AGTACTTTGAACTTCTCCTATACTGT 57.347 34.615 0.00 0.00 0.00 3.55
4291 5765 7.494625 TCCTTTAACTGTTTCTAATATGAGCCG 59.505 37.037 0.00 0.00 0.00 5.52
4294 5768 5.339008 ACTGTTTCTAATATGAGCCGTGA 57.661 39.130 0.00 0.00 0.00 4.35
4320 5794 5.723492 TTGCATTATCACGACTTCATCTG 57.277 39.130 0.00 0.00 0.00 2.90
4329 5803 3.610242 CACGACTTCATCTGAGTACTTGC 59.390 47.826 0.00 0.00 0.00 4.01
4433 5907 4.214332 GCAGACACTAACTTCTTTTCCCAG 59.786 45.833 0.00 0.00 0.00 4.45
4446 5920 2.673775 TTCCCAGAACTGCATTCCAA 57.326 45.000 0.00 0.00 38.16 3.53
4613 6087 8.177119 AGACAGAAACCATTAACAATGCTTTA 57.823 30.769 0.00 0.00 37.57 1.85
4656 6130 2.302445 AGCTCTCCATCAGATGCCATAC 59.698 50.000 4.68 0.00 0.00 2.39
4801 6275 3.926616 AGTCCGAAGTCCTTGTATGTTG 58.073 45.455 0.00 0.00 0.00 3.33
4932 6411 8.281529 AGGAGGATAAGCTGGAACTTAAATAT 57.718 34.615 0.00 0.00 35.82 1.28
4933 6412 9.393786 AGGAGGATAAGCTGGAACTTAAATATA 57.606 33.333 0.00 0.00 35.82 0.86
5083 6562 3.264450 CCATCTCAGGTCATAATACCCCC 59.736 52.174 0.00 0.00 40.71 5.40
5188 7050 3.850273 GCTGTCAGCATTTCTTTGAATCG 59.150 43.478 20.16 0.00 41.89 3.34
5278 7140 1.344114 GATTTGGGGCAGTTTGAGCAA 59.656 47.619 0.00 0.00 0.00 3.91
5424 7288 1.154197 GCGGCGTTTTTCTCCTTACT 58.846 50.000 9.37 0.00 0.00 2.24
5654 9394 5.360144 TGGAAAAAGACGACAACCCAAATAA 59.640 36.000 0.00 0.00 0.00 1.40
5655 9395 6.127423 TGGAAAAAGACGACAACCCAAATAAA 60.127 34.615 0.00 0.00 0.00 1.40
5656 9396 6.419710 GGAAAAAGACGACAACCCAAATAAAG 59.580 38.462 0.00 0.00 0.00 1.85
6055 9798 3.058293 CCGCTCAAACAATCTGCTAACAA 60.058 43.478 0.00 0.00 0.00 2.83
6058 9801 4.860907 GCTCAAACAATCTGCTAACAATGG 59.139 41.667 0.00 0.00 0.00 3.16
6192 10182 7.492352 ACTGTGGTTTTAGTCTTACATTGAC 57.508 36.000 0.00 0.00 34.88 3.18
6382 10375 5.873179 TTTCTGGTCTATAAAAACCTGCG 57.127 39.130 0.00 0.00 36.47 5.18
6647 10640 5.280654 AGCAACCAAACTTTGATGTTCAT 57.719 34.783 2.87 0.00 0.00 2.57
6654 10647 8.862325 ACCAAACTTTGATGTTCATATCAGTA 57.138 30.769 2.87 0.00 38.25 2.74
6657 10650 8.655970 CAAACTTTGATGTTCATATCAGTACGA 58.344 33.333 0.00 0.00 38.25 3.43
6658 10651 8.771920 AACTTTGATGTTCATATCAGTACGAA 57.228 30.769 0.00 0.00 38.25 3.85
6659 10652 8.412608 ACTTTGATGTTCATATCAGTACGAAG 57.587 34.615 0.00 0.00 38.25 3.79
6660 10653 8.035394 ACTTTGATGTTCATATCAGTACGAAGT 58.965 33.333 0.00 0.00 40.57 3.01
6661 10654 7.987268 TTGATGTTCATATCAGTACGAAGTC 57.013 36.000 0.00 0.00 39.09 3.01
6662 10655 6.504398 TGATGTTCATATCAGTACGAAGTCC 58.496 40.000 0.00 0.00 35.42 3.85
6665 10658 5.184287 TGTTCATATCAGTACGAAGTCCACA 59.816 40.000 0.00 0.00 43.93 4.17
6666 10659 6.127451 TGTTCATATCAGTACGAAGTCCACAT 60.127 38.462 0.00 0.00 43.93 3.21
6724 13258 2.543653 GCTTCAAACATTTGGCTCACGT 60.544 45.455 4.58 0.00 38.66 4.49
7244 18606 2.028130 TGCCAATGGAAAACAGAACGT 58.972 42.857 2.05 0.00 0.00 3.99
7435 18797 5.008217 GGCTTTGTGTTACATTGACTACACA 59.992 40.000 14.60 14.60 46.41 3.72
7552 19284 4.142293 GGATTTTTCTCCAGACCTGCAATC 60.142 45.833 0.00 0.00 35.24 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 7.538575 CAATTCCCACTACCTCACTAAATTTG 58.461 38.462 0.00 0.00 0.00 2.32
51 53 5.652452 GCAATTCCCACTACCTCACTAAATT 59.348 40.000 0.00 0.00 0.00 1.82
52 54 5.193679 GCAATTCCCACTACCTCACTAAAT 58.806 41.667 0.00 0.00 0.00 1.40
53 55 4.566907 GGCAATTCCCACTACCTCACTAAA 60.567 45.833 0.00 0.00 0.00 1.85
54 56 3.054655 GGCAATTCCCACTACCTCACTAA 60.055 47.826 0.00 0.00 0.00 2.24
119 121 4.275689 TGCTTACATGAGAACCAACACAAG 59.724 41.667 0.00 0.00 0.00 3.16
135 137 7.011499 TCTTTAGAATTACAGGGTGCTTACA 57.989 36.000 0.00 0.00 0.00 2.41
181 184 2.028125 GCATCCATGGCTTGCAGCAT 62.028 55.000 25.80 3.92 44.75 3.79
219 222 6.179756 TCAAGTTATGTGCTGATGGTAATGT 58.820 36.000 0.00 0.00 0.00 2.71
238 241 3.068165 CCTTTCTTTTTCGGCCTTCAAGT 59.932 43.478 0.00 0.00 0.00 3.16
300 303 1.447838 CCCGACGACTCAACCATGG 60.448 63.158 11.19 11.19 0.00 3.66
305 308 1.860078 CTTTGCCCGACGACTCAAC 59.140 57.895 0.00 0.00 0.00 3.18
306 309 1.959226 GCTTTGCCCGACGACTCAA 60.959 57.895 0.00 0.00 0.00 3.02
307 310 2.357034 GCTTTGCCCGACGACTCA 60.357 61.111 0.00 0.00 0.00 3.41
308 311 1.696832 GATGCTTTGCCCGACGACTC 61.697 60.000 0.00 0.00 0.00 3.36
309 312 1.741770 GATGCTTTGCCCGACGACT 60.742 57.895 0.00 0.00 0.00 4.18
310 313 2.750888 GGATGCTTTGCCCGACGAC 61.751 63.158 0.00 0.00 0.00 4.34
311 314 2.435938 GGATGCTTTGCCCGACGA 60.436 61.111 0.00 0.00 0.00 4.20
312 315 1.982073 GAAGGATGCTTTGCCCGACG 61.982 60.000 0.00 0.00 0.00 5.12
313 316 1.657751 GGAAGGATGCTTTGCCCGAC 61.658 60.000 0.00 0.00 0.00 4.79
314 317 1.378514 GGAAGGATGCTTTGCCCGA 60.379 57.895 0.00 0.00 0.00 5.14
315 318 1.660560 CTGGAAGGATGCTTTGCCCG 61.661 60.000 0.00 0.00 0.00 6.13
316 319 2.196319 CTGGAAGGATGCTTTGCCC 58.804 57.895 0.00 0.00 0.00 5.36
349 352 2.124695 GGGTGGAATCAGACCGGC 60.125 66.667 0.00 0.00 32.48 6.13
363 366 0.251608 GGTGGCCTATGTTTGTGGGT 60.252 55.000 3.32 0.00 0.00 4.51
390 393 1.684734 ATCCCGCTGTCCTTACCGT 60.685 57.895 0.00 0.00 0.00 4.83
404 407 2.435693 CCTCCTCCGTCACCATCCC 61.436 68.421 0.00 0.00 0.00 3.85
407 410 1.381872 CCTCCTCCTCCGTCACCAT 60.382 63.158 0.00 0.00 0.00 3.55
411 414 2.944954 TCCCCTCCTCCTCCGTCA 60.945 66.667 0.00 0.00 0.00 4.35
412 415 2.123640 CTCCCCTCCTCCTCCGTC 60.124 72.222 0.00 0.00 0.00 4.79
413 416 3.756783 CCTCCCCTCCTCCTCCGT 61.757 72.222 0.00 0.00 0.00 4.69
417 420 4.814041 GCTGCCTCCCCTCCTCCT 62.814 72.222 0.00 0.00 0.00 3.69
444 447 4.382541 TCTCCTCCGCCTCTGCCA 62.383 66.667 0.00 0.00 0.00 4.92
458 461 2.815647 CTTTCCGCGGCACCTCTC 60.816 66.667 23.51 0.00 0.00 3.20
473 476 1.623686 ATCCTGCCCCACCATCCTT 60.624 57.895 0.00 0.00 0.00 3.36
474 477 2.045132 ATCCTGCCCCACCATCCT 59.955 61.111 0.00 0.00 0.00 3.24
476 479 1.152881 GTCATCCTGCCCCACCATC 60.153 63.158 0.00 0.00 0.00 3.51
477 480 1.620589 AGTCATCCTGCCCCACCAT 60.621 57.895 0.00 0.00 0.00 3.55
478 481 2.204136 AGTCATCCTGCCCCACCA 60.204 61.111 0.00 0.00 0.00 4.17
479 482 2.273449 CAGTCATCCTGCCCCACC 59.727 66.667 0.00 0.00 33.59 4.61
480 483 2.273449 CCAGTCATCCTGCCCCAC 59.727 66.667 0.00 0.00 40.06 4.61
481 484 3.016971 CCCAGTCATCCTGCCCCA 61.017 66.667 0.00 0.00 40.06 4.96
483 486 2.505364 AAAGCCCAGTCATCCTGCCC 62.505 60.000 0.00 0.00 40.06 5.36
484 487 1.000396 AAAGCCCAGTCATCCTGCC 60.000 57.895 0.00 0.00 40.06 4.85
485 488 0.034670 AGAAAGCCCAGTCATCCTGC 60.035 55.000 0.00 0.00 40.06 4.85
486 489 2.363683 GAAGAAAGCCCAGTCATCCTG 58.636 52.381 0.00 0.00 41.15 3.86
487 490 1.283321 GGAAGAAAGCCCAGTCATCCT 59.717 52.381 0.00 0.00 30.58 3.24
488 491 1.683319 GGGAAGAAAGCCCAGTCATCC 60.683 57.143 0.00 0.00 45.31 3.51
489 492 1.756430 GGGAAGAAAGCCCAGTCATC 58.244 55.000 0.00 0.00 45.31 2.92
490 493 3.987594 GGGAAGAAAGCCCAGTCAT 57.012 52.632 0.00 0.00 45.31 3.06
508 525 3.300009 GAAGGTGTCAATTCGCAAACAG 58.700 45.455 0.00 0.00 0.00 3.16
548 565 2.710377 TGCATGTGGTCGCTCTATTTT 58.290 42.857 0.00 0.00 0.00 1.82
552 569 0.608130 ACTTGCATGTGGTCGCTCTA 59.392 50.000 4.14 0.00 0.00 2.43
561 578 8.877808 TCTATTAACATCTAGACTTGCATGTG 57.122 34.615 10.37 0.00 29.78 3.21
606 624 7.675062 TGCAACCTAACCACATTATCAATTTT 58.325 30.769 0.00 0.00 0.00 1.82
609 627 6.380846 ACATGCAACCTAACCACATTATCAAT 59.619 34.615 0.00 0.00 0.00 2.57
611 629 5.260424 ACATGCAACCTAACCACATTATCA 58.740 37.500 0.00 0.00 0.00 2.15
612 630 5.356751 TGACATGCAACCTAACCACATTATC 59.643 40.000 0.00 0.00 0.00 1.75
613 631 5.260424 TGACATGCAACCTAACCACATTAT 58.740 37.500 0.00 0.00 0.00 1.28
614 632 4.657013 TGACATGCAACCTAACCACATTA 58.343 39.130 0.00 0.00 0.00 1.90
615 633 3.495331 TGACATGCAACCTAACCACATT 58.505 40.909 0.00 0.00 0.00 2.71
683 701 8.138074 GCTCTGCATTCGAATACCTCATATATA 58.862 37.037 10.97 0.00 0.00 0.86
684 702 6.983307 GCTCTGCATTCGAATACCTCATATAT 59.017 38.462 10.97 0.00 0.00 0.86
685 703 6.333416 GCTCTGCATTCGAATACCTCATATA 58.667 40.000 10.97 0.00 0.00 0.86
686 704 5.174395 GCTCTGCATTCGAATACCTCATAT 58.826 41.667 10.97 0.00 0.00 1.78
710 734 4.388499 ATGTGCCCGGACACGTCC 62.388 66.667 16.55 6.12 43.74 4.79
729 753 0.034477 CCAGGCCCTAAAATGTCCGT 60.034 55.000 0.00 0.00 0.00 4.69
733 757 3.106827 CCAAATCCAGGCCCTAAAATGT 58.893 45.455 0.00 0.00 0.00 2.71
735 759 3.106827 CACCAAATCCAGGCCCTAAAAT 58.893 45.455 0.00 0.00 0.00 1.82
745 769 0.667184 GCCGCAAACACCAAATCCAG 60.667 55.000 0.00 0.00 0.00 3.86
779 811 9.607988 ATGTTACTATCTCCTACTCTATCGATG 57.392 37.037 8.54 0.00 0.00 3.84
787 819 8.865420 TCCATGTATGTTACTATCTCCTACTC 57.135 38.462 0.00 0.00 0.00 2.59
795 827 8.247562 GGAGTCAGATCCATGTATGTTACTATC 58.752 40.741 0.00 0.00 39.34 2.08
806 838 3.198635 ACATTTCGGAGTCAGATCCATGT 59.801 43.478 0.00 1.33 39.53 3.21
809 841 2.159240 CGACATTTCGGAGTCAGATCCA 60.159 50.000 0.00 0.00 41.89 3.41
815 883 0.456142 CGCTCGACATTTCGGAGTCA 60.456 55.000 0.73 0.00 45.90 3.41
830 898 1.938625 AGTACTCCTACGTCTCGCTC 58.061 55.000 0.00 0.00 0.00 5.03
842 910 3.795623 TGATCCAACGCTTAGTACTCC 57.204 47.619 0.00 0.00 0.00 3.85
933 1010 1.878102 GCTCGCCTTATATGGTGGTGG 60.878 57.143 15.99 9.25 38.11 4.61
934 1011 1.512926 GCTCGCCTTATATGGTGGTG 58.487 55.000 15.99 11.19 38.11 4.17
935 1012 0.033504 CGCTCGCCTTATATGGTGGT 59.966 55.000 15.99 0.00 38.11 4.16
977 1058 2.583593 GTGCAGACTCGATCGGGC 60.584 66.667 16.63 8.21 34.27 6.13
1512 1606 2.265739 GCCTCGTGCATCTCCACA 59.734 61.111 0.00 0.00 40.77 4.17
1539 1633 1.302832 CCACAGGTGGTTCTGCTCC 60.303 63.158 10.34 0.00 45.53 4.70
1626 1723 1.725665 CGGCTCCGTAATCTCGTCA 59.274 57.895 0.00 0.00 34.35 4.35
1941 3306 6.627087 TCCACTGAATCCTTAGTTGATTCT 57.373 37.500 12.60 0.00 45.34 2.40
2047 3418 4.527038 TGAGATAGGCCTTATAAACCGGAG 59.473 45.833 12.58 0.00 0.00 4.63
2107 3480 8.491331 AATGCGCATTGGAAACTAAAAATAAT 57.509 26.923 33.48 3.62 0.00 1.28
2194 3567 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
2195 3568 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
2206 3579 9.174166 TGCCTAGAAAGACAAATATTTAGGAAC 57.826 33.333 11.79 0.00 0.00 3.62
2217 3590 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
2230 3687 8.143193 TCCATATATTGTGTCCATTTGAAATGC 58.857 33.333 12.26 0.87 0.00 3.56
2240 3697 8.539544 CCTACATACATCCATATATTGTGTCCA 58.460 37.037 0.00 0.00 0.00 4.02
2241 3698 7.495934 GCCTACATACATCCATATATTGTGTCC 59.504 40.741 0.00 0.00 0.00 4.02
2243 3700 7.917003 TGCCTACATACATCCATATATTGTGT 58.083 34.615 0.00 0.66 0.00 3.72
2244 3701 8.969260 ATGCCTACATACATCCATATATTGTG 57.031 34.615 0.00 0.00 33.67 3.33
2253 3710 9.860650 ACTTTAAAATATGCCTACATACATCCA 57.139 29.630 0.00 0.00 41.50 3.41
2260 3723 8.980481 AGCTACACTTTAAAATATGCCTACAT 57.020 30.769 0.00 0.00 40.49 2.29
2263 3726 8.889717 GTGAAGCTACACTTTAAAATATGCCTA 58.110 33.333 0.00 0.00 39.29 3.93
2265 3728 7.971004 GTGAAGCTACACTTTAAAATATGCC 57.029 36.000 0.00 0.00 39.29 4.40
2278 3741 4.756084 AGCAAAATGAGTGAAGCTACAC 57.244 40.909 0.00 0.00 40.60 2.90
2280 3743 4.083802 ACGAAGCAAAATGAGTGAAGCTAC 60.084 41.667 0.00 0.00 0.00 3.58
2282 3745 2.880890 ACGAAGCAAAATGAGTGAAGCT 59.119 40.909 0.00 0.00 0.00 3.74
2283 3746 3.273919 ACGAAGCAAAATGAGTGAAGC 57.726 42.857 0.00 0.00 0.00 3.86
2286 3749 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2290 3753 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2294 3757 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2295 3758 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2296 3759 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2297 3760 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
2298 3761 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
2300 3763 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
2301 3764 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2302 3765 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2303 3766 9.856488 GTAGAGATTTCAACAAGTGACTACATA 57.144 33.333 0.00 0.00 35.39 2.29
2304 3767 8.367911 TGTAGAGATTTCAACAAGTGACTACAT 58.632 33.333 0.00 0.00 36.58 2.29
2308 3771 7.987458 TCTTTGTAGAGATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
2309 3772 8.064814 GTCTTTGTAGAGATTTCAACAAGTGAC 58.935 37.037 0.00 0.00 35.39 3.67
2310 3773 7.768582 TGTCTTTGTAGAGATTTCAACAAGTGA 59.231 33.333 0.00 0.00 33.70 3.41
2311 3774 7.919690 TGTCTTTGTAGAGATTTCAACAAGTG 58.080 34.615 0.00 0.00 33.70 3.16
2312 3775 8.506168 TTGTCTTTGTAGAGATTTCAACAAGT 57.494 30.769 0.00 0.00 33.70 3.16
2313 3776 9.956720 ATTTGTCTTTGTAGAGATTTCAACAAG 57.043 29.630 0.00 0.00 33.70 3.16
2324 3787 7.962918 CGTTCCCAAATATTTGTCTTTGTAGAG 59.037 37.037 23.24 7.00 36.45 2.43
2329 3792 6.019779 TCCGTTCCCAAATATTTGTCTTTG 57.980 37.500 23.24 10.08 36.45 2.77
2336 3799 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
2337 3800 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
2344 3807 0.468648 CCATTACTCCCTCCGTTCCC 59.531 60.000 0.00 0.00 0.00 3.97
2479 3942 3.835395 TCGGTTTATGGGGCTCAAATTTT 59.165 39.130 0.00 0.00 0.00 1.82
2481 3944 3.094484 TCGGTTTATGGGGCTCAAATT 57.906 42.857 0.00 0.00 0.00 1.82
2607 4070 4.972591 GCATGACAGCGGCTTTTT 57.027 50.000 0.00 0.00 0.00 1.94
2735 4208 2.191400 TGAGGCTGCTGAATTAGAGGT 58.809 47.619 0.00 0.00 0.00 3.85
2819 4292 7.881142 TGCTGTTGCTAGTGTATGTTAAATTT 58.119 30.769 0.00 0.00 40.48 1.82
2822 4295 6.261158 TGTTGCTGTTGCTAGTGTATGTTAAA 59.739 34.615 0.00 0.00 40.48 1.52
2824 4297 5.178623 GTGTTGCTGTTGCTAGTGTATGTTA 59.821 40.000 0.00 0.00 40.48 2.41
2832 4305 3.131709 AGATGTGTTGCTGTTGCTAGT 57.868 42.857 0.00 0.00 40.48 2.57
3093 4567 5.063204 TGGGATCAAGTAATATGCGAAAGG 58.937 41.667 0.00 0.00 0.00 3.11
3153 4627 0.169672 CAAGTTCTTCAGCATGCCCG 59.830 55.000 15.66 6.18 34.76 6.13
3287 4761 0.535335 TATCGGCACTCACCAGGAAC 59.465 55.000 0.00 0.00 0.00 3.62
3528 5002 7.522721 CATATGTTTATGGATTACCCGTGGGG 61.523 46.154 10.28 2.83 39.18 4.96
4291 5765 3.551890 AGTCGTGATAATGCAATCGTCAC 59.448 43.478 12.25 12.25 37.30 3.67
4294 5768 4.180817 TGAAGTCGTGATAATGCAATCGT 58.819 39.130 0.00 0.00 0.00 3.73
4320 5794 5.500645 ACTGGAAAAACAAGCAAGTACTC 57.499 39.130 0.00 0.00 0.00 2.59
4329 5803 5.296035 AGGTAGAAACGACTGGAAAAACAAG 59.704 40.000 0.00 0.00 0.00 3.16
4433 5907 2.548057 TCGTCAAGTTGGAATGCAGTTC 59.452 45.455 2.34 0.00 36.04 3.01
4965 6444 1.139226 GCACACACACTTGGTTTGCG 61.139 55.000 0.00 0.00 30.10 4.85
5083 6562 5.625311 GCACACGTAATTTCCTTTCTCTTTG 59.375 40.000 0.00 0.00 0.00 2.77
5188 7050 7.894753 ACACTACTAGTTTAGGGATCTTACC 57.105 40.000 0.00 0.00 0.00 2.85
5278 7140 6.543831 GTGAGGAACATGCCTACATTATTCTT 59.456 38.462 0.00 0.00 38.73 2.52
5409 7273 8.436200 CAAGTCTATCAAGTAAGGAGAAAAACG 58.564 37.037 0.00 0.00 0.00 3.60
5412 7276 6.879458 GCCAAGTCTATCAAGTAAGGAGAAAA 59.121 38.462 0.00 0.00 0.00 2.29
5424 7288 6.767902 GGAATGTGAATAGCCAAGTCTATCAA 59.232 38.462 0.00 0.00 0.00 2.57
5613 9353 9.739276 TCTTTTTCCAAATATCTCTTTAGCTGA 57.261 29.630 0.00 0.00 0.00 4.26
5654 9394 7.890127 TCCATTTCTCCAACATTGTATCTTCTT 59.110 33.333 0.00 0.00 0.00 2.52
5655 9395 7.405292 TCCATTTCTCCAACATTGTATCTTCT 58.595 34.615 0.00 0.00 0.00 2.85
5656 9396 7.630242 TCCATTTCTCCAACATTGTATCTTC 57.370 36.000 0.00 0.00 0.00 2.87
6055 9798 2.689785 CGCGTTGCCATGTGACCAT 61.690 57.895 0.00 0.00 0.00 3.55
6058 9801 4.759096 GCCGCGTTGCCATGTGAC 62.759 66.667 4.92 0.00 0.00 3.67
6167 9914 7.225931 TGTCAATGTAAGACTAAAACCACAGTC 59.774 37.037 0.00 0.00 41.25 3.51
6382 10375 4.453136 TGGCGAGTACAAATTTGAGTTACC 59.547 41.667 24.64 16.67 0.00 2.85
6558 10551 5.061721 ACAAAAGATGGTACCTCCTGTTT 57.938 39.130 14.36 6.27 37.07 2.83
6647 10640 7.255486 CCTGATTATGTGGACTTCGTACTGATA 60.255 40.741 0.00 0.00 0.00 2.15
6654 10647 3.260884 ACACCTGATTATGTGGACTTCGT 59.739 43.478 0.00 0.00 36.80 3.85
6657 10650 6.814954 AGATACACCTGATTATGTGGACTT 57.185 37.500 0.00 0.00 36.80 3.01
6658 10651 6.814954 AAGATACACCTGATTATGTGGACT 57.185 37.500 0.00 0.00 36.80 3.85
6659 10652 9.862371 CTATAAGATACACCTGATTATGTGGAC 57.138 37.037 0.00 0.00 36.80 4.02
6660 10653 9.035890 CCTATAAGATACACCTGATTATGTGGA 57.964 37.037 0.00 0.00 36.80 4.02
6661 10654 9.035890 TCCTATAAGATACACCTGATTATGTGG 57.964 37.037 0.00 0.00 36.80 4.17
6959 13522 9.045223 TCAGTCGTATGGAATTTGAGAATATTG 57.955 33.333 0.00 0.00 0.00 1.90
7552 19284 5.885230 TTAAATCTGCACTTGATGGTCTG 57.115 39.130 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.