Multiple sequence alignment - TraesCS4B01G115300

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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 TraesCS4B01G115300 chr4B 100.000 3458 0 0 1 3458 132057738 132054281 0.000000e+00 6386.0
1 TraesCS4B01G115300 chr4B 79.616 1408 248 28 975 2369 132295269 132293888 0.000000e+00 974.0
2 TraesCS4B01G115300 chr4B 75.614 1140 220 44 1295 2399 139627379 139626263 2.380000e-141 512.0
3 TraesCS4B01G115300 chr4B 80.423 378 67 7 2880 3254 132293750 132293377 7.310000e-72 281.0
4 TraesCS4B01G115300 chr4B 79.487 234 42 6 158 390 529145742 529145970 9.930000e-36 161.0
5 TraesCS4B01G115300 chr4B 100.000 30 0 0 2485 2514 303833631 303833602 4.820000e-04 56.5
6 TraesCS4B01G115300 chr4B 100.000 29 0 0 2486 2514 392588645 392588617 2.000000e-03 54.7
7 TraesCS4B01G115300 chr4D 95.334 1693 69 8 887 2574 93612979 93611292 0.000000e+00 2680.0
8 TraesCS4B01G115300 chr4D 93.236 887 43 6 2588 3458 93611306 93610421 0.000000e+00 1290.0
9 TraesCS4B01G115300 chr4D 79.957 1407 249 20 976 2369 93761531 93760145 0.000000e+00 1005.0
10 TraesCS4B01G115300 chr4D 80.426 470 87 5 2798 3264 93760036 93759569 1.530000e-93 353.0
11 TraesCS4B01G115300 chr4D 81.356 413 63 12 1294 1699 98078656 98078251 1.200000e-84 324.0
12 TraesCS4B01G115300 chr4D 87.562 201 20 3 562 762 93614906 93614711 9.650000e-56 228.0
13 TraesCS4B01G115300 chr4A 96.555 1132 33 4 879 2006 488248730 488249859 0.000000e+00 1869.0
14 TraesCS4B01G115300 chr4A 91.950 882 50 13 2588 3458 488250373 488251244 0.000000e+00 1216.0
15 TraesCS4B01G115300 chr4A 79.688 1408 251 24 975 2369 487916348 487917733 0.000000e+00 983.0
16 TraesCS4B01G115300 chr4A 91.902 531 31 6 2052 2574 488249861 488250387 0.000000e+00 732.0
17 TraesCS4B01G115300 chr4A 82.299 435 71 6 2794 3225 487917830 487918261 4.210000e-99 372.0
18 TraesCS4B01G115300 chr4A 95.349 43 1 1 816 858 488248625 488248666 2.230000e-07 67.6
19 TraesCS4B01G115300 chr2B 78.814 590 93 23 1288 1868 49981364 49980798 5.450000e-98 368.0
20 TraesCS4B01G115300 chr2A 78.571 588 98 23 1285 1862 32503543 32504112 2.540000e-96 363.0
21 TraesCS4B01G115300 chr2A 84.892 139 17 4 2590 2726 47781126 47781262 1.670000e-28 137.0
22 TraesCS4B01G115300 chr2A 100.000 29 0 0 2486 2514 583737942 583737970 2.000000e-03 54.7
23 TraesCS4B01G115300 chr7D 79.773 529 68 21 1 495 82928774 82928251 7.100000e-92 348.0
24 TraesCS4B01G115300 chr6D 83.065 372 54 8 179 546 80047031 80047397 2.570000e-86 329.0
25 TraesCS4B01G115300 chr6D 75.672 670 123 31 1285 1938 56211716 56212361 7.260000e-77 298.0
26 TraesCS4B01G115300 chr6D 77.958 431 49 17 1295 1721 61003133 61003521 9.650000e-56 228.0
27 TraesCS4B01G115300 chr6D 72.775 573 125 29 1309 1862 101720847 101721407 7.680000e-37 165.0
28 TraesCS4B01G115300 chr5B 75.354 706 134 28 1237 1938 63844350 63845019 1.560000e-78 303.0
29 TraesCS4B01G115300 chr5B 74.612 709 144 23 1237 1937 63632027 63632707 2.630000e-71 279.0
30 TraesCS4B01G115300 chr5B 80.233 172 21 6 2589 2754 53021970 53022134 2.180000e-22 117.0
31 TraesCS4B01G115300 chr5D 75.319 705 134 28 1238 1938 58677778 58678446 5.610000e-78 302.0
32 TraesCS4B01G115300 chr5D 74.471 709 147 27 1237 1938 58947049 58947730 3.400000e-70 276.0
33 TraesCS4B01G115300 chr2D 77.203 522 85 23 1357 1868 30462726 30462229 1.220000e-69 274.0
34 TraesCS4B01G115300 chr2D 75.694 576 118 16 1285 1853 8976731 8977291 5.690000e-68 268.0
35 TraesCS4B01G115300 chr3D 73.710 601 121 29 1223 1802 560198828 560198244 2.100000e-47 200.0
36 TraesCS4B01G115300 chrUn 100.000 29 0 0 2486 2514 98816809 98816781 2.000000e-03 54.7
37 TraesCS4B01G115300 chr7A 100.000 29 0 0 2486 2514 422402265 422402293 2.000000e-03 54.7
38 TraesCS4B01G115300 chr3B 100.000 29 0 0 2486 2514 468452256 468452284 2.000000e-03 54.7
39 TraesCS4B01G115300 chr1B 100.000 29 0 0 2486 2514 463996173 463996145 2.000000e-03 54.7


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 TraesCS4B01G115300 chr4B 132054281 132057738 3457 True 6386.000000 6386 100.0000 1 3458 1 chr4B.!!$R1 3457
1 TraesCS4B01G115300 chr4B 132293377 132295269 1892 True 627.500000 974 80.0195 975 3254 2 chr4B.!!$R5 2279
2 TraesCS4B01G115300 chr4B 139626263 139627379 1116 True 512.000000 512 75.6140 1295 2399 1 chr4B.!!$R2 1104
3 TraesCS4B01G115300 chr4D 93610421 93614906 4485 True 1399.333333 2680 92.0440 562 3458 3 chr4D.!!$R2 2896
4 TraesCS4B01G115300 chr4D 93759569 93761531 1962 True 679.000000 1005 80.1915 976 3264 2 chr4D.!!$R3 2288
5 TraesCS4B01G115300 chr4A 488248625 488251244 2619 False 971.150000 1869 93.9390 816 3458 4 chr4A.!!$F2 2642
6 TraesCS4B01G115300 chr4A 487916348 487918261 1913 False 677.500000 983 80.9935 975 3225 2 chr4A.!!$F1 2250
7 TraesCS4B01G115300 chr2B 49980798 49981364 566 True 368.000000 368 78.8140 1288 1868 1 chr2B.!!$R1 580
8 TraesCS4B01G115300 chr2A 32503543 32504112 569 False 363.000000 363 78.5710 1285 1862 1 chr2A.!!$F1 577
9 TraesCS4B01G115300 chr7D 82928251 82928774 523 True 348.000000 348 79.7730 1 495 1 chr7D.!!$R1 494
10 TraesCS4B01G115300 chr6D 56211716 56212361 645 False 298.000000 298 75.6720 1285 1938 1 chr6D.!!$F1 653
11 TraesCS4B01G115300 chr5B 63844350 63845019 669 False 303.000000 303 75.3540 1237 1938 1 chr5B.!!$F3 701
12 TraesCS4B01G115300 chr5B 63632027 63632707 680 False 279.000000 279 74.6120 1237 1937 1 chr5B.!!$F2 700
13 TraesCS4B01G115300 chr5D 58677778 58678446 668 False 302.000000 302 75.3190 1238 1938 1 chr5D.!!$F1 700
14 TraesCS4B01G115300 chr5D 58947049 58947730 681 False 276.000000 276 74.4710 1237 1938 1 chr5D.!!$F2 701
15 TraesCS4B01G115300 chr2D 8976731 8977291 560 False 268.000000 268 75.6940 1285 1853 1 chr2D.!!$F1 568

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
730 763 0.038310 GGAGTTTGAGGACTTGGGGG 59.962 60.000 0.0 0.0 0.00 5.40 F
877 995 0.908910 TCCCATCTAAGCTTTGCCGA 59.091 50.000 3.2 0.0 0.00 5.54 F
1965 3688 1.333881 GCATTGATCTGAGCATCGCAC 60.334 52.381 10.9 0.0 38.61 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3688 0.038159 AGGTTCGGAGCGTCTTTCAG 60.038 55.0 0.0 0.0 0.00 3.02 R
2025 3754 0.326264 ATCTTGACACTCCTGGGCAC 59.674 55.0 0.0 0.0 0.00 5.01 R
2861 4663 0.855349 GACTGCACGCATTCGATAGG 59.145 55.0 0.0 0.0 39.41 2.57 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
28 29 0.320421 CGAGACCGAGCAAGGGAAAA 60.320 55.000 2.52 0.00 38.22 2.29
42 43 1.337447 GGGAAAACCATCTGACGACGA 60.337 52.381 0.00 0.00 39.85 4.20
43 44 1.993370 GGAAAACCATCTGACGACGAG 59.007 52.381 0.00 0.00 0.00 4.18
48 49 1.611977 ACCATCTGACGACGAGAACAA 59.388 47.619 0.00 0.00 0.00 2.83
53 54 2.292292 TCTGACGACGAGAACAACATGA 59.708 45.455 0.00 0.00 0.00 3.07
55 56 1.719780 GACGACGAGAACAACATGACC 59.280 52.381 0.00 0.00 0.00 4.02
58 59 1.455786 GACGAGAACAACATGACCGTG 59.544 52.381 0.00 0.00 0.00 4.94
59 60 0.163788 CGAGAACAACATGACCGTGC 59.836 55.000 0.00 0.00 0.00 5.34
61 62 0.249699 AGAACAACATGACCGTGCGA 60.250 50.000 0.00 0.00 0.00 5.10
79 80 1.737793 CGAAAGTTAAGCCGGCTCAAT 59.262 47.619 32.93 17.93 0.00 2.57
92 93 1.602311 GCTCAATAGCCTCCACCATG 58.398 55.000 0.00 0.00 43.40 3.66
93 94 1.602311 CTCAATAGCCTCCACCATGC 58.398 55.000 0.00 0.00 0.00 4.06
94 95 0.183492 TCAATAGCCTCCACCATGCC 59.817 55.000 0.00 0.00 0.00 4.40
95 96 0.106569 CAATAGCCTCCACCATGCCA 60.107 55.000 0.00 0.00 0.00 4.92
96 97 0.184451 AATAGCCTCCACCATGCCAG 59.816 55.000 0.00 0.00 0.00 4.85
97 98 0.695462 ATAGCCTCCACCATGCCAGA 60.695 55.000 0.00 0.00 0.00 3.86
98 99 0.695462 TAGCCTCCACCATGCCAGAT 60.695 55.000 0.00 0.00 0.00 2.90
100 120 0.685458 GCCTCCACCATGCCAGATTT 60.685 55.000 0.00 0.00 0.00 2.17
101 121 1.396653 CCTCCACCATGCCAGATTTC 58.603 55.000 0.00 0.00 0.00 2.17
123 143 4.704833 GGTCGCTTGGGCTGAGCA 62.705 66.667 6.82 0.00 40.13 4.26
127 147 2.282745 GCTTGGGCTGAGCAAGGT 60.283 61.111 6.82 0.00 39.89 3.50
131 151 1.003580 CTTGGGCTGAGCAAGGTAGAA 59.996 52.381 6.82 0.00 0.00 2.10
133 153 1.271379 TGGGCTGAGCAAGGTAGAAAC 60.271 52.381 6.82 0.00 0.00 2.78
160 192 1.729881 GGCCTTGCCTTTATCAGCG 59.270 57.895 0.00 0.00 46.69 5.18
170 202 2.292267 CTTTATCAGCGCATCCCAGTT 58.708 47.619 11.47 0.00 0.00 3.16
171 203 1.667236 TTATCAGCGCATCCCAGTTG 58.333 50.000 11.47 0.00 0.00 3.16
175 207 2.124736 GCGCATCCCAGTTGGCTA 60.125 61.111 0.30 0.00 0.00 3.93
180 212 0.537188 CATCCCAGTTGGCTACGACT 59.463 55.000 0.00 0.00 42.17 4.18
187 219 1.067495 AGTTGGCTACGACTCTGAAGC 60.067 52.381 0.00 0.00 36.60 3.86
192 224 1.407258 GCTACGACTCTGAAGCAGGAT 59.593 52.381 0.00 0.00 35.05 3.24
207 239 2.542411 GCAGGATGAAAATCCATCACGC 60.542 50.000 7.46 0.00 43.49 5.34
208 240 2.033801 CAGGATGAAAATCCATCACGCC 59.966 50.000 7.46 0.00 43.49 5.68
212 244 0.395724 GAAAATCCATCACGCCCCCT 60.396 55.000 0.00 0.00 0.00 4.79
220 252 0.105453 ATCACGCCCCCTAGATCTGT 60.105 55.000 5.18 0.00 0.00 3.41
221 253 0.325296 TCACGCCCCCTAGATCTGTT 60.325 55.000 5.18 0.00 0.00 3.16
225 257 1.120530 GCCCCCTAGATCTGTTTCGA 58.879 55.000 5.18 0.00 0.00 3.71
229 261 2.035632 CCCTAGATCTGTTTCGAGGCT 58.964 52.381 5.18 0.00 37.24 4.58
231 263 2.428890 CCTAGATCTGTTTCGAGGCTGT 59.571 50.000 5.18 0.00 32.72 4.40
240 272 1.266178 TTCGAGGCTGTCTCAATGGA 58.734 50.000 10.25 0.00 42.55 3.41
243 275 1.198713 GAGGCTGTCTCAATGGAGGA 58.801 55.000 4.02 0.00 41.69 3.71
244 276 1.138661 GAGGCTGTCTCAATGGAGGAG 59.861 57.143 4.02 0.00 41.69 3.69
247 279 1.473080 GCTGTCTCAATGGAGGAGAGC 60.473 57.143 0.00 0.57 41.77 4.09
305 337 3.633094 CTGGTCGTGAGCACCTCCG 62.633 68.421 0.00 0.00 34.78 4.63
333 365 4.069232 CTGACTCCCAGGCGCGAA 62.069 66.667 12.10 0.00 39.23 4.70
334 366 3.997064 CTGACTCCCAGGCGCGAAG 62.997 68.421 12.10 0.00 39.23 3.79
344 376 3.119096 GCGCGAAGGGAAGTCCAC 61.119 66.667 12.10 0.00 46.37 4.02
353 385 4.329545 GAAGTCCACCCAGCGGCA 62.330 66.667 1.45 0.00 0.00 5.69
356 388 4.947147 GTCCACCCAGCGGCAACA 62.947 66.667 1.45 0.00 0.00 3.33
366 398 2.182842 GCGGCAACATGCTCTAGGG 61.183 63.158 2.00 0.00 44.28 3.53
374 406 0.625849 CATGCTCTAGGGTTTGGGGT 59.374 55.000 0.00 0.00 0.00 4.95
377 409 0.919710 GCTCTAGGGTTTGGGGTGAT 59.080 55.000 0.00 0.00 0.00 3.06
380 412 1.203505 TCTAGGGTTTGGGGTGATGGA 60.204 52.381 0.00 0.00 0.00 3.41
386 418 2.562738 GGTTTGGGGTGATGGAAGAAAG 59.437 50.000 0.00 0.00 0.00 2.62
398 430 0.393132 GAAGAAAGGGGGAAGGAGCG 60.393 60.000 0.00 0.00 0.00 5.03
444 477 1.896660 CACCCACACCGGACCTTTG 60.897 63.158 9.46 0.00 36.56 2.77
445 478 2.983592 CCCACACCGGACCTTTGC 60.984 66.667 9.46 0.00 36.56 3.68
446 479 2.983592 CCACACCGGACCTTTGCC 60.984 66.667 9.46 0.00 36.56 4.52
447 480 2.983592 CACACCGGACCTTTGCCC 60.984 66.667 9.46 0.00 0.00 5.36
448 481 4.636435 ACACCGGACCTTTGCCCG 62.636 66.667 9.46 0.00 44.94 6.13
482 515 4.222847 GCGGCGAGGGGGAAGTAG 62.223 72.222 12.98 0.00 0.00 2.57
483 516 4.222847 CGGCGAGGGGGAAGTAGC 62.223 72.222 0.00 0.00 0.00 3.58
484 517 4.222847 GGCGAGGGGGAAGTAGCG 62.223 72.222 0.00 0.00 0.00 4.26
485 518 3.145551 GCGAGGGGGAAGTAGCGA 61.146 66.667 0.00 0.00 0.00 4.93
486 519 3.121019 CGAGGGGGAAGTAGCGAG 58.879 66.667 0.00 0.00 0.00 5.03
487 520 2.491022 CGAGGGGGAAGTAGCGAGG 61.491 68.421 0.00 0.00 0.00 4.63
488 521 1.076192 GAGGGGGAAGTAGCGAGGA 60.076 63.158 0.00 0.00 0.00 3.71
489 522 1.075896 AGGGGGAAGTAGCGAGGAG 60.076 63.158 0.00 0.00 0.00 3.69
490 523 2.134933 GGGGGAAGTAGCGAGGAGG 61.135 68.421 0.00 0.00 0.00 4.30
491 524 2.134933 GGGGAAGTAGCGAGGAGGG 61.135 68.421 0.00 0.00 0.00 4.30
492 525 1.076192 GGGAAGTAGCGAGGAGGGA 60.076 63.158 0.00 0.00 0.00 4.20
493 526 1.110518 GGGAAGTAGCGAGGAGGGAG 61.111 65.000 0.00 0.00 0.00 4.30
494 527 1.737201 GAAGTAGCGAGGAGGGAGC 59.263 63.158 0.00 0.00 0.00 4.70
495 528 2.065906 GAAGTAGCGAGGAGGGAGCG 62.066 65.000 0.00 0.00 35.78 5.03
512 545 4.537433 GCCGGCAGCGAGAGGATT 62.537 66.667 24.80 0.00 0.00 3.01
513 546 2.587194 CCGGCAGCGAGAGGATTG 60.587 66.667 0.00 0.00 0.00 2.67
514 547 2.587194 CGGCAGCGAGAGGATTGG 60.587 66.667 0.00 0.00 0.00 3.16
515 548 2.203126 GGCAGCGAGAGGATTGGG 60.203 66.667 0.00 0.00 0.00 4.12
516 549 2.735772 GGCAGCGAGAGGATTGGGA 61.736 63.158 0.00 0.00 0.00 4.37
517 550 1.227497 GCAGCGAGAGGATTGGGAG 60.227 63.158 0.00 0.00 0.00 4.30
518 551 1.227497 CAGCGAGAGGATTGGGAGC 60.227 63.158 0.00 0.00 0.00 4.70
519 552 2.110006 GCGAGAGGATTGGGAGCC 59.890 66.667 0.00 0.00 0.00 4.70
520 553 2.419198 CGAGAGGATTGGGAGCCG 59.581 66.667 0.00 0.00 36.12 5.52
521 554 2.110006 GAGAGGATTGGGAGCCGC 59.890 66.667 0.00 0.00 36.12 6.53
522 555 3.468326 GAGAGGATTGGGAGCCGCC 62.468 68.421 0.00 0.00 36.12 6.13
578 611 3.194861 TCAATCGGTGCTAATTCCTTCG 58.805 45.455 0.00 0.00 0.00 3.79
581 614 3.155093 TCGGTGCTAATTCCTTCGTAC 57.845 47.619 0.00 0.00 0.00 3.67
591 624 4.755266 ATTCCTTCGTACCTAAGCACAT 57.245 40.909 0.00 0.00 0.00 3.21
595 628 7.534723 TTCCTTCGTACCTAAGCACATATAT 57.465 36.000 0.00 0.00 0.00 0.86
612 645 8.715998 GCACATATATAGTTTCAGATTGAGGTG 58.284 37.037 0.00 0.00 0.00 4.00
623 656 2.171448 AGATTGAGGTGGTAGCCATGTC 59.829 50.000 0.00 0.00 35.28 3.06
641 674 7.231925 AGCCATGTCTAATTCAAATGCATATGA 59.768 33.333 6.97 0.00 0.00 2.15
644 677 8.912658 CATGTCTAATTCAAATGCATATGAAGC 58.087 33.333 6.97 0.00 38.80 3.86
647 680 8.347771 GTCTAATTCAAATGCATATGAAGCTCA 58.652 33.333 6.97 0.00 38.80 4.26
653 686 5.769484 AATGCATATGAAGCTCAAAGAGG 57.231 39.130 6.97 0.00 0.00 3.69
654 687 4.492494 TGCATATGAAGCTCAAAGAGGA 57.508 40.909 6.97 0.00 0.00 3.71
655 688 4.449131 TGCATATGAAGCTCAAAGAGGAG 58.551 43.478 6.97 0.00 37.97 3.69
656 689 4.080695 TGCATATGAAGCTCAAAGAGGAGT 60.081 41.667 6.97 0.00 37.24 3.85
663 696 2.029470 AGCTCAAAGAGGAGTGAAGTCG 60.029 50.000 0.00 0.00 37.24 4.18
667 700 0.605589 AAGAGGAGTGAAGTCGGCTG 59.394 55.000 0.00 0.00 0.00 4.85
678 711 2.386661 AGTCGGCTGAGTTTGTATGG 57.613 50.000 0.00 0.00 0.00 2.74
686 719 0.451383 GAGTTTGTATGGCGCATGCA 59.549 50.000 19.57 8.13 45.35 3.96
691 724 1.031029 TGTATGGCGCATGCATGTGT 61.031 50.000 33.99 20.96 45.35 3.72
708 741 0.400213 TGTCCTTGTCATGGGTCCAC 59.600 55.000 4.99 0.00 0.00 4.02
715 748 1.078823 TGTCATGGGTCCACTAGGAGT 59.921 52.381 0.00 0.00 46.92 3.85
717 750 2.572104 GTCATGGGTCCACTAGGAGTTT 59.428 50.000 0.00 0.00 46.92 2.66
730 763 0.038310 GGAGTTTGAGGACTTGGGGG 59.962 60.000 0.00 0.00 0.00 5.40
736 769 1.920835 GAGGACTTGGGGGTGAGCT 60.921 63.158 0.00 0.00 0.00 4.09
752 785 1.670406 GCTATGAGATGCCCCGCAG 60.670 63.158 0.00 0.00 43.65 5.18
775 829 4.095632 GCAGAGAAGGAAGCAAGGAAATAC 59.904 45.833 0.00 0.00 0.00 1.89
776 830 5.495640 CAGAGAAGGAAGCAAGGAAATACT 58.504 41.667 0.00 0.00 0.00 2.12
778 832 6.093357 CAGAGAAGGAAGCAAGGAAATACTTC 59.907 42.308 0.00 0.00 38.22 3.01
790 844 4.828829 GGAAATACTTCCTTCGTTCCAGA 58.171 43.478 0.00 0.00 46.80 3.86
791 845 5.243207 GGAAATACTTCCTTCGTTCCAGAA 58.757 41.667 0.00 0.00 46.80 3.02
792 846 5.880887 GGAAATACTTCCTTCGTTCCAGAAT 59.119 40.000 0.00 0.00 46.80 2.40
793 847 6.183360 GGAAATACTTCCTTCGTTCCAGAATG 60.183 42.308 0.00 0.00 46.80 2.67
812 866 8.370493 CAGAATGGATGATACGAACTTTATGT 57.630 34.615 0.00 0.00 0.00 2.29
813 867 8.491152 CAGAATGGATGATACGAACTTTATGTC 58.509 37.037 0.00 0.00 0.00 3.06
814 868 8.204160 AGAATGGATGATACGAACTTTATGTCA 58.796 33.333 0.00 0.00 0.00 3.58
858 912 4.684134 AGCAAAGCCACGGCCCAT 62.684 61.111 3.95 0.00 43.17 4.00
860 914 3.451894 CAAAGCCACGGCCCATCC 61.452 66.667 3.95 0.00 43.17 3.51
861 915 4.759205 AAAGCCACGGCCCATCCC 62.759 66.667 3.95 0.00 43.17 3.85
865 919 3.492353 CCACGGCCCATCCCATCT 61.492 66.667 0.00 0.00 0.00 2.90
866 920 2.146724 CCACGGCCCATCCCATCTA 61.147 63.158 0.00 0.00 0.00 1.98
877 995 0.908910 TCCCATCTAAGCTTTGCCGA 59.091 50.000 3.20 0.00 0.00 5.54
895 1013 3.340789 GGTGGCACTTTCACCGTC 58.659 61.111 18.45 0.00 44.16 4.79
896 1014 2.258726 GGTGGCACTTTCACCGTCC 61.259 63.158 18.45 0.00 44.16 4.79
1455 3138 2.678934 CTCCTCCCCGTCCGAACA 60.679 66.667 0.00 0.00 0.00 3.18
1458 3141 2.995574 CTCCCCGTCCGAACAGGT 60.996 66.667 0.00 0.00 41.99 4.00
1901 3624 3.253921 TGAACATGCTGATGAAACACCTG 59.746 43.478 0.00 0.00 33.36 4.00
1965 3688 1.333881 GCATTGATCTGAGCATCGCAC 60.334 52.381 10.90 0.00 38.61 5.34
1976 3699 1.630244 GCATCGCACTGAAAGACGCT 61.630 55.000 0.00 0.00 37.07 5.07
2047 3776 1.003580 GCCCAGGAGTGTCAAGATTGA 59.996 52.381 0.00 0.00 34.20 2.57
2134 3863 2.779755 ACCGTCATCAAGGTGCATAA 57.220 45.000 0.00 0.00 39.66 1.90
2179 3919 3.332761 TCGATTCGCCAATGTAAATGC 57.667 42.857 0.00 0.00 0.00 3.56
2182 3922 2.999507 TTCGCCAATGTAAATGCGTT 57.000 40.000 0.00 0.00 46.57 4.84
2187 3927 3.783943 CGCCAATGTAAATGCGTTAACTC 59.216 43.478 3.71 0.00 41.95 3.01
2215 3955 5.526846 TCTGAAAAATGGAAATTTGGTGCAC 59.473 36.000 8.80 8.80 0.00 4.57
2363 4103 0.108424 GTCGAGAGGCTGCATCTTGT 60.108 55.000 25.69 2.94 31.22 3.16
2385 4125 2.608752 GGTGACACCACTACCACTTACG 60.609 54.545 20.14 0.00 42.77 3.18
2403 4143 3.235157 ACGTTGGCATCAATTTCCATG 57.765 42.857 0.00 0.00 35.10 3.66
2466 4206 2.493278 TGCTTCCATTTAGAGCCAAAGC 59.507 45.455 0.00 0.00 38.43 3.51
2503 4248 6.075762 TGCAGAAATGATAAATCCCGAATG 57.924 37.500 0.00 0.00 0.00 2.67
2504 4249 5.593909 TGCAGAAATGATAAATCCCGAATGT 59.406 36.000 0.00 0.00 0.00 2.71
2505 4250 6.096705 TGCAGAAATGATAAATCCCGAATGTT 59.903 34.615 0.00 0.00 0.00 2.71
2506 4251 6.638468 GCAGAAATGATAAATCCCGAATGTTC 59.362 38.462 0.00 0.00 0.00 3.18
2507 4252 7.681782 GCAGAAATGATAAATCCCGAATGTTCA 60.682 37.037 0.00 0.00 0.00 3.18
2521 4266 0.896923 TGTTCAGGATTTGCCCATGC 59.103 50.000 0.00 0.00 37.37 4.06
2531 4276 3.511182 TGCCCATGCAAATCAAACG 57.489 47.368 0.00 0.00 46.66 3.60
2532 4277 0.678395 TGCCCATGCAAATCAAACGT 59.322 45.000 0.00 0.00 46.66 3.99
2565 4310 4.445452 AACTTTAGTTGACGCGAGGATA 57.555 40.909 15.93 0.00 36.80 2.59
2566 4311 4.445452 ACTTTAGTTGACGCGAGGATAA 57.555 40.909 15.93 2.12 0.00 1.75
2567 4312 4.171754 ACTTTAGTTGACGCGAGGATAAC 58.828 43.478 15.93 10.13 0.00 1.89
2568 4313 3.853831 TTAGTTGACGCGAGGATAACA 57.146 42.857 15.93 0.00 0.00 2.41
2569 4314 2.736144 AGTTGACGCGAGGATAACAA 57.264 45.000 15.93 4.53 0.00 2.83
2570 4315 2.607187 AGTTGACGCGAGGATAACAAG 58.393 47.619 15.93 0.00 0.00 3.16
2571 4316 2.029290 AGTTGACGCGAGGATAACAAGT 60.029 45.455 15.93 7.27 0.00 3.16
2572 4317 2.735134 GTTGACGCGAGGATAACAAGTT 59.265 45.455 15.93 0.00 0.00 2.66
2573 4318 3.034721 TGACGCGAGGATAACAAGTTT 57.965 42.857 15.93 0.00 0.00 2.66
2574 4319 3.395639 TGACGCGAGGATAACAAGTTTT 58.604 40.909 15.93 0.00 0.00 2.43
2575 4320 3.810941 TGACGCGAGGATAACAAGTTTTT 59.189 39.130 15.93 0.00 0.00 1.94
2627 4372 5.321959 TGACAAGCACAACAATTTTCTGA 57.678 34.783 0.00 0.00 0.00 3.27
2632 4377 6.091169 ACAAGCACAACAATTTTCTGACAAAG 59.909 34.615 0.00 0.00 0.00 2.77
2633 4378 5.723295 AGCACAACAATTTTCTGACAAAGT 58.277 33.333 0.00 0.00 0.00 2.66
2644 4389 7.681939 TTTTCTGACAAAGTACAAACTGAGT 57.318 32.000 0.00 0.00 35.62 3.41
2654 4399 2.571212 ACAAACTGAGTGCGGAATTGA 58.429 42.857 0.00 0.00 0.00 2.57
2677 4422 4.582656 ACATGCTTACCAACTAAACTTGCA 59.417 37.500 0.00 0.00 0.00 4.08
2679 4424 5.782893 TGCTTACCAACTAAACTTGCAAT 57.217 34.783 0.00 0.00 0.00 3.56
2681 4426 4.851558 GCTTACCAACTAAACTTGCAATCG 59.148 41.667 0.00 0.00 0.00 3.34
2684 4429 3.058224 ACCAACTAAACTTGCAATCGCTC 60.058 43.478 0.00 0.00 39.64 5.03
2687 4432 0.094558 TAAACTTGCAATCGCTCGCG 59.905 50.000 0.00 0.00 39.64 5.87
2770 4521 2.346847 CGTCCTTTCTTTGAGATGAGCG 59.653 50.000 0.00 0.00 0.00 5.03
3243 5045 5.222631 GTGTTTGCGGAAGATTGAAAAGAT 58.777 37.500 0.00 0.00 0.00 2.40
3332 5134 2.893441 TGCAAGGCACTGTTTTGGA 58.107 47.368 0.00 0.00 40.86 3.53
3335 5137 1.666888 GCAAGGCACTGTTTTGGATCG 60.667 52.381 0.00 0.00 40.86 3.69
3347 5149 1.686355 TTGGATCGTTGGCTTGTGTT 58.314 45.000 0.00 0.00 0.00 3.32
3351 5153 3.049912 GGATCGTTGGCTTGTGTTTTTC 58.950 45.455 0.00 0.00 0.00 2.29
3366 5170 5.710099 TGTGTTTTTCTTGTCAGAGTTCCTT 59.290 36.000 0.00 0.00 0.00 3.36
3368 5172 5.943416 TGTTTTTCTTGTCAGAGTTCCTTGA 59.057 36.000 0.00 0.00 0.00 3.02
3404 5208 1.325640 CGACCTTGAGATGTTGATGCG 59.674 52.381 0.00 0.00 0.00 4.73
3428 5238 2.551459 AGTGTTGCTCAAATGCAGTCTC 59.449 45.455 0.00 0.00 44.27 3.36
3437 5247 5.664457 CTCAAATGCAGTCTCTGTATGGTA 58.336 41.667 0.00 0.00 36.94 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.244816 TGTTCTCGTCGTCAGATGGT 58.755 50.000 0.00 0.00 34.23 3.55
42 43 0.249699 TCGCACGGTCATGTTGTTCT 60.250 50.000 0.00 0.00 0.00 3.01
43 44 0.584396 TTCGCACGGTCATGTTGTTC 59.416 50.000 0.00 0.00 0.00 3.18
48 49 2.157834 TAACTTTCGCACGGTCATGT 57.842 45.000 0.00 0.00 0.00 3.21
53 54 1.562575 CGGCTTAACTTTCGCACGGT 61.563 55.000 0.00 0.00 0.00 4.83
55 56 1.131826 CCGGCTTAACTTTCGCACG 59.868 57.895 0.00 0.00 0.00 5.34
58 59 1.296056 TGAGCCGGCTTAACTTTCGC 61.296 55.000 33.34 15.01 0.00 4.70
59 60 1.153353 TTGAGCCGGCTTAACTTTCG 58.847 50.000 33.34 0.00 0.00 3.46
61 62 2.683362 GCTATTGAGCCGGCTTAACTTT 59.317 45.455 33.20 21.08 43.49 2.66
79 80 0.695462 ATCTGGCATGGTGGAGGCTA 60.695 55.000 0.00 0.00 0.00 3.93
93 94 2.890474 CGACCCGCCGAAATCTGG 60.890 66.667 0.00 0.00 0.00 3.86
107 127 2.669569 TTGCTCAGCCCAAGCGAC 60.670 61.111 0.00 0.00 46.67 5.19
108 128 2.359107 CTTGCTCAGCCCAAGCGA 60.359 61.111 0.00 0.00 46.67 4.93
114 134 1.454201 GTTTCTACCTTGCTCAGCCC 58.546 55.000 0.00 0.00 0.00 5.19
118 138 0.321298 GCCGGTTTCTACCTTGCTCA 60.321 55.000 1.90 0.00 42.66 4.26
122 142 0.320073 TGACGCCGGTTTCTACCTTG 60.320 55.000 1.90 0.00 42.66 3.61
123 143 0.037605 CTGACGCCGGTTTCTACCTT 60.038 55.000 1.90 0.00 42.66 3.50
127 147 2.263540 GCCTGACGCCGGTTTCTA 59.736 61.111 1.90 0.00 0.00 2.10
153 174 0.179048 CCAACTGGGATGCGCTGATA 60.179 55.000 9.73 0.00 40.01 2.15
157 178 2.669133 TAGCCAACTGGGATGCGCT 61.669 57.895 9.73 0.00 40.01 5.92
160 192 1.090052 GTCGTAGCCAACTGGGATGC 61.090 60.000 0.00 0.00 40.01 3.91
170 202 0.528017 CTGCTTCAGAGTCGTAGCCA 59.472 55.000 10.37 0.00 32.44 4.75
171 203 0.179124 CCTGCTTCAGAGTCGTAGCC 60.179 60.000 10.37 0.00 32.44 3.93
175 207 1.550327 TCATCCTGCTTCAGAGTCGT 58.450 50.000 0.00 0.00 32.44 4.34
192 224 0.682855 GGGGGCGTGATGGATTTTCA 60.683 55.000 0.00 0.00 0.00 2.69
207 239 1.689273 CCTCGAAACAGATCTAGGGGG 59.311 57.143 0.00 0.00 30.58 5.40
208 240 1.069358 GCCTCGAAACAGATCTAGGGG 59.931 57.143 8.69 3.26 33.88 4.79
212 244 3.357203 AGACAGCCTCGAAACAGATCTA 58.643 45.455 0.00 0.00 0.00 1.98
220 252 1.623311 TCCATTGAGACAGCCTCGAAA 59.377 47.619 0.00 0.00 44.92 3.46
221 253 1.205655 CTCCATTGAGACAGCCTCGAA 59.794 52.381 0.00 0.00 44.92 3.71
225 257 1.202330 CTCCTCCATTGAGACAGCCT 58.798 55.000 0.00 0.00 41.42 4.58
229 261 2.106566 GAGCTCTCCTCCATTGAGACA 58.893 52.381 6.43 0.00 41.42 3.41
243 275 3.004951 CCTTGGCATGGGAGCTCT 58.995 61.111 14.64 0.00 34.17 4.09
244 276 2.832201 GCCTTGGCATGGGAGCTC 60.832 66.667 19.82 4.71 34.17 4.09
247 279 2.515523 CTCGCCTTGGCATGGGAG 60.516 66.667 19.82 18.37 35.60 4.30
294 326 3.062466 CTCGGACGGAGGTGCTCA 61.062 66.667 2.13 0.00 39.22 4.26
333 365 3.322466 CGCTGGGTGGACTTCCCT 61.322 66.667 2.65 0.00 44.84 4.20
334 366 4.410400 CCGCTGGGTGGACTTCCC 62.410 72.222 0.00 0.00 44.81 3.97
338 370 4.643387 GTTGCCGCTGGGTGGACT 62.643 66.667 0.93 0.00 34.74 3.85
344 376 2.874648 TAGAGCATGTTGCCGCTGGG 62.875 60.000 0.00 0.00 46.52 4.45
353 385 1.005924 CCCCAAACCCTAGAGCATGTT 59.994 52.381 0.00 0.00 0.00 2.71
356 388 0.625849 CACCCCAAACCCTAGAGCAT 59.374 55.000 0.00 0.00 0.00 3.79
366 398 2.562738 CCTTTCTTCCATCACCCCAAAC 59.437 50.000 0.00 0.00 0.00 2.93
374 406 1.640670 CCTTCCCCCTTTCTTCCATCA 59.359 52.381 0.00 0.00 0.00 3.07
377 409 1.372501 CTCCTTCCCCCTTTCTTCCA 58.627 55.000 0.00 0.00 0.00 3.53
380 412 1.134438 ACGCTCCTTCCCCCTTTCTT 61.134 55.000 0.00 0.00 0.00 2.52
386 418 4.475135 GCTCACGCTCCTTCCCCC 62.475 72.222 0.00 0.00 0.00 5.40
465 498 4.222847 CTACTTCCCCCTCGCCGC 62.223 72.222 0.00 0.00 0.00 6.53
466 499 4.222847 GCTACTTCCCCCTCGCCG 62.223 72.222 0.00 0.00 0.00 6.46
467 500 4.222847 CGCTACTTCCCCCTCGCC 62.223 72.222 0.00 0.00 0.00 5.54
468 501 3.140225 CTCGCTACTTCCCCCTCGC 62.140 68.421 0.00 0.00 0.00 5.03
469 502 2.491022 CCTCGCTACTTCCCCCTCG 61.491 68.421 0.00 0.00 0.00 4.63
470 503 1.076192 TCCTCGCTACTTCCCCCTC 60.076 63.158 0.00 0.00 0.00 4.30
471 504 1.075896 CTCCTCGCTACTTCCCCCT 60.076 63.158 0.00 0.00 0.00 4.79
472 505 2.134933 CCTCCTCGCTACTTCCCCC 61.135 68.421 0.00 0.00 0.00 5.40
473 506 2.134933 CCCTCCTCGCTACTTCCCC 61.135 68.421 0.00 0.00 0.00 4.81
474 507 1.076192 TCCCTCCTCGCTACTTCCC 60.076 63.158 0.00 0.00 0.00 3.97
475 508 1.740332 GCTCCCTCCTCGCTACTTCC 61.740 65.000 0.00 0.00 0.00 3.46
476 509 1.737201 GCTCCCTCCTCGCTACTTC 59.263 63.158 0.00 0.00 0.00 3.01
477 510 2.122167 CGCTCCCTCCTCGCTACTT 61.122 63.158 0.00 0.00 0.00 2.24
478 511 2.517402 CGCTCCCTCCTCGCTACT 60.517 66.667 0.00 0.00 0.00 2.57
479 512 4.273257 GCGCTCCCTCCTCGCTAC 62.273 72.222 0.00 0.00 44.79 3.58
495 528 4.537433 AATCCTCTCGCTGCCGGC 62.537 66.667 22.73 22.73 34.56 6.13
496 529 2.587194 CAATCCTCTCGCTGCCGG 60.587 66.667 0.00 0.00 34.56 6.13
497 530 2.587194 CCAATCCTCTCGCTGCCG 60.587 66.667 0.00 0.00 0.00 5.69
498 531 2.203126 CCCAATCCTCTCGCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
499 532 1.227497 CTCCCAATCCTCTCGCTGC 60.227 63.158 0.00 0.00 0.00 5.25
500 533 1.227497 GCTCCCAATCCTCTCGCTG 60.227 63.158 0.00 0.00 0.00 5.18
501 534 2.439104 GGCTCCCAATCCTCTCGCT 61.439 63.158 0.00 0.00 0.00 4.93
502 535 2.110006 GGCTCCCAATCCTCTCGC 59.890 66.667 0.00 0.00 0.00 5.03
503 536 2.419198 CGGCTCCCAATCCTCTCG 59.581 66.667 0.00 0.00 0.00 4.04
504 537 2.110006 GCGGCTCCCAATCCTCTC 59.890 66.667 0.00 0.00 0.00 3.20
505 538 3.483869 GGCGGCTCCCAATCCTCT 61.484 66.667 0.00 0.00 0.00 3.69
542 575 3.122613 CCGATTGAGAAATAGCGATCTGC 59.877 47.826 1.92 1.92 46.98 4.26
543 576 4.149571 CACCGATTGAGAAATAGCGATCTG 59.850 45.833 0.00 0.00 0.00 2.90
544 577 4.302455 CACCGATTGAGAAATAGCGATCT 58.698 43.478 0.00 0.00 0.00 2.75
545 578 3.120854 GCACCGATTGAGAAATAGCGATC 60.121 47.826 0.00 0.00 0.00 3.69
546 579 2.802816 GCACCGATTGAGAAATAGCGAT 59.197 45.455 0.00 0.00 0.00 4.58
547 580 2.159099 AGCACCGATTGAGAAATAGCGA 60.159 45.455 0.00 0.00 0.00 4.93
548 581 2.205074 AGCACCGATTGAGAAATAGCG 58.795 47.619 0.00 0.00 0.00 4.26
549 582 5.931441 ATTAGCACCGATTGAGAAATAGC 57.069 39.130 0.00 0.00 0.00 2.97
550 583 6.708054 AGGAATTAGCACCGATTGAGAAATAG 59.292 38.462 0.00 0.00 0.00 1.73
551 584 6.591935 AGGAATTAGCACCGATTGAGAAATA 58.408 36.000 0.00 0.00 0.00 1.40
552 585 5.440610 AGGAATTAGCACCGATTGAGAAAT 58.559 37.500 0.00 0.00 0.00 2.17
553 586 4.843728 AGGAATTAGCACCGATTGAGAAA 58.156 39.130 0.00 0.00 0.00 2.52
554 587 4.487714 AGGAATTAGCACCGATTGAGAA 57.512 40.909 0.00 0.00 0.00 2.87
555 588 4.442706 GAAGGAATTAGCACCGATTGAGA 58.557 43.478 0.00 0.00 0.00 3.27
556 589 3.246226 CGAAGGAATTAGCACCGATTGAG 59.754 47.826 0.00 0.00 0.00 3.02
557 590 3.194861 CGAAGGAATTAGCACCGATTGA 58.805 45.455 0.00 0.00 0.00 2.57
558 591 2.936498 ACGAAGGAATTAGCACCGATTG 59.064 45.455 0.00 0.00 0.00 2.67
559 592 3.261981 ACGAAGGAATTAGCACCGATT 57.738 42.857 0.00 0.00 0.00 3.34
560 593 2.981859 ACGAAGGAATTAGCACCGAT 57.018 45.000 0.00 0.00 0.00 4.18
591 624 8.585881 GCTACCACCTCAATCTGAAACTATATA 58.414 37.037 0.00 0.00 0.00 0.86
595 628 4.081087 GGCTACCACCTCAATCTGAAACTA 60.081 45.833 0.00 0.00 0.00 2.24
612 645 5.067674 TGCATTTGAATTAGACATGGCTACC 59.932 40.000 8.12 1.24 0.00 3.18
623 656 9.524106 TTTGAGCTTCATATGCATTTGAATTAG 57.476 29.630 26.18 18.36 31.83 1.73
641 674 3.553922 CGACTTCACTCCTCTTTGAGCTT 60.554 47.826 0.00 0.00 35.72 3.74
644 677 2.928731 GCCGACTTCACTCCTCTTTGAG 60.929 54.545 0.00 0.00 38.37 3.02
647 680 1.001406 CAGCCGACTTCACTCCTCTTT 59.999 52.381 0.00 0.00 0.00 2.52
653 686 1.795286 CAAACTCAGCCGACTTCACTC 59.205 52.381 0.00 0.00 0.00 3.51
654 687 1.139058 ACAAACTCAGCCGACTTCACT 59.861 47.619 0.00 0.00 0.00 3.41
655 688 1.583054 ACAAACTCAGCCGACTTCAC 58.417 50.000 0.00 0.00 0.00 3.18
656 689 3.325870 CATACAAACTCAGCCGACTTCA 58.674 45.455 0.00 0.00 0.00 3.02
663 696 1.305219 TGCGCCATACAAACTCAGCC 61.305 55.000 4.18 0.00 0.00 4.85
667 700 0.451383 TGCATGCGCCATACAAACTC 59.549 50.000 14.09 0.00 37.32 3.01
678 711 1.515519 CAAGGACACATGCATGCGC 60.516 57.895 26.53 15.07 39.24 6.09
686 719 1.004745 GGACCCATGACAAGGACACAT 59.995 52.381 0.00 0.00 0.00 3.21
691 724 2.187958 CTAGTGGACCCATGACAAGGA 58.812 52.381 0.00 0.00 0.00 3.36
708 741 2.237392 CCCCAAGTCCTCAAACTCCTAG 59.763 54.545 0.00 0.00 0.00 3.02
715 748 0.771127 CTCACCCCCAAGTCCTCAAA 59.229 55.000 0.00 0.00 0.00 2.69
717 750 2.224159 GCTCACCCCCAAGTCCTCA 61.224 63.158 0.00 0.00 0.00 3.86
730 763 0.320247 CGGGGCATCTCATAGCTCAC 60.320 60.000 0.00 0.00 31.24 3.51
736 769 2.387476 CTGCTGCGGGGCATCTCATA 62.387 60.000 0.00 0.00 41.63 2.15
752 785 2.191128 TTCCTTGCTTCCTTCTCTGC 57.809 50.000 0.00 0.00 0.00 4.26
755 788 6.429791 GAAGTATTTCCTTGCTTCCTTCTC 57.570 41.667 0.00 0.00 33.30 2.87
775 829 3.334583 TCCATTCTGGAACGAAGGAAG 57.665 47.619 0.00 0.00 45.00 3.46
786 840 7.442364 ACATAAAGTTCGTATCATCCATTCTGG 59.558 37.037 0.00 0.00 39.43 3.86
787 841 8.370493 ACATAAAGTTCGTATCATCCATTCTG 57.630 34.615 0.00 0.00 0.00 3.02
788 842 8.204160 TGACATAAAGTTCGTATCATCCATTCT 58.796 33.333 0.00 0.00 0.00 2.40
789 843 8.365399 TGACATAAAGTTCGTATCATCCATTC 57.635 34.615 0.00 0.00 0.00 2.67
790 844 8.204160 TCTGACATAAAGTTCGTATCATCCATT 58.796 33.333 0.00 0.00 0.00 3.16
791 845 7.726216 TCTGACATAAAGTTCGTATCATCCAT 58.274 34.615 0.00 0.00 0.00 3.41
792 846 7.107639 TCTGACATAAAGTTCGTATCATCCA 57.892 36.000 0.00 0.00 0.00 3.41
793 847 6.642950 CCTCTGACATAAAGTTCGTATCATCC 59.357 42.308 0.00 0.00 0.00 3.51
794 848 7.426410 TCCTCTGACATAAAGTTCGTATCATC 58.574 38.462 0.00 0.00 0.00 2.92
795 849 7.348080 TCCTCTGACATAAAGTTCGTATCAT 57.652 36.000 0.00 0.00 0.00 2.45
796 850 6.183360 CCTCCTCTGACATAAAGTTCGTATCA 60.183 42.308 0.00 0.00 0.00 2.15
797 851 6.039493 TCCTCCTCTGACATAAAGTTCGTATC 59.961 42.308 0.00 0.00 0.00 2.24
798 852 5.892119 TCCTCCTCTGACATAAAGTTCGTAT 59.108 40.000 0.00 0.00 0.00 3.06
799 853 5.258841 TCCTCCTCTGACATAAAGTTCGTA 58.741 41.667 0.00 0.00 0.00 3.43
800 854 4.087182 TCCTCCTCTGACATAAAGTTCGT 58.913 43.478 0.00 0.00 0.00 3.85
801 855 4.440802 CCTCCTCCTCTGACATAAAGTTCG 60.441 50.000 0.00 0.00 0.00 3.95
802 856 4.141824 CCCTCCTCCTCTGACATAAAGTTC 60.142 50.000 0.00 0.00 0.00 3.01
803 857 3.777522 CCCTCCTCCTCTGACATAAAGTT 59.222 47.826 0.00 0.00 0.00 2.66
804 858 3.012959 TCCCTCCTCCTCTGACATAAAGT 59.987 47.826 0.00 0.00 0.00 2.66
805 859 3.647636 TCCCTCCTCCTCTGACATAAAG 58.352 50.000 0.00 0.00 0.00 1.85
806 860 3.776731 TCCCTCCTCCTCTGACATAAA 57.223 47.619 0.00 0.00 0.00 1.40
807 861 3.581101 CATCCCTCCTCCTCTGACATAA 58.419 50.000 0.00 0.00 0.00 1.90
808 862 2.158249 CCATCCCTCCTCCTCTGACATA 60.158 54.545 0.00 0.00 0.00 2.29
809 863 1.414245 CCATCCCTCCTCCTCTGACAT 60.414 57.143 0.00 0.00 0.00 3.06
810 864 0.031716 CCATCCCTCCTCCTCTGACA 60.032 60.000 0.00 0.00 0.00 3.58
811 865 0.263172 TCCATCCCTCCTCCTCTGAC 59.737 60.000 0.00 0.00 0.00 3.51
812 866 0.560193 CTCCATCCCTCCTCCTCTGA 59.440 60.000 0.00 0.00 0.00 3.27
813 867 0.471591 CCTCCATCCCTCCTCCTCTG 60.472 65.000 0.00 0.00 0.00 3.35
814 868 1.673928 CCCTCCATCCCTCCTCCTCT 61.674 65.000 0.00 0.00 0.00 3.69
858 912 0.908910 TCGGCAAAGCTTAGATGGGA 59.091 50.000 0.00 0.00 0.00 4.37
860 914 1.303309 CCTCGGCAAAGCTTAGATGG 58.697 55.000 0.00 0.00 0.00 3.51
861 915 1.667724 CACCTCGGCAAAGCTTAGATG 59.332 52.381 0.00 0.00 0.00 2.90
862 916 1.407437 CCACCTCGGCAAAGCTTAGAT 60.407 52.381 0.00 0.00 0.00 1.98
865 919 4.713946 CCACCTCGGCAAAGCTTA 57.286 55.556 0.00 0.00 0.00 3.09
893 1011 4.443266 AGGAAGCGCGCTCTGGAC 62.443 66.667 36.57 21.51 0.00 4.02
894 1012 4.135153 GAGGAAGCGCGCTCTGGA 62.135 66.667 36.57 0.00 0.00 3.86
942 2619 1.670083 CGGACGAGGGTTTTGGGAC 60.670 63.158 0.00 0.00 0.00 4.46
1181 2858 4.699522 GGAGGGTCACCGTGTGCC 62.700 72.222 0.00 2.69 43.47 5.01
1599 3318 4.828925 GCGAGGAGCTGGAGCCAC 62.829 72.222 0.00 0.00 44.04 5.01
1965 3688 0.038159 AGGTTCGGAGCGTCTTTCAG 60.038 55.000 0.00 0.00 0.00 3.02
1976 3699 1.183030 TGAGCCTTTCGAGGTTCGGA 61.183 55.000 5.10 0.00 41.33 4.55
2025 3754 0.326264 ATCTTGACACTCCTGGGCAC 59.674 55.000 0.00 0.00 0.00 5.01
2179 3919 5.404366 TCCATTTTTCAGAGACGAGTTAACG 59.596 40.000 0.00 0.00 39.31 3.18
2182 3922 7.979444 ATTTCCATTTTTCAGAGACGAGTTA 57.021 32.000 0.00 0.00 0.00 2.24
2187 3927 6.144402 CACCAAATTTCCATTTTTCAGAGACG 59.856 38.462 0.00 0.00 29.41 4.18
2215 3955 3.052082 CGTTGTCCCAGCCTGCAG 61.052 66.667 6.78 6.78 0.00 4.41
2302 4042 1.688772 CAGGGCAGCATCTTAGCAAT 58.311 50.000 0.00 0.00 36.85 3.56
2385 4125 4.756135 ACAAACATGGAAATTGATGCCAAC 59.244 37.500 0.00 0.00 34.95 3.77
2437 4177 6.380846 TGGCTCTAAATGGAAGCATTATTGTT 59.619 34.615 0.00 0.00 0.00 2.83
2466 4206 6.441274 TCATTTCTGCAAAGAAAAGCTACAG 58.559 36.000 5.35 0.00 40.60 2.74
2503 4248 3.746900 GCATGGGCAAATCCTGAAC 57.253 52.632 0.00 0.00 40.72 3.18
2576 4321 7.654022 AACTTGTTATCCTCACCTTCAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
2577 4322 7.654022 AAACTTGTTATCCTCACCTTCAAAA 57.346 32.000 0.00 0.00 0.00 2.44
2578 4323 7.996644 ACTAAACTTGTTATCCTCACCTTCAAA 59.003 33.333 0.00 0.00 0.00 2.69
2579 4324 7.514721 ACTAAACTTGTTATCCTCACCTTCAA 58.485 34.615 0.00 0.00 0.00 2.69
2580 4325 7.074653 ACTAAACTTGTTATCCTCACCTTCA 57.925 36.000 0.00 0.00 0.00 3.02
2581 4326 7.660208 TCAACTAAACTTGTTATCCTCACCTTC 59.340 37.037 0.00 0.00 0.00 3.46
2582 4327 7.444487 GTCAACTAAACTTGTTATCCTCACCTT 59.556 37.037 0.00 0.00 0.00 3.50
2583 4328 6.935208 GTCAACTAAACTTGTTATCCTCACCT 59.065 38.462 0.00 0.00 0.00 4.00
2584 4329 6.708949 TGTCAACTAAACTTGTTATCCTCACC 59.291 38.462 0.00 0.00 0.00 4.02
2585 4330 7.724305 TGTCAACTAAACTTGTTATCCTCAC 57.276 36.000 0.00 0.00 0.00 3.51
2586 4331 7.041372 GCTTGTCAACTAAACTTGTTATCCTCA 60.041 37.037 0.00 0.00 0.00 3.86
2587 4332 7.041372 TGCTTGTCAACTAAACTTGTTATCCTC 60.041 37.037 0.00 0.00 0.00 3.71
2588 4333 6.770785 TGCTTGTCAACTAAACTTGTTATCCT 59.229 34.615 0.00 0.00 0.00 3.24
2589 4334 6.856426 GTGCTTGTCAACTAAACTTGTTATCC 59.144 38.462 0.00 0.00 0.00 2.59
2590 4335 7.414436 TGTGCTTGTCAACTAAACTTGTTATC 58.586 34.615 0.00 0.00 0.00 1.75
2591 4336 7.328277 TGTGCTTGTCAACTAAACTTGTTAT 57.672 32.000 0.00 0.00 0.00 1.89
2592 4337 6.745159 TGTGCTTGTCAACTAAACTTGTTA 57.255 33.333 0.00 0.00 0.00 2.41
2593 4338 5.637006 TGTGCTTGTCAACTAAACTTGTT 57.363 34.783 0.00 0.00 0.00 2.83
2594 4339 5.048364 TGTTGTGCTTGTCAACTAAACTTGT 60.048 36.000 9.57 0.00 43.54 3.16
2627 4372 2.612212 CCGCACTCAGTTTGTACTTTGT 59.388 45.455 0.00 0.00 30.26 2.83
2632 4377 3.496884 TCAATTCCGCACTCAGTTTGTAC 59.503 43.478 0.00 0.00 0.00 2.90
2633 4378 3.496884 GTCAATTCCGCACTCAGTTTGTA 59.503 43.478 0.00 0.00 0.00 2.41
2644 4389 1.742831 GGTAAGCATGTCAATTCCGCA 59.257 47.619 0.00 0.00 0.00 5.69
2654 4399 4.582656 TGCAAGTTTAGTTGGTAAGCATGT 59.417 37.500 0.00 0.00 0.00 3.21
2677 4422 4.201685 GGCAATTTATATACGCGAGCGATT 60.202 41.667 24.72 12.56 42.83 3.34
2679 4424 2.664568 GGCAATTTATATACGCGAGCGA 59.335 45.455 24.72 8.20 42.83 4.93
2681 4426 3.185594 TGTGGCAATTTATATACGCGAGC 59.814 43.478 15.93 0.28 0.00 5.03
2684 4429 6.798207 TTTTTGTGGCAATTTATATACGCG 57.202 33.333 3.53 3.53 0.00 6.01
2770 4521 7.913674 ATGAAGTAAATCAGTGAGAACTTCC 57.086 36.000 26.32 16.59 41.20 3.46
2861 4663 0.855349 GACTGCACGCATTCGATAGG 59.145 55.000 0.00 0.00 39.41 2.57
2972 4774 1.291877 AACACGATCACCAGCTTCGC 61.292 55.000 4.70 0.00 36.37 4.70
3024 4826 3.725754 GGTTTCACCTTGGAGCTGA 57.274 52.632 0.00 0.00 34.73 4.26
3243 5045 4.407621 TCACCTGGTAGAGAACTCAAAACA 59.592 41.667 0.00 0.61 0.00 2.83
3332 5134 4.111916 CAAGAAAAACACAAGCCAACGAT 58.888 39.130 0.00 0.00 0.00 3.73
3335 5137 4.241681 TGACAAGAAAAACACAAGCCAAC 58.758 39.130 0.00 0.00 0.00 3.77
3347 5149 7.645058 AAATCAAGGAACTCTGACAAGAAAA 57.355 32.000 0.00 0.00 38.49 2.29
3351 5153 9.971922 AAATAAAAATCAAGGAACTCTGACAAG 57.028 29.630 0.00 0.00 38.49 3.16
3366 5170 3.367910 GGTCGCCAGGCAAATAAAAATCA 60.368 43.478 13.30 0.00 0.00 2.57
3368 5172 2.831526 AGGTCGCCAGGCAAATAAAAAT 59.168 40.909 13.30 0.00 0.00 1.82
3404 5208 4.023707 AGACTGCATTTGAGCAACACTTAC 60.024 41.667 0.00 0.00 45.13 2.34


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

AutoCloner maintained by Alex Coulton.