Multiple sequence alignment - TraesCS2D01G054100

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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 TraesCS2D01G054100 chr2D 100.000 4782 0 0 1 4782 21606694 21611475 0.000000e+00 8831.0
1 TraesCS2D01G054100 chr2D 82.309 944 108 29 986 1889 22419603 22420527 0.000000e+00 763.0
2 TraesCS2D01G054100 chr2D 86.096 187 16 9 4213 4394 293173782 293173963 4.880000e-45 193.0
3 TraesCS2D01G054100 chr2D 78.730 315 39 22 4240 4547 570084039 570084332 8.170000e-43 185.0
4 TraesCS2D01G054100 chr2D 84.615 104 15 1 1925 2027 22423639 22423742 8.470000e-18 102.0
5 TraesCS2D01G054100 chr2B 93.145 2757 164 13 2039 4782 35028892 35026148 0.000000e+00 4021.0
6 TraesCS2D01G054100 chr2B 93.651 1134 54 9 930 2046 35030533 35029401 0.000000e+00 1679.0
7 TraesCS2D01G054100 chr2B 87.100 1062 121 14 2042 3094 34887429 34886375 0.000000e+00 1188.0
8 TraesCS2D01G054100 chr2B 84.006 1238 160 16 3362 4586 34886376 34885164 0.000000e+00 1155.0
9 TraesCS2D01G054100 chr2B 80.255 1413 249 27 2444 3847 39238446 39239837 0.000000e+00 1037.0
10 TraesCS2D01G054100 chr2B 84.349 722 56 27 1 705 35032028 35031347 0.000000e+00 654.0
11 TraesCS2D01G054100 chr2B 84.615 208 29 3 4432 4637 15000003 15000209 2.260000e-48 204.0
12 TraesCS2D01G054100 chr2B 100.000 30 0 0 170 199 35031722 35031751 6.690000e-04 56.5
13 TraesCS2D01G054100 chr2A 92.698 2205 139 13 2039 4227 23804544 23806742 0.000000e+00 3160.0
14 TraesCS2D01G054100 chr2A 85.974 2089 231 24 2036 4113 23831787 23833824 0.000000e+00 2178.0
15 TraesCS2D01G054100 chr2A 93.042 1121 53 10 951 2046 23802985 23804105 0.000000e+00 1615.0
16 TraesCS2D01G054100 chr2A 83.087 881 105 19 1040 1889 24128511 24129378 0.000000e+00 761.0
17 TraesCS2D01G054100 chr2A 88.991 545 57 2 4241 4782 23820711 23821255 0.000000e+00 671.0
18 TraesCS2D01G054100 chrUn 82.421 950 110 26 986 1889 16951272 16952210 0.000000e+00 776.0
19 TraesCS2D01G054100 chrUn 82.421 950 110 26 986 1889 266455518 266456456 0.000000e+00 776.0
20 TraesCS2D01G054100 chrUn 82.421 950 110 26 986 1889 282234019 282233081 0.000000e+00 776.0
21 TraesCS2D01G054100 chrUn 79.880 333 43 13 4300 4626 16172657 16172343 6.230000e-54 222.0
22 TraesCS2D01G054100 chrUn 83.654 104 16 1 1928 2030 360308524 360308421 3.940000e-16 97.1
23 TraesCS2D01G054100 chr5D 86.500 200 22 4 4432 4626 536288694 536288495 1.040000e-51 215.0
24 TraesCS2D01G054100 chr5D 83.410 217 30 5 4446 4658 461086637 461086851 3.780000e-46 196.0
25 TraesCS2D01G054100 chr5D 82.096 229 38 3 4174 4399 257732385 257732157 4.880000e-45 193.0
26 TraesCS2D01G054100 chr5D 77.202 386 53 23 4239 4608 477882275 477881909 4.880000e-45 193.0
27 TraesCS2D01G054100 chr5D 83.173 208 33 2 4455 4662 300172646 300172441 6.320000e-44 189.0
28 TraesCS2D01G054100 chr5D 74.942 431 66 33 4213 4618 7917023 7916610 4.950000e-35 159.0
29 TraesCS2D01G054100 chr4D 82.258 248 39 4 4429 4673 352673308 352673063 4.850000e-50 209.0
30 TraesCS2D01G054100 chr3A 83.721 215 27 7 4453 4661 639089660 639089872 3.780000e-46 196.0
31 TraesCS2D01G054100 chr5A 74.638 414 70 29 4213 4605 263591696 263592095 2.980000e-32 150.0
32 TraesCS2D01G054100 chr5A 81.053 190 31 5 4213 4399 191310682 191310495 3.860000e-31 147.0
33 TraesCS2D01G054100 chr4A 79.670 182 30 7 4174 4351 165899891 165900069 1.810000e-24 124.0


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 TraesCS2D01G054100 chr2D 21606694 21611475 4781 False 8831.0 8831 100.000000 1 4782 1 chr2D.!!$F1 4781
1 TraesCS2D01G054100 chr2D 22419603 22423742 4139 False 432.5 763 83.462000 986 2027 2 chr2D.!!$F4 1041
2 TraesCS2D01G054100 chr2B 35026148 35032028 5880 True 2118.0 4021 90.381667 1 4782 3 chr2B.!!$R2 4781
3 TraesCS2D01G054100 chr2B 34885164 34887429 2265 True 1171.5 1188 85.553000 2042 4586 2 chr2B.!!$R1 2544
4 TraesCS2D01G054100 chr2B 39238446 39239837 1391 False 1037.0 1037 80.255000 2444 3847 1 chr2B.!!$F3 1403
5 TraesCS2D01G054100 chr2A 23802985 23806742 3757 False 2387.5 3160 92.870000 951 4227 2 chr2A.!!$F4 3276
6 TraesCS2D01G054100 chr2A 23831787 23833824 2037 False 2178.0 2178 85.974000 2036 4113 1 chr2A.!!$F2 2077
7 TraesCS2D01G054100 chr2A 24128511 24129378 867 False 761.0 761 83.087000 1040 1889 1 chr2A.!!$F3 849
8 TraesCS2D01G054100 chr2A 23820711 23821255 544 False 671.0 671 88.991000 4241 4782 1 chr2A.!!$F1 541
9 TraesCS2D01G054100 chrUn 16951272 16952210 938 False 776.0 776 82.421000 986 1889 1 chrUn.!!$F1 903
10 TraesCS2D01G054100 chrUn 266455518 266456456 938 False 776.0 776 82.421000 986 1889 1 chrUn.!!$F2 903
11 TraesCS2D01G054100 chrUn 282233081 282234019 938 True 776.0 776 82.421000 986 1889 1 chrUn.!!$R2 903

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
496 501 0.179111 CAGTGTCTGTGTCACCACGT 60.179 55.000 0.00 0.0 44.92 4.49 F
1111 1746 0.179936 GCCTGATCAGCTGCTACCTT 59.820 55.000 17.76 0.0 0.00 3.50 F
1383 2033 1.330521 CAACACAACGGACAACTCCAG 59.669 52.381 0.00 0.0 36.12 3.86 F
2737 5297 1.337728 CCGGGAAAAATCCAAGTTGCC 60.338 52.381 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 2442 0.312416 CGTCGTCCCTGAGATCCATC 59.688 60.000 0.00 0.00 0.00 3.51 R
2306 4842 0.597568 TGAAACATTGGCTTGGCTCG 59.402 50.000 0.00 0.00 0.00 5.03 R
2800 5360 1.305213 GCCAAAGGATCCCTTGCCA 60.305 57.895 16.52 0.00 43.92 4.92 R
4729 8179 0.036875 AGGTAACCAGCTGAGTTGGC 59.963 55.000 22.99 16.97 37.43 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.785453 CCGGCCAGCCCACTTCTC 62.785 72.222 2.24 0.00 0.00 2.87
105 109 4.111016 CTCGCCGCGTCCACACTA 62.111 66.667 13.39 0.00 0.00 2.74
106 110 4.409218 TCGCCGCGTCCACACTAC 62.409 66.667 13.39 0.00 0.00 2.73
112 116 1.863662 CGCGTCCACACTACTCCACT 61.864 60.000 0.00 0.00 0.00 4.00
117 121 2.548480 GTCCACACTACTCCACTTTTGC 59.452 50.000 0.00 0.00 0.00 3.68
128 132 3.620488 TCCACTTTTGCAAGTTCTGAGT 58.380 40.909 0.00 0.00 40.66 3.41
151 155 4.000988 TGCGAGTTAAAGATTTGAGTCCC 58.999 43.478 0.00 0.00 0.00 4.46
254 258 4.762251 GTCCTTGACTTGGCAGTTATTTCT 59.238 41.667 0.00 0.00 31.22 2.52
262 266 6.449698 ACTTGGCAGTTATTTCTGAACAATG 58.550 36.000 0.00 0.00 37.61 2.82
270 275 8.230486 CAGTTATTTCTGAACAATGTGGTCTAC 58.770 37.037 0.00 0.00 34.53 2.59
279 284 1.257750 ATGTGGTCTACGCTGGCTGA 61.258 55.000 0.00 0.00 0.00 4.26
326 331 0.381801 GCATATGGAAGGGTGCGTTG 59.618 55.000 4.56 0.00 0.00 4.10
340 345 2.363683 TGCGTTGCACATATGATTGGA 58.636 42.857 10.38 0.00 31.71 3.53
341 346 2.355444 TGCGTTGCACATATGATTGGAG 59.645 45.455 10.38 0.00 31.71 3.86
364 369 6.653020 AGTAGATGAAAATGTGCTCCATGTA 58.347 36.000 0.00 0.00 32.82 2.29
373 378 2.695147 TGTGCTCCATGTACAGATCGAT 59.305 45.455 0.00 0.00 36.38 3.59
381 386 3.047613 TGTACAGATCGATCGTTGACG 57.952 47.619 21.77 10.72 41.45 4.35
395 400 2.962253 GACGATGCTAGCCGGCAC 60.962 66.667 31.54 18.33 45.36 5.01
396 401 3.432051 GACGATGCTAGCCGGCACT 62.432 63.158 31.54 12.06 45.36 4.40
402 407 0.539518 TGCTAGCCGGCACTGATTTA 59.460 50.000 31.54 9.35 37.29 1.40
406 411 3.730963 GCTAGCCGGCACTGATTTAAAAC 60.731 47.826 31.54 0.00 0.00 2.43
407 412 2.514803 AGCCGGCACTGATTTAAAACT 58.485 42.857 31.54 0.00 0.00 2.66
408 413 2.488153 AGCCGGCACTGATTTAAAACTC 59.512 45.455 31.54 0.00 0.00 3.01
409 414 2.727916 GCCGGCACTGATTTAAAACTCG 60.728 50.000 24.80 0.00 0.00 4.18
410 415 2.505866 CGGCACTGATTTAAAACTCGC 58.494 47.619 0.00 0.00 0.00 5.03
411 416 2.727916 CGGCACTGATTTAAAACTCGCC 60.728 50.000 10.96 10.96 0.00 5.54
412 417 2.415491 GGCACTGATTTAAAACTCGCCC 60.415 50.000 10.28 0.00 0.00 6.13
413 418 2.488153 GCACTGATTTAAAACTCGCCCT 59.512 45.455 0.00 0.00 0.00 5.19
414 419 3.670627 GCACTGATTTAAAACTCGCCCTG 60.671 47.826 0.00 0.00 0.00 4.45
415 420 3.081804 ACTGATTTAAAACTCGCCCTGG 58.918 45.455 0.00 0.00 0.00 4.45
416 421 3.081804 CTGATTTAAAACTCGCCCTGGT 58.918 45.455 0.00 0.00 0.00 4.00
417 422 4.258543 CTGATTTAAAACTCGCCCTGGTA 58.741 43.478 0.00 0.00 0.00 3.25
418 423 4.653868 TGATTTAAAACTCGCCCTGGTAA 58.346 39.130 0.00 0.00 0.00 2.85
434 439 1.933853 GGTAAGCCATTACTGCTGTCG 59.066 52.381 0.00 0.00 40.99 4.35
464 469 3.513909 TTATGGATCCAGGGAATGCAG 57.486 47.619 21.33 0.00 0.00 4.41
467 472 0.548031 GGATCCAGGGAATGCAGACA 59.452 55.000 6.95 0.00 0.00 3.41
468 473 1.144503 GGATCCAGGGAATGCAGACAT 59.855 52.381 6.95 0.00 38.49 3.06
469 474 2.373169 GGATCCAGGGAATGCAGACATA 59.627 50.000 6.95 0.00 34.62 2.29
477 482 5.471456 CAGGGAATGCAGACATAGATAAACC 59.529 44.000 0.00 0.00 34.62 3.27
493 498 0.908910 AACCAGTGTCTGTGTCACCA 59.091 50.000 0.00 0.00 36.58 4.17
496 501 0.179111 CAGTGTCTGTGTCACCACGT 60.179 55.000 0.00 0.00 44.92 4.49
497 502 1.066454 CAGTGTCTGTGTCACCACGTA 59.934 52.381 0.00 0.00 44.92 3.57
512 517 4.024387 CACCACGTATACAACAACAAAGCT 60.024 41.667 3.32 0.00 0.00 3.74
515 520 5.407387 CCACGTATACAACAACAAAGCTACT 59.593 40.000 3.32 0.00 0.00 2.57
517 522 7.349711 CACGTATACAACAACAAAGCTACTTT 58.650 34.615 3.32 0.00 33.58 2.66
519 524 7.225145 ACGTATACAACAACAAAGCTACTTTCA 59.775 33.333 3.32 0.00 30.60 2.69
524 529 6.918022 ACAACAACAAAGCTACTTTCATTAGC 59.082 34.615 0.00 0.00 42.06 3.09
525 530 6.633500 ACAACAAAGCTACTTTCATTAGCA 57.367 33.333 4.31 0.00 43.85 3.49
526 531 6.672147 ACAACAAAGCTACTTTCATTAGCAG 58.328 36.000 4.31 0.00 43.85 4.24
527 532 6.263168 ACAACAAAGCTACTTTCATTAGCAGT 59.737 34.615 4.31 0.00 43.85 4.40
529 534 7.602517 ACAAAGCTACTTTCATTAGCAGTAG 57.397 36.000 4.31 0.00 43.85 2.57
535 540 7.227992 CTACTTTCATTAGCAGTAGCAAGTC 57.772 40.000 0.00 0.00 45.49 3.01
536 541 5.799213 ACTTTCATTAGCAGTAGCAAGTCT 58.201 37.500 0.00 0.00 45.49 3.24
537 542 5.872070 ACTTTCATTAGCAGTAGCAAGTCTC 59.128 40.000 0.00 0.00 45.49 3.36
538 543 5.667539 TTCATTAGCAGTAGCAAGTCTCT 57.332 39.130 0.00 0.00 45.49 3.10
539 544 5.003692 TCATTAGCAGTAGCAAGTCTCTG 57.996 43.478 0.00 0.00 45.49 3.35
540 545 4.464244 TCATTAGCAGTAGCAAGTCTCTGT 59.536 41.667 0.00 0.00 45.49 3.41
541 546 2.739885 AGCAGTAGCAAGTCTCTGTG 57.260 50.000 0.00 0.00 45.49 3.66
542 547 2.242926 AGCAGTAGCAAGTCTCTGTGA 58.757 47.619 0.00 0.00 45.49 3.58
543 548 2.630098 AGCAGTAGCAAGTCTCTGTGAA 59.370 45.455 0.00 0.00 45.49 3.18
544 549 2.992543 GCAGTAGCAAGTCTCTGTGAAG 59.007 50.000 0.00 0.00 41.58 3.02
545 550 3.305676 GCAGTAGCAAGTCTCTGTGAAGA 60.306 47.826 0.00 0.00 41.58 2.87
546 551 4.620332 GCAGTAGCAAGTCTCTGTGAAGAT 60.620 45.833 0.00 0.00 41.58 2.40
547 552 4.863689 CAGTAGCAAGTCTCTGTGAAGATG 59.136 45.833 0.00 0.00 0.00 2.90
548 553 4.526262 AGTAGCAAGTCTCTGTGAAGATGT 59.474 41.667 0.00 0.00 0.00 3.06
549 554 5.712446 AGTAGCAAGTCTCTGTGAAGATGTA 59.288 40.000 0.00 0.00 0.00 2.29
550 555 4.815269 AGCAAGTCTCTGTGAAGATGTAC 58.185 43.478 0.00 0.00 0.00 2.90
551 556 4.281941 AGCAAGTCTCTGTGAAGATGTACA 59.718 41.667 0.00 0.00 0.00 2.90
552 557 5.046735 AGCAAGTCTCTGTGAAGATGTACAT 60.047 40.000 8.43 8.43 0.00 2.29
553 558 6.153510 AGCAAGTCTCTGTGAAGATGTACATA 59.846 38.462 8.71 0.00 0.00 2.29
554 559 6.254589 GCAAGTCTCTGTGAAGATGTACATAC 59.745 42.308 8.71 3.88 0.00 2.39
555 560 7.315890 CAAGTCTCTGTGAAGATGTACATACA 58.684 38.462 8.71 8.59 40.98 2.29
556 561 7.468141 AGTCTCTGTGAAGATGTACATACAA 57.532 36.000 8.71 0.88 39.99 2.41
557 562 8.072321 AGTCTCTGTGAAGATGTACATACAAT 57.928 34.615 8.71 0.00 39.99 2.71
577 582 5.590259 ACAATAATGAACCTGCACATAGTCC 59.410 40.000 0.00 0.00 0.00 3.85
585 590 4.493618 ACCTGCACATAGTCCCATAGTAT 58.506 43.478 0.00 0.00 0.00 2.12
586 591 5.651303 ACCTGCACATAGTCCCATAGTATA 58.349 41.667 0.00 0.00 0.00 1.47
587 592 5.480772 ACCTGCACATAGTCCCATAGTATAC 59.519 44.000 0.00 0.00 0.00 1.47
588 593 5.393135 CCTGCACATAGTCCCATAGTATACG 60.393 48.000 0.00 0.00 0.00 3.06
589 594 4.082408 TGCACATAGTCCCATAGTATACGC 60.082 45.833 0.00 0.00 0.00 4.42
590 595 4.158025 GCACATAGTCCCATAGTATACGCT 59.842 45.833 0.00 0.00 0.00 5.07
591 596 5.336531 GCACATAGTCCCATAGTATACGCTT 60.337 44.000 0.00 0.00 0.00 4.68
592 597 6.688578 CACATAGTCCCATAGTATACGCTTT 58.311 40.000 0.00 0.00 0.00 3.51
593 598 6.807230 CACATAGTCCCATAGTATACGCTTTC 59.193 42.308 0.00 0.00 0.00 2.62
596 601 6.481434 AGTCCCATAGTATACGCTTTCTTT 57.519 37.500 0.00 0.00 0.00 2.52
597 602 7.592885 AGTCCCATAGTATACGCTTTCTTTA 57.407 36.000 0.00 0.00 0.00 1.85
599 604 7.287235 AGTCCCATAGTATACGCTTTCTTTACT 59.713 37.037 0.00 0.00 0.00 2.24
600 605 7.594386 GTCCCATAGTATACGCTTTCTTTACTC 59.406 40.741 0.00 0.00 0.00 2.59
601 606 7.504911 TCCCATAGTATACGCTTTCTTTACTCT 59.495 37.037 0.00 0.00 0.00 3.24
602 607 8.142551 CCCATAGTATACGCTTTCTTTACTCTT 58.857 37.037 0.00 0.00 0.00 2.85
603 608 9.530633 CCATAGTATACGCTTTCTTTACTCTTT 57.469 33.333 0.00 0.00 0.00 2.52
606 611 8.914328 AGTATACGCTTTCTTTACTCTTTCTC 57.086 34.615 0.00 0.00 0.00 2.87
635 651 2.037772 CCGGCTGCCAGAGTAATAGAAT 59.962 50.000 20.29 0.00 0.00 2.40
643 659 6.359804 TGCCAGAGTAATAGAATTTGCTCAT 58.640 36.000 5.34 0.00 39.82 2.90
665 682 2.169769 CTGCTCTTAACCCCAACCGATA 59.830 50.000 0.00 0.00 0.00 2.92
666 683 2.572556 TGCTCTTAACCCCAACCGATAA 59.427 45.455 0.00 0.00 0.00 1.75
667 684 3.201266 TGCTCTTAACCCCAACCGATAAT 59.799 43.478 0.00 0.00 0.00 1.28
671 688 4.944930 TCTTAACCCCAACCGATAATTGTG 59.055 41.667 0.00 0.00 0.00 3.33
674 691 3.613030 ACCCCAACCGATAATTGTGTAC 58.387 45.455 0.00 0.00 0.00 2.90
701 718 2.083774 CATGTGGCTTCGGTTACATGT 58.916 47.619 2.69 2.69 43.19 3.21
704 721 3.741249 TGTGGCTTCGGTTACATGTAAA 58.259 40.909 19.63 2.07 0.00 2.01
705 722 4.135306 TGTGGCTTCGGTTACATGTAAAA 58.865 39.130 19.63 9.99 0.00 1.52
735 1238 8.871125 ACTATTTTCTCTCTTTCTAACACTCCA 58.129 33.333 0.00 0.00 0.00 3.86
745 1248 0.766674 TAACACTCCACACTGGCCCT 60.767 55.000 0.00 0.00 37.47 5.19
746 1249 1.645402 AACACTCCACACTGGCCCTT 61.645 55.000 0.00 0.00 37.47 3.95
748 1251 2.352805 CTCCACACTGGCCCTTCC 59.647 66.667 0.00 0.00 37.47 3.46
755 1258 1.992557 ACACTGGCCCTTCCAAATAGA 59.007 47.619 0.00 0.00 46.01 1.98
757 1260 3.011708 ACACTGGCCCTTCCAAATAGAAT 59.988 43.478 0.00 0.00 46.01 2.40
758 1261 3.382546 CACTGGCCCTTCCAAATAGAATG 59.617 47.826 0.00 0.00 46.01 2.67
768 1272 6.206243 CCTTCCAAATAGAATGCTCTACCATG 59.794 42.308 0.00 0.00 36.98 3.66
774 1278 4.414337 AGAATGCTCTACCATGAGTTCC 57.586 45.455 0.00 0.00 36.51 3.62
788 1292 2.029290 TGAGTTCCAGGTTCGAAGTAGC 60.029 50.000 0.00 0.00 0.00 3.58
799 1303 1.279527 CGAAGTAGCGCGGAAACACA 61.280 55.000 8.83 0.00 0.00 3.72
868 1375 8.034313 ACTAAGATATTATTCCTGAACAGCCA 57.966 34.615 0.00 0.00 0.00 4.75
875 1383 0.478072 TCCTGAACAGCCACCAACAT 59.522 50.000 0.00 0.00 0.00 2.71
879 1387 1.168714 GAACAGCCACCAACATCTCC 58.831 55.000 0.00 0.00 0.00 3.71
932 1440 2.658285 CAGTTGTCACAATCAGCTTGC 58.342 47.619 0.00 0.00 38.50 4.01
933 1441 2.033675 CAGTTGTCACAATCAGCTTGCA 59.966 45.455 0.00 0.00 38.50 4.08
934 1442 2.689471 AGTTGTCACAATCAGCTTGCAA 59.311 40.909 0.00 0.00 38.50 4.08
935 1443 3.319972 AGTTGTCACAATCAGCTTGCAAT 59.680 39.130 0.00 0.00 38.50 3.56
937 1445 2.624364 TGTCACAATCAGCTTGCAATGT 59.376 40.909 0.00 0.00 38.50 2.71
938 1446 3.240069 GTCACAATCAGCTTGCAATGTC 58.760 45.455 0.00 0.00 38.50 3.06
939 1447 3.057736 GTCACAATCAGCTTGCAATGTCT 60.058 43.478 0.00 0.00 38.50 3.41
941 1449 4.154737 TCACAATCAGCTTGCAATGTCTAC 59.845 41.667 0.00 0.00 38.50 2.59
942 1450 4.074259 ACAATCAGCTTGCAATGTCTACA 58.926 39.130 0.00 0.00 38.50 2.74
943 1451 4.155462 ACAATCAGCTTGCAATGTCTACAG 59.845 41.667 0.00 0.00 38.50 2.74
944 1452 2.703416 TCAGCTTGCAATGTCTACAGG 58.297 47.619 0.00 0.00 0.00 4.00
1007 1615 0.815734 GCATGAGCAAGCAACCTGAT 59.184 50.000 0.00 0.00 41.58 2.90
1032 1645 2.805194 ACGGACCACTAGCTTAACTCT 58.195 47.619 0.00 0.00 0.00 3.24
1092 1721 0.397254 ATCCTCCTCCCCACGTACTG 60.397 60.000 0.00 0.00 0.00 2.74
1111 1746 0.179936 GCCTGATCAGCTGCTACCTT 59.820 55.000 17.76 0.00 0.00 3.50
1129 1770 2.614481 CCTTTTTCTAGCCGCCTACACA 60.614 50.000 0.00 0.00 0.00 3.72
1185 1832 3.387091 CACCATCCCGACGGACCA 61.387 66.667 17.49 0.00 42.48 4.02
1383 2033 1.330521 CAACACAACGGACAACTCCAG 59.669 52.381 0.00 0.00 36.12 3.86
1768 2442 1.393597 CCTACGAGTTCAACGCGACG 61.394 60.000 21.10 9.91 44.09 5.12
1889 2563 6.025989 GGTCCTTCCACTCAACAGGTAACT 62.026 50.000 0.00 0.00 42.23 2.24
1923 3761 1.611977 GTGTGTTTTTCCTGGCCTACC 59.388 52.381 3.32 0.00 0.00 3.18
1926 3764 3.244770 TGTGTTTTTCCTGGCCTACCTAG 60.245 47.826 3.32 0.00 36.63 3.02
2037 4558 4.671766 GCCCGACTTTCACATCATTGTTAC 60.672 45.833 0.00 0.00 32.34 2.50
2278 4814 8.763356 CAGAACATGATGATTTAGAGAGTTAGC 58.237 37.037 0.00 0.00 0.00 3.09
2729 5289 2.452505 TCCAATCACCGGGAAAAATCC 58.547 47.619 6.32 0.00 0.00 3.01
2737 5297 1.337728 CCGGGAAAAATCCAAGTTGCC 60.338 52.381 0.00 0.00 0.00 4.52
2743 5303 4.309933 GAAAAATCCAAGTTGCCAGGAAG 58.690 43.478 0.00 0.00 34.62 3.46
2769 5329 3.197333 TCGTACTCTGAGCTAGTAGTGGT 59.803 47.826 4.19 3.13 30.26 4.16
2800 5360 9.634021 GATAACTTCTCCAAGGATAGGAAAATT 57.366 33.333 0.00 0.00 34.08 1.82
3051 5611 1.938657 CTCAGCGACCATCTCCACGT 61.939 60.000 0.00 0.00 0.00 4.49
3181 5747 1.669999 GGTACGTGCTACACCGGGAT 61.670 60.000 6.32 0.00 0.00 3.85
3460 6026 4.388499 AACCTCATCGCCGCCGTT 62.388 61.111 0.00 0.00 35.54 4.44
3520 6086 0.178909 ATGAGCGGATGAGAGGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
3557 6123 0.742281 GCAGATGGAGCGTGTCATGT 60.742 55.000 0.00 0.00 0.00 3.21
3558 6124 1.284657 CAGATGGAGCGTGTCATGTC 58.715 55.000 0.00 0.00 0.00 3.06
3565 6131 2.860293 CGTGTCATGTCAACCGGC 59.140 61.111 0.00 0.00 0.00 6.13
3974 6546 2.229543 GGTTGCTTGATGATGCTCACAA 59.770 45.455 0.00 0.00 0.00 3.33
3975 6547 3.119245 GGTTGCTTGATGATGCTCACAAT 60.119 43.478 0.00 0.00 0.00 2.71
3976 6548 4.096833 GGTTGCTTGATGATGCTCACAATA 59.903 41.667 0.00 0.00 0.00 1.90
3977 6549 5.393352 GGTTGCTTGATGATGCTCACAATAA 60.393 40.000 0.00 0.00 0.00 1.40
3978 6550 6.270815 GTTGCTTGATGATGCTCACAATAAT 58.729 36.000 0.00 0.00 0.00 1.28
3979 6551 6.459670 TGCTTGATGATGCTCACAATAATT 57.540 33.333 0.00 0.00 0.00 1.40
3980 6552 6.270064 TGCTTGATGATGCTCACAATAATTG 58.730 36.000 0.00 0.00 0.00 2.32
3983 6555 6.778834 TGATGATGCTCACAATAATTGGTT 57.221 33.333 0.00 0.00 34.12 3.67
3991 7433 5.336372 GCTCACAATAATTGGTTGCCTACAA 60.336 40.000 5.59 0.00 34.12 2.41
3992 7434 6.627953 GCTCACAATAATTGGTTGCCTACAAT 60.628 38.462 5.59 0.00 38.27 2.71
3993 7435 7.416213 GCTCACAATAATTGGTTGCCTACAATA 60.416 37.037 5.59 0.00 38.27 1.90
4003 7446 5.046950 TGGTTGCCTACAATAATTTTGGTCC 60.047 40.000 0.00 0.00 38.27 4.46
4012 7455 4.918810 ATAATTTTGGTCCTTCGATGCC 57.081 40.909 0.00 0.00 0.00 4.40
4057 7500 6.194967 TCCTAGATGATGTGTGTTCCTCTTA 58.805 40.000 0.00 0.00 0.00 2.10
4059 7502 4.764172 AGATGATGTGTGTTCCTCTTAGC 58.236 43.478 0.00 0.00 0.00 3.09
4141 7584 0.254178 GCATGATGGTGTCCAGGACT 59.746 55.000 20.82 0.00 36.75 3.85
4207 7653 1.232909 TACTCCTAGCTAGGTGGGCT 58.767 55.000 34.11 21.57 44.02 5.19
4209 7655 0.397816 CTCCTAGCTAGGTGGGCTGT 60.398 60.000 33.84 0.00 44.02 4.40
4233 7679 1.176619 GGACCCCCTTTGTCGGTTTG 61.177 60.000 0.00 0.00 33.46 2.93
4237 7683 0.179001 CCCCTTTGTCGGTTTGGTCT 60.179 55.000 0.00 0.00 0.00 3.85
4238 7684 1.235724 CCCTTTGTCGGTTTGGTCTC 58.764 55.000 0.00 0.00 0.00 3.36
4370 7818 9.570468 CCTAGGCCTACGATACATTATATAAGA 57.430 37.037 8.91 0.00 0.00 2.10
4414 7862 7.415592 AGATCATTAGAGTCTCAACACATCA 57.584 36.000 0.00 0.00 0.00 3.07
4443 7891 9.862371 GAGATGAAACTACTCTCATAGACAAAA 57.138 33.333 0.00 0.00 36.31 2.44
4534 7982 3.115556 CTCTTCGAGAGAGCCCGG 58.884 66.667 10.36 0.00 45.07 5.73
4605 8053 1.074699 GGACCCCCTACCCGAGATT 60.075 63.158 0.00 0.00 0.00 2.40
4608 8056 0.253020 ACCCCCTACCCGAGATTTGT 60.253 55.000 0.00 0.00 0.00 2.83
4618 8066 4.344104 ACCCGAGATTTGTTGGATTTGAT 58.656 39.130 0.00 0.00 0.00 2.57
4688 8138 6.073276 TGTGTGACAAAAGATTAGATCGGTTG 60.073 38.462 0.00 5.59 35.44 3.77
4694 8144 0.874607 GATTAGATCGGTTGCGGCGT 60.875 55.000 9.37 0.00 0.00 5.68
4729 8179 2.806288 ACGAATTTTCATCTTCGGCG 57.194 45.000 0.00 0.00 46.37 6.46
4737 8187 1.741401 CATCTTCGGCGCCAACTCA 60.741 57.895 28.98 5.83 0.00 3.41
4758 8208 0.112412 CTGGTTACCTGGGCCAAGTT 59.888 55.000 14.01 0.00 0.00 2.66
4778 8228 1.203250 TGAGGACTACACCCCATGTCA 60.203 52.381 0.00 0.00 42.09 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.675714 CGGTCCACAGCTTCAGCATTA 60.676 52.381 0.75 0.00 45.16 1.90
29 30 2.743928 CCGGTCCACAGCTTCAGC 60.744 66.667 0.00 0.00 42.49 4.26
64 65 0.861837 CAGTGAAAGAGTGTGGACGC 59.138 55.000 0.00 0.00 0.00 5.19
69 73 0.890996 GGGGGCAGTGAAAGAGTGTG 60.891 60.000 0.00 0.00 0.00 3.82
103 107 4.816385 TCAGAACTTGCAAAAGTGGAGTAG 59.184 41.667 0.00 0.00 32.47 2.57
105 109 3.620488 TCAGAACTTGCAAAAGTGGAGT 58.380 40.909 0.00 0.00 32.47 3.85
106 110 3.629398 ACTCAGAACTTGCAAAAGTGGAG 59.371 43.478 0.00 7.94 34.85 3.86
112 116 2.421775 TCGCAACTCAGAACTTGCAAAA 59.578 40.909 0.00 0.00 42.50 2.44
117 121 5.234329 TCTTTAACTCGCAACTCAGAACTTG 59.766 40.000 0.00 0.00 0.00 3.16
128 132 4.454504 GGGACTCAAATCTTTAACTCGCAA 59.545 41.667 0.00 0.00 0.00 4.85
162 166 4.175337 GCTAGCACATGCCCGGGA 62.175 66.667 29.31 10.35 43.38 5.14
165 169 1.434622 CTGAAGCTAGCACATGCCCG 61.435 60.000 18.83 1.10 43.38 6.13
237 241 5.689383 TGTTCAGAAATAACTGCCAAGTC 57.311 39.130 0.00 0.00 34.77 3.01
254 258 2.412870 CAGCGTAGACCACATTGTTCA 58.587 47.619 0.00 0.00 0.00 3.18
262 266 0.108138 AATCAGCCAGCGTAGACCAC 60.108 55.000 0.00 0.00 0.00 4.16
270 275 3.207669 GGAGCCAATCAGCCAGCG 61.208 66.667 0.00 0.00 0.00 5.18
326 331 7.734924 TTTCATCTACTCCAATCATATGTGC 57.265 36.000 1.90 0.00 0.00 4.57
340 345 5.503927 ACATGGAGCACATTTTCATCTACT 58.496 37.500 0.00 0.00 37.84 2.57
341 346 5.824904 ACATGGAGCACATTTTCATCTAC 57.175 39.130 0.00 0.00 37.84 2.59
381 386 0.533755 AATCAGTGCCGGCTAGCATC 60.534 55.000 29.70 10.71 46.24 3.91
395 400 3.081804 ACCAGGGCGAGTTTTAAATCAG 58.918 45.455 0.00 0.00 0.00 2.90
396 401 3.149005 ACCAGGGCGAGTTTTAAATCA 57.851 42.857 0.00 0.00 0.00 2.57
402 407 0.608308 GGCTTACCAGGGCGAGTTTT 60.608 55.000 0.00 0.00 35.26 2.43
414 419 1.933853 CGACAGCAGTAATGGCTTACC 59.066 52.381 0.00 0.00 40.23 2.85
415 420 2.618053 ACGACAGCAGTAATGGCTTAC 58.382 47.619 0.00 0.00 40.23 2.34
416 421 3.000041 CAACGACAGCAGTAATGGCTTA 59.000 45.455 0.00 0.00 40.23 3.09
417 422 1.806542 CAACGACAGCAGTAATGGCTT 59.193 47.619 0.00 0.00 40.23 4.35
418 423 1.442769 CAACGACAGCAGTAATGGCT 58.557 50.000 0.00 0.00 43.77 4.75
434 439 4.038402 CCCTGGATCCATAAAAGATGCAAC 59.962 45.833 16.63 0.00 40.89 4.17
464 469 6.398918 ACACAGACACTGGTTTATCTATGTC 58.601 40.000 0.00 0.00 35.51 3.06
467 472 6.398918 GTGACACAGACACTGGTTTATCTAT 58.601 40.000 0.00 0.00 35.51 1.98
468 473 5.279306 GGTGACACAGACACTGGTTTATCTA 60.279 44.000 8.08 0.00 38.20 1.98
469 474 4.503296 GGTGACACAGACACTGGTTTATCT 60.503 45.833 8.08 0.00 38.20 1.98
493 498 7.225145 TGAAAGTAGCTTTGTTGTTGTATACGT 59.775 33.333 0.00 0.00 33.49 3.57
512 517 6.936279 AGACTTGCTACTGCTAATGAAAGTA 58.064 36.000 0.00 0.00 40.48 2.24
515 520 5.871524 CAGAGACTTGCTACTGCTAATGAAA 59.128 40.000 0.00 0.00 40.48 2.69
517 522 4.464244 ACAGAGACTTGCTACTGCTAATGA 59.536 41.667 0.00 0.00 40.48 2.57
519 524 4.464244 TCACAGAGACTTGCTACTGCTAAT 59.536 41.667 0.00 0.00 40.48 1.73
523 528 2.732412 TCACAGAGACTTGCTACTGC 57.268 50.000 0.00 0.00 40.20 4.40
524 529 4.511617 TCTTCACAGAGACTTGCTACTG 57.488 45.455 0.00 0.00 36.58 2.74
525 530 4.526262 ACATCTTCACAGAGACTTGCTACT 59.474 41.667 0.00 0.00 30.36 2.57
526 531 4.815269 ACATCTTCACAGAGACTTGCTAC 58.185 43.478 0.00 0.00 30.36 3.58
527 532 5.476945 TGTACATCTTCACAGAGACTTGCTA 59.523 40.000 0.00 0.00 30.36 3.49
529 534 4.560128 TGTACATCTTCACAGAGACTTGC 58.440 43.478 0.00 0.00 30.36 4.01
530 535 7.315890 TGTATGTACATCTTCACAGAGACTTG 58.684 38.462 12.68 0.00 30.36 3.16
531 536 7.468141 TGTATGTACATCTTCACAGAGACTT 57.532 36.000 12.68 0.00 30.36 3.01
533 538 9.803315 TTATTGTATGTACATCTTCACAGAGAC 57.197 33.333 12.68 1.34 35.89 3.36
542 547 8.840321 GCAGGTTCATTATTGTATGTACATCTT 58.160 33.333 12.68 0.00 35.89 2.40
543 548 7.992608 TGCAGGTTCATTATTGTATGTACATCT 59.007 33.333 12.68 0.00 35.89 2.90
544 549 8.070171 GTGCAGGTTCATTATTGTATGTACATC 58.930 37.037 12.68 5.06 35.89 3.06
545 550 7.555914 TGTGCAGGTTCATTATTGTATGTACAT 59.444 33.333 13.93 13.93 35.89 2.29
546 551 6.881602 TGTGCAGGTTCATTATTGTATGTACA 59.118 34.615 0.00 0.00 30.18 2.90
547 552 7.315247 TGTGCAGGTTCATTATTGTATGTAC 57.685 36.000 0.00 0.00 0.00 2.90
548 553 9.271828 CTATGTGCAGGTTCATTATTGTATGTA 57.728 33.333 0.00 0.00 0.00 2.29
549 554 7.775093 ACTATGTGCAGGTTCATTATTGTATGT 59.225 33.333 0.00 0.00 0.00 2.29
550 555 8.158169 ACTATGTGCAGGTTCATTATTGTATG 57.842 34.615 0.00 0.00 0.00 2.39
551 556 7.445402 GGACTATGTGCAGGTTCATTATTGTAT 59.555 37.037 0.00 0.00 0.00 2.29
552 557 6.765989 GGACTATGTGCAGGTTCATTATTGTA 59.234 38.462 0.00 0.00 0.00 2.41
553 558 5.590259 GGACTATGTGCAGGTTCATTATTGT 59.410 40.000 0.00 0.00 0.00 2.71
554 559 5.009010 GGGACTATGTGCAGGTTCATTATTG 59.991 44.000 0.00 0.00 0.00 1.90
555 560 5.133221 GGGACTATGTGCAGGTTCATTATT 58.867 41.667 0.00 0.00 0.00 1.40
556 561 4.165950 TGGGACTATGTGCAGGTTCATTAT 59.834 41.667 0.00 0.00 0.00 1.28
557 562 3.521531 TGGGACTATGTGCAGGTTCATTA 59.478 43.478 0.00 0.00 0.00 1.90
564 569 5.393135 CGTATACTATGGGACTATGTGCAGG 60.393 48.000 0.56 0.00 0.00 4.85
577 582 9.530633 AAAGAGTAAAGAAAGCGTATACTATGG 57.469 33.333 0.56 0.00 0.00 2.74
585 590 5.766222 ACGAGAAAGAGTAAAGAAAGCGTA 58.234 37.500 0.00 0.00 0.00 4.42
586 591 4.618965 ACGAGAAAGAGTAAAGAAAGCGT 58.381 39.130 0.00 0.00 0.00 5.07
587 592 5.857517 ACTACGAGAAAGAGTAAAGAAAGCG 59.142 40.000 0.00 0.00 0.00 4.68
588 593 6.032670 CGACTACGAGAAAGAGTAAAGAAAGC 59.967 42.308 0.00 0.00 42.66 3.51
589 594 6.032670 GCGACTACGAGAAAGAGTAAAGAAAG 59.967 42.308 0.00 0.00 42.66 2.62
590 595 5.855395 GCGACTACGAGAAAGAGTAAAGAAA 59.145 40.000 0.00 0.00 42.66 2.52
591 596 5.388944 GCGACTACGAGAAAGAGTAAAGAA 58.611 41.667 0.00 0.00 42.66 2.52
592 597 4.142730 GGCGACTACGAGAAAGAGTAAAGA 60.143 45.833 0.00 0.00 42.66 2.52
593 598 4.097012 GGCGACTACGAGAAAGAGTAAAG 58.903 47.826 0.00 0.00 42.66 1.85
596 601 1.662629 CGGCGACTACGAGAAAGAGTA 59.337 52.381 0.00 0.00 42.66 2.59
597 602 0.447011 CGGCGACTACGAGAAAGAGT 59.553 55.000 0.00 0.00 42.66 3.24
599 604 1.798735 CCGGCGACTACGAGAAAGA 59.201 57.895 9.30 0.00 42.66 2.52
600 605 1.872679 GCCGGCGACTACGAGAAAG 60.873 63.158 12.58 0.00 42.66 2.62
601 606 2.180017 GCCGGCGACTACGAGAAA 59.820 61.111 12.58 0.00 42.66 2.52
602 607 2.749044 AGCCGGCGACTACGAGAA 60.749 61.111 23.20 0.00 42.66 2.87
603 608 3.506096 CAGCCGGCGACTACGAGA 61.506 66.667 23.20 0.00 42.66 4.04
621 637 7.307870 GCAGATGAGCAAATTCTATTACTCTGG 60.308 40.741 0.00 0.00 0.00 3.86
624 640 7.656948 AGAGCAGATGAGCAAATTCTATTACTC 59.343 37.037 0.00 0.00 36.85 2.59
635 651 3.347216 GGGTTAAGAGCAGATGAGCAAA 58.653 45.455 0.00 0.00 36.85 3.68
643 659 0.323629 CGGTTGGGGTTAAGAGCAGA 59.676 55.000 0.00 0.00 0.00 4.26
709 726 8.871125 TGGAGTGTTAGAAAGAGAGAAAATAGT 58.129 33.333 0.00 0.00 0.00 2.12
710 727 9.145865 GTGGAGTGTTAGAAAGAGAGAAAATAG 57.854 37.037 0.00 0.00 0.00 1.73
711 728 8.647796 TGTGGAGTGTTAGAAAGAGAGAAAATA 58.352 33.333 0.00 0.00 0.00 1.40
712 729 7.442666 GTGTGGAGTGTTAGAAAGAGAGAAAAT 59.557 37.037 0.00 0.00 0.00 1.82
721 1224 2.808543 GCCAGTGTGGAGTGTTAGAAAG 59.191 50.000 0.00 0.00 40.96 2.62
730 1233 2.529744 GGAAGGGCCAGTGTGGAGT 61.530 63.158 6.18 0.00 40.96 3.85
745 1248 6.899089 TCATGGTAGAGCATTCTATTTGGAA 58.101 36.000 0.00 0.00 38.17 3.53
746 1249 6.100279 ACTCATGGTAGAGCATTCTATTTGGA 59.900 38.462 0.00 0.00 38.17 3.53
748 1251 7.041508 GGAACTCATGGTAGAGCATTCTATTTG 60.042 40.741 0.00 0.00 38.17 2.32
755 1258 3.118112 CCTGGAACTCATGGTAGAGCATT 60.118 47.826 0.00 0.00 39.26 3.56
757 1260 1.833630 CCTGGAACTCATGGTAGAGCA 59.166 52.381 0.00 0.00 39.26 4.26
758 1261 1.834263 ACCTGGAACTCATGGTAGAGC 59.166 52.381 0.00 0.00 39.26 4.09
768 1272 2.608268 GCTACTTCGAACCTGGAACTC 58.392 52.381 0.00 0.00 0.00 3.01
774 1278 2.158959 CCGCGCTACTTCGAACCTG 61.159 63.158 5.56 0.00 0.00 4.00
788 1292 8.775220 TTCAATATTTATATTGTGTTTCCGCG 57.225 30.769 17.53 0.00 46.04 6.46
862 1369 0.700564 ATGGAGATGTTGGTGGCTGT 59.299 50.000 0.00 0.00 0.00 4.40
868 1375 2.885135 TGCTGAATGGAGATGTTGGT 57.115 45.000 0.00 0.00 0.00 3.67
895 1403 6.266558 TGACAACTGCAACCCTATACATTTTT 59.733 34.615 0.00 0.00 0.00 1.94
896 1404 5.772672 TGACAACTGCAACCCTATACATTTT 59.227 36.000 0.00 0.00 0.00 1.82
905 1413 1.956477 GATTGTGACAACTGCAACCCT 59.044 47.619 0.00 0.00 0.00 4.34
910 1418 1.971481 AGCTGATTGTGACAACTGCA 58.029 45.000 21.41 12.14 0.00 4.41
915 1423 3.068448 ACATTGCAAGCTGATTGTGACAA 59.932 39.130 4.94 0.00 41.29 3.18
932 1440 1.556911 AGAGTGGGCCTGTAGACATTG 59.443 52.381 4.53 0.00 0.00 2.82
933 1441 1.556911 CAGAGTGGGCCTGTAGACATT 59.443 52.381 4.53 0.00 0.00 2.71
934 1442 1.198713 CAGAGTGGGCCTGTAGACAT 58.801 55.000 4.53 0.00 0.00 3.06
935 1443 1.544825 GCAGAGTGGGCCTGTAGACA 61.545 60.000 4.53 0.00 34.29 3.41
937 1445 0.545309 AAGCAGAGTGGGCCTGTAGA 60.545 55.000 4.53 0.00 34.29 2.59
938 1446 0.392193 CAAGCAGAGTGGGCCTGTAG 60.392 60.000 4.53 0.00 34.29 2.74
939 1447 0.835971 TCAAGCAGAGTGGGCCTGTA 60.836 55.000 4.53 0.00 34.29 2.74
941 1449 1.073722 TTCAAGCAGAGTGGGCCTG 59.926 57.895 4.53 0.00 34.88 4.85
942 1450 1.073897 GTTCAAGCAGAGTGGGCCT 59.926 57.895 4.53 0.00 0.00 5.19
943 1451 1.973812 GGTTCAAGCAGAGTGGGCC 60.974 63.158 0.00 0.00 0.00 5.80
944 1452 1.973812 GGGTTCAAGCAGAGTGGGC 60.974 63.158 0.00 0.00 0.00 5.36
1007 1615 2.814805 AAGCTAGTGGTCCGTACCTA 57.185 50.000 0.00 0.00 46.91 3.08
1012 1625 2.754002 GAGAGTTAAGCTAGTGGTCCGT 59.246 50.000 0.00 0.00 0.00 4.69
1017 1630 3.732471 GCACGAGAGAGTTAAGCTAGTGG 60.732 52.174 0.00 0.00 36.29 4.00
1092 1721 0.179936 AAGGTAGCAGCTGATCAGGC 59.820 55.000 23.89 18.67 0.00 4.85
1111 1746 1.674817 GCTGTGTAGGCGGCTAGAAAA 60.675 52.381 20.35 9.12 37.74 2.29
1185 1832 1.001293 TGATGAAGTTGAGCTGCTCGT 59.999 47.619 23.35 8.97 32.35 4.18
1362 2012 1.375551 GGAGTTGTCCGTTGTGTTGT 58.624 50.000 0.00 0.00 31.37 3.32
1466 2128 2.639286 GCCGGTGCTGTTCTTGTG 59.361 61.111 1.90 0.00 33.53 3.33
1768 2442 0.312416 CGTCGTCCCTGAGATCCATC 59.688 60.000 0.00 0.00 0.00 3.51
1889 2563 6.655848 GGAAAAACACACACATGGTATAGGTA 59.344 38.462 0.00 0.00 0.00 3.08
1892 2566 6.349280 CCAGGAAAAACACACACATGGTATAG 60.349 42.308 0.00 0.00 0.00 1.31
1923 3761 6.829811 AGAAGGAAACTAGCTAGTACACCTAG 59.170 42.308 29.59 9.14 42.92 3.02
1926 3764 5.918426 AGAAGGAAACTAGCTAGTACACC 57.082 43.478 26.29 25.01 42.68 4.16
2187 4719 6.359480 ACGGCTGTAAACTTTAAGATATGC 57.641 37.500 0.00 1.67 0.00 3.14
2193 4728 8.739461 CAAAAAGTTACGGCTGTAAACTTTAAG 58.261 33.333 27.55 22.37 41.99 1.85
2298 4834 2.192664 TGGCTTGGCTCGTATTTTCA 57.807 45.000 0.00 0.00 0.00 2.69
2306 4842 0.597568 TGAAACATTGGCTTGGCTCG 59.402 50.000 0.00 0.00 0.00 5.03
2535 5072 2.696187 GAGAACACTGGATAGGAGACCC 59.304 54.545 0.00 0.00 0.00 4.46
2729 5289 1.532868 CGAGAACTTCCTGGCAACTTG 59.467 52.381 0.00 0.00 37.61 3.16
2737 5297 3.426963 GCTCAGAGTACGAGAACTTCCTG 60.427 52.174 0.00 0.00 31.84 3.86
2743 5303 5.005971 CACTACTAGCTCAGAGTACGAGAAC 59.994 48.000 0.00 0.00 31.84 3.01
2769 5329 3.437213 TCCTTGGAGAAGTTATCCGTCA 58.563 45.455 11.81 0.00 39.91 4.35
2800 5360 1.305213 GCCAAAGGATCCCTTGCCA 60.305 57.895 16.52 0.00 43.92 4.92
3181 5747 3.457234 CATCACGTTGCTAGGCTTGATA 58.543 45.455 0.00 0.00 0.00 2.15
3205 5771 4.214327 GCCTCGAAGCCCTCTCCG 62.214 72.222 0.00 0.00 0.00 4.63
3406 5972 1.185618 TTCCTGGGACGACTGGTCTG 61.186 60.000 0.00 0.00 45.35 3.51
3460 6026 3.498121 CGTCCCTGCTATAAGACTCCCTA 60.498 52.174 0.00 0.00 0.00 3.53
3520 6086 2.594303 CACCGCCACTGCTCCAAA 60.594 61.111 0.00 0.00 34.43 3.28
3557 6123 1.302431 CACACATCAGGCCGGTTGA 60.302 57.895 19.20 8.27 0.00 3.18
3558 6124 1.577328 GACACACATCAGGCCGGTTG 61.577 60.000 11.85 11.85 0.00 3.77
3565 6131 1.073964 CTTGCTCGACACACATCAGG 58.926 55.000 0.00 0.00 0.00 3.86
3592 6158 0.819582 CTTTGATGGATGGCCGCTTT 59.180 50.000 0.00 0.00 36.79 3.51
3895 6467 6.295859 GCCTTGGAACCCTATTCAAGAAAAAT 60.296 38.462 0.00 0.00 38.96 1.82
3910 6482 0.919710 ATCTGGTAGGCCTTGGAACC 59.080 55.000 12.58 13.87 35.27 3.62
3974 6546 9.612066 CCAAAATTATTGTAGGCAACCAATTAT 57.388 29.630 2.40 0.00 37.44 1.28
3975 6547 8.598041 ACCAAAATTATTGTAGGCAACCAATTA 58.402 29.630 2.40 0.00 37.44 1.40
3976 6548 7.457561 ACCAAAATTATTGTAGGCAACCAATT 58.542 30.769 2.40 0.00 37.44 2.32
3977 6549 7.014988 ACCAAAATTATTGTAGGCAACCAAT 57.985 32.000 0.00 0.00 37.44 3.16
3978 6550 6.426646 ACCAAAATTATTGTAGGCAACCAA 57.573 33.333 0.00 0.00 37.44 3.67
3979 6551 5.046950 GGACCAAAATTATTGTAGGCAACCA 60.047 40.000 0.00 0.00 37.44 3.67
3980 6552 5.186992 AGGACCAAAATTATTGTAGGCAACC 59.813 40.000 0.00 0.00 37.44 3.77
3983 6555 5.124776 CGAAGGACCAAAATTATTGTAGGCA 59.875 40.000 0.00 0.00 0.00 4.75
3991 7433 3.636764 GGGCATCGAAGGACCAAAATTAT 59.363 43.478 7.43 0.00 0.00 1.28
3992 7434 3.020984 GGGCATCGAAGGACCAAAATTA 58.979 45.455 7.43 0.00 0.00 1.40
3993 7435 1.824852 GGGCATCGAAGGACCAAAATT 59.175 47.619 7.43 0.00 0.00 1.82
4012 7455 1.202382 GGTAACAAGGGAGACGATCGG 60.202 57.143 20.98 0.81 0.00 4.18
4057 7500 1.409427 GTAAGGCTCGTAGTGATGGCT 59.591 52.381 0.00 0.00 33.97 4.75
4059 7502 2.427453 ACTGTAAGGCTCGTAGTGATGG 59.573 50.000 0.00 0.00 39.30 3.51
4188 7634 1.133450 CAGCCCACCTAGCTAGGAGTA 60.133 57.143 40.40 0.00 46.63 2.59
4207 7653 0.991355 ACAAAGGGGGTCCTCACACA 60.991 55.000 0.00 0.00 44.07 3.72
4209 7655 1.764571 CGACAAAGGGGGTCCTCACA 61.765 60.000 0.00 0.00 44.07 3.58
4233 7679 2.572284 CCGAAGTGACCCGAGACC 59.428 66.667 0.00 0.00 0.00 3.85
4237 7683 3.235481 TTGCCCGAAGTGACCCGA 61.235 61.111 0.00 0.00 0.00 5.14
4238 7684 3.047877 GTTGCCCGAAGTGACCCG 61.048 66.667 0.00 0.00 0.00 5.28
4370 7818 1.038130 ATCGACTAGCCAAGCCTCGT 61.038 55.000 0.00 0.00 0.00 4.18
4443 7891 8.417106 AGTACATGTTGATCTATCACGAGATTT 58.583 33.333 2.30 0.00 36.27 2.17
4453 7901 7.620094 GGGGGTATAGAGTACATGTTGATCTAT 59.380 40.741 21.25 21.25 37.11 1.98
4534 7982 5.409826 CAGAGACACAAATTTCACCTAGGTC 59.590 44.000 12.84 0.00 0.00 3.85
4618 8066 2.689175 GGGCCACCCATGATGGAA 59.311 61.111 14.26 0.00 44.65 3.53
4636 8084 3.065510 CGACTACACAGATGGACCTGTAG 59.934 52.174 13.62 13.62 44.87 2.74
4670 8118 3.788797 GCCGCAACCGATCTAATCTTTTG 60.789 47.826 0.00 0.00 36.29 2.44
4671 8119 2.354821 GCCGCAACCGATCTAATCTTTT 59.645 45.455 0.00 0.00 36.29 2.27
4694 8144 1.138036 CGTTCCGGCGTGTAGATCA 59.862 57.895 6.01 0.00 0.00 2.92
4729 8179 0.036875 AGGTAACCAGCTGAGTTGGC 59.963 55.000 22.99 16.97 37.43 4.52
4737 8187 2.142292 CTTGGCCCAGGTAACCAGCT 62.142 60.000 0.00 0.00 34.28 4.24
4758 8208 1.203250 TGACATGGGGTGTAGTCCTCA 60.203 52.381 0.00 0.00 42.36 3.86


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

AutoCloner maintained by Alex Coulton.