Multiple sequence alignment - TraesCS3B01G043200

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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 TraesCS3B01G043200 chr3B 100.000 2429 0 0 1 2429 22198623 22201051 0.000000e+00 4486.0
1 TraesCS3B01G043200 chr3B 84.146 492 73 3 10 496 22172216 22171725 2.830000e-129 472.0
2 TraesCS3B01G043200 chr3B 77.797 572 80 22 1 543 22180249 22179696 2.350000e-80 309.0
3 TraesCS3B01G043200 chr3B 85.526 228 29 3 317 543 22165289 22165065 4.040000e-58 235.0
4 TraesCS3B01G043200 chr3A 89.590 586 38 7 802 1373 21176185 21175609 0.000000e+00 723.0
5 TraesCS3B01G043200 chr3A 85.578 631 71 8 752 1366 21290900 21291526 0.000000e+00 643.0
6 TraesCS3B01G043200 chr3A 84.879 496 67 3 1 488 21267627 21268122 6.030000e-136 494.0
7 TraesCS3B01G043200 chr3A 83.398 518 54 15 1926 2429 21072205 21071706 3.680000e-123 451.0
8 TraesCS3B01G043200 chr3A 87.728 383 42 5 980 1359 21315915 21316295 2.220000e-120 442.0
9 TraesCS3B01G043200 chr3A 81.933 476 69 11 899 1371 21272572 21273033 1.050000e-103 387.0
10 TraesCS3B01G043200 chr3A 85.484 310 22 11 1579 1880 21072599 21072305 3.920000e-78 302.0
11 TraesCS3B01G043200 chr3A 77.148 547 98 16 1 543 21177247 21176724 2.360000e-75 292.0
12 TraesCS3B01G043200 chr3A 90.000 220 22 0 1 220 21169485 21169266 3.950000e-73 285.0
13 TraesCS3B01G043200 chr3A 90.476 210 20 0 11 220 21289805 21290014 6.610000e-71 278.0
14 TraesCS3B01G043200 chr3A 84.921 252 22 6 750 987 21314886 21315135 8.680000e-60 241.0
15 TraesCS3B01G043200 chr3A 79.018 224 43 3 323 544 21169137 21168916 1.500000e-32 150.0
16 TraesCS3B01G043200 chr3A 86.735 98 13 0 447 544 21277616 21277713 2.550000e-20 110.0
17 TraesCS3B01G043200 chr3A 93.617 47 1 2 499 544 21268190 21268235 4.330000e-08 69.4
18 TraesCS3B01G043200 chr3D 93.750 464 15 3 1626 2089 15323940 15324389 0.000000e+00 684.0
19 TraesCS3B01G043200 chr3D 94.344 389 14 1 1 381 15209096 15209484 7.480000e-165 590.0
20 TraesCS3B01G043200 chr3D 89.605 481 25 6 750 1216 15211169 15211638 2.690000e-164 588.0
21 TraesCS3B01G043200 chr3D 83.780 635 74 9 755 1373 15100539 15099918 2.090000e-160 575.0
22 TraesCS3B01G043200 chr3D 93.956 364 11 4 2076 2429 15326117 15326479 7.640000e-150 540.0
23 TraesCS3B01G043200 chr3D 79.474 570 71 28 1 543 15201931 15201381 1.780000e-96 363.0
24 TraesCS3B01G043200 chr3D 80.160 499 76 12 1 486 15156424 15155936 3.840000e-93 351.0
25 TraesCS3B01G043200 chr3D 77.091 550 74 24 802 1326 15219565 15220087 1.110000e-68 270.0
26 TraesCS3B01G043200 chr3D 88.636 220 25 0 1 220 15218377 15218596 3.980000e-68 268.0
27 TraesCS3B01G043200 chr3D 93.038 158 11 0 1216 1373 15212645 15212802 5.220000e-57 231.0
28 TraesCS3B01G043200 chr3D 83.700 227 30 4 319 544 15123711 15123491 8.800000e-50 207.0
29 TraesCS3B01G043200 chr3D 90.062 161 15 1 578 738 15209481 15209640 8.800000e-50 207.0
30 TraesCS3B01G043200 chr1D 85.920 625 60 13 761 1362 46361387 46362006 2.040000e-180 641.0
31 TraesCS3B01G043200 chr1D 80.952 105 7 10 547 651 46360291 46360382 1.200000e-08 71.3
32 TraesCS3B01G043200 chr1B 91.837 49 1 2 547 595 65704250 65704205 5.610000e-07 65.8


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 TraesCS3B01G043200 chr3B 22198623 22201051 2428 False 4486.00 4486 100.00000 1 2429 1 chr3B.!!$F1 2428
1 TraesCS3B01G043200 chr3B 22179696 22180249 553 True 309.00 309 77.79700 1 543 1 chr3B.!!$R3 542
2 TraesCS3B01G043200 chr3A 21175609 21177247 1638 True 507.50 723 83.36900 1 1373 2 chr3A.!!$R3 1372
3 TraesCS3B01G043200 chr3A 21289805 21291526 1721 False 460.50 643 88.02700 11 1366 2 chr3A.!!$F4 1355
4 TraesCS3B01G043200 chr3A 21071706 21072599 893 True 376.50 451 84.44100 1579 2429 2 chr3A.!!$R1 850
5 TraesCS3B01G043200 chr3A 21314886 21316295 1409 False 341.50 442 86.32450 750 1359 2 chr3A.!!$F5 609
6 TraesCS3B01G043200 chr3A 21267627 21268235 608 False 281.70 494 89.24800 1 544 2 chr3A.!!$F3 543
7 TraesCS3B01G043200 chr3A 21168916 21169485 569 True 217.50 285 84.50900 1 544 2 chr3A.!!$R2 543
8 TraesCS3B01G043200 chr3D 15323940 15326479 2539 False 612.00 684 93.85300 1626 2429 2 chr3D.!!$F3 803
9 TraesCS3B01G043200 chr3D 15099918 15100539 621 True 575.00 575 83.78000 755 1373 1 chr3D.!!$R1 618
10 TraesCS3B01G043200 chr3D 15209096 15212802 3706 False 404.00 590 91.76225 1 1373 4 chr3D.!!$F1 1372
11 TraesCS3B01G043200 chr3D 15201381 15201931 550 True 363.00 363 79.47400 1 543 1 chr3D.!!$R4 542
12 TraesCS3B01G043200 chr3D 15218377 15220087 1710 False 269.00 270 82.86350 1 1326 2 chr3D.!!$F2 1325
13 TraesCS3B01G043200 chr1D 46360291 46362006 1715 False 356.15 641 83.43600 547 1362 2 chr1D.!!$F1 815

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
408 489 0.172578 TGACGTTGTCGGGATAGCAG 59.827 55.0 0.00 0.0 41.85 4.24 F
1383 6036 0.240945 CGGACCTGCGCAAAGAAATT 59.759 50.0 13.05 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 6046 0.175760 GGTATGCAACTGCCTCTCGA 59.824 55.0 0.0 0.0 41.18 4.04 R
2277 8746 2.098117 GGTACTGCAATAAGCCAGCAAG 59.902 50.0 0.0 0.0 44.83 4.01 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
216 217 1.105457 TACCTCGGGATTGTGGTACG 58.895 55.000 0.00 0.00 37.03 3.67
407 488 0.821517 ATGACGTTGTCGGGATAGCA 59.178 50.000 0.00 0.00 41.85 3.49
408 489 0.172578 TGACGTTGTCGGGATAGCAG 59.827 55.000 0.00 0.00 41.85 4.24
409 490 1.146358 GACGTTGTCGGGATAGCAGC 61.146 60.000 0.00 0.00 41.85 5.25
410 491 1.883084 CGTTGTCGGGATAGCAGCC 60.883 63.158 0.00 0.00 0.00 4.85
411 492 1.883084 GTTGTCGGGATAGCAGCCG 60.883 63.158 0.00 0.00 0.00 5.52
412 493 3.088941 TTGTCGGGATAGCAGCCGG 62.089 63.158 0.00 0.00 0.00 6.13
431 518 4.388499 GCCGACGCCAGGGAGAAA 62.388 66.667 0.00 0.00 0.00 2.52
544 691 2.809601 CAAAGGCGTCCGACGAGG 60.810 66.667 24.78 4.46 46.05 4.63
545 692 4.065281 AAAGGCGTCCGACGAGGG 62.065 66.667 24.78 0.00 46.05 4.30
548 695 3.443045 GGCGTCCGACGAGGGTAA 61.443 66.667 24.78 0.00 46.05 2.85
549 696 2.202531 GCGTCCGACGAGGGTAAC 60.203 66.667 24.78 0.88 46.05 2.50
551 698 1.805254 CGTCCGACGAGGGTAACAT 59.195 57.895 16.03 0.00 46.05 2.71
552 699 1.016627 CGTCCGACGAGGGTAACATA 58.983 55.000 16.03 0.00 46.05 2.29
553 700 1.605710 CGTCCGACGAGGGTAACATAT 59.394 52.381 16.03 0.00 46.05 1.78
689 1494 1.967066 CCAGCTCGGAATCAGACCTAT 59.033 52.381 0.00 0.00 36.56 2.57
690 1495 2.288702 CCAGCTCGGAATCAGACCTATG 60.289 54.545 0.00 0.00 36.56 2.23
717 1526 8.902540 ACCTCTAATTGCATCAATATAAACGA 57.097 30.769 0.00 0.00 32.43 3.85
795 3618 0.685097 AGTGAAGCTAGTCCGGCAAA 59.315 50.000 0.00 0.00 0.00 3.68
798 3621 0.931005 GAAGCTAGTCCGGCAAATCG 59.069 55.000 0.00 0.00 0.00 3.34
1175 4818 0.731514 GACGATGACGACGAAGGCAA 60.732 55.000 0.00 0.00 42.66 4.52
1229 5879 2.517402 CCTCCTCCTCGTCCTCCG 60.517 72.222 0.00 0.00 38.13 4.63
1253 5906 1.602771 GGTGCCCAAGAGGTAGGAC 59.397 63.158 0.00 0.00 38.26 3.85
1345 5998 9.661954 TCTATAATGTTAAGGAGAAGATCTGGT 57.338 33.333 0.00 0.00 0.00 4.00
1349 6002 8.560124 AATGTTAAGGAGAAGATCTGGTCTAT 57.440 34.615 0.00 0.00 35.67 1.98
1353 6006 4.479158 AGGAGAAGATCTGGTCTATGGAC 58.521 47.826 0.00 0.00 41.43 4.02
1373 6026 2.819595 CATTCCACCGGACCTGCG 60.820 66.667 9.46 0.00 0.00 5.18
1374 6027 4.778143 ATTCCACCGGACCTGCGC 62.778 66.667 9.46 0.00 0.00 6.09
1378 6031 3.726517 CACCGGACCTGCGCAAAG 61.727 66.667 13.05 8.76 0.00 2.77
1379 6032 3.936203 ACCGGACCTGCGCAAAGA 61.936 61.111 13.05 0.00 0.00 2.52
1380 6033 2.668212 CCGGACCTGCGCAAAGAA 60.668 61.111 13.05 0.00 0.00 2.52
1381 6034 2.258013 CCGGACCTGCGCAAAGAAA 61.258 57.895 13.05 0.00 0.00 2.52
1382 6035 1.586154 CCGGACCTGCGCAAAGAAAT 61.586 55.000 13.05 0.00 0.00 2.17
1383 6036 0.240945 CGGACCTGCGCAAAGAAATT 59.759 50.000 13.05 0.00 0.00 1.82
1384 6037 1.729149 CGGACCTGCGCAAAGAAATTC 60.729 52.381 13.05 0.00 0.00 2.17
1385 6038 1.402852 GGACCTGCGCAAAGAAATTCC 60.403 52.381 13.05 5.18 0.00 3.01
1386 6039 1.269448 GACCTGCGCAAAGAAATTCCA 59.731 47.619 13.05 0.00 0.00 3.53
1387 6040 1.270550 ACCTGCGCAAAGAAATTCCAG 59.729 47.619 13.05 0.00 0.00 3.86
1388 6041 1.270550 CCTGCGCAAAGAAATTCCAGT 59.729 47.619 13.05 0.00 0.00 4.00
1389 6042 2.322161 CTGCGCAAAGAAATTCCAGTG 58.678 47.619 13.05 0.00 0.00 3.66
1390 6043 1.680735 TGCGCAAAGAAATTCCAGTGT 59.319 42.857 8.16 0.00 0.00 3.55
1391 6044 2.053627 GCGCAAAGAAATTCCAGTGTG 58.946 47.619 0.30 0.00 0.00 3.82
1392 6045 2.053627 CGCAAAGAAATTCCAGTGTGC 58.946 47.619 0.00 0.00 0.00 4.57
1393 6046 2.287788 CGCAAAGAAATTCCAGTGTGCT 60.288 45.455 0.00 0.00 0.00 4.40
1394 6047 3.311966 GCAAAGAAATTCCAGTGTGCTC 58.688 45.455 0.00 0.00 0.00 4.26
1395 6048 3.558505 CAAAGAAATTCCAGTGTGCTCG 58.441 45.455 0.00 0.00 0.00 5.03
1396 6049 2.839486 AGAAATTCCAGTGTGCTCGA 57.161 45.000 0.00 0.00 0.00 4.04
1397 6050 2.693069 AGAAATTCCAGTGTGCTCGAG 58.307 47.619 8.45 8.45 0.00 4.04
1398 6051 2.300152 AGAAATTCCAGTGTGCTCGAGA 59.700 45.455 18.75 0.00 0.00 4.04
1399 6052 2.376808 AATTCCAGTGTGCTCGAGAG 57.623 50.000 18.75 0.00 0.00 3.20
1400 6053 0.534412 ATTCCAGTGTGCTCGAGAGG 59.466 55.000 18.75 7.33 0.00 3.69
1401 6054 2.125753 CCAGTGTGCTCGAGAGGC 60.126 66.667 18.75 1.58 0.00 4.70
1402 6055 2.653115 CAGTGTGCTCGAGAGGCA 59.347 61.111 18.75 4.92 35.45 4.75
1403 6056 1.445754 CAGTGTGCTCGAGAGGCAG 60.446 63.158 18.75 0.00 37.82 4.85
1404 6057 1.905843 AGTGTGCTCGAGAGGCAGT 60.906 57.895 18.75 10.89 37.82 4.40
1405 6058 1.005630 GTGTGCTCGAGAGGCAGTT 60.006 57.895 18.75 0.00 37.82 3.16
1406 6059 1.005748 TGTGCTCGAGAGGCAGTTG 60.006 57.895 18.75 0.00 37.82 3.16
1407 6060 2.047844 TGCTCGAGAGGCAGTTGC 60.048 61.111 18.75 0.00 41.14 4.17
1408 6061 2.047844 GCTCGAGAGGCAGTTGCA 60.048 61.111 18.75 0.00 44.36 4.08
1409 6062 1.449246 GCTCGAGAGGCAGTTGCAT 60.449 57.895 18.75 0.00 44.36 3.96
1410 6063 0.179100 GCTCGAGAGGCAGTTGCATA 60.179 55.000 18.75 0.00 44.36 3.14
1411 6064 1.565305 CTCGAGAGGCAGTTGCATAC 58.435 55.000 6.58 0.00 44.36 2.39
1412 6065 0.175760 TCGAGAGGCAGTTGCATACC 59.824 55.000 6.43 0.00 44.36 2.73
1413 6066 0.176680 CGAGAGGCAGTTGCATACCT 59.823 55.000 6.43 0.00 44.36 3.08
1414 6067 1.661341 GAGAGGCAGTTGCATACCTG 58.339 55.000 6.43 3.58 44.36 4.00
1415 6068 1.208052 GAGAGGCAGTTGCATACCTGA 59.792 52.381 11.48 0.00 44.36 3.86
1416 6069 1.630369 AGAGGCAGTTGCATACCTGAA 59.370 47.619 11.48 0.00 44.36 3.02
1417 6070 1.740025 GAGGCAGTTGCATACCTGAAC 59.260 52.381 11.48 4.81 44.36 3.18
1418 6071 1.073763 AGGCAGTTGCATACCTGAACA 59.926 47.619 11.48 0.00 44.36 3.18
1419 6072 1.470098 GGCAGTTGCATACCTGAACAG 59.530 52.381 11.48 0.00 44.36 3.16
1420 6073 2.426522 GCAGTTGCATACCTGAACAGA 58.573 47.619 11.48 0.00 41.59 3.41
1421 6074 2.813754 GCAGTTGCATACCTGAACAGAA 59.186 45.455 11.48 0.00 41.59 3.02
1422 6075 3.253188 GCAGTTGCATACCTGAACAGAAA 59.747 43.478 11.48 0.00 41.59 2.52
1423 6076 4.082571 GCAGTTGCATACCTGAACAGAAAT 60.083 41.667 11.48 0.00 41.59 2.17
1424 6077 5.565439 GCAGTTGCATACCTGAACAGAAATT 60.565 40.000 11.48 0.00 41.59 1.82
1425 6078 6.088824 CAGTTGCATACCTGAACAGAAATTC 58.911 40.000 3.19 0.00 0.00 2.17
1426 6079 6.006449 AGTTGCATACCTGAACAGAAATTCT 58.994 36.000 3.19 0.00 0.00 2.40
1448 6101 2.947852 ACGGAGAGTCAACGAGATTTG 58.052 47.619 12.54 0.00 0.00 2.32
1449 6102 2.263077 CGGAGAGTCAACGAGATTTGG 58.737 52.381 0.73 0.00 0.00 3.28
1450 6103 2.622436 GGAGAGTCAACGAGATTTGGG 58.378 52.381 0.00 0.00 0.00 4.12
1451 6104 2.622436 GAGAGTCAACGAGATTTGGGG 58.378 52.381 0.00 0.00 0.00 4.96
1452 6105 2.233922 GAGAGTCAACGAGATTTGGGGA 59.766 50.000 0.00 0.00 0.00 4.81
1453 6106 2.637872 AGAGTCAACGAGATTTGGGGAA 59.362 45.455 0.00 0.00 0.00 3.97
1454 6107 3.003480 GAGTCAACGAGATTTGGGGAAG 58.997 50.000 0.00 0.00 0.00 3.46
1455 6108 2.372172 AGTCAACGAGATTTGGGGAAGT 59.628 45.455 0.00 0.00 0.00 3.01
1456 6109 2.742589 GTCAACGAGATTTGGGGAAGTC 59.257 50.000 0.00 0.00 0.00 3.01
1457 6110 2.637872 TCAACGAGATTTGGGGAAGTCT 59.362 45.455 0.00 0.00 0.00 3.24
1458 6111 3.072476 TCAACGAGATTTGGGGAAGTCTT 59.928 43.478 0.00 0.00 0.00 3.01
1459 6112 3.790089 ACGAGATTTGGGGAAGTCTTT 57.210 42.857 0.00 0.00 0.00 2.52
1460 6113 3.676093 ACGAGATTTGGGGAAGTCTTTC 58.324 45.455 0.00 0.00 0.00 2.62
1461 6114 3.328050 ACGAGATTTGGGGAAGTCTTTCT 59.672 43.478 0.00 0.00 33.68 2.52
1462 6115 3.686726 CGAGATTTGGGGAAGTCTTTCTG 59.313 47.826 0.00 0.00 33.68 3.02
1463 6116 4.563580 CGAGATTTGGGGAAGTCTTTCTGA 60.564 45.833 0.00 0.00 33.68 3.27
1464 6117 5.316987 GAGATTTGGGGAAGTCTTTCTGAA 58.683 41.667 0.00 0.00 33.68 3.02
1465 6118 5.705400 AGATTTGGGGAAGTCTTTCTGAAA 58.295 37.500 2.44 2.44 33.68 2.69
1466 6119 6.318112 AGATTTGGGGAAGTCTTTCTGAAAT 58.682 36.000 2.88 0.00 33.68 2.17
1467 6120 5.789643 TTTGGGGAAGTCTTTCTGAAATG 57.210 39.130 2.88 0.00 33.68 2.32
1468 6121 4.453480 TGGGGAAGTCTTTCTGAAATGT 57.547 40.909 2.88 0.00 33.68 2.71
1469 6122 4.398319 TGGGGAAGTCTTTCTGAAATGTC 58.602 43.478 2.88 0.00 33.68 3.06
1470 6123 4.104738 TGGGGAAGTCTTTCTGAAATGTCT 59.895 41.667 2.88 0.48 33.68 3.41
1471 6124 5.309543 TGGGGAAGTCTTTCTGAAATGTCTA 59.690 40.000 2.88 0.00 33.68 2.59
1472 6125 5.877564 GGGGAAGTCTTTCTGAAATGTCTAG 59.122 44.000 2.88 0.00 33.68 2.43
1473 6126 6.295916 GGGGAAGTCTTTCTGAAATGTCTAGA 60.296 42.308 2.88 0.00 33.68 2.43
1474 6127 7.162082 GGGAAGTCTTTCTGAAATGTCTAGAA 58.838 38.462 2.88 0.00 33.68 2.10
1475 6128 7.661847 GGGAAGTCTTTCTGAAATGTCTAGAAA 59.338 37.037 2.88 9.02 37.91 2.52
1476 6129 9.225436 GGAAGTCTTTCTGAAATGTCTAGAAAT 57.775 33.333 2.88 0.00 39.07 2.17
1479 6132 9.377312 AGTCTTTCTGAAATGTCTAGAAATAGC 57.623 33.333 2.88 0.00 39.07 2.97
1480 6133 9.377312 GTCTTTCTGAAATGTCTAGAAATAGCT 57.623 33.333 2.88 0.00 39.07 3.32
1481 6134 9.376075 TCTTTCTGAAATGTCTAGAAATAGCTG 57.624 33.333 2.88 0.00 39.07 4.24
1482 6135 8.498054 TTTCTGAAATGTCTAGAAATAGCTGG 57.502 34.615 0.00 0.00 36.00 4.85
1483 6136 7.187824 TCTGAAATGTCTAGAAATAGCTGGT 57.812 36.000 0.00 0.00 0.00 4.00
1484 6137 7.624549 TCTGAAATGTCTAGAAATAGCTGGTT 58.375 34.615 0.00 0.00 0.00 3.67
1485 6138 7.550551 TCTGAAATGTCTAGAAATAGCTGGTTG 59.449 37.037 0.00 0.00 0.00 3.77
1486 6139 6.599244 TGAAATGTCTAGAAATAGCTGGTTGG 59.401 38.462 0.00 0.00 0.00 3.77
1487 6140 3.873910 TGTCTAGAAATAGCTGGTTGGC 58.126 45.455 0.00 0.00 0.00 4.52
1488 6141 2.866762 GTCTAGAAATAGCTGGTTGGCG 59.133 50.000 0.00 0.00 37.29 5.69
1489 6142 2.500098 TCTAGAAATAGCTGGTTGGCGT 59.500 45.455 0.00 0.00 37.29 5.68
1490 6143 1.739067 AGAAATAGCTGGTTGGCGTC 58.261 50.000 0.00 0.00 37.29 5.19
1491 6144 1.003118 AGAAATAGCTGGTTGGCGTCA 59.997 47.619 0.00 0.00 37.29 4.35
1492 6145 2.017049 GAAATAGCTGGTTGGCGTCAT 58.983 47.619 0.00 0.00 37.29 3.06
1493 6146 3.118408 AGAAATAGCTGGTTGGCGTCATA 60.118 43.478 0.00 0.00 37.29 2.15
1494 6147 3.492102 AATAGCTGGTTGGCGTCATAT 57.508 42.857 0.00 0.00 37.29 1.78
1495 6148 2.238942 TAGCTGGTTGGCGTCATATG 57.761 50.000 0.00 0.00 37.29 1.78
1496 6149 0.464373 AGCTGGTTGGCGTCATATGG 60.464 55.000 2.13 0.00 37.29 2.74
1497 6150 0.748005 GCTGGTTGGCGTCATATGGT 60.748 55.000 2.13 0.00 0.00 3.55
1498 6151 1.750193 CTGGTTGGCGTCATATGGTT 58.250 50.000 2.13 0.00 0.00 3.67
1499 6152 1.670811 CTGGTTGGCGTCATATGGTTC 59.329 52.381 2.13 0.00 0.00 3.62
1500 6153 1.021968 GGTTGGCGTCATATGGTTCC 58.978 55.000 2.13 2.30 0.00 3.62
1501 6154 1.680555 GGTTGGCGTCATATGGTTCCA 60.681 52.381 2.13 4.90 0.00 3.53
1502 6155 2.297701 GTTGGCGTCATATGGTTCCAT 58.702 47.619 9.37 9.37 0.00 3.41
1503 6156 1.965935 TGGCGTCATATGGTTCCATG 58.034 50.000 13.86 0.76 0.00 3.66
1504 6157 1.238439 GGCGTCATATGGTTCCATGG 58.762 55.000 4.97 4.97 0.00 3.66
1505 6158 1.476833 GGCGTCATATGGTTCCATGGT 60.477 52.381 12.58 0.00 0.00 3.55
1506 6159 1.603802 GCGTCATATGGTTCCATGGTG 59.396 52.381 12.58 11.98 0.00 4.17
1507 6160 2.744823 GCGTCATATGGTTCCATGGTGA 60.745 50.000 12.58 13.75 0.00 4.02
1508 6161 3.133691 CGTCATATGGTTCCATGGTGAG 58.866 50.000 12.58 8.43 0.00 3.51
1509 6162 3.432186 CGTCATATGGTTCCATGGTGAGT 60.432 47.826 12.58 0.00 0.00 3.41
1510 6163 4.526970 GTCATATGGTTCCATGGTGAGTT 58.473 43.478 12.58 0.00 0.00 3.01
1511 6164 4.949856 GTCATATGGTTCCATGGTGAGTTT 59.050 41.667 12.58 0.00 0.00 2.66
1512 6165 5.418840 GTCATATGGTTCCATGGTGAGTTTT 59.581 40.000 12.58 0.00 0.00 2.43
1513 6166 5.652014 TCATATGGTTCCATGGTGAGTTTTC 59.348 40.000 12.58 0.00 0.00 2.29
1514 6167 3.593442 TGGTTCCATGGTGAGTTTTCT 57.407 42.857 12.58 0.00 0.00 2.52
1515 6168 3.221771 TGGTTCCATGGTGAGTTTTCTG 58.778 45.455 12.58 0.00 0.00 3.02
1516 6169 3.222603 GGTTCCATGGTGAGTTTTCTGT 58.777 45.455 12.58 0.00 0.00 3.41
1517 6170 3.636764 GGTTCCATGGTGAGTTTTCTGTT 59.363 43.478 12.58 0.00 0.00 3.16
1518 6171 4.261614 GGTTCCATGGTGAGTTTTCTGTTC 60.262 45.833 12.58 0.00 0.00 3.18
1519 6172 3.486383 TCCATGGTGAGTTTTCTGTTCC 58.514 45.455 12.58 0.00 0.00 3.62
1520 6173 3.138283 TCCATGGTGAGTTTTCTGTTCCT 59.862 43.478 12.58 0.00 0.00 3.36
1521 6174 4.349636 TCCATGGTGAGTTTTCTGTTCCTA 59.650 41.667 12.58 0.00 0.00 2.94
1522 6175 4.455877 CCATGGTGAGTTTTCTGTTCCTAC 59.544 45.833 2.57 0.00 0.00 3.18
1523 6176 5.308825 CATGGTGAGTTTTCTGTTCCTACT 58.691 41.667 0.00 0.00 0.00 2.57
1524 6177 4.703897 TGGTGAGTTTTCTGTTCCTACTG 58.296 43.478 0.00 0.00 0.00 2.74
1525 6178 3.498777 GGTGAGTTTTCTGTTCCTACTGC 59.501 47.826 0.00 0.00 0.00 4.40
1526 6179 4.381411 GTGAGTTTTCTGTTCCTACTGCT 58.619 43.478 0.00 0.00 0.00 4.24
1527 6180 4.212214 GTGAGTTTTCTGTTCCTACTGCTG 59.788 45.833 0.00 0.00 0.00 4.41
1528 6181 4.141711 TGAGTTTTCTGTTCCTACTGCTGT 60.142 41.667 0.66 0.66 0.00 4.40
1529 6182 5.069914 TGAGTTTTCTGTTCCTACTGCTGTA 59.930 40.000 3.25 3.25 0.00 2.74
1530 6183 5.925509 AGTTTTCTGTTCCTACTGCTGTAA 58.074 37.500 4.91 0.00 0.00 2.41
1531 6184 6.354130 AGTTTTCTGTTCCTACTGCTGTAAA 58.646 36.000 4.91 0.00 0.00 2.01
1532 6185 6.260271 AGTTTTCTGTTCCTACTGCTGTAAAC 59.740 38.462 4.91 7.88 0.00 2.01
1533 6186 5.546621 TTCTGTTCCTACTGCTGTAAACT 57.453 39.130 15.22 0.00 0.00 2.66
1534 6187 5.546621 TCTGTTCCTACTGCTGTAAACTT 57.453 39.130 15.22 0.00 0.00 2.66
1535 6188 5.539048 TCTGTTCCTACTGCTGTAAACTTC 58.461 41.667 15.22 4.01 0.00 3.01
1536 6189 4.638304 TGTTCCTACTGCTGTAAACTTCC 58.362 43.478 15.22 1.18 0.00 3.46
1537 6190 3.975168 TCCTACTGCTGTAAACTTCCC 57.025 47.619 4.91 0.00 0.00 3.97
1538 6191 3.517612 TCCTACTGCTGTAAACTTCCCT 58.482 45.455 4.91 0.00 0.00 4.20
1539 6192 3.908103 TCCTACTGCTGTAAACTTCCCTT 59.092 43.478 4.91 0.00 0.00 3.95
1540 6193 4.003648 CCTACTGCTGTAAACTTCCCTTG 58.996 47.826 4.91 0.00 0.00 3.61
1541 6194 3.857157 ACTGCTGTAAACTTCCCTTGA 57.143 42.857 0.00 0.00 0.00 3.02
1542 6195 4.164843 ACTGCTGTAAACTTCCCTTGAA 57.835 40.909 0.00 0.00 0.00 2.69
1543 6196 4.532834 ACTGCTGTAAACTTCCCTTGAAA 58.467 39.130 0.00 0.00 0.00 2.69
1544 6197 5.140454 ACTGCTGTAAACTTCCCTTGAAAT 58.860 37.500 0.00 0.00 0.00 2.17
1545 6198 6.303839 ACTGCTGTAAACTTCCCTTGAAATA 58.696 36.000 0.00 0.00 0.00 1.40
1546 6199 6.206829 ACTGCTGTAAACTTCCCTTGAAATAC 59.793 38.462 0.00 0.00 0.00 1.89
1547 6200 5.180492 TGCTGTAAACTTCCCTTGAAATACG 59.820 40.000 0.00 0.00 0.00 3.06
1548 6201 5.616488 TGTAAACTTCCCTTGAAATACGC 57.384 39.130 0.00 0.00 0.00 4.42
1549 6202 3.824414 AAACTTCCCTTGAAATACGCG 57.176 42.857 3.53 3.53 0.00 6.01
1550 6203 1.084289 ACTTCCCTTGAAATACGCGC 58.916 50.000 5.73 0.00 0.00 6.86
1551 6204 1.083489 CTTCCCTTGAAATACGCGCA 58.917 50.000 5.73 0.00 0.00 6.09
1552 6205 1.062587 CTTCCCTTGAAATACGCGCAG 59.937 52.381 5.73 2.42 0.00 5.18
1565 6218 4.223800 CGCAGCCTAAAGATGCCA 57.776 55.556 0.00 0.00 36.60 4.92
1566 6219 1.723870 CGCAGCCTAAAGATGCCAC 59.276 57.895 0.00 0.00 36.60 5.01
1567 6220 0.745845 CGCAGCCTAAAGATGCCACT 60.746 55.000 0.00 0.00 36.60 4.00
1568 6221 1.020437 GCAGCCTAAAGATGCCACTC 58.980 55.000 0.00 0.00 33.81 3.51
1569 6222 1.679944 GCAGCCTAAAGATGCCACTCA 60.680 52.381 0.00 0.00 33.81 3.41
1570 6223 2.715046 CAGCCTAAAGATGCCACTCAA 58.285 47.619 0.00 0.00 0.00 3.02
1571 6224 2.421424 CAGCCTAAAGATGCCACTCAAC 59.579 50.000 0.00 0.00 0.00 3.18
1572 6225 2.307098 AGCCTAAAGATGCCACTCAACT 59.693 45.455 0.00 0.00 0.00 3.16
1573 6226 3.084786 GCCTAAAGATGCCACTCAACTT 58.915 45.455 0.00 0.00 39.15 2.66
1574 6227 3.127721 GCCTAAAGATGCCACTCAACTTC 59.872 47.826 0.00 0.00 36.88 3.01
1575 6228 3.372206 CCTAAAGATGCCACTCAACTTCG 59.628 47.826 0.00 0.00 36.88 3.79
1576 6229 2.839486 AAGATGCCACTCAACTTCGA 57.161 45.000 0.00 0.00 33.17 3.71
1577 6230 2.376808 AGATGCCACTCAACTTCGAG 57.623 50.000 0.00 0.00 39.05 4.04
1579 6232 2.037772 AGATGCCACTCAACTTCGAGTT 59.962 45.455 0.00 0.00 43.84 3.01
1656 6309 2.106566 TGGGCTGCAAGTTCAAAAAGA 58.893 42.857 0.50 0.00 35.30 2.52
1743 6402 9.793245 CTTTTAAGACAATGTACTGTTACGAAG 57.207 33.333 0.00 0.00 0.00 3.79
1753 6412 7.591006 TGTACTGTTACGAAGGATCAAAATC 57.409 36.000 0.00 0.00 0.00 2.17
1855 6515 3.594603 ATCAGTCTCCACAGTTAACCG 57.405 47.619 0.88 0.00 0.00 4.44
1972 6686 1.066858 ACCTGCAACACTAGATGGTCG 60.067 52.381 0.00 0.00 0.00 4.79
1973 6687 1.002366 CTGCAACACTAGATGGTCGC 58.998 55.000 0.00 0.00 0.00 5.19
1974 6688 0.391130 TGCAACACTAGATGGTCGCC 60.391 55.000 0.00 0.00 0.00 5.54
2053 6767 4.750941 TCCATCCTCCAAACCAGAAAAAT 58.249 39.130 0.00 0.00 0.00 1.82
2055 6769 5.606329 TCCATCCTCCAAACCAGAAAAATTT 59.394 36.000 0.00 0.00 0.00 1.82
2056 6770 6.784969 TCCATCCTCCAAACCAGAAAAATTTA 59.215 34.615 0.00 0.00 0.00 1.40
2057 6771 7.291182 TCCATCCTCCAAACCAGAAAAATTTAA 59.709 33.333 0.00 0.00 0.00 1.52
2058 6772 7.936301 CCATCCTCCAAACCAGAAAAATTTAAA 59.064 33.333 0.00 0.00 0.00 1.52
2178 8638 1.680314 CTTGCCTGGAGCTTTCCCC 60.680 63.158 0.00 0.00 44.23 4.81
2229 8698 9.498176 AACGGACTAAAACTTGAGTTAATATGT 57.502 29.630 0.00 0.00 37.25 2.29
2230 8699 9.148104 ACGGACTAAAACTTGAGTTAATATGTC 57.852 33.333 0.00 2.94 37.25 3.06
2277 8746 4.933400 ACTTCTTTTGCATCATTGGATTGC 59.067 37.500 0.00 0.00 0.00 3.56
2389 8859 1.651240 CTTCCATTCACTGGGCGCTG 61.651 60.000 7.64 6.09 45.98 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 217 1.880027 GTGGGTCAATGTGAAGTCCAC 59.120 52.381 9.43 9.43 45.88 4.02
388 457 0.821517 TGCTATCCCGACAACGTCAT 59.178 50.000 0.00 0.00 37.88 3.06
418 499 4.394712 CCGCTTTCTCCCTGGCGT 62.395 66.667 0.00 0.00 45.11 5.68
499 643 4.388499 CGTCCCCTTCACCACCGG 62.388 72.222 0.00 0.00 0.00 5.28
500 644 3.307906 TCGTCCCCTTCACCACCG 61.308 66.667 0.00 0.00 0.00 4.94
502 646 2.048503 CGTCGTCCCCTTCACCAC 60.049 66.667 0.00 0.00 0.00 4.16
539 686 5.009811 GCAGTTCTCTATATGTTACCCTCGT 59.990 44.000 0.00 0.00 0.00 4.18
544 691 6.041069 ACTGGAGCAGTTCTCTATATGTTACC 59.959 42.308 0.00 0.00 42.59 2.85
545 692 6.920758 CACTGGAGCAGTTCTCTATATGTTAC 59.079 42.308 0.00 0.00 42.59 2.50
546 693 6.461648 GCACTGGAGCAGTTCTCTATATGTTA 60.462 42.308 0.00 0.00 42.59 2.41
548 695 4.202202 GCACTGGAGCAGTTCTCTATATGT 60.202 45.833 0.00 0.00 42.59 2.29
549 696 4.305769 GCACTGGAGCAGTTCTCTATATG 58.694 47.826 0.00 0.00 42.59 1.78
551 698 2.359214 CGCACTGGAGCAGTTCTCTATA 59.641 50.000 0.00 0.00 42.59 1.31
552 699 1.135915 CGCACTGGAGCAGTTCTCTAT 59.864 52.381 0.00 0.00 42.59 1.98
553 700 0.528017 CGCACTGGAGCAGTTCTCTA 59.472 55.000 0.00 0.00 42.59 2.43
714 1523 0.465824 CAGAGGAGGGTATCGGTCGT 60.466 60.000 0.00 0.00 0.00 4.34
717 1526 2.946785 CTTACAGAGGAGGGTATCGGT 58.053 52.381 0.00 0.00 0.00 4.69
795 3618 1.869767 GAAAATCTGCATCCTCGCGAT 59.130 47.619 10.36 0.00 33.35 4.58
798 3621 1.009829 ACGAAAATCTGCATCCTCGC 58.990 50.000 0.00 0.00 0.00 5.03
991 4620 5.701750 CCACATGGATCTTCATCTTCTCATC 59.298 44.000 0.00 0.00 37.39 2.92
1161 4795 1.006571 GGTCTTGCCTTCGTCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
1163 4797 2.207924 AGGGTCTTGCCTTCGTCGT 61.208 57.895 0.00 0.00 37.43 4.34
1165 4799 1.376037 CCAGGGTCTTGCCTTCGTC 60.376 63.158 0.00 0.00 37.43 4.20
1166 4800 2.750350 CCAGGGTCTTGCCTTCGT 59.250 61.111 0.00 0.00 37.43 3.85
1167 4801 2.747855 GCCAGGGTCTTGCCTTCG 60.748 66.667 0.00 0.00 37.43 3.79
1175 4818 3.846405 TTGAGGTCCGCCAGGGTCT 62.846 63.158 0.00 0.00 38.33 3.85
1248 5898 4.093998 GTCTTCACGTAGATGTTCGTCCTA 59.906 45.833 0.00 0.00 38.23 2.94
1373 6026 3.311966 GAGCACACTGGAATTTCTTTGC 58.688 45.455 0.00 0.00 0.00 3.68
1374 6027 3.250762 TCGAGCACACTGGAATTTCTTTG 59.749 43.478 0.00 0.00 0.00 2.77
1375 6028 3.476552 TCGAGCACACTGGAATTTCTTT 58.523 40.909 0.00 0.00 0.00 2.52
1376 6029 3.070018 CTCGAGCACACTGGAATTTCTT 58.930 45.455 0.00 0.00 29.43 2.52
1377 6030 2.300152 TCTCGAGCACACTGGAATTTCT 59.700 45.455 7.81 0.00 29.43 2.52
1378 6031 2.670414 CTCTCGAGCACACTGGAATTTC 59.330 50.000 7.81 0.00 29.43 2.17
1379 6032 2.613977 CCTCTCGAGCACACTGGAATTT 60.614 50.000 7.81 0.00 29.43 1.82
1380 6033 1.066573 CCTCTCGAGCACACTGGAATT 60.067 52.381 7.81 0.00 29.43 2.17
1381 6034 0.534412 CCTCTCGAGCACACTGGAAT 59.466 55.000 7.81 0.00 29.43 3.01
1382 6035 1.967535 CCTCTCGAGCACACTGGAA 59.032 57.895 7.81 0.00 29.43 3.53
1383 6036 2.640302 GCCTCTCGAGCACACTGGA 61.640 63.158 7.81 0.00 0.00 3.86
1384 6037 2.125753 GCCTCTCGAGCACACTGG 60.126 66.667 7.81 4.04 0.00 4.00
1385 6038 1.445754 CTGCCTCTCGAGCACACTG 60.446 63.158 7.81 0.00 36.01 3.66
1386 6039 1.467678 AACTGCCTCTCGAGCACACT 61.468 55.000 7.81 0.00 36.01 3.55
1387 6040 1.005630 AACTGCCTCTCGAGCACAC 60.006 57.895 7.81 0.00 36.01 3.82
1388 6041 1.005748 CAACTGCCTCTCGAGCACA 60.006 57.895 7.81 4.63 36.01 4.57
1389 6042 2.386660 GCAACTGCCTCTCGAGCAC 61.387 63.158 7.81 0.00 36.01 4.40
1390 6043 2.047844 GCAACTGCCTCTCGAGCA 60.048 61.111 7.81 2.09 38.82 4.26
1391 6044 0.179100 TATGCAACTGCCTCTCGAGC 60.179 55.000 7.81 0.00 41.18 5.03
1392 6045 1.565305 GTATGCAACTGCCTCTCGAG 58.435 55.000 5.93 5.93 41.18 4.04
1393 6046 0.175760 GGTATGCAACTGCCTCTCGA 59.824 55.000 0.00 0.00 41.18 4.04
1394 6047 0.176680 AGGTATGCAACTGCCTCTCG 59.823 55.000 0.00 0.00 41.18 4.04
1395 6048 1.208052 TCAGGTATGCAACTGCCTCTC 59.792 52.381 10.53 0.00 41.18 3.20
1396 6049 1.279496 TCAGGTATGCAACTGCCTCT 58.721 50.000 10.53 0.00 41.18 3.69
1397 6050 1.740025 GTTCAGGTATGCAACTGCCTC 59.260 52.381 10.53 2.32 41.18 4.70
1398 6051 1.073763 TGTTCAGGTATGCAACTGCCT 59.926 47.619 10.53 1.67 41.18 4.75
1399 6052 1.470098 CTGTTCAGGTATGCAACTGCC 59.530 52.381 10.53 0.00 41.18 4.85
1400 6053 2.426522 TCTGTTCAGGTATGCAACTGC 58.573 47.619 10.53 0.00 42.50 4.40
1401 6054 5.633830 ATTTCTGTTCAGGTATGCAACTG 57.366 39.130 9.41 9.41 36.07 3.16
1402 6055 6.006449 AGAATTTCTGTTCAGGTATGCAACT 58.994 36.000 0.00 0.00 0.00 3.16
1403 6056 6.072508 TCAGAATTTCTGTTCAGGTATGCAAC 60.073 38.462 22.44 0.00 44.58 4.17
1404 6057 6.003326 TCAGAATTTCTGTTCAGGTATGCAA 58.997 36.000 22.44 0.00 44.58 4.08
1405 6058 5.412594 GTCAGAATTTCTGTTCAGGTATGCA 59.587 40.000 22.44 0.00 44.58 3.96
1406 6059 5.446473 CGTCAGAATTTCTGTTCAGGTATGC 60.446 44.000 22.44 4.66 44.58 3.14
1407 6060 5.063944 CCGTCAGAATTTCTGTTCAGGTATG 59.936 44.000 22.44 9.41 44.58 2.39
1408 6061 5.046591 TCCGTCAGAATTTCTGTTCAGGTAT 60.047 40.000 22.44 0.00 44.58 2.73
1409 6062 4.282449 TCCGTCAGAATTTCTGTTCAGGTA 59.718 41.667 22.44 2.52 44.58 3.08
1410 6063 3.071023 TCCGTCAGAATTTCTGTTCAGGT 59.929 43.478 22.44 0.00 44.58 4.00
1411 6064 3.664107 TCCGTCAGAATTTCTGTTCAGG 58.336 45.455 22.44 19.58 44.58 3.86
1412 6065 4.560128 TCTCCGTCAGAATTTCTGTTCAG 58.440 43.478 22.44 14.97 44.58 3.02
1413 6066 4.039245 ACTCTCCGTCAGAATTTCTGTTCA 59.961 41.667 22.44 4.51 44.58 3.18
1414 6067 4.561105 ACTCTCCGTCAGAATTTCTGTTC 58.439 43.478 22.44 16.23 44.58 3.18
1415 6068 4.561105 GACTCTCCGTCAGAATTTCTGTT 58.439 43.478 22.44 2.55 44.58 3.16
1416 6069 4.181309 GACTCTCCGTCAGAATTTCTGT 57.819 45.455 22.44 4.29 44.58 3.41
1427 6080 2.917971 CAAATCTCGTTGACTCTCCGTC 59.082 50.000 0.00 0.00 43.14 4.79
1428 6081 2.352814 CCAAATCTCGTTGACTCTCCGT 60.353 50.000 0.00 0.00 0.00 4.69
1429 6082 2.263077 CCAAATCTCGTTGACTCTCCG 58.737 52.381 0.00 0.00 0.00 4.63
1430 6083 2.622436 CCCAAATCTCGTTGACTCTCC 58.378 52.381 0.00 0.00 0.00 3.71
1431 6084 2.233922 TCCCCAAATCTCGTTGACTCTC 59.766 50.000 0.00 0.00 0.00 3.20
1432 6085 2.257207 TCCCCAAATCTCGTTGACTCT 58.743 47.619 0.00 0.00 0.00 3.24
1433 6086 2.762535 TCCCCAAATCTCGTTGACTC 57.237 50.000 0.00 0.00 0.00 3.36
1434 6087 2.372172 ACTTCCCCAAATCTCGTTGACT 59.628 45.455 0.00 0.00 0.00 3.41
1435 6088 2.742589 GACTTCCCCAAATCTCGTTGAC 59.257 50.000 0.00 0.00 0.00 3.18
1436 6089 2.637872 AGACTTCCCCAAATCTCGTTGA 59.362 45.455 0.00 0.00 0.00 3.18
1437 6090 3.059352 AGACTTCCCCAAATCTCGTTG 57.941 47.619 0.00 0.00 0.00 4.10
1438 6091 3.790089 AAGACTTCCCCAAATCTCGTT 57.210 42.857 0.00 0.00 0.00 3.85
1439 6092 3.328050 AGAAAGACTTCCCCAAATCTCGT 59.672 43.478 0.00 0.00 31.28 4.18
1440 6093 3.686726 CAGAAAGACTTCCCCAAATCTCG 59.313 47.826 0.00 0.00 31.28 4.04
1441 6094 4.911390 TCAGAAAGACTTCCCCAAATCTC 58.089 43.478 0.00 0.00 31.28 2.75
1442 6095 5.324832 TTCAGAAAGACTTCCCCAAATCT 57.675 39.130 0.00 0.00 31.28 2.40
1443 6096 6.015095 ACATTTCAGAAAGACTTCCCCAAATC 60.015 38.462 1.28 0.00 31.28 2.17
1444 6097 5.840693 ACATTTCAGAAAGACTTCCCCAAAT 59.159 36.000 1.28 0.00 31.28 2.32
1445 6098 5.208121 ACATTTCAGAAAGACTTCCCCAAA 58.792 37.500 1.28 0.00 31.28 3.28
1446 6099 4.803452 ACATTTCAGAAAGACTTCCCCAA 58.197 39.130 1.28 0.00 31.28 4.12
1447 6100 4.104738 AGACATTTCAGAAAGACTTCCCCA 59.895 41.667 1.28 0.00 31.28 4.96
1448 6101 4.657013 AGACATTTCAGAAAGACTTCCCC 58.343 43.478 1.28 0.00 31.28 4.81
1449 6102 6.702329 TCTAGACATTTCAGAAAGACTTCCC 58.298 40.000 1.28 0.00 31.28 3.97
1450 6103 8.608844 TTTCTAGACATTTCAGAAAGACTTCC 57.391 34.615 1.28 0.00 34.28 3.46
1453 6106 9.377312 GCTATTTCTAGACATTTCAGAAAGACT 57.623 33.333 1.28 3.66 40.54 3.24
1454 6107 9.377312 AGCTATTTCTAGACATTTCAGAAAGAC 57.623 33.333 1.28 0.00 40.54 3.01
1455 6108 9.376075 CAGCTATTTCTAGACATTTCAGAAAGA 57.624 33.333 1.28 6.72 40.54 2.52
1456 6109 8.610896 CCAGCTATTTCTAGACATTTCAGAAAG 58.389 37.037 1.28 0.00 40.54 2.62
1457 6110 8.103305 ACCAGCTATTTCTAGACATTTCAGAAA 58.897 33.333 0.00 0.00 41.22 2.52
1458 6111 7.624549 ACCAGCTATTTCTAGACATTTCAGAA 58.375 34.615 0.00 0.00 0.00 3.02
1459 6112 7.187824 ACCAGCTATTTCTAGACATTTCAGA 57.812 36.000 0.00 0.00 0.00 3.27
1460 6113 7.201679 CCAACCAGCTATTTCTAGACATTTCAG 60.202 40.741 0.00 0.00 0.00 3.02
1461 6114 6.599244 CCAACCAGCTATTTCTAGACATTTCA 59.401 38.462 0.00 0.00 0.00 2.69
1462 6115 6.458888 GCCAACCAGCTATTTCTAGACATTTC 60.459 42.308 0.00 0.00 0.00 2.17
1463 6116 5.358160 GCCAACCAGCTATTTCTAGACATTT 59.642 40.000 0.00 0.00 0.00 2.32
1464 6117 4.884164 GCCAACCAGCTATTTCTAGACATT 59.116 41.667 0.00 0.00 0.00 2.71
1465 6118 4.455606 GCCAACCAGCTATTTCTAGACAT 58.544 43.478 0.00 0.00 0.00 3.06
1466 6119 3.678806 CGCCAACCAGCTATTTCTAGACA 60.679 47.826 0.00 0.00 0.00 3.41
1467 6120 2.866762 CGCCAACCAGCTATTTCTAGAC 59.133 50.000 0.00 0.00 0.00 2.59
1468 6121 2.500098 ACGCCAACCAGCTATTTCTAGA 59.500 45.455 0.00 0.00 0.00 2.43
1469 6122 2.866762 GACGCCAACCAGCTATTTCTAG 59.133 50.000 0.00 0.00 0.00 2.43
1470 6123 2.235155 TGACGCCAACCAGCTATTTCTA 59.765 45.455 0.00 0.00 0.00 2.10
1471 6124 1.003118 TGACGCCAACCAGCTATTTCT 59.997 47.619 0.00 0.00 0.00 2.52
1472 6125 1.448985 TGACGCCAACCAGCTATTTC 58.551 50.000 0.00 0.00 0.00 2.17
1473 6126 2.128771 ATGACGCCAACCAGCTATTT 57.871 45.000 0.00 0.00 0.00 1.40
1474 6127 3.141398 CATATGACGCCAACCAGCTATT 58.859 45.455 0.00 0.00 0.00 1.73
1475 6128 2.550855 CCATATGACGCCAACCAGCTAT 60.551 50.000 3.65 0.00 0.00 2.97
1476 6129 1.202639 CCATATGACGCCAACCAGCTA 60.203 52.381 3.65 0.00 0.00 3.32
1477 6130 0.464373 CCATATGACGCCAACCAGCT 60.464 55.000 3.65 0.00 0.00 4.24
1478 6131 0.748005 ACCATATGACGCCAACCAGC 60.748 55.000 3.65 0.00 0.00 4.85
1479 6132 1.670811 GAACCATATGACGCCAACCAG 59.329 52.381 3.65 0.00 0.00 4.00
1480 6133 1.680555 GGAACCATATGACGCCAACCA 60.681 52.381 3.65 0.00 0.00 3.67
1481 6134 1.021968 GGAACCATATGACGCCAACC 58.978 55.000 3.65 0.00 0.00 3.77
1482 6135 1.745232 TGGAACCATATGACGCCAAC 58.255 50.000 3.65 0.00 0.00 3.77
1483 6136 2.296792 CATGGAACCATATGACGCCAA 58.703 47.619 3.65 0.00 34.91 4.52
1484 6137 1.476652 CCATGGAACCATATGACGCCA 60.477 52.381 5.56 8.43 34.91 5.69
1485 6138 1.238439 CCATGGAACCATATGACGCC 58.762 55.000 5.56 2.64 34.91 5.68
1486 6139 1.603802 CACCATGGAACCATATGACGC 59.396 52.381 21.47 0.00 34.91 5.19
1487 6140 3.133691 CTCACCATGGAACCATATGACG 58.866 50.000 21.47 0.60 34.91 4.35
1488 6141 4.156455 ACTCACCATGGAACCATATGAC 57.844 45.455 21.47 0.00 34.91 3.06
1489 6142 4.860802 AACTCACCATGGAACCATATGA 57.139 40.909 21.47 8.83 34.91 2.15
1490 6143 5.653769 AGAAAACTCACCATGGAACCATATG 59.346 40.000 21.47 4.07 34.91 1.78
1491 6144 5.653769 CAGAAAACTCACCATGGAACCATAT 59.346 40.000 21.47 0.00 34.91 1.78
1492 6145 5.009631 CAGAAAACTCACCATGGAACCATA 58.990 41.667 21.47 0.00 34.91 2.74
1493 6146 3.828451 CAGAAAACTCACCATGGAACCAT 59.172 43.478 21.47 0.00 37.08 3.55
1494 6147 3.221771 CAGAAAACTCACCATGGAACCA 58.778 45.455 21.47 0.00 0.00 3.67
1495 6148 3.222603 ACAGAAAACTCACCATGGAACC 58.777 45.455 21.47 0.00 0.00 3.62
1496 6149 4.261614 GGAACAGAAAACTCACCATGGAAC 60.262 45.833 21.47 0.29 0.00 3.62
1497 6150 3.888930 GGAACAGAAAACTCACCATGGAA 59.111 43.478 21.47 4.97 0.00 3.53
1498 6151 3.138283 AGGAACAGAAAACTCACCATGGA 59.862 43.478 21.47 0.00 0.00 3.41
1499 6152 3.490348 AGGAACAGAAAACTCACCATGG 58.510 45.455 11.19 11.19 0.00 3.66
1500 6153 5.180117 CAGTAGGAACAGAAAACTCACCATG 59.820 44.000 0.00 0.00 0.00 3.66
1501 6154 5.308825 CAGTAGGAACAGAAAACTCACCAT 58.691 41.667 0.00 0.00 0.00 3.55
1502 6155 4.703897 CAGTAGGAACAGAAAACTCACCA 58.296 43.478 0.00 0.00 0.00 4.17
1503 6156 3.498777 GCAGTAGGAACAGAAAACTCACC 59.501 47.826 0.00 0.00 0.00 4.02
1504 6157 4.212214 CAGCAGTAGGAACAGAAAACTCAC 59.788 45.833 0.00 0.00 0.00 3.51
1505 6158 4.141711 ACAGCAGTAGGAACAGAAAACTCA 60.142 41.667 0.00 0.00 0.00 3.41
1506 6159 4.381411 ACAGCAGTAGGAACAGAAAACTC 58.619 43.478 0.00 0.00 0.00 3.01
1507 6160 4.423625 ACAGCAGTAGGAACAGAAAACT 57.576 40.909 0.00 0.00 0.00 2.66
1508 6161 6.260271 AGTTTACAGCAGTAGGAACAGAAAAC 59.740 38.462 6.61 0.23 0.00 2.43
1509 6162 6.354130 AGTTTACAGCAGTAGGAACAGAAAA 58.646 36.000 6.61 0.00 0.00 2.29
1510 6163 5.925509 AGTTTACAGCAGTAGGAACAGAAA 58.074 37.500 6.61 0.00 0.00 2.52
1511 6164 5.546621 AGTTTACAGCAGTAGGAACAGAA 57.453 39.130 6.61 0.00 0.00 3.02
1512 6165 5.510861 GGAAGTTTACAGCAGTAGGAACAGA 60.511 44.000 6.61 0.00 0.00 3.41
1513 6166 4.691216 GGAAGTTTACAGCAGTAGGAACAG 59.309 45.833 6.61 0.00 0.00 3.16
1514 6167 4.504340 GGGAAGTTTACAGCAGTAGGAACA 60.504 45.833 6.61 0.00 0.00 3.18
1515 6168 4.001652 GGGAAGTTTACAGCAGTAGGAAC 58.998 47.826 0.00 0.00 0.00 3.62
1516 6169 3.908103 AGGGAAGTTTACAGCAGTAGGAA 59.092 43.478 0.00 0.00 0.00 3.36
1517 6170 3.517612 AGGGAAGTTTACAGCAGTAGGA 58.482 45.455 0.00 0.00 0.00 2.94
1518 6171 3.983044 AGGGAAGTTTACAGCAGTAGG 57.017 47.619 0.00 0.00 0.00 3.18
1519 6172 4.894784 TCAAGGGAAGTTTACAGCAGTAG 58.105 43.478 0.00 0.00 0.00 2.57
1520 6173 4.967084 TCAAGGGAAGTTTACAGCAGTA 57.033 40.909 0.00 0.00 0.00 2.74
1521 6174 3.857157 TCAAGGGAAGTTTACAGCAGT 57.143 42.857 0.00 0.00 0.00 4.40
1522 6175 5.712152 ATTTCAAGGGAAGTTTACAGCAG 57.288 39.130 0.00 0.00 33.82 4.24
1523 6176 5.180492 CGTATTTCAAGGGAAGTTTACAGCA 59.820 40.000 0.00 0.00 33.82 4.41
1524 6177 5.628134 CGTATTTCAAGGGAAGTTTACAGC 58.372 41.667 0.00 0.00 33.82 4.40
1525 6178 5.628134 GCGTATTTCAAGGGAAGTTTACAG 58.372 41.667 0.00 0.00 33.82 2.74
1526 6179 4.152759 CGCGTATTTCAAGGGAAGTTTACA 59.847 41.667 0.00 0.00 33.82 2.41
1527 6180 4.644954 CGCGTATTTCAAGGGAAGTTTAC 58.355 43.478 0.00 0.00 33.82 2.01
1528 6181 3.125658 GCGCGTATTTCAAGGGAAGTTTA 59.874 43.478 8.43 0.00 33.82 2.01
1529 6182 2.095415 GCGCGTATTTCAAGGGAAGTTT 60.095 45.455 8.43 0.00 33.82 2.66
1530 6183 1.467342 GCGCGTATTTCAAGGGAAGTT 59.533 47.619 8.43 0.00 33.82 2.66
1531 6184 1.084289 GCGCGTATTTCAAGGGAAGT 58.916 50.000 8.43 0.00 33.82 3.01
1532 6185 1.062587 CTGCGCGTATTTCAAGGGAAG 59.937 52.381 8.43 0.00 33.82 3.46
1533 6186 1.083489 CTGCGCGTATTTCAAGGGAA 58.917 50.000 8.43 0.00 0.00 3.97
1534 6187 1.366111 GCTGCGCGTATTTCAAGGGA 61.366 55.000 8.43 0.00 0.00 4.20
1535 6188 1.062525 GCTGCGCGTATTTCAAGGG 59.937 57.895 8.43 0.00 0.00 3.95
1536 6189 1.062525 GGCTGCGCGTATTTCAAGG 59.937 57.895 8.43 0.00 0.00 3.61
1537 6190 1.286501 TAGGCTGCGCGTATTTCAAG 58.713 50.000 8.43 0.00 0.00 3.02
1538 6191 1.728068 TTAGGCTGCGCGTATTTCAA 58.272 45.000 8.43 0.00 0.00 2.69
1539 6192 1.663643 CTTTAGGCTGCGCGTATTTCA 59.336 47.619 8.43 0.00 0.00 2.69
1540 6193 1.931172 TCTTTAGGCTGCGCGTATTTC 59.069 47.619 8.43 0.00 0.00 2.17
1541 6194 2.018542 TCTTTAGGCTGCGCGTATTT 57.981 45.000 8.43 0.00 0.00 1.40
1542 6195 1.867233 CATCTTTAGGCTGCGCGTATT 59.133 47.619 8.43 0.00 0.00 1.89
1543 6196 1.502231 CATCTTTAGGCTGCGCGTAT 58.498 50.000 8.43 0.00 0.00 3.06
1544 6197 1.151777 GCATCTTTAGGCTGCGCGTA 61.152 55.000 8.43 0.71 0.00 4.42
1545 6198 2.464459 GCATCTTTAGGCTGCGCGT 61.464 57.895 8.43 0.00 0.00 6.01
1546 6199 2.325857 GCATCTTTAGGCTGCGCG 59.674 61.111 0.00 0.00 0.00 6.86
1547 6200 2.114670 TGGCATCTTTAGGCTGCGC 61.115 57.895 0.00 0.00 36.76 6.09
1548 6201 0.745845 AGTGGCATCTTTAGGCTGCG 60.746 55.000 0.00 0.00 36.76 5.18
1549 6202 1.020437 GAGTGGCATCTTTAGGCTGC 58.980 55.000 0.00 0.00 31.60 5.25
1550 6203 2.408271 TGAGTGGCATCTTTAGGCTG 57.592 50.000 0.00 0.00 31.60 4.85
1551 6204 2.307098 AGTTGAGTGGCATCTTTAGGCT 59.693 45.455 0.00 0.00 31.60 4.58
1552 6205 2.716217 AGTTGAGTGGCATCTTTAGGC 58.284 47.619 0.00 0.00 0.00 3.93
1553 6206 3.372206 CGAAGTTGAGTGGCATCTTTAGG 59.628 47.826 0.00 0.00 36.82 2.69
1554 6207 4.245660 TCGAAGTTGAGTGGCATCTTTAG 58.754 43.478 0.00 0.00 36.82 1.85
1555 6208 4.245660 CTCGAAGTTGAGTGGCATCTTTA 58.754 43.478 0.00 0.00 36.82 1.85
1556 6209 3.070018 CTCGAAGTTGAGTGGCATCTTT 58.930 45.455 0.00 0.00 36.82 2.52
1557 6210 2.693069 CTCGAAGTTGAGTGGCATCTT 58.307 47.619 0.00 0.00 38.82 2.40
1558 6211 2.376808 CTCGAAGTTGAGTGGCATCT 57.623 50.000 0.00 0.00 0.00 2.90
1569 6222 5.582665 GCTAATTCATCTCCAACTCGAAGTT 59.417 40.000 0.00 0.00 39.39 2.66
1570 6223 5.105146 AGCTAATTCATCTCCAACTCGAAGT 60.105 40.000 0.00 0.00 0.00 3.01
1571 6224 5.355596 AGCTAATTCATCTCCAACTCGAAG 58.644 41.667 0.00 0.00 0.00 3.79
1572 6225 5.344743 AGCTAATTCATCTCCAACTCGAA 57.655 39.130 0.00 0.00 0.00 3.71
1573 6226 5.344743 AAGCTAATTCATCTCCAACTCGA 57.655 39.130 0.00 0.00 0.00 4.04
1574 6227 5.176590 GCTAAGCTAATTCATCTCCAACTCG 59.823 44.000 0.00 0.00 0.00 4.18
1575 6228 6.287525 AGCTAAGCTAATTCATCTCCAACTC 58.712 40.000 0.00 0.00 36.99 3.01
1576 6229 6.245890 AGCTAAGCTAATTCATCTCCAACT 57.754 37.500 0.00 0.00 36.99 3.16
1577 6230 7.437748 TCTAGCTAAGCTAATTCATCTCCAAC 58.562 38.462 0.00 0.00 40.82 3.77
1578 6231 7.507277 TCTCTAGCTAAGCTAATTCATCTCCAA 59.493 37.037 0.00 0.00 40.82 3.53
1579 6232 7.007116 TCTCTAGCTAAGCTAATTCATCTCCA 58.993 38.462 0.00 0.00 40.82 3.86
1580 6233 7.461182 TCTCTAGCTAAGCTAATTCATCTCC 57.539 40.000 0.00 0.00 40.82 3.71
1609 6262 1.419387 GAGCCAGGCCTAGTTCATCAT 59.581 52.381 3.98 0.00 0.00 2.45
1620 6273 1.397390 CCCATGAATTGAGCCAGGCC 61.397 60.000 8.22 0.00 0.00 5.19
1621 6274 2.024590 GCCCATGAATTGAGCCAGGC 62.025 60.000 1.84 1.84 0.00 4.85
1656 6309 9.317936 GAGGTGAACTGAAGAAAAATTTGAATT 57.682 29.630 0.00 0.00 0.00 2.17
1743 6402 4.789012 TTGTTCCTGCTGATTTTGATCC 57.211 40.909 0.00 0.00 0.00 3.36
1855 6515 5.294306 CCACACAATACATGTACCATCAGAC 59.706 44.000 7.96 0.00 41.46 3.51
1899 6585 6.704289 TTCAATGATGAAGGAAAGCATAGG 57.296 37.500 0.00 0.00 40.59 2.57
1972 6686 0.249398 AGAGTACCAACGACCATGGC 59.751 55.000 13.04 3.65 41.89 4.40
1973 6687 1.469251 CGAGAGTACCAACGACCATGG 60.469 57.143 11.19 11.19 43.84 3.66
1974 6688 1.471287 TCGAGAGTACCAACGACCATG 59.529 52.381 0.00 0.00 0.00 3.66
2058 6772 9.803315 GACGTGACATCACAACCATATATATAT 57.197 33.333 12.32 0.00 46.75 0.86
2061 6775 7.145323 CAGACGTGACATCACAACCATATATA 58.855 38.462 12.32 0.00 46.75 0.86
2234 8703 9.890629 AAGAAGTAGCACAATGATGTATCTTAA 57.109 29.630 0.00 0.00 37.82 1.85
2277 8746 2.098117 GGTACTGCAATAAGCCAGCAAG 59.902 50.000 0.00 0.00 44.83 4.01
2389 8859 4.930405 GGGAGTTGTACAAGAAAGAGTAGC 59.070 45.833 8.98 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.