Multiple sequence alignment - TraesCS5D01G265500

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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 TraesCS5D01G265500 chr5D 100.000 2423 0 0 1 2423 369869152 369871574 0.000000e+00 4475
1 TraesCS5D01G265500 chr5D 93.162 117 1 1 2155 2271 369871249 369871358 5.360000e-37 165
2 TraesCS5D01G265500 chr5D 93.162 117 1 1 2098 2207 369871306 369871422 5.360000e-37 165
3 TraesCS5D01G265500 chr5A 89.636 1100 40 22 574 1608 472341712 472342802 0.000000e+00 1332
4 TraesCS5D01G265500 chr5A 82.588 626 75 13 1616 2207 472343022 472343647 2.760000e-144 521
5 TraesCS5D01G265500 chr5A 94.424 269 15 0 2155 2423 472343531 472343799 4.820000e-112 414
6 TraesCS5D01G265500 chr5B 88.230 1113 48 30 564 1608 439227119 439228216 0.000000e+00 1253
7 TraesCS5D01G265500 chr5B 89.831 413 38 2 1 409 439226096 439226508 5.930000e-146 527
8 TraesCS5D01G265500 chr5B 81.331 616 69 13 1615 2207 439228453 439229045 2.200000e-125 459
9 TraesCS5D01G265500 chr5B 94.709 189 8 2 2155 2343 439228931 439229117 2.360000e-75 292
10 TraesCS5D01G265500 chr5B 98.947 95 1 0 2329 2423 439230132 439230226 1.150000e-38 171
11 TraesCS5D01G265500 chr7D 84.770 348 44 6 1615 1955 136414892 136414547 8.300000e-90 340
12 TraesCS5D01G265500 chr3D 84.393 346 49 3 1615 1955 134007708 134007363 3.860000e-88 335
13 TraesCS5D01G265500 chr6A 84.241 349 46 6 1615 1956 573641312 573641658 4.990000e-87 331
14 TraesCS5D01G265500 chr2D 84.195 348 46 6 1615 1955 87830477 87830132 1.800000e-86 329
15 TraesCS5D01G265500 chr2D 83.430 344 52 2 1615 1953 112538788 112538445 5.030000e-82 315
16 TraesCS5D01G265500 chr4B 83.815 346 50 3 1615 1955 64076983 64076639 8.360000e-85 324
17 TraesCS5D01G265500 chr2B 83.526 346 52 2 1615 1955 162860808 162860463 3.890000e-83 318
18 TraesCS5D01G265500 chr2A 83.526 346 52 3 1615 1955 765573894 765574239 3.890000e-83 318
19 TraesCS5D01G265500 chr1A 83.526 346 48 6 1615 1955 285980405 285980064 5.030000e-82 315


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 TraesCS5D01G265500 chr5D 369869152 369871574 2422 False 1601.666667 4475 95.441333 1 2423 3 chr5D.!!$F1 2422
1 TraesCS5D01G265500 chr5A 472341712 472343799 2087 False 755.666667 1332 88.882667 574 2423 3 chr5A.!!$F1 1849
2 TraesCS5D01G265500 chr5B 439226096 439230226 4130 False 540.400000 1253 90.609600 1 2423 5 chr5B.!!$F1 2422

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
468 473 0.039074 AAGTTGTCGTCTCTGGCTCG 60.039 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2619 0.179137 CACGCTACTCTTCATCGGCA 60.179 55.0 0.0 0.0 0.0 5.69 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
55 56 0.755686 CCCCATCCACTAGCTCAGTC 59.244 60.000 0.00 0.00 34.26 3.51
61 62 1.813178 TCCACTAGCTCAGTCGAGTTG 59.187 52.381 0.00 0.00 41.71 3.16
75 76 3.253677 GTCGAGTTGTCCTTCTCAGAAGA 59.746 47.826 16.64 0.00 0.00 2.87
76 77 4.082463 GTCGAGTTGTCCTTCTCAGAAGAT 60.082 45.833 16.64 0.00 0.00 2.40
78 79 4.502962 GAGTTGTCCTTCTCAGAAGATGG 58.497 47.826 16.64 0.00 44.53 3.51
88 89 2.962421 CTCAGAAGATGGGTCCTCCTAC 59.038 54.545 0.00 0.00 36.20 3.18
110 111 1.067283 CCGCGCAGGAGATGAATAGAT 60.067 52.381 8.75 0.00 45.00 1.98
125 126 4.654262 TGAATAGATGACTAACTCCACCCC 59.346 45.833 0.00 0.00 32.04 4.95
130 131 1.697432 TGACTAACTCCACCCCAACAG 59.303 52.381 0.00 0.00 0.00 3.16
137 138 2.198426 CACCCCAACAGCCAACCT 59.802 61.111 0.00 0.00 0.00 3.50
145 146 0.771127 AACAGCCAACCTAGCTTGGA 59.229 50.000 21.63 0.00 43.19 3.53
147 148 1.168714 CAGCCAACCTAGCTTGGAAC 58.831 55.000 21.63 6.79 43.19 3.62
171 175 2.350522 CTCCCAATGAAACTGGAGTCG 58.649 52.381 0.00 0.00 39.64 4.18
173 177 1.806542 CCCAATGAAACTGGAGTCGTG 59.193 52.381 0.00 0.00 0.00 4.35
183 188 3.914312 ACTGGAGTCGTGTCATTAACAG 58.086 45.455 0.00 0.00 38.97 3.16
193 198 3.368236 GTGTCATTAACAGGAAGCGAGAC 59.632 47.826 0.00 0.00 38.97 3.36
215 220 2.109126 GCACACTTCCCGAGCATCC 61.109 63.158 0.00 0.00 0.00 3.51
279 284 0.387367 CGAACCACGAGTGACTCAGG 60.387 60.000 13.67 15.39 45.77 3.86
283 288 0.673985 CCACGAGTGACTCAGGTGAA 59.326 55.000 18.24 0.00 28.16 3.18
287 292 2.223829 ACGAGTGACTCAGGTGAACAAG 60.224 50.000 13.67 0.00 0.00 3.16
288 293 2.139118 GAGTGACTCAGGTGAACAAGC 58.861 52.381 7.90 0.00 0.00 4.01
292 297 1.071471 CTCAGGTGAACAAGCCCGT 59.929 57.895 0.00 0.00 0.00 5.28
295 300 1.086696 CAGGTGAACAAGCCCGTATG 58.913 55.000 0.00 0.00 0.00 2.39
350 355 0.527565 AATCTTCGCATGGCCACAAC 59.472 50.000 8.16 0.00 0.00 3.32
366 371 6.551601 TGGCCACAACTTCCTAAATTTAAAGA 59.448 34.615 0.00 5.39 0.00 2.52
383 388 7.520119 TTTAAAGAGTACACATATGCGACAG 57.480 36.000 1.58 0.00 0.00 3.51
393 398 4.006989 ACATATGCGACAGTTGCCTAAAA 58.993 39.130 10.50 0.00 0.00 1.52
396 401 4.519540 ATGCGACAGTTGCCTAAAATTT 57.480 36.364 10.50 0.00 0.00 1.82
409 414 7.023171 TGCCTAAAATTTCCCTAACTACTCA 57.977 36.000 0.00 0.00 0.00 3.41
410 415 7.110155 TGCCTAAAATTTCCCTAACTACTCAG 58.890 38.462 0.00 0.00 0.00 3.35
411 416 7.037873 TGCCTAAAATTTCCCTAACTACTCAGA 60.038 37.037 0.00 0.00 0.00 3.27
413 418 9.331282 CCTAAAATTTCCCTAACTACTCAGATG 57.669 37.037 0.00 0.00 0.00 2.90
416 421 7.741554 AATTTCCCTAACTACTCAGATGACT 57.258 36.000 0.00 0.00 0.00 3.41
417 422 8.840200 AATTTCCCTAACTACTCAGATGACTA 57.160 34.615 0.00 0.00 0.00 2.59
418 423 8.840200 ATTTCCCTAACTACTCAGATGACTAA 57.160 34.615 0.00 0.00 0.00 2.24
419 424 7.883391 TTCCCTAACTACTCAGATGACTAAG 57.117 40.000 0.00 0.00 0.00 2.18
422 427 4.640789 AACTACTCAGATGACTAAGCCG 57.359 45.455 0.00 0.00 0.00 5.52
423 428 2.952978 ACTACTCAGATGACTAAGCCGG 59.047 50.000 0.00 0.00 0.00 6.13
425 430 1.342076 ACTCAGATGACTAAGCCGGGA 60.342 52.381 2.18 0.00 0.00 5.14
426 431 1.757118 CTCAGATGACTAAGCCGGGAA 59.243 52.381 2.18 0.00 0.00 3.97
439 444 2.949106 GGGAACGAGTCGACGACA 59.051 61.111 28.31 0.00 34.60 4.35
442 447 0.447011 GGAACGAGTCGACGACATCT 59.553 55.000 28.31 9.37 34.60 2.90
443 448 1.529418 GGAACGAGTCGACGACATCTC 60.529 57.143 28.31 16.58 34.60 2.75
444 449 0.447011 AACGAGTCGACGACATCTCC 59.553 55.000 28.31 11.40 34.60 3.71
445 450 0.672711 ACGAGTCGACGACATCTCCA 60.673 55.000 28.31 0.00 34.60 3.86
446 451 0.247735 CGAGTCGACGACATCTCCAC 60.248 60.000 28.31 10.10 34.60 4.02
447 452 0.099082 GAGTCGACGACATCTCCACC 59.901 60.000 28.31 0.00 34.60 4.61
448 453 0.608308 AGTCGACGACATCTCCACCA 60.608 55.000 28.31 0.00 34.60 4.17
449 454 0.242825 GTCGACGACATCTCCACCAA 59.757 55.000 22.66 0.00 32.09 3.67
450 455 0.963225 TCGACGACATCTCCACCAAA 59.037 50.000 0.00 0.00 0.00 3.28
451 456 1.067846 TCGACGACATCTCCACCAAAG 60.068 52.381 0.00 0.00 0.00 2.77
452 457 1.336887 CGACGACATCTCCACCAAAGT 60.337 52.381 0.00 0.00 0.00 2.66
453 458 2.767505 GACGACATCTCCACCAAAGTT 58.232 47.619 0.00 0.00 0.00 2.66
454 459 2.480419 GACGACATCTCCACCAAAGTTG 59.520 50.000 0.00 0.00 0.00 3.16
457 462 2.480419 GACATCTCCACCAAAGTTGTCG 59.520 50.000 0.00 0.00 35.14 4.35
458 463 2.158813 ACATCTCCACCAAAGTTGTCGT 60.159 45.455 0.00 0.00 0.00 4.34
460 465 1.760613 TCTCCACCAAAGTTGTCGTCT 59.239 47.619 0.00 0.00 0.00 4.18
461 466 2.135933 CTCCACCAAAGTTGTCGTCTC 58.864 52.381 0.00 0.00 0.00 3.36
462 467 1.760613 TCCACCAAAGTTGTCGTCTCT 59.239 47.619 0.00 0.00 0.00 3.10
463 468 1.867233 CCACCAAAGTTGTCGTCTCTG 59.133 52.381 0.00 0.00 0.00 3.35
464 469 1.867233 CACCAAAGTTGTCGTCTCTGG 59.133 52.381 0.00 0.00 0.00 3.86
465 470 0.868406 CCAAAGTTGTCGTCTCTGGC 59.132 55.000 0.00 0.00 0.00 4.85
468 473 0.039074 AAGTTGTCGTCTCTGGCTCG 60.039 55.000 0.00 0.00 0.00 5.03
469 474 1.173444 AGTTGTCGTCTCTGGCTCGT 61.173 55.000 0.00 0.00 0.00 4.18
471 476 0.039437 TTGTCGTCTCTGGCTCGTTC 60.039 55.000 0.00 0.00 0.00 3.95
472 477 1.153997 GTCGTCTCTGGCTCGTTCC 60.154 63.158 0.00 0.00 0.00 3.62
473 478 2.182030 CGTCTCTGGCTCGTTCCC 59.818 66.667 0.00 0.00 0.00 3.97
474 479 2.636412 CGTCTCTGGCTCGTTCCCA 61.636 63.158 0.00 0.00 0.00 4.37
478 483 2.348998 CTGGCTCGTTCCCAGCTT 59.651 61.111 5.98 0.00 42.98 3.74
479 484 2.032528 TGGCTCGTTCCCAGCTTG 59.967 61.111 0.00 0.00 37.05 4.01
482 487 2.747855 CTCGTTCCCAGCTTGCCC 60.748 66.667 0.00 0.00 0.00 5.36
485 490 2.747855 GTTCCCAGCTTGCCCTCG 60.748 66.667 0.00 0.00 0.00 4.63
486 491 3.249189 TTCCCAGCTTGCCCTCGT 61.249 61.111 0.00 0.00 0.00 4.18
487 492 3.551496 TTCCCAGCTTGCCCTCGTG 62.551 63.158 0.00 0.00 0.00 4.35
489 494 4.020617 CCAGCTTGCCCTCGTGGA 62.021 66.667 4.76 0.00 35.39 4.02
490 495 2.435586 CAGCTTGCCCTCGTGGAG 60.436 66.667 4.76 0.00 35.39 3.86
504 509 4.436998 GGAGGACGCCACGACTGG 62.437 72.222 0.00 0.00 41.13 4.00
523 528 3.367743 CGTCGTCCCCGTCTCCAA 61.368 66.667 0.00 0.00 35.01 3.53
524 529 2.260743 GTCGTCCCCGTCTCCAAC 59.739 66.667 0.00 0.00 35.01 3.77
525 530 2.116772 TCGTCCCCGTCTCCAACT 59.883 61.111 0.00 0.00 35.01 3.16
527 532 2.273179 CGTCCCCGTCTCCAACTCA 61.273 63.158 0.00 0.00 0.00 3.41
529 534 0.898789 GTCCCCGTCTCCAACTCAGA 60.899 60.000 0.00 0.00 0.00 3.27
530 535 0.898789 TCCCCGTCTCCAACTCAGAC 60.899 60.000 0.00 0.00 37.51 3.51
535 540 1.634702 GTCTCCAACTCAGACGATGC 58.365 55.000 0.00 0.00 31.33 3.91
537 542 2.423892 GTCTCCAACTCAGACGATGCTA 59.576 50.000 0.00 0.00 31.33 3.49
538 543 2.423892 TCTCCAACTCAGACGATGCTAC 59.576 50.000 0.00 0.00 0.00 3.58
539 544 2.425312 CTCCAACTCAGACGATGCTACT 59.575 50.000 0.00 0.00 0.00 2.57
540 545 2.423892 TCCAACTCAGACGATGCTACTC 59.576 50.000 0.00 0.00 0.00 2.59
541 546 2.425312 CCAACTCAGACGATGCTACTCT 59.575 50.000 0.00 0.00 0.00 3.24
542 547 3.488384 CCAACTCAGACGATGCTACTCTC 60.488 52.174 0.00 0.00 0.00 3.20
543 548 3.275617 ACTCAGACGATGCTACTCTCT 57.724 47.619 0.00 0.00 0.00 3.10
544 549 3.202906 ACTCAGACGATGCTACTCTCTC 58.797 50.000 0.00 0.00 0.00 3.20
545 550 3.118408 ACTCAGACGATGCTACTCTCTCT 60.118 47.826 0.00 0.00 0.00 3.10
547 552 3.133901 TCAGACGATGCTACTCTCTCTCT 59.866 47.826 0.00 0.00 0.00 3.10
549 554 3.133901 AGACGATGCTACTCTCTCTCTCA 59.866 47.826 0.00 0.00 0.00 3.27
551 556 3.202097 CGATGCTACTCTCTCTCTCACA 58.798 50.000 0.00 0.00 0.00 3.58
553 558 3.425162 TGCTACTCTCTCTCTCACACA 57.575 47.619 0.00 0.00 0.00 3.72
554 559 3.078097 TGCTACTCTCTCTCTCACACAC 58.922 50.000 0.00 0.00 0.00 3.82
555 560 3.078097 GCTACTCTCTCTCTCACACACA 58.922 50.000 0.00 0.00 0.00 3.72
556 561 3.119990 GCTACTCTCTCTCTCACACACAC 60.120 52.174 0.00 0.00 0.00 3.82
557 562 2.937519 ACTCTCTCTCTCACACACACA 58.062 47.619 0.00 0.00 0.00 3.72
558 563 2.621055 ACTCTCTCTCTCACACACACAC 59.379 50.000 0.00 0.00 0.00 3.82
559 564 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
560 565 2.359214 TCTCTCTCTCACACACACACAC 59.641 50.000 0.00 0.00 0.00 3.82
561 566 1.409064 TCTCTCTCACACACACACACC 59.591 52.381 0.00 0.00 0.00 4.16
562 567 0.102300 TCTCTCACACACACACACCG 59.898 55.000 0.00 0.00 0.00 4.94
607 1071 1.733360 CGGGATTAGGAAACGCGAAAA 59.267 47.619 15.93 0.00 41.18 2.29
610 1074 4.673320 CGGGATTAGGAAACGCGAAAATTT 60.673 41.667 15.93 1.61 41.18 1.82
641 1109 1.153597 TGCGAGGTTCATATGCTGCG 61.154 55.000 0.00 0.00 0.00 5.18
675 1143 0.535102 CTTCTTCACGTGCCCTTGGT 60.535 55.000 11.67 0.00 0.00 3.67
732 1211 1.272715 CACACAAGCGACACGTCAC 59.727 57.895 0.00 0.00 0.00 3.67
733 1212 1.153726 ACACAAGCGACACGTCACA 60.154 52.632 0.00 0.00 0.00 3.58
734 1213 1.145759 ACACAAGCGACACGTCACAG 61.146 55.000 0.00 0.00 0.00 3.66
735 1214 1.141019 ACAAGCGACACGTCACAGT 59.859 52.632 0.00 0.00 0.00 3.55
736 1215 1.145759 ACAAGCGACACGTCACAGTG 61.146 55.000 0.00 0.00 46.83 3.66
737 1216 1.591594 AAGCGACACGTCACAGTGG 60.592 57.895 0.00 0.00 45.80 4.00
767 1246 2.365617 ACTTGCCGTGAGAAGAGAAGAA 59.634 45.455 0.00 0.00 0.00 2.52
768 1247 2.732412 TGCCGTGAGAAGAGAAGAAG 57.268 50.000 0.00 0.00 0.00 2.85
830 1313 3.136123 GCCACACGCCATGAGCAT 61.136 61.111 0.00 0.00 44.04 3.79
963 1464 4.903010 ACTCGCCGCACGTTGGTT 62.903 61.111 5.55 0.00 44.19 3.67
969 1476 1.278637 CCGCACGTTGGTTCTTGAC 59.721 57.895 0.00 0.00 0.00 3.18
981 1488 1.134220 GTTCTTGACCACCCACACAGA 60.134 52.381 0.00 0.00 0.00 3.41
985 1492 1.079127 GACCACCCACACAGATCCG 60.079 63.158 0.00 0.00 0.00 4.18
986 1493 1.535444 ACCACCCACACAGATCCGA 60.535 57.895 0.00 0.00 0.00 4.55
987 1494 1.219124 CCACCCACACAGATCCGAG 59.781 63.158 0.00 0.00 0.00 4.63
989 1496 1.990060 ACCCACACAGATCCGAGGG 60.990 63.158 7.95 7.95 42.07 4.30
1426 1947 1.147153 CCCTTCTTCGGCTGATCCC 59.853 63.158 0.00 0.00 0.00 3.85
1437 1958 0.108207 GCTGATCCCTCCCATGTCTG 59.892 60.000 0.00 0.00 0.00 3.51
1478 2008 0.451783 CCGGCTTGCTGTTGTAATCC 59.548 55.000 0.00 0.00 0.00 3.01
1499 2029 3.424433 CCGCCGTGTTTTCATTAGTTCTC 60.424 47.826 0.00 0.00 0.00 2.87
1512 2045 7.745620 TCATTAGTTCTCTATACGCTGATGA 57.254 36.000 0.00 0.00 32.36 2.92
1608 2161 4.707030 TTCAGTGCCACATGAATGATTC 57.293 40.909 0.00 0.00 30.67 2.52
1609 2162 2.679336 TCAGTGCCACATGAATGATTCG 59.321 45.455 0.00 0.00 0.00 3.34
1610 2163 2.421073 CAGTGCCACATGAATGATTCGT 59.579 45.455 0.00 0.00 0.00 3.85
1641 2424 4.096231 TCTTCAATCATGGCAATACAACGG 59.904 41.667 0.00 0.00 0.00 4.44
1687 2470 0.824109 CAGATCCGCAGACCACCTAA 59.176 55.000 0.00 0.00 0.00 2.69
1692 2475 1.287815 CGCAGACCACCTAACGACA 59.712 57.895 0.00 0.00 0.00 4.35
1700 2483 4.099881 AGACCACCTAACGACAACTACAAA 59.900 41.667 0.00 0.00 0.00 2.83
1710 2493 3.601586 CGACAACTACAAACACTGAAGCG 60.602 47.826 0.00 0.00 0.00 4.68
1718 2501 0.531974 AACACTGAAGCGAGCCGAAA 60.532 50.000 0.00 0.00 0.00 3.46
1730 2515 3.913573 CCGAAAGCGCCATCGTCG 61.914 66.667 24.83 16.85 37.36 5.12
1767 2552 5.114081 GCCGGAGCTAGACAAAACTTATTA 58.886 41.667 5.05 0.00 35.50 0.98
1788 2573 7.973048 ATTATAGTAGACAGTTGGGAAGTCA 57.027 36.000 0.00 0.00 34.80 3.41
1791 2576 5.153950 AGTAGACAGTTGGGAAGTCATTC 57.846 43.478 0.00 0.00 34.80 2.67
1801 2586 2.092699 GGGAAGTCATTCTGCTAAGGCT 60.093 50.000 0.00 0.00 35.63 4.58
1803 2588 2.998316 AGTCATTCTGCTAAGGCTCC 57.002 50.000 0.00 0.00 39.59 4.70
1811 2596 3.374764 TCTGCTAAGGCTCCATAGAACA 58.625 45.455 2.63 0.00 39.59 3.18
1818 2603 0.654683 GCTCCATAGAACAAGCGCAG 59.345 55.000 11.47 3.78 0.00 5.18
1819 2604 2.009042 GCTCCATAGAACAAGCGCAGT 61.009 52.381 11.47 4.59 0.00 4.40
1821 2606 3.521560 CTCCATAGAACAAGCGCAGTAA 58.478 45.455 11.47 0.00 0.00 2.24
1844 2629 2.787249 CAACCGCTGCCGATGAAG 59.213 61.111 0.00 0.00 36.29 3.02
1853 2638 0.179137 TGCCGATGAAGAGTAGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
1896 2681 7.957484 CCTAAAAACACATGAATGTAGACGAAG 59.043 37.037 0.00 0.00 39.39 3.79
1926 2714 5.029650 TCCGAACAAATTCATCAAGAACG 57.970 39.130 0.00 0.00 39.49 3.95
1934 2722 0.824109 TCATCAAGAACGGATCCGCT 59.176 50.000 33.62 23.23 44.19 5.52
1956 2744 1.956170 GACACACCTCCACACGCTG 60.956 63.158 0.00 0.00 0.00 5.18
1957 2745 2.666190 CACACCTCCACACGCTGG 60.666 66.667 0.00 0.00 42.29 4.85
1965 2764 1.956170 CCACACGCTGGAGACACAC 60.956 63.158 0.00 0.00 43.95 3.82
1970 2769 1.448540 CGCTGGAGACACACCATCC 60.449 63.158 0.00 0.00 36.79 3.51
1971 2770 1.448540 GCTGGAGACACACCATCCG 60.449 63.158 0.00 0.00 36.79 4.18
1982 2781 2.355756 CACACCATCCGGACAATGAATC 59.644 50.000 6.12 0.00 35.59 2.52
1990 2789 1.744522 CGGACAATGAATCCATGCACA 59.255 47.619 0.00 0.00 35.83 4.57
2146 2961 2.772287 AGACTTTAGCTGCCAACTGAC 58.228 47.619 0.00 0.00 0.00 3.51
2182 2997 8.638873 TCATCAATATGATTACTTACCAGACGT 58.361 33.333 0.00 0.00 37.20 4.34
2183 2998 9.908152 CATCAATATGATTACTTACCAGACGTA 57.092 33.333 0.00 0.00 34.28 3.57
2185 3000 9.346005 TCAATATGATTACTTACCAGACGTAGA 57.654 33.333 0.00 0.00 0.00 2.59
2186 3001 9.395707 CAATATGATTACTTACCAGACGTAGAC 57.604 37.037 0.00 0.00 0.00 2.59
2187 3002 8.921353 ATATGATTACTTACCAGACGTAGACT 57.079 34.615 0.00 0.00 0.00 3.24
2188 3003 7.642082 ATGATTACTTACCAGACGTAGACTT 57.358 36.000 0.00 0.00 0.00 3.01
2189 3004 7.458409 TGATTACTTACCAGACGTAGACTTT 57.542 36.000 0.00 0.00 0.00 2.66
2190 3005 8.565896 TGATTACTTACCAGACGTAGACTTTA 57.434 34.615 0.00 0.00 0.00 1.85
2191 3006 8.671921 TGATTACTTACCAGACGTAGACTTTAG 58.328 37.037 0.00 0.00 0.00 1.85
2192 3007 5.307926 ACTTACCAGACGTAGACTTTAGC 57.692 43.478 0.00 0.00 0.00 3.09
2193 3008 5.008980 ACTTACCAGACGTAGACTTTAGCT 58.991 41.667 0.00 0.00 0.00 3.32
2194 3009 3.851976 ACCAGACGTAGACTTTAGCTG 57.148 47.619 0.00 0.00 0.00 4.24
2195 3010 2.094649 ACCAGACGTAGACTTTAGCTGC 60.095 50.000 0.00 0.00 0.00 5.25
2196 3011 2.531206 CAGACGTAGACTTTAGCTGCC 58.469 52.381 0.00 0.00 0.00 4.85
2197 3012 2.094700 CAGACGTAGACTTTAGCTGCCA 60.095 50.000 0.00 0.00 0.00 4.92
2198 3013 2.561419 AGACGTAGACTTTAGCTGCCAA 59.439 45.455 0.00 0.00 0.00 4.52
2199 3014 2.666994 GACGTAGACTTTAGCTGCCAAC 59.333 50.000 0.00 0.00 0.00 3.77
2200 3015 2.299297 ACGTAGACTTTAGCTGCCAACT 59.701 45.455 0.00 0.00 0.00 3.16
2201 3016 2.668457 CGTAGACTTTAGCTGCCAACTG 59.332 50.000 0.00 0.00 0.00 3.16
2202 3017 3.614150 CGTAGACTTTAGCTGCCAACTGA 60.614 47.826 0.00 0.00 0.00 3.41
2203 3018 2.772287 AGACTTTAGCTGCCAACTGAC 58.228 47.619 0.00 0.00 0.00 3.51
2204 3019 2.370189 AGACTTTAGCTGCCAACTGACT 59.630 45.455 0.00 0.00 0.00 3.41
2205 3020 2.739379 GACTTTAGCTGCCAACTGACTC 59.261 50.000 0.00 0.00 0.00 3.36
2206 3021 2.104792 ACTTTAGCTGCCAACTGACTCA 59.895 45.455 0.00 0.00 0.00 3.41
2207 3022 2.462456 TTAGCTGCCAACTGACTCAG 57.538 50.000 4.36 4.36 37.52 3.35
2209 3024 1.342074 AGCTGCCAACTGACTCAGTA 58.658 50.000 12.22 0.00 44.62 2.74
2210 3025 1.001406 AGCTGCCAACTGACTCAGTAC 59.999 52.381 12.22 6.07 44.62 2.73
2211 3026 1.001406 GCTGCCAACTGACTCAGTACT 59.999 52.381 12.22 0.00 44.62 2.73
2212 3027 2.231478 GCTGCCAACTGACTCAGTACTA 59.769 50.000 12.22 0.00 44.62 1.82
2213 3028 3.118956 GCTGCCAACTGACTCAGTACTAT 60.119 47.826 12.22 0.00 44.62 2.12
2214 3029 4.677584 CTGCCAACTGACTCAGTACTATC 58.322 47.826 12.22 0.00 44.62 2.08
2215 3030 4.086457 TGCCAACTGACTCAGTACTATCA 58.914 43.478 12.22 0.00 44.62 2.15
2216 3031 4.711846 TGCCAACTGACTCAGTACTATCAT 59.288 41.667 12.22 0.00 44.62 2.45
2217 3032 5.163509 TGCCAACTGACTCAGTACTATCATC 60.164 44.000 12.22 0.00 44.62 2.92
2218 3033 5.163509 GCCAACTGACTCAGTACTATCATCA 60.164 44.000 12.22 0.00 44.62 3.07
2219 3034 6.628175 GCCAACTGACTCAGTACTATCATCAA 60.628 42.308 12.22 0.00 44.62 2.57
2220 3035 7.495901 CCAACTGACTCAGTACTATCATCAAT 58.504 38.462 12.22 0.00 44.62 2.57
2221 3036 8.633561 CCAACTGACTCAGTACTATCATCAATA 58.366 37.037 12.22 0.00 44.62 1.90
2224 3039 9.579932 ACTGACTCAGTACTATCATCAATATGA 57.420 33.333 10.13 0.00 43.46 2.15
2282 3097 5.163814 GCCAACTGAATCATGAGACAGTTAC 60.164 44.000 31.18 25.55 46.94 2.50
2318 3133 7.277760 GTGACAGTTATGTTCAGTATGTATGCA 59.722 37.037 0.00 0.00 40.68 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.852842 TGCATCTAATCCCCTTGGGG 59.147 55.000 18.54 18.54 44.51 4.96
7 8 1.496429 AGTGCATCTAATCCCCTTGGG 59.504 52.381 0.00 0.00 46.11 4.12
16 17 1.672881 GCGGCTGAAAGTGCATCTAAT 59.327 47.619 0.00 0.00 37.40 1.73
55 56 3.924918 TCTTCTGAGAAGGACAACTCG 57.075 47.619 21.04 0.00 36.11 4.18
61 62 2.169561 GGACCCATCTTCTGAGAAGGAC 59.830 54.545 21.04 7.17 42.16 3.85
75 76 2.838225 CGGCGTAGGAGGACCCAT 60.838 66.667 0.00 0.00 37.41 4.00
104 105 4.631234 TGGGGTGGAGTTAGTCATCTATT 58.369 43.478 0.00 0.00 0.00 1.73
110 111 1.697432 CTGTTGGGGTGGAGTTAGTCA 59.303 52.381 0.00 0.00 0.00 3.41
125 126 0.883833 CCAAGCTAGGTTGGCTGTTG 59.116 55.000 34.14 14.71 40.70 3.33
130 131 1.271379 TGAGTTCCAAGCTAGGTTGGC 60.271 52.381 37.78 27.89 45.89 4.52
137 138 2.024176 TGGGAGTGAGTTCCAAGCTA 57.976 50.000 0.00 0.00 39.09 3.32
145 146 3.138283 TCCAGTTTCATTGGGAGTGAGTT 59.862 43.478 0.00 0.00 36.34 3.01
147 148 3.341823 CTCCAGTTTCATTGGGAGTGAG 58.658 50.000 0.00 0.00 41.58 3.51
171 175 3.368236 GTCTCGCTTCCTGTTAATGACAC 59.632 47.826 0.00 0.00 33.82 3.67
173 177 2.599082 CGTCTCGCTTCCTGTTAATGAC 59.401 50.000 0.00 0.00 0.00 3.06
196 201 2.045926 ATGCTCGGGAAGTGTGCC 60.046 61.111 0.00 0.00 0.00 5.01
197 202 2.109126 GGATGCTCGGGAAGTGTGC 61.109 63.158 0.00 0.00 0.00 4.57
215 220 1.136695 CTGCACTGCCTTCCTAGAGAG 59.863 57.143 0.00 0.00 0.00 3.20
240 245 4.439057 TCGTGTTGCTTTTGACTCTACTT 58.561 39.130 0.00 0.00 0.00 2.24
241 246 4.054780 TCGTGTTGCTTTTGACTCTACT 57.945 40.909 0.00 0.00 0.00 2.57
268 273 2.139118 GCTTGTTCACCTGAGTCACTC 58.861 52.381 0.00 0.00 0.00 3.51
279 284 4.634443 ACTATTTCATACGGGCTTGTTCAC 59.366 41.667 0.00 0.00 0.00 3.18
283 288 7.443272 GGTATTTACTATTTCATACGGGCTTGT 59.557 37.037 0.00 0.00 0.00 3.16
287 292 7.733402 TTGGTATTTACTATTTCATACGGGC 57.267 36.000 0.00 0.00 0.00 6.13
366 371 2.930040 GCAACTGTCGCATATGTGTACT 59.070 45.455 15.62 0.00 0.00 2.73
383 388 7.392393 TGAGTAGTTAGGGAAATTTTAGGCAAC 59.608 37.037 0.00 0.00 0.00 4.17
393 398 8.840200 TTAGTCATCTGAGTAGTTAGGGAAAT 57.160 34.615 0.00 0.00 32.15 2.17
396 401 5.828859 GCTTAGTCATCTGAGTAGTTAGGGA 59.171 44.000 0.00 0.00 32.15 4.20
409 414 0.460311 CGTTCCCGGCTTAGTCATCT 59.540 55.000 0.00 0.00 0.00 2.90
410 415 0.458669 TCGTTCCCGGCTTAGTCATC 59.541 55.000 0.00 0.00 33.95 2.92
411 416 0.460311 CTCGTTCCCGGCTTAGTCAT 59.540 55.000 0.00 0.00 33.95 3.06
413 418 0.179142 GACTCGTTCCCGGCTTAGTC 60.179 60.000 0.00 0.15 30.36 2.59
414 419 1.888736 GACTCGTTCCCGGCTTAGT 59.111 57.895 0.00 0.00 33.95 2.24
416 421 1.675310 TCGACTCGTTCCCGGCTTA 60.675 57.895 0.00 0.00 33.95 3.09
417 422 2.987547 TCGACTCGTTCCCGGCTT 60.988 61.111 0.00 0.00 33.95 4.35
418 423 3.745803 GTCGACTCGTTCCCGGCT 61.746 66.667 8.70 0.00 33.95 5.52
422 427 0.522915 GATGTCGTCGACTCGTTCCC 60.523 60.000 24.75 0.00 33.15 3.97
423 428 0.447011 AGATGTCGTCGACTCGTTCC 59.553 55.000 24.75 8.54 33.15 3.62
425 430 0.447011 GGAGATGTCGTCGACTCGTT 59.553 55.000 24.75 9.07 33.15 3.85
426 431 0.672711 TGGAGATGTCGTCGACTCGT 60.673 55.000 24.75 11.80 33.15 4.18
428 433 0.099082 GGTGGAGATGTCGTCGACTC 59.901 60.000 24.75 18.46 33.15 3.36
429 434 0.608308 TGGTGGAGATGTCGTCGACT 60.608 55.000 24.75 11.40 33.15 4.18
430 435 0.242825 TTGGTGGAGATGTCGTCGAC 59.757 55.000 18.51 18.51 0.00 4.20
432 437 1.336887 ACTTTGGTGGAGATGTCGTCG 60.337 52.381 0.00 0.00 0.00 5.12
433 438 2.457366 ACTTTGGTGGAGATGTCGTC 57.543 50.000 0.00 0.00 0.00 4.20
434 439 2.158813 ACAACTTTGGTGGAGATGTCGT 60.159 45.455 0.00 0.00 0.00 4.34
435 440 2.480419 GACAACTTTGGTGGAGATGTCG 59.520 50.000 0.00 0.00 37.25 4.35
436 441 2.480419 CGACAACTTTGGTGGAGATGTC 59.520 50.000 4.93 4.93 41.07 3.06
437 442 2.158813 ACGACAACTTTGGTGGAGATGT 60.159 45.455 0.00 0.00 33.52 3.06
438 443 2.480419 GACGACAACTTTGGTGGAGATG 59.520 50.000 0.00 0.00 0.00 2.90
439 444 2.368875 AGACGACAACTTTGGTGGAGAT 59.631 45.455 0.00 0.00 0.00 2.75
442 447 1.760613 AGAGACGACAACTTTGGTGGA 59.239 47.619 0.00 0.00 0.00 4.02
443 448 1.867233 CAGAGACGACAACTTTGGTGG 59.133 52.381 0.00 0.00 0.00 4.61
444 449 1.867233 CCAGAGACGACAACTTTGGTG 59.133 52.381 0.00 0.00 35.69 4.17
445 450 1.810412 GCCAGAGACGACAACTTTGGT 60.810 52.381 0.00 0.00 40.36 3.67
446 451 0.868406 GCCAGAGACGACAACTTTGG 59.132 55.000 0.00 0.00 40.92 3.28
447 452 1.795286 GAGCCAGAGACGACAACTTTG 59.205 52.381 0.00 0.00 0.00 2.77
448 453 1.603172 CGAGCCAGAGACGACAACTTT 60.603 52.381 0.00 0.00 0.00 2.66
449 454 0.039074 CGAGCCAGAGACGACAACTT 60.039 55.000 0.00 0.00 0.00 2.66
450 455 1.173444 ACGAGCCAGAGACGACAACT 61.173 55.000 0.00 0.00 0.00 3.16
451 456 0.318784 AACGAGCCAGAGACGACAAC 60.319 55.000 0.00 0.00 0.00 3.32
452 457 0.039437 GAACGAGCCAGAGACGACAA 60.039 55.000 0.00 0.00 0.00 3.18
453 458 1.579932 GAACGAGCCAGAGACGACA 59.420 57.895 0.00 0.00 0.00 4.35
454 459 1.153997 GGAACGAGCCAGAGACGAC 60.154 63.158 0.00 0.00 0.00 4.34
457 462 1.216710 CTGGGAACGAGCCAGAGAC 59.783 63.158 0.00 0.00 33.87 3.36
458 463 2.650116 GCTGGGAACGAGCCAGAGA 61.650 63.158 0.00 0.00 33.87 3.10
460 465 2.217038 AAGCTGGGAACGAGCCAGA 61.217 57.895 0.00 0.00 35.80 3.86
461 466 2.037136 CAAGCTGGGAACGAGCCAG 61.037 63.158 0.00 0.00 35.80 4.85
462 467 2.032528 CAAGCTGGGAACGAGCCA 59.967 61.111 0.00 0.00 35.80 4.75
463 468 3.435186 GCAAGCTGGGAACGAGCC 61.435 66.667 0.00 0.00 35.80 4.70
464 469 3.435186 GGCAAGCTGGGAACGAGC 61.435 66.667 0.00 0.00 35.54 5.03
465 470 2.747855 GGGCAAGCTGGGAACGAG 60.748 66.667 0.00 0.00 0.00 4.18
468 473 2.747855 CGAGGGCAAGCTGGGAAC 60.748 66.667 0.00 0.00 0.00 3.62
469 474 3.249189 ACGAGGGCAAGCTGGGAA 61.249 61.111 0.00 0.00 0.00 3.97
472 477 3.965539 CTCCACGAGGGCAAGCTGG 62.966 68.421 0.00 0.00 36.21 4.85
473 478 2.435586 CTCCACGAGGGCAAGCTG 60.436 66.667 0.00 0.00 36.21 4.24
474 479 3.710722 CCTCCACGAGGGCAAGCT 61.711 66.667 0.00 0.00 45.43 3.74
486 491 3.680786 CAGTCGTGGCGTCCTCCA 61.681 66.667 0.00 0.00 0.00 3.86
487 492 4.436998 CCAGTCGTGGCGTCCTCC 62.437 72.222 0.00 0.00 36.89 4.30
510 515 0.898789 TCTGAGTTGGAGACGGGGAC 60.899 60.000 0.00 0.00 0.00 4.46
511 516 0.898789 GTCTGAGTTGGAGACGGGGA 60.899 60.000 0.00 0.00 31.01 4.81
512 517 1.592223 GTCTGAGTTGGAGACGGGG 59.408 63.158 0.00 0.00 31.01 5.73
516 521 1.203523 AGCATCGTCTGAGTTGGAGAC 59.796 52.381 0.00 0.00 37.14 3.36
517 522 1.550327 AGCATCGTCTGAGTTGGAGA 58.450 50.000 0.00 0.00 0.00 3.71
519 524 2.423892 GAGTAGCATCGTCTGAGTTGGA 59.576 50.000 0.00 0.00 0.00 3.53
521 526 3.376859 AGAGAGTAGCATCGTCTGAGTTG 59.623 47.826 0.00 0.00 0.00 3.16
522 527 3.616219 AGAGAGTAGCATCGTCTGAGTT 58.384 45.455 0.00 0.00 0.00 3.01
523 528 3.118408 AGAGAGAGTAGCATCGTCTGAGT 60.118 47.826 0.00 0.00 0.00 3.41
524 529 3.466836 AGAGAGAGTAGCATCGTCTGAG 58.533 50.000 0.00 0.00 0.00 3.35
525 530 3.133901 AGAGAGAGAGTAGCATCGTCTGA 59.866 47.826 0.00 0.00 0.00 3.27
527 532 3.133901 TGAGAGAGAGAGTAGCATCGTCT 59.866 47.826 0.00 0.00 0.00 4.18
529 534 3.202906 GTGAGAGAGAGAGTAGCATCGT 58.797 50.000 0.00 0.00 0.00 3.73
530 535 3.002246 GTGTGAGAGAGAGAGTAGCATCG 59.998 52.174 0.00 0.00 0.00 3.84
532 537 3.694072 GTGTGTGAGAGAGAGAGTAGCAT 59.306 47.826 0.00 0.00 0.00 3.79
535 540 4.068599 TGTGTGTGTGAGAGAGAGAGTAG 58.931 47.826 0.00 0.00 0.00 2.57
537 542 2.621055 GTGTGTGTGTGAGAGAGAGAGT 59.379 50.000 0.00 0.00 0.00 3.24
538 543 2.620585 TGTGTGTGTGTGAGAGAGAGAG 59.379 50.000 0.00 0.00 0.00 3.20
539 544 2.359214 GTGTGTGTGTGTGAGAGAGAGA 59.641 50.000 0.00 0.00 0.00 3.10
540 545 2.544694 GGTGTGTGTGTGTGAGAGAGAG 60.545 54.545 0.00 0.00 0.00 3.20
541 546 1.409064 GGTGTGTGTGTGTGAGAGAGA 59.591 52.381 0.00 0.00 0.00 3.10
542 547 1.858091 GGTGTGTGTGTGTGAGAGAG 58.142 55.000 0.00 0.00 0.00 3.20
543 548 0.102300 CGGTGTGTGTGTGTGAGAGA 59.898 55.000 0.00 0.00 0.00 3.10
544 549 0.875908 CCGGTGTGTGTGTGTGAGAG 60.876 60.000 0.00 0.00 0.00 3.20
545 550 1.142965 CCGGTGTGTGTGTGTGAGA 59.857 57.895 0.00 0.00 0.00 3.27
547 552 2.512745 GCCGGTGTGTGTGTGTGA 60.513 61.111 1.90 0.00 0.00 3.58
549 554 2.513666 CAGCCGGTGTGTGTGTGT 60.514 61.111 1.90 0.00 0.00 3.72
551 556 1.817941 GTTCAGCCGGTGTGTGTGT 60.818 57.895 1.90 0.00 0.00 3.72
553 558 1.523711 CAGTTCAGCCGGTGTGTGT 60.524 57.895 1.90 0.00 0.00 3.72
554 559 1.095228 AACAGTTCAGCCGGTGTGTG 61.095 55.000 1.90 0.00 0.00 3.82
555 560 0.393808 AAACAGTTCAGCCGGTGTGT 60.394 50.000 1.90 0.00 0.00 3.72
556 561 0.738389 AAAACAGTTCAGCCGGTGTG 59.262 50.000 1.90 0.61 0.00 3.82
557 562 1.470051 AAAAACAGTTCAGCCGGTGT 58.530 45.000 1.90 0.00 0.00 4.16
587 1051 1.361793 TTTCGCGTTTCCTAATCCCG 58.638 50.000 5.77 0.00 0.00 5.14
607 1071 6.575162 AACCTCGCAGTTCAGATTTTAAAT 57.425 33.333 0.00 0.00 0.00 1.40
641 1109 4.982701 AAGGTGGCTGTGCAGGGC 62.983 66.667 6.27 6.27 0.00 5.19
657 1125 0.534203 GACCAAGGGCACGTGAAGAA 60.534 55.000 22.23 0.00 0.00 2.52
732 1211 1.947013 CAAGTCAGCACTGCCACTG 59.053 57.895 4.36 0.00 31.06 3.66
733 1212 1.895707 GCAAGTCAGCACTGCCACT 60.896 57.895 0.00 0.00 31.06 4.00
734 1213 2.641559 GCAAGTCAGCACTGCCAC 59.358 61.111 0.00 0.00 31.06 5.01
735 1214 2.595463 GGCAAGTCAGCACTGCCA 60.595 61.111 7.42 0.00 42.20 4.92
736 1215 3.730761 CGGCAAGTCAGCACTGCC 61.731 66.667 2.15 2.15 40.61 4.85
737 1216 2.974698 ACGGCAAGTCAGCACTGC 60.975 61.111 0.00 0.00 35.83 4.40
848 1331 1.218316 CGAGGTTAGTGGTGGAGGC 59.782 63.158 0.00 0.00 0.00 4.70
963 1464 1.347707 GATCTGTGTGGGTGGTCAAGA 59.652 52.381 0.00 0.00 0.00 3.02
969 1476 1.219124 CTCGGATCTGTGTGGGTGG 59.781 63.158 0.42 0.00 0.00 4.61
981 1488 1.289982 TGGTCCTCTCTCCCTCGGAT 61.290 60.000 0.00 0.00 0.00 4.18
985 1492 1.406860 GCCATGGTCCTCTCTCCCTC 61.407 65.000 14.67 0.00 0.00 4.30
986 1493 1.383803 GCCATGGTCCTCTCTCCCT 60.384 63.158 14.67 0.00 0.00 4.20
987 1494 2.447714 GGCCATGGTCCTCTCTCCC 61.448 68.421 14.67 0.00 0.00 4.30
989 1496 1.524482 GTGGCCATGGTCCTCTCTC 59.476 63.158 15.27 0.00 0.00 3.20
1287 1808 1.026718 CGTTGGACTTGAGGATGCCC 61.027 60.000 0.00 0.00 0.00 5.36
1426 1947 2.124403 GGCAGGCAGACATGGGAG 60.124 66.667 0.00 0.00 0.00 4.30
1459 1989 0.451783 GGATTACAACAGCAAGCCGG 59.548 55.000 0.00 0.00 0.00 6.13
1478 2008 3.432252 AGAGAACTAATGAAAACACGGCG 59.568 43.478 4.80 4.80 0.00 6.46
1499 2029 8.401709 ACATGATAGTACATCATCAGCGTATAG 58.598 37.037 14.21 6.46 36.69 1.31
1608 2161 4.560035 GCCATGATTGAAGATGAAAACACG 59.440 41.667 0.00 0.00 0.00 4.49
1609 2162 5.472148 TGCCATGATTGAAGATGAAAACAC 58.528 37.500 0.00 0.00 0.00 3.32
1610 2163 5.725325 TGCCATGATTGAAGATGAAAACA 57.275 34.783 0.00 0.00 0.00 2.83
1611 2164 7.760794 TGTATTGCCATGATTGAAGATGAAAAC 59.239 33.333 0.00 0.00 0.00 2.43
1612 2165 7.838884 TGTATTGCCATGATTGAAGATGAAAA 58.161 30.769 0.00 0.00 0.00 2.29
1687 2470 3.308866 GCTTCAGTGTTTGTAGTTGTCGT 59.691 43.478 0.00 0.00 0.00 4.34
1692 2475 2.544267 GCTCGCTTCAGTGTTTGTAGTT 59.456 45.455 0.00 0.00 0.00 2.24
1700 2483 0.946221 CTTTCGGCTCGCTTCAGTGT 60.946 55.000 0.00 0.00 0.00 3.55
1724 2509 3.782443 GGGAGGGGCAACGACGAT 61.782 66.667 0.00 0.00 37.60 3.73
1767 2552 6.670027 AGAATGACTTCCCAACTGTCTACTAT 59.330 38.462 0.00 0.00 31.27 2.12
1782 2567 3.202097 GGAGCCTTAGCAGAATGACTTC 58.798 50.000 0.00 0.00 43.56 3.01
1788 2573 4.410228 TGTTCTATGGAGCCTTAGCAGAAT 59.590 41.667 4.93 0.00 43.56 2.40
1791 2576 3.827008 TGTTCTATGGAGCCTTAGCAG 57.173 47.619 4.93 0.00 43.56 4.24
1801 2586 3.603158 TTACTGCGCTTGTTCTATGGA 57.397 42.857 9.73 0.00 0.00 3.41
1803 2588 5.029650 TGTTTTACTGCGCTTGTTCTATG 57.970 39.130 9.73 0.00 0.00 2.23
1811 2596 1.269051 GGTTGCTGTTTTACTGCGCTT 60.269 47.619 9.73 0.00 44.63 4.68
1834 2619 0.179137 CACGCTACTCTTCATCGGCA 60.179 55.000 0.00 0.00 0.00 5.69
1844 2629 1.404391 TCCTTTCGATCCACGCTACTC 59.596 52.381 0.00 0.00 42.26 2.59
1896 2681 3.343617 TGAATTTGTTCGGATCTGGTCC 58.656 45.455 0.62 0.00 44.10 4.46
1909 2697 4.094887 CGGATCCGTTCTTGATGAATTTGT 59.905 41.667 26.35 0.00 36.99 2.83
1926 2714 1.153549 GTGTGTCTCCAGCGGATCC 60.154 63.158 0.00 0.00 0.00 3.36
1956 2744 1.218316 GTCCGGATGGTGTGTCTCC 59.782 63.158 7.81 0.00 36.30 3.71
1957 2745 0.320374 TTGTCCGGATGGTGTGTCTC 59.680 55.000 7.81 0.00 36.30 3.36
1965 2764 2.346766 TGGATTCATTGTCCGGATGG 57.653 50.000 7.81 0.00 38.64 3.51
1970 2769 1.744522 TGTGCATGGATTCATTGTCCG 59.255 47.619 0.00 0.00 38.64 4.79
1971 2770 2.756760 ACTGTGCATGGATTCATTGTCC 59.243 45.455 0.00 0.00 36.26 4.02
1982 2781 1.065926 TGGCTTCTCTACTGTGCATGG 60.066 52.381 0.00 0.00 0.00 3.66
1990 2789 5.424895 AGATGTTGAGATTGGCTTCTCTACT 59.575 40.000 22.12 13.70 44.02 2.57
2027 2826 4.398044 CCATTGCGACCCTGTAAAAAGTAT 59.602 41.667 0.00 0.00 0.00 2.12
2030 2829 2.094752 CCCATTGCGACCCTGTAAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
2177 2992 2.168496 TGGCAGCTAAAGTCTACGTCT 58.832 47.619 0.00 0.00 0.00 4.18
2178 2993 2.649331 TGGCAGCTAAAGTCTACGTC 57.351 50.000 0.00 0.00 0.00 4.34
2179 2994 2.299297 AGTTGGCAGCTAAAGTCTACGT 59.701 45.455 0.52 0.00 0.00 3.57
2180 2995 2.668457 CAGTTGGCAGCTAAAGTCTACG 59.332 50.000 2.72 0.00 0.00 3.51
2181 2996 3.680458 GTCAGTTGGCAGCTAAAGTCTAC 59.320 47.826 2.72 0.00 0.00 2.59
2182 2997 3.578716 AGTCAGTTGGCAGCTAAAGTCTA 59.421 43.478 2.72 0.00 0.00 2.59
2183 2998 2.370189 AGTCAGTTGGCAGCTAAAGTCT 59.630 45.455 2.72 0.00 0.00 3.24
2184 2999 2.739379 GAGTCAGTTGGCAGCTAAAGTC 59.261 50.000 2.72 4.44 0.00 3.01
2185 3000 2.104792 TGAGTCAGTTGGCAGCTAAAGT 59.895 45.455 2.72 0.00 0.00 2.66
2186 3001 2.740981 CTGAGTCAGTTGGCAGCTAAAG 59.259 50.000 12.28 0.00 0.00 1.85
2187 3002 2.104792 ACTGAGTCAGTTGGCAGCTAAA 59.895 45.455 20.34 0.00 42.59 1.85
2188 3003 1.694150 ACTGAGTCAGTTGGCAGCTAA 59.306 47.619 20.34 0.00 42.59 3.09
2189 3004 1.342074 ACTGAGTCAGTTGGCAGCTA 58.658 50.000 20.34 0.00 42.59 3.32
2190 3005 1.001406 GTACTGAGTCAGTTGGCAGCT 59.999 52.381 29.84 6.00 42.59 4.24
2191 3006 1.001406 AGTACTGAGTCAGTTGGCAGC 59.999 52.381 29.84 13.43 42.59 5.25
2192 3007 4.158579 TGATAGTACTGAGTCAGTTGGCAG 59.841 45.833 29.84 1.15 42.59 4.85
2193 3008 4.086457 TGATAGTACTGAGTCAGTTGGCA 58.914 43.478 29.84 17.52 42.59 4.92
2194 3009 4.720649 TGATAGTACTGAGTCAGTTGGC 57.279 45.455 29.84 19.38 42.59 4.52
2195 3010 6.456795 TGATGATAGTACTGAGTCAGTTGG 57.543 41.667 29.84 3.13 42.59 3.77
2198 3013 9.579932 TCATATTGATGATAGTACTGAGTCAGT 57.420 33.333 27.98 27.98 41.32 3.41
2219 3034 9.321562 CGTTTGGTAACTGGTAAGTAATCATAT 57.678 33.333 0.00 0.00 34.77 1.78
2220 3035 8.313292 ACGTTTGGTAACTGGTAAGTAATCATA 58.687 33.333 0.00 0.00 34.77 2.15
2221 3036 7.163441 ACGTTTGGTAACTGGTAAGTAATCAT 58.837 34.615 0.00 0.00 34.77 2.45
2222 3037 6.523840 ACGTTTGGTAACTGGTAAGTAATCA 58.476 36.000 0.00 0.00 34.77 2.57
2223 3038 8.028938 TCTACGTTTGGTAACTGGTAAGTAATC 58.971 37.037 0.00 0.00 34.77 1.75
2224 3039 7.814587 GTCTACGTTTGGTAACTGGTAAGTAAT 59.185 37.037 0.00 0.00 34.77 1.89
2225 3040 7.014230 AGTCTACGTTTGGTAACTGGTAAGTAA 59.986 37.037 0.00 0.00 34.77 2.24
2226 3041 6.490040 AGTCTACGTTTGGTAACTGGTAAGTA 59.510 38.462 0.00 0.00 34.77 2.24
2227 3042 5.302823 AGTCTACGTTTGGTAACTGGTAAGT 59.697 40.000 0.00 0.00 38.71 2.24
2228 3043 5.776744 AGTCTACGTTTGGTAACTGGTAAG 58.223 41.667 0.00 0.00 37.61 2.34
2229 3044 5.789643 AGTCTACGTTTGGTAACTGGTAA 57.210 39.130 0.00 0.00 37.61 2.85
2230 3045 5.789643 AAGTCTACGTTTGGTAACTGGTA 57.210 39.130 0.00 0.00 37.61 3.25
2231 3046 4.677673 AAGTCTACGTTTGGTAACTGGT 57.322 40.909 0.00 0.00 37.61 4.00
2232 3047 5.119743 GCTAAAGTCTACGTTTGGTAACTGG 59.880 44.000 0.00 0.00 37.61 4.00
2233 3048 5.924825 AGCTAAAGTCTACGTTTGGTAACTG 59.075 40.000 0.00 0.00 37.61 3.16
2234 3049 5.924825 CAGCTAAAGTCTACGTTTGGTAACT 59.075 40.000 0.00 0.00 37.61 2.24
2282 3097 5.319626 AACATAACTGTCACGTGGAGAACG 61.320 45.833 17.00 5.69 46.34 3.95
2293 3108 7.277760 GTGCATACATACTGAACATAACTGTCA 59.722 37.037 0.00 0.00 33.36 3.58


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

AutoCloner maintained by Alex Coulton.