Multiple sequence alignment - TraesCS3B01G073700

Loading Multiple Alignment...

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 TraesCS3B01G073700 chr3B 100.000 3567 0 0 1 3567 44285540 44281974 0.000000e+00 6588
1 TraesCS3B01G073700 chr3A 96.740 2914 92 3 655 3567 36493525 36490614 0.000000e+00 4852
2 TraesCS3B01G073700 chr3A 98.182 165 3 0 1 165 36493709 36493545 4.510000e-74 289
3 TraesCS3B01G073700 chr3D 96.203 2923 78 11 655 3567 26456260 26453361 0.000000e+00 4752
4 TraesCS3B01G073700 chr3D 83.483 557 52 21 94 649 26457135 26456618 1.930000e-132 483


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 TraesCS3B01G073700 chr3B 44281974 44285540 3566 True 6588.0 6588 100.000 1 3567 1 chr3B.!!$R1 3566
1 TraesCS3B01G073700 chr3A 36490614 36493709 3095 True 2570.5 4852 97.461 1 3567 2 chr3A.!!$R1 3566
2 TraesCS3B01G073700 chr3D 26453361 26457135 3774 True 2617.5 4752 89.843 94 3567 2 chr3D.!!$R1 3473

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
898 1259 0.038744 AGGTCCAGCAGAACCCATTG 59.961 55.0 0.00 0.0 29.47 2.82 F
1410 1775 0.175760 TCATTGAGGACGCTACAGGC 59.824 55.0 0.00 0.0 37.64 4.85 F
2143 2508 0.326522 TCCAGGCTGCCCTCAAGATA 60.327 55.0 16.57 0.0 40.33 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2337 0.951558 TTTTGACCCGCAGCTTCTTC 59.048 50.000 0.00 0.00 0.0 2.87 R
2326 2691 1.131883 CTCTGCATCAAAGGCCTTTCG 59.868 52.381 28.16 21.50 0.0 3.46 R
3192 3557 2.033151 CAGTGACATGCATGACGCTATG 60.033 50.000 33.70 23.73 40.3 2.23 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
23 24 4.506288 TCGTAACATCTTGCACGATTATGG 59.494 41.667 2.37 0.00 34.58 2.74
127 128 3.489785 GTGCGTTGCTACAGGTATATGTC 59.510 47.826 0.00 0.00 34.56 3.06
208 209 7.274033 CCTATGTTCATTGTTTGTGTGCTTATG 59.726 37.037 0.00 0.00 0.00 1.90
220 221 5.409211 TGTGTGCTTATGTATTGGCATTTG 58.591 37.500 0.00 0.00 37.05 2.32
278 279 4.488126 TGCTTTGTCATGCTAACTGAAC 57.512 40.909 0.00 0.00 0.00 3.18
340 341 7.553881 AAAAACTAGTATGTTCATGGATCCG 57.446 36.000 7.39 0.00 0.00 4.18
341 342 4.258702 ACTAGTATGTTCATGGATCCGC 57.741 45.455 7.39 0.00 0.00 5.54
343 344 3.845781 AGTATGTTCATGGATCCGCTT 57.154 42.857 7.39 0.00 0.00 4.68
345 346 4.130118 AGTATGTTCATGGATCCGCTTTC 58.870 43.478 7.39 0.00 0.00 2.62
346 347 2.488204 TGTTCATGGATCCGCTTTCA 57.512 45.000 7.39 0.98 0.00 2.69
347 348 2.083774 TGTTCATGGATCCGCTTTCAC 58.916 47.619 7.39 0.00 0.00 3.18
348 349 1.401905 GTTCATGGATCCGCTTTCACC 59.598 52.381 7.39 0.00 0.00 4.02
349 350 0.617935 TCATGGATCCGCTTTCACCA 59.382 50.000 7.39 0.00 35.09 4.17
350 351 1.212688 TCATGGATCCGCTTTCACCAT 59.787 47.619 7.39 0.00 41.25 3.55
351 352 2.026641 CATGGATCCGCTTTCACCATT 58.973 47.619 7.39 0.00 38.99 3.16
352 353 1.462616 TGGATCCGCTTTCACCATTG 58.537 50.000 7.39 0.00 0.00 2.82
353 354 0.740737 GGATCCGCTTTCACCATTGG 59.259 55.000 0.00 0.00 0.00 3.16
354 355 0.101219 GATCCGCTTTCACCATTGGC 59.899 55.000 1.54 0.00 0.00 4.52
355 356 0.323725 ATCCGCTTTCACCATTGGCT 60.324 50.000 1.54 0.00 0.00 4.75
356 357 0.539438 TCCGCTTTCACCATTGGCTT 60.539 50.000 1.54 0.00 0.00 4.35
357 358 0.109132 CCGCTTTCACCATTGGCTTC 60.109 55.000 1.54 0.00 0.00 3.86
358 359 0.109132 CGCTTTCACCATTGGCTTCC 60.109 55.000 1.54 0.00 0.00 3.46
359 360 1.260544 GCTTTCACCATTGGCTTCCT 58.739 50.000 1.54 0.00 0.00 3.36
360 361 2.446435 GCTTTCACCATTGGCTTCCTA 58.554 47.619 1.54 0.00 0.00 2.94
361 362 2.825532 GCTTTCACCATTGGCTTCCTAA 59.174 45.455 1.54 0.00 0.00 2.69
362 363 3.258123 GCTTTCACCATTGGCTTCCTAAA 59.742 43.478 1.54 0.00 0.00 1.85
363 364 4.262420 GCTTTCACCATTGGCTTCCTAAAA 60.262 41.667 1.54 0.00 0.00 1.52
364 365 5.741673 GCTTTCACCATTGGCTTCCTAAAAA 60.742 40.000 1.54 0.00 0.00 1.94
392 393 4.810191 ATCTAGTTTCAAAGGTCTCGCT 57.190 40.909 0.00 0.00 0.00 4.93
393 394 3.914312 TCTAGTTTCAAAGGTCTCGCTG 58.086 45.455 0.00 0.00 0.00 5.18
404 405 1.908299 TCTCGCTGTGAGGAAGCCA 60.908 57.895 17.44 0.00 45.32 4.75
421 422 0.378257 CCAATGGTGAAAGCGGATCG 59.622 55.000 0.00 0.00 36.92 3.69
436 437 3.541516 GCGGATCGTCAATCAAGTTAACG 60.542 47.826 0.00 0.00 35.96 3.18
443 444 5.467399 TCGTCAATCAAGTTAACGGTTTGAT 59.533 36.000 20.04 16.98 41.84 2.57
449 450 8.405531 CAATCAAGTTAACGGTTTGATGGATAT 58.594 33.333 17.48 4.30 39.82 1.63
488 489 9.927668 ATTCATATTTTGAGTAACCTTTGTTGG 57.072 29.630 0.00 0.00 35.27 3.77
489 490 7.375053 TCATATTTTGAGTAACCTTTGTTGGC 58.625 34.615 0.00 0.00 35.87 4.52
490 491 5.869649 ATTTTGAGTAACCTTTGTTGGCT 57.130 34.783 0.00 0.00 35.87 4.75
491 492 5.669164 TTTTGAGTAACCTTTGTTGGCTT 57.331 34.783 0.00 0.00 35.87 4.35
492 493 5.669164 TTTGAGTAACCTTTGTTGGCTTT 57.331 34.783 0.00 0.00 35.87 3.51
493 494 5.669164 TTGAGTAACCTTTGTTGGCTTTT 57.331 34.783 0.00 0.00 35.87 2.27
494 495 6.777213 TTGAGTAACCTTTGTTGGCTTTTA 57.223 33.333 0.00 0.00 35.87 1.52
495 496 6.969993 TGAGTAACCTTTGTTGGCTTTTAT 57.030 33.333 0.00 0.00 35.87 1.40
496 497 7.354751 TGAGTAACCTTTGTTGGCTTTTATT 57.645 32.000 0.00 0.00 35.87 1.40
497 498 7.787028 TGAGTAACCTTTGTTGGCTTTTATTT 58.213 30.769 0.00 0.00 35.87 1.40
498 499 8.915036 TGAGTAACCTTTGTTGGCTTTTATTTA 58.085 29.630 0.00 0.00 35.87 1.40
499 500 9.923143 GAGTAACCTTTGTTGGCTTTTATTTAT 57.077 29.630 0.00 0.00 35.87 1.40
500 501 9.923143 AGTAACCTTTGTTGGCTTTTATTTATC 57.077 29.630 0.00 0.00 35.87 1.75
501 502 9.923143 GTAACCTTTGTTGGCTTTTATTTATCT 57.077 29.630 0.00 0.00 35.87 1.98
503 504 9.845740 AACCTTTGTTGGCTTTTATTTATCTTT 57.154 25.926 0.00 0.00 32.13 2.52
504 505 9.271828 ACCTTTGTTGGCTTTTATTTATCTTTG 57.728 29.630 0.00 0.00 0.00 2.77
505 506 9.271828 CCTTTGTTGGCTTTTATTTATCTTTGT 57.728 29.630 0.00 0.00 0.00 2.83
508 509 9.823647 TTGTTGGCTTTTATTTATCTTTGTTGA 57.176 25.926 0.00 0.00 0.00 3.18
509 510 9.995003 TGTTGGCTTTTATTTATCTTTGTTGAT 57.005 25.926 0.00 0.00 0.00 2.57
536 544 8.816640 AAAACATAAACAAAGATGATGGTCAC 57.183 30.769 0.00 0.00 0.00 3.67
537 545 7.523293 AACATAAACAAAGATGATGGTCACA 57.477 32.000 0.00 0.00 0.00 3.58
543 551 8.408043 AAACAAAGATGATGGTCACAAGATTA 57.592 30.769 0.00 0.00 0.00 1.75
546 554 9.113838 ACAAAGATGATGGTCACAAGATTATAC 57.886 33.333 0.00 0.00 0.00 1.47
553 561 6.806668 TGGTCACAAGATTATACCATCTCA 57.193 37.500 0.00 0.00 35.34 3.27
562 570 7.854166 AGATTATACCATCTCAAAGCTCTCT 57.146 36.000 0.00 0.00 0.00 3.10
630 638 8.233868 TGTCTTGATAAAACACATATGGAAACG 58.766 33.333 7.80 0.00 0.00 3.60
639 647 5.670485 ACACATATGGAAACGAGCTCATAA 58.330 37.500 15.40 0.00 0.00 1.90
645 653 9.208022 CATATGGAAACGAGCTCATAAATCTTA 57.792 33.333 15.40 2.02 0.00 2.10
649 657 6.422400 GGAAACGAGCTCATAAATCTTAGAGG 59.578 42.308 15.40 0.00 0.00 3.69
650 658 6.716934 AACGAGCTCATAAATCTTAGAGGA 57.283 37.500 15.40 0.00 0.00 3.71
651 659 6.909550 ACGAGCTCATAAATCTTAGAGGAT 57.090 37.500 15.40 0.00 0.00 3.24
652 660 8.410673 AACGAGCTCATAAATCTTAGAGGATA 57.589 34.615 15.40 0.00 0.00 2.59
653 661 8.410673 ACGAGCTCATAAATCTTAGAGGATAA 57.589 34.615 15.40 0.00 0.00 1.75
667 1027 3.325135 AGAGGATAAAATCTAGCCACCGG 59.675 47.826 0.00 0.00 0.00 5.28
714 1074 4.568359 TGAGCGAGAAGTAAAGCAATGATC 59.432 41.667 0.00 0.00 0.00 2.92
715 1075 4.764172 AGCGAGAAGTAAAGCAATGATCT 58.236 39.130 0.00 0.00 0.00 2.75
795 1156 0.312416 AAATAGCACGGCAAAACGCA 59.688 45.000 0.00 0.00 45.17 5.24
834 1195 1.452651 CACCCCTGCTGCCACTATG 60.453 63.158 0.00 0.00 0.00 2.23
898 1259 0.038744 AGGTCCAGCAGAACCCATTG 59.961 55.000 0.00 0.00 29.47 2.82
925 1286 2.668279 GCCTTTTACCAGCACAACATCG 60.668 50.000 0.00 0.00 0.00 3.84
1036 1397 3.744940 AATTGAAGAAGGGGATCAGCA 57.255 42.857 0.00 0.00 0.00 4.41
1138 1499 1.707989 TCCCCTAAGCACATGTTTCCA 59.292 47.619 0.00 0.00 0.00 3.53
1146 1507 2.489329 AGCACATGTTTCCAATTCCTCG 59.511 45.455 0.00 0.00 0.00 4.63
1190 1551 4.908601 TGTTTTGCCATTCTCTCCTCTA 57.091 40.909 0.00 0.00 0.00 2.43
1374 1739 2.125512 GAGCGCTTCACCACGGAT 60.126 61.111 13.26 0.00 0.00 4.18
1394 1759 2.270205 CGCTGGTGAGCCCTTCAT 59.730 61.111 0.00 0.00 42.91 2.57
1404 1769 1.078143 GCCCTTCATTGAGGACGCT 60.078 57.895 0.00 0.00 39.25 5.07
1405 1770 0.178068 GCCCTTCATTGAGGACGCTA 59.822 55.000 0.00 0.00 39.25 4.26
1407 1772 1.207089 CCCTTCATTGAGGACGCTACA 59.793 52.381 0.00 0.00 39.25 2.74
1410 1775 0.175760 TCATTGAGGACGCTACAGGC 59.824 55.000 0.00 0.00 37.64 4.85
1485 1850 1.557269 GGAGGGAGCCAGAAGAAGCA 61.557 60.000 0.00 0.00 0.00 3.91
1506 1871 1.144913 AGTGCTGGGCAAGGTAAAGAA 59.855 47.619 0.00 0.00 41.47 2.52
1551 1916 4.261909 CCTTCTGCATCACAAAAAGAAGCT 60.262 41.667 5.42 0.00 41.54 3.74
1556 1921 3.862264 GCATCACAAAAAGAAGCTTCCCC 60.862 47.826 22.81 0.00 0.00 4.81
1721 2086 6.068010 TCAAATGAAACACCACCTGTCTAAT 58.932 36.000 0.00 0.00 30.29 1.73
1779 2144 6.588756 TCTTTATAGTTCAGTTGCGACGAAAT 59.411 34.615 13.37 13.37 0.00 2.17
1795 2160 9.705471 TGCGACGAAATACGATAAATTTTTATT 57.295 25.926 0.00 0.00 45.77 1.40
1822 2187 1.134431 TGAACTGCAGTTGCTGAGTCA 60.134 47.619 35.67 22.20 41.71 3.41
2059 2424 3.735746 GGCCAGAAATCGAAAACAAAGTG 59.264 43.478 0.00 0.00 0.00 3.16
2066 2431 1.329292 TCGAAAACAAAGTGTGGAGCG 59.671 47.619 0.00 0.00 0.00 5.03
2143 2508 0.326522 TCCAGGCTGCCCTCAAGATA 60.327 55.000 16.57 0.00 40.33 1.98
2150 2515 2.224018 GCTGCCCTCAAGATAGTCTCTG 60.224 54.545 0.00 0.00 33.29 3.35
2205 2570 4.072131 GACAAAAGGCACATGGTAGAGAA 58.928 43.478 0.00 0.00 0.00 2.87
2292 2657 1.277557 GGAAGTCATCACTGAGGCTGT 59.722 52.381 0.00 0.00 31.06 4.40
2326 2691 0.388649 ACGCGTGGACTGAGAATGTC 60.389 55.000 12.93 0.00 0.00 3.06
2423 2788 0.520404 TTCGCTGTCTACACGTCCTC 59.480 55.000 0.00 0.00 0.00 3.71
2481 2846 8.078596 GGACAATCCTATCTGCAAAAATATGTC 58.921 37.037 0.00 0.00 32.53 3.06
2524 2889 4.012374 ACTGGAAACTTATGACATGCAGG 58.988 43.478 0.00 0.00 34.25 4.85
2597 2962 1.221466 AACACAGTGACACGGCATCG 61.221 55.000 7.81 0.00 43.02 3.84
2661 3026 2.045045 CCAAGAGCATGCCCCGAA 60.045 61.111 15.66 0.00 0.00 4.30
2723 3088 7.962964 TGTGTGTTGTAAAATGAAACCAAAA 57.037 28.000 0.00 0.00 0.00 2.44
2802 3167 5.331876 AGTTCCTCTTCAGATAAACCTCG 57.668 43.478 0.00 0.00 0.00 4.63
2828 3193 5.461407 CACTATGATTCTGTCACAGATTCCG 59.539 44.000 21.62 14.37 40.39 4.30
3079 3444 4.771903 TGGCACAACCGTACATACATAAT 58.228 39.130 0.00 0.00 43.94 1.28
3168 3533 0.662619 CAAGCACAGAAAGTTCGCCA 59.337 50.000 0.00 0.00 0.00 5.69
3192 3557 5.645497 AGTGTAATCTCTGCCACTTCAATTC 59.355 40.000 0.00 0.00 34.64 2.17
3369 3739 4.228912 AGCTTGCAATGTGTAAACTGTC 57.771 40.909 0.00 0.00 0.00 3.51
3545 3915 5.958955 AGCATCAGAAAATTGGAAGCTAAC 58.041 37.500 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 4.153296 CGCACAGGTACAATCAACATAACA 59.847 41.667 0.00 0.00 0.00 2.41
185 186 6.514947 ACATAAGCACACAAACAATGAACAT 58.485 32.000 0.00 0.00 0.00 2.71
198 199 4.805192 CCAAATGCCAATACATAAGCACAC 59.195 41.667 0.00 0.00 38.21 3.82
208 209 4.218312 AGGGATTCTCCAAATGCCAATAC 58.782 43.478 10.38 0.00 40.17 1.89
231 232 4.454847 GCAGATCCATGAACATACCATGAG 59.545 45.833 0.00 0.00 42.89 2.90
237 238 4.337555 AGCAAAGCAGATCCATGAACATAC 59.662 41.667 0.00 0.00 0.00 2.39
278 279 5.661056 TGTCACATTACTCTTACTCAGGG 57.339 43.478 0.00 0.00 0.00 4.45
318 319 5.057149 GCGGATCCATGAACATACTAGTTT 58.943 41.667 13.41 0.00 0.00 2.66
319 320 4.345257 AGCGGATCCATGAACATACTAGTT 59.655 41.667 13.41 0.00 0.00 2.24
320 321 3.898123 AGCGGATCCATGAACATACTAGT 59.102 43.478 13.41 0.00 0.00 2.57
321 322 4.527509 AGCGGATCCATGAACATACTAG 57.472 45.455 13.41 0.00 0.00 2.57
323 324 3.845781 AAGCGGATCCATGAACATACT 57.154 42.857 13.41 0.00 0.00 2.12
324 325 3.876914 TGAAAGCGGATCCATGAACATAC 59.123 43.478 13.41 0.00 0.00 2.39
325 326 3.876914 GTGAAAGCGGATCCATGAACATA 59.123 43.478 13.41 0.00 0.00 2.29
326 327 2.684881 GTGAAAGCGGATCCATGAACAT 59.315 45.455 13.41 0.00 0.00 2.71
327 328 2.083774 GTGAAAGCGGATCCATGAACA 58.916 47.619 13.41 3.25 0.00 3.18
328 329 1.401905 GGTGAAAGCGGATCCATGAAC 59.598 52.381 13.41 1.78 0.00 3.18
329 330 1.004161 TGGTGAAAGCGGATCCATGAA 59.996 47.619 13.41 0.00 36.92 2.57
330 331 0.617935 TGGTGAAAGCGGATCCATGA 59.382 50.000 13.41 0.00 36.92 3.07
331 332 1.683943 ATGGTGAAAGCGGATCCATG 58.316 50.000 13.41 0.00 37.48 3.66
332 333 2.026641 CAATGGTGAAAGCGGATCCAT 58.973 47.619 13.41 0.00 40.10 3.41
333 334 1.462616 CAATGGTGAAAGCGGATCCA 58.537 50.000 13.41 0.00 36.92 3.41
334 335 0.740737 CCAATGGTGAAAGCGGATCC 59.259 55.000 0.00 0.00 36.92 3.36
336 337 0.323725 AGCCAATGGTGAAAGCGGAT 60.324 50.000 0.00 0.00 36.92 4.18
337 338 0.539438 AAGCCAATGGTGAAAGCGGA 60.539 50.000 0.00 0.00 36.92 5.54
338 339 0.109132 GAAGCCAATGGTGAAAGCGG 60.109 55.000 0.00 0.00 36.92 5.52
339 340 0.109132 GGAAGCCAATGGTGAAAGCG 60.109 55.000 0.00 0.00 36.92 4.68
340 341 1.260544 AGGAAGCCAATGGTGAAAGC 58.739 50.000 0.00 0.00 0.00 3.51
341 342 5.467035 TTTTAGGAAGCCAATGGTGAAAG 57.533 39.130 0.00 0.00 0.00 2.62
365 366 8.451748 GCGAGACCTTTGAAACTAGATTTTATT 58.548 33.333 0.00 0.00 0.00 1.40
366 367 7.824779 AGCGAGACCTTTGAAACTAGATTTTAT 59.175 33.333 0.00 0.00 0.00 1.40
367 368 7.117812 CAGCGAGACCTTTGAAACTAGATTTTA 59.882 37.037 0.00 0.00 0.00 1.52
368 369 5.998363 AGCGAGACCTTTGAAACTAGATTTT 59.002 36.000 0.00 0.00 0.00 1.82
381 382 1.001406 CTTCCTCACAGCGAGACCTTT 59.999 52.381 0.00 0.00 45.45 3.11
392 393 0.770499 TCACCATTGGCTTCCTCACA 59.230 50.000 1.54 0.00 0.00 3.58
393 394 1.909700 TTCACCATTGGCTTCCTCAC 58.090 50.000 1.54 0.00 0.00 3.51
404 405 1.338674 TGACGATCCGCTTTCACCATT 60.339 47.619 0.00 0.00 0.00 3.16
421 422 5.856455 CCATCAAACCGTTAACTTGATTGAC 59.144 40.000 15.29 0.00 37.63 3.18
473 474 9.923143 ATAAATAAAAGCCAACAAAGGTTACTC 57.077 29.630 0.00 0.00 34.87 2.59
479 480 9.271828 ACAAAGATAAATAAAAGCCAACAAAGG 57.728 29.630 0.00 0.00 0.00 3.11
510 511 9.260002 GTGACCATCATCTTTGTTTATGTTTTT 57.740 29.630 0.00 0.00 0.00 1.94
511 512 8.420222 TGTGACCATCATCTTTGTTTATGTTTT 58.580 29.630 0.00 0.00 0.00 2.43
512 513 7.950512 TGTGACCATCATCTTTGTTTATGTTT 58.049 30.769 0.00 0.00 0.00 2.83
536 544 8.149647 AGAGAGCTTTGAGATGGTATAATCTTG 58.850 37.037 0.00 0.00 37.03 3.02
537 545 8.261349 AGAGAGCTTTGAGATGGTATAATCTT 57.739 34.615 0.00 0.00 37.03 2.40
543 551 7.508636 TCTGAATAGAGAGCTTTGAGATGGTAT 59.491 37.037 0.00 0.00 0.00 2.73
546 554 6.159299 TCTGAATAGAGAGCTTTGAGATGG 57.841 41.667 0.00 0.00 0.00 3.51
612 620 5.935206 TGAGCTCGTTTCCATATGTGTTTTA 59.065 36.000 9.64 0.00 0.00 1.52
619 627 7.664082 AGATTTATGAGCTCGTTTCCATATG 57.336 36.000 14.93 0.00 0.00 1.78
624 632 6.422400 CCTCTAAGATTTATGAGCTCGTTTCC 59.578 42.308 14.93 1.75 0.00 3.13
639 647 8.379331 GGTGGCTAGATTTTATCCTCTAAGATT 58.621 37.037 0.00 0.00 0.00 2.40
645 653 3.325135 CCGGTGGCTAGATTTTATCCTCT 59.675 47.826 0.00 0.00 0.00 3.69
649 657 3.557264 CCTCCCGGTGGCTAGATTTTATC 60.557 52.174 0.00 0.00 0.00 1.75
650 658 2.372172 CCTCCCGGTGGCTAGATTTTAT 59.628 50.000 0.00 0.00 0.00 1.40
651 659 1.766496 CCTCCCGGTGGCTAGATTTTA 59.234 52.381 0.00 0.00 0.00 1.52
652 660 0.546598 CCTCCCGGTGGCTAGATTTT 59.453 55.000 0.00 0.00 0.00 1.82
653 661 0.326238 TCCTCCCGGTGGCTAGATTT 60.326 55.000 0.00 0.00 0.00 2.17
667 1027 1.844687 ATTGCCTTTCTTGCTCCTCC 58.155 50.000 0.00 0.00 0.00 4.30
795 1156 1.269703 ATTTCGGGAGGGTAGCGGTT 61.270 55.000 0.00 0.00 0.00 4.44
834 1195 3.049912 GTTGCCATTCCGTTTTGAAGTC 58.950 45.455 0.00 0.00 0.00 3.01
898 1259 0.673437 TGCTGGTAAAAGGCAAGCAC 59.327 50.000 0.00 0.00 37.93 4.40
903 1264 1.769026 TGTTGTGCTGGTAAAAGGCA 58.231 45.000 0.00 0.00 0.00 4.75
960 1321 1.065418 AGGCGAATCCGGAAACTGAAT 60.065 47.619 9.01 0.00 40.77 2.57
1146 1507 4.487412 GAAGCCATGCAGCACCGC 62.487 66.667 0.00 1.58 34.23 5.68
1190 1551 0.598065 GAGCGCCCAAACATCTTTGT 59.402 50.000 2.29 0.00 35.84 2.83
1410 1775 4.796231 CCCGCGGTGAAGGACTCG 62.796 72.222 26.12 0.00 0.00 4.18
1453 1818 3.922366 CCTCCTGGGGTCTTTGGT 58.078 61.111 0.00 0.00 0.00 3.67
1485 1850 1.144913 TCTTTACCTTGCCCAGCACTT 59.855 47.619 0.00 0.00 38.71 3.16
1506 1871 3.445096 GTGCATCCATTTCTTAGCCTTGT 59.555 43.478 0.00 0.00 0.00 3.16
1551 1916 2.063979 ATCTCATCGTGCGGGGGAA 61.064 57.895 0.00 0.00 0.00 3.97
1556 1921 1.725164 CATCATCATCTCATCGTGCGG 59.275 52.381 0.00 0.00 0.00 5.69
1721 2086 4.890158 TGCTGAACTGAACTGGAGATAA 57.110 40.909 0.00 0.00 0.00 1.75
1795 2160 1.337703 GCAACTGCAGTTCACATGGAA 59.662 47.619 28.97 0.00 41.59 3.53
1822 2187 2.296073 AGACCTCAGGTTCGAACTCT 57.704 50.000 26.32 18.56 35.25 3.24
1972 2337 0.951558 TTTTGACCCGCAGCTTCTTC 59.048 50.000 0.00 0.00 0.00 2.87
2059 2424 3.550656 CGTTCCTTGTCGCTCCAC 58.449 61.111 0.00 0.00 0.00 4.02
2066 2431 1.087501 GATTCAGGGCGTTCCTTGTC 58.912 55.000 0.00 0.00 45.47 3.18
2143 2508 6.409005 CCATTGTATCTTGGATTCCAGAGACT 60.409 42.308 20.56 12.91 33.81 3.24
2150 2515 5.376625 TGCTACCATTGTATCTTGGATTCC 58.623 41.667 0.00 0.00 36.79 3.01
2224 2589 3.330267 CTCCAGTTTGAGCAGAAGGTAC 58.670 50.000 0.00 0.00 0.00 3.34
2278 2643 3.616956 TTTAGGACAGCCTCAGTGATG 57.383 47.619 0.00 0.00 45.54 3.07
2292 2657 3.428452 CCACGCGTCTAACAGATTTAGGA 60.428 47.826 9.86 0.00 0.00 2.94
2326 2691 1.131883 CTCTGCATCAAAGGCCTTTCG 59.868 52.381 28.16 21.50 0.00 3.46
2355 2720 3.415212 TGCAGGAACCAAGAAGAGATTG 58.585 45.455 0.00 0.00 0.00 2.67
2423 2788 1.207593 GCTTACCTTGTGCAGCACG 59.792 57.895 20.67 9.10 37.14 5.34
2432 2797 3.081061 TGCACAATAGTGGCTTACCTTG 58.919 45.455 0.00 0.00 45.98 3.61
2481 2846 8.414003 TCCAGTTAGCTAATATAGTGTTCAGTG 58.586 37.037 9.88 0.00 0.00 3.66
2524 2889 9.255304 CCTCTAATTAATAGAACTCTTCTGCAC 57.745 37.037 0.00 0.00 40.12 4.57
2597 2962 7.407393 ACTGTAAGGTGAATAACTCTCTACC 57.593 40.000 0.00 0.00 39.30 3.18
2802 3167 4.128925 TCTGTGACAGAATCATAGTGCC 57.871 45.455 13.74 0.00 44.71 5.01
2997 3362 5.124457 TCCTTTTGCAATCTCAGTATTCTGC 59.876 40.000 0.00 0.00 41.10 4.26
3079 3444 9.958180 TGATGTTCCTTTGAAATAGTTGAGATA 57.042 29.630 0.00 0.00 30.79 1.98
3168 3533 4.623932 TTGAAGTGGCAGAGATTACACT 57.376 40.909 0.00 0.00 45.34 3.55
3192 3557 2.033151 CAGTGACATGCATGACGCTATG 60.033 50.000 33.70 23.73 40.30 2.23
3330 3695 8.792830 TGCAAGCTTACTACAGAATTTCTTAT 57.207 30.769 0.00 0.00 0.00 1.73
3369 3739 5.581605 ACAGCAGGTAATGAATAATTTGCG 58.418 37.500 0.00 0.00 35.54 4.85


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

AutoCloner maintained by Alex Coulton.