Multiple sequence alignment - TraesCS7B01G220400

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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 TraesCS7B01G220400 chr7B 100.000 4874 0 0 1 4874 411605402 411610275 0.000000e+00 9001.0
1 TraesCS7B01G220400 chr7B 92.123 292 21 1 520 809 747298898 747298607 1.260000e-110 411.0
2 TraesCS7B01G220400 chr6B 97.108 4391 118 7 488 4874 375642109 375637724 0.000000e+00 7396.0
3 TraesCS7B01G220400 chr6B 96.596 3202 95 10 1677 4873 196484764 196487956 0.000000e+00 5297.0
4 TraesCS7B01G220400 chr6B 97.447 2703 64 3 488 3188 710547754 710545055 0.000000e+00 4604.0
5 TraesCS7B01G220400 chr6B 97.328 1160 26 3 488 1646 196483613 196484768 0.000000e+00 1965.0
6 TraesCS7B01G220400 chr6B 97.692 1083 21 2 488 1570 393072281 393073359 0.000000e+00 1858.0
7 TraesCS7B01G220400 chr6B 96.073 1044 34 6 3837 4874 393090021 393091063 0.000000e+00 1694.0
8 TraesCS7B01G220400 chr6B 97.602 417 10 0 1 417 196483203 196483619 0.000000e+00 715.0
9 TraesCS7B01G220400 chr6B 96.882 417 13 0 1 417 393071871 393072287 0.000000e+00 699.0
10 TraesCS7B01G220400 chr6B 96.429 420 15 0 1 420 375642519 375642100 0.000000e+00 693.0
11 TraesCS7B01G220400 chr6B 95.714 420 18 0 1 420 710548164 710547745 0.000000e+00 676.0
12 TraesCS7B01G220400 chr6B 95.719 327 14 0 3 329 720620651 720620977 1.200000e-145 527.0
13 TraesCS7B01G220400 chr5B 97.062 4391 120 6 488 4874 446179195 446174810 0.000000e+00 7385.0
14 TraesCS7B01G220400 chr5B 95.476 420 17 2 1 420 446179603 446179186 0.000000e+00 669.0
15 TraesCS7B01G220400 chr2B 97.017 3922 91 8 977 4874 779303542 779307461 0.000000e+00 6571.0
16 TraesCS7B01G220400 chr2B 85.714 126 9 4 340 464 188832783 188832900 1.840000e-24 124.0
17 TraesCS7B01G220400 chr2B 92.135 89 3 1 390 478 3644428 3644512 6.630000e-24 122.0
18 TraesCS7B01G220400 chr7D 94.023 3798 195 14 1090 4874 625868598 625872376 0.000000e+00 5727.0
19 TraesCS7B01G220400 chr2D 93.049 3798 199 30 1090 4874 97593096 97596841 0.000000e+00 5491.0
20 TraesCS7B01G220400 chr3A 92.656 3799 219 28 1090 4872 468236759 468233005 0.000000e+00 5415.0
21 TraesCS7B01G220400 chr3A 93.555 481 27 4 617 1093 500017623 500018103 0.000000e+00 713.0
22 TraesCS7B01G220400 chr3A 90.659 182 14 1 340 521 723997291 723997113 6.300000e-59 239.0
23 TraesCS7B01G220400 chr3A 94.737 57 2 1 339 395 468237539 468237484 2.420000e-13 87.9
24 TraesCS7B01G220400 chr6A 92.429 3817 231 18 1090 4874 343410387 343406597 0.000000e+00 5395.0
25 TraesCS7B01G220400 chr1B 96.879 2948 77 8 1934 4874 586566841 586569780 0.000000e+00 4920.0
26 TraesCS7B01G220400 chr1B 97.460 630 12 2 488 1117 586559151 586559776 0.000000e+00 1072.0
27 TraesCS7B01G220400 chr1B 95.444 417 15 1 1 417 586558745 586559157 0.000000e+00 662.0
28 TraesCS7B01G220400 chr6D 94.573 2985 132 12 1090 4061 62081459 62078492 0.000000e+00 4588.0
29 TraesCS7B01G220400 chr6D 95.634 481 17 1 617 1093 54816047 54816527 0.000000e+00 769.0
30 TraesCS7B01G220400 chr6D 95.218 481 19 1 617 1093 156017551 156017071 0.000000e+00 758.0
31 TraesCS7B01G220400 chr6D 76.261 337 36 23 517 809 11769934 11770270 6.580000e-29 139.0
32 TraesCS7B01G220400 chr1A 86.772 1270 137 23 3624 4874 517804749 517806006 0.000000e+00 1386.0
33 TraesCS7B01G220400 chr1A 94.495 327 18 0 3 329 379472939 379473265 5.630000e-139 505.0
34 TraesCS7B01G220400 chr1A 86.408 206 12 5 299 504 474581979 474581790 1.370000e-50 211.0
35 TraesCS7B01G220400 chr1A 94.643 56 3 0 336 391 434043971 434044026 2.420000e-13 87.9
36 TraesCS7B01G220400 chr2A 95.107 327 16 0 3 329 90615404 90615078 2.600000e-142 516.0
37 TraesCS7B01G220400 chr4A 89.011 182 8 4 340 521 293245166 293244997 1.060000e-51 215.0
38 TraesCS7B01G220400 chr5D 81.503 173 23 6 340 511 33108619 33108455 3.060000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G220400 chr7B 411605402 411610275 4873 False 9001.00 9001 100.000000 1 4874 1 chr7B.!!$F1 4873
1 TraesCS7B01G220400 chr6B 375637724 375642519 4795 True 4044.50 7396 96.768500 1 4874 2 chr6B.!!$R1 4873
2 TraesCS7B01G220400 chr6B 196483203 196487956 4753 False 2659.00 5297 97.175333 1 4873 3 chr6B.!!$F3 4872
3 TraesCS7B01G220400 chr6B 710545055 710548164 3109 True 2640.00 4604 96.580500 1 3188 2 chr6B.!!$R2 3187
4 TraesCS7B01G220400 chr6B 393090021 393091063 1042 False 1694.00 1694 96.073000 3837 4874 1 chr6B.!!$F1 1037
5 TraesCS7B01G220400 chr6B 393071871 393073359 1488 False 1278.50 1858 97.287000 1 1570 2 chr6B.!!$F4 1569
6 TraesCS7B01G220400 chr5B 446174810 446179603 4793 True 4027.00 7385 96.269000 1 4874 2 chr5B.!!$R1 4873
7 TraesCS7B01G220400 chr2B 779303542 779307461 3919 False 6571.00 6571 97.017000 977 4874 1 chr2B.!!$F3 3897
8 TraesCS7B01G220400 chr7D 625868598 625872376 3778 False 5727.00 5727 94.023000 1090 4874 1 chr7D.!!$F1 3784
9 TraesCS7B01G220400 chr2D 97593096 97596841 3745 False 5491.00 5491 93.049000 1090 4874 1 chr2D.!!$F1 3784
10 TraesCS7B01G220400 chr3A 468233005 468237539 4534 True 2751.45 5415 93.696500 339 4872 2 chr3A.!!$R2 4533
11 TraesCS7B01G220400 chr6A 343406597 343410387 3790 True 5395.00 5395 92.429000 1090 4874 1 chr6A.!!$R1 3784
12 TraesCS7B01G220400 chr1B 586566841 586569780 2939 False 4920.00 4920 96.879000 1934 4874 1 chr1B.!!$F1 2940
13 TraesCS7B01G220400 chr1B 586558745 586559776 1031 False 867.00 1072 96.452000 1 1117 2 chr1B.!!$F2 1116
14 TraesCS7B01G220400 chr6D 62078492 62081459 2967 True 4588.00 4588 94.573000 1090 4061 1 chr6D.!!$R1 2971
15 TraesCS7B01G220400 chr1A 517804749 517806006 1257 False 1386.00 1386 86.772000 3624 4874 1 chr1A.!!$F3 1250

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
484 485 0.036105 TGATGCTTCATCTGCACGGT 60.036 50.000 8.11 0.0 43.59 4.83 F
485 486 1.206849 TGATGCTTCATCTGCACGGTA 59.793 47.619 8.11 0.0 43.59 4.02 F
2252 2646 0.028902 GAACGCAGCCAAAAGAACGT 59.971 50.000 0.00 0.0 34.85 3.99 F
3141 3537 0.890683 CAGATGGAAACCCAACAGGC 59.109 55.000 0.00 0.0 40.58 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2051 1.470979 GCTTTGCAGATCCATTGGCAG 60.471 52.381 0.0 0.0 37.59 4.85 R
2421 2815 2.777832 ACAATCTGGCTCTTCTCCAC 57.222 50.000 0.0 0.0 0.00 4.02 R
3665 4065 0.249955 TCATCAGCGAAGGCATCACA 59.750 50.000 0.0 0.0 43.41 3.58 R
4267 4709 0.029567 GTGCCCGTGATCTAGAGTCG 59.970 60.000 0.0 3.0 0.00 4.18 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
220 221 2.921500 ATGACATGGTGGCCAGGCA 61.921 57.895 15.19 2.05 39.09 4.75
223 224 2.196997 GACATGGTGGCCAGGCACTA 62.197 60.000 21.78 17.46 39.09 2.74
313 314 0.108615 CGCTCTGTTTCCTCGTGGAT 60.109 55.000 7.11 0.00 42.81 3.41
415 416 5.833082 TCTGTATGTACAAAGCTAGCTAGC 58.167 41.667 33.96 33.96 41.62 3.42
417 418 6.771267 TCTGTATGTACAAAGCTAGCTAGCTA 59.229 38.462 40.88 27.65 45.67 3.32
418 419 7.041030 TCTGTATGTACAAAGCTAGCTAGCTAG 60.041 40.741 40.88 37.09 45.67 3.42
430 431 3.992260 GCTAGCTAGCTACTACAAGCA 57.008 47.619 33.71 4.28 45.30 3.91
432 433 2.880963 AGCTAGCTACTACAAGCAGC 57.119 50.000 17.69 10.35 45.30 5.25
434 435 2.763448 AGCTAGCTACTACAAGCAGCTT 59.237 45.455 17.69 0.21 42.03 3.74
436 437 4.402793 AGCTAGCTACTACAAGCAGCTTAA 59.597 41.667 17.69 0.00 42.03 1.85
438 439 5.755861 GCTAGCTACTACAAGCAGCTTAATT 59.244 40.000 7.52 0.00 42.03 1.40
439 440 6.292596 GCTAGCTACTACAAGCAGCTTAATTG 60.293 42.308 7.52 0.00 42.03 2.32
440 441 5.734720 AGCTACTACAAGCAGCTTAATTGA 58.265 37.500 7.52 0.00 42.03 2.57
441 442 6.352516 AGCTACTACAAGCAGCTTAATTGAT 58.647 36.000 7.52 0.00 42.03 2.57
442 443 6.825721 AGCTACTACAAGCAGCTTAATTGATT 59.174 34.615 7.52 0.00 42.03 2.57
443 444 6.909357 GCTACTACAAGCAGCTTAATTGATTG 59.091 38.462 7.52 13.42 44.93 2.67
450 451 7.891782 CAAGCAGCTTAATTGATTGTTGTATG 58.108 34.615 7.52 0.00 37.22 2.39
451 452 7.395190 AGCAGCTTAATTGATTGTTGTATGA 57.605 32.000 0.00 0.00 0.00 2.15
452 453 7.478322 AGCAGCTTAATTGATTGTTGTATGAG 58.522 34.615 0.00 0.00 0.00 2.90
453 454 6.197842 GCAGCTTAATTGATTGTTGTATGAGC 59.802 38.462 0.00 0.00 0.00 4.26
454 455 7.252708 CAGCTTAATTGATTGTTGTATGAGCA 58.747 34.615 0.00 0.00 0.00 4.26
455 456 7.431376 CAGCTTAATTGATTGTTGTATGAGCAG 59.569 37.037 0.00 0.00 0.00 4.24
456 457 6.197842 GCTTAATTGATTGTTGTATGAGCAGC 59.802 38.462 0.00 0.00 0.00 5.25
457 458 5.909621 AATTGATTGTTGTATGAGCAGCT 57.090 34.783 0.00 0.00 0.00 4.24
458 459 5.909621 ATTGATTGTTGTATGAGCAGCTT 57.090 34.783 0.00 0.00 0.00 3.74
459 460 4.952262 TGATTGTTGTATGAGCAGCTTC 57.048 40.909 0.00 0.00 0.00 3.86
460 461 3.691118 TGATTGTTGTATGAGCAGCTTCC 59.309 43.478 0.00 0.00 0.00 3.46
461 462 3.423539 TTGTTGTATGAGCAGCTTCCT 57.576 42.857 0.00 0.00 0.00 3.36
462 463 2.703416 TGTTGTATGAGCAGCTTCCTG 58.297 47.619 0.00 0.00 42.13 3.86
474 475 1.171308 GCTTCCTGCTTGATGCTTCA 58.829 50.000 0.00 0.00 43.37 3.02
475 476 1.749634 GCTTCCTGCTTGATGCTTCAT 59.250 47.619 2.75 0.00 43.37 2.57
476 477 2.223525 GCTTCCTGCTTGATGCTTCATC 60.224 50.000 2.75 0.13 43.37 2.92
477 478 3.280295 CTTCCTGCTTGATGCTTCATCT 58.720 45.455 2.75 0.00 41.06 2.90
478 479 2.640184 TCCTGCTTGATGCTTCATCTG 58.360 47.619 2.75 3.43 41.06 2.90
479 480 1.065701 CCTGCTTGATGCTTCATCTGC 59.934 52.381 2.75 8.93 41.06 4.26
480 481 1.743394 CTGCTTGATGCTTCATCTGCA 59.257 47.619 17.67 17.67 42.86 4.41
481 482 1.471287 TGCTTGATGCTTCATCTGCAC 59.529 47.619 15.95 4.47 41.59 4.57
482 483 1.531264 GCTTGATGCTTCATCTGCACG 60.531 52.381 2.75 0.00 43.59 5.34
483 484 1.063616 CTTGATGCTTCATCTGCACGG 59.936 52.381 2.75 0.00 43.59 4.94
484 485 0.036105 TGATGCTTCATCTGCACGGT 60.036 50.000 8.11 0.00 43.59 4.83
485 486 1.206849 TGATGCTTCATCTGCACGGTA 59.793 47.619 8.11 0.00 43.59 4.02
486 487 1.594862 GATGCTTCATCTGCACGGTAC 59.405 52.381 0.00 0.00 43.59 3.34
671 676 1.681793 AGAATCCTACCATCACCGTCG 59.318 52.381 0.00 0.00 0.00 5.12
812 817 9.522804 CTTATACATCCTACAGTCACTTTCTTC 57.477 37.037 0.00 0.00 0.00 2.87
813 818 7.726033 ATACATCCTACAGTCACTTTCTTCT 57.274 36.000 0.00 0.00 0.00 2.85
814 819 6.426646 ACATCCTACAGTCACTTTCTTCTT 57.573 37.500 0.00 0.00 0.00 2.52
1013 1037 2.993899 GGTCTTACACGAGTCACATTGG 59.006 50.000 0.00 0.00 0.00 3.16
1303 1694 5.455056 AACGGCATACAAAAACCAACATA 57.545 34.783 0.00 0.00 0.00 2.29
1506 1897 1.354155 CGTGCGCGACTACAGGATA 59.646 57.895 16.08 0.00 41.33 2.59
1527 1918 7.491696 AGGATAGTACTTGCTTTCGTTTACATC 59.508 37.037 0.00 0.00 0.00 3.06
1528 1919 5.857822 AGTACTTGCTTTCGTTTACATCC 57.142 39.130 0.00 0.00 0.00 3.51
1660 2051 6.523546 GGTTTTAAAGCATCTAAGAAGCGTTC 59.476 38.462 4.36 0.00 31.63 3.95
1824 2216 4.141390 GGACATTCACCCTACCATTCATCT 60.141 45.833 0.00 0.00 0.00 2.90
2163 2557 7.640597 TTTCAGGTTATCTCTAAGATCACGA 57.359 36.000 0.00 0.00 36.20 4.35
2252 2646 0.028902 GAACGCAGCCAAAAGAACGT 59.971 50.000 0.00 0.00 34.85 3.99
2956 3350 2.996621 AGATCAACTACAAGCTGAACGC 59.003 45.455 0.00 0.00 39.57 4.84
3141 3537 0.890683 CAGATGGAAACCCAACAGGC 59.109 55.000 0.00 0.00 40.58 4.85
3285 3683 9.729281 ATCCAAACTTGCAAAATATTCTTTCAT 57.271 25.926 0.00 0.00 0.00 2.57
3344 3742 4.095483 CCGACTGCTATTTCTTCAAATGCT 59.905 41.667 0.00 0.00 33.95 3.79
3389 3787 6.972328 GGCAATCTCGAATGTTTAAAGCAATA 59.028 34.615 0.00 0.00 0.00 1.90
3409 3809 6.603095 CAATAGTAAGTCACAACCTTGCTTC 58.397 40.000 0.00 0.00 36.47 3.86
3492 3892 6.826231 TCTTCTCTTTTACCATGTGTTGTTGA 59.174 34.615 0.00 0.00 0.00 3.18
3555 3955 6.040616 GCTAGCTAGGGACATGAACTTAACTA 59.959 42.308 22.10 0.00 0.00 2.24
3556 3956 6.472686 AGCTAGGGACATGAACTTAACTAG 57.527 41.667 0.00 2.80 0.00 2.57
3665 4065 2.490991 CAGGATGTCATGATCATGCGT 58.509 47.619 27.68 22.60 38.37 5.24
3734 4134 4.890988 TCTTCCTGTTGATATAGGGGTCA 58.109 43.478 0.00 0.00 33.67 4.02
3826 4226 3.152341 GGCCTATGCTGCTGTTATTGAT 58.848 45.455 0.00 0.00 37.74 2.57
4092 4530 1.474077 GCCTTAGCCATTCACACTTGG 59.526 52.381 0.00 0.00 36.03 3.61
4178 4620 6.868339 GCAATAGTTTTTAACAATGGAGCTGT 59.132 34.615 0.00 0.00 0.00 4.40
4267 4709 3.963428 TCCAAAGAACTAGCTGGACTC 57.037 47.619 3.17 0.00 32.97 3.36
4286 4728 0.029567 CGACTCTAGATCACGGGCAC 59.970 60.000 0.00 0.00 0.00 5.01
4346 4788 8.816640 ACATTTGAGTTTTATTTGATGGACAC 57.183 30.769 0.00 0.00 0.00 3.67
4663 5128 5.079689 TGTTGAAATAGAGTATCGCCACA 57.920 39.130 0.00 0.00 42.67 4.17
4747 5212 7.581213 ATTTGTCACCATCAAAAGAAGTACA 57.419 32.000 0.00 0.00 38.11 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 2.592993 CCCAGTTCAAGGCCGAGGA 61.593 63.158 0.00 0.00 0.00 3.71
202 203 2.043652 GCCTGGCCACCATGTCAT 60.044 61.111 7.66 0.00 30.82 3.06
220 221 1.595357 GGGTGCGGCAGTAACTAGT 59.405 57.895 1.18 0.00 0.00 2.57
223 224 3.307906 TCGGGTGCGGCAGTAACT 61.308 61.111 1.18 0.00 0.00 2.24
313 314 3.172106 TCACGACCCCCTTTGGCA 61.172 61.111 0.00 0.00 0.00 4.92
419 420 7.978982 ACAATCAATTAAGCTGCTTGTAGTAG 58.021 34.615 24.35 9.55 32.81 2.57
420 421 7.921786 ACAATCAATTAAGCTGCTTGTAGTA 57.078 32.000 24.35 7.93 32.81 1.82
422 423 7.086376 ACAACAATCAATTAAGCTGCTTGTAG 58.914 34.615 24.35 11.50 33.29 2.74
423 424 6.980593 ACAACAATCAATTAAGCTGCTTGTA 58.019 32.000 24.35 12.66 33.29 2.41
428 429 6.197842 GCTCATACAACAATCAATTAAGCTGC 59.802 38.462 0.00 0.00 0.00 5.25
429 430 7.252708 TGCTCATACAACAATCAATTAAGCTG 58.747 34.615 0.00 0.00 0.00 4.24
430 431 7.395190 TGCTCATACAACAATCAATTAAGCT 57.605 32.000 0.00 0.00 0.00 3.74
432 433 7.478322 AGCTGCTCATACAACAATCAATTAAG 58.522 34.615 0.00 0.00 0.00 1.85
434 435 7.395190 AAGCTGCTCATACAACAATCAATTA 57.605 32.000 1.00 0.00 0.00 1.40
436 437 5.163581 GGAAGCTGCTCATACAACAATCAAT 60.164 40.000 1.00 0.00 0.00 2.57
438 439 3.691118 GGAAGCTGCTCATACAACAATCA 59.309 43.478 1.00 0.00 0.00 2.57
439 440 3.944015 AGGAAGCTGCTCATACAACAATC 59.056 43.478 1.00 0.00 0.00 2.67
440 441 3.693085 CAGGAAGCTGCTCATACAACAAT 59.307 43.478 1.00 0.00 0.00 2.71
441 442 3.076621 CAGGAAGCTGCTCATACAACAA 58.923 45.455 1.00 0.00 0.00 2.83
442 443 2.703416 CAGGAAGCTGCTCATACAACA 58.297 47.619 1.00 0.00 0.00 3.33
443 444 1.399791 GCAGGAAGCTGCTCATACAAC 59.600 52.381 1.00 0.00 46.04 3.32
444 445 1.742761 GCAGGAAGCTGCTCATACAA 58.257 50.000 1.00 0.00 46.04 2.41
445 446 3.465990 GCAGGAAGCTGCTCATACA 57.534 52.632 1.00 0.00 46.04 2.29
453 454 6.503261 GATGAAGCATCAAGCAGGAAGCTG 62.503 50.000 7.91 0.00 45.20 4.24
454 455 6.690068 AGATGAAGCATCAAGCAGGAAGCT 62.690 45.833 9.77 2.07 46.28 3.74
459 460 5.571640 GTGCAGATGAAGCATCAAGCAGG 62.572 52.174 20.22 1.65 46.36 4.85
460 461 2.478031 GTGCAGATGAAGCATCAAGCAG 60.478 50.000 20.22 1.55 46.36 4.24
462 463 1.531264 CGTGCAGATGAAGCATCAAGC 60.531 52.381 9.77 12.23 44.79 4.01
463 464 1.063616 CCGTGCAGATGAAGCATCAAG 59.936 52.381 9.77 3.52 44.79 3.02
464 465 1.089112 CCGTGCAGATGAAGCATCAA 58.911 50.000 9.77 0.00 44.79 2.57
465 466 0.036105 ACCGTGCAGATGAAGCATCA 60.036 50.000 9.77 0.00 44.79 3.07
466 467 1.594862 GTACCGTGCAGATGAAGCATC 59.405 52.381 0.00 0.00 44.79 3.91
467 468 1.656652 GTACCGTGCAGATGAAGCAT 58.343 50.000 0.00 0.00 44.79 3.79
468 469 0.735978 CGTACCGTGCAGATGAAGCA 60.736 55.000 0.00 0.00 40.19 3.91
469 470 1.999051 CGTACCGTGCAGATGAAGC 59.001 57.895 0.00 0.00 0.00 3.86
470 471 0.458543 AGCGTACCGTGCAGATGAAG 60.459 55.000 0.00 0.00 33.85 3.02
471 472 0.037697 AAGCGTACCGTGCAGATGAA 60.038 50.000 0.00 0.00 33.85 2.57
472 473 0.735978 CAAGCGTACCGTGCAGATGA 60.736 55.000 0.00 0.00 33.85 2.92
473 474 1.709760 CAAGCGTACCGTGCAGATG 59.290 57.895 0.00 0.00 33.85 2.90
474 475 2.100631 GCAAGCGTACCGTGCAGAT 61.101 57.895 14.11 0.00 46.38 2.90
475 476 2.736995 GCAAGCGTACCGTGCAGA 60.737 61.111 14.11 0.00 46.38 4.26
479 480 1.911293 ATGCAAGCAAGCGTACCGTG 61.911 55.000 0.00 0.00 37.31 4.94
480 481 1.234615 AATGCAAGCAAGCGTACCGT 61.235 50.000 0.00 0.00 37.31 4.83
481 482 0.109781 AAATGCAAGCAAGCGTACCG 60.110 50.000 0.00 0.00 37.31 4.02
482 483 2.064573 AAAATGCAAGCAAGCGTACC 57.935 45.000 0.00 0.00 37.31 3.34
483 484 5.761818 AATAAAAATGCAAGCAAGCGTAC 57.238 34.783 0.00 0.00 37.31 3.67
484 485 6.847400 TCTAATAAAAATGCAAGCAAGCGTA 58.153 32.000 0.00 0.00 37.31 4.42
485 486 5.708948 TCTAATAAAAATGCAAGCAAGCGT 58.291 33.333 0.00 0.00 37.31 5.07
486 487 6.817270 ATCTAATAAAAATGCAAGCAAGCG 57.183 33.333 0.00 0.00 37.31 4.68
487 488 9.305925 ACTTATCTAATAAAAATGCAAGCAAGC 57.694 29.630 0.00 0.00 0.00 4.01
490 491 9.787532 GACACTTATCTAATAAAAATGCAAGCA 57.212 29.630 0.00 0.00 0.00 3.91
491 492 8.947940 CGACACTTATCTAATAAAAATGCAAGC 58.052 33.333 0.00 0.00 0.00 4.01
671 676 2.416747 TGTTGTATGCAGAGTGACAGC 58.583 47.619 0.00 0.00 0.00 4.40
718 723 9.136952 ACGGATAATATTACATCGAAAGCTAAC 57.863 33.333 15.96 0.00 0.00 2.34
776 781 8.822805 ACTGTAGGATGTATAAGAAGAAACCAA 58.177 33.333 0.00 0.00 0.00 3.67
1506 1897 4.387862 CGGATGTAAACGAAAGCAAGTACT 59.612 41.667 0.00 0.00 0.00 2.73
1527 1918 6.668541 AGATTGTAAGAAATGATGACACGG 57.331 37.500 0.00 0.00 0.00 4.94
1528 1919 9.642312 CATTAGATTGTAAGAAATGATGACACG 57.358 33.333 0.00 0.00 30.77 4.49
1660 2051 1.470979 GCTTTGCAGATCCATTGGCAG 60.471 52.381 0.00 0.00 37.59 4.85
1824 2216 7.386025 GCACTATCATATCTGCAACAATGAGTA 59.614 37.037 9.55 3.85 32.25 2.59
2076 2470 6.931281 CACTCTTCTGGTTGTAAATCTTCTGA 59.069 38.462 0.00 0.00 0.00 3.27
2078 2472 6.234177 CCACTCTTCTGGTTGTAAATCTTCT 58.766 40.000 0.00 0.00 0.00 2.85
2252 2646 7.211573 TGTCTTCTGTTTCTTACGGTTATCAA 58.788 34.615 0.00 0.00 34.56 2.57
2421 2815 2.777832 ACAATCTGGCTCTTCTCCAC 57.222 50.000 0.00 0.00 0.00 4.02
2956 3350 2.724977 TCCTCTCTTGTGTGTTAGCG 57.275 50.000 0.00 0.00 0.00 4.26
3094 3490 6.155827 GCTCAATTGTACAAACTTTGCCATA 58.844 36.000 13.23 0.00 0.00 2.74
3110 3506 4.687483 GGTTTCCATCTGTTTGCTCAATTG 59.313 41.667 0.00 0.00 0.00 2.32
3141 3537 5.233225 AGCATATGACTGTAATCACCATCG 58.767 41.667 6.97 0.00 0.00 3.84
3213 3610 7.014422 CCTCTTCGTAGGAACCTGTAAATAGAT 59.986 40.741 3.36 0.00 39.15 1.98
3285 3683 8.946248 TGGAGTCTTATTAGGACTAGATGTCTA 58.054 37.037 8.31 0.00 43.13 2.59
3344 3742 2.353323 CTTGCTGCAGCTTGTATGAGA 58.647 47.619 36.61 12.87 42.66 3.27
3389 3787 3.136626 AGGAAGCAAGGTTGTGACTTACT 59.863 43.478 0.00 0.00 0.00 2.24
3409 3809 2.189594 TGCAGGTGAACATGAAGAGG 57.810 50.000 0.00 0.00 0.00 3.69
3492 3892 4.754618 TGTTTAAGTTGTGACTCGATGCAT 59.245 37.500 0.00 0.00 34.21 3.96
3665 4065 0.249955 TCATCAGCGAAGGCATCACA 59.750 50.000 0.00 0.00 43.41 3.58
3826 4226 1.855295 TGAGCGGGTACTTGGTATCA 58.145 50.000 0.00 0.00 0.00 2.15
3885 4302 3.641031 GCAACAAAGTTTGCCGAGT 57.359 47.368 15.59 0.00 45.22 4.18
3917 4340 8.475639 GTTAGGTTCTAACATCCTATCAAGACA 58.524 37.037 11.58 0.00 34.40 3.41
4092 4530 9.032420 GTAACTAAGGCATCAGAACAACTATAC 57.968 37.037 0.00 0.00 0.00 1.47
4186 4628 6.989759 TGAGTCAAACATAACATACGCCATAT 59.010 34.615 0.00 0.00 0.00 1.78
4242 4684 4.406003 GTCCAGCTAGTTCTTTGGATCCTA 59.594 45.833 14.23 1.56 41.41 2.94
4267 4709 0.029567 GTGCCCGTGATCTAGAGTCG 59.970 60.000 0.00 3.00 0.00 4.18
4747 5212 3.749088 TCGTCGTAACAGGAAATTGCAAT 59.251 39.130 5.99 5.99 0.00 3.56


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

AutoCloner maintained by Alex Coulton.