Multiple sequence alignment - TraesCS3B01G474100

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 TraesCS3B01G474100 chr3B 100.000 2867 0 0 1 2867 723277461 723274595 0.000000e+00 5295.0
1 TraesCS3B01G474100 chr3B 100.000 52 0 0 2470 2521 723274943 723274892 2.350000e-16 97.1
2 TraesCS3B01G474100 chr3B 100.000 52 0 0 2519 2570 723274992 723274941 2.350000e-16 97.1
3 TraesCS3B01G474100 chr3A 92.883 2515 125 22 52 2525 683072554 683070053 0.000000e+00 3603.0
4 TraesCS3B01G474100 chr3A 94.220 173 9 1 2519 2690 683070108 683069936 2.190000e-66 263.0
5 TraesCS3B01G474100 chr3A 94.326 141 7 1 2728 2867 683069734 683069594 6.220000e-52 215.0
6 TraesCS3B01G474100 chr3D 93.039 2356 104 20 55 2395 546322799 546320489 0.000000e+00 3387.0
7 TraesCS3B01G474100 chr3D 89.049 347 36 2 2522 2867 546320379 546320034 2.040000e-116 429.0
8 TraesCS3B01G474100 chr3D 94.595 37 2 0 1 37 546322839 546322803 1.110000e-04 58.4


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 TraesCS3B01G474100 chr3B 723274595 723277461 2866 True 1829.733333 5295 100.000000 1 2867 3 chr3B.!!$R1 2866
1 TraesCS3B01G474100 chr3A 683069594 683072554 2960 True 1360.333333 3603 93.809667 52 2867 3 chr3A.!!$R1 2815
2 TraesCS3B01G474100 chr3D 546320034 546322839 2805 True 1291.466667 3387 92.227667 1 2867 3 chr3D.!!$R1 2866

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
136 140 0.323302 TATGTGGCGAAGGTGCTTGA 59.677 50.0 0.0 0.0 34.52 3.02 F
446 453 0.334676 CCCTATCCAAACAAGGCCCA 59.665 55.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1345 0.041684 TGGCCTCTGAGAGATGACCA 59.958 55.0 11.82 9.9 0.00 4.02 R
1938 1958 0.319083 TTGGGTGTAAGACGCGACAT 59.681 50.0 15.93 1.0 40.44 3.06 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
28 29 3.604582 CCTTCCTCCTTGCAGAGTAAAG 58.395 50.000 2.63 5.63 31.53 1.85
29 30 3.604582 CTTCCTCCTTGCAGAGTAAAGG 58.395 50.000 2.63 0.00 43.72 3.11
37 38 1.351017 TGCAGAGTAAAGGAGGGGTTG 59.649 52.381 0.00 0.00 0.00 3.77
38 39 1.340114 GCAGAGTAAAGGAGGGGTTGG 60.340 57.143 0.00 0.00 0.00 3.77
39 40 2.266279 CAGAGTAAAGGAGGGGTTGGA 58.734 52.381 0.00 0.00 0.00 3.53
40 41 2.237392 CAGAGTAAAGGAGGGGTTGGAG 59.763 54.545 0.00 0.00 0.00 3.86
41 42 0.992695 AGTAAAGGAGGGGTTGGAGC 59.007 55.000 0.00 0.00 0.00 4.70
42 43 0.392595 GTAAAGGAGGGGTTGGAGCG 60.393 60.000 0.00 0.00 0.00 5.03
43 44 0.545787 TAAAGGAGGGGTTGGAGCGA 60.546 55.000 0.00 0.00 0.00 4.93
44 45 2.125766 AAAGGAGGGGTTGGAGCGAC 62.126 60.000 0.00 0.00 0.00 5.19
45 46 3.003763 GGAGGGGTTGGAGCGACT 61.004 66.667 0.00 0.00 0.00 4.18
46 47 2.593956 GGAGGGGTTGGAGCGACTT 61.594 63.158 0.00 0.00 0.00 3.01
47 48 1.376037 GAGGGGTTGGAGCGACTTG 60.376 63.158 0.00 0.00 0.00 3.16
48 49 2.113243 GAGGGGTTGGAGCGACTTGT 62.113 60.000 0.00 0.00 0.00 3.16
49 50 1.671379 GGGGTTGGAGCGACTTGTC 60.671 63.158 0.00 0.00 0.00 3.18
50 51 1.671379 GGGTTGGAGCGACTTGTCC 60.671 63.158 0.00 0.00 0.00 4.02
77 78 1.616865 GCCCCAAGGTAAAAGTCCAAC 59.383 52.381 0.00 0.00 34.57 3.77
88 89 0.696501 AAGTCCAACCGTATTGCCCT 59.303 50.000 0.00 0.00 0.00 5.19
99 100 2.225467 GTATTGCCCTTGGATCTCTGC 58.775 52.381 0.00 0.00 0.00 4.26
125 129 6.523201 GTCTTGTTTAATTCTTGTATGTGGCG 59.477 38.462 0.00 0.00 0.00 5.69
136 140 0.323302 TATGTGGCGAAGGTGCTTGA 59.677 50.000 0.00 0.00 34.52 3.02
183 187 1.196766 TGCATCAGCTGGGTCTCAGT 61.197 55.000 15.13 0.00 45.08 3.41
373 380 6.003326 TGTAAGAATTGATTCTGGAGTTGCA 58.997 36.000 6.98 0.00 45.83 4.08
390 397 1.359848 GCAGCTGCATGTACGTAGTT 58.640 50.000 33.36 0.00 41.23 2.24
419 426 4.095610 GCGTGTTTGTGGAATATACTTGC 58.904 43.478 0.00 0.00 0.00 4.01
428 435 4.389077 GTGGAATATACTTGCGTGCTATCC 59.611 45.833 0.00 0.00 0.00 2.59
429 436 3.933332 GGAATATACTTGCGTGCTATCCC 59.067 47.826 0.00 0.00 0.00 3.85
430 437 4.322801 GGAATATACTTGCGTGCTATCCCT 60.323 45.833 0.00 0.00 0.00 4.20
431 438 5.105473 GGAATATACTTGCGTGCTATCCCTA 60.105 44.000 0.00 0.00 0.00 3.53
432 439 6.407074 GGAATATACTTGCGTGCTATCCCTAT 60.407 42.308 0.00 0.00 0.00 2.57
433 440 2.821991 ACTTGCGTGCTATCCCTATC 57.178 50.000 0.00 0.00 0.00 2.08
442 449 4.137543 GTGCTATCCCTATCCAAACAAGG 58.862 47.826 0.00 0.00 0.00 3.61
446 453 0.334676 CCCTATCCAAACAAGGCCCA 59.665 55.000 0.00 0.00 0.00 5.36
448 455 1.824852 CCTATCCAAACAAGGCCCAAC 59.175 52.381 0.00 0.00 0.00 3.77
458 465 3.637769 ACAAGGCCCAACAGTTTTTCTA 58.362 40.909 0.00 0.00 0.00 2.10
459 466 3.383505 ACAAGGCCCAACAGTTTTTCTAC 59.616 43.478 0.00 0.00 0.00 2.59
460 467 3.306472 AGGCCCAACAGTTTTTCTACA 57.694 42.857 0.00 0.00 0.00 2.74
461 468 3.222603 AGGCCCAACAGTTTTTCTACAG 58.777 45.455 0.00 0.00 0.00 2.74
471 486 3.832490 AGTTTTTCTACAGGGGAAATGGC 59.168 43.478 0.00 0.00 33.51 4.40
488 503 1.313091 GGCTTCCGGTGGTTTCATCC 61.313 60.000 0.00 0.00 0.00 3.51
492 507 1.004320 CCGGTGGTTTCATCCGTGA 60.004 57.895 0.00 0.00 42.30 4.35
509 524 3.451902 CCGTGACCAGTAAAATACCCCTA 59.548 47.826 0.00 0.00 0.00 3.53
514 530 7.095270 GTGACCAGTAAAATACCCCTATATCG 58.905 42.308 0.00 0.00 0.00 2.92
544 560 8.868522 ACAGCTGCATATATTTACATGGTATT 57.131 30.769 15.27 0.00 0.00 1.89
555 571 1.005805 ACATGGTATTCAAGCAGGGCA 59.994 47.619 0.00 0.00 41.55 5.36
614 630 3.449737 CCTACGGTATCCCTTTCAGTTGA 59.550 47.826 0.00 0.00 0.00 3.18
629 645 5.488262 TCAGTTGATTGGACTGATCTTCA 57.512 39.130 3.03 0.00 46.21 3.02
660 676 4.105697 AGGTCCCTATGGTTTTTGTCTTCA 59.894 41.667 0.00 0.00 0.00 3.02
664 680 5.073144 TCCCTATGGTTTTTGTCTTCAGAGT 59.927 40.000 0.00 0.00 0.00 3.24
670 686 6.987386 TGGTTTTTGTCTTCAGAGTTTTTGA 58.013 32.000 0.00 0.00 0.00 2.69
763 779 4.713553 TGCACAATGTTAAGAAGTCCTCA 58.286 39.130 0.00 0.00 0.00 3.86
764 780 5.316167 TGCACAATGTTAAGAAGTCCTCAT 58.684 37.500 0.00 0.00 0.00 2.90
787 803 2.356135 ACGCAGTTCGCTTATTTGGAT 58.644 42.857 0.00 0.00 37.78 3.41
824 840 2.514803 ACATGCCCCTACTGTTTTCAC 58.485 47.619 0.00 0.00 0.00 3.18
829 845 2.557056 GCCCCTACTGTTTTCACCTTTC 59.443 50.000 0.00 0.00 0.00 2.62
1179 1195 2.649531 TTCATCGTGACCCAAGGTTT 57.350 45.000 0.00 0.00 35.25 3.27
1446 1462 4.213531 TGGGCCTGGATTAGAAGATCTA 57.786 45.455 4.53 0.00 0.00 1.98
1506 1522 2.234143 CCTGCCTCTCAGTCATCGATA 58.766 52.381 0.00 0.00 41.25 2.92
1592 1608 2.687935 GCAAGGACAAGTTTGAACTGGA 59.312 45.455 5.30 0.00 39.66 3.86
1596 1612 3.815401 AGGACAAGTTTGAACTGGAATCG 59.185 43.478 5.30 0.00 39.66 3.34
1904 1923 4.009675 TGGTTGGAGTTCACAATGCTATC 58.990 43.478 0.00 0.00 0.00 2.08
1913 1933 7.334421 GGAGTTCACAATGCTATCTTAGTGAAA 59.666 37.037 7.30 0.00 44.49 2.69
1923 1943 6.201615 TGCTATCTTAGTGAAAATGCTGATCG 59.798 38.462 0.00 0.00 0.00 3.69
1938 1958 4.065088 GCTGATCGAATGGGCTTTATGTA 58.935 43.478 0.00 0.00 0.00 2.29
2074 2094 7.715265 TTTTGTTTGCTTTTACACAAGTCAA 57.285 28.000 0.00 0.00 31.00 3.18
2078 2098 8.572828 TGTTTGCTTTTACACAAGTCAATATG 57.427 30.769 0.00 0.00 0.00 1.78
2167 2187 6.095580 TGCTGTATTGGTTGTTTTGTAGTTGA 59.904 34.615 0.00 0.00 0.00 3.18
2242 2262 1.001378 GAACATGGTTTCAAGCGCACT 60.001 47.619 11.47 0.00 0.00 4.40
2377 2402 9.245962 AGTATGATTCTAAAAATACCGAAGACG 57.754 33.333 0.00 0.00 39.43 4.18
2381 2406 7.816031 TGATTCTAAAAATACCGAAGACGAACT 59.184 33.333 0.00 0.00 42.66 3.01
2389 2414 0.038159 CGAAGACGAACTCTTGCCCT 60.038 55.000 0.00 0.00 39.53 5.19
2390 2415 1.201647 CGAAGACGAACTCTTGCCCTA 59.798 52.381 0.00 0.00 39.53 3.53
2391 2416 2.159226 CGAAGACGAACTCTTGCCCTAT 60.159 50.000 0.00 0.00 39.53 2.57
2392 2417 3.066342 CGAAGACGAACTCTTGCCCTATA 59.934 47.826 0.00 0.00 39.53 1.31
2433 2486 6.475727 CAGTAGTTGATATTAGTGGGTTGACG 59.524 42.308 0.00 0.00 0.00 4.35
2435 2488 6.534475 AGTTGATATTAGTGGGTTGACGTA 57.466 37.500 0.00 0.00 0.00 3.57
2519 2579 3.401033 TCCTCGAGCTGACATGAAAAA 57.599 42.857 6.99 0.00 0.00 1.94
2540 2600 6.937436 AAAAATTACGGTGGGATCTCATAC 57.063 37.500 0.00 0.00 0.00 2.39
2541 2601 5.888982 AAATTACGGTGGGATCTCATACT 57.111 39.130 0.00 0.00 0.00 2.12
2542 2602 6.989155 AAATTACGGTGGGATCTCATACTA 57.011 37.500 0.00 0.00 0.00 1.82
2543 2603 6.591750 AATTACGGTGGGATCTCATACTAG 57.408 41.667 0.00 0.00 0.00 2.57
2544 2604 3.596940 ACGGTGGGATCTCATACTAGT 57.403 47.619 0.00 0.00 0.00 2.57
2545 2605 3.223435 ACGGTGGGATCTCATACTAGTG 58.777 50.000 5.39 0.00 0.00 2.74
2546 2606 2.558795 CGGTGGGATCTCATACTAGTGG 59.441 54.545 5.39 0.00 0.00 4.00
2547 2607 3.750922 CGGTGGGATCTCATACTAGTGGA 60.751 52.174 5.39 2.18 0.00 4.02
2548 2608 4.421131 GGTGGGATCTCATACTAGTGGAT 58.579 47.826 5.39 4.10 0.00 3.41
2549 2609 4.464597 GGTGGGATCTCATACTAGTGGATC 59.535 50.000 5.39 12.18 34.00 3.36
2550 2610 4.464597 GTGGGATCTCATACTAGTGGATCC 59.535 50.000 24.72 24.72 46.79 3.36
2551 2611 4.358310 TGGGATCTCATACTAGTGGATCCT 59.642 45.833 27.83 0.00 46.73 3.24
2552 2612 4.953579 GGGATCTCATACTAGTGGATCCTC 59.046 50.000 27.83 20.78 46.73 3.71
2553 2613 4.638421 GGATCTCATACTAGTGGATCCTCG 59.362 50.000 25.07 0.08 45.14 4.63
2554 2614 4.976540 TCTCATACTAGTGGATCCTCGA 57.023 45.455 14.23 4.78 0.00 4.04
2555 2615 4.900684 TCTCATACTAGTGGATCCTCGAG 58.099 47.826 18.89 18.89 0.00 4.04
2556 2616 3.413327 TCATACTAGTGGATCCTCGAGC 58.587 50.000 20.01 3.89 0.00 5.03
2557 2617 3.073209 TCATACTAGTGGATCCTCGAGCT 59.927 47.826 20.01 11.85 0.00 4.09
2558 2618 1.686355 ACTAGTGGATCCTCGAGCTG 58.314 55.000 20.01 7.96 0.00 4.24
2559 2619 1.213182 ACTAGTGGATCCTCGAGCTGA 59.787 52.381 20.01 0.00 0.00 4.26
2560 2620 1.606668 CTAGTGGATCCTCGAGCTGAC 59.393 57.143 14.23 0.00 0.00 3.51
2561 2621 0.323816 AGTGGATCCTCGAGCTGACA 60.324 55.000 14.23 0.19 0.00 3.58
2562 2622 0.749649 GTGGATCCTCGAGCTGACAT 59.250 55.000 14.23 0.00 0.00 3.06
2563 2623 0.749049 TGGATCCTCGAGCTGACATG 59.251 55.000 14.23 0.00 0.00 3.21
2564 2624 1.035923 GGATCCTCGAGCTGACATGA 58.964 55.000 6.99 0.00 0.00 3.07
2565 2625 1.410517 GGATCCTCGAGCTGACATGAA 59.589 52.381 6.99 0.00 0.00 2.57
2566 2626 2.159043 GGATCCTCGAGCTGACATGAAA 60.159 50.000 6.99 0.00 0.00 2.69
2655 2715 2.925170 CGGCCATCCCCCTCCTAG 60.925 72.222 2.24 0.00 0.00 3.02
2673 2733 3.771160 CCGTCCTTCCCACCCTCG 61.771 72.222 0.00 0.00 0.00 4.63
2678 2738 4.452733 CTTCCCACCCTCGTCGCC 62.453 72.222 0.00 0.00 0.00 5.54
2709 2769 3.322466 CTCCCCGCCTCAGGTGTT 61.322 66.667 2.86 0.00 0.00 3.32
2711 2771 3.953775 CCCCGCCTCAGGTGTTGT 61.954 66.667 2.86 0.00 0.00 3.32
2736 2960 2.175715 GCTTCCTCCCCATCCAACTATT 59.824 50.000 0.00 0.00 0.00 1.73
2823 3047 0.187361 TGCACCACCTTTAGGCCTTT 59.813 50.000 12.58 0.00 39.32 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.593956 AAGTCGCTCCAACCCCTCC 61.594 63.158 0.00 0.00 0.00 4.30
29 30 1.376037 CAAGTCGCTCCAACCCCTC 60.376 63.158 0.00 0.00 0.00 4.30
37 38 4.452733 CGGGGGACAAGTCGCTCC 62.453 72.222 15.47 13.46 39.58 4.70
38 39 3.358076 CTCGGGGGACAAGTCGCTC 62.358 68.421 15.47 11.51 41.61 5.03
39 40 3.382832 CTCGGGGGACAAGTCGCT 61.383 66.667 15.47 0.00 41.61 4.93
40 41 4.452733 CCTCGGGGGACAAGTCGC 62.453 72.222 8.58 8.58 41.23 5.19
41 42 4.452733 GCCTCGGGGGACAAGTCG 62.453 72.222 1.90 0.00 37.23 4.18
42 43 4.097361 GGCCTCGGGGGACAAGTC 62.097 72.222 1.90 0.00 44.40 3.01
77 78 1.417890 AGAGATCCAAGGGCAATACGG 59.582 52.381 0.00 0.00 0.00 4.02
88 89 2.839486 AACAAGACGCAGAGATCCAA 57.161 45.000 0.00 0.00 0.00 3.53
99 100 6.523201 GCCACATACAAGAATTAAACAAGACG 59.477 38.462 0.00 0.00 0.00 4.18
125 129 0.232303 CGTTCACGTCAAGCACCTTC 59.768 55.000 0.00 0.00 34.11 3.46
136 140 1.306642 TTGTTTGTGGGCGTTCACGT 61.307 50.000 0.62 0.00 40.31 4.49
183 187 7.642194 GTGTGTCAAATCAAATACAAGACGAAA 59.358 33.333 0.00 0.00 0.00 3.46
266 270 9.086336 CATAAACATCAATTTGGGACACATAAC 57.914 33.333 0.00 0.00 39.29 1.89
316 321 5.239306 ACAGTCACACCACAGATGTAAATTG 59.761 40.000 0.00 0.00 0.00 2.32
373 380 1.337728 TGCAACTACGTACATGCAGCT 60.338 47.619 20.76 0.00 43.32 4.24
390 397 0.817229 TCCACAAACACGCATCTGCA 60.817 50.000 2.72 0.00 42.21 4.41
419 426 3.469008 TGTTTGGATAGGGATAGCACG 57.531 47.619 0.00 0.00 0.00 5.34
428 435 1.824852 GTTGGGCCTTGTTTGGATAGG 59.175 52.381 4.53 0.00 0.00 2.57
429 436 2.493278 CTGTTGGGCCTTGTTTGGATAG 59.507 50.000 4.53 0.00 0.00 2.08
430 437 2.158385 ACTGTTGGGCCTTGTTTGGATA 60.158 45.455 4.53 0.00 0.00 2.59
431 438 1.341080 CTGTTGGGCCTTGTTTGGAT 58.659 50.000 4.53 0.00 0.00 3.41
432 439 0.032615 ACTGTTGGGCCTTGTTTGGA 60.033 50.000 4.53 0.00 0.00 3.53
433 440 0.829990 AACTGTTGGGCCTTGTTTGG 59.170 50.000 4.53 0.00 0.00 3.28
442 449 2.296190 CCCTGTAGAAAAACTGTTGGGC 59.704 50.000 0.00 0.00 0.00 5.36
446 453 5.304357 CCATTTCCCCTGTAGAAAAACTGTT 59.696 40.000 0.00 0.00 36.83 3.16
448 455 4.321974 GCCATTTCCCCTGTAGAAAAACTG 60.322 45.833 0.00 0.00 36.83 3.16
471 486 2.466867 CGGATGAAACCACCGGAAG 58.533 57.895 9.46 0.00 42.48 3.46
488 503 3.622166 AGGGGTATTTTACTGGTCACG 57.378 47.619 0.00 0.00 0.00 4.35
492 507 8.725606 TTACGATATAGGGGTATTTTACTGGT 57.274 34.615 0.00 0.00 0.00 4.00
544 560 2.571653 ACTACACTAATGCCCTGCTTGA 59.428 45.455 0.00 0.00 0.00 3.02
555 571 8.011844 TCATCAGCTGACAATACTACACTAAT 57.988 34.615 20.97 0.00 0.00 1.73
614 630 5.233083 TCACAGTTGAAGATCAGTCCAAT 57.767 39.130 0.00 0.00 0.00 3.16
629 645 2.632537 ACCATAGGGACCTTCACAGTT 58.367 47.619 0.00 0.00 38.05 3.16
660 676 8.519799 TCCAACAAAGATAAGTCAAAAACTCT 57.480 30.769 0.00 0.00 37.17 3.24
787 803 5.316167 GGCATGTATATGGTCCAAGATCAA 58.684 41.667 0.00 0.00 34.79 2.57
824 840 3.701040 CCCAACATGGATAAGTGGAAAGG 59.299 47.826 0.00 0.00 40.96 3.11
1012 1028 2.648059 GAAGCACCAATATGTCTGCCT 58.352 47.619 0.00 0.00 0.00 4.75
1068 1084 4.836825 CATCACAGTAAGGACACTCCATT 58.163 43.478 0.00 0.00 39.61 3.16
1137 1153 8.519526 TGAAAATCACTATACATCCCAACAAAC 58.480 33.333 0.00 0.00 0.00 2.93
1179 1195 2.242965 AGACATTGCTTCCATGATCCCA 59.757 45.455 0.00 0.00 0.00 4.37
1191 1207 1.656652 GCATCACGGTAGACATTGCT 58.343 50.000 0.00 0.00 0.00 3.91
1329 1345 0.041684 TGGCCTCTGAGAGATGACCA 59.958 55.000 11.82 9.90 0.00 4.02
1394 1410 3.197790 CAACATCTGCCCTCCGCG 61.198 66.667 0.00 0.00 42.08 6.46
1446 1462 7.254692 CGATCATTATGAGTCAACTGCTCAATT 60.255 37.037 0.00 0.00 44.82 2.32
1506 1522 2.105477 CCTAACACTAGGCATGGCATCT 59.895 50.000 22.64 3.11 38.50 2.90
1592 1608 2.559440 GCATCTCTCTTGCTTCCGATT 58.441 47.619 0.00 0.00 37.14 3.34
1596 1612 1.948145 CATGGCATCTCTCTTGCTTCC 59.052 52.381 0.00 0.00 40.03 3.46
1904 1923 6.197276 CCATTCGATCAGCATTTTCACTAAG 58.803 40.000 0.00 0.00 0.00 2.18
1913 1933 2.062971 AAGCCCATTCGATCAGCATT 57.937 45.000 0.00 0.00 0.00 3.56
1923 1943 3.363970 CGCGACATACATAAAGCCCATTC 60.364 47.826 0.00 0.00 0.00 2.67
1938 1958 0.319083 TTGGGTGTAAGACGCGACAT 59.681 50.000 15.93 1.00 40.44 3.06
2095 2115 8.714906 TCACCCCCAAAAAGTTTATATTGAAAA 58.285 29.630 0.95 0.00 0.00 2.29
2291 2316 4.170468 ACAATCAACAGGTTTCTCAGGT 57.830 40.909 0.00 0.00 0.00 4.00
2406 2459 8.472413 GTCAACCCACTAATATCAACTACTGTA 58.528 37.037 0.00 0.00 0.00 2.74
2519 2579 5.888982 AGTATGAGATCCCACCGTAATTT 57.111 39.130 0.00 0.00 0.00 1.82
2520 2580 6.015350 CACTAGTATGAGATCCCACCGTAATT 60.015 42.308 0.00 0.00 0.00 1.40
2521 2581 5.477291 CACTAGTATGAGATCCCACCGTAAT 59.523 44.000 0.00 0.00 0.00 1.89
2522 2582 4.825634 CACTAGTATGAGATCCCACCGTAA 59.174 45.833 0.00 0.00 0.00 3.18
2523 2583 4.395625 CACTAGTATGAGATCCCACCGTA 58.604 47.826 0.00 0.00 0.00 4.02
2524 2584 3.223435 CACTAGTATGAGATCCCACCGT 58.777 50.000 0.00 0.00 0.00 4.83
2525 2585 2.558795 CCACTAGTATGAGATCCCACCG 59.441 54.545 0.00 0.00 0.00 4.94
2526 2586 3.845860 TCCACTAGTATGAGATCCCACC 58.154 50.000 0.00 0.00 0.00 4.61
2527 2587 4.464597 GGATCCACTAGTATGAGATCCCAC 59.535 50.000 21.70 7.32 44.81 4.61
2528 2588 4.678256 GGATCCACTAGTATGAGATCCCA 58.322 47.826 21.70 0.00 44.81 4.37
2531 2591 5.492895 TCGAGGATCCACTAGTATGAGATC 58.507 45.833 15.82 12.56 34.01 2.75
2532 2592 5.496556 CTCGAGGATCCACTAGTATGAGAT 58.503 45.833 15.82 0.00 0.00 2.75
2533 2593 4.804597 GCTCGAGGATCCACTAGTATGAGA 60.805 50.000 15.82 0.00 0.00 3.27
2534 2594 3.438781 GCTCGAGGATCCACTAGTATGAG 59.561 52.174 15.82 9.52 0.00 2.90
2535 2595 3.073209 AGCTCGAGGATCCACTAGTATGA 59.927 47.826 15.82 0.00 0.00 2.15
2536 2596 3.190327 CAGCTCGAGGATCCACTAGTATG 59.810 52.174 15.82 8.74 0.00 2.39
2537 2597 3.073209 TCAGCTCGAGGATCCACTAGTAT 59.927 47.826 15.82 0.00 0.00 2.12
2538 2598 2.438392 TCAGCTCGAGGATCCACTAGTA 59.562 50.000 15.82 0.00 0.00 1.82
2539 2599 1.213182 TCAGCTCGAGGATCCACTAGT 59.787 52.381 15.82 0.00 0.00 2.57
2540 2600 1.606668 GTCAGCTCGAGGATCCACTAG 59.393 57.143 15.82 10.49 0.00 2.57
2541 2601 1.064685 TGTCAGCTCGAGGATCCACTA 60.065 52.381 15.82 0.00 0.00 2.74
2542 2602 0.323816 TGTCAGCTCGAGGATCCACT 60.324 55.000 15.82 0.00 0.00 4.00
2543 2603 0.749649 ATGTCAGCTCGAGGATCCAC 59.250 55.000 15.82 6.85 0.00 4.02
2544 2604 0.749049 CATGTCAGCTCGAGGATCCA 59.251 55.000 15.82 0.00 0.00 3.41
2545 2605 1.035923 TCATGTCAGCTCGAGGATCC 58.964 55.000 15.58 2.48 0.00 3.36
2546 2606 2.879002 TTCATGTCAGCTCGAGGATC 57.121 50.000 15.58 0.00 0.00 3.36
2547 2607 3.616956 TTTTCATGTCAGCTCGAGGAT 57.383 42.857 15.58 0.00 0.00 3.24
2548 2608 3.401033 TTTTTCATGTCAGCTCGAGGA 57.599 42.857 15.58 0.22 0.00 3.71
2565 2625 1.173913 GGCGGGCATGACTACTTTTT 58.826 50.000 0.00 0.00 0.00 1.94
2566 2626 0.679960 GGGCGGGCATGACTACTTTT 60.680 55.000 0.00 0.00 0.00 2.27
2591 2651 0.527817 GAAGCCGGTGGACTATCACG 60.528 60.000 1.90 0.00 38.46 4.35
2644 2704 4.153330 GGACGGCTAGGAGGGGGA 62.153 72.222 0.00 0.00 0.00 4.81
2655 2715 4.097361 GAGGGTGGGAAGGACGGC 62.097 72.222 0.00 0.00 0.00 5.68
2707 2767 2.035783 GGGAGGAAGCCCCACAAC 59.964 66.667 0.00 0.00 42.62 3.32
2804 3028 0.187361 AAAGGCCTAAAGGTGGTGCA 59.813 50.000 5.16 0.00 37.57 4.57
2823 3047 4.271533 GTGTCGGTAAGAACAACACAATGA 59.728 41.667 0.00 0.00 40.67 2.57


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

AutoCloner maintained by Alex Coulton.