Multiple sequence alignment - TraesCS5A01G311700

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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 TraesCS5A01G311700 chr5A 100.000 2242 0 0 461 2702 523449544 523451785 0.000000e+00 4141.0
1 TraesCS5A01G311700 chr5A 76.600 1500 230 70 809 2251 523136504 523137939 0.000000e+00 713.0
2 TraesCS5A01G311700 chr5A 85.246 366 44 8 1067 1424 522066671 522067034 4.250000e-98 368.0
3 TraesCS5A01G311700 chr5A 100.000 198 0 0 1 198 523449084 523449281 1.530000e-97 366.0
4 TraesCS5A01G311700 chr5D 95.255 1981 77 9 558 2527 411627183 411629157 0.000000e+00 3121.0
5 TraesCS5A01G311700 chr5D 81.102 926 126 33 813 1700 411196551 411197465 0.000000e+00 695.0
6 TraesCS5A01G311700 chr5D 85.833 360 46 5 1067 1424 410444223 410444579 7.060000e-101 377.0
7 TraesCS5A01G311700 chr5D 78.053 647 101 23 1050 1668 411225770 411225137 1.180000e-98 370.0
8 TraesCS5A01G311700 chr5D 88.000 175 14 2 2528 2702 411629394 411629561 1.640000e-47 200.0
9 TraesCS5A01G311700 chr5D 84.091 88 9 3 112 195 411627064 411627150 2.230000e-11 80.5
10 TraesCS5A01G311700 chr5B 91.357 2071 114 30 559 2612 493930992 493933014 0.000000e+00 2772.0
11 TraesCS5A01G311700 chr5B 76.282 1501 229 77 813 2253 493673860 493675293 0.000000e+00 682.0
12 TraesCS5A01G311700 chr5B 84.958 359 50 4 1068 1424 492619519 492619875 7.110000e-96 361.0
13 TraesCS5A01G311700 chr5B 100.000 46 0 0 69 114 493930828 493930873 4.790000e-13 86.1
14 TraesCS5A01G311700 chr5B 86.765 68 5 3 496 560 347686965 347687031 3.730000e-09 73.1
15 TraesCS5A01G311700 chrUn 87.671 73 4 4 488 557 470950218 470950148 2.230000e-11 80.5
16 TraesCS5A01G311700 chr3A 86.111 72 7 2 488 557 531947947 531947877 1.040000e-09 75.0
17 TraesCS5A01G311700 chr3A 97.619 42 1 0 519 560 601564397 601564356 3.730000e-09 73.1
18 TraesCS5A01G311700 chr7A 97.500 40 1 0 518 557 669548879 669548840 4.830000e-08 69.4


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 TraesCS5A01G311700 chr5A 523449084 523451785 2701 False 2253.500000 4141 100.000000 1 2702 2 chr5A.!!$F3 2701
1 TraesCS5A01G311700 chr5A 523136504 523137939 1435 False 713.000000 713 76.600000 809 2251 1 chr5A.!!$F2 1442
2 TraesCS5A01G311700 chr5D 411627064 411629561 2497 False 1133.833333 3121 89.115333 112 2702 3 chr5D.!!$F3 2590
3 TraesCS5A01G311700 chr5D 411196551 411197465 914 False 695.000000 695 81.102000 813 1700 1 chr5D.!!$F2 887
4 TraesCS5A01G311700 chr5D 411225137 411225770 633 True 370.000000 370 78.053000 1050 1668 1 chr5D.!!$R1 618
5 TraesCS5A01G311700 chr5B 493930828 493933014 2186 False 1429.050000 2772 95.678500 69 2612 2 chr5B.!!$F4 2543
6 TraesCS5A01G311700 chr5B 493673860 493675293 1433 False 682.000000 682 76.282000 813 2253 1 chr5B.!!$F3 1440

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
665 691 1.271817 CCTTGGAGCTTTCTTGCCTCT 60.272 52.381 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2145 0.61782 TACTTGGCCCACCTCTCTCC 60.618 60.0 0.0 0.0 36.63 3.71 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
46 47 4.173036 GTTTTCGAAATCCTGCCAATCA 57.827 40.909 12.12 0.00 0.00 2.57
47 48 4.555262 GTTTTCGAAATCCTGCCAATCAA 58.445 39.130 12.12 0.00 0.00 2.57
48 49 4.862902 TTTCGAAATCCTGCCAATCAAA 57.137 36.364 6.47 0.00 0.00 2.69
49 50 4.439305 TTCGAAATCCTGCCAATCAAAG 57.561 40.909 0.00 0.00 0.00 2.77
50 51 3.684908 TCGAAATCCTGCCAATCAAAGA 58.315 40.909 0.00 0.00 0.00 2.52
51 52 3.691118 TCGAAATCCTGCCAATCAAAGAG 59.309 43.478 0.00 0.00 0.00 2.85
52 53 3.181493 CGAAATCCTGCCAATCAAAGAGG 60.181 47.826 0.00 0.00 0.00 3.69
56 57 4.440145 GCCAATCAAAGAGGCCCA 57.560 55.556 0.00 0.00 42.58 5.36
57 58 2.906268 GCCAATCAAAGAGGCCCAT 58.094 52.632 0.00 0.00 42.58 4.00
58 59 2.071778 GCCAATCAAAGAGGCCCATA 57.928 50.000 0.00 0.00 42.58 2.74
59 60 1.959282 GCCAATCAAAGAGGCCCATAG 59.041 52.381 0.00 0.00 42.58 2.23
60 61 2.687914 GCCAATCAAAGAGGCCCATAGT 60.688 50.000 0.00 0.00 42.58 2.12
61 62 2.954318 CCAATCAAAGAGGCCCATAGTG 59.046 50.000 0.00 0.00 0.00 2.74
62 63 3.624777 CAATCAAAGAGGCCCATAGTGT 58.375 45.455 0.00 0.00 0.00 3.55
63 64 4.019174 CAATCAAAGAGGCCCATAGTGTT 58.981 43.478 0.00 0.00 0.00 3.32
64 65 3.806949 TCAAAGAGGCCCATAGTGTTT 57.193 42.857 0.00 0.00 0.00 2.83
65 66 4.112634 TCAAAGAGGCCCATAGTGTTTT 57.887 40.909 0.00 0.00 0.00 2.43
66 67 4.479158 TCAAAGAGGCCCATAGTGTTTTT 58.521 39.130 0.00 0.00 0.00 1.94
114 133 4.229876 GCTTGTGATTGCAAAAGTAGGTC 58.770 43.478 1.71 0.00 40.75 3.85
124 143 8.615878 ATTGCAAAAGTAGGTCGCATATTATA 57.384 30.769 1.71 0.00 31.67 0.98
153 172 7.852945 CAGTAACATTCTTGTTTCTCTGTGTTC 59.147 37.037 0.00 0.00 43.57 3.18
159 178 6.757897 TCTTGTTTCTCTGTGTTCAACATT 57.242 33.333 0.00 0.00 38.39 2.71
160 179 7.156876 TCTTGTTTCTCTGTGTTCAACATTT 57.843 32.000 0.00 0.00 38.39 2.32
480 506 3.604875 GGTCTACCCTCGTGAAAATCA 57.395 47.619 0.00 0.00 0.00 2.57
481 507 3.522553 GGTCTACCCTCGTGAAAATCAG 58.477 50.000 0.00 0.00 0.00 2.90
482 508 3.194968 GGTCTACCCTCGTGAAAATCAGA 59.805 47.826 0.00 0.00 0.00 3.27
483 509 4.425520 GTCTACCCTCGTGAAAATCAGAG 58.574 47.826 0.00 0.00 0.00 3.35
487 513 3.550437 CCTCGTGAAAATCAGAGGGAT 57.450 47.619 13.54 0.00 44.78 3.85
488 514 3.201290 CCTCGTGAAAATCAGAGGGATG 58.799 50.000 13.54 0.00 44.78 3.51
489 515 3.201290 CTCGTGAAAATCAGAGGGATGG 58.799 50.000 0.00 0.00 36.02 3.51
490 516 2.571653 TCGTGAAAATCAGAGGGATGGT 59.428 45.455 0.00 0.00 36.02 3.55
491 517 3.009033 TCGTGAAAATCAGAGGGATGGTT 59.991 43.478 0.00 0.00 36.02 3.67
492 518 4.224147 TCGTGAAAATCAGAGGGATGGTTA 59.776 41.667 0.00 0.00 36.02 2.85
493 519 4.572389 CGTGAAAATCAGAGGGATGGTTAG 59.428 45.833 0.00 0.00 36.02 2.34
494 520 4.336713 GTGAAAATCAGAGGGATGGTTAGC 59.663 45.833 0.00 0.00 36.02 3.09
495 521 4.228210 TGAAAATCAGAGGGATGGTTAGCT 59.772 41.667 0.00 0.00 36.02 3.32
496 522 5.428457 TGAAAATCAGAGGGATGGTTAGCTA 59.572 40.000 0.00 0.00 36.02 3.32
497 523 5.559148 AAATCAGAGGGATGGTTAGCTAG 57.441 43.478 0.00 0.00 36.02 3.42
498 524 3.973472 TCAGAGGGATGGTTAGCTAGA 57.027 47.619 0.00 0.00 0.00 2.43
499 525 4.265856 TCAGAGGGATGGTTAGCTAGAA 57.734 45.455 0.00 0.00 0.00 2.10
500 526 4.820775 TCAGAGGGATGGTTAGCTAGAAT 58.179 43.478 0.00 0.00 0.00 2.40
501 527 4.590647 TCAGAGGGATGGTTAGCTAGAATG 59.409 45.833 0.00 0.00 0.00 2.67
502 528 4.590647 CAGAGGGATGGTTAGCTAGAATGA 59.409 45.833 0.00 0.00 0.00 2.57
503 529 5.070981 CAGAGGGATGGTTAGCTAGAATGAA 59.929 44.000 0.00 0.00 0.00 2.57
504 530 5.667626 AGAGGGATGGTTAGCTAGAATGAAA 59.332 40.000 0.00 0.00 0.00 2.69
505 531 6.158695 AGAGGGATGGTTAGCTAGAATGAAAA 59.841 38.462 0.00 0.00 0.00 2.29
506 532 6.731467 AGGGATGGTTAGCTAGAATGAAAAA 58.269 36.000 0.00 0.00 0.00 1.94
529 555 8.682128 AAAATTGTAGCCAATGTAATTACGTG 57.318 30.769 11.06 10.83 40.42 4.49
530 556 6.995511 ATTGTAGCCAATGTAATTACGTGT 57.004 33.333 11.06 0.00 39.81 4.49
531 557 8.495361 AATTGTAGCCAATGTAATTACGTGTA 57.505 30.769 11.06 0.00 40.42 2.90
532 558 7.902387 TTGTAGCCAATGTAATTACGTGTAA 57.098 32.000 11.06 0.00 32.46 2.41
533 559 7.293402 TGTAGCCAATGTAATTACGTGTAAC 57.707 36.000 11.06 8.97 32.46 2.50
534 560 7.098477 TGTAGCCAATGTAATTACGTGTAACT 58.902 34.615 11.06 8.95 32.46 2.24
535 561 6.657836 AGCCAATGTAATTACGTGTAACTC 57.342 37.500 11.06 0.00 32.46 3.01
536 562 6.403878 AGCCAATGTAATTACGTGTAACTCT 58.596 36.000 11.06 1.50 32.46 3.24
537 563 6.877322 AGCCAATGTAATTACGTGTAACTCTT 59.123 34.615 11.06 0.00 32.46 2.85
538 564 7.389607 AGCCAATGTAATTACGTGTAACTCTTT 59.610 33.333 11.06 0.00 32.46 2.52
539 565 7.480542 GCCAATGTAATTACGTGTAACTCTTTG 59.519 37.037 11.06 2.86 32.46 2.77
540 566 8.500773 CCAATGTAATTACGTGTAACTCTTTGT 58.499 33.333 11.06 0.00 32.46 2.83
544 570 9.695526 TGTAATTACGTGTAACTCTTTGTATGT 57.304 29.630 10.92 0.00 31.75 2.29
548 574 9.784680 ATTACGTGTAACTCTTTGTATGTCTAG 57.215 33.333 0.00 0.00 31.75 2.43
549 575 6.091437 ACGTGTAACTCTTTGTATGTCTAGC 58.909 40.000 0.00 0.00 31.75 3.42
550 576 6.090783 CGTGTAACTCTTTGTATGTCTAGCA 58.909 40.000 0.00 0.00 31.75 3.49
551 577 6.752351 CGTGTAACTCTTTGTATGTCTAGCAT 59.248 38.462 5.25 5.25 36.70 3.79
552 578 7.275779 CGTGTAACTCTTTGTATGTCTAGCATT 59.724 37.037 5.22 0.00 35.02 3.56
553 579 9.582431 GTGTAACTCTTTGTATGTCTAGCATTA 57.418 33.333 5.22 0.00 38.94 1.90
646 672 1.648467 GCGCTCCTTGTCCAATGTCC 61.648 60.000 0.00 0.00 0.00 4.02
665 691 1.271817 CCTTGGAGCTTTCTTGCCTCT 60.272 52.381 0.00 0.00 0.00 3.69
932 963 1.280133 CCCATCTCAAGCTCAACCTGA 59.720 52.381 0.00 0.00 0.00 3.86
994 1029 4.643387 GCCAGCACCGACCACCTT 62.643 66.667 0.00 0.00 0.00 3.50
1036 1074 1.606531 GACCAGCAATGGAGCTCCT 59.393 57.895 32.28 15.91 44.54 3.69
1767 1866 8.139989 GCAGTTGATTCCAGCATAATAAAATCT 58.860 33.333 0.00 0.00 0.00 2.40
1769 1868 8.139989 AGTTGATTCCAGCATAATAAAATCTGC 58.860 33.333 0.00 0.00 34.85 4.26
1847 1946 3.911989 GCAATCAGATGCGGTTCTG 57.088 52.632 5.10 5.10 43.70 3.02
1915 2029 2.602257 TGCTGGATGAATAGTCGTGG 57.398 50.000 0.00 0.00 0.00 4.94
2027 2145 3.201290 AGATCAACGCTTGCTAATCAGG 58.799 45.455 0.00 0.00 0.00 3.86
2259 2390 3.731264 GCTGATGTGTCACGTAGTACCTC 60.731 52.174 0.00 0.00 41.61 3.85
2322 2453 4.607293 TCAGATTTAGTGTGACTGTGCT 57.393 40.909 0.00 0.00 0.00 4.40
2345 2479 7.280428 TGCTAGTGACTAGTACTTGATAGTGTC 59.720 40.741 19.80 5.10 36.53 3.67
2358 2492 8.420374 ACTTGATAGTGTCGTACAATAATTGG 57.580 34.615 0.00 0.00 32.13 3.16
2415 2549 3.059884 GCATTCTTCGAGTGAACAGTCA 58.940 45.455 9.76 0.00 0.00 3.41
2519 2654 3.258372 TCTTGTACTGCTGGAATCGTCTT 59.742 43.478 0.00 0.00 0.00 3.01
2520 2655 2.959516 TGTACTGCTGGAATCGTCTTG 58.040 47.619 0.00 0.00 0.00 3.02
2521 2656 2.299013 TGTACTGCTGGAATCGTCTTGT 59.701 45.455 0.00 0.00 0.00 3.16
2522 2657 3.508402 TGTACTGCTGGAATCGTCTTGTA 59.492 43.478 0.00 0.00 0.00 2.41
2523 2658 2.960819 ACTGCTGGAATCGTCTTGTAC 58.039 47.619 0.00 0.00 0.00 2.90
2524 2659 2.299013 ACTGCTGGAATCGTCTTGTACA 59.701 45.455 0.00 0.00 0.00 2.90
2525 2660 3.055819 ACTGCTGGAATCGTCTTGTACAT 60.056 43.478 0.00 0.00 0.00 2.29
2526 2661 4.159693 ACTGCTGGAATCGTCTTGTACATA 59.840 41.667 0.00 0.00 0.00 2.29
2573 2945 1.780860 CCGCGCAAACAAGAAAGAAAG 59.219 47.619 8.75 0.00 0.00 2.62
2643 3018 1.270907 ACTCCAACTCCCAGCTAGTG 58.729 55.000 0.00 0.00 0.00 2.74
2670 3045 4.475135 GGCTCCGCTTCCAGGGTC 62.475 72.222 0.00 0.00 0.00 4.46
2692 3067 3.959975 GCGCGTGTGGCTCCAAAA 61.960 61.111 8.43 0.00 40.44 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.012232 AGGATTTCGAAAACGTGGTAGTAAAAA 59.988 33.333 15.66 0.00 0.00 1.94
13 14 6.482973 AGGATTTCGAAAACGTGGTAGTAAAA 59.517 34.615 15.66 0.00 0.00 1.52
14 15 5.990996 AGGATTTCGAAAACGTGGTAGTAAA 59.009 36.000 15.66 0.00 0.00 2.01
15 16 5.406175 CAGGATTTCGAAAACGTGGTAGTAA 59.594 40.000 24.66 0.00 0.00 2.24
16 17 4.925054 CAGGATTTCGAAAACGTGGTAGTA 59.075 41.667 24.66 0.00 0.00 1.82
17 18 3.744426 CAGGATTTCGAAAACGTGGTAGT 59.256 43.478 24.66 4.12 0.00 2.73
18 19 3.424433 GCAGGATTTCGAAAACGTGGTAG 60.424 47.826 29.66 13.96 30.43 3.18
19 20 2.481185 GCAGGATTTCGAAAACGTGGTA 59.519 45.455 29.66 4.02 30.43 3.25
20 21 1.265905 GCAGGATTTCGAAAACGTGGT 59.734 47.619 29.66 10.33 30.43 4.16
21 22 1.401018 GGCAGGATTTCGAAAACGTGG 60.401 52.381 29.66 17.87 30.43 4.94
22 23 1.265635 TGGCAGGATTTCGAAAACGTG 59.734 47.619 26.75 26.75 32.14 4.49
23 24 1.600023 TGGCAGGATTTCGAAAACGT 58.400 45.000 15.66 11.11 0.00 3.99
24 25 2.697431 TTGGCAGGATTTCGAAAACG 57.303 45.000 15.66 4.89 0.00 3.60
25 26 4.173036 TGATTGGCAGGATTTCGAAAAC 57.827 40.909 15.66 12.33 0.00 2.43
26 27 4.862902 TTGATTGGCAGGATTTCGAAAA 57.137 36.364 15.66 0.00 0.00 2.29
27 28 4.522405 TCTTTGATTGGCAGGATTTCGAAA 59.478 37.500 13.91 13.91 0.00 3.46
28 29 4.078537 TCTTTGATTGGCAGGATTTCGAA 58.921 39.130 0.00 0.00 0.00 3.71
29 30 3.684908 TCTTTGATTGGCAGGATTTCGA 58.315 40.909 0.00 0.00 0.00 3.71
30 31 3.181493 CCTCTTTGATTGGCAGGATTTCG 60.181 47.826 0.00 0.00 0.00 3.46
31 32 3.429960 GCCTCTTTGATTGGCAGGATTTC 60.430 47.826 0.00 0.00 45.46 2.17
32 33 2.498885 GCCTCTTTGATTGGCAGGATTT 59.501 45.455 0.00 0.00 45.46 2.17
33 34 2.105766 GCCTCTTTGATTGGCAGGATT 58.894 47.619 0.00 0.00 45.46 3.01
34 35 1.772836 GCCTCTTTGATTGGCAGGAT 58.227 50.000 0.00 0.00 45.46 3.24
35 36 3.271250 GCCTCTTTGATTGGCAGGA 57.729 52.632 0.00 0.00 45.46 3.86
39 40 1.959282 CTATGGGCCTCTTTGATTGGC 59.041 52.381 4.53 0.00 45.42 4.52
40 41 2.954318 CACTATGGGCCTCTTTGATTGG 59.046 50.000 4.53 0.00 0.00 3.16
41 42 3.624777 ACACTATGGGCCTCTTTGATTG 58.375 45.455 4.53 0.00 0.00 2.67
42 43 4.322057 AACACTATGGGCCTCTTTGATT 57.678 40.909 4.53 0.00 0.00 2.57
43 44 4.322057 AAACACTATGGGCCTCTTTGAT 57.678 40.909 4.53 0.00 0.00 2.57
44 45 3.806949 AAACACTATGGGCCTCTTTGA 57.193 42.857 4.53 0.00 0.00 2.69
45 46 4.871933 AAAAACACTATGGGCCTCTTTG 57.128 40.909 4.53 0.00 0.00 2.77
64 65 3.766676 TTGAGCGTACACAAGCAAAAA 57.233 38.095 0.00 0.00 35.48 1.94
65 66 3.563808 AGATTGAGCGTACACAAGCAAAA 59.436 39.130 12.60 0.12 35.55 2.44
66 67 3.058983 CAGATTGAGCGTACACAAGCAAA 60.059 43.478 12.60 0.40 35.55 3.68
67 68 2.480037 CAGATTGAGCGTACACAAGCAA 59.520 45.455 12.60 0.00 35.55 3.91
159 178 9.478768 TCGTGTACAATATACTCTTGTGAAAAA 57.521 29.630 0.00 0.00 37.41 1.94
160 179 9.135843 CTCGTGTACAATATACTCTTGTGAAAA 57.864 33.333 0.00 0.00 37.41 2.29
164 183 7.429630 CAGTCTCGTGTACAATATACTCTTGTG 59.570 40.741 0.00 0.00 37.41 3.33
165 184 7.120873 ACAGTCTCGTGTACAATATACTCTTGT 59.879 37.037 0.00 0.00 39.93 3.16
166 185 7.473366 ACAGTCTCGTGTACAATATACTCTTG 58.527 38.462 0.00 0.00 0.00 3.02
167 186 7.627298 ACAGTCTCGTGTACAATATACTCTT 57.373 36.000 0.00 0.00 0.00 2.85
168 187 7.986320 ACTACAGTCTCGTGTACAATATACTCT 59.014 37.037 0.00 0.00 31.46 3.24
170 189 9.605275 TTACTACAGTCTCGTGTACAATATACT 57.395 33.333 0.00 0.00 31.46 2.12
460 486 3.194968 TCTGATTTTCACGAGGGTAGACC 59.805 47.826 0.00 0.00 40.67 3.85
461 487 4.425520 CTCTGATTTTCACGAGGGTAGAC 58.574 47.826 0.00 0.00 0.00 2.59
462 488 3.447586 CCTCTGATTTTCACGAGGGTAGA 59.552 47.826 11.84 0.00 37.76 2.59
463 489 3.430929 CCCTCTGATTTTCACGAGGGTAG 60.431 52.174 21.62 7.78 45.99 3.18
464 490 2.500098 CCCTCTGATTTTCACGAGGGTA 59.500 50.000 21.62 0.00 45.99 3.69
465 491 1.279271 CCCTCTGATTTTCACGAGGGT 59.721 52.381 21.62 0.00 45.99 4.34
466 492 2.029838 CCCTCTGATTTTCACGAGGG 57.970 55.000 18.95 18.95 45.95 4.30
467 493 3.201290 CATCCCTCTGATTTTCACGAGG 58.799 50.000 12.36 12.36 39.43 4.63
468 494 3.201290 CCATCCCTCTGATTTTCACGAG 58.799 50.000 0.00 0.00 0.00 4.18
469 495 2.571653 ACCATCCCTCTGATTTTCACGA 59.428 45.455 0.00 0.00 0.00 4.35
470 496 2.991250 ACCATCCCTCTGATTTTCACG 58.009 47.619 0.00 0.00 0.00 4.35
471 497 4.336713 GCTAACCATCCCTCTGATTTTCAC 59.663 45.833 0.00 0.00 0.00 3.18
472 498 4.228210 AGCTAACCATCCCTCTGATTTTCA 59.772 41.667 0.00 0.00 0.00 2.69
473 499 4.786425 AGCTAACCATCCCTCTGATTTTC 58.214 43.478 0.00 0.00 0.00 2.29
474 500 4.870021 AGCTAACCATCCCTCTGATTTT 57.130 40.909 0.00 0.00 0.00 1.82
475 501 5.219739 TCTAGCTAACCATCCCTCTGATTT 58.780 41.667 0.00 0.00 0.00 2.17
476 502 4.820775 TCTAGCTAACCATCCCTCTGATT 58.179 43.478 0.00 0.00 0.00 2.57
477 503 4.477536 TCTAGCTAACCATCCCTCTGAT 57.522 45.455 0.00 0.00 0.00 2.90
478 504 3.973472 TCTAGCTAACCATCCCTCTGA 57.027 47.619 0.00 0.00 0.00 3.27
479 505 4.590647 TCATTCTAGCTAACCATCCCTCTG 59.409 45.833 0.00 0.00 0.00 3.35
480 506 4.820775 TCATTCTAGCTAACCATCCCTCT 58.179 43.478 0.00 0.00 0.00 3.69
481 507 5.552870 TTCATTCTAGCTAACCATCCCTC 57.447 43.478 0.00 0.00 0.00 4.30
482 508 5.975988 TTTCATTCTAGCTAACCATCCCT 57.024 39.130 0.00 0.00 0.00 4.20
503 529 9.134734 CACGTAATTACATTGGCTACAATTTTT 57.865 29.630 15.67 0.00 44.69 1.94
504 530 8.301002 ACACGTAATTACATTGGCTACAATTTT 58.699 29.630 15.67 0.00 44.69 1.82
505 531 7.822658 ACACGTAATTACATTGGCTACAATTT 58.177 30.769 15.67 0.00 44.69 1.82
506 532 7.385778 ACACGTAATTACATTGGCTACAATT 57.614 32.000 15.67 0.00 44.69 2.32
508 534 7.603404 AGTTACACGTAATTACATTGGCTACAA 59.397 33.333 15.67 0.00 41.59 2.41
509 535 7.098477 AGTTACACGTAATTACATTGGCTACA 58.902 34.615 15.67 0.00 0.00 2.74
510 536 7.490402 AGAGTTACACGTAATTACATTGGCTAC 59.510 37.037 15.67 10.35 0.00 3.58
511 537 7.549839 AGAGTTACACGTAATTACATTGGCTA 58.450 34.615 15.67 0.00 0.00 3.93
512 538 6.403878 AGAGTTACACGTAATTACATTGGCT 58.596 36.000 15.67 10.61 0.00 4.75
513 539 6.657836 AGAGTTACACGTAATTACATTGGC 57.342 37.500 15.67 6.90 0.00 4.52
514 540 8.500773 ACAAAGAGTTACACGTAATTACATTGG 58.499 33.333 15.67 1.93 0.00 3.16
518 544 9.695526 ACATACAAAGAGTTACACGTAATTACA 57.304 29.630 15.67 0.00 0.00 2.41
522 548 9.784680 CTAGACATACAAAGAGTTACACGTAAT 57.215 33.333 0.00 0.00 0.00 1.89
523 549 7.752239 GCTAGACATACAAAGAGTTACACGTAA 59.248 37.037 0.00 0.00 0.00 3.18
524 550 7.094677 TGCTAGACATACAAAGAGTTACACGTA 60.095 37.037 0.00 0.00 0.00 3.57
525 551 6.091437 GCTAGACATACAAAGAGTTACACGT 58.909 40.000 0.00 0.00 0.00 4.49
526 552 6.090783 TGCTAGACATACAAAGAGTTACACG 58.909 40.000 0.00 0.00 0.00 4.49
527 553 8.480643 AATGCTAGACATACAAAGAGTTACAC 57.519 34.615 0.00 0.00 38.34 2.90
553 579 8.707449 ACCAAGATGGATAATTGTTAATGCAAT 58.293 29.630 2.85 0.00 40.96 3.56
554 580 8.076910 ACCAAGATGGATAATTGTTAATGCAA 57.923 30.769 2.85 0.00 40.96 4.08
555 581 7.341512 TGACCAAGATGGATAATTGTTAATGCA 59.658 33.333 2.85 0.00 40.96 3.96
556 582 7.715657 TGACCAAGATGGATAATTGTTAATGC 58.284 34.615 2.85 0.00 40.96 3.56
646 672 1.811359 CAGAGGCAAGAAAGCTCCAAG 59.189 52.381 0.00 0.00 34.17 3.61
665 691 2.223502 CGCGTTATCTTGTCCTCTAGCA 60.224 50.000 0.00 0.00 0.00 3.49
932 963 3.034635 GGTGGTCTATGGAGTGTGAGAT 58.965 50.000 0.00 0.00 0.00 2.75
994 1029 1.141665 CGGTCATGTCCATCGCTGA 59.858 57.895 9.71 0.00 0.00 4.26
1036 1074 3.796443 CGACGACGGCGAGGAAGA 61.796 66.667 22.49 0.00 41.64 2.87
1206 1247 1.288127 GTCGGCTGTGAGGTACGTT 59.712 57.895 0.00 0.00 0.00 3.99
1815 1914 6.016860 GCATCTGATTGCATGTATACCAAAGA 60.017 38.462 0.00 0.00 42.31 2.52
1915 2029 2.667199 CCGTTTGTCCGGGACCAC 60.667 66.667 23.81 18.28 44.32 4.16
1939 2053 6.371278 AGTGATAGTACCCTCCTTTCGAATA 58.629 40.000 0.00 0.00 0.00 1.75
2001 2119 4.928661 TTAGCAAGCGTTGATCTTTCTC 57.071 40.909 0.00 0.00 0.00 2.87
2027 2145 0.617820 TACTTGGCCCACCTCTCTCC 60.618 60.000 0.00 0.00 36.63 3.71
2259 2390 8.965172 CACATGTCATCTTCAAAAGAAAGAAAG 58.035 33.333 0.00 0.00 41.63 2.62
2322 2453 7.326454 ACGACACTATCAAGTACTAGTCACTA 58.674 38.462 0.00 0.00 33.48 2.74
2345 2479 6.130298 TCAATTCTGCCCAATTATTGTACG 57.870 37.500 4.15 0.00 0.00 3.67
2358 2492 5.010012 CCTATACACCCAAATCAATTCTGCC 59.990 44.000 0.00 0.00 0.00 4.85
2462 2596 1.073923 TGCCAAAGGAGGGAGAAGAAC 59.926 52.381 0.00 0.00 0.00 3.01
2526 2661 9.397280 GAGGAAAGGACAGCTTAAAATATACTT 57.603 33.333 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.