Multiple sequence alignment - TraesCS4A01G084800

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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 TraesCS4A01G084800 chr4A 100.000 3138 0 0 1 3138 89450166 89447029 0.000000e+00 5795.0
1 TraesCS4A01G084800 chr4A 100.000 30 0 0 2499 2528 89447632 89447603 4.370000e-04 56.5
2 TraesCS4A01G084800 chr4A 100.000 30 0 0 2535 2564 89447668 89447639 4.370000e-04 56.5
3 TraesCS4A01G084800 chr4D 92.960 1946 86 26 614 2532 375118642 375120563 0.000000e+00 2787.0
4 TraesCS4A01G084800 chr4D 91.497 541 23 6 1 541 375076335 375076852 0.000000e+00 723.0
5 TraesCS4A01G084800 chr4D 88.468 581 11 11 2582 3136 375120547 375121097 0.000000e+00 651.0
6 TraesCS4A01G084800 chr4D 96.053 76 2 1 535 610 375077706 375077780 4.250000e-24 122.0
7 TraesCS4A01G084800 chr4B 90.417 1847 132 29 649 2486 462211269 462213079 0.000000e+00 2388.0
8 TraesCS4A01G084800 chr4B 87.193 570 27 17 2582 3136 462213123 462213661 9.630000e-170 606.0
9 TraesCS4A01G084800 chr4B 98.039 255 5 0 1 255 462206969 462207223 7.990000e-121 444.0
10 TraesCS4A01G084800 chr4B 100.000 61 0 0 550 610 462207240 462207300 2.560000e-21 113.0
11 TraesCS4A01G084800 chr5D 82.313 147 20 5 2992 3136 69099957 69099815 4.250000e-24 122.0
12 TraesCS4A01G084800 chr5A 82.313 147 20 5 2992 3136 59704452 59704310 4.250000e-24 122.0


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 TraesCS4A01G084800 chr4A 89447029 89450166 3137 True 1969.333333 5795 100.00000 1 3138 3 chr4A.!!$R1 3137
1 TraesCS4A01G084800 chr4D 375118642 375121097 2455 False 1719.000000 2787 90.71400 614 3136 2 chr4D.!!$F2 2522
2 TraesCS4A01G084800 chr4D 375076335 375077780 1445 False 422.500000 723 93.77500 1 610 2 chr4D.!!$F1 609
3 TraesCS4A01G084800 chr4B 462206969 462213661 6692 False 887.750000 2388 93.91225 1 3136 4 chr4B.!!$F1 3135

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
876 5670 0.109597 CCACGCAAAGGATCAGCAAC 60.110 55.0 0.0 0.0 0.00 4.17 F
1196 5991 0.455464 CATACCGACGACACGAAGCA 60.455 55.0 0.0 0.0 35.09 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 6494 0.249911 GACAACGCCTGTGAACTCCT 60.250 55.0 0.00 0.0 38.84 3.69 R
2342 7140 0.255890 CCACTAGGGGTTGGTCCATG 59.744 60.0 1.53 0.0 38.11 3.66 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
105 106 6.820470 TTAAAAAGCAAGTCGGACATTTTG 57.180 33.333 11.27 7.50 0.00 2.44
263 264 7.106239 ACTATTAATTTGAGTGACAGACCTGG 58.894 38.462 0.00 0.00 34.19 4.45
270 271 3.157518 TGACAGACCTGGCACCTTA 57.842 52.632 0.59 0.00 45.07 2.69
380 381 1.282157 ACTCCCTGGCAATGTTCCTAC 59.718 52.381 0.00 0.00 0.00 3.18
389 390 3.265791 GCAATGTTCCTACTGTCTGGAG 58.734 50.000 3.32 0.00 33.46 3.86
390 391 3.055819 GCAATGTTCCTACTGTCTGGAGA 60.056 47.826 3.32 0.00 33.46 3.71
391 392 4.383552 GCAATGTTCCTACTGTCTGGAGAT 60.384 45.833 3.32 0.00 33.46 2.75
392 393 5.738909 CAATGTTCCTACTGTCTGGAGATT 58.261 41.667 3.32 4.08 33.46 2.40
532 533 3.643320 TGAACATGAGTCCTCTTGTCACT 59.357 43.478 14.07 2.17 44.08 3.41
651 4647 2.721797 GCGTGTGCAAAATACACTCTCG 60.722 50.000 0.00 0.00 44.70 4.04
673 5463 2.582978 GGTAACCAGCGAGGGTCC 59.417 66.667 3.26 0.00 41.32 4.46
681 5471 3.140814 GCGAGGGTCCCATTTGCC 61.141 66.667 11.55 0.00 0.00 4.52
752 5542 5.202765 TGGATGTCATGGCATGTTAAATCT 58.797 37.500 25.62 6.31 0.00 2.40
851 5645 3.502672 CCATCTGATCATCTCCCTCCTCT 60.503 52.174 0.00 0.00 0.00 3.69
852 5646 3.524095 TCTGATCATCTCCCTCCTCTC 57.476 52.381 0.00 0.00 0.00 3.20
876 5670 0.109597 CCACGCAAAGGATCAGCAAC 60.110 55.000 0.00 0.00 0.00 4.17
905 5699 0.960364 ATCAGCATCCAAACGCCGTT 60.960 50.000 0.00 0.00 0.00 4.44
934 5728 3.715628 GCAATTAGCAATCCACCGAAT 57.284 42.857 0.00 0.00 44.79 3.34
935 5729 4.829064 GCAATTAGCAATCCACCGAATA 57.171 40.909 0.00 0.00 44.79 1.75
936 5730 5.376854 GCAATTAGCAATCCACCGAATAT 57.623 39.130 0.00 0.00 44.79 1.28
939 5733 6.801862 GCAATTAGCAATCCACCGAATATAAC 59.198 38.462 0.00 0.00 44.79 1.89
949 5743 9.793259 AATCCACCGAATATAACATAACAGAAT 57.207 29.630 0.00 0.00 0.00 2.40
960 5754 5.824904 ACATAACAGAATAGCAAAGCCAG 57.175 39.130 0.00 0.00 0.00 4.85
1014 5809 1.152368 GGCCATGGGATTCCTCCAG 59.848 63.158 15.13 0.00 44.08 3.86
1032 5827 0.605589 AGAAGACCTCCAAGCAGACG 59.394 55.000 0.00 0.00 0.00 4.18
1190 5985 2.785105 GCGTGCATACCGACGACAC 61.785 63.158 0.00 0.00 37.81 3.67
1196 5991 0.455464 CATACCGACGACACGAAGCA 60.455 55.000 0.00 0.00 35.09 3.91
1209 6004 1.831389 CGAAGCAAGACGTGGTGGTG 61.831 60.000 0.00 0.00 38.21 4.17
1225 6020 3.664888 TGCCCTTGGATGCAGGCT 61.665 61.111 16.71 0.00 45.94 4.58
1343 6138 2.056815 ATCGAGCAGGCTGAGCAGA 61.057 57.895 20.86 11.51 0.00 4.26
1412 6207 6.333416 TCTCATCTTTGGTTCTCTATGTTCG 58.667 40.000 0.00 0.00 0.00 3.95
1421 6216 4.151867 GGTTCTCTATGTTCGTTGGACAAC 59.848 45.833 5.14 5.14 37.92 3.32
1447 6242 1.176527 TGCTATTCTGTTTGGGCTGC 58.823 50.000 0.00 0.00 0.00 5.25
1655 6452 4.963276 TTTGATCATTTTCTAGCGGGTG 57.037 40.909 0.00 0.00 0.00 4.61
1682 6479 1.434555 TCCGCAGTGTAAAATGGACG 58.565 50.000 0.00 0.00 0.00 4.79
1686 6483 2.695359 GCAGTGTAAAATGGACGGAGA 58.305 47.619 0.00 0.00 0.00 3.71
1716 6514 0.249911 AGGAGTTCACAGGCGTTGTC 60.250 55.000 0.00 0.00 38.16 3.18
1802 6600 0.976641 AGTGACCAAAGAGATCGCCA 59.023 50.000 0.00 0.00 0.00 5.69
1867 6665 1.416401 ACGGAGGATGGCAACGATATT 59.584 47.619 0.00 0.00 42.51 1.28
1901 6699 0.473755 TGAGCTCCAAGAAGCAACCA 59.526 50.000 12.15 0.00 45.00 3.67
2038 6836 2.531483 ATACACCCGGGCTGGAGAGT 62.531 60.000 24.08 11.49 42.00 3.24
2053 6851 2.417924 GGAGAGTGACGAGAATGTGCAT 60.418 50.000 0.00 0.00 0.00 3.96
2090 6888 3.838903 TGATGGATCAGATGATGAGGAGG 59.161 47.826 0.00 0.00 42.53 4.30
2145 6943 1.142667 TGGGTGTGCATGAGAACTGAA 59.857 47.619 0.00 0.00 0.00 3.02
2167 6965 0.820871 GACGACCTTCCTCTGCATCT 59.179 55.000 0.00 0.00 0.00 2.90
2255 7053 7.595311 TGTGAATAGACATGAATACACACAC 57.405 36.000 0.00 0.00 33.22 3.82
2274 7072 7.348956 CACACACGTGTAATTTCAAACTATCA 58.651 34.615 22.90 0.00 42.83 2.15
2276 7074 7.853929 ACACACGTGTAATTTCAAACTATCAAC 59.146 33.333 22.90 0.00 42.90 3.18
2277 7075 8.067784 CACACGTGTAATTTCAAACTATCAACT 58.932 33.333 22.90 0.00 0.00 3.16
2329 7127 9.072375 CAGTCAACTGGAGTATCATCTATAAGA 57.928 37.037 2.08 0.00 40.20 2.10
2349 7147 6.521151 AAGAAATGTCAATTCTCATGGACC 57.479 37.500 3.61 0.00 36.14 4.46
2350 7148 5.573219 AGAAATGTCAATTCTCATGGACCA 58.427 37.500 0.00 0.00 31.61 4.02
2399 7206 5.789643 AACCACATTGCTTAACAGTCATT 57.210 34.783 0.00 0.00 0.00 2.57
2429 7236 0.107508 TCACCTATCTGCTGCTTGGC 60.108 55.000 0.00 0.00 0.00 4.52
2469 7276 7.762615 CACCTTGATTTGATGATGTTGCTTTAT 59.237 33.333 0.00 0.00 0.00 1.40
2488 7307 6.824704 GCTTTATAGTAACCACCATACCAACA 59.175 38.462 0.00 0.00 0.00 3.33
2509 7328 9.859427 CCAACATATCTTTAATGTCATGTTGTT 57.141 29.630 26.27 12.84 45.91 2.83
2541 7360 9.979578 ATTTTTGTAACATATGTTGTGTCATGT 57.020 25.926 27.62 3.92 38.99 3.21
2542 7361 9.809096 TTTTTGTAACATATGTTGTGTCATGTT 57.191 25.926 27.62 4.99 42.57 2.71
2543 7362 8.794308 TTTGTAACATATGTTGTGTCATGTTG 57.206 30.769 27.62 0.00 40.73 3.33
2544 7363 7.503521 TGTAACATATGTTGTGTCATGTTGT 57.496 32.000 27.62 2.50 40.73 3.32
2545 7364 7.935520 TGTAACATATGTTGTGTCATGTTGTT 58.064 30.769 27.62 2.88 40.73 2.83
2546 7365 8.073167 TGTAACATATGTTGTGTCATGTTGTTC 58.927 33.333 27.62 0.00 40.73 3.18
2547 7366 6.631971 ACATATGTTGTGTCATGTTGTTCA 57.368 33.333 1.41 0.00 37.11 3.18
2548 7367 7.036996 ACATATGTTGTGTCATGTTGTTCAA 57.963 32.000 1.41 0.00 37.11 2.69
2549 7368 7.140705 ACATATGTTGTGTCATGTTGTTCAAG 58.859 34.615 1.41 0.00 37.11 3.02
2550 7369 5.581126 ATGTTGTGTCATGTTGTTCAAGT 57.419 34.783 0.00 0.00 0.00 3.16
2551 7370 6.691754 ATGTTGTGTCATGTTGTTCAAGTA 57.308 33.333 0.00 0.00 0.00 2.24
2552 7371 6.691754 TGTTGTGTCATGTTGTTCAAGTAT 57.308 33.333 0.00 0.00 0.00 2.12
2553 7372 7.094508 TGTTGTGTCATGTTGTTCAAGTATT 57.905 32.000 0.00 0.00 0.00 1.89
2554 7373 7.542890 TGTTGTGTCATGTTGTTCAAGTATTT 58.457 30.769 0.00 0.00 0.00 1.40
2555 7374 8.031864 TGTTGTGTCATGTTGTTCAAGTATTTT 58.968 29.630 0.00 0.00 0.00 1.82
2556 7375 8.868916 GTTGTGTCATGTTGTTCAAGTATTTTT 58.131 29.630 0.00 0.00 0.00 1.94
2557 7376 8.404889 TGTGTCATGTTGTTCAAGTATTTTTG 57.595 30.769 0.00 0.00 0.00 2.44
2558 7377 8.031864 TGTGTCATGTTGTTCAAGTATTTTTGT 58.968 29.630 0.00 0.00 0.00 2.83
2559 7378 9.509855 GTGTCATGTTGTTCAAGTATTTTTGTA 57.490 29.630 0.00 0.00 0.00 2.41
2629 7448 7.039363 AGGTATAATTGCTAGCAAACCAACAAA 60.039 33.333 34.37 15.01 39.55 2.83
2630 7449 7.763985 GGTATAATTGCTAGCAAACCAACAAAT 59.236 33.333 30.94 19.23 39.55 2.32
2680 7499 2.933769 CCAAAGATGGTCAAACTTCGC 58.066 47.619 0.00 0.00 42.18 4.70
2681 7500 2.351738 CCAAAGATGGTCAAACTTCGCC 60.352 50.000 0.00 0.00 42.18 5.54
2682 7501 1.534729 AAGATGGTCAAACTTCGCCC 58.465 50.000 0.00 0.00 0.00 6.13
2683 7502 0.400213 AGATGGTCAAACTTCGCCCA 59.600 50.000 0.00 0.00 0.00 5.36
2684 7503 1.202879 AGATGGTCAAACTTCGCCCAA 60.203 47.619 0.00 0.00 0.00 4.12
2685 7504 0.958822 ATGGTCAAACTTCGCCCAAC 59.041 50.000 0.00 0.00 0.00 3.77
2686 7505 0.394488 TGGTCAAACTTCGCCCAACA 60.394 50.000 0.00 0.00 0.00 3.33
2687 7506 0.958822 GGTCAAACTTCGCCCAACAT 59.041 50.000 0.00 0.00 0.00 2.71
2688 7507 1.339929 GGTCAAACTTCGCCCAACATT 59.660 47.619 0.00 0.00 0.00 2.71
2689 7508 2.393764 GTCAAACTTCGCCCAACATTG 58.606 47.619 0.00 0.00 0.00 2.82
2737 7556 1.419381 TGCACAGGGGCGAAGATATA 58.581 50.000 0.00 0.00 36.28 0.86
2748 7567 4.563786 GGGCGAAGATATAGAAGGGGAAAG 60.564 50.000 0.00 0.00 0.00 2.62
2910 7731 1.208052 AGTTCGGTAGCTGATGTGCAT 59.792 47.619 0.00 0.00 34.99 3.96
2912 7733 2.509052 TCGGTAGCTGATGTGCATAC 57.491 50.000 0.00 0.00 34.99 2.39
2913 7734 1.754226 TCGGTAGCTGATGTGCATACA 59.246 47.619 0.00 0.00 41.89 2.29
3004 7849 8.478877 CCACTATTCACAGAAGTATAGAACCTT 58.521 37.037 0.00 0.00 0.00 3.50
3136 7981 2.232208 GGCCTCAAGTCAAATCCCTTTG 59.768 50.000 0.00 0.00 42.60 2.77
3137 7982 3.157087 GCCTCAAGTCAAATCCCTTTGA 58.843 45.455 0.00 0.00 46.53 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 6.166982 GTCTCATACCTCCATATTAAGGTGC 58.833 44.000 13.77 0.00 45.49 5.01
266 267 6.835819 TCGTCTCATACCTCCATATTAAGG 57.164 41.667 0.00 0.00 38.70 2.69
270 271 5.012148 CCCTTTCGTCTCATACCTCCATATT 59.988 44.000 0.00 0.00 0.00 1.28
356 357 1.004277 GAACATTGCCAGGGAGTACCA 59.996 52.381 0.00 0.00 43.89 3.25
365 366 3.005554 CAGACAGTAGGAACATTGCCAG 58.994 50.000 0.00 0.00 0.00 4.85
380 381 6.763610 GGTAGGTATTTTCAATCTCCAGACAG 59.236 42.308 0.00 0.00 0.00 3.51
390 391 9.533831 ACTTGAATTCTGGTAGGTATTTTCAAT 57.466 29.630 7.05 0.00 33.05 2.57
391 392 8.934023 ACTTGAATTCTGGTAGGTATTTTCAA 57.066 30.769 7.05 0.00 32.66 2.69
427 428 9.106070 GGTTAGCAGCTTATTTTTAGCTAGTAA 57.894 33.333 0.00 0.00 46.80 2.24
444 445 5.118990 TGAAGATTATCTGTGGTTAGCAGC 58.881 41.667 0.00 0.00 34.21 5.25
485 486 6.315891 AGAGCAGAATAAGCAAGTCAAATCTC 59.684 38.462 0.00 0.00 0.00 2.75
541 1401 3.814945 GCTCTACAGCAACAACACATTC 58.185 45.455 0.00 0.00 46.06 2.67
610 1470 5.795939 CACGCAAGAGTGAGTAGTACTTTAG 59.204 44.000 0.00 0.00 44.43 1.85
651 4647 0.177373 CCCTCGCTGGTTACCCTTAC 59.823 60.000 0.00 0.00 0.00 2.34
664 5454 3.140814 GGCAAATGGGACCCTCGC 61.141 66.667 13.00 8.67 0.00 5.03
673 5463 6.428385 TTTTAAAATATTGCGGGCAAATGG 57.572 33.333 10.45 0.00 39.55 3.16
681 5471 9.471742 GCTACAAATGTTTTTAAAATATTGCGG 57.528 29.630 11.96 8.32 0.00 5.69
710 5500 6.205464 ACATCCAATTTATATGTCCTTCGCTG 59.795 38.462 0.00 0.00 0.00 5.18
717 5507 6.209192 TGCCATGACATCCAATTTATATGTCC 59.791 38.462 16.34 6.76 45.74 4.02
752 5542 6.460953 GGCTCTTGTGTTTTCAATCCTTGTAA 60.461 38.462 0.00 0.00 0.00 2.41
851 5645 0.537188 GATCCTTTGCGTGGAGAGGA 59.463 55.000 3.16 3.16 42.13 3.71
852 5646 0.250234 TGATCCTTTGCGTGGAGAGG 59.750 55.000 0.00 0.00 36.99 3.69
876 5670 0.379669 GGATGCTGATCTTGGTTGCG 59.620 55.000 0.00 0.00 0.00 4.85
926 5720 8.656849 GCTATTCTGTTATGTTATATTCGGTGG 58.343 37.037 0.00 0.00 0.00 4.61
933 5727 9.573166 TGGCTTTGCTATTCTGTTATGTTATAT 57.427 29.630 0.00 0.00 0.00 0.86
934 5728 8.972458 TGGCTTTGCTATTCTGTTATGTTATA 57.028 30.769 0.00 0.00 0.00 0.98
935 5729 7.469181 GCTGGCTTTGCTATTCTGTTATGTTAT 60.469 37.037 0.00 0.00 0.00 1.89
936 5730 6.183360 GCTGGCTTTGCTATTCTGTTATGTTA 60.183 38.462 0.00 0.00 0.00 2.41
939 5733 4.096833 TGCTGGCTTTGCTATTCTGTTATG 59.903 41.667 0.00 0.00 0.00 1.90
949 5743 1.603455 GTGGGTGCTGGCTTTGCTA 60.603 57.895 0.00 0.00 0.00 3.49
1014 5809 0.390472 CCGTCTGCTTGGAGGTCTTC 60.390 60.000 0.00 0.00 0.00 2.87
1032 5827 1.448717 GAGGGACTTGAGCTTCGCC 60.449 63.158 0.00 0.00 41.55 5.54
1127 5922 4.154347 GGACGAGGAGCTGGCTGG 62.154 72.222 0.00 0.00 0.00 4.85
1178 5973 0.241749 TTGCTTCGTGTCGTCGGTAT 59.758 50.000 0.00 0.00 0.00 2.73
1190 5985 1.594293 ACCACCACGTCTTGCTTCG 60.594 57.895 0.00 0.00 0.00 3.79
1209 6004 1.076777 TAAGCCTGCATCCAAGGGC 60.077 57.895 4.28 4.28 44.38 5.19
1225 6020 2.813754 GCAGAAACACCAGCATCAGTAA 59.186 45.455 0.00 0.00 0.00 2.24
1255 6050 0.761802 CCTCCTGGATAACCTGCTCC 59.238 60.000 0.00 0.00 37.04 4.70
1343 6138 3.941483 GCAACATACTGTGGCTTGTCTAT 59.059 43.478 0.00 0.00 43.82 1.98
1365 6160 2.513204 CGTGATGAGGCAGGCAGG 60.513 66.667 0.00 0.00 0.00 4.85
1412 6207 6.144402 CAGAATAGCAATGTTTGTTGTCCAAC 59.856 38.462 3.21 3.21 41.50 3.77
1645 6442 1.412710 GGATCAATGACACCCGCTAGA 59.587 52.381 0.00 0.00 0.00 2.43
1655 6452 4.678509 TTTTACACTGCGGATCAATGAC 57.321 40.909 0.00 0.00 0.00 3.06
1682 6479 2.747855 CCTGCCCGCAGTTTCTCC 60.748 66.667 15.22 0.00 42.15 3.71
1686 6483 1.600916 GAACTCCTGCCCGCAGTTT 60.601 57.895 15.22 5.68 42.15 2.66
1697 6494 0.249911 GACAACGCCTGTGAACTCCT 60.250 55.000 0.00 0.00 38.84 3.69
1802 6600 2.494059 CACCAAGATGTTGTTCTCCGT 58.506 47.619 1.49 0.00 30.95 4.69
1867 6665 3.214328 GAGCTCAAAGAAGTCCACCAAA 58.786 45.455 9.40 0.00 0.00 3.28
1901 6699 3.181466 GGAACATTGTTGTTGCCTTCCTT 60.181 43.478 6.80 0.00 46.01 3.36
2038 6836 3.436700 ACGATATGCACATTCTCGTCA 57.563 42.857 12.42 0.00 34.88 4.35
2053 6851 5.596772 TGATCCATCAGAGTTGGTAACGATA 59.403 40.000 0.00 0.00 35.64 2.92
2088 6886 2.285024 TTACGCCGGCCTGTAACCT 61.285 57.895 23.46 0.00 0.00 3.50
2089 6887 2.102438 GTTACGCCGGCCTGTAACC 61.102 63.158 31.29 20.14 42.80 2.85
2090 6888 2.102438 GGTTACGCCGGCCTGTAAC 61.102 63.158 32.51 32.51 46.06 2.50
2145 6943 0.976641 TGCAGAGGAAGGTCGTCATT 59.023 50.000 1.28 0.00 34.00 2.57
2167 6965 5.547465 CCCATATCGTTACATTTCTAGCCA 58.453 41.667 0.00 0.00 0.00 4.75
2287 7085 6.097554 CAGTTGACTGGACTAGTTGGATATCT 59.902 42.308 2.05 0.00 40.53 1.98
2288 7086 6.276847 CAGTTGACTGGACTAGTTGGATATC 58.723 44.000 0.00 0.00 40.53 1.63
2325 7123 7.174413 TGGTCCATGAGAATTGACATTTCTTA 58.826 34.615 12.58 9.70 33.65 2.10
2329 7127 5.047092 GGTTGGTCCATGAGAATTGACATTT 60.047 40.000 0.00 0.00 35.97 2.32
2332 7130 3.420893 GGTTGGTCCATGAGAATTGACA 58.579 45.455 0.00 0.00 35.97 3.58
2333 7131 2.755103 GGGTTGGTCCATGAGAATTGAC 59.245 50.000 0.00 0.00 38.11 3.18
2334 7132 2.291540 GGGGTTGGTCCATGAGAATTGA 60.292 50.000 0.00 0.00 38.11 2.57
2335 7133 2.102578 GGGGTTGGTCCATGAGAATTG 58.897 52.381 0.00 0.00 38.11 2.32
2336 7134 2.003072 AGGGGTTGGTCCATGAGAATT 58.997 47.619 0.00 0.00 38.11 2.17
2338 7136 2.196595 CTAGGGGTTGGTCCATGAGAA 58.803 52.381 0.00 0.00 38.11 2.87
2339 7137 1.080498 ACTAGGGGTTGGTCCATGAGA 59.920 52.381 0.00 0.00 38.11 3.27
2340 7138 1.210478 CACTAGGGGTTGGTCCATGAG 59.790 57.143 0.00 0.00 38.11 2.90
2341 7139 1.285280 CACTAGGGGTTGGTCCATGA 58.715 55.000 0.00 0.00 38.11 3.07
2342 7140 0.255890 CCACTAGGGGTTGGTCCATG 59.744 60.000 1.53 0.00 38.11 3.66
2343 7141 1.571773 GCCACTAGGGGTTGGTCCAT 61.572 60.000 13.95 0.00 38.11 3.41
2344 7142 2.228480 GCCACTAGGGGTTGGTCCA 61.228 63.158 13.95 0.00 38.11 4.02
2345 7143 2.675371 GCCACTAGGGGTTGGTCC 59.325 66.667 13.95 0.00 37.04 4.46
2347 7145 1.146544 ATTGGCCACTAGGGGTTGGT 61.147 55.000 13.95 0.00 37.04 3.67
2348 7146 0.684153 CATTGGCCACTAGGGGTTGG 60.684 60.000 13.95 2.48 37.04 3.77
2349 7147 1.322538 GCATTGGCCACTAGGGGTTG 61.323 60.000 13.95 6.94 37.04 3.77
2350 7148 1.000359 GCATTGGCCACTAGGGGTT 60.000 57.895 13.95 0.00 37.04 4.11
2375 7182 5.682943 TGACTGTTAAGCAATGTGGTTAC 57.317 39.130 0.00 0.00 39.68 2.50
2429 7236 3.124921 GGTGATGAACGGCGGTGG 61.125 66.667 13.24 0.00 0.00 4.61
2469 7276 7.924358 AGATATGTTGGTATGGTGGTTACTA 57.076 36.000 0.00 0.00 0.00 1.82
2525 7344 7.140705 ACTTGAACAACATGACACAACATATG 58.859 34.615 0.00 0.00 0.00 1.78
2526 7345 7.275888 ACTTGAACAACATGACACAACATAT 57.724 32.000 0.00 0.00 0.00 1.78
2527 7346 6.691754 ACTTGAACAACATGACACAACATA 57.308 33.333 0.00 0.00 0.00 2.29
2528 7347 5.581126 ACTTGAACAACATGACACAACAT 57.419 34.783 0.00 0.00 0.00 2.71
2529 7348 6.691754 ATACTTGAACAACATGACACAACA 57.308 33.333 0.00 0.00 0.00 3.33
2530 7349 7.985634 AAATACTTGAACAACATGACACAAC 57.014 32.000 0.00 0.00 0.00 3.32
2531 7350 8.867935 CAAAAATACTTGAACAACATGACACAA 58.132 29.630 0.00 0.00 0.00 3.33
2532 7351 8.031864 ACAAAAATACTTGAACAACATGACACA 58.968 29.630 0.00 0.00 0.00 3.72
2533 7352 8.406172 ACAAAAATACTTGAACAACATGACAC 57.594 30.769 0.00 0.00 0.00 3.67
2575 7394 7.602265 GCCCACATAATGTTTACAAAATTGTCT 59.398 33.333 1.37 0.00 42.35 3.41
2576 7395 7.148490 GGCCCACATAATGTTTACAAAATTGTC 60.148 37.037 1.37 0.00 42.35 3.18
2577 7396 6.652900 GGCCCACATAATGTTTACAAAATTGT 59.347 34.615 4.01 4.01 44.86 2.71
2578 7397 6.652481 TGGCCCACATAATGTTTACAAAATTG 59.348 34.615 0.00 0.00 0.00 2.32
2579 7398 6.773638 TGGCCCACATAATGTTTACAAAATT 58.226 32.000 0.00 0.00 0.00 1.82
2580 7399 6.365970 TGGCCCACATAATGTTTACAAAAT 57.634 33.333 0.00 0.00 0.00 1.82
2581 7400 5.279708 CCTGGCCCACATAATGTTTACAAAA 60.280 40.000 0.00 0.00 0.00 2.44
2582 7401 4.221703 CCTGGCCCACATAATGTTTACAAA 59.778 41.667 0.00 0.00 0.00 2.83
2583 7402 3.766591 CCTGGCCCACATAATGTTTACAA 59.233 43.478 0.00 0.00 0.00 2.41
2584 7403 3.245443 ACCTGGCCCACATAATGTTTACA 60.245 43.478 0.00 0.00 0.00 2.41
2585 7404 3.361786 ACCTGGCCCACATAATGTTTAC 58.638 45.455 0.00 0.00 0.00 2.01
2586 7405 3.748645 ACCTGGCCCACATAATGTTTA 57.251 42.857 0.00 0.00 0.00 2.01
2587 7406 2.621556 ACCTGGCCCACATAATGTTT 57.378 45.000 0.00 0.00 0.00 2.83
2588 7407 3.971468 ATACCTGGCCCACATAATGTT 57.029 42.857 0.00 0.00 0.00 2.71
2600 7419 4.261614 GGTTTGCTAGCAATTATACCTGGC 60.262 45.833 29.59 12.50 35.70 4.85
2629 7448 9.433153 TGTACTGATCTCGTCGAGTAAATATAT 57.567 33.333 21.15 6.13 0.00 0.86
2630 7449 8.822652 TGTACTGATCTCGTCGAGTAAATATA 57.177 34.615 21.15 1.04 0.00 0.86
2697 7516 4.381398 GCATTTTTGTTGGGCCAAGTTTTT 60.381 37.500 21.62 0.09 0.00 1.94
2698 7517 3.130164 GCATTTTTGTTGGGCCAAGTTTT 59.870 39.130 21.62 0.00 0.00 2.43
2737 7556 1.074566 CACTGGCTTCTTTCCCCTTCT 59.925 52.381 0.00 0.00 0.00 2.85
2748 7567 2.970974 GCGCACCTTCACTGGCTTC 61.971 63.158 0.30 0.00 0.00 3.86
2910 7731 2.094575 GCGTATGCCGACAAATTGTGTA 59.905 45.455 2.20 0.00 36.21 2.90
2912 7733 1.135831 TGCGTATGCCGACAAATTGTG 60.136 47.619 2.20 0.00 41.78 3.33
2913 7734 1.160989 TGCGTATGCCGACAAATTGT 58.839 45.000 4.05 0.00 41.78 2.71
3034 7879 5.105187 TGTTTTCCACAAATGTCATTCCACA 60.105 36.000 0.00 0.00 29.87 4.17


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

AutoCloner maintained by Alex Coulton.