Multiple sequence alignment - TraesCS2A01G316600

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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 TraesCS2A01G316600 chr2A 100.000 3470 0 0 1 3470 542548901 542552370 0.000000e+00 6408.0
1 TraesCS2A01G316600 chr2D 90.798 3510 227 39 1 3468 404118951 404122406 0.000000e+00 4604.0
2 TraesCS2A01G316600 chr2B 89.976 2504 171 31 1 2473 478183268 478185722 0.000000e+00 3160.0
3 TraesCS2A01G316600 chr2B 92.089 986 56 14 2492 3470 478187928 478188898 0.000000e+00 1369.0
4 TraesCS2A01G316600 chr2B 85.714 315 30 7 2554 2865 478185785 478186087 5.590000e-83 318.0
5 TraesCS2A01G316600 chr2B 80.804 224 20 7 2928 3128 478187696 478187919 1.670000e-33 154.0
6 TraesCS2A01G316600 chr3B 93.023 43 3 0 700 742 157230446 157230488 2.890000e-06 63.9
7 TraesCS2A01G316600 chr3B 90.698 43 4 0 710 752 187904285 187904327 1.350000e-04 58.4
8 TraesCS2A01G316600 chr3B 89.130 46 5 0 709 754 252558345 252558300 1.350000e-04 58.4
9 TraesCS2A01G316600 chr7D 90.909 44 4 0 709 752 387221913 387221870 3.740000e-05 60.2
10 TraesCS2A01G316600 chr6B 90.698 43 4 0 709 751 408680860 408680818 1.350000e-04 58.4
11 TraesCS2A01G316600 chr3D 97.059 34 1 0 709 742 105428559 105428592 1.350000e-04 58.4
12 TraesCS2A01G316600 chr5A 90.476 42 4 0 713 754 636630915 636630874 4.840000e-04 56.5


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 TraesCS2A01G316600 chr2A 542548901 542552370 3469 False 6408.00 6408 100.00000 1 3470 1 chr2A.!!$F1 3469
1 TraesCS2A01G316600 chr2D 404118951 404122406 3455 False 4604.00 4604 90.79800 1 3468 1 chr2D.!!$F1 3467
2 TraesCS2A01G316600 chr2B 478183268 478188898 5630 False 1250.25 3160 87.14575 1 3470 4 chr2B.!!$F1 3469

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
432 438 0.108186 TAGCTCGATGTGGGCACAAG 60.108 55.0 0.00 0.0 45.41 3.16 F
1169 1215 0.321653 ACCGGAAGCCTCAACATCAC 60.322 55.0 9.46 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2123 0.039437 ATGATCATCCCGTACGCGTC 60.039 55.000 18.63 6.85 36.15 5.19 R
2527 2616 1.065701 GAAGCAGAGCTCAATGCCATG 59.934 52.381 20.84 8.21 43.60 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
22 23 2.656646 ACGAGCGTGATGGAAGCA 59.343 55.556 0.00 0.00 0.00 3.91
47 48 3.270877 GCCTAGAACACCATTCACGATT 58.729 45.455 0.00 0.00 0.00 3.34
59 60 4.876107 CCATTCACGATTAGCTTGGTACTT 59.124 41.667 0.00 0.00 0.00 2.24
78 79 5.464030 ACTTGCCTAGTAAAGAAGAACGA 57.536 39.130 8.27 0.00 34.56 3.85
93 94 2.427453 AGAACGACGATCCAACATAGCT 59.573 45.455 0.00 0.00 0.00 3.32
117 118 0.473755 TGAGCCAAAGACTTCAGCCA 59.526 50.000 5.93 2.56 0.00 4.75
119 120 2.305635 TGAGCCAAAGACTTCAGCCATA 59.694 45.455 5.93 0.00 0.00 2.74
176 177 8.776376 AATTAAATGCCTTTGTAATGTCAAGG 57.224 30.769 0.00 0.00 0.00 3.61
216 219 4.472833 ACTCTTTCCTAGCATGGATCTTGT 59.527 41.667 0.00 0.00 35.83 3.16
229 232 2.440409 GATCTTGTGTGCAACCTGGAT 58.560 47.619 0.00 0.00 34.36 3.41
310 313 3.795101 CGTACTATTTCCGACATGTGACC 59.205 47.826 1.15 0.00 0.00 4.02
311 314 3.973206 ACTATTTCCGACATGTGACCA 57.027 42.857 1.15 0.00 0.00 4.02
337 340 2.278330 GGGTGGCAAGGAGCTTTGG 61.278 63.158 0.52 0.00 44.79 3.28
366 369 3.973472 TGTAGAAGCTATGAGGGAGGA 57.027 47.619 0.00 0.00 0.00 3.71
367 370 3.567397 TGTAGAAGCTATGAGGGAGGAC 58.433 50.000 0.00 0.00 0.00 3.85
372 375 4.591072 AGAAGCTATGAGGGAGGACAATAC 59.409 45.833 0.00 0.00 0.00 1.89
391 397 0.179134 CGTCTAAAGTCGCCCTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
408 414 1.354368 CCAGGGCCTCAACCTTCTTAA 59.646 52.381 0.95 0.00 35.78 1.85
431 437 0.323302 TTAGCTCGATGTGGGCACAA 59.677 50.000 0.00 0.00 45.41 3.33
432 438 0.108186 TAGCTCGATGTGGGCACAAG 60.108 55.000 0.00 0.00 45.41 3.16
475 481 2.623878 TCACCCACGAACAGCTTAAA 57.376 45.000 0.00 0.00 0.00 1.52
500 508 1.202510 GCCGCCATGATGCCATTTTTA 60.203 47.619 0.00 0.00 0.00 1.52
503 511 4.798924 GCCGCCATGATGCCATTTTTAATA 60.799 41.667 0.00 0.00 0.00 0.98
504 512 5.295950 CCGCCATGATGCCATTTTTAATAA 58.704 37.500 0.00 0.00 0.00 1.40
505 513 5.933463 CCGCCATGATGCCATTTTTAATAAT 59.067 36.000 0.00 0.00 0.00 1.28
506 514 6.091169 CCGCCATGATGCCATTTTTAATAATC 59.909 38.462 0.00 0.00 0.00 1.75
507 515 6.645827 CGCCATGATGCCATTTTTAATAATCA 59.354 34.615 0.00 0.00 0.00 2.57
541 549 8.750515 TTATGATAGAAAGCACCAATGAATCA 57.249 30.769 0.00 0.00 0.00 2.57
542 550 6.688637 TGATAGAAAGCACCAATGAATCAG 57.311 37.500 0.00 0.00 0.00 2.90
543 551 3.863142 AGAAAGCACCAATGAATCAGC 57.137 42.857 0.00 0.00 0.00 4.26
544 552 3.428532 AGAAAGCACCAATGAATCAGCT 58.571 40.909 0.00 0.00 0.00 4.24
545 553 3.442977 AGAAAGCACCAATGAATCAGCTC 59.557 43.478 0.00 0.00 0.00 4.09
546 554 2.803030 AGCACCAATGAATCAGCTCT 57.197 45.000 0.00 0.00 0.00 4.09
550 558 3.607741 CACCAATGAATCAGCTCTGTCT 58.392 45.455 0.00 0.00 0.00 3.41
564 584 2.433970 CTCTGTCTGGGGGATCTCTTTC 59.566 54.545 0.00 0.00 0.00 2.62
575 595 5.423290 GGGGGATCTCTTTCATGATGTTTTT 59.577 40.000 0.00 0.00 0.00 1.94
576 596 6.335777 GGGGATCTCTTTCATGATGTTTTTG 58.664 40.000 0.00 0.00 0.00 2.44
584 604 5.720371 TTCATGATGTTTTTGTAGGGTGG 57.280 39.130 0.00 0.00 0.00 4.61
588 608 6.778069 TCATGATGTTTTTGTAGGGTGGTTTA 59.222 34.615 0.00 0.00 0.00 2.01
589 609 6.642707 TGATGTTTTTGTAGGGTGGTTTAG 57.357 37.500 0.00 0.00 0.00 1.85
590 610 5.536916 TGATGTTTTTGTAGGGTGGTTTAGG 59.463 40.000 0.00 0.00 0.00 2.69
591 611 4.869451 TGTTTTTGTAGGGTGGTTTAGGT 58.131 39.130 0.00 0.00 0.00 3.08
592 612 4.645588 TGTTTTTGTAGGGTGGTTTAGGTG 59.354 41.667 0.00 0.00 0.00 4.00
593 613 4.523168 TTTTGTAGGGTGGTTTAGGTGT 57.477 40.909 0.00 0.00 0.00 4.16
594 614 4.523168 TTTGTAGGGTGGTTTAGGTGTT 57.477 40.909 0.00 0.00 0.00 3.32
595 615 3.775261 TGTAGGGTGGTTTAGGTGTTC 57.225 47.619 0.00 0.00 0.00 3.18
596 616 2.372837 TGTAGGGTGGTTTAGGTGTTCC 59.627 50.000 0.00 0.00 0.00 3.62
598 618 2.141067 AGGGTGGTTTAGGTGTTCCTT 58.859 47.619 0.00 0.00 42.12 3.36
599 619 2.107726 AGGGTGGTTTAGGTGTTCCTTC 59.892 50.000 0.00 0.00 42.12 3.46
600 620 2.511659 GGTGGTTTAGGTGTTCCTTCC 58.488 52.381 0.00 0.00 42.12 3.46
601 621 2.148768 GTGGTTTAGGTGTTCCTTCCG 58.851 52.381 0.00 0.00 42.12 4.30
602 622 1.072648 TGGTTTAGGTGTTCCTTCCGG 59.927 52.381 0.00 0.00 42.12 5.14
603 623 1.348696 GGTTTAGGTGTTCCTTCCGGA 59.651 52.381 0.00 0.00 42.12 5.14
604 624 2.224597 GGTTTAGGTGTTCCTTCCGGAA 60.225 50.000 17.73 17.73 46.90 4.30
615 635 5.799827 TTCCTTCCGGAACAAATTCATTT 57.200 34.783 14.35 0.00 44.28 2.32
616 636 5.132897 TCCTTCCGGAACAAATTCATTTG 57.867 39.130 14.35 10.19 42.51 2.32
617 637 4.560513 TCCTTCCGGAACAAATTCATTTGC 60.561 41.667 14.35 0.00 41.55 3.68
627 647 4.644498 CAAATTCATTTGCTGGGTTCCTT 58.356 39.130 0.00 0.00 40.42 3.36
630 650 0.527565 CATTTGCTGGGTTCCTTCCG 59.472 55.000 0.00 0.00 0.00 4.30
635 655 1.144057 CTGGGTTCCTTCCGGATCG 59.856 63.158 4.15 0.00 39.58 3.69
637 657 1.143401 GGGTTCCTTCCGGATCGAC 59.857 63.158 4.15 1.84 39.58 4.20
640 660 0.535797 GTTCCTTCCGGATCGACCTT 59.464 55.000 4.15 0.00 39.58 3.50
645 665 0.970640 TTCCGGATCGACCTTGTTCA 59.029 50.000 4.15 0.00 36.31 3.18
646 666 0.970640 TCCGGATCGACCTTGTTCAA 59.029 50.000 0.00 0.00 36.31 2.69
653 673 2.500229 TCGACCTTGTTCAATGGGTTC 58.500 47.619 0.00 0.00 31.60 3.62
654 674 1.539827 CGACCTTGTTCAATGGGTTCC 59.460 52.381 0.00 0.00 31.60 3.62
656 676 1.503347 ACCTTGTTCAATGGGTTCCCT 59.497 47.619 9.43 0.00 0.00 4.20
681 715 6.725364 AGTTTGATATTGTGGTCCTTGATCT 58.275 36.000 0.00 0.00 0.00 2.75
684 718 8.562892 GTTTGATATTGTGGTCCTTGATCTATG 58.437 37.037 0.00 0.00 0.00 2.23
689 723 4.832248 TGTGGTCCTTGATCTATGTGTTC 58.168 43.478 0.00 0.00 0.00 3.18
700 734 6.401394 TGATCTATGTGTTCTTTGTCTCCTG 58.599 40.000 0.00 0.00 0.00 3.86
702 736 2.708216 TGTGTTCTTTGTCTCCTGCA 57.292 45.000 0.00 0.00 0.00 4.41
703 737 3.213206 TGTGTTCTTTGTCTCCTGCAT 57.787 42.857 0.00 0.00 0.00 3.96
706 740 5.316167 TGTGTTCTTTGTCTCCTGCATAAT 58.684 37.500 0.00 0.00 0.00 1.28
707 741 5.769662 TGTGTTCTTTGTCTCCTGCATAATT 59.230 36.000 0.00 0.00 0.00 1.40
745 779 5.758296 AGCAACACTTATTTTGAGACGAAGA 59.242 36.000 0.00 0.00 0.00 2.87
746 780 5.846473 GCAACACTTATTTTGAGACGAAGAC 59.154 40.000 0.00 0.00 0.00 3.01
762 796 9.224058 GAGACGAAGACAGTAGAACATAATTAC 57.776 37.037 0.00 0.00 0.00 1.89
815 854 5.180492 TGGTAATTAGCAAACTCCGAAACTG 59.820 40.000 14.77 0.00 0.00 3.16
820 859 3.070018 AGCAAACTCCGAAACTGATGAG 58.930 45.455 0.00 0.00 0.00 2.90
874 916 1.658717 CGAAGCGATGCTACCCTCG 60.659 63.158 0.00 0.00 38.25 4.63
896 938 1.545651 CCAGTTCACCTTTCCTCCACC 60.546 57.143 0.00 0.00 0.00 4.61
903 945 0.960861 CCTTTCCTCCACCGCCTTTC 60.961 60.000 0.00 0.00 0.00 2.62
911 953 1.302033 CACCGCCTTTCTGTGCTCT 60.302 57.895 0.00 0.00 0.00 4.09
936 978 6.452244 GAACAAATCGGGAACAAAGAATTG 57.548 37.500 0.00 0.00 42.46 2.32
937 979 4.881920 ACAAATCGGGAACAAAGAATTGG 58.118 39.130 0.00 0.00 41.01 3.16
965 1011 7.229506 GCTGCTTGATCTACTTAACCCATTTAT 59.770 37.037 0.00 0.00 0.00 1.40
1076 1122 4.214327 CTTCCTCGCCCTCCTCGC 62.214 72.222 0.00 0.00 0.00 5.03
1152 1198 2.342648 GTGGACTCCGTGGACACC 59.657 66.667 0.00 0.00 0.00 4.16
1169 1215 0.321653 ACCGGAAGCCTCAACATCAC 60.322 55.000 9.46 0.00 0.00 3.06
1176 1222 1.298859 GCCTCAACATCACCGACCAC 61.299 60.000 0.00 0.00 0.00 4.16
1320 1366 1.218316 GTACCTGGTGAAGCTCGGG 59.782 63.158 10.23 0.00 35.60 5.14
1413 1459 1.663702 GTGCGTCAAGTGCTACCGT 60.664 57.895 0.00 0.00 0.00 4.83
1458 1504 4.849329 GCCTCGACCACCTACGCG 62.849 72.222 3.53 3.53 0.00 6.01
1912 1958 1.263356 CTACCTCAACCTCAACGGGA 58.737 55.000 0.00 0.00 36.97 5.14
1947 1993 1.225704 GGCCATGTCCTCCTCCTTG 59.774 63.158 0.00 0.00 0.00 3.61
1969 2015 4.505217 GCAGCATGAACGCGACGG 62.505 66.667 15.93 4.24 39.69 4.79
1980 2026 4.509737 GCGACGGCTCCAGGTACC 62.510 72.222 2.73 2.73 35.83 3.34
1981 2027 3.834799 CGACGGCTCCAGGTACCC 61.835 72.222 8.74 0.00 0.00 3.69
1985 2031 4.791069 GGCTCCAGGTACCCCCGA 62.791 72.222 8.74 0.30 38.74 5.14
1986 2032 3.468140 GCTCCAGGTACCCCCGAC 61.468 72.222 8.74 0.00 38.74 4.79
1987 2033 2.762875 CTCCAGGTACCCCCGACC 60.763 72.222 8.74 0.00 38.74 4.79
1988 2034 4.403502 TCCAGGTACCCCCGACCC 62.404 72.222 8.74 0.00 37.73 4.46
2097 2155 0.317854 TGATCATCGACATCGCGTCC 60.318 55.000 5.77 0.00 42.07 4.79
2218 2276 1.523258 CTCTGCTTCATCCTGCCGG 60.523 63.158 0.00 0.00 0.00 6.13
2220 2278 1.523258 CTGCTTCATCCTGCCGGAG 60.523 63.158 5.05 0.00 44.06 4.63
2299 2357 0.107752 GCTCAAGCTGGAGAAGGAGG 60.108 60.000 22.98 0.00 37.05 4.30
2300 2358 1.566211 CTCAAGCTGGAGAAGGAGGA 58.434 55.000 13.35 0.00 37.05 3.71
2317 2375 1.079750 GAGCTGTTCGTGGAGGACC 60.080 63.158 0.00 0.00 0.00 4.46
2455 2513 0.508641 CGTCAAGACCAACTGCGAAG 59.491 55.000 0.00 0.00 0.00 3.79
2477 2535 4.100808 AGCCATGACTCACTAGGATTTCTC 59.899 45.833 0.00 0.00 0.00 2.87
2510 2599 9.693739 ATTTACCCATAACAAATGTAGACATCA 57.306 29.630 0.00 0.00 35.10 3.07
2513 2602 8.593945 ACCCATAACAAATGTAGACATCAAAT 57.406 30.769 0.00 0.00 35.10 2.32
2527 2616 5.047235 AGACATCAAATAGGATAGGTACGGC 60.047 44.000 0.00 0.00 0.00 5.68
2629 2730 8.836268 ATGAATTTGTGAGTGCATTTTTACAT 57.164 26.923 0.00 0.00 0.00 2.29
2687 2788 4.717877 TGATACAATGGTCTAAGGGCATG 58.282 43.478 0.00 0.00 0.00 4.06
2694 2795 2.825532 TGGTCTAAGGGCATGCTTTTTC 59.174 45.455 18.92 0.00 0.00 2.29
2700 2801 3.407424 AGGGCATGCTTTTTCCTTTTC 57.593 42.857 18.92 0.00 0.00 2.29
2702 2803 2.038952 GGGCATGCTTTTTCCTTTTCCT 59.961 45.455 18.92 0.00 0.00 3.36
2710 2811 5.651576 TGCTTTTTCCTTTTCCTTTTTGCAT 59.348 32.000 0.00 0.00 0.00 3.96
2712 2813 7.132213 GCTTTTTCCTTTTCCTTTTTGCATAC 58.868 34.615 0.00 0.00 0.00 2.39
2716 2817 7.589958 TTCCTTTTCCTTTTTGCATACTGTA 57.410 32.000 0.00 0.00 0.00 2.74
2717 2818 7.775053 TCCTTTTCCTTTTTGCATACTGTAT 57.225 32.000 0.00 0.00 0.00 2.29
2718 2819 8.871629 TCCTTTTCCTTTTTGCATACTGTATA 57.128 30.769 0.00 0.00 0.00 1.47
2783 2884 4.664150 TTCGCACAAGGGAATTCTTTTT 57.336 36.364 5.23 0.00 41.18 1.94
2809 2910 6.457159 TTTCTTTTGGGTCCCATTCTACTA 57.543 37.500 12.68 0.00 31.53 1.82
2826 2927 5.208890 TCTACTATTTCTAGGCTCCTTGCA 58.791 41.667 0.00 0.00 45.15 4.08
2867 5182 7.928873 AGTAAAATGGAAGGAGAACCAATAGA 58.071 34.615 0.00 0.00 39.69 1.98
2868 5183 8.049721 AGTAAAATGGAAGGAGAACCAATAGAG 58.950 37.037 0.00 0.00 39.69 2.43
2869 5184 6.394345 AAATGGAAGGAGAACCAATAGAGT 57.606 37.500 0.00 0.00 39.69 3.24
2870 5185 4.826274 TGGAAGGAGAACCAATAGAGTG 57.174 45.455 0.00 0.00 38.94 3.51
2871 5186 3.055094 TGGAAGGAGAACCAATAGAGTGC 60.055 47.826 0.00 0.00 38.94 4.40
2872 5187 2.969628 AGGAGAACCAATAGAGTGCG 57.030 50.000 0.00 0.00 38.94 5.34
2873 5188 1.482593 AGGAGAACCAATAGAGTGCGG 59.517 52.381 0.00 0.00 38.94 5.69
2874 5189 1.480954 GGAGAACCAATAGAGTGCGGA 59.519 52.381 0.00 0.00 35.97 5.54
2875 5190 2.093658 GGAGAACCAATAGAGTGCGGAA 60.094 50.000 0.00 0.00 35.97 4.30
2876 5191 3.596214 GAGAACCAATAGAGTGCGGAAA 58.404 45.455 0.00 0.00 0.00 3.13
2877 5192 3.335579 AGAACCAATAGAGTGCGGAAAC 58.664 45.455 0.00 0.00 0.00 2.78
2878 5193 2.851263 ACCAATAGAGTGCGGAAACA 57.149 45.000 0.00 0.00 0.00 2.83
2896 5211 6.094048 CGGAAACATCATTACCATCTCACTTT 59.906 38.462 0.00 0.00 0.00 2.66
2955 5272 9.264719 CATGATATATTCACAACTCACAAGCTA 57.735 33.333 0.00 0.00 37.11 3.32
3021 5339 6.174720 TCCACCTTCATGTGATCCTATAAC 57.825 41.667 0.00 0.00 38.55 1.89
3034 5352 9.687210 TGTGATCCTATAACGACATTATTACAC 57.313 33.333 0.00 0.00 35.08 2.90
3048 5366 6.257849 ACATTATTACACGGTGTCTGCATAAG 59.742 38.462 18.43 11.36 0.00 1.73
3117 5435 3.129113 TGCCATGAACACATAACTGATGC 59.871 43.478 0.00 0.00 39.39 3.91
3142 5460 7.361201 GCACACACTTGCAGATTTTCTATAAGA 60.361 37.037 0.00 0.00 42.49 2.10
3213 5531 6.367422 GTCCTCAAGTTTGAACAGATACTCTG 59.633 42.308 2.65 2.65 40.39 3.35
3276 5594 9.440773 GCCTGAACATAACATAGATTATCATCA 57.559 33.333 0.00 0.00 0.00 3.07
3433 5752 4.517285 TGGTAGAATTCAGTTCCATCAGC 58.483 43.478 8.44 0.00 37.56 4.26
3436 5755 5.295540 GGTAGAATTCAGTTCCATCAGCTTC 59.704 44.000 8.44 0.00 37.56 3.86
3442 5761 6.560253 TTCAGTTCCATCAGCTTCTTTAAC 57.440 37.500 0.00 0.00 0.00 2.01
3448 5767 7.669722 AGTTCCATCAGCTTCTTTAACCAATTA 59.330 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.985159 TGAATGGTGTTCTAGGCAGGT 59.015 47.619 0.00 0.00 0.00 4.00
47 48 5.718130 TCTTTACTAGGCAAGTACCAAGCTA 59.282 40.000 0.00 0.00 40.48 3.32
59 60 3.503363 TCGTCGTTCTTCTTTACTAGGCA 59.497 43.478 0.00 0.00 0.00 4.75
78 79 5.339008 TCAAGTTAGCTATGTTGGATCGT 57.661 39.130 13.09 0.00 0.00 3.73
93 94 3.815401 GCTGAAGTCTTTGGCTCAAGTTA 59.185 43.478 4.22 0.00 0.00 2.24
142 143 7.150783 ACAAAGGCATTTAATTCTCTCTCAC 57.849 36.000 0.00 0.00 0.00 3.51
216 219 2.235016 GTTGGTTATCCAGGTTGCACA 58.765 47.619 0.00 0.00 45.22 4.57
229 232 7.888021 ACATCCATGATAACTTCTTGTTGGTTA 59.112 33.333 0.00 0.00 39.55 2.85
274 277 5.623956 AATAGTACGGATCAACCAATCCA 57.376 39.130 0.00 0.00 44.73 3.41
289 292 4.565564 GTGGTCACATGTCGGAAATAGTAC 59.434 45.833 0.00 0.00 0.00 2.73
337 340 5.582665 CCTCATAGCTTCTACAAGTTGTTCC 59.417 44.000 14.90 0.00 31.45 3.62
366 369 2.494870 AGGGCGACTTTAGACGTATTGT 59.505 45.455 0.00 0.00 35.76 2.71
367 370 3.114065 GAGGGCGACTTTAGACGTATTG 58.886 50.000 0.00 0.00 35.76 1.90
372 375 0.179134 CTGGAGGGCGACTTTAGACG 60.179 60.000 0.00 0.00 36.38 4.18
391 397 2.130272 CCTTAAGAAGGTTGAGGCCC 57.870 55.000 3.36 0.00 43.95 5.80
408 414 0.394565 GCCCACATCGAGCTAATCCT 59.605 55.000 0.00 0.00 0.00 3.24
431 437 1.202976 AGGGCAATTCACAAGCTCACT 60.203 47.619 0.00 0.00 0.00 3.41
432 438 1.068055 CAGGGCAATTCACAAGCTCAC 60.068 52.381 0.00 0.00 0.00 3.51
445 451 3.588511 TGGGTGATGGCAGGGCAA 61.589 61.111 0.00 0.00 0.00 4.52
500 508 9.866655 TTCTATCATAAAGCTTGGGTGATTATT 57.133 29.630 20.02 6.14 32.31 1.40
503 511 8.230472 CTTTCTATCATAAAGCTTGGGTGATT 57.770 34.615 20.02 9.64 32.31 2.57
504 512 7.814264 CTTTCTATCATAAAGCTTGGGTGAT 57.186 36.000 19.22 19.22 34.26 3.06
541 549 0.398381 GAGATCCCCCAGACAGAGCT 60.398 60.000 0.00 0.00 0.00 4.09
542 550 0.398381 AGAGATCCCCCAGACAGAGC 60.398 60.000 0.00 0.00 0.00 4.09
543 551 2.173126 AAGAGATCCCCCAGACAGAG 57.827 55.000 0.00 0.00 0.00 3.35
544 552 2.225624 TGAAAGAGATCCCCCAGACAGA 60.226 50.000 0.00 0.00 0.00 3.41
545 553 2.191400 TGAAAGAGATCCCCCAGACAG 58.809 52.381 0.00 0.00 0.00 3.51
546 554 2.342406 TGAAAGAGATCCCCCAGACA 57.658 50.000 0.00 0.00 0.00 3.41
550 558 3.125656 ACATCATGAAAGAGATCCCCCA 58.874 45.455 0.00 0.00 0.00 4.96
564 584 5.467035 AACCACCCTACAAAAACATCATG 57.533 39.130 0.00 0.00 0.00 3.07
575 595 2.372837 GGAACACCTAAACCACCCTACA 59.627 50.000 0.00 0.00 0.00 2.74
576 596 2.641321 AGGAACACCTAAACCACCCTAC 59.359 50.000 0.00 0.00 31.52 3.18
596 616 4.386652 CAGCAAATGAATTTGTTCCGGAAG 59.613 41.667 19.50 1.89 46.63 3.46
597 617 4.305769 CAGCAAATGAATTTGTTCCGGAA 58.694 39.130 14.35 14.35 46.63 4.30
598 618 3.305950 CCAGCAAATGAATTTGTTCCGGA 60.306 43.478 15.27 0.00 46.63 5.14
599 619 2.995258 CCAGCAAATGAATTTGTTCCGG 59.005 45.455 15.27 0.00 46.63 5.14
600 620 2.995258 CCCAGCAAATGAATTTGTTCCG 59.005 45.455 15.27 4.24 46.63 4.30
601 621 4.006780 ACCCAGCAAATGAATTTGTTCC 57.993 40.909 15.27 1.86 46.63 3.62
602 622 4.452114 GGAACCCAGCAAATGAATTTGTTC 59.548 41.667 15.27 10.82 46.63 3.18
603 623 4.102996 AGGAACCCAGCAAATGAATTTGTT 59.897 37.500 15.27 8.18 46.63 2.83
604 624 3.647590 AGGAACCCAGCAAATGAATTTGT 59.352 39.130 15.27 2.49 46.63 2.83
606 626 4.263025 GGAAGGAACCCAGCAAATGAATTT 60.263 41.667 0.00 0.00 0.00 1.82
607 627 3.261643 GGAAGGAACCCAGCAAATGAATT 59.738 43.478 0.00 0.00 0.00 2.17
608 628 2.833943 GGAAGGAACCCAGCAAATGAAT 59.166 45.455 0.00 0.00 0.00 2.57
609 629 2.247358 GGAAGGAACCCAGCAAATGAA 58.753 47.619 0.00 0.00 0.00 2.57
610 630 1.886222 CGGAAGGAACCCAGCAAATGA 60.886 52.381 0.00 0.00 0.00 2.57
611 631 0.527565 CGGAAGGAACCCAGCAAATG 59.472 55.000 0.00 0.00 0.00 2.32
612 632 2.961424 CGGAAGGAACCCAGCAAAT 58.039 52.632 0.00 0.00 0.00 2.32
613 633 4.492604 CGGAAGGAACCCAGCAAA 57.507 55.556 0.00 0.00 0.00 3.68
627 647 0.970640 TTGAACAAGGTCGATCCGGA 59.029 50.000 6.61 6.61 41.99 5.14
630 650 2.017049 CCCATTGAACAAGGTCGATCC 58.983 52.381 0.00 0.00 0.00 3.36
653 673 5.373812 AGGACCACAATATCAAACTAGGG 57.626 43.478 0.00 0.00 0.00 3.53
654 674 6.414732 TCAAGGACCACAATATCAAACTAGG 58.585 40.000 0.00 0.00 0.00 3.02
656 676 7.861629 AGATCAAGGACCACAATATCAAACTA 58.138 34.615 0.00 0.00 0.00 2.24
681 715 4.350368 TGCAGGAGACAAAGAACACATA 57.650 40.909 0.00 0.00 0.00 2.29
684 718 5.886960 ATTATGCAGGAGACAAAGAACAC 57.113 39.130 0.00 0.00 0.00 3.32
689 723 8.299570 AGTACAAAAATTATGCAGGAGACAAAG 58.700 33.333 0.00 0.00 0.00 2.77
722 756 5.846473 GTCTTCGTCTCAAAATAAGTGTTGC 59.154 40.000 0.00 0.00 0.00 4.17
793 832 6.476243 TCAGTTTCGGAGTTTGCTAATTAC 57.524 37.500 0.00 0.00 0.00 1.89
874 916 1.420138 TGGAGGAAAGGTGAACTGGTC 59.580 52.381 0.00 0.00 0.00 4.02
896 938 0.667487 TTCGAGAGCACAGAAAGGCG 60.667 55.000 0.00 0.00 34.54 5.52
936 978 2.225068 TAAGTAGATCAAGCAGCGCC 57.775 50.000 2.29 0.00 0.00 6.53
937 979 2.285488 GGTTAAGTAGATCAAGCAGCGC 59.715 50.000 0.00 0.00 0.00 5.92
965 1011 2.605837 TTTGCGTGTTGGTCAGTAGA 57.394 45.000 0.00 0.00 0.00 2.59
1152 1198 1.361668 CGGTGATGTTGAGGCTTCCG 61.362 60.000 0.00 0.00 0.00 4.30
1169 1215 3.827898 GGAGGAGCTCGTGGTCGG 61.828 72.222 14.78 0.00 41.26 4.79
1413 1459 0.761323 TGAACACGGGGTCCTTCTGA 60.761 55.000 0.00 0.00 0.00 3.27
1458 1504 3.964875 CTGTTGCACGGCACCACC 61.965 66.667 0.00 0.00 38.71 4.61
1605 1651 2.509336 CCGATGGTCAGCGTGTCC 60.509 66.667 7.81 0.00 38.74 4.02
1912 1958 1.153369 CCTTGTCGCCGATGGACAT 60.153 57.895 0.00 0.00 43.37 3.06
1947 1993 2.806856 CGCGTTCATGCTGCTCCTC 61.807 63.158 0.00 0.00 0.00 3.71
1987 2033 4.671590 GTTGGGGTTGGGGTCGGG 62.672 72.222 0.00 0.00 0.00 5.14
1989 2035 4.259131 ACGTTGGGGTTGGGGTCG 62.259 66.667 0.00 0.00 0.00 4.79
2065 2123 0.039437 ATGATCATCCCGTACGCGTC 60.039 55.000 18.63 6.85 36.15 5.19
2072 2130 1.068264 CGATGTCGATGATCATCCCGT 60.068 52.381 26.30 18.83 43.02 5.28
2186 2244 4.748798 AGAGGTCCAGCCCCAGGG 62.749 72.222 0.00 0.00 38.26 4.45
2218 2276 4.554036 GCTCATCGGCACCCCCTC 62.554 72.222 0.00 0.00 0.00 4.30
2299 2357 1.079750 GGTCCTCCACGAACAGCTC 60.080 63.158 0.00 0.00 0.00 4.09
2300 2358 2.932234 CGGTCCTCCACGAACAGCT 61.932 63.158 0.00 0.00 0.00 4.24
2317 2375 2.341543 CATCATCCCGCTCTCCCG 59.658 66.667 0.00 0.00 0.00 5.14
2455 2513 4.100808 AGAGAAATCCTAGTGAGTCATGGC 59.899 45.833 0.00 0.00 0.00 4.40
2501 2590 7.536855 CCGTACCTATCCTATTTGATGTCTAC 58.463 42.308 0.00 0.00 0.00 2.59
2510 2599 3.307480 GCCATGCCGTACCTATCCTATTT 60.307 47.826 0.00 0.00 0.00 1.40
2513 2602 1.263356 GCCATGCCGTACCTATCCTA 58.737 55.000 0.00 0.00 0.00 2.94
2527 2616 1.065701 GAAGCAGAGCTCAATGCCATG 59.934 52.381 20.84 8.21 43.60 3.66
2604 2705 8.836268 ATGTAAAAATGCACTCACAAATTCAT 57.164 26.923 0.00 0.00 0.00 2.57
2687 2788 5.559427 TGCAAAAAGGAAAAGGAAAAAGC 57.441 34.783 0.00 0.00 0.00 3.51
2694 2795 9.921637 TTTATACAGTATGCAAAAAGGAAAAGG 57.078 29.630 3.03 0.00 42.53 3.11
2700 2801 9.009327 CGTTCATTTATACAGTATGCAAAAAGG 57.991 33.333 3.03 0.00 42.53 3.11
2716 2817 9.139174 GTGGATTCACAAATTTCGTTCATTTAT 57.861 29.630 0.00 0.00 43.13 1.40
2717 2818 8.514136 GTGGATTCACAAATTTCGTTCATTTA 57.486 30.769 0.00 0.00 43.13 1.40
2718 2819 7.406799 GTGGATTCACAAATTTCGTTCATTT 57.593 32.000 0.00 0.00 43.13 2.32
2743 2844 8.465999 TGTGCGAATATAAAATTCACATTCCTT 58.534 29.630 0.00 0.00 0.00 3.36
2745 2846 8.627487 TTGTGCGAATATAAAATTCACATTCC 57.373 30.769 0.00 0.00 0.00 3.01
2761 2862 4.871933 AAAAGAATTCCCTTGTGCGAAT 57.128 36.364 0.65 0.00 0.00 3.34
2784 2885 6.140377 AGTAGAATGGGACCCAAAAGAAAAA 58.860 36.000 19.58 0.00 36.95 1.94
2785 2886 5.711698 AGTAGAATGGGACCCAAAAGAAAA 58.288 37.500 19.58 0.00 36.95 2.29
2789 2890 7.119387 AGAAATAGTAGAATGGGACCCAAAAG 58.881 38.462 19.58 0.00 36.95 2.27
2794 2895 5.280062 GCCTAGAAATAGTAGAATGGGACCC 60.280 48.000 2.45 2.45 0.00 4.46
2795 2896 5.544562 AGCCTAGAAATAGTAGAATGGGACC 59.455 44.000 0.00 0.00 0.00 4.46
2809 2910 3.294214 CCAATGCAAGGAGCCTAGAAAT 58.706 45.455 2.49 0.00 44.83 2.17
2867 5182 3.066291 TGGTAATGATGTTTCCGCACT 57.934 42.857 0.00 0.00 0.00 4.40
2868 5183 3.627577 AGATGGTAATGATGTTTCCGCAC 59.372 43.478 0.00 0.00 0.00 5.34
2869 5184 3.876914 GAGATGGTAATGATGTTTCCGCA 59.123 43.478 0.00 0.00 0.00 5.69
2870 5185 3.876914 TGAGATGGTAATGATGTTTCCGC 59.123 43.478 0.00 0.00 0.00 5.54
2871 5186 5.118990 AGTGAGATGGTAATGATGTTTCCG 58.881 41.667 0.00 0.00 0.00 4.30
2872 5187 7.396540 AAAGTGAGATGGTAATGATGTTTCC 57.603 36.000 0.00 0.00 0.00 3.13
2873 5188 9.941664 CATAAAGTGAGATGGTAATGATGTTTC 57.058 33.333 0.00 0.00 0.00 2.78
2874 5189 9.466497 ACATAAAGTGAGATGGTAATGATGTTT 57.534 29.630 0.00 0.00 0.00 2.83
2911 5227 4.492646 TCATGCCCCTCTATAGATGACAA 58.507 43.478 2.11 0.00 0.00 3.18
3021 5339 3.000078 GCAGACACCGTGTAATAATGTCG 60.000 47.826 3.58 0.00 43.54 4.35
3117 5435 8.032952 TCTTATAGAAAATCTGCAAGTGTGTG 57.967 34.615 0.00 0.00 33.76 3.82
3158 5476 7.648039 AAACAAAATAGGTAAGGTTGTCACA 57.352 32.000 0.00 0.00 31.41 3.58
3185 5503 1.939934 CTGTTCAAACTTGAGGACGCA 59.060 47.619 0.00 0.00 38.61 5.24
3213 5531 2.343484 GGCCCAACTGGACCTAATAC 57.657 55.000 0.00 0.00 35.25 1.89
3236 5554 3.206964 GTTCAGGCAAATCTACCTAGCC 58.793 50.000 0.00 0.00 45.54 3.93
3276 5594 6.210287 TGAACTGAAACCGTGGTTAATTTT 57.790 33.333 4.41 0.00 37.35 1.82
3288 5606 8.063630 CAGCATTATTTTGTTTGAACTGAAACC 58.936 33.333 0.00 0.00 35.34 3.27
3364 5683 3.076032 AGGAGGCCAACCAAAACTATCTT 59.924 43.478 18.84 0.00 39.06 2.40
3433 5752 9.178758 AGCTCTTGGTATAATTGGTTAAAGAAG 57.821 33.333 0.00 0.00 0.00 2.85
3436 5755 8.506168 TGAGCTCTTGGTATAATTGGTTAAAG 57.494 34.615 16.19 0.00 0.00 1.85
3442 5761 9.956720 CTTAAAATGAGCTCTTGGTATAATTGG 57.043 33.333 16.19 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.