Multiple sequence alignment - TraesCS5D01G534300

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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 TraesCS5D01G534300 chr5D 100.000 2757 0 0 1 2757 548478594 548481350 0.000000e+00 5092
1 TraesCS5D01G534300 chr5D 83.019 1113 92 56 668 1714 548460143 548461224 0.000000e+00 918
2 TraesCS5D01G534300 chr5D 84.823 481 49 14 63 531 548468506 548468974 1.930000e-126 462
3 TraesCS5D01G534300 chr5D 76.949 295 21 17 1401 1692 548374347 548374597 1.040000e-24 124
4 TraesCS5D01G534300 chr5B 86.368 2252 135 64 608 2757 692690729 692692910 0.000000e+00 2300
5 TraesCS5D01G534300 chr5B 79.983 1179 128 65 594 1714 692678235 692679363 0.000000e+00 771
6 TraesCS5D01G534300 chr5B 83.133 498 57 14 40 531 692690224 692690700 1.960000e-116 429
7 TraesCS5D01G534300 chr5B 79.495 317 37 10 936 1240 692648690 692648990 1.670000e-47 200
8 TraesCS5D01G534300 chr5B 81.481 243 16 13 671 900 692648482 692648708 3.650000e-39 172
9 TraesCS5D01G534300 chr4A 87.781 1866 107 47 965 2755 619369940 619371759 0.000000e+00 2071
10 TraesCS5D01G534300 chr4A 83.531 844 77 41 907 1714 619333527 619334344 0.000000e+00 732
11 TraesCS5D01G534300 chr4A 81.688 557 58 27 64 586 619369015 619369561 9.130000e-115 424
12 TraesCS5D01G534300 chr4A 79.639 609 71 26 1102 1689 619312346 619312922 3.330000e-104 388
13 TraesCS5D01G534300 chr4A 85.068 221 18 11 602 814 619333129 619333342 7.740000e-51 211
14 TraesCS5D01G534300 chr4B 88.788 553 46 6 2220 2757 650049572 650050123 0.000000e+00 664
15 TraesCS5D01G534300 chr4B 88.788 553 46 7 2220 2757 650179629 650180180 0.000000e+00 664
16 TraesCS5D01G534300 chr4B 88.427 553 48 6 2220 2757 650059181 650059732 0.000000e+00 652
17 TraesCS5D01G534300 chr4B 87.884 553 50 7 2220 2757 650117969 650118519 3.870000e-178 634
18 TraesCS5D01G534300 chr6B 87.477 551 51 7 2222 2757 49267878 49268425 1.080000e-173 619


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 TraesCS5D01G534300 chr5D 548478594 548481350 2756 False 5092.0 5092 100.0000 1 2757 1 chr5D.!!$F4 2756
1 TraesCS5D01G534300 chr5D 548460143 548461224 1081 False 918.0 918 83.0190 668 1714 1 chr5D.!!$F2 1046
2 TraesCS5D01G534300 chr5B 692690224 692692910 2686 False 1364.5 2300 84.7505 40 2757 2 chr5B.!!$F3 2717
3 TraesCS5D01G534300 chr5B 692678235 692679363 1128 False 771.0 771 79.9830 594 1714 1 chr5B.!!$F1 1120
4 TraesCS5D01G534300 chr4A 619369015 619371759 2744 False 1247.5 2071 84.7345 64 2755 2 chr4A.!!$F3 2691
5 TraesCS5D01G534300 chr4A 619333129 619334344 1215 False 471.5 732 84.2995 602 1714 2 chr4A.!!$F2 1112
6 TraesCS5D01G534300 chr4A 619312346 619312922 576 False 388.0 388 79.6390 1102 1689 1 chr4A.!!$F1 587
7 TraesCS5D01G534300 chr4B 650049572 650050123 551 False 664.0 664 88.7880 2220 2757 1 chr4B.!!$F1 537
8 TraesCS5D01G534300 chr4B 650179629 650180180 551 False 664.0 664 88.7880 2220 2757 1 chr4B.!!$F4 537
9 TraesCS5D01G534300 chr4B 650059181 650059732 551 False 652.0 652 88.4270 2220 2757 1 chr4B.!!$F2 537
10 TraesCS5D01G534300 chr4B 650117969 650118519 550 False 634.0 634 87.8840 2220 2757 1 chr4B.!!$F3 537
11 TraesCS5D01G534300 chr6B 49267878 49268425 547 False 619.0 619 87.4770 2222 2757 1 chr6B.!!$F1 535

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
900 1009 0.041982 ACCCTGTCTCCCTCTTCCTC 59.958 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2674 3054 0.251354 TTCAGACTGAGGCCTGCATC 59.749 55.0 12.0 3.94 0.0 3.91 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
37 38 8.498054 AAACATGTTACATTATGAGACTGAGG 57.502 34.615 12.39 0.00 0.00 3.86
38 39 6.586344 ACATGTTACATTATGAGACTGAGGG 58.414 40.000 0.00 0.00 0.00 4.30
55 56 8.282982 AGACTGAGGGAGTAGTAATTATGAAGA 58.717 37.037 0.00 0.00 33.83 2.87
142 145 3.006752 GGAACCAATCCTTGCACATTTCA 59.993 43.478 0.00 0.00 45.56 2.69
145 148 4.634199 ACCAATCCTTGCACATTTCAAAG 58.366 39.130 0.00 0.00 0.00 2.77
155 158 8.400186 CCTTGCACATTTCAAAGAAAGAAAAAT 58.600 29.630 0.00 0.00 38.36 1.82
170 173 7.715686 AGAAAGAAAAATATTAGCCTAGACCCG 59.284 37.037 0.00 0.00 0.00 5.28
174 177 4.473477 AATATTAGCCTAGACCCGATGC 57.527 45.455 0.00 0.00 0.00 3.91
183 186 1.156736 AGACCCGATGCAAAAGTTCG 58.843 50.000 0.00 0.00 0.00 3.95
212 215 8.501904 TCCTATGAATGAAATGACATCCCTTTA 58.498 33.333 0.00 0.00 0.00 1.85
217 220 9.565090 TGAATGAAATGACATCCCTTTATCTAG 57.435 33.333 0.00 0.00 0.00 2.43
228 231 9.890915 ACATCCCTTTATCTAGAGAACTAAGAT 57.109 33.333 0.00 0.00 0.00 2.40
260 263 9.480861 TTCTCACGATATTCCTATCCTATGAAT 57.519 33.333 0.00 0.00 31.67 2.57
276 279 6.769822 TCCTATGAATCAAAGAAGCCTTCATC 59.230 38.462 7.29 0.00 37.62 2.92
287 290 5.809001 AGAAGCCTTCATCTGAAACATACA 58.191 37.500 7.29 0.00 33.07 2.29
334 341 2.077627 TGCGATAACTTTTTAGCCGCA 58.922 42.857 0.00 0.00 44.20 5.69
388 396 5.547465 TCAACCATAATCTCAAGTCACGTT 58.453 37.500 0.00 0.00 0.00 3.99
391 399 5.305585 ACCATAATCTCAAGTCACGTTGTT 58.694 37.500 0.00 0.00 0.00 2.83
403 411 4.083217 AGTCACGTTGTTGCACTTTTACAA 60.083 37.500 0.00 0.00 0.00 2.41
408 416 7.541091 TCACGTTGTTGCACTTTTACAATTTTA 59.459 29.630 4.34 0.00 34.63 1.52
409 417 8.162880 CACGTTGTTGCACTTTTACAATTTTAA 58.837 29.630 4.34 0.00 34.63 1.52
410 418 8.709646 ACGTTGTTGCACTTTTACAATTTTAAA 58.290 25.926 4.34 0.00 34.63 1.52
411 419 9.193602 CGTTGTTGCACTTTTACAATTTTAAAG 57.806 29.630 4.34 0.00 34.63 1.85
412 420 9.484326 GTTGTTGCACTTTTACAATTTTAAAGG 57.516 29.630 4.34 5.05 34.63 3.11
413 421 9.436957 TTGTTGCACTTTTACAATTTTAAAGGA 57.563 25.926 11.79 0.00 34.10 3.36
415 423 8.874816 GTTGCACTTTTACAATTTTAAAGGACA 58.125 29.630 11.79 7.52 34.10 4.02
457 500 1.546476 CGTCAAGAGAGTAGGGTGCTT 59.454 52.381 0.00 0.00 0.00 3.91
458 501 2.672478 CGTCAAGAGAGTAGGGTGCTTG 60.672 54.545 0.00 0.00 37.79 4.01
515 558 6.421202 CCAGTTTATATGAGAAACTAGGTCGC 59.579 42.308 2.52 0.00 43.59 5.19
531 574 0.107410 TCGCAAACCACACTTCCACT 60.107 50.000 0.00 0.00 0.00 4.00
532 575 1.139256 TCGCAAACCACACTTCCACTA 59.861 47.619 0.00 0.00 0.00 2.74
533 576 2.151202 CGCAAACCACACTTCCACTAT 58.849 47.619 0.00 0.00 0.00 2.12
534 577 2.552315 CGCAAACCACACTTCCACTATT 59.448 45.455 0.00 0.00 0.00 1.73
543 586 4.675114 CACACTTCCACTATTCGCAAAAAC 59.325 41.667 0.00 0.00 0.00 2.43
545 588 4.675114 CACTTCCACTATTCGCAAAAACAC 59.325 41.667 0.00 0.00 0.00 3.32
547 590 4.217754 TCCACTATTCGCAAAAACACAC 57.782 40.909 0.00 0.00 0.00 3.82
549 592 3.728718 CCACTATTCGCAAAAACACACAC 59.271 43.478 0.00 0.00 0.00 3.82
551 594 4.204168 CACTATTCGCAAAAACACACACAC 59.796 41.667 0.00 0.00 0.00 3.82
554 597 1.266989 TCGCAAAAACACACACACACA 59.733 42.857 0.00 0.00 0.00 3.72
555 598 1.385075 CGCAAAAACACACACACACAC 59.615 47.619 0.00 0.00 0.00 3.82
556 599 2.398498 GCAAAAACACACACACACACA 58.602 42.857 0.00 0.00 0.00 3.72
557 600 2.154772 GCAAAAACACACACACACACAC 59.845 45.455 0.00 0.00 0.00 3.82
558 601 3.375642 CAAAAACACACACACACACACA 58.624 40.909 0.00 0.00 0.00 3.72
559 602 2.697431 AAACACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
560 603 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
562 605 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
563 606 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
564 607 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
565 608 1.535028 CACACACACACACACACACTT 59.465 47.619 0.00 0.00 0.00 3.16
570 613 2.076100 ACACACACACACACTTCACAG 58.924 47.619 0.00 0.00 0.00 3.66
579 622 2.545526 ACACACTTCACAGCGAATTGAG 59.454 45.455 0.00 0.00 36.61 3.02
586 629 2.560981 TCACAGCGAATTGAGACACCTA 59.439 45.455 0.00 0.00 0.00 3.08
588 631 3.745975 CACAGCGAATTGAGACACCTAAA 59.254 43.478 0.00 0.00 0.00 1.85
589 632 4.393062 CACAGCGAATTGAGACACCTAAAT 59.607 41.667 0.00 0.00 0.00 1.40
591 634 4.872691 CAGCGAATTGAGACACCTAAATCT 59.127 41.667 0.00 0.00 0.00 2.40
592 635 4.872691 AGCGAATTGAGACACCTAAATCTG 59.127 41.667 0.00 0.00 0.00 2.90
600 643 9.911788 ATTGAGACACCTAAATCTGTAATTCAT 57.088 29.630 0.00 0.00 0.00 2.57
632 676 1.243902 GCCCAAAAGGATGACACGAA 58.756 50.000 0.00 0.00 38.24 3.85
639 683 5.215160 CAAAAGGATGACACGAAAAAGAGG 58.785 41.667 0.00 0.00 0.00 3.69
642 686 3.003480 GGATGACACGAAAAAGAGGGAG 58.997 50.000 0.00 0.00 0.00 4.30
643 687 2.543777 TGACACGAAAAAGAGGGAGG 57.456 50.000 0.00 0.00 0.00 4.30
646 690 1.348036 ACACGAAAAAGAGGGAGGAGG 59.652 52.381 0.00 0.00 0.00 4.30
647 691 1.623811 CACGAAAAAGAGGGAGGAGGA 59.376 52.381 0.00 0.00 0.00 3.71
648 692 1.903183 ACGAAAAAGAGGGAGGAGGAG 59.097 52.381 0.00 0.00 0.00 3.69
649 693 1.208293 CGAAAAAGAGGGAGGAGGAGG 59.792 57.143 0.00 0.00 0.00 4.30
650 694 2.552367 GAAAAAGAGGGAGGAGGAGGA 58.448 52.381 0.00 0.00 0.00 3.71
655 699 0.185175 GAGGGAGGAGGAGGAGAGAC 59.815 65.000 0.00 0.00 0.00 3.36
698 749 1.209261 TCCACTAGCGAAATGATGGCA 59.791 47.619 0.00 0.00 34.79 4.92
758 819 1.121850 CGCAATTGATGTGCACGTCG 61.122 55.000 28.96 18.04 42.33 5.12
780 841 3.222855 CCCGGCACCAGCAACAAA 61.223 61.111 0.00 0.00 44.61 2.83
781 842 2.790791 CCCGGCACCAGCAACAAAA 61.791 57.895 0.00 0.00 44.61 2.44
871 953 4.332828 ACCATGCTACCAAAACTAACCTC 58.667 43.478 0.00 0.00 0.00 3.85
872 954 3.694566 CCATGCTACCAAAACTAACCTCC 59.305 47.826 0.00 0.00 0.00 4.30
873 959 4.331968 CATGCTACCAAAACTAACCTCCA 58.668 43.478 0.00 0.00 0.00 3.86
881 967 6.969043 ACCAAAACTAACCTCCATGATGATA 58.031 36.000 0.00 0.00 0.00 2.15
896 1005 3.051803 TGATGATACCCTGTCTCCCTCTT 60.052 47.826 0.00 0.00 0.00 2.85
897 1006 3.033659 TGATACCCTGTCTCCCTCTTC 57.966 52.381 0.00 0.00 0.00 2.87
898 1007 2.321719 GATACCCTGTCTCCCTCTTCC 58.678 57.143 0.00 0.00 0.00 3.46
899 1008 1.394532 TACCCTGTCTCCCTCTTCCT 58.605 55.000 0.00 0.00 0.00 3.36
900 1009 0.041982 ACCCTGTCTCCCTCTTCCTC 59.958 60.000 0.00 0.00 0.00 3.71
901 1010 1.040339 CCCTGTCTCCCTCTTCCTCG 61.040 65.000 0.00 0.00 0.00 4.63
905 1066 0.681564 GTCTCCCTCTTCCTCGCTCA 60.682 60.000 0.00 0.00 0.00 4.26
939 1100 0.110486 TCTCTCACCAAACCTTGCCC 59.890 55.000 0.00 0.00 0.00 5.36
949 1110 0.540597 AACCTTGCCCTGCTTTCCTC 60.541 55.000 0.00 0.00 0.00 3.71
1030 1220 3.013219 GCATCTTTCTTCCAACCCTCTC 58.987 50.000 0.00 0.00 0.00 3.20
1062 1252 2.162608 CAGAACCTCCGTAGTCTCAGTG 59.837 54.545 0.00 0.00 0.00 3.66
1074 1270 3.417101 AGTCTCAGTGTCAATCGTCTCT 58.583 45.455 0.00 0.00 0.00 3.10
1300 1530 4.025040 TCATATGAAGATCCATGCCACC 57.975 45.455 1.98 0.00 0.00 4.61
1327 1564 3.334691 TCCACATACTAACAGCAAGCAC 58.665 45.455 0.00 0.00 0.00 4.40
1460 1727 2.047179 AAGACCTTCTTCGCGGCC 60.047 61.111 6.13 0.00 28.99 6.13
1478 1745 2.821366 TACGACGGCGAGGAGGAC 60.821 66.667 22.49 0.00 41.64 3.85
1736 2023 2.027625 CGAGCTCGACAAACCACCC 61.028 63.158 32.06 0.00 43.02 4.61
1843 2131 9.757227 TTACCTTGTCATTTGGTAAAATCTTTG 57.243 29.630 9.03 0.00 41.59 2.77
1856 2147 9.384764 TGGTAAAATCTTTGTTTTAACTTTGGG 57.615 29.630 8.19 0.00 40.32 4.12
1857 2148 9.386010 GGTAAAATCTTTGTTTTAACTTTGGGT 57.614 29.630 1.14 0.00 37.93 4.51
1863 2154 8.754991 TCTTTGTTTTAACTTTGGGTGAGATA 57.245 30.769 0.00 0.00 0.00 1.98
1893 2184 9.958180 AAGCATATGCATAGGTTTGTGTATATA 57.042 29.630 28.62 0.00 45.16 0.86
1900 2191 9.732130 TGCATAGGTTTGTGTATATATTATGCA 57.268 29.630 14.52 14.52 44.78 3.96
1994 2286 4.760220 TGGGGCCCCCTCTCTTCC 62.760 72.222 38.81 10.43 45.70 3.46
2099 2401 7.618502 TGGTACAATAATAGTCGTGCAAATT 57.381 32.000 0.00 0.00 31.92 1.82
2100 2402 8.046294 TGGTACAATAATAGTCGTGCAAATTT 57.954 30.769 0.00 0.00 31.92 1.82
2111 2413 7.667043 AGTCGTGCAAATTTATTCAAGTCTA 57.333 32.000 0.00 0.00 0.00 2.59
2179 2496 4.127171 AGTACTGCATAATGGTTAAGGCG 58.873 43.478 0.00 0.00 0.00 5.52
2211 2528 5.127194 TCGTTTGTTCATCATAGACCTAGCT 59.873 40.000 0.00 0.00 0.00 3.32
2214 2543 5.713792 TGTTCATCATAGACCTAGCTAGC 57.286 43.478 15.74 6.62 0.00 3.42
2216 2545 6.543735 TGTTCATCATAGACCTAGCTAGCTA 58.456 40.000 22.85 22.85 0.00 3.32
2217 2546 6.657117 TGTTCATCATAGACCTAGCTAGCTAG 59.343 42.308 35.39 35.39 44.07 3.42
2218 2547 6.628644 TCATCATAGACCTAGCTAGCTAGA 57.371 41.667 40.98 27.02 46.56 2.43
2220 2549 7.053498 TCATCATAGACCTAGCTAGCTAGATG 58.947 42.308 40.98 34.17 46.56 2.90
2221 2550 5.189928 TCATAGACCTAGCTAGCTAGATGC 58.810 45.833 40.98 30.12 46.56 3.91
2222 2551 2.802719 AGACCTAGCTAGCTAGATGCC 58.197 52.381 40.98 27.88 46.56 4.40
2223 2552 2.109128 AGACCTAGCTAGCTAGATGCCA 59.891 50.000 40.98 15.96 46.56 4.92
2225 2554 2.109128 ACCTAGCTAGCTAGATGCCAGA 59.891 50.000 40.98 14.57 46.56 3.86
2229 2579 1.622811 GCTAGCTAGATGCCAGATGGT 59.377 52.381 25.15 0.00 44.23 3.55
2304 2654 7.973944 CAGAATCATGATCAAATCTGCTTTCAA 59.026 33.333 17.82 0.00 0.00 2.69
2314 2664 7.995289 TCAAATCTGCTTTCAACTTAGACAAA 58.005 30.769 0.00 0.00 0.00 2.83
2363 2713 3.000727 GTCGACCCGATCAAAATTCAGT 58.999 45.455 3.51 0.00 38.42 3.41
2401 2757 4.693566 ACAGTATAAACGTGTTCACATGGG 59.306 41.667 0.00 0.00 37.19 4.00
2426 2782 4.627035 GGCAGTCCTACAAAAATGCAAATC 59.373 41.667 0.00 0.00 35.40 2.17
2489 2851 0.605319 GTGAATCCGTGGCCACTGAA 60.605 55.000 30.39 17.57 0.00 3.02
2503 2865 3.898627 CTGAACCGAGCTGACGCGT 62.899 63.158 13.85 13.85 42.32 6.01
2519 2881 1.193874 CGCGTTCCTTAACCAGTCAAC 59.806 52.381 0.00 0.00 31.46 3.18
2628 2995 7.429920 CGTGACTCACTACTTAGCTTCTTTATC 59.570 40.741 7.58 0.00 31.34 1.75
2637 3017 7.141758 ACTTAGCTTCTTTATCATCATGGGA 57.858 36.000 0.00 0.00 0.00 4.37
2674 3054 5.240891 TCAAGTTCAAGACAGATTAGCAGG 58.759 41.667 0.00 0.00 0.00 4.85
2723 3103 0.168128 CGCAACGGGGAACAGATTTC 59.832 55.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.950210 CCTCAGTCTCATAATGTAACATGTTTT 58.050 33.333 17.78 7.81 0.00 2.43
12 13 7.554118 CCCTCAGTCTCATAATGTAACATGTTT 59.446 37.037 17.78 0.51 0.00 2.83
13 14 7.050377 CCCTCAGTCTCATAATGTAACATGTT 58.950 38.462 16.68 16.68 0.00 2.71
14 15 6.384015 TCCCTCAGTCTCATAATGTAACATGT 59.616 38.462 0.00 0.00 0.00 3.21
15 16 6.820335 TCCCTCAGTCTCATAATGTAACATG 58.180 40.000 0.00 0.00 0.00 3.21
16 17 6.613271 ACTCCCTCAGTCTCATAATGTAACAT 59.387 38.462 0.00 0.00 0.00 2.71
17 18 5.958380 ACTCCCTCAGTCTCATAATGTAACA 59.042 40.000 0.00 0.00 0.00 2.41
18 19 6.472686 ACTCCCTCAGTCTCATAATGTAAC 57.527 41.667 0.00 0.00 0.00 2.50
19 20 7.355101 ACTACTCCCTCAGTCTCATAATGTAA 58.645 38.462 0.00 0.00 36.43 2.41
20 21 6.912426 ACTACTCCCTCAGTCTCATAATGTA 58.088 40.000 0.00 0.00 36.43 2.29
21 22 5.772004 ACTACTCCCTCAGTCTCATAATGT 58.228 41.667 0.00 0.00 36.43 2.71
22 23 7.825331 TTACTACTCCCTCAGTCTCATAATG 57.175 40.000 0.00 0.00 36.43 1.90
25 26 9.521841 CATAATTACTACTCCCTCAGTCTCATA 57.478 37.037 0.00 0.00 36.43 2.15
26 27 8.228206 TCATAATTACTACTCCCTCAGTCTCAT 58.772 37.037 0.00 0.00 36.43 2.90
27 28 7.583625 TCATAATTACTACTCCCTCAGTCTCA 58.416 38.462 0.00 0.00 36.43 3.27
28 29 8.466617 TTCATAATTACTACTCCCTCAGTCTC 57.533 38.462 0.00 0.00 36.43 3.36
29 30 8.282982 TCTTCATAATTACTACTCCCTCAGTCT 58.717 37.037 0.00 0.00 36.43 3.24
30 31 8.466617 TCTTCATAATTACTACTCCCTCAGTC 57.533 38.462 0.00 0.00 36.43 3.51
31 32 8.840200 TTCTTCATAATTACTACTCCCTCAGT 57.160 34.615 0.00 0.00 39.41 3.41
83 86 4.825085 TCATTTCTACAACCCAACAGTTCC 59.175 41.667 0.00 0.00 0.00 3.62
89 92 6.443792 ACGAAATTCATTTCTACAACCCAAC 58.556 36.000 9.95 0.00 42.96 3.77
145 148 7.713942 TCGGGTCTAGGCTAATATTTTTCTTTC 59.286 37.037 0.00 0.00 0.00 2.62
155 158 2.884320 TGCATCGGGTCTAGGCTAATA 58.116 47.619 0.00 0.00 0.00 0.98
170 173 6.844696 TCATAGGATACGAACTTTTGCATC 57.155 37.500 0.00 0.00 46.39 3.91
183 186 8.105829 AGGGATGTCATTTCATTCATAGGATAC 58.894 37.037 0.00 0.00 0.00 2.24
247 250 6.777782 AGGCTTCTTTGATTCATAGGATAGG 58.222 40.000 4.57 0.00 0.00 2.57
260 263 5.132502 TGTTTCAGATGAAGGCTTCTTTGA 58.867 37.500 26.26 21.64 35.21 2.69
300 303 6.268825 AGTTATCGCAGAGTCTTCACTAAA 57.731 37.500 0.00 0.00 43.63 1.85
304 307 5.847670 AAAAGTTATCGCAGAGTCTTCAC 57.152 39.130 0.00 0.00 43.63 3.18
351 358 0.037232 GGTTGAACTCTCCCGGTCTG 60.037 60.000 0.00 0.00 0.00 3.51
388 396 8.874816 GTCCTTTAAAATTGTAAAAGTGCAACA 58.125 29.630 2.51 0.00 41.43 3.33
391 399 9.606631 ATTGTCCTTTAAAATTGTAAAAGTGCA 57.393 25.926 2.51 0.00 0.00 4.57
408 416 6.101005 TCCCATCCAAAAGAAAATTGTCCTTT 59.899 34.615 0.00 0.00 0.00 3.11
409 417 5.606329 TCCCATCCAAAAGAAAATTGTCCTT 59.394 36.000 0.00 0.00 0.00 3.36
410 418 5.012046 GTCCCATCCAAAAGAAAATTGTCCT 59.988 40.000 0.00 0.00 0.00 3.85
411 419 5.237815 GTCCCATCCAAAAGAAAATTGTCC 58.762 41.667 0.00 0.00 0.00 4.02
412 420 5.012046 AGGTCCCATCCAAAAGAAAATTGTC 59.988 40.000 0.00 0.00 0.00 3.18
413 421 4.907269 AGGTCCCATCCAAAAGAAAATTGT 59.093 37.500 0.00 0.00 0.00 2.71
415 423 4.220602 CGAGGTCCCATCCAAAAGAAAATT 59.779 41.667 0.00 0.00 0.00 1.82
418 426 2.107552 ACGAGGTCCCATCCAAAAGAAA 59.892 45.455 0.00 0.00 0.00 2.52
421 462 1.003118 TGACGAGGTCCCATCCAAAAG 59.997 52.381 0.00 0.00 0.00 2.27
429 470 0.112606 ACTCTCTTGACGAGGTCCCA 59.887 55.000 0.00 0.00 40.30 4.37
479 522 7.466804 TCTCATATAAACTGGACCAAGGTTTT 58.533 34.615 14.94 6.31 35.29 2.43
484 527 9.319143 CTAGTTTCTCATATAAACTGGACCAAG 57.681 37.037 10.93 0.00 43.95 3.61
515 558 3.364964 GCGAATAGTGGAAGTGTGGTTTG 60.365 47.826 0.00 0.00 0.00 2.93
531 574 4.099120 GTGTGTGTGTGTTTTTGCGAATA 58.901 39.130 0.00 0.00 0.00 1.75
532 575 2.920490 GTGTGTGTGTGTTTTTGCGAAT 59.080 40.909 0.00 0.00 0.00 3.34
533 576 2.287608 TGTGTGTGTGTGTTTTTGCGAA 60.288 40.909 0.00 0.00 0.00 4.70
534 577 1.266989 TGTGTGTGTGTGTTTTTGCGA 59.733 42.857 0.00 0.00 0.00 5.10
543 586 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
545 588 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
547 590 1.803555 TGAAGTGTGTGTGTGTGTGTG 59.196 47.619 0.00 0.00 0.00 3.82
549 592 1.803555 TGTGAAGTGTGTGTGTGTGTG 59.196 47.619 0.00 0.00 0.00 3.82
551 594 1.202065 GCTGTGAAGTGTGTGTGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
554 597 0.108377 TCGCTGTGAAGTGTGTGTGT 60.108 50.000 0.00 0.00 0.00 3.72
555 598 1.006086 TTCGCTGTGAAGTGTGTGTG 58.994 50.000 0.00 0.00 31.44 3.82
556 599 1.953559 ATTCGCTGTGAAGTGTGTGT 58.046 45.000 9.71 0.00 40.65 3.72
557 600 2.642995 CAATTCGCTGTGAAGTGTGTG 58.357 47.619 19.76 5.46 45.24 3.82
562 605 2.802816 GTGTCTCAATTCGCTGTGAAGT 59.197 45.455 9.71 3.84 40.65 3.01
563 606 2.158449 GGTGTCTCAATTCGCTGTGAAG 59.842 50.000 9.71 0.00 40.65 3.02
564 607 2.143122 GGTGTCTCAATTCGCTGTGAA 58.857 47.619 6.06 6.06 41.81 3.18
565 608 1.344438 AGGTGTCTCAATTCGCTGTGA 59.656 47.619 0.00 0.00 0.00 3.58
570 613 4.631813 ACAGATTTAGGTGTCTCAATTCGC 59.368 41.667 0.00 0.00 0.00 4.70
586 629 7.013655 GGGTGCAGTGATATGAATTACAGATTT 59.986 37.037 0.00 0.00 30.06 2.17
588 631 6.000219 GGGTGCAGTGATATGAATTACAGAT 59.000 40.000 0.00 0.00 32.79 2.90
589 632 5.368145 GGGTGCAGTGATATGAATTACAGA 58.632 41.667 0.00 0.00 0.00 3.41
591 634 4.126437 CGGGTGCAGTGATATGAATTACA 58.874 43.478 0.00 0.00 0.00 2.41
592 635 3.058914 GCGGGTGCAGTGATATGAATTAC 60.059 47.826 0.00 0.00 42.15 1.89
600 643 2.130821 TTTGGGCGGGTGCAGTGATA 62.131 55.000 0.00 0.00 45.35 2.15
632 676 1.725182 TCTCCTCCTCCTCCCTCTTTT 59.275 52.381 0.00 0.00 0.00 2.27
639 683 1.499007 AGATGTCTCTCCTCCTCCTCC 59.501 57.143 0.00 0.00 0.00 4.30
655 699 0.870393 AGCACGCACACAAAGAGATG 59.130 50.000 0.00 0.00 0.00 2.90
698 749 0.482446 TGGGGTGAGCTTGATTTGGT 59.518 50.000 0.00 0.00 0.00 3.67
780 841 3.379452 TCCCATGGTGTGTTTCCTTTTT 58.621 40.909 11.73 0.00 0.00 1.94
781 842 3.039252 TCCCATGGTGTGTTTCCTTTT 57.961 42.857 11.73 0.00 0.00 2.27
871 953 2.304180 GGGAGACAGGGTATCATCATGG 59.696 54.545 0.00 0.00 0.00 3.66
872 954 3.246301 AGGGAGACAGGGTATCATCATG 58.754 50.000 0.00 0.00 0.00 3.07
873 959 3.143741 AGAGGGAGACAGGGTATCATCAT 59.856 47.826 0.00 0.00 0.00 2.45
881 967 0.041982 GAGGAAGAGGGAGACAGGGT 59.958 60.000 0.00 0.00 0.00 4.34
896 1005 0.244994 GACAGAAAGCTGAGCGAGGA 59.755 55.000 0.00 0.00 45.17 3.71
897 1006 0.246086 AGACAGAAAGCTGAGCGAGG 59.754 55.000 0.00 0.00 45.17 4.63
898 1007 2.077413 AAGACAGAAAGCTGAGCGAG 57.923 50.000 0.00 0.00 45.17 5.03
899 1008 2.036475 AGAAAGACAGAAAGCTGAGCGA 59.964 45.455 0.00 0.00 45.17 4.93
900 1009 2.411409 GAGAAAGACAGAAAGCTGAGCG 59.589 50.000 0.00 0.00 45.17 5.03
901 1010 3.663025 AGAGAAAGACAGAAAGCTGAGC 58.337 45.455 0.00 0.00 45.17 4.26
905 1066 4.262420 GGTGAGAGAGAAAGACAGAAAGCT 60.262 45.833 0.00 0.00 0.00 3.74
939 1100 1.077858 GGGGAGCAGAGGAAAGCAG 60.078 63.158 0.00 0.00 0.00 4.24
967 1141 1.593479 GGCCCGGCGTGTCTTATAC 60.593 63.158 6.01 0.00 0.00 1.47
1030 1220 1.104630 GAGGTTCTGACGGAGGGTAG 58.895 60.000 0.00 0.00 0.00 3.18
1062 1252 0.526524 CGGAGCCAGAGACGATTGAC 60.527 60.000 0.00 0.00 0.00 3.18
1074 1270 2.721167 CGGTCCTTCATCGGAGCCA 61.721 63.158 3.72 0.00 46.28 4.75
1112 1314 1.340399 ATGCAGCCGATGGAGAAGGA 61.340 55.000 0.00 0.00 30.11 3.36
1159 1361 2.048127 GGCTTCTTGTCGAGCGGT 60.048 61.111 0.00 0.00 0.00 5.68
1300 1530 2.540515 CTGTTAGTATGTGGAGTGCCG 58.459 52.381 0.00 0.00 36.79 5.69
1307 1538 3.073678 TGTGCTTGCTGTTAGTATGTGG 58.926 45.455 0.00 0.00 0.00 4.17
1327 1564 3.626670 GCCTCTCTCTGAAATGGATGTTG 59.373 47.826 0.00 0.00 0.00 3.33
1460 1727 2.513204 TCCTCCTCGCCGTCGTAG 60.513 66.667 0.00 0.00 36.96 3.51
1478 1745 0.039035 CCCTATCCTCCTCCTCCTCG 59.961 65.000 0.00 0.00 0.00 4.63
1612 1897 3.773154 GGGAGAGGGAGGAGGGCT 61.773 72.222 0.00 0.00 0.00 5.19
1666 1951 3.189376 TTGATGCAGGTGGTGGCGA 62.189 57.895 0.00 0.00 0.00 5.54
1727 2014 1.072331 AGCACTAGTGAGGGTGGTTTG 59.928 52.381 27.08 0.00 40.57 2.93
1767 2055 7.221838 GGAAGAACTAAAAGATGAGATCACTCG 59.778 40.741 0.00 0.00 45.25 4.18
1770 2058 7.201478 CGTGGAAGAACTAAAAGATGAGATCAC 60.201 40.741 0.00 0.00 0.00 3.06
1843 2131 9.678941 CTTCTTTATCTCACCCAAAGTTAAAAC 57.321 33.333 0.00 0.00 32.36 2.43
1856 2147 7.605691 ACCTATGCATATGCTTCTTTATCTCAC 59.394 37.037 27.13 0.00 42.66 3.51
1857 2148 7.683578 ACCTATGCATATGCTTCTTTATCTCA 58.316 34.615 27.13 3.88 42.66 3.27
1863 2154 6.153340 ACACAAACCTATGCATATGCTTCTTT 59.847 34.615 27.13 15.51 42.66 2.52
1893 2184 4.795469 TCCACTCCACATGAATGCATAAT 58.205 39.130 0.00 0.00 32.27 1.28
1894 2185 4.201657 CTCCACTCCACATGAATGCATAA 58.798 43.478 0.00 0.00 32.27 1.90
1895 2186 3.200605 ACTCCACTCCACATGAATGCATA 59.799 43.478 0.00 0.00 32.27 3.14
1896 2187 2.025605 ACTCCACTCCACATGAATGCAT 60.026 45.455 0.00 0.00 34.29 3.96
1897 2188 1.352017 ACTCCACTCCACATGAATGCA 59.648 47.619 0.00 0.00 0.00 3.96
1898 2189 2.119801 ACTCCACTCCACATGAATGC 57.880 50.000 0.00 0.00 0.00 3.56
1899 2190 3.189910 CACAACTCCACTCCACATGAATG 59.810 47.826 0.00 0.00 0.00 2.67
1900 2191 3.181440 ACACAACTCCACTCCACATGAAT 60.181 43.478 0.00 0.00 0.00 2.57
1901 2192 2.172505 ACACAACTCCACTCCACATGAA 59.827 45.455 0.00 0.00 0.00 2.57
1902 2193 1.768275 ACACAACTCCACTCCACATGA 59.232 47.619 0.00 0.00 0.00 3.07
1903 2194 2.260844 ACACAACTCCACTCCACATG 57.739 50.000 0.00 0.00 0.00 3.21
1962 2254 1.674057 CCCATGGCCCGTAGAGATC 59.326 63.158 6.09 0.00 0.00 2.75
1986 2278 6.237154 ACTTCAATGGAAAAGAGGAAGAGAG 58.763 40.000 0.00 0.00 36.24 3.20
1987 2279 6.192970 ACTTCAATGGAAAAGAGGAAGAGA 57.807 37.500 0.00 0.00 36.24 3.10
1994 2286 5.702349 AGAGCAACTTCAATGGAAAAGAG 57.298 39.130 0.00 0.00 31.35 2.85
2099 2401 8.564574 GTCCAACAAACATGTAGACTTGAATAA 58.435 33.333 13.56 0.00 0.00 1.40
2100 2402 7.936847 AGTCCAACAAACATGTAGACTTGAATA 59.063 33.333 13.56 0.00 34.13 1.75
2111 2413 3.888323 TGCATGTAGTCCAACAAACATGT 59.112 39.130 18.58 0.00 46.93 3.21
2154 2459 5.179555 GCCTTAACCATTATGCAGTACTAGC 59.820 44.000 0.00 2.56 0.00 3.42
2179 2496 9.690434 GTCTATGATGAACAAACGAGTTAATTC 57.310 33.333 0.00 5.62 0.00 2.17
2211 2528 3.574396 GTGTACCATCTGGCATCTAGCTA 59.426 47.826 0.00 0.00 44.79 3.32
2214 2543 4.141846 ACAAGTGTACCATCTGGCATCTAG 60.142 45.833 0.00 0.00 39.32 2.43
2216 2545 2.573462 ACAAGTGTACCATCTGGCATCT 59.427 45.455 0.00 0.00 39.32 2.90
2217 2546 2.939103 GACAAGTGTACCATCTGGCATC 59.061 50.000 0.00 0.00 39.32 3.91
2218 2547 2.573462 AGACAAGTGTACCATCTGGCAT 59.427 45.455 0.00 0.00 39.32 4.40
2220 2549 2.028112 TGAGACAAGTGTACCATCTGGC 60.028 50.000 0.00 0.00 39.32 4.85
2221 2550 3.961480 TGAGACAAGTGTACCATCTGG 57.039 47.619 0.00 0.00 42.17 3.86
2222 2551 4.021104 TCCTTGAGACAAGTGTACCATCTG 60.021 45.833 9.99 0.00 0.00 2.90
2223 2552 4.160329 TCCTTGAGACAAGTGTACCATCT 58.840 43.478 9.99 0.00 0.00 2.90
2225 2554 4.974645 TTCCTTGAGACAAGTGTACCAT 57.025 40.909 9.99 0.00 0.00 3.55
2229 2579 7.873719 TTTTCATTTCCTTGAGACAAGTGTA 57.126 32.000 9.99 0.00 0.00 2.90
2401 2757 2.819608 TGCATTTTTGTAGGACTGCCTC 59.180 45.455 0.00 0.00 45.54 4.70
2460 2816 2.987149 CCACGGATTCACATATAGCGAC 59.013 50.000 0.00 0.00 0.00 5.19
2463 2819 2.076863 GGCCACGGATTCACATATAGC 58.923 52.381 0.00 0.00 0.00 2.97
2489 2851 4.719369 GGAACGCGTCAGCTCGGT 62.719 66.667 14.44 0.00 42.32 4.69
2503 2865 4.141367 TGGTGATGTTGACTGGTTAAGGAA 60.141 41.667 0.00 0.00 0.00 3.36
2519 2881 5.703978 TTGTTAATCAGTGGTTGGTGATG 57.296 39.130 0.00 0.00 33.58 3.07
2637 3017 7.013369 GTCTTGAACTTGAAGTGGGATTAAGTT 59.987 37.037 0.00 0.00 42.39 2.66
2674 3054 0.251354 TTCAGACTGAGGCCTGCATC 59.749 55.000 12.00 3.94 0.00 3.91
2723 3103 2.210961 AGCGATGAAGCATCACATCAG 58.789 47.619 8.02 0.00 40.54 2.90


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

AutoCloner maintained by Alex Coulton.