Multiple sequence alignment - TraesCS2A01G298500

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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 TraesCS2A01G298500 chr2A 100.000 2270 0 0 1 2270 513854770 513852501 0.000000e+00 4193
1 TraesCS2A01G298500 chr2B 88.123 1785 84 45 529 2270 450258702 450257003 0.000000e+00 2004
2 TraesCS2A01G298500 chr2B 91.647 419 20 9 49 457 450259412 450258999 1.180000e-157 566
3 TraesCS2A01G298500 chr2D 91.264 1282 52 24 966 2231 378909826 378908589 0.000000e+00 1692
4 TraesCS2A01G298500 chr2D 90.643 513 24 12 1 506 378910829 378910334 0.000000e+00 660
5 TraesCS2A01G298500 chr2D 90.252 318 15 11 532 841 378910203 378909894 3.510000e-108 401
6 TraesCS2A01G298500 chr6B 96.667 90 3 0 882 971 592983721 592983810 1.400000e-32 150


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 TraesCS2A01G298500 chr2A 513852501 513854770 2269 True 4193.000000 4193 100.000000 1 2270 1 chr2A.!!$R1 2269
1 TraesCS2A01G298500 chr2B 450257003 450259412 2409 True 1285.000000 2004 89.885000 49 2270 2 chr2B.!!$R1 2221
2 TraesCS2A01G298500 chr2D 378908589 378910829 2240 True 917.666667 1692 90.719667 1 2231 3 chr2D.!!$R1 2230

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
108 109 0.112995 TGGCCATGAACCTTCTTGCT 59.887 50.0 0.0 0.0 32.7 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2236 0.249868 CCTGCTTAATCCGCGATCCA 60.25 55.0 8.23 0.0 0.0 3.41 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 1.518133 GCGAATGCAGAGCTCTCGT 60.518 57.895 14.96 7.64 42.15 4.18
105 106 3.269381 TCCTTATGGCCATGAACCTTCTT 59.731 43.478 29.04 0.13 0.00 2.52
106 107 3.382546 CCTTATGGCCATGAACCTTCTTG 59.617 47.826 29.04 5.34 33.53 3.02
107 108 1.188863 ATGGCCATGAACCTTCTTGC 58.811 50.000 20.04 0.00 32.70 4.01
108 109 0.112995 TGGCCATGAACCTTCTTGCT 59.887 50.000 0.00 0.00 32.70 3.91
133 145 2.499289 TGCCTTGTCCTTTTCTTTTGCA 59.501 40.909 0.00 0.00 0.00 4.08
134 146 3.134442 TGCCTTGTCCTTTTCTTTTGCAT 59.866 39.130 0.00 0.00 0.00 3.96
135 147 4.343526 TGCCTTGTCCTTTTCTTTTGCATA 59.656 37.500 0.00 0.00 0.00 3.14
136 148 5.011943 TGCCTTGTCCTTTTCTTTTGCATAT 59.988 36.000 0.00 0.00 0.00 1.78
137 149 5.578336 GCCTTGTCCTTTTCTTTTGCATATC 59.422 40.000 0.00 0.00 0.00 1.63
138 150 6.573094 GCCTTGTCCTTTTCTTTTGCATATCT 60.573 38.462 0.00 0.00 0.00 1.98
139 151 7.031975 CCTTGTCCTTTTCTTTTGCATATCTC 58.968 38.462 0.00 0.00 0.00 2.75
140 152 7.094032 CCTTGTCCTTTTCTTTTGCATATCTCT 60.094 37.037 0.00 0.00 0.00 3.10
141 153 7.383102 TGTCCTTTTCTTTTGCATATCTCTC 57.617 36.000 0.00 0.00 0.00 3.20
142 154 6.942005 TGTCCTTTTCTTTTGCATATCTCTCA 59.058 34.615 0.00 0.00 0.00 3.27
225 237 0.318441 CTCCTCTCCAACACGCTCAA 59.682 55.000 0.00 0.00 0.00 3.02
262 277 1.218047 CACCGTCCATGTCCATCGT 59.782 57.895 0.00 0.00 0.00 3.73
381 404 1.950472 CACCAACTCGAACGATTTGC 58.050 50.000 17.40 0.00 34.69 3.68
396 419 5.608676 CGATTTGCTCGTAGACTATAGGA 57.391 43.478 4.43 0.00 42.56 2.94
403 426 1.197264 CGTAGACTATAGGAGCGCACC 59.803 57.143 16.88 16.88 0.00 5.01
404 427 1.197264 GTAGACTATAGGAGCGCACCG 59.803 57.143 18.47 6.59 34.73 4.94
405 428 1.173444 AGACTATAGGAGCGCACCGG 61.173 60.000 18.47 11.97 34.73 5.28
406 429 2.143594 GACTATAGGAGCGCACCGGG 62.144 65.000 18.47 11.64 34.73 5.73
407 430 3.575351 CTATAGGAGCGCACCGGGC 62.575 68.421 18.47 5.50 41.91 6.13
431 454 2.796032 GCGCAGGCACAAAATTATCCTC 60.796 50.000 0.30 0.00 39.62 3.71
432 455 2.539547 CGCAGGCACAAAATTATCCTCG 60.540 50.000 0.00 0.00 0.00 4.63
439 462 4.782195 GCACAAAATTATCCTCGCGTGTAG 60.782 45.833 5.77 0.00 0.00 2.74
441 464 4.565564 ACAAAATTATCCTCGCGTGTAGAC 59.434 41.667 5.77 0.00 0.00 2.59
447 470 1.445582 CTCGCGTGTAGACAACCCC 60.446 63.158 5.77 0.00 0.00 4.95
453 476 1.269936 CGTGTAGACAACCCCGAGTTT 60.270 52.381 0.00 0.00 36.18 2.66
458 515 1.344763 AGACAACCCCGAGTTTCTCAG 59.655 52.381 0.00 0.00 36.18 3.35
463 520 1.344763 ACCCCGAGTTTCTCAGTCTTG 59.655 52.381 0.00 0.00 0.00 3.02
476 533 4.883585 TCTCAGTCTTGCAAACTGTGAATT 59.116 37.500 26.21 5.24 41.63 2.17
477 534 6.054941 TCTCAGTCTTGCAAACTGTGAATTA 58.945 36.000 26.21 14.83 41.63 1.40
478 535 6.017934 TCTCAGTCTTGCAAACTGTGAATTAC 60.018 38.462 26.21 4.88 41.63 1.89
506 565 5.541845 TGATCCGACTATGCAGAAAATAGG 58.458 41.667 0.00 0.00 32.81 2.57
507 566 3.728845 TCCGACTATGCAGAAAATAGGC 58.271 45.455 0.00 0.00 33.03 3.93
511 570 5.758296 CCGACTATGCAGAAAATAGGCTTTA 59.242 40.000 0.00 0.00 34.04 1.85
512 571 6.292919 CCGACTATGCAGAAAATAGGCTTTAC 60.293 42.308 0.00 0.00 34.04 2.01
515 574 7.989826 ACTATGCAGAAAATAGGCTTTACTTG 58.010 34.615 0.00 0.00 32.81 3.16
517 576 4.522405 TGCAGAAAATAGGCTTTACTTGCA 59.478 37.500 0.00 0.00 32.44 4.08
518 577 5.098211 GCAGAAAATAGGCTTTACTTGCAG 58.902 41.667 0.00 0.00 0.00 4.41
519 578 5.644644 CAGAAAATAGGCTTTACTTGCAGG 58.355 41.667 0.00 0.00 0.00 4.85
521 580 3.372440 AATAGGCTTTACTTGCAGGCT 57.628 42.857 0.00 0.00 46.95 4.58
522 581 2.113860 TAGGCTTTACTTGCAGGCTG 57.886 50.000 10.94 10.94 45.13 4.85
523 582 0.401738 AGGCTTTACTTGCAGGCTGA 59.598 50.000 20.86 0.00 43.94 4.26
524 583 0.523519 GGCTTTACTTGCAGGCTGAC 59.476 55.000 20.86 10.37 32.83 3.51
527 808 2.351157 GCTTTACTTGCAGGCTGACAAG 60.351 50.000 31.66 31.66 46.91 3.16
545 826 2.494870 CAAGGCTTTTCCCCTCTCATTG 59.505 50.000 0.00 0.00 34.51 2.82
557 838 2.223900 CCTCTCATTGCTCAGCGTGATA 60.224 50.000 5.13 0.00 0.00 2.15
565 846 1.598132 GCTCAGCGTGATACTAGTCGA 59.402 52.381 0.00 0.00 0.00 4.20
567 848 3.665848 GCTCAGCGTGATACTAGTCGATC 60.666 52.174 0.00 0.00 0.00 3.69
568 849 2.475487 TCAGCGTGATACTAGTCGATCG 59.525 50.000 9.36 9.36 0.00 3.69
569 850 1.799403 AGCGTGATACTAGTCGATCGG 59.201 52.381 16.41 0.89 0.00 4.18
601 882 3.055591 GTCATGTCACAGACTCACAGTG 58.944 50.000 0.00 0.00 37.35 3.66
602 883 2.695147 TCATGTCACAGACTCACAGTGT 59.305 45.455 0.00 0.00 37.31 3.55
603 884 2.584492 TGTCACAGACTCACAGTGTG 57.416 50.000 17.53 17.53 44.20 3.82
604 885 1.212616 GTCACAGACTCACAGTGTGC 58.787 55.000 18.80 4.82 42.61 4.57
605 886 1.114627 TCACAGACTCACAGTGTGCT 58.885 50.000 18.80 7.22 42.61 4.40
606 887 2.034685 GTCACAGACTCACAGTGTGCTA 59.965 50.000 18.80 1.16 42.61 3.49
607 888 2.893489 TCACAGACTCACAGTGTGCTAT 59.107 45.455 18.80 5.94 42.61 2.97
608 889 4.079253 TCACAGACTCACAGTGTGCTATA 58.921 43.478 18.80 0.00 42.61 1.31
609 890 4.706962 TCACAGACTCACAGTGTGCTATAT 59.293 41.667 18.80 0.62 42.61 0.86
611 892 6.377146 TCACAGACTCACAGTGTGCTATATAA 59.623 38.462 18.80 0.00 42.61 0.98
612 893 7.068716 TCACAGACTCACAGTGTGCTATATAAT 59.931 37.037 18.80 0.00 42.61 1.28
613 894 7.708322 CACAGACTCACAGTGTGCTATATAATT 59.292 37.037 18.80 0.00 42.61 1.40
614 895 8.914011 ACAGACTCACAGTGTGCTATATAATTA 58.086 33.333 18.80 0.00 42.61 1.40
615 896 9.920133 CAGACTCACAGTGTGCTATATAATTAT 57.080 33.333 18.80 2.97 32.63 1.28
706 996 7.430992 TGCATGTAGATTGCATATCTTTCTC 57.569 36.000 14.02 6.49 44.73 2.87
711 1003 5.240013 AGATTGCATATCTTTCTCTCCCC 57.760 43.478 5.80 0.00 0.00 4.81
862 1158 2.361610 CCCCGCCATTTGCACTCT 60.362 61.111 0.00 0.00 41.33 3.24
865 1161 2.753966 CCGCCATTTGCACTCTCCG 61.754 63.158 0.00 0.00 41.33 4.63
895 1192 3.859961 CACCAGTCATCACGTACATCTTC 59.140 47.826 0.00 0.00 0.00 2.87
923 1220 2.113139 AAACCTCCACACCTGGCG 59.887 61.111 0.00 0.00 37.49 5.69
1015 1313 3.709880 TACATGGGGCGAACGAGCG 62.710 63.158 0.00 0.00 38.18 5.03
1033 1331 2.507324 GCAGGCGGACGACTCTTC 60.507 66.667 0.00 0.00 0.00 2.87
1034 1332 2.995872 GCAGGCGGACGACTCTTCT 61.996 63.158 0.00 0.00 0.00 2.85
1035 1333 1.654954 GCAGGCGGACGACTCTTCTA 61.655 60.000 0.00 0.00 0.00 2.10
1078 1376 4.337304 TGCCCCTGCTCCTCCTCA 62.337 66.667 0.00 0.00 38.71 3.86
1086 1384 0.105760 TGCTCCTCCTCATCCTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
1275 1573 0.179032 TGGAGAAGCCGTGAAGCAAA 60.179 50.000 0.00 0.00 40.66 3.68
1281 1579 0.603975 AGCCGTGAAGCAAAGGAGAC 60.604 55.000 0.00 0.00 34.23 3.36
1288 1586 4.090057 GCAAAGGAGACGGTGCGC 62.090 66.667 0.00 0.00 35.73 6.09
1367 1666 6.285990 ACATATGGGTTGGTTAATCGTAGAC 58.714 40.000 7.80 0.00 42.51 2.59
1450 1749 4.530946 TGGAGAGGTTCCTTCGTTTCTTAT 59.469 41.667 0.00 0.00 46.92 1.73
1451 1750 5.012768 TGGAGAGGTTCCTTCGTTTCTTATT 59.987 40.000 0.00 0.00 46.92 1.40
1452 1751 6.211986 TGGAGAGGTTCCTTCGTTTCTTATTA 59.788 38.462 0.00 0.00 46.92 0.98
1453 1752 6.534436 GGAGAGGTTCCTTCGTTTCTTATTAC 59.466 42.308 0.00 0.00 43.16 1.89
1454 1753 6.404708 AGAGGTTCCTTCGTTTCTTATTACC 58.595 40.000 0.00 0.00 0.00 2.85
1455 1754 6.212993 AGAGGTTCCTTCGTTTCTTATTACCT 59.787 38.462 0.00 0.00 35.13 3.08
1456 1755 6.776744 AGGTTCCTTCGTTTCTTATTACCTT 58.223 36.000 0.00 0.00 0.00 3.50
1457 1756 7.229308 AGGTTCCTTCGTTTCTTATTACCTTT 58.771 34.615 0.00 0.00 0.00 3.11
1458 1757 7.174426 AGGTTCCTTCGTTTCTTATTACCTTTG 59.826 37.037 0.00 0.00 0.00 2.77
1459 1758 7.303261 GTTCCTTCGTTTCTTATTACCTTTGG 58.697 38.462 0.00 0.00 0.00 3.28
1460 1759 6.536447 TCCTTCGTTTCTTATTACCTTTGGT 58.464 36.000 0.00 0.00 40.16 3.67
1461 1760 6.999871 TCCTTCGTTTCTTATTACCTTTGGTT 59.000 34.615 0.00 0.00 37.09 3.67
1462 1761 7.503230 TCCTTCGTTTCTTATTACCTTTGGTTT 59.497 33.333 0.00 0.00 37.09 3.27
1463 1762 7.593644 CCTTCGTTTCTTATTACCTTTGGTTTG 59.406 37.037 0.00 0.00 37.09 2.93
1464 1763 7.804843 TCGTTTCTTATTACCTTTGGTTTGA 57.195 32.000 0.00 0.00 37.09 2.69
1465 1764 8.223177 TCGTTTCTTATTACCTTTGGTTTGAA 57.777 30.769 0.00 0.00 37.09 2.69
1466 1765 8.130469 TCGTTTCTTATTACCTTTGGTTTGAAC 58.870 33.333 0.00 0.00 37.09 3.18
1515 1830 1.000274 CCCAACTTTCCTTCCTTTGCG 60.000 52.381 0.00 0.00 0.00 4.85
1568 1885 8.618702 AAGCTAAAGGATGATTGATATGTGAG 57.381 34.615 0.00 0.00 0.00 3.51
1583 1900 8.697507 TGATATGTGAGATGATATATACCGCT 57.302 34.615 0.00 0.00 0.00 5.52
1584 1901 8.571336 TGATATGTGAGATGATATATACCGCTG 58.429 37.037 0.00 0.00 0.00 5.18
1585 1902 4.998788 TGTGAGATGATATATACCGCTGC 58.001 43.478 0.00 0.00 0.00 5.25
1586 1903 4.462483 TGTGAGATGATATATACCGCTGCA 59.538 41.667 0.00 0.00 0.00 4.41
1587 1904 5.047377 TGTGAGATGATATATACCGCTGCAA 60.047 40.000 0.00 0.00 0.00 4.08
1637 1954 2.813754 GTCTGGTAATGACTTTGCTGCA 59.186 45.455 0.00 0.00 0.00 4.41
1728 2046 6.046593 CGTTGCACCTTCCTTTGACTATATA 58.953 40.000 0.00 0.00 0.00 0.86
1730 2048 7.870954 CGTTGCACCTTCCTTTGACTATATATA 59.129 37.037 0.00 0.00 0.00 0.86
1733 2051 7.231925 TGCACCTTCCTTTGACTATATATACGA 59.768 37.037 0.00 0.00 0.00 3.43
1734 2052 8.251721 GCACCTTCCTTTGACTATATATACGAT 58.748 37.037 0.00 0.00 0.00 3.73
1775 2093 9.877137 CAAGCCAACATTAATTCCTTTTTAAAC 57.123 29.630 0.00 0.00 0.00 2.01
1893 2236 2.158856 AGGATGATGCATGTCATGTCGT 60.159 45.455 14.26 6.31 38.88 4.34
1994 2337 1.982660 TTTGCCCGTGACATTTGGTA 58.017 45.000 0.00 0.00 0.00 3.25
2000 2343 3.365969 GCCCGTGACATTTGGTAAAAGAG 60.366 47.826 0.00 0.00 0.00 2.85
2098 2441 1.478631 CATCCTTTTTCCTGGCCTCC 58.521 55.000 3.32 0.00 0.00 4.30
2099 2442 1.084018 ATCCTTTTTCCTGGCCTCCA 58.916 50.000 3.32 0.00 0.00 3.86
2220 2567 3.078594 ACAAACACGGTTTGATTGCTC 57.921 42.857 26.05 0.00 40.75 4.26
2231 2578 4.441792 GTTTGATTGCTCCACCAAAGTTT 58.558 39.130 0.00 0.00 0.00 2.66
2232 2579 4.751767 TTGATTGCTCCACCAAAGTTTT 57.248 36.364 0.00 0.00 0.00 2.43
2233 2580 5.860941 TTGATTGCTCCACCAAAGTTTTA 57.139 34.783 0.00 0.00 0.00 1.52
2234 2581 6.418057 TTGATTGCTCCACCAAAGTTTTAT 57.582 33.333 0.00 0.00 0.00 1.40
2235 2582 6.418057 TGATTGCTCCACCAAAGTTTTATT 57.582 33.333 0.00 0.00 0.00 1.40
2239 2586 6.969993 TGCTCCACCAAAGTTTTATTACTT 57.030 33.333 0.00 0.00 39.97 2.24
2244 2591 7.375053 TCCACCAAAGTTTTATTACTTCATGC 58.625 34.615 0.00 0.00 37.37 4.06
2248 2595 9.777297 ACCAAAGTTTTATTACTTCATGCAATT 57.223 25.926 0.00 0.00 37.37 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.033405 CTCCTCCCCGAGTAGGTGAA 60.033 60.000 0.00 0.00 38.74 3.18
106 107 0.540597 AAAAGGACAAGGCAGGGAGC 60.541 55.000 0.00 0.00 44.65 4.70
107 108 1.074566 AGAAAAGGACAAGGCAGGGAG 59.925 52.381 0.00 0.00 0.00 4.30
108 109 1.149101 AGAAAAGGACAAGGCAGGGA 58.851 50.000 0.00 0.00 0.00 4.20
133 145 6.882768 AAAGGAAGTGGAAGTGAGAGATAT 57.117 37.500 0.00 0.00 0.00 1.63
134 146 6.498651 AGAAAAGGAAGTGGAAGTGAGAGATA 59.501 38.462 0.00 0.00 0.00 1.98
135 147 5.309282 AGAAAAGGAAGTGGAAGTGAGAGAT 59.691 40.000 0.00 0.00 0.00 2.75
136 148 4.656112 AGAAAAGGAAGTGGAAGTGAGAGA 59.344 41.667 0.00 0.00 0.00 3.10
137 149 4.967036 AGAAAAGGAAGTGGAAGTGAGAG 58.033 43.478 0.00 0.00 0.00 3.20
138 150 5.126067 CAAGAAAAGGAAGTGGAAGTGAGA 58.874 41.667 0.00 0.00 0.00 3.27
139 151 4.276926 CCAAGAAAAGGAAGTGGAAGTGAG 59.723 45.833 0.00 0.00 0.00 3.51
140 152 4.207165 CCAAGAAAAGGAAGTGGAAGTGA 58.793 43.478 0.00 0.00 0.00 3.41
141 153 3.954258 ACCAAGAAAAGGAAGTGGAAGTG 59.046 43.478 0.00 0.00 33.39 3.16
142 154 3.954258 CACCAAGAAAAGGAAGTGGAAGT 59.046 43.478 0.00 0.00 33.39 3.01
381 404 2.158058 GTGCGCTCCTATAGTCTACGAG 59.842 54.545 9.73 0.00 0.00 4.18
407 430 2.206515 TAATTTTGTGCCTGCGCCGG 62.207 55.000 14.29 14.29 0.00 6.13
415 438 1.400494 ACGCGAGGATAATTTTGTGCC 59.600 47.619 15.93 0.00 0.00 5.01
420 443 4.751060 TGTCTACACGCGAGGATAATTTT 58.249 39.130 15.93 0.00 0.00 1.82
431 454 2.807895 CGGGGTTGTCTACACGCG 60.808 66.667 3.53 3.53 0.00 6.01
432 455 1.445582 CTCGGGGTTGTCTACACGC 60.446 63.158 0.00 0.00 0.00 5.34
439 462 1.070289 ACTGAGAAACTCGGGGTTGTC 59.930 52.381 2.63 2.63 40.86 3.18
441 464 1.344763 AGACTGAGAAACTCGGGGTTG 59.655 52.381 0.00 0.00 40.86 3.77
447 470 3.557595 AGTTTGCAAGACTGAGAAACTCG 59.442 43.478 11.78 0.00 34.25 4.18
453 476 3.541996 TCACAGTTTGCAAGACTGAGA 57.458 42.857 30.94 27.28 45.72 3.27
458 515 6.073003 AGCTAGTAATTCACAGTTTGCAAGAC 60.073 38.462 0.00 1.42 0.00 3.01
463 520 5.862924 TCAGCTAGTAATTCACAGTTTGC 57.137 39.130 0.00 0.00 0.00 3.68
476 533 3.751518 TGCATAGTCGGATCAGCTAGTA 58.248 45.455 0.00 0.00 0.00 1.82
477 534 2.556189 CTGCATAGTCGGATCAGCTAGT 59.444 50.000 0.00 0.00 0.00 2.57
478 535 2.816672 TCTGCATAGTCGGATCAGCTAG 59.183 50.000 0.00 0.00 0.00 3.42
506 565 1.238439 TGTCAGCCTGCAAGTAAAGC 58.762 50.000 0.00 0.00 0.00 3.51
507 566 2.227388 CCTTGTCAGCCTGCAAGTAAAG 59.773 50.000 20.05 7.71 40.13 1.85
511 570 1.900498 GCCTTGTCAGCCTGCAAGT 60.900 57.895 20.05 0.00 40.13 3.16
512 571 1.177256 AAGCCTTGTCAGCCTGCAAG 61.177 55.000 16.87 16.87 41.08 4.01
515 574 0.038801 GAAAAGCCTTGTCAGCCTGC 60.039 55.000 0.00 0.00 0.00 4.85
517 576 0.540597 GGGAAAAGCCTTGTCAGCCT 60.541 55.000 0.00 0.00 36.66 4.58
518 577 1.536073 GGGGAAAAGCCTTGTCAGCC 61.536 60.000 0.00 0.00 36.66 4.85
519 578 0.540597 AGGGGAAAAGCCTTGTCAGC 60.541 55.000 0.00 0.00 36.66 4.26
521 580 1.073923 GAGAGGGGAAAAGCCTTGTCA 59.926 52.381 0.00 0.00 36.66 3.58
522 581 1.073923 TGAGAGGGGAAAAGCCTTGTC 59.926 52.381 0.00 0.00 36.66 3.18
523 582 1.149101 TGAGAGGGGAAAAGCCTTGT 58.851 50.000 0.00 0.00 36.66 3.16
524 583 2.494870 CAATGAGAGGGGAAAAGCCTTG 59.505 50.000 0.00 0.00 36.66 3.61
527 808 0.820226 GCAATGAGAGGGGAAAAGCC 59.180 55.000 0.00 0.00 0.00 4.35
530 811 2.881403 GCTGAGCAATGAGAGGGGAAAA 60.881 50.000 0.00 0.00 0.00 2.29
535 816 1.088340 CACGCTGAGCAATGAGAGGG 61.088 60.000 4.88 0.00 0.00 4.30
545 826 1.598132 TCGACTAGTATCACGCTGAGC 59.402 52.381 0.00 0.00 0.00 4.26
557 838 5.065218 ACAATTTACGTACCGATCGACTAGT 59.935 40.000 18.66 13.34 0.00 2.57
565 846 5.290158 GTGACATGACAATTTACGTACCGAT 59.710 40.000 0.00 0.00 0.00 4.18
567 848 4.386350 TGTGACATGACAATTTACGTACCG 59.614 41.667 0.00 0.00 0.00 4.02
568 849 5.636121 TCTGTGACATGACAATTTACGTACC 59.364 40.000 0.00 0.00 0.00 3.34
569 850 6.365247 AGTCTGTGACATGACAATTTACGTAC 59.635 38.462 14.43 0.00 34.60 3.67
575 856 5.125356 TGTGAGTCTGTGACATGACAATTT 58.875 37.500 14.43 0.00 34.60 1.82
577 858 4.202295 ACTGTGAGTCTGTGACATGACAAT 60.202 41.667 14.43 0.00 34.60 2.71
580 861 3.055591 CACTGTGAGTCTGTGACATGAC 58.944 50.000 0.32 6.96 44.93 3.06
589 870 9.920133 ATAATTATATAGCACACTGTGAGTCTG 57.080 33.333 15.86 3.18 35.23 3.51
612 893 9.383519 GCTGCTTTAATAGTGCCTCATATATAA 57.616 33.333 0.00 0.00 0.00 0.98
613 894 7.987458 GGCTGCTTTAATAGTGCCTCATATATA 59.013 37.037 0.00 0.00 40.24 0.86
614 895 6.825721 GGCTGCTTTAATAGTGCCTCATATAT 59.174 38.462 0.00 0.00 40.24 0.86
615 896 6.173339 GGCTGCTTTAATAGTGCCTCATATA 58.827 40.000 0.00 0.00 40.24 0.86
616 897 5.006386 GGCTGCTTTAATAGTGCCTCATAT 58.994 41.667 0.00 0.00 40.24 1.78
617 898 4.141505 TGGCTGCTTTAATAGTGCCTCATA 60.142 41.667 0.00 0.00 42.29 2.15
618 899 3.217626 GGCTGCTTTAATAGTGCCTCAT 58.782 45.455 0.00 0.00 40.24 2.90
704 994 0.401738 TTCACAAGCAAGGGGGAGAG 59.598 55.000 0.00 0.00 0.00 3.20
706 996 0.178992 TGTTCACAAGCAAGGGGGAG 60.179 55.000 0.00 0.00 0.00 4.30
862 1158 1.124780 TGACTGGTGAAGGTTTCGGA 58.875 50.000 0.00 0.00 0.00 4.55
865 1161 2.480419 CGTGATGACTGGTGAAGGTTTC 59.520 50.000 0.00 0.00 0.00 2.78
895 1192 1.681264 GTGGAGGTTTGTGGTTTGAGG 59.319 52.381 0.00 0.00 0.00 3.86
939 1236 2.503382 GGTCGATGAGGAGGGGAGC 61.503 68.421 0.00 0.00 0.00 4.70
1015 1313 3.991536 GAAGAGTCGTCCGCCTGCC 62.992 68.421 0.00 0.00 0.00 4.85
1021 1319 1.062206 GCGGTAGAAGAGTCGTCCG 59.938 63.158 2.15 1.60 43.04 4.79
1027 1325 2.885861 CTGCGGCGGTAGAAGAGT 59.114 61.111 9.78 0.00 0.00 3.24
1288 1586 1.107114 ATATCTCTATCGGCGGCCAG 58.893 55.000 20.71 11.98 0.00 4.85
1349 1648 3.508744 TCGTCTACGATTAACCAACCC 57.491 47.619 0.14 0.00 44.22 4.11
1450 1749 5.394773 GCTCCAAAGTTCAAACCAAAGGTAA 60.395 40.000 0.00 0.00 33.12 2.85
1451 1750 4.098807 GCTCCAAAGTTCAAACCAAAGGTA 59.901 41.667 0.00 0.00 33.12 3.08
1452 1751 3.118775 GCTCCAAAGTTCAAACCAAAGGT 60.119 43.478 0.00 0.00 37.65 3.50
1453 1752 3.457234 GCTCCAAAGTTCAAACCAAAGG 58.543 45.455 0.00 0.00 0.00 3.11
1454 1753 3.457234 GGCTCCAAAGTTCAAACCAAAG 58.543 45.455 0.00 0.00 0.00 2.77
1455 1754 2.159170 CGGCTCCAAAGTTCAAACCAAA 60.159 45.455 0.00 0.00 0.00 3.28
1456 1755 1.407258 CGGCTCCAAAGTTCAAACCAA 59.593 47.619 0.00 0.00 0.00 3.67
1457 1756 1.028905 CGGCTCCAAAGTTCAAACCA 58.971 50.000 0.00 0.00 0.00 3.67
1458 1757 0.313987 CCGGCTCCAAAGTTCAAACC 59.686 55.000 0.00 0.00 0.00 3.27
1459 1758 0.318699 GCCGGCTCCAAAGTTCAAAC 60.319 55.000 22.15 0.00 0.00 2.93
1460 1759 0.753479 TGCCGGCTCCAAAGTTCAAA 60.753 50.000 29.70 0.00 0.00 2.69
1461 1760 1.152860 TGCCGGCTCCAAAGTTCAA 60.153 52.632 29.70 0.00 0.00 2.69
1462 1761 1.600636 CTGCCGGCTCCAAAGTTCA 60.601 57.895 29.70 1.03 0.00 3.18
1463 1762 1.301677 CTCTGCCGGCTCCAAAGTTC 61.302 60.000 29.70 0.00 0.00 3.01
1464 1763 1.302832 CTCTGCCGGCTCCAAAGTT 60.303 57.895 29.70 0.00 0.00 2.66
1465 1764 2.056906 AACTCTGCCGGCTCCAAAGT 62.057 55.000 29.70 19.16 0.00 2.66
1466 1765 1.302832 AACTCTGCCGGCTCCAAAG 60.303 57.895 29.70 16.58 0.00 2.77
1534 1849 8.906867 TCAATCATCCTTTAGCTTTATCCAAAG 58.093 33.333 0.00 0.00 43.46 2.77
1568 1885 4.571984 TGCATTGCAGCGGTATATATCATC 59.428 41.667 7.38 0.00 37.31 2.92
1583 1900 5.417894 AGAGAGAAAGATGATTTGCATTGCA 59.582 36.000 7.38 7.38 37.34 4.08
1584 1901 5.892568 AGAGAGAAAGATGATTTGCATTGC 58.107 37.500 0.46 0.46 37.34 3.56
1637 1954 1.337728 TGCTCACACCAAATCGACGAT 60.338 47.619 4.05 4.05 0.00 3.73
1672 1990 1.732683 CCGCCATTTTGTCAACGCC 60.733 57.895 0.00 0.00 0.00 5.68
1744 2062 8.744568 AAAGGAATTAATGTTGGCTTGAAAAA 57.255 26.923 0.00 0.00 0.00 1.94
1745 2063 8.744568 AAAAGGAATTAATGTTGGCTTGAAAA 57.255 26.923 0.00 0.00 0.00 2.29
1775 2093 3.128242 AGGAACAAGATGTACGTACTCGG 59.872 47.826 25.12 17.65 41.85 4.63
1823 2141 9.699410 ACCAATCACATCTTGGATCTTAATAAA 57.301 29.630 8.96 0.00 44.95 1.40
1825 2143 7.229306 GCACCAATCACATCTTGGATCTTAATA 59.771 37.037 8.96 0.00 44.95 0.98
1827 2145 5.357878 GCACCAATCACATCTTGGATCTTAA 59.642 40.000 8.96 0.00 44.95 1.85
1828 2146 4.883585 GCACCAATCACATCTTGGATCTTA 59.116 41.667 8.96 0.00 44.95 2.10
1829 2147 3.698040 GCACCAATCACATCTTGGATCTT 59.302 43.478 8.96 0.00 44.95 2.40
1830 2148 3.285484 GCACCAATCACATCTTGGATCT 58.715 45.455 8.96 0.00 44.95 2.75
1831 2149 3.018856 TGCACCAATCACATCTTGGATC 58.981 45.455 8.96 0.00 44.95 3.36
1868 2200 3.181448 ACATGACATGCATCATCCTAGCA 60.181 43.478 15.49 0.00 43.14 3.49
1893 2236 0.249868 CCTGCTTAATCCGCGATCCA 60.250 55.000 8.23 0.00 0.00 3.41
1994 2337 7.392953 GTCTTTCCATCCATCTTTCTCTCTTTT 59.607 37.037 0.00 0.00 0.00 2.27
2000 2343 3.873952 CCGTCTTTCCATCCATCTTTCTC 59.126 47.826 0.00 0.00 0.00 2.87
2098 2441 4.381398 CCATGACAAGTCTACTCTGGACTG 60.381 50.000 0.00 0.00 42.39 3.51
2099 2442 3.766591 CCATGACAAGTCTACTCTGGACT 59.233 47.826 0.00 0.00 44.73 3.85
2100 2443 3.677424 GCCATGACAAGTCTACTCTGGAC 60.677 52.174 0.00 0.00 0.00 4.02
2101 2444 2.497675 GCCATGACAAGTCTACTCTGGA 59.502 50.000 0.00 0.00 0.00 3.86
2102 2445 2.419297 GGCCATGACAAGTCTACTCTGG 60.419 54.545 0.00 2.83 0.00 3.86
2162 2505 4.569023 TCCTAGCCGCGTGCATCG 62.569 66.667 19.30 0.00 44.83 3.84
2163 2506 2.962253 GTCCTAGCCGCGTGCATC 60.962 66.667 19.30 3.94 44.83 3.91
2164 2507 3.309436 TTGTCCTAGCCGCGTGCAT 62.309 57.895 19.30 8.83 44.83 3.96
2165 2508 3.932580 CTTGTCCTAGCCGCGTGCA 62.933 63.158 19.30 6.86 44.83 4.57
2174 2521 1.115467 AGATGTCGCCCTTGTCCTAG 58.885 55.000 0.00 0.00 0.00 3.02
2220 2567 7.151308 TGCATGAAGTAATAAAACTTTGGTGG 58.849 34.615 0.00 0.00 39.78 4.61
2231 2578 8.279970 AGCAGTACAATTGCATGAAGTAATAA 57.720 30.769 5.05 0.00 43.92 1.40
2232 2579 7.864108 AGCAGTACAATTGCATGAAGTAATA 57.136 32.000 5.05 0.00 43.92 0.98
2233 2580 6.764308 AGCAGTACAATTGCATGAAGTAAT 57.236 33.333 5.05 0.00 43.92 1.89
2234 2581 6.573664 AAGCAGTACAATTGCATGAAGTAA 57.426 33.333 5.05 0.00 43.92 2.24
2235 2582 6.380995 CAAAGCAGTACAATTGCATGAAGTA 58.619 36.000 5.05 0.00 43.92 2.24
2239 2586 3.573538 ACCAAAGCAGTACAATTGCATGA 59.426 39.130 5.05 0.00 43.92 3.07
2244 2591 4.320608 ACCAACCAAAGCAGTACAATTG 57.679 40.909 3.24 3.24 0.00 2.32
2248 2595 2.028130 CCAACCAACCAAAGCAGTACA 58.972 47.619 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.