Multiple sequence alignment - TraesCS4A01G022100

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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 TraesCS4A01G022100 chr4A 100.000 2636 0 0 1 2636 15889649 15892284 0.000000e+00 4868
1 TraesCS4A01G022100 chr4A 92.866 841 45 10 1805 2636 682762023 682761189 0.000000e+00 1206
2 TraesCS4A01G022100 chr4D 93.218 1799 82 17 873 2636 451057328 451055535 0.000000e+00 2610
3 TraesCS4A01G022100 chr4D 84.848 726 94 14 54 774 451058134 451057420 0.000000e+00 717
4 TraesCS4A01G022100 chr4B 94.850 932 35 8 873 1802 564223918 564222998 0.000000e+00 1443
5 TraesCS4A01G022100 chr4B 93.895 475 29 0 2079 2553 564188064 564187590 0.000000e+00 717
6 TraesCS4A01G022100 chr4B 91.928 223 17 1 1806 2028 564194073 564193852 7.080000e-81 311
7 TraesCS4A01G022100 chr4B 86.475 244 29 3 54 296 564226347 564226107 5.590000e-67 265
8 TraesCS4A01G022100 chr4B 86.066 244 30 2 54 296 564241750 564241510 2.600000e-65 259
9 TraesCS4A01G022100 chr4B 96.591 88 3 0 2549 2636 564184574 564184487 2.110000e-31 147
10 TraesCS4A01G022100 chr6D 85.810 599 57 11 2049 2634 420225811 420226394 6.240000e-171 610
11 TraesCS4A01G022100 chr5A 83.025 595 74 7 1810 2381 645603039 645602449 5.030000e-142 514
12 TraesCS4A01G022100 chr5A 88.655 238 27 0 1806 2043 611974777 611975014 9.230000e-75 291
13 TraesCS4A01G022100 chr5A 88.940 217 17 7 2165 2378 626249744 626249956 7.240000e-66 261
14 TraesCS4A01G022100 chr5D 82.828 594 56 27 1815 2381 501063855 501063281 8.480000e-135 490
15 TraesCS4A01G022100 chr1D 80.628 382 39 14 1846 2193 464738680 464739060 2.010000e-66 263
16 TraesCS4A01G022100 chr1A 89.017 173 10 5 2465 2636 538763691 538763527 3.440000e-49 206
17 TraesCS4A01G022100 chr5B 84.951 206 24 5 54 257 604850664 604850464 4.450000e-48 202
18 TraesCS4A01G022100 chr2D 86.486 185 21 4 2198 2381 606113770 606113589 1.600000e-47 200
19 TraesCS4A01G022100 chr2A 84.699 183 25 3 2200 2381 748814581 748814401 2.080000e-41 180


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 TraesCS4A01G022100 chr4A 15889649 15892284 2635 False 4868.0 4868 100.0000 1 2636 1 chr4A.!!$F1 2635
1 TraesCS4A01G022100 chr4A 682761189 682762023 834 True 1206.0 1206 92.8660 1805 2636 1 chr4A.!!$R1 831
2 TraesCS4A01G022100 chr4D 451055535 451058134 2599 True 1663.5 2610 89.0330 54 2636 2 chr4D.!!$R1 2582
3 TraesCS4A01G022100 chr4B 564222998 564226347 3349 True 854.0 1443 90.6625 54 1802 2 chr4B.!!$R4 1748
4 TraesCS4A01G022100 chr4B 564184487 564188064 3577 True 432.0 717 95.2430 2079 2636 2 chr4B.!!$R3 557
5 TraesCS4A01G022100 chr6D 420225811 420226394 583 False 610.0 610 85.8100 2049 2634 1 chr6D.!!$F1 585
6 TraesCS4A01G022100 chr5A 645602449 645603039 590 True 514.0 514 83.0250 1810 2381 1 chr5A.!!$R1 571
7 TraesCS4A01G022100 chr5D 501063281 501063855 574 True 490.0 490 82.8280 1815 2381 1 chr5D.!!$R1 566

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
573 1124 0.03831 AACCAAAGTCCTAGGGCAGC 59.962 55.0 17.52 0.8 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3436 0.811915 GCTGCTCCGTCTCTTACTGA 59.188 55.0 0.0 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
36 37 2.733945 CAAAAGGTTGCCACCCCG 59.266 61.111 2.72 0.00 45.63 5.73
37 38 3.230990 AAAAGGTTGCCACCCCGC 61.231 61.111 2.72 0.00 45.63 6.13
38 39 3.749284 AAAAGGTTGCCACCCCGCT 62.749 57.895 2.72 0.00 45.63 5.52
39 40 3.749284 AAAGGTTGCCACCCCGCTT 62.749 57.895 2.72 0.00 45.63 4.68
40 41 3.749284 AAGGTTGCCACCCCGCTTT 62.749 57.895 2.72 0.00 45.63 3.51
41 42 2.282603 GGTTGCCACCCCGCTTTA 60.283 61.111 0.00 0.00 37.03 1.85
42 43 1.680989 GGTTGCCACCCCGCTTTAT 60.681 57.895 0.00 0.00 37.03 1.40
43 44 0.394625 GGTTGCCACCCCGCTTTATA 60.395 55.000 0.00 0.00 37.03 0.98
44 45 1.687563 GTTGCCACCCCGCTTTATAT 58.312 50.000 0.00 0.00 0.00 0.86
45 46 2.487625 GGTTGCCACCCCGCTTTATATA 60.488 50.000 0.00 0.00 37.03 0.86
46 47 3.418047 GTTGCCACCCCGCTTTATATAT 58.582 45.455 0.00 0.00 0.00 0.86
47 48 4.566070 GGTTGCCACCCCGCTTTATATATA 60.566 45.833 0.00 0.00 37.03 0.86
48 49 4.912317 TGCCACCCCGCTTTATATATAA 57.088 40.909 0.81 0.81 0.00 0.98
49 50 5.244189 TGCCACCCCGCTTTATATATAAA 57.756 39.130 15.47 15.47 0.00 1.40
50 51 9.177671 GGTTGCCACCCCGCTTTATATATAAAG 62.178 44.444 29.34 29.34 42.88 1.85
124 125 8.615211 CAAGATGCTAAATAACAGCTAACATGA 58.385 33.333 0.00 0.00 39.83 3.07
126 127 9.347240 AGATGCTAAATAACAGCTAACATGATT 57.653 29.630 0.00 0.00 39.83 2.57
127 128 9.956720 GATGCTAAATAACAGCTAACATGATTT 57.043 29.630 0.00 0.00 39.83 2.17
128 129 9.740239 ATGCTAAATAACAGCTAACATGATTTG 57.260 29.630 0.00 0.00 39.83 2.32
154 155 3.635331 CACCAAGAACACTTGAGCATTG 58.365 45.455 10.89 0.00 42.26 2.82
208 209 3.686916 AGAAACTAAGTCAGGTGAGCC 57.313 47.619 0.00 0.00 0.00 4.70
262 263 0.486879 TCCCTTGAGGCCAACCATTT 59.513 50.000 5.01 0.00 39.06 2.32
263 264 1.713647 TCCCTTGAGGCCAACCATTTA 59.286 47.619 5.01 0.00 39.06 1.40
264 265 2.102578 CCCTTGAGGCCAACCATTTAG 58.897 52.381 5.01 0.00 39.06 1.85
271 272 2.590704 CCAACCATTTAGGCACCCC 58.409 57.895 0.00 0.00 43.14 4.95
275 276 0.915387 ACCATTTAGGCACCCCCGTA 60.915 55.000 0.00 0.00 43.14 4.02
276 277 0.464916 CCATTTAGGCACCCCCGTAC 60.465 60.000 0.00 0.00 39.21 3.67
277 278 0.464916 CATTTAGGCACCCCCGTACC 60.465 60.000 0.00 0.00 39.21 3.34
284 285 1.390383 GCACCCCCGTACCTCTCTAC 61.390 65.000 0.00 0.00 0.00 2.59
302 853 3.157949 CTCCGAAGAGGCCTCCCC 61.158 72.222 29.54 19.32 40.77 4.81
303 854 3.984186 CTCCGAAGAGGCCTCCCCA 62.984 68.421 29.54 8.16 40.77 4.96
322 873 1.000896 CCCTCGCACCTTTGGGATT 60.001 57.895 0.00 0.00 43.30 3.01
337 888 4.388499 ATTGAAGGACGCCGCGGT 62.388 61.111 28.70 7.71 0.00 5.68
349 900 2.876955 CGCGGTCGGTGGTAGTAA 59.123 61.111 0.00 0.00 0.00 2.24
354 905 1.801395 CGGTCGGTGGTAGTAATGCTG 60.801 57.143 0.00 0.00 0.00 4.41
359 910 1.838077 GGTGGTAGTAATGCTGACCCT 59.162 52.381 0.00 0.00 0.00 4.34
376 927 2.301870 ACCCTCGAGCAAGTATGAACAA 59.698 45.455 6.99 0.00 0.00 2.83
394 945 4.947147 GGCCAACACGGTGCCAGA 62.947 66.667 8.30 0.00 44.70 3.86
413 964 4.988598 AGCGGACCACAAGCACGG 62.989 66.667 0.00 0.00 0.00 4.94
431 982 1.070786 GTCACCTCACCCTGCGAAA 59.929 57.895 0.00 0.00 0.00 3.46
444 995 1.368374 GCGAAACAAACCACCGACG 60.368 57.895 0.00 0.00 0.00 5.12
448 999 0.459934 AAACAAACCACCGACGTCGA 60.460 50.000 37.65 0.00 43.02 4.20
450 1001 2.353839 AAACCACCGACGTCGACG 60.354 61.111 37.65 34.58 43.02 5.12
477 1028 2.828520 TCTAGCCAAGACCAAGACAGAG 59.171 50.000 0.00 0.00 0.00 3.35
487 1038 1.338579 CCAAGACAGAGACCTCAAGCC 60.339 57.143 0.00 0.00 0.00 4.35
490 1041 1.882989 GACAGAGACCTCAAGCCGCT 61.883 60.000 0.00 0.00 0.00 5.52
496 1047 0.674895 GACCTCAAGCCGCTGAACAT 60.675 55.000 0.00 0.00 0.00 2.71
499 1050 1.376543 CTCAAGCCGCTGAACATGAT 58.623 50.000 0.00 0.00 0.00 2.45
507 1058 3.457234 CCGCTGAACATGATTAGCACTA 58.543 45.455 17.85 0.00 35.98 2.74
515 1066 8.352752 TGAACATGATTAGCACTAAAGATACG 57.647 34.615 0.00 0.00 0.00 3.06
522 1073 1.647346 CACTAAAGATACGCCGGCAA 58.353 50.000 28.98 14.85 0.00 4.52
523 1074 2.210116 CACTAAAGATACGCCGGCAAT 58.790 47.619 28.98 19.48 0.00 3.56
530 1081 3.993376 TACGCCGGCAATCGACCAC 62.993 63.158 28.98 0.00 42.43 4.16
565 1116 1.541672 CCCACCCAACCAAAGTCCT 59.458 57.895 0.00 0.00 0.00 3.85
573 1124 0.038310 AACCAAAGTCCTAGGGCAGC 59.962 55.000 17.52 0.80 0.00 5.25
574 1125 0.842467 ACCAAAGTCCTAGGGCAGCT 60.842 55.000 17.52 3.27 0.00 4.24
581 1132 1.279271 GTCCTAGGGCAGCTTCTTCAA 59.721 52.381 9.01 0.00 0.00 2.69
607 1159 0.322816 AATGATGCCGTTGGAGCACT 60.323 50.000 0.00 0.00 44.40 4.40
608 1160 0.745845 ATGATGCCGTTGGAGCACTC 60.746 55.000 0.00 0.00 44.40 3.51
623 1175 1.982395 ACTCTCGCCGTCCAATCCA 60.982 57.895 0.00 0.00 0.00 3.41
627 1179 2.238847 CTCGCCGTCCAATCCAAGGA 62.239 60.000 0.00 0.00 0.00 3.36
632 1184 2.233676 GCCGTCCAATCCAAGGAATTTT 59.766 45.455 0.00 0.00 36.80 1.82
644 1196 4.309933 CAAGGAATTTTGAGCTTTCACCC 58.690 43.478 0.00 0.00 0.00 4.61
645 1197 2.558359 AGGAATTTTGAGCTTTCACCCG 59.442 45.455 0.00 0.00 0.00 5.28
648 1200 0.183971 TTTTGAGCTTTCACCCGGGA 59.816 50.000 32.02 1.07 0.00 5.14
649 1201 0.404040 TTTGAGCTTTCACCCGGGAT 59.596 50.000 32.02 8.96 0.00 3.85
650 1202 0.322456 TTGAGCTTTCACCCGGGATG 60.322 55.000 32.02 21.65 0.00 3.51
656 1208 1.847798 TTTCACCCGGGATGTGGAGG 61.848 60.000 32.02 5.68 34.46 4.30
661 1213 2.136878 CCGGGATGTGGAGGAGGAG 61.137 68.421 0.00 0.00 0.00 3.69
694 1246 9.066892 GGTTGAACCTTTGATATAATCTATGCA 57.933 33.333 7.20 0.00 34.73 3.96
711 1263 2.777094 TGCATTTTCGAGATGTGGTGA 58.223 42.857 11.13 0.00 0.00 4.02
733 1285 5.415701 TGATCAAGCTTAGATGGTTTGGTTC 59.584 40.000 13.78 0.00 0.00 3.62
745 1297 4.601084 TGGTTTGGTTCTTTTGGTACTGA 58.399 39.130 0.00 0.00 0.00 3.41
761 1313 9.932207 TTTGGTACTGAAACTAGATTCGATAAA 57.068 29.630 8.08 2.29 31.80 1.40
900 2547 8.661352 TTTTCCATTTTGAAAATCTGGACTTC 57.339 30.769 11.43 0.00 38.84 3.01
901 2548 6.012658 TCCATTTTGAAAATCTGGACTTCG 57.987 37.500 8.50 0.00 31.19 3.79
904 2551 2.859165 TGAAAATCTGGACTTCGGCT 57.141 45.000 0.00 0.00 0.00 5.52
910 2557 1.743252 CTGGACTTCGGCTTCTGGC 60.743 63.158 0.00 0.00 40.90 4.85
1080 2729 1.757699 ACTTCTATCTTCCGCCTCCAC 59.242 52.381 0.00 0.00 0.00 4.02
1254 2903 2.434359 CCGGCGGACCAAGAAGAC 60.434 66.667 24.41 0.00 34.57 3.01
1272 2921 1.297456 ACGAAGACGACGAGGAGGAC 61.297 60.000 0.00 0.00 42.66 3.85
1279 2928 0.040870 CGACGAGGAGGACGATGATG 60.041 60.000 0.00 0.00 34.70 3.07
1280 2929 1.309950 GACGAGGAGGACGATGATGA 58.690 55.000 0.00 0.00 34.70 2.92
1281 2930 1.265635 GACGAGGAGGACGATGATGAG 59.734 57.143 0.00 0.00 34.70 2.90
1521 3170 2.673523 GTGTCAGCCAGCTGGGAT 59.326 61.111 33.46 11.06 43.75 3.85
1530 3179 4.804420 AGCTGGGATCCCGCCAGA 62.804 66.667 31.30 14.22 39.42 3.86
1670 3322 4.628766 GGTGGTAACTCGGTTAAGCTTAAG 59.371 45.833 19.16 10.00 37.61 1.85
1673 3325 6.309009 GTGGTAACTCGGTTAAGCTTAAGTAC 59.691 42.308 19.16 8.59 37.61 2.73
1674 3326 6.209391 TGGTAACTCGGTTAAGCTTAAGTACT 59.791 38.462 19.16 2.84 37.61 2.73
1680 3332 6.385033 TCGGTTAAGCTTAAGTACTCTTGTC 58.615 40.000 19.16 3.67 35.36 3.18
1741 3393 3.579709 CTGTAGATGTTCTTGTGAGCGT 58.420 45.455 0.00 0.00 0.00 5.07
1752 3406 2.232756 TGTGAGCGTGTGTGTGTAAT 57.767 45.000 0.00 0.00 0.00 1.89
1774 3428 4.261578 ACAATGAGATTTTGTTGGCCAG 57.738 40.909 5.11 0.00 33.64 4.85
1782 3436 2.363306 TTTGTTGGCCAGTCACTCAT 57.637 45.000 5.11 0.00 0.00 2.90
1813 3470 4.100189 AGACGGAGCAGCATAAGTAGAAAT 59.900 41.667 0.00 0.00 0.00 2.17
1824 3481 9.803130 CAGCATAAGTAGAAATCATTCATTACG 57.197 33.333 0.00 0.00 38.06 3.18
1892 3550 3.944087 AGGAAGAAACATCCACTGCTAC 58.056 45.455 0.00 0.00 39.55 3.58
2057 3715 2.697229 CTCTAGGTGTGAGCCATCATCA 59.303 50.000 0.00 0.00 37.87 3.07
2058 3716 2.432146 TCTAGGTGTGAGCCATCATCAC 59.568 50.000 0.00 0.00 45.88 3.06
2128 3815 0.612229 AGTGTGATGTCCTGGCTCAG 59.388 55.000 0.00 0.00 0.00 3.35
2342 4029 6.313411 CAGATTCAGAGTTGTTTCATCTCTCC 59.687 42.308 7.20 0.64 38.14 3.71
2346 4033 4.928615 CAGAGTTGTTTCATCTCTCCTGTC 59.071 45.833 7.20 0.00 38.14 3.51
2378 4065 4.242475 TGCGTCGAGATTGTACAAGAATT 58.758 39.130 14.65 0.00 0.00 2.17
2386 4073 6.259550 AGATTGTACAAGAATTTGCCAGTC 57.740 37.500 14.65 2.15 37.85 3.51
2495 4193 3.856900 ACCAGCCCTTAAAATGTTTCCT 58.143 40.909 0.00 0.00 0.00 3.36
2601 7320 5.526111 GTCACTAACTTCAGTTTTGGCTACA 59.474 40.000 0.00 0.00 39.31 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.733945 CGGGGTGGCAACCTTTTG 59.266 61.111 23.12 5.37 46.70 2.44
20 21 3.230990 GCGGGGTGGCAACCTTTT 61.231 61.111 23.12 0.00 46.70 2.27
21 22 3.749284 AAGCGGGGTGGCAACCTTT 62.749 57.895 23.12 10.95 46.70 3.11
22 23 2.360439 TAAAGCGGGGTGGCAACCTT 62.360 55.000 23.12 10.41 46.70 3.50
23 24 2.150014 ATAAAGCGGGGTGGCAACCT 62.150 55.000 23.12 3.05 46.70 3.50
24 25 0.394625 TATAAAGCGGGGTGGCAACC 60.395 55.000 14.87 14.87 46.81 3.77
25 26 1.687563 ATATAAAGCGGGGTGGCAAC 58.312 50.000 0.00 0.00 34.64 4.17
26 27 3.799432 ATATATAAAGCGGGGTGGCAA 57.201 42.857 0.00 0.00 34.64 4.52
27 28 4.912317 TTATATATAAAGCGGGGTGGCA 57.088 40.909 2.56 0.00 34.64 4.92
28 29 5.813080 CTTTATATATAAAGCGGGGTGGC 57.187 43.478 25.10 0.00 41.69 5.01
115 116 4.746729 TGGTGCATTCAAATCATGTTAGC 58.253 39.130 0.00 0.00 0.00 3.09
124 125 4.942761 AGTGTTCTTGGTGCATTCAAAT 57.057 36.364 0.00 0.00 0.00 2.32
126 127 4.044336 CAAGTGTTCTTGGTGCATTCAA 57.956 40.909 0.00 0.00 45.02 2.69
127 128 3.713858 CAAGTGTTCTTGGTGCATTCA 57.286 42.857 0.00 0.00 45.02 2.57
165 166 0.179073 ATGGCTTGACCTCGGATTCG 60.179 55.000 0.00 0.00 40.22 3.34
168 169 1.043116 TCGATGGCTTGACCTCGGAT 61.043 55.000 1.67 0.00 38.69 4.18
169 170 1.254975 TTCGATGGCTTGACCTCGGA 61.255 55.000 1.67 0.00 38.69 4.55
170 171 0.807667 CTTCGATGGCTTGACCTCGG 60.808 60.000 1.67 0.00 38.69 4.63
171 172 0.173481 TCTTCGATGGCTTGACCTCG 59.827 55.000 0.00 0.00 40.22 4.63
219 220 1.718280 ACGGAGTGAGGTCTTCCTTT 58.282 50.000 0.00 0.00 45.24 3.11
262 263 2.042639 GAGGTACGGGGGTGCCTA 60.043 66.667 3.81 0.00 39.56 3.93
263 264 3.978410 GAGAGGTACGGGGGTGCCT 62.978 68.421 3.45 3.45 42.16 4.75
264 265 2.578586 TAGAGAGGTACGGGGGTGCC 62.579 65.000 0.00 0.00 0.00 5.01
267 268 0.923233 AGGTAGAGAGGTACGGGGGT 60.923 60.000 0.00 0.00 0.00 4.95
271 272 0.467384 TCGGAGGTAGAGAGGTACGG 59.533 60.000 0.00 0.00 0.00 4.02
275 276 2.721425 CTCTTCGGAGGTAGAGAGGT 57.279 55.000 0.00 0.00 38.40 3.85
298 299 4.974438 AAGGTGCGAGGGTGGGGA 62.974 66.667 0.00 0.00 0.00 4.81
302 853 2.484287 ATCCCAAAGGTGCGAGGGTG 62.484 60.000 0.00 0.00 42.12 4.61
303 854 1.789576 AATCCCAAAGGTGCGAGGGT 61.790 55.000 0.00 0.00 42.12 4.34
309 860 1.546029 GTCCTTCAATCCCAAAGGTGC 59.454 52.381 1.41 0.00 42.28 5.01
311 862 1.886655 GCGTCCTTCAATCCCAAAGGT 60.887 52.381 1.41 0.00 42.28 3.50
314 865 0.958382 CGGCGTCCTTCAATCCCAAA 60.958 55.000 0.00 0.00 0.00 3.28
337 888 1.479323 GGTCAGCATTACTACCACCGA 59.521 52.381 0.00 0.00 32.04 4.69
341 892 1.754803 CGAGGGTCAGCATTACTACCA 59.245 52.381 0.00 0.00 33.46 3.25
347 898 0.901827 TTGCTCGAGGGTCAGCATTA 59.098 50.000 15.58 0.00 45.03 1.90
349 900 1.220206 CTTGCTCGAGGGTCAGCAT 59.780 57.895 15.58 0.00 45.03 3.79
354 905 2.094182 TGTTCATACTTGCTCGAGGGTC 60.094 50.000 15.58 0.00 0.00 4.46
359 910 2.346803 GCCTTGTTCATACTTGCTCGA 58.653 47.619 0.00 0.00 0.00 4.04
392 943 1.148273 TGCTTGTGGTCCGCTTTCT 59.852 52.632 3.62 0.00 0.00 2.52
394 945 2.542907 CGTGCTTGTGGTCCGCTTT 61.543 57.895 3.62 0.00 0.00 3.51
413 964 1.070786 TTTCGCAGGGTGAGGTGAC 59.929 57.895 0.00 0.00 0.00 3.67
414 965 1.070786 GTTTCGCAGGGTGAGGTGA 59.929 57.895 0.00 0.00 0.00 4.02
431 982 1.589727 GTCGACGTCGGTGGTTTGT 60.590 57.895 35.05 0.00 40.29 2.83
448 999 1.677966 TCTTGGCTAGAGGCGACGT 60.678 57.895 0.00 0.00 44.42 4.34
450 1001 1.142097 GGTCTTGGCTAGAGGCGAC 59.858 63.158 0.00 1.20 44.42 5.19
459 1010 1.346068 GTCTCTGTCTTGGTCTTGGCT 59.654 52.381 0.00 0.00 0.00 4.75
477 1028 0.674895 ATGTTCAGCGGCTTGAGGTC 60.675 55.000 0.00 0.00 0.00 3.85
487 1038 5.291858 TCTTTAGTGCTAATCATGTTCAGCG 59.708 40.000 9.49 0.00 36.81 5.18
490 1041 7.042725 GCGTATCTTTAGTGCTAATCATGTTCA 60.043 37.037 0.00 0.00 0.00 3.18
496 1047 4.295870 CGGCGTATCTTTAGTGCTAATCA 58.704 43.478 0.00 0.00 0.00 2.57
499 1050 2.800629 GCCGGCGTATCTTTAGTGCTAA 60.801 50.000 12.58 0.00 0.00 3.09
507 1058 0.179094 TCGATTGCCGGCGTATCTTT 60.179 50.000 28.23 8.95 39.14 2.52
522 1073 2.167398 CTTCGGTGTGGGTGGTCGAT 62.167 60.000 0.00 0.00 0.00 3.59
523 1074 2.838693 TTCGGTGTGGGTGGTCGA 60.839 61.111 0.00 0.00 0.00 4.20
542 1093 2.082629 CTTTGGTTGGGTGGGCGAAC 62.083 60.000 0.00 0.00 0.00 3.95
543 1094 1.830408 CTTTGGTTGGGTGGGCGAA 60.830 57.895 0.00 0.00 0.00 4.70
547 1098 0.774908 TAGGACTTTGGTTGGGTGGG 59.225 55.000 0.00 0.00 0.00 4.61
565 1116 3.788227 TTTCTTGAAGAAGCTGCCCTA 57.212 42.857 7.76 0.00 35.37 3.53
599 1151 3.749064 GACGGCGAGAGTGCTCCA 61.749 66.667 16.62 0.00 37.91 3.86
607 1159 1.218047 CTTGGATTGGACGGCGAGA 59.782 57.895 16.62 0.00 0.00 4.04
608 1160 1.815421 CCTTGGATTGGACGGCGAG 60.815 63.158 16.62 0.00 0.00 5.03
623 1175 3.005791 CGGGTGAAAGCTCAAAATTCCTT 59.994 43.478 0.00 0.00 31.88 3.36
627 1179 1.618343 CCCGGGTGAAAGCTCAAAATT 59.382 47.619 14.18 0.00 31.88 1.82
632 1184 1.299648 CATCCCGGGTGAAAGCTCA 59.700 57.895 22.86 0.00 0.00 4.26
644 1196 2.136878 CCTCCTCCTCCACATCCCG 61.137 68.421 0.00 0.00 0.00 5.14
645 1197 1.768077 CCCTCCTCCTCCACATCCC 60.768 68.421 0.00 0.00 0.00 3.85
648 1200 0.327000 CCTTCCCTCCTCCTCCACAT 60.327 60.000 0.00 0.00 0.00 3.21
649 1201 1.081092 CCTTCCCTCCTCCTCCACA 59.919 63.158 0.00 0.00 0.00 4.17
650 1202 1.690985 CCCTTCCCTCCTCCTCCAC 60.691 68.421 0.00 0.00 0.00 4.02
656 1208 0.328592 GTTCAACCCCTTCCCTCCTC 59.671 60.000 0.00 0.00 0.00 3.71
661 1213 1.133294 TCAAAGGTTCAACCCCTTCCC 60.133 52.381 1.75 0.00 41.47 3.97
683 1235 7.663081 ACCACATCTCGAAAATGCATAGATTAT 59.337 33.333 0.00 0.00 0.00 1.28
694 1246 4.095483 GCTTGATCACCACATCTCGAAAAT 59.905 41.667 0.00 0.00 0.00 1.82
695 1247 3.436704 GCTTGATCACCACATCTCGAAAA 59.563 43.478 0.00 0.00 0.00 2.29
702 1254 4.514441 CCATCTAAGCTTGATCACCACATC 59.486 45.833 9.86 0.00 0.00 3.06
711 1263 5.574188 AGAACCAAACCATCTAAGCTTGAT 58.426 37.500 9.86 7.36 0.00 2.57
733 1285 7.884816 TCGAATCTAGTTTCAGTACCAAAAG 57.115 36.000 12.80 0.00 0.00 2.27
835 2464 9.454859 CCTTTACTTTATGTTCAGAGAAGGATT 57.545 33.333 0.00 0.00 32.26 3.01
836 2465 8.606830 ACCTTTACTTTATGTTCAGAGAAGGAT 58.393 33.333 0.00 0.00 33.56 3.24
837 2466 7.974504 ACCTTTACTTTATGTTCAGAGAAGGA 58.025 34.615 0.00 0.00 33.56 3.36
890 2537 0.539051 CCAGAAGCCGAAGTCCAGAT 59.461 55.000 0.00 0.00 0.00 2.90
900 2547 1.227205 CTAGAGCAGCCAGAAGCCG 60.227 63.158 0.00 0.00 45.47 5.52
901 2548 1.145819 CCTAGAGCAGCCAGAAGCC 59.854 63.158 0.00 0.00 45.47 4.35
910 2557 3.127352 GACGGACGGCCTAGAGCAG 62.127 68.421 5.33 0.00 46.50 4.24
1239 2888 1.005394 TTCGTCTTCTTGGTCCGCC 60.005 57.895 0.00 0.00 0.00 6.13
1254 2903 1.424635 GTCCTCCTCGTCGTCTTCG 59.575 63.158 0.00 0.00 38.55 3.79
1272 2921 0.595588 CGTCCTCCTCCTCATCATCG 59.404 60.000 0.00 0.00 0.00 3.84
1279 2928 1.152839 CCCTCTCGTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1280 2929 1.619975 TCCCTCTCGTCCTCCTCCT 60.620 63.158 0.00 0.00 0.00 3.69
1281 2930 1.454295 GTCCCTCTCGTCCTCCTCC 60.454 68.421 0.00 0.00 0.00 4.30
1637 3289 2.738643 CGAGTTACCACCACAGCCTATG 60.739 54.545 0.00 0.00 0.00 2.23
1680 3332 4.522022 AGCAAGAAGAAGAAATTGTGGGAG 59.478 41.667 0.00 0.00 0.00 4.30
1741 3393 8.845227 ACAAAATCTCATTGTATTACACACACA 58.155 29.630 0.00 0.00 39.14 3.72
1752 3406 4.832266 ACTGGCCAACAAAATCTCATTGTA 59.168 37.500 7.01 0.00 39.98 2.41
1774 3428 3.690139 TCCGTCTCTTACTGATGAGTGAC 59.310 47.826 0.00 0.00 33.71 3.67
1782 3436 0.811915 GCTGCTCCGTCTCTTACTGA 59.188 55.000 0.00 0.00 0.00 3.41
1813 3470 6.514870 GCTTTGGATTATGCCGTAATGAATGA 60.515 38.462 0.00 0.00 33.16 2.57
1824 3481 9.793252 CAGTAATTATATGCTTTGGATTATGCC 57.207 33.333 0.00 0.00 0.00 4.40
1892 3550 5.277490 CGTGGGAATTGATATGTAACAGCAG 60.277 44.000 0.00 0.00 0.00 4.24
2057 3715 5.024118 AGTAGTAACCATCTTGGCACTAGT 58.976 41.667 8.21 8.66 42.67 2.57
2058 3716 5.599999 AGTAGTAACCATCTTGGCACTAG 57.400 43.478 8.21 0.00 42.67 2.57
2128 3815 3.142174 CCCTTGAAGAGTCTGGACAAAC 58.858 50.000 0.00 0.00 0.00 2.93
2301 3988 6.053632 TGAATCTGAAGAGCAATGGAAGTA 57.946 37.500 0.00 0.00 0.00 2.24
2342 4029 3.179048 TCGACGCAGATACATTTGACAG 58.821 45.455 0.00 0.00 0.00 3.51
2346 4033 4.268644 ACAATCTCGACGCAGATACATTTG 59.731 41.667 9.29 7.61 32.46 2.32
2378 4065 6.493115 TCTTATGAAAATTGAAGGACTGGCAA 59.507 34.615 0.00 0.00 0.00 4.52
2495 4193 2.714259 GTGGCAAACACTACCAGCA 58.286 52.632 0.00 0.00 46.72 4.41
2601 7320 3.243771 CCGATAAATGGAGAACGTAGGCT 60.244 47.826 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.