Multiple sequence alignment - TraesCS2A01G040500

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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 TraesCS2A01G040500 chr2A 100.000 2906 0 0 1 2906 16609003 16606098 0.000000e+00 5367.0
1 TraesCS2A01G040500 chr2A 89.508 1992 137 41 6 1970 16623547 16621601 0.000000e+00 2455.0
2 TraesCS2A01G040500 chr2A 92.439 1058 27 13 1896 2906 16621600 16620549 0.000000e+00 1461.0
3 TraesCS2A01G040500 chr2A 90.385 104 7 2 2193 2294 102694874 102694772 1.820000e-27 134.0
4 TraesCS2A01G040500 chr2D 92.536 1447 73 16 657 2081 14379815 14381248 0.000000e+00 2041.0
5 TraesCS2A01G040500 chr2B 90.988 1387 81 17 697 2044 26135306 26136687 0.000000e+00 1829.0
6 TraesCS2A01G040500 chr2B 90.466 902 49 15 1167 2044 26201391 26202279 0.000000e+00 1155.0
7 TraesCS2A01G040500 chr2B 87.097 124 13 2 2449 2570 26138119 26138241 1.400000e-28 137.0
8 TraesCS2A01G040500 chr2B 100.000 31 0 0 2330 2360 769004222 769004252 1.120000e-04 58.4
9 TraesCS2A01G040500 chr1A 78.354 559 90 20 1097 1632 536974478 536975028 1.670000e-87 333.0
10 TraesCS2A01G040500 chr1A 94.286 70 4 0 2290 2359 100084879 100084810 1.100000e-19 108.0
11 TraesCS2A01G040500 chr1A 83.133 83 12 2 2290 2371 472524254 472524173 1.120000e-09 75.0
12 TraesCS2A01G040500 chr1B 78.285 548 96 13 1100 1628 598844454 598843911 6.000000e-87 331.0
13 TraesCS2A01G040500 chr1B 94.286 70 4 0 2290 2359 472046198 472046129 1.100000e-19 108.0
14 TraesCS2A01G040500 chr5D 76.923 546 107 15 1091 1628 417607967 417608501 2.830000e-75 292.0
15 TraesCS2A01G040500 chr5D 90.728 151 11 3 467 616 537178351 537178203 6.350000e-47 198.0
16 TraesCS2A01G040500 chr5B 76.782 547 106 15 1091 1628 504775470 504776004 1.320000e-73 287.0
17 TraesCS2A01G040500 chr5B 89.610 154 13 3 464 616 539322888 539322737 2.960000e-45 193.0
18 TraesCS2A01G040500 chr1D 91.275 149 10 3 469 616 427827082 427826936 1.770000e-47 200.0
19 TraesCS2A01G040500 chr1D 93.000 100 5 1 2194 2291 469051090 469051189 8.390000e-31 145.0
20 TraesCS2A01G040500 chr1D 89.524 105 9 1 2192 2294 481633875 481633771 6.530000e-27 132.0
21 TraesCS2A01G040500 chr1D 94.286 70 4 0 2290 2359 62800308 62800377 1.100000e-19 108.0
22 TraesCS2A01G040500 chr1D 92.857 70 5 0 2290 2359 45499747 45499816 5.120000e-18 102.0
23 TraesCS2A01G040500 chr4B 90.132 152 11 4 466 616 659160701 659160849 8.220000e-46 195.0
24 TraesCS2A01G040500 chr4B 89.933 149 12 3 469 616 41528096 41528242 3.820000e-44 189.0
25 TraesCS2A01G040500 chr4B 88.393 112 10 2 2185 2294 4182397 4182287 6.530000e-27 132.0
26 TraesCS2A01G040500 chr3D 89.542 153 13 3 465 616 238999410 238999560 1.060000e-44 191.0
27 TraesCS2A01G040500 chr3D 89.815 108 6 4 2187 2291 179355783 179355678 1.820000e-27 134.0
28 TraesCS2A01G040500 chr3D 90.909 99 7 1 2195 2291 598117216 598117314 6.530000e-27 132.0
29 TraesCS2A01G040500 chrUn 89.933 149 12 3 469 616 31220657 31220511 3.820000e-44 189.0
30 TraesCS2A01G040500 chr4D 89.474 152 13 3 466 616 230542547 230542696 3.820000e-44 189.0
31 TraesCS2A01G040500 chr4D 76.577 111 20 6 2748 2855 484773545 484773438 4.050000e-04 56.5
32 TraesCS2A01G040500 chr6D 90.909 99 7 1 2195 2291 471190864 471190766 6.530000e-27 132.0
33 TraesCS2A01G040500 chr6D 94.286 70 4 0 2290 2359 255009514 255009583 1.100000e-19 108.0
34 TraesCS2A01G040500 chr5A 90.196 102 8 1 2195 2294 267945434 267945333 6.530000e-27 132.0
35 TraesCS2A01G040500 chr5A 94.286 70 4 0 2290 2359 9566573 9566642 1.100000e-19 108.0
36 TraesCS2A01G040500 chr7D 94.286 70 4 0 2290 2359 51464245 51464176 1.100000e-19 108.0
37 TraesCS2A01G040500 chr3B 94.286 70 4 0 2290 2359 43339554 43339623 1.100000e-19 108.0
38 TraesCS2A01G040500 chr3A 91.549 71 6 0 2290 2360 219179704 219179774 6.630000e-17 99.0
39 TraesCS2A01G040500 chr6B 85.714 63 8 1 2808 2869 716994709 716994771 6.720000e-07 65.8
40 TraesCS2A01G040500 chr6B 100.000 33 0 0 2329 2361 3268597 3268629 8.700000e-06 62.1


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 TraesCS2A01G040500 chr2A 16606098 16609003 2905 True 5367 5367 100.0000 1 2906 1 chr2A.!!$R1 2905
1 TraesCS2A01G040500 chr2A 16620549 16623547 2998 True 1958 2455 90.9735 6 2906 2 chr2A.!!$R3 2900
2 TraesCS2A01G040500 chr2D 14379815 14381248 1433 False 2041 2041 92.5360 657 2081 1 chr2D.!!$F1 1424
3 TraesCS2A01G040500 chr2B 26201391 26202279 888 False 1155 1155 90.4660 1167 2044 1 chr2B.!!$F1 877
4 TraesCS2A01G040500 chr2B 26135306 26138241 2935 False 983 1829 89.0425 697 2570 2 chr2B.!!$F3 1873
5 TraesCS2A01G040500 chr1A 536974478 536975028 550 False 333 333 78.3540 1097 1632 1 chr1A.!!$F1 535
6 TraesCS2A01G040500 chr1B 598843911 598844454 543 True 331 331 78.2850 1100 1628 1 chr1B.!!$R2 528
7 TraesCS2A01G040500 chr5D 417607967 417608501 534 False 292 292 76.9230 1091 1628 1 chr5D.!!$F1 537
8 TraesCS2A01G040500 chr5B 504775470 504776004 534 False 287 287 76.7820 1091 1628 1 chr5B.!!$F1 537

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
933 1001 0.622136 AGACTTGGGCATGATCAGCA 59.378 50.0 15.83 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2636 4176 0.099436 GTCCAGAACATGCAATCCGC 59.901 55.0 0.0 0.0 42.89 5.54 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
21 22 3.357203 AGATGTCGTCTCTAGCAGGAAA 58.643 45.455 0.00 0.00 28.45 3.13
29 30 4.636249 GTCTCTAGCAGGAAATACCATGG 58.364 47.826 11.19 11.19 42.04 3.66
183 184 2.276732 TCAGGGGCAACAAGAGAAAG 57.723 50.000 0.00 0.00 39.74 2.62
188 189 4.030216 AGGGGCAACAAGAGAAAGAAAAA 58.970 39.130 0.00 0.00 39.74 1.94
189 190 4.655649 AGGGGCAACAAGAGAAAGAAAAAT 59.344 37.500 0.00 0.00 39.74 1.82
211 212 5.621197 TTACGCCATAATATTGGATGTGC 57.379 39.130 0.00 0.95 39.25 4.57
213 214 3.253188 ACGCCATAATATTGGATGTGCAC 59.747 43.478 10.75 10.75 39.25 4.57
218 219 6.366877 GCCATAATATTGGATGTGCACAATTC 59.633 38.462 25.72 17.66 39.25 2.17
230 231 3.803231 GTGCACAATTCTTGACAAATGCA 59.197 39.130 13.17 0.00 35.95 3.96
241 242 5.827797 TCTTGACAAATGCAAGTTTAGGACT 59.172 36.000 13.43 0.00 42.49 3.85
262 263 7.952930 AGGACTATATATCCACAGTTCACATCT 59.047 37.037 11.47 0.00 38.86 2.90
273 274 8.739039 TCCACAGTTCACATCTATTATTTTTGG 58.261 33.333 0.00 0.00 0.00 3.28
276 277 6.980397 CAGTTCACATCTATTATTTTTGGGGC 59.020 38.462 0.00 0.00 0.00 5.80
286 287 1.120184 TTTTTGGGGCTGCATGCTCA 61.120 50.000 20.33 6.69 46.01 4.26
292 293 4.309347 GCTGCATGCTCATCGGCG 62.309 66.667 20.33 0.00 38.95 6.46
294 295 2.586914 TGCATGCTCATCGGCGAG 60.587 61.111 20.33 7.89 36.02 5.03
369 370 2.741517 TGGCGACAACAACATAGATGTG 59.258 45.455 0.00 0.00 38.22 3.21
374 375 4.690748 CGACAACAACATAGATGTGAAGGT 59.309 41.667 0.00 0.00 41.61 3.50
383 384 3.134574 AGATGTGAAGGTTTGGCGTTA 57.865 42.857 0.00 0.00 0.00 3.18
384 385 3.074412 AGATGTGAAGGTTTGGCGTTAG 58.926 45.455 0.00 0.00 0.00 2.34
385 386 2.335316 TGTGAAGGTTTGGCGTTAGT 57.665 45.000 0.00 0.00 0.00 2.24
387 388 3.806380 TGTGAAGGTTTGGCGTTAGTTA 58.194 40.909 0.00 0.00 0.00 2.24
388 389 3.810941 TGTGAAGGTTTGGCGTTAGTTAG 59.189 43.478 0.00 0.00 0.00 2.34
389 390 3.811497 GTGAAGGTTTGGCGTTAGTTAGT 59.189 43.478 0.00 0.00 0.00 2.24
390 391 4.990426 GTGAAGGTTTGGCGTTAGTTAGTA 59.010 41.667 0.00 0.00 0.00 1.82
391 392 5.640783 GTGAAGGTTTGGCGTTAGTTAGTAT 59.359 40.000 0.00 0.00 0.00 2.12
392 393 6.813152 GTGAAGGTTTGGCGTTAGTTAGTATA 59.187 38.462 0.00 0.00 0.00 1.47
393 394 6.813152 TGAAGGTTTGGCGTTAGTTAGTATAC 59.187 38.462 0.00 0.00 0.00 1.47
394 395 6.284891 AGGTTTGGCGTTAGTTAGTATACA 57.715 37.500 5.50 0.00 0.00 2.29
400 401 5.868801 TGGCGTTAGTTAGTATACACCAAAC 59.131 40.000 5.50 4.30 0.00 2.93
477 478 1.065928 GCGTGGATGTACTCCCTCG 59.934 63.158 17.82 17.82 44.23 4.63
478 479 1.734137 CGTGGATGTACTCCCTCGG 59.266 63.158 15.71 3.74 44.23 4.63
493 494 7.063934 ACTCCCTCGGTTCCTAAATATAAAG 57.936 40.000 0.00 0.00 0.00 1.85
500 501 9.379791 CTCGGTTCCTAAATATAAAGTCTTTGT 57.620 33.333 8.14 3.93 0.00 2.83
521 522 7.921786 TTGTAAAGATTTCACTATGGACCAG 57.078 36.000 0.00 0.00 0.00 4.00
530 531 5.251182 TCACTATGGACCAGATACGGATA 57.749 43.478 0.00 0.00 0.00 2.59
533 534 7.583625 TCACTATGGACCAGATACGGATATAT 58.416 38.462 0.00 0.00 0.00 0.86
540 541 7.502561 TGGACCAGATACGGATATATGTAGATG 59.497 40.741 0.00 0.00 29.44 2.90
559 560 9.534565 TGTAGATGCATTTTAGAGTGTAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
560 561 7.706281 AGATGCATTTTAGAGTGTAGATTCG 57.294 36.000 0.00 0.00 0.00 3.34
563 564 5.520288 TGCATTTTAGAGTGTAGATTCGCTC 59.480 40.000 0.00 0.00 42.95 5.03
569 570 8.547967 TTTAGAGTGTAGATTCGCTCATTTTT 57.452 30.769 9.37 0.00 44.43 1.94
570 571 6.414408 AGAGTGTAGATTCGCTCATTTTTG 57.586 37.500 9.37 0.00 44.43 2.44
571 572 4.974591 AGTGTAGATTCGCTCATTTTTGC 58.025 39.130 0.00 0.00 0.00 3.68
572 573 4.697352 AGTGTAGATTCGCTCATTTTTGCT 59.303 37.500 0.00 0.00 0.00 3.91
574 575 4.694982 TGTAGATTCGCTCATTTTTGCTCA 59.305 37.500 0.00 0.00 0.00 4.26
575 576 4.352600 AGATTCGCTCATTTTTGCTCAG 57.647 40.909 0.00 0.00 0.00 3.35
584 586 6.402550 CGCTCATTTTTGCTCAGTATGTAGTT 60.403 38.462 0.00 0.00 37.40 2.24
641 643 6.074544 ACAGTATTTAGGAACTAGCTAGCG 57.925 41.667 20.91 0.00 44.25 4.26
642 644 5.593502 ACAGTATTTAGGAACTAGCTAGCGT 59.406 40.000 20.91 8.99 44.25 5.07
751 753 1.757118 AGAGCTAGCATCTGCCGTTTA 59.243 47.619 18.83 0.00 43.38 2.01
752 754 2.168521 AGAGCTAGCATCTGCCGTTTAA 59.831 45.455 18.83 0.00 43.38 1.52
753 755 3.134458 GAGCTAGCATCTGCCGTTTAAT 58.866 45.455 18.83 0.00 43.38 1.40
759 762 4.737054 AGCATCTGCCGTTTAATTTTCTG 58.263 39.130 0.00 0.00 43.38 3.02
773 776 1.662517 TTTCTGCGCTTGACTTGTGA 58.337 45.000 9.73 0.00 0.00 3.58
816 820 1.296392 CATCCAGACCAGTTGGCGA 59.704 57.895 0.00 0.00 39.32 5.54
901 943 1.373570 CCTTTCTTCCTTGCCTAGCG 58.626 55.000 0.00 0.00 0.00 4.26
922 964 5.825679 AGCGCTCTCTATATATAGACTTGGG 59.174 44.000 16.95 16.55 35.64 4.12
931 999 9.140874 TCTATATATAGACTTGGGCATGATCAG 57.859 37.037 16.95 0.00 34.63 2.90
932 1000 2.627515 TAGACTTGGGCATGATCAGC 57.372 50.000 0.09 5.10 0.00 4.26
933 1001 0.622136 AGACTTGGGCATGATCAGCA 59.378 50.000 15.83 0.00 0.00 4.41
934 1002 1.214673 AGACTTGGGCATGATCAGCAT 59.785 47.619 15.83 0.00 37.85 3.79
935 1003 2.029623 GACTTGGGCATGATCAGCATT 58.970 47.619 15.83 0.00 34.15 3.56
936 1004 2.029623 ACTTGGGCATGATCAGCATTC 58.970 47.619 15.83 7.84 34.15 2.67
937 1005 2.307768 CTTGGGCATGATCAGCATTCT 58.692 47.619 15.83 0.00 34.15 2.40
938 1006 2.447408 TGGGCATGATCAGCATTCTT 57.553 45.000 15.83 0.00 34.15 2.52
939 1007 2.304092 TGGGCATGATCAGCATTCTTC 58.696 47.619 15.83 1.72 34.15 2.87
940 1008 2.304092 GGGCATGATCAGCATTCTTCA 58.696 47.619 15.83 0.00 34.15 3.02
941 1009 2.034305 GGGCATGATCAGCATTCTTCAC 59.966 50.000 15.83 0.63 34.15 3.18
942 1010 2.686405 GGCATGATCAGCATTCTTCACA 59.314 45.455 15.83 0.00 34.15 3.58
943 1011 3.243101 GGCATGATCAGCATTCTTCACAG 60.243 47.826 15.83 0.00 34.15 3.66
944 1012 3.792459 GCATGATCAGCATTCTTCACAGC 60.792 47.826 0.09 0.00 34.15 4.40
945 1013 3.062122 TGATCAGCATTCTTCACAGCA 57.938 42.857 0.00 0.00 0.00 4.41
946 1014 3.414269 TGATCAGCATTCTTCACAGCAA 58.586 40.909 0.00 0.00 0.00 3.91
947 1015 3.189910 TGATCAGCATTCTTCACAGCAAC 59.810 43.478 0.00 0.00 0.00 4.17
948 1016 1.881973 TCAGCATTCTTCACAGCAACC 59.118 47.619 0.00 0.00 0.00 3.77
949 1017 1.610038 CAGCATTCTTCACAGCAACCA 59.390 47.619 0.00 0.00 0.00 3.67
950 1018 2.034939 CAGCATTCTTCACAGCAACCAA 59.965 45.455 0.00 0.00 0.00 3.67
951 1019 2.295349 AGCATTCTTCACAGCAACCAAG 59.705 45.455 0.00 0.00 0.00 3.61
952 1020 2.294233 GCATTCTTCACAGCAACCAAGA 59.706 45.455 0.00 0.00 0.00 3.02
953 1021 3.243501 GCATTCTTCACAGCAACCAAGAA 60.244 43.478 4.11 4.11 38.80 2.52
954 1022 4.560108 GCATTCTTCACAGCAACCAAGAAT 60.560 41.667 7.53 7.53 43.34 2.40
955 1023 4.836125 TTCTTCACAGCAACCAAGAATC 57.164 40.909 0.00 0.00 31.40 2.52
956 1024 3.819368 TCTTCACAGCAACCAAGAATCA 58.181 40.909 0.00 0.00 0.00 2.57
986 1054 6.929606 TGTAACTAACCAGAAGAAGAAGAAGC 59.070 38.462 0.00 0.00 0.00 3.86
992 1060 4.102367 ACCAGAAGAAGAAGAAGCAGAAGT 59.898 41.667 0.00 0.00 0.00 3.01
1005 1091 1.740380 GCAGAAGTAGAAGCGATGGCA 60.740 52.381 1.50 0.00 43.41 4.92
1020 1106 3.564027 GCATTCCGACGCCCTTCG 61.564 66.667 0.00 0.00 45.38 3.79
1179 1271 3.244561 ACAACACCGTCATCATCTCCTTT 60.245 43.478 0.00 0.00 0.00 3.11
1332 1424 3.506096 TACTCGCTGCCGTCCTCG 61.506 66.667 0.00 0.00 35.54 4.63
1800 1918 1.596603 TGCAATATGACCTCATGCCG 58.403 50.000 0.00 0.00 37.15 5.69
1944 2138 5.326292 CATGCATTATAGTGTGTGTGTGTG 58.674 41.667 0.00 0.00 0.00 3.82
1945 2139 4.384940 TGCATTATAGTGTGTGTGTGTGT 58.615 39.130 0.00 0.00 0.00 3.72
1946 2140 4.213059 TGCATTATAGTGTGTGTGTGTGTG 59.787 41.667 0.00 0.00 0.00 3.82
1947 2141 4.213270 GCATTATAGTGTGTGTGTGTGTGT 59.787 41.667 0.00 0.00 0.00 3.72
1948 2142 5.407084 GCATTATAGTGTGTGTGTGTGTGTA 59.593 40.000 0.00 0.00 0.00 2.90
1949 2143 6.401047 GCATTATAGTGTGTGTGTGTGTGTAG 60.401 42.308 0.00 0.00 0.00 2.74
2602 4142 7.202195 CCTCCTAATTAACTAGGTAAGGGCATT 60.202 40.741 9.71 0.00 39.70 3.56
2614 4154 4.081476 GGTAAGGGCATTTTCAAAGCTGAT 60.081 41.667 0.00 0.00 0.00 2.90
2626 4166 3.254166 TCAAAGCTGATTCTCAAACTGCC 59.746 43.478 0.00 0.00 0.00 4.85
2629 4169 1.135460 GCTGATTCTCAAACTGCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
2636 4176 0.675083 TCAAACTGCCTGCAACCATG 59.325 50.000 0.00 0.00 0.00 3.66
2691 4231 0.533491 AGCAGGCGTGTATCGGTTTA 59.467 50.000 8.40 0.00 40.26 2.01
2699 4239 3.802423 CGTGTATCGGTTTATCGATCGA 58.198 45.455 21.86 21.86 45.43 3.59
2706 4246 2.593257 GGTTTATCGATCGATCCGGAC 58.407 52.381 32.50 23.42 36.17 4.79
2711 4251 0.883370 TCGATCGATCCGGACGTGAT 60.883 55.000 19.51 17.15 0.00 3.06
2737 4277 2.134346 CCACAAACCGGAAAATTGCTG 58.866 47.619 9.46 8.55 0.00 4.41
2769 4338 0.179089 CCGATTCTGACTGCCCTGAG 60.179 60.000 0.00 0.00 0.00 3.35
2842 4411 2.813042 GCTCCAGAGCGTCAGTGC 60.813 66.667 3.49 0.00 45.29 4.40
2858 4427 1.202770 AGTGCTGTATTTATCCCCGCC 60.203 52.381 0.00 0.00 0.00 6.13
2900 4469 3.118454 ACTCCGCGCATTGAACCG 61.118 61.111 8.75 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.719531 TCCTGCTAGAGACGACATCT 57.280 50.000 0.00 0.00 41.91 2.90
1 2 3.784701 TTTCCTGCTAGAGACGACATC 57.215 47.619 0.00 0.00 0.00 3.06
3 4 3.380637 GGTATTTCCTGCTAGAGACGACA 59.619 47.826 0.00 0.00 0.00 4.35
4 5 3.380637 TGGTATTTCCTGCTAGAGACGAC 59.619 47.826 0.00 0.00 37.07 4.34
94 95 5.915196 CGCAATAATCTTGATCGTCTGTAGA 59.085 40.000 0.00 0.00 0.00 2.59
104 105 7.099266 TCATTTCAACCGCAATAATCTTGAT 57.901 32.000 0.00 0.00 0.00 2.57
183 184 9.691362 ACATCCAATATTATGGCGTAATTTTTC 57.309 29.630 16.58 0.00 40.46 2.29
188 189 5.709631 TGCACATCCAATATTATGGCGTAAT 59.290 36.000 15.75 15.75 40.46 1.89
189 190 5.049060 GTGCACATCCAATATTATGGCGTAA 60.049 40.000 13.17 0.91 40.46 3.18
218 219 6.076981 AGTCCTAAACTTGCATTTGTCAAG 57.923 37.500 10.92 10.92 44.71 3.02
262 263 4.070630 GCATGCAGCCCCAAAAATAATA 57.929 40.909 14.21 0.00 37.23 0.98
276 277 2.586914 TCGCCGATGAGCATGCAG 60.587 61.111 21.98 5.35 0.00 4.41
286 287 1.226974 CGTCATCAACCTCGCCGAT 60.227 57.895 0.00 0.00 0.00 4.18
292 293 0.388649 ACACGCTCGTCATCAACCTC 60.389 55.000 0.00 0.00 0.00 3.85
294 295 1.269166 CTACACGCTCGTCATCAACC 58.731 55.000 0.00 0.00 0.00 3.77
315 316 1.202348 GCCACAACCATGTAAAGCTCC 59.798 52.381 0.00 0.00 37.82 4.70
348 349 2.741517 CACATCTATGTTGTTGTCGCCA 59.258 45.455 0.00 0.00 39.39 5.69
349 350 3.000041 TCACATCTATGTTGTTGTCGCC 59.000 45.455 0.00 0.00 39.39 5.54
355 356 5.278957 GCCAAACCTTCACATCTATGTTGTT 60.279 40.000 0.00 0.00 39.39 2.83
358 359 3.440173 CGCCAAACCTTCACATCTATGTT 59.560 43.478 0.00 0.00 39.39 2.71
369 370 6.813152 TGTATACTAACTAACGCCAAACCTTC 59.187 38.462 4.17 0.00 0.00 3.46
374 375 6.035368 TGGTGTATACTAACTAACGCCAAA 57.965 37.500 4.17 0.00 46.50 3.28
383 384 6.579666 TCGTCTGTTTGGTGTATACTAACT 57.420 37.500 4.17 0.00 0.00 2.24
384 385 6.810182 ACATCGTCTGTTTGGTGTATACTAAC 59.190 38.462 4.17 4.53 32.90 2.34
385 386 6.927416 ACATCGTCTGTTTGGTGTATACTAA 58.073 36.000 4.17 0.00 32.90 2.24
387 388 5.401531 ACATCGTCTGTTTGGTGTATACT 57.598 39.130 4.17 0.00 32.90 2.12
388 389 6.755141 ACATACATCGTCTGTTTGGTGTATAC 59.245 38.462 12.77 0.00 40.07 1.47
389 390 6.869695 ACATACATCGTCTGTTTGGTGTATA 58.130 36.000 12.77 0.00 40.07 1.47
390 391 5.730550 ACATACATCGTCTGTTTGGTGTAT 58.269 37.500 12.77 0.00 40.07 2.29
391 392 5.142061 ACATACATCGTCTGTTTGGTGTA 57.858 39.130 12.77 0.00 40.07 2.90
392 393 4.002906 ACATACATCGTCTGTTTGGTGT 57.997 40.909 12.77 0.00 40.07 4.16
393 394 7.651704 TGATATACATACATCGTCTGTTTGGTG 59.348 37.037 12.77 5.61 40.07 4.17
394 395 7.722363 TGATATACATACATCGTCTGTTTGGT 58.278 34.615 12.77 6.63 40.07 3.67
400 401 7.699812 CACCTCATGATATACATACATCGTCTG 59.300 40.741 0.00 0.00 37.46 3.51
493 494 8.451748 GGTCCATAGTGAAATCTTTACAAAGAC 58.548 37.037 6.56 0.00 46.80 3.01
500 501 8.141909 CGTATCTGGTCCATAGTGAAATCTTTA 58.858 37.037 0.00 0.00 0.00 1.85
502 503 6.463049 CCGTATCTGGTCCATAGTGAAATCTT 60.463 42.308 0.00 0.00 0.00 2.40
509 510 7.285629 ACATATATCCGTATCTGGTCCATAGTG 59.714 40.741 0.00 0.00 0.00 2.74
511 512 7.825331 ACATATATCCGTATCTGGTCCATAG 57.175 40.000 0.00 0.00 0.00 2.23
513 514 7.583625 TCTACATATATCCGTATCTGGTCCAT 58.416 38.462 0.00 0.00 0.00 3.41
515 516 7.522399 GCATCTACATATATCCGTATCTGGTCC 60.522 44.444 0.00 0.00 0.00 4.46
516 517 7.013369 TGCATCTACATATATCCGTATCTGGTC 59.987 40.741 0.00 0.00 0.00 4.02
533 534 9.534565 GAATCTACACTCTAAAATGCATCTACA 57.465 33.333 0.00 0.00 0.00 2.74
540 541 5.520288 TGAGCGAATCTACACTCTAAAATGC 59.480 40.000 0.00 0.00 0.00 3.56
548 549 5.024555 GCAAAAATGAGCGAATCTACACTC 58.975 41.667 0.00 0.00 0.00 3.51
558 559 4.002982 ACATACTGAGCAAAAATGAGCGA 58.997 39.130 0.00 0.00 35.48 4.93
559 560 4.346734 ACATACTGAGCAAAAATGAGCG 57.653 40.909 0.00 0.00 35.48 5.03
560 561 6.428385 ACTACATACTGAGCAAAAATGAGC 57.572 37.500 0.00 0.00 0.00 4.26
615 617 8.298140 CGCTAGCTAGTTCCTAAATACTGTATT 58.702 37.037 21.62 7.22 0.00 1.89
616 618 7.447853 ACGCTAGCTAGTTCCTAAATACTGTAT 59.552 37.037 21.62 0.00 0.00 2.29
617 619 6.769822 ACGCTAGCTAGTTCCTAAATACTGTA 59.230 38.462 21.62 0.00 0.00 2.74
619 621 5.915758 CACGCTAGCTAGTTCCTAAATACTG 59.084 44.000 21.62 0.00 0.00 2.74
620 622 5.826737 TCACGCTAGCTAGTTCCTAAATACT 59.173 40.000 21.62 0.00 0.00 2.12
622 624 5.009410 GGTCACGCTAGCTAGTTCCTAAATA 59.991 44.000 21.62 0.00 0.00 1.40
623 625 4.202131 GGTCACGCTAGCTAGTTCCTAAAT 60.202 45.833 21.62 0.00 0.00 1.40
625 627 2.686915 GGTCACGCTAGCTAGTTCCTAA 59.313 50.000 21.62 1.14 0.00 2.69
626 628 2.295885 GGTCACGCTAGCTAGTTCCTA 58.704 52.381 21.62 2.14 0.00 2.94
627 629 1.104630 GGTCACGCTAGCTAGTTCCT 58.895 55.000 21.62 0.00 0.00 3.36
628 630 0.815734 TGGTCACGCTAGCTAGTTCC 59.184 55.000 21.62 15.71 0.00 3.62
630 632 3.064931 GTTTTGGTCACGCTAGCTAGTT 58.935 45.455 21.62 6.89 0.00 2.24
631 633 2.685100 GTTTTGGTCACGCTAGCTAGT 58.315 47.619 21.62 0.65 0.00 2.57
632 634 1.654105 CGTTTTGGTCACGCTAGCTAG 59.346 52.381 16.84 16.84 0.00 3.42
633 635 1.705256 CGTTTTGGTCACGCTAGCTA 58.295 50.000 13.93 0.00 0.00 3.32
634 636 2.528797 CGTTTTGGTCACGCTAGCT 58.471 52.632 13.93 0.00 0.00 3.32
751 753 3.066621 TCACAAGTCAAGCGCAGAAAATT 59.933 39.130 11.47 0.47 0.00 1.82
752 754 2.618241 TCACAAGTCAAGCGCAGAAAAT 59.382 40.909 11.47 0.00 0.00 1.82
753 755 2.013400 TCACAAGTCAAGCGCAGAAAA 58.987 42.857 11.47 0.00 0.00 2.29
759 762 1.002366 ATCGATCACAAGTCAAGCGC 58.998 50.000 0.00 0.00 0.00 5.92
773 776 4.302455 GTCAAATCAGATGGACGATCGAT 58.698 43.478 24.34 4.53 36.04 3.59
816 820 0.881118 ACAATTTCGATTGGCTGCGT 59.119 45.000 3.94 0.00 35.93 5.24
901 943 7.286546 TCATGCCCAAGTCTATATATAGAGAGC 59.713 40.741 20.55 17.61 39.87 4.09
922 964 3.792459 GCTGTGAAGAATGCTGATCATGC 60.792 47.826 0.00 2.91 35.13 4.06
931 999 2.294233 TCTTGGTTGCTGTGAAGAATGC 59.706 45.455 0.00 0.00 0.00 3.56
932 1000 4.572985 TTCTTGGTTGCTGTGAAGAATG 57.427 40.909 0.00 0.00 31.13 2.67
933 1001 4.828939 TGATTCTTGGTTGCTGTGAAGAAT 59.171 37.500 0.00 0.00 44.20 2.40
934 1002 4.206375 TGATTCTTGGTTGCTGTGAAGAA 58.794 39.130 0.00 0.00 38.46 2.52
935 1003 3.819368 TGATTCTTGGTTGCTGTGAAGA 58.181 40.909 0.00 0.00 0.00 2.87
936 1004 4.216902 TGATGATTCTTGGTTGCTGTGAAG 59.783 41.667 0.00 0.00 0.00 3.02
937 1005 4.022935 GTGATGATTCTTGGTTGCTGTGAA 60.023 41.667 0.00 0.00 0.00 3.18
938 1006 3.503363 GTGATGATTCTTGGTTGCTGTGA 59.497 43.478 0.00 0.00 0.00 3.58
939 1007 3.504906 AGTGATGATTCTTGGTTGCTGTG 59.495 43.478 0.00 0.00 0.00 3.66
940 1008 3.504906 CAGTGATGATTCTTGGTTGCTGT 59.495 43.478 0.00 0.00 0.00 4.40
941 1009 3.504906 ACAGTGATGATTCTTGGTTGCTG 59.495 43.478 0.00 0.00 0.00 4.41
942 1010 3.759581 ACAGTGATGATTCTTGGTTGCT 58.240 40.909 0.00 0.00 0.00 3.91
943 1011 5.182001 AGTTACAGTGATGATTCTTGGTTGC 59.818 40.000 0.00 0.00 0.00 4.17
944 1012 6.808008 AGTTACAGTGATGATTCTTGGTTG 57.192 37.500 0.00 0.00 0.00 3.77
945 1013 7.390718 GGTTAGTTACAGTGATGATTCTTGGTT 59.609 37.037 0.00 0.00 0.00 3.67
946 1014 6.879458 GGTTAGTTACAGTGATGATTCTTGGT 59.121 38.462 0.00 0.00 0.00 3.67
947 1015 6.878923 TGGTTAGTTACAGTGATGATTCTTGG 59.121 38.462 0.00 0.00 0.00 3.61
948 1016 7.819415 TCTGGTTAGTTACAGTGATGATTCTTG 59.181 37.037 0.00 0.00 36.17 3.02
949 1017 7.907389 TCTGGTTAGTTACAGTGATGATTCTT 58.093 34.615 0.00 0.00 36.17 2.52
950 1018 7.482169 TCTGGTTAGTTACAGTGATGATTCT 57.518 36.000 0.00 0.00 36.17 2.40
951 1019 8.035394 TCTTCTGGTTAGTTACAGTGATGATTC 58.965 37.037 0.00 0.00 36.17 2.52
952 1020 7.907389 TCTTCTGGTTAGTTACAGTGATGATT 58.093 34.615 0.00 0.00 36.17 2.57
953 1021 7.482169 TCTTCTGGTTAGTTACAGTGATGAT 57.518 36.000 0.00 0.00 36.17 2.45
954 1022 6.911250 TCTTCTGGTTAGTTACAGTGATGA 57.089 37.500 0.00 0.00 36.17 2.92
955 1023 7.378966 TCTTCTTCTGGTTAGTTACAGTGATG 58.621 38.462 0.00 0.00 36.17 3.07
956 1024 7.540474 TCTTCTTCTGGTTAGTTACAGTGAT 57.460 36.000 0.00 0.00 36.17 3.06
986 1054 2.299993 TGCCATCGCTTCTACTTCTG 57.700 50.000 0.00 0.00 35.36 3.02
992 1060 0.750249 TCGGAATGCCATCGCTTCTA 59.250 50.000 0.00 0.00 35.36 2.10
1020 1106 2.202892 GCCCCTGCTACTACGCAC 60.203 66.667 0.00 0.00 35.74 5.34
1179 1271 1.373748 GTGGCCGAAGACGCTGTAA 60.374 57.895 0.00 0.00 38.29 2.41
1708 1812 0.462047 CCGATGTACACCTTGCTCCC 60.462 60.000 0.00 0.00 0.00 4.30
1744 1848 4.011517 GTCGTTCCTCCCCGGCAA 62.012 66.667 0.00 0.00 0.00 4.52
2193 3715 3.525537 GCTAGAGCATGCACTTCTACAA 58.474 45.455 22.83 2.96 41.59 2.41
2205 3727 3.931907 TGGTTACATTGGCTAGAGCAT 57.068 42.857 3.54 0.00 44.36 3.79
2614 4154 1.032014 GGTTGCAGGCAGTTTGAGAA 58.968 50.000 0.00 0.00 0.00 2.87
2636 4176 0.099436 GTCCAGAACATGCAATCCGC 59.901 55.000 0.00 0.00 42.89 5.54
2691 4231 0.883370 TCACGTCCGGATCGATCGAT 60.883 55.000 29.76 29.76 37.59 3.59
2753 4322 1.203441 TGGCTCAGGGCAGTCAGAAT 61.203 55.000 0.00 0.00 43.20 2.40
2809 4378 3.414700 GCGGTGCTGACCACTTCG 61.415 66.667 0.00 0.00 43.33 3.79
2831 4400 3.491267 GGATAAATACAGCACTGACGCTC 59.509 47.826 4.31 0.00 41.38 5.03
2842 4411 1.697432 TCTGGGCGGGGATAAATACAG 59.303 52.381 0.00 0.00 0.00 2.74
2849 4418 2.844362 CTGCTCTGGGCGGGGATA 60.844 66.667 0.00 0.00 45.43 2.59
2875 4444 3.567478 ATGCGCGGAGTGACGTGAA 62.567 57.895 8.83 0.00 46.47 3.18


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

AutoCloner maintained by Alex Coulton.