Multiple sequence alignment - TraesCS5A01G511500

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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 TraesCS5A01G511500 chr5A 100.000 2540 0 0 1 2540 675320624 675318085 0.000000e+00 4691
1 TraesCS5A01G511500 chr5A 85.094 1013 101 34 1205 2185 675155105 675154111 0.000000e+00 989
2 TraesCS5A01G511500 chr5A 87.500 680 49 14 562 1217 675161162 675160495 0.000000e+00 752
3 TraesCS5A01G511500 chr5A 84.192 582 69 11 1 566 675189989 675189415 6.180000e-151 544
4 TraesCS5A01G511500 chr5A 77.700 574 83 25 1021 1567 674852036 674852591 2.450000e-80 309
5 TraesCS5A01G511500 chr5A 77.700 574 83 25 1021 1567 674893248 674893803 2.450000e-80 309
6 TraesCS5A01G511500 chr5A 84.000 225 26 6 2285 2507 675154022 675153806 9.210000e-50 207
7 TraesCS5A01G511500 chr4D 88.362 1349 95 28 1 1295 495637607 495638947 0.000000e+00 1565
8 TraesCS5A01G511500 chr4D 91.010 723 43 11 915 1615 495520285 495521007 0.000000e+00 955
9 TraesCS5A01G511500 chr4D 87.344 561 40 19 337 878 495519406 495519954 4.640000e-172 614
10 TraesCS5A01G511500 chr4D 87.727 440 39 5 1705 2137 495521000 495521431 1.360000e-137 499
11 TraesCS5A01G511500 chr4D 86.073 438 33 10 1760 2185 495639364 495639785 1.790000e-121 446
12 TraesCS5A01G511500 chr4D 89.459 351 26 2 1 341 495473315 495473664 1.400000e-117 433
13 TraesCS5A01G511500 chr4D 79.862 581 79 17 995 1541 495129587 495130163 8.520000e-105 390
14 TraesCS5A01G511500 chr4D 85.321 327 25 14 1321 1642 495638943 495639251 1.470000e-82 316
15 TraesCS5A01G511500 chr4D 78.613 519 78 19 1073 1567 495074508 495075017 1.900000e-81 313
16 TraesCS5A01G511500 chr4D 85.135 222 24 5 2286 2507 495639880 495640092 4.250000e-53 219
17 TraesCS5A01G511500 chr4D 84.615 221 21 3 2319 2539 495521556 495521763 9.210000e-50 207
18 TraesCS5A01G511500 chr4B 89.048 977 67 21 677 1615 635460235 635461209 0.000000e+00 1175
19 TraesCS5A01G511500 chr4B 91.107 551 27 4 1 529 635459361 635459911 0.000000e+00 726
20 TraesCS5A01G511500 chr4B 78.448 580 87 18 995 1540 635029918 635030493 6.730000e-91 344
21 TraesCS5A01G511500 chr4B 82.251 231 25 6 2285 2507 635461769 635461991 4.320000e-43 185
22 TraesCS5A01G511500 chrUn 77.700 574 83 25 1021 1567 283623695 283624250 2.450000e-80 309


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 TraesCS5A01G511500 chr5A 675318085 675320624 2539 True 4691.000000 4691 100.000000 1 2540 1 chr5A.!!$R3 2539
1 TraesCS5A01G511500 chr5A 675160495 675161162 667 True 752.000000 752 87.500000 562 1217 1 chr5A.!!$R1 655
2 TraesCS5A01G511500 chr5A 675153806 675155105 1299 True 598.000000 989 84.547000 1205 2507 2 chr5A.!!$R4 1302
3 TraesCS5A01G511500 chr5A 675189415 675189989 574 True 544.000000 544 84.192000 1 566 1 chr5A.!!$R2 565
4 TraesCS5A01G511500 chr5A 674852036 674852591 555 False 309.000000 309 77.700000 1021 1567 1 chr5A.!!$F1 546
5 TraesCS5A01G511500 chr5A 674893248 674893803 555 False 309.000000 309 77.700000 1021 1567 1 chr5A.!!$F2 546
6 TraesCS5A01G511500 chr4D 495637607 495640092 2485 False 636.500000 1565 86.222750 1 2507 4 chr4D.!!$F5 2506
7 TraesCS5A01G511500 chr4D 495519406 495521763 2357 False 568.750000 955 87.674000 337 2539 4 chr4D.!!$F4 2202
8 TraesCS5A01G511500 chr4D 495129587 495130163 576 False 390.000000 390 79.862000 995 1541 1 chr4D.!!$F2 546
9 TraesCS5A01G511500 chr4D 495074508 495075017 509 False 313.000000 313 78.613000 1073 1567 1 chr4D.!!$F1 494
10 TraesCS5A01G511500 chr4B 635459361 635461991 2630 False 695.333333 1175 87.468667 1 2507 3 chr4B.!!$F2 2506
11 TraesCS5A01G511500 chr4B 635029918 635030493 575 False 344.000000 344 78.448000 995 1540 1 chr4B.!!$F1 545
12 TraesCS5A01G511500 chrUn 283623695 283624250 555 False 309.000000 309 77.700000 1021 1567 1 chrUn.!!$F1 546

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
773 1002 0.321298 ACTGCACCGGTTGTATGGAC 60.321 55.0 2.97 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 3154 0.038526 AGCAGGACCGTACGTTCTTG 60.039 55.0 18.56 18.56 0.0 3.02 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
80 81 1.734655 TCTTCCTCCCATCCTATGCC 58.265 55.000 0.00 0.00 0.00 4.40
117 118 3.501349 ACTGCTTCTGAAGAGACTACCA 58.499 45.455 21.06 6.54 0.00 3.25
121 122 6.127479 ACTGCTTCTGAAGAGACTACCATTAG 60.127 42.308 21.06 0.00 0.00 1.73
163 164 1.643286 TGCCTGGGAATGTTGGGATTA 59.357 47.619 0.00 0.00 0.00 1.75
167 168 4.352893 CCTGGGAATGTTGGGATTACTTT 58.647 43.478 0.00 0.00 0.00 2.66
247 250 7.661040 CAAGAACTTCCACCTAAATTTGATGT 58.339 34.615 0.00 0.00 0.00 3.06
459 477 4.082125 AGGCTTTCCTAGAATTGGTGTTG 58.918 43.478 0.00 0.00 42.06 3.33
465 483 6.887626 TTCCTAGAATTGGTGTTGGTTAAC 57.112 37.500 0.00 0.00 37.32 2.01
470 488 6.538945 AGAATTGGTGTTGGTTAACTTTGT 57.461 33.333 5.42 0.00 37.68 2.83
472 490 7.039270 AGAATTGGTGTTGGTTAACTTTGTTC 58.961 34.615 5.42 0.00 37.68 3.18
473 491 5.723672 TTGGTGTTGGTTAACTTTGTTCA 57.276 34.783 5.42 0.00 37.68 3.18
711 940 8.528643 TCAGATTCGTCCAAATAGAAAGTTAGA 58.471 33.333 0.00 0.00 0.00 2.10
768 997 1.345089 ACATGTACTGCACCGGTTGTA 59.655 47.619 2.97 6.03 0.00 2.41
773 1002 0.321298 ACTGCACCGGTTGTATGGAC 60.321 55.000 2.97 0.00 0.00 4.02
800 1029 2.727123 TCAAGCACTTCCTCCACAAA 57.273 45.000 0.00 0.00 0.00 2.83
839 1068 1.986378 CGGTGACTCGCTTGACTTTAG 59.014 52.381 0.00 0.00 0.00 1.85
845 1074 6.183360 GGTGACTCGCTTGACTTTAGTATCTA 60.183 42.308 0.00 0.00 0.00 1.98
857 1086 0.324923 AGTATCTACACCGCACCCCA 60.325 55.000 0.00 0.00 0.00 4.96
899 1412 8.043710 TCTCTATTTTCTCACTTGGGAAGATTC 58.956 37.037 0.54 0.00 0.00 2.52
913 1437 6.441222 TGGGAAGATTCAGTAGTGGTATACT 58.559 40.000 2.25 0.00 43.56 2.12
1140 1693 2.734723 CAGACGGTGTGCGTGGAG 60.735 66.667 0.00 0.00 0.00 3.86
1493 2097 2.359354 CGGCATGGGTCGGTCAAA 60.359 61.111 0.00 0.00 38.79 2.69
1577 2208 2.813754 GCCGGCTGCTGAATTTCATATA 59.186 45.455 22.15 0.00 36.87 0.86
1589 2220 5.523552 TGAATTTCATATAGCACAGGTGACG 59.476 40.000 3.10 0.00 0.00 4.35
1605 2236 3.553511 GGTGACGCTAATCAGTTCATCTG 59.446 47.826 0.00 0.00 44.85 2.90
1607 2238 3.190079 GACGCTAATCAGTTCATCTGCA 58.810 45.455 0.00 0.00 43.32 4.41
1615 2246 1.802960 CAGTTCATCTGCAACTCGCTT 59.197 47.619 0.00 0.00 43.06 4.68
1644 2277 2.957402 AGAAAAGCAGGATCACCACA 57.043 45.000 0.00 0.00 38.94 4.17
1648 2281 1.495579 AAGCAGGATCACCACAGGCT 61.496 55.000 0.00 0.00 38.94 4.58
1651 2284 0.393537 CAGGATCACCACAGGCTTCC 60.394 60.000 0.00 0.00 38.94 3.46
1657 2293 2.046023 CCACAGGCTTCCGCATCA 60.046 61.111 0.00 0.00 38.10 3.07
1672 2308 2.684754 CATCACAACGATGCACACAA 57.315 45.000 0.00 0.00 44.95 3.33
1673 2309 2.309693 CATCACAACGATGCACACAAC 58.690 47.619 0.00 0.00 44.95 3.32
1680 2316 4.097714 CAACGATGCACACAACCATATTC 58.902 43.478 0.00 0.00 0.00 1.75
1683 2319 5.368145 ACGATGCACACAACCATATTCTAT 58.632 37.500 0.00 0.00 0.00 1.98
1685 2321 6.989759 ACGATGCACACAACCATATTCTATTA 59.010 34.615 0.00 0.00 0.00 0.98
1686 2322 7.497579 ACGATGCACACAACCATATTCTATTAA 59.502 33.333 0.00 0.00 0.00 1.40
1688 2324 9.669353 GATGCACACAACCATATTCTATTAAAG 57.331 33.333 0.00 0.00 0.00 1.85
1689 2325 8.574251 TGCACACAACCATATTCTATTAAAGT 57.426 30.769 0.00 0.00 0.00 2.66
1690 2326 9.019656 TGCACACAACCATATTCTATTAAAGTT 57.980 29.630 0.00 0.00 0.00 2.66
1691 2327 9.503427 GCACACAACCATATTCTATTAAAGTTC 57.497 33.333 0.00 0.00 0.00 3.01
1721 2357 9.436957 AATGTCTTGTACTTGTTCTTATCGATT 57.563 29.630 1.71 0.00 0.00 3.34
1755 2391 5.209818 TGCTATAATTAACTGGGTCCTCG 57.790 43.478 0.00 0.00 0.00 4.63
1758 2394 5.695363 GCTATAATTAACTGGGTCCTCGAAC 59.305 44.000 0.00 0.00 0.00 3.95
1769 2438 3.617284 GGTCCTCGAACCAATTAACCAT 58.383 45.455 1.23 0.00 39.27 3.55
1770 2439 4.384427 GGGTCCTCGAACCAATTAACCATA 60.384 45.833 8.50 0.00 39.63 2.74
1816 2486 0.093026 CGTCGACGGAAACATTCAGC 59.907 55.000 29.70 0.00 35.37 4.26
1822 2492 3.609175 CGACGGAAACATTCAGCAACAAT 60.609 43.478 0.00 0.00 0.00 2.71
1824 2494 4.050553 ACGGAAACATTCAGCAACAATTG 58.949 39.130 3.24 3.24 0.00 2.32
1895 2565 5.730550 TCTCGGTATATTTGTGTTCTTGCT 58.269 37.500 0.00 0.00 0.00 3.91
1897 2567 6.312918 TCTCGGTATATTTGTGTTCTTGCTTC 59.687 38.462 0.00 0.00 0.00 3.86
1937 2607 0.039527 GCATTGTGGTTTCACCCGTC 60.040 55.000 0.00 0.00 42.98 4.79
1942 2612 2.773487 TGTGGTTTCACCCGTCAATAG 58.227 47.619 0.00 0.00 42.98 1.73
1993 2675 0.298707 CTCGTTCATCAATCCGCACG 59.701 55.000 0.00 0.00 0.00 5.34
2011 2693 1.134640 ACGGCATGTAATAACGGCTCA 60.135 47.619 0.00 0.00 0.00 4.26
2013 2695 2.548057 CGGCATGTAATAACGGCTCAAT 59.452 45.455 0.00 0.00 0.00 2.57
2077 2762 2.039216 TGTCCGGTTTTGCTATTCCTCA 59.961 45.455 0.00 0.00 0.00 3.86
2083 2768 4.396166 CGGTTTTGCTATTCCTCAGACAAT 59.604 41.667 0.00 0.00 0.00 2.71
2132 2819 7.062957 ACCGATAGAGGAAATCCATTGAAAAT 58.937 34.615 1.67 0.00 38.89 1.82
2133 2820 7.561356 ACCGATAGAGGAAATCCATTGAAAATT 59.439 33.333 1.67 0.00 38.89 1.82
2134 2821 9.066892 CCGATAGAGGAAATCCATTGAAAATTA 57.933 33.333 1.67 0.00 38.89 1.40
2135 2822 9.884465 CGATAGAGGAAATCCATTGAAAATTAC 57.116 33.333 1.67 0.00 38.89 1.89
2165 2929 6.755461 ATATTTTCAGTCGCTTGATCTACG 57.245 37.500 0.00 0.00 0.00 3.51
2181 2945 7.605410 TGATCTACGGTGGTTCTTATTTTTC 57.395 36.000 4.54 0.00 0.00 2.29
2188 2952 6.543100 ACGGTGGTTCTTATTTTTCACTACAA 59.457 34.615 0.00 0.00 0.00 2.41
2190 2954 7.749126 CGGTGGTTCTTATTTTTCACTACAATC 59.251 37.037 0.00 0.00 0.00 2.67
2200 2996 7.609760 TTTTTCACTACAATCGCTCATGTAT 57.390 32.000 0.00 0.00 32.02 2.29
2205 3001 1.942657 ACAATCGCTCATGTATGCACC 59.057 47.619 0.00 0.00 0.00 5.01
2233 3029 4.227300 TGGATGGACCAAACAAGTATAGCT 59.773 41.667 0.00 0.00 46.75 3.32
2234 3030 4.816925 GGATGGACCAAACAAGTATAGCTC 59.183 45.833 0.00 0.00 38.79 4.09
2238 3034 4.081087 GGACCAAACAAGTATAGCTCCTGA 60.081 45.833 0.00 0.00 0.00 3.86
2244 3040 6.485830 AACAAGTATAGCTCCTGATGCTTA 57.514 37.500 0.00 0.00 41.46 3.09
2245 3041 6.485830 ACAAGTATAGCTCCTGATGCTTAA 57.514 37.500 0.00 0.00 41.46 1.85
2247 3043 8.195165 ACAAGTATAGCTCCTGATGCTTAATA 57.805 34.615 0.00 0.00 41.46 0.98
2250 3046 7.790027 AGTATAGCTCCTGATGCTTAATATGG 58.210 38.462 0.00 0.00 41.46 2.74
2251 3047 4.989875 AGCTCCTGATGCTTAATATGGT 57.010 40.909 0.00 0.00 37.52 3.55
2252 3048 7.739995 ATAGCTCCTGATGCTTAATATGGTA 57.260 36.000 0.00 0.00 41.46 3.25
2253 3049 6.439636 AGCTCCTGATGCTTAATATGGTAA 57.560 37.500 0.00 0.00 37.52 2.85
2254 3050 7.025520 AGCTCCTGATGCTTAATATGGTAAT 57.974 36.000 0.00 0.00 37.52 1.89
2255 3051 6.883217 AGCTCCTGATGCTTAATATGGTAATG 59.117 38.462 0.00 0.00 37.52 1.90
2256 3052 6.656693 GCTCCTGATGCTTAATATGGTAATGT 59.343 38.462 0.00 0.00 0.00 2.71
2257 3053 7.824289 GCTCCTGATGCTTAATATGGTAATGTA 59.176 37.037 0.00 0.00 0.00 2.29
2258 3054 9.376075 CTCCTGATGCTTAATATGGTAATGTAG 57.624 37.037 0.00 0.00 0.00 2.74
2259 3055 8.880244 TCCTGATGCTTAATATGGTAATGTAGT 58.120 33.333 0.00 0.00 0.00 2.73
2260 3056 9.507329 CCTGATGCTTAATATGGTAATGTAGTT 57.493 33.333 0.00 0.00 0.00 2.24
2266 3062 9.646336 GCTTAATATGGTAATGTAGTTTCAACG 57.354 33.333 0.00 0.00 0.00 4.10
2268 3064 9.669887 TTAATATGGTAATGTAGTTTCAACGGT 57.330 29.630 0.00 0.00 0.00 4.83
2269 3065 8.570068 AATATGGTAATGTAGTTTCAACGGTT 57.430 30.769 0.00 0.00 0.00 4.44
2270 3066 6.887626 ATGGTAATGTAGTTTCAACGGTTT 57.112 33.333 0.00 0.00 0.00 3.27
2271 3067 6.303021 TGGTAATGTAGTTTCAACGGTTTC 57.697 37.500 0.00 0.00 0.00 2.78
2272 3068 6.056884 TGGTAATGTAGTTTCAACGGTTTCT 58.943 36.000 0.00 0.00 0.00 2.52
2273 3069 6.203338 TGGTAATGTAGTTTCAACGGTTTCTC 59.797 38.462 0.00 0.00 0.00 2.87
2274 3070 5.684550 AATGTAGTTTCAACGGTTTCTCC 57.315 39.130 0.00 0.00 0.00 3.71
2275 3071 4.411256 TGTAGTTTCAACGGTTTCTCCT 57.589 40.909 0.00 0.00 0.00 3.69
2276 3072 5.534207 TGTAGTTTCAACGGTTTCTCCTA 57.466 39.130 0.00 0.00 0.00 2.94
2277 3073 5.535333 TGTAGTTTCAACGGTTTCTCCTAG 58.465 41.667 0.00 0.00 0.00 3.02
2278 3074 4.950205 AGTTTCAACGGTTTCTCCTAGA 57.050 40.909 0.00 0.00 0.00 2.43
2279 3075 5.485209 AGTTTCAACGGTTTCTCCTAGAT 57.515 39.130 0.00 0.00 0.00 1.98
2280 3076 6.600882 AGTTTCAACGGTTTCTCCTAGATA 57.399 37.500 0.00 0.00 0.00 1.98
2281 3077 6.396450 AGTTTCAACGGTTTCTCCTAGATAC 58.604 40.000 0.00 0.00 0.00 2.24
2282 3078 6.210984 AGTTTCAACGGTTTCTCCTAGATACT 59.789 38.462 0.00 0.00 0.00 2.12
2283 3079 5.578005 TCAACGGTTTCTCCTAGATACTG 57.422 43.478 0.00 5.21 38.16 2.74
2364 3169 1.412387 GACACAAGAACGTACGGTCC 58.588 55.000 28.78 11.83 30.85 4.46
2368 3173 0.038526 CAAGAACGTACGGTCCTGCT 60.039 55.000 28.78 8.41 30.85 4.24
2388 3193 1.837439 TGTGGAGTTGTGGAGTGACTT 59.163 47.619 0.00 0.00 0.00 3.01
2404 3210 1.379916 CTTGGATGGCAGTGGACCA 59.620 57.895 0.00 0.00 42.61 4.02
2406 3212 0.539438 TTGGATGGCAGTGGACCAAC 60.539 55.000 0.00 0.00 41.49 3.77
2407 3213 1.380302 GGATGGCAGTGGACCAACT 59.620 57.895 0.00 0.00 41.49 3.16
2408 3214 0.618458 GGATGGCAGTGGACCAACTA 59.382 55.000 0.00 0.00 41.49 2.24
2409 3215 1.407437 GGATGGCAGTGGACCAACTAG 60.407 57.143 0.00 0.00 41.49 2.57
2410 3216 1.279271 GATGGCAGTGGACCAACTAGT 59.721 52.381 0.00 0.00 41.49 2.57
2411 3217 2.018355 TGGCAGTGGACCAACTAGTA 57.982 50.000 0.00 0.00 33.12 1.82
2412 3218 1.621814 TGGCAGTGGACCAACTAGTAC 59.378 52.381 0.00 0.00 33.12 2.73
2413 3219 1.900486 GGCAGTGGACCAACTAGTACT 59.100 52.381 0.00 0.00 0.00 2.73
2414 3220 3.094572 GGCAGTGGACCAACTAGTACTA 58.905 50.000 1.89 1.89 0.00 1.82
2415 3221 3.119209 GGCAGTGGACCAACTAGTACTAC 60.119 52.174 0.00 0.00 0.00 2.73
2416 3222 3.762823 GCAGTGGACCAACTAGTACTACT 59.237 47.826 0.00 0.00 0.00 2.57
2459 3265 2.288458 CCTCCGCTGTTTGTTTCGTTTA 59.712 45.455 0.00 0.00 0.00 2.01
2467 3273 1.881591 TTGTTTCGTTTAGGGACCGG 58.118 50.000 0.00 0.00 0.00 5.28
2492 3298 5.047188 AGGCTGTTTGTTTAATTTTGGACG 58.953 37.500 0.00 0.00 0.00 4.79
2496 3302 5.035443 TGTTTGTTTAATTTTGGACGGACG 58.965 37.500 0.00 0.00 0.00 4.79
2527 3333 2.347490 CCACCGTGGGTTCTCCTG 59.653 66.667 9.99 0.00 31.02 3.86
2529 3335 1.301716 CACCGTGGGTTCTCCTGTG 60.302 63.158 0.00 0.00 31.02 3.66
2535 3341 2.168521 CGTGGGTTCTCCTGTGATGTAT 59.831 50.000 0.00 0.00 36.20 2.29
2536 3342 3.738281 CGTGGGTTCTCCTGTGATGTATC 60.738 52.174 0.00 0.00 36.20 2.24
2538 3344 4.080863 GTGGGTTCTCCTGTGATGTATCTT 60.081 45.833 0.00 0.00 36.20 2.40
2539 3345 4.080919 TGGGTTCTCCTGTGATGTATCTTG 60.081 45.833 0.00 0.00 36.20 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 8.973182 GTTAATAAAGTAATCCCAACATTCCCA 58.027 33.333 0.00 0.00 0.00 4.37
148 149 8.973182 TGTTAATAAAGTAATCCCAACATTCCC 58.027 33.333 0.00 0.00 0.00 3.97
163 164 6.655425 GGCTCTCTTCCTGTTGTTAATAAAGT 59.345 38.462 0.00 0.00 0.00 2.66
167 168 5.755409 TGGCTCTCTTCCTGTTGTTAATA 57.245 39.130 0.00 0.00 0.00 0.98
247 250 6.184068 TCCAGCAAGCCATACTAACAAATTA 58.816 36.000 0.00 0.00 0.00 1.40
363 379 5.994668 AGGTCTCTTGATTCTTTCTGTTGAC 59.005 40.000 0.00 0.00 0.00 3.18
451 467 5.723672 TGAACAAAGTTAACCAACACCAA 57.276 34.783 0.88 0.00 37.10 3.67
459 477 7.770801 AAGCTCAAAATGAACAAAGTTAACC 57.229 32.000 0.88 0.00 0.00 2.85
529 556 2.479049 ACCGTGGAACGATCGTTCTATG 60.479 50.000 42.86 40.70 0.00 2.23
568 600 8.918202 ACACTATTTGTTCTTCCTCAACATAA 57.082 30.769 0.00 0.00 33.09 1.90
574 606 5.376625 AGCAACACTATTTGTTCTTCCTCA 58.623 37.500 0.00 0.00 46.05 3.86
655 703 4.526970 ACTCAGAATTTGTGTTGTCCACT 58.473 39.130 0.00 0.00 44.81 4.00
666 714 5.994250 TCTGATCCCCTAACTCAGAATTTG 58.006 41.667 0.00 0.00 41.71 2.32
667 715 6.838401 ATCTGATCCCCTAACTCAGAATTT 57.162 37.500 5.67 0.00 46.07 1.82
670 718 4.342378 CGAATCTGATCCCCTAACTCAGAA 59.658 45.833 5.67 0.00 46.07 3.02
745 974 1.295101 CCGGTGCAGTACATGTGGA 59.705 57.895 9.11 0.00 0.00 4.02
768 997 5.221322 GGAAGTGCTTGAAAGAAAAGTCCAT 60.221 40.000 0.00 0.00 0.00 3.41
773 1002 4.339247 TGGAGGAAGTGCTTGAAAGAAAAG 59.661 41.667 0.00 0.00 0.00 2.27
839 1068 0.179092 GTGGGGTGCGGTGTAGATAC 60.179 60.000 0.00 0.00 0.00 2.24
845 1074 2.845317 TAGTGTGGGGTGCGGTGT 60.845 61.111 0.00 0.00 0.00 4.16
857 1086 8.653036 AAAATAGAGAGGTTCTACAGTAGTGT 57.347 34.615 8.55 8.55 41.10 3.55
899 1412 6.474819 CTCTCGATGAGTATACCACTACTG 57.525 45.833 0.00 0.00 37.72 2.74
913 1437 6.931840 CGATCCTATATATGGACTCTCGATGA 59.068 42.308 14.20 0.00 36.36 2.92
1156 1709 1.815408 GCAGAAGAGGCACTGGAACAA 60.815 52.381 0.00 0.00 41.55 2.83
1485 2089 3.068881 CCAGAGGCCTTTGACCGA 58.931 61.111 24.46 0.00 0.00 4.69
1567 2198 4.273480 GCGTCACCTGTGCTATATGAAATT 59.727 41.667 0.00 0.00 0.00 1.82
1568 2199 3.809832 GCGTCACCTGTGCTATATGAAAT 59.190 43.478 0.00 0.00 0.00 2.17
1577 2208 0.608130 TGATTAGCGTCACCTGTGCT 59.392 50.000 0.00 0.00 42.58 4.40
1627 2260 1.915141 CCTGTGGTGATCCTGCTTTT 58.085 50.000 0.00 0.00 34.23 2.27
1631 2264 1.001641 AAGCCTGTGGTGATCCTGC 60.002 57.895 0.00 0.00 34.23 4.85
1632 2265 0.393537 GGAAGCCTGTGGTGATCCTG 60.394 60.000 0.00 0.00 34.23 3.86
1657 2293 1.317613 ATGGTTGTGTGCATCGTTGT 58.682 45.000 0.00 0.00 0.00 3.32
1692 2328 8.926710 CGATAAGAACAAGTACAAGACATTCTT 58.073 33.333 0.00 4.55 38.98 2.52
1693 2329 8.304596 TCGATAAGAACAAGTACAAGACATTCT 58.695 33.333 0.00 0.00 31.73 2.40
1694 2330 8.462143 TCGATAAGAACAAGTACAAGACATTC 57.538 34.615 0.00 0.00 0.00 2.67
1695 2331 9.436957 AATCGATAAGAACAAGTACAAGACATT 57.563 29.630 0.00 0.00 0.00 2.71
1696 2332 9.436957 AAATCGATAAGAACAAGTACAAGACAT 57.563 29.630 0.00 0.00 0.00 3.06
1697 2333 8.827177 AAATCGATAAGAACAAGTACAAGACA 57.173 30.769 0.00 0.00 0.00 3.41
1698 2334 9.141400 AGAAATCGATAAGAACAAGTACAAGAC 57.859 33.333 0.00 0.00 0.00 3.01
1699 2335 9.706691 AAGAAATCGATAAGAACAAGTACAAGA 57.293 29.630 0.00 0.00 0.00 3.02
1702 2338 9.268268 ACAAAGAAATCGATAAGAACAAGTACA 57.732 29.630 0.00 0.00 0.00 2.90
1749 2385 6.937436 AATATGGTTAATTGGTTCGAGGAC 57.063 37.500 0.00 0.00 0.00 3.85
1787 2456 2.354188 CGTCGACGACACCTGCAA 60.354 61.111 33.35 0.00 43.02 4.08
1816 2486 5.072823 CGACACAGACGATTACAATTGTTG 58.927 41.667 17.78 9.43 33.21 3.33
1822 2492 1.705256 GCCGACACAGACGATTACAA 58.295 50.000 0.00 0.00 0.00 2.41
1824 2494 0.179181 TCGCCGACACAGACGATTAC 60.179 55.000 0.00 0.00 0.00 1.89
1895 2565 4.503817 CCAGCTAGCTGCCTACAATATGAA 60.504 45.833 34.82 0.00 44.23 2.57
1897 2567 3.332919 CCAGCTAGCTGCCTACAATATG 58.667 50.000 34.82 16.02 44.23 1.78
1993 2675 3.363970 CGATTGAGCCGTTATTACATGCC 60.364 47.826 0.00 0.00 0.00 4.40
2104 2790 6.522054 TCAATGGATTTCCTCTATCGGTAAC 58.478 40.000 0.00 0.00 36.82 2.50
2105 2791 6.740944 TCAATGGATTTCCTCTATCGGTAA 57.259 37.500 0.00 0.00 36.82 2.85
2106 2792 6.740944 TTCAATGGATTTCCTCTATCGGTA 57.259 37.500 0.00 0.00 36.82 4.02
2109 2795 9.884465 GTAATTTTCAATGGATTTCCTCTATCG 57.116 33.333 0.00 0.00 36.82 2.92
2112 2798 9.753674 ACTGTAATTTTCAATGGATTTCCTCTA 57.246 29.630 0.00 0.00 36.82 2.43
2132 2819 8.440059 CAAGCGACTGAAAATATTGTACTGTAA 58.560 33.333 0.00 0.00 0.00 2.41
2133 2820 7.815549 TCAAGCGACTGAAAATATTGTACTGTA 59.184 33.333 0.00 0.00 0.00 2.74
2134 2821 6.649141 TCAAGCGACTGAAAATATTGTACTGT 59.351 34.615 0.00 0.00 0.00 3.55
2135 2822 7.060600 TCAAGCGACTGAAAATATTGTACTG 57.939 36.000 0.00 0.00 0.00 2.74
2136 2823 7.766278 AGATCAAGCGACTGAAAATATTGTACT 59.234 33.333 0.00 0.00 0.00 2.73
2137 2824 7.910304 AGATCAAGCGACTGAAAATATTGTAC 58.090 34.615 0.00 0.00 0.00 2.90
2165 2929 7.749126 CGATTGTAGTGAAAAATAAGAACCACC 59.251 37.037 0.00 0.00 0.00 4.61
2181 2945 3.803778 TGCATACATGAGCGATTGTAGTG 59.196 43.478 0.00 0.00 32.24 2.74
2188 2952 0.761187 AGGGTGCATACATGAGCGAT 59.239 50.000 0.00 0.00 0.00 4.58
2190 2954 2.238942 TTAGGGTGCATACATGAGCG 57.761 50.000 0.00 0.00 0.00 5.03
2200 2996 0.550914 GGTCCATCCATTAGGGTGCA 59.449 55.000 0.00 0.00 45.19 4.57
2205 3001 4.344104 ACTTGTTTGGTCCATCCATTAGG 58.656 43.478 0.00 0.00 46.60 2.69
2231 3027 6.656693 ACATTACCATATTAAGCATCAGGAGC 59.343 38.462 0.00 0.00 0.00 4.70
2233 3029 8.880244 ACTACATTACCATATTAAGCATCAGGA 58.120 33.333 0.00 0.00 0.00 3.86
2234 3030 9.507329 AACTACATTACCATATTAAGCATCAGG 57.493 33.333 0.00 0.00 0.00 3.86
2244 3040 8.570068 AACCGTTGAAACTACATTACCATATT 57.430 30.769 0.00 0.00 0.00 1.28
2245 3041 8.570068 AAACCGTTGAAACTACATTACCATAT 57.430 30.769 0.00 0.00 0.00 1.78
2247 3043 6.713450 AGAAACCGTTGAAACTACATTACCAT 59.287 34.615 0.00 0.00 0.00 3.55
2250 3046 6.426025 AGGAGAAACCGTTGAAACTACATTAC 59.574 38.462 0.00 0.00 44.74 1.89
2251 3047 6.527423 AGGAGAAACCGTTGAAACTACATTA 58.473 36.000 0.00 0.00 44.74 1.90
2252 3048 5.374071 AGGAGAAACCGTTGAAACTACATT 58.626 37.500 0.00 0.00 44.74 2.71
2253 3049 4.969484 AGGAGAAACCGTTGAAACTACAT 58.031 39.130 0.00 0.00 44.74 2.29
2254 3050 4.411256 AGGAGAAACCGTTGAAACTACA 57.589 40.909 0.00 0.00 44.74 2.74
2255 3051 5.776744 TCTAGGAGAAACCGTTGAAACTAC 58.223 41.667 0.00 0.00 44.74 2.73
2256 3052 6.600882 ATCTAGGAGAAACCGTTGAAACTA 57.399 37.500 0.00 0.00 44.74 2.24
2257 3053 4.950205 TCTAGGAGAAACCGTTGAAACT 57.050 40.909 0.00 0.00 44.74 2.66
2258 3054 6.310711 CAGTATCTAGGAGAAACCGTTGAAAC 59.689 42.308 0.00 0.00 44.74 2.78
2259 3055 6.014840 ACAGTATCTAGGAGAAACCGTTGAAA 60.015 38.462 0.00 0.00 44.74 2.69
2260 3056 5.479375 ACAGTATCTAGGAGAAACCGTTGAA 59.521 40.000 0.00 0.00 44.74 2.69
2261 3057 5.014858 ACAGTATCTAGGAGAAACCGTTGA 58.985 41.667 0.00 0.00 44.74 3.18
2262 3058 5.326200 ACAGTATCTAGGAGAAACCGTTG 57.674 43.478 0.00 0.00 44.74 4.10
2263 3059 6.606395 ACATACAGTATCTAGGAGAAACCGTT 59.394 38.462 0.00 0.00 44.74 4.44
2264 3060 6.127793 ACATACAGTATCTAGGAGAAACCGT 58.872 40.000 0.00 0.00 44.74 4.83
2265 3061 6.636562 ACATACAGTATCTAGGAGAAACCG 57.363 41.667 0.00 0.00 44.74 4.44
2266 3062 9.134055 AGTAACATACAGTATCTAGGAGAAACC 57.866 37.037 0.00 0.00 39.35 3.27
2267 3063 9.953697 CAGTAACATACAGTATCTAGGAGAAAC 57.046 37.037 0.00 0.00 0.00 2.78
2268 3064 8.630917 GCAGTAACATACAGTATCTAGGAGAAA 58.369 37.037 0.00 0.00 0.00 2.52
2269 3065 7.778382 TGCAGTAACATACAGTATCTAGGAGAA 59.222 37.037 0.00 0.00 0.00 2.87
2270 3066 7.228906 GTGCAGTAACATACAGTATCTAGGAGA 59.771 40.741 0.00 0.00 0.00 3.71
2271 3067 7.364200 GTGCAGTAACATACAGTATCTAGGAG 58.636 42.308 0.00 0.00 0.00 3.69
2272 3068 6.264744 GGTGCAGTAACATACAGTATCTAGGA 59.735 42.308 0.00 0.00 0.00 2.94
2273 3069 6.448006 GGTGCAGTAACATACAGTATCTAGG 58.552 44.000 0.00 0.00 0.00 3.02
2274 3070 6.040504 TGGGTGCAGTAACATACAGTATCTAG 59.959 42.308 0.00 0.00 0.00 2.43
2275 3071 5.894964 TGGGTGCAGTAACATACAGTATCTA 59.105 40.000 0.00 0.00 0.00 1.98
2276 3072 4.714802 TGGGTGCAGTAACATACAGTATCT 59.285 41.667 0.00 0.00 0.00 1.98
2277 3073 5.018539 TGGGTGCAGTAACATACAGTATC 57.981 43.478 0.00 0.00 0.00 2.24
2278 3074 5.104527 ACATGGGTGCAGTAACATACAGTAT 60.105 40.000 0.00 0.00 0.00 2.12
2279 3075 4.224147 ACATGGGTGCAGTAACATACAGTA 59.776 41.667 0.00 0.00 0.00 2.74
2280 3076 3.009033 ACATGGGTGCAGTAACATACAGT 59.991 43.478 0.00 0.00 0.00 3.55
2281 3077 3.374988 CACATGGGTGCAGTAACATACAG 59.625 47.826 0.00 0.00 38.37 2.74
2282 3078 3.008485 TCACATGGGTGCAGTAACATACA 59.992 43.478 0.00 0.00 44.87 2.29
2283 3079 3.605634 TCACATGGGTGCAGTAACATAC 58.394 45.455 0.00 0.00 44.87 2.39
2340 3145 1.201661 CGTACGTTCTTGTGTCGCATG 60.202 52.381 7.22 0.00 0.00 4.06
2349 3154 0.038526 AGCAGGACCGTACGTTCTTG 60.039 55.000 18.56 18.56 0.00 3.02
2364 3169 0.107456 ACTCCACAACTCCACAGCAG 59.893 55.000 0.00 0.00 0.00 4.24
2368 3173 1.496060 AGTCACTCCACAACTCCACA 58.504 50.000 0.00 0.00 0.00 4.17
2388 3193 1.074775 GTTGGTCCACTGCCATCCA 59.925 57.895 0.00 0.00 35.71 3.41
2408 3214 8.584157 ACACGACTAGCATATAGTAGTAGTACT 58.416 37.037 14.57 14.57 42.49 2.73
2409 3215 8.755696 ACACGACTAGCATATAGTAGTAGTAC 57.244 38.462 0.00 0.00 34.51 2.73
2410 3216 7.752686 CGACACGACTAGCATATAGTAGTAGTA 59.247 40.741 8.29 0.00 34.51 1.82
2411 3217 6.585702 CGACACGACTAGCATATAGTAGTAGT 59.414 42.308 0.00 4.51 36.04 2.73
2412 3218 6.805760 TCGACACGACTAGCATATAGTAGTAG 59.194 42.308 0.00 0.92 32.89 2.57
2413 3219 6.681777 TCGACACGACTAGCATATAGTAGTA 58.318 40.000 0.00 0.00 32.89 1.82
2414 3220 5.536260 TCGACACGACTAGCATATAGTAGT 58.464 41.667 0.00 0.00 34.50 2.73
2429 3235 3.733960 CAGCGGAGGTCGACACGA 61.734 66.667 24.20 0.00 42.43 4.35
2467 3273 4.813697 TCCAAAATTAAACAAACAGCCTGC 59.186 37.500 0.00 0.00 0.00 4.85
2492 3298 2.286025 GTGGTGTACAAACAACTCGTCC 59.714 50.000 0.00 0.00 44.16 4.79
2496 3302 2.031191 CACGGTGGTGTACAAACAACTC 59.969 50.000 13.17 0.00 44.16 3.01


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

AutoCloner maintained by Alex Coulton.