Multiple sequence alignment - TraesCS2A01G296800

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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 TraesCS2A01G296800 chr2A 100.000 3223 0 0 1 3223 510947291 510950513 0.000000e+00 5952.0
1 TraesCS2A01G296800 chr2A 86.667 645 44 12 2593 3221 36242357 36241739 0.000000e+00 676.0
2 TraesCS2A01G296800 chr2A 88.309 479 34 6 2709 3172 751272957 751272486 3.630000e-154 555.0
3 TraesCS2A01G296800 chr2A 88.100 479 35 5 2709 3172 751242378 751241907 1.690000e-152 549.0
4 TraesCS2A01G296800 chr2A 84.170 518 47 15 2716 3221 136747653 136748147 1.350000e-128 470.0
5 TraesCS2A01G296800 chr2A 92.908 141 9 1 2595 2734 136747499 136747639 1.520000e-48 204.0
6 TraesCS2A01G296800 chr2D 94.444 2088 82 17 511 2596 377055335 377057390 0.000000e+00 3182.0
7 TraesCS2A01G296800 chr2D 88.048 251 27 1 1 251 377055082 377055329 8.740000e-76 294.0
8 TraesCS2A01G296800 chr2B 95.172 1947 66 14 654 2596 448477242 448479164 0.000000e+00 3049.0
9 TraesCS2A01G296800 chr2B 99.683 630 2 0 2594 3223 183062543 183061914 0.000000e+00 1153.0
10 TraesCS2A01G296800 chr2B 86.905 252 26 4 1 250 448474599 448474845 3.170000e-70 276.0
11 TraesCS2A01G296800 chr2B 93.711 159 10 0 505 663 448474843 448475001 4.160000e-59 239.0
12 TraesCS2A01G296800 chr2B 79.279 111 18 4 2590 2696 526500948 526501057 4.460000e-09 73.1
13 TraesCS2A01G296800 chr3B 88.608 632 62 7 2595 3221 791819550 791820176 0.000000e+00 760.0
14 TraesCS2A01G296800 chr5B 87.092 643 41 12 2595 3221 659550670 659551286 0.000000e+00 689.0
15 TraesCS2A01G296800 chr7A 86.916 642 42 12 2595 3221 62483004 62483618 0.000000e+00 682.0
16 TraesCS2A01G296800 chr6B 85.164 519 37 12 2717 3221 439476493 439476985 2.230000e-136 496.0
17 TraesCS2A01G296800 chr6B 86.280 379 34 7 2595 2958 704704433 704704808 2.330000e-106 396.0
18 TraesCS2A01G296800 chr6B 87.452 263 23 7 248 501 629198090 629198351 8.740000e-76 294.0
19 TraesCS2A01G296800 chr6A 89.272 261 21 4 248 501 600289578 600289838 1.440000e-83 320.0
20 TraesCS2A01G296800 chr1B 89.231 260 20 5 248 501 540717702 540717959 5.190000e-83 318.0
21 TraesCS2A01G296800 chr7D 87.407 270 24 7 243 502 591013270 591013001 5.230000e-78 302.0
22 TraesCS2A01G296800 chr7B 87.786 262 26 4 248 503 431976780 431976519 5.230000e-78 302.0
23 TraesCS2A01G296800 chr7B 87.547 265 27 4 244 502 677406528 677406264 5.230000e-78 302.0
24 TraesCS2A01G296800 chr7B 87.266 267 21 6 248 501 267173866 267173600 3.140000e-75 292.0
25 TraesCS2A01G296800 chr4B 86.312 263 27 6 248 501 395666002 395665740 8.810000e-71 278.0
26 TraesCS2A01G296800 chr4A 84.962 266 34 3 243 502 641844774 641844509 6.860000e-67 265.0
27 TraesCS2A01G296800 chr4A 100.000 38 0 0 2595 2632 605539592 605539629 1.600000e-08 71.3
28 TraesCS2A01G296800 chrUn 100.000 39 0 0 2594 2632 43007674 43007636 4.460000e-09 73.1
29 TraesCS2A01G296800 chrUn 100.000 39 0 0 2594 2632 43189594 43189632 4.460000e-09 73.1
30 TraesCS2A01G296800 chrUn 100.000 39 0 0 2594 2632 178611984 178612022 4.460000e-09 73.1
31 TraesCS2A01G296800 chrUn 100.000 39 0 0 2594 2632 364116439 364116477 4.460000e-09 73.1
32 TraesCS2A01G296800 chrUn 100.000 39 0 0 2594 2632 364118176 364118138 4.460000e-09 73.1


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 TraesCS2A01G296800 chr2A 510947291 510950513 3222 False 5952 5952 100.000000 1 3223 1 chr2A.!!$F1 3222
1 TraesCS2A01G296800 chr2A 36241739 36242357 618 True 676 676 86.667000 2593 3221 1 chr2A.!!$R1 628
2 TraesCS2A01G296800 chr2A 136747499 136748147 648 False 337 470 88.539000 2595 3221 2 chr2A.!!$F2 626
3 TraesCS2A01G296800 chr2D 377055082 377057390 2308 False 1738 3182 91.246000 1 2596 2 chr2D.!!$F1 2595
4 TraesCS2A01G296800 chr2B 448474599 448479164 4565 False 1188 3049 91.929333 1 2596 3 chr2B.!!$F2 2595
5 TraesCS2A01G296800 chr2B 183061914 183062543 629 True 1153 1153 99.683000 2594 3223 1 chr2B.!!$R1 629
6 TraesCS2A01G296800 chr3B 791819550 791820176 626 False 760 760 88.608000 2595 3221 1 chr3B.!!$F1 626
7 TraesCS2A01G296800 chr5B 659550670 659551286 616 False 689 689 87.092000 2595 3221 1 chr5B.!!$F1 626
8 TraesCS2A01G296800 chr7A 62483004 62483618 614 False 682 682 86.916000 2595 3221 1 chr7A.!!$F1 626

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
642 645 0.03759 TCCCATTCACCTTTCCCGTG 59.962 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 4482 0.315568 CCACGACCATCCTAGCTAGC 59.684 60.0 15.74 6.62 0.0 3.42 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
127 130 9.976511 CAGACGGAGGTAATATAAGACAAATTA 57.023 33.333 0.00 0.00 0.00 1.40
204 207 2.693591 GTCATATCCGGAGTCAGTTCCA 59.306 50.000 11.34 0.00 37.05 3.53
215 218 4.220821 GGAGTCAGTTCCAGTCAGTCAATA 59.779 45.833 0.00 0.00 37.20 1.90
221 224 3.319137 TCCAGTCAGTCAATAGTGTGC 57.681 47.619 0.00 0.00 0.00 4.57
224 227 2.027745 CAGTCAGTCAATAGTGTGCCCT 60.028 50.000 0.00 0.00 0.00 5.19
229 232 0.692476 TCAATAGTGTGCCCTGCTGT 59.308 50.000 0.00 0.00 0.00 4.40
246 249 5.066117 CCTGCTGTATAGAGACGACACTAAA 59.934 44.000 0.05 0.00 0.00 1.85
251 254 4.640789 ATAGAGACGACACTAAAGCTGG 57.359 45.455 0.00 0.00 0.00 4.85
252 255 2.240279 AGAGACGACACTAAAGCTGGT 58.760 47.619 0.00 0.00 0.00 4.00
254 257 2.731976 GAGACGACACTAAAGCTGGTTG 59.268 50.000 0.00 0.00 0.00 3.77
255 258 2.102588 AGACGACACTAAAGCTGGTTGT 59.897 45.455 0.00 0.00 0.00 3.32
256 259 3.319972 AGACGACACTAAAGCTGGTTGTA 59.680 43.478 0.00 0.00 0.00 2.41
257 260 4.053295 GACGACACTAAAGCTGGTTGTAA 58.947 43.478 0.00 0.00 0.00 2.41
258 261 4.638304 ACGACACTAAAGCTGGTTGTAAT 58.362 39.130 0.00 0.00 0.00 1.89
259 262 4.451096 ACGACACTAAAGCTGGTTGTAATG 59.549 41.667 0.00 0.00 0.00 1.90
260 263 4.142902 CGACACTAAAGCTGGTTGTAATGG 60.143 45.833 0.00 0.00 0.00 3.16
261 264 4.079253 ACACTAAAGCTGGTTGTAATGGG 58.921 43.478 0.00 0.00 0.00 4.00
262 265 3.443681 CACTAAAGCTGGTTGTAATGGGG 59.556 47.826 0.00 0.00 0.00 4.96
263 266 2.990740 AAAGCTGGTTGTAATGGGGA 57.009 45.000 0.00 0.00 0.00 4.81
264 267 2.514458 AAGCTGGTTGTAATGGGGAG 57.486 50.000 0.00 0.00 0.00 4.30
265 268 1.372501 AGCTGGTTGTAATGGGGAGT 58.627 50.000 0.00 0.00 0.00 3.85
266 269 2.557869 AGCTGGTTGTAATGGGGAGTA 58.442 47.619 0.00 0.00 0.00 2.59
267 270 3.123273 AGCTGGTTGTAATGGGGAGTAT 58.877 45.455 0.00 0.00 0.00 2.12
268 271 3.136626 AGCTGGTTGTAATGGGGAGTATC 59.863 47.826 0.00 0.00 0.00 2.24
269 272 3.118038 GCTGGTTGTAATGGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
270 273 4.446311 GCTGGTTGTAATGGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
271 274 5.221843 GCTGGTTGTAATGGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
272 275 6.522459 GCTGGTTGTAATGGGGAGTATCATAT 60.522 42.308 0.00 0.00 36.25 1.78
273 276 7.311046 GCTGGTTGTAATGGGGAGTATCATATA 60.311 40.741 0.00 0.00 36.25 0.86
274 277 7.913789 TGGTTGTAATGGGGAGTATCATATAC 58.086 38.462 0.00 0.00 36.25 1.47
275 278 7.737607 TGGTTGTAATGGGGAGTATCATATACT 59.262 37.037 0.00 0.00 36.25 2.12
276 279 9.263446 GGTTGTAATGGGGAGTATCATATACTA 57.737 37.037 0.00 0.00 36.25 1.82
278 281 8.534954 TGTAATGGGGAGTATCATATACTAGC 57.465 38.462 0.00 0.00 36.25 3.42
279 282 8.119891 TGTAATGGGGAGTATCATATACTAGCA 58.880 37.037 0.00 0.00 36.25 3.49
280 283 9.148879 GTAATGGGGAGTATCATATACTAGCAT 57.851 37.037 0.00 0.00 36.25 3.79
281 284 7.609097 ATGGGGAGTATCATATACTAGCATG 57.391 40.000 0.00 0.00 36.25 4.06
282 285 5.363868 TGGGGAGTATCATATACTAGCATGC 59.636 44.000 10.51 10.51 36.25 4.06
283 286 5.363868 GGGGAGTATCATATACTAGCATGCA 59.636 44.000 21.98 5.01 36.25 3.96
284 287 6.042552 GGGGAGTATCATATACTAGCATGCAT 59.957 42.308 21.98 6.99 36.25 3.96
285 288 7.233553 GGGGAGTATCATATACTAGCATGCATA 59.766 40.741 21.98 9.21 36.25 3.14
286 289 8.811017 GGGAGTATCATATACTAGCATGCATAT 58.189 37.037 21.98 16.02 36.25 1.78
371 374 7.982761 TCATGCATGACACATATTAGCATAA 57.017 32.000 25.42 0.00 39.00 1.90
372 375 7.809665 TCATGCATGACACATATTAGCATAAC 58.190 34.615 25.42 0.00 39.00 1.89
373 376 7.444792 TCATGCATGACACATATTAGCATAACA 59.555 33.333 25.42 0.00 39.00 2.41
374 377 7.748691 TGCATGACACATATTAGCATAACAT 57.251 32.000 0.00 0.00 0.00 2.71
375 378 8.168790 TGCATGACACATATTAGCATAACATT 57.831 30.769 0.00 0.00 0.00 2.71
376 379 8.631797 TGCATGACACATATTAGCATAACATTT 58.368 29.630 0.00 0.00 0.00 2.32
416 419 8.437360 TCATGATATGATACTCAACGCTTTTT 57.563 30.769 0.00 0.00 33.59 1.94
444 447 9.904198 TTCATTTAATTCTATGACACCTCATCA 57.096 29.630 2.75 0.00 38.21 3.07
445 448 9.904198 TCATTTAATTCTATGACACCTCATCAA 57.096 29.630 0.00 0.00 38.21 2.57
459 462 9.573133 GACACCTCATCAAAATTATTTAGTTGG 57.427 33.333 0.00 0.00 0.00 3.77
460 463 8.034804 ACACCTCATCAAAATTATTTAGTTGGC 58.965 33.333 0.00 0.00 0.00 4.52
461 464 8.034215 CACCTCATCAAAATTATTTAGTTGGCA 58.966 33.333 0.00 0.00 0.00 4.92
462 465 8.761689 ACCTCATCAAAATTATTTAGTTGGCAT 58.238 29.630 0.00 0.00 0.00 4.40
498 501 7.476667 AGCTATGATACTACATTACGATCAGC 58.523 38.462 0.00 0.00 30.49 4.26
499 502 6.693545 GCTATGATACTACATTACGATCAGCC 59.306 42.308 0.00 0.00 30.49 4.85
500 503 6.842437 ATGATACTACATTACGATCAGCCT 57.158 37.500 0.00 0.00 30.49 4.58
501 504 7.939784 ATGATACTACATTACGATCAGCCTA 57.060 36.000 0.00 0.00 30.49 3.93
502 505 7.142306 TGATACTACATTACGATCAGCCTAC 57.858 40.000 0.00 0.00 0.00 3.18
503 506 4.850347 ACTACATTACGATCAGCCTACC 57.150 45.455 0.00 0.00 0.00 3.18
504 507 2.795175 ACATTACGATCAGCCTACCG 57.205 50.000 0.00 0.00 0.00 4.02
505 508 1.269621 ACATTACGATCAGCCTACCGC 60.270 52.381 0.00 0.00 37.98 5.68
586 589 7.445096 CACACCATCTAATAGCACCAAATCATA 59.555 37.037 0.00 0.00 0.00 2.15
618 621 7.388460 ACATTATTGAGCTCTCCTTTTTCTG 57.612 36.000 16.19 3.85 0.00 3.02
642 645 0.037590 TCCCATTCACCTTTCCCGTG 59.962 55.000 0.00 0.00 0.00 4.94
742 2995 6.102468 TGAATCAATCCCATGACCCACTAATA 59.898 38.462 0.00 0.00 30.82 0.98
750 3003 5.445069 CCATGACCCACTAATAATTGACCA 58.555 41.667 0.00 0.00 0.00 4.02
795 3048 1.997606 CCGTAAATTCCGTTTCGAGCT 59.002 47.619 0.00 0.00 0.00 4.09
977 3230 1.009429 AGATCTTGGCCTCCTCTTCCT 59.991 52.381 3.32 0.00 0.00 3.36
986 3239 2.503356 GCCTCCTCTTCCTGAGAATTCA 59.497 50.000 8.44 0.00 45.39 2.57
993 3246 0.391130 TCCTGAGAATTCAACGCCGG 60.391 55.000 8.44 0.00 31.69 6.13
1054 3307 0.250513 AGTGGATTTCTCCGTGCTCC 59.749 55.000 0.00 0.00 45.37 4.70
1081 3334 6.303839 TCTACCTCTGTTGCCTGTAATTTTT 58.696 36.000 0.00 0.00 0.00 1.94
1107 3360 2.498885 GGATTTTCCATGCCTCTGCTTT 59.501 45.455 0.00 0.00 36.28 3.51
1108 3361 3.429960 GGATTTTCCATGCCTCTGCTTTC 60.430 47.826 0.00 0.00 36.28 2.62
1112 3365 1.094073 CCATGCCTCTGCTTTCTCGG 61.094 60.000 0.00 0.00 38.71 4.63
1316 3569 0.862701 CGTCCGTACGCGATGCTTAA 60.863 55.000 15.93 0.00 43.12 1.85
1368 3621 5.600696 CCAGTACCAAGTTTCAGCAATTTT 58.399 37.500 0.00 0.00 0.00 1.82
1414 3667 6.422776 AAATGCCTATGTAGTTTGACTTCG 57.577 37.500 0.00 0.00 0.00 3.79
1519 3772 4.592485 AGTCATCCTGGTCATATTCGAC 57.408 45.455 0.00 0.00 35.03 4.20
1590 3843 1.452110 TGACTCATCAAATGTGGCCG 58.548 50.000 0.00 0.00 30.89 6.13
1660 3913 4.201871 TGTTGTCTGACAAACCATTTCGTC 60.202 41.667 23.55 8.78 40.15 4.20
1749 4003 2.444010 ACAAGGGTAGGTTGCCAAGTTA 59.556 45.455 0.00 0.00 0.00 2.24
1980 4234 1.446272 GGGTCCTTGACTTCGCTCG 60.446 63.158 0.00 0.00 32.47 5.03
2226 4482 0.597637 CGGTGCTGATTACTAGCGGG 60.598 60.000 0.00 0.00 44.01 6.13
2285 4541 3.853104 CCTGAATGGTTGTAGCCGA 57.147 52.632 0.00 0.00 0.00 5.54
2286 4542 1.369625 CCTGAATGGTTGTAGCCGAC 58.630 55.000 0.00 0.00 0.00 4.79
2287 4543 1.066143 CCTGAATGGTTGTAGCCGACT 60.066 52.381 0.00 0.00 0.00 4.18
2288 4544 2.615493 CCTGAATGGTTGTAGCCGACTT 60.615 50.000 0.00 0.00 0.00 3.01
2289 4545 2.416547 CTGAATGGTTGTAGCCGACTTG 59.583 50.000 0.00 0.00 0.00 3.16
2290 4546 2.224426 TGAATGGTTGTAGCCGACTTGT 60.224 45.455 0.00 0.00 0.00 3.16
2291 4547 3.007074 TGAATGGTTGTAGCCGACTTGTA 59.993 43.478 0.00 0.00 0.00 2.41
2292 4548 2.736144 TGGTTGTAGCCGACTTGTAG 57.264 50.000 0.00 0.00 0.00 2.74
2299 4555 3.259876 TGTAGCCGACTTGTAGGACAAAT 59.740 43.478 4.11 0.00 37.69 2.32
2310 4566 7.315142 ACTTGTAGGACAAATATCGAAACGTA 58.685 34.615 0.00 0.00 37.69 3.57
2315 4571 9.977762 GTAGGACAAATATCGAAACGTAAAAAT 57.022 29.630 0.00 0.00 0.00 1.82
2405 4661 5.219343 TCGATGTTCAGGCTGATTATCAT 57.781 39.130 27.01 22.69 0.00 2.45
2406 4662 5.614308 TCGATGTTCAGGCTGATTATCATT 58.386 37.500 27.01 9.88 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 130 4.970640 TCTTATATTACCCCCGTCCAAACT 59.029 41.667 0.00 0.00 0.00 2.66
128 131 5.059161 GTCTTATATTACCCCCGTCCAAAC 58.941 45.833 0.00 0.00 0.00 2.93
165 168 9.593134 GGATATGACATGAACTATATGACCTTC 57.407 37.037 0.00 0.00 0.00 3.46
166 169 8.253810 CGGATATGACATGAACTATATGACCTT 58.746 37.037 0.00 0.00 0.00 3.50
171 174 7.776107 ACTCCGGATATGACATGAACTATATG 58.224 38.462 3.57 0.00 0.00 1.78
177 180 4.202161 ACTGACTCCGGATATGACATGAAC 60.202 45.833 3.57 0.00 0.00 3.18
183 186 2.693591 TGGAACTGACTCCGGATATGAC 59.306 50.000 3.57 0.00 38.44 3.06
184 187 2.959030 CTGGAACTGACTCCGGATATGA 59.041 50.000 3.57 0.00 43.68 2.15
204 207 2.027745 CAGGGCACACTATTGACTGACT 60.028 50.000 0.00 0.00 0.00 3.41
215 218 1.759445 CTCTATACAGCAGGGCACACT 59.241 52.381 0.00 0.00 0.00 3.55
221 224 2.033550 GTGTCGTCTCTATACAGCAGGG 59.966 54.545 0.00 0.00 0.00 4.45
224 227 5.448768 GCTTTAGTGTCGTCTCTATACAGCA 60.449 44.000 10.40 0.00 0.00 4.41
229 232 5.191426 ACCAGCTTTAGTGTCGTCTCTATA 58.809 41.667 0.00 0.00 0.00 1.31
246 249 1.372501 ACTCCCCATTACAACCAGCT 58.627 50.000 0.00 0.00 0.00 4.24
252 255 8.978472 GCTAGTATATGATACTCCCCATTACAA 58.022 37.037 2.44 0.00 0.00 2.41
254 257 8.534954 TGCTAGTATATGATACTCCCCATTAC 57.465 38.462 2.44 0.00 0.00 1.89
255 258 9.147732 CATGCTAGTATATGATACTCCCCATTA 57.852 37.037 2.44 0.00 0.00 1.90
256 259 7.419518 GCATGCTAGTATATGATACTCCCCATT 60.420 40.741 11.37 0.00 0.00 3.16
257 260 6.042552 GCATGCTAGTATATGATACTCCCCAT 59.957 42.308 11.37 2.77 0.00 4.00
258 261 5.363868 GCATGCTAGTATATGATACTCCCCA 59.636 44.000 11.37 0.79 0.00 4.96
259 262 5.363868 TGCATGCTAGTATATGATACTCCCC 59.636 44.000 20.33 0.00 0.00 4.81
260 263 6.471233 TGCATGCTAGTATATGATACTCCC 57.529 41.667 20.33 0.00 0.00 4.30
347 350 7.444792 TGTTATGCTAATATGTGTCATGCATGA 59.555 33.333 25.42 25.42 39.53 3.07
348 351 7.586747 TGTTATGCTAATATGTGTCATGCATG 58.413 34.615 21.07 21.07 39.53 4.06
349 352 7.748691 TGTTATGCTAATATGTGTCATGCAT 57.251 32.000 0.00 0.00 41.60 3.96
350 353 7.748691 ATGTTATGCTAATATGTGTCATGCA 57.251 32.000 0.00 0.00 0.00 3.96
418 421 9.904198 TGATGAGGTGTCATAGAATTAAATGAA 57.096 29.630 4.25 0.00 43.92 2.57
419 422 9.904198 TTGATGAGGTGTCATAGAATTAAATGA 57.096 29.630 0.00 0.00 43.92 2.57
433 436 9.573133 CCAACTAAATAATTTTGATGAGGTGTC 57.427 33.333 0.00 0.00 0.00 3.67
434 437 8.034804 GCCAACTAAATAATTTTGATGAGGTGT 58.965 33.333 0.00 0.00 0.00 4.16
435 438 8.034215 TGCCAACTAAATAATTTTGATGAGGTG 58.966 33.333 0.00 0.00 0.00 4.00
436 439 8.133024 TGCCAACTAAATAATTTTGATGAGGT 57.867 30.769 0.00 0.00 0.00 3.85
472 475 8.613482 GCTGATCGTAATGTAGTATCATAGCTA 58.387 37.037 0.00 0.00 0.00 3.32
473 476 7.415765 GGCTGATCGTAATGTAGTATCATAGCT 60.416 40.741 0.00 0.00 0.00 3.32
474 477 6.693545 GGCTGATCGTAATGTAGTATCATAGC 59.306 42.308 0.00 0.00 0.00 2.97
475 478 7.990917 AGGCTGATCGTAATGTAGTATCATAG 58.009 38.462 0.00 0.00 0.00 2.23
476 479 7.939784 AGGCTGATCGTAATGTAGTATCATA 57.060 36.000 0.00 0.00 0.00 2.15
477 480 6.842437 AGGCTGATCGTAATGTAGTATCAT 57.158 37.500 0.00 0.00 0.00 2.45
478 481 6.150641 GGTAGGCTGATCGTAATGTAGTATCA 59.849 42.308 0.00 0.00 0.00 2.15
479 482 6.553524 GGTAGGCTGATCGTAATGTAGTATC 58.446 44.000 0.00 0.00 0.00 2.24
480 483 5.123502 CGGTAGGCTGATCGTAATGTAGTAT 59.876 44.000 0.00 0.00 0.00 2.12
481 484 4.453478 CGGTAGGCTGATCGTAATGTAGTA 59.547 45.833 0.00 0.00 0.00 1.82
482 485 3.252701 CGGTAGGCTGATCGTAATGTAGT 59.747 47.826 0.00 0.00 0.00 2.73
483 486 3.822996 CGGTAGGCTGATCGTAATGTAG 58.177 50.000 0.00 0.00 0.00 2.74
484 487 2.030540 GCGGTAGGCTGATCGTAATGTA 60.031 50.000 0.00 0.00 39.11 2.29
485 488 1.269621 GCGGTAGGCTGATCGTAATGT 60.270 52.381 0.00 0.00 39.11 2.71
486 489 1.419374 GCGGTAGGCTGATCGTAATG 58.581 55.000 0.00 0.00 39.11 1.90
487 490 3.888093 GCGGTAGGCTGATCGTAAT 57.112 52.632 0.00 0.00 39.11 1.89
497 500 0.311477 GCTACTACAGAGCGGTAGGC 59.689 60.000 14.76 7.89 43.99 3.93
498 501 1.874872 GAGCTACTACAGAGCGGTAGG 59.125 57.143 14.76 0.00 43.99 3.18
499 502 2.562635 TGAGCTACTACAGAGCGGTAG 58.437 52.381 10.45 10.45 44.98 3.18
500 503 2.704464 TGAGCTACTACAGAGCGGTA 57.296 50.000 0.00 0.00 44.98 4.02
501 504 1.835494 TTGAGCTACTACAGAGCGGT 58.165 50.000 0.00 0.00 44.98 5.68
502 505 4.569761 TTATTGAGCTACTACAGAGCGG 57.430 45.455 0.00 0.00 44.98 5.52
503 506 6.362016 CAGAATTATTGAGCTACTACAGAGCG 59.638 42.308 0.00 0.00 44.98 5.03
504 507 7.429633 TCAGAATTATTGAGCTACTACAGAGC 58.570 38.462 0.00 0.00 40.42 4.09
505 508 9.624697 GATCAGAATTATTGAGCTACTACAGAG 57.375 37.037 0.00 0.00 0.00 3.35
506 509 9.360901 AGATCAGAATTATTGAGCTACTACAGA 57.639 33.333 8.08 0.00 39.34 3.41
586 589 6.043411 GGAGAGCTCAATAATGTTAAGTCGT 58.957 40.000 17.77 0.00 0.00 4.34
618 621 2.437413 GGAAAGGTGAATGGGAGTGTC 58.563 52.381 0.00 0.00 0.00 3.67
742 2995 0.951558 GCTCCGTTGTGTGGTCAATT 59.048 50.000 0.00 0.00 0.00 2.32
750 3003 1.597027 CCTTTCGGCTCCGTTGTGT 60.597 57.895 8.28 0.00 40.74 3.72
770 3023 5.231991 GCTCGAAACGGAATTTACGGTATTA 59.768 40.000 5.91 0.00 35.23 0.98
795 3048 0.108329 GTTAGCTTAGCTCGGCCACA 60.108 55.000 11.09 0.00 40.44 4.17
977 3230 1.153353 GAACCGGCGTTGAATTCTCA 58.847 50.000 6.01 0.00 30.30 3.27
986 3239 2.025418 GACATCGTGAACCGGCGTT 61.025 57.895 6.01 0.00 37.11 4.84
993 3246 0.985549 GCTCGACAGACATCGTGAAC 59.014 55.000 1.78 0.00 42.80 3.18
1040 3293 3.369576 GGTAGAAAGGAGCACGGAGAAAT 60.370 47.826 0.00 0.00 0.00 2.17
1043 3296 1.183549 GGTAGAAAGGAGCACGGAGA 58.816 55.000 0.00 0.00 0.00 3.71
1049 3302 2.289694 GCAACAGAGGTAGAAAGGAGCA 60.290 50.000 0.00 0.00 0.00 4.26
1050 3303 2.351455 GCAACAGAGGTAGAAAGGAGC 58.649 52.381 0.00 0.00 0.00 4.70
1054 3307 3.409026 ACAGGCAACAGAGGTAGAAAG 57.591 47.619 0.00 0.00 41.41 2.62
1081 3334 3.614806 GCATGGAAAATCCCGCCA 58.385 55.556 0.00 0.00 35.03 5.69
1107 3360 1.846849 GATCAGCGATCGAGCCGAGA 61.847 60.000 21.57 6.67 39.91 4.04
1108 3361 1.441849 GATCAGCGATCGAGCCGAG 60.442 63.158 21.57 0.90 39.91 4.63
1316 3569 9.057089 CGTCCTAAATCCTAATTCTAGCAATTT 57.943 33.333 5.76 0.00 0.00 1.82
1414 3667 6.226787 CAGTTATTCCATCCCAGTATCTCAC 58.773 44.000 0.00 0.00 0.00 3.51
1660 3913 2.728180 TCGGAATCCTGCGATCCG 59.272 61.111 7.09 7.09 40.84 4.18
1749 4003 3.010472 TGGATCAATCAACAGACCACCAT 59.990 43.478 0.00 0.00 0.00 3.55
2129 4385 2.676822 ACGAAGCTCGGCCTCTCA 60.677 61.111 0.00 0.00 45.59 3.27
2226 4482 0.315568 CCACGACCATCCTAGCTAGC 59.684 60.000 15.74 6.62 0.00 3.42
2282 4538 4.928601 TCGATATTTGTCCTACAAGTCGG 58.071 43.478 16.69 0.00 39.53 4.79
2283 4539 6.505888 CGTTTCGATATTTGTCCTACAAGTCG 60.506 42.308 13.38 13.38 39.53 4.18
2284 4540 6.309737 ACGTTTCGATATTTGTCCTACAAGTC 59.690 38.462 0.00 0.00 39.53 3.01
2285 4541 6.161381 ACGTTTCGATATTTGTCCTACAAGT 58.839 36.000 0.00 0.00 39.53 3.16
2286 4542 6.642683 ACGTTTCGATATTTGTCCTACAAG 57.357 37.500 0.00 0.00 39.53 3.16
2287 4543 8.531622 TTTACGTTTCGATATTTGTCCTACAA 57.468 30.769 0.00 0.00 36.11 2.41
2288 4544 8.531622 TTTTACGTTTCGATATTTGTCCTACA 57.468 30.769 0.00 0.00 0.00 2.74
2289 4545 9.977762 ATTTTTACGTTTCGATATTTGTCCTAC 57.022 29.630 0.00 0.00 0.00 3.18
2290 4546 9.976255 CATTTTTACGTTTCGATATTTGTCCTA 57.024 29.630 0.00 0.00 0.00 2.94
2291 4547 7.966204 CCATTTTTACGTTTCGATATTTGTCCT 59.034 33.333 0.00 0.00 0.00 3.85
2292 4548 7.751793 ACCATTTTTACGTTTCGATATTTGTCC 59.248 33.333 0.00 0.00 0.00 4.02
2299 4555 7.187244 TGTCAACCATTTTTACGTTTCGATA 57.813 32.000 0.00 0.00 0.00 2.92
2310 4566 5.069516 AGCTCTGTTCATGTCAACCATTTTT 59.930 36.000 0.00 0.00 0.00 1.94
2315 4571 2.936919 AGCTCTGTTCATGTCAACCA 57.063 45.000 0.00 0.00 0.00 3.67
2479 4737 7.372451 TCTTAAAATCGGATTGTTGGTGTAG 57.628 36.000 3.59 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.