Multiple sequence alignment - TraesCS1A01G265600

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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 TraesCS1A01G265600 chr1A 100.000 2382 0 0 1 2382 461336663 461339044 0.000000e+00 4399
1 TraesCS1A01G265600 chr1A 80.619 485 51 26 636 1099 461356453 461356915 3.790000e-88 335
2 TraesCS1A01G265600 chr1A 80.196 409 45 25 1168 1552 461357023 461357419 8.390000e-70 274
3 TraesCS1A01G265600 chr1D 93.124 1687 88 17 714 2382 361802297 361803973 0.000000e+00 2447
4 TraesCS1A01G265600 chr1D 86.351 718 89 6 1 714 361801541 361802253 0.000000e+00 774
5 TraesCS1A01G265600 chr1D 80.860 465 50 25 652 1099 361907285 361907727 1.770000e-86 329
6 TraesCS1A01G265600 chr1D 81.841 402 39 23 1175 1552 361907842 361908233 8.270000e-80 307
7 TraesCS1A01G265600 chr1B 89.174 1247 83 16 1151 2382 484297417 484298626 0.000000e+00 1507
8 TraesCS1A01G265600 chr1B 91.444 374 20 5 709 1082 484296959 484297320 9.830000e-139 503
9 TraesCS1A01G265600 chr1B 82.553 470 47 22 652 1099 484365689 484366145 4.800000e-102 381
10 TraesCS1A01G265600 chr1B 80.988 405 45 24 1168 1549 484366253 484366648 2.320000e-75 292
11 TraesCS1A01G265600 chr1B 85.841 226 28 4 1162 1384 484147212 484147436 1.100000e-58 237
12 TraesCS1A01G265600 chr1B 85.841 226 28 4 1162 1384 484214199 484214423 1.100000e-58 237
13 TraesCS1A01G265600 chr1B 75.493 355 70 16 28 373 654039405 654039751 8.810000e-35 158
14 TraesCS1A01G265600 chr7D 81.373 408 64 9 27 425 74954027 74954431 2.950000e-84 322
15 TraesCS1A01G265600 chr7D 80.247 405 69 9 12 408 626480312 626480713 6.440000e-76 294
16 TraesCS1A01G265600 chr7D 79.330 358 64 9 4 354 608288075 608288429 2.370000e-60 243
17 TraesCS1A01G265600 chr7D 82.883 222 35 3 15 235 14798223 14798442 1.870000e-46 196
18 TraesCS1A01G265600 chr7B 76.840 462 95 10 28 480 77568566 77569024 1.410000e-62 250
19 TraesCS1A01G265600 chr4A 78.072 415 69 15 12 408 75468132 75467722 2.370000e-60 243
20 TraesCS1A01G265600 chr4A 76.227 387 73 15 4 378 500122872 500122493 1.120000e-43 187
21 TraesCS1A01G265600 chrUn 79.514 288 54 5 12 296 127023020 127022735 1.440000e-47 200


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 TraesCS1A01G265600 chr1A 461336663 461339044 2381 False 4399.0 4399 100.0000 1 2382 1 chr1A.!!$F1 2381
1 TraesCS1A01G265600 chr1A 461356453 461357419 966 False 304.5 335 80.4075 636 1552 2 chr1A.!!$F2 916
2 TraesCS1A01G265600 chr1D 361801541 361803973 2432 False 1610.5 2447 89.7375 1 2382 2 chr1D.!!$F1 2381
3 TraesCS1A01G265600 chr1D 361907285 361908233 948 False 318.0 329 81.3505 652 1552 2 chr1D.!!$F2 900
4 TraesCS1A01G265600 chr1B 484296959 484298626 1667 False 1005.0 1507 90.3090 709 2382 2 chr1B.!!$F4 1673
5 TraesCS1A01G265600 chr1B 484365689 484366648 959 False 336.5 381 81.7705 652 1549 2 chr1B.!!$F5 897

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
397 400 0.104304 GCAACGGACCGATACAGGAT 59.896 55.0 23.38 0.0 34.73 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2539 1.610522 GCAAGAGTTGACATTGGTGCT 59.389 47.619 0.0 0.0 0.0 4.4 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
23 24 2.023414 TAATACTGGCCCGCTCGTGG 62.023 60.000 0.00 0.00 0.00 4.94
45 46 3.352338 GACGTGTGGCCGGAGTAGG 62.352 68.421 5.05 0.00 0.00 3.18
47 48 2.048023 CGTGTGGCCGGAGTAGGTA 61.048 63.158 5.05 0.00 0.00 3.08
54 55 1.864725 GCCGGAGTAGGTATCTCGGC 61.865 65.000 5.05 9.77 40.80 5.54
70 71 1.967494 GGCTTCCACGCGGGTTTAA 60.967 57.895 12.47 0.00 38.11 1.52
74 75 0.250814 TTCCACGCGGGTTTAATGGT 60.251 50.000 12.47 0.00 38.11 3.55
90 91 2.642700 GTGGCGTTTGAATGCGGT 59.357 55.556 2.17 0.00 41.81 5.68
99 100 2.892425 GAATGCGGTGAGGAGGCG 60.892 66.667 0.00 0.00 0.00 5.52
109 110 1.070786 GAGGAGGCGTGTTCAACCA 59.929 57.895 0.00 0.00 0.00 3.67
111 112 1.070786 GGAGGCGTGTTCAACCAGA 59.929 57.895 0.00 0.00 0.00 3.86
154 155 2.877691 GGCGCGCCTCTTCAATTT 59.122 55.556 41.71 0.00 0.00 1.82
155 156 1.514873 GGCGCGCCTCTTCAATTTG 60.515 57.895 41.71 0.00 0.00 2.32
156 157 1.210155 GCGCGCCTCTTCAATTTGT 59.790 52.632 23.24 0.00 0.00 2.83
162 163 3.012518 CGCCTCTTCAATTTGTGGAGAT 58.987 45.455 16.68 0.00 41.35 2.75
167 168 6.409704 CCTCTTCAATTTGTGGAGATAGTGA 58.590 40.000 16.68 0.00 41.35 3.41
172 173 5.104776 TCAATTTGTGGAGATAGTGAGAGGG 60.105 44.000 0.00 0.00 0.00 4.30
173 174 1.781786 TGTGGAGATAGTGAGAGGGC 58.218 55.000 0.00 0.00 0.00 5.19
180 181 1.384989 ATAGTGAGAGGGCGTGTCCG 61.385 60.000 1.68 0.00 34.94 4.79
199 200 1.526887 CCCTGAGCCGCCTTCAATA 59.473 57.895 0.00 0.00 0.00 1.90
209 210 0.819259 GCCTTCAATATGGAGCGGCA 60.819 55.000 14.50 0.00 36.08 5.69
241 242 0.463654 GCATGAATGCGGGTAGGTGA 60.464 55.000 0.00 0.00 44.67 4.02
242 243 1.299541 CATGAATGCGGGTAGGTGAC 58.700 55.000 0.00 0.00 0.00 3.67
264 266 2.356278 GGGGGAAGCATGTGCAGA 59.644 61.111 7.83 0.00 45.16 4.26
268 270 0.322816 GGGAAGCATGTGCAGAAGGA 60.323 55.000 7.83 0.00 45.16 3.36
269 271 1.684248 GGGAAGCATGTGCAGAAGGAT 60.684 52.381 7.83 0.00 45.16 3.24
273 275 0.394762 GCATGTGCAGAAGGATGGGA 60.395 55.000 0.00 0.00 41.59 4.37
281 283 1.565759 CAGAAGGATGGGATTGGTGGA 59.434 52.381 0.00 0.00 0.00 4.02
298 300 0.606673 GGACCAGGGCAGTCAGAAAC 60.607 60.000 0.00 0.00 35.89 2.78
302 304 1.841556 AGGGCAGTCAGAAACGGGA 60.842 57.895 0.00 0.00 0.00 5.14
311 313 1.134521 TCAGAAACGGGATTGGGATCG 60.135 52.381 0.00 0.00 32.84 3.69
312 314 0.180406 AGAAACGGGATTGGGATCGG 59.820 55.000 0.00 0.00 32.84 4.18
320 322 1.682451 GATTGGGATCGGTCCGGACA 61.682 60.000 34.40 17.10 46.09 4.02
323 326 3.846430 GGATCGGTCCGGACACCC 61.846 72.222 34.40 23.55 34.13 4.61
346 349 4.403453 GCAAATATTCTCGCGTTTGTCTT 58.597 39.130 15.95 0.03 34.82 3.01
348 351 5.617609 CAAATATTCTCGCGTTTGTCTTCA 58.382 37.500 5.77 0.00 0.00 3.02
393 396 2.507547 GCGCAACGGACCGATACA 60.508 61.111 23.38 0.00 0.00 2.29
397 400 0.104304 GCAACGGACCGATACAGGAT 59.896 55.000 23.38 0.00 34.73 3.24
398 401 1.852942 CAACGGACCGATACAGGATG 58.147 55.000 23.38 2.46 46.00 3.51
410 413 4.039245 CGATACAGGATGGTGTTGGATAGT 59.961 45.833 0.00 0.00 43.62 2.12
413 416 4.998051 ACAGGATGGTGTTGGATAGTTTT 58.002 39.130 0.00 0.00 43.62 2.43
425 428 0.462789 ATAGTTTTCGCGGTCCGGAT 59.537 50.000 14.38 0.00 37.59 4.18
427 430 0.179119 AGTTTTCGCGGTCCGGATAG 60.179 55.000 14.38 6.03 37.59 2.08
430 433 2.894240 TTTCGCGGTCCGGATAGCAC 62.894 60.000 26.39 8.13 37.59 4.40
432 435 4.203076 GCGGTCCGGATAGCACGT 62.203 66.667 23.62 0.00 0.00 4.49
436 439 0.108520 GGTCCGGATAGCACGTTTCA 60.109 55.000 7.81 0.00 0.00 2.69
437 440 1.673626 GGTCCGGATAGCACGTTTCAA 60.674 52.381 7.81 0.00 0.00 2.69
438 441 2.070783 GTCCGGATAGCACGTTTCAAA 58.929 47.619 7.81 0.00 0.00 2.69
439 442 2.676342 GTCCGGATAGCACGTTTCAAAT 59.324 45.455 7.81 0.00 0.00 2.32
445 448 4.500477 GGATAGCACGTTTCAAATGATTGC 59.500 41.667 0.00 0.00 36.45 3.56
463 466 1.874345 GCGGGAGGTTTGAGAGTCGA 61.874 60.000 0.00 0.00 0.00 4.20
464 467 0.109226 CGGGAGGTTTGAGAGTCGAC 60.109 60.000 7.70 7.70 0.00 4.20
469 472 0.507358 GGTTTGAGAGTCGACGTTGC 59.493 55.000 10.46 1.91 0.00 4.17
471 474 1.190323 GTTTGAGAGTCGACGTTGCAG 59.810 52.381 10.46 0.00 0.00 4.41
483 486 2.283298 ACGTTGCAGATGCTCTTATGG 58.717 47.619 6.35 0.00 42.66 2.74
510 513 7.594714 TCTAAATTAGCATCACTAGATCCGTC 58.405 38.462 0.00 0.00 30.20 4.79
513 516 3.724508 AGCATCACTAGATCCGTCTTG 57.275 47.619 0.00 0.00 35.87 3.02
701 707 0.610174 ACGTGATCTGATGTGCTGGT 59.390 50.000 0.00 0.00 0.00 4.00
754 808 1.088306 CCACGCCGCCTATAAAACAA 58.912 50.000 0.00 0.00 0.00 2.83
831 902 6.117488 CCACCTAACCAAATAATAACGACCT 58.883 40.000 0.00 0.00 0.00 3.85
832 903 6.037830 CCACCTAACCAAATAATAACGACCTG 59.962 42.308 0.00 0.00 0.00 4.00
846 921 1.306141 ACCTGTAGCCTAGCAGCCA 60.306 57.895 0.00 0.00 0.00 4.75
996 1078 1.069973 TGCACGAAAAGTTCATCAGCG 60.070 47.619 0.00 0.00 0.00 5.18
1083 1165 0.506932 CACACGTGAACGGTAAGCAG 59.493 55.000 25.01 0.00 44.95 4.24
1128 1223 2.093921 TGTAGTTCGATCGATTTGGGCA 60.094 45.455 20.18 10.56 0.00 5.36
1142 1273 2.472695 TGGGCAGTCATGTCTTGTAC 57.527 50.000 0.00 0.00 0.00 2.90
1145 1276 2.094390 GGGCAGTCATGTCTTGTACGTA 60.094 50.000 0.00 0.00 0.00 3.57
1146 1277 3.179830 GGCAGTCATGTCTTGTACGTAG 58.820 50.000 0.00 0.00 0.00 3.51
1386 1534 1.929836 CTGCAAGAAGTACTGATCGGC 59.070 52.381 0.00 1.95 34.07 5.54
1414 1570 2.998670 CAGCATGATATGTTCCGCCTAG 59.001 50.000 0.00 0.00 39.69 3.02
1418 1574 4.093998 GCATGATATGTTCCGCCTAGAATG 59.906 45.833 0.00 0.00 0.00 2.67
1474 1630 1.911293 GCCTATGCGTGTGTGTGTGG 61.911 60.000 0.00 0.00 0.00 4.17
1499 1667 7.305474 GCCAACAAATATGTATACCAGTATGC 58.695 38.462 0.00 0.00 39.40 3.14
1559 1727 2.441410 TGGTGTTGCTTGTTGTTCAGA 58.559 42.857 0.00 0.00 0.00 3.27
1600 1774 6.247903 CGTGAATAAGTAATGATTGTGCGTT 58.752 36.000 0.00 0.00 0.00 4.84
1602 1776 6.468956 GTGAATAAGTAATGATTGTGCGTTGG 59.531 38.462 0.00 0.00 0.00 3.77
1605 1779 2.487762 AGTAATGATTGTGCGTTGGTGG 59.512 45.455 0.00 0.00 0.00 4.61
1633 1807 0.318699 TGAGTTCTCTTGTCCACGCG 60.319 55.000 3.53 3.53 0.00 6.01
1685 1860 6.983307 CCTCTCCGATATGATATCCATTGTTC 59.017 42.308 6.85 0.00 36.71 3.18
1715 1890 4.889832 AGCAGTATGTTAGATGCTTTGC 57.110 40.909 0.00 0.00 46.46 3.68
1725 1900 6.630071 TGTTAGATGCTTTGCTTATTTTCCC 58.370 36.000 0.00 0.00 0.00 3.97
1894 2074 7.420002 TCGCACATACAATAACTATTCTACGT 58.580 34.615 0.00 0.00 0.00 3.57
1948 2130 8.400947 CACACCTTTCATCCTGACTAATATTTG 58.599 37.037 0.00 0.00 0.00 2.32
2134 2316 7.821846 TGCAAATGGTAAAAGGTTCCATATTTC 59.178 33.333 0.00 0.00 40.52 2.17
2231 2414 5.007823 TGACAAAAGAATTCGTAAAAGCGGA 59.992 36.000 0.00 0.00 0.00 5.54
2237 2420 8.483307 AAAGAATTCGTAAAAGCGGACTAATA 57.517 30.769 0.00 0.00 0.00 0.98
2282 2469 9.358406 ACAATGAGATCATGCAATTAGGAATTA 57.642 29.630 0.00 0.00 36.56 1.40
2329 2516 5.183904 GTCATGCAAAAGACTTATTCCAGGT 59.816 40.000 9.32 0.00 0.00 4.00
2359 2546 2.016318 CGATGCCTTCAATAGCACCAA 58.984 47.619 0.00 0.00 42.84 3.67
2374 2561 1.069022 CACCAATGTCAACTCTTGCCG 60.069 52.381 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.104304 ACGAGCGGGCCAGTATTAAG 59.896 55.000 4.39 0.00 0.00 1.85
29 30 1.389609 ATACCTACTCCGGCCACACG 61.390 60.000 2.24 0.00 0.00 4.49
45 46 1.944676 CGCGTGGAAGCCGAGATAC 60.945 63.158 0.00 0.00 0.00 2.24
47 48 4.514577 CCGCGTGGAAGCCGAGAT 62.515 66.667 10.20 0.00 37.49 2.75
54 55 0.450184 CCATTAAACCCGCGTGGAAG 59.550 55.000 18.79 2.60 37.49 3.46
70 71 1.212490 CGCATTCAAACGCCACCAT 59.788 52.632 0.00 0.00 0.00 3.55
74 75 1.851021 CTCACCGCATTCAAACGCCA 61.851 55.000 0.00 0.00 0.00 5.69
90 91 1.070786 GGTTGAACACGCCTCCTCA 59.929 57.895 0.00 0.00 0.00 3.86
99 100 0.304705 CTGCACGTCTGGTTGAACAC 59.695 55.000 0.00 0.00 0.00 3.32
145 146 7.244886 TCTCACTATCTCCACAAATTGAAGA 57.755 36.000 0.00 0.12 0.00 2.87
146 147 6.538021 CCTCTCACTATCTCCACAAATTGAAG 59.462 42.308 0.00 0.00 0.00 3.02
154 155 1.781786 GCCCTCTCACTATCTCCACA 58.218 55.000 0.00 0.00 0.00 4.17
155 156 0.671251 CGCCCTCTCACTATCTCCAC 59.329 60.000 0.00 0.00 0.00 4.02
156 157 0.259065 ACGCCCTCTCACTATCTCCA 59.741 55.000 0.00 0.00 0.00 3.86
162 163 2.044555 CGGACACGCCCTCTCACTA 61.045 63.158 0.00 0.00 0.00 2.74
180 181 2.608970 TATTGAAGGCGGCTCAGGGC 62.609 60.000 13.70 0.17 40.90 5.19
187 188 1.845809 CGCTCCATATTGAAGGCGGC 61.846 60.000 0.00 0.00 39.12 6.53
189 190 1.845809 GCCGCTCCATATTGAAGGCG 61.846 60.000 7.05 5.62 41.84 5.52
209 210 0.035317 TTCATGCCACTCTTGAGCGT 59.965 50.000 0.00 0.00 31.57 5.07
211 212 2.846039 CATTCATGCCACTCTTGAGC 57.154 50.000 0.00 0.00 31.57 4.26
223 224 1.299541 GTCACCTACCCGCATTCATG 58.700 55.000 0.00 0.00 0.00 3.07
248 250 1.318158 CCTTCTGCACATGCTTCCCC 61.318 60.000 5.31 0.00 42.66 4.81
256 258 2.662866 CAATCCCATCCTTCTGCACAT 58.337 47.619 0.00 0.00 0.00 3.21
257 259 1.341285 CCAATCCCATCCTTCTGCACA 60.341 52.381 0.00 0.00 0.00 4.57
259 261 1.002069 ACCAATCCCATCCTTCTGCA 58.998 50.000 0.00 0.00 0.00 4.41
262 264 1.566231 GTCCACCAATCCCATCCTTCT 59.434 52.381 0.00 0.00 0.00 2.85
264 266 0.631212 GGTCCACCAATCCCATCCTT 59.369 55.000 0.00 0.00 35.64 3.36
268 270 1.583784 CCCTGGTCCACCAATCCCAT 61.584 60.000 0.00 0.00 46.97 4.00
269 271 2.237965 CCCTGGTCCACCAATCCCA 61.238 63.158 0.00 0.00 46.97 4.37
273 275 2.142292 GACTGCCCTGGTCCACCAAT 62.142 60.000 0.00 0.00 46.97 3.16
281 283 1.071471 CGTTTCTGACTGCCCTGGT 59.929 57.895 0.00 0.00 0.00 4.00
289 291 1.358152 TCCCAATCCCGTTTCTGACT 58.642 50.000 0.00 0.00 0.00 3.41
298 300 2.426023 GGACCGATCCCAATCCCG 59.574 66.667 0.00 0.00 39.39 5.14
302 304 1.687840 TGTCCGGACCGATCCCAAT 60.688 57.895 31.19 0.00 42.83 3.16
320 322 2.307363 CGCGAGAATATTTGCGGGT 58.693 52.632 17.64 0.00 45.07 5.28
329 332 3.909430 ACTGAAGACAAACGCGAGAATA 58.091 40.909 15.93 0.00 0.00 1.75
330 333 2.755650 ACTGAAGACAAACGCGAGAAT 58.244 42.857 15.93 0.00 0.00 2.40
332 335 2.218953 AACTGAAGACAAACGCGAGA 57.781 45.000 15.93 0.00 0.00 4.04
346 349 1.269448 GCATTTTCTCCCGCAAACTGA 59.731 47.619 0.00 0.00 0.00 3.41
348 351 0.240945 CGCATTTTCTCCCGCAAACT 59.759 50.000 0.00 0.00 0.00 2.66
379 382 1.538204 CCATCCTGTATCGGTCCGTTG 60.538 57.143 11.88 0.00 0.00 4.10
380 383 0.750850 CCATCCTGTATCGGTCCGTT 59.249 55.000 11.88 5.52 0.00 4.44
381 384 0.396695 ACCATCCTGTATCGGTCCGT 60.397 55.000 11.88 1.23 0.00 4.69
383 386 1.120530 ACACCATCCTGTATCGGTCC 58.879 55.000 0.00 0.00 0.00 4.46
393 396 4.261801 CGAAAACTATCCAACACCATCCT 58.738 43.478 0.00 0.00 0.00 3.24
397 400 1.801771 CGCGAAAACTATCCAACACCA 59.198 47.619 0.00 0.00 0.00 4.17
398 401 1.129811 CCGCGAAAACTATCCAACACC 59.870 52.381 8.23 0.00 0.00 4.16
410 413 1.519898 GCTATCCGGACCGCGAAAA 60.520 57.895 6.12 0.15 0.00 2.29
413 416 3.896133 GTGCTATCCGGACCGCGA 61.896 66.667 6.12 7.99 0.00 5.87
425 428 3.487536 CGCAATCATTTGAAACGTGCTA 58.512 40.909 0.00 0.00 34.60 3.49
427 430 1.386412 CCGCAATCATTTGAAACGTGC 59.614 47.619 0.00 0.00 34.60 5.34
430 433 2.518949 CTCCCGCAATCATTTGAAACG 58.481 47.619 0.00 0.00 34.60 3.60
432 435 2.524306 ACCTCCCGCAATCATTTGAAA 58.476 42.857 0.00 0.00 34.60 2.69
436 439 2.493278 CTCAAACCTCCCGCAATCATTT 59.507 45.455 0.00 0.00 0.00 2.32
437 440 2.094675 CTCAAACCTCCCGCAATCATT 58.905 47.619 0.00 0.00 0.00 2.57
438 441 1.281867 TCTCAAACCTCCCGCAATCAT 59.718 47.619 0.00 0.00 0.00 2.45
439 442 0.690192 TCTCAAACCTCCCGCAATCA 59.310 50.000 0.00 0.00 0.00 2.57
445 448 0.109226 GTCGACTCTCAAACCTCCCG 60.109 60.000 8.70 0.00 0.00 5.14
469 472 7.148440 GCTAATTTAGAGCCATAAGAGCATCTG 60.148 40.741 7.63 0.00 38.81 2.90
471 474 6.652481 TGCTAATTTAGAGCCATAAGAGCATC 59.348 38.462 7.63 0.00 39.30 3.91
483 486 6.529829 CGGATCTAGTGATGCTAATTTAGAGC 59.470 42.308 7.63 0.00 38.64 4.09
577 580 9.985318 TTACGAGTCAAAGTTTTAAAATTTCGA 57.015 25.926 16.48 6.99 0.00 3.71
605 608 9.740239 TCCGTGTATAATTGTACATCTAGTTTC 57.260 33.333 16.79 2.66 36.98 2.78
701 707 9.374838 GACATGCATTGTATATATCACTCATGA 57.625 33.333 16.86 0.00 39.18 3.07
831 902 0.681733 GCTATGGCTGCTAGGCTACA 59.318 55.000 0.00 0.00 41.96 2.74
832 903 0.681733 TGCTATGGCTGCTAGGCTAC 59.318 55.000 1.68 0.00 41.96 3.58
846 921 6.258727 CGTAACTTGATTGACAATCCTGCTAT 59.741 38.462 22.44 8.90 37.88 2.97
996 1078 1.598701 GCTTGGTGCCCTTCATGGTC 61.599 60.000 0.00 0.00 35.15 4.02
1029 1111 2.765807 AGGACGGCCTGGAGGATG 60.766 66.667 10.54 0.00 44.90 3.51
1083 1165 2.005451 AGAACGATTGAGCATGAGCAC 58.995 47.619 0.00 0.00 45.49 4.40
1128 1223 6.429078 TCACTTACTACGTACAAGACATGACT 59.571 38.462 15.67 0.00 0.00 3.41
1142 1273 6.807230 GGCATCAGGTAATATCACTTACTACG 59.193 42.308 0.00 0.00 33.13 3.51
1145 1276 5.538813 TCGGCATCAGGTAATATCACTTACT 59.461 40.000 0.00 0.00 33.13 2.24
1146 1277 5.779922 TCGGCATCAGGTAATATCACTTAC 58.220 41.667 0.00 0.00 0.00 2.34
1149 1280 4.284490 ACATCGGCATCAGGTAATATCACT 59.716 41.667 0.00 0.00 0.00 3.41
1155 1286 3.470709 CAAGACATCGGCATCAGGTAAT 58.529 45.455 0.00 0.00 0.00 1.89
1156 1287 2.905075 CAAGACATCGGCATCAGGTAA 58.095 47.619 0.00 0.00 0.00 2.85
1394 1542 2.899900 TCTAGGCGGAACATATCATGCT 59.100 45.455 0.00 0.00 33.04 3.79
1414 1570 7.295952 TCTCGTCTGAGCTTTTATTTCATTC 57.704 36.000 0.00 0.00 42.26 2.67
1418 1574 6.893958 TCATCTCGTCTGAGCTTTTATTTC 57.106 37.500 0.00 0.00 42.26 2.17
1474 1630 7.305474 GCATACTGGTATACATATTTGTTGGC 58.695 38.462 5.01 0.00 37.28 4.52
1499 1667 2.050351 ACAGCGACGAAGACACGG 60.050 61.111 0.00 0.00 37.61 4.94
1600 1774 6.252599 AGAGAACTCATATTATTGCCACCA 57.747 37.500 4.64 0.00 0.00 4.17
1602 1776 7.254932 GGACAAGAGAACTCATATTATTGCCAC 60.255 40.741 4.64 0.00 0.00 5.01
1605 1779 7.517417 CGTGGACAAGAGAACTCATATTATTGC 60.517 40.741 4.64 0.00 0.00 3.56
1660 1835 6.477053 ACAATGGATATCATATCGGAGAGG 57.523 41.667 4.83 0.00 35.48 3.69
1685 1860 7.011763 AGCATCTAACATACTGCTTAACATGTG 59.988 37.037 0.00 0.00 42.03 3.21
1810 1990 4.864806 CAGCTCGTGTGAGTATGTGTTAAT 59.135 41.667 0.00 0.00 44.48 1.40
1814 1994 1.886542 TCAGCTCGTGTGAGTATGTGT 59.113 47.619 0.00 0.00 44.48 3.72
1870 2050 7.618964 ACGTAGAATAGTTATTGTATGTGCG 57.381 36.000 11.10 4.96 39.05 5.34
1888 2068 9.486497 CATAGTAAGATGGTAAGAGTACGTAGA 57.514 37.037 0.00 0.00 0.00 2.59
1894 2074 6.378745 TGCCCATAGTAAGATGGTAAGAGTA 58.621 40.000 1.96 0.00 44.37 2.59
1913 2095 1.907807 GAAAGGTGTGGCATGCCCA 60.908 57.895 33.44 26.07 42.79 5.36
1948 2130 1.732405 GCCCGTTTAGCAAACATCAGC 60.732 52.381 10.82 0.00 41.44 4.26
2352 2539 1.610522 GCAAGAGTTGACATTGGTGCT 59.389 47.619 0.00 0.00 0.00 4.40
2359 2546 2.699954 CCTAACGGCAAGAGTTGACAT 58.300 47.619 0.00 0.00 39.16 3.06


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

AutoCloner maintained by Alex Coulton.