Multiple sequence alignment - TraesCS1A01G262400

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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 TraesCS1A01G262400 chr1A 100.000 1406 0 0 1 1406 457371180 457372585 0.000000e+00 2597.0
1 TraesCS1A01G262400 chr1A 100.000 1287 0 0 1707 2993 457372886 457374172 0.000000e+00 2377.0
2 TraesCS1A01G262400 chr1A 89.177 462 37 4 932 1384 457945254 457945711 5.600000e-157 564.0
3 TraesCS1A01G262400 chr1A 88.301 359 34 3 1768 2126 457945726 457946076 9.920000e-115 424.0
4 TraesCS1A01G262400 chr1A 92.208 77 3 1 1707 1780 457945779 457945855 4.080000e-19 106.0
5 TraesCS1A01G262400 chr1A 84.404 109 13 3 1821 1928 457372886 457372991 1.470000e-18 104.0
6 TraesCS1A01G262400 chr1A 84.404 109 13 3 1707 1812 457373000 457373107 1.470000e-18 104.0
7 TraesCS1A01G262400 chr1A 77.019 161 27 3 2545 2696 457954793 457954952 1.910000e-12 84.2
8 TraesCS1A01G262400 chr1D 89.530 1404 120 12 3 1381 356362149 356360748 0.000000e+00 1753.0
9 TraesCS1A01G262400 chr1D 93.049 892 37 6 1707 2593 356360707 356359836 0.000000e+00 1280.0
10 TraesCS1A01G262400 chr1D 89.868 454 31 4 940 1384 356859288 356859735 1.200000e-158 569.0
11 TraesCS1A01G262400 chr1D 82.353 510 44 21 1814 2291 356860261 356860756 4.650000e-108 401.0
12 TraesCS1A01G262400 chr1D 87.466 367 13 13 2645 2993 356359819 356359468 2.800000e-105 392.0
13 TraesCS1A01G262400 chr1D 83.803 142 21 2 281 422 4045473 4045612 1.870000e-27 134.0
14 TraesCS1A01G262400 chr1D 81.208 149 25 1 1707 1855 356360593 356360448 1.890000e-22 117.0
15 TraesCS1A01G262400 chr1D 79.605 152 28 1 1707 1855 356860268 356860419 4.080000e-19 106.0
16 TraesCS1A01G262400 chr1B 87.396 1325 113 25 89 1381 479792291 479793593 0.000000e+00 1472.0
17 TraesCS1A01G262400 chr1B 87.719 1140 61 36 1784 2887 479794007 479795103 0.000000e+00 1256.0
18 TraesCS1A01G262400 chr1B 87.427 517 54 4 879 1384 480326619 480327135 4.300000e-163 584.0
19 TraesCS1A01G262400 chr1B 81.455 550 59 24 1769 2290 480327151 480327685 7.720000e-111 411.0
20 TraesCS1A01G262400 chr1B 77.465 284 45 10 2545 2811 480359588 480359869 5.170000e-33 152.0
21 TraesCS1A01G262400 chr1B 82.237 152 21 2 1707 1855 479794044 479794192 3.130000e-25 126.0
22 TraesCS1A01G262400 chr1B 81.081 148 22 6 281 425 50397434 50397290 2.440000e-21 113.0
23 TraesCS1A01G262400 chr1B 98.361 61 1 0 2910 2970 479795177 479795237 1.130000e-19 108.0
24 TraesCS1A01G262400 chr1B 78.710 155 24 3 1707 1855 480327203 480327354 8.830000e-16 95.3
25 TraesCS1A01G262400 chr6B 83.333 210 33 2 1000 1208 69707783 69707991 3.040000e-45 193.0
26 TraesCS1A01G262400 chr7B 84.884 172 23 3 86 255 605996489 605996319 1.430000e-38 171.0
27 TraesCS1A01G262400 chr7B 81.560 141 24 2 281 421 630501256 630501394 6.780000e-22 115.0
28 TraesCS1A01G262400 chr7B 94.444 36 1 1 668 703 503471244 503471210 1.000000e-03 54.7
29 TraesCS1A01G262400 chrUn 82.199 191 32 2 82 271 52721114 52720925 2.390000e-36 163.0
30 TraesCS1A01G262400 chr5D 82.447 188 29 4 86 271 534079804 534079619 8.590000e-36 161.0
31 TraesCS1A01G262400 chr5D 85.612 139 18 2 289 426 452491535 452491672 8.650000e-31 145.0
32 TraesCS1A01G262400 chr5A 81.915 188 31 3 85 270 246831073 246831259 3.990000e-34 156.0
33 TraesCS1A01G262400 chr5A 81.283 187 28 6 86 268 246825350 246825533 8.650000e-31 145.0
34 TraesCS1A01G262400 chr2D 81.383 188 32 3 86 271 77457770 77457584 1.860000e-32 150.0
35 TraesCS1A01G262400 chr2D 83.803 142 19 4 281 421 366095825 366095687 6.730000e-27 132.0
36 TraesCS1A01G262400 chr3A 79.787 188 36 2 86 271 7689756 7689569 5.200000e-28 135.0
37 TraesCS1A01G262400 chr7D 81.657 169 24 7 64 228 5019124 5019289 1.870000e-27 134.0
38 TraesCS1A01G262400 chr7A 83.803 142 21 2 281 422 695822314 695822453 1.870000e-27 134.0
39 TraesCS1A01G262400 chr5B 84.733 131 17 3 85 213 176597389 176597518 8.710000e-26 128.0
40 TraesCS1A01G262400 chr3B 82.432 148 23 3 281 428 683833933 683833789 3.130000e-25 126.0


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 TraesCS1A01G262400 chr1A 457371180 457374172 2992 False 1295.500000 2597 92.202000 1 2993 4 chr1A.!!$F2 2992
1 TraesCS1A01G262400 chr1A 457945254 457946076 822 False 364.666667 564 89.895333 932 2126 3 chr1A.!!$F3 1194
2 TraesCS1A01G262400 chr1D 356359468 356362149 2681 True 885.500000 1753 87.813250 3 2993 4 chr1D.!!$R1 2990
3 TraesCS1A01G262400 chr1D 356859288 356860756 1468 False 358.666667 569 83.942000 940 2291 3 chr1D.!!$F2 1351
4 TraesCS1A01G262400 chr1B 479792291 479795237 2946 False 740.500000 1472 88.928250 89 2970 4 chr1B.!!$F2 2881
5 TraesCS1A01G262400 chr1B 480326619 480327685 1066 False 363.433333 584 82.530667 879 2290 3 chr1B.!!$F3 1411

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
120 121 0.101759 GGCGCGTAGTTGATCTACCA 59.898 55.0 8.43 0.0 44.3 3.25 F
290 291 0.107831 TGCCGCATATGTCTAACCCC 59.892 55.0 4.29 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1189 0.959372 ATGACCTCGAACTCGACGGT 60.959 55.0 17.48 17.48 45.48 4.83 R
2128 2987 0.321671 TCTTCTGGAACCAAGCTCGG 59.678 55.0 0.00 0.00 0.00 4.63 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
29 30 4.843220 ACAAGGTGAAATTCTGAAGCAG 57.157 40.909 0.00 0.00 0.00 4.24
47 48 9.255304 CTGAAGCAGATAGTTTATCTAAGTTCC 57.745 37.037 0.00 0.00 43.41 3.62
79 80 2.759535 TGGATGTGGGCAAACATGTATG 59.240 45.455 9.48 0.00 40.87 2.39
84 85 3.389329 TGTGGGCAAACATGTATGGTTTT 59.611 39.130 0.00 0.00 35.04 2.43
120 121 0.101759 GGCGCGTAGTTGATCTACCA 59.898 55.000 8.43 0.00 44.30 3.25
145 146 3.262420 ACCAAGCAATCATACGAGACAC 58.738 45.455 0.00 0.00 0.00 3.67
152 153 1.817357 TCATACGAGACACGACACCT 58.183 50.000 0.00 0.00 45.77 4.00
164 165 6.698380 AGACACGACACCTAGATTTGTTAAT 58.302 36.000 0.00 0.00 0.00 1.40
165 166 6.590292 AGACACGACACCTAGATTTGTTAATG 59.410 38.462 0.00 0.00 0.00 1.90
175 176 5.880054 AGATTTGTTAATGAGGTTCACCG 57.120 39.130 0.00 0.00 42.08 4.94
181 182 2.113860 AATGAGGTTCACCGTCATGG 57.886 50.000 10.09 0.00 46.41 3.66
195 196 2.039831 ATGGCTACATCCCCGGGT 60.040 61.111 21.85 2.42 29.20 5.28
204 205 1.211949 ACATCCCCGGGTTTGACTATG 59.788 52.381 21.85 12.76 0.00 2.23
208 209 0.461339 CCCGGGTTTGACTATGGACG 60.461 60.000 14.18 0.00 0.00 4.79
213 214 1.653151 GTTTGACTATGGACGCTCCC 58.347 55.000 2.23 0.00 35.03 4.30
214 215 1.207329 GTTTGACTATGGACGCTCCCT 59.793 52.381 2.23 0.00 35.03 4.20
231 232 1.136984 CTCTCACGACACCGCTACC 59.863 63.158 0.00 0.00 39.95 3.18
233 234 0.963856 TCTCACGACACCGCTACCAT 60.964 55.000 0.00 0.00 39.95 3.55
234 235 0.802222 CTCACGACACCGCTACCATG 60.802 60.000 0.00 0.00 39.95 3.66
283 284 4.017877 GCCGCTGCCGCATATGTC 62.018 66.667 8.09 0.00 35.30 3.06
284 285 2.280389 CCGCTGCCGCATATGTCT 60.280 61.111 4.29 0.00 35.30 3.41
285 286 1.006220 CCGCTGCCGCATATGTCTA 60.006 57.895 4.29 0.00 35.30 2.59
286 287 0.599991 CCGCTGCCGCATATGTCTAA 60.600 55.000 4.29 0.00 35.30 2.10
287 288 0.508641 CGCTGCCGCATATGTCTAAC 59.491 55.000 4.29 0.00 35.30 2.34
288 289 0.868406 GCTGCCGCATATGTCTAACC 59.132 55.000 4.29 0.00 35.78 2.85
290 291 0.107831 TGCCGCATATGTCTAACCCC 59.892 55.000 4.29 0.00 0.00 4.95
295 311 3.513912 CCGCATATGTCTAACCCCTCATA 59.486 47.826 4.29 0.00 0.00 2.15
322 338 8.728596 ATATAAGAGGCCTAGAATACAAGTGT 57.271 34.615 4.42 0.00 0.00 3.55
356 375 8.807118 GGACATGACTCCATATTCTATCTACAA 58.193 37.037 0.00 0.00 0.00 2.41
369 388 8.873215 ATTCTATCTACAAACCATACAACTCG 57.127 34.615 0.00 0.00 0.00 4.18
389 408 8.883731 CAACTCGGAGTTCAATTGTAATCTATT 58.116 33.333 20.03 0.00 36.03 1.73
413 432 8.549777 TTTTTGTACACAATATTCGACACAAC 57.450 30.769 0.00 0.00 35.55 3.32
414 433 5.849357 TGTACACAATATTCGACACAACC 57.151 39.130 0.00 0.00 0.00 3.77
474 493 6.724893 TCTTATGGACCTCGTTGATCAATA 57.275 37.500 12.12 2.38 0.00 1.90
482 501 4.759693 ACCTCGTTGATCAATAAAGCAACA 59.240 37.500 12.12 0.00 40.32 3.33
488 507 6.022251 CGTTGATCAATAAAGCAACATCGTTC 60.022 38.462 12.12 0.00 40.32 3.95
524 543 7.871853 TGAAAAAGACAAGTTAACATAGAGGC 58.128 34.615 8.61 0.00 0.00 4.70
532 551 0.384309 TAACATAGAGGCCTCGCGTG 59.616 55.000 26.95 25.43 34.09 5.34
559 578 2.398554 CGTGGGAAATGGAGCACCG 61.399 63.158 0.00 0.00 39.42 4.94
570 589 1.003839 GAGCACCGGGACATGAACA 60.004 57.895 6.32 0.00 0.00 3.18
618 637 1.067495 AGCTACGTGCCAAGTTCTCTC 60.067 52.381 0.00 0.00 44.23 3.20
632 651 3.639094 AGTTCTCTCAGCAAGTGTACTGT 59.361 43.478 0.00 0.00 35.37 3.55
642 661 6.210784 TCAGCAAGTGTACTGTTATTACCTCT 59.789 38.462 0.00 0.00 35.37 3.69
645 664 6.649557 GCAAGTGTACTGTTATTACCTCTGTT 59.350 38.462 0.00 0.00 0.00 3.16
647 666 6.932947 AGTGTACTGTTATTACCTCTGTTCC 58.067 40.000 0.00 0.00 0.00 3.62
666 685 8.675504 TCTGTTCCAAATTACGTGTCTTAAAAA 58.324 29.630 0.00 0.00 0.00 1.94
741 760 4.837093 ACAAATAATTCAGGACGGAGGA 57.163 40.909 0.00 0.00 0.00 3.71
889 920 2.824041 CCCGCAAAGCCGCTGTAT 60.824 61.111 0.00 0.00 0.00 2.29
934 966 4.400251 CGACCCCCACCTCCTCCT 62.400 72.222 0.00 0.00 0.00 3.69
984 1023 1.949079 GCTAGGGTTTTGGTCCTTCGG 60.949 57.143 0.00 0.00 34.75 4.30
1147 1189 0.318699 CAGCCTCAACGAGAACGACA 60.319 55.000 0.00 0.00 42.66 4.35
1221 1263 4.316823 ACCGCACCAGGAGGAGGA 62.317 66.667 11.48 0.00 39.08 3.71
1782 1857 2.095978 GATACGGCGGTGGTGGCTAT 62.096 60.000 13.24 0.00 0.00 2.97
2128 2987 2.257409 TTTCCCCCTGCTGCTCGATC 62.257 60.000 0.00 0.00 0.00 3.69
2168 3027 1.092921 TTGCTGGTGGTGTGTTCGTC 61.093 55.000 0.00 0.00 0.00 4.20
2169 3028 2.594962 GCTGGTGGTGTGTTCGTCG 61.595 63.158 0.00 0.00 0.00 5.12
2170 3029 1.227147 CTGGTGGTGTGTTCGTCGT 60.227 57.895 0.00 0.00 0.00 4.34
2262 3131 6.937436 AAGTTATCGAAGTCAAGTTTGGTT 57.063 33.333 0.00 0.00 0.00 3.67
2291 3160 6.371825 TGAGATTGATCTATGATCTTGCATGC 59.628 38.462 11.82 11.82 37.25 4.06
2295 3164 5.731591 TGATCTATGATCTTGCATGCCTAG 58.268 41.667 16.68 12.74 0.00 3.02
2310 3179 5.516996 CATGCCTAGTGTTTATCTTGCATG 58.483 41.667 6.73 6.73 0.00 4.06
2346 3215 7.008440 TGAAAGCGTTGATTCTGATATTCTG 57.992 36.000 0.00 0.00 0.00 3.02
2354 3223 7.095857 CGTTGATTCTGATATTCTGTTCTAGGC 60.096 40.741 0.00 0.00 0.00 3.93
2357 3226 8.801299 TGATTCTGATATTCTGTTCTAGGCTAG 58.199 37.037 15.56 15.56 0.00 3.42
2358 3227 8.719645 ATTCTGATATTCTGTTCTAGGCTAGT 57.280 34.615 20.45 2.80 0.00 2.57
2359 3228 7.517614 TCTGATATTCTGTTCTAGGCTAGTG 57.482 40.000 20.45 10.01 0.00 2.74
2395 3264 5.528600 TTGGAATCCTGTTCTCCCATTTA 57.471 39.130 0.00 0.00 0.00 1.40
2397 3266 5.448654 TGGAATCCTGTTCTCCCATTTATG 58.551 41.667 0.00 0.00 0.00 1.90
2451 3321 3.921119 TTCGCAAGTTTGATGCTTCAT 57.079 38.095 2.75 0.00 41.64 2.57
2472 3342 2.955660 TGTTCAACAGGTTCATGGTTCC 59.044 45.455 0.00 0.00 0.00 3.62
2489 3364 3.888930 GGTTCCAAATCTTCAACAGGTCA 59.111 43.478 0.00 0.00 0.00 4.02
2502 3377 9.739276 TCTTCAACAGGTCAATTCTTATATGTT 57.261 29.630 0.00 0.00 0.00 2.71
2516 3391 5.874810 TCTTATATGTTCTTGTGCCACTGTC 59.125 40.000 0.00 0.00 0.00 3.51
2517 3392 2.645838 ATGTTCTTGTGCCACTGTCT 57.354 45.000 0.00 0.00 0.00 3.41
2518 3393 1.667236 TGTTCTTGTGCCACTGTCTG 58.333 50.000 0.00 0.00 0.00 3.51
2521 3396 0.533531 TCTTGTGCCACTGTCTGCTG 60.534 55.000 0.00 0.00 0.00 4.41
2536 3432 6.209589 ACTGTCTGCTGTTAGTAGATTCTTCA 59.790 38.462 0.14 0.00 39.13 3.02
2546 3442 5.939764 AGTAGATTCTTCACATGCCACTA 57.060 39.130 0.00 0.00 0.00 2.74
2559 3455 1.337074 TGCCACTAGCTTGCAAAATGC 60.337 47.619 0.00 0.00 43.10 3.56
2561 3457 5.184212 TGCCACTAGCTTGCAAAATGCAT 62.184 43.478 11.26 0.00 46.67 3.96
2583 3483 4.442706 TCCTAGATCTTTTTGCATCCGTC 58.557 43.478 0.00 0.00 0.00 4.79
2594 3494 1.291132 GCATCCGTCCTAAGCAAGAC 58.709 55.000 0.00 0.00 0.00 3.01
2595 3495 1.405526 GCATCCGTCCTAAGCAAGACA 60.406 52.381 0.00 0.00 33.08 3.41
2598 3498 0.038526 CCGTCCTAAGCAAGACACGT 60.039 55.000 0.00 0.00 32.37 4.49
2610 3510 2.549754 CAAGACACGTTGATTCCTTGCT 59.450 45.455 0.00 0.00 0.00 3.91
2616 3516 5.670485 ACACGTTGATTCCTTGCTATGATA 58.330 37.500 0.00 0.00 0.00 2.15
2621 3521 6.925718 CGTTGATTCCTTGCTATGATAGAAGA 59.074 38.462 3.13 0.00 0.00 2.87
2657 3564 1.377987 GCTGTTCCCATTACGCCCA 60.378 57.895 0.00 0.00 0.00 5.36
2694 3601 5.816777 AGCTTAATCTGAATTCAGCAGTCTC 59.183 40.000 27.45 15.60 42.22 3.36
2695 3602 5.816777 GCTTAATCTGAATTCAGCAGTCTCT 59.183 40.000 27.45 10.54 40.38 3.10
2696 3603 6.315891 GCTTAATCTGAATTCAGCAGTCTCTT 59.684 38.462 27.45 14.34 40.38 2.85
2697 3604 7.606858 TTAATCTGAATTCAGCAGTCTCTTG 57.393 36.000 27.45 4.31 43.46 3.02
2715 3622 3.821033 TCTTGCTTAAGAAAGAAGGCACC 59.179 43.478 21.62 0.00 36.79 5.01
2776 3684 2.802816 GTGGAGTAGTGTGCTTTGTCTG 59.197 50.000 0.00 0.00 0.00 3.51
2785 3693 2.229792 GTGCTTTGTCTGGGATGAACA 58.770 47.619 0.00 0.00 0.00 3.18
2812 3720 4.631377 TGGAATCATGTCGCTTTAGACTTG 59.369 41.667 6.65 6.65 43.45 3.16
2813 3721 4.034510 GGAATCATGTCGCTTTAGACTTGG 59.965 45.833 11.33 0.00 42.78 3.61
2843 3751 7.375053 TGCGAAGAATAACAGCCTAAATTTTT 58.625 30.769 0.00 0.00 0.00 1.94
2870 3778 6.042638 TCCTTCCAACAAATGACTCTAGAG 57.957 41.667 18.49 18.49 0.00 2.43
2875 3783 4.940046 CCAACAAATGACTCTAGAGCACAT 59.060 41.667 19.97 20.19 32.87 3.21
2979 3938 8.267183 TGAAACCATGATATGAAGTACACATCT 58.733 33.333 8.45 0.99 33.97 2.90
2980 3939 8.668510 AAACCATGATATGAAGTACACATCTC 57.331 34.615 8.45 9.16 33.97 2.75
2981 3940 7.365497 ACCATGATATGAAGTACACATCTCA 57.635 36.000 16.76 16.76 33.97 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.364522 TCAGAATTTCACCTTGTAGATTTCG 57.635 36.000 0.00 0.00 0.00 3.46
1 2 7.752686 GCTTCAGAATTTCACCTTGTAGATTTC 59.247 37.037 0.00 0.00 0.00 2.17
8 9 4.464008 TCTGCTTCAGAATTTCACCTTGT 58.536 39.130 0.00 0.00 37.57 3.16
21 22 9.255304 GGAACTTAGATAAACTATCTGCTTCAG 57.745 37.037 6.46 0.00 44.81 3.02
47 48 4.272489 TGCCCACATCCAGAGATTAAAAG 58.728 43.478 0.00 0.00 0.00 2.27
59 60 2.101249 CCATACATGTTTGCCCACATCC 59.899 50.000 2.30 0.00 35.03 3.51
79 80 8.377681 GCGCCTTAAATTATTCTAACAAAAACC 58.622 33.333 0.00 0.00 0.00 3.27
84 85 6.425577 ACGCGCCTTAAATTATTCTAACAA 57.574 33.333 5.73 0.00 0.00 2.83
97 98 2.953466 AGATCAACTACGCGCCTTAA 57.047 45.000 5.73 0.00 0.00 1.85
98 99 3.344904 GTAGATCAACTACGCGCCTTA 57.655 47.619 5.73 0.00 41.36 2.69
99 100 2.205307 GTAGATCAACTACGCGCCTT 57.795 50.000 5.73 0.00 41.36 4.35
120 121 3.197766 TCTCGTATGATTGCTTGGTCCTT 59.802 43.478 0.00 0.00 0.00 3.36
145 146 6.106673 ACCTCATTAACAAATCTAGGTGTCG 58.893 40.000 0.00 0.00 34.64 4.35
152 153 6.469410 ACGGTGAACCTCATTAACAAATCTA 58.531 36.000 0.00 0.00 0.00 1.98
164 165 1.003839 GCCATGACGGTGAACCTCA 60.004 57.895 0.00 1.55 36.97 3.86
165 166 0.535335 TAGCCATGACGGTGAACCTC 59.465 55.000 0.00 0.00 36.97 3.85
175 176 1.071471 CCGGGGATGTAGCCATGAC 59.929 63.158 0.00 0.00 0.00 3.06
181 182 0.746923 GTCAAACCCGGGGATGTAGC 60.747 60.000 27.92 13.29 0.00 3.58
195 196 1.480954 GAGGGAGCGTCCATAGTCAAA 59.519 52.381 6.41 0.00 38.64 2.69
204 205 2.750637 TCGTGAGAGGGAGCGTCC 60.751 66.667 0.00 0.00 34.84 4.79
208 209 2.574399 GGTGTCGTGAGAGGGAGC 59.426 66.667 0.00 0.00 43.49 4.70
213 214 1.136984 GGTAGCGGTGTCGTGAGAG 59.863 63.158 0.00 0.00 43.49 3.20
214 215 0.963856 ATGGTAGCGGTGTCGTGAGA 60.964 55.000 0.00 0.00 38.89 3.27
271 272 0.107831 GGGGTTAGACATATGCGGCA 59.892 55.000 4.58 4.58 0.00 5.69
273 274 1.691976 TGAGGGGTTAGACATATGCGG 59.308 52.381 1.58 0.00 0.00 5.69
280 281 9.937876 CCTCTTATATATATGAGGGGTTAGACA 57.062 37.037 30.31 0.56 44.65 3.41
281 282 8.862085 GCCTCTTATATATATGAGGGGTTAGAC 58.138 40.741 34.29 21.96 46.68 2.59
283 284 8.013667 AGGCCTCTTATATATATGAGGGGTTAG 58.986 40.741 34.29 20.07 46.68 2.34
284 285 7.905412 AGGCCTCTTATATATATGAGGGGTTA 58.095 38.462 34.29 4.59 46.68 2.85
285 286 6.767854 AGGCCTCTTATATATATGAGGGGTT 58.232 40.000 34.29 16.46 46.68 4.11
286 287 6.377158 AGGCCTCTTATATATATGAGGGGT 57.623 41.667 34.29 11.45 46.68 4.95
287 288 7.770662 TCTAGGCCTCTTATATATATGAGGGG 58.229 42.308 34.29 23.36 46.68 4.79
288 289 9.836179 ATTCTAGGCCTCTTATATATATGAGGG 57.164 37.037 34.29 24.93 46.68 4.30
305 321 4.833390 ACAAGACACTTGTATTCTAGGCC 58.167 43.478 14.21 0.00 0.00 5.19
322 338 7.345653 AGAATATGGAGTCATGTCCTAACAAGA 59.654 37.037 4.17 0.00 39.30 3.02
356 375 4.345859 TTGAACTCCGAGTTGTATGGTT 57.654 40.909 18.59 0.00 38.80 3.67
364 383 9.449719 AAATAGATTACAATTGAACTCCGAGTT 57.550 29.630 13.75 13.75 41.95 3.01
389 408 7.133513 GGTTGTGTCGAATATTGTGTACAAAA 58.866 34.615 0.00 0.00 39.55 2.44
393 412 4.933400 AGGGTTGTGTCGAATATTGTGTAC 59.067 41.667 0.00 0.00 0.00 2.90
404 423 3.547054 AAGTTGTTAGGGTTGTGTCGA 57.453 42.857 0.00 0.00 0.00 4.20
413 432 3.252215 TGTTGATGCGAAAGTTGTTAGGG 59.748 43.478 0.00 0.00 0.00 3.53
414 433 4.481930 TGTTGATGCGAAAGTTGTTAGG 57.518 40.909 0.00 0.00 0.00 2.69
474 493 2.871096 TAGGGGAACGATGTTGCTTT 57.129 45.000 0.00 0.00 0.00 3.51
482 501 7.715686 GTCTTTTTCATCTATTAGGGGAACGAT 59.284 37.037 0.00 0.00 0.00 3.73
488 507 8.581253 AACTTGTCTTTTTCATCTATTAGGGG 57.419 34.615 0.00 0.00 0.00 4.79
559 578 2.362077 ACTTGCAAGTTGTTCATGTCCC 59.638 45.455 26.36 0.00 35.21 4.46
570 589 0.103572 CTGCTTGGCACTTGCAAGTT 59.896 50.000 29.23 12.23 44.36 2.66
595 614 3.006537 AGAGAACTTGGCACGTAGCTTAA 59.993 43.478 0.00 5.47 44.79 1.85
597 616 1.344763 AGAGAACTTGGCACGTAGCTT 59.655 47.619 0.00 0.00 44.79 3.74
618 637 6.311445 CAGAGGTAATAACAGTACACTTGCTG 59.689 42.308 0.00 0.00 41.06 4.41
632 651 7.879160 ACACGTAATTTGGAACAGAGGTAATAA 59.121 33.333 0.00 0.00 42.39 1.40
642 661 9.804758 AATTTTTAAGACACGTAATTTGGAACA 57.195 25.926 0.00 0.00 0.00 3.18
741 760 8.970859 AGATCAGCTTTGCTTGTATAATACTT 57.029 30.769 0.00 0.00 36.40 2.24
874 905 0.316196 GCTTATACAGCGGCTTTGCG 60.316 55.000 0.00 0.00 39.29 4.85
889 920 2.616489 GGCCTCTTAGGTGGGCTTA 58.384 57.895 11.64 0.00 44.76 3.09
897 928 6.183360 GGGTCGATATAAATAGGCCTCTTAGG 60.183 46.154 9.68 0.54 33.33 2.69
934 966 0.904865 AGATCGGTGTGGAGGCTGAA 60.905 55.000 0.00 0.00 0.00 3.02
984 1023 3.799755 ATCTTGCGCCGCCGAAAC 61.800 61.111 6.63 0.00 36.29 2.78
1147 1189 0.959372 ATGACCTCGAACTCGACGGT 60.959 55.000 17.48 17.48 45.48 4.83
1764 1839 2.138179 ATAGCCACCACCGCCGTAT 61.138 57.895 0.00 0.00 0.00 3.06
1806 2177 2.730672 GCCGCACTTGTAGCACTCG 61.731 63.158 0.00 0.00 0.00 4.18
2128 2987 0.321671 TCTTCTGGAACCAAGCTCGG 59.678 55.000 0.00 0.00 0.00 4.63
2168 3027 9.113876 GACAACAAAATAACTTGGATCTTAACG 57.886 33.333 0.00 0.00 0.00 3.18
2262 3131 8.208903 TGCAAGATCATAGATCAATCTCAAGAA 58.791 33.333 9.43 0.00 38.32 2.52
2291 3160 6.355397 CAGACATGCAAGATAAACACTAGG 57.645 41.667 0.00 0.00 0.00 3.02
2310 3179 1.583477 GCTTTCAAGCCTGGCAGAC 59.417 57.895 22.65 3.71 46.20 3.51
2328 3197 7.095857 GCCTAGAACAGAATATCAGAATCAACG 60.096 40.741 0.00 0.00 0.00 4.10
2346 3215 1.207329 CCACCACCACTAGCCTAGAAC 59.793 57.143 5.58 0.00 0.00 3.01
2354 3223 5.505780 TCCAAAATAATCCACCACCACTAG 58.494 41.667 0.00 0.00 0.00 2.57
2357 3226 5.660460 GATTCCAAAATAATCCACCACCAC 58.340 41.667 0.00 0.00 0.00 4.16
2358 3227 5.930837 GATTCCAAAATAATCCACCACCA 57.069 39.130 0.00 0.00 0.00 4.17
2395 3264 1.031571 ACGCCAATGGAATCGCACAT 61.032 50.000 2.05 0.00 0.00 3.21
2397 3266 0.109319 AAACGCCAATGGAATCGCAC 60.109 50.000 2.05 0.00 0.00 5.34
2451 3321 2.955660 GGAACCATGAACCTGTTGAACA 59.044 45.455 0.00 0.00 0.00 3.18
2489 3364 7.394359 ACAGTGGCACAAGAACATATAAGAATT 59.606 33.333 21.41 0.00 44.16 2.17
2502 3377 0.533531 CAGCAGACAGTGGCACAAGA 60.534 55.000 21.41 0.00 44.16 3.02
2516 3391 6.238049 GCATGTGAAGAATCTACTAACAGCAG 60.238 42.308 0.00 0.00 0.00 4.24
2517 3392 5.582269 GCATGTGAAGAATCTACTAACAGCA 59.418 40.000 0.00 0.00 0.00 4.41
2518 3393 5.007136 GGCATGTGAAGAATCTACTAACAGC 59.993 44.000 0.00 0.00 0.00 4.40
2521 3396 6.109359 AGTGGCATGTGAAGAATCTACTAAC 58.891 40.000 0.00 0.00 0.00 2.34
2536 3432 1.619654 TTTGCAAGCTAGTGGCATGT 58.380 45.000 5.59 0.00 44.79 3.21
2559 3455 4.818546 ACGGATGCAAAAAGATCTAGGATG 59.181 41.667 0.00 0.00 0.00 3.51
2561 3457 4.442706 GACGGATGCAAAAAGATCTAGGA 58.557 43.478 0.00 0.00 0.00 2.94
2583 3483 3.125316 GGAATCAACGTGTCTTGCTTAGG 59.875 47.826 0.00 0.00 0.00 2.69
2594 3494 5.985530 TCTATCATAGCAAGGAATCAACGTG 59.014 40.000 0.00 0.00 0.00 4.49
2595 3495 6.161855 TCTATCATAGCAAGGAATCAACGT 57.838 37.500 0.00 0.00 0.00 3.99
2598 3498 7.795047 TGTCTTCTATCATAGCAAGGAATCAA 58.205 34.615 0.00 0.00 0.00 2.57
2610 3510 9.842775 AGCTGATTGAATTTGTCTTCTATCATA 57.157 29.630 10.01 0.00 42.39 2.15
2616 3516 5.106237 GCAGAGCTGATTGAATTTGTCTTCT 60.106 40.000 0.85 0.00 0.00 2.85
2644 3544 1.004862 TGAAATGTGGGCGTAATGGGA 59.995 47.619 0.00 0.00 0.00 4.37
2645 3545 1.468985 TGAAATGTGGGCGTAATGGG 58.531 50.000 0.00 0.00 0.00 4.00
2646 3546 3.799281 AATGAAATGTGGGCGTAATGG 57.201 42.857 0.00 0.00 0.00 3.16
2647 3547 6.582295 GCTTATAATGAAATGTGGGCGTAATG 59.418 38.462 0.00 0.00 0.00 1.90
2648 3548 6.490040 AGCTTATAATGAAATGTGGGCGTAAT 59.510 34.615 0.00 0.00 0.00 1.89
2649 3549 5.825679 AGCTTATAATGAAATGTGGGCGTAA 59.174 36.000 0.00 0.00 0.00 3.18
2650 3550 5.373222 AGCTTATAATGAAATGTGGGCGTA 58.627 37.500 0.00 0.00 0.00 4.42
2651 3551 4.207165 AGCTTATAATGAAATGTGGGCGT 58.793 39.130 0.00 0.00 0.00 5.68
2694 3601 3.823304 AGGTGCCTTCTTTCTTAAGCAAG 59.177 43.478 8.40 8.40 0.00 4.01
2695 3602 3.832527 AGGTGCCTTCTTTCTTAAGCAA 58.167 40.909 0.00 0.00 0.00 3.91
2696 3603 3.508845 AGGTGCCTTCTTTCTTAAGCA 57.491 42.857 0.00 0.00 0.00 3.91
2697 3604 4.142578 GCTAAGGTGCCTTCTTTCTTAAGC 60.143 45.833 6.77 4.75 37.47 3.09
2776 3684 4.891756 ACATGATTCCATTCTGTTCATCCC 59.108 41.667 0.00 0.00 0.00 3.85
2785 3693 5.525378 GTCTAAAGCGACATGATTCCATTCT 59.475 40.000 0.00 0.00 34.11 2.40
2812 3720 2.222027 CTGTTATTCTTCGCATCCCCC 58.778 52.381 0.00 0.00 0.00 5.40
2813 3721 1.604278 GCTGTTATTCTTCGCATCCCC 59.396 52.381 0.00 0.00 0.00 4.81
2843 3751 6.627087 AGAGTCATTTGTTGGAAGGAGATA 57.373 37.500 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.