Multiple sequence alignment - TraesCS4A01G382200

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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 TraesCS4A01G382200 chr4A 100.000 2912 0 0 1 2912 660451213 660454124 0.000000e+00 5378.0
1 TraesCS4A01G382200 chr4A 83.040 908 113 23 1238 2130 660624767 660625648 0.000000e+00 785.0
2 TraesCS4A01G382200 chr4A 86.411 287 34 3 1443 1728 660654515 660654797 2.820000e-80 309.0
3 TraesCS4A01G382200 chr4A 84.167 120 19 0 1218 1337 660654270 660654389 1.830000e-22 117.0
4 TraesCS4A01G382200 chr7A 92.164 2935 178 30 1 2912 48524739 48527644 0.000000e+00 4098.0
5 TraesCS4A01G382200 chr7A 80.797 1104 150 33 1238 2306 48715649 48716725 0.000000e+00 808.0
6 TraesCS4A01G382200 chr7A 78.816 963 153 29 1218 2154 48583658 48584595 4.150000e-168 601.0
7 TraesCS4A01G382200 chr7A 86.218 312 28 8 2309 2605 48716610 48716921 1.010000e-84 324.0
8 TraesCS4A01G382200 chr7A 79.531 469 69 19 1218 1665 48756002 48756464 2.820000e-80 309.0
9 TraesCS4A01G382200 chr7A 81.298 262 28 5 2370 2620 48584999 48585250 2.960000e-45 193.0
10 TraesCS4A01G382200 chr7D 89.421 1985 135 32 363 2306 46712997 46711047 0.000000e+00 2433.0
11 TraesCS4A01G382200 chr7D 84.800 875 103 12 1449 2306 46670549 46669688 0.000000e+00 852.0
12 TraesCS4A01G382200 chr7D 84.992 613 68 15 2301 2895 46711175 46710569 4.150000e-168 601.0
13 TraesCS4A01G382200 chr7D 93.151 219 12 3 1443 1659 46586136 46585919 4.680000e-83 318.0
14 TraesCS4A01G382200 chr3B 83.607 122 13 5 1223 1337 191290484 191290605 1.100000e-19 108.0
15 TraesCS4A01G382200 chr1D 81.452 124 16 4 1219 1337 308459964 308459843 8.590000e-16 95.3


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 TraesCS4A01G382200 chr4A 660451213 660454124 2911 False 5378 5378 100.0000 1 2912 1 chr4A.!!$F1 2911
1 TraesCS4A01G382200 chr4A 660624767 660625648 881 False 785 785 83.0400 1238 2130 1 chr4A.!!$F2 892
2 TraesCS4A01G382200 chr4A 660654270 660654797 527 False 213 309 85.2890 1218 1728 2 chr4A.!!$F3 510
3 TraesCS4A01G382200 chr7A 48524739 48527644 2905 False 4098 4098 92.1640 1 2912 1 chr7A.!!$F1 2911
4 TraesCS4A01G382200 chr7A 48715649 48716921 1272 False 566 808 83.5075 1238 2605 2 chr7A.!!$F4 1367
5 TraesCS4A01G382200 chr7A 48583658 48585250 1592 False 397 601 80.0570 1218 2620 2 chr7A.!!$F3 1402
6 TraesCS4A01G382200 chr7D 46710569 46712997 2428 True 1517 2433 87.2065 363 2895 2 chr7D.!!$R3 2532
7 TraesCS4A01G382200 chr7D 46669688 46670549 861 True 852 852 84.8000 1449 2306 1 chr7D.!!$R2 857

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
81 82 0.319469 GAACAATTGTGGCCGGTTGG 60.319 55.0 12.82 0.0 38.77 3.77 F
219 226 0.389817 TCTCCAGATTTGCCGACACG 60.390 55.0 0.00 0.0 0.00 4.49 F
1421 1474 0.683973 CTTGGAGATCGAGGATGGGG 59.316 60.0 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 1088 0.900647 AGTACCAGAAGCTCGGCTGT 60.901 55.000 9.47 0.0 39.62 4.40 R
1698 1767 1.001641 GCAGGAGAGGCACATGGTT 60.002 57.895 0.00 0.0 0.00 3.67 R
2724 3151 0.175989 GGTCCTTTGGCGACCTCTAG 59.824 60.000 2.45 0.0 45.41 2.43 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
52 53 9.768662 ATTTAAACATGCTTGAAATCAGAAAGT 57.231 25.926 6.60 0.00 0.00 2.66
65 66 6.473397 AATCAGAAAGTTGACGAGATGAAC 57.527 37.500 0.00 0.00 0.00 3.18
66 67 4.944048 TCAGAAAGTTGACGAGATGAACA 58.056 39.130 0.00 0.00 0.00 3.18
68 69 5.991606 TCAGAAAGTTGACGAGATGAACAAT 59.008 36.000 0.00 0.00 0.00 2.71
69 70 6.483307 TCAGAAAGTTGACGAGATGAACAATT 59.517 34.615 0.00 0.00 0.00 2.32
81 82 0.319469 GAACAATTGTGGCCGGTTGG 60.319 55.000 12.82 0.00 38.77 3.77
110 111 0.885196 GGTTGCGCCTTGTAAATCCA 59.115 50.000 4.18 0.00 0.00 3.41
135 136 9.773328 CAAATTTCTTTGTTTTTCTTCTTTCCC 57.227 29.630 0.00 0.00 37.54 3.97
141 142 3.697045 TGTTTTTCTTCTTTCCCAGCGAA 59.303 39.130 0.00 0.00 0.00 4.70
145 146 1.971357 TCTTCTTTCCCAGCGAAGTCT 59.029 47.619 0.00 0.00 36.44 3.24
183 190 2.257034 GTTTCCATCTACGTGACGTCC 58.743 52.381 16.19 3.43 41.54 4.79
213 220 2.632377 TCGTCAATCTCCAGATTTGCC 58.368 47.619 0.00 0.00 42.41 4.52
219 226 0.389817 TCTCCAGATTTGCCGACACG 60.390 55.000 0.00 0.00 0.00 4.49
239 246 2.706890 GGTTTCCCGAAAGTGCTCATA 58.293 47.619 0.00 0.00 0.00 2.15
245 252 2.544685 CCGAAAGTGCTCATAGGAGTG 58.455 52.381 6.23 0.00 43.37 3.51
255 262 2.290916 CTCATAGGAGTGTGATACGCGT 59.709 50.000 19.17 19.17 36.36 6.01
261 268 0.732880 AGTGTGATACGCGTCTGTGC 60.733 55.000 18.63 4.26 33.01 4.57
275 282 3.789756 CGTCTGTGCGTTTATACAGGTAG 59.210 47.826 0.00 0.00 43.40 3.18
282 289 4.628333 TGCGTTTATACAGGTAGCTGTTTC 59.372 41.667 30.71 15.69 38.64 2.78
300 307 3.640436 CTGTGTGCATGCGAGCGTG 62.640 63.158 14.09 12.54 37.31 5.34
303 310 1.447663 TGTGCATGCGAGCGTGTAT 60.448 52.632 14.09 0.00 37.31 2.29
308 315 1.852077 GCATGCGAGCGTGTATGTTTC 60.852 52.381 17.28 0.00 35.52 2.78
309 316 1.393196 CATGCGAGCGTGTATGTTTCA 59.607 47.619 8.99 0.00 0.00 2.69
310 317 1.067693 TGCGAGCGTGTATGTTTCAG 58.932 50.000 0.00 0.00 0.00 3.02
311 318 1.068474 GCGAGCGTGTATGTTTCAGT 58.932 50.000 0.00 0.00 0.00 3.41
312 319 2.256174 GCGAGCGTGTATGTTTCAGTA 58.744 47.619 0.00 0.00 0.00 2.74
313 320 2.664568 GCGAGCGTGTATGTTTCAGTAA 59.335 45.455 0.00 0.00 0.00 2.24
314 321 3.241678 GCGAGCGTGTATGTTTCAGTAAG 60.242 47.826 0.00 0.00 0.00 2.34
315 322 4.163552 CGAGCGTGTATGTTTCAGTAAGA 58.836 43.478 0.00 0.00 0.00 2.10
317 324 5.386958 AGCGTGTATGTTTCAGTAAGAGA 57.613 39.130 0.00 0.00 0.00 3.10
318 325 5.967088 AGCGTGTATGTTTCAGTAAGAGAT 58.033 37.500 0.00 0.00 0.00 2.75
319 326 6.398918 AGCGTGTATGTTTCAGTAAGAGATT 58.601 36.000 0.00 0.00 0.00 2.40
320 327 6.311445 AGCGTGTATGTTTCAGTAAGAGATTG 59.689 38.462 0.00 0.00 0.00 2.67
321 328 6.470160 CGTGTATGTTTCAGTAAGAGATTGC 58.530 40.000 0.00 0.00 0.00 3.56
323 330 7.201556 CGTGTATGTTTCAGTAAGAGATTGCAT 60.202 37.037 0.00 0.00 0.00 3.96
324 331 8.454106 GTGTATGTTTCAGTAAGAGATTGCATT 58.546 33.333 0.00 0.00 0.00 3.56
325 332 9.665719 TGTATGTTTCAGTAAGAGATTGCATTA 57.334 29.630 0.00 0.00 0.00 1.90
326 333 9.922305 GTATGTTTCAGTAAGAGATTGCATTAC 57.078 33.333 0.00 0.00 0.00 1.89
327 334 7.060600 TGTTTCAGTAAGAGATTGCATTACG 57.939 36.000 0.00 0.00 35.14 3.18
328 335 6.871492 TGTTTCAGTAAGAGATTGCATTACGA 59.129 34.615 0.00 0.00 35.14 3.43
329 336 7.549134 TGTTTCAGTAAGAGATTGCATTACGAT 59.451 33.333 0.00 0.00 35.14 3.73
333 340 8.414003 TCAGTAAGAGATTGCATTACGATAAGT 58.586 33.333 0.00 0.00 35.14 2.24
361 368 5.527214 TCACAATAAGGCATGATTAGTTCCG 59.473 40.000 0.00 0.00 0.00 4.30
428 435 2.169561 CTCTCTCCCACTAAAAGGCTCC 59.830 54.545 0.00 0.00 0.00 4.70
443 461 1.173913 GCTCCAACCCATGTTACCAC 58.826 55.000 0.00 0.00 32.09 4.16
503 521 3.810310 AATCACGTCCTTGATCTCCTC 57.190 47.619 0.00 0.00 35.02 3.71
515 533 3.921104 TGATCTCCTCCAGAAGCACTAT 58.079 45.455 0.00 0.00 33.62 2.12
613 631 5.174579 CACACTGATTGTACTATCATGAGCG 59.825 44.000 18.31 10.20 35.67 5.03
630 648 7.837505 TCATGAGCGTAATTATTTTACACGAG 58.162 34.615 2.66 0.00 34.66 4.18
644 665 2.509336 CGAGCCGGTGCGATTTCT 60.509 61.111 11.86 0.00 44.33 2.52
833 859 1.522355 AGCTCATCATTGTCGCCCG 60.522 57.895 0.00 0.00 0.00 6.13
834 860 3.017323 CTCATCATTGTCGCCCGC 58.983 61.111 0.00 0.00 0.00 6.13
835 861 2.513666 TCATCATTGTCGCCCGCC 60.514 61.111 0.00 0.00 0.00 6.13
836 862 3.585990 CATCATTGTCGCCCGCCC 61.586 66.667 0.00 0.00 0.00 6.13
983 1009 1.153862 CGGACAGACAGAGCTCAGC 60.154 63.158 17.77 4.37 0.00 4.26
993 1019 4.398044 AGACAGAGCTCAGCTAGTTAGTTC 59.602 45.833 17.77 0.00 39.88 3.01
996 1022 5.186797 ACAGAGCTCAGCTAGTTAGTTCAAT 59.813 40.000 17.77 0.00 39.88 2.57
998 1024 7.069331 ACAGAGCTCAGCTAGTTAGTTCAATAT 59.931 37.037 17.77 0.00 39.88 1.28
1055 1081 4.778143 CCTGGGCCTCGTTTCCCG 62.778 72.222 4.53 0.00 45.60 5.14
1062 1088 3.702048 CTCGTTTCCCGGCCCTCA 61.702 66.667 0.00 0.00 37.11 3.86
1155 1181 1.079438 GGTGGAGGAGAGGAGGTGT 59.921 63.158 0.00 0.00 0.00 4.16
1161 1187 2.283529 GGAGAGGAGGTGTTCGCCA 61.284 63.158 5.19 0.00 37.84 5.69
1296 1328 2.046892 CTGTCCAAGGACCAGGCG 60.047 66.667 16.18 0.00 43.97 5.52
1365 1397 1.737735 TGTCTCGCCTCATTGCACG 60.738 57.895 0.00 0.00 0.00 5.34
1367 1399 3.120385 CTCGCCTCATTGCACGCA 61.120 61.111 0.00 0.00 0.00 5.24
1368 1400 2.667874 TCGCCTCATTGCACGCAA 60.668 55.556 6.95 6.95 40.47 4.85
1370 1402 2.502510 GCCTCATTGCACGCAACG 60.503 61.111 6.60 0.00 38.88 4.10
1372 1404 2.251963 CTCATTGCACGCAACGCA 59.748 55.556 6.60 0.00 38.88 5.24
1421 1474 0.683973 CTTGGAGATCGAGGATGGGG 59.316 60.000 0.00 0.00 0.00 4.96
1698 1767 4.752594 GGGCCCCTCACCACCCTA 62.753 72.222 12.23 0.00 39.42 3.53
1806 1875 3.228759 ATGCCAATGCCATCGCCC 61.229 61.111 0.00 0.00 36.33 6.13
1919 1991 1.437573 CGGCCAGATAGAACGAGCA 59.562 57.895 2.24 0.00 0.00 4.26
1934 2006 0.390340 GAGCAATCTCTGTGACGCCA 60.390 55.000 0.00 0.00 36.42 5.69
1937 2009 1.079819 AATCTCTGTGACGCCACCG 60.080 57.895 0.00 0.00 42.53 4.94
2029 2103 8.100508 AGTGTAGCAGAAAGTTTAATCCTTTC 57.899 34.615 15.35 15.35 45.20 2.62
2030 2104 7.175119 AGTGTAGCAGAAAGTTTAATCCTTTCC 59.825 37.037 17.81 8.97 45.72 3.13
2053 2129 4.224818 CCTTCTCTGTCTCTGAGGGAAATT 59.775 45.833 4.59 0.00 29.37 1.82
2102 2187 0.109458 CGGTCAATCGACGAGTTCCA 60.109 55.000 3.01 0.00 43.61 3.53
2279 2688 6.921857 CGAGGGTTGGTGTATTATTACTAGTG 59.078 42.308 5.39 0.00 0.00 2.74
2306 2725 4.458989 GGCTTGGTTTGTCTGATGTATCAA 59.541 41.667 0.00 0.00 36.18 2.57
2359 2778 1.945394 CTGTCCTGCATAGATGTTGCC 59.055 52.381 0.00 0.00 39.39 4.52
2364 2783 0.179097 TGCATAGATGTTGCCGCGTA 60.179 50.000 4.92 0.00 39.39 4.42
2365 2784 0.508641 GCATAGATGTTGCCGCGTAG 59.491 55.000 4.92 0.00 33.95 3.51
2375 2794 1.284408 GCCGCGTAGAGATCAGGAG 59.716 63.158 4.92 0.00 0.00 3.69
2384 2803 4.580995 CGTAGAGATCAGGAGTTGGTGTAT 59.419 45.833 0.00 0.00 0.00 2.29
2400 2819 7.610305 AGTTGGTGTATTATTACTTGACTTGGG 59.390 37.037 0.00 0.00 0.00 4.12
2497 2916 3.347216 TGGCCATCTAGCAAAAGAAGTC 58.653 45.455 0.00 0.00 0.00 3.01
2584 3011 0.545171 AGGTGCATGGTCTCCTCATG 59.455 55.000 0.00 0.00 43.39 3.07
2620 3047 8.543774 CAGGTATTTCATCTTGTCGTTTCTATC 58.456 37.037 0.00 0.00 0.00 2.08
2651 3078 4.461198 CTTTTATATTGGCCTCCGGAGTT 58.539 43.478 29.25 11.32 0.00 3.01
2667 3094 0.400213 AGTTGCAACCGGAAGATCCA 59.600 50.000 25.62 0.00 35.91 3.41
2681 3108 2.977808 AGATCCACATATCCCGACCTT 58.022 47.619 0.00 0.00 0.00 3.50
2709 3136 1.696336 AGCTCACATGAGTCACAAGGT 59.304 47.619 10.50 0.00 43.85 3.50
2724 3151 1.459592 CAAGGTCGAACCAACGTGATC 59.540 52.381 0.00 0.00 41.95 2.92
2784 3213 4.072088 CGCCGCTCACCGACAAAC 62.072 66.667 0.00 0.00 40.02 2.93
2789 3218 1.484227 CGCTCACCGACAAACGTTGA 61.484 55.000 0.00 0.00 40.80 3.18
2794 3223 0.176219 ACCGACAAACGTTGAGGACA 59.824 50.000 0.00 0.00 40.78 4.02
2847 3276 2.076100 TCTACGCCAACAAGCAATCAG 58.924 47.619 0.00 0.00 0.00 2.90
2865 3294 4.926140 TCAGCATTCTCGTAGATGACAT 57.074 40.909 0.00 0.00 33.89 3.06
2891 3320 2.174424 GAGATTGGGAGGCTTGAGGAAT 59.826 50.000 0.00 0.00 0.00 3.01
2898 3327 2.439507 GGAGGCTTGAGGAATATGGTCA 59.560 50.000 0.00 0.00 0.00 4.02
2902 3331 4.414846 AGGCTTGAGGAATATGGTCAGATT 59.585 41.667 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.712241 TCATCTCGTCAACTTTCTGATTTC 57.288 37.500 0.00 0.00 0.00 2.17
51 52 4.466828 CCACAATTGTTCATCTCGTCAAC 58.533 43.478 8.77 0.00 0.00 3.18
52 53 3.058293 GCCACAATTGTTCATCTCGTCAA 60.058 43.478 8.77 0.00 0.00 3.18
88 89 2.288518 GGATTTACAAGGCGCAACCAAA 60.289 45.455 10.83 2.65 43.14 3.28
92 93 2.715737 TTGGATTTACAAGGCGCAAC 57.284 45.000 10.83 0.00 0.00 4.17
93 94 3.951775 ATTTGGATTTACAAGGCGCAA 57.048 38.095 10.83 0.00 0.00 4.85
110 111 9.513906 TGGGAAAGAAGAAAAACAAAGAAATTT 57.486 25.926 0.00 0.00 0.00 1.82
135 136 2.872245 TCCAACTGAAAAGACTTCGCTG 59.128 45.455 0.00 0.00 0.00 5.18
141 142 3.718815 GTCGTCTCCAACTGAAAAGACT 58.281 45.455 0.00 0.00 36.77 3.24
145 146 2.589798 ACGTCGTCTCCAACTGAAAA 57.410 45.000 0.00 0.00 0.00 2.29
183 190 3.641439 GAGATTGACGAAATCACCACG 57.359 47.619 14.85 0.00 46.21 4.94
225 232 2.093973 ACACTCCTATGAGCACTTTCGG 60.094 50.000 0.00 0.00 42.74 4.30
228 235 4.833478 ATCACACTCCTATGAGCACTTT 57.167 40.909 0.00 0.00 42.74 2.66
239 246 0.452184 CAGACGCGTATCACACTCCT 59.548 55.000 13.97 0.00 0.00 3.69
255 262 3.446161 AGCTACCTGTATAAACGCACAGA 59.554 43.478 3.37 0.00 43.99 3.41
269 276 1.532868 GCACACAGAAACAGCTACCTG 59.467 52.381 0.00 0.00 44.80 4.00
270 277 1.140852 TGCACACAGAAACAGCTACCT 59.859 47.619 0.00 0.00 0.00 3.08
275 282 1.000233 CGCATGCACACAGAAACAGC 61.000 55.000 19.57 0.00 0.00 4.40
282 289 3.417224 ACGCTCGCATGCACACAG 61.417 61.111 19.57 8.45 0.00 3.66
300 307 9.922305 GTAATGCAATCTCTTACTGAAACATAC 57.078 33.333 0.00 0.00 0.00 2.39
303 310 6.871492 TCGTAATGCAATCTCTTACTGAAACA 59.129 34.615 0.00 0.00 0.00 2.83
308 315 8.581057 ACTTATCGTAATGCAATCTCTTACTG 57.419 34.615 0.00 0.00 0.00 2.74
309 316 9.035607 CAACTTATCGTAATGCAATCTCTTACT 57.964 33.333 0.00 0.00 0.00 2.24
310 317 8.818057 ACAACTTATCGTAATGCAATCTCTTAC 58.182 33.333 0.00 0.00 0.00 2.34
311 318 8.942338 ACAACTTATCGTAATGCAATCTCTTA 57.058 30.769 0.00 0.00 0.00 2.10
312 319 7.849804 ACAACTTATCGTAATGCAATCTCTT 57.150 32.000 0.00 0.00 0.00 2.85
313 320 7.549134 TGAACAACTTATCGTAATGCAATCTCT 59.451 33.333 0.00 0.00 0.00 3.10
314 321 7.636359 GTGAACAACTTATCGTAATGCAATCTC 59.364 37.037 0.00 0.00 0.00 2.75
315 322 7.119116 TGTGAACAACTTATCGTAATGCAATCT 59.881 33.333 0.00 0.00 0.00 2.40
317 324 7.139896 TGTGAACAACTTATCGTAATGCAAT 57.860 32.000 0.00 0.00 0.00 3.56
318 325 6.546972 TGTGAACAACTTATCGTAATGCAA 57.453 33.333 0.00 0.00 0.00 4.08
319 326 6.546972 TTGTGAACAACTTATCGTAATGCA 57.453 33.333 0.00 0.00 0.00 3.96
320 327 9.210426 CTTATTGTGAACAACTTATCGTAATGC 57.790 33.333 0.00 0.00 38.86 3.56
321 328 9.702726 CCTTATTGTGAACAACTTATCGTAATG 57.297 33.333 0.00 0.00 38.86 1.90
323 330 7.388224 TGCCTTATTGTGAACAACTTATCGTAA 59.612 33.333 0.00 0.00 38.86 3.18
324 331 6.874664 TGCCTTATTGTGAACAACTTATCGTA 59.125 34.615 0.00 0.00 38.86 3.43
325 332 5.703592 TGCCTTATTGTGAACAACTTATCGT 59.296 36.000 0.00 0.00 38.86 3.73
326 333 6.176975 TGCCTTATTGTGAACAACTTATCG 57.823 37.500 0.00 0.00 38.86 2.92
327 334 7.761409 TCATGCCTTATTGTGAACAACTTATC 58.239 34.615 0.00 0.00 38.86 1.75
328 335 7.701539 TCATGCCTTATTGTGAACAACTTAT 57.298 32.000 0.00 0.00 38.86 1.73
329 336 7.701539 ATCATGCCTTATTGTGAACAACTTA 57.298 32.000 0.00 0.00 38.86 2.24
333 340 7.701539 ACTAATCATGCCTTATTGTGAACAA 57.298 32.000 0.00 0.00 40.51 2.83
443 461 3.295093 TCTGTCAGGAGATTAGCAGAGG 58.705 50.000 0.00 0.00 0.00 3.69
481 499 4.261825 GGAGGAGATCAAGGACGTGATTAG 60.262 50.000 0.00 0.00 38.38 1.73
613 631 5.495502 CACCGGCTCGTGTAAAATAATTAC 58.504 41.667 0.00 0.00 0.00 1.89
630 648 1.425428 CAAGAGAAATCGCACCGGC 59.575 57.895 0.00 0.00 0.00 6.13
644 665 2.353704 CGTTAGGGTCATGTGAGCAAGA 60.354 50.000 13.49 0.00 43.82 3.02
833 859 3.584403 GGGATGATGGGAGGGGGC 61.584 72.222 0.00 0.00 0.00 5.80
834 860 2.860971 GGGGATGATGGGAGGGGG 60.861 72.222 0.00 0.00 0.00 5.40
835 861 3.252284 CGGGGATGATGGGAGGGG 61.252 72.222 0.00 0.00 0.00 4.79
836 862 3.252284 CCGGGGATGATGGGAGGG 61.252 72.222 0.00 0.00 0.00 4.30
983 1009 6.874134 AGGCGCCATTATATTGAACTAACTAG 59.126 38.462 31.54 0.00 0.00 2.57
993 1019 2.417933 GCTCTGAGGCGCCATTATATTG 59.582 50.000 31.54 11.47 0.00 1.90
996 1022 0.321671 GGCTCTGAGGCGCCATTATA 59.678 55.000 31.54 8.85 45.59 0.98
998 1024 2.505982 GGCTCTGAGGCGCCATTA 59.494 61.111 31.54 13.36 45.59 1.90
1062 1088 0.900647 AGTACCAGAAGCTCGGCTGT 60.901 55.000 9.47 0.00 39.62 4.40
1296 1328 3.827898 CACTCCTCGAGGACGGCC 61.828 72.222 30.49 0.00 39.78 6.13
1370 1402 3.109547 TGTGATCGACCGCGTTGC 61.110 61.111 4.92 0.00 38.98 4.17
1372 1404 2.431942 GGTGTGATCGACCGCGTT 60.432 61.111 4.92 0.00 38.98 4.84
1385 1417 3.010472 TCCAAGAATCATCCATGTGGTGT 59.990 43.478 0.00 0.00 36.34 4.16
1421 1474 8.369218 ACACAAAAGAAATCCATGTCATTTTC 57.631 30.769 0.00 1.68 0.00 2.29
1698 1767 1.001641 GCAGGAGAGGCACATGGTT 60.002 57.895 0.00 0.00 0.00 3.67
1875 1947 4.446413 ACCTTCGTTAGCCCGGCG 62.446 66.667 3.05 0.00 0.00 6.46
1884 1956 1.597027 CGCCTTGACCACCTTCGTT 60.597 57.895 0.00 0.00 0.00 3.85
1885 1957 2.030562 CGCCTTGACCACCTTCGT 59.969 61.111 0.00 0.00 0.00 3.85
1919 1991 1.079819 CGGTGGCGTCACAGAGATT 60.080 57.895 23.45 0.00 45.32 2.40
1934 2006 3.848301 TTGGCATGCTGAGCACGGT 62.848 57.895 18.92 0.00 43.04 4.83
1937 2009 2.149803 TTGCTTGGCATGCTGAGCAC 62.150 55.000 32.95 13.60 44.07 4.40
2029 2103 1.006519 TCCCTCAGAGACAGAGAAGGG 59.993 57.143 0.00 0.00 35.09 3.95
2030 2104 2.523325 TCCCTCAGAGACAGAGAAGG 57.477 55.000 0.00 0.00 35.09 3.46
2102 2187 1.434188 TGGATACATTCATCCCCGCT 58.566 50.000 0.00 0.00 46.17 5.52
2146 2234 8.714179 CAACATGTTGGTACGAATTAGTTTCTA 58.286 33.333 27.60 0.00 36.95 2.10
2159 2261 8.066000 GTGTACTTTTACTCAACATGTTGGTAC 58.934 37.037 32.54 29.45 40.78 3.34
2250 2371 2.596904 AATACACCAACCCTCGATCG 57.403 50.000 9.36 9.36 0.00 3.69
2279 2688 1.032014 TCAGACAAACCAAGCCAAGC 58.968 50.000 0.00 0.00 0.00 4.01
2359 2778 1.268794 CCAACTCCTGATCTCTACGCG 60.269 57.143 3.53 3.53 0.00 6.01
2364 2783 7.682787 AATAATACACCAACTCCTGATCTCT 57.317 36.000 0.00 0.00 0.00 3.10
2365 2784 8.643324 AGTAATAATACACCAACTCCTGATCTC 58.357 37.037 0.00 0.00 34.29 2.75
2375 2794 7.392393 ACCCAAGTCAAGTAATAATACACCAAC 59.608 37.037 0.00 0.00 34.29 3.77
2384 2803 7.780745 TCCAGAAAAACCCAAGTCAAGTAATAA 59.219 33.333 0.00 0.00 0.00 1.40
2400 2819 9.606631 ATTGAGTAGATGATACTCCAGAAAAAC 57.393 33.333 11.44 0.00 42.32 2.43
2584 3011 6.575162 AGATGAAATACCTGAACAACCAAC 57.425 37.500 0.00 0.00 0.00 3.77
2620 3047 6.212888 AGGCCAATATAAAAGCTCAAACAG 57.787 37.500 5.01 0.00 0.00 3.16
2651 3078 0.327924 ATGTGGATCTTCCGGTTGCA 59.672 50.000 0.00 0.00 40.17 4.08
2688 3115 2.105477 ACCTTGTGACTCATGTGAGCTT 59.895 45.455 9.84 0.00 45.79 3.74
2699 3126 1.805120 CGTTGGTTCGACCTTGTGACT 60.805 52.381 5.77 0.00 39.58 3.41
2709 3136 2.422479 CCTCTAGATCACGTTGGTTCGA 59.578 50.000 0.00 0.00 34.70 3.71
2724 3151 0.175989 GGTCCTTTGGCGACCTCTAG 59.824 60.000 2.45 0.00 45.41 2.43
2747 3174 1.875963 CGACGGCTTTCCTTTGCAT 59.124 52.632 0.00 0.00 0.00 3.96
2789 3218 1.476007 GCTGGTGAGGTCAGTGTCCT 61.476 60.000 8.81 8.81 38.09 3.85
2794 3223 0.612229 CTGATGCTGGTGAGGTCAGT 59.388 55.000 0.00 0.00 34.89 3.41
2806 3235 0.680280 CTTTGCCAGCCTCTGATGCT 60.680 55.000 1.31 1.31 40.41 3.79
2847 3276 3.633235 ACGATGTCATCTACGAGAATGC 58.367 45.455 11.04 0.00 0.00 3.56
2853 3282 2.817901 TCTCGACGATGTCATCTACGA 58.182 47.619 21.09 21.09 34.98 3.43
2859 3288 2.031870 TCCCAATCTCGACGATGTCAT 58.968 47.619 0.00 0.00 32.09 3.06
2865 3294 0.970937 AAGCCTCCCAATCTCGACGA 60.971 55.000 0.00 0.00 0.00 4.20
2891 3320 3.452755 CTACGCACCAATCTGACCATA 57.547 47.619 0.00 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.