Multiple sequence alignment - TraesCS5D01G492700

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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 TraesCS5D01G492700 chr5D 100.000 2797 0 0 1 2797 525731186 525733982 0.000000e+00 5166.0
1 TraesCS5D01G492700 chr5D 90.649 1433 81 24 482 1891 525760810 525762212 0.000000e+00 1855.0
2 TraesCS5D01G492700 chr5B 91.626 2448 152 23 365 2794 660185714 660188126 0.000000e+00 3336.0
3 TraesCS5D01G492700 chr5B 89.624 1436 110 22 482 1889 660209136 660210560 0.000000e+00 1790.0
4 TraesCS5D01G492700 chr5B 87.083 240 28 2 46 284 660185139 660185376 4.590000e-68 268.0
5 TraesCS5D01G492700 chr5A 91.690 1805 106 24 611 2391 652049968 652051752 0.000000e+00 2462.0
6 TraesCS5D01G492700 chr5A 90.340 1325 85 23 597 1891 652064036 652065347 0.000000e+00 1698.0
7 TraesCS5D01G492700 chr5A 87.621 412 35 7 2390 2794 652051856 652052258 5.460000e-127 464.0
8 TraesCS5D01G492700 chr5A 84.307 274 24 8 245 503 652046704 652046973 1.660000e-62 250.0
9 TraesCS5D01G492700 chr3B 91.026 78 6 1 452 528 115399165 115399088 1.370000e-18 104.0
10 TraesCS5D01G492700 chr2D 100.000 31 0 0 452 482 81330112 81330082 1.080000e-04 58.4
11 TraesCS5D01G492700 chr6A 94.444 36 1 1 494 528 542199763 542199728 1.000000e-03 54.7
12 TraesCS5D01G492700 chr1B 100.000 29 0 0 2043 2071 633788876 633788904 1.000000e-03 54.7
13 TraesCS5D01G492700 chr1B 100.000 29 0 0 2043 2071 633794212 633794240 1.000000e-03 54.7
14 TraesCS5D01G492700 chr3D 96.875 32 0 1 449 479 598856280 598856311 5.000000e-03 52.8


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 TraesCS5D01G492700 chr5D 525731186 525733982 2796 False 5166.000000 5166 100.000000 1 2797 1 chr5D.!!$F1 2796
1 TraesCS5D01G492700 chr5D 525760810 525762212 1402 False 1855.000000 1855 90.649000 482 1891 1 chr5D.!!$F2 1409
2 TraesCS5D01G492700 chr5B 660185139 660188126 2987 False 1802.000000 3336 89.354500 46 2794 2 chr5B.!!$F2 2748
3 TraesCS5D01G492700 chr5B 660209136 660210560 1424 False 1790.000000 1790 89.624000 482 1889 1 chr5B.!!$F1 1407
4 TraesCS5D01G492700 chr5A 652064036 652065347 1311 False 1698.000000 1698 90.340000 597 1891 1 chr5A.!!$F1 1294
5 TraesCS5D01G492700 chr5A 652046704 652052258 5554 False 1058.666667 2462 87.872667 245 2794 3 chr5A.!!$F2 2549

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
545 977 0.179018 AACCCTGCACAAGTCCTCAC 60.179 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 5519 0.107945 GGCTGCTCAAGGACGAGAAT 60.108 55.0 0.0 0.0 34.79 2.4 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
25 26 3.113325 CATCGATTGATGCATAAGCCG 57.887 47.619 10.05 1.75 45.06 5.52
26 27 2.524569 TCGATTGATGCATAAGCCGA 57.475 45.000 0.00 4.37 41.13 5.54
27 28 2.407090 TCGATTGATGCATAAGCCGAG 58.593 47.619 0.00 0.00 41.13 4.63
28 29 1.462283 CGATTGATGCATAAGCCGAGG 59.538 52.381 0.00 0.00 41.13 4.63
29 30 1.808945 GATTGATGCATAAGCCGAGGG 59.191 52.381 0.00 0.00 41.13 4.30
30 31 0.546122 TTGATGCATAAGCCGAGGGT 59.454 50.000 0.00 0.00 41.13 4.34
31 32 0.546122 TGATGCATAAGCCGAGGGTT 59.454 50.000 11.51 11.51 41.13 4.11
32 33 1.064758 TGATGCATAAGCCGAGGGTTT 60.065 47.619 12.04 0.00 41.13 3.27
33 34 2.171659 TGATGCATAAGCCGAGGGTTTA 59.828 45.455 12.04 1.41 41.13 2.01
34 35 2.325583 TGCATAAGCCGAGGGTTTAG 57.674 50.000 12.04 6.50 41.13 1.85
35 36 0.945099 GCATAAGCCGAGGGTTTAGC 59.055 55.000 12.04 12.16 32.29 3.09
36 37 1.594331 CATAAGCCGAGGGTTTAGCC 58.406 55.000 12.04 0.00 32.29 3.93
37 38 1.141053 CATAAGCCGAGGGTTTAGCCT 59.859 52.381 12.04 0.00 32.29 4.58
38 39 0.828677 TAAGCCGAGGGTTTAGCCTC 59.171 55.000 16.21 16.21 37.08 4.70
39 40 1.911702 AAGCCGAGGGTTTAGCCTCC 61.912 60.000 19.35 8.75 37.43 4.30
40 41 2.368011 GCCGAGGGTTTAGCCTCCT 61.368 63.158 19.35 0.00 37.43 3.69
41 42 1.911702 GCCGAGGGTTTAGCCTCCTT 61.912 60.000 19.35 0.00 37.43 3.36
42 43 0.618981 CCGAGGGTTTAGCCTCCTTT 59.381 55.000 19.35 0.00 37.43 3.11
43 44 1.835531 CCGAGGGTTTAGCCTCCTTTA 59.164 52.381 19.35 0.00 37.43 1.85
44 45 2.419713 CCGAGGGTTTAGCCTCCTTTAC 60.420 54.545 19.35 0.00 37.43 2.01
49 50 6.458630 AGGGTTTAGCCTCCTTTACTAAAA 57.541 37.500 0.00 0.00 37.56 1.52
67 68 9.846248 TTACTAAAAACCTATGACTAAGTCGAC 57.154 33.333 7.70 7.70 34.95 4.20
69 70 9.236006 ACTAAAAACCTATGACTAAGTCGACTA 57.764 33.333 20.39 2.37 34.95 2.59
73 74 6.923928 ACCTATGACTAAGTCGACTACTTC 57.076 41.667 20.39 14.91 45.64 3.01
79 80 5.118642 ACTAAGTCGACTACTTCCACAAC 57.881 43.478 20.39 0.00 45.64 3.32
82 83 3.714391 AGTCGACTACTTCCACAACAAC 58.286 45.455 18.46 0.00 33.35 3.32
83 84 3.131577 AGTCGACTACTTCCACAACAACA 59.868 43.478 18.46 0.00 33.35 3.33
96 97 5.588648 TCCACAACAACACCTTAAAGAAGAG 59.411 40.000 0.00 0.00 34.25 2.85
119 120 1.089481 AACATCATCGCGCCATCGTT 61.089 50.000 0.00 0.00 38.14 3.85
121 122 2.246739 ATCATCGCGCCATCGTTGG 61.247 57.895 8.23 8.23 46.66 3.77
139 140 1.134699 TGGCAAATCTAGGCAGAGACG 60.135 52.381 0.00 0.00 36.56 4.18
144 145 3.724508 AATCTAGGCAGAGACGACATG 57.275 47.619 0.00 0.00 33.22 3.21
150 151 1.608025 GGCAGAGACGACATGGACAAA 60.608 52.381 0.00 0.00 0.00 2.83
151 152 2.350522 GCAGAGACGACATGGACAAAT 58.649 47.619 0.00 0.00 0.00 2.32
156 157 6.403636 GCAGAGACGACATGGACAAATATTTT 60.404 38.462 0.00 0.00 0.00 1.82
161 162 7.554118 AGACGACATGGACAAATATTTTCATCT 59.446 33.333 0.00 0.00 0.00 2.90
162 163 7.475015 ACGACATGGACAAATATTTTCATCTG 58.525 34.615 0.00 0.00 0.00 2.90
177 179 1.667724 CATCTGGTTGCCAAGATCGAC 59.332 52.381 0.00 0.00 30.80 4.20
185 187 2.789213 TGCCAAGATCGACCAATGAAA 58.211 42.857 0.00 0.00 0.00 2.69
186 188 3.153130 TGCCAAGATCGACCAATGAAAA 58.847 40.909 0.00 0.00 0.00 2.29
187 189 3.057596 TGCCAAGATCGACCAATGAAAAC 60.058 43.478 0.00 0.00 0.00 2.43
213 215 5.596845 ACACAACAACAAGTCAACAAAACT 58.403 33.333 0.00 0.00 0.00 2.66
264 266 3.689649 ACCATTCAGCTCGACCAATAAAC 59.310 43.478 0.00 0.00 0.00 2.01
268 270 1.076332 AGCTCGACCAATAAACGTGC 58.924 50.000 0.00 0.00 43.45 5.34
284 286 2.939756 ACGTGCGCCAAATACATTGATA 59.060 40.909 4.18 0.00 41.85 2.15
286 288 3.242576 CGTGCGCCAAATACATTGATACA 60.243 43.478 4.18 0.00 41.85 2.29
293 295 5.734220 GCCAAATACATTGATACACCTGCAG 60.734 44.000 6.78 6.78 41.85 4.41
295 297 6.263842 CCAAATACATTGATACACCTGCAGAT 59.736 38.462 17.39 0.00 41.85 2.90
296 298 6.872628 AATACATTGATACACCTGCAGATG 57.127 37.500 17.39 12.07 0.00 2.90
298 300 1.655484 TTGATACACCTGCAGATGCG 58.345 50.000 17.39 0.00 45.83 4.73
324 333 3.717294 GTGGGCATCGAGGGGTGT 61.717 66.667 0.00 0.00 0.00 4.16
327 336 2.125106 GGCATCGAGGGGTGTCAC 60.125 66.667 0.00 0.00 0.00 3.67
345 354 3.136123 CCCTGCCGCAATGACCAG 61.136 66.667 0.00 0.00 0.00 4.00
545 977 0.179018 AACCCTGCACAAGTCCTCAC 60.179 55.000 0.00 0.00 0.00 3.51
613 3319 5.250543 TCTCATCTAGACTAGAGCTAGCCAT 59.749 44.000 17.02 2.38 38.38 4.40
663 3809 5.405873 GCAATTTATAGCCCTTCGACTAGAC 59.594 44.000 0.00 0.00 0.00 2.59
669 3815 3.371965 AGCCCTTCGACTAGACCATTTA 58.628 45.455 0.00 0.00 0.00 1.40
670 3816 3.773119 AGCCCTTCGACTAGACCATTTAA 59.227 43.478 0.00 0.00 0.00 1.52
773 3924 8.577296 GTCCTTGGTCTAAAAGCTAAAGAAATT 58.423 33.333 0.00 0.00 0.00 1.82
792 3943 5.584551 AATTCTTAACTTCTCCTGGGTGT 57.415 39.130 0.00 0.00 0.00 4.16
849 4000 6.596888 ACTAGCACAGTAGATGAACGTAAGTA 59.403 38.462 0.00 0.00 44.01 2.24
871 4031 9.967346 AAGTATATATATATAGCTTGCACGGTG 57.033 33.333 11.94 3.15 0.00 4.94
878 4038 2.594303 CTTGCACGGTGGAAGCCA 60.594 61.111 25.80 5.45 38.90 4.75
1083 4249 1.741770 GAAGACGGTGGAGCGCAAT 60.742 57.895 11.47 0.00 0.00 3.56
1190 4358 4.447389 TGCACATGTTATATCGATTGACCG 59.553 41.667 1.71 0.00 0.00 4.79
1208 4376 7.561021 TTGACCGCATATGTATATGTGTTTT 57.439 32.000 18.77 7.50 45.25 2.43
1401 4577 2.280524 CGACAACCGAACTGGGCA 60.281 61.111 0.00 0.00 44.64 5.36
1472 4648 1.630126 ATCTTGGCTCCGGTCTGCAT 61.630 55.000 15.87 1.89 0.00 3.96
1638 4817 3.192922 GCTCGCGCCGTTAACCAT 61.193 61.111 0.00 0.00 0.00 3.55
1639 4818 2.746803 GCTCGCGCCGTTAACCATT 61.747 57.895 0.00 0.00 0.00 3.16
1736 4922 6.294010 CGATATCGATCTTGTAGGTTGGAGAA 60.294 42.308 20.50 0.00 43.02 2.87
1742 4928 3.135712 TCTTGTAGGTTGGAGAACAGCAA 59.864 43.478 0.00 0.00 33.27 3.91
2010 5202 1.334960 GCGGCATGCAATGGTATACAC 60.335 52.381 21.36 0.00 46.86 2.90
2188 5381 6.431198 TGTCTTACTTTTGGTGACTGTTTC 57.569 37.500 0.00 0.00 0.00 2.78
2265 5458 6.072119 CCCTAAGACGAAATATAAATTGGGGC 60.072 42.308 0.00 0.00 0.00 5.80
2278 5472 5.794767 AAATTGGGGCCCTAAAATTTGAT 57.205 34.783 26.05 2.96 32.48 2.57
2312 5506 4.848562 ATTCATGTGCCTGCTTGATATG 57.151 40.909 0.00 0.00 0.00 1.78
2325 5519 5.939447 TGCTTGATATGGATGGATGTGTTA 58.061 37.500 0.00 0.00 0.00 2.41
2330 5524 8.853077 TTGATATGGATGGATGTGTTATTCTC 57.147 34.615 0.00 0.00 0.00 2.87
2431 5731 1.552578 TTGTACTTCAGCGGGCTAGA 58.447 50.000 0.00 0.00 0.00 2.43
2435 5735 0.247736 ACTTCAGCGGGCTAGAGTTG 59.752 55.000 0.00 0.00 0.00 3.16
2441 5741 2.187163 GGGCTAGAGTTGGACCGC 59.813 66.667 0.00 0.00 0.00 5.68
2443 5743 2.707849 GGCTAGAGTTGGACCGCGA 61.708 63.158 8.23 0.00 0.00 5.87
2466 5766 2.756400 GTGGTGGTGGCCAGATCA 59.244 61.111 5.11 0.00 39.53 2.92
2493 5793 1.573857 GGATGGGGTTAGGGGAATTGT 59.426 52.381 0.00 0.00 0.00 2.71
2514 5814 0.951040 GGAAGCACGAGTGAGTTGGG 60.951 60.000 7.50 0.00 0.00 4.12
2729 6035 2.270986 GCAGCCAACCAACTCCAGG 61.271 63.158 0.00 0.00 0.00 4.45
2794 6100 8.697846 AATCAATTCAAGTATGCAATTCACTG 57.302 30.769 0.00 0.00 0.00 3.66
2795 6101 7.451501 TCAATTCAAGTATGCAATTCACTGA 57.548 32.000 0.00 0.00 0.00 3.41
2796 6102 7.307694 TCAATTCAAGTATGCAATTCACTGAC 58.692 34.615 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.998670 CTCGGCTTATGCATCAATCGAT 59.001 45.455 0.19 0.00 41.91 3.59
7 8 2.407090 CTCGGCTTATGCATCAATCGA 58.593 47.619 0.19 8.60 41.91 3.59
8 9 1.462283 CCTCGGCTTATGCATCAATCG 59.538 52.381 0.19 4.23 41.91 3.34
9 10 1.808945 CCCTCGGCTTATGCATCAATC 59.191 52.381 0.19 0.00 41.91 2.67
10 11 1.143684 ACCCTCGGCTTATGCATCAAT 59.856 47.619 0.19 0.00 41.91 2.57
11 12 0.546122 ACCCTCGGCTTATGCATCAA 59.454 50.000 0.19 0.00 41.91 2.57
12 13 0.546122 AACCCTCGGCTTATGCATCA 59.454 50.000 0.19 0.00 41.91 3.07
13 14 1.680338 AAACCCTCGGCTTATGCATC 58.320 50.000 0.19 0.00 41.91 3.91
14 15 2.851195 CTAAACCCTCGGCTTATGCAT 58.149 47.619 3.79 3.79 41.91 3.96
15 16 1.745827 GCTAAACCCTCGGCTTATGCA 60.746 52.381 2.72 0.00 41.91 3.96
16 17 0.945099 GCTAAACCCTCGGCTTATGC 59.055 55.000 0.00 0.00 38.76 3.14
17 18 1.141053 AGGCTAAACCCTCGGCTTATG 59.859 52.381 0.00 0.00 40.58 1.90
18 19 1.416772 GAGGCTAAACCCTCGGCTTAT 59.583 52.381 0.00 0.00 41.79 1.73
19 20 0.828677 GAGGCTAAACCCTCGGCTTA 59.171 55.000 0.00 0.00 41.79 3.09
20 21 1.602771 GAGGCTAAACCCTCGGCTT 59.397 57.895 0.00 0.00 41.79 4.35
21 22 3.310652 GAGGCTAAACCCTCGGCT 58.689 61.111 0.00 0.00 41.79 5.52
26 27 6.458630 TTTTAGTAAAGGAGGCTAAACCCT 57.541 37.500 0.00 0.00 40.58 4.34
27 28 6.071728 GGTTTTTAGTAAAGGAGGCTAAACCC 60.072 42.308 9.15 0.00 40.58 4.11
28 29 6.718454 AGGTTTTTAGTAAAGGAGGCTAAACC 59.282 38.462 11.45 11.45 35.31 3.27
29 30 7.756395 AGGTTTTTAGTAAAGGAGGCTAAAC 57.244 36.000 0.00 0.00 35.31 2.01
30 31 9.457436 CATAGGTTTTTAGTAAAGGAGGCTAAA 57.543 33.333 0.00 0.00 34.21 1.85
31 32 8.828751 TCATAGGTTTTTAGTAAAGGAGGCTAA 58.171 33.333 0.00 0.00 0.00 3.09
32 33 8.262933 GTCATAGGTTTTTAGTAAAGGAGGCTA 58.737 37.037 0.00 0.00 0.00 3.93
33 34 7.037514 AGTCATAGGTTTTTAGTAAAGGAGGCT 60.038 37.037 0.00 0.00 0.00 4.58
34 35 7.110810 AGTCATAGGTTTTTAGTAAAGGAGGC 58.889 38.462 0.00 0.00 0.00 4.70
41 42 9.846248 GTCGACTTAGTCATAGGTTTTTAGTAA 57.154 33.333 13.14 0.00 32.09 2.24
42 43 9.236006 AGTCGACTTAGTCATAGGTTTTTAGTA 57.764 33.333 13.58 0.00 32.09 1.82
43 44 8.120140 AGTCGACTTAGTCATAGGTTTTTAGT 57.880 34.615 13.58 0.00 32.09 2.24
44 45 9.500864 GTAGTCGACTTAGTCATAGGTTTTTAG 57.499 37.037 25.44 0.00 32.09 1.85
67 68 6.540914 TCTTTAAGGTGTTGTTGTGGAAGTAG 59.459 38.462 0.00 0.00 0.00 2.57
69 70 5.258051 TCTTTAAGGTGTTGTTGTGGAAGT 58.742 37.500 0.00 0.00 0.00 3.01
72 73 5.502079 TCTTCTTTAAGGTGTTGTTGTGGA 58.498 37.500 0.00 0.00 33.22 4.02
73 74 5.588648 TCTCTTCTTTAAGGTGTTGTTGTGG 59.411 40.000 0.00 0.00 33.22 4.17
79 80 7.496529 TGTTCATCTCTTCTTTAAGGTGTTG 57.503 36.000 0.00 0.00 33.22 3.33
82 83 7.912056 TGATGTTCATCTCTTCTTTAAGGTG 57.088 36.000 12.94 0.00 33.22 4.00
113 114 2.016318 TGCCTAGATTTGCCAACGATG 58.984 47.619 0.00 0.00 0.00 3.84
119 120 1.134699 CGTCTCTGCCTAGATTTGCCA 60.135 52.381 0.00 0.00 31.21 4.92
121 122 2.197577 GTCGTCTCTGCCTAGATTTGC 58.802 52.381 0.00 0.00 31.21 3.68
125 126 1.959985 CCATGTCGTCTCTGCCTAGAT 59.040 52.381 0.00 0.00 31.21 1.98
131 132 1.795768 TTTGTCCATGTCGTCTCTGC 58.204 50.000 0.00 0.00 0.00 4.26
139 140 7.775120 ACCAGATGAAAATATTTGTCCATGTC 58.225 34.615 0.39 0.00 0.00 3.06
144 145 5.812127 GGCAACCAGATGAAAATATTTGTCC 59.188 40.000 0.39 0.00 0.00 4.02
150 151 6.238842 CGATCTTGGCAACCAGATGAAAATAT 60.239 38.462 4.94 0.00 33.81 1.28
151 152 5.066375 CGATCTTGGCAACCAGATGAAAATA 59.934 40.000 4.94 0.00 33.81 1.40
156 157 1.554617 TCGATCTTGGCAACCAGATGA 59.445 47.619 4.94 0.00 33.81 2.92
161 162 0.109532 TTGGTCGATCTTGGCAACCA 59.890 50.000 2.40 2.40 38.20 3.67
162 163 1.133025 CATTGGTCGATCTTGGCAACC 59.867 52.381 0.00 0.00 0.00 3.77
177 179 4.692625 TGTTGTTGTGTTGGTTTTCATTGG 59.307 37.500 0.00 0.00 0.00 3.16
185 187 4.202161 TGTTGACTTGTTGTTGTGTTGGTT 60.202 37.500 0.00 0.00 0.00 3.67
186 188 3.319405 TGTTGACTTGTTGTTGTGTTGGT 59.681 39.130 0.00 0.00 0.00 3.67
187 189 3.906998 TGTTGACTTGTTGTTGTGTTGG 58.093 40.909 0.00 0.00 0.00 3.77
213 215 9.770097 TGAATTTGCATTGTTACCTTATTGAAA 57.230 25.926 0.00 0.00 0.00 2.69
264 266 2.473530 ATCAATGTATTTGGCGCACG 57.526 45.000 10.83 0.00 35.92 5.34
268 270 4.789481 GCAGGTGTATCAATGTATTTGGCG 60.789 45.833 0.00 0.00 35.92 5.69
286 288 4.039092 AAGGGCGCATCTGCAGGT 62.039 61.111 15.13 2.68 42.21 4.00
293 295 2.568090 CCACAACAAGGGCGCATC 59.432 61.111 10.83 0.00 0.00 3.91
311 320 2.125106 GGTGACACCCCTCGATGC 60.125 66.667 14.16 0.00 30.04 3.91
324 333 3.645660 TCATTGCGGCAGGGGTGA 61.646 61.111 1.67 4.21 0.00 4.02
327 336 4.738998 TGGTCATTGCGGCAGGGG 62.739 66.667 1.67 0.00 0.00 4.79
347 356 4.829518 GCGTTGGCGGCGAATTCC 62.830 66.667 12.98 1.84 38.78 3.01
358 373 0.030638 CAACCTGAACTTGGCGTTGG 59.969 55.000 0.00 0.00 35.56 3.77
361 376 1.528309 CCCAACCTGAACTTGGCGT 60.528 57.895 0.00 0.00 37.45 5.68
440 699 9.899226 GATGAGAATTAGCAAACCCAAATATAC 57.101 33.333 0.00 0.00 0.00 1.47
532 964 3.955771 TTTTTACGTGAGGACTTGTGC 57.044 42.857 0.00 0.00 0.00 4.57
541 973 7.802738 TCTACACCATTTGATTTTTACGTGAG 58.197 34.615 0.00 0.00 0.00 3.51
630 3775 3.681593 GGCTATAAATTGCCACCGGATA 58.318 45.455 9.46 0.00 45.97 2.59
643 3789 4.539726 TGGTCTAGTCGAAGGGCTATAAA 58.460 43.478 0.00 0.00 0.00 1.40
644 3790 4.174704 TGGTCTAGTCGAAGGGCTATAA 57.825 45.455 0.00 0.00 0.00 0.98
648 3794 1.867363 AATGGTCTAGTCGAAGGGCT 58.133 50.000 0.00 0.00 0.00 5.19
652 3798 6.395629 TGAGGTTTAAATGGTCTAGTCGAAG 58.604 40.000 0.00 0.00 0.00 3.79
656 3802 9.668497 AATAGTTGAGGTTTAAATGGTCTAGTC 57.332 33.333 0.00 0.00 0.00 2.59
694 3844 2.306847 AGTTTCAGCACCGTCCATTTT 58.693 42.857 0.00 0.00 0.00 1.82
773 3924 5.189145 GGAATACACCCAGGAGAAGTTAAGA 59.811 44.000 0.00 0.00 0.00 2.10
792 3943 3.193903 TCCGAGTCGTTTGATGTGGAATA 59.806 43.478 12.31 0.00 0.00 1.75
849 4000 7.597288 TCCACCGTGCAAGCTATATATATAT 57.403 36.000 10.10 10.10 0.00 0.86
870 4030 2.037902 TGTGATACTCGTTTGGCTTCCA 59.962 45.455 0.00 0.00 0.00 3.53
871 4031 2.415512 GTGTGATACTCGTTTGGCTTCC 59.584 50.000 0.00 0.00 0.00 3.46
878 4038 0.390735 GCCCGGTGTGATACTCGTTT 60.391 55.000 0.00 0.00 0.00 3.60
943 4103 1.265568 GGTCAGCGTGTATGTACGTG 58.734 55.000 0.00 0.00 45.36 4.49
1083 4249 2.032634 GTTCATCTGGTTGCGGCGA 61.033 57.895 12.98 0.00 0.00 5.54
1174 4342 6.887376 ACATATGCGGTCAATCGATATAAC 57.113 37.500 1.58 0.00 0.00 1.89
1401 4577 1.613630 ATGAGGAACCAGAGCCGGT 60.614 57.895 1.90 0.00 42.71 5.28
1437 4613 1.293062 AGATGCTGAACCTCCACCAT 58.707 50.000 0.00 0.00 0.00 3.55
1736 4922 1.744368 CTCGATGCTGCCTTGCTGT 60.744 57.895 0.00 0.00 0.00 4.40
1742 4928 2.364842 ACCCTCTCGATGCTGCCT 60.365 61.111 0.00 0.00 0.00 4.75
2010 5202 4.445385 GGTTTTGTAGCACATTTTGAGCTG 59.555 41.667 9.28 0.00 43.86 4.24
2024 5216 3.877508 GCATAGGGCTACTGGTTTTGTAG 59.122 47.826 0.00 0.00 40.05 2.74
2188 5381 0.907837 CTGCAACACGTCGTAGATCG 59.092 55.000 0.00 0.00 40.67 3.69
2265 5458 7.843490 TTAGTCGACTCATCAAATTTTAGGG 57.157 36.000 23.89 0.00 0.00 3.53
2278 5472 4.391830 GGCACATGAATTTTAGTCGACTCA 59.608 41.667 23.89 13.44 0.00 3.41
2312 5506 4.058817 GGACGAGAATAACACATCCATCC 58.941 47.826 0.00 0.00 0.00 3.51
2325 5519 0.107945 GGCTGCTCAAGGACGAGAAT 60.108 55.000 0.00 0.00 34.79 2.40
2330 5524 1.302033 ACTTGGCTGCTCAAGGACG 60.302 57.895 24.58 9.56 46.04 4.79
2431 5731 2.342648 GGTCTTCGCGGTCCAACT 59.657 61.111 6.13 0.00 0.00 3.16
2466 5766 0.403453 CCTAACCCCATCCCCATCCT 60.403 60.000 0.00 0.00 0.00 3.24
2493 5793 1.581934 CAACTCACTCGTGCTTCCAA 58.418 50.000 0.00 0.00 0.00 3.53
2529 5830 3.243941 CCCCTTAAAAACCCTCAAAACCG 60.244 47.826 0.00 0.00 0.00 4.44
2677 5983 6.976349 TCTGCTTGTAAGTATGTACATAACGG 59.024 38.462 17.07 9.82 34.05 4.44
2678 5984 7.701078 ACTCTGCTTGTAAGTATGTACATAACG 59.299 37.037 17.07 0.92 34.05 3.18
2716 6022 2.880890 CAGAGAAACCTGGAGTTGGTTG 59.119 50.000 0.00 0.00 45.99 3.77


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

AutoCloner maintained by Alex Coulton.