Multiple sequence alignment - TraesCS5B01G408600

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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 TraesCS5B01G408600 chr5B 100.000 2863 0 0 1 2863 584112690 584115552 0 5288
1 TraesCS5B01G408600 chr5D 89.163 2713 160 66 198 2841 476695943 476698590 0 3258
2 TraesCS5B01G408600 chr5A 88.916 1624 95 36 1283 2863 596020079 596021660 0 1923
3 TraesCS5B01G408600 chr5A 87.469 1221 78 42 11 1176 596018752 596019952 0 1338


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 TraesCS5B01G408600 chr5B 584112690 584115552 2862 False 5288.0 5288 100.0000 1 2863 1 chr5B.!!$F1 2862
1 TraesCS5B01G408600 chr5D 476695943 476698590 2647 False 3258.0 3258 89.1630 198 2841 1 chr5D.!!$F1 2643
2 TraesCS5B01G408600 chr5A 596018752 596021660 2908 False 1630.5 1923 88.1925 11 2863 2 chr5A.!!$F1 2852

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
655 716 0.107831 AGAGAGATCGAGACCGGGAG 59.892 60.0 6.32 0.0 36.24 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 2802 1.138266 GCAAAGCTATCCACGGGTAGA 59.862 52.381 7.59 0.0 0.0 2.59 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
49 53 1.195674 GGAAAGAGTTCAAGCGCTGAC 59.804 52.381 12.58 10.91 35.25 3.51
50 54 1.195674 GAAAGAGTTCAAGCGCTGACC 59.804 52.381 12.58 3.23 32.21 4.02
54 58 1.204312 GTTCAAGCGCTGACCGAAC 59.796 57.895 12.58 17.53 40.02 3.95
55 59 1.069090 TTCAAGCGCTGACCGAACT 59.931 52.632 12.58 0.00 40.02 3.01
58 62 2.867855 AAGCGCTGACCGAACTGGA 61.868 57.895 12.58 0.00 42.00 3.86
59 63 2.771763 AAGCGCTGACCGAACTGGAG 62.772 60.000 12.58 0.00 42.00 3.86
60 64 2.962569 CGCTGACCGAACTGGAGA 59.037 61.111 0.00 0.00 42.00 3.71
61 65 1.289066 CGCTGACCGAACTGGAGAA 59.711 57.895 0.00 0.00 42.00 2.87
62 66 0.108615 CGCTGACCGAACTGGAGAAT 60.109 55.000 0.00 0.00 42.00 2.40
63 67 1.363744 GCTGACCGAACTGGAGAATG 58.636 55.000 0.00 0.00 42.00 2.67
64 68 2.009042 GCTGACCGAACTGGAGAATGG 61.009 57.143 0.00 0.00 42.00 3.16
65 69 0.613260 TGACCGAACTGGAGAATGGG 59.387 55.000 0.00 0.00 42.00 4.00
66 70 0.744771 GACCGAACTGGAGAATGGGC 60.745 60.000 0.00 0.00 42.00 5.36
88 92 5.088739 GCACCATTTCTAGATTGACGTTTG 58.911 41.667 0.00 0.00 0.00 2.93
95 99 2.270352 AGATTGACGTTTGGGCTGAA 57.730 45.000 0.00 0.00 0.00 3.02
101 105 2.357637 TGACGTTTGGGCTGAAGAAAAG 59.642 45.455 0.00 0.00 0.00 2.27
102 106 1.067060 ACGTTTGGGCTGAAGAAAAGC 59.933 47.619 0.00 0.00 40.06 3.51
103 107 1.338020 CGTTTGGGCTGAAGAAAAGCT 59.662 47.619 0.00 0.00 40.64 3.74
105 109 2.071778 TTGGGCTGAAGAAAAGCTGT 57.928 45.000 0.00 0.00 40.64 4.40
107 111 3.222173 TGGGCTGAAGAAAAGCTGTAA 57.778 42.857 0.00 0.00 40.64 2.41
108 112 2.884639 TGGGCTGAAGAAAAGCTGTAAC 59.115 45.455 0.00 0.00 40.64 2.50
109 113 2.229062 GGGCTGAAGAAAAGCTGTAACC 59.771 50.000 0.00 0.00 40.64 2.85
110 114 2.095718 GGCTGAAGAAAAGCTGTAACCG 60.096 50.000 0.00 0.00 40.64 4.44
111 115 2.548480 GCTGAAGAAAAGCTGTAACCGT 59.452 45.455 0.00 0.00 37.69 4.83
112 116 3.003378 GCTGAAGAAAAGCTGTAACCGTT 59.997 43.478 0.00 0.00 37.69 4.44
113 117 4.497507 GCTGAAGAAAAGCTGTAACCGTTT 60.498 41.667 0.00 0.00 37.69 3.60
114 118 5.570234 TGAAGAAAAGCTGTAACCGTTTT 57.430 34.783 0.00 0.00 0.00 2.43
117 121 5.169836 AGAAAAGCTGTAACCGTTTTCTG 57.830 39.130 7.85 0.00 43.99 3.02
124 128 5.124936 AGCTGTAACCGTTTTCTGTCTTTTT 59.875 36.000 0.00 0.00 0.00 1.94
271 279 2.494870 GGCAAAGCACATCATTCTTCCT 59.505 45.455 0.00 0.00 0.00 3.36
288 296 0.179936 CCTCTCAAGGCTGTCATCCC 59.820 60.000 0.00 0.00 35.37 3.85
308 317 4.013050 CCCATCCTCTGTCCTTTTTCTTC 58.987 47.826 0.00 0.00 0.00 2.87
361 373 3.325293 TCTCCACTCTCATCAACTTGC 57.675 47.619 0.00 0.00 0.00 4.01
379 395 0.109272 GCTCGAACAGTGACCGATCA 60.109 55.000 10.83 0.00 0.00 2.92
381 397 2.881074 CTCGAACAGTGACCGATCATT 58.119 47.619 10.83 0.00 37.14 2.57
460 478 2.208619 TCACCGCCCCTTGTTACGA 61.209 57.895 0.00 0.00 0.00 3.43
461 479 2.030958 CACCGCCCCTTGTTACGAC 61.031 63.158 0.00 0.00 0.00 4.34
462 480 2.435410 CCGCCCCTTGTTACGACC 60.435 66.667 0.00 0.00 0.00 4.79
463 481 2.812178 CGCCCCTTGTTACGACCG 60.812 66.667 0.00 0.00 0.00 4.79
464 482 2.344872 GCCCCTTGTTACGACCGT 59.655 61.111 0.00 0.00 0.00 4.83
465 483 1.739196 GCCCCTTGTTACGACCGTC 60.739 63.158 0.00 0.00 0.00 4.79
466 484 1.444895 CCCCTTGTTACGACCGTCG 60.445 63.158 19.24 19.24 46.93 5.12
553 572 3.991999 CGTCTCCCCACGTCTACA 58.008 61.111 0.00 0.00 34.95 2.74
554 573 2.490165 CGTCTCCCCACGTCTACAT 58.510 57.895 0.00 0.00 34.95 2.29
555 574 0.815734 CGTCTCCCCACGTCTACATT 59.184 55.000 0.00 0.00 34.95 2.71
556 575 1.469251 CGTCTCCCCACGTCTACATTG 60.469 57.143 0.00 0.00 34.95 2.82
557 576 0.535335 TCTCCCCACGTCTACATTGC 59.465 55.000 0.00 0.00 0.00 3.56
558 577 0.249120 CTCCCCACGTCTACATTGCA 59.751 55.000 0.00 0.00 0.00 4.08
559 578 0.249120 TCCCCACGTCTACATTGCAG 59.751 55.000 0.00 0.00 0.00 4.41
584 645 2.594962 CGTGATCGGCGGCCAATAC 61.595 63.158 20.71 10.79 0.00 1.89
655 716 0.107831 AGAGAGATCGAGACCGGGAG 59.892 60.000 6.32 0.00 36.24 4.30
691 752 3.679980 CGATCAAAAGGCTCTCGAGAAAA 59.320 43.478 17.36 0.00 0.00 2.29
857 926 6.760466 TCATCATTCCCTCCATATATCTCCT 58.240 40.000 0.00 0.00 0.00 3.69
999 1072 3.345808 GCGCGTTGCTTCCAGTGA 61.346 61.111 8.43 0.00 41.73 3.41
1012 1085 1.889105 CAGTGAATGGATCGCGGGG 60.889 63.158 6.13 0.00 43.53 5.73
1191 1336 4.938080 TCTCTCTGATCTTCGGTTTATGC 58.062 43.478 0.00 0.00 0.00 3.14
1203 1348 2.684881 CGGTTTATGCTTCAGCCTTCAT 59.315 45.455 0.00 0.00 41.18 2.57
1267 1412 9.253275 GAAACATTTGAAAATGAATTACATGCG 57.747 29.630 19.85 0.00 46.72 4.73
1273 1425 9.549509 TTTGAAAATGAATTACATGCGTAGTAC 57.450 29.630 0.00 0.00 39.39 2.73
1274 1426 7.395645 TGAAAATGAATTACATGCGTAGTACG 58.604 34.615 18.37 18.37 40.62 3.67
1275 1427 6.897259 AAATGAATTACATGCGTAGTACGT 57.103 33.333 22.81 6.66 40.13 3.57
1276 1428 7.990541 AAATGAATTACATGCGTAGTACGTA 57.009 32.000 22.81 19.50 40.13 3.57
1277 1429 6.981379 ATGAATTACATGCGTAGTACGTAC 57.019 37.500 22.81 18.10 44.73 3.67
1278 1430 6.122850 TGAATTACATGCGTAGTACGTACT 57.877 37.500 29.62 29.62 44.73 2.73
1279 1431 7.245419 TGAATTACATGCGTAGTACGTACTA 57.755 36.000 27.51 27.51 44.73 1.82
1280 1432 7.864686 TGAATTACATGCGTAGTACGTACTAT 58.135 34.615 32.03 20.08 44.73 2.12
1281 1433 7.799914 TGAATTACATGCGTAGTACGTACTATG 59.200 37.037 35.25 35.25 44.73 2.23
1325 1477 6.015856 AGACATGGAAATATAGACCTCTCGTG 60.016 42.308 0.00 0.00 0.00 4.35
1409 1561 9.436957 TGAAGACTATCATTTGTTCTAAACTCC 57.563 33.333 0.00 0.00 0.00 3.85
1411 1563 7.612677 AGACTATCATTTGTTCTAAACTCCGT 58.387 34.615 0.00 0.00 0.00 4.69
1580 1732 0.248289 ATGTACCACACCACGTAGCC 59.752 55.000 0.00 0.00 0.00 3.93
1841 1996 0.247736 CGTCCTCCCTCTTCAACCTG 59.752 60.000 0.00 0.00 0.00 4.00
1882 2047 4.077184 GTGGGTGGTCGCCGATGA 62.077 66.667 0.00 0.00 0.00 2.92
1885 2050 3.771160 GGTGGTCGCCGATGAGGT 61.771 66.667 0.00 0.00 43.70 3.85
1900 2065 2.574399 GGTCGCCAGACTCTGACC 59.426 66.667 7.69 3.81 46.29 4.02
1906 2071 1.979155 CCAGACTCTGACCCGCTGA 60.979 63.158 7.69 0.00 32.44 4.26
1916 2081 0.809241 GACCCGCTGAAGCATCTCTG 60.809 60.000 2.79 0.00 42.21 3.35
1924 2091 4.208873 CGCTGAAGCATCTCTGAATTCTAC 59.791 45.833 7.05 0.00 42.21 2.59
1933 2100 9.532494 AGCATCTCTGAATTCTACTCTGTATAT 57.468 33.333 7.05 0.00 0.00 0.86
1962 2129 7.827729 GGAAGGAAGGTTTTGTATGTGTATAGT 59.172 37.037 0.00 0.00 0.00 2.12
1963 2130 9.880157 GAAGGAAGGTTTTGTATGTGTATAGTA 57.120 33.333 0.00 0.00 0.00 1.82
1964 2131 9.886132 AAGGAAGGTTTTGTATGTGTATAGTAG 57.114 33.333 0.00 0.00 0.00 2.57
1965 2132 7.985752 AGGAAGGTTTTGTATGTGTATAGTAGC 59.014 37.037 0.00 0.00 0.00 3.58
1966 2133 7.985752 GGAAGGTTTTGTATGTGTATAGTAGCT 59.014 37.037 0.00 0.00 0.00 3.32
1967 2134 8.718102 AAGGTTTTGTATGTGTATAGTAGCTG 57.282 34.615 0.00 0.00 0.00 4.24
1968 2135 7.272978 AGGTTTTGTATGTGTATAGTAGCTGG 58.727 38.462 0.00 0.00 0.00 4.85
1969 2136 7.125204 AGGTTTTGTATGTGTATAGTAGCTGGA 59.875 37.037 0.00 0.00 0.00 3.86
1970 2137 7.767198 GGTTTTGTATGTGTATAGTAGCTGGAA 59.233 37.037 0.00 0.00 0.00 3.53
1984 2151 4.388577 AGCTGGAAGGAAGGTTTTGTAT 57.611 40.909 0.00 0.00 0.00 2.29
2005 2176 6.889177 TGTATTCAGATTTCATAAACCTGCCA 59.111 34.615 0.00 0.00 0.00 4.92
2052 2224 2.799126 TGGATGCCGAACTGGTAAAT 57.201 45.000 0.00 0.00 41.21 1.40
2110 2282 5.858381 TCAGCTCTTTGCATAATAGGGTAG 58.142 41.667 0.00 0.00 45.94 3.18
2143 2317 4.761975 TGTTTTCGTTTCTGGTCAGTACT 58.238 39.130 0.00 0.00 0.00 2.73
2212 2390 1.661112 GCTGCTGAAGACGGAACATAC 59.339 52.381 0.00 0.00 0.00 2.39
2253 2435 5.157781 GGATGTTATGTTTTTGTAGCGCAA 58.842 37.500 11.47 0.00 34.87 4.85
2254 2436 5.804979 GGATGTTATGTTTTTGTAGCGCAAT 59.195 36.000 11.47 0.00 36.89 3.56
2255 2437 6.020678 GGATGTTATGTTTTTGTAGCGCAATC 60.021 38.462 11.47 0.00 36.89 2.67
2279 2462 4.806640 TTTCATTTTCTGAGGGAATGGC 57.193 40.909 8.21 0.00 34.68 4.40
2324 2507 2.037902 TCGGTGCAAAGTAGACATTCCA 59.962 45.455 0.00 0.00 0.00 3.53
2331 2514 4.635765 GCAAAGTAGACATTCCAGCATGTA 59.364 41.667 0.00 0.00 37.52 2.29
2334 2517 5.016051 AGTAGACATTCCAGCATGTACAG 57.984 43.478 0.33 0.00 37.52 2.74
2361 2544 4.550422 GCTATCTTAGCGATGTCACATCA 58.450 43.478 18.05 0.00 42.62 3.07
2390 2573 5.215252 TGTTGAGGTGTAGGAAAGAGAAG 57.785 43.478 0.00 0.00 0.00 2.85
2427 2629 7.309194 GCCTTTGCCTTCTCTTAAGAACAAATA 60.309 37.037 6.63 0.00 37.11 1.40
2478 2680 9.401058 AGATAAGATTAAGAGAACAACCATTGG 57.599 33.333 0.00 0.00 34.12 3.16
2489 2691 2.498481 ACAACCATTGGGCATCATCTTG 59.502 45.455 7.78 2.50 37.90 3.02
2516 2719 6.399743 TGTTATTTCTAGATTACGTGGCACA 58.600 36.000 19.09 0.00 0.00 4.57
2599 2802 1.637553 ACCAAGCTCATCTTCCACCAT 59.362 47.619 0.00 0.00 31.27 3.55
2606 2809 2.036475 CTCATCTTCCACCATCTACCCG 59.964 54.545 0.00 0.00 0.00 5.28
2647 2850 3.424962 GCTGACAACTAGTTCCGCAATTC 60.425 47.826 4.77 0.00 0.00 2.17
2858 3065 8.650143 ATTTGTGACCCAGATACTGTAAAAAT 57.350 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.884472 TCCTCTATTGGAATTACAGACCAA 57.116 37.500 0.00 0.00 45.64 3.67
9 10 6.884472 TTCCTCTATTGGAATTACAGACCA 57.116 37.500 0.00 0.00 40.80 4.02
12 13 8.380742 ACTCTTTCCTCTATTGGAATTACAGA 57.619 34.615 0.00 0.00 44.55 3.41
25 26 2.563179 AGCGCTTGAACTCTTTCCTCTA 59.437 45.455 2.64 0.00 0.00 2.43
26 27 1.346068 AGCGCTTGAACTCTTTCCTCT 59.654 47.619 2.64 0.00 0.00 3.69
36 37 1.204312 GTTCGGTCAGCGCTTGAAC 59.796 57.895 7.50 15.85 40.28 3.18
49 53 1.026718 GTGCCCATTCTCCAGTTCGG 61.027 60.000 0.00 0.00 0.00 4.30
50 54 1.026718 GGTGCCCATTCTCCAGTTCG 61.027 60.000 0.00 0.00 0.00 3.95
62 66 3.620488 GTCAATCTAGAAATGGTGCCCA 58.380 45.455 0.00 0.00 38.19 5.36
63 67 2.614057 CGTCAATCTAGAAATGGTGCCC 59.386 50.000 0.00 0.00 0.00 5.36
64 68 3.270877 ACGTCAATCTAGAAATGGTGCC 58.729 45.455 0.00 0.00 0.00 5.01
65 69 4.946784 AACGTCAATCTAGAAATGGTGC 57.053 40.909 0.00 0.00 0.00 5.01
66 70 5.391950 CCCAAACGTCAATCTAGAAATGGTG 60.392 44.000 0.00 0.00 0.00 4.17
88 92 2.229062 GGTTACAGCTTTTCTTCAGCCC 59.771 50.000 0.00 0.00 38.09 5.19
95 99 4.638865 ACAGAAAACGGTTACAGCTTTTCT 59.361 37.500 14.34 14.34 41.50 2.52
101 105 4.547406 AAAGACAGAAAACGGTTACAGC 57.453 40.909 0.00 0.00 0.00 4.40
124 128 5.317733 ACGTTCACAATTTGTTCAGGAAA 57.682 34.783 0.00 0.00 0.00 3.13
125 129 4.974368 ACGTTCACAATTTGTTCAGGAA 57.026 36.364 0.00 0.00 0.00 3.36
127 131 4.862018 ACAAACGTTCACAATTTGTTCAGG 59.138 37.500 0.00 0.00 42.43 3.86
128 132 5.799936 AGACAAACGTTCACAATTTGTTCAG 59.200 36.000 0.00 0.00 44.45 3.02
129 133 5.570973 CAGACAAACGTTCACAATTTGTTCA 59.429 36.000 0.00 0.00 44.45 3.18
130 134 5.571357 ACAGACAAACGTTCACAATTTGTTC 59.429 36.000 0.00 0.00 44.45 3.18
131 135 5.465935 ACAGACAAACGTTCACAATTTGTT 58.534 33.333 0.00 0.00 44.45 2.83
132 136 5.054390 ACAGACAAACGTTCACAATTTGT 57.946 34.783 0.00 0.00 46.48 2.83
133 137 5.331902 AGACAGACAAACGTTCACAATTTG 58.668 37.500 0.00 0.00 38.89 2.32
134 138 5.560966 AGACAGACAAACGTTCACAATTT 57.439 34.783 0.00 0.00 0.00 1.82
135 139 5.560966 AAGACAGACAAACGTTCACAATT 57.439 34.783 0.00 0.00 0.00 2.32
136 140 5.560966 AAAGACAGACAAACGTTCACAAT 57.439 34.783 0.00 0.00 0.00 2.71
137 141 5.365403 AAAAGACAGACAAACGTTCACAA 57.635 34.783 0.00 0.00 0.00 3.33
250 255 2.494870 AGGAAGAATGATGTGCTTTGCC 59.505 45.455 0.00 0.00 0.00 4.52
260 268 3.522750 ACAGCCTTGAGAGGAAGAATGAT 59.477 43.478 0.00 0.00 46.74 2.45
261 269 2.909006 ACAGCCTTGAGAGGAAGAATGA 59.091 45.455 0.00 0.00 46.74 2.57
262 270 3.269178 GACAGCCTTGAGAGGAAGAATG 58.731 50.000 0.00 0.00 46.74 2.67
271 279 1.487976 GATGGGATGACAGCCTTGAGA 59.512 52.381 10.08 0.00 0.00 3.27
288 296 4.655963 TGGAAGAAAAAGGACAGAGGATG 58.344 43.478 0.00 0.00 0.00 3.51
308 317 4.083110 GCAATGGAATCCGACAATATCTGG 60.083 45.833 0.00 0.00 0.00 3.86
361 373 2.568696 ATGATCGGTCACTGTTCGAG 57.431 50.000 0.00 0.00 37.14 4.04
379 395 0.767375 ACAGTGCCAGTGGTCTGAAT 59.233 50.000 29.53 14.61 43.76 2.57
381 397 1.447217 CACAGTGCCAGTGGTCTGA 59.553 57.895 29.53 6.01 43.76 3.27
445 463 2.435410 GGTCGTAACAAGGGGCGG 60.435 66.667 0.00 0.00 0.00 6.13
460 478 1.093159 GAGTATGACTGGTCGACGGT 58.907 55.000 9.92 10.90 42.79 4.83
461 479 1.092348 TGAGTATGACTGGTCGACGG 58.908 55.000 9.92 7.53 0.00 4.79
462 480 4.666908 CGATATGAGTATGACTGGTCGACG 60.667 50.000 9.92 0.00 0.00 5.12
463 481 4.713806 CGATATGAGTATGACTGGTCGAC 58.286 47.826 7.13 7.13 0.00 4.20
464 482 3.188667 GCGATATGAGTATGACTGGTCGA 59.811 47.826 0.00 0.00 0.00 4.20
465 483 3.493272 GCGATATGAGTATGACTGGTCG 58.507 50.000 0.00 0.00 0.00 4.79
466 484 3.670895 CGGCGATATGAGTATGACTGGTC 60.671 52.174 0.00 0.00 0.00 4.02
545 564 0.108804 CGTCCCTGCAATGTAGACGT 60.109 55.000 0.00 0.00 43.89 4.34
546 565 2.665777 CGTCCCTGCAATGTAGACG 58.334 57.895 0.00 0.00 43.52 4.18
547 566 1.641577 GACGTCCCTGCAATGTAGAC 58.358 55.000 3.51 0.00 0.00 2.59
548 567 0.172578 CGACGTCCCTGCAATGTAGA 59.827 55.000 10.58 0.00 0.00 2.59
549 568 0.108804 ACGACGTCCCTGCAATGTAG 60.109 55.000 10.58 0.00 0.00 2.74
550 569 0.389296 CACGACGTCCCTGCAATGTA 60.389 55.000 10.58 0.00 0.00 2.29
551 570 1.667830 CACGACGTCCCTGCAATGT 60.668 57.895 10.58 0.00 0.00 2.71
552 571 0.740868 ATCACGACGTCCCTGCAATG 60.741 55.000 10.58 0.00 0.00 2.82
553 572 0.460284 GATCACGACGTCCCTGCAAT 60.460 55.000 10.58 0.00 0.00 3.56
554 573 1.080093 GATCACGACGTCCCTGCAA 60.080 57.895 10.58 0.00 0.00 4.08
555 574 2.571757 GATCACGACGTCCCTGCA 59.428 61.111 10.58 0.00 0.00 4.41
556 575 2.579787 CGATCACGACGTCCCTGC 60.580 66.667 10.58 0.00 42.66 4.85
557 576 2.102357 CCGATCACGACGTCCCTG 59.898 66.667 10.58 5.75 42.66 4.45
558 577 3.823330 GCCGATCACGACGTCCCT 61.823 66.667 10.58 0.00 42.66 4.20
584 645 1.196127 TGTACACGACACTGCGTAGAG 59.804 52.381 7.78 0.99 43.59 2.43
691 752 3.486383 CTCTTCCTCTAGATTCTCCGCT 58.514 50.000 0.00 0.00 0.00 5.52
946 1015 4.054825 CCATGCGCGCCCAAAACT 62.055 61.111 30.77 0.88 0.00 2.66
1092 1165 0.647410 CGACGGACATGAACATGAGC 59.353 55.000 19.56 11.32 41.20 4.26
1191 1336 0.609957 TGCACCCATGAAGGCTGAAG 60.610 55.000 0.00 0.00 35.39 3.02
1203 1348 3.159615 TGCTGATCACTGCACCCA 58.840 55.556 5.58 0.00 43.83 4.51
1273 1425 6.579292 CGGAGAAAGAAAGATAGCATAGTACG 59.421 42.308 0.00 0.00 0.00 3.67
1274 1426 7.649973 TCGGAGAAAGAAAGATAGCATAGTAC 58.350 38.462 0.00 0.00 0.00 2.73
1275 1427 7.818997 TCGGAGAAAGAAAGATAGCATAGTA 57.181 36.000 0.00 0.00 0.00 1.82
1276 1428 6.716934 TCGGAGAAAGAAAGATAGCATAGT 57.283 37.500 0.00 0.00 0.00 2.12
1277 1429 7.381139 GTCTTCGGAGAAAGAAAGATAGCATAG 59.619 40.741 0.00 0.00 45.90 2.23
1278 1430 7.147897 TGTCTTCGGAGAAAGAAAGATAGCATA 60.148 37.037 0.00 0.00 45.90 3.14
1279 1431 6.045955 GTCTTCGGAGAAAGAAAGATAGCAT 58.954 40.000 0.00 0.00 45.90 3.79
1280 1432 5.047306 TGTCTTCGGAGAAAGAAAGATAGCA 60.047 40.000 0.00 0.00 45.90 3.49
1281 1433 5.411781 TGTCTTCGGAGAAAGAAAGATAGC 58.588 41.667 0.00 0.00 45.90 2.97
1388 1540 6.092259 GCACGGAGTTTAGAACAAATGATAGT 59.908 38.462 0.00 0.00 41.61 2.12
1391 1543 4.759693 TGCACGGAGTTTAGAACAAATGAT 59.240 37.500 0.00 0.00 41.61 2.45
1394 1546 5.508200 TTTGCACGGAGTTTAGAACAAAT 57.492 34.783 0.00 0.00 41.61 2.32
1403 1555 1.537990 GCCATGTTTTGCACGGAGTTT 60.538 47.619 0.00 0.00 41.61 2.66
1409 1561 0.598158 AAGCTGCCATGTTTTGCACG 60.598 50.000 0.00 0.00 33.17 5.34
1411 1563 0.033781 GGAAGCTGCCATGTTTTGCA 59.966 50.000 5.59 0.00 35.86 4.08
1580 1732 2.303549 GACACGAGGGGGAGATGCTG 62.304 65.000 0.00 0.00 0.00 4.41
1841 1996 1.144057 CCTGGAGGCGATGTACCAC 59.856 63.158 0.00 0.00 0.00 4.16
1865 2020 4.077184 TCATCGGCGACCACCCAC 62.077 66.667 13.76 0.00 0.00 4.61
1866 2021 3.770040 CTCATCGGCGACCACCCA 61.770 66.667 13.76 0.00 0.00 4.51
1882 2047 1.979693 GGTCAGAGTCTGGCGACCT 60.980 63.158 19.99 1.82 43.79 3.85
1885 2050 3.062466 CGGGTCAGAGTCTGGCGA 61.062 66.667 19.99 0.00 36.90 5.54
1900 2065 1.950828 ATTCAGAGATGCTTCAGCGG 58.049 50.000 2.07 0.00 45.83 5.52
1906 2071 6.543430 ACAGAGTAGAATTCAGAGATGCTT 57.457 37.500 8.44 0.00 0.00 3.91
1916 2081 9.303116 TCCTTCCAGATATACAGAGTAGAATTC 57.697 37.037 0.00 0.00 0.00 2.17
1924 2091 6.739331 AACCTTCCTTCCAGATATACAGAG 57.261 41.667 0.00 0.00 0.00 3.35
1933 2100 5.070001 CACATACAAAACCTTCCTTCCAGA 58.930 41.667 0.00 0.00 0.00 3.86
1962 2129 3.876309 ACAAAACCTTCCTTCCAGCTA 57.124 42.857 0.00 0.00 0.00 3.32
1963 2130 2.755952 ACAAAACCTTCCTTCCAGCT 57.244 45.000 0.00 0.00 0.00 4.24
1964 2131 4.522789 TGAATACAAAACCTTCCTTCCAGC 59.477 41.667 0.00 0.00 0.00 4.85
1965 2132 6.003950 TCTGAATACAAAACCTTCCTTCCAG 58.996 40.000 0.00 0.00 0.00 3.86
1966 2133 5.947663 TCTGAATACAAAACCTTCCTTCCA 58.052 37.500 0.00 0.00 0.00 3.53
1967 2134 7.468141 AATCTGAATACAAAACCTTCCTTCC 57.532 36.000 0.00 0.00 0.00 3.46
1968 2135 8.576442 TGAAATCTGAATACAAAACCTTCCTTC 58.424 33.333 0.00 0.00 0.00 3.46
1969 2136 8.477419 TGAAATCTGAATACAAAACCTTCCTT 57.523 30.769 0.00 0.00 0.00 3.36
1970 2137 8.655935 ATGAAATCTGAATACAAAACCTTCCT 57.344 30.769 0.00 0.00 0.00 3.36
2212 2390 2.860009 TCCATCAGCCTACTACCTACG 58.140 52.381 0.00 0.00 0.00 3.51
2253 2435 7.618137 CCATTCCCTCAGAAAATGAAAAAGAT 58.382 34.615 1.62 0.00 38.21 2.40
2254 2436 6.518875 GCCATTCCCTCAGAAAATGAAAAAGA 60.519 38.462 1.62 0.00 38.21 2.52
2255 2437 5.640783 GCCATTCCCTCAGAAAATGAAAAAG 59.359 40.000 1.62 0.00 38.21 2.27
2351 2534 5.182570 CCTCAACATTTGTCTGATGTGACAT 59.817 40.000 0.00 0.00 45.03 3.06
2358 2541 5.013079 TCCTACACCTCAACATTTGTCTGAT 59.987 40.000 0.00 0.00 0.00 2.90
2361 2544 4.974645 TCCTACACCTCAACATTTGTCT 57.025 40.909 0.00 0.00 0.00 3.41
2390 2573 2.648318 GCAAAGGCTTTTCGCGTGC 61.648 57.895 10.36 6.67 40.44 5.34
2427 2629 7.458397 TCTAGTTCATAAAAATGTGGTGAGGT 58.542 34.615 0.00 0.00 0.00 3.85
2468 2670 2.498481 CAAGATGATGCCCAATGGTTGT 59.502 45.455 0.00 0.00 0.00 3.32
2471 2673 2.537633 ACAAGATGATGCCCAATGGT 57.462 45.000 0.00 0.00 0.00 3.55
2478 2680 8.677300 TCTAGAAATAACAAACAAGATGATGCC 58.323 33.333 0.00 0.00 0.00 4.40
2489 2691 7.691050 GTGCCACGTAATCTAGAAATAACAAAC 59.309 37.037 0.00 0.00 0.00 2.93
2599 2802 1.138266 GCAAAGCTATCCACGGGTAGA 59.862 52.381 7.59 0.00 0.00 2.59
2606 2809 2.813779 CTTGACGCAAAGCTATCCAC 57.186 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.