Multiple sequence alignment - TraesCS6D01G251800

Loading Multiple Alignment...

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 TraesCS6D01G251800 chr6D 100.000 3920 0 0 1 3920 355860470 355856551 0.000000e+00 7239.0
1 TraesCS6D01G251800 chr6A 94.141 3345 116 31 628 3920 498531223 498527907 0.000000e+00 5018.0
2 TraesCS6D01G251800 chr6A 88.158 456 31 7 72 523 498531677 498531241 4.490000e-144 521.0
3 TraesCS6D01G251800 chr6A 91.860 86 7 0 1 86 5939150 5939065 1.910000e-23 121.0
4 TraesCS6D01G251800 chr6B 91.753 3650 179 48 348 3920 536817202 536813598 0.000000e+00 4961.0
5 TraesCS6D01G251800 chr6B 92.941 85 4 2 1 84 8123119 8123202 5.320000e-24 122.0
6 TraesCS6D01G251800 chr5B 97.297 74 2 0 1 74 248390273 248390200 4.110000e-25 126.0
7 TraesCS6D01G251800 chr5B 84.483 58 8 1 1594 1650 29337979 29338036 5.470000e-04 56.5
8 TraesCS6D01G251800 chr5A 97.297 74 2 0 1 74 297722941 297722868 4.110000e-25 126.0
9 TraesCS6D01G251800 chr5A 88.421 95 10 1 1 95 585431700 585431793 3.200000e-21 113.0
10 TraesCS6D01G251800 chr5A 78.378 111 17 6 1544 1650 27516507 27516614 9.090000e-07 65.8
11 TraesCS6D01G251800 chr3B 97.297 74 2 0 1 74 154663132 154663205 4.110000e-25 126.0
12 TraesCS6D01G251800 chr3A 93.827 81 5 0 1 81 393104296 393104216 5.320000e-24 122.0
13 TraesCS6D01G251800 chr3A 88.889 72 7 1 641 711 278111313 278111242 1.940000e-13 87.9
14 TraesCS6D01G251800 chr1B 93.902 82 4 1 1 81 497266679 497266598 5.320000e-24 122.0
15 TraesCS6D01G251800 chr2D 88.660 97 5 5 1 94 624881873 624881966 3.200000e-21 113.0
16 TraesCS6D01G251800 chr5D 78.378 111 17 6 1544 1650 38724309 38724416 9.090000e-07 65.8


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 TraesCS6D01G251800 chr6D 355856551 355860470 3919 True 7239.0 7239 100.0000 1 3920 1 chr6D.!!$R1 3919
1 TraesCS6D01G251800 chr6A 498527907 498531677 3770 True 2769.5 5018 91.1495 72 3920 2 chr6A.!!$R2 3848
2 TraesCS6D01G251800 chr6B 536813598 536817202 3604 True 4961.0 4961 91.7530 348 3920 1 chr6B.!!$R1 3572

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
565 570 0.033366 GGGTGTGTTTGGATTGCCAC 59.967 55.0 0.0 0.0 45.94 5.01 F
940 962 0.182775 ACTCACCTGGGTTCCAACAC 59.817 55.0 0.0 0.0 30.80 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2086 1.268899 CTGAAGTAGGTGACGAACGGT 59.731 52.381 0.0 0.0 0.00 4.83 R
2936 2970 0.816018 AAACATCGGACGTGTTGGCA 60.816 50.000 0.0 0.0 39.57 4.92 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
24 25 7.946655 TTCACTCATTTTGCTCCGTATATAG 57.053 36.000 0.00 0.00 0.00 1.31
25 26 7.050970 TCACTCATTTTGCTCCGTATATAGT 57.949 36.000 0.00 0.00 0.00 2.12
26 27 7.145985 TCACTCATTTTGCTCCGTATATAGTC 58.854 38.462 0.00 0.00 0.00 2.59
27 28 7.014326 TCACTCATTTTGCTCCGTATATAGTCT 59.986 37.037 0.00 0.00 0.00 3.24
28 29 8.297426 CACTCATTTTGCTCCGTATATAGTCTA 58.703 37.037 0.00 0.00 0.00 2.59
29 30 9.026121 ACTCATTTTGCTCCGTATATAGTCTAT 57.974 33.333 0.00 0.00 0.00 1.98
68 69 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
69 70 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
70 71 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
83 84 5.011840 GGAACGGAGGGAGTAATTTATAGCT 59.988 44.000 0.00 0.00 0.00 3.32
85 86 5.145564 ACGGAGGGAGTAATTTATAGCTGA 58.854 41.667 0.00 0.00 0.00 4.26
89 90 7.039923 CGGAGGGAGTAATTTATAGCTGAACTA 60.040 40.741 0.00 0.00 34.64 2.24
112 113 3.287222 ACAGTTGCCTAGCACTTCAAAA 58.713 40.909 0.00 0.00 38.71 2.44
123 124 7.648142 CCTAGCACTTCAAAAGAAATTGTGTA 58.352 34.615 0.00 0.00 0.00 2.90
129 130 5.858159 TCAAAAGAAATTGTGTAAACGCG 57.142 34.783 3.53 3.53 0.00 6.01
141 142 0.250381 TAAACGCGCCCTTTCCAAGA 60.250 50.000 5.73 0.00 0.00 3.02
146 147 1.448119 GCGCCCTTTCCAAGATAGCC 61.448 60.000 0.00 0.00 0.00 3.93
159 160 5.013704 TCCAAGATAGCCACTTGAAAACCTA 59.986 40.000 14.01 0.00 44.92 3.08
160 161 5.355350 CCAAGATAGCCACTTGAAAACCTAG 59.645 44.000 14.01 0.00 44.92 3.02
167 171 3.253432 CCACTTGAAAACCTAGGCACTTC 59.747 47.826 9.30 9.72 41.75 3.01
178 182 4.716784 ACCTAGGCACTTCTTCATACATGA 59.283 41.667 9.30 0.00 41.75 3.07
184 188 4.024218 GCACTTCTTCATACATGATCCAGC 60.024 45.833 0.00 0.00 36.56 4.85
192 196 0.254178 ACATGATCCAGCCACCAGTC 59.746 55.000 0.00 0.00 0.00 3.51
194 198 1.639635 ATGATCCAGCCACCAGTCCC 61.640 60.000 0.00 0.00 0.00 4.46
235 239 9.770097 TCTTCCTAGATCACATCAACAATAATC 57.230 33.333 0.00 0.00 0.00 1.75
237 241 9.904198 TTCCTAGATCACATCAACAATAATCAA 57.096 29.630 0.00 0.00 0.00 2.57
292 296 0.782384 GTTGCGAGTGTAGACCGTTG 59.218 55.000 0.00 0.00 0.00 4.10
303 307 0.537188 AGACCGTTGGATGGCTACTG 59.463 55.000 0.00 0.00 0.00 2.74
319 323 4.702131 GGCTACTGACAAATTCACCATCTT 59.298 41.667 0.00 0.00 0.00 2.40
324 328 6.533730 ACTGACAAATTCACCATCTTAGTCA 58.466 36.000 0.00 0.00 33.11 3.41
393 397 9.372369 GTATGATACTTATTGTGGCTAGATTCC 57.628 37.037 0.00 0.00 0.00 3.01
404 408 5.136105 GTGGCTAGATTCCATCAAAATCCT 58.864 41.667 0.00 0.00 35.81 3.24
503 508 2.375146 GGCGAACCCAATCACCTAATT 58.625 47.619 0.00 0.00 0.00 1.40
532 537 6.365789 TCTGAAATTTGATGAACCGAAATTGC 59.634 34.615 0.00 0.00 31.31 3.56
538 543 0.594110 TGAACCGAAATTGCGAACCC 59.406 50.000 7.61 0.00 0.00 4.11
565 570 0.033366 GGGTGTGTTTGGATTGCCAC 59.967 55.000 0.00 0.00 45.94 5.01
567 572 0.318614 GTGTGTTTGGATTGCCACCG 60.319 55.000 0.00 0.00 45.94 4.94
585 590 1.156736 CGAAGTGCACCCTACCAAAG 58.843 55.000 14.63 0.00 0.00 2.77
596 601 4.827284 CACCCTACCAAAGAAAGTTCATGT 59.173 41.667 0.00 0.00 0.00 3.21
637 642 7.579589 TGTTGGATGATTGCTAAATTTTTCG 57.420 32.000 0.00 0.00 0.00 3.46
662 667 7.587757 CGAACAACTCTAGTTCATTTTTCTTGG 59.412 37.037 6.83 0.00 44.22 3.61
782 790 2.887568 GCGGTCGCTGTGATCCAG 60.888 66.667 8.20 6.79 44.53 3.86
892 907 3.771577 ACAAGTAGCAAAGGCAGTAGT 57.228 42.857 0.00 0.00 44.61 2.73
911 926 1.887242 GTGCGAACTGGTGTCAGCA 60.887 57.895 4.37 4.37 44.59 4.41
940 962 0.182775 ACTCACCTGGGTTCCAACAC 59.817 55.000 0.00 0.00 30.80 3.32
942 964 0.626382 TCACCTGGGTTCCAACACAA 59.374 50.000 0.00 0.00 42.67 3.33
952 974 4.749598 GGGTTCCAACACAAAAATTGCTAG 59.250 41.667 0.00 0.00 31.01 3.42
954 976 5.815222 GGTTCCAACACAAAAATTGCTAGTT 59.185 36.000 0.00 0.00 0.00 2.24
1249 1271 1.333177 ACAAGAGACGGAAGAGCACT 58.667 50.000 0.00 0.00 0.00 4.40
1277 1299 5.417425 GACACGTCGACTAACAATGTAAG 57.583 43.478 14.70 0.00 0.00 2.34
1280 1302 3.671928 ACGTCGACTAACAATGTAAGTGC 59.328 43.478 14.70 0.00 33.50 4.40
1285 1307 6.364165 GTCGACTAACAATGTAAGTGCTACAA 59.636 38.462 8.70 0.00 43.75 2.41
1291 1313 5.853936 ACAATGTAAGTGCTACAAGAGTGA 58.146 37.500 0.00 0.00 43.75 3.41
1317 1339 2.992114 AGAACGAGCAGGCCGTCT 60.992 61.111 0.00 0.00 39.57 4.18
1443 1477 4.129737 CTGCGTCCGTCGGTGGAT 62.130 66.667 11.88 0.00 40.91 3.41
1749 1783 2.264794 CCCAACGTCTTCTCCGGG 59.735 66.667 0.00 0.00 0.00 5.73
1755 1789 0.903454 ACGTCTTCTCCGGGTTCCAT 60.903 55.000 0.00 0.00 0.00 3.41
2016 2050 0.995024 CCAAGAAGGACCCCATCACT 59.005 55.000 0.00 0.00 41.22 3.41
2071 2105 1.001048 CACCGTTCGTCACCTACTTCA 60.001 52.381 0.00 0.00 0.00 3.02
2133 2167 3.573772 CTCCGTCAAGCAGCCGTCA 62.574 63.158 0.00 0.00 0.00 4.35
2812 2846 4.758251 TGGTGATGGACGCGCAGG 62.758 66.667 5.73 0.00 0.00 4.85
2936 2970 6.486993 CACCAATGATCATCAGATTCAGACAT 59.513 38.462 9.06 0.00 33.72 3.06
2947 2981 1.225855 TTCAGACATGCCAACACGTC 58.774 50.000 0.00 0.00 39.28 4.34
2979 3013 1.428370 GCCATAGATTGCGTGCGACA 61.428 55.000 0.00 0.00 0.00 4.35
2985 3019 1.393539 AGATTGCGTGCGACAATGTAC 59.606 47.619 14.97 0.00 37.85 2.90
2997 3031 4.440103 GCGACAATGTACAATAGTAGACCG 59.560 45.833 0.00 0.53 0.00 4.79
3095 3129 6.640499 TGTAGCATTTACATGTTTGCAAGAAC 59.360 34.615 22.31 16.32 37.56 3.01
3112 3146 5.625311 GCAAGAACGAACTATTGGTGAAAAG 59.375 40.000 0.00 0.00 0.00 2.27
3118 3152 5.938125 ACGAACTATTGGTGAAAAGCATACT 59.062 36.000 0.00 0.00 0.00 2.12
3119 3153 6.430000 ACGAACTATTGGTGAAAAGCATACTT 59.570 34.615 0.00 0.00 37.90 2.24
3120 3154 6.742718 CGAACTATTGGTGAAAAGCATACTTG 59.257 38.462 0.00 0.00 35.85 3.16
3137 3171 4.331356 GCAGGTGCAGTGCAAAAG 57.669 55.556 21.67 13.18 41.47 2.27
3147 3181 1.677576 CAGTGCAAAAGAACAGCCTGA 59.322 47.619 0.00 0.00 32.16 3.86
3154 3188 5.984926 TGCAAAAGAACAGCCTGAAAAATAG 59.015 36.000 0.00 0.00 0.00 1.73
3164 3198 3.425193 GCCTGAAAAATAGTTGCAACACG 59.575 43.478 30.11 7.91 0.00 4.49
3172 3206 2.202946 TTGCAACACGCGTCCAGA 60.203 55.556 9.86 0.00 46.97 3.86
3226 3260 6.865205 AGTACGAAACAAGGTATGAACTACAC 59.135 38.462 0.00 0.00 31.44 2.90
3332 3394 5.895636 ACATGCTATTGGATTTCACGAAA 57.104 34.783 0.00 0.00 34.46 3.46
3356 3418 2.436417 GTGGAGCTACCTTGCATTTGA 58.564 47.619 0.00 0.00 39.86 2.69
3360 3422 4.640201 TGGAGCTACCTTGCATTTGATTAC 59.360 41.667 0.00 0.00 39.86 1.89
3361 3423 4.640201 GGAGCTACCTTGCATTTGATTACA 59.360 41.667 0.00 0.00 35.41 2.41
3362 3424 5.220931 GGAGCTACCTTGCATTTGATTACAG 60.221 44.000 0.00 0.00 35.41 2.74
3363 3425 5.500234 AGCTACCTTGCATTTGATTACAGA 58.500 37.500 0.00 0.00 34.99 3.41
3411 3475 8.836413 TCAATGTTGTTAGTCTAGAAAAACAGG 58.164 33.333 16.46 7.32 33.70 4.00
3471 3535 4.756564 TGCTCCTATGGAAGGTATGAGAT 58.243 43.478 0.00 0.00 46.62 2.75
3486 3567 7.640313 AGGTATGAGATTATGATGATGCCAAT 58.360 34.615 0.00 0.00 0.00 3.16
3505 3586 8.750515 TGCCAATATCATTAACAATCTTCAGA 57.249 30.769 0.00 0.00 0.00 3.27
3541 3622 4.187694 CAGCACTTCTCTTCCTAACATCC 58.812 47.826 0.00 0.00 0.00 3.51
3597 3689 8.256356 AGATACCTAACAGAAGTTGCATAGAT 57.744 34.615 0.00 0.00 38.69 1.98
3598 3690 8.364142 AGATACCTAACAGAAGTTGCATAGATC 58.636 37.037 0.00 0.00 38.69 2.75
3599 3691 6.299805 ACCTAACAGAAGTTGCATAGATCA 57.700 37.500 0.00 0.00 38.69 2.92
3623 3715 5.005740 CCAACTTCTCAAGATTCATGTGGA 58.994 41.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.497595 ACTATATACGGAGCAAAATGAGTGAA 58.502 34.615 0.00 0.00 0.00 3.18
1 2 7.014326 AGACTATATACGGAGCAAAATGAGTGA 59.986 37.037 0.00 0.00 0.00 3.41
2 3 7.148641 AGACTATATACGGAGCAAAATGAGTG 58.851 38.462 0.00 0.00 0.00 3.51
3 4 7.291411 AGACTATATACGGAGCAAAATGAGT 57.709 36.000 0.00 0.00 0.00 3.41
42 43 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
43 44 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
44 45 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
45 46 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
46 47 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
47 48 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
48 49 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
49 50 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
50 51 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
51 52 8.731591 AATTACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
52 53 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
53 54 7.441903 AAATTACTCCCTCCGTTCCTAAATA 57.558 36.000 0.00 0.00 0.00 1.40
54 55 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
55 56 5.767277 AAATTACTCCCTCCGTTCCTAAA 57.233 39.130 0.00 0.00 0.00 1.85
56 57 7.256083 GCTATAAATTACTCCCTCCGTTCCTAA 60.256 40.741 0.00 0.00 0.00 2.69
57 58 6.210185 GCTATAAATTACTCCCTCCGTTCCTA 59.790 42.308 0.00 0.00 0.00 2.94
58 59 5.011840 GCTATAAATTACTCCCTCCGTTCCT 59.988 44.000 0.00 0.00 0.00 3.36
59 60 5.011840 AGCTATAAATTACTCCCTCCGTTCC 59.988 44.000 0.00 0.00 0.00 3.62
60 61 5.927115 CAGCTATAAATTACTCCCTCCGTTC 59.073 44.000 0.00 0.00 0.00 3.95
61 62 5.601313 TCAGCTATAAATTACTCCCTCCGTT 59.399 40.000 0.00 0.00 0.00 4.44
62 63 5.145564 TCAGCTATAAATTACTCCCTCCGT 58.854 41.667 0.00 0.00 0.00 4.69
63 64 5.723672 TCAGCTATAAATTACTCCCTCCG 57.276 43.478 0.00 0.00 0.00 4.63
64 65 7.068686 AGTTCAGCTATAAATTACTCCCTCC 57.931 40.000 0.00 0.00 0.00 4.30
65 66 9.080097 TCTAGTTCAGCTATAAATTACTCCCTC 57.920 37.037 0.00 0.00 0.00 4.30
66 67 8.862085 GTCTAGTTCAGCTATAAATTACTCCCT 58.138 37.037 0.00 0.00 0.00 4.20
67 68 8.639761 TGTCTAGTTCAGCTATAAATTACTCCC 58.360 37.037 0.00 0.00 0.00 4.30
68 69 9.685828 CTGTCTAGTTCAGCTATAAATTACTCC 57.314 37.037 0.00 0.00 0.00 3.85
112 113 1.068816 GGGCGCGTTTACACAATTTCT 60.069 47.619 8.43 0.00 0.00 2.52
123 124 0.893727 ATCTTGGAAAGGGCGCGTTT 60.894 50.000 8.43 3.26 46.24 3.60
129 130 1.064389 AGTGGCTATCTTGGAAAGGGC 60.064 52.381 0.00 0.00 46.24 5.19
141 142 3.010138 TGCCTAGGTTTTCAAGTGGCTAT 59.990 43.478 11.31 0.00 39.57 2.97
146 147 4.137543 AGAAGTGCCTAGGTTTTCAAGTG 58.862 43.478 11.31 0.00 0.00 3.16
159 160 4.164796 TGGATCATGTATGAAGAAGTGCCT 59.835 41.667 0.00 0.00 40.69 4.75
160 161 4.454678 TGGATCATGTATGAAGAAGTGCC 58.545 43.478 0.00 0.00 40.69 5.01
167 171 3.144506 GGTGGCTGGATCATGTATGAAG 58.855 50.000 0.00 0.00 40.69 3.02
178 182 2.204136 TGGGACTGGTGGCTGGAT 60.204 61.111 0.00 0.00 0.00 3.41
192 196 8.119246 TCTAGGAAGATAAGATAGAATCCTGGG 58.881 40.741 0.00 0.00 36.54 4.45
277 281 1.469251 CCATCCAACGGTCTACACTCG 60.469 57.143 0.00 0.00 0.00 4.18
292 296 3.378427 GGTGAATTTGTCAGTAGCCATCC 59.622 47.826 0.00 0.00 36.74 3.51
303 307 6.038714 GGGATGACTAAGATGGTGAATTTGTC 59.961 42.308 0.00 0.00 31.93 3.18
324 328 2.287584 TCTTTGGAGGGTCATTGGGAT 58.712 47.619 0.00 0.00 0.00 3.85
378 382 6.041296 GGATTTTGATGGAATCTAGCCACAAT 59.959 38.462 0.00 0.00 45.81 2.71
393 397 6.222389 TGTGCCAAAACTTAGGATTTTGATG 58.778 36.000 10.89 0.00 45.75 3.07
404 408 8.149647 AGATTCATCAAATTGTGCCAAAACTTA 58.850 29.630 0.00 0.00 0.00 2.24
473 478 2.414785 GGGTTCGCCGGAATTGCAT 61.415 57.895 5.05 0.00 38.45 3.96
503 508 4.819088 TCGGTTCATCAAATTTCAGACACA 59.181 37.500 0.00 0.00 0.00 3.72
538 543 2.299521 TCCAAACACACCCTAAAACCG 58.700 47.619 0.00 0.00 0.00 4.44
565 570 0.250553 TTTGGTAGGGTGCACTTCGG 60.251 55.000 17.98 0.00 0.00 4.30
567 572 2.561478 TCTTTGGTAGGGTGCACTTC 57.439 50.000 17.98 9.64 0.00 3.01
585 590 3.660904 CGACGTTTCGGACATGAACTTTC 60.661 47.826 0.00 0.00 41.89 2.62
607 612 0.176449 GCAATCATCCAACAAGGGCC 59.824 55.000 0.00 0.00 38.24 5.80
637 642 7.379797 GCCAAGAAAAATGAACTAGAGTTGTTC 59.620 37.037 0.00 0.00 42.77 3.18
662 667 2.353011 CCCATGAGTTGGTCAACAATGC 60.353 50.000 15.12 3.68 44.83 3.56
692 697 7.768582 ACAAGTTTTCCTAAAATTTGGTTGAGG 59.231 33.333 18.49 0.00 46.25 3.86
782 790 1.717194 TCAAAGATTACGTGGACCGC 58.283 50.000 0.00 0.00 41.42 5.68
877 890 1.808411 GCACACTACTGCCTTTGCTA 58.192 50.000 0.00 0.00 38.71 3.49
892 907 1.887242 GCTGACACCAGTTCGCACA 60.887 57.895 0.00 0.00 42.35 4.57
952 974 6.706716 GGCTCTTTGGATTACTAGTGGATAAC 59.293 42.308 5.39 0.00 0.00 1.89
954 976 5.903010 TGGCTCTTTGGATTACTAGTGGATA 59.097 40.000 5.39 0.00 0.00 2.59
964 986 4.581824 GCAGATCAATGGCTCTTTGGATTA 59.418 41.667 0.00 0.00 0.00 1.75
1215 1237 1.901650 CTTGTTGCTCGACCGGCTTC 61.902 60.000 0.00 0.00 0.00 3.86
1266 1288 7.384115 GTCACTCTTGTAGCACTTACATTGTTA 59.616 37.037 0.00 0.00 41.72 2.41
1274 1296 4.155462 CGGTAGTCACTCTTGTAGCACTTA 59.845 45.833 0.00 0.00 0.00 2.24
1277 1299 2.864968 CGGTAGTCACTCTTGTAGCAC 58.135 52.381 0.00 0.00 0.00 4.40
1280 1302 1.736126 TCGCGGTAGTCACTCTTGTAG 59.264 52.381 6.13 0.00 0.00 2.74
1285 1307 0.803740 GTTCTCGCGGTAGTCACTCT 59.196 55.000 6.13 0.00 0.00 3.24
1291 1313 2.254703 CTGCTCGTTCTCGCGGTAGT 62.255 60.000 6.13 0.00 36.96 2.73
1314 1336 2.583593 GACCGAGGCGCATCAGAC 60.584 66.667 23.09 7.48 0.00 3.51
1317 1339 4.492160 GACGACCGAGGCGCATCA 62.492 66.667 23.09 0.00 0.00 3.07
1542 1576 4.089239 TTGCGGATGTAGGCGCCA 62.089 61.111 31.54 12.31 0.00 5.69
2052 2086 1.268899 CTGAAGTAGGTGACGAACGGT 59.731 52.381 0.00 0.00 0.00 4.83
2133 2167 1.741770 GGCGAAGTCGTGCAGGAAT 60.742 57.895 11.28 7.18 42.22 3.01
2936 2970 0.816018 AAACATCGGACGTGTTGGCA 60.816 50.000 0.00 0.00 39.57 4.92
2947 2981 1.831389 CTATGGCGCGGAAACATCGG 61.831 60.000 8.83 0.00 0.00 4.18
2973 3007 5.345702 GGTCTACTATTGTACATTGTCGCA 58.654 41.667 0.00 0.00 0.00 5.10
2979 3013 6.602406 ACTCTGTCGGTCTACTATTGTACATT 59.398 38.462 0.00 0.00 0.00 2.71
2985 3019 3.695060 ACCACTCTGTCGGTCTACTATTG 59.305 47.826 0.00 0.00 0.00 1.90
2997 3031 0.613260 TACCCATGCACCACTCTGTC 59.387 55.000 0.00 0.00 0.00 3.51
3088 3122 4.742438 TTCACCAATAGTTCGTTCTTGC 57.258 40.909 0.00 0.00 0.00 4.01
3095 3129 6.422776 AGTATGCTTTTCACCAATAGTTCG 57.577 37.500 0.00 0.00 0.00 3.95
3120 3154 0.102844 TTCTTTTGCACTGCACCTGC 59.897 50.000 2.26 4.87 38.71 4.85
3121 3155 1.134753 TGTTCTTTTGCACTGCACCTG 59.865 47.619 2.26 0.00 38.71 4.00
3122 3156 1.406539 CTGTTCTTTTGCACTGCACCT 59.593 47.619 2.26 0.00 38.71 4.00
3123 3157 1.843992 CTGTTCTTTTGCACTGCACC 58.156 50.000 2.26 0.00 38.71 5.01
3124 3158 1.203065 GCTGTTCTTTTGCACTGCAC 58.797 50.000 2.26 0.00 39.45 4.57
3131 3165 5.985530 ACTATTTTTCAGGCTGTTCTTTTGC 59.014 36.000 15.27 0.00 0.00 3.68
3137 3171 4.870363 TGCAACTATTTTTCAGGCTGTTC 58.130 39.130 15.27 0.00 0.00 3.18
3147 3181 3.040099 GACGCGTGTTGCAACTATTTTT 58.960 40.909 28.61 10.07 46.97 1.94
3154 3188 2.052237 CTGGACGCGTGTTGCAAC 60.052 61.111 20.70 22.83 46.97 4.17
3164 3198 0.445436 CAATTCTGCAGTCTGGACGC 59.555 55.000 14.67 9.37 36.20 5.19
3185 3219 7.806487 TGTTTCGTACTACTACTCAATGAGTTG 59.194 37.037 21.83 20.88 40.28 3.16
3226 3260 4.506886 ACTCTCTTACCTGTGAAGTTCG 57.493 45.455 0.00 0.00 0.00 3.95
3311 3351 6.981379 GATTTCGTGAAATCCAATAGCATG 57.019 37.500 19.81 0.00 46.68 4.06
3332 3394 1.264749 TGCAAGGTAGCTCCACCGAT 61.265 55.000 0.00 0.00 43.84 4.18
3356 3418 8.515695 TGCTGAATTGATGATTCTTCTGTAAT 57.484 30.769 1.76 0.00 43.74 1.89
3360 3422 6.263392 AGGATGCTGAATTGATGATTCTTCTG 59.737 38.462 0.00 0.00 43.74 3.02
3361 3423 6.366340 AGGATGCTGAATTGATGATTCTTCT 58.634 36.000 0.00 0.00 43.74 2.85
3362 3424 6.262496 TGAGGATGCTGAATTGATGATTCTTC 59.738 38.462 0.00 0.00 43.74 2.87
3363 3425 6.127101 TGAGGATGCTGAATTGATGATTCTT 58.873 36.000 0.00 0.00 43.74 2.52
3411 3475 5.182760 AGACAAAAGAGAAGCCATGTTCATC 59.817 40.000 0.00 0.00 0.00 2.92
3486 3567 9.842775 AGATTGCTCTGAAGATTGTTAATGATA 57.157 29.630 0.00 0.00 0.00 2.15
3505 3586 1.003349 AGTGCTGCAGAGAAGATTGCT 59.997 47.619 20.43 0.00 40.87 3.91
3541 3622 9.791820 TGATGAGTAAAAATACAGAATGCATTG 57.208 29.630 18.59 6.76 42.53 2.82
3581 3670 4.558226 TGGTGATCTATGCAACTTCTGT 57.442 40.909 0.00 0.00 0.00 3.41
3597 3689 5.471116 CACATGAATCTTGAGAAGTTGGTGA 59.529 40.000 0.00 0.00 0.00 4.02
3598 3690 5.335426 CCACATGAATCTTGAGAAGTTGGTG 60.335 44.000 0.00 0.00 0.00 4.17
3599 3691 4.763793 CCACATGAATCTTGAGAAGTTGGT 59.236 41.667 0.00 0.00 0.00 3.67
3623 3715 3.562176 CCCTTTCTAGGCTGTGGAATGTT 60.562 47.826 0.00 0.00 40.50 2.71
3829 3921 9.147732 TCTTTTGATCTGAGGTATAATCTGCTA 57.852 33.333 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.