Multiple sequence alignment - TraesCS7D01G317100

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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 TraesCS7D01G317100 chr7D 100.000 3221 0 0 1 3221 403646870 403643650 0.000000e+00 5949.0
1 TraesCS7D01G317100 chr7B 94.336 2260 79 16 1 2223 412904650 412902403 0.000000e+00 3419.0
2 TraesCS7D01G317100 chr7B 81.000 800 126 20 2215 2999 412902224 412901436 2.120000e-171 612.0
3 TraesCS7D01G317100 chr7B 74.265 408 93 10 2807 3209 737002866 737002466 9.250000e-36 161.0
4 TraesCS7D01G317100 chr7B 74.576 354 82 7 2836 3186 737178422 737178074 7.200000e-32 148.0
5 TraesCS7D01G317100 chr7B 74.160 387 84 15 2807 3186 737682092 737681715 2.590000e-31 147.0
6 TraesCS7D01G317100 chr7A 88.783 2318 180 51 928 3221 462302107 462299846 0.000000e+00 2767.0
7 TraesCS7D01G317100 chr7A 96.244 213 8 0 708 920 462302783 462302571 1.840000e-92 350.0
8 TraesCS7D01G317100 chr7A 87.552 241 30 0 2402 2642 127570364 127570124 2.450000e-71 279.0
9 TraesCS7D01G317100 chr7A 89.894 188 5 6 462 640 462319049 462318867 2.500000e-56 230.0
10 TraesCS7D01G317100 chr7A 95.890 73 3 0 1 73 462320114 462320042 5.640000e-23 119.0
11 TraesCS7D01G317100 chr4A 77.890 493 91 12 2722 3207 537537821 537537340 1.130000e-74 291.0
12 TraesCS7D01G317100 chr4A 74.603 315 64 8 2896 3209 8581068 8581367 1.210000e-24 124.0
13 TraesCS7D01G317100 chr4A 80.303 132 23 1 388 516 540477979 540477848 2.640000e-16 97.1
14 TraesCS7D01G317100 chr3D 84.906 265 37 3 2379 2641 606746493 606746756 6.850000e-67 265.0
15 TraesCS7D01G317100 chr2D 85.115 262 35 2 2381 2641 180090099 180089841 6.850000e-67 265.0
16 TraesCS7D01G317100 chr2D 85.214 257 37 1 2377 2632 68920666 68920410 2.460000e-66 263.0
17 TraesCS7D01G317100 chr2D 83.889 180 24 4 344 520 87787056 87786879 1.990000e-37 167.0
18 TraesCS7D01G317100 chr2D 83.626 171 23 5 1565 1732 524564808 524564976 4.300000e-34 156.0
19 TraesCS7D01G317100 chr1D 85.057 261 36 2 2375 2632 447926308 447926568 2.460000e-66 263.0
20 TraesCS7D01G317100 chr1D 87.879 66 7 1 3142 3207 373377260 373377196 3.450000e-10 76.8
21 TraesCS7D01G317100 chr6B 84.733 262 36 2 2381 2641 626818728 626818470 3.190000e-65 259.0
22 TraesCS7D01G317100 chr6B 75.385 195 41 6 2962 3153 90282326 90282516 1.590000e-13 87.9
23 TraesCS7D01G317100 chr5D 84.586 266 36 3 2377 2641 357501092 357500831 3.190000e-65 259.0
24 TraesCS7D01G317100 chr5B 84.270 267 38 2 2377 2642 646377947 646377684 1.150000e-64 257.0
25 TraesCS7D01G317100 chr3B 78.478 381 70 10 2834 3209 566474785 566475158 4.150000e-59 239.0
26 TraesCS7D01G317100 chr3B 81.879 149 27 0 3039 3187 792820041 792819893 3.370000e-25 126.0
27 TraesCS7D01G317100 chr1A 75.495 404 93 6 2806 3207 547694878 547695277 3.280000e-45 193.0
28 TraesCS7D01G317100 chr2A 84.211 171 22 5 1565 1732 670220100 670220268 9.250000e-36 161.0
29 TraesCS7D01G317100 chr2B 83.041 171 24 5 1565 1732 620642126 620641958 2.000000e-32 150.0
30 TraesCS7D01G317100 chr2B 83.333 96 12 3 19 111 111443223 111443129 5.730000e-13 86.1
31 TraesCS7D01G317100 chr4D 78.169 142 25 4 379 516 56696546 56696685 5.730000e-13 86.1


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 TraesCS7D01G317100 chr7D 403643650 403646870 3220 True 5949.0 5949 100.0000 1 3221 1 chr7D.!!$R1 3220
1 TraesCS7D01G317100 chr7B 412901436 412904650 3214 True 2015.5 3419 87.6680 1 2999 2 chr7B.!!$R4 2998
2 TraesCS7D01G317100 chr7A 462299846 462302783 2937 True 1558.5 2767 92.5135 708 3221 2 chr7A.!!$R2 2513

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
184 185 0.620556 TCCTTGATGTTGGAGCCCTC 59.379 55.0 0.0 0.0 0.0 4.30 F
1743 2232 0.250513 CCCTCTACCTCAACTGCACC 59.749 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2316 0.028374 CGAACGCGAACCCTGTTTTT 59.972 50.0 15.93 0.00 40.82 1.94 R
3148 3850 0.036294 AGAGCCGGCTTAACCTTGTC 60.036 55.0 33.34 14.79 35.61 3.18 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
50 51 2.806244 GAGCGAAGTATTGTTGTGTGGT 59.194 45.455 0.00 0.00 0.00 4.16
60 61 7.103641 AGTATTGTTGTGTGGTTACATAGAGG 58.896 38.462 0.00 0.00 39.39 3.69
64 65 3.786553 TGTGTGGTTACATAGAGGACCT 58.213 45.455 0.00 0.00 39.39 3.85
65 66 3.767673 TGTGTGGTTACATAGAGGACCTC 59.232 47.826 14.15 14.15 39.39 3.85
69 70 4.406003 GTGGTTACATAGAGGACCTCATGT 59.594 45.833 27.77 27.77 36.74 3.21
99 100 9.785982 GAGGATTTTTGCCTCTAGATTATAACT 57.214 33.333 0.00 0.00 46.70 2.24
124 125 9.420118 CTCTATCATTATGAGTAAGGCTCCTAT 57.580 37.037 0.29 0.00 43.48 2.57
146 147 9.651913 CCTATTTAAATAAAGAAAAAGCCTGCA 57.348 29.630 9.15 0.00 0.00 4.41
149 150 9.723601 ATTTAAATAAAGAAAAAGCCTGCATCA 57.276 25.926 0.00 0.00 0.00 3.07
150 151 9.723601 TTTAAATAAAGAAAAAGCCTGCATCAT 57.276 25.926 0.00 0.00 0.00 2.45
151 152 7.838771 AAATAAAGAAAAAGCCTGCATCATC 57.161 32.000 0.00 0.00 0.00 2.92
152 153 6.786967 ATAAAGAAAAAGCCTGCATCATCT 57.213 33.333 0.00 0.00 0.00 2.90
153 154 7.886629 ATAAAGAAAAAGCCTGCATCATCTA 57.113 32.000 0.00 0.00 0.00 1.98
154 155 6.594788 AAAGAAAAAGCCTGCATCATCTAA 57.405 33.333 0.00 0.00 0.00 2.10
164 165 4.753610 CCTGCATCATCTAATACACTGTGG 59.246 45.833 13.09 0.00 0.00 4.17
173 174 5.977635 TCTAATACACTGTGGTCCTTGATG 58.022 41.667 13.09 0.00 0.00 3.07
184 185 0.620556 TCCTTGATGTTGGAGCCCTC 59.379 55.000 0.00 0.00 0.00 4.30
197 198 2.624029 GGAGCCCTCCCATTCAATTGAA 60.624 50.000 22.52 22.52 43.94 2.69
208 209 9.143631 CTCCCATTCAATTGAAATGTTTAGTTC 57.856 33.333 23.91 0.00 37.61 3.01
235 236 6.295236 GGATTTGGTTGATGATTTTGACCAGA 60.295 38.462 0.00 0.00 41.06 3.86
255 256 6.054295 CCAGATCAACTATTTCTCAAGGAGG 58.946 44.000 0.00 0.00 0.00 4.30
258 259 6.671779 AGATCAACTATTTCTCAAGGAGGTCT 59.328 38.462 0.00 0.00 0.00 3.85
359 360 1.259840 ATTGCACATCCCCTTGCCAC 61.260 55.000 0.00 0.00 38.00 5.01
416 417 7.561251 TGTAGCACCAATATAATATATGCGGT 58.439 34.615 8.17 8.17 36.71 5.68
423 424 7.335924 ACCAATATAATATATGCGGTCACCAAC 59.664 37.037 0.00 0.00 0.00 3.77
533 534 2.254546 AACACTCACCATCTTTCGCA 57.745 45.000 0.00 0.00 0.00 5.10
555 556 3.704061 AGGCGCCAAACCAAATATACAAT 59.296 39.130 31.54 0.00 0.00 2.71
556 557 4.161377 AGGCGCCAAACCAAATATACAATT 59.839 37.500 31.54 0.00 0.00 2.32
606 607 1.062148 GCGAATAGCGTTCAACCCTTC 59.938 52.381 5.86 0.00 43.41 3.46
758 760 1.972872 AGCACTCACTCAAAACTGGG 58.027 50.000 0.00 0.00 0.00 4.45
959 1445 7.164803 AGTAGTCATAAGAAAGAAGCAAAGCT 58.835 34.615 0.00 0.00 42.56 3.74
1149 1638 1.191535 CCACCGATCCTCTGGTACAA 58.808 55.000 0.00 0.00 38.70 2.41
1743 2232 0.250513 CCCTCTACCTCAACTGCACC 59.749 60.000 0.00 0.00 0.00 5.01
1848 2337 1.493134 AAACAGGGTTCGCGTTCGTC 61.493 55.000 5.77 0.00 36.96 4.20
2158 2647 2.829720 CCACCACTGCCAGTAGTACTAA 59.170 50.000 3.61 0.00 0.00 2.24
2160 2649 3.257375 CACCACTGCCAGTAGTACTAACA 59.743 47.826 3.61 3.54 0.00 2.41
2166 2655 2.418334 GCCAGTAGTACTAACACTGCCC 60.418 54.545 15.90 7.67 38.67 5.36
2265 2943 1.573108 TTGCCCTTTTTGTGGGTTCA 58.427 45.000 0.00 0.00 46.22 3.18
2280 2958 4.026062 GTGGGTTCAATTTCGTTTTTCTGC 60.026 41.667 0.00 0.00 0.00 4.26
2281 2959 4.116238 GGGTTCAATTTCGTTTTTCTGCA 58.884 39.130 0.00 0.00 0.00 4.41
2286 2967 8.003784 GGTTCAATTTCGTTTTTCTGCAATTAG 58.996 33.333 0.00 0.00 0.00 1.73
2325 3012 1.875576 GCCGCAGATCATAGGTTCCAG 60.876 57.143 0.00 0.00 0.00 3.86
2329 3016 3.181471 CGCAGATCATAGGTTCCAGTTCT 60.181 47.826 0.00 0.00 0.00 3.01
2409 3101 6.488006 ACATCCAATATAGCACCTTCAATCAC 59.512 38.462 0.00 0.00 0.00 3.06
2411 3103 4.214119 CCAATATAGCACCTTCAATCACGG 59.786 45.833 0.00 0.00 0.00 4.94
2420 3116 4.992319 CACCTTCAATCACGGTAGTACAAA 59.008 41.667 2.06 0.00 0.00 2.83
2426 3122 6.460781 TCAATCACGGTAGTACAAAGAACAT 58.539 36.000 2.06 0.00 0.00 2.71
2468 3164 2.242965 TCCAGATCCGTAGACCACCTAA 59.757 50.000 0.00 0.00 0.00 2.69
2469 3165 3.117246 TCCAGATCCGTAGACCACCTAAT 60.117 47.826 0.00 0.00 0.00 1.73
2470 3166 3.005897 CCAGATCCGTAGACCACCTAATG 59.994 52.174 0.00 0.00 0.00 1.90
2472 3168 3.890147 AGATCCGTAGACCACCTAATGAC 59.110 47.826 0.00 0.00 0.00 3.06
2480 3176 4.279145 AGACCACCTAATGACGACTACAT 58.721 43.478 0.00 0.00 0.00 2.29
2483 3179 3.430236 CCACCTAATGACGACTACATGCA 60.430 47.826 0.00 0.00 0.00 3.96
2499 3195 1.100463 TGCACTGAAGCAAGCCGAAA 61.100 50.000 0.00 0.00 42.46 3.46
2526 3222 2.107141 CGTCATCGCCCCTCCTTC 59.893 66.667 0.00 0.00 0.00 3.46
2553 3249 3.638484 AGCCGAGCAAAATTTGTTGTAC 58.362 40.909 7.60 0.00 0.00 2.90
2558 3254 6.622896 GCCGAGCAAAATTTGTTGTACTAGAT 60.623 38.462 7.60 0.00 0.00 1.98
2585 3281 1.445871 AAATCGTCGTGTTAAGGCCC 58.554 50.000 0.00 0.00 0.00 5.80
2598 3294 0.698886 AAGGCCCCATAGGATCAGCA 60.699 55.000 0.00 0.00 38.24 4.41
2604 3300 1.212688 CCCATAGGATCAGCACACCAA 59.787 52.381 0.00 0.00 33.47 3.67
2607 3303 3.763360 CCATAGGATCAGCACACCAAAAA 59.237 43.478 0.00 0.00 0.00 1.94
2643 3339 4.883585 TGATGAAAAGTGGCATAGATCACC 59.116 41.667 0.00 0.00 34.67 4.02
2656 3352 6.145696 GGCATAGATCACCGATTTAGTACAAC 59.854 42.308 0.00 0.00 0.00 3.32
2658 3354 7.306632 GCATAGATCACCGATTTAGTACAACAC 60.307 40.741 0.00 0.00 0.00 3.32
2717 3413 1.282653 CCCTTCTTCCCTTCCCCTCC 61.283 65.000 0.00 0.00 0.00 4.30
2720 3416 3.009115 CTTCCCTTCCCCTCCGCA 61.009 66.667 0.00 0.00 0.00 5.69
2748 3446 2.417719 CAAACTCTCCCTCCAGTTTCG 58.582 52.381 0.00 0.00 40.19 3.46
2749 3447 0.321996 AACTCTCCCTCCAGTTTCGC 59.678 55.000 0.00 0.00 27.81 4.70
2756 3454 1.301401 CTCCAGTTTCGCCGGTGAA 60.301 57.895 26.19 26.19 0.00 3.18
2760 3458 3.343421 GTTTCGCCGGTGAACGCT 61.343 61.111 29.44 0.00 42.52 5.07
2761 3459 2.589442 TTTCGCCGGTGAACGCTT 60.589 55.556 29.44 0.00 42.52 4.68
2765 3463 2.746277 GCCGGTGAACGCTTGGAT 60.746 61.111 1.90 0.00 42.52 3.41
2767 3465 1.862602 GCCGGTGAACGCTTGGATTT 61.863 55.000 1.90 0.00 42.52 2.17
2778 3476 0.627986 CTTGGATTTGCCTCCCCTCT 59.372 55.000 0.00 0.00 37.63 3.69
2788 3486 1.916874 GCCTCCCCTCTTACCTTTCTT 59.083 52.381 0.00 0.00 0.00 2.52
2798 3496 1.344065 TACCTTTCTTCGGTGGCTGA 58.656 50.000 0.00 0.00 35.98 4.26
2827 3525 2.365617 GAGGAGAATACCGATGCCTTCA 59.634 50.000 0.00 0.00 34.73 3.02
2849 3547 8.647256 TTCACTCTAGCTAGTAGTTTAGGTTT 57.353 34.615 20.10 0.00 33.70 3.27
2865 3563 7.450634 AGTTTAGGTTTGGGTTTTCTAATCCTC 59.549 37.037 0.00 0.00 35.41 3.71
2914 3612 6.492254 ACAACGCTTTTTCTTCGAGTTTATT 58.508 32.000 0.00 0.00 0.00 1.40
2936 3634 2.731374 GGGCTCCGATTCTCCTCG 59.269 66.667 0.00 0.00 38.37 4.63
2941 3639 1.268845 GCTCCGATTCTCCTCGAGTTC 60.269 57.143 12.31 0.00 41.12 3.01
2942 3640 2.017782 CTCCGATTCTCCTCGAGTTCA 58.982 52.381 12.31 0.00 41.12 3.18
2948 3646 5.046529 CGATTCTCCTCGAGTTCATTCATT 58.953 41.667 12.31 0.00 41.12 2.57
2951 3649 4.507710 TCTCCTCGAGTTCATTCATTTGG 58.492 43.478 12.31 0.00 0.00 3.28
2960 3658 3.342377 TCATTCATTTGGACGTAGCCA 57.658 42.857 0.00 0.00 35.78 4.75
2985 3683 1.751349 GCCCCGGCGTAGATTCCTTA 61.751 60.000 6.01 0.00 0.00 2.69
3009 3707 2.426431 TCCTTGGGGAGTGAGGTTAA 57.574 50.000 0.00 0.00 36.57 2.01
3025 3723 2.349155 GGTTAAGGTTTCTCGTTGTGCG 60.349 50.000 0.00 0.00 43.01 5.34
3031 3729 0.027455 TTTCTCGTTGTGCGTGCAAG 59.973 50.000 0.00 0.00 42.13 4.01
3035 3733 1.440850 CGTTGTGCGTGCAAGATGG 60.441 57.895 2.99 0.00 35.54 3.51
3044 3742 2.256174 CGTGCAAGATGGCAAGATTTG 58.744 47.619 0.00 0.00 46.93 2.32
3049 3747 6.278363 GTGCAAGATGGCAAGATTTGATATT 58.722 36.000 0.00 0.00 46.93 1.28
3050 3748 7.428020 GTGCAAGATGGCAAGATTTGATATTA 58.572 34.615 0.00 0.00 46.93 0.98
3051 3749 7.594015 GTGCAAGATGGCAAGATTTGATATTAG 59.406 37.037 0.00 0.00 46.93 1.73
3058 3756 7.839907 TGGCAAGATTTGATATTAGTTGCTTT 58.160 30.769 0.00 0.00 39.01 3.51
3073 3771 8.964476 TTAGTTGCTTTAGATCTATTCAAGGG 57.036 34.615 2.58 0.00 0.00 3.95
3117 3819 0.899720 ATCGCGTTGGTCCTTAAGGA 59.100 50.000 20.72 20.72 43.08 3.36
3135 3837 3.786635 AGGATACATGCACGAAGACTTC 58.213 45.455 5.03 5.03 41.41 3.01
3136 3838 2.866762 GGATACATGCACGAAGACTTCC 59.133 50.000 9.63 0.00 0.00 3.46
3138 3840 4.202121 GGATACATGCACGAAGACTTCCTA 60.202 45.833 9.63 0.00 0.00 2.94
3139 3841 2.960819 ACATGCACGAAGACTTCCTAC 58.039 47.619 9.63 0.00 0.00 3.18
3140 3842 2.271800 CATGCACGAAGACTTCCTACC 58.728 52.381 9.63 0.00 0.00 3.18
3141 3843 1.629043 TGCACGAAGACTTCCTACCT 58.371 50.000 9.63 0.00 0.00 3.08
3148 3850 3.487711 CGAAGACTTCCTACCTGTCATCG 60.488 52.174 9.63 0.00 42.41 3.84
3156 3858 2.233922 CCTACCTGTCATCGACAAGGTT 59.766 50.000 17.46 7.60 42.26 3.50
3160 3862 2.673368 CCTGTCATCGACAAGGTTAAGC 59.327 50.000 0.00 0.00 42.26 3.09
3163 3865 1.006832 CATCGACAAGGTTAAGCCGG 58.993 55.000 0.00 0.00 43.70 6.13
3167 3869 0.036294 GACAAGGTTAAGCCGGCTCT 60.036 55.000 32.93 20.23 43.70 4.09
3168 3870 0.321653 ACAAGGTTAAGCCGGCTCTG 60.322 55.000 32.93 20.82 43.70 3.35
3169 3871 1.026718 CAAGGTTAAGCCGGCTCTGG 61.027 60.000 32.93 16.58 43.70 3.86
3173 3875 0.179081 GTTAAGCCGGCTCTGGTAGG 60.179 60.000 32.93 0.00 0.00 3.18
3181 3883 3.541713 CTCTGGTAGGGGAGCGGC 61.542 72.222 0.00 0.00 0.00 6.53
3187 3889 2.762459 TAGGGGAGCGGCGACAAT 60.762 61.111 12.98 0.00 0.00 2.71
3188 3890 3.088941 TAGGGGAGCGGCGACAATG 62.089 63.158 12.98 0.00 0.00 2.82
3196 3898 3.047280 GGCGACAATGGCACGTCA 61.047 61.111 16.48 0.00 32.24 4.35
3211 3913 1.874466 GTCAGCGGCTCGTTCTAGC 60.874 63.158 0.00 0.00 41.99 3.42
3215 3917 2.951745 CGGCTCGTTCTAGCAGCG 60.952 66.667 0.00 0.00 44.64 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.806244 ACCACACAACAATACTTCGCTC 59.194 45.455 0.00 0.00 0.00 5.03
31 32 3.619233 AACCACACAACAATACTTCGC 57.381 42.857 0.00 0.00 0.00 4.70
33 34 8.542497 TCTATGTAACCACACAACAATACTTC 57.458 34.615 0.00 0.00 37.54 3.01
34 35 7.606456 CCTCTATGTAACCACACAACAATACTT 59.394 37.037 0.00 0.00 37.54 2.24
116 117 9.314321 GGCTTTTTCTTTATTTAAATAGGAGCC 57.686 33.333 7.91 13.78 0.00 4.70
124 125 9.723601 ATGATGCAGGCTTTTTCTTTATTTAAA 57.276 25.926 0.00 0.00 0.00 1.52
146 147 6.384015 TCAAGGACCACAGTGTATTAGATGAT 59.616 38.462 0.00 0.00 0.00 2.45
147 148 5.719563 TCAAGGACCACAGTGTATTAGATGA 59.280 40.000 0.00 0.00 0.00 2.92
148 149 5.977635 TCAAGGACCACAGTGTATTAGATG 58.022 41.667 0.00 0.00 0.00 2.90
149 150 6.156949 ACATCAAGGACCACAGTGTATTAGAT 59.843 38.462 0.00 0.00 0.00 1.98
150 151 5.483937 ACATCAAGGACCACAGTGTATTAGA 59.516 40.000 0.00 0.00 0.00 2.10
151 152 5.734720 ACATCAAGGACCACAGTGTATTAG 58.265 41.667 0.00 0.00 0.00 1.73
152 153 5.755409 ACATCAAGGACCACAGTGTATTA 57.245 39.130 0.00 0.00 0.00 0.98
153 154 4.640771 ACATCAAGGACCACAGTGTATT 57.359 40.909 0.00 0.00 0.00 1.89
154 155 4.326826 CAACATCAAGGACCACAGTGTAT 58.673 43.478 0.00 0.00 0.00 2.29
164 165 0.329596 AGGGCTCCAACATCAAGGAC 59.670 55.000 0.00 0.00 0.00 3.85
184 185 8.928733 CAGAACTAAACATTTCAATTGAATGGG 58.071 33.333 21.10 15.11 33.54 4.00
197 198 7.595819 TCAACCAAATCCAGAACTAAACATT 57.404 32.000 0.00 0.00 0.00 2.71
208 209 5.870978 GGTCAAAATCATCAACCAAATCCAG 59.129 40.000 0.00 0.00 0.00 3.86
235 236 6.882768 AGACCTCCTTGAGAAATAGTTGAT 57.117 37.500 0.00 0.00 0.00 2.57
310 311 5.419788 TGCTGCCATTTGAGAAATAGTTGAT 59.580 36.000 0.00 0.00 0.00 2.57
344 345 0.107017 CTAGGTGGCAAGGGGATGTG 60.107 60.000 0.00 0.00 0.00 3.21
359 360 3.451141 TGGCACTTTTTGTTTGCTAGG 57.549 42.857 0.00 0.00 36.46 3.02
390 391 8.044309 ACCGCATATATTATATTGGTGCTACAA 58.956 33.333 13.12 0.00 34.41 2.41
519 520 1.741401 CGCCTGCGAAAGATGGTGA 60.741 57.895 5.43 0.00 42.83 4.02
533 534 2.729194 TGTATATTTGGTTTGGCGCCT 58.271 42.857 29.70 6.93 0.00 5.52
564 565 4.216257 GCTACACCATTGATGTTGTTGAGT 59.784 41.667 7.14 0.00 35.05 3.41
579 580 1.202817 TGAACGCTATTCGCTACACCA 59.797 47.619 0.00 0.00 43.23 4.17
606 607 7.012138 GCCTATACCATGATGAATCAATGCTAG 59.988 40.741 0.00 0.00 40.69 3.42
905 934 4.363999 GCACTTGCTATCCAGTAGTAGTG 58.636 47.826 0.00 0.00 42.16 2.74
959 1445 2.629617 TGGCTTGCATGATCTCGATCTA 59.370 45.455 3.33 0.00 38.60 1.98
1132 1621 1.486211 CCTTGTACCAGAGGATCGGT 58.514 55.000 0.00 0.00 42.81 4.69
1476 1965 2.126031 GCGAGGACGGTGAAGGTC 60.126 66.667 0.00 0.00 40.15 3.85
1827 2316 0.028374 CGAACGCGAACCCTGTTTTT 59.972 50.000 15.93 0.00 40.82 1.94
1833 2322 4.712425 CCGACGAACGCGAACCCT 62.712 66.667 15.93 0.00 41.64 4.34
2139 2628 3.257624 GTGTTAGTACTACTGGCAGTGGT 59.742 47.826 34.05 34.05 42.72 4.16
2256 2934 5.105752 CAGAAAAACGAAATTGAACCCACA 58.894 37.500 0.00 0.00 0.00 4.17
2265 2943 8.432110 AAACCTAATTGCAGAAAAACGAAATT 57.568 26.923 0.00 0.00 0.00 1.82
2300 2981 2.224606 ACCTATGATCTGCGGCATTTG 58.775 47.619 1.75 0.00 0.00 2.32
2380 3071 7.716799 TGAAGGTGCTATATTGGATGTTTTT 57.283 32.000 0.00 0.00 0.00 1.94
2385 3076 6.347969 CGTGATTGAAGGTGCTATATTGGATG 60.348 42.308 0.00 0.00 0.00 3.51
2386 3077 5.702670 CGTGATTGAAGGTGCTATATTGGAT 59.297 40.000 0.00 0.00 0.00 3.41
2388 3079 4.214119 CCGTGATTGAAGGTGCTATATTGG 59.786 45.833 0.00 0.00 0.00 3.16
2390 3081 5.036117 ACCGTGATTGAAGGTGCTATATT 57.964 39.130 0.00 0.00 34.71 1.28
2393 3084 3.451178 ACTACCGTGATTGAAGGTGCTAT 59.549 43.478 0.00 0.00 37.00 2.97
2396 3087 2.094762 ACTACCGTGATTGAAGGTGC 57.905 50.000 0.00 0.00 37.00 5.01
2399 3091 5.475719 TCTTTGTACTACCGTGATTGAAGG 58.524 41.667 0.00 0.00 0.00 3.46
2409 3101 7.596749 ATTTCTGATGTTCTTTGTACTACCG 57.403 36.000 0.00 0.00 0.00 4.02
2468 3164 3.515630 CTTCAGTGCATGTAGTCGTCAT 58.484 45.455 0.00 0.00 0.00 3.06
2469 3165 2.926586 GCTTCAGTGCATGTAGTCGTCA 60.927 50.000 0.00 0.00 0.00 4.35
2470 3166 1.656095 GCTTCAGTGCATGTAGTCGTC 59.344 52.381 0.00 0.00 0.00 4.20
2472 3168 1.713597 TGCTTCAGTGCATGTAGTCG 58.286 50.000 0.00 0.00 38.12 4.18
2480 3176 1.100463 TTTCGGCTTGCTTCAGTGCA 61.100 50.000 0.00 0.00 41.65 4.57
2483 3179 1.845809 CGCTTTCGGCTTGCTTCAGT 61.846 55.000 0.00 0.00 39.13 3.41
2508 3204 2.363795 AAGGAGGGGCGATGACGA 60.364 61.111 0.00 0.00 42.66 4.20
2531 3227 3.177997 ACAACAAATTTTGCTCGGCTT 57.822 38.095 9.04 0.00 0.00 4.35
2553 3249 5.964168 ACACGACGATTTTTCGACTATCTAG 59.036 40.000 0.00 0.00 39.83 2.43
2558 3254 5.343058 CCTTAACACGACGATTTTTCGACTA 59.657 40.000 0.00 0.00 39.83 2.59
2565 3261 1.808343 GGGCCTTAACACGACGATTTT 59.192 47.619 0.84 0.00 0.00 1.82
2585 3281 2.715749 TTGGTGTGCTGATCCTATGG 57.284 50.000 0.00 0.00 0.00 2.74
2604 3300 1.805428 ATCAGCGGCGGTTGCTTTTT 61.805 50.000 9.73 0.00 41.72 1.94
2607 3303 3.434319 CATCAGCGGCGGTTGCTT 61.434 61.111 9.73 0.00 41.72 3.91
2609 3305 2.470801 TTTTCATCAGCGGCGGTTGC 62.471 55.000 9.73 0.00 41.71 4.17
2616 3312 0.813184 ATGCCACTTTTCATCAGCGG 59.187 50.000 0.00 0.00 0.00 5.52
2633 3329 7.921214 AGTGTTGTACTAAATCGGTGATCTATG 59.079 37.037 0.00 0.00 38.04 2.23
2643 3339 9.577110 TTTGGAGTATAGTGTTGTACTAAATCG 57.423 33.333 0.00 0.00 44.64 3.34
2717 3413 1.078848 AGAGTTTGCCCTAGCTGCG 60.079 57.895 0.00 0.00 40.80 5.18
2720 3416 2.302019 GGGAGAGTTTGCCCTAGCT 58.698 57.895 0.00 0.00 41.31 3.32
2741 3439 2.549282 CGTTCACCGGCGAAACTG 59.451 61.111 9.30 0.00 0.00 3.16
2748 3446 1.862602 AAATCCAAGCGTTCACCGGC 61.863 55.000 0.00 0.00 36.94 6.13
2749 3447 0.109781 CAAATCCAAGCGTTCACCGG 60.110 55.000 0.00 0.00 36.94 5.28
2756 3454 1.678970 GGGAGGCAAATCCAAGCGT 60.679 57.895 4.47 0.00 41.52 5.07
2760 3458 1.084018 AAGAGGGGAGGCAAATCCAA 58.916 50.000 4.47 0.00 41.52 3.53
2761 3459 1.564348 GTAAGAGGGGAGGCAAATCCA 59.436 52.381 4.47 0.00 41.52 3.41
2765 3463 1.755200 AAGGTAAGAGGGGAGGCAAA 58.245 50.000 0.00 0.00 0.00 3.68
2767 3465 1.203440 AGAAAGGTAAGAGGGGAGGCA 60.203 52.381 0.00 0.00 0.00 4.75
2778 3476 1.695242 TCAGCCACCGAAGAAAGGTAA 59.305 47.619 0.00 0.00 40.59 2.85
2788 3486 2.046023 CTTGCCATCAGCCACCGA 60.046 61.111 0.00 0.00 42.71 4.69
2798 3496 1.417890 CGGTATTCTCCTCCTTGCCAT 59.582 52.381 0.00 0.00 0.00 4.40
2804 3502 1.133009 AGGCATCGGTATTCTCCTCCT 60.133 52.381 0.00 0.00 0.00 3.69
2827 3525 6.380560 CCCAAACCTAAACTACTAGCTAGAGT 59.619 42.308 27.45 20.58 0.00 3.24
2849 3547 2.355716 CCTGCGAGGATTAGAAAACCCA 60.356 50.000 0.00 0.00 37.67 4.51
2932 3630 3.062639 CGTCCAAATGAATGAACTCGAGG 59.937 47.826 18.41 0.00 0.00 4.63
2936 3634 4.201822 GGCTACGTCCAAATGAATGAACTC 60.202 45.833 0.00 0.00 0.00 3.01
2941 3639 3.727673 CGTTGGCTACGTCCAAATGAATG 60.728 47.826 13.26 0.00 46.63 2.67
2942 3640 2.418628 CGTTGGCTACGTCCAAATGAAT 59.581 45.455 13.26 0.00 46.63 2.57
2979 3677 3.214694 TCCCCAAGGAGATGTAAGGAA 57.785 47.619 0.00 0.00 37.19 3.36
3001 3699 4.124238 CACAACGAGAAACCTTAACCTCA 58.876 43.478 0.00 0.00 0.00 3.86
3025 3723 3.581024 TCAAATCTTGCCATCTTGCAC 57.419 42.857 0.00 0.00 41.88 4.57
3031 3729 7.655490 AGCAACTAATATCAAATCTTGCCATC 58.345 34.615 0.00 0.00 34.39 3.51
3049 3747 8.090788 ACCCTTGAATAGATCTAAAGCAACTA 57.909 34.615 6.52 0.00 0.00 2.24
3050 3748 6.963322 ACCCTTGAATAGATCTAAAGCAACT 58.037 36.000 6.52 0.00 0.00 3.16
3051 3749 7.336931 TGAACCCTTGAATAGATCTAAAGCAAC 59.663 37.037 6.52 1.22 0.00 4.17
3058 3756 6.785337 TCGTTGAACCCTTGAATAGATCTA 57.215 37.500 4.57 4.57 0.00 1.98
3067 3765 1.418264 TCACCATCGTTGAACCCTTGA 59.582 47.619 0.00 0.00 0.00 3.02
3068 3766 1.890876 TCACCATCGTTGAACCCTTG 58.109 50.000 0.00 0.00 0.00 3.61
3069 3767 2.819608 CAATCACCATCGTTGAACCCTT 59.180 45.455 0.00 0.00 0.00 3.95
3070 3768 2.436417 CAATCACCATCGTTGAACCCT 58.564 47.619 0.00 0.00 0.00 4.34
3071 3769 1.135402 GCAATCACCATCGTTGAACCC 60.135 52.381 0.00 0.00 0.00 4.11
3072 3770 1.465689 CGCAATCACCATCGTTGAACC 60.466 52.381 0.00 0.00 0.00 3.62
3073 3771 1.465689 CCGCAATCACCATCGTTGAAC 60.466 52.381 0.00 0.00 0.00 3.18
3117 3819 3.895232 AGGAAGTCTTCGTGCATGTAT 57.105 42.857 6.99 0.00 0.00 2.29
3118 3820 3.119245 GGTAGGAAGTCTTCGTGCATGTA 60.119 47.826 20.30 0.00 32.83 2.29
3127 3829 3.695060 TCGATGACAGGTAGGAAGTCTTC 59.305 47.826 3.80 3.80 34.78 2.87
3135 3837 1.825474 ACCTTGTCGATGACAGGTAGG 59.175 52.381 14.98 13.76 43.69 3.18
3136 3838 3.594603 AACCTTGTCGATGACAGGTAG 57.405 47.619 16.15 6.03 43.69 3.18
3138 3840 3.864921 GCTTAACCTTGTCGATGACAGGT 60.865 47.826 12.34 12.34 43.69 4.00
3139 3841 2.673368 GCTTAACCTTGTCGATGACAGG 59.327 50.000 11.41 11.41 43.69 4.00
3140 3842 2.673368 GGCTTAACCTTGTCGATGACAG 59.327 50.000 0.00 0.00 43.69 3.51
3141 3843 2.695359 GGCTTAACCTTGTCGATGACA 58.305 47.619 0.00 0.00 41.09 3.58
3148 3850 0.036294 AGAGCCGGCTTAACCTTGTC 60.036 55.000 33.34 14.79 35.61 3.18
3156 3858 1.760875 CCCTACCAGAGCCGGCTTA 60.761 63.158 33.34 18.08 0.00 3.09
3160 3862 2.840102 CTCCCCTACCAGAGCCGG 60.840 72.222 0.00 0.00 0.00 6.13
3169 3871 3.090219 ATTGTCGCCGCTCCCCTAC 62.090 63.158 0.00 0.00 0.00 3.18
3181 3883 2.476051 GCTGACGTGCCATTGTCG 59.524 61.111 0.00 0.00 37.94 4.35
3191 3893 2.254703 CTAGAACGAGCCGCTGACGT 62.255 60.000 0.00 0.00 41.97 4.34
3196 3898 2.492090 CTGCTAGAACGAGCCGCT 59.508 61.111 0.00 0.00 42.11 5.52


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

AutoCloner maintained by Alex Coulton.