Multiple sequence alignment - TraesCS1B01G292400

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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 TraesCS1B01G292400 chr1B 100.000 3510 0 0 1 3510 509893675 509890166 0.000000e+00 6482.0
1 TraesCS1B01G292400 chr1D 94.040 1745 71 16 845 2572 379798001 379796273 0.000000e+00 2615.0
2 TraesCS1B01G292400 chr1D 93.581 888 36 8 2632 3510 379796271 379795396 0.000000e+00 1304.0
3 TraesCS1B01G292400 chr1D 90.068 876 37 19 4 838 379798914 379798048 0.000000e+00 1090.0
4 TraesCS1B01G292400 chr1A 94.715 1438 50 16 845 2270 480832890 480831467 0.000000e+00 2211.0
5 TraesCS1B01G292400 chr1A 90.113 708 30 10 2804 3510 480830941 480830273 0.000000e+00 883.0
6 TraesCS1B01G292400 chr1A 89.142 571 31 15 141 701 480833872 480833323 0.000000e+00 682.0
7 TraesCS1B01G292400 chr1A 91.429 490 23 12 2282 2768 480831408 480830935 0.000000e+00 654.0
8 TraesCS1B01G292400 chr1A 78.360 439 46 23 6 417 480883990 480883574 4.530000e-59 239.0
9 TraesCS1B01G292400 chr1A 92.661 109 6 2 739 846 480833037 480832930 4.690000e-34 156.0
10 TraesCS1B01G292400 chr5B 100.000 28 0 0 2591 2618 21431926 21431953 6.000000e-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 TraesCS1B01G292400 chr1B 509890166 509893675 3509 True 6482.000000 6482 100.000 1 3510 1 chr1B.!!$R1 3509
1 TraesCS1B01G292400 chr1D 379795396 379798914 3518 True 1669.666667 2615 92.563 4 3510 3 chr1D.!!$R1 3506
2 TraesCS1B01G292400 chr1A 480830273 480833872 3599 True 917.200000 2211 91.612 141 3510 5 chr1A.!!$R2 3369

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
186 198 0.246360 TCCGTAGTAGTGACGACCGA 59.754 55.000 0.0 0.0 42.98 4.69 F
713 753 1.001068 GAAGATCTAAGTAGGGCCGCC 59.999 57.143 0.0 0.0 0.00 6.13 F
2009 2338 0.325933 TGATCTGTGGAGGTTGGCAG 59.674 55.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2338 0.328258 TTCCTTAGCTCCCTGCCAAC 59.672 55.0 0.00 0.0 44.23 3.77 R
2392 2775 0.251077 CTTCCTCTTTGGTGGCAGCT 60.251 55.0 18.53 0.0 37.07 4.24 R
2894 3334 1.419874 GCAGAGACTGAGATGCACGC 61.420 60.0 2.81 0.0 38.54 5.34 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
179 191 7.443575 GGAGAATATTACAGTCCGTAGTAGTGA 59.556 40.741 0.00 0.00 0.00 3.41
184 196 1.396301 CAGTCCGTAGTAGTGACGACC 59.604 57.143 0.00 0.00 42.98 4.79
185 197 0.371645 GTCCGTAGTAGTGACGACCG 59.628 60.000 0.00 0.00 42.98 4.79
186 198 0.246360 TCCGTAGTAGTGACGACCGA 59.754 55.000 0.00 0.00 42.98 4.69
187 199 1.078709 CCGTAGTAGTGACGACCGAA 58.921 55.000 0.00 0.00 42.98 4.30
188 200 1.667724 CCGTAGTAGTGACGACCGAAT 59.332 52.381 0.00 0.00 42.98 3.34
254 266 1.275238 ACCATCCTCTGATTCCCCCTT 60.275 52.381 0.00 0.00 0.00 3.95
364 384 1.255882 CATCCATCTCCCTCCTCTCG 58.744 60.000 0.00 0.00 0.00 4.04
476 497 3.005578 GCCGATCCGAGGTAAATTCTACT 59.994 47.826 0.00 0.00 0.00 2.57
551 572 5.119694 GCCTTTAGGTCTCCAATACTTGAG 58.880 45.833 0.00 0.00 37.57 3.02
558 579 4.319177 GTCTCCAATACTTGAGCACAGTT 58.681 43.478 0.00 0.00 0.00 3.16
654 677 1.139498 TGTTGATCTGGGAGGGGCAA 61.139 55.000 0.00 0.00 0.00 4.52
713 753 1.001068 GAAGATCTAAGTAGGGCCGCC 59.999 57.143 0.00 0.00 0.00 6.13
789 1065 4.839121 TGTGAGACTGGTACTGTGTTTTT 58.161 39.130 0.00 0.00 41.64 1.94
835 1112 8.798859 AAACGGTTATAGAGTCTACTTGAGTA 57.201 34.615 0.85 0.00 0.00 2.59
838 1115 9.054922 ACGGTTATAGAGTCTACTTGAGTATTC 57.945 37.037 0.85 0.00 0.00 1.75
843 1160 6.687081 AGAGTCTACTTGAGTATTCCTTCG 57.313 41.667 0.00 0.00 0.00 3.79
855 1172 4.379243 CCTTCGGTCGCACTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
864 1181 1.144057 CGCACTGCCTACCCTAAGG 59.856 63.158 0.00 0.00 39.87 2.69
955 1277 6.206438 TGACTATGCATTTTCAAGTGCTTGTA 59.794 34.615 3.54 0.00 41.78 2.41
960 1282 4.298332 CATTTTCAAGTGCTTGTACCCAC 58.702 43.478 11.17 0.00 41.16 4.61
1028 1350 6.462067 CCCTGTTCTTTCTTGCTTTCAGAATT 60.462 38.462 0.00 0.00 0.00 2.17
1032 1354 6.713762 TCTTTCTTGCTTTCAGAATTTCCA 57.286 33.333 0.00 0.00 0.00 3.53
1113 1435 2.096248 ACGGTGGTCAGAAAAGCAAAA 58.904 42.857 0.00 0.00 0.00 2.44
1137 1459 4.277515 TGATGCTATAAGCCCATCTGAC 57.722 45.455 0.00 0.00 41.51 3.51
1323 1645 3.747708 GCTACTTTGCCCCCGAATCTTAT 60.748 47.826 0.00 0.00 0.00 1.73
1526 1854 3.019564 AGCTGTCATTAAAGCATGGGAC 58.980 45.455 0.00 0.00 42.06 4.46
1559 1887 6.648725 AGAACTATGAAAGTATGTGAACGC 57.351 37.500 0.00 0.00 37.50 4.84
1618 1946 5.772825 TTCTTTCTAATATGGCATGGTGC 57.227 39.130 10.98 0.00 44.08 5.01
1696 2025 3.706373 GGAAGTCCAGGCTCGCCA 61.706 66.667 11.02 0.00 38.92 5.69
1711 2040 1.147153 GCCACCAGAGATACCAGCC 59.853 63.158 0.00 0.00 0.00 4.85
1970 2299 2.093181 CCCAATAATCAGACGGTGGTCA 60.093 50.000 0.00 0.00 45.92 4.02
1978 2307 4.074627 TCAGACGGTGGTCAACAAAATA 57.925 40.909 0.00 0.00 45.92 1.40
2009 2338 0.325933 TGATCTGTGGAGGTTGGCAG 59.674 55.000 0.00 0.00 0.00 4.85
2028 2357 0.328258 GTTGGCAGGGAGCTAAGGAA 59.672 55.000 0.00 0.00 44.87 3.36
2243 2579 7.850193 ACCCAATAATCATGTTAAACAGCATT 58.150 30.769 0.00 0.00 0.00 3.56
2263 2599 8.361889 CAGCATTGGACATCATATTGGAATTAA 58.638 33.333 0.00 0.00 0.00 1.40
2292 2675 8.749841 ATAGATTTGAGAACTACGTATCATGC 57.250 34.615 0.00 0.00 0.00 4.06
2329 2712 8.749026 TTTGTAGTACCCTTGTGATTGTTAAA 57.251 30.769 0.00 0.00 0.00 1.52
2572 3004 2.064014 GTGCCGACTGTTGTAACCTAC 58.936 52.381 0.00 0.00 0.00 3.18
2573 3005 1.965643 TGCCGACTGTTGTAACCTACT 59.034 47.619 0.00 0.00 0.00 2.57
2574 3006 2.029649 TGCCGACTGTTGTAACCTACTC 60.030 50.000 0.00 0.00 0.00 2.59
2575 3007 2.673326 GCCGACTGTTGTAACCTACTCC 60.673 54.545 0.00 0.00 0.00 3.85
2576 3008 2.094338 CCGACTGTTGTAACCTACTCCC 60.094 54.545 0.00 0.00 0.00 4.30
2577 3009 2.824341 CGACTGTTGTAACCTACTCCCT 59.176 50.000 0.00 0.00 0.00 4.20
2578 3010 3.119566 CGACTGTTGTAACCTACTCCCTC 60.120 52.174 0.00 0.00 0.00 4.30
2579 3011 3.171528 ACTGTTGTAACCTACTCCCTCC 58.828 50.000 0.00 0.00 0.00 4.30
2580 3012 2.165845 CTGTTGTAACCTACTCCCTCCG 59.834 54.545 0.00 0.00 0.00 4.63
2581 3013 2.174360 GTTGTAACCTACTCCCTCCGT 58.826 52.381 0.00 0.00 0.00 4.69
2582 3014 2.134789 TGTAACCTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
2583 3015 1.020437 GTAACCTACTCCCTCCGTCG 58.980 60.000 0.00 0.00 0.00 5.12
2584 3016 0.749454 TAACCTACTCCCTCCGTCGC 60.749 60.000 0.00 0.00 0.00 5.19
2585 3017 2.439701 CCTACTCCCTCCGTCGCA 60.440 66.667 0.00 0.00 0.00 5.10
2586 3018 1.828660 CCTACTCCCTCCGTCGCAT 60.829 63.158 0.00 0.00 0.00 4.73
2587 3019 0.536687 CCTACTCCCTCCGTCGCATA 60.537 60.000 0.00 0.00 0.00 3.14
2588 3020 1.315690 CTACTCCCTCCGTCGCATAA 58.684 55.000 0.00 0.00 0.00 1.90
2589 3021 1.679680 CTACTCCCTCCGTCGCATAAA 59.320 52.381 0.00 0.00 0.00 1.40
2590 3022 0.899720 ACTCCCTCCGTCGCATAAAA 59.100 50.000 0.00 0.00 0.00 1.52
2591 3023 1.134788 ACTCCCTCCGTCGCATAAAAG 60.135 52.381 0.00 0.00 0.00 2.27
2592 3024 1.136305 CTCCCTCCGTCGCATAAAAGA 59.864 52.381 0.00 0.00 0.00 2.52
2593 3025 1.551430 TCCCTCCGTCGCATAAAAGAA 59.449 47.619 0.00 0.00 0.00 2.52
2594 3026 2.027929 TCCCTCCGTCGCATAAAAGAAA 60.028 45.455 0.00 0.00 0.00 2.52
2595 3027 2.745281 CCCTCCGTCGCATAAAAGAAAA 59.255 45.455 0.00 0.00 0.00 2.29
2596 3028 3.425758 CCCTCCGTCGCATAAAAGAAAAC 60.426 47.826 0.00 0.00 0.00 2.43
2597 3029 3.187637 CCTCCGTCGCATAAAAGAAAACA 59.812 43.478 0.00 0.00 0.00 2.83
2598 3030 4.142687 CCTCCGTCGCATAAAAGAAAACAT 60.143 41.667 0.00 0.00 0.00 2.71
2599 3031 4.965062 TCCGTCGCATAAAAGAAAACATC 58.035 39.130 0.00 0.00 0.00 3.06
2600 3032 4.693566 TCCGTCGCATAAAAGAAAACATCT 59.306 37.500 0.00 0.00 41.32 2.90
2613 3045 6.575162 AGAAAACATCTTACATTGTGGGAC 57.425 37.500 0.00 0.00 33.39 4.46
2614 3046 5.181245 AGAAAACATCTTACATTGTGGGACG 59.819 40.000 0.00 0.00 33.39 4.79
2615 3047 3.973206 ACATCTTACATTGTGGGACGA 57.027 42.857 0.00 0.00 0.00 4.20
2616 3048 4.280436 ACATCTTACATTGTGGGACGAA 57.720 40.909 0.00 0.00 0.00 3.85
2617 3049 4.253685 ACATCTTACATTGTGGGACGAAG 58.746 43.478 0.00 0.00 0.00 3.79
2630 3062 3.118261 TGGGACGAAGTAGTACGGAGTAT 60.118 47.826 0.00 0.00 45.41 2.12
2634 3066 6.205658 GGGACGAAGTAGTACGGAGTATAAAT 59.794 42.308 0.00 0.00 45.41 1.40
2660 3092 0.453950 GCACAAAGCATCAGACTGCG 60.454 55.000 0.00 0.00 46.86 5.18
2705 3144 1.454847 TTTGGGGGATGCCGTATGC 60.455 57.895 0.00 0.00 41.77 3.14
2775 3214 7.707104 ACTTCTCTTGGTTTTTACACAAGATG 58.293 34.615 6.78 4.20 46.50 2.90
2857 3297 8.206189 TGTCTGAGATAATGTAATTGCAGATGA 58.794 33.333 1.90 0.00 36.99 2.92
2858 3298 8.710551 GTCTGAGATAATGTAATTGCAGATGAG 58.289 37.037 1.90 0.00 36.99 2.90
2859 3299 8.427276 TCTGAGATAATGTAATTGCAGATGAGT 58.573 33.333 1.90 0.00 36.99 3.41
2860 3300 8.374327 TGAGATAATGTAATTGCAGATGAGTG 57.626 34.615 1.90 0.00 36.99 3.51
2870 3310 4.470334 TGCAGATGAGTGTATACAGCAA 57.530 40.909 5.62 0.00 0.00 3.91
2876 3316 5.819379 AGATGAGTGTATACAGCAAATGTGG 59.181 40.000 5.62 0.00 43.80 4.17
2894 3334 3.820467 TGTGGCATTTACTTCTGAACAGG 59.180 43.478 0.00 0.00 0.00 4.00
2901 3341 0.250467 ACTTCTGAACAGGCGTGCAT 60.250 50.000 6.26 0.00 27.15 3.96
2902 3342 0.445436 CTTCTGAACAGGCGTGCATC 59.555 55.000 6.26 6.10 27.15 3.91
2903 3343 0.035317 TTCTGAACAGGCGTGCATCT 59.965 50.000 6.26 0.00 27.15 2.90
2904 3344 0.390340 TCTGAACAGGCGTGCATCTC 60.390 55.000 6.26 0.00 27.15 2.75
2905 3345 0.671472 CTGAACAGGCGTGCATCTCA 60.671 55.000 6.26 3.91 27.15 3.27
2906 3346 0.671472 TGAACAGGCGTGCATCTCAG 60.671 55.000 6.26 0.00 0.00 3.35
2911 3351 0.969917 AGGCGTGCATCTCAGTCTCT 60.970 55.000 0.00 0.00 0.00 3.10
3045 3486 0.809241 GGCAGCAGTCATCTTCCTCG 60.809 60.000 0.00 0.00 0.00 4.63
3073 3514 4.201783 GGAAATACGACCATCTCAAAACGG 60.202 45.833 0.00 0.00 0.00 4.44
3089 3530 1.913762 CGGAACCCTGGAGAGGTGT 60.914 63.158 0.00 0.00 37.78 4.16
3109 3550 5.057149 GTGTAAATACTTCTGGATCCGCAT 58.943 41.667 7.39 0.00 0.00 4.73
3168 3609 4.708421 AGAAGTATCCGCTAACCTGTTACA 59.292 41.667 0.00 0.00 0.00 2.41
3189 3630 4.463891 ACAATCCGAAATGGCTCAGAAATT 59.536 37.500 0.00 0.00 37.80 1.82
3230 3671 9.372189 CTTGAATAGGAATATCAATCCCCTTTT 57.628 33.333 0.00 0.00 37.71 2.27
3315 3757 7.277981 GGCGGTGTAGATGGTAAAATATCATAG 59.722 40.741 0.00 0.00 27.47 2.23
3409 3851 4.032960 AGCACCTGTGGATAAACAATCA 57.967 40.909 0.00 0.00 36.20 2.57
3471 3913 2.892374 AGAAAGCAACCAAGCAAACAC 58.108 42.857 0.00 0.00 36.85 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.495754 GACTCAATATCTTTTGTGCAAAGTATC 57.504 33.333 0.00 0.00 42.47 2.24
161 173 3.679980 GTCGTCACTACTACGGACTGTAA 59.320 47.826 0.00 0.00 40.68 2.41
188 200 1.268386 CCCTTCGTCGATTCGATTCGA 60.268 52.381 24.07 24.07 45.27 3.71
254 266 1.961381 ATCTGGATGGGACGAGGGGA 61.961 60.000 0.00 0.00 0.00 4.81
364 384 1.213296 TGGGATTAGAAGGGTGAGCC 58.787 55.000 0.00 0.00 0.00 4.70
437 458 0.456221 GGCGACGATTTGGAGAGAGA 59.544 55.000 0.00 0.00 0.00 3.10
459 480 6.403878 CAAAGGAAGTAGAATTTACCTCGGA 58.596 40.000 0.00 0.00 0.00 4.55
476 497 4.262549 CCATGACAAAATCAGGCAAAGGAA 60.263 41.667 0.00 0.00 41.91 3.36
546 567 3.003068 CCTGAACTGAAACTGTGCTCAAG 59.997 47.826 0.00 0.00 0.00 3.02
551 572 2.423538 ACAACCTGAACTGAAACTGTGC 59.576 45.455 0.00 0.00 0.00 4.57
558 579 3.892633 TGGCACAACCTGAACTGAA 57.107 47.368 0.00 0.00 40.22 3.02
713 753 7.975616 CACAAAACAATTCCAATAGGTGATAGG 59.024 37.037 0.00 0.00 35.89 2.57
717 757 6.723298 ACACAAAACAATTCCAATAGGTGA 57.277 33.333 0.00 0.00 35.89 4.02
721 761 9.398170 CTGAGTTACACAAAACAATTCCAATAG 57.602 33.333 0.00 0.00 0.00 1.73
789 1065 8.386606 CCGTTTTTCTCATCAAAACAAAAATGA 58.613 29.630 8.54 0.00 42.07 2.57
842 1159 4.814294 GGGTAGGCAGTGCGACCG 62.814 72.222 24.03 0.00 36.49 4.79
843 1160 1.610554 TTAGGGTAGGCAGTGCGACC 61.611 60.000 23.34 23.34 35.39 4.79
864 1181 8.067784 GCCAGTTTTAAAATAAAAGGTTTCAGC 58.932 33.333 3.52 0.00 0.00 4.26
917 1234 5.738619 TGCATAGTCAGTTCCTTCACTTA 57.261 39.130 0.00 0.00 0.00 2.24
955 1277 5.838521 ACCAAATTTGATCAAACTAGTGGGT 59.161 36.000 27.80 22.58 32.51 4.51
960 1282 8.369218 AGCAAAACCAAATTTGATCAAACTAG 57.631 30.769 22.71 14.22 41.73 2.57
1028 1350 2.942804 TGACCTTGCTGTTGAATGGAA 58.057 42.857 0.00 0.00 0.00 3.53
1032 1354 1.547372 GCCATGACCTTGCTGTTGAAT 59.453 47.619 0.00 0.00 0.00 2.57
1137 1459 2.953466 CATCAACCAATGGAAGGCTG 57.047 50.000 6.16 0.00 0.00 4.85
1323 1645 2.561858 TGCATAGAAAAGTGCATTGCCA 59.438 40.909 6.12 0.00 45.60 4.92
1408 1736 4.458989 GTGTCCCTTCATAATGAACTGCAA 59.541 41.667 0.00 0.00 32.21 4.08
1485 1813 1.133199 TCCCTGGCCAACTTCAAATGT 60.133 47.619 7.01 0.00 0.00 2.71
1559 1887 9.661187 CTATCAAAGTGAGCAAGCAATTATAAG 57.339 33.333 0.00 0.00 0.00 1.73
1618 1946 1.135315 CCAACCTTCAACATGCCGATG 60.135 52.381 0.00 0.00 35.49 3.84
1696 2025 1.958288 ACTTGGCTGGTATCTCTGGT 58.042 50.000 0.00 0.00 0.00 4.00
1711 2040 4.190772 AGGTGAAATGGCAAACAAACTTG 58.809 39.130 0.00 0.00 0.00 3.16
1934 2263 8.759481 TGATTATTGGGTACTTGATGCATTAA 57.241 30.769 0.00 1.27 0.00 1.40
1935 2264 8.217111 TCTGATTATTGGGTACTTGATGCATTA 58.783 33.333 0.00 0.00 0.00 1.90
1936 2265 7.013655 GTCTGATTATTGGGTACTTGATGCATT 59.986 37.037 0.00 0.00 0.00 3.56
1937 2266 6.488006 GTCTGATTATTGGGTACTTGATGCAT 59.512 38.462 0.00 0.00 0.00 3.96
1938 2267 5.822519 GTCTGATTATTGGGTACTTGATGCA 59.177 40.000 0.00 0.00 0.00 3.96
1970 2299 8.242053 CAGATCAGCTTCATTGAGTATTTTGTT 58.758 33.333 0.00 0.00 0.00 2.83
1978 2307 3.262660 TCCACAGATCAGCTTCATTGAGT 59.737 43.478 0.00 0.00 0.00 3.41
2009 2338 0.328258 TTCCTTAGCTCCCTGCCAAC 59.672 55.000 0.00 0.00 44.23 3.77
2028 2357 4.515361 CATTCAGAGGCAGAGTTCTCAAT 58.485 43.478 2.64 0.00 32.76 2.57
2138 2473 1.708341 AACAGCAAAAGCTCCACCAT 58.292 45.000 0.00 0.00 0.00 3.55
2140 2475 2.602257 AAAACAGCAAAAGCTCCACC 57.398 45.000 0.00 0.00 0.00 4.61
2270 2606 5.986135 AGGCATGATACGTAGTTCTCAAATC 59.014 40.000 0.08 0.00 37.78 2.17
2272 2608 5.339008 AGGCATGATACGTAGTTCTCAAA 57.661 39.130 0.08 0.00 37.78 2.69
2292 2675 9.284968 CAAGGGTACTACAAAATGGATAATAGG 57.715 37.037 0.00 0.00 0.00 2.57
2392 2775 0.251077 CTTCCTCTTTGGTGGCAGCT 60.251 55.000 18.53 0.00 37.07 4.24
2572 3004 1.136305 TCTTTTATGCGACGGAGGGAG 59.864 52.381 0.00 0.00 0.00 4.30
2573 3005 1.187974 TCTTTTATGCGACGGAGGGA 58.812 50.000 0.00 0.00 0.00 4.20
2574 3006 2.018542 TTCTTTTATGCGACGGAGGG 57.981 50.000 0.00 0.00 0.00 4.30
2575 3007 3.187637 TGTTTTCTTTTATGCGACGGAGG 59.812 43.478 0.00 0.00 0.00 4.30
2576 3008 4.398549 TGTTTTCTTTTATGCGACGGAG 57.601 40.909 0.00 0.00 0.00 4.63
2577 3009 4.693566 AGATGTTTTCTTTTATGCGACGGA 59.306 37.500 0.00 0.00 0.00 4.69
2578 3010 4.969816 AGATGTTTTCTTTTATGCGACGG 58.030 39.130 0.00 0.00 0.00 4.79
2579 3011 7.012943 TGTAAGATGTTTTCTTTTATGCGACG 58.987 34.615 0.00 0.00 42.15 5.12
2580 3012 8.895932 ATGTAAGATGTTTTCTTTTATGCGAC 57.104 30.769 0.00 0.00 42.15 5.19
2581 3013 9.340695 CAATGTAAGATGTTTTCTTTTATGCGA 57.659 29.630 0.00 0.00 42.15 5.10
2582 3014 9.128107 ACAATGTAAGATGTTTTCTTTTATGCG 57.872 29.630 0.00 0.00 42.15 4.73
2585 3017 9.927668 CCCACAATGTAAGATGTTTTCTTTTAT 57.072 29.630 0.00 0.00 42.15 1.40
2586 3018 9.137459 TCCCACAATGTAAGATGTTTTCTTTTA 57.863 29.630 0.00 0.00 42.15 1.52
2587 3019 7.926018 GTCCCACAATGTAAGATGTTTTCTTTT 59.074 33.333 0.00 0.00 42.15 2.27
2588 3020 7.433680 GTCCCACAATGTAAGATGTTTTCTTT 58.566 34.615 0.00 0.00 42.15 2.52
2589 3021 6.293955 CGTCCCACAATGTAAGATGTTTTCTT 60.294 38.462 0.00 0.00 46.53 2.52
2590 3022 5.181245 CGTCCCACAATGTAAGATGTTTTCT 59.819 40.000 0.00 0.00 35.70 2.52
2591 3023 5.180492 TCGTCCCACAATGTAAGATGTTTTC 59.820 40.000 0.00 0.00 0.00 2.29
2592 3024 5.067273 TCGTCCCACAATGTAAGATGTTTT 58.933 37.500 0.00 0.00 0.00 2.43
2593 3025 4.647611 TCGTCCCACAATGTAAGATGTTT 58.352 39.130 0.00 0.00 0.00 2.83
2594 3026 4.280436 TCGTCCCACAATGTAAGATGTT 57.720 40.909 0.00 0.00 0.00 2.71
2595 3027 3.973206 TCGTCCCACAATGTAAGATGT 57.027 42.857 0.00 0.00 0.00 3.06
2596 3028 4.253685 ACTTCGTCCCACAATGTAAGATG 58.746 43.478 0.00 0.00 0.00 2.90
2597 3029 4.553330 ACTTCGTCCCACAATGTAAGAT 57.447 40.909 0.00 0.00 0.00 2.40
2598 3030 4.525487 ACTACTTCGTCCCACAATGTAAGA 59.475 41.667 0.00 0.00 0.00 2.10
2599 3031 4.817517 ACTACTTCGTCCCACAATGTAAG 58.182 43.478 0.00 0.00 0.00 2.34
2600 3032 4.877378 ACTACTTCGTCCCACAATGTAA 57.123 40.909 0.00 0.00 0.00 2.41
2601 3033 4.142622 CGTACTACTTCGTCCCACAATGTA 60.143 45.833 0.00 0.00 0.00 2.29
2602 3034 3.366679 CGTACTACTTCGTCCCACAATGT 60.367 47.826 0.00 0.00 0.00 2.71
2603 3035 3.176708 CGTACTACTTCGTCCCACAATG 58.823 50.000 0.00 0.00 0.00 2.82
2604 3036 2.165030 CCGTACTACTTCGTCCCACAAT 59.835 50.000 0.00 0.00 0.00 2.71
2605 3037 1.541147 CCGTACTACTTCGTCCCACAA 59.459 52.381 0.00 0.00 0.00 3.33
2606 3038 1.167851 CCGTACTACTTCGTCCCACA 58.832 55.000 0.00 0.00 0.00 4.17
2607 3039 1.399791 CTCCGTACTACTTCGTCCCAC 59.600 57.143 0.00 0.00 0.00 4.61
2608 3040 1.003580 ACTCCGTACTACTTCGTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
2609 3041 1.743996 ACTCCGTACTACTTCGTCCC 58.256 55.000 0.00 0.00 0.00 4.46
2610 3042 6.604735 TTTATACTCCGTACTACTTCGTCC 57.395 41.667 0.00 0.00 0.00 4.79
2617 3049 9.903682 TGCAGATTAATTTATACTCCGTACTAC 57.096 33.333 0.00 0.00 0.00 2.73
2618 3050 9.903682 GTGCAGATTAATTTATACTCCGTACTA 57.096 33.333 0.00 0.00 0.00 1.82
2619 3051 8.418662 TGTGCAGATTAATTTATACTCCGTACT 58.581 33.333 0.00 0.00 0.00 2.73
2620 3052 8.583810 TGTGCAGATTAATTTATACTCCGTAC 57.416 34.615 0.00 0.00 0.00 3.67
2621 3053 9.602568 TTTGTGCAGATTAATTTATACTCCGTA 57.397 29.630 0.00 0.00 0.00 4.02
2622 3054 8.500753 TTTGTGCAGATTAATTTATACTCCGT 57.499 30.769 0.00 0.00 0.00 4.69
2623 3055 7.587757 GCTTTGTGCAGATTAATTTATACTCCG 59.412 37.037 0.00 0.00 42.31 4.63
2624 3056 8.788409 GCTTTGTGCAGATTAATTTATACTCC 57.212 34.615 0.00 0.00 42.31 3.85
2660 3092 4.006319 AGTAGCCAACAAGCAATCTTCTC 58.994 43.478 0.00 0.00 34.23 2.87
2705 3144 3.272364 TAAGGCTGGTGCTGGGCAG 62.272 63.158 0.00 0.00 40.08 4.85
2750 3189 7.339466 ACATCTTGTGTAAAAACCAAGAGAAGT 59.661 33.333 7.32 3.86 39.91 3.01
2786 3225 5.696724 AGTAAAAATGACTCGTCAGAAGTGG 59.303 40.000 5.91 0.00 43.61 4.00
2788 3227 5.177696 GCAGTAAAAATGACTCGTCAGAAGT 59.822 40.000 5.91 0.00 43.61 3.01
2836 3276 8.375608 ACACTCATCTGCAATTACATTATCTC 57.624 34.615 0.00 0.00 0.00 2.75
2857 3297 3.684908 TGCCACATTTGCTGTATACACT 58.315 40.909 0.08 0.00 35.91 3.55
2858 3298 4.637483 ATGCCACATTTGCTGTATACAC 57.363 40.909 0.08 0.16 35.91 2.90
2859 3299 5.657826 AAATGCCACATTTGCTGTATACA 57.342 34.783 5.25 5.25 35.91 2.29
2860 3300 6.795399 AGTAAATGCCACATTTGCTGTATAC 58.205 36.000 18.69 7.13 35.91 1.47
2870 3310 5.047802 CCTGTTCAGAAGTAAATGCCACATT 60.048 40.000 1.00 0.00 0.00 2.71
2876 3316 2.484264 ACGCCTGTTCAGAAGTAAATGC 59.516 45.455 1.00 0.00 0.00 3.56
2894 3334 1.419874 GCAGAGACTGAGATGCACGC 61.420 60.000 2.81 0.00 38.54 5.34
2961 3401 6.859017 AGTTTAACCCTTGTGTTGTAAAGTG 58.141 36.000 0.00 0.00 0.00 3.16
3045 3486 3.067180 TGAGATGGTCGTATTTCCGGTAC 59.933 47.826 0.00 0.00 0.00 3.34
3073 3514 4.470304 AGTATTTACACCTCTCCAGGGTTC 59.530 45.833 0.00 0.00 45.53 3.62
3089 3530 5.290493 ACATGCGGATCCAGAAGTATTTA 57.710 39.130 13.41 0.00 0.00 1.40
3168 3609 4.463891 ACAATTTCTGAGCCATTTCGGATT 59.536 37.500 0.00 0.00 36.56 3.01
3189 3630 2.719531 TCAAGTGCCCAAAGTGTACA 57.280 45.000 0.00 0.00 0.00 2.90
3315 3757 1.520787 CCTACGGTTCCGTGCATCC 60.521 63.158 24.37 0.00 42.91 3.51
3337 3779 4.375272 CCAGTATCAGTCAATACAGGCAG 58.625 47.826 0.00 0.00 33.63 4.85
3409 3851 7.817478 TCGTGTGTTATATGTTCTGATGTTTCT 59.183 33.333 0.00 0.00 0.00 2.52
3443 3885 3.305403 GCTTGGTTGCTTTCTTAACCCTC 60.305 47.826 0.00 0.00 44.48 4.30
3471 3913 2.325761 CCGCTTCCCGAACTATAATCG 58.674 52.381 1.58 1.58 40.02 3.34


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

AutoCloner maintained by Alex Coulton.