Multiple sequence alignment - TraesCS4A01G316700

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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 TraesCS4A01G316700 chr4A 100.000 3626 0 0 1 3626 606522492 606526117 0.000000e+00 6697.0
1 TraesCS4A01G316700 chr5B 91.368 2989 130 47 676 3626 708240095 708237197 0.000000e+00 3973.0
2 TraesCS4A01G316700 chr5B 91.085 673 40 9 1 665 708240812 708240152 0.000000e+00 893.0
3 TraesCS4A01G316700 chr5B 81.188 101 19 0 2853 2953 589999828 589999928 8.340000e-12 82.4
4 TraesCS4A01G316700 chr5D 95.593 2065 63 12 793 2850 565050038 565052081 0.000000e+00 3284.0
5 TraesCS4A01G316700 chr5D 91.916 668 44 5 1 666 565049137 565049796 0.000000e+00 926.0
6 TraesCS4A01G316700 chr5D 88.245 604 11 19 3027 3626 565052145 565052692 0.000000e+00 667.0
7 TraesCS4A01G316700 chr1D 87.963 108 12 1 2840 2947 332929737 332929631 3.800000e-25 126.0
8 TraesCS4A01G316700 chr1D 83.696 92 15 0 2853 2944 272317204 272317295 1.790000e-13 87.9
9 TraesCS4A01G316700 chr7B 90.805 87 8 0 2853 2939 246518673 246518587 2.290000e-22 117.0
10 TraesCS4A01G316700 chr4D 87.129 101 12 1 2845 2945 293138813 293138912 2.960000e-21 113.0
11 TraesCS4A01G316700 chr1B 84.946 93 14 0 2852 2944 371447798 371447890 1.070000e-15 95.3
12 TraesCS4A01G316700 chr1A 83.696 92 15 0 2853 2944 344476049 344476140 1.790000e-13 87.9
13 TraesCS4A01G316700 chr2D 81.319 91 17 0 2854 2944 82095083 82095173 1.400000e-09 75.0
14 TraesCS4A01G316700 chr4B 97.436 39 1 0 1 39 507907429 507907391 2.340000e-07 67.6
15 TraesCS4A01G316700 chr3B 97.436 39 0 1 1 39 475437844 475437807 8.400000e-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 TraesCS4A01G316700 chr4A 606522492 606526117 3625 False 6697.000000 6697 100.0000 1 3626 1 chr4A.!!$F1 3625
1 TraesCS4A01G316700 chr5B 708237197 708240812 3615 True 2433.000000 3973 91.2265 1 3626 2 chr5B.!!$R1 3625
2 TraesCS4A01G316700 chr5D 565049137 565052692 3555 False 1625.666667 3284 91.9180 1 3626 3 chr5D.!!$F1 3625

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
87 88 0.108424 CCCTCTTCTCCTCTGTTGCG 60.108 60.0 0.0 0.0 0.00 4.85 F
413 422 0.326264 GAGGTTGACACTCCATGCCT 59.674 55.0 0.0 0.0 0.00 4.75 F
1110 1240 0.102300 GTGGCAAGAAAGGCAACGTT 59.898 50.0 0.0 0.0 46.19 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1231 0.108329 CGAGGATACCAACGTTGCCT 60.108 55.000 22.93 21.72 37.17 4.75 R
2022 2155 1.220749 GATCACCAGCCCTGCGTAA 59.779 57.895 0.00 0.00 0.00 3.18 R
2697 2846 0.045162 TTAACTAGGGGGAGGGGTGG 59.955 60.000 0.00 0.00 0.00 4.61 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
82 83 2.430610 CGCCCCCTCTTCTCCTCTG 61.431 68.421 0.00 0.00 0.00 3.35
87 88 0.108424 CCCTCTTCTCCTCTGTTGCG 60.108 60.000 0.00 0.00 0.00 4.85
139 140 7.840342 AGAGAACATATGCGATAAATCATCC 57.160 36.000 1.58 0.00 0.00 3.51
140 141 6.533012 AGAGAACATATGCGATAAATCATCCG 59.467 38.462 1.58 0.00 0.00 4.18
141 142 4.864916 ACATATGCGATAAATCATCCGC 57.135 40.909 1.58 0.00 35.26 5.54
200 206 3.361794 TTTGTGCAGCTATTTTTCGCA 57.638 38.095 0.00 0.00 0.00 5.10
210 216 6.247903 CAGCTATTTTTCGCAGATTTCGTAA 58.752 36.000 0.00 0.00 35.04 3.18
214 220 8.831372 GCTATTTTTCGCAGATTTCGTAATATG 58.169 33.333 5.16 5.16 36.33 1.78
286 295 7.167924 TGATGCACACAACCATACATTATTT 57.832 32.000 0.00 0.00 0.00 1.40
287 296 8.286191 TGATGCACACAACCATACATTATTTA 57.714 30.769 0.00 0.00 0.00 1.40
288 297 8.911965 TGATGCACACAACCATACATTATTTAT 58.088 29.630 0.00 0.00 0.00 1.40
289 298 9.748708 GATGCACACAACCATACATTATTTATT 57.251 29.630 0.00 0.00 0.00 1.40
312 321 4.448537 TTGAAAACAATGATTAGCCCCG 57.551 40.909 0.00 0.00 0.00 5.73
360 369 5.468540 TTTGATCCGGTGGTATGATCTAG 57.531 43.478 0.00 0.00 36.65 2.43
413 422 0.326264 GAGGTTGACACTCCATGCCT 59.674 55.000 0.00 0.00 0.00 4.75
434 443 2.430694 TCCACCATCCTACAACTCATCG 59.569 50.000 0.00 0.00 0.00 3.84
441 450 5.235186 CCATCCTACAACTCATCGTCAAATC 59.765 44.000 0.00 0.00 0.00 2.17
455 464 3.126858 CGTCAAATCGATGTGTTCCCATT 59.873 43.478 15.20 0.00 0.00 3.16
456 465 4.662145 GTCAAATCGATGTGTTCCCATTC 58.338 43.478 15.20 0.00 0.00 2.67
483 492 2.976185 TCACCATCACCACTCACCTTTA 59.024 45.455 0.00 0.00 0.00 1.85
577 591 6.088085 CGCGCTTACAAATCATTCTTTCTTTT 59.912 34.615 5.56 0.00 0.00 2.27
666 681 7.389803 TCAATGGATATTTATGGCATTACCG 57.610 36.000 4.78 0.00 43.94 4.02
669 684 8.469200 CAATGGATATTTATGGCATTACCGAAT 58.531 33.333 4.78 2.09 43.94 3.34
670 685 9.693739 AATGGATATTTATGGCATTACCGAATA 57.306 29.630 4.78 4.19 43.94 1.75
725 789 7.134815 CACTCTACTTTCCACAACATTCAAAG 58.865 38.462 0.00 0.00 0.00 2.77
748 843 5.007528 AGCATTTCAAACCAAAATTCAACCG 59.992 36.000 0.00 0.00 0.00 4.44
749 844 4.866682 TTTCAAACCAAAATTCAACCGC 57.133 36.364 0.00 0.00 0.00 5.68
758 853 3.916405 AAATTCAACCGCGTGTTTTTG 57.084 38.095 4.92 0.27 34.00 2.44
762 857 2.251893 TCAACCGCGTGTTTTTGTTTC 58.748 42.857 4.92 0.00 34.00 2.78
763 858 1.986378 CAACCGCGTGTTTTTGTTTCA 59.014 42.857 4.92 0.00 34.00 2.69
766 861 1.446465 CCGCGTGTTTTTGTTTCATCG 59.554 47.619 4.92 0.00 0.00 3.84
840 969 4.399303 GCTTGCATCCCTAATAGTGTTGTT 59.601 41.667 0.00 0.00 0.00 2.83
841 970 5.677091 GCTTGCATCCCTAATAGTGTTGTTG 60.677 44.000 0.00 0.00 0.00 3.33
844 973 5.878116 TGCATCCCTAATAGTGTTGTTGTAC 59.122 40.000 0.00 0.00 0.00 2.90
845 974 6.113411 GCATCCCTAATAGTGTTGTTGTACT 58.887 40.000 0.00 0.00 0.00 2.73
846 975 7.093245 TGCATCCCTAATAGTGTTGTTGTACTA 60.093 37.037 0.00 0.00 34.23 1.82
847 976 7.438459 GCATCCCTAATAGTGTTGTTGTACTAG 59.562 40.741 0.00 0.00 33.32 2.57
858 987 5.482526 TGTTGTTGTACTAGGATAGGAAGCA 59.517 40.000 0.00 0.00 44.97 3.91
880 1009 5.232838 GCACTTGAAACATTTTGACCTTGAG 59.767 40.000 0.00 0.00 0.00 3.02
887 1016 6.544928 AACATTTTGACCTTGAGACCTTTT 57.455 33.333 0.00 0.00 0.00 2.27
889 1018 5.069119 ACATTTTGACCTTGAGACCTTTTCC 59.931 40.000 0.00 0.00 0.00 3.13
890 1019 3.943671 TTGACCTTGAGACCTTTTCCA 57.056 42.857 0.00 0.00 0.00 3.53
892 1021 4.453480 TGACCTTGAGACCTTTTCCATT 57.547 40.909 0.00 0.00 0.00 3.16
894 1023 3.759086 GACCTTGAGACCTTTTCCATTCC 59.241 47.826 0.00 0.00 0.00 3.01
895 1024 3.399305 ACCTTGAGACCTTTTCCATTCCT 59.601 43.478 0.00 0.00 0.00 3.36
999 1129 1.067821 GACAGACAGATCGATCCACCC 59.932 57.143 21.66 8.89 0.00 4.61
1059 1189 2.586357 GCCATCTCGTCGAAGCCC 60.586 66.667 0.00 0.00 0.00 5.19
1110 1240 0.102300 GTGGCAAGAAAGGCAACGTT 59.898 50.000 0.00 0.00 46.19 3.99
1113 1243 0.102300 GCAAGAAAGGCAACGTTGGT 59.898 50.000 28.33 0.00 46.39 3.67
1390 1520 3.573772 CTGCTGGAGTTCGCCGACA 62.574 63.158 0.00 0.00 0.00 4.35
1512 1642 4.166888 GCCATGGAGGAGCTCGCA 62.167 66.667 18.40 0.00 41.22 5.10
2572 2717 1.684049 CGAGGAGGAGGAAGCCACT 60.684 63.158 0.00 0.00 0.00 4.00
2695 2844 5.796350 AATCGTTCCTCTTATTTTGTCCG 57.204 39.130 0.00 0.00 0.00 4.79
2696 2845 2.997986 TCGTTCCTCTTATTTTGTCCGC 59.002 45.455 0.00 0.00 0.00 5.54
2697 2846 2.095372 CGTTCCTCTTATTTTGTCCGCC 59.905 50.000 0.00 0.00 0.00 6.13
2698 2847 2.413310 TCCTCTTATTTTGTCCGCCC 57.587 50.000 0.00 0.00 0.00 6.13
2699 2848 1.631388 TCCTCTTATTTTGTCCGCCCA 59.369 47.619 0.00 0.00 0.00 5.36
2700 2849 1.743394 CCTCTTATTTTGTCCGCCCAC 59.257 52.381 0.00 0.00 0.00 4.61
2701 2850 1.743394 CTCTTATTTTGTCCGCCCACC 59.257 52.381 0.00 0.00 0.00 4.61
2702 2851 0.815095 CTTATTTTGTCCGCCCACCC 59.185 55.000 0.00 0.00 0.00 4.61
2703 2852 0.612453 TTATTTTGTCCGCCCACCCC 60.612 55.000 0.00 0.00 0.00 4.95
2704 2853 1.502527 TATTTTGTCCGCCCACCCCT 61.503 55.000 0.00 0.00 0.00 4.79
2760 2909 2.105477 CCGGATGGGATCTCTTGTTCAT 59.895 50.000 0.00 0.00 38.47 2.57
2770 2919 6.482973 GGGATCTCTTGTTCATCTTCATCTTC 59.517 42.308 0.00 0.00 0.00 2.87
2771 2920 7.046652 GGATCTCTTGTTCATCTTCATCTTCA 58.953 38.462 0.00 0.00 0.00 3.02
2772 2921 7.716123 GGATCTCTTGTTCATCTTCATCTTCAT 59.284 37.037 0.00 0.00 0.00 2.57
2773 2922 8.665643 ATCTCTTGTTCATCTTCATCTTCATC 57.334 34.615 0.00 0.00 0.00 2.92
2774 2923 7.849160 TCTCTTGTTCATCTTCATCTTCATCT 58.151 34.615 0.00 0.00 0.00 2.90
2775 2924 8.319881 TCTCTTGTTCATCTTCATCTTCATCTT 58.680 33.333 0.00 0.00 0.00 2.40
2873 3025 7.047460 ACGTACTACCTTCGATCCATAAAAT 57.953 36.000 0.00 0.00 0.00 1.82
2877 3029 4.900635 ACCTTCGATCCATAAAATGTGC 57.099 40.909 0.00 0.00 0.00 4.57
2881 3033 1.660052 CGATCCATAAAATGTGCCGCG 60.660 52.381 0.00 0.00 0.00 6.46
2884 3036 0.172352 CCATAAAATGTGCCGCGGTT 59.828 50.000 28.70 14.47 0.00 4.44
2887 3039 3.502920 CATAAAATGTGCCGCGGTTTTA 58.497 40.909 28.70 26.26 32.53 1.52
2896 3048 1.536766 GCCGCGGTTTTAAACTAACCT 59.463 47.619 28.70 0.00 42.31 3.50
2898 3050 2.807392 CCGCGGTTTTAAACTAACCTCA 59.193 45.455 19.50 0.00 42.31 3.86
2899 3051 3.364267 CCGCGGTTTTAAACTAACCTCAC 60.364 47.826 19.50 0.00 42.31 3.51
2900 3052 3.495753 CGCGGTTTTAAACTAACCTCACT 59.504 43.478 7.79 0.00 42.31 3.41
2901 3053 4.024641 CGCGGTTTTAAACTAACCTCACTT 60.025 41.667 7.79 0.00 42.31 3.16
2902 3054 5.446709 GCGGTTTTAAACTAACCTCACTTC 58.553 41.667 7.79 0.00 42.31 3.01
2903 3055 5.007921 GCGGTTTTAAACTAACCTCACTTCA 59.992 40.000 7.79 0.00 42.31 3.02
2904 3056 6.458615 GCGGTTTTAAACTAACCTCACTTCAA 60.459 38.462 7.79 0.00 42.31 2.69
2905 3057 7.474190 CGGTTTTAAACTAACCTCACTTCAAA 58.526 34.615 7.79 0.00 42.31 2.69
2906 3058 7.969508 CGGTTTTAAACTAACCTCACTTCAAAA 59.030 33.333 7.79 0.00 42.31 2.44
2907 3059 9.079833 GGTTTTAAACTAACCTCACTTCAAAAC 57.920 33.333 7.79 0.00 41.46 2.43
2908 3060 9.850628 GTTTTAAACTAACCTCACTTCAAAACT 57.149 29.630 0.00 0.00 32.31 2.66
2925 3077 5.122554 TCAAAACTAGTTCAAAACTGCGACA 59.877 36.000 8.95 0.00 42.84 4.35
2939 3091 4.323417 ACTGCGACACTTATTTTGGATCA 58.677 39.130 0.00 0.00 0.00 2.92
2942 3094 4.631377 TGCGACACTTATTTTGGATCAGAG 59.369 41.667 0.00 0.00 0.00 3.35
2947 3099 7.020827 ACACTTATTTTGGATCAGAGGAAGA 57.979 36.000 0.00 0.00 0.00 2.87
2957 3109 5.532406 TGGATCAGAGGAAGAAGTGTTTTTG 59.468 40.000 0.00 0.00 0.00 2.44
2970 3122 6.316140 AGAAGTGTTTTTGCCATTTTCTTTCC 59.684 34.615 0.00 0.00 0.00 3.13
3007 3161 5.479027 AGATGAGATGAGAGATGATGGTGAG 59.521 44.000 0.00 0.00 0.00 3.51
3023 3177 2.033801 GGTGAGCCAACATACATGCATC 59.966 50.000 0.00 0.00 34.09 3.91
3070 3224 1.128200 ACAGACAGCAACCCTACACA 58.872 50.000 0.00 0.00 0.00 3.72
3189 3347 1.582389 AGATTTGCTGCTCCTCTCCT 58.418 50.000 0.00 0.00 0.00 3.69
3190 3348 1.485895 AGATTTGCTGCTCCTCTCCTC 59.514 52.381 0.00 0.00 0.00 3.71
3191 3349 1.209019 GATTTGCTGCTCCTCTCCTCA 59.791 52.381 0.00 0.00 0.00 3.86
3192 3350 1.059098 TTTGCTGCTCCTCTCCTCAA 58.941 50.000 0.00 0.00 0.00 3.02
3193 3351 0.322975 TTGCTGCTCCTCTCCTCAAC 59.677 55.000 0.00 0.00 0.00 3.18
3194 3352 0.833409 TGCTGCTCCTCTCCTCAACA 60.833 55.000 0.00 0.00 0.00 3.33
3195 3353 0.540923 GCTGCTCCTCTCCTCAACAT 59.459 55.000 0.00 0.00 0.00 2.71
3238 3396 7.898014 TCTAATCTACCAATCTACTCAAGCA 57.102 36.000 0.00 0.00 0.00 3.91
3239 3397 7.717568 TCTAATCTACCAATCTACTCAAGCAC 58.282 38.462 0.00 0.00 0.00 4.40
3240 3398 6.552445 AATCTACCAATCTACTCAAGCACT 57.448 37.500 0.00 0.00 0.00 4.40
3241 3399 5.584253 TCTACCAATCTACTCAAGCACTC 57.416 43.478 0.00 0.00 0.00 3.51
3257 3415 2.356535 GCACTCACCCTTTCCATCTCAT 60.357 50.000 0.00 0.00 0.00 2.90
3261 3419 3.453717 CTCACCCTTTCCATCTCATCTCA 59.546 47.826 0.00 0.00 0.00 3.27
3363 3538 5.153950 AGGTGAGGTTTGAGATGTAGAAC 57.846 43.478 0.00 0.00 0.00 3.01
3481 3656 3.396560 TGAATCACAGAGACACTTGCAG 58.603 45.455 0.00 0.00 0.00 4.41
3496 3671 2.033757 CAGGAGCCTGCTTGCACT 59.966 61.111 3.18 0.00 37.24 4.40
3497 3672 1.297689 CAGGAGCCTGCTTGCACTA 59.702 57.895 3.18 0.00 37.24 2.74
3498 3673 0.743701 CAGGAGCCTGCTTGCACTAG 60.744 60.000 3.18 0.00 37.24 2.57
3509 3684 6.091986 GCCTGCTTGCACTAGATTAATCTATC 59.908 42.308 22.46 15.50 38.60 2.08
3574 3754 2.910199 TGCATGCACCTCTCTGTATTC 58.090 47.619 18.46 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 3.607370 GAGGGTGGAGGGTCGCAAC 62.607 68.421 0.00 0.00 0.00 4.17
87 88 2.760385 CGAGGAGGGTGGAGGGTC 60.760 72.222 0.00 0.00 0.00 4.46
137 138 5.403166 CGGTATTATTTTGAACGATAGCGGA 59.597 40.000 4.97 0.00 43.17 5.54
138 139 5.403166 TCGGTATTATTTTGAACGATAGCGG 59.597 40.000 4.97 0.00 41.68 5.52
139 140 6.442487 TCGGTATTATTTTGAACGATAGCG 57.558 37.500 0.00 0.00 42.31 4.26
140 141 9.659830 ATTTTCGGTATTATTTTGAACGATAGC 57.340 29.630 0.00 0.00 42.67 2.97
200 206 9.887406 ACGAAACAAAAACATATTACGAAATCT 57.113 25.926 0.00 0.00 0.00 2.40
214 220 7.114388 GGTGATCATCCTTTACGAAACAAAAAC 59.886 37.037 0.00 0.00 0.00 2.43
360 369 1.442769 ATGACATGCCTTGTGTCGTC 58.557 50.000 0.00 0.00 46.89 4.20
413 422 2.430694 CGATGAGTTGTAGGATGGTGGA 59.569 50.000 0.00 0.00 0.00 4.02
447 456 3.593442 TGGTGATATGGGAATGGGAAC 57.407 47.619 0.00 0.00 0.00 3.62
448 457 3.726328 TGATGGTGATATGGGAATGGGAA 59.274 43.478 0.00 0.00 0.00 3.97
450 459 3.424703 GTGATGGTGATATGGGAATGGG 58.575 50.000 0.00 0.00 0.00 4.00
455 464 2.705658 GAGTGGTGATGGTGATATGGGA 59.294 50.000 0.00 0.00 0.00 4.37
456 465 2.439135 TGAGTGGTGATGGTGATATGGG 59.561 50.000 0.00 0.00 0.00 4.00
483 492 4.507794 GCGAAATTGCGACGTGTT 57.492 50.000 10.87 0.00 0.00 3.32
643 658 7.389803 TCGGTAATGCCATAAATATCCATTG 57.610 36.000 0.00 0.00 36.97 2.82
666 681 9.659830 CGCAGGTGTTAAAAGGTTTATATATTC 57.340 33.333 0.00 0.00 0.00 1.75
669 684 6.238157 CGCGCAGGTGTTAAAAGGTTTATATA 60.238 38.462 8.75 0.00 0.00 0.86
670 685 5.448089 CGCGCAGGTGTTAAAAGGTTTATAT 60.448 40.000 8.75 0.00 0.00 0.86
674 735 1.268845 CGCGCAGGTGTTAAAAGGTTT 60.269 47.619 8.75 0.00 0.00 3.27
683 744 1.596752 TGTGAATCGCGCAGGTGTT 60.597 52.632 8.75 0.00 32.23 3.32
688 749 0.917259 GTAGAGTGTGAATCGCGCAG 59.083 55.000 8.75 0.00 37.76 5.18
725 789 5.204101 CGGTTGAATTTTGGTTTGAAATGC 58.796 37.500 0.00 0.00 0.00 3.56
748 843 3.062124 GTGTCGATGAAACAAAAACACGC 60.062 43.478 0.00 0.00 0.00 5.34
749 844 4.339429 AGTGTCGATGAAACAAAAACACG 58.661 39.130 0.00 0.00 40.22 4.49
758 853 6.414408 AGATGATCAAAGTGTCGATGAAAC 57.586 37.500 0.00 0.00 0.00 2.78
762 857 5.349543 TCACAAGATGATCAAAGTGTCGATG 59.650 40.000 0.00 0.47 29.99 3.84
763 858 5.482006 TCACAAGATGATCAAAGTGTCGAT 58.518 37.500 0.00 0.00 29.99 3.59
818 947 5.415701 ACAACAACACTATTAGGGATGCAAG 59.584 40.000 0.00 0.00 0.00 4.01
821 950 6.113411 AGTACAACAACACTATTAGGGATGC 58.887 40.000 0.00 0.00 0.00 3.91
823 952 7.842743 TCCTAGTACAACAACACTATTAGGGAT 59.157 37.037 0.00 0.00 0.00 3.85
828 957 9.925545 TCCTATCCTAGTACAACAACACTATTA 57.074 33.333 0.00 0.00 0.00 0.98
840 969 5.516044 TCAAGTGCTTCCTATCCTAGTACA 58.484 41.667 0.00 0.00 0.00 2.90
841 970 6.466885 TTCAAGTGCTTCCTATCCTAGTAC 57.533 41.667 0.00 0.00 0.00 2.73
844 973 5.734720 TGTTTCAAGTGCTTCCTATCCTAG 58.265 41.667 0.00 0.00 0.00 3.02
845 974 5.755409 TGTTTCAAGTGCTTCCTATCCTA 57.245 39.130 0.00 0.00 0.00 2.94
846 975 4.640771 TGTTTCAAGTGCTTCCTATCCT 57.359 40.909 0.00 0.00 0.00 3.24
847 976 5.904362 AATGTTTCAAGTGCTTCCTATCC 57.096 39.130 0.00 0.00 0.00 2.59
858 987 6.405842 GGTCTCAAGGTCAAAATGTTTCAAGT 60.406 38.462 0.00 0.00 0.00 3.16
889 1018 6.653989 AGGATAGTTGTAGTCCAAAGGAATG 58.346 40.000 0.00 0.00 34.07 2.67
890 1019 6.674419 AGAGGATAGTTGTAGTCCAAAGGAAT 59.326 38.462 0.00 0.00 34.07 3.01
892 1021 5.590818 AGAGGATAGTTGTAGTCCAAAGGA 58.409 41.667 0.00 0.00 34.07 3.36
933 1062 1.028868 CAAGAGCTAGCCACTTGCCC 61.029 60.000 27.25 5.12 42.71 5.36
956 1085 2.949106 CACGCACCAGCAAGAAGG 59.051 61.111 0.00 0.00 42.27 3.46
1101 1231 0.108329 CGAGGATACCAACGTTGCCT 60.108 55.000 22.93 21.72 37.17 4.75
1110 1240 4.670199 TCGAAGGCGAGGATACCA 57.330 55.556 0.00 0.00 42.51 3.25
2022 2155 1.220749 GATCACCAGCCCTGCGTAA 59.779 57.895 0.00 0.00 0.00 3.18
2028 2161 1.459455 CGATCGAGATCACCAGCCCT 61.459 60.000 10.26 0.00 37.69 5.19
2304 2437 1.298190 GGCTATGTCCGTCGTCGAC 60.298 63.158 15.51 15.51 39.71 4.20
2353 2486 4.025401 CAGGAACGTGTTGCCGCC 62.025 66.667 0.32 0.00 0.00 6.13
2433 2575 1.375523 CCACACGTAGTTCAGCCCC 60.376 63.158 0.00 0.00 41.61 5.80
2493 2635 4.351938 TCCACGAACTCGCGGTGG 62.352 66.667 21.14 21.14 41.85 4.61
2696 2845 1.905141 TAACTAGGGGGAGGGGTGGG 61.905 65.000 0.00 0.00 0.00 4.61
2697 2846 0.045162 TTAACTAGGGGGAGGGGTGG 59.955 60.000 0.00 0.00 0.00 4.61
2698 2847 1.844497 CTTTAACTAGGGGGAGGGGTG 59.156 57.143 0.00 0.00 0.00 4.61
2699 2848 1.274825 CCTTTAACTAGGGGGAGGGGT 60.275 57.143 0.00 0.00 0.00 4.95
2700 2849 1.010419 TCCTTTAACTAGGGGGAGGGG 59.990 57.143 0.00 0.00 35.90 4.79
2701 2850 2.581479 TCCTTTAACTAGGGGGAGGG 57.419 55.000 0.00 0.00 35.90 4.30
2702 2851 5.467668 AAAATCCTTTAACTAGGGGGAGG 57.532 43.478 0.00 0.00 35.90 4.30
2703 2852 6.152831 CACAAAAATCCTTTAACTAGGGGGAG 59.847 42.308 0.00 0.00 35.90 4.30
2704 2853 6.014012 CACAAAAATCCTTTAACTAGGGGGA 58.986 40.000 0.00 0.00 35.90 4.81
2760 2909 6.817140 CACTCACATCAAGATGAAGATGAAGA 59.183 38.462 16.39 5.98 43.28 2.87
2770 2919 7.066163 TGCTAATTAACCACTCACATCAAGATG 59.934 37.037 8.45 8.45 44.15 2.90
2771 2920 7.112122 TGCTAATTAACCACTCACATCAAGAT 58.888 34.615 0.00 0.00 0.00 2.40
2772 2921 6.472016 TGCTAATTAACCACTCACATCAAGA 58.528 36.000 0.00 0.00 0.00 3.02
2773 2922 6.741992 TGCTAATTAACCACTCACATCAAG 57.258 37.500 0.00 0.00 0.00 3.02
2774 2923 6.658816 ACATGCTAATTAACCACTCACATCAA 59.341 34.615 0.00 0.00 0.00 2.57
2775 2924 6.179756 ACATGCTAATTAACCACTCACATCA 58.820 36.000 0.00 0.00 0.00 3.07
2851 3003 7.307219 GCACATTTTATGGATCGAAGGTAGTAC 60.307 40.741 0.00 0.00 33.60 2.73
2852 3004 6.704493 GCACATTTTATGGATCGAAGGTAGTA 59.296 38.462 0.00 0.00 33.60 1.82
2853 3005 5.527582 GCACATTTTATGGATCGAAGGTAGT 59.472 40.000 0.00 0.00 33.60 2.73
2854 3006 5.049405 GGCACATTTTATGGATCGAAGGTAG 60.049 44.000 0.00 0.00 33.60 3.18
2873 3025 1.590932 TAGTTTAAAACCGCGGCACA 58.409 45.000 28.58 4.91 0.00 4.57
2881 3033 9.079833 GTTTTGAAGTGAGGTTAGTTTAAAACC 57.920 33.333 11.96 0.01 45.65 3.27
2887 3039 8.803397 AACTAGTTTTGAAGTGAGGTTAGTTT 57.197 30.769 1.12 0.00 0.00 2.66
2896 3048 7.027161 GCAGTTTTGAACTAGTTTTGAAGTGA 58.973 34.615 23.52 3.57 40.46 3.41
2898 3050 6.027749 CGCAGTTTTGAACTAGTTTTGAAGT 58.972 36.000 10.02 5.16 40.46 3.01
2899 3051 6.194692 GTCGCAGTTTTGAACTAGTTTTGAAG 59.805 38.462 10.02 0.00 40.46 3.02
2900 3052 6.025280 GTCGCAGTTTTGAACTAGTTTTGAA 58.975 36.000 10.02 2.63 40.46 2.69
2901 3053 5.122554 TGTCGCAGTTTTGAACTAGTTTTGA 59.877 36.000 10.02 0.00 40.46 2.69
2902 3054 5.227184 GTGTCGCAGTTTTGAACTAGTTTTG 59.773 40.000 10.02 3.71 40.46 2.44
2903 3055 5.123344 AGTGTCGCAGTTTTGAACTAGTTTT 59.877 36.000 10.02 0.00 40.46 2.43
2904 3056 4.634443 AGTGTCGCAGTTTTGAACTAGTTT 59.366 37.500 10.02 0.00 40.46 2.66
2905 3057 4.189231 AGTGTCGCAGTTTTGAACTAGTT 58.811 39.130 8.13 8.13 40.46 2.24
2906 3058 3.793559 AGTGTCGCAGTTTTGAACTAGT 58.206 40.909 0.00 0.00 40.46 2.57
2907 3059 4.795970 AAGTGTCGCAGTTTTGAACTAG 57.204 40.909 0.00 0.00 40.46 2.57
2908 3060 6.854496 AATAAGTGTCGCAGTTTTGAACTA 57.146 33.333 5.46 0.00 40.46 2.24
2925 3077 7.609532 CACTTCTTCCTCTGATCCAAAATAAGT 59.390 37.037 0.00 0.00 0.00 2.24
2939 3091 3.631250 TGGCAAAAACACTTCTTCCTCT 58.369 40.909 0.00 0.00 0.00 3.69
2942 3094 5.817296 AGAAAATGGCAAAAACACTTCTTCC 59.183 36.000 0.00 0.00 0.00 3.46
2947 3099 5.064579 CGGAAAGAAAATGGCAAAAACACTT 59.935 36.000 0.00 0.00 0.00 3.16
2957 3109 4.082787 TCTCAATCACGGAAAGAAAATGGC 60.083 41.667 0.00 0.00 0.00 4.40
2970 3122 6.755607 TCTCATCTCATCTTTTCTCAATCACG 59.244 38.462 0.00 0.00 0.00 4.35
3007 3161 2.424601 ACACAGATGCATGTATGTTGGC 59.575 45.455 2.46 0.00 0.00 4.52
3023 3177 0.617413 AGGGGCTTCATCAGACACAG 59.383 55.000 0.00 0.00 35.54 3.66
3070 3224 2.418368 TGCTCACTTCAACTGGTGTT 57.582 45.000 0.00 0.00 36.75 3.32
3137 3291 0.323360 TACTGTTGCCTCCATTGCCC 60.323 55.000 0.00 0.00 0.00 5.36
3189 3347 9.891828 GATATGTAACAACTTGTTGAATGTTGA 57.108 29.630 18.82 1.15 41.30 3.18
3190 3348 9.897744 AGATATGTAACAACTTGTTGAATGTTG 57.102 29.630 18.82 3.46 41.30 3.33
3232 3390 0.843309 TGGAAAGGGTGAGTGCTTGA 59.157 50.000 0.00 0.00 0.00 3.02
3234 3392 1.707427 AGATGGAAAGGGTGAGTGCTT 59.293 47.619 0.00 0.00 0.00 3.91
3235 3393 1.280421 GAGATGGAAAGGGTGAGTGCT 59.720 52.381 0.00 0.00 0.00 4.40
3236 3394 1.003580 TGAGATGGAAAGGGTGAGTGC 59.996 52.381 0.00 0.00 0.00 4.40
3238 3396 3.454082 GAGATGAGATGGAAAGGGTGAGT 59.546 47.826 0.00 0.00 0.00 3.41
3239 3397 3.453717 TGAGATGAGATGGAAAGGGTGAG 59.546 47.826 0.00 0.00 0.00 3.51
3240 3398 3.453868 TGAGATGAGATGGAAAGGGTGA 58.546 45.455 0.00 0.00 0.00 4.02
3241 3399 3.920231 TGAGATGAGATGGAAAGGGTG 57.080 47.619 0.00 0.00 0.00 4.61
3257 3415 3.006003 GCTGCTGATGAGATGAGATGAGA 59.994 47.826 0.00 0.00 0.00 3.27
3261 3419 3.840124 TTGCTGCTGATGAGATGAGAT 57.160 42.857 0.00 0.00 0.00 2.75
3363 3538 3.743017 CCCCCATGTGTCCCCCAG 61.743 72.222 0.00 0.00 0.00 4.45
3445 3620 7.412173 CTGTGATTCAGGAGCAGCTAGCTTA 62.412 48.000 16.46 0.00 45.11 3.09
3446 3621 6.719353 CTGTGATTCAGGAGCAGCTAGCTT 62.719 50.000 16.46 0.21 45.11 3.74
3447 3622 5.306593 CTGTGATTCAGGAGCAGCTAGCT 62.307 52.174 12.68 12.68 45.52 3.32
3481 3656 0.179936 ATCTAGTGCAAGCAGGCTCC 59.820 55.000 0.00 0.00 34.04 4.70
3489 3664 8.976471 CACACAGATAGATTAATCTAGTGCAAG 58.024 37.037 27.24 20.90 42.20 4.01
3490 3665 8.478066 ACACACAGATAGATTAATCTAGTGCAA 58.522 33.333 27.24 12.30 42.20 4.08
3491 3666 8.011844 ACACACAGATAGATTAATCTAGTGCA 57.988 34.615 27.24 12.86 42.20 4.57
3497 3672 7.875041 GCCACATACACACAGATAGATTAATCT 59.125 37.037 21.28 21.28 40.86 2.40
3498 3673 7.657354 TGCCACATACACACAGATAGATTAATC 59.343 37.037 7.41 7.41 0.00 1.75
3509 3684 2.481568 CTGAACTGCCACATACACACAG 59.518 50.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.