Multiple sequence alignment - TraesCS1D01G122600

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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 TraesCS1D01G122600 chr1D 100.000 3626 0 0 1 3626 123701435 123697810 0.000000e+00 6697.0
1 TraesCS1D01G122600 chr1A 96.178 3166 84 10 1 3154 135969571 135966431 0.000000e+00 5142.0
2 TraesCS1D01G122600 chr1A 85.201 473 42 17 3173 3626 135966445 135965982 9.170000e-126 460.0
3 TraesCS1D01G122600 chr1B 95.938 3151 82 12 7 3135 188263231 188260105 0.000000e+00 5068.0
4 TraesCS1D01G122600 chr1B 84.146 164 21 3 3417 3575 47500736 47500899 1.740000e-33 154.0
5 TraesCS1D01G122600 chr2D 85.064 1011 129 8 1170 2171 43285094 43284097 0.000000e+00 1011.0
6 TraesCS1D01G122600 chr2D 87.912 91 10 1 3488 3577 197839996 197839906 4.950000e-19 106.0
7 TraesCS1D01G122600 chr2B 80.648 987 148 28 1161 2133 68150738 68149781 0.000000e+00 725.0
8 TraesCS1D01G122600 chr2B 85.075 134 19 1 3445 3577 680077975 680077842 6.320000e-28 135.0
9 TraesCS1D01G122600 chr3A 74.053 898 196 28 1230 2104 77410178 77411061 2.090000e-87 333.0
10 TraesCS1D01G122600 chr2A 82.095 296 43 6 1661 1947 44850030 44849736 1.010000e-60 244.0
11 TraesCS1D01G122600 chr2A 80.000 135 24 3 3445 3577 69329538 69329405 2.980000e-16 97.1
12 TraesCS1D01G122600 chr3D 72.414 841 195 27 1230 2047 66311222 66310396 2.180000e-57 233.0
13 TraesCS1D01G122600 chr3B 82.530 166 23 4 3417 3577 72926319 72926483 1.360000e-29 141.0
14 TraesCS1D01G122600 chr5B 89.333 75 3 4 3333 3402 213479691 213479765 4.990000e-14 89.8
15 TraesCS1D01G122600 chr7A 92.857 42 1 2 3299 3338 102290887 102290928 3.910000e-05 60.2


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 TraesCS1D01G122600 chr1D 123697810 123701435 3625 True 6697 6697 100.0000 1 3626 1 chr1D.!!$R1 3625
1 TraesCS1D01G122600 chr1A 135965982 135969571 3589 True 2801 5142 90.6895 1 3626 2 chr1A.!!$R1 3625
2 TraesCS1D01G122600 chr1B 188260105 188263231 3126 True 5068 5068 95.9380 7 3135 1 chr1B.!!$R1 3128
3 TraesCS1D01G122600 chr2D 43284097 43285094 997 True 1011 1011 85.0640 1170 2171 1 chr2D.!!$R1 1001
4 TraesCS1D01G122600 chr2B 68149781 68150738 957 True 725 725 80.6480 1161 2133 1 chr2B.!!$R1 972
5 TraesCS1D01G122600 chr3A 77410178 77411061 883 False 333 333 74.0530 1230 2104 1 chr3A.!!$F1 874
6 TraesCS1D01G122600 chr3D 66310396 66311222 826 True 233 233 72.4140 1230 2047 1 chr3D.!!$R1 817

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
552 563 0.739813 CACGAGACCCGGATGGAAAC 60.740 60.0 0.73 0.0 43.93 2.78 F
1212 1224 0.178944 TGGGAGAGTTCGGACTGGAA 60.179 55.0 0.00 0.0 35.88 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 2654 1.697982 TCCTCCTCCTCGTCGATCATA 59.302 52.381 0.0 0.0 0.0 2.15 R
2636 2669 0.178935 CCATCTCCTCCTCCTCCTCC 60.179 65.000 0.0 0.0 0.0 4.30 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
93 94 2.106511 CTCTGGAAAAACCTGTCCTGGA 59.893 50.000 0.00 0.00 39.86 3.86
138 139 7.386059 AGAAATTGTTGAAAGGTGTCAAAAGT 58.614 30.769 0.00 0.00 39.18 2.66
225 226 7.636150 AAGACTGGTCAATTGATTTCTATGG 57.364 36.000 12.12 0.00 0.00 2.74
241 242 9.979578 GATTTCTATGGATCTCGAGCATATTAT 57.020 33.333 7.81 0.00 0.00 1.28
262 263 2.371841 TGTCCACATGACTTTAGCACCT 59.628 45.455 0.00 0.00 44.75 4.00
318 319 6.533730 AGACTCACTGTTCCATGTTTTATGA 58.466 36.000 0.00 0.00 0.00 2.15
352 353 2.858344 CTCTTAGTTGACATTACCGCGG 59.142 50.000 26.86 26.86 0.00 6.46
410 421 6.912203 TTTGCAATTCATTATGCTGGATTG 57.088 33.333 0.00 1.22 42.63 2.67
470 481 4.055360 CGACAACACAATGACCTTCTACA 58.945 43.478 0.00 0.00 0.00 2.74
479 490 2.684943 TGACCTTCTACACCTTGACCA 58.315 47.619 0.00 0.00 0.00 4.02
552 563 0.739813 CACGAGACCCGGATGGAAAC 60.740 60.000 0.73 0.00 43.93 2.78
590 601 5.580691 CACAAGTGTAACAAGTGAGAGTCAA 59.419 40.000 0.00 0.00 43.60 3.18
980 992 2.158957 TCCCATCCGAAAGCTGTATGTC 60.159 50.000 0.00 0.00 0.00 3.06
1023 1035 4.194640 TGCTTTCATGGAAGATCAGTAGC 58.805 43.478 18.45 0.16 0.00 3.58
1212 1224 0.178944 TGGGAGAGTTCGGACTGGAA 60.179 55.000 0.00 0.00 35.88 3.53
1876 1909 2.725312 GCAGGTGGAGATGCCGAGA 61.725 63.158 0.00 0.00 40.66 4.04
2222 2255 4.148825 CCTTCCTCCTGACCGCCG 62.149 72.222 0.00 0.00 0.00 6.46
2381 2414 1.669999 GCCGCCGTAGTAAGGGAAGA 61.670 60.000 4.19 0.00 31.98 2.87
2620 2653 0.894184 GACGCGGGATGAGGAGGATA 60.894 60.000 12.47 0.00 0.00 2.59
2621 2654 0.251832 ACGCGGGATGAGGAGGATAT 60.252 55.000 12.47 0.00 0.00 1.63
2622 2655 1.005569 ACGCGGGATGAGGAGGATATA 59.994 52.381 12.47 0.00 0.00 0.86
2623 2656 2.311463 CGCGGGATGAGGAGGATATAT 58.689 52.381 0.00 0.00 0.00 0.86
2626 2659 3.900601 GCGGGATGAGGAGGATATATGAT 59.099 47.826 0.00 0.00 0.00 2.45
2627 2660 4.021544 GCGGGATGAGGAGGATATATGATC 60.022 50.000 0.00 0.00 0.00 2.92
2628 2661 4.217334 CGGGATGAGGAGGATATATGATCG 59.783 50.000 0.00 0.00 0.00 3.69
2629 2662 5.389520 GGGATGAGGAGGATATATGATCGA 58.610 45.833 0.00 0.00 0.00 3.59
2630 2663 5.242838 GGGATGAGGAGGATATATGATCGAC 59.757 48.000 0.00 0.00 0.00 4.20
2631 2664 5.049060 GGATGAGGAGGATATATGATCGACG 60.049 48.000 0.00 0.00 0.00 5.12
2632 2665 5.099042 TGAGGAGGATATATGATCGACGA 57.901 43.478 0.00 0.00 0.00 4.20
2633 2666 5.119694 TGAGGAGGATATATGATCGACGAG 58.880 45.833 3.01 0.00 0.00 4.18
2634 2667 4.456535 AGGAGGATATATGATCGACGAGG 58.543 47.826 3.01 0.00 0.00 4.63
2635 2668 4.164413 AGGAGGATATATGATCGACGAGGA 59.836 45.833 3.01 0.00 0.00 3.71
2636 2669 4.513692 GGAGGATATATGATCGACGAGGAG 59.486 50.000 3.01 0.00 0.00 3.69
2637 2670 4.456535 AGGATATATGATCGACGAGGAGG 58.543 47.826 3.01 0.00 0.00 4.30
2638 2671 4.164413 AGGATATATGATCGACGAGGAGGA 59.836 45.833 3.01 0.00 0.00 3.71
2639 2672 4.513692 GGATATATGATCGACGAGGAGGAG 59.486 50.000 3.01 0.00 0.00 3.69
2669 2702 2.237143 GGAGATGGTTGAGGTGTGATGA 59.763 50.000 0.00 0.00 0.00 2.92
2729 2766 4.509737 GAGCTGGGGACGCGGTAC 62.510 72.222 12.47 0.71 35.50 3.34
2871 2914 4.273257 GGCCGAGCCGAGTAGAGC 62.273 72.222 0.00 0.00 39.62 4.09
2944 2989 7.175797 GGTTCTATTATAGAGGGGAAAATGGG 58.824 42.308 2.00 0.00 35.96 4.00
3077 3123 0.107831 TCTTTTGTCACGACCCCTGG 59.892 55.000 0.00 0.00 0.00 4.45
3078 3124 0.107831 CTTTTGTCACGACCCCTGGA 59.892 55.000 0.00 0.00 0.00 3.86
3154 3200 3.183775 CACCGTGCACTACAAAACTACTC 59.816 47.826 16.19 0.00 0.00 2.59
3156 3202 4.056050 CCGTGCACTACAAAACTACTCTT 58.944 43.478 16.19 0.00 0.00 2.85
3157 3203 4.510340 CCGTGCACTACAAAACTACTCTTT 59.490 41.667 16.19 0.00 0.00 2.52
3158 3204 5.007332 CCGTGCACTACAAAACTACTCTTTT 59.993 40.000 16.19 0.00 0.00 2.27
3159 3205 6.457799 CCGTGCACTACAAAACTACTCTTTTT 60.458 38.462 16.19 0.00 0.00 1.94
3181 3227 4.451629 TTTTTGCGGGAACACTACAAAA 57.548 36.364 0.00 0.00 38.16 2.44
3182 3228 3.423996 TTTGCGGGAACACTACAAAAC 57.576 42.857 0.00 0.00 0.00 2.43
3183 3229 2.335316 TGCGGGAACACTACAAAACT 57.665 45.000 0.00 0.00 0.00 2.66
3184 3230 3.472283 TGCGGGAACACTACAAAACTA 57.528 42.857 0.00 0.00 0.00 2.24
3185 3231 3.132925 TGCGGGAACACTACAAAACTAC 58.867 45.455 0.00 0.00 0.00 2.73
3186 3232 3.181463 TGCGGGAACACTACAAAACTACT 60.181 43.478 0.00 0.00 0.00 2.57
3187 3233 3.431233 GCGGGAACACTACAAAACTACTC 59.569 47.826 0.00 0.00 0.00 2.59
3188 3234 3.671928 CGGGAACACTACAAAACTACTCG 59.328 47.826 0.00 0.00 0.00 4.18
3191 3237 4.304939 GAACACTACAAAACTACTCGCCT 58.695 43.478 0.00 0.00 0.00 5.52
3195 3241 4.056050 ACTACAAAACTACTCGCCTTGTG 58.944 43.478 0.00 0.00 32.69 3.33
3219 3265 6.468109 GGTTCTAGAAAGAAGCGGATTACCG 61.468 48.000 6.78 4.21 46.84 4.02
3236 3282 8.456904 GGATTACCGTAATGTTTTTCTTTTCC 57.543 34.615 8.55 0.00 0.00 3.13
3237 3283 7.271868 GGATTACCGTAATGTTTTTCTTTTCCG 59.728 37.037 8.55 0.00 0.00 4.30
3239 3285 4.579753 ACCGTAATGTTTTTCTTTTCCGGA 59.420 37.500 0.00 0.00 34.21 5.14
3240 3286 5.242171 ACCGTAATGTTTTTCTTTTCCGGAT 59.758 36.000 4.15 0.00 34.21 4.18
3241 3287 6.153756 CCGTAATGTTTTTCTTTTCCGGATT 58.846 36.000 4.15 0.00 33.09 3.01
3242 3288 7.040548 ACCGTAATGTTTTTCTTTTCCGGATTA 60.041 33.333 4.15 0.00 34.21 1.75
3244 3290 9.182933 CGTAATGTTTTTCTTTTCCGGATTAAA 57.817 29.630 4.15 2.51 0.00 1.52
3275 3326 2.223711 GGTCAAGTTTTTGTGACGGCAT 60.224 45.455 0.00 0.00 44.19 4.40
3282 3333 0.874390 TTTGTGACGGCATGCTCTTC 59.126 50.000 18.92 11.75 0.00 2.87
3287 3338 2.030805 GTGACGGCATGCTCTTCTTTTT 60.031 45.455 18.92 0.00 0.00 1.94
3288 3339 3.188460 GTGACGGCATGCTCTTCTTTTTA 59.812 43.478 18.92 0.00 0.00 1.52
3289 3340 4.009675 TGACGGCATGCTCTTCTTTTTAT 58.990 39.130 18.92 0.00 0.00 1.40
3290 3341 4.458989 TGACGGCATGCTCTTCTTTTTATT 59.541 37.500 18.92 0.00 0.00 1.40
3291 3342 5.048083 TGACGGCATGCTCTTCTTTTTATTT 60.048 36.000 18.92 0.00 0.00 1.40
3292 3343 6.150307 TGACGGCATGCTCTTCTTTTTATTTA 59.850 34.615 18.92 0.00 0.00 1.40
3293 3344 6.919721 ACGGCATGCTCTTCTTTTTATTTAA 58.080 32.000 18.92 0.00 0.00 1.52
3294 3345 6.806739 ACGGCATGCTCTTCTTTTTATTTAAC 59.193 34.615 18.92 0.00 0.00 2.01
3295 3346 7.029563 CGGCATGCTCTTCTTTTTATTTAACT 58.970 34.615 18.92 0.00 0.00 2.24
3355 3406 7.889589 AAAAACAAACTTCACCTCAAAAGAG 57.110 32.000 0.00 0.00 0.00 2.85
3363 3419 4.836125 TCACCTCAAAAGAGCAATGAAC 57.164 40.909 0.00 0.00 0.00 3.18
3389 3445 2.644992 GCGCAACAAAGGTCCTGG 59.355 61.111 0.30 0.00 0.00 4.45
3406 3462 0.320683 TGGTGAGTTGACGGATGCTG 60.321 55.000 0.00 0.00 0.00 4.41
3426 3482 2.370445 CCAGTGGCCAGGGGTAGAG 61.370 68.421 5.11 0.00 0.00 2.43
3434 3490 0.325671 CCAGGGGTAGAGCCAGAGAA 60.326 60.000 0.00 0.00 39.65 2.87
3536 3592 3.587923 ACCATGGAATCAATTTTGCACG 58.412 40.909 21.47 0.00 29.29 5.34
3538 3594 3.368539 CCATGGAATCAATTTTGCACGTG 59.631 43.478 12.28 12.28 29.29 4.49
3550 3606 2.625906 CACGTGGTGTCTTGTGCG 59.374 61.111 7.95 0.00 0.00 5.34
3565 3622 2.669569 GCGCCAGGAAGCTGAACA 60.670 61.111 0.00 0.00 0.00 3.18
3569 3626 1.318158 GCCAGGAAGCTGAACATGGG 61.318 60.000 16.92 2.65 38.23 4.00
3614 3672 0.779997 ACCCCCTCTTCATGTGCTTT 59.220 50.000 0.00 0.00 0.00 3.51
3617 3675 2.954318 CCCCCTCTTCATGTGCTTTATG 59.046 50.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 1.404035 GACCGCACTTTTGACACCTTT 59.596 47.619 0.00 0.00 0.00 3.11
138 139 4.729227 TCAACTATAACATCAGACCGCA 57.271 40.909 0.00 0.00 0.00 5.69
223 224 4.772100 TGGACATAATATGCTCGAGATCCA 59.228 41.667 18.75 4.98 0.00 3.41
225 226 5.714047 TGTGGACATAATATGCTCGAGATC 58.286 41.667 18.75 0.00 0.00 2.75
262 263 6.156775 TCTCATGTCAAAGAGATGGGAATGTA 59.843 38.462 4.44 0.00 39.37 2.29
352 353 8.283291 GCAACATTATAAAGTCATAGTAGGTGC 58.717 37.037 0.00 0.00 0.00 5.01
437 448 1.134371 TGTGTTGTCGGACAATGGACA 60.134 47.619 24.81 22.14 40.59 4.02
470 481 0.994247 TCCTGCATCATGGTCAAGGT 59.006 50.000 3.84 0.00 0.00 3.50
479 490 3.474600 GTGTAGCTGATTCCTGCATCAT 58.525 45.455 0.00 0.00 39.38 2.45
552 563 2.970609 CACTTGTGTAAATTCCAACGCG 59.029 45.455 3.53 3.53 0.00 6.01
576 587 5.888161 AGTTGGAAATTTGACTCTCACTTGT 59.112 36.000 0.00 0.00 0.00 3.16
590 601 5.531287 GTGAGGTGTGTTCTAGTTGGAAATT 59.469 40.000 0.00 0.00 0.00 1.82
757 768 6.107901 TGGCTAACATTTTAAATGCCAGTT 57.892 33.333 16.57 6.97 43.09 3.16
765 776 8.207545 ACAGACCAAATTGGCTAACATTTTAAA 58.792 29.630 12.67 0.00 42.67 1.52
952 964 2.982488 AGCTTTCGGATGGGATTAGGAT 59.018 45.455 0.00 0.00 0.00 3.24
1023 1035 2.868583 CGGGCTTCTGTAATGTGATGAG 59.131 50.000 0.00 0.00 0.00 2.90
1183 1195 1.536943 AACTCTCCCAGCAGGACGAC 61.537 60.000 0.00 0.00 40.93 4.34
2620 2653 2.306219 TCCTCCTCCTCGTCGATCATAT 59.694 50.000 0.00 0.00 0.00 1.78
2621 2654 1.697982 TCCTCCTCCTCGTCGATCATA 59.302 52.381 0.00 0.00 0.00 2.15
2622 2655 0.474614 TCCTCCTCCTCGTCGATCAT 59.525 55.000 0.00 0.00 0.00 2.45
2623 2656 0.179043 CTCCTCCTCCTCGTCGATCA 60.179 60.000 0.00 0.00 0.00 2.92
2626 2659 1.973816 CTCCTCCTCCTCCTCGTCGA 61.974 65.000 0.00 0.00 0.00 4.20
2627 2660 1.525077 CTCCTCCTCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
2628 2661 1.152839 CCTCCTCCTCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
2629 2662 1.619975 TCCTCCTCCTCCTCCTCGT 60.620 63.158 0.00 0.00 0.00 4.18
2630 2663 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
2631 2664 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2632 2665 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2633 2666 0.996762 TCTCCTCCTCCTCCTCCTCC 60.997 65.000 0.00 0.00 0.00 4.30
2634 2667 1.158007 ATCTCCTCCTCCTCCTCCTC 58.842 60.000 0.00 0.00 0.00 3.71
2635 2668 0.859760 CATCTCCTCCTCCTCCTCCT 59.140 60.000 0.00 0.00 0.00 3.69
2636 2669 0.178935 CCATCTCCTCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
2637 2670 0.560688 ACCATCTCCTCCTCCTCCTC 59.439 60.000 0.00 0.00 0.00 3.71
2638 2671 1.022903 AACCATCTCCTCCTCCTCCT 58.977 55.000 0.00 0.00 0.00 3.69
2639 2672 1.127343 CAACCATCTCCTCCTCCTCC 58.873 60.000 0.00 0.00 0.00 4.30
2729 2766 0.387622 TTTTAGTCTCCCGTCACGCG 60.388 55.000 3.53 3.53 40.95 6.01
2871 2914 1.220206 CAGCCCACCACTCTAGCAG 59.780 63.158 0.00 0.00 0.00 4.24
2913 2956 4.596212 CCCCTCTATAATAGAACCCCGTTT 59.404 45.833 0.00 0.00 33.75 3.60
2944 2989 4.935808 ACACCACAGACGATATTTTCCTTC 59.064 41.667 0.00 0.00 0.00 3.46
3077 3123 1.344763 AGACTAGCCGGCCATACAATC 59.655 52.381 26.15 11.46 0.00 2.67
3078 3124 1.424638 AGACTAGCCGGCCATACAAT 58.575 50.000 26.15 4.77 0.00 2.71
3160 3206 4.082136 AGTTTTGTAGTGTTCCCGCAAAAA 60.082 37.500 0.00 0.00 39.63 1.94
3161 3207 3.444388 AGTTTTGTAGTGTTCCCGCAAAA 59.556 39.130 0.00 0.00 36.90 2.44
3162 3208 3.018149 AGTTTTGTAGTGTTCCCGCAAA 58.982 40.909 0.00 0.00 0.00 3.68
3163 3209 2.645802 AGTTTTGTAGTGTTCCCGCAA 58.354 42.857 0.00 0.00 0.00 4.85
3164 3210 2.335316 AGTTTTGTAGTGTTCCCGCA 57.665 45.000 0.00 0.00 0.00 5.69
3165 3211 3.396560 AGTAGTTTTGTAGTGTTCCCGC 58.603 45.455 0.00 0.00 0.00 6.13
3166 3212 3.671928 CGAGTAGTTTTGTAGTGTTCCCG 59.328 47.826 0.00 0.00 0.00 5.14
3167 3213 3.431233 GCGAGTAGTTTTGTAGTGTTCCC 59.569 47.826 0.00 0.00 0.00 3.97
3168 3214 3.431233 GGCGAGTAGTTTTGTAGTGTTCC 59.569 47.826 0.00 0.00 0.00 3.62
3169 3215 4.304939 AGGCGAGTAGTTTTGTAGTGTTC 58.695 43.478 0.00 0.00 0.00 3.18
3170 3216 4.332428 AGGCGAGTAGTTTTGTAGTGTT 57.668 40.909 0.00 0.00 0.00 3.32
3171 3217 4.056050 CAAGGCGAGTAGTTTTGTAGTGT 58.944 43.478 0.00 0.00 0.00 3.55
3172 3218 4.056050 ACAAGGCGAGTAGTTTTGTAGTG 58.944 43.478 0.00 0.00 30.79 2.74
3173 3219 4.056050 CACAAGGCGAGTAGTTTTGTAGT 58.944 43.478 0.00 0.00 31.34 2.73
3174 3220 3.432252 CCACAAGGCGAGTAGTTTTGTAG 59.568 47.826 0.00 0.00 31.34 2.74
3175 3221 3.181463 ACCACAAGGCGAGTAGTTTTGTA 60.181 43.478 0.00 0.00 39.06 2.41
3176 3222 2.218603 CCACAAGGCGAGTAGTTTTGT 58.781 47.619 0.00 0.00 32.60 2.83
3177 3223 2.218603 ACCACAAGGCGAGTAGTTTTG 58.781 47.619 0.00 0.00 39.06 2.44
3178 3224 2.632987 ACCACAAGGCGAGTAGTTTT 57.367 45.000 0.00 0.00 39.06 2.43
3179 3225 2.104281 AGAACCACAAGGCGAGTAGTTT 59.896 45.455 0.00 0.00 39.06 2.66
3180 3226 1.692519 AGAACCACAAGGCGAGTAGTT 59.307 47.619 0.00 0.00 39.06 2.24
3181 3227 1.339097 AGAACCACAAGGCGAGTAGT 58.661 50.000 0.00 0.00 39.06 2.73
3182 3228 2.753452 TCTAGAACCACAAGGCGAGTAG 59.247 50.000 0.00 0.00 39.06 2.57
3183 3229 2.799017 TCTAGAACCACAAGGCGAGTA 58.201 47.619 0.00 0.00 39.06 2.59
3184 3230 1.629043 TCTAGAACCACAAGGCGAGT 58.371 50.000 0.00 0.00 39.06 4.18
3185 3231 2.743636 TTCTAGAACCACAAGGCGAG 57.256 50.000 0.00 0.00 39.06 5.03
3186 3232 2.631062 TCTTTCTAGAACCACAAGGCGA 59.369 45.455 4.18 0.00 39.06 5.54
3187 3233 3.040147 TCTTTCTAGAACCACAAGGCG 57.960 47.619 4.18 0.00 39.06 5.52
3188 3234 3.189495 GCTTCTTTCTAGAACCACAAGGC 59.811 47.826 4.18 0.51 35.49 4.35
3191 3237 3.070446 TCCGCTTCTTTCTAGAACCACAA 59.930 43.478 4.18 0.00 35.49 3.33
3195 3241 4.809958 GGTAATCCGCTTCTTTCTAGAACC 59.190 45.833 4.18 0.00 35.49 3.62
3244 3290 4.693095 ACAAAAACTTGACCGCAACATTTT 59.307 33.333 0.00 0.00 32.59 1.82
3245 3291 4.092675 CACAAAAACTTGACCGCAACATTT 59.907 37.500 0.00 0.00 0.00 2.32
3260 3311 1.001378 AGAGCATGCCGTCACAAAAAC 60.001 47.619 15.66 0.00 0.00 2.43
3289 3340 8.339714 GCACTGACATTTGTGTTAGTAGTTAAA 58.660 33.333 5.80 0.00 36.66 1.52
3290 3341 7.306925 CGCACTGACATTTGTGTTAGTAGTTAA 60.307 37.037 5.80 0.00 36.66 2.01
3291 3342 6.144886 CGCACTGACATTTGTGTTAGTAGTTA 59.855 38.462 5.80 0.00 36.66 2.24
3292 3343 5.050363 CGCACTGACATTTGTGTTAGTAGTT 60.050 40.000 5.80 0.00 36.66 2.24
3293 3344 4.447724 CGCACTGACATTTGTGTTAGTAGT 59.552 41.667 5.80 0.00 36.66 2.73
3294 3345 4.447724 ACGCACTGACATTTGTGTTAGTAG 59.552 41.667 5.80 6.26 36.66 2.57
3295 3346 4.373527 ACGCACTGACATTTGTGTTAGTA 58.626 39.130 5.80 0.00 36.66 1.82
3333 3384 5.047377 TGCTCTTTTGAGGTGAAGTTTGTTT 60.047 36.000 0.00 0.00 46.30 2.83
3351 3402 2.298163 CCTTTGCTGGTTCATTGCTCTT 59.702 45.455 0.00 0.00 0.00 2.85
3355 3406 1.010419 CGCCTTTGCTGGTTCATTGC 61.010 55.000 0.00 0.00 34.43 3.56
3363 3419 1.216941 CTTTGTTGCGCCTTTGCTGG 61.217 55.000 4.18 0.00 35.36 4.85
3378 3434 2.222027 GTCAACTCACCAGGACCTTTG 58.778 52.381 0.00 0.00 0.00 2.77
3379 3435 1.202651 CGTCAACTCACCAGGACCTTT 60.203 52.381 0.00 0.00 0.00 3.11
3389 3445 1.639298 GCCAGCATCCGTCAACTCAC 61.639 60.000 0.00 0.00 0.00 3.51
3434 3490 6.642707 TTTTACACTGGGACGATCATTTTT 57.357 33.333 0.00 0.00 0.00 1.94
3442 3498 3.395639 GTGTGATTTTACACTGGGACGA 58.604 45.455 0.00 0.00 45.70 4.20
3443 3499 3.806316 GTGTGATTTTACACTGGGACG 57.194 47.619 0.00 0.00 45.70 4.79
3472 3528 5.761234 GTGTGTGACACCCTGTTTTTAGATA 59.239 40.000 13.85 0.00 43.05 1.98
3500 3556 9.693739 TGATTCCATGGTAATTTTGTGTATAGT 57.306 29.630 12.58 0.00 0.00 2.12
3519 3575 2.363680 ACCACGTGCAAAATTGATTCCA 59.636 40.909 10.91 0.00 0.00 3.53
3536 3592 2.896801 CTGGCGCACAAGACACCAC 61.897 63.158 10.83 0.00 0.00 4.16
3538 3594 3.357079 CCTGGCGCACAAGACACC 61.357 66.667 10.83 0.00 0.00 4.16
3550 3606 1.318158 CCCATGTTCAGCTTCCTGGC 61.318 60.000 0.00 0.00 39.61 4.85
3592 3650 1.204146 GCACATGAAGAGGGGGTCTA 58.796 55.000 0.00 0.00 32.65 2.59
3594 3652 0.329596 AAGCACATGAAGAGGGGGTC 59.670 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.