Multiple sequence alignment - TraesCS5D01G149100

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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 TraesCS5D01G149100 chr5D 100.000 2808 0 0 1 2808 238151495 238148688 0.000000e+00 5186
1 TraesCS5D01G149100 chr5D 89.922 129 13 0 2680 2808 281171213 281171341 1.730000e-37 167
2 TraesCS5D01G149100 chr5B 94.400 1893 50 13 847 2683 267417202 267419094 0.000000e+00 2857
3 TraesCS5D01G149100 chr5B 90.368 706 42 2 1 681 267308021 267308725 0.000000e+00 904
4 TraesCS5D01G149100 chr5B 95.187 187 6 3 672 855 267415702 267415888 2.740000e-75 292
5 TraesCS5D01G149100 chr5A 91.865 1893 75 31 847 2682 316659015 316660885 0.000000e+00 2569
6 TraesCS5D01G149100 chr5A 96.330 109 4 0 2700 2808 389723303 389723411 2.220000e-41 180
7 TraesCS5D01G149100 chr5A 90.152 132 9 3 2680 2808 439182262 439182132 4.810000e-38 169
8 TraesCS5D01G149100 chr2A 82.367 431 43 15 1750 2174 56885092 56885495 7.450000e-91 344
9 TraesCS5D01G149100 chr2A 81.903 431 45 22 1750 2174 56882052 56881649 1.610000e-87 333
10 TraesCS5D01G149100 chr2A 83.051 177 15 12 1998 2174 56534227 56534388 2.250000e-31 147
11 TraesCS5D01G149100 chr7D 96.330 109 4 0 2700 2808 363148966 363148858 2.220000e-41 180
12 TraesCS5D01G149100 chr4A 96.330 109 4 0 2698 2806 95308510 95308402 2.220000e-41 180
13 TraesCS5D01G149100 chr3A 96.330 109 4 0 2700 2808 214611877 214611769 2.220000e-41 180
14 TraesCS5D01G149100 chr6D 95.495 111 5 0 2698 2808 41542621 41542511 7.990000e-41 178
15 TraesCS5D01G149100 chr4D 95.495 111 5 0 2698 2808 461321835 461321725 7.990000e-41 178
16 TraesCS5D01G149100 chr4D 95.495 111 5 0 2698 2808 461340110 461340000 7.990000e-41 178


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 TraesCS5D01G149100 chr5D 238148688 238151495 2807 True 5186.0 5186 100.0000 1 2808 1 chr5D.!!$R1 2807
1 TraesCS5D01G149100 chr5B 267415702 267419094 3392 False 1574.5 2857 94.7935 672 2683 2 chr5B.!!$F2 2011
2 TraesCS5D01G149100 chr5B 267308021 267308725 704 False 904.0 904 90.3680 1 681 1 chr5B.!!$F1 680
3 TraesCS5D01G149100 chr5A 316659015 316660885 1870 False 2569.0 2569 91.8650 847 2682 1 chr5A.!!$F1 1835

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
258 259 0.251209 TCGTGGTGCAGTACTCCTCT 60.251 55.0 0.0 0.0 32.83 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 3363 0.72914 GCCGGAACAAAGCATCAACG 60.729 55.0 5.05 0.0 0.0 4.1 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
34 35 6.948353 TCTTCTGCACATATAAATCTTTCGC 58.052 36.000 0.00 0.00 0.00 4.70
35 36 5.673337 TCTGCACATATAAATCTTTCGCC 57.327 39.130 0.00 0.00 0.00 5.54
39 40 5.207768 GCACATATAAATCTTTCGCCAGTG 58.792 41.667 0.00 0.00 0.00 3.66
63 64 2.885861 CCTCTCCGACTCCCAACG 59.114 66.667 0.00 0.00 0.00 4.10
76 77 3.060602 CTCCCAACGACTTGAGAGTTTC 58.939 50.000 0.00 0.00 35.88 2.78
94 95 4.407296 AGTTTCCGGATCAGCTAGATTTCT 59.593 41.667 4.15 0.00 37.00 2.52
95 96 4.327982 TTCCGGATCAGCTAGATTTCTG 57.672 45.455 4.15 0.00 37.00 3.02
99 100 3.733224 CGGATCAGCTAGATTTCTGAACG 59.267 47.826 0.00 2.96 41.96 3.95
118 119 0.817654 GTAATGCAAGAAGCCCCCAC 59.182 55.000 0.00 0.00 44.83 4.61
130 131 1.695114 GCCCCCACAAAACTGCCTTT 61.695 55.000 0.00 0.00 0.00 3.11
156 157 2.031258 TCGACACACCACAACAACAT 57.969 45.000 0.00 0.00 0.00 2.71
160 161 1.748493 ACACACCACAACAACATCACC 59.252 47.619 0.00 0.00 0.00 4.02
168 169 4.328983 CCACAACAACATCACCGTATCTAC 59.671 45.833 0.00 0.00 0.00 2.59
169 170 4.328983 CACAACAACATCACCGTATCTACC 59.671 45.833 0.00 0.00 0.00 3.18
182 183 0.390735 ATCTACCGTTCCGTGCAACC 60.391 55.000 0.00 0.00 0.00 3.77
223 224 2.276732 ACATGTTCAACTGGTGGAGG 57.723 50.000 0.00 0.00 0.00 4.30
258 259 0.251209 TCGTGGTGCAGTACTCCTCT 60.251 55.000 0.00 0.00 32.83 3.69
280 281 1.045911 TGGGTTGTCCTTGGTTTGGC 61.046 55.000 0.00 0.00 36.20 4.52
288 289 4.532834 TGTCCTTGGTTTGGCTAATATCC 58.467 43.478 0.00 0.00 0.00 2.59
294 295 4.144297 TGGTTTGGCTAATATCCTGATGC 58.856 43.478 0.00 0.00 0.00 3.91
320 321 7.705325 CCAGCCAAGAAAGATTTGATGAAATAG 59.295 37.037 0.00 0.00 31.58 1.73
377 378 3.057245 GGATTGCTTTTCTCCTCGCTTTT 60.057 43.478 0.00 0.00 0.00 2.27
416 417 3.382865 TCACTACCATCAGCTCATGAGAC 59.617 47.826 27.04 16.75 42.53 3.36
439 465 3.449737 AGTCCCTTGCATTCAAATCATGG 59.550 43.478 0.00 0.00 0.00 3.66
468 494 6.349611 GCACACATATGTTCAACCATCTCTTT 60.350 38.462 5.37 0.00 36.72 2.52
478 504 3.963428 ACCATCTCTTTTGTAGCGAGT 57.037 42.857 0.00 0.00 0.00 4.18
482 508 3.299340 TCTCTTTTGTAGCGAGTGACC 57.701 47.619 0.00 0.00 0.00 4.02
516 542 2.991190 CCAACATGCATTCAAACAGAGC 59.009 45.455 0.00 0.00 0.00 4.09
543 569 5.611796 TTCCAATTGTCTTCAGATGAACG 57.388 39.130 4.43 0.00 0.00 3.95
551 577 2.603110 TCTTCAGATGAACGTATTGCGC 59.397 45.455 0.00 0.00 46.11 6.09
566 592 1.517694 GCGCGGACGGAAGATGTTA 60.518 57.895 8.83 0.00 40.57 2.41
601 627 3.610040 ATGCAACACATCCGAAGTAGA 57.390 42.857 0.00 0.00 31.52 2.59
608 634 3.065510 ACACATCCGAAGTAGACATCGAG 59.934 47.826 8.74 1.91 39.14 4.04
613 639 3.374367 TCCGAAGTAGACATCGAGTTCTG 59.626 47.826 8.74 0.00 39.14 3.02
669 695 4.024809 GTCACTGTAGTGTTCCAAAGCTTC 60.025 45.833 11.44 0.00 45.76 3.86
685 711 2.614057 AGCTTCGTCCAGTTTTGTTCTG 59.386 45.455 0.00 0.00 0.00 3.02
759 785 9.638239 TTTGTTTTGATCAGCATCTTATTAACC 57.362 29.630 0.00 0.00 0.00 2.85
763 789 5.297547 TGATCAGCATCTTATTAACCGACC 58.702 41.667 0.00 0.00 0.00 4.79
801 827 4.100084 CGGTCAGCTCCCATGCCA 62.100 66.667 0.15 0.00 0.00 4.92
865 2216 4.939368 TTGGCGGTCGGTGGGTTG 62.939 66.667 0.00 0.00 0.00 3.77
917 2269 4.058817 CGAGAGAAGGCCCAACATATTAC 58.941 47.826 0.00 0.00 0.00 1.89
958 2314 0.958876 CTGACTAAACCCCAACGCCC 60.959 60.000 0.00 0.00 0.00 6.13
960 2316 2.748647 CTAAACCCCAACGCCCCG 60.749 66.667 0.00 0.00 0.00 5.73
980 2336 2.800629 CGGACGTATAAAATCGCCCACT 60.801 50.000 0.00 0.00 30.43 4.00
1073 2438 2.598394 ACCGCAAACATGGCTGCT 60.598 55.556 16.41 0.00 36.38 4.24
1184 2549 2.034879 CATCAAGGTGAACGGCGCT 61.035 57.895 6.90 0.00 0.00 5.92
1289 2654 1.226974 CGACATGAGGATCCGCGTT 60.227 57.895 7.58 0.05 0.00 4.84
1534 2900 3.838271 GGCCTGCAGGATCGTCGA 61.838 66.667 37.21 0.00 37.39 4.20
1566 2932 3.497942 GGTTTTCTCTGCTTTACCTCCCA 60.498 47.826 0.00 0.00 0.00 4.37
1595 2961 4.205587 AGACTCCGTATGATTAGTTCCGT 58.794 43.478 0.00 0.00 0.00 4.69
1622 2988 6.266103 CCTTGGCAAGATATTGTGGTATGATT 59.734 38.462 28.18 0.00 0.00 2.57
1672 3039 3.007074 TGGGTAGTTGCTCGATTGTGTTA 59.993 43.478 0.00 0.00 0.00 2.41
1756 3173 4.751600 TGTTGTCTGATGACTGATGTTGTC 59.248 41.667 0.00 0.00 43.29 3.18
1774 3191 4.546829 TGTCTTTAAGTTAGCCGGATGT 57.453 40.909 5.05 0.00 0.00 3.06
1787 3204 1.167851 CGGATGTGTTGAATGGTGCT 58.832 50.000 0.00 0.00 0.00 4.40
1946 3363 7.041372 TGTGCTTTACCTCACAAATTCTAGAAC 60.041 37.037 7.48 0.00 39.91 3.01
2012 3431 4.939439 TGTGATGTGAGATGTTTGAGGATG 59.061 41.667 0.00 0.00 0.00 3.51
2120 3554 7.147312 TCCAGTTTCATTAGATTGTTGCAAAG 58.853 34.615 0.00 0.00 0.00 2.77
2237 3671 7.796054 ACTGGTATTCAACTATATCAGCACTT 58.204 34.615 0.00 0.00 41.09 3.16
2559 4010 4.691860 ACCTTGAAAGAGCATTTCATCG 57.308 40.909 15.32 11.49 38.12 3.84
2569 4020 4.396166 AGAGCATTTCATCGTTTGGTTAGG 59.604 41.667 0.00 0.00 0.00 2.69
2683 4134 3.323403 GCCATTCCTGACTATCTGCTACT 59.677 47.826 0.00 0.00 0.00 2.57
2684 4135 4.560513 GCCATTCCTGACTATCTGCTACTC 60.561 50.000 0.00 0.00 0.00 2.59
2685 4136 4.021544 CCATTCCTGACTATCTGCTACTCC 60.022 50.000 0.00 0.00 0.00 3.85
2686 4137 3.231207 TCCTGACTATCTGCTACTCCC 57.769 52.381 0.00 0.00 0.00 4.30
2687 4138 2.786445 TCCTGACTATCTGCTACTCCCT 59.214 50.000 0.00 0.00 0.00 4.20
2688 4139 3.153919 CCTGACTATCTGCTACTCCCTC 58.846 54.545 0.00 0.00 0.00 4.30
2689 4140 3.153919 CTGACTATCTGCTACTCCCTCC 58.846 54.545 0.00 0.00 0.00 4.30
2690 4141 2.156098 GACTATCTGCTACTCCCTCCG 58.844 57.143 0.00 0.00 0.00 4.63
2691 4142 1.495574 ACTATCTGCTACTCCCTCCGT 59.504 52.381 0.00 0.00 0.00 4.69
2692 4143 2.091775 ACTATCTGCTACTCCCTCCGTT 60.092 50.000 0.00 0.00 0.00 4.44
2693 4144 1.404843 ATCTGCTACTCCCTCCGTTC 58.595 55.000 0.00 0.00 0.00 3.95
2694 4145 0.683504 TCTGCTACTCCCTCCGTTCC 60.684 60.000 0.00 0.00 0.00 3.62
2695 4146 1.677637 CTGCTACTCCCTCCGTTCCC 61.678 65.000 0.00 0.00 0.00 3.97
2696 4147 1.684734 GCTACTCCCTCCGTTCCCA 60.685 63.158 0.00 0.00 0.00 4.37
2697 4148 1.049289 GCTACTCCCTCCGTTCCCAT 61.049 60.000 0.00 0.00 0.00 4.00
2698 4149 1.041437 CTACTCCCTCCGTTCCCATC 58.959 60.000 0.00 0.00 0.00 3.51
2699 4150 0.635009 TACTCCCTCCGTTCCCATCT 59.365 55.000 0.00 0.00 0.00 2.90
2700 4151 0.635009 ACTCCCTCCGTTCCCATCTA 59.365 55.000 0.00 0.00 0.00 1.98
2701 4152 1.333177 CTCCCTCCGTTCCCATCTAG 58.667 60.000 0.00 0.00 0.00 2.43
2702 4153 0.931468 TCCCTCCGTTCCCATCTAGA 59.069 55.000 0.00 0.00 0.00 2.43
2703 4154 1.133450 TCCCTCCGTTCCCATCTAGAG 60.133 57.143 0.00 0.00 0.00 2.43
2704 4155 1.133450 CCCTCCGTTCCCATCTAGAGA 60.133 57.143 0.00 0.00 0.00 3.10
2705 4156 2.491825 CCCTCCGTTCCCATCTAGAGAT 60.492 54.545 0.00 0.00 34.56 2.75
2706 4157 3.235200 CCTCCGTTCCCATCTAGAGATT 58.765 50.000 0.00 0.00 31.21 2.40
2707 4158 3.257127 CCTCCGTTCCCATCTAGAGATTC 59.743 52.174 0.00 0.00 31.21 2.52
2708 4159 3.231818 TCCGTTCCCATCTAGAGATTCC 58.768 50.000 0.00 0.00 31.21 3.01
2709 4160 2.965831 CCGTTCCCATCTAGAGATTCCA 59.034 50.000 0.00 0.00 31.21 3.53
2710 4161 3.388024 CCGTTCCCATCTAGAGATTCCAA 59.612 47.826 0.00 0.00 31.21 3.53
2711 4162 4.372656 CGTTCCCATCTAGAGATTCCAAC 58.627 47.826 0.00 0.00 31.21 3.77
2712 4163 4.141937 CGTTCCCATCTAGAGATTCCAACA 60.142 45.833 0.00 0.00 31.21 3.33
2713 4164 5.626809 CGTTCCCATCTAGAGATTCCAACAA 60.627 44.000 0.00 0.00 31.21 2.83
2714 4165 5.620738 TCCCATCTAGAGATTCCAACAAG 57.379 43.478 0.00 0.00 31.21 3.16
2715 4166 5.032846 TCCCATCTAGAGATTCCAACAAGT 58.967 41.667 0.00 0.00 31.21 3.16
2716 4167 5.104776 TCCCATCTAGAGATTCCAACAAGTG 60.105 44.000 0.00 0.00 31.21 3.16
2717 4168 5.104776 CCCATCTAGAGATTCCAACAAGTGA 60.105 44.000 0.00 0.00 31.21 3.41
2718 4169 5.814705 CCATCTAGAGATTCCAACAAGTGAC 59.185 44.000 0.00 0.00 31.21 3.67
2719 4170 6.351711 CCATCTAGAGATTCCAACAAGTGACT 60.352 42.308 0.00 0.00 31.21 3.41
2720 4171 7.147828 CCATCTAGAGATTCCAACAAGTGACTA 60.148 40.741 0.00 0.00 31.21 2.59
2721 4172 7.159322 TCTAGAGATTCCAACAAGTGACTAC 57.841 40.000 0.00 0.00 0.00 2.73
2722 4173 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
2723 4174 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
2724 4175 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
2725 4176 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
2726 4177 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
2727 4178 5.456548 TTCCAACAAGTGACTACATACGA 57.543 39.130 0.00 0.00 0.00 3.43
2728 4179 5.456548 TCCAACAAGTGACTACATACGAA 57.543 39.130 0.00 0.00 0.00 3.85
2729 4180 5.466819 TCCAACAAGTGACTACATACGAAG 58.533 41.667 0.00 0.00 0.00 3.79
2730 4181 4.091509 CCAACAAGTGACTACATACGAAGC 59.908 45.833 0.00 0.00 0.00 3.86
2731 4182 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2732 4183 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2733 4184 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2734 4185 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2735 4186 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2736 4187 7.041372 ACAAGTGACTACATACGAAGCAAAATT 60.041 33.333 0.00 0.00 0.00 1.82
2737 4188 8.440059 CAAGTGACTACATACGAAGCAAAATTA 58.560 33.333 0.00 0.00 0.00 1.40
2738 4189 8.186178 AGTGACTACATACGAAGCAAAATTAG 57.814 34.615 0.00 0.00 0.00 1.73
2739 4190 7.817962 AGTGACTACATACGAAGCAAAATTAGT 59.182 33.333 0.00 0.00 0.00 2.24
2740 4191 7.898309 GTGACTACATACGAAGCAAAATTAGTG 59.102 37.037 0.00 0.00 0.00 2.74
2741 4192 7.815549 TGACTACATACGAAGCAAAATTAGTGA 59.184 33.333 0.00 0.00 0.00 3.41
2742 4193 8.542497 ACTACATACGAAGCAAAATTAGTGAA 57.458 30.769 0.00 0.00 0.00 3.18
2743 4194 9.162764 ACTACATACGAAGCAAAATTAGTGAAT 57.837 29.630 0.00 0.00 0.00 2.57
2744 4195 9.638300 CTACATACGAAGCAAAATTAGTGAATC 57.362 33.333 0.00 0.00 0.00 2.52
2745 4196 8.268850 ACATACGAAGCAAAATTAGTGAATCT 57.731 30.769 0.00 0.00 0.00 2.40
2746 4197 9.378551 ACATACGAAGCAAAATTAGTGAATCTA 57.621 29.630 0.00 0.00 0.00 1.98
2747 4198 9.638300 CATACGAAGCAAAATTAGTGAATCTAC 57.362 33.333 0.00 0.00 0.00 2.59
2748 4199 7.667043 ACGAAGCAAAATTAGTGAATCTACA 57.333 32.000 0.00 0.00 0.00 2.74
2749 4200 7.519002 ACGAAGCAAAATTAGTGAATCTACAC 58.481 34.615 0.00 0.00 40.60 2.90
2751 4202 7.900352 CGAAGCAAAATTAGTGAATCTACACTC 59.100 37.037 4.63 0.00 46.36 3.51
2752 4203 8.854614 AAGCAAAATTAGTGAATCTACACTCT 57.145 30.769 4.63 0.00 46.36 3.24
2753 4204 9.944376 AAGCAAAATTAGTGAATCTACACTCTA 57.056 29.630 4.63 0.00 46.36 2.43
2754 4205 9.944376 AGCAAAATTAGTGAATCTACACTCTAA 57.056 29.630 4.63 0.00 46.36 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.823098 GATTTATATGTGCAGAAGATTCATGTC 57.177 33.333 0.00 0.00 0.00 3.06
14 15 5.008019 ACTGGCGAAAGATTTATATGTGCAG 59.992 40.000 0.00 0.00 0.00 4.41
34 35 0.460987 CGGAGAGGCTTTAGCACTGG 60.461 60.000 3.88 0.00 44.36 4.00
35 36 0.532573 TCGGAGAGGCTTTAGCACTG 59.467 55.000 3.88 0.00 44.36 3.66
39 40 0.103390 GGAGTCGGAGAGGCTTTAGC 59.897 60.000 0.00 0.00 36.95 3.09
63 64 3.516615 CTGATCCGGAAACTCTCAAGTC 58.483 50.000 9.01 0.00 33.48 3.01
76 77 4.054671 GTTCAGAAATCTAGCTGATCCGG 58.945 47.826 0.00 0.00 40.51 5.14
94 95 1.810151 GGGCTTCTTGCATTACGTTCA 59.190 47.619 0.00 0.00 45.15 3.18
95 96 1.132453 GGGGCTTCTTGCATTACGTTC 59.868 52.381 0.00 0.00 45.15 3.95
99 100 0.817654 GTGGGGGCTTCTTGCATTAC 59.182 55.000 0.00 0.00 45.15 1.89
130 131 4.381411 TGTTGTGGTGTGTCGATATTCAA 58.619 39.130 0.00 0.00 0.00 2.69
136 137 2.031258 TGTTGTTGTGGTGTGTCGAT 57.969 45.000 0.00 0.00 0.00 3.59
182 183 1.568612 AACTCAACACGGATGCAGCG 61.569 55.000 0.00 0.00 0.00 5.18
184 185 3.249799 TGTAAAACTCAACACGGATGCAG 59.750 43.478 0.00 0.00 0.00 4.41
235 236 1.812686 GAGTACTGCACCACGACCCA 61.813 60.000 0.00 0.00 0.00 4.51
258 259 2.315176 CAAACCAAGGACAACCCATCA 58.685 47.619 0.00 0.00 37.41 3.07
280 281 3.708403 TGGCTGGCATCAGGATATTAG 57.292 47.619 0.00 0.00 41.19 1.73
288 289 1.830279 TCTTTCTTGGCTGGCATCAG 58.170 50.000 4.22 0.04 43.64 2.90
294 295 5.395682 TTCATCAAATCTTTCTTGGCTGG 57.604 39.130 0.00 0.00 0.00 4.85
377 378 2.236146 AGTGACCATGTAGGCGATTTGA 59.764 45.455 0.00 0.00 43.14 2.69
416 417 4.430007 CATGATTTGAATGCAAGGGACTG 58.570 43.478 0.00 0.00 40.86 3.51
468 494 0.747852 TGTGTGGTCACTCGCTACAA 59.252 50.000 2.66 0.00 44.14 2.41
478 504 1.419381 TGGCTAGAAGTGTGTGGTCA 58.581 50.000 0.00 0.00 0.00 4.02
482 508 2.095567 GCATGTTGGCTAGAAGTGTGTG 60.096 50.000 0.00 0.00 0.00 3.82
516 542 2.807967 TCTGAAGACAATTGGAAGCACG 59.192 45.455 10.83 0.00 0.00 5.34
543 569 0.874607 ATCTTCCGTCCGCGCAATAC 60.875 55.000 8.75 0.25 36.67 1.89
551 577 0.174845 TGGCTAACATCTTCCGTCCG 59.825 55.000 0.00 0.00 0.00 4.79
566 592 0.469494 TGCATCACCGTCATATGGCT 59.531 50.000 5.65 0.00 0.00 4.75
596 622 1.751924 GGGCAGAACTCGATGTCTACT 59.248 52.381 0.00 0.00 0.00 2.57
601 627 0.321653 GTTGGGGCAGAACTCGATGT 60.322 55.000 0.00 0.00 0.00 3.06
608 634 1.303643 CTGGAGGTTGGGGCAGAAC 60.304 63.158 0.00 0.00 0.00 3.01
613 639 0.322906 CTTCTTCTGGAGGTTGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
669 695 4.988540 TCTGATACAGAACAAAACTGGACG 59.011 41.667 0.00 0.00 37.57 4.79
685 711 1.555075 TGTTCAGGGCCAGTCTGATAC 59.445 52.381 6.18 9.79 40.46 2.24
758 784 2.622436 GGAGATTTTCTGTCAGGTCGG 58.378 52.381 0.00 0.00 0.00 4.79
759 785 2.028112 TGGGAGATTTTCTGTCAGGTCG 60.028 50.000 0.00 0.00 0.00 4.79
763 789 2.996621 GTCGTGGGAGATTTTCTGTCAG 59.003 50.000 0.00 0.00 0.00 3.51
801 827 3.412386 CAACGGAGGTGGAAGATTTCTT 58.588 45.455 0.00 0.00 39.23 2.52
865 2216 6.039382 AGTCATTTGGTCCTTGTGTTAGAAAC 59.961 38.462 0.00 0.00 0.00 2.78
958 2314 1.142474 GGGCGATTTTATACGTCCGG 58.858 55.000 0.00 0.00 43.94 5.14
963 2319 3.057734 GAGGAGTGGGCGATTTTATACG 58.942 50.000 0.00 0.00 0.00 3.06
980 2336 0.975556 TAGGCAGGTGATTGCGAGGA 60.976 55.000 0.00 0.00 45.00 3.71
1063 2428 1.002868 GTGAGGACAGCAGCCATGT 60.003 57.895 0.00 0.00 0.00 3.21
1184 2549 2.861101 GCGGATCAGCTCGATGGGA 61.861 63.158 10.86 0.00 33.17 4.37
1226 2591 4.547859 AGCATGATGGGCTCGAAC 57.452 55.556 0.00 0.00 36.81 3.95
1534 2900 3.074538 AGCAGAGAAAACCACCCAATAGT 59.925 43.478 0.00 0.00 0.00 2.12
1566 2932 9.583765 GAACTAATCATACGGAGTCTAAAACTT 57.416 33.333 0.00 0.00 43.93 2.66
1595 2961 4.584638 ACCACAATATCTTGCCAAGGTA 57.415 40.909 4.30 1.56 35.69 3.08
1622 2988 7.217200 AGTAGTCTTAAAACATCTCACAGCAA 58.783 34.615 0.00 0.00 0.00 3.91
1756 3173 4.693566 TCAACACATCCGGCTAACTTAAAG 59.306 41.667 0.00 0.00 0.00 1.85
1774 3191 6.658816 AGTGATTGTATTAGCACCATTCAACA 59.341 34.615 0.00 0.00 31.85 3.33
1874 3291 8.485976 AAGCAAATCAGTCTTACAATACTCTC 57.514 34.615 0.00 0.00 0.00 3.20
1883 3300 8.983724 GTATCATCCTAAGCAAATCAGTCTTAC 58.016 37.037 0.00 0.00 0.00 2.34
1946 3363 0.729140 GCCGGAACAAAGCATCAACG 60.729 55.000 5.05 0.00 0.00 4.10
2012 3431 2.547826 GTATTCCAGCAACTACCCGAC 58.452 52.381 0.00 0.00 0.00 4.79
2237 3671 2.237643 ACACACAATATGCAACAGCCA 58.762 42.857 0.00 0.00 0.00 4.75
2391 3842 3.251479 TGTATGCAAGGAGCTACACTG 57.749 47.619 0.00 0.00 45.94 3.66
2542 3993 4.278170 ACCAAACGATGAAATGCTCTTTCA 59.722 37.500 14.57 14.57 41.91 2.69
2545 3996 4.853924 AACCAAACGATGAAATGCTCTT 57.146 36.364 0.00 0.00 0.00 2.85
2559 4010 9.820725 AGTACCAATTTTAAAACCTAACCAAAC 57.179 29.630 1.97 0.00 0.00 2.93
2683 4134 0.931468 TCTAGATGGGAACGGAGGGA 59.069 55.000 0.00 0.00 0.00 4.20
2684 4135 1.133450 TCTCTAGATGGGAACGGAGGG 60.133 57.143 0.00 0.00 0.00 4.30
2685 4136 2.366640 TCTCTAGATGGGAACGGAGG 57.633 55.000 0.00 0.00 0.00 4.30
2686 4137 3.257127 GGAATCTCTAGATGGGAACGGAG 59.743 52.174 0.00 0.00 34.49 4.63
2687 4138 3.231818 GGAATCTCTAGATGGGAACGGA 58.768 50.000 0.00 0.00 34.49 4.69
2688 4139 2.965831 TGGAATCTCTAGATGGGAACGG 59.034 50.000 0.00 0.00 34.49 4.44
2689 4140 4.141937 TGTTGGAATCTCTAGATGGGAACG 60.142 45.833 0.00 0.00 34.49 3.95
2690 4141 5.359194 TGTTGGAATCTCTAGATGGGAAC 57.641 43.478 0.00 0.00 34.49 3.62
2691 4142 5.488919 ACTTGTTGGAATCTCTAGATGGGAA 59.511 40.000 0.00 0.00 34.49 3.97
2692 4143 5.032846 ACTTGTTGGAATCTCTAGATGGGA 58.967 41.667 0.00 0.00 34.49 4.37
2693 4144 5.104776 TCACTTGTTGGAATCTCTAGATGGG 60.105 44.000 0.00 0.00 34.49 4.00
2694 4145 5.814705 GTCACTTGTTGGAATCTCTAGATGG 59.185 44.000 0.00 0.00 34.49 3.51
2695 4146 6.638610 AGTCACTTGTTGGAATCTCTAGATG 58.361 40.000 0.00 0.00 34.49 2.90
2696 4147 6.865834 AGTCACTTGTTGGAATCTCTAGAT 57.134 37.500 0.00 0.00 36.07 1.98
2697 4148 6.719829 TGTAGTCACTTGTTGGAATCTCTAGA 59.280 38.462 0.00 0.00 0.00 2.43
2698 4149 6.925211 TGTAGTCACTTGTTGGAATCTCTAG 58.075 40.000 0.00 0.00 0.00 2.43
2699 4150 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
2700 4151 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
2701 4152 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
2702 4153 6.071560 TCGTATGTAGTCACTTGTTGGAATCT 60.072 38.462 0.00 0.00 0.00 2.40
2703 4154 6.097356 TCGTATGTAGTCACTTGTTGGAATC 58.903 40.000 0.00 0.00 0.00 2.52
2704 4155 6.032956 TCGTATGTAGTCACTTGTTGGAAT 57.967 37.500 0.00 0.00 0.00 3.01
2705 4156 5.456548 TCGTATGTAGTCACTTGTTGGAA 57.543 39.130 0.00 0.00 0.00 3.53
2706 4157 5.456548 TTCGTATGTAGTCACTTGTTGGA 57.543 39.130 0.00 0.00 0.00 3.53
2707 4158 4.091509 GCTTCGTATGTAGTCACTTGTTGG 59.908 45.833 0.00 0.00 0.00 3.77
2708 4159 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
2709 4160 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
2710 4161 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2711 4162 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2712 4163 7.435068 AATTTTGCTTCGTATGTAGTCACTT 57.565 32.000 0.00 0.00 0.00 3.16
2713 4164 7.817962 ACTAATTTTGCTTCGTATGTAGTCACT 59.182 33.333 0.00 0.00 0.00 3.41
2714 4165 7.898309 CACTAATTTTGCTTCGTATGTAGTCAC 59.102 37.037 0.00 0.00 0.00 3.67
2715 4166 7.815549 TCACTAATTTTGCTTCGTATGTAGTCA 59.184 33.333 0.00 0.00 0.00 3.41
2716 4167 8.181487 TCACTAATTTTGCTTCGTATGTAGTC 57.819 34.615 0.00 0.00 0.00 2.59
2717 4168 8.542497 TTCACTAATTTTGCTTCGTATGTAGT 57.458 30.769 0.00 0.00 0.00 2.73
2718 4169 9.638300 GATTCACTAATTTTGCTTCGTATGTAG 57.362 33.333 0.00 0.00 0.00 2.74
2719 4170 9.378551 AGATTCACTAATTTTGCTTCGTATGTA 57.621 29.630 0.00 0.00 0.00 2.29
2720 4171 8.268850 AGATTCACTAATTTTGCTTCGTATGT 57.731 30.769 0.00 0.00 0.00 2.29
2721 4172 9.638300 GTAGATTCACTAATTTTGCTTCGTATG 57.362 33.333 0.00 0.00 32.49 2.39
2722 4173 9.378551 TGTAGATTCACTAATTTTGCTTCGTAT 57.621 29.630 0.00 0.00 32.49 3.06
2723 4174 8.653338 GTGTAGATTCACTAATTTTGCTTCGTA 58.347 33.333 0.00 0.00 35.68 3.43
2724 4175 7.387948 AGTGTAGATTCACTAATTTTGCTTCGT 59.612 33.333 0.00 0.00 45.31 3.85
2725 4176 7.743104 AGTGTAGATTCACTAATTTTGCTTCG 58.257 34.615 0.00 0.00 45.31 3.79
2726 4177 8.940952 AGAGTGTAGATTCACTAATTTTGCTTC 58.059 33.333 0.00 0.00 46.81 3.86
2727 4178 8.854614 AGAGTGTAGATTCACTAATTTTGCTT 57.145 30.769 0.00 0.00 46.81 3.91
2728 4179 9.944376 TTAGAGTGTAGATTCACTAATTTTGCT 57.056 29.630 0.00 0.00 46.81 3.91


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

AutoCloner maintained by Alex Coulton.