Multiple sequence alignment - TraesCS3D01G163000

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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 TraesCS3D01G163000 chr3D 100.000 3480 0 0 1 3480 134555828 134559307 0.000000e+00 6427.0
1 TraesCS3D01G163000 chr3A 88.657 2592 163 75 193 2727 148615090 148617607 0.000000e+00 3037.0
2 TraesCS3D01G163000 chr3A 89.947 189 12 1 1 189 148613896 148614077 1.610000e-58 237.0
3 TraesCS3D01G163000 chr3A 86.076 79 6 2 2727 2800 148617637 148617715 2.880000e-11 80.5
4 TraesCS3D01G163000 chr3B 93.948 1867 58 12 349 2183 190909814 190911657 0.000000e+00 2771.0
5 TraesCS3D01G163000 chr3B 87.155 1339 99 40 2184 3479 190911757 190913065 0.000000e+00 1452.0
6 TraesCS3D01G163000 chr3B 83.601 311 28 9 65 353 190909190 190909499 1.590000e-68 270.0


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 TraesCS3D01G163000 chr3D 134555828 134559307 3479 False 6427.000000 6427 100.000000 1 3480 1 chr3D.!!$F1 3479
1 TraesCS3D01G163000 chr3A 148613896 148617715 3819 False 1118.166667 3037 88.226667 1 2800 3 chr3A.!!$F1 2799
2 TraesCS3D01G163000 chr3B 190909190 190913065 3875 False 1497.666667 2771 88.234667 65 3479 3 chr3B.!!$F1 3414

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
379 1733 0.173481 TCGCACACCTAGCTAAGCTG 59.827 55.0 0.0 0.0 40.1 4.24 F
1290 2670 0.246635 GTAAAGAGCAGAGGTCGCCA 59.753 55.0 0.0 0.0 35.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 3728 0.317479 GTTACAGAGCCTGTCCACGT 59.683 55.0 10.6 0.0 41.21 4.49 R
2856 4442 0.250295 TTCCTTTCTGCCGTCTGGTG 60.250 55.0 0.0 0.0 37.67 4.17 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
20 21 3.991536 GAGACGCTCTTCCCGCCAC 62.992 68.421 0.37 0.00 0.00 5.01
52 53 4.105697 TCAAAATGTTGGGAGTTAGACCCT 59.894 41.667 0.00 0.00 46.82 4.34
53 54 4.302559 AAATGTTGGGAGTTAGACCCTC 57.697 45.455 0.00 0.00 46.82 4.30
54 55 2.715763 TGTTGGGAGTTAGACCCTCT 57.284 50.000 0.00 0.00 46.82 3.69
55 56 2.537143 TGTTGGGAGTTAGACCCTCTC 58.463 52.381 0.00 0.00 46.82 3.20
56 57 2.158219 TGTTGGGAGTTAGACCCTCTCA 60.158 50.000 0.00 0.00 46.82 3.27
57 58 2.904434 GTTGGGAGTTAGACCCTCTCAA 59.096 50.000 0.00 0.00 44.94 3.02
58 59 3.269592 TGGGAGTTAGACCCTCTCAAA 57.730 47.619 0.00 0.00 46.82 2.69
104 105 4.196971 ACCTACGAAACAAATAGATGGCC 58.803 43.478 0.00 0.00 0.00 5.36
135 136 2.178984 ACAACCCCCAAATCCTCTTTCA 59.821 45.455 0.00 0.00 0.00 2.69
143 144 3.311871 CCAAATCCTCTTTCATCGCTCAG 59.688 47.826 0.00 0.00 0.00 3.35
189 191 5.590259 CACAAATTACTAGAAGGTCATGGGG 59.410 44.000 0.00 0.00 0.00 4.96
191 193 1.802553 TACTAGAAGGTCATGGGGCC 58.197 55.000 0.00 0.00 0.00 5.80
285 1313 8.542497 TTTTGTGTATGTGTCTAAGTCATACC 57.458 34.615 10.58 4.91 41.50 2.73
295 1323 7.147620 TGTGTCTAAGTCATACCCCGATATTTT 60.148 37.037 0.00 0.00 0.00 1.82
301 1329 6.062095 AGTCATACCCCGATATTTTTCAAGG 58.938 40.000 0.00 0.00 0.00 3.61
362 1716 3.004419 TCTGTCAACTAAGTGACCACTCG 59.996 47.826 2.84 1.16 46.13 4.18
379 1733 0.173481 TCGCACACCTAGCTAAGCTG 59.827 55.000 0.00 0.00 40.10 4.24
402 1756 7.031226 TGGCTATCTTGCTCAAACATTAATC 57.969 36.000 0.00 0.00 0.00 1.75
502 1856 7.044181 CAGATTGCCAAAAGATACTCTACTCA 58.956 38.462 0.00 0.00 0.00 3.41
663 2020 0.326264 AAGCCTGACAGTGTCATCCC 59.674 55.000 25.65 16.06 41.94 3.85
751 2108 5.163703 ACTCTCAGCTCTAAGTTGTGTATCG 60.164 44.000 0.00 0.00 0.00 2.92
791 2148 8.873830 CAGATAGTTAATACTCCAAGTTGTGTG 58.126 37.037 1.45 0.00 35.78 3.82
805 2162 4.060900 AGTTGTGTGTCTAGTTGATGCTG 58.939 43.478 0.00 0.00 0.00 4.41
895 2265 3.377172 TGTGATTCTCAGCTGCAATCATG 59.623 43.478 29.02 9.21 38.48 3.07
900 2270 4.950205 TCTCAGCTGCAATCATGAGATA 57.050 40.909 9.47 0.00 42.36 1.98
926 2296 6.633500 AACTGCTGACATTTTTAAGCTGTA 57.367 33.333 6.49 0.00 44.05 2.74
938 2308 9.559958 CATTTTTAAGCTGTAGAATGTTCGAAT 57.440 29.630 0.00 0.00 0.00 3.34
939 2309 8.948853 TTTTTAAGCTGTAGAATGTTCGAATG 57.051 30.769 0.00 0.00 0.00 2.67
954 2328 6.482835 TGTTCGAATGTTTGACTTTGTGTAG 58.517 36.000 0.00 0.00 0.00 2.74
964 2338 7.921214 TGTTTGACTTTGTGTAGTTTTGTTCAA 59.079 29.630 0.00 0.00 0.00 2.69
992 2366 6.287589 AGTAACATTTACCTCCTGACTCTG 57.712 41.667 0.00 0.00 0.00 3.35
1050 2427 2.670509 GCAGAAGAAGAACAGCAATGGC 60.671 50.000 0.00 0.00 41.61 4.40
1290 2670 0.246635 GTAAAGAGCAGAGGTCGCCA 59.753 55.000 0.00 0.00 35.00 5.69
1584 2997 2.047443 GTTCTCGTCCTCGCCTCCT 61.047 63.158 0.00 0.00 36.96 3.69
1585 2998 2.046864 TTCTCGTCCTCGCCTCCTG 61.047 63.158 0.00 0.00 36.96 3.86
1785 3198 1.810853 CGACATCATGGCGCTGACA 60.811 57.895 0.00 0.00 44.33 3.58
1967 3380 2.181021 GAGGCAGGGTACGTCGTG 59.819 66.667 8.47 0.00 0.00 4.35
1973 3386 2.126189 GGGTACGTCGTGCCACTC 60.126 66.667 29.87 12.34 40.07 3.51
1975 3388 2.503375 GTACGTCGTGCCACTCCG 60.503 66.667 8.47 0.00 0.00 4.63
1977 3390 2.042259 TACGTCGTGCCACTCCGAT 61.042 57.895 8.47 0.00 35.30 4.18
1978 3391 1.985447 TACGTCGTGCCACTCCGATC 61.985 60.000 8.47 0.00 35.30 3.69
1979 3392 2.579787 GTCGTGCCACTCCGATCG 60.580 66.667 8.51 8.51 35.30 3.69
1980 3393 3.060000 TCGTGCCACTCCGATCGT 61.060 61.111 15.09 0.00 0.00 3.73
1981 3394 1.746239 TCGTGCCACTCCGATCGTA 60.746 57.895 15.09 0.00 0.00 3.43
1982 3395 1.099295 TCGTGCCACTCCGATCGTAT 61.099 55.000 15.09 0.00 0.00 3.06
1983 3396 0.660595 CGTGCCACTCCGATCGTATC 60.661 60.000 15.09 0.00 0.00 2.24
1984 3397 0.318784 GTGCCACTCCGATCGTATCC 60.319 60.000 15.09 0.00 0.00 2.59
1985 3398 1.081376 GCCACTCCGATCGTATCCG 60.081 63.158 15.09 0.00 0.00 4.18
2089 3502 0.250901 ATTGGAAGCTTGTGACGGCT 60.251 50.000 2.10 0.00 40.85 5.52
2177 3590 5.189928 TCAAGACCAAGAAGTGTAAGCAAA 58.810 37.500 0.00 0.00 0.00 3.68
2203 3715 6.702716 ACTAGTACTTCTGAATCCACTAGC 57.297 41.667 21.16 0.00 39.24 3.42
2214 3726 4.470876 CACTAGCGTGGTGGTACG 57.529 61.111 0.00 0.00 46.28 3.67
2215 3727 1.582968 CACTAGCGTGGTGGTACGT 59.417 57.895 0.00 0.00 45.36 3.57
2216 3728 0.804364 CACTAGCGTGGTGGTACGTA 59.196 55.000 0.00 0.00 45.36 3.57
2217 3729 0.804989 ACTAGCGTGGTGGTACGTAC 59.195 55.000 17.56 17.56 45.36 3.67
2218 3730 0.247814 CTAGCGTGGTGGTACGTACG 60.248 60.000 18.98 15.01 45.36 3.67
2225 3737 0.109597 GGTGGTACGTACGTGGACAG 60.110 60.000 30.25 0.00 0.00 3.51
2250 3762 3.062909 TCTGTAACTGTGACGTGTTTTGC 59.937 43.478 0.00 0.00 0.00 3.68
2251 3763 3.004171 TGTAACTGTGACGTGTTTTGCT 58.996 40.909 0.00 0.00 0.00 3.91
2268 3793 0.242017 GCTCATTCAGGTGTTGTGGC 59.758 55.000 0.00 0.00 0.00 5.01
2537 4065 2.159627 GTGCTATTCTGGTTTCGTGTGG 59.840 50.000 0.00 0.00 0.00 4.17
2581 4109 8.839310 ATATATGTTACTCCTTGTGATTCAGC 57.161 34.615 0.00 0.00 0.00 4.26
2583 4111 4.065088 TGTTACTCCTTGTGATTCAGCAC 58.935 43.478 0.00 0.00 39.22 4.40
2584 4112 2.191128 ACTCCTTGTGATTCAGCACC 57.809 50.000 0.00 0.00 37.99 5.01
2585 4113 1.421268 ACTCCTTGTGATTCAGCACCA 59.579 47.619 0.00 0.00 37.99 4.17
2599 4128 2.070262 GCACCAGCTTTGGTTGAATC 57.930 50.000 0.00 0.00 40.85 2.52
2606 4135 2.875933 AGCTTTGGTTGAATCGAACGAA 59.124 40.909 0.12 0.00 0.00 3.85
2615 4144 4.661993 TGAATCGAACGAACTTTGGATG 57.338 40.909 0.12 0.00 0.00 3.51
2618 4147 0.787787 CGAACGAACTTTGGATGCGA 59.212 50.000 0.00 0.00 0.00 5.10
2619 4148 1.201812 CGAACGAACTTTGGATGCGAG 60.202 52.381 0.00 0.00 0.00 5.03
2625 4161 3.546670 CGAACTTTGGATGCGAGTACTAC 59.453 47.826 0.00 0.00 0.00 2.73
2651 4187 3.998672 GAACGCCACGAGTCCCCA 61.999 66.667 0.00 0.00 0.00 4.96
2652 4188 4.309950 AACGCCACGAGTCCCCAC 62.310 66.667 0.00 0.00 0.00 4.61
2656 4192 2.973899 CCACGAGTCCCCACTCTG 59.026 66.667 0.00 0.00 46.31 3.35
2657 4193 2.262915 CACGAGTCCCCACTCTGC 59.737 66.667 0.00 0.00 46.31 4.26
2658 4194 2.118513 ACGAGTCCCCACTCTGCT 59.881 61.111 0.00 0.00 46.31 4.24
2659 4195 1.979693 ACGAGTCCCCACTCTGCTC 60.980 63.158 0.00 0.00 46.31 4.26
2660 4196 2.888863 GAGTCCCCACTCTGCTCG 59.111 66.667 0.00 0.00 45.20 5.03
2661 4197 1.979693 GAGTCCCCACTCTGCTCGT 60.980 63.158 0.00 0.00 45.20 4.18
2662 4198 0.680280 GAGTCCCCACTCTGCTCGTA 60.680 60.000 0.00 0.00 45.20 3.43
2663 4199 0.681564 AGTCCCCACTCTGCTCGTAG 60.682 60.000 0.00 0.00 0.00 3.51
2664 4200 0.966370 GTCCCCACTCTGCTCGTAGT 60.966 60.000 0.00 0.00 0.00 2.73
2665 4201 0.251653 TCCCCACTCTGCTCGTAGTT 60.252 55.000 0.00 0.00 0.00 2.24
2666 4202 0.108615 CCCCACTCTGCTCGTAGTTG 60.109 60.000 0.00 0.00 0.00 3.16
2667 4203 0.888619 CCCACTCTGCTCGTAGTTGA 59.111 55.000 0.00 0.00 0.00 3.18
2668 4204 1.135257 CCCACTCTGCTCGTAGTTGAG 60.135 57.143 0.00 0.00 39.05 3.02
2669 4205 1.542030 CCACTCTGCTCGTAGTTGAGT 59.458 52.381 0.00 0.00 38.28 3.41
2671 4207 2.983136 CACTCTGCTCGTAGTTGAGTTG 59.017 50.000 0.00 0.00 38.28 3.16
2675 4211 2.917971 CTGCTCGTAGTTGAGTTGTAGC 59.082 50.000 0.00 0.00 38.28 3.58
2676 4212 2.557056 TGCTCGTAGTTGAGTTGTAGCT 59.443 45.455 0.00 0.00 38.28 3.32
2677 4213 3.754850 TGCTCGTAGTTGAGTTGTAGCTA 59.245 43.478 0.00 0.00 38.28 3.32
2703 4243 1.021920 GGGCGCTCTCCTCTGTTTTC 61.022 60.000 7.64 0.00 0.00 2.29
2706 4246 0.321671 CGCTCTCCTCTGTTTTCCCA 59.678 55.000 0.00 0.00 0.00 4.37
2707 4247 1.270839 CGCTCTCCTCTGTTTTCCCAA 60.271 52.381 0.00 0.00 0.00 4.12
2708 4248 2.431454 GCTCTCCTCTGTTTTCCCAAG 58.569 52.381 0.00 0.00 0.00 3.61
2709 4249 2.224646 GCTCTCCTCTGTTTTCCCAAGT 60.225 50.000 0.00 0.00 0.00 3.16
2711 4251 2.372172 TCTCCTCTGTTTTCCCAAGTCC 59.628 50.000 0.00 0.00 0.00 3.85
2712 4252 1.423921 TCCTCTGTTTTCCCAAGTCCC 59.576 52.381 0.00 0.00 0.00 4.46
2713 4253 1.144913 CCTCTGTTTTCCCAAGTCCCA 59.855 52.381 0.00 0.00 0.00 4.37
2714 4254 2.508526 CTCTGTTTTCCCAAGTCCCAG 58.491 52.381 0.00 0.00 0.00 4.45
2715 4255 1.144913 TCTGTTTTCCCAAGTCCCAGG 59.855 52.381 0.00 0.00 0.00 4.45
2717 4257 0.178961 GTTTTCCCAAGTCCCAGGCT 60.179 55.000 0.00 0.00 0.00 4.58
2718 4258 0.112412 TTTTCCCAAGTCCCAGGCTC 59.888 55.000 0.00 0.00 0.00 4.70
2719 4259 1.789576 TTTCCCAAGTCCCAGGCTCC 61.790 60.000 0.00 0.00 0.00 4.70
2723 4263 1.920325 CAAGTCCCAGGCTCCCAGA 60.920 63.158 0.00 0.00 0.00 3.86
2752 4319 4.519437 TCGCAGCGCCTCATCCTG 62.519 66.667 10.87 0.00 0.00 3.86
2754 4321 2.501128 GCAGCGCCTCATCCTGTA 59.499 61.111 2.29 0.00 0.00 2.74
2755 4322 1.593750 GCAGCGCCTCATCCTGTAG 60.594 63.158 2.29 0.00 0.00 2.74
2757 4324 2.280457 GCGCCTCATCCTGTAGCC 60.280 66.667 0.00 0.00 0.00 3.93
2758 4325 2.028190 CGCCTCATCCTGTAGCCG 59.972 66.667 0.00 0.00 0.00 5.52
2802 4380 1.524165 GCTCTCTCGCGAGGTAGGA 60.524 63.158 33.98 23.49 37.86 2.94
2803 4381 1.503818 GCTCTCTCGCGAGGTAGGAG 61.504 65.000 33.98 29.99 37.86 3.69
2804 4382 1.503818 CTCTCTCGCGAGGTAGGAGC 61.504 65.000 33.98 0.00 37.86 4.70
2805 4383 1.820056 CTCTCGCGAGGTAGGAGCA 60.820 63.158 33.98 12.73 33.51 4.26
2806 4384 1.781025 CTCTCGCGAGGTAGGAGCAG 61.781 65.000 33.98 18.27 33.51 4.24
2807 4385 2.045242 TCGCGAGGTAGGAGCAGT 60.045 61.111 3.71 0.00 0.00 4.40
2808 4386 0.814410 CTCGCGAGGTAGGAGCAGTA 60.814 60.000 28.40 0.00 0.00 2.74
2809 4387 1.094073 TCGCGAGGTAGGAGCAGTAC 61.094 60.000 3.71 0.00 0.00 2.73
2810 4388 1.096386 CGCGAGGTAGGAGCAGTACT 61.096 60.000 0.00 0.00 0.00 2.73
2835 4419 2.358582 CCATGCCATTGAATCGCTGTTA 59.641 45.455 0.00 0.00 0.00 2.41
2839 4425 4.450976 TGCCATTGAATCGCTGTTATACT 58.549 39.130 0.00 0.00 0.00 2.12
2842 4428 5.465390 GCCATTGAATCGCTGTTATACTACA 59.535 40.000 0.00 0.00 0.00 2.74
2843 4429 6.346919 GCCATTGAATCGCTGTTATACTACAG 60.347 42.308 0.87 0.87 46.55 2.74
2844 4430 6.701841 CCATTGAATCGCTGTTATACTACAGT 59.298 38.462 6.46 0.00 45.76 3.55
2845 4431 7.865889 CCATTGAATCGCTGTTATACTACAGTA 59.134 37.037 6.46 0.00 45.76 2.74
2846 4432 8.691727 CATTGAATCGCTGTTATACTACAGTAC 58.308 37.037 6.46 0.00 45.76 2.73
2875 4461 0.250295 CACCAGACGGCAGAAAGGAA 60.250 55.000 0.00 0.00 34.57 3.36
2876 4462 0.472471 ACCAGACGGCAGAAAGGAAA 59.528 50.000 0.00 0.00 34.57 3.13
2877 4463 1.073923 ACCAGACGGCAGAAAGGAAAT 59.926 47.619 0.00 0.00 34.57 2.17
2878 4464 1.740025 CCAGACGGCAGAAAGGAAATC 59.260 52.381 0.00 0.00 0.00 2.17
2879 4465 1.740025 CAGACGGCAGAAAGGAAATCC 59.260 52.381 0.00 0.00 0.00 3.01
2880 4466 1.095600 GACGGCAGAAAGGAAATCCC 58.904 55.000 0.00 0.00 36.42 3.85
2990 4592 1.932604 GCGATCTCCTGCATCCTAACG 60.933 57.143 0.00 0.00 0.00 3.18
2994 4596 0.811616 CTCCTGCATCCTAACGCCAC 60.812 60.000 0.00 0.00 0.00 5.01
3107 4710 6.525629 CCTCCAGGTTACAATTCCTACTATG 58.474 44.000 0.00 0.00 32.26 2.23
3108 4711 6.326583 CCTCCAGGTTACAATTCCTACTATGA 59.673 42.308 0.00 0.00 32.26 2.15
3109 4712 7.016661 CCTCCAGGTTACAATTCCTACTATGAT 59.983 40.741 0.00 0.00 32.26 2.45
3110 4713 7.735917 TCCAGGTTACAATTCCTACTATGATG 58.264 38.462 0.00 0.00 32.26 3.07
3112 4715 7.993183 CCAGGTTACAATTCCTACTATGATGTT 59.007 37.037 0.00 0.00 32.26 2.71
3134 4740 0.813821 GCTTCTGTGATTTGCCCCTC 59.186 55.000 0.00 0.00 0.00 4.30
3143 4749 4.081531 TGTGATTTGCCCCTCATGAATTTC 60.082 41.667 0.00 0.00 0.00 2.17
3172 4780 9.540538 TCCCCTTTATATTGTCAAAAAGAATCA 57.459 29.630 9.01 0.00 31.96 2.57
3266 4874 0.729116 GCTGCCTCGTACGTACTACA 59.271 55.000 22.55 13.61 0.00 2.74
3294 4902 2.425312 TGTTTATATGCCGGTGCTTTGG 59.575 45.455 1.90 0.00 38.71 3.28
3310 4918 0.322816 TTGGCTTGCAGGGATCAGTC 60.323 55.000 0.00 0.00 0.00 3.51
3331 4939 2.100749 CGGTCCAAATAATTTGCCCTCC 59.899 50.000 0.00 0.00 39.31 4.30
3332 4940 3.374764 GGTCCAAATAATTTGCCCTCCT 58.625 45.455 0.00 0.00 39.31 3.69
3333 4941 3.384789 GGTCCAAATAATTTGCCCTCCTC 59.615 47.826 0.00 0.00 39.31 3.71
3347 4955 0.176680 CTCCTCTGTCATGGAACGGG 59.823 60.000 0.00 0.00 31.23 5.28
3397 5005 4.724279 ACACAGGAAAACTAATCCACCT 57.276 40.909 0.00 0.00 39.55 4.00
3398 5006 4.652822 ACACAGGAAAACTAATCCACCTC 58.347 43.478 0.00 0.00 39.55 3.85
3421 5029 1.142748 GACATGGAGGCCAGTCTCG 59.857 63.158 5.01 0.00 36.75 4.04
3470 5078 2.429610 TGCTACCTGATTCCGTACCTTC 59.570 50.000 0.00 0.00 0.00 3.46
3479 5087 6.128363 CCTGATTCCGTACCTTCAACTAAAAC 60.128 42.308 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.119931 TCCCAACATTTTGATGAGAAACG 57.880 39.130 0.00 0.00 34.24 3.60
82 83 4.196971 GGCCATCTATTTGTTTCGTAGGT 58.803 43.478 0.00 0.00 0.00 3.08
91 92 7.066142 TGTTGGTTATATGGCCATCTATTTGT 58.934 34.615 24.80 0.00 34.37 2.83
104 105 5.163353 GGATTTGGGGGTTGTTGGTTATATG 60.163 44.000 0.00 0.00 0.00 1.78
135 136 3.562973 CACATCTTATTTGCCTGAGCGAT 59.437 43.478 0.00 0.00 44.31 4.58
143 144 5.576774 GTGTAAAAGCCACATCTTATTTGCC 59.423 40.000 0.00 0.00 33.00 4.52
194 196 7.117236 TGTTGCTAGTTTTAGAAAGTGGATACG 59.883 37.037 0.00 0.00 42.51 3.06
336 1366 4.270325 GTGGTCACTTAGTTGACAGAACAC 59.730 45.833 13.72 8.88 46.68 3.32
379 1733 7.012704 TCAGATTAATGTTTGAGCAAGATAGCC 59.987 37.037 0.00 0.00 34.23 3.93
402 1756 7.198390 AGTGTTGTTTTGATCTCACATTTCAG 58.802 34.615 0.00 0.00 0.00 3.02
663 2020 5.188327 TGAGAGTTCAGTCAAGTACACAG 57.812 43.478 0.00 0.00 0.00 3.66
751 2108 7.539712 TTAACTATCTGACATAAGCAACTGC 57.460 36.000 0.00 0.00 42.49 4.40
805 2162 4.194640 TGATGCTAGGACAAAGCTCAATC 58.805 43.478 0.00 0.00 40.73 2.67
900 2270 6.263168 ACAGCTTAAAAATGTCAGCAGTTAGT 59.737 34.615 0.00 0.00 34.49 2.24
926 2296 6.692681 CACAAAGTCAAACATTCGAACATTCT 59.307 34.615 0.00 0.00 0.00 2.40
938 2308 7.426410 TGAACAAAACTACACAAAGTCAAACA 58.574 30.769 0.00 0.00 0.00 2.83
939 2309 7.861176 TGAACAAAACTACACAAAGTCAAAC 57.139 32.000 0.00 0.00 0.00 2.93
964 2338 6.606395 AGTCAGGAGGTAAATGTTACTCGTAT 59.394 38.462 0.00 0.00 0.00 3.06
992 2366 0.743097 GCATTCCTCCATTGCCTGAC 59.257 55.000 0.00 0.00 0.00 3.51
1050 2427 2.757508 TCGAGCCTCTGGAGCTGG 60.758 66.667 0.00 0.00 41.75 4.85
1827 3240 2.853542 TCCTTGTGGAGCCTGGCA 60.854 61.111 22.65 0.00 37.46 4.92
1965 3378 0.318784 GGATACGATCGGAGTGGCAC 60.319 60.000 20.98 10.29 0.00 5.01
1967 3380 4.968197 GGATACGATCGGAGTGGC 57.032 61.111 20.98 1.86 0.00 5.01
1979 3392 1.401148 CGATCATCCACGGACGGATAC 60.401 57.143 3.30 0.00 44.28 2.24
1980 3393 0.879090 CGATCATCCACGGACGGATA 59.121 55.000 3.30 0.00 44.28 2.59
1982 3395 1.452470 TCGATCATCCACGGACGGA 60.452 57.895 0.00 0.00 40.07 4.69
1983 3396 1.299165 GTCGATCATCCACGGACGG 60.299 63.158 0.00 0.00 0.00 4.79
1984 3397 1.299165 GGTCGATCATCCACGGACG 60.299 63.158 0.00 0.00 0.00 4.79
1985 3398 0.527817 GTGGTCGATCATCCACGGAC 60.528 60.000 16.85 3.89 43.34 4.79
2089 3502 3.521937 CCTGGAAGTTGGGGTCTATGTAA 59.478 47.826 0.00 0.00 0.00 2.41
2177 3590 8.852135 GCTAGTGGATTCAGAAGTACTAGTAAT 58.148 37.037 20.99 0.00 39.63 1.89
2214 3726 1.171308 TACAGAGCCTGTCCACGTAC 58.829 55.000 10.60 0.00 41.21 3.67
2215 3727 1.542915 GTTACAGAGCCTGTCCACGTA 59.457 52.381 10.60 0.00 41.21 3.57
2216 3728 0.317479 GTTACAGAGCCTGTCCACGT 59.683 55.000 10.60 0.00 41.21 4.49
2217 3729 0.603569 AGTTACAGAGCCTGTCCACG 59.396 55.000 10.60 0.00 41.21 4.94
2218 3730 1.344763 ACAGTTACAGAGCCTGTCCAC 59.655 52.381 10.60 9.32 41.21 4.02
2225 3737 1.269621 ACACGTCACAGTTACAGAGCC 60.270 52.381 0.00 0.00 0.00 4.70
2250 3762 0.518636 CGCCACAACACCTGAATGAG 59.481 55.000 0.00 0.00 0.00 2.90
2251 3763 0.888736 CCGCCACAACACCTGAATGA 60.889 55.000 0.00 0.00 0.00 2.57
2302 3827 2.366167 CCCTCCTCCACCTCCCTG 60.366 72.222 0.00 0.00 0.00 4.45
2537 4065 7.704047 ACATATATACATGCAGATGTGATCGAC 59.296 37.037 4.50 0.00 43.03 4.20
2584 4112 2.223144 TCGTTCGATTCAACCAAAGCTG 59.777 45.455 0.00 0.00 0.00 4.24
2585 4113 2.489971 TCGTTCGATTCAACCAAAGCT 58.510 42.857 0.00 0.00 0.00 3.74
2591 4120 3.249080 TCCAAAGTTCGTTCGATTCAACC 59.751 43.478 0.00 0.00 0.00 3.77
2598 4127 0.787787 CGCATCCAAAGTTCGTTCGA 59.212 50.000 0.00 0.00 0.00 3.71
2599 4128 0.787787 TCGCATCCAAAGTTCGTTCG 59.212 50.000 0.00 0.00 0.00 3.95
2606 4135 3.510360 ACAGTAGTACTCGCATCCAAAGT 59.490 43.478 0.00 0.00 0.00 2.66
2615 4144 3.826236 TCACAGAACAGTAGTACTCGC 57.174 47.619 0.00 0.00 0.00 5.03
2618 4147 3.305199 GGCGTTCACAGAACAGTAGTACT 60.305 47.826 0.00 0.00 0.00 2.73
2619 4148 2.985139 GGCGTTCACAGAACAGTAGTAC 59.015 50.000 10.15 0.00 0.00 2.73
2625 4161 0.874175 TCGTGGCGTTCACAGAACAG 60.874 55.000 10.15 4.57 46.36 3.16
2645 4181 0.966370 ACTACGAGCAGAGTGGGGAC 60.966 60.000 0.00 0.00 0.00 4.46
2651 4187 2.623889 ACAACTCAACTACGAGCAGAGT 59.376 45.455 0.00 0.00 40.99 3.24
2652 4188 3.290308 ACAACTCAACTACGAGCAGAG 57.710 47.619 0.00 0.00 36.42 3.35
2653 4189 3.366070 GCTACAACTCAACTACGAGCAGA 60.366 47.826 0.00 0.00 36.42 4.26
2656 4192 3.219052 AGCTACAACTCAACTACGAGC 57.781 47.619 0.00 0.00 36.42 5.03
2657 4193 4.201930 CCCTAGCTACAACTCAACTACGAG 60.202 50.000 0.00 0.00 39.05 4.18
2658 4194 3.693085 CCCTAGCTACAACTCAACTACGA 59.307 47.826 0.00 0.00 0.00 3.43
2659 4195 3.181489 CCCCTAGCTACAACTCAACTACG 60.181 52.174 0.00 0.00 0.00 3.51
2660 4196 3.430513 GCCCCTAGCTACAACTCAACTAC 60.431 52.174 0.00 0.00 38.99 2.73
2661 4197 2.764572 GCCCCTAGCTACAACTCAACTA 59.235 50.000 0.00 0.00 38.99 2.24
2662 4198 1.555533 GCCCCTAGCTACAACTCAACT 59.444 52.381 0.00 0.00 38.99 3.16
2663 4199 1.739371 CGCCCCTAGCTACAACTCAAC 60.739 57.143 0.00 0.00 40.39 3.18
2664 4200 0.535335 CGCCCCTAGCTACAACTCAA 59.465 55.000 0.00 0.00 40.39 3.02
2665 4201 1.327690 CCGCCCCTAGCTACAACTCA 61.328 60.000 0.00 0.00 40.39 3.41
2666 4202 1.442148 CCGCCCCTAGCTACAACTC 59.558 63.158 0.00 0.00 40.39 3.01
2667 4203 2.064581 CCCGCCCCTAGCTACAACT 61.065 63.158 0.00 0.00 40.39 3.16
2668 4204 2.504519 CCCGCCCCTAGCTACAAC 59.495 66.667 0.00 0.00 40.39 3.32
2669 4205 2.766651 CCCCGCCCCTAGCTACAA 60.767 66.667 0.00 0.00 40.39 2.41
2683 4223 2.470938 AAAACAGAGGAGAGCGCCCC 62.471 60.000 2.29 2.83 0.00 5.80
2688 4228 2.224646 ACTTGGGAAAACAGAGGAGAGC 60.225 50.000 0.00 0.00 0.00 4.09
2703 4243 3.732849 GGGAGCCTGGGACTTGGG 61.733 72.222 0.00 0.00 0.00 4.12
2706 4246 0.772124 TTTCTGGGAGCCTGGGACTT 60.772 55.000 0.00 0.00 0.00 3.01
2707 4247 1.151810 TTTCTGGGAGCCTGGGACT 60.152 57.895 0.00 0.00 0.00 3.85
2708 4248 1.002011 GTTTCTGGGAGCCTGGGAC 60.002 63.158 0.00 0.00 0.00 4.46
2709 4249 2.231380 GGTTTCTGGGAGCCTGGGA 61.231 63.158 0.00 0.00 0.00 4.37
2711 4251 2.045926 CGGTTTCTGGGAGCCTGG 60.046 66.667 0.00 0.00 0.00 4.45
2712 4252 2.747855 GCGGTTTCTGGGAGCCTG 60.748 66.667 0.00 0.00 0.00 4.85
2713 4253 4.035102 GGCGGTTTCTGGGAGCCT 62.035 66.667 0.00 0.00 44.06 4.58
2735 4302 4.519437 CAGGATGAGGCGCTGCGA 62.519 66.667 28.07 4.65 39.69 5.10
2744 4311 1.365633 GAGGCGGCTACAGGATGAG 59.634 63.158 13.24 0.00 39.69 2.90
2758 4325 2.740714 GAACATGACACGCGGAGGC 61.741 63.158 12.47 5.15 0.00 4.70
2802 4380 1.866015 TGGCATGGAGTAGTACTGCT 58.134 50.000 20.83 13.82 37.46 4.24
2803 4381 2.874701 CAATGGCATGGAGTAGTACTGC 59.125 50.000 14.46 14.46 37.06 4.40
2804 4382 4.406648 TCAATGGCATGGAGTAGTACTG 57.593 45.455 7.76 0.00 0.00 2.74
2805 4383 5.615289 GATTCAATGGCATGGAGTAGTACT 58.385 41.667 4.45 1.37 0.00 2.73
2806 4384 4.449068 CGATTCAATGGCATGGAGTAGTAC 59.551 45.833 4.45 0.00 0.00 2.73
2807 4385 4.631131 CGATTCAATGGCATGGAGTAGTA 58.369 43.478 4.45 0.00 0.00 1.82
2808 4386 3.470709 CGATTCAATGGCATGGAGTAGT 58.529 45.455 4.45 0.00 0.00 2.73
2809 4387 2.225019 GCGATTCAATGGCATGGAGTAG 59.775 50.000 4.45 3.96 33.87 2.57
2810 4388 2.158769 AGCGATTCAATGGCATGGAGTA 60.159 45.455 7.17 0.00 36.36 2.59
2854 4440 2.664851 TTTCTGCCGTCTGGTGCG 60.665 61.111 0.00 0.00 37.67 5.34
2855 4441 2.328099 CCTTTCTGCCGTCTGGTGC 61.328 63.158 0.00 0.00 37.67 5.01
2856 4442 0.250295 TTCCTTTCTGCCGTCTGGTG 60.250 55.000 0.00 0.00 37.67 4.17
2857 4443 0.472471 TTTCCTTTCTGCCGTCTGGT 59.528 50.000 0.00 0.00 37.67 4.00
2858 4444 1.740025 GATTTCCTTTCTGCCGTCTGG 59.260 52.381 0.00 0.00 38.77 3.86
2861 4447 1.095600 GGGATTTCCTTTCTGCCGTC 58.904 55.000 0.00 0.00 35.95 4.79
2864 4450 2.493675 GTTCAGGGATTTCCTTTCTGCC 59.506 50.000 0.00 0.00 45.47 4.85
2875 4461 3.307762 CGGAGAGGAAAAGTTCAGGGATT 60.308 47.826 0.00 0.00 0.00 3.01
2876 4462 2.237392 CGGAGAGGAAAAGTTCAGGGAT 59.763 50.000 0.00 0.00 0.00 3.85
2877 4463 1.623811 CGGAGAGGAAAAGTTCAGGGA 59.376 52.381 0.00 0.00 0.00 4.20
2878 4464 1.623811 TCGGAGAGGAAAAGTTCAGGG 59.376 52.381 0.00 0.00 0.00 4.45
2879 4465 3.402628 TTCGGAGAGGAAAAGTTCAGG 57.597 47.619 0.00 0.00 38.43 3.86
2880 4466 3.614616 CGATTCGGAGAGGAAAAGTTCAG 59.385 47.826 0.00 0.00 38.43 3.02
2881 4467 3.257375 TCGATTCGGAGAGGAAAAGTTCA 59.743 43.478 6.18 0.00 38.43 3.18
2882 4468 3.846360 TCGATTCGGAGAGGAAAAGTTC 58.154 45.455 6.18 0.00 38.43 3.01
2953 4539 3.881783 GCCGCGCGAGTAAATTTTA 57.118 47.368 34.63 0.00 0.00 1.52
2954 4540 4.757554 GCCGCGCGAGTAAATTTT 57.242 50.000 34.63 0.00 0.00 1.82
3001 4603 1.625511 AGCAAGCAAGAAAAGAGGGG 58.374 50.000 0.00 0.00 0.00 4.79
3005 4607 6.560253 CTAAACCTAGCAAGCAAGAAAAGA 57.440 37.500 0.00 0.00 0.00 2.52
3083 4686 6.326583 TCATAGTAGGAATTGTAACCTGGAGG 59.673 42.308 0.00 0.00 37.68 4.30
3094 4697 9.553064 AGAAGCTTAACATCATAGTAGGAATTG 57.447 33.333 0.00 0.00 0.00 2.32
3105 4708 6.327934 GCAAATCACAGAAGCTTAACATCAT 58.672 36.000 0.00 0.00 0.00 2.45
3107 4710 5.098211 GGCAAATCACAGAAGCTTAACATC 58.902 41.667 0.00 0.00 0.00 3.06
3108 4711 4.082026 GGGCAAATCACAGAAGCTTAACAT 60.082 41.667 0.00 0.00 0.00 2.71
3109 4712 3.255642 GGGCAAATCACAGAAGCTTAACA 59.744 43.478 0.00 0.00 0.00 2.41
3110 4713 3.367395 GGGGCAAATCACAGAAGCTTAAC 60.367 47.826 0.00 0.00 0.00 2.01
3112 4715 2.041620 AGGGGCAAATCACAGAAGCTTA 59.958 45.455 0.00 0.00 0.00 3.09
3172 4780 8.691661 AACAGGTAGAAACATACAAATGACTT 57.308 30.769 0.00 0.00 36.54 3.01
3176 4784 8.237267 GGAAGAACAGGTAGAAACATACAAATG 58.763 37.037 0.00 0.00 39.17 2.32
3266 4874 4.304110 CACCGGCATATAAACATCGTACT 58.696 43.478 0.00 0.00 0.00 2.73
3294 4902 1.817099 CCGACTGATCCCTGCAAGC 60.817 63.158 0.00 0.00 0.00 4.01
3310 4918 2.100749 GGAGGGCAAATTATTTGGACCG 59.899 50.000 17.89 0.00 40.94 4.79
3331 4939 1.811266 CGCCCGTTCCATGACAGAG 60.811 63.158 0.00 0.00 0.00 3.35
3332 4940 2.264480 CGCCCGTTCCATGACAGA 59.736 61.111 0.00 0.00 0.00 3.41
3333 4941 3.499737 GCGCCCGTTCCATGACAG 61.500 66.667 0.00 0.00 0.00 3.51
3397 5005 1.907222 CTGGCCTCCATGTCTGCAGA 61.907 60.000 13.74 13.74 30.82 4.26
3398 5006 1.451567 CTGGCCTCCATGTCTGCAG 60.452 63.158 7.63 7.63 30.82 4.41
3421 5029 1.450312 CCGGGGAGATGCTTGTGTC 60.450 63.158 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.