Multiple sequence alignment - TraesCS4D01G133600

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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 TraesCS4D01G133600 chr4D 100.000 2945 0 0 1 2945 120073314 120070370 0.000000e+00 5439.0
1 TraesCS4D01G133600 chr4B 93.804 1985 69 25 765 2705 183003275 183001301 0.000000e+00 2935.0
2 TraesCS4D01G133600 chr4A 96.936 1534 35 5 747 2275 451595486 451593960 0.000000e+00 2562.0
3 TraesCS4D01G133600 chr4A 86.810 743 57 17 1 709 451598236 451597501 0.000000e+00 791.0
4 TraesCS4D01G133600 chr4A 93.013 229 10 3 2405 2633 451593583 451593361 2.190000e-86 329.0
5 TraesCS4D01G133600 chr4A 90.323 62 6 0 357 418 451597928 451597867 6.760000e-12 82.4
6 TraesCS4D01G133600 chr4A 95.745 47 2 0 2274 2320 451593713 451593667 3.150000e-10 76.8
7 TraesCS4D01G133600 chr4A 100.000 35 0 0 2274 2308 451593658 451593624 6.810000e-07 65.8
8 TraesCS4D01G133600 chr2D 89.340 863 90 2 1082 1943 327623101 327623962 0.000000e+00 1083.0
9 TraesCS4D01G133600 chr2D 93.069 202 13 1 2711 2911 640312130 640311929 7.980000e-76 294.0
10 TraesCS4D01G133600 chr2B 89.224 863 91 2 1082 1943 396956911 396957772 0.000000e+00 1077.0
11 TraesCS4D01G133600 chr2B 90.338 207 17 3 2706 2911 283190466 283190262 4.840000e-68 268.0
12 TraesCS4D01G133600 chr2B 89.831 59 1 4 2886 2942 715721714 715721769 1.460000e-08 71.3
13 TraesCS4D01G133600 chr2A 88.876 863 94 2 1082 1943 432591809 432592670 0.000000e+00 1061.0
14 TraesCS4D01G133600 chr7D 94.203 207 11 1 2706 2911 43692409 43692615 6.130000e-82 315.0
15 TraesCS4D01G133600 chr7D 94.330 194 11 0 2706 2899 43692832 43693025 6.170000e-77 298.0
16 TraesCS4D01G133600 chr7D 85.294 68 7 3 2880 2945 10560583 10560649 1.890000e-07 67.6
17 TraesCS4D01G133600 chr6A 93.810 210 12 1 2702 2911 405696389 405696181 6.130000e-82 315.0
18 TraesCS4D01G133600 chrUn 93.365 211 12 2 2701 2911 89955733 89955525 7.930000e-81 311.0
19 TraesCS4D01G133600 chr5A 93.204 206 12 1 2706 2911 346536510 346536307 4.770000e-78 302.0
20 TraesCS4D01G133600 chr5D 90.865 208 18 1 2704 2911 434358719 434358925 8.040000e-71 278.0
21 TraesCS4D01G133600 chr5D 93.878 49 3 0 2894 2942 475004838 475004886 1.130000e-09 75.0
22 TraesCS4D01G133600 chr5D 90.909 55 3 2 2890 2942 235640359 235640413 4.070000e-09 73.1
23 TraesCS4D01G133600 chr6D 90.431 209 16 4 2705 2911 125241960 125242166 3.740000e-69 272.0
24 TraesCS4D01G133600 chr1A 97.826 46 1 0 2898 2943 550138450 550138405 2.430000e-11 80.5
25 TraesCS4D01G133600 chr7B 100.000 42 0 0 2904 2945 440013440 440013399 8.750000e-11 78.7
26 TraesCS4D01G133600 chr1D 100.000 41 0 0 2905 2945 464031286 464031246 3.150000e-10 76.8
27 TraesCS4D01G133600 chr5B 94.000 50 2 1 2894 2943 231730657 231730609 1.130000e-09 75.0
28 TraesCS4D01G133600 chr5B 87.500 64 7 1 357 419 685622381 685622444 4.070000e-09 73.1
29 TraesCS4D01G133600 chr7A 95.556 45 2 0 2901 2945 716275396 716275352 4.070000e-09 73.1


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 TraesCS4D01G133600 chr4D 120070370 120073314 2944 True 5439.000000 5439 100.0000 1 2945 1 chr4D.!!$R1 2944
1 TraesCS4D01G133600 chr4B 183001301 183003275 1974 True 2935.000000 2935 93.8040 765 2705 1 chr4B.!!$R1 1940
2 TraesCS4D01G133600 chr4A 451593361 451598236 4875 True 651.166667 2562 93.8045 1 2633 6 chr4A.!!$R1 2632
3 TraesCS4D01G133600 chr2D 327623101 327623962 861 False 1083.000000 1083 89.3400 1082 1943 1 chr2D.!!$F1 861
4 TraesCS4D01G133600 chr2B 396956911 396957772 861 False 1077.000000 1077 89.2240 1082 1943 1 chr2B.!!$F1 861
5 TraesCS4D01G133600 chr2A 432591809 432592670 861 False 1061.000000 1061 88.8760 1082 1943 1 chr2A.!!$F1 861
6 TraesCS4D01G133600 chr7D 43692409 43693025 616 False 306.500000 315 94.2665 2706 2911 2 chr7D.!!$F2 205

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
213 214 0.099968 TGAGATACCCGTTTCGAGCG 59.900 55.000 4.76 4.76 0.0 5.03 F
214 215 0.100146 GAGATACCCGTTTCGAGCGT 59.900 55.000 9.89 0.00 0.0 5.07 F
223 224 1.267632 CGTTTCGAGCGTAGAGAGAGG 60.268 57.143 3.73 0.00 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 3652 1.518572 CATCACCAGGTCGTACGGC 60.519 63.158 16.52 14.54 0.00 5.68 R
1890 3907 1.550130 GGTCGGACAGGTTGATCCCA 61.550 60.000 10.76 0.00 36.75 4.37 R
2025 4043 2.811431 CGATGCACCTAGAGTAGAGGAG 59.189 54.545 0.00 0.00 37.53 3.69 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
88 89 2.549611 CTTGTCGAGAGGGAGTGGCG 62.550 65.000 0.00 0.00 0.00 5.69
109 110 0.105194 TCACCTTGGAGTGGGTCTCA 60.105 55.000 0.00 0.00 44.40 3.27
114 115 2.840651 CCTTGGAGTGGGTCTCATTACT 59.159 50.000 0.00 0.00 44.40 2.24
115 116 3.369892 CCTTGGAGTGGGTCTCATTACTG 60.370 52.174 0.00 0.00 44.40 2.74
136 137 9.778741 TTACTGTTCATTCTTGAAACTGATAGT 57.221 29.630 0.00 0.00 43.29 2.12
138 139 8.778358 ACTGTTCATTCTTGAAACTGATAGTTC 58.222 33.333 0.00 0.00 43.29 3.01
144 145 7.426929 TTCTTGAAACTGATAGTTCTGAAGC 57.573 36.000 0.00 0.00 37.47 3.86
192 193 2.071540 CTCGTGATGCATGTCTTGTGT 58.928 47.619 2.46 0.00 0.00 3.72
203 204 4.752101 GCATGTCTTGTGTATGAGATACCC 59.248 45.833 0.00 0.00 34.86 3.69
207 208 5.046878 TGTCTTGTGTATGAGATACCCGTTT 60.047 40.000 0.00 0.00 34.86 3.60
213 214 0.099968 TGAGATACCCGTTTCGAGCG 59.900 55.000 4.76 4.76 0.00 5.03
214 215 0.100146 GAGATACCCGTTTCGAGCGT 59.900 55.000 9.89 0.00 0.00 5.07
223 224 1.267632 CGTTTCGAGCGTAGAGAGAGG 60.268 57.143 3.73 0.00 0.00 3.69
224 225 1.738908 GTTTCGAGCGTAGAGAGAGGT 59.261 52.381 0.00 0.00 0.00 3.85
225 226 1.370609 TTCGAGCGTAGAGAGAGGTG 58.629 55.000 0.00 0.00 0.00 4.00
239 250 2.691011 GAGAGGTGGAGGTGAGACATAC 59.309 54.545 0.00 0.00 0.00 2.39
244 255 3.627747 GGTGGAGGTGAGACATACTAGGT 60.628 52.174 0.00 0.00 0.00 3.08
275 286 8.159344 AGAAATAATGTTAGCCATGAGTTAGC 57.841 34.615 0.00 0.00 32.82 3.09
278 289 3.931907 TGTTAGCCATGAGTTAGCCAT 57.068 42.857 0.00 0.00 0.00 4.40
304 315 3.818773 AGGGCGAATGGATATTAAAACCG 59.181 43.478 0.00 0.00 0.00 4.44
379 390 2.591715 GCAGTGTGGTTGCGGTCT 60.592 61.111 0.00 0.00 0.00 3.85
380 391 2.896801 GCAGTGTGGTTGCGGTCTG 61.897 63.158 0.00 0.00 0.00 3.51
460 491 8.216453 CCTGCAAAAATAAATAAATATGCTCGC 58.784 33.333 0.00 0.00 33.87 5.03
542 574 5.890985 TGAGGGAAACAACTTGAGAATTCAA 59.109 36.000 8.44 0.00 40.92 2.69
544 576 7.069826 TGAGGGAAACAACTTGAGAATTCAAAT 59.930 33.333 8.44 0.00 42.48 2.32
585 618 9.719355 AATTTTTAGGCAACCGAGATTTTATTT 57.281 25.926 0.00 0.00 37.17 1.40
612 645 2.605837 TTGAACACAGTAAGGACGCA 57.394 45.000 0.00 0.00 0.00 5.24
631 664 4.446234 CGCAAGTGCTTATATAAACGAGC 58.554 43.478 1.21 0.00 39.32 5.03
638 671 7.214381 AGTGCTTATATAAACGAGCCAACATA 58.786 34.615 0.00 0.00 34.30 2.29
640 673 8.169268 GTGCTTATATAAACGAGCCAACATATC 58.831 37.037 0.00 0.00 34.30 1.63
675 709 8.250332 ACATTACAAAATCATCGTAAAGCCATT 58.750 29.630 0.00 0.00 0.00 3.16
679 713 4.536364 AATCATCGTAAAGCCATTCACG 57.464 40.909 0.00 0.00 35.78 4.35
688 722 6.757478 TCGTAAAGCCATTCACGATAAATACA 59.243 34.615 0.00 0.00 38.40 2.29
697 731 7.041848 CCATTCACGATAAATACAAGCATCAGA 60.042 37.037 0.00 0.00 0.00 3.27
700 734 8.076714 TCACGATAAATACAAGCATCAGAATC 57.923 34.615 0.00 0.00 0.00 2.52
701 735 7.710475 TCACGATAAATACAAGCATCAGAATCA 59.290 33.333 0.00 0.00 0.00 2.57
709 743 4.590222 ACAAGCATCAGAATCAAAAACCCT 59.410 37.500 0.00 0.00 0.00 4.34
710 744 5.774690 ACAAGCATCAGAATCAAAAACCCTA 59.225 36.000 0.00 0.00 0.00 3.53
711 745 6.267471 ACAAGCATCAGAATCAAAAACCCTAA 59.733 34.615 0.00 0.00 0.00 2.69
712 746 7.038799 ACAAGCATCAGAATCAAAAACCCTAAT 60.039 33.333 0.00 0.00 0.00 1.73
713 747 6.870769 AGCATCAGAATCAAAAACCCTAATG 58.129 36.000 0.00 0.00 0.00 1.90
714 748 6.044682 GCATCAGAATCAAAAACCCTAATGG 58.955 40.000 0.00 0.00 41.37 3.16
729 763 4.583871 CCTAATGGGCTGAGAATATCACC 58.416 47.826 0.00 0.00 33.22 4.02
731 765 1.496060 TGGGCTGAGAATATCACCGT 58.504 50.000 0.00 0.00 33.22 4.83
738 1949 4.615949 CTGAGAATATCACCGTCCTTCTG 58.384 47.826 0.00 0.00 33.22 3.02
739 1950 4.278310 TGAGAATATCACCGTCCTTCTGA 58.722 43.478 0.00 0.00 31.12 3.27
746 1957 4.386867 TCACCGTCCTTCTGATCATAAC 57.613 45.455 0.00 0.00 0.00 1.89
747 1958 3.767131 TCACCGTCCTTCTGATCATAACA 59.233 43.478 0.00 0.00 0.00 2.41
748 1959 4.115516 CACCGTCCTTCTGATCATAACAG 58.884 47.826 0.00 0.00 36.80 3.16
751 1962 3.553511 CGTCCTTCTGATCATAACAGCAC 59.446 47.826 0.00 0.00 35.61 4.40
752 1963 4.507710 GTCCTTCTGATCATAACAGCACA 58.492 43.478 0.00 0.00 35.61 4.57
753 1964 4.569966 GTCCTTCTGATCATAACAGCACAG 59.430 45.833 0.00 0.00 35.61 3.66
785 2794 3.627395 TTAGGCAACCGAGATGATTGT 57.373 42.857 0.00 0.00 37.17 2.71
787 2796 2.086869 AGGCAACCGAGATGATTGTTG 58.913 47.619 0.00 0.00 37.17 3.33
793 2802 4.771114 ACCGAGATGATTGTTGGGATAA 57.229 40.909 0.00 0.00 0.00 1.75
794 2803 5.110814 ACCGAGATGATTGTTGGGATAAA 57.889 39.130 0.00 0.00 0.00 1.40
795 2804 5.505780 ACCGAGATGATTGTTGGGATAAAA 58.494 37.500 0.00 0.00 0.00 1.52
796 2805 6.129179 ACCGAGATGATTGTTGGGATAAAAT 58.871 36.000 0.00 0.00 0.00 1.82
797 2806 6.039717 ACCGAGATGATTGTTGGGATAAAATG 59.960 38.462 0.00 0.00 0.00 2.32
1032 3049 3.315949 GTGGTGGCCCTGTACGGA 61.316 66.667 2.31 0.00 33.16 4.69
1620 3637 1.583967 CGAGGTCTTCAGCTACGCG 60.584 63.158 3.53 3.53 0.00 6.01
1788 3805 2.176273 CGGCATCTTCAAGAGCGGG 61.176 63.158 0.00 0.00 0.00 6.13
1890 3907 3.411517 CTCGGGGAGGCCATGGTT 61.412 66.667 14.67 1.53 0.00 3.67
2025 4043 2.049077 TGCATCATGTGTCGTTTTGC 57.951 45.000 0.00 0.00 0.00 3.68
2046 4064 2.811431 CTCCTCTACTCTAGGTGCATCG 59.189 54.545 0.00 0.00 35.48 3.84
2088 4109 1.040339 TTGGGTGTTGGTTGCCAGTC 61.040 55.000 0.00 0.00 33.81 3.51
2097 4118 0.460987 GGTTGCCAGTCGAGATCAGG 60.461 60.000 0.00 0.00 0.00 3.86
2129 4150 1.592081 GCTCTTCAAGTGCTATGCTCG 59.408 52.381 4.13 0.00 32.42 5.03
2130 4151 2.736719 GCTCTTCAAGTGCTATGCTCGA 60.737 50.000 4.13 0.00 32.42 4.04
2219 4241 1.798223 CGAAAATGACTGGTCTTGCGA 59.202 47.619 2.38 0.00 0.00 5.10
2231 4253 2.617021 GGTCTTGCGATGGTTTCCCTAA 60.617 50.000 0.00 0.00 0.00 2.69
2255 4277 2.091610 TGACCAGACAACAAAATCCCCA 60.092 45.455 0.00 0.00 0.00 4.96
2260 4282 4.563374 CCAGACAACAAAATCCCCATTTCC 60.563 45.833 0.00 0.00 30.37 3.13
2261 4283 4.284234 CAGACAACAAAATCCCCATTTCCT 59.716 41.667 0.00 0.00 30.37 3.36
2334 4644 4.475944 CAAGTAATTTTGCACGGAGGAAG 58.524 43.478 0.00 0.00 0.00 3.46
2377 4714 5.035443 CAGATTCCTACACGCTACTTGTAC 58.965 45.833 0.00 0.00 0.00 2.90
2378 4715 4.948621 AGATTCCTACACGCTACTTGTACT 59.051 41.667 0.00 0.00 0.00 2.73
2379 4716 4.430137 TTCCTACACGCTACTTGTACTG 57.570 45.455 0.00 0.00 0.00 2.74
2380 4717 3.415212 TCCTACACGCTACTTGTACTGT 58.585 45.455 0.00 0.00 0.00 3.55
2402 4742 2.034812 AGCAATGCTCGGTAGTACTAGC 59.965 50.000 19.94 19.94 30.62 3.42
2407 4747 3.087031 TGCTCGGTAGTACTAGCAAACT 58.913 45.455 26.90 0.00 41.74 2.66
2412 4752 4.574013 TCGGTAGTACTAGCAAACTCTAGC 59.426 45.833 26.90 3.87 39.64 3.42
2503 4843 2.046892 ATCACTCGTGGTGCAGGC 60.047 61.111 0.00 0.00 44.98 4.85
2504 4844 3.612247 ATCACTCGTGGTGCAGGCC 62.612 63.158 0.00 0.00 44.98 5.19
2664 5011 6.878389 TGATGATTAGCATATTGCCGTTGATA 59.122 34.615 0.00 0.00 46.52 2.15
2685 5032 2.118679 TGGCTGTGTGCATATAGAGGT 58.881 47.619 11.41 0.00 45.15 3.85
2689 5036 1.068588 TGTGTGCATATAGAGGTCGGC 59.931 52.381 0.00 0.00 0.00 5.54
2697 5044 3.843166 TATAGAGGTCGGCTGTGGGGG 62.843 61.905 0.00 0.00 0.00 5.40
2730 5077 5.367060 GGGGAGACTTGTATAGGATCTGTTT 59.633 44.000 0.00 0.00 0.00 2.83
2738 5085 8.822805 ACTTGTATAGGATCTGTTTTTAGGTGA 58.177 33.333 0.00 0.00 0.00 4.02
2836 5183 5.342806 TGTTTGATGTACGAGCTCAAAAG 57.657 39.130 15.40 0.00 39.74 2.27
2874 5221 8.761497 CAAATCGAACTACACTTAGAGAAACAA 58.239 33.333 0.00 0.00 0.00 2.83
2906 5253 8.509690 ACAAAATCAGATGTGAATAGTGTCAAG 58.490 33.333 0.00 0.00 35.88 3.02
2911 5258 7.539436 TCAGATGTGAATAGTGTCAAGTACTC 58.461 38.462 0.00 0.00 0.00 2.59
2912 5259 6.754209 CAGATGTGAATAGTGTCAAGTACTCC 59.246 42.308 0.00 0.00 0.00 3.85
2913 5260 5.401531 TGTGAATAGTGTCAAGTACTCCC 57.598 43.478 0.00 0.00 0.00 4.30
2915 5262 5.185249 TGTGAATAGTGTCAAGTACTCCCTC 59.815 44.000 0.00 0.00 0.00 4.30
2916 5263 4.710375 TGAATAGTGTCAAGTACTCCCTCC 59.290 45.833 0.00 0.00 0.00 4.30
2917 5264 1.546961 AGTGTCAAGTACTCCCTCCG 58.453 55.000 0.00 0.00 0.00 4.63
2918 5265 1.203025 AGTGTCAAGTACTCCCTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
2919 5266 2.040813 AGTGTCAAGTACTCCCTCCGTA 59.959 50.000 0.00 0.00 0.00 4.02
2922 5269 3.256631 TGTCAAGTACTCCCTCCGTAAAC 59.743 47.826 0.00 0.00 0.00 2.01
2923 5270 3.509184 GTCAAGTACTCCCTCCGTAAACT 59.491 47.826 0.00 0.00 0.00 2.66
2924 5271 4.702131 GTCAAGTACTCCCTCCGTAAACTA 59.298 45.833 0.00 0.00 0.00 2.24
2925 5272 5.183904 GTCAAGTACTCCCTCCGTAAACTAA 59.816 44.000 0.00 0.00 0.00 2.24
2926 5273 5.954150 TCAAGTACTCCCTCCGTAAACTAAT 59.046 40.000 0.00 0.00 0.00 1.73
2930 5277 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
2931 5278 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2933 5280 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2934 5281 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2935 5282 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2936 5283 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2938 5285 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2940 5287 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2941 5288 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.948623 CGGACCACAGCAATGTTCGA 60.949 55.000 0.00 0.00 0.00 3.71
17 18 1.497278 CGGACCACAGCAATGTTCG 59.503 57.895 0.00 0.00 0.00 3.95
18 19 0.605319 TCCGGACCACAGCAATGTTC 60.605 55.000 0.00 0.00 0.00 3.18
19 20 0.179004 TTCCGGACCACAGCAATGTT 60.179 50.000 1.83 0.00 0.00 2.71
88 89 1.003233 GACCCACTCCAAGGTGAGC 60.003 63.158 0.00 0.00 39.34 4.26
114 115 8.777413 CAGAACTATCAGTTTCAAGAATGAACA 58.223 33.333 0.00 0.00 45.01 3.18
115 116 8.993121 TCAGAACTATCAGTTTCAAGAATGAAC 58.007 33.333 0.00 0.00 45.01 3.18
136 137 6.071108 ACTCATCTAGTTAAGCTGCTTCAGAA 60.071 38.462 19.62 5.00 33.35 3.02
138 139 5.659463 ACTCATCTAGTTAAGCTGCTTCAG 58.341 41.667 19.62 11.73 33.35 3.02
144 145 9.853555 CCTATCAATACTCATCTAGTTAAGCTG 57.146 37.037 0.00 0.00 39.80 4.24
192 193 2.031420 CGCTCGAAACGGGTATCTCATA 60.031 50.000 0.00 0.00 0.00 2.15
203 204 1.267632 CCTCTCTCTACGCTCGAAACG 60.268 57.143 6.00 6.00 0.00 3.60
207 208 0.462225 CCACCTCTCTCTACGCTCGA 60.462 60.000 0.00 0.00 0.00 4.04
213 214 2.240160 TCTCACCTCCACCTCTCTCTAC 59.760 54.545 0.00 0.00 0.00 2.59
214 215 2.240160 GTCTCACCTCCACCTCTCTCTA 59.760 54.545 0.00 0.00 0.00 2.43
223 224 3.381908 CACCTAGTATGTCTCACCTCCAC 59.618 52.174 0.00 0.00 0.00 4.02
224 225 3.632333 CACCTAGTATGTCTCACCTCCA 58.368 50.000 0.00 0.00 0.00 3.86
225 226 2.362717 GCACCTAGTATGTCTCACCTCC 59.637 54.545 0.00 0.00 0.00 4.30
239 250 7.171678 GGCTAACATTATTTCTAGTGCACCTAG 59.828 40.741 14.63 14.14 43.97 3.02
244 255 7.053498 TCATGGCTAACATTATTTCTAGTGCA 58.947 34.615 0.00 0.00 37.84 4.57
275 286 2.795231 ATCCATTCGCCCTATCATGG 57.205 50.000 0.00 0.00 38.04 3.66
278 289 6.657541 GGTTTTAATATCCATTCGCCCTATCA 59.342 38.462 0.00 0.00 0.00 2.15
323 334 3.763057 AGTTTTACAACCCCATCCTGAC 58.237 45.455 0.00 0.00 32.70 3.51
354 365 0.738389 CAACCACACTGCGGTTTTCT 59.262 50.000 0.00 0.00 44.46 2.52
378 389 1.268992 TACAACCCCATCCGGACCAG 61.269 60.000 6.12 0.00 0.00 4.00
379 390 0.841158 TTACAACCCCATCCGGACCA 60.841 55.000 6.12 0.00 0.00 4.02
380 391 0.328926 TTTACAACCCCATCCGGACC 59.671 55.000 6.12 0.00 0.00 4.46
385 396 5.258051 TCACATAGTTTTACAACCCCATCC 58.742 41.667 0.00 0.00 32.70 3.51
416 427 9.674068 TTTTGCAGGTAAAAGAAGGTTTTAATT 57.326 25.926 0.00 0.00 0.00 1.40
417 428 9.674068 TTTTTGCAGGTAAAAGAAGGTTTTAAT 57.326 25.926 0.00 0.00 31.80 1.40
418 429 9.674068 ATTTTTGCAGGTAAAAGAAGGTTTTAA 57.326 25.926 1.68 0.00 31.80 1.52
420 431 9.674068 TTATTTTTGCAGGTAAAAGAAGGTTTT 57.326 25.926 1.68 0.00 31.80 2.43
421 432 9.674068 TTTATTTTTGCAGGTAAAAGAAGGTTT 57.326 25.926 3.27 0.00 30.32 3.27
508 539 5.023452 AGTTGTTTCCCTCAAAGAAAAGGT 58.977 37.500 0.00 0.00 35.13 3.50
510 541 6.630071 TCAAGTTGTTTCCCTCAAAGAAAAG 58.370 36.000 2.11 0.00 35.13 2.27
585 618 8.231837 GCGTCCTTACTGTGTTCAAAATAAATA 58.768 33.333 0.00 0.00 0.00 1.40
586 619 7.081976 GCGTCCTTACTGTGTTCAAAATAAAT 58.918 34.615 0.00 0.00 0.00 1.40
591 624 3.271729 TGCGTCCTTACTGTGTTCAAAA 58.728 40.909 0.00 0.00 0.00 2.44
610 643 4.272504 TGGCTCGTTTATATAAGCACTTGC 59.727 41.667 9.62 7.05 42.49 4.01
612 645 5.878116 TGTTGGCTCGTTTATATAAGCACTT 59.122 36.000 9.62 0.00 36.47 3.16
615 648 7.875554 TGATATGTTGGCTCGTTTATATAAGCA 59.124 33.333 9.62 0.00 36.47 3.91
646 679 8.921670 GGCTTTACGATGATTTTGTAATGTTTT 58.078 29.630 0.00 0.00 34.76 2.43
656 689 5.123186 TCGTGAATGGCTTTACGATGATTTT 59.877 36.000 10.79 0.00 45.09 1.82
665 698 7.376072 GCTTGTATTTATCGTGAATGGCTTTAC 59.624 37.037 0.00 0.00 0.00 2.01
670 703 5.168526 TGCTTGTATTTATCGTGAATGGC 57.831 39.130 0.00 0.00 0.00 4.40
675 709 7.710475 TGATTCTGATGCTTGTATTTATCGTGA 59.290 33.333 0.00 0.00 0.00 4.35
688 722 6.916360 TTAGGGTTTTTGATTCTGATGCTT 57.084 33.333 0.00 0.00 0.00 3.91
715 749 3.068873 AGAAGGACGGTGATATTCTCAGC 59.931 47.826 0.00 0.00 46.66 4.26
717 751 4.278310 TCAGAAGGACGGTGATATTCTCA 58.722 43.478 0.00 0.00 0.00 3.27
718 752 4.920640 TCAGAAGGACGGTGATATTCTC 57.079 45.455 0.00 0.00 0.00 2.87
719 753 4.895889 TGATCAGAAGGACGGTGATATTCT 59.104 41.667 0.00 0.00 30.93 2.40
720 754 5.201713 TGATCAGAAGGACGGTGATATTC 57.798 43.478 0.00 0.00 30.93 1.75
721 755 5.815233 ATGATCAGAAGGACGGTGATATT 57.185 39.130 0.09 0.00 30.93 1.28
722 756 6.267699 TGTTATGATCAGAAGGACGGTGATAT 59.732 38.462 2.29 0.00 30.93 1.63
723 757 5.596772 TGTTATGATCAGAAGGACGGTGATA 59.403 40.000 2.29 0.00 30.93 2.15
724 758 4.405680 TGTTATGATCAGAAGGACGGTGAT 59.594 41.667 2.29 0.00 33.53 3.06
726 760 4.115516 CTGTTATGATCAGAAGGACGGTG 58.884 47.826 2.29 0.00 35.20 4.94
727 761 3.430929 GCTGTTATGATCAGAAGGACGGT 60.431 47.826 2.29 0.00 35.20 4.83
729 763 3.553511 GTGCTGTTATGATCAGAAGGACG 59.446 47.826 2.29 0.00 35.20 4.79
731 765 4.383444 CCTGTGCTGTTATGATCAGAAGGA 60.383 45.833 2.29 0.00 34.49 3.36
738 1949 3.347216 ACCAACCTGTGCTGTTATGATC 58.653 45.455 0.00 0.00 0.00 2.92
739 1950 3.439857 ACCAACCTGTGCTGTTATGAT 57.560 42.857 0.00 0.00 0.00 2.45
746 1957 1.447317 AAGCGAACCAACCTGTGCTG 61.447 55.000 0.00 0.00 32.14 4.41
747 1958 0.751643 AAAGCGAACCAACCTGTGCT 60.752 50.000 0.00 0.00 0.00 4.40
748 1959 0.948678 TAAAGCGAACCAACCTGTGC 59.051 50.000 0.00 0.00 0.00 4.57
751 1962 0.521735 GCCTAAAGCGAACCAACCTG 59.478 55.000 0.00 0.00 0.00 4.00
752 1963 2.942641 GCCTAAAGCGAACCAACCT 58.057 52.632 0.00 0.00 0.00 3.50
785 2794 9.228949 CAACAATCCAATTTCATTTTATCCCAA 57.771 29.630 0.00 0.00 0.00 4.12
787 2796 8.046107 TCCAACAATCCAATTTCATTTTATCCC 58.954 33.333 0.00 0.00 0.00 3.85
793 2802 5.237048 CGGTCCAACAATCCAATTTCATTT 58.763 37.500 0.00 0.00 0.00 2.32
794 2803 4.322650 CCGGTCCAACAATCCAATTTCATT 60.323 41.667 0.00 0.00 0.00 2.57
795 2804 3.195396 CCGGTCCAACAATCCAATTTCAT 59.805 43.478 0.00 0.00 0.00 2.57
796 2805 2.560542 CCGGTCCAACAATCCAATTTCA 59.439 45.455 0.00 0.00 0.00 2.69
797 2806 2.823154 TCCGGTCCAACAATCCAATTTC 59.177 45.455 0.00 0.00 0.00 2.17
1032 3049 1.671901 CCACCACCGCCTTGTTGTTT 61.672 55.000 0.00 0.00 0.00 2.83
1635 3652 1.518572 CATCACCAGGTCGTACGGC 60.519 63.158 16.52 14.54 0.00 5.68
1890 3907 1.550130 GGTCGGACAGGTTGATCCCA 61.550 60.000 10.76 0.00 36.75 4.37
2025 4043 2.811431 CGATGCACCTAGAGTAGAGGAG 59.189 54.545 0.00 0.00 37.53 3.69
2046 4064 7.815068 CCAAGATAGTACTGCTGGATAATACAC 59.185 40.741 5.39 0.00 0.00 2.90
2088 4109 3.201290 CAAAATCCCTCACCTGATCTCG 58.799 50.000 0.00 0.00 0.00 4.04
2097 4118 3.823304 ACTTGAAGAGCAAAATCCCTCAC 59.177 43.478 0.00 0.00 35.74 3.51
2231 4253 3.222603 GGATTTTGTTGTCTGGTCAGGT 58.777 45.455 0.00 0.00 0.00 4.00
2255 4277 8.554490 AGTACATAGGTGTAAGATGAGGAAAT 57.446 34.615 0.00 0.00 42.18 2.17
2260 4282 7.670140 TGGGATAGTACATAGGTGTAAGATGAG 59.330 40.741 0.00 0.00 42.18 2.90
2261 4283 7.450634 GTGGGATAGTACATAGGTGTAAGATGA 59.549 40.741 0.00 0.00 42.18 2.92
2334 4644 8.494016 AATCTGGTTAAGCTGTAATCAAGTAC 57.506 34.615 6.19 0.00 0.00 2.73
2377 4714 2.586258 ACTACCGAGCATTGCTACAG 57.414 50.000 11.96 8.66 39.88 2.74
2378 4715 3.021695 AGTACTACCGAGCATTGCTACA 58.978 45.455 11.96 0.00 39.88 2.74
2379 4716 3.712091 AGTACTACCGAGCATTGCTAC 57.288 47.619 11.96 4.23 39.88 3.58
2380 4717 3.252701 GCTAGTACTACCGAGCATTGCTA 59.747 47.826 11.96 0.00 39.88 3.49
2384 4724 4.159879 AGTTTGCTAGTACTACCGAGCATT 59.840 41.667 16.71 5.62 44.02 3.56
2385 4725 3.700038 AGTTTGCTAGTACTACCGAGCAT 59.300 43.478 16.71 2.27 44.02 3.79
2460 4800 4.760047 CTGACGGGACCGCCTTGG 62.760 72.222 11.21 0.00 44.19 3.61
2503 4843 0.396278 GGCCATTGAAAGAGAGGGGG 60.396 60.000 0.00 0.00 0.00 5.40
2504 4844 0.396278 GGGCCATTGAAAGAGAGGGG 60.396 60.000 4.39 0.00 0.00 4.79
2664 5011 2.707791 ACCTCTATATGCACACAGCCAT 59.292 45.455 0.00 0.00 44.83 4.40
2697 5044 1.703513 ACAAGTCTCCCCCAGTTTACC 59.296 52.381 0.00 0.00 0.00 2.85
2705 5052 3.835395 CAGATCCTATACAAGTCTCCCCC 59.165 52.174 0.00 0.00 0.00 5.40
2706 5053 4.484912 ACAGATCCTATACAAGTCTCCCC 58.515 47.826 0.00 0.00 0.00 4.81
2707 5054 6.487299 AAACAGATCCTATACAAGTCTCCC 57.513 41.667 0.00 0.00 0.00 4.30
2708 5055 9.535878 CTAAAAACAGATCCTATACAAGTCTCC 57.464 37.037 0.00 0.00 0.00 3.71
2709 5056 9.535878 CCTAAAAACAGATCCTATACAAGTCTC 57.464 37.037 0.00 0.00 0.00 3.36
2790 5137 9.643693 ACATGGATGTATGTCTTCAAATTTTTC 57.356 29.630 0.00 0.00 39.68 2.29
2796 5143 7.757941 TCAAACATGGATGTATGTCTTCAAA 57.242 32.000 0.00 0.00 40.24 2.69
2798 5145 7.324354 CATCAAACATGGATGTATGTCTTCA 57.676 36.000 0.00 0.00 40.24 3.02
2826 5173 2.227626 GGAGCTGAAACCTTTTGAGCTC 59.772 50.000 23.79 23.79 44.27 4.09
2836 5183 1.821216 TCGATTTGGGAGCTGAAACC 58.179 50.000 0.00 0.00 0.00 3.27
2881 5228 8.509690 ACTTGACACTATTCACATCTGATTTTG 58.490 33.333 0.00 0.00 0.00 2.44
2906 5253 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2911 5258 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2912 5259 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2913 5260 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2915 5262 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02


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

AutoCloner maintained by Alex Coulton.