Multiple sequence alignment - TraesCS6A01G249200

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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 TraesCS6A01G249200 chr6A 100.000 2719 0 0 451 3169 461988261 461985543 0.000000e+00 5022.0
1 TraesCS6A01G249200 chr6A 76.375 1236 199 53 994 2178 462225848 462227041 2.120000e-161 579.0
2 TraesCS6A01G249200 chr6A 100.000 267 0 0 1 267 461988711 461988445 7.900000e-136 494.0
3 TraesCS6A01G249200 chr6D 93.515 2745 125 22 451 3169 324599972 324597255 0.000000e+00 4034.0
4 TraesCS6A01G249200 chr6D 87.798 336 35 3 1836 2171 324783996 324784325 3.830000e-104 388.0
5 TraesCS6A01G249200 chr6D 88.627 255 27 2 1 254 324600268 324600015 3.070000e-80 309.0
6 TraesCS6A01G249200 chr6D 74.343 799 132 42 981 1737 324783127 324783894 4.030000e-69 272.0
7 TraesCS6A01G249200 chr6B 95.336 1308 56 4 1499 2804 498852226 498853530 0.000000e+00 2073.0
8 TraesCS6A01G249200 chr6B 94.955 674 25 6 782 1450 498851469 498852138 0.000000e+00 1048.0
9 TraesCS6A01G249200 chr6B 76.375 1236 200 55 994 2178 498544056 498542862 5.890000e-162 580.0
10 TraesCS6A01G249200 chr6B 88.629 299 20 8 2877 3169 498854124 498854414 5.030000e-93 351.0
11 TraesCS6A01G249200 chr6B 88.889 252 19 6 471 713 498851088 498851339 5.140000e-78 302.0
12 TraesCS6A01G249200 chr6B 86.296 270 33 3 1 267 498850480 498850748 1.110000e-74 291.0
13 TraesCS6A01G249200 chr3D 79.848 660 104 22 1527 2175 580522320 580522961 3.730000e-124 455.0
14 TraesCS6A01G249200 chr3D 75.703 498 74 30 981 1449 580521754 580522233 4.140000e-49 206.0
15 TraesCS6A01G249200 chr3D 80.916 262 44 6 3 260 610803288 610803547 5.360000e-48 202.0
16 TraesCS6A01G249200 chr3A 79.066 664 108 24 1527 2178 715974327 715974971 8.120000e-116 427.0
17 TraesCS6A01G249200 chr3A 75.299 502 74 32 981 1450 715973758 715974241 8.970000e-46 195.0
18 TraesCS6A01G249200 chr1A 80.989 263 45 5 1 260 558836203 558836463 1.490000e-48 204.0
19 TraesCS6A01G249200 chr4A 80.608 263 46 5 1 260 733564848 733565108 6.930000e-47 198.0
20 TraesCS6A01G249200 chr3B 75.296 506 71 33 981 1450 775735525 775736012 3.230000e-45 193.0
21 TraesCS6A01G249200 chr3B 83.491 212 30 4 1527 1737 775736098 775736305 3.230000e-45 193.0
22 TraesCS6A01G249200 chr2A 79.926 269 48 6 3 267 702078842 702079108 3.230000e-45 193.0
23 TraesCS6A01G249200 chr2A 91.489 47 2 2 612 656 724506685 724506731 2.640000e-06 63.9
24 TraesCS6A01G249200 chr7A 80.738 244 43 4 20 260 706098131 706098373 1.500000e-43 187.0
25 TraesCS6A01G249200 chr2D 79.771 262 49 4 1 260 17602313 17602572 1.500000e-43 187.0
26 TraesCS6A01G249200 chr2D 79.771 262 49 4 1 260 17625524 17625783 1.500000e-43 187.0
27 TraesCS6A01G249200 chr5A 87.059 85 11 0 571 655 41902130 41902046 2.600000e-16 97.1
28 TraesCS6A01G249200 chr5B 86.047 86 12 0 571 656 579143977 579143892 3.370000e-15 93.5
29 TraesCS6A01G249200 chr5D 90.741 54 5 0 602 655 489297325 489297272 4.380000e-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 TraesCS6A01G249200 chr6A 461985543 461988711 3168 True 2758.0 5022 100.0000 1 3169 2 chr6A.!!$R1 3168
1 TraesCS6A01G249200 chr6A 462225848 462227041 1193 False 579.0 579 76.3750 994 2178 1 chr6A.!!$F1 1184
2 TraesCS6A01G249200 chr6D 324597255 324600268 3013 True 2171.5 4034 91.0710 1 3169 2 chr6D.!!$R1 3168
3 TraesCS6A01G249200 chr6D 324783127 324784325 1198 False 330.0 388 81.0705 981 2171 2 chr6D.!!$F1 1190
4 TraesCS6A01G249200 chr6B 498850480 498854414 3934 False 813.0 2073 90.8210 1 3169 5 chr6B.!!$F1 3168
5 TraesCS6A01G249200 chr6B 498542862 498544056 1194 True 580.0 580 76.3750 994 2178 1 chr6B.!!$R1 1184
6 TraesCS6A01G249200 chr3D 580521754 580522961 1207 False 330.5 455 77.7755 981 2175 2 chr3D.!!$F2 1194
7 TraesCS6A01G249200 chr3A 715973758 715974971 1213 False 311.0 427 77.1825 981 2178 2 chr3A.!!$F1 1197

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
107 108 0.396811 AACTGCGGCTGTCTAAACCT 59.603 50.0 13.03 0.0 0.0 3.50 F
591 893 1.361668 ATCAACGGCTCACATGCGTC 61.362 55.0 0.00 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1536 1.139095 CAGACGACGAAGGGGTAGC 59.861 63.158 0.00 0.0 0.00 3.58 R
2368 2897 0.179936 GACCATGGAGGGAAGAGCTG 59.820 60.000 21.47 0.0 43.89 4.24 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
30 31 5.495640 AGATCCTCTCGAAAATTTCAGCTT 58.504 37.500 6.53 0.00 0.00 3.74
32 33 6.760770 AGATCCTCTCGAAAATTTCAGCTTAG 59.239 38.462 6.53 0.00 0.00 2.18
53 54 3.587506 AGTTGGACACTATTTGCCTACCT 59.412 43.478 0.00 0.00 31.97 3.08
57 58 5.521696 TGGACACTATTTGCCTACCTAGTA 58.478 41.667 0.00 0.00 0.00 1.82
69 70 4.458397 CCTACCTAGTATGTTCGTCTCCA 58.542 47.826 0.00 0.00 0.00 3.86
94 95 6.567769 AAAATACTTTGTGTTGAAACTGCG 57.432 33.333 0.00 0.00 0.00 5.18
97 98 0.814457 TTTGTGTTGAAACTGCGGCT 59.186 45.000 0.00 0.00 0.00 5.52
107 108 0.396811 AACTGCGGCTGTCTAAACCT 59.603 50.000 13.03 0.00 0.00 3.50
140 142 3.603532 TCAAATCTGATGCTCCACTGAC 58.396 45.455 0.00 0.00 0.00 3.51
141 143 3.262660 TCAAATCTGATGCTCCACTGACT 59.737 43.478 0.00 0.00 0.00 3.41
146 148 3.262660 TCTGATGCTCCACTGACTCAATT 59.737 43.478 0.00 0.00 0.00 2.32
179 181 6.754209 CAGTTAAGCAGATCGAAGTACTCAAT 59.246 38.462 0.00 0.00 0.00 2.57
190 192 6.338146 TCGAAGTACTCAATGTAAGGAATGG 58.662 40.000 0.00 0.00 32.25 3.16
193 195 2.643551 ACTCAATGTAAGGAATGGGCG 58.356 47.619 0.00 0.00 0.00 6.13
227 231 4.679373 TGCCAATCCAAGCACTTTAAAA 57.321 36.364 0.00 0.00 33.08 1.52
485 774 6.144078 TGTATTCTTATTGTGCGCTCTCTA 57.856 37.500 9.73 0.00 0.00 2.43
493 782 2.095461 TGTGCGCTCTCTAAGTCTCAT 58.905 47.619 9.73 0.00 0.00 2.90
511 800 1.920734 ATAATGGCAGCCACCACCGA 61.921 55.000 19.10 0.00 44.17 4.69
591 893 1.361668 ATCAACGGCTCACATGCGTC 61.362 55.000 0.00 0.00 0.00 5.19
648 950 2.171448 CCTTCATGTGGAGGGACTTAGG 59.829 54.545 0.00 0.00 45.42 2.69
649 951 2.642171 TCATGTGGAGGGACTTAGGT 57.358 50.000 0.00 0.00 41.55 3.08
700 1003 7.663493 TCTCAATGGTATGTTGTGAAATGTACA 59.337 33.333 0.00 0.00 0.00 2.90
724 1027 5.520632 TCGCAATCCATTTTCGTTACAAAA 58.479 33.333 0.00 0.00 0.00 2.44
726 1029 5.401079 CGCAATCCATTTTCGTTACAAAAGT 59.599 36.000 0.00 0.00 0.00 2.66
727 1030 6.579292 CGCAATCCATTTTCGTTACAAAAGTA 59.421 34.615 0.00 0.00 0.00 2.24
728 1031 7.201232 CGCAATCCATTTTCGTTACAAAAGTAG 60.201 37.037 0.00 0.00 0.00 2.57
729 1032 7.806014 GCAATCCATTTTCGTTACAAAAGTAGA 59.194 33.333 0.00 0.00 0.00 2.59
730 1033 9.329913 CAATCCATTTTCGTTACAAAAGTAGAG 57.670 33.333 0.00 0.00 0.00 2.43
731 1034 8.617290 ATCCATTTTCGTTACAAAAGTAGAGT 57.383 30.769 0.00 0.00 0.00 3.24
732 1035 9.715121 ATCCATTTTCGTTACAAAAGTAGAGTA 57.285 29.630 0.00 0.00 0.00 2.59
733 1036 9.715121 TCCATTTTCGTTACAAAAGTAGAGTAT 57.285 29.630 0.00 0.00 0.00 2.12
738 1041 9.754382 TTTCGTTACAAAAGTAGAGTATTGTCT 57.246 29.630 0.00 0.00 37.25 3.41
866 1252 2.579860 AGCAGAATCCCCACATCTCTTT 59.420 45.455 0.00 0.00 0.00 2.52
891 1277 2.479049 CGTACGTCTACATCCCCACAAG 60.479 54.545 7.22 0.00 0.00 3.16
914 1300 4.321230 GGTACACTATAAATACCCGTCCCG 60.321 50.000 0.00 0.00 33.54 5.14
941 1327 1.529010 CCCTGCAACTCACCAAGCA 60.529 57.895 0.00 0.00 35.43 3.91
1047 1433 1.993370 CTACTTAGCGCACTGGTTGTC 59.007 52.381 11.47 0.00 0.00 3.18
1129 1536 1.648720 CACAAGAACCACACCGCTG 59.351 57.895 0.00 0.00 0.00 5.18
1137 1544 3.706373 CACACCGCTGCTACCCCT 61.706 66.667 0.00 0.00 0.00 4.79
1283 1706 1.801771 GTACATTAACTGCACCGCACA 59.198 47.619 0.00 0.00 33.79 4.57
1357 1785 4.129737 TACCAGAGCGCTGTCGGC 62.130 66.667 18.48 0.00 40.63 5.54
1443 1871 1.211969 GAGCGTGCTACGAGGTCAA 59.788 57.895 11.94 0.00 46.05 3.18
1460 1920 5.098663 AGGTCAAGATAACCCCTAAACAGA 58.901 41.667 0.00 0.00 37.52 3.41
1469 1929 1.625818 CCCCTAAACAGAGTGCTGACT 59.374 52.381 0.00 0.00 45.17 3.41
1470 1930 2.039084 CCCCTAAACAGAGTGCTGACTT 59.961 50.000 0.00 0.00 45.17 3.01
1519 2028 8.746052 AATGGTCCTAACGAAATGAATTCATA 57.254 30.769 21.00 3.89 37.96 2.15
1787 2313 3.253188 TGCAGCACAAATTAACAGAGACC 59.747 43.478 0.00 0.00 0.00 3.85
1922 2451 2.901975 CCTGGAGGTCCTGATCGAA 58.098 57.895 0.00 0.00 37.15 3.71
2265 2794 2.349580 GGTCGTGGTAATTTAGAACCGC 59.650 50.000 0.00 0.00 41.82 5.68
2280 2809 2.028420 ACCGCGGGTTAATTTCTACC 57.972 50.000 31.76 0.00 27.29 3.18
2337 2866 1.079266 GCAGGAGGCTGTGTCAGAG 60.079 63.158 0.00 0.00 40.25 3.35
2347 2876 0.613292 TGTGTCAGAGGAGGAGGAGC 60.613 60.000 0.00 0.00 0.00 4.70
2368 2897 0.741927 GGCCATGCAAAGATTGTGCC 60.742 55.000 0.00 0.00 41.49 5.01
2395 2924 2.415010 CTCCATGGTCTCTCGGCG 59.585 66.667 12.58 0.00 0.00 6.46
2426 2955 1.915350 GATGCGTGTCGTCGATTTGTA 59.085 47.619 0.00 0.00 0.00 2.41
2456 2985 6.436843 TTGTTTCTCTTCCTCTGTTTTGTC 57.563 37.500 0.00 0.00 0.00 3.18
2488 3017 1.679139 AGCTTGTAGTGCAGTGCAAA 58.321 45.000 21.67 9.68 41.47 3.68
2534 3067 4.173036 AGTTGTGTGAGTGTGTTTTTGG 57.827 40.909 0.00 0.00 0.00 3.28
2538 3071 1.748493 TGTGAGTGTGTTTTTGGAGCC 59.252 47.619 0.00 0.00 0.00 4.70
2603 3136 3.863142 ACTGAAATCTGCAATTCCAGC 57.137 42.857 7.43 0.00 32.87 4.85
2644 3186 2.628657 ACCAAGCGTAAAGTCACTCTCT 59.371 45.455 0.00 0.00 0.00 3.10
2645 3187 2.989840 CCAAGCGTAAAGTCACTCTCTG 59.010 50.000 0.00 0.00 0.00 3.35
2646 3188 3.305403 CCAAGCGTAAAGTCACTCTCTGA 60.305 47.826 0.00 0.00 0.00 3.27
2647 3189 4.299155 CAAGCGTAAAGTCACTCTCTGAA 58.701 43.478 0.00 0.00 0.00 3.02
2648 3190 3.903360 AGCGTAAAGTCACTCTCTGAAC 58.097 45.455 0.00 0.00 0.00 3.18
2649 3191 3.570550 AGCGTAAAGTCACTCTCTGAACT 59.429 43.478 0.00 0.00 0.00 3.01
2650 3192 3.915569 GCGTAAAGTCACTCTCTGAACTC 59.084 47.826 0.00 0.00 0.00 3.01
2651 3193 4.320641 GCGTAAAGTCACTCTCTGAACTCT 60.321 45.833 0.00 0.00 0.00 3.24
2652 3194 5.387279 CGTAAAGTCACTCTCTGAACTCTC 58.613 45.833 0.00 0.00 0.00 3.20
2694 3236 1.414061 AACTGCACCTGAGCCACTCT 61.414 55.000 0.00 0.00 0.00 3.24
2776 3318 3.316308 AGCACTGATGTTTTTCACACTCC 59.684 43.478 0.00 0.00 38.61 3.85
2804 3346 4.900684 TCATTCTTCATGGACCGTGTAAA 58.099 39.130 13.49 7.02 33.07 2.01
2805 3347 4.935205 TCATTCTTCATGGACCGTGTAAAG 59.065 41.667 13.49 10.56 33.07 1.85
2806 3348 4.345859 TTCTTCATGGACCGTGTAAAGT 57.654 40.909 13.49 0.00 0.00 2.66
2807 3349 5.471556 TTCTTCATGGACCGTGTAAAGTA 57.528 39.130 13.49 2.51 0.00 2.24
2808 3350 4.813027 TCTTCATGGACCGTGTAAAGTAC 58.187 43.478 13.49 0.00 0.00 2.73
2809 3351 3.598019 TCATGGACCGTGTAAAGTACC 57.402 47.619 13.49 0.00 0.00 3.34
2865 3652 7.094762 GGAAAATGAGTACTAGGAACTTTGGTG 60.095 40.741 0.00 0.00 41.75 4.17
2882 3945 1.734465 GGTGATCAGTTTTGCTCCTCG 59.266 52.381 0.00 0.00 0.00 4.63
2890 3953 2.074576 GTTTTGCTCCTCGGTTACTCC 58.925 52.381 0.00 0.00 0.00 3.85
2926 3989 2.012673 GATGACACATGCAGTTCTCCC 58.987 52.381 0.00 0.00 0.00 4.30
2951 4020 2.031495 AAGTACAGGAAGGCAGAGGT 57.969 50.000 0.00 0.00 0.00 3.85
2965 4034 2.685897 GCAGAGGTAGAGACTGTACTGG 59.314 54.545 9.43 0.00 34.60 4.00
2972 4041 4.705507 GGTAGAGACTGTACTGGTCATCAA 59.294 45.833 17.21 2.87 36.29 2.57
2973 4042 5.361285 GGTAGAGACTGTACTGGTCATCAAT 59.639 44.000 17.21 1.88 36.29 2.57
2974 4043 6.127310 GGTAGAGACTGTACTGGTCATCAATT 60.127 42.308 17.21 1.33 36.29 2.32
2977 4046 7.721402 AGAGACTGTACTGGTCATCAATTATC 58.279 38.462 17.21 7.32 36.29 1.75
2981 4050 7.795047 ACTGTACTGGTCATCAATTATCATCA 58.205 34.615 4.66 0.00 0.00 3.07
3005 4074 3.249559 CACAAGAACTGTTCTCAGAAGGC 59.750 47.826 22.24 0.00 43.76 4.35
3016 4088 4.785511 TCTCAGAAGGCACTACTGTTAC 57.214 45.455 0.00 0.00 38.49 2.50
3046 4119 2.025418 CGGTTGTACGAGCACCACC 61.025 63.158 12.65 0.00 35.47 4.61
3063 4136 1.346395 CACCCTACAAGCCTACACACA 59.654 52.381 0.00 0.00 0.00 3.72
3080 4153 4.122776 CACACAAGAGCTTCAGTTGTACT 58.877 43.478 0.00 0.00 33.10 2.73
3081 4154 5.163447 ACACACAAGAGCTTCAGTTGTACTA 60.163 40.000 0.00 0.00 33.10 1.82
3082 4155 5.175856 CACACAAGAGCTTCAGTTGTACTAC 59.824 44.000 0.00 0.00 33.10 2.73
3149 4222 6.507023 GGCATGTGGGTCTGATAAAATAAAG 58.493 40.000 0.00 0.00 0.00 1.85
3152 4225 7.631377 GCATGTGGGTCTGATAAAATAAAGCTT 60.631 37.037 0.00 0.00 0.00 3.74
3158 4231 8.523658 GGGTCTGATAAAATAAAGCTTTCAAGT 58.476 33.333 16.57 2.85 0.00 3.16
3161 4234 8.575589 TCTGATAAAATAAAGCTTTCAAGTGCA 58.424 29.630 16.57 6.63 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.739112 AGTGTCCAACTAAGCTGAAATTTTC 58.261 36.000 2.05 2.05 37.36 2.29
30 31 4.781087 AGGTAGGCAAATAGTGTCCAACTA 59.219 41.667 0.00 0.00 45.47 2.24
32 33 3.951663 AGGTAGGCAAATAGTGTCCAAC 58.048 45.455 0.00 0.00 29.16 3.77
84 85 2.248280 TTAGACAGCCGCAGTTTCAA 57.752 45.000 0.00 0.00 0.00 2.69
94 95 5.246307 AGTGATTTGTAGGTTTAGACAGCC 58.754 41.667 0.00 0.00 0.00 4.85
97 98 7.297936 TGAGAGTGATTTGTAGGTTTAGACA 57.702 36.000 0.00 0.00 0.00 3.41
107 108 7.108194 AGCATCAGATTTGAGAGTGATTTGTA 58.892 34.615 0.00 0.00 36.61 2.41
140 142 8.037382 TCTGCTTAACTGATTTGAGAATTGAG 57.963 34.615 0.00 0.00 0.00 3.02
141 143 7.984422 TCTGCTTAACTGATTTGAGAATTGA 57.016 32.000 0.00 0.00 0.00 2.57
146 148 5.965922 TCGATCTGCTTAACTGATTTGAGA 58.034 37.500 0.00 0.00 37.10 3.27
179 181 1.377987 GGTGCGCCCATTCCTTACA 60.378 57.895 4.45 0.00 0.00 2.41
235 239 7.519488 CGTGACTAGACAGTGTTCAAACTAGTA 60.519 40.741 17.14 7.42 39.96 1.82
485 774 2.648059 GTGGCTGCCATTATGAGACTT 58.352 47.619 26.22 0.00 35.28 3.01
493 782 2.045438 CGGTGGTGGCTGCCATTA 60.045 61.111 26.22 14.07 41.08 1.90
511 800 5.005628 AGGAGAAAACTCTAGTCAGTCCT 57.994 43.478 0.00 0.00 0.00 3.85
537 830 3.887621 ACAACTGATAGCGCTTCCTTA 57.112 42.857 18.68 0.00 0.00 2.69
538 831 2.770164 ACAACTGATAGCGCTTCCTT 57.230 45.000 18.68 0.00 0.00 3.36
546 848 4.208047 CAGCTACATCGAACAACTGATAGC 59.792 45.833 0.00 0.00 0.00 2.97
591 893 6.390721 CCTAACATCAGTCCATATAAGACCG 58.609 44.000 3.33 0.00 34.67 4.79
700 1003 4.955925 TGTAACGAAAATGGATTGCGAT 57.044 36.364 0.00 0.00 0.00 4.58
732 1035 9.449719 ACGAACAAAATTTATAGGAGAGACAAT 57.550 29.630 0.00 0.00 0.00 2.71
733 1036 8.717821 CACGAACAAAATTTATAGGAGAGACAA 58.282 33.333 0.00 0.00 0.00 3.18
734 1037 7.148474 GCACGAACAAAATTTATAGGAGAGACA 60.148 37.037 0.00 0.00 0.00 3.41
735 1038 7.064728 AGCACGAACAAAATTTATAGGAGAGAC 59.935 37.037 0.00 0.00 0.00 3.36
736 1039 7.064609 CAGCACGAACAAAATTTATAGGAGAGA 59.935 37.037 0.00 0.00 0.00 3.10
737 1040 7.182761 CAGCACGAACAAAATTTATAGGAGAG 58.817 38.462 0.00 0.00 0.00 3.20
738 1041 6.403200 GCAGCACGAACAAAATTTATAGGAGA 60.403 38.462 0.00 0.00 0.00 3.71
866 1252 1.382522 GGGATGTAGACGTACGTGGA 58.617 55.000 28.16 10.40 30.95 4.02
891 1277 5.139435 GGGACGGGTATTTATAGTGTACC 57.861 47.826 0.00 0.00 37.69 3.34
914 1300 0.603975 GAGTTGCAGGGAGTGTCCAC 60.604 60.000 0.00 0.00 38.64 4.02
941 1327 7.852263 ACTAGATATGGTTAGCTCAAGTGTTT 58.148 34.615 0.00 0.00 0.00 2.83
954 1340 7.129425 GGAGAGGATATGGACTAGATATGGTT 58.871 42.308 0.00 0.00 0.00 3.67
1129 1536 1.139095 CAGACGACGAAGGGGTAGC 59.861 63.158 0.00 0.00 0.00 3.58
1283 1706 1.599047 CTCCACCCATCTCAACGCT 59.401 57.895 0.00 0.00 0.00 5.07
1357 1785 3.110178 GACGAGAACGGCCGGTTG 61.110 66.667 31.76 19.46 42.35 3.77
1443 1871 4.080863 CAGCACTCTGTTTAGGGGTTATCT 60.081 45.833 0.00 0.00 35.61 1.98
1460 1920 3.927142 GCTATACACGAAAAGTCAGCACT 59.073 43.478 0.00 0.00 31.28 4.40
1469 1929 3.512329 TGGAGTGGAGCTATACACGAAAA 59.488 43.478 9.26 0.00 45.79 2.29
1470 1930 3.093814 TGGAGTGGAGCTATACACGAAA 58.906 45.455 9.26 0.00 45.79 3.46
2199 2728 2.125832 TAGCCAAGCACGTACGGC 60.126 61.111 21.06 19.03 45.23 5.68
2265 2794 0.932399 CCGCGGTAGAAATTAACCCG 59.068 55.000 19.50 0.00 41.50 5.28
2280 2809 3.577667 TCGTATAAATACAATCCCCGCG 58.422 45.455 0.00 0.00 32.87 6.46
2337 2866 2.771762 ATGGCCTGCTCCTCCTCC 60.772 66.667 3.32 0.00 0.00 4.30
2347 2876 2.004583 CACAATCTTTGCATGGCCTG 57.995 50.000 3.32 0.34 0.00 4.85
2368 2897 0.179936 GACCATGGAGGGAAGAGCTG 59.820 60.000 21.47 0.00 43.89 4.24
2395 2924 1.227380 CACGCATCACTAGGGGAGC 60.227 63.158 0.00 0.00 0.00 4.70
2426 2955 8.697507 AACAGAGGAAGAGAAACAAAATACAT 57.302 30.769 0.00 0.00 0.00 2.29
2456 2985 4.328440 CACTACAAGCTTTTCTCCTCATCG 59.672 45.833 0.00 0.00 0.00 3.84
2488 3017 0.796312 CATCGGCGTGCAACTTTAGT 59.204 50.000 6.85 0.00 31.75 2.24
2603 3136 9.353999 GCTTGGTAATTAAACTGAATAAAGTGG 57.646 33.333 0.00 0.00 0.00 4.00
2644 3186 8.803235 AGTAGTAATACACACATTGAGAGTTCA 58.197 33.333 2.81 0.00 0.00 3.18
2645 3187 9.640963 AAGTAGTAATACACACATTGAGAGTTC 57.359 33.333 2.81 0.00 0.00 3.01
2646 3188 9.424319 CAAGTAGTAATACACACATTGAGAGTT 57.576 33.333 2.81 0.00 0.00 3.01
2647 3189 7.545965 GCAAGTAGTAATACACACATTGAGAGT 59.454 37.037 2.81 0.00 0.00 3.24
2648 3190 7.545615 TGCAAGTAGTAATACACACATTGAGAG 59.454 37.037 2.81 0.00 0.00 3.20
2649 3191 7.382898 TGCAAGTAGTAATACACACATTGAGA 58.617 34.615 2.81 0.00 0.00 3.27
2650 3192 7.595311 TGCAAGTAGTAATACACACATTGAG 57.405 36.000 2.81 0.00 0.00 3.02
2651 3193 7.971183 TTGCAAGTAGTAATACACACATTGA 57.029 32.000 2.81 0.00 0.00 2.57
2652 3194 8.289618 AGTTTGCAAGTAGTAATACACACATTG 58.710 33.333 0.00 0.00 0.00 2.82
2733 3275 2.167281 TCATAGGAAGAGCTCTGCACAC 59.833 50.000 23.57 6.20 0.00 3.82
2776 3318 2.939103 GGTCCATGAAGAATGAAGGACG 59.061 50.000 0.00 0.00 44.89 4.79
2804 3346 3.181478 GCGCTCCTATAAACACAGGTACT 60.181 47.826 0.00 0.00 43.88 2.73
2805 3347 3.121544 GCGCTCCTATAAACACAGGTAC 58.878 50.000 0.00 0.00 0.00 3.34
2806 3348 2.101917 GGCGCTCCTATAAACACAGGTA 59.898 50.000 7.64 0.00 0.00 3.08
2807 3349 1.134491 GGCGCTCCTATAAACACAGGT 60.134 52.381 7.64 0.00 0.00 4.00
2808 3350 1.134521 TGGCGCTCCTATAAACACAGG 60.135 52.381 7.64 0.00 0.00 4.00
2809 3351 2.309528 TGGCGCTCCTATAAACACAG 57.690 50.000 7.64 0.00 0.00 3.66
2865 3652 2.100605 ACCGAGGAGCAAAACTGATC 57.899 50.000 0.00 0.00 0.00 2.92
2882 3945 1.154197 GCAGAACAACCGGAGTAACC 58.846 55.000 9.46 0.00 0.00 2.85
2951 4020 8.768501 ATAATTGATGACCAGTACAGTCTCTA 57.231 34.615 14.81 8.72 35.21 2.43
2965 4034 9.282247 GTTCTTGTGTTGATGATAATTGATGAC 57.718 33.333 0.00 0.00 0.00 3.06
2972 4041 8.627208 AGAACAGTTCTTGTGTTGATGATAAT 57.373 30.769 10.27 0.00 40.74 1.28
2973 4042 7.714813 TGAGAACAGTTCTTGTGTTGATGATAA 59.285 33.333 17.19 0.00 40.87 1.75
2974 4043 7.216494 TGAGAACAGTTCTTGTGTTGATGATA 58.784 34.615 17.19 0.00 40.87 2.15
2977 4046 5.525012 TCTGAGAACAGTTCTTGTGTTGATG 59.475 40.000 17.19 1.47 43.81 3.07
2981 4050 4.878397 CCTTCTGAGAACAGTTCTTGTGTT 59.122 41.667 17.19 0.00 43.81 3.32
3005 4074 5.508573 CGACGATCTTTCAGTAACAGTAGTG 59.491 44.000 0.00 0.00 32.64 2.74
3016 4088 2.592897 CGTACAACCGACGATCTTTCAG 59.407 50.000 0.00 0.00 42.98 3.02
3046 4119 3.589988 CTCTTGTGTGTAGGCTTGTAGG 58.410 50.000 0.00 0.00 0.00 3.18
3063 4136 7.120873 TCGAATAGTAGTACAACTGAAGCTCTT 59.879 37.037 2.52 0.00 0.00 2.85
3081 4154 9.406113 ACCTTCTAGTATGTAAAGTCGAATAGT 57.594 33.333 0.00 0.00 0.00 2.12
3082 4155 9.666626 CACCTTCTAGTATGTAAAGTCGAATAG 57.333 37.037 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.