Multiple sequence alignment - TraesCS1D01G064200

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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 TraesCS1D01G064200 chr1D 100.000 4422 0 0 1 4422 44652976 44648555 0.000000e+00 8167
1 TraesCS1D01G064200 chr1D 83.906 466 43 9 185 642 97221845 97222286 2.460000e-112 416
2 TraesCS1D01G064200 chr1D 82.080 452 41 14 4006 4422 44692866 44692420 2.530000e-92 350
3 TraesCS1D01G064200 chr1D 81.416 452 44 18 4006 4422 44664869 44664423 2.550000e-87 333
4 TraesCS1D01G064200 chr1D 90.909 187 10 3 185 364 97221781 97221967 1.230000e-60 244
5 TraesCS1D01G064200 chr1D 88.649 185 14 3 187 364 97221719 97221903 7.450000e-53 219
6 TraesCS1D01G064200 chr1B 96.712 3011 99 0 974 3984 63969371 63966361 0.000000e+00 5012
7 TraesCS1D01G064200 chr1B 92.127 3493 219 23 974 4419 64431371 64427888 0.000000e+00 4876
8 TraesCS1D01G064200 chr1B 92.072 3494 211 32 974 4419 64281793 64278318 0.000000e+00 4857
9 TraesCS1D01G064200 chr6B 84.656 2822 384 39 997 3798 156689111 156686319 0.000000e+00 2767
10 TraesCS1D01G064200 chr2D 97.994 947 13 2 1 942 88688018 88688963 0.000000e+00 1639
11 TraesCS1D01G064200 chr2D 75.793 2805 609 61 1000 3769 528077103 528079872 0.000000e+00 1354
12 TraesCS1D01G064200 chr2B 75.284 2820 622 66 987 3769 625917085 625919866 0.000000e+00 1277
13 TraesCS1D01G064200 chr2B 79.114 474 68 27 190 642 773342302 773341839 9.300000e-77 298
14 TraesCS1D01G064200 chr5D 95.419 764 21 4 185 934 334693649 334694412 0.000000e+00 1205
15 TraesCS1D01G064200 chr5D 88.136 236 15 9 170 398 334693575 334693804 7.290000e-68 268
16 TraesCS1D01G064200 chr5D 88.136 118 14 0 481 598 378789277 378789160 1.660000e-29 141
17 TraesCS1D01G064200 chr4D 97.633 338 2 4 1 332 7866180 7865843 3.840000e-160 575
18 TraesCS1D01G064200 chr4D 87.829 304 30 5 185 481 455085844 455086147 2.530000e-92 350
19 TraesCS1D01G064200 chr4D 84.426 244 24 11 410 642 455086107 455086347 1.240000e-55 228
20 TraesCS1D01G064200 chr7A 83.878 459 34 22 201 642 636696327 636696762 6.890000e-108 401
21 TraesCS1D01G064200 chr2A 83.261 460 45 11 194 645 510989443 510989008 1.150000e-105 394
22 TraesCS1D01G064200 chr3B 83.019 477 37 25 185 642 758611917 758612368 4.150000e-105 392
23 TraesCS1D01G064200 chr7D 98.995 199 2 0 1 199 557075981 557076179 1.510000e-94 357
24 TraesCS1D01G064200 chr3D 96.711 152 5 0 1 152 588360694 588360845 2.040000e-63 254
25 TraesCS1D01G064200 chrUn 82.818 291 35 10 362 642 315779759 315780044 3.420000e-61 246
26 TraesCS1D01G064200 chr7B 85.542 166 22 2 481 645 437677012 437676848 5.880000e-39 172
27 TraesCS1D01G064200 chr6D 89.706 136 10 4 8 140 48516058 48516192 2.110000e-38 171
28 TraesCS1D01G064200 chr4A 85.366 123 13 2 481 598 624608522 624608400 6.010000e-24 122
29 TraesCS1D01G064200 chr1A 76.744 258 25 14 373 595 569474831 569475088 1.300000e-20 111


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 TraesCS1D01G064200 chr1D 44648555 44652976 4421 True 8167.0 8167 100.000000 1 4422 1 chr1D.!!$R1 4421
1 TraesCS1D01G064200 chr1D 97221719 97222286 567 False 293.0 416 87.821333 185 642 3 chr1D.!!$F1 457
2 TraesCS1D01G064200 chr1B 63966361 63969371 3010 True 5012.0 5012 96.712000 974 3984 1 chr1B.!!$R1 3010
3 TraesCS1D01G064200 chr1B 64427888 64431371 3483 True 4876.0 4876 92.127000 974 4419 1 chr1B.!!$R3 3445
4 TraesCS1D01G064200 chr1B 64278318 64281793 3475 True 4857.0 4857 92.072000 974 4419 1 chr1B.!!$R2 3445
5 TraesCS1D01G064200 chr6B 156686319 156689111 2792 True 2767.0 2767 84.656000 997 3798 1 chr6B.!!$R1 2801
6 TraesCS1D01G064200 chr2D 88688018 88688963 945 False 1639.0 1639 97.994000 1 942 1 chr2D.!!$F1 941
7 TraesCS1D01G064200 chr2D 528077103 528079872 2769 False 1354.0 1354 75.793000 1000 3769 1 chr2D.!!$F2 2769
8 TraesCS1D01G064200 chr2B 625917085 625919866 2781 False 1277.0 1277 75.284000 987 3769 1 chr2B.!!$F1 2782
9 TraesCS1D01G064200 chr5D 334693575 334694412 837 False 736.5 1205 91.777500 170 934 2 chr5D.!!$F1 764
10 TraesCS1D01G064200 chr4D 455085844 455086347 503 False 289.0 350 86.127500 185 642 2 chr4D.!!$F1 457

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
123 124 1.645034 CTCATTGTAGCACTGGACGG 58.355 55.000 0.0 0.0 0.0 4.79 F
1029 1280 1.480137 CTGATCGCCATATCCCTCTCC 59.520 57.143 0.0 0.0 0.0 3.71 F
2222 2485 1.269012 CATGGAATTGGGCAAGTGGT 58.731 50.000 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2215 0.454600 CTGCAACATGATGGTCCTGC 59.545 55.0 0.0 1.0 0.00 4.85 R
2404 2667 1.136690 CGTTGCACTAGCTCGTTCAA 58.863 50.0 0.0 0.0 42.74 2.69 R
4143 4428 0.108804 TCTCCGACAACCTTGATCGC 60.109 55.0 0.0 0.0 33.52 4.58 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
123 124 1.645034 CTCATTGTAGCACTGGACGG 58.355 55.000 0.00 0.00 0.00 4.79
598 849 4.015406 CACTACCACGCAGCCCCA 62.015 66.667 0.00 0.00 0.00 4.96
693 944 3.066190 GATGCAGCAAGCCAGCCA 61.066 61.111 0.00 0.00 44.83 4.75
740 991 1.893808 CTGCTTTGGTGGTGCTCGT 60.894 57.895 0.00 0.00 0.00 4.18
756 1007 2.379972 CTCGTCATGGGTACTCTCCTT 58.620 52.381 0.00 0.00 0.00 3.36
934 1185 3.447586 CGGTGGATCTAGAGACTTTTCCA 59.552 47.826 6.43 6.43 0.00 3.53
935 1186 4.081642 CGGTGGATCTAGAGACTTTTCCAA 60.082 45.833 11.25 0.00 35.19 3.53
938 1189 6.887002 GGTGGATCTAGAGACTTTTCCAATTT 59.113 38.462 11.25 0.00 35.19 1.82
946 1197 9.394477 CTAGAGACTTTTCCAATTTAAAAACCG 57.606 33.333 0.00 0.00 0.00 4.44
947 1198 7.207383 AGAGACTTTTCCAATTTAAAAACCGG 58.793 34.615 0.00 0.00 0.00 5.28
948 1199 6.880484 AGACTTTTCCAATTTAAAAACCGGT 58.120 32.000 0.00 0.00 0.00 5.28
949 1200 6.759356 AGACTTTTCCAATTTAAAAACCGGTG 59.241 34.615 8.52 0.00 0.00 4.94
950 1201 5.818336 ACTTTTCCAATTTAAAAACCGGTGG 59.182 36.000 8.52 0.70 0.00 4.61
951 1202 5.354842 TTTCCAATTTAAAAACCGGTGGT 57.645 34.783 8.52 0.00 37.65 4.16
952 1203 4.323553 TCCAATTTAAAAACCGGTGGTG 57.676 40.909 8.52 0.00 35.34 4.17
953 1204 3.705072 TCCAATTTAAAAACCGGTGGTGT 59.295 39.130 8.52 0.00 35.34 4.16
954 1205 4.891756 TCCAATTTAAAAACCGGTGGTGTA 59.108 37.500 8.52 0.00 35.34 2.90
955 1206 5.361857 TCCAATTTAAAAACCGGTGGTGTAA 59.638 36.000 8.52 1.99 35.34 2.41
956 1207 6.041751 TCCAATTTAAAAACCGGTGGTGTAAT 59.958 34.615 8.52 3.09 35.34 1.89
957 1208 6.706716 CCAATTTAAAAACCGGTGGTGTAATT 59.293 34.615 8.52 9.51 35.34 1.40
958 1209 7.307455 CCAATTTAAAAACCGGTGGTGTAATTG 60.307 37.037 23.91 23.91 35.34 2.32
959 1210 6.461110 TTTAAAAACCGGTGGTGTAATTGA 57.539 33.333 8.52 0.00 35.34 2.57
960 1211 3.994204 AAAACCGGTGGTGTAATTGAC 57.006 42.857 8.52 0.00 35.34 3.18
961 1212 2.943036 AACCGGTGGTGTAATTGACT 57.057 45.000 8.52 0.00 35.34 3.41
962 1213 2.467566 ACCGGTGGTGTAATTGACTC 57.532 50.000 6.12 0.00 32.98 3.36
963 1214 1.695242 ACCGGTGGTGTAATTGACTCA 59.305 47.619 6.12 0.00 32.98 3.41
964 1215 2.105134 ACCGGTGGTGTAATTGACTCAA 59.895 45.455 6.12 0.00 32.98 3.02
965 1216 3.244770 ACCGGTGGTGTAATTGACTCAAT 60.245 43.478 6.12 0.00 32.66 2.57
966 1217 3.756434 CCGGTGGTGTAATTGACTCAATT 59.244 43.478 18.76 18.76 44.74 2.32
967 1218 4.217550 CCGGTGGTGTAATTGACTCAATTT 59.782 41.667 19.72 6.91 40.60 1.82
968 1219 5.153513 CGGTGGTGTAATTGACTCAATTTG 58.846 41.667 19.72 0.00 40.60 2.32
969 1220 5.049060 CGGTGGTGTAATTGACTCAATTTGA 60.049 40.000 19.72 6.67 40.60 2.69
970 1221 6.514212 CGGTGGTGTAATTGACTCAATTTGAA 60.514 38.462 19.72 2.44 40.60 2.69
971 1222 6.640907 GGTGGTGTAATTGACTCAATTTGAAC 59.359 38.462 19.72 13.40 40.60 3.18
972 1223 6.640907 GTGGTGTAATTGACTCAATTTGAACC 59.359 38.462 19.72 21.12 40.60 3.62
978 1229 5.917541 TTGACTCAATTTGAACCTCGTAC 57.082 39.130 0.01 0.00 0.00 3.67
1029 1280 1.480137 CTGATCGCCATATCCCTCTCC 59.520 57.143 0.00 0.00 0.00 3.71
1093 1344 1.595993 CGTCTTCCTCGCCTCCTTCA 61.596 60.000 0.00 0.00 0.00 3.02
1612 1875 5.140747 CAAGACTACTCTTGCCACTAACT 57.859 43.478 0.00 0.00 45.43 2.24
1870 2133 3.121030 CCTGGTTTCAGCTCCGCG 61.121 66.667 0.00 0.00 39.61 6.46
2082 2345 3.634397 TGGGCTTTCAAGATACTGGAG 57.366 47.619 0.00 0.00 0.00 3.86
2222 2485 1.269012 CATGGAATTGGGCAAGTGGT 58.731 50.000 0.00 0.00 0.00 4.16
2404 2667 1.673808 GGAGGTCGCGGATGGTTACT 61.674 60.000 6.13 0.00 0.00 2.24
2521 2784 7.303998 GGAGATTGCTGCATATAGATCAAAAC 58.696 38.462 1.84 0.00 31.98 2.43
2688 2954 3.440173 ACCTGGATGTTGCACTATTTTCG 59.560 43.478 0.00 0.00 0.00 3.46
3121 3387 7.126061 TGGAGTAGACCAGAGAATTCTTATCA 58.874 38.462 9.87 0.00 34.77 2.15
3513 3779 6.095440 GCATAGAATTTCAAAAGGACAGCCTA 59.905 38.462 0.00 0.00 46.28 3.93
3798 4067 1.730501 AGACGGATGCAGTCACATTG 58.269 50.000 7.27 0.00 40.84 2.82
3960 4229 1.541588 GCCCACAGCTTCGAAAAGATT 59.458 47.619 0.00 0.00 38.99 2.40
3975 4244 0.253630 AGATTGGGCTACTTGGGGGA 60.254 55.000 0.00 0.00 0.00 4.81
3976 4245 0.853530 GATTGGGCTACTTGGGGGAT 59.146 55.000 0.00 0.00 0.00 3.85
3977 4246 2.062636 GATTGGGCTACTTGGGGGATA 58.937 52.381 0.00 0.00 0.00 2.59
4004 4273 5.858581 GCAAAACTCTGCATTTTACTACCTG 59.141 40.000 0.00 0.00 42.17 4.00
4020 4289 1.315257 CCTGGTGCAGCATTGGGTAC 61.315 60.000 20.52 0.00 0.00 3.34
4029 4298 2.159627 CAGCATTGGGTACGTTCTGAAC 59.840 50.000 10.48 10.48 0.00 3.18
4035 4304 3.981211 TGGGTACGTTCTGAACTTGTAC 58.019 45.455 20.89 20.89 35.75 2.90
4058 4327 9.226345 GTACTTTTGCTATTATTGTTCTGATGC 57.774 33.333 0.00 0.00 0.00 3.91
4059 4328 8.059798 ACTTTTGCTATTATTGTTCTGATGCT 57.940 30.769 0.00 0.00 0.00 3.79
4060 4329 9.177608 ACTTTTGCTATTATTGTTCTGATGCTA 57.822 29.630 0.00 0.00 0.00 3.49
4066 4335 9.322776 GCTATTATTGTTCTGATGCTATTTTCG 57.677 33.333 0.00 0.00 0.00 3.46
4069 4338 6.741992 ATTGTTCTGATGCTATTTTCGTCA 57.258 33.333 0.00 0.00 0.00 4.35
4070 4339 5.784750 TGTTCTGATGCTATTTTCGTCAG 57.215 39.130 6.00 6.00 44.72 3.51
4071 4340 4.093408 TGTTCTGATGCTATTTTCGTCAGC 59.907 41.667 7.20 0.00 43.65 4.26
4088 4357 4.945090 GTCAGCAACGGCAAAAATTTATG 58.055 39.130 0.00 0.00 44.61 1.90
4089 4358 3.993081 TCAGCAACGGCAAAAATTTATGG 59.007 39.130 0.00 0.00 44.61 2.74
4090 4359 3.124976 CAGCAACGGCAAAAATTTATGGG 59.875 43.478 0.00 0.00 44.61 4.00
4092 4361 3.500299 GCAACGGCAAAAATTTATGGGTT 59.500 39.130 0.00 0.00 40.72 4.11
4093 4362 4.023622 GCAACGGCAAAAATTTATGGGTTT 60.024 37.500 0.00 0.00 40.72 3.27
4121 4406 6.899393 TTTTGAAGTGCTTGTCTAATGGAT 57.101 33.333 0.00 0.00 0.00 3.41
4126 4411 6.149973 TGAAGTGCTTGTCTAATGGATTTCTG 59.850 38.462 0.00 0.00 0.00 3.02
4129 4414 6.541641 AGTGCTTGTCTAATGGATTTCTGATC 59.458 38.462 0.00 0.00 0.00 2.92
4131 4416 6.541278 TGCTTGTCTAATGGATTTCTGATCAG 59.459 38.462 17.07 17.07 0.00 2.90
4143 4428 0.094216 CTGATCAGACGCGTGCAAAG 59.906 55.000 20.70 2.30 0.00 2.77
4168 4453 3.202906 TCAAGGTTGTCGGAGAAGTTTG 58.797 45.455 5.45 5.45 39.69 2.93
4187 4472 3.806949 TGGCTGGTACAATTTTCCTCT 57.193 42.857 0.00 0.00 38.70 3.69
4201 4486 4.989279 TTTCCTCTGCTAAATTGGCATC 57.011 40.909 4.11 0.00 39.07 3.91
4230 4515 0.947244 GTGGAACAGTTCACAGCCAG 59.053 55.000 15.36 0.00 41.80 4.85
4234 4519 0.839946 AACAGTTCACAGCCAGGACT 59.160 50.000 0.00 0.00 0.00 3.85
4235 4520 1.717032 ACAGTTCACAGCCAGGACTA 58.283 50.000 0.00 0.00 0.00 2.59
4276 4561 5.240891 TGACTTGTGACTGATGGATTCTTC 58.759 41.667 0.00 0.00 0.00 2.87
4280 4565 3.002791 GTGACTGATGGATTCTTCGCAA 58.997 45.455 0.00 0.00 0.00 4.85
4335 4624 2.486966 GGGGTACGACCGACTTCG 59.513 66.667 0.00 0.00 44.87 3.79
4361 4671 0.874607 GTGAAGAACTCACGCCGTGT 60.875 55.000 17.83 0.00 44.95 4.49
4384 4694 1.010935 CGACGCAGCTGTTCATGTCT 61.011 55.000 16.64 0.00 0.00 3.41
4419 4729 0.610174 TGGGTGAGCAGCTAAGACTG 59.390 55.000 0.00 0.00 40.80 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 384 2.663808 TGTAATGAAGCGTCGTCGAAA 58.336 42.857 6.17 0.00 39.71 3.46
740 991 1.559682 GCCAAAGGAGAGTACCCATGA 59.440 52.381 0.00 0.00 0.00 3.07
756 1007 0.324552 CCATTCATCCCCACAGCCAA 60.325 55.000 0.00 0.00 0.00 4.52
889 1140 6.531948 CCGACTGATTTCTTCTTCTCGTAAAT 59.468 38.462 0.00 0.00 0.00 1.40
934 1185 7.438757 GTCAATTACACCACCGGTTTTTAAATT 59.561 33.333 2.97 6.25 31.02 1.82
935 1186 6.924612 GTCAATTACACCACCGGTTTTTAAAT 59.075 34.615 2.97 0.00 31.02 1.40
938 1189 5.131784 AGTCAATTACACCACCGGTTTTTA 58.868 37.500 2.97 0.00 31.02 1.52
941 1192 3.143728 GAGTCAATTACACCACCGGTTT 58.856 45.455 2.97 0.00 31.02 3.27
942 1193 2.105134 TGAGTCAATTACACCACCGGTT 59.895 45.455 2.97 0.00 31.02 4.44
943 1194 1.695242 TGAGTCAATTACACCACCGGT 59.305 47.619 0.00 0.00 35.62 5.28
944 1195 2.465860 TGAGTCAATTACACCACCGG 57.534 50.000 0.00 0.00 0.00 5.28
945 1196 5.049060 TCAAATTGAGTCAATTACACCACCG 60.049 40.000 27.15 11.27 42.32 4.94
946 1197 6.325919 TCAAATTGAGTCAATTACACCACC 57.674 37.500 27.15 0.00 42.32 4.61
947 1198 6.640907 GGTTCAAATTGAGTCAATTACACCAC 59.359 38.462 28.69 21.30 42.32 4.16
948 1199 6.549364 AGGTTCAAATTGAGTCAATTACACCA 59.451 34.615 31.58 17.00 42.32 4.17
949 1200 6.981722 AGGTTCAAATTGAGTCAATTACACC 58.018 36.000 27.15 27.42 42.32 4.16
950 1201 6.797033 CGAGGTTCAAATTGAGTCAATTACAC 59.203 38.462 27.15 21.92 42.32 2.90
951 1202 6.485313 ACGAGGTTCAAATTGAGTCAATTACA 59.515 34.615 27.15 15.90 42.32 2.41
952 1203 6.899114 ACGAGGTTCAAATTGAGTCAATTAC 58.101 36.000 27.15 21.37 42.32 1.89
953 1204 7.118680 GGTACGAGGTTCAAATTGAGTCAATTA 59.881 37.037 27.15 13.13 42.32 1.40
954 1205 6.072673 GGTACGAGGTTCAAATTGAGTCAATT 60.073 38.462 22.70 22.70 44.62 2.32
955 1206 5.411669 GGTACGAGGTTCAAATTGAGTCAAT 59.588 40.000 12.75 12.75 35.39 2.57
956 1207 4.753107 GGTACGAGGTTCAAATTGAGTCAA 59.247 41.667 8.27 8.27 0.00 3.18
957 1208 4.202274 TGGTACGAGGTTCAAATTGAGTCA 60.202 41.667 0.00 0.00 0.00 3.41
958 1209 4.151867 GTGGTACGAGGTTCAAATTGAGTC 59.848 45.833 0.00 0.00 0.00 3.36
959 1210 4.062991 GTGGTACGAGGTTCAAATTGAGT 58.937 43.478 0.00 0.00 0.00 3.41
960 1211 3.435671 GGTGGTACGAGGTTCAAATTGAG 59.564 47.826 0.00 0.00 0.00 3.02
961 1212 3.404899 GGTGGTACGAGGTTCAAATTGA 58.595 45.455 0.00 0.00 0.00 2.57
962 1213 2.486592 GGGTGGTACGAGGTTCAAATTG 59.513 50.000 0.00 0.00 0.00 2.32
963 1214 2.374170 AGGGTGGTACGAGGTTCAAATT 59.626 45.455 0.00 0.00 0.00 1.82
964 1215 1.982958 AGGGTGGTACGAGGTTCAAAT 59.017 47.619 0.00 0.00 0.00 2.32
965 1216 1.426751 AGGGTGGTACGAGGTTCAAA 58.573 50.000 0.00 0.00 0.00 2.69
966 1217 1.895131 GTAGGGTGGTACGAGGTTCAA 59.105 52.381 0.00 0.00 0.00 2.69
967 1218 1.076024 AGTAGGGTGGTACGAGGTTCA 59.924 52.381 0.00 0.00 0.00 3.18
968 1219 1.844687 AGTAGGGTGGTACGAGGTTC 58.155 55.000 0.00 0.00 0.00 3.62
969 1220 2.728007 GTAGTAGGGTGGTACGAGGTT 58.272 52.381 0.00 0.00 0.00 3.50
970 1221 1.407437 CGTAGTAGGGTGGTACGAGGT 60.407 57.143 0.00 0.00 41.64 3.85
971 1222 1.134401 TCGTAGTAGGGTGGTACGAGG 60.134 57.143 0.00 0.00 42.60 4.63
972 1223 2.315925 TCGTAGTAGGGTGGTACGAG 57.684 55.000 0.00 0.00 42.60 4.18
978 1229 1.445716 CTCGGCTCGTAGTAGGGTGG 61.446 65.000 0.00 0.00 0.00 4.61
1067 1318 4.796231 CGAGGAAGACGGCCGTGG 62.796 72.222 39.65 7.25 0.00 4.94
1612 1875 4.560136 TTGCAGCGATTTTCTTGTACAA 57.440 36.364 8.28 8.28 0.00 2.41
1870 2133 4.168760 GTTTCACTATCAAGCAATGCACC 58.831 43.478 8.35 0.00 0.00 5.01
1952 2215 0.454600 CTGCAACATGATGGTCCTGC 59.545 55.000 0.00 1.00 0.00 4.85
2082 2345 3.631453 TGGCAGACCACAACATCTC 57.369 52.632 0.00 0.00 42.67 2.75
2404 2667 1.136690 CGTTGCACTAGCTCGTTCAA 58.863 50.000 0.00 0.00 42.74 2.69
2565 2831 8.504005 AGTGTAAGATAACGGATTTTCTGTTTG 58.496 33.333 7.00 0.00 42.95 2.93
2688 2954 3.664025 GCACAGTTAACAATCTGAAACGC 59.336 43.478 8.61 0.00 35.84 4.84
3798 4067 1.600916 GTTGACTGACCCCACTGGC 60.601 63.158 0.00 0.00 37.83 4.85
3960 4229 1.052124 CGTATCCCCCAAGTAGCCCA 61.052 60.000 0.00 0.00 0.00 5.36
3975 4244 4.519540 AAAATGCAGAGTTTTGCCGTAT 57.480 36.364 0.00 0.00 43.43 3.06
3976 4245 4.517453 AGTAAAATGCAGAGTTTTGCCGTA 59.483 37.500 6.74 0.00 43.43 4.02
3977 4246 2.888834 AAAATGCAGAGTTTTGCCGT 57.111 40.000 0.00 0.00 43.43 5.68
4004 4273 1.241315 AACGTACCCAATGCTGCACC 61.241 55.000 3.57 0.00 0.00 5.01
4020 4289 5.156804 AGCAAAAGTACAAGTTCAGAACG 57.843 39.130 7.68 0.00 36.23 3.95
4050 4319 4.252878 TGCTGACGAAAATAGCATCAGAA 58.747 39.130 3.80 0.00 42.05 3.02
4066 4335 4.143137 CCATAAATTTTTGCCGTTGCTGAC 60.143 41.667 0.00 0.00 38.71 3.51
4069 4338 3.244387 ACCCATAAATTTTTGCCGTTGCT 60.244 39.130 0.00 0.00 38.71 3.91
4070 4339 3.070748 ACCCATAAATTTTTGCCGTTGC 58.929 40.909 0.00 0.00 38.26 4.17
4071 4340 5.681337 AAACCCATAAATTTTTGCCGTTG 57.319 34.783 0.00 0.00 0.00 4.10
4072 4341 6.701145 AAAAACCCATAAATTTTTGCCGTT 57.299 29.167 0.00 1.75 36.80 4.44
4097 4382 6.707440 TCCATTAGACAAGCACTTCAAAAA 57.293 33.333 0.00 0.00 0.00 1.94
4102 4387 6.372659 TCAGAAATCCATTAGACAAGCACTTC 59.627 38.462 0.00 0.00 0.00 3.01
4116 4401 2.159043 ACGCGTCTGATCAGAAATCCAT 60.159 45.455 26.70 8.15 39.48 3.41
4117 4402 1.204704 ACGCGTCTGATCAGAAATCCA 59.795 47.619 26.70 0.75 39.48 3.41
4121 4406 0.319469 TGCACGCGTCTGATCAGAAA 60.319 50.000 26.70 3.20 39.48 2.52
4126 4411 1.225854 GCTTTGCACGCGTCTGATC 60.226 57.895 9.86 0.00 0.00 2.92
4143 4428 0.108804 TCTCCGACAACCTTGATCGC 60.109 55.000 0.00 0.00 33.52 4.58
4168 4453 2.164422 GCAGAGGAAAATTGTACCAGCC 59.836 50.000 0.00 0.00 0.00 4.85
4230 4515 8.131731 GTCATGATTAGGCAAATTTTCTAGTCC 58.868 37.037 0.00 1.16 0.00 3.85
4234 4519 9.023962 ACAAGTCATGATTAGGCAAATTTTCTA 57.976 29.630 0.00 0.00 0.00 2.10
4235 4520 7.816031 CACAAGTCATGATTAGGCAAATTTTCT 59.184 33.333 0.00 0.00 0.00 2.52
4280 4565 1.483827 TGCATCAGATCCTTTCGCTCT 59.516 47.619 0.00 0.00 0.00 4.09
4335 4624 3.706055 TGAGTTCTTCACCTGCACC 57.294 52.632 0.00 0.00 0.00 5.01
4357 4667 2.880879 AGCTGCGTCGCATACACG 60.881 61.111 22.03 9.79 38.13 4.49
4361 4671 0.460109 ATGAACAGCTGCGTCGCATA 60.460 50.000 22.03 0.00 38.13 3.14
4369 4679 0.441533 CGTGAGACATGAACAGCTGC 59.558 55.000 15.27 0.00 0.00 5.25
4398 4708 1.484240 AGTCTTAGCTGCTCACCCATC 59.516 52.381 4.91 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.