Multiple sequence alignment - TraesCS3D01G011400

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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 TraesCS3D01G011400 chr3D 100.000 4189 0 0 1 4189 4074960 4079148 0.000000e+00 7736.0
1 TraesCS3D01G011400 chr3D 91.533 1429 111 5 1846 3266 4168453 4167027 0.000000e+00 1960.0
2 TraesCS3D01G011400 chr3D 85.691 1803 190 32 1 1751 4170300 4168514 0.000000e+00 1838.0
3 TraesCS3D01G011400 chr3D 79.254 2092 376 40 1064 3122 28382982 28380916 0.000000e+00 1406.0
4 TraesCS3D01G011400 chr3D 94.279 402 23 0 3371 3772 4167010 4166609 2.140000e-172 616.0
5 TraesCS3D01G011400 chr3D 98.507 67 1 0 3906 3972 4166439 4166373 7.360000e-23 119.0
6 TraesCS3D01G011400 chr3D 98.000 50 1 0 3861 3910 4166505 4166456 2.070000e-13 87.9
7 TraesCS3D01G011400 chrUn 93.450 3084 111 24 753 3804 246339355 246342379 0.000000e+00 4492.0
8 TraesCS3D01G011400 chrUn 90.501 779 51 11 1 757 246338519 246339296 0.000000e+00 1007.0
9 TraesCS3D01G011400 chrUn 85.714 84 6 3 3728 3806 35383883 35383965 2.680000e-12 84.2
10 TraesCS3D01G011400 chrUn 85.714 84 6 3 3728 3806 300614690 300614772 2.680000e-12 84.2
11 TraesCS3D01G011400 chrUn 100.000 31 0 0 1 31 469290923 469290953 1.630000e-04 58.4
12 TraesCS3D01G011400 chr3B 93.450 3084 111 24 753 3804 6393455 6396479 0.000000e+00 4492.0
13 TraesCS3D01G011400 chr3B 86.642 2141 244 30 1146 3262 6667670 6665548 0.000000e+00 2331.0
14 TraesCS3D01G011400 chr3B 90.704 1108 69 13 2193 3267 13937795 13936689 0.000000e+00 1445.0
15 TraesCS3D01G011400 chr3B 90.501 779 51 11 1 757 6392619 6393396 0.000000e+00 1007.0
16 TraesCS3D01G011400 chr3B 84.854 515 25 21 3374 3859 13936572 13936082 1.760000e-128 470.0
17 TraesCS3D01G011400 chr3B 87.607 234 29 0 988 1221 13939516 13939283 5.340000e-69 272.0
18 TraesCS3D01G011400 chr3B 83.548 310 27 11 3371 3658 6665540 6665233 6.900000e-68 268.0
19 TraesCS3D01G011400 chr3B 85.321 109 4 3 3980 4088 6664979 6664883 7.410000e-18 102.0
20 TraesCS3D01G011400 chr3B 85.714 84 6 3 3728 3806 6547173 6547091 2.680000e-12 84.2
21 TraesCS3D01G011400 chr3B 80.247 81 12 4 4108 4188 6664883 6664807 1.630000e-04 58.4
22 TraesCS3D01G011400 chr3A 90.797 1869 116 8 1846 3703 9614058 9615881 0.000000e+00 2447.0
23 TraesCS3D01G011400 chr3A 86.205 1805 174 35 1 1751 9612214 9613997 0.000000e+00 1884.0
24 TraesCS3D01G011400 chr3A 90.064 1409 113 8 1865 3266 9779210 9777822 0.000000e+00 1801.0
25 TraesCS3D01G011400 chr3A 85.412 994 126 13 765 1751 9780258 9779277 0.000000e+00 1014.0
26 TraesCS3D01G011400 chr3A 93.774 514 29 1 1 514 9781388 9780878 0.000000e+00 769.0
27 TraesCS3D01G011400 chr3A 93.471 291 16 2 3873 4163 9615967 9616254 2.990000e-116 429.0
28 TraesCS3D01G011400 chr3A 84.367 371 21 21 3666 4021 9777562 9777214 3.120000e-86 329.0
29 TraesCS3D01G011400 chr3A 89.655 261 14 2 3371 3631 9777805 9777558 1.880000e-83 320.0
30 TraesCS3D01G011400 chr3A 91.057 123 7 1 4038 4160 9777113 9776995 3.350000e-36 163.0
31 TraesCS3D01G011400 chr3A 98.438 64 0 1 3785 3848 9615909 9615971 1.230000e-20 111.0
32 TraesCS3D01G011400 chr6A 86.087 920 57 17 3273 4163 609888433 609889310 0.000000e+00 924.0
33 TraesCS3D01G011400 chr6A 87.950 722 69 12 1 707 609885848 609886566 0.000000e+00 835.0
34 TraesCS3D01G011400 chr6A 93.360 497 33 0 2230 2726 609887491 609887987 0.000000e+00 736.0
35 TraesCS3D01G011400 chr6A 92.000 450 36 0 2757 3206 609887984 609888433 2.120000e-177 632.0
36 TraesCS3D01G011400 chr6A 91.643 347 23 4 1771 2117 609886914 609887254 3.790000e-130 475.0
37 TraesCS3D01G011400 chr6A 93.367 196 13 0 2028 2223 609887263 609887458 1.470000e-74 291.0


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 TraesCS3D01G011400 chr3D 4074960 4079148 4188 False 7736.000000 7736 100.000000 1 4189 1 chr3D.!!$F1 4188
1 TraesCS3D01G011400 chr3D 28380916 28382982 2066 True 1406.000000 1406 79.254000 1064 3122 1 chr3D.!!$R1 2058
2 TraesCS3D01G011400 chr3D 4166373 4170300 3927 True 924.180000 1960 93.602000 1 3972 5 chr3D.!!$R2 3971
3 TraesCS3D01G011400 chrUn 246338519 246342379 3860 False 2749.500000 4492 91.975500 1 3804 2 chrUn.!!$F4 3803
4 TraesCS3D01G011400 chr3B 6392619 6396479 3860 False 2749.500000 4492 91.975500 1 3804 2 chr3B.!!$F1 3803
5 TraesCS3D01G011400 chr3B 13936082 13939516 3434 True 729.000000 1445 87.721667 988 3859 3 chr3B.!!$R3 2871
6 TraesCS3D01G011400 chr3B 6664807 6667670 2863 True 689.850000 2331 83.939500 1146 4188 4 chr3B.!!$R2 3042
7 TraesCS3D01G011400 chr3A 9612214 9616254 4040 False 1217.750000 2447 92.227750 1 4163 4 chr3A.!!$F1 4162
8 TraesCS3D01G011400 chr3A 9776995 9781388 4393 True 732.666667 1801 89.054833 1 4160 6 chr3A.!!$R1 4159
9 TraesCS3D01G011400 chr6A 609885848 609889310 3462 False 648.833333 924 90.734500 1 4163 6 chr6A.!!$F1 4162

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
551 926 0.456221 GATCTCTGTTCCGCCTTCGA 59.544 55.0 0.0 0.00 38.10 3.71 F
1030 1557 0.309302 CGTTGCATTTCCACGTTCCA 59.691 50.0 0.0 0.00 0.00 3.53 F
1573 2105 0.727398 GCCTTCACGTGGATACTTGC 59.273 55.0 17.0 5.61 37.61 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 2078 0.518636 CCACGTGAAGGCTCAACATG 59.481 55.0 19.30 0.0 31.88 3.21 R
2864 4466 0.539986 GATCCACGTTCCTTAGCCCA 59.460 55.0 0.00 0.0 0.00 5.36 R
3223 4871 0.041386 ACCTGAGGTGGGTAGAGGAC 59.959 60.0 1.77 0.0 32.98 3.85 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
25 26 3.489355 TGTCTCACCAAATGCAATGACT 58.511 40.909 4.54 0.00 0.00 3.41
29 30 4.828939 TCTCACCAAATGCAATGACTCTTT 59.171 37.500 4.54 0.00 0.00 2.52
50 51 2.706890 TGGCTCTTTCGGTGAATAACC 58.293 47.619 0.00 0.00 46.60 2.85
83 84 0.534203 ATCATAATCCCGCGGCGTTT 60.534 50.000 22.85 16.19 0.00 3.60
84 85 1.010125 CATAATCCCGCGGCGTTTG 60.010 57.895 22.85 5.67 0.00 2.93
177 178 1.610522 GAACTGGCTTGTGTTGCTCAT 59.389 47.619 0.00 0.00 0.00 2.90
209 210 1.029947 GCCAACAATACTGTCCCCCG 61.030 60.000 0.00 0.00 33.45 5.73
218 219 1.000739 CTGTCCCCCGTACCTGGTA 59.999 63.158 1.49 1.49 0.00 3.25
240 241 1.019805 GTACCGGCCTTCTCTGTTGC 61.020 60.000 0.00 0.00 0.00 4.17
285 286 0.779997 AGGATTGCAGTTTCACCCCT 59.220 50.000 0.00 0.00 0.00 4.79
387 388 0.467384 AGCGGGATGACATTCAGGAG 59.533 55.000 0.00 0.00 0.00 3.69
551 926 0.456221 GATCTCTGTTCCGCCTTCGA 59.544 55.000 0.00 0.00 38.10 3.71
576 960 1.063717 CCTGGATGGTGGGCAGTTATT 60.064 52.381 0.00 0.00 0.00 1.40
580 964 3.096092 GGATGGTGGGCAGTTATTGAAA 58.904 45.455 0.00 0.00 0.00 2.69
676 1067 6.019318 CCAAAGCTTCAAACATTTCTGTGAAG 60.019 38.462 0.00 7.69 37.96 3.02
684 1075 7.428020 TCAAACATTTCTGTGAAGAATGAAGG 58.572 34.615 2.66 0.00 35.22 3.46
707 1098 3.574354 AGGAGGAAATGAGATGAAGCC 57.426 47.619 0.00 0.00 0.00 4.35
709 1100 2.948315 GGAGGAAATGAGATGAAGCCAC 59.052 50.000 0.00 0.00 0.00 5.01
772 1250 5.104485 GGCTACCTTTCTTCCTTATCTTCCA 60.104 44.000 0.00 0.00 0.00 3.53
841 1350 6.321181 AGTTTGACTAAGAAAACCAGCAATCA 59.679 34.615 0.00 0.00 37.04 2.57
842 1351 5.947228 TGACTAAGAAAACCAGCAATCAG 57.053 39.130 0.00 0.00 0.00 2.90
843 1352 4.761739 TGACTAAGAAAACCAGCAATCAGG 59.238 41.667 0.00 0.00 0.00 3.86
844 1353 4.729868 ACTAAGAAAACCAGCAATCAGGT 58.270 39.130 0.00 0.00 40.61 4.00
845 1354 4.520492 ACTAAGAAAACCAGCAATCAGGTG 59.480 41.667 0.00 0.00 45.23 4.00
850 1359 4.084265 CAGCAATCAGGTGGCACA 57.916 55.556 20.82 0.00 41.98 4.57
906 1423 4.009675 TCAGTCCATATGCACCAGAAAAC 58.990 43.478 0.00 0.00 0.00 2.43
928 1445 3.618594 CACGTATGTCATTCAAGACCAGG 59.381 47.826 0.00 0.00 37.73 4.45
960 1477 9.990360 ATAATTAGCCTTCTTCTTAACTCTAGC 57.010 33.333 0.00 0.00 0.00 3.42
964 1481 4.425520 CCTTCTTCTTAACTCTAGCACCG 58.574 47.826 0.00 0.00 0.00 4.94
1029 1556 0.386731 CCGTTGCATTTCCACGTTCC 60.387 55.000 7.07 0.00 0.00 3.62
1030 1557 0.309302 CGTTGCATTTCCACGTTCCA 59.691 50.000 0.00 0.00 0.00 3.53
1042 1569 5.423704 TCCACGTTCCATTATACTCCAAA 57.576 39.130 0.00 0.00 0.00 3.28
1049 1576 8.044908 ACGTTCCATTATACTCCAAACATTAGT 58.955 33.333 0.00 0.00 0.00 2.24
1075 1602 4.164221 TCTCCTCCACACTTTCAGTTCTTT 59.836 41.667 0.00 0.00 0.00 2.52
1104 1631 4.207165 AGACTGGAGCAGAAGATACTCTC 58.793 47.826 0.00 0.00 35.18 3.20
1105 1632 3.951037 GACTGGAGCAGAAGATACTCTCA 59.049 47.826 0.00 0.00 35.18 3.27
1170 1697 4.331968 ACATCAAGCATCCTTTCCGTTTA 58.668 39.130 0.00 0.00 0.00 2.01
1171 1698 4.396166 ACATCAAGCATCCTTTCCGTTTAG 59.604 41.667 0.00 0.00 0.00 1.85
1546 2078 5.180680 ACCGTGCTTTCTTATTGGTCTAAAC 59.819 40.000 0.00 0.00 0.00 2.01
1561 2093 4.083271 GGTCTAAACATGTTGAGCCTTCAC 60.083 45.833 17.14 9.97 31.71 3.18
1573 2105 0.727398 GCCTTCACGTGGATACTTGC 59.273 55.000 17.00 5.61 37.61 4.01
1708 2252 5.708736 TTTTGCTCCCTGGACATATTCTA 57.291 39.130 0.00 0.00 0.00 2.10
1721 2265 7.674120 TGGACATATTCTAGGATCATCAACAG 58.326 38.462 0.00 0.00 0.00 3.16
1897 2455 8.697507 AGTTCAAACATCCTAAATCAGACTTT 57.302 30.769 0.00 0.00 0.00 2.66
2195 3762 7.341805 ACTGGCTAACAAAGATATCAGTTGAT 58.658 34.615 20.17 13.57 38.51 2.57
2846 4448 3.093814 TGTCTACAGCTTCGGGATGTTA 58.906 45.455 5.65 0.00 42.37 2.41
2864 4466 1.344953 TATTGCTGGAGATGGCCGGT 61.345 55.000 1.90 0.00 36.65 5.28
2897 4502 1.519455 GGATCCACGAGCGTCAAGG 60.519 63.158 6.95 0.00 0.00 3.61
2938 4543 3.251729 GCATGGGTATACAATCAGCTGTG 59.748 47.826 14.67 8.27 0.00 3.66
3041 4684 0.820226 TCCAGATGAAGCCAGACGAG 59.180 55.000 0.00 0.00 0.00 4.18
3206 4854 6.923508 CAGAGTGAAATGCCTATACATCGTAA 59.076 38.462 0.00 0.00 0.00 3.18
3207 4855 6.924060 AGAGTGAAATGCCTATACATCGTAAC 59.076 38.462 0.00 0.00 0.00 2.50
3223 4871 6.699642 ACATCGTAACTTTGGACCAAATTTTG 59.300 34.615 23.01 17.88 32.70 2.44
3266 4990 4.726416 CGCTCAGCAAGTCAATATTTGTT 58.274 39.130 0.00 0.00 0.00 2.83
3267 4991 5.156355 CGCTCAGCAAGTCAATATTTGTTT 58.844 37.500 0.00 0.00 0.00 2.83
3268 4992 5.630680 CGCTCAGCAAGTCAATATTTGTTTT 59.369 36.000 0.00 0.00 0.00 2.43
3269 4993 6.399249 CGCTCAGCAAGTCAATATTTGTTTTG 60.399 38.462 0.00 0.00 0.00 2.44
3270 4994 6.128742 GCTCAGCAAGTCAATATTTGTTTTGG 60.129 38.462 0.00 0.00 0.00 3.28
3271 4995 7.048629 TCAGCAAGTCAATATTTGTTTTGGA 57.951 32.000 0.00 0.00 0.00 3.53
3272 4996 7.495901 TCAGCAAGTCAATATTTGTTTTGGAA 58.504 30.769 0.00 0.00 0.00 3.53
3273 4997 7.652909 TCAGCAAGTCAATATTTGTTTTGGAAG 59.347 33.333 0.00 0.00 0.00 3.46
3275 4999 6.705825 GCAAGTCAATATTTGTTTTGGAAGGT 59.294 34.615 0.00 0.00 0.00 3.50
3278 5002 8.661352 AGTCAATATTTGTTTTGGAAGGTTTG 57.339 30.769 0.00 0.00 0.00 2.93
3279 5003 8.482128 AGTCAATATTTGTTTTGGAAGGTTTGA 58.518 29.630 0.00 0.00 0.00 2.69
3280 5004 9.103861 GTCAATATTTGTTTTGGAAGGTTTGAA 57.896 29.630 0.00 0.00 0.00 2.69
3282 5006 9.934190 CAATATTTGTTTTGGAAGGTTTGAAAG 57.066 29.630 0.00 0.00 0.00 2.62
3284 5008 6.793492 TTTGTTTTGGAAGGTTTGAAAGTG 57.207 33.333 0.00 0.00 0.00 3.16
3287 5011 6.994221 TGTTTTGGAAGGTTTGAAAGTGTAA 58.006 32.000 0.00 0.00 0.00 2.41
3288 5012 7.093992 TGTTTTGGAAGGTTTGAAAGTGTAAG 58.906 34.615 0.00 0.00 0.00 2.34
3289 5013 7.039644 TGTTTTGGAAGGTTTGAAAGTGTAAGA 60.040 33.333 0.00 0.00 0.00 2.10
3290 5014 7.654022 TTTGGAAGGTTTGAAAGTGTAAGAT 57.346 32.000 0.00 0.00 0.00 2.40
3292 5016 8.754991 TTGGAAGGTTTGAAAGTGTAAGATTA 57.245 30.769 0.00 0.00 0.00 1.75
3294 5018 9.010029 TGGAAGGTTTGAAAGTGTAAGATTATC 57.990 33.333 0.00 0.00 0.00 1.75
3296 5020 9.232473 GAAGGTTTGAAAGTGTAAGATTATCCT 57.768 33.333 0.00 0.00 0.00 3.24
3297 5021 9.588096 AAGGTTTGAAAGTGTAAGATTATCCTT 57.412 29.630 0.00 0.00 0.00 3.36
3298 5022 9.014297 AGGTTTGAAAGTGTAAGATTATCCTTG 57.986 33.333 0.00 0.00 0.00 3.61
3299 5023 8.244113 GGTTTGAAAGTGTAAGATTATCCTTGG 58.756 37.037 0.00 0.00 0.00 3.61
3301 5025 8.934023 TTGAAAGTGTAAGATTATCCTTGGTT 57.066 30.769 0.00 0.00 0.00 3.67
3303 5027 9.667107 TGAAAGTGTAAGATTATCCTTGGTTAG 57.333 33.333 0.00 0.00 0.00 2.34
3309 5033 9.627123 TGTAAGATTATCCTTGGTTAGATTTGG 57.373 33.333 0.00 0.00 0.00 3.28
3315 5054 5.431179 TCCTTGGTTAGATTTGGACCTAC 57.569 43.478 0.00 0.00 34.52 3.18
3326 5065 2.112279 TGGACCTACCACAGAAGGTT 57.888 50.000 0.00 0.00 46.22 3.50
3327 5066 1.975680 TGGACCTACCACAGAAGGTTC 59.024 52.381 0.00 0.00 46.22 3.62
3328 5067 2.258109 GGACCTACCACAGAAGGTTCT 58.742 52.381 0.00 0.00 46.22 3.01
3329 5068 4.576137 TGGACCTACCACAGAAGGTTCTG 61.576 52.174 16.57 16.57 46.22 3.02
3350 5089 4.522114 TGTTGTGTCCAATGTGAAGAAGA 58.478 39.130 0.00 0.00 32.11 2.87
3351 5090 5.132502 TGTTGTGTCCAATGTGAAGAAGAT 58.867 37.500 0.00 0.00 32.11 2.40
3352 5091 6.295249 TGTTGTGTCCAATGTGAAGAAGATA 58.705 36.000 0.00 0.00 32.11 1.98
3353 5092 6.204688 TGTTGTGTCCAATGTGAAGAAGATAC 59.795 38.462 0.00 0.00 32.11 2.24
3354 5093 6.114187 TGTGTCCAATGTGAAGAAGATACT 57.886 37.500 0.00 0.00 0.00 2.12
3355 5094 6.166279 TGTGTCCAATGTGAAGAAGATACTC 58.834 40.000 0.00 0.00 0.00 2.59
3356 5095 6.014242 TGTGTCCAATGTGAAGAAGATACTCT 60.014 38.462 0.00 0.00 0.00 3.24
3357 5096 6.876257 GTGTCCAATGTGAAGAAGATACTCTT 59.124 38.462 0.00 0.00 39.87 2.85
3358 5097 7.389053 GTGTCCAATGTGAAGAAGATACTCTTT 59.611 37.037 0.00 0.00 36.73 2.52
3359 5098 7.939039 TGTCCAATGTGAAGAAGATACTCTTTT 59.061 33.333 0.00 0.00 36.73 2.27
3360 5099 8.447053 GTCCAATGTGAAGAAGATACTCTTTTC 58.553 37.037 0.00 0.00 36.73 2.29
3361 5100 8.378565 TCCAATGTGAAGAAGATACTCTTTTCT 58.621 33.333 10.36 0.00 36.73 2.52
3362 5101 9.007901 CCAATGTGAAGAAGATACTCTTTTCTT 57.992 33.333 0.00 0.00 42.21 2.52
3654 5440 1.086634 GCAGGAAGAGATGGCGTGAC 61.087 60.000 0.00 0.00 0.00 3.67
3849 5708 2.155279 GAAGAACCAAAGGAGAGGTGC 58.845 52.381 0.00 0.00 38.37 5.01
3893 5805 1.880027 AGGTTACTGAAAGCTTTGCCG 59.120 47.619 18.30 6.91 43.37 5.69
3917 5852 6.036517 CGTTCTTCTTATGCTCTGCTTGTTAT 59.963 38.462 0.00 0.00 0.00 1.89
4073 6095 3.861569 GTTCAGGAACTCTGTTTCACG 57.138 47.619 4.95 0.00 43.76 4.35
4147 6169 3.441922 TGTGCTGTTTGTTGCTAGTTCAA 59.558 39.130 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.631160 TCACCGAAAGAGCCAAAAGA 57.369 45.000 0.00 0.00 0.00 2.52
29 30 3.078837 GGTTATTCACCGAAAGAGCCAA 58.921 45.455 0.00 0.00 35.12 4.52
50 51 7.752239 GCGGGATTATGATATCAAATCTGTTTG 59.248 37.037 24.22 16.52 44.81 2.93
51 52 7.361201 CGCGGGATTATGATATCAAATCTGTTT 60.361 37.037 24.22 7.93 31.66 2.83
53 54 5.582269 CGCGGGATTATGATATCAAATCTGT 59.418 40.000 24.22 9.00 31.66 3.41
83 84 4.035792 CACAGTGGTTTCAAACGGTATTCA 59.964 41.667 0.00 0.00 0.00 2.57
84 85 4.533222 CACAGTGGTTTCAAACGGTATTC 58.467 43.478 0.00 0.00 0.00 1.75
177 178 0.178967 TGTTGGCCCAATCTCTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
218 219 1.276622 ACAGAGAAGGCCGGTACAAT 58.723 50.000 1.90 0.00 0.00 2.71
240 241 4.489810 ACGCTGTTCAAGAGAGTTGATAG 58.510 43.478 0.00 0.00 0.00 2.08
285 286 9.557061 CTAGTCTATACATACCTGACAGTTACA 57.443 37.037 0.93 0.00 0.00 2.41
306 307 5.023533 TGCCACCAATCTATCAACTAGTC 57.976 43.478 0.00 0.00 0.00 2.59
343 344 0.846693 AATCATGGACTAGGTGCCCC 59.153 55.000 0.00 0.00 0.00 5.80
387 388 3.932710 TGCAATCGACTACAGATTTGGTC 59.067 43.478 0.00 0.00 36.30 4.02
580 964 2.633488 GCAACTAGCGAGGGAGATTTT 58.367 47.619 0.00 0.00 0.00 1.82
592 976 0.890996 ACAGGGCAACAGCAACTAGC 60.891 55.000 0.00 0.00 46.19 3.42
596 980 0.675633 ATCAACAGGGCAACAGCAAC 59.324 50.000 0.00 0.00 39.74 4.17
676 1067 6.653989 TCTCATTTCCTCCTTACCTTCATTC 58.346 40.000 0.00 0.00 0.00 2.67
684 1075 4.819088 GGCTTCATCTCATTTCCTCCTTAC 59.181 45.833 0.00 0.00 0.00 2.34
772 1250 2.887152 GACTTGTCAAAGGCAACATCCT 59.113 45.455 0.00 0.00 41.57 3.24
843 1352 2.203337 TCAAGCCTGGTGTGCCAC 60.203 61.111 0.00 0.00 40.46 5.01
844 1353 1.414866 TAGTCAAGCCTGGTGTGCCA 61.415 55.000 0.00 0.00 43.73 4.92
845 1354 0.035056 ATAGTCAAGCCTGGTGTGCC 60.035 55.000 0.00 0.00 0.00 5.01
846 1355 1.740025 GAATAGTCAAGCCTGGTGTGC 59.260 52.381 0.00 0.00 0.00 4.57
847 1356 3.340814 AGAATAGTCAAGCCTGGTGTG 57.659 47.619 0.00 0.00 0.00 3.82
848 1357 3.307762 GGAAGAATAGTCAAGCCTGGTGT 60.308 47.826 0.00 0.00 0.00 4.16
849 1358 3.054802 AGGAAGAATAGTCAAGCCTGGTG 60.055 47.826 0.00 0.00 0.00 4.17
850 1359 3.185455 AGGAAGAATAGTCAAGCCTGGT 58.815 45.455 0.00 0.00 0.00 4.00
851 1360 3.454082 AGAGGAAGAATAGTCAAGCCTGG 59.546 47.826 3.70 0.00 0.00 4.45
852 1361 4.751767 AGAGGAAGAATAGTCAAGCCTG 57.248 45.455 3.70 0.00 0.00 4.85
906 1423 3.618594 CCTGGTCTTGAATGACATACGTG 59.381 47.826 0.00 0.00 38.61 4.49
928 1445 6.852858 AAGAAGAAGGCTAATTATCGAAGC 57.147 37.500 0.00 0.00 35.47 3.86
973 1500 0.179702 TCACAGATGCAGGATCAGGC 59.820 55.000 4.52 0.00 32.86 4.85
974 1501 2.562635 CTTCACAGATGCAGGATCAGG 58.437 52.381 4.52 0.00 32.86 3.86
975 1502 1.941294 GCTTCACAGATGCAGGATCAG 59.059 52.381 4.52 0.00 33.71 2.90
976 1503 1.558294 AGCTTCACAGATGCAGGATCA 59.442 47.619 4.52 0.00 35.57 2.92
977 1504 2.158928 AGAGCTTCACAGATGCAGGATC 60.159 50.000 7.49 0.00 35.57 3.36
978 1505 1.838715 AGAGCTTCACAGATGCAGGAT 59.161 47.619 7.49 0.00 35.57 3.24
979 1506 1.206610 GAGAGCTTCACAGATGCAGGA 59.793 52.381 7.49 0.00 35.57 3.86
980 1507 1.066358 TGAGAGCTTCACAGATGCAGG 60.066 52.381 7.49 0.00 35.57 4.85
981 1508 2.381725 TGAGAGCTTCACAGATGCAG 57.618 50.000 7.49 0.00 35.57 4.41
982 1509 2.235402 TCATGAGAGCTTCACAGATGCA 59.765 45.455 7.49 0.00 38.99 3.96
1042 1569 6.875972 AAGTGTGGAGGAGATTACTAATGT 57.124 37.500 0.00 0.00 0.00 2.71
1075 1602 1.644509 TCTGCTCCAGTCTTGGCTAA 58.355 50.000 0.00 0.00 44.63 3.09
1153 1680 3.610911 CTCCTAAACGGAAAGGATGCTT 58.389 45.455 0.00 0.00 42.53 3.91
1171 1698 2.670148 AACCAGGCGGATCACCTCC 61.670 63.158 3.60 0.00 41.06 4.30
1546 2078 0.518636 CCACGTGAAGGCTCAACATG 59.481 55.000 19.30 0.00 31.88 3.21
1561 2093 1.134401 AGTCATGGGCAAGTATCCACG 60.134 52.381 0.00 0.00 35.67 4.94
1721 2265 4.583489 ACCTCATTGAATCATTCAGGCATC 59.417 41.667 0.00 0.00 41.38 3.91
1897 2455 1.339535 TGTCGATGCCAACAATAGCCA 60.340 47.619 0.00 0.00 0.00 4.75
2195 3762 0.687354 GGAGGAACCTCTCAACTGCA 59.313 55.000 18.54 0.00 42.38 4.41
2846 4448 2.194056 CCGGCCATCTCCAGCAAT 59.806 61.111 2.24 0.00 0.00 3.56
2864 4466 0.539986 GATCCACGTTCCTTAGCCCA 59.460 55.000 0.00 0.00 0.00 5.36
2897 4502 1.722636 CCGGGTAGTACGTCTGGCTC 61.723 65.000 0.00 0.00 0.00 4.70
2924 4529 1.066215 TGCCGACACAGCTGATTGTAT 60.066 47.619 23.35 0.00 0.00 2.29
2938 4543 2.358737 CACCCACCTCTTGCCGAC 60.359 66.667 0.00 0.00 0.00 4.79
3174 4821 4.564782 AGGCATTTCACTCTGAGAATGA 57.435 40.909 12.44 2.62 32.12 2.57
3223 4871 0.041386 ACCTGAGGTGGGTAGAGGAC 59.959 60.000 1.77 0.00 32.98 3.85
3266 4990 7.654022 ATCTTACACTTTCAAACCTTCCAAA 57.346 32.000 0.00 0.00 0.00 3.28
3267 4991 7.654022 AATCTTACACTTTCAAACCTTCCAA 57.346 32.000 0.00 0.00 0.00 3.53
3268 4992 8.934023 ATAATCTTACACTTTCAAACCTTCCA 57.066 30.769 0.00 0.00 0.00 3.53
3269 4993 8.459635 GGATAATCTTACACTTTCAAACCTTCC 58.540 37.037 0.00 0.00 0.00 3.46
3270 4994 9.232473 AGGATAATCTTACACTTTCAAACCTTC 57.768 33.333 0.00 0.00 0.00 3.46
3271 4995 9.588096 AAGGATAATCTTACACTTTCAAACCTT 57.412 29.630 0.00 0.00 0.00 3.50
3272 4996 9.014297 CAAGGATAATCTTACACTTTCAAACCT 57.986 33.333 0.00 0.00 0.00 3.50
3273 4997 8.244113 CCAAGGATAATCTTACACTTTCAAACC 58.756 37.037 0.00 0.00 0.00 3.27
3275 4999 8.934023 ACCAAGGATAATCTTACACTTTCAAA 57.066 30.769 0.00 0.00 0.00 2.69
3278 5002 9.886132 TCTAACCAAGGATAATCTTACACTTTC 57.114 33.333 0.00 0.00 0.00 2.62
3284 5008 9.847224 TCCAAATCTAACCAAGGATAATCTTAC 57.153 33.333 0.00 0.00 0.00 2.34
3287 5011 7.129504 AGGTCCAAATCTAACCAAGGATAATCT 59.870 37.037 0.00 0.00 35.43 2.40
3288 5012 7.290813 AGGTCCAAATCTAACCAAGGATAATC 58.709 38.462 0.00 0.00 35.43 1.75
3289 5013 7.226059 AGGTCCAAATCTAACCAAGGATAAT 57.774 36.000 0.00 0.00 35.43 1.28
3290 5014 6.652205 AGGTCCAAATCTAACCAAGGATAA 57.348 37.500 0.00 0.00 35.43 1.75
3292 5016 5.104067 GGTAGGTCCAAATCTAACCAAGGAT 60.104 44.000 0.00 0.00 35.43 3.24
3294 5018 4.018779 TGGTAGGTCCAAATCTAACCAAGG 60.019 45.833 0.00 0.00 44.12 3.61
3308 5032 2.258109 AGAACCTTCTGTGGTAGGTCC 58.742 52.381 0.00 0.00 41.41 4.46
3320 5059 3.632145 ACATTGGACACAACAGAACCTTC 59.368 43.478 0.00 0.00 39.87 3.46
3324 5063 4.335315 TCTTCACATTGGACACAACAGAAC 59.665 41.667 0.00 0.00 39.87 3.01
3326 5065 4.149511 TCTTCACATTGGACACAACAGA 57.850 40.909 0.00 0.00 39.87 3.41
3327 5066 4.576053 TCTTCTTCACATTGGACACAACAG 59.424 41.667 0.00 0.00 39.87 3.16
3328 5067 4.522114 TCTTCTTCACATTGGACACAACA 58.478 39.130 0.00 0.00 39.87 3.33
3329 5068 5.695851 ATCTTCTTCACATTGGACACAAC 57.304 39.130 0.00 0.00 39.87 3.32
3330 5069 6.533730 AGTATCTTCTTCACATTGGACACAA 58.466 36.000 0.00 0.00 41.59 3.33
3331 5070 6.114187 AGTATCTTCTTCACATTGGACACA 57.886 37.500 0.00 0.00 0.00 3.72
3332 5071 6.654793 GAGTATCTTCTTCACATTGGACAC 57.345 41.667 0.00 0.00 0.00 3.67
3397 5137 7.332430 ACAATTTGCATCATCATTTTCGATGTT 59.668 29.630 0.00 0.00 42.82 2.71
3654 5440 0.819259 ATGAAACCCCGGCATGATCG 60.819 55.000 0.00 0.00 0.00 3.69
3849 5708 0.396695 ATTGCAGCAGATGGGAAGGG 60.397 55.000 0.00 0.00 0.00 3.95
3893 5805 5.619625 AACAAGCAGAGCATAAGAAGAAC 57.380 39.130 0.00 0.00 0.00 3.01
3917 5852 3.351794 TGTGTGGGTGTGTAACTTGAA 57.648 42.857 0.00 0.00 38.04 2.69
4049 6071 4.876107 GTGAAACAGAGTTCCTGAACTTCA 59.124 41.667 13.40 9.87 44.08 3.02
4072 6094 0.934496 TCCGTGTCTGAACTTTTGCG 59.066 50.000 0.00 0.00 0.00 4.85
4073 6095 1.264288 CCTCCGTGTCTGAACTTTTGC 59.736 52.381 0.00 0.00 0.00 3.68
4147 6169 6.058183 CCTCACCGGAGATTATGATCTTTTT 58.942 40.000 9.46 0.00 42.66 1.94


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

AutoCloner maintained by Alex Coulton.