Multiple sequence alignment - TraesCS6D01G069400

Loading Multiple Alignment...

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 TraesCS6D01G069400 chr6D 100.000 4192 0 0 1 4192 34926251 34930442 0.000000e+00 7742.0
1 TraesCS6D01G069400 chr6D 90.450 2000 104 35 1355 3294 34735995 34734023 0.000000e+00 2555.0
2 TraesCS6D01G069400 chr6D 78.520 1108 94 71 355 1358 34737096 34736029 2.790000e-166 595.0
3 TraesCS6D01G069400 chr6D 88.596 342 26 8 1399 1735 34647729 34648062 1.820000e-108 403.0
4 TraesCS6D01G069400 chr6D 88.959 317 33 2 2043 2359 34648153 34648467 1.410000e-104 390.0
5 TraesCS6D01G069400 chr6D 88.789 223 13 6 938 1153 34594067 34594284 3.210000e-66 263.0
6 TraesCS6D01G069400 chr6D 85.052 194 15 9 1171 1358 34611858 34612043 7.160000e-43 185.0
7 TraesCS6D01G069400 chr6D 74.522 628 60 56 355 916 34593400 34593993 9.260000e-42 182.0
8 TraesCS6D01G069400 chr6D 84.559 136 8 3 11 135 34591624 34591757 5.690000e-24 122.0
9 TraesCS6D01G069400 chr6D 94.737 57 3 0 13 69 34737505 34737449 5.770000e-14 89.8
10 TraesCS6D01G069400 chr6D 100.000 39 0 0 161 199 34737300 34737262 5.810000e-09 73.1
11 TraesCS6D01G069400 chr6B 90.843 3298 150 48 155 3348 71838943 71842192 0.000000e+00 4277.0
12 TraesCS6D01G069400 chr6B 91.816 1845 100 24 1422 3238 71707594 71705773 0.000000e+00 2523.0
13 TraesCS6D01G069400 chr6B 86.509 593 53 14 1296 1885 71591210 71591778 9.890000e-176 627.0
14 TraesCS6D01G069400 chr6B 85.333 450 26 20 941 1358 71708150 71707709 2.990000e-116 429.0
15 TraesCS6D01G069400 chr6B 91.060 302 23 3 2043 2344 71591761 71592058 5.050000e-109 405.0
16 TraesCS6D01G069400 chr6B 76.406 640 48 49 355 916 71708823 71708209 2.500000e-62 250.0
17 TraesCS6D01G069400 chr6B 75.518 531 46 43 381 865 71590646 71591138 2.570000e-42 183.0
18 TraesCS6D01G069400 chr6B 85.350 157 14 3 1 151 71838748 71838901 2.020000e-33 154.0
19 TraesCS6D01G069400 chr6B 80.383 209 20 8 1 199 71709186 71708989 5.650000e-29 139.0
20 TraesCS6D01G069400 chr6B 86.325 117 6 1 1 107 71585044 71585160 7.360000e-23 119.0
21 TraesCS6D01G069400 chr6B 93.617 47 1 2 867 911 71591156 71591202 7.520000e-08 69.4
22 TraesCS6D01G069400 chr6A 89.872 3278 129 66 188 3348 39129361 39132552 0.000000e+00 4026.0
23 TraesCS6D01G069400 chr6A 89.851 1941 119 38 1355 3240 39048943 39047026 0.000000e+00 2422.0
24 TraesCS6D01G069400 chr6A 77.113 1136 80 85 355 1358 39050061 39048974 3.770000e-135 492.0
25 TraesCS6D01G069400 chr6A 83.432 338 41 10 2154 2477 39002137 39002473 2.450000e-77 300.0
26 TraesCS6D01G069400 chr6A 82.275 378 35 13 1087 1433 38870883 38871259 8.810000e-77 298.0
27 TraesCS6D01G069400 chr6A 90.455 220 18 1 2362 2581 39001926 39002142 1.910000e-73 287.0
28 TraesCS6D01G069400 chr6A 94.152 171 10 0 1427 1597 38893080 38893250 1.160000e-65 261.0
29 TraesCS6D01G069400 chr6A 88.535 157 11 2 1 151 39129145 39129300 2.570000e-42 183.0
30 TraesCS6D01G069400 chr6A 74.520 573 64 45 412 930 38869885 38870429 1.550000e-39 174.0
31 TraesCS6D01G069400 chr6A 82.993 147 18 5 1 140 39050468 39050322 4.400000e-25 126.0
32 TraesCS6D01G069400 chr6A 92.188 64 5 0 155 218 38869622 38869685 1.600000e-14 91.6
33 TraesCS6D01G069400 chr6A 97.778 45 1 0 155 199 39050272 39050228 1.250000e-10 78.7
34 TraesCS6D01G069400 chr6A 91.304 46 1 2 1030 1075 38870846 38870888 4.530000e-05 60.2
35 TraesCS6D01G069400 chr4D 91.404 826 70 1 3367 4192 447649903 447650727 0.000000e+00 1131.0
36 TraesCS6D01G069400 chr3D 91.283 826 71 1 3367 4192 253380557 253381381 0.000000e+00 1125.0
37 TraesCS6D01G069400 chr3D 88.996 827 87 4 3367 4192 19891883 19892706 0.000000e+00 1020.0
38 TraesCS6D01G069400 chr7B 89.238 827 86 3 3367 4192 219653316 219654140 0.000000e+00 1031.0
39 TraesCS6D01G069400 chr2B 88.150 827 93 4 3367 4192 489828591 489827769 0.000000e+00 979.0
40 TraesCS6D01G069400 chr5B 87.636 825 99 3 3369 4192 299905462 299904640 0.000000e+00 955.0
41 TraesCS6D01G069400 chr4A 86.962 836 99 6 3359 4192 195990811 195991638 0.000000e+00 931.0
42 TraesCS6D01G069400 chr4A 87.062 827 98 5 3367 4192 195979719 195980537 0.000000e+00 926.0
43 TraesCS6D01G069400 chr3B 85.386 828 115 6 3367 4192 445199408 445198585 0.000000e+00 854.0
44 TraesCS6D01G069400 chr3B 91.237 194 12 4 2472 2661 424780841 424781033 4.160000e-65 259.0
45 TraesCS6D01G069400 chr1D 94.841 252 13 0 2466 2717 308198065 308197814 1.090000e-105 394.0
46 TraesCS6D01G069400 chr1D 97.619 42 1 0 2948 2989 308197818 308197777 5.810000e-09 73.1
47 TraesCS6D01G069400 chr5D 91.729 266 19 1 2441 2706 455834383 455834645 2.380000e-97 366.0
48 TraesCS6D01G069400 chr5A 92.683 205 12 2 2830 3031 652055853 652055649 4.100000e-75 292.0
49 TraesCS6D01G069400 chr3A 93.846 130 8 0 2541 2670 49472908 49472779 3.310000e-46 196.0


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 TraesCS6D01G069400 chr6D 34926251 34930442 4191 False 7742.000 7742 100.00000 1 4192 1 chr6D.!!$F2 4191
1 TraesCS6D01G069400 chr6D 34734023 34737505 3482 True 828.225 2555 90.92675 13 3294 4 chr6D.!!$R1 3281
2 TraesCS6D01G069400 chr6D 34647729 34648467 738 False 396.500 403 88.77750 1399 2359 2 chr6D.!!$F4 960
3 TraesCS6D01G069400 chr6B 71838748 71842192 3444 False 2215.500 4277 88.09650 1 3348 2 chr6B.!!$F3 3347
4 TraesCS6D01G069400 chr6B 71705773 71709186 3413 True 835.250 2523 83.48450 1 3238 4 chr6B.!!$R1 3237
5 TraesCS6D01G069400 chr6B 71590646 71592058 1412 False 321.100 627 86.67600 381 2344 4 chr6B.!!$F2 1963
6 TraesCS6D01G069400 chr6A 39129145 39132552 3407 False 2104.500 4026 89.20350 1 3348 2 chr6A.!!$F4 3347
7 TraesCS6D01G069400 chr6A 39047026 39050468 3442 True 779.675 2422 86.93375 1 3240 4 chr6A.!!$R1 3239
8 TraesCS6D01G069400 chr6A 39001926 39002473 547 False 293.500 300 86.94350 2154 2581 2 chr6A.!!$F3 427
9 TraesCS6D01G069400 chr4D 447649903 447650727 824 False 1131.000 1131 91.40400 3367 4192 1 chr4D.!!$F1 825
10 TraesCS6D01G069400 chr3D 253380557 253381381 824 False 1125.000 1125 91.28300 3367 4192 1 chr3D.!!$F2 825
11 TraesCS6D01G069400 chr3D 19891883 19892706 823 False 1020.000 1020 88.99600 3367 4192 1 chr3D.!!$F1 825
12 TraesCS6D01G069400 chr7B 219653316 219654140 824 False 1031.000 1031 89.23800 3367 4192 1 chr7B.!!$F1 825
13 TraesCS6D01G069400 chr2B 489827769 489828591 822 True 979.000 979 88.15000 3367 4192 1 chr2B.!!$R1 825
14 TraesCS6D01G069400 chr5B 299904640 299905462 822 True 955.000 955 87.63600 3369 4192 1 chr5B.!!$R1 823
15 TraesCS6D01G069400 chr4A 195990811 195991638 827 False 931.000 931 86.96200 3359 4192 1 chr4A.!!$F2 833
16 TraesCS6D01G069400 chr4A 195979719 195980537 818 False 926.000 926 87.06200 3367 4192 1 chr4A.!!$F1 825
17 TraesCS6D01G069400 chr3B 445198585 445199408 823 True 854.000 854 85.38600 3367 4192 1 chr3B.!!$R1 825

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
424 541 0.039527 CGATCACGGCGATGATACCA 60.040 55.000 16.62 0.0 39.48 3.25 F
443 563 1.082756 GCGCGGCGATGGATAAAAG 60.083 57.895 28.54 0.0 0.00 2.27 F
2361 2873 0.099968 CCATGCACGATTCTTGGCTG 59.900 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1772 0.038159 CCGGCCAAAAATTAACGGCA 60.038 50.0 2.24 0.00 46.75 5.69 R
2372 2884 0.387202 CGACATGGATCGAAGCTCCT 59.613 55.0 5.20 0.00 45.13 3.69 R
3352 3925 0.036858 GAGACTTTCGGCCAGAAGCT 60.037 55.0 13.51 11.53 43.05 3.74 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
92 103 0.687354 AAACAGCCTCCGATGTCACT 59.313 50.000 0.00 0.00 0.00 3.41
109 120 2.096248 CACTCCGTCCTTCTCTTAGCT 58.904 52.381 0.00 0.00 0.00 3.32
130 145 2.031919 TGGGCGAAATGACGTGCT 59.968 55.556 0.00 0.00 35.59 4.40
135 150 1.868997 CGAAATGACGTGCTTGCCT 59.131 52.632 0.00 0.00 0.00 4.75
138 153 1.174712 AAATGACGTGCTTGCCTGCT 61.175 50.000 0.00 0.00 0.00 4.24
201 260 1.210204 ACACTGCATCCCCATGAGGT 61.210 55.000 0.00 0.00 30.57 3.85
244 307 0.257039 ATAGCAGAACTGGGGGCTTG 59.743 55.000 3.99 0.00 37.79 4.01
332 412 3.872511 TTGCATTGGCCATCTTTACTG 57.127 42.857 6.09 0.00 40.13 2.74
342 422 4.442192 GGCCATCTTTACTGGTAGAGTCAG 60.442 50.000 0.00 0.00 35.96 3.51
360 465 8.558973 AGAGTCAGGATAAATCAAGTTTTGAG 57.441 34.615 0.00 0.00 43.98 3.02
424 541 0.039527 CGATCACGGCGATGATACCA 60.040 55.000 16.62 0.00 39.48 3.25
443 563 1.082756 GCGCGGCGATGGATAAAAG 60.083 57.895 28.54 0.00 0.00 2.27
574 710 5.641209 GCCCTATACATACTTTGCTGATGAG 59.359 44.000 0.00 0.00 0.00 2.90
656 827 3.515286 GGCTGATCCGTCGACCGA 61.515 66.667 10.58 9.74 39.56 4.69
658 829 2.408022 CTGATCCGTCGACCGACC 59.592 66.667 15.74 0.00 41.76 4.79
659 830 3.450559 CTGATCCGTCGACCGACCG 62.451 68.421 15.74 10.18 41.76 4.79
697 872 5.070446 TCTGAAAGGTAGCTTTCTTCTGACA 59.930 40.000 34.86 20.00 42.17 3.58
723 902 4.933330 TCCAAGAACAGCTAGCTATAACG 58.067 43.478 18.86 7.23 0.00 3.18
780 965 5.624159 TCACACTTGATTTTGATCCTCTGT 58.376 37.500 0.00 0.00 0.00 3.41
849 1058 6.645306 TGTATAATGTACTACCTTTGCTGCA 58.355 36.000 0.00 0.00 0.00 4.41
954 1236 1.723542 GATGTGTCACTCACTTGCTCG 59.276 52.381 4.27 0.00 46.27 5.03
1004 1292 3.270839 GCTGAGCTGAGCGATGGC 61.271 66.667 10.09 0.00 40.37 4.40
1235 1545 5.352846 CAGAGCTTGATGATGATGATCCATC 59.647 44.000 5.31 5.31 42.38 3.51
1381 1776 3.864686 CGGCCAAGTCGATTGCCG 61.865 66.667 20.07 20.07 45.38 5.69
1411 1810 0.247736 GCCGGATCTCTGACTGTTGT 59.752 55.000 5.05 0.00 0.00 3.32
1415 1814 3.187227 CCGGATCTCTGACTGTTGTTTTG 59.813 47.826 0.00 0.00 0.00 2.44
1444 1849 4.479993 AGGATGCACGCTCAGGCC 62.480 66.667 0.00 0.00 34.44 5.19
1601 2006 3.482833 GCTCTTCGCTTCAAGATACGTAC 59.517 47.826 0.00 0.00 31.84 3.67
1602 2007 3.677601 TCTTCGCTTCAAGATACGTACG 58.322 45.455 15.01 15.01 0.00 3.67
1603 2008 3.125829 TCTTCGCTTCAAGATACGTACGT 59.874 43.478 25.98 25.98 0.00 3.57
1604 2009 2.777494 TCGCTTCAAGATACGTACGTG 58.223 47.619 30.25 13.59 0.00 4.49
1641 2054 1.542328 CGTGGCCGATGATGGGAAATA 60.542 52.381 0.00 0.00 35.63 1.40
1642 2055 2.582052 GTGGCCGATGATGGGAAATAA 58.418 47.619 0.00 0.00 0.00 1.40
1643 2056 2.955660 GTGGCCGATGATGGGAAATAAA 59.044 45.455 0.00 0.00 0.00 1.40
1686 2105 3.305177 TTAGGGAGCACGCGGTTCC 62.305 63.158 12.47 15.91 45.56 3.62
1771 2202 5.423931 TCCATGGTGCGTGGTGTATATATAT 59.576 40.000 12.58 0.00 41.03 0.86
2138 2605 3.336568 TCGGGGTCGGAGAGGAGT 61.337 66.667 0.00 0.00 36.95 3.85
2359 2871 1.226773 GCCATGCACGATTCTTGGC 60.227 57.895 9.33 9.33 44.05 4.52
2360 2872 1.660560 GCCATGCACGATTCTTGGCT 61.661 55.000 16.22 0.00 45.72 4.75
2361 2873 0.099968 CCATGCACGATTCTTGGCTG 59.900 55.000 0.00 0.00 0.00 4.85
2362 2874 0.524816 CATGCACGATTCTTGGCTGC 60.525 55.000 0.00 0.00 0.00 5.25
2365 2877 0.455633 GCACGATTCTTGGCTGCTTG 60.456 55.000 0.00 0.00 0.00 4.01
2368 2880 2.030893 CACGATTCTTGGCTGCTTGAAA 60.031 45.455 0.00 0.00 0.00 2.69
2369 2881 2.030805 ACGATTCTTGGCTGCTTGAAAC 60.031 45.455 0.00 0.59 0.00 2.78
2370 2882 2.227388 CGATTCTTGGCTGCTTGAAACT 59.773 45.455 0.00 0.00 0.00 2.66
2371 2883 3.436704 CGATTCTTGGCTGCTTGAAACTA 59.563 43.478 0.00 0.00 0.00 2.24
2372 2884 4.083324 CGATTCTTGGCTGCTTGAAACTAA 60.083 41.667 0.00 0.00 0.00 2.24
2373 2885 4.836125 TTCTTGGCTGCTTGAAACTAAG 57.164 40.909 0.00 0.00 0.00 2.18
2374 2886 3.149196 TCTTGGCTGCTTGAAACTAAGG 58.851 45.455 0.00 0.00 0.00 2.69
2910 3437 1.729276 CCGATCGCCATTGTTGCAT 59.271 52.632 10.32 0.00 0.00 3.96
3158 3702 1.071385 CAGGTGCTGGGAGGATATCAC 59.929 57.143 4.83 0.00 0.00 3.06
3213 3760 8.691661 TTGATTGATTCCCTTTATTACTAGCC 57.308 34.615 0.00 0.00 0.00 3.93
3275 3840 1.867363 AGTTCCCTTCCTGCTCGTAT 58.133 50.000 0.00 0.00 0.00 3.06
3285 3850 5.048713 CCTTCCTGCTCGTATTTTGTTTTCT 60.049 40.000 0.00 0.00 0.00 2.52
3291 3862 7.022055 TGCTCGTATTTTGTTTTCTCTTTCA 57.978 32.000 0.00 0.00 0.00 2.69
3294 3865 8.968242 GCTCGTATTTTGTTTTCTCTTTCATTT 58.032 29.630 0.00 0.00 0.00 2.32
3328 3901 9.635520 TGAAGTTTAACTAATTAACTCGAGGAG 57.364 33.333 18.41 6.31 35.52 3.69
3348 3921 7.401955 AGGAGAGGACAATGAAATCAAATTC 57.598 36.000 0.00 0.00 0.00 2.17
3349 3922 6.094603 AGGAGAGGACAATGAAATCAAATTCG 59.905 38.462 0.00 0.00 31.80 3.34
3350 3923 6.094048 GGAGAGGACAATGAAATCAAATTCGA 59.906 38.462 0.00 0.00 31.80 3.71
3351 3924 7.362056 GGAGAGGACAATGAAATCAAATTCGAA 60.362 37.037 0.00 0.00 31.80 3.71
3352 3925 7.885297 AGAGGACAATGAAATCAAATTCGAAA 58.115 30.769 0.00 0.00 31.80 3.46
3353 3926 8.025445 AGAGGACAATGAAATCAAATTCGAAAG 58.975 33.333 0.00 0.00 31.80 2.62
3354 3927 6.587608 AGGACAATGAAATCAAATTCGAAAGC 59.412 34.615 0.00 0.00 31.80 3.51
3355 3928 6.587608 GGACAATGAAATCAAATTCGAAAGCT 59.412 34.615 0.00 0.00 31.80 3.74
3356 3929 7.116805 GGACAATGAAATCAAATTCGAAAGCTT 59.883 33.333 0.00 0.00 31.80 3.74
3357 3930 8.011067 ACAATGAAATCAAATTCGAAAGCTTC 57.989 30.769 0.00 0.82 31.80 3.86
3358 3931 7.869429 ACAATGAAATCAAATTCGAAAGCTTCT 59.131 29.630 0.00 0.00 31.80 2.85
3359 3932 7.807687 ATGAAATCAAATTCGAAAGCTTCTG 57.192 32.000 0.00 0.00 31.80 3.02
3360 3933 6.151691 TGAAATCAAATTCGAAAGCTTCTGG 58.848 36.000 0.00 0.00 31.80 3.86
3361 3934 3.559238 TCAAATTCGAAAGCTTCTGGC 57.441 42.857 0.00 0.00 42.19 4.85
3362 3935 2.228822 TCAAATTCGAAAGCTTCTGGCC 59.771 45.455 0.00 0.00 43.05 5.36
3365 3938 0.250124 TTCGAAAGCTTCTGGCCGAA 60.250 50.000 0.00 7.82 43.05 4.30
3383 3956 4.033990 CGAAAGTCTCGGATCATTCTCA 57.966 45.455 0.00 0.00 44.20 3.27
3540 4114 2.214376 TGGCCCTGGATAACAAACTG 57.786 50.000 0.00 0.00 0.00 3.16
3566 4140 0.879839 ACGGCCAAAGCATTGCAAAC 60.880 50.000 11.91 0.00 42.56 2.93
3600 4174 4.273318 AGTGGATTGGGAATGTTAAGCTC 58.727 43.478 0.00 0.00 0.00 4.09
3693 4267 5.445939 CGACGAACATGGATTAAGGAAGTTG 60.446 44.000 0.00 0.00 0.00 3.16
3705 4279 2.273619 AGGAAGTTGCTGAAGAGGGAT 58.726 47.619 0.00 0.00 0.00 3.85
3726 4300 2.511145 CTTGGCCTCTGCTCGCTC 60.511 66.667 3.32 0.00 37.74 5.03
3783 4357 0.618981 AACTTAAAGAGGGGGAGGCG 59.381 55.000 0.00 0.00 0.00 5.52
3918 4492 5.278808 GGTGGATGACTACTACGATGCATTA 60.279 44.000 0.00 0.00 0.00 1.90
3940 4514 4.736896 GTTCTTCGGCTCGGCGGT 62.737 66.667 7.21 0.00 0.00 5.68
4088 4662 3.427670 CGGTTTCACTGGCCGTTT 58.572 55.556 0.00 0.00 40.53 3.60
4102 4676 2.223711 GGCCGTTTTCTTTGTGTCATGT 60.224 45.455 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.431942 GTACCGTCCACGCACCAG 60.432 66.667 0.00 0.00 38.18 4.00
9 10 0.039256 TTACTGTACCGTCCACGCAC 60.039 55.000 0.00 0.00 38.18 5.34
92 103 0.818296 GCAGCTAAGAGAAGGACGGA 59.182 55.000 0.00 0.00 0.00 4.69
109 120 2.745884 CGTCATTTCGCCCAGGCA 60.746 61.111 9.78 0.00 42.06 4.75
130 145 1.002746 TAATGGCACGAGCAGGCAA 60.003 52.632 7.26 0.00 45.03 4.52
135 150 1.809619 GACGCTAATGGCACGAGCA 60.810 57.895 19.19 0.00 44.61 4.26
138 153 2.883730 GCGACGCTAATGGCACGA 60.884 61.111 13.73 0.00 40.65 4.35
140 155 2.703409 CAGCGACGCTAATGGCAC 59.297 61.111 24.00 0.00 41.91 5.01
201 260 2.334977 AGGTAAGGTGTGGTGTCATGA 58.665 47.619 0.00 0.00 0.00 3.07
244 307 2.048444 TGCAATTCTGATGAGAGGCC 57.952 50.000 0.00 0.00 0.00 5.19
332 412 8.669243 CAAAACTTGATTTATCCTGACTCTACC 58.331 37.037 0.00 0.00 0.00 3.18
342 422 7.557719 TGAGGGATCTCAAAACTTGATTTATCC 59.442 37.037 0.00 12.64 46.08 2.59
360 465 2.087646 GCAAGAAAGGTGTGAGGGATC 58.912 52.381 0.00 0.00 0.00 3.36
424 541 1.498865 CTTTTATCCATCGCCGCGCT 61.499 55.000 8.21 0.00 0.00 5.92
443 563 1.354506 GCATGAATGTGCTCTCGCC 59.645 57.895 0.00 0.00 41.82 5.54
574 710 0.813184 CAGGGGTGTTGCATCATCAC 59.187 55.000 10.12 6.26 34.47 3.06
666 838 3.127425 AGCTACCTTTCAGAACGCTTT 57.873 42.857 0.00 0.00 0.00 3.51
697 872 1.912043 AGCTAGCTGTTCTTGGATGGT 59.088 47.619 18.57 0.00 0.00 3.55
723 902 1.933853 CATAAACCTAGCACGACTGCC 59.066 52.381 0.00 0.00 45.53 4.85
780 965 4.642885 TCATCATGATCATCAGCAAGCAAA 59.357 37.500 4.86 0.00 0.00 3.68
837 1045 1.016627 GATCGCATGCAGCAAAGGTA 58.983 50.000 19.57 0.00 46.13 3.08
838 1046 1.805254 GATCGCATGCAGCAAAGGT 59.195 52.632 19.57 0.00 46.13 3.50
839 1047 1.298116 CGATCGCATGCAGCAAAGG 60.298 57.895 19.57 0.00 46.13 3.11
849 1058 1.227263 GGGCTACACACGATCGCAT 60.227 57.895 16.60 0.00 0.00 4.73
954 1236 2.111384 TGGTCAGCTTGTCCTAGGATC 58.889 52.381 16.27 9.46 0.00 3.36
1004 1292 1.686052 GCTGGTGATAGTCTCCTCCTG 59.314 57.143 0.49 0.00 31.62 3.86
1235 1545 2.426024 CTCCAAGAACCTGCCATGAATG 59.574 50.000 0.00 0.00 0.00 2.67
1236 1546 2.309755 TCTCCAAGAACCTGCCATGAAT 59.690 45.455 0.00 0.00 0.00 2.57
1237 1547 1.704628 TCTCCAAGAACCTGCCATGAA 59.295 47.619 0.00 0.00 0.00 2.57
1238 1548 1.361204 TCTCCAAGAACCTGCCATGA 58.639 50.000 0.00 0.00 0.00 3.07
1370 1758 4.481463 CCAAAAATTAACGGCAATCGACT 58.519 39.130 0.00 0.00 42.43 4.18
1377 1772 0.038159 CCGGCCAAAAATTAACGGCA 60.038 50.000 2.24 0.00 46.75 5.69
1381 1776 4.398044 TCAGAGATCCGGCCAAAAATTAAC 59.602 41.667 2.24 0.00 0.00 2.01
1411 1810 2.534042 TCCTGACCAACCAACCAAAA 57.466 45.000 0.00 0.00 0.00 2.44
1415 1814 0.539438 TGCATCCTGACCAACCAACC 60.539 55.000 0.00 0.00 0.00 3.77
1771 2202 2.930019 CCCCAGTCAGGTCAGCCA 60.930 66.667 0.00 0.00 37.19 4.75
1865 2308 3.474570 GCCTCCGTCTCCTGCCAT 61.475 66.667 0.00 0.00 0.00 4.40
2030 2488 3.932580 CTCTGCCGCGTACTGCCAA 62.933 63.158 4.92 0.00 42.08 4.52
2138 2605 2.934932 TCCCCCAGCTGCATGTCA 60.935 61.111 8.66 0.00 0.00 3.58
2359 2871 3.124297 CGAAGCTCCTTAGTTTCAAGCAG 59.876 47.826 0.00 0.00 41.59 4.24
2360 2872 3.067106 CGAAGCTCCTTAGTTTCAAGCA 58.933 45.455 0.00 0.00 41.59 3.91
2361 2873 3.326747 TCGAAGCTCCTTAGTTTCAAGC 58.673 45.455 0.00 0.00 41.59 4.01
2362 2874 4.568760 GGATCGAAGCTCCTTAGTTTCAAG 59.431 45.833 0.00 0.00 41.59 3.02
2365 2877 4.124851 TGGATCGAAGCTCCTTAGTTTC 57.875 45.455 5.20 0.00 39.01 2.78
2368 2880 3.034635 ACATGGATCGAAGCTCCTTAGT 58.965 45.455 5.20 0.00 33.69 2.24
2369 2881 3.648009 GACATGGATCGAAGCTCCTTAG 58.352 50.000 5.20 0.00 33.69 2.18
2370 2882 2.034685 CGACATGGATCGAAGCTCCTTA 59.965 50.000 5.20 0.00 45.13 2.69
2371 2883 1.202463 CGACATGGATCGAAGCTCCTT 60.202 52.381 5.20 0.00 45.13 3.36
2372 2884 0.387202 CGACATGGATCGAAGCTCCT 59.613 55.000 5.20 0.00 45.13 3.69
2373 2885 0.598680 CCGACATGGATCGAAGCTCC 60.599 60.000 7.25 0.00 45.13 4.70
2374 2886 1.218230 GCCGACATGGATCGAAGCTC 61.218 60.000 7.25 0.00 45.13 4.09
2378 2903 0.752658 ATCTGCCGACATGGATCGAA 59.247 50.000 7.25 0.00 45.13 3.71
2765 3290 1.658717 CGGCGATCTCGTCCATGAC 60.659 63.158 0.00 0.00 41.58 3.06
2910 3437 2.641321 CCATGAATCCCTATCAGCAGGA 59.359 50.000 0.00 0.00 38.00 3.86
3158 3702 0.745845 GGTACTGCAGATGCTGGTGG 60.746 60.000 23.35 0.00 43.15 4.61
3246 3811 4.807834 GCAGGAAGGGAACTAATTACGTAC 59.192 45.833 0.00 0.00 42.68 3.67
3328 3901 7.201384 GCTTTCGAATTTGATTTCATTGTCCTC 60.201 37.037 0.00 0.00 0.00 3.71
3348 3921 0.166814 CTTTCGGCCAGAAGCTTTCG 59.833 55.000 2.24 0.74 43.05 3.46
3349 3922 1.197949 GACTTTCGGCCAGAAGCTTTC 59.802 52.381 13.51 2.72 43.05 2.62
3350 3923 1.202818 AGACTTTCGGCCAGAAGCTTT 60.203 47.619 13.51 0.00 43.05 3.51
3351 3924 0.398318 AGACTTTCGGCCAGAAGCTT 59.602 50.000 13.51 0.00 43.05 3.74
3352 3925 0.036858 GAGACTTTCGGCCAGAAGCT 60.037 55.000 13.51 11.53 43.05 3.74
3353 3926 1.355066 CGAGACTTTCGGCCAGAAGC 61.355 60.000 13.51 7.80 45.54 3.86
3354 3927 2.743195 CGAGACTTTCGGCCAGAAG 58.257 57.895 2.24 8.64 45.54 2.85
3355 3928 4.988065 CGAGACTTTCGGCCAGAA 57.012 55.556 2.24 4.57 45.54 3.02
3365 3938 3.370104 AGGTGAGAATGATCCGAGACTT 58.630 45.455 0.00 0.00 0.00 3.01
3383 3956 1.276421 CGTCCAGATCCACAAAGAGGT 59.724 52.381 0.00 0.00 0.00 3.85
3566 4140 1.800586 CAATCCACTTGTCACTCCACG 59.199 52.381 0.00 0.00 0.00 4.94
3670 4244 5.673818 GCAACTTCCTTAATCCATGTTCGTC 60.674 44.000 0.00 0.00 0.00 4.20
3675 4249 4.922206 TCAGCAACTTCCTTAATCCATGT 58.078 39.130 0.00 0.00 0.00 3.21
3705 4279 1.593787 CGAGCAGAGGCCAAGAAGA 59.406 57.895 5.01 0.00 42.56 2.87
3726 4300 0.943359 GCCTCGCAATGGATCTCTCG 60.943 60.000 0.00 0.00 0.00 4.04
3783 4357 0.238553 GCTGGAAGAAAGCCGTGTTC 59.761 55.000 0.00 0.00 34.07 3.18
3815 4389 5.048504 GTGATCACATTCTTCTTTTGCCTGA 60.049 40.000 21.07 0.00 0.00 3.86
3918 4492 1.305930 GCCGAGCCGAAGAACCAAAT 61.306 55.000 0.00 0.00 0.00 2.32
3940 4514 0.690192 TCCAAGTTGATCGAGGCCAA 59.310 50.000 5.01 0.00 0.00 4.52
3943 4517 1.667724 CATGTCCAAGTTGATCGAGGC 59.332 52.381 3.87 0.00 0.00 4.70
4004 4578 3.318313 TCAACCTCCTCTTCCTCAAACT 58.682 45.455 0.00 0.00 0.00 2.66
4063 4637 3.239253 AGTGAAACCGTCCGGGCT 61.239 61.111 3.66 0.00 40.62 5.19
4088 4662 2.757314 TGTGCCAACATGACACAAAGAA 59.243 40.909 0.00 0.00 41.11 2.52
4135 4709 2.747460 GCATGGAACTGCCGCAGA 60.747 61.111 27.12 4.56 40.66 4.26


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

AutoCloner maintained by Alex Coulton.