Multiple sequence alignment - TraesCS3D01G278800

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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 TraesCS3D01G278800 chr3D 100.000 5393 0 0 1792 7184 386434133 386439525 0.000000e+00 9960.0
1 TraesCS3D01G278800 chr3D 100.000 1466 0 0 1 1466 386432342 386433807 0.000000e+00 2708.0
2 TraesCS3D01G278800 chr3A 96.264 4711 118 22 1792 6464 508162590 508167280 0.000000e+00 7672.0
3 TraesCS3D01G278800 chr3A 92.533 1500 60 16 1 1465 508161096 508162578 0.000000e+00 2102.0
4 TraesCS3D01G278800 chr3A 87.244 439 28 14 6769 7181 508168086 508168522 6.520000e-130 475.0
5 TraesCS3D01G278800 chr3A 92.096 291 4 6 6462 6750 508167380 508167653 6.760000e-105 392.0
6 TraesCS3D01G278800 chr3B 96.000 3800 81 22 2984 6725 502640508 502644294 0.000000e+00 6109.0
7 TraesCS3D01G278800 chr3B 93.006 1487 73 11 1 1465 502637701 502639178 0.000000e+00 2141.0
8 TraesCS3D01G278800 chr3B 95.108 1206 46 9 1792 2989 502639190 502640390 0.000000e+00 1888.0
9 TraesCS3D01G278800 chr3B 91.910 445 27 2 6748 7184 502645435 502645878 1.320000e-171 614.0
10 TraesCS3D01G278800 chr3B 91.422 443 38 0 1936 2378 793293927 793294369 6.160000e-170 608.0
11 TraesCS3D01G278800 chr3B 91.071 448 34 3 1936 2378 793334361 793334807 1.030000e-167 601.0
12 TraesCS3D01G278800 chr3B 86.412 471 28 10 2559 3000 793334989 793335452 3.900000e-132 483.0
13 TraesCS3D01G278800 chr3B 86.316 475 25 19 2559 3000 793294551 793295018 1.400000e-131 481.0
14 TraesCS3D01G278800 chr3B 94.444 108 6 0 3038 3145 793295022 793295129 4.460000e-37 167.0
15 TraesCS3D01G278800 chr3B 83.654 104 10 6 3085 3186 793335476 793335574 2.760000e-14 91.6
16 TraesCS3D01G278800 chr3B 90.909 66 2 3 2494 2556 793334814 793334878 1.280000e-12 86.1
17 TraesCS3D01G278800 chr2D 90.015 651 27 15 2560 3181 582153479 582152838 0.000000e+00 808.0
18 TraesCS3D01G278800 chr4A 86.942 605 40 9 2597 3175 359953847 359954438 1.690000e-180 643.0
19 TraesCS3D01G278800 chr5D 87.805 533 34 13 2032 2556 479386103 479386612 4.800000e-166 595.0
20 TraesCS3D01G278800 chr5D 87.430 533 36 13 2032 2556 371030774 371030265 1.040000e-162 584.0
21 TraesCS3D01G278800 chr5D 87.937 315 32 4 1154 1465 371031330 371031019 4.090000e-97 366.0
22 TraesCS3D01G278800 chr5D 83.898 236 15 2 1792 2004 479385870 479386105 3.400000e-48 204.0
23 TraesCS3D01G278800 chr5D 83.475 236 16 1 1792 2004 371031007 371030772 1.580000e-46 198.0
24 TraesCS3D01G278800 chr1D 87.782 532 34 14 2032 2555 469879233 469878725 1.730000e-165 593.0
25 TraesCS3D01G278800 chr1D 87.937 315 32 4 1154 1465 469879789 469879478 4.090000e-97 366.0
26 TraesCS3D01G278800 chr1D 83.475 236 16 3 1792 2004 469879466 469879231 1.580000e-46 198.0
27 TraesCS3D01G278800 chr1D 100.000 41 0 0 6438 6478 157979168 157979208 7.730000e-10 76.8
28 TraesCS3D01G278800 chr4B 86.867 533 39 11 2032 2556 62873336 62872827 1.050000e-157 568.0
29 TraesCS3D01G278800 chr4B 86.032 315 34 6 1154 1465 62873885 62873578 5.370000e-86 329.0
30 TraesCS3D01G278800 chr6A 86.867 533 37 12 2032 2556 598147479 598146972 3.760000e-157 566.0
31 TraesCS3D01G278800 chr6A 90.972 144 13 0 1861 2004 598147620 598147477 2.040000e-45 195.0
32 TraesCS3D01G278800 chr5B 90.754 411 27 2 2771 3181 81271192 81270793 8.200000e-149 538.0
33 TraesCS3D01G278800 chr5B 86.412 471 29 10 2559 3000 387887506 387887042 3.900000e-132 483.0
34 TraesCS3D01G278800 chr5B 92.814 167 10 1 2836 3000 330634530 330634364 2.590000e-59 241.0
35 TraesCS3D01G278800 chr5B 85.430 151 14 6 3038 3186 330634360 330634216 4.490000e-32 150.0
36 TraesCS3D01G278800 chr6D 85.849 530 35 19 2032 2556 418222116 418221622 1.780000e-145 527.0
37 TraesCS3D01G278800 chr6D 82.627 236 18 6 1792 2004 418222349 418222114 3.420000e-43 187.0
38 TraesCS3D01G278800 chr2B 91.111 45 0 4 6636 6677 8936845 8936888 2.800000e-04 58.4


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 TraesCS3D01G278800 chr3D 386432342 386439525 7183 False 6334.000000 9960 100.000000 1 7184 2 chr3D.!!$F1 7183
1 TraesCS3D01G278800 chr3A 508161096 508168522 7426 False 2660.250000 7672 92.034250 1 7181 4 chr3A.!!$F1 7180
2 TraesCS3D01G278800 chr3B 502637701 502645878 8177 False 2688.000000 6109 94.006000 1 7184 4 chr3B.!!$F1 7183
3 TraesCS3D01G278800 chr3B 793293927 793295129 1202 False 418.666667 608 90.727333 1936 3145 3 chr3B.!!$F2 1209
4 TraesCS3D01G278800 chr3B 793334361 793335574 1213 False 315.425000 601 88.011500 1936 3186 4 chr3B.!!$F3 1250
5 TraesCS3D01G278800 chr2D 582152838 582153479 641 True 808.000000 808 90.015000 2560 3181 1 chr2D.!!$R1 621
6 TraesCS3D01G278800 chr4A 359953847 359954438 591 False 643.000000 643 86.942000 2597 3175 1 chr4A.!!$F1 578
7 TraesCS3D01G278800 chr5D 479385870 479386612 742 False 399.500000 595 85.851500 1792 2556 2 chr5D.!!$F1 764
8 TraesCS3D01G278800 chr5D 371030265 371031330 1065 True 382.666667 584 86.280667 1154 2556 3 chr5D.!!$R1 1402
9 TraesCS3D01G278800 chr1D 469878725 469879789 1064 True 385.666667 593 86.398000 1154 2555 3 chr1D.!!$R1 1401
10 TraesCS3D01G278800 chr4B 62872827 62873885 1058 True 448.500000 568 86.449500 1154 2556 2 chr4B.!!$R1 1402
11 TraesCS3D01G278800 chr6A 598146972 598147620 648 True 380.500000 566 88.919500 1861 2556 2 chr6A.!!$R1 695
12 TraesCS3D01G278800 chr6D 418221622 418222349 727 True 357.000000 527 84.238000 1792 2556 2 chr6D.!!$R1 764

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
207 208 0.592637 CAGGCAAGAAACATGCGTCA 59.407 50.000 0.00 0.0 44.75 4.35 F
785 796 1.153429 CTGCCCTACGGTGGTTAGC 60.153 63.158 0.00 0.0 0.00 3.09 F
1387 1436 2.361737 GGGCTTCAGGGCTTGGTC 60.362 66.667 0.00 0.0 40.65 4.02 F
2165 2248 2.008268 GATGGTTCATGGGCTTGCGG 62.008 60.000 0.00 0.0 0.00 5.69 F
3377 3751 3.932089 GTCTGCTCTTGGAGAAAGATGTC 59.068 47.826 0.00 0.0 44.02 3.06 F
4378 4782 2.171027 TCACAACCTCGGGTAGTTTTGT 59.829 45.455 0.00 0.0 33.12 2.83 F
5032 5437 0.322277 AGCCACATGTTCTGCTCCAG 60.322 55.000 8.16 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1436 0.242286 CCTATCTGATCTCCGCACCG 59.758 60.000 0.00 0.00 0.00 4.94 R
1833 1885 0.811281 GACACCTAATTGGCAGCACC 59.189 55.000 0.00 0.00 40.22 5.01 R
2521 2608 3.156293 TGTGCAACCAGAGCATATTGTT 58.844 40.909 0.00 0.00 44.79 2.83 R
3676 4059 3.492313 GCAACCTAAATCTCAACAAGCG 58.508 45.455 0.00 0.00 0.00 4.68 R
4464 4868 2.547218 GGTCGTTAGAGGTTGCAACTCA 60.547 50.000 27.64 8.91 37.43 3.41 R
6027 6458 0.034198 TTGCGCTGTACTGGCTAACA 59.966 50.000 9.73 5.29 0.00 2.41 R
6374 6805 0.179073 CATCCCCGAGACATGTGACC 60.179 60.000 1.15 0.00 0.00 4.02 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
185 186 7.216881 CAGAATAGCAAACATGTCACGTTAATG 59.783 37.037 0.00 0.00 0.00 1.90
207 208 0.592637 CAGGCAAGAAACATGCGTCA 59.407 50.000 0.00 0.00 44.75 4.35
248 249 1.168714 GGAGGCGTCAAAGCAATCTT 58.831 50.000 8.91 0.00 39.27 2.40
377 378 2.579684 ATCTCAAGCTCCGGCCGAAC 62.580 60.000 30.73 15.71 39.73 3.95
395 396 6.238130 GGCCGAACTTGATTTCTTCTACATAC 60.238 42.308 0.00 0.00 0.00 2.39
439 443 8.580720 TCTTCTATATCTAACTCATGTGGCTTC 58.419 37.037 0.00 0.00 0.00 3.86
464 469 2.352651 TCTATCGCAAATGAGCACAAGC 59.647 45.455 0.00 0.00 42.56 4.01
674 679 1.229359 CATGGCAGCCATCTCCCTT 59.771 57.895 25.23 0.00 43.15 3.95
782 793 4.029809 GGCTGCCCTACGGTGGTT 62.030 66.667 7.66 0.00 0.00 3.67
783 794 2.662070 GGCTGCCCTACGGTGGTTA 61.662 63.158 7.66 0.00 0.00 2.85
785 796 1.153429 CTGCCCTACGGTGGTTAGC 60.153 63.158 0.00 0.00 0.00 3.09
939 963 3.312736 TTTCACTTTCAGGCCTTCCTT 57.687 42.857 0.00 0.00 41.93 3.36
945 969 2.586648 TTCAGGCCTTCCTTCCTTTC 57.413 50.000 0.00 0.00 41.93 2.62
1387 1436 2.361737 GGGCTTCAGGGCTTGGTC 60.362 66.667 0.00 0.00 40.65 4.02
1465 1517 8.486210 ACTGATAAATTCACCTATGTAGCAGAA 58.514 33.333 6.18 0.00 34.93 3.02
1823 1875 3.243234 TGTGGTACCAAAATGTTTGCTCG 60.243 43.478 18.31 0.00 0.00 5.03
1833 1885 4.410492 AATGTTTGCTCGTAGAAGCTTG 57.590 40.909 2.10 0.00 34.09 4.01
1859 1932 4.389077 GCTGCCAATTAGGTGTCGTATATC 59.611 45.833 0.00 0.00 40.61 1.63
1873 1948 4.743644 GTCGTATATCAGTGTGCCCTTTAC 59.256 45.833 0.00 0.00 0.00 2.01
1879 1954 2.955660 TCAGTGTGCCCTTTACTTTTGG 59.044 45.455 0.00 0.00 0.00 3.28
1938 2014 2.225068 ATACCGAGCTTTGATCGTGG 57.775 50.000 4.60 0.00 38.50 4.94
2165 2248 2.008268 GATGGTTCATGGGCTTGCGG 62.008 60.000 0.00 0.00 0.00 5.69
2279 2362 4.818005 TGTATGGATATCTTGCTGCAGTTG 59.182 41.667 16.64 6.01 0.00 3.16
2304 2387 9.685828 TGGCAGTTAAATTTTGATAACACTTAC 57.314 29.630 0.00 0.00 35.06 2.34
2641 2836 7.220030 AGATACCCATTTGCAGATACAGTAAG 58.780 38.462 0.00 0.00 0.00 2.34
2989 3239 9.816787 AACCATTTTAGGGTTATAAGAACTTCA 57.183 29.630 0.00 0.00 46.47 3.02
3377 3751 3.932089 GTCTGCTCTTGGAGAAAGATGTC 59.068 47.826 0.00 0.00 44.02 3.06
3676 4059 9.937175 GTTTCTGTTGCCATTCTCTAATATTAC 57.063 33.333 0.00 0.00 0.00 1.89
3763 4146 4.764823 TGGAAACTACATAGCAAGGTTTGG 59.235 41.667 0.00 0.00 31.51 3.28
3948 4340 3.583966 TGGTGGGTACGTTTCTAAGGATT 59.416 43.478 0.00 0.00 0.00 3.01
3959 4351 6.102663 CGTTTCTAAGGATTGTCTCTGATGT 58.897 40.000 0.00 0.00 0.00 3.06
4166 4569 7.039293 TCCTTCTATTACAGTGTGTATGTGTGT 60.039 37.037 5.88 0.00 32.20 3.72
4378 4782 2.171027 TCACAACCTCGGGTAGTTTTGT 59.829 45.455 0.00 0.00 33.12 2.83
4464 4868 8.450964 CAAATCTAACAACCGAAACATATGTCT 58.549 33.333 9.23 0.00 0.00 3.41
4509 4913 5.869888 CGGAGCTGTCTACTTTACAATCTTT 59.130 40.000 0.00 0.00 0.00 2.52
5032 5437 0.322277 AGCCACATGTTCTGCTCCAG 60.322 55.000 8.16 0.00 0.00 3.86
5192 5597 4.703575 TCATCTGGATTGGCTTCAGAAAAG 59.296 41.667 0.00 0.00 40.37 2.27
5601 6028 5.478233 TGCTTAATAACCTGCGTTACATG 57.522 39.130 0.00 0.00 37.28 3.21
5794 6225 1.268999 TGCTTTGCGCACAGGTAAAAG 60.269 47.619 23.94 17.01 45.47 2.27
5873 6304 6.862711 TCAAATTTTTGAGCATGCATTTCA 57.137 29.167 21.98 12.41 41.88 2.69
5916 6347 6.972328 TCAGCTTTGAAAGTTCATGTTGTAAC 59.028 34.615 6.81 0.00 37.00 2.50
6177 6608 3.515901 AGGCCTATGAGTTCTTTTCGAGT 59.484 43.478 1.29 0.00 0.00 4.18
6243 6674 4.612939 CGATCTGTGATATTGCATGGCTTG 60.613 45.833 0.00 0.00 0.00 4.01
6374 6805 1.675415 GGTGAGAGGCTGAGCTCTTTG 60.675 57.143 16.19 6.44 32.44 2.77
6421 6855 1.063649 GCATTGCTGACTGATGCCG 59.936 57.895 0.16 0.00 40.10 5.69
6458 6892 1.137086 ACTCGTGCTCGGCATCTTAAT 59.863 47.619 8.49 0.00 41.91 1.40
6539 7075 2.168106 ACTCACAAAGTGGCAATGCAAA 59.832 40.909 7.79 0.00 36.65 3.68
6540 7076 3.181463 ACTCACAAAGTGGCAATGCAAAT 60.181 39.130 7.79 0.00 36.65 2.32
6607 7143 6.948309 AGGCTTGTGGATCTGTTTAGTTTATT 59.052 34.615 0.00 0.00 0.00 1.40
6608 7144 8.107095 AGGCTTGTGGATCTGTTTAGTTTATTA 58.893 33.333 0.00 0.00 0.00 0.98
6609 7145 8.903820 GGCTTGTGGATCTGTTTAGTTTATTAT 58.096 33.333 0.00 0.00 0.00 1.28
6694 7234 6.013379 ACTCTGAATAGTCAAGAATCAACCCA 60.013 38.462 8.62 0.00 31.88 4.51
6833 8714 1.227205 GAGTGATCCTGGCTCGCAG 60.227 63.158 13.04 0.00 0.00 5.18
6867 8748 1.675641 GGGTGCGCTTGATGGACTT 60.676 57.895 9.73 0.00 0.00 3.01
6888 8770 2.270297 AAGGCGGTGATGAATTGCGC 62.270 55.000 0.00 0.00 0.00 6.09
6940 8822 3.487942 GGTGCAATTTTTGTTGTACGGTC 59.512 43.478 0.00 0.00 43.04 4.79
7072 8976 7.235079 TCATAGGAAGTGGAAACCAAATGTTA 58.765 34.615 0.00 0.00 35.67 2.41
7074 8979 4.277423 AGGAAGTGGAAACCAAATGTTACG 59.723 41.667 0.00 0.00 35.67 3.18
7081 8986 6.752815 GTGGAAACCAAATGTTACGAAAAAGA 59.247 34.615 0.00 0.00 35.67 2.52
7129 9034 5.233083 TGGGAGCTATGATAAAGGACATG 57.767 43.478 0.00 0.00 0.00 3.21
7169 9076 7.470289 AGCGAGACATGAAAATATGAGTTAC 57.530 36.000 0.00 0.00 0.00 2.50
7170 9077 6.199154 AGCGAGACATGAAAATATGAGTTACG 59.801 38.462 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
185 186 0.109597 CGCATGTTTCTTGCCTGGAC 60.110 55.000 0.00 0.00 36.75 4.02
207 208 4.463891 CCAACTGGCCACTATGATTTCTTT 59.536 41.667 0.00 0.00 0.00 2.52
248 249 1.142667 TCAGTGTTCACATGGCCAAGA 59.857 47.619 16.33 8.46 0.00 3.02
411 412 8.748412 AGCCACATGAGTTAGATATAGAAGATC 58.252 37.037 0.00 0.00 0.00 2.75
413 414 8.484214 AAGCCACATGAGTTAGATATAGAAGA 57.516 34.615 0.00 0.00 0.00 2.87
423 427 3.997021 AGAAACGAAGCCACATGAGTTAG 59.003 43.478 0.00 0.00 0.00 2.34
439 443 3.181521 TGTGCTCATTTGCGATAGAAACG 60.182 43.478 0.00 0.00 29.09 3.60
464 469 3.829601 AGTGGTTTAGTCCTCTCTGTGAG 59.170 47.826 0.00 0.00 42.30 3.51
691 696 2.031516 CACGGAACAGCAGGAGCAG 61.032 63.158 0.00 0.00 45.49 4.24
808 819 0.331278 GGATCATTCCCACCACCACA 59.669 55.000 0.00 0.00 35.84 4.17
939 963 3.992943 TGCCGATAAAGGAAGAAAGGA 57.007 42.857 0.00 0.00 0.00 3.36
945 969 5.237344 AGAAATTCGATGCCGATAAAGGAAG 59.763 40.000 0.00 0.00 45.10 3.46
1387 1436 0.242286 CCTATCTGATCTCCGCACCG 59.758 60.000 0.00 0.00 0.00 4.94
1423 1475 1.089920 CAGTGAGCTTCCAATTCCGG 58.910 55.000 0.00 0.00 0.00 5.14
1426 1478 7.699812 GTGAATTTATCAGTGAGCTTCCAATTC 59.300 37.037 0.00 6.72 39.19 2.17
1833 1885 0.811281 GACACCTAATTGGCAGCACC 59.189 55.000 0.00 0.00 40.22 5.01
1859 1932 2.545742 GCCAAAAGTAAAGGGCACACTG 60.546 50.000 0.00 0.00 45.70 3.66
1873 1948 4.348857 GCCAGTGCTTGCCAAAAG 57.651 55.556 0.00 0.00 33.53 2.27
1938 2014 1.775869 GCCTGCAGCAGAAGAAAAAC 58.224 50.000 24.90 0.00 42.97 2.43
2069 2149 1.140312 AACCAGGGACGGCATATGAT 58.860 50.000 6.97 0.00 0.00 2.45
2074 2154 3.876309 AATATAAACCAGGGACGGCAT 57.124 42.857 0.00 0.00 0.00 4.40
2165 2248 0.874390 TCAAGCGTTTCATCCAGCAC 59.126 50.000 0.00 0.00 0.00 4.40
2279 2362 8.846607 CGTAAGTGTTATCAAAATTTAACTGCC 58.153 33.333 0.00 0.00 31.16 4.85
2304 2387 9.155975 AGTTTTCAGCATATATATCCTTAAGCG 57.844 33.333 0.00 0.00 0.00 4.68
2521 2608 3.156293 TGTGCAACCAGAGCATATTGTT 58.844 40.909 0.00 0.00 44.79 2.83
2747 2947 7.865530 ACCTAAATGTGGGGAATTAAAAAGT 57.134 32.000 0.00 0.00 0.00 2.66
3392 3766 7.333921 TGACAACTTAGAACGGTTAAGAAAACA 59.666 33.333 9.71 3.59 33.40 2.83
3676 4059 3.492313 GCAACCTAAATCTCAACAAGCG 58.508 45.455 0.00 0.00 0.00 4.68
4166 4569 6.989169 ACTAATTGCAACCAAAATTAGCACAA 59.011 30.769 0.00 0.00 44.66 3.33
4378 4782 4.661222 TCCATGCCAGTCAAAAATACTCA 58.339 39.130 0.00 0.00 0.00 3.41
4464 4868 2.547218 GGTCGTTAGAGGTTGCAACTCA 60.547 50.000 27.64 8.91 37.43 3.41
4509 4913 8.674263 AGATTTTTGATATTTGCAAAACACCA 57.326 26.923 17.19 9.12 42.82 4.17
4739 5144 6.543831 ACTCTGAACTATTGCAAAAGTGAACT 59.456 34.615 1.71 0.00 0.00 3.01
4740 5145 6.729187 ACTCTGAACTATTGCAAAAGTGAAC 58.271 36.000 1.71 0.00 0.00 3.18
4742 5147 6.238731 CCAACTCTGAACTATTGCAAAAGTGA 60.239 38.462 1.71 0.00 0.00 3.41
4743 5148 5.916883 CCAACTCTGAACTATTGCAAAAGTG 59.083 40.000 1.71 0.00 0.00 3.16
5192 5597 8.947115 AGCACAAAATACTTACCAATAGAAGAC 58.053 33.333 0.00 0.00 0.00 3.01
5280 5685 6.500684 TCACCAGATATTTGAAGCAGAAAC 57.499 37.500 0.00 0.00 0.00 2.78
5584 6011 4.570772 CACTAGCATGTAACGCAGGTTATT 59.429 41.667 0.00 0.00 40.53 1.40
5601 6028 6.590292 TGTAAATCAAAGCACTAGACACTAGC 59.410 38.462 0.00 0.00 0.00 3.42
5794 6225 8.709386 TCTATGCAAGAAGTAAGATGTTCTTC 57.291 34.615 0.00 6.66 40.32 2.87
5843 6274 6.262496 TGCATGCTCAAAAATTTGAAATTCCA 59.738 30.769 20.33 3.14 45.61 3.53
5848 6279 7.704271 TGAAATGCATGCTCAAAAATTTGAAA 58.296 26.923 20.33 2.53 45.61 2.69
5864 6295 7.613022 AGAATTATATCCCGTCATGAAATGCAT 59.387 33.333 0.00 0.00 46.21 3.96
5873 6304 6.365970 AGCTGAAGAATTATATCCCGTCAT 57.634 37.500 0.00 0.00 0.00 3.06
6027 6458 0.034198 TTGCGCTGTACTGGCTAACA 59.966 50.000 9.73 5.29 0.00 2.41
6177 6608 7.220740 TGTAAAGGTGTACATTTGATCACTCA 58.779 34.615 0.00 0.00 31.84 3.41
6243 6674 4.058817 CGCAGAAATATCCCCAGTACTTC 58.941 47.826 0.00 0.00 0.00 3.01
6308 6739 1.812571 CACGGTGCAAGGAGCTTAATT 59.187 47.619 0.00 0.00 45.94 1.40
6313 6744 0.391661 CATACACGGTGCAAGGAGCT 60.392 55.000 8.30 0.00 45.94 4.09
6374 6805 0.179073 CATCCCCGAGACATGTGACC 60.179 60.000 1.15 0.00 0.00 4.02
6421 6855 5.336744 CACGAGTTAGGAAGAGAATGTCTC 58.663 45.833 0.00 0.00 43.70 3.36
6458 6892 4.155826 CCTATCCAACGTTGCATTTGAAGA 59.844 41.667 22.93 11.93 0.00 2.87
6539 7075 5.938125 GGAACAGGCCACGAAACATATATAT 59.062 40.000 5.01 0.00 0.00 0.86
6540 7076 5.302360 GGAACAGGCCACGAAACATATATA 58.698 41.667 5.01 0.00 0.00 0.86
6694 7234 2.949644 CCTTGGACGGTTTCAAAGTTCT 59.050 45.455 0.00 0.00 33.70 3.01
6811 8692 1.607801 CGAGCCAGGATCACTCACCA 61.608 60.000 5.34 0.00 0.00 4.17
6815 8696 1.227205 CTGCGAGCCAGGATCACTC 60.227 63.158 5.34 0.00 37.93 3.51
6848 8729 3.134127 GTCCATCAAGCGCACCCC 61.134 66.667 11.47 0.00 0.00 4.95
6867 8748 0.810648 GCAATTCATCACCGCCTTCA 59.189 50.000 0.00 0.00 0.00 3.02
6888 8770 3.888930 ACACACACAAATCCCCTTAACAG 59.111 43.478 0.00 0.00 0.00 3.16
6997 8899 5.047306 TCTCTTGAAATAGACTTTCGCCTCA 60.047 40.000 0.00 0.00 0.00 3.86
7072 8976 7.254932 CCTCTCTCATTTTTCAGTCTTTTTCGT 60.255 37.037 0.00 0.00 0.00 3.85
7074 8979 6.860539 GCCTCTCTCATTTTTCAGTCTTTTTC 59.139 38.462 0.00 0.00 0.00 2.29
7081 8986 2.039084 ACCGCCTCTCTCATTTTTCAGT 59.961 45.455 0.00 0.00 0.00 3.41
7147 9052 6.695713 TCCGTAACTCATATTTTCATGTCTCG 59.304 38.462 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.