Multiple sequence alignment - TraesCS4D01G084300

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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 TraesCS4D01G084300 chr4D 100.000 2935 0 0 893 3827 58144605 58147539 0.000000e+00 5421.0
1 TraesCS4D01G084300 chr4D 100.000 562 0 0 1 562 58143713 58144274 0.000000e+00 1038.0
2 TraesCS4D01G084300 chr4D 91.011 89 3 4 3247 3334 58146896 58146980 8.690000e-22 115.0
3 TraesCS4D01G084300 chr4D 91.011 89 3 4 3184 3268 58146959 58147046 8.690000e-22 115.0
4 TraesCS4D01G084300 chr4D 100.000 28 0 0 412 439 5529422 5529449 7.000000e-03 52.8
5 TraesCS4D01G084300 chr4B 95.346 2385 71 17 895 3268 87412407 87414762 0.000000e+00 3753.0
6 TraesCS4D01G084300 chr4B 94.326 282 7 3 3247 3522 87414675 87414953 1.270000e-114 424.0
7 TraesCS4D01G084300 chr4B 84.464 457 37 17 131 562 87411866 87412313 1.640000e-113 420.0
8 TraesCS4D01G084300 chr4B 87.241 290 21 5 3538 3827 87414937 87415210 2.220000e-82 316.0
9 TraesCS4D01G084300 chr4B 89.683 126 12 1 1 126 87410065 87410189 3.960000e-35 159.0
10 TraesCS4D01G084300 chr4B 93.182 44 3 0 343 386 644323756 644323799 8.870000e-07 65.8
11 TraesCS4D01G084300 chr4A 94.492 1979 84 16 899 2865 537599967 537598002 0.000000e+00 3027.0
12 TraesCS4D01G084300 chr4A 90.110 637 38 10 899 1526 537601979 537601359 0.000000e+00 804.0
13 TraesCS4D01G084300 chr4A 89.247 651 38 11 3184 3827 537597530 537596905 0.000000e+00 785.0
14 TraesCS4D01G084300 chr4A 94.606 482 12 6 2862 3334 537597922 537597446 0.000000e+00 734.0
15 TraesCS4D01G084300 chr4A 82.016 367 42 11 1 366 537600923 537600580 1.340000e-74 291.0
16 TraesCS4D01G084300 chr4A 85.340 191 25 2 176 366 537602560 537602373 1.080000e-45 195.0
17 TraesCS4D01G084300 chr4A 79.412 238 27 9 1 238 537948228 537948013 8.570000e-32 148.0
18 TraesCS4D01G084300 chr4A 90.000 90 3 4 3184 3268 537597467 537597379 1.120000e-20 111.0
19 TraesCS4D01G084300 chr4A 90.588 85 4 3 3247 3331 537597593 537597513 4.040000e-20 110.0
20 TraesCS4D01G084300 chr4A 80.208 96 17 2 141 236 591891163 591891256 1.910000e-08 71.3
21 TraesCS4D01G084300 chr7A 84.810 79 12 0 138 216 688307087 688307165 3.170000e-11 80.5
22 TraesCS4D01G084300 chr7A 80.000 110 18 3 133 242 688618349 688618244 1.140000e-10 78.7
23 TraesCS4D01G084300 chr7A 87.931 58 5 2 343 400 613630018 613629963 2.470000e-07 67.6
24 TraesCS4D01G084300 chr7B 92.727 55 2 2 346 400 641330441 641330389 1.140000e-10 78.7
25 TraesCS4D01G084300 chr7B 79.592 98 16 4 341 438 663115813 663115906 2.470000e-07 67.6
26 TraesCS4D01G084300 chr2A 81.250 96 17 1 141 236 602365453 602365547 4.100000e-10 76.8
27 TraesCS4D01G084300 chr2A 81.250 96 16 2 141 236 628488315 628488408 4.100000e-10 76.8
28 TraesCS4D01G084300 chr2A 79.798 99 18 2 144 242 295033842 295033746 1.910000e-08 71.3
29 TraesCS4D01G084300 chr6A 89.474 57 4 2 344 400 18652572 18652518 1.910000e-08 71.3
30 TraesCS4D01G084300 chr3A 79.245 106 19 3 137 242 68122444 68122342 1.910000e-08 71.3
31 TraesCS4D01G084300 chr3A 79.798 99 18 2 144 242 122155215 122155119 1.910000e-08 71.3
32 TraesCS4D01G084300 chr1D 81.319 91 13 4 344 434 487188587 487188501 1.910000e-08 71.3
33 TraesCS4D01G084300 chr7D 93.478 46 3 0 343 388 101395309 101395264 6.860000e-08 69.4
34 TraesCS4D01G084300 chr2D 80.435 92 14 4 343 434 500486428 500486341 2.470000e-07 67.6


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 TraesCS4D01G084300 chr4D 58143713 58147539 3826 False 1672.250 5421 95.505500 1 3827 4 chr4D.!!$F2 3826
1 TraesCS4D01G084300 chr4B 87410065 87415210 5145 False 1014.400 3753 90.212000 1 3827 5 chr4B.!!$F2 3826
2 TraesCS4D01G084300 chr4A 537596905 537602560 5655 True 757.125 3027 89.549875 1 3827 8 chr4A.!!$R2 3826

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
126 1764 0.664767 GAGTACATCATCGGAGCGGC 60.665 60.0 0.00 0.0 0.00 6.53 F
133 3443 0.897621 TCATCGGAGCGGCATATGAT 59.102 50.0 6.97 0.0 0.00 2.45 F
1323 4987 1.040339 GTCTGCCGGATCAGGAGTCT 61.040 60.0 16.86 0.0 34.91 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 5494 0.382636 CTTCGTCGAACAAACACGCC 60.383 55.0 2.90 0.0 33.46 5.68 R
1917 5599 1.089920 CAAAATCCAGCAGACCTCCG 58.910 55.0 0.00 0.0 0.00 4.63 R
2961 6729 0.675208 TGCGCTGCCGGAAAAAGATA 60.675 50.0 5.05 0.0 34.32 1.98 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
23 1661 6.357579 TGACACCTTGCCATTATGAAAATT 57.642 33.333 0.00 0.00 0.00 1.82
25 1663 7.546358 TGACACCTTGCCATTATGAAAATTAG 58.454 34.615 0.00 0.00 0.00 1.73
27 1665 7.547227 ACACCTTGCCATTATGAAAATTAGTC 58.453 34.615 0.00 0.00 0.00 2.59
28 1666 6.692681 CACCTTGCCATTATGAAAATTAGTCG 59.307 38.462 0.00 0.00 0.00 4.18
29 1667 6.183360 ACCTTGCCATTATGAAAATTAGTCGG 60.183 38.462 0.00 0.00 0.00 4.79
31 1669 7.397892 TTGCCATTATGAAAATTAGTCGGAA 57.602 32.000 0.00 0.00 0.00 4.30
33 1671 8.006298 TGCCATTATGAAAATTAGTCGGAATT 57.994 30.769 0.00 0.00 0.00 2.17
35 1673 9.959749 GCCATTATGAAAATTAGTCGGAATTAA 57.040 29.630 0.00 0.00 0.00 1.40
41 1679 8.682128 TGAAAATTAGTCGGAATTAATGCAAC 57.318 30.769 0.00 0.00 0.00 4.17
126 1764 0.664767 GAGTACATCATCGGAGCGGC 60.665 60.000 0.00 0.00 0.00 6.53
129 1767 1.067846 GTACATCATCGGAGCGGCATA 60.068 52.381 1.45 0.00 0.00 3.14
133 3443 0.897621 TCATCGGAGCGGCATATGAT 59.102 50.000 6.97 0.00 0.00 2.45
142 3452 5.605534 GGAGCGGCATATGATGTTAGATAT 58.394 41.667 6.97 0.00 0.00 1.63
145 3455 6.051717 AGCGGCATATGATGTTAGATATTCC 58.948 40.000 6.97 0.00 0.00 3.01
148 3458 6.703607 CGGCATATGATGTTAGATATTCCCTC 59.296 42.308 6.97 0.00 0.00 4.30
158 3468 6.447084 TGTTAGATATTCCCTCTGGTCCTTTT 59.553 38.462 0.00 0.00 0.00 2.27
168 3478 1.804748 CTGGTCCTTTTTACTCCGCAC 59.195 52.381 0.00 0.00 0.00 5.34
172 3482 2.812011 GTCCTTTTTACTCCGCACATGT 59.188 45.455 0.00 0.00 0.00 3.21
181 3491 1.805943 CTCCGCACATGTGATTTGTCA 59.194 47.619 29.80 4.19 0.00 3.58
1042 4706 2.283966 CCTCCTCCACGTCCCAGT 60.284 66.667 0.00 0.00 0.00 4.00
1044 4708 2.283676 TCCTCCACGTCCCAGTCC 60.284 66.667 0.00 0.00 0.00 3.85
1323 4987 1.040339 GTCTGCCGGATCAGGAGTCT 61.040 60.000 16.86 0.00 34.91 3.24
1331 4995 1.337118 GATCAGGAGTCTAGGGCCAG 58.663 60.000 6.18 0.85 0.00 4.85
1947 5629 2.622011 GGATTTTGACACGCCGGCA 61.622 57.895 28.98 2.40 0.00 5.69
2091 5773 0.476338 TAAGCTCCTTGTGTGCCCAA 59.524 50.000 0.00 0.00 33.94 4.12
2163 5845 1.135257 GTCTCTGGTGAGTCATGGTCG 60.135 57.143 0.00 0.00 40.98 4.79
2223 5905 0.970640 TTAGCAGTCGCCCACTAACA 59.029 50.000 0.00 0.00 39.83 2.41
2602 6284 1.702491 GGCGTTGCCCGATACAACTC 61.702 60.000 11.56 5.49 44.06 3.01
2604 6286 1.722011 CGTTGCCCGATACAACTCTT 58.278 50.000 11.56 0.00 44.15 2.85
2612 6294 2.093973 CCGATACAACTCTTCAGCCAGT 60.094 50.000 0.00 0.00 0.00 4.00
2615 6297 5.168569 CGATACAACTCTTCAGCCAGTTAA 58.831 41.667 0.00 0.00 31.41 2.01
2631 6313 0.741326 TTAACGCTTGTTGCCTGCAA 59.259 45.000 0.00 0.00 38.78 4.08
2652 6334 2.106166 AGAGGATAGCAAGCAATCTGGG 59.894 50.000 0.00 0.00 0.00 4.45
2658 6340 1.937546 GCAAGCAATCTGGGTTCGGG 61.938 60.000 0.00 0.00 0.00 5.14
2661 6343 1.002624 GCAATCTGGGTTCGGGTCA 60.003 57.895 0.00 0.00 0.00 4.02
2681 6363 0.307760 GTCGAGTTTGGTTGCAGTGG 59.692 55.000 0.00 0.00 0.00 4.00
2706 6388 7.773690 GGTGGTGGATTAAATTATGACAGTAGT 59.226 37.037 0.00 0.00 0.00 2.73
2720 6402 2.567615 ACAGTAGTAAGGCCACTCCAAG 59.432 50.000 5.01 0.00 37.29 3.61
2833 6515 5.222631 GCTTGTTTGAAACATGAGGTTAGG 58.777 41.667 22.99 0.00 41.79 2.69
2835 6517 4.798882 TGTTTGAAACATGAGGTTAGGGT 58.201 39.130 6.66 0.00 39.29 4.34
2836 6518 5.205056 TGTTTGAAACATGAGGTTAGGGTT 58.795 37.500 6.66 0.00 39.29 4.11
2837 6519 6.366340 TGTTTGAAACATGAGGTTAGGGTTA 58.634 36.000 6.66 0.00 39.29 2.85
2839 6521 7.175990 TGTTTGAAACATGAGGTTAGGGTTATC 59.824 37.037 6.66 0.00 39.29 1.75
2840 6522 5.751586 TGAAACATGAGGTTAGGGTTATCC 58.248 41.667 0.00 0.00 39.29 2.59
2843 6525 5.373812 ACATGAGGTTAGGGTTATCCTTG 57.626 43.478 0.00 0.00 45.47 3.61
2844 6526 4.788617 ACATGAGGTTAGGGTTATCCTTGT 59.211 41.667 0.00 0.00 45.47 3.16
2845 6527 5.104485 ACATGAGGTTAGGGTTATCCTTGTC 60.104 44.000 0.00 0.00 45.47 3.18
3166 6942 7.624549 TCAGAAAGCAGTAATCTGGAGTTTAT 58.375 34.615 2.53 0.00 40.71 1.40
3180 6956 8.547481 TCTGGAGTTTATGGTGTTCTGATATA 57.453 34.615 0.00 0.00 0.00 0.86
3244 7083 9.334693 CTTGTTTGTCTAAAATTCAGTATCTGC 57.665 33.333 0.00 0.00 0.00 4.26
3245 7084 7.518161 TGTTTGTCTAAAATTCAGTATCTGCG 58.482 34.615 0.00 0.00 0.00 5.18
3246 7085 6.662414 TTGTCTAAAATTCAGTATCTGCGG 57.338 37.500 0.00 0.00 0.00 5.69
3247 7086 5.972935 TGTCTAAAATTCAGTATCTGCGGA 58.027 37.500 0.00 0.00 0.00 5.54
3248 7087 6.582636 TGTCTAAAATTCAGTATCTGCGGAT 58.417 36.000 13.70 13.70 36.07 4.18
3249 7088 7.722363 TGTCTAAAATTCAGTATCTGCGGATA 58.278 34.615 11.36 11.36 33.71 2.59
3250 7089 8.367911 TGTCTAAAATTCAGTATCTGCGGATAT 58.632 33.333 18.11 5.28 36.88 1.63
3251 7090 9.209175 GTCTAAAATTCAGTATCTGCGGATATT 57.791 33.333 18.11 11.48 36.88 1.28
3252 7091 9.424319 TCTAAAATTCAGTATCTGCGGATATTC 57.576 33.333 18.11 6.77 36.88 1.75
3253 7092 9.429359 CTAAAATTCAGTATCTGCGGATATTCT 57.571 33.333 18.11 8.95 36.88 2.40
3254 7093 8.682936 AAAATTCAGTATCTGCGGATATTCTT 57.317 30.769 18.11 5.18 36.88 2.52
3255 7094 7.664082 AATTCAGTATCTGCGGATATTCTTG 57.336 36.000 18.11 13.55 36.88 3.02
3256 7095 5.139435 TCAGTATCTGCGGATATTCTTGG 57.861 43.478 18.11 3.08 36.88 3.61
3257 7096 4.832823 TCAGTATCTGCGGATATTCTTGGA 59.167 41.667 18.11 5.31 36.88 3.53
3258 7097 5.304357 TCAGTATCTGCGGATATTCTTGGAA 59.696 40.000 18.11 0.00 36.88 3.53
3259 7098 5.636965 CAGTATCTGCGGATATTCTTGGAAG 59.363 44.000 18.11 0.00 36.88 3.46
3260 7099 4.963318 ATCTGCGGATATTCTTGGAAGA 57.037 40.909 6.14 0.00 0.00 2.87
3261 7100 6.042093 AGTATCTGCGGATATTCTTGGAAGAA 59.958 38.462 18.11 4.34 39.82 2.52
3262 7101 4.442706 TCTGCGGATATTCTTGGAAGAAC 58.557 43.478 3.95 0.00 46.80 3.01
3263 7102 4.081142 TCTGCGGATATTCTTGGAAGAACA 60.081 41.667 3.95 0.00 46.80 3.18
3264 7103 4.780815 TGCGGATATTCTTGGAAGAACAT 58.219 39.130 3.95 0.00 46.80 2.71
3265 7104 4.816385 TGCGGATATTCTTGGAAGAACATC 59.184 41.667 10.65 10.65 46.80 3.06
3266 7105 4.816385 GCGGATATTCTTGGAAGAACATCA 59.184 41.667 17.84 1.58 45.98 3.07
3267 7106 5.277538 GCGGATATTCTTGGAAGAACATCAC 60.278 44.000 17.84 8.83 45.98 3.06
3268 7107 5.817296 CGGATATTCTTGGAAGAACATCACA 59.183 40.000 17.84 0.00 45.98 3.58
3269 7108 6.018425 CGGATATTCTTGGAAGAACATCACAG 60.018 42.308 17.84 8.25 45.98 3.66
3270 7109 6.825721 GGATATTCTTGGAAGAACATCACAGT 59.174 38.462 17.84 0.00 45.98 3.55
3271 7110 7.011857 GGATATTCTTGGAAGAACATCACAGTC 59.988 40.741 17.84 1.98 45.98 3.51
3272 7111 4.008074 TCTTGGAAGAACATCACAGTCC 57.992 45.455 0.00 0.00 30.73 3.85
3273 7112 3.648067 TCTTGGAAGAACATCACAGTCCT 59.352 43.478 0.00 0.00 30.73 3.85
3274 7113 4.103153 TCTTGGAAGAACATCACAGTCCTT 59.897 41.667 0.00 0.00 30.73 3.36
3275 7114 4.008074 TGGAAGAACATCACAGTCCTTC 57.992 45.455 0.00 0.00 0.00 3.46
3276 7115 3.390967 TGGAAGAACATCACAGTCCTTCA 59.609 43.478 0.00 0.00 33.63 3.02
3277 7116 4.042062 TGGAAGAACATCACAGTCCTTCAT 59.958 41.667 0.00 0.00 33.63 2.57
3278 7117 5.248248 TGGAAGAACATCACAGTCCTTCATA 59.752 40.000 0.00 0.00 33.63 2.15
3279 7118 6.173339 GGAAGAACATCACAGTCCTTCATAA 58.827 40.000 0.00 0.00 33.63 1.90
3280 7119 6.655003 GGAAGAACATCACAGTCCTTCATAAA 59.345 38.462 0.00 0.00 33.63 1.40
3281 7120 7.361286 GGAAGAACATCACAGTCCTTCATAAAC 60.361 40.741 0.00 0.00 33.63 2.01
3282 7121 6.773638 AGAACATCACAGTCCTTCATAAACT 58.226 36.000 0.00 0.00 0.00 2.66
3283 7122 7.227156 AGAACATCACAGTCCTTCATAAACTT 58.773 34.615 0.00 0.00 0.00 2.66
3284 7123 6.808008 ACATCACAGTCCTTCATAAACTTG 57.192 37.500 0.00 0.00 0.00 3.16
3285 7124 6.299141 ACATCACAGTCCTTCATAAACTTGT 58.701 36.000 0.00 0.00 0.00 3.16
3286 7125 6.428159 ACATCACAGTCCTTCATAAACTTGTC 59.572 38.462 0.00 0.00 0.00 3.18
3287 7126 6.174720 TCACAGTCCTTCATAAACTTGTCT 57.825 37.500 0.00 0.00 0.00 3.41
3288 7127 5.991606 TCACAGTCCTTCATAAACTTGTCTG 59.008 40.000 0.00 0.00 0.00 3.51
3289 7128 5.760253 CACAGTCCTTCATAAACTTGTCTGT 59.240 40.000 0.00 0.00 33.62 3.41
3290 7129 5.992217 ACAGTCCTTCATAAACTTGTCTGTC 59.008 40.000 0.00 0.00 0.00 3.51
3291 7130 6.183361 ACAGTCCTTCATAAACTTGTCTGTCT 60.183 38.462 0.00 0.00 0.00 3.41
3292 7131 7.015292 ACAGTCCTTCATAAACTTGTCTGTCTA 59.985 37.037 0.00 0.00 0.00 2.59
3293 7132 7.872993 CAGTCCTTCATAAACTTGTCTGTCTAA 59.127 37.037 0.00 0.00 0.00 2.10
3294 7133 8.429641 AGTCCTTCATAAACTTGTCTGTCTAAA 58.570 33.333 0.00 0.00 0.00 1.85
3295 7134 9.052759 GTCCTTCATAAACTTGTCTGTCTAAAA 57.947 33.333 0.00 0.00 0.00 1.52
3296 7135 9.793259 TCCTTCATAAACTTGTCTGTCTAAAAT 57.207 29.630 0.00 0.00 0.00 1.82
3475 7384 6.607198 ACCCAGTTCAGTTCCATATAAAATGG 59.393 38.462 0.00 0.00 40.48 3.16
3491 7400 5.333566 AAAATGGAAGGGTTTCTCCTGTA 57.666 39.130 0.00 0.00 37.20 2.74
3492 7401 5.333566 AAATGGAAGGGTTTCTCCTGTAA 57.666 39.130 0.00 0.00 37.20 2.41
3496 7405 5.321927 TGGAAGGGTTTCTCCTGTAAATTC 58.678 41.667 0.00 0.00 37.20 2.17
3636 7550 7.613411 TGAAAATGGACAAATTTGACCCTTTTT 59.387 29.630 33.20 32.10 44.01 1.94
3690 7604 5.636965 TGCACAAAATTCATAAAATGACCCG 59.363 36.000 0.00 0.00 39.39 5.28
3693 7607 7.329717 GCACAAAATTCATAAAATGACCCGTTA 59.670 33.333 0.00 0.00 39.39 3.18
3696 7610 8.652463 CAAAATTCATAAAATGACCCGTTAACC 58.348 33.333 0.00 0.00 39.39 2.85
3699 7613 2.275134 AAAATGACCCGTTAACCCGT 57.725 45.000 0.00 0.00 0.00 5.28
3725 7639 4.076244 GCTGGGATGCCATGCTAG 57.924 61.111 6.34 5.17 32.41 3.42
3726 7640 1.453235 GCTGGGATGCCATGCTAGA 59.547 57.895 13.66 0.00 30.81 2.43
3727 7641 0.037877 GCTGGGATGCCATGCTAGAT 59.962 55.000 13.66 0.00 30.81 1.98
3728 7642 1.280133 GCTGGGATGCCATGCTAGATA 59.720 52.381 13.66 0.00 30.81 1.98
3729 7643 2.290514 GCTGGGATGCCATGCTAGATAA 60.291 50.000 13.66 0.00 30.81 1.75
3730 7644 3.341823 CTGGGATGCCATGCTAGATAAC 58.658 50.000 6.34 0.00 30.81 1.89
3731 7645 2.710471 TGGGATGCCATGCTAGATAACA 59.290 45.455 0.00 0.00 0.00 2.41
3732 7646 3.331591 TGGGATGCCATGCTAGATAACAT 59.668 43.478 0.00 0.00 0.00 2.71
3733 7647 3.693085 GGGATGCCATGCTAGATAACATG 59.307 47.826 0.00 0.00 42.67 3.21
3734 7648 4.330250 GGATGCCATGCTAGATAACATGT 58.670 43.478 0.00 0.00 41.69 3.21
3735 7649 4.394300 GGATGCCATGCTAGATAACATGTC 59.606 45.833 0.00 0.00 41.69 3.06
3736 7650 4.420522 TGCCATGCTAGATAACATGTCA 57.579 40.909 0.00 0.00 41.69 3.58
3737 7651 4.129380 TGCCATGCTAGATAACATGTCAC 58.871 43.478 0.00 0.00 41.69 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.692681 CGACTAATTTTCATAATGGCAAGGTG 59.307 38.462 0.00 0.00 0.00 4.00
8 1646 7.581213 ATTCCGACTAATTTTCATAATGGCA 57.419 32.000 0.00 0.00 0.00 4.92
21 1659 9.120538 ACATTAGTTGCATTAATTCCGACTAAT 57.879 29.630 20.54 20.54 42.58 1.73
23 1661 8.500753 AACATTAGTTGCATTAATTCCGACTA 57.499 30.769 8.13 8.13 36.39 2.59
25 1663 9.730420 AATAACATTAGTTGCATTAATTCCGAC 57.270 29.630 0.00 0.00 38.69 4.79
84 1722 1.164411 TCACCGCATCACCAACAATC 58.836 50.000 0.00 0.00 0.00 2.67
126 1764 8.766476 ACCAGAGGGAATATCTAACATCATATG 58.234 37.037 0.00 0.00 38.05 1.78
129 1767 6.214412 GGACCAGAGGGAATATCTAACATCAT 59.786 42.308 0.00 0.00 38.05 2.45
133 3443 5.157770 AGGACCAGAGGGAATATCTAACA 57.842 43.478 0.00 0.00 38.05 2.41
142 3452 3.329814 GGAGTAAAAAGGACCAGAGGGAA 59.670 47.826 0.00 0.00 38.05 3.97
145 3455 2.935676 GCGGAGTAAAAAGGACCAGAGG 60.936 54.545 0.00 0.00 0.00 3.69
148 3458 1.804748 GTGCGGAGTAAAAAGGACCAG 59.195 52.381 0.00 0.00 0.00 4.00
158 3468 3.407698 ACAAATCACATGTGCGGAGTAA 58.592 40.909 21.38 2.02 0.00 2.24
168 3478 6.732154 AGTTTGACTTCTGACAAATCACATG 58.268 36.000 0.00 0.00 39.24 3.21
892 4547 2.158755 GGACAGGAGGAGAGAGAGAGAG 60.159 59.091 0.00 0.00 0.00 3.20
893 4548 1.843851 GGACAGGAGGAGAGAGAGAGA 59.156 57.143 0.00 0.00 0.00 3.10
894 4549 1.563879 TGGACAGGAGGAGAGAGAGAG 59.436 57.143 0.00 0.00 0.00 3.20
895 4550 1.675007 TGGACAGGAGGAGAGAGAGA 58.325 55.000 0.00 0.00 0.00 3.10
896 4551 2.495669 GTTTGGACAGGAGGAGAGAGAG 59.504 54.545 0.00 0.00 0.00 3.20
897 4552 2.530701 GTTTGGACAGGAGGAGAGAGA 58.469 52.381 0.00 0.00 0.00 3.10
1349 5013 0.666577 CCGTCTTCTGGGTTCACGAC 60.667 60.000 0.00 0.00 32.08 4.34
1494 5164 1.609501 TCCAGAGGACGGGTTGGAG 60.610 63.158 0.00 0.00 34.90 3.86
1812 5494 0.382636 CTTCGTCGAACAAACACGCC 60.383 55.000 2.90 0.00 33.46 5.68
1917 5599 1.089920 CAAAATCCAGCAGACCTCCG 58.910 55.000 0.00 0.00 0.00 4.63
2091 5773 3.699894 CTGCTGCCCAGTCCTCGT 61.700 66.667 0.00 0.00 36.79 4.18
2163 5845 1.079612 GCCTGTGCTGCCATTTTCC 60.080 57.895 0.00 0.00 33.53 3.13
2223 5905 1.062428 TCTACCACCGGATCCATCCTT 60.062 52.381 9.46 0.00 44.93 3.36
2235 5917 1.112113 TCTCGAGGCATTCTACCACC 58.888 55.000 13.56 0.00 0.00 4.61
2412 6094 2.472695 TCCCCTTCAATTCTGTGTCG 57.527 50.000 0.00 0.00 0.00 4.35
2599 6281 1.344763 AGCGTTAACTGGCTGAAGAGT 59.655 47.619 7.14 0.00 38.27 3.24
2602 6284 1.873591 ACAAGCGTTAACTGGCTGAAG 59.126 47.619 8.51 5.43 39.93 3.02
2604 6286 1.601903 CAACAAGCGTTAACTGGCTGA 59.398 47.619 8.51 0.00 39.93 4.26
2631 6313 2.106166 CCCAGATTGCTTGCTATCCTCT 59.894 50.000 12.03 0.00 0.00 3.69
2652 6334 1.137513 CAAACTCGACTGACCCGAAC 58.862 55.000 0.00 0.00 35.48 3.95
2658 6340 1.261619 CTGCAACCAAACTCGACTGAC 59.738 52.381 0.00 0.00 0.00 3.51
2661 6343 1.299541 CACTGCAACCAAACTCGACT 58.700 50.000 0.00 0.00 0.00 4.18
2681 6363 8.732746 ACTACTGTCATAATTTAATCCACCAC 57.267 34.615 0.00 0.00 0.00 4.16
2706 6388 3.087065 GGGCTTGGAGTGGCCTTA 58.913 61.111 3.32 0.00 46.80 2.69
2720 6402 1.228245 TCTGCCACTTGAACAGGGC 60.228 57.895 0.00 0.00 46.58 5.19
2833 6515 5.352569 CACAACATCTGAGACAAGGATAACC 59.647 44.000 0.00 0.00 0.00 2.85
2835 6517 6.114187 ACACAACATCTGAGACAAGGATAA 57.886 37.500 0.00 0.00 0.00 1.75
2836 6518 5.745312 ACACAACATCTGAGACAAGGATA 57.255 39.130 0.00 0.00 0.00 2.59
2837 6519 4.630644 ACACAACATCTGAGACAAGGAT 57.369 40.909 0.00 0.00 0.00 3.24
2839 6521 4.887748 AGTACACAACATCTGAGACAAGG 58.112 43.478 0.00 0.00 0.00 3.61
2840 6522 6.682746 AGTAGTACACAACATCTGAGACAAG 58.317 40.000 2.52 0.00 0.00 3.16
2841 6523 6.650427 AGTAGTACACAACATCTGAGACAA 57.350 37.500 2.52 0.00 0.00 3.18
2843 6525 7.380431 ACTAGTAGTACACAACATCTGAGAC 57.620 40.000 0.00 0.00 0.00 3.36
2844 6526 7.997773 AACTAGTAGTACACAACATCTGAGA 57.002 36.000 2.50 0.00 0.00 3.27
2845 6527 8.948145 ACTAACTAGTAGTACACAACATCTGAG 58.052 37.037 2.50 0.00 41.51 3.35
2961 6729 0.675208 TGCGCTGCCGGAAAAAGATA 60.675 50.000 5.05 0.00 34.32 1.98
3045 6813 1.486310 ACTGTGAGCTCACTTGGTTCA 59.514 47.619 38.81 21.25 46.55 3.18
3051 6819 2.697751 ACTCTGAACTGTGAGCTCACTT 59.302 45.455 38.81 28.86 46.55 3.16
3102 6878 3.309682 AGAATTACATGTCGAATGCCACG 59.690 43.478 0.00 0.00 0.00 4.94
3166 6942 9.987272 CAAGAATATCAGTATATCAGAACACCA 57.013 33.333 0.00 0.00 0.00 4.17
3235 7074 5.139435 TCCAAGAATATCCGCAGATACTG 57.861 43.478 0.00 0.00 37.80 2.74
3236 7075 5.540337 TCTTCCAAGAATATCCGCAGATACT 59.460 40.000 0.00 0.00 37.80 2.12
3237 7076 5.784177 TCTTCCAAGAATATCCGCAGATAC 58.216 41.667 0.00 0.00 37.80 2.24
3238 7077 6.183360 TGTTCTTCCAAGAATATCCGCAGATA 60.183 38.462 5.07 0.00 45.83 1.98
3239 7078 4.963318 TCTTCCAAGAATATCCGCAGAT 57.037 40.909 0.00 0.00 32.32 2.90
3240 7079 4.081142 TGTTCTTCCAAGAATATCCGCAGA 60.081 41.667 5.07 0.00 45.83 4.26
3241 7080 4.191544 TGTTCTTCCAAGAATATCCGCAG 58.808 43.478 5.07 0.00 45.83 5.18
3242 7081 4.214986 TGTTCTTCCAAGAATATCCGCA 57.785 40.909 5.07 0.00 45.83 5.69
3247 7086 6.825721 GGACTGTGATGTTCTTCCAAGAATAT 59.174 38.462 10.19 10.19 45.65 1.28
3248 7087 6.013379 AGGACTGTGATGTTCTTCCAAGAATA 60.013 38.462 5.07 3.21 45.83 1.75
3249 7088 5.006386 GGACTGTGATGTTCTTCCAAGAAT 58.994 41.667 5.07 0.00 45.83 2.40
3250 7089 4.103153 AGGACTGTGATGTTCTTCCAAGAA 59.897 41.667 0.00 0.00 42.41 2.52
3251 7090 3.648067 AGGACTGTGATGTTCTTCCAAGA 59.352 43.478 0.00 0.00 0.00 3.02
3252 7091 4.013267 AGGACTGTGATGTTCTTCCAAG 57.987 45.455 0.00 0.00 0.00 3.61
3253 7092 4.141505 TGAAGGACTGTGATGTTCTTCCAA 60.142 41.667 11.69 0.00 46.67 3.53
3254 7093 3.390967 TGAAGGACTGTGATGTTCTTCCA 59.609 43.478 11.69 0.53 46.67 3.53
3255 7094 4.008074 TGAAGGACTGTGATGTTCTTCC 57.992 45.455 11.69 0.00 46.67 3.46
3257 7096 7.227156 AGTTTATGAAGGACTGTGATGTTCTT 58.773 34.615 0.00 0.00 38.39 2.52
3258 7097 6.773638 AGTTTATGAAGGACTGTGATGTTCT 58.226 36.000 0.00 0.00 0.00 3.01
3259 7098 7.041098 ACAAGTTTATGAAGGACTGTGATGTTC 60.041 37.037 0.00 0.00 0.00 3.18
3260 7099 6.772716 ACAAGTTTATGAAGGACTGTGATGTT 59.227 34.615 0.00 0.00 0.00 2.71
3261 7100 6.299141 ACAAGTTTATGAAGGACTGTGATGT 58.701 36.000 0.00 0.00 0.00 3.06
3262 7101 6.652481 AGACAAGTTTATGAAGGACTGTGATG 59.348 38.462 0.00 0.00 0.00 3.07
3263 7102 6.652481 CAGACAAGTTTATGAAGGACTGTGAT 59.348 38.462 0.00 0.00 0.00 3.06
3264 7103 5.991606 CAGACAAGTTTATGAAGGACTGTGA 59.008 40.000 0.00 0.00 0.00 3.58
3265 7104 5.760253 ACAGACAAGTTTATGAAGGACTGTG 59.240 40.000 0.00 0.00 34.39 3.66
3266 7105 5.930135 ACAGACAAGTTTATGAAGGACTGT 58.070 37.500 0.00 0.00 0.00 3.55
3267 7106 6.226787 AGACAGACAAGTTTATGAAGGACTG 58.773 40.000 0.00 0.00 0.00 3.51
3268 7107 6.426646 AGACAGACAAGTTTATGAAGGACT 57.573 37.500 0.00 0.00 0.00 3.85
3269 7108 8.603242 TTTAGACAGACAAGTTTATGAAGGAC 57.397 34.615 0.00 0.00 0.00 3.85
3270 7109 9.793259 ATTTTAGACAGACAAGTTTATGAAGGA 57.207 29.630 0.00 0.00 0.00 3.36
3280 7119 9.429359 CAGATACTGAATTTTAGACAGACAAGT 57.571 33.333 0.00 0.00 35.85 3.16
3281 7120 8.386606 GCAGATACTGAATTTTAGACAGACAAG 58.613 37.037 0.00 0.00 35.85 3.16
3282 7121 7.063426 CGCAGATACTGAATTTTAGACAGACAA 59.937 37.037 0.00 0.00 35.85 3.18
3283 7122 6.531594 CGCAGATACTGAATTTTAGACAGACA 59.468 38.462 0.00 0.00 35.85 3.41
3284 7123 6.531948 ACGCAGATACTGAATTTTAGACAGAC 59.468 38.462 0.00 0.00 35.85 3.51
3285 7124 6.631016 ACGCAGATACTGAATTTTAGACAGA 58.369 36.000 0.00 0.00 35.85 3.41
3286 7125 6.019479 GGACGCAGATACTGAATTTTAGACAG 60.019 42.308 2.81 0.00 37.62 3.51
3287 7126 5.810587 GGACGCAGATACTGAATTTTAGACA 59.189 40.000 2.81 0.00 32.44 3.41
3288 7127 6.019479 CAGGACGCAGATACTGAATTTTAGAC 60.019 42.308 2.81 0.00 32.44 2.59
3289 7128 6.042777 CAGGACGCAGATACTGAATTTTAGA 58.957 40.000 2.81 0.00 32.44 2.10
3290 7129 6.042777 TCAGGACGCAGATACTGAATTTTAG 58.957 40.000 2.81 0.00 37.06 1.85
3291 7130 5.972935 TCAGGACGCAGATACTGAATTTTA 58.027 37.500 2.81 0.00 37.06 1.52
3292 7131 4.832248 TCAGGACGCAGATACTGAATTTT 58.168 39.130 2.81 0.00 37.06 1.82
3293 7132 4.437239 CTCAGGACGCAGATACTGAATTT 58.563 43.478 2.81 0.00 39.26 1.82
3294 7133 3.181471 CCTCAGGACGCAGATACTGAATT 60.181 47.826 2.81 0.00 39.26 2.17
3295 7134 2.363680 CCTCAGGACGCAGATACTGAAT 59.636 50.000 2.81 0.00 39.26 2.57
3296 7135 1.751351 CCTCAGGACGCAGATACTGAA 59.249 52.381 2.81 0.00 39.26 3.02
3297 7136 1.341089 ACCTCAGGACGCAGATACTGA 60.341 52.381 0.00 0.00 37.61 3.41
3441 7350 1.625818 ACTGAACTGGGTAGGAGCAAG 59.374 52.381 0.00 0.00 0.00 4.01
3475 7384 7.526142 AAAGAATTTACAGGAGAAACCCTTC 57.474 36.000 0.00 0.00 35.86 3.46
3491 7400 7.655732 CGAACCCCAACTCAATAAAAAGAATTT 59.344 33.333 0.00 0.00 42.41 1.82
3492 7401 7.151976 CGAACCCCAACTCAATAAAAAGAATT 58.848 34.615 0.00 0.00 0.00 2.17
3496 7405 5.447624 ACGAACCCCAACTCAATAAAAAG 57.552 39.130 0.00 0.00 0.00 2.27
3717 7631 4.067896 GGGTGACATGTTATCTAGCATGG 58.932 47.826 15.55 2.20 45.50 3.66
3719 7633 4.202398 CCAGGGTGACATGTTATCTAGCAT 60.202 45.833 0.00 0.00 41.51 3.79
3720 7634 3.134623 CCAGGGTGACATGTTATCTAGCA 59.865 47.826 0.00 0.00 41.51 3.49
3721 7635 3.733337 CCAGGGTGACATGTTATCTAGC 58.267 50.000 0.00 0.00 41.51 3.42
3722 7636 3.495100 GGCCAGGGTGACATGTTATCTAG 60.495 52.174 0.00 0.00 41.51 2.43
3723 7637 2.438021 GGCCAGGGTGACATGTTATCTA 59.562 50.000 0.00 0.00 41.51 1.98
3724 7638 1.212935 GGCCAGGGTGACATGTTATCT 59.787 52.381 0.00 0.00 41.51 1.98
3725 7639 1.212935 AGGCCAGGGTGACATGTTATC 59.787 52.381 5.01 0.00 41.51 1.75
3726 7640 1.064463 CAGGCCAGGGTGACATGTTAT 60.064 52.381 5.01 0.00 41.51 1.89
3727 7641 0.327924 CAGGCCAGGGTGACATGTTA 59.672 55.000 5.01 0.00 41.51 2.41
3728 7642 1.075482 CAGGCCAGGGTGACATGTT 59.925 57.895 5.01 0.00 41.51 2.71
3729 7643 1.845627 CTCAGGCCAGGGTGACATGT 61.846 60.000 5.01 0.00 41.51 3.21
3730 7644 1.077930 CTCAGGCCAGGGTGACATG 60.078 63.158 5.01 0.00 43.08 3.21
3731 7645 2.304056 CCTCAGGCCAGGGTGACAT 61.304 63.158 5.01 0.00 0.00 3.06
3732 7646 2.930019 CCTCAGGCCAGGGTGACA 60.930 66.667 5.01 0.00 0.00 3.58
3733 7647 4.416738 GCCTCAGGCCAGGGTGAC 62.417 72.222 3.37 0.00 44.06 3.67
3751 7665 3.884350 CGCGCCATCAAGCATGCT 61.884 61.111 16.30 16.30 0.00 3.79
3752 7666 4.918129 CCGCGCCATCAAGCATGC 62.918 66.667 10.51 10.51 0.00 4.06


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

AutoCloner maintained by Alex Coulton.