Multiple sequence alignment - TraesCS4A01G134600

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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 TraesCS4A01G134600 chr4A 100.000 4129 0 0 1 4129 182921250 182925378 0.000000e+00 7625.0
1 TraesCS4A01G134600 chr4D 92.947 3261 137 32 920 4129 300282666 300279448 0.000000e+00 4662.0
2 TraesCS4A01G134600 chr4D 88.163 980 41 27 1 922 300283658 300282696 0.000000e+00 1098.0
3 TraesCS4A01G134600 chr4B 90.292 2977 177 38 1213 4128 373763096 373760171 0.000000e+00 3794.0
4 TraesCS4A01G134600 chr4B 88.132 1247 67 30 1 1171 373764341 373763100 0.000000e+00 1408.0
5 TraesCS4A01G134600 chr1B 82.979 94 14 2 3845 3938 593602813 593602722 2.650000e-12 84.2
6 TraesCS4A01G134600 chr1B 85.000 60 8 1 3879 3938 593495815 593495757 4.460000e-05 60.2
7 TraesCS4A01G134600 chr3D 84.211 76 12 0 3863 3938 526908817 526908742 1.590000e-09 75.0
8 TraesCS4A01G134600 chr1D 77.778 117 25 1 3822 3938 437903653 437903538 2.060000e-08 71.3
9 TraesCS4A01G134600 chr1A 83.333 78 11 2 3861 3938 534564260 534564185 2.060000e-08 71.3
10 TraesCS4A01G134600 chr2B 85.714 63 9 0 3872 3934 1212309 1212247 2.660000e-07 67.6
11 TraesCS4A01G134600 chr2B 96.970 33 0 1 459 491 743320259 743320228 2.000000e-03 54.7
12 TraesCS4A01G134600 chr5B 84.058 69 10 1 3866 3933 501959551 501959619 9.580000e-07 65.8


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 TraesCS4A01G134600 chr4A 182921250 182925378 4128 False 7625 7625 100.000 1 4129 1 chr4A.!!$F1 4128
1 TraesCS4A01G134600 chr4D 300279448 300283658 4210 True 2880 4662 90.555 1 4129 2 chr4D.!!$R1 4128
2 TraesCS4A01G134600 chr4B 373760171 373764341 4170 True 2601 3794 89.212 1 4128 2 chr4B.!!$R1 4127

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
47 49 0.034896 GAAACCACGAGGAGGAAGCA 59.965 55.0 5.68 0.0 38.69 3.91 F
1487 1614 0.105760 AACTGGGTTCCATTGGTGCA 60.106 50.0 1.86 0.0 30.82 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1676 0.459237 CTTCTCGCTGCTTCCGATGT 60.459 55.0 0.0 0.0 33.83 3.06 R
3150 3289 0.250513 AACTCGCCAATCCTGAGTCC 59.749 55.0 0.0 0.0 41.88 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
33 35 0.251209 GGGGAAGAGTGGTGGAAACC 60.251 60.000 0.00 0.00 0.00 3.27
47 49 0.034896 GAAACCACGAGGAGGAAGCA 59.965 55.000 5.68 0.00 38.69 3.91
48 50 0.693049 AAACCACGAGGAGGAAGCAT 59.307 50.000 5.68 0.00 38.69 3.79
95 100 1.578897 GCTTCTTCCCCTCTTCCTCT 58.421 55.000 0.00 0.00 0.00 3.69
96 101 1.912731 GCTTCTTCCCCTCTTCCTCTT 59.087 52.381 0.00 0.00 0.00 2.85
97 102 2.093181 GCTTCTTCCCCTCTTCCTCTTC 60.093 54.545 0.00 0.00 0.00 2.87
98 103 3.177228 CTTCTTCCCCTCTTCCTCTTCA 58.823 50.000 0.00 0.00 0.00 3.02
99 104 3.498614 TCTTCCCCTCTTCCTCTTCAT 57.501 47.619 0.00 0.00 0.00 2.57
100 105 3.379452 TCTTCCCCTCTTCCTCTTCATC 58.621 50.000 0.00 0.00 0.00 2.92
137 148 0.107459 GGTGCCTTTCCAGAGCCTAG 60.107 60.000 0.00 0.00 0.00 3.02
138 149 0.615850 GTGCCTTTCCAGAGCCTAGT 59.384 55.000 0.00 0.00 0.00 2.57
169 183 1.952621 TCCCTCATCTCCTCCGTTTT 58.047 50.000 0.00 0.00 0.00 2.43
175 193 5.396884 CCCTCATCTCCTCCGTTTTATTCTT 60.397 44.000 0.00 0.00 0.00 2.52
179 197 7.042335 TCATCTCCTCCGTTTTATTCTTTCTC 58.958 38.462 0.00 0.00 0.00 2.87
180 198 6.607004 TCTCCTCCGTTTTATTCTTTCTCT 57.393 37.500 0.00 0.00 0.00 3.10
181 199 6.631962 TCTCCTCCGTTTTATTCTTTCTCTC 58.368 40.000 0.00 0.00 0.00 3.20
182 200 5.731591 TCCTCCGTTTTATTCTTTCTCTCC 58.268 41.667 0.00 0.00 0.00 3.71
199 217 2.578178 CGTCTCGAGCTGGCTTCG 60.578 66.667 7.81 2.75 0.00 3.79
220 238 4.399303 TCGAGATTACTCTCTTCATGTGCA 59.601 41.667 8.31 0.00 44.92 4.57
221 239 5.105063 CGAGATTACTCTCTTCATGTGCAA 58.895 41.667 8.31 0.00 44.92 4.08
286 328 6.808321 TTCTACTAGGTTGCAACTCCATAT 57.192 37.500 27.64 12.05 0.00 1.78
287 329 7.907841 TTCTACTAGGTTGCAACTCCATATA 57.092 36.000 27.64 12.49 0.00 0.86
443 491 9.310716 GTACCAACAATCAGTACCTTATTACTC 57.689 37.037 0.00 0.00 32.07 2.59
533 584 6.072673 ACAATCACTACCTTCCGATTTGTTTC 60.073 38.462 0.00 0.00 0.00 2.78
661 742 1.607801 GCCCCTGCATTTCTTGGTCC 61.608 60.000 0.00 0.00 37.47 4.46
668 756 2.040544 ATTTCTTGGTCCGCAGCCG 61.041 57.895 0.00 0.00 0.00 5.52
715 803 7.557719 AGCAGCTAATCTTATTTGTATGTGGTT 59.442 33.333 0.00 0.00 0.00 3.67
719 807 8.345565 GCTAATCTTATTTGTATGTGGTTCTGG 58.654 37.037 0.00 0.00 0.00 3.86
736 824 5.452777 GTTCTGGAACTGTATTTCTTGCAC 58.547 41.667 6.26 0.00 38.25 4.57
745 833 3.317711 TGTATTTCTTGCACCACCTTGTG 59.682 43.478 0.00 0.00 39.29 3.33
746 834 1.846007 TTTCTTGCACCACCTTGTGT 58.154 45.000 0.00 0.00 38.52 3.72
800 888 5.518847 ACGGATACATGTTATTCACGTTCAG 59.481 40.000 2.30 0.00 0.00 3.02
862 956 2.555227 CCAACCAGGTGCTAGTGGAATT 60.555 50.000 1.25 0.00 37.27 2.17
864 958 2.795329 ACCAGGTGCTAGTGGAATTTG 58.205 47.619 4.21 0.00 37.27 2.32
870 964 4.885907 AGGTGCTAGTGGAATTTGATCATG 59.114 41.667 0.00 0.00 0.00 3.07
924 1051 3.041211 TGGATTCTGGACCTGGTATCAG 58.959 50.000 18.27 18.27 40.59 2.90
946 1073 4.781087 AGTTTGGTGGTAGCTGGTAGATAA 59.219 41.667 0.00 0.00 0.00 1.75
951 1078 5.139001 GGTGGTAGCTGGTAGATAACTACT 58.861 45.833 9.72 0.00 45.70 2.57
1065 1192 6.238648 CCCAAAGTGTCTTAACATTCTACCT 58.761 40.000 0.00 0.00 37.81 3.08
1196 1323 5.186198 CCCCTCCGATCCATATTAATTGTC 58.814 45.833 0.00 0.00 0.00 3.18
1200 1327 6.275494 TCCGATCCATATTAATTGTCGCTA 57.725 37.500 0.00 0.00 0.00 4.26
1201 1328 6.873997 TCCGATCCATATTAATTGTCGCTAT 58.126 36.000 0.00 0.00 0.00 2.97
1478 1605 1.029681 AAAGCAACGAACTGGGTTCC 58.970 50.000 5.06 0.00 39.14 3.62
1487 1614 0.105760 AACTGGGTTCCATTGGTGCA 60.106 50.000 1.86 0.00 30.82 4.57
1505 1632 1.879372 GCAGCTGCGGATGATTCCATA 60.879 52.381 25.23 0.00 42.74 2.74
1549 1676 0.543277 ATCGAGCAAGAGGGCAATGA 59.457 50.000 0.00 0.00 35.83 2.57
1552 1679 1.760192 GAGCAAGAGGGCAATGACAT 58.240 50.000 0.00 0.00 35.83 3.06
1604 1731 5.988561 GTCAGATGAGGAGAATGTTATGGAC 59.011 44.000 0.00 0.00 0.00 4.02
1619 1746 5.470437 TGTTATGGACGTTGCAAATACTGAA 59.530 36.000 0.00 0.00 0.00 3.02
1626 1753 3.641648 GTTGCAAATACTGAAAGCAGCA 58.358 40.909 0.00 0.00 46.26 4.41
1665 1792 1.952367 GCCAGGACACCAATGGAGAAG 60.952 57.143 6.16 0.00 36.09 2.85
1667 1794 2.571653 CCAGGACACCAATGGAGAAGTA 59.428 50.000 6.16 0.00 36.09 2.24
1686 1813 2.125773 AGAAGATCTTGCTGCCCTTG 57.874 50.000 14.00 0.00 0.00 3.61
1779 1912 2.693069 CAGGGAATATAGAGGCTTGCG 58.307 52.381 0.00 0.00 0.00 4.85
1781 1914 2.564947 AGGGAATATAGAGGCTTGCGAG 59.435 50.000 0.00 0.00 0.00 5.03
1797 1930 4.642445 TGCGAGATAAACGAAGATGGTA 57.358 40.909 0.00 0.00 0.00 3.25
1811 1944 5.991606 CGAAGATGGTAATATGGAAAGCAGA 59.008 40.000 0.00 0.00 0.00 4.26
1844 1977 5.657474 TCAGAACAGAACATACCGTTATCC 58.343 41.667 0.00 0.00 38.19 2.59
1850 1983 3.956199 AGAACATACCGTTATCCGAGGAA 59.044 43.478 0.00 0.00 38.19 3.36
1931 2070 0.311790 CGGCAAGCAAGAGAAGCAAA 59.688 50.000 0.00 0.00 0.00 3.68
1951 2090 2.672961 CTCGTAAGGGTGCATTCTCA 57.327 50.000 0.00 0.00 38.47 3.27
1978 2117 0.529555 GATCTCCGAGAAGTGCCTGC 60.530 60.000 1.27 0.00 0.00 4.85
2204 2343 4.965200 ACCTCTTACAGCTTATCATCCC 57.035 45.455 0.00 0.00 0.00 3.85
2207 2346 2.037251 TCTTACAGCTTATCATCCCGCC 59.963 50.000 0.00 0.00 0.00 6.13
2609 2748 1.795889 GCGCAAGTTCTCTCCTACTCG 60.796 57.143 0.30 0.00 41.68 4.18
2825 2964 2.497138 CTGCATGTGTCAAGGAACTCA 58.503 47.619 0.00 0.00 38.49 3.41
3026 3165 2.009051 TCAGATGCTAAACATGGTGCG 58.991 47.619 0.00 0.00 39.84 5.34
3146 3285 8.179615 GGGTCATAGGTAATTTAACTTCGTTTG 58.820 37.037 0.00 0.00 0.00 2.93
3147 3286 8.724229 GGTCATAGGTAATTTAACTTCGTTTGT 58.276 33.333 0.00 0.00 0.00 2.83
3148 3287 9.750882 GTCATAGGTAATTTAACTTCGTTTGTC 57.249 33.333 0.00 0.00 0.00 3.18
3149 3288 8.649841 TCATAGGTAATTTAACTTCGTTTGTCG 58.350 33.333 0.00 0.00 41.41 4.35
3150 3289 6.232139 AGGTAATTTAACTTCGTTTGTCGG 57.768 37.500 0.00 0.00 40.32 4.79
3151 3290 5.179929 AGGTAATTTAACTTCGTTTGTCGGG 59.820 40.000 0.00 0.00 40.32 5.14
3152 3291 5.179182 GGTAATTTAACTTCGTTTGTCGGGA 59.821 40.000 0.00 0.00 40.32 5.14
3180 3319 2.094762 TGGCGAGTTTAGGAGAAAGC 57.905 50.000 0.00 0.00 0.00 3.51
3219 3360 7.337689 TGAGTTTTTGGAATGATGATAGAGTGG 59.662 37.037 0.00 0.00 0.00 4.00
3235 3376 8.438373 TGATAGAGTGGTAGCTATTACTGTAGT 58.562 37.037 15.11 7.75 32.61 2.73
3236 3377 9.941325 GATAGAGTGGTAGCTATTACTGTAGTA 57.059 37.037 15.11 1.01 32.61 1.82
3237 3378 9.723601 ATAGAGTGGTAGCTATTACTGTAGTAC 57.276 37.037 15.11 0.00 32.61 2.73
3238 3379 7.804147 AGAGTGGTAGCTATTACTGTAGTACT 58.196 38.462 15.11 0.00 32.61 2.73
3239 3380 8.932610 AGAGTGGTAGCTATTACTGTAGTACTA 58.067 37.037 15.11 0.00 32.61 1.82
3270 3415 2.592102 AATGAATGTGTGGGCTCACT 57.408 45.000 19.48 0.00 43.94 3.41
3304 3449 4.125703 CCATTCATCTGTCTACAAGGCTC 58.874 47.826 0.00 0.00 0.00 4.70
3305 3450 4.141756 CCATTCATCTGTCTACAAGGCTCT 60.142 45.833 0.00 0.00 0.00 4.09
3306 3451 5.069648 CCATTCATCTGTCTACAAGGCTCTA 59.930 44.000 0.00 0.00 0.00 2.43
3307 3452 5.584253 TTCATCTGTCTACAAGGCTCTAC 57.416 43.478 0.00 0.00 0.00 2.59
3308 3453 4.861196 TCATCTGTCTACAAGGCTCTACT 58.139 43.478 0.00 0.00 0.00 2.57
3416 3575 7.063426 GCTTTATTAGTTCTCCATTTTGTTGGC 59.937 37.037 0.00 0.00 36.66 4.52
3420 3579 4.696455 AGTTCTCCATTTTGTTGGCTTTG 58.304 39.130 0.00 0.00 36.66 2.77
3430 3589 1.879380 TGTTGGCTTTGATCTTGACGG 59.121 47.619 0.00 0.00 0.00 4.79
3450 3609 3.161866 GGGGAGATGTTGTGCCTTTTTA 58.838 45.455 0.00 0.00 0.00 1.52
3455 3615 2.160721 TGTTGTGCCTTTTTACCCCA 57.839 45.000 0.00 0.00 0.00 4.96
3499 3659 4.379339 TTTGTTGGCTTTATTATCGCCC 57.621 40.909 0.00 0.00 43.12 6.13
3524 3684 8.087750 CCTTGTCATGGCTTTATTCTTTGTAAA 58.912 33.333 0.00 0.00 0.00 2.01
3634 3795 3.054361 AGGTAAAGATGGAAGCGTGGAAT 60.054 43.478 0.00 0.00 0.00 3.01
3642 3803 2.227865 TGGAAGCGTGGAATTAAAGCAC 59.772 45.455 2.28 0.00 0.00 4.40
3718 3879 1.811266 CATCTCCAACGCCGACCTG 60.811 63.158 0.00 0.00 0.00 4.00
3725 3886 0.938713 CAACGCCGACCTGTAAAACA 59.061 50.000 0.00 0.00 0.00 2.83
3729 3890 1.658094 CGCCGACCTGTAAAACAAACG 60.658 52.381 0.00 0.00 0.00 3.60
3740 3905 5.933790 TGTAAAACAAACGCCACATCTATC 58.066 37.500 0.00 0.00 0.00 2.08
3776 3941 1.064906 ACAGGAGTCCAGGCATTGATG 60.065 52.381 12.86 0.00 0.00 3.07
3796 3962 2.044946 GGAGCCGGCATCCAAAGT 60.045 61.111 31.54 4.27 36.79 2.66
3809 3975 4.399303 GCATCCAAAGTAACTAGCCACAAT 59.601 41.667 0.00 0.00 0.00 2.71
3815 3981 5.700402 AAGTAACTAGCCACAATCATCCT 57.300 39.130 0.00 0.00 0.00 3.24
3827 3993 3.833650 ACAATCATCCTGCCACATTTGAA 59.166 39.130 0.00 0.00 0.00 2.69
3828 3994 4.178540 CAATCATCCTGCCACATTTGAAC 58.821 43.478 0.00 0.00 0.00 3.18
3829 3995 2.874014 TCATCCTGCCACATTTGAACA 58.126 42.857 0.00 0.00 0.00 3.18
3832 3998 3.451141 TCCTGCCACATTTGAACAAAC 57.549 42.857 2.03 0.00 32.51 2.93
3833 3999 2.102252 TCCTGCCACATTTGAACAAACC 59.898 45.455 2.03 0.00 32.51 3.27
3861 4038 8.232913 ACAACTTCCATTCAAGCTTAAGTAAA 57.767 30.769 9.79 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 0.179089 CTGGATGCTTCCTCCTCGTG 60.179 60.000 18.67 0.00 43.07 4.35
47 49 0.845102 ACCTTTCCCGTTCCCTGGAT 60.845 55.000 0.00 0.00 0.00 3.41
48 50 1.462627 ACCTTTCCCGTTCCCTGGA 60.463 57.895 0.00 0.00 0.00 3.86
95 100 3.634397 ATGCGGAAGGAAGAAGATGAA 57.366 42.857 0.00 0.00 32.68 2.57
96 101 3.535561 GAATGCGGAAGGAAGAAGATGA 58.464 45.455 0.00 0.00 32.68 2.92
97 102 2.286294 CGAATGCGGAAGGAAGAAGATG 59.714 50.000 0.00 0.00 32.68 2.90
98 103 2.555199 CGAATGCGGAAGGAAGAAGAT 58.445 47.619 0.00 0.00 32.68 2.40
99 104 2.010145 CGAATGCGGAAGGAAGAAGA 57.990 50.000 0.00 0.00 32.68 2.87
169 183 3.312973 GCTCGAGACGGAGAGAAAGAATA 59.687 47.826 18.75 0.00 36.65 1.75
175 193 1.027255 CCAGCTCGAGACGGAGAGAA 61.027 60.000 18.75 0.00 36.65 2.87
179 197 2.606155 GAAGCCAGCTCGAGACGGAG 62.606 65.000 18.75 0.03 37.11 4.63
180 198 2.676822 AAGCCAGCTCGAGACGGA 60.677 61.111 18.75 0.00 0.00 4.69
181 199 2.202676 GAAGCCAGCTCGAGACGG 60.203 66.667 18.75 16.22 0.00 4.79
182 200 2.578178 CGAAGCCAGCTCGAGACG 60.578 66.667 18.75 5.50 0.00 4.18
199 217 8.654230 TTATTGCACATGAAGAGAGTAATCTC 57.346 34.615 12.25 12.25 40.70 2.75
220 238 6.810911 ACAGAGCAATCGATACTGACTTATT 58.189 36.000 20.40 3.36 33.53 1.40
221 239 6.264292 AGACAGAGCAATCGATACTGACTTAT 59.736 38.462 20.40 5.69 32.10 1.73
257 290 6.485648 GGAGTTGCAACCTAGTAGAAAGAAAA 59.514 38.462 25.62 0.00 0.00 2.29
261 296 4.894784 TGGAGTTGCAACCTAGTAGAAAG 58.105 43.478 25.62 0.00 0.00 2.62
262 297 4.967084 TGGAGTTGCAACCTAGTAGAAA 57.033 40.909 25.62 0.00 0.00 2.52
264 299 6.015350 GCTATATGGAGTTGCAACCTAGTAGA 60.015 42.308 25.62 10.57 0.00 2.59
265 300 6.159988 GCTATATGGAGTTGCAACCTAGTAG 58.840 44.000 25.62 18.89 0.00 2.57
266 301 5.600898 TGCTATATGGAGTTGCAACCTAGTA 59.399 40.000 25.62 14.09 0.00 1.82
286 328 6.876789 TCTCGGAAACAAAATCTTATGTGCTA 59.123 34.615 0.00 0.00 0.00 3.49
287 329 5.705441 TCTCGGAAACAAAATCTTATGTGCT 59.295 36.000 0.00 0.00 0.00 4.40
441 489 5.576384 ACAAAGACGTCGAGTACTAGTAGAG 59.424 44.000 10.46 0.00 0.00 2.43
442 490 5.473931 ACAAAGACGTCGAGTACTAGTAGA 58.526 41.667 10.46 0.00 0.00 2.59
443 491 5.220378 GGACAAAGACGTCGAGTACTAGTAG 60.220 48.000 10.46 0.00 36.73 2.57
449 497 1.267806 TGGGACAAAGACGTCGAGTAC 59.732 52.381 10.46 10.54 36.73 2.73
455 503 3.870633 ATCTACTGGGACAAAGACGTC 57.129 47.619 7.70 7.70 38.70 4.34
533 584 4.455606 AGGAATTGGCCGATTAGAGAAAG 58.544 43.478 18.67 0.00 0.00 2.62
661 742 1.069296 TGAAAAACAAGATCGGCTGCG 60.069 47.619 0.00 0.00 0.00 5.18
668 756 5.576384 TGCTGTTTGTGTGAAAAACAAGATC 59.424 36.000 3.62 0.00 46.38 2.75
715 803 4.072131 GGTGCAAGAAATACAGTTCCAGA 58.928 43.478 0.00 0.00 0.00 3.86
719 807 3.821033 AGGTGGTGCAAGAAATACAGTTC 59.179 43.478 0.00 0.00 0.00 3.01
736 824 6.568869 TGAAGAAACATAAAACACAAGGTGG 58.431 36.000 1.07 0.00 37.94 4.61
820 909 5.815581 TGGACTAATAGCATGAAAACCTGT 58.184 37.500 0.00 0.00 0.00 4.00
839 933 0.321653 CCACTAGCACCTGGTTGGAC 60.322 60.000 8.52 0.00 39.71 4.02
862 956 7.383029 GCAAACATTCAAGAGAAACATGATCAA 59.617 33.333 0.00 0.00 37.29 2.57
864 958 6.864685 TGCAAACATTCAAGAGAAACATGATC 59.135 34.615 0.00 0.00 37.29 2.92
870 964 7.362662 TGTATCTGCAAACATTCAAGAGAAAC 58.637 34.615 0.00 0.00 37.29 2.78
924 1051 3.629142 ATCTACCAGCTACCACCAAAC 57.371 47.619 0.00 0.00 0.00 2.93
946 1073 3.947834 GCACAATATTTCCAGGCAGTAGT 59.052 43.478 0.00 0.00 0.00 2.73
951 1078 2.378038 GGAGCACAATATTTCCAGGCA 58.622 47.619 0.00 0.00 0.00 4.75
1065 1192 3.953612 AGACTGAAACATTTGCAGGTTCA 59.046 39.130 4.98 4.98 34.05 3.18
1172 1299 4.601857 ACAATTAATATGGATCGGAGGGGT 59.398 41.667 0.00 0.00 0.00 4.95
1196 1323 9.814507 TTTGTGTGTATTTGTACTAAAATAGCG 57.185 29.630 0.00 0.00 33.71 4.26
1200 1327 9.834628 CCGATTTGTGTGTATTTGTACTAAAAT 57.165 29.630 0.00 0.00 34.24 1.82
1201 1328 8.838365 ACCGATTTGTGTGTATTTGTACTAAAA 58.162 29.630 0.00 0.00 0.00 1.52
1478 1605 2.412323 ATCCGCAGCTGCACCAATG 61.412 57.895 36.03 19.47 42.21 2.82
1549 1676 0.459237 CTTCTCGCTGCTTCCGATGT 60.459 55.000 0.00 0.00 33.83 3.06
1552 1679 2.573869 CCTTCTCGCTGCTTCCGA 59.426 61.111 0.00 0.00 0.00 4.55
1604 1731 2.658325 GCTGCTTTCAGTATTTGCAACG 59.342 45.455 0.00 0.00 42.29 4.10
1619 1746 1.599542 GAACTGTCGTCTTTGCTGCTT 59.400 47.619 0.00 0.00 0.00 3.91
1626 1753 2.417719 GCCATCAGAACTGTCGTCTTT 58.582 47.619 1.73 0.00 0.00 2.52
1665 1792 2.941720 CAAGGGCAGCAAGATCTTCTAC 59.058 50.000 4.57 1.27 0.00 2.59
1667 1794 1.353694 ACAAGGGCAGCAAGATCTTCT 59.646 47.619 4.57 3.39 0.00 2.85
1686 1813 1.834188 CCATTCCCACTGGGTTGTAC 58.166 55.000 14.25 0.00 44.74 2.90
1718 1851 5.119434 GTCGTTCTCTTCTTTGTCAGAATCC 59.881 44.000 0.00 0.00 40.95 3.01
1762 1895 3.944055 TCTCGCAAGCCTCTATATTCC 57.056 47.619 0.00 0.00 37.18 3.01
1767 1900 3.318275 TCGTTTATCTCGCAAGCCTCTAT 59.682 43.478 0.00 0.00 37.18 1.98
1768 1901 2.686405 TCGTTTATCTCGCAAGCCTCTA 59.314 45.455 0.00 0.00 37.18 2.43
1779 1912 9.706691 TTCCATATTACCATCTTCGTTTATCTC 57.293 33.333 0.00 0.00 0.00 2.75
1797 1930 6.904626 AGGTATTCAGTCTGCTTTCCATATT 58.095 36.000 0.00 0.00 0.00 1.28
1826 1959 3.067742 CCTCGGATAACGGTATGTTCTGT 59.932 47.826 0.00 0.00 44.45 3.41
1835 1968 2.731572 TCTCTTTCCTCGGATAACGGT 58.268 47.619 0.00 0.00 44.45 4.83
1844 1977 4.938080 TGCTAGCTAATTCTCTTTCCTCG 58.062 43.478 17.23 0.00 0.00 4.63
1850 1983 5.653769 TGGCAAATTGCTAGCTAATTCTCTT 59.346 36.000 18.04 3.14 44.28 2.85
1931 2070 1.899814 TGAGAATGCACCCTTACGAGT 59.100 47.619 0.00 0.00 0.00 4.18
1951 2090 3.192422 CACTTCTCGGAGATCACAAGACT 59.808 47.826 8.81 0.00 33.89 3.24
1978 2117 3.055530 AGCAAGGGAGTCAACTGATACTG 60.056 47.826 0.00 0.00 0.00 2.74
2204 2343 2.787249 CCAGAATGCTTGACGGCG 59.213 61.111 4.80 4.80 34.52 6.46
2207 2346 1.003116 GCATAGCCAGAATGCTTGACG 60.003 52.381 0.93 0.00 45.05 4.35
2609 2748 3.323979 TCTTTCTGTTGGGGTCTCTGTAC 59.676 47.826 0.00 0.00 0.00 2.90
2716 2855 3.430790 CGAGTATGGTTCAGCTTGATGGA 60.431 47.826 0.00 0.00 0.00 3.41
3026 3165 4.039124 TCTTTTGCTTTTGATCCCTTCACC 59.961 41.667 0.00 0.00 32.84 4.02
3146 3285 1.153349 GCCAATCCTGAGTCCCGAC 60.153 63.158 0.00 0.00 0.00 4.79
3147 3286 2.721167 CGCCAATCCTGAGTCCCGA 61.721 63.158 0.00 0.00 0.00 5.14
3148 3287 2.202932 CGCCAATCCTGAGTCCCG 60.203 66.667 0.00 0.00 0.00 5.14
3149 3288 1.144936 CTCGCCAATCCTGAGTCCC 59.855 63.158 0.00 0.00 0.00 4.46
3150 3289 0.250513 AACTCGCCAATCCTGAGTCC 59.749 55.000 0.00 0.00 41.88 3.85
3151 3290 2.100605 AAACTCGCCAATCCTGAGTC 57.899 50.000 0.00 0.00 41.88 3.36
3152 3291 2.093447 CCTAAACTCGCCAATCCTGAGT 60.093 50.000 0.00 0.00 44.46 3.41
3180 3319 4.487948 CAAAAACTCACCCTGCATGTATG 58.512 43.478 0.00 0.00 0.00 2.39
3270 3415 5.316167 ACAGATGAATGGCAGACAACTAAA 58.684 37.500 0.00 0.00 0.00 1.85
3304 3449 5.323900 CACACATAATCGCCAAACAAGTAG 58.676 41.667 0.00 0.00 0.00 2.57
3305 3450 4.378978 GCACACATAATCGCCAAACAAGTA 60.379 41.667 0.00 0.00 0.00 2.24
3306 3451 3.611530 GCACACATAATCGCCAAACAAGT 60.612 43.478 0.00 0.00 0.00 3.16
3307 3452 2.916716 GCACACATAATCGCCAAACAAG 59.083 45.455 0.00 0.00 0.00 3.16
3308 3453 2.556189 AGCACACATAATCGCCAAACAA 59.444 40.909 0.00 0.00 0.00 2.83
3310 3455 2.420022 AGAGCACACATAATCGCCAAAC 59.580 45.455 0.00 0.00 0.00 2.93
3416 3575 3.201290 CATCTCCCCGTCAAGATCAAAG 58.799 50.000 0.00 0.00 29.77 2.77
3420 3579 2.093447 ACAACATCTCCCCGTCAAGATC 60.093 50.000 0.00 0.00 29.77 2.75
3430 3589 3.056821 GGTAAAAAGGCACAACATCTCCC 60.057 47.826 0.00 0.00 0.00 4.30
3450 3609 3.498661 GGATTCAGTTGTCTTCTTGGGGT 60.499 47.826 0.00 0.00 0.00 4.95
3455 3615 7.830099 AATTCAAGGATTCAGTTGTCTTCTT 57.170 32.000 0.00 0.00 0.00 2.52
3499 3659 8.915654 GTTTACAAAGAATAAAGCCATGACAAG 58.084 33.333 0.00 0.00 0.00 3.16
3586 3747 6.640518 TGGTTTGGCTTTTAAAATGTGTGTA 58.359 32.000 0.09 0.00 0.00 2.90
3634 3795 4.705337 ACCGAAGTTTTGTGTGCTTTAA 57.295 36.364 0.00 0.00 0.00 1.52
3642 3803 1.199624 GCAGCAACCGAAGTTTTGTG 58.800 50.000 0.00 0.00 32.45 3.33
3676 3837 4.565166 CCGTGATGTAATCTTTGCGAACTA 59.435 41.667 0.00 0.00 45.81 2.24
3718 3879 5.329493 GGATAGATGTGGCGTTTGTTTTAC 58.671 41.667 0.00 0.00 0.00 2.01
3725 3886 0.179056 CCCGGATAGATGTGGCGTTT 60.179 55.000 0.73 0.00 0.00 3.60
3729 3890 1.371558 GTCCCCGGATAGATGTGGC 59.628 63.158 0.73 0.00 0.00 5.01
3796 3962 3.433598 GGCAGGATGATTGTGGCTAGTTA 60.434 47.826 0.00 0.00 39.69 2.24
3809 3975 2.874014 TGTTCAAATGTGGCAGGATGA 58.126 42.857 0.00 0.00 39.69 2.92
3815 3981 1.202463 CCGGTTTGTTCAAATGTGGCA 60.202 47.619 0.00 0.00 0.00 4.92
3941 4119 8.337532 CGATGAGCATTTAGTTGAAATATGTCA 58.662 33.333 0.00 0.00 35.45 3.58
3942 4120 7.800380 CCGATGAGCATTTAGTTGAAATATGTC 59.200 37.037 0.00 0.00 35.45 3.06
3945 4123 7.283127 ACACCGATGAGCATTTAGTTGAAATAT 59.717 33.333 0.00 0.00 35.45 1.28
3946 4124 6.597672 ACACCGATGAGCATTTAGTTGAAATA 59.402 34.615 0.00 0.00 35.45 1.40
3947 4125 5.415701 ACACCGATGAGCATTTAGTTGAAAT 59.584 36.000 0.00 0.00 38.34 2.17
3948 4126 4.759693 ACACCGATGAGCATTTAGTTGAAA 59.240 37.500 0.00 0.00 0.00 2.69
3949 4127 4.323417 ACACCGATGAGCATTTAGTTGAA 58.677 39.130 0.00 0.00 0.00 2.69
3951 4129 3.063997 GGACACCGATGAGCATTTAGTTG 59.936 47.826 0.00 0.00 0.00 3.16
3952 4130 3.270877 GGACACCGATGAGCATTTAGTT 58.729 45.455 0.00 0.00 0.00 2.24
3953 4131 2.906354 GGACACCGATGAGCATTTAGT 58.094 47.619 0.00 0.00 0.00 2.24
3975 4163 4.136796 TGGAGAAGACATGTTGTGGAAAG 58.863 43.478 0.00 0.00 0.00 2.62
4033 4221 1.453155 GCTGAAGCTTCAATTCCCGA 58.547 50.000 28.16 4.72 36.64 5.14
4057 4245 2.464865 CGGAAGCCACTATTCTTCTCG 58.535 52.381 0.00 0.00 38.86 4.04
4082 4270 4.722700 GAGCTTGCCCCCTTCGCA 62.723 66.667 0.00 0.00 0.00 5.10
4084 4272 2.747855 GTGAGCTTGCCCCCTTCG 60.748 66.667 0.00 0.00 0.00 3.79
4089 4277 4.660938 AACCGGTGAGCTTGCCCC 62.661 66.667 8.52 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.