Multiple sequence alignment - TraesCS1D01G085900

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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 TraesCS1D01G085900 chr1D 100.000 3287 0 0 1 3287 70345044 70348330 0.000000e+00 6071.0
1 TraesCS1D01G085900 chr1A 92.745 2605 106 27 731 3287 70701812 70704381 0.000000e+00 3687.0
2 TraesCS1D01G085900 chr1A 92.699 452 18 5 282 726 70701225 70701668 3.580000e-179 638.0
3 TraesCS1D01G085900 chr1A 94.915 59 3 0 1 59 70700975 70701033 3.490000e-15 93.5
4 TraesCS1D01G085900 chr1B 94.281 2378 93 17 731 3086 111669268 111671624 0.000000e+00 3598.0
5 TraesCS1D01G085900 chr1B 93.962 530 22 3 203 726 111668318 111668843 0.000000e+00 793.0
6 TraesCS1D01G085900 chr1B 96.552 203 6 1 3085 3287 111671786 111671987 5.260000e-88 335.0
7 TraesCS1D01G085900 chr4D 97.368 38 1 0 62 99 489228345 489228382 7.610000e-07 65.8
8 TraesCS1D01G085900 chr6B 95.000 40 2 0 62 101 5615087 5615126 2.740000e-06 63.9
9 TraesCS1D01G085900 chr6B 94.737 38 1 1 64 101 5597116 5597152 1.270000e-04 58.4
10 TraesCS1D01G085900 chr4B 94.872 39 0 2 62 99 608385040 608385003 3.540000e-05 60.2
11 TraesCS1D01G085900 chr7B 92.105 38 3 0 62 99 548395990 548396027 2.000000e-03 54.7


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 TraesCS1D01G085900 chr1D 70345044 70348330 3286 False 6071.000000 6071 100.000000 1 3287 1 chr1D.!!$F1 3286
1 TraesCS1D01G085900 chr1A 70700975 70704381 3406 False 1472.833333 3687 93.453000 1 3287 3 chr1A.!!$F1 3286
2 TraesCS1D01G085900 chr1B 111668318 111671987 3669 False 1575.333333 3598 94.931667 203 3287 3 chr1B.!!$F1 3084

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
519 565 0.243365 GTTTCACATTGCGGCCATGA 59.757 50.0 19.57 4.94 0.0 3.07 F
1145 1675 0.036732 TGTTGCTCTCCATCACCCAC 59.963 55.0 0.00 0.00 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2343 1.287425 GGTTCGGTTCATCCATCGAC 58.713 55.0 0.0 0.0 35.57 4.20 R
2782 3322 0.322008 CAACCAGAGCACCCTCTTCC 60.322 60.0 0.0 0.0 46.16 3.46 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
47 48 5.186198 GGCACACTAACTTGATAGACCAAT 58.814 41.667 0.00 0.00 0.00 3.16
59 60 8.680903 ACTTGATAGACCAATCAATTTGCTAAG 58.319 33.333 0.14 0.00 43.16 2.18
60 61 7.031226 TGATAGACCAATCAATTTGCTAAGC 57.969 36.000 0.00 0.00 32.97 3.09
61 62 6.602803 TGATAGACCAATCAATTTGCTAAGCA 59.397 34.615 0.00 0.00 32.97 3.91
62 63 5.064441 AGACCAATCAATTTGCTAAGCAC 57.936 39.130 0.00 0.00 38.71 4.40
63 64 4.768968 AGACCAATCAATTTGCTAAGCACT 59.231 37.500 0.00 0.00 38.71 4.40
64 65 5.064441 ACCAATCAATTTGCTAAGCACTC 57.936 39.130 0.00 0.00 38.71 3.51
65 66 4.082026 ACCAATCAATTTGCTAAGCACTCC 60.082 41.667 0.00 0.00 38.71 3.85
66 67 4.159135 CCAATCAATTTGCTAAGCACTCCT 59.841 41.667 0.00 0.00 38.71 3.69
67 68 5.337009 CCAATCAATTTGCTAAGCACTCCTT 60.337 40.000 0.00 0.00 38.71 3.36
68 69 5.573337 ATCAATTTGCTAAGCACTCCTTC 57.427 39.130 0.00 0.00 38.71 3.46
69 70 3.758554 TCAATTTGCTAAGCACTCCTTCC 59.241 43.478 0.00 0.00 38.71 3.46
70 71 1.808411 TTTGCTAAGCACTCCTTCCG 58.192 50.000 0.00 0.00 38.71 4.30
71 72 0.673644 TTGCTAAGCACTCCTTCCGC 60.674 55.000 0.00 0.00 38.71 5.54
72 73 1.815840 GCTAAGCACTCCTTCCGCC 60.816 63.158 0.00 0.00 34.95 6.13
73 74 1.153349 CTAAGCACTCCTTCCGCCC 60.153 63.158 0.00 0.00 34.95 6.13
74 75 2.595009 CTAAGCACTCCTTCCGCCCC 62.595 65.000 0.00 0.00 34.95 5.80
77 78 3.072468 CACTCCTTCCGCCCCGTA 61.072 66.667 0.00 0.00 0.00 4.02
78 79 2.284112 ACTCCTTCCGCCCCGTAA 60.284 61.111 0.00 0.00 0.00 3.18
79 80 1.688187 ACTCCTTCCGCCCCGTAAT 60.688 57.895 0.00 0.00 0.00 1.89
80 81 0.397535 ACTCCTTCCGCCCCGTAATA 60.398 55.000 0.00 0.00 0.00 0.98
81 82 0.974383 CTCCTTCCGCCCCGTAATAT 59.026 55.000 0.00 0.00 0.00 1.28
82 83 2.173519 CTCCTTCCGCCCCGTAATATA 58.826 52.381 0.00 0.00 0.00 0.86
83 84 2.564062 CTCCTTCCGCCCCGTAATATAA 59.436 50.000 0.00 0.00 0.00 0.98
84 85 2.564062 TCCTTCCGCCCCGTAATATAAG 59.436 50.000 0.00 0.00 0.00 1.73
85 86 2.564062 CCTTCCGCCCCGTAATATAAGA 59.436 50.000 0.00 0.00 0.00 2.10
86 87 3.368116 CCTTCCGCCCCGTAATATAAGAG 60.368 52.174 0.00 0.00 0.00 2.85
87 88 1.547372 TCCGCCCCGTAATATAAGAGC 59.453 52.381 0.00 0.00 0.00 4.09
88 89 1.625616 CGCCCCGTAATATAAGAGCG 58.374 55.000 0.00 0.00 36.06 5.03
89 90 1.068055 CGCCCCGTAATATAAGAGCGT 60.068 52.381 0.00 0.00 37.69 5.07
90 91 2.608752 CGCCCCGTAATATAAGAGCGTT 60.609 50.000 0.00 0.00 37.69 4.84
91 92 3.396560 GCCCCGTAATATAAGAGCGTTT 58.603 45.455 0.00 0.00 0.00 3.60
92 93 3.811497 GCCCCGTAATATAAGAGCGTTTT 59.189 43.478 0.00 0.00 0.00 2.43
93 94 4.274214 GCCCCGTAATATAAGAGCGTTTTT 59.726 41.667 0.00 0.00 0.00 1.94
94 95 5.744490 CCCCGTAATATAAGAGCGTTTTTG 58.256 41.667 0.00 0.00 0.00 2.44
95 96 5.524646 CCCCGTAATATAAGAGCGTTTTTGA 59.475 40.000 0.00 0.00 0.00 2.69
96 97 6.416514 CCCGTAATATAAGAGCGTTTTTGAC 58.583 40.000 0.00 0.00 0.00 3.18
97 98 6.036300 CCCGTAATATAAGAGCGTTTTTGACA 59.964 38.462 0.00 0.00 0.00 3.58
98 99 6.898189 CCGTAATATAAGAGCGTTTTTGACAC 59.102 38.462 0.00 0.00 0.00 3.67
99 100 6.618308 CGTAATATAAGAGCGTTTTTGACACG 59.382 38.462 0.00 0.00 40.75 4.49
100 101 6.476243 AATATAAGAGCGTTTTTGACACGT 57.524 33.333 0.00 0.00 39.92 4.49
101 102 7.585286 AATATAAGAGCGTTTTTGACACGTA 57.415 32.000 0.00 0.00 39.92 3.57
102 103 7.766219 ATATAAGAGCGTTTTTGACACGTAT 57.234 32.000 0.00 0.00 39.92 3.06
103 104 4.806342 AAGAGCGTTTTTGACACGTATT 57.194 36.364 0.00 0.00 39.92 1.89
104 105 5.910637 AAGAGCGTTTTTGACACGTATTA 57.089 34.783 0.00 0.00 39.92 0.98
105 106 5.260027 AGAGCGTTTTTGACACGTATTAC 57.740 39.130 0.00 0.00 39.92 1.89
142 143 7.743749 AGTAGATAGATTGCCATTGTTCATCT 58.256 34.615 0.00 0.00 0.00 2.90
151 152 3.777478 CCATTGTTCATCTTGACCATGC 58.223 45.455 0.00 0.00 0.00 4.06
152 153 3.193903 CCATTGTTCATCTTGACCATGCA 59.806 43.478 0.00 0.00 0.00 3.96
153 154 4.142026 CCATTGTTCATCTTGACCATGCAT 60.142 41.667 0.00 0.00 0.00 3.96
154 155 5.068067 CCATTGTTCATCTTGACCATGCATA 59.932 40.000 0.00 0.00 0.00 3.14
155 156 6.239204 CCATTGTTCATCTTGACCATGCATAT 60.239 38.462 0.00 0.00 0.00 1.78
156 157 7.040271 CCATTGTTCATCTTGACCATGCATATA 60.040 37.037 0.00 0.00 0.00 0.86
157 158 8.520351 CATTGTTCATCTTGACCATGCATATAT 58.480 33.333 0.00 0.00 0.00 0.86
158 159 8.467963 TTGTTCATCTTGACCATGCATATATT 57.532 30.769 0.00 0.00 0.00 1.28
159 160 7.878036 TGTTCATCTTGACCATGCATATATTG 58.122 34.615 0.00 0.00 0.00 1.90
160 161 7.720515 TGTTCATCTTGACCATGCATATATTGA 59.279 33.333 0.00 0.00 0.00 2.57
161 162 8.737175 GTTCATCTTGACCATGCATATATTGAT 58.263 33.333 0.00 0.00 0.00 2.57
162 163 8.276252 TCATCTTGACCATGCATATATTGATG 57.724 34.615 0.00 9.66 0.00 3.07
171 172 2.223641 GCATATATTGATGCCATGGCCG 60.224 50.000 33.44 9.81 45.41 6.13
186 187 2.345991 CCGGCCGGGTATATGTGG 59.654 66.667 37.42 6.27 0.00 4.17
198 199 2.370281 ATATGTGGCCGTCGATCATC 57.630 50.000 0.00 0.00 0.00 2.92
215 229 8.810652 TCGATCATCGAATGTGTGATTAATTA 57.189 30.769 7.45 0.00 46.90 1.40
382 428 2.111878 CATCATCCGGCCTCCACC 59.888 66.667 0.00 0.00 0.00 4.61
436 482 2.865308 CTGTGTCGTGCATGCAGG 59.135 61.111 29.80 29.80 0.00 4.85
516 562 2.642129 CGTTTCACATTGCGGCCA 59.358 55.556 2.24 0.00 0.00 5.36
517 563 1.212490 CGTTTCACATTGCGGCCAT 59.788 52.632 2.24 0.00 0.00 4.40
518 564 1.072116 CGTTTCACATTGCGGCCATG 61.072 55.000 12.06 12.06 0.00 3.66
519 565 0.243365 GTTTCACATTGCGGCCATGA 59.757 50.000 19.57 4.94 0.00 3.07
729 785 7.224297 AGAGGAGTAAATTACAAGAAACTGCA 58.776 34.615 5.89 0.00 0.00 4.41
775 1279 9.034800 ACCATGGTAATTTCATCATAACAAACT 57.965 29.630 18.10 0.00 0.00 2.66
777 1281 8.810427 CATGGTAATTTCATCATAACAAACTGC 58.190 33.333 0.00 0.00 0.00 4.40
870 1397 5.170748 AGCGATGGAAAAATTCATGGAAAC 58.829 37.500 0.00 0.00 0.00 2.78
887 1414 7.648510 TCATGGAAACGGTAAAAATTAACACAC 59.351 33.333 0.00 0.00 0.00 3.82
940 1467 8.631797 CCAAGGAAATTGAAATCCATTGTTTTT 58.368 29.630 3.65 0.00 41.83 1.94
1072 1599 0.107945 GGCCGAAGCAAGAGAGACAT 60.108 55.000 0.00 0.00 42.56 3.06
1077 1604 2.192624 GAAGCAAGAGAGACATCGCTC 58.807 52.381 4.61 4.61 42.11 5.03
1145 1675 0.036732 TGTTGCTCTCCATCACCCAC 59.963 55.000 0.00 0.00 0.00 4.61
1770 2303 3.792736 CGATTCCCCTTCCGCCCA 61.793 66.667 0.00 0.00 0.00 5.36
1904 2437 2.268920 GCTGGATCCGAGCACCAA 59.731 61.111 23.33 0.00 36.40 3.67
2209 2742 1.512926 CACCTTCTTCGACAACTGGG 58.487 55.000 0.00 0.00 0.00 4.45
2395 2928 0.179307 CGCGAAGTTCTTCGACAACG 60.179 55.000 30.39 21.79 46.52 4.10
2463 2999 1.063806 CGAACTGACCTGCTCTTTCG 58.936 55.000 0.00 0.00 32.35 3.46
2497 3033 9.140286 CGTCAAAGTTCTTCAGATTTGATACTA 57.860 33.333 8.24 0.00 41.97 1.82
2528 3066 2.840038 TCCGCCATGGATGAATATAGCT 59.160 45.455 18.40 0.00 43.74 3.32
2556 3095 5.817296 GCTGGTTTCCTTTTTGTTGAATTCT 59.183 36.000 7.05 0.00 0.00 2.40
2611 3150 6.029346 ACGATTTGGAGAAATGCAGAAATT 57.971 33.333 0.00 0.00 31.58 1.82
2672 3211 4.686191 TCTGCATGTTTTGGTTTCCATT 57.314 36.364 0.00 0.00 31.53 3.16
2684 3223 6.885952 TTGGTTTCCATTTCGTTCTGATTA 57.114 33.333 0.00 0.00 31.53 1.75
2711 3250 8.112099 CAAGTTTATTTGCACTATGCTCATTC 57.888 34.615 2.02 0.00 45.31 2.67
2717 3256 6.519679 TTTGCACTATGCTCATTCAATTCT 57.480 33.333 2.02 0.00 45.31 2.40
2732 3271 7.391554 TCATTCAATTCTCAACCTGTTCTTAGG 59.608 37.037 0.00 0.00 43.71 2.69
2740 3279 6.781014 TCTCAACCTGTTCTTAGGAGTTCTTA 59.219 38.462 0.00 0.00 40.42 2.10
2782 3322 2.046313 GATGCTATTTGCGGAAATGCG 58.954 47.619 23.28 15.11 46.63 4.73
2787 3327 1.173043 ATTTGCGGAAATGCGGAAGA 58.827 45.000 14.55 0.00 37.81 2.87
2814 3354 1.978473 TGGTTGAGAGCAGAGCCTC 59.022 57.895 0.00 0.00 0.00 4.70
2815 3355 1.220477 GGTTGAGAGCAGAGCCTCC 59.780 63.158 0.00 0.00 32.17 4.30
2873 3432 8.477256 GGAATAGGATGATTTTTGGTTCAATCA 58.523 33.333 0.00 0.00 42.27 2.57
2875 3434 6.669125 AGGATGATTTTTGGTTCAATCACA 57.331 33.333 0.00 0.00 41.18 3.58
2903 3462 7.013846 ACCTGTTCATAGCTAGACTCTGAATAC 59.986 40.741 9.34 1.08 41.78 1.89
2919 3478 8.910944 ACTCTGAATACGATTTAGGCTTTAGTA 58.089 33.333 0.00 0.00 0.00 1.82
3127 3849 4.202070 CCTTTTCTACGGCTTTGTTTTGGA 60.202 41.667 0.00 0.00 0.00 3.53
3219 3941 7.112122 ACACCAGAACATTATTATCTGAGCAA 58.888 34.615 3.70 0.00 42.48 3.91
3269 3991 1.747709 GAGCACTGTAGTACCCGAGA 58.252 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.288752 GCCCAATTGGTCGGTTGTG 59.711 57.895 22.91 6.26 36.04 3.33
12 13 1.901464 GTGTGCCCAATTGGTCGGT 60.901 57.895 22.91 0.00 36.04 4.69
47 48 3.758554 GGAAGGAGTGCTTAGCAAATTGA 59.241 43.478 9.05 0.00 41.47 2.57
60 61 1.968050 ATTACGGGGCGGAAGGAGTG 61.968 60.000 0.00 0.00 31.47 3.51
61 62 0.397535 TATTACGGGGCGGAAGGAGT 60.398 55.000 0.00 0.00 31.47 3.85
62 63 0.974383 ATATTACGGGGCGGAAGGAG 59.026 55.000 0.00 0.00 31.47 3.69
63 64 2.307496 TATATTACGGGGCGGAAGGA 57.693 50.000 0.00 0.00 31.47 3.36
64 65 2.564062 TCTTATATTACGGGGCGGAAGG 59.436 50.000 0.00 0.00 31.47 3.46
65 66 3.846360 CTCTTATATTACGGGGCGGAAG 58.154 50.000 0.00 0.00 31.47 3.46
66 67 2.028748 GCTCTTATATTACGGGGCGGAA 60.029 50.000 0.00 0.00 32.91 4.30
67 68 1.547372 GCTCTTATATTACGGGGCGGA 59.453 52.381 0.00 0.00 0.00 5.54
68 69 1.734707 CGCTCTTATATTACGGGGCGG 60.735 57.143 0.00 0.00 38.12 6.13
69 70 1.068055 ACGCTCTTATATTACGGGGCG 60.068 52.381 4.51 4.51 45.49 6.13
70 71 2.738013 ACGCTCTTATATTACGGGGC 57.262 50.000 0.00 0.00 0.00 5.80
71 72 5.524646 TCAAAAACGCTCTTATATTACGGGG 59.475 40.000 0.00 0.00 0.00 5.73
72 73 6.036300 TGTCAAAAACGCTCTTATATTACGGG 59.964 38.462 0.00 0.00 0.00 5.28
73 74 6.898189 GTGTCAAAAACGCTCTTATATTACGG 59.102 38.462 0.00 0.00 35.42 4.02
74 75 6.618308 CGTGTCAAAAACGCTCTTATATTACG 59.382 38.462 0.00 0.00 36.18 3.18
75 76 7.450627 ACGTGTCAAAAACGCTCTTATATTAC 58.549 34.615 0.00 0.00 44.80 1.89
76 77 7.585286 ACGTGTCAAAAACGCTCTTATATTA 57.415 32.000 0.00 0.00 44.80 0.98
77 78 6.476243 ACGTGTCAAAAACGCTCTTATATT 57.524 33.333 0.00 0.00 44.80 1.28
78 79 7.766219 ATACGTGTCAAAAACGCTCTTATAT 57.234 32.000 0.00 0.00 44.80 0.86
79 80 7.585286 AATACGTGTCAAAAACGCTCTTATA 57.415 32.000 0.00 0.00 44.80 0.98
80 81 6.476243 AATACGTGTCAAAAACGCTCTTAT 57.524 33.333 0.00 0.00 44.80 1.73
81 82 5.910637 AATACGTGTCAAAAACGCTCTTA 57.089 34.783 0.00 0.00 44.80 2.10
82 83 4.806342 AATACGTGTCAAAAACGCTCTT 57.194 36.364 0.00 0.00 44.80 2.85
83 84 4.143473 CGTAATACGTGTCAAAAACGCTCT 60.143 41.667 4.41 0.00 44.80 4.09
84 85 4.070224 CGTAATACGTGTCAAAAACGCTC 58.930 43.478 4.41 0.00 44.80 5.03
85 86 3.120923 CCGTAATACGTGTCAAAAACGCT 60.121 43.478 12.05 0.00 44.80 5.07
86 87 3.147740 CCGTAATACGTGTCAAAAACGC 58.852 45.455 12.05 0.00 44.80 4.84
87 88 3.428198 TCCCGTAATACGTGTCAAAAACG 59.572 43.478 12.05 0.00 46.32 3.60
88 89 4.663889 CGTCCCGTAATACGTGTCAAAAAC 60.664 45.833 12.05 0.00 40.58 2.43
89 90 3.428198 CGTCCCGTAATACGTGTCAAAAA 59.572 43.478 12.05 0.00 40.58 1.94
90 91 2.985809 CGTCCCGTAATACGTGTCAAAA 59.014 45.455 12.05 0.00 40.58 2.44
91 92 2.594321 CGTCCCGTAATACGTGTCAAA 58.406 47.619 12.05 0.00 40.58 2.69
92 93 1.135431 CCGTCCCGTAATACGTGTCAA 60.135 52.381 12.05 0.00 40.58 3.18
93 94 0.451383 CCGTCCCGTAATACGTGTCA 59.549 55.000 12.05 0.00 40.58 3.58
94 95 0.732571 TCCGTCCCGTAATACGTGTC 59.267 55.000 12.05 0.00 40.58 3.67
95 96 0.734889 CTCCGTCCCGTAATACGTGT 59.265 55.000 12.05 0.00 40.58 4.49
96 97 0.029834 CCTCCGTCCCGTAATACGTG 59.970 60.000 12.05 0.00 40.58 4.49
97 98 1.103398 CCCTCCGTCCCGTAATACGT 61.103 60.000 12.05 0.00 40.58 3.57
98 99 0.819259 TCCCTCCGTCCCGTAATACG 60.819 60.000 5.74 5.74 42.11 3.06
99 100 0.957362 CTCCCTCCGTCCCGTAATAC 59.043 60.000 0.00 0.00 0.00 1.89
100 101 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
101 102 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
102 103 0.107017 CTACTCCCTCCGTCCCGTAA 60.107 60.000 0.00 0.00 0.00 3.18
103 104 0.982852 TCTACTCCCTCCGTCCCGTA 60.983 60.000 0.00 0.00 0.00 4.02
104 105 1.643475 ATCTACTCCCTCCGTCCCGT 61.643 60.000 0.00 0.00 0.00 5.28
105 106 0.399454 TATCTACTCCCTCCGTCCCG 59.601 60.000 0.00 0.00 0.00 5.14
106 107 1.704070 TCTATCTACTCCCTCCGTCCC 59.296 57.143 0.00 0.00 0.00 4.46
107 108 3.724732 ATCTATCTACTCCCTCCGTCC 57.275 52.381 0.00 0.00 0.00 4.79
108 109 3.191791 GCAATCTATCTACTCCCTCCGTC 59.808 52.174 0.00 0.00 0.00 4.79
109 110 3.158676 GCAATCTATCTACTCCCTCCGT 58.841 50.000 0.00 0.00 0.00 4.69
110 111 2.494073 GGCAATCTATCTACTCCCTCCG 59.506 54.545 0.00 0.00 0.00 4.63
111 112 3.511477 TGGCAATCTATCTACTCCCTCC 58.489 50.000 0.00 0.00 0.00 4.30
112 113 5.012561 ACAATGGCAATCTATCTACTCCCTC 59.987 44.000 0.00 0.00 0.00 4.30
113 114 4.910304 ACAATGGCAATCTATCTACTCCCT 59.090 41.667 0.00 0.00 0.00 4.20
114 115 5.234466 ACAATGGCAATCTATCTACTCCC 57.766 43.478 0.00 0.00 0.00 4.30
115 116 6.291377 TGAACAATGGCAATCTATCTACTCC 58.709 40.000 0.00 0.00 0.00 3.85
116 117 7.877097 AGATGAACAATGGCAATCTATCTACTC 59.123 37.037 0.00 0.00 0.00 2.59
117 118 7.743749 AGATGAACAATGGCAATCTATCTACT 58.256 34.615 0.00 0.00 0.00 2.57
118 119 7.976135 AGATGAACAATGGCAATCTATCTAC 57.024 36.000 0.00 0.00 0.00 2.59
151 152 2.359848 CCGGCCATGGCATCAATATATG 59.640 50.000 36.56 12.66 44.11 1.78
152 153 2.658285 CCGGCCATGGCATCAATATAT 58.342 47.619 36.56 0.00 44.11 0.86
153 154 2.127271 CCGGCCATGGCATCAATATA 57.873 50.000 36.56 0.00 44.11 0.86
154 155 2.965805 CCGGCCATGGCATCAATAT 58.034 52.632 36.56 0.00 44.11 1.28
155 156 4.498346 CCGGCCATGGCATCAATA 57.502 55.556 36.56 0.00 44.11 1.90
164 165 2.966732 ATATACCCGGCCGGCCATG 61.967 63.158 42.78 33.66 35.37 3.66
165 166 2.609610 ATATACCCGGCCGGCCAT 60.610 61.111 42.78 31.61 35.37 4.40
166 167 3.632080 CATATACCCGGCCGGCCA 61.632 66.667 42.78 27.55 35.37 5.36
167 168 3.633116 ACATATACCCGGCCGGCC 61.633 66.667 39.46 36.69 33.26 6.13
215 229 6.506538 ACATCTTCTCCTACCATATGCTTT 57.493 37.500 0.00 0.00 0.00 3.51
382 428 6.253298 CGGTGCTTTTGTTTTGGATATGTATG 59.747 38.462 0.00 0.00 0.00 2.39
516 562 1.225373 ATACCCCACACATGGCTCAT 58.775 50.000 0.00 0.00 45.76 2.90
517 563 0.998928 AATACCCCACACATGGCTCA 59.001 50.000 0.00 0.00 45.76 4.26
518 564 2.143876 AAATACCCCACACATGGCTC 57.856 50.000 0.00 0.00 45.76 4.70
519 565 2.456577 GAAAATACCCCACACATGGCT 58.543 47.619 0.00 0.00 45.76 4.75
597 653 2.433491 CGTCGCCACCGATTCCAA 60.433 61.111 0.00 0.00 46.38 3.53
726 782 0.537143 AGCATCTCAACCCGTTTGCA 60.537 50.000 5.14 0.00 34.88 4.08
727 783 0.598065 AAGCATCTCAACCCGTTTGC 59.402 50.000 0.00 0.00 34.88 3.68
729 785 3.254903 GGTTAAAGCATCTCAACCCGTTT 59.745 43.478 0.00 0.00 35.43 3.60
775 1279 7.038659 ACTACAGCAAGTTTTTAACATTTGCA 58.961 30.769 12.46 0.00 42.00 4.08
777 1281 9.730420 ACTACTACAGCAAGTTTTTAACATTTG 57.270 29.630 0.00 0.00 0.00 2.32
812 1320 7.508687 TGTATGCTACCATTGTATCACAGATT 58.491 34.615 0.00 0.00 32.85 2.40
870 1397 7.172019 ACAGGAGTAGTGTGTTAATTTTTACCG 59.828 37.037 0.00 0.00 0.00 4.02
887 1414 8.576442 ACAAATTTCCAAATTGTACAGGAGTAG 58.424 33.333 0.00 0.00 38.53 2.57
940 1467 4.262635 GCTGCTCCTCCTGCAATATACTAA 60.263 45.833 0.00 0.00 40.13 2.24
941 1468 3.259374 GCTGCTCCTCCTGCAATATACTA 59.741 47.826 0.00 0.00 40.13 1.82
943 1470 2.224378 TGCTGCTCCTCCTGCAATATAC 60.224 50.000 0.00 0.00 40.13 1.47
944 1471 2.049372 TGCTGCTCCTCCTGCAATATA 58.951 47.619 0.00 0.00 40.13 0.86
945 1472 0.841961 TGCTGCTCCTCCTGCAATAT 59.158 50.000 0.00 0.00 40.13 1.28
946 1473 0.841961 ATGCTGCTCCTCCTGCAATA 59.158 50.000 0.00 0.00 41.83 1.90
947 1474 0.752009 CATGCTGCTCCTCCTGCAAT 60.752 55.000 0.00 0.00 41.83 3.56
948 1475 1.378119 CATGCTGCTCCTCCTGCAA 60.378 57.895 0.00 0.00 41.83 4.08
982 1509 6.138761 CAGACATTTCTTGTTACTGCAAGTC 58.861 40.000 5.84 0.00 41.06 3.01
1062 1589 0.459489 GCTGGAGCGATGTCTCTCTT 59.541 55.000 0.63 0.00 33.70 2.85
1145 1675 1.227249 TAGAGGAGAGAGGAGGTGGG 58.773 60.000 0.00 0.00 0.00 4.61
1196 1726 1.225855 GCGTGGTGAGAATGACAACA 58.774 50.000 0.00 0.00 32.30 3.33
1197 1727 0.163788 CGCGTGGTGAGAATGACAAC 59.836 55.000 0.00 0.00 0.00 3.32
1198 1728 0.032815 TCGCGTGGTGAGAATGACAA 59.967 50.000 5.77 0.00 0.00 3.18
1306 1836 1.453745 GGATGATCCGCTTGGGCAA 60.454 57.895 0.00 0.00 38.60 4.52
1781 2314 2.730404 GGAGAAGAGAAAAACCGACGAC 59.270 50.000 0.00 0.00 0.00 4.34
1810 2343 1.287425 GGTTCGGTTCATCCATCGAC 58.713 55.000 0.00 0.00 35.57 4.20
1904 2437 2.743718 CCAGGTTGGTCTCGCAGT 59.256 61.111 0.00 0.00 31.35 4.40
2209 2742 2.725008 CTCCTCTGGCGGATCGAC 59.275 66.667 0.00 0.00 34.27 4.20
2240 2773 3.423154 CTTGTTCCTGGCGGTCGC 61.423 66.667 6.83 6.83 41.06 5.19
2395 2928 5.428184 TTCTCTTCTTCTGAATCCTTCCC 57.572 43.478 0.00 0.00 0.00 3.97
2463 2999 7.230466 TCTGAAGAACTTTGACGAAACTAAC 57.770 36.000 0.00 0.00 0.00 2.34
2528 3066 4.580995 TCAACAAAAAGGAAACCAGCGATA 59.419 37.500 0.00 0.00 0.00 2.92
2556 3095 7.949690 TGTCTAGCTACTATGAACAGGTTTA 57.050 36.000 0.00 0.00 0.00 2.01
2611 3150 0.836606 TGTTCTCAACCAGAGCACCA 59.163 50.000 0.00 0.00 44.35 4.17
2672 3211 7.537306 GCAAATAAACTTGCTAATCAGAACGAA 59.463 33.333 1.15 0.00 46.66 3.85
2698 3237 6.318144 AGGTTGAGAATTGAATGAGCATAGTG 59.682 38.462 0.00 0.00 0.00 2.74
2711 3250 6.234177 ACTCCTAAGAACAGGTTGAGAATTG 58.766 40.000 4.17 0.00 36.99 2.32
2717 3256 5.888982 AAGAACTCCTAAGAACAGGTTGA 57.111 39.130 0.00 0.00 36.99 3.18
2758 3298 4.734402 GCATTTCCGCAAATAGCATCTCAA 60.734 41.667 2.60 0.00 46.13 3.02
2773 3313 1.078426 ACCCTCTTCCGCATTTCCG 60.078 57.895 0.00 0.00 0.00 4.30
2782 3322 0.322008 CAACCAGAGCACCCTCTTCC 60.322 60.000 0.00 0.00 46.16 3.46
2787 3327 2.370718 CTCTCAACCAGAGCACCCT 58.629 57.895 0.00 0.00 42.56 4.34
2814 3354 0.830648 TAAGCATGAGGAACCTCCGG 59.169 55.000 16.85 0.00 42.75 5.14
2815 3355 2.874701 CAATAAGCATGAGGAACCTCCG 59.125 50.000 16.85 9.94 42.75 4.63
2873 3432 5.482175 AGAGTCTAGCTATGAACAGGTTTGT 59.518 40.000 0.00 0.00 39.87 2.83
2875 3434 5.717178 TCAGAGTCTAGCTATGAACAGGTTT 59.283 40.000 8.44 0.00 41.88 3.27
2942 3501 4.869297 CCATTTTCAAAGCACAGACAAACA 59.131 37.500 0.00 0.00 0.00 2.83
3053 3612 8.147058 AGAAACATGTAGAACCATATCTAGCTG 58.853 37.037 0.00 0.00 32.72 4.24
3219 3941 6.119536 TGTGAACAGAGACTACCAAACAAAT 58.880 36.000 0.00 0.00 0.00 2.32
3263 3985 1.474077 CTGCCAAAGGAAATTCTCGGG 59.526 52.381 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.