Multiple sequence alignment - TraesCS7D01G323100

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 TraesCS7D01G323100 chr7D 100.000 3936 0 0 1 3936 412888335 412884400 0.000000e+00 7269
1 TraesCS7D01G323100 chr7A 93.196 3116 132 34 1 3103 474298850 474295802 0.000000e+00 4506
2 TraesCS7D01G323100 chr7A 93.622 831 27 4 3111 3936 474295747 474294938 0.000000e+00 1218
3 TraesCS7D01G323100 chr7B 94.319 2922 117 29 218 3115 427305300 427302404 0.000000e+00 4431
4 TraesCS7D01G323100 chr7B 96.083 817 24 4 3120 3936 427302332 427301524 0.000000e+00 1325
5 TraesCS7D01G323100 chr7B 95.205 146 3 1 1 146 427305438 427305297 1.100000e-55 228
6 TraesCS7D01G323100 chr7B 88.710 124 14 0 656 779 517901171 517901294 6.810000e-33 152
7 TraesCS7D01G323100 chr1B 72.774 584 123 23 2147 2702 491983447 491982872 8.750000e-37 165
8 TraesCS7D01G323100 chr1B 88.710 124 14 0 2814 2937 491982789 491982666 6.810000e-33 152
9 TraesCS7D01G323100 chr1A 89.516 124 13 0 2814 2937 466927484 466927361 1.460000e-34 158
10 TraesCS7D01G323100 chr1A 73.561 469 94 19 2259 2702 466928036 466927573 6.810000e-33 152
11 TraesCS7D01G323100 chr4B 88.281 128 15 0 2571 2698 126597716 126597589 1.890000e-33 154
12 TraesCS7D01G323100 chr4A 88.281 128 15 0 2571 2698 502028245 502028118 1.890000e-33 154
13 TraesCS7D01G323100 chr6B 88.710 124 14 0 656 779 138632187 138632310 6.810000e-33 152
14 TraesCS7D01G323100 chr6B 87.097 124 16 0 656 779 138656920 138657043 1.470000e-29 141
15 TraesCS7D01G323100 chr4D 87.692 130 16 0 2571 2700 89537823 89537694 6.810000e-33 152
16 TraesCS7D01G323100 chr1D 88.710 124 14 0 2814 2937 367429300 367429177 6.810000e-33 152
17 TraesCS7D01G323100 chr3A 88.095 126 14 1 2562 2686 627864865 627864990 8.810000e-32 148
18 TraesCS7D01G323100 chrUn 87.903 124 15 0 656 779 194986370 194986247 3.170000e-31 147
19 TraesCS7D01G323100 chr3B 86.822 129 16 1 2562 2689 647680712 647680840 4.100000e-30 143


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 TraesCS7D01G323100 chr7D 412884400 412888335 3935 True 7269.000000 7269 100.000000 1 3936 1 chr7D.!!$R1 3935
1 TraesCS7D01G323100 chr7A 474294938 474298850 3912 True 2862.000000 4506 93.409000 1 3936 2 chr7A.!!$R1 3935
2 TraesCS7D01G323100 chr7B 427301524 427305438 3914 True 1994.666667 4431 95.202333 1 3936 3 chr7B.!!$R1 3935

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
189 196 0.032952 TTTTGGGTCGTCAGGTCGAG 59.967 55.0 0.00 0.0 40.52 4.04 F
300 307 0.179032 TCCTCCACTTTTTGCAGCGA 60.179 50.0 0.00 0.0 0.00 4.93 F
340 347 0.179179 GTTTCCAGCGCTCTGATTGC 60.179 55.0 7.13 0.0 42.95 3.56 F
1664 1698 0.314302 ATGCCTACCTACGTCGATGC 59.686 55.0 4.06 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1507 0.604073 TAAGATTCACGCGACCACCA 59.396 50.000 15.93 0.0 0.00 4.17 R
1685 1725 1.069204 TCAGAGTCAGACAGGTGCAAC 59.931 52.381 2.66 0.0 0.00 4.17 R
1877 1918 2.548057 AGCAACATTGACTACCACGTTG 59.452 45.455 0.00 0.0 37.41 4.10 R
3521 3663 0.179124 GGCGCAAACCAACAAGTTGA 60.179 50.000 10.83 0.0 42.93 3.18 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
141 148 2.728007 CAAAAGGTTGGGATCTCCTCC 58.272 52.381 0.00 0.00 44.11 4.30
148 155 4.916314 GGATCTCCTCCCCGCGGA 62.916 72.222 30.73 6.52 38.19 5.54
149 156 2.838225 GATCTCCTCCCCGCGGAA 60.838 66.667 30.73 13.89 37.86 4.30
150 157 2.840102 ATCTCCTCCCCGCGGAAG 60.840 66.667 30.73 22.85 37.86 3.46
151 158 3.375443 ATCTCCTCCCCGCGGAAGA 62.375 63.158 30.73 21.87 37.86 2.87
173 180 8.759481 AAGAGGAAGAATCTCTTTCAAGTTTT 57.241 30.769 0.00 0.00 46.01 2.43
176 183 6.266330 AGGAAGAATCTCTTTCAAGTTTTGGG 59.734 38.462 0.00 0.00 36.73 4.12
177 184 6.040955 GGAAGAATCTCTTTCAAGTTTTGGGT 59.959 38.462 0.00 0.00 36.73 4.51
178 185 6.641169 AGAATCTCTTTCAAGTTTTGGGTC 57.359 37.500 0.00 0.00 36.75 4.46
179 186 5.239525 AGAATCTCTTTCAAGTTTTGGGTCG 59.760 40.000 0.00 0.00 36.75 4.79
180 187 3.881220 TCTCTTTCAAGTTTTGGGTCGT 58.119 40.909 0.00 0.00 0.00 4.34
181 188 3.875134 TCTCTTTCAAGTTTTGGGTCGTC 59.125 43.478 0.00 0.00 0.00 4.20
182 189 3.611970 TCTTTCAAGTTTTGGGTCGTCA 58.388 40.909 0.00 0.00 0.00 4.35
183 190 3.625764 TCTTTCAAGTTTTGGGTCGTCAG 59.374 43.478 0.00 0.00 0.00 3.51
184 191 1.961793 TCAAGTTTTGGGTCGTCAGG 58.038 50.000 0.00 0.00 0.00 3.86
185 192 1.210967 TCAAGTTTTGGGTCGTCAGGT 59.789 47.619 0.00 0.00 0.00 4.00
186 193 1.602377 CAAGTTTTGGGTCGTCAGGTC 59.398 52.381 0.00 0.00 0.00 3.85
187 194 0.249741 AGTTTTGGGTCGTCAGGTCG 60.250 55.000 0.00 0.00 0.00 4.79
188 195 0.249573 GTTTTGGGTCGTCAGGTCGA 60.250 55.000 0.00 0.00 37.51 4.20
189 196 0.032952 TTTTGGGTCGTCAGGTCGAG 59.967 55.000 0.00 0.00 40.52 4.04
228 235 2.841988 AGATGGCCGCTCCTCCTC 60.842 66.667 0.00 0.00 35.26 3.71
230 237 4.488911 ATGGCCGCTCCTCCTCCT 62.489 66.667 0.00 0.00 35.26 3.69
231 238 4.722535 TGGCCGCTCCTCCTCCTT 62.723 66.667 0.00 0.00 35.26 3.36
232 239 3.855853 GGCCGCTCCTCCTCCTTC 61.856 72.222 0.00 0.00 0.00 3.46
233 240 3.077556 GCCGCTCCTCCTCCTTCA 61.078 66.667 0.00 0.00 0.00 3.02
234 241 2.896443 CCGCTCCTCCTCCTTCAC 59.104 66.667 0.00 0.00 0.00 3.18
300 307 0.179032 TCCTCCACTTTTTGCAGCGA 60.179 50.000 0.00 0.00 0.00 4.93
307 314 3.374745 CACTTTTTGCAGCGAACTTCAT 58.625 40.909 0.00 0.00 0.00 2.57
309 316 5.156355 CACTTTTTGCAGCGAACTTCATAT 58.844 37.500 0.00 0.00 0.00 1.78
318 325 5.809562 GCAGCGAACTTCATATATCTAGCAT 59.190 40.000 0.00 0.00 0.00 3.79
319 326 6.975197 GCAGCGAACTTCATATATCTAGCATA 59.025 38.462 0.00 0.00 0.00 3.14
320 327 7.651304 GCAGCGAACTTCATATATCTAGCATAT 59.349 37.037 0.00 0.00 0.00 1.78
340 347 0.179179 GTTTCCAGCGCTCTGATTGC 60.179 55.000 7.13 0.00 42.95 3.56
342 349 0.742281 TTCCAGCGCTCTGATTGCTC 60.742 55.000 7.13 0.00 42.95 4.26
343 350 2.523507 CCAGCGCTCTGATTGCTCG 61.524 63.158 7.13 0.00 42.95 5.03
424 432 6.961359 TCCATTTCACAACATAGAAGTACG 57.039 37.500 0.00 0.00 0.00 3.67
425 433 5.872617 TCCATTTCACAACATAGAAGTACGG 59.127 40.000 0.00 0.00 0.00 4.02
478 486 2.676839 CTGCCACAGTAGCAAAGAGATG 59.323 50.000 0.00 0.00 40.35 2.90
479 487 2.038952 TGCCACAGTAGCAAAGAGATGT 59.961 45.455 0.00 0.00 37.28 3.06
542 562 5.008118 GGTCAAACTTTGTTCCTCTGAGAAG 59.992 44.000 6.17 3.99 0.00 2.85
572 592 0.542467 AATTGTGGTGCCATGCCTGA 60.542 50.000 0.00 0.00 0.00 3.86
635 659 1.003118 TGTTAGCCTTTCGCCATCAGT 59.997 47.619 0.00 0.00 38.78 3.41
666 690 2.884997 TTTCCATCCACCCATCGCCG 62.885 60.000 0.00 0.00 0.00 6.46
766 790 5.461526 CACTGACTCGAGACTATTCAAACA 58.538 41.667 21.68 2.68 0.00 2.83
897 924 6.487299 AGACGCTAATCTTCCTCCTATTTT 57.513 37.500 0.00 0.00 0.00 1.82
950 977 3.557898 GCTCATTCAGAAGACCTTGACCA 60.558 47.826 0.00 0.00 0.00 4.02
957 984 3.578716 CAGAAGACCTTGACCACTAGGAA 59.421 47.826 0.00 0.00 40.51 3.36
963 990 2.420129 CCTTGACCACTAGGAAATCGGG 60.420 54.545 0.00 0.00 40.51 5.14
1119 1146 1.612513 CCATCATCACCGGGGGAAA 59.387 57.895 2.42 0.00 0.00 3.13
1185 1212 0.685458 ATCAGAATGGCTGGGTTGGC 60.685 55.000 0.00 0.00 44.98 4.52
1266 1293 0.800683 CCTCGCGCAAAGATGTCGTA 60.801 55.000 8.75 0.00 0.00 3.43
1381 1408 5.049267 TCGCTTAAACAGGTAAACATCCAAC 60.049 40.000 0.00 0.00 0.00 3.77
1387 1414 6.976934 AACAGGTAAACATCCAACTGAATT 57.023 33.333 0.00 0.00 0.00 2.17
1535 1566 8.779096 AATAGTAGTTGGTATGCTTACCTAGT 57.221 34.615 24.67 21.87 46.96 2.57
1591 1622 7.553881 TGAAAAGTAAGATATGCCTGCTTAC 57.446 36.000 0.00 0.00 42.52 2.34
1653 1687 3.618690 AGTGAGAAAGACATGCCTACC 57.381 47.619 0.00 0.00 0.00 3.18
1656 1690 4.160626 AGTGAGAAAGACATGCCTACCTAC 59.839 45.833 0.00 0.00 0.00 3.18
1657 1691 3.130516 TGAGAAAGACATGCCTACCTACG 59.869 47.826 0.00 0.00 0.00 3.51
1658 1692 3.097614 AGAAAGACATGCCTACCTACGT 58.902 45.455 0.00 0.00 0.00 3.57
1660 1694 1.022735 AGACATGCCTACCTACGTCG 58.977 55.000 0.00 0.00 0.00 5.12
1661 1695 1.019673 GACATGCCTACCTACGTCGA 58.980 55.000 0.00 0.00 0.00 4.20
1662 1696 1.607628 GACATGCCTACCTACGTCGAT 59.392 52.381 0.00 0.00 0.00 3.59
1663 1697 1.337071 ACATGCCTACCTACGTCGATG 59.663 52.381 2.26 2.26 0.00 3.84
1664 1698 0.314302 ATGCCTACCTACGTCGATGC 59.686 55.000 4.06 0.00 0.00 3.91
1667 1701 1.888215 CCTACCTACGTCGATGCCTA 58.112 55.000 4.06 0.00 0.00 3.93
1668 1702 1.534595 CCTACCTACGTCGATGCCTAC 59.465 57.143 4.06 0.00 0.00 3.18
1670 1704 1.688772 ACCTACGTCGATGCCTACAT 58.311 50.000 4.06 0.00 39.98 2.29
1673 1707 2.812591 CCTACGTCGATGCCTACATAGT 59.187 50.000 4.06 0.00 36.35 2.12
1685 1725 5.308014 TGCCTACATAGTGCATATGAAAGG 58.692 41.667 21.16 21.16 43.54 3.11
1850 1890 6.927936 GCTGCTTCTCTCATTAATCTCATACA 59.072 38.462 0.00 0.00 0.00 2.29
1877 1918 3.025866 GCTGTGTGCATTGCTTAGC 57.974 52.632 10.49 10.07 42.31 3.09
1892 1933 3.000727 GCTTAGCAACGTGGTAGTCAAT 58.999 45.455 0.00 0.00 31.46 2.57
1972 2013 1.090728 GAAAGTTCCTGCTAGCAGCC 58.909 55.000 34.82 24.22 41.51 4.85
1987 2028 0.173481 CAGCCAAGAGGAATCGACGA 59.827 55.000 0.00 0.00 36.89 4.20
2093 2134 4.146745 AGTACCTTCCTTCACAACGTTT 57.853 40.909 0.00 0.00 0.00 3.60
2094 2135 4.520179 AGTACCTTCCTTCACAACGTTTT 58.480 39.130 0.00 0.00 0.00 2.43
2095 2136 4.945543 AGTACCTTCCTTCACAACGTTTTT 59.054 37.500 0.00 0.00 0.00 1.94
2152 2201 4.967084 TTGTATGTACACCAACAGGTCT 57.033 40.909 0.00 0.00 35.64 3.85
2260 2309 0.179936 GCATCTCTTCCAGGAGGGTG 59.820 60.000 0.00 0.00 38.11 4.61
2263 2312 0.487325 TCTCTTCCAGGAGGGTGTCA 59.513 55.000 0.00 0.00 38.11 3.58
2371 2420 1.221566 CACGATGCACTCCATCCCA 59.778 57.895 0.00 0.00 46.17 4.37
2554 2603 4.388499 GGGTTGCGGCGAGAGGAA 62.388 66.667 12.98 0.00 0.00 3.36
2659 2708 2.203788 TTCCGAGGCAGGGTGACT 60.204 61.111 0.00 0.00 39.41 3.41
2788 2837 2.927014 GCCTTCAAGTTCATCGTCGTCT 60.927 50.000 0.00 0.00 0.00 4.18
2809 2858 0.179207 CGACGTCCGATCACGAGAAA 60.179 55.000 10.58 0.00 42.69 2.52
2941 2990 4.148128 ACTGGCCTGTGAATGAATAGAG 57.852 45.455 15.36 0.00 0.00 2.43
2944 2993 3.282021 GGCCTGTGAATGAATAGAGCAA 58.718 45.455 0.00 0.00 0.00 3.91
2988 3037 5.674525 TGTGTGATAAGTCCATCAAGATCC 58.325 41.667 0.00 0.00 36.71 3.36
3063 3112 9.241919 TGTCAAGAATGGCAAGAAATATAAAGA 57.758 29.630 0.00 0.00 38.47 2.52
3078 3127 9.434559 GAAATATAAAGATTTGGTCGTTGCTAC 57.565 33.333 0.00 0.00 30.94 3.58
3116 3165 6.762187 TCCGAACTTTTCTGTACATTGTAACA 59.238 34.615 0.00 0.00 0.00 2.41
3126 3243 5.996219 TGTACATTGTAACACACATGAAGC 58.004 37.500 0.00 0.00 36.90 3.86
3130 3247 5.709631 ACATTGTAACACACATGAAGCCATA 59.290 36.000 0.00 0.00 36.90 2.74
3192 3310 1.337703 TCTGCATGTCAAACCAGCAAC 59.662 47.619 0.00 0.00 34.45 4.17
3224 3342 1.056125 ATCATCAGATGGCCGGTGGA 61.056 55.000 10.67 0.00 31.91 4.02
3225 3343 1.224315 CATCAGATGGCCGGTGGAA 59.776 57.895 1.90 0.00 0.00 3.53
3226 3344 0.816825 CATCAGATGGCCGGTGGAAG 60.817 60.000 1.90 0.00 0.00 3.46
3227 3345 1.987807 ATCAGATGGCCGGTGGAAGG 61.988 60.000 1.90 0.00 0.00 3.46
3228 3346 2.285368 AGATGGCCGGTGGAAGGA 60.285 61.111 1.90 0.00 0.00 3.36
3229 3347 2.190578 GATGGCCGGTGGAAGGAG 59.809 66.667 1.90 0.00 0.00 3.69
3230 3348 4.115199 ATGGCCGGTGGAAGGAGC 62.115 66.667 1.90 0.00 0.00 4.70
3232 3350 4.115199 GGCCGGTGGAAGGAGCAT 62.115 66.667 1.90 0.00 0.00 3.79
3233 3351 2.044946 GCCGGTGGAAGGAGCATT 60.045 61.111 1.90 0.00 0.00 3.56
3234 3352 1.678970 GCCGGTGGAAGGAGCATTT 60.679 57.895 1.90 0.00 0.00 2.32
3235 3353 0.393808 GCCGGTGGAAGGAGCATTTA 60.394 55.000 1.90 0.00 0.00 1.40
3236 3354 1.668419 CCGGTGGAAGGAGCATTTAG 58.332 55.000 0.00 0.00 0.00 1.85
3237 3355 1.209504 CCGGTGGAAGGAGCATTTAGA 59.790 52.381 0.00 0.00 0.00 2.10
3238 3356 2.280628 CGGTGGAAGGAGCATTTAGAC 58.719 52.381 0.00 0.00 0.00 2.59
3239 3357 2.354704 CGGTGGAAGGAGCATTTAGACA 60.355 50.000 0.00 0.00 0.00 3.41
3240 3358 3.274288 GGTGGAAGGAGCATTTAGACAG 58.726 50.000 0.00 0.00 0.00 3.51
3241 3359 3.274288 GTGGAAGGAGCATTTAGACAGG 58.726 50.000 0.00 0.00 0.00 4.00
3242 3360 3.055094 GTGGAAGGAGCATTTAGACAGGA 60.055 47.826 0.00 0.00 0.00 3.86
3243 3361 3.198635 TGGAAGGAGCATTTAGACAGGAG 59.801 47.826 0.00 0.00 0.00 3.69
3280 3418 4.406648 TCAATGGTCTACACCTATGCAG 57.593 45.455 0.00 0.00 44.17 4.41
3286 3424 6.346477 TGGTCTACACCTATGCAGATTATC 57.654 41.667 0.00 0.00 44.17 1.75
3313 3451 6.367969 ACAATTAACAATCCACAGTCGACTAC 59.632 38.462 19.57 0.00 0.00 2.73
3521 3663 4.148825 GCGGCCCTCACTGACGAT 62.149 66.667 0.00 0.00 0.00 3.73
3550 3692 0.597377 GGTTTGCGCCCTGAAAACTG 60.597 55.000 16.73 0.00 34.84 3.16
3690 3832 5.105146 AGTTTGATCGGAGCTCTCAGTAATT 60.105 40.000 14.64 0.00 0.00 1.40
3816 3958 1.546029 CGTGAGGTCTTCAGGATGTCA 59.454 52.381 0.00 0.00 42.85 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.942879 CGAGCGATCTCTCCTCCG 59.057 66.667 7.12 0.00 37.19 4.63
114 121 3.291383 CCAACCTTTTGCGGCCGA 61.291 61.111 33.48 11.82 0.00 5.54
115 122 4.356442 CCCAACCTTTTGCGGCCG 62.356 66.667 24.05 24.05 0.00 6.13
116 123 2.225791 GATCCCAACCTTTTGCGGCC 62.226 60.000 0.00 0.00 0.00 6.13
117 124 1.215382 GATCCCAACCTTTTGCGGC 59.785 57.895 0.00 0.00 0.00 6.53
118 125 0.811281 GAGATCCCAACCTTTTGCGG 59.189 55.000 0.00 0.00 0.00 5.69
119 126 0.811281 GGAGATCCCAACCTTTTGCG 59.189 55.000 0.00 0.00 34.14 4.85
141 148 0.530870 GATTCTTCCTCTTCCGCGGG 60.531 60.000 27.83 10.69 0.00 6.13
146 153 6.472016 ACTTGAAAGAGATTCTTCCTCTTCC 58.528 40.000 5.94 0.00 46.80 3.46
147 154 7.977789 AACTTGAAAGAGATTCTTCCTCTTC 57.022 36.000 5.94 2.13 46.80 2.87
149 156 7.230309 CCAAAACTTGAAAGAGATTCTTCCTCT 59.770 37.037 0.00 0.00 42.37 3.69
150 157 7.366513 CCAAAACTTGAAAGAGATTCTTCCTC 58.633 38.462 0.00 0.00 35.27 3.71
151 158 6.266330 CCCAAAACTTGAAAGAGATTCTTCCT 59.734 38.462 0.00 0.00 35.27 3.36
173 180 2.675423 CCTCGACCTGACGACCCA 60.675 66.667 0.00 0.00 37.37 4.51
176 183 1.984321 GAGCTCCTCGACCTGACGAC 61.984 65.000 0.87 0.00 37.37 4.34
177 184 1.745864 GAGCTCCTCGACCTGACGA 60.746 63.158 0.87 0.00 40.00 4.20
178 185 2.795297 GAGCTCCTCGACCTGACG 59.205 66.667 0.87 0.00 0.00 4.35
187 194 1.524849 GCCCCAAATCGAGCTCCTC 60.525 63.158 8.47 0.00 0.00 3.71
188 195 2.592308 GCCCCAAATCGAGCTCCT 59.408 61.111 8.47 0.00 0.00 3.69
189 196 2.517166 GGCCCCAAATCGAGCTCC 60.517 66.667 8.47 0.00 0.00 4.70
228 235 1.206849 GCAGAGGAGGAAGAGTGAAGG 59.793 57.143 0.00 0.00 0.00 3.46
230 237 2.015456 TGCAGAGGAGGAAGAGTGAA 57.985 50.000 0.00 0.00 0.00 3.18
231 238 2.106566 GATGCAGAGGAGGAAGAGTGA 58.893 52.381 0.00 0.00 0.00 3.41
232 239 1.138661 GGATGCAGAGGAGGAAGAGTG 59.861 57.143 0.00 0.00 0.00 3.51
233 240 1.273495 TGGATGCAGAGGAGGAAGAGT 60.273 52.381 0.00 0.00 0.00 3.24
234 241 1.138661 GTGGATGCAGAGGAGGAAGAG 59.861 57.143 0.00 0.00 0.00 2.85
307 314 6.042777 GCGCTGGAAACATATGCTAGATATA 58.957 40.000 0.00 0.00 41.51 0.86
309 316 4.021104 AGCGCTGGAAACATATGCTAGATA 60.021 41.667 10.39 0.00 39.30 1.98
318 325 2.938451 CAATCAGAGCGCTGGAAACATA 59.062 45.455 18.48 0.00 42.53 2.29
319 326 1.741706 CAATCAGAGCGCTGGAAACAT 59.258 47.619 18.48 0.00 42.53 2.71
320 327 1.159285 CAATCAGAGCGCTGGAAACA 58.841 50.000 18.48 0.00 42.53 2.83
325 332 2.523507 CGAGCAATCAGAGCGCTGG 61.524 63.158 18.48 7.07 42.53 4.85
340 347 9.410556 ACAAAAGAAAATAAACATGGAATCGAG 57.589 29.630 0.00 0.00 0.00 4.04
398 405 7.330946 CGTACTTCTATGTTGTGAAATGGAAGA 59.669 37.037 13.54 0.00 41.42 2.87
424 432 6.289064 TCTACAGAAACTTCAGAGAAAACCC 58.711 40.000 0.00 0.00 0.00 4.11
425 433 7.875554 AGATCTACAGAAACTTCAGAGAAAACC 59.124 37.037 0.00 0.00 0.00 3.27
542 562 2.545742 GCACCACAATTTTGACCCACTC 60.546 50.000 0.00 0.00 0.00 3.51
666 690 1.342819 ACAGACAGCCAACTCTCTGAC 59.657 52.381 5.51 0.00 40.36 3.51
737 761 0.736053 GTCTCGAGTCAGTGGGCTAG 59.264 60.000 13.13 0.00 0.00 3.42
766 790 7.328737 ACAGCTTCGTTACTAATACCATTCTT 58.671 34.615 0.00 0.00 0.00 2.52
897 924 4.395854 CACTGCATATACACAAGGAAAGCA 59.604 41.667 0.00 0.00 0.00 3.91
950 977 3.197983 CAGAACTTCCCCGATTTCCTAGT 59.802 47.826 0.00 0.00 0.00 2.57
957 984 1.423921 ACAACCAGAACTTCCCCGATT 59.576 47.619 0.00 0.00 0.00 3.34
963 990 1.464997 GCGATGACAACCAGAACTTCC 59.535 52.381 0.00 0.00 0.00 3.46
1185 1212 4.081642 TCACGAAGTAATTCAGGAGGAAGG 60.082 45.833 3.55 0.00 41.61 3.46
1381 1408 9.692749 AGCTGCAAATATTCATGATAAATTCAG 57.307 29.630 1.02 3.56 37.89 3.02
1387 1414 6.260714 ACGACAGCTGCAAATATTCATGATAA 59.739 34.615 15.27 0.00 0.00 1.75
1478 1507 0.604073 TAAGATTCACGCGACCACCA 59.396 50.000 15.93 0.00 0.00 4.17
1479 1508 1.659098 CTTAAGATTCACGCGACCACC 59.341 52.381 15.93 0.00 0.00 4.61
1533 1564 9.216117 ACGAGAAAATTGCTACAAATTACTACT 57.784 29.630 0.00 0.00 0.00 2.57
1591 1622 7.914537 CTACTTTTCAGTAGGCAAACTTTTG 57.085 36.000 1.97 0.00 46.37 2.44
1653 1687 3.811514 CACTATGTAGGCATCGACGTAG 58.188 50.000 0.00 0.00 41.12 3.51
1656 1690 1.269051 TGCACTATGTAGGCATCGACG 60.269 52.381 0.00 0.00 36.58 5.12
1657 1691 2.509052 TGCACTATGTAGGCATCGAC 57.491 50.000 0.00 0.00 36.58 4.20
1658 1692 4.462483 TCATATGCACTATGTAGGCATCGA 59.538 41.667 14.85 11.71 44.41 3.59
1660 1694 6.093219 CCTTTCATATGCACTATGTAGGCATC 59.907 42.308 14.85 0.00 44.41 3.91
1662 1696 5.163205 ACCTTTCATATGCACTATGTAGGCA 60.163 40.000 21.84 0.00 40.51 4.75
1663 1697 5.308825 ACCTTTCATATGCACTATGTAGGC 58.691 41.667 21.84 0.00 40.51 3.93
1664 1698 6.293626 GCAACCTTTCATATGCACTATGTAGG 60.294 42.308 21.18 21.18 41.45 3.18
1667 1701 4.949238 TGCAACCTTTCATATGCACTATGT 59.051 37.500 0.00 0.00 43.32 2.29
1668 1702 5.503662 TGCAACCTTTCATATGCACTATG 57.496 39.130 0.00 0.00 43.32 2.23
1685 1725 1.069204 TCAGAGTCAGACAGGTGCAAC 59.931 52.381 2.66 0.00 0.00 4.17
1877 1918 2.548057 AGCAACATTGACTACCACGTTG 59.452 45.455 0.00 0.00 37.41 4.10
1972 2013 3.057019 TGTTGTTCGTCGATTCCTCTTG 58.943 45.455 0.00 0.00 0.00 3.02
2152 2201 2.754946 ACTTCGTGCCGAGGAAATTA 57.245 45.000 12.34 0.00 36.48 1.40
2371 2420 3.386237 GGGTCGACTGCAGAGGCT 61.386 66.667 23.35 0.00 41.91 4.58
2554 2603 1.284841 CCTTGGCCTCCCCATCTTCT 61.285 60.000 3.32 0.00 44.89 2.85
2659 2708 1.070786 GTTCTTCACGGAGGCCACA 59.929 57.895 5.01 0.00 0.00 4.17
2719 2768 2.746277 GGTTCAGACGGCGGCAAT 60.746 61.111 18.30 0.00 0.00 3.56
2720 2769 3.469863 AAGGTTCAGACGGCGGCAA 62.470 57.895 18.30 0.00 0.00 4.52
2770 2819 2.977829 CGAAGACGACGATGAACTTGAA 59.022 45.455 0.00 0.00 42.66 2.69
2809 2858 3.560025 CCTTACCAAACTGCAGGATCACT 60.560 47.826 19.93 0.00 0.00 3.41
2988 3037 9.086336 TCAACAACAGCAATAGAAAAAGAAAAG 57.914 29.630 0.00 0.00 0.00 2.27
3086 3135 1.594331 ACAGAAAAGTTCGGAGGCAC 58.406 50.000 0.00 0.00 34.02 5.01
3093 3142 7.372396 GTGTGTTACAATGTACAGAAAAGTTCG 59.628 37.037 0.33 0.00 34.02 3.95
3126 3243 8.918658 GTTTGCAGCATGATTTATTACATATGG 58.081 33.333 7.80 0.00 39.69 2.74
3130 3247 7.549839 ACTGTTTGCAGCATGATTTATTACAT 58.450 30.769 0.00 0.00 46.30 2.29
3192 3310 2.507058 TCTGATGATCCCAGAAACCCAG 59.493 50.000 11.20 0.00 37.68 4.45
3196 3314 2.883386 GCCATCTGATGATCCCAGAAAC 59.117 50.000 18.92 7.48 43.07 2.78
3224 3342 5.505181 TTTCTCCTGTCTAAATGCTCCTT 57.495 39.130 0.00 0.00 0.00 3.36
3225 3343 5.707066 ATTTCTCCTGTCTAAATGCTCCT 57.293 39.130 0.00 0.00 0.00 3.69
3226 3344 8.457238 AATTATTTCTCCTGTCTAAATGCTCC 57.543 34.615 0.00 0.00 0.00 4.70
3286 3424 6.590292 AGTCGACTGTGGATTGTTAATTGTAG 59.410 38.462 19.30 0.00 0.00 2.74
3521 3663 0.179124 GGCGCAAACCAACAAGTTGA 60.179 50.000 10.83 0.00 42.93 3.18
3550 3692 2.021722 TGCCGTTGCAGTGAGAAAC 58.978 52.632 0.00 0.00 44.23 2.78
3690 3832 1.646912 TCCCGGTTATGACCAGAACA 58.353 50.000 7.52 0.00 46.91 3.18
3755 3897 2.037772 AGTGACTTAGAGTTGGGCACTG 59.962 50.000 0.00 0.00 35.01 3.66
3816 3958 1.213926 GATGACCTTGAGATGGGCCTT 59.786 52.381 4.53 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.