Multiple sequence alignment - TraesCS6D01G030700

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 TraesCS6D01G030700 chr6D 100.000 4214 0 0 1 4214 12312507 12308294 0.000000e+00 7782.0
1 TraesCS6D01G030700 chr6D 85.311 177 19 3 1084 1256 12311376 12311203 4.330000e-40 176.0
2 TraesCS6D01G030700 chr6D 85.311 177 19 3 1132 1305 12311424 12311252 4.330000e-40 176.0
3 TraesCS6D01G030700 chr6A 94.616 3622 101 38 611 4214 13667955 13664410 0.000000e+00 5522.0
4 TraesCS6D01G030700 chr6A 92.045 176 13 1 874 1048 14659655 14659480 3.250000e-61 246.0
5 TraesCS6D01G030700 chr6A 85.542 166 15 3 4 163 13668598 13668436 9.370000e-37 165.0
6 TraesCS6D01G030700 chr6B 93.374 3109 126 34 1132 4214 22558961 22555907 0.000000e+00 4527.0
7 TraesCS6D01G030700 chr6B 84.134 1103 84 44 190 1256 22559841 22558794 0.000000e+00 983.0
8 TraesCS6D01G030700 chr2D 90.634 331 28 2 2281 2609 556200430 556200101 1.800000e-118 436.0
9 TraesCS6D01G030700 chr2D 89.426 331 33 1 2281 2609 564446426 564446096 2.340000e-112 416.0
10 TraesCS6D01G030700 chr2D 97.436 39 1 0 4176 4214 564446074 564446036 2.720000e-07 67.6
11 TraesCS6D01G030700 chr2D 94.872 39 2 0 4176 4214 556200079 556200041 1.270000e-05 62.1
12 TraesCS6D01G030700 chr2D 97.222 36 1 0 4179 4214 564584306 564584271 1.270000e-05 62.1
13 TraesCS6D01G030700 chr2A 89.297 327 32 2 2281 2605 695952130 695951805 1.410000e-109 407.0
14 TraesCS6D01G030700 chr2A 88.991 327 33 2 2281 2605 695776414 695776089 6.560000e-108 401.0
15 TraesCS6D01G030700 chr4A 89.623 318 30 3 2294 2609 30742638 30742322 6.560000e-108 401.0
16 TraesCS6D01G030700 chr4B 88.520 331 35 2 2281 2609 22464845 22465174 8.490000e-107 398.0
17 TraesCS6D01G030700 chr4B 97.436 39 1 0 4176 4214 22465196 22465234 2.720000e-07 67.6
18 TraesCS6D01G030700 chr3D 88.788 330 29 6 2282 2609 482857506 482857829 8.490000e-107 398.0
19 TraesCS6D01G030700 chr3D 97.436 39 1 0 4176 4214 482857851 482857889 2.720000e-07 67.6
20 TraesCS6D01G030700 chr2B 97.436 39 1 0 4176 4214 601695564 601695526 2.720000e-07 67.6
21 TraesCS6D01G030700 chr2B 97.436 39 1 0 4176 4214 663367387 663367425 2.720000e-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 TraesCS6D01G030700 chr6D 12308294 12312507 4213 True 2711.333333 7782 90.207333 1 4214 3 chr6D.!!$R1 4213
1 TraesCS6D01G030700 chr6A 13664410 13668598 4188 True 2843.500000 5522 90.079000 4 4214 2 chr6A.!!$R2 4210
2 TraesCS6D01G030700 chr6B 22555907 22559841 3934 True 2755.000000 4527 88.754000 190 4214 2 chr6B.!!$R1 4024

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
436 857 0.692419 TCCCATGCCTTCCTCTCTCC 60.692 60.0 0.00 0.0 0.00 3.71 F
1919 2383 0.105593 CTCATGTGCGGCTACAGGAT 59.894 55.0 16.06 0.0 40.14 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 2446 0.031857 CGCTGCACATCCCAAAAACA 59.968 50.0 0.0 0.0 0.0 2.83 R
3484 3956 0.030603 ATTGGTTTGTGGTTGGGGGT 60.031 50.0 0.0 0.0 0.0 4.95 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
26 27 8.081633 TGTTTATTCATCTTTCATGTGTGTTCC 58.918 33.333 0.00 0.00 0.00 3.62
31 32 5.702670 TCATCTTTCATGTGTGTTCCTCTTC 59.297 40.000 0.00 0.00 0.00 2.87
34 35 4.422073 TTCATGTGTGTTCCTCTTCAGT 57.578 40.909 0.00 0.00 0.00 3.41
38 39 6.533730 TCATGTGTGTTCCTCTTCAGTAAAT 58.466 36.000 0.00 0.00 0.00 1.40
40 41 8.321353 TCATGTGTGTTCCTCTTCAGTAAATAT 58.679 33.333 0.00 0.00 0.00 1.28
42 43 9.823647 ATGTGTGTTCCTCTTCAGTAAATATAG 57.176 33.333 0.00 0.00 0.00 1.31
43 44 8.812972 TGTGTGTTCCTCTTCAGTAAATATAGT 58.187 33.333 0.00 0.00 0.00 2.12
44 45 9.654663 GTGTGTTCCTCTTCAGTAAATATAGTT 57.345 33.333 0.00 0.00 0.00 2.24
100 103 5.934935 AGTAAAACATAACCGGTGTTCAG 57.065 39.130 8.52 0.00 38.76 3.02
158 165 4.694982 TGCGCTCAAGAATGTTATCTCAAA 59.305 37.500 9.73 0.00 0.00 2.69
163 170 8.443160 CGCTCAAGAATGTTATCTCAAAGTTTA 58.557 33.333 0.00 0.00 0.00 2.01
169 176 8.504005 AGAATGTTATCTCAAAGTTTAACACCG 58.496 33.333 3.60 0.00 37.37 4.94
170 177 6.548441 TGTTATCTCAAAGTTTAACACCGG 57.452 37.500 0.00 0.00 31.51 5.28
171 178 5.470777 TGTTATCTCAAAGTTTAACACCGGG 59.529 40.000 6.32 0.00 31.51 5.73
172 179 2.853705 TCTCAAAGTTTAACACCGGGG 58.146 47.619 0.00 0.00 0.00 5.73
174 181 3.390639 TCTCAAAGTTTAACACCGGGGTA 59.609 43.478 11.42 0.00 0.00 3.69
175 182 3.475575 TCAAAGTTTAACACCGGGGTAC 58.524 45.455 11.42 4.50 0.00 3.34
176 183 3.118112 TCAAAGTTTAACACCGGGGTACA 60.118 43.478 11.42 0.00 0.00 2.90
177 184 3.793819 AAGTTTAACACCGGGGTACAT 57.206 42.857 11.42 0.00 0.00 2.29
179 186 1.469703 GTTTAACACCGGGGTACATGC 59.530 52.381 11.42 0.00 0.00 4.06
188 606 2.014128 CGGGGTACATGCCAAAACTAG 58.986 52.381 0.00 0.00 0.00 2.57
202 620 7.526608 TGCCAAAACTAGTAAAATTCTCGATG 58.473 34.615 0.00 0.00 0.00 3.84
203 621 7.174253 TGCCAAAACTAGTAAAATTCTCGATGT 59.826 33.333 0.00 0.00 0.00 3.06
204 622 7.692705 GCCAAAACTAGTAAAATTCTCGATGTC 59.307 37.037 0.00 0.00 0.00 3.06
205 623 8.175716 CCAAAACTAGTAAAATTCTCGATGTCC 58.824 37.037 0.00 0.00 0.00 4.02
249 667 6.875948 AATACGCTATGGCATCACAATTTA 57.124 33.333 1.65 0.00 38.60 1.40
259 677 4.402155 GGCATCACAATTTAGAATGGTGGA 59.598 41.667 8.01 0.00 0.00 4.02
292 710 6.092955 TCGAATTTAGATATAACCGGTGCT 57.907 37.500 8.52 0.00 0.00 4.40
293 711 6.154445 TCGAATTTAGATATAACCGGTGCTC 58.846 40.000 8.52 2.54 0.00 4.26
300 718 1.635817 ATAACCGGTGCTCCCATGCT 61.636 55.000 8.52 0.00 0.00 3.79
302 720 4.100084 CCGGTGCTCCCATGCTCA 62.100 66.667 0.00 0.00 0.00 4.26
303 721 2.821366 CGGTGCTCCCATGCTCAC 60.821 66.667 0.00 0.00 0.00 3.51
324 742 2.358737 GCCGCAGCTTACACAGGT 60.359 61.111 0.00 0.00 35.50 4.00
327 745 1.626654 CCGCAGCTTACACAGGTTCG 61.627 60.000 0.00 0.00 39.09 3.95
332 750 2.357760 TTACACAGGTTCGGCGGC 60.358 61.111 7.21 0.00 0.00 6.53
348 766 2.048597 GCACCGATGACGTCACCA 60.049 61.111 22.71 0.00 37.88 4.17
375 793 2.027377 ACATGAGCAACCTTCCTCTCAG 60.027 50.000 0.00 0.00 38.74 3.35
395 814 4.040829 TCAGGAGAAGAAAAGACATGAGCA 59.959 41.667 0.00 0.00 0.00 4.26
397 816 5.240183 CAGGAGAAGAAAAGACATGAGCAAA 59.760 40.000 0.00 0.00 0.00 3.68
436 857 0.692419 TCCCATGCCTTCCTCTCTCC 60.692 60.000 0.00 0.00 0.00 3.71
441 862 1.207791 TGCCTTCCTCTCTCCATTCC 58.792 55.000 0.00 0.00 0.00 3.01
443 864 1.490574 CCTTCCTCTCTCCATTCCGT 58.509 55.000 0.00 0.00 0.00 4.69
452 873 4.714632 TCTCTCCATTCCGTTTCTTGTTT 58.285 39.130 0.00 0.00 0.00 2.83
453 874 5.130350 TCTCTCCATTCCGTTTCTTGTTTT 58.870 37.500 0.00 0.00 0.00 2.43
454 875 6.292923 TCTCTCCATTCCGTTTCTTGTTTTA 58.707 36.000 0.00 0.00 0.00 1.52
455 876 6.768861 TCTCTCCATTCCGTTTCTTGTTTTAA 59.231 34.615 0.00 0.00 0.00 1.52
538 975 7.710475 CACAGACAATTTTGGAAAATACAGGTT 59.290 33.333 0.00 0.00 37.62 3.50
588 1029 6.798427 AGAATCCTCTTGAGCACACTATAA 57.202 37.500 0.00 0.00 0.00 0.98
649 1090 5.185249 GGATGTAACTGGTCTTGACTCTGTA 59.815 44.000 0.61 0.00 0.00 2.74
654 1095 6.726490 AACTGGTCTTGACTCTGTAGTTTA 57.274 37.500 0.61 0.00 35.56 2.01
655 1096 6.919775 ACTGGTCTTGACTCTGTAGTTTAT 57.080 37.500 0.61 0.00 35.56 1.40
656 1097 8.418597 AACTGGTCTTGACTCTGTAGTTTATA 57.581 34.615 0.61 0.00 35.56 0.98
697 1138 4.996788 AATCAATGGGCTCAAGAATGTC 57.003 40.909 0.00 0.00 0.00 3.06
707 1150 4.252073 GCTCAAGAATGTCATCACAGAGT 58.748 43.478 0.00 0.00 35.41 3.24
717 1160 6.596309 TGTCATCACAGAGTAGATTTCACT 57.404 37.500 0.00 0.00 0.00 3.41
721 1164 6.663523 TCATCACAGAGTAGATTTCACTGGTA 59.336 38.462 0.00 0.00 33.57 3.25
722 1165 6.911250 TCACAGAGTAGATTTCACTGGTAA 57.089 37.500 0.00 0.00 33.57 2.85
724 1167 7.378966 TCACAGAGTAGATTTCACTGGTAAAG 58.621 38.462 0.00 0.00 33.57 1.85
725 1168 7.015292 TCACAGAGTAGATTTCACTGGTAAAGT 59.985 37.037 0.00 0.00 40.93 2.66
728 1171 9.141400 CAGAGTAGATTTCACTGGTAAAGTAAC 57.859 37.037 0.00 0.00 36.83 2.50
729 1172 8.867097 AGAGTAGATTTCACTGGTAAAGTAACA 58.133 33.333 0.00 0.00 36.83 2.41
731 1174 8.426489 AGTAGATTTCACTGGTAAAGTAACACA 58.574 33.333 0.00 0.00 36.83 3.72
732 1175 9.048446 GTAGATTTCACTGGTAAAGTAACACAA 57.952 33.333 0.00 0.00 36.83 3.33
733 1176 8.154649 AGATTTCACTGGTAAAGTAACACAAG 57.845 34.615 0.00 0.00 36.83 3.16
734 1177 7.773690 AGATTTCACTGGTAAAGTAACACAAGT 59.226 33.333 0.00 0.00 36.83 3.16
735 1178 7.690952 TTTCACTGGTAAAGTAACACAAGTT 57.309 32.000 0.00 0.00 36.83 2.66
819 1263 2.358582 GAGAGTAAACTAGGTCGCTCCC 59.641 54.545 7.65 0.00 36.75 4.30
854 1298 1.403679 CAAGCCGTCTTGGAAAACACA 59.596 47.619 0.00 0.00 44.53 3.72
858 1302 2.561569 CCGTCTTGGAAAACACACTCT 58.438 47.619 0.00 0.00 42.00 3.24
885 1329 1.153529 CTGCTCTGCTCAGCTCAGG 60.154 63.158 0.00 0.00 40.39 3.86
926 1371 4.747108 CAGCCGCAGAGCATATATATTACC 59.253 45.833 0.00 0.00 34.23 2.85
962 1407 3.813529 GCACACTTGCTACTTGGTAAG 57.186 47.619 0.00 0.00 46.17 2.34
964 1409 2.484264 CACACTTGCTACTTGGTAAGGC 59.516 50.000 0.00 0.00 34.13 4.35
973 1418 1.003233 ACTTGGTAAGGCTGTAGCACC 59.997 52.381 6.18 5.65 44.36 5.01
994 1439 2.367202 ATACCACCACCAGGGCGAG 61.367 63.158 0.00 0.00 42.05 5.03
1057 1502 4.471908 TCATCGCATGGCAGCCGT 62.472 61.111 7.03 2.72 0.00 5.68
1098 1543 3.201494 CTGGACGAGCAGGACGAT 58.799 61.111 0.00 0.00 34.70 3.73
1110 1555 2.049985 GACGATGATCCTCCCGCG 60.050 66.667 0.00 0.00 0.00 6.46
1191 1636 3.125573 TCGTCGGACGAGCAGGAG 61.126 66.667 27.66 0.00 46.73 3.69
1208 1653 2.359850 GGACAATCCGCCTGTGCA 60.360 61.111 0.00 0.00 35.41 4.57
1293 1744 4.477975 CCGTCGGACGAGCAGGAC 62.478 72.222 30.33 0.00 46.05 3.85
1360 1814 3.781770 GAGGAGTCCGATGCGCCAG 62.782 68.421 4.18 0.00 0.00 4.85
1374 1828 3.082579 GCCAGGAGTACCCTCGCTG 62.083 68.421 11.07 4.19 44.56 5.18
1626 2089 1.051812 CTGGGAGGCCGATCAACTAT 58.948 55.000 0.00 0.00 0.00 2.12
1909 2373 2.046988 TGGTGGAGCTCATGTGCG 60.047 61.111 17.19 0.00 38.13 5.34
1919 2383 0.105593 CTCATGTGCGGCTACAGGAT 59.894 55.000 16.06 0.00 40.14 3.24
1982 2446 2.093181 TCAGTATGGCATTTACGGTGCT 60.093 45.455 4.78 0.00 42.16 4.40
2200 2665 5.936686 AGTCAGGCAAATCATATGAATCG 57.063 39.130 9.99 2.01 0.00 3.34
2208 2673 5.468072 GCAAATCATATGAATCGAGTCAGGT 59.532 40.000 21.10 7.93 0.00 4.00
2289 2754 9.654663 AACAAAACAGATGAGGTATAGTTAGTC 57.345 33.333 0.00 0.00 0.00 2.59
2824 3295 3.507233 TGAACTCCATGGCAACTTCATTC 59.493 43.478 6.96 2.50 37.61 2.67
2839 3310 4.042187 ACTTCATTCAACAGAAGGCTAGGT 59.958 41.667 7.05 0.00 44.20 3.08
2906 3377 9.632969 CTACTTTTATTGACGTTTATCCAATCG 57.367 33.333 2.99 0.00 33.21 3.34
3025 3497 1.459450 TTTCTTATGAACGCCAGGGC 58.541 50.000 0.00 0.00 37.85 5.19
3461 3933 2.678336 GGCCCTGTCTATTTGTTCTTCG 59.322 50.000 0.00 0.00 0.00 3.79
3481 3953 4.263572 CTCCGCACACCCCCACAA 62.264 66.667 0.00 0.00 0.00 3.33
3482 3954 4.572571 TCCGCACACCCCCACAAC 62.573 66.667 0.00 0.00 0.00 3.32
3483 3955 4.885270 CCGCACACCCCCACAACA 62.885 66.667 0.00 0.00 0.00 3.33
3484 3956 2.830827 CGCACACCCCCACAACAA 60.831 61.111 0.00 0.00 0.00 2.83
3550 4022 2.257034 CGTAGAACAAACCGGTCTAGC 58.743 52.381 8.04 0.00 0.00 3.42
3564 4036 0.395724 TCTAGCACTCCTGATCCGCA 60.396 55.000 0.00 0.00 0.00 5.69
3682 4154 4.880164 TGCTTAGAACACCTAGGACCTAT 58.120 43.478 17.98 0.56 0.00 2.57
3692 4164 6.372104 ACACCTAGGACCTATAGAACCTTAC 58.628 44.000 17.98 0.00 34.42 2.34
3693 4165 6.068616 ACACCTAGGACCTATAGAACCTTACA 60.069 42.308 17.98 5.12 34.42 2.41
3709 4181 5.690997 CCTTACAAGGGAGAGTTGTTTTC 57.309 43.478 0.00 0.00 42.66 2.29
3766 4238 2.409948 ATGTAGAAGAGGCCAGCAAC 57.590 50.000 5.01 0.00 0.00 4.17
3871 4348 5.789574 ATGAAATGGTTAAGGTACCTCCA 57.210 39.130 20.12 20.12 39.04 3.86
4041 4518 6.888105 TCAGACAGGACAAAATATATGAGCA 58.112 36.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.081633 GGAACACACATGAAAGATGAATAAACA 58.918 33.333 0.00 0.00 0.00 2.83
1 2 8.299570 AGGAACACACATGAAAGATGAATAAAC 58.700 33.333 0.00 0.00 0.00 2.01
2 3 8.408043 AGGAACACACATGAAAGATGAATAAA 57.592 30.769 0.00 0.00 0.00 1.40
8 9 5.471116 TGAAGAGGAACACACATGAAAGATG 59.529 40.000 0.00 0.00 0.00 2.90
11 12 4.818546 ACTGAAGAGGAACACACATGAAAG 59.181 41.667 0.00 0.00 0.00 2.62
40 41 8.726988 CAAGAGGAATAAAACGGATGAAAACTA 58.273 33.333 0.00 0.00 0.00 2.24
42 43 7.590279 TCAAGAGGAATAAAACGGATGAAAAC 58.410 34.615 0.00 0.00 0.00 2.43
43 44 7.753309 TCAAGAGGAATAAAACGGATGAAAA 57.247 32.000 0.00 0.00 0.00 2.29
44 45 7.753309 TTCAAGAGGAATAAAACGGATGAAA 57.247 32.000 0.00 0.00 0.00 2.69
77 80 6.523840 ACTGAACACCGGTTATGTTTTACTA 58.476 36.000 2.97 0.00 40.36 1.82
78 81 5.370679 ACTGAACACCGGTTATGTTTTACT 58.629 37.500 2.97 0.00 40.36 2.24
79 82 5.467735 AGACTGAACACCGGTTATGTTTTAC 59.532 40.000 2.97 0.00 40.36 2.01
158 165 2.876892 GCATGTACCCCGGTGTTAAACT 60.877 50.000 0.00 0.00 0.00 2.66
163 170 2.070399 TTGGCATGTACCCCGGTGTT 62.070 55.000 0.00 0.00 0.00 3.32
164 171 2.070399 TTTGGCATGTACCCCGGTGT 62.070 55.000 0.00 0.00 0.00 4.16
165 172 0.896019 TTTTGGCATGTACCCCGGTG 60.896 55.000 0.00 0.00 0.00 4.94
166 173 0.896479 GTTTTGGCATGTACCCCGGT 60.896 55.000 0.00 0.00 0.00 5.28
167 174 0.610785 AGTTTTGGCATGTACCCCGG 60.611 55.000 0.00 0.00 0.00 5.73
168 175 2.014128 CTAGTTTTGGCATGTACCCCG 58.986 52.381 0.00 0.00 0.00 5.73
169 176 3.081710 ACTAGTTTTGGCATGTACCCC 57.918 47.619 0.00 0.00 0.00 4.95
170 177 6.578163 TTTTACTAGTTTTGGCATGTACCC 57.422 37.500 0.00 0.00 0.00 3.69
171 178 8.520351 AGAATTTTACTAGTTTTGGCATGTACC 58.480 33.333 0.00 0.00 0.00 3.34
172 179 9.556030 GAGAATTTTACTAGTTTTGGCATGTAC 57.444 33.333 0.00 0.00 0.00 2.90
174 181 7.174253 TCGAGAATTTTACTAGTTTTGGCATGT 59.826 33.333 0.00 0.00 0.00 3.21
175 182 7.526608 TCGAGAATTTTACTAGTTTTGGCATG 58.473 34.615 0.00 0.00 0.00 4.06
176 183 7.681939 TCGAGAATTTTACTAGTTTTGGCAT 57.318 32.000 0.00 0.00 0.00 4.40
177 184 7.174253 ACATCGAGAATTTTACTAGTTTTGGCA 59.826 33.333 0.00 0.00 0.00 4.92
179 186 8.175716 GGACATCGAGAATTTTACTAGTTTTGG 58.824 37.037 0.00 0.00 0.00 3.28
188 606 6.404712 AAAGACGGACATCGAGAATTTTAC 57.595 37.500 0.00 0.00 42.43 2.01
226 644 5.772825 AAATTGTGATGCCATAGCGTATT 57.227 34.783 0.00 0.00 44.31 1.89
227 645 6.230472 TCTAAATTGTGATGCCATAGCGTAT 58.770 36.000 0.00 0.00 44.31 3.06
228 646 5.606505 TCTAAATTGTGATGCCATAGCGTA 58.393 37.500 0.00 0.00 44.31 4.42
229 647 4.450976 TCTAAATTGTGATGCCATAGCGT 58.549 39.130 0.00 0.00 44.31 5.07
230 648 5.422666 TTCTAAATTGTGATGCCATAGCG 57.577 39.130 0.00 0.00 44.31 4.26
231 649 6.154445 CCATTCTAAATTGTGATGCCATAGC 58.846 40.000 0.00 0.00 40.48 2.97
232 650 7.143340 CACCATTCTAAATTGTGATGCCATAG 58.857 38.462 0.00 0.00 0.00 2.23
233 651 6.040729 CCACCATTCTAAATTGTGATGCCATA 59.959 38.462 5.68 0.00 0.00 2.74
249 667 3.753272 CGATTGTGTTTCTCCACCATTCT 59.247 43.478 0.00 0.00 34.35 2.40
284 702 4.101448 GAGCATGGGAGCACCGGT 62.101 66.667 0.00 0.00 44.64 5.28
286 704 2.821366 GTGAGCATGGGAGCACCG 60.821 66.667 0.00 0.00 44.64 4.94
307 725 1.912371 GAACCTGTGTAAGCTGCGGC 61.912 60.000 10.33 10.33 39.06 6.53
332 750 2.086426 CGTGGTGACGTCATCGGTG 61.086 63.158 23.12 10.84 40.91 4.94
336 754 1.269166 GTCATCGTGGTGACGTCATC 58.731 55.000 23.12 22.57 46.20 2.92
348 766 2.350522 GAAGGTTGCTCATGTCATCGT 58.649 47.619 0.00 0.00 0.00 3.73
375 793 5.456265 GTTTGCTCATGTCTTTTCTTCTCC 58.544 41.667 0.00 0.00 0.00 3.71
395 814 2.026014 CGTGCTTGCGCTTGGTTT 59.974 55.556 9.73 0.00 36.97 3.27
397 816 3.649986 GACGTGCTTGCGCTTGGT 61.650 61.111 9.73 0.00 36.97 3.67
412 831 2.124695 GGAAGGCATGGGACGGAC 60.125 66.667 0.00 0.00 0.00 4.79
414 833 2.190578 GAGGAAGGCATGGGACGG 59.809 66.667 0.00 0.00 0.00 4.79
415 834 1.144936 GAGAGGAAGGCATGGGACG 59.855 63.158 0.00 0.00 0.00 4.79
416 835 0.467804 GAGAGAGGAAGGCATGGGAC 59.532 60.000 0.00 0.00 0.00 4.46
496 917 3.570550 GTCTGTGTAGTCCTCTGTGTTCT 59.429 47.826 0.00 0.00 0.00 3.01
497 918 3.318275 TGTCTGTGTAGTCCTCTGTGTTC 59.682 47.826 0.00 0.00 0.00 3.18
498 919 3.296854 TGTCTGTGTAGTCCTCTGTGTT 58.703 45.455 0.00 0.00 0.00 3.32
500 921 4.527509 ATTGTCTGTGTAGTCCTCTGTG 57.472 45.455 0.00 0.00 0.00 3.66
504 941 5.305585 TCCAAAATTGTCTGTGTAGTCCTC 58.694 41.667 0.00 0.00 0.00 3.71
538 975 2.567169 CCTCCACATGTTCACCTACTCA 59.433 50.000 0.00 0.00 0.00 3.41
618 1059 6.093633 GTCAAGACCAGTTACATCCCATTTAC 59.906 42.308 0.00 0.00 0.00 2.01
626 1067 5.140747 ACAGAGTCAAGACCAGTTACATC 57.859 43.478 0.00 0.00 0.00 3.06
697 1138 5.728471 ACCAGTGAAATCTACTCTGTGATG 58.272 41.667 0.00 0.00 0.00 3.07
707 1150 9.268268 CTTGTGTTACTTTACCAGTGAAATCTA 57.732 33.333 0.00 0.00 35.97 1.98
721 1164 9.844790 GGTGTTTAACTTAACTTGTGTTACTTT 57.155 29.630 0.00 0.00 38.26 2.66
722 1165 9.012161 TGGTGTTTAACTTAACTTGTGTTACTT 57.988 29.630 0.00 0.00 38.26 2.24
724 1167 7.697710 GGTGGTGTTTAACTTAACTTGTGTTAC 59.302 37.037 0.00 0.00 38.26 2.50
725 1168 7.392673 TGGTGGTGTTTAACTTAACTTGTGTTA 59.607 33.333 0.00 0.00 37.59 2.41
728 1171 6.197364 TGGTGGTGTTTAACTTAACTTGTG 57.803 37.500 0.00 0.00 0.00 3.33
729 1172 6.626402 GCTTGGTGGTGTTTAACTTAACTTGT 60.626 38.462 0.00 0.00 0.00 3.16
731 1174 5.655090 AGCTTGGTGGTGTTTAACTTAACTT 59.345 36.000 0.00 0.00 0.00 2.66
732 1175 5.067283 CAGCTTGGTGGTGTTTAACTTAACT 59.933 40.000 0.00 0.00 39.17 2.24
733 1176 5.278604 CAGCTTGGTGGTGTTTAACTTAAC 58.721 41.667 0.00 0.00 39.17 2.01
734 1177 5.508200 CAGCTTGGTGGTGTTTAACTTAA 57.492 39.130 0.00 0.00 39.17 1.85
766 1209 5.467035 TGTGTGACATGATTACTCTGTGA 57.533 39.130 0.00 0.00 0.00 3.58
819 1263 1.237285 GCTTGGTGCTGTGTAGGTGG 61.237 60.000 0.00 0.00 38.95 4.61
854 1298 0.612732 AGAGCAGAGCAGAGCAGAGT 60.613 55.000 0.00 0.00 0.00 3.24
858 1302 2.228389 GAGCAGAGCAGAGCAGAGCA 62.228 60.000 0.00 0.00 0.00 4.26
885 1329 2.435059 GAACCTCTGCCGCTCCAC 60.435 66.667 0.00 0.00 0.00 4.02
900 1344 1.047801 TATATGCTCTGCGGCTGGAA 58.952 50.000 7.03 0.00 0.00 3.53
961 1406 0.541863 GGTATGTGGTGCTACAGCCT 59.458 55.000 0.00 0.00 41.18 4.58
962 1407 0.251916 TGGTATGTGGTGCTACAGCC 59.748 55.000 0.00 5.57 41.18 4.85
964 1409 1.277842 TGGTGGTATGTGGTGCTACAG 59.722 52.381 0.00 0.00 33.44 2.74
973 1418 1.378514 GCCCTGGTGGTGGTATGTG 60.379 63.158 0.00 0.00 36.04 3.21
994 1439 3.866582 CGGCCTCCTCATGGGTCC 61.867 72.222 0.00 0.00 36.25 4.46
1191 1636 1.523154 TTTGCACAGGCGGATTGTCC 61.523 55.000 0.00 0.00 45.35 4.02
1360 1814 4.208686 CGGCAGCGAGGGTACTCC 62.209 72.222 0.00 0.00 40.77 3.85
1591 2054 4.431131 AGGAGCCGGCATTGGTGG 62.431 66.667 31.54 0.00 0.00 4.61
1705 2168 1.064166 CAGGAAGTTGGCCCTCATCAT 60.064 52.381 0.00 0.00 0.00 2.45
1909 2373 5.170748 CCAAAAACATCAAATCCTGTAGCC 58.829 41.667 0.00 0.00 0.00 3.93
1919 2383 5.105716 TCACCTTTCGACCAAAAACATCAAA 60.106 36.000 0.00 0.00 0.00 2.69
1970 2434 3.056304 CCCAAAAACAGCACCGTAAATG 58.944 45.455 0.00 0.00 0.00 2.32
1982 2446 0.031857 CGCTGCACATCCCAAAAACA 59.968 50.000 0.00 0.00 0.00 2.83
2200 2665 7.730364 TGTTTTCTTTAGATTCACCTGACTC 57.270 36.000 0.00 0.00 0.00 3.36
2253 2718 6.024552 TCATCTGTTTTGTTAGCCCATTTC 57.975 37.500 0.00 0.00 0.00 2.17
2289 2754 7.730364 ATAAACGGAATAGCTTGGATTAGTG 57.270 36.000 0.00 0.00 0.00 2.74
2749 3220 2.230660 AGCAAGGTTCTAACAAGTGGC 58.769 47.619 0.00 0.00 0.00 5.01
2824 3295 3.070018 CACTTCACCTAGCCTTCTGTTG 58.930 50.000 0.00 0.00 0.00 3.33
2839 3310 0.179059 TCAGAAAGCGCACCACTTCA 60.179 50.000 11.47 0.00 0.00 3.02
2906 3377 2.544267 GGTCTATTGTCGCCATGCTTAC 59.456 50.000 0.00 0.00 0.00 2.34
3025 3497 2.496871 AGCCTCTTGATGTCTCTGTCAG 59.503 50.000 0.00 0.00 0.00 3.51
3403 3875 2.284754 TGCAAGCACTTCCATTACCA 57.715 45.000 0.00 0.00 0.00 3.25
3481 3953 0.978667 GGTTTGTGGTTGGGGGTTGT 60.979 55.000 0.00 0.00 0.00 3.32
3482 3954 0.978146 TGGTTTGTGGTTGGGGGTTG 60.978 55.000 0.00 0.00 0.00 3.77
3483 3955 0.252742 TTGGTTTGTGGTTGGGGGTT 60.253 50.000 0.00 0.00 0.00 4.11
3484 3956 0.030603 ATTGGTTTGTGGTTGGGGGT 60.031 50.000 0.00 0.00 0.00 4.95
3525 3997 1.571215 CCGGTTTGTTCTACGGGTGC 61.571 60.000 0.00 0.00 42.48 5.01
3535 4007 1.270678 GGAGTGCTAGACCGGTTTGTT 60.271 52.381 9.42 0.00 0.00 2.83
3550 4022 1.039785 TCCTCTGCGGATCAGGAGTG 61.040 60.000 13.61 11.18 43.06 3.51
3564 4036 4.922206 TGACTGCATGGTTTATTTCCTCT 58.078 39.130 0.00 0.00 0.00 3.69
3682 4154 5.152934 ACAACTCTCCCTTGTAAGGTTCTA 58.847 41.667 9.65 0.00 44.98 2.10
3871 4348 5.014966 AGGCCTATTCAAGATCCATGCTAAT 59.985 40.000 1.29 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.