Multiple sequence alignment - TraesCS5D01G382600

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 TraesCS5D01G382600 chr5D 100.000 2903 0 0 1 2903 452363472 452366374 0.000000e+00 5361.0
1 TraesCS5D01G382600 chr5D 84.671 1109 107 32 875 1966 70521728 70520666 0.000000e+00 1048.0
2 TraesCS5D01G382600 chr5D 90.476 63 4 2 474 536 498015275 498015215 6.670000e-12 82.4
3 TraesCS5D01G382600 chr5D 88.889 63 5 2 474 535 460397722 460397661 3.100000e-10 76.8
4 TraesCS5D01G382600 chr5D 76.596 141 27 5 2114 2251 462744017 462743880 4.010000e-09 73.1
5 TraesCS5D01G382600 chr5D 83.871 62 7 3 476 535 135236332 135236392 4.040000e-04 56.5
6 TraesCS5D01G382600 chr5B 92.247 2928 170 25 1 2901 552563168 552566065 0.000000e+00 4096.0
7 TraesCS5D01G382600 chr5B 84.731 1061 106 26 875 1914 75812005 75810980 0.000000e+00 1011.0
8 TraesCS5D01G382600 chr5A 92.637 1426 72 17 533 1936 571304018 571305432 0.000000e+00 2021.0
9 TraesCS5D01G382600 chr5A 84.581 1109 107 28 875 1966 60414466 60413405 0.000000e+00 1042.0
10 TraesCS5D01G382600 chr3D 88.438 493 55 2 1 492 283615569 283615078 6.930000e-166 593.0
11 TraesCS5D01G382600 chr3D 75.655 267 55 9 2165 2425 86970823 86971085 1.090000e-24 124.0
12 TraesCS5D01G382600 chr3D 84.483 58 9 0 474 531 91382858 91382801 1.120000e-04 58.4
13 TraesCS5D01G382600 chr6D 89.241 474 48 2 1 472 115644581 115645053 8.960000e-165 590.0
14 TraesCS5D01G382600 chr6D 86.383 470 64 0 1 470 111625751 111626220 5.550000e-142 514.0
15 TraesCS5D01G382600 chr6D 85.481 489 69 2 1 488 421797849 421798336 2.580000e-140 508.0
16 TraesCS5D01G382600 chr6D 80.921 152 21 7 2194 2342 276019733 276019587 2.360000e-21 113.0
17 TraesCS5D01G382600 chr3A 87.810 484 58 1 1 483 371161453 371160970 1.510000e-157 566.0
18 TraesCS5D01G382600 chr2D 87.891 479 53 5 2 477 423282037 423282513 2.530000e-155 558.0
19 TraesCS5D01G382600 chr2D 75.524 286 59 8 2143 2426 354816038 354815762 2.350000e-26 130.0
20 TraesCS5D01G382600 chr4A 85.206 534 70 7 1 532 606341794 606342320 9.150000e-150 540.0
21 TraesCS5D01G382600 chr4A 92.973 185 12 1 1087 1271 688857688 688857505 4.770000e-68 268.0
22 TraesCS5D01G382600 chr4A 73.793 290 68 7 2196 2480 87969033 87969319 1.100000e-19 108.0
23 TraesCS5D01G382600 chr4A 75.000 192 43 4 2143 2334 27662557 27662371 1.850000e-12 84.2
24 TraesCS5D01G382600 chr4A 90.000 60 4 2 476 534 608272809 608272751 3.100000e-10 76.8
25 TraesCS5D01G382600 chr4A 85.484 62 7 2 474 534 552850253 552850193 2.420000e-06 63.9
26 TraesCS5D01G382600 chr6A 85.098 510 74 2 20 527 136229500 136228991 1.190000e-143 520.0
27 TraesCS5D01G382600 chr6A 90.476 189 15 2 1057 1244 104399235 104399421 2.230000e-61 246.0
28 TraesCS5D01G382600 chr7D 82.069 145 22 4 1713 1855 428952610 428952752 1.410000e-23 121.0
29 TraesCS5D01G382600 chr7B 82.069 145 22 4 1713 1855 446665463 446665605 1.410000e-23 121.0
30 TraesCS5D01G382600 chr7B 75.099 253 49 13 2181 2425 686894393 686894639 3.960000e-19 106.0
31 TraesCS5D01G382600 chr7A 82.069 145 22 4 1713 1855 503052290 503052148 1.410000e-23 121.0
32 TraesCS5D01G382600 chr1D 81.250 144 25 2 1713 1855 283617795 283617937 6.570000e-22 115.0
33 TraesCS5D01G382600 chr1A 81.250 144 25 2 1713 1855 355343679 355343821 6.570000e-22 115.0
34 TraesCS5D01G382600 chr2A 73.443 305 71 9 2176 2473 52153099 52152798 3.960000e-19 106.0
35 TraesCS5D01G382600 chr6B 87.778 90 8 3 1053 1140 134670460 134670372 5.120000e-18 102.0
36 TraesCS5D01G382600 chr4D 86.154 65 7 2 471 534 81923957 81924020 5.190000e-08 69.4


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 TraesCS5D01G382600 chr5D 452363472 452366374 2902 False 5361 5361 100.000 1 2903 1 chr5D.!!$F2 2902
1 TraesCS5D01G382600 chr5D 70520666 70521728 1062 True 1048 1048 84.671 875 1966 1 chr5D.!!$R1 1091
2 TraesCS5D01G382600 chr5B 552563168 552566065 2897 False 4096 4096 92.247 1 2901 1 chr5B.!!$F1 2900
3 TraesCS5D01G382600 chr5B 75810980 75812005 1025 True 1011 1011 84.731 875 1914 1 chr5B.!!$R1 1039
4 TraesCS5D01G382600 chr5A 571304018 571305432 1414 False 2021 2021 92.637 533 1936 1 chr5A.!!$F1 1403
5 TraesCS5D01G382600 chr5A 60413405 60414466 1061 True 1042 1042 84.581 875 1966 1 chr5A.!!$R1 1091
6 TraesCS5D01G382600 chr4A 606341794 606342320 526 False 540 540 85.206 1 532 1 chr4A.!!$F2 531
7 TraesCS5D01G382600 chr6A 136228991 136229500 509 True 520 520 85.098 20 527 1 chr6A.!!$R1 507

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
170 173 0.457443 TCCGCAGACTCATACAGCTG 59.543 55.0 13.48 13.48 32.41 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2244 1.205655 CAGGATGCTTGAGACTTCCGA 59.794 52.381 0.0 0.0 36.67 4.55 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
25 26 3.497932 CGAAGGCAGCAGCAGAGC 61.498 66.667 2.65 0.00 44.61 4.09
72 74 4.394078 CAAGACCGCGTCGTCCGA 62.394 66.667 4.92 0.00 39.56 4.55
101 103 2.937519 AGGCTACATCGTCATCTCTGA 58.062 47.619 0.00 0.00 0.00 3.27
105 107 4.022416 GGCTACATCGTCATCTCTGATTCT 60.022 45.833 0.00 0.00 32.98 2.40
108 110 4.942852 ACATCGTCATCTCTGATTCTTCC 58.057 43.478 0.00 0.00 32.98 3.46
109 111 4.648762 ACATCGTCATCTCTGATTCTTCCT 59.351 41.667 0.00 0.00 32.98 3.36
110 112 4.909696 TCGTCATCTCTGATTCTTCCTC 57.090 45.455 0.00 0.00 32.98 3.71
114 117 3.634448 TCATCTCTGATTCTTCCTCCGAC 59.366 47.826 0.00 0.00 0.00 4.79
133 136 3.343788 GACAGGTCTGACGGCTCCG 62.344 68.421 6.79 6.79 46.03 4.63
151 154 1.752833 GACGTGAACCCACCTCCTT 59.247 57.895 0.00 0.00 40.12 3.36
162 165 1.228894 ACCTCCTTCCGCAGACTCA 60.229 57.895 0.00 0.00 0.00 3.41
165 168 1.067821 CCTCCTTCCGCAGACTCATAC 59.932 57.143 0.00 0.00 0.00 2.39
170 173 0.457443 TCCGCAGACTCATACAGCTG 59.543 55.000 13.48 13.48 32.41 4.24
171 174 1.150567 CCGCAGACTCATACAGCTGC 61.151 60.000 15.27 0.00 43.41 5.25
173 176 1.760268 GCAGACTCATACAGCTGCGC 61.760 60.000 15.27 0.00 40.28 6.09
241 244 5.243283 TCGCCCTCTCCTGTTTATAATCTAC 59.757 44.000 0.00 0.00 0.00 2.59
266 269 9.991906 ACTTGTAGTATGTAGTTACAATGTGTT 57.008 29.630 0.00 0.00 39.99 3.32
285 288 4.688879 GTGTTGGATCGTTGAACTATGTGA 59.311 41.667 0.00 0.00 0.00 3.58
305 308 1.423921 ACTTCCCCGTTTGGTGATCTT 59.576 47.619 0.00 0.00 0.00 2.40
309 312 1.272212 CCCCGTTTGGTGATCTTTTGG 59.728 52.381 0.00 0.00 0.00 3.28
332 335 4.864247 GGTGATGTTTATGTGAATTGTGCC 59.136 41.667 0.00 0.00 0.00 5.01
333 336 4.864247 GTGATGTTTATGTGAATTGTGCCC 59.136 41.667 0.00 0.00 0.00 5.36
334 337 4.525874 TGATGTTTATGTGAATTGTGCCCA 59.474 37.500 0.00 0.00 0.00 5.36
352 355 3.767131 GCCCATTTGGTACCAGTTTGTAT 59.233 43.478 15.65 0.80 36.04 2.29
354 357 4.381505 CCCATTTGGTACCAGTTTGTATGC 60.382 45.833 15.65 0.00 0.00 3.14
355 358 4.381505 CCATTTGGTACCAGTTTGTATGCC 60.382 45.833 15.65 0.00 0.00 4.40
362 365 2.159382 CCAGTTTGTATGCCCGTTTCT 58.841 47.619 0.00 0.00 0.00 2.52
366 369 3.252458 AGTTTGTATGCCCGTTTCTTGTC 59.748 43.478 0.00 0.00 0.00 3.18
382 385 5.915812 TCTTGTCGATTTTGATCGTTTCA 57.084 34.783 8.43 4.93 43.85 2.69
414 417 8.936070 ACGTACTAGTTGCATGAATTTGTATA 57.064 30.769 0.00 0.00 0.00 1.47
415 418 9.373603 ACGTACTAGTTGCATGAATTTGTATAA 57.626 29.630 0.00 0.00 0.00 0.98
476 479 1.379527 GAATTTAGGGAGTGCACGGG 58.620 55.000 12.01 0.00 0.00 5.28
477 480 0.679960 AATTTAGGGAGTGCACGGGC 60.680 55.000 12.01 0.34 41.68 6.13
499 502 0.882042 GTCCGCGGACGTATAGGAGA 60.882 60.000 39.77 6.59 37.70 3.71
500 503 0.882042 TCCGCGGACGTATAGGAGAC 60.882 60.000 27.28 0.00 37.70 3.36
509 512 4.299978 GACGTATAGGAGACCAGATTTGC 58.700 47.826 0.00 0.00 0.00 3.68
543 546 6.560003 TGTAGATGCTCTAAATTTGAGGGA 57.440 37.500 15.09 2.65 29.58 4.20
568 577 1.805945 GTCACGGTCCGCTGACATC 60.806 63.158 27.58 11.83 43.65 3.06
572 581 1.226802 CGGTCCGCTGACATCTGAG 60.227 63.158 10.60 0.00 43.65 3.35
708 726 1.977293 GCATCTCCACTCCACCTCCC 61.977 65.000 0.00 0.00 0.00 4.30
711 729 4.316823 TCCACTCCACCTCCCGCT 62.317 66.667 0.00 0.00 0.00 5.52
811 829 1.541588 GATCAGTGCTTTGTGTTCCCC 59.458 52.381 0.00 0.00 0.00 4.81
847 865 5.245301 CCAATCCATTGACTTGCATCCATAT 59.755 40.000 0.56 0.00 40.14 1.78
873 891 3.862264 GCTCCTCCCATTTCAACTTTTGC 60.862 47.826 0.00 0.00 0.00 3.68
1940 1985 1.448540 CCGACAGGACTGGATGTGC 60.449 63.158 4.14 0.00 41.02 4.57
1945 1990 1.002888 ACAGGACTGGATGTGCTCTTG 59.997 52.381 4.14 0.00 44.20 3.02
1965 2010 3.958704 TGCATTTGTTCTTTGTACACGG 58.041 40.909 0.00 0.00 0.00 4.94
1993 2038 5.175127 CACATGCATGTACACCACTAACTA 58.825 41.667 30.92 0.00 39.39 2.24
1994 2039 5.641636 CACATGCATGTACACCACTAACTAA 59.358 40.000 30.92 0.00 39.39 2.24
1995 2040 6.148645 CACATGCATGTACACCACTAACTAAA 59.851 38.462 30.92 0.00 39.39 1.85
1996 2041 6.712998 ACATGCATGTACACCACTAACTAAAA 59.287 34.615 30.50 0.00 39.68 1.52
2063 2220 1.209128 ATGCAGTATACTTGCGCGAC 58.791 50.000 12.10 0.88 0.00 5.19
2075 2232 1.503294 TGCGCGACAAACATAGTGAA 58.497 45.000 12.10 0.00 0.00 3.18
2087 2244 6.936900 ACAAACATAGTGAAAGCATCTACAGT 59.063 34.615 0.00 0.00 0.00 3.55
2107 2264 1.205655 TCGGAAGTCTCAAGCATCCTG 59.794 52.381 0.00 0.00 0.00 3.86
2118 2277 0.325296 AGCATCCTGTAAGTCCGGGA 60.325 55.000 0.00 0.00 0.00 5.14
2138 2297 2.367567 GAGGACGGCCCAATCACTAATA 59.632 50.000 1.76 0.00 37.41 0.98
2188 2347 3.426615 TCAATAACCGGCCTCAAATGTT 58.573 40.909 0.00 0.00 0.00 2.71
2195 2354 1.466167 CGGCCTCAAATGTTCAGACTG 59.534 52.381 0.00 0.00 0.00 3.51
2197 2356 2.485814 GGCCTCAAATGTTCAGACTGAC 59.514 50.000 4.15 1.51 0.00 3.51
2204 2363 1.668151 GTTCAGACTGACCGGCACC 60.668 63.158 4.15 0.00 0.00 5.01
2213 2372 1.371558 GACCGGCACCCCTCATATC 59.628 63.158 0.00 0.00 0.00 1.63
2216 2375 1.372683 CGGCACCCCTCATATCCAG 59.627 63.158 0.00 0.00 0.00 3.86
2274 2453 2.202756 GGATGCGTCCGTCAGGTC 60.203 66.667 9.75 0.00 39.05 3.85
2300 2479 4.489771 CCCACGATGGCCCACCTC 62.490 72.222 0.00 0.00 35.79 3.85
2321 2500 3.919223 GACTCCACATATAGTCGTCCC 57.081 52.381 0.00 0.00 33.38 4.46
2342 2521 0.464373 ATCCGCTCACCGCATCAAAT 60.464 50.000 0.00 0.00 39.08 2.32
2368 2547 2.279069 CCACTCCACTCAGCTCCGT 61.279 63.158 0.00 0.00 0.00 4.69
2369 2548 1.668294 CACTCCACTCAGCTCCGTT 59.332 57.895 0.00 0.00 0.00 4.44
2370 2549 0.034059 CACTCCACTCAGCTCCGTTT 59.966 55.000 0.00 0.00 0.00 3.60
2371 2550 0.318762 ACTCCACTCAGCTCCGTTTC 59.681 55.000 0.00 0.00 0.00 2.78
2372 2551 0.390472 CTCCACTCAGCTCCGTTTCC 60.390 60.000 0.00 0.00 0.00 3.13
2394 2573 1.068250 CTCCCTTTCGGCGATCTCC 59.932 63.158 11.76 0.00 0.00 3.71
2450 2629 1.000163 CCGACCACTCCTAATCCATCG 60.000 57.143 0.00 0.00 0.00 3.84
2543 2723 3.991536 GAAGGAGTGCGCTCGACCC 62.992 68.421 20.49 7.89 42.53 4.46
2602 2782 4.514577 ACAAGCGCTCGGATCCGG 62.515 66.667 32.79 23.49 40.25 5.14
2632 2812 1.219124 GCTCGAGGTCCATCTTGCA 59.781 57.895 15.58 0.00 0.00 4.08
2642 2822 0.622665 CCATCTTGCACCCCTTCTCT 59.377 55.000 0.00 0.00 0.00 3.10
2648 2828 2.224159 GCACCCCTTCTCTGGTCCA 61.224 63.158 0.00 0.00 30.70 4.02
2649 2829 1.986413 CACCCCTTCTCTGGTCCAG 59.014 63.158 13.21 13.21 30.70 3.86
2663 2843 1.552719 GGTCCAGAGGAGTACAAGGGT 60.553 57.143 0.00 0.00 29.39 4.34
2681 2861 2.305052 GGGTTATAGGGATAGGTGTGCC 59.695 54.545 0.00 0.00 0.00 5.01
2684 2864 0.105142 ATAGGGATAGGTGTGCCCGT 60.105 55.000 0.00 0.00 46.68 5.28
2685 2865 0.757935 TAGGGATAGGTGTGCCCGTC 60.758 60.000 0.00 0.00 46.68 4.79
2788 2968 2.046892 TGGCGCAGAAGAGGAAGC 60.047 61.111 10.83 0.00 0.00 3.86
2792 2972 1.028868 GCGCAGAAGAGGAAGCCATT 61.029 55.000 0.30 0.00 0.00 3.16
2800 2980 0.744771 GAGGAAGCCATTCGTGTCCC 60.745 60.000 0.00 0.00 36.19 4.46
2806 2986 0.466189 GCCATTCGTGTCCCCATCAT 60.466 55.000 0.00 0.00 0.00 2.45
2828 3008 0.883833 ACAAGCGGCAAAGGATGAAG 59.116 50.000 1.45 0.00 0.00 3.02
2833 3013 0.443869 CGGCAAAGGATGAAGACACG 59.556 55.000 0.00 0.00 0.00 4.49
2856 3036 1.521681 CTCGCCCGAGAACAATCCC 60.522 63.158 12.04 0.00 44.53 3.85
2861 3041 2.267642 CGAGAACAATCCCGGGCA 59.732 61.111 18.49 5.14 0.00 5.36
2865 3045 1.201429 AGAACAATCCCGGGCAGTCT 61.201 55.000 18.49 10.84 0.00 3.24
2878 3058 2.044555 CAGTCTGTGCCATGGCCAG 61.045 63.158 32.88 32.88 41.09 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 74 2.420022 GACGATGTAGCCTTGCAAATGT 59.580 45.455 0.00 0.00 0.00 2.71
74 76 2.710377 TGACGATGTAGCCTTGCAAAT 58.290 42.857 0.00 0.00 0.00 2.32
101 103 0.818296 CCTGTCGTCGGAGGAAGAAT 59.182 55.000 1.41 0.00 32.42 2.40
105 107 1.074423 AGACCTGTCGTCGGAGGAA 59.926 57.895 15.67 0.00 46.92 3.36
108 110 1.502640 GTCAGACCTGTCGTCGGAG 59.497 63.158 0.00 0.00 44.88 4.63
109 111 2.322830 CGTCAGACCTGTCGTCGGA 61.323 63.158 8.16 0.00 46.92 4.55
110 112 2.176055 CGTCAGACCTGTCGTCGG 59.824 66.667 8.16 0.00 46.92 4.79
114 117 2.179517 GAGCCGTCAGACCTGTCG 59.820 66.667 9.13 9.13 40.71 4.35
127 130 3.998672 TGGGTTCACGTCGGAGCC 61.999 66.667 7.36 7.36 37.43 4.70
128 131 2.737376 GTGGGTTCACGTCGGAGC 60.737 66.667 0.00 0.00 33.87 4.70
139 142 2.852075 TGCGGAAGGAGGTGGGTT 60.852 61.111 0.00 0.00 0.00 4.11
151 154 0.457443 CAGCTGTATGAGTCTGCGGA 59.543 55.000 5.25 0.00 35.48 5.54
197 200 4.735132 TTCACCGCTTCCTCGCCG 62.735 66.667 0.00 0.00 0.00 6.46
208 211 3.708220 GAGAGGGCGAGCTTCACCG 62.708 68.421 0.00 0.00 0.00 4.94
218 221 4.608948 AGATTATAAACAGGAGAGGGCG 57.391 45.455 0.00 0.00 0.00 6.13
266 269 4.801330 AGTCACATAGTTCAACGATCCA 57.199 40.909 0.00 0.00 0.00 3.41
285 288 1.064825 AGATCACCAAACGGGGAAGT 58.935 50.000 0.00 0.00 40.18 3.01
305 308 6.927936 CACAATTCACATAAACATCACCCAAA 59.072 34.615 0.00 0.00 0.00 3.28
309 312 4.864247 GGCACAATTCACATAAACATCACC 59.136 41.667 0.00 0.00 0.00 4.02
332 335 4.381505 GGCATACAAACTGGTACCAAATGG 60.382 45.833 17.11 6.69 42.17 3.16
333 336 4.381505 GGGCATACAAACTGGTACCAAATG 60.382 45.833 17.11 16.39 0.00 2.32
334 337 3.767131 GGGCATACAAACTGGTACCAAAT 59.233 43.478 17.11 4.09 0.00 2.32
352 355 1.600023 AAATCGACAAGAAACGGGCA 58.400 45.000 0.00 0.00 0.00 5.36
354 357 3.889196 TCAAAATCGACAAGAAACGGG 57.111 42.857 0.00 0.00 0.00 5.28
382 385 6.635030 TCATGCAACTAGTACGTAGATCAT 57.365 37.500 0.00 0.00 32.41 2.45
427 430 2.029290 ACACCCGCGTATCTCATATTCC 60.029 50.000 4.92 0.00 0.00 3.01
456 459 1.006832 CCGTGCACTCCCTAAATTCG 58.993 55.000 16.19 0.00 0.00 3.34
457 460 1.379527 CCCGTGCACTCCCTAAATTC 58.620 55.000 16.19 0.00 0.00 2.17
458 461 0.679960 GCCCGTGCACTCCCTAAATT 60.680 55.000 16.19 0.00 37.47 1.82
499 502 0.609131 CCGGAGTTGGCAAATCTGGT 60.609 55.000 35.69 5.44 35.18 4.00
500 503 2.183409 CCGGAGTTGGCAAATCTGG 58.817 57.895 33.37 33.37 33.32 3.86
509 512 0.811616 GCATCTACAGCCGGAGTTGG 60.812 60.000 5.05 0.00 0.00 3.77
568 577 1.271379 ACACAAAATCCGACCCCTCAG 60.271 52.381 0.00 0.00 0.00 3.35
572 581 1.092348 GCTACACAAAATCCGACCCC 58.908 55.000 0.00 0.00 0.00 4.95
612 624 0.693049 CCAACAACTGCCTCTACCCT 59.307 55.000 0.00 0.00 0.00 4.34
708 726 6.017852 GGTCTCCTCCTTTTTAATATTCAGCG 60.018 42.308 0.00 0.00 0.00 5.18
711 729 7.125204 TCTCGGTCTCCTCCTTTTTAATATTCA 59.875 37.037 0.00 0.00 0.00 2.57
748 766 4.590222 TGGAGATGAGCATAGAATACAGCA 59.410 41.667 0.00 0.00 0.00 4.41
763 781 2.061848 TGGGTTGGACTTTGGAGATGA 58.938 47.619 0.00 0.00 0.00 2.92
811 829 4.082081 TCAATGGATTGGTTAGCAGCAAAG 60.082 41.667 0.00 0.00 43.52 2.77
847 865 2.376518 AGTTGAAATGGGAGGAGCAGAA 59.623 45.455 0.00 0.00 0.00 3.02
873 891 1.071857 GGAGGCCGAGGGGTTTTATAG 59.928 57.143 0.00 0.00 34.97 1.31
1940 1985 5.396362 CGTGTACAAAGAACAAATGCAAGAG 59.604 40.000 0.00 0.00 0.00 2.85
1945 1990 2.724174 GCCGTGTACAAAGAACAAATGC 59.276 45.455 0.00 0.00 0.00 3.56
1965 2010 1.670811 GGTGTACATGCATGTGTAGGC 59.329 52.381 36.72 22.25 41.89 3.93
2063 2220 7.369803 ACTGTAGATGCTTTCACTATGTTTG 57.630 36.000 0.00 0.00 0.00 2.93
2075 2232 3.093057 AGACTTCCGACTGTAGATGCTT 58.907 45.455 0.00 0.00 0.00 3.91
2087 2244 1.205655 CAGGATGCTTGAGACTTCCGA 59.794 52.381 0.00 0.00 36.67 4.55
2118 2277 1.213296 ATTAGTGATTGGGCCGTCCT 58.787 50.000 0.00 2.45 36.20 3.85
2157 2316 1.737793 CCGGTTATTGAGGCTTGTGTC 59.262 52.381 0.00 0.00 0.00 3.67
2188 2347 3.311110 GGGTGCCGGTCAGTCTGA 61.311 66.667 1.90 0.00 0.00 3.27
2195 2354 1.371558 GATATGAGGGGTGCCGGTC 59.628 63.158 1.90 0.00 0.00 4.79
2197 2356 2.116983 CTGGATATGAGGGGTGCCGG 62.117 65.000 0.00 0.00 0.00 6.13
2204 2363 2.377869 AGATTTGGGCTGGATATGAGGG 59.622 50.000 0.00 0.00 0.00 4.30
2256 2435 2.994995 ACCTGACGGACGCATCCA 60.995 61.111 0.00 0.00 46.67 3.41
2274 2453 4.969196 CATCGTGGGCCGGATCCG 62.969 72.222 27.65 27.65 37.11 4.18
2286 2465 3.771160 GTCGAGGTGGGCCATCGT 61.771 66.667 24.33 13.64 37.02 3.73
2287 2466 3.432051 GAGTCGAGGTGGGCCATCG 62.432 68.421 20.71 20.71 37.03 3.84
2335 2514 1.667724 GAGTGGAGTGCCGATTTGATG 59.332 52.381 0.00 0.00 36.79 3.07
2342 2521 2.203640 AGTGGAGTGGAGTGCCGA 60.204 61.111 0.00 0.00 36.79 5.54
2469 2649 2.443016 CTCCTGACCTCCTCCCCG 60.443 72.222 0.00 0.00 0.00 5.73
2470 2650 2.041405 CCTCCTGACCTCCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
2526 2706 4.070552 GGGTCGAGCGCACTCCTT 62.071 66.667 11.47 0.00 40.03 3.36
2543 2723 1.688735 TGCCAGATCGAATCCTACCTG 59.311 52.381 0.00 0.00 0.00 4.00
2602 2782 4.087892 TCGAGCTTCCAGCCCAGC 62.088 66.667 0.00 0.00 43.77 4.85
2604 2784 3.393970 CCTCGAGCTTCCAGCCCA 61.394 66.667 6.99 0.00 43.77 5.36
2608 2788 0.103937 GATGGACCTCGAGCTTCCAG 59.896 60.000 28.10 10.44 42.72 3.86
2632 2812 1.868810 TCTGGACCAGAGAAGGGGT 59.131 57.895 20.74 0.00 40.96 4.95
2642 2822 1.552486 CCCTTGTACTCCTCTGGACCA 60.552 57.143 0.00 0.00 0.00 4.02
2648 2828 4.485021 TCCCTATAACCCTTGTACTCCTCT 59.515 45.833 0.00 0.00 0.00 3.69
2649 2829 4.812653 TCCCTATAACCCTTGTACTCCTC 58.187 47.826 0.00 0.00 0.00 3.71
2663 2843 2.253610 CGGGCACACCTATCCCTATAA 58.746 52.381 0.00 0.00 37.89 0.98
2681 2861 2.800544 CCCATCTGCTTATTTACGACGG 59.199 50.000 0.00 0.00 0.00 4.79
2684 2864 3.491964 CGTCCCCATCTGCTTATTTACGA 60.492 47.826 0.00 0.00 0.00 3.43
2685 2865 2.800544 CGTCCCCATCTGCTTATTTACG 59.199 50.000 0.00 0.00 0.00 3.18
2730 2910 4.521062 ATCGACAGCAGAGCGGGC 62.521 66.667 0.00 0.00 0.00 6.13
2731 2911 2.584418 CATCGACAGCAGAGCGGG 60.584 66.667 0.00 0.00 0.00 6.13
2732 2912 2.163390 CACATCGACAGCAGAGCGG 61.163 63.158 0.00 0.00 0.00 5.52
2733 2913 2.163390 CCACATCGACAGCAGAGCG 61.163 63.158 0.00 0.00 0.00 5.03
2734 2914 2.459442 GCCACATCGACAGCAGAGC 61.459 63.158 0.00 0.00 0.00 4.09
2735 2915 2.163390 CGCCACATCGACAGCAGAG 61.163 63.158 0.00 0.00 0.00 3.35
2736 2916 2.125952 CGCCACATCGACAGCAGA 60.126 61.111 0.00 0.00 0.00 4.26
2737 2917 3.190849 CCGCCACATCGACAGCAG 61.191 66.667 0.00 0.00 0.00 4.24
2738 2918 3.647649 CTCCGCCACATCGACAGCA 62.648 63.158 0.00 0.00 0.00 4.41
2739 2919 2.887568 CTCCGCCACATCGACAGC 60.888 66.667 0.00 0.00 0.00 4.40
2740 2920 2.202797 CCTCCGCCACATCGACAG 60.203 66.667 0.00 0.00 0.00 3.51
2741 2921 4.451150 GCCTCCGCCACATCGACA 62.451 66.667 0.00 0.00 0.00 4.35
2767 2947 3.123620 CCTCTTCTGCGCCAGTGC 61.124 66.667 4.18 0.00 32.61 4.40
2769 2949 1.294780 CTTCCTCTTCTGCGCCAGT 59.705 57.895 4.18 0.00 32.61 4.00
2773 2953 1.028868 AATGGCTTCCTCTTCTGCGC 61.029 55.000 0.00 0.00 0.00 6.09
2783 2963 1.749258 GGGGACACGAATGGCTTCC 60.749 63.158 0.00 0.00 32.54 3.46
2800 2980 1.314534 TTGCCGCTTGTGGATGATGG 61.315 55.000 4.17 0.00 0.00 3.51
2806 2986 1.074775 ATCCTTTGCCGCTTGTGGA 59.925 52.632 4.17 0.00 0.00 4.02
2878 3058 2.747855 CCTCTTTGGGGCGCAGTC 60.748 66.667 10.83 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.