Multiple sequence alignment - TraesCS5A01G170400

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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 TraesCS5A01G170400 chr5A 100.000 3296 0 0 1 3296 363599549 363596254 0.000000e+00 6087
1 TraesCS5A01G170400 chr5A 81.004 1195 201 18 1109 2287 364198632 364199816 0.000000e+00 926
2 TraesCS5A01G170400 chr5A 79.251 1229 222 26 1135 2343 363919808 363921023 0.000000e+00 826
3 TraesCS5A01G170400 chr5A 78.117 1147 204 40 1169 2287 364349567 364350694 0.000000e+00 684
4 TraesCS5A01G170400 chr5D 92.278 3328 149 45 1 3296 274573557 274570306 0.000000e+00 4623
5 TraesCS5A01G170400 chr5D 82.665 998 146 20 1102 2084 275195250 275196235 0.000000e+00 859
6 TraesCS5A01G170400 chr5D 79.299 1227 225 22 1135 2343 275147031 275148246 0.000000e+00 832
7 TraesCS5A01G170400 chr5D 77.885 1144 202 34 1169 2287 275404801 275405918 0.000000e+00 664
8 TraesCS5A01G170400 chr5B 94.958 2598 75 17 733 3296 309666221 309663646 0.000000e+00 4021
9 TraesCS5A01G170400 chr5B 80.932 1180 195 23 1126 2287 312261198 312262365 0.000000e+00 905
10 TraesCS5A01G170400 chr5B 79.708 1232 211 27 1135 2343 309817035 309818250 0.000000e+00 854
11 TraesCS5A01G170400 chr5B 79.899 1189 196 35 1109 2287 310034929 310036084 0.000000e+00 832
12 TraesCS5A01G170400 chr5B 78.291 1147 202 35 1169 2287 312592519 312593646 0.000000e+00 695
13 TraesCS5A01G170400 chr5B 85.082 429 55 9 151 574 309674207 309673783 2.350000e-116 429


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 TraesCS5A01G170400 chr5A 363596254 363599549 3295 True 6087 6087 100.000 1 3296 1 chr5A.!!$R1 3295
1 TraesCS5A01G170400 chr5A 364198632 364199816 1184 False 926 926 81.004 1109 2287 1 chr5A.!!$F2 1178
2 TraesCS5A01G170400 chr5A 363919808 363921023 1215 False 826 826 79.251 1135 2343 1 chr5A.!!$F1 1208
3 TraesCS5A01G170400 chr5A 364349567 364350694 1127 False 684 684 78.117 1169 2287 1 chr5A.!!$F3 1118
4 TraesCS5A01G170400 chr5D 274570306 274573557 3251 True 4623 4623 92.278 1 3296 1 chr5D.!!$R1 3295
5 TraesCS5A01G170400 chr5D 275195250 275196235 985 False 859 859 82.665 1102 2084 1 chr5D.!!$F2 982
6 TraesCS5A01G170400 chr5D 275147031 275148246 1215 False 832 832 79.299 1135 2343 1 chr5D.!!$F1 1208
7 TraesCS5A01G170400 chr5D 275404801 275405918 1117 False 664 664 77.885 1169 2287 1 chr5D.!!$F3 1118
8 TraesCS5A01G170400 chr5B 309663646 309666221 2575 True 4021 4021 94.958 733 3296 1 chr5B.!!$R1 2563
9 TraesCS5A01G170400 chr5B 312261198 312262365 1167 False 905 905 80.932 1126 2287 1 chr5B.!!$F3 1161
10 TraesCS5A01G170400 chr5B 309817035 309818250 1215 False 854 854 79.708 1135 2343 1 chr5B.!!$F1 1208
11 TraesCS5A01G170400 chr5B 310034929 310036084 1155 False 832 832 79.899 1109 2287 1 chr5B.!!$F2 1178
12 TraesCS5A01G170400 chr5B 312592519 312593646 1127 False 695 695 78.291 1169 2287 1 chr5B.!!$F4 1118

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
861 879 0.039618 TCAAATCTGCCCACCCCTTC 59.960 55.000 0.0 0.0 0.0 3.46 F
876 894 1.133356 CCCTTCCATCTCCCCATTTCC 60.133 57.143 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1854 1.375908 GCCGGACTTGCAGATGTGA 60.376 57.895 5.05 0.0 0.0 3.58 R
2751 2824 1.811965 TGCCATCAAACTTCATCCGTG 59.188 47.619 0.00 0.0 0.0 4.94 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
103 104 0.612744 TGGCTCATCGGTTCATGTGA 59.387 50.000 0.00 0.00 0.00 3.58
123 126 6.503524 TGTGACACTCTTTGAAAAATAAGGC 58.496 36.000 7.20 0.00 0.00 4.35
126 129 4.825085 ACACTCTTTGAAAAATAAGGCGGA 59.175 37.500 0.00 0.00 0.00 5.54
127 130 5.048713 ACACTCTTTGAAAAATAAGGCGGAG 60.049 40.000 0.00 0.00 0.00 4.63
133 136 0.551396 AAAATAAGGCGGAGGGAGGG 59.449 55.000 0.00 0.00 0.00 4.30
135 138 2.562973 AATAAGGCGGAGGGAGGGGT 62.563 60.000 0.00 0.00 0.00 4.95
136 139 1.671925 ATAAGGCGGAGGGAGGGGTA 61.672 60.000 0.00 0.00 0.00 3.69
137 140 1.671925 TAAGGCGGAGGGAGGGGTAT 61.672 60.000 0.00 0.00 0.00 2.73
138 141 2.447959 GGCGGAGGGAGGGGTATT 60.448 66.667 0.00 0.00 0.00 1.89
139 142 2.517798 GGCGGAGGGAGGGGTATTC 61.518 68.421 0.00 0.00 0.00 1.75
140 143 2.868986 GCGGAGGGAGGGGTATTCG 61.869 68.421 0.00 0.00 0.00 3.34
141 144 2.868986 CGGAGGGAGGGGTATTCGC 61.869 68.421 0.00 0.00 0.00 4.70
142 145 2.517798 GGAGGGAGGGGTATTCGCC 61.518 68.421 0.00 0.00 45.51 5.54
143 146 2.447959 AGGGAGGGGTATTCGCCC 60.448 66.667 1.54 0.00 46.19 6.13
195 198 8.646900 GCTTATAAGGCTAATAGGATCTGCTAT 58.353 37.037 14.28 0.00 0.00 2.97
226 230 0.486879 TGAAGGGAGGGGTTGCAAAT 59.513 50.000 0.00 0.00 0.00 2.32
228 232 2.110899 TGAAGGGAGGGGTTGCAAATAA 59.889 45.455 0.00 0.00 0.00 1.40
253 257 5.820423 GGAAAGCACAAACAAAATTAGGGTT 59.180 36.000 0.00 0.00 0.00 4.11
261 265 3.423749 ACAAAATTAGGGTTACACCGGG 58.576 45.455 6.32 0.00 39.83 5.73
264 269 3.639672 AATTAGGGTTACACCGGGAAG 57.360 47.619 6.32 0.00 39.83 3.46
271 276 2.410939 GTTACACCGGGAAGTCTTGAC 58.589 52.381 6.32 0.00 0.00 3.18
297 303 6.483640 CCATGCCTTAGGATAGTTCTACAAAC 59.516 42.308 0.69 0.00 0.00 2.93
302 308 6.476053 CCTTAGGATAGTTCTACAAACGAAGC 59.524 42.308 0.00 0.00 0.00 3.86
303 309 5.662674 AGGATAGTTCTACAAACGAAGCT 57.337 39.130 0.00 0.00 0.00 3.74
304 310 6.038997 AGGATAGTTCTACAAACGAAGCTT 57.961 37.500 0.00 0.00 0.00 3.74
334 341 0.320421 AACACCACGAAGGACATCCG 60.320 55.000 5.70 0.00 41.22 4.18
337 344 2.885644 CACGAAGGACATCCGCGG 60.886 66.667 22.12 22.12 40.95 6.46
346 353 2.324477 CATCCGCGGCGATGTTTC 59.676 61.111 25.92 0.00 35.83 2.78
348 355 0.874175 CATCCGCGGCGATGTTTCTA 60.874 55.000 25.92 0.00 35.83 2.10
353 360 0.249911 GCGGCGATGTTTCTAGGGAT 60.250 55.000 12.98 0.00 0.00 3.85
359 366 3.743396 GCGATGTTTCTAGGGATGACATC 59.257 47.826 6.91 6.91 39.41 3.06
367 374 1.514983 AGGGATGACATCAGGCATCA 58.485 50.000 17.08 0.00 42.00 3.07
391 398 4.025040 TGCTGAGATTGAAAGACCATGT 57.975 40.909 0.00 0.00 0.00 3.21
394 401 4.248859 CTGAGATTGAAAGACCATGTCGT 58.751 43.478 0.00 0.00 37.67 4.34
395 402 4.641396 TGAGATTGAAAGACCATGTCGTT 58.359 39.130 0.00 0.00 37.01 3.85
396 403 4.452114 TGAGATTGAAAGACCATGTCGTTG 59.548 41.667 0.22 0.00 34.74 4.10
415 422 2.683933 GGCTCTTCCGGACCCTCA 60.684 66.667 1.83 0.00 0.00 3.86
423 430 0.539986 TCCGGACCCTCAAATAGCAC 59.460 55.000 0.00 0.00 0.00 4.40
424 431 0.251916 CCGGACCCTCAAATAGCACA 59.748 55.000 0.00 0.00 0.00 4.57
438 445 1.889573 GCACAGAGATAAGGGCGGC 60.890 63.158 0.00 0.00 0.00 6.53
439 446 1.522092 CACAGAGATAAGGGCGGCA 59.478 57.895 12.47 0.00 0.00 5.69
455 462 3.902515 GCAGAGAGCAGACACAGAA 57.097 52.632 0.00 0.00 44.79 3.02
509 516 2.709475 GAGGTATGCGGCAAAGCG 59.291 61.111 6.82 0.00 40.67 4.68
537 544 3.305720 AGAACCACACTCCAGACACTTA 58.694 45.455 0.00 0.00 0.00 2.24
593 600 7.649306 TGATGTTATCATGTTCGTATGTGAGAG 59.351 37.037 0.00 0.00 33.59 3.20
639 654 4.210331 GGCTGAATCACCTAAATCCACAT 58.790 43.478 0.00 0.00 0.00 3.21
660 675 9.454585 CCACATGCAGTAATTATTAGTCAAATG 57.545 33.333 0.00 0.00 0.00 2.32
661 676 8.961092 CACATGCAGTAATTATTAGTCAAATGC 58.039 33.333 0.00 0.00 0.00 3.56
662 677 8.906867 ACATGCAGTAATTATTAGTCAAATGCT 58.093 29.630 0.00 0.00 0.00 3.79
665 680 9.571810 TGCAGTAATTATTAGTCAAATGCTTTG 57.428 29.630 0.00 3.17 41.96 2.77
666 681 9.573133 GCAGTAATTATTAGTCAAATGCTTTGT 57.427 29.630 8.01 0.00 41.36 2.83
672 687 9.846248 ATTATTAGTCAAATGCTTTGTCTTCAC 57.154 29.630 11.29 3.20 39.24 3.18
673 688 4.214980 AGTCAAATGCTTTGTCTTCACG 57.785 40.909 8.01 0.00 41.36 4.35
674 689 3.876914 AGTCAAATGCTTTGTCTTCACGA 59.123 39.130 0.00 0.00 41.36 4.35
675 690 4.024556 AGTCAAATGCTTTGTCTTCACGAG 60.025 41.667 0.00 0.00 41.36 4.18
677 692 5.050363 GTCAAATGCTTTGTCTTCACGAGTA 60.050 40.000 0.00 0.00 41.36 2.59
678 693 5.525745 TCAAATGCTTTGTCTTCACGAGTAA 59.474 36.000 0.00 0.00 41.36 2.24
679 694 6.037720 TCAAATGCTTTGTCTTCACGAGTAAA 59.962 34.615 0.00 0.00 41.36 2.01
680 695 6.371809 AATGCTTTGTCTTCACGAGTAAAA 57.628 33.333 0.00 0.00 0.00 1.52
681 696 5.804692 TGCTTTGTCTTCACGAGTAAAAA 57.195 34.783 0.00 0.00 0.00 1.94
682 697 6.371809 TGCTTTGTCTTCACGAGTAAAAAT 57.628 33.333 0.00 0.00 0.00 1.82
683 698 7.485418 TGCTTTGTCTTCACGAGTAAAAATA 57.515 32.000 0.00 0.00 0.00 1.40
684 699 7.349711 TGCTTTGTCTTCACGAGTAAAAATAC 58.650 34.615 0.00 0.00 0.00 1.89
685 700 7.011576 TGCTTTGTCTTCACGAGTAAAAATACA 59.988 33.333 0.00 0.00 0.00 2.29
686 701 8.015658 GCTTTGTCTTCACGAGTAAAAATACAT 58.984 33.333 0.00 0.00 0.00 2.29
687 702 9.530129 CTTTGTCTTCACGAGTAAAAATACATC 57.470 33.333 0.00 0.00 0.00 3.06
688 703 8.596271 TTGTCTTCACGAGTAAAAATACATCA 57.404 30.769 0.00 0.00 0.00 3.07
689 704 8.771920 TGTCTTCACGAGTAAAAATACATCAT 57.228 30.769 0.00 0.00 0.00 2.45
690 705 9.863845 TGTCTTCACGAGTAAAAATACATCATA 57.136 29.630 0.00 0.00 0.00 2.15
692 707 9.863845 TCTTCACGAGTAAAAATACATCATACA 57.136 29.630 0.00 0.00 0.00 2.29
716 731 9.872757 ACATTTACATTCTTATTATAAACGGCG 57.127 29.630 4.80 4.80 0.00 6.46
786 801 9.851043 GAAAGATAAGCGTGTAAAATAAGCTAG 57.149 33.333 0.00 0.00 37.15 3.42
787 802 8.943909 AAGATAAGCGTGTAAAATAAGCTAGT 57.056 30.769 0.00 0.00 37.15 2.57
851 869 8.538409 ACCAATTCTAAAATGTTCAAATCTGC 57.462 30.769 0.00 0.00 0.00 4.26
861 879 0.039618 TCAAATCTGCCCACCCCTTC 59.960 55.000 0.00 0.00 0.00 3.46
876 894 1.133356 CCCTTCCATCTCCCCATTTCC 60.133 57.143 0.00 0.00 0.00 3.13
894 913 1.764054 CTCCTTCCCCGGAGCAGAT 60.764 63.158 0.73 0.00 43.69 2.90
1026 1052 2.171840 CCGAAGACTGGGAAGAAGAGA 58.828 52.381 0.00 0.00 0.00 3.10
1087 1113 1.512735 AACCCCATCTTCCTCTAGCC 58.487 55.000 0.00 0.00 0.00 3.93
1371 1416 4.150454 CCCCTCGGCTCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
1809 1854 1.144057 CGCCGGGAAGCTCTATTGT 59.856 57.895 2.18 0.00 0.00 2.71
1821 1866 4.190001 AGCTCTATTGTCACATCTGCAAG 58.810 43.478 0.00 0.00 0.00 4.01
2328 2391 4.552166 ATTTCGGCCATTTGTAAGATCG 57.448 40.909 2.24 0.00 0.00 3.69
2380 2444 7.431249 CCAGTGATATTGCTTGATAAAATGCT 58.569 34.615 0.00 0.00 0.00 3.79
2385 2449 8.911965 TGATATTGCTTGATAAAATGCTTACCA 58.088 29.630 0.00 0.00 0.00 3.25
2486 2553 2.158755 AGGCTAATAGCGTTGGAAGCAT 60.159 45.455 6.15 0.00 43.62 3.79
2503 2570 8.641989 TTGGAAGCATAAGCGTATCCATTAGTG 61.642 40.741 13.36 0.00 45.51 2.74
2553 2622 2.749839 CCCGCGGCAAGGAATGAA 60.750 61.111 22.85 0.00 0.00 2.57
2562 2631 3.610114 CGGCAAGGAATGAAAAGTCACTG 60.610 47.826 0.00 0.00 36.31 3.66
2751 2824 9.899226 ATCTTTACATTAACTTGAAAGCACTTC 57.101 29.630 0.00 0.00 34.31 3.01
2799 2872 7.328404 TGGCACTATATCCCTTCAATTATGA 57.672 36.000 0.00 0.00 0.00 2.15
2855 2928 1.504359 CACGCGGGAAGTAAAGTTCA 58.496 50.000 12.47 0.00 0.00 3.18
2925 2998 2.095110 TGGATTGCATTGAGTTTCAGCG 60.095 45.455 0.00 0.00 0.00 5.18
3102 3190 7.671398 ACTTGTAATTTTCATGGTGATTCCTCT 59.329 33.333 0.00 0.00 37.07 3.69
3103 3191 8.421249 TTGTAATTTTCATGGTGATTCCTCTT 57.579 30.769 0.00 0.00 37.07 2.85
3175 3263 9.701098 ATTGCTAATATTTGTTATGCAATCTGG 57.299 29.630 0.00 0.00 43.31 3.86
3187 3275 1.457346 CAATCTGGCCCAGAACAGAC 58.543 55.000 19.17 0.00 45.54 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.118261 ACATGAACCGATGAGCCAATACT 60.118 43.478 0.00 0.00 0.00 2.12
103 104 4.825085 TCCGCCTTATTTTTCAAAGAGTGT 59.175 37.500 0.00 0.00 0.00 3.55
123 126 2.868986 GCGAATACCCCTCCCTCCG 61.869 68.421 0.00 0.00 0.00 4.63
126 129 2.447959 GGGCGAATACCCCTCCCT 60.448 66.667 0.00 0.00 45.00 4.20
139 142 6.879188 ATTAAAAATATGTTTCGTTGGGCG 57.121 33.333 0.00 0.00 43.01 6.13
166 169 7.364232 GCAGATCCTATTAGCCTTATAAGCAGA 60.364 40.741 6.99 0.00 0.00 4.26
195 198 3.526019 CCCTCCCTTCATAAACACCCTTA 59.474 47.826 0.00 0.00 0.00 2.69
226 230 7.147637 ACCCTAATTTTGTTTGTGCTTTCCTTA 60.148 33.333 0.00 0.00 0.00 2.69
228 232 5.130311 ACCCTAATTTTGTTTGTGCTTTCCT 59.870 36.000 0.00 0.00 0.00 3.36
253 257 0.971386 GGTCAAGACTTCCCGGTGTA 59.029 55.000 0.00 0.00 0.00 2.90
261 265 2.206576 AAGGCATGGGTCAAGACTTC 57.793 50.000 0.00 0.00 21.72 3.01
264 269 1.559682 TCCTAAGGCATGGGTCAAGAC 59.440 52.381 0.00 0.00 0.00 3.01
271 276 4.593206 TGTAGAACTATCCTAAGGCATGGG 59.407 45.833 0.00 0.00 0.00 4.00
302 308 2.253452 GTGTTGGCGCTGCTCAAG 59.747 61.111 7.64 0.00 0.00 3.02
303 309 3.286751 GGTGTTGGCGCTGCTCAA 61.287 61.111 7.64 0.00 0.00 3.02
304 310 4.560743 TGGTGTTGGCGCTGCTCA 62.561 61.111 7.64 0.00 0.00 4.26
334 341 0.249911 ATCCCTAGAAACATCGCCGC 60.250 55.000 0.00 0.00 0.00 6.53
337 344 3.179443 TGTCATCCCTAGAAACATCGC 57.821 47.619 0.00 0.00 0.00 4.58
339 346 5.303971 CCTGATGTCATCCCTAGAAACATC 58.696 45.833 10.36 6.80 43.19 3.06
346 353 2.636403 TGATGCCTGATGTCATCCCTAG 59.364 50.000 10.36 1.40 38.57 3.02
348 355 1.420514 CTGATGCCTGATGTCATCCCT 59.579 52.381 10.36 0.00 38.57 4.20
367 374 4.090761 TGGTCTTTCAATCTCAGCAACT 57.909 40.909 0.00 0.00 0.00 3.16
372 379 4.248859 ACGACATGGTCTTTCAATCTCAG 58.751 43.478 0.00 0.00 0.00 3.35
375 382 3.189287 GCAACGACATGGTCTTTCAATCT 59.811 43.478 0.00 0.00 0.00 2.40
377 384 2.095768 CGCAACGACATGGTCTTTCAAT 60.096 45.455 0.00 0.00 0.00 2.57
378 385 1.262950 CGCAACGACATGGTCTTTCAA 59.737 47.619 0.00 0.00 0.00 2.69
379 386 0.865111 CGCAACGACATGGTCTTTCA 59.135 50.000 0.00 0.00 0.00 2.69
407 414 2.501723 TCTCTGTGCTATTTGAGGGTCC 59.498 50.000 0.00 0.00 0.00 4.46
408 415 3.895232 TCTCTGTGCTATTTGAGGGTC 57.105 47.619 0.00 0.00 0.00 4.46
409 416 5.163258 CCTTATCTCTGTGCTATTTGAGGGT 60.163 44.000 0.00 0.00 0.00 4.34
413 420 4.708177 GCCCTTATCTCTGTGCTATTTGA 58.292 43.478 0.00 0.00 0.00 2.69
415 422 3.495100 CCGCCCTTATCTCTGTGCTATTT 60.495 47.826 0.00 0.00 0.00 1.40
423 430 0.033228 CTCTGCCGCCCTTATCTCTG 59.967 60.000 0.00 0.00 0.00 3.35
424 431 0.105964 TCTCTGCCGCCCTTATCTCT 60.106 55.000 0.00 0.00 0.00 3.10
438 445 1.067000 CCCTTCTGTGTCTGCTCTCTG 60.067 57.143 0.00 0.00 0.00 3.35
439 446 1.203112 TCCCTTCTGTGTCTGCTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
448 455 1.417890 CTGAGGTTGTCCCTTCTGTGT 59.582 52.381 0.00 0.00 46.51 3.72
452 459 1.903183 GCTACTGAGGTTGTCCCTTCT 59.097 52.381 0.00 0.00 46.51 2.85
509 516 4.681978 AGTGTGGTTCTCCGCGGC 62.682 66.667 23.51 6.01 46.30 6.53
554 561 7.833682 ACATGATAACATCAATTTCCTACCACA 59.166 33.333 0.00 0.00 43.50 4.17
606 613 4.716784 AGGTGATTCAGCCATGAGTAAGTA 59.283 41.667 12.07 0.00 36.61 2.24
660 675 7.349711 TGTATTTTTACTCGTGAAGACAAAGC 58.650 34.615 0.00 0.00 0.00 3.51
661 676 9.530129 GATGTATTTTTACTCGTGAAGACAAAG 57.470 33.333 0.00 0.00 0.00 2.77
662 677 9.047371 TGATGTATTTTTACTCGTGAAGACAAA 57.953 29.630 0.00 0.00 0.00 2.83
664 679 8.771920 ATGATGTATTTTTACTCGTGAAGACA 57.228 30.769 0.00 0.00 0.00 3.41
666 681 9.863845 TGTATGATGTATTTTTACTCGTGAAGA 57.136 29.630 0.00 0.00 0.00 2.87
690 705 9.872757 CGCCGTTTATAATAAGAATGTAAATGT 57.127 29.630 0.00 0.00 0.00 2.71
693 708 9.531942 TCTCGCCGTTTATAATAAGAATGTAAA 57.468 29.630 0.00 0.00 0.00 2.01
694 709 9.188588 CTCTCGCCGTTTATAATAAGAATGTAA 57.811 33.333 0.00 0.00 0.00 2.41
695 710 8.570488 TCTCTCGCCGTTTATAATAAGAATGTA 58.430 33.333 0.00 0.00 0.00 2.29
696 711 7.431249 TCTCTCGCCGTTTATAATAAGAATGT 58.569 34.615 0.00 0.00 0.00 2.71
697 712 7.595502 ACTCTCTCGCCGTTTATAATAAGAATG 59.404 37.037 0.00 0.00 0.00 2.67
698 713 7.659186 ACTCTCTCGCCGTTTATAATAAGAAT 58.341 34.615 0.00 0.00 0.00 2.40
699 714 7.035840 ACTCTCTCGCCGTTTATAATAAGAA 57.964 36.000 0.00 0.00 0.00 2.52
700 715 6.630444 ACTCTCTCGCCGTTTATAATAAGA 57.370 37.500 0.00 0.00 0.00 2.10
701 716 8.452534 AGATACTCTCTCGCCGTTTATAATAAG 58.547 37.037 0.00 0.00 0.00 1.73
716 731 3.129638 AGAACGCAACCAGATACTCTCTC 59.870 47.826 0.00 0.00 29.16 3.20
800 815 6.846870 TCGAAATGCAATTGTATTTTCGAC 57.153 33.333 29.26 20.17 39.76 4.20
851 869 2.386935 GGGAGATGGAAGGGGTGGG 61.387 68.421 0.00 0.00 0.00 4.61
861 879 1.527457 AGGAGGAAATGGGGAGATGG 58.473 55.000 0.00 0.00 0.00 3.51
894 913 3.353836 GCAGCGGAAAAGGCACGA 61.354 61.111 0.00 0.00 0.00 4.35
1047 1073 0.264955 TGGGTTTGGGTTTGGGCTTA 59.735 50.000 0.00 0.00 0.00 3.09
1312 1338 1.174712 GGCTGGTGCTTCTGCTTGAA 61.175 55.000 8.13 0.00 40.48 2.69
1371 1416 4.426313 TCGAGGGAGCTGAGCGGA 62.426 66.667 0.00 0.00 0.00 5.54
1809 1854 1.375908 GCCGGACTTGCAGATGTGA 60.376 57.895 5.05 0.00 0.00 3.58
2328 2391 3.922171 ATGACATGAAGAGGGAAGGAC 57.078 47.619 0.00 0.00 0.00 3.85
2380 2444 8.773645 CATATGAAAATGAATACGAGCTGGTAA 58.226 33.333 12.87 0.00 0.00 2.85
2385 2449 7.792374 ACACATATGAAAATGAATACGAGCT 57.208 32.000 10.38 0.00 0.00 4.09
2394 2458 8.803201 TTAAACGCAAACACATATGAAAATGA 57.197 26.923 10.38 0.00 0.00 2.57
2454 2520 4.238514 CGCTATTAGCCTAGTAAAGCTGG 58.761 47.826 10.04 0.00 40.28 4.85
2486 2553 7.834681 AGATCCTATCACTAATGGATACGCTTA 59.165 37.037 0.00 0.00 39.19 3.09
2724 2797 9.899226 AAGTGCTTTCAAGTTAATGTAAAGATC 57.101 29.630 0.00 0.00 30.44 2.75
2751 2824 1.811965 TGCCATCAAACTTCATCCGTG 59.188 47.619 0.00 0.00 0.00 4.94
2799 2872 3.933861 ATGGAAGTCGCTTAAAGGGAT 57.066 42.857 0.00 0.00 39.44 3.85
2855 2928 1.824230 ACATTATGTTGGCATTGGCGT 59.176 42.857 5.68 0.00 42.47 5.68
2857 2930 3.859443 TGAACATTATGTTGGCATTGGC 58.141 40.909 15.83 2.73 41.28 4.52
2891 2964 4.662468 TGCAATCCAAGTAAAAGTTGCA 57.338 36.364 6.50 6.50 46.52 4.08
2925 2998 1.956477 ACAAGAACAGGTGGAATGTGC 59.044 47.619 0.00 0.00 0.00 4.57
3156 3244 4.900652 TGGGCCAGATTGCATAACAAATAT 59.099 37.500 0.00 0.00 42.86 1.28
3172 3260 0.397941 TCAAGTCTGTTCTGGGCCAG 59.602 55.000 28.01 28.01 0.00 4.85
3175 3263 0.398318 ACCTCAAGTCTGTTCTGGGC 59.602 55.000 0.00 0.00 0.00 5.36
3212 3300 1.923356 AAAATGAGGCGGTTCATGGT 58.077 45.000 0.00 0.00 37.83 3.55


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

AutoCloner maintained by Alex Coulton.