Multiple sequence alignment - TraesCS3A01G151000

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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 TraesCS3A01G151000 chr3A 100.000 3297 0 0 1 3297 138286994 138283698 0.000000e+00 6089
1 TraesCS3A01G151000 chr3B 90.428 2758 152 48 522 3251 181678033 181675360 0.000000e+00 3528
2 TraesCS3A01G151000 chr3B 88.272 486 22 13 1 475 181678507 181678046 1.730000e-152 549
3 TraesCS3A01G151000 chr3B 87.709 179 20 2 1 178 181891827 181891650 1.200000e-49 207
4 TraesCS3A01G151000 chr3D 92.158 2512 113 39 1 2488 127656571 127654120 0.000000e+00 3470
5 TraesCS3A01G151000 chr3D 87.372 681 41 23 2627 3297 127654044 127653399 0.000000e+00 739
6 TraesCS3A01G151000 chr3D 95.238 63 3 0 2513 2575 127654124 127654062 2.090000e-17 100


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 TraesCS3A01G151000 chr3A 138283698 138286994 3296 True 6089.000000 6089 100.000000 1 3297 1 chr3A.!!$R1 3296
1 TraesCS3A01G151000 chr3B 181675360 181678507 3147 True 2038.500000 3528 89.350000 1 3251 2 chr3B.!!$R2 3250
2 TraesCS3A01G151000 chr3D 127653399 127656571 3172 True 1436.333333 3470 91.589333 1 3297 3 chr3D.!!$R1 3296

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
886 913 0.041982 ACCTTGTCCTCCTCCTCCTC 59.958 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2484 0.16923 AAGAGAGTAGAGCGCACACG 59.831 55.0 11.47 0.0 44.07 4.49 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
89 90 9.830975 CAAGGAAAGAAAAAGGAAAAAGGATTA 57.169 29.630 0.00 0.00 0.00 1.75
161 162 9.760077 TTCCTCGGTCATAAGTAAGAAATTATC 57.240 33.333 0.00 0.00 0.00 1.75
226 236 4.191544 CAGAAGCCCATCGACTTTTATCA 58.808 43.478 0.00 0.00 0.00 2.15
266 276 1.645704 GCATCTCCTGTGCTGTGCTG 61.646 60.000 0.00 0.00 39.45 4.41
267 277 0.321387 CATCTCCTGTGCTGTGCTGT 60.321 55.000 0.00 0.00 0.00 4.40
268 278 0.321387 ATCTCCTGTGCTGTGCTGTG 60.321 55.000 0.00 0.00 0.00 3.66
269 279 1.227764 CTCCTGTGCTGTGCTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
271 281 2.330393 CTGTGCTGTGCTGTGTGC 59.670 61.111 0.00 0.00 43.25 4.57
272 282 2.124612 TGTGCTGTGCTGTGTGCT 60.125 55.556 0.00 0.00 43.37 4.40
273 283 2.114331 CTGTGCTGTGCTGTGTGCTC 62.114 60.000 0.00 0.00 43.37 4.26
274 284 2.592574 TGCTGTGCTGTGTGCTCC 60.593 61.111 0.00 0.00 43.37 4.70
275 285 2.592574 GCTGTGCTGTGTGCTCCA 60.593 61.111 0.00 0.00 43.37 3.86
276 286 2.188829 GCTGTGCTGTGTGCTCCAA 61.189 57.895 0.00 0.00 43.37 3.53
277 287 1.947013 CTGTGCTGTGTGCTCCAAG 59.053 57.895 0.00 0.00 43.37 3.61
278 288 0.533531 CTGTGCTGTGTGCTCCAAGA 60.534 55.000 0.00 0.00 43.37 3.02
279 289 0.533531 TGTGCTGTGTGCTCCAAGAG 60.534 55.000 0.00 0.00 43.37 2.85
280 290 1.071987 TGCTGTGTGCTCCAAGAGG 59.928 57.895 0.00 0.00 43.37 3.69
281 291 2.331132 GCTGTGTGCTCCAAGAGGC 61.331 63.158 0.00 0.00 38.95 4.70
282 292 1.071987 CTGTGTGCTCCAAGAGGCA 59.928 57.895 0.00 0.00 36.01 4.75
283 293 0.954449 CTGTGTGCTCCAAGAGGCAG 60.954 60.000 0.00 0.00 39.22 4.85
284 294 1.372683 GTGTGCTCCAAGAGGCAGA 59.627 57.895 0.00 0.00 39.22 4.26
386 404 0.755686 GTCTCCAGGATCGGATGCTT 59.244 55.000 9.49 0.00 33.56 3.91
387 405 1.139853 GTCTCCAGGATCGGATGCTTT 59.860 52.381 9.49 0.00 33.56 3.51
388 406 1.139654 TCTCCAGGATCGGATGCTTTG 59.860 52.381 9.49 4.55 33.56 2.77
389 407 1.139654 CTCCAGGATCGGATGCTTTGA 59.860 52.381 9.49 8.49 33.56 2.69
418 443 4.036144 TGCACAAAATCAAGTGACGATTGA 59.964 37.500 0.00 0.00 40.72 2.57
428 453 6.216569 TCAAGTGACGATTGAATAGATAGGC 58.783 40.000 0.00 0.00 33.85 3.93
447 472 1.984297 GCGTTTTGTCTCTAGTCGGAC 59.016 52.381 0.00 0.00 0.00 4.79
460 485 1.000736 GTCGGACGGTCGTTGAACTC 61.001 60.000 1.43 0.00 0.00 3.01
486 511 9.877178 CCGATTAGATAAAGCTAGATTTACCAT 57.123 33.333 15.04 7.14 0.00 3.55
496 521 1.065491 AGATTTACCATCCGCAGCACA 60.065 47.619 0.00 0.00 0.00 4.57
560 586 1.445582 GAGCATGTGCAGCCAAAGC 60.446 57.895 7.83 0.00 45.16 3.51
572 598 2.317609 CCAAAGCCCACGTCACTCG 61.318 63.158 0.00 0.00 46.00 4.18
590 616 1.501337 CGTGCCATGTGATCCATCGG 61.501 60.000 0.00 0.39 0.00 4.18
635 661 3.126831 GTCTGGTCACTCACAGTTTCAG 58.873 50.000 0.00 0.00 36.17 3.02
636 662 1.869767 CTGGTCACTCACAGTTTCAGC 59.130 52.381 0.00 0.00 0.00 4.26
648 675 7.379529 ACTCACAGTTTCAGCAAAATAAATTCG 59.620 33.333 0.00 0.00 0.00 3.34
668 695 1.209747 GAAGAAATCCGGTGGCTACCT 59.790 52.381 18.03 0.00 45.22 3.08
672 699 3.458487 AGAAATCCGGTGGCTACCTATTT 59.542 43.478 21.56 21.56 45.22 1.40
676 703 1.070289 CCGGTGGCTACCTATTTCCTC 59.930 57.143 18.03 0.00 45.22 3.71
693 720 4.514577 CGTTCGATCCTGGCGGCT 62.515 66.667 11.43 0.00 0.00 5.52
729 756 2.024871 CGAGATCACGCGAGACCC 59.975 66.667 15.93 6.37 41.48 4.46
730 757 2.024871 GAGATCACGCGAGACCCG 59.975 66.667 15.93 0.00 42.21 5.28
843 870 4.529769 TCATGAGCTCATCTATTACCCCAG 59.470 45.833 26.44 10.70 33.61 4.45
886 913 0.041982 ACCTTGTCCTCCTCCTCCTC 59.958 60.000 0.00 0.00 0.00 3.71
932 964 7.078228 CCCGAAAGAGTCTTTTTATTTGAGTG 58.922 38.462 18.96 1.04 0.00 3.51
934 966 7.587757 CCGAAAGAGTCTTTTTATTTGAGTGTG 59.412 37.037 18.96 0.00 0.00 3.82
940 972 7.509546 AGTCTTTTTATTTGAGTGTGGAGAGA 58.490 34.615 0.00 0.00 0.00 3.10
943 975 7.657761 TCTTTTTATTTGAGTGTGGAGAGAGAC 59.342 37.037 0.00 0.00 0.00 3.36
945 977 4.963318 ATTTGAGTGTGGAGAGAGACAA 57.037 40.909 0.00 0.00 0.00 3.18
946 978 4.963318 TTTGAGTGTGGAGAGAGACAAT 57.037 40.909 0.00 0.00 0.00 2.71
947 979 4.527509 TTGAGTGTGGAGAGAGACAATC 57.472 45.455 0.00 0.00 37.62 2.67
948 980 3.500343 TGAGTGTGGAGAGAGACAATCA 58.500 45.455 0.00 0.00 42.97 2.57
949 981 3.897505 TGAGTGTGGAGAGAGACAATCAA 59.102 43.478 0.00 0.00 42.43 2.57
950 982 4.021632 TGAGTGTGGAGAGAGACAATCAAG 60.022 45.833 0.00 0.00 42.43 3.02
951 983 4.155709 AGTGTGGAGAGAGACAATCAAGA 58.844 43.478 0.00 0.00 0.00 3.02
952 984 4.220382 AGTGTGGAGAGAGACAATCAAGAG 59.780 45.833 0.00 0.00 0.00 2.85
953 985 4.219507 GTGTGGAGAGAGACAATCAAGAGA 59.780 45.833 0.00 0.00 0.00 3.10
954 986 4.835056 TGTGGAGAGAGACAATCAAGAGAA 59.165 41.667 0.00 0.00 0.00 2.87
955 987 5.047448 TGTGGAGAGAGACAATCAAGAGAAG 60.047 44.000 0.00 0.00 0.00 2.85
956 988 5.047377 GTGGAGAGAGACAATCAAGAGAAGT 60.047 44.000 0.00 0.00 0.00 3.01
962 994 5.656416 AGAGACAATCAAGAGAAGTAGAGGG 59.344 44.000 0.00 0.00 0.00 4.30
1005 1041 1.440893 CTCTCTGGGCGTGATGGAG 59.559 63.158 0.00 0.00 0.00 3.86
1017 1053 0.976641 TGATGGAGTCGTTCAGCCTT 59.023 50.000 0.00 0.00 0.00 4.35
1091 1127 3.722295 CACGACCATTGCCGCGTT 61.722 61.111 4.92 0.00 34.37 4.84
1104 1140 2.970324 GCGTTGGCGTGTGAGGAA 60.970 61.111 0.00 0.00 40.81 3.36
1107 1143 1.227853 GTTGGCGTGTGAGGAAGGT 60.228 57.895 0.00 0.00 0.00 3.50
1290 1326 4.394712 GAGGTGGTGGCCGTGGAG 62.395 72.222 0.00 0.00 0.00 3.86
1312 1348 3.625897 TGGTGCCGGTCAGTGAGG 61.626 66.667 1.90 0.00 0.00 3.86
1407 1443 2.203153 ACCAAGTTCCGCGTGCTT 60.203 55.556 4.92 3.13 0.00 3.91
1504 1549 1.004918 CCCAAGACGAACCGCTTCT 60.005 57.895 0.00 0.00 0.00 2.85
2206 2257 1.072331 TCTGCTTTCTCTCACAACCCC 59.928 52.381 0.00 0.00 0.00 4.95
2425 2477 1.789054 GCCGGATTAAGAAAACGTGCG 60.789 52.381 5.05 0.00 0.00 5.34
2426 2478 1.461897 CCGGATTAAGAAAACGTGCGT 59.538 47.619 0.00 0.00 0.00 5.24
2427 2479 2.492001 CGGATTAAGAAAACGTGCGTG 58.508 47.619 0.00 0.00 0.00 5.34
2428 2480 2.239201 GGATTAAGAAAACGTGCGTGC 58.761 47.619 0.00 0.00 0.00 5.34
2429 2481 2.350007 GGATTAAGAAAACGTGCGTGCA 60.350 45.455 0.00 0.00 0.00 4.57
2430 2482 3.488489 GATTAAGAAAACGTGCGTGCAT 58.512 40.909 0.00 0.00 0.00 3.96
2431 2483 4.436317 GGATTAAGAAAACGTGCGTGCATA 60.436 41.667 0.00 0.00 0.00 3.14
2432 2484 2.309898 AAGAAAACGTGCGTGCATAC 57.690 45.000 0.00 0.00 0.00 2.39
2444 2496 4.395080 GCATACGTGTGCGCTCTA 57.605 55.556 21.65 0.00 42.83 2.43
2445 2497 1.917921 GCATACGTGTGCGCTCTAC 59.082 57.895 21.65 3.95 42.83 2.59
2465 2517 2.364324 ACTCTCTTGTCTTAACGTGGCA 59.636 45.455 0.00 0.00 0.00 4.92
2526 2578 2.202797 CTCGCCACCGTCTGGATG 60.203 66.667 0.50 0.00 43.95 3.51
2578 2630 9.594038 GTAGTATGCATGTAAAATATTTCCGTG 57.406 33.333 10.16 8.12 0.00 4.94
2589 2641 1.257055 ATTTCCGTGCCCCCAATGTG 61.257 55.000 0.00 0.00 0.00 3.21
2608 2660 7.307751 CCAATGTGAAGTCGCTTTTCTAGTAAA 60.308 37.037 0.00 0.00 0.00 2.01
2609 2661 6.520792 TGTGAAGTCGCTTTTCTAGTAAAC 57.479 37.500 0.00 0.00 0.00 2.01
2610 2662 6.278363 TGTGAAGTCGCTTTTCTAGTAAACT 58.722 36.000 0.00 0.00 0.00 2.66
2611 2663 6.759827 TGTGAAGTCGCTTTTCTAGTAAACTT 59.240 34.615 0.00 0.00 0.00 2.66
2612 2664 7.042925 TGTGAAGTCGCTTTTCTAGTAAACTTC 60.043 37.037 13.40 13.40 38.21 3.01
2619 2671 7.328737 TCGCTTTTCTAGTAAACTTCTTGCTAG 59.671 37.037 3.93 3.93 0.00 3.42
2620 2672 7.328737 CGCTTTTCTAGTAAACTTCTTGCTAGA 59.671 37.037 7.86 7.86 37.11 2.43
2621 2673 8.989980 GCTTTTCTAGTAAACTTCTTGCTAGAA 58.010 33.333 16.29 16.29 43.06 2.10
2636 2688 5.314923 TGCTAGAAGTTGGCATTTCATTC 57.685 39.130 12.83 3.29 38.49 2.67
2640 2692 5.649782 AGAAGTTGGCATTTCATTCGAAT 57.350 34.783 4.39 4.39 0.00 3.34
2641 2693 6.029346 AGAAGTTGGCATTTCATTCGAATT 57.971 33.333 8.21 0.00 0.00 2.17
2679 2731 2.252072 TAATGCGACTGGTCTGGGCC 62.252 60.000 0.00 0.00 0.00 5.80
2682 2734 4.135153 CGACTGGTCTGGGCCGAG 62.135 72.222 8.78 8.78 0.00 4.63
2704 2756 2.253758 CGACAGTGCAAGGGTGTGG 61.254 63.158 0.00 0.00 0.00 4.17
2741 2793 1.056660 TCGCTGAGAAAAGAGGGGTT 58.943 50.000 0.00 0.00 0.00 4.11
2947 3005 0.456653 CCGAAATCCGCTGCCTTTTG 60.457 55.000 0.00 0.00 36.84 2.44
3004 3068 1.153745 CTTTCTGTCCGCTCCGAGG 60.154 63.158 0.00 0.00 0.00 4.63
3133 3201 3.151022 GGCGTGGAGGGAGGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
3134 3202 3.151022 GCGTGGAGGGAGGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
3135 3203 2.684104 CGTGGAGGGAGGAGAGGA 59.316 66.667 0.00 0.00 0.00 3.71
3136 3204 1.454847 CGTGGAGGGAGGAGAGGAG 60.455 68.421 0.00 0.00 0.00 3.69
3137 3205 1.075600 GTGGAGGGAGGAGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
3176 3244 4.385405 GCAGTCTGGGCGTGCTCT 62.385 66.667 1.14 0.00 34.23 4.09
3206 3279 3.282920 GCGGCTGGCTGGCTAATC 61.283 66.667 15.58 0.00 39.11 1.75
3207 3280 2.507944 CGGCTGGCTGGCTAATCT 59.492 61.111 15.58 0.00 39.32 2.40
3208 3281 1.153086 CGGCTGGCTGGCTAATCTT 60.153 57.895 15.58 0.00 39.32 2.40
3209 3282 0.749454 CGGCTGGCTGGCTAATCTTT 60.749 55.000 15.58 0.00 39.32 2.52
3227 3300 1.808531 TTACGTGGAGTGTCCGTGGG 61.809 60.000 0.00 0.00 40.17 4.61
3254 3327 4.794241 GCGCGCGATTGTGTGGTC 62.794 66.667 37.18 7.60 36.62 4.02
3255 3328 3.410516 CGCGCGATTGTGTGGTCA 61.411 61.111 28.94 0.00 32.50 4.02
3256 3329 2.173382 GCGCGATTGTGTGGTCAC 59.827 61.111 12.10 0.00 44.08 3.67
3257 3330 2.317609 GCGCGATTGTGTGGTCACT 61.318 57.895 12.10 0.00 44.14 3.41
3261 3334 1.626654 CGATTGTGTGGTCACTCGCC 61.627 60.000 2.66 0.00 44.14 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 200 0.460987 GTCGATGGGCTTCTGTCAGG 60.461 60.000 0.00 0.00 0.00 3.86
226 236 4.141779 TGCATGCTACACTGAATCTGATCT 60.142 41.667 20.33 0.00 0.00 2.75
266 276 0.952984 GTCTGCCTCTTGGAGCACAC 60.953 60.000 0.00 0.00 34.68 3.82
267 277 1.372683 GTCTGCCTCTTGGAGCACA 59.627 57.895 0.00 0.00 34.68 4.57
268 278 0.673022 CTGTCTGCCTCTTGGAGCAC 60.673 60.000 0.00 0.00 34.68 4.40
269 279 0.833409 TCTGTCTGCCTCTTGGAGCA 60.833 55.000 0.00 0.00 37.46 4.26
271 281 1.554836 TCTCTGTCTGCCTCTTGGAG 58.445 55.000 0.00 0.00 34.57 3.86
272 282 2.106566 GATCTCTGTCTGCCTCTTGGA 58.893 52.381 0.00 0.00 34.57 3.53
273 283 1.829849 TGATCTCTGTCTGCCTCTTGG 59.170 52.381 0.00 0.00 0.00 3.61
274 284 3.823281 ATGATCTCTGTCTGCCTCTTG 57.177 47.619 0.00 0.00 0.00 3.02
275 285 3.518705 ACAATGATCTCTGTCTGCCTCTT 59.481 43.478 0.00 0.00 0.00 2.85
276 286 3.106054 ACAATGATCTCTGTCTGCCTCT 58.894 45.455 0.00 0.00 0.00 3.69
277 287 3.118847 TCACAATGATCTCTGTCTGCCTC 60.119 47.826 0.00 0.00 0.00 4.70
278 288 2.836372 TCACAATGATCTCTGTCTGCCT 59.164 45.455 0.00 0.00 0.00 4.75
279 289 3.257469 TCACAATGATCTCTGTCTGCC 57.743 47.619 0.00 0.00 0.00 4.85
386 404 5.692654 CACTTGATTTTGTGCACATCATCAA 59.307 36.000 32.10 32.10 35.31 2.57
387 405 5.009811 TCACTTGATTTTGTGCACATCATCA 59.990 36.000 26.38 26.38 34.49 3.07
388 406 5.344128 GTCACTTGATTTTGTGCACATCATC 59.656 40.000 22.39 22.81 34.49 2.92
389 407 5.224888 GTCACTTGATTTTGTGCACATCAT 58.775 37.500 22.39 15.45 34.49 2.45
418 443 7.349412 ACTAGAGACAAAACGCCTATCTATT 57.651 36.000 0.00 0.00 0.00 1.73
428 453 2.240040 CGTCCGACTAGAGACAAAACG 58.760 52.381 0.00 0.00 33.08 3.60
447 472 2.159476 TCTAATCGGAGTTCAACGACCG 60.159 50.000 18.60 18.60 42.39 4.79
460 485 9.877178 ATGGTAAATCTAGCTTTATCTAATCGG 57.123 33.333 9.98 0.00 0.00 4.18
572 598 0.179048 TCCGATGGATCACATGGCAC 60.179 55.000 0.00 0.00 40.72 5.01
590 616 5.028549 TCTCACTGGGATTTTCTATGCTC 57.971 43.478 0.00 0.00 0.00 4.26
596 622 4.263243 CCAGACTTCTCACTGGGATTTTCT 60.263 45.833 0.00 0.00 46.76 2.52
635 661 6.530181 ACCGGATTTCTTCGAATTTATTTTGC 59.470 34.615 9.46 0.00 0.00 3.68
636 662 7.009174 CCACCGGATTTCTTCGAATTTATTTTG 59.991 37.037 9.46 0.00 0.00 2.44
648 675 1.664873 GGTAGCCACCGGATTTCTTC 58.335 55.000 9.46 0.00 34.36 2.87
668 695 2.223971 GCCAGGATCGAACGAGGAAATA 60.224 50.000 6.27 0.00 0.00 1.40
672 699 2.771639 CGCCAGGATCGAACGAGGA 61.772 63.158 6.27 0.00 0.00 3.71
676 703 4.514577 AGCCGCCAGGATCGAACG 62.515 66.667 0.00 0.00 41.02 3.95
693 720 4.812476 CCGCTCGTCGCCCAATCA 62.812 66.667 0.00 0.00 36.73 2.57
733 760 4.293648 TGTCCGTGTGCCGTCTGG 62.294 66.667 0.00 0.00 38.77 3.86
734 761 3.036084 GTGTCCGTGTGCCGTCTG 61.036 66.667 0.00 0.00 33.66 3.51
886 913 1.460504 GAGGCTTTTACCTTTCGGGG 58.539 55.000 0.00 0.00 41.32 5.73
896 923 1.280998 CTCTTTCGGGGGAGGCTTTTA 59.719 52.381 0.00 0.00 0.00 1.52
906 933 6.206829 ACTCAAATAAAAAGACTCTTTCGGGG 59.793 38.462 4.46 0.00 0.00 5.73
932 964 5.047377 ACTTCTCTTGATTGTCTCTCTCCAC 60.047 44.000 0.00 0.00 0.00 4.02
934 966 5.659440 ACTTCTCTTGATTGTCTCTCTCC 57.341 43.478 0.00 0.00 0.00 3.71
940 972 4.714308 CCCCTCTACTTCTCTTGATTGTCT 59.286 45.833 0.00 0.00 0.00 3.41
943 975 4.467795 TCACCCCTCTACTTCTCTTGATTG 59.532 45.833 0.00 0.00 0.00 2.67
945 977 4.285863 CTCACCCCTCTACTTCTCTTGAT 58.714 47.826 0.00 0.00 0.00 2.57
946 978 3.564571 CCTCACCCCTCTACTTCTCTTGA 60.565 52.174 0.00 0.00 0.00 3.02
947 979 2.763448 CCTCACCCCTCTACTTCTCTTG 59.237 54.545 0.00 0.00 0.00 3.02
948 980 2.292587 CCCTCACCCCTCTACTTCTCTT 60.293 54.545 0.00 0.00 0.00 2.85
949 981 1.289530 CCCTCACCCCTCTACTTCTCT 59.710 57.143 0.00 0.00 0.00 3.10
950 982 1.288335 TCCCTCACCCCTCTACTTCTC 59.712 57.143 0.00 0.00 0.00 2.87
951 983 1.289530 CTCCCTCACCCCTCTACTTCT 59.710 57.143 0.00 0.00 0.00 2.85
952 984 1.007359 ACTCCCTCACCCCTCTACTTC 59.993 57.143 0.00 0.00 0.00 3.01
953 985 1.094269 ACTCCCTCACCCCTCTACTT 58.906 55.000 0.00 0.00 0.00 2.24
954 986 0.336737 CACTCCCTCACCCCTCTACT 59.663 60.000 0.00 0.00 0.00 2.57
955 987 0.688087 CCACTCCCTCACCCCTCTAC 60.688 65.000 0.00 0.00 0.00 2.59
956 988 0.854039 TCCACTCCCTCACCCCTCTA 60.854 60.000 0.00 0.00 0.00 2.43
962 994 1.893919 GCTCACTCCACTCCCTCACC 61.894 65.000 0.00 0.00 0.00 4.02
996 1032 1.078759 GGCTGAACGACTCCATCACG 61.079 60.000 0.00 0.00 0.00 4.35
1005 1041 2.156343 ACTTGAGAAGGCTGAACGAC 57.844 50.000 0.00 0.00 0.00 4.34
1017 1053 2.571757 CCGCGCAGGTACTTGAGA 59.428 61.111 12.86 0.00 34.60 3.27
1091 1127 2.425592 CACCTTCCTCACACGCCA 59.574 61.111 0.00 0.00 0.00 5.69
1104 1140 2.858974 CCACCCCCTTCACCACCT 60.859 66.667 0.00 0.00 0.00 4.00
1107 1143 1.386772 ACTTCCACCCCCTTCACCA 60.387 57.895 0.00 0.00 0.00 4.17
1136 1172 2.430244 CGTCTTCCACCACGTCCG 60.430 66.667 0.00 0.00 0.00 4.79
1407 1443 2.393271 GCTTCCTCAGCTTAAGCAGA 57.607 50.000 28.39 23.99 46.27 4.26
1504 1549 1.060729 TCCACCCGGAACTTGATCAA 58.939 50.000 0.73 8.12 38.83 2.57
2168 2219 6.297080 AGCAGAGGGATGTTATCATCTATG 57.703 41.667 12.41 4.23 46.74 2.23
2206 2257 3.885521 GGCGACTCGGACCCTACG 61.886 72.222 0.00 0.00 0.00 3.51
2396 2448 5.694231 TTTCTTAATCCGGCATCATGATG 57.306 39.130 28.04 28.04 41.60 3.07
2425 2477 0.800683 TAGAGCGCACACGTATGCAC 60.801 55.000 20.22 9.52 46.47 4.57
2426 2478 0.800683 GTAGAGCGCACACGTATGCA 60.801 55.000 20.22 0.00 46.47 3.96
2427 2479 0.525668 AGTAGAGCGCACACGTATGC 60.526 55.000 9.22 9.22 42.83 3.14
2428 2480 1.064208 AGAGTAGAGCGCACACGTATG 59.936 52.381 11.47 0.00 42.83 2.39
2429 2481 1.331138 GAGAGTAGAGCGCACACGTAT 59.669 52.381 11.47 0.00 42.83 3.06
2430 2482 0.725686 GAGAGTAGAGCGCACACGTA 59.274 55.000 11.47 0.00 42.83 3.57
2431 2483 0.956410 AGAGAGTAGAGCGCACACGT 60.956 55.000 11.47 0.00 42.83 4.49
2432 2484 0.169230 AAGAGAGTAGAGCGCACACG 59.831 55.000 11.47 0.00 44.07 4.49
2433 2485 1.068194 ACAAGAGAGTAGAGCGCACAC 60.068 52.381 11.47 3.75 0.00 3.82
2434 2486 1.200252 GACAAGAGAGTAGAGCGCACA 59.800 52.381 11.47 0.00 0.00 4.57
2435 2487 1.470890 AGACAAGAGAGTAGAGCGCAC 59.529 52.381 11.47 2.25 0.00 5.34
2436 2488 1.827681 AGACAAGAGAGTAGAGCGCA 58.172 50.000 11.47 0.00 0.00 6.09
2444 2496 2.364324 TGCCACGTTAAGACAAGAGAGT 59.636 45.455 0.00 0.00 0.00 3.24
2445 2497 3.026630 TGCCACGTTAAGACAAGAGAG 57.973 47.619 0.00 0.00 0.00 3.20
2515 2567 3.470709 CAGATTATTGCATCCAGACGGT 58.529 45.455 0.00 0.00 0.00 4.83
2522 2574 1.267806 CACCGCCAGATTATTGCATCC 59.732 52.381 0.00 0.00 0.00 3.51
2526 2578 1.532868 CTAGCACCGCCAGATTATTGC 59.467 52.381 0.00 0.00 0.00 3.56
2576 2628 1.586154 CGACTTCACATTGGGGGCAC 61.586 60.000 0.00 0.00 0.00 5.01
2578 2630 2.700773 GCGACTTCACATTGGGGGC 61.701 63.158 0.00 0.00 0.00 5.80
2589 2641 7.640616 AGAAGTTTACTAGAAAAGCGACTTC 57.359 36.000 0.00 7.04 39.52 3.01
2610 2662 4.826733 TGAAATGCCAACTTCTAGCAAGAA 59.173 37.500 8.38 0.00 40.46 2.52
2611 2663 4.397420 TGAAATGCCAACTTCTAGCAAGA 58.603 39.130 8.38 0.00 40.46 3.02
2612 2664 4.771590 TGAAATGCCAACTTCTAGCAAG 57.228 40.909 0.00 0.00 40.46 4.01
2619 2671 6.710692 AAATTCGAATGAAATGCCAACTTC 57.289 33.333 12.25 0.00 37.71 3.01
2620 2672 6.705381 TGAAAATTCGAATGAAATGCCAACTT 59.295 30.769 12.25 0.00 37.71 2.66
2621 2673 6.146021 GTGAAAATTCGAATGAAATGCCAACT 59.854 34.615 12.25 0.00 37.71 3.16
2622 2674 6.073873 TGTGAAAATTCGAATGAAATGCCAAC 60.074 34.615 12.25 2.33 37.71 3.77
2623 2675 5.987953 TGTGAAAATTCGAATGAAATGCCAA 59.012 32.000 12.25 0.00 37.71 4.52
2624 2676 5.536260 TGTGAAAATTCGAATGAAATGCCA 58.464 33.333 12.25 0.65 37.71 4.92
2625 2677 6.532657 AGATGTGAAAATTCGAATGAAATGCC 59.467 34.615 12.25 0.00 37.71 4.40
2654 2706 0.713883 GACCAGTCGCATTACACACG 59.286 55.000 0.00 0.00 0.00 4.49
2679 2731 3.008240 CTTGCACTGTCGCTGCTCG 62.008 63.158 0.00 0.00 35.53 5.03
2682 2734 3.730761 CCCTTGCACTGTCGCTGC 61.731 66.667 0.00 0.00 35.03 5.25
2871 2927 3.708220 CTCGAGCCGGAACAGAGCC 62.708 68.421 5.05 0.00 0.00 4.70
2875 2931 0.737715 CCTTTCTCGAGCCGGAACAG 60.738 60.000 5.05 0.00 0.00 3.16
2974 3038 2.603776 AGAAAGAGGACGGGCCGT 60.604 61.111 34.81 34.81 45.10 5.68
2975 3039 2.125512 CAGAAAGAGGACGGGCCG 60.126 66.667 27.06 27.06 43.43 6.13
2977 3041 1.079057 GGACAGAAAGAGGACGGGC 60.079 63.158 0.00 0.00 0.00 6.13
2978 3042 1.215647 CGGACAGAAAGAGGACGGG 59.784 63.158 0.00 0.00 0.00 5.28
2979 3043 1.446272 GCGGACAGAAAGAGGACGG 60.446 63.158 0.00 0.00 0.00 4.79
2980 3044 0.456995 GAGCGGACAGAAAGAGGACG 60.457 60.000 0.00 0.00 0.00 4.79
2981 3045 0.108567 GGAGCGGACAGAAAGAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
2982 3046 1.595993 CGGAGCGGACAGAAAGAGGA 61.596 60.000 0.00 0.00 0.00 3.71
2983 3047 1.153745 CGGAGCGGACAGAAAGAGG 60.154 63.158 0.00 0.00 0.00 3.69
2984 3048 0.179150 CTCGGAGCGGACAGAAAGAG 60.179 60.000 0.00 0.00 0.00 2.85
2985 3049 1.595993 CCTCGGAGCGGACAGAAAGA 61.596 60.000 0.00 0.00 31.34 2.52
3123 3191 4.150454 CCGCCTCCTCTCCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
3159 3227 4.385405 AGAGCACGCCCAGACTGC 62.385 66.667 0.00 0.00 0.00 4.40
3160 3228 2.433838 CAGAGCACGCCCAGACTG 60.434 66.667 0.00 0.00 0.00 3.51
3161 3229 3.699894 CCAGAGCACGCCCAGACT 61.700 66.667 0.00 0.00 0.00 3.24
3199 3272 3.858247 ACACTCCACGTAAAGATTAGCC 58.142 45.455 3.57 0.00 0.00 3.93
3200 3273 3.864003 GGACACTCCACGTAAAGATTAGC 59.136 47.826 3.57 0.00 36.28 3.09
3203 3276 2.298163 ACGGACACTCCACGTAAAGATT 59.702 45.455 3.57 0.00 39.30 2.40
3204 3277 1.891150 ACGGACACTCCACGTAAAGAT 59.109 47.619 3.57 0.00 39.30 2.40
3205 3278 1.001048 CACGGACACTCCACGTAAAGA 60.001 52.381 3.57 0.00 39.02 2.52
3206 3279 1.415374 CACGGACACTCCACGTAAAG 58.585 55.000 0.00 0.00 39.02 1.85
3207 3280 0.032403 CCACGGACACTCCACGTAAA 59.968 55.000 0.00 0.00 39.02 2.01
3208 3281 1.661480 CCACGGACACTCCACGTAA 59.339 57.895 0.00 0.00 39.02 3.18
3209 3282 2.270257 CCCACGGACACTCCACGTA 61.270 63.158 0.00 0.00 39.02 3.57


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

AutoCloner maintained by Alex Coulton.