Multiple sequence alignment - TraesCS3D01G252700

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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 TraesCS3D01G252700 chr3D 100.000 3327 0 0 1 3327 354072171 354075497 0.000000e+00 6144
1 TraesCS3D01G252700 chr3A 94.404 1787 57 19 680 2438 472790797 472792568 0.000000e+00 2706
2 TraesCS3D01G252700 chr3A 86.872 716 42 24 2 692 472790080 472790768 0.000000e+00 754
3 TraesCS3D01G252700 chr3A 89.541 392 10 9 2796 3168 472793134 472793513 5.030000e-128 468
4 TraesCS3D01G252700 chr3A 95.181 166 0 2 3166 3327 472795243 472795404 4.260000e-64 255
5 TraesCS3D01G252700 chr3B 92.881 1826 62 21 680 2490 452461961 452463733 0.000000e+00 2590
6 TraesCS3D01G252700 chr3B 91.644 742 29 15 2559 3283 452463899 452464624 0.000000e+00 996
7 TraesCS3D01G252700 chr3B 87.518 705 36 17 6 694 452461262 452461930 0.000000e+00 767
8 TraesCS3D01G252700 chr3B 81.538 325 50 8 1707 2028 362054314 362053997 3.290000e-65 259
9 TraesCS3D01G252700 chr1D 80.692 347 42 17 1696 2018 447550955 447551300 2.560000e-61 246


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 TraesCS3D01G252700 chr3D 354072171 354075497 3326 False 6144.00 6144 100.0000 1 3327 1 chr3D.!!$F1 3326
1 TraesCS3D01G252700 chr3A 472790080 472795404 5324 False 1045.75 2706 91.4995 2 3327 4 chr3A.!!$F1 3325
2 TraesCS3D01G252700 chr3B 452461262 452464624 3362 False 1451.00 2590 90.6810 6 3283 3 chr3B.!!$F1 3277

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
400 405 0.106708 TCGGTCTTTCAAGCTGTGCT 59.893 50.0 0.0 0.0 42.56 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2500 0.39034 TCTCACGCTGCACCTGAATC 60.39 55.0 0.0 0.0 0.0 2.52 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
113 114 2.096819 GTCTACTCCTCTCTGCAAGACG 59.903 54.545 0.00 0.00 38.67 4.18
168 169 3.252974 AGTACTTCAAATCTCCGGCTG 57.747 47.619 0.00 0.00 0.00 4.85
186 187 2.117865 CTGCATCTTCTCCTCCTCCTT 58.882 52.381 0.00 0.00 0.00 3.36
187 188 2.504996 CTGCATCTTCTCCTCCTCCTTT 59.495 50.000 0.00 0.00 0.00 3.11
189 190 3.054802 TGCATCTTCTCCTCCTCCTTTTC 60.055 47.826 0.00 0.00 0.00 2.29
190 191 3.054802 GCATCTTCTCCTCCTCCTTTTCA 60.055 47.826 0.00 0.00 0.00 2.69
192 193 4.833478 TCTTCTCCTCCTCCTTTTCATG 57.167 45.455 0.00 0.00 0.00 3.07
217 218 1.810755 GTAGCTTGCTTGGTTGGGTAC 59.189 52.381 0.00 0.00 0.00 3.34
334 335 2.047655 TCGCCGGCGTTTCTTGAT 60.048 55.556 44.16 0.00 40.74 2.57
336 337 2.387445 CGCCGGCGTTTCTTGATGA 61.387 57.895 39.71 0.00 34.35 2.92
352 353 2.202810 GACGTGCTAGCTCCCTGC 60.203 66.667 17.23 0.00 43.29 4.85
371 376 2.282462 CAAGGAGTTGCCGGCCTT 60.282 61.111 26.77 16.73 42.52 4.35
383 388 1.447317 CCGGCCTTGGAATTGGATCG 61.447 60.000 0.00 0.00 0.00 3.69
384 389 1.447317 CGGCCTTGGAATTGGATCGG 61.447 60.000 0.00 0.00 0.00 4.18
391 396 3.712016 TGGAATTGGATCGGTCTTTCA 57.288 42.857 0.00 0.00 0.00 2.69
392 397 4.027674 TGGAATTGGATCGGTCTTTCAA 57.972 40.909 0.00 0.00 0.00 2.69
393 398 4.009675 TGGAATTGGATCGGTCTTTCAAG 58.990 43.478 0.00 0.00 0.00 3.02
394 399 3.181496 GGAATTGGATCGGTCTTTCAAGC 60.181 47.826 0.00 0.00 0.00 4.01
395 400 2.859165 TTGGATCGGTCTTTCAAGCT 57.141 45.000 0.00 0.00 0.00 3.74
396 401 2.099141 TGGATCGGTCTTTCAAGCTG 57.901 50.000 0.00 0.00 0.00 4.24
397 402 1.347707 TGGATCGGTCTTTCAAGCTGT 59.652 47.619 0.00 0.00 0.00 4.40
398 403 1.734465 GGATCGGTCTTTCAAGCTGTG 59.266 52.381 0.00 0.00 0.00 3.66
399 404 1.129437 GATCGGTCTTTCAAGCTGTGC 59.871 52.381 0.00 0.00 0.00 4.57
400 405 0.106708 TCGGTCTTTCAAGCTGTGCT 59.893 50.000 0.00 0.00 42.56 4.40
401 406 0.514691 CGGTCTTTCAAGCTGTGCTC 59.485 55.000 0.00 0.00 38.25 4.26
402 407 0.877743 GGTCTTTCAAGCTGTGCTCC 59.122 55.000 0.00 0.00 38.25 4.70
403 408 1.597742 GTCTTTCAAGCTGTGCTCCA 58.402 50.000 0.00 0.00 38.25 3.86
452 457 1.205417 CCCATTGTTGTTCCATCCAGC 59.795 52.381 0.00 0.00 0.00 4.85
457 462 1.355381 TGTTGTTCCATCCAGCCATCT 59.645 47.619 0.00 0.00 0.00 2.90
505 510 5.406780 AGCTGCAAAGAATCTATACGCATAC 59.593 40.000 1.02 0.00 0.00 2.39
507 512 6.617317 GCTGCAAAGAATCTATACGCATACTG 60.617 42.308 0.00 0.00 0.00 2.74
516 521 5.061179 TCTATACGCATACTGACTAGCACA 58.939 41.667 0.00 0.00 0.00 4.57
523 529 6.016192 ACGCATACTGACTAGCACATATAGTT 60.016 38.462 0.00 0.00 33.64 2.24
524 530 7.174426 ACGCATACTGACTAGCACATATAGTTA 59.826 37.037 0.00 0.00 33.64 2.24
525 531 7.694367 CGCATACTGACTAGCACATATAGTTAG 59.306 40.741 4.04 4.04 40.72 2.34
529 535 8.982091 ACTGACTAGCACATATAGTTAGAGAA 57.018 34.615 10.70 0.00 38.49 2.87
530 536 9.581289 ACTGACTAGCACATATAGTTAGAGAAT 57.419 33.333 10.70 0.00 38.49 2.40
531 537 9.838975 CTGACTAGCACATATAGTTAGAGAATG 57.161 37.037 5.58 0.00 38.49 2.67
532 538 8.300286 TGACTAGCACATATAGTTAGAGAATGC 58.700 37.037 5.58 0.00 33.64 3.56
533 539 7.309177 ACTAGCACATATAGTTAGAGAATGCG 58.691 38.462 5.58 0.00 35.72 4.73
534 540 5.473931 AGCACATATAGTTAGAGAATGCGG 58.526 41.667 0.00 0.00 35.72 5.69
535 541 5.011125 AGCACATATAGTTAGAGAATGCGGT 59.989 40.000 0.00 0.00 35.72 5.68
536 542 5.696724 GCACATATAGTTAGAGAATGCGGTT 59.303 40.000 0.00 0.00 0.00 4.44
537 543 6.202954 GCACATATAGTTAGAGAATGCGGTTT 59.797 38.462 0.00 0.00 0.00 3.27
538 544 7.254795 GCACATATAGTTAGAGAATGCGGTTTT 60.255 37.037 0.00 0.00 0.00 2.43
573 579 6.920758 CACTTAATCAGGCTGCTTAGTACTAG 59.079 42.308 10.34 7.34 0.00 2.57
575 581 7.778853 ACTTAATCAGGCTGCTTAGTACTAGTA 59.221 37.037 10.34 0.00 0.00 1.82
576 582 6.394025 AATCAGGCTGCTTAGTACTAGTAC 57.606 41.667 23.03 23.03 36.35 2.73
577 583 4.851843 TCAGGCTGCTTAGTACTAGTACA 58.148 43.478 29.87 15.95 38.48 2.90
711 786 8.209584 TGAGATTGGTAGTAAGTCGTAGAGTAT 58.790 37.037 0.00 0.00 40.67 2.12
712 787 9.703892 GAGATTGGTAGTAAGTCGTAGAGTATA 57.296 37.037 0.00 0.00 40.67 1.47
1012 1098 4.135153 CGCCAGTCGCTGCCTAGT 62.135 66.667 0.00 0.00 34.21 2.57
1015 1101 0.108329 GCCAGTCGCTGCCTAGTTAA 60.108 55.000 0.00 0.00 0.00 2.01
1091 1189 4.509737 GACGACGCCTACCTGCCC 62.510 72.222 0.00 0.00 0.00 5.36
1689 1799 2.747443 TTCGGCCAGGACACCAACA 61.747 57.895 2.24 0.00 0.00 3.33
1925 2035 2.125350 CTGCAGAAGCTCGTCCCC 60.125 66.667 8.42 0.00 42.74 4.81
2092 2205 3.641906 AGGTTACAGTTACACTCACAGCT 59.358 43.478 0.00 0.00 0.00 4.24
2158 2271 6.640907 AGAAATAACAACAACATTTCTTCCGC 59.359 34.615 3.56 0.00 43.21 5.54
2171 2284 1.909302 TCTTCCGCCTTCAGAAATCCT 59.091 47.619 0.00 0.00 0.00 3.24
2266 2382 1.208358 CGCCGTGTCAAGACTACGA 59.792 57.895 19.30 0.00 37.73 3.43
2282 2398 5.932303 AGACTACGAACGTGGTTAAGTAGTA 59.068 40.000 16.27 5.39 43.27 1.82
2340 2458 2.853594 GTGTCGTCGTGTACTTTTGTCA 59.146 45.455 0.00 0.00 0.00 3.58
2343 2461 3.792956 GTCGTCGTGTACTTTTGTCAAGA 59.207 43.478 0.00 0.00 0.00 3.02
2382 2500 4.214383 CGCTGCATCGTGGAAGCG 62.214 66.667 15.01 15.01 39.33 4.68
2389 2507 4.910956 TCGTGGAAGCGATTCAGG 57.089 55.556 16.24 7.37 35.83 3.86
2432 2550 0.680921 CCGGTGGCAGGACATCATTT 60.681 55.000 0.00 0.00 0.00 2.32
2433 2551 1.408127 CCGGTGGCAGGACATCATTTA 60.408 52.381 0.00 0.00 0.00 1.40
2513 2633 4.712122 TTTTGCGGGGTTTGAGATATTC 57.288 40.909 0.00 0.00 0.00 1.75
2516 2636 3.897239 TGCGGGGTTTGAGATATTCATT 58.103 40.909 0.00 0.00 35.27 2.57
2518 2638 4.097741 TGCGGGGTTTGAGATATTCATTTG 59.902 41.667 0.00 0.00 35.27 2.32
2519 2639 4.097892 GCGGGGTTTGAGATATTCATTTGT 59.902 41.667 0.00 0.00 35.27 2.83
2522 2642 6.350110 CGGGGTTTGAGATATTCATTTGTGTT 60.350 38.462 0.00 0.00 35.27 3.32
2523 2643 7.035612 GGGGTTTGAGATATTCATTTGTGTTC 58.964 38.462 0.00 0.00 35.27 3.18
2525 2645 8.956426 GGGTTTGAGATATTCATTTGTGTTCTA 58.044 33.333 0.00 0.00 35.27 2.10
2526 2646 9.774742 GGTTTGAGATATTCATTTGTGTTCTAC 57.225 33.333 0.00 0.00 35.27 2.59
2534 2654 6.554334 TTCATTTGTGTTCTACTAAGTGGC 57.446 37.500 0.00 0.00 0.00 5.01
2536 2656 5.700832 TCATTTGTGTTCTACTAAGTGGCTG 59.299 40.000 0.00 0.00 0.00 4.85
2537 2657 3.678056 TGTGTTCTACTAAGTGGCTGG 57.322 47.619 0.00 0.00 0.00 4.85
2538 2658 2.301870 TGTGTTCTACTAAGTGGCTGGG 59.698 50.000 0.00 0.00 0.00 4.45
2539 2659 2.565834 GTGTTCTACTAAGTGGCTGGGA 59.434 50.000 0.00 0.00 0.00 4.37
2540 2660 2.565834 TGTTCTACTAAGTGGCTGGGAC 59.434 50.000 0.00 0.00 0.00 4.46
2541 2661 2.565834 GTTCTACTAAGTGGCTGGGACA 59.434 50.000 0.00 0.00 0.00 4.02
2542 2662 2.176889 TCTACTAAGTGGCTGGGACAC 58.823 52.381 0.00 0.00 42.83 3.67
2543 2663 1.207329 CTACTAAGTGGCTGGGACACC 59.793 57.143 0.00 0.00 43.69 4.16
2544 2664 1.299976 CTAAGTGGCTGGGACACCC 59.700 63.158 0.00 0.00 43.69 4.61
2624 2847 2.699846 GTGAGAGCCTCTCTTCCATGAT 59.300 50.000 21.72 0.00 43.73 2.45
2626 2849 4.343526 GTGAGAGCCTCTCTTCCATGATTA 59.656 45.833 21.72 0.00 43.73 1.75
2627 2850 5.011943 GTGAGAGCCTCTCTTCCATGATTAT 59.988 44.000 21.72 0.00 43.73 1.28
2628 2851 6.210385 GTGAGAGCCTCTCTTCCATGATTATA 59.790 42.308 21.72 0.00 43.73 0.98
2629 2852 6.958778 TGAGAGCCTCTCTTCCATGATTATAT 59.041 38.462 21.72 0.00 43.73 0.86
2630 2853 8.118600 TGAGAGCCTCTCTTCCATGATTATATA 58.881 37.037 21.72 0.00 43.73 0.86
2632 2855 8.121833 AGAGCCTCTCTTCCATGATTATATACT 58.878 37.037 0.00 0.00 37.60 2.12
2633 2856 9.415008 GAGCCTCTCTTCCATGATTATATACTA 57.585 37.037 0.00 0.00 0.00 1.82
2663 3154 8.682936 ATAGCATAGGAAGTTACTTTGAATGG 57.317 34.615 9.53 0.00 0.00 3.16
2755 3246 0.105778 TGCCGTCACTCACACAATGA 59.894 50.000 0.00 0.00 35.45 2.57
2758 3249 2.609491 GCCGTCACTCACACAATGACTA 60.609 50.000 0.00 0.00 40.51 2.59
2783 3274 4.273480 GCTAGCATAGGTACAAATGTGTGG 59.727 45.833 10.63 0.00 39.70 4.17
2790 3281 7.307989 GCATAGGTACAAATGTGTGGATCATAC 60.308 40.741 0.00 0.00 38.82 2.39
2791 3282 5.116180 AGGTACAAATGTGTGGATCATACG 58.884 41.667 0.00 0.00 38.82 3.06
2792 3283 4.873827 GGTACAAATGTGTGGATCATACGT 59.126 41.667 0.00 0.00 38.82 3.57
2793 3284 6.044046 GGTACAAATGTGTGGATCATACGTA 58.956 40.000 0.00 0.00 38.82 3.57
2969 3502 3.927854 TGCAAATGTGAATCATTGGGTG 58.072 40.909 0.00 0.00 44.85 4.61
2982 3515 0.323633 TTGGGTGCATGGATGAGGTG 60.324 55.000 0.00 0.00 0.00 4.00
2983 3516 1.304282 GGGTGCATGGATGAGGTGT 59.696 57.895 0.00 0.00 0.00 4.16
2985 3518 0.749454 GGTGCATGGATGAGGTGTCC 60.749 60.000 0.00 0.00 36.26 4.02
2986 3519 0.749454 GTGCATGGATGAGGTGTCCC 60.749 60.000 0.00 0.00 34.76 4.46
2989 3522 1.616725 GCATGGATGAGGTGTCCCAAA 60.617 52.381 0.00 0.00 34.76 3.28
3308 5584 6.456988 CCCGTGTCTTTTTATCTTATCTGCAC 60.457 42.308 0.00 0.00 0.00 4.57
3309 5585 6.092122 CCGTGTCTTTTTATCTTATCTGCACA 59.908 38.462 0.00 0.00 0.00 4.57
3310 5586 7.176075 CGTGTCTTTTTATCTTATCTGCACAG 58.824 38.462 0.00 0.00 0.00 3.66
3311 5587 6.963805 GTGTCTTTTTATCTTATCTGCACAGC 59.036 38.462 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.130693 CGGTCTAGCAACCTAGCTTACTT 59.869 47.826 0.00 0.00 43.70 2.24
32 33 1.472376 GGCTTTGGACCTGATCGAGAG 60.472 57.143 0.00 0.00 0.00 3.20
33 34 0.537188 GGCTTTGGACCTGATCGAGA 59.463 55.000 0.00 0.00 0.00 4.04
113 114 6.544564 GGATAGATAGATGTAGACCTACCTGC 59.455 46.154 4.88 0.00 35.26 4.85
168 169 3.054802 TGAAAAGGAGGAGGAGAAGATGC 60.055 47.826 0.00 0.00 0.00 3.91
186 187 2.449464 AGCAAGCTACCATGCATGAAA 58.551 42.857 28.31 13.85 44.95 2.69
187 188 2.133281 AGCAAGCTACCATGCATGAA 57.867 45.000 28.31 14.21 44.95 2.57
189 190 1.202371 CCAAGCAAGCTACCATGCATG 60.202 52.381 20.19 20.19 44.95 4.06
190 191 1.108776 CCAAGCAAGCTACCATGCAT 58.891 50.000 10.57 0.00 44.95 3.96
192 193 0.890683 AACCAAGCAAGCTACCATGC 59.109 50.000 0.00 0.00 42.87 4.06
217 218 6.428385 AGAAGCAAATTTCTTCATAGACCG 57.572 37.500 21.75 0.00 41.68 4.79
334 335 3.006756 GCAGGGAGCTAGCACGTCA 62.007 63.158 18.83 0.00 41.15 4.35
336 337 3.775654 GGCAGGGAGCTAGCACGT 61.776 66.667 18.83 8.15 44.79 4.49
371 376 3.712016 TGAAAGACCGATCCAATTCCA 57.288 42.857 0.00 0.00 0.00 3.53
383 388 0.877743 GGAGCACAGCTTGAAAGACC 59.122 55.000 0.00 0.00 39.88 3.85
384 389 1.265365 GTGGAGCACAGCTTGAAAGAC 59.735 52.381 0.00 0.00 39.88 3.01
394 399 2.821366 GCCGATGGTGGAGCACAG 60.821 66.667 0.00 0.00 35.86 3.66
395 400 4.758251 CGCCGATGGTGGAGCACA 62.758 66.667 0.00 0.00 35.86 4.57
403 408 2.901051 CTAACTTCGCCGCCGATGGT 62.901 60.000 6.63 1.98 43.97 3.55
419 424 0.034186 CAATGGGAGGCACCAGCTAA 60.034 55.000 2.69 0.00 45.20 3.09
452 457 3.276857 CCTGTGAGATGAAACCAGATGG 58.723 50.000 0.00 0.00 42.17 3.51
457 462 3.622206 GCCATACCTGTGAGATGAAACCA 60.622 47.826 0.00 0.00 0.00 3.67
485 490 6.642950 AGTCAGTATGCGTATAGATTCTTTGC 59.357 38.462 0.00 0.00 34.76 3.68
505 510 9.838975 CATTCTCTAACTATATGTGCTAGTCAG 57.161 37.037 0.00 0.00 0.00 3.51
507 512 7.483375 CGCATTCTCTAACTATATGTGCTAGTC 59.517 40.741 0.00 0.00 0.00 2.59
516 521 8.936864 GCATAAAACCGCATTCTCTAACTATAT 58.063 33.333 0.00 0.00 0.00 0.86
523 529 4.261155 GCATGCATAAAACCGCATTCTCTA 60.261 41.667 14.21 0.00 46.49 2.43
524 530 3.489738 GCATGCATAAAACCGCATTCTCT 60.490 43.478 14.21 0.00 46.49 3.10
525 531 2.791004 GCATGCATAAAACCGCATTCTC 59.209 45.455 14.21 0.00 46.49 2.87
527 533 2.282290 GTGCATGCATAAAACCGCATTC 59.718 45.455 25.64 1.60 46.49 2.67
528 534 2.270047 GTGCATGCATAAAACCGCATT 58.730 42.857 25.64 0.00 46.49 3.56
530 536 0.600057 TGTGCATGCATAAAACCGCA 59.400 45.000 25.64 11.55 43.45 5.69
531 537 0.991344 GTGTGCATGCATAAAACCGC 59.009 50.000 25.64 12.52 0.00 5.68
532 538 2.634982 AGTGTGCATGCATAAAACCG 57.365 45.000 25.64 0.00 0.00 4.44
533 539 6.098679 TGATTAAGTGTGCATGCATAAAACC 58.901 36.000 25.64 10.35 0.00 3.27
534 540 6.254157 CCTGATTAAGTGTGCATGCATAAAAC 59.746 38.462 25.64 18.73 0.00 2.43
535 541 6.331845 CCTGATTAAGTGTGCATGCATAAAA 58.668 36.000 25.64 15.86 0.00 1.52
536 542 5.679382 GCCTGATTAAGTGTGCATGCATAAA 60.679 40.000 25.64 12.97 0.00 1.40
537 543 4.202040 GCCTGATTAAGTGTGCATGCATAA 60.202 41.667 25.64 18.04 0.00 1.90
538 544 3.316029 GCCTGATTAAGTGTGCATGCATA 59.684 43.478 25.64 19.63 0.00 3.14
654 680 0.179181 CGACTTGCCATGCACATGTC 60.179 55.000 16.58 16.58 38.71 3.06
670 696 5.163499 ACCAATCTCAAGAATCCTACTCGAC 60.163 44.000 0.00 0.00 0.00 4.20
671 697 4.956700 ACCAATCTCAAGAATCCTACTCGA 59.043 41.667 0.00 0.00 0.00 4.04
711 786 4.617253 ATAATTACACCGCCATCTGCTA 57.383 40.909 0.00 0.00 38.05 3.49
712 787 3.492102 ATAATTACACCGCCATCTGCT 57.508 42.857 0.00 0.00 38.05 4.24
733 808 1.038130 CCGGAGATGTCTCGAACCCT 61.038 60.000 0.00 0.00 43.76 4.34
1009 1095 3.243636 CGCCGGGAGAAGCTAATTAACTA 60.244 47.826 2.18 0.00 0.00 2.24
1010 1096 2.483188 CGCCGGGAGAAGCTAATTAACT 60.483 50.000 2.18 0.00 0.00 2.24
1011 1097 1.865340 CGCCGGGAGAAGCTAATTAAC 59.135 52.381 2.18 0.00 0.00 2.01
1012 1098 1.202604 CCGCCGGGAGAAGCTAATTAA 60.203 52.381 2.18 0.00 34.06 1.40
1015 1101 2.822399 CCGCCGGGAGAAGCTAAT 59.178 61.111 2.18 0.00 34.06 1.73
1222 1329 1.153127 CCCAGCGGGCCGTTATTAA 60.153 57.895 28.82 0.00 35.35 1.40
1775 1885 1.080705 CTCCGTGACGAGGTTCACC 60.081 63.158 6.54 0.00 42.63 4.02
1925 2035 1.883084 GTCCATCTTGCTACCGCCG 60.883 63.158 0.00 0.00 34.43 6.46
1931 2041 1.153647 CGCCGTGTCCATCTTGCTA 60.154 57.895 0.00 0.00 0.00 3.49
2092 2205 4.082300 CAGGGTTGTTGCTGTAATAATGCA 60.082 41.667 0.00 0.00 34.69 3.96
2158 2271 8.530804 AGAATTTCCATTAGGATTTCTGAAGG 57.469 34.615 8.55 0.00 45.26 3.46
2171 2284 4.922206 ACAGTCTGGCAGAATTTCCATTA 58.078 39.130 20.62 0.00 0.00 1.90
2266 2382 6.263168 ACAGTACTGTACTACTTAACCACGTT 59.737 38.462 26.91 0.00 42.90 3.99
2340 2458 8.349983 CGGACCGATCCAAATTAATTAATTCTT 58.650 33.333 20.86 6.60 46.67 2.52
2343 2461 6.264518 AGCGGACCGATCCAAATTAATTAATT 59.735 34.615 20.50 16.15 46.67 1.40
2382 2500 0.390340 TCTCACGCTGCACCTGAATC 60.390 55.000 0.00 0.00 0.00 2.52
2389 2507 1.136872 GTCTCGATCTCACGCTGCAC 61.137 60.000 0.00 0.00 0.00 4.57
2432 2550 8.101309 TCCTTTTCTTCTCCATCCAATACATA 57.899 34.615 0.00 0.00 0.00 2.29
2433 2551 6.973642 TCCTTTTCTTCTCCATCCAATACAT 58.026 36.000 0.00 0.00 0.00 2.29
2492 2612 4.082845 TGAATATCTCAAACCCCGCAAAA 58.917 39.130 0.00 0.00 0.00 2.44
2496 2616 4.097892 ACAAATGAATATCTCAAACCCCGC 59.902 41.667 0.00 0.00 37.67 6.13
2498 2618 6.530019 ACACAAATGAATATCTCAAACCCC 57.470 37.500 0.00 0.00 37.67 4.95
2499 2619 7.830739 AGAACACAAATGAATATCTCAAACCC 58.169 34.615 0.00 0.00 37.67 4.11
2500 2620 9.774742 GTAGAACACAAATGAATATCTCAAACC 57.225 33.333 0.00 0.00 37.67 3.27
2508 2628 8.893727 GCCACTTAGTAGAACACAAATGAATAT 58.106 33.333 0.00 0.00 0.00 1.28
2510 2630 6.942576 AGCCACTTAGTAGAACACAAATGAAT 59.057 34.615 0.00 0.00 0.00 2.57
2512 2632 5.700832 CAGCCACTTAGTAGAACACAAATGA 59.299 40.000 0.00 0.00 0.00 2.57
2513 2633 5.106555 CCAGCCACTTAGTAGAACACAAATG 60.107 44.000 0.00 0.00 0.00 2.32
2516 2636 3.244422 CCCAGCCACTTAGTAGAACACAA 60.244 47.826 0.00 0.00 0.00 3.33
2518 2638 2.565834 TCCCAGCCACTTAGTAGAACAC 59.434 50.000 0.00 0.00 0.00 3.32
2519 2639 2.565834 GTCCCAGCCACTTAGTAGAACA 59.434 50.000 0.00 0.00 0.00 3.18
2522 2642 2.176889 GTGTCCCAGCCACTTAGTAGA 58.823 52.381 0.00 0.00 0.00 2.59
2523 2643 1.207329 GGTGTCCCAGCCACTTAGTAG 59.793 57.143 0.00 0.00 33.31 2.57
2525 2645 2.067197 GGTGTCCCAGCCACTTAGT 58.933 57.895 0.00 0.00 33.31 2.24
2556 2676 0.106918 TCGTGTCCCAGGCACTTTTT 60.107 50.000 0.00 0.00 34.60 1.94
2557 2677 0.818040 GTCGTGTCCCAGGCACTTTT 60.818 55.000 0.00 0.00 34.60 2.27
2585 2802 4.868171 TCTCACTACGATTTTACATGCACC 59.132 41.667 0.00 0.00 0.00 5.01
2686 3177 7.013559 CAGATGATCCATGCATGTAAGGTTTAA 59.986 37.037 24.58 1.76 0.00 1.52
2755 3246 6.986817 CACATTTGTACCTATGCTAGCTTAGT 59.013 38.462 27.01 19.76 0.00 2.24
2758 3249 5.586243 CACACATTTGTACCTATGCTAGCTT 59.414 40.000 17.23 12.56 33.30 3.74
2790 3281 9.781633 ACCTCCTATGCTACTATAAGATATACG 57.218 37.037 0.00 0.00 0.00 3.06
2803 3325 7.873505 CCATTCTAAACTAACCTCCTATGCTAC 59.126 40.741 0.00 0.00 0.00 3.58
2863 3396 2.357009 AGCGGAAGAAATCATCATGCAC 59.643 45.455 0.00 0.00 0.00 4.57
2969 3502 0.034186 TTGGGACACCTCATCCATGC 60.034 55.000 0.00 0.00 39.29 4.06
3007 3540 1.003839 GAGACCGACCAATGCACCA 60.004 57.895 0.00 0.00 0.00 4.17
3309 5585 3.499737 GCCAGCATTACACGCGCT 61.500 61.111 5.73 0.00 36.10 5.92


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

AutoCloner maintained by Alex Coulton.