Multiple sequence alignment - TraesCS3A01G160200

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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 TraesCS3A01G160200 chr3A 100.000 2661 0 0 1 2661 160073462 160076122 0.000000e+00 4915.0
1 TraesCS3A01G160200 chr3A 83.333 138 20 3 185 321 114543259 114543124 1.000000e-24 124.0
2 TraesCS3A01G160200 chr3B 92.311 2055 113 22 185 2222 203642154 203644180 0.000000e+00 2878.0
3 TraesCS3A01G160200 chr3B 90.782 358 23 6 2228 2581 203644289 203644640 1.120000e-128 470.0
4 TraesCS3A01G160200 chr3B 89.759 166 16 1 23 188 203641941 203642105 7.460000e-51 211.0
5 TraesCS3A01G160200 chr3D 91.930 1772 90 22 185 1931 141657310 141659053 0.000000e+00 2431.0
6 TraesCS3A01G160200 chr3D 92.868 673 33 7 1919 2581 141659505 141660172 0.000000e+00 963.0
7 TraesCS3A01G160200 chr3D 78.491 265 48 8 247 510 96672300 96672044 5.890000e-37 165.0
8 TraesCS3A01G160200 chrUn 83.681 288 42 3 205 487 10264189 10263902 1.570000e-67 267.0
9 TraesCS3A01G160200 chr7D 83.162 291 46 2 185 475 138285592 138285305 2.030000e-66 263.0
10 TraesCS3A01G160200 chr5A 82.374 278 49 0 185 462 356103428 356103151 2.650000e-60 243.0
11 TraesCS3A01G160200 chr2A 80.678 295 53 3 185 478 749909324 749909033 2.670000e-55 226.0
12 TraesCS3A01G160200 chr2B 79.870 308 56 3 185 487 569978937 569978631 1.240000e-53 220.0
13 TraesCS3A01G160200 chr6D 93.056 72 5 0 117 188 453964281 453964210 3.620000e-19 106.0
14 TraesCS3A01G160200 chr1A 81.731 104 16 1 352 455 373786532 373786432 1.700000e-12 84.2


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 TraesCS3A01G160200 chr3A 160073462 160076122 2660 False 4915.000000 4915 100.000000 1 2661 1 chr3A.!!$F1 2660
1 TraesCS3A01G160200 chr3B 203641941 203644640 2699 False 1186.333333 2878 90.950667 23 2581 3 chr3B.!!$F1 2558
2 TraesCS3A01G160200 chr3D 141657310 141660172 2862 False 1697.000000 2431 92.399000 185 2581 2 chr3D.!!$F1 2396

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
100 101 0.108585 TGCTTTGTGGTGAGGAGTCC 59.891 55.0 0.0 0.0 0.0 3.85 F
888 956 0.466543 ACAAACCACACCTAGTCGCA 59.533 50.0 0.0 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1274 1.135053 TCGTTCGTTCTTGGTGACACA 60.135 47.619 8.08 0.0 42.67 3.72 R
2513 3175 0.105658 TTAGGGTGAGGGAGGGATCG 60.106 60.000 0.00 0.0 0.00 3.69 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
73 74 3.848726 AGTGTTGCTTTTGTGGTGAAAG 58.151 40.909 0.00 0.00 37.21 2.62
78 79 4.040445 TGCTTTTGTGGTGAAAGTAAGC 57.960 40.909 0.00 0.00 36.67 3.09
100 101 0.108585 TGCTTTGTGGTGAGGAGTCC 59.891 55.000 0.00 0.00 0.00 3.85
115 116 5.105187 TGAGGAGTCCATTCAGTGTCTATTG 60.105 44.000 12.86 0.00 0.00 1.90
122 123 4.095483 CCATTCAGTGTCTATTGCTTCACC 59.905 45.833 0.00 0.00 0.00 4.02
154 155 4.067896 CCAAGCTATTATGGCGATCTGTT 58.932 43.478 0.00 0.00 34.52 3.16
161 162 8.140628 AGCTATTATGGCGATCTGTTCATATAG 58.859 37.037 0.00 0.00 34.52 1.31
162 163 7.923344 GCTATTATGGCGATCTGTTCATATAGT 59.077 37.037 0.00 0.00 0.00 2.12
191 244 0.962489 ACCTCCAGTCACAAGTCTCG 59.038 55.000 0.00 0.00 0.00 4.04
196 249 1.468224 CCAGTCACAAGTCTCGGATCG 60.468 57.143 0.00 0.00 0.00 3.69
229 282 1.066215 GGGCTTTACTTTGGGCCATTG 60.066 52.381 7.26 5.83 45.68 2.82
236 289 2.893424 ACTTTGGGCCATTGAGAACAT 58.107 42.857 7.26 0.00 0.00 2.71
243 296 4.021544 TGGGCCATTGAGAACATTTGTAAC 60.022 41.667 0.00 0.00 0.00 2.50
322 376 3.520290 TCAGTTGGATCCATACGTGAC 57.480 47.619 17.06 9.69 0.00 3.67
339 393 3.592059 GTGACCGTTACTATGCAAGGAA 58.408 45.455 0.00 0.00 0.00 3.36
365 419 2.359975 GGAGCCCACGGTCTTTGG 60.360 66.667 0.00 0.00 36.70 3.28
373 427 0.673437 CACGGTCTTTGGGTGCAATT 59.327 50.000 0.00 0.00 0.00 2.32
440 494 4.404715 GTGGGCTACTAGTAGGATTTGTGA 59.595 45.833 27.24 0.00 33.87 3.58
484 542 8.811994 TCTACTATTGCTTTTTATTTGCCCTTT 58.188 29.630 0.00 0.00 0.00 3.11
508 566 5.811399 GCAACTATGTGTGGCAGTTATTA 57.189 39.130 0.00 0.00 44.85 0.98
523 581 9.440773 TGGCAGTTATTATGATCAGATATTGAC 57.559 33.333 0.09 7.05 38.99 3.18
559 617 8.617290 ATCGATAAAAGGTTATATGAACCACC 57.383 34.615 12.46 0.00 42.69 4.61
565 626 3.714798 AGGTTATATGAACCACCCGATGT 59.285 43.478 12.46 0.00 42.69 3.06
618 683 9.217223 CGAAATATATTCGTTTCCGTCAAAAAT 57.783 29.630 0.00 0.00 37.18 1.82
620 685 8.762149 AATATATTCGTTTCCGTCAAAAATCG 57.238 30.769 0.00 0.00 35.01 3.34
621 686 3.948196 TTCGTTTCCGTCAAAAATCGT 57.052 38.095 0.00 0.00 35.01 3.73
622 687 5.594724 ATTCGTTTCCGTCAAAAATCGTA 57.405 34.783 0.00 0.00 35.01 3.43
623 688 4.373532 TCGTTTCCGTCAAAAATCGTAC 57.626 40.909 0.00 0.00 35.01 3.67
803 869 2.496070 CAGGAAACGAGGTAGTCCATCA 59.504 50.000 0.00 0.00 35.89 3.07
809 875 2.163815 ACGAGGTAGTCCATCAACTTCG 59.836 50.000 4.92 4.92 45.04 3.79
810 876 2.541556 GAGGTAGTCCATCAACTTCGC 58.458 52.381 0.00 0.00 35.89 4.70
833 899 8.684655 TCGCAATTTAAGATAATAACGACTACG 58.315 33.333 0.00 0.00 45.75 3.51
888 956 0.466543 ACAAACCACACCTAGTCGCA 59.533 50.000 0.00 0.00 0.00 5.10
967 1035 6.513180 TCTACCGAACATATTTCAGCCTAAG 58.487 40.000 0.00 0.00 0.00 2.18
1149 1217 0.734942 AGTTCCAATACACGCCGTCG 60.735 55.000 0.00 0.00 42.43 5.12
1192 1260 0.609957 TGCTCCCAGCTGTTTCCATG 60.610 55.000 13.81 0.00 42.97 3.66
1206 1274 2.512286 CATGTCATCGTGCCGGCT 60.512 61.111 29.70 3.37 0.00 5.52
1215 1283 4.927782 GTGCCGGCTGTGTCACCA 62.928 66.667 29.70 0.00 0.00 4.17
1274 1344 2.033448 TTCTTCGTGGCCGCCAAT 59.967 55.556 15.39 0.00 34.18 3.16
1305 1375 2.759973 CCTACAGCCTCCTCGCCA 60.760 66.667 0.00 0.00 0.00 5.69
1453 1533 1.376812 TCATGAGCTGCAGGTGCTG 60.377 57.895 25.60 19.14 41.30 4.41
1603 1683 1.005037 TCTCGCATGTGGCTTCGTT 60.005 52.632 6.39 0.00 41.67 3.85
1667 1747 1.409241 CCATGAACAGCTAGGGCATGT 60.409 52.381 13.52 0.00 41.70 3.21
1668 1748 1.674441 CATGAACAGCTAGGGCATGTG 59.326 52.381 0.00 0.00 41.70 3.21
1669 1749 0.983467 TGAACAGCTAGGGCATGTGA 59.017 50.000 0.00 0.00 41.70 3.58
1775 1859 9.624697 TTGTGATATTCTGAAATTACTTGCAAC 57.375 29.630 0.00 0.00 0.00 4.17
1823 1907 9.654663 CTAGTATTGCTTTGGTAGAACTAAAGT 57.345 33.333 14.70 1.84 45.05 2.66
1824 1908 8.549338 AGTATTGCTTTGGTAGAACTAAAGTC 57.451 34.615 14.70 9.28 45.05 3.01
1827 1911 6.169557 TGCTTTGGTAGAACTAAAGTCTCA 57.830 37.500 14.70 4.85 45.05 3.27
1829 1913 7.224297 TGCTTTGGTAGAACTAAAGTCTCATT 58.776 34.615 14.70 0.00 45.05 2.57
1915 1999 7.757941 TGATCCATGAGACAAACAATGTTTA 57.242 32.000 11.33 0.00 44.12 2.01
1941 2489 2.886523 CACTTTGAGTTGGCCAAGATCA 59.113 45.455 21.21 22.54 0.00 2.92
2141 2689 3.679502 TGATACACACAATCAAGAGCACG 59.320 43.478 0.00 0.00 30.52 5.34
2144 2692 2.800544 ACACACAATCAAGAGCACGTAC 59.199 45.455 0.00 0.00 0.00 3.67
2145 2693 3.059884 CACACAATCAAGAGCACGTACT 58.940 45.455 0.00 0.00 0.00 2.73
2146 2694 4.234574 CACACAATCAAGAGCACGTACTA 58.765 43.478 0.00 0.00 0.00 1.82
2147 2695 4.684242 CACACAATCAAGAGCACGTACTAA 59.316 41.667 0.00 0.00 0.00 2.24
2148 2696 4.684703 ACACAATCAAGAGCACGTACTAAC 59.315 41.667 0.00 0.00 0.00 2.34
2305 2963 5.045942 ACAAGGTTCCAAATCAAAAGGTGTT 60.046 36.000 0.00 0.00 0.00 3.32
2331 2989 1.710816 GAGTACTCCCTCCATCCCAG 58.289 60.000 12.13 0.00 0.00 4.45
2350 3009 9.135189 CATCCCAGAATAAGACAATTATTTGGA 57.865 33.333 15.48 12.11 37.15 3.53
2408 3067 1.731093 AACGTCCAGTTTTTGCGGG 59.269 52.632 0.00 0.00 40.88 6.13
2436 3097 4.462508 TGTTGATTTGCAGTTTGGTTGA 57.537 36.364 0.00 0.00 0.00 3.18
2536 3198 2.942905 TCCCTCCCTCACCCTAAAATT 58.057 47.619 0.00 0.00 0.00 1.82
2575 3237 9.881529 TCGTTATTCTTGGTTAAAATGTGTTAC 57.118 29.630 0.00 0.00 0.00 2.50
2582 3244 9.881529 TCTTGGTTAAAATGTGTTACGATTTAC 57.118 29.630 0.00 0.00 0.00 2.01
2583 3245 9.666626 CTTGGTTAAAATGTGTTACGATTTACA 57.333 29.630 0.00 0.00 0.00 2.41
2585 3247 9.613957 TGGTTAAAATGTGTTACGATTTACATG 57.386 29.630 0.00 0.00 34.28 3.21
2586 3248 8.580431 GGTTAAAATGTGTTACGATTTACATGC 58.420 33.333 0.00 0.00 34.28 4.06
2587 3249 6.846870 AAAATGTGTTACGATTTACATGCG 57.153 33.333 0.00 0.00 34.28 4.73
2588 3250 5.788055 AATGTGTTACGATTTACATGCGA 57.212 34.783 0.00 0.00 34.28 5.10
2589 3251 4.571375 TGTGTTACGATTTACATGCGAC 57.429 40.909 0.00 0.00 0.00 5.19
2590 3252 4.239304 TGTGTTACGATTTACATGCGACT 58.761 39.130 0.00 0.00 0.00 4.18
2591 3253 4.687018 TGTGTTACGATTTACATGCGACTT 59.313 37.500 0.00 0.00 0.00 3.01
2592 3254 5.177881 TGTGTTACGATTTACATGCGACTTT 59.822 36.000 0.00 0.00 0.00 2.66
2593 3255 6.075280 GTGTTACGATTTACATGCGACTTTT 58.925 36.000 0.00 0.00 0.00 2.27
2594 3256 6.575942 GTGTTACGATTTACATGCGACTTTTT 59.424 34.615 0.00 0.00 0.00 1.94
2595 3257 6.575572 TGTTACGATTTACATGCGACTTTTTG 59.424 34.615 0.00 0.00 0.00 2.44
2596 3258 4.472286 ACGATTTACATGCGACTTTTTGG 58.528 39.130 0.00 0.00 0.00 3.28
2597 3259 4.214545 ACGATTTACATGCGACTTTTTGGA 59.785 37.500 0.00 0.00 0.00 3.53
2598 3260 5.106317 ACGATTTACATGCGACTTTTTGGAT 60.106 36.000 0.00 0.00 0.00 3.41
2599 3261 5.227805 CGATTTACATGCGACTTTTTGGATG 59.772 40.000 0.00 0.00 40.14 3.51
2600 3262 5.697473 TTTACATGCGACTTTTTGGATGA 57.303 34.783 0.00 0.00 37.16 2.92
2601 3263 3.837213 ACATGCGACTTTTTGGATGAG 57.163 42.857 0.00 0.00 37.16 2.90
2602 3264 3.149196 ACATGCGACTTTTTGGATGAGT 58.851 40.909 0.00 0.00 37.16 3.41
2603 3265 4.323417 ACATGCGACTTTTTGGATGAGTA 58.677 39.130 0.00 0.00 37.16 2.59
2604 3266 4.759693 ACATGCGACTTTTTGGATGAGTAA 59.240 37.500 0.00 0.00 37.16 2.24
2605 3267 5.240623 ACATGCGACTTTTTGGATGAGTAAA 59.759 36.000 0.00 0.00 37.16 2.01
2606 3268 5.759506 TGCGACTTTTTGGATGAGTAAAA 57.240 34.783 0.00 0.00 0.00 1.52
2607 3269 6.137794 TGCGACTTTTTGGATGAGTAAAAA 57.862 33.333 0.00 0.00 35.29 1.94
2639 3301 2.571548 CAAGGGGTCTTGTGATGCC 58.428 57.895 0.00 0.00 43.92 4.40
2640 3302 0.251297 CAAGGGGTCTTGTGATGCCA 60.251 55.000 0.00 0.00 43.92 4.92
2641 3303 0.482446 AAGGGGTCTTGTGATGCCAA 59.518 50.000 0.00 0.00 0.00 4.52
2642 3304 0.038744 AGGGGTCTTGTGATGCCAAG 59.961 55.000 0.00 0.00 42.57 3.61
2643 3305 0.038166 GGGGTCTTGTGATGCCAAGA 59.962 55.000 0.00 0.00 46.43 3.02
2646 3308 3.650647 TCTTGTGATGCCAAGACCC 57.349 52.632 0.00 0.00 44.39 4.46
2647 3309 0.770499 TCTTGTGATGCCAAGACCCA 59.230 50.000 0.00 0.00 44.39 4.51
2648 3310 1.355381 TCTTGTGATGCCAAGACCCAT 59.645 47.619 0.00 0.00 44.39 4.00
2649 3311 2.173519 CTTGTGATGCCAAGACCCATT 58.826 47.619 0.00 0.00 43.65 3.16
2650 3312 2.307496 TGTGATGCCAAGACCCATTT 57.693 45.000 0.00 0.00 0.00 2.32
2651 3313 1.894466 TGTGATGCCAAGACCCATTTG 59.106 47.619 0.00 0.00 0.00 2.32
2652 3314 2.170166 GTGATGCCAAGACCCATTTGA 58.830 47.619 0.00 0.00 0.00 2.69
2653 3315 2.094545 GTGATGCCAAGACCCATTTGAC 60.095 50.000 0.00 0.00 0.00 3.18
2654 3316 2.170166 GATGCCAAGACCCATTTGACA 58.830 47.619 0.00 0.00 0.00 3.58
2655 3317 2.307496 TGCCAAGACCCATTTGACAT 57.693 45.000 0.00 0.00 0.00 3.06
2656 3318 2.607499 TGCCAAGACCCATTTGACATT 58.393 42.857 0.00 0.00 0.00 2.71
2657 3319 2.971330 TGCCAAGACCCATTTGACATTT 59.029 40.909 0.00 0.00 0.00 2.32
2658 3320 3.244146 TGCCAAGACCCATTTGACATTTG 60.244 43.478 0.00 0.00 0.00 2.32
2659 3321 3.865684 GCCAAGACCCATTTGACATTTGG 60.866 47.826 0.00 0.00 37.48 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.722094 TCACCACAAAAGCAACACTCT 58.278 42.857 0.00 0.00 0.00 3.24
52 53 3.258123 ACTTTCACCACAAAAGCAACACT 59.742 39.130 0.00 0.00 37.26 3.55
78 79 0.588252 CTCCTCACCACAAAGCAACG 59.412 55.000 0.00 0.00 0.00 4.10
87 88 1.625818 ACTGAATGGACTCCTCACCAC 59.374 52.381 0.00 0.00 39.06 4.16
100 101 4.201753 CGGTGAAGCAATAGACACTGAATG 60.202 45.833 0.00 0.00 40.66 2.67
115 116 4.043200 GCAAGTGGGCGGTGAAGC 62.043 66.667 0.00 0.00 0.00 3.86
161 162 7.444487 ACTTGTGACTGGAGGTAGATTAAAAAC 59.556 37.037 0.00 0.00 0.00 2.43
162 163 7.514721 ACTTGTGACTGGAGGTAGATTAAAAA 58.485 34.615 0.00 0.00 0.00 1.94
177 178 1.468224 CCGATCCGAGACTTGTGACTG 60.468 57.143 0.00 0.00 0.00 3.51
179 180 0.526662 ACCGATCCGAGACTTGTGAC 59.473 55.000 0.00 0.00 0.00 3.67
180 181 2.118313 TACCGATCCGAGACTTGTGA 57.882 50.000 0.00 0.00 0.00 3.58
191 244 3.636764 AGCCCAAATTTTCATACCGATCC 59.363 43.478 0.00 0.00 0.00 3.36
196 249 7.119116 CCAAAGTAAAGCCCAAATTTTCATACC 59.881 37.037 0.00 0.00 0.00 2.73
243 296 8.237267 ACTTTCCTTCTGCTAAAAATACAATCG 58.763 33.333 0.00 0.00 0.00 3.34
276 329 6.070653 TGGCCTTGAAGATAATCTGCAATTTT 60.071 34.615 3.32 0.00 41.01 1.82
277 330 5.422970 TGGCCTTGAAGATAATCTGCAATTT 59.577 36.000 3.32 0.00 41.01 1.82
278 331 4.957954 TGGCCTTGAAGATAATCTGCAATT 59.042 37.500 3.32 0.00 41.01 2.32
279 332 4.539726 TGGCCTTGAAGATAATCTGCAAT 58.460 39.130 3.32 0.00 41.01 3.56
318 372 3.241067 TCCTTGCATAGTAACGGTCAC 57.759 47.619 0.00 0.00 0.00 3.67
322 376 3.132289 TCCTCTTCCTTGCATAGTAACGG 59.868 47.826 0.00 0.00 0.00 4.44
365 419 3.206150 ACCATCTCGTATCAATTGCACC 58.794 45.455 0.00 0.00 0.00 5.01
484 542 0.110295 ACTGCCACACATAGTTGCCA 59.890 50.000 0.00 0.00 38.06 4.92
497 555 9.440773 GTCAATATCTGATCATAATAACTGCCA 57.559 33.333 0.00 0.00 36.14 4.92
537 595 6.993902 TCGGGTGGTTCATATAACCTTTTATC 59.006 38.462 8.29 0.00 40.88 1.75
550 608 1.762957 CCTCTACATCGGGTGGTTCAT 59.237 52.381 0.00 0.00 0.00 2.57
555 613 2.822399 GGCCTCTACATCGGGTGG 59.178 66.667 0.00 0.00 0.00 4.61
559 617 2.565645 CCCTCGGCCTCTACATCGG 61.566 68.421 0.00 0.00 0.00 4.18
565 626 0.178941 GGAATACCCCTCGGCCTCTA 60.179 60.000 0.00 0.00 0.00 2.43
618 683 8.562892 GGAATAGCACTAGTAATTACAGTACGA 58.437 37.037 17.65 9.91 0.00 3.43
619 684 8.566260 AGGAATAGCACTAGTAATTACAGTACG 58.434 37.037 17.65 8.92 0.00 3.67
620 685 9.896263 GAGGAATAGCACTAGTAATTACAGTAC 57.104 37.037 17.65 12.45 0.00 2.73
621 686 8.781196 CGAGGAATAGCACTAGTAATTACAGTA 58.219 37.037 17.65 1.81 0.00 2.74
622 687 7.501559 TCGAGGAATAGCACTAGTAATTACAGT 59.498 37.037 17.65 14.51 0.00 3.55
623 688 7.872881 TCGAGGAATAGCACTAGTAATTACAG 58.127 38.462 17.65 13.95 0.00 2.74
803 869 9.698617 GTCGTTATTATCTTAAATTGCGAAGTT 57.301 29.630 0.00 0.00 30.98 2.66
833 899 4.398673 ACTCCTACTACGATTCCAGTCAAC 59.601 45.833 0.00 0.00 0.00 3.18
888 956 2.028385 GGAGGGAACTGAATACGTGTGT 60.028 50.000 0.00 0.00 44.43 3.72
967 1035 3.419915 CAATTATGACGAGCACTTGTGC 58.580 45.455 16.98 16.98 0.00 4.57
980 1048 5.132502 CCATGGTTGTCTAGGCAATTATGA 58.867 41.667 25.61 7.96 31.89 2.15
986 1054 0.676466 CGCCATGGTTGTCTAGGCAA 60.676 55.000 14.67 5.45 45.47 4.52
1083 1151 1.733399 GGTCGTCTTGTGGCTCGTC 60.733 63.158 0.00 0.00 0.00 4.20
1149 1217 6.579292 CAGCAGCTATAGATACTTACACGAAC 59.421 42.308 3.21 0.00 0.00 3.95
1206 1274 1.135053 TCGTTCGTTCTTGGTGACACA 60.135 47.619 8.08 0.00 42.67 3.72
1215 1283 1.561250 CGGCGTTTCGTTCGTTCTT 59.439 52.632 0.00 0.00 0.00 2.52
1591 1671 2.281484 ACCGCAACGAAGCCACAT 60.281 55.556 0.00 0.00 0.00 3.21
1603 1683 1.604308 TAAGTGGAGGACGACCGCA 60.604 57.895 9.99 0.00 41.83 5.69
1698 1778 8.675705 TTCGAATTTATTCTCTCCATGCAATA 57.324 30.769 0.00 0.00 34.69 1.90
1699 1779 7.572523 TTCGAATTTATTCTCTCCATGCAAT 57.427 32.000 0.00 0.00 34.69 3.56
1700 1780 7.572523 ATTCGAATTTATTCTCTCCATGCAA 57.427 32.000 4.39 0.00 34.69 4.08
1707 1787 9.130312 AGCGTGTATATTCGAATTTATTCTCTC 57.870 33.333 17.19 0.91 34.69 3.20
1823 1907 6.867519 TTTACATAGTCTGGGTCAATGAGA 57.132 37.500 0.00 0.00 0.00 3.27
1824 1908 9.613428 TTAATTTACATAGTCTGGGTCAATGAG 57.387 33.333 0.00 0.00 0.00 2.90
1829 1913 9.967451 TCAAATTAATTTACATAGTCTGGGTCA 57.033 29.630 12.98 0.00 0.00 4.02
1915 1999 2.665165 TGGCCAACTCAAAGTGACAAT 58.335 42.857 0.61 0.00 0.00 2.71
1924 2008 4.410099 AGAATTGATCTTGGCCAACTCAA 58.590 39.130 28.23 28.23 33.39 3.02
1965 2513 1.405463 TCTCGCATTACTCGCTCATGT 59.595 47.619 0.00 0.00 0.00 3.21
1966 2514 2.049959 CTCTCGCATTACTCGCTCATG 58.950 52.381 0.00 0.00 0.00 3.07
2066 2614 4.328208 AGGAGATCCTGCCATCCC 57.672 61.111 0.00 0.00 46.55 3.85
2141 2689 4.341520 AGCTGTACATGGGCTAGTTAGTAC 59.658 45.833 6.32 0.00 34.31 2.73
2144 2692 4.262079 GGTAGCTGTACATGGGCTAGTTAG 60.262 50.000 13.84 0.00 38.91 2.34
2145 2693 3.640029 GGTAGCTGTACATGGGCTAGTTA 59.360 47.826 13.84 0.00 38.91 2.24
2146 2694 2.434702 GGTAGCTGTACATGGGCTAGTT 59.565 50.000 13.84 0.00 38.91 2.24
2147 2695 2.040178 GGTAGCTGTACATGGGCTAGT 58.960 52.381 13.84 0.00 38.91 2.57
2148 2696 1.344763 GGGTAGCTGTACATGGGCTAG 59.655 57.143 13.84 0.00 38.91 3.42
2277 2935 5.294060 CCTTTTGATTTGGAACCTTGTGTTG 59.706 40.000 0.00 0.00 37.29 3.33
2282 2940 5.022282 ACACCTTTTGATTTGGAACCTTG 57.978 39.130 0.00 0.00 0.00 3.61
2331 2989 9.971922 CCTCCATTCCAAATAATTGTCTTATTC 57.028 33.333 0.00 0.00 34.60 1.75
2350 3009 8.798975 TCAGTCTAATAAATACTCCCTCCATT 57.201 34.615 0.00 0.00 0.00 3.16
2470 3132 3.372440 AACCTATGCCTTCTTTCCCAG 57.628 47.619 0.00 0.00 0.00 4.45
2513 3175 0.105658 TTAGGGTGAGGGAGGGATCG 60.106 60.000 0.00 0.00 0.00 3.69
2536 3198 6.346096 CAAGAATAACGAGATCACCCCTTTA 58.654 40.000 0.00 0.00 0.00 1.85
2575 3237 4.717991 TCCAAAAAGTCGCATGTAAATCG 58.282 39.130 0.00 0.00 0.00 3.34
2581 3243 3.149196 ACTCATCCAAAAAGTCGCATGT 58.851 40.909 0.00 0.00 0.00 3.21
2582 3244 3.837213 ACTCATCCAAAAAGTCGCATG 57.163 42.857 0.00 0.00 0.00 4.06
2583 3245 5.957842 TTTACTCATCCAAAAAGTCGCAT 57.042 34.783 0.00 0.00 0.00 4.73
2584 3246 5.759506 TTTTACTCATCCAAAAAGTCGCA 57.240 34.783 0.00 0.00 0.00 5.10
2608 3270 4.400529 GACCCCTTGTCAACACATTTTT 57.599 40.909 0.00 0.00 43.85 1.94
2622 3284 0.482446 TTGGCATCACAAGACCCCTT 59.518 50.000 0.00 0.00 0.00 3.95
2623 3285 2.163454 TTGGCATCACAAGACCCCT 58.837 52.632 0.00 0.00 0.00 4.79
2624 3286 4.841441 TTGGCATCACAAGACCCC 57.159 55.556 0.00 0.00 0.00 4.95
2630 3292 2.299582 CAAATGGGTCTTGGCATCACAA 59.700 45.455 0.00 0.00 0.00 3.33
2631 3293 1.894466 CAAATGGGTCTTGGCATCACA 59.106 47.619 0.00 0.00 0.00 3.58
2632 3294 2.094545 GTCAAATGGGTCTTGGCATCAC 60.095 50.000 0.00 0.00 0.00 3.06
2633 3295 2.170166 GTCAAATGGGTCTTGGCATCA 58.830 47.619 0.00 0.00 0.00 3.07
2634 3296 2.170166 TGTCAAATGGGTCTTGGCATC 58.830 47.619 0.00 0.00 33.60 3.91
2635 3297 2.307496 TGTCAAATGGGTCTTGGCAT 57.693 45.000 0.00 0.00 33.60 4.40
2636 3298 2.307496 ATGTCAAATGGGTCTTGGCA 57.693 45.000 0.00 0.00 42.22 4.92
2637 3299 3.328505 CAAATGTCAAATGGGTCTTGGC 58.671 45.455 0.00 0.00 0.00 4.52
2638 3300 3.929094 CCAAATGTCAAATGGGTCTTGG 58.071 45.455 0.33 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.