Multiple sequence alignment - TraesCS6D01G153000

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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 TraesCS6D01G153000 chr6D 100.000 3188 0 0 1 3188 127082857 127086044 0.000000e+00 5888.0
1 TraesCS6D01G153000 chr6A 93.025 2939 117 35 260 3188 151529147 151526287 0.000000e+00 4211.0
2 TraesCS6D01G153000 chr6A 93.208 265 17 1 1 264 151566091 151565827 3.860000e-104 388.0
3 TraesCS6D01G153000 chr6B 95.023 2431 89 18 1 2424 226138990 226141395 0.000000e+00 3790.0
4 TraesCS6D01G153000 chr6B 88.531 715 48 17 2479 3188 226141395 226142080 0.000000e+00 835.0
5 TraesCS6D01G153000 chr2B 78.125 160 18 12 340 487 673937694 673937540 5.670000e-13 86.1
6 TraesCS6D01G153000 chr1A 81.731 104 16 3 384 484 38853098 38852995 2.040000e-12 84.2
7 TraesCS6D01G153000 chr1A 79.630 108 18 4 381 484 430237908 430238015 1.230000e-09 75.0
8 TraesCS6D01G153000 chr1A 75.000 188 30 13 311 486 492227823 492227641 1.590000e-08 71.3
9 TraesCS6D01G153000 chr7B 81.553 103 14 5 387 486 64723825 64723725 2.640000e-11 80.5
10 TraesCS6D01G153000 chr5D 91.667 60 2 3 384 440 546857804 546857863 2.640000e-11 80.5
11 TraesCS6D01G153000 chr4D 76.064 188 24 15 312 484 507755787 507755606 9.480000e-11 78.7


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 TraesCS6D01G153000 chr6D 127082857 127086044 3187 False 5888.0 5888 100.000 1 3188 1 chr6D.!!$F1 3187
1 TraesCS6D01G153000 chr6A 151526287 151529147 2860 True 4211.0 4211 93.025 260 3188 1 chr6A.!!$R1 2928
2 TraesCS6D01G153000 chr6B 226138990 226142080 3090 False 2312.5 3790 91.777 1 3188 2 chr6B.!!$F1 3187

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
776 785 0.108089 GAGGAAAACGCTCTCCCTCC 60.108 60.0 0.0 0.0 37.91 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2511 0.043334 CCCCTTCTCTTCTCCCTCCA 59.957 60.0 0.0 0.0 0.0 3.86 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
84 86 5.374921 AGATCCAACATGTCCATTCTGATC 58.625 41.667 0.00 3.82 0.00 2.92
93 95 5.964958 TGTCCATTCTGATCCTGTTTTTC 57.035 39.130 0.00 0.00 0.00 2.29
149 151 4.012374 TCTAGGCTCCATTCTTGCAAAAG 58.988 43.478 0.00 0.00 0.00 2.27
156 158 5.314923 TCCATTCTTGCAAAAGATAGTGC 57.685 39.130 0.00 0.00 41.29 4.40
174 176 7.936301 AGATAGTGCATTTCTCCCTCTATTTTC 59.064 37.037 0.00 0.00 0.00 2.29
189 191 8.636213 CCCTCTATTTTCTGCATGTATTTTGAT 58.364 33.333 0.00 0.00 0.00 2.57
197 199 9.585099 TTTCTGCATGTATTTTGATTAACCATC 57.415 29.630 0.00 0.00 0.00 3.51
198 200 8.523915 TCTGCATGTATTTTGATTAACCATCT 57.476 30.769 0.00 0.00 32.34 2.90
199 201 9.625747 TCTGCATGTATTTTGATTAACCATCTA 57.374 29.630 0.00 0.00 32.34 1.98
233 235 7.127012 TGTAGTCCCGGATGAACAATAAATA 57.873 36.000 0.73 0.00 0.00 1.40
294 296 1.206371 AGGAGTGTTTCGGGTTATCGG 59.794 52.381 0.00 0.00 0.00 4.18
330 332 0.447801 ATCGCATTCGTGGAAGTTGC 59.552 50.000 0.00 0.00 36.96 4.17
380 382 6.634805 TGCTACTTTCAAACACATTTTGGAA 58.365 32.000 0.00 0.00 0.00 3.53
382 384 6.291585 GCTACTTTCAAACACATTTTGGAACG 60.292 38.462 0.00 0.00 0.00 3.95
444 446 9.545105 TGATGAAACTTTGTAAGCATTTCAAAT 57.455 25.926 2.19 0.00 42.91 2.32
533 539 2.403252 ACCCGAGCTTACTTTCATGG 57.597 50.000 0.00 0.00 0.00 3.66
547 553 9.280174 CTTACTTTCATGGTCTAACAAGGTAAA 57.720 33.333 0.00 0.00 0.00 2.01
563 569 7.609960 ACAAGGTAAACTTTCTACTAGCCTAC 58.390 38.462 0.00 0.00 37.29 3.18
564 570 7.454066 ACAAGGTAAACTTTCTACTAGCCTACT 59.546 37.037 0.00 0.00 37.29 2.57
565 571 8.964772 CAAGGTAAACTTTCTACTAGCCTACTA 58.035 37.037 0.00 0.00 37.29 1.82
566 572 8.518430 AGGTAAACTTTCTACTAGCCTACTAC 57.482 38.462 0.00 0.00 0.00 2.73
766 775 4.893424 CTCCTAGAGAGAGAGGAAAACG 57.107 50.000 0.00 0.00 46.50 3.60
776 785 0.108089 GAGGAAAACGCTCTCCCTCC 60.108 60.000 0.00 0.00 37.91 4.30
778 787 1.078356 GAAAACGCTCTCCCTCCCC 60.078 63.158 0.00 0.00 0.00 4.81
816 826 9.287373 GAGTACTACCTATTGCATAGTCTACTT 57.713 37.037 0.00 0.00 31.65 2.24
818 828 7.291411 ACTACCTATTGCATAGTCTACTTGG 57.709 40.000 0.00 0.00 0.00 3.61
819 829 4.962155 ACCTATTGCATAGTCTACTTGGC 58.038 43.478 0.00 0.00 0.00 4.52
1167 1177 4.135153 CTCTCCGGTGCTGACCCG 62.135 72.222 0.00 0.00 45.07 5.28
1243 1253 3.966026 GCCGACGAGGGACGAAGTG 62.966 68.421 0.00 0.00 45.77 3.16
1532 1542 2.805353 CGACCTTGACGTGCTCCG 60.805 66.667 0.00 0.00 44.03 4.63
1599 1609 2.363975 ATTCCGCTTCCACCCGCTA 61.364 57.895 0.00 0.00 0.00 4.26
1743 1753 1.308069 CCGCATTCTTGAGGTGGGTG 61.308 60.000 0.00 0.00 37.97 4.61
2121 2131 3.857038 GGGTATGCGGCGGAGGAA 61.857 66.667 9.78 0.00 0.00 3.36
2192 2202 1.929836 CTCTTCGTGGCACTAGCAATC 59.070 52.381 16.72 0.00 44.61 2.67
2223 2233 1.067295 TCCATGCTGTTGGACCTCTT 58.933 50.000 0.00 0.00 40.90 2.85
2299 2309 2.286950 CGCAATGAACCATATGGAACCG 60.287 50.000 28.77 14.92 38.94 4.44
2424 2462 0.038599 ATGCATGCAAGGACCAGTGA 59.961 50.000 26.68 0.00 0.00 3.41
2425 2463 0.607217 TGCATGCAAGGACCAGTGAG 60.607 55.000 20.30 0.00 0.00 3.51
2426 2464 1.310933 GCATGCAAGGACCAGTGAGG 61.311 60.000 14.21 0.00 45.67 3.86
2427 2465 1.001641 ATGCAAGGACCAGTGAGGC 60.002 57.895 0.00 0.00 43.14 4.70
2428 2466 1.495579 ATGCAAGGACCAGTGAGGCT 61.496 55.000 0.00 0.00 43.14 4.58
2429 2467 0.835971 TGCAAGGACCAGTGAGGCTA 60.836 55.000 0.00 0.00 43.14 3.93
2430 2468 0.107945 GCAAGGACCAGTGAGGCTAG 60.108 60.000 0.00 0.00 43.14 3.42
2431 2469 0.107945 CAAGGACCAGTGAGGCTAGC 60.108 60.000 6.04 6.04 43.14 3.42
2432 2470 0.252467 AAGGACCAGTGAGGCTAGCT 60.252 55.000 15.72 0.00 43.14 3.32
2433 2471 0.686112 AGGACCAGTGAGGCTAGCTC 60.686 60.000 15.72 10.64 43.14 4.09
2434 2472 0.686112 GGACCAGTGAGGCTAGCTCT 60.686 60.000 15.72 10.10 43.14 4.09
2435 2473 1.190643 GACCAGTGAGGCTAGCTCTT 58.809 55.000 15.72 0.21 43.14 2.85
2436 2474 2.379972 GACCAGTGAGGCTAGCTCTTA 58.620 52.381 15.72 4.17 43.14 2.10
2437 2475 2.962421 GACCAGTGAGGCTAGCTCTTAT 59.038 50.000 15.72 0.00 43.14 1.73
2438 2476 3.379452 ACCAGTGAGGCTAGCTCTTATT 58.621 45.455 15.72 1.19 43.14 1.40
2439 2477 3.777522 ACCAGTGAGGCTAGCTCTTATTT 59.222 43.478 15.72 0.00 43.14 1.40
2440 2478 4.962995 ACCAGTGAGGCTAGCTCTTATTTA 59.037 41.667 15.72 0.00 43.14 1.40
2441 2479 5.604650 ACCAGTGAGGCTAGCTCTTATTTAT 59.395 40.000 15.72 0.00 43.14 1.40
2442 2480 6.162777 CCAGTGAGGCTAGCTCTTATTTATC 58.837 44.000 15.72 0.00 0.00 1.75
2443 2481 6.162777 CAGTGAGGCTAGCTCTTATTTATCC 58.837 44.000 15.72 0.00 0.00 2.59
2444 2482 6.014669 CAGTGAGGCTAGCTCTTATTTATCCT 60.015 42.308 15.72 0.00 0.00 3.24
2445 2483 7.177568 CAGTGAGGCTAGCTCTTATTTATCCTA 59.822 40.741 15.72 0.00 0.00 2.94
2446 2484 7.396055 AGTGAGGCTAGCTCTTATTTATCCTAG 59.604 40.741 15.72 0.00 0.00 3.02
2447 2485 6.153680 TGAGGCTAGCTCTTATTTATCCTAGC 59.846 42.308 15.72 8.52 44.17 3.42
2448 2486 6.260663 AGGCTAGCTCTTATTTATCCTAGCT 58.739 40.000 15.72 0.00 44.27 3.32
2449 2487 7.415086 AGGCTAGCTCTTATTTATCCTAGCTA 58.585 38.462 15.72 0.00 44.27 3.32
2454 2492 8.288689 AGCTCTTATTTATCCTAGCTAGCTAC 57.711 38.462 20.67 5.81 38.48 3.58
2455 2493 8.113462 AGCTCTTATTTATCCTAGCTAGCTACT 58.887 37.037 20.67 10.56 38.48 2.57
2456 2494 8.188139 GCTCTTATTTATCCTAGCTAGCTACTG 58.812 40.741 20.67 14.21 0.00 2.74
2457 2495 9.238368 CTCTTATTTATCCTAGCTAGCTACTGT 57.762 37.037 20.67 11.06 0.00 3.55
2461 2499 8.943594 ATTTATCCTAGCTAGCTACTGTACTT 57.056 34.615 20.67 1.64 0.00 2.24
2462 2500 7.747155 TTATCCTAGCTAGCTACTGTACTTG 57.253 40.000 20.67 8.23 0.00 3.16
2463 2501 3.884091 TCCTAGCTAGCTACTGTACTTGC 59.116 47.826 20.67 12.20 35.30 4.01
2464 2502 3.004944 CCTAGCTAGCTACTGTACTTGCC 59.995 52.174 20.67 0.00 35.61 4.52
2465 2503 2.457598 AGCTAGCTACTGTACTTGCCA 58.542 47.619 17.69 0.00 35.61 4.92
2466 2504 3.034635 AGCTAGCTACTGTACTTGCCAT 58.965 45.455 17.69 0.00 35.61 4.40
2467 2505 3.452627 AGCTAGCTACTGTACTTGCCATT 59.547 43.478 17.69 0.00 35.61 3.16
2468 2506 3.804873 GCTAGCTACTGTACTTGCCATTC 59.195 47.826 7.70 0.00 0.00 2.67
2469 2507 4.442192 GCTAGCTACTGTACTTGCCATTCT 60.442 45.833 7.70 0.00 0.00 2.40
2470 2508 4.559862 AGCTACTGTACTTGCCATTCTT 57.440 40.909 0.00 0.00 0.00 2.52
2471 2509 4.256920 AGCTACTGTACTTGCCATTCTTG 58.743 43.478 0.00 0.00 0.00 3.02
2472 2510 4.003648 GCTACTGTACTTGCCATTCTTGT 58.996 43.478 0.00 0.00 0.00 3.16
2473 2511 4.455877 GCTACTGTACTTGCCATTCTTGTT 59.544 41.667 0.00 0.00 0.00 2.83
2474 2512 4.836125 ACTGTACTTGCCATTCTTGTTG 57.164 40.909 0.00 0.00 0.00 3.33
2475 2513 3.569701 ACTGTACTTGCCATTCTTGTTGG 59.430 43.478 0.00 0.00 37.31 3.77
2476 2514 3.820467 CTGTACTTGCCATTCTTGTTGGA 59.180 43.478 0.00 0.00 36.26 3.53
2477 2515 3.820467 TGTACTTGCCATTCTTGTTGGAG 59.180 43.478 0.00 0.00 36.26 3.86
2478 2516 2.242043 ACTTGCCATTCTTGTTGGAGG 58.758 47.619 0.00 0.00 36.26 4.30
2683 2721 9.897744 CAGTTATTTCTTCTTTGCTTTACATCA 57.102 29.630 0.00 0.00 0.00 3.07
2738 2776 2.158667 TGTTCAACTTCCCCTCTCCAAC 60.159 50.000 0.00 0.00 0.00 3.77
2798 2836 9.833917 ACTACTTAAAAATATGTTCTAGAGCCC 57.166 33.333 3.94 0.00 0.00 5.19
2799 2837 9.274206 CTACTTAAAAATATGTTCTAGAGCCCC 57.726 37.037 3.94 0.00 0.00 5.80
2800 2838 7.873195 ACTTAAAAATATGTTCTAGAGCCCCT 58.127 34.615 3.94 0.00 0.00 4.79
2801 2839 8.999895 ACTTAAAAATATGTTCTAGAGCCCCTA 58.000 33.333 3.94 0.00 0.00 3.53
2802 2840 9.847224 CTTAAAAATATGTTCTAGAGCCCCTAA 57.153 33.333 3.94 0.00 0.00 2.69
2830 2868 5.304686 TGTTCTAGAGTGGATGGTGTTTT 57.695 39.130 0.00 0.00 0.00 2.43
2874 2912 9.743057 CACTGAACAAATTTGACCACTATTTTA 57.257 29.630 24.64 2.23 0.00 1.52
3027 3069 3.325135 ACTTGTCTCCACACTTTCTAGGG 59.675 47.826 0.00 0.00 29.76 3.53
3042 3084 0.179094 TAGGGCGCGATGTACTTTGG 60.179 55.000 12.10 0.00 0.00 3.28
3054 3096 6.475402 GCGATGTACTTTGGATTTTAAATGGG 59.525 38.462 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.656040 ATGTGCATTTTTATGAAATGTGTATGT 57.344 25.926 14.19 0.36 39.25 2.29
52 53 4.581824 GGACATGTTGGATCTATGTGCATT 59.418 41.667 0.00 0.00 41.14 3.56
54 55 3.054508 TGGACATGTTGGATCTATGTGCA 60.055 43.478 16.46 16.46 46.26 4.57
84 86 7.026631 TGTTCTTGTATGTCAGAAAAACAGG 57.973 36.000 0.00 0.00 0.00 4.00
93 95 8.571336 AGAATTTCCTTTGTTCTTGTATGTCAG 58.429 33.333 0.00 0.00 0.00 3.51
149 151 7.936301 AGAAAATAGAGGGAGAAATGCACTATC 59.064 37.037 0.00 0.00 0.00 2.08
156 158 6.320672 ACATGCAGAAAATAGAGGGAGAAATG 59.679 38.462 0.00 0.00 0.00 2.32
157 159 6.430007 ACATGCAGAAAATAGAGGGAGAAAT 58.570 36.000 0.00 0.00 0.00 2.17
189 191 8.574251 ACTACATGCACAAAATAGATGGTTAA 57.426 30.769 0.00 0.00 0.00 2.01
197 199 3.312421 CCGGGACTACATGCACAAAATAG 59.688 47.826 0.00 0.00 0.00 1.73
198 200 3.055021 TCCGGGACTACATGCACAAAATA 60.055 43.478 0.00 0.00 0.00 1.40
199 201 2.091541 CCGGGACTACATGCACAAAAT 58.908 47.619 0.00 0.00 0.00 1.82
200 202 1.072489 TCCGGGACTACATGCACAAAA 59.928 47.619 0.00 0.00 0.00 2.44
201 203 0.687920 TCCGGGACTACATGCACAAA 59.312 50.000 0.00 0.00 0.00 2.83
202 204 0.908910 ATCCGGGACTACATGCACAA 59.091 50.000 0.00 0.00 0.00 3.33
203 205 0.177836 CATCCGGGACTACATGCACA 59.822 55.000 0.00 0.00 0.00 4.57
253 255 5.757320 TCCTTAATGTTTGCCACACAATTTG 59.243 36.000 0.00 0.00 38.61 2.32
254 256 5.923204 TCCTTAATGTTTGCCACACAATTT 58.077 33.333 0.00 0.00 38.61 1.82
255 257 5.070313 ACTCCTTAATGTTTGCCACACAATT 59.930 36.000 0.00 0.00 38.61 2.32
256 258 4.588528 ACTCCTTAATGTTTGCCACACAAT 59.411 37.500 0.00 0.00 38.61 2.71
257 259 3.957497 ACTCCTTAATGTTTGCCACACAA 59.043 39.130 0.00 0.00 38.61 3.33
258 260 3.317711 CACTCCTTAATGTTTGCCACACA 59.682 43.478 0.00 0.00 38.61 3.72
294 296 6.610741 ATGCGATTCTAGGATCAAACTTTC 57.389 37.500 11.68 0.00 0.00 2.62
330 332 1.666888 GGAGCACTGATTGTTTTGCCG 60.667 52.381 0.00 0.00 35.47 5.69
487 489 9.679661 TCAAATGCTCCTTATATGAACAGTAAA 57.320 29.630 0.00 0.00 0.00 2.01
501 506 1.826385 CTCGGGTTCAAATGCTCCTT 58.174 50.000 0.00 0.00 0.00 3.36
533 539 9.138062 GCTAGTAGAAAGTTTACCTTGTTAGAC 57.862 37.037 0.00 0.00 32.32 2.59
547 553 9.697990 ACAAATAGTAGTAGGCTAGTAGAAAGT 57.302 33.333 9.34 2.26 36.77 2.66
637 643 5.124617 GGGAATGGTCAAGATGTCTTCTTTC 59.875 44.000 0.00 0.00 42.15 2.62
639 645 4.568592 GGGGAATGGTCAAGATGTCTTCTT 60.569 45.833 0.00 0.00 45.83 2.52
658 665 2.824880 CGTGGACTTTGGTGGGGGA 61.825 63.158 0.00 0.00 0.00 4.81
766 775 2.123033 GAGAGGGGGAGGGAGAGC 60.123 72.222 0.00 0.00 0.00 4.09
771 780 0.777446 CTAGAGAGAGAGGGGGAGGG 59.223 65.000 0.00 0.00 0.00 4.30
772 781 1.827792 TCTAGAGAGAGAGGGGGAGG 58.172 60.000 0.00 0.00 0.00 4.30
816 826 2.852075 AGGTGTTCCCTTCCGCCA 60.852 61.111 0.00 0.00 42.73 5.69
818 828 0.391263 CTACAGGTGTTCCCTTCCGC 60.391 60.000 0.00 0.00 42.73 5.54
819 829 0.974383 ACTACAGGTGTTCCCTTCCG 59.026 55.000 0.00 0.00 42.73 4.30
839 849 4.962122 CTGCAACACGCGCACACC 62.962 66.667 5.73 0.00 46.97 4.16
1484 1494 2.038813 TGATCCTGACCTCGGGCA 59.961 61.111 0.00 0.00 42.21 5.36
1599 1609 4.021925 GCCGTGCAGGGAAGGAGT 62.022 66.667 29.10 0.00 41.48 3.85
2163 2173 0.802607 GCCACGAAGAGACCGACATC 60.803 60.000 0.00 0.00 0.00 3.06
2192 2202 4.082665 ACAGCATGGATAGATCACTTGG 57.917 45.455 0.00 0.00 43.62 3.61
2287 2297 1.673033 GCTCGATCCGGTTCCATATGG 60.673 57.143 16.25 16.25 0.00 2.74
2288 2298 1.000843 TGCTCGATCCGGTTCCATATG 59.999 52.381 0.00 0.00 0.00 1.78
2299 2309 1.092345 GCCTCCAACTTGCTCGATCC 61.092 60.000 0.00 0.00 0.00 3.36
2424 2462 6.260663 AGCTAGGATAAATAAGAGCTAGCCT 58.739 40.000 12.13 5.44 38.46 4.58
2425 2463 6.538945 AGCTAGGATAAATAAGAGCTAGCC 57.461 41.667 12.13 2.81 38.46 3.93
2428 2466 9.398538 GTAGCTAGCTAGGATAAATAAGAGCTA 57.601 37.037 24.78 11.79 40.58 3.32
2429 2467 8.113462 AGTAGCTAGCTAGGATAAATAAGAGCT 58.887 37.037 24.78 12.78 42.64 4.09
2430 2468 8.188139 CAGTAGCTAGCTAGGATAAATAAGAGC 58.812 40.741 24.78 7.80 0.00 4.09
2431 2469 9.238368 ACAGTAGCTAGCTAGGATAAATAAGAG 57.762 37.037 24.78 5.26 0.00 2.85
2436 2474 8.798402 CAAGTACAGTAGCTAGCTAGGATAAAT 58.202 37.037 24.78 7.11 0.00 1.40
2437 2475 7.255520 GCAAGTACAGTAGCTAGCTAGGATAAA 60.256 40.741 24.78 0.13 0.00 1.40
2438 2476 6.207025 GCAAGTACAGTAGCTAGCTAGGATAA 59.793 42.308 24.78 7.12 0.00 1.75
2439 2477 5.706369 GCAAGTACAGTAGCTAGCTAGGATA 59.294 44.000 24.78 13.53 0.00 2.59
2440 2478 4.521256 GCAAGTACAGTAGCTAGCTAGGAT 59.479 45.833 24.78 14.50 0.00 3.24
2441 2479 3.884091 GCAAGTACAGTAGCTAGCTAGGA 59.116 47.826 24.78 8.29 0.00 2.94
2442 2480 3.004944 GGCAAGTACAGTAGCTAGCTAGG 59.995 52.174 24.78 20.62 0.00 3.02
2443 2481 3.632604 TGGCAAGTACAGTAGCTAGCTAG 59.367 47.826 24.78 16.84 0.00 3.42
2444 2482 3.628008 TGGCAAGTACAGTAGCTAGCTA 58.372 45.455 20.67 20.67 0.00 3.32
2445 2483 2.457598 TGGCAAGTACAGTAGCTAGCT 58.542 47.619 23.12 23.12 0.00 3.32
2446 2484 2.961526 TGGCAAGTACAGTAGCTAGC 57.038 50.000 6.62 6.62 0.00 3.42
2447 2485 5.269505 AGAATGGCAAGTACAGTAGCTAG 57.730 43.478 0.00 0.00 0.00 3.42
2448 2486 5.046591 ACAAGAATGGCAAGTACAGTAGCTA 60.047 40.000 0.00 0.00 0.00 3.32
2449 2487 4.256920 CAAGAATGGCAAGTACAGTAGCT 58.743 43.478 0.00 0.00 0.00 3.32
2450 2488 4.003648 ACAAGAATGGCAAGTACAGTAGC 58.996 43.478 0.00 0.00 0.00 3.58
2451 2489 5.106555 CCAACAAGAATGGCAAGTACAGTAG 60.107 44.000 0.00 0.00 0.00 2.57
2452 2490 4.759693 CCAACAAGAATGGCAAGTACAGTA 59.240 41.667 0.00 0.00 0.00 2.74
2453 2491 3.569701 CCAACAAGAATGGCAAGTACAGT 59.430 43.478 0.00 0.00 0.00 3.55
2454 2492 3.820467 TCCAACAAGAATGGCAAGTACAG 59.180 43.478 0.00 0.00 37.88 2.74
2455 2493 3.820467 CTCCAACAAGAATGGCAAGTACA 59.180 43.478 0.00 0.00 37.88 2.90
2456 2494 3.191371 CCTCCAACAAGAATGGCAAGTAC 59.809 47.826 0.00 0.00 37.88 2.73
2457 2495 3.420893 CCTCCAACAAGAATGGCAAGTA 58.579 45.455 0.00 0.00 37.88 2.24
2458 2496 2.242043 CCTCCAACAAGAATGGCAAGT 58.758 47.619 0.00 0.00 37.88 3.16
2459 2497 1.547372 CCCTCCAACAAGAATGGCAAG 59.453 52.381 0.00 0.00 37.88 4.01
2460 2498 1.146774 TCCCTCCAACAAGAATGGCAA 59.853 47.619 0.00 0.00 37.88 4.52
2461 2499 0.776810 TCCCTCCAACAAGAATGGCA 59.223 50.000 0.00 0.00 37.88 4.92
2462 2500 1.004745 TCTCCCTCCAACAAGAATGGC 59.995 52.381 0.00 0.00 37.88 4.40
2463 2501 3.009473 TCTTCTCCCTCCAACAAGAATGG 59.991 47.826 0.00 0.00 39.41 3.16
2464 2502 4.019860 TCTCTTCTCCCTCCAACAAGAATG 60.020 45.833 0.00 0.00 0.00 2.67
2465 2503 4.171234 TCTCTTCTCCCTCCAACAAGAAT 58.829 43.478 0.00 0.00 0.00 2.40
2466 2504 3.587498 TCTCTTCTCCCTCCAACAAGAA 58.413 45.455 0.00 0.00 0.00 2.52
2467 2505 3.260269 TCTCTTCTCCCTCCAACAAGA 57.740 47.619 0.00 0.00 0.00 3.02
2468 2506 3.307339 CCTTCTCTTCTCCCTCCAACAAG 60.307 52.174 0.00 0.00 0.00 3.16
2469 2507 2.639839 CCTTCTCTTCTCCCTCCAACAA 59.360 50.000 0.00 0.00 0.00 2.83
2470 2508 2.260822 CCTTCTCTTCTCCCTCCAACA 58.739 52.381 0.00 0.00 0.00 3.33
2471 2509 1.557371 CCCTTCTCTTCTCCCTCCAAC 59.443 57.143 0.00 0.00 0.00 3.77
2472 2510 1.555765 CCCCTTCTCTTCTCCCTCCAA 60.556 57.143 0.00 0.00 0.00 3.53
2473 2511 0.043334 CCCCTTCTCTTCTCCCTCCA 59.957 60.000 0.00 0.00 0.00 3.86
2474 2512 0.340208 TCCCCTTCTCTTCTCCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
2475 2513 1.691163 CCTCCCCTTCTCTTCTCCCTC 60.691 61.905 0.00 0.00 0.00 4.30
2476 2514 0.341609 CCTCCCCTTCTCTTCTCCCT 59.658 60.000 0.00 0.00 0.00 4.20
2477 2515 0.043485 ACCTCCCCTTCTCTTCTCCC 59.957 60.000 0.00 0.00 0.00 4.30
2478 2516 1.491668 GACCTCCCCTTCTCTTCTCC 58.508 60.000 0.00 0.00 0.00 3.71
2738 2776 7.482169 TCTATAGCAACTCCACCAATATAGG 57.518 40.000 0.00 0.00 0.00 2.57
2803 2841 6.306987 ACACCATCCACTCTAGAACATTTTT 58.693 36.000 0.00 0.00 0.00 1.94
2806 2844 5.505181 AACACCATCCACTCTAGAACATT 57.495 39.130 0.00 0.00 0.00 2.71
2830 2868 2.559668 AGTGGAGACGGTACAAATTCGA 59.440 45.455 0.00 0.00 0.00 3.71
2874 2912 8.757982 AAATGACCTGCTTCAATATTCATACT 57.242 30.769 0.00 0.00 0.00 2.12
3027 3069 2.825086 AAATCCAAAGTACATCGCGC 57.175 45.000 0.00 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.