Multiple sequence alignment - TraesCS5A01G225900

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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 TraesCS5A01G225900 chr5A 100.000 2840 0 0 1 2840 441705784 441702945 0.000000e+00 5245
1 TraesCS5A01G225900 chr5A 88.889 90 7 3 2152 2240 652000425 652000512 1.080000e-19 108
2 TraesCS5A01G225900 chr5A 87.500 88 11 0 2152 2239 536773610 536773523 5.010000e-18 102
3 TraesCS5A01G225900 chr5B 93.619 2053 91 21 410 2438 399813377 399811341 0.000000e+00 3029
4 TraesCS5A01G225900 chr5B 92.442 172 9 4 2670 2839 399811019 399810850 2.830000e-60 243
5 TraesCS5A01G225900 chr5D 93.730 1531 67 15 847 2358 340760261 340758741 0.000000e+00 2268
6 TraesCS5A01G225900 chr5D 89.012 810 55 17 1 793 340761391 340760599 0.000000e+00 972
7 TraesCS5A01G225900 chr5D 90.517 116 9 1 2438 2551 340758533 340758418 4.900000e-33 152
8 TraesCS5A01G225900 chr5D 88.298 94 7 4 2147 2238 188826624 188826533 2.990000e-20 110
9 TraesCS5A01G225900 chr3D 90.722 97 8 1 2151 2247 136724314 136724219 8.260000e-26 128
10 TraesCS5A01G225900 chr2B 89.130 92 10 0 2152 2243 379950452 379950361 6.430000e-22 115
11 TraesCS5A01G225900 chr2D 90.588 85 8 0 2152 2236 628571449 628571533 2.310000e-21 113
12 TraesCS5A01G225900 chr2D 86.170 94 11 2 2148 2240 610470748 610470840 1.800000e-17 100
13 TraesCS5A01G225900 chr2D 86.170 94 11 2 2148 2240 610493411 610493503 1.800000e-17 100
14 TraesCS5A01G225900 chr1A 87.912 91 7 4 2152 2240 436259737 436259649 1.390000e-18 104


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 TraesCS5A01G225900 chr5A 441702945 441705784 2839 True 5245.000000 5245 100.000000 1 2840 1 chr5A.!!$R1 2839
1 TraesCS5A01G225900 chr5B 399810850 399813377 2527 True 1636.000000 3029 93.030500 410 2839 2 chr5B.!!$R1 2429
2 TraesCS5A01G225900 chr5D 340758418 340761391 2973 True 1130.666667 2268 91.086333 1 2551 3 chr5D.!!$R2 2550

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
996 1303 0.101219 GAATCTTTGATGCCCGGCAC 59.899 55.0 16.16 9.58 43.04 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2907 0.177604 GTCTGAGCTCATGACTGGGG 59.822 60.0 26.07 12.16 0.0 4.96 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
26 27 4.558178 TCACTATTTGGTGCAAAATGCTG 58.442 39.130 6.62 2.72 45.31 4.41
52 53 0.818040 GTGAACCCGCACCTTTGACT 60.818 55.000 0.00 0.00 32.68 3.41
76 77 9.762381 ACTTTGGTTTAATATCCTGGTTCAATA 57.238 29.630 0.00 0.00 0.00 1.90
143 150 8.989131 ACATGGAAACTAAATTACCTAGAGCTA 58.011 33.333 0.00 0.00 0.00 3.32
168 175 1.425267 TTGTGTGTCTCGTGGCGTTG 61.425 55.000 0.00 0.00 0.00 4.10
180 187 1.720852 GTGGCGTTGCATTTTTGCTAG 59.279 47.619 0.00 0.00 35.49 3.42
185 192 2.346244 CGTTGCATTTTTGCTAGCATGG 59.654 45.455 20.13 7.67 36.80 3.66
236 243 4.009675 TCATTGCCATGGTTGTACTTCTC 58.990 43.478 14.67 0.00 0.00 2.87
261 268 1.208358 GGCGGTCCGTTTTTAGTGC 59.792 57.895 13.94 0.00 0.00 4.40
296 303 2.992124 TTCACAAGAGTCGGGTTTCA 57.008 45.000 0.00 0.00 0.00 2.69
299 306 4.610605 TCACAAGAGTCGGGTTTCATTA 57.389 40.909 0.00 0.00 0.00 1.90
301 308 3.435671 CACAAGAGTCGGGTTTCATTACC 59.564 47.826 0.00 0.00 37.47 2.85
327 334 2.288579 TGTATCTTTTCACCGCGACAGT 60.289 45.455 8.23 0.00 0.00 3.55
331 338 2.230508 TCTTTTCACCGCGACAGTCTAT 59.769 45.455 8.23 0.00 0.00 1.98
337 344 4.751060 TCACCGCGACAGTCTATTTTTAT 58.249 39.130 8.23 0.00 0.00 1.40
338 345 5.172934 TCACCGCGACAGTCTATTTTTATT 58.827 37.500 8.23 0.00 0.00 1.40
344 351 7.425595 CCGCGACAGTCTATTTTTATTCTTTTC 59.574 37.037 8.23 0.00 0.00 2.29
368 375 8.247666 TCTAAGTCTAGCCTATTTTTACTCCC 57.752 38.462 0.00 0.00 0.00 4.30
373 380 6.706716 GTCTAGCCTATTTTTACTCCCATGTC 59.293 42.308 0.00 0.00 0.00 3.06
379 386 8.515414 GCCTATTTTTACTCCCATGTCAATATC 58.485 37.037 0.00 0.00 0.00 1.63
398 405 0.591170 CTTCGTTGCAAACCACGGAT 59.409 50.000 0.00 0.00 46.28 4.18
416 423 7.040062 ACCACGGATATTTTTCATGTGAAGAAA 60.040 33.333 3.29 4.83 32.90 2.52
444 453 8.142551 AGAAGAAGACTAAAGAAAAGCGTAGAA 58.857 33.333 0.00 0.00 0.00 2.10
468 477 5.534207 AATGAAGACTTGCATTGACCAAA 57.466 34.783 10.29 0.00 33.74 3.28
490 499 2.628178 CCCAAGTCAAAGAAAACCCTCC 59.372 50.000 0.00 0.00 0.00 4.30
492 501 3.319122 CCAAGTCAAAGAAAACCCTCCTG 59.681 47.826 0.00 0.00 0.00 3.86
494 503 3.821748 AGTCAAAGAAAACCCTCCTGAC 58.178 45.455 0.00 0.00 32.99 3.51
497 506 2.887152 CAAAGAAAACCCTCCTGACTGG 59.113 50.000 0.00 0.00 37.10 4.00
498 507 2.118403 AGAAAACCCTCCTGACTGGA 57.882 50.000 0.64 0.64 43.86 3.86
499 508 2.418669 AGAAAACCCTCCTGACTGGAA 58.581 47.619 2.38 0.00 45.63 3.53
500 509 2.373502 AGAAAACCCTCCTGACTGGAAG 59.626 50.000 2.38 0.00 45.63 3.46
501 510 2.118403 AAACCCTCCTGACTGGAAGA 57.882 50.000 2.38 0.00 45.63 2.87
502 511 1.650528 AACCCTCCTGACTGGAAGAG 58.349 55.000 2.38 0.00 45.63 2.85
503 512 0.907230 ACCCTCCTGACTGGAAGAGC 60.907 60.000 2.38 0.00 45.63 4.09
504 513 1.621672 CCCTCCTGACTGGAAGAGCC 61.622 65.000 2.38 0.00 45.63 4.70
510 519 0.891373 TGACTGGAAGAGCCGAAGAG 59.109 55.000 0.00 0.00 40.66 2.85
539 548 4.808364 ACAAAACCAAATTGTTCATCCACG 59.192 37.500 0.00 0.00 37.74 4.94
566 575 2.695147 CCTTGTTTTCCTTGCTGGTTCT 59.305 45.455 0.00 0.00 37.07 3.01
567 576 3.132824 CCTTGTTTTCCTTGCTGGTTCTT 59.867 43.478 0.00 0.00 37.07 2.52
568 577 4.363138 CTTGTTTTCCTTGCTGGTTCTTC 58.637 43.478 0.00 0.00 37.07 2.87
577 590 1.425066 TGCTGGTTCTTCCAATCCAGT 59.575 47.619 10.94 0.00 46.59 4.00
614 627 2.810400 CGTCCTCACCTCCACACAAAAT 60.810 50.000 0.00 0.00 0.00 1.82
619 632 2.697751 TCACCTCCACACAAAATTTGGG 59.302 45.455 6.40 6.40 40.79 4.12
691 715 4.033776 CATGCCACGGGACCCACT 62.034 66.667 12.15 0.00 0.00 4.00
701 725 2.119029 GGACCCACTATTTGCGGGC 61.119 63.158 0.00 0.00 41.73 6.13
841 865 1.152139 CCTCCCCTGGATCTCCTCC 60.152 68.421 0.00 0.00 45.19 4.30
974 1281 1.007842 GAAGGAGAGGGGAGGAGAAGT 59.992 57.143 0.00 0.00 0.00 3.01
994 1301 1.095228 TCGAATCTTTGATGCCCGGC 61.095 55.000 1.04 1.04 0.00 6.13
996 1303 0.101219 GAATCTTTGATGCCCGGCAC 59.899 55.000 16.16 9.58 43.04 5.01
1533 1840 1.226686 ACTTGCTCAAGCTGCTCACG 61.227 55.000 1.00 0.00 41.99 4.35
1615 1922 4.842139 GTGATCTACGACATCAAACACC 57.158 45.455 0.00 0.00 31.98 4.16
1912 2219 2.153645 TGTCTGGTGAATGTGTGATGC 58.846 47.619 0.00 0.00 0.00 3.91
1979 2286 4.406972 TCCCTCAATTGTGATACTCCTCAG 59.593 45.833 9.06 0.00 31.85 3.35
2105 2412 1.996191 GCTGATTCTTCACACGTCCTC 59.004 52.381 0.00 0.00 0.00 3.71
2114 2421 4.694509 TCTTCACACGTCCTCTAGAGTTAC 59.305 45.833 18.42 14.20 0.00 2.50
2161 2472 3.907474 TCTTTTGTCATGTACTCCCTCCA 59.093 43.478 0.00 0.00 0.00 3.86
2163 2474 4.487714 TTTGTCATGTACTCCCTCCATC 57.512 45.455 0.00 0.00 0.00 3.51
2164 2475 2.398588 TGTCATGTACTCCCTCCATCC 58.601 52.381 0.00 0.00 0.00 3.51
2165 2476 1.694696 GTCATGTACTCCCTCCATCCC 59.305 57.143 0.00 0.00 0.00 3.85
2166 2477 1.293763 TCATGTACTCCCTCCATCCCA 59.706 52.381 0.00 0.00 0.00 4.37
2167 2478 1.417890 CATGTACTCCCTCCATCCCAC 59.582 57.143 0.00 0.00 0.00 4.61
2169 2480 0.831307 GTACTCCCTCCATCCCACAC 59.169 60.000 0.00 0.00 0.00 3.82
2177 2488 4.140447 TCCCTCCATCCCACACTATAAGAT 60.140 45.833 0.00 0.00 0.00 2.40
2183 2494 6.055588 CCATCCCACACTATAAGATCGTTTT 58.944 40.000 0.00 0.00 0.00 2.43
2184 2495 6.542370 CCATCCCACACTATAAGATCGTTTTT 59.458 38.462 0.00 0.00 0.00 1.94
2185 2496 7.254795 CCATCCCACACTATAAGATCGTTTTTC 60.255 40.741 0.00 0.00 0.00 2.29
2186 2497 6.703319 TCCCACACTATAAGATCGTTTTTCA 58.297 36.000 0.00 0.00 0.00 2.69
2187 2498 7.162761 TCCCACACTATAAGATCGTTTTTCAA 58.837 34.615 0.00 0.00 0.00 2.69
2188 2499 7.333423 TCCCACACTATAAGATCGTTTTTCAAG 59.667 37.037 0.00 0.00 0.00 3.02
2190 2501 7.360861 CCACACTATAAGATCGTTTTTCAAGCA 60.361 37.037 0.00 0.00 0.00 3.91
2192 2503 8.564574 ACACTATAAGATCGTTTTTCAAGCAAA 58.435 29.630 0.00 0.00 0.00 3.68
2193 2504 8.840867 CACTATAAGATCGTTTTTCAAGCAAAC 58.159 33.333 0.00 0.00 0.00 2.93
2194 2505 8.564574 ACTATAAGATCGTTTTTCAAGCAAACA 58.435 29.630 0.00 0.00 34.33 2.83
2198 2509 5.858581 AGATCGTTTTTCAAGCAAACATAGC 59.141 36.000 0.00 0.00 34.33 2.97
2222 2533 9.643693 AGCTTGAAAAACAATCTTATATTGTGG 57.356 29.630 4.27 0.00 40.94 4.17
2223 2534 8.872845 GCTTGAAAAACAATCTTATATTGTGGG 58.127 33.333 4.27 0.00 40.94 4.61
2226 2537 8.240682 TGAAAAACAATCTTATATTGTGGGACG 58.759 33.333 4.27 0.00 40.94 4.79
2229 2540 5.611374 ACAATCTTATATTGTGGGACGGAG 58.389 41.667 2.72 0.00 40.37 4.63
2267 2578 4.515191 TGATTGCTTACTGTTCTGTGTTCC 59.485 41.667 0.00 0.00 0.00 3.62
2312 2634 3.506808 TGGGCTAACCATGGCAGT 58.493 55.556 13.04 0.00 46.80 4.40
2347 2669 7.607991 CCAATTCTATCACTAGTTGGTTCAAGT 59.392 37.037 0.00 0.00 31.24 3.16
2352 2674 8.188799 TCTATCACTAGTTGGTTCAAGTTATCG 58.811 37.037 0.00 0.00 0.00 2.92
2353 2675 6.092955 TCACTAGTTGGTTCAAGTTATCGT 57.907 37.500 0.00 0.00 0.00 3.73
2361 2777 9.578439 AGTTGGTTCAAGTTATCGTAGTATTAC 57.422 33.333 0.00 0.00 0.00 1.89
2378 2794 3.469008 TTACATAGGTCCATGCTTCCG 57.531 47.619 0.00 0.00 0.00 4.30
2386 2802 2.365582 GTCCATGCTTCCGTACCAATT 58.634 47.619 0.00 0.00 0.00 2.32
2407 2823 6.658188 ATTGGGTTCTTTTTGGTATCGAAA 57.342 33.333 0.00 0.00 0.00 3.46
2425 2841 9.106070 GTATCGAAATTACCAAGGACTGTATTT 57.894 33.333 0.00 0.00 0.00 1.40
2443 2892 4.934797 ATTTTGTGAAGAGGGGAGATGA 57.065 40.909 0.00 0.00 0.00 2.92
2450 2899 2.350863 AGAGGGGAGATGACCAAAGT 57.649 50.000 0.00 0.00 0.00 2.66
2476 2926 0.177604 CCCCAGTCATGAGCTCAGAC 59.822 60.000 26.05 26.05 0.00 3.51
2519 2971 7.095439 GGATAAGCTCAGCTGTTGTTCATATAC 60.095 40.741 14.67 2.43 39.62 1.47
2540 2992 5.886960 ACATTGTCAGGATTCTGTTTAGC 57.113 39.130 0.00 0.00 41.59 3.09
2575 3069 7.736447 GCATTTAGCAAGGACTGTCTATTAT 57.264 36.000 7.85 0.00 44.79 1.28
2576 3070 7.579726 GCATTTAGCAAGGACTGTCTATTATG 58.420 38.462 7.85 5.14 44.79 1.90
2577 3071 7.227512 GCATTTAGCAAGGACTGTCTATTATGT 59.772 37.037 7.85 0.00 44.79 2.29
2578 3072 9.764363 CATTTAGCAAGGACTGTCTATTATGTA 57.236 33.333 7.85 0.00 0.00 2.29
2581 3075 9.817809 TTAGCAAGGACTGTCTATTATGTAAAG 57.182 33.333 7.85 0.00 0.00 1.85
2582 3076 8.079211 AGCAAGGACTGTCTATTATGTAAAGA 57.921 34.615 7.85 0.00 0.00 2.52
2583 3077 8.540388 AGCAAGGACTGTCTATTATGTAAAGAA 58.460 33.333 7.85 0.00 0.00 2.52
2584 3078 8.821894 GCAAGGACTGTCTATTATGTAAAGAAG 58.178 37.037 7.85 0.00 0.00 2.85
2587 3081 8.417884 AGGACTGTCTATTATGTAAAGAAGAGC 58.582 37.037 7.85 0.00 0.00 4.09
2588 3082 8.198109 GGACTGTCTATTATGTAAAGAAGAGCA 58.802 37.037 7.85 0.00 0.00 4.26
2589 3083 9.587772 GACTGTCTATTATGTAAAGAAGAGCAA 57.412 33.333 0.00 0.00 0.00 3.91
2597 3091 6.851222 ATGTAAAGAAGAGCAATCATACCG 57.149 37.500 0.00 0.00 0.00 4.02
2598 3092 5.972935 TGTAAAGAAGAGCAATCATACCGA 58.027 37.500 0.00 0.00 0.00 4.69
2624 3118 9.862149 AAATAAGTCAAGAAACTTTCCCTAGAA 57.138 29.630 0.00 0.00 40.01 2.10
2630 3124 8.454894 GTCAAGAAACTTTCCCTAGAATTGATC 58.545 37.037 0.00 0.00 0.00 2.92
2633 3127 5.796502 AACTTTCCCTAGAATTGATCCCA 57.203 39.130 0.00 0.00 0.00 4.37
2651 3145 4.832248 TCCCAAGTCTCAACATCATGTAC 58.168 43.478 0.00 0.00 0.00 2.90
2652 3146 4.532126 TCCCAAGTCTCAACATCATGTACT 59.468 41.667 0.00 0.00 0.00 2.73
2653 3147 5.013079 TCCCAAGTCTCAACATCATGTACTT 59.987 40.000 0.00 0.00 32.06 2.24
2654 3148 6.212589 TCCCAAGTCTCAACATCATGTACTTA 59.787 38.462 3.78 0.00 31.32 2.24
2666 3160 5.864418 TCATGTACTTATGTACCAGGACC 57.136 43.478 14.44 0.00 46.19 4.46
2667 3161 5.274015 TCATGTACTTATGTACCAGGACCA 58.726 41.667 14.44 0.00 46.19 4.02
2681 3220 1.429687 AGGACCAGGTCAGTAGTCTGT 59.570 52.381 21.75 0.00 41.91 3.41
2743 3282 1.988107 AGTCTGGTCACACCCATCAAT 59.012 47.619 0.00 0.00 37.50 2.57
2749 3288 2.301346 GTCACACCCATCAATCCATCC 58.699 52.381 0.00 0.00 0.00 3.51
2761 3300 6.830324 CCATCAATCCATCCTCTTCTTTGTTA 59.170 38.462 0.00 0.00 0.00 2.41
2770 3309 6.783708 TCCTCTTCTTTGTTATCCTCTCTC 57.216 41.667 0.00 0.00 0.00 3.20
2782 3321 6.038382 TGTTATCCTCTCTCGTTCAGTCATAC 59.962 42.308 0.00 0.00 0.00 2.39
2783 3322 3.951663 TCCTCTCTCGTTCAGTCATACA 58.048 45.455 0.00 0.00 0.00 2.29
2784 3323 3.690139 TCCTCTCTCGTTCAGTCATACAC 59.310 47.826 0.00 0.00 0.00 2.90
2785 3324 3.692101 CCTCTCTCGTTCAGTCATACACT 59.308 47.826 0.00 0.00 34.67 3.55
2820 3361 4.896482 AGAGCGACCTCTCTAATTATGGTT 59.104 41.667 0.00 0.00 45.21 3.67
2821 3362 6.069331 AGAGCGACCTCTCTAATTATGGTTA 58.931 40.000 0.00 0.00 45.21 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.574428 GTGCGGGTTCACACATCAC 59.426 57.895 0.00 0.00 36.77 3.06
52 53 9.535170 TGTATTGAACCAGGATATTAAACCAAA 57.465 29.630 0.00 0.00 0.00 3.28
95 96 9.665264 CATGTCAATCATCAACTATCATGAAAG 57.335 33.333 0.00 0.00 34.09 2.62
114 115 9.667107 CTCTAGGTAATTTAGTTTCCATGTCAA 57.333 33.333 0.00 0.00 30.14 3.18
116 117 7.988028 AGCTCTAGGTAATTTAGTTTCCATGTC 59.012 37.037 0.00 0.00 30.14 3.06
149 156 1.153529 AACGCCACGAGACACACAA 60.154 52.632 0.00 0.00 0.00 3.33
160 167 1.720852 CTAGCAAAAATGCAACGCCAC 59.279 47.619 3.41 0.00 37.25 5.01
168 175 2.012937 TGCCATGCTAGCAAAAATGC 57.987 45.000 23.54 18.73 37.28 3.56
180 187 5.917541 CATGGAAGAAAAATATGCCATGC 57.082 39.130 0.00 0.00 44.10 4.06
185 192 8.937634 ATGTTTCTCATGGAAGAAAAATATGC 57.062 30.769 10.29 0.54 44.54 3.14
198 205 9.000859 CATGGCAATGAAACATGTTTCTCATGG 62.001 40.741 37.76 27.88 45.29 3.66
203 210 4.040706 ACCATGGCAATGAAACATGTTTCT 59.959 37.500 37.76 25.90 46.67 2.52
215 222 3.129287 GGAGAAGTACAACCATGGCAATG 59.871 47.826 13.04 11.41 0.00 2.82
244 251 1.208358 GGCACTAAAAACGGACCGC 59.792 57.895 15.39 0.00 0.00 5.68
250 257 6.436843 AAAGATCCTATGGCACTAAAAACG 57.563 37.500 0.00 0.00 0.00 3.60
277 284 2.992124 TGAAACCCGACTCTTGTGAA 57.008 45.000 0.00 0.00 0.00 3.18
278 285 3.485463 AATGAAACCCGACTCTTGTGA 57.515 42.857 0.00 0.00 0.00 3.58
296 303 6.038356 CGGTGAAAAGATACACTACGGTAAT 58.962 40.000 0.00 0.00 37.22 1.89
299 306 3.841643 CGGTGAAAAGATACACTACGGT 58.158 45.455 0.00 0.00 37.22 4.83
301 308 2.278094 CGCGGTGAAAAGATACACTACG 59.722 50.000 0.00 0.00 37.22 3.51
302 309 3.302699 GTCGCGGTGAAAAGATACACTAC 59.697 47.826 6.13 0.00 37.22 2.73
344 351 8.019656 TGGGAGTAAAAATAGGCTAGACTTAG 57.980 38.462 1.68 0.00 0.00 2.18
350 357 6.591935 TGACATGGGAGTAAAAATAGGCTAG 58.408 40.000 0.00 0.00 0.00 3.42
353 360 6.715347 ATTGACATGGGAGTAAAAATAGGC 57.285 37.500 0.00 0.00 0.00 3.93
367 374 4.880886 TGCAACGAAGATATTGACATGG 57.119 40.909 0.00 0.00 0.00 3.66
368 375 5.512788 GGTTTGCAACGAAGATATTGACATG 59.487 40.000 0.00 0.00 0.00 3.21
373 380 3.845775 CGTGGTTTGCAACGAAGATATTG 59.154 43.478 0.00 0.00 44.42 1.90
379 386 0.591170 ATCCGTGGTTTGCAACGAAG 59.409 50.000 10.13 1.09 44.42 3.79
416 423 7.555306 ACGCTTTTCTTTAGTCTTCTTCTTT 57.445 32.000 0.00 0.00 0.00 2.52
444 453 5.534207 TGGTCAATGCAAGTCTTCATTTT 57.466 34.783 0.00 0.00 31.15 1.82
468 477 3.296854 GAGGGTTTTCTTTGACTTGGGT 58.703 45.455 0.00 0.00 0.00 4.51
490 499 0.891373 TCTTCGGCTCTTCCAGTCAG 59.109 55.000 0.00 0.00 34.01 3.51
492 501 0.174617 CCTCTTCGGCTCTTCCAGTC 59.825 60.000 0.00 0.00 34.01 3.51
503 512 2.159170 TGGTTTTGTTTTGCCTCTTCGG 60.159 45.455 0.00 0.00 0.00 4.30
504 513 3.157932 TGGTTTTGTTTTGCCTCTTCG 57.842 42.857 0.00 0.00 0.00 3.79
510 519 5.703876 TGAACAATTTGGTTTTGTTTTGCC 58.296 33.333 0.78 0.00 44.90 4.52
539 548 1.869774 CAAGGAAAACAAGGGCAAGC 58.130 50.000 0.00 0.00 0.00 4.01
566 575 1.630369 CAGGTCAGGACTGGATTGGAA 59.370 52.381 0.00 0.00 32.38 3.53
567 576 1.203300 TCAGGTCAGGACTGGATTGGA 60.203 52.381 0.00 0.00 36.62 3.53
568 577 1.065854 GTCAGGTCAGGACTGGATTGG 60.066 57.143 0.00 0.00 36.62 3.16
974 1281 1.378531 CCGGGCATCAAAGATTCGAA 58.621 50.000 0.00 0.00 0.00 3.71
1615 1922 4.643463 AGGCTATTGCAGAATCTCATCAG 58.357 43.478 0.66 0.00 41.91 2.90
1704 2011 1.068921 GAGCAGAGAATCGGAGCCC 59.931 63.158 0.00 0.00 42.67 5.19
1912 2219 6.426328 GTGTCAAGCAAGAGGATATAATCAGG 59.574 42.308 0.00 0.00 0.00 3.86
1979 2286 7.571428 GCAGTCATCTAACCTAAACAAACTCAC 60.571 40.741 0.00 0.00 0.00 3.51
2105 2412 8.534333 TTTTGCTATCAAGTGTGTAACTCTAG 57.466 34.615 0.00 0.00 40.23 2.43
2114 2421 6.498304 AGTGTTCTTTTTGCTATCAAGTGTG 58.502 36.000 0.00 0.00 33.12 3.82
2161 2472 7.335627 TGAAAAACGATCTTATAGTGTGGGAT 58.664 34.615 0.00 0.00 0.00 3.85
2163 2474 6.978343 TGAAAAACGATCTTATAGTGTGGG 57.022 37.500 0.00 0.00 0.00 4.61
2164 2475 6.961554 GCTTGAAAAACGATCTTATAGTGTGG 59.038 38.462 0.00 0.00 0.00 4.17
2165 2476 7.518161 TGCTTGAAAAACGATCTTATAGTGTG 58.482 34.615 0.00 0.00 0.00 3.82
2166 2477 7.667043 TGCTTGAAAAACGATCTTATAGTGT 57.333 32.000 0.00 0.00 0.00 3.55
2167 2478 8.840867 GTTTGCTTGAAAAACGATCTTATAGTG 58.159 33.333 0.00 0.00 0.00 2.74
2169 2480 8.948853 TGTTTGCTTGAAAAACGATCTTATAG 57.051 30.769 0.00 0.00 39.81 1.31
2177 2488 5.181690 AGCTATGTTTGCTTGAAAAACGA 57.818 34.783 0.00 0.00 39.81 3.85
2187 2498 7.412137 GATTGTTTTTCAAGCTATGTTTGCT 57.588 32.000 0.00 0.00 43.32 3.91
2201 2512 7.700656 CCGTCCCACAATATAAGATTGTTTTTC 59.299 37.037 0.00 0.00 39.94 2.29
2202 2513 7.394923 TCCGTCCCACAATATAAGATTGTTTTT 59.605 33.333 0.00 0.00 39.94 1.94
2203 2514 6.887545 TCCGTCCCACAATATAAGATTGTTTT 59.112 34.615 0.00 0.00 39.94 2.43
2207 2518 4.997395 CCTCCGTCCCACAATATAAGATTG 59.003 45.833 0.00 0.00 35.29 2.67
2208 2519 4.041691 CCCTCCGTCCCACAATATAAGATT 59.958 45.833 0.00 0.00 0.00 2.40
2209 2520 3.583086 CCCTCCGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
2219 2530 2.305858 ATATACTCCCTCCGTCCCAC 57.694 55.000 0.00 0.00 0.00 4.61
2220 2531 2.991713 ACTATATACTCCCTCCGTCCCA 59.008 50.000 0.00 0.00 0.00 4.37
2221 2532 3.245193 ACACTATATACTCCCTCCGTCCC 60.245 52.174 0.00 0.00 0.00 4.46
2222 2533 4.031636 ACACTATATACTCCCTCCGTCC 57.968 50.000 0.00 0.00 0.00 4.79
2223 2534 5.068636 TCAACACTATATACTCCCTCCGTC 58.931 45.833 0.00 0.00 0.00 4.79
2226 2537 6.014156 AGCAATCAACACTATATACTCCCTCC 60.014 42.308 0.00 0.00 0.00 4.30
2229 2540 8.368668 AGTAAGCAATCAACACTATATACTCCC 58.631 37.037 0.00 0.00 0.00 4.30
2259 2570 3.058914 GTGATTCCTCAAACGGAACACAG 60.059 47.826 14.54 0.00 45.24 3.66
2267 2578 2.629051 GGGTAGGTGATTCCTCAAACG 58.371 52.381 0.00 0.00 44.42 3.60
2312 2634 6.897966 ACTAGTGATAGAATTGGAGTCCTTGA 59.102 38.462 11.33 0.00 0.00 3.02
2347 2669 8.464404 GCATGGACCTATGTAATACTACGATAA 58.536 37.037 0.00 0.00 0.00 1.75
2352 2674 7.097834 GGAAGCATGGACCTATGTAATACTAC 58.902 42.308 0.00 0.00 0.00 2.73
2353 2675 6.071560 CGGAAGCATGGACCTATGTAATACTA 60.072 42.308 0.00 0.00 0.00 1.82
2361 2777 2.548067 GGTACGGAAGCATGGACCTATG 60.548 54.545 0.00 0.00 0.00 2.23
2386 2802 6.658188 AATTTCGATACCAAAAAGAACCCA 57.342 33.333 0.00 0.00 0.00 4.51
2401 2817 8.458843 CAAAATACAGTCCTTGGTAATTTCGAT 58.541 33.333 0.00 0.00 0.00 3.59
2407 2823 7.942341 TCTTCACAAAATACAGTCCTTGGTAAT 59.058 33.333 0.00 0.00 0.00 1.89
2425 2841 1.909302 GGTCATCTCCCCTCTTCACAA 59.091 52.381 0.00 0.00 0.00 3.33
2456 2906 0.979709 TCTGAGCTCATGACTGGGGG 60.980 60.000 18.63 1.85 0.00 5.40
2457 2907 0.177604 GTCTGAGCTCATGACTGGGG 59.822 60.000 26.07 12.16 0.00 4.96
2476 2926 5.508825 GCTTATCCTGGTCTATGACACAGAG 60.509 48.000 13.68 0.00 34.88 3.35
2487 2939 1.761784 CAGCTGAGCTTATCCTGGTCT 59.238 52.381 8.42 0.00 36.40 3.85
2519 2971 6.149973 TGAAGCTAAACAGAATCCTGACAATG 59.850 38.462 0.00 0.00 43.02 2.82
2540 2992 8.844244 AGTCCTTGCTAAATGCTAATTATGAAG 58.156 33.333 0.00 0.00 43.37 3.02
2571 3065 8.993121 CGGTATGATTGCTCTTCTTTACATAAT 58.007 33.333 0.00 0.00 0.00 1.28
2572 3066 8.201464 TCGGTATGATTGCTCTTCTTTACATAA 58.799 33.333 0.00 0.00 0.00 1.90
2573 3067 7.722363 TCGGTATGATTGCTCTTCTTTACATA 58.278 34.615 0.00 0.00 0.00 2.29
2574 3068 6.582636 TCGGTATGATTGCTCTTCTTTACAT 58.417 36.000 0.00 0.00 0.00 2.29
2575 3069 5.972935 TCGGTATGATTGCTCTTCTTTACA 58.027 37.500 0.00 0.00 0.00 2.41
2576 3070 6.903883 TTCGGTATGATTGCTCTTCTTTAC 57.096 37.500 0.00 0.00 0.00 2.01
2577 3071 9.607988 TTATTTCGGTATGATTGCTCTTCTTTA 57.392 29.630 0.00 0.00 0.00 1.85
2578 3072 8.506168 TTATTTCGGTATGATTGCTCTTCTTT 57.494 30.769 0.00 0.00 0.00 2.52
2579 3073 7.770897 ACTTATTTCGGTATGATTGCTCTTCTT 59.229 33.333 0.00 0.00 0.00 2.52
2580 3074 7.275920 ACTTATTTCGGTATGATTGCTCTTCT 58.724 34.615 0.00 0.00 0.00 2.85
2581 3075 7.224753 TGACTTATTTCGGTATGATTGCTCTTC 59.775 37.037 0.00 0.00 0.00 2.87
2582 3076 7.047891 TGACTTATTTCGGTATGATTGCTCTT 58.952 34.615 0.00 0.00 0.00 2.85
2583 3077 6.582636 TGACTTATTTCGGTATGATTGCTCT 58.417 36.000 0.00 0.00 0.00 4.09
2584 3078 6.844696 TGACTTATTTCGGTATGATTGCTC 57.155 37.500 0.00 0.00 0.00 4.26
2585 3079 7.047891 TCTTGACTTATTTCGGTATGATTGCT 58.952 34.615 0.00 0.00 0.00 3.91
2586 3080 7.246674 TCTTGACTTATTTCGGTATGATTGC 57.753 36.000 0.00 0.00 0.00 3.56
2587 3081 9.490663 GTTTCTTGACTTATTTCGGTATGATTG 57.509 33.333 0.00 0.00 0.00 2.67
2588 3082 9.449719 AGTTTCTTGACTTATTTCGGTATGATT 57.550 29.630 0.00 0.00 0.00 2.57
2589 3083 9.449719 AAGTTTCTTGACTTATTTCGGTATGAT 57.550 29.630 0.00 0.00 38.06 2.45
2590 3084 8.842358 AAGTTTCTTGACTTATTTCGGTATGA 57.158 30.769 0.00 0.00 38.06 2.15
2591 3085 9.543018 GAAAGTTTCTTGACTTATTTCGGTATG 57.457 33.333 8.41 0.00 38.86 2.39
2592 3086 8.727910 GGAAAGTTTCTTGACTTATTTCGGTAT 58.272 33.333 15.05 0.00 38.86 2.73
2593 3087 7.173735 GGGAAAGTTTCTTGACTTATTTCGGTA 59.826 37.037 15.05 0.00 38.86 4.02
2594 3088 6.016527 GGGAAAGTTTCTTGACTTATTTCGGT 60.017 38.462 15.05 0.00 38.86 4.69
2595 3089 6.206829 AGGGAAAGTTTCTTGACTTATTTCGG 59.793 38.462 15.05 0.00 38.86 4.30
2596 3090 7.203255 AGGGAAAGTTTCTTGACTTATTTCG 57.797 36.000 15.05 0.00 38.86 3.46
2597 3091 9.503399 TCTAGGGAAAGTTTCTTGACTTATTTC 57.497 33.333 15.05 0.00 38.86 2.17
2598 3092 9.862149 TTCTAGGGAAAGTTTCTTGACTTATTT 57.138 29.630 15.05 0.00 38.86 1.40
2624 3118 5.183530 TGATGTTGAGACTTGGGATCAAT 57.816 39.130 0.00 0.00 35.56 2.57
2625 3119 4.639078 TGATGTTGAGACTTGGGATCAA 57.361 40.909 0.00 0.00 0.00 2.57
2630 3124 4.836825 AGTACATGATGTTGAGACTTGGG 58.163 43.478 2.29 0.00 0.00 4.12
2651 3145 3.104512 TGACCTGGTCCTGGTACATAAG 58.895 50.000 23.42 0.00 38.20 1.73
2652 3146 3.104512 CTGACCTGGTCCTGGTACATAA 58.895 50.000 23.42 0.35 38.20 1.90
2653 3147 2.043939 ACTGACCTGGTCCTGGTACATA 59.956 50.000 23.42 6.90 38.20 2.29
2654 3148 1.203313 ACTGACCTGGTCCTGGTACAT 60.203 52.381 23.42 6.03 38.20 2.29
2666 3160 2.752354 CCTCAGACAGACTACTGACCTG 59.248 54.545 0.00 0.00 46.03 4.00
2667 3161 2.645297 TCCTCAGACAGACTACTGACCT 59.355 50.000 0.00 0.00 46.03 3.85
2711 3250 1.006162 GACCAGACTACCAGAGAGGGT 59.994 57.143 0.00 0.00 43.89 4.34
2743 3282 5.966935 AGAGGATAACAAAGAAGAGGATGGA 59.033 40.000 0.00 0.00 0.00 3.41
2749 3288 6.202516 ACGAGAGAGGATAACAAAGAAGAG 57.797 41.667 0.00 0.00 0.00 2.85
2761 3300 4.336993 GTGTATGACTGAACGAGAGAGGAT 59.663 45.833 0.00 0.00 0.00 3.24
2770 3309 4.806330 ACTACCAAGTGTATGACTGAACG 58.194 43.478 0.00 0.00 34.02 3.95
2782 3321 3.184581 GTCGCTCTCAAAACTACCAAGTG 59.815 47.826 0.00 0.00 35.62 3.16
2783 3322 3.391049 GTCGCTCTCAAAACTACCAAGT 58.609 45.455 0.00 0.00 37.65 3.16
2784 3323 2.737252 GGTCGCTCTCAAAACTACCAAG 59.263 50.000 0.00 0.00 0.00 3.61
2785 3324 2.367567 AGGTCGCTCTCAAAACTACCAA 59.632 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.