Multiple sequence alignment - TraesCS6A01G217000

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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 TraesCS6A01G217000 chr6A 100.000 2706 0 0 1 2706 399700429 399697724 0.000000e+00 4998.0
1 TraesCS6A01G217000 chr6D 88.693 2724 202 37 1 2706 276681585 276684220 0.000000e+00 3227.0
2 TraesCS6A01G217000 chr6B 91.779 1265 63 18 571 1826 438406292 438407524 0.000000e+00 1722.0
3 TraesCS6A01G217000 chr6B 93.189 323 18 1 1828 2150 438407686 438408004 3.150000e-129 472.0
4 TraesCS6A01G217000 chr4B 82.759 87 13 2 784 869 285576766 285576681 2.890000e-10 76.8
5 TraesCS6A01G217000 chr3A 89.583 48 5 0 301 348 50361643 50361690 8.090000e-06 62.1
6 TraesCS6A01G217000 chr7A 97.059 34 1 0 2182 2215 712673623 712673590 1.050000e-04 58.4
7 TraesCS6A01G217000 chr4A 100.000 31 0 0 784 814 255338356 255338326 1.050000e-04 58.4
8 TraesCS6A01G217000 chr1A 100.000 28 0 0 786 813 24947295 24947268 5.000000e-03 52.8


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 TraesCS6A01G217000 chr6A 399697724 399700429 2705 True 4998 4998 100.000 1 2706 1 chr6A.!!$R1 2705
1 TraesCS6A01G217000 chr6D 276681585 276684220 2635 False 3227 3227 88.693 1 2706 1 chr6D.!!$F1 2705
2 TraesCS6A01G217000 chr6B 438406292 438408004 1712 False 1097 1722 92.484 571 2150 2 chr6B.!!$F1 1579

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
365 367 0.249489 CACTGCCCTACGCCTCATAC 60.249 60.0 0.0 0.0 36.24 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2343 0.18135 CCCAGGGATGCTAGGTTGTC 59.819 60.0 0.0 0.0 0.0 3.18 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
45 46 7.481275 TTTTTCATTTTTGAGAAGCACATCC 57.519 32.000 0.00 0.00 0.00 3.51
113 114 7.777910 TGATTTTTGTCTTCTCCAAAACCTAGA 59.222 33.333 0.00 0.00 40.44 2.43
159 160 6.056090 AGAAAGCCAACTAAAACCCAAAAA 57.944 33.333 0.00 0.00 0.00 1.94
161 162 5.429681 AAGCCAACTAAAACCCAAAAACT 57.570 34.783 0.00 0.00 0.00 2.66
162 163 5.018539 AGCCAACTAAAACCCAAAAACTC 57.981 39.130 0.00 0.00 0.00 3.01
166 168 6.422701 GCCAACTAAAACCCAAAAACTCATAC 59.577 38.462 0.00 0.00 0.00 2.39
168 170 7.651704 CCAACTAAAACCCAAAAACTCATACAG 59.348 37.037 0.00 0.00 0.00 2.74
171 173 8.973182 ACTAAAACCCAAAAACTCATACAGAAA 58.027 29.630 0.00 0.00 0.00 2.52
197 199 0.329596 AAAATTGAGAGGGAGCGCCT 59.670 50.000 2.29 0.00 0.00 5.52
215 217 1.269051 CCTAGCACGCGACATGTGATA 60.269 52.381 15.93 1.59 39.73 2.15
223 225 1.868109 GCGACATGTGATAGCGGCTAA 60.868 52.381 14.54 0.00 0.00 3.09
224 226 2.469826 CGACATGTGATAGCGGCTAAA 58.530 47.619 14.54 2.65 0.00 1.85
235 237 2.750237 GGCTAAACGTGCCCCCAG 60.750 66.667 4.06 0.00 44.32 4.45
258 260 3.129988 GGCATCCAAAATGACCTCTGAAG 59.870 47.826 0.00 0.00 0.00 3.02
290 292 5.752650 AGGGGATAACCTTTAGTTAGTTGC 58.247 41.667 0.00 0.00 44.07 4.17
295 297 6.476053 GGATAACCTTTAGTTAGTTGCTCTCG 59.524 42.308 0.00 0.00 44.07 4.04
299 301 4.691216 CCTTTAGTTAGTTGCTCTCGCTTT 59.309 41.667 0.00 0.00 36.97 3.51
301 303 6.035112 CCTTTAGTTAGTTGCTCTCGCTTTAG 59.965 42.308 0.00 0.00 36.97 1.85
314 316 1.276622 GCTTTAGGGAGGTGGTCAGA 58.723 55.000 0.00 0.00 0.00 3.27
318 320 2.940514 TAGGGAGGTGGTCAGATCAA 57.059 50.000 0.00 0.00 0.00 2.57
328 330 3.058914 GTGGTCAGATCAAACAAGTTCGG 60.059 47.826 0.00 0.00 0.00 4.30
350 352 1.000060 CAGGCATCCAACCAAACACTG 60.000 52.381 0.00 0.00 0.00 3.66
356 358 0.958822 CCAACCAAACACTGCCCTAC 59.041 55.000 0.00 0.00 0.00 3.18
364 366 0.686441 ACACTGCCCTACGCCTCATA 60.686 55.000 0.00 0.00 36.24 2.15
365 367 0.249489 CACTGCCCTACGCCTCATAC 60.249 60.000 0.00 0.00 36.24 2.39
368 370 2.880380 GCCCTACGCCTCATACCCC 61.880 68.421 0.00 0.00 0.00 4.95
371 373 1.129058 CCTACGCCTCATACCCCTTT 58.871 55.000 0.00 0.00 0.00 3.11
395 397 0.603707 CACAGTGACCATGCGAAGGT 60.604 55.000 0.00 0.00 43.46 3.50
398 400 2.224426 ACAGTGACCATGCGAAGGTTTA 60.224 45.455 0.00 0.00 40.09 2.01
405 407 3.118738 ACCATGCGAAGGTTTAGAGTAGG 60.119 47.826 0.00 0.00 35.33 3.18
411 413 4.039366 GCGAAGGTTTAGAGTAGGGATCAT 59.961 45.833 0.00 0.00 0.00 2.45
423 425 5.440610 AGTAGGGATCATCCATGACAAAAC 58.559 41.667 5.89 0.00 40.03 2.43
427 429 4.891756 GGGATCATCCATGACAAAACAGAT 59.108 41.667 5.89 0.00 40.03 2.90
455 457 2.664081 CCAGGACTCCAGTGGCTCC 61.664 68.421 15.03 15.03 0.00 4.70
478 480 1.242076 GAAGGCTTCAAGCAGCTTGA 58.758 50.000 30.44 30.44 46.93 3.02
489 491 6.330004 TCAAGCAGCTTGAAAATGTATTCA 57.670 33.333 31.66 7.91 45.84 2.57
509 511 4.370049 TCAATGCATCCATTTTTATGGCG 58.630 39.130 0.00 0.00 39.60 5.69
544 546 6.309251 CACCAATGACACACTTTAAAACGTTT 59.691 34.615 7.96 7.96 0.00 3.60
545 547 7.485277 CACCAATGACACACTTTAAAACGTTTA 59.515 33.333 15.03 0.00 0.00 2.01
546 548 8.027771 ACCAATGACACACTTTAAAACGTTTAA 58.972 29.630 15.03 4.98 0.00 1.52
547 549 8.861101 CCAATGACACACTTTAAAACGTTTAAA 58.139 29.630 15.03 13.14 0.00 1.52
582 584 8.565896 AAAGAATAGCTCATTGACACAACATA 57.434 30.769 0.00 0.00 0.00 2.29
644 649 2.540265 AGCTTGAGATTATCTGCGGG 57.460 50.000 0.00 0.00 34.69 6.13
697 702 6.909550 ATTCAAAGCCCAACTTGTGTTATA 57.090 33.333 0.00 0.00 39.09 0.98
703 708 9.730420 CAAAGCCCAACTTGTGTTATATATTAC 57.270 33.333 0.00 0.00 39.09 1.89
779 793 8.776376 AACATGGGTTGATGTTTGATATTTTC 57.224 30.769 0.00 0.00 42.69 2.29
781 795 8.596293 ACATGGGTTGATGTTTGATATTTTCTT 58.404 29.630 0.00 0.00 32.38 2.52
822 836 9.462174 CATTTTAAAATGTGCTACAGAAGTTCA 57.538 29.630 26.14 0.00 40.61 3.18
884 898 1.821258 CCTCTTGGGGCTACGGTAC 59.179 63.158 0.00 0.00 0.00 3.34
957 973 4.627058 TCTTGCGTTCTCAAACACTGATA 58.373 39.130 0.00 0.00 34.93 2.15
958 974 5.237815 TCTTGCGTTCTCAAACACTGATAT 58.762 37.500 0.00 0.00 34.93 1.63
959 975 5.348724 TCTTGCGTTCTCAAACACTGATATC 59.651 40.000 0.00 0.00 34.93 1.63
960 976 3.612423 TGCGTTCTCAAACACTGATATCG 59.388 43.478 0.00 0.00 34.93 2.92
961 977 3.857665 GCGTTCTCAAACACTGATATCGA 59.142 43.478 0.00 0.00 34.93 3.59
1071 1087 0.103208 GCTCCTTGGATGACGACGAT 59.897 55.000 0.00 0.00 0.00 3.73
1075 1091 1.404181 CCTTGGATGACGACGATGTGT 60.404 52.381 0.00 0.00 0.00 3.72
1286 1306 1.278985 TCCTGCTGTCCATTGATCGTT 59.721 47.619 0.00 0.00 0.00 3.85
1973 2153 3.325425 TCAAAAGTGTGGATAAGTCCCGA 59.675 43.478 0.00 0.00 44.41 5.14
1980 2160 3.181442 TGTGGATAAGTCCCGAAAACCAA 60.181 43.478 0.00 0.00 44.41 3.67
2079 2259 3.055458 TCATTCATGTCTTGTCCGGCTAA 60.055 43.478 0.00 0.00 0.00 3.09
2099 2279 5.748630 GCTAATTTTGTTCCATTCCGAATCC 59.251 40.000 0.00 0.00 0.00 3.01
2100 2280 3.840890 TTTTGTTCCATTCCGAATCCG 57.159 42.857 0.00 0.00 0.00 4.18
2122 2302 3.777910 GTTCCTTCCGGCCGCCTA 61.778 66.667 22.85 3.89 0.00 3.93
2125 2305 2.591715 CCTTCCGGCCGCCTAATG 60.592 66.667 22.85 4.77 0.00 1.90
2133 2313 0.107831 GGCCGCCTAATGTGTGGATA 59.892 55.000 0.71 0.00 35.32 2.59
2141 2321 4.611943 CCTAATGTGTGGATAGAGTGACG 58.388 47.826 0.00 0.00 0.00 4.35
2163 2343 1.445716 CTACGCCACTAGAGACCGGG 61.446 65.000 6.32 0.00 0.00 5.73
2165 2345 2.772691 CGCCACTAGAGACCGGGAC 61.773 68.421 6.32 0.00 0.00 4.46
2174 2354 1.229082 AGACCGGGACAACCTAGCA 60.229 57.895 6.32 0.00 36.97 3.49
2175 2355 0.617820 AGACCGGGACAACCTAGCAT 60.618 55.000 6.32 0.00 36.97 3.79
2180 2360 0.181350 GGGACAACCTAGCATCCCTG 59.819 60.000 10.20 0.00 46.43 4.45
2196 2376 1.452108 CTGGGAGGCCGAAATCACC 60.452 63.158 0.00 0.00 0.00 4.02
2202 2382 0.899720 AGGCCGAAATCACCGTTCTA 59.100 50.000 0.00 0.00 0.00 2.10
2210 2390 5.445939 CCGAAATCACCGTTCTAATCTTGTG 60.446 44.000 0.00 0.00 0.00 3.33
2230 2410 4.760204 TGTGAGAACTCTTCATCACTCGTA 59.240 41.667 5.84 0.00 38.01 3.43
2233 2413 5.049398 AGAACTCTTCATCACTCGTACAC 57.951 43.478 0.00 0.00 0.00 2.90
2235 2415 2.812591 ACTCTTCATCACTCGTACACGT 59.187 45.455 1.19 0.00 40.80 4.49
2245 2425 8.588789 TCATCACTCGTACACGTAATTATTTTG 58.411 33.333 1.19 0.00 40.80 2.44
2290 2470 3.591835 CACAGCCCGTGCCGTTTT 61.592 61.111 0.00 0.00 39.19 2.43
2315 2495 3.849911 TGAACATGAAAACGCCAAACAA 58.150 36.364 0.00 0.00 0.00 2.83
2320 2500 1.208259 GAAAACGCCAAACAAGCCAG 58.792 50.000 0.00 0.00 0.00 4.85
2334 2514 4.047059 CCAGCAACCAAGCCAGCG 62.047 66.667 0.00 0.00 34.23 5.18
2335 2515 4.712425 CAGCAACCAAGCCAGCGC 62.712 66.667 0.00 0.00 34.23 5.92
2352 2532 4.641645 CTGGTGCCTTGGCCGACA 62.642 66.667 9.35 4.73 0.00 4.35
2355 2535 2.594592 GTGCCTTGGCCGACAGTT 60.595 61.111 9.35 0.00 0.00 3.16
2376 2556 4.093952 CCTCGCTGGCGTTGCAAG 62.094 66.667 14.55 4.48 40.74 4.01
2377 2557 3.349006 CTCGCTGGCGTTGCAAGT 61.349 61.111 14.55 0.00 40.74 3.16
2382 2562 1.726865 CTGGCGTTGCAAGTTGACA 59.273 52.632 7.16 0.00 0.00 3.58
2386 2566 0.310543 GCGTTGCAAGTTGACATGGA 59.689 50.000 7.16 0.00 0.00 3.41
2402 2586 0.539438 TGGATTGAAACGCCAAGGCT 60.539 50.000 9.73 0.00 39.32 4.58
2440 2624 0.965363 CAAACGCCAAGGCCTATGGT 60.965 55.000 25.51 12.56 40.23 3.55
2448 2632 2.555227 CCAAGGCCTATGGTGTTTCTGT 60.555 50.000 20.06 0.00 33.08 3.41
2450 2634 3.525800 AGGCCTATGGTGTTTCTGTTT 57.474 42.857 1.29 0.00 0.00 2.83
2453 2637 5.010282 AGGCCTATGGTGTTTCTGTTTTAG 58.990 41.667 1.29 0.00 0.00 1.85
2478 2662 3.297134 TTAAATGGTGATGGGGCTCTC 57.703 47.619 0.00 0.00 0.00 3.20
2480 2664 1.229131 AATGGTGATGGGGCTCTCAT 58.771 50.000 0.00 0.00 0.00 2.90
2482 2666 1.348008 TGGTGATGGGGCTCTCATCC 61.348 60.000 11.20 4.59 40.02 3.51
2484 2668 0.179034 GTGATGGGGCTCTCATCCAC 60.179 60.000 11.20 7.04 40.02 4.02
2491 2675 0.835941 GGCTCTCATCCACCACTCAT 59.164 55.000 0.00 0.00 0.00 2.90
2497 2681 2.498885 CTCATCCACCACTCATCACTCA 59.501 50.000 0.00 0.00 0.00 3.41
2502 2686 2.301296 CCACCACTCATCACTCACTCTT 59.699 50.000 0.00 0.00 0.00 2.85
2508 2692 5.279406 CCACTCATCACTCACTCTTTTCTCT 60.279 44.000 0.00 0.00 0.00 3.10
2509 2693 6.222389 CACTCATCACTCACTCTTTTCTCTT 58.778 40.000 0.00 0.00 0.00 2.85
2510 2694 6.705381 CACTCATCACTCACTCTTTTCTCTTT 59.295 38.462 0.00 0.00 0.00 2.52
2511 2695 7.226325 CACTCATCACTCACTCTTTTCTCTTTT 59.774 37.037 0.00 0.00 0.00 2.27
2512 2696 7.226325 ACTCATCACTCACTCTTTTCTCTTTTG 59.774 37.037 0.00 0.00 0.00 2.44
2517 2701 5.946377 ACTCACTCTTTTCTCTTTTGTTGGT 59.054 36.000 0.00 0.00 0.00 3.67
2520 2704 7.335627 TCACTCTTTTCTCTTTTGTTGGTCTA 58.664 34.615 0.00 0.00 0.00 2.59
2524 2708 8.980481 TCTTTTCTCTTTTGTTGGTCTATCTT 57.020 30.769 0.00 0.00 0.00 2.40
2530 2714 5.934625 TCTTTTGTTGGTCTATCTTCAGCTC 59.065 40.000 0.00 0.00 0.00 4.09
2536 2720 2.433970 GGTCTATCTTCAGCTCTTGCCT 59.566 50.000 0.00 0.00 40.80 4.75
2540 2724 5.064579 GTCTATCTTCAGCTCTTGCCTTTTC 59.935 44.000 0.00 0.00 40.80 2.29
2543 2727 2.664402 TCAGCTCTTGCCTTTTCCTT 57.336 45.000 0.00 0.00 40.80 3.36
2544 2728 2.233271 TCAGCTCTTGCCTTTTCCTTG 58.767 47.619 0.00 0.00 40.80 3.61
2548 2732 3.452264 AGCTCTTGCCTTTTCCTTGTTTT 59.548 39.130 0.00 0.00 40.80 2.43
2556 2740 4.499865 GCCTTTTCCTTGTTTTGTCTCCTC 60.500 45.833 0.00 0.00 0.00 3.71
2573 2757 3.583086 CTCCTCCACTTAAACCCTCTCAA 59.417 47.826 0.00 0.00 0.00 3.02
2576 2760 5.074515 TCCTCCACTTAAACCCTCTCAAATT 59.925 40.000 0.00 0.00 0.00 1.82
2577 2761 5.416013 CCTCCACTTAAACCCTCTCAAATTC 59.584 44.000 0.00 0.00 0.00 2.17
2580 2764 7.751646 TCCACTTAAACCCTCTCAAATTCTTA 58.248 34.615 0.00 0.00 0.00 2.10
2583 2767 8.507249 CACTTAAACCCTCTCAAATTCTTACAG 58.493 37.037 0.00 0.00 0.00 2.74
2594 2778 5.580691 TCAAATTCTTACAGATCGATTGCGT 59.419 36.000 0.00 0.00 38.98 5.24
2595 2779 6.092122 TCAAATTCTTACAGATCGATTGCGTT 59.908 34.615 0.00 0.00 38.98 4.84
2596 2780 4.840401 TTCTTACAGATCGATTGCGTTG 57.160 40.909 0.00 0.00 38.98 4.10
2597 2781 3.186909 TCTTACAGATCGATTGCGTTGG 58.813 45.455 0.00 0.00 38.98 3.77
2598 2782 2.665649 TACAGATCGATTGCGTTGGT 57.334 45.000 0.00 0.00 38.98 3.67
2599 2783 1.359848 ACAGATCGATTGCGTTGGTC 58.640 50.000 0.00 0.00 38.98 4.02
2600 2784 0.652592 CAGATCGATTGCGTTGGTCC 59.347 55.000 0.00 0.00 38.98 4.46
2601 2785 0.806102 AGATCGATTGCGTTGGTCCG 60.806 55.000 0.00 0.00 38.98 4.79
2602 2786 1.079405 ATCGATTGCGTTGGTCCGT 60.079 52.632 0.00 0.00 38.98 4.69
2603 2787 0.672401 ATCGATTGCGTTGGTCCGTT 60.672 50.000 0.00 0.00 38.98 4.44
2604 2788 0.038435 TCGATTGCGTTGGTCCGTTA 60.038 50.000 0.00 0.00 38.98 3.18
2605 2789 0.791422 CGATTGCGTTGGTCCGTTAA 59.209 50.000 0.00 0.00 0.00 2.01
2663 2847 7.814107 TCTTTCATCTCACAAATTTGTATTGGC 59.186 33.333 22.87 0.00 39.91 4.52
2686 2870 5.127682 GCTGGATTTGTCTATTTGGATGGTT 59.872 40.000 0.00 0.00 0.00 3.67
2687 2871 6.351286 GCTGGATTTGTCTATTTGGATGGTTT 60.351 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.191162 CGGGATGTGCTTCTCAAAAATGA 59.809 43.478 0.00 0.00 0.00 2.57
77 78 7.928167 GGAGAAGACAAAAATCATGGAGTTTTT 59.072 33.333 2.08 9.70 37.66 1.94
137 138 5.878116 AGTTTTTGGGTTTTAGTTGGCTTTC 59.122 36.000 0.00 0.00 0.00 2.62
145 146 8.528044 TTCTGTATGAGTTTTTGGGTTTTAGT 57.472 30.769 0.00 0.00 0.00 2.24
171 173 5.869344 GCGCTCCCTCTCAATTTTAAATTTT 59.131 36.000 0.00 0.00 0.00 1.82
174 176 3.381590 GGCGCTCCCTCTCAATTTTAAAT 59.618 43.478 7.64 0.00 0.00 1.40
184 186 2.835431 TGCTAGGCGCTCCCTCTC 60.835 66.667 7.64 0.00 44.96 3.20
185 187 3.151022 GTGCTAGGCGCTCCCTCT 61.151 66.667 7.64 0.00 44.96 3.69
197 199 1.864029 GCTATCACATGTCGCGTGCTA 60.864 52.381 5.77 0.00 34.27 3.49
202 204 2.932083 GCCGCTATCACATGTCGCG 61.932 63.158 16.75 16.75 43.08 5.87
232 234 0.826062 GGTCATTTTGGATGCCCTGG 59.174 55.000 0.00 0.00 0.00 4.45
235 237 1.753073 CAGAGGTCATTTTGGATGCCC 59.247 52.381 0.00 0.00 0.00 5.36
266 268 6.675303 AGCAACTAACTAAAGGTTATCCCCTA 59.325 38.462 0.00 0.00 39.36 3.53
290 292 0.461961 CCACCTCCCTAAAGCGAGAG 59.538 60.000 0.00 0.00 0.00 3.20
295 297 1.276622 TCTGACCACCTCCCTAAAGC 58.723 55.000 0.00 0.00 0.00 3.51
299 301 2.838202 GTTTGATCTGACCACCTCCCTA 59.162 50.000 0.00 0.00 0.00 3.53
301 303 1.351017 TGTTTGATCTGACCACCTCCC 59.649 52.381 0.00 0.00 0.00 4.30
314 316 1.880027 GCCTGACCGAACTTGTTTGAT 59.120 47.619 2.52 0.00 0.00 2.57
318 320 1.523758 GATGCCTGACCGAACTTGTT 58.476 50.000 0.00 0.00 0.00 2.83
328 330 1.000274 GTGTTTGGTTGGATGCCTGAC 60.000 52.381 0.00 0.00 0.00 3.51
350 352 2.741747 GGGTATGAGGCGTAGGGC 59.258 66.667 0.00 0.00 42.51 5.19
356 358 4.559502 CCAAAGGGGTATGAGGCG 57.440 61.111 0.00 0.00 0.00 5.52
368 370 0.540365 ATGGTCACTGTGGCCCAAAG 60.540 55.000 27.26 0.00 42.76 2.77
371 373 2.435663 CATGGTCACTGTGGCCCA 59.564 61.111 27.26 22.12 42.76 5.36
374 376 1.915614 CTTCGCATGGTCACTGTGGC 61.916 60.000 8.11 5.79 0.00 5.01
395 397 6.143206 TGTCATGGATGATCCCTACTCTAAA 58.857 40.000 9.36 0.00 39.30 1.85
398 400 4.204792 TGTCATGGATGATCCCTACTCT 57.795 45.455 9.36 0.00 39.30 3.24
405 407 7.572523 TTATCTGTTTTGTCATGGATGATCC 57.427 36.000 4.05 4.05 39.30 3.36
433 435 0.329596 GCCACTGGAGTCCTGGAAAT 59.670 55.000 19.36 0.00 0.00 2.17
438 440 2.985456 GGAGCCACTGGAGTCCTG 59.015 66.667 14.16 14.16 0.00 3.86
489 491 3.132925 GCGCCATAAAAATGGATGCATT 58.867 40.909 6.63 6.63 44.39 3.56
509 511 1.376683 TCATTGGTGCACCGGTAGC 60.377 57.895 30.07 14.59 39.43 3.58
555 557 7.715657 TGTTGTGTCAATGAGCTATTCTTTTT 58.284 30.769 0.00 0.00 0.00 1.94
556 558 7.275888 TGTTGTGTCAATGAGCTATTCTTTT 57.724 32.000 0.00 0.00 0.00 2.27
557 559 6.882610 TGTTGTGTCAATGAGCTATTCTTT 57.117 33.333 0.00 0.00 0.00 2.52
558 560 8.565896 TTATGTTGTGTCAATGAGCTATTCTT 57.434 30.769 0.00 0.00 0.00 2.52
559 561 8.454106 GTTTATGTTGTGTCAATGAGCTATTCT 58.546 33.333 0.00 0.00 0.00 2.40
560 562 7.698130 GGTTTATGTTGTGTCAATGAGCTATTC 59.302 37.037 0.00 0.00 0.00 1.75
582 584 8.558973 TTGAAATTTTCTGACAACATTGGTTT 57.441 26.923 10.33 0.00 34.21 3.27
638 643 8.954950 ATCTCTATTGATAATAAATCCCGCAG 57.045 34.615 0.00 0.00 0.00 5.18
703 708 8.583810 TTAGGGTACGAAAAATCGATATTGAG 57.416 34.615 0.00 0.00 36.85 3.02
738 743 8.619546 CAACCCATGTTGTTACAATCAAATTTT 58.380 29.630 0.00 0.00 45.51 1.82
814 828 1.202758 TCACCGGTGCATTGAACTTCT 60.203 47.619 30.25 0.00 0.00 2.85
822 836 1.896660 GTGGTGTCACCGGTGCATT 60.897 57.895 30.25 0.00 42.58 3.56
848 862 6.294473 CAAGAGGGAAGAATATATGTGCACT 58.706 40.000 19.41 6.22 0.00 4.40
884 898 2.124403 GGCTCCAGCATCCACCTG 60.124 66.667 0.03 0.00 44.36 4.00
957 973 1.270518 ACACTGAAGCTGCAAGTCGAT 60.271 47.619 1.02 0.00 35.30 3.59
958 974 0.104855 ACACTGAAGCTGCAAGTCGA 59.895 50.000 1.02 0.00 35.30 4.20
959 975 0.510359 GACACTGAAGCTGCAAGTCG 59.490 55.000 10.33 0.00 35.30 4.18
960 976 0.510359 CGACACTGAAGCTGCAAGTC 59.490 55.000 14.32 14.32 35.30 3.01
961 977 0.179073 ACGACACTGAAGCTGCAAGT 60.179 50.000 1.02 0.00 35.30 3.16
1071 1087 1.487452 GCTTCACGACGCAGAACACA 61.487 55.000 0.00 0.00 0.00 3.72
1075 1091 2.733218 CGGCTTCACGACGCAGAA 60.733 61.111 0.00 0.00 37.31 3.02
1230 1246 3.066291 AGGCATGTACCGTGAAATTGA 57.934 42.857 0.00 0.00 33.69 2.57
1731 1751 3.118775 TCACGACTGCCAAGCTAATACAT 60.119 43.478 0.00 0.00 0.00 2.29
1913 2093 3.027974 AGGAAAGGAAAGAACGACTCG 57.972 47.619 0.00 0.00 0.00 4.18
1973 2153 2.096248 TGCGTCTGTCCTTTTGGTTTT 58.904 42.857 0.00 0.00 41.38 2.43
1980 2160 1.600916 GCCCTTGCGTCTGTCCTTT 60.601 57.895 0.00 0.00 0.00 3.11
2032 2212 3.500299 TCAGAAAGAGACGAGACAGACAG 59.500 47.826 0.00 0.00 0.00 3.51
2033 2213 3.251245 GTCAGAAAGAGACGAGACAGACA 59.749 47.826 0.00 0.00 0.00 3.41
2035 2215 3.745799 AGTCAGAAAGAGACGAGACAGA 58.254 45.455 0.00 0.00 40.84 3.41
2122 2302 2.735444 CGCGTCACTCTATCCACACATT 60.735 50.000 0.00 0.00 0.00 2.71
2125 2305 1.140407 GCGCGTCACTCTATCCACAC 61.140 60.000 8.43 0.00 0.00 3.82
2154 2334 0.971447 GCTAGGTTGTCCCGGTCTCT 60.971 60.000 0.00 0.00 38.74 3.10
2163 2343 0.181350 CCCAGGGATGCTAGGTTGTC 59.819 60.000 0.00 0.00 0.00 3.18
2165 2345 0.471617 CTCCCAGGGATGCTAGGTTG 59.528 60.000 9.31 0.00 0.00 3.77
2174 2354 1.697754 ATTTCGGCCTCCCAGGGAT 60.698 57.895 9.31 0.00 35.37 3.85
2175 2355 2.286121 ATTTCGGCCTCCCAGGGA 60.286 61.111 8.35 8.35 35.37 4.20
2180 2360 2.513897 CGGTGATTTCGGCCTCCC 60.514 66.667 0.00 0.00 0.00 4.30
2202 2382 6.767456 AGTGATGAAGAGTTCTCACAAGATT 58.233 36.000 15.42 0.00 38.81 2.40
2210 2390 5.090083 GTGTACGAGTGATGAAGAGTTCTC 58.910 45.833 0.00 0.00 0.00 2.87
2281 2461 4.678509 TCATGTTCATCTAAAACGGCAC 57.321 40.909 0.00 0.00 0.00 5.01
2290 2470 5.009110 TGTTTGGCGTTTTCATGTTCATCTA 59.991 36.000 0.00 0.00 0.00 1.98
2315 2495 2.599578 CTGGCTTGGTTGCTGGCT 60.600 61.111 0.00 0.00 0.00 4.75
2335 2515 4.641645 TGTCGGCCAAGGCACCAG 62.642 66.667 13.87 1.33 44.11 4.00
2338 2518 1.298859 CTAACTGTCGGCCAAGGCAC 61.299 60.000 13.87 4.00 44.11 5.01
2349 2529 1.153549 CCAGCGAGGCCTAACTGTC 60.154 63.158 25.40 5.66 0.00 3.51
2362 2542 2.726912 CAACTTGCAACGCCAGCG 60.727 61.111 11.05 11.05 46.03 5.18
2376 2556 2.030363 TGGCGTTTCAATCCATGTCAAC 60.030 45.455 0.00 0.00 0.00 3.18
2377 2557 2.234143 TGGCGTTTCAATCCATGTCAA 58.766 42.857 0.00 0.00 0.00 3.18
2382 2562 0.532115 GCCTTGGCGTTTCAATCCAT 59.468 50.000 0.00 0.00 0.00 3.41
2386 2566 1.203052 CATGAGCCTTGGCGTTTCAAT 59.797 47.619 5.95 0.00 0.00 2.57
2402 2586 2.361104 GGCCCAGAAACGCCATGA 60.361 61.111 0.00 0.00 45.01 3.07
2409 2593 1.285950 GCGTTTGAGGCCCAGAAAC 59.714 57.895 0.00 5.43 0.00 2.78
2448 2632 8.646900 GCCCCATCACCATTTAAATATCTAAAA 58.353 33.333 0.00 0.00 0.00 1.52
2450 2634 7.534852 AGCCCCATCACCATTTAAATATCTAA 58.465 34.615 0.00 0.00 0.00 2.10
2453 2637 6.012745 AGAGCCCCATCACCATTTAAATATC 58.987 40.000 0.00 0.00 0.00 1.63
2462 2646 0.769873 GATGAGAGCCCCATCACCAT 59.230 55.000 0.00 0.00 39.98 3.55
2465 2649 0.179034 GTGGATGAGAGCCCCATCAC 60.179 60.000 11.19 5.65 41.52 3.06
2467 2651 1.348008 TGGTGGATGAGAGCCCCATC 61.348 60.000 0.00 0.00 39.61 3.51
2468 2652 1.308128 TGGTGGATGAGAGCCCCAT 60.308 57.895 0.00 0.00 31.94 4.00
2478 2662 2.235650 AGTGAGTGATGAGTGGTGGATG 59.764 50.000 0.00 0.00 0.00 3.51
2480 2664 1.895798 GAGTGAGTGATGAGTGGTGGA 59.104 52.381 0.00 0.00 0.00 4.02
2482 2666 3.674528 AAGAGTGAGTGATGAGTGGTG 57.325 47.619 0.00 0.00 0.00 4.17
2484 2668 4.892433 AGAAAAGAGTGAGTGATGAGTGG 58.108 43.478 0.00 0.00 0.00 4.00
2491 2675 6.094048 CCAACAAAAGAGAAAAGAGTGAGTGA 59.906 38.462 0.00 0.00 0.00 3.41
2497 2681 8.214364 AGATAGACCAACAAAAGAGAAAAGAGT 58.786 33.333 0.00 0.00 0.00 3.24
2502 2686 7.041098 GCTGAAGATAGACCAACAAAAGAGAAA 60.041 37.037 0.00 0.00 0.00 2.52
2508 2692 5.869579 AGAGCTGAAGATAGACCAACAAAA 58.130 37.500 0.00 0.00 0.00 2.44
2509 2693 5.489792 AGAGCTGAAGATAGACCAACAAA 57.510 39.130 0.00 0.00 0.00 2.83
2510 2694 5.240891 CAAGAGCTGAAGATAGACCAACAA 58.759 41.667 0.00 0.00 0.00 2.83
2511 2695 4.825422 CAAGAGCTGAAGATAGACCAACA 58.175 43.478 0.00 0.00 0.00 3.33
2512 2696 3.620821 GCAAGAGCTGAAGATAGACCAAC 59.379 47.826 0.00 0.00 37.91 3.77
2517 2701 4.833478 AAAGGCAAGAGCTGAAGATAGA 57.167 40.909 0.00 0.00 41.70 1.98
2520 2704 3.087781 GGAAAAGGCAAGAGCTGAAGAT 58.912 45.455 0.00 0.00 41.70 2.40
2524 2708 2.233271 CAAGGAAAAGGCAAGAGCTGA 58.767 47.619 0.00 0.00 41.70 4.26
2530 2714 4.758688 AGACAAAACAAGGAAAAGGCAAG 58.241 39.130 0.00 0.00 0.00 4.01
2536 2720 4.401202 GTGGAGGAGACAAAACAAGGAAAA 59.599 41.667 0.00 0.00 0.00 2.29
2540 2724 3.214696 AGTGGAGGAGACAAAACAAGG 57.785 47.619 0.00 0.00 0.00 3.61
2543 2727 4.885325 GGTTTAAGTGGAGGAGACAAAACA 59.115 41.667 0.00 0.00 0.00 2.83
2544 2728 4.277672 GGGTTTAAGTGGAGGAGACAAAAC 59.722 45.833 0.00 0.00 0.00 2.43
2548 2732 2.904434 GAGGGTTTAAGTGGAGGAGACA 59.096 50.000 0.00 0.00 0.00 3.41
2556 2740 6.901081 AAGAATTTGAGAGGGTTTAAGTGG 57.099 37.500 0.00 0.00 0.00 4.00
2573 2757 5.220662 CCAACGCAATCGATCTGTAAGAATT 60.221 40.000 0.00 0.00 42.93 2.17
2576 2760 3.186909 CCAACGCAATCGATCTGTAAGA 58.813 45.455 0.00 0.00 43.55 2.10
2577 2761 2.930040 ACCAACGCAATCGATCTGTAAG 59.070 45.455 0.00 0.00 39.41 2.34
2580 2764 1.359848 GACCAACGCAATCGATCTGT 58.640 50.000 0.00 0.00 39.41 3.41
2583 2767 1.082117 ACGGACCAACGCAATCGATC 61.082 55.000 0.00 0.00 39.41 3.69
2600 2784 4.704457 ACGAAAATGACACCGAATTAACG 58.296 39.130 0.00 0.00 0.00 3.18
2601 2785 5.566395 GGAACGAAAATGACACCGAATTAAC 59.434 40.000 0.00 0.00 0.00 2.01
2602 2786 5.470777 AGGAACGAAAATGACACCGAATTAA 59.529 36.000 0.00 0.00 0.00 1.40
2603 2787 4.998672 AGGAACGAAAATGACACCGAATTA 59.001 37.500 0.00 0.00 0.00 1.40
2604 2788 3.818773 AGGAACGAAAATGACACCGAATT 59.181 39.130 0.00 0.00 0.00 2.17
2605 2789 3.408634 AGGAACGAAAATGACACCGAAT 58.591 40.909 0.00 0.00 0.00 3.34
2639 2823 7.599621 CAGCCAATACAAATTTGTGAGATGAAA 59.400 33.333 29.72 10.85 42.31 2.69
2663 2847 6.780457 AACCATCCAAATAGACAAATCCAG 57.220 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.