Multiple sequence alignment - TraesCS2D01G452300

Loading Multiple Alignment...

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 TraesCS2D01G452300 chr2D 100.000 2736 0 0 515 3250 561909645 561906910 0.000000e+00 5053
1 TraesCS2D01G452300 chr2D 85.637 1664 136 57 659 2265 561851272 561852889 0.000000e+00 1653
2 TraesCS2D01G452300 chr2D 100.000 171 0 0 1 171 561910159 561909989 1.880000e-82 316
3 TraesCS2D01G452300 chr2B 93.774 1815 72 8 515 2290 671040573 671038761 0.000000e+00 2687
4 TraesCS2D01G452300 chr2B 89.805 1285 94 22 998 2261 670853254 670854522 0.000000e+00 1613
5 TraesCS2D01G452300 chr2B 89.655 638 51 11 2595 3232 671036982 671036360 0.000000e+00 798
6 TraesCS2D01G452300 chr2B 86.905 168 15 6 8 170 671041155 671040990 7.160000e-42 182
7 TraesCS2D01G452300 chr2A 94.724 1668 61 6 619 2260 701868757 701867091 0.000000e+00 2567
8 TraesCS2D01G452300 chr2A 89.984 1288 93 23 998 2265 701497127 701498398 0.000000e+00 1631
9 TraesCS2D01G452300 chr2A 91.120 777 58 5 2474 3250 701866496 701865731 0.000000e+00 1042
10 TraesCS2D01G452300 chr2A 93.195 338 22 1 1186 1523 628063331 628062995 2.250000e-136 496
11 TraesCS2D01G452300 chr2A 92.593 108 5 3 2362 2466 701867031 701866924 5.620000e-33 152
12 TraesCS2D01G452300 chr7B 96.212 132 5 0 1546 1677 506596659 506596790 1.960000e-52 217
13 TraesCS2D01G452300 chr5D 97.368 114 3 0 1301 1414 436205412 436205525 9.200000e-46 195
14 TraesCS2D01G452300 chr1B 91.270 126 8 3 2474 2596 41855003 41855128 5.580000e-38 169


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 TraesCS2D01G452300 chr2D 561906910 561910159 3249 True 2684.500000 5053 100.000000 1 3250 2 chr2D.!!$R1 3249
1 TraesCS2D01G452300 chr2D 561851272 561852889 1617 False 1653.000000 1653 85.637000 659 2265 1 chr2D.!!$F1 1606
2 TraesCS2D01G452300 chr2B 670853254 670854522 1268 False 1613.000000 1613 89.805000 998 2261 1 chr2B.!!$F1 1263
3 TraesCS2D01G452300 chr2B 671036360 671041155 4795 True 1222.333333 2687 90.111333 8 3232 3 chr2B.!!$R1 3224
4 TraesCS2D01G452300 chr2A 701497127 701498398 1271 False 1631.000000 1631 89.984000 998 2265 1 chr2A.!!$F1 1267
5 TraesCS2D01G452300 chr2A 701865731 701868757 3026 True 1253.666667 2567 92.812333 619 3250 3 chr2A.!!$R2 2631

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
986 1099 1.743772 CGGGTTTGCAGGATACAGAGG 60.744 57.143 0.0 0.0 41.41 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 4364 0.108615 AACCGAGACCGAGCTTCATG 60.109 55.0 0.0 0.0 38.22 3.07 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
74 75 4.746611 CAGGAACTTTCAGCAATTCCAAAC 59.253 41.667 4.78 0.00 42.66 2.93
75 76 4.651045 AGGAACTTTCAGCAATTCCAAACT 59.349 37.500 4.78 0.00 42.66 2.66
76 77 5.129320 AGGAACTTTCAGCAATTCCAAACTT 59.871 36.000 4.78 0.00 42.66 2.66
77 78 5.817296 GGAACTTTCAGCAATTCCAAACTTT 59.183 36.000 0.00 0.00 40.38 2.66
78 79 6.316140 GGAACTTTCAGCAATTCCAAACTTTT 59.684 34.615 0.00 0.00 40.38 2.27
111 112 9.672673 TTGAAAATTTCAAATTCCAACTTGGTA 57.327 25.926 17.69 0.00 45.94 3.25
146 152 2.100631 CGGAGGGTCACATGAACGC 61.101 63.158 0.00 5.83 30.99 4.84
156 162 4.393155 ATGAACGCGCCTGCAGGA 62.393 61.111 37.21 14.16 42.97 3.86
170 176 1.970352 GCAGGAGAGAGAAGGCTGGG 61.970 65.000 0.00 0.00 0.00 4.45
532 610 1.880894 GGACGAGTGGACACGATCA 59.119 57.895 3.58 0.00 36.20 2.92
607 685 8.118976 TGTCAGATCCCTAAATATACGTTAGG 57.881 38.462 13.74 13.74 44.97 2.69
686 764 2.842394 ATCAACGGCTCCAGTGCTCG 62.842 60.000 0.00 0.00 34.52 5.03
707 785 2.499205 CTGGCGCCGTCTGGATTA 59.501 61.111 23.90 0.00 37.49 1.75
880 979 2.480416 CCGATTTCAACGAGAGGAGGAG 60.480 54.545 0.00 0.00 0.00 3.69
941 1054 2.203209 CTGCCCCGGTTGCTATCC 60.203 66.667 13.63 0.00 0.00 2.59
943 1056 2.111251 GCCCCGGTTGCTATCCTC 59.889 66.667 0.00 0.00 0.00 3.71
986 1099 1.743772 CGGGTTTGCAGGATACAGAGG 60.744 57.143 0.00 0.00 41.41 3.69
1076 1212 7.554118 TCCATCTTGAATTCTTGATACTGGAAC 59.446 37.037 7.05 0.00 0.00 3.62
1151 1298 0.456221 CAGGTACACGAGGCGAAGAT 59.544 55.000 0.00 0.00 0.00 2.40
1159 1306 1.205485 CGAGGCGAAGATGAAGCTCG 61.205 60.000 0.00 0.00 0.00 5.03
1162 1309 1.486644 GGCGAAGATGAAGCTCGAGC 61.487 60.000 30.01 30.01 42.49 5.03
1256 1418 0.599991 TCAACATCGTGCTCGTGCTT 60.600 50.000 11.19 0.00 40.48 3.91
1383 1545 1.064946 CCGCTGCTCCTCTACTTCG 59.935 63.158 0.00 0.00 0.00 3.79
1811 1973 2.028130 CTCAGGAGCGACACCTTCTAT 58.972 52.381 0.00 0.00 35.35 1.98
2276 2453 0.734942 TCGCCGGAATTCGAGTTGAC 60.735 55.000 5.05 0.00 42.43 3.18
2277 2454 1.011968 CGCCGGAATTCGAGTTGACA 61.012 55.000 5.05 0.00 42.43 3.58
2290 2467 1.069823 AGTTGACACTCTGCTCACCAG 59.930 52.381 0.00 0.00 43.17 4.00
2292 2469 0.676184 TGACACTCTGCTCACCAGAC 59.324 55.000 0.00 0.00 45.44 3.51
2295 2472 0.678395 CACTCTGCTCACCAGACTGT 59.322 55.000 0.93 0.00 45.44 3.55
2296 2473 1.889170 CACTCTGCTCACCAGACTGTA 59.111 52.381 0.93 0.00 45.44 2.74
2297 2474 2.297315 CACTCTGCTCACCAGACTGTAA 59.703 50.000 0.93 0.00 45.44 2.41
2298 2475 2.965831 ACTCTGCTCACCAGACTGTAAA 59.034 45.455 0.93 0.00 45.44 2.01
2299 2476 3.388024 ACTCTGCTCACCAGACTGTAAAA 59.612 43.478 0.93 0.00 45.44 1.52
2300 2477 3.728845 TCTGCTCACCAGACTGTAAAAC 58.271 45.455 0.93 0.00 45.44 2.43
2301 2478 3.388024 TCTGCTCACCAGACTGTAAAACT 59.612 43.478 0.93 0.00 45.44 2.66
2302 2479 4.587262 TCTGCTCACCAGACTGTAAAACTA 59.413 41.667 0.93 0.00 45.44 2.24
2303 2480 4.883083 TGCTCACCAGACTGTAAAACTAG 58.117 43.478 0.93 0.00 0.00 2.57
2304 2481 3.680458 GCTCACCAGACTGTAAAACTAGC 59.320 47.826 0.93 0.00 0.00 3.42
2306 2483 4.883083 TCACCAGACTGTAAAACTAGCTG 58.117 43.478 0.00 0.00 0.00 4.24
2331 4129 2.868964 AGGACTTCCTATAGGTGCCA 57.131 50.000 18.51 0.00 46.48 4.92
2354 4152 4.954875 ACTCTATGATGAGCTTTGCTACC 58.045 43.478 0.00 0.00 39.88 3.18
2357 4155 2.472695 TGATGAGCTTTGCTACCGTT 57.527 45.000 0.00 0.00 39.88 4.44
2366 4164 4.024302 AGCTTTGCTACCGTTTTAACTCAC 60.024 41.667 0.00 0.00 36.99 3.51
2368 4166 3.367992 TGCTACCGTTTTAACTCACGA 57.632 42.857 0.00 0.00 38.76 4.35
2373 4171 1.193874 CCGTTTTAACTCACGAGGTGC 59.806 52.381 0.00 0.00 38.76 5.01
2466 4266 4.929479 GGGGGATTTATGTATGTATGCCA 58.071 43.478 0.00 0.00 30.86 4.92
2467 4267 5.518865 GGGGGATTTATGTATGTATGCCAT 58.481 41.667 0.00 0.00 37.58 4.40
2468 4268 6.668645 GGGGGATTTATGTATGTATGCCATA 58.331 40.000 0.00 0.00 34.86 2.74
2469 4269 6.772716 GGGGGATTTATGTATGTATGCCATAG 59.227 42.308 0.00 0.00 36.71 2.23
2470 4270 7.346471 GGGGATTTATGTATGTATGCCATAGT 58.654 38.462 0.00 0.00 36.71 2.12
2471 4271 7.834181 GGGGATTTATGTATGTATGCCATAGTT 59.166 37.037 0.00 0.00 36.71 2.24
2472 4272 9.243105 GGGATTTATGTATGTATGCCATAGTTT 57.757 33.333 0.00 0.00 36.71 2.66
2479 4279 8.432110 TGTATGTATGCCATAGTTTTGTACTG 57.568 34.615 0.00 0.00 36.71 2.74
2480 4280 8.044309 TGTATGTATGCCATAGTTTTGTACTGT 58.956 33.333 0.00 0.00 36.71 3.55
2481 4281 9.537192 GTATGTATGCCATAGTTTTGTACTGTA 57.463 33.333 0.00 0.00 36.71 2.74
2482 4282 7.837202 TGTATGCCATAGTTTTGTACTGTAC 57.163 36.000 10.98 10.98 37.73 2.90
2483 4283 7.387643 TGTATGCCATAGTTTTGTACTGTACA 58.612 34.615 16.26 16.26 37.73 2.90
2484 4284 8.044309 TGTATGCCATAGTTTTGTACTGTACAT 58.956 33.333 20.31 8.95 38.68 2.29
2485 4285 6.978343 TGCCATAGTTTTGTACTGTACATC 57.022 37.500 20.31 13.67 38.68 3.06
2486 4286 5.878116 TGCCATAGTTTTGTACTGTACATCC 59.122 40.000 20.31 11.48 38.68 3.51
2487 4287 5.006358 GCCATAGTTTTGTACTGTACATCCG 59.994 44.000 20.31 6.34 38.68 4.18
2488 4288 6.103997 CCATAGTTTTGTACTGTACATCCGT 58.896 40.000 20.31 9.37 38.68 4.69
2489 4289 7.259882 CCATAGTTTTGTACTGTACATCCGTA 58.740 38.462 20.31 11.01 38.68 4.02
2490 4290 7.924412 CCATAGTTTTGTACTGTACATCCGTAT 59.076 37.037 20.31 12.50 38.68 3.06
2491 4291 8.965172 CATAGTTTTGTACTGTACATCCGTATC 58.035 37.037 20.31 8.09 38.68 2.24
2492 4292 6.927416 AGTTTTGTACTGTACATCCGTATCA 58.073 36.000 20.31 1.34 38.68 2.15
2493 4293 7.380536 AGTTTTGTACTGTACATCCGTATCAA 58.619 34.615 20.31 7.31 38.68 2.57
2494 4294 7.330208 AGTTTTGTACTGTACATCCGTATCAAC 59.670 37.037 20.31 12.43 38.68 3.18
2495 4295 5.900865 TGTACTGTACATCCGTATCAACA 57.099 39.130 16.26 0.00 32.89 3.33
2496 4296 5.643664 TGTACTGTACATCCGTATCAACAC 58.356 41.667 16.26 0.00 32.89 3.32
2497 4297 3.766151 ACTGTACATCCGTATCAACACG 58.234 45.455 0.00 0.00 41.59 4.49
2498 4298 3.192001 ACTGTACATCCGTATCAACACGT 59.808 43.478 0.00 0.00 40.31 4.49
2499 4299 3.503891 TGTACATCCGTATCAACACGTG 58.496 45.455 15.48 15.48 40.31 4.49
2500 4300 2.736144 ACATCCGTATCAACACGTGT 57.264 45.000 17.22 17.22 40.31 4.49
2501 4301 2.333926 ACATCCGTATCAACACGTGTG 58.666 47.619 24.16 16.12 40.31 3.82
2502 4302 2.029739 ACATCCGTATCAACACGTGTGA 60.030 45.455 24.16 20.74 40.31 3.58
2503 4303 3.186909 CATCCGTATCAACACGTGTGAT 58.813 45.455 24.16 25.28 40.31 3.06
2504 4304 3.306917 TCCGTATCAACACGTGTGATT 57.693 42.857 26.99 16.74 40.31 2.57
2505 4305 3.655486 TCCGTATCAACACGTGTGATTT 58.345 40.909 26.99 15.33 40.31 2.17
2506 4306 4.059511 TCCGTATCAACACGTGTGATTTT 58.940 39.130 26.99 10.68 40.31 1.82
2507 4307 4.512198 TCCGTATCAACACGTGTGATTTTT 59.488 37.500 26.99 10.03 40.31 1.94
2568 4368 9.558396 AAATTTTGAAAATAAAGTGCTCCATGA 57.442 25.926 3.26 0.00 0.00 3.07
2569 4369 9.558396 AATTTTGAAAATAAAGTGCTCCATGAA 57.442 25.926 3.26 0.00 0.00 2.57
2570 4370 8.592105 TTTTGAAAATAAAGTGCTCCATGAAG 57.408 30.769 0.00 0.00 0.00 3.02
2571 4371 5.713025 TGAAAATAAAGTGCTCCATGAAGC 58.287 37.500 0.00 0.00 42.82 3.86
2572 4372 5.477984 TGAAAATAAAGTGCTCCATGAAGCT 59.522 36.000 5.24 0.00 42.94 3.74
2573 4373 5.573337 AAATAAAGTGCTCCATGAAGCTC 57.427 39.130 5.24 0.78 42.94 4.09
2574 4374 1.446907 AAAGTGCTCCATGAAGCTCG 58.553 50.000 5.24 0.00 42.94 5.03
2575 4375 0.392193 AAGTGCTCCATGAAGCTCGG 60.392 55.000 5.24 0.00 42.94 4.63
2576 4376 1.078848 GTGCTCCATGAAGCTCGGT 60.079 57.895 5.24 0.00 42.94 4.69
2577 4377 1.086634 GTGCTCCATGAAGCTCGGTC 61.087 60.000 5.24 0.00 42.94 4.79
2578 4378 1.260538 TGCTCCATGAAGCTCGGTCT 61.261 55.000 5.24 0.00 42.94 3.85
2579 4379 0.529555 GCTCCATGAAGCTCGGTCTC 60.530 60.000 0.00 0.00 39.27 3.36
2580 4380 0.248825 CTCCATGAAGCTCGGTCTCG 60.249 60.000 0.00 0.00 37.82 4.04
2581 4381 1.227089 CCATGAAGCTCGGTCTCGG 60.227 63.158 0.00 0.00 36.95 4.63
2582 4382 1.513158 CATGAAGCTCGGTCTCGGT 59.487 57.895 0.00 0.00 36.95 4.69
2583 4383 0.108615 CATGAAGCTCGGTCTCGGTT 60.109 55.000 0.00 0.00 36.95 4.44
2584 4384 0.608640 ATGAAGCTCGGTCTCGGTTT 59.391 50.000 0.00 0.00 36.95 3.27
2585 4385 1.250328 TGAAGCTCGGTCTCGGTTTA 58.750 50.000 0.00 0.00 36.95 2.01
2586 4386 1.201647 TGAAGCTCGGTCTCGGTTTAG 59.798 52.381 0.00 0.00 36.95 1.85
2587 4387 0.108756 AAGCTCGGTCTCGGTTTAGC 60.109 55.000 0.00 0.00 36.95 3.09
2588 4388 1.214589 GCTCGGTCTCGGTTTAGCA 59.785 57.895 0.00 0.00 34.16 3.49
2589 4389 0.179108 GCTCGGTCTCGGTTTAGCAT 60.179 55.000 0.00 0.00 34.16 3.79
2590 4390 1.739371 GCTCGGTCTCGGTTTAGCATT 60.739 52.381 0.00 0.00 34.16 3.56
2591 4391 2.618053 CTCGGTCTCGGTTTAGCATTT 58.382 47.619 0.00 0.00 36.95 2.32
2592 4392 2.603560 CTCGGTCTCGGTTTAGCATTTC 59.396 50.000 0.00 0.00 36.95 2.17
2593 4393 1.664151 CGGTCTCGGTTTAGCATTTCC 59.336 52.381 0.00 0.00 0.00 3.13
2594 4394 1.664151 GGTCTCGGTTTAGCATTTCCG 59.336 52.381 0.00 0.00 43.65 4.30
2595 4395 2.344025 GTCTCGGTTTAGCATTTCCGT 58.656 47.619 9.44 0.00 42.95 4.69
2596 4396 2.093783 GTCTCGGTTTAGCATTTCCGTG 59.906 50.000 9.44 7.80 42.95 4.94
2597 4397 2.028839 TCTCGGTTTAGCATTTCCGTGA 60.029 45.455 9.44 9.58 42.95 4.35
2713 5073 5.702065 TCCACAGTTTATTATACCTGCCA 57.298 39.130 0.00 0.00 0.00 4.92
2718 5078 6.767902 CACAGTTTATTATACCTGCCATCACT 59.232 38.462 0.00 0.00 0.00 3.41
2719 5079 7.283127 CACAGTTTATTATACCTGCCATCACTT 59.717 37.037 0.00 0.00 0.00 3.16
2799 5159 4.744137 TGTTCCATTGTTCAATCTTTTGCG 59.256 37.500 0.00 0.00 32.61 4.85
2836 5196 1.996191 GTGACAAGAATCGTGAGGAGC 59.004 52.381 2.68 0.00 0.00 4.70
2887 5247 0.618458 AGCCGGTAAGAAATGCAGGA 59.382 50.000 1.90 0.00 30.63 3.86
2893 5253 3.368427 CGGTAAGAAATGCAGGAGAGTGA 60.368 47.826 0.00 0.00 0.00 3.41
2977 5337 6.978343 TGCGTAGAGTATGTAAGCATTTTT 57.022 33.333 0.00 0.00 43.60 1.94
3002 5362 1.583495 CTCGGCCAGTCACTGTCGTA 61.583 60.000 14.76 4.60 31.77 3.43
3017 5377 4.142513 ACTGTCGTATAACCCGAAGTTCTC 60.143 45.833 0.56 0.00 40.05 2.87
3051 5411 0.830444 AACCTAGTGGCGTCTCACCA 60.830 55.000 0.00 0.00 38.34 4.17
3070 5430 2.143925 CACCTCCTCGAGACAAAAACC 58.856 52.381 15.71 0.00 0.00 3.27
3139 5501 8.997323 TGCAACCATATTATCAAAACAAAAAGG 58.003 29.630 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.871125 CGCCTCCCCTTTTAGTATCATATATAT 58.129 37.037 0.00 0.00 0.00 0.86
1 2 7.201974 GCGCCTCCCCTTTTAGTATCATATATA 60.202 40.741 0.00 0.00 0.00 0.86
2 3 6.408206 GCGCCTCCCCTTTTAGTATCATATAT 60.408 42.308 0.00 0.00 0.00 0.86
3 4 5.105064 GCGCCTCCCCTTTTAGTATCATATA 60.105 44.000 0.00 0.00 0.00 0.86
4 5 4.323562 GCGCCTCCCCTTTTAGTATCATAT 60.324 45.833 0.00 0.00 0.00 1.78
5 6 3.007614 GCGCCTCCCCTTTTAGTATCATA 59.992 47.826 0.00 0.00 0.00 2.15
6 7 2.224548 GCGCCTCCCCTTTTAGTATCAT 60.225 50.000 0.00 0.00 0.00 2.45
33 34 1.453524 CTGAAGAAGAACAGCACGACG 59.546 52.381 0.00 0.00 0.00 5.12
113 114 7.449086 TGTGACCCTCCGAGTAATTTAATTTTT 59.551 33.333 0.00 0.00 0.00 1.94
114 115 6.943718 TGTGACCCTCCGAGTAATTTAATTTT 59.056 34.615 0.00 0.00 0.00 1.82
118 119 5.188163 TCATGTGACCCTCCGAGTAATTTAA 59.812 40.000 0.00 0.00 0.00 1.52
119 120 4.712829 TCATGTGACCCTCCGAGTAATTTA 59.287 41.667 0.00 0.00 0.00 1.40
122 123 2.747177 TCATGTGACCCTCCGAGTAAT 58.253 47.619 0.00 0.00 0.00 1.89
124 125 1.822990 GTTCATGTGACCCTCCGAGTA 59.177 52.381 0.00 0.00 0.00 2.59
126 127 0.458543 CGTTCATGTGACCCTCCGAG 60.459 60.000 0.00 0.00 0.00 4.63
127 128 1.589630 CGTTCATGTGACCCTCCGA 59.410 57.895 0.00 0.00 0.00 4.55
128 129 2.100631 GCGTTCATGTGACCCTCCG 61.101 63.158 0.00 0.00 0.00 4.63
129 130 2.100631 CGCGTTCATGTGACCCTCC 61.101 63.158 0.00 0.00 0.00 4.30
133 139 2.742372 AGGCGCGTTCATGTGACC 60.742 61.111 8.43 0.00 0.00 4.02
146 152 1.141449 CTTCTCTCTCCTGCAGGCG 59.859 63.158 28.91 22.98 34.44 5.52
532 610 2.237392 CGAGATTTTTCTCTCCCCAGGT 59.763 50.000 1.90 0.00 38.78 4.00
559 637 8.586570 ACAGTTCATCGCAATTTTAAATCAAA 57.413 26.923 0.00 0.00 0.00 2.69
573 651 1.137872 AGGGATCTGACAGTTCATCGC 59.862 52.381 14.08 11.99 0.00 4.58
663 741 1.078759 CACTGGAGCCGTTGATCGTC 61.079 60.000 0.00 0.00 37.94 4.20
707 785 0.614697 CGGCCCCTTGGAGGAAAAAT 60.615 55.000 0.00 0.00 37.67 1.82
787 865 3.063997 GGTCTTAATCTGCGGTCAACATG 59.936 47.826 0.00 0.00 0.00 3.21
880 979 2.158959 CGGATGCGTGTCGTCTTCC 61.159 63.158 0.00 0.00 0.00 3.46
906 1005 3.308046 GGCAGGGGAATAATCTGATCCTC 60.308 52.174 0.00 0.00 33.68 3.71
941 1054 1.135575 GCCGAAAAGGATGTGCAAGAG 60.136 52.381 0.00 0.00 45.00 2.85
943 1056 0.597568 TGCCGAAAAGGATGTGCAAG 59.402 50.000 0.00 0.00 45.00 4.01
986 1099 0.601311 GCCCATATCCGCACAGAGTC 60.601 60.000 0.00 0.00 0.00 3.36
1076 1212 1.535462 CGGCCTACAACCACAAGAAAG 59.465 52.381 0.00 0.00 0.00 2.62
1151 1298 2.046864 AGCTACGGCTCGAGCTTCA 61.047 57.895 34.46 18.97 46.99 3.02
1162 1309 2.438254 TGCCATTGCCAGCTACGG 60.438 61.111 0.00 0.00 36.33 4.02
1811 1973 0.897621 ACTGCATCTCCATCACGTCA 59.102 50.000 0.00 0.00 0.00 4.35
2108 2270 1.303888 CATGGCCAGCACCTTCACT 60.304 57.895 13.05 0.00 0.00 3.41
2276 2453 3.511182 CAGTCTGGTGAGCAGAGTG 57.489 57.895 28.36 28.36 41.77 3.51
2277 2454 2.294449 TACAGTCTGGTGAGCAGAGT 57.706 50.000 15.44 15.57 32.98 3.24
2290 2467 6.043411 CCTATCCACAGCTAGTTTTACAGTC 58.957 44.000 0.00 0.00 0.00 3.51
2291 2468 5.720041 TCCTATCCACAGCTAGTTTTACAGT 59.280 40.000 0.00 0.00 0.00 3.55
2292 2469 6.043411 GTCCTATCCACAGCTAGTTTTACAG 58.957 44.000 0.00 0.00 0.00 2.74
2295 2472 6.127140 GGAAGTCCTATCCACAGCTAGTTTTA 60.127 42.308 0.00 0.00 36.92 1.52
2296 2473 5.338463 GGAAGTCCTATCCACAGCTAGTTTT 60.338 44.000 0.00 0.00 36.92 2.43
2297 2474 4.162509 GGAAGTCCTATCCACAGCTAGTTT 59.837 45.833 0.00 0.00 36.92 2.66
2298 2475 3.707102 GGAAGTCCTATCCACAGCTAGTT 59.293 47.826 0.00 0.00 36.92 2.24
2299 2476 3.052490 AGGAAGTCCTATCCACAGCTAGT 60.052 47.826 0.00 0.00 46.48 2.57
2300 2477 3.571590 AGGAAGTCCTATCCACAGCTAG 58.428 50.000 0.00 0.00 46.48 3.42
2301 2478 3.689872 AGGAAGTCCTATCCACAGCTA 57.310 47.619 0.00 0.00 46.48 3.32
2302 2479 2.559381 AGGAAGTCCTATCCACAGCT 57.441 50.000 0.00 0.00 46.48 4.24
2324 4122 2.158842 GCTCATCATAGAGTTGGCACCT 60.159 50.000 0.00 0.00 37.94 4.00
2331 4129 5.363939 GGTAGCAAAGCTCATCATAGAGTT 58.636 41.667 0.00 0.00 40.44 3.01
2354 4152 1.193874 GGCACCTCGTGAGTTAAAACG 59.806 52.381 0.00 1.30 41.11 3.60
2357 4155 0.390124 ACGGCACCTCGTGAGTTAAA 59.610 50.000 0.00 0.00 42.21 1.52
2373 4171 1.068434 ACCAACAAAAAGATGCCACGG 59.932 47.619 0.00 0.00 0.00 4.94
2387 4185 1.065491 AGCCTGCGATCATAACCAACA 60.065 47.619 0.00 0.00 0.00 3.33
2458 4258 7.387643 TGTACAGTACAAAACTATGGCATACA 58.612 34.615 11.21 0.00 35.76 2.29
2459 4259 7.837202 TGTACAGTACAAAACTATGGCATAC 57.163 36.000 11.21 0.00 35.76 2.39
2460 4260 7.713507 GGATGTACAGTACAAAACTATGGCATA 59.286 37.037 17.43 7.06 42.76 3.14
2461 4261 6.542370 GGATGTACAGTACAAAACTATGGCAT 59.458 38.462 17.43 4.88 42.76 4.40
2462 4262 5.878116 GGATGTACAGTACAAAACTATGGCA 59.122 40.000 17.43 0.00 42.76 4.92
2463 4263 5.006358 CGGATGTACAGTACAAAACTATGGC 59.994 44.000 17.43 0.00 42.76 4.40
2464 4264 6.103997 ACGGATGTACAGTACAAAACTATGG 58.896 40.000 17.43 4.42 42.76 2.74
2465 4265 8.867112 ATACGGATGTACAGTACAAAACTATG 57.133 34.615 17.43 6.28 42.76 2.23
2466 4266 8.689061 TGATACGGATGTACAGTACAAAACTAT 58.311 33.333 17.43 9.91 42.76 2.12
2467 4267 8.054152 TGATACGGATGTACAGTACAAAACTA 57.946 34.615 17.43 5.89 42.76 2.24
2468 4268 6.927416 TGATACGGATGTACAGTACAAAACT 58.073 36.000 17.43 0.66 42.76 2.66
2469 4269 7.116662 TGTTGATACGGATGTACAGTACAAAAC 59.883 37.037 17.43 11.33 42.76 2.43
2470 4270 7.116662 GTGTTGATACGGATGTACAGTACAAAA 59.883 37.037 17.43 2.47 42.76 2.44
2471 4271 6.587226 GTGTTGATACGGATGTACAGTACAAA 59.413 38.462 17.43 2.09 42.76 2.83
2472 4272 6.094719 GTGTTGATACGGATGTACAGTACAA 58.905 40.000 17.43 0.95 42.76 2.41
2473 4273 5.643664 GTGTTGATACGGATGTACAGTACA 58.356 41.667 15.90 15.90 43.80 2.90
2474 4274 4.731961 CGTGTTGATACGGATGTACAGTAC 59.268 45.833 0.33 3.49 40.22 2.73
2475 4275 4.912214 CGTGTTGATACGGATGTACAGTA 58.088 43.478 0.33 0.00 40.22 2.74
2476 4276 3.766151 CGTGTTGATACGGATGTACAGT 58.234 45.455 0.33 0.00 40.22 3.55
2542 4342 9.558396 TCATGGAGCACTTTATTTTCAAAATTT 57.442 25.926 0.00 0.00 0.00 1.82
2543 4343 9.558396 TTCATGGAGCACTTTATTTTCAAAATT 57.442 25.926 0.00 0.00 0.00 1.82
2544 4344 9.211485 CTTCATGGAGCACTTTATTTTCAAAAT 57.789 29.630 0.02 0.02 0.00 1.82
2545 4345 7.171337 GCTTCATGGAGCACTTTATTTTCAAAA 59.829 33.333 21.68 0.00 42.25 2.44
2546 4346 6.646240 GCTTCATGGAGCACTTTATTTTCAAA 59.354 34.615 21.68 0.00 42.25 2.69
2547 4347 6.015180 AGCTTCATGGAGCACTTTATTTTCAA 60.015 34.615 27.76 0.00 45.12 2.69
2548 4348 5.477984 AGCTTCATGGAGCACTTTATTTTCA 59.522 36.000 27.76 0.00 45.12 2.69
2549 4349 5.958955 AGCTTCATGGAGCACTTTATTTTC 58.041 37.500 27.76 0.00 45.12 2.29
2550 4350 5.392380 CGAGCTTCATGGAGCACTTTATTTT 60.392 40.000 27.76 3.34 45.12 1.82
2551 4351 4.095483 CGAGCTTCATGGAGCACTTTATTT 59.905 41.667 27.76 4.14 45.12 1.40
2552 4352 3.624861 CGAGCTTCATGGAGCACTTTATT 59.375 43.478 27.76 4.96 45.12 1.40
2553 4353 3.201290 CGAGCTTCATGGAGCACTTTAT 58.799 45.455 27.76 5.76 45.12 1.40
2554 4354 2.621338 CGAGCTTCATGGAGCACTTTA 58.379 47.619 27.76 0.00 45.12 1.85
2555 4355 1.446907 CGAGCTTCATGGAGCACTTT 58.553 50.000 27.76 7.00 45.12 2.66
2556 4356 0.392193 CCGAGCTTCATGGAGCACTT 60.392 55.000 27.76 7.40 45.12 3.16
2557 4357 1.220206 CCGAGCTTCATGGAGCACT 59.780 57.895 27.76 8.23 45.12 4.40
2558 4358 1.078848 ACCGAGCTTCATGGAGCAC 60.079 57.895 27.76 20.40 45.12 4.40
2559 4359 1.219124 GACCGAGCTTCATGGAGCA 59.781 57.895 27.76 0.00 45.12 4.26
2560 4360 0.529555 GAGACCGAGCTTCATGGAGC 60.530 60.000 19.03 19.03 43.02 4.70
2561 4361 0.248825 CGAGACCGAGCTTCATGGAG 60.249 60.000 0.00 0.00 38.22 3.86
2562 4362 1.667154 CCGAGACCGAGCTTCATGGA 61.667 60.000 0.00 0.00 38.22 3.41
2563 4363 1.227089 CCGAGACCGAGCTTCATGG 60.227 63.158 0.00 0.00 38.22 3.66
2564 4364 0.108615 AACCGAGACCGAGCTTCATG 60.109 55.000 0.00 0.00 38.22 3.07
2565 4365 0.608640 AAACCGAGACCGAGCTTCAT 59.391 50.000 0.00 0.00 38.22 2.57
2566 4366 1.201647 CTAAACCGAGACCGAGCTTCA 59.798 52.381 0.00 0.00 38.22 3.02
2567 4367 1.910688 CTAAACCGAGACCGAGCTTC 58.089 55.000 0.00 0.00 38.22 3.86
2568 4368 0.108756 GCTAAACCGAGACCGAGCTT 60.109 55.000 0.00 0.00 38.22 3.74
2569 4369 1.248785 TGCTAAACCGAGACCGAGCT 61.249 55.000 0.00 0.00 38.22 4.09
2570 4370 0.179108 ATGCTAAACCGAGACCGAGC 60.179 55.000 0.00 0.00 38.22 5.03
2571 4371 2.295253 AATGCTAAACCGAGACCGAG 57.705 50.000 0.00 0.00 38.22 4.63
2572 4372 2.613691 GAAATGCTAAACCGAGACCGA 58.386 47.619 0.00 0.00 38.22 4.69
2573 4373 1.664151 GGAAATGCTAAACCGAGACCG 59.336 52.381 0.00 0.00 0.00 4.79
2574 4374 1.664151 CGGAAATGCTAAACCGAGACC 59.336 52.381 0.00 0.00 46.94 3.85
2575 4375 2.093783 CACGGAAATGCTAAACCGAGAC 59.906 50.000 16.57 0.00 46.94 3.36
2576 4376 2.028839 TCACGGAAATGCTAAACCGAGA 60.029 45.455 16.57 12.31 46.94 4.04
2577 4377 2.343101 TCACGGAAATGCTAAACCGAG 58.657 47.619 16.57 10.58 46.94 4.63
2578 4378 2.459060 TCACGGAAATGCTAAACCGA 57.541 45.000 16.57 0.00 46.94 4.69
2580 4380 5.510671 CATACATCACGGAAATGCTAAACC 58.489 41.667 0.00 0.00 0.00 3.27
2581 4381 4.970003 GCATACATCACGGAAATGCTAAAC 59.030 41.667 0.00 0.00 39.80 2.01
2582 4382 5.168526 GCATACATCACGGAAATGCTAAA 57.831 39.130 0.00 0.00 39.80 1.85
2583 4383 4.811555 GCATACATCACGGAAATGCTAA 57.188 40.909 0.00 0.00 39.80 3.09
2585 4385 2.923121 AGCATACATCACGGAAATGCT 58.077 42.857 2.42 2.42 46.28 3.79
2586 4386 2.874701 AGAGCATACATCACGGAAATGC 59.125 45.455 0.00 0.00 42.52 3.56
2587 4387 5.928264 TGATAGAGCATACATCACGGAAATG 59.072 40.000 0.00 0.00 0.00 2.32
2588 4388 6.101650 TGATAGAGCATACATCACGGAAAT 57.898 37.500 0.00 0.00 0.00 2.17
2589 4389 5.529581 TGATAGAGCATACATCACGGAAA 57.470 39.130 0.00 0.00 0.00 3.13
2590 4390 5.728637 ATGATAGAGCATACATCACGGAA 57.271 39.130 0.00 0.00 31.83 4.30
2591 4391 6.196079 GTATGATAGAGCATACATCACGGA 57.804 41.667 11.98 0.00 46.20 4.69
2669 5029 1.564348 GAGATATGTTGGGTGGTGGGT 59.436 52.381 0.00 0.00 0.00 4.51
2707 5067 4.521146 AGATAACAGAAAGTGATGGCAGG 58.479 43.478 0.00 0.00 0.00 4.85
2718 5078 6.701841 CGCCAAAGAGCTATAGATAACAGAAA 59.298 38.462 3.21 0.00 0.00 2.52
2719 5079 6.183360 ACGCCAAAGAGCTATAGATAACAGAA 60.183 38.462 3.21 0.00 0.00 3.02
2799 5159 7.553334 TCTTGTCACTTATGGTCCAACTATAC 58.447 38.462 0.00 0.00 0.00 1.47
2836 5196 1.202879 TGCCTCCACCCACTTACAAAG 60.203 52.381 0.00 0.00 0.00 2.77
2887 5247 1.067565 CCGTGTGTGTAGCATCACTCT 60.068 52.381 11.42 0.00 38.90 3.24
2893 5253 2.238847 ATCCGCCGTGTGTGTAGCAT 62.239 55.000 0.00 0.00 0.00 3.79
2977 5337 0.830444 AGTGACTGGCCGAGGTACAA 60.830 55.000 0.00 0.00 0.00 2.41
2982 5342 2.262915 GACAGTGACTGGCCGAGG 59.737 66.667 17.92 0.00 32.43 4.63
3002 5362 3.941483 CTGCATTGAGAACTTCGGGTTAT 59.059 43.478 0.00 0.00 38.41 1.89
3051 5411 1.766496 TGGTTTTTGTCTCGAGGAGGT 59.234 47.619 13.56 0.00 0.00 3.85
3052 5412 2.543777 TGGTTTTTGTCTCGAGGAGG 57.456 50.000 13.56 0.00 0.00 4.30
3053 5413 5.438761 AAAATGGTTTTTGTCTCGAGGAG 57.561 39.130 13.56 0.00 33.79 3.69
3095 5455 2.090400 CATATGATGCAGAGTCCGGG 57.910 55.000 0.00 0.00 0.00 5.73
3150 5512 4.134563 AGACTTTGTACCGCACTTCATTT 58.865 39.130 0.00 0.00 0.00 2.32
3152 5514 3.402628 AGACTTTGTACCGCACTTCAT 57.597 42.857 0.00 0.00 0.00 2.57
3153 5515 2.869801 CAAGACTTTGTACCGCACTTCA 59.130 45.455 0.00 0.00 0.00 3.02
3154 5516 3.128349 TCAAGACTTTGTACCGCACTTC 58.872 45.455 0.00 0.00 35.73 3.01


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

AutoCloner maintained by Alex Coulton.