Multiple sequence alignment - TraesCS6A01G412800

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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 TraesCS6A01G412800 chr6A 100.000 1737 0 0 861 2597 614381484 614383220 0.000000e+00 3208
1 TraesCS6A01G412800 chr6A 100.000 552 0 0 1 552 614380624 614381175 0.000000e+00 1020
2 TraesCS6A01G412800 chr6A 88.021 192 23 0 956 1147 441486255 441486446 7.230000e-56 228
3 TraesCS6A01G412800 chr6D 84.830 1826 130 73 861 2596 469205271 469207039 0.000000e+00 1701
4 TraesCS6A01G412800 chr6D 84.364 582 58 14 1 552 469204243 469204821 8.180000e-150 540
5 TraesCS6A01G412800 chr6D 87.255 204 26 0 956 1159 306129277 306129480 1.550000e-57 233
6 TraesCS6A01G412800 chr6D 83.186 226 20 10 2085 2305 469224345 469224557 9.490000e-45 191
7 TraesCS6A01G412800 chr6B 90.162 1047 65 23 926 1949 715448862 715449893 0.000000e+00 1328
8 TraesCS6A01G412800 chr6B 81.157 674 72 41 1948 2596 715449923 715450566 8.350000e-135 490
9 TraesCS6A01G412800 chr6B 83.527 516 59 17 1 506 715447860 715448359 2.360000e-125 459
10 TraesCS6A01G412800 chr6B 87.019 208 26 1 956 1162 473055963 473056170 1.550000e-57 233
11 TraesCS6A01G412800 chr7A 89.731 633 46 15 920 1544 165448389 165447768 0.000000e+00 791
12 TraesCS6A01G412800 chr2B 87.168 226 27 2 954 1178 557227662 557227438 3.320000e-64 255
13 TraesCS6A01G412800 chr2A 86.726 226 28 2 954 1178 618267351 618267127 1.540000e-62 250
14 TraesCS6A01G412800 chr2D 86.667 225 26 3 954 1175 476345881 476345658 2.000000e-61 246


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 TraesCS6A01G412800 chr6A 614380624 614383220 2596 False 2114.0 3208 100.000000 1 2597 2 chr6A.!!$F2 2596
1 TraesCS6A01G412800 chr6D 469204243 469207039 2796 False 1120.5 1701 84.597000 1 2596 2 chr6D.!!$F3 2595
2 TraesCS6A01G412800 chr6B 715447860 715450566 2706 False 759.0 1328 84.948667 1 2596 3 chr6B.!!$F2 2595
3 TraesCS6A01G412800 chr7A 165447768 165448389 621 True 791.0 791 89.731000 920 1544 1 chr7A.!!$R1 624

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
331 361 0.694783 TTACCCCACCCTCACACACA 60.695 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 2607 1.135139 TGCACTCTTCTATCGGCTGTC 59.865 52.381 0.0 0.0 0.0 3.51 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
47 50 2.309528 ACGTGTGCGGATGACATAAT 57.690 45.000 0.00 0.00 43.45 1.28
51 54 2.806244 GTGTGCGGATGACATAATACCC 59.194 50.000 0.00 0.00 0.00 3.69
53 56 3.898741 TGTGCGGATGACATAATACCCTA 59.101 43.478 0.00 0.00 0.00 3.53
56 59 4.462834 TGCGGATGACATAATACCCTAGAG 59.537 45.833 0.00 0.00 0.00 2.43
57 60 4.463186 GCGGATGACATAATACCCTAGAGT 59.537 45.833 0.00 0.00 0.00 3.24
60 63 6.127869 CGGATGACATAATACCCTAGAGTCAG 60.128 46.154 0.00 0.00 37.85 3.51
79 82 3.266772 TCAGGGAAGACCATGTTTAGCAT 59.733 43.478 0.00 0.00 46.50 3.79
94 97 4.503741 TTAGCATGTGCAGGTTTTTCTC 57.496 40.909 7.83 0.00 45.16 2.87
97 100 2.819608 GCATGTGCAGGTTTTTCTCCTA 59.180 45.455 0.00 0.00 41.59 2.94
255 260 1.608590 CCAGGCTGTCAAAAACGTCAT 59.391 47.619 14.43 0.00 0.00 3.06
323 353 1.633945 GACAACTCATTACCCCACCCT 59.366 52.381 0.00 0.00 0.00 4.34
328 358 0.988832 TCATTACCCCACCCTCACAC 59.011 55.000 0.00 0.00 0.00 3.82
330 360 0.696501 ATTACCCCACCCTCACACAC 59.303 55.000 0.00 0.00 0.00 3.82
331 361 0.694783 TTACCCCACCCTCACACACA 60.695 55.000 0.00 0.00 0.00 3.72
345 375 1.277842 ACACACACCACTCACTGACAA 59.722 47.619 0.00 0.00 0.00 3.18
348 378 2.205074 CACACCACTCACTGACAACTC 58.795 52.381 0.00 0.00 0.00 3.01
357 387 1.079543 CTGACAACTCGGCTCCAGG 60.080 63.158 0.00 0.00 0.00 4.45
366 396 2.123982 GGCTCCAGGGAAGCATGG 60.124 66.667 2.65 0.00 37.97 3.66
372 402 3.747579 AGGGAAGCATGGCCCCAG 61.748 66.667 0.00 0.00 45.89 4.45
373 403 3.743017 GGGAAGCATGGCCCCAGA 61.743 66.667 0.00 0.00 39.89 3.86
374 404 2.605299 GGAAGCATGGCCCCAGAT 59.395 61.111 0.00 0.00 0.00 2.90
380 410 1.177256 GCATGGCCCCAGATGTCATC 61.177 60.000 0.00 4.52 0.00 2.92
382 412 2.060567 ATGGCCCCAGATGTCATCGG 62.061 60.000 0.00 10.99 0.00 4.18
383 413 2.111878 GCCCCAGATGTCATCGGG 59.888 66.667 24.58 24.58 43.23 5.14
391 421 2.034432 CAGATGTCATCGGGAGAGAGTG 59.966 54.545 7.18 0.00 45.48 3.51
395 425 2.444895 ATCGGGAGAGAGTGGGGC 60.445 66.667 0.00 0.00 45.48 5.80
399 429 2.363172 GGGAGAGAGTGGGGCTCAC 61.363 68.421 10.20 10.20 46.47 3.51
407 437 1.376037 GTGGGGCTCACTGCTGTAC 60.376 63.158 11.06 0.00 42.86 2.90
411 442 1.801913 GGCTCACTGCTGTACGTCG 60.802 63.158 0.00 0.00 42.39 5.12
885 1059 1.004440 GGAGGACAAGCAGCTCGTT 60.004 57.895 0.00 0.00 0.00 3.85
892 1066 3.165160 AAGCAGCTCGTTCCGGTGT 62.165 57.895 0.00 0.00 32.75 4.16
894 1068 2.432628 CAGCTCGTTCCGGTGTCC 60.433 66.667 0.00 0.00 0.00 4.02
1539 1760 2.756283 CTCGCCTCCTTCTCCGGT 60.756 66.667 0.00 0.00 0.00 5.28
1597 1818 2.203788 AGGAGACCGCCCACTGAA 60.204 61.111 0.00 0.00 0.00 3.02
1646 1870 0.394488 GCAGGGCTAGGGTTTCTTCC 60.394 60.000 0.00 0.00 0.00 3.46
1720 1950 5.163814 CGGCAAGAGGAAAAGATTACTGAAG 60.164 44.000 0.00 0.00 26.43 3.02
1782 2024 0.539051 TAAGCTTGCTCCTCTGCTCC 59.461 55.000 9.86 0.00 34.38 4.70
1788 2030 1.381056 GCTCCTCTGCTCCCTCTCA 60.381 63.158 0.00 0.00 0.00 3.27
1789 2031 1.394266 GCTCCTCTGCTCCCTCTCAG 61.394 65.000 0.00 0.00 0.00 3.35
1792 2034 1.641192 TCCTCTGCTCCCTCTCAGTTA 59.359 52.381 0.00 0.00 0.00 2.24
1800 2052 3.511934 GCTCCCTCTCAGTTAAGTTCAGA 59.488 47.826 0.00 0.00 0.00 3.27
1821 2073 1.132977 TGGTTAGGTCAGGTCAGGTCA 60.133 52.381 0.00 0.00 0.00 4.02
1822 2074 1.550976 GGTTAGGTCAGGTCAGGTCAG 59.449 57.143 0.00 0.00 0.00 3.51
1823 2075 1.550976 GTTAGGTCAGGTCAGGTCAGG 59.449 57.143 0.00 0.00 0.00 3.86
1824 2076 0.784495 TAGGTCAGGTCAGGTCAGGT 59.216 55.000 0.00 0.00 0.00 4.00
1825 2077 0.543174 AGGTCAGGTCAGGTCAGGTC 60.543 60.000 0.00 0.00 0.00 3.85
1826 2078 0.832135 GGTCAGGTCAGGTCAGGTCA 60.832 60.000 0.00 0.00 0.00 4.02
1827 2079 0.605589 GTCAGGTCAGGTCAGGTCAG 59.394 60.000 0.00 0.00 0.00 3.51
1828 2080 0.542938 TCAGGTCAGGTCAGGTCAGG 60.543 60.000 0.00 0.00 0.00 3.86
1829 2081 0.833834 CAGGTCAGGTCAGGTCAGGT 60.834 60.000 0.00 0.00 0.00 4.00
1830 2082 0.833834 AGGTCAGGTCAGGTCAGGTG 60.834 60.000 0.00 0.00 0.00 4.00
1870 2122 3.700577 CGGGTAGCAACAGCAATTG 57.299 52.632 0.00 0.00 0.00 2.32
2010 2297 5.619533 GCTGCTGATTCCAAGAAAGAAGAAG 60.620 44.000 0.00 0.00 0.00 2.85
2029 2316 4.160252 AGAAGAAGAAAAGGCTTGCACAAA 59.840 37.500 0.00 0.00 0.00 2.83
2031 2318 4.625028 AGAAGAAAAGGCTTGCACAAATC 58.375 39.130 0.00 0.00 0.00 2.17
2032 2319 4.343239 AGAAGAAAAGGCTTGCACAAATCT 59.657 37.500 0.00 0.00 0.00 2.40
2037 2324 4.612264 AAGGCTTGCACAAATCTCAAAT 57.388 36.364 0.00 0.00 0.00 2.32
2038 2325 3.921677 AGGCTTGCACAAATCTCAAATG 58.078 40.909 0.00 0.00 0.00 2.32
2039 2326 3.322828 AGGCTTGCACAAATCTCAAATGT 59.677 39.130 0.00 0.00 0.00 2.71
2079 2367 1.453762 GGAGGATGAGCAAGCATGGC 61.454 60.000 0.00 0.00 32.57 4.40
2094 2382 2.161855 CATGGCCTTCAGTAAGTTGCA 58.838 47.619 3.32 0.00 0.00 4.08
2106 2394 0.888285 AAGTTGCACCTCTGCTCTGC 60.888 55.000 0.00 0.00 44.57 4.26
2119 2407 3.194542 TCTGCTCTGCTTCTTAGGTCTTC 59.805 47.826 0.00 0.00 0.00 2.87
2124 2412 5.471797 GCTCTGCTTCTTAGGTCTTCTTTTT 59.528 40.000 0.00 0.00 0.00 1.94
2193 2490 9.113838 AGTGCTTGGTGAGAATAATAATAAGTG 57.886 33.333 0.00 0.00 0.00 3.16
2258 2557 5.128499 TCTTTTGATTGTTTGATGGGTGTGT 59.872 36.000 0.00 0.00 0.00 3.72
2275 2574 2.682352 TGTGTCAATTGTGTGTCACCAG 59.318 45.455 5.13 0.00 32.73 4.00
2277 2576 2.092699 TGTCAATTGTGTGTCACCAGGA 60.093 45.455 5.13 0.00 32.73 3.86
2291 2590 4.337555 GTCACCAGGAATGGAATTGATCAG 59.662 45.833 0.31 0.00 36.07 2.90
2305 2604 8.814931 TGGAATTGATCAGTGGACAAAAATAAT 58.185 29.630 0.00 0.00 0.00 1.28
2306 2605 9.090692 GGAATTGATCAGTGGACAAAAATAATG 57.909 33.333 0.00 0.00 0.00 1.90
2308 2607 9.865321 AATTGATCAGTGGACAAAAATAATGAG 57.135 29.630 0.00 0.00 0.00 2.90
2313 2612 6.072508 TCAGTGGACAAAAATAATGAGACAGC 60.073 38.462 0.00 0.00 0.00 4.40
2314 2613 5.183904 AGTGGACAAAAATAATGAGACAGCC 59.816 40.000 0.00 0.00 0.00 4.85
2317 2616 5.066505 GGACAAAAATAATGAGACAGCCGAT 59.933 40.000 0.00 0.00 0.00 4.18
2319 2618 7.251704 ACAAAAATAATGAGACAGCCGATAG 57.748 36.000 0.00 0.00 0.00 2.08
2321 2620 7.552687 ACAAAAATAATGAGACAGCCGATAGAA 59.447 33.333 0.00 0.00 39.76 2.10
2322 2621 7.721286 AAAATAATGAGACAGCCGATAGAAG 57.279 36.000 0.00 0.00 39.76 2.85
2323 2622 6.656632 AATAATGAGACAGCCGATAGAAGA 57.343 37.500 0.00 0.00 39.76 2.87
2325 2624 3.006112 TGAGACAGCCGATAGAAGAGT 57.994 47.619 0.00 0.00 39.76 3.24
2326 2625 2.685388 TGAGACAGCCGATAGAAGAGTG 59.315 50.000 0.00 0.00 39.76 3.51
2331 2630 2.034878 AGCCGATAGAAGAGTGCATCA 58.965 47.619 0.00 0.00 39.76 3.07
2333 2632 2.992543 GCCGATAGAAGAGTGCATCATC 59.007 50.000 0.00 0.00 39.76 2.92
2335 2634 4.236147 CCGATAGAAGAGTGCATCATCTG 58.764 47.826 11.60 0.36 36.65 2.90
2338 2637 5.506982 CGATAGAAGAGTGCATCATCTGTCA 60.507 44.000 18.41 3.68 41.39 3.58
2343 2642 2.871022 GAGTGCATCATCTGTCATGTCC 59.129 50.000 0.00 0.00 0.00 4.02
2344 2643 2.237893 AGTGCATCATCTGTCATGTCCA 59.762 45.455 0.00 0.00 0.00 4.02
2345 2644 3.118000 AGTGCATCATCTGTCATGTCCAT 60.118 43.478 0.00 0.00 0.00 3.41
2346 2645 3.250280 GTGCATCATCTGTCATGTCCATC 59.750 47.826 0.00 0.00 0.00 3.51
2347 2646 2.812591 GCATCATCTGTCATGTCCATCC 59.187 50.000 0.00 0.00 0.00 3.51
2348 2647 3.746432 GCATCATCTGTCATGTCCATCCA 60.746 47.826 0.00 0.00 0.00 3.41
2350 2649 2.158856 TCATCTGTCATGTCCATCCAGC 60.159 50.000 0.00 0.00 0.00 4.85
2351 2650 1.278537 TCTGTCATGTCCATCCAGCA 58.721 50.000 0.00 0.00 0.00 4.41
2352 2651 1.208776 TCTGTCATGTCCATCCAGCAG 59.791 52.381 0.00 0.00 0.00 4.24
2353 2652 0.393402 TGTCATGTCCATCCAGCAGC 60.393 55.000 0.00 0.00 0.00 5.25
2354 2653 0.393402 GTCATGTCCATCCAGCAGCA 60.393 55.000 0.00 0.00 0.00 4.41
2355 2654 0.393402 TCATGTCCATCCAGCAGCAC 60.393 55.000 0.00 0.00 0.00 4.40
2356 2655 1.077212 ATGTCCATCCAGCAGCACC 60.077 57.895 0.00 0.00 0.00 5.01
2357 2656 2.439156 GTCCATCCAGCAGCACCC 60.439 66.667 0.00 0.00 0.00 4.61
2359 2658 2.124403 CCATCCAGCAGCACCCTC 60.124 66.667 0.00 0.00 0.00 4.30
2360 2659 2.677289 CCATCCAGCAGCACCCTCT 61.677 63.158 0.00 0.00 0.00 3.69
2361 2660 1.153208 CATCCAGCAGCACCCTCTC 60.153 63.158 0.00 0.00 0.00 3.20
2362 2661 1.614525 ATCCAGCAGCACCCTCTCA 60.615 57.895 0.00 0.00 0.00 3.27
2363 2662 0.987081 ATCCAGCAGCACCCTCTCAT 60.987 55.000 0.00 0.00 0.00 2.90
2380 2692 1.018148 CATCCGCTACGTCTCTGTCT 58.982 55.000 0.00 0.00 0.00 3.41
2396 2708 5.893824 TCTCTGTCTTTGCATCCTAGTATCA 59.106 40.000 0.00 0.00 0.00 2.15
2404 2716 3.244318 TGCATCCTAGTATCATGCCACTG 60.244 47.826 8.75 1.23 41.97 3.66
2407 2719 5.802465 CATCCTAGTATCATGCCACTGATT 58.198 41.667 8.75 0.00 37.13 2.57
2408 2720 5.894298 TCCTAGTATCATGCCACTGATTT 57.106 39.130 8.75 0.00 37.13 2.17
2410 2722 6.291377 TCCTAGTATCATGCCACTGATTTTC 58.709 40.000 8.75 0.00 37.13 2.29
2415 2727 7.285566 AGTATCATGCCACTGATTTTCACTAT 58.714 34.615 0.00 0.00 37.13 2.12
2434 2758 7.860613 TCACTATTATCATACCATTGTTTGCG 58.139 34.615 0.00 0.00 0.00 4.85
2446 2770 2.791383 TGTTTGCGAAATTCAGGTGG 57.209 45.000 0.00 0.00 0.00 4.61
2456 2780 3.918253 TTCAGGTGGCGATGCACCC 62.918 63.158 6.27 0.00 42.21 4.61
2519 2865 3.788616 TTTTGCGGCTGCTGTTGCC 62.789 57.895 20.27 0.00 46.42 4.52
2528 2874 4.332637 GCTGTTGCCGGCACTGTG 62.333 66.667 32.95 20.19 42.86 3.66
2529 2875 2.591429 CTGTTGCCGGCACTGTGA 60.591 61.111 32.95 12.15 0.00 3.58
2539 2885 3.168628 GCACTGTGATGTGTTGTGC 57.831 52.632 12.86 0.00 45.23 4.57
2579 2925 7.450634 AGCTGTGGAGGTAGAATAATAATCGTA 59.549 37.037 0.00 0.00 0.00 3.43
2580 2926 7.755822 GCTGTGGAGGTAGAATAATAATCGTAG 59.244 40.741 0.00 0.00 0.00 3.51
2581 2927 8.118976 TGTGGAGGTAGAATAATAATCGTAGG 57.881 38.462 0.00 0.00 0.00 3.18
2596 2942 0.470268 GTAGGGAGTGGGGGCTCTAG 60.470 65.000 0.00 0.00 35.89 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.419922 CGCACACGTATCAGGTTGC 59.580 57.895 0.00 0.00 33.53 4.17
19 20 0.389296 TCCGCACACGTATCAGGTTG 60.389 55.000 0.00 0.00 37.70 3.77
21 24 0.179111 CATCCGCACACGTATCAGGT 60.179 55.000 0.00 0.00 37.70 4.00
24 27 0.528470 TGTCATCCGCACACGTATCA 59.472 50.000 0.00 0.00 37.70 2.15
27 30 2.943449 TTATGTCATCCGCACACGTA 57.057 45.000 0.00 0.00 37.70 3.57
29 32 2.475111 GGTATTATGTCATCCGCACACG 59.525 50.000 0.00 0.00 39.67 4.49
51 54 3.370104 ACATGGTCTTCCCTGACTCTAG 58.630 50.000 0.00 0.00 37.16 2.43
53 56 2.334006 ACATGGTCTTCCCTGACTCT 57.666 50.000 0.00 0.00 37.16 3.24
56 59 3.010420 GCTAAACATGGTCTTCCCTGAC 58.990 50.000 0.00 0.00 34.26 3.51
57 60 2.642311 TGCTAAACATGGTCTTCCCTGA 59.358 45.455 0.00 0.00 34.26 3.86
79 82 6.539173 TCTTATTAGGAGAAAAACCTGCACA 58.461 36.000 0.00 0.00 38.31 4.57
137 140 4.493618 TGGTGAAATAATTCCCCCACAAA 58.506 39.130 0.00 0.00 32.58 2.83
139 142 3.835395 GTTGGTGAAATAATTCCCCCACA 59.165 43.478 0.00 0.00 36.10 4.17
140 143 3.119280 CGTTGGTGAAATAATTCCCCCAC 60.119 47.826 0.00 0.00 36.10 4.61
141 144 3.093057 CGTTGGTGAAATAATTCCCCCA 58.907 45.455 0.00 0.00 32.58 4.96
142 145 2.429250 CCGTTGGTGAAATAATTCCCCC 59.571 50.000 0.00 0.00 32.58 5.40
144 147 4.794278 AACCGTTGGTGAAATAATTCCC 57.206 40.909 0.00 0.00 35.34 3.97
255 260 2.025321 GGCAATTACCTCTTTCCAGGGA 60.025 50.000 0.00 0.00 37.96 4.20
323 353 1.134818 GTCAGTGAGTGGTGTGTGTGA 60.135 52.381 0.00 0.00 0.00 3.58
328 358 2.205074 GAGTTGTCAGTGAGTGGTGTG 58.795 52.381 0.00 0.00 0.00 3.82
330 360 1.491670 CGAGTTGTCAGTGAGTGGTG 58.508 55.000 0.00 0.00 0.00 4.17
331 361 0.389391 CCGAGTTGTCAGTGAGTGGT 59.611 55.000 0.00 0.00 0.00 4.16
345 375 3.394836 GCTTCCCTGGAGCCGAGT 61.395 66.667 0.00 0.00 0.00 4.18
348 378 2.515523 CATGCTTCCCTGGAGCCG 60.516 66.667 5.07 0.00 0.00 5.52
357 387 1.831286 CATCTGGGGCCATGCTTCC 60.831 63.158 4.39 0.00 0.00 3.46
366 396 2.111878 CCCGATGACATCTGGGGC 59.888 66.667 25.63 0.00 38.56 5.80
372 402 1.339610 CCACTCTCTCCCGATGACATC 59.660 57.143 5.28 5.28 0.00 3.06
373 403 1.407936 CCACTCTCTCCCGATGACAT 58.592 55.000 0.00 0.00 0.00 3.06
374 404 0.684479 CCCACTCTCTCCCGATGACA 60.684 60.000 0.00 0.00 0.00 3.58
380 410 3.151022 GAGCCCCACTCTCTCCCG 61.151 72.222 0.00 0.00 42.62 5.14
382 412 3.304251 GTGAGCCCCACTCTCTCC 58.696 66.667 0.07 0.00 46.41 3.71
395 425 0.794981 GCTCGACGTACAGCAGTGAG 60.795 60.000 12.30 0.00 35.56 3.51
864 1038 2.925170 AGCTGCTTGTCCTCCGGT 60.925 61.111 0.00 0.00 0.00 5.28
865 1039 2.125350 GAGCTGCTTGTCCTCCGG 60.125 66.667 2.53 0.00 0.00 5.14
894 1068 3.550992 CCATTCGTCCCGTTCGCG 61.551 66.667 0.00 0.00 40.93 5.87
951 1144 2.046892 CTGTGCCGGTCCTTGGAG 60.047 66.667 1.90 0.00 0.00 3.86
1234 1442 4.660938 GAGGTGGTGGTGGTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
1235 1443 4.660938 GGAGGTGGTGGTGGTGGC 62.661 72.222 0.00 0.00 0.00 5.01
1236 1444 3.966543 GGGAGGTGGTGGTGGTGG 61.967 72.222 0.00 0.00 0.00 4.61
1293 1508 4.595538 TTGCCGTTGCCGTCGTCT 62.596 61.111 0.00 0.00 36.33 4.18
1578 1799 2.681778 CAGTGGGCGGTCTCCTCT 60.682 66.667 0.00 0.00 0.00 3.69
1720 1950 2.154462 CCACCTTGTCTGATGAACACC 58.846 52.381 0.00 0.00 0.00 4.16
1782 2024 5.413309 ACCATCTGAACTTAACTGAGAGG 57.587 43.478 0.00 0.00 0.00 3.69
1788 2030 6.295916 CCTGACCTAACCATCTGAACTTAACT 60.296 42.308 0.00 0.00 0.00 2.24
1789 2031 5.875359 CCTGACCTAACCATCTGAACTTAAC 59.125 44.000 0.00 0.00 0.00 2.01
1792 2034 3.910627 ACCTGACCTAACCATCTGAACTT 59.089 43.478 0.00 0.00 0.00 2.66
1800 2052 2.188817 GACCTGACCTGACCTAACCAT 58.811 52.381 0.00 0.00 0.00 3.55
1821 2073 1.630878 GAGACCCAATTCACCTGACCT 59.369 52.381 0.00 0.00 0.00 3.85
1822 2074 1.630878 AGAGACCCAATTCACCTGACC 59.369 52.381 0.00 0.00 0.00 4.02
1823 2075 4.553330 TTAGAGACCCAATTCACCTGAC 57.447 45.455 0.00 0.00 0.00 3.51
1824 2076 5.779241 ATTTAGAGACCCAATTCACCTGA 57.221 39.130 0.00 0.00 0.00 3.86
1825 2077 6.660949 AGAAATTTAGAGACCCAATTCACCTG 59.339 38.462 0.00 0.00 0.00 4.00
1826 2078 6.660949 CAGAAATTTAGAGACCCAATTCACCT 59.339 38.462 0.00 0.00 0.00 4.00
1827 2079 6.625960 GCAGAAATTTAGAGACCCAATTCACC 60.626 42.308 0.00 0.00 0.00 4.02
1828 2080 6.325596 GCAGAAATTTAGAGACCCAATTCAC 58.674 40.000 0.00 0.00 0.00 3.18
1829 2081 5.123820 CGCAGAAATTTAGAGACCCAATTCA 59.876 40.000 0.00 0.00 0.00 2.57
1830 2082 5.449177 CCGCAGAAATTTAGAGACCCAATTC 60.449 44.000 0.00 0.00 0.00 2.17
2010 2297 4.625028 AGATTTGTGCAAGCCTTTTCTTC 58.375 39.130 0.00 0.00 0.00 2.87
2029 2316 4.768448 TGCAGAATTGTGGACATTTGAGAT 59.232 37.500 4.57 0.00 0.00 2.75
2031 2318 4.508461 TGCAGAATTGTGGACATTTGAG 57.492 40.909 4.57 0.00 0.00 3.02
2032 2319 4.523558 TGATGCAGAATTGTGGACATTTGA 59.476 37.500 4.57 0.00 0.00 2.69
2037 2324 3.753815 TCTTGATGCAGAATTGTGGACA 58.246 40.909 4.57 0.59 0.00 4.02
2038 2325 4.439700 CCATCTTGATGCAGAATTGTGGAC 60.440 45.833 4.57 0.00 0.00 4.02
2039 2326 3.697542 CCATCTTGATGCAGAATTGTGGA 59.302 43.478 4.57 1.35 0.00 4.02
2079 2367 3.070018 CAGAGGTGCAACTTACTGAAGG 58.930 50.000 13.86 0.00 36.95 3.46
2094 2382 1.830477 CCTAAGAAGCAGAGCAGAGGT 59.170 52.381 0.00 0.00 0.00 3.85
2138 2432 6.040729 TCAATCCAGAGCACAAAAGAAATGAA 59.959 34.615 0.00 0.00 0.00 2.57
2140 2434 5.775686 TCAATCCAGAGCACAAAAGAAATG 58.224 37.500 0.00 0.00 0.00 2.32
2141 2435 6.409524 TTCAATCCAGAGCACAAAAGAAAT 57.590 33.333 0.00 0.00 0.00 2.17
2152 2446 4.201990 CCAAGCACTAATTCAATCCAGAGC 60.202 45.833 0.00 0.00 0.00 4.09
2258 2557 3.289407 TTCCTGGTGACACACAATTGA 57.711 42.857 13.59 0.00 35.86 2.57
2275 2574 4.272489 TGTCCACTGATCAATTCCATTCC 58.728 43.478 0.00 0.00 0.00 3.01
2277 2576 6.669125 TTTTGTCCACTGATCAATTCCATT 57.331 33.333 0.00 0.00 0.00 3.16
2291 2590 5.402398 GGCTGTCTCATTATTTTTGTCCAC 58.598 41.667 0.00 0.00 0.00 4.02
2305 2604 2.685388 CACTCTTCTATCGGCTGTCTCA 59.315 50.000 0.00 0.00 0.00 3.27
2306 2605 2.542824 GCACTCTTCTATCGGCTGTCTC 60.543 54.545 0.00 0.00 0.00 3.36
2308 2607 1.135139 TGCACTCTTCTATCGGCTGTC 59.865 52.381 0.00 0.00 0.00 3.51
2313 2612 4.236147 CAGATGATGCACTCTTCTATCGG 58.764 47.826 11.48 1.40 36.51 4.18
2314 2613 4.869215 ACAGATGATGCACTCTTCTATCG 58.131 43.478 11.48 5.80 36.51 2.92
2317 2616 5.128335 ACATGACAGATGATGCACTCTTCTA 59.872 40.000 0.00 2.26 36.51 2.10
2319 2618 4.190001 ACATGACAGATGATGCACTCTTC 58.810 43.478 0.00 0.00 0.00 2.87
2321 2620 3.431905 GGACATGACAGATGATGCACTCT 60.432 47.826 0.00 0.00 0.00 3.24
2322 2621 2.871022 GGACATGACAGATGATGCACTC 59.129 50.000 0.00 0.00 0.00 3.51
2323 2622 2.237893 TGGACATGACAGATGATGCACT 59.762 45.455 0.00 0.00 0.00 4.40
2325 2624 3.473625 GATGGACATGACAGATGATGCA 58.526 45.455 0.00 0.00 0.00 3.96
2326 2625 2.812591 GGATGGACATGACAGATGATGC 59.187 50.000 0.00 0.00 0.00 3.91
2331 2630 1.841919 TGCTGGATGGACATGACAGAT 59.158 47.619 14.28 0.00 0.00 2.90
2333 2632 1.664873 CTGCTGGATGGACATGACAG 58.335 55.000 0.00 8.45 0.00 3.51
2335 2634 0.393402 TGCTGCTGGATGGACATGAC 60.393 55.000 0.00 0.00 0.00 3.06
2338 2637 1.077212 GGTGCTGCTGGATGGACAT 60.077 57.895 0.00 0.00 0.00 3.06
2343 2642 1.153208 GAGAGGGTGCTGCTGGATG 60.153 63.158 0.00 0.00 0.00 3.51
2344 2643 0.987081 ATGAGAGGGTGCTGCTGGAT 60.987 55.000 0.00 0.00 0.00 3.41
2345 2644 1.614525 ATGAGAGGGTGCTGCTGGA 60.615 57.895 0.00 0.00 0.00 3.86
2346 2645 1.153208 GATGAGAGGGTGCTGCTGG 60.153 63.158 0.00 0.00 0.00 4.85
2347 2646 1.153208 GGATGAGAGGGTGCTGCTG 60.153 63.158 0.00 0.00 0.00 4.41
2348 2647 2.729479 CGGATGAGAGGGTGCTGCT 61.729 63.158 0.00 0.00 0.00 4.24
2350 2649 1.395045 TAGCGGATGAGAGGGTGCTG 61.395 60.000 0.00 0.00 34.08 4.41
2351 2650 1.075970 TAGCGGATGAGAGGGTGCT 60.076 57.895 0.00 0.00 36.51 4.40
2352 2651 1.068250 GTAGCGGATGAGAGGGTGC 59.932 63.158 0.00 0.00 0.00 5.01
2353 2652 1.360551 CGTAGCGGATGAGAGGGTG 59.639 63.158 0.00 0.00 0.00 4.61
2354 2653 1.076923 ACGTAGCGGATGAGAGGGT 60.077 57.895 0.00 0.00 0.00 4.34
2355 2654 0.820074 AGACGTAGCGGATGAGAGGG 60.820 60.000 0.00 0.00 0.00 4.30
2356 2655 0.589223 GAGACGTAGCGGATGAGAGG 59.411 60.000 0.00 0.00 0.00 3.69
2357 2656 1.262950 CAGAGACGTAGCGGATGAGAG 59.737 57.143 0.00 0.00 0.00 3.20
2359 2658 1.003331 GACAGAGACGTAGCGGATGAG 60.003 57.143 0.00 0.00 0.00 2.90
2360 2659 1.015109 GACAGAGACGTAGCGGATGA 58.985 55.000 0.00 0.00 0.00 2.92
2361 2660 1.018148 AGACAGAGACGTAGCGGATG 58.982 55.000 0.00 0.00 0.00 3.51
2362 2661 1.752683 AAGACAGAGACGTAGCGGAT 58.247 50.000 0.00 0.00 0.00 4.18
2363 2662 1.199327 CAAAGACAGAGACGTAGCGGA 59.801 52.381 0.00 0.00 0.00 5.54
2380 2692 4.136796 GTGGCATGATACTAGGATGCAAA 58.863 43.478 15.75 5.35 43.58 3.68
2396 2708 8.701908 ATGATAATAGTGAAAATCAGTGGCAT 57.298 30.769 0.00 0.00 32.25 4.40
2408 2720 8.341903 CGCAAACAATGGTATGATAATAGTGAA 58.658 33.333 0.00 0.00 0.00 3.18
2410 2722 7.860613 TCGCAAACAATGGTATGATAATAGTG 58.139 34.615 0.00 0.00 0.00 2.74
2415 2727 8.246871 TGAATTTCGCAAACAATGGTATGATAA 58.753 29.630 0.00 0.00 0.00 1.75
2434 2758 0.810648 TGCATCGCCACCTGAATTTC 59.189 50.000 0.00 0.00 0.00 2.17
2456 2780 3.316308 ACTTCTAAACAACAAGCTGCTGG 59.684 43.478 1.35 1.47 0.00 4.85
2519 2865 0.041047 CACAACACATCACAGTGCCG 60.041 55.000 0.00 0.00 43.23 5.69
2522 2868 1.598676 GCAGCACAACACATCACAGTG 60.599 52.381 0.00 0.00 44.93 3.66
2525 2871 1.001158 CATGCAGCACAACACATCACA 60.001 47.619 0.00 0.00 0.00 3.58
2526 2872 1.001048 ACATGCAGCACAACACATCAC 60.001 47.619 0.00 0.00 0.00 3.06
2527 2873 1.001158 CACATGCAGCACAACACATCA 60.001 47.619 0.00 0.00 0.00 3.07
2528 2874 1.693467 CACATGCAGCACAACACATC 58.307 50.000 0.00 0.00 0.00 3.06
2529 2875 0.319211 GCACATGCAGCACAACACAT 60.319 50.000 0.00 0.00 41.59 3.21
2539 2885 2.745100 AGCTGACCGCACATGCAG 60.745 61.111 4.49 0.00 42.61 4.41
2579 2925 2.699496 CTAGAGCCCCCACTCCCT 59.301 66.667 0.00 0.00 37.39 4.20


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

AutoCloner maintained by Alex Coulton.