Multiple sequence alignment - TraesCS7D01G081100

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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 TraesCS7D01G081100 chr7D 100.000 2448 0 0 1 2448 47810090 47807643 0.000000e+00 4521.0
1 TraesCS7D01G081100 chr7D 82.262 902 124 17 793 1664 48173612 48174507 0.000000e+00 747.0
2 TraesCS7D01G081100 chr7D 82.048 908 130 16 793 1672 48257340 48258242 0.000000e+00 743.0
3 TraesCS7D01G081100 chr7D 82.151 902 125 17 793 1664 48166625 48167520 0.000000e+00 741.0
4 TraesCS7D01G081100 chr7D 81.978 910 127 17 793 1671 48127671 48128574 0.000000e+00 737.0
5 TraesCS7D01G081100 chr7D 81.718 908 131 18 793 1671 48209635 48210536 0.000000e+00 725.0
6 TraesCS7D01G081100 chr7D 81.873 822 110 23 755 1540 47516182 47517000 0.000000e+00 656.0
7 TraesCS7D01G081100 chr7D 82.431 757 97 25 933 1654 22414415 22413660 1.600000e-176 628.0
8 TraesCS7D01G081100 chr7D 82.095 754 96 25 933 1648 10725549 10726301 2.080000e-170 608.0
9 TraesCS7D01G081100 chr7D 85.821 134 16 3 1 131 439997275 439997408 3.280000e-29 139.0
10 TraesCS7D01G081100 chr7A 95.188 1434 58 6 506 1935 50425936 50424510 0.000000e+00 2255.0
11 TraesCS7D01G081100 chr7A 80.851 987 129 41 707 1648 9823865 9824836 0.000000e+00 721.0
12 TraesCS7D01G081100 chr7A 80.851 987 129 41 707 1648 9880442 9881413 0.000000e+00 721.0
13 TraesCS7D01G081100 chr7A 81.931 642 75 27 933 1533 9976756 9977397 2.810000e-139 505.0
14 TraesCS7D01G081100 chr7A 90.501 379 26 5 126 500 50426922 50426550 2.190000e-135 492.0
15 TraesCS7D01G081100 chr7A 90.625 192 10 3 1938 2129 50424479 50424296 5.230000e-62 248.0
16 TraesCS7D01G081100 chr7A 91.729 133 8 2 2247 2376 50424077 50423945 5.380000e-42 182.0
17 TraesCS7D01G081100 chr7A 90.551 127 12 0 1 127 50427265 50427139 4.190000e-38 169.0
18 TraesCS7D01G081100 chr4A 87.500 1400 109 31 574 1934 662451493 662452865 0.000000e+00 1555.0
19 TraesCS7D01G081100 chr4A 78.993 914 123 28 793 1672 663211513 663212391 5.910000e-156 560.0
20 TraesCS7D01G081100 chr4A 85.000 520 73 3 1139 1654 727966172 727965654 7.760000e-145 523.0
21 TraesCS7D01G081100 chr4A 83.721 387 55 5 1996 2376 662454224 662454608 2.310000e-95 359.0
22 TraesCS7D01G081100 chr4A 83.835 266 23 6 1 250 662450803 662451064 4.070000e-58 235.0
23 TraesCS7D01G081100 chr4A 89.286 112 11 1 265 376 662451048 662451158 3.280000e-29 139.0
24 TraesCS7D01G081100 chr4A 96.610 59 1 1 392 450 662451445 662451502 2.000000e-16 97.1
25 TraesCS7D01G081100 chr5A 77.712 839 129 34 734 1542 139071190 139072000 6.170000e-126 460.0
26 TraesCS7D01G081100 chr7B 89.565 115 11 1 1 114 705592920 705593034 7.050000e-31 145.0
27 TraesCS7D01G081100 chr7B 85.455 55 5 3 2050 2103 685112015 685111963 1.000000e-03 54.7
28 TraesCS7D01G081100 chr2B 87.121 132 6 3 1 121 741971779 741971910 3.280000e-29 139.0
29 TraesCS7D01G081100 chr2A 91.892 74 6 0 1 74 119341923 119341850 1.200000e-18 104.0
30 TraesCS7D01G081100 chr6D 90.541 74 7 0 1 74 68075100 68075027 5.570000e-17 99.0
31 TraesCS7D01G081100 chr6D 87.692 65 7 1 51 115 197314385 197314448 9.390000e-10 75.0
32 TraesCS7D01G081100 chr6A 90.541 74 7 0 1 74 200240544 200240471 5.570000e-17 99.0
33 TraesCS7D01G081100 chr6A 90.541 74 7 0 1 74 609882206 609882279 5.570000e-17 99.0
34 TraesCS7D01G081100 chr6A 89.062 64 6 1 52 115 245764517 245764579 7.260000e-11 78.7
35 TraesCS7D01G081100 chr4D 91.549 71 6 0 1 71 349158160 349158230 5.570000e-17 99.0
36 TraesCS7D01G081100 chr5D 90.541 74 6 1 1 74 269336375 269336303 2.000000e-16 97.1
37 TraesCS7D01G081100 chr1A 80.435 138 10 7 1 121 62255846 62255709 3.350000e-14 89.8
38 TraesCS7D01G081100 chr6B 87.500 64 7 1 52 115 302595972 302596034 3.380000e-09 73.1


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 TraesCS7D01G081100 chr7D 47807643 47810090 2447 True 4521.00 4521 100.0000 1 2448 1 chr7D.!!$R2 2447
1 TraesCS7D01G081100 chr7D 48173612 48174507 895 False 747.00 747 82.2620 793 1664 1 chr7D.!!$F5 871
2 TraesCS7D01G081100 chr7D 48257340 48258242 902 False 743.00 743 82.0480 793 1672 1 chr7D.!!$F7 879
3 TraesCS7D01G081100 chr7D 48166625 48167520 895 False 741.00 741 82.1510 793 1664 1 chr7D.!!$F4 871
4 TraesCS7D01G081100 chr7D 48127671 48128574 903 False 737.00 737 81.9780 793 1671 1 chr7D.!!$F3 878
5 TraesCS7D01G081100 chr7D 48209635 48210536 901 False 725.00 725 81.7180 793 1671 1 chr7D.!!$F6 878
6 TraesCS7D01G081100 chr7D 47516182 47517000 818 False 656.00 656 81.8730 755 1540 1 chr7D.!!$F2 785
7 TraesCS7D01G081100 chr7D 22413660 22414415 755 True 628.00 628 82.4310 933 1654 1 chr7D.!!$R1 721
8 TraesCS7D01G081100 chr7D 10725549 10726301 752 False 608.00 608 82.0950 933 1648 1 chr7D.!!$F1 715
9 TraesCS7D01G081100 chr7A 9823865 9824836 971 False 721.00 721 80.8510 707 1648 1 chr7A.!!$F1 941
10 TraesCS7D01G081100 chr7A 9880442 9881413 971 False 721.00 721 80.8510 707 1648 1 chr7A.!!$F2 941
11 TraesCS7D01G081100 chr7A 50423945 50427265 3320 True 669.20 2255 91.7188 1 2376 5 chr7A.!!$R1 2375
12 TraesCS7D01G081100 chr7A 9976756 9977397 641 False 505.00 505 81.9310 933 1533 1 chr7A.!!$F3 600
13 TraesCS7D01G081100 chr4A 663211513 663212391 878 False 560.00 560 78.9930 793 1672 1 chr4A.!!$F1 879
14 TraesCS7D01G081100 chr4A 727965654 727966172 518 True 523.00 523 85.0000 1139 1654 1 chr4A.!!$R1 515
15 TraesCS7D01G081100 chr4A 662450803 662454608 3805 False 477.02 1555 88.1904 1 2376 5 chr4A.!!$F2 2375
16 TraesCS7D01G081100 chr5A 139071190 139072000 810 False 460.00 460 77.7120 734 1542 1 chr5A.!!$F1 808

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
525 1645 0.038744 CACCTTGGAGCATTGGGACT 59.961 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 5072 0.03601 GGGATCGGGCTGGTATCATG 60.036 60.0 0.0 0.0 0.0 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
115 132 6.403878 CAGAGTAAATAAAAACGGAGGGAGA 58.596 40.000 0.00 0.00 0.00 3.71
245 486 2.761786 AGGCATTCCCATTGCACTAT 57.238 45.000 0.00 0.00 41.95 2.12
246 487 3.882102 AGGCATTCCCATTGCACTATA 57.118 42.857 0.00 0.00 41.95 1.31
247 488 4.393239 AGGCATTCCCATTGCACTATAT 57.607 40.909 0.00 0.00 41.95 0.86
248 489 4.744237 AGGCATTCCCATTGCACTATATT 58.256 39.130 0.00 0.00 41.95 1.28
286 527 5.203528 ACCCAATGCACTATATTTGAAGCT 58.796 37.500 0.00 0.00 0.00 3.74
468 980 0.523072 CCTCAGAAAATGTGGTGCCG 59.477 55.000 0.00 0.00 37.71 5.69
470 982 1.080569 CAGAAAATGTGGTGCCGCC 60.081 57.895 0.00 0.00 37.90 6.13
484 996 1.821332 CCGCCTCAGATTTCTGCCC 60.821 63.158 2.60 0.00 43.46 5.36
500 1012 1.304282 CCCTGGTGGCATGCTTAGT 59.696 57.895 18.92 0.00 0.00 2.24
501 1013 0.546122 CCCTGGTGGCATGCTTAGTA 59.454 55.000 18.92 0.00 0.00 1.82
502 1014 1.668419 CCTGGTGGCATGCTTAGTAC 58.332 55.000 18.92 9.02 0.00 2.73
503 1015 1.210478 CCTGGTGGCATGCTTAGTACT 59.790 52.381 18.92 0.00 0.00 2.73
504 1016 2.356125 CCTGGTGGCATGCTTAGTACTT 60.356 50.000 18.92 0.00 0.00 2.24
525 1645 0.038744 CACCTTGGAGCATTGGGACT 59.961 55.000 0.00 0.00 0.00 3.85
528 1648 1.651240 CTTGGAGCATTGGGACTGCG 61.651 60.000 0.00 0.00 44.38 5.18
689 1809 5.675684 TTGTTAGACACCTGATGCATCTA 57.324 39.130 26.32 12.54 0.00 1.98
725 1851 6.678568 AGCTTAAGATATAGTGCACTGGAT 57.321 37.500 29.57 20.71 0.00 3.41
731 1857 0.921896 ATAGTGCACTGGATTGCCCT 59.078 50.000 29.57 0.97 42.25 5.19
841 1971 5.049828 TGAACGTATATCTCATGCACTTGG 58.950 41.667 0.00 0.00 0.00 3.61
848 1987 7.148672 CGTATATCTCATGCACTTGGAATCTTC 60.149 40.741 0.00 0.00 0.00 2.87
949 2098 3.117474 TGGAGTCCAACCATTTTGTACCA 60.117 43.478 10.20 0.00 32.03 3.25
1088 2279 9.590451 TGCACAGTGTATGTATATATCATCATG 57.410 33.333 1.61 0.00 41.41 3.07
1136 2366 8.409358 TCTATATATACACACACACATCTGCT 57.591 34.615 0.00 0.00 0.00 4.24
1494 2741 4.517952 TCGTCGGTAATAAAAGTCACCA 57.482 40.909 0.00 0.00 0.00 4.17
1582 2829 4.572985 TCAGCAAGACAAACTTTGATGG 57.427 40.909 8.55 0.00 36.61 3.51
1743 2991 1.729586 TCCTTGTACAGCACCCTCTT 58.270 50.000 0.00 0.00 0.00 2.85
1888 3145 4.341806 TGTGATTGATCAGTTTGGCACTTT 59.658 37.500 8.55 0.00 37.51 2.66
1947 3232 2.627945 GGCAAATGATCGACACTACCA 58.372 47.619 0.00 0.00 0.00 3.25
1955 3240 2.047560 GACACTACCACACGGCCC 60.048 66.667 0.00 0.00 34.57 5.80
2094 4648 8.134905 TGTTTGAATACATCGATCATCTTGAG 57.865 34.615 0.00 0.00 0.00 3.02
2109 4663 4.744795 TCTTGAGCTAGAGGATGGAAAC 57.255 45.455 0.00 0.00 0.00 2.78
2124 4678 4.686191 TGGAAACAGATTTGCCAAATGT 57.314 36.364 7.53 0.00 35.38 2.71
2129 4683 2.629137 ACAGATTTGCCAAATGTGCTCA 59.371 40.909 22.86 0.00 43.68 4.26
2161 4715 3.372954 CACCTGTCGGTTCTATTCGATC 58.627 50.000 0.00 0.00 42.13 3.69
2167 4721 1.666311 CGGTTCTATTCGATCTCGGCC 60.666 57.143 0.00 0.00 40.29 6.13
2171 4725 1.880675 TCTATTCGATCTCGGCCAGTC 59.119 52.381 2.24 0.00 40.29 3.51
2174 4728 4.193334 CGATCTCGGCCAGTCGCA 62.193 66.667 2.24 0.00 40.31 5.10
2188 4742 2.507992 CGCAGAGGTCGGAGCAAG 60.508 66.667 10.15 0.00 0.00 4.01
2202 4756 3.689414 CAAGCATGCAAGCAGGGA 58.311 55.556 21.98 0.00 36.85 4.20
2205 4759 0.033405 AAGCATGCAAGCAGGGAGAT 60.033 50.000 21.98 0.00 36.85 2.75
2210 4764 1.676635 GCAAGCAGGGAGATGTGCA 60.677 57.895 0.00 0.00 42.47 4.57
2213 4767 2.045634 GCAGGGAGATGTGCAGCA 60.046 61.111 0.00 0.00 39.62 4.41
2263 4918 0.604511 CAGGCAGTGTGCTGTGATCA 60.605 55.000 0.00 0.00 44.28 2.92
2297 4958 2.459060 TTTTTAGACACGATCGGGCA 57.541 45.000 19.30 0.00 0.00 5.36
2305 4966 1.153706 ACGATCGGGCAAACGTAGG 60.154 57.895 20.98 0.00 37.22 3.18
2371 5032 3.329889 AGGCATGCGGAAGGACCA 61.330 61.111 12.44 0.00 38.90 4.02
2376 5037 2.293318 ATGCGGAAGGACCAGCAGA 61.293 57.895 9.24 0.00 45.40 4.26
2377 5038 2.435059 GCGGAAGGACCAGCAGAC 60.435 66.667 0.00 0.00 37.82 3.51
2378 5039 2.125912 CGGAAGGACCAGCAGACG 60.126 66.667 0.00 0.00 38.90 4.18
2379 5040 2.932234 CGGAAGGACCAGCAGACGT 61.932 63.158 0.00 0.00 38.90 4.34
2380 5041 1.592400 CGGAAGGACCAGCAGACGTA 61.592 60.000 0.00 0.00 38.90 3.57
2381 5042 0.173708 GGAAGGACCAGCAGACGTAG 59.826 60.000 0.00 0.00 38.79 3.51
2382 5043 0.458716 GAAGGACCAGCAGACGTAGC 60.459 60.000 4.40 4.40 0.00 3.58
2383 5044 0.900647 AAGGACCAGCAGACGTAGCT 60.901 55.000 9.02 9.02 44.62 3.32
2388 5049 4.996976 AGCAGACGTAGCTGGTTG 57.003 55.556 13.55 0.00 43.51 3.77
2389 5050 1.293498 AGCAGACGTAGCTGGTTGG 59.707 57.895 13.55 0.00 43.51 3.77
2390 5051 1.185618 AGCAGACGTAGCTGGTTGGA 61.186 55.000 13.55 0.00 43.51 3.53
2391 5052 0.320421 GCAGACGTAGCTGGTTGGAA 60.320 55.000 0.00 0.00 36.41 3.53
2392 5053 1.676014 GCAGACGTAGCTGGTTGGAAT 60.676 52.381 0.00 0.00 36.41 3.01
2393 5054 2.002586 CAGACGTAGCTGGTTGGAATG 58.997 52.381 0.00 0.00 32.26 2.67
2394 5055 0.727398 GACGTAGCTGGTTGGAATGC 59.273 55.000 0.00 0.00 0.00 3.56
2395 5056 0.036164 ACGTAGCTGGTTGGAATGCA 59.964 50.000 0.00 0.00 0.00 3.96
2396 5057 0.447801 CGTAGCTGGTTGGAATGCAC 59.552 55.000 0.00 0.00 0.00 4.57
2397 5058 1.826385 GTAGCTGGTTGGAATGCACT 58.174 50.000 0.00 0.00 0.00 4.40
2398 5059 1.740025 GTAGCTGGTTGGAATGCACTC 59.260 52.381 0.00 0.00 0.00 3.51
2399 5060 0.610232 AGCTGGTTGGAATGCACTCC 60.610 55.000 7.40 7.40 35.88 3.85
2400 5061 0.895100 GCTGGTTGGAATGCACTCCA 60.895 55.000 14.04 14.04 43.99 3.86
2408 5069 4.589216 TGGAATGCACTCCAAGAAAAAG 57.411 40.909 15.90 0.00 42.69 2.27
2409 5070 3.243839 TGGAATGCACTCCAAGAAAAAGC 60.244 43.478 15.90 0.00 42.69 3.51
2410 5071 3.006217 GGAATGCACTCCAAGAAAAAGCT 59.994 43.478 9.87 0.00 35.36 3.74
2411 5072 3.930634 ATGCACTCCAAGAAAAAGCTC 57.069 42.857 0.00 0.00 0.00 4.09
2412 5073 2.653726 TGCACTCCAAGAAAAAGCTCA 58.346 42.857 0.00 0.00 0.00 4.26
2413 5074 3.225104 TGCACTCCAAGAAAAAGCTCAT 58.775 40.909 0.00 0.00 0.00 2.90
2414 5075 3.005050 TGCACTCCAAGAAAAAGCTCATG 59.995 43.478 0.00 0.00 0.00 3.07
2415 5076 3.254166 GCACTCCAAGAAAAAGCTCATGA 59.746 43.478 0.00 0.00 0.00 3.07
2416 5077 4.082354 GCACTCCAAGAAAAAGCTCATGAT 60.082 41.667 0.00 0.00 0.00 2.45
2417 5078 5.124457 GCACTCCAAGAAAAAGCTCATGATA 59.876 40.000 0.00 0.00 0.00 2.15
2418 5079 6.549952 CACTCCAAGAAAAAGCTCATGATAC 58.450 40.000 0.00 0.00 0.00 2.24
2419 5080 5.649831 ACTCCAAGAAAAAGCTCATGATACC 59.350 40.000 0.00 0.00 0.00 2.73
2420 5081 5.569355 TCCAAGAAAAAGCTCATGATACCA 58.431 37.500 0.00 0.00 0.00 3.25
2421 5082 5.649395 TCCAAGAAAAAGCTCATGATACCAG 59.351 40.000 0.00 0.00 0.00 4.00
2422 5083 5.338365 CAAGAAAAAGCTCATGATACCAGC 58.662 41.667 0.00 0.00 0.00 4.85
2423 5084 3.950395 AGAAAAAGCTCATGATACCAGCC 59.050 43.478 0.00 0.00 33.28 4.85
2424 5085 2.355010 AAAGCTCATGATACCAGCCC 57.645 50.000 0.00 0.00 33.28 5.19
2425 5086 0.107456 AAGCTCATGATACCAGCCCG 59.893 55.000 0.00 0.00 33.28 6.13
2426 5087 0.760567 AGCTCATGATACCAGCCCGA 60.761 55.000 0.00 0.00 33.28 5.14
2427 5088 0.322975 GCTCATGATACCAGCCCGAT 59.677 55.000 0.00 0.00 0.00 4.18
2428 5089 1.674221 GCTCATGATACCAGCCCGATC 60.674 57.143 0.00 0.00 0.00 3.69
2429 5090 0.976641 TCATGATACCAGCCCGATCC 59.023 55.000 0.00 0.00 0.00 3.36
2430 5091 0.036010 CATGATACCAGCCCGATCCC 60.036 60.000 0.00 0.00 0.00 3.85
2431 5092 1.201429 ATGATACCAGCCCGATCCCC 61.201 60.000 0.00 0.00 0.00 4.81
2432 5093 1.536662 GATACCAGCCCGATCCCCT 60.537 63.158 0.00 0.00 0.00 4.79
2433 5094 1.536662 ATACCAGCCCGATCCCCTC 60.537 63.158 0.00 0.00 0.00 4.30
2434 5095 2.326529 ATACCAGCCCGATCCCCTCA 62.327 60.000 0.00 0.00 0.00 3.86
2435 5096 2.539277 TACCAGCCCGATCCCCTCAA 62.539 60.000 0.00 0.00 0.00 3.02
2436 5097 2.455565 CCAGCCCGATCCCCTCAAT 61.456 63.158 0.00 0.00 0.00 2.57
2437 5098 1.127567 CCAGCCCGATCCCCTCAATA 61.128 60.000 0.00 0.00 0.00 1.90
2438 5099 0.764890 CAGCCCGATCCCCTCAATAA 59.235 55.000 0.00 0.00 0.00 1.40
2439 5100 1.142870 CAGCCCGATCCCCTCAATAAA 59.857 52.381 0.00 0.00 0.00 1.40
2440 5101 1.421646 AGCCCGATCCCCTCAATAAAG 59.578 52.381 0.00 0.00 0.00 1.85
2441 5102 1.897560 CCCGATCCCCTCAATAAAGC 58.102 55.000 0.00 0.00 0.00 3.51
2442 5103 1.512926 CCGATCCCCTCAATAAAGCG 58.487 55.000 0.00 0.00 0.00 4.68
2443 5104 1.512926 CGATCCCCTCAATAAAGCGG 58.487 55.000 0.00 0.00 0.00 5.52
2444 5105 1.878102 CGATCCCCTCAATAAAGCGGG 60.878 57.143 0.00 0.00 36.42 6.13
2445 5106 0.178990 ATCCCCTCAATAAAGCGGGC 60.179 55.000 0.00 0.00 35.29 6.13
2446 5107 1.227383 CCCCTCAATAAAGCGGGCT 59.773 57.895 0.00 0.00 35.29 5.19
2447 5108 1.103398 CCCCTCAATAAAGCGGGCTG 61.103 60.000 0.00 0.00 35.29 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 368 5.882557 AGATGTCTTGTATTTGGTGCTAAGG 59.117 40.000 0.00 0.00 0.00 2.69
147 382 8.316946 TGAGTGAGAAATTATGAGATGTCTTGT 58.683 33.333 0.00 0.00 0.00 3.16
221 462 4.545678 AGTGCAATGGGAATGCCTTTATA 58.454 39.130 0.00 0.00 43.16 0.98
222 463 3.377573 AGTGCAATGGGAATGCCTTTAT 58.622 40.909 0.00 0.00 43.16 1.40
223 464 2.818921 AGTGCAATGGGAATGCCTTTA 58.181 42.857 0.00 0.00 43.16 1.85
224 465 1.648116 AGTGCAATGGGAATGCCTTT 58.352 45.000 0.00 0.00 43.16 3.11
315 556 7.727181 ACTATAGTCCATTGGAGAACATGTAC 58.273 38.462 5.39 0.00 29.39 2.90
320 561 8.603898 TCTAAACTATAGTCCATTGGAGAACA 57.396 34.615 5.39 0.00 29.39 3.18
384 625 2.371841 AGAAAACCAATGCTTTTCCCCC 59.628 45.455 9.43 0.00 38.05 5.40
439 951 7.989741 CACCACATTTTCTGAGGAGTATATCTT 59.010 37.037 0.00 0.00 37.79 2.40
441 953 6.203723 GCACCACATTTTCTGAGGAGTATATC 59.796 42.308 0.00 0.00 37.79 1.63
449 961 0.523072 CGGCACCACATTTTCTGAGG 59.477 55.000 0.00 0.00 41.08 3.86
454 966 1.212751 GAGGCGGCACCACATTTTC 59.787 57.895 13.08 0.00 43.14 2.29
468 980 0.750911 CCAGGGCAGAAATCTGAGGC 60.751 60.000 14.43 0.46 46.59 4.70
470 982 1.681166 CCACCAGGGCAGAAATCTGAG 60.681 57.143 14.43 1.02 46.59 3.35
484 996 2.698855 AGTACTAAGCATGCCACCAG 57.301 50.000 15.66 8.90 0.00 4.00
500 1012 3.308117 CCCAATGCTCCAAGGTGTAAGTA 60.308 47.826 0.00 0.00 0.00 2.24
501 1013 2.555227 CCCAATGCTCCAAGGTGTAAGT 60.555 50.000 0.00 0.00 0.00 2.24
502 1014 2.094675 CCCAATGCTCCAAGGTGTAAG 58.905 52.381 0.00 0.00 0.00 2.34
503 1015 1.707989 TCCCAATGCTCCAAGGTGTAA 59.292 47.619 0.00 0.00 0.00 2.41
504 1016 1.004277 GTCCCAATGCTCCAAGGTGTA 59.996 52.381 0.00 0.00 0.00 2.90
525 1645 1.396648 CAGTTTCCGTGCATTATCGCA 59.603 47.619 0.00 0.00 40.32 5.10
528 1648 4.752101 AGATAGCAGTTTCCGTGCATTATC 59.248 41.667 0.00 0.00 43.82 1.75
588 1708 8.514594 TGAATGCCTTTCTCATAAGTGTTAAAG 58.485 33.333 0.00 0.00 35.23 1.85
592 1712 6.899393 TTGAATGCCTTTCTCATAAGTGTT 57.101 33.333 0.00 0.00 35.23 3.32
689 1809 3.912248 TCTTAAGCTATTCCCTCCGTCT 58.088 45.455 0.00 0.00 0.00 4.18
725 1851 4.711355 CCTTAATGAATTCTCCAAGGGCAA 59.289 41.667 17.74 0.00 30.97 4.52
731 1857 6.891361 TCTTGCATCCTTAATGAATTCTCCAA 59.109 34.615 7.05 0.00 37.59 3.53
832 1962 5.171339 ACTACAGAAGATTCCAAGTGCAT 57.829 39.130 0.00 0.00 0.00 3.96
938 2087 9.226606 TCAAGTATAAGGTTCTGGTACAAAATG 57.773 33.333 0.00 0.00 38.70 2.32
949 2098 8.880991 TCAGTTCTAGTCAAGTATAAGGTTCT 57.119 34.615 0.00 0.00 0.00 3.01
1121 2344 3.308053 GCAGTATAGCAGATGTGTGTGTG 59.692 47.826 0.00 0.00 0.00 3.82
1122 2345 3.055891 TGCAGTATAGCAGATGTGTGTGT 60.056 43.478 0.00 0.00 40.11 3.72
1494 2741 6.070824 GGGACCTGATTGTTCAAACCAAATAT 60.071 38.462 0.00 0.00 0.00 1.28
1529 2776 3.685139 AACATGCGGGATATCCTGTAG 57.315 47.619 27.80 20.20 44.34 2.74
1582 2829 6.993079 ACAACAAATTACTGGGGATTCTTTC 58.007 36.000 0.00 0.00 0.00 2.62
1750 2998 0.535102 AAAGAGGGTGCTGTGTTCGG 60.535 55.000 0.00 0.00 0.00 4.30
1751 2999 0.588252 CAAAGAGGGTGCTGTGTTCG 59.412 55.000 0.00 0.00 0.00 3.95
1752 3000 1.680338 ACAAAGAGGGTGCTGTGTTC 58.320 50.000 0.00 0.00 32.45 3.18
1753 3001 2.143876 AACAAAGAGGGTGCTGTGTT 57.856 45.000 0.00 0.00 40.59 3.32
1841 3098 1.138069 TGGTCTCATGTGTGTTCGTGT 59.862 47.619 0.00 0.00 0.00 4.49
1888 3145 3.903208 GCCCCAGGCTGAGAAAATA 57.097 52.632 17.94 0.00 46.69 1.40
1947 3232 2.683933 AGATCCTTCGGGCCGTGT 60.684 61.111 27.32 8.39 34.44 4.49
1955 3240 3.059352 ACAAGGTTTGGAGATCCTTCG 57.941 47.619 0.00 0.00 39.22 3.79
2089 4643 4.161189 TCTGTTTCCATCCTCTAGCTCAAG 59.839 45.833 0.00 0.00 0.00 3.02
2094 4648 4.036144 GCAAATCTGTTTCCATCCTCTAGC 59.964 45.833 0.00 0.00 0.00 3.42
2109 4663 3.306917 TGAGCACATTTGGCAAATCTG 57.693 42.857 22.02 20.83 0.00 2.90
2129 4683 3.965539 GACAGGTGCCGCTGCTGAT 62.966 63.158 0.70 0.00 38.71 2.90
2148 4702 1.340248 TGGCCGAGATCGAATAGAACC 59.660 52.381 3.31 0.00 43.02 3.62
2150 4704 2.293677 GACTGGCCGAGATCGAATAGAA 59.706 50.000 3.31 0.00 43.02 2.10
2151 4705 1.880675 GACTGGCCGAGATCGAATAGA 59.119 52.381 3.31 0.00 43.02 1.98
2167 4721 2.487428 CTCCGACCTCTGCGACTG 59.513 66.667 0.00 0.00 0.00 3.51
2171 4725 2.507992 CTTGCTCCGACCTCTGCG 60.508 66.667 0.00 0.00 0.00 5.18
2174 4728 1.220206 CATGCTTGCTCCGACCTCT 59.780 57.895 0.00 0.00 0.00 3.69
2188 4742 1.035932 ACATCTCCCTGCTTGCATGC 61.036 55.000 17.19 17.19 0.00 4.06
2202 4756 0.806868 CGACCAATTGCTGCACATCT 59.193 50.000 0.00 0.00 0.00 2.90
2205 4759 1.528076 ACCGACCAATTGCTGCACA 60.528 52.632 0.00 0.00 0.00 4.57
2210 4764 0.744414 CGATCCACCGACCAATTGCT 60.744 55.000 0.00 0.00 0.00 3.91
2213 4767 1.538204 CGATCGATCCACCGACCAATT 60.538 52.381 19.51 0.00 41.70 2.32
2297 4958 1.594836 TTGCGCCGTTCCTACGTTT 60.595 52.632 4.18 0.00 46.20 3.60
2358 5019 2.270205 CTGCTGGTCCTTCCGCAT 59.730 61.111 0.00 0.00 41.76 4.73
2371 5032 1.185618 TCCAACCAGCTACGTCTGCT 61.186 55.000 9.76 9.76 42.06 4.24
2376 5037 0.036164 TGCATTCCAACCAGCTACGT 59.964 50.000 0.00 0.00 0.00 3.57
2377 5038 0.447801 GTGCATTCCAACCAGCTACG 59.552 55.000 0.00 0.00 0.00 3.51
2378 5039 1.740025 GAGTGCATTCCAACCAGCTAC 59.260 52.381 0.00 0.00 0.00 3.58
2379 5040 1.340017 GGAGTGCATTCCAACCAGCTA 60.340 52.381 22.46 0.00 37.20 3.32
2380 5041 0.610232 GGAGTGCATTCCAACCAGCT 60.610 55.000 22.46 0.00 37.20 4.24
2381 5042 0.895100 TGGAGTGCATTCCAACCAGC 60.895 55.000 27.11 0.56 44.09 4.85
2382 5043 3.344703 TGGAGTGCATTCCAACCAG 57.655 52.632 27.11 0.00 44.09 4.00
2387 5048 3.243839 GCTTTTTCTTGGAGTGCATTCCA 60.244 43.478 25.75 25.75 45.34 3.53
2388 5049 3.006217 AGCTTTTTCTTGGAGTGCATTCC 59.994 43.478 20.81 20.81 37.77 3.01
2389 5050 4.233005 GAGCTTTTTCTTGGAGTGCATTC 58.767 43.478 0.00 0.00 0.00 2.67
2390 5051 3.638160 TGAGCTTTTTCTTGGAGTGCATT 59.362 39.130 0.00 0.00 0.00 3.56
2391 5052 3.225104 TGAGCTTTTTCTTGGAGTGCAT 58.775 40.909 0.00 0.00 0.00 3.96
2392 5053 2.653726 TGAGCTTTTTCTTGGAGTGCA 58.346 42.857 0.00 0.00 0.00 4.57
2393 5054 3.254166 TCATGAGCTTTTTCTTGGAGTGC 59.746 43.478 0.00 0.00 0.00 4.40
2394 5055 5.640189 ATCATGAGCTTTTTCTTGGAGTG 57.360 39.130 0.09 0.00 0.00 3.51
2395 5056 5.649831 GGTATCATGAGCTTTTTCTTGGAGT 59.350 40.000 0.09 0.00 0.00 3.85
2396 5057 5.649395 TGGTATCATGAGCTTTTTCTTGGAG 59.351 40.000 0.09 0.00 0.00 3.86
2397 5058 5.569355 TGGTATCATGAGCTTTTTCTTGGA 58.431 37.500 0.09 0.00 0.00 3.53
2398 5059 5.678107 GCTGGTATCATGAGCTTTTTCTTGG 60.678 44.000 0.09 0.00 0.00 3.61
2399 5060 5.338365 GCTGGTATCATGAGCTTTTTCTTG 58.662 41.667 0.09 0.00 0.00 3.02
2400 5061 4.400567 GGCTGGTATCATGAGCTTTTTCTT 59.599 41.667 0.09 0.00 33.03 2.52
2401 5062 3.950395 GGCTGGTATCATGAGCTTTTTCT 59.050 43.478 0.09 0.00 33.03 2.52
2402 5063 3.067320 GGGCTGGTATCATGAGCTTTTTC 59.933 47.826 0.09 0.00 33.03 2.29
2403 5064 3.026694 GGGCTGGTATCATGAGCTTTTT 58.973 45.455 0.09 0.00 33.03 1.94
2404 5065 2.659428 GGGCTGGTATCATGAGCTTTT 58.341 47.619 0.09 0.00 33.03 2.27
2405 5066 1.475751 CGGGCTGGTATCATGAGCTTT 60.476 52.381 0.09 0.00 33.03 3.51
2406 5067 0.107456 CGGGCTGGTATCATGAGCTT 59.893 55.000 0.09 0.00 33.03 3.74
2407 5068 0.760567 TCGGGCTGGTATCATGAGCT 60.761 55.000 0.09 0.00 33.03 4.09
2408 5069 0.322975 ATCGGGCTGGTATCATGAGC 59.677 55.000 0.09 0.00 0.00 4.26
2409 5070 1.066573 GGATCGGGCTGGTATCATGAG 60.067 57.143 0.09 0.00 0.00 2.90
2410 5071 0.976641 GGATCGGGCTGGTATCATGA 59.023 55.000 0.00 0.00 0.00 3.07
2411 5072 0.036010 GGGATCGGGCTGGTATCATG 60.036 60.000 0.00 0.00 0.00 3.07
2412 5073 1.201429 GGGGATCGGGCTGGTATCAT 61.201 60.000 0.00 0.00 0.00 2.45
2413 5074 1.841556 GGGGATCGGGCTGGTATCA 60.842 63.158 0.00 0.00 0.00 2.15
2414 5075 1.536662 AGGGGATCGGGCTGGTATC 60.537 63.158 0.00 0.00 0.00 2.24
2415 5076 1.536662 GAGGGGATCGGGCTGGTAT 60.537 63.158 0.00 0.00 0.00 2.73
2416 5077 2.122989 GAGGGGATCGGGCTGGTA 60.123 66.667 0.00 0.00 0.00 3.25
2417 5078 3.810931 TATTGAGGGGATCGGGCTGGT 62.811 57.143 0.00 0.00 0.00 4.00
2418 5079 1.127567 TATTGAGGGGATCGGGCTGG 61.128 60.000 0.00 0.00 0.00 4.85
2419 5080 0.764890 TTATTGAGGGGATCGGGCTG 59.235 55.000 0.00 0.00 0.00 4.85
2420 5081 1.421646 CTTTATTGAGGGGATCGGGCT 59.578 52.381 0.00 0.00 0.00 5.19
2421 5082 1.897560 CTTTATTGAGGGGATCGGGC 58.102 55.000 0.00 0.00 0.00 6.13
2422 5083 1.878102 CGCTTTATTGAGGGGATCGGG 60.878 57.143 0.00 0.00 0.00 5.14
2423 5084 1.512926 CGCTTTATTGAGGGGATCGG 58.487 55.000 0.00 0.00 0.00 4.18
2428 5089 1.103398 CAGCCCGCTTTATTGAGGGG 61.103 60.000 5.54 1.36 45.53 4.79


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

AutoCloner maintained by Alex Coulton.