Multiple sequence alignment - TraesCS1D01G373100

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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 TraesCS1D01G373100 chr1D 100.000 3401 0 0 1 3401 451141706 451138306 0.000000e+00 6281.0
1 TraesCS1D01G373100 chr1D 93.968 746 44 1 1 745 451245009 451244264 0.000000e+00 1127.0
2 TraesCS1D01G373100 chr1D 89.417 737 66 4 6 733 451195983 451195250 0.000000e+00 918.0
3 TraesCS1D01G373100 chr1D 89.822 619 35 2 1861 2451 451243605 451242987 0.000000e+00 769.0
4 TraesCS1D01G373100 chr1D 91.400 500 42 1 978 1476 473862706 473863205 0.000000e+00 684.0
5 TraesCS1D01G373100 chr1D 85.972 499 40 9 2930 3401 451227931 451227436 1.090000e-139 507.0
6 TraesCS1D01G373100 chr1D 93.056 288 12 3 1326 1605 451243887 451243600 6.790000e-112 414.0
7 TraesCS1D01G373100 chr1A 93.974 1593 84 8 864 2451 545896837 545895252 0.000000e+00 2399.0
8 TraesCS1D01G373100 chr1A 91.169 770 44 10 1 770 545897600 545896855 0.000000e+00 1024.0
9 TraesCS1D01G373100 chr1A 88.948 751 68 7 6 745 545908931 545908185 0.000000e+00 913.0
10 TraesCS1D01G373100 chr1A 84.164 903 95 15 2538 3396 545895232 545894334 0.000000e+00 832.0
11 TraesCS1D01G373100 chr1A 91.617 501 41 1 977 1476 568108564 568109064 0.000000e+00 691.0
12 TraesCS1D01G373100 chr1A 96.443 253 9 0 1001 1253 9255276 9255024 5.250000e-113 418.0
13 TraesCS1D01G373100 chr1A 100.000 32 0 0 801 832 545896858 545896827 3.670000e-05 60.2
14 TraesCS1D01G373100 chr1B 91.199 1568 77 26 1 1532 619530316 619528774 0.000000e+00 2074.0
15 TraesCS1D01G373100 chr1B 91.673 1405 86 12 1078 2451 619430534 619429130 0.000000e+00 1917.0
16 TraesCS1D01G373100 chr1B 92.250 929 69 2 1526 2451 619433757 619432829 0.000000e+00 1314.0
17 TraesCS1D01G373100 chr1B 90.777 824 70 3 6 823 619431354 619430531 0.000000e+00 1096.0
18 TraesCS1D01G373100 chr1B 87.191 929 83 16 1554 2453 619543385 619542464 0.000000e+00 1024.0
19 TraesCS1D01G373100 chr1B 90.566 742 70 0 1 742 619545728 619544987 0.000000e+00 983.0
20 TraesCS1D01G373100 chr1B 85.116 907 88 19 2538 3401 619429109 619428207 0.000000e+00 883.0
21 TraesCS1D01G373100 chr1B 85.887 829 80 14 1578 2370 619585616 619584789 0.000000e+00 848.0
22 TraesCS1D01G373100 chr1B 86.104 734 97 5 1 733 619536613 619535884 0.000000e+00 785.0
23 TraesCS1D01G373100 chr1B 91.617 501 40 2 978 1476 658915129 658915629 0.000000e+00 691.0
24 TraesCS1D01G373100 chr1B 84.906 636 85 7 1 629 619586806 619586175 1.720000e-177 632.0
25 TraesCS1D01G373100 chr1B 89.815 432 44 0 1027 1458 619535631 619535200 3.830000e-154 555.0
26 TraesCS1D01G373100 chr1B 88.473 347 26 7 1248 1594 619544271 619543939 1.140000e-109 407.0
27 TraesCS1D01G373100 chr1B 85.648 216 23 4 2634 2848 619542382 619542174 1.590000e-53 220.0
28 TraesCS1D01G373100 chr1B 92.222 90 7 0 1917 2006 619543908 619543819 9.910000e-26 128.0
29 TraesCS1D01G373100 chr6D 96.838 253 8 0 1001 1253 318999232 318999484 1.130000e-114 424.0
30 TraesCS1D01G373100 chr5A 95.982 224 9 0 1161 1384 364528630 364528407 6.940000e-97 364.0
31 TraesCS1D01G373100 chr3B 93.000 200 14 0 1185 1384 379341406 379341207 3.320000e-75 292.0


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 TraesCS1D01G373100 chr1D 451138306 451141706 3400 True 6281.0 6281 100.00000 1 3401 1 chr1D.!!$R1 3400
1 TraesCS1D01G373100 chr1D 451195250 451195983 733 True 918.0 918 89.41700 6 733 1 chr1D.!!$R2 727
2 TraesCS1D01G373100 chr1D 451242987 451245009 2022 True 770.0 1127 92.28200 1 2451 3 chr1D.!!$R4 2450
3 TraesCS1D01G373100 chr1A 545894334 545897600 3266 True 1078.8 2399 92.32675 1 3396 4 chr1A.!!$R3 3395
4 TraesCS1D01G373100 chr1A 545908185 545908931 746 True 913.0 913 88.94800 6 745 1 chr1A.!!$R2 739
5 TraesCS1D01G373100 chr1A 568108564 568109064 500 False 691.0 691 91.61700 977 1476 1 chr1A.!!$F1 499
6 TraesCS1D01G373100 chr1B 619528774 619530316 1542 True 2074.0 2074 91.19900 1 1532 1 chr1B.!!$R1 1531
7 TraesCS1D01G373100 chr1B 619428207 619433757 5550 True 1302.5 1917 89.95400 6 3401 4 chr1B.!!$R2 3395
8 TraesCS1D01G373100 chr1B 619584789 619586806 2017 True 740.0 848 85.39650 1 2370 2 chr1B.!!$R5 2369
9 TraesCS1D01G373100 chr1B 658915129 658915629 500 False 691.0 691 91.61700 978 1476 1 chr1B.!!$F1 498
10 TraesCS1D01G373100 chr1B 619535200 619536613 1413 True 670.0 785 87.95950 1 1458 2 chr1B.!!$R3 1457
11 TraesCS1D01G373100 chr1B 619542174 619545728 3554 True 552.4 1024 88.82000 1 2848 5 chr1B.!!$R4 2847

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
855 3771 0.170561 CGTGACTCGGACGGAATCTT 59.829 55.0 0.0 0.0 35.71 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 6148 0.877071 ACTTGACTCAATGCCTTGCG 59.123 50.0 0.0 0.0 32.11 4.85 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
718 3179 3.048602 CGGGAGTTCTGACCACGT 58.951 61.111 0.00 0.00 0.00 4.49
721 3182 1.658673 GGAGTTCTGACCACGTCGT 59.341 57.895 0.00 0.00 34.95 4.34
782 3276 0.321653 AAGGCTCGTAACCTTGGCAG 60.322 55.000 5.74 0.00 45.88 4.85
851 3767 1.283793 GAACGTGACTCGGACGGAA 59.716 57.895 1.62 0.00 44.69 4.30
854 3770 0.959372 ACGTGACTCGGACGGAATCT 60.959 55.000 1.62 0.00 44.69 2.40
855 3771 0.170561 CGTGACTCGGACGGAATCTT 59.829 55.000 0.00 0.00 35.71 2.40
856 3772 1.402456 CGTGACTCGGACGGAATCTTT 60.402 52.381 0.00 0.00 35.71 2.52
911 3874 1.024271 GCCTGGCATAGCAAAATCGA 58.976 50.000 15.17 0.00 0.00 3.59
934 3897 3.370421 CCAGGCCCATATAATATCACGCA 60.370 47.826 0.00 0.00 0.00 5.24
936 3899 3.519510 AGGCCCATATAATATCACGCACT 59.480 43.478 0.00 0.00 0.00 4.40
937 3900 4.019321 AGGCCCATATAATATCACGCACTT 60.019 41.667 0.00 0.00 0.00 3.16
938 3901 4.700213 GGCCCATATAATATCACGCACTTT 59.300 41.667 0.00 0.00 0.00 2.66
939 3902 5.183140 GGCCCATATAATATCACGCACTTTT 59.817 40.000 0.00 0.00 0.00 2.27
1467 4447 2.362889 CCCAAGGGCGCCTTCATT 60.363 61.111 28.56 13.43 42.67 2.57
1689 5271 0.105593 AGAGCATGCCTACGGATGTG 59.894 55.000 15.66 0.00 0.00 3.21
1707 5292 2.284190 GTGCTTGATCCTAAGAGTGCC 58.716 52.381 0.00 0.00 0.00 5.01
1719 5304 2.849294 AGAGTGCCAAGAAGAGAACC 57.151 50.000 0.00 0.00 0.00 3.62
1815 5400 2.084546 CAGAAACCACGGGATTTCCTC 58.915 52.381 0.00 0.00 35.77 3.71
2055 5667 6.624423 ACAAGAAATGGAAGAAATGGATTCG 58.376 36.000 0.00 0.00 43.15 3.34
2085 5697 0.908198 ACCAACTGGAGGAGATGCTC 59.092 55.000 1.86 0.00 38.94 4.26
2151 5763 1.889891 AACAAGAACACAAACGTGCG 58.110 45.000 0.00 0.00 37.97 5.34
2202 5818 4.618920 TTTGTTAGAGGGAGGTGAAGAC 57.381 45.455 0.00 0.00 0.00 3.01
2216 5832 0.669318 GAAGACGATGGTGGCAACGA 60.669 55.000 0.00 0.00 42.51 3.85
2250 5866 6.537355 TCAAGGTTCTGACAAAGATCAAGAT 58.463 36.000 0.00 0.00 33.93 2.40
2262 5878 7.000472 ACAAAGATCAAGATCAAGAGACCAAA 59.000 34.615 12.21 0.00 40.22 3.28
2307 5923 2.046507 AAGCCAGCGGAAGAGCAG 60.047 61.111 0.00 0.00 40.15 4.24
2333 5949 4.127171 GTTAAAGCAGTGGTTCAGTCAGA 58.873 43.478 8.24 0.00 0.00 3.27
2433 6050 2.097825 GCCAGAAGAAATGAGGCATGT 58.902 47.619 0.00 0.00 44.59 3.21
2453 6070 3.117888 TGTGAGGGAAAGCTGAGAAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
2454 6071 3.885901 GTGAGGGAAAGCTGAGAAGTTTT 59.114 43.478 0.00 0.00 0.00 2.43
2455 6072 4.339530 GTGAGGGAAAGCTGAGAAGTTTTT 59.660 41.667 0.00 0.00 0.00 1.94
2480 6097 5.748670 TTTTGACTATACACAGTAGGGCA 57.251 39.130 0.00 0.00 0.00 5.36
2481 6098 5.748670 TTTGACTATACACAGTAGGGCAA 57.251 39.130 0.00 0.00 0.00 4.52
2482 6099 5.748670 TTGACTATACACAGTAGGGCAAA 57.251 39.130 0.00 0.00 0.00 3.68
2483 6100 5.748670 TGACTATACACAGTAGGGCAAAA 57.251 39.130 0.00 0.00 0.00 2.44
2484 6101 6.116711 TGACTATACACAGTAGGGCAAAAA 57.883 37.500 0.00 0.00 0.00 1.94
2505 6122 6.616774 AAAACCCACTGCAATTTTTATGTG 57.383 33.333 0.00 0.00 0.00 3.21
2506 6123 5.543507 AACCCACTGCAATTTTTATGTGA 57.456 34.783 0.45 0.00 0.00 3.58
2507 6124 5.138125 ACCCACTGCAATTTTTATGTGAG 57.862 39.130 0.45 0.00 0.00 3.51
2508 6125 4.832266 ACCCACTGCAATTTTTATGTGAGA 59.168 37.500 0.45 0.00 0.00 3.27
2509 6126 5.304101 ACCCACTGCAATTTTTATGTGAGAA 59.696 36.000 0.45 0.00 0.00 2.87
2510 6127 5.865552 CCCACTGCAATTTTTATGTGAGAAG 59.134 40.000 0.45 0.00 0.00 2.85
2511 6128 6.449698 CCACTGCAATTTTTATGTGAGAAGT 58.550 36.000 0.45 0.00 0.00 3.01
2512 6129 6.925165 CCACTGCAATTTTTATGTGAGAAGTT 59.075 34.615 0.45 0.00 0.00 2.66
2513 6130 7.115378 CCACTGCAATTTTTATGTGAGAAGTTC 59.885 37.037 0.00 0.00 0.00 3.01
2514 6131 7.648908 CACTGCAATTTTTATGTGAGAAGTTCA 59.351 33.333 5.50 0.00 0.00 3.18
2515 6132 7.864379 ACTGCAATTTTTATGTGAGAAGTTCAG 59.136 33.333 5.50 0.00 36.21 3.02
2516 6133 6.642131 TGCAATTTTTATGTGAGAAGTTCAGC 59.358 34.615 5.50 0.00 36.21 4.26
2517 6134 6.642131 GCAATTTTTATGTGAGAAGTTCAGCA 59.358 34.615 5.50 0.00 36.21 4.41
2518 6135 7.148853 GCAATTTTTATGTGAGAAGTTCAGCAG 60.149 37.037 5.50 0.00 36.21 4.24
2519 6136 5.362556 TTTTATGTGAGAAGTTCAGCAGC 57.637 39.130 5.50 0.00 36.21 5.25
2520 6137 2.556144 ATGTGAGAAGTTCAGCAGCA 57.444 45.000 5.50 4.98 36.21 4.41
2521 6138 1.875009 TGTGAGAAGTTCAGCAGCAG 58.125 50.000 5.50 0.00 36.21 4.24
2522 6139 1.413812 TGTGAGAAGTTCAGCAGCAGA 59.586 47.619 5.50 0.00 36.21 4.26
2523 6140 2.067766 GTGAGAAGTTCAGCAGCAGAG 58.932 52.381 5.50 0.00 36.21 3.35
2524 6141 1.690893 TGAGAAGTTCAGCAGCAGAGT 59.309 47.619 5.50 0.00 0.00 3.24
2525 6142 2.103771 TGAGAAGTTCAGCAGCAGAGTT 59.896 45.455 5.50 0.00 0.00 3.01
2526 6143 3.321968 TGAGAAGTTCAGCAGCAGAGTTA 59.678 43.478 5.50 0.00 0.00 2.24
2527 6144 3.924144 AGAAGTTCAGCAGCAGAGTTAG 58.076 45.455 5.50 0.00 0.00 2.34
2528 6145 3.323403 AGAAGTTCAGCAGCAGAGTTAGT 59.677 43.478 5.50 0.00 0.00 2.24
2529 6146 3.760580 AGTTCAGCAGCAGAGTTAGTT 57.239 42.857 0.00 0.00 0.00 2.24
2530 6147 4.078639 AGTTCAGCAGCAGAGTTAGTTT 57.921 40.909 0.00 0.00 0.00 2.66
2531 6148 4.061596 AGTTCAGCAGCAGAGTTAGTTTC 58.938 43.478 0.00 0.00 0.00 2.78
2532 6149 2.677199 TCAGCAGCAGAGTTAGTTTCG 58.323 47.619 0.00 0.00 0.00 3.46
2533 6150 1.127582 CAGCAGCAGAGTTAGTTTCGC 59.872 52.381 0.00 0.00 0.00 4.70
2534 6151 1.148310 GCAGCAGAGTTAGTTTCGCA 58.852 50.000 0.00 0.00 0.00 5.10
2535 6152 1.531149 GCAGCAGAGTTAGTTTCGCAA 59.469 47.619 0.00 0.00 0.00 4.85
2536 6153 2.412065 GCAGCAGAGTTAGTTTCGCAAG 60.412 50.000 0.00 0.00 0.00 4.01
2557 6174 5.948992 AGGCATTGAGTCAAGTTAGTTTC 57.051 39.130 11.91 0.00 0.00 2.78
2573 6190 1.202114 GTTTCGCAAGGCATGGATGAA 59.798 47.619 0.00 0.00 38.47 2.57
2622 6240 7.049140 GCATTTATGTGCTTTTTGGTACTTC 57.951 36.000 0.00 0.00 41.82 3.01
2632 6250 5.239525 GCTTTTTGGTACTTCTCTGTGATGT 59.760 40.000 0.00 4.13 37.00 3.06
2677 6296 8.712363 CGATGTAGTCCATTCTATTAAACCATG 58.288 37.037 0.00 0.00 32.56 3.66
2685 6304 7.122055 TCCATTCTATTAAACCATGTGGACAAC 59.878 37.037 5.96 0.00 38.94 3.32
2717 6336 3.071457 TGTCTGAGAGAACATTTGCTCCA 59.929 43.478 0.00 0.00 0.00 3.86
2721 6340 4.654915 TGAGAGAACATTTGCTCCATCAA 58.345 39.130 0.00 0.00 0.00 2.57
2724 6343 6.209986 TGAGAGAACATTTGCTCCATCAATTT 59.790 34.615 0.00 0.00 0.00 1.82
2733 6352 4.019174 TGCTCCATCAATTTCTTTCCTCC 58.981 43.478 0.00 0.00 0.00 4.30
2779 6398 7.828508 ATAATTGTGTCACTGGCATAATGAT 57.171 32.000 6.40 2.28 30.13 2.45
2797 6416 7.148035 CATAATGATGAAGACAATTGGTGTCCA 60.148 37.037 10.83 1.63 45.56 4.02
2851 6470 2.093890 TGAATGTCAAATCGGCAGCAT 58.906 42.857 0.00 0.00 0.00 3.79
2853 6472 3.884693 TGAATGTCAAATCGGCAGCATAT 59.115 39.130 0.00 0.00 0.00 1.78
2898 6517 8.682936 AAGATTCATCTTACAACAGTGTTCTT 57.317 30.769 5.27 0.00 44.80 2.52
2900 6519 7.933577 AGATTCATCTTACAACAGTGTTCTTCA 59.066 33.333 5.27 0.00 39.30 3.02
2906 6525 8.138365 TCTTACAACAGTGTTCTTCATGTTAC 57.862 34.615 5.27 0.00 39.30 2.50
2914 6533 8.812972 ACAGTGTTCTTCATGTTACCTTATCTA 58.187 33.333 0.00 0.00 0.00 1.98
2925 6544 7.360113 TGTTACCTTATCTACATGATGCAGA 57.640 36.000 0.00 0.00 36.65 4.26
2926 6545 7.210174 TGTTACCTTATCTACATGATGCAGAC 58.790 38.462 0.00 0.00 36.65 3.51
2928 6547 5.605534 ACCTTATCTACATGATGCAGACAC 58.394 41.667 0.00 0.00 36.65 3.67
2929 6548 5.365025 ACCTTATCTACATGATGCAGACACT 59.635 40.000 0.00 0.00 36.65 3.55
2930 6549 6.551227 ACCTTATCTACATGATGCAGACACTA 59.449 38.462 0.00 0.00 36.65 2.74
2931 6550 7.089538 CCTTATCTACATGATGCAGACACTAG 58.910 42.308 0.00 0.00 36.65 2.57
2932 6551 4.313277 TCTACATGATGCAGACACTAGC 57.687 45.455 0.00 0.00 0.00 3.42
2937 6584 2.079158 TGATGCAGACACTAGCTTTGC 58.921 47.619 0.00 0.00 35.42 3.68
2948 6595 6.934645 AGACACTAGCTTTGCTGTTTGTTATA 59.065 34.615 0.00 0.00 40.10 0.98
2958 6605 9.713740 CTTTGCTGTTTGTTATATTCTCTCATC 57.286 33.333 0.00 0.00 0.00 2.92
3010 6657 4.970662 ATGATGAAGAACAATTGGTCCG 57.029 40.909 19.90 0.00 30.36 4.79
3012 6659 3.751175 TGATGAAGAACAATTGGTCCGTC 59.249 43.478 19.90 17.04 30.36 4.79
3051 6698 5.796935 GTGATGATTTCCAATGAAACACTCG 59.203 40.000 0.00 0.00 42.97 4.18
3072 6719 5.423015 TCGATGCTTCTGATTCTAAAAGCT 58.577 37.500 14.73 0.00 43.48 3.74
3111 6758 9.295825 ACTGTCCATTCTGTTTATTGTAATCAA 57.704 29.630 0.00 0.00 37.98 2.57
3130 6777 7.935338 AATCAAGTTTTGCTGTTATGTTCAG 57.065 32.000 0.00 0.00 36.18 3.02
3164 6811 7.093354 CACTACATTTCTGTGTACTGATGAGT 58.907 38.462 0.00 0.00 36.79 3.41
3270 6923 8.696374 TGAAAGCAGCTGTACTAGTTTATATCT 58.304 33.333 16.64 0.00 0.00 1.98
3295 6948 5.970592 GCAGATGCCCTTTCTTTTTAGATT 58.029 37.500 0.00 0.00 34.31 2.40
3306 6959 8.462016 CCTTTCTTTTTAGATTGAATGGATCGT 58.538 33.333 0.00 0.00 36.47 3.73
3384 7048 1.542472 TGCATCTTTGAGTGTGCCATG 59.458 47.619 0.00 0.00 36.79 3.66
3388 7052 2.778299 TCTTTGAGTGTGCCATGTACC 58.222 47.619 0.00 0.00 0.00 3.34
3389 7053 2.371841 TCTTTGAGTGTGCCATGTACCT 59.628 45.455 0.00 0.00 0.00 3.08
3396 7060 5.116084 AGTGTGCCATGTACCTAAATGAT 57.884 39.130 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
423 2824 1.000938 GTTCTACACACCTTCGGACGT 60.001 52.381 0.00 0.00 0.00 4.34
721 3182 3.884350 CGGCCTCGTCGATTCCGA 61.884 66.667 22.98 2.74 42.43 4.55
782 3276 2.673368 GAGCTGTTATATATGTGCGGCC 59.327 50.000 0.00 0.00 32.33 6.13
789 3283 8.438513 CAAATTCGGACTGAGCTGTTATATATG 58.561 37.037 0.00 0.00 0.00 1.78
851 3767 7.365840 GTGAGAGACACGGAAATAAAAAGAT 57.634 36.000 0.00 0.00 39.78 2.40
911 3874 3.370527 GCGTGATATTATATGGGCCTGGT 60.371 47.826 4.53 0.00 0.00 4.00
947 3910 9.314321 TCGATTCCTTCTGATACTTTTATCAAC 57.686 33.333 0.00 0.00 42.93 3.18
1037 4009 0.970937 CTCCTTGGCGAGGTGGTAGA 60.971 60.000 20.33 0.00 46.39 2.59
1467 4447 3.165875 CTGAGACCTGAAGACCTTGGTA 58.834 50.000 0.00 0.00 32.30 3.25
1545 4528 1.519455 CCGGCTCGCTCTAGGTTTG 60.519 63.158 0.00 0.00 0.00 2.93
1689 5271 2.698855 TGGCACTCTTAGGATCAAGC 57.301 50.000 0.00 0.00 0.00 4.01
1707 5292 1.291877 CGCCACGGGTTCTCTTCTTG 61.292 60.000 0.00 0.00 0.00 3.02
2034 5646 5.509498 TCCGAATCCATTTCTTCCATTTCT 58.491 37.500 0.00 0.00 31.73 2.52
2055 5667 3.077359 CTCCAGTTGGTGTTCTTCATCC 58.923 50.000 0.00 0.00 36.34 3.51
2085 5697 4.445718 ACATAACGCTCATAAGCTTCATCG 59.554 41.667 0.00 3.61 46.91 3.84
2120 5732 6.591750 TGTGTTCTTGTTTTACTTTCCCAA 57.408 33.333 0.00 0.00 0.00 4.12
2123 5735 6.583427 ACGTTTGTGTTCTTGTTTTACTTTCC 59.417 34.615 0.00 0.00 0.00 3.13
2124 5736 7.433979 CACGTTTGTGTTCTTGTTTTACTTTC 58.566 34.615 0.00 0.00 41.34 2.62
2125 5737 7.328157 CACGTTTGTGTTCTTGTTTTACTTT 57.672 32.000 0.00 0.00 41.34 2.66
2151 5763 4.097437 TCAGCATCAGGATTGATTTGCTTC 59.903 41.667 3.58 0.00 43.62 3.86
2180 5792 4.322801 CGTCTTCACCTCCCTCTAACAAAT 60.323 45.833 0.00 0.00 0.00 2.32
2202 5818 3.101209 CCATCGTTGCCACCATCG 58.899 61.111 0.00 0.00 35.92 3.84
2216 5832 2.171237 TCAGAACCTTGATCGATGCCAT 59.829 45.455 0.54 0.00 0.00 4.40
2250 5866 3.680777 AAAAGGGGTTTGGTCTCTTGA 57.319 42.857 0.00 0.00 0.00 3.02
2262 5878 9.670442 TCTGTATCTAGACATAATAAAAGGGGT 57.330 33.333 0.00 0.00 0.00 4.95
2307 5923 3.821033 ACTGAACCACTGCTTTAACATCC 59.179 43.478 0.00 0.00 0.00 3.51
2333 5949 5.809001 TCTTCCTGCTTCTGTGAACATATT 58.191 37.500 0.00 0.00 0.00 1.28
2433 6050 3.864789 AAACTTCTCAGCTTTCCCTCA 57.135 42.857 0.00 0.00 0.00 3.86
2457 6074 6.116711 TGCCCTACTGTGTATAGTCAAAAA 57.883 37.500 0.00 0.00 32.19 1.94
2458 6075 5.748670 TGCCCTACTGTGTATAGTCAAAA 57.251 39.130 0.00 0.00 32.19 2.44
2459 6076 5.748670 TTGCCCTACTGTGTATAGTCAAA 57.251 39.130 0.00 0.00 32.19 2.69
2460 6077 5.748670 TTTGCCCTACTGTGTATAGTCAA 57.251 39.130 0.00 0.00 32.19 3.18
2461 6078 5.748670 TTTTGCCCTACTGTGTATAGTCA 57.251 39.130 0.00 0.00 32.19 3.41
2481 6098 6.825721 TCACATAAAAATTGCAGTGGGTTTTT 59.174 30.769 0.00 10.90 37.48 1.94
2482 6099 6.352516 TCACATAAAAATTGCAGTGGGTTTT 58.647 32.000 0.00 0.00 0.00 2.43
2483 6100 5.923204 TCACATAAAAATTGCAGTGGGTTT 58.077 33.333 0.00 0.00 0.00 3.27
2484 6101 5.304101 TCTCACATAAAAATTGCAGTGGGTT 59.696 36.000 0.00 0.00 0.00 4.11
2485 6102 4.832266 TCTCACATAAAAATTGCAGTGGGT 59.168 37.500 0.00 0.00 0.00 4.51
2486 6103 5.389859 TCTCACATAAAAATTGCAGTGGG 57.610 39.130 0.00 0.00 0.00 4.61
2487 6104 6.449698 ACTTCTCACATAAAAATTGCAGTGG 58.550 36.000 0.00 0.00 0.00 4.00
2488 6105 7.648908 TGAACTTCTCACATAAAAATTGCAGTG 59.351 33.333 0.00 0.00 0.00 3.66
2489 6106 7.715657 TGAACTTCTCACATAAAAATTGCAGT 58.284 30.769 0.00 0.00 0.00 4.40
2490 6107 7.148853 GCTGAACTTCTCACATAAAAATTGCAG 60.149 37.037 0.00 0.00 0.00 4.41
2491 6108 6.642131 GCTGAACTTCTCACATAAAAATTGCA 59.358 34.615 0.00 0.00 0.00 4.08
2492 6109 6.642131 TGCTGAACTTCTCACATAAAAATTGC 59.358 34.615 0.00 0.00 0.00 3.56
2493 6110 7.148853 GCTGCTGAACTTCTCACATAAAAATTG 60.149 37.037 0.00 0.00 0.00 2.32
2494 6111 6.865205 GCTGCTGAACTTCTCACATAAAAATT 59.135 34.615 0.00 0.00 0.00 1.82
2495 6112 6.016024 TGCTGCTGAACTTCTCACATAAAAAT 60.016 34.615 0.00 0.00 0.00 1.82
2496 6113 5.299028 TGCTGCTGAACTTCTCACATAAAAA 59.701 36.000 0.00 0.00 0.00 1.94
2497 6114 4.821260 TGCTGCTGAACTTCTCACATAAAA 59.179 37.500 0.00 0.00 0.00 1.52
2498 6115 4.388485 TGCTGCTGAACTTCTCACATAAA 58.612 39.130 0.00 0.00 0.00 1.40
2499 6116 3.999001 CTGCTGCTGAACTTCTCACATAA 59.001 43.478 0.00 0.00 0.00 1.90
2500 6117 3.259123 TCTGCTGCTGAACTTCTCACATA 59.741 43.478 6.77 0.00 0.00 2.29
2501 6118 2.038164 TCTGCTGCTGAACTTCTCACAT 59.962 45.455 6.77 0.00 0.00 3.21
2502 6119 1.413812 TCTGCTGCTGAACTTCTCACA 59.586 47.619 6.77 0.00 0.00 3.58
2503 6120 2.067766 CTCTGCTGCTGAACTTCTCAC 58.932 52.381 10.47 0.00 0.00 3.51
2504 6121 1.690893 ACTCTGCTGCTGAACTTCTCA 59.309 47.619 10.47 0.00 0.00 3.27
2505 6122 2.453983 ACTCTGCTGCTGAACTTCTC 57.546 50.000 10.47 0.00 0.00 2.87
2506 6123 2.926778 AACTCTGCTGCTGAACTTCT 57.073 45.000 10.47 0.00 0.00 2.85
2507 6124 3.658709 ACTAACTCTGCTGCTGAACTTC 58.341 45.455 10.47 0.00 0.00 3.01
2508 6125 3.760580 ACTAACTCTGCTGCTGAACTT 57.239 42.857 10.47 7.34 0.00 2.66
2509 6126 3.760580 AACTAACTCTGCTGCTGAACT 57.239 42.857 10.47 3.49 0.00 3.01
2510 6127 3.120854 CGAAACTAACTCTGCTGCTGAAC 60.121 47.826 10.47 0.00 0.00 3.18
2511 6128 3.059884 CGAAACTAACTCTGCTGCTGAA 58.940 45.455 10.47 0.00 0.00 3.02
2512 6129 2.677199 CGAAACTAACTCTGCTGCTGA 58.323 47.619 8.95 8.95 0.00 4.26
2513 6130 1.127582 GCGAAACTAACTCTGCTGCTG 59.872 52.381 0.00 0.00 0.00 4.41
2514 6131 1.270305 TGCGAAACTAACTCTGCTGCT 60.270 47.619 0.00 0.00 0.00 4.24
2515 6132 1.148310 TGCGAAACTAACTCTGCTGC 58.852 50.000 0.00 0.00 0.00 5.25
2516 6133 2.158449 CCTTGCGAAACTAACTCTGCTG 59.842 50.000 0.00 0.00 0.00 4.41
2517 6134 2.417719 CCTTGCGAAACTAACTCTGCT 58.582 47.619 0.00 0.00 0.00 4.24
2518 6135 1.135944 GCCTTGCGAAACTAACTCTGC 60.136 52.381 0.00 0.00 0.00 4.26
2519 6136 2.143122 TGCCTTGCGAAACTAACTCTG 58.857 47.619 0.00 0.00 0.00 3.35
2520 6137 2.543777 TGCCTTGCGAAACTAACTCT 57.456 45.000 0.00 0.00 0.00 3.24
2521 6138 3.188460 TCAATGCCTTGCGAAACTAACTC 59.812 43.478 0.00 0.00 32.11 3.01
2522 6139 3.146066 TCAATGCCTTGCGAAACTAACT 58.854 40.909 0.00 0.00 32.11 2.24
2523 6140 3.058224 ACTCAATGCCTTGCGAAACTAAC 60.058 43.478 0.00 0.00 32.11 2.34
2524 6141 3.146066 ACTCAATGCCTTGCGAAACTAA 58.854 40.909 0.00 0.00 32.11 2.24
2525 6142 2.742053 GACTCAATGCCTTGCGAAACTA 59.258 45.455 0.00 0.00 32.11 2.24
2526 6143 1.537202 GACTCAATGCCTTGCGAAACT 59.463 47.619 0.00 0.00 32.11 2.66
2527 6144 1.266718 TGACTCAATGCCTTGCGAAAC 59.733 47.619 0.00 0.00 32.11 2.78
2528 6145 1.603456 TGACTCAATGCCTTGCGAAA 58.397 45.000 0.00 0.00 32.11 3.46
2529 6146 1.536766 CTTGACTCAATGCCTTGCGAA 59.463 47.619 0.00 0.00 32.11 4.70
2530 6147 1.159285 CTTGACTCAATGCCTTGCGA 58.841 50.000 0.00 0.00 32.11 5.10
2531 6148 0.877071 ACTTGACTCAATGCCTTGCG 59.123 50.000 0.00 0.00 32.11 4.85
2532 6149 3.503748 ACTAACTTGACTCAATGCCTTGC 59.496 43.478 0.00 0.00 32.11 4.01
2533 6150 5.695851 AACTAACTTGACTCAATGCCTTG 57.304 39.130 0.00 0.00 0.00 3.61
2534 6151 5.049405 CGAAACTAACTTGACTCAATGCCTT 60.049 40.000 0.00 0.00 0.00 4.35
2535 6152 4.452455 CGAAACTAACTTGACTCAATGCCT 59.548 41.667 0.00 0.00 0.00 4.75
2536 6153 4.712763 CGAAACTAACTTGACTCAATGCC 58.287 43.478 0.00 0.00 0.00 4.40
2557 6174 2.358582 TGTTATTCATCCATGCCTTGCG 59.641 45.455 0.00 0.00 0.00 4.85
2573 6190 7.071069 TCTGATCTCACATAATGCCTGTTAT 57.929 36.000 0.00 0.00 0.00 1.89
2615 6233 6.260050 TGTTTTCAACATCACAGAGAAGTACC 59.740 38.462 0.00 0.00 36.25 3.34
2632 6250 7.624360 ACATCGGCTAATTATCTGTTTTCAA 57.376 32.000 0.00 0.00 0.00 2.69
2647 6265 7.770366 TTAATAGAATGGACTACATCGGCTA 57.230 36.000 0.00 0.00 39.40 3.93
2650 6268 7.214381 TGGTTTAATAGAATGGACTACATCGG 58.786 38.462 0.00 0.00 39.40 4.18
2677 6296 2.712057 CAAATGCCTCAGTTGTCCAC 57.288 50.000 0.00 0.00 35.19 4.02
2685 6304 3.606595 TCTCTCAGACAAATGCCTCAG 57.393 47.619 0.00 0.00 0.00 3.35
2740 6359 5.646360 ACACAATTATACGAAAAGGAGTGGG 59.354 40.000 0.00 0.00 0.00 4.61
2746 6365 6.542852 CCAGTGACACAATTATACGAAAAGG 58.457 40.000 8.59 0.00 0.00 3.11
2826 6445 4.595116 CTGCCGATTTGACATTCAGAATC 58.405 43.478 0.00 0.00 0.00 2.52
2867 6486 9.429359 CACTGTTGTAAGATGAATCTTTCTAGT 57.571 33.333 10.66 8.94 44.28 2.57
2868 6487 9.429359 ACACTGTTGTAAGATGAATCTTTCTAG 57.571 33.333 10.66 8.46 44.28 2.43
2869 6488 9.778741 AACACTGTTGTAAGATGAATCTTTCTA 57.221 29.630 10.66 1.02 45.71 2.10
2884 6503 6.588204 AGGTAACATGAAGAACACTGTTGTA 58.412 36.000 0.00 0.00 34.24 2.41
2900 6519 7.875041 GTCTGCATCATGTAGATAAGGTAACAT 59.125 37.037 8.85 0.00 41.02 2.71
2906 6525 5.851720 AGTGTCTGCATCATGTAGATAAGG 58.148 41.667 8.85 0.00 41.02 2.69
2914 6533 3.623906 AAGCTAGTGTCTGCATCATGT 57.376 42.857 0.00 0.00 0.00 3.21
2925 6544 7.687941 ATATAACAAACAGCAAAGCTAGTGT 57.312 32.000 0.00 0.00 36.40 3.55
2926 6545 8.454106 AGAATATAACAAACAGCAAAGCTAGTG 58.546 33.333 0.00 0.00 36.40 2.74
2928 6547 8.887717 AGAGAATATAACAAACAGCAAAGCTAG 58.112 33.333 0.00 0.00 36.40 3.42
2929 6548 8.792830 AGAGAATATAACAAACAGCAAAGCTA 57.207 30.769 0.00 0.00 36.40 3.32
2930 6549 7.391554 TGAGAGAATATAACAAACAGCAAAGCT 59.608 33.333 0.00 0.00 40.77 3.74
2931 6550 7.530010 TGAGAGAATATAACAAACAGCAAAGC 58.470 34.615 0.00 0.00 0.00 3.51
2932 6551 9.713740 GATGAGAGAATATAACAAACAGCAAAG 57.286 33.333 0.00 0.00 0.00 2.77
3032 6679 4.795278 GCATCGAGTGTTTCATTGGAAATC 59.205 41.667 0.00 0.00 44.32 2.17
3044 6691 4.199432 AGAATCAGAAGCATCGAGTGTT 57.801 40.909 0.00 0.00 0.00 3.32
3051 6698 6.238429 CCTGAGCTTTTAGAATCAGAAGCATC 60.238 42.308 14.38 10.40 45.17 3.91
3072 6719 6.825213 CAGAATGGACAGTAATTCAATCCTGA 59.175 38.462 9.92 0.00 35.63 3.86
3102 6749 9.243637 GAACATAACAGCAAAACTTGATTACAA 57.756 29.630 0.00 0.00 34.65 2.41
3111 6758 7.362662 CACATACTGAACATAACAGCAAAACT 58.637 34.615 0.00 0.00 38.74 2.66
3130 6777 5.179368 ACACAGAAATGTAGTGTGCACATAC 59.821 40.000 24.69 23.06 44.51 2.39
3295 6948 3.119137 AGACATGACGAACGATCCATTCA 60.119 43.478 0.00 0.00 0.00 2.57
3306 6959 6.929049 ACTAGATTTGTTTCAGACATGACGAA 59.071 34.615 0.00 0.00 38.26 3.85


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

AutoCloner maintained by Alex Coulton.