Multiple sequence alignment - TraesCS3A01G343700

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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 TraesCS3A01G343700 chr3A 100.000 2970 0 0 1 2970 593175757 593178726 0.000000e+00 5485.0
1 TraesCS3A01G343700 chr3A 83.885 1359 107 57 710 1973 593339621 593340962 0.000000e+00 1194.0
2 TraesCS3A01G343700 chr3A 72.517 604 115 28 1 558 739664135 739663537 6.630000e-32 148.0
3 TraesCS3A01G343700 chr3A 80.189 212 23 9 366 560 629625352 629625143 1.110000e-29 141.0
4 TraesCS3A01G343700 chr3A 90.000 50 3 2 719 766 593107339 593107388 2.470000e-06 63.9
5 TraesCS3A01G343700 chr3D 90.111 2518 144 40 520 2970 449540270 449542749 0.000000e+00 3173.0
6 TraesCS3A01G343700 chr3D 92.184 499 36 3 1 498 449539807 449540303 0.000000e+00 702.0
7 TraesCS3A01G343700 chr3D 84.379 717 72 17 1284 1973 449737750 449738453 0.000000e+00 667.0
8 TraesCS3A01G343700 chr3D 84.890 589 51 22 719 1274 449737129 449737712 7.190000e-156 560.0
9 TraesCS3A01G343700 chr3D 91.150 113 6 4 448 558 607210932 607210822 1.840000e-32 150.0
10 TraesCS3A01G343700 chr3D 75.850 294 45 14 1 272 486125385 486125096 3.110000e-25 126.0
11 TraesCS3A01G343700 chr3D 79.720 143 20 6 164 299 58394962 58395102 8.760000e-16 95.3
12 TraesCS3A01G343700 chr3B 89.940 1501 97 13 789 2265 590623404 590624874 0.000000e+00 1886.0
13 TraesCS3A01G343700 chr3B 83.929 784 81 26 1284 2035 591365381 591366151 0.000000e+00 708.0
14 TraesCS3A01G343700 chr3B 86.957 575 47 19 719 1269 591364761 591365331 3.250000e-174 621.0
15 TraesCS3A01G343700 chr3B 81.062 829 102 27 1 796 590622426 590623232 7.040000e-171 610.0
16 TraesCS3A01G343700 chr3B 78.279 244 33 13 336 562 719912146 719912386 3.990000e-29 139.0
17 TraesCS3A01G343700 chr3B 86.486 111 13 1 448 558 816611049 816610941 1.450000e-23 121.0
18 TraesCS3A01G343700 chr5A 81.053 285 28 9 2710 2968 691841476 691841192 1.400000e-48 204.0
19 TraesCS3A01G343700 chr5A 79.137 139 22 6 2707 2841 616604967 616604832 4.080000e-14 89.8
20 TraesCS3A01G343700 chr5A 78.417 139 23 6 2707 2841 616610431 616610296 1.900000e-12 84.2
21 TraesCS3A01G343700 chr4D 80.247 243 29 11 336 561 67806320 67806080 6.590000e-37 165.0
22 TraesCS3A01G343700 chr4A 83.529 170 24 3 395 562 33655741 33655908 3.960000e-34 156.0
23 TraesCS3A01G343700 chr4A 79.851 134 24 3 2707 2838 726403207 726403339 8.760000e-16 95.3
24 TraesCS3A01G343700 chr6B 78.750 240 31 9 336 558 679240075 679240311 3.090000e-30 143.0
25 TraesCS3A01G343700 chr2A 76.678 283 40 10 2710 2966 303628001 303628283 1.860000e-27 134.0
26 TraesCS3A01G343700 chr2A 79.545 132 21 5 2714 2841 48345324 48345195 4.080000e-14 89.8
27 TraesCS3A01G343700 chr2D 78.696 230 26 10 2710 2926 262428621 262428840 6.680000e-27 132.0
28 TraesCS3A01G343700 chr7B 86.555 119 15 1 448 566 557056502 557056619 2.400000e-26 130.0
29 TraesCS3A01G343700 chr7B 86.957 115 11 4 448 560 698723638 698723526 3.110000e-25 126.0
30 TraesCS3A01G343700 chr7B 86.667 75 9 1 180 254 284016167 284016240 6.820000e-12 82.4
31 TraesCS3A01G343700 chr2B 81.890 127 15 7 179 299 706715607 706715483 1.880000e-17 100.0
32 TraesCS3A01G343700 chr2B 92.857 56 3 1 1 55 778461317 778461372 2.450000e-11 80.5
33 TraesCS3A01G343700 chr7D 72.727 308 75 5 1 300 434232831 434232525 8.760000e-16 95.3
34 TraesCS3A01G343700 chr7A 79.104 134 25 3 2707 2838 92431787 92431919 4.080000e-14 89.8
35 TraesCS3A01G343700 chr7A 78.417 139 23 6 2707 2841 30754389 30754254 1.900000e-12 84.2
36 TraesCS3A01G343700 chr1A 79.104 134 25 3 2707 2838 569994925 569995057 4.080000e-14 89.8
37 TraesCS3A01G343700 chr6D 96.970 33 1 0 692 724 78277314 78277346 4.140000e-04 56.5


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 TraesCS3A01G343700 chr3A 593175757 593178726 2969 False 5485.0 5485 100.0000 1 2970 1 chr3A.!!$F2 2969
1 TraesCS3A01G343700 chr3A 593339621 593340962 1341 False 1194.0 1194 83.8850 710 1973 1 chr3A.!!$F3 1263
2 TraesCS3A01G343700 chr3D 449539807 449542749 2942 False 1937.5 3173 91.1475 1 2970 2 chr3D.!!$F2 2969
3 TraesCS3A01G343700 chr3D 449737129 449738453 1324 False 613.5 667 84.6345 719 1973 2 chr3D.!!$F3 1254
4 TraesCS3A01G343700 chr3B 590622426 590624874 2448 False 1248.0 1886 85.5010 1 2265 2 chr3B.!!$F2 2264
5 TraesCS3A01G343700 chr3B 591364761 591366151 1390 False 664.5 708 85.4430 719 2035 2 chr3B.!!$F3 1316

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
463 480 0.037734 AGTCCGGACATGGGGAAAAC 59.962 55.0 35.0 5.32 33.27 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 2464 0.396811 CTCAAAAGACCCCACCGACT 59.603 55.0 0.0 0.0 0.0 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.661178 GCGACACAGACAACATTGCTG 60.661 52.381 11.87 11.87 37.90 4.41
114 115 0.817654 CGTGTCATACTGCTCCTCCA 59.182 55.000 0.00 0.00 0.00 3.86
119 121 0.250640 CATACTGCTCCTCCATGCCC 60.251 60.000 0.00 0.00 0.00 5.36
155 157 1.336702 GCCATCAACATTTGCGGAACA 60.337 47.619 0.00 0.00 0.00 3.18
166 168 4.335647 CGGAACAGTGCCCTGCCT 62.336 66.667 0.00 0.00 42.81 4.75
249 251 2.327325 AAGTAGAACAGGAGAGGCCA 57.673 50.000 5.01 0.00 40.02 5.36
257 259 4.021925 GGAGAGGCCACCGCTTGT 62.022 66.667 5.01 0.00 32.83 3.16
270 272 1.167851 CGCTTGTGTCCCATGAATGT 58.832 50.000 0.00 0.00 0.00 2.71
275 277 4.578871 CTTGTGTCCCATGAATGTCACTA 58.421 43.478 0.00 0.00 0.00 2.74
279 281 1.484653 TCCCATGAATGTCACTACCGG 59.515 52.381 0.00 0.00 0.00 5.28
301 303 3.980989 TCGCCGGCGTACACAACT 61.981 61.111 44.16 0.00 40.74 3.16
318 320 4.701651 CACAACTGGAGGAATATGCTTCAA 59.298 41.667 0.00 0.00 0.00 2.69
430 432 2.099141 TGCGCTGAAGCACTTATCTT 57.901 45.000 9.73 0.00 42.92 2.40
463 480 0.037734 AGTCCGGACATGGGGAAAAC 59.962 55.000 35.00 5.32 33.27 2.43
481 498 4.471904 AAACAATAGAGATCTGCCGTGA 57.528 40.909 0.00 0.00 0.00 4.35
503 520 1.669779 CGACCGTAGACTAGTCAAGGG 59.330 57.143 24.44 21.25 0.00 3.95
508 525 3.819902 CCGTAGACTAGTCAAGGGTATCC 59.180 52.174 24.44 0.00 0.00 2.59
522 539 2.701951 GGGTATCCTTGTCGTGGGAATA 59.298 50.000 0.00 0.00 35.08 1.75
566 599 7.631377 GCCGTAGACTAGTTTTACCTTAATCCA 60.631 40.741 0.00 0.00 0.00 3.41
582 615 7.505585 ACCTTAATCCAGTTTGAATGAAGTTCA 59.494 33.333 8.27 8.27 44.87 3.18
584 617 9.350357 CTTAATCCAGTTTGAATGAAGTTCATG 57.650 33.333 18.94 6.29 45.77 3.07
592 625 5.375417 TGAATGAAGTTCATGCGATTTGT 57.625 34.783 18.94 0.60 41.79 2.83
627 661 7.824704 TTTTAAATGTACGCGGATAGTGTTA 57.175 32.000 12.47 0.00 44.20 2.41
640 674 1.853963 AGTGTTAGATGTCCGGCTCT 58.146 50.000 0.00 0.94 0.00 4.09
643 677 0.461961 GTTAGATGTCCGGCTCTGCT 59.538 55.000 0.00 0.00 0.00 4.24
648 682 0.461961 ATGTCCGGCTCTGCTTCTAC 59.538 55.000 0.00 0.00 0.00 2.59
659 693 2.157073 GCTTCTACGTTCGCGGACC 61.157 63.158 12.96 0.00 46.45 4.46
682 716 1.691976 TCCCGTCGGCTGATGAATATT 59.308 47.619 16.68 0.00 32.56 1.28
701 735 2.022718 TGGAGGAAATTTTGGGGGTG 57.977 50.000 0.00 0.00 0.00 4.61
954 1196 0.249741 GTTGGTGCACGTACTGTCCT 60.250 55.000 11.45 0.00 0.00 3.85
1213 1459 1.569548 AGAGGAAGATGACGGACCCTA 59.430 52.381 0.00 0.00 0.00 3.53
1345 1633 1.140161 CCGTCGATTTCGCAGGGTA 59.860 57.895 0.00 0.00 39.60 3.69
1461 1749 0.883833 CACCCGAGGTACGTACAGTT 59.116 55.000 26.02 11.66 40.78 3.16
1837 2164 3.315140 TCGCGGGGATGGTTGTCA 61.315 61.111 6.13 0.00 0.00 3.58
1883 2213 1.215423 AGGTGGAACTTGGTGCTTCTT 59.785 47.619 0.00 0.00 36.74 2.52
1906 2236 1.134491 GTCGGGGAATTTCTCGATGGT 60.134 52.381 12.87 0.00 34.13 3.55
2011 2349 1.941812 CTTGCGACACAACCTCACC 59.058 57.895 0.00 0.00 33.68 4.02
2041 2379 4.246458 GGACAGATCCGGAGTATATTTGC 58.754 47.826 11.34 0.00 34.48 3.68
2046 2384 3.102052 TCCGGAGTATATTTGCGTTCC 57.898 47.619 0.00 0.00 0.00 3.62
2053 2391 4.689071 AGTATATTTGCGTTCCGACATGA 58.311 39.130 0.00 0.00 0.00 3.07
2068 2406 0.232046 CATGAACGTGTCACCGTGTG 59.768 55.000 0.00 0.00 41.65 3.82
2076 2414 1.997606 GTGTCACCGTGTGCCTATAAC 59.002 52.381 0.00 0.00 32.98 1.89
2092 2430 1.029408 TAACCATGCCATGTCGCCAC 61.029 55.000 3.63 0.00 0.00 5.01
2101 2439 0.249120 CATGTCGCCACAGGGAACTA 59.751 55.000 0.00 0.00 40.21 2.24
2118 2456 2.240279 ACTAGTCGGGAGCATGATACC 58.760 52.381 0.63 0.63 0.00 2.73
2126 2464 3.069586 CGGGAGCATGATACCTAAGACAA 59.930 47.826 11.24 0.00 0.00 3.18
2134 2472 3.446161 TGATACCTAAGACAAGTCGGTGG 59.554 47.826 8.07 7.40 34.09 4.61
2146 2484 1.072505 TCGGTGGGGTCTTTTGAGC 59.927 57.895 0.00 0.00 45.49 4.26
2163 2501 3.669536 TGAGCATCCAAAACGTCACATA 58.330 40.909 0.00 0.00 0.00 2.29
2165 2503 4.094739 TGAGCATCCAAAACGTCACATATG 59.905 41.667 0.00 0.00 0.00 1.78
2167 2505 3.181497 GCATCCAAAACGTCACATATGCT 60.181 43.478 14.34 0.00 36.44 3.79
2170 2508 2.159393 CCAAAACGTCACATATGCTGGG 60.159 50.000 1.58 0.00 0.00 4.45
2171 2509 2.746904 CAAAACGTCACATATGCTGGGA 59.253 45.455 1.58 0.00 33.87 4.37
2174 2512 0.250038 CGTCACATATGCTGGGAGGG 60.250 60.000 1.58 0.00 38.18 4.30
2199 2544 1.340248 CACGAGACGGTTATGGGCTAT 59.660 52.381 0.00 0.00 0.00 2.97
2237 2582 0.250081 CCTAGGGCCTTGAGATTCGC 60.250 60.000 13.45 0.00 0.00 4.70
2241 2586 2.609747 AGGGCCTTGAGATTCGCTATA 58.390 47.619 0.00 0.00 0.00 1.31
2243 2588 3.007398 AGGGCCTTGAGATTCGCTATAAG 59.993 47.826 0.00 0.00 0.00 1.73
2244 2589 3.244249 GGGCCTTGAGATTCGCTATAAGT 60.244 47.826 0.84 0.00 0.00 2.24
2245 2590 3.743396 GGCCTTGAGATTCGCTATAAGTG 59.257 47.826 0.00 0.00 0.00 3.16
2252 2597 5.985530 TGAGATTCGCTATAAGTGAACATGG 59.014 40.000 5.13 0.00 46.10 3.66
2266 2621 3.071023 TGAACATGGAGAACGAGGAAGTT 59.929 43.478 0.00 0.00 36.99 2.66
2368 2723 3.972950 TGTGGTGTTTAATTGGTCGTG 57.027 42.857 0.00 0.00 0.00 4.35
2369 2724 2.619177 TGTGGTGTTTAATTGGTCGTGG 59.381 45.455 0.00 0.00 0.00 4.94
2378 2733 3.703001 AATTGGTCGTGGTCTCTCATT 57.297 42.857 0.00 0.00 0.00 2.57
2382 2737 5.925506 TTGGTCGTGGTCTCTCATTTATA 57.074 39.130 0.00 0.00 0.00 0.98
2387 2742 7.232737 TGGTCGTGGTCTCTCATTTATATATGT 59.767 37.037 0.00 0.00 0.00 2.29
2390 2745 8.297426 TCGTGGTCTCTCATTTATATATGTGAC 58.703 37.037 0.00 9.27 0.00 3.67
2407 2762 3.251571 GTGACAGATGGACTTTCCGTAC 58.748 50.000 0.00 0.00 40.17 3.67
2408 2763 2.894765 TGACAGATGGACTTTCCGTACA 59.105 45.455 0.00 0.00 41.72 2.90
2428 2783 7.008901 CCGTACAAAGAAAAAGACTCAAAAACC 59.991 37.037 0.00 0.00 0.00 3.27
2438 2793 5.567138 AGACTCAAAAACCTGTTCAACAG 57.433 39.130 10.91 10.91 45.53 3.16
2471 2826 5.074584 AGACTAACTCGGACAGAAAATCC 57.925 43.478 0.00 0.00 0.00 3.01
2482 2837 5.949735 GGACAGAAAATCCGCAAAGAAATA 58.050 37.500 0.00 0.00 0.00 1.40
2495 2859 4.462483 GCAAAGAAATAGGACATGTTGGGA 59.538 41.667 0.00 0.00 0.00 4.37
2526 2890 7.736447 AGTTGAAACAGAGAATCCACTAAAG 57.264 36.000 0.00 0.00 33.66 1.85
2527 2891 7.283329 AGTTGAAACAGAGAATCCACTAAAGT 58.717 34.615 0.00 0.00 33.66 2.66
2528 2892 7.442666 AGTTGAAACAGAGAATCCACTAAAGTC 59.557 37.037 0.00 0.00 33.66 3.01
2529 2893 5.926542 TGAAACAGAGAATCCACTAAAGTCG 59.073 40.000 0.00 0.00 33.66 4.18
2530 2894 4.457834 ACAGAGAATCCACTAAAGTCGG 57.542 45.455 0.00 0.00 33.66 4.79
2531 2895 4.087182 ACAGAGAATCCACTAAAGTCGGA 58.913 43.478 4.48 4.48 33.66 4.55
2532 2896 4.082136 ACAGAGAATCCACTAAAGTCGGAC 60.082 45.833 0.00 0.00 33.66 4.79
2533 2897 4.082190 CAGAGAATCCACTAAAGTCGGACA 60.082 45.833 11.27 0.00 33.66 4.02
2534 2898 4.712337 AGAGAATCCACTAAAGTCGGACAT 59.288 41.667 11.27 0.00 33.66 3.06
2535 2899 5.187967 AGAGAATCCACTAAAGTCGGACATT 59.812 40.000 11.27 7.40 33.66 2.71
2536 2900 5.178797 AGAATCCACTAAAGTCGGACATTG 58.821 41.667 11.27 2.73 31.50 2.82
2537 2901 3.328382 TCCACTAAAGTCGGACATTGG 57.672 47.619 11.27 9.31 0.00 3.16
2559 2923 3.937079 GGTCGGACATTTAAGTCGGAATT 59.063 43.478 10.76 0.00 45.46 2.17
2574 2938 5.359860 AGTCGGAATTTCCAACTTGACTTTT 59.640 36.000 15.58 0.00 35.91 2.27
2577 2941 6.039616 CGGAATTTCCAACTTGACTTTTCAA 58.960 36.000 15.58 0.00 36.42 2.69
2579 2943 7.224557 CGGAATTTCCAACTTGACTTTTCAATT 59.775 33.333 15.58 0.00 37.48 2.32
2580 2944 8.892723 GGAATTTCCAACTTGACTTTTCAATTT 58.107 29.630 10.67 0.00 37.53 1.82
2581 2945 9.920826 GAATTTCCAACTTGACTTTTCAATTTC 57.079 29.630 0.00 0.00 41.05 2.17
2593 2957 6.122277 ACTTTTCAATTTCTGTCTCTGACCA 58.878 36.000 0.00 0.00 0.00 4.02
2631 2995 4.380867 GGTTGTATGCCACTTTGGATTGAG 60.381 45.833 0.00 0.00 40.96 3.02
2643 3007 9.793252 CCACTTTGGATTGAGATAATACAAAAG 57.207 33.333 10.28 6.86 40.96 2.27
2663 3027 1.069227 GGCAAAGTTGTTCGCTTCGAT 60.069 47.619 0.00 0.00 35.23 3.59
2703 3067 4.584874 TGTTGAGGACTTTTGTGTTGAGA 58.415 39.130 0.00 0.00 0.00 3.27
2704 3068 5.007034 TGTTGAGGACTTTTGTGTTGAGAA 58.993 37.500 0.00 0.00 0.00 2.87
2705 3069 5.475220 TGTTGAGGACTTTTGTGTTGAGAAA 59.525 36.000 0.00 0.00 0.00 2.52
2706 3070 6.015856 TGTTGAGGACTTTTGTGTTGAGAAAA 60.016 34.615 0.00 0.00 0.00 2.29
2707 3071 6.773976 TGAGGACTTTTGTGTTGAGAAAAT 57.226 33.333 0.00 0.00 0.00 1.82
2708 3072 7.873719 TGAGGACTTTTGTGTTGAGAAAATA 57.126 32.000 0.00 0.00 0.00 1.40
2709 3073 7.930217 TGAGGACTTTTGTGTTGAGAAAATAG 58.070 34.615 0.00 0.00 0.00 1.73
2710 3074 7.773224 TGAGGACTTTTGTGTTGAGAAAATAGA 59.227 33.333 0.00 0.00 0.00 1.98
2711 3075 8.159344 AGGACTTTTGTGTTGAGAAAATAGAG 57.841 34.615 0.00 0.00 0.00 2.43
2781 3147 7.851387 TTATGGCATGAAAGTATTAACGACA 57.149 32.000 10.98 0.00 0.00 4.35
2786 3152 7.011016 TGGCATGAAAGTATTAACGACATACTG 59.989 37.037 0.00 0.00 37.49 2.74
2805 3171 5.582439 ACTGATTGCGATCTAAATAAGCG 57.418 39.130 15.08 0.00 33.28 4.68
2807 3173 4.058124 TGATTGCGATCTAAATAAGCGCT 58.942 39.130 15.08 2.64 46.95 5.92
2857 3238 5.604565 TGCACATAGAATGACATACTGGAG 58.395 41.667 0.00 0.00 0.00 3.86
2871 3252 1.271054 ACTGGAGCGGGATAATCATGC 60.271 52.381 0.00 0.00 0.00 4.06
2880 3261 4.740934 GCGGGATAATCATGCTATACCCTC 60.741 50.000 9.28 2.26 34.55 4.30
2881 3262 4.651503 CGGGATAATCATGCTATACCCTCT 59.348 45.833 9.28 0.00 34.55 3.69
2906 3287 3.490759 CAGTTGGCCGTAGCAGCG 61.491 66.667 0.00 0.00 42.56 5.18
2932 3313 1.079543 CGACAGCCTCCTTCTGGTG 60.080 63.158 0.00 0.00 35.94 4.17
2938 3319 2.125350 CTCCTTCTGGTGAGCGGC 60.125 66.667 0.00 0.00 34.23 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 157 2.599578 CAAAGCAGGCAGGGCACT 60.600 61.111 0.00 0.00 0.00 4.40
166 168 0.388006 TCGTCGATCTTCGCAAAGCA 60.388 50.000 0.00 0.00 40.21 3.91
175 177 4.554363 CGCCGCCTCGTCGATCTT 62.554 66.667 0.00 0.00 0.00 2.40
227 229 3.394606 TGGCCTCTCCTGTTCTACTTTTT 59.605 43.478 3.32 0.00 35.26 1.94
301 303 5.396772 CCACTAGTTGAAGCATATTCCTCCA 60.397 44.000 0.00 0.00 0.00 3.86
318 320 1.923909 GGCACCCTTCCCCACTAGT 60.924 63.158 0.00 0.00 0.00 2.57
423 425 3.881688 CTGTCATGAGCCCCAAAGATAAG 59.118 47.826 0.00 0.00 0.00 1.73
424 426 3.266772 ACTGTCATGAGCCCCAAAGATAA 59.733 43.478 0.00 0.00 0.00 1.75
427 429 1.003580 GACTGTCATGAGCCCCAAAGA 59.996 52.381 2.24 0.00 0.00 2.52
430 432 1.685224 GGACTGTCATGAGCCCCAA 59.315 57.895 10.38 0.00 0.00 4.12
463 480 2.748605 GGTCACGGCAGATCTCTATTG 58.251 52.381 0.00 0.00 0.00 1.90
481 498 2.354259 CTTGACTAGTCTACGGTCGGT 58.646 52.381 23.01 0.00 33.21 4.69
503 520 4.931661 TCTATTCCCACGACAAGGATAC 57.068 45.455 0.00 0.00 30.55 2.24
508 525 4.486090 CGGATATCTATTCCCACGACAAG 58.514 47.826 2.05 0.00 0.00 3.16
509 526 3.305813 GCGGATATCTATTCCCACGACAA 60.306 47.826 2.05 0.00 0.00 3.18
510 527 2.230508 GCGGATATCTATTCCCACGACA 59.769 50.000 2.05 0.00 0.00 4.35
619 653 3.319405 CAGAGCCGGACATCTAACACTAT 59.681 47.826 5.05 0.00 0.00 2.12
623 657 0.175760 GCAGAGCCGGACATCTAACA 59.824 55.000 5.05 0.00 0.00 2.41
627 661 0.975040 AGAAGCAGAGCCGGACATCT 60.975 55.000 5.05 1.15 0.00 2.90
640 674 1.443194 GTCCGCGAACGTAGAAGCA 60.443 57.895 8.23 0.00 37.70 3.91
643 677 2.176546 CGGTCCGCGAACGTAGAA 59.823 61.111 8.23 0.00 38.03 2.10
659 693 4.873129 CATCAGCCGACGGGACCG 62.873 72.222 17.22 9.56 46.03 4.79
682 716 1.505538 TCACCCCCAAAATTTCCTCCA 59.494 47.619 0.00 0.00 0.00 3.86
701 735 3.135530 AGATAAGGGCATCTCCAACACTC 59.864 47.826 0.00 0.00 36.21 3.51
826 1058 2.035155 GGAACCAACGGGGAAGGG 59.965 66.667 2.06 0.00 41.15 3.95
889 1125 2.160219 GCTTGTGAGTGCGAATGAATCA 59.840 45.455 0.00 0.00 0.00 2.57
954 1196 2.729882 GCTCGAACTTCGCACTAGAAAA 59.270 45.455 6.29 0.00 40.21 2.29
1365 1653 2.283604 TGTGCGCCTGGACCTCTA 60.284 61.111 4.18 0.00 35.21 2.43
1461 1749 4.059773 ACCATTAGGGGCATTTCTTTCA 57.940 40.909 0.00 0.00 42.91 2.69
1494 1811 4.257731 TGCAACAAAATAGCGTCAGGATA 58.742 39.130 0.00 0.00 0.00 2.59
1496 1813 2.499197 TGCAACAAAATAGCGTCAGGA 58.501 42.857 0.00 0.00 0.00 3.86
1837 2164 1.743252 GTAGGACGAGGACGACGGT 60.743 63.158 0.00 0.00 42.66 4.83
1883 2213 1.552578 TCGAGAAATTCCCCGACAGA 58.447 50.000 4.41 0.00 0.00 3.41
1906 2236 0.970937 CCCACTCCCAGTCGAAGCTA 60.971 60.000 0.00 0.00 0.00 3.32
1977 2307 1.654317 CAAGCTGAGGCAGACATCTC 58.346 55.000 0.00 0.00 41.70 2.75
2011 2349 3.133003 ACTCCGGATCTGTCCACTAAATG 59.867 47.826 3.57 0.00 45.37 2.32
2053 2391 2.018727 TAGGCACACGGTGACACGTT 62.019 55.000 16.29 0.00 45.35 3.99
2056 2394 1.997606 GTTATAGGCACACGGTGACAC 59.002 52.381 16.29 0.00 45.35 3.67
2058 2396 1.066716 TGGTTATAGGCACACGGTGAC 60.067 52.381 16.29 6.26 42.83 3.67
2068 2406 1.806542 CGACATGGCATGGTTATAGGC 59.193 52.381 29.49 3.39 33.60 3.93
2092 2430 0.970937 TGCTCCCGACTAGTTCCCTG 60.971 60.000 0.00 0.00 0.00 4.45
2097 2435 2.628657 GGTATCATGCTCCCGACTAGTT 59.371 50.000 0.00 0.00 0.00 2.24
2098 2436 2.158445 AGGTATCATGCTCCCGACTAGT 60.158 50.000 0.00 0.00 0.00 2.57
2101 2439 2.677542 TAGGTATCATGCTCCCGACT 57.322 50.000 0.00 0.00 0.00 4.18
2118 2456 0.974383 ACCCCACCGACTTGTCTTAG 59.026 55.000 0.00 0.00 0.00 2.18
2126 2464 0.396811 CTCAAAAGACCCCACCGACT 59.603 55.000 0.00 0.00 0.00 4.18
2134 2472 3.653344 GTTTTGGATGCTCAAAAGACCC 58.347 45.455 11.41 0.00 44.22 4.46
2146 2484 4.345288 CAGCATATGTGACGTTTTGGATG 58.655 43.478 4.29 0.00 0.00 3.51
2170 2508 4.477975 CGTCTCGTGCCGTCCCTC 62.478 72.222 0.00 0.00 0.00 4.30
2174 2512 1.138047 CATAACCGTCTCGTGCCGTC 61.138 60.000 0.00 0.00 0.00 4.79
2193 2538 2.508751 GGGTCGACCTGGATAGCCC 61.509 68.421 32.52 10.42 35.85 5.19
2216 2561 1.069358 CGAATCTCAAGGCCCTAGGAC 59.931 57.143 11.48 0.00 0.00 3.85
2237 2582 5.980116 CCTCGTTCTCCATGTTCACTTATAG 59.020 44.000 0.00 0.00 0.00 1.31
2241 2586 2.632996 TCCTCGTTCTCCATGTTCACTT 59.367 45.455 0.00 0.00 0.00 3.16
2243 2588 2.743636 TCCTCGTTCTCCATGTTCAC 57.256 50.000 0.00 0.00 0.00 3.18
2244 2589 2.632996 ACTTCCTCGTTCTCCATGTTCA 59.367 45.455 0.00 0.00 0.00 3.18
2245 2590 3.320673 ACTTCCTCGTTCTCCATGTTC 57.679 47.619 0.00 0.00 0.00 3.18
2378 2733 8.088365 CGGAAAGTCCATCTGTCACATATATAA 58.912 37.037 0.00 0.00 35.91 0.98
2382 2737 4.162320 ACGGAAAGTCCATCTGTCACATAT 59.838 41.667 0.00 0.00 35.91 1.78
2387 2742 2.894765 TGTACGGAAAGTCCATCTGTCA 59.105 45.455 0.00 0.00 37.56 3.58
2390 2745 4.566004 TCTTTGTACGGAAAGTCCATCTG 58.434 43.478 5.79 0.00 35.91 2.90
2402 2757 7.008901 GGTTTTTGAGTCTTTTTCTTTGTACGG 59.991 37.037 0.00 0.00 0.00 4.02
2407 2762 7.889589 ACAGGTTTTTGAGTCTTTTTCTTTG 57.110 32.000 0.00 0.00 0.00 2.77
2408 2763 8.147704 TGAACAGGTTTTTGAGTCTTTTTCTTT 58.852 29.630 0.00 0.00 0.00 2.52
2428 2783 5.007724 GTCTAGGTTTTGACCTGTTGAACAG 59.992 44.000 18.04 18.04 45.53 3.16
2438 2793 4.219288 TCCGAGTTAGTCTAGGTTTTGACC 59.781 45.833 0.00 0.00 39.47 4.02
2471 2826 4.414852 CCAACATGTCCTATTTCTTTGCG 58.585 43.478 0.00 0.00 0.00 4.85
2472 2827 4.462483 TCCCAACATGTCCTATTTCTTTGC 59.538 41.667 0.00 0.00 0.00 3.68
2475 2830 6.078456 TCATCCCAACATGTCCTATTTCTT 57.922 37.500 0.00 0.00 0.00 2.52
2477 2832 6.773976 TTTCATCCCAACATGTCCTATTTC 57.226 37.500 0.00 0.00 0.00 2.17
2482 2837 5.456921 ACTATTTCATCCCAACATGTCCT 57.543 39.130 0.00 0.00 0.00 3.85
2495 2859 8.734386 GTGGATTCTCTGTTTCAACTATTTCAT 58.266 33.333 0.00 0.00 0.00 2.57
2526 2890 1.447314 GTCCGACCCAATGTCCGAC 60.447 63.158 0.00 0.00 42.30 4.79
2527 2891 1.261938 ATGTCCGACCCAATGTCCGA 61.262 55.000 0.00 0.00 41.18 4.55
2528 2892 0.392461 AATGTCCGACCCAATGTCCG 60.392 55.000 0.00 0.00 41.18 4.79
2529 2893 1.834188 AAATGTCCGACCCAATGTCC 58.166 50.000 0.00 0.00 41.18 4.02
2530 2894 4.007659 ACTTAAATGTCCGACCCAATGTC 58.992 43.478 0.00 0.00 40.81 3.06
2531 2895 4.007659 GACTTAAATGTCCGACCCAATGT 58.992 43.478 0.00 0.00 0.00 2.71
2532 2896 3.063452 CGACTTAAATGTCCGACCCAATG 59.937 47.826 0.00 0.00 33.70 2.82
2533 2897 3.267483 CGACTTAAATGTCCGACCCAAT 58.733 45.455 0.00 0.00 33.70 3.16
2534 2898 2.613474 CCGACTTAAATGTCCGACCCAA 60.613 50.000 0.00 0.00 33.70 4.12
2535 2899 1.066716 CCGACTTAAATGTCCGACCCA 60.067 52.381 0.00 0.00 33.70 4.51
2536 2900 1.205417 TCCGACTTAAATGTCCGACCC 59.795 52.381 0.00 0.00 33.70 4.46
2537 2901 2.660189 TCCGACTTAAATGTCCGACC 57.340 50.000 0.00 0.00 33.70 4.79
2574 2938 4.005650 GCATGGTCAGAGACAGAAATTGA 58.994 43.478 0.00 0.00 33.68 2.57
2577 2941 3.708403 TGCATGGTCAGAGACAGAAAT 57.292 42.857 0.00 0.00 33.68 2.17
2579 2943 2.417787 CGATGCATGGTCAGAGACAGAA 60.418 50.000 2.46 0.00 33.68 3.02
2580 2944 1.135721 CGATGCATGGTCAGAGACAGA 59.864 52.381 2.46 0.00 33.68 3.41
2581 2945 1.568606 CGATGCATGGTCAGAGACAG 58.431 55.000 2.46 0.00 33.68 3.51
2593 2957 2.238521 ACAACCTCAAAACCGATGCAT 58.761 42.857 0.00 0.00 0.00 3.96
2631 2995 7.410407 GCGAACAACTTTGCCTTTTGTATTATC 60.410 37.037 0.00 0.00 33.10 1.75
2643 3007 0.306533 TCGAAGCGAACAACTTTGCC 59.693 50.000 0.00 0.00 37.49 4.52
2682 3046 5.560966 TTCTCAACACAAAAGTCCTCAAC 57.439 39.130 0.00 0.00 0.00 3.18
2743 3108 9.814899 TTTCATGCCATAATCACGATTATTTTT 57.185 25.926 9.14 0.00 40.84 1.94
2744 3109 9.467258 CTTTCATGCCATAATCACGATTATTTT 57.533 29.630 9.14 0.00 40.84 1.82
2752 3117 7.530525 CGTTAATACTTTCATGCCATAATCACG 59.469 37.037 0.00 0.00 0.00 4.35
2753 3118 8.556194 TCGTTAATACTTTCATGCCATAATCAC 58.444 33.333 0.00 0.00 0.00 3.06
2756 3121 8.445275 TGTCGTTAATACTTTCATGCCATAAT 57.555 30.769 0.00 0.00 0.00 1.28
2757 3122 7.851387 TGTCGTTAATACTTTCATGCCATAA 57.149 32.000 0.00 0.00 0.00 1.90
2768 3134 6.976349 TCGCAATCAGTATGTCGTTAATACTT 59.024 34.615 5.17 0.00 38.50 2.24
2781 3147 6.183360 GCGCTTATTTAGATCGCAATCAGTAT 60.183 38.462 0.00 0.00 44.50 2.12
2805 3171 8.967552 ATGTTTCTACTATATGCGTAGTAAGC 57.032 34.615 0.60 0.60 36.88 3.09
2827 3193 8.591940 AGTATGTCATTCTATGTGCATAGATGT 58.408 33.333 18.99 10.67 46.38 3.06
2834 3200 5.604565 CTCCAGTATGTCATTCTATGTGCA 58.395 41.667 0.00 0.00 0.00 4.57
2843 3209 1.496060 TCCCGCTCCAGTATGTCATT 58.504 50.000 0.00 0.00 0.00 2.57
2844 3210 1.722034 ATCCCGCTCCAGTATGTCAT 58.278 50.000 0.00 0.00 0.00 3.06
2845 3211 2.375014 TATCCCGCTCCAGTATGTCA 57.625 50.000 0.00 0.00 0.00 3.58
2847 3213 3.239449 TGATTATCCCGCTCCAGTATGT 58.761 45.455 0.00 0.00 0.00 2.29
2849 3215 3.369892 GCATGATTATCCCGCTCCAGTAT 60.370 47.826 0.00 0.00 0.00 2.12
2853 3234 1.059098 AGCATGATTATCCCGCTCCA 58.941 50.000 0.00 0.00 0.00 3.86
2857 3238 3.134804 AGGGTATAGCATGATTATCCCGC 59.865 47.826 4.02 0.00 38.72 6.13
2871 3252 3.577919 ACTGGCCAACTAGAGGGTATAG 58.422 50.000 7.01 0.00 0.00 1.31
2916 3297 1.835927 GCTCACCAGAAGGAGGCTGT 61.836 60.000 0.00 0.00 38.69 4.40
2918 3299 2.654079 CGCTCACCAGAAGGAGGCT 61.654 63.158 0.00 0.00 38.69 4.58


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

AutoCloner maintained by Alex Coulton.