Multiple sequence alignment - TraesCS6D01G054800

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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 TraesCS6D01G054800 chr6D 100.000 3159 0 0 1 3159 25881103 25877945 0.000000e+00 5834.0
1 TraesCS6D01G054800 chr6D 83.716 1437 183 26 783 2179 25827834 25826409 0.000000e+00 1310.0
2 TraesCS6D01G054800 chr6D 84.774 1307 145 31 887 2157 25852755 25851467 0.000000e+00 1262.0
3 TraesCS6D01G054800 chr6D 89.043 575 63 0 1588 2162 25915640 25916214 0.000000e+00 713.0
4 TraesCS6D01G054800 chr6D 81.950 482 67 12 779 1249 25805311 25804839 1.060000e-104 390.0
5 TraesCS6D01G054800 chr6A 89.778 2387 130 46 1 2317 24032435 24030093 0.000000e+00 2952.0
6 TraesCS6D01G054800 chr6A 83.253 1451 189 27 783 2188 23952611 23951170 0.000000e+00 1284.0
7 TraesCS6D01G054800 chr6A 88.046 870 87 12 1305 2162 24048988 24049852 0.000000e+00 1014.0
8 TraesCS6D01G054800 chr6A 87.456 845 86 10 2321 3159 24007406 24006576 0.000000e+00 955.0
9 TraesCS6D01G054800 chr6A 85.391 883 105 14 1277 2157 23962875 23962015 0.000000e+00 894.0
10 TraesCS6D01G054800 chr6A 85.192 520 60 10 770 1276 24048382 24048897 4.670000e-143 518.0
11 TraesCS6D01G054800 chr6A 92.308 52 4 0 23 74 490841508 490841457 1.220000e-09 75.0
12 TraesCS6D01G054800 chr6B 94.512 911 43 7 1283 2188 42318467 42317559 0.000000e+00 1399.0
13 TraesCS6D01G054800 chr6B 84.314 1428 189 21 783 2179 42212215 42210792 0.000000e+00 1363.0
14 TraesCS6D01G054800 chr6B 83.671 1433 173 35 766 2160 42392804 42394213 0.000000e+00 1293.0
15 TraesCS6D01G054800 chr6B 83.183 886 108 27 1277 2157 42231339 42230490 0.000000e+00 773.0
16 TraesCS6D01G054800 chr6B 89.796 392 20 6 876 1262 42318986 42318610 4.740000e-133 484.0
17 TraesCS6D01G054800 chr6B 81.729 509 65 16 779 1266 42005966 42005465 1.770000e-107 399.0
18 TraesCS6D01G054800 chr6B 87.821 312 14 2 467 754 42319349 42319038 8.390000e-91 344.0
19 TraesCS6D01G054800 chr6B 89.630 135 10 1 2193 2323 42317516 42317382 5.420000e-38 169.0
20 TraesCS6D01G054800 chr6B 98.039 51 1 0 2268 2318 458503475 458503525 4.340000e-14 89.8
21 TraesCS6D01G054800 chr6B 94.643 56 1 2 2264 2318 13827513 13827567 5.610000e-13 86.1
22 TraesCS6D01G054800 chr5B 96.364 55 1 1 2262 2316 269975142 269975195 4.340000e-14 89.8
23 TraesCS6D01G054800 chr5B 91.667 60 4 1 2261 2320 62980487 62980429 7.260000e-12 82.4
24 TraesCS6D01G054800 chr3B 98.039 51 1 0 2270 2320 65214147 65214097 4.340000e-14 89.8
25 TraesCS6D01G054800 chr1B 92.982 57 3 1 2261 2317 548535443 548535498 7.260000e-12 82.4
26 TraesCS6D01G054800 chr7B 91.228 57 5 0 18 74 72281634 72281690 9.390000e-11 78.7
27 TraesCS6D01G054800 chr4B 97.778 45 1 0 2274 2318 269170795 269170751 9.390000e-11 78.7
28 TraesCS6D01G054800 chr2B 87.500 64 7 1 11 74 762361080 762361018 4.370000e-09 73.1
29 TraesCS6D01G054800 chr5D 90.385 52 5 0 15 66 14756355 14756304 5.650000e-08 69.4
30 TraesCS6D01G054800 chr7D 84.483 58 7 1 18 73 617833882 617833939 4.400000e-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 TraesCS6D01G054800 chr6D 25877945 25881103 3158 True 5834 5834 100.00000 1 3159 1 chr6D.!!$R4 3158
1 TraesCS6D01G054800 chr6D 25826409 25827834 1425 True 1310 1310 83.71600 783 2179 1 chr6D.!!$R2 1396
2 TraesCS6D01G054800 chr6D 25851467 25852755 1288 True 1262 1262 84.77400 887 2157 1 chr6D.!!$R3 1270
3 TraesCS6D01G054800 chr6D 25915640 25916214 574 False 713 713 89.04300 1588 2162 1 chr6D.!!$F1 574
4 TraesCS6D01G054800 chr6A 24030093 24032435 2342 True 2952 2952 89.77800 1 2317 1 chr6A.!!$R4 2316
5 TraesCS6D01G054800 chr6A 23951170 23952611 1441 True 1284 1284 83.25300 783 2188 1 chr6A.!!$R1 1405
6 TraesCS6D01G054800 chr6A 24006576 24007406 830 True 955 955 87.45600 2321 3159 1 chr6A.!!$R3 838
7 TraesCS6D01G054800 chr6A 23962015 23962875 860 True 894 894 85.39100 1277 2157 1 chr6A.!!$R2 880
8 TraesCS6D01G054800 chr6A 24048382 24049852 1470 False 766 1014 86.61900 770 2162 2 chr6A.!!$F1 1392
9 TraesCS6D01G054800 chr6B 42210792 42212215 1423 True 1363 1363 84.31400 783 2179 1 chr6B.!!$R2 1396
10 TraesCS6D01G054800 chr6B 42392804 42394213 1409 False 1293 1293 83.67100 766 2160 1 chr6B.!!$F2 1394
11 TraesCS6D01G054800 chr6B 42230490 42231339 849 True 773 773 83.18300 1277 2157 1 chr6B.!!$R3 880
12 TraesCS6D01G054800 chr6B 42317382 42319349 1967 True 599 1399 90.43975 467 2323 4 chr6B.!!$R4 1856
13 TraesCS6D01G054800 chr6B 42005465 42005966 501 True 399 399 81.72900 779 1266 1 chr6B.!!$R1 487

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
155 162 0.118952 ACCCAGGGCCAAAAATCCAT 59.881 50.0 4.91 0.0 0.0 3.41 F
932 987 0.387239 GCCACAGTTAAGCAAAGCCG 60.387 55.0 0.00 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2390 0.325860 TACGCCTAATCTGGGTGGGT 60.326 55.0 0.00 0.0 38.54 4.51 R
2740 3062 0.036388 ATTCGTTGGAGCCACATCGT 60.036 50.0 8.09 0.0 35.63 3.73 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
35 36 6.896860 TGAAATCTTGGGATATCAAACATGGT 59.103 34.615 4.83 0.00 0.00 3.55
45 46 2.607499 TCAAACATGGTTGCCCAATCT 58.393 42.857 19.00 0.00 46.04 2.40
50 51 3.778265 ACATGGTTGCCCAATCTACTTT 58.222 40.909 0.00 0.00 46.04 2.66
51 52 4.159557 ACATGGTTGCCCAATCTACTTTT 58.840 39.130 0.00 0.00 46.04 2.27
52 53 4.021192 ACATGGTTGCCCAATCTACTTTTG 60.021 41.667 0.00 0.00 46.04 2.44
55 56 3.320826 GGTTGCCCAATCTACTTTTGTGT 59.679 43.478 0.00 0.00 0.00 3.72
64 65 7.114811 CCCAATCTACTTTTGTGTGAAATTTCG 59.885 37.037 13.34 0.00 0.00 3.46
154 161 0.835543 CACCCAGGGCCAAAAATCCA 60.836 55.000 4.91 0.00 0.00 3.41
155 162 0.118952 ACCCAGGGCCAAAAATCCAT 59.881 50.000 4.91 0.00 0.00 3.41
172 179 4.090761 TCCATGTCCCTTTGATATGCTC 57.909 45.455 0.00 0.00 40.28 4.26
173 180 3.459227 TCCATGTCCCTTTGATATGCTCA 59.541 43.478 0.00 0.00 40.28 4.26
188 195 0.654683 GCTCAATACTCCTGCTTGCG 59.345 55.000 0.00 0.00 0.00 4.85
217 224 8.653338 CAAAGCAATCCTTATGTTTCTGAATTG 58.347 33.333 0.00 0.00 32.20 2.32
239 246 9.545105 AATTGAAAAGAAAATGCATGACTGTTA 57.455 25.926 0.00 0.00 0.00 2.41
306 314 3.615224 AAAAATACCAAGGCAGGCATG 57.385 42.857 0.00 0.00 0.00 4.06
307 315 1.488390 AAATACCAAGGCAGGCATGG 58.512 50.000 16.37 16.37 40.16 3.66
309 317 0.396139 ATACCAAGGCAGGCATGGTG 60.396 55.000 29.08 7.01 46.56 4.17
310 318 1.496444 TACCAAGGCAGGCATGGTGA 61.496 55.000 29.08 13.43 46.56 4.02
311 319 2.345760 CCAAGGCAGGCATGGTGAC 61.346 63.158 10.08 0.00 0.00 3.67
337 345 7.368480 AGCTTGGTTTGCAATTTCATTTATC 57.632 32.000 0.00 0.00 0.00 1.75
344 352 7.390162 GGTTTGCAATTTCATTTATCCAAAGGA 59.610 33.333 0.00 0.00 32.89 3.36
352 360 6.057321 TCATTTATCCAAAGGACGGTAAGT 57.943 37.500 0.00 0.00 32.98 2.24
436 445 5.520649 GGAGCTAGAAAATGAGACCTTAACG 59.479 44.000 0.00 0.00 0.00 3.18
437 446 4.870991 AGCTAGAAAATGAGACCTTAACGC 59.129 41.667 0.00 0.00 0.00 4.84
438 447 4.034163 GCTAGAAAATGAGACCTTAACGCC 59.966 45.833 0.00 0.00 0.00 5.68
440 449 4.589908 AGAAAATGAGACCTTAACGCCAT 58.410 39.130 0.00 0.00 0.00 4.40
441 450 4.396166 AGAAAATGAGACCTTAACGCCATG 59.604 41.667 0.00 0.00 0.00 3.66
442 451 2.332063 ATGAGACCTTAACGCCATGG 57.668 50.000 7.63 7.63 0.00 3.66
443 452 0.392461 TGAGACCTTAACGCCATGGC 60.392 55.000 27.67 27.67 37.85 4.40
461 472 1.173913 GCCCATGGGTTTACTCACAC 58.826 55.000 31.58 7.31 37.65 3.82
462 473 1.546773 GCCCATGGGTTTACTCACACA 60.547 52.381 31.58 0.00 37.65 3.72
463 474 2.870175 CCCATGGGTTTACTCACACAA 58.130 47.619 23.93 0.00 32.47 3.33
464 475 2.556622 CCCATGGGTTTACTCACACAAC 59.443 50.000 23.93 0.00 32.47 3.32
481 493 1.927174 CAACGGCTTACATCCTTCTCG 59.073 52.381 0.00 0.00 0.00 4.04
637 673 7.828508 TTTCAATTAGCTGGCTGAATATGAT 57.171 32.000 5.25 0.00 0.00 2.45
727 765 6.298361 TGAACAAAGATGGATCAGTTTCTGA 58.702 36.000 1.92 1.92 44.99 3.27
737 775 4.710375 GGATCAGTTTCTGACACCTACCTA 59.290 45.833 1.44 0.00 43.63 3.08
738 776 5.187186 GGATCAGTTTCTGACACCTACCTAA 59.813 44.000 1.44 0.00 43.63 2.69
739 777 5.464030 TCAGTTTCTGACACCTACCTAAC 57.536 43.478 0.00 0.00 35.39 2.34
740 778 4.022589 TCAGTTTCTGACACCTACCTAACG 60.023 45.833 0.00 0.00 35.39 3.18
741 779 4.022589 CAGTTTCTGACACCTACCTAACGA 60.023 45.833 0.00 0.00 32.44 3.85
742 780 4.771054 AGTTTCTGACACCTACCTAACGAT 59.229 41.667 0.00 0.00 0.00 3.73
743 781 4.713824 TTCTGACACCTACCTAACGATG 57.286 45.455 0.00 0.00 0.00 3.84
744 782 2.426024 TCTGACACCTACCTAACGATGC 59.574 50.000 0.00 0.00 0.00 3.91
745 783 1.133598 TGACACCTACCTAACGATGCG 59.866 52.381 0.00 0.00 0.00 4.73
746 784 1.133790 GACACCTACCTAACGATGCGT 59.866 52.381 0.00 0.00 43.97 5.24
747 785 1.133790 ACACCTACCTAACGATGCGTC 59.866 52.381 0.00 0.00 39.99 5.19
756 794 4.003534 CGATGCGTCGCTCTTGAT 57.996 55.556 16.48 2.34 41.49 2.57
757 795 1.556958 CGATGCGTCGCTCTTGATG 59.443 57.895 16.48 0.00 41.49 3.07
764 802 4.845177 CGCTCTTGATGCGCAAAA 57.155 50.000 17.11 11.73 46.72 2.44
765 803 3.090598 CGCTCTTGATGCGCAAAAA 57.909 47.368 17.11 11.32 46.72 1.94
812 850 2.802816 CAGAGAAAGAAACCACGTGGAG 59.197 50.000 40.21 16.12 38.94 3.86
837 881 4.798882 TGTCATACTTTTCCACAACCCTT 58.201 39.130 0.00 0.00 0.00 3.95
932 987 0.387239 GCCACAGTTAAGCAAAGCCG 60.387 55.000 0.00 0.00 0.00 5.52
993 1054 3.004106 AGCCTACGTACGTATCCACATTC 59.996 47.826 26.98 10.69 0.00 2.67
1098 1161 1.226575 CTCGCCGTCATTCTACGCA 60.227 57.895 0.00 0.00 41.51 5.24
1110 1173 1.375908 CTACGCAAAGAGCTGCCCA 60.376 57.895 0.00 0.00 42.61 5.36
1296 1514 1.733912 GGTCGGGATTAACGGTGAAAC 59.266 52.381 0.00 0.00 0.00 2.78
1301 1519 3.571571 GGGATTAACGGTGAAACTTTGC 58.428 45.455 0.00 0.00 36.74 3.68
1303 1521 4.473199 GGATTAACGGTGAAACTTTGCTC 58.527 43.478 0.00 0.00 36.74 4.26
1955 2229 1.203994 ACAACGCCTACTATCGCAACT 59.796 47.619 0.00 0.00 0.00 3.16
2173 2447 2.879026 CAGCTGATCCAACATCCATCTG 59.121 50.000 8.42 0.00 0.00 2.90
2175 2449 2.228059 CTGATCCAACATCCATCTGCC 58.772 52.381 0.00 0.00 0.00 4.85
2179 2453 1.288633 TCCAACATCCATCTGCCCATT 59.711 47.619 0.00 0.00 0.00 3.16
2327 2648 6.183360 GCGTTTAGATCACTACAGAGGTTTTC 60.183 42.308 0.00 0.00 0.00 2.29
2332 2653 3.128349 TCACTACAGAGGTTTTCGTTGC 58.872 45.455 0.00 0.00 0.00 4.17
2337 2658 0.663153 AGAGGTTTTCGTTGCAGTGC 59.337 50.000 8.58 8.58 0.00 4.40
2363 2684 3.147595 TCGCTGACATCCCTCCCG 61.148 66.667 0.00 0.00 0.00 5.14
2369 2691 1.198094 TGACATCCCTCCCGCTTGAA 61.198 55.000 0.00 0.00 0.00 2.69
2402 2724 1.342275 CCCAAGCCAATGATGAAGGGA 60.342 52.381 0.00 0.00 37.22 4.20
2404 2726 2.167075 CCAAGCCAATGATGAAGGGAAC 59.833 50.000 0.00 0.00 0.00 3.62
2421 2743 0.107654 AACCGCTCCTTGATAGCCAC 60.108 55.000 0.00 0.00 36.60 5.01
2459 2781 2.288273 GCGTCTAGTATGGCAGGGTTAG 60.288 54.545 0.00 0.00 0.00 2.34
2484 2806 0.478072 TGAACCAGGACATGCACCTT 59.522 50.000 9.01 0.00 35.35 3.50
2486 2808 0.251341 AACCAGGACATGCACCTTCC 60.251 55.000 9.01 0.00 35.35 3.46
2503 2825 2.380410 CCGACTTGTAGGTGCACGC 61.380 63.158 11.45 3.85 0.00 5.34
2509 2831 4.109675 GTAGGTGCACGCCCCCAT 62.110 66.667 11.45 0.00 0.00 4.00
2530 2852 7.358066 CCCATCGACATCAAGAATTTCAATAG 58.642 38.462 0.00 0.00 0.00 1.73
2556 2878 5.248640 AGAAGTGGGTCATCAGTAACAATG 58.751 41.667 0.00 0.00 0.00 2.82
2557 2879 3.955471 AGTGGGTCATCAGTAACAATGG 58.045 45.455 0.00 0.00 0.00 3.16
2569 2891 5.468746 TCAGTAACAATGGGAAGTTCTTTCG 59.531 40.000 2.25 0.00 36.62 3.46
2580 2902 4.575236 GGAAGTTCTTTCGAAACAGGAGTT 59.425 41.667 6.47 2.05 36.72 3.01
2594 2916 1.283321 AGGAGTTCCTGGGATGAAAGC 59.717 52.381 0.00 0.00 46.55 3.51
2597 2919 1.005215 AGTTCCTGGGATGAAAGCCTG 59.995 52.381 0.00 0.00 46.10 4.85
2599 2921 0.620556 TCCTGGGATGAAAGCCTGAC 59.379 55.000 0.00 0.00 46.10 3.51
2603 2925 1.073125 TGGGATGAAAGCCTGACGAAA 59.927 47.619 0.00 0.00 46.10 3.46
2685 3007 3.869272 CACGGCGGCAGCTTGATC 61.869 66.667 13.24 0.00 44.37 2.92
2689 3011 2.815211 GCGGCAGCTTGATCGACA 60.815 61.111 0.00 0.00 41.01 4.35
2690 3012 3.084579 CGGCAGCTTGATCGACAC 58.915 61.111 0.00 0.00 0.00 3.67
2691 3013 1.446792 CGGCAGCTTGATCGACACT 60.447 57.895 0.00 0.00 0.00 3.55
2696 3018 0.108424 AGCTTGATCGACACTGAGCC 60.108 55.000 0.00 0.00 0.00 4.70
2699 3021 0.388520 TTGATCGACACTGAGCCGTG 60.389 55.000 0.00 0.00 40.67 4.94
2723 3045 1.043673 GGAGGCCTGGTCGACTACAT 61.044 60.000 12.00 0.00 0.00 2.29
2733 3055 2.361119 GGTCGACTACATGGAGCATACA 59.639 50.000 16.46 0.00 34.00 2.29
2740 3062 1.762370 ACATGGAGCATACATCACGGA 59.238 47.619 0.00 0.00 0.00 4.69
2762 3084 0.744414 ATGTGGCTCCAACGAATCCG 60.744 55.000 0.00 0.00 42.50 4.18
2764 3086 2.287274 TGGCTCCAACGAATCCGGA 61.287 57.895 6.61 6.61 40.78 5.14
2773 3095 3.279875 GAATCCGGATGGCGGTGC 61.280 66.667 19.95 0.00 34.14 5.01
2786 3108 3.749064 GGTGCCAGACGCTCTCGA 61.749 66.667 0.00 0.00 39.41 4.04
2811 3134 1.067582 CGGTTGCTCTATCCCCGAC 59.932 63.158 0.00 0.00 41.08 4.79
2816 3139 0.818445 TGCTCTATCCCCGACGTCTC 60.818 60.000 14.70 0.00 0.00 3.36
2817 3140 0.818445 GCTCTATCCCCGACGTCTCA 60.818 60.000 14.70 0.00 0.00 3.27
2819 3142 1.334243 CTCTATCCCCGACGTCTCAAC 59.666 57.143 14.70 0.00 0.00 3.18
2842 3165 1.472990 TTGTATGCGTAGACGATGCG 58.527 50.000 6.19 0.00 43.67 4.73
2857 3180 2.031683 CGATGCGGAGGTAAATTTCCAC 59.968 50.000 0.00 0.00 32.87 4.02
2874 3197 1.586422 CACGATGTGGATGGATGGAC 58.414 55.000 0.00 0.00 0.00 4.02
2885 3208 1.679139 TGGATGGACGATGCAAATCC 58.321 50.000 7.20 7.20 37.83 3.01
2952 3275 8.352201 TCATCAATCTTTCTGGTTAACACAAAG 58.648 33.333 8.10 11.36 36.69 2.77
2955 3278 9.179909 TCAATCTTTCTGGTTAACACAAAGTTA 57.820 29.630 8.10 0.00 41.64 2.24
2970 3293 7.748847 ACACAAAGTTAACAGATATAAAGGCG 58.251 34.615 8.61 0.00 0.00 5.52
2976 3299 3.093717 ACAGATATAAAGGCGTGACGG 57.906 47.619 7.25 0.00 0.00 4.79
2979 3302 4.116961 CAGATATAAAGGCGTGACGGAAA 58.883 43.478 7.25 0.00 0.00 3.13
3006 3329 6.717084 AGAACCAAGAAATCTTACTCCCTTTG 59.283 38.462 0.00 0.00 34.28 2.77
3008 3331 7.086685 ACCAAGAAATCTTACTCCCTTTGTA 57.913 36.000 0.00 0.00 34.28 2.41
3069 3392 5.648960 GGGTACATTTCCATCCTTTTCGTTA 59.351 40.000 0.00 0.00 0.00 3.18
3109 3432 2.211250 ATGGCATGTTGTCTGCTCTT 57.789 45.000 0.00 0.00 39.60 2.85
3120 3445 3.411446 TGTCTGCTCTTTTATGTGTGGG 58.589 45.455 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.566138 ACCATGTTTGATATCCCAAGATTTCAT 59.434 33.333 0.00 0.00 39.33 2.57
35 36 4.211125 TCACACAAAAGTAGATTGGGCAA 58.789 39.130 0.00 0.00 34.49 4.52
45 46 8.744008 TTTTCACGAAATTTCACACAAAAGTA 57.256 26.923 17.99 0.00 0.00 2.24
172 179 1.009829 GGTCGCAAGCAGGAGTATTG 58.990 55.000 0.00 0.00 37.18 1.90
173 180 0.613260 TGGTCGCAAGCAGGAGTATT 59.387 50.000 0.00 0.00 37.18 1.89
188 195 6.071952 TCAGAAACATAAGGATTGCTTTGGTC 60.072 38.462 0.00 0.00 0.00 4.02
304 312 1.069049 GCAAACCAAGCTTGTCACCAT 59.931 47.619 24.35 2.51 0.00 3.55
305 313 0.459489 GCAAACCAAGCTTGTCACCA 59.541 50.000 24.35 0.00 0.00 4.17
306 314 0.459489 TGCAAACCAAGCTTGTCACC 59.541 50.000 24.35 9.54 0.00 4.02
307 315 2.292103 TTGCAAACCAAGCTTGTCAC 57.708 45.000 24.35 9.93 0.00 3.67
308 316 3.540314 AATTGCAAACCAAGCTTGTCA 57.460 38.095 24.35 11.16 36.76 3.58
309 317 3.870419 TGAAATTGCAAACCAAGCTTGTC 59.130 39.130 24.35 11.76 36.76 3.18
310 318 3.871485 TGAAATTGCAAACCAAGCTTGT 58.129 36.364 24.35 10.37 36.76 3.16
311 319 5.427036 AATGAAATTGCAAACCAAGCTTG 57.573 34.783 19.93 19.93 36.76 4.01
312 320 7.094677 GGATAAATGAAATTGCAAACCAAGCTT 60.095 33.333 1.71 0.00 36.10 3.74
313 321 6.372381 GGATAAATGAAATTGCAAACCAAGCT 59.628 34.615 1.71 0.00 36.10 3.74
314 322 6.149142 TGGATAAATGAAATTGCAAACCAAGC 59.851 34.615 1.71 0.00 36.10 4.01
315 323 7.670009 TGGATAAATGAAATTGCAAACCAAG 57.330 32.000 1.71 0.00 36.10 3.61
316 324 8.455903 TTTGGATAAATGAAATTGCAAACCAA 57.544 26.923 1.71 0.00 36.10 3.67
317 325 7.174599 CCTTTGGATAAATGAAATTGCAAACCA 59.825 33.333 1.71 1.94 36.10 3.67
318 326 7.390162 TCCTTTGGATAAATGAAATTGCAAACC 59.610 33.333 1.71 0.00 36.10 3.27
319 327 8.229811 GTCCTTTGGATAAATGAAATTGCAAAC 58.770 33.333 1.71 0.00 32.31 2.93
337 345 2.946990 ACAAACACTTACCGTCCTTTGG 59.053 45.455 0.00 0.00 30.00 3.28
344 352 2.946990 CCTTTGGACAAACACTTACCGT 59.053 45.455 0.00 0.00 0.00 4.83
352 360 4.083565 GGTAATAGGCCTTTGGACAAACA 58.916 43.478 12.58 0.00 29.21 2.83
438 447 1.341877 TGAGTAAACCCATGGGCCATG 60.342 52.381 34.76 34.76 41.10 3.66
440 449 0.039035 GTGAGTAAACCCATGGGCCA 59.961 55.000 31.73 9.61 39.32 5.36
441 450 0.039035 TGTGAGTAAACCCATGGGCC 59.961 55.000 31.73 15.90 39.32 5.80
442 451 1.173913 GTGTGAGTAAACCCATGGGC 58.826 55.000 31.73 14.55 39.32 5.36
443 452 2.556622 GTTGTGTGAGTAAACCCATGGG 59.443 50.000 30.23 30.23 42.03 4.00
560 572 4.796830 GGGTTGTTTCGTGAACTTCTTTTC 59.203 41.667 6.12 0.00 39.08 2.29
727 765 1.133790 GACGCATCGTTAGGTAGGTGT 59.866 52.381 0.00 0.00 41.37 4.16
740 778 1.275066 GCATCAAGAGCGACGCATC 59.725 57.895 23.70 15.88 0.00 3.91
741 779 3.403277 GCATCAAGAGCGACGCAT 58.597 55.556 23.70 7.23 0.00 4.73
765 803 4.254492 GACTAAGAGCGACCCATCTTTTT 58.746 43.478 0.00 0.00 37.05 1.94
774 812 1.544691 TCTGGTTGACTAAGAGCGACC 59.455 52.381 0.00 0.00 38.75 4.79
812 850 4.546570 GGTTGTGGAAAAGTATGACAAGC 58.453 43.478 0.00 0.00 0.00 4.01
1296 1514 3.999663 GCAGCCCTATACATAGAGCAAAG 59.000 47.826 5.66 0.00 36.67 2.77
1301 1519 2.159503 CGTCGCAGCCCTATACATAGAG 60.160 54.545 0.00 0.00 32.05 2.43
1303 1521 1.135373 CCGTCGCAGCCCTATACATAG 60.135 57.143 0.00 0.00 0.00 2.23
1560 1813 1.468914 TGCAGTCTACGTAGTCAGCAG 59.531 52.381 26.93 13.48 43.93 4.24
1723 1997 1.673665 CGGGCTCAGCTGCTTCTTT 60.674 57.895 9.47 0.00 0.00 2.52
1928 2202 3.486375 CGATAGTAGGCGTTGTCGAAGAA 60.486 47.826 0.00 0.00 39.69 2.52
2116 2390 0.325860 TACGCCTAATCTGGGTGGGT 60.326 55.000 0.00 0.00 38.54 4.51
2173 2447 3.933955 TGTAACACGTACATACAATGGGC 59.066 43.478 5.17 0.00 37.81 5.36
2175 2449 5.636121 ACACTGTAACACGTACATACAATGG 59.364 40.000 15.64 8.43 41.93 3.16
2179 2453 7.424803 ACTTAACACTGTAACACGTACATACA 58.575 34.615 0.00 0.00 41.93 2.29
2244 2560 5.722021 ATCTGAACCAAACGGCTTTATTT 57.278 34.783 0.00 0.00 0.00 1.40
2318 2639 0.663153 GCACTGCAACGAAAACCTCT 59.337 50.000 0.00 0.00 0.00 3.69
2327 2648 2.743752 CCCAGATCGCACTGCAACG 61.744 63.158 1.11 0.00 36.67 4.10
2337 2658 0.596083 GATGTCAGCGACCCAGATCG 60.596 60.000 6.30 0.00 45.09 3.69
2363 2684 1.081175 GACAAGCCGCCTTTCAAGC 60.081 57.895 0.00 0.00 0.00 4.01
2402 2724 0.107654 GTGGCTATCAAGGAGCGGTT 60.108 55.000 0.00 0.00 41.06 4.44
2404 2726 1.592669 CGTGGCTATCAAGGAGCGG 60.593 63.158 0.00 0.00 41.06 5.52
2405 2727 0.872021 GTCGTGGCTATCAAGGAGCG 60.872 60.000 0.00 0.00 41.06 5.03
2416 2738 2.284625 TGGGAGGATGTCGTGGCT 60.285 61.111 0.00 0.00 0.00 4.75
2421 2743 2.184322 CCGTGTGGGAGGATGTCG 59.816 66.667 0.00 0.00 38.47 4.35
2459 2781 1.813513 CATGTCCTGGTTCACTGGTC 58.186 55.000 0.00 0.00 39.12 4.02
2484 2806 1.287815 CGTGCACCTACAAGTCGGA 59.712 57.895 12.15 0.00 0.00 4.55
2486 2808 2.380410 GGCGTGCACCTACAAGTCG 61.380 63.158 12.15 0.00 0.00 4.18
2503 2825 2.645838 ATTCTTGATGTCGATGGGGG 57.354 50.000 0.00 0.00 0.00 5.40
2509 2831 6.649155 TCCCTATTGAAATTCTTGATGTCGA 58.351 36.000 0.00 0.00 0.00 4.20
2530 2852 1.280457 ACTGATGACCCACTTCTCCC 58.720 55.000 0.00 0.00 0.00 4.30
2580 2902 0.620556 GTCAGGCTTTCATCCCAGGA 59.379 55.000 0.00 0.00 0.00 3.86
2585 2907 3.440173 TCAATTTCGTCAGGCTTTCATCC 59.560 43.478 0.00 0.00 0.00 3.51
2594 2916 4.455533 TCCATGTTTCTCAATTTCGTCAGG 59.544 41.667 0.00 0.00 0.00 3.86
2597 2919 5.625311 GTGTTCCATGTTTCTCAATTTCGTC 59.375 40.000 0.00 0.00 0.00 4.20
2599 2921 5.626543 CAGTGTTCCATGTTTCTCAATTTCG 59.373 40.000 0.00 0.00 0.00 3.46
2603 2925 4.728772 TCCAGTGTTCCATGTTTCTCAAT 58.271 39.130 0.00 0.00 0.00 2.57
2621 2943 2.426024 CCAAGCTCCAATGTTCATCCAG 59.574 50.000 0.00 0.00 0.00 3.86
2625 2947 2.622452 CCCTCCAAGCTCCAATGTTCAT 60.622 50.000 0.00 0.00 0.00 2.57
2631 2953 1.283321 GAACTCCCTCCAAGCTCCAAT 59.717 52.381 0.00 0.00 0.00 3.16
2672 2994 2.815211 TGTCGATCAAGCTGCCGC 60.815 61.111 0.00 0.00 0.00 6.53
2716 3038 3.983988 CGTGATGTATGCTCCATGTAGTC 59.016 47.826 0.00 0.00 0.00 2.59
2723 3045 0.102300 CGTCCGTGATGTATGCTCCA 59.898 55.000 0.00 0.00 0.00 3.86
2733 3055 1.141881 GAGCCACATCGTCCGTGAT 59.858 57.895 0.00 0.00 36.43 3.06
2740 3062 0.036388 ATTCGTTGGAGCCACATCGT 60.036 50.000 8.09 0.00 35.63 3.73
2773 3095 1.999071 CTCCCTTCGAGAGCGTCTGG 61.999 65.000 0.00 0.00 41.63 3.86
2774 3096 1.431440 CTCCCTTCGAGAGCGTCTG 59.569 63.158 0.00 0.00 41.63 3.51
2795 3117 0.248949 GACGTCGGGGATAGAGCAAC 60.249 60.000 0.00 0.00 0.00 4.17
2816 3139 3.544682 TCGTCTACGCATACAAATCGTTG 59.455 43.478 0.00 0.00 38.85 4.10
2817 3140 3.761657 TCGTCTACGCATACAAATCGTT 58.238 40.909 0.00 0.00 39.60 3.85
2819 3142 3.420544 GCATCGTCTACGCATACAAATCG 60.421 47.826 0.00 0.00 39.60 3.34
2831 3154 2.857592 TTTACCTCCGCATCGTCTAC 57.142 50.000 0.00 0.00 0.00 2.59
2842 3165 4.616181 CACATCGTGGAAATTTACCTCC 57.384 45.455 0.00 0.00 0.00 4.30
2857 3180 0.389025 TCGTCCATCCATCCACATCG 59.611 55.000 0.00 0.00 0.00 3.84
2866 3189 1.212688 AGGATTTGCATCGTCCATCCA 59.787 47.619 13.14 0.00 36.60 3.41
2917 3240 9.525826 AACCAGAAAGATTGATGACTAAGATTT 57.474 29.630 0.00 0.00 0.00 2.17
2926 3249 7.815840 TTGTGTTAACCAGAAAGATTGATGA 57.184 32.000 2.48 0.00 0.00 2.92
2945 3268 7.389607 ACGCCTTTATATCTGTTAACTTTGTGT 59.610 33.333 7.22 0.00 0.00 3.72
2952 3275 5.051240 CCGTCACGCCTTTATATCTGTTAAC 60.051 44.000 0.00 0.00 0.00 2.01
2955 3278 3.131577 TCCGTCACGCCTTTATATCTGTT 59.868 43.478 0.00 0.00 0.00 3.16
2958 3281 4.098960 TCTTTCCGTCACGCCTTTATATCT 59.901 41.667 0.00 0.00 0.00 1.98
2969 3292 1.792949 CTTGGTTCTCTTTCCGTCACG 59.207 52.381 0.00 0.00 0.00 4.35
2970 3293 3.107642 TCTTGGTTCTCTTTCCGTCAC 57.892 47.619 0.00 0.00 0.00 3.67
2976 3299 7.119992 GGGAGTAAGATTTCTTGGTTCTCTTTC 59.880 40.741 3.07 0.00 37.40 2.62
2979 3302 5.788014 AGGGAGTAAGATTTCTTGGTTCTCT 59.212 40.000 3.07 1.27 37.40 3.10
3039 3362 3.788142 AGGATGGAAATGTACCCACATCT 59.212 43.478 0.00 0.27 44.83 2.90
3040 3363 4.170468 AGGATGGAAATGTACCCACATC 57.830 45.455 0.00 0.00 44.83 3.06
3042 3365 4.396357 AAAGGATGGAAATGTACCCACA 57.604 40.909 0.00 0.00 39.52 4.17
3043 3366 4.142469 CGAAAAGGATGGAAATGTACCCAC 60.142 45.833 0.00 0.00 34.92 4.61
3044 3367 4.013728 CGAAAAGGATGGAAATGTACCCA 58.986 43.478 0.00 0.00 36.79 4.51
3047 3370 7.813645 AGTTAACGAAAAGGATGGAAATGTAC 58.186 34.615 0.00 0.00 0.00 2.90
3054 3377 9.947433 TTTAATAGAGTTAACGAAAAGGATGGA 57.053 29.630 0.00 0.00 0.00 3.41
3084 3407 3.137176 AGCAGACAACATGCCATATAGGT 59.863 43.478 0.00 0.00 44.97 3.08
3086 3409 4.639334 AGAGCAGACAACATGCCATATAG 58.361 43.478 0.00 0.00 44.97 1.31
3088 3411 3.572632 AGAGCAGACAACATGCCATAT 57.427 42.857 0.00 0.00 44.97 1.78
3089 3412 3.354948 AAGAGCAGACAACATGCCATA 57.645 42.857 0.00 0.00 44.97 2.74
3101 3424 3.559171 GGACCCACACATAAAAGAGCAGA 60.559 47.826 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.