Multiple sequence alignment - TraesCS6D01G129400

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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 TraesCS6D01G129400 chr6D 100.000 2780 0 0 1 2780 94601293 94604072 0.000000e+00 5134.0
1 TraesCS6D01G129400 chr6D 84.872 390 55 4 1075 1462 296348046 296347659 9.340000e-105 390.0
2 TraesCS6D01G129400 chr6A 92.377 2112 71 27 17 2087 114460050 114457988 0.000000e+00 2926.0
3 TraesCS6D01G129400 chr6A 85.090 389 56 2 1075 1462 422328667 422328280 2.010000e-106 396.0
4 TraesCS6D01G129400 chr6A 84.211 399 55 7 1068 1462 598619731 598619337 5.620000e-102 381.0
5 TraesCS6D01G129400 chr6A 92.405 158 11 1 2071 2227 114457976 114457819 1.000000e-54 224.0
6 TraesCS6D01G129400 chr6A 95.522 67 3 0 2582 2648 114457714 114457648 1.050000e-19 108.0
7 TraesCS6D01G129400 chr6B 92.227 1994 71 36 1 1947 178274308 178272352 0.000000e+00 2747.0
8 TraesCS6D01G129400 chr6B 84.615 390 56 4 1075 1462 460928701 460929088 4.340000e-103 385.0
9 TraesCS6D01G129400 chr6B 91.633 251 17 4 2072 2319 178272067 178271818 7.370000e-91 344.0
10 TraesCS6D01G129400 chr6B 91.549 142 9 1 1948 2086 178272258 178272117 2.830000e-45 193.0
11 TraesCS6D01G129400 chr6B 93.548 93 6 0 2582 2674 178271041 178270949 3.730000e-29 139.0
12 TraesCS6D01G129400 chr6B 89.474 95 9 1 2685 2779 178270818 178270725 4.860000e-23 119.0
13 TraesCS6D01G129400 chr6B 86.667 90 8 1 2431 2516 704956572 704956483 2.280000e-16 97.1
14 TraesCS6D01G129400 chr6B 90.141 71 2 4 2508 2577 659585054 659584988 1.370000e-13 87.9
15 TraesCS6D01G129400 chr6B 89.706 68 3 3 2508 2575 55649760 55649697 1.770000e-12 84.2
16 TraesCS6D01G129400 chr6B 90.476 63 4 2 2519 2580 76671328 76671267 6.380000e-12 82.4
17 TraesCS6D01G129400 chr7A 88.124 421 47 3 1071 1491 662967093 662967510 5.350000e-137 497.0
18 TraesCS6D01G129400 chr7A 86.667 90 6 2 2431 2516 28153759 28153672 8.200000e-16 95.3
19 TraesCS6D01G129400 chr7D 87.059 425 52 3 1067 1491 573192880 573193301 6.970000e-131 477.0
20 TraesCS6D01G129400 chr7D 86.022 93 8 4 2431 2519 159659619 159659528 8.200000e-16 95.3
21 TraesCS6D01G129400 chr7D 90.323 62 4 2 2519 2580 567656275 567656216 2.300000e-11 80.5
22 TraesCS6D01G129400 chr7B 86.468 436 56 3 1056 1491 631405249 631405681 2.510000e-130 475.0
23 TraesCS6D01G129400 chr7B 90.625 64 1 5 2507 2569 304515582 304515641 2.300000e-11 80.5
24 TraesCS6D01G129400 chr5B 88.043 92 6 2 2429 2516 595288844 595288754 1.360000e-18 104.0
25 TraesCS6D01G129400 chr5B 87.097 93 8 1 2431 2519 671350756 671350664 4.900000e-18 102.0
26 TraesCS6D01G129400 chr4A 86.364 88 6 3 2433 2516 59560071 59560156 1.060000e-14 91.6
27 TraesCS6D01G129400 chr1D 85.556 90 9 1 2431 2516 42812744 42812833 1.060000e-14 91.6
28 TraesCS6D01G129400 chr4B 83.333 102 11 3 2420 2516 535249745 535249845 3.810000e-14 89.8
29 TraesCS6D01G129400 chr1B 84.043 94 11 1 2430 2519 68248145 68248052 1.370000e-13 87.9
30 TraesCS6D01G129400 chr2B 93.103 58 2 2 2523 2579 184953906 184953962 1.770000e-12 84.2
31 TraesCS6D01G129400 chr2B 90.476 63 2 3 2508 2570 694547238 694547180 2.300000e-11 80.5
32 TraesCS6D01G129400 chrUn 85.714 77 5 5 2508 2582 2945602 2945530 2.970000e-10 76.8
33 TraesCS6D01G129400 chr3B 86.301 73 5 5 2508 2579 136894335 136894403 1.070000e-09 75.0


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 TraesCS6D01G129400 chr6D 94601293 94604072 2779 False 5134.0 5134 100.000000 1 2780 1 chr6D.!!$F1 2779
1 TraesCS6D01G129400 chr6A 114457648 114460050 2402 True 1086.0 2926 93.434667 17 2648 3 chr6A.!!$R3 2631
2 TraesCS6D01G129400 chr6B 178270725 178274308 3583 True 708.4 2747 91.686200 1 2779 5 chr6B.!!$R5 2778

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
775 826 0.179062 GCTGAATCCTCATCTGCCGT 60.179 55.0 0.0 0.0 36.2 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1895 0.390209 GCATCGCCATTGCCAAAACT 60.39 50.0 0.0 0.0 33.95 2.66 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
67 68 5.010719 ACTTTCATCGTCTTCTTGGTGAGTA 59.989 40.000 0.00 0.00 0.00 2.59
90 91 2.163818 ACGTTTTCTGCTTCATCGGA 57.836 45.000 0.00 0.00 0.00 4.55
111 112 2.281664 GCAGATTTGCGCGCGATTC 61.282 57.895 37.18 27.74 41.13 2.52
117 118 3.950794 TTGCGCGCGATTCCCTCTT 62.951 57.895 37.18 0.00 0.00 2.85
136 137 5.369409 TCTTGATCTTGATCCATGCTCTT 57.631 39.130 7.99 0.00 0.00 2.85
143 144 6.845758 TCTTGATCCATGCTCTTTGATTTT 57.154 33.333 0.00 0.00 0.00 1.82
144 145 6.627243 TCTTGATCCATGCTCTTTGATTTTG 58.373 36.000 0.00 0.00 0.00 2.44
145 146 4.751060 TGATCCATGCTCTTTGATTTTGC 58.249 39.130 0.00 0.00 0.00 3.68
146 147 4.221041 TGATCCATGCTCTTTGATTTTGCA 59.779 37.500 0.00 0.00 38.05 4.08
147 148 3.916761 TCCATGCTCTTTGATTTTGCAC 58.083 40.909 0.00 0.00 36.44 4.57
148 149 2.997986 CCATGCTCTTTGATTTTGCACC 59.002 45.455 0.00 0.00 36.44 5.01
149 150 2.420628 TGCTCTTTGATTTTGCACCG 57.579 45.000 0.00 0.00 0.00 4.94
150 151 1.680735 TGCTCTTTGATTTTGCACCGT 59.319 42.857 0.00 0.00 0.00 4.83
151 152 2.287547 TGCTCTTTGATTTTGCACCGTC 60.288 45.455 0.00 0.00 0.00 4.79
152 153 2.574322 CTCTTTGATTTTGCACCGTCG 58.426 47.619 0.00 0.00 0.00 5.12
153 154 1.265635 TCTTTGATTTTGCACCGTCGG 59.734 47.619 10.48 10.48 0.00 4.79
154 155 1.001815 CTTTGATTTTGCACCGTCGGT 60.002 47.619 12.23 12.23 35.62 4.69
176 177 3.762823 TGTGCTTGATTGATTATGTGCCA 59.237 39.130 0.00 0.00 0.00 4.92
245 246 4.708726 GCATGAGCATGACTAAACCTTT 57.291 40.909 14.27 0.00 41.20 3.11
400 417 6.806751 ACCAAGAAAGAAAGAAAAAGCTACC 58.193 36.000 0.00 0.00 0.00 3.18
402 419 6.920210 CCAAGAAAGAAAGAAAAAGCTACCAG 59.080 38.462 0.00 0.00 0.00 4.00
403 420 7.201821 CCAAGAAAGAAAGAAAAAGCTACCAGA 60.202 37.037 0.00 0.00 0.00 3.86
404 421 8.355913 CAAGAAAGAAAGAAAAAGCTACCAGAT 58.644 33.333 0.00 0.00 0.00 2.90
405 422 8.105097 AGAAAGAAAGAAAAAGCTACCAGATC 57.895 34.615 0.00 0.00 0.00 2.75
406 423 7.941790 AGAAAGAAAGAAAAAGCTACCAGATCT 59.058 33.333 0.00 0.00 0.00 2.75
446 483 3.832527 AGGGTTCCATTAATTCCATCCG 58.167 45.455 0.00 0.00 0.00 4.18
584 621 3.450457 TGTTTCTGTTTTTGCCATGTCCT 59.550 39.130 0.00 0.00 0.00 3.85
715 766 3.808728 CCTGAGAAACACTTGTCCTCAA 58.191 45.455 12.59 0.00 34.01 3.02
726 777 3.526534 CTTGTCCTCAAGCTAGTTAGGC 58.473 50.000 0.00 0.00 43.34 3.93
766 817 2.035321 CCCTAGTTCTCGCTGAATCCTC 59.965 54.545 0.00 0.00 36.99 3.71
774 825 1.220169 CGCTGAATCCTCATCTGCCG 61.220 60.000 0.00 0.00 38.19 5.69
775 826 0.179062 GCTGAATCCTCATCTGCCGT 60.179 55.000 0.00 0.00 36.20 5.68
776 827 1.069204 GCTGAATCCTCATCTGCCGTA 59.931 52.381 0.00 0.00 36.20 4.02
777 828 2.865670 GCTGAATCCTCATCTGCCGTAG 60.866 54.545 0.00 0.00 36.20 3.51
778 829 1.069204 TGAATCCTCATCTGCCGTAGC 59.931 52.381 0.00 0.00 40.48 3.58
804 855 4.707934 GCTAGGATTGGAGGGAGATACTAC 59.292 50.000 0.00 0.00 0.00 2.73
841 892 1.068194 AGAAACCGACGAGCTCTTGAG 60.068 52.381 12.85 0.00 0.00 3.02
876 929 8.578151 GGGACACTATAAGCCATATAGCTATAC 58.422 40.741 15.67 3.84 45.02 1.47
932 985 4.458989 TCAAGGCCAGCATTGTTTACTAAG 59.541 41.667 15.71 0.00 38.63 2.18
1039 1092 3.636231 CGGTGGACAGCCCTGGAA 61.636 66.667 0.00 0.00 35.38 3.53
1260 1313 3.646715 CCCTTCTTCGGCCACCCA 61.647 66.667 2.24 0.00 0.00 4.51
1799 1855 1.924191 GCTAGCTCGACGCAGAGAATC 60.924 57.143 7.70 0.00 42.61 2.52
1839 1895 3.313012 AGTAAGTCAAGCGTGCATGTA 57.687 42.857 7.93 0.00 0.00 2.29
1840 1896 3.254060 AGTAAGTCAAGCGTGCATGTAG 58.746 45.455 7.93 0.00 0.00 2.74
1972 2124 5.270893 TGCATTAGCGACTGAGGTAATTA 57.729 39.130 8.65 0.00 46.23 1.40
1973 2125 5.289595 TGCATTAGCGACTGAGGTAATTAG 58.710 41.667 8.65 0.00 46.23 1.73
2215 2435 9.693739 AATAGTGAATATAAATGTTGGGACACA 57.306 29.630 0.00 0.00 39.29 3.72
2231 2460 6.348498 TGGGACACATGTCATATCTAGTTTG 58.652 40.000 13.77 0.00 46.47 2.93
2260 2489 4.522722 AGGTTTTCTAAGTCTCAGTCGG 57.477 45.455 0.00 0.00 0.00 4.79
2271 2500 3.820595 TCAGTCGGCTGAGTTGATG 57.179 52.632 17.42 0.00 45.94 3.07
2274 2503 1.134995 CAGTCGGCTGAGTTGATGCTA 60.135 52.381 12.86 0.00 45.28 3.49
2279 2508 4.752101 GTCGGCTGAGTTGATGCTATATTT 59.248 41.667 0.00 0.00 0.00 1.40
2367 2664 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
2368 2665 0.905337 ACTGAGACCTAGCCACACCC 60.905 60.000 0.00 0.00 0.00 4.61
2369 2666 0.616111 CTGAGACCTAGCCACACCCT 60.616 60.000 0.00 0.00 0.00 4.34
2370 2667 0.708209 TGAGACCTAGCCACACCCTA 59.292 55.000 0.00 0.00 0.00 3.53
2385 2682 2.747446 CACCCTAAAATCAGTCCCAACG 59.253 50.000 0.00 0.00 0.00 4.10
2427 2726 9.837525 ACTTTATTTTCCTACTCGTATATAGCG 57.162 33.333 0.00 0.00 0.00 4.26
2442 3193 2.119801 TAGCGAGTACTCCCTTCGTT 57.880 50.000 15.02 5.79 36.74 3.85
2443 3194 1.254954 AGCGAGTACTCCCTTCGTTT 58.745 50.000 17.23 0.00 36.74 3.60
2445 3196 1.201880 GCGAGTACTCCCTTCGTTTCT 59.798 52.381 17.23 0.00 36.74 2.52
2457 3208 8.979534 ACTCCCTTCGTTTCTAAATATAAGTCT 58.020 33.333 0.00 0.00 0.00 3.24
2480 3231 9.406828 GTCTTTGTAAAGATTTTACCATGAACC 57.593 33.333 9.98 0.00 45.83 3.62
2481 3232 9.137459 TCTTTGTAAAGATTTTACCATGAACCA 57.863 29.630 3.05 0.00 39.95 3.67
2482 3233 9.191995 CTTTGTAAAGATTTTACCATGAACCAC 57.808 33.333 8.70 0.00 38.28 4.16
2483 3234 6.904498 TGTAAAGATTTTACCATGAACCACG 58.096 36.000 8.70 0.00 0.00 4.94
2484 3235 6.487331 TGTAAAGATTTTACCATGAACCACGT 59.513 34.615 8.70 0.00 0.00 4.49
2485 3236 7.660617 TGTAAAGATTTTACCATGAACCACGTA 59.339 33.333 8.70 0.00 0.00 3.57
2486 3237 7.696992 AAAGATTTTACCATGAACCACGTAT 57.303 32.000 0.00 0.00 0.00 3.06
2487 3238 6.677781 AGATTTTACCATGAACCACGTATG 57.322 37.500 0.00 0.00 0.00 2.39
2502 3253 5.929697 CACGTATGGATGTAGATGCATTT 57.070 39.130 12.10 0.00 40.76 2.32
2503 3254 6.304356 CACGTATGGATGTAGATGCATTTT 57.696 37.500 12.10 0.00 40.76 1.82
2504 3255 7.420184 CACGTATGGATGTAGATGCATTTTA 57.580 36.000 12.10 0.00 40.76 1.52
2505 3256 7.860613 CACGTATGGATGTAGATGCATTTTAA 58.139 34.615 12.10 0.00 40.76 1.52
2506 3257 8.341903 CACGTATGGATGTAGATGCATTTTAAA 58.658 33.333 12.10 0.00 40.76 1.52
2507 3258 8.898761 ACGTATGGATGTAGATGCATTTTAAAA 58.101 29.630 12.10 2.51 40.76 1.52
2508 3259 9.897744 CGTATGGATGTAGATGCATTTTAAAAT 57.102 29.630 12.10 7.64 40.76 1.82
2530 3281 8.585471 AAATGTAGATTGACATGGTGAAATCT 57.415 30.769 14.71 14.71 39.99 2.40
2534 3285 7.981789 TGTAGATTGACATGGTGAAATCTCTAC 59.018 37.037 14.07 10.76 36.49 2.59
2540 3291 6.650807 TGACATGGTGAAATCTCTACAAAGAC 59.349 38.462 0.00 0.00 0.00 3.01
2544 3295 9.388506 CATGGTGAAATCTCTACAAAGACTTAT 57.611 33.333 0.00 0.00 0.00 1.73
2561 3312 9.828039 AAAGACTTATATTTAAGTAACGGAGGG 57.172 33.333 8.35 0.00 46.32 4.30
2562 3313 8.773033 AGACTTATATTTAAGTAACGGAGGGA 57.227 34.615 8.35 0.00 46.32 4.20
2564 3315 8.544687 ACTTATATTTAAGTAACGGAGGGAGT 57.455 34.615 6.77 0.00 44.90 3.85
2684 3582 4.791974 ACTTGTCAAGTAGTACTACACGC 58.208 43.478 29.87 18.36 40.69 5.34
2688 3586 4.164294 GTCAAGTAGTACTACACGCTTGG 58.836 47.826 29.87 10.76 41.32 3.61
2689 3587 3.822735 TCAAGTAGTACTACACGCTTGGT 59.177 43.478 29.87 8.33 41.32 3.67
2691 3589 4.170292 AGTAGTACTACACGCTTGGTTG 57.830 45.455 29.87 0.00 38.48 3.77
2693 3591 4.761739 AGTAGTACTACACGCTTGGTTGTA 59.238 41.667 29.87 0.00 38.48 2.41
2694 3592 3.905784 AGTACTACACGCTTGGTTGTAC 58.094 45.455 0.00 12.46 43.23 2.90
2695 3593 2.894763 ACTACACGCTTGGTTGTACA 57.105 45.000 0.00 0.00 0.00 2.90
2696 3594 2.476821 ACTACACGCTTGGTTGTACAC 58.523 47.619 0.00 0.00 0.00 2.90
2697 3595 7.734287 AGTACTACACGCTTGGTTGTACACC 62.734 48.000 18.29 0.96 44.40 4.16
2755 3659 5.641209 ACGTACGTCAGATTTCAGTACTACT 59.359 40.000 16.72 0.00 36.48 2.57
2757 3661 7.493971 ACGTACGTCAGATTTCAGTACTACTAT 59.506 37.037 16.72 0.00 36.48 2.12
2758 3662 7.792967 CGTACGTCAGATTTCAGTACTACTATG 59.207 40.741 7.22 0.00 36.48 2.23
2761 3665 8.182881 ACGTCAGATTTCAGTACTACTATGAAC 58.817 37.037 0.00 0.00 32.91 3.18
2779 3683 2.698855 ACCAACGATCCATTCTCCAG 57.301 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.514691 GCAAGCAGAGAAGAACACCG 59.485 55.000 0.00 0.00 0.00 4.94
11 12 2.645838 ACAAGAAGGCAAGCAGAGAA 57.354 45.000 0.00 0.00 0.00 2.87
13 14 1.196354 CGAACAAGAAGGCAAGCAGAG 59.804 52.381 0.00 0.00 0.00 3.35
14 15 1.229428 CGAACAAGAAGGCAAGCAGA 58.771 50.000 0.00 0.00 0.00 4.26
15 16 0.947244 ACGAACAAGAAGGCAAGCAG 59.053 50.000 0.00 0.00 0.00 4.24
67 68 2.407361 CGATGAAGCAGAAAACGTACGT 59.593 45.455 16.72 16.72 0.00 3.57
108 109 5.632118 CATGGATCAAGATCAAGAGGGAAT 58.368 41.667 11.78 0.00 39.54 3.01
111 112 3.147629 GCATGGATCAAGATCAAGAGGG 58.852 50.000 11.78 0.00 39.54 4.30
117 118 5.106876 TCAAAGAGCATGGATCAAGATCA 57.893 39.130 11.78 0.00 39.54 2.92
136 137 2.709170 ACCGACGGTGCAAAATCAA 58.291 47.368 21.02 0.00 32.98 2.57
146 147 1.070786 AATCAAGCACACCGACGGT 59.929 52.632 15.37 15.37 35.62 4.83
147 148 0.948623 TCAATCAAGCACACCGACGG 60.949 55.000 13.61 13.61 0.00 4.79
148 149 1.078709 ATCAATCAAGCACACCGACG 58.921 50.000 0.00 0.00 0.00 5.12
149 150 4.094887 ACATAATCAATCAAGCACACCGAC 59.905 41.667 0.00 0.00 0.00 4.79
150 151 4.094739 CACATAATCAATCAAGCACACCGA 59.905 41.667 0.00 0.00 0.00 4.69
151 152 4.345288 CACATAATCAATCAAGCACACCG 58.655 43.478 0.00 0.00 0.00 4.94
152 153 4.107622 GCACATAATCAATCAAGCACACC 58.892 43.478 0.00 0.00 0.00 4.16
153 154 4.107622 GGCACATAATCAATCAAGCACAC 58.892 43.478 0.00 0.00 0.00 3.82
154 155 3.762823 TGGCACATAATCAATCAAGCACA 59.237 39.130 0.00 0.00 0.00 4.57
176 177 0.731417 GCGAAGATGCAGCAGTTCAT 59.269 50.000 16.78 0.00 34.15 2.57
226 227 5.184892 AGGAAAGGTTTAGTCATGCTCAT 57.815 39.130 0.00 0.00 0.00 2.90
241 242 6.112927 TGATTCCCAAATTGAAAGGAAAGG 57.887 37.500 6.34 0.00 41.53 3.11
242 243 7.444299 TCTTGATTCCCAAATTGAAAGGAAAG 58.556 34.615 6.34 1.54 41.53 2.62
243 244 7.372260 TCTTGATTCCCAAATTGAAAGGAAA 57.628 32.000 6.34 0.00 41.53 3.13
244 245 6.992664 TCTTGATTCCCAAATTGAAAGGAA 57.007 33.333 5.00 5.00 42.36 3.36
245 246 6.239572 GGTTCTTGATTCCCAAATTGAAAGGA 60.240 38.462 0.00 0.00 33.76 3.36
400 417 5.180492 AGCTAGCGCTAGTAGTAAAGATCTG 59.820 44.000 37.37 14.78 46.79 2.90
402 419 5.616488 AGCTAGCGCTAGTAGTAAAGATC 57.384 43.478 37.37 20.81 46.79 2.75
446 483 4.059459 CGGTCAACTCGCACGCAC 62.059 66.667 0.00 0.00 0.00 5.34
469 506 6.325596 GGTGAGATTACTTCATTGAAAAGCC 58.674 40.000 0.01 0.00 0.00 4.35
471 508 7.452880 TGGGTGAGATTACTTCATTGAAAAG 57.547 36.000 0.01 0.00 0.00 2.27
602 639 1.141657 ACACAACCTGAGACATGCAGT 59.858 47.619 0.00 0.00 0.00 4.40
666 709 5.462530 TGTTTCTCAAACCTACGATCTGA 57.537 39.130 0.00 0.00 40.67 3.27
667 710 5.446473 GCATGTTTCTCAAACCTACGATCTG 60.446 44.000 0.00 0.00 40.67 2.90
715 766 0.173708 GCTGACACGCCTAACTAGCT 59.826 55.000 0.00 0.00 0.00 3.32
725 776 1.194772 GTTTCAGGTTAGCTGACACGC 59.805 52.381 14.03 1.38 0.00 5.34
726 777 1.798813 GGTTTCAGGTTAGCTGACACG 59.201 52.381 19.84 0.62 33.68 4.49
766 817 1.201181 CCTAGCTAGCTACGGCAGATG 59.799 57.143 20.67 8.23 41.70 2.90
774 825 2.829120 CCCTCCAATCCTAGCTAGCTAC 59.171 54.545 20.67 0.00 0.00 3.58
775 826 2.722458 TCCCTCCAATCCTAGCTAGCTA 59.278 50.000 22.85 22.85 0.00 3.32
776 827 1.505538 TCCCTCCAATCCTAGCTAGCT 59.494 52.381 23.12 23.12 0.00 3.32
777 828 1.899142 CTCCCTCCAATCCTAGCTAGC 59.101 57.143 15.74 6.62 0.00 3.42
778 829 3.534357 TCTCCCTCCAATCCTAGCTAG 57.466 52.381 14.20 14.20 0.00 3.42
804 855 4.282873 GTTTCTTGAAGTTCTTGGCGAAG 58.717 43.478 1.39 1.39 30.85 3.79
841 892 4.202131 GGCTTATAGTGTCCCAGTGTACTC 60.202 50.000 0.00 0.00 0.00 2.59
876 929 9.586150 GTCAAACGACTGCAATAAATATATCTG 57.414 33.333 0.00 0.00 0.00 2.90
878 931 8.556194 TGGTCAAACGACTGCAATAAATATATC 58.444 33.333 0.00 0.00 33.65 1.63
917 970 3.131046 GCATGGCCTTAGTAAACAATGCT 59.869 43.478 3.32 0.00 0.00 3.79
1839 1895 0.390209 GCATCGCCATTGCCAAAACT 60.390 50.000 0.00 0.00 33.95 2.66
1840 1896 2.080700 GCATCGCCATTGCCAAAAC 58.919 52.632 0.00 0.00 33.95 2.43
1972 2124 8.417106 CAGAGTACATTACAGATAACCATGACT 58.583 37.037 0.00 0.00 0.00 3.41
1973 2125 7.169982 GCAGAGTACATTACAGATAACCATGAC 59.830 40.741 0.00 0.00 0.00 3.06
1994 2146 1.460743 CACGTACACAACCATGCAGAG 59.539 52.381 0.00 0.00 0.00 3.35
2022 2177 3.181466 ACATTTCAAACCTGCCAACTTCC 60.181 43.478 0.00 0.00 0.00 3.46
2023 2178 4.058721 ACATTTCAAACCTGCCAACTTC 57.941 40.909 0.00 0.00 0.00 3.01
2231 2460 9.274206 ACTGAGACTTAGAAAACCTAATTTGAC 57.726 33.333 0.47 0.00 36.80 3.18
2238 2467 4.082354 GCCGACTGAGACTTAGAAAACCTA 60.082 45.833 0.47 0.00 0.00 3.08
2260 2489 7.923888 TCAAAGAAATATAGCATCAACTCAGC 58.076 34.615 0.00 0.00 0.00 4.26
2335 2565 9.463902 GCTAGGTCTCAGTCCAATAATATAGTA 57.536 37.037 0.00 0.00 0.00 1.82
2337 2567 7.397476 TGGCTAGGTCTCAGTCCAATAATATAG 59.603 40.741 0.00 0.00 0.00 1.31
2338 2568 7.178628 GTGGCTAGGTCTCAGTCCAATAATATA 59.821 40.741 0.00 0.00 0.00 0.86
2339 2569 6.014156 GTGGCTAGGTCTCAGTCCAATAATAT 60.014 42.308 0.00 0.00 0.00 1.28
2340 2570 5.304614 GTGGCTAGGTCTCAGTCCAATAATA 59.695 44.000 0.00 0.00 0.00 0.98
2342 2572 3.451178 GTGGCTAGGTCTCAGTCCAATAA 59.549 47.826 0.00 0.00 0.00 1.40
2343 2573 3.031736 GTGGCTAGGTCTCAGTCCAATA 58.968 50.000 0.00 0.00 0.00 1.90
2344 2574 1.834263 GTGGCTAGGTCTCAGTCCAAT 59.166 52.381 0.00 0.00 0.00 3.16
2367 2664 3.007635 GACCGTTGGGACTGATTTTAGG 58.992 50.000 0.00 0.00 36.97 2.69
2368 2665 3.670625 TGACCGTTGGGACTGATTTTAG 58.329 45.455 0.00 0.00 36.97 1.85
2369 2666 3.773418 TGACCGTTGGGACTGATTTTA 57.227 42.857 0.00 0.00 36.97 1.52
2370 2667 2.649531 TGACCGTTGGGACTGATTTT 57.350 45.000 0.00 0.00 36.97 1.82
2425 2724 1.201880 AGAAACGAAGGGAGTACTCGC 59.798 52.381 27.68 27.68 42.14 5.03
2454 3205 9.406828 GGTTCATGGTAAAATCTTTACAAAGAC 57.593 33.333 6.56 0.00 46.80 3.01
2456 3207 9.191995 GTGGTTCATGGTAAAATCTTTACAAAG 57.808 33.333 10.54 0.00 37.36 2.77
2457 3208 7.863375 CGTGGTTCATGGTAAAATCTTTACAAA 59.137 33.333 10.54 0.65 0.00 2.83
2460 3211 6.905578 ACGTGGTTCATGGTAAAATCTTTAC 58.094 36.000 0.00 1.44 0.00 2.01
2462 3213 7.362574 CCATACGTGGTTCATGGTAAAATCTTT 60.363 37.037 0.00 0.00 40.83 2.52
2463 3214 6.094881 CCATACGTGGTTCATGGTAAAATCTT 59.905 38.462 0.00 0.00 40.83 2.40
2464 3215 5.588648 CCATACGTGGTTCATGGTAAAATCT 59.411 40.000 0.00 0.00 40.83 2.40
2465 3216 5.587043 TCCATACGTGGTTCATGGTAAAATC 59.413 40.000 12.80 0.00 46.16 2.17
2466 3217 5.502079 TCCATACGTGGTTCATGGTAAAAT 58.498 37.500 12.80 0.00 46.16 1.82
2469 3220 4.080807 ACATCCATACGTGGTTCATGGTAA 60.081 41.667 12.80 0.00 46.16 2.85
2470 3221 3.452990 ACATCCATACGTGGTTCATGGTA 59.547 43.478 12.80 2.64 46.16 3.25
2472 3223 2.917933 ACATCCATACGTGGTTCATGG 58.082 47.619 7.82 7.82 46.16 3.66
2473 3224 4.944048 TCTACATCCATACGTGGTTCATG 58.056 43.478 0.00 0.00 46.16 3.07
2474 3225 5.541845 CATCTACATCCATACGTGGTTCAT 58.458 41.667 0.00 0.00 46.16 2.57
2475 3226 4.739436 GCATCTACATCCATACGTGGTTCA 60.739 45.833 0.00 0.00 46.16 3.18
2476 3227 3.741344 GCATCTACATCCATACGTGGTTC 59.259 47.826 0.00 0.00 46.16 3.62
2477 3228 3.133901 TGCATCTACATCCATACGTGGTT 59.866 43.478 0.00 0.00 46.16 3.67
2478 3229 2.698274 TGCATCTACATCCATACGTGGT 59.302 45.455 0.00 0.00 46.16 4.16
2480 3231 5.929697 AAATGCATCTACATCCATACGTG 57.070 39.130 0.00 0.00 0.00 4.49
2481 3232 8.445275 TTTAAAATGCATCTACATCCATACGT 57.555 30.769 0.00 0.00 0.00 3.57
2482 3233 9.897744 ATTTTAAAATGCATCTACATCCATACG 57.102 29.630 12.62 0.00 0.00 3.06
2504 3255 9.028284 AGATTTCACCATGTCAATCTACATTTT 57.972 29.630 0.00 0.00 38.01 1.82
2505 3256 8.585471 AGATTTCACCATGTCAATCTACATTT 57.415 30.769 0.00 0.00 38.01 2.32
2506 3257 8.051535 AGAGATTTCACCATGTCAATCTACATT 58.948 33.333 6.11 0.00 38.01 2.71
2507 3258 7.571919 AGAGATTTCACCATGTCAATCTACAT 58.428 34.615 6.11 0.00 40.75 2.29
2508 3259 6.950842 AGAGATTTCACCATGTCAATCTACA 58.049 36.000 6.11 0.00 36.35 2.74
2509 3260 7.981789 TGTAGAGATTTCACCATGTCAATCTAC 59.018 37.037 0.00 0.00 36.35 2.59
2512 3263 7.615582 TTGTAGAGATTTCACCATGTCAATC 57.384 36.000 0.00 0.00 0.00 2.67
2516 3267 6.876257 AGTCTTTGTAGAGATTTCACCATGTC 59.124 38.462 0.00 0.00 0.00 3.06
2571 3346 5.722021 TGCCATCAGAAGCGATAGTAATA 57.278 39.130 0.00 0.00 39.35 0.98
2578 3353 1.696336 AGGTATGCCATCAGAAGCGAT 59.304 47.619 1.54 0.00 37.19 4.58
2666 3451 4.164294 CCAAGCGTGTAGTACTACTTGAC 58.836 47.826 28.56 19.25 40.63 3.18
2674 3572 3.426525 GTGTACAACCAAGCGTGTAGTAC 59.573 47.826 14.75 14.75 32.68 2.73
2688 3586 1.650363 GCCACAACCGGTGTACAAC 59.350 57.895 8.52 0.00 46.44 3.32
2689 3587 1.888172 CGCCACAACCGGTGTACAA 60.888 57.895 8.52 0.00 46.44 2.41
2691 3589 2.029369 TCGCCACAACCGGTGTAC 59.971 61.111 8.52 3.77 46.44 2.90
2693 3591 4.922026 GGTCGCCACAACCGGTGT 62.922 66.667 8.52 5.76 46.44 4.16
2696 3594 4.636435 AAGGGTCGCCACAACCGG 62.636 66.667 0.00 0.00 37.69 5.28
2697 3595 2.593436 AAAGGGTCGCCACAACCG 60.593 61.111 0.00 0.00 37.69 4.44
2699 3597 2.265904 GGGAAAGGGTCGCCACAAC 61.266 63.158 0.00 0.00 33.06 3.32
2700 3598 2.114411 GGGAAAGGGTCGCCACAA 59.886 61.111 0.00 0.00 33.06 3.33
2708 3612 0.856982 TGTGATGTTGGGGAAAGGGT 59.143 50.000 0.00 0.00 0.00 4.34
2711 3615 3.716601 GTTGTTGTGATGTTGGGGAAAG 58.283 45.455 0.00 0.00 0.00 2.62
2755 3659 4.163268 TGGAGAATGGATCGTTGGTTCATA 59.837 41.667 0.00 0.00 0.00 2.15
2757 3661 2.304470 TGGAGAATGGATCGTTGGTTCA 59.696 45.455 0.00 0.00 0.00 3.18
2758 3662 2.939103 CTGGAGAATGGATCGTTGGTTC 59.061 50.000 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.