Multiple sequence alignment - TraesCS1D01G356700

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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 TraesCS1D01G356700 chr1D 100.000 3491 0 0 1 3491 441033833 441030343 0.000000e+00 6447.0
1 TraesCS1D01G356700 chr1D 90.048 1859 158 16 746 2590 441019319 441017474 0.000000e+00 2383.0
2 TraesCS1D01G356700 chr1D 81.813 1721 269 23 772 2483 441008190 441006505 0.000000e+00 1404.0
3 TraesCS1D01G356700 chr1D 81.180 1525 262 20 971 2483 441016537 441015026 0.000000e+00 1203.0
4 TraesCS1D01G356700 chr1D 91.295 471 39 1 2728 3196 441017256 441016786 2.940000e-180 641.0
5 TraesCS1D01G356700 chr1D 85.556 90 10 3 3078 3166 441008744 441008657 1.330000e-14 91.6
6 TraesCS1D01G356700 chr1D 94.595 37 2 0 2692 2728 172052210 172052246 1.350000e-04 58.4
7 TraesCS1D01G356700 chr1D 100.000 29 0 0 2694 2722 7705896 7705868 2.000000e-03 54.7
8 TraesCS1D01G356700 chr1B 88.193 3481 308 47 1 3451 598702062 598698655 0.000000e+00 4056.0
9 TraesCS1D01G356700 chr1B 83.333 1692 261 15 791 2469 598698302 598696619 0.000000e+00 1543.0
10 TraesCS1D01G356700 chr1B 87.129 101 10 3 3078 3177 598690488 598690390 1.020000e-20 111.0
11 TraesCS1D01G356700 chr1B 95.455 66 3 0 771 836 598689948 598689883 4.770000e-19 106.0
12 TraesCS1D01G356700 chr1A 90.791 1770 149 8 852 2612 537072024 537073788 0.000000e+00 2353.0
13 TraesCS1D01G356700 chr1A 87.848 1868 197 20 746 2597 537081748 537083601 0.000000e+00 2165.0
14 TraesCS1D01G356700 chr1A 82.312 1730 267 30 771 2483 537093578 537095285 0.000000e+00 1463.0
15 TraesCS1D01G356700 chr1A 82.332 1698 265 26 781 2463 537089992 537091669 0.000000e+00 1441.0
16 TraesCS1D01G356700 chr1A 93.312 942 35 14 1 936 537070959 537071878 0.000000e+00 1365.0
17 TraesCS1D01G356700 chr1A 90.720 722 64 2 2722 3440 537083806 537084527 0.000000e+00 959.0
18 TraesCS1D01G356700 chr1A 86.865 571 53 11 2828 3376 537074096 537074666 1.380000e-173 619.0
19 TraesCS1D01G356700 chr1A 79.894 378 52 16 3077 3451 537092858 537093214 4.470000e-64 255.0
20 TraesCS1D01G356700 chr6D 100.000 31 0 0 2692 2722 132286835 132286865 1.350000e-04 58.4
21 TraesCS1D01G356700 chr7D 97.059 34 0 1 2694 2727 545806558 545806590 4.870000e-04 56.5
22 TraesCS1D01G356700 chr7D 96.970 33 0 1 2694 2726 28015885 28015916 2.000000e-03 54.7
23 TraesCS1D01G356700 chr7D 94.118 34 2 0 2694 2727 260385155 260385122 6.000000e-03 52.8
24 TraesCS1D01G356700 chr7D 94.118 34 2 0 2694 2727 427915595 427915562 6.000000e-03 52.8
25 TraesCS1D01G356700 chr7D 100.000 28 0 0 2694 2721 604312079 604312106 6.000000e-03 52.8
26 TraesCS1D01G356700 chr2D 100.000 28 0 0 2694 2721 72794578 72794605 6.000000e-03 52.8


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 TraesCS1D01G356700 chr1D 441030343 441033833 3490 True 6447.000000 6447 100.000000 1 3491 1 chr1D.!!$R2 3490
1 TraesCS1D01G356700 chr1D 441015026 441019319 4293 True 1409.000000 2383 87.507667 746 3196 3 chr1D.!!$R4 2450
2 TraesCS1D01G356700 chr1D 441006505 441008744 2239 True 747.800000 1404 83.684500 772 3166 2 chr1D.!!$R3 2394
3 TraesCS1D01G356700 chr1B 598696619 598702062 5443 True 2799.500000 4056 85.763000 1 3451 2 chr1B.!!$R2 3450
4 TraesCS1D01G356700 chr1A 537081748 537084527 2779 False 1562.000000 2165 89.284000 746 3440 2 chr1A.!!$F2 2694
5 TraesCS1D01G356700 chr1A 537070959 537074666 3707 False 1445.666667 2353 90.322667 1 3376 3 chr1A.!!$F1 3375
6 TraesCS1D01G356700 chr1A 537089992 537095285 5293 False 1053.000000 1463 81.512667 771 3451 3 chr1A.!!$F3 2680

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
737 763 1.140452 CTGAGCTCCCACATGCTGTAT 59.860 52.381 12.15 0.0 39.91 2.29 F
1259 4336 0.108233 GCCTTCAGGTGCAGAGAGAG 60.108 60.000 0.00 0.0 37.57 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 5236 0.252239 TCTGCCTGTGCTCCCTAAGA 60.252 55.0 0.0 0.0 38.71 2.10 R
3127 6437 1.012841 GCTCCAGCTATCTGTGTTGC 58.987 55.0 0.0 0.0 38.66 4.17 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
232 241 8.730680 TGATAGCAGATGATTGATGAATGAATG 58.269 33.333 0.00 0.00 0.00 2.67
271 281 6.072397 TGGTGGATTTGGTTGTACTTTAATCG 60.072 38.462 0.00 0.00 0.00 3.34
391 410 6.882610 TGATGATGCCACATACTAAATTCC 57.117 37.500 0.00 0.00 0.00 3.01
694 720 8.589701 TCATCTCTTTGTAGTTGTAGGACATA 57.410 34.615 0.00 0.00 0.00 2.29
696 722 9.254133 CATCTCTTTGTAGTTGTAGGACATATG 57.746 37.037 0.00 0.00 0.00 1.78
697 723 7.782049 TCTCTTTGTAGTTGTAGGACATATGG 58.218 38.462 7.80 0.00 0.00 2.74
698 724 6.346096 TCTTTGTAGTTGTAGGACATATGGC 58.654 40.000 7.80 3.17 0.00 4.40
705 731 3.103742 TGTAGGACATATGGCTGTGTGA 58.896 45.455 8.85 0.00 0.00 3.58
737 763 1.140452 CTGAGCTCCCACATGCTGTAT 59.860 52.381 12.15 0.00 39.91 2.29
814 3647 1.588674 AACAATGTCGCCTTCGTTGA 58.411 45.000 8.63 0.00 36.19 3.18
836 3669 5.104776 TGAATGGGTCAATGAAGACTAGGAG 60.105 44.000 0.00 0.00 38.57 3.69
837 3670 4.061131 TGGGTCAATGAAGACTAGGAGA 57.939 45.455 0.00 0.00 38.57 3.71
838 3671 3.769844 TGGGTCAATGAAGACTAGGAGAC 59.230 47.826 0.00 0.00 38.57 3.36
847 3683 6.235231 TGAAGACTAGGAGACAAAAACACT 57.765 37.500 0.00 0.00 0.00 3.55
891 3795 1.237285 TTGCCTTCTGAAGCTTCCGC 61.237 55.000 23.42 16.02 0.00 5.54
902 3806 2.035442 GCTTCCGCCTGACTGTTCC 61.035 63.158 0.00 0.00 0.00 3.62
925 3840 4.910746 AGTCATCGAGTCAACAAATTCG 57.089 40.909 0.00 0.00 34.56 3.34
926 3841 4.556233 AGTCATCGAGTCAACAAATTCGA 58.444 39.130 0.00 0.00 44.88 3.71
952 3867 3.699538 TCTTTCGAGCTAAGAGCACCATA 59.300 43.478 0.64 0.00 45.56 2.74
953 3868 3.438297 TTCGAGCTAAGAGCACCATAC 57.562 47.619 0.64 0.00 45.56 2.39
957 3872 4.023107 TCGAGCTAAGAGCACCATACATAC 60.023 45.833 0.64 0.00 45.56 2.39
990 3905 1.636003 GGAGGGGTTCCTGTTCATTCT 59.364 52.381 0.00 0.00 45.05 2.40
992 3907 2.305927 GAGGGGTTCCTGTTCATTCTCA 59.694 50.000 0.00 0.00 45.05 3.27
1009 3924 2.082231 CTCACTTCACAATGGAGGCAG 58.918 52.381 0.00 0.00 0.00 4.85
1060 4137 2.558795 GGCAGAGCTATATCCTTCGTGA 59.441 50.000 0.00 0.00 0.00 4.35
1074 4151 2.094659 CGTGATCAAGAAGCGCCGT 61.095 57.895 2.29 0.00 0.00 5.68
1086 4163 2.356313 CGCCGTGAGCAGACAACT 60.356 61.111 0.00 0.00 44.04 3.16
1174 4251 1.822186 GGGCGGTGTGTCACAAACT 60.822 57.895 7.38 0.00 35.86 2.66
1186 4263 4.872691 GTGTCACAAACTGAGGGATGATAG 59.127 45.833 0.00 0.00 0.00 2.08
1207 4284 0.741326 TCAGGCTAGCACGATGAGAC 59.259 55.000 18.24 0.00 0.00 3.36
1259 4336 0.108233 GCCTTCAGGTGCAGAGAGAG 60.108 60.000 0.00 0.00 37.57 3.20
1267 4344 1.261480 GTGCAGAGAGAGGAAGACCA 58.739 55.000 0.00 0.00 38.94 4.02
1280 4357 2.570135 GAAGACCAATGATGAGGAGGC 58.430 52.381 0.00 0.00 0.00 4.70
1306 4383 2.589014 GCTTCTTGTTTGCTCAATCCG 58.411 47.619 0.00 0.00 0.00 4.18
1317 4394 3.619419 TGCTCAATCCGATTTCAATCCA 58.381 40.909 0.00 0.00 31.68 3.41
1390 4467 5.489792 AATTGGTAGAGAAAGCAGTCAGA 57.510 39.130 0.00 0.00 0.00 3.27
1408 4485 6.093495 CAGTCAGAAGTTGAAACAGGTTGTTA 59.907 38.462 0.00 0.00 40.14 2.41
1421 4498 5.390387 ACAGGTTGTTATTGGCCTAGAAAA 58.610 37.500 3.32 0.00 0.00 2.29
1440 4517 7.230849 AGAAAACATGGTTGCTGATATGAAA 57.769 32.000 2.12 0.00 0.00 2.69
1452 4529 7.255491 TGCTGATATGAAAGAGTTTGCTATG 57.745 36.000 0.00 0.00 0.00 2.23
1549 4626 2.460669 GCCAAATGGAGAGGGAACAAT 58.539 47.619 2.98 0.00 37.39 2.71
1602 4679 2.158173 AGGGAATGGAAATGTGGGTGTT 60.158 45.455 0.00 0.00 0.00 3.32
1606 4683 4.770010 GGAATGGAAATGTGGGTGTTCTTA 59.230 41.667 0.00 0.00 0.00 2.10
1614 4691 5.705609 ATGTGGGTGTTCTTACAATTGTC 57.294 39.130 15.85 0.34 35.69 3.18
1632 4709 2.110213 GGTCCTGCACGTGTTGGA 59.890 61.111 21.78 21.78 0.00 3.53
1847 4926 4.562757 CGTGGACAAAGGAGTATGGAAGAA 60.563 45.833 0.00 0.00 0.00 2.52
2157 5236 0.326264 GGTGCAGGGTTCTCAGACAT 59.674 55.000 0.00 0.00 0.00 3.06
2190 5269 5.586243 GCACAGGCAGAAGAATATCTTGTTA 59.414 40.000 0.00 0.00 37.06 2.41
2235 5314 5.106908 GGAAGATCAGCCTCGTTATATTTGC 60.107 44.000 0.00 0.00 0.00 3.68
2248 5327 2.453983 TATTTGCAGCTTGGCCAAAC 57.546 45.000 20.91 15.93 0.00 2.93
2251 5330 3.605664 GCAGCTTGGCCAAACGGT 61.606 61.111 20.91 11.75 0.00 4.83
2269 5348 1.471676 GGTGGCGAGGTTCTGAGTATG 60.472 57.143 0.00 0.00 0.00 2.39
2274 5353 3.864003 GGCGAGGTTCTGAGTATGTTAAC 59.136 47.826 0.00 0.00 0.00 2.01
2339 5418 3.112263 ACAGTGGGATTCCGAGGATAAA 58.888 45.455 0.00 0.00 35.24 1.40
2376 5455 2.856628 CGGCACCTGGAGCGCTATA 61.857 63.158 11.50 0.29 0.00 1.31
2484 5565 3.128938 ACGAGAAGTACCACAGCATAGAC 59.871 47.826 0.00 0.00 0.00 2.59
2492 5573 4.060038 ACCACAGCATAGACGAATAAGG 57.940 45.455 0.00 0.00 0.00 2.69
2526 5607 2.629002 ACCGTGGTGACATTGCTTC 58.371 52.632 0.00 0.00 46.14 3.86
2543 5624 2.028748 GCTTCGAGTTACTGGTGGGTTA 60.029 50.000 0.00 0.00 0.00 2.85
2556 5638 5.046520 ACTGGTGGGTTATCTTCTTGTCTAC 60.047 44.000 0.00 0.00 0.00 2.59
2557 5639 4.841813 TGGTGGGTTATCTTCTTGTCTACA 59.158 41.667 0.00 0.00 0.00 2.74
2558 5640 5.308497 TGGTGGGTTATCTTCTTGTCTACAA 59.692 40.000 0.00 0.00 0.00 2.41
2625 5733 6.625873 AAAAGTTGATCTGGTTCTTGAGTC 57.374 37.500 0.00 0.00 0.00 3.36
2627 5735 5.559148 AGTTGATCTGGTTCTTGAGTCTT 57.441 39.130 0.00 0.00 0.00 3.01
2628 5736 5.546526 AGTTGATCTGGTTCTTGAGTCTTC 58.453 41.667 0.00 0.00 0.00 2.87
2696 5895 4.640201 GGCTCCTTAAATACTGATTGTGCA 59.360 41.667 0.00 0.00 0.00 4.57
2697 5896 5.449177 GGCTCCTTAAATACTGATTGTGCAC 60.449 44.000 10.75 10.75 0.00 4.57
2698 5897 5.727791 GCTCCTTAAATACTGATTGTGCACG 60.728 44.000 13.13 0.00 0.00 5.34
2699 5898 5.242434 TCCTTAAATACTGATTGTGCACGT 58.758 37.500 13.13 5.95 0.00 4.49
2700 5899 6.399743 TCCTTAAATACTGATTGTGCACGTA 58.600 36.000 13.13 8.15 0.00 3.57
2701 5900 6.533723 TCCTTAAATACTGATTGTGCACGTAG 59.466 38.462 13.13 9.82 0.00 3.51
2702 5901 6.238103 CCTTAAATACTGATTGTGCACGTAGG 60.238 42.308 13.13 3.10 0.00 3.18
2703 5902 4.465632 AATACTGATTGTGCACGTAGGA 57.534 40.909 13.13 4.63 0.00 2.94
2704 5903 2.370281 ACTGATTGTGCACGTAGGAG 57.630 50.000 13.13 6.75 0.00 3.69
2705 5904 1.002366 CTGATTGTGCACGTAGGAGC 58.998 55.000 13.13 0.00 0.00 4.70
2706 5905 0.320050 TGATTGTGCACGTAGGAGCA 59.680 50.000 13.13 3.32 40.12 4.26
2707 5906 1.270571 TGATTGTGCACGTAGGAGCAA 60.271 47.619 13.13 0.00 43.55 3.91
2708 5907 1.804151 GATTGTGCACGTAGGAGCAAA 59.196 47.619 13.13 1.16 43.55 3.68
2709 5908 1.669604 TTGTGCACGTAGGAGCAAAA 58.330 45.000 13.13 7.67 43.55 2.44
2710 5909 1.225855 TGTGCACGTAGGAGCAAAAG 58.774 50.000 13.13 0.00 43.55 2.27
2711 5910 0.517316 GTGCACGTAGGAGCAAAAGG 59.483 55.000 9.11 0.00 43.55 3.11
2712 5911 0.605319 TGCACGTAGGAGCAAAAGGG 60.605 55.000 5.02 0.00 39.51 3.95
2713 5912 0.321298 GCACGTAGGAGCAAAAGGGA 60.321 55.000 0.00 0.00 32.99 4.20
2714 5913 1.880646 GCACGTAGGAGCAAAAGGGAA 60.881 52.381 0.00 0.00 32.99 3.97
2715 5914 2.711542 CACGTAGGAGCAAAAGGGAAT 58.288 47.619 0.00 0.00 0.00 3.01
2716 5915 3.869065 CACGTAGGAGCAAAAGGGAATA 58.131 45.455 0.00 0.00 0.00 1.75
2717 5916 4.451900 CACGTAGGAGCAAAAGGGAATAT 58.548 43.478 0.00 0.00 0.00 1.28
2718 5917 4.511826 CACGTAGGAGCAAAAGGGAATATC 59.488 45.833 0.00 0.00 0.00 1.63
2719 5918 4.065789 CGTAGGAGCAAAAGGGAATATCC 58.934 47.826 0.00 0.00 35.23 2.59
2760 5959 5.569355 TCTTCATCTGAATAAACAAGCCCA 58.431 37.500 0.00 0.00 33.01 5.36
2871 6173 0.318441 CAACCACTCGAGAAGCCTGA 59.682 55.000 21.68 0.00 0.00 3.86
2924 6226 0.037975 GGGCGACGAAGGACAAGTAA 60.038 55.000 0.00 0.00 0.00 2.24
3039 6348 1.529865 GCTGGTTAACGGTGTCTTGTC 59.470 52.381 0.00 0.00 0.00 3.18
3040 6349 2.828877 CTGGTTAACGGTGTCTTGTCA 58.171 47.619 0.00 0.00 0.00 3.58
3054 6363 5.011451 GTCTTGTCAAAGAAGACATCACG 57.989 43.478 10.97 0.00 46.90 4.35
3067 6376 1.734477 ATCACGCACACGAGTCTGC 60.734 57.895 0.00 0.00 43.93 4.26
3077 6387 1.153939 CGAGTCTGCGGAGTTCAGG 60.154 63.158 3.90 0.00 32.63 3.86
3079 6389 0.318762 GAGTCTGCGGAGTTCAGGTT 59.681 55.000 3.90 0.00 32.63 3.50
3127 6437 6.867662 AAGATCAGTACCACAAGTGAAAAG 57.132 37.500 0.94 0.00 32.71 2.27
3160 6470 4.348198 GCTGGAGCTAACAAGATGAAAC 57.652 45.455 0.00 0.00 38.21 2.78
3179 6489 4.622701 AACAACAGCTGAAAGAACAGAC 57.377 40.909 23.35 0.00 39.94 3.51
3185 6495 3.060003 CAGCTGAAAGAACAGACTGAACG 60.060 47.826 8.42 0.00 40.64 3.95
3205 6517 1.408702 GAACACAACCACTGCCATTGT 59.591 47.619 0.00 0.00 37.02 2.71
3216 6535 1.117994 TGCCATTGTGCAGGTTTTGA 58.882 45.000 0.00 0.00 36.04 2.69
3224 6543 4.527509 TGTGCAGGTTTTGAAAAGAACA 57.472 36.364 0.00 0.00 0.00 3.18
3303 6622 4.447138 TCCACCACACTGACCTTTATTT 57.553 40.909 0.00 0.00 0.00 1.40
3311 6630 7.942341 ACCACACTGACCTTTATTTAATCAGAA 59.058 33.333 6.56 0.00 39.33 3.02
3313 6632 9.612620 CACACTGACCTTTATTTAATCAGAAAC 57.387 33.333 6.56 0.00 39.33 2.78
3379 6710 5.247110 GGGTCAGATGCCTATTCTCTGAATA 59.753 44.000 3.26 0.00 45.02 1.75
3454 7278 2.932614 CAGCAACTTCCTAACTCCATCG 59.067 50.000 0.00 0.00 0.00 3.84
3478 7302 3.756434 GCTCAGAGTACCATCTAGCTAGG 59.244 52.174 20.58 8.41 0.00 3.02
3482 7306 3.139397 AGAGTACCATCTAGCTAGGCAGT 59.861 47.826 20.58 16.05 0.00 4.40
3483 7307 3.892588 GAGTACCATCTAGCTAGGCAGTT 59.107 47.826 20.58 4.73 0.00 3.16
3484 7308 4.290942 AGTACCATCTAGCTAGGCAGTTT 58.709 43.478 20.58 3.73 0.00 2.66
3485 7309 4.717280 AGTACCATCTAGCTAGGCAGTTTT 59.283 41.667 20.58 4.96 0.00 2.43
3486 7310 3.878778 ACCATCTAGCTAGGCAGTTTTG 58.121 45.455 20.58 7.25 0.00 2.44
3488 7312 3.118261 CCATCTAGCTAGGCAGTTTTGGA 60.118 47.826 20.58 0.00 0.00 3.53
3489 7313 4.517285 CATCTAGCTAGGCAGTTTTGGAA 58.483 43.478 20.58 0.00 0.00 3.53
3490 7314 3.939066 TCTAGCTAGGCAGTTTTGGAAC 58.061 45.455 20.58 0.00 35.97 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.228769 TGTAGTCGGACCACTGCCT 60.229 57.895 8.14 0.00 0.00 4.75
128 130 2.821969 AGTTGATGTTCATCCACAAGCC 59.178 45.455 15.78 0.00 0.00 4.35
271 281 7.009540 CAGAAAAGCATGATTAATCCGGAAAAC 59.990 37.037 9.01 0.00 0.00 2.43
356 366 2.009051 GCATCATCATCGGTTCACACA 58.991 47.619 0.00 0.00 0.00 3.72
391 410 4.330250 AGTGGGATCTGAAAACATGTCTG 58.670 43.478 0.00 0.00 0.00 3.51
473 494 3.689649 CCCGTTCCAGAACTTAAGAATGG 59.310 47.826 10.09 13.25 42.57 3.16
705 731 3.245016 TGGGAGCTCAGTGATTGTGAAAT 60.245 43.478 17.19 0.00 0.00 2.17
714 740 1.196766 AGCATGTGGGAGCTCAGTGA 61.197 55.000 17.19 0.00 36.00 3.41
814 3647 5.032846 TCTCCTAGTCTTCATTGACCCATT 58.967 41.667 0.00 0.00 37.66 3.16
891 3795 2.029020 TCGATGACTTGGAACAGTCAGG 60.029 50.000 9.28 4.54 44.67 3.86
902 3806 5.075448 CGAATTTGTTGACTCGATGACTTG 58.925 41.667 0.00 0.00 33.13 3.16
925 3840 4.090786 GTGCTCTTAGCTCGAAAGACTTTC 59.909 45.833 16.58 16.58 42.97 2.62
926 3841 3.991121 GTGCTCTTAGCTCGAAAGACTTT 59.009 43.478 0.00 0.00 42.97 2.66
941 3856 4.678044 CGTCACTGTATGTATGGTGCTCTT 60.678 45.833 0.00 0.00 0.00 2.85
952 3867 0.037326 CCCAGCACGTCACTGTATGT 60.037 55.000 12.75 0.00 33.09 2.29
953 3868 0.246360 TCCCAGCACGTCACTGTATG 59.754 55.000 12.75 3.34 33.09 2.39
957 3872 2.047844 CCTCCCAGCACGTCACTG 60.048 66.667 7.93 7.93 34.82 3.66
990 3905 1.421268 ACTGCCTCCATTGTGAAGTGA 59.579 47.619 0.00 0.00 0.00 3.41
992 3907 1.421268 TGACTGCCTCCATTGTGAAGT 59.579 47.619 0.00 0.00 0.00 3.01
1009 3924 1.880027 ACCAAGAACCGCAGAAATGAC 59.120 47.619 0.00 0.00 0.00 3.06
1060 4137 2.103042 GCTCACGGCGCTTCTTGAT 61.103 57.895 6.90 0.00 0.00 2.57
1086 4163 0.325016 TCTGCAGATCCTCCTCAGCA 60.325 55.000 13.74 0.00 35.59 4.41
1174 4251 3.556862 AGCCTGATCTATCATCCCTCA 57.443 47.619 0.00 0.00 36.02 3.86
1186 4263 1.611006 TCTCATCGTGCTAGCCTGATC 59.389 52.381 13.29 0.00 0.00 2.92
1207 4284 3.679389 AGTACCCTCTGAACATTTGCTG 58.321 45.455 0.00 0.00 0.00 4.41
1259 4336 2.747799 GCCTCCTCATCATTGGTCTTCC 60.748 54.545 0.00 0.00 0.00 3.46
1267 4344 0.387202 CGACTCGCCTCCTCATCATT 59.613 55.000 0.00 0.00 0.00 2.57
1280 4357 0.861837 AGCAAACAAGAAGCGACTCG 59.138 50.000 0.00 0.00 0.00 4.18
1306 4383 4.622701 AACGCTTAGCTGGATTGAAATC 57.377 40.909 1.76 0.00 34.66 2.17
1317 4394 0.796927 GAAGGCGAAAACGCTTAGCT 59.203 50.000 13.81 0.00 34.92 3.32
1334 4411 6.524734 TCAATCTGAGTGTTGCTAGAAAGAA 58.475 36.000 4.92 0.00 0.00 2.52
1390 4467 5.356426 GCCAATAACAACCTGTTTCAACTT 58.644 37.500 0.00 0.00 41.45 2.66
1408 4485 3.055891 GCAACCATGTTTTCTAGGCCAAT 60.056 43.478 5.01 0.00 0.00 3.16
1421 4498 5.503927 ACTCTTTCATATCAGCAACCATGT 58.496 37.500 0.00 0.00 0.00 3.21
1440 4517 5.353678 GCTCATCAGAAACATAGCAAACTCT 59.646 40.000 0.00 0.00 0.00 3.24
1452 4529 2.815478 CGAGGGTAGCTCATCAGAAAC 58.185 52.381 0.00 0.00 0.00 2.78
1558 4635 1.882623 AGGCTCAGCTTGTAGCAAAAC 59.117 47.619 13.02 0.00 45.56 2.43
1560 4637 1.611673 GGAGGCTCAGCTTGTAGCAAA 60.612 52.381 17.69 0.00 45.56 3.68
1602 4679 2.037902 TGCAGGACCGACAATTGTAAGA 59.962 45.455 11.95 0.00 0.00 2.10
1606 4683 1.227999 CGTGCAGGACCGACAATTGT 61.228 55.000 11.78 11.78 0.00 2.71
1614 4691 3.345808 CCAACACGTGCAGGACCG 61.346 66.667 17.22 2.71 0.00 4.79
1632 4709 1.490490 TGGTCCACAAGAGTGCTCTTT 59.510 47.619 11.38 2.22 46.95 2.52
1847 4926 0.395686 TTCAGAAGAGTGCAGCAGCT 59.604 50.000 1.76 0.00 42.74 4.24
2157 5236 0.252239 TCTGCCTGTGCTCCCTAAGA 60.252 55.000 0.00 0.00 38.71 2.10
2190 5269 5.158141 TCCTCAGCAGGATATTCACCTAAT 58.842 41.667 0.00 0.00 44.75 1.73
2226 5305 4.502962 GTTTGGCCAAGCTGCAAATATAA 58.497 39.130 23.72 0.00 0.00 0.98
2235 5314 2.336088 CACCGTTTGGCCAAGCTG 59.664 61.111 27.08 23.36 39.70 4.24
2248 5327 1.592400 TACTCAGAACCTCGCCACCG 61.592 60.000 0.00 0.00 0.00 4.94
2251 5330 1.557099 ACATACTCAGAACCTCGCCA 58.443 50.000 0.00 0.00 0.00 5.69
2269 5348 5.062308 CACTACATCGCAGAAGGAAGTTAAC 59.938 44.000 0.00 0.00 43.58 2.01
2274 5353 3.119316 AGTCACTACATCGCAGAAGGAAG 60.119 47.826 0.00 0.00 43.58 3.46
2339 5418 3.007398 GCCGGATAGAAGATCCATCACTT 59.993 47.826 5.05 0.00 38.08 3.16
2376 5455 1.133294 ACCTCAAATTTTCCCCGTGGT 60.133 47.619 0.00 0.00 0.00 4.16
2484 5565 3.375299 CCAAAGAGTGCTTCCCTTATTCG 59.625 47.826 0.00 0.00 31.82 3.34
2492 5573 1.856265 CGGTGCCAAAGAGTGCTTCC 61.856 60.000 0.00 0.00 31.82 3.46
2526 5607 4.159879 AGAAGATAACCCACCAGTAACTCG 59.840 45.833 0.00 0.00 0.00 4.18
2543 5624 4.762251 GCCTTGGTTTGTAGACAAGAAGAT 59.238 41.667 5.31 0.00 43.13 2.40
2556 5638 1.915141 ATCTGGTGAGCCTTGGTTTG 58.085 50.000 0.00 0.00 35.27 2.93
2557 5639 2.242043 CAATCTGGTGAGCCTTGGTTT 58.758 47.619 0.00 0.00 35.27 3.27
2558 5640 1.548582 CCAATCTGGTGAGCCTTGGTT 60.549 52.381 0.00 0.00 31.70 3.67
2639 5747 8.555896 TGGGTATCAGTTACAATACTCCATAA 57.444 34.615 5.67 0.00 30.45 1.90
2658 5768 2.455163 AGGAGCCCTATGTACTGGGTAT 59.545 50.000 16.55 8.86 45.06 2.73
2696 5895 4.444449 GGATATTCCCTTTTGCTCCTACGT 60.444 45.833 0.00 0.00 0.00 3.57
2697 5896 4.065789 GGATATTCCCTTTTGCTCCTACG 58.934 47.826 0.00 0.00 0.00 3.51
2711 5910 8.146412 AGTACACAAGTTATTACGGGATATTCC 58.854 37.037 0.00 0.00 35.23 3.01
2712 5911 9.189723 GAGTACACAAGTTATTACGGGATATTC 57.810 37.037 0.00 0.00 0.00 1.75
2713 5912 8.921205 AGAGTACACAAGTTATTACGGGATATT 58.079 33.333 0.00 0.00 0.00 1.28
2714 5913 8.474710 AGAGTACACAAGTTATTACGGGATAT 57.525 34.615 0.00 0.00 0.00 1.63
2715 5914 7.886629 AGAGTACACAAGTTATTACGGGATA 57.113 36.000 0.00 0.00 0.00 2.59
2716 5915 6.786967 AGAGTACACAAGTTATTACGGGAT 57.213 37.500 0.00 0.00 0.00 3.85
2717 5916 6.209192 TGAAGAGTACACAAGTTATTACGGGA 59.791 38.462 0.00 0.00 0.00 5.14
2718 5917 6.392354 TGAAGAGTACACAAGTTATTACGGG 58.608 40.000 0.00 0.00 0.00 5.28
2719 5918 7.974501 AGATGAAGAGTACACAAGTTATTACGG 59.025 37.037 0.00 0.00 0.00 4.02
2720 5919 8.799091 CAGATGAAGAGTACACAAGTTATTACG 58.201 37.037 0.00 0.00 0.00 3.18
2760 5959 9.979578 CAGAAGAAATATCAGCTACTTAGTCAT 57.020 33.333 0.00 0.00 0.00 3.06
2811 6013 8.195436 TGTTAGTACTAGCAAGATATGTCAACC 58.805 37.037 16.15 0.00 0.00 3.77
2924 6226 2.185310 GATGTTGAGGACGCCCAGGT 62.185 60.000 0.00 0.00 33.88 4.00
3039 6348 2.660094 CGTGTGCGTGATGTCTTCTTTG 60.660 50.000 0.00 0.00 0.00 2.77
3040 6349 1.526887 CGTGTGCGTGATGTCTTCTTT 59.473 47.619 0.00 0.00 0.00 2.52
3054 6363 2.807045 CTCCGCAGACTCGTGTGC 60.807 66.667 8.92 8.92 45.19 4.57
3067 6376 1.439679 GTTGCCTAACCTGAACTCCG 58.560 55.000 0.00 0.00 0.00 4.63
3127 6437 1.012841 GCTCCAGCTATCTGTGTTGC 58.987 55.000 0.00 0.00 38.66 4.17
3160 6470 3.873361 TCAGTCTGTTCTTTCAGCTGTTG 59.127 43.478 14.67 5.36 38.89 3.33
3179 6489 1.268032 GCAGTGGTTGTGTTCGTTCAG 60.268 52.381 0.00 0.00 0.00 3.02
3185 6495 1.408702 ACAATGGCAGTGGTTGTGTTC 59.591 47.619 19.96 0.00 34.98 3.18
3205 6517 5.184864 TCTTCTGTTCTTTTCAAAACCTGCA 59.815 36.000 0.00 0.00 0.00 4.41
3454 7278 3.486383 AGCTAGATGGTACTCTGAGCTC 58.514 50.000 6.82 6.82 32.00 4.09


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

AutoCloner maintained by Alex Coulton.