Multiple sequence alignment - TraesCS2D01G356200

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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 TraesCS2D01G356200 chr2D 100.000 3833 0 0 1 3833 458665787 458669619 0.000000e+00 7079.0
1 TraesCS2D01G356200 chr2A 93.342 3154 135 43 475 3612 601848017 601851111 0.000000e+00 4591.0
2 TraesCS2D01G356200 chr2A 94.456 469 24 2 3 470 601847393 601847860 0.000000e+00 721.0
3 TraesCS2D01G356200 chr2A 87.778 180 15 1 3661 3833 601987694 601987873 1.810000e-48 204.0
4 TraesCS2D01G356200 chr2B 89.227 1643 103 34 2137 3753 539476527 539478121 0.000000e+00 1986.0
5 TraesCS2D01G356200 chr2B 94.527 1206 58 7 826 2030 539475285 539476483 0.000000e+00 1855.0
6 TraesCS2D01G356200 chr2B 91.289 287 10 4 1 274 539474247 539474531 1.010000e-100 377.0
7 TraesCS2D01G356200 chr2B 100.000 29 0 0 3805 3833 539478122 539478150 2.000000e-03 54.7


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 TraesCS2D01G356200 chr2D 458665787 458669619 3832 False 7079.000 7079 100.00000 1 3833 1 chr2D.!!$F1 3832
1 TraesCS2D01G356200 chr2A 601847393 601851111 3718 False 2656.000 4591 93.89900 3 3612 2 chr2A.!!$F2 3609
2 TraesCS2D01G356200 chr2B 539474247 539478150 3903 False 1068.175 1986 93.76075 1 3833 4 chr2B.!!$F1 3832

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
361 395 0.673644 CTCACTGTGCCGGTAAAGGG 60.674 60.0 14.85 10.53 0.00 3.95 F
1395 1917 1.037493 TGGCTACAATACTCGGCGAT 58.963 50.0 11.27 3.37 0.00 4.58 F
1815 2337 0.318441 GCACTGGTGTCACTGCTCTA 59.682 55.0 8.11 0.00 32.42 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 2027 0.912486 GCTGGCCTTCTCCTCCTTTA 59.088 55.0 3.32 0.0 0.00 1.85 R
2787 3325 0.601558 GTCTGAACGACCCACTAGCA 59.398 55.0 0.00 0.0 36.62 3.49 R
3763 4326 0.108424 CCACACTGGAGACTAGCTGC 60.108 60.0 0.00 0.0 40.96 5.25 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
24 25 1.132453 GTAGGCCAGAATTGGTTTCGC 59.868 52.381 5.01 0.00 46.80 4.70
42 43 2.701006 CGTTGGACCGCGCAATAG 59.299 61.111 8.75 0.00 0.00 1.73
140 146 6.814954 AAGCAGATCTTCCTACCTGATTTA 57.185 37.500 0.00 0.00 32.17 1.40
165 171 3.329225 TGATGTTGGATATGCGGGGAATA 59.671 43.478 0.00 0.00 0.00 1.75
205 211 9.237846 GTTTGTAGAGAGAAATTTGGTGAAAAG 57.762 33.333 0.00 0.00 0.00 2.27
318 352 5.011635 TGCAAATCACTTCAGTACTGTAGGA 59.988 40.000 27.08 21.59 33.07 2.94
322 356 9.653287 CAAATCACTTCAGTACTGTAGGATTAA 57.347 33.333 26.99 14.39 32.55 1.40
329 363 9.307121 CTTCAGTACTGTAGGATTAACAGAATG 57.693 37.037 21.99 5.75 45.89 2.67
361 395 0.673644 CTCACTGTGCCGGTAAAGGG 60.674 60.000 14.85 10.53 0.00 3.95
387 421 8.702163 ATGAGCATTTTAAATAGGGAAAAACG 57.298 30.769 0.00 0.00 0.00 3.60
393 427 6.844097 TTTAAATAGGGAAAAACGATGGCT 57.156 33.333 0.00 0.00 0.00 4.75
406 440 1.402968 CGATGGCTGCTGCTAATTTGT 59.597 47.619 15.64 0.00 39.59 2.83
426 460 9.612066 AATTTGTTTGTCACCAACATAAAGAAT 57.388 25.926 0.00 0.00 37.82 2.40
470 504 7.864108 TCTTGTCATAATGTAGGGTGATTTG 57.136 36.000 0.00 0.00 0.00 2.32
472 506 7.552687 TCTTGTCATAATGTAGGGTGATTTGTC 59.447 37.037 0.00 0.00 0.00 3.18
473 507 6.716284 TGTCATAATGTAGGGTGATTTGTCA 58.284 36.000 0.00 0.00 0.00 3.58
537 724 7.051623 TCGCCCTAAACAAATGTTGATAGTAT 58.948 34.615 0.00 0.00 38.44 2.12
538 725 8.205512 TCGCCCTAAACAAATGTTGATAGTATA 58.794 33.333 0.00 0.00 38.44 1.47
539 726 8.280497 CGCCCTAAACAAATGTTGATAGTATAC 58.720 37.037 0.00 0.00 38.44 1.47
642 837 7.151976 ACACTATTTGGCTTATTGTGAAAACC 58.848 34.615 15.96 0.00 34.36 3.27
696 891 3.323751 GCAAGAAACCAGATTTGCCAT 57.676 42.857 0.00 0.00 39.88 4.40
790 1311 3.829948 CATCACCAGACAAATGAACTGC 58.170 45.455 0.00 0.00 0.00 4.40
930 1452 6.926313 AGTTCTCTTCTGAGTAATGTGGTAC 58.074 40.000 0.00 0.00 40.98 3.34
952 1474 6.169557 ACCTTGATGAATAAGCCGTATACA 57.830 37.500 3.32 0.00 0.00 2.29
1206 1728 6.585702 CGTTCAATGGAATGCTTAACAATTCA 59.414 34.615 7.38 0.00 35.05 2.57
1224 1746 3.019799 TCACCCACAAACCTTTTGCTA 57.980 42.857 0.00 0.00 0.00 3.49
1314 1836 3.567164 CACTGGATGAGGATAATGCAACC 59.433 47.826 0.00 0.00 0.00 3.77
1395 1917 1.037493 TGGCTACAATACTCGGCGAT 58.963 50.000 11.27 3.37 0.00 4.58
1505 2027 6.655078 AATGACACTTTATCCAAGCAAACT 57.345 33.333 0.00 0.00 35.65 2.66
1707 2229 6.488006 CAGTGAATTTGAAGAAGAGGAAAGGA 59.512 38.462 0.00 0.00 0.00 3.36
1749 2271 4.905429 TCACATTTGCTGAAGCCTTAGTA 58.095 39.130 0.00 0.00 41.18 1.82
1815 2337 0.318441 GCACTGGTGTCACTGCTCTA 59.682 55.000 8.11 0.00 32.42 2.43
1881 2403 3.782889 ACTGTTTTGTTGTGCCTCTTC 57.217 42.857 0.00 0.00 0.00 2.87
1935 2457 9.790344 CTTGGTGGATCTATCTCTGAATATTTT 57.210 33.333 0.00 0.00 0.00 1.82
1973 2495 7.713507 TCTCTTTTAACTAGTTTGCAGCAACTA 59.286 33.333 14.49 11.51 0.00 2.24
1976 2498 8.795786 TTTTAACTAGTTTGCAGCAACTATTG 57.204 30.769 14.49 5.20 0.00 1.90
1977 2499 7.504924 TTAACTAGTTTGCAGCAACTATTGT 57.495 32.000 14.49 5.76 0.00 2.71
1978 2500 6.391227 AACTAGTTTGCAGCAACTATTGTT 57.609 33.333 7.54 10.67 36.75 2.83
1979 2501 6.391227 ACTAGTTTGCAGCAACTATTGTTT 57.609 33.333 7.54 0.00 33.52 2.83
1980 2502 6.438763 ACTAGTTTGCAGCAACTATTGTTTC 58.561 36.000 7.54 0.00 33.52 2.78
1997 2519 6.748333 TTGTTTCTTCTAAGGATGCATCAG 57.252 37.500 27.25 16.40 0.00 2.90
2008 2530 3.389329 AGGATGCATCAGAAGGATTACGT 59.611 43.478 27.25 0.00 32.57 3.57
2010 2532 4.212214 GGATGCATCAGAAGGATTACGTTC 59.788 45.833 27.25 1.07 40.03 3.95
2101 2623 7.839611 GTTCACAAGAATTAAGCAGCAGCTAAT 60.840 37.037 3.18 2.26 42.83 1.73
2148 2679 7.320443 TCACTCCATGTTAAATCACTAATGC 57.680 36.000 0.00 0.00 0.00 3.56
2149 2680 7.112122 TCACTCCATGTTAAATCACTAATGCT 58.888 34.615 0.00 0.00 0.00 3.79
2150 2681 7.280876 TCACTCCATGTTAAATCACTAATGCTC 59.719 37.037 0.00 0.00 0.00 4.26
2151 2682 7.066163 CACTCCATGTTAAATCACTAATGCTCA 59.934 37.037 0.00 0.00 0.00 4.26
2152 2683 7.776969 ACTCCATGTTAAATCACTAATGCTCAT 59.223 33.333 0.00 0.00 0.00 2.90
2153 2684 7.933396 TCCATGTTAAATCACTAATGCTCATG 58.067 34.615 0.00 0.00 0.00 3.07
2154 2685 6.639686 CCATGTTAAATCACTAATGCTCATGC 59.360 38.462 0.00 0.00 40.20 4.06
2170 2701 7.019774 TGCTCATGCATTTCTGTTAACTATC 57.980 36.000 7.22 0.00 45.31 2.08
2171 2702 6.132056 GCTCATGCATTTCTGTTAACTATCG 58.868 40.000 7.22 0.00 39.41 2.92
2172 2703 6.603237 TCATGCATTTCTGTTAACTATCGG 57.397 37.500 7.22 0.00 0.00 4.18
2173 2704 6.112734 TCATGCATTTCTGTTAACTATCGGT 58.887 36.000 7.22 0.00 0.00 4.69
2174 2705 7.269316 TCATGCATTTCTGTTAACTATCGGTA 58.731 34.615 7.22 0.00 0.00 4.02
2175 2706 7.766738 TCATGCATTTCTGTTAACTATCGGTAA 59.233 33.333 7.22 0.00 0.00 2.85
2193 2724 4.499357 CGGTAACCCTTCAGACATACTAGC 60.499 50.000 0.00 0.00 0.00 3.42
2199 2730 4.437239 CCTTCAGACATACTAGCTGTTGG 58.563 47.826 0.00 0.00 0.00 3.77
2243 2775 5.873712 TGCATCTGTTTGAACACACATTTTT 59.126 32.000 0.00 0.00 34.70 1.94
2248 2780 5.541845 TGTTTGAACACACATTTTTCCACA 58.458 33.333 0.00 0.00 33.17 4.17
2314 2850 9.766277 GAAATAATTTGAGTTGCTACTTCTGAG 57.234 33.333 1.43 0.00 33.84 3.35
2430 2968 2.048503 CTCCTTTTCGCGACCGGT 60.049 61.111 9.15 6.92 34.56 5.28
2542 3080 1.460699 GGGCTCAAGGACTTTGGGT 59.539 57.895 0.00 0.00 39.60 4.51
2604 3142 1.064825 TCTTTTTCTCGGCCCTCCTT 58.935 50.000 0.00 0.00 0.00 3.36
2784 3322 3.133901 TCAAGCCGGTTTATCAGATGCTA 59.866 43.478 2.14 0.00 0.00 3.49
2787 3325 5.683876 AGCCGGTTTATCAGATGCTATAT 57.316 39.130 1.90 0.00 0.00 0.86
2790 3328 5.423015 CCGGTTTATCAGATGCTATATGCT 58.577 41.667 0.00 0.00 43.37 3.79
2793 3331 7.261325 CGGTTTATCAGATGCTATATGCTAGT 58.739 38.462 0.00 0.00 43.37 2.57
2854 3395 5.366477 TGATGGAGTAAGTGGCATCAATAGA 59.634 40.000 0.00 0.00 0.00 1.98
2858 3400 6.599244 TGGAGTAAGTGGCATCAATAGAAAAG 59.401 38.462 0.00 0.00 0.00 2.27
3014 3568 6.014669 GGTATTGGAGCATATGAGAGAGTTCT 60.015 42.308 6.97 0.00 36.01 3.01
3035 3589 9.300681 AGTTCTCTTGATTCCATAATTTGTTCA 57.699 29.630 0.00 0.00 0.00 3.18
3058 3615 7.214381 TCATGTTGTGTAAGGTATATACAGCC 58.786 38.462 14.70 0.00 34.14 4.85
3060 3617 5.360429 TGTTGTGTAAGGTATATACAGCCGA 59.640 40.000 14.70 0.00 34.14 5.54
3198 3756 1.303236 TGCATTCCCCTTCGTGGTG 60.303 57.895 0.00 0.00 0.00 4.17
3219 3777 7.225145 GTGGTGCCACGAGTTTATTATGTATTA 59.775 37.037 5.53 0.00 37.19 0.98
3254 3812 8.152898 TCTCAGCAATAGCATCTTGTATTGTAT 58.847 33.333 0.00 0.00 45.49 2.29
3255 3813 8.315391 TCAGCAATAGCATCTTGTATTGTATC 57.685 34.615 0.00 0.00 45.49 2.24
3259 3817 8.013947 GCAATAGCATCTTGTATTGTATCTGTG 58.986 37.037 0.00 0.00 38.42 3.66
3264 3822 9.049523 AGCATCTTGTATTGTATCTGTGTATTG 57.950 33.333 0.00 0.00 0.00 1.90
3270 3828 8.487313 TGTATTGTATCTGTGTATTGTGAACC 57.513 34.615 0.00 0.00 0.00 3.62
3446 4008 5.232463 TGGTATCCGTTGTTTCTTACAGTC 58.768 41.667 0.00 0.00 38.19 3.51
3528 4091 4.899239 CGGCCGGAGTGGAGATGC 62.899 72.222 20.10 0.00 42.00 3.91
3530 4093 3.838271 GCCGGAGTGGAGATGCGA 61.838 66.667 5.05 0.00 42.00 5.10
3561 4124 4.151867 CGGTGCTCTCTTGTTTTTAGTACC 59.848 45.833 0.00 0.00 38.94 3.34
3562 4125 5.306394 GGTGCTCTCTTGTTTTTAGTACCT 58.694 41.667 0.00 0.00 39.16 3.08
3563 4126 6.461640 GGTGCTCTCTTGTTTTTAGTACCTA 58.538 40.000 0.00 0.00 39.16 3.08
3566 4129 7.116519 GTGCTCTCTTGTTTTTAGTACCTACTG 59.883 40.741 0.00 0.00 37.10 2.74
3567 4130 7.153315 GCTCTCTTGTTTTTAGTACCTACTGT 58.847 38.462 0.00 0.00 37.10 3.55
3568 4131 8.302438 GCTCTCTTGTTTTTAGTACCTACTGTA 58.698 37.037 0.00 0.00 37.10 2.74
3589 4152 5.359576 TGTACTTTGCAATCCAAAACAGAGT 59.640 36.000 0.00 0.00 42.51 3.24
3628 4191 0.858583 GTGCGTTGCAATCCAAAACC 59.141 50.000 0.59 0.00 41.47 3.27
3633 4196 3.452474 CGTTGCAATCCAAAACCAAGAA 58.548 40.909 0.59 0.00 34.68 2.52
3634 4197 3.490526 CGTTGCAATCCAAAACCAAGAAG 59.509 43.478 0.59 0.00 34.68 2.85
3635 4198 3.749665 TGCAATCCAAAACCAAGAAGG 57.250 42.857 0.00 0.00 45.67 3.46
3636 4199 2.368221 TGCAATCCAAAACCAAGAAGGG 59.632 45.455 0.00 0.00 43.89 3.95
3637 4200 2.289631 GCAATCCAAAACCAAGAAGGGG 60.290 50.000 0.00 0.00 43.89 4.79
3638 4201 3.238597 CAATCCAAAACCAAGAAGGGGA 58.761 45.455 0.00 0.00 43.89 4.81
3639 4202 3.628832 ATCCAAAACCAAGAAGGGGAA 57.371 42.857 0.00 0.00 43.89 3.97
3640 4203 3.406512 TCCAAAACCAAGAAGGGGAAA 57.593 42.857 0.00 0.00 43.89 3.13
3641 4204 3.035363 TCCAAAACCAAGAAGGGGAAAC 58.965 45.455 0.00 0.00 43.89 2.78
3642 4205 3.038280 CCAAAACCAAGAAGGGGAAACT 58.962 45.455 0.00 0.00 43.89 2.66
3643 4206 3.181466 CCAAAACCAAGAAGGGGAAACTG 60.181 47.826 0.00 0.00 43.89 3.16
3644 4207 3.680777 AAACCAAGAAGGGGAAACTGA 57.319 42.857 0.00 0.00 43.89 3.41
3645 4208 3.680777 AACCAAGAAGGGGAAACTGAA 57.319 42.857 0.00 0.00 43.89 3.02
3646 4209 3.680777 ACCAAGAAGGGGAAACTGAAA 57.319 42.857 0.00 0.00 43.89 2.69
3647 4210 3.566351 ACCAAGAAGGGGAAACTGAAAG 58.434 45.455 0.00 0.00 43.89 2.62
3697 4260 5.867903 AGCACAGCTAAGATAGACAAGAT 57.132 39.130 0.00 0.00 36.99 2.40
3712 4275 8.868522 ATAGACAAGATCAAAGTTCCATCAAA 57.131 30.769 0.00 0.00 0.00 2.69
3775 4338 1.435515 CGACCAGCAGCTAGTCTCC 59.564 63.158 17.54 0.00 0.00 3.71
3776 4339 1.315981 CGACCAGCAGCTAGTCTCCA 61.316 60.000 17.54 0.00 0.00 3.86
3777 4340 0.459489 GACCAGCAGCTAGTCTCCAG 59.541 60.000 13.26 0.00 0.00 3.86
3778 4341 0.252012 ACCAGCAGCTAGTCTCCAGT 60.252 55.000 0.00 0.00 0.00 4.00
3779 4342 0.175302 CCAGCAGCTAGTCTCCAGTG 59.825 60.000 0.00 0.00 0.00 3.66
3780 4343 0.894141 CAGCAGCTAGTCTCCAGTGT 59.106 55.000 0.00 0.00 0.00 3.55
3781 4344 0.894141 AGCAGCTAGTCTCCAGTGTG 59.106 55.000 0.00 0.00 0.00 3.82
3782 4345 0.108424 GCAGCTAGTCTCCAGTGTGG 60.108 60.000 0.00 0.00 39.43 4.17
3783 4346 1.550327 CAGCTAGTCTCCAGTGTGGA 58.450 55.000 0.00 0.00 45.98 4.02
3784 4347 1.203523 CAGCTAGTCTCCAGTGTGGAC 59.796 57.143 0.00 5.03 42.67 4.02
3785 4348 0.171455 GCTAGTCTCCAGTGTGGACG 59.829 60.000 0.00 0.00 42.67 4.79
3786 4349 0.171455 CTAGTCTCCAGTGTGGACGC 59.829 60.000 0.00 0.00 42.67 5.19
3787 4350 0.251209 TAGTCTCCAGTGTGGACGCT 60.251 55.000 0.00 0.00 42.67 5.07
3793 4356 3.640407 AGTGTGGACGCTGGGCAT 61.640 61.111 0.00 0.00 35.04 4.40
3794 4357 2.267642 GTGTGGACGCTGGGCATA 59.732 61.111 0.00 0.00 0.00 3.14
3795 4358 1.815421 GTGTGGACGCTGGGCATAG 60.815 63.158 0.00 0.00 0.00 2.23
3796 4359 2.203070 GTGGACGCTGGGCATAGG 60.203 66.667 0.00 0.00 0.00 2.57
3797 4360 2.364973 TGGACGCTGGGCATAGGA 60.365 61.111 0.00 0.00 0.00 2.94
3798 4361 1.992834 TGGACGCTGGGCATAGGAA 60.993 57.895 0.00 0.00 0.00 3.36
3799 4362 1.523938 GGACGCTGGGCATAGGAAC 60.524 63.158 0.00 0.00 0.00 3.62
3800 4363 1.220749 GACGCTGGGCATAGGAACA 59.779 57.895 0.00 0.00 0.00 3.18
3801 4364 1.078426 ACGCTGGGCATAGGAACAC 60.078 57.895 0.00 0.00 0.00 3.32
3802 4365 1.078497 CGCTGGGCATAGGAACACA 60.078 57.895 0.00 0.00 0.00 3.72
3803 4366 0.464373 CGCTGGGCATAGGAACACAT 60.464 55.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.808958 CTATTGCGCGGTCCAACGG 61.809 63.158 8.83 0.00 0.00 4.44
42 43 6.331369 TGAACAGAATTGAAAACCCAGATC 57.669 37.500 0.00 0.00 0.00 2.75
140 146 1.202806 CCCGCATATCCAACATCACCT 60.203 52.381 0.00 0.00 0.00 4.00
165 171 7.231317 TCTCTCTACAAACTGGCATTGAAAAAT 59.769 33.333 7.77 0.00 0.00 1.82
284 298 3.071874 AGTGATTTGCAGATTTCCCGA 57.928 42.857 0.00 0.00 0.00 5.14
322 356 8.559536 CAGTGAGTGTAAATACAAACATTCTGT 58.440 33.333 0.00 0.00 38.04 3.41
341 375 0.034896 CCTTTACCGGCACAGTGAGT 59.965 55.000 4.15 0.46 0.00 3.41
346 380 0.251916 TCATCCCTTTACCGGCACAG 59.748 55.000 0.00 0.00 0.00 3.66
361 395 8.807581 CGTTTTTCCCTATTTAAAATGCTCATC 58.192 33.333 0.00 0.00 0.00 2.92
387 421 3.515330 AACAAATTAGCAGCAGCCATC 57.485 42.857 0.00 0.00 43.56 3.51
393 427 3.382865 TGGTGACAAACAAATTAGCAGCA 59.617 39.130 0.00 0.00 37.44 4.41
459 493 6.126409 AGTTCTTGTTTGACAAATCACCCTA 58.874 36.000 3.49 0.00 37.69 3.53
470 504 8.290325 CCTTATGTCCTTTAGTTCTTGTTTGAC 58.710 37.037 0.00 0.00 0.00 3.18
472 506 8.076178 CACCTTATGTCCTTTAGTTCTTGTTTG 58.924 37.037 0.00 0.00 0.00 2.93
473 507 7.255486 GCACCTTATGTCCTTTAGTTCTTGTTT 60.255 37.037 0.00 0.00 0.00 2.83
514 701 9.116067 TGTATACTATCAACATTTGTTTAGGGC 57.884 33.333 4.17 0.00 35.83 5.19
537 724 8.692710 CAAAGGGTGAAGTGTCTATATAGTGTA 58.307 37.037 9.58 0.00 0.00 2.90
538 725 7.556844 CAAAGGGTGAAGTGTCTATATAGTGT 58.443 38.462 9.58 0.00 0.00 3.55
539 726 6.480320 GCAAAGGGTGAAGTGTCTATATAGTG 59.520 42.308 9.58 0.00 0.00 2.74
558 745 2.880890 AGCACTCACTGTTAAGCAAAGG 59.119 45.455 0.00 0.00 0.00 3.11
696 891 5.132502 CCCATCATGGCTCAGTAAAATGTA 58.867 41.667 0.00 0.00 35.79 2.29
752 947 5.067283 TGGTGATGCATCAATCAGATTTGAG 59.933 40.000 30.24 0.00 38.90 3.02
930 1452 7.672983 ATTGTATACGGCTTATTCATCAAGG 57.327 36.000 0.00 0.00 0.00 3.61
1206 1728 3.494223 GCAATAGCAAAAGGTTTGTGGGT 60.494 43.478 2.92 0.00 41.58 4.51
1224 1746 1.197812 GGATCCCCAAAGCAAGCAAT 58.802 50.000 0.00 0.00 0.00 3.56
1314 1836 4.027755 ACGAAGTGGCTGTGTTCG 57.972 55.556 2.35 2.35 46.64 3.95
1395 1917 2.029649 AGTCGCGCTTAGGTTCAAAGTA 60.030 45.455 5.56 0.00 0.00 2.24
1505 2027 0.912486 GCTGGCCTTCTCCTCCTTTA 59.088 55.000 3.32 0.00 0.00 1.85
1707 2229 1.657804 AATCGTCCCCTCTTCTTGGT 58.342 50.000 0.00 0.00 0.00 3.67
1749 2271 3.245052 ACAGTAGCCAGAAATCTGCCTTT 60.245 43.478 4.87 0.00 42.47 3.11
1815 2337 3.330701 TCCCAATCTGAGCTAGGTTGTTT 59.669 43.478 12.33 0.00 44.45 2.83
1881 2403 1.480205 CAACAAAGTTGCAGAAGCCG 58.520 50.000 0.00 0.00 41.13 5.52
1935 2457 9.086758 ACTAGTTAAAAGAGAGCTTACCTTACA 57.913 33.333 0.00 0.00 32.98 2.41
1943 2465 6.293680 GCTGCAAACTAGTTAAAAGAGAGCTT 60.294 38.462 8.92 0.00 35.37 3.74
1946 2468 6.545504 TGCTGCAAACTAGTTAAAAGAGAG 57.454 37.500 8.92 0.19 0.00 3.20
1973 2495 7.114754 TCTGATGCATCCTTAGAAGAAACAAT 58.885 34.615 23.67 0.00 0.00 2.71
1976 2498 6.038050 CCTTCTGATGCATCCTTAGAAGAAAC 59.962 42.308 34.83 10.36 44.32 2.78
1977 2499 6.070021 TCCTTCTGATGCATCCTTAGAAGAAA 60.070 38.462 34.83 25.80 44.32 2.52
1978 2500 5.426509 TCCTTCTGATGCATCCTTAGAAGAA 59.573 40.000 34.83 27.33 44.32 2.52
1979 2501 4.964897 TCCTTCTGATGCATCCTTAGAAGA 59.035 41.667 34.83 24.88 44.32 2.87
1980 2502 5.287674 TCCTTCTGATGCATCCTTAGAAG 57.712 43.478 30.47 30.47 42.34 2.85
1997 2519 4.267928 CCAACTCATCGAACGTAATCCTTC 59.732 45.833 0.00 0.00 0.00 3.46
2008 2530 4.819105 ACAGATAACCCAACTCATCGAA 57.181 40.909 0.00 0.00 0.00 3.71
2010 2532 4.503910 TGAACAGATAACCCAACTCATCG 58.496 43.478 0.00 0.00 0.00 3.84
2147 2678 6.132056 CGATAGTTAACAGAAATGCATGAGC 58.868 40.000 8.61 0.00 42.57 4.26
2148 2679 6.258727 ACCGATAGTTAACAGAAATGCATGAG 59.741 38.462 8.61 0.00 0.00 2.90
2149 2680 6.112734 ACCGATAGTTAACAGAAATGCATGA 58.887 36.000 8.61 0.00 0.00 3.07
2150 2681 6.363577 ACCGATAGTTAACAGAAATGCATG 57.636 37.500 8.61 0.00 0.00 4.06
2151 2682 7.012044 GGTTACCGATAGTTAACAGAAATGCAT 59.988 37.037 8.61 0.00 0.00 3.96
2152 2683 6.314400 GGTTACCGATAGTTAACAGAAATGCA 59.686 38.462 8.61 0.00 0.00 3.96
2153 2684 6.238293 GGGTTACCGATAGTTAACAGAAATGC 60.238 42.308 8.61 0.00 0.00 3.56
2154 2685 7.046033 AGGGTTACCGATAGTTAACAGAAATG 58.954 38.462 8.61 0.00 43.47 2.32
2155 2686 7.191593 AGGGTTACCGATAGTTAACAGAAAT 57.808 36.000 8.61 0.00 43.47 2.17
2156 2687 6.610075 AGGGTTACCGATAGTTAACAGAAA 57.390 37.500 8.61 0.00 43.47 2.52
2157 2688 6.211184 TGAAGGGTTACCGATAGTTAACAGAA 59.789 38.462 8.61 0.00 43.47 3.02
2158 2689 5.716228 TGAAGGGTTACCGATAGTTAACAGA 59.284 40.000 8.61 0.00 43.47 3.41
2159 2690 5.969423 TGAAGGGTTACCGATAGTTAACAG 58.031 41.667 8.61 0.00 43.47 3.16
2160 2691 5.716228 TCTGAAGGGTTACCGATAGTTAACA 59.284 40.000 8.61 0.00 43.47 2.41
2161 2692 6.038985 GTCTGAAGGGTTACCGATAGTTAAC 58.961 44.000 0.00 0.00 43.47 2.01
2162 2693 5.716228 TGTCTGAAGGGTTACCGATAGTTAA 59.284 40.000 0.00 0.00 43.47 2.01
2163 2694 5.263599 TGTCTGAAGGGTTACCGATAGTTA 58.736 41.667 0.00 0.00 43.47 2.24
2164 2695 4.091549 TGTCTGAAGGGTTACCGATAGTT 58.908 43.478 0.00 0.00 43.47 2.24
2165 2696 3.705051 TGTCTGAAGGGTTACCGATAGT 58.295 45.455 0.00 0.00 43.47 2.12
2166 2697 4.939052 ATGTCTGAAGGGTTACCGATAG 57.061 45.455 0.00 0.00 43.47 2.08
2167 2698 5.452255 AGTATGTCTGAAGGGTTACCGATA 58.548 41.667 0.00 0.00 43.47 2.92
2168 2699 4.287552 AGTATGTCTGAAGGGTTACCGAT 58.712 43.478 0.00 0.00 43.47 4.18
2169 2700 3.705051 AGTATGTCTGAAGGGTTACCGA 58.295 45.455 0.00 0.00 43.47 4.69
2170 2701 4.499357 GCTAGTATGTCTGAAGGGTTACCG 60.499 50.000 0.00 0.00 43.47 4.02
2171 2702 4.650131 AGCTAGTATGTCTGAAGGGTTACC 59.350 45.833 0.00 0.00 0.00 2.85
2172 2703 5.127356 ACAGCTAGTATGTCTGAAGGGTTAC 59.873 44.000 1.83 0.00 0.00 2.50
2173 2704 5.269991 ACAGCTAGTATGTCTGAAGGGTTA 58.730 41.667 1.83 0.00 0.00 2.85
2174 2705 4.097418 ACAGCTAGTATGTCTGAAGGGTT 58.903 43.478 1.83 0.00 0.00 4.11
2175 2706 3.714144 ACAGCTAGTATGTCTGAAGGGT 58.286 45.455 1.83 0.00 0.00 4.34
2193 2724 5.702670 ACATACAAGACAATGAGACCAACAG 59.297 40.000 0.00 0.00 0.00 3.16
2199 2730 6.000891 TGCAAACATACAAGACAATGAGAC 57.999 37.500 0.00 0.00 0.00 3.36
2341 2879 5.012239 AGGAAGCATTCTTGTTCTGCAATA 58.988 37.500 0.00 0.00 46.56 1.90
2430 2968 1.341089 ACGTAGATCAGGCTGTGGAGA 60.341 52.381 15.27 0.00 0.00 3.71
2542 3080 5.124297 CCATGAGCATGAAGTTGTACATCAA 59.876 40.000 11.84 0.00 41.20 2.57
2784 3322 3.068307 GTCTGAACGACCCACTAGCATAT 59.932 47.826 0.00 0.00 36.62 1.78
2787 3325 0.601558 GTCTGAACGACCCACTAGCA 59.398 55.000 0.00 0.00 36.62 3.49
2790 3328 0.963962 GGTGTCTGAACGACCCACTA 59.036 55.000 0.00 0.00 42.13 2.74
2793 3331 1.458777 AGGGTGTCTGAACGACCCA 60.459 57.895 18.25 0.00 43.57 4.51
2854 3395 7.042797 TCTTTTCTCATACTTGCAAGCTTTT 57.957 32.000 26.27 9.43 0.00 2.27
2858 3400 7.141363 TCTTTTCTTTTCTCATACTTGCAAGC 58.859 34.615 26.27 0.00 0.00 4.01
2945 3491 3.322828 ACAACCGTGGGATAATATACGCT 59.677 43.478 0.00 0.00 35.39 5.07
3014 3568 9.642327 CAACATGAACAAATTATGGAATCAAGA 57.358 29.630 0.00 0.00 0.00 3.02
3015 3569 9.426837 ACAACATGAACAAATTATGGAATCAAG 57.573 29.630 0.00 0.00 0.00 3.02
3018 3572 8.761575 ACACAACATGAACAAATTATGGAATC 57.238 30.769 0.00 0.00 0.00 2.52
3035 3589 6.041182 TCGGCTGTATATACCTTACACAACAT 59.959 38.462 10.38 0.00 0.00 2.71
3122 3680 4.111577 TCCCTGGTCTCCTGATTTACAAT 58.888 43.478 0.00 0.00 0.00 2.71
3179 3737 1.002134 ACCACGAAGGGGAATGCAG 60.002 57.895 0.00 0.00 43.89 4.41
3238 3796 9.049523 CAATACACAGATACAATACAAGATGCT 57.950 33.333 0.00 0.00 0.00 3.79
3239 3797 8.830580 ACAATACACAGATACAATACAAGATGC 58.169 33.333 0.00 0.00 0.00 3.91
3242 3800 9.936759 TTCACAATACACAGATACAATACAAGA 57.063 29.630 0.00 0.00 0.00 3.02
3243 3801 9.973246 GTTCACAATACACAGATACAATACAAG 57.027 33.333 0.00 0.00 0.00 3.16
3244 3802 8.941977 GGTTCACAATACACAGATACAATACAA 58.058 33.333 0.00 0.00 0.00 2.41
3254 3812 4.504864 CCTTCAGGGTTCACAATACACAGA 60.505 45.833 0.00 0.00 0.00 3.41
3255 3813 3.753272 CCTTCAGGGTTCACAATACACAG 59.247 47.826 0.00 0.00 0.00 3.66
3270 3828 3.066814 GCAAGCTGCCCCTTCAGG 61.067 66.667 0.00 0.00 37.42 3.86
3356 3917 1.003355 CACACTAGCACAGGGGTGG 60.003 63.158 0.00 0.00 45.38 4.61
3358 3919 2.895424 GCCACACTAGCACAGGGGT 61.895 63.158 0.00 0.00 28.64 4.95
3446 4008 1.129624 CTTGGAGACGACGACTCTCAG 59.870 57.143 22.92 15.98 36.61 3.35
3561 4124 6.734137 TGTTTTGGATTGCAAAGTACAGTAG 58.266 36.000 1.71 0.00 0.00 2.57
3562 4125 6.544197 TCTGTTTTGGATTGCAAAGTACAGTA 59.456 34.615 23.38 14.01 34.53 2.74
3563 4126 5.359576 TCTGTTTTGGATTGCAAAGTACAGT 59.640 36.000 23.38 0.00 34.53 3.55
3566 4129 5.831997 ACTCTGTTTTGGATTGCAAAGTAC 58.168 37.500 1.71 1.65 0.00 2.73
3567 4130 7.067615 TGTTACTCTGTTTTGGATTGCAAAGTA 59.932 33.333 1.71 0.00 0.00 2.24
3568 4131 6.127479 TGTTACTCTGTTTTGGATTGCAAAGT 60.127 34.615 1.71 0.35 0.00 2.66
3569 4132 6.272318 TGTTACTCTGTTTTGGATTGCAAAG 58.728 36.000 1.71 0.00 0.00 2.77
3589 4152 4.142447 GCACTACGTTCTGGATCTCTGTTA 60.142 45.833 0.00 0.00 0.00 2.41
3628 4191 6.709018 TTAACTTTCAGTTTCCCCTTCTTG 57.291 37.500 0.00 0.00 39.51 3.02
3633 4196 6.183360 GCTCTTTTTAACTTTCAGTTTCCCCT 60.183 38.462 0.00 0.00 39.51 4.79
3634 4197 5.983720 GCTCTTTTTAACTTTCAGTTTCCCC 59.016 40.000 0.00 0.00 39.51 4.81
3635 4198 5.685954 CGCTCTTTTTAACTTTCAGTTTCCC 59.314 40.000 0.00 0.00 39.51 3.97
3636 4199 6.414109 GTCGCTCTTTTTAACTTTCAGTTTCC 59.586 38.462 0.00 0.00 39.51 3.13
3637 4200 7.187480 AGTCGCTCTTTTTAACTTTCAGTTTC 58.813 34.615 0.00 0.00 39.51 2.78
3638 4201 7.085052 AGTCGCTCTTTTTAACTTTCAGTTT 57.915 32.000 0.00 0.00 39.51 2.66
3639 4202 6.679327 AGTCGCTCTTTTTAACTTTCAGTT 57.321 33.333 0.00 0.00 41.97 3.16
3640 4203 7.208080 TCTAGTCGCTCTTTTTAACTTTCAGT 58.792 34.615 0.00 0.00 0.00 3.41
3641 4204 7.639162 TCTAGTCGCTCTTTTTAACTTTCAG 57.361 36.000 0.00 0.00 0.00 3.02
3642 4205 7.493320 TGTTCTAGTCGCTCTTTTTAACTTTCA 59.507 33.333 0.00 0.00 0.00 2.69
3643 4206 7.848491 TGTTCTAGTCGCTCTTTTTAACTTTC 58.152 34.615 0.00 0.00 0.00 2.62
3644 4207 7.781548 TGTTCTAGTCGCTCTTTTTAACTTT 57.218 32.000 0.00 0.00 0.00 2.66
3645 4208 7.571428 GCATGTTCTAGTCGCTCTTTTTAACTT 60.571 37.037 0.00 0.00 0.00 2.66
3646 4209 6.128526 GCATGTTCTAGTCGCTCTTTTTAACT 60.129 38.462 0.00 0.00 0.00 2.24
3647 4210 6.016111 GCATGTTCTAGTCGCTCTTTTTAAC 58.984 40.000 0.00 0.00 0.00 2.01
3648 4211 5.932303 AGCATGTTCTAGTCGCTCTTTTTAA 59.068 36.000 0.00 0.00 0.00 1.52
3649 4212 5.479306 AGCATGTTCTAGTCGCTCTTTTTA 58.521 37.500 0.00 0.00 0.00 1.52
3650 4213 4.319177 AGCATGTTCTAGTCGCTCTTTTT 58.681 39.130 0.00 0.00 0.00 1.94
3651 4214 3.929610 GAGCATGTTCTAGTCGCTCTTTT 59.070 43.478 1.76 0.00 44.47 2.27
3689 4252 6.208204 CCTTTGATGGAACTTTGATCTTGTCT 59.792 38.462 0.00 0.00 0.00 3.41
3712 4275 0.551131 AGAAGGCCAAGACCATCCCT 60.551 55.000 5.01 0.00 0.00 4.20
3718 4281 0.600057 CTGCAAAGAAGGCCAAGACC 59.400 55.000 5.01 0.00 0.00 3.85
3753 4316 3.826754 CTAGCTGCTGGTCGCCGA 61.827 66.667 13.43 0.00 38.05 5.54
3754 4317 4.135153 ACTAGCTGCTGGTCGCCG 62.135 66.667 13.27 0.00 38.05 6.46
3755 4318 2.202810 GACTAGCTGCTGGTCGCC 60.203 66.667 26.65 8.76 32.76 5.54
3756 4319 1.226831 GAGACTAGCTGCTGGTCGC 60.227 63.158 31.54 29.59 44.77 5.19
3757 4320 1.315981 TGGAGACTAGCTGCTGGTCG 61.316 60.000 31.54 12.86 44.77 4.79
3758 4321 0.459489 CTGGAGACTAGCTGCTGGTC 59.541 60.000 31.33 31.33 41.33 4.02
3759 4322 0.252012 ACTGGAGACTAGCTGCTGGT 60.252 55.000 19.01 19.01 38.05 4.00
3760 4323 0.175302 CACTGGAGACTAGCTGCTGG 59.825 60.000 13.43 12.56 38.05 4.85
3761 4324 0.894141 ACACTGGAGACTAGCTGCTG 59.106 55.000 13.43 4.99 39.32 4.41
3762 4325 0.894141 CACACTGGAGACTAGCTGCT 59.106 55.000 7.57 7.57 35.71 4.24
3763 4326 0.108424 CCACACTGGAGACTAGCTGC 60.108 60.000 0.00 0.00 40.96 5.25
3764 4327 1.550327 TCCACACTGGAGACTAGCTG 58.450 55.000 0.00 0.00 42.67 4.24
3775 4338 2.520465 TATGCCCAGCGTCCACACTG 62.520 60.000 0.00 0.00 0.00 3.66
3776 4339 2.244117 CTATGCCCAGCGTCCACACT 62.244 60.000 0.00 0.00 0.00 3.55
3777 4340 1.815421 CTATGCCCAGCGTCCACAC 60.815 63.158 0.00 0.00 0.00 3.82
3778 4341 2.584064 CTATGCCCAGCGTCCACA 59.416 61.111 0.00 0.00 0.00 4.17
3779 4342 2.203070 CCTATGCCCAGCGTCCAC 60.203 66.667 0.00 0.00 0.00 4.02
3780 4343 1.992834 TTCCTATGCCCAGCGTCCA 60.993 57.895 0.00 0.00 0.00 4.02
3781 4344 1.523938 GTTCCTATGCCCAGCGTCC 60.524 63.158 0.00 0.00 0.00 4.79
3782 4345 1.090052 GTGTTCCTATGCCCAGCGTC 61.090 60.000 0.00 0.00 0.00 5.19
3783 4346 1.078426 GTGTTCCTATGCCCAGCGT 60.078 57.895 0.00 0.00 0.00 5.07
3784 4347 0.464373 ATGTGTTCCTATGCCCAGCG 60.464 55.000 0.00 0.00 0.00 5.18
3785 4348 1.027357 CATGTGTTCCTATGCCCAGC 58.973 55.000 0.00 0.00 0.00 4.85
3786 4349 1.027357 GCATGTGTTCCTATGCCCAG 58.973 55.000 0.00 0.00 42.88 4.45
3787 4350 3.189568 GCATGTGTTCCTATGCCCA 57.810 52.632 0.00 0.00 42.88 5.36
3791 4354 5.121105 TGATGAGAAGCATGTGTTCCTATG 58.879 41.667 0.00 0.00 37.34 2.23
3792 4355 5.104610 ACTGATGAGAAGCATGTGTTCCTAT 60.105 40.000 0.00 0.00 37.34 2.57
3793 4356 4.223700 ACTGATGAGAAGCATGTGTTCCTA 59.776 41.667 0.00 0.00 37.34 2.94
3794 4357 3.008813 ACTGATGAGAAGCATGTGTTCCT 59.991 43.478 0.00 0.00 37.34 3.36
3795 4358 3.341823 ACTGATGAGAAGCATGTGTTCC 58.658 45.455 0.00 0.00 37.34 3.62
3796 4359 4.252073 AGACTGATGAGAAGCATGTGTTC 58.748 43.478 0.00 0.00 37.34 3.18
3797 4360 4.283363 AGACTGATGAGAAGCATGTGTT 57.717 40.909 0.00 0.00 37.34 3.32
3798 4361 3.977134 AGACTGATGAGAAGCATGTGT 57.023 42.857 0.00 0.00 37.34 3.72
3799 4362 3.181509 GCAAGACTGATGAGAAGCATGTG 60.182 47.826 0.00 0.00 37.34 3.21
3800 4363 3.008330 GCAAGACTGATGAGAAGCATGT 58.992 45.455 0.00 0.00 37.34 3.21
3801 4364 2.355132 GGCAAGACTGATGAGAAGCATG 59.645 50.000 0.00 0.00 37.34 4.06
3802 4365 2.239150 AGGCAAGACTGATGAGAAGCAT 59.761 45.455 0.00 0.00 40.77 3.79
3803 4366 1.627329 AGGCAAGACTGATGAGAAGCA 59.373 47.619 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.