Multiple sequence alignment - TraesCS1A01G197700

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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 TraesCS1A01G197700 chr1A 100.000 3746 0 0 1 3746 355628543 355632288 0.000000e+00 6918.0
1 TraesCS1A01G197700 chr1D 94.369 2930 103 18 12 2911 284045836 284048733 0.000000e+00 4440.0
2 TraesCS1A01G197700 chr1D 98.113 53 0 1 2949 3000 284051337 284051389 1.430000e-14 91.6
3 TraesCS1A01G197700 chr1B 92.562 3025 138 44 13 2988 385656431 385659417 0.000000e+00 4259.0
4 TraesCS1A01G197700 chr1B 94.253 87 2 2 2946 3031 385659406 385659490 3.040000e-26 130.0
5 TraesCS1A01G197700 chr1B 88.000 75 4 3 3676 3746 385659538 385659611 2.400000e-12 84.2
6 TraesCS1A01G197700 chr4A 92.767 553 35 5 3056 3608 520957829 520957282 0.000000e+00 795.0
7 TraesCS1A01G197700 chr4D 89.661 590 52 8 3091 3676 506218526 506217942 0.000000e+00 743.0
8 TraesCS1A01G197700 chr6D 87.917 629 66 9 3056 3678 131025643 131026267 0.000000e+00 732.0
9 TraesCS1A01G197700 chr6D 90.244 123 12 0 1183 1305 336210019 336209897 1.080000e-35 161.0
10 TraesCS1A01G197700 chr6A 87.299 622 69 8 3056 3673 196336703 196337318 0.000000e+00 702.0
11 TraesCS1A01G197700 chr6A 80.426 235 31 5 1072 1305 475438701 475438481 8.320000e-37 165.0
12 TraesCS1A01G197700 chr5B 87.159 623 69 10 3055 3673 458699741 458700356 0.000000e+00 697.0
13 TraesCS1A01G197700 chr3A 86.804 629 67 9 3056 3676 742880177 742880797 0.000000e+00 688.0
14 TraesCS1A01G197700 chr3D 85.692 629 74 9 3056 3676 34048559 34047939 0.000000e+00 649.0
15 TraesCS1A01G197700 chrUn 85.533 629 73 12 3056 3676 161630807 161630189 3.150000e-180 641.0
16 TraesCS1A01G197700 chr2B 85.096 624 83 8 3056 3675 569126835 569127452 2.460000e-176 628.0
17 TraesCS1A01G197700 chr6B 79.498 239 30 7 1072 1305 484526931 484527155 6.480000e-33 152.0


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 TraesCS1A01G197700 chr1A 355628543 355632288 3745 False 6918.000000 6918 100.000 1 3746 1 chr1A.!!$F1 3745
1 TraesCS1A01G197700 chr1D 284045836 284051389 5553 False 2265.800000 4440 96.241 12 3000 2 chr1D.!!$F1 2988
2 TraesCS1A01G197700 chr1B 385656431 385659611 3180 False 1491.066667 4259 91.605 13 3746 3 chr1B.!!$F1 3733
3 TraesCS1A01G197700 chr4A 520957282 520957829 547 True 795.000000 795 92.767 3056 3608 1 chr4A.!!$R1 552
4 TraesCS1A01G197700 chr4D 506217942 506218526 584 True 743.000000 743 89.661 3091 3676 1 chr4D.!!$R1 585
5 TraesCS1A01G197700 chr6D 131025643 131026267 624 False 732.000000 732 87.917 3056 3678 1 chr6D.!!$F1 622
6 TraesCS1A01G197700 chr6A 196336703 196337318 615 False 702.000000 702 87.299 3056 3673 1 chr6A.!!$F1 617
7 TraesCS1A01G197700 chr5B 458699741 458700356 615 False 697.000000 697 87.159 3055 3673 1 chr5B.!!$F1 618
8 TraesCS1A01G197700 chr3A 742880177 742880797 620 False 688.000000 688 86.804 3056 3676 1 chr3A.!!$F1 620
9 TraesCS1A01G197700 chr3D 34047939 34048559 620 True 649.000000 649 85.692 3056 3676 1 chr3D.!!$R1 620
10 TraesCS1A01G197700 chrUn 161630189 161630807 618 True 641.000000 641 85.533 3056 3676 1 chrUn.!!$R1 620
11 TraesCS1A01G197700 chr2B 569126835 569127452 617 False 628.000000 628 85.096 3056 3675 1 chr2B.!!$F1 619

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
761 807 0.034186 TTCATTTCATCCCGCTGCCT 60.034 50.0 0.0 0.0 0.0 4.75 F
774 820 0.250038 GCTGCCTTGTCTGTCTGTCA 60.250 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2082 3.202706 GATTCCACGGGCCTTCGC 61.203 66.667 0.84 0.0 0.0 4.70 R
2790 2881 7.875327 ACATCATCATTCAGACATTTCATCA 57.125 32.000 0.00 0.0 0.0 3.07 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
61 76 2.468831 CTCTCCTCGCTGTTATCTTGC 58.531 52.381 0.00 0.00 0.00 4.01
72 87 4.659088 CTGTTATCTTGCAGCAATGTCAG 58.341 43.478 8.67 9.37 0.00 3.51
75 90 5.352293 TGTTATCTTGCAGCAATGTCAGTAG 59.648 40.000 8.67 0.00 0.00 2.57
103 118 6.807230 CAGTAGTATGTTAGTGACAACTGGAC 59.193 42.308 8.87 3.85 42.62 4.02
107 122 1.792949 GTTAGTGACAACTGGACGCAG 59.207 52.381 0.00 0.00 37.19 5.18
123 138 1.196130 GCAGTATCAAATGCGCGTGC 61.196 55.000 15.48 15.48 43.20 5.34
135 150 2.184579 GCGTGCCTGGTCTACTCC 59.815 66.667 0.00 0.00 0.00 3.85
158 173 2.087646 GCTTAACTCTGAGGCCAAAGG 58.912 52.381 5.01 0.00 0.00 3.11
202 221 2.283617 GCGATCTTGTGCTACATCACTG 59.716 50.000 0.00 0.00 37.81 3.66
256 275 2.956964 GAGCGGCATCGAAGGACG 60.957 66.667 10.99 10.99 44.09 4.79
275 294 1.153429 GTTGGGTAGGCCGTAGCTG 60.153 63.158 0.00 0.00 39.73 4.24
342 378 1.515521 GGTTGCAAGGGAAGGTGACG 61.516 60.000 0.00 0.00 0.00 4.35
369 405 2.744377 GCCTATCCCTCCGCCTTC 59.256 66.667 0.00 0.00 0.00 3.46
386 422 0.831288 TTCTGCCCCAACAACCATGG 60.831 55.000 11.19 11.19 37.71 3.66
467 503 0.096454 GGTACGCCGCACATCTTTTC 59.904 55.000 0.00 0.00 0.00 2.29
468 504 1.076332 GTACGCCGCACATCTTTTCT 58.924 50.000 0.00 0.00 0.00 2.52
469 505 1.463444 GTACGCCGCACATCTTTTCTT 59.537 47.619 0.00 0.00 0.00 2.52
470 506 0.951558 ACGCCGCACATCTTTTCTTT 59.048 45.000 0.00 0.00 0.00 2.52
471 507 1.330306 CGCCGCACATCTTTTCTTTG 58.670 50.000 0.00 0.00 0.00 2.77
474 510 1.613437 CCGCACATCTTTTCTTTGGGT 59.387 47.619 0.00 0.00 0.00 4.51
486 522 3.518634 TCTTTGGGTTTTTCAGTGCAC 57.481 42.857 9.40 9.40 0.00 4.57
490 531 0.594796 GGGTTTTTCAGTGCACTGCG 60.595 55.000 36.76 18.97 43.46 5.18
521 562 2.642700 CCGCGGGTTTGGTTCAAG 59.357 61.111 20.10 0.00 0.00 3.02
522 563 2.642700 CGCGGGTTTGGTTCAAGG 59.357 61.111 0.00 0.00 0.00 3.61
523 564 1.894756 CGCGGGTTTGGTTCAAGGA 60.895 57.895 0.00 0.00 0.00 3.36
524 565 1.852067 CGCGGGTTTGGTTCAAGGAG 61.852 60.000 0.00 0.00 0.00 3.69
525 566 1.524008 GCGGGTTTGGTTCAAGGAGG 61.524 60.000 0.00 0.00 0.00 4.30
526 567 0.893727 CGGGTTTGGTTCAAGGAGGG 60.894 60.000 0.00 0.00 0.00 4.30
527 568 0.481128 GGGTTTGGTTCAAGGAGGGA 59.519 55.000 0.00 0.00 0.00 4.20
528 569 1.547901 GGGTTTGGTTCAAGGAGGGAG 60.548 57.143 0.00 0.00 0.00 4.30
570 611 2.548920 CCATCCAGCTCGTTTATCCTCC 60.549 54.545 0.00 0.00 0.00 4.30
581 622 3.815407 TATCCTCCCCGCCCGTACC 62.815 68.421 0.00 0.00 0.00 3.34
636 677 2.496817 CTGCCCTCGTCCTGTAGC 59.503 66.667 0.00 0.00 0.00 3.58
653 694 2.170985 CTTGACTTTCACCGCGCG 59.829 61.111 25.67 25.67 0.00 6.86
686 727 0.882042 CGAGCTCATCAATTCCGGGG 60.882 60.000 15.40 0.00 0.00 5.73
695 736 2.423064 AATTCCGGGGGATTTGCGC 61.423 57.895 0.00 0.00 0.00 6.09
723 764 2.925563 CGGTCTCGCGGTTTACTATTTT 59.074 45.455 6.13 0.00 0.00 1.82
761 807 0.034186 TTCATTTCATCCCGCTGCCT 60.034 50.000 0.00 0.00 0.00 4.75
766 812 1.841302 TTCATCCCGCTGCCTTGTCT 61.841 55.000 0.00 0.00 0.00 3.41
770 816 2.345244 CCGCTGCCTTGTCTGTCT 59.655 61.111 0.00 0.00 0.00 3.41
774 820 0.250038 GCTGCCTTGTCTGTCTGTCA 60.250 55.000 0.00 0.00 0.00 3.58
775 821 1.610102 GCTGCCTTGTCTGTCTGTCAT 60.610 52.381 0.00 0.00 0.00 3.06
776 822 2.354103 GCTGCCTTGTCTGTCTGTCATA 60.354 50.000 0.00 0.00 0.00 2.15
804 854 0.765510 AACCTTCCGTCTTTGCTCCT 59.234 50.000 0.00 0.00 0.00 3.69
813 863 1.205893 GTCTTTGCTCCTGGTCGATCT 59.794 52.381 0.00 0.00 0.00 2.75
899 949 4.899239 GCTCGAGTCCGGCCATGG 62.899 72.222 15.13 7.63 36.24 3.66
921 974 1.820481 GTCGTCCTCCTCCTCCTCG 60.820 68.421 0.00 0.00 0.00 4.63
1050 1134 3.369242 TCCATTGATTCATGTGGCTGA 57.631 42.857 11.74 0.00 0.00 4.26
1055 1139 5.394773 CCATTGATTCATGTGGCTGAATGAA 60.395 40.000 5.31 8.41 44.00 2.57
1068 1153 2.422479 CTGAATGAATGACTGGCTGTGG 59.578 50.000 0.29 0.00 0.00 4.17
1197 1282 2.737376 GTCGACACCTGGAACGGC 60.737 66.667 11.55 0.49 0.00 5.68
1354 1439 2.750948 TCAGTCAGGCAAAAGTCGTAC 58.249 47.619 0.00 0.00 0.00 3.67
1355 1440 2.364324 TCAGTCAGGCAAAAGTCGTACT 59.636 45.455 0.00 0.00 0.00 2.73
1356 1441 2.476619 CAGTCAGGCAAAAGTCGTACTG 59.523 50.000 0.00 0.00 0.00 2.74
1357 1442 2.102588 AGTCAGGCAAAAGTCGTACTGT 59.897 45.455 0.00 0.00 0.00 3.55
1358 1443 3.319972 AGTCAGGCAAAAGTCGTACTGTA 59.680 43.478 0.00 0.00 0.00 2.74
1371 1456 7.860918 AGTCGTACTGTAGTTGAGATTGATA 57.139 36.000 0.00 0.00 0.00 2.15
1385 1470 8.689972 GTTGAGATTGATAGGGAAATGAAATGT 58.310 33.333 0.00 0.00 0.00 2.71
1387 1472 7.227314 TGAGATTGATAGGGAAATGAAATGTCG 59.773 37.037 0.00 0.00 28.48 4.35
1500 1585 1.592223 CTCACGGACCCAGTTCTCC 59.408 63.158 0.00 0.00 0.00 3.71
1522 1607 3.277211 TTCTTCGCGGCGCTGTACT 62.277 57.895 30.54 0.00 0.00 2.73
1950 2035 3.259425 GAAGCTGGCGCACACCAAG 62.259 63.158 10.83 0.00 39.86 3.61
1962 2047 3.971702 ACCAAGGGGCTCAGGTGC 61.972 66.667 0.23 0.00 37.90 5.01
2088 2173 4.961511 TGGGTGACGTGCGTGCTC 62.962 66.667 0.67 0.00 0.00 4.26
2260 2345 4.159901 TCATCATGCCGCTCGCCA 62.160 61.111 0.00 0.00 36.24 5.69
2340 2425 2.358737 GTCCTGGTGGTTCTGGCG 60.359 66.667 0.00 0.00 34.23 5.69
2785 2876 2.295253 AATGCACTGCTCCGTACTAC 57.705 50.000 1.98 0.00 0.00 2.73
2786 2877 1.475403 ATGCACTGCTCCGTACTACT 58.525 50.000 1.98 0.00 0.00 2.57
2787 2878 0.526211 TGCACTGCTCCGTACTACTG 59.474 55.000 1.98 0.00 0.00 2.74
2789 2880 1.741706 GCACTGCTCCGTACTACTGTA 59.258 52.381 0.00 0.00 0.00 2.74
2790 2881 2.358267 GCACTGCTCCGTACTACTGTAT 59.642 50.000 0.00 0.00 0.00 2.29
2791 2882 3.792459 GCACTGCTCCGTACTACTGTATG 60.792 52.174 0.00 0.00 35.89 2.39
2792 2883 3.626217 CACTGCTCCGTACTACTGTATGA 59.374 47.826 0.00 0.00 37.76 2.15
2793 2884 4.276183 CACTGCTCCGTACTACTGTATGAT 59.724 45.833 0.00 0.00 37.76 2.45
2794 2885 4.276183 ACTGCTCCGTACTACTGTATGATG 59.724 45.833 0.00 0.00 37.76 3.07
2795 2886 4.457466 TGCTCCGTACTACTGTATGATGA 58.543 43.478 0.00 0.00 37.76 2.92
2844 2935 1.544691 ACATCACGCCGTAGAAGTCTT 59.455 47.619 0.00 0.00 0.00 3.01
2898 2989 5.008019 TCAGAGAGTGTCGTTAACGTTAACT 59.992 40.000 35.52 23.72 40.57 2.24
2929 5555 7.669722 TGGGAGATATGTAAGGGCAATTTTATC 59.330 37.037 0.00 0.00 0.00 1.75
2953 5579 6.705381 TCTTTTAGCAAAACAATGGGTGAATG 59.295 34.615 0.00 0.00 0.00 2.67
3007 5664 9.632638 ATGCAATCATAGTTTCTTGGTTATACT 57.367 29.630 0.00 0.00 0.00 2.12
3008 5665 8.892723 TGCAATCATAGTTTCTTGGTTATACTG 58.107 33.333 0.00 0.00 0.00 2.74
3031 5688 2.892373 TCGCATAAGGTTTTCTTGCG 57.108 45.000 9.13 9.13 44.28 4.85
3033 5690 3.327626 TCGCATAAGGTTTTCTTGCGTA 58.672 40.909 14.22 0.69 43.74 4.42
3034 5691 3.123959 TCGCATAAGGTTTTCTTGCGTAC 59.876 43.478 14.22 0.00 43.74 3.67
3035 5692 3.120477 CGCATAAGGTTTTCTTGCGTACA 60.120 43.478 7.38 0.00 40.65 2.90
3037 5694 5.399013 GCATAAGGTTTTCTTGCGTACAAT 58.601 37.500 0.00 0.00 36.93 2.71
3038 5695 5.861787 GCATAAGGTTTTCTTGCGTACAATT 59.138 36.000 0.00 0.00 36.93 2.32
3039 5696 6.364976 GCATAAGGTTTTCTTGCGTACAATTT 59.635 34.615 0.00 0.00 36.93 1.82
3079 5758 8.589629 CATAATTTTCTGCAACAATACTCTTGC 58.410 33.333 0.00 0.00 42.67 4.01
3258 5942 4.365514 TTCTGCAACAAGACCCTTGATA 57.634 40.909 13.00 0.00 0.00 2.15
3454 6146 2.025699 ACCCCATTTGTTGCGGTATACT 60.026 45.455 2.25 0.00 34.63 2.12
3477 6169 3.462483 TTCGAAACAGGTGCTCAGTTA 57.538 42.857 0.00 0.00 0.00 2.24
3492 6184 8.414778 GGTGCTCAGTTATAAGAACTGTAGTAT 58.585 37.037 14.61 0.00 45.75 2.12
3498 6190 8.414003 CAGTTATAAGAACTGTAGTATGGAGCA 58.586 37.037 8.40 0.00 41.90 4.26
3579 6274 6.239148 CCATTTCGTCAGAGATAGAGATGGAA 60.239 42.308 14.18 0.00 43.78 3.53
3607 6307 2.625790 GGTGCACTTACCCATCAAAACA 59.374 45.455 17.98 0.00 34.56 2.83
3611 6311 4.236935 GCACTTACCCATCAAAACATGTG 58.763 43.478 0.00 0.00 0.00 3.21
3612 6312 4.261994 GCACTTACCCATCAAAACATGTGT 60.262 41.667 0.00 0.00 0.00 3.72
3613 6313 5.460646 CACTTACCCATCAAAACATGTGTC 58.539 41.667 0.00 0.00 0.00 3.67
3614 6314 5.009510 CACTTACCCATCAAAACATGTGTCA 59.990 40.000 0.00 0.00 0.00 3.58
3619 6319 4.370049 CCATCAAAACATGTGTCAAAGCA 58.630 39.130 0.00 0.00 0.00 3.91
3678 6378 5.221441 GGTTGACCACTAGCTTTTTCCAATT 60.221 40.000 0.00 0.00 35.64 2.32
3679 6379 6.280643 GTTGACCACTAGCTTTTTCCAATTT 58.719 36.000 0.00 0.00 0.00 1.82
3680 6380 6.084326 TGACCACTAGCTTTTTCCAATTTC 57.916 37.500 0.00 0.00 0.00 2.17
3681 6381 5.596361 TGACCACTAGCTTTTTCCAATTTCA 59.404 36.000 0.00 0.00 0.00 2.69
3682 6382 6.097554 TGACCACTAGCTTTTTCCAATTTCAA 59.902 34.615 0.00 0.00 0.00 2.69
3683 6383 7.066307 ACCACTAGCTTTTTCCAATTTCAAT 57.934 32.000 0.00 0.00 0.00 2.57
3684 6384 7.508687 ACCACTAGCTTTTTCCAATTTCAATT 58.491 30.769 0.00 0.00 0.00 2.32
3685 6385 7.992608 ACCACTAGCTTTTTCCAATTTCAATTT 59.007 29.630 0.00 0.00 0.00 1.82
3686 6386 9.487790 CCACTAGCTTTTTCCAATTTCAATTTA 57.512 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.550327 TCCAGATTCAGACGAGCAGT 58.450 50.000 0.00 0.00 0.00 4.40
10 11 2.471818 CATCCAGATTCAGACGAGCAG 58.528 52.381 0.00 0.00 0.00 4.24
40 41 2.468831 CAAGATAACAGCGAGGAGAGC 58.531 52.381 0.00 0.00 0.00 4.09
61 76 2.420642 ACTGCACTACTGACATTGCTG 58.579 47.619 0.00 0.00 39.18 4.41
72 87 6.849502 TGTCACTAACATACTACTGCACTAC 58.150 40.000 0.00 0.00 31.20 2.73
75 90 6.089551 CAGTTGTCACTAACATACTACTGCAC 59.910 42.308 0.00 0.00 39.09 4.57
107 122 0.589729 CAGGCACGCGCATTTGATAC 60.590 55.000 5.73 0.00 41.24 2.24
123 138 2.054232 TAAGCTCGGAGTAGACCAGG 57.946 55.000 6.90 0.00 0.00 4.45
150 165 2.299867 TGCTTCTCATTTTCCTTTGGCC 59.700 45.455 0.00 0.00 0.00 5.36
248 267 1.217244 CCTACCCAACCGTCCTTCG 59.783 63.158 0.00 0.00 39.52 3.79
256 275 2.188731 GCTACGGCCTACCCAACC 59.811 66.667 0.00 0.00 0.00 3.77
342 378 4.603946 GGATAGGCGGCGGGTCAC 62.604 72.222 9.78 0.00 0.00 3.67
364 400 2.574018 GGTTGTTGGGGCAGAAGGC 61.574 63.158 0.00 0.00 43.74 4.35
369 405 0.615544 ATCCATGGTTGTTGGGGCAG 60.616 55.000 12.58 0.00 34.85 4.85
386 422 3.512516 GTGAGCCTTGGCGCCATC 61.513 66.667 33.25 24.99 0.00 3.51
445 481 1.884075 AAGATGTGCGGCGTACCTCA 61.884 55.000 27.97 11.92 0.00 3.86
467 503 3.189285 CAGTGCACTGAAAAACCCAAAG 58.811 45.455 38.12 9.27 46.59 2.77
468 504 2.676463 GCAGTGCACTGAAAAACCCAAA 60.676 45.455 43.32 0.00 46.59 3.28
469 505 1.134848 GCAGTGCACTGAAAAACCCAA 60.135 47.619 43.32 0.00 46.59 4.12
470 506 0.459489 GCAGTGCACTGAAAAACCCA 59.541 50.000 43.32 0.00 46.59 4.51
471 507 0.594796 CGCAGTGCACTGAAAAACCC 60.595 55.000 43.32 25.24 46.59 4.11
474 510 0.100325 CACCGCAGTGCACTGAAAAA 59.900 50.000 43.32 0.00 46.59 1.94
505 546 1.852067 CTCCTTGAACCAAACCCGCG 61.852 60.000 0.00 0.00 0.00 6.46
521 562 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
522 563 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
525 566 4.179599 CTCCCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
526 567 4.179599 CCTCCCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
550 591 2.548920 GGGAGGATAAACGAGCTGGATG 60.549 54.545 1.44 0.00 0.00 3.51
618 659 2.496817 CTACAGGACGAGGGCAGC 59.503 66.667 0.00 0.00 0.00 5.25
636 677 2.170985 CGCGCGGTGAAAGTCAAG 59.829 61.111 24.84 0.00 0.00 3.02
686 727 3.508840 CGGAGTGGGCGCAAATCC 61.509 66.667 20.53 20.53 0.00 3.01
743 789 0.034186 AAGGCAGCGGGATGAAATGA 60.034 50.000 0.00 0.00 0.00 2.57
744 790 0.101759 CAAGGCAGCGGGATGAAATG 59.898 55.000 0.00 0.00 0.00 2.32
745 791 0.323725 ACAAGGCAGCGGGATGAAAT 60.324 50.000 0.00 0.00 0.00 2.17
746 792 0.960364 GACAAGGCAGCGGGATGAAA 60.960 55.000 0.00 0.00 0.00 2.69
747 793 1.377202 GACAAGGCAGCGGGATGAA 60.377 57.895 0.00 0.00 0.00 2.57
752 798 2.743928 GACAGACAAGGCAGCGGG 60.744 66.667 0.00 0.00 0.00 6.13
761 807 7.703058 TCTAATGACTATGACAGACAGACAA 57.297 36.000 0.00 0.00 32.40 3.18
766 812 7.363880 GGAAGGTTCTAATGACTATGACAGACA 60.364 40.741 0.00 0.00 33.43 3.41
770 816 5.421056 ACGGAAGGTTCTAATGACTATGACA 59.579 40.000 0.00 0.00 0.00 3.58
774 820 6.793505 AAGACGGAAGGTTCTAATGACTAT 57.206 37.500 0.00 0.00 0.00 2.12
775 821 6.395629 CAAAGACGGAAGGTTCTAATGACTA 58.604 40.000 0.00 0.00 0.00 2.59
776 822 5.238583 CAAAGACGGAAGGTTCTAATGACT 58.761 41.667 0.00 0.00 0.00 3.41
804 854 2.089201 TCAGCGAGTAAAGATCGACCA 58.911 47.619 0.00 0.00 42.76 4.02
813 863 3.198068 GCATCCAGATTCAGCGAGTAAA 58.802 45.455 0.00 0.00 0.00 2.01
897 947 2.360852 GAGGAGGACGACGACCCA 60.361 66.667 12.78 0.00 0.00 4.51
899 949 2.045143 AGGAGGAGGACGACGACC 60.045 66.667 8.37 8.37 0.00 4.79
939 992 3.499737 GCCACCGCCGTCATCTTG 61.500 66.667 0.00 0.00 0.00 3.02
980 1033 2.085343 AACAATGGCAGGCCCTGTCT 62.085 55.000 17.72 0.00 36.97 3.41
1008 1061 0.384230 TCGTCGTCGTCGTTGGTTAC 60.384 55.000 11.41 0.00 38.33 2.50
1010 1063 0.318107 AATCGTCGTCGTCGTTGGTT 60.318 50.000 11.41 0.00 38.33 3.67
1014 1067 0.040157 TGGAAATCGTCGTCGTCGTT 60.040 50.000 11.41 0.87 38.33 3.85
1050 1134 2.165167 CACCACAGCCAGTCATTCATT 58.835 47.619 0.00 0.00 0.00 2.57
1055 1139 1.601759 GCACACCACAGCCAGTCAT 60.602 57.895 0.00 0.00 0.00 3.06
1068 1153 1.571460 CAACTCGAAGCCTGCACAC 59.429 57.895 0.00 0.00 0.00 3.82
1197 1282 1.078426 GGGGACGATGAAGGTGGTG 60.078 63.158 0.00 0.00 0.00 4.17
1354 1439 8.206867 TCATTTCCCTATCAATCTCAACTACAG 58.793 37.037 0.00 0.00 0.00 2.74
1355 1440 8.089625 TCATTTCCCTATCAATCTCAACTACA 57.910 34.615 0.00 0.00 0.00 2.74
1356 1441 8.964476 TTCATTTCCCTATCAATCTCAACTAC 57.036 34.615 0.00 0.00 0.00 2.73
1358 1443 8.910944 CATTTCATTTCCCTATCAATCTCAACT 58.089 33.333 0.00 0.00 0.00 3.16
1371 1456 4.137116 TCGATCGACATTTCATTTCCCT 57.863 40.909 15.15 0.00 0.00 4.20
1385 1470 1.667722 CCCTGCATCCATCGATCGA 59.332 57.895 21.86 21.86 0.00 3.59
1387 1472 1.673665 GGCCCTGCATCCATCGATC 60.674 63.158 0.00 0.00 0.00 3.69
1522 1607 2.264480 CGTGCCGATGGAGGTCAA 59.736 61.111 0.00 0.00 0.00 3.18
1997 2082 3.202706 GATTCCACGGGCCTTCGC 61.203 66.667 0.84 0.00 0.00 4.70
2785 2876 9.052759 TCATCATTCAGACATTTCATCATACAG 57.947 33.333 0.00 0.00 0.00 2.74
2786 2877 8.967664 TCATCATTCAGACATTTCATCATACA 57.032 30.769 0.00 0.00 0.00 2.29
2787 2878 9.827411 CATCATCATTCAGACATTTCATCATAC 57.173 33.333 0.00 0.00 0.00 2.39
2789 2880 8.465273 ACATCATCATTCAGACATTTCATCAT 57.535 30.769 0.00 0.00 0.00 2.45
2790 2881 7.875327 ACATCATCATTCAGACATTTCATCA 57.125 32.000 0.00 0.00 0.00 3.07
2791 2882 9.661187 GTTACATCATCATTCAGACATTTCATC 57.339 33.333 0.00 0.00 0.00 2.92
2792 2883 9.404848 AGTTACATCATCATTCAGACATTTCAT 57.595 29.630 0.00 0.00 0.00 2.57
2793 2884 8.797350 AGTTACATCATCATTCAGACATTTCA 57.203 30.769 0.00 0.00 0.00 2.69
2794 2885 9.499585 CAAGTTACATCATCATTCAGACATTTC 57.500 33.333 0.00 0.00 0.00 2.17
2795 2886 8.464404 CCAAGTTACATCATCATTCAGACATTT 58.536 33.333 0.00 0.00 0.00 2.32
2844 2935 5.250200 ACAAAACAAGAGTTATATCCGGCA 58.750 37.500 0.00 0.00 36.84 5.69
2898 2989 3.583086 GCCCTTACATATCTCCCAGCTTA 59.417 47.826 0.00 0.00 0.00 3.09
2929 5555 6.705381 TCATTCACCCATTGTTTTGCTAAAAG 59.295 34.615 0.00 0.00 0.00 2.27
2947 5573 7.428826 AGGACAAAGAACTGAAAATCATTCAC 58.571 34.615 0.00 0.00 0.00 3.18
2953 5579 7.745620 TCCTAAGGACAAAGAACTGAAAATC 57.254 36.000 0.00 0.00 0.00 2.17
3007 5664 5.636837 GCAAGAAAACCTTATGCGATTACA 58.363 37.500 0.00 0.00 32.86 2.41
3008 5665 4.728608 CGCAAGAAAACCTTATGCGATTAC 59.271 41.667 12.56 0.00 44.88 1.89
3012 5669 2.147958 ACGCAAGAAAACCTTATGCGA 58.852 42.857 22.95 0.00 44.88 5.10
3039 5696 8.550376 GCAGAAAATTATGCTTTTCAGAAAACA 58.450 29.630 4.06 8.41 44.11 2.83
3079 5758 5.467063 AGTTAGAGAAGAAAAGGTTTCGCAG 59.533 40.000 0.00 0.00 0.00 5.18
3402 6091 0.734253 CACGGGTTGCTCTCTTCGAG 60.734 60.000 0.00 0.00 42.88 4.04
3403 6092 1.289066 CACGGGTTGCTCTCTTCGA 59.711 57.895 0.00 0.00 0.00 3.71
3415 6104 1.913262 TGATGCAGAGACCACGGGT 60.913 57.895 0.00 0.00 39.44 5.28
3454 6146 3.013921 ACTGAGCACCTGTTTCGAAAAA 58.986 40.909 13.10 6.34 0.00 1.94
3477 6169 6.836527 AGAGTGCTCCATACTACAGTTCTTAT 59.163 38.462 0.00 0.00 0.00 1.73
3492 6184 1.297689 GACCATGCAGAGTGCTCCA 59.702 57.895 0.00 0.00 45.31 3.86
3579 6274 0.605589 GGGTAAGTGCACCGCTTCTT 60.606 55.000 14.63 2.28 39.69 2.52
3607 6307 3.436704 CCACGTTCTATGCTTTGACACAT 59.563 43.478 0.00 0.00 0.00 3.21
3611 6311 2.159627 CCACCACGTTCTATGCTTTGAC 59.840 50.000 0.00 0.00 0.00 3.18
3612 6312 2.037902 TCCACCACGTTCTATGCTTTGA 59.962 45.455 0.00 0.00 0.00 2.69
3613 6313 2.422597 TCCACCACGTTCTATGCTTTG 58.577 47.619 0.00 0.00 0.00 2.77
3614 6314 2.851263 TCCACCACGTTCTATGCTTT 57.149 45.000 0.00 0.00 0.00 3.51
3619 6319 3.096852 TCTCACATCCACCACGTTCTAT 58.903 45.455 0.00 0.00 0.00 1.98
3690 6390 8.817876 CCCCCATAAAACTATGAAAACCTTTAA 58.182 33.333 0.00 0.00 0.00 1.52
3691 6391 7.093245 GCCCCCATAAAACTATGAAAACCTTTA 60.093 37.037 0.00 0.00 0.00 1.85
3692 6392 6.296202 GCCCCCATAAAACTATGAAAACCTTT 60.296 38.462 0.00 0.00 0.00 3.11
3693 6393 5.188948 GCCCCCATAAAACTATGAAAACCTT 59.811 40.000 0.00 0.00 0.00 3.50
3694 6394 4.714802 GCCCCCATAAAACTATGAAAACCT 59.285 41.667 0.00 0.00 0.00 3.50
3695 6395 4.714802 AGCCCCCATAAAACTATGAAAACC 59.285 41.667 0.00 0.00 0.00 3.27
3696 6396 5.932619 AGCCCCCATAAAACTATGAAAAC 57.067 39.130 0.00 0.00 0.00 2.43
3697 6397 6.260663 AGAAGCCCCCATAAAACTATGAAAA 58.739 36.000 0.00 0.00 0.00 2.29
3698 6398 5.837829 AGAAGCCCCCATAAAACTATGAAA 58.162 37.500 0.00 0.00 0.00 2.69
3699 6399 5.466127 AGAAGCCCCCATAAAACTATGAA 57.534 39.130 0.00 0.00 0.00 2.57
3700 6400 6.584471 TTAGAAGCCCCCATAAAACTATGA 57.416 37.500 0.00 0.00 0.00 2.15
3701 6401 6.265422 CCTTTAGAAGCCCCCATAAAACTATG 59.735 42.308 0.00 0.00 0.00 2.23
3702 6402 6.373759 CCTTTAGAAGCCCCCATAAAACTAT 58.626 40.000 0.00 0.00 0.00 2.12
3714 6414 5.351458 CAATATGTTTGCCTTTAGAAGCCC 58.649 41.667 0.00 0.00 0.00 5.19
3715 6415 5.105351 ACCAATATGTTTGCCTTTAGAAGCC 60.105 40.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.