Multiple sequence alignment - TraesCS2A01G192600

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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 TraesCS2A01G192600 chr2A 100.000 3785 0 0 1 3785 160685645 160689429 0.000000e+00 6990
1 TraesCS2A01G192600 chr2D 95.762 3327 88 22 130 3432 140551904 140548607 0.000000e+00 5313
2 TraesCS2A01G192600 chr2D 91.641 323 22 3 3466 3785 140548600 140548280 3.470000e-120 442
3 TraesCS2A01G192600 chr2B 94.331 3140 84 40 372 3467 199529792 199532881 0.000000e+00 4726
4 TraesCS2A01G192600 chr6B 78.736 174 21 9 117 275 6318799 6318627 6.690000e-18 102


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 TraesCS2A01G192600 chr2A 160685645 160689429 3784 False 6990.0 6990 100.0000 1 3785 1 chr2A.!!$F1 3784
1 TraesCS2A01G192600 chr2D 140548280 140551904 3624 True 2877.5 5313 93.7015 130 3785 2 chr2D.!!$R1 3655
2 TraesCS2A01G192600 chr2B 199529792 199532881 3089 False 4726.0 4726 94.3310 372 3467 1 chr2B.!!$F1 3095

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
54 55 0.037975 CTTGCCAACCACTGCATTCC 60.038 55.0 0.00 0.00 37.33 3.01 F
58 59 0.251297 CCAACCACTGCATTCCAGGA 60.251 55.0 0.00 0.00 46.14 3.86 F
923 947 0.315568 CCAGCTGATCCCTACGTAGC 59.684 60.0 17.39 6.59 34.71 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1737 1.517257 CTGCAGGAAGTAGGACGCG 60.517 63.158 5.57 3.53 0.0 6.01 R
2394 2448 2.154462 CCGAACACCTTCAAGAATGCT 58.846 47.619 0.00 0.00 0.0 3.79 R
2793 2847 0.033228 CTGACCTCGCTCCATCCATC 59.967 60.000 0.00 0.00 0.0 3.51 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
23 24 6.916360 ACTATCCAACAATTCACCAACATT 57.084 33.333 0.00 0.00 0.00 2.71
25 26 8.593945 ACTATCCAACAATTCACCAACATTAT 57.406 30.769 0.00 0.00 0.00 1.28
26 27 8.469200 ACTATCCAACAATTCACCAACATTATG 58.531 33.333 0.00 0.00 0.00 1.90
27 28 6.907853 TCCAACAATTCACCAACATTATGA 57.092 33.333 0.00 0.00 0.00 2.15
28 29 6.686630 TCCAACAATTCACCAACATTATGAC 58.313 36.000 0.00 0.00 0.00 3.06
29 30 5.868801 CCAACAATTCACCAACATTATGACC 59.131 40.000 0.00 0.00 0.00 4.02
30 31 6.453943 CAACAATTCACCAACATTATGACCA 58.546 36.000 0.00 0.00 0.00 4.02
31 32 6.024552 ACAATTCACCAACATTATGACCAC 57.975 37.500 0.00 0.00 0.00 4.16
32 33 5.538053 ACAATTCACCAACATTATGACCACA 59.462 36.000 0.00 0.00 0.00 4.17
33 34 5.902613 ATTCACCAACATTATGACCACAG 57.097 39.130 0.00 0.00 0.00 3.66
34 35 3.684908 TCACCAACATTATGACCACAGG 58.315 45.455 0.00 0.00 0.00 4.00
35 36 2.164219 CACCAACATTATGACCACAGGC 59.836 50.000 0.00 0.00 0.00 4.85
36 37 2.041620 ACCAACATTATGACCACAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
37 38 3.091545 CCAACATTATGACCACAGGCTT 58.908 45.455 0.00 0.00 0.00 4.35
38 39 3.119388 CCAACATTATGACCACAGGCTTG 60.119 47.826 0.00 0.00 0.00 4.01
39 40 2.094675 ACATTATGACCACAGGCTTGC 58.905 47.619 0.00 0.00 0.00 4.01
40 41 1.406539 CATTATGACCACAGGCTTGCC 59.593 52.381 2.97 2.97 0.00 4.52
41 42 0.403655 TTATGACCACAGGCTTGCCA 59.596 50.000 14.54 0.00 0.00 4.92
42 43 0.403655 TATGACCACAGGCTTGCCAA 59.596 50.000 14.54 0.00 0.00 4.52
43 44 1.181098 ATGACCACAGGCTTGCCAAC 61.181 55.000 14.54 0.00 0.00 3.77
44 45 2.521708 ACCACAGGCTTGCCAACC 60.522 61.111 14.54 0.00 0.00 3.77
45 46 2.521465 CCACAGGCTTGCCAACCA 60.521 61.111 14.54 0.00 0.00 3.67
46 47 2.730094 CACAGGCTTGCCAACCAC 59.270 61.111 14.54 0.00 0.00 4.16
47 48 1.829533 CACAGGCTTGCCAACCACT 60.830 57.895 14.54 0.00 0.00 4.00
48 49 1.829533 ACAGGCTTGCCAACCACTG 60.830 57.895 14.54 4.71 0.00 3.66
49 50 2.914097 AGGCTTGCCAACCACTGC 60.914 61.111 14.54 0.00 0.00 4.40
50 51 3.225798 GGCTTGCCAACCACTGCA 61.226 61.111 6.79 0.00 35.27 4.41
51 52 2.576832 GGCTTGCCAACCACTGCAT 61.577 57.895 6.79 0.00 37.33 3.96
52 53 1.368579 GCTTGCCAACCACTGCATT 59.631 52.632 0.00 0.00 37.33 3.56
53 54 0.668401 GCTTGCCAACCACTGCATTC 60.668 55.000 0.00 0.00 37.33 2.67
54 55 0.037975 CTTGCCAACCACTGCATTCC 60.038 55.000 0.00 0.00 37.33 3.01
55 56 0.758310 TTGCCAACCACTGCATTCCA 60.758 50.000 0.00 0.00 37.33 3.53
57 58 1.880819 GCCAACCACTGCATTCCAGG 61.881 60.000 0.00 0.00 46.14 4.45
58 59 0.251297 CCAACCACTGCATTCCAGGA 60.251 55.000 0.00 0.00 46.14 3.86
59 60 1.617804 CCAACCACTGCATTCCAGGAT 60.618 52.381 0.00 0.00 46.14 3.24
60 61 1.747355 CAACCACTGCATTCCAGGATC 59.253 52.381 0.00 0.00 46.14 3.36
61 62 1.293062 ACCACTGCATTCCAGGATCT 58.707 50.000 0.00 0.00 46.14 2.75
62 63 1.637553 ACCACTGCATTCCAGGATCTT 59.362 47.619 0.00 0.00 46.14 2.40
63 64 2.295885 CCACTGCATTCCAGGATCTTC 58.704 52.381 0.00 0.00 46.14 2.87
64 65 1.938577 CACTGCATTCCAGGATCTTCG 59.061 52.381 0.00 0.00 46.14 3.79
65 66 1.556911 ACTGCATTCCAGGATCTTCGT 59.443 47.619 0.00 0.00 46.14 3.85
66 67 1.938577 CTGCATTCCAGGATCTTCGTG 59.061 52.381 0.00 0.00 37.93 4.35
70 71 4.528674 CCAGGATCTTCGTGGCAG 57.471 61.111 3.54 0.00 44.19 4.85
71 72 1.599047 CCAGGATCTTCGTGGCAGT 59.401 57.895 3.54 0.00 44.19 4.40
72 73 0.460987 CCAGGATCTTCGTGGCAGTC 60.461 60.000 3.54 0.00 44.19 3.51
73 74 0.534412 CAGGATCTTCGTGGCAGTCT 59.466 55.000 0.00 0.00 0.00 3.24
74 75 1.066573 CAGGATCTTCGTGGCAGTCTT 60.067 52.381 0.00 0.00 0.00 3.01
75 76 1.625818 AGGATCTTCGTGGCAGTCTTT 59.374 47.619 0.00 0.00 0.00 2.52
76 77 1.734465 GGATCTTCGTGGCAGTCTTTG 59.266 52.381 0.00 0.00 0.00 2.77
86 87 3.389741 CAGTCTTTGCATCGCCAAC 57.610 52.632 0.00 0.00 0.00 3.77
87 88 0.453282 CAGTCTTTGCATCGCCAACG 60.453 55.000 0.00 0.00 42.01 4.10
88 89 1.797537 GTCTTTGCATCGCCAACGC 60.798 57.895 0.00 0.00 39.84 4.84
89 90 2.504681 CTTTGCATCGCCAACGCC 60.505 61.111 0.00 0.00 39.84 5.68
90 91 4.397090 TTTGCATCGCCAACGCCG 62.397 61.111 0.00 0.00 39.84 6.46
117 118 4.143333 CCGTGGGGGTGTAGAGCG 62.143 72.222 0.00 0.00 0.00 5.03
118 119 3.379445 CGTGGGGGTGTAGAGCGT 61.379 66.667 0.00 0.00 0.00 5.07
119 120 2.264794 GTGGGGGTGTAGAGCGTG 59.735 66.667 0.00 0.00 0.00 5.34
120 121 2.118732 TGGGGGTGTAGAGCGTGA 59.881 61.111 0.00 0.00 0.00 4.35
121 122 2.280552 TGGGGGTGTAGAGCGTGAC 61.281 63.158 0.00 0.00 0.00 3.67
122 123 2.280552 GGGGGTGTAGAGCGTGACA 61.281 63.158 0.00 0.00 0.00 3.58
123 124 1.614241 GGGGGTGTAGAGCGTGACAT 61.614 60.000 0.00 0.00 0.00 3.06
124 125 1.108776 GGGGTGTAGAGCGTGACATA 58.891 55.000 0.00 0.00 0.00 2.29
125 126 1.687123 GGGGTGTAGAGCGTGACATAT 59.313 52.381 0.00 0.00 0.00 1.78
126 127 2.288273 GGGGTGTAGAGCGTGACATATC 60.288 54.545 0.00 0.00 0.00 1.63
127 128 2.623889 GGGTGTAGAGCGTGACATATCT 59.376 50.000 0.00 0.00 0.00 1.98
128 129 3.819337 GGGTGTAGAGCGTGACATATCTA 59.181 47.826 0.00 0.00 0.00 1.98
129 130 4.459685 GGGTGTAGAGCGTGACATATCTAT 59.540 45.833 0.00 0.00 0.00 1.98
130 131 5.646793 GGGTGTAGAGCGTGACATATCTATA 59.353 44.000 0.00 0.00 0.00 1.31
131 132 6.403418 GGGTGTAGAGCGTGACATATCTATAC 60.403 46.154 10.40 10.40 36.32 1.47
132 133 6.372103 GGTGTAGAGCGTGACATATCTATACT 59.628 42.308 14.90 0.00 36.89 2.12
133 134 7.094720 GGTGTAGAGCGTGACATATCTATACTT 60.095 40.741 14.90 0.00 36.89 2.24
134 135 8.933807 GTGTAGAGCGTGACATATCTATACTTA 58.066 37.037 11.09 0.00 35.03 2.24
215 216 4.435651 GGTTAGTTGACTTATCACGCAAGC 60.436 45.833 0.00 0.00 45.62 4.01
219 230 4.330074 AGTTGACTTATCACGCAAGCATAC 59.670 41.667 0.00 0.00 45.62 2.39
223 234 5.160699 ACTTATCACGCAAGCATACATTG 57.839 39.130 0.00 0.00 45.62 2.82
231 242 3.778718 CGCAAGCATACATTGTAACGAAC 59.221 43.478 0.00 0.00 0.00 3.95
233 244 5.022021 GCAAGCATACATTGTAACGAACTC 58.978 41.667 0.00 0.00 0.00 3.01
254 265 3.932710 TCCGATGAATACAGTTGAGTTGC 59.067 43.478 0.00 0.00 0.00 4.17
257 268 5.496387 CGATGAATACAGTTGAGTTGCATC 58.504 41.667 0.00 0.00 0.00 3.91
264 275 5.683876 ACAGTTGAGTTGCATCCTATAGT 57.316 39.130 0.00 0.00 0.00 2.12
273 284 8.486210 TGAGTTGCATCCTATAGTTTTCTACAT 58.514 33.333 0.00 0.00 35.02 2.29
274 285 9.982651 GAGTTGCATCCTATAGTTTTCTACATA 57.017 33.333 0.00 0.00 35.02 2.29
323 334 1.355210 GACAACACAACCACGCCAG 59.645 57.895 0.00 0.00 0.00 4.85
334 345 0.742990 CCACGCCAGCTATTTCCGAA 60.743 55.000 0.00 0.00 0.00 4.30
335 346 1.299541 CACGCCAGCTATTTCCGAAT 58.700 50.000 0.00 0.00 0.00 3.34
336 347 1.261619 CACGCCAGCTATTTCCGAATC 59.738 52.381 0.00 0.00 0.00 2.52
337 348 0.508641 CGCCAGCTATTTCCGAATCG 59.491 55.000 0.00 0.00 0.00 3.34
382 393 1.609208 ACCCATGTGCAGTCAAAGTC 58.391 50.000 0.00 0.00 0.00 3.01
423 436 2.166829 TGCATGTACATTGTCCCAACC 58.833 47.619 5.37 0.00 0.00 3.77
455 477 1.031235 TGTGTGTTGATGCAGGGTTG 58.969 50.000 0.00 0.00 0.00 3.77
507 529 1.887242 CGGCAAAGCGCTATGGCTA 60.887 57.895 12.05 0.00 43.93 3.93
642 664 6.272324 AGAATCTCCCCAATAATATGGTCGAA 59.728 38.462 0.00 0.00 38.91 3.71
751 775 2.159517 GCCGCAAAAGATACAAGTGGAG 60.160 50.000 0.00 0.00 31.69 3.86
840 864 2.032528 CATCGCCACACCACACCT 59.967 61.111 0.00 0.00 0.00 4.00
854 878 1.522355 CACCTCACCGCATAGCCTG 60.522 63.158 0.00 0.00 0.00 4.85
923 947 0.315568 CCAGCTGATCCCTACGTAGC 59.684 60.000 17.39 6.59 34.71 3.58
2340 2394 3.827898 GTGGTCGAGGAGGAGGCG 61.828 72.222 0.00 0.00 0.00 5.52
2793 2847 1.070445 GAGGCCATGATCGGTGGAG 59.930 63.158 18.31 0.00 39.12 3.86
2794 2848 1.383109 AGGCCATGATCGGTGGAGA 60.383 57.895 18.31 0.00 39.12 3.71
2795 2849 0.765903 AGGCCATGATCGGTGGAGAT 60.766 55.000 18.31 3.10 39.12 2.75
2796 2850 0.604780 GGCCATGATCGGTGGAGATG 60.605 60.000 18.31 1.18 39.12 2.90
2817 2871 1.069204 GATGGAGCGAGGTCAGCAATA 59.931 52.381 4.64 0.00 37.01 1.90
2876 2930 1.153349 GGGTCCTCAGATCAACGGC 60.153 63.158 0.00 0.00 0.00 5.68
2904 2961 1.539388 CGCATGTAGGGTTTTGAAGCA 59.461 47.619 0.00 0.00 0.00 3.91
2907 2964 1.234821 TGTAGGGTTTTGAAGCAGCG 58.765 50.000 0.00 0.00 0.00 5.18
2908 2965 0.109735 GTAGGGTTTTGAAGCAGCGC 60.110 55.000 0.00 0.00 0.00 5.92
2909 2966 1.241315 TAGGGTTTTGAAGCAGCGCC 61.241 55.000 2.29 0.00 0.00 6.53
2910 2967 2.727544 GGTTTTGAAGCAGCGCCA 59.272 55.556 2.29 0.00 0.00 5.69
2911 2968 1.372128 GGTTTTGAAGCAGCGCCAG 60.372 57.895 2.29 0.00 0.00 4.85
3097 3154 8.871686 TGTTTCCTTAATTTCTTTGCTCTTTC 57.128 30.769 0.00 0.00 0.00 2.62
3202 3260 0.896226 GCCGGAACCCCTATAGCTAG 59.104 60.000 5.05 0.00 0.00 3.42
3203 3261 0.896226 CCGGAACCCCTATAGCTAGC 59.104 60.000 6.62 6.62 0.00 3.42
3204 3262 1.629043 CGGAACCCCTATAGCTAGCA 58.371 55.000 18.83 3.19 0.00 3.49
3205 3263 2.180276 CGGAACCCCTATAGCTAGCAT 58.820 52.381 18.83 10.87 0.00 3.79
3206 3264 2.093973 CGGAACCCCTATAGCTAGCATG 60.094 54.545 18.83 3.46 0.00 4.06
3207 3265 2.355209 GGAACCCCTATAGCTAGCATGC 60.355 54.545 18.83 10.51 0.00 4.06
3208 3266 2.334006 ACCCCTATAGCTAGCATGCT 57.666 50.000 25.99 25.99 46.11 3.79
3210 3268 3.100671 ACCCCTATAGCTAGCATGCTAC 58.899 50.000 23.52 18.70 46.60 3.58
3211 3269 3.245803 ACCCCTATAGCTAGCATGCTACT 60.246 47.826 23.52 23.75 46.60 2.57
3212 3270 3.383185 CCCCTATAGCTAGCATGCTACTC 59.617 52.174 23.52 16.97 46.60 2.59
3216 3274 6.068010 CCTATAGCTAGCATGCTACTCCTAT 58.932 44.000 23.52 24.88 46.60 2.57
3218 3276 4.046286 AGCTAGCATGCTACTCCTATCT 57.954 45.455 23.52 3.33 42.10 1.98
3220 3278 4.837860 AGCTAGCATGCTACTCCTATCTTT 59.162 41.667 23.52 0.00 42.10 2.52
3264 3338 7.284261 TGATTTACATGTTCCTTGTCTTGTTGA 59.716 33.333 2.30 0.00 0.00 3.18
3458 3533 9.511272 TTTTTCTCCTAGTATTACCCTGTTTTC 57.489 33.333 0.00 0.00 0.00 2.29
3460 3535 5.361857 TCTCCTAGTATTACCCTGTTTTCGG 59.638 44.000 0.00 0.00 0.00 4.30
3462 3537 5.484998 TCCTAGTATTACCCTGTTTTCGGTT 59.515 40.000 0.00 0.00 33.36 4.44
3463 3538 6.667414 TCCTAGTATTACCCTGTTTTCGGTTA 59.333 38.462 0.00 0.00 33.36 2.85
3464 3539 6.982724 CCTAGTATTACCCTGTTTTCGGTTAG 59.017 42.308 0.00 0.00 33.36 2.34
3488 3563 7.305474 AGCAACACGAAAGAAAACTATATTGG 58.695 34.615 0.00 0.00 0.00 3.16
3498 3573 5.812642 AGAAAACTATATTGGACAGCGTCAG 59.187 40.000 10.14 1.96 33.68 3.51
3500 3575 5.847111 AACTATATTGGACAGCGTCAGTA 57.153 39.130 10.14 1.94 33.68 2.74
3522 3597 9.632969 CAGTACGTAAACAAAGATTATGTATGC 57.367 33.333 0.00 0.00 37.19 3.14
3532 3607 9.243105 ACAAAGATTATGTATGCCACTTACTTT 57.757 29.630 0.00 0.00 0.00 2.66
3539 3615 5.815581 TGTATGCCACTTACTTTCCTGATT 58.184 37.500 0.00 0.00 0.00 2.57
3542 3618 4.072131 TGCCACTTACTTTCCTGATTCAC 58.928 43.478 0.00 0.00 0.00 3.18
3553 3629 5.426689 TTCCTGATTCACAAGAGTAGCAT 57.573 39.130 0.00 0.00 0.00 3.79
3573 3649 4.626287 GCATTAGGTCAATGTTCAGAGGGA 60.626 45.833 0.00 0.00 45.05 4.20
3580 3656 5.248640 GTCAATGTTCAGAGGGATCTTTGA 58.751 41.667 0.00 0.00 37.19 2.69
3596 3672 2.079170 TTGAGAGATCTCCGGCTGAT 57.921 50.000 19.30 9.10 42.20 2.90
3603 3679 4.346418 AGAGATCTCCGGCTGATACAAAAT 59.654 41.667 19.30 0.00 0.00 1.82
3652 3728 3.828875 AGCTAGTGCCAAATACCTCTC 57.171 47.619 0.00 0.00 40.80 3.20
3653 3729 3.379452 AGCTAGTGCCAAATACCTCTCT 58.621 45.455 0.00 0.00 40.80 3.10
3654 3730 3.386402 AGCTAGTGCCAAATACCTCTCTC 59.614 47.826 0.00 0.00 40.80 3.20
3655 3731 2.969628 AGTGCCAAATACCTCTCTCG 57.030 50.000 0.00 0.00 0.00 4.04
3683 3759 1.209019 AGGTTCTGCTGCATAGACCTG 59.791 52.381 22.73 4.16 30.07 4.00
3693 3769 6.814043 TGCTGCATAGACCTGATATGATATC 58.186 40.000 5.50 5.50 33.30 1.63
3707 3783 8.584063 TGATATGATATCATTGGGGTTTCATG 57.416 34.615 22.84 0.00 37.76 3.07
3775 3853 5.670792 AGACAATATCTGGTGAAACGGTA 57.329 39.130 0.00 0.00 38.12 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.916360 AATGTTGGTGAATTGTTGGATAGT 57.084 33.333 0.00 0.00 0.00 2.12
1 2 8.685427 TCATAATGTTGGTGAATTGTTGGATAG 58.315 33.333 0.00 0.00 0.00 2.08
2 3 8.465999 GTCATAATGTTGGTGAATTGTTGGATA 58.534 33.333 0.00 0.00 0.00 2.59
3 4 7.322664 GTCATAATGTTGGTGAATTGTTGGAT 58.677 34.615 0.00 0.00 0.00 3.41
4 5 6.295011 GGTCATAATGTTGGTGAATTGTTGGA 60.295 38.462 0.00 0.00 0.00 3.53
5 6 5.868801 GGTCATAATGTTGGTGAATTGTTGG 59.131 40.000 0.00 0.00 0.00 3.77
6 7 6.365789 GTGGTCATAATGTTGGTGAATTGTTG 59.634 38.462 0.00 0.00 0.00 3.33
7 8 6.041409 TGTGGTCATAATGTTGGTGAATTGTT 59.959 34.615 0.00 0.00 0.00 2.83
8 9 5.538053 TGTGGTCATAATGTTGGTGAATTGT 59.462 36.000 0.00 0.00 0.00 2.71
9 10 6.023357 TGTGGTCATAATGTTGGTGAATTG 57.977 37.500 0.00 0.00 0.00 2.32
10 11 5.185635 CCTGTGGTCATAATGTTGGTGAATT 59.814 40.000 0.00 0.00 0.00 2.17
11 12 4.706476 CCTGTGGTCATAATGTTGGTGAAT 59.294 41.667 0.00 0.00 0.00 2.57
12 13 4.078537 CCTGTGGTCATAATGTTGGTGAA 58.921 43.478 0.00 0.00 0.00 3.18
13 14 3.684908 CCTGTGGTCATAATGTTGGTGA 58.315 45.455 0.00 0.00 0.00 4.02
14 15 2.164219 GCCTGTGGTCATAATGTTGGTG 59.836 50.000 0.00 0.00 0.00 4.17
15 16 2.041620 AGCCTGTGGTCATAATGTTGGT 59.958 45.455 0.00 0.00 0.00 3.67
16 17 2.726821 AGCCTGTGGTCATAATGTTGG 58.273 47.619 0.00 0.00 0.00 3.77
17 18 3.674138 GCAAGCCTGTGGTCATAATGTTG 60.674 47.826 0.00 0.00 0.00 3.33
18 19 2.493278 GCAAGCCTGTGGTCATAATGTT 59.507 45.455 0.00 0.00 0.00 2.71
19 20 2.094675 GCAAGCCTGTGGTCATAATGT 58.905 47.619 0.00 0.00 0.00 2.71
20 21 1.406539 GGCAAGCCTGTGGTCATAATG 59.593 52.381 3.29 0.00 0.00 1.90
21 22 1.005805 TGGCAAGCCTGTGGTCATAAT 59.994 47.619 12.96 0.00 36.94 1.28
22 23 0.403655 TGGCAAGCCTGTGGTCATAA 59.596 50.000 12.96 0.00 36.94 1.90
23 24 0.403655 TTGGCAAGCCTGTGGTCATA 59.596 50.000 12.96 0.00 36.94 2.15
24 25 1.153524 TTGGCAAGCCTGTGGTCAT 59.846 52.632 12.96 0.00 36.94 3.06
25 26 1.827789 GTTGGCAAGCCTGTGGTCA 60.828 57.895 12.96 0.00 36.94 4.02
26 27 2.564721 GGTTGGCAAGCCTGTGGTC 61.565 63.158 18.29 0.00 36.94 4.02
27 28 2.521708 GGTTGGCAAGCCTGTGGT 60.522 61.111 18.29 0.00 36.94 4.16
28 29 2.521465 TGGTTGGCAAGCCTGTGG 60.521 61.111 25.02 0.00 36.94 4.17
29 30 1.829533 AGTGGTTGGCAAGCCTGTG 60.830 57.895 25.02 0.00 36.94 3.66
30 31 1.829533 CAGTGGTTGGCAAGCCTGT 60.830 57.895 25.02 8.08 36.94 4.00
31 32 3.045142 CAGTGGTTGGCAAGCCTG 58.955 61.111 25.02 24.14 36.94 4.85
32 33 2.914097 GCAGTGGTTGGCAAGCCT 60.914 61.111 25.02 18.23 36.94 4.58
33 34 2.103339 AATGCAGTGGTTGGCAAGCC 62.103 55.000 25.02 17.26 44.20 4.35
34 35 0.668401 GAATGCAGTGGTTGGCAAGC 60.668 55.000 21.83 21.83 44.20 4.01
35 36 0.037975 GGAATGCAGTGGTTGGCAAG 60.038 55.000 0.00 0.00 44.20 4.01
36 37 0.758310 TGGAATGCAGTGGTTGGCAA 60.758 50.000 0.00 0.00 44.20 4.52
37 38 1.152589 TGGAATGCAGTGGTTGGCA 60.153 52.632 0.00 0.00 45.23 4.92
38 39 1.588082 CTGGAATGCAGTGGTTGGC 59.412 57.895 0.00 0.00 0.00 4.52
39 40 0.251297 TCCTGGAATGCAGTGGTTGG 60.251 55.000 0.21 0.00 0.00 3.77
40 41 1.747355 GATCCTGGAATGCAGTGGTTG 59.253 52.381 0.00 0.00 0.00 3.77
41 42 1.637553 AGATCCTGGAATGCAGTGGTT 59.362 47.619 0.00 0.00 0.00 3.67
42 43 1.293062 AGATCCTGGAATGCAGTGGT 58.707 50.000 0.00 0.00 0.00 4.16
43 44 2.295885 GAAGATCCTGGAATGCAGTGG 58.704 52.381 0.00 0.00 0.00 4.00
44 45 1.938577 CGAAGATCCTGGAATGCAGTG 59.061 52.381 0.00 0.00 0.00 3.66
45 46 1.556911 ACGAAGATCCTGGAATGCAGT 59.443 47.619 0.00 0.00 0.00 4.40
46 47 1.938577 CACGAAGATCCTGGAATGCAG 59.061 52.381 0.00 0.00 0.00 4.41
47 48 1.407299 CCACGAAGATCCTGGAATGCA 60.407 52.381 0.00 0.00 0.00 3.96
48 49 1.303309 CCACGAAGATCCTGGAATGC 58.697 55.000 0.00 0.00 0.00 3.56
49 50 1.303309 GCCACGAAGATCCTGGAATG 58.697 55.000 0.00 0.00 0.00 2.67
50 51 0.911769 TGCCACGAAGATCCTGGAAT 59.088 50.000 0.00 0.00 0.00 3.01
51 52 0.250234 CTGCCACGAAGATCCTGGAA 59.750 55.000 0.00 0.00 0.00 3.53
52 53 0.904865 ACTGCCACGAAGATCCTGGA 60.905 55.000 0.00 0.00 0.00 3.86
53 54 0.460987 GACTGCCACGAAGATCCTGG 60.461 60.000 0.00 0.00 0.00 4.45
54 55 0.534412 AGACTGCCACGAAGATCCTG 59.466 55.000 0.00 0.00 0.00 3.86
55 56 1.270907 AAGACTGCCACGAAGATCCT 58.729 50.000 0.00 0.00 0.00 3.24
56 57 1.734465 CAAAGACTGCCACGAAGATCC 59.266 52.381 0.00 0.00 0.00 3.36
57 58 1.129437 GCAAAGACTGCCACGAAGATC 59.871 52.381 0.00 0.00 46.13 2.75
58 59 1.160137 GCAAAGACTGCCACGAAGAT 58.840 50.000 0.00 0.00 46.13 2.40
59 60 2.616969 GCAAAGACTGCCACGAAGA 58.383 52.632 0.00 0.00 46.13 2.87
68 69 0.453282 CGTTGGCGATGCAAAGACTG 60.453 55.000 0.00 0.00 41.33 3.51
69 70 1.868997 CGTTGGCGATGCAAAGACT 59.131 52.632 0.00 0.00 41.33 3.24
70 71 1.797537 GCGTTGGCGATGCAAAGAC 60.798 57.895 14.13 0.00 40.14 3.01
71 72 2.560861 GCGTTGGCGATGCAAAGA 59.439 55.556 14.13 0.00 40.14 2.52
72 73 2.504681 GGCGTTGGCGATGCAAAG 60.505 61.111 20.14 0.00 42.27 2.77
83 84 4.117372 GTCGAAGCGACGGCGTTG 62.117 66.667 22.69 22.69 46.56 4.10
94 95 2.221906 CTACACCCCCACGGTCGAAG 62.222 65.000 0.00 0.00 43.58 3.79
95 96 2.203611 TACACCCCCACGGTCGAA 60.204 61.111 0.00 0.00 43.58 3.71
96 97 2.677524 CTACACCCCCACGGTCGA 60.678 66.667 0.00 0.00 43.58 4.20
97 98 2.677524 TCTACACCCCCACGGTCG 60.678 66.667 0.00 0.00 43.58 4.79
98 99 3.015312 GCTCTACACCCCCACGGTC 62.015 68.421 0.00 0.00 43.58 4.79
100 101 4.143333 CGCTCTACACCCCCACGG 62.143 72.222 0.00 0.00 37.81 4.94
101 102 3.379445 ACGCTCTACACCCCCACG 61.379 66.667 0.00 0.00 0.00 4.94
102 103 2.264794 CACGCTCTACACCCCCAC 59.735 66.667 0.00 0.00 0.00 4.61
103 104 2.118732 TCACGCTCTACACCCCCA 59.881 61.111 0.00 0.00 0.00 4.96
104 105 1.614241 ATGTCACGCTCTACACCCCC 61.614 60.000 0.00 0.00 0.00 5.40
105 106 1.108776 TATGTCACGCTCTACACCCC 58.891 55.000 0.00 0.00 0.00 4.95
106 107 2.623889 AGATATGTCACGCTCTACACCC 59.376 50.000 0.00 0.00 0.00 4.61
107 108 3.992260 AGATATGTCACGCTCTACACC 57.008 47.619 0.00 0.00 0.00 4.16
108 109 7.367159 AGTATAGATATGTCACGCTCTACAC 57.633 40.000 0.00 0.00 0.00 2.90
109 110 7.981102 AAGTATAGATATGTCACGCTCTACA 57.019 36.000 0.00 0.00 0.00 2.74
113 114 9.291664 GGAAATAAGTATAGATATGTCACGCTC 57.708 37.037 0.00 0.00 0.00 5.03
114 115 8.803235 TGGAAATAAGTATAGATATGTCACGCT 58.197 33.333 0.00 0.00 0.00 5.07
115 116 8.981724 TGGAAATAAGTATAGATATGTCACGC 57.018 34.615 0.00 0.00 0.00 5.34
177 178 9.747898 AGTCAACTAACCCTATCATATCTCTAG 57.252 37.037 0.00 0.00 0.00 2.43
185 186 7.434492 CGTGATAAGTCAACTAACCCTATCAT 58.566 38.462 5.32 0.00 35.80 2.45
188 189 5.128171 TGCGTGATAAGTCAACTAACCCTAT 59.872 40.000 0.00 0.00 35.80 2.57
201 202 4.635765 ACAATGTATGCTTGCGTGATAAGT 59.364 37.500 0.00 0.00 0.00 2.24
205 206 4.494035 CGTTACAATGTATGCTTGCGTGAT 60.494 41.667 0.00 0.00 0.00 3.06
207 208 3.090699 CGTTACAATGTATGCTTGCGTG 58.909 45.455 0.00 0.00 0.00 5.34
209 210 3.649870 TCGTTACAATGTATGCTTGCG 57.350 42.857 0.00 0.00 0.00 4.85
215 216 5.746721 TCATCGGAGTTCGTTACAATGTATG 59.253 40.000 0.00 0.00 40.32 2.39
219 230 5.718649 ATTCATCGGAGTTCGTTACAATG 57.281 39.130 0.00 0.00 40.32 2.82
223 234 5.338365 ACTGTATTCATCGGAGTTCGTTAC 58.662 41.667 0.00 0.00 40.32 2.50
231 242 4.033358 GCAACTCAACTGTATTCATCGGAG 59.967 45.833 0.00 0.00 0.00 4.63
233 244 3.684305 TGCAACTCAACTGTATTCATCGG 59.316 43.478 0.00 0.00 0.00 4.18
264 275 6.183360 CCACGCCAGCTATTTTATGTAGAAAA 60.183 38.462 0.00 0.00 33.04 2.29
273 284 5.247084 TCTAAAACCACGCCAGCTATTTTA 58.753 37.500 0.00 0.00 0.00 1.52
274 285 4.076394 TCTAAAACCACGCCAGCTATTTT 58.924 39.130 0.00 0.00 0.00 1.82
334 345 2.359981 TGTACTCCTTCCGATCCGAT 57.640 50.000 0.00 0.00 0.00 4.18
335 346 2.133281 TTGTACTCCTTCCGATCCGA 57.867 50.000 0.00 0.00 0.00 4.55
336 347 3.123804 CAATTGTACTCCTTCCGATCCG 58.876 50.000 0.00 0.00 0.00 4.18
337 348 4.099573 TCTCAATTGTACTCCTTCCGATCC 59.900 45.833 5.13 0.00 0.00 3.36
338 349 5.263968 TCTCAATTGTACTCCTTCCGATC 57.736 43.478 5.13 0.00 0.00 3.69
339 350 5.878406 ATCTCAATTGTACTCCTTCCGAT 57.122 39.130 5.13 0.00 0.00 4.18
382 393 2.847327 AAGGATGCATGGGTAGATCG 57.153 50.000 2.46 0.00 0.00 3.69
423 436 0.996462 ACACACACTGTCACGTTTCG 59.004 50.000 0.00 0.00 0.00 3.46
507 529 2.928334 TCTCGATCTTACGGCCTACTT 58.072 47.619 0.00 0.00 0.00 2.24
557 579 1.244019 GGGTGTGGTTCAGTGGATGC 61.244 60.000 0.00 0.00 0.00 3.91
642 664 3.052455 TGTGGTGATATGTGCTTTCGT 57.948 42.857 0.00 0.00 0.00 3.85
751 775 3.689002 CTTTCCTCCTCCCCGCAGC 62.689 68.421 0.00 0.00 0.00 5.25
840 864 4.175337 GGCCAGGCTATGCGGTGA 62.175 66.667 12.43 0.00 0.00 4.02
854 878 3.247886 GCGAATTGTTAGTTAGCTAGGCC 59.752 47.826 0.00 0.00 0.00 5.19
1452 1506 3.372554 GAGGTCCGGCGGGAAAGAG 62.373 68.421 27.98 0.00 46.08 2.85
1683 1737 1.517257 CTGCAGGAAGTAGGACGCG 60.517 63.158 5.57 3.53 0.00 6.01
2394 2448 2.154462 CCGAACACCTTCAAGAATGCT 58.846 47.619 0.00 0.00 0.00 3.79
2793 2847 0.033228 CTGACCTCGCTCCATCCATC 59.967 60.000 0.00 0.00 0.00 3.51
2794 2848 2.037620 GCTGACCTCGCTCCATCCAT 62.038 60.000 0.00 0.00 0.00 3.41
2795 2849 2.725312 GCTGACCTCGCTCCATCCA 61.725 63.158 0.00 0.00 0.00 3.41
2796 2850 2.107953 GCTGACCTCGCTCCATCC 59.892 66.667 0.00 0.00 0.00 3.51
2817 2871 1.167851 CATCCAATCCTTGCACGTGT 58.832 50.000 18.38 0.00 0.00 4.49
2876 2930 2.228241 CCCTACATGCGCGTACGTG 61.228 63.158 23.94 23.94 42.83 4.49
2907 2964 3.044059 CTACGCTTGCTTGCCTGGC 62.044 63.158 12.87 12.87 0.00 4.85
2908 2965 2.401766 CCTACGCTTGCTTGCCTGG 61.402 63.158 0.00 0.00 0.00 4.45
2909 2966 1.364626 CTCCTACGCTTGCTTGCCTG 61.365 60.000 0.00 0.00 0.00 4.85
2910 2967 1.078848 CTCCTACGCTTGCTTGCCT 60.079 57.895 0.00 0.00 0.00 4.75
2911 2968 2.109126 CCTCCTACGCTTGCTTGCC 61.109 63.158 0.00 0.00 0.00 4.52
3055 3112 4.091800 GGAAACAAATCAAATCATGGCGTG 59.908 41.667 0.00 0.00 0.00 5.34
3097 3154 3.247648 ACAAGACGATCGAAACACAAAGG 59.752 43.478 24.34 2.32 0.00 3.11
3140 3198 3.391506 AAGTTTGCTCCAAAAGGATGC 57.608 42.857 0.00 0.00 35.03 3.91
3142 3200 4.766404 CGTAAGTTTGCTCCAAAAGGAT 57.234 40.909 0.00 0.00 35.03 3.24
3202 3260 4.213059 GCAAGAAAGATAGGAGTAGCATGC 59.787 45.833 10.51 10.51 0.00 4.06
3203 3261 5.363101 TGCAAGAAAGATAGGAGTAGCATG 58.637 41.667 0.00 0.00 0.00 4.06
3204 3262 5.620738 TGCAAGAAAGATAGGAGTAGCAT 57.379 39.130 0.00 0.00 0.00 3.79
3205 3263 5.620738 ATGCAAGAAAGATAGGAGTAGCA 57.379 39.130 0.00 0.00 0.00 3.49
3206 3264 7.062839 CGATAATGCAAGAAAGATAGGAGTAGC 59.937 40.741 0.00 0.00 0.00 3.58
3207 3265 8.300286 TCGATAATGCAAGAAAGATAGGAGTAG 58.700 37.037 0.00 0.00 0.00 2.57
3208 3266 8.178313 TCGATAATGCAAGAAAGATAGGAGTA 57.822 34.615 0.00 0.00 0.00 2.59
3209 3267 7.055667 TCGATAATGCAAGAAAGATAGGAGT 57.944 36.000 0.00 0.00 0.00 3.85
3210 3268 7.961855 CATCGATAATGCAAGAAAGATAGGAG 58.038 38.462 0.00 0.00 0.00 3.69
3211 3269 7.895975 CATCGATAATGCAAGAAAGATAGGA 57.104 36.000 0.00 0.00 0.00 2.94
3264 3338 5.988561 GTCAAGAAGACAAGAACTGACATCT 59.011 40.000 0.00 0.00 46.77 2.90
3439 3514 5.349061 ACCGAAAACAGGGTAATACTAGG 57.651 43.478 0.00 0.00 33.95 3.02
3442 3517 5.181009 GCTAACCGAAAACAGGGTAATACT 58.819 41.667 0.00 0.00 34.85 2.12
3444 3519 5.163281 TGCTAACCGAAAACAGGGTAATA 57.837 39.130 0.00 0.00 34.85 0.98
3447 3522 3.140623 GTTGCTAACCGAAAACAGGGTA 58.859 45.455 0.00 0.00 34.85 3.69
3448 3523 1.951602 GTTGCTAACCGAAAACAGGGT 59.048 47.619 0.00 0.00 38.44 4.34
3452 3527 2.277969 TCGTGTTGCTAACCGAAAACA 58.722 42.857 0.00 0.00 33.40 2.83
3453 3528 3.322230 TTCGTGTTGCTAACCGAAAAC 57.678 42.857 15.46 0.00 39.40 2.43
3457 3532 2.512485 TCTTTCGTGTTGCTAACCGA 57.488 45.000 0.00 0.00 34.10 4.69
3458 3533 3.595709 TTTCTTTCGTGTTGCTAACCG 57.404 42.857 0.00 0.00 0.00 4.44
3460 3535 9.821662 AATATAGTTTTCTTTCGTGTTGCTAAC 57.178 29.630 0.00 0.00 0.00 2.34
3462 3537 8.447833 CCAATATAGTTTTCTTTCGTGTTGCTA 58.552 33.333 0.00 0.00 0.00 3.49
3463 3538 7.174253 TCCAATATAGTTTTCTTTCGTGTTGCT 59.826 33.333 0.00 0.00 0.00 3.91
3464 3539 7.270579 GTCCAATATAGTTTTCTTTCGTGTTGC 59.729 37.037 0.00 0.00 0.00 4.17
3498 3573 8.605746 TGGCATACATAATCTTTGTTTACGTAC 58.394 33.333 0.00 0.00 0.00 3.67
3500 3575 7.335924 AGTGGCATACATAATCTTTGTTTACGT 59.664 33.333 0.00 0.00 0.00 3.57
3522 3597 5.997746 TCTTGTGAATCAGGAAAGTAAGTGG 59.002 40.000 0.00 0.00 0.00 4.00
3528 3603 5.221722 TGCTACTCTTGTGAATCAGGAAAGT 60.222 40.000 0.00 0.00 31.90 2.66
3532 3607 5.426689 AATGCTACTCTTGTGAATCAGGA 57.573 39.130 0.00 0.00 0.00 3.86
3539 3615 5.738619 TTGACCTAATGCTACTCTTGTGA 57.261 39.130 0.00 0.00 0.00 3.58
3553 3629 5.032846 AGATCCCTCTGAACATTGACCTAA 58.967 41.667 0.00 0.00 0.00 2.69
3580 3656 2.666272 TGTATCAGCCGGAGATCTCT 57.334 50.000 21.81 3.24 0.00 3.10
3596 3672 8.137437 GCACTACTCGTAATACCCTATTTTGTA 58.863 37.037 0.00 0.00 0.00 2.41
3603 3679 4.139786 CCAGCACTACTCGTAATACCCTA 58.860 47.826 0.00 0.00 0.00 3.53
3652 3728 1.079543 CAGAACCTGCCTGGACGAG 60.080 63.158 0.00 0.00 39.71 4.18
3653 3729 3.059982 CAGAACCTGCCTGGACGA 58.940 61.111 0.00 0.00 39.71 4.20
3678 3754 6.319048 ACCCCAATGATATCATATCAGGTC 57.681 41.667 18.47 0.00 35.10 3.85
3683 3759 7.835682 TCCATGAAACCCCAATGATATCATATC 59.164 37.037 18.47 8.95 35.10 1.63
3693 3769 4.025360 TCAATCTCCATGAAACCCCAATG 58.975 43.478 0.00 0.00 0.00 2.82
3707 3783 3.376546 GCCATTTGTCACTCTCAATCTCC 59.623 47.826 0.00 0.00 0.00 3.71
3761 3839 1.000506 GCTCTGTACCGTTTCACCAGA 59.999 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.