Multiple sequence alignment - TraesCS5A01G189700

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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 TraesCS5A01G189700 chr5A 100.000 3272 0 0 1 3272 393251902 393255173 0.000000e+00 6043
1 TraesCS5A01G189700 chr5D 94.353 3099 103 35 196 3272 304876108 304879156 0.000000e+00 4687
2 TraesCS5A01G189700 chr5B 92.265 3038 119 38 106 3106 349711202 349714160 0.000000e+00 4202
3 TraesCS5A01G189700 chr5B 95.652 92 2 2 3161 3252 349714637 349714726 2.630000e-31 147


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 TraesCS5A01G189700 chr5A 393251902 393255173 3271 False 6043.0 6043 100.0000 1 3272 1 chr5A.!!$F1 3271
1 TraesCS5A01G189700 chr5D 304876108 304879156 3048 False 4687.0 4687 94.3530 196 3272 1 chr5D.!!$F1 3076
2 TraesCS5A01G189700 chr5B 349711202 349714726 3524 False 2174.5 4202 93.9585 106 3252 2 chr5B.!!$F1 3146

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
105 106 0.246360 CCCGCATCAGTGTCTGTGTA 59.754 55.0 7.78 0.0 32.61 2.90 F
158 159 0.613853 TGTCCGATTCGAGGGTCCTT 60.614 55.0 7.83 0.0 0.00 3.36 F
1872 1894 1.051812 ACAGCAGCAACTACCTGTCT 58.948 50.0 0.00 0.0 33.57 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1894 0.836400 AGCCGAGGAGGTTCTGGAAA 60.836 55.000 0.0 0.0 43.7 3.13 R
2143 2165 2.148052 TGTGGGGCGGGTAGTTCAA 61.148 57.895 0.0 0.0 0.0 2.69 R
3148 3207 0.321671 TCCTTCTCGCCAAACCTCTG 59.678 55.000 0.0 0.0 0.0 3.35 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
21 22 4.632538 AAACCAAAACTAGATATGCGGC 57.367 40.909 0.00 0.00 0.00 6.53
22 23 3.560636 ACCAAAACTAGATATGCGGCT 57.439 42.857 0.00 0.00 0.00 5.52
23 24 4.682778 ACCAAAACTAGATATGCGGCTA 57.317 40.909 0.00 0.00 0.00 3.93
24 25 5.228945 ACCAAAACTAGATATGCGGCTAT 57.771 39.130 0.00 0.00 0.00 2.97
25 26 5.621193 ACCAAAACTAGATATGCGGCTATT 58.379 37.500 0.00 0.00 0.00 1.73
26 27 5.701290 ACCAAAACTAGATATGCGGCTATTC 59.299 40.000 0.00 0.00 0.00 1.75
27 28 5.934625 CCAAAACTAGATATGCGGCTATTCT 59.065 40.000 0.00 3.13 0.00 2.40
28 29 6.128445 CCAAAACTAGATATGCGGCTATTCTG 60.128 42.308 0.00 0.00 0.00 3.02
29 30 5.984695 AACTAGATATGCGGCTATTCTGA 57.015 39.130 0.00 0.00 0.00 3.27
30 31 6.537453 AACTAGATATGCGGCTATTCTGAT 57.463 37.500 0.00 0.00 0.00 2.90
31 32 6.142818 ACTAGATATGCGGCTATTCTGATC 57.857 41.667 0.00 0.00 0.00 2.92
32 33 4.039151 AGATATGCGGCTATTCTGATCG 57.961 45.455 0.00 0.00 0.00 3.69
33 34 3.445450 AGATATGCGGCTATTCTGATCGT 59.555 43.478 0.00 0.00 0.00 3.73
34 35 1.788258 ATGCGGCTATTCTGATCGTG 58.212 50.000 0.00 0.00 0.00 4.35
35 36 0.875908 TGCGGCTATTCTGATCGTGC 60.876 55.000 0.00 0.00 0.00 5.34
36 37 0.875908 GCGGCTATTCTGATCGTGCA 60.876 55.000 0.00 0.00 0.00 4.57
37 38 1.135046 CGGCTATTCTGATCGTGCAG 58.865 55.000 0.00 1.67 37.24 4.41
38 39 1.269257 CGGCTATTCTGATCGTGCAGA 60.269 52.381 6.00 6.00 42.81 4.26
39 40 2.131183 GGCTATTCTGATCGTGCAGAC 58.869 52.381 8.99 0.15 44.08 3.51
40 41 2.223923 GGCTATTCTGATCGTGCAGACT 60.224 50.000 8.99 7.23 44.08 3.24
41 42 3.004839 GGCTATTCTGATCGTGCAGACTA 59.995 47.826 8.99 7.86 44.08 2.59
42 43 4.499865 GGCTATTCTGATCGTGCAGACTAA 60.500 45.833 8.99 0.00 44.08 2.24
43 44 5.043903 GCTATTCTGATCGTGCAGACTAAA 58.956 41.667 8.99 0.00 44.08 1.85
44 45 5.520288 GCTATTCTGATCGTGCAGACTAAAA 59.480 40.000 8.99 0.00 44.08 1.52
45 46 6.036083 GCTATTCTGATCGTGCAGACTAAAAA 59.964 38.462 8.99 0.00 44.08 1.94
60 61 4.167597 AAAAATGGGTGCGGACGT 57.832 50.000 0.00 0.00 0.00 4.34
61 62 3.325902 AAAAATGGGTGCGGACGTA 57.674 47.368 0.00 0.00 0.00 3.57
62 63 1.828979 AAAAATGGGTGCGGACGTAT 58.171 45.000 0.00 0.00 0.00 3.06
63 64 1.091537 AAAATGGGTGCGGACGTATG 58.908 50.000 0.00 0.00 0.00 2.39
64 65 1.373590 AAATGGGTGCGGACGTATGC 61.374 55.000 0.00 4.63 0.00 3.14
65 66 4.805231 TGGGTGCGGACGTATGCG 62.805 66.667 0.19 0.19 43.57 4.73
66 67 4.501714 GGGTGCGGACGTATGCGA 62.502 66.667 11.07 0.00 43.37 5.10
67 68 3.252484 GGTGCGGACGTATGCGAC 61.252 66.667 11.07 3.13 43.37 5.19
68 69 2.202570 GTGCGGACGTATGCGACT 60.203 61.111 11.07 0.00 43.37 4.18
69 70 1.063006 GTGCGGACGTATGCGACTA 59.937 57.895 11.07 0.00 43.37 2.59
70 71 0.317603 GTGCGGACGTATGCGACTAT 60.318 55.000 11.07 0.00 43.37 2.12
71 72 1.069703 GTGCGGACGTATGCGACTATA 60.070 52.381 11.07 0.00 43.37 1.31
72 73 1.808343 TGCGGACGTATGCGACTATAT 59.192 47.619 11.07 0.00 43.37 0.86
73 74 2.227149 TGCGGACGTATGCGACTATATT 59.773 45.455 11.07 0.00 43.37 1.28
74 75 2.592897 GCGGACGTATGCGACTATATTG 59.407 50.000 11.07 0.00 43.37 1.90
75 76 3.168963 CGGACGTATGCGACTATATTGG 58.831 50.000 11.07 0.00 43.37 3.16
76 77 3.120095 CGGACGTATGCGACTATATTGGA 60.120 47.826 11.07 0.00 43.37 3.53
77 78 4.438336 CGGACGTATGCGACTATATTGGAT 60.438 45.833 11.07 0.00 43.37 3.41
78 79 4.798907 GGACGTATGCGACTATATTGGATG 59.201 45.833 11.07 0.00 42.00 3.51
79 80 4.744570 ACGTATGCGACTATATTGGATGG 58.255 43.478 11.07 0.00 42.00 3.51
80 81 3.551890 CGTATGCGACTATATTGGATGGC 59.448 47.826 0.00 0.00 41.33 4.40
81 82 2.472695 TGCGACTATATTGGATGGCC 57.527 50.000 0.00 0.00 0.00 5.36
82 83 1.337728 TGCGACTATATTGGATGGCCG 60.338 52.381 0.00 0.00 36.79 6.13
83 84 1.337823 GCGACTATATTGGATGGCCGT 60.338 52.381 0.00 0.00 36.79 5.68
84 85 2.607187 CGACTATATTGGATGGCCGTC 58.393 52.381 17.28 17.28 36.79 4.79
85 86 2.231478 CGACTATATTGGATGGCCGTCT 59.769 50.000 24.11 7.67 36.79 4.18
86 87 3.673594 CGACTATATTGGATGGCCGTCTC 60.674 52.174 24.11 14.61 36.79 3.36
87 88 2.567615 ACTATATTGGATGGCCGTCTCC 59.432 50.000 24.11 17.14 36.79 3.71
88 89 0.693049 ATATTGGATGGCCGTCTCCC 59.307 55.000 24.11 9.57 36.79 4.30
89 90 1.754380 TATTGGATGGCCGTCTCCCG 61.754 60.000 24.11 0.00 36.79 5.14
92 93 4.241555 GATGGCCGTCTCCCGCAT 62.242 66.667 18.25 0.00 34.38 4.73
93 94 4.241555 ATGGCCGTCTCCCGCATC 62.242 66.667 0.00 0.00 34.38 3.91
95 96 4.899239 GGCCGTCTCCCGCATCAG 62.899 72.222 0.00 0.00 34.38 2.90
96 97 4.148825 GCCGTCTCCCGCATCAGT 62.149 66.667 0.00 0.00 34.38 3.41
97 98 2.202797 CCGTCTCCCGCATCAGTG 60.203 66.667 0.00 0.00 34.38 3.66
98 99 2.573869 CGTCTCCCGCATCAGTGT 59.426 61.111 0.00 0.00 0.00 3.55
99 100 1.517257 CGTCTCCCGCATCAGTGTC 60.517 63.158 0.00 0.00 0.00 3.67
100 101 1.893786 GTCTCCCGCATCAGTGTCT 59.106 57.895 0.00 0.00 0.00 3.41
101 102 0.459237 GTCTCCCGCATCAGTGTCTG 60.459 60.000 0.00 0.00 0.00 3.51
102 103 0.900182 TCTCCCGCATCAGTGTCTGT 60.900 55.000 0.00 0.00 32.61 3.41
103 104 0.738762 CTCCCGCATCAGTGTCTGTG 60.739 60.000 0.00 0.00 32.61 3.66
104 105 1.004560 CCCGCATCAGTGTCTGTGT 60.005 57.895 7.78 0.00 32.61 3.72
105 106 0.246360 CCCGCATCAGTGTCTGTGTA 59.754 55.000 7.78 0.00 32.61 2.90
106 107 1.350193 CCGCATCAGTGTCTGTGTAC 58.650 55.000 7.78 0.00 32.61 2.90
107 108 1.067565 CCGCATCAGTGTCTGTGTACT 60.068 52.381 0.00 0.00 32.61 2.73
108 109 1.988467 CGCATCAGTGTCTGTGTACTG 59.012 52.381 0.00 0.00 44.31 2.74
109 110 2.341257 GCATCAGTGTCTGTGTACTGG 58.659 52.381 0.00 0.00 43.40 4.00
110 111 2.289072 GCATCAGTGTCTGTGTACTGGT 60.289 50.000 0.00 0.00 43.40 4.00
111 112 3.579709 CATCAGTGTCTGTGTACTGGTC 58.420 50.000 0.00 0.00 43.40 4.02
119 120 1.993948 GTGTACTGGTCCCCCTCCC 60.994 68.421 0.00 0.00 0.00 4.30
156 157 1.141234 GTGTCCGATTCGAGGGTCC 59.859 63.158 7.83 0.00 0.00 4.46
157 158 1.000019 TGTCCGATTCGAGGGTCCT 60.000 57.895 7.83 0.00 0.00 3.85
158 159 0.613853 TGTCCGATTCGAGGGTCCTT 60.614 55.000 7.83 0.00 0.00 3.36
173 174 1.923356 TCCTTGTTGGAAATGCCCTC 58.077 50.000 0.00 0.00 42.94 4.30
192 193 6.183360 TGCCCTCATACTACATTTTAGAGGAC 60.183 42.308 7.12 0.00 42.87 3.85
194 195 7.473511 GCCCTCATACTACATTTTAGAGGACAT 60.474 40.741 7.12 0.00 42.87 3.06
241 242 9.154847 CTTGACAGAATTTCTTTGTTTTTCCTT 57.845 29.630 0.00 0.00 0.00 3.36
243 244 8.934825 TGACAGAATTTCTTTGTTTTTCCTTTG 58.065 29.630 0.00 0.00 0.00 2.77
276 277 2.884997 TTCCATCGAACCGCATGGGG 62.885 60.000 26.22 26.22 40.21 4.96
277 278 2.189257 CATCGAACCGCATGGGGA 59.811 61.111 33.50 12.98 41.60 4.81
278 279 1.227943 CATCGAACCGCATGGGGAT 60.228 57.895 33.50 23.35 41.60 3.85
287 288 2.290896 ACCGCATGGGGATATATGGTTG 60.291 50.000 33.50 4.36 41.60 3.77
329 330 6.957920 TGAACACTCTTCCATCAAAATTCA 57.042 33.333 0.00 0.00 0.00 2.57
332 333 5.717119 ACACTCTTCCATCAAAATTCATGC 58.283 37.500 0.00 0.00 0.00 4.06
354 355 5.240623 TGCAGTTTTGTAATCTTACACAGGG 59.759 40.000 2.33 0.00 42.84 4.45
408 409 2.969628 ACGTTCTCAGAGGCCATAAG 57.030 50.000 5.01 0.00 0.00 1.73
409 410 2.457598 ACGTTCTCAGAGGCCATAAGA 58.542 47.619 5.01 0.00 0.00 2.10
566 573 5.514274 AACAATGTAGTTCACCAAACCAG 57.486 39.130 0.00 0.00 38.76 4.00
653 661 1.472552 GCAACAACAACAAACCTCCCC 60.473 52.381 0.00 0.00 0.00 4.81
712 720 4.072088 GAACGTGCGCCGAACCAG 62.072 66.667 22.10 1.40 40.70 4.00
787 802 3.117888 TCACACCAAAGCTTCTCTTCCTT 60.118 43.478 0.00 0.00 32.88 3.36
792 807 3.755905 CCAAAGCTTCTCTTCCTTCCTTC 59.244 47.826 0.00 0.00 32.88 3.46
793 808 3.712016 AAGCTTCTCTTCCTTCCTTCC 57.288 47.619 0.00 0.00 0.00 3.46
794 809 2.914536 AGCTTCTCTTCCTTCCTTCCT 58.085 47.619 0.00 0.00 0.00 3.36
795 810 2.837591 AGCTTCTCTTCCTTCCTTCCTC 59.162 50.000 0.00 0.00 0.00 3.71
796 811 2.093181 GCTTCTCTTCCTTCCTTCCTCC 60.093 54.545 0.00 0.00 0.00 4.30
797 812 2.255770 TCTCTTCCTTCCTTCCTCCC 57.744 55.000 0.00 0.00 0.00 4.30
798 813 1.725182 TCTCTTCCTTCCTTCCTCCCT 59.275 52.381 0.00 0.00 0.00 4.20
799 814 2.115427 CTCTTCCTTCCTTCCTCCCTC 58.885 57.143 0.00 0.00 0.00 4.30
863 878 2.409870 GGGCGCTTGTGGAATGGAG 61.410 63.158 7.64 0.00 0.00 3.86
970 989 2.950638 TCGGGGGAGGGAGAAGGA 60.951 66.667 0.00 0.00 0.00 3.36
972 991 2.764547 GGGGGAGGGAGAAGGACG 60.765 72.222 0.00 0.00 0.00 4.79
974 993 1.758906 GGGGAGGGAGAAGGACGAG 60.759 68.421 0.00 0.00 0.00 4.18
1180 1199 1.136305 TCTACGGCCTTCAGGATTTCG 59.864 52.381 0.00 0.00 37.39 3.46
1240 1262 2.908940 ACCAGCAACACCAGCAGC 60.909 61.111 0.00 0.00 0.00 5.25
1241 1263 2.908428 CCAGCAACACCAGCAGCA 60.908 61.111 0.00 0.00 0.00 4.41
1242 1264 2.643272 CAGCAACACCAGCAGCAG 59.357 61.111 0.00 0.00 0.00 4.24
1872 1894 1.051812 ACAGCAGCAACTACCTGTCT 58.948 50.000 0.00 0.00 33.57 3.41
2298 2320 5.136105 AGAGAAAGAGAAAGGTGCATGTTT 58.864 37.500 0.00 0.00 0.00 2.83
2329 2351 3.560105 GCTCCCTGATTAATTTGCTCCT 58.440 45.455 0.00 0.00 0.00 3.69
2330 2352 3.567585 GCTCCCTGATTAATTTGCTCCTC 59.432 47.826 0.00 0.00 0.00 3.71
2331 2353 3.808728 TCCCTGATTAATTTGCTCCTCG 58.191 45.455 0.00 0.00 0.00 4.63
2332 2354 2.291741 CCCTGATTAATTTGCTCCTCGC 59.708 50.000 0.00 0.00 39.77 5.03
2333 2355 3.209410 CCTGATTAATTTGCTCCTCGCT 58.791 45.455 0.00 0.00 40.11 4.93
2334 2356 3.629398 CCTGATTAATTTGCTCCTCGCTT 59.371 43.478 0.00 0.00 40.11 4.68
2387 2409 9.343539 AGGTCTGGTTAATCATCTTTATTTAGC 57.656 33.333 0.00 0.00 0.00 3.09
2414 2440 9.893305 ATTATACCTTTTGTTGCTTATTATCGC 57.107 29.630 0.00 0.00 0.00 4.58
2434 2460 2.891580 GCCTTCTATCTCCGTCACCATA 59.108 50.000 0.00 0.00 0.00 2.74
2475 2501 4.425577 AAACATCATCTTTGGTTCGCTC 57.574 40.909 0.00 0.00 0.00 5.03
2488 2514 3.884091 TGGTTCGCTCCTCTCTTAGATAC 59.116 47.826 0.00 0.00 0.00 2.24
2553 2584 7.009179 ACAGACATTGATTTCTTGTCCTCTA 57.991 36.000 9.25 0.00 40.46 2.43
2554 2585 6.876257 ACAGACATTGATTTCTTGTCCTCTAC 59.124 38.462 9.25 0.00 40.46 2.59
2555 2586 7.102346 CAGACATTGATTTCTTGTCCTCTACT 58.898 38.462 9.25 0.00 40.46 2.57
2556 2587 8.253810 CAGACATTGATTTCTTGTCCTCTACTA 58.746 37.037 9.25 0.00 40.46 1.82
2557 2588 8.986991 AGACATTGATTTCTTGTCCTCTACTAT 58.013 33.333 9.25 0.00 40.46 2.12
2558 2589 8.954950 ACATTGATTTCTTGTCCTCTACTATG 57.045 34.615 0.00 0.00 0.00 2.23
2559 2590 8.543774 ACATTGATTTCTTGTCCTCTACTATGT 58.456 33.333 0.00 0.00 0.00 2.29
2616 2647 4.640201 GCATCACTAAAGCTGGTTTATCCA 59.360 41.667 11.96 0.79 45.01 3.41
2725 2757 4.938226 GGTGTGTCATAAAGAAAGGAGGAG 59.062 45.833 0.00 0.00 0.00 3.69
2779 2811 4.219033 CGTAACTCATCAAACTGCCAAAC 58.781 43.478 0.00 0.00 0.00 2.93
2795 2827 3.803778 GCCAAACAAGTCATTTTCTGGTG 59.196 43.478 0.00 0.00 0.00 4.17
2977 3018 8.850156 AGAATAAACCCCGATTTGATTAATCTG 58.150 33.333 16.24 2.04 40.46 2.90
3134 3183 2.550830 ACTGATGAAACGAAGGCAGT 57.449 45.000 0.00 0.00 0.00 4.40
3146 3205 2.223548 CGAAGGCAGTGAGAGAGAGATG 60.224 54.545 0.00 0.00 0.00 2.90
3148 3207 0.104671 GGCAGTGAGAGAGAGATGCC 59.895 60.000 0.00 0.00 45.61 4.40
3157 3216 2.500910 AGAGAGAGATGCCAGAGGTTTG 59.499 50.000 0.00 0.00 0.00 2.93
3175 3646 2.680312 TGGCGAGAAGGAGATCTTTG 57.320 50.000 0.00 0.00 35.50 2.77
3218 3689 1.134877 AGGACGACGACGATGTAGAGA 60.135 52.381 15.32 0.00 42.66 3.10
3238 3709 7.862274 AGAGATAGATTGAGAGAGAGAGAGA 57.138 40.000 0.00 0.00 0.00 3.10
3240 3711 7.013823 AGATAGATTGAGAGAGAGAGAGAGG 57.986 44.000 0.00 0.00 0.00 3.69
3241 3712 6.789457 AGATAGATTGAGAGAGAGAGAGAGGA 59.211 42.308 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.886123 AGCCGCATATCTAGTTTTGGTT 58.114 40.909 0.00 0.00 0.00 3.67
2 3 3.560636 AGCCGCATATCTAGTTTTGGT 57.439 42.857 0.00 0.00 0.00 3.67
3 4 5.934625 AGAATAGCCGCATATCTAGTTTTGG 59.065 40.000 0.00 0.00 0.00 3.28
4 5 6.646653 TCAGAATAGCCGCATATCTAGTTTTG 59.353 38.462 0.00 0.00 0.00 2.44
5 6 6.759272 TCAGAATAGCCGCATATCTAGTTTT 58.241 36.000 0.00 0.00 0.00 2.43
7 8 5.984695 TCAGAATAGCCGCATATCTAGTT 57.015 39.130 0.00 0.00 0.00 2.24
8 9 5.220951 CGATCAGAATAGCCGCATATCTAGT 60.221 44.000 0.00 0.00 0.00 2.57
9 10 5.211454 CGATCAGAATAGCCGCATATCTAG 58.789 45.833 0.00 0.00 0.00 2.43
10 11 4.640647 ACGATCAGAATAGCCGCATATCTA 59.359 41.667 0.00 0.00 0.00 1.98
11 12 3.445450 ACGATCAGAATAGCCGCATATCT 59.555 43.478 0.00 0.00 0.00 1.98
12 13 3.549471 CACGATCAGAATAGCCGCATATC 59.451 47.826 0.00 0.00 0.00 1.63
13 14 3.515630 CACGATCAGAATAGCCGCATAT 58.484 45.455 0.00 0.00 0.00 1.78
14 15 2.926586 GCACGATCAGAATAGCCGCATA 60.927 50.000 0.00 0.00 0.00 3.14
15 16 1.788258 CACGATCAGAATAGCCGCAT 58.212 50.000 0.00 0.00 0.00 4.73
16 17 0.875908 GCACGATCAGAATAGCCGCA 60.876 55.000 0.00 0.00 0.00 5.69
17 18 0.875908 TGCACGATCAGAATAGCCGC 60.876 55.000 0.00 0.00 0.00 6.53
18 19 1.135046 CTGCACGATCAGAATAGCCG 58.865 55.000 0.00 0.00 36.19 5.52
19 20 2.131183 GTCTGCACGATCAGAATAGCC 58.869 52.381 11.65 0.00 43.89 3.93
20 21 3.090952 AGTCTGCACGATCAGAATAGC 57.909 47.619 11.65 2.33 43.89 2.97
21 22 7.525688 TTTTTAGTCTGCACGATCAGAATAG 57.474 36.000 14.48 0.00 42.29 1.73
43 44 1.470890 CATACGTCCGCACCCATTTTT 59.529 47.619 0.00 0.00 0.00 1.94
44 45 1.091537 CATACGTCCGCACCCATTTT 58.908 50.000 0.00 0.00 0.00 1.82
45 46 1.373590 GCATACGTCCGCACCCATTT 61.374 55.000 0.00 0.00 0.00 2.32
46 47 1.817941 GCATACGTCCGCACCCATT 60.818 57.895 0.00 0.00 0.00 3.16
47 48 2.203015 GCATACGTCCGCACCCAT 60.203 61.111 0.00 0.00 0.00 4.00
48 49 4.805231 CGCATACGTCCGCACCCA 62.805 66.667 9.49 0.00 33.53 4.51
49 50 4.501714 TCGCATACGTCCGCACCC 62.502 66.667 9.49 0.00 41.18 4.61
50 51 2.327002 TAGTCGCATACGTCCGCACC 62.327 60.000 9.49 0.00 41.18 5.01
51 52 0.317603 ATAGTCGCATACGTCCGCAC 60.318 55.000 9.49 6.72 41.18 5.34
52 53 1.228533 TATAGTCGCATACGTCCGCA 58.771 50.000 9.49 0.00 41.18 5.69
53 54 2.539346 ATATAGTCGCATACGTCCGC 57.461 50.000 0.00 0.00 41.18 5.54
54 55 3.120095 TCCAATATAGTCGCATACGTCCG 60.120 47.826 0.00 0.00 41.18 4.79
55 56 4.430137 TCCAATATAGTCGCATACGTCC 57.570 45.455 0.00 0.00 41.18 4.79
56 57 4.798907 CCATCCAATATAGTCGCATACGTC 59.201 45.833 0.00 0.00 41.18 4.34
57 58 4.744570 CCATCCAATATAGTCGCATACGT 58.255 43.478 0.00 0.00 41.18 3.57
58 59 3.551890 GCCATCCAATATAGTCGCATACG 59.448 47.826 0.00 0.00 42.01 3.06
59 60 3.871594 GGCCATCCAATATAGTCGCATAC 59.128 47.826 0.00 0.00 0.00 2.39
60 61 3.430236 CGGCCATCCAATATAGTCGCATA 60.430 47.826 2.24 0.00 0.00 3.14
61 62 2.677902 CGGCCATCCAATATAGTCGCAT 60.678 50.000 2.24 0.00 0.00 4.73
62 63 1.337728 CGGCCATCCAATATAGTCGCA 60.338 52.381 2.24 0.00 0.00 5.10
63 64 1.337823 ACGGCCATCCAATATAGTCGC 60.338 52.381 2.24 0.00 0.00 5.19
64 65 2.231478 AGACGGCCATCCAATATAGTCG 59.769 50.000 2.24 0.00 33.15 4.18
65 66 3.368531 GGAGACGGCCATCCAATATAGTC 60.369 52.174 12.64 3.28 35.54 2.59
66 67 2.567615 GGAGACGGCCATCCAATATAGT 59.432 50.000 12.64 0.00 35.54 2.12
67 68 2.093447 GGGAGACGGCCATCCAATATAG 60.093 54.545 17.85 0.00 37.33 1.31
68 69 1.906574 GGGAGACGGCCATCCAATATA 59.093 52.381 17.85 0.00 37.33 0.86
69 70 0.693049 GGGAGACGGCCATCCAATAT 59.307 55.000 17.85 0.00 37.33 1.28
70 71 1.754380 CGGGAGACGGCCATCCAATA 61.754 60.000 17.85 0.00 37.33 1.90
71 72 2.919043 GGGAGACGGCCATCCAAT 59.081 61.111 17.85 0.00 37.33 3.16
72 73 3.781307 CGGGAGACGGCCATCCAA 61.781 66.667 17.85 0.00 37.33 3.53
80 81 2.202797 CACTGATGCGGGAGACGG 60.203 66.667 0.00 0.00 44.51 4.79
82 83 0.459237 CAGACACTGATGCGGGAGAC 60.459 60.000 0.00 0.00 32.44 3.36
83 84 0.900182 ACAGACACTGATGCGGGAGA 60.900 55.000 5.76 0.00 35.18 3.71
84 85 0.738762 CACAGACACTGATGCGGGAG 60.739 60.000 5.76 0.00 35.18 4.30
85 86 1.293179 CACAGACACTGATGCGGGA 59.707 57.895 5.76 0.00 35.18 5.14
86 87 0.246360 TACACAGACACTGATGCGGG 59.754 55.000 5.76 0.00 35.18 6.13
87 88 1.067565 AGTACACAGACACTGATGCGG 60.068 52.381 5.76 0.00 35.18 5.69
88 89 1.988467 CAGTACACAGACACTGATGCG 59.012 52.381 5.76 0.00 43.99 4.73
89 90 2.289072 ACCAGTACACAGACACTGATGC 60.289 50.000 5.76 0.00 43.99 3.91
90 91 3.579709 GACCAGTACACAGACACTGATG 58.420 50.000 5.76 3.48 43.99 3.07
91 92 2.563179 GGACCAGTACACAGACACTGAT 59.437 50.000 5.76 0.00 43.99 2.90
92 93 1.961394 GGACCAGTACACAGACACTGA 59.039 52.381 5.76 0.00 43.99 3.41
93 94 1.000955 GGGACCAGTACACAGACACTG 59.999 57.143 0.00 0.00 41.51 3.66
94 95 1.339097 GGGACCAGTACACAGACACT 58.661 55.000 0.00 0.00 0.00 3.55
95 96 3.908737 GGGACCAGTACACAGACAC 57.091 57.895 0.00 0.00 0.00 3.67
153 154 5.112668 TATGAGGGCATTTCCAACAAGGAC 61.113 45.833 0.00 0.00 40.09 3.85
156 157 4.019174 AGTATGAGGGCATTTCCAACAAG 58.981 43.478 0.00 0.00 35.94 3.16
157 158 4.046286 AGTATGAGGGCATTTCCAACAA 57.954 40.909 0.00 0.00 35.94 2.83
158 159 3.737559 AGTATGAGGGCATTTCCAACA 57.262 42.857 0.00 0.00 35.94 3.33
192 193 7.884816 AGAAATTTGAGTGCATGAAAAGATG 57.115 32.000 0.00 0.00 0.00 2.90
194 195 7.436080 GTCAAGAAATTTGAGTGCATGAAAAGA 59.564 33.333 0.00 0.00 0.00 2.52
241 242 7.265647 TCGATGGAAAAGTGTTTGATAACAA 57.734 32.000 0.00 0.00 45.33 2.83
243 244 6.581166 GGTTCGATGGAAAAGTGTTTGATAAC 59.419 38.462 0.00 0.00 33.05 1.89
287 288 1.464219 CATGCGAATTTTGGGTTTGCC 59.536 47.619 0.00 0.00 35.54 4.52
303 304 4.771590 TTTGATGGAAGAGTGTTCATGC 57.228 40.909 2.06 0.00 0.00 4.06
329 330 6.071952 CCCTGTGTAAGATTACAAAACTGCAT 60.072 38.462 6.99 0.00 44.46 3.96
332 333 5.240623 TGCCCTGTGTAAGATTACAAAACTG 59.759 40.000 6.99 0.80 44.46 3.16
354 355 7.948278 AAAACGTAGGAATAGAGTATCATGC 57.052 36.000 0.00 0.00 37.82 4.06
613 620 4.918060 CGTGTGTGTGTGTGCGCG 62.918 66.667 0.00 0.00 0.00 6.86
615 622 4.589700 GGCGTGTGTGTGTGTGCG 62.590 66.667 0.00 0.00 0.00 5.34
616 623 4.589700 CGGCGTGTGTGTGTGTGC 62.590 66.667 0.00 0.00 0.00 4.57
624 632 2.691771 TTGTTGTTGCGGCGTGTGT 61.692 52.632 9.37 0.00 0.00 3.72
863 878 1.671328 GTGGCTAAAAAGAGCGGATCC 59.329 52.381 0.00 0.00 43.83 3.36
953 968 2.950638 TCCTTCTCCCTCCCCCGA 60.951 66.667 0.00 0.00 0.00 5.14
954 969 2.764547 GTCCTTCTCCCTCCCCCG 60.765 72.222 0.00 0.00 0.00 5.73
956 971 1.758906 CTCGTCCTTCTCCCTCCCC 60.759 68.421 0.00 0.00 0.00 4.81
972 991 1.372128 CAAAAGCAGCAACGCCCTC 60.372 57.895 0.00 0.00 0.00 4.30
974 993 1.661509 GACAAAAGCAGCAACGCCC 60.662 57.895 0.00 0.00 0.00 6.13
1198 1217 3.968568 TTGCTGTTGCTGCTGCGG 61.969 61.111 11.21 3.55 43.34 5.69
1199 1218 2.728383 GTTGCTGTTGCTGCTGCG 60.728 61.111 11.21 0.00 43.34 5.18
1284 1306 3.978867 GACACGCGACGACGAGGAG 62.979 68.421 15.93 7.76 43.08 3.69
1383 1405 4.148825 CTCTTCCGCGACCCCCTG 62.149 72.222 8.23 0.00 0.00 4.45
1422 1444 4.295119 GTGAGCACCGTCGTGGGT 62.295 66.667 1.73 0.00 44.64 4.51
1806 1828 1.261480 ACGTCAGCTGGAAGTCATCT 58.739 50.000 15.13 0.00 32.45 2.90
1872 1894 0.836400 AGCCGAGGAGGTTCTGGAAA 60.836 55.000 0.00 0.00 43.70 3.13
2143 2165 2.148052 TGTGGGGCGGGTAGTTCAA 61.148 57.895 0.00 0.00 0.00 2.69
2332 2354 1.153107 TGATGCATGGAGGCGGAAG 60.153 57.895 2.46 0.00 36.28 3.46
2333 2355 1.451927 GTGATGCATGGAGGCGGAA 60.452 57.895 2.46 0.00 36.28 4.30
2334 2356 2.190313 GTGATGCATGGAGGCGGA 59.810 61.111 2.46 0.00 36.28 5.54
2403 2429 5.038033 CGGAGATAGAAGGCGATAATAAGC 58.962 45.833 0.00 0.00 0.00 3.09
2414 2440 4.399219 TCTATGGTGACGGAGATAGAAGG 58.601 47.826 0.00 0.00 0.00 3.46
2434 2460 5.708230 TGTTTTAAATGTACAAGGCCGATCT 59.292 36.000 0.00 0.00 0.00 2.75
2475 2501 7.383572 GCACATGTGTAATGTATCTAAGAGAGG 59.616 40.741 26.01 0.00 0.00 3.69
2488 2514 4.256110 TCTCTCCTTGCACATGTGTAATG 58.744 43.478 26.43 23.26 34.80 1.90
2553 2584 5.068591 TGTGCCGATCAACATAGTACATAGT 59.931 40.000 0.00 0.00 0.00 2.12
2554 2585 5.528870 TGTGCCGATCAACATAGTACATAG 58.471 41.667 0.00 0.00 0.00 2.23
2555 2586 5.068591 ACTGTGCCGATCAACATAGTACATA 59.931 40.000 11.24 0.00 36.60 2.29
2556 2587 4.141937 ACTGTGCCGATCAACATAGTACAT 60.142 41.667 11.24 0.00 36.60 2.29
2557 2588 3.194755 ACTGTGCCGATCAACATAGTACA 59.805 43.478 11.24 0.04 36.60 2.90
2558 2589 3.551890 CACTGTGCCGATCAACATAGTAC 59.448 47.826 12.19 0.00 36.27 2.73
2559 2590 3.194755 ACACTGTGCCGATCAACATAGTA 59.805 43.478 7.90 0.00 36.27 1.82
2560 2591 2.028112 ACACTGTGCCGATCAACATAGT 60.028 45.455 7.90 8.12 38.59 2.12
2561 2592 2.349580 CACACTGTGCCGATCAACATAG 59.650 50.000 7.90 7.05 0.00 2.23
2586 2617 3.119291 CAGCTTTAGTGATGCTACTCGG 58.881 50.000 0.00 0.00 36.69 4.63
2688 2720 4.452733 CACCGCCGGAGAACTCCC 62.453 72.222 11.71 1.86 46.96 4.30
2702 2734 4.906618 TCCTCCTTTCTTTATGACACACC 58.093 43.478 0.00 0.00 0.00 4.16
2725 2757 0.460459 GCAACTACGCCTTCTCTCCC 60.460 60.000 0.00 0.00 0.00 4.30
2779 2811 5.220643 GGTTTTTGCACCAGAAAATGACTTG 60.221 40.000 0.00 0.00 36.73 3.16
2795 2827 0.581529 GGCTTTTCGCTGGTTTTTGC 59.418 50.000 0.00 0.00 39.13 3.68
2977 3018 2.520741 CTCCTCCTCCTCCTCGCC 60.521 72.222 0.00 0.00 0.00 5.54
3134 3183 1.287442 ACCTCTGGCATCTCTCTCTCA 59.713 52.381 0.00 0.00 0.00 3.27
3148 3207 0.321671 TCCTTCTCGCCAAACCTCTG 59.678 55.000 0.00 0.00 0.00 3.35
3157 3216 2.682155 ACAAAGATCTCCTTCTCGCC 57.318 50.000 0.00 0.00 33.02 5.54
3175 3646 3.614588 GTCGACACCTAGCAACAAAAAC 58.385 45.455 11.55 0.00 0.00 2.43
3218 3689 7.392766 TTCCTCTCTCTCTCTCTCAATCTAT 57.607 40.000 0.00 0.00 0.00 1.98
3238 3709 2.624838 CAACTTGTCACTGCCAATTCCT 59.375 45.455 0.00 0.00 0.00 3.36
3240 3711 3.715628 ACAACTTGTCACTGCCAATTC 57.284 42.857 0.00 0.00 0.00 2.17
3241 3712 3.784338 CAACAACTTGTCACTGCCAATT 58.216 40.909 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.