Multiple sequence alignment - TraesCS3B01G576500

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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 TraesCS3B01G576500 chr3B 100.000 2996 0 0 1 2996 806274625 806271630 0.000000e+00 5533.0
1 TraesCS3B01G576500 chr3B 94.266 1587 57 13 597 2157 807074523 807072945 0.000000e+00 2396.0
2 TraesCS3B01G576500 chr3B 93.308 523 24 6 2322 2837 807072945 807072427 0.000000e+00 761.0
3 TraesCS3B01G576500 chr3B 96.078 153 5 1 2170 2321 507737927 507738079 6.410000e-62 248.0
4 TraesCS3B01G576500 chr3B 82.553 235 41 0 965 1199 380868221 380868455 1.090000e-49 207.0
5 TraesCS3B01G576500 chr3B 83.182 220 26 7 1785 2000 380871139 380871351 1.100000e-44 191.0
6 TraesCS3B01G576500 chr3A 88.258 1320 113 18 783 2087 729173866 729172574 0.000000e+00 1541.0
7 TraesCS3B01G576500 chr3A 87.013 693 75 12 2 686 729180537 729179852 0.000000e+00 767.0
8 TraesCS3B01G576500 chr3A 91.388 209 11 3 2324 2529 729172446 729172242 2.270000e-71 279.0
9 TraesCS3B01G576500 chr3A 82.787 244 40 2 957 1199 377648142 377648384 1.810000e-52 217.0
10 TraesCS3B01G576500 chr3D 84.696 1333 120 28 777 2087 599054621 599053351 0.000000e+00 1254.0
11 TraesCS3B01G576500 chr3D 82.979 235 40 0 965 1199 288096199 288096433 2.340000e-51 213.0
12 TraesCS3B01G576500 chr3D 83.562 219 27 5 1785 2000 288099411 288099623 2.360000e-46 196.0
13 TraesCS3B01G576500 chr3D 81.215 181 6 12 866 1046 598995658 598995810 1.460000e-23 121.0
14 TraesCS3B01G576500 chr7A 86.199 413 37 13 1683 2087 688857318 688857718 2.130000e-116 429.0
15 TraesCS3B01G576500 chr7A 97.386 153 3 1 2170 2321 698893517 698893669 2.960000e-65 259.0
16 TraesCS3B01G576500 chr7A 96.732 153 4 1 2170 2321 698788769 698788921 1.380000e-63 254.0
17 TraesCS3B01G576500 chr7A 96.078 153 5 1 2170 2321 698895279 698895431 6.410000e-62 248.0
18 TraesCS3B01G576500 chr7D 96.732 153 4 1 2170 2321 196009215 196009367 1.380000e-63 254.0
19 TraesCS3B01G576500 chr4A 96.078 153 5 1 2170 2321 27645192 27645344 6.410000e-62 248.0
20 TraesCS3B01G576500 chr4A 96.667 150 4 1 2173 2321 554647232 554647083 6.410000e-62 248.0
21 TraesCS3B01G576500 chr2B 96.078 153 5 1 2170 2321 656166565 656166717 6.410000e-62 248.0
22 TraesCS3B01G576500 chr2B 86.935 199 26 0 1001 1199 464432425 464432623 1.080000e-54 224.0
23 TraesCS3B01G576500 chr1A 96.078 153 5 1 2170 2321 10743921 10744073 6.410000e-62 248.0
24 TraesCS3B01G576500 chr2A 87.437 199 25 0 1001 1199 530350488 530350686 2.320000e-56 230.0
25 TraesCS3B01G576500 chr4D 85.882 85 12 0 48 132 487458777 487458861 1.140000e-14 91.6
26 TraesCS3B01G576500 chr5A 86.250 80 9 2 52 130 384128265 384128343 5.320000e-13 86.1
27 TraesCS3B01G576500 chr6D 86.885 61 7 1 54 113 89519933 89519993 1.930000e-07 67.6
28 TraesCS3B01G576500 chr6A 100.000 31 0 0 329 359 548744504 548744534 1.160000e-04 58.4


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 TraesCS3B01G576500 chr3B 806271630 806274625 2995 True 5533.0 5533 100.0000 1 2996 1 chr3B.!!$R1 2995
1 TraesCS3B01G576500 chr3B 807072427 807074523 2096 True 1578.5 2396 93.7870 597 2837 2 chr3B.!!$R2 2240
2 TraesCS3B01G576500 chr3A 729172242 729173866 1624 True 910.0 1541 89.8230 783 2529 2 chr3A.!!$R2 1746
3 TraesCS3B01G576500 chr3A 729179852 729180537 685 True 767.0 767 87.0130 2 686 1 chr3A.!!$R1 684
4 TraesCS3B01G576500 chr3D 599053351 599054621 1270 True 1254.0 1254 84.6960 777 2087 1 chr3D.!!$R1 1310
5 TraesCS3B01G576500 chr3D 288096199 288099623 3424 False 204.5 213 83.2705 965 2000 2 chr3D.!!$F2 1035
6 TraesCS3B01G576500 chr7A 698893517 698895431 1914 False 253.5 259 96.7320 2170 2321 2 chr7A.!!$F3 151

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
290 292 0.113190 AGGGAAGGAAAGTTGGGCAG 59.887 55.0 0.0 0.0 0.0 4.85 F
563 566 0.321671 CAGTTGGGTGATGAGGTCGT 59.678 55.0 0.0 0.0 0.0 4.34 F
568 571 0.460311 GGGTGATGAGGTCGTGTAGG 59.540 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 4269 0.037160 TGAGGATTTGCAGCAGCTGA 59.963 50.000 27.39 5.57 42.74 4.26 R
1833 4271 0.327259 TCTGAGGATTTGCAGCAGCT 59.673 50.000 1.76 0.00 42.74 4.24 R
2146 4652 2.752354 TGATGATGGGCAGTTTTAACCG 59.248 45.455 0.00 0.00 0.00 4.44 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
35 36 6.687105 AGAATAACTCAAATAAAATGCGTCGC 59.313 34.615 11.10 11.10 0.00 5.19
40 41 3.308595 TCAAATAAAATGCGTCGCGATCT 59.691 39.130 14.06 0.00 0.00 2.75
50 51 1.202043 CGTCGCGATCTGTCTAAGTGT 60.202 52.381 14.06 0.00 0.00 3.55
73 75 4.260334 GCACCTGCGAGAACTATAAAAC 57.740 45.455 0.00 0.00 0.00 2.43
82 84 7.107542 TGCGAGAACTATAAAACCCTAACATT 58.892 34.615 0.00 0.00 0.00 2.71
83 85 8.259411 TGCGAGAACTATAAAACCCTAACATTA 58.741 33.333 0.00 0.00 0.00 1.90
94 96 5.526506 ACCCTAACATTAACTACTAGCCG 57.473 43.478 0.00 0.00 0.00 5.52
127 129 0.621862 AGGATTCTCCTCCCCACCAC 60.622 60.000 0.00 0.00 45.66 4.16
130 132 4.715130 TCTCCTCCCCACCACCGG 62.715 72.222 0.00 0.00 0.00 5.28
139 141 4.308458 CACCACCGGCGAACTGGA 62.308 66.667 20.48 0.00 46.41 3.86
166 168 2.093447 GGGTTGTCAAGGATCGACATCT 60.093 50.000 3.21 0.00 42.69 2.90
172 174 1.857217 CAAGGATCGACATCTGCGAAG 59.143 52.381 0.00 0.00 41.52 3.79
186 188 1.289066 CGAAGGCAGAGAACGACCA 59.711 57.895 0.00 0.00 0.00 4.02
192 194 2.026822 AGGCAGAGAACGACCAATGATT 60.027 45.455 0.00 0.00 0.00 2.57
194 196 4.130118 GGCAGAGAACGACCAATGATTAT 58.870 43.478 0.00 0.00 0.00 1.28
215 217 0.179108 GAGCCGCGTAGGAGAATGTT 60.179 55.000 4.92 0.00 45.00 2.71
216 218 0.460284 AGCCGCGTAGGAGAATGTTG 60.460 55.000 4.92 0.00 45.00 3.33
217 219 2.006772 CCGCGTAGGAGAATGTTGC 58.993 57.895 4.92 0.00 45.00 4.17
227 229 2.032204 GGAGAATGTTGCGATGAGATGC 60.032 50.000 0.00 0.00 0.00 3.91
248 250 2.541346 CTGCTATTGTACTGGACATGCG 59.459 50.000 0.00 0.00 38.07 4.73
249 251 1.261619 GCTATTGTACTGGACATGCGC 59.738 52.381 0.00 0.00 38.07 6.09
253 255 0.670239 TGTACTGGACATGCGCTGTG 60.670 55.000 15.61 13.33 38.54 3.66
256 258 1.668793 CTGGACATGCGCTGTGACA 60.669 57.895 18.00 13.90 38.54 3.58
273 275 1.210722 GACAGGGCTAGAAGGGAAAGG 59.789 57.143 0.00 0.00 0.00 3.11
290 292 0.113190 AGGGAAGGAAAGTTGGGCAG 59.887 55.000 0.00 0.00 0.00 4.85
307 309 3.138798 GGCAGCACATGGGAGCAG 61.139 66.667 13.77 5.36 32.55 4.24
309 311 3.506096 CAGCACATGGGAGCAGCG 61.506 66.667 0.00 0.00 32.55 5.18
327 329 1.820906 GCATGAGATTGGCGAGGCA 60.821 57.895 0.00 0.00 0.00 4.75
331 333 0.749091 TGAGATTGGCGAGGCAATGG 60.749 55.000 25.94 0.00 0.00 3.16
341 343 1.734465 CGAGGCAATGGTTCTCACTTC 59.266 52.381 0.00 0.00 0.00 3.01
342 344 1.734465 GAGGCAATGGTTCTCACTTCG 59.266 52.381 0.00 0.00 0.00 3.79
403 406 8.620416 ACATCAAAATATTTCAGCTATACGCAA 58.380 29.630 0.10 0.00 42.61 4.85
476 479 3.005367 GTCCACCGAAACCAATGAAATGT 59.995 43.478 0.00 0.00 0.00 2.71
477 480 3.005261 TCCACCGAAACCAATGAAATGTG 59.995 43.478 0.00 0.00 0.00 3.21
491 494 5.018539 TGAAATGTGGTAATCTCGGTAGG 57.981 43.478 0.00 0.00 0.00 3.18
515 518 6.688813 GGCGCTGAAATATTTCTCAAACTTAG 59.311 38.462 24.77 14.15 38.02 2.18
534 537 7.695869 ACTTAGATTTATAAAACGAGCTCGG 57.304 36.000 36.93 20.54 44.95 4.63
559 562 1.687612 AGCCAGTTGGGTGATGAGG 59.312 57.895 1.37 0.00 45.50 3.86
561 564 0.678048 GCCAGTTGGGTGATGAGGTC 60.678 60.000 0.00 0.00 39.65 3.85
562 565 0.391661 CCAGTTGGGTGATGAGGTCG 60.392 60.000 0.00 0.00 0.00 4.79
563 566 0.321671 CAGTTGGGTGATGAGGTCGT 59.678 55.000 0.00 0.00 0.00 4.34
566 569 1.274167 GTTGGGTGATGAGGTCGTGTA 59.726 52.381 0.00 0.00 0.00 2.90
568 571 0.460311 GGGTGATGAGGTCGTGTAGG 59.540 60.000 0.00 0.00 0.00 3.18
571 574 1.549170 GTGATGAGGTCGTGTAGGGTT 59.451 52.381 0.00 0.00 0.00 4.11
586 589 1.203125 AGGGTTGGGTTGGGTGTAATG 60.203 52.381 0.00 0.00 0.00 1.90
630 633 1.888512 ACGAACTTTACGGACCTGCTA 59.111 47.619 0.00 0.00 34.93 3.49
650 653 7.255451 CCTGCTAACCTGTCTTGTTTTATTTGA 60.255 37.037 0.00 0.00 0.00 2.69
693 698 5.502089 TTAACCGTCCCTCCTGAATTTTA 57.498 39.130 0.00 0.00 0.00 1.52
727 733 5.622233 GCAACCCTGATGAATTTAACTGGTC 60.622 44.000 3.49 0.00 0.00 4.02
728 734 5.520748 ACCCTGATGAATTTAACTGGTCT 57.479 39.130 3.49 0.00 0.00 3.85
756 762 1.822186 CCAGCCCGTAAAATCCCCG 60.822 63.158 0.00 0.00 0.00 5.73
757 763 2.124445 AGCCCGTAAAATCCCCGC 60.124 61.111 0.00 0.00 0.00 6.13
763 769 1.528161 CCGTAAAATCCCCGCGTAATC 59.472 52.381 4.92 0.00 0.00 1.75
774 780 1.255342 CCGCGTAATCGTCAGTTGATG 59.745 52.381 4.92 0.00 39.49 3.07
781 787 5.275927 CGTAATCGTCAGTTGATGTAGCAAG 60.276 44.000 1.60 0.00 33.00 4.01
889 915 4.497507 CGAAGGGATTTTTAAGAATCGGCC 60.498 45.833 11.42 8.61 36.99 6.13
937 968 3.757270 GATCTCTCGAATCCTCTACCCA 58.243 50.000 0.00 0.00 0.00 4.51
1564 2851 9.932699 CTTCTACTGCTCATCATCAAAATTTAG 57.067 33.333 0.00 0.00 0.00 1.85
1575 2862 8.921205 CATCATCAAAATTTAGAGGAGGGAAAT 58.079 33.333 0.00 0.00 0.00 2.17
1585 2878 8.530804 TTTAGAGGAGGGAAATACAGTACTAC 57.469 38.462 0.00 0.00 0.00 2.73
1586 2879 6.344232 AGAGGAGGGAAATACAGTACTACT 57.656 41.667 0.00 0.00 0.00 2.57
1587 2880 6.743788 AGAGGAGGGAAATACAGTACTACTT 58.256 40.000 0.00 0.00 0.00 2.24
1594 2890 6.127423 GGGAAATACAGTACTACTTGCAGAGA 60.127 42.308 0.00 0.00 0.00 3.10
1783 4221 7.391833 AGAGTGCCAATAAAGAAGAAGTAAAGG 59.608 37.037 0.00 0.00 0.00 3.11
1830 4268 7.309744 CCCAAATTGATAGTAAAGCCAAAGTCA 60.310 37.037 0.00 0.00 0.00 3.41
1831 4269 8.253113 CCAAATTGATAGTAAAGCCAAAGTCAT 58.747 33.333 0.00 0.00 0.00 3.06
1832 4270 9.294030 CAAATTGATAGTAAAGCCAAAGTCATC 57.706 33.333 0.00 0.00 0.00 2.92
1833 4271 8.579850 AATTGATAGTAAAGCCAAAGTCATCA 57.420 30.769 0.00 0.00 0.00 3.07
2000 4444 4.031089 CGATGAAAGTGATGAGTGAAGACG 59.969 45.833 0.00 0.00 0.00 4.18
2027 4471 2.736144 TTCGAGTCATAACCGCACTT 57.264 45.000 0.00 0.00 0.00 3.16
2039 4483 0.034059 CCGCACTTCAGGAGACAAGT 59.966 55.000 0.00 0.00 32.87 3.16
2158 4664 8.959734 AATATTAACTTGACGGTTAAAACTGC 57.040 30.769 1.54 0.00 42.46 4.40
2159 4665 3.703286 AACTTGACGGTTAAAACTGCC 57.297 42.857 1.54 0.00 38.89 4.85
2160 4666 1.951602 ACTTGACGGTTAAAACTGCCC 59.048 47.619 1.54 0.00 38.89 5.36
2161 4667 1.950909 CTTGACGGTTAAAACTGCCCA 59.049 47.619 1.54 0.00 38.89 5.36
2162 4668 2.279935 TGACGGTTAAAACTGCCCAT 57.720 45.000 1.54 0.00 38.89 4.00
2163 4669 2.156098 TGACGGTTAAAACTGCCCATC 58.844 47.619 1.54 0.00 38.89 3.51
2164 4670 2.156098 GACGGTTAAAACTGCCCATCA 58.844 47.619 1.54 0.00 38.89 3.07
2165 4671 2.752903 GACGGTTAAAACTGCCCATCAT 59.247 45.455 1.54 0.00 38.89 2.45
2166 4672 2.752903 ACGGTTAAAACTGCCCATCATC 59.247 45.455 1.54 0.00 38.89 2.92
2167 4673 2.752354 CGGTTAAAACTGCCCATCATCA 59.248 45.455 0.00 0.00 0.00 3.07
2168 4674 3.192422 CGGTTAAAACTGCCCATCATCAA 59.808 43.478 0.00 0.00 0.00 2.57
2175 4681 4.307032 ACTGCCCATCATCAAAACTAGT 57.693 40.909 0.00 0.00 0.00 2.57
2284 4791 4.342092 GGTGGCCTTGTATAGATGCAAAAT 59.658 41.667 3.32 0.00 32.12 1.82
2352 5871 3.499737 CCAATCAGGTCGGCGCAC 61.500 66.667 10.83 0.00 0.00 5.34
2360 5879 2.456119 GGTCGGCGCACTCAGATTG 61.456 63.158 10.83 0.00 0.00 2.67
2417 5958 2.039746 TCATTTTGACATGGACGAGGGT 59.960 45.455 0.00 0.00 0.00 4.34
2451 5992 9.921637 GGAATACTCTGATTTTGATCTACCTAG 57.078 37.037 0.00 0.00 0.00 3.02
2568 6581 5.749109 CCTATGACACTACGACAATTCCTTC 59.251 44.000 0.00 0.00 0.00 3.46
2589 6602 0.611340 AGTCCGGTACCACTCCAGTC 60.611 60.000 13.54 0.00 0.00 3.51
2599 6612 3.162666 ACCACTCCAGTCTTGATCGTAA 58.837 45.455 0.00 0.00 0.00 3.18
2661 6678 5.928839 GCTGTTCTTCTCTCTCAAACATGTA 59.071 40.000 0.00 0.00 0.00 2.29
2665 6682 9.591792 TGTTCTTCTCTCTCAAACATGTATATG 57.408 33.333 0.00 0.00 40.24 1.78
2681 6698 4.225042 TGTATATGCCGCCCTTCAATATCT 59.775 41.667 0.00 0.00 0.00 1.98
2688 6705 3.694072 CCGCCCTTCAATATCTTTGTTCA 59.306 43.478 0.00 0.00 0.00 3.18
2708 6725 4.744570 TCAACATGTAAAACGTTTTGCCA 58.255 34.783 31.26 26.18 32.72 4.92
2725 6742 4.926140 TGCCAAACACATGTTGAACATA 57.074 36.364 10.89 0.00 36.53 2.29
2824 6841 7.476667 TGTCACAAACATTCTTTTCGTAACAT 58.523 30.769 0.00 0.00 31.20 2.71
2825 6842 7.430793 TGTCACAAACATTCTTTTCGTAACATG 59.569 33.333 0.00 0.00 31.20 3.21
2833 6850 8.779303 ACATTCTTTTCGTAACATGTGAACATA 58.221 29.630 0.00 0.00 34.26 2.29
2969 6986 9.710900 ACAAAATAAATGAGGAGGAAAATTGAC 57.289 29.630 0.00 0.00 0.00 3.18
2970 6987 9.709495 CAAAATAAATGAGGAGGAAAATTGACA 57.291 29.630 0.00 0.00 0.00 3.58
2972 6989 9.933723 AAATAAATGAGGAGGAAAATTGACAAG 57.066 29.630 0.00 0.00 0.00 3.16
2973 6990 8.884124 ATAAATGAGGAGGAAAATTGACAAGA 57.116 30.769 0.00 0.00 0.00 3.02
2974 6991 7.601705 AAATGAGGAGGAAAATTGACAAGAA 57.398 32.000 0.00 0.00 0.00 2.52
2975 6992 7.601705 AATGAGGAGGAAAATTGACAAGAAA 57.398 32.000 0.00 0.00 0.00 2.52
2976 6993 7.787623 ATGAGGAGGAAAATTGACAAGAAAT 57.212 32.000 0.00 0.00 0.00 2.17
2977 6994 7.601705 TGAGGAGGAAAATTGACAAGAAATT 57.398 32.000 0.00 0.00 0.00 1.82
2978 6995 8.704849 TGAGGAGGAAAATTGACAAGAAATTA 57.295 30.769 0.00 0.00 0.00 1.40
2979 6996 8.796475 TGAGGAGGAAAATTGACAAGAAATTAG 58.204 33.333 0.00 0.00 0.00 1.73
2980 6997 8.940397 AGGAGGAAAATTGACAAGAAATTAGA 57.060 30.769 0.00 0.00 0.00 2.10
2981 6998 9.367160 AGGAGGAAAATTGACAAGAAATTAGAA 57.633 29.630 0.00 0.00 0.00 2.10
2982 6999 9.981114 GGAGGAAAATTGACAAGAAATTAGAAA 57.019 29.630 0.00 0.00 0.00 2.52
2988 7005 8.593492 AATTGACAAGAAATTAGAAAACTGCC 57.407 30.769 0.00 0.00 0.00 4.85
2989 7006 6.707440 TGACAAGAAATTAGAAAACTGCCA 57.293 33.333 0.00 0.00 0.00 4.92
2990 7007 7.106439 TGACAAGAAATTAGAAAACTGCCAA 57.894 32.000 0.00 0.00 0.00 4.52
2991 7008 7.551585 TGACAAGAAATTAGAAAACTGCCAAA 58.448 30.769 0.00 0.00 0.00 3.28
2992 7009 8.037758 TGACAAGAAATTAGAAAACTGCCAAAA 58.962 29.630 0.00 0.00 0.00 2.44
2993 7010 8.785329 ACAAGAAATTAGAAAACTGCCAAAAA 57.215 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.343155 CGCGACGCATTTTATTTGAGTTATTC 60.343 38.462 21.35 0.00 0.00 1.75
23 24 1.586578 GACAGATCGCGACGCATTTTA 59.413 47.619 21.35 0.00 0.00 1.52
26 27 0.380733 TAGACAGATCGCGACGCATT 59.619 50.000 21.35 5.87 0.00 3.56
32 33 1.062148 CGACACTTAGACAGATCGCGA 59.938 52.381 13.09 13.09 31.14 5.87
35 36 2.177977 GTGCGACACTTAGACAGATCG 58.822 52.381 3.20 0.00 37.57 3.69
40 41 0.319555 GCAGGTGCGACACTTAGACA 60.320 55.000 9.31 0.00 34.40 3.41
68 69 7.981225 CGGCTAGTAGTTAATGTTAGGGTTTTA 59.019 37.037 0.00 0.00 0.00 1.52
73 75 4.586001 TCCGGCTAGTAGTTAATGTTAGGG 59.414 45.833 0.00 0.00 0.00 3.53
82 84 2.422519 CCTCCACTCCGGCTAGTAGTTA 60.423 54.545 0.00 0.00 33.14 2.24
83 85 1.685491 CCTCCACTCCGGCTAGTAGTT 60.685 57.143 0.00 0.00 33.14 2.24
94 96 1.566298 AATCCTGGTGCCTCCACTCC 61.566 60.000 0.00 0.00 41.93 3.85
127 129 2.738521 CACTGTCCAGTTCGCCGG 60.739 66.667 0.00 0.00 40.20 6.13
130 132 2.358737 CCCCACTGTCCAGTTCGC 60.359 66.667 0.00 0.00 40.20 4.70
137 139 0.537371 CCTTGACAACCCCACTGTCC 60.537 60.000 0.82 0.00 42.13 4.02
139 141 1.073923 GATCCTTGACAACCCCACTGT 59.926 52.381 0.00 0.00 0.00 3.55
166 168 1.372997 GTCGTTCTCTGCCTTCGCA 60.373 57.895 0.00 0.00 44.78 5.10
172 174 2.029838 ATCATTGGTCGTTCTCTGCC 57.970 50.000 0.00 0.00 0.00 4.85
186 188 3.067106 CCTACGCGGCTCAATAATCATT 58.933 45.455 12.47 0.00 0.00 2.57
192 194 1.395635 TTCTCCTACGCGGCTCAATA 58.604 50.000 12.47 0.00 0.00 1.90
194 196 0.179111 CATTCTCCTACGCGGCTCAA 60.179 55.000 12.47 0.00 0.00 3.02
215 217 2.140717 CAATAGCAGCATCTCATCGCA 58.859 47.619 0.00 0.00 0.00 5.10
216 218 2.141517 ACAATAGCAGCATCTCATCGC 58.858 47.619 0.00 0.00 0.00 4.58
217 219 4.385146 CAGTACAATAGCAGCATCTCATCG 59.615 45.833 0.00 0.00 0.00 3.84
227 229 2.541346 CGCATGTCCAGTACAATAGCAG 59.459 50.000 0.00 0.00 42.70 4.24
248 250 0.107945 CCTTCTAGCCCTGTCACAGC 60.108 60.000 0.00 0.00 0.00 4.40
249 251 0.539051 CCCTTCTAGCCCTGTCACAG 59.461 60.000 0.00 0.00 0.00 3.66
253 255 1.210722 CCTTTCCCTTCTAGCCCTGTC 59.789 57.143 0.00 0.00 0.00 3.51
256 258 0.421904 TCCCTTTCCCTTCTAGCCCT 59.578 55.000 0.00 0.00 0.00 5.19
261 263 4.248652 ACTTTCCTTCCCTTTCCCTTCTA 58.751 43.478 0.00 0.00 0.00 2.10
262 264 3.064412 ACTTTCCTTCCCTTTCCCTTCT 58.936 45.455 0.00 0.00 0.00 2.85
273 275 1.536073 GCCTGCCCAACTTTCCTTCC 61.536 60.000 0.00 0.00 0.00 3.46
290 292 3.138798 CTGCTCCCATGTGCTGCC 61.139 66.667 0.00 0.00 32.27 4.85
309 311 1.378882 TTGCCTCGCCAATCTCATGC 61.379 55.000 0.00 0.00 0.00 4.06
314 316 0.323725 AACCATTGCCTCGCCAATCT 60.324 50.000 0.00 0.00 33.35 2.40
341 343 5.824904 AGGAATTCATCAAAATCTCACCG 57.175 39.130 7.93 0.00 0.00 4.94
452 455 1.890876 TCATTGGTTTCGGTGGACTG 58.109 50.000 0.00 0.00 0.00 3.51
476 479 0.754217 AGCGCCTACCGAGATTACCA 60.754 55.000 2.29 0.00 40.02 3.25
477 480 0.318784 CAGCGCCTACCGAGATTACC 60.319 60.000 2.29 0.00 40.02 2.85
482 485 1.395635 TATTTCAGCGCCTACCGAGA 58.604 50.000 2.29 0.00 40.02 4.04
483 486 2.440539 ATATTTCAGCGCCTACCGAG 57.559 50.000 2.29 0.00 40.02 4.63
491 494 7.464358 TCTAAGTTTGAGAAATATTTCAGCGC 58.536 34.615 26.02 14.38 39.61 5.92
515 518 4.789095 TGCCGAGCTCGTTTTATAAATC 57.211 40.909 32.41 9.93 37.74 2.17
524 527 2.571757 TCGATTGCCGAGCTCGTT 59.428 55.556 32.41 15.58 43.23 3.85
534 537 1.675641 ACCCAACTGGCTCGATTGC 60.676 57.895 0.00 0.00 37.83 3.56
545 548 0.321671 CACGACCTCATCACCCAACT 59.678 55.000 0.00 0.00 0.00 3.16
556 559 1.190178 ACCCAACCCTACACGACCTC 61.190 60.000 0.00 0.00 0.00 3.85
558 561 0.604511 CAACCCAACCCTACACGACC 60.605 60.000 0.00 0.00 0.00 4.79
559 562 0.604511 CCAACCCAACCCTACACGAC 60.605 60.000 0.00 0.00 0.00 4.34
561 564 1.302993 CCCAACCCAACCCTACACG 60.303 63.158 0.00 0.00 0.00 4.49
562 565 0.538746 CACCCAACCCAACCCTACAC 60.539 60.000 0.00 0.00 0.00 2.90
563 566 0.994591 ACACCCAACCCAACCCTACA 60.995 55.000 0.00 0.00 0.00 2.74
566 569 1.163408 ATTACACCCAACCCAACCCT 58.837 50.000 0.00 0.00 0.00 4.34
568 571 0.606096 GCATTACACCCAACCCAACC 59.394 55.000 0.00 0.00 0.00 3.77
571 574 2.026636 GTCTAGCATTACACCCAACCCA 60.027 50.000 0.00 0.00 0.00 4.51
586 589 1.446272 GGCAGTCCGTGTGTCTAGC 60.446 63.158 0.00 0.00 0.00 3.42
609 612 1.066136 GCAGGTCCGTAAAGTTCGTC 58.934 55.000 0.00 0.00 0.00 4.20
612 615 2.998670 GGTTAGCAGGTCCGTAAAGTTC 59.001 50.000 0.00 0.00 0.00 3.01
668 673 5.703730 AATTCAGGAGGGACGGTTAATTA 57.296 39.130 0.00 0.00 0.00 1.40
707 713 4.096984 GCAGACCAGTTAAATTCATCAGGG 59.903 45.833 0.00 0.00 0.00 4.45
713 719 3.420893 CCCAGCAGACCAGTTAAATTCA 58.579 45.455 0.00 0.00 0.00 2.57
714 720 2.164422 GCCCAGCAGACCAGTTAAATTC 59.836 50.000 0.00 0.00 0.00 2.17
715 721 2.171003 GCCCAGCAGACCAGTTAAATT 58.829 47.619 0.00 0.00 0.00 1.82
756 762 3.061139 GCTACATCAACTGACGATTACGC 60.061 47.826 0.00 0.00 43.96 4.42
757 763 4.102649 TGCTACATCAACTGACGATTACG 58.897 43.478 0.00 0.00 45.75 3.18
763 769 4.667668 GCTTTCTTGCTACATCAACTGACG 60.668 45.833 0.00 0.00 0.00 4.35
889 915 2.935481 TGGGAGGGGACAGGCTTG 60.935 66.667 0.00 0.00 0.00 4.01
1383 2409 0.977627 TCATGGTGTCGCCCATCTCT 60.978 55.000 0.00 0.00 43.46 3.10
1564 2851 6.683360 GCAAGTAGTACTGTATTTCCCTCCTC 60.683 46.154 5.39 0.00 0.00 3.71
1575 2862 6.348295 CGTCTTTCTCTGCAAGTAGTACTGTA 60.348 42.308 5.39 0.00 33.76 2.74
1585 2878 2.411409 GCTCTTCGTCTTTCTCTGCAAG 59.589 50.000 0.00 0.00 0.00 4.01
1586 2879 2.036475 AGCTCTTCGTCTTTCTCTGCAA 59.964 45.455 0.00 0.00 0.00 4.08
1587 2880 1.615883 AGCTCTTCGTCTTTCTCTGCA 59.384 47.619 0.00 0.00 0.00 4.41
1739 3868 5.668471 CACTCTCAGGATCATTAGCTTTGA 58.332 41.667 0.00 0.00 0.00 2.69
1783 4221 2.807392 GCATCTTAGATGCCAAGCTCTC 59.193 50.000 30.61 5.58 39.01 3.20
1812 4250 5.819901 AGCTGATGACTTTGGCTTTACTATC 59.180 40.000 0.00 0.00 0.00 2.08
1830 4268 1.340697 TGAGGATTTGCAGCAGCTGAT 60.341 47.619 27.39 8.90 42.74 2.90
1831 4269 0.037160 TGAGGATTTGCAGCAGCTGA 59.963 50.000 27.39 5.57 42.74 4.26
1832 4270 0.452184 CTGAGGATTTGCAGCAGCTG 59.548 55.000 18.93 18.93 42.74 4.24
1833 4271 0.327259 TCTGAGGATTTGCAGCAGCT 59.673 50.000 1.76 0.00 42.74 4.24
2000 4444 4.296690 CGGTTATGACTCGAATAAGGGTC 58.703 47.826 0.00 0.00 41.82 4.46
2039 4483 3.781965 TGATGATGATCTTGTTCCAGGGA 59.218 43.478 0.00 0.00 0.00 4.20
2146 4652 2.752354 TGATGATGGGCAGTTTTAACCG 59.248 45.455 0.00 0.00 0.00 4.44
2156 4662 4.458989 GTCAACTAGTTTTGATGATGGGCA 59.541 41.667 5.07 0.00 37.80 5.36
2157 4663 4.702131 AGTCAACTAGTTTTGATGATGGGC 59.298 41.667 5.07 0.00 37.80 5.36
2158 4664 5.707298 ACAGTCAACTAGTTTTGATGATGGG 59.293 40.000 5.07 0.00 37.80 4.00
2159 4665 6.427853 TGACAGTCAACTAGTTTTGATGATGG 59.572 38.462 5.07 0.31 37.80 3.51
2160 4666 7.425577 TGACAGTCAACTAGTTTTGATGATG 57.574 36.000 5.07 5.78 37.80 3.07
2161 4667 8.627208 AATGACAGTCAACTAGTTTTGATGAT 57.373 30.769 7.50 0.00 37.80 2.45
2162 4668 9.725019 ATAATGACAGTCAACTAGTTTTGATGA 57.275 29.630 7.50 0.00 37.80 2.92
2163 4669 9.764870 CATAATGACAGTCAACTAGTTTTGATG 57.235 33.333 7.50 5.46 37.80 3.07
2164 4670 9.725019 TCATAATGACAGTCAACTAGTTTTGAT 57.275 29.630 7.50 0.00 37.80 2.57
2165 4671 8.988934 GTCATAATGACAGTCAACTAGTTTTGA 58.011 33.333 7.50 5.27 46.22 2.69
2226 4732 8.282592 TCGAGGCAAAATTAATGATATTTCTCG 58.717 33.333 11.50 11.50 37.74 4.04
2284 4791 5.904984 ACAAGGCCACTATGGAATATACA 57.095 39.130 5.01 0.00 40.96 2.29
2352 5871 4.331992 AGTGATGCAACGAATCAATCTGAG 59.668 41.667 0.00 0.00 35.87 3.35
2360 5879 4.871993 AATCTGAGTGATGCAACGAATC 57.128 40.909 0.00 0.00 35.21 2.52
2451 5992 7.010552 CGGCCTAGAATCATGCATAAATAGTAC 59.989 40.741 0.00 0.00 0.00 2.73
2568 6581 0.246635 CTGGAGTGGTACCGGACTTG 59.753 60.000 9.46 0.00 35.98 3.16
2589 6602 4.375405 GCATGCGTCTATGTTACGATCAAG 60.375 45.833 0.00 0.00 42.90 3.02
2640 6657 8.547069 GCATATACATGTTTGAGAGAGAAGAAC 58.453 37.037 2.30 0.00 34.40 3.01
2661 6678 4.307032 AAGATATTGAAGGGCGGCATAT 57.693 40.909 12.47 4.80 0.00 1.78
2665 6682 2.024414 ACAAAGATATTGAAGGGCGGC 58.976 47.619 0.00 0.00 0.00 6.53
2681 6698 7.010023 GCAAAACGTTTTACATGTTGAACAAA 58.990 30.769 24.79 0.00 34.59 2.83
2688 6705 5.859557 GTTTGGCAAAACGTTTTACATGTT 58.140 33.333 24.79 0.00 36.60 2.71
2943 6960 9.710900 GTCAATTTTCCTCCTCATTTATTTTGT 57.289 29.630 0.00 0.00 0.00 2.83
2944 6961 9.709495 TGTCAATTTTCCTCCTCATTTATTTTG 57.291 29.630 0.00 0.00 0.00 2.44
2946 6963 9.933723 CTTGTCAATTTTCCTCCTCATTTATTT 57.066 29.630 0.00 0.00 0.00 1.40
2947 6964 9.312904 TCTTGTCAATTTTCCTCCTCATTTATT 57.687 29.630 0.00 0.00 0.00 1.40
2948 6965 8.884124 TCTTGTCAATTTTCCTCCTCATTTAT 57.116 30.769 0.00 0.00 0.00 1.40
2949 6966 8.704849 TTCTTGTCAATTTTCCTCCTCATTTA 57.295 30.769 0.00 0.00 0.00 1.40
2950 6967 7.601705 TTCTTGTCAATTTTCCTCCTCATTT 57.398 32.000 0.00 0.00 0.00 2.32
2951 6968 7.601705 TTTCTTGTCAATTTTCCTCCTCATT 57.398 32.000 0.00 0.00 0.00 2.57
2952 6969 7.787623 ATTTCTTGTCAATTTTCCTCCTCAT 57.212 32.000 0.00 0.00 0.00 2.90
2953 6970 7.601705 AATTTCTTGTCAATTTTCCTCCTCA 57.398 32.000 0.00 0.00 0.00 3.86
2954 6971 9.014297 TCTAATTTCTTGTCAATTTTCCTCCTC 57.986 33.333 0.00 0.00 0.00 3.71
2955 6972 8.940397 TCTAATTTCTTGTCAATTTTCCTCCT 57.060 30.769 0.00 0.00 0.00 3.69
2956 6973 9.981114 TTTCTAATTTCTTGTCAATTTTCCTCC 57.019 29.630 0.00 0.00 0.00 4.30
2962 6979 9.045223 GGCAGTTTTCTAATTTCTTGTCAATTT 57.955 29.630 0.00 0.00 0.00 1.82
2963 6980 8.203485 TGGCAGTTTTCTAATTTCTTGTCAATT 58.797 29.630 0.00 0.00 0.00 2.32
2964 6981 7.725251 TGGCAGTTTTCTAATTTCTTGTCAAT 58.275 30.769 0.00 0.00 0.00 2.57
2965 6982 7.106439 TGGCAGTTTTCTAATTTCTTGTCAA 57.894 32.000 0.00 0.00 0.00 3.18
2966 6983 6.707440 TGGCAGTTTTCTAATTTCTTGTCA 57.293 33.333 0.00 0.00 0.00 3.58
2967 6984 8.419076 TTTTGGCAGTTTTCTAATTTCTTGTC 57.581 30.769 0.00 0.00 0.00 3.18
2968 6985 8.785329 TTTTTGGCAGTTTTCTAATTTCTTGT 57.215 26.923 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.