Multiple sequence alignment - TraesCS6D01G337400

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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 TraesCS6D01G337400 chr6D 100.000 8789 0 0 1 8789 437943539 437952327 0.000000e+00 16231
1 TraesCS6D01G337400 chr6D 84.667 887 127 9 2945 3828 437946375 437947255 0.000000e+00 876
2 TraesCS6D01G337400 chr6D 84.667 887 127 9 2837 3717 437946483 437947366 0.000000e+00 876
3 TraesCS6D01G337400 chr6D 83.523 789 124 6 3140 3925 437946456 437947241 0.000000e+00 732
4 TraesCS6D01G337400 chr6D 83.523 789 124 6 2918 3703 437946678 437947463 0.000000e+00 732
5 TraesCS6D01G337400 chr6A 97.227 6455 114 17 1148 7581 586317216 586323626 0.000000e+00 10868
6 TraesCS6D01G337400 chr6A 95.592 1225 40 10 7573 8789 586323693 586324911 0.000000e+00 1951
7 TraesCS6D01G337400 chr6A 84.684 1234 62 52 4 1176 586316119 586317286 0.000000e+00 1114
8 TraesCS6D01G337400 chr6A 84.528 879 131 5 2843 3717 586319013 586319890 0.000000e+00 865
9 TraesCS6D01G337400 chr6A 88.295 692 81 0 3137 3828 586319088 586319779 0.000000e+00 830
10 TraesCS6D01G337400 chr6A 83.270 789 126 6 2918 3703 586319202 586319987 0.000000e+00 721
11 TraesCS6D01G337400 chr6A 76.275 451 103 4 2922 3370 586319539 586319987 4.100000e-58 237
12 TraesCS6D01G337400 chr6B 96.240 4282 125 21 3313 7581 662888721 662892979 0.000000e+00 6983
13 TraesCS6D01G337400 chr6B 91.677 3088 146 45 281 3297 662885267 662888314 0.000000e+00 4176
14 TraesCS6D01G337400 chr6B 93.624 1239 40 20 7573 8789 662893049 662894270 0.000000e+00 1814
15 TraesCS6D01G337400 chr6B 85.342 614 37 28 4 582 662884540 662885135 3.540000e-163 586
16 TraesCS6D01G337400 chr6B 76.950 282 61 4 3646 3925 662888721 662889000 3.280000e-34 158


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 TraesCS6D01G337400 chr6D 437943539 437952327 8788 False 16231.0 16231 100.000000 1 8789 1 chr6D.!!$F1 8788
1 TraesCS6D01G337400 chr6D 437946375 437947463 1088 False 804.0 876 84.095000 2837 3925 4 chr6D.!!$F2 1088
2 TraesCS6D01G337400 chr6A 586316119 586323626 7507 False 5991.0 10868 90.955500 4 7581 2 chr6A.!!$F1 7577
3 TraesCS6D01G337400 chr6A 586319013 586324911 5898 False 920.8 1951 85.592000 2843 8789 5 chr6A.!!$F2 5946
4 TraesCS6D01G337400 chr6B 662884540 662892979 8439 False 3915.0 6983 91.086333 4 7581 3 chr6B.!!$F3 7577
5 TraesCS6D01G337400 chr6B 662893049 662894270 1221 False 1814.0 1814 93.624000 7573 8789 1 chr6B.!!$F2 1216

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
239 257 0.236711 CCACACAGAAAGAGCAAGCG 59.763 55.000 0.00 0.00 0.00 4.68 F
496 1006 0.251832 TGCCTCCGTTTCTCTCTCCT 60.252 55.000 0.00 0.00 0.00 3.69 F
617 1144 0.739112 GCCAGCACTGAGTCACTAGC 60.739 60.000 0.00 0.00 0.00 3.42 F
876 1435 1.517242 GTTGCTGGTCCTTGTCTGAG 58.483 55.000 0.00 0.00 0.00 3.35 F
2789 3358 1.135575 CGCTGAAAAGGATGGCAGAAC 60.136 52.381 0.00 0.00 0.00 3.01 F
2801 3370 0.538287 GGCAGAACTGTGGCCTCTTT 60.538 55.000 3.32 0.00 44.32 2.52 F
4406 5366 4.110036 TGTCAGTATCATCACGTGGAAG 57.890 45.455 17.00 6.09 0.00 3.46 F
5400 6363 4.273318 AGAGGTCAAATTGGGAATAGTGC 58.727 43.478 0.00 0.00 0.00 4.40 F
5953 6917 2.351157 GCTTGTGTTGCTTCATGAGTCC 60.351 50.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2420 1.289530 CTAGGTGACTCCTCCCCTCTT 59.710 57.143 0.00 0.00 44.42 2.85 R
2493 3062 1.416401 TCAGAACCAAGCCTTCTTCGT 59.584 47.619 0.00 0.00 0.00 3.85 R
2789 3358 0.037326 TGCGACTAAAGAGGCCACAG 60.037 55.000 5.01 0.00 0.00 3.66 R
2801 3370 0.952280 GATCCCTCGATGTGCGACTA 59.048 55.000 0.00 0.00 45.59 2.59 R
4258 5218 2.482142 CCTTTACCGAGATGGCTCTGTC 60.482 54.545 0.00 0.00 43.94 3.51 R
5110 6070 6.835488 AGAATAAATGGCCACTGATACATGTT 59.165 34.615 8.16 0.00 0.00 2.71 R
5953 6917 4.393062 ACAAAAGATGCAATAGTGAGGTCG 59.607 41.667 0.00 0.00 0.00 4.79 R
6791 7765 1.002544 GACTACCAGCTTGGCAGAAGT 59.997 52.381 8.82 5.19 42.67 3.01 R
8095 9158 3.720949 ACAACGGGCTTTAAGGTTTTC 57.279 42.857 0.00 0.00 0.00 2.29 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
33 34 4.803426 CGCTCGCTCGGCTTCCTT 62.803 66.667 0.00 0.00 0.00 3.36
122 123 2.202932 CTAGCCGTTGCCATCGCT 60.203 61.111 0.00 0.00 38.69 4.93
124 125 2.635229 CTAGCCGTTGCCATCGCTCT 62.635 60.000 0.00 0.00 38.69 4.09
127 128 3.869272 CGTTGCCATCGCTCTGCC 61.869 66.667 0.00 0.00 35.36 4.85
128 129 2.437359 GTTGCCATCGCTCTGCCT 60.437 61.111 0.00 0.00 35.36 4.75
129 130 2.124983 TTGCCATCGCTCTGCCTC 60.125 61.111 0.00 0.00 35.36 4.70
130 131 2.663075 TTGCCATCGCTCTGCCTCT 61.663 57.895 0.00 0.00 35.36 3.69
132 133 2.108566 CCATCGCTCTGCCTCTGG 59.891 66.667 0.00 0.00 0.00 3.86
223 241 1.525941 TGCTTTTTACTACCCGCCAC 58.474 50.000 0.00 0.00 0.00 5.01
225 243 1.198408 GCTTTTTACTACCCGCCACAC 59.802 52.381 0.00 0.00 0.00 3.82
234 252 2.328099 CCCGCCACACAGAAAGAGC 61.328 63.158 0.00 0.00 0.00 4.09
235 253 1.597854 CCGCCACACAGAAAGAGCA 60.598 57.895 0.00 0.00 0.00 4.26
239 257 0.236711 CCACACAGAAAGAGCAAGCG 59.763 55.000 0.00 0.00 0.00 4.68
241 259 1.070309 CACACAGAAAGAGCAAGCGAC 60.070 52.381 0.00 0.00 0.00 5.19
242 260 1.220529 CACAGAAAGAGCAAGCGACA 58.779 50.000 0.00 0.00 0.00 4.35
255 278 2.765807 CGACAGAGATGGCCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
259 282 1.237163 CAGAGATGGCCCCCTCCTA 59.763 63.158 15.47 0.00 0.00 2.94
271 294 1.408822 CCCCTCCTACCACTTGCATTC 60.409 57.143 0.00 0.00 0.00 2.67
275 298 3.118112 CCTCCTACCACTTGCATTCATCT 60.118 47.826 0.00 0.00 0.00 2.90
278 301 3.118112 CCTACCACTTGCATTCATCTCCT 60.118 47.826 0.00 0.00 0.00 3.69
280 303 4.574674 ACCACTTGCATTCATCTCCTTA 57.425 40.909 0.00 0.00 0.00 2.69
282 305 5.513233 ACCACTTGCATTCATCTCCTTAAT 58.487 37.500 0.00 0.00 0.00 1.40
283 306 5.954150 ACCACTTGCATTCATCTCCTTAATT 59.046 36.000 0.00 0.00 0.00 1.40
284 307 7.118723 ACCACTTGCATTCATCTCCTTAATTA 58.881 34.615 0.00 0.00 0.00 1.40
285 308 7.615365 ACCACTTGCATTCATCTCCTTAATTAA 59.385 33.333 0.00 0.00 0.00 1.40
286 309 8.636213 CCACTTGCATTCATCTCCTTAATTAAT 58.364 33.333 0.00 0.00 0.00 1.40
287 310 9.674824 CACTTGCATTCATCTCCTTAATTAATC 57.325 33.333 0.00 0.00 0.00 1.75
290 313 9.631257 TTGCATTCATCTCCTTAATTAATCTCA 57.369 29.630 0.00 0.00 0.00 3.27
291 314 9.631257 TGCATTCATCTCCTTAATTAATCTCAA 57.369 29.630 0.00 0.00 0.00 3.02
343 380 2.500392 TAATGTGGGCTTGGGTGTAC 57.500 50.000 0.00 0.00 0.00 2.90
345 382 1.663911 ATGTGGGCTTGGGTGTACTA 58.336 50.000 0.00 0.00 0.00 1.82
347 384 0.981943 GTGGGCTTGGGTGTACTAGT 59.018 55.000 0.00 0.00 0.00 2.57
349 386 2.093816 GTGGGCTTGGGTGTACTAGTAC 60.094 54.545 23.58 23.58 36.63 2.73
351 388 2.836372 GGGCTTGGGTGTACTAGTACTT 59.164 50.000 28.56 0.00 37.00 2.24
472 982 0.998945 CTCCCCCTCCCTCTCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
473 983 0.996762 TCCCCCTCCCTCTCTCTCTC 60.997 65.000 0.00 0.00 0.00 3.20
496 1006 0.251832 TGCCTCCGTTTCTCTCTCCT 60.252 55.000 0.00 0.00 0.00 3.69
526 1048 4.225497 GCCATTACTCGGCTTGCT 57.775 55.556 0.00 0.00 46.56 3.91
588 1114 2.040464 TCCCTCCCTCCATCAGGC 60.040 66.667 0.00 0.00 41.80 4.85
617 1144 0.739112 GCCAGCACTGAGTCACTAGC 60.739 60.000 0.00 0.00 0.00 3.42
757 1307 1.716028 AAAACAACCTCCGGCCCTCT 61.716 55.000 0.00 0.00 0.00 3.69
759 1309 3.003173 CAACCTCCGGCCCTCTCA 61.003 66.667 0.00 0.00 0.00 3.27
775 1333 4.264128 CCCTCTCATCCCCTTTTCTTTTCT 60.264 45.833 0.00 0.00 0.00 2.52
876 1435 1.517242 GTTGCTGGTCCTTGTCTGAG 58.483 55.000 0.00 0.00 0.00 3.35
879 1438 2.061220 CTGGTCCTTGTCTGAGCCA 58.939 57.895 0.00 0.00 0.00 4.75
896 1456 2.427232 CCACATTGGCTTGTCTTGTG 57.573 50.000 0.00 0.00 37.90 3.33
897 1457 1.682854 CCACATTGGCTTGTCTTGTGT 59.317 47.619 0.00 0.00 36.75 3.72
898 1458 2.101249 CCACATTGGCTTGTCTTGTGTT 59.899 45.455 0.00 0.00 36.75 3.32
1181 1747 4.845580 CTCGCCGAATGCTGCCCT 62.846 66.667 0.00 0.00 38.05 5.19
1272 1838 2.283966 AGGTCCCAGTCCACCGAG 60.284 66.667 0.00 0.00 37.79 4.63
1845 2414 4.759782 ACAAAATCGATCGATTGGTCTCT 58.240 39.130 36.54 21.16 43.26 3.10
1851 2420 3.632145 TCGATCGATTGGTCTCTTCATCA 59.368 43.478 15.15 0.00 0.00 3.07
2305 2874 2.540361 GCTTCTGATGGCGTTAATGCTG 60.540 50.000 18.76 5.49 34.52 4.41
2310 2879 3.339141 TGATGGCGTTAATGCTGTTGTA 58.661 40.909 18.76 0.00 34.52 2.41
2421 2990 6.501805 AGGCCTCTGATGGTATTGATGTTATA 59.498 38.462 0.00 0.00 0.00 0.98
2493 3062 2.429930 CTGCGTGGGGTTTCTCCA 59.570 61.111 0.00 0.00 38.11 3.86
2701 3270 5.999600 CCATCAACCTCATATGCTACATCAA 59.000 40.000 0.00 0.00 0.00 2.57
2789 3358 1.135575 CGCTGAAAAGGATGGCAGAAC 60.136 52.381 0.00 0.00 0.00 3.01
2801 3370 0.538287 GGCAGAACTGTGGCCTCTTT 60.538 55.000 3.32 0.00 44.32 2.52
4072 5032 5.734720 CTCAAGTAGAAGCCATCCAGTTTA 58.265 41.667 0.00 0.00 0.00 2.01
4258 5218 4.209703 GTGTGGATGCAACTCAAAAACATG 59.790 41.667 0.00 0.00 0.00 3.21
4406 5366 4.110036 TGTCAGTATCATCACGTGGAAG 57.890 45.455 17.00 6.09 0.00 3.46
5108 6068 5.848369 AGGTAAACACTCTAAAGTTACCCCT 59.152 40.000 7.17 0.00 31.71 4.79
5110 6070 7.513781 AGGTAAACACTCTAAAGTTACCCCTTA 59.486 37.037 7.17 0.00 31.71 2.69
5400 6363 4.273318 AGAGGTCAAATTGGGAATAGTGC 58.727 43.478 0.00 0.00 0.00 4.40
5841 6805 7.647907 AAGTTTACATGTTTCCGTACTAGTG 57.352 36.000 2.30 0.00 0.00 2.74
5953 6917 2.351157 GCTTGTGTTGCTTCATGAGTCC 60.351 50.000 0.00 0.00 0.00 3.85
6791 7765 0.615331 CTAGCTTTCTGGCCAGTCCA 59.385 55.000 31.58 14.75 44.18 4.02
6994 7968 6.426980 TGATTTTCTATGCTTGCTACACTG 57.573 37.500 0.00 0.00 0.00 3.66
7217 8191 6.484643 CACTGCAGGTACAAGCTTGATATATT 59.515 38.462 32.50 11.72 32.89 1.28
7491 8470 6.919662 CACTGACTGAAACATAAGCAATTGTT 59.080 34.615 7.40 0.00 37.66 2.83
7682 8741 1.174712 TCCAGGCTTGAAGCTGCAAC 61.175 55.000 17.59 0.63 41.99 4.17
7934 8993 1.374572 CCCTTTGTTAGGTACCCCCA 58.625 55.000 8.74 0.00 43.07 4.96
7937 8996 3.245839 CCCTTTGTTAGGTACCCCCAAAT 60.246 47.826 8.74 0.00 43.07 2.32
7940 8999 5.046878 CCTTTGTTAGGTACCCCCAAATTTC 60.047 44.000 8.74 0.00 39.39 2.17
7941 9000 5.342361 TTGTTAGGTACCCCCAAATTTCT 57.658 39.130 8.74 0.00 34.66 2.52
7942 9001 4.925836 TGTTAGGTACCCCCAAATTTCTC 58.074 43.478 8.74 0.00 34.66 2.87
8013 9076 3.867600 GCATGGAAGAGAAGTCAGCAAGA 60.868 47.826 0.00 0.00 0.00 3.02
8086 9149 3.144506 CAGCTCACAAACTGAGGATGTT 58.855 45.455 0.00 0.00 46.08 2.71
8095 9158 1.276421 ACTGAGGATGTTGAGGTTCCG 59.724 52.381 0.00 0.00 34.61 4.30
8096 9159 1.550524 CTGAGGATGTTGAGGTTCCGA 59.449 52.381 0.00 0.00 34.61 4.55
8110 9173 2.029649 GGTTCCGAAAACCTTAAAGCCC 60.030 50.000 11.22 0.00 37.34 5.19
8278 9345 2.097110 TGACAGGTTCCTGGTACACT 57.903 50.000 20.88 0.93 38.30 3.55
8302 9370 6.050432 TGACTTCATTTACCTACACGTTTGT 58.950 36.000 0.00 0.00 40.02 2.83
8312 9381 2.963320 ACGTTTGTGGTCGCCGTC 60.963 61.111 0.00 0.00 0.00 4.79
8320 9389 1.602605 TGGTCGCCGTCTCAAGAGA 60.603 57.895 0.00 0.00 34.56 3.10
8324 9393 2.452105 GTCGCCGTCTCAAGAGAATAC 58.548 52.381 0.57 0.00 39.48 1.89
8353 9422 6.546395 ACGCTTTCTTGATATGTCAATGTTC 58.454 36.000 5.26 0.00 43.08 3.18
8383 9457 6.533730 TCTATGAAATGTGTGGTTTGTCTCT 58.466 36.000 0.00 0.00 0.00 3.10
8419 9493 2.691409 TAGTGCTGGAACTGTATGGC 57.309 50.000 0.00 0.00 0.00 4.40
8422 9496 1.470098 GTGCTGGAACTGTATGGCTTG 59.530 52.381 0.00 0.00 0.00 4.01
8571 9646 7.785033 TGTATACAACTAGTTTAGTTAGGCCC 58.215 38.462 5.07 0.00 46.66 5.80
8588 9663 1.447217 CCTACGCCATCATCCTGCA 59.553 57.895 0.00 0.00 0.00 4.41
8770 9848 4.517285 TCCCATGTAGATCAGCAACTTTC 58.483 43.478 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.389576 CGGGTCAAGCGCTGCAAC 62.390 66.667 12.58 9.78 0.00 4.17
24 25 1.078848 CAGTCAGGGAAGGAAGCCG 60.079 63.158 0.00 0.00 0.00 5.52
33 34 3.733960 CGTCGTCGCAGTCAGGGA 61.734 66.667 0.00 0.00 36.77 4.20
130 131 1.303561 GTTGTGCTGGATGGAGCCA 60.304 57.895 0.00 0.00 38.28 4.75
132 133 2.401766 CCGTTGTGCTGGATGGAGC 61.402 63.158 0.00 0.00 39.62 4.70
133 134 2.401766 GCCGTTGTGCTGGATGGAG 61.402 63.158 0.00 0.00 0.00 3.86
134 135 2.359850 GCCGTTGTGCTGGATGGA 60.360 61.111 0.00 0.00 0.00 3.41
135 136 2.267351 TTGCCGTTGTGCTGGATGG 61.267 57.895 0.00 0.00 0.00 3.51
136 137 1.081242 GTTGCCGTTGTGCTGGATG 60.081 57.895 0.00 0.00 0.00 3.51
137 138 0.895100 ATGTTGCCGTTGTGCTGGAT 60.895 50.000 0.00 0.00 0.00 3.41
144 145 2.627699 AGAAATGGAATGTTGCCGTTGT 59.372 40.909 0.00 0.00 34.94 3.32
193 208 8.241367 CGGGTAGTAAAAAGCATTAAGAATTGT 58.759 33.333 0.00 0.00 0.00 2.71
223 241 1.194098 CTGTCGCTTGCTCTTTCTGTG 59.806 52.381 0.00 0.00 0.00 3.66
225 243 1.725706 CTCTGTCGCTTGCTCTTTCTG 59.274 52.381 0.00 0.00 0.00 3.02
234 252 1.817099 GGGCCATCTCTGTCGCTTG 60.817 63.158 4.39 0.00 0.00 4.01
235 253 2.586792 GGGCCATCTCTGTCGCTT 59.413 61.111 4.39 0.00 0.00 4.68
239 257 2.447714 GGAGGGGGCCATCTCTGTC 61.448 68.421 20.50 5.86 0.00 3.51
241 259 1.124477 GTAGGAGGGGGCCATCTCTG 61.124 65.000 20.50 0.00 0.00 3.35
242 260 1.237458 GTAGGAGGGGGCCATCTCT 59.763 63.158 20.50 12.51 0.00 3.10
255 278 3.118261 GGAGATGAATGCAAGTGGTAGGA 60.118 47.826 0.00 0.00 0.00 2.94
259 282 3.446442 AAGGAGATGAATGCAAGTGGT 57.554 42.857 0.00 0.00 0.00 4.16
291 314 8.409371 GGCGTAGGAGTAATAAAAGTAAGTACT 58.591 37.037 0.00 0.00 38.39 2.73
292 315 7.377131 CGGCGTAGGAGTAATAAAAGTAAGTAC 59.623 40.741 0.00 0.00 0.00 2.73
293 316 7.417612 CGGCGTAGGAGTAATAAAAGTAAGTA 58.582 38.462 0.00 0.00 0.00 2.24
343 380 9.119329 GAATGCGATGATTAGTACAAGTACTAG 57.881 37.037 16.88 8.31 45.92 2.57
347 384 7.489160 ACTGAATGCGATGATTAGTACAAGTA 58.511 34.615 0.00 0.00 0.00 2.24
349 386 6.834959 ACTGAATGCGATGATTAGTACAAG 57.165 37.500 0.00 0.00 0.00 3.16
351 388 5.006649 GCAACTGAATGCGATGATTAGTACA 59.993 40.000 0.00 0.00 36.45 2.90
472 982 0.251832 AGAGAAACGGAGGCAGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
473 983 0.174617 GAGAGAAACGGAGGCAGAGG 59.825 60.000 0.00 0.00 0.00 3.69
544 1066 2.432628 CTCACGGGAACTCCACGC 60.433 66.667 0.00 0.00 37.91 5.34
757 1307 4.832823 GTGGAAGAAAAGAAAAGGGGATGA 59.167 41.667 0.00 0.00 0.00 2.92
759 1309 4.160329 GGTGGAAGAAAAGAAAAGGGGAT 58.840 43.478 0.00 0.00 0.00 3.85
844 1403 1.228552 AGCAACCAACCGGCAGATT 60.229 52.632 0.00 0.00 34.57 2.40
879 1438 3.784338 CAAACACAAGACAAGCCAATGT 58.216 40.909 0.00 0.00 35.90 2.71
891 1451 1.659335 CAGCGCCTGCAAACACAAG 60.659 57.895 2.29 0.00 46.23 3.16
1032 1598 2.819595 TCAGATTTCTGCGGCGGC 60.820 61.111 9.78 9.68 43.46 6.53
1033 1599 2.802667 CGTCAGATTTCTGCGGCGG 61.803 63.158 9.78 1.35 43.46 6.13
1034 1600 2.697425 CGTCAGATTTCTGCGGCG 59.303 61.111 0.51 0.51 43.46 6.46
1035 1601 2.401195 GCGTCAGATTTCTGCGGC 59.599 61.111 18.83 13.35 43.46 6.53
1036 1602 1.298157 TTGGCGTCAGATTTCTGCGG 61.298 55.000 18.83 8.89 43.46 5.69
1037 1603 0.179215 GTTGGCGTCAGATTTCTGCG 60.179 55.000 15.35 15.35 43.46 5.18
1038 1604 0.179215 CGTTGGCGTCAGATTTCTGC 60.179 55.000 2.60 0.00 43.46 4.26
1039 1605 0.179215 GCGTTGGCGTCAGATTTCTG 60.179 55.000 0.97 0.97 40.83 3.02
1040 1606 1.298859 GGCGTTGGCGTCAGATTTCT 61.299 55.000 0.00 0.00 43.09 2.52
1251 1817 1.679898 GGTGGACTGGGACCTCTTG 59.320 63.158 0.00 0.00 0.00 3.02
1326 1892 2.764128 GAGATCCTGGACGGGGCA 60.764 66.667 0.00 0.00 0.00 5.36
1329 1895 3.917760 GCGGAGATCCTGGACGGG 61.918 72.222 0.00 0.00 0.00 5.28
1639 2208 4.743018 GTGGTCAATCACCCTGGG 57.257 61.111 12.28 12.28 46.18 4.45
1776 2345 1.587088 GCTTGCGGCGGATGAAATG 60.587 57.895 18.00 0.00 0.00 2.32
1845 2414 2.225624 TGACTCCTCCCCTCTTGATGAA 60.226 50.000 0.00 0.00 0.00 2.57
1851 2420 1.289530 CTAGGTGACTCCTCCCCTCTT 59.710 57.143 0.00 0.00 44.42 2.85
2421 2990 2.808543 AGAAAAATCTGCGCTTCTTCGT 59.191 40.909 9.73 0.00 0.00 3.85
2493 3062 1.416401 TCAGAACCAAGCCTTCTTCGT 59.584 47.619 0.00 0.00 0.00 3.85
2789 3358 0.037326 TGCGACTAAAGAGGCCACAG 60.037 55.000 5.01 0.00 0.00 3.66
2801 3370 0.952280 GATCCCTCGATGTGCGACTA 59.048 55.000 0.00 0.00 45.59 2.59
4258 5218 2.482142 CCTTTACCGAGATGGCTCTGTC 60.482 54.545 0.00 0.00 43.94 3.51
5108 6068 8.532186 AATAAATGGCCACTGATACATGTTAA 57.468 30.769 8.16 0.00 0.00 2.01
5110 6070 6.835488 AGAATAAATGGCCACTGATACATGTT 59.165 34.615 8.16 0.00 0.00 2.71
5400 6363 9.817365 CTCAACATATCTTACTTGTTGTTTCAG 57.183 33.333 12.98 2.32 46.43 3.02
5665 6629 7.461182 AAACAGACATGATCGGGAATTTTAA 57.539 32.000 0.00 0.00 0.00 1.52
5850 6814 9.844790 CACAGAATATAAAACTTGCTTCATGAA 57.155 29.630 8.12 8.12 0.00 2.57
5851 6815 8.461222 CCACAGAATATAAAACTTGCTTCATGA 58.539 33.333 0.00 0.00 0.00 3.07
5855 6819 7.121315 ACCTCCACAGAATATAAAACTTGCTTC 59.879 37.037 0.00 0.00 0.00 3.86
5953 6917 4.393062 ACAAAAGATGCAATAGTGAGGTCG 59.607 41.667 0.00 0.00 0.00 4.79
6751 7725 2.826428 CATAATGTCACCACCCTCTCG 58.174 52.381 0.00 0.00 0.00 4.04
6791 7765 1.002544 GACTACCAGCTTGGCAGAAGT 59.997 52.381 8.82 5.19 42.67 3.01
8095 9158 3.720949 ACAACGGGCTTTAAGGTTTTC 57.279 42.857 0.00 0.00 0.00 2.29
8096 9159 5.595257 TTTACAACGGGCTTTAAGGTTTT 57.405 34.783 0.00 0.00 0.00 2.43
8110 9173 5.986135 AGAGGAGCTGCTATAATTTACAACG 59.014 40.000 8.12 0.00 0.00 4.10
8278 9345 6.018588 CACAAACGTGTAGGTAAATGAAGTCA 60.019 38.462 0.00 0.00 35.72 3.41
8302 9370 1.176619 TTCTCTTGAGACGGCGACCA 61.177 55.000 16.62 5.07 0.00 4.02
8312 9381 2.159366 AGCGTCACCGTATTCTCTTGAG 60.159 50.000 0.00 0.00 36.15 3.02
8320 9389 3.034721 TCAAGAAAGCGTCACCGTATT 57.965 42.857 0.00 0.00 36.15 1.89
8324 9393 2.930040 ACATATCAAGAAAGCGTCACCG 59.070 45.455 0.00 0.00 37.07 4.94
8353 9422 4.511527 ACCACACATTTCATAGAGCTGAG 58.488 43.478 0.00 0.00 0.00 3.35
8419 9493 5.873712 AGAGCATCACTAGAATCAACACAAG 59.126 40.000 0.00 0.00 37.82 3.16
8422 9496 6.478344 CCTTAGAGCATCACTAGAATCAACAC 59.522 42.308 0.00 0.00 37.82 3.32
8571 9646 1.534163 CAATGCAGGATGATGGCGTAG 59.466 52.381 0.00 0.00 39.69 3.51
8588 9663 2.162681 GTGGCTGTCAACCTAAGCAAT 58.837 47.619 0.00 0.00 38.73 3.56
8745 9823 5.220710 AGTTGCTGATCTACATGGGATAC 57.779 43.478 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.