Multiple sequence alignment - TraesCS6A01G338900

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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 TraesCS6A01G338900 chr6A 100.000 3653 0 0 1 3653 572143267 572139615 0.000000e+00 6746
1 TraesCS6A01G338900 chr6A 85.902 305 37 6 3326 3628 73639200 73639500 1.640000e-83 320
2 TraesCS6A01G338900 chr6B 92.063 3402 218 17 266 3652 643270269 643266905 0.000000e+00 4739
3 TraesCS6A01G338900 chr6B 91.723 2513 168 14 341 2836 643437372 643434883 0.000000e+00 3452
4 TraesCS6A01G338900 chr6B 94.131 443 25 1 3212 3653 643431034 643430592 0.000000e+00 673
5 TraesCS6A01G338900 chr6B 83.934 305 34 10 3326 3628 130965357 130965648 9.990000e-71 278
6 TraesCS6A01G338900 chr6B 96.154 130 2 3 230 357 643437512 643437384 3.700000e-50 209
7 TraesCS6A01G338900 chr6B 90.698 129 8 3 2875 3000 643431617 643431490 6.270000e-38 169
8 TraesCS6A01G338900 chr6D 92.213 2273 136 20 521 2774 427496169 427493919 0.000000e+00 3179
9 TraesCS6A01G338900 chr6D 90.271 884 53 11 2240 3120 427492369 427491516 0.000000e+00 1125
10 TraesCS6A01G338900 chr6D 94.595 444 22 2 3212 3653 427493690 427493247 0.000000e+00 686
11 TraesCS6A01G338900 chr6D 90.323 527 30 12 1 523 427496761 427496252 0.000000e+00 671
12 TraesCS6A01G338900 chr6D 92.308 442 34 0 3212 3653 427486760 427486319 2.390000e-176 628
13 TraesCS6A01G338900 chr6D 93.333 360 24 0 3212 3571 427965755 427966114 1.930000e-147 532
14 TraesCS6A01G338900 chr6D 86.287 474 50 6 3182 3653 427491429 427490969 5.450000e-138 501
15 TraesCS6A01G338900 chr6D 86.897 290 34 4 3326 3613 58446631 58446918 4.550000e-84 322
16 TraesCS6A01G338900 chr6D 94.048 84 5 0 3570 3653 427966196 427966279 1.060000e-25 128


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 TraesCS6A01G338900 chr6A 572139615 572143267 3652 True 6746.00 6746 100.0000 1 3653 1 chr6A.!!$R1 3652
1 TraesCS6A01G338900 chr6B 643266905 643270269 3364 True 4739.00 4739 92.0630 266 3652 1 chr6B.!!$R1 3386
2 TraesCS6A01G338900 chr6B 643430592 643437512 6920 True 1125.75 3452 93.1765 230 3653 4 chr6B.!!$R2 3423
3 TraesCS6A01G338900 chr6D 427490969 427496761 5792 True 1232.40 3179 90.7378 1 3653 5 chr6D.!!$R2 3652
4 TraesCS6A01G338900 chr6D 427965755 427966279 524 False 330.00 532 93.6905 3212 3653 2 chr6D.!!$F2 441

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
932 1055 1.382522 CCTCGTGGGTCCAATCAATG 58.617 55.0 0.00 0.0 0.00 2.82 F
1775 1909 0.108424 CTGTGGGCTGACTCAGTAGC 60.108 60.0 7.89 0.0 39.17 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2616 0.448990 CGTCGTACATCCTCAACCGA 59.551 55.0 0.0 0.0 0.0 4.69 R
3005 6443 0.036306 GTACTTGGTGGTGACTGGGG 59.964 60.0 0.0 0.0 0.0 4.96 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
25 26 7.581213 TGACATGAATAAATACCCATGTTCC 57.419 36.000 0.00 0.00 46.49 3.62
27 28 5.838521 ACATGAATAAATACCCATGTTCCCC 59.161 40.000 0.00 0.00 44.88 4.81
44 45 4.837093 TCCCCTAAACGAATCTGAACAT 57.163 40.909 0.00 0.00 0.00 2.71
98 99 7.744087 TGACAACAATATAGCTTGTCTTTGT 57.256 32.000 12.35 6.53 42.82 2.83
102 103 9.062524 ACAACAATATAGCTTGTCTTTGTACAA 57.937 29.630 3.59 3.59 38.38 2.41
158 159 1.745489 CGTGAAGCTAACTGCCCCC 60.745 63.158 0.00 0.00 44.23 5.40
192 193 2.993899 CCGTCCGATCCATATTACTTGC 59.006 50.000 0.00 0.00 0.00 4.01
195 196 2.631062 TCCGATCCATATTACTTGCCGT 59.369 45.455 0.00 0.00 0.00 5.68
196 197 2.993899 CCGATCCATATTACTTGCCGTC 59.006 50.000 0.00 0.00 0.00 4.79
197 198 3.554129 CCGATCCATATTACTTGCCGTCA 60.554 47.826 0.00 0.00 0.00 4.35
200 201 5.558273 CGATCCATATTACTTGCCGTCAAAC 60.558 44.000 0.00 0.00 0.00 2.93
201 202 3.619483 TCCATATTACTTGCCGTCAAACG 59.381 43.478 0.00 0.00 42.11 3.60
213 214 1.860950 CGTCAAACGGATGCATCTAGG 59.139 52.381 25.28 16.82 38.08 3.02
214 215 2.738643 CGTCAAACGGATGCATCTAGGT 60.739 50.000 25.28 17.42 38.08 3.08
215 216 2.609459 GTCAAACGGATGCATCTAGGTG 59.391 50.000 25.28 19.19 0.00 4.00
216 217 2.236146 TCAAACGGATGCATCTAGGTGT 59.764 45.455 25.28 13.47 0.00 4.16
217 218 3.449377 TCAAACGGATGCATCTAGGTGTA 59.551 43.478 25.28 0.00 0.00 2.90
218 219 4.100963 TCAAACGGATGCATCTAGGTGTAT 59.899 41.667 25.28 6.25 0.00 2.29
220 221 4.689612 ACGGATGCATCTAGGTGTATTT 57.310 40.909 25.28 1.13 0.00 1.40
223 224 5.304614 ACGGATGCATCTAGGTGTATTTAGT 59.695 40.000 25.28 6.19 0.00 2.24
225 226 5.409826 GGATGCATCTAGGTGTATTTAGTGC 59.590 44.000 25.28 0.00 0.00 4.40
226 227 5.614324 TGCATCTAGGTGTATTTAGTGCT 57.386 39.130 4.60 0.00 31.37 4.40
227 228 6.724893 TGCATCTAGGTGTATTTAGTGCTA 57.275 37.500 4.60 0.00 31.37 3.49
228 229 6.749139 TGCATCTAGGTGTATTTAGTGCTAG 58.251 40.000 4.60 0.00 31.37 3.42
229 230 6.549736 TGCATCTAGGTGTATTTAGTGCTAGA 59.450 38.462 4.60 0.00 31.37 2.43
230 231 7.233553 TGCATCTAGGTGTATTTAGTGCTAGAT 59.766 37.037 4.60 0.00 34.44 1.98
231 232 7.543868 GCATCTAGGTGTATTTAGTGCTAGATG 59.456 40.741 10.48 10.48 45.72 2.90
232 233 7.526142 TCTAGGTGTATTTAGTGCTAGATGG 57.474 40.000 0.00 0.00 0.00 3.51
233 234 7.295340 TCTAGGTGTATTTAGTGCTAGATGGA 58.705 38.462 0.00 0.00 0.00 3.41
234 235 7.950684 TCTAGGTGTATTTAGTGCTAGATGGAT 59.049 37.037 0.00 0.00 0.00 3.41
235 236 6.998802 AGGTGTATTTAGTGCTAGATGGATC 58.001 40.000 0.00 0.00 0.00 3.36
236 237 5.864474 GGTGTATTTAGTGCTAGATGGATCG 59.136 44.000 0.00 0.00 0.00 3.69
237 238 5.864474 GTGTATTTAGTGCTAGATGGATCGG 59.136 44.000 0.00 0.00 0.00 4.18
238 239 5.773176 TGTATTTAGTGCTAGATGGATCGGA 59.227 40.000 0.00 0.00 0.00 4.55
365 395 7.854557 AGAAATGACTAATTTTACCCCGTAC 57.145 36.000 0.00 0.00 38.64 3.67
400 430 2.020720 TGTTAGTGTGTGCCTTTGTGG 58.979 47.619 0.00 0.00 39.35 4.17
466 496 5.995282 ACTTCCATTTGATTCACTTCACGTA 59.005 36.000 0.00 0.00 0.00 3.57
507 537 6.872920 TCAAATGATGGTTTTAGGGCATTAC 58.127 36.000 0.00 0.00 0.00 1.89
509 539 7.836685 TCAAATGATGGTTTTAGGGCATTACTA 59.163 33.333 0.00 0.00 0.00 1.82
551 666 6.893020 AATACTCCCAAGAGACAATTACCT 57.107 37.500 0.00 0.00 43.39 3.08
576 691 2.670905 CGGATCATTGTACGAAGTTGCA 59.329 45.455 0.00 0.00 37.78 4.08
650 768 5.523552 ACAAAATAGTCAAAACCAAGCTTGC 59.476 36.000 21.43 5.41 0.00 4.01
777 898 9.346725 GCATTCTCTCGAAAATAAAAAGTTGAT 57.653 29.630 0.00 0.00 31.91 2.57
822 943 6.038271 AGTTTAGAAACGAAAGCATCACTTGT 59.962 34.615 0.00 0.00 43.51 3.16
922 1045 2.203640 TGAGACTGCCTCGTGGGT 60.204 61.111 5.54 0.00 44.92 4.51
932 1055 1.382522 CCTCGTGGGTCCAATCAATG 58.617 55.000 0.00 0.00 0.00 2.82
947 1070 5.010922 CCAATCAATGTGGAGTCCTTTGAAA 59.989 40.000 19.69 5.78 38.54 2.69
950 1073 3.884037 ATGTGGAGTCCTTTGAAACCT 57.116 42.857 11.33 0.00 0.00 3.50
1141 1272 4.760047 CCGCCGTCACCCTCCTTG 62.760 72.222 0.00 0.00 0.00 3.61
1227 1361 4.013702 GTCTACCTCTGGACGGCA 57.986 61.111 0.00 0.00 0.00 5.69
1233 1367 0.907704 ACCTCTGGACGGCAACCATA 60.908 55.000 0.00 0.00 36.79 2.74
1346 1480 2.651361 CTTCACCGTGAGCTCCGT 59.349 61.111 12.15 1.49 0.00 4.69
1416 1550 2.325082 CGGGTTCTTGGTGAAGGCG 61.325 63.158 0.00 0.00 35.01 5.52
1469 1603 2.971660 TTGCTCGATTCGTATGGGAA 57.028 45.000 5.89 0.89 0.00 3.97
1470 1604 3.469008 TTGCTCGATTCGTATGGGAAT 57.531 42.857 5.89 0.00 39.27 3.01
1478 1612 1.507140 TCGTATGGGAATCTTGGCCT 58.493 50.000 3.32 0.00 0.00 5.19
1506 1640 1.079127 CGCAAGGAGGGTGTTCGAT 60.079 57.895 0.00 0.00 0.00 3.59
1590 1724 4.704833 GTGGAGGCTGCGCAGGAA 62.705 66.667 36.47 1.48 0.00 3.36
1607 1741 1.329599 GGAAATGTTCGACGGTATGGC 59.670 52.381 0.00 0.00 0.00 4.40
1732 1866 0.454600 GCACAGCTGGAACATGATGG 59.545 55.000 19.93 0.00 38.20 3.51
1770 1904 3.640407 GGGCTGTGGGCTGACTCA 61.640 66.667 0.00 0.00 41.46 3.41
1775 1909 0.108424 CTGTGGGCTGACTCAGTAGC 60.108 60.000 7.89 0.00 39.17 3.58
1798 1932 1.819208 TTCAATCGGATGCGGCTGG 60.819 57.895 6.82 0.00 0.00 4.85
1956 2093 4.827304 TTCTTTGATCGACATGTTTGCA 57.173 36.364 0.00 0.00 0.00 4.08
2071 2208 3.130869 GCAACATGGACATGGCAAAGATA 59.869 43.478 15.94 0.00 42.91 1.98
2088 2225 6.865205 GCAAAGATACACTGAAGCTTTTCAAT 59.135 34.615 0.00 0.00 0.00 2.57
2140 2277 1.872952 CAGTGACATTTCTTGGCGTGA 59.127 47.619 0.00 0.00 35.37 4.35
2154 2291 1.765161 GCGTGATATCAGCTTGCGCA 61.765 55.000 24.46 5.66 42.44 6.09
2235 2372 5.505819 CGCAATTCAGAAATCTGCAGATCAT 60.506 40.000 28.83 20.40 43.46 2.45
2310 2447 2.919666 CCTTTGTGAAGGTAATGCCG 57.080 50.000 0.00 0.00 46.16 5.69
2382 2519 3.765511 AGCATTGCAATGTTGATGTAGGT 59.234 39.130 33.67 12.79 38.65 3.08
2465 2602 2.556257 TGCAAACACACTAGCTCGAAA 58.444 42.857 0.00 0.00 0.00 3.46
2479 2616 0.251916 TCGAAACCAGCGATGGGATT 59.748 50.000 25.79 18.36 32.09 3.01
2481 2618 0.657840 GAAACCAGCGATGGGATTCG 59.342 55.000 25.79 0.00 41.99 3.34
2482 2619 0.748005 AAACCAGCGATGGGATTCGG 60.748 55.000 25.79 0.00 39.49 4.30
2553 2693 0.324943 GGCTCAGCTGGGTTGAAGTA 59.675 55.000 16.66 0.00 0.00 2.24
2595 2735 1.749258 GACGGGGGATTTCAGCCAC 60.749 63.158 0.00 0.00 0.00 5.01
2725 2866 4.578928 AGGACAACACAACTACCATGAAAC 59.421 41.667 0.00 0.00 0.00 2.78
2801 2942 7.439108 AAATGTATGAGCTTAGGGTAGTTCT 57.561 36.000 0.00 0.00 0.00 3.01
2836 2985 5.455326 GCCTGAAGGATTAAGATCAAGGCTA 60.455 44.000 0.00 0.00 39.97 3.93
2848 2997 7.661536 AAGATCAAGGCTATCAAGTGTAGTA 57.338 36.000 0.00 0.00 0.00 1.82
2983 6419 9.937175 GAAAAGCAAATGTATATACAAGAGTCC 57.063 33.333 19.11 6.59 39.99 3.85
3003 6441 3.118408 TCCATAGGTTTGGTCGATGAAGG 60.118 47.826 0.00 0.00 38.01 3.46
3004 6442 2.396590 TAGGTTTGGTCGATGAAGGC 57.603 50.000 0.00 0.00 0.00 4.35
3005 6443 0.322546 AGGTTTGGTCGATGAAGGCC 60.323 55.000 0.00 0.00 36.18 5.19
3006 6444 1.313091 GGTTTGGTCGATGAAGGCCC 61.313 60.000 0.00 0.00 34.30 5.80
3007 6445 1.001393 TTTGGTCGATGAAGGCCCC 60.001 57.895 0.00 0.00 34.30 5.80
3008 6446 2.493273 TTTGGTCGATGAAGGCCCCC 62.493 60.000 0.00 0.00 34.30 5.40
3009 6447 3.407967 GGTCGATGAAGGCCCCCA 61.408 66.667 0.00 0.00 0.00 4.96
3010 6448 2.190578 GTCGATGAAGGCCCCCAG 59.809 66.667 0.00 0.00 0.00 4.45
3013 6451 2.669133 CGATGAAGGCCCCCAGTCA 61.669 63.158 0.00 0.00 0.00 3.41
3031 6469 4.451096 CAGTCACCACCAAGTACATGTAAC 59.549 45.833 7.25 2.37 0.00 2.50
3040 6478 6.882140 CACCAAGTACATGTAACCCTTTCATA 59.118 38.462 7.25 0.00 0.00 2.15
3063 6501 0.535102 AGGCAACACTGTACAGCACC 60.535 55.000 22.90 15.74 41.41 5.01
3108 6546 2.158813 TGTCTCTTGTGGTGGAAAGTCC 60.159 50.000 0.00 0.00 36.96 3.85
3189 6675 6.775088 CACATACAAACGTGCATAGAAAGAT 58.225 36.000 0.00 0.00 0.00 2.40
3194 6680 4.946784 AACGTGCATAGAAAGATGGAAC 57.053 40.909 0.00 0.00 0.00 3.62
3247 6888 7.033530 TCGTTTCTTTCTTTTTCCTATGCAA 57.966 32.000 0.00 0.00 0.00 4.08
3275 6916 3.051081 TGTTTTATTGCAATGGGGTGC 57.949 42.857 22.27 7.70 45.15 5.01
3424 7073 7.492524 TGTAGTCCTAGCTTTATTGTCATGAG 58.507 38.462 0.00 0.00 0.00 2.90
3468 7120 8.485976 TTTTTCCTTGTTTTGATTACCTTGTG 57.514 30.769 0.00 0.00 0.00 3.33
3490 7142 5.239306 GTGACAGAATGAAAACATCACCAGA 59.761 40.000 0.00 0.00 41.93 3.86
3545 7197 6.589135 TGCAATGTCTTCATGATCTCTACAT 58.411 36.000 0.00 0.00 34.19 2.29
3567 7219 3.842007 TTCCCCGTTCTTCAGTAAACA 57.158 42.857 0.00 0.00 0.00 2.83
3575 7310 6.537301 CCCGTTCTTCAGTAAACAATAGCATA 59.463 38.462 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.549082 TCGTTTAGGGGAACATGGGTA 58.451 47.619 0.00 0.00 0.00 3.69
25 26 8.438676 AATTCTATGTTCAGATTCGTTTAGGG 57.561 34.615 0.00 0.00 0.00 3.53
98 99 6.993308 TGTCCTTACACAAGTAGCAAATTGTA 59.007 34.615 0.00 0.00 37.54 2.41
102 103 5.240844 GGTTGTCCTTACACAAGTAGCAAAT 59.759 40.000 0.00 0.00 36.94 2.32
195 196 2.236146 ACACCTAGATGCATCCGTTTGA 59.764 45.455 23.06 1.40 0.00 2.69
196 197 2.632377 ACACCTAGATGCATCCGTTTG 58.368 47.619 23.06 16.73 0.00 2.93
197 198 4.689612 ATACACCTAGATGCATCCGTTT 57.310 40.909 23.06 12.05 0.00 3.60
200 201 5.635280 CACTAAATACACCTAGATGCATCCG 59.365 44.000 23.06 14.09 0.00 4.18
201 202 5.409826 GCACTAAATACACCTAGATGCATCC 59.590 44.000 23.06 5.58 0.00 3.51
202 203 6.226787 AGCACTAAATACACCTAGATGCATC 58.773 40.000 19.37 19.37 32.99 3.91
203 204 6.179906 AGCACTAAATACACCTAGATGCAT 57.820 37.500 0.00 0.00 32.99 3.96
204 205 5.614324 AGCACTAAATACACCTAGATGCA 57.386 39.130 0.00 0.00 32.99 3.96
205 206 6.982852 TCTAGCACTAAATACACCTAGATGC 58.017 40.000 0.00 0.00 29.68 3.91
206 207 8.978564 CATCTAGCACTAAATACACCTAGATG 57.021 38.462 16.40 16.40 45.79 2.90
207 208 7.950684 TCCATCTAGCACTAAATACACCTAGAT 59.049 37.037 0.00 0.00 41.04 1.98
208 209 7.295340 TCCATCTAGCACTAAATACACCTAGA 58.705 38.462 0.00 0.00 36.64 2.43
209 210 7.526142 TCCATCTAGCACTAAATACACCTAG 57.474 40.000 0.00 0.00 0.00 3.02
212 213 5.864474 CGATCCATCTAGCACTAAATACACC 59.136 44.000 0.00 0.00 0.00 4.16
213 214 5.864474 CCGATCCATCTAGCACTAAATACAC 59.136 44.000 0.00 0.00 0.00 2.90
214 215 5.773176 TCCGATCCATCTAGCACTAAATACA 59.227 40.000 0.00 0.00 0.00 2.29
215 216 6.268825 TCCGATCCATCTAGCACTAAATAC 57.731 41.667 0.00 0.00 0.00 1.89
216 217 5.419155 CCTCCGATCCATCTAGCACTAAATA 59.581 44.000 0.00 0.00 0.00 1.40
217 218 4.221703 CCTCCGATCCATCTAGCACTAAAT 59.778 45.833 0.00 0.00 0.00 1.40
218 219 3.574396 CCTCCGATCCATCTAGCACTAAA 59.426 47.826 0.00 0.00 0.00 1.85
220 221 2.375509 TCCTCCGATCCATCTAGCACTA 59.624 50.000 0.00 0.00 0.00 2.74
223 224 1.145945 ACTCCTCCGATCCATCTAGCA 59.854 52.381 0.00 0.00 0.00 3.49
225 226 4.295141 ACTACTCCTCCGATCCATCTAG 57.705 50.000 0.00 0.00 0.00 2.43
226 227 4.726035 AACTACTCCTCCGATCCATCTA 57.274 45.455 0.00 0.00 0.00 1.98
227 228 3.603965 AACTACTCCTCCGATCCATCT 57.396 47.619 0.00 0.00 0.00 2.90
228 229 3.243907 CCAAACTACTCCTCCGATCCATC 60.244 52.174 0.00 0.00 0.00 3.51
229 230 2.700897 CCAAACTACTCCTCCGATCCAT 59.299 50.000 0.00 0.00 0.00 3.41
230 231 2.108168 CCAAACTACTCCTCCGATCCA 58.892 52.381 0.00 0.00 0.00 3.41
231 232 2.108970 ACCAAACTACTCCTCCGATCC 58.891 52.381 0.00 0.00 0.00 3.36
232 233 3.522553 CAACCAAACTACTCCTCCGATC 58.477 50.000 0.00 0.00 0.00 3.69
233 234 2.236395 CCAACCAAACTACTCCTCCGAT 59.764 50.000 0.00 0.00 0.00 4.18
234 235 1.621814 CCAACCAAACTACTCCTCCGA 59.378 52.381 0.00 0.00 0.00 4.55
235 236 1.621814 TCCAACCAAACTACTCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
236 237 3.782656 TTCCAACCAAACTACTCCTCC 57.217 47.619 0.00 0.00 0.00 4.30
237 238 6.650427 ATTTTTCCAACCAAACTACTCCTC 57.350 37.500 0.00 0.00 0.00 3.71
238 239 8.721133 AATATTTTTCCAACCAAACTACTCCT 57.279 30.769 0.00 0.00 0.00 3.69
365 395 7.218773 CACACACTAACACTGAAAAATGTCAAG 59.781 37.037 0.00 0.00 0.00 3.02
445 475 6.622679 GCATTACGTGAAGTGAATCAAATGGA 60.623 38.462 0.00 0.00 30.83 3.41
466 496 6.703319 TCATTTGAATTCTTCATGGTGCATT 58.297 32.000 7.05 0.00 39.84 3.56
507 537 9.894783 AGTATTACATTGTAGTTATCTGCGTAG 57.105 33.333 0.00 0.00 0.00 3.51
509 539 7.866393 GGAGTATTACATTGTAGTTATCTGCGT 59.134 37.037 0.00 0.00 0.00 5.24
541 656 4.608948 ATGATCCGAGGAGGTAATTGTC 57.391 45.455 0.00 0.00 41.99 3.18
551 666 3.021695 ACTTCGTACAATGATCCGAGGA 58.978 45.455 6.05 0.00 31.79 3.71
576 691 0.396556 GTTGCCCGGGGGTAATTGAT 60.397 55.000 25.28 0.00 41.62 2.57
650 768 5.835113 AAAAACAGTTGATATGGATCGGG 57.165 39.130 0.00 0.00 34.49 5.14
790 911 6.945072 TGCTTTCGTTTCTAAACTCTCTTTC 58.055 36.000 4.24 0.00 36.77 2.62
822 943 5.429681 TTTTCCATCCCTCAACTTATCGA 57.570 39.130 0.00 0.00 0.00 3.59
922 1045 4.081406 CAAAGGACTCCACATTGATTGGA 58.919 43.478 0.00 0.00 41.06 3.53
932 1055 2.879026 GTGAGGTTTCAAAGGACTCCAC 59.121 50.000 0.00 0.00 34.49 4.02
947 1070 3.454587 TTTGCTGGCGTCGTGAGGT 62.455 57.895 0.00 0.00 0.00 3.85
950 1073 2.970324 GGTTTGCTGGCGTCGTGA 60.970 61.111 0.00 0.00 0.00 4.35
1140 1271 3.157252 GAGGAGGAGGATGCGGCA 61.157 66.667 4.58 4.58 0.00 5.69
1141 1272 3.934962 GGAGGAGGAGGATGCGGC 61.935 72.222 0.00 0.00 0.00 6.53
1227 1361 2.097110 TGGCGTAGGAGGATATGGTT 57.903 50.000 0.00 0.00 0.00 3.67
1233 1367 1.522569 GTGCTTGGCGTAGGAGGAT 59.477 57.895 0.00 0.00 0.00 3.24
1346 1480 1.587043 CGTCGAGAGGGACTTGAGCA 61.587 60.000 0.00 0.00 41.55 4.26
1378 1512 4.624364 CACCTGGCACACCTCGCA 62.624 66.667 0.00 0.00 36.63 5.10
1416 1550 4.862823 ACGGAGGAGCCTAGGCCC 62.863 72.222 30.42 27.73 43.17 5.80
1449 1583 3.469008 TTCCCATACGAATCGAGCAAT 57.531 42.857 10.55 0.00 0.00 3.56
1469 1603 1.229951 TCCCTCACCAGGCCAAGAT 60.230 57.895 5.01 0.00 38.72 2.40
1470 1604 2.206900 TCCCTCACCAGGCCAAGA 59.793 61.111 5.01 0.00 38.72 3.02
1478 1612 2.525629 TCCTTGCGTCCCTCACCA 60.526 61.111 0.00 0.00 0.00 4.17
1506 1640 1.298157 CGTTCCTCGCAGGCATTTCA 61.298 55.000 0.00 0.00 34.61 2.69
1590 1724 0.808453 CCGCCATACCGTCGAACATT 60.808 55.000 0.00 0.00 0.00 2.71
1607 1741 0.825840 GGAGATGAGGTCCCTCTCCG 60.826 65.000 14.20 0.00 44.05 4.63
1732 1866 3.041940 CTGGGAACACGCGGTGAC 61.042 66.667 12.47 6.58 36.96 3.67
1770 1904 0.892755 TCCGATTGAACACCGCTACT 59.107 50.000 0.00 0.00 0.00 2.57
1775 1909 1.348250 CGCATCCGATTGAACACCG 59.652 57.895 0.00 0.00 36.29 4.94
1809 1943 1.140161 CATTGTTGCAGCATCGGGG 59.860 57.895 3.36 0.00 0.00 5.73
1812 1949 1.517694 GGCCATTGTTGCAGCATCG 60.518 57.895 3.36 0.00 0.00 3.84
1887 2024 1.535462 CAGCCCTTGTGTAAAAGTCCG 59.465 52.381 0.00 0.00 0.00 4.79
1973 2110 3.621794 CCAAACAAGAAACGAGCTTCAG 58.378 45.455 0.00 0.00 0.00 3.02
2006 2143 4.698201 TTGTAAGACACCACATCCTTCA 57.302 40.909 0.00 0.00 0.00 3.02
2071 2208 5.300034 TCATGTCATTGAAAAGCTTCAGTGT 59.700 36.000 0.00 0.00 45.08 3.55
2088 2225 3.949754 GCAATCCTTCCTCAATCATGTCA 59.050 43.478 0.00 0.00 0.00 3.58
2154 2291 1.604378 GTCCACTAGCCCAGCATGT 59.396 57.895 0.00 0.00 0.00 3.21
2235 2372 3.117776 AGAGATCCACCATGCAAGCATAA 60.118 43.478 7.29 0.00 34.91 1.90
2310 2447 1.604593 ACCTGCATGTGGCTTCACC 60.605 57.895 6.77 0.00 45.15 4.02
2382 2519 2.570284 TTCTCTTGCGGCGACCTCA 61.570 57.895 12.98 0.00 0.00 3.86
2465 2602 1.910580 AACCGAATCCCATCGCTGGT 61.911 55.000 4.31 0.00 41.37 4.00
2479 2616 0.448990 CGTCGTACATCCTCAACCGA 59.551 55.000 0.00 0.00 0.00 4.69
2481 2618 1.471684 AGTCGTCGTACATCCTCAACC 59.528 52.381 0.00 0.00 0.00 3.77
2482 2619 2.161012 TCAGTCGTCGTACATCCTCAAC 59.839 50.000 0.00 0.00 0.00 3.18
2483 2620 2.429478 TCAGTCGTCGTACATCCTCAA 58.571 47.619 0.00 0.00 0.00 3.02
2553 2693 5.028549 AGAACTCATGAACAACAGTGTCT 57.971 39.130 0.00 0.00 36.80 3.41
2595 2735 8.894768 TGTTGTAAATTTGATTAAAACTGGGG 57.105 30.769 0.00 0.00 35.12 4.96
2801 2942 7.833682 TCTTAATCCTTCAGGCATTGTGAATTA 59.166 33.333 0.00 0.00 33.49 1.40
2836 2985 7.014711 CACTACCTCCATGATACTACACTTGAT 59.985 40.741 0.00 0.00 0.00 2.57
2848 2997 4.964897 TCATTGAGACACTACCTCCATGAT 59.035 41.667 0.00 0.00 37.67 2.45
2873 3022 6.485830 TCTGCTGCCATATAAAACTAGACT 57.514 37.500 0.00 0.00 0.00 3.24
2983 6419 2.614057 GCCTTCATCGACCAAACCTATG 59.386 50.000 0.00 0.00 0.00 2.23
3003 6441 3.868200 CTTGGTGGTGACTGGGGGC 62.868 68.421 0.00 0.00 0.00 5.80
3004 6442 1.131303 TACTTGGTGGTGACTGGGGG 61.131 60.000 0.00 0.00 0.00 5.40
3005 6443 0.036306 GTACTTGGTGGTGACTGGGG 59.964 60.000 0.00 0.00 0.00 4.96
3006 6444 0.762418 TGTACTTGGTGGTGACTGGG 59.238 55.000 0.00 0.00 0.00 4.45
3007 6445 2.224523 ACATGTACTTGGTGGTGACTGG 60.225 50.000 12.86 0.00 0.00 4.00
3008 6446 3.126001 ACATGTACTTGGTGGTGACTG 57.874 47.619 12.86 0.00 0.00 3.51
3009 6447 4.504340 GGTTACATGTACTTGGTGGTGACT 60.504 45.833 4.68 0.00 0.00 3.41
3010 6448 3.749609 GGTTACATGTACTTGGTGGTGAC 59.250 47.826 4.68 0.00 0.00 3.67
3013 6451 2.983898 AGGGTTACATGTACTTGGTGGT 59.016 45.455 4.68 0.00 0.00 4.16
3031 6469 4.019174 AGTGTTGCCTGAATATGAAAGGG 58.981 43.478 0.00 0.00 0.00 3.95
3040 6478 2.154462 GCTGTACAGTGTTGCCTGAAT 58.846 47.619 23.44 0.00 36.30 2.57
3073 6511 5.067805 CACAAGAGACAGGCTAAAGGTTTTT 59.932 40.000 0.00 0.00 0.00 1.94
3074 6512 4.580580 CACAAGAGACAGGCTAAAGGTTTT 59.419 41.667 0.00 0.00 0.00 2.43
3075 6513 4.137543 CACAAGAGACAGGCTAAAGGTTT 58.862 43.478 0.00 0.00 0.00 3.27
3076 6514 3.496870 CCACAAGAGACAGGCTAAAGGTT 60.497 47.826 0.00 0.00 0.00 3.50
3077 6515 2.039084 CCACAAGAGACAGGCTAAAGGT 59.961 50.000 0.00 0.00 0.00 3.50
3078 6516 2.039084 ACCACAAGAGACAGGCTAAAGG 59.961 50.000 0.00 0.00 0.00 3.11
3093 6531 2.649531 AATCGGACTTTCCACCACAA 57.350 45.000 0.00 0.00 35.91 3.33
3108 6546 9.916397 CACAAAGTAAATAGCTTACCTTAATCG 57.084 33.333 0.00 0.00 40.84 3.34
3165 6651 6.164408 TCTTTCTATGCACGTTTGTATGTG 57.836 37.500 0.00 0.00 42.92 3.21
3166 6652 6.183360 CCATCTTTCTATGCACGTTTGTATGT 60.183 38.462 0.00 0.00 29.75 2.29
3171 6657 4.944962 TCCATCTTTCTATGCACGTTTG 57.055 40.909 0.00 0.00 0.00 2.93
3187 6673 4.451096 TCAGTAAAGCTCGTTTGTTCCATC 59.549 41.667 0.00 0.00 0.00 3.51
3189 6675 3.799366 TCAGTAAAGCTCGTTTGTTCCA 58.201 40.909 0.00 0.00 0.00 3.53
3194 6680 6.223138 TGTATGTTCAGTAAAGCTCGTTTG 57.777 37.500 0.00 0.00 0.00 2.93
3424 7073 3.487120 AAGACTAACCAGTTGACACCC 57.513 47.619 0.00 0.00 34.21 4.61
3468 7120 5.947228 TCTGGTGATGTTTTCATTCTGTC 57.053 39.130 0.00 0.00 41.05 3.51
3490 7142 7.968405 GCGATAACATTAACAAAAACCAGAGAT 59.032 33.333 0.00 0.00 0.00 2.75
3545 7197 4.525024 TGTTTACTGAAGAACGGGGAAAA 58.475 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.