Multiple sequence alignment - TraesCS3D01G095500

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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 TraesCS3D01G095500 chr3D 100.000 4355 0 0 1 4355 48445831 48441477 0.000000e+00 8043
1 TraesCS3D01G095500 chr3A 93.554 2932 144 31 631 3537 60666965 60664054 0.000000e+00 4325
2 TraesCS3D01G095500 chr3A 90.402 771 37 16 3604 4355 60662237 60661485 0.000000e+00 979
3 TraesCS3D01G095500 chr3A 85.110 591 46 15 1 573 60667523 60666957 2.270000e-157 566
4 TraesCS3D01G095500 chr3B 94.991 2276 100 6 709 2982 76510653 76508390 0.000000e+00 3559
5 TraesCS3D01G095500 chr3B 88.851 583 29 15 3166 3729 76506657 76506092 0.000000e+00 684
6 TraesCS3D01G095500 chr3B 81.982 666 57 18 1 640 76514737 76514109 1.400000e-139 507
7 TraesCS3D01G095500 chr3B 86.797 409 26 10 3956 4355 76505387 76504998 8.650000e-117 431
8 TraesCS3D01G095500 chr3B 90.476 189 17 1 2986 3173 76508251 76508063 9.350000e-62 248


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 TraesCS3D01G095500 chr3D 48441477 48445831 4354 True 8043.000000 8043 100.000000 1 4355 1 chr3D.!!$R1 4354
1 TraesCS3D01G095500 chr3A 60661485 60667523 6038 True 1956.666667 4325 89.688667 1 4355 3 chr3A.!!$R1 4354
2 TraesCS3D01G095500 chr3B 76504998 76514737 9739 True 1085.800000 3559 88.619400 1 4355 5 chr3B.!!$R1 4354

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
584 603 0.111639 TAGGTTGTTTGAGGTGGGGC 59.888 55.0 0.00 0.00 0.00 5.80 F
735 4152 0.792640 GCACATCCTCGACAGTGTTG 59.207 55.0 3.89 3.89 34.59 3.33 F
1713 5134 0.451783 CAACGGCAAGTATGAAGGGC 59.548 55.0 0.00 0.00 0.00 5.19 F
2607 6037 0.036010 AGCAAGGGGTCAAGATCACG 60.036 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 5110 0.036164 TCATACTTGCCGTTGCCAGT 59.964 50.0 0.0 0.0 44.84 4.00 R
2584 6014 0.323178 ATCTTGACCCCTTGCTGCTG 60.323 55.0 0.0 0.0 0.00 4.41 R
3224 8213 0.248296 GCAAACGGCAAAAGTCGACA 60.248 50.0 19.5 0.0 43.97 4.35 R
4214 11473 0.542333 TACCCAAATCATTCGGGCGA 59.458 50.0 0.0 0.0 44.49 5.54 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
38 39 1.646540 CCTCTCTCTAGCAGCGTCG 59.353 63.158 0.00 0.00 0.00 5.12
73 74 1.988982 GACCTGGATCTCCCTTGCCC 61.989 65.000 0.00 0.00 35.38 5.36
118 120 2.386064 TTTCCGTGGTTCTGGGGACG 62.386 60.000 0.00 0.00 0.00 4.79
135 137 2.354773 GTCCCGCGGATGTCGATC 60.355 66.667 30.73 5.98 42.43 3.69
202 204 1.561769 ATTGATCGGGAGGTGGTGCA 61.562 55.000 0.00 0.00 0.00 4.57
203 205 1.561769 TTGATCGGGAGGTGGTGCAT 61.562 55.000 0.00 0.00 0.00 3.96
204 206 1.227674 GATCGGGAGGTGGTGCATC 60.228 63.158 0.00 0.00 0.00 3.91
205 207 2.978452 GATCGGGAGGTGGTGCATCG 62.978 65.000 0.00 0.00 0.00 3.84
206 208 3.770040 CGGGAGGTGGTGCATCGA 61.770 66.667 0.00 0.00 0.00 3.59
207 209 2.911143 GGGAGGTGGTGCATCGAT 59.089 61.111 0.00 0.00 0.00 3.59
209 211 1.097547 GGGAGGTGGTGCATCGATTG 61.098 60.000 0.00 0.00 0.00 2.67
211 213 1.718757 GAGGTGGTGCATCGATTGGC 61.719 60.000 0.00 0.00 0.00 4.52
212 214 1.750399 GGTGGTGCATCGATTGGCT 60.750 57.895 8.93 0.00 0.00 4.75
213 215 1.718757 GGTGGTGCATCGATTGGCTC 61.719 60.000 8.93 5.47 0.00 4.70
214 216 1.451927 TGGTGCATCGATTGGCTCC 60.452 57.895 17.45 17.45 42.47 4.70
215 217 1.153086 GGTGCATCGATTGGCTCCT 60.153 57.895 17.16 0.00 39.82 3.69
216 218 1.162800 GGTGCATCGATTGGCTCCTC 61.163 60.000 17.16 4.04 39.82 3.71
217 219 1.146930 TGCATCGATTGGCTCCTCC 59.853 57.895 8.93 0.00 0.00 4.30
218 220 1.599240 GCATCGATTGGCTCCTCCC 60.599 63.158 0.00 0.00 0.00 4.30
219 221 1.832219 CATCGATTGGCTCCTCCCA 59.168 57.895 0.00 0.00 0.00 4.37
220 222 0.533755 CATCGATTGGCTCCTCCCAC 60.534 60.000 0.00 0.00 33.82 4.61
221 223 0.692419 ATCGATTGGCTCCTCCCACT 60.692 55.000 0.00 0.00 33.82 4.00
222 224 1.153289 CGATTGGCTCCTCCCACTG 60.153 63.158 0.00 0.00 33.82 3.66
223 225 1.225704 GATTGGCTCCTCCCACTGG 59.774 63.158 0.00 0.00 33.82 4.00
224 226 1.229951 ATTGGCTCCTCCCACTGGA 60.230 57.895 0.00 0.00 38.75 3.86
225 227 0.625683 ATTGGCTCCTCCCACTGGAT 60.626 55.000 0.00 0.00 40.80 3.41
226 228 1.565390 TTGGCTCCTCCCACTGGATG 61.565 60.000 0.00 0.00 40.80 3.51
305 310 1.826385 AGCCGGAATTTGGAGTTCTG 58.174 50.000 5.05 0.00 0.00 3.02
315 320 3.526931 TTGGAGTTCTGATTAGAGCGG 57.473 47.619 0.00 0.00 38.96 5.52
394 413 0.529992 GGTAGAATTGGGCGGTCGAG 60.530 60.000 0.00 0.00 0.00 4.04
397 416 1.375523 GAATTGGGCGGTCGAGTGT 60.376 57.895 0.00 0.00 0.00 3.55
400 419 0.390735 ATTGGGCGGTCGAGTGTTAC 60.391 55.000 0.00 0.00 0.00 2.50
409 428 4.673580 GCGGTCGAGTGTTACAATCTCTTA 60.674 45.833 11.01 0.00 0.00 2.10
439 458 3.277142 TGCCGATCTCACACTCTAGTA 57.723 47.619 0.00 0.00 0.00 1.82
490 509 1.201855 CGCGTGTTTGAGCTGAGATTC 60.202 52.381 0.00 0.00 0.00 2.52
501 520 5.423015 TGAGCTGAGATTCTCACCATTTAC 58.577 41.667 12.38 1.96 35.39 2.01
505 524 6.888632 AGCTGAGATTCTCACCATTTACAATT 59.111 34.615 12.38 0.00 35.39 2.32
526 545 2.102070 ATCGGTAACAATTCGTGGCA 57.898 45.000 0.00 0.00 0.00 4.92
535 554 4.156455 ACAATTCGTGGCAAGAGGATAT 57.844 40.909 2.85 0.00 0.00 1.63
537 556 3.845781 ATTCGTGGCAAGAGGATATGT 57.154 42.857 2.85 0.00 0.00 2.29
544 563 2.364324 GGCAAGAGGATATGTGTCGGTA 59.636 50.000 0.00 0.00 0.00 4.02
545 564 3.181469 GGCAAGAGGATATGTGTCGGTAA 60.181 47.826 0.00 0.00 0.00 2.85
575 594 2.668144 TTGGGGTCCTAGGTTGTTTG 57.332 50.000 9.08 0.00 0.00 2.93
584 603 0.111639 TAGGTTGTTTGAGGTGGGGC 59.888 55.000 0.00 0.00 0.00 5.80
586 605 2.203422 TTGTTTGAGGTGGGGCGG 60.203 61.111 0.00 0.00 0.00 6.13
587 606 2.758207 TTGTTTGAGGTGGGGCGGA 61.758 57.895 0.00 0.00 0.00 5.54
588 607 2.359975 GTTTGAGGTGGGGCGGAG 60.360 66.667 0.00 0.00 0.00 4.63
621 651 6.823689 GTCCGGTAATATGATAATCCAGCAAT 59.176 38.462 0.00 0.00 0.00 3.56
628 658 5.936686 ATGATAATCCAGCAATTCAGTCG 57.063 39.130 0.00 0.00 0.00 4.18
699 812 9.860393 ACCCCTATATAATCCCAGGATAATATC 57.140 37.037 0.00 0.00 33.97 1.63
707 820 7.639062 AATCCCAGGATAATATCAGACTGTT 57.361 36.000 1.59 0.00 33.97 3.16
735 4152 0.792640 GCACATCCTCGACAGTGTTG 59.207 55.000 3.89 3.89 34.59 3.33
776 4193 7.819900 ACCTAGATCTGTATCACTTGTTTGAAC 59.180 37.037 5.18 0.00 34.28 3.18
831 4248 7.717436 TGAATGGTTTGTTCACTACATTCAGTA 59.283 33.333 12.29 0.00 45.15 2.74
852 4269 9.997482 TCAGTACAAGATGTTTTTGTTTTAGTC 57.003 29.630 0.00 0.00 39.36 2.59
863 4280 5.502153 TTTGTTTTAGTCGCCTTTTGCTA 57.498 34.783 0.00 0.00 38.05 3.49
890 4307 3.340814 TCTCTTTGTTGCAGGATCTCC 57.659 47.619 0.00 0.00 0.00 3.71
893 4310 2.237143 TCTTTGTTGCAGGATCTCCGAT 59.763 45.455 0.00 0.00 42.08 4.18
896 4313 4.422073 TTGTTGCAGGATCTCCGATAAT 57.578 40.909 0.00 0.00 42.08 1.28
902 4319 5.305585 TGCAGGATCTCCGATAATTTAACC 58.694 41.667 0.00 0.00 42.08 2.85
907 4328 5.179555 GGATCTCCGATAATTTAACCTGTGC 59.820 44.000 0.00 0.00 0.00 4.57
909 4330 3.864243 TCCGATAATTTAACCTGTGCGT 58.136 40.909 0.00 0.00 0.00 5.24
927 4348 0.856641 GTGTTGTCGCTGTCGCTTAA 59.143 50.000 0.00 0.00 35.26 1.85
983 4404 4.165779 GCGTTTGGAATCGATTCATTTGT 58.834 39.130 32.92 1.60 38.53 2.83
1014 4435 5.128663 TGGCTTGTATATGAGCTCACAAGTA 59.871 40.000 30.19 22.11 46.12 2.24
1182 4603 2.146073 ATTGTGGTTGCTTCGCTGCC 62.146 55.000 0.00 0.00 0.00 4.85
1224 4645 4.695928 AGAATCTTTAACTGCGACCCTTTC 59.304 41.667 0.00 0.00 0.00 2.62
1449 4870 7.415653 GGGAAAGATAACATTGTGATTGTCCTC 60.416 40.741 9.74 1.39 0.00 3.71
1638 5059 6.456988 GGCTAAAGGTGACAAAGATGATTACG 60.457 42.308 0.00 0.00 0.00 3.18
1671 5092 3.056678 CACACATTTCTTGCATGGCCTTA 60.057 43.478 3.32 0.00 0.00 2.69
1689 5110 5.307196 GGCCTTAACTATGGATGGTCTCTTA 59.693 44.000 0.00 0.00 0.00 2.10
1713 5134 0.451783 CAACGGCAAGTATGAAGGGC 59.548 55.000 0.00 0.00 0.00 5.19
1771 5192 2.012673 GCCTGCAAGAGGTGAGTAATG 58.987 52.381 0.00 0.00 44.97 1.90
1777 5198 4.756642 TGCAAGAGGTGAGTAATGTTTCAG 59.243 41.667 0.00 0.00 0.00 3.02
1779 5200 5.239525 GCAAGAGGTGAGTAATGTTTCAGTT 59.760 40.000 0.00 0.00 0.00 3.16
1978 5399 7.617723 AGAGGTCTTGATAAAGCCGAGATATAT 59.382 37.037 0.00 0.00 0.00 0.86
2210 5631 6.591935 TCACTGTCTTTCATGAAAGGTTAGT 58.408 36.000 36.07 31.42 45.80 2.24
2244 5665 3.181507 GCTCGCACTATTTGATTGCTCAA 60.182 43.478 0.00 0.00 39.62 3.02
2294 5715 5.381184 TTGGCATAATGAAGGGCTAACTA 57.619 39.130 0.00 0.00 0.00 2.24
2377 5798 3.624861 CAGAGGACTAATGGATGCACAAC 59.375 47.826 0.00 0.00 0.00 3.32
2433 5855 8.864087 TGATGTGATGAATAGTCTAGCTAATGT 58.136 33.333 0.00 0.00 32.72 2.71
2449 5871 5.873732 GCTAATGTGGAAAAGTTAGCTCAG 58.126 41.667 8.31 0.00 43.38 3.35
2495 5917 9.521503 TTGTCAATTTCGTAAAATGATGTGAAA 57.478 25.926 0.00 0.00 35.27 2.69
2545 5973 2.094854 GCAAACTGCTGCTCTGCTATTT 60.095 45.455 0.00 0.00 40.96 1.40
2584 6014 7.551262 AGAAAACAGTAAACAAAACCCAATTCC 59.449 33.333 0.00 0.00 0.00 3.01
2597 6027 0.901580 CAATTCCAGCAGCAAGGGGT 60.902 55.000 0.00 0.00 0.00 4.95
2607 6037 0.036010 AGCAAGGGGTCAAGATCACG 60.036 55.000 0.00 0.00 0.00 4.35
2734 6164 8.892723 TCAGTTAGTCAAGGCATTAACATATTG 58.107 33.333 0.00 0.00 0.00 1.90
2994 6561 9.249457 CCATATACCTGTAGCACATATAATTCG 57.751 37.037 0.00 0.00 0.00 3.34
2996 6563 4.315803 ACCTGTAGCACATATAATTCGGC 58.684 43.478 0.00 0.00 0.00 5.54
2997 6564 3.684788 CCTGTAGCACATATAATTCGGCC 59.315 47.826 0.00 0.00 0.00 6.13
2999 6566 4.709250 TGTAGCACATATAATTCGGCCAA 58.291 39.130 2.24 0.00 0.00 4.52
3026 6593 5.029650 TGCTGTCAATACACGTTTGATTC 57.970 39.130 4.58 0.00 35.68 2.52
3089 6657 4.092968 CAGAAAATTACACCAGTCGGTAGC 59.907 45.833 0.00 0.00 46.94 3.58
3136 6710 6.109359 CAGGCTAAAGCTGTTTCAGTAGTAT 58.891 40.000 1.39 0.00 41.70 2.12
3164 6738 5.240183 CCTCAGCAGATTTTTGTTCTTCTCA 59.760 40.000 0.00 0.00 0.00 3.27
3214 8201 7.066887 TGCTCTTGTATTTGTTGAAACTCTCAA 59.933 33.333 0.00 0.00 41.93 3.02
3238 8227 3.924686 ACTAACTATGTCGACTTTTGCCG 59.075 43.478 17.92 3.46 0.00 5.69
3282 8271 0.106335 TTGACCAAGTAAACGGCGGA 59.894 50.000 13.24 0.00 0.00 5.54
3321 8310 0.319641 ACTCGCGGTTTCTCAAGACC 60.320 55.000 6.13 0.00 0.00 3.85
3351 8340 1.599047 CCTGAGGACATTGACCGCT 59.401 57.895 9.86 0.00 0.00 5.52
3365 8354 2.472934 CGCTTAAACCGCGTGACC 59.527 61.111 4.92 0.00 45.13 4.02
3366 8355 2.865308 GCTTAAACCGCGTGACCC 59.135 61.111 4.92 0.00 0.00 4.46
3367 8356 1.670083 GCTTAAACCGCGTGACCCT 60.670 57.895 4.92 0.00 0.00 4.34
3406 8395 6.736123 ACGACATGTACATACATAGAAGGTC 58.264 40.000 8.32 7.47 44.57 3.85
3440 8429 5.337330 CCATTGTATATAACCGTCCTCCTCC 60.337 48.000 0.00 0.00 0.00 4.30
3441 8430 4.736611 TGTATATAACCGTCCTCCTCCT 57.263 45.455 0.00 0.00 0.00 3.69
3442 8431 4.660168 TGTATATAACCGTCCTCCTCCTC 58.340 47.826 0.00 0.00 0.00 3.71
3481 8470 1.442148 GTCGCCGGAATAAGGAGCT 59.558 57.895 5.05 0.00 0.00 4.09
3560 8560 7.655328 TCCAAATTGCATTGTTTATTCGACTTT 59.345 29.630 0.00 0.00 0.00 2.66
3561 8561 8.920665 CCAAATTGCATTGTTTATTCGACTTTA 58.079 29.630 0.00 0.00 0.00 1.85
3573 8575 7.899178 TTATTCGACTTTATGAACAAGAGCA 57.101 32.000 0.00 0.00 0.00 4.26
3854 10797 1.008538 GTGGTTCTTGTGCTTGGCG 60.009 57.895 0.00 0.00 0.00 5.69
3870 10813 1.795872 TGGCGTGTTTGATCAAGTACG 59.204 47.619 27.93 27.93 35.80 3.67
3874 10817 3.426191 GCGTGTTTGATCAAGTACGTACA 59.574 43.478 30.10 19.99 35.44 2.90
3875 10818 4.090930 GCGTGTTTGATCAAGTACGTACAT 59.909 41.667 30.10 13.27 35.44 2.29
3876 10819 5.286797 GCGTGTTTGATCAAGTACGTACATA 59.713 40.000 30.10 12.14 35.44 2.29
4029 11286 1.066071 TCTGATCTCGTGTCGTCCTCT 60.066 52.381 0.00 0.00 0.00 3.69
4045 11302 1.579698 CTCTTGATGTGCCCATCTCG 58.420 55.000 10.62 1.90 46.38 4.04
4050 11307 1.202568 TGATGTGCCCATCTCGTCATC 60.203 52.381 10.62 0.00 46.38 2.92
4051 11308 0.832626 ATGTGCCCATCTCGTCATCA 59.167 50.000 0.00 0.00 0.00 3.07
4052 11309 0.612744 TGTGCCCATCTCGTCATCAA 59.387 50.000 0.00 0.00 0.00 2.57
4053 11310 1.210234 TGTGCCCATCTCGTCATCAAT 59.790 47.619 0.00 0.00 0.00 2.57
4054 11311 2.292267 GTGCCCATCTCGTCATCAATT 58.708 47.619 0.00 0.00 0.00 2.32
4055 11312 2.289002 GTGCCCATCTCGTCATCAATTC 59.711 50.000 0.00 0.00 0.00 2.17
4056 11313 2.093021 TGCCCATCTCGTCATCAATTCA 60.093 45.455 0.00 0.00 0.00 2.57
4057 11314 3.144506 GCCCATCTCGTCATCAATTCAT 58.855 45.455 0.00 0.00 0.00 2.57
4058 11315 3.188048 GCCCATCTCGTCATCAATTCATC 59.812 47.826 0.00 0.00 0.00 2.92
4059 11316 4.383173 CCCATCTCGTCATCAATTCATCA 58.617 43.478 0.00 0.00 0.00 3.07
4060 11317 5.001874 CCCATCTCGTCATCAATTCATCAT 58.998 41.667 0.00 0.00 0.00 2.45
4061 11318 6.168389 CCCATCTCGTCATCAATTCATCATA 58.832 40.000 0.00 0.00 0.00 2.15
4062 11319 6.822170 CCCATCTCGTCATCAATTCATCATAT 59.178 38.462 0.00 0.00 0.00 1.78
4063 11320 7.983484 CCCATCTCGTCATCAATTCATCATATA 59.017 37.037 0.00 0.00 0.00 0.86
4064 11321 8.815189 CCATCTCGTCATCAATTCATCATATAC 58.185 37.037 0.00 0.00 0.00 1.47
4065 11322 9.583765 CATCTCGTCATCAATTCATCATATACT 57.416 33.333 0.00 0.00 0.00 2.12
4101 11358 2.154854 TCCTCTTCTTTGTCTGTGCG 57.845 50.000 0.00 0.00 0.00 5.34
4106 11363 2.866156 TCTTCTTTGTCTGTGCGAACTG 59.134 45.455 0.00 0.00 0.00 3.16
4120 11377 1.463056 CGAACTGTTTATTCCAGCGCA 59.537 47.619 11.47 0.00 33.09 6.09
4137 11394 1.409227 GCAGATGACTCGTCGCTGTG 61.409 60.000 16.03 6.82 37.13 3.66
4145 11402 1.328439 CTCGTCGCTGTGAAGTGTAC 58.672 55.000 4.18 0.00 0.00 2.90
4162 11421 4.098960 AGTGTACACGAAGGAGACAAAGAA 59.901 41.667 19.93 0.00 36.20 2.52
4164 11423 5.118817 GTGTACACGAAGGAGACAAAGAATC 59.881 44.000 10.84 0.00 0.00 2.52
4206 11465 0.963355 TTAGGGCCATTTGTCACGCC 60.963 55.000 6.18 0.00 40.85 5.68
4211 11470 1.353609 GCCATTTGTCACGCCATTGC 61.354 55.000 0.00 0.00 0.00 3.56
4214 11473 2.406130 CATTTGTCACGCCATTGCTTT 58.594 42.857 0.00 0.00 34.43 3.51
4215 11474 2.132740 TTTGTCACGCCATTGCTTTC 57.867 45.000 0.00 0.00 34.43 2.62
4216 11475 0.040514 TTGTCACGCCATTGCTTTCG 60.041 50.000 0.00 0.00 34.43 3.46
4219 11478 3.747976 ACGCCATTGCTTTCGCCC 61.748 61.111 0.00 0.00 34.43 6.13
4220 11479 4.834892 CGCCATTGCTTTCGCCCG 62.835 66.667 0.00 0.00 34.43 6.13
4344 11608 2.554142 GAGTGATGTCATGGATTCGCA 58.446 47.619 0.00 0.00 0.00 5.10
4350 11614 4.641541 TGATGTCATGGATTCGCAGAAAAT 59.358 37.500 0.00 0.00 45.90 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 120 2.354773 GATCGACATCCGCGGGAC 60.355 66.667 27.83 9.66 38.37 4.46
128 130 0.326143 TCCCAATCCCCAGATCGACA 60.326 55.000 0.00 0.00 0.00 4.35
170 172 1.076777 ATCAATCAACCAGCCCGGG 60.077 57.895 19.09 19.09 40.22 5.73
177 179 1.065491 CACCTCCCGATCAATCAACCA 60.065 52.381 0.00 0.00 0.00 3.67
179 181 1.065418 ACCACCTCCCGATCAATCAAC 60.065 52.381 0.00 0.00 0.00 3.18
202 204 0.692419 AGTGGGAGGAGCCAATCGAT 60.692 55.000 0.00 0.00 38.95 3.59
203 205 1.306141 AGTGGGAGGAGCCAATCGA 60.306 57.895 0.00 0.00 38.95 3.59
204 206 1.153289 CAGTGGGAGGAGCCAATCG 60.153 63.158 0.00 0.00 38.95 3.34
205 207 1.225704 CCAGTGGGAGGAGCCAATC 59.774 63.158 0.00 0.00 38.95 2.67
206 208 1.229951 TCCAGTGGGAGGAGCCAAT 60.230 57.895 9.92 0.00 38.64 3.16
207 209 2.206900 TCCAGTGGGAGGAGCCAA 59.793 61.111 9.92 0.00 38.64 4.52
218 220 1.461091 GCCATGGCATCCATCCAGTG 61.461 60.000 32.08 0.00 43.15 3.66
219 221 1.152610 GCCATGGCATCCATCCAGT 60.153 57.895 32.08 0.00 43.15 4.00
220 222 1.906824 GGCCATGGCATCCATCCAG 60.907 63.158 36.56 0.00 43.15 3.86
221 223 2.199257 GGCCATGGCATCCATCCA 59.801 61.111 36.56 0.00 43.15 3.41
222 224 2.602568 GGGCCATGGCATCCATCC 60.603 66.667 36.56 23.59 43.15 3.51
223 225 1.906824 CAGGGCCATGGCATCCATC 60.907 63.158 36.56 18.69 43.15 3.51
224 226 2.200370 CAGGGCCATGGCATCCAT 59.800 61.111 36.56 15.88 46.37 3.41
225 227 4.845447 GCAGGGCCATGGCATCCA 62.845 66.667 36.56 0.00 44.11 3.41
257 259 2.103538 TATTCGCGTCCCGTCAGC 59.896 61.111 5.77 0.00 38.35 4.26
258 260 1.588139 GGTATTCGCGTCCCGTCAG 60.588 63.158 5.77 0.00 38.35 3.51
259 261 2.491152 GGTATTCGCGTCCCGTCA 59.509 61.111 5.77 0.00 38.35 4.35
260 262 2.653130 CGGTATTCGCGTCCCGTC 60.653 66.667 5.77 0.00 38.35 4.79
261 263 4.197498 CCGGTATTCGCGTCCCGT 62.197 66.667 20.38 3.22 38.79 5.28
262 264 4.936823 CCCGGTATTCGCGTCCCG 62.937 72.222 5.77 13.27 40.12 5.14
305 310 0.455295 CGCTCCGATCCGCTCTAATC 60.455 60.000 0.00 0.00 0.00 1.75
394 413 9.282247 CATTGATTTGCTAAGAGATTGTAACAC 57.718 33.333 0.00 0.00 0.00 3.32
397 416 7.483307 GGCATTGATTTGCTAAGAGATTGTAA 58.517 34.615 0.00 0.00 42.38 2.41
400 419 4.974275 CGGCATTGATTTGCTAAGAGATTG 59.026 41.667 0.00 0.00 42.38 2.67
409 428 2.357009 GTGAGATCGGCATTGATTTGCT 59.643 45.455 0.00 0.00 42.38 3.91
459 478 1.025812 AAACACGCGGGATTCAAACA 58.974 45.000 19.19 0.00 0.00 2.83
490 509 8.670135 TGTTACCGATAAATTGTAAATGGTGAG 58.330 33.333 0.00 0.00 0.00 3.51
501 520 5.454232 GCCACGAATTGTTACCGATAAATTG 59.546 40.000 0.00 0.00 0.00 2.32
505 524 3.597255 TGCCACGAATTGTTACCGATAA 58.403 40.909 0.00 0.00 0.00 1.75
526 545 8.880991 ACTATATTACCGACACATATCCTCTT 57.119 34.615 0.00 0.00 0.00 2.85
535 554 6.764085 CCCAAATCAACTATATTACCGACACA 59.236 38.462 0.00 0.00 0.00 3.72
537 556 6.126710 ACCCCAAATCAACTATATTACCGACA 60.127 38.462 0.00 0.00 0.00 4.35
544 563 6.624021 ACCTAGGACCCCAAATCAACTATATT 59.376 38.462 17.98 0.00 0.00 1.28
545 564 6.158260 ACCTAGGACCCCAAATCAACTATAT 58.842 40.000 17.98 0.00 0.00 0.86
584 603 1.592400 TACCGGACAGTTCTGCTCCG 61.592 60.000 23.36 23.36 42.91 4.63
586 605 2.674796 ATTACCGGACAGTTCTGCTC 57.325 50.000 9.46 0.00 0.00 4.26
587 606 3.704566 TCATATTACCGGACAGTTCTGCT 59.295 43.478 9.46 0.00 0.00 4.24
588 607 4.054780 TCATATTACCGGACAGTTCTGC 57.945 45.455 9.46 0.00 0.00 4.26
599 629 8.267620 TGAATTGCTGGATTATCATATTACCG 57.732 34.615 0.00 0.00 0.00 4.02
621 651 5.685841 GTTGCTACAAAATAAGCGACTGAA 58.314 37.500 7.32 0.00 45.71 3.02
628 658 7.437124 CGCTTAAAAGTTGCTACAAAATAAGC 58.563 34.615 18.51 18.51 39.33 3.09
699 812 5.007039 GGATGTGCATATGTACAACAGTCTG 59.993 44.000 27.05 0.00 43.49 3.51
707 820 3.383185 TGTCGAGGATGTGCATATGTACA 59.617 43.478 25.82 25.82 44.32 2.90
735 4152 6.423302 CAGATCTAGGTACAATGTCAGCATTC 59.577 42.308 0.00 0.00 42.91 2.67
776 4193 6.270064 ACCTTCCAAACAAAAACAGTAATCG 58.730 36.000 0.00 0.00 0.00 3.34
831 4248 5.746721 GGCGACTAAAACAAAAACATCTTGT 59.253 36.000 0.00 0.00 38.65 3.16
863 4280 5.596836 TCCTGCAACAAAGAGAAAACATT 57.403 34.783 0.00 0.00 0.00 2.71
890 4307 4.593597 ACACGCACAGGTTAAATTATCG 57.406 40.909 0.00 0.00 0.00 2.92
893 4310 4.318903 CGACAACACGCACAGGTTAAATTA 60.319 41.667 0.00 0.00 0.00 1.40
896 4313 1.328069 CGACAACACGCACAGGTTAAA 59.672 47.619 0.00 0.00 0.00 1.52
921 4342 3.806316 AAGGTTGTCGATGTTTAAGCG 57.194 42.857 0.00 0.00 0.00 4.68
927 4348 0.591170 CGCCAAAGGTTGTCGATGTT 59.409 50.000 0.00 0.00 0.00 2.71
954 4375 1.737236 TCGATTCCAAACGCAATGAGG 59.263 47.619 0.00 0.00 0.00 3.86
983 4404 4.080919 AGCTCATATACAAGCCAGACACAA 60.081 41.667 4.89 0.00 39.39 3.33
1014 4435 0.463116 GTAAACCCCGCGATGTGGAT 60.463 55.000 8.23 0.00 34.74 3.41
1224 4645 2.260822 TCCCTCCTGAAAGTCTCCTTG 58.739 52.381 0.00 0.00 0.00 3.61
1479 4900 4.224762 TCTGATGGAGCATCTTCAGATCT 58.775 43.478 15.74 0.00 43.88 2.75
1530 4951 2.485903 GAATGATGAGAGAGGCAGCAG 58.514 52.381 0.00 0.00 34.91 4.24
1536 4957 6.824553 TGAAGTATTGGAATGATGAGAGAGG 58.175 40.000 0.00 0.00 0.00 3.69
1638 5059 2.762327 AGAAATGTGTGAATCATGGGCC 59.238 45.455 0.00 0.00 0.00 5.80
1671 5092 4.101741 GCCAGTAAGAGACCATCCATAGTT 59.898 45.833 0.00 0.00 0.00 2.24
1689 5110 0.036164 TCATACTTGCCGTTGCCAGT 59.964 50.000 0.00 0.00 44.84 4.00
1771 5192 5.173774 TGTCATCAAAGAGCAACTGAAAC 57.826 39.130 0.00 0.00 0.00 2.78
1777 5198 3.084039 TGGGATGTCATCAAAGAGCAAC 58.916 45.455 14.72 0.00 0.00 4.17
1779 5200 3.657398 ATGGGATGTCATCAAAGAGCA 57.343 42.857 14.72 0.00 0.00 4.26
1894 5315 2.457813 TGCCCATGCTAACCATCAAT 57.542 45.000 0.00 0.00 38.71 2.57
1978 5399 2.268762 TTGGTGACAGTGCAATGCTA 57.731 45.000 15.18 0.00 44.54 3.49
2210 5631 2.100197 AGTGCGAGCAGAAGTACCATA 58.900 47.619 0.00 0.00 0.00 2.74
2244 5665 3.900601 ACACAGAACTCTCAAGACCAGAT 59.099 43.478 0.00 0.00 0.00 2.90
2433 5855 6.620877 TTCTATCCTGAGCTAACTTTTCCA 57.379 37.500 0.00 0.00 0.00 3.53
2499 5921 8.462016 GCCTGTTTAATGTTTTGAGATCACTAT 58.538 33.333 0.00 0.00 0.00 2.12
2584 6014 0.323178 ATCTTGACCCCTTGCTGCTG 60.323 55.000 0.00 0.00 0.00 4.41
2597 6027 8.771920 ATGATAAGTAAAACACGTGATCTTGA 57.228 30.769 25.01 2.60 0.00 3.02
2627 6057 5.845985 ATGAAGTGAATCACAAGTACGTG 57.154 39.130 16.38 7.29 36.74 4.49
2734 6164 2.991250 TCCCTAGAGAAATGCAGCAAC 58.009 47.619 0.00 0.00 0.00 4.17
2994 6561 0.681175 ATTGACAGCAAAGGTTGGCC 59.319 50.000 0.00 0.00 37.59 5.36
2996 6563 3.609175 CGTGTATTGACAGCAAAGGTTGG 60.609 47.826 0.00 0.00 37.59 3.77
2997 6564 3.003275 ACGTGTATTGACAGCAAAGGTTG 59.997 43.478 0.00 0.00 37.59 3.77
2999 6566 2.846193 ACGTGTATTGACAGCAAAGGT 58.154 42.857 0.00 0.00 37.59 3.50
3026 6593 4.115401 TGATCGGACATTCAGAAGTGAG 57.885 45.455 0.00 0.00 32.98 3.51
3089 6657 7.220683 CCTGTAACAAGAACTGTCATTGTTTTG 59.779 37.037 21.04 14.03 42.82 2.44
3155 6729 3.808174 ACGGTTACTTGCTTGAGAAGAAC 59.192 43.478 0.00 0.00 0.00 3.01
3214 8201 4.689345 GGCAAAAGTCGACATAGTTAGTGT 59.311 41.667 19.50 0.00 0.00 3.55
3224 8213 0.248296 GCAAACGGCAAAAGTCGACA 60.248 50.000 19.50 0.00 43.97 4.35
3238 8227 1.068954 GCACCTGTAGAAGCTGCAAAC 60.069 52.381 1.02 0.00 0.00 2.93
3282 8271 3.449018 AGTATTCCTTCTGCGTCATCTGT 59.551 43.478 0.00 0.00 0.00 3.41
3321 8310 4.261701 CTCAGGGGAGGGTAGTCG 57.738 66.667 0.00 0.00 37.51 4.18
3351 8340 1.962306 GCAGGGTCACGCGGTTTAA 60.962 57.895 12.47 0.00 0.00 1.52
3379 8368 7.014326 ACCTTCTATGTATGTACATGTCGTCAT 59.986 37.037 18.81 14.98 45.77 3.06
3406 8395 5.405571 GGTTATATACAATGGACAGAGCACG 59.594 44.000 0.00 0.00 0.00 5.34
3440 8429 1.880340 CTAGAGCTTTGCCGGCGAG 60.880 63.158 23.90 22.56 34.52 5.03
3441 8430 2.184322 CTAGAGCTTTGCCGGCGA 59.816 61.111 23.90 19.26 34.52 5.54
3442 8431 2.892425 CCTAGAGCTTTGCCGGCG 60.892 66.667 23.90 8.96 34.52 6.46
3507 8496 2.266689 CAAAATGGGCAGGCAGGC 59.733 61.111 0.00 0.00 43.27 4.85
3560 8560 7.940688 ACATATCAATGGATGCTCTTGTTCATA 59.059 33.333 0.00 0.00 37.43 2.15
3561 8561 6.776116 ACATATCAATGGATGCTCTTGTTCAT 59.224 34.615 0.00 0.00 37.43 2.57
3726 10475 2.176148 TCCACAATGGCATCCATCAGAT 59.824 45.455 0.00 0.00 44.40 2.90
4045 11302 9.662947 TGATGGAGTATATGATGAATTGATGAC 57.337 33.333 0.00 0.00 0.00 3.06
4050 11307 9.591792 ACGTATGATGGAGTATATGATGAATTG 57.408 33.333 0.00 0.00 0.00 2.32
4052 11309 9.809096 GAACGTATGATGGAGTATATGATGAAT 57.191 33.333 0.00 0.00 0.00 2.57
4053 11310 8.802267 TGAACGTATGATGGAGTATATGATGAA 58.198 33.333 0.00 0.00 0.00 2.57
4054 11311 8.348285 TGAACGTATGATGGAGTATATGATGA 57.652 34.615 0.00 0.00 0.00 2.92
4055 11312 9.591792 AATGAACGTATGATGGAGTATATGATG 57.408 33.333 0.00 0.00 0.00 3.07
4057 11314 9.639601 GAAATGAACGTATGATGGAGTATATGA 57.360 33.333 0.00 0.00 0.00 2.15
4058 11315 8.873830 GGAAATGAACGTATGATGGAGTATATG 58.126 37.037 0.00 0.00 0.00 1.78
4059 11316 8.816894 AGGAAATGAACGTATGATGGAGTATAT 58.183 33.333 0.00 0.00 0.00 0.86
4060 11317 8.190326 AGGAAATGAACGTATGATGGAGTATA 57.810 34.615 0.00 0.00 0.00 1.47
4061 11318 7.015682 AGAGGAAATGAACGTATGATGGAGTAT 59.984 37.037 0.00 0.00 0.00 2.12
4062 11319 6.323996 AGAGGAAATGAACGTATGATGGAGTA 59.676 38.462 0.00 0.00 0.00 2.59
4063 11320 5.129485 AGAGGAAATGAACGTATGATGGAGT 59.871 40.000 0.00 0.00 0.00 3.85
4064 11321 5.605534 AGAGGAAATGAACGTATGATGGAG 58.394 41.667 0.00 0.00 0.00 3.86
4065 11322 5.614324 AGAGGAAATGAACGTATGATGGA 57.386 39.130 0.00 0.00 0.00 3.41
4077 11334 4.516698 GCACAGACAAAGAAGAGGAAATGA 59.483 41.667 0.00 0.00 0.00 2.57
4101 11358 2.742053 TCTGCGCTGGAATAAACAGTTC 59.258 45.455 14.70 0.00 38.22 3.01
4106 11363 2.939103 AGTCATCTGCGCTGGAATAAAC 59.061 45.455 14.70 5.05 0.00 2.01
4120 11377 0.881796 TTCACAGCGACGAGTCATCT 59.118 50.000 0.00 0.00 0.00 2.90
4137 11394 3.637998 TGTCTCCTTCGTGTACACTTC 57.362 47.619 23.01 0.00 0.00 3.01
4145 11402 3.575630 TCGATTCTTTGTCTCCTTCGTG 58.424 45.455 0.00 0.00 0.00 4.35
4162 11421 3.481903 CGCTGCGTGTTGCTCGAT 61.482 61.111 14.93 0.00 46.63 3.59
4211 11470 1.202290 CCCAAATCATTCGGGCGAAAG 60.202 52.381 0.00 0.00 37.69 2.62
4214 11473 0.542333 TACCCAAATCATTCGGGCGA 59.458 50.000 0.00 0.00 44.49 5.54
4215 11474 1.384525 TTACCCAAATCATTCGGGCG 58.615 50.000 0.00 0.00 44.49 6.13
4216 11475 2.296190 GGATTACCCAAATCATTCGGGC 59.704 50.000 0.00 0.00 45.05 6.13
4219 11478 2.031157 GCCGGATTACCCAAATCATTCG 60.031 50.000 5.05 0.00 45.05 3.34
4220 11479 2.296190 GGCCGGATTACCCAAATCATTC 59.704 50.000 5.05 0.00 45.05 2.67
4283 11542 1.823169 TTGGTTCCCTCCTCCGTTCG 61.823 60.000 0.00 0.00 0.00 3.95
4310 11569 9.583765 CATGACATCACTCCTACAATATGATAG 57.416 37.037 0.00 0.00 0.00 2.08
4315 11574 7.565190 ATCCATGACATCACTCCTACAATAT 57.435 36.000 0.00 0.00 0.00 1.28
4318 11577 5.674525 GAATCCATGACATCACTCCTACAA 58.325 41.667 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.