Multiple sequence alignment - TraesCS5D01G429900

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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 TraesCS5D01G429900 chr5D 100.000 4768 0 0 1 4768 487291643 487286876 0.000000e+00 8805
1 TraesCS5D01G429900 chr5B 94.588 4804 150 41 1 4768 599656282 599651553 0.000000e+00 7330
2 TraesCS5D01G429900 chr5A 95.005 2823 114 9 172 2991 607684098 607681300 0.000000e+00 4407
3 TraesCS5D01G429900 chr5A 91.882 1047 53 17 3017 4057 607681314 607680294 0.000000e+00 1434
4 TraesCS5D01G429900 chr5A 81.757 444 46 14 4105 4519 607680287 607679850 5.910000e-89 339
5 TraesCS5D01G429900 chr5A 87.081 209 24 1 4563 4768 607679849 607679641 2.870000e-57 233
6 TraesCS5D01G429900 chr1B 84.778 427 43 14 1 422 173132272 173131863 4.440000e-110 409
7 TraesCS5D01G429900 chr1A 85.266 414 38 14 1 409 121136499 121136104 5.750000e-109 405
8 TraesCS5D01G429900 chr4D 82.069 435 44 21 1 422 123147137 123146724 1.640000e-89 340
9 TraesCS5D01G429900 chr4B 84.726 347 35 10 1 345 187734496 187734166 9.890000e-87 331
10 TraesCS5D01G429900 chr4A 83.923 311 32 11 1 309 446594871 446595165 1.010000e-71 281
11 TraesCS5D01G429900 chr4A 87.500 120 15 0 301 420 446607085 446607204 6.430000e-29 139
12 TraesCS5D01G429900 chr2B 84.459 296 32 11 1 296 489351747 489352028 3.630000e-71 279
13 TraesCS5D01G429900 chr7D 82.390 159 17 3 275 422 590518835 590518677 1.390000e-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 TraesCS5D01G429900 chr5D 487286876 487291643 4767 True 8805.00 8805 100.00000 1 4768 1 chr5D.!!$R1 4767
1 TraesCS5D01G429900 chr5B 599651553 599656282 4729 True 7330.00 7330 94.58800 1 4768 1 chr5B.!!$R1 4767
2 TraesCS5D01G429900 chr5A 607679641 607684098 4457 True 1603.25 4407 88.93125 172 4768 4 chr5A.!!$R1 4596

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
866 870 2.061028 GTCTTGCCCAAATTTGCTTCG 58.939 47.619 12.92 0.0 0.00 3.79 F
1422 1426 0.887387 CTCCTTTTCCGTGGCCGAAA 60.887 55.000 0.00 0.0 35.63 3.46 F
1557 1561 1.071471 ACAGTTTCCTCAGGGTGCG 59.929 57.895 0.00 0.0 0.00 5.34 F
2715 2721 1.168714 CAGGTCTTGGTAGCTTTGCC 58.831 55.000 0.00 0.0 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2158 0.034089 TCTGCTCACTCCGGAGATCA 60.034 55.000 37.69 24.05 37.05 2.92 R
2932 2938 1.111277 AAAGGCCTGTTGCGAAAAGT 58.889 45.000 5.69 0.00 42.61 2.66 R
3181 3189 1.699634 TGAAGAGTTTCCCAGGTGAGG 59.300 52.381 0.00 0.00 32.09 3.86 R
4107 4124 0.243095 GCTGCTGCTTCTCCAAAAGG 59.757 55.000 8.53 0.00 36.03 3.11 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
54 55 5.876651 TGCCTATTCATCTGTCAGTATGT 57.123 39.130 0.00 0.00 37.40 2.29
518 522 3.915437 AGGTTCATTTTACGGTTGCTG 57.085 42.857 0.00 0.00 0.00 4.41
551 555 7.569591 GCCACGCTGAACTTATGTTATAATCTC 60.570 40.741 0.00 0.00 36.39 2.75
746 750 4.331168 GGCTGCTACACTGAGAAGTTATTG 59.669 45.833 0.00 0.00 0.00 1.90
781 785 7.346751 TGCTTCCTCAAAAACAGAAAATACT 57.653 32.000 0.00 0.00 0.00 2.12
866 870 2.061028 GTCTTGCCCAAATTTGCTTCG 58.939 47.619 12.92 0.00 0.00 3.79
1056 1060 3.370978 CCGCTCTATTTGTACTTGTGGTG 59.629 47.826 0.00 0.00 0.00 4.17
1182 1186 6.703165 GTCTGAAACTGCCAAATCTGAATTTT 59.297 34.615 0.00 0.00 32.69 1.82
1419 1423 3.431725 GCTCCTTTTCCGTGGCCG 61.432 66.667 0.00 0.00 0.00 6.13
1422 1426 0.887387 CTCCTTTTCCGTGGCCGAAA 60.887 55.000 0.00 0.00 35.63 3.46
1539 1543 1.527380 GTTTCCTGGTGGCGGAACA 60.527 57.895 0.00 0.00 40.09 3.18
1557 1561 1.071471 ACAGTTTCCTCAGGGTGCG 59.929 57.895 0.00 0.00 0.00 5.34
1601 1605 3.564225 GCTTCTGTTATCCCAATTACCGG 59.436 47.826 0.00 0.00 0.00 5.28
1606 1610 4.076509 TCCCAATTACCGGGGGAG 57.923 61.111 11.11 0.00 45.83 4.30
1779 1783 3.253432 GGGTGCTTACCTGTTGAAGAAAG 59.747 47.826 0.00 0.00 0.00 2.62
2004 2008 3.197766 TGGTTGACTCATATGGTCTCCAC 59.802 47.826 21.74 16.22 35.80 4.02
2019 2023 9.881441 TATGGTCTCCACAGAAATTCTGAACCG 62.881 44.444 27.63 13.47 46.84 4.44
2153 2158 1.463674 GATGGCAACGGACCAAAGAT 58.536 50.000 0.00 0.00 41.49 2.40
2279 2284 1.740025 GACAAATCTTGCCCGAGGAAG 59.260 52.381 0.00 0.00 0.00 3.46
2321 2326 1.858091 AGTGTGAGTTGACAAGCGAG 58.142 50.000 0.00 0.00 0.00 5.03
2349 2354 5.178096 TGTATGGTGAGTGTCATTCCATT 57.822 39.130 4.82 0.00 35.60 3.16
2715 2721 1.168714 CAGGTCTTGGTAGCTTTGCC 58.831 55.000 0.00 0.00 0.00 4.52
2921 2927 7.853437 TGTTCGTTGTACATTGTTTCTACATTG 59.147 33.333 0.00 0.00 40.04 2.82
2932 2938 9.214957 CATTGTTTCTACATTGTGGTAGTTCTA 57.785 33.333 0.00 0.00 41.20 2.10
2946 2952 4.151867 GGTAGTTCTACTTTTCGCAACAGG 59.848 45.833 9.40 0.00 0.00 4.00
3043 3049 9.490379 GGAACTTCTCTTTTCTGTTATGAAGTA 57.510 33.333 0.00 0.00 40.81 2.24
3115 3121 5.809562 GTGTGTGAAGATAGAAGGATGTGAG 59.190 44.000 0.00 0.00 0.00 3.51
3181 3189 6.699575 ATAATGGCATCTCTTGTTACCAAC 57.300 37.500 0.00 0.00 0.00 3.77
3202 3210 2.289945 CCTCACCTGGGAAACTCTTCAG 60.290 54.545 0.00 0.00 32.75 3.02
3448 3459 2.800544 CGGTGTCTTCAGTTTGTACCAG 59.199 50.000 0.00 0.00 0.00 4.00
3521 3532 7.660617 ACTTGTTGGCTGATATTATCTGATCTG 59.339 37.037 13.09 0.00 0.00 2.90
3522 3533 7.307131 TGTTGGCTGATATTATCTGATCTGA 57.693 36.000 13.09 4.63 0.00 3.27
3523 3534 7.914859 TGTTGGCTGATATTATCTGATCTGAT 58.085 34.615 17.88 17.88 0.00 2.90
3524 3535 8.380867 TGTTGGCTGATATTATCTGATCTGATT 58.619 33.333 18.83 6.27 0.00 2.57
3525 3536 9.881649 GTTGGCTGATATTATCTGATCTGATTA 57.118 33.333 18.83 11.43 0.00 1.75
3716 3727 2.417924 CCCTCGTGTTCCTGAGAAGATG 60.418 54.545 0.00 0.00 34.38 2.90
3846 3858 3.991773 TCGTTGCAAGTACACATTAGACC 59.008 43.478 0.00 0.00 0.00 3.85
3875 3887 3.117888 AGAGAACTGAAGAACCAAGCCAA 60.118 43.478 0.00 0.00 0.00 4.52
3888 3900 4.469657 ACCAAGCCAATGACAAACTAGAA 58.530 39.130 0.00 0.00 0.00 2.10
3889 3901 4.520492 ACCAAGCCAATGACAAACTAGAAG 59.480 41.667 0.00 0.00 0.00 2.85
3890 3902 4.761739 CCAAGCCAATGACAAACTAGAAGA 59.238 41.667 0.00 0.00 0.00 2.87
3963 3980 6.223138 TGTTCGTGCTGTATTCTTGTTTAG 57.777 37.500 0.00 0.00 0.00 1.85
3972 3989 8.462811 TGCTGTATTCTTGTTTAGTTTTGTTCA 58.537 29.630 0.00 0.00 0.00 3.18
4062 4079 7.964604 AACATACTAGGAACAGTTTTGAGTC 57.035 36.000 0.00 0.00 0.00 3.36
4063 4080 7.304497 ACATACTAGGAACAGTTTTGAGTCT 57.696 36.000 0.00 0.00 0.00 3.24
4064 4081 7.736893 ACATACTAGGAACAGTTTTGAGTCTT 58.263 34.615 0.00 0.00 0.00 3.01
4065 4082 7.657761 ACATACTAGGAACAGTTTTGAGTCTTG 59.342 37.037 0.00 0.00 0.00 3.02
4066 4083 4.816925 ACTAGGAACAGTTTTGAGTCTTGC 59.183 41.667 0.00 0.00 0.00 4.01
4067 4084 3.891049 AGGAACAGTTTTGAGTCTTGCT 58.109 40.909 0.00 0.00 0.00 3.91
4068 4085 3.879892 AGGAACAGTTTTGAGTCTTGCTC 59.120 43.478 0.00 0.00 44.36 4.26
4073 4090 1.333619 GTTTTGAGTCTTGCTCGGCAA 59.666 47.619 10.28 10.28 46.80 4.52
4107 4124 6.843069 AAAGAAATGTGCATTGTTGTTACC 57.157 33.333 0.00 0.00 0.00 2.85
4156 4174 4.335647 CGCTGCCCTCCACCTGTT 62.336 66.667 0.00 0.00 0.00 3.16
4188 4206 1.623811 CCAGCGGCCAGGTAGTAATAT 59.376 52.381 2.24 0.00 0.00 1.28
4243 4278 3.706373 GGAGGCTCCAAGGCGACA 61.706 66.667 28.55 0.00 46.58 4.35
4257 4292 1.716826 GCGACAACGACACCCCAAAA 61.717 55.000 0.00 0.00 42.66 2.44
4259 4294 1.069500 CGACAACGACACCCCAAAATC 60.069 52.381 0.00 0.00 42.66 2.17
4261 4296 2.359531 GACAACGACACCCCAAAATCAA 59.640 45.455 0.00 0.00 0.00 2.57
4262 4297 2.761208 ACAACGACACCCCAAAATCAAA 59.239 40.909 0.00 0.00 0.00 2.69
4457 4508 1.688735 ACTACAACTCTGCAGCACTCA 59.311 47.619 9.47 0.00 0.00 3.41
4459 4510 1.805869 ACAACTCTGCAGCACTCATC 58.194 50.000 9.47 0.00 0.00 2.92
4462 4513 2.096220 ACTCTGCAGCACTCATCTTG 57.904 50.000 9.47 0.00 0.00 3.02
4465 4516 2.415857 CTCTGCAGCACTCATCTTGTTC 59.584 50.000 9.47 0.00 0.00 3.18
4470 4521 3.979495 GCAGCACTCATCTTGTTCTTTTG 59.021 43.478 0.00 0.00 0.00 2.44
4471 4522 4.498682 GCAGCACTCATCTTGTTCTTTTGT 60.499 41.667 0.00 0.00 0.00 2.83
4473 4524 6.038356 CAGCACTCATCTTGTTCTTTTGTTT 58.962 36.000 0.00 0.00 0.00 2.83
4474 4525 6.197842 CAGCACTCATCTTGTTCTTTTGTTTC 59.802 38.462 0.00 0.00 0.00 2.78
4475 4526 5.172053 GCACTCATCTTGTTCTTTTGTTTCG 59.828 40.000 0.00 0.00 0.00 3.46
4476 4527 5.172053 CACTCATCTTGTTCTTTTGTTTCGC 59.828 40.000 0.00 0.00 0.00 4.70
4484 4535 1.337703 TCTTTTGTTTCGCAGCAGCAT 59.662 42.857 0.82 0.00 42.27 3.79
4494 4545 5.497635 TTCGCAGCAGCATTCATAATTTA 57.502 34.783 0.82 0.00 42.27 1.40
4521 4572 6.128117 GCATACACTTGTAAATTTCCTCCGAA 60.128 38.462 0.00 0.00 33.76 4.30
4531 4582 4.680171 ATTTCCTCCGAACGAACAATTC 57.320 40.909 0.00 0.00 0.00 2.17
4538 4589 3.431912 TCCGAACGAACAATTCATGACTG 59.568 43.478 0.00 0.00 0.00 3.51
4539 4590 3.431912 CCGAACGAACAATTCATGACTGA 59.568 43.478 10.31 0.00 0.00 3.41
4541 4592 4.386230 GAACGAACAATTCATGACTGACG 58.614 43.478 10.31 14.65 0.00 4.35
4546 4597 2.289631 ACAATTCATGACTGACGCCTCA 60.290 45.455 10.31 0.00 0.00 3.86
4553 4604 0.249489 GACTGACGCCTCAACTGTGT 60.249 55.000 0.00 0.00 0.00 3.72
4554 4605 0.530650 ACTGACGCCTCAACTGTGTG 60.531 55.000 0.00 0.00 0.00 3.82
4555 4606 1.224069 CTGACGCCTCAACTGTGTGG 61.224 60.000 0.00 0.00 40.72 4.17
4557 4608 0.814010 GACGCCTCAACTGTGTGGTT 60.814 55.000 0.00 0.00 40.04 3.67
4559 4610 0.029300 CGCCTCAACTGTGTGGTTTG 59.971 55.000 0.00 0.00 40.04 2.93
4560 4611 1.102978 GCCTCAACTGTGTGGTTTGT 58.897 50.000 0.00 0.00 40.04 2.83
4561 4612 2.294074 GCCTCAACTGTGTGGTTTGTA 58.706 47.619 0.00 0.00 40.04 2.41
4567 4618 6.293407 CCTCAACTGTGTGGTTTGTAAGTATG 60.293 42.308 0.00 0.00 34.30 2.39
4619 4673 2.264005 TGCCGCTTTTGAGGAACTTA 57.736 45.000 0.00 0.00 41.55 2.24
4627 4681 5.617087 CGCTTTTGAGGAACTTAAGCCTAAC 60.617 44.000 1.29 0.00 41.55 2.34
4634 4695 8.370266 TGAGGAACTTAAGCCTAACTATTGTA 57.630 34.615 1.29 0.00 41.55 2.41
4635 4696 8.818860 TGAGGAACTTAAGCCTAACTATTGTAA 58.181 33.333 1.29 0.00 41.55 2.41
4636 4697 9.096160 GAGGAACTTAAGCCTAACTATTGTAAC 57.904 37.037 1.29 0.00 41.55 2.50
4637 4698 8.823794 AGGAACTTAAGCCTAACTATTGTAACT 58.176 33.333 1.29 0.00 27.25 2.24
4667 4728 5.913137 AGTCTTTGTCCATGTGTTTGAAA 57.087 34.783 0.00 0.00 0.00 2.69
4670 4731 7.425606 AGTCTTTGTCCATGTGTTTGAAATAC 58.574 34.615 0.00 0.00 0.00 1.89
4673 4734 7.920151 TCTTTGTCCATGTGTTTGAAATACTTG 59.080 33.333 11.84 11.84 0.00 3.16
4680 4741 5.587289 TGTGTTTGAAATACTTGAGCCAAC 58.413 37.500 6.38 0.00 0.00 3.77
4723 4790 4.962362 TCTCTCAATTAGGATGCTGTGGTA 59.038 41.667 0.00 0.00 0.00 3.25
4765 4832 4.046462 CGAAAACAAGACTAGAACCGTCA 58.954 43.478 0.00 0.00 33.89 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.550712 AGGCAATGACCTAAATGAAAGAAATC 58.449 34.615 0.00 0.00 38.67 2.17
18 19 8.000709 AGATGAATAGGCAATGACCTAAATGAA 58.999 33.333 7.35 0.00 45.35 2.57
54 55 7.395617 TGGTTTATTTATGCTACCACAGTACA 58.604 34.615 0.00 0.00 34.13 2.90
263 264 6.970191 AGCTATACCAAAATACAGTTTCCCT 58.030 36.000 0.00 0.00 0.00 4.20
505 509 2.223386 GCACAGTTCAGCAACCGTAAAA 60.223 45.455 0.00 0.00 32.22 1.52
518 522 1.160329 AGTTCAGCGTGGCACAGTTC 61.160 55.000 19.09 3.33 41.80 3.01
746 750 6.985188 TTTTGAGGAAGCATGACTATGTAC 57.015 37.500 0.00 0.00 36.65 2.90
781 785 5.994416 AAGGGATTATTCTCTTTGCCCTA 57.006 39.130 0.00 0.00 39.81 3.53
844 848 3.667360 GAAGCAAATTTGGGCAAGACAT 58.333 40.909 19.47 0.00 0.00 3.06
1056 1060 2.278332 AGAAGGAACAGAGCCCAAAC 57.722 50.000 0.00 0.00 0.00 2.93
1137 1141 3.755378 GACATTTGGTCTGCTCATTCACT 59.245 43.478 0.00 0.00 43.46 3.41
1182 1186 1.486310 GATGCACTATGGTGGGTCTCA 59.514 52.381 11.53 0.16 43.18 3.27
1419 1423 4.016113 AGAAACATAATCGCGGCTTTTC 57.984 40.909 6.13 7.28 0.00 2.29
1422 1426 4.554723 GCATAAGAAACATAATCGCGGCTT 60.555 41.667 6.13 2.83 0.00 4.35
1539 1543 1.071471 CGCACCCTGAGGAAACTGT 59.929 57.895 0.00 0.00 44.43 3.55
1557 1561 4.991687 GCAAGCTGGTCTATATACTTGTCC 59.008 45.833 9.16 0.00 37.44 4.02
1601 1605 0.687354 TGCAGTTCTCACTTCTCCCC 59.313 55.000 0.00 0.00 0.00 4.81
1605 1609 1.957177 TCGAGTGCAGTTCTCACTTCT 59.043 47.619 0.00 0.00 44.09 2.85
1606 1610 2.055100 GTCGAGTGCAGTTCTCACTTC 58.945 52.381 0.00 0.00 44.09 3.01
1779 1783 6.111768 AGCGAATGACATAGTCAAAACATC 57.888 37.500 3.74 0.00 45.96 3.06
1865 1869 3.689347 CTTCATTGATCCAAGGACACCA 58.311 45.455 0.00 0.00 33.90 4.17
2004 2008 2.480419 AGCGAACGGTTCAGAATTTCTG 59.520 45.455 18.49 18.49 45.59 3.02
2019 2023 2.657372 CGTCTGTAGAACAAGAGCGAAC 59.343 50.000 0.00 0.00 0.00 3.95
2153 2158 0.034089 TCTGCTCACTCCGGAGATCA 60.034 55.000 37.69 24.05 37.05 2.92
2279 2284 6.424812 ACTTGGCAACTTTTGAATTATCTTGC 59.575 34.615 0.00 0.00 33.38 4.01
2321 2326 4.456280 TGACACTCACCATACATCACTC 57.544 45.455 0.00 0.00 0.00 3.51
2715 2721 2.568003 TGGAGACTCCAGTACAGCG 58.432 57.895 20.74 0.00 42.67 5.18
2921 2927 4.508861 TGTTGCGAAAAGTAGAACTACCAC 59.491 41.667 8.16 0.00 36.75 4.16
2932 2938 1.111277 AAAGGCCTGTTGCGAAAAGT 58.889 45.000 5.69 0.00 42.61 2.66
2946 2952 2.519377 ACCGGCAAAAGTAAAAAGGC 57.481 45.000 0.00 0.00 0.00 4.35
3073 3079 7.386059 TCACACACAACAATACATGAGTATCT 58.614 34.615 0.00 0.00 40.00 1.98
3075 3081 7.877612 TCTTCACACACAACAATACATGAGTAT 59.122 33.333 0.00 0.00 42.66 2.12
3115 3121 8.556194 TGGCACACGAAGATTTTAATGATATAC 58.444 33.333 0.00 0.00 0.00 1.47
3181 3189 1.699634 TGAAGAGTTTCCCAGGTGAGG 59.300 52.381 0.00 0.00 32.09 3.86
3202 3210 7.169645 ACATCATCATTTAACAACAGCACAAAC 59.830 33.333 0.00 0.00 0.00 2.93
3358 3369 6.130298 TCACACCTGTAACAAGAACAAATG 57.870 37.500 0.00 0.00 0.00 2.32
3448 3459 6.072112 TGGTCTTTCAATGCTTACTTGTTC 57.928 37.500 0.00 0.00 0.00 3.18
3846 3858 2.613730 TCTTCAGTTCTCTACACGCG 57.386 50.000 3.53 3.53 0.00 6.01
4063 4080 7.773213 CTTTAACAAGAGCATTGCCGAGCAA 62.773 44.000 12.63 12.63 41.72 3.91
4064 4081 0.890542 AACAAGAGCATTGCCGAGCA 60.891 50.000 4.70 0.00 36.47 4.26
4065 4082 1.086696 TAACAAGAGCATTGCCGAGC 58.913 50.000 4.70 0.00 0.00 5.03
4066 4083 3.436704 TCTTTAACAAGAGCATTGCCGAG 59.563 43.478 4.70 0.00 33.80 4.63
4067 4084 3.407698 TCTTTAACAAGAGCATTGCCGA 58.592 40.909 4.70 0.00 33.80 5.54
4068 4085 3.829886 TCTTTAACAAGAGCATTGCCG 57.170 42.857 4.70 0.00 33.80 5.69
4069 4086 5.928264 ACATTTCTTTAACAAGAGCATTGCC 59.072 36.000 4.70 0.00 40.28 4.52
4070 4087 6.617105 GCACATTTCTTTAACAAGAGCATTGC 60.617 38.462 0.00 0.00 40.28 3.56
4071 4088 6.421501 TGCACATTTCTTTAACAAGAGCATTG 59.578 34.615 0.51 0.51 40.28 2.82
4072 4089 6.514947 TGCACATTTCTTTAACAAGAGCATT 58.485 32.000 0.00 0.00 40.28 3.56
4073 4090 6.088016 TGCACATTTCTTTAACAAGAGCAT 57.912 33.333 0.00 0.00 40.28 3.79
4074 4091 5.512753 TGCACATTTCTTTAACAAGAGCA 57.487 34.783 0.00 0.00 40.28 4.26
4075 4092 6.421801 ACAATGCACATTTCTTTAACAAGAGC 59.578 34.615 0.00 0.00 40.28 4.09
4076 4093 7.935338 ACAATGCACATTTCTTTAACAAGAG 57.065 32.000 0.00 0.00 40.28 2.85
4107 4124 0.243095 GCTGCTGCTTCTCCAAAAGG 59.757 55.000 8.53 0.00 36.03 3.11
4188 4206 3.394274 CCCATGGGTGATGTCCACTATAA 59.606 47.826 23.93 0.00 45.03 0.98
4235 4270 2.280592 GGGTGTCGTTGTCGCCTT 60.281 61.111 0.00 0.00 35.96 4.35
4243 4278 4.681074 ATTTTGATTTTGGGGTGTCGTT 57.319 36.364 0.00 0.00 0.00 3.85
4253 4288 7.020602 GGGGCGTATCAAAAATTTTGATTTTG 58.979 34.615 30.98 22.65 44.97 2.44
4257 4292 5.413309 TGGGGCGTATCAAAAATTTTGAT 57.587 34.783 29.42 29.42 41.54 2.57
4259 4294 3.932089 CCTGGGGCGTATCAAAAATTTTG 59.068 43.478 11.92 11.92 0.00 2.44
4261 4296 2.093711 GCCTGGGGCGTATCAAAAATTT 60.094 45.455 0.00 0.00 39.62 1.82
4262 4297 1.480545 GCCTGGGGCGTATCAAAAATT 59.519 47.619 0.00 0.00 39.62 1.82
4421 4472 7.556996 AGAGTTGTAGTAGTACCTATGTCTTGG 59.443 40.741 5.26 0.00 0.00 3.61
4437 4488 1.688735 TGAGTGCTGCAGAGTTGTAGT 59.311 47.619 20.43 0.00 39.03 2.73
4440 4491 1.347050 AGATGAGTGCTGCAGAGTTGT 59.653 47.619 20.43 0.00 0.00 3.32
4443 4494 1.347050 ACAAGATGAGTGCTGCAGAGT 59.653 47.619 20.43 5.50 0.00 3.24
4457 4508 4.044426 GCTGCGAAACAAAAGAACAAGAT 58.956 39.130 0.00 0.00 0.00 2.40
4459 4510 3.178267 TGCTGCGAAACAAAAGAACAAG 58.822 40.909 0.00 0.00 0.00 3.16
4462 4513 1.518515 GCTGCTGCGAAACAAAAGAAC 59.481 47.619 0.00 0.00 0.00 3.01
4465 4516 1.774639 ATGCTGCTGCGAAACAAAAG 58.225 45.000 11.21 0.00 43.34 2.27
4470 4521 2.830772 TATGAATGCTGCTGCGAAAC 57.169 45.000 11.21 3.43 43.34 2.78
4471 4522 4.374843 AATTATGAATGCTGCTGCGAAA 57.625 36.364 11.21 0.00 43.34 3.46
4473 4524 5.454520 CATAAATTATGAATGCTGCTGCGA 58.545 37.500 7.17 0.80 39.16 5.10
4474 4525 4.089493 GCATAAATTATGAATGCTGCTGCG 59.911 41.667 16.45 0.00 42.15 5.18
4475 4526 4.986034 TGCATAAATTATGAATGCTGCTGC 59.014 37.500 16.45 8.89 44.96 5.25
4476 4527 7.810759 TGTATGCATAAATTATGAATGCTGCTG 59.189 33.333 18.58 0.00 44.96 4.41
4494 4545 6.183360 CGGAGGAAATTTACAAGTGTATGCAT 60.183 38.462 3.79 3.79 0.00 3.96
4521 4572 2.157668 GCGTCAGTCATGAATTGTTCGT 59.842 45.455 0.00 0.00 37.14 3.85
4531 4582 1.073964 CAGTTGAGGCGTCAGTCATG 58.926 55.000 9.34 3.92 32.98 3.07
4538 4589 0.814010 AACCACACAGTTGAGGCGTC 60.814 55.000 0.00 0.00 36.98 5.19
4539 4590 0.393808 AAACCACACAGTTGAGGCGT 60.394 50.000 0.00 0.00 36.98 5.68
4541 4592 1.102978 ACAAACCACACAGTTGAGGC 58.897 50.000 0.00 0.00 36.98 4.70
4546 4597 9.953565 ATATACATACTTACAAACCACACAGTT 57.046 29.630 0.00 0.00 0.00 3.16
4567 4618 9.221775 CGTGCTGGATTTTTAGTCAAAATATAC 57.778 33.333 0.00 0.00 43.89 1.47
4579 4630 1.803334 ACGAGCGTGCTGGATTTTTA 58.197 45.000 10.94 0.00 0.00 1.52
4581 4632 1.665679 CATACGAGCGTGCTGGATTTT 59.334 47.619 10.94 0.00 0.00 1.82
4634 4695 8.950210 CACATGGACAAAGACTATCAAATAGTT 58.050 33.333 0.00 0.00 45.64 2.24
4636 4697 8.498054 ACACATGGACAAAGACTATCAAATAG 57.502 34.615 0.00 0.00 38.81 1.73
4637 4698 8.862325 AACACATGGACAAAGACTATCAAATA 57.138 30.769 0.00 0.00 0.00 1.40
4638 4699 7.765695 AACACATGGACAAAGACTATCAAAT 57.234 32.000 0.00 0.00 0.00 2.32
4639 4700 7.284261 TCAAACACATGGACAAAGACTATCAAA 59.716 33.333 0.00 0.00 0.00 2.69
4640 4701 6.770303 TCAAACACATGGACAAAGACTATCAA 59.230 34.615 0.00 0.00 0.00 2.57
4646 4707 7.425606 AGTATTTCAAACACATGGACAAAGAC 58.574 34.615 0.00 0.00 0.00 3.01
4656 4717 6.040842 AGTTGGCTCAAGTATTTCAAACACAT 59.959 34.615 0.00 0.00 0.00 3.21
4667 4728 5.749462 AGCTTGAATAGTTGGCTCAAGTAT 58.251 37.500 11.90 9.40 45.13 2.12
4670 4731 6.690194 ATTAGCTTGAATAGTTGGCTCAAG 57.310 37.500 7.37 7.37 45.78 3.02
4673 4734 8.383318 TGATAATTAGCTTGAATAGTTGGCTC 57.617 34.615 1.93 0.00 34.88 4.70
4723 4790 4.827087 CGCTGAGCTCCGTGCCAT 62.827 66.667 12.15 0.00 44.23 4.40


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

AutoCloner maintained by Alex Coulton.