Multiple sequence alignment - TraesCS1A01G245700

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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 TraesCS1A01G245700 chr1A 100.000 7282 0 0 1 7282 435056160 435063441 0.000000e+00 13448.0
1 TraesCS1A01G245700 chr1B 97.019 3422 71 12 3869 7282 452314648 452318046 0.000000e+00 5725.0
2 TraesCS1A01G245700 chr1B 94.857 3247 124 25 647 3864 452311224 452314456 0.000000e+00 5031.0
3 TraesCS1A01G245700 chr1B 87.789 303 28 8 1 294 452310399 452310701 5.410000e-91 346.0
4 TraesCS1A01G245700 chr1B 85.393 356 18 8 296 648 452310786 452311110 9.050000e-89 339.0
5 TraesCS1A01G245700 chr1D 96.567 3437 73 13 3869 7282 336550373 336553787 0.000000e+00 5651.0
6 TraesCS1A01G245700 chr1D 96.157 3227 90 15 646 3864 336546986 336550186 0.000000e+00 5241.0
7 TraesCS1A01G245700 chr1D 89.362 423 32 8 1 410 336545993 336546415 3.010000e-143 520.0
8 TraesCS1A01G245700 chr1D 93.671 237 10 4 417 648 336546649 336546885 4.180000e-92 350.0
9 TraesCS1A01G245700 chr1D 91.045 67 4 2 433 497 336546584 336546650 1.010000e-13 89.8
10 TraesCS1A01G245700 chr3B 83.853 353 35 12 6015 6358 16225863 16225524 4.240000e-82 316.0
11 TraesCS1A01G245700 chr2B 82.000 100 17 1 304 402 223715923 223715824 4.680000e-12 84.2


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 TraesCS1A01G245700 chr1A 435056160 435063441 7281 False 13448.00 13448 100.0000 1 7282 1 chr1A.!!$F1 7281
1 TraesCS1A01G245700 chr1B 452310399 452318046 7647 False 2860.25 5725 91.2645 1 7282 4 chr1B.!!$F1 7281
2 TraesCS1A01G245700 chr1D 336545993 336553787 7794 False 2370.36 5651 93.3604 1 7282 5 chr1D.!!$F1 7281

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
924 1373 0.688087 CTGACTCCTCCTACCCCCAC 60.688 65.000 0.0 0.0 0.0 4.61 F
1706 2172 0.037160 GGGCTTAAAGGTCGTGGGAA 59.963 55.000 0.0 0.0 0.0 3.97 F
1975 2444 0.982852 TGGTGGCGATCTGGAGGAAT 60.983 55.000 0.0 0.0 0.0 3.01 F
3709 4185 0.249398 ACCTAATGTGACGCTGACCC 59.751 55.000 0.0 0.0 0.0 4.46 F
3713 4189 0.324614 AATGTGACGCTGACCCATCA 59.675 50.000 0.0 0.0 0.0 3.07 F
4384 5047 2.357009 CTCCTTGGCGAAATGGATCTTG 59.643 50.000 0.0 0.0 0.0 3.02 F
6197 6860 1.992557 ACCTCCCATGACCAGCTAAAA 59.007 47.619 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2618 3087 0.106419 CCCGGCCCTTATTTTAGCCA 60.106 55.000 0.00 0.00 46.08 4.75 R
3701 4177 1.202568 TGAAGCTATGATGGGTCAGCG 60.203 52.381 0.00 0.00 37.87 5.18 R
3825 4301 3.937814 TCTGTGTCAACATTAGCCGATT 58.062 40.909 0.00 0.00 35.22 3.34 R
5501 6164 1.205893 AGAGAAGGATGTGTCGAAGCC 59.794 52.381 0.00 0.00 0.00 4.35 R
5600 6263 8.929487 ACAAATCTTGTTTTAACCCCTTCATAA 58.071 29.630 0.00 0.00 42.22 1.90 R
6257 6920 1.280133 CTCAACTCAGGGGCAATCTGA 59.720 52.381 4.77 4.77 38.75 3.27 R
7173 7857 3.057104 CCATTCTCATGCAACAAAGCTCA 60.057 43.478 0.00 0.00 34.99 4.26 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 28 8.908786 CTTCTCCACTTAATAGGATAATGCAA 57.091 34.615 0.00 0.00 32.53 4.08
138 142 3.265479 CCCCTCTCTCAGTTTTGATTCCT 59.735 47.826 0.00 0.00 31.68 3.36
152 160 4.841813 TGATTCCTCCCTCCTATCTCTT 57.158 45.455 0.00 0.00 0.00 2.85
158 166 5.707495 TCCTCCCTCCTATCTCTTAGTTTC 58.293 45.833 0.00 0.00 0.00 2.78
159 167 4.836175 CCTCCCTCCTATCTCTTAGTTTCC 59.164 50.000 0.00 0.00 0.00 3.13
161 169 4.486529 TCCCTCCTATCTCTTAGTTTCCCT 59.513 45.833 0.00 0.00 0.00 4.20
162 170 5.042523 TCCCTCCTATCTCTTAGTTTCCCTT 60.043 44.000 0.00 0.00 0.00 3.95
163 171 5.071115 CCCTCCTATCTCTTAGTTTCCCTTG 59.929 48.000 0.00 0.00 0.00 3.61
164 172 5.663556 CCTCCTATCTCTTAGTTTCCCTTGT 59.336 44.000 0.00 0.00 0.00 3.16
168 177 8.101419 TCCTATCTCTTAGTTTCCCTTGTTTTC 58.899 37.037 0.00 0.00 0.00 2.29
187 196 2.232399 TCCTTGAAAACCGCCTTAACC 58.768 47.619 0.00 0.00 0.00 2.85
188 197 1.957877 CCTTGAAAACCGCCTTAACCA 59.042 47.619 0.00 0.00 0.00 3.67
238 247 5.143376 AGATGATGTTTTCTTTGGCAAGG 57.857 39.130 2.45 2.45 0.00 3.61
278 288 9.066892 CCAATAAGATCCTAAAATTCATTCGGA 57.933 33.333 0.00 0.00 0.00 4.55
294 304 7.214467 TCATTCGGAAAGATAAATAATGGGC 57.786 36.000 0.00 0.00 0.00 5.36
300 393 6.127897 CGGAAAGATAAATAATGGGCAGGATC 60.128 42.308 0.00 0.00 0.00 3.36
315 408 5.598417 GGGCAGGATCTTATTTGGTAAACAT 59.402 40.000 0.00 0.00 0.00 2.71
363 456 6.260377 TGAGTATGTAAATCACGGACTAACG 58.740 40.000 0.00 0.00 40.31 3.18
404 501 4.244066 TGTTGCAATGCATGGACAATTAC 58.756 39.130 9.39 0.95 38.76 1.89
410 507 5.528690 GCAATGCATGGACAATTACTCTAGA 59.471 40.000 4.87 0.00 0.00 2.43
411 508 6.038603 GCAATGCATGGACAATTACTCTAGAA 59.961 38.462 4.87 0.00 0.00 2.10
413 510 8.461222 CAATGCATGGACAATTACTCTAGAAAA 58.539 33.333 0.00 0.00 0.00 2.29
443 767 8.208718 TGTAGATAAAATGTGCAGTGGTTATC 57.791 34.615 10.20 10.20 0.00 1.75
466 792 5.235616 TCACAGTTTTAACCTAACTTGCTCG 59.764 40.000 0.00 0.00 33.73 5.03
512 838 4.849329 GTCGCCCGCTTCGACGAT 62.849 66.667 0.00 0.00 45.19 3.73
616 946 4.120589 CAGCTCGAAAGGGAGTAAATACC 58.879 47.826 0.00 0.00 36.41 2.73
656 1101 1.600636 CGCAGTGGCCCAGAAAAGA 60.601 57.895 0.00 0.00 36.38 2.52
901 1350 4.353489 AGGAGTAGGAGTAGTACCATACCC 59.647 50.000 0.00 5.29 0.00 3.69
917 1366 1.311403 CCCCTGCTGACTCCTCCTA 59.689 63.158 0.00 0.00 0.00 2.94
918 1367 1.045911 CCCCTGCTGACTCCTCCTAC 61.046 65.000 0.00 0.00 0.00 3.18
923 1372 1.704082 CTGACTCCTCCTACCCCCA 59.296 63.158 0.00 0.00 0.00 4.96
924 1373 0.688087 CTGACTCCTCCTACCCCCAC 60.688 65.000 0.00 0.00 0.00 4.61
926 1375 1.867487 ACTCCTCCTACCCCCACCT 60.867 63.158 0.00 0.00 0.00 4.00
927 1376 1.383248 CTCCTCCTACCCCCACCTG 60.383 68.421 0.00 0.00 0.00 4.00
928 1377 1.865045 TCCTCCTACCCCCACCTGA 60.865 63.158 0.00 0.00 0.00 3.86
1514 1977 1.472201 GCGAGGTGATGATGCTTCTGA 60.472 52.381 0.88 0.00 0.00 3.27
1609 2072 3.430218 CGCTAGTGGGAATCGAATCAATC 59.570 47.826 2.36 0.00 0.00 2.67
1705 2171 1.681076 GGGCTTAAAGGTCGTGGGA 59.319 57.895 0.00 0.00 0.00 4.37
1706 2172 0.037160 GGGCTTAAAGGTCGTGGGAA 59.963 55.000 0.00 0.00 0.00 3.97
1716 2182 4.452733 CGTGGGAACGAGGGAGGC 62.453 72.222 0.00 0.00 34.64 4.70
1762 2228 3.949754 GGATGAGGAGCACATGAATGAAA 59.050 43.478 0.00 0.00 0.00 2.69
1869 2338 5.823209 TTGGAGATTACTATGACGACGAA 57.177 39.130 0.00 0.00 0.00 3.85
1873 2342 6.183360 TGGAGATTACTATGACGACGAAATGT 60.183 38.462 0.00 0.00 0.00 2.71
1890 2359 2.638480 TGTTGGAGGAAAGACTGGTG 57.362 50.000 0.00 0.00 0.00 4.17
1906 2375 1.040646 GGTGGCAGATCTGATCCGTA 58.959 55.000 27.04 1.27 0.00 4.02
1975 2444 0.982852 TGGTGGCGATCTGGAGGAAT 60.983 55.000 0.00 0.00 0.00 3.01
2028 2497 4.151335 GGTGATGATGACGATTCTATGCAC 59.849 45.833 0.00 0.00 0.00 4.57
2066 2535 2.414559 GCATGTCTGAACCAATCAACGG 60.415 50.000 0.00 0.00 37.67 4.44
2084 2553 2.709475 CGATGCTAAGGCGCCAAC 59.291 61.111 31.54 15.14 42.25 3.77
2165 2634 1.204146 GTTAGGTGCCATGAGGAGGA 58.796 55.000 0.00 0.00 36.89 3.71
2166 2635 1.771255 GTTAGGTGCCATGAGGAGGAT 59.229 52.381 0.00 0.00 36.89 3.24
2167 2636 1.427809 TAGGTGCCATGAGGAGGATG 58.572 55.000 0.00 0.00 36.89 3.51
2202 2671 5.610132 AGATGTTATCAAGGATGAGGTGGAT 59.390 40.000 0.00 0.00 39.39 3.41
2218 2687 3.243468 GGTGGATACTAAGCGAGAAGGAC 60.243 52.174 0.00 0.00 37.61 3.85
2324 2793 2.135933 CTCGAAGAAGAAACCGTTGCT 58.864 47.619 0.00 0.00 34.09 3.91
2553 3022 3.416156 ACTGGAAGAAGAGGATGCAAAC 58.584 45.455 0.00 0.00 37.43 2.93
2618 3087 5.930569 GCAAGAAAGAAATTGCCTCATCTTT 59.069 36.000 1.16 1.16 44.76 2.52
3093 3562 5.656213 AATCTGGAAAATCTGCCAAGAAG 57.344 39.130 0.00 0.00 35.59 2.85
3095 3564 4.473444 TCTGGAAAATCTGCCAAGAAGTT 58.527 39.130 0.00 0.00 35.59 2.66
3116 3585 2.955660 TCAGCCGTTCAGGTTCAAAAAT 59.044 40.909 0.00 0.00 43.70 1.82
3203 3672 2.909006 TCTCTCCTTTTGACCAGCATCT 59.091 45.455 0.00 0.00 0.00 2.90
3418 3887 2.756840 TGTCTCTGACCTTGCAGATG 57.243 50.000 0.00 0.00 43.43 2.90
3438 3907 7.307278 GCAGATGCATGACTGTTATTCTTCTAG 60.307 40.741 2.46 0.00 41.59 2.43
3571 4047 1.332195 ACTGCACAGACTGAGCTGTA 58.668 50.000 27.35 8.89 46.80 2.74
3572 4048 1.898472 ACTGCACAGACTGAGCTGTAT 59.102 47.619 27.35 10.98 46.80 2.29
3573 4049 2.094286 ACTGCACAGACTGAGCTGTATC 60.094 50.000 27.35 1.74 46.80 2.24
3574 4050 1.135286 TGCACAGACTGAGCTGTATCG 60.135 52.381 22.78 0.65 46.80 2.92
3575 4051 1.133216 GCACAGACTGAGCTGTATCGA 59.867 52.381 16.55 0.00 46.80 3.59
3576 4052 2.794282 GCACAGACTGAGCTGTATCGAG 60.794 54.545 16.55 0.08 46.80 4.04
3577 4053 2.680339 CACAGACTGAGCTGTATCGAGA 59.320 50.000 10.08 0.00 46.80 4.04
3578 4054 3.314913 CACAGACTGAGCTGTATCGAGAT 59.685 47.826 10.08 0.00 46.80 2.75
3579 4055 3.314913 ACAGACTGAGCTGTATCGAGATG 59.685 47.826 10.08 0.00 46.67 2.90
3628 4104 2.217510 ACTTCGGAAGGCTCAGACTA 57.782 50.000 20.97 0.00 0.00 2.59
3684 4160 4.022849 ACGCTGATCAAGAAAGAAAAAGGG 60.023 41.667 0.00 0.00 0.00 3.95
3709 4185 0.249398 ACCTAATGTGACGCTGACCC 59.751 55.000 0.00 0.00 0.00 4.46
3713 4189 0.324614 AATGTGACGCTGACCCATCA 59.675 50.000 0.00 0.00 0.00 3.07
3731 4207 5.426504 CCATCATAGCTTCATCCCTGTATC 58.573 45.833 0.00 0.00 0.00 2.24
3825 4301 5.306419 AGAGTGATTATCTCTGCTTGGCATA 59.694 40.000 1.22 0.00 40.26 3.14
3829 4305 5.640783 TGATTATCTCTGCTTGGCATAATCG 59.359 40.000 13.78 0.00 38.52 3.34
3845 4321 5.741425 CATAATCGGCTAATGTTGACACAG 58.259 41.667 0.00 0.00 35.94 3.66
3847 4323 3.394674 TCGGCTAATGTTGACACAGAA 57.605 42.857 0.00 0.00 35.94 3.02
3864 4340 7.545615 TGACACAGAACATACTTTATGCTACTG 59.454 37.037 0.00 0.00 39.79 2.74
3866 4342 8.094548 ACACAGAACATACTTTATGCTACTGAA 58.905 33.333 15.32 0.00 39.79 3.02
3867 4343 8.598924 CACAGAACATACTTTATGCTACTGAAG 58.401 37.037 15.32 0.00 39.79 3.02
3868 4344 8.314751 ACAGAACATACTTTATGCTACTGAAGT 58.685 33.333 15.32 2.72 39.79 3.01
3869 4345 9.803315 CAGAACATACTTTATGCTACTGAAGTA 57.197 33.333 0.00 0.00 39.79 2.24
3870 4346 9.804758 AGAACATACTTTATGCTACTGAAGTAC 57.195 33.333 0.00 0.00 39.79 2.73
3871 4347 9.804758 GAACATACTTTATGCTACTGAAGTACT 57.195 33.333 0.00 0.00 39.79 2.73
3877 4353 9.021807 ACTTTATGCTACTGAAGTACTAACAGA 57.978 33.333 26.16 14.45 35.85 3.41
3879 4355 9.803315 TTTATGCTACTGAAGTACTAACAGATG 57.197 33.333 26.16 19.92 35.85 2.90
3889 4550 7.668469 TGAAGTACTAACAGATGTACCTCTGAA 59.332 37.037 28.31 17.04 44.48 3.02
3898 4559 6.772716 ACAGATGTACCTCTGAACATTTGTTT 59.227 34.615 28.31 5.27 44.44 2.83
3902 4563 7.639113 TGTACCTCTGAACATTTGTTTCTTT 57.361 32.000 0.00 0.00 38.56 2.52
4057 4720 8.681486 TGCTTATATTTACAGCATCATCTTGT 57.319 30.769 0.00 0.00 38.65 3.16
4058 4721 9.123902 TGCTTATATTTACAGCATCATCTTGTT 57.876 29.630 0.00 0.00 38.65 2.83
4059 4722 9.390795 GCTTATATTTACAGCATCATCTTGTTG 57.609 33.333 0.00 0.00 34.39 3.33
4062 4725 8.969260 ATATTTACAGCATCATCTTGTTGAGA 57.031 30.769 0.00 0.00 39.13 3.27
4063 4726 6.486253 TTTACAGCATCATCTTGTTGAGAC 57.514 37.500 0.00 0.00 37.17 3.36
4064 4727 4.011966 ACAGCATCATCTTGTTGAGACA 57.988 40.909 0.00 0.00 37.17 3.41
4065 4728 4.392047 ACAGCATCATCTTGTTGAGACAA 58.608 39.130 0.00 0.00 43.23 3.18
4066 4729 4.214971 ACAGCATCATCTTGTTGAGACAAC 59.785 41.667 7.55 7.55 40.71 3.32
4067 4730 4.454847 CAGCATCATCTTGTTGAGACAACT 59.545 41.667 14.19 0.00 40.71 3.16
4068 4731 4.454847 AGCATCATCTTGTTGAGACAACTG 59.545 41.667 14.19 8.36 40.71 3.16
4072 4735 5.924356 TCATCTTGTTGAGACAACTGGTTA 58.076 37.500 14.19 0.00 40.71 2.85
4135 4798 4.697514 GCAATGTGCTAGATCTTGGACTA 58.302 43.478 24.28 14.07 40.96 2.59
4204 4867 5.104941 TGACGACCAAATAGGAATCAGATGT 60.105 40.000 0.00 0.00 41.22 3.06
4249 4912 6.908825 TCTGGAAATCAGATTTGTTTTACCG 58.091 36.000 13.38 4.46 46.71 4.02
4301 4964 5.049680 TCGAAATTTTAGCTCACTCCACAAC 60.050 40.000 0.00 0.00 0.00 3.32
4384 5047 2.357009 CTCCTTGGCGAAATGGATCTTG 59.643 50.000 0.00 0.00 0.00 3.02
4934 5597 9.057089 GGTATTCTTGGAATAAGTTATGGTCTG 57.943 37.037 0.00 0.00 0.00 3.51
5111 5774 4.871993 AACTGAGAAGCGCATAATTCTG 57.128 40.909 13.66 8.14 35.93 3.02
5600 6263 6.118852 GCTTGAGAGATTAAGGTCAAATCCT 58.881 40.000 0.00 0.00 39.84 3.24
6197 6860 1.992557 ACCTCCCATGACCAGCTAAAA 59.007 47.619 0.00 0.00 0.00 1.52
6257 6920 7.781056 AGTCAAACATGGTTTTCACTTACAAT 58.219 30.769 0.00 0.00 0.00 2.71
6422 7085 6.121590 TCTGTGGATGCTAGCATTATTTTGA 58.878 36.000 30.08 19.80 36.70 2.69
6665 7343 8.651389 CATCTTACAAGAGGAAATGGACCTATA 58.349 37.037 0.00 0.00 39.04 1.31
6695 7373 4.462132 TGTGCAATGCTATAAGCCTGAAAA 59.538 37.500 6.82 0.00 41.51 2.29
6696 7374 5.039333 GTGCAATGCTATAAGCCTGAAAAG 58.961 41.667 6.82 0.00 41.51 2.27
6732 7411 5.295292 AGCCTTCATTTCATTGTCTGATACG 59.705 40.000 0.00 0.00 32.72 3.06
6827 7508 5.631512 GTCTGCTCATCGAGTCATTTATACC 59.368 44.000 0.00 0.00 31.39 2.73
6843 7525 2.121291 TACCGATGCCAGCAAAATGA 57.879 45.000 0.00 0.00 0.00 2.57
6898 7580 7.391620 GTCAGAGGCTACTAGATCATAGTACT 58.608 42.308 0.00 0.00 0.00 2.73
7148 7832 9.981114 AGCATGTTTTAGCATAGTAAACTTTTT 57.019 25.926 0.00 0.00 33.92 1.94
7200 7887 3.144657 TGTTGCATGAGAATGGTGACT 57.855 42.857 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.271458 TCACTTTGCATTATCCTATTAAGTGGA 58.729 33.333 16.39 2.27 40.76 4.02
25 28 5.560966 AACAATGAACGTCAAACTCACTT 57.439 34.783 0.00 0.00 0.00 3.16
80 83 1.812571 GTGGGTGATGTGCGAAAGAAT 59.187 47.619 0.00 0.00 0.00 2.40
138 142 4.486529 AGGGAAACTAAGAGATAGGAGGGA 59.513 45.833 0.00 0.00 35.81 4.20
152 160 7.483580 TTTTCAAGGAAAACAAGGGAAACTA 57.516 32.000 0.28 0.00 36.73 2.24
164 172 4.441773 GGTTAAGGCGGTTTTCAAGGAAAA 60.442 41.667 0.28 0.28 38.90 2.29
168 177 1.957877 TGGTTAAGGCGGTTTTCAAGG 59.042 47.619 0.00 0.00 0.00 3.61
180 189 1.694844 AAAACGTGGGGTGGTTAAGG 58.305 50.000 0.00 0.00 0.00 2.69
187 196 4.379082 GCTAAGTCAATAAAACGTGGGGTG 60.379 45.833 0.00 0.00 0.00 4.61
188 197 3.754850 GCTAAGTCAATAAAACGTGGGGT 59.245 43.478 0.00 0.00 0.00 4.95
220 229 2.802247 GTGCCTTGCCAAAGAAAACATC 59.198 45.455 0.00 0.00 35.19 3.06
341 434 6.199937 ACGTTAGTCCGTGATTTACATACT 57.800 37.500 0.00 0.00 40.08 2.12
343 436 6.855836 AGAACGTTAGTCCGTGATTTACATA 58.144 36.000 0.00 0.00 41.65 2.29
411 508 9.248291 CACTGCACATTTTATCTACAACTTTTT 57.752 29.630 0.00 0.00 0.00 1.94
413 510 7.014230 ACCACTGCACATTTTATCTACAACTTT 59.986 33.333 0.00 0.00 0.00 2.66
418 742 7.826744 TGATAACCACTGCACATTTTATCTACA 59.173 33.333 11.71 0.00 30.54 2.74
443 767 5.235616 TCGAGCAAGTTAGGTTAAAACTGTG 59.764 40.000 0.00 0.00 37.26 3.66
466 792 0.232303 CGCTAATTTCGCCGTGGATC 59.768 55.000 0.00 0.00 0.00 3.36
514 840 4.436998 CTGACTGACGACGGGGGC 62.437 72.222 0.00 0.00 0.00 5.80
515 841 1.654954 CTACTGACTGACGACGGGGG 61.655 65.000 0.00 0.00 0.00 5.40
616 946 1.741770 CTTCCTTCGTTCTGGCCCG 60.742 63.158 0.00 0.00 0.00 6.13
656 1101 2.338984 GTGTCCTTGTCGTCGCCT 59.661 61.111 0.00 0.00 0.00 5.52
901 1350 1.045911 GGGTAGGAGGAGTCAGCAGG 61.046 65.000 0.00 0.00 0.00 4.85
917 1366 2.923035 CGTCAGTCAGGTGGGGGT 60.923 66.667 0.00 0.00 0.00 4.95
918 1367 2.603473 TCGTCAGTCAGGTGGGGG 60.603 66.667 0.00 0.00 0.00 5.40
923 1372 1.579084 GCGAGAGTCGTCAGTCAGGT 61.579 60.000 0.00 0.00 42.81 4.00
924 1373 1.135731 GCGAGAGTCGTCAGTCAGG 59.864 63.158 0.00 0.00 42.81 3.86
926 1375 3.264947 GGCGAGAGTCGTCAGTCA 58.735 61.111 0.00 0.00 45.01 3.41
1403 1866 2.588989 CCTCTGCCTCCTTGCTCC 59.411 66.667 0.00 0.00 0.00 4.70
1514 1977 3.245797 CGAGATTCGCCATTATCATCGT 58.754 45.455 0.00 0.00 31.14 3.73
1609 2072 2.593978 CCCACTCCCCTGATGCTG 59.406 66.667 0.00 0.00 0.00 4.41
1716 2182 2.125202 GAAAACCAACACCGAGCCCG 62.125 60.000 0.00 0.00 0.00 6.13
1722 2188 1.678627 TCCACATGAAAACCAACACCG 59.321 47.619 0.00 0.00 0.00 4.94
1727 2193 4.081406 CTCCTCATCCACATGAAAACCAA 58.919 43.478 0.00 0.00 38.63 3.67
1869 2338 3.490348 CACCAGTCTTTCCTCCAACATT 58.510 45.455 0.00 0.00 0.00 2.71
1873 2342 0.110486 GCCACCAGTCTTTCCTCCAA 59.890 55.000 0.00 0.00 0.00 3.53
1890 2359 3.318275 TGTAAGTACGGATCAGATCTGCC 59.682 47.826 18.36 13.07 39.30 4.85
1975 2444 2.251818 GAATCCCATCTCATCCTCGGA 58.748 52.381 0.00 0.00 0.00 4.55
2028 2497 1.018910 TGCCACATTCATCTGCATCG 58.981 50.000 0.00 0.00 0.00 3.84
2084 2553 0.583438 CGCCTTAGCATCATCGTTGG 59.417 55.000 0.00 0.00 39.83 3.77
2165 2634 7.419981 CCTTGATAACATCTTCTTCCTCCTCAT 60.420 40.741 0.00 0.00 0.00 2.90
2166 2635 6.126940 CCTTGATAACATCTTCTTCCTCCTCA 60.127 42.308 0.00 0.00 0.00 3.86
2167 2636 6.098982 TCCTTGATAACATCTTCTTCCTCCTC 59.901 42.308 0.00 0.00 0.00 3.71
2202 2671 3.201290 CGTAGGTCCTTCTCGCTTAGTA 58.799 50.000 0.00 0.00 0.00 1.82
2218 2687 2.171870 TCCCTTGATTAAAGCCCGTAGG 59.828 50.000 0.00 0.00 39.52 3.18
2312 2781 0.736053 TTTTCGCAGCAACGGTTTCT 59.264 45.000 0.00 0.00 0.00 2.52
2474 2943 1.156645 GGCACTGTCATCATCCTCGC 61.157 60.000 0.00 0.00 0.00 5.03
2553 3022 4.752101 TCTTCTTCCTCTTTCGCTTTCTTG 59.248 41.667 0.00 0.00 0.00 3.02
2618 3087 0.106419 CCCGGCCCTTATTTTAGCCA 60.106 55.000 0.00 0.00 46.08 4.75
3093 3562 1.305201 TTGAACCTGAACGGCTGAAC 58.695 50.000 0.00 0.00 35.61 3.18
3095 3564 2.045561 TTTTGAACCTGAACGGCTGA 57.954 45.000 0.00 0.00 35.61 4.26
3116 3585 2.035961 AGAAGTGACTGTCGCTTTAGCA 59.964 45.455 30.54 0.00 46.13 3.49
3203 3672 9.314321 GATCCTTGAAATTATAGTCGAACTGAA 57.686 33.333 0.00 0.00 0.00 3.02
3418 3887 7.550906 AGGAAACTAGAAGAATAACAGTCATGC 59.449 37.037 0.00 0.00 40.61 4.06
3438 3907 6.385649 TCAAATCAACACCACTAAGGAAAC 57.614 37.500 0.00 0.00 41.22 2.78
3515 3991 6.013639 AGCCAGGTCTAGTTAAACAACTACAT 60.014 38.462 0.00 0.00 34.37 2.29
3571 4047 6.957920 ATTCAGATCGGATATCATCTCGAT 57.042 37.500 12.53 12.53 41.76 3.59
3572 4048 9.732130 ATATATTCAGATCGGATATCATCTCGA 57.268 33.333 4.83 4.70 36.76 4.04
3614 4090 1.754226 CTGGTCTAGTCTGAGCCTTCC 59.246 57.143 0.00 0.00 33.93 3.46
3619 4095 3.843999 CTCAAACTGGTCTAGTCTGAGC 58.156 50.000 6.74 0.00 44.89 4.26
3628 4104 2.711009 TCCATGTTCCTCAAACTGGTCT 59.289 45.455 0.00 0.00 38.76 3.85
3701 4177 1.202568 TGAAGCTATGATGGGTCAGCG 60.203 52.381 0.00 0.00 37.87 5.18
3709 4185 5.189342 AGGATACAGGGATGAAGCTATGATG 59.811 44.000 0.00 0.00 41.41 3.07
3713 4189 4.756564 TGAGGATACAGGGATGAAGCTAT 58.243 43.478 0.00 0.00 41.41 2.97
3731 4207 7.176589 ACTAGTCCTGTTCTTTTATCTGAGG 57.823 40.000 0.00 0.00 0.00 3.86
3825 4301 3.937814 TCTGTGTCAACATTAGCCGATT 58.062 40.909 0.00 0.00 35.22 3.34
3829 4305 5.643777 AGTATGTTCTGTGTCAACATTAGCC 59.356 40.000 3.53 0.00 40.83 3.93
3845 4321 9.804758 AGTACTTCAGTAGCATAAAGTATGTTC 57.195 33.333 0.00 0.00 36.79 3.18
3864 4340 7.627298 TCAGAGGTACATCTGTTAGTACTTC 57.373 40.000 30.51 0.00 45.70 3.01
3866 4342 6.946583 TGTTCAGAGGTACATCTGTTAGTACT 59.053 38.462 30.51 0.00 45.70 2.73
3867 4343 7.154435 TGTTCAGAGGTACATCTGTTAGTAC 57.846 40.000 30.51 21.69 45.70 2.73
3868 4344 7.956328 ATGTTCAGAGGTACATCTGTTAGTA 57.044 36.000 30.51 13.40 45.70 1.82
3869 4345 6.859112 ATGTTCAGAGGTACATCTGTTAGT 57.141 37.500 30.51 16.43 45.70 2.24
3870 4346 7.604164 ACAAATGTTCAGAGGTACATCTGTTAG 59.396 37.037 30.51 18.60 45.70 2.34
3871 4347 7.450074 ACAAATGTTCAGAGGTACATCTGTTA 58.550 34.615 30.51 19.79 45.70 2.41
3873 4349 5.869579 ACAAATGTTCAGAGGTACATCTGT 58.130 37.500 30.51 13.74 45.70 3.41
3874 4350 6.808008 AACAAATGTTCAGAGGTACATCTG 57.192 37.500 27.48 27.48 46.70 2.90
3875 4351 7.227156 AGAAACAAATGTTCAGAGGTACATCT 58.773 34.615 3.73 3.73 37.25 2.90
3876 4352 7.440523 AGAAACAAATGTTCAGAGGTACATC 57.559 36.000 0.00 0.00 37.25 3.06
3877 4353 7.823745 AAGAAACAAATGTTCAGAGGTACAT 57.176 32.000 0.00 0.00 37.25 2.29
3878 4354 7.639113 AAAGAAACAAATGTTCAGAGGTACA 57.361 32.000 0.00 0.00 37.25 2.90
3879 4355 7.648112 GGAAAAGAAACAAATGTTCAGAGGTAC 59.352 37.037 0.00 0.00 37.25 3.34
4007 4670 6.049149 TGCGACAAATAGAAATTCTAGGAGG 58.951 40.000 8.78 1.50 31.67 4.30
4023 4686 6.183360 TGCTGTAAATATAAGCATGCGACAAA 60.183 34.615 13.01 0.00 41.83 2.83
4050 4713 6.618287 TTAACCAGTTGTCTCAACAAGATG 57.382 37.500 13.74 4.59 45.78 2.90
4051 4714 7.639113 TTTTAACCAGTTGTCTCAACAAGAT 57.361 32.000 13.74 3.65 45.78 2.40
4052 4715 7.338196 TCATTTTAACCAGTTGTCTCAACAAGA 59.662 33.333 13.74 0.00 45.78 3.02
4053 4716 7.479980 TCATTTTAACCAGTTGTCTCAACAAG 58.520 34.615 13.74 7.58 45.78 3.16
4054 4717 7.397892 TCATTTTAACCAGTTGTCTCAACAA 57.602 32.000 13.74 0.00 43.06 2.83
4055 4718 7.581213 ATCATTTTAACCAGTTGTCTCAACA 57.419 32.000 13.74 0.00 0.00 3.33
4056 4719 9.612620 CTAATCATTTTAACCAGTTGTCTCAAC 57.387 33.333 4.69 4.69 0.00 3.18
4057 4720 8.296713 GCTAATCATTTTAACCAGTTGTCTCAA 58.703 33.333 0.00 0.00 0.00 3.02
4058 4721 7.094377 GGCTAATCATTTTAACCAGTTGTCTCA 60.094 37.037 0.00 0.00 0.00 3.27
4059 4722 7.121315 AGGCTAATCATTTTAACCAGTTGTCTC 59.879 37.037 0.00 0.00 0.00 3.36
4060 4723 6.948309 AGGCTAATCATTTTAACCAGTTGTCT 59.052 34.615 0.00 0.00 0.00 3.41
4061 4724 7.029563 CAGGCTAATCATTTTAACCAGTTGTC 58.970 38.462 0.00 0.00 0.00 3.18
4062 4725 6.493458 ACAGGCTAATCATTTTAACCAGTTGT 59.507 34.615 0.00 0.00 0.00 3.32
4063 4726 6.924111 ACAGGCTAATCATTTTAACCAGTTG 58.076 36.000 0.00 0.00 0.00 3.16
4064 4727 8.823220 ATACAGGCTAATCATTTTAACCAGTT 57.177 30.769 0.00 0.00 0.00 3.16
4065 4728 8.823220 AATACAGGCTAATCATTTTAACCAGT 57.177 30.769 0.00 0.00 0.00 4.00
4135 4798 4.814771 CGAGAACAAGGTGTTTTAGAAGGT 59.185 41.667 0.00 0.00 41.28 3.50
4204 4867 7.054124 CCAGATTTACCAAGGAGCAGTATTTA 58.946 38.462 0.00 0.00 0.00 1.40
4301 4964 8.621286 AGTTAACTGATGAAACTTACCTTTGTG 58.379 33.333 7.48 0.00 29.25 3.33
4384 5047 3.626028 ACATCAACGCTTCCTTCAAAC 57.374 42.857 0.00 0.00 0.00 2.93
4733 5396 2.575805 ACTCCTCTTCCCAAGCAAAG 57.424 50.000 0.00 0.00 0.00 2.77
5501 6164 1.205893 AGAGAAGGATGTGTCGAAGCC 59.794 52.381 0.00 0.00 0.00 4.35
5600 6263 8.929487 ACAAATCTTGTTTTAACCCCTTCATAA 58.071 29.630 0.00 0.00 42.22 1.90
6197 6860 7.934120 GGATAGTGTATCTTTAAGAACATGCCT 59.066 37.037 0.00 2.58 35.52 4.75
6257 6920 1.280133 CTCAACTCAGGGGCAATCTGA 59.720 52.381 4.77 4.77 38.75 3.27
6422 7085 9.499479 CTATATATGACAGCAAACAAGAGGAAT 57.501 33.333 0.00 0.00 0.00 3.01
6665 7343 5.639082 GGCTTATAGCATTGCACAAAAACTT 59.361 36.000 11.91 0.00 44.75 2.66
6732 7411 6.697892 GGTACATCAGATAGTAAACACTGAGC 59.302 42.308 0.00 0.00 41.55 4.26
6827 7508 5.005971 CCTTTATTTCATTTTGCTGGCATCG 59.994 40.000 0.00 0.00 0.00 3.84
6843 7525 5.193099 ACATGTGGTAGGCTCCTTTATTT 57.807 39.130 0.00 0.00 0.00 1.40
6898 7580 2.803386 TGAAAACGCGTTCTGCATAGAA 59.197 40.909 26.77 0.90 46.97 2.10
7104 7788 8.668510 AACATGCTTCCATACAAAGTAGATAG 57.331 34.615 0.00 0.00 0.00 2.08
7173 7857 3.057104 CCATTCTCATGCAACAAAGCTCA 60.057 43.478 0.00 0.00 34.99 4.26


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

AutoCloner maintained by Alex Coulton.