Multiple sequence alignment - TraesCS6D01G111600

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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 TraesCS6D01G111600 chr6D 100.000 6219 0 0 1 6219 78263701 78269919 0.000000e+00 11485
1 TraesCS6D01G111600 chr6B 94.042 5841 224 59 12 5802 151126218 151131984 0.000000e+00 8745
2 TraesCS6D01G111600 chr6B 86.280 328 19 7 5810 6113 151132960 151133285 3.590000e-87 333
3 TraesCS6D01G111600 chr6B 84.492 187 22 4 1094 1273 694674556 694674742 1.780000e-40 178
4 TraesCS6D01G111600 chr6A 94.221 4603 163 44 1239 5802 93810940 93815478 0.000000e+00 6931
5 TraesCS6D01G111600 chr6A 88.221 1664 113 46 10 1647 93809340 93810946 0.000000e+00 1910
6 TraesCS6D01G111600 chr6A 95.722 187 8 0 6033 6219 93817369 93817555 1.010000e-77 302
7 TraesCS6D01G111600 chr6A 87.879 165 14 3 5810 5973 93815527 93815686 8.230000e-44 189
8 TraesCS6D01G111600 chr7D 79.151 1602 316 14 3614 5203 543728162 543729757 0.000000e+00 1092
9 TraesCS6D01G111600 chr7D 83.938 193 22 6 1094 1278 543725269 543725460 6.410000e-40 176
10 TraesCS6D01G111600 chr7A 83.938 193 22 6 1094 1278 625636004 625636195 6.410000e-40 176


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 TraesCS6D01G111600 chr6D 78263701 78269919 6218 False 11485 11485 100.00000 1 6219 1 chr6D.!!$F1 6218
1 TraesCS6D01G111600 chr6B 151126218 151133285 7067 False 4539 8745 90.16100 12 6113 2 chr6B.!!$F2 6101
2 TraesCS6D01G111600 chr6A 93809340 93817555 8215 False 2333 6931 91.51075 10 6219 4 chr6A.!!$F1 6209
3 TraesCS6D01G111600 chr7D 543725269 543729757 4488 False 634 1092 81.54450 1094 5203 2 chr7D.!!$F1 4109

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
229 231 1.070134 AGGCGGTTGCATATACGACAT 59.930 47.619 8.13 0.00 45.35 3.06 F
259 261 1.199852 GCACGCCAAACACAAAGTCG 61.200 55.000 0.00 0.00 0.00 4.18 F
1409 1730 1.272147 GCTTTTGTGGGGGATCTGAGT 60.272 52.381 0.00 0.00 0.00 3.41 F
1722 2429 1.133544 ACGTAGATCTACCTCCCCACC 60.134 57.143 24.01 0.00 32.61 4.61 F
2475 3188 2.584791 GTGTTGCGCTCCTGTTAATTG 58.415 47.619 9.73 0.00 0.00 2.32 F
3345 4995 0.687354 TGAAGTTGTGAGGAGCTCCC 59.313 55.000 29.54 20.23 36.42 4.30 F
3453 5349 1.946768 TCAACTTGCTAGCAACACCAC 59.053 47.619 26.06 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1605 0.597568 CACAGAAGGCAAAATCGGCA 59.402 50.000 0.0 0.0 0.00 5.69 R
1688 2395 2.160205 TCTACGTTCTCAGTGTGGAGG 58.840 52.381 0.0 0.0 35.58 4.30 R
3072 4722 0.174845 TCTAATCCCGCCTCGTTGTG 59.825 55.000 0.0 0.0 0.00 3.33 R
3078 4728 2.910688 TGTTCATCTAATCCCGCCTC 57.089 50.000 0.0 0.0 0.00 4.70 R
4135 6269 0.323451 TCTCAAGAGCCCGAGTAGCA 60.323 55.000 0.0 0.0 0.00 3.49 R
4394 6528 0.324645 GGAGCCAACCCCACATTGAT 60.325 55.000 0.0 0.0 0.00 2.57 R
5363 7520 0.181114 AGACCAAACAGACAGCAGCA 59.819 50.000 0.0 0.0 0.00 4.41 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
95 97 4.320456 CTGACAGCCGTGGCCTGT 62.320 66.667 7.39 11.09 43.17 4.00
96 98 4.624364 TGACAGCCGTGGCCTGTG 62.624 66.667 16.94 8.48 43.17 3.66
144 146 4.454678 AGAGAGCTTCATTTTGTGTGACA 58.545 39.130 0.00 0.00 0.00 3.58
146 148 3.002656 AGAGCTTCATTTTGTGTGACACG 59.997 43.478 11.51 0.00 37.14 4.49
147 149 2.682856 AGCTTCATTTTGTGTGACACGT 59.317 40.909 11.51 0.00 37.14 4.49
154 156 4.329296 TTTTGTGTGACACGTGTAACTG 57.671 40.909 31.30 2.19 37.14 3.16
173 175 7.994911 TGTAACTGAGAAGATGGCATATTTGAT 59.005 33.333 8.97 0.00 0.00 2.57
174 176 9.494271 GTAACTGAGAAGATGGCATATTTGATA 57.506 33.333 8.97 0.00 0.00 2.15
175 177 7.976135 ACTGAGAAGATGGCATATTTGATAC 57.024 36.000 8.97 0.00 0.00 2.24
229 231 1.070134 AGGCGGTTGCATATACGACAT 59.930 47.619 8.13 0.00 45.35 3.06
233 235 3.047093 CGGTTGCATATACGACATTCGA 58.953 45.455 1.94 0.00 43.74 3.71
240 242 4.143597 GCATATACGACATTCGACCGAAAG 60.144 45.833 8.97 7.34 43.74 2.62
256 258 1.587946 GAAAGCACGCCAAACACAAAG 59.412 47.619 0.00 0.00 0.00 2.77
259 261 1.199852 GCACGCCAAACACAAAGTCG 61.200 55.000 0.00 0.00 0.00 4.18
299 301 4.324267 ACCCAACGACTTTTATCCTCTTG 58.676 43.478 0.00 0.00 0.00 3.02
302 304 5.484715 CCAACGACTTTTATCCTCTTGGTA 58.515 41.667 0.00 0.00 34.23 3.25
380 382 2.524951 TAACCCCCGCACCGTGAATC 62.525 60.000 1.65 0.00 0.00 2.52
394 396 2.804572 CGTGAATCTTCATCCTCGCCAT 60.805 50.000 0.00 0.00 39.73 4.40
400 402 2.171237 TCTTCATCCTCGCCATCACATT 59.829 45.455 0.00 0.00 0.00 2.71
410 412 1.614051 GCCATCACATTGTCTCCACCA 60.614 52.381 0.00 0.00 0.00 4.17
414 416 1.667830 ACATTGTCTCCACCACGCG 60.668 57.895 3.53 3.53 0.00 6.01
460 462 5.488919 TCCAAACTTACCTCTCCATCTCAAT 59.511 40.000 0.00 0.00 0.00 2.57
471 473 7.671398 ACCTCTCCATCTCAATAAACACAAAAT 59.329 33.333 0.00 0.00 0.00 1.82
534 536 9.065871 GCAGTACAATTTCATGAAATTACAGTC 57.934 33.333 34.62 24.37 46.01 3.51
901 934 1.360393 ACTCCCACTTTTCCCCAGCA 61.360 55.000 0.00 0.00 0.00 4.41
904 937 1.531365 CCACTTTTCCCCAGCAGCA 60.531 57.895 0.00 0.00 0.00 4.41
905 938 1.530013 CCACTTTTCCCCAGCAGCAG 61.530 60.000 0.00 0.00 0.00 4.24
992 1028 4.227197 CATGGGATAGGTAGTGGTTCTCT 58.773 47.826 0.00 0.00 0.00 3.10
1268 1313 2.529744 GGAACTGGTGAGTGCCCCT 61.530 63.158 0.00 0.00 41.89 4.79
1284 1605 2.441901 CTCTCCGCCTCTCAGCCT 60.442 66.667 0.00 0.00 0.00 4.58
1315 1636 2.893637 CCTTCTGTGAGTGATTACGGG 58.106 52.381 0.00 0.00 0.00 5.28
1340 1661 2.885644 TGCGGCGAATTCGAGCTC 60.886 61.111 32.72 18.15 42.13 4.09
1409 1730 1.272147 GCTTTTGTGGGGGATCTGAGT 60.272 52.381 0.00 0.00 0.00 3.41
1421 1742 4.101741 GGGGATCTGAGTTACATACTGCTT 59.898 45.833 0.00 0.00 37.17 3.91
1427 1750 9.619316 GATCTGAGTTACATACTGCTTATACTG 57.381 37.037 0.00 0.00 37.17 2.74
1576 1899 6.157820 TGTGTCAAATCAGGGAGATGGTTATA 59.842 38.462 0.00 0.00 36.96 0.98
1639 2346 2.644676 GGCCCCTGATCACTTACTTTC 58.355 52.381 0.00 0.00 0.00 2.62
1669 2376 9.263538 TGCTTTATATTTGATGGATTTCAATGC 57.736 29.630 0.00 0.00 35.64 3.56
1677 2384 2.300433 TGGATTTCAATGCGGGAGATG 58.700 47.619 0.00 0.00 0.00 2.90
1722 2429 1.133544 ACGTAGATCTACCTCCCCACC 60.134 57.143 24.01 0.00 32.61 4.61
2229 2937 6.888632 TCGTAGTTAGGAGTCCAGAGTATTTT 59.111 38.462 12.86 0.00 0.00 1.82
2230 2938 8.049117 TCGTAGTTAGGAGTCCAGAGTATTTTA 58.951 37.037 12.86 0.00 0.00 1.52
2231 2939 8.848182 CGTAGTTAGGAGTCCAGAGTATTTTAT 58.152 37.037 12.86 0.00 0.00 1.40
2391 3104 4.404073 GTCTATCTGCTCTTCTCCTCCAAA 59.596 45.833 0.00 0.00 0.00 3.28
2445 3158 5.822278 TGCACTTCTACGATGAGTTATCTC 58.178 41.667 0.00 0.00 40.79 2.75
2475 3188 2.584791 GTGTTGCGCTCCTGTTAATTG 58.415 47.619 9.73 0.00 0.00 2.32
2641 3354 3.100671 ACTTGCCCTTCCTCTAGTAGTG 58.899 50.000 0.00 0.00 0.00 2.74
2877 4525 6.041511 CAGTTTGTGGTTGATGATGTTTGAA 58.958 36.000 0.00 0.00 0.00 2.69
2894 4542 7.320443 TGTTTGAAAGATGTGGCTATATGTC 57.680 36.000 0.00 0.00 0.00 3.06
2937 4585 6.979465 TGACAAAACATCATAATGCTGTTCA 58.021 32.000 0.00 0.00 35.89 3.18
2941 4589 8.767085 ACAAAACATCATAATGCTGTTCAAAAG 58.233 29.630 0.00 0.00 35.89 2.27
2943 4591 9.545105 AAAACATCATAATGCTGTTCAAAAGAA 57.455 25.926 0.00 0.00 35.89 2.52
2944 4592 9.715121 AAACATCATAATGCTGTTCAAAAGAAT 57.285 25.926 0.00 0.00 35.89 2.40
3072 4722 2.726633 ACAAGTAATGTTTGTGCGTGC 58.273 42.857 0.00 0.00 40.06 5.34
3135 4785 7.615757 AGAGGAAGGTAAACAAAATCCATTAGG 59.384 37.037 0.00 0.00 0.00 2.69
3345 4995 0.687354 TGAAGTTGTGAGGAGCTCCC 59.313 55.000 29.54 20.23 36.42 4.30
3354 5004 2.103263 GTGAGGAGCTCCCGAACATAAT 59.897 50.000 29.54 7.15 40.87 1.28
3453 5349 1.946768 TCAACTTGCTAGCAACACCAC 59.053 47.619 26.06 0.00 0.00 4.16
3463 5359 4.142687 GCTAGCAACACCACGATACATTTT 60.143 41.667 10.63 0.00 0.00 1.82
3553 5452 8.881743 TGTAACTTAGTCAAACACGTTACATTT 58.118 29.630 8.27 0.00 40.68 2.32
3571 5470 6.940831 ACATTTGCCATTTTACTTTGCTTT 57.059 29.167 0.00 0.00 0.00 3.51
3573 5472 4.809815 TTGCCATTTTACTTTGCTTTGC 57.190 36.364 0.00 0.00 0.00 3.68
3961 6095 3.958147 CAACAGGGAAGGGTAACTTTTGT 59.042 43.478 0.00 0.00 40.21 2.83
4066 6200 9.973450 ATAGCATCTGTAAACTCTGTATGTAAG 57.027 33.333 0.00 0.00 0.00 2.34
4070 6204 6.320171 TCTGTAAACTCTGTATGTAAGCGTC 58.680 40.000 0.00 0.00 0.00 5.19
4813 6947 1.816224 CTTGCTAAAAGCGGCCCTTTA 59.184 47.619 16.58 8.77 46.26 1.85
4864 6998 2.032376 TTGAGTGATGCTGCGCCA 59.968 55.556 4.18 0.00 0.00 5.69
5011 7145 3.088532 CTCAGTAGCAGGTCTTCACTCT 58.911 50.000 0.00 0.00 0.00 3.24
5191 7325 3.932710 GGACGCTGACTGAAATACATGAA 59.067 43.478 0.00 0.00 0.00 2.57
5229 7363 4.628074 TCGTTAGTTTGAGACCAGAAAGG 58.372 43.478 0.00 0.00 45.67 3.11
5233 7367 1.801178 GTTTGAGACCAGAAAGGCTCG 59.199 52.381 0.00 0.00 43.14 5.03
5234 7368 1.048601 TTGAGACCAGAAAGGCTCGT 58.951 50.000 0.00 0.00 43.14 4.18
5236 7370 0.390472 GAGACCAGAAAGGCTCGTGG 60.390 60.000 7.91 7.91 43.14 4.94
5237 7371 2.032681 ACCAGAAAGGCTCGTGGC 59.967 61.111 2.35 2.35 43.14 5.01
5239 7373 2.037136 CCAGAAAGGCTCGTGGCAG 61.037 63.158 13.78 0.00 44.01 4.85
5644 7801 4.742201 TCCGCGAGCTGCTTGGTC 62.742 66.667 18.18 2.01 43.27 4.02
5689 7849 5.857822 ACTAATACCGCTGACAAAAACTC 57.142 39.130 0.00 0.00 0.00 3.01
5745 7905 8.506168 TGATTGTAGCTAAAAAGTTATCAGGG 57.494 34.615 0.00 0.00 0.00 4.45
5758 7918 1.595311 ATCAGGGCTGGTTGTATGGA 58.405 50.000 0.00 0.00 0.00 3.41
5802 7963 3.191669 CCCGCGACATTTGTTGTAGATA 58.808 45.455 8.23 0.00 39.18 1.98
5803 7964 3.807622 CCCGCGACATTTGTTGTAGATAT 59.192 43.478 8.23 0.00 39.18 1.63
5804 7965 4.986034 CCCGCGACATTTGTTGTAGATATA 59.014 41.667 8.23 0.00 39.18 0.86
5805 7966 5.107607 CCCGCGACATTTGTTGTAGATATAC 60.108 44.000 8.23 0.00 39.18 1.47
5806 7967 5.387035 CCGCGACATTTGTTGTAGATATACG 60.387 44.000 8.23 0.00 39.18 3.06
5808 7969 6.357766 CGCGACATTTGTTGTAGATATACGTA 59.642 38.462 0.00 0.00 39.18 3.57
5826 8955 9.719355 ATATACGTACTTATGATGCCATTTTGA 57.281 29.630 0.00 0.00 34.31 2.69
5900 9030 1.210538 TCAGCTCCTGATTGGATGCT 58.789 50.000 0.00 0.00 45.16 3.79
5902 9032 2.103771 TCAGCTCCTGATTGGATGCTAC 59.896 50.000 7.81 0.00 45.16 3.58
5904 9034 2.104451 AGCTCCTGATTGGATGCTACTG 59.896 50.000 0.00 0.00 45.16 2.74
5905 9035 2.158842 GCTCCTGATTGGATGCTACTGT 60.159 50.000 0.00 0.00 45.16 3.55
5913 9043 5.128663 TGATTGGATGCTACTGTAGTTGCTA 59.871 40.000 15.71 7.20 44.85 3.49
6024 10761 1.661480 GCTGCTGCAACCATGACAA 59.339 52.632 11.11 0.00 39.41 3.18
6026 10763 0.956633 CTGCTGCAACCATGACAAGT 59.043 50.000 3.02 0.00 0.00 3.16
6116 10874 3.073678 TGCATCTTCTAAAGAAAGCGCA 58.926 40.909 11.47 5.83 42.21 6.09
6130 10888 2.888834 AGCGCAAAACAAACAGGATT 57.111 40.000 11.47 0.00 0.00 3.01
6136 10894 4.025813 CGCAAAACAAACAGGATTCCAAAG 60.026 41.667 5.29 0.00 0.00 2.77
6193 10951 1.633432 TCCAAGTCAACCCGGAATCAT 59.367 47.619 0.73 0.00 0.00 2.45
6198 10956 1.031571 TCAACCCGGAATCATGCAGC 61.032 55.000 0.73 0.00 0.00 5.25
6202 10960 0.101759 CCCGGAATCATGCAGCAAAG 59.898 55.000 0.73 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.365582 CCCACCTACCAGTTAATGCAC 58.634 52.381 0.00 0.00 0.00 4.57
23 24 1.340600 GCCCACCTACCAGTTAATGCA 60.341 52.381 0.00 0.00 0.00 3.96
52 54 5.240121 TCTAGGCGTTATTTTCCTCGTTTT 58.760 37.500 0.00 0.00 0.00 2.43
144 146 2.299013 TGCCATCTTCTCAGTTACACGT 59.701 45.455 0.00 0.00 0.00 4.49
146 148 7.280876 TCAAATATGCCATCTTCTCAGTTACAC 59.719 37.037 0.00 0.00 0.00 2.90
147 149 7.337938 TCAAATATGCCATCTTCTCAGTTACA 58.662 34.615 0.00 0.00 0.00 2.41
173 175 4.503910 AGCGTGCAAGATGTGAAATAGTA 58.496 39.130 2.99 0.00 0.00 1.82
174 176 3.338249 AGCGTGCAAGATGTGAAATAGT 58.662 40.909 2.99 0.00 0.00 2.12
175 177 4.025396 CCTAGCGTGCAAGATGTGAAATAG 60.025 45.833 2.99 0.00 0.00 1.73
229 231 3.039588 GGCGTGCTTTCGGTCGAA 61.040 61.111 1.33 1.33 0.00 3.71
233 235 2.115911 TGTTTGGCGTGCTTTCGGT 61.116 52.632 0.00 0.00 0.00 4.69
240 242 1.199852 CGACTTTGTGTTTGGCGTGC 61.200 55.000 0.00 0.00 0.00 5.34
256 258 4.379499 GGTTCCAAACTCATCCAAATCGAC 60.379 45.833 0.00 0.00 0.00 4.20
259 261 3.831911 TGGGTTCCAAACTCATCCAAATC 59.168 43.478 0.00 0.00 36.84 2.17
272 274 3.822167 GGATAAAAGTCGTTGGGTTCCAA 59.178 43.478 0.00 0.00 41.69 3.53
299 301 0.240145 GTTGAGCTGGCGGTTTTACC 59.760 55.000 0.00 0.00 34.05 2.85
302 304 1.152756 AGGTTGAGCTGGCGGTTTT 60.153 52.632 0.00 0.00 0.00 2.43
380 382 2.251409 ATGTGATGGCGAGGATGAAG 57.749 50.000 0.00 0.00 0.00 3.02
394 396 0.602638 GCGTGGTGGAGACAATGTGA 60.603 55.000 0.00 0.00 46.06 3.58
400 402 4.337060 CGACGCGTGGTGGAGACA 62.337 66.667 20.70 0.00 38.70 3.41
422 424 2.111999 TTTGGACCGAGCTGGAGGTG 62.112 60.000 9.56 0.00 41.51 4.00
423 425 1.841556 TTTGGACCGAGCTGGAGGT 60.842 57.895 8.91 6.98 44.64 3.85
429 431 1.275573 GAGGTAAGTTTGGACCGAGCT 59.724 52.381 0.00 0.00 40.91 4.09
430 432 1.275573 AGAGGTAAGTTTGGACCGAGC 59.724 52.381 0.00 0.00 40.91 5.03
507 509 8.796475 ACTGTAATTTCATGAAATTGTACTGCT 58.204 29.630 38.71 24.75 46.80 4.24
508 510 8.970691 ACTGTAATTTCATGAAATTGTACTGC 57.029 30.769 38.71 24.72 46.80 4.40
534 536 0.025513 GCTTTGCTACATCGCACTCG 59.974 55.000 0.00 0.00 40.09 4.18
714 731 2.575455 TTTGGTTTGTGGGGGCGAGT 62.575 55.000 0.00 0.00 0.00 4.18
928 961 2.202676 GGTTGGCTCTCTCGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
930 963 1.000486 TAGGGTTGGCTCTCTCGCT 60.000 57.895 0.00 0.00 0.00 4.93
932 965 1.439644 GCTAGGGTTGGCTCTCTCG 59.560 63.158 0.00 0.00 0.00 4.04
1268 1313 2.757508 CAGGCTGAGAGGCGGAGA 60.758 66.667 9.42 0.00 46.58 3.71
1284 1605 0.597568 CACAGAAGGCAAAATCGGCA 59.402 50.000 0.00 0.00 0.00 5.69
1409 1730 9.687210 CGAATAACCAGTATAAGCAGTATGTAA 57.313 33.333 0.00 0.00 39.31 2.41
1421 1742 8.014070 TCACTTCCAATCGAATAACCAGTATA 57.986 34.615 0.00 0.00 0.00 1.47
1427 1750 8.122952 CACTAAATCACTTCCAATCGAATAACC 58.877 37.037 0.00 0.00 0.00 2.85
1434 1757 5.411361 TGTTCCACTAAATCACTTCCAATCG 59.589 40.000 0.00 0.00 0.00 3.34
1576 1899 3.681593 GTGAGCTCGTCTCCCTCTATAT 58.318 50.000 9.64 0.00 41.18 0.86
1639 2346 8.415553 TGAAATCCATCAAATATAAAGCACTGG 58.584 33.333 0.00 0.00 0.00 4.00
1677 2384 3.384789 TCAGTGTGGAGGTAGATGTATGC 59.615 47.826 0.00 0.00 0.00 3.14
1688 2395 2.160205 TCTACGTTCTCAGTGTGGAGG 58.840 52.381 0.00 0.00 35.58 4.30
1722 2429 3.040147 TGGCTTCCTTTACTGTTCTCG 57.960 47.619 0.00 0.00 0.00 4.04
2116 2823 7.069208 AGCTAGATGTGTGTATCTCTTTCATCA 59.931 37.037 0.00 0.00 38.35 3.07
2229 2937 6.786122 ACAAAGCCCTTAACTGGACTAAATA 58.214 36.000 0.00 0.00 0.00 1.40
2230 2938 5.641155 ACAAAGCCCTTAACTGGACTAAAT 58.359 37.500 0.00 0.00 0.00 1.40
2231 2939 5.056553 ACAAAGCCCTTAACTGGACTAAA 57.943 39.130 0.00 0.00 0.00 1.85
2232 2940 4.717279 ACAAAGCCCTTAACTGGACTAA 57.283 40.909 0.00 0.00 0.00 2.24
2445 3158 0.882042 AGCGCAACACCTGAAGACAG 60.882 55.000 11.47 0.00 43.12 3.51
2475 3188 8.477256 TCCATCCTAAATCAATTTCCAATGAAC 58.523 33.333 0.00 0.00 0.00 3.18
2641 3354 4.081050 GTCACCAACCAGGGAAGC 57.919 61.111 0.00 0.00 43.89 3.86
2813 4459 7.434492 TGCTCAGCTTTGTTATATACTCCTAC 58.566 38.462 0.00 0.00 0.00 3.18
2814 4460 7.505923 TCTGCTCAGCTTTGTTATATACTCCTA 59.494 37.037 0.00 0.00 0.00 2.94
2816 4462 6.516718 TCTGCTCAGCTTTGTTATATACTCC 58.483 40.000 0.00 0.00 0.00 3.85
2817 4463 8.425577 TTTCTGCTCAGCTTTGTTATATACTC 57.574 34.615 0.00 0.00 0.00 2.59
2877 4525 5.830799 TCATGGACATATAGCCACATCTT 57.169 39.130 0.00 0.00 36.92 2.40
2894 4542 2.616376 TCAAGTGAACACCGTTTCATGG 59.384 45.455 1.11 0.00 37.80 3.66
3072 4722 0.174845 TCTAATCCCGCCTCGTTGTG 59.825 55.000 0.00 0.00 0.00 3.33
3078 4728 2.910688 TGTTCATCTAATCCCGCCTC 57.089 50.000 0.00 0.00 0.00 4.70
3553 5452 4.070630 AGCAAAGCAAAGTAAAATGGCA 57.929 36.364 0.00 0.00 0.00 4.92
3571 5470 6.714810 ACAATTGTCAATAACAGAGGTAAGCA 59.285 34.615 4.92 0.00 39.58 3.91
3573 5472 9.965824 AAAACAATTGTCAATAACAGAGGTAAG 57.034 29.630 12.39 0.00 39.58 2.34
3814 5942 7.289310 TGAAGAACTGAATGCCCATATAATGA 58.711 34.615 0.00 0.00 0.00 2.57
4066 6200 3.926527 TCTTTGTCATGTGATACAGACGC 59.073 43.478 0.00 0.00 32.63 5.19
4070 6204 8.121086 GTGATCATTCTTTGTCATGTGATACAG 58.879 37.037 0.00 0.00 0.00 2.74
4135 6269 0.323451 TCTCAAGAGCCCGAGTAGCA 60.323 55.000 0.00 0.00 0.00 3.49
4394 6528 0.324645 GGAGCCAACCCCACATTGAT 60.325 55.000 0.00 0.00 0.00 2.57
4645 6779 1.827969 GTATCACTGAGGAGCACACCT 59.172 52.381 0.00 0.00 43.64 4.00
4864 6998 2.124570 GTGATGCACCGCCAGGAT 60.125 61.111 0.00 0.00 41.02 3.24
5011 7145 0.898320 GGAGGTAGAGCTGTGAAGCA 59.102 55.000 0.00 0.00 37.25 3.91
5113 7247 4.275810 CCTTTGATCCTTCCATGACACAT 58.724 43.478 0.00 0.00 0.00 3.21
5229 7363 0.602905 ACAACTAACCTGCCACGAGC 60.603 55.000 0.00 0.00 44.14 5.03
5233 7367 2.161609 GCATACACAACTAACCTGCCAC 59.838 50.000 0.00 0.00 0.00 5.01
5234 7368 2.039746 AGCATACACAACTAACCTGCCA 59.960 45.455 0.00 0.00 0.00 4.92
5236 7370 3.119849 CCAAGCATACACAACTAACCTGC 60.120 47.826 0.00 0.00 0.00 4.85
5237 7371 4.323417 TCCAAGCATACACAACTAACCTG 58.677 43.478 0.00 0.00 0.00 4.00
5239 7373 4.156008 CCTTCCAAGCATACACAACTAACC 59.844 45.833 0.00 0.00 0.00 2.85
5363 7520 0.181114 AGACCAAACAGACAGCAGCA 59.819 50.000 0.00 0.00 0.00 4.41
5364 7521 1.801178 GTAGACCAAACAGACAGCAGC 59.199 52.381 0.00 0.00 0.00 5.25
5365 7522 3.393089 AGTAGACCAAACAGACAGCAG 57.607 47.619 0.00 0.00 0.00 4.24
5546 7703 5.647658 TCAGGACCAATTACAACATCATCAC 59.352 40.000 0.00 0.00 0.00 3.06
5644 7801 5.505173 AAACAAACAATGTGAGAGGAGTG 57.495 39.130 0.00 0.00 42.99 3.51
5745 7905 3.306019 CCCTGTTTTTCCATACAACCAGC 60.306 47.826 0.00 0.00 0.00 4.85
5758 7918 4.141937 GGAAGCAAAACTCTCCCTGTTTTT 60.142 41.667 0.00 0.00 42.68 1.94
5802 7963 7.931407 TCTCAAAATGGCATCATAAGTACGTAT 59.069 33.333 0.00 0.00 32.44 3.06
5803 7964 7.269316 TCTCAAAATGGCATCATAAGTACGTA 58.731 34.615 0.00 0.00 32.44 3.57
5804 7965 6.112734 TCTCAAAATGGCATCATAAGTACGT 58.887 36.000 0.00 0.00 32.44 3.57
5805 7966 6.603237 TCTCAAAATGGCATCATAAGTACG 57.397 37.500 0.00 0.00 32.44 3.67
5806 7967 8.288208 CAGATCTCAAAATGGCATCATAAGTAC 58.712 37.037 0.00 0.00 32.44 2.73
5808 7969 6.264744 CCAGATCTCAAAATGGCATCATAAGT 59.735 38.462 0.00 0.00 32.44 2.24
5826 8955 4.537688 TCATTCTTCCCAGAAACCAGATCT 59.462 41.667 0.00 0.00 42.53 2.75
5872 9002 1.149101 TCAGGAGCTGAAAAAGGGGT 58.851 50.000 0.00 0.00 37.57 4.95
5900 9030 3.253921 TGTTCACGCTAGCAACTACAGTA 59.746 43.478 16.45 0.00 0.00 2.74
5902 9032 2.663602 CTGTTCACGCTAGCAACTACAG 59.336 50.000 16.45 16.96 0.00 2.74
5904 9034 2.673833 ACTGTTCACGCTAGCAACTAC 58.326 47.619 16.45 7.73 0.00 2.73
5905 9035 3.380479 AACTGTTCACGCTAGCAACTA 57.620 42.857 16.45 2.65 0.00 2.24
5913 9043 1.270678 GGGTTCCTAACTGTTCACGCT 60.271 52.381 0.00 0.00 0.00 5.07
5973 9103 2.741122 TGTTTTCAGTAAACCACGCG 57.259 45.000 3.53 3.53 44.49 6.01
6024 10761 1.298667 GCCACGGAACCATGGTACT 59.701 57.895 20.12 2.44 38.34 2.73
6026 10763 1.567208 ATGGCCACGGAACCATGGTA 61.567 55.000 20.12 0.00 45.03 3.25
6116 10874 4.080638 TGCCTTTGGAATCCTGTTTGTTTT 60.081 37.500 0.00 0.00 0.00 2.43
6130 10888 1.886222 CGGGTTGAAGATGCCTTTGGA 60.886 52.381 0.00 0.00 31.62 3.53
6136 10894 1.883021 CCAACGGGTTGAAGATGCC 59.117 57.895 12.89 0.00 42.93 4.40
6163 10921 2.285977 GTTGACTTGGACTTCCGTTGT 58.714 47.619 0.00 0.00 39.43 3.32
6193 10951 2.721231 GTCAACCGCTTTGCTGCA 59.279 55.556 0.00 0.00 34.88 4.41
6198 10956 1.082104 GCTTCCGTCAACCGCTTTG 60.082 57.895 0.00 0.00 36.42 2.77


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

AutoCloner maintained by Alex Coulton.