Multiple sequence alignment - TraesCS4D01G155400

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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 TraesCS4D01G155400 chr4D 100.000 4243 0 0 1 4243 207362816 207367058 0 7836
1 TraesCS4D01G155400 chr5D 95.717 4249 173 9 1 4243 503225672 503221427 0 6830
2 TraesCS4D01G155400 chr5D 95.034 4249 200 10 1 4243 6196390 6192147 0 6667
3 TraesCS4D01G155400 chr3A 95.670 4249 174 10 1 4243 66010169 66014413 0 6818
4 TraesCS4D01G155400 chr3A 94.987 4249 204 9 1 4243 672902559 672906804 0 6658
5 TraesCS4D01G155400 chrUn 95.504 4248 181 9 1 4243 216511154 216515396 0 6778
6 TraesCS4D01G155400 chrUn 95.565 4239 178 9 10 4243 286272220 286267987 0 6778
7 TraesCS4D01G155400 chr3B 95.154 4251 195 9 1 4243 201534483 201530236 0 6698
8 TraesCS4D01G155400 chr2B 95.164 4239 194 11 10 4243 474915885 474911653 0 6682
9 TraesCS4D01G155400 chr1B 95.471 3974 176 4 1 3972 633746444 633750415 0 6338


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 TraesCS4D01G155400 chr4D 207362816 207367058 4242 False 7836 7836 100.000 1 4243 1 chr4D.!!$F1 4242
1 TraesCS4D01G155400 chr5D 503221427 503225672 4245 True 6830 6830 95.717 1 4243 1 chr5D.!!$R2 4242
2 TraesCS4D01G155400 chr5D 6192147 6196390 4243 True 6667 6667 95.034 1 4243 1 chr5D.!!$R1 4242
3 TraesCS4D01G155400 chr3A 66010169 66014413 4244 False 6818 6818 95.670 1 4243 1 chr3A.!!$F1 4242
4 TraesCS4D01G155400 chr3A 672902559 672906804 4245 False 6658 6658 94.987 1 4243 1 chr3A.!!$F2 4242
5 TraesCS4D01G155400 chrUn 216511154 216515396 4242 False 6778 6778 95.504 1 4243 1 chrUn.!!$F1 4242
6 TraesCS4D01G155400 chrUn 286267987 286272220 4233 True 6778 6778 95.565 10 4243 1 chrUn.!!$R1 4233
7 TraesCS4D01G155400 chr3B 201530236 201534483 4247 True 6698 6698 95.154 1 4243 1 chr3B.!!$R1 4242
8 TraesCS4D01G155400 chr2B 474911653 474915885 4232 True 6682 6682 95.164 10 4243 1 chr2B.!!$R1 4233
9 TraesCS4D01G155400 chr1B 633746444 633750415 3971 False 6338 6338 95.471 1 3972 1 chr1B.!!$F1 3971


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
127 128 1.561542 GCTTGGAGGGAGATCTTTCCA 59.438 52.381 16.31 16.31 39.09 3.53 F
572 575 1.758122 ATCCCAAAAGCATCCGGGC 60.758 57.895 0.00 0.00 38.68 6.13 F
1735 1744 1.217942 ACTTGGGTTTCAGCTTTCCCT 59.782 47.619 11.80 0.00 40.48 4.20 F
1881 1891 0.750850 ATGTTATCCCCACTCCGACG 59.249 55.000 0.00 0.00 0.00 5.12 F
1964 1974 1.165270 CAGGGTCCGGAACAATGAAC 58.835 55.000 23.64 1.83 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1734 0.332972 AAAGGGGCTAGGGAAAGCTG 59.667 55.0 0.00 0.0 42.37 4.24 R
1865 1875 1.108776 CTTCGTCGGAGTGGGGATAA 58.891 55.0 0.00 0.0 0.00 1.75 R
2970 2981 0.037975 GCTTGCCATCCACACCAAAG 60.038 55.0 0.00 0.0 0.00 2.77 R
3014 3025 0.179142 GAACGCTCGTAAGGAGTCCC 60.179 60.0 5.25 0.0 45.03 4.46 R
3564 3575 1.103398 GCCCAAAGAGGCGCATATGT 61.103 55.0 10.83 0.0 44.57 2.29 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
50 51 9.575783 GAGTAAATAGAATTCCATACTCGATCC 57.424 37.037 15.69 2.22 32.62 3.36
127 128 1.561542 GCTTGGAGGGAGATCTTTCCA 59.438 52.381 16.31 16.31 39.09 3.53
130 131 4.459330 CTTGGAGGGAGATCTTTCCAATC 58.541 47.826 25.19 13.64 45.70 2.67
145 147 1.765314 CCAATCCTTCGAGATCCACCT 59.235 52.381 0.00 0.00 0.00 4.00
226 229 4.911390 ACGGATTCTTGAACCTCTTTCAT 58.089 39.130 0.00 0.00 43.99 2.57
227 230 6.049955 ACGGATTCTTGAACCTCTTTCATA 57.950 37.500 0.00 0.00 43.99 2.15
292 295 6.935741 ATCCGATCCAATTTTTCGTAATCA 57.064 33.333 0.00 0.00 0.00 2.57
407 410 6.564328 ACAAAAGACAGAAACAAATCCACTC 58.436 36.000 0.00 0.00 0.00 3.51
418 421 6.783708 AACAAATCCACTCTTGGTTTTACA 57.216 33.333 0.50 0.00 41.16 2.41
451 454 6.572167 ACGTAGAGTAACTCCCAATATAGC 57.428 41.667 0.00 0.00 0.00 2.97
460 463 9.614792 AGTAACTCCCAATATAGCAGTAAAAAG 57.385 33.333 0.00 0.00 0.00 2.27
464 467 7.775561 ACTCCCAATATAGCAGTAAAAAGAAGG 59.224 37.037 0.00 0.00 0.00 3.46
466 469 6.321181 CCCAATATAGCAGTAAAAAGAAGGCA 59.679 38.462 0.00 0.00 0.00 4.75
513 516 7.041712 GGAAAGTTCCGATTGAAATAGGATCTC 60.042 40.741 13.10 5.63 38.48 2.75
565 568 5.127031 GGTTATTAGAAGCATCCCAAAAGCA 59.873 40.000 0.00 0.00 0.00 3.91
572 575 1.758122 ATCCCAAAAGCATCCGGGC 60.758 57.895 0.00 0.00 38.68 6.13
634 639 2.440599 CAAAGGGAGTGGGGGTGG 59.559 66.667 0.00 0.00 0.00 4.61
673 678 2.625314 CGACTCATAGAATGGCAGAGGA 59.375 50.000 0.00 0.00 0.00 3.71
687 692 4.716784 TGGCAGAGGAAAATAGAGCTCTTA 59.283 41.667 23.84 8.44 0.00 2.10
740 745 7.010160 TCTATGTATGTAGACACATGGATCCA 58.990 38.462 18.88 18.88 45.17 3.41
745 750 5.276461 TGTAGACACATGGATCCATACAC 57.724 43.478 26.87 17.09 34.91 2.90
753 758 2.957474 TGGATCCATACACCTCGATCA 58.043 47.619 11.44 0.00 34.14 2.92
782 787 7.552050 AGAATCAATAGAAGGAGAATCGGAT 57.448 36.000 0.00 0.00 34.37 4.18
787 792 7.831753 TCAATAGAAGGAGAATCGGATGATAC 58.168 38.462 0.00 0.00 34.37 2.24
794 799 5.011533 AGGAGAATCGGATGATACCTTTCTG 59.988 44.000 0.00 0.00 33.45 3.02
795 800 5.011125 GGAGAATCGGATGATACCTTTCTGA 59.989 44.000 0.00 0.00 33.45 3.27
853 858 8.829373 AAAATCATTATCAACTAAGCCCTCTT 57.171 30.769 0.00 0.00 36.35 2.85
937 943 4.041691 ACCTATTCATGGGGATTCCGTAAG 59.958 45.833 0.00 0.00 38.76 2.34
965 971 7.212976 TCCCATTTCAAAAATCGAAACAATCA 58.787 30.769 0.00 0.00 35.31 2.57
967 973 7.384660 CCCATTTCAAAAATCGAAACAATCAGA 59.615 33.333 0.00 0.00 35.31 3.27
975 981 8.925161 AAAATCGAAACAATCAGAACTTTTCA 57.075 26.923 0.00 0.00 0.00 2.69
976 982 9.533253 AAAATCGAAACAATCAGAACTTTTCAT 57.467 25.926 0.00 0.00 0.00 2.57
1188 1194 9.790344 AAAGATAGACCTTGGATCTATTTCATG 57.210 33.333 10.70 0.00 39.09 3.07
1197 1203 7.201767 CCTTGGATCTATTTCATGTCTTCAACC 60.202 40.741 0.00 0.00 0.00 3.77
1218 1224 9.727859 TCAACCAGTTTAGTAATAAGCATAACA 57.272 29.630 0.00 0.00 0.00 2.41
1455 1461 9.386010 TGTGGTGCTAACGATTTAATAACTATT 57.614 29.630 0.00 0.00 0.00 1.73
1499 1505 8.786826 TTCAGTTTATGTTCCTACCTATTGTG 57.213 34.615 0.00 0.00 0.00 3.33
1532 1538 5.457140 CAAGAGAGATCTACGGTCTAATGC 58.543 45.833 0.00 0.00 0.00 3.56
1542 1548 2.626743 ACGGTCTAATGCGGCTACTATT 59.373 45.455 0.00 0.00 0.00 1.73
1618 1624 3.326521 TGGCTATATGGTTCATCTGGGT 58.673 45.455 0.00 0.00 0.00 4.51
1628 1637 2.366916 GTTCATCTGGGTGGAGATCGAT 59.633 50.000 0.00 0.00 29.72 3.59
1629 1638 2.682594 TCATCTGGGTGGAGATCGATT 58.317 47.619 0.00 0.00 29.72 3.34
1643 1652 8.450964 GTGGAGATCGATTTTCAAGAAATTGTA 58.549 33.333 0.00 0.00 0.00 2.41
1656 1665 7.735500 TCAAGAAATTGTAAACGGTCTTATCG 58.264 34.615 0.00 0.00 0.00 2.92
1690 1699 9.719355 AATGTATAACTCCCCAAAAATTTCAAC 57.281 29.630 0.00 0.00 0.00 3.18
1725 1734 3.764237 TCACTGTAGGACTTGGGTTTC 57.236 47.619 0.00 0.00 0.00 2.78
1735 1744 1.217942 ACTTGGGTTTCAGCTTTCCCT 59.782 47.619 11.80 0.00 40.48 4.20
1820 1830 9.791781 TTCCTACCTCTATATCTATCTCTGAGA 57.208 37.037 10.23 10.23 0.00 3.27
1834 1844 5.047566 TCTCTGAGATGTTTGGGTTTTGA 57.952 39.130 2.58 0.00 0.00 2.69
1835 1845 5.634118 TCTCTGAGATGTTTGGGTTTTGAT 58.366 37.500 2.58 0.00 0.00 2.57
1846 1856 8.251383 TGTTTGGGTTTTGATAAACTCCATAA 57.749 30.769 9.95 6.72 42.88 1.90
1865 1875 9.388506 CTCCATAAACATGTAGAAGAGAAATGT 57.611 33.333 0.00 0.00 32.99 2.71
1881 1891 0.750850 ATGTTATCCCCACTCCGACG 59.249 55.000 0.00 0.00 0.00 5.12
1952 1962 2.755103 CAATTTAGGTGAAGCAGGGTCC 59.245 50.000 0.00 0.00 0.00 4.46
1964 1974 1.165270 CAGGGTCCGGAACAATGAAC 58.835 55.000 23.64 1.83 0.00 3.18
2029 2039 5.012354 ACGGGTAGTTCCTACAAAGAATCAA 59.988 40.000 4.01 0.00 38.58 2.57
2076 2086 8.243289 TGAATTATCGATGTACATGCTACATG 57.757 34.615 14.43 6.03 38.18 3.21
2183 2193 4.989279 ATTGGGAACGAATCAAATCAGG 57.011 40.909 0.00 0.00 0.00 3.86
2185 2195 3.343617 TGGGAACGAATCAAATCAGGTC 58.656 45.455 0.00 0.00 0.00 3.85
2207 2217 6.091034 GGTCGTTCTATTTCTCAACCTTTCTC 59.909 42.308 0.00 0.00 0.00 2.87
2338 2348 9.933723 AAATCGATTTTGAAAAAGAATGGATCT 57.066 25.926 17.60 0.00 41.32 2.75
2350 2360 8.738645 AAAAGAATGGATCTGGTCTTATACAC 57.261 34.615 0.00 0.00 38.79 2.90
2353 2363 6.384015 AGAATGGATCTGGTCTTATACACACA 59.616 38.462 0.00 0.00 36.88 3.72
2419 2429 1.480789 TATCACTTAGGAGCCGTGCA 58.519 50.000 0.00 0.00 0.00 4.57
2457 2467 3.612479 GCACGGTTTTGCATGAGAGAAAT 60.612 43.478 0.00 0.00 42.49 2.17
2491 2501 3.196685 CCTCTTTTCGAATCTGACTCCCT 59.803 47.826 0.00 0.00 0.00 4.20
2606 2616 6.845758 TCAAATGAATGGCATCTTCTTCTT 57.154 33.333 0.00 0.00 35.78 2.52
2607 2617 6.860080 TCAAATGAATGGCATCTTCTTCTTC 58.140 36.000 0.00 0.00 35.78 2.87
2613 2623 4.952262 TGGCATCTTCTTCTTCAAATCG 57.048 40.909 0.00 0.00 0.00 3.34
2642 2652 5.659440 TTCTTAGCATGATTTTGGGGAAC 57.341 39.130 0.00 0.00 0.00 3.62
2700 2710 3.557054 GCTTGCATATTCGTCCATAGGGA 60.557 47.826 0.00 0.00 42.29 4.20
2714 2724 6.448369 TCCATAGGGAAAATCGGATATGTT 57.552 37.500 0.00 0.00 41.32 2.71
2742 2752 6.817765 TTGGAATAATTGTTGGAGACTCAC 57.182 37.500 4.53 0.00 0.00 3.51
2832 2842 8.236585 TGCTTGCATTGTATTATTTGGTCTAT 57.763 30.769 0.00 0.00 0.00 1.98
2843 2853 3.615224 TTTGGTCTATGTACCGGAACC 57.385 47.619 9.46 4.34 42.91 3.62
2918 2929 5.596361 TCTCTCTTTAGCCCTATGTCTCTTG 59.404 44.000 0.00 0.00 0.00 3.02
2970 2981 7.522901 GGTTTCTTCGGAAAACTCTATCTAC 57.477 40.000 5.55 0.00 45.35 2.59
2972 2983 7.818446 GGTTTCTTCGGAAAACTCTATCTACTT 59.182 37.037 5.55 0.00 45.35 2.24
3012 3023 5.221126 GCAGGCCTATATTTCTTGGTTTCAG 60.221 44.000 3.98 0.00 0.00 3.02
3014 3025 5.888161 AGGCCTATATTTCTTGGTTTCAGTG 59.112 40.000 1.29 0.00 0.00 3.66
3109 3120 4.099419 CCAAGAAATAACCCCTTATGTGCC 59.901 45.833 0.00 0.00 0.00 5.01
3182 3193 5.596836 TGACTGTATGTGTGATAGCATCA 57.403 39.130 0.00 0.00 36.84 3.07
3212 3223 4.525487 CCAGGAATATCAATGAACCCCATG 59.475 45.833 0.00 0.00 35.24 3.66
3572 3583 8.450964 CCTATTCTTATTTGGGTAACATATGCG 58.549 37.037 1.58 0.00 39.74 4.73
3617 3628 9.261180 GAATCGAGAAATTGGATTGTACATCTA 57.739 33.333 0.00 0.00 34.78 1.98
3672 3683 9.352191 GATACATATAAGGTGTCCTACGGATAT 57.648 37.037 0.00 0.00 32.73 1.63
3716 3727 4.148838 GTCTGACTCAGGCCTATATGACT 58.851 47.826 3.98 0.00 28.61 3.41
3721 3732 4.745351 ACTCAGGCCTATATGACTGATCA 58.255 43.478 13.31 0.00 39.06 2.92
3840 3851 6.406370 CCTTGATAGTGAAATGGTAGACACA 58.594 40.000 0.00 0.00 35.97 3.72
3844 3855 4.537135 AGTGAAATGGTAGACACACGAT 57.463 40.909 0.00 0.00 35.97 3.73
3865 3876 5.062183 CGATACTCAAAATCTCGTGCTGAAA 59.938 40.000 0.00 0.00 0.00 2.69
4003 4014 3.133183 GTCCTTAACCATCTCCCTGAGAC 59.867 52.174 0.00 0.00 41.76 3.36
4030 4041 9.569122 AAGTAGACAGTAAAAGCCAAAATAGAA 57.431 29.630 0.00 0.00 0.00 2.10
4095 4107 7.182060 AGGAGATAATAAAGAACCCAAAGCAA 58.818 34.615 0.00 0.00 0.00 3.91
4099 4111 7.765819 AGATAATAAAGAACCCAAAGCAAATGC 59.234 33.333 0.00 0.00 42.49 3.56
4132 4144 4.265073 CAAGGGTGGTCTTAAGAATCCAG 58.735 47.826 13.66 1.06 0.00 3.86
4138 4150 5.046231 GGTGGTCTTAAGAATCCAGAAGAGT 60.046 44.000 13.66 0.00 0.00 3.24
4162 4174 9.360901 AGTTTGCTCAGAAGAGATAGATGTATA 57.639 33.333 0.00 0.00 44.98 1.47
4170 4182 8.865090 CAGAAGAGATAGATGTATACCAACCTT 58.135 37.037 0.00 0.00 0.00 3.50
4180 4192 9.838339 AGATGTATACCAACCTTATTTTCTCAG 57.162 33.333 0.00 0.00 0.00 3.35
4182 4194 7.924541 TGTATACCAACCTTATTTTCTCAGGT 58.075 34.615 0.00 0.00 43.17 4.00
4230 4243 3.345508 AAAGTGACTACGAATTCCCCC 57.654 47.619 0.00 0.00 0.00 5.40
4238 4251 3.824443 ACTACGAATTCCCCCTTTTGTTG 59.176 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.410991 TCTATGGGATCGAGTATGGAATTCTA 58.589 38.462 5.23 0.00 0.00 2.10
50 51 7.621285 TCCACAGAATTCTATAGGGATCTATGG 59.379 40.741 7.86 15.23 36.87 2.74
127 128 4.030913 TGTAAGGTGGATCTCGAAGGATT 58.969 43.478 0.00 0.00 0.00 3.01
130 131 3.887621 TTGTAAGGTGGATCTCGAAGG 57.112 47.619 0.00 0.00 0.00 3.46
145 147 5.087323 TGGCTTTTTGACCCCATATTGTAA 58.913 37.500 0.00 0.00 0.00 2.41
171 173 9.796120 TTTATAAGGGCGAAAATCACTTATTTG 57.204 29.630 3.26 0.00 37.85 2.32
186 189 8.132995 AGAATCCGTTTTATTTTTATAAGGGCG 58.867 33.333 0.00 0.00 0.00 6.13
200 203 6.768861 TGAAAGAGGTTCAAGAATCCGTTTTA 59.231 34.615 0.00 0.00 43.43 1.52
226 229 4.335594 CAGTACCTCGATGTGACATGAGTA 59.664 45.833 1.23 0.00 0.00 2.59
227 230 3.129462 CAGTACCTCGATGTGACATGAGT 59.871 47.826 1.23 0.00 0.00 3.41
407 410 6.378582 ACGTATTGCTTGATGTAAAACCAAG 58.621 36.000 0.00 0.00 40.00 3.61
418 421 6.461231 GGGAGTTACTCTACGTATTGCTTGAT 60.461 42.308 12.41 0.00 0.00 2.57
513 516 1.000938 GGCAAGTGCTCTTCCTTGTTG 60.001 52.381 2.85 0.00 40.13 3.33
565 568 1.303317 GCCATATTTCGGCCCGGAT 60.303 57.895 0.73 0.17 44.22 4.18
572 575 8.702163 AACTTAATTTGAAAGCCATATTTCGG 57.298 30.769 0.00 0.00 41.21 4.30
673 678 8.324163 ACGAAAATGTGTAAGAGCTCTATTTT 57.676 30.769 24.32 24.32 0.00 1.82
687 692 6.976088 TGTTCATGGATTAACGAAAATGTGT 58.024 32.000 0.00 0.00 0.00 3.72
740 745 6.878317 TGATTCTTTTCTGATCGAGGTGTAT 58.122 36.000 0.00 0.00 0.00 2.29
745 750 8.654230 TTCTATTGATTCTTTTCTGATCGAGG 57.346 34.615 0.00 0.00 0.00 4.63
753 758 9.323985 CGATTCTCCTTCTATTGATTCTTTTCT 57.676 33.333 0.00 0.00 0.00 2.52
782 787 9.712305 TTTTTGTTTGTTTTCAGAAAGGTATCA 57.288 25.926 0.00 0.00 0.00 2.15
826 831 9.920946 AGAGGGCTTAGTTGATAATGATTTTTA 57.079 29.630 0.00 0.00 0.00 1.52
828 833 8.689972 CAAGAGGGCTTAGTTGATAATGATTTT 58.310 33.333 0.00 0.00 31.81 1.82
853 858 5.435686 TCTTATTCTTAAGCAAGCCCTCA 57.564 39.130 0.00 0.00 35.72 3.86
937 943 8.527567 TTGTTTCGATTTTTGAAATGGGATAC 57.472 30.769 0.00 0.00 37.62 2.24
965 971 6.888632 ACTGCATCCAATCTATGAAAAGTTCT 59.111 34.615 0.00 0.00 0.00 3.01
967 973 7.472334 AACTGCATCCAATCTATGAAAAGTT 57.528 32.000 0.00 0.00 0.00 2.66
976 982 9.276590 CATGAATTAGTAACTGCATCCAATCTA 57.723 33.333 0.00 0.00 0.00 1.98
1137 1143 8.737168 TTTTATCAGAGGTTGAATCGATCATT 57.263 30.769 0.00 0.00 39.77 2.57
1177 1183 8.641498 AAACTGGTTGAAGACATGAAATAGAT 57.359 30.769 0.00 0.00 0.00 1.98
1188 1194 8.319143 TGCTTATTACTAAACTGGTTGAAGAC 57.681 34.615 0.00 0.00 0.00 3.01
1197 1203 9.174166 AGGGTTGTTATGCTTATTACTAAACTG 57.826 33.333 0.00 0.00 0.00 3.16
1218 1224 3.112263 TCTCCATCGGAACAATAGGGTT 58.888 45.455 0.00 0.00 0.00 4.11
1219 1225 2.700897 CTCTCCATCGGAACAATAGGGT 59.299 50.000 0.00 0.00 0.00 4.34
1357 1363 9.113838 CTCTGTTATAGCCATTTCTGTACATTT 57.886 33.333 0.00 0.00 0.00 2.32
1455 1461 5.827797 ACTGAAACATTCTGGAGCTACAAAA 59.172 36.000 0.00 0.00 33.45 2.44
1542 1548 6.436027 TGCCCAACCCATGAGTAAATATTTA 58.564 36.000 3.71 3.71 0.00 1.40
1561 1567 2.092753 CCAGAATAGAAGAGCTTGCCCA 60.093 50.000 0.00 0.00 0.00 5.36
1618 1624 7.452880 ACAATTTCTTGAAAATCGATCTCCA 57.547 32.000 0.00 0.00 36.20 3.86
1629 1638 9.887406 GATAAGACCGTTTACAATTTCTTGAAA 57.113 29.630 0.00 0.00 36.20 2.69
1643 1652 6.592607 ACATTTGTGTATCGATAAGACCGTTT 59.407 34.615 6.72 0.00 0.00 3.60
1656 1665 8.514330 TTTGGGGAGTTATACATTTGTGTATC 57.486 34.615 4.49 0.00 36.50 2.24
1680 1689 9.807649 GATGGATATAAGTGCAGTTGAAATTTT 57.192 29.630 17.21 0.00 0.00 1.82
1681 1690 8.970020 TGATGGATATAAGTGCAGTTGAAATTT 58.030 29.630 17.21 0.00 0.00 1.82
1690 1699 6.015095 TCCTACAGTGATGGATATAAGTGCAG 60.015 42.308 0.00 0.00 0.00 4.41
1725 1734 0.332972 AAAGGGGCTAGGGAAAGCTG 59.667 55.000 0.00 0.00 42.37 4.24
1735 1744 4.141251 GGAGTCCATTATGAAAAGGGGCTA 60.141 45.833 3.60 0.00 0.00 3.93
1820 1830 6.739331 TGGAGTTTATCAAAACCCAAACAT 57.261 33.333 8.04 0.00 45.11 2.71
1846 1856 7.775561 GGGGATAACATTTCTCTTCTACATGTT 59.224 37.037 2.30 0.00 40.38 2.71
1865 1875 1.108776 CTTCGTCGGAGTGGGGATAA 58.891 55.000 0.00 0.00 0.00 1.75
1936 1946 1.987855 CCGGACCCTGCTTCACCTA 60.988 63.158 0.00 0.00 0.00 3.08
1952 1962 6.683974 ATCATAAAGAGGTTCATTGTTCCG 57.316 37.500 0.00 0.00 0.00 4.30
2066 2076 2.292267 GAGAACCCACCATGTAGCATG 58.708 52.381 2.38 2.38 0.00 4.06
2076 2086 1.909302 TCTGAAGGATGAGAACCCACC 59.091 52.381 0.00 0.00 0.00 4.61
2183 2193 6.645415 TGAGAAAGGTTGAGAAATAGAACGAC 59.355 38.462 0.00 0.00 0.00 4.34
2185 2195 6.647067 AGTGAGAAAGGTTGAGAAATAGAACG 59.353 38.462 0.00 0.00 0.00 3.95
2337 2347 3.442625 TCCTCGTGTGTGTATAAGACCAG 59.557 47.826 0.00 0.00 0.00 4.00
2338 2348 3.423749 TCCTCGTGTGTGTATAAGACCA 58.576 45.455 0.00 0.00 0.00 4.02
2350 2360 5.682943 TTTTTGATTACCTTCCTCGTGTG 57.317 39.130 0.00 0.00 0.00 3.82
2419 2429 3.005554 CCGTGCATGAGACTTTCATCTT 58.994 45.455 7.72 0.00 44.76 2.40
2480 2490 1.360852 ACTGGAGTGAGGGAGTCAGAT 59.639 52.381 0.00 0.00 35.13 2.90
2491 2501 2.158957 AGAAAAGCAACGACTGGAGTGA 60.159 45.455 0.00 0.00 0.00 3.41
2588 2598 6.403964 CGATTTGAAGAAGAAGATGCCATTCA 60.404 38.462 0.00 0.00 0.00 2.57
2642 2652 5.163713 GCTTGTTTGAGTAATAGCAAGGAGG 60.164 44.000 0.00 0.00 35.31 4.30
2742 2752 5.582689 ATCATGCTTGCATATCCATCATG 57.417 39.130 7.84 4.03 32.28 3.07
2799 2809 9.492973 AAATAATACAATGCAAGCAAAAGTTCT 57.507 25.926 0.00 0.00 0.00 3.01
2832 2842 3.734597 CGAATGTTATCGGTTCCGGTACA 60.735 47.826 13.64 12.33 39.12 2.90
2843 2853 5.863935 TCCTGCATAATCTCGAATGTTATCG 59.136 40.000 0.00 0.00 44.04 2.92
2918 2929 3.973458 GGAAGGCCTCCTAGGGAC 58.027 66.667 5.23 0.00 41.61 4.46
2970 2981 0.037975 GCTTGCCATCCACACCAAAG 60.038 55.000 0.00 0.00 0.00 2.77
2972 2983 1.152589 TGCTTGCCATCCACACCAA 60.153 52.632 0.00 0.00 0.00 3.67
3012 3023 1.139095 CGCTCGTAAGGAGTCCCAC 59.861 63.158 5.25 3.34 45.03 4.61
3014 3025 0.179142 GAACGCTCGTAAGGAGTCCC 60.179 60.000 5.25 0.00 45.03 4.46
3078 3089 4.077108 GGGGTTATTTCTTGGTTTCGTCT 58.923 43.478 0.00 0.00 0.00 4.18
3182 3193 8.164070 GGGTTCATTGATATTCCTGGTATAGTT 58.836 37.037 0.00 0.00 0.00 2.24
3212 3223 2.223665 GGTATCCTGAGCAATTGCAAGC 60.224 50.000 30.89 19.59 45.16 4.01
3328 3339 9.726438 GATTATAAGTTCATAACCCTAGCACAT 57.274 33.333 0.00 0.00 0.00 3.21
3329 3340 8.710239 TGATTATAAGTTCATAACCCTAGCACA 58.290 33.333 0.00 0.00 0.00 4.57
3331 3342 9.725019 CATGATTATAAGTTCATAACCCTAGCA 57.275 33.333 2.05 0.00 31.50 3.49
3392 3403 2.355756 GTGCACGGTCTAGTTCGGTATA 59.644 50.000 0.00 0.00 0.00 1.47
3402 3413 6.811954 TCATAATAAGAATGTGCACGGTCTA 58.188 36.000 19.17 7.22 0.00 2.59
3564 3575 1.103398 GCCCAAAGAGGCGCATATGT 61.103 55.000 10.83 0.00 44.57 2.29
3672 3683 5.953183 ACATCAAATAGCTTCGATTTGCAA 58.047 33.333 13.39 0.00 41.86 4.08
3716 3727 6.878317 AGTCTTGGAGTATTTCGATTGATCA 58.122 36.000 0.00 0.00 0.00 2.92
3721 3732 5.420409 GTGGAGTCTTGGAGTATTTCGATT 58.580 41.667 0.00 0.00 0.00 3.34
3823 3834 4.537135 ATCGTGTGTCTACCATTTCACT 57.463 40.909 0.00 0.00 0.00 3.41
3840 3851 3.859961 CAGCACGAGATTTTGAGTATCGT 59.140 43.478 0.00 0.00 46.63 3.73
3844 3855 5.334105 GCTTTTCAGCACGAGATTTTGAGTA 60.334 40.000 0.00 0.00 46.49 2.59
3865 3876 1.289380 GACTCGAACCTCCACGCTT 59.711 57.895 0.00 0.00 0.00 4.68
3959 3970 3.476552 CTCAGAAGATAGAGGAGAGCGT 58.523 50.000 0.00 0.00 0.00 5.07
4003 4014 8.999431 TCTATTTTGGCTTTTACTGTCTACTTG 58.001 33.333 0.00 0.00 0.00 3.16
4045 4056 5.057149 CGAGGGATTTTTAGGATCGTTCAT 58.943 41.667 0.00 0.00 0.00 2.57
4095 4107 2.780010 ACCCTTGCACTAGGATAGCATT 59.220 45.455 5.98 0.00 44.39 3.56
4099 4111 2.103263 GACCACCCTTGCACTAGGATAG 59.897 54.545 5.98 0.00 46.50 2.08
4107 4119 2.561478 TCTTAAGACCACCCTTGCAC 57.439 50.000 0.00 0.00 0.00 4.57
4132 4144 6.862209 TCTATCTCTTCTGAGCAAACTCTTC 58.138 40.000 0.00 0.00 43.85 2.87
4138 4150 8.580720 GGTATACATCTATCTCTTCTGAGCAAA 58.419 37.037 5.01 0.00 40.03 3.68
4162 4174 5.061721 ACACCTGAGAAAATAAGGTTGGT 57.938 39.130 0.00 0.00 41.65 3.67
4201 4214 4.659111 TCGTAGTCACTTTTTCCTGTCA 57.341 40.909 0.00 0.00 0.00 3.58



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

AutoCloner maintained by Alex Coulton.