Multiple sequence alignment - TraesCS4D01G158200

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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 TraesCS4D01G158200 chr4D 100.000 6338 0 0 1 6338 220470159 220463822 0.000000e+00 11705.0
1 TraesCS4D01G158200 chr4B 94.550 3376 128 20 1 3324 316665431 316662060 0.000000e+00 5164.0
2 TraesCS4D01G158200 chr4B 96.067 3026 76 12 3319 6338 316656355 316653367 0.000000e+00 4889.0
3 TraesCS4D01G158200 chr4B 81.553 206 26 10 56 257 285587182 285586985 6.580000e-35 159.0
4 TraesCS4D01G158200 chr4B 79.021 143 23 7 6108 6246 342842060 342842199 2.430000e-14 91.6
5 TraesCS4D01G158200 chr4A 94.617 2322 101 8 2590 4889 306318586 306316267 0.000000e+00 3574.0
6 TraesCS4D01G158200 chr4A 94.568 1841 48 14 783 2576 306320870 306319035 0.000000e+00 2798.0
7 TraesCS4D01G158200 chr4A 92.451 1126 47 9 4871 5970 306315911 306314798 0.000000e+00 1574.0
8 TraesCS4D01G158200 chr4A 88.114 774 64 16 1 763 306321694 306320938 0.000000e+00 894.0
9 TraesCS4D01G158200 chrUn 100.000 397 0 0 2250 2646 479107641 479107245 0.000000e+00 734.0
10 TraesCS4D01G158200 chr5B 90.847 295 18 1 4631 4925 33540378 33540093 2.770000e-103 387.0
11 TraesCS4D01G158200 chr5B 88.696 230 13 6 4928 5157 33538981 33538765 1.050000e-67 268.0
12 TraesCS4D01G158200 chr5B 80.000 220 32 12 56 270 367239521 367239309 1.100000e-32 152.0
13 TraesCS4D01G158200 chr5A 85.581 215 24 5 6040 6253 137284374 137284582 1.070000e-52 219.0
14 TraesCS4D01G158200 chr5A 80.357 224 29 12 56 270 412455118 412454901 8.510000e-34 156.0
15 TraesCS4D01G158200 chr7D 80.797 276 45 8 6045 6317 211881418 211881688 6.440000e-50 209.0
16 TraesCS4D01G158200 chr7D 80.995 221 28 12 56 270 326044400 326044188 5.080000e-36 163.0
17 TraesCS4D01G158200 chr1A 82.266 203 32 4 6045 6246 188142443 188142642 8.450000e-39 172.0
18 TraesCS4D01G158200 chr3B 81.364 220 30 11 56 270 317605067 317604854 1.090000e-37 169.0
19 TraesCS4D01G158200 chr1D 81.281 203 33 5 6045 6246 128522417 128522615 6.580000e-35 159.0
20 TraesCS4D01G158200 chr3A 80.455 220 31 12 56 270 283089044 283088832 2.370000e-34 158.0
21 TraesCS4D01G158200 chr2B 78.710 155 20 10 6103 6252 230336932 230337078 2.430000e-14 91.6
22 TraesCS4D01G158200 chr7B 77.852 149 26 7 6108 6252 227271726 227271581 1.130000e-12 86.1
23 TraesCS4D01G158200 chr6B 78.322 143 24 7 6108 6246 351023716 351023855 1.130000e-12 86.1


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 TraesCS4D01G158200 chr4D 220463822 220470159 6337 True 11705.0 11705 100.0000 1 6338 1 chr4D.!!$R1 6337
1 TraesCS4D01G158200 chr4B 316662060 316665431 3371 True 5164.0 5164 94.5500 1 3324 1 chr4B.!!$R3 3323
2 TraesCS4D01G158200 chr4B 316653367 316656355 2988 True 4889.0 4889 96.0670 3319 6338 1 chr4B.!!$R2 3019
3 TraesCS4D01G158200 chr4A 306314798 306321694 6896 True 2210.0 3574 92.4375 1 5970 4 chr4A.!!$R1 5969
4 TraesCS4D01G158200 chr5B 33538765 33540378 1613 True 327.5 387 89.7715 4631 5157 2 chr5B.!!$R2 526

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
310 316 0.340208 TCTCCTCTCCCCCTTCCTTC 59.660 60.000 0.00 0.0 0.00 3.46 F
539 545 1.378514 GGAAGGAGCGGCAATGGAA 60.379 57.895 1.45 0.0 0.00 3.53 F
1574 1695 0.684153 ACTGTTGCTGCCCAAGTTGT 60.684 50.000 1.45 0.0 33.21 3.32 F
1932 2061 0.037590 TTGGGTGTGTACTGATGGCC 59.962 55.000 0.00 0.0 0.00 5.36 F
2746 3309 1.202927 ACTTTGGCACCATGTACAGCT 60.203 47.619 0.33 0.0 0.00 4.24 F
3284 3849 1.070786 GGAACTCCGTGAGCCACAA 59.929 57.895 6.21 0.0 33.40 3.33 F
3399 3964 1.209747 CCAAACAGGCCCTAGGTCTAC 59.790 57.143 8.29 0.0 34.19 2.59 F
4674 5248 1.197721 GAGATTGTCAACAAGGTGCCG 59.802 52.381 1.69 0.0 39.47 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1695 1.227527 CGATCGCCCATGCTACCAA 60.228 57.895 0.26 0.0 34.43 3.67 R
1783 1912 1.860078 CGGAAAGGTCTCGTGCAAC 59.140 57.895 0.00 0.0 0.00 4.17 R
3145 3710 0.034089 TGTCTCTCTCGCCCTCATCA 60.034 55.000 0.00 0.0 0.00 3.07 R
3284 3849 0.676782 CCGCTTTCACCTCCCGAAAT 60.677 55.000 0.00 0.0 32.21 2.17 R
4003 4577 0.315568 GACGACCAGCAGAACTCAGT 59.684 55.000 0.00 0.0 0.00 3.41 R
4674 5248 0.394352 ATTCACCGCCACCAAGATCC 60.394 55.000 0.00 0.0 0.00 3.36 R
5295 7367 1.003580 TCTTCCTCATCAACCTGCACC 59.996 52.381 0.00 0.0 0.00 5.01 R
6070 8173 1.225373 TGGATTCCCCCTCCAAGATG 58.775 55.000 0.00 0.0 39.83 2.90 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
93 94 5.321927 TGGATTTGAGAAGAACCTTTACCC 58.678 41.667 0.00 0.00 0.00 3.69
123 124 2.224042 CCCCCTTTTGACTTGTTCTTGC 60.224 50.000 0.00 0.00 0.00 4.01
176 177 6.017400 AGTGATGTGTGATTTGGATTTGTC 57.983 37.500 0.00 0.00 0.00 3.18
184 185 6.016777 GTGTGATTTGGATTTGTCTGAGTCTT 60.017 38.462 0.00 0.00 0.00 3.01
198 203 4.022416 TCTGAGTCTTTCTCTCTCTTGTGC 60.022 45.833 0.00 0.00 43.13 4.57
301 307 2.612251 CCCCTCCTCTCCTCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
310 316 0.340208 TCTCCTCTCCCCCTTCCTTC 59.660 60.000 0.00 0.00 0.00 3.46
383 389 3.786809 CGTAGGTCGTTGAGCAAGA 57.213 52.632 0.00 0.00 31.89 3.02
409 415 4.555709 TGGGCAAACGTGACGGCT 62.556 61.111 10.66 0.00 31.03 5.52
479 485 1.558233 GAGGAGGAAGTCGGAGGAAA 58.442 55.000 0.00 0.00 0.00 3.13
483 489 2.448453 GAGGAAGTCGGAGGAAAGAGA 58.552 52.381 0.00 0.00 0.00 3.10
496 502 4.704103 AGAGAGGTGGCGGGCAGA 62.704 66.667 3.75 0.00 0.00 4.26
539 545 1.378514 GGAAGGAGCGGCAATGGAA 60.379 57.895 1.45 0.00 0.00 3.53
606 613 4.966787 GGTCGGTTGCAGGGCCAA 62.967 66.667 6.18 0.00 0.00 4.52
687 694 1.405121 CGCGGGTAGAAAAAGGTAGCT 60.405 52.381 0.00 0.00 0.00 3.32
698 705 6.311735 AGAAAAAGGTAGCTATTGGGTTTCA 58.688 36.000 15.91 0.00 0.00 2.69
720 730 3.286353 TGATGCAACCACTCTTTTGTGA 58.714 40.909 0.00 0.00 40.12 3.58
725 735 2.684881 CAACCACTCTTTTGTGACAGCT 59.315 45.455 0.00 0.00 40.12 4.24
753 763 5.114785 ACTACTCTATATTCGCTGCACTG 57.885 43.478 0.00 0.00 0.00 3.66
754 764 4.822350 ACTACTCTATATTCGCTGCACTGA 59.178 41.667 0.00 0.00 0.00 3.41
755 765 4.235939 ACTCTATATTCGCTGCACTGAG 57.764 45.455 0.00 0.00 0.00 3.35
757 767 3.222603 TCTATATTCGCTGCACTGAGGA 58.777 45.455 0.00 0.00 0.00 3.71
829 890 4.634004 TCGTGTGTGAAAATAATAGGGCTG 59.366 41.667 0.00 0.00 0.00 4.85
843 915 1.451936 GGCTGGGAGATGCGGTAAT 59.548 57.895 0.00 0.00 0.00 1.89
865 949 3.295228 CTTTTGGCACGAGTCCGCG 62.295 63.158 0.00 0.00 39.95 6.46
866 950 4.595538 TTTGGCACGAGTCCGCGT 62.596 61.111 4.92 0.00 46.88 6.01
1181 1268 1.862201 CTTCTTGTGGTGCGTTTCGTA 59.138 47.619 0.00 0.00 0.00 3.43
1269 1356 1.538512 CGGGCGAGGAATCTAATCGTA 59.461 52.381 0.00 0.00 38.66 3.43
1314 1401 5.130145 TGAATTGATTTTGTCCCCTTGTGTT 59.870 36.000 0.00 0.00 0.00 3.32
1574 1695 0.684153 ACTGTTGCTGCCCAAGTTGT 60.684 50.000 1.45 0.00 33.21 3.32
1679 1808 6.476053 GGCTCAGCAGTGTAGTAGTATAAAAC 59.524 42.308 0.00 0.00 0.00 2.43
1698 1827 1.820519 ACTTGGCACATGCAACCTATG 59.179 47.619 6.15 0.00 44.36 2.23
1726 1855 4.724399 TGAGCCTTAATGTTTTCAGGACA 58.276 39.130 0.00 0.00 29.03 4.02
1843 1972 8.328864 GTTCCTTTAGCGTGATAGTCATTTTAG 58.671 37.037 0.00 0.00 0.00 1.85
1892 2021 3.577649 TCCTTGTTGAGAGAACTAGCG 57.422 47.619 0.00 0.00 0.00 4.26
1932 2061 0.037590 TTGGGTGTGTACTGATGGCC 59.962 55.000 0.00 0.00 0.00 5.36
2022 2151 1.270839 TGTTGGCTAGTGTGGCTCTTC 60.271 52.381 0.00 0.00 0.00 2.87
2686 3248 8.025445 CCTCAAAATCTACCAAATTCTCAACTG 58.975 37.037 0.00 0.00 0.00 3.16
2714 3276 1.649664 CTCTGATTCCAGTTCCGCAG 58.350 55.000 0.00 0.00 41.16 5.18
2717 3279 3.983317 CTGATTCCAGTTCCGCAGGCA 62.983 57.143 0.00 0.00 41.04 4.75
2746 3309 1.202927 ACTTTGGCACCATGTACAGCT 60.203 47.619 0.33 0.00 0.00 4.24
2842 3406 2.666098 CCGTTCGGTGGGGAAGGAT 61.666 63.158 2.82 0.00 34.58 3.24
2965 3530 1.805945 CGTTACTGCCGTCCTCTGC 60.806 63.158 0.00 0.00 0.00 4.26
3142 3707 3.117512 GGCTGATGGGAGGGAGAAATAAA 60.118 47.826 0.00 0.00 0.00 1.40
3145 3710 5.760131 CTGATGGGAGGGAGAAATAAAAGT 58.240 41.667 0.00 0.00 0.00 2.66
3154 3719 4.339530 GGGAGAAATAAAAGTGATGAGGGC 59.660 45.833 0.00 0.00 0.00 5.19
3173 3738 2.080693 GCGAGAGAGACAAGAGAGACA 58.919 52.381 0.00 0.00 0.00 3.41
3284 3849 1.070786 GGAACTCCGTGAGCCACAA 59.929 57.895 6.21 0.00 33.40 3.33
3399 3964 1.209747 CCAAACAGGCCCTAGGTCTAC 59.790 57.143 8.29 0.00 34.19 2.59
3626 4193 5.350633 TGATGTTCTTGGCAAAAGTTTCTG 58.649 37.500 0.00 0.00 0.00 3.02
3881 4455 1.424302 CCCTCCATGGAAGCATCATCT 59.576 52.381 17.00 0.00 38.35 2.90
3886 4460 3.713248 TCCATGGAAGCATCATCTGTAGT 59.287 43.478 13.46 0.00 0.00 2.73
3900 4474 5.070981 TCATCTGTAGTTCCCTTCATCATCC 59.929 44.000 0.00 0.00 0.00 3.51
4003 4577 5.451937 CGAGTCTGGTGGCTAGATGAATTAA 60.452 44.000 0.00 0.00 0.00 1.40
4162 4736 8.567104 ACAAGAAAAACATTGGGAAATTATTGC 58.433 29.630 0.00 0.00 0.00 3.56
4674 5248 1.197721 GAGATTGTCAACAAGGTGCCG 59.802 52.381 1.69 0.00 39.47 5.69
4768 5342 9.181805 CATAGTCAAATTCTCATGAATCATTGC 57.818 33.333 0.00 0.00 41.62 3.56
5594 7666 7.878644 TGTACATGTTGTAACCAGCAGTAATTA 59.121 33.333 2.30 0.00 35.13 1.40
5636 7717 1.745087 ACCATCATGCCACGAAATCAC 59.255 47.619 0.00 0.00 0.00 3.06
5637 7718 1.268184 CCATCATGCCACGAAATCACG 60.268 52.381 0.00 0.00 39.31 4.35
5639 7720 1.075542 TCATGCCACGAAATCACGTC 58.924 50.000 0.00 0.00 44.76 4.34
5640 7721 0.795698 CATGCCACGAAATCACGTCA 59.204 50.000 0.00 0.00 44.76 4.35
5654 7735 2.159099 TCACGTCATTCAGATGTAGCCC 60.159 50.000 0.00 0.00 44.59 5.19
5770 7873 6.626302 AGAGAAATCTAGAGGAAAACACTCG 58.374 40.000 0.00 0.00 39.90 4.18
5772 7875 6.626302 AGAAATCTAGAGGAAAACACTCGAG 58.374 40.000 11.84 11.84 39.90 4.04
5805 7908 3.392947 TCACACCAACTACCCTCAAATCA 59.607 43.478 0.00 0.00 0.00 2.57
5840 7943 4.082787 AGGTACATTTTGCATCCAAGAACG 60.083 41.667 0.00 0.00 31.52 3.95
5845 7948 2.254546 TTGCATCCAAGAACGACACT 57.745 45.000 0.00 0.00 0.00 3.55
5913 8016 4.342665 GGAGAGATGGTTCGTCCTTAATCT 59.657 45.833 0.00 0.00 37.07 2.40
5914 8017 5.269505 AGAGATGGTTCGTCCTTAATCTG 57.730 43.478 0.00 0.00 37.07 2.90
5941 8044 7.939039 AAAGGATTCTTCCAAAAGGATTTTTCC 59.061 33.333 0.00 0.00 42.01 3.13
5985 8088 7.951347 ATGAGGAAATAAGATGAGCAAAACT 57.049 32.000 0.00 0.00 0.00 2.66
6070 8173 4.103311 ACCCTAGATGGCCTAATCTTTCAC 59.897 45.833 10.65 0.00 37.98 3.18
6072 8175 5.222007 CCCTAGATGGCCTAATCTTTCACAT 60.222 44.000 10.65 0.00 37.98 3.21
6234 8338 5.688807 AGTAAGGTCCATCTCAAATCCATG 58.311 41.667 0.00 0.00 0.00 3.66
6259 8363 4.078922 AGGACATGAGATCTTGGAGGTAGA 60.079 45.833 0.00 0.00 0.00 2.59
6274 8378 5.788533 TGGAGGTAGATAGTTCTTCCCAAAA 59.211 40.000 0.00 0.00 39.59 2.44
6294 8398 2.143602 ACTCTAGGAGAGATGGAGGCT 58.856 52.381 10.42 0.00 45.07 4.58
6327 8431 5.513094 CGAGAGGATATTCCAATAAAGGGCA 60.513 44.000 0.00 0.00 39.61 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.341209 GTCAAAAGGGGGAAGCACAAG 59.659 52.381 0.00 0.00 0.00 3.16
123 124 7.683437 AGCATACATGAGATCCACAAATATG 57.317 36.000 0.00 13.72 0.00 1.78
184 185 3.894427 ACTCAAGAGCACAAGAGAGAGAA 59.106 43.478 9.22 0.00 32.59 2.87
198 203 4.934602 GGAGAAAGGATGAACACTCAAGAG 59.065 45.833 0.00 0.00 34.49 2.85
301 307 4.115199 CCTGCGGGGAAGGAAGGG 62.115 72.222 2.57 0.00 36.91 3.95
336 342 1.075896 GAGGAGAGGGACCCGACAT 60.076 63.158 4.40 0.00 0.00 3.06
383 389 0.889186 ACGTTTGCCCAGCTCGATTT 60.889 50.000 0.00 0.00 0.00 2.17
427 433 2.884207 GCGTCGGATCCGGACAAC 60.884 66.667 32.79 21.98 40.25 3.32
479 485 4.704103 TCTGCCCGCCACCTCTCT 62.704 66.667 0.00 0.00 0.00 3.10
595 601 2.601367 GCTCCTTTGGCCCTGCAA 60.601 61.111 0.00 0.00 0.00 4.08
603 610 2.056223 CCATGGCCAGCTCCTTTGG 61.056 63.158 13.05 8.43 38.78 3.28
606 613 4.809496 CGCCATGGCCAGCTCCTT 62.809 66.667 30.79 0.00 37.98 3.36
673 680 7.463431 TGAAACCCAATAGCTACCTTTTTCTA 58.537 34.615 0.00 0.00 0.00 2.10
698 705 3.890756 TCACAAAAGAGTGGTTGCATCAT 59.109 39.130 0.00 0.00 39.93 2.45
720 730 0.034380 TAGAGTAGTCGGGCAGCTGT 60.034 55.000 16.64 0.00 0.00 4.40
725 735 2.486982 GCGAATATAGAGTAGTCGGGCA 59.513 50.000 6.98 0.00 35.84 5.36
779 816 1.717194 TTAAGCACGAAAGGCTACCG 58.283 50.000 6.87 6.87 41.66 4.02
781 818 4.851010 TGTTTTTAAGCACGAAAGGCTAC 58.149 39.130 0.00 0.00 41.66 3.58
786 823 6.020995 ACACGAATTGTTTTTAAGCACGAAAG 60.021 34.615 0.00 0.00 33.09 2.62
829 890 5.048713 CCAAAAGATAATTACCGCATCTCCC 60.049 44.000 0.00 0.00 0.00 4.30
843 915 2.343101 CGGACTCGTGCCAAAAGATAA 58.657 47.619 0.00 0.00 0.00 1.75
865 949 0.533308 TCCACCAACTTACACGGCAC 60.533 55.000 0.00 0.00 0.00 5.01
866 950 0.180642 TTCCACCAACTTACACGGCA 59.819 50.000 0.00 0.00 0.00 5.69
867 951 1.265905 CTTTCCACCAACTTACACGGC 59.734 52.381 0.00 0.00 0.00 5.68
868 952 2.546789 GTCTTTCCACCAACTTACACGG 59.453 50.000 0.00 0.00 0.00 4.94
869 953 3.199677 TGTCTTTCCACCAACTTACACG 58.800 45.455 0.00 0.00 0.00 4.49
873 959 6.015350 TGTTTTGTTGTCTTTCCACCAACTTA 60.015 34.615 0.00 0.00 39.30 2.24
987 1074 1.808411 TCCTCATCTTTGACGCAACC 58.192 50.000 0.00 0.00 0.00 3.77
994 1081 3.307975 CCCAGCTTCTTCCTCATCTTTGA 60.308 47.826 0.00 0.00 0.00 2.69
1269 1356 3.248602 CACTAGCGAGACAAAGCAAAAGT 59.751 43.478 0.00 0.00 35.48 2.66
1314 1401 2.217750 CATCCACCACAAACGAACTCA 58.782 47.619 0.00 0.00 0.00 3.41
1574 1695 1.227527 CGATCGCCCATGCTACCAA 60.228 57.895 0.26 0.00 34.43 3.67
1679 1808 2.093890 TCATAGGTTGCATGTGCCAAG 58.906 47.619 2.07 0.00 41.18 3.61
1698 1827 7.031975 CCTGAAAACATTAAGGCTCAAGATTC 58.968 38.462 0.00 0.00 0.00 2.52
1783 1912 1.860078 CGGAAAGGTCTCGTGCAAC 59.140 57.895 0.00 0.00 0.00 4.17
1843 1972 8.584600 CACAAGTCATGTTACGAGAAGTATTAC 58.415 37.037 0.00 0.00 41.46 1.89
1892 2021 2.686558 AAATGTGTGCACGATGTCAC 57.313 45.000 13.13 4.04 0.00 3.67
1932 2061 8.126700 AGTAACAGACATAAACAAAAACTTCCG 58.873 33.333 0.00 0.00 0.00 4.30
2022 2151 6.369890 ACAGAATACAACATAACACAGAGCAG 59.630 38.462 0.00 0.00 0.00 4.24
2646 3208 1.285280 TTGAGGACATCCGAATGGGT 58.715 50.000 0.00 0.00 42.08 4.51
2686 3248 1.330655 TGGAATCAGAGGGAGTCGGC 61.331 60.000 0.00 0.00 41.45 5.54
2717 3279 0.102300 GGTGCCAAAGTTCACGCTTT 59.898 50.000 0.00 0.00 39.05 3.51
2746 3309 2.109834 ACCAACCCATGAAGACCATTCA 59.890 45.455 0.00 0.00 31.94 2.57
2772 3335 4.142038 ACGAGCCAAGTCCTAACAAAATT 58.858 39.130 0.00 0.00 0.00 1.82
2925 3490 2.048222 CCTTCTGGCGCTGTTCGA 60.048 61.111 7.64 0.00 41.67 3.71
2950 3515 3.449227 CCGCAGAGGACGGCAGTA 61.449 66.667 0.00 0.00 44.90 2.74
3012 3577 1.135527 TCGCCCTACTCACCGTTATTG 59.864 52.381 0.00 0.00 0.00 1.90
3039 3604 1.153369 ATCCACAATCGCAGACGGG 60.153 57.895 0.00 0.00 42.51 5.28
3142 3707 1.110442 CTCTCTCGCCCTCATCACTT 58.890 55.000 0.00 0.00 0.00 3.16
3145 3710 0.034089 TGTCTCTCTCGCCCTCATCA 60.034 55.000 0.00 0.00 0.00 3.07
3154 3719 2.677836 CCTGTCTCTCTTGTCTCTCTCG 59.322 54.545 0.00 0.00 0.00 4.04
3173 3738 1.680651 CAGAGCGAGTCTCCACCCT 60.681 63.158 0.00 0.00 42.90 4.34
3284 3849 0.676782 CCGCTTTCACCTCCCGAAAT 60.677 55.000 0.00 0.00 32.21 2.17
3881 4455 3.104512 ACGGATGATGAAGGGAACTACA 58.895 45.455 0.00 0.00 42.68 2.74
3886 4460 5.630415 AGAATTACGGATGATGAAGGGAA 57.370 39.130 0.00 0.00 0.00 3.97
3900 4474 3.688272 CAGCAGCCATGAAAGAATTACG 58.312 45.455 0.00 0.00 0.00 3.18
3990 4564 6.760770 AGCAGAACTCAGTTAATTCATCTAGC 59.239 38.462 0.00 0.00 0.00 3.42
4003 4577 0.315568 GACGACCAGCAGAACTCAGT 59.684 55.000 0.00 0.00 0.00 3.41
4128 4702 6.072728 TCCCAATGTTTTTCTTGTACTCATCG 60.073 38.462 0.00 0.00 0.00 3.84
4131 4705 7.411486 TTTCCCAATGTTTTTCTTGTACTCA 57.589 32.000 0.00 0.00 0.00 3.41
4162 4736 2.877168 GCTGATACATCTTGAGCCTTGG 59.123 50.000 0.00 0.00 0.00 3.61
4674 5248 0.394352 ATTCACCGCCACCAAGATCC 60.394 55.000 0.00 0.00 0.00 3.36
4768 5342 9.727403 CATTAATAACATGCTCGTTACTTATCG 57.273 33.333 0.00 0.00 34.31 2.92
4886 5849 7.584987 TGCTAAGAAAATTTAACTCTGCTGAC 58.415 34.615 15.57 0.00 0.00 3.51
5177 7249 1.291184 TGAAATCACAGCTGGCGTCG 61.291 55.000 19.93 0.75 0.00 5.12
5295 7367 1.003580 TCTTCCTCATCAACCTGCACC 59.996 52.381 0.00 0.00 0.00 5.01
5484 7556 6.587990 CACATCCTAGTCAGTTAAGTCAACAG 59.412 42.308 0.00 0.00 39.81 3.16
5594 7666 8.178313 TGGTCACGACATGATATACTAGAAAT 57.822 34.615 0.00 0.00 40.28 2.17
5636 7717 2.477825 CTGGGCTACATCTGAATGACG 58.522 52.381 0.00 0.00 36.67 4.35
5637 7718 2.216898 GCTGGGCTACATCTGAATGAC 58.783 52.381 0.00 0.00 36.67 3.06
5638 7719 1.839354 TGCTGGGCTACATCTGAATGA 59.161 47.619 0.00 0.00 36.67 2.57
5639 7720 2.336945 TGCTGGGCTACATCTGAATG 57.663 50.000 0.00 0.00 38.93 2.67
5640 7721 2.928334 CTTGCTGGGCTACATCTGAAT 58.072 47.619 0.00 0.00 0.00 2.57
5654 7735 1.530720 TCGTACACACATTGCTTGCTG 59.469 47.619 0.00 0.00 0.00 4.41
5805 7908 6.266558 TGCAAAATGTACCTGTATTGACCTTT 59.733 34.615 0.00 0.00 0.00 3.11
5840 7943 8.727910 CCTTTGGTTACCTTTATTTCTAGTGTC 58.272 37.037 2.07 0.00 0.00 3.67
5897 8000 4.285003 TCCTTTCAGATTAAGGACGAACCA 59.715 41.667 0.00 0.00 44.72 3.67
5941 8044 4.827835 TCATAGAGGATGAAGACCTAACGG 59.172 45.833 0.00 0.00 41.80 4.44
5978 8081 4.837972 ACTAGATCTTGAGGGAGTTTTGC 58.162 43.478 11.29 0.00 0.00 3.68
5985 8088 6.814954 AAGCATAAACTAGATCTTGAGGGA 57.185 37.500 11.29 0.00 0.00 4.20
6020 8123 4.745620 ACTCTTCGTAGTTCTTGCACTTTC 59.254 41.667 0.00 0.00 0.00 2.62
6070 8173 1.225373 TGGATTCCCCCTCCAAGATG 58.775 55.000 0.00 0.00 39.83 2.90
6072 8175 3.530685 TTGGATTCCCCCTCCAAGA 57.469 52.632 0.00 0.00 45.56 3.02
6189 8293 5.707764 ACTCTTCTTGCTATTTTCCTTGGAC 59.292 40.000 0.00 0.00 0.00 4.02
6197 8301 6.779860 TGGACCTTACTCTTCTTGCTATTTT 58.220 36.000 0.00 0.00 0.00 1.82
6234 8338 2.368221 CCTCCAAGATCTCATGTCCTCC 59.632 54.545 0.00 0.00 0.00 4.30
6246 8350 5.841783 GGGAAGAACTATCTACCTCCAAGAT 59.158 44.000 0.00 0.00 33.46 2.40
6259 8363 6.960542 TCTCCTAGAGTTTTGGGAAGAACTAT 59.039 38.462 0.00 0.00 36.31 2.12
6274 8378 2.143602 AGCCTCCATCTCTCCTAGAGT 58.856 52.381 3.98 0.00 42.83 3.24
6294 8398 4.653801 TGGAATATCCTCTCGTGGATTCAA 59.346 41.667 11.25 0.00 43.79 2.69
6312 8416 7.018150 TGGATATCAATGCCCTTTATTGGAAT 58.982 34.615 4.83 0.00 36.44 3.01


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

AutoCloner maintained by Alex Coulton.