Multiple sequence alignment - TraesCS1D01G113700

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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 TraesCS1D01G113700 chr1D 100.000 4515 0 0 1 4515 109976933 109972419 0.000000e+00 8338
1 TraesCS1D01G113700 chr1A 93.503 4294 150 36 1 4258 113862143 113857943 0.000000e+00 6264
2 TraesCS1D01G113700 chr1A 96.923 260 8 0 4256 4515 113857905 113857646 1.930000e-118 436
3 TraesCS1D01G113700 chr1B 93.630 4066 171 42 1 3995 166595605 166591557 0.000000e+00 5993
4 TraesCS1D01G113700 chr1B 93.657 268 9 2 4256 4515 166591068 166590801 1.180000e-105 394
5 TraesCS1D01G113700 chr1B 90.813 283 15 5 3978 4258 166591379 166591106 7.140000e-98 368
6 TraesCS1D01G113700 chr7A 93.061 245 17 0 3776 4020 149286837 149286593 4.290000e-95 359
7 TraesCS1D01G113700 chr7A 96.203 79 3 0 4010 4088 149284999 149284921 3.670000e-26 130
8 TraesCS1D01G113700 chr3B 79.085 306 49 12 2267 2563 79121444 79121743 3.560000e-46 196
9 TraesCS1D01G113700 chr3B 85.890 163 21 2 995 1155 79120327 79120489 6.000000e-39 172
10 TraesCS1D01G113700 chr3D 78.689 305 51 12 2267 2563 49639510 49639808 1.660000e-44 191
11 TraesCS1D01G113700 chr3D 85.802 162 22 1 995 1155 49638360 49638521 2.160000e-38 171
12 TraesCS1D01G113700 chr3A 85.890 163 21 2 995 1155 63065925 63066087 6.000000e-39 172
13 TraesCS1D01G113700 chr3A 77.346 309 52 15 2267 2563 63067031 63067333 2.790000e-37 167


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 TraesCS1D01G113700 chr1D 109972419 109976933 4514 True 8338.000000 8338 100.000 1 4515 1 chr1D.!!$R1 4514
1 TraesCS1D01G113700 chr1A 113857646 113862143 4497 True 3350.000000 6264 95.213 1 4515 2 chr1A.!!$R1 4514
2 TraesCS1D01G113700 chr1B 166590801 166595605 4804 True 2251.666667 5993 92.700 1 4515 3 chr1B.!!$R1 4514
3 TraesCS1D01G113700 chr7A 149284921 149286837 1916 True 244.500000 359 94.632 3776 4088 2 chr7A.!!$R1 312

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
87 88 0.179936 GAGAAGGCAGATCTGGTGGG 59.820 60.0 23.89 0.0 0.00 4.61 F
239 246 0.605319 GTGGTGATGAAGGACGGCAA 60.605 55.0 0.00 0.0 0.00 4.52 F
893 918 0.664761 ATTGGCTGATCGAAATGGCG 59.335 50.0 0.00 0.0 0.00 5.69 F
963 988 1.383523 GGGGAGGCTCGATCTTTTTG 58.616 55.0 8.69 0.0 0.00 2.44 F
2028 2072 0.034476 TCACTCCAGCTCTGCACTTG 59.966 55.0 0.00 0.0 0.00 3.16 F
2033 2077 0.036577 CCAGCTCTGCACTTGCTACT 60.037 55.0 2.33 0.0 42.66 2.57 F
2436 2509 0.394565 GCAGCCGGACTATCCAGATT 59.605 55.0 5.05 0.0 35.91 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1601 0.035317 TACACTCCAGGCAGCACAAG 59.965 55.000 0.00 0.0 0.0 3.16 R
1757 1798 0.317160 TCGTCAAGGTGGTAGCTGTG 59.683 55.000 0.00 0.0 0.0 3.66 R
1758 1799 0.603569 CTCGTCAAGGTGGTAGCTGT 59.396 55.000 0.00 0.0 0.0 4.40 R
2102 2168 1.282382 TAACCTGCACCCCTAACTCC 58.718 55.000 0.00 0.0 0.0 3.85 R
2981 3055 0.100503 AAACTGCACACGGAACAAGC 59.899 50.000 0.00 0.0 0.0 4.01 R
3503 3577 1.000717 ACGAAATTTTCACGCCCTTGG 60.001 47.619 9.66 0.0 0.0 3.61 R
4354 6307 1.140852 CGAGGGGCTGTTGGATTATCA 59.859 52.381 0.00 0.0 0.0 2.15 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
20 21 0.884704 GCTCTCGTGAAGGGTTTGCA 60.885 55.000 0.00 0.00 0.00 4.08
44 45 2.025981 TGGAAGGATGGTGGATTCAGTG 60.026 50.000 0.00 0.00 0.00 3.66
45 46 2.239654 GGAAGGATGGTGGATTCAGTGA 59.760 50.000 0.00 0.00 0.00 3.41
81 82 1.649321 TGTGTGGAGAAGGCAGATCT 58.351 50.000 0.00 0.00 0.00 2.75
87 88 0.179936 GAGAAGGCAGATCTGGTGGG 59.820 60.000 23.89 0.00 0.00 4.61
116 117 2.079158 TCCTAGGACGACACGTTACAG 58.921 52.381 7.62 0.00 41.37 2.74
197 204 2.294074 CCGACAGTTCTTTGGTTGGAA 58.706 47.619 0.00 0.00 38.17 3.53
200 207 3.625764 CGACAGTTCTTTGGTTGGAAGAA 59.374 43.478 0.00 0.00 39.95 2.52
218 225 5.616270 GAAGAACTTGTCTCTTCCTCCTTT 58.384 41.667 1.86 0.00 41.95 3.11
221 228 5.841783 AGAACTTGTCTCTTCCTCCTTTAGT 59.158 40.000 0.00 0.00 0.00 2.24
224 231 3.858135 TGTCTCTTCCTCCTTTAGTGGT 58.142 45.455 0.00 0.00 0.00 4.16
239 246 0.605319 GTGGTGATGAAGGACGGCAA 60.605 55.000 0.00 0.00 0.00 4.52
254 261 4.904590 CAACAACCGCCCCACCCA 62.905 66.667 0.00 0.00 0.00 4.51
255 262 4.906537 AACAACCGCCCCACCCAC 62.907 66.667 0.00 0.00 0.00 4.61
288 295 9.990868 AGGGACCTTGTTGTAATTTTCTATTAT 57.009 29.630 0.00 0.00 0.00 1.28
341 348 1.975407 GTCCCCTCTCGTCGGTTCA 60.975 63.158 0.00 0.00 0.00 3.18
379 386 1.203313 GTGGCGCGTGTTGTACTTC 59.797 57.895 8.43 0.00 0.00 3.01
410 417 1.004628 TGAATGTACACATGGCAGCCT 59.995 47.619 14.15 0.00 36.56 4.58
414 421 1.078497 TACACATGGCAGCCTTCGG 60.078 57.895 14.15 3.14 0.00 4.30
415 422 2.535485 TACACATGGCAGCCTTCGGG 62.535 60.000 14.15 4.41 38.37 5.14
416 423 4.431131 ACATGGCAGCCTTCGGGG 62.431 66.667 14.15 0.00 35.16 5.73
578 602 2.972505 CAAGCGACGTGGCCAACT 60.973 61.111 19.50 0.00 0.00 3.16
815 839 4.530857 CCCAGATCCACCGACGCC 62.531 72.222 0.00 0.00 0.00 5.68
864 889 1.208614 GTTTCTTGGCAGAGCGCTG 59.791 57.895 18.48 13.73 45.13 5.18
893 918 0.664761 ATTGGCTGATCGAAATGGCG 59.335 50.000 0.00 0.00 0.00 5.69
963 988 1.383523 GGGGAGGCTCGATCTTTTTG 58.616 55.000 8.69 0.00 0.00 2.44
1150 1175 6.767902 TGTGAGATCTAACTGTTTCTTGCTTT 59.232 34.615 11.67 0.00 0.00 3.51
1277 1303 8.562892 GGTTCAGATTATTAACACCAGATGATG 58.437 37.037 0.00 0.00 0.00 3.07
1328 1354 4.021544 GGAGTGCCAATTGAATTTGGTGTA 60.022 41.667 7.12 0.00 46.54 2.90
1331 1357 6.165577 AGTGCCAATTGAATTTGGTGTATTC 58.834 36.000 7.12 0.00 46.54 1.75
1480 1511 4.737855 ATGAACGAGGTTGTGTAGCTAT 57.262 40.909 0.00 0.00 33.94 2.97
1563 1601 6.037610 CAGATGGGAGTAGTATCTTTGTTTGC 59.962 42.308 0.00 0.00 0.00 3.68
1671 1712 7.994425 TGTTGCTTATTTCCTTGTGAATAGA 57.006 32.000 0.00 0.00 31.67 1.98
1680 1721 5.336150 TCCTTGTGAATAGAGAGAGCTTG 57.664 43.478 0.00 0.00 0.00 4.01
1757 1798 4.274950 TCCTTTGAGACGGAATTGTGTTTC 59.725 41.667 0.00 0.00 0.00 2.78
1758 1799 4.036262 CCTTTGAGACGGAATTGTGTTTCA 59.964 41.667 0.00 0.00 0.00 2.69
1814 1855 2.746362 CACTTTCTGCTCCCTTCATGTC 59.254 50.000 0.00 0.00 0.00 3.06
1937 1978 4.956075 AGTCTTGGTTTCAATTCTGTTGGT 59.044 37.500 0.00 0.00 31.75 3.67
1952 1993 6.497624 TCTGTTGGTTTTTACCAGGTACTA 57.502 37.500 0.00 0.00 41.35 1.82
1968 2009 5.859114 CAGGTACTACACATTATGCGATCTC 59.141 44.000 0.00 0.00 36.02 2.75
1970 2011 5.859114 GGTACTACACATTATGCGATCTCTG 59.141 44.000 0.00 0.00 0.00 3.35
1983 2024 5.664457 TGCGATCTCTGTACATTGATTCTT 58.336 37.500 10.71 0.00 0.00 2.52
2018 2062 5.760743 GGATTCCTAGTTAATTCACTCCAGC 59.239 44.000 0.00 0.00 0.00 4.85
2028 2072 0.034476 TCACTCCAGCTCTGCACTTG 59.966 55.000 0.00 0.00 0.00 3.16
2033 2077 0.036577 CCAGCTCTGCACTTGCTACT 60.037 55.000 2.33 0.00 42.66 2.57
2045 2089 4.753107 GCACTTGCTACTTTTGGTAGTACA 59.247 41.667 2.06 0.00 46.99 2.90
2046 2090 5.107065 GCACTTGCTACTTTTGGTAGTACAG 60.107 44.000 2.06 0.00 46.99 2.74
2061 2126 8.905660 TGGTAGTACAGCAGTAAAAATGTAAA 57.094 30.769 2.06 0.00 30.45 2.01
2102 2168 4.093850 GCGGTACAACAATAGTTACTTGGG 59.906 45.833 0.00 0.00 35.85 4.12
2112 2178 2.558974 AGTTACTTGGGGAGTTAGGGG 58.441 52.381 0.00 0.00 39.86 4.79
2132 2202 7.830848 AGGGGTGCAGGTTAATTATATCTAT 57.169 36.000 0.00 0.00 0.00 1.98
2271 2341 5.183904 ACTGATGCTGAATTGTCCTTTTACC 59.816 40.000 0.00 0.00 0.00 2.85
2356 2429 6.014584 AGGAAGAAGTTCAGGTTTGTGTTTTT 60.015 34.615 5.50 0.00 33.93 1.94
2436 2509 0.394565 GCAGCCGGACTATCCAGATT 59.605 55.000 5.05 0.00 35.91 2.40
2553 2626 1.806542 ACGACTTGCATCGCTCAAATT 59.193 42.857 9.55 0.00 46.22 1.82
2611 2684 5.935789 CACAAATCAAAATTTCCTGGCATCT 59.064 36.000 0.00 0.00 32.69 2.90
2648 2721 1.818060 TGGAATTTGCATCTGGTTCCG 59.182 47.619 0.00 0.00 40.89 4.30
2665 2738 4.381932 GGTTCCGGAATGAAGAATTTGCAT 60.382 41.667 22.04 0.00 0.00 3.96
2701 2774 8.635328 TGACTGTTCATTACTACTCTGTTACAA 58.365 33.333 0.00 0.00 0.00 2.41
2717 2790 8.284945 TCTGTTACAATCACGTATTACTACCT 57.715 34.615 0.00 0.00 0.00 3.08
2929 3003 1.574134 AACGTTGTGGTAAGTCACGG 58.426 50.000 0.00 0.00 40.31 4.94
2931 3005 1.136695 ACGTTGTGGTAAGTCACGGAA 59.863 47.619 0.00 0.00 40.31 4.30
2981 3055 6.968131 TGTTAATCTGTTTCTGATTCTCCG 57.032 37.500 5.43 0.00 34.69 4.63
3108 3182 1.743394 GTCCTGGGCCATCTTAAAACG 59.257 52.381 6.72 0.00 0.00 3.60
3503 3577 2.271800 CGATGTGGAGCTCAAAGTACC 58.728 52.381 17.19 0.00 0.00 3.34
3628 3702 5.733620 AATGAAGCAATGGACATTTCAGT 57.266 34.783 0.00 0.00 30.31 3.41
3629 3703 5.733620 ATGAAGCAATGGACATTTCAGTT 57.266 34.783 0.00 0.00 0.00 3.16
3630 3704 6.839124 ATGAAGCAATGGACATTTCAGTTA 57.161 33.333 0.00 0.00 0.00 2.24
3631 3705 6.012658 TGAAGCAATGGACATTTCAGTTAC 57.987 37.500 0.00 0.00 0.00 2.50
3632 3706 5.534278 TGAAGCAATGGACATTTCAGTTACA 59.466 36.000 0.00 0.00 0.00 2.41
3633 3707 6.040278 TGAAGCAATGGACATTTCAGTTACAA 59.960 34.615 0.00 0.00 0.00 2.41
3634 3708 6.017400 AGCAATGGACATTTCAGTTACAAG 57.983 37.500 0.00 0.00 0.00 3.16
3635 3709 5.536161 AGCAATGGACATTTCAGTTACAAGT 59.464 36.000 0.00 0.00 0.00 3.16
3636 3710 6.714810 AGCAATGGACATTTCAGTTACAAGTA 59.285 34.615 0.00 0.00 0.00 2.24
3637 3711 7.230510 AGCAATGGACATTTCAGTTACAAGTAA 59.769 33.333 0.00 0.00 0.00 2.24
3638 3712 8.028938 GCAATGGACATTTCAGTTACAAGTAAT 58.971 33.333 0.00 0.00 0.00 1.89
3639 3713 9.345517 CAATGGACATTTCAGTTACAAGTAATG 57.654 33.333 0.00 0.00 0.00 1.90
3640 3714 7.447374 TGGACATTTCAGTTACAAGTAATGG 57.553 36.000 10.12 0.00 29.95 3.16
3641 3715 7.227873 TGGACATTTCAGTTACAAGTAATGGA 58.772 34.615 10.12 0.00 29.95 3.41
3642 3716 7.174253 TGGACATTTCAGTTACAAGTAATGGAC 59.826 37.037 10.12 5.20 29.95 4.02
3643 3717 7.174253 GGACATTTCAGTTACAAGTAATGGACA 59.826 37.037 10.12 0.00 29.95 4.02
3644 3718 8.635765 ACATTTCAGTTACAAGTAATGGACAT 57.364 30.769 10.12 0.00 29.95 3.06
3645 3719 8.514594 ACATTTCAGTTACAAGTAATGGACATG 58.485 33.333 14.52 14.52 31.71 3.21
3646 3720 8.514594 CATTTCAGTTACAAGTAATGGACATGT 58.485 33.333 0.00 0.00 42.47 3.21
3647 3721 7.667043 TTCAGTTACAAGTAATGGACATGTC 57.333 36.000 17.91 17.91 39.20 3.06
3648 3722 6.764379 TCAGTTACAAGTAATGGACATGTCA 58.236 36.000 26.47 13.45 39.20 3.58
3649 3723 6.873605 TCAGTTACAAGTAATGGACATGTCAG 59.126 38.462 26.47 8.32 39.20 3.51
3730 3837 9.015367 TCTACCATGAAACTAGATAGCAGATAC 57.985 37.037 0.00 0.00 0.00 2.24
3916 4025 7.361457 TCAGATTTACCTTGGACCATAGTAG 57.639 40.000 0.00 0.00 0.00 2.57
4008 5914 4.042187 ACAGCTACAGTTCAAGGAGGAATT 59.958 41.667 0.00 0.00 0.00 2.17
4095 6001 5.506649 CGGTGCCTGTTTTTACTTACACATT 60.507 40.000 0.00 0.00 0.00 2.71
4215 6121 7.970384 TCAGTTTGCTAAATGTTCCGTTATAG 58.030 34.615 8.12 0.00 31.55 1.31
4308 6261 1.301677 CCACGCTCCCAAGAAAGCTC 61.302 60.000 0.00 0.00 36.35 4.09
4309 6262 0.603707 CACGCTCCCAAGAAAGCTCA 60.604 55.000 0.00 0.00 36.35 4.26
4440 6393 2.735762 GCTATCAGAAACCGCTTCTCGT 60.736 50.000 0.00 0.00 42.84 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.566231 GAATCCACCATCCTTCCACCT 59.434 52.381 0.00 0.00 0.00 4.00
44 45 2.854777 CACAATGTCGTCGAGGAAGATC 59.145 50.000 9.78 0.00 0.00 2.75
45 46 2.231478 ACACAATGTCGTCGAGGAAGAT 59.769 45.455 9.78 2.35 0.00 2.40
81 82 2.639673 TAGGACAACCCCACCCACCA 62.640 60.000 0.00 0.00 36.73 4.17
87 88 0.901580 TCGTCCTAGGACAACCCCAC 60.902 60.000 35.32 12.16 44.77 4.61
116 117 3.482472 CGTGAACGAGTAGCACATATCAC 59.518 47.826 0.00 0.00 43.02 3.06
171 172 0.307760 CAAAGAACTGTCGGTGCACC 59.692 55.000 26.78 26.78 0.00 5.01
197 204 5.841783 ACTAAAGGAGGAAGAGACAAGTTCT 59.158 40.000 0.00 0.00 37.23 3.01
200 207 4.284746 CCACTAAAGGAGGAAGAGACAAGT 59.715 45.833 0.00 0.00 0.00 3.16
212 219 4.508662 GTCCTTCATCACCACTAAAGGAG 58.491 47.826 2.50 0.00 44.53 3.69
218 225 0.535335 GCCGTCCTTCATCACCACTA 59.465 55.000 0.00 0.00 0.00 2.74
221 228 0.605319 GTTGCCGTCCTTCATCACCA 60.605 55.000 0.00 0.00 0.00 4.17
224 231 1.234821 GTTGTTGCCGTCCTTCATCA 58.765 50.000 0.00 0.00 0.00 3.07
260 267 5.701224 AGAAAATTACAACAAGGTCCCTGA 58.299 37.500 0.00 0.00 0.00 3.86
288 295 4.571984 CACAGACAAGAAACACATCTCACA 59.428 41.667 0.00 0.00 0.00 3.58
341 348 1.636988 GCGTGCCGTAGAACATACTT 58.363 50.000 0.00 0.00 0.00 2.24
379 386 1.181001 GTACATTCAGTCGAGCGTCG 58.819 55.000 0.00 1.67 42.10 5.12
389 396 1.402968 GGCTGCCATGTGTACATTCAG 59.597 52.381 15.17 14.68 37.40 3.02
451 475 5.028549 TGCCAAATTTGCCTTTTTGTAGA 57.971 34.783 12.92 0.00 32.23 2.59
578 602 9.162764 GATTAAAGGAAGCGGCAATTAGATATA 57.837 33.333 1.45 0.00 0.00 0.86
815 839 4.894772 CGAAACATACCGCGCGCG 62.895 66.667 43.73 43.73 39.44 6.86
864 889 4.189188 CAGCCAATCGCAGCAGCC 62.189 66.667 0.00 0.00 41.38 4.85
893 918 0.673022 CACCTGCAGGCAAGAGAGAC 60.673 60.000 33.06 0.00 39.32 3.36
947 972 2.162408 CCAACCAAAAAGATCGAGCCTC 59.838 50.000 0.00 0.00 0.00 4.70
963 988 0.465460 TCCAGACAACAGCACCAACC 60.465 55.000 0.00 0.00 0.00 3.77
1150 1175 3.250744 CGTAACGAATCAAGAAGCTGGA 58.749 45.455 0.00 0.00 0.00 3.86
1328 1354 7.921214 ACGAATCACAACAGATAGTTATCGAAT 59.079 33.333 0.00 0.00 38.74 3.34
1331 1357 6.129691 CGACGAATCACAACAGATAGTTATCG 60.130 42.308 0.00 0.00 38.74 2.92
1341 1372 0.179240 GCTGCGACGAATCACAACAG 60.179 55.000 0.00 0.00 0.00 3.16
1343 1374 0.443869 ATGCTGCGACGAATCACAAC 59.556 50.000 0.00 0.00 0.00 3.32
1563 1601 0.035317 TACACTCCAGGCAGCACAAG 59.965 55.000 0.00 0.00 0.00 3.16
1680 1721 6.760298 TCATATTCTCATTCACTTCTCAGCAC 59.240 38.462 0.00 0.00 0.00 4.40
1687 1728 6.709397 TGGCATCTCATATTCTCATTCACTTC 59.291 38.462 0.00 0.00 0.00 3.01
1738 1779 3.942115 TGTGAAACACAATTCCGTCTCAA 59.058 39.130 1.99 0.00 45.67 3.02
1742 1783 2.290641 AGCTGTGAAACACAATTCCGTC 59.709 45.455 6.08 0.00 45.67 4.79
1744 1785 3.364964 GGTAGCTGTGAAACACAATTCCG 60.365 47.826 0.00 0.00 45.67 4.30
1757 1798 0.317160 TCGTCAAGGTGGTAGCTGTG 59.683 55.000 0.00 0.00 0.00 3.66
1758 1799 0.603569 CTCGTCAAGGTGGTAGCTGT 59.396 55.000 0.00 0.00 0.00 4.40
1814 1855 4.092821 TCGAAAAACTTCATCCATAGTGCG 59.907 41.667 0.00 0.00 0.00 5.34
1937 1978 7.064847 CGCATAATGTGTAGTACCTGGTAAAAA 59.935 37.037 8.40 0.00 0.00 1.94
1952 1993 5.262588 TGTACAGAGATCGCATAATGTGT 57.737 39.130 0.00 0.00 0.00 3.72
1983 2024 9.710818 AATTAACTAGGAATCCTGACTAGTACA 57.289 33.333 12.96 0.00 44.76 2.90
2018 2062 2.880890 ACCAAAAGTAGCAAGTGCAGAG 59.119 45.455 6.00 0.00 45.16 3.35
2033 2077 8.228035 ACATTTTTACTGCTGTACTACCAAAA 57.772 30.769 2.52 7.65 0.00 2.44
2061 2126 1.439679 GCCTAGCGCAAGTAAGTGTT 58.560 50.000 11.47 0.00 41.68 3.32
2086 2152 6.296836 CCCTAACTCCCCAAGTAACTATTGTT 60.297 42.308 0.00 0.00 37.17 2.83
2102 2168 1.282382 TAACCTGCACCCCTAACTCC 58.718 55.000 0.00 0.00 0.00 3.85
2157 2227 3.342377 ACTCTAGCCAAAAGCCTTCTC 57.658 47.619 0.00 0.00 45.47 2.87
2271 2341 2.093288 TGGCCAGCTTTGTCATCTAGAG 60.093 50.000 0.00 0.00 0.00 2.43
2436 2509 2.358322 AAAGAAGCACGGAAAGGGAA 57.642 45.000 0.00 0.00 0.00 3.97
2553 2626 5.335897 GCAAAAGCTGTCATCAAAGGATACA 60.336 40.000 0.00 0.00 41.41 2.29
2648 2721 5.634859 ACGTCAAATGCAAATTCTTCATTCC 59.365 36.000 0.00 0.00 30.84 3.01
2665 2738 5.989168 AGTAATGAACAGTCATCACGTCAAA 59.011 36.000 0.00 0.00 44.02 2.69
2701 2774 7.062605 CACGACAAAAAGGTAGTAATACGTGAT 59.937 37.037 0.00 0.00 45.29 3.06
2717 2790 5.373981 ACTACAAAACCACACGACAAAAA 57.626 34.783 0.00 0.00 0.00 1.94
2929 3003 3.443099 AGAAGTTTGCCAAAGCTGTTC 57.557 42.857 0.00 0.00 40.80 3.18
2931 3005 3.893326 AAAGAAGTTTGCCAAAGCTGT 57.107 38.095 0.00 0.00 40.80 4.40
2981 3055 0.100503 AAACTGCACACGGAACAAGC 59.899 50.000 0.00 0.00 0.00 4.01
3257 3331 1.897560 AAAGCAAGGTACCTGCTGTC 58.102 50.000 28.36 15.64 39.06 3.51
3503 3577 1.000717 ACGAAATTTTCACGCCCTTGG 60.001 47.619 9.66 0.00 0.00 3.61
3628 3702 8.151596 TGTAACTGACATGTCCATTACTTGTAA 58.848 33.333 30.20 18.04 44.19 2.41
3629 3703 7.672240 TGTAACTGACATGTCCATTACTTGTA 58.328 34.615 30.20 18.28 44.19 2.41
3630 3704 6.530120 TGTAACTGACATGTCCATTACTTGT 58.470 36.000 30.20 14.76 46.15 3.16
3631 3705 7.433708 TTGTAACTGACATGTCCATTACTTG 57.566 36.000 30.20 14.33 38.07 3.16
3632 3706 8.635765 AATTGTAACTGACATGTCCATTACTT 57.364 30.769 30.20 21.78 38.07 2.24
3633 3707 9.733556 TTAATTGTAACTGACATGTCCATTACT 57.266 29.630 30.20 20.98 38.07 2.24
3637 3711 9.859427 CATTTTAATTGTAACTGACATGTCCAT 57.141 29.630 22.85 11.28 38.07 3.41
3638 3712 9.072375 TCATTTTAATTGTAACTGACATGTCCA 57.928 29.630 22.85 10.29 38.07 4.02
3916 4025 5.362556 ACTGAAATGTACATCACTTGCAC 57.637 39.130 9.23 0.00 0.00 4.57
4008 5914 2.929641 TGCTTCATCTGTGAAACACCA 58.070 42.857 0.00 0.00 45.67 4.17
4215 6121 8.907885 AGAGATGAATTATAGGTTTTTCCTTGC 58.092 33.333 0.00 0.00 45.67 4.01
4254 6160 2.901192 TCTGAAGAACCGGTGAACCATA 59.099 45.455 8.52 0.00 35.14 2.74
4354 6307 1.140852 CGAGGGGCTGTTGGATTATCA 59.859 52.381 0.00 0.00 0.00 2.15
4440 6393 5.240623 CACCATTCTGCTTTGTAGGTTTGTA 59.759 40.000 0.00 0.00 0.00 2.41
4491 6445 6.164417 CCTTTCATGCCCATCATTCAAATA 57.836 37.500 0.00 0.00 31.79 1.40


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

AutoCloner maintained by Alex Coulton.