Multiple sequence alignment - TraesCS5B01G151700

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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 TraesCS5B01G151700 chr5B 100.000 4711 0 0 1 4711 280977501 280982211 0.000000e+00 8700.0
1 TraesCS5B01G151700 chr5D 94.848 4717 203 20 17 4711 246295456 246300154 0.000000e+00 7328.0
2 TraesCS5B01G151700 chr5A 96.184 3905 106 19 811 4711 330191361 330195226 0.000000e+00 6346.0
3 TraesCS5B01G151700 chr5A 83.892 627 64 13 437 1044 330169533 330170141 8.850000e-157 564.0
4 TraesCS5B01G151700 chr4D 75.000 400 75 18 420 798 281304277 281303882 1.360000e-35 161.0
5 TraesCS5B01G151700 chr4D 73.310 281 56 13 535 799 482769238 482769515 8.400000e-13 86.1
6 TraesCS5B01G151700 chr4B 86.916 107 12 2 2216 2321 653520760 653520865 8.280000e-23 119.0
7 TraesCS5B01G151700 chr7D 72.727 396 89 15 420 799 139748839 139748447 1.070000e-21 115.0
8 TraesCS5B01G151700 chr2A 72.796 397 87 15 420 799 729228081 729228473 1.070000e-21 115.0
9 TraesCS5B01G151700 chr2A 75.088 285 52 14 531 799 743570548 743570267 1.070000e-21 115.0
10 TraesCS5B01G151700 chr7A 72.074 376 84 15 441 799 189350452 189350823 5.020000e-15 93.5
11 TraesCS5B01G151700 chr3D 88.889 72 8 0 728 799 378776340 378776269 6.490000e-14 89.8
12 TraesCS5B01G151700 chr2D 88.889 72 8 0 728 799 617903688 617903617 6.490000e-14 89.8


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 TraesCS5B01G151700 chr5B 280977501 280982211 4710 False 8700 8700 100.000 1 4711 1 chr5B.!!$F1 4710
1 TraesCS5B01G151700 chr5D 246295456 246300154 4698 False 7328 7328 94.848 17 4711 1 chr5D.!!$F1 4694
2 TraesCS5B01G151700 chr5A 330191361 330195226 3865 False 6346 6346 96.184 811 4711 1 chr5A.!!$F2 3900
3 TraesCS5B01G151700 chr5A 330169533 330170141 608 False 564 564 83.892 437 1044 1 chr5A.!!$F1 607

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
99 100 0.046242 TGAGGTCCAGGATCCCCATT 59.954 55.0 8.55 0.0 33.88 3.16 F
162 163 0.249657 CCCTCTAATGCTCACTCCGC 60.250 60.0 0.00 0.0 0.00 5.54 F
315 316 0.325671 TGCTTGGCTCTAGCTAGGGT 60.326 55.0 21.71 0.0 41.70 4.34 F
416 417 0.391263 CCGCTCTGTTGGACCTAACC 60.391 60.0 0.00 0.0 0.00 2.85 F
2066 2096 0.694783 TGTAGGTTGGTGTGGGTCCA 60.695 55.0 0.00 0.0 0.00 4.02 F
2687 2717 0.179020 CCCCAGACAGCAAGAACACA 60.179 55.0 0.00 0.0 0.00 3.72 F
3077 3113 0.557729 GGGGTCATCCATCCATTGGT 59.442 55.0 1.86 0.0 46.52 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2096 1.076513 GATTAACACAACCCCCACCCT 59.923 52.381 0.0 0.0 0.00 4.34 R
2104 2134 2.769095 ACTCCCTACCAGAAGAGATTGC 59.231 50.000 0.0 0.0 0.00 3.56 R
2106 2136 4.482772 TCCTACTCCCTACCAGAAGAGATT 59.517 45.833 0.0 0.0 0.00 2.40 R
2329 2359 3.646162 TCTCGGTATTATGGCTCCAACAT 59.354 43.478 0.0 0.0 0.00 2.71 R
3077 3113 1.649321 AGAGCCTGTTGATCCTGTGA 58.351 50.000 0.0 0.0 0.00 3.58 R
3624 3660 2.234661 TGTGGCAGTAGTTCATCTGGAG 59.765 50.000 0.0 0.0 32.94 3.86 R
3968 4005 3.503827 TCTCCGTACACATCACATCAC 57.496 47.619 0.0 0.0 0.00 3.06 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
39 40 1.407025 GGGTTTCCTTCCTCTTAGGCG 60.407 57.143 0.00 0.00 34.61 5.52
45 46 1.134401 CCTTCCTCTTAGGCGATTGCA 60.134 52.381 7.38 0.00 45.35 4.08
68 69 2.298163 TCGTCTTCAAGTCCAACCTACC 59.702 50.000 0.00 0.00 0.00 3.18
71 72 2.038557 TCTTCAAGTCCAACCTACCTGC 59.961 50.000 0.00 0.00 0.00 4.85
88 89 3.691342 CGTTCGGCCTGAGGTCCA 61.691 66.667 0.00 0.00 0.00 4.02
97 98 1.003442 CTGAGGTCCAGGATCCCCA 59.997 63.158 8.55 0.00 39.23 4.96
99 100 0.046242 TGAGGTCCAGGATCCCCATT 59.954 55.000 8.55 0.00 33.88 3.16
104 105 1.149174 CCAGGATCCCCATTGTCCG 59.851 63.158 8.55 0.00 37.12 4.79
111 112 1.131303 TCCCCATTGTCCGTCTTGGT 61.131 55.000 0.00 0.00 39.52 3.67
115 116 1.375523 ATTGTCCGTCTTGGTCGGC 60.376 57.895 0.00 0.00 46.49 5.54
121 122 4.097361 GTCTTGGTCGGCCCTCCC 62.097 72.222 2.12 0.00 0.00 4.30
149 150 1.503784 ACCGGATGAAGATCCCCTCTA 59.496 52.381 9.46 0.00 45.12 2.43
158 159 3.342926 AGATCCCCTCTAATGCTCACT 57.657 47.619 0.00 0.00 30.26 3.41
162 163 0.249657 CCCTCTAATGCTCACTCCGC 60.250 60.000 0.00 0.00 0.00 5.54
271 272 3.050835 TGTCATGGTGGATGAGGATGAT 58.949 45.455 0.00 0.00 42.00 2.45
273 274 3.327172 GTCATGGTGGATGAGGATGATCT 59.673 47.826 0.00 0.00 42.00 2.75
293 294 5.480642 TCTAGAGATCAATGATGGCCTTC 57.519 43.478 11.69 11.69 0.00 3.46
294 295 4.903649 TCTAGAGATCAATGATGGCCTTCA 59.096 41.667 22.42 22.42 0.00 3.02
315 316 0.325671 TGCTTGGCTCTAGCTAGGGT 60.326 55.000 21.71 0.00 41.70 4.34
330 331 5.735766 AGCTAGGGTTCATACTCAGAAAAC 58.264 41.667 0.00 0.00 0.00 2.43
334 335 5.953571 AGGGTTCATACTCAGAAAACCTTT 58.046 37.500 0.00 0.00 39.45 3.11
335 336 7.086685 AGGGTTCATACTCAGAAAACCTTTA 57.913 36.000 0.00 0.00 39.45 1.85
360 361 6.326064 AGCCAATCTGTGTTCTATAGAGACAT 59.674 38.462 14.04 2.31 29.49 3.06
389 390 0.958091 TTGGAATCCGGTGCAAAGTG 59.042 50.000 0.00 0.00 0.00 3.16
401 402 1.235724 GCAAAGTGTAAGGTTCCGCT 58.764 50.000 0.00 0.00 0.00 5.52
406 407 1.692519 AGTGTAAGGTTCCGCTCTGTT 59.307 47.619 0.00 0.00 0.00 3.16
416 417 0.391263 CCGCTCTGTTGGACCTAACC 60.391 60.000 0.00 0.00 0.00 2.85
447 448 8.564574 TGCAACTTATCGAGTTATTTTTCACTT 58.435 29.630 0.00 0.00 46.75 3.16
481 482 1.661341 AAGCGGAGATTCATGCACTC 58.339 50.000 0.00 0.00 0.00 3.51
484 485 2.366590 AGCGGAGATTCATGCACTCATA 59.633 45.455 12.83 0.00 33.00 2.15
517 518 4.783227 ACCCTCACTATCCAACATACAACT 59.217 41.667 0.00 0.00 0.00 3.16
533 534 8.691661 ACATACAACTCTTTCAGTTATGGTTT 57.308 30.769 0.00 0.00 44.14 3.27
546 547 8.070034 TCAGTTATGGTTTAGTCGGATTCTTA 57.930 34.615 0.00 0.00 0.00 2.10
560 561 6.701841 GTCGGATTCTTATGAAGCACTATCAA 59.298 38.462 8.63 0.00 40.08 2.57
595 596 2.031560 TGCATTGATTCGTTCGGCATAC 59.968 45.455 0.00 0.00 0.00 2.39
639 640 8.980481 ATAAAAGAGTTGATGTGTAATAGGGG 57.020 34.615 0.00 0.00 0.00 4.79
640 641 6.388619 AAAGAGTTGATGTGTAATAGGGGT 57.611 37.500 0.00 0.00 0.00 4.95
679 682 5.808366 TTCACCAGTCAGAATAGAGTTGT 57.192 39.130 0.00 0.00 0.00 3.32
687 690 5.009210 AGTCAGAATAGAGTTGTAGATCGGC 59.991 44.000 0.00 0.00 0.00 5.54
701 704 1.618837 GATCGGCTGGCCAACTATAGA 59.381 52.381 7.01 0.90 35.37 1.98
718 721 8.651588 CAACTATAGATGCTCCGAATTTATCAC 58.348 37.037 6.78 0.00 0.00 3.06
726 729 4.212214 GCTCCGAATTTATCACTGATGTCC 59.788 45.833 1.42 0.00 0.00 4.02
763 766 1.425066 AGGATTTGTGGCCTCTCAACA 59.575 47.619 3.32 0.00 0.00 3.33
783 786 6.645003 TCAACAGTAACACTACTACAATGCAG 59.355 38.462 0.00 0.00 36.14 4.41
803 823 5.300792 TGCAGTAAAACTCCCTTTACCAAAG 59.699 40.000 3.28 0.00 40.97 2.77
847 867 9.045745 ACAAATACCCATGATTATGTTTTTCCT 57.954 29.630 0.00 0.00 32.21 3.36
883 903 8.023706 GCAACTTGTTAGAAAAAGAGATAAGGG 58.976 37.037 0.00 0.00 0.00 3.95
884 904 8.515414 CAACTTGTTAGAAAAAGAGATAAGGGG 58.485 37.037 0.00 0.00 0.00 4.79
991 1018 1.561643 CTAGCTGTGTTCTCCCTCCA 58.438 55.000 0.00 0.00 0.00 3.86
1098 1125 3.917760 GATGACGAGCCCTCCCGG 61.918 72.222 0.00 0.00 0.00 5.73
1533 1560 1.503542 GGCTGACTTGCACGATTGG 59.496 57.895 0.00 0.00 34.04 3.16
1536 1563 1.804151 GCTGACTTGCACGATTGGTTA 59.196 47.619 0.00 0.00 0.00 2.85
1582 1609 6.252995 ACAGCCTTAATTCAATTTAGGGACA 58.747 36.000 15.45 0.00 38.99 4.02
1714 1744 5.307196 TCCCTTGGTATGTAGCCTTTATCTC 59.693 44.000 0.00 0.00 0.00 2.75
1814 1844 2.641305 AGAATGGAGCATGCAGTTCTC 58.359 47.619 21.98 7.97 42.42 2.87
1836 1866 6.369340 TCTCGCATTTACTATGGAAAAACGAA 59.631 34.615 0.00 0.00 31.33 3.85
1837 1867 6.539324 TCGCATTTACTATGGAAAAACGAAG 58.461 36.000 0.00 0.00 29.76 3.79
1840 1870 7.535940 CGCATTTACTATGGAAAAACGAAGAAA 59.464 33.333 0.00 0.00 0.00 2.52
1841 1871 8.850452 GCATTTACTATGGAAAAACGAAGAAAG 58.150 33.333 0.00 0.00 0.00 2.62
1842 1872 9.893305 CATTTACTATGGAAAAACGAAGAAAGT 57.107 29.630 0.00 0.00 0.00 2.66
1912 1942 2.433145 ATGCACTCTGTGGCGTCG 60.433 61.111 0.00 0.00 33.64 5.12
1950 1980 9.344772 TGCTAACATTTCCTAGTTTTTCTACAA 57.655 29.630 0.00 0.00 0.00 2.41
2055 2085 3.009723 CTGCATAACTGGGTGTAGGTTG 58.990 50.000 0.00 0.00 0.00 3.77
2066 2096 0.694783 TGTAGGTTGGTGTGGGTCCA 60.695 55.000 0.00 0.00 0.00 4.02
2104 2134 8.345565 GTGTTAATCATGCAAGGGTATTTCTAG 58.654 37.037 0.00 0.00 0.00 2.43
2106 2136 4.502105 TCATGCAAGGGTATTTCTAGCA 57.498 40.909 0.00 0.00 34.78 3.49
2329 2359 5.682234 TTAGATCAGACAATGGAGCTCAA 57.318 39.130 17.19 4.05 31.35 3.02
2411 2441 4.020751 TCATTTCTCTCTGAGGACTGGTTG 60.021 45.833 4.59 0.00 0.00 3.77
2472 2502 1.338200 GGTTGCTCTCCACGATGAACT 60.338 52.381 0.00 0.00 0.00 3.01
2516 2546 6.765989 TCTCATGGAAAACTATAATTGACCCG 59.234 38.462 0.00 0.00 0.00 5.28
2625 2655 7.289782 AGAGAGATTCAAGCATAAGACCTACAT 59.710 37.037 0.00 0.00 0.00 2.29
2645 2675 5.883661 ACATGTGGATATGCTTTTCTTTCG 58.116 37.500 0.00 0.00 0.00 3.46
2687 2717 0.179020 CCCCAGACAGCAAGAACACA 60.179 55.000 0.00 0.00 0.00 3.72
3077 3113 0.557729 GGGGTCATCCATCCATTGGT 59.442 55.000 1.86 0.00 46.52 3.67
3153 3189 3.188460 GCAATAAGTCTCTTGTTTGCCGA 59.812 43.478 14.87 0.00 34.79 5.54
3814 3851 0.036858 AAGAACTTGCGAGCCTCTCC 60.037 55.000 0.00 0.00 0.00 3.71
3952 3989 6.519679 TCAATGCTTATCAACATGCTTCTT 57.480 33.333 0.00 0.00 0.00 2.52
3960 3997 7.627939 GCTTATCAACATGCTTCTTGAAGTGAT 60.628 37.037 11.41 12.84 30.32 3.06
3968 4005 9.107177 ACATGCTTCTTGAAGTGATAGAAATAG 57.893 33.333 11.41 0.00 0.00 1.73
3969 4006 9.107177 CATGCTTCTTGAAGTGATAGAAATAGT 57.893 33.333 11.41 0.00 0.00 2.12
3970 4007 8.484641 TGCTTCTTGAAGTGATAGAAATAGTG 57.515 34.615 11.41 0.00 0.00 2.74
3971 4008 8.314021 TGCTTCTTGAAGTGATAGAAATAGTGA 58.686 33.333 11.41 0.00 0.00 3.41
3972 4009 9.323985 GCTTCTTGAAGTGATAGAAATAGTGAT 57.676 33.333 11.41 0.00 0.00 3.06
4148 4185 5.285134 CCGTGTAAAACATTAGCCGATTTTG 59.715 40.000 0.00 0.00 0.00 2.44
4433 4470 4.421058 CGTACTGTTGATCGAATTCTCCA 58.579 43.478 3.52 0.00 0.00 3.86
4474 4511 5.476945 ACCTGCACCCTTAACTAATTTCTTG 59.523 40.000 0.00 0.00 0.00 3.02
4514 4551 7.502120 TTCTTTCTTTGTGGAGATTCTCTTG 57.498 36.000 13.22 0.00 0.00 3.02
4593 4630 8.480501 AGCCTGCATGAAACAGATAAATTTATT 58.519 29.630 11.92 0.00 37.32 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.580580 GGAAACCCTAATCTTGTGCATAGG 59.419 45.833 2.33 2.33 35.68 2.57
4 5 5.440610 AGGAAACCCTAATCTTGTGCATAG 58.559 41.667 0.00 0.00 30.72 2.23
5 6 5.450818 AGGAAACCCTAATCTTGTGCATA 57.549 39.130 0.00 0.00 30.72 3.14
6 7 4.322057 AGGAAACCCTAATCTTGTGCAT 57.678 40.909 0.00 0.00 30.72 3.96
7 8 3.806949 AGGAAACCCTAATCTTGTGCA 57.193 42.857 0.00 0.00 30.72 4.57
8 9 3.444034 GGAAGGAAACCCTAATCTTGTGC 59.556 47.826 0.00 0.00 32.65 4.57
9 10 4.923415 AGGAAGGAAACCCTAATCTTGTG 58.077 43.478 0.00 0.00 32.65 3.33
10 11 4.852697 AGAGGAAGGAAACCCTAATCTTGT 59.147 41.667 0.00 0.00 32.65 3.16
11 12 5.443230 AGAGGAAGGAAACCCTAATCTTG 57.557 43.478 0.00 0.00 32.65 3.02
12 13 6.158871 CCTAAGAGGAAGGAAACCCTAATCTT 59.841 42.308 0.00 0.00 37.67 2.40
13 14 5.668080 CCTAAGAGGAAGGAAACCCTAATCT 59.332 44.000 0.00 0.00 37.67 2.40
14 15 5.687970 GCCTAAGAGGAAGGAAACCCTAATC 60.688 48.000 0.00 0.00 37.67 1.75
15 16 4.166337 GCCTAAGAGGAAGGAAACCCTAAT 59.834 45.833 0.00 0.00 37.67 1.73
18 19 1.916874 GCCTAAGAGGAAGGAAACCCT 59.083 52.381 0.00 0.00 37.67 4.34
39 40 3.436704 TGGACTTGAAGACGATTGCAATC 59.563 43.478 26.42 26.42 0.00 2.67
45 46 3.771577 AGGTTGGACTTGAAGACGATT 57.228 42.857 0.00 0.00 0.00 3.34
55 56 0.763035 AACGCAGGTAGGTTGGACTT 59.237 50.000 0.00 0.00 0.00 3.01
68 69 4.379243 ACCTCAGGCCGAACGCAG 62.379 66.667 0.00 0.00 40.31 5.18
71 72 3.649277 CTGGACCTCAGGCCGAACG 62.649 68.421 0.00 0.00 39.76 3.95
88 89 0.326618 AGACGGACAATGGGGATCCT 60.327 55.000 12.58 0.00 0.00 3.24
104 105 4.097361 GGGAGGGCCGACCAAGAC 62.097 72.222 20.67 3.79 43.89 3.01
121 122 1.141881 CTTCATCCGGTGGAGGTCG 59.858 63.158 0.00 0.00 34.82 4.79
133 134 4.285517 TGAGCATTAGAGGGGATCTTCATC 59.714 45.833 0.00 0.00 39.64 2.92
137 138 3.645687 GAGTGAGCATTAGAGGGGATCTT 59.354 47.826 0.00 0.00 39.64 2.40
149 150 2.434884 CGTGGCGGAGTGAGCATT 60.435 61.111 0.00 0.00 36.08 3.56
215 216 9.140286 CTCTTCGTCATTAAGAACAAGTTGATA 57.860 33.333 10.54 0.00 32.77 2.15
253 254 4.776308 TCTAGATCATCCTCATCCACCATG 59.224 45.833 0.00 0.00 0.00 3.66
254 255 5.020941 TCTAGATCATCCTCATCCACCAT 57.979 43.478 0.00 0.00 0.00 3.55
271 272 4.903649 TGAAGGCCATCATTGATCTCTAGA 59.096 41.667 6.57 0.00 0.00 2.43
273 274 4.657504 ACTGAAGGCCATCATTGATCTCTA 59.342 41.667 11.80 0.00 0.00 2.43
282 283 1.471119 CAAGCACTGAAGGCCATCAT 58.529 50.000 11.80 0.00 0.00 2.45
283 284 0.609957 CCAAGCACTGAAGGCCATCA 60.610 55.000 10.80 10.80 0.00 3.07
289 290 2.011046 GCTAGAGCCAAGCACTGAAGG 61.011 57.143 0.00 0.00 39.83 3.46
290 291 1.066286 AGCTAGAGCCAAGCACTGAAG 60.066 52.381 0.00 0.00 42.62 3.02
293 294 1.202510 CCTAGCTAGAGCCAAGCACTG 60.203 57.143 22.70 0.00 42.62 3.66
294 295 1.118838 CCTAGCTAGAGCCAAGCACT 58.881 55.000 22.70 0.00 42.62 4.40
315 316 6.539173 TGGCTAAAGGTTTTCTGAGTATGAA 58.461 36.000 0.00 0.00 0.00 2.57
330 331 7.500992 TCTATAGAACACAGATTGGCTAAAGG 58.499 38.462 0.00 0.00 0.00 3.11
334 335 6.833933 TGTCTCTATAGAACACAGATTGGCTA 59.166 38.462 3.57 0.00 32.16 3.93
335 336 5.658634 TGTCTCTATAGAACACAGATTGGCT 59.341 40.000 3.57 0.00 32.16 4.75
360 361 1.221840 GGATTCCAAGCCGCTCTCA 59.778 57.895 0.00 0.00 0.00 3.27
389 390 1.001633 TCCAACAGAGCGGAACCTTAC 59.998 52.381 0.00 0.00 0.00 2.34
401 402 4.042311 TGCAAATAGGTTAGGTCCAACAGA 59.958 41.667 0.00 0.00 0.00 3.41
406 407 4.650972 AGTTGCAAATAGGTTAGGTCCA 57.349 40.909 0.00 0.00 0.00 4.02
442 443 4.379394 GCTTCCAATGCATCGTTAAAGTGA 60.379 41.667 0.00 0.00 0.00 3.41
447 448 1.400142 CCGCTTCCAATGCATCGTTAA 59.600 47.619 0.00 0.00 0.00 2.01
499 500 7.604164 ACTGAAAGAGTTGTATGTTGGATAGTG 59.396 37.037 0.00 0.00 37.43 2.74
500 501 7.680730 ACTGAAAGAGTTGTATGTTGGATAGT 58.319 34.615 0.00 0.00 37.43 2.12
517 518 6.349243 TCCGACTAAACCATAACTGAAAGA 57.651 37.500 0.00 0.00 37.43 2.52
533 534 5.854010 AGTGCTTCATAAGAATCCGACTA 57.146 39.130 0.00 0.00 32.31 2.59
546 547 9.399797 TGTTTGATAGAATTGATAGTGCTTCAT 57.600 29.630 0.00 0.00 0.00 2.57
560 561 8.192774 ACGAATCAATGCATTGTTTGATAGAAT 58.807 29.630 30.80 16.45 40.70 2.40
616 617 6.790319 ACCCCTATTACACATCAACTCTTTT 58.210 36.000 0.00 0.00 0.00 2.27
639 640 5.163561 TGGTGAATCTTCTGTGGACAAAAAC 60.164 40.000 0.00 0.00 0.00 2.43
640 641 4.952957 TGGTGAATCTTCTGTGGACAAAAA 59.047 37.500 0.00 0.00 0.00 1.94
679 682 1.717032 ATAGTTGGCCAGCCGATCTA 58.283 50.000 16.95 8.75 39.42 1.98
687 690 2.611473 CGGAGCATCTATAGTTGGCCAG 60.611 54.545 5.11 0.00 33.73 4.85
701 704 5.371526 ACATCAGTGATAAATTCGGAGCAT 58.628 37.500 5.03 0.00 0.00 3.79
718 721 1.270839 ACAAGGTGGAACGGACATCAG 60.271 52.381 0.00 0.00 38.12 2.90
726 729 3.328382 TCCTCAATACAAGGTGGAACG 57.672 47.619 0.00 0.00 38.12 3.95
763 766 8.985805 GTTTTACTGCATTGTAGTAGTGTTACT 58.014 33.333 13.28 0.00 42.66 2.24
783 786 8.252417 TGTTTTCTTTGGTAAAGGGAGTTTTAC 58.748 33.333 1.88 1.12 40.91 2.01
803 823 9.783256 GGTATTTGTATTCTGGTGTATGTTTTC 57.217 33.333 0.00 0.00 0.00 2.29
978 1005 1.210722 GGAGGAATGGAGGGAGAACAC 59.789 57.143 0.00 0.00 0.00 3.32
991 1018 0.324645 GTGGTGGCCATTGGAGGAAT 60.325 55.000 9.72 0.00 35.28 3.01
1714 1744 2.485426 CCAGGCATTGCATATACCTTCG 59.515 50.000 11.39 0.00 0.00 3.79
1814 1844 6.539324 TCTTCGTTTTTCCATAGTAAATGCG 58.461 36.000 0.00 0.00 0.00 4.73
1840 1870 8.523658 GTCCATTCCTTTGCTAATAAGAAAACT 58.476 33.333 0.00 0.00 0.00 2.66
1841 1871 8.523658 AGTCCATTCCTTTGCTAATAAGAAAAC 58.476 33.333 0.00 0.00 0.00 2.43
1842 1872 8.522830 CAGTCCATTCCTTTGCTAATAAGAAAA 58.477 33.333 0.00 0.00 0.00 2.29
1845 1875 6.599244 CACAGTCCATTCCTTTGCTAATAAGA 59.401 38.462 0.00 0.00 0.00 2.10
1846 1876 6.599244 TCACAGTCCATTCCTTTGCTAATAAG 59.401 38.462 0.00 0.00 0.00 1.73
1848 1878 6.061022 TCACAGTCCATTCCTTTGCTAATA 57.939 37.500 0.00 0.00 0.00 0.98
1849 1879 4.922206 TCACAGTCCATTCCTTTGCTAAT 58.078 39.130 0.00 0.00 0.00 1.73
1902 1932 2.049526 TACAGTGCGACGCCACAG 60.050 61.111 18.69 14.10 38.18 3.66
1912 1942 5.629435 GGAAATGTTAGCAAAACTACAGTGC 59.371 40.000 3.94 0.00 38.59 4.40
1974 2004 4.154195 CACGAAGGGTTAGAACAGGAAATG 59.846 45.833 0.00 0.00 0.00 2.32
2006 2036 5.124776 GCCATGGCTGTACTAACATAAACAA 59.875 40.000 29.98 0.00 38.26 2.83
2055 2085 3.966543 CCACCCTGGACCCACACC 61.967 72.222 0.00 0.00 40.96 4.16
2066 2096 1.076513 GATTAACACAACCCCCACCCT 59.923 52.381 0.00 0.00 0.00 4.34
2104 2134 2.769095 ACTCCCTACCAGAAGAGATTGC 59.231 50.000 0.00 0.00 0.00 3.56
2106 2136 4.482772 TCCTACTCCCTACCAGAAGAGATT 59.517 45.833 0.00 0.00 0.00 2.40
2329 2359 3.646162 TCTCGGTATTATGGCTCCAACAT 59.354 43.478 0.00 0.00 0.00 2.71
2340 2370 7.166167 GGTATTGGTCCAATTCTCGGTATTAT 58.834 38.462 22.13 0.00 35.54 1.28
2472 2502 7.933577 CCATGAGAGATTGTAAGCAAGGTTATA 59.066 37.037 0.00 0.00 38.10 0.98
2546 2576 5.946972 GGATAGTAGGCTATGCTCTAACTGA 59.053 44.000 0.00 0.00 41.17 3.41
2625 2655 5.245531 AGACGAAAGAAAAGCATATCCACA 58.754 37.500 0.00 0.00 0.00 4.17
2645 2675 2.164338 AGACCTCCGACTTGAGAAGAC 58.836 52.381 0.00 0.00 34.11 3.01
2681 2711 4.093850 ACCTGTCTAACAAAACGTGTGTTC 59.906 41.667 18.24 7.94 40.60 3.18
2900 2936 8.311836 ACTTCTAGATGTTTCCGTTTGAATAGA 58.688 33.333 5.47 0.00 31.67 1.98
3077 3113 1.649321 AGAGCCTGTTGATCCTGTGA 58.351 50.000 0.00 0.00 0.00 3.58
3624 3660 2.234661 TGTGGCAGTAGTTCATCTGGAG 59.765 50.000 0.00 0.00 32.94 3.86
3814 3851 6.430451 GTCACCTACAGTTTGTGAATTTCTG 58.570 40.000 6.45 0.00 40.41 3.02
3952 3989 9.538508 CATCACATCACTATTTCTATCACTTCA 57.461 33.333 0.00 0.00 0.00 3.02
3960 3997 7.067737 TCCGTACACATCACATCACTATTTCTA 59.932 37.037 0.00 0.00 0.00 2.10
3968 4005 3.503827 TCTCCGTACACATCACATCAC 57.496 47.619 0.00 0.00 0.00 3.06
3969 4006 4.219725 TCTTTCTCCGTACACATCACATCA 59.780 41.667 0.00 0.00 0.00 3.07
3970 4007 4.744570 TCTTTCTCCGTACACATCACATC 58.255 43.478 0.00 0.00 0.00 3.06
3971 4008 4.801330 TCTTTCTCCGTACACATCACAT 57.199 40.909 0.00 0.00 0.00 3.21
3972 4009 4.801330 ATCTTTCTCCGTACACATCACA 57.199 40.909 0.00 0.00 0.00 3.58
4260 4297 6.239064 GCCGTCCTCTTAGAAATCTGAATCTA 60.239 42.308 0.00 0.87 0.00 1.98
4514 4551 4.381411 AGGTAGACTGAAACAGAAACTGC 58.619 43.478 5.76 5.67 34.37 4.40


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

AutoCloner maintained by Alex Coulton.