Multiple sequence alignment - TraesCS4A01G428600

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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 TraesCS4A01G428600 chr4A 100.000 4553 0 0 1 4553 699792967 699797519 0.000000e+00 8408
1 TraesCS4A01G428600 chr4A 92.000 1975 116 20 2020 3972 699844472 699846426 0.000000e+00 2734
2 TraesCS4A01G428600 chr4A 84.515 1298 136 36 3022 4298 699851306 699852559 0.000000e+00 1223
3 TraesCS4A01G428600 chr4A 86.013 622 43 22 1420 2026 699803581 699804173 1.080000e-175 627
4 TraesCS4A01G428600 chr4A 91.083 157 14 0 2871 3027 699850617 699850773 3.570000e-51 213
5 TraesCS4A01G428600 chr4A 89.510 143 10 4 4050 4187 699846446 699846588 4.680000e-40 176
6 TraesCS4A01G428600 chr7D 90.778 4652 247 85 1 4553 29875945 29871377 0.000000e+00 6047
7 TraesCS4A01G428600 chr7D 89.157 1660 155 14 2669 4326 29861899 29860263 0.000000e+00 2045
8 TraesCS4A01G428600 chr7A 90.623 2570 134 44 1 2528 30137907 30135403 0.000000e+00 3312
9 TraesCS4A01G428600 chr7A 85.775 1167 131 19 3175 4326 30134678 30133532 0.000000e+00 1203
10 TraesCS4A01G428600 chr7A 88.548 620 53 10 2534 3143 30135294 30134683 0.000000e+00 736
11 TraesCS4A01G428600 chr1B 79.378 611 67 20 1 589 53999594 54000167 4.300000e-100 375
12 TraesCS4A01G428600 chr6B 85.855 304 31 7 362 663 456578152 456578445 3.420000e-81 313
13 TraesCS4A01G428600 chrUn 88.235 238 27 1 438 675 231905398 231905162 2.680000e-72 283
14 TraesCS4A01G428600 chr3D 86.473 207 14 4 398 600 203918297 203918101 9.920000e-52 215
15 TraesCS4A01G428600 chr2B 92.308 143 11 0 534 676 102553163 102553021 2.150000e-48 204
16 TraesCS4A01G428600 chr5B 91.971 137 11 0 534 670 561794935 561795071 4.650000e-45 193
17 TraesCS4A01G428600 chr4B 90.210 143 14 0 534 676 610015044 610014902 2.160000e-43 187
18 TraesCS4A01G428600 chr3B 90.210 143 14 0 534 676 604555028 604555170 2.160000e-43 187


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 TraesCS4A01G428600 chr4A 699792967 699797519 4552 False 8408.000000 8408 100.000000 1 4553 1 chr4A.!!$F1 4552
1 TraesCS4A01G428600 chr4A 699844472 699846588 2116 False 1455.000000 2734 90.755000 2020 4187 2 chr4A.!!$F3 2167
2 TraesCS4A01G428600 chr4A 699850617 699852559 1942 False 718.000000 1223 87.799000 2871 4298 2 chr4A.!!$F4 1427
3 TraesCS4A01G428600 chr4A 699803581 699804173 592 False 627.000000 627 86.013000 1420 2026 1 chr4A.!!$F2 606
4 TraesCS4A01G428600 chr7D 29871377 29875945 4568 True 6047.000000 6047 90.778000 1 4553 1 chr7D.!!$R2 4552
5 TraesCS4A01G428600 chr7D 29860263 29861899 1636 True 2045.000000 2045 89.157000 2669 4326 1 chr7D.!!$R1 1657
6 TraesCS4A01G428600 chr7A 30133532 30137907 4375 True 1750.333333 3312 88.315333 1 4326 3 chr7A.!!$R1 4325
7 TraesCS4A01G428600 chr1B 53999594 54000167 573 False 375.000000 375 79.378000 1 589 1 chr1B.!!$F1 588

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
869 900 0.108756 GAGTGGGCTTCGAGTGGTAC 60.109 60.0 0.0 0.0 0.00 3.34 F
1402 1472 0.595588 ATGGAATCAACGCAACGCAA 59.404 45.0 0.0 0.0 0.00 4.85 F
2661 2875 0.249911 AGTTGGTGTGAGAAGTCGCC 60.250 55.0 0.0 0.0 31.59 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1851 0.392729 GAGGCTGAGAGCTGCAACAT 60.393 55.0 1.02 0.0 41.99 2.71 R
3070 3828 0.039437 ACACGTAGAGGTCAGCAACG 60.039 55.0 0.00 0.0 39.37 4.10 R
4517 5365 0.103208 CTCCTCGAAACCTAGCGCAT 59.897 55.0 11.47 0.0 0.00 4.73 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
40 41 1.694150 CAACACTGGACAGAGGGAGAA 59.306 52.381 6.29 0.00 0.00 2.87
68 69 1.002274 AGGACACCTAGAGGGGCAG 59.998 63.158 0.00 0.00 44.30 4.85
72 73 0.910088 ACACCTAGAGGGGCAGTTCC 60.910 60.000 0.00 0.00 44.30 3.62
73 74 0.909610 CACCTAGAGGGGCAGTTCCA 60.910 60.000 0.00 0.00 40.27 3.53
106 112 4.590918 TCAACACTTACCCTTGTTTCACA 58.409 39.130 0.00 0.00 33.59 3.58
119 125 2.286125 TGTTTCACACAGCAATTCGACG 60.286 45.455 0.00 0.00 0.00 5.12
136 142 3.339061 CGGCATCGTTACACTAGCA 57.661 52.632 0.00 0.00 0.00 3.49
137 143 0.921347 CGGCATCGTTACACTAGCAC 59.079 55.000 0.00 0.00 0.00 4.40
138 144 1.734377 CGGCATCGTTACACTAGCACA 60.734 52.381 0.00 0.00 0.00 4.57
139 145 2.550978 GGCATCGTTACACTAGCACAT 58.449 47.619 0.00 0.00 0.00 3.21
140 146 2.285220 GGCATCGTTACACTAGCACATG 59.715 50.000 0.00 0.00 0.00 3.21
141 147 3.186909 GCATCGTTACACTAGCACATGA 58.813 45.455 0.00 0.00 0.00 3.07
142 148 3.000322 GCATCGTTACACTAGCACATGAC 60.000 47.826 0.00 0.00 0.00 3.06
143 149 4.424626 CATCGTTACACTAGCACATGACT 58.575 43.478 0.00 0.00 0.00 3.41
144 150 5.578776 CATCGTTACACTAGCACATGACTA 58.421 41.667 0.00 0.00 0.00 2.59
145 151 5.632244 TCGTTACACTAGCACATGACTAA 57.368 39.130 0.00 0.00 0.00 2.24
146 152 6.016213 TCGTTACACTAGCACATGACTAAA 57.984 37.500 0.00 0.00 0.00 1.85
147 153 6.448852 TCGTTACACTAGCACATGACTAAAA 58.551 36.000 0.00 0.00 0.00 1.52
148 154 6.924612 TCGTTACACTAGCACATGACTAAAAA 59.075 34.615 0.00 0.00 0.00 1.94
166 176 1.395635 AAAAACCCACAACGACCTCC 58.604 50.000 0.00 0.00 0.00 4.30
172 182 1.762957 CCCACAACGACCTCCATATCT 59.237 52.381 0.00 0.00 0.00 1.98
182 192 4.155826 CGACCTCCATATCTAGAGAGCAAG 59.844 50.000 0.00 0.00 31.43 4.01
185 195 4.467082 CCTCCATATCTAGAGAGCAAGCAT 59.533 45.833 0.00 0.00 31.43 3.79
200 211 4.640201 AGCAAGCATACAACACGGATAATT 59.360 37.500 0.00 0.00 0.00 1.40
233 244 0.178964 TTCCAGAGGGCCAAACAAGG 60.179 55.000 6.18 0.00 0.00 3.61
393 424 3.845259 GCGGAGGGCATCACGGTA 61.845 66.667 0.08 0.00 42.87 4.02
478 509 4.228567 GGGCGGTAGAGCTCCTGC 62.229 72.222 10.93 12.58 37.29 4.85
767 798 2.670148 CCCTCCACTAGCCACCACC 61.670 68.421 0.00 0.00 0.00 4.61
768 799 1.918293 CCTCCACTAGCCACCACCA 60.918 63.158 0.00 0.00 0.00 4.17
869 900 0.108756 GAGTGGGCTTCGAGTGGTAC 60.109 60.000 0.00 0.00 0.00 3.34
870 901 0.830444 AGTGGGCTTCGAGTGGTACA 60.830 55.000 0.00 0.00 0.00 2.90
898 929 2.434359 GTTGGGTTCTCTCGGCGG 60.434 66.667 7.21 0.00 0.00 6.13
963 995 2.612251 GGGGGAGAGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
964 996 2.123033 GGGGAGAGGAGAGGGAGC 60.123 72.222 0.00 0.00 0.00 4.70
1330 1380 2.408835 CGCCCATTTCGGTGATGC 59.591 61.111 0.00 0.00 35.25 3.91
1349 1399 1.337823 GCGATCCACCCAACGCTATAT 60.338 52.381 0.00 0.00 46.06 0.86
1353 1403 4.438880 CGATCCACCCAACGCTATATAGAG 60.439 50.000 14.16 12.76 0.00 2.43
1354 1404 4.108501 TCCACCCAACGCTATATAGAGA 57.891 45.455 18.98 0.00 0.00 3.10
1355 1405 4.476297 TCCACCCAACGCTATATAGAGAA 58.524 43.478 18.98 0.00 0.00 2.87
1356 1406 4.523173 TCCACCCAACGCTATATAGAGAAG 59.477 45.833 18.98 10.61 0.00 2.85
1357 1407 4.523173 CCACCCAACGCTATATAGAGAAGA 59.477 45.833 18.98 0.00 0.00 2.87
1380 1450 1.694169 ACTGGATACTGGGGCCTGG 60.694 63.158 0.84 0.00 40.36 4.45
1402 1472 0.595588 ATGGAATCAACGCAACGCAA 59.404 45.000 0.00 0.00 0.00 4.85
1455 1525 5.385198 TCAATGGGGGAAATGCTAACTATC 58.615 41.667 0.00 0.00 0.00 2.08
1516 1587 1.281867 CAGTAGGAGCATTGGGGAACA 59.718 52.381 0.00 0.00 0.00 3.18
1528 1599 2.875296 TGGGGAACATCTGTTGGAAAG 58.125 47.619 0.00 0.00 38.56 2.62
1552 1645 1.866059 GCGGTTATTTTGTCGGCGC 60.866 57.895 0.00 0.00 0.00 6.53
1574 1667 2.799562 GCTGTTTTGTGGGAGCAGTTTC 60.800 50.000 0.00 0.00 0.00 2.78
1576 1669 3.096092 TGTTTTGTGGGAGCAGTTTCTT 58.904 40.909 0.00 0.00 0.00 2.52
1577 1670 3.130340 TGTTTTGTGGGAGCAGTTTCTTC 59.870 43.478 0.00 0.00 0.00 2.87
1610 1704 8.893727 GCTGTTCAGTATTAGGTGATAAATGTT 58.106 33.333 1.78 0.00 0.00 2.71
1640 1734 2.543012 CTCCATCATCTGTCATTCGTGC 59.457 50.000 0.00 0.00 0.00 5.34
1676 1770 1.798813 GCGCGTGCTATATTAGGCTTT 59.201 47.619 15.02 0.00 38.39 3.51
1696 1790 8.102676 AGGCTTTGCTTGTTATAAATGGAAAAT 58.897 29.630 0.00 0.00 0.00 1.82
1756 1851 6.189133 GTTTTATACCCCACAACCCTCATAA 58.811 40.000 0.00 0.00 0.00 1.90
1816 1911 4.468643 TGAACCGCGAATTTTGATACAAC 58.531 39.130 8.23 0.00 0.00 3.32
1818 1913 2.814919 ACCGCGAATTTTGATACAACCA 59.185 40.909 8.23 0.00 0.00 3.67
1906 2001 2.093106 AGGGTCTAATATAGCTCGCCG 58.907 52.381 0.00 0.00 0.00 6.46
1962 2057 5.067954 TGTCCCTTACTTGGTTCTTTTAGC 58.932 41.667 0.00 0.00 0.00 3.09
2066 2164 5.398176 TGTTGACACGTTTATGTTCTGTC 57.602 39.130 0.00 0.00 31.24 3.51
2120 2219 2.752903 GCATCAACCAAAGGATACCGTT 59.247 45.455 0.00 0.00 37.17 4.44
2122 2221 2.156098 TCAACCAAAGGATACCGTTGC 58.844 47.619 10.09 0.00 40.65 4.17
2296 2395 0.671251 TCCGCCGCTCATTTGTTTTT 59.329 45.000 0.00 0.00 0.00 1.94
2332 2431 4.761739 TGTTCTTGGGTCTTCTTAATGCAG 59.238 41.667 0.00 0.00 0.00 4.41
2339 2438 6.480763 TGGGTCTTCTTAATGCAGTTAATGA 58.519 36.000 0.00 0.00 32.12 2.57
2340 2439 6.374333 TGGGTCTTCTTAATGCAGTTAATGAC 59.626 38.462 0.00 6.53 32.12 3.06
2470 2569 4.119442 TCAGATTGTACGCTTTACCTCC 57.881 45.455 0.00 0.00 0.00 4.30
2496 2595 4.865365 CCTGAATCTCTTACGGTTGTCTTC 59.135 45.833 0.00 0.00 0.00 2.87
2661 2875 0.249911 AGTTGGTGTGAGAAGTCGCC 60.250 55.000 0.00 0.00 31.59 5.54
2685 2901 6.704050 CCGGTTAAATAAATTATTGGGCTTGG 59.296 38.462 0.00 0.00 0.00 3.61
2689 2905 9.660180 GTTAAATAAATTATTGGGCTTGGTTGA 57.340 29.630 0.00 0.00 0.00 3.18
2716 2932 4.142138 TGGTCACTGCGGTTATTTTTGTTT 60.142 37.500 0.00 0.00 0.00 2.83
2717 2933 4.806775 GGTCACTGCGGTTATTTTTGTTTT 59.193 37.500 0.00 0.00 0.00 2.43
2876 3092 7.446625 AGTGTTCTTATTTCAACTCTGAATGCT 59.553 33.333 0.00 0.00 41.22 3.79
3033 3791 3.007614 TGTCCAAGTCTGGCTTAGTTACC 59.992 47.826 0.00 0.00 43.17 2.85
3055 3813 4.092968 CCGAAATGTCCACTACAAAGCTAC 59.907 45.833 0.00 0.00 42.70 3.58
3070 3828 5.180680 ACAAAGCTACCGTTGAAAAGTATCC 59.819 40.000 2.92 0.00 34.97 2.59
3137 3903 1.217882 AGCGTGTACACAGTGAAAGC 58.782 50.000 24.98 17.30 0.00 3.51
3212 3978 7.118496 TGCTTTCCTAGTTTTGAATTTCCAA 57.882 32.000 0.00 0.00 0.00 3.53
3280 4046 6.647334 TCAACTGCATATTTGTTTCTCCAA 57.353 33.333 0.00 0.00 0.00 3.53
3583 4372 1.066716 CCAATGTGTTCCTGGCAATGG 60.067 52.381 0.00 0.00 0.00 3.16
3619 4408 3.691118 GGTCTCAGTTGCATGCTTCATTA 59.309 43.478 20.33 0.00 0.00 1.90
3628 4417 4.025360 TGCATGCTTCATTATTTCCCAGT 58.975 39.130 20.33 0.00 0.00 4.00
3705 4494 6.035327 CCTTTTGTCTTTCTTTTTCTGTGCAG 59.965 38.462 0.00 0.00 0.00 4.41
4007 4809 1.838112 TGTTGCCTTAGCCTGATTGG 58.162 50.000 0.00 0.00 38.69 3.16
4011 4813 1.017387 GCCTTAGCCTGATTGGTTCG 58.983 55.000 0.00 0.00 38.35 3.95
4013 4815 2.280628 CCTTAGCCTGATTGGTTCGAC 58.719 52.381 0.00 0.00 38.35 4.20
4079 4883 7.177392 GCCTATTTTATTCTGGCATTATGAGGT 59.823 37.037 0.00 0.00 42.79 3.85
4125 4934 4.439426 GCATGCGTGGGTTGTTTGAATATA 60.439 41.667 8.27 0.00 0.00 0.86
4175 4984 6.956202 AAATCAGATTGGATCCAAGATGAC 57.044 37.500 31.64 20.66 39.47 3.06
4176 4985 5.641789 ATCAGATTGGATCCAAGATGACA 57.358 39.130 31.64 19.34 39.47 3.58
4200 5009 7.615365 ACAACATGTCATTGTAATCCTATGGTT 59.385 33.333 0.00 0.00 38.51 3.67
4201 5010 8.469200 CAACATGTCATTGTAATCCTATGGTTT 58.531 33.333 0.00 0.00 0.00 3.27
4202 5011 8.593945 ACATGTCATTGTAATCCTATGGTTTT 57.406 30.769 0.00 0.00 0.00 2.43
4203 5012 9.034800 ACATGTCATTGTAATCCTATGGTTTTT 57.965 29.630 0.00 0.00 0.00 1.94
4234 5043 8.690203 TTGTTCTAGTGAAATGGATCAAAGAA 57.310 30.769 0.00 0.00 34.09 2.52
4236 5045 6.992063 TCTAGTGAAATGGATCAAAGAAGC 57.008 37.500 0.00 0.00 0.00 3.86
4242 5051 3.550437 ATGGATCAAAGAAGCGCTAGT 57.450 42.857 12.05 0.00 0.00 2.57
4264 5073 1.293924 GCATCACTTCCGTGGATCTG 58.706 55.000 0.00 0.00 41.53 2.90
4273 5095 2.376109 TCCGTGGATCTGTAACTCCTC 58.624 52.381 0.00 0.00 32.47 3.71
4286 5108 0.539051 ACTCCTCCGAAATGCAGAGG 59.461 55.000 11.77 11.77 0.00 3.69
4298 5120 0.320683 TGCAGAGGACCAATGTGTCG 60.321 55.000 0.00 0.00 36.07 4.35
4326 5149 9.581099 TTCTTTCCTTCAACATTTTTGAGTAAC 57.419 29.630 0.00 0.00 0.00 2.50
4327 5150 8.966868 TCTTTCCTTCAACATTTTTGAGTAACT 58.033 29.630 0.00 0.00 0.00 2.24
4330 5153 9.621629 TTCCTTCAACATTTTTGAGTAACTAGA 57.378 29.630 0.00 0.00 0.00 2.43
4331 5154 9.621629 TCCTTCAACATTTTTGAGTAACTAGAA 57.378 29.630 0.00 0.00 0.00 2.10
4377 5225 1.623542 GGTGGTCGGCTAGGGATTGT 61.624 60.000 0.00 0.00 0.00 2.71
4439 5287 3.503363 GCATGCTGTCAGGCCGAC 61.503 66.667 11.37 17.43 43.58 4.79
4447 5295 2.678580 TCAGGCCGACGTGATGGA 60.679 61.111 0.00 0.00 35.83 3.41
4450 5298 2.509336 GGCCGACGTGATGGACAG 60.509 66.667 0.00 0.00 31.69 3.51
4452 5300 1.805945 GCCGACGTGATGGACAGTC 60.806 63.158 0.00 0.00 0.00 3.51
4474 5322 2.677228 CAGACCCATTTCGCCCCT 59.323 61.111 0.00 0.00 0.00 4.79
4475 5323 1.750399 CAGACCCATTTCGCCCCTG 60.750 63.158 0.00 0.00 0.00 4.45
4479 5327 0.106719 ACCCATTTCGCCCCTGTATG 60.107 55.000 0.00 0.00 0.00 2.39
4484 5332 0.916086 TTTCGCCCCTGTATGTGGAT 59.084 50.000 0.00 0.00 0.00 3.41
4486 5334 1.796017 TCGCCCCTGTATGTGGATTA 58.204 50.000 0.00 0.00 0.00 1.75
4498 5346 3.951563 TGTGGATTAGATTTGGGGGAG 57.048 47.619 0.00 0.00 0.00 4.30
4531 5379 2.097396 CGAACATATGCGCTAGGTTTCG 60.097 50.000 9.73 13.66 34.62 3.46
4541 5389 2.630592 CTAGGTTTCGAGGAGCCCGC 62.631 65.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.656112 CCTCTAGGTGTCCTCCATTTATGT 59.344 45.833 0.00 0.00 34.61 2.29
68 69 7.538303 AAGTGTTGAAACATTGAAATGGAAC 57.462 32.000 7.87 5.61 41.59 3.62
72 73 7.209475 AGGGTAAGTGTTGAAACATTGAAATG 58.791 34.615 0.00 1.45 41.59 2.32
73 74 7.360113 AGGGTAAGTGTTGAAACATTGAAAT 57.640 32.000 0.00 0.00 41.59 2.17
106 112 2.089854 GATGCCGTCGAATTGCTGT 58.910 52.632 0.00 0.00 0.00 4.40
119 125 2.004583 TGTGCTAGTGTAACGATGCC 57.995 50.000 0.00 0.00 45.86 4.40
147 153 1.341187 TGGAGGTCGTTGTGGGTTTTT 60.341 47.619 0.00 0.00 0.00 1.94
148 154 0.256464 TGGAGGTCGTTGTGGGTTTT 59.744 50.000 0.00 0.00 0.00 2.43
149 155 0.476771 ATGGAGGTCGTTGTGGGTTT 59.523 50.000 0.00 0.00 0.00 3.27
150 156 1.354101 TATGGAGGTCGTTGTGGGTT 58.646 50.000 0.00 0.00 0.00 4.11
151 157 1.485066 GATATGGAGGTCGTTGTGGGT 59.515 52.381 0.00 0.00 0.00 4.51
162 172 3.831333 TGCTTGCTCTCTAGATATGGAGG 59.169 47.826 0.50 0.00 0.00 4.30
166 176 7.116090 GTGTTGTATGCTTGCTCTCTAGATATG 59.884 40.741 0.00 0.00 0.00 1.78
172 182 3.511699 CGTGTTGTATGCTTGCTCTCTA 58.488 45.455 0.00 0.00 0.00 2.43
182 192 9.677567 AATTTGATAATTATCCGTGTTGTATGC 57.322 29.630 20.29 0.00 32.25 3.14
200 211 5.536161 GCCCTCTGGAATGCTTAATTTGATA 59.464 40.000 0.00 0.00 0.00 2.15
233 244 0.317020 GTAGGCCGCAAAATCATCGC 60.317 55.000 0.00 0.00 0.00 4.58
268 279 5.874261 TGTCATGCAAAGATCGAGATTTGTA 59.126 36.000 20.12 17.63 38.41 2.41
392 423 1.605058 GCCTCGGTTCCTGCTCTGTA 61.605 60.000 0.00 0.00 0.00 2.74
393 424 2.948720 GCCTCGGTTCCTGCTCTGT 61.949 63.158 0.00 0.00 0.00 3.41
862 893 1.692519 ACGCCTTCTTCTTGTACCACT 59.307 47.619 0.00 0.00 0.00 4.00
869 900 1.266989 GAACCCAACGCCTTCTTCTTG 59.733 52.381 0.00 0.00 0.00 3.02
870 901 1.143073 AGAACCCAACGCCTTCTTCTT 59.857 47.619 0.00 0.00 0.00 2.52
898 929 1.908299 CCTTTTGCCCCTGGGTCAC 60.908 63.158 12.71 1.08 37.65 3.67
1236 1281 2.511145 CGGAAGAGGAGCAGCTGC 60.511 66.667 31.53 31.53 42.49 5.25
1237 1282 2.511145 GCGGAAGAGGAGCAGCTG 60.511 66.667 10.11 10.11 0.00 4.24
1238 1283 3.780173 GGCGGAAGAGGAGCAGCT 61.780 66.667 0.00 0.00 0.00 4.24
1330 1380 2.743636 ATATAGCGTTGGGTGGATCG 57.256 50.000 0.00 0.00 0.00 3.69
1349 1399 5.419155 CCAGTATCCAGTGTGTTCTTCTCTA 59.581 44.000 0.00 0.00 0.00 2.43
1353 1403 3.600388 CCCAGTATCCAGTGTGTTCTTC 58.400 50.000 0.00 0.00 0.00 2.87
1354 1404 2.305927 CCCCAGTATCCAGTGTGTTCTT 59.694 50.000 0.00 0.00 0.00 2.52
1355 1405 1.909302 CCCCAGTATCCAGTGTGTTCT 59.091 52.381 0.00 0.00 0.00 3.01
1356 1406 1.679032 GCCCCAGTATCCAGTGTGTTC 60.679 57.143 0.00 0.00 0.00 3.18
1357 1407 0.328258 GCCCCAGTATCCAGTGTGTT 59.672 55.000 0.00 0.00 0.00 3.32
1380 1450 1.882198 CGTTGCGTTGATTCCATCAC 58.118 50.000 0.00 0.00 39.39 3.06
1402 1472 1.153568 CACCCACTGATCATCGCGT 60.154 57.895 5.77 0.00 0.00 6.01
1455 1525 5.521906 TTGCTACTAGAGACAGGCATAAG 57.478 43.478 0.00 0.00 0.00 1.73
1516 1587 2.066262 CGCGTGTACTTTCCAACAGAT 58.934 47.619 0.00 0.00 0.00 2.90
1528 1599 2.472723 CCGACAAAATAACCGCGTGTAC 60.473 50.000 4.92 0.00 0.00 2.90
1552 1645 1.283793 CTGCTCCCACAAAACAGCG 59.716 57.895 0.00 0.00 34.39 5.18
1574 1667 7.653713 ACCTAATACTGAACAGCATATTCGAAG 59.346 37.037 3.35 0.00 0.00 3.79
1576 1669 6.923508 CACCTAATACTGAACAGCATATTCGA 59.076 38.462 1.46 0.00 0.00 3.71
1577 1670 6.923508 TCACCTAATACTGAACAGCATATTCG 59.076 38.462 1.46 0.00 0.00 3.34
1610 1704 0.397675 AGATGATGGAGCTGGTCGGA 60.398 55.000 0.00 0.00 0.00 4.55
1651 1745 1.583856 CTAATATAGCACGCGCCGATG 59.416 52.381 5.73 0.00 39.83 3.84
1696 1790 4.702831 TGCATCCGTATCAGCAAGATTAA 58.297 39.130 0.00 0.00 38.19 1.40
1756 1851 0.392729 GAGGCTGAGAGCTGCAACAT 60.393 55.000 1.02 0.00 41.99 2.71
1818 1913 0.489567 AGACAAGGGAGTCCAGTCCT 59.510 55.000 19.25 2.99 39.59 3.85
1902 1997 1.438651 TTCTTTGGAATCTCACGGCG 58.561 50.000 4.80 4.80 0.00 6.46
1906 2001 6.877611 TGGTAGTTTTCTTTGGAATCTCAC 57.122 37.500 0.00 0.00 0.00 3.51
1940 2035 4.153655 CGCTAAAAGAACCAAGTAAGGGAC 59.846 45.833 0.00 0.00 0.00 4.46
1941 2036 4.202388 ACGCTAAAAGAACCAAGTAAGGGA 60.202 41.667 0.00 0.00 0.00 4.20
1951 2046 3.805971 ACACTGTACACGCTAAAAGAACC 59.194 43.478 0.00 0.00 0.00 3.62
2046 2144 4.870991 TGTGACAGAACATAAACGTGTCAA 59.129 37.500 5.11 0.00 46.69 3.18
2066 2164 6.931281 TCTGAAAGAGAACTGGAATAACTGTG 59.069 38.462 0.00 0.00 38.67 3.66
2120 2219 4.996758 CCAAATATATGATCCAGTGTCGCA 59.003 41.667 0.00 0.00 0.00 5.10
2122 2221 6.459066 ACTCCAAATATATGATCCAGTGTCG 58.541 40.000 0.00 0.00 0.00 4.35
2296 2395 6.775629 AGACCCAAGAACAAATAGTGCTAAAA 59.224 34.615 0.00 0.00 33.87 1.52
2332 2431 5.751243 ACACCAACTGAAGTGTCATTAAC 57.249 39.130 0.00 0.00 43.62 2.01
2340 2439 4.307432 CAGTACCTACACCAACTGAAGTG 58.693 47.826 0.00 0.00 41.47 3.16
2470 2569 4.822026 ACAACCGTAAGAGATTCAGGAAG 58.178 43.478 0.00 0.00 43.02 3.46
2496 2595 9.237846 GGAACTTCTTTCTTCTACACAAAATTG 57.762 33.333 0.00 0.00 34.26 2.32
2605 2810 8.101309 TCTGGGATGAAATTTAATACTCAGGA 57.899 34.615 12.75 0.33 0.00 3.86
2661 2875 7.269316 ACCAAGCCCAATAATTTATTTAACCG 58.731 34.615 0.00 0.00 0.00 4.44
2685 2901 0.798776 CCGCAGTGACCAGAATCAAC 59.201 55.000 0.00 0.00 0.00 3.18
2689 2905 3.350219 AATAACCGCAGTGACCAGAAT 57.650 42.857 0.00 0.00 0.00 2.40
2863 3079 1.250328 TGGGCAAGCATTCAGAGTTG 58.750 50.000 0.00 0.00 0.00 3.16
2876 3092 1.757118 TCGGTTCAAATTGTTGGGCAA 59.243 42.857 0.00 0.00 41.89 4.52
3033 3791 4.092968 GGTAGCTTTGTAGTGGACATTTCG 59.907 45.833 0.00 0.00 38.07 3.46
3055 3813 2.482721 AGCAACGGATACTTTTCAACGG 59.517 45.455 0.00 0.00 0.00 4.44
3070 3828 0.039437 ACACGTAGAGGTCAGCAACG 60.039 55.000 0.00 0.00 39.37 4.10
3137 3903 8.048534 ACAATAATGAACTGGATCAACTCAAG 57.951 34.615 0.00 0.00 32.06 3.02
3173 3939 7.939039 ACTAGGAAAGCATAATATTAAGCTGCA 59.061 33.333 22.20 8.23 37.71 4.41
3212 3978 2.906389 TGGAGTGGACAGAGCTTTGTAT 59.094 45.455 10.30 0.00 0.00 2.29
3280 4046 4.864704 ATCGGGCAACAACTAAACAAAT 57.135 36.364 0.00 0.00 39.74 2.32
3589 4378 1.300620 CAACTGAGACCGGCGACAA 60.301 57.895 9.30 0.00 0.00 3.18
3619 4408 3.328535 ACACCCTTTTCACTGGGAAAT 57.671 42.857 5.83 0.00 44.59 2.17
3628 4417 4.331968 CAAGGCTACATACACCCTTTTCA 58.668 43.478 0.00 0.00 35.59 2.69
3705 4494 2.481952 ACAGCAAACTCAAGAATCGCTC 59.518 45.455 0.00 0.00 0.00 5.03
4007 4809 7.653767 ATCCTCATTTTATATTCCGTCGAAC 57.346 36.000 0.00 0.00 0.00 3.95
4041 4845 9.495572 CAGAATAAAATAGGCCTAGTTCTAAGG 57.504 37.037 24.72 10.24 37.17 2.69
4052 4856 7.363268 CCTCATAATGCCAGAATAAAATAGGCC 60.363 40.741 0.00 0.00 44.60 5.19
4175 4984 7.572523 ACCATAGGATTACAATGACATGTTG 57.427 36.000 0.00 0.00 34.75 3.33
4176 4985 8.593945 AAACCATAGGATTACAATGACATGTT 57.406 30.769 0.00 0.00 34.75 2.71
4222 5031 3.550437 ACTAGCGCTTCTTTGATCCAT 57.450 42.857 18.68 0.00 0.00 3.41
4223 5032 3.334583 AACTAGCGCTTCTTTGATCCA 57.665 42.857 18.68 0.00 0.00 3.41
4234 5043 1.734465 GAAGTGATGCAAACTAGCGCT 59.266 47.619 17.26 17.26 37.31 5.92
4236 5045 1.061131 CGGAAGTGATGCAAACTAGCG 59.939 52.381 5.89 0.00 37.31 4.26
4264 5073 3.190874 CTCTGCATTTCGGAGGAGTTAC 58.809 50.000 0.00 0.00 43.10 2.50
4273 5095 1.402968 CATTGGTCCTCTGCATTTCGG 59.597 52.381 0.00 0.00 0.00 4.30
4286 5108 3.564225 AGGAAAGAAACGACACATTGGTC 59.436 43.478 0.00 0.00 34.42 4.02
4298 5120 8.479313 ACTCAAAAATGTTGAAGGAAAGAAAC 57.521 30.769 0.00 0.00 0.00 2.78
4357 5205 2.432300 AATCCCTAGCCGACCACCG 61.432 63.158 0.00 0.00 38.18 4.94
4364 5212 1.819632 GCCACACAATCCCTAGCCG 60.820 63.158 0.00 0.00 0.00 5.52
4395 5243 2.488836 CCCCTTTATACCCAGTCCACT 58.511 52.381 0.00 0.00 0.00 4.00
4396 5244 1.493446 CCCCCTTTATACCCAGTCCAC 59.507 57.143 0.00 0.00 0.00 4.02
4401 5249 0.850784 CCCACCCCCTTTATACCCAG 59.149 60.000 0.00 0.00 0.00 4.45
4429 5277 2.509336 CCATCACGTCGGCCTGAC 60.509 66.667 15.15 15.15 44.53 3.51
4439 5287 0.320683 TGCCAAGACTGTCCATCACG 60.321 55.000 3.76 0.00 0.00 4.35
4452 5300 1.508088 GCGAAATGGGTCTGCCAAG 59.492 57.895 0.00 0.00 36.17 3.61
4468 5316 1.691976 TCTAATCCACATACAGGGGCG 59.308 52.381 0.00 0.00 42.23 6.13
4474 5322 4.729370 TCCCCCAAATCTAATCCACATACA 59.271 41.667 0.00 0.00 0.00 2.29
4475 5323 5.073144 TCTCCCCCAAATCTAATCCACATAC 59.927 44.000 0.00 0.00 0.00 2.39
4479 5327 3.435169 GGTCTCCCCCAAATCTAATCCAC 60.435 52.174 0.00 0.00 0.00 4.02
4484 5332 1.209621 CCGGTCTCCCCCAAATCTAA 58.790 55.000 0.00 0.00 0.00 2.10
4486 5334 0.549169 TTCCGGTCTCCCCCAAATCT 60.549 55.000 0.00 0.00 0.00 2.40
4512 5360 3.123804 CTCGAAACCTAGCGCATATGTT 58.876 45.455 11.47 4.33 0.00 2.71
4517 5365 0.103208 CTCCTCGAAACCTAGCGCAT 59.897 55.000 11.47 0.00 0.00 4.73
4520 5368 1.227002 GGCTCCTCGAAACCTAGCG 60.227 63.158 0.00 0.00 33.96 4.26
4531 5379 4.247380 CCATCCAGCGGGCTCCTC 62.247 72.222 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.