Multiple sequence alignment - TraesCS1A01G193900

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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 TraesCS1A01G193900 chr1A 100.000 2573 0 0 1 2573 351345970 351343398 0.000000e+00 4752
1 TraesCS1A01G193900 chr1B 89.600 2375 130 40 260 2573 378834163 378831845 0.000000e+00 2909
2 TraesCS1A01G193900 chr1B 89.035 228 13 4 1 220 378834388 378834165 3.260000e-69 272
3 TraesCS1A01G193900 chr1B 84.247 146 20 3 2429 2573 378831676 378831533 3.450000e-29 139
4 TraesCS1A01G193900 chr1D 90.491 1651 78 29 260 1892 279099688 279098099 0.000000e+00 2106
5 TraesCS1A01G193900 chr1D 93.313 329 15 4 1876 2199 279096560 279096234 1.790000e-131 479
6 TraesCS1A01G193900 chr1D 90.749 227 10 4 1 220 279099912 279099690 2.500000e-75 292
7 TraesCS1A01G193900 chr1D 89.944 179 16 2 2397 2573 279095851 279095673 1.990000e-56 230


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 TraesCS1A01G193900 chr1A 351343398 351345970 2572 True 4752.000000 4752 100.000000 1 2573 1 chr1A.!!$R1 2572
1 TraesCS1A01G193900 chr1B 378831533 378834388 2855 True 1106.666667 2909 87.627333 1 2573 3 chr1B.!!$R1 2572
2 TraesCS1A01G193900 chr1D 279095673 279099912 4239 True 776.750000 2106 91.124250 1 2573 4 chr1D.!!$R1 2572

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
956 973 0.105709 TGAGTCTGACCAGTGACCCA 60.106 55.0 3.76 0.0 34.02 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 3537 0.250467 TGCTGGTCAAGACTGAAGGC 60.25 55.0 0.0 0.0 31.88 4.35 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
85 87 3.317993 ACCAGTGCTAATGTTTGGTGTTC 59.682 43.478 0.00 0.00 40.47 3.18
86 88 3.569701 CCAGTGCTAATGTTTGGTGTTCT 59.430 43.478 0.00 0.00 0.00 3.01
87 89 4.759693 CCAGTGCTAATGTTTGGTGTTCTA 59.240 41.667 0.00 0.00 0.00 2.10
95 97 7.816031 GCTAATGTTTGGTGTTCTACTACTACA 59.184 37.037 0.00 0.00 0.00 2.74
96 98 7.958053 AATGTTTGGTGTTCTACTACTACAC 57.042 36.000 0.00 0.00 41.01 2.90
125 127 3.828875 AGCTCCCAACTATCTAAGCAC 57.171 47.619 0.00 0.00 32.25 4.40
155 157 4.022849 GTGACCCCAAACAGAAATCTGAAG 60.023 45.833 16.93 6.10 46.59 3.02
157 159 3.891366 ACCCCAAACAGAAATCTGAAGTG 59.109 43.478 16.93 10.49 46.59 3.16
161 163 4.261741 CCAAACAGAAATCTGAAGTGGGTG 60.262 45.833 16.93 4.31 46.59 4.61
202 211 9.836076 CATTAATCATGTGCATTTCACTATAGG 57.164 33.333 4.43 0.00 45.81 2.57
224 233 2.519002 GCATCGTGCGTACATTTGAA 57.481 45.000 4.09 0.00 31.71 2.69
225 234 2.845486 GCATCGTGCGTACATTTGAAA 58.155 42.857 4.09 0.00 31.71 2.69
226 235 2.588106 GCATCGTGCGTACATTTGAAAC 59.412 45.455 4.09 0.00 31.71 2.78
227 236 3.804688 CATCGTGCGTACATTTGAAACA 58.195 40.909 4.09 0.00 0.00 2.83
228 237 3.946308 TCGTGCGTACATTTGAAACAA 57.054 38.095 4.09 0.00 0.00 2.83
229 238 4.274421 TCGTGCGTACATTTGAAACAAA 57.726 36.364 4.09 0.00 0.00 2.83
230 239 4.849883 TCGTGCGTACATTTGAAACAAAT 58.150 34.783 4.09 4.22 0.00 2.32
231 240 4.907010 TCGTGCGTACATTTGAAACAAATC 59.093 37.500 4.09 0.00 0.00 2.17
232 241 4.672862 CGTGCGTACATTTGAAACAAATCA 59.327 37.500 4.09 0.64 0.00 2.57
233 242 5.341993 CGTGCGTACATTTGAAACAAATCAT 59.658 36.000 4.09 2.47 0.00 2.45
234 243 6.515882 GTGCGTACATTTGAAACAAATCATG 58.484 36.000 0.00 0.00 0.00 3.07
235 244 6.143758 GTGCGTACATTTGAAACAAATCATGT 59.856 34.615 0.00 6.88 46.82 3.21
236 245 6.143598 TGCGTACATTTGAAACAAATCATGTG 59.856 34.615 6.73 1.28 42.99 3.21
237 246 6.515882 CGTACATTTGAAACAAATCATGTGC 58.484 36.000 6.73 6.97 42.99 4.57
238 247 6.143598 CGTACATTTGAAACAAATCATGTGCA 59.856 34.615 6.73 0.00 42.99 4.57
239 248 7.148771 CGTACATTTGAAACAAATCATGTGCAT 60.149 33.333 6.73 0.00 42.99 3.96
240 249 9.138062 GTACATTTGAAACAAATCATGTGCATA 57.862 29.630 6.73 0.00 42.99 3.14
241 250 8.604640 ACATTTGAAACAAATCATGTGCATAA 57.395 26.923 6.73 0.00 42.99 1.90
242 251 9.221933 ACATTTGAAACAAATCATGTGCATAAT 57.778 25.926 6.73 0.00 42.99 1.28
246 255 9.926158 TTGAAACAAATCATGTGCATAATAACT 57.074 25.926 0.00 0.00 42.99 2.24
258 267 8.370493 TGTGCATAATAACTAAGATTCTGAGC 57.630 34.615 0.00 0.00 0.00 4.26
300 309 2.238847 CTCCATTCCAGGAACGGCGA 62.239 60.000 16.62 0.00 37.20 5.54
394 403 2.435372 TCAGCCAGTGAAACAAACCT 57.565 45.000 0.00 0.00 41.43 3.50
402 411 4.216257 CCAGTGAAACAAACCTAGACCATG 59.784 45.833 0.00 0.00 41.43 3.66
425 434 4.227864 CCTGAAGGCAGAGTTAGGATTT 57.772 45.455 0.00 0.00 45.17 2.17
592 601 0.465705 GGATGATCTTGGCGGTCTCA 59.534 55.000 0.00 0.00 0.00 3.27
770 779 2.123897 GCCGGCCTCTCTCTCTCT 60.124 66.667 18.11 0.00 0.00 3.10
771 780 2.193536 GCCGGCCTCTCTCTCTCTC 61.194 68.421 18.11 0.00 0.00 3.20
772 781 1.531748 CCGGCCTCTCTCTCTCTCT 59.468 63.158 0.00 0.00 0.00 3.10
865 882 0.324943 TGGCTTCCCACTTACAGAGC 59.675 55.000 0.00 0.00 35.79 4.09
955 972 1.048601 TTGAGTCTGACCAGTGACCC 58.951 55.000 3.76 0.00 34.02 4.46
956 973 0.105709 TGAGTCTGACCAGTGACCCA 60.106 55.000 3.76 0.00 34.02 4.51
958 975 0.398522 AGTCTGACCAGTGACCCACA 60.399 55.000 3.76 0.00 36.74 4.17
1256 1276 2.134287 GGAGGTCATGGAGGCGCTA 61.134 63.158 7.64 0.00 0.00 4.26
1274 1294 2.303311 GCTACAAAAGGAGGTCAGGTCT 59.697 50.000 0.00 0.00 0.00 3.85
1348 1368 0.109723 TCCAGGCCAGGTAACAACAC 59.890 55.000 14.79 0.00 41.41 3.32
1353 1373 1.675552 GCCAGGTAACAACACACAGT 58.324 50.000 0.00 0.00 41.41 3.55
1354 1374 1.333619 GCCAGGTAACAACACACAGTG 59.666 52.381 0.00 0.00 38.34 3.66
1360 1380 1.083489 AACAACACACAGTGACACCG 58.917 50.000 7.81 0.00 36.96 4.94
1370 1390 4.245660 CACAGTGACACCGTAAATCTCAT 58.754 43.478 0.84 0.00 0.00 2.90
1372 1392 4.690748 ACAGTGACACCGTAAATCTCATTG 59.309 41.667 0.84 0.00 0.00 2.82
1380 1400 7.974675 ACACCGTAAATCTCATTGAAATACAG 58.025 34.615 0.00 0.00 0.00 2.74
1389 1409 7.312657 TCTCATTGAAATACAGAATGAGCAC 57.687 36.000 13.66 0.00 40.67 4.40
1391 1411 6.845302 TCATTGAAATACAGAATGAGCACAC 58.155 36.000 0.00 0.00 39.69 3.82
1398 1418 2.545526 ACAGAATGAGCACACGAGTTTG 59.454 45.455 0.00 0.00 39.69 2.93
1424 1444 6.957020 AGGTTGATTATGGTTTATTGTTCCCA 59.043 34.615 0.00 0.00 0.00 4.37
1449 1470 6.595716 AGCTAGGAATTGAGATTGTGTGTAAC 59.404 38.462 0.00 0.00 37.35 2.50
1473 1518 5.344933 CACGATCACGAGAGTTTATGTTTGA 59.655 40.000 0.00 0.00 46.40 2.69
1485 1530 1.923356 ATGTTTGATTCCGGCTTGGT 58.077 45.000 0.00 0.00 39.52 3.67
1486 1531 1.698506 TGTTTGATTCCGGCTTGGTT 58.301 45.000 0.00 0.00 39.52 3.67
1494 1539 1.770294 TCCGGCTTGGTTTGTTCTTT 58.230 45.000 0.00 0.00 39.52 2.52
1598 1643 2.190398 TAGGCTTTCCATCCAGGCTA 57.810 50.000 0.00 0.00 43.80 3.93
1601 1646 1.133668 GGCTTTCCATCCAGGCTATGT 60.134 52.381 0.00 0.00 37.29 2.29
1617 1662 3.777522 GCTATGTTCCTAGGGGCTATCAT 59.222 47.826 9.46 3.19 0.00 2.45
1618 1663 4.141824 GCTATGTTCCTAGGGGCTATCATC 60.142 50.000 9.46 0.00 0.00 2.92
1619 1664 3.637821 TGTTCCTAGGGGCTATCATCT 57.362 47.619 9.46 0.00 0.00 2.90
1620 1665 3.242867 TGTTCCTAGGGGCTATCATCTG 58.757 50.000 9.46 0.00 0.00 2.90
1621 1666 3.116746 TGTTCCTAGGGGCTATCATCTGA 60.117 47.826 9.46 0.00 0.00 3.27
1622 1667 4.100373 GTTCCTAGGGGCTATCATCTGAT 58.900 47.826 9.46 0.00 38.51 2.90
1623 1668 4.426357 TCCTAGGGGCTATCATCTGATT 57.574 45.455 9.46 0.00 36.05 2.57
1624 1669 4.357325 TCCTAGGGGCTATCATCTGATTC 58.643 47.826 9.46 0.00 36.05 2.52
1625 1670 3.454082 CCTAGGGGCTATCATCTGATTCC 59.546 52.174 0.00 1.10 36.05 3.01
1626 1671 2.995746 AGGGGCTATCATCTGATTCCA 58.004 47.619 0.00 0.00 36.05 3.53
1627 1672 2.641815 AGGGGCTATCATCTGATTCCAC 59.358 50.000 0.00 2.25 36.05 4.02
1628 1673 2.641815 GGGGCTATCATCTGATTCCACT 59.358 50.000 0.00 0.00 36.05 4.00
1629 1674 3.307339 GGGGCTATCATCTGATTCCACTC 60.307 52.174 0.00 0.00 36.05 3.51
1630 1675 3.326006 GGGCTATCATCTGATTCCACTCA 59.674 47.826 0.00 0.00 36.05 3.41
1661 1721 7.542025 AGTTCATTCTGCTAAATCATTTCCAC 58.458 34.615 0.00 0.00 0.00 4.02
1697 1760 0.473755 AGTGACCCAAGTGTGATGCA 59.526 50.000 0.00 0.00 0.00 3.96
1706 1769 0.954449 AGTGTGATGCAGCTGCTCAC 60.954 55.000 37.41 37.41 43.20 3.51
1714 1777 2.942342 TGCAGCTGCTCACAACTTGTG 61.942 52.381 36.61 14.79 43.39 3.33
1737 1800 7.176515 TGTGTAAATCATTTTCAGGTACATGCT 59.823 33.333 1.79 0.00 0.00 3.79
1781 1844 6.557110 TGCAAGTGTTATGATGATGTTCATG 58.443 36.000 0.00 0.00 37.20 3.07
1821 1884 4.193865 CCAAATCCTTGCAAATTGATCCC 58.806 43.478 0.00 0.00 0.00 3.85
1822 1885 4.193865 CAAATCCTTGCAAATTGATCCCC 58.806 43.478 0.00 0.00 0.00 4.81
1826 1889 3.649981 TCCTTGCAAATTGATCCCCAAAA 59.350 39.130 0.00 0.00 38.43 2.44
1918 3537 7.765307 AGCACATACACTTTCATTATCTTTGG 58.235 34.615 0.00 0.00 0.00 3.28
1919 3538 6.473455 GCACATACACTTTCATTATCTTTGGC 59.527 38.462 0.00 0.00 0.00 4.52
1951 3574 0.378257 CCAGCAATACATCGTGGTGC 59.622 55.000 0.00 0.00 40.96 5.01
1955 3578 1.405105 GCAATACATCGTGGTGCCAAT 59.595 47.619 0.00 0.00 0.00 3.16
2088 3713 0.984230 TGGTCAACTGGGTCATCCTC 59.016 55.000 0.00 0.00 36.20 3.71
2127 3752 7.172532 TGTTTCGTAGCTGTTTGTGATCTTATT 59.827 33.333 0.00 0.00 0.00 1.40
2136 3761 5.711506 TGTTTGTGATCTTATTCATGCCTGT 59.288 36.000 0.00 0.00 0.00 4.00
2195 3820 6.913170 TCCAATTGCTTACTCTTTGTTCATC 58.087 36.000 0.00 0.00 0.00 2.92
2226 3883 6.348498 TGAACACTTCTGAGTTGATCTTCAA 58.652 36.000 0.00 0.00 32.54 2.69
2237 3894 6.099413 TGAGTTGATCTTCAATCTGATAGCCT 59.901 38.462 0.00 0.00 38.79 4.58
2245 3902 3.704566 TCAATCTGATAGCCTAACACGGT 59.295 43.478 0.00 0.00 0.00 4.83
2248 3905 3.894759 TCTGATAGCCTAACACGGTACT 58.105 45.455 0.00 0.00 0.00 2.73
2269 3926 2.162208 TCTTTGATGTTGCTGCGGAATC 59.838 45.455 0.00 0.00 0.00 2.52
2292 3949 7.395190 TCACTATTGACCCAAATGAAGAATG 57.605 36.000 0.00 0.00 0.00 2.67
2298 3955 3.365472 ACCCAAATGAAGAATGTAGGCC 58.635 45.455 0.00 0.00 0.00 5.19
2301 3958 1.680338 AATGAAGAATGTAGGCCGGC 58.320 50.000 21.18 21.18 0.00 6.13
2304 3961 1.300481 GAAGAATGTAGGCCGGCTTC 58.700 55.000 28.56 21.15 0.00 3.86
2305 3962 0.912486 AAGAATGTAGGCCGGCTTCT 59.088 50.000 28.56 23.13 0.00 2.85
2306 3963 1.789523 AGAATGTAGGCCGGCTTCTA 58.210 50.000 28.56 17.47 0.00 2.10
2307 3964 1.413077 AGAATGTAGGCCGGCTTCTAC 59.587 52.381 28.56 27.50 37.09 2.59
2308 3965 1.413077 GAATGTAGGCCGGCTTCTACT 59.587 52.381 30.60 21.18 37.37 2.57
2309 3966 1.041437 ATGTAGGCCGGCTTCTACTC 58.959 55.000 30.60 14.65 37.37 2.59
2310 3967 0.323999 TGTAGGCCGGCTTCTACTCA 60.324 55.000 30.60 17.08 37.37 3.41
2325 3982 6.237701 GCTTCTACTCAAAAGCTAGACGATTG 60.238 42.308 0.00 0.00 43.57 2.67
2350 4007 7.560991 TGAAAACTATCTTTGCACCCATGATAT 59.439 33.333 0.00 0.00 0.00 1.63
2358 4015 3.289836 TGCACCCATGATATTTCTGTGG 58.710 45.455 0.00 2.66 0.00 4.17
2366 4023 5.808540 CCATGATATTTCTGTGGTTTTGCTG 59.191 40.000 0.00 0.00 0.00 4.41
2400 4057 6.478512 TGCTTTTGTTTTTCTCCCAAGTAT 57.521 33.333 0.00 0.00 0.00 2.12
2401 4058 7.589958 TGCTTTTGTTTTTCTCCCAAGTATA 57.410 32.000 0.00 0.00 0.00 1.47
2402 4059 8.189119 TGCTTTTGTTTTTCTCCCAAGTATAT 57.811 30.769 0.00 0.00 0.00 0.86
2403 4060 9.303116 TGCTTTTGTTTTTCTCCCAAGTATATA 57.697 29.630 0.00 0.00 0.00 0.86
2424 4243 8.995027 ATATATAAATGGCCAGTGTTCTTGAA 57.005 30.769 13.05 0.00 0.00 2.69
2433 4252 4.458989 GCCAGTGTTCTTGAATAATCACCA 59.541 41.667 0.00 0.00 34.61 4.17
2434 4253 5.126061 GCCAGTGTTCTTGAATAATCACCAT 59.874 40.000 0.00 0.00 34.61 3.55
2438 4257 8.464404 CAGTGTTCTTGAATAATCACCATTCAT 58.536 33.333 0.00 0.00 40.94 2.57
2456 4275 1.129917 ATCCTGTCCATCTGCCTCTG 58.870 55.000 0.00 0.00 0.00 3.35
2457 4276 0.252421 TCCTGTCCATCTGCCTCTGT 60.252 55.000 0.00 0.00 0.00 3.41
2468 4287 2.020720 CTGCCTCTGTATCGTCTCTGT 58.979 52.381 0.00 0.00 0.00 3.41
2505 4324 6.420306 CACAGACTTGCAGTGCTATTCTATAG 59.580 42.308 17.60 8.59 0.00 1.31
2562 4381 3.641906 AGTAATGTGAGGGGAAGGATACG 59.358 47.826 0.00 0.00 46.39 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 4.406003 AGCTTGGGAATGGTGTAGTAGTAG 59.594 45.833 0.00 0.00 0.00 2.57
86 88 4.359105 AGCTTGGGAATGGTGTAGTAGTA 58.641 43.478 0.00 0.00 0.00 1.82
87 89 3.182152 AGCTTGGGAATGGTGTAGTAGT 58.818 45.455 0.00 0.00 0.00 2.73
95 97 0.251787 GTTGGGAGCTTGGGAATGGT 60.252 55.000 0.00 0.00 0.00 3.55
96 98 0.040204 AGTTGGGAGCTTGGGAATGG 59.960 55.000 0.00 0.00 0.00 3.16
125 127 2.359354 TTTGGGGTCACATCGCCG 60.359 61.111 0.00 0.00 42.29 6.46
155 157 5.913137 TGTTTATCATTCCATTCACCCAC 57.087 39.130 0.00 0.00 0.00 4.61
157 159 9.696917 GATTAATGTTTATCATTCCATTCACCC 57.303 33.333 0.00 0.00 44.50 4.61
197 206 0.955905 TACGCACGATGCAGCCTATA 59.044 50.000 0.00 0.00 45.36 1.31
201 210 1.705337 AATGTACGCACGATGCAGCC 61.705 55.000 0.00 0.00 45.36 4.85
202 211 0.096976 AAATGTACGCACGATGCAGC 59.903 50.000 9.95 0.00 45.36 5.25
220 229 9.926158 AGTTATTATGCACATGATTTGTTTCAA 57.074 25.926 0.00 0.00 36.00 2.69
232 241 8.997323 GCTCAGAATCTTAGTTATTATGCACAT 58.003 33.333 0.00 0.00 0.00 3.21
233 242 7.986889 TGCTCAGAATCTTAGTTATTATGCACA 59.013 33.333 0.00 0.00 0.00 4.57
234 243 8.370493 TGCTCAGAATCTTAGTTATTATGCAC 57.630 34.615 0.00 0.00 0.00 4.57
243 252 9.160496 CTTCTTGTTATGCTCAGAATCTTAGTT 57.840 33.333 0.00 0.00 0.00 2.24
244 253 7.279758 GCTTCTTGTTATGCTCAGAATCTTAGT 59.720 37.037 0.00 0.00 0.00 2.24
245 254 7.279536 TGCTTCTTGTTATGCTCAGAATCTTAG 59.720 37.037 0.00 0.00 0.00 2.18
246 255 7.065085 GTGCTTCTTGTTATGCTCAGAATCTTA 59.935 37.037 0.00 0.00 0.00 2.10
247 256 5.942236 TGCTTCTTGTTATGCTCAGAATCTT 59.058 36.000 0.00 0.00 0.00 2.40
248 257 5.353678 GTGCTTCTTGTTATGCTCAGAATCT 59.646 40.000 0.00 0.00 0.00 2.40
249 258 5.448360 GGTGCTTCTTGTTATGCTCAGAATC 60.448 44.000 0.00 0.00 0.00 2.52
250 259 4.397417 GGTGCTTCTTGTTATGCTCAGAAT 59.603 41.667 0.00 0.00 0.00 2.40
251 260 3.753272 GGTGCTTCTTGTTATGCTCAGAA 59.247 43.478 0.00 0.00 0.00 3.02
252 261 3.338249 GGTGCTTCTTGTTATGCTCAGA 58.662 45.455 0.00 0.00 0.00 3.27
253 262 2.421424 GGGTGCTTCTTGTTATGCTCAG 59.579 50.000 0.00 0.00 0.00 3.35
254 263 2.040278 AGGGTGCTTCTTGTTATGCTCA 59.960 45.455 0.00 0.00 0.00 4.26
255 264 2.421424 CAGGGTGCTTCTTGTTATGCTC 59.579 50.000 0.00 0.00 0.00 4.26
256 265 2.040278 TCAGGGTGCTTCTTGTTATGCT 59.960 45.455 0.00 0.00 0.00 3.79
257 266 2.162408 GTCAGGGTGCTTCTTGTTATGC 59.838 50.000 0.00 0.00 0.00 3.14
258 267 2.749621 GGTCAGGGTGCTTCTTGTTATG 59.250 50.000 0.00 0.00 0.00 1.90
308 317 1.428620 GTCGAGGAGTAGCACGGTC 59.571 63.158 0.00 0.00 0.00 4.79
592 601 1.765314 CGGGAGAAGTGGATCCAGATT 59.235 52.381 16.81 13.46 37.33 2.40
770 779 1.360852 AGAGGCCAAGAAGAGAGGAGA 59.639 52.381 5.01 0.00 0.00 3.71
771 780 1.481772 CAGAGGCCAAGAAGAGAGGAG 59.518 57.143 5.01 0.00 0.00 3.69
772 781 1.566211 CAGAGGCCAAGAAGAGAGGA 58.434 55.000 5.01 0.00 0.00 3.71
918 935 3.110358 TCAACAGCGAATTATACGACCG 58.890 45.455 0.00 0.00 0.00 4.79
923 940 5.232414 GGTCAGACTCAACAGCGAATTATAC 59.768 44.000 0.00 0.00 0.00 1.47
955 972 3.345808 CGCCCTTCCGTGTGTGTG 61.346 66.667 0.00 0.00 0.00 3.82
1256 1276 2.635427 GAGAGACCTGACCTCCTTTTGT 59.365 50.000 0.00 0.00 0.00 2.83
1274 1294 1.170290 TCCAGCTGTTGTCGTCGAGA 61.170 55.000 13.81 0.00 0.00 4.04
1348 1368 3.649073 TGAGATTTACGGTGTCACTGTG 58.351 45.455 24.88 0.17 38.36 3.66
1353 1373 7.604545 TGTATTTCAATGAGATTTACGGTGTCA 59.395 33.333 0.00 0.00 0.00 3.58
1354 1374 7.970384 TGTATTTCAATGAGATTTACGGTGTC 58.030 34.615 0.00 0.00 0.00 3.67
1370 1390 4.994217 TCGTGTGCTCATTCTGTATTTCAA 59.006 37.500 0.00 0.00 0.00 2.69
1372 1392 4.627467 ACTCGTGTGCTCATTCTGTATTTC 59.373 41.667 0.00 0.00 0.00 2.17
1380 1400 2.158449 CCTCAAACTCGTGTGCTCATTC 59.842 50.000 0.00 0.00 0.00 2.67
1389 1409 4.695455 ACCATAATCAACCTCAAACTCGTG 59.305 41.667 0.00 0.00 0.00 4.35
1391 1411 5.880054 AACCATAATCAACCTCAAACTCG 57.120 39.130 0.00 0.00 0.00 4.18
1398 1418 7.123547 TGGGAACAATAAACCATAATCAACCTC 59.876 37.037 0.00 0.00 37.44 3.85
1424 1444 5.171339 ACACACAATCTCAATTCCTAGCT 57.829 39.130 0.00 0.00 0.00 3.32
1449 1470 5.344933 TCAAACATAAACTCTCGTGATCGTG 59.655 40.000 0.00 0.00 38.33 4.35
1458 1479 4.636206 AGCCGGAATCAAACATAAACTCTC 59.364 41.667 5.05 0.00 0.00 3.20
1473 1518 1.995376 AGAACAAACCAAGCCGGAAT 58.005 45.000 5.05 0.00 38.63 3.01
1485 1530 5.585820 GGTAACCACCTGAAAAGAACAAA 57.414 39.130 0.00 0.00 42.11 2.83
1598 1643 3.843027 CAGATGATAGCCCCTAGGAACAT 59.157 47.826 11.48 0.00 33.47 2.71
1601 1646 3.923273 TCAGATGATAGCCCCTAGGAA 57.077 47.619 11.48 0.00 33.47 3.36
1617 1662 3.779444 ACTACAGGTGAGTGGAATCAGA 58.221 45.455 0.00 0.00 0.00 3.27
1618 1663 4.021104 TGAACTACAGGTGAGTGGAATCAG 60.021 45.833 0.00 0.00 0.00 2.90
1619 1664 3.901222 TGAACTACAGGTGAGTGGAATCA 59.099 43.478 0.00 0.00 0.00 2.57
1620 1665 4.537135 TGAACTACAGGTGAGTGGAATC 57.463 45.455 0.00 0.00 0.00 2.52
1621 1666 5.249393 AGAATGAACTACAGGTGAGTGGAAT 59.751 40.000 0.00 0.00 0.00 3.01
1622 1667 4.593206 AGAATGAACTACAGGTGAGTGGAA 59.407 41.667 0.00 0.00 0.00 3.53
1623 1668 4.021104 CAGAATGAACTACAGGTGAGTGGA 60.021 45.833 0.00 0.00 39.69 4.02
1624 1669 4.248859 CAGAATGAACTACAGGTGAGTGG 58.751 47.826 0.00 0.00 39.69 4.00
1625 1670 3.681897 GCAGAATGAACTACAGGTGAGTG 59.318 47.826 0.00 0.00 39.69 3.51
1626 1671 3.580458 AGCAGAATGAACTACAGGTGAGT 59.420 43.478 0.00 0.00 39.69 3.41
1627 1672 4.199432 AGCAGAATGAACTACAGGTGAG 57.801 45.455 0.00 0.00 39.69 3.51
1628 1673 5.738619 TTAGCAGAATGAACTACAGGTGA 57.261 39.130 0.00 0.00 39.69 4.02
1629 1674 6.595326 TGATTTAGCAGAATGAACTACAGGTG 59.405 38.462 0.00 0.00 39.69 4.00
1630 1675 6.711277 TGATTTAGCAGAATGAACTACAGGT 58.289 36.000 0.00 0.00 39.69 4.00
1661 1721 6.926826 TGGGTCACTTAAATATAGCATGTACG 59.073 38.462 0.00 0.00 0.00 3.67
1706 1769 9.180678 GTACCTGAAAATGATTTACACAAGTTG 57.819 33.333 0.00 0.00 0.00 3.16
1714 1777 9.669353 CATAGCATGTACCTGAAAATGATTTAC 57.331 33.333 1.92 0.00 0.00 2.01
1758 1821 6.690098 GTCATGAACATCATCATAACACTTGC 59.310 38.462 0.00 0.00 37.96 4.01
1918 3537 0.250467 TGCTGGTCAAGACTGAAGGC 60.250 55.000 0.00 0.00 31.88 4.35
1919 3538 2.260844 TTGCTGGTCAAGACTGAAGG 57.739 50.000 0.00 0.00 31.88 3.46
2006 3630 9.722056 GCTATTTGTATTCTAGGACAAAATGTG 57.278 33.333 16.96 11.05 45.78 3.21
2007 3631 8.903820 GGCTATTTGTATTCTAGGACAAAATGT 58.096 33.333 16.96 8.20 45.78 2.71
2088 3713 5.354234 AGCTACGAAACAATCCCATACAAAG 59.646 40.000 0.00 0.00 0.00 2.77
2136 3761 0.465705 CATAAGAGGAAGCCGCCAGA 59.534 55.000 0.00 0.00 0.00 3.86
2195 3820 4.608948 ACTCAGAAGTGTTCAGGTAAGG 57.391 45.455 0.00 0.00 33.32 2.69
2226 3883 4.471548 AGTACCGTGTTAGGCTATCAGAT 58.528 43.478 5.55 0.00 33.69 2.90
2237 3894 4.449743 GCAACATCAAAGAGTACCGTGTTA 59.550 41.667 0.00 0.00 0.00 2.41
2245 3902 2.076100 CCGCAGCAACATCAAAGAGTA 58.924 47.619 0.00 0.00 0.00 2.59
2248 3905 1.603456 TTCCGCAGCAACATCAAAGA 58.397 45.000 0.00 0.00 0.00 2.52
2269 3926 7.161773 ACATTCTTCATTTGGGTCAATAGTG 57.838 36.000 0.00 0.00 0.00 2.74
2292 3949 0.822164 TTGAGTAGAAGCCGGCCTAC 59.178 55.000 26.48 26.48 36.42 3.18
2301 3958 7.030165 TCAATCGTCTAGCTTTTGAGTAGAAG 58.970 38.462 0.00 0.00 0.00 2.85
2304 3961 7.582435 TTTCAATCGTCTAGCTTTTGAGTAG 57.418 36.000 0.00 0.00 0.00 2.57
2305 3962 7.656137 AGTTTTCAATCGTCTAGCTTTTGAGTA 59.344 33.333 0.00 0.00 0.00 2.59
2306 3963 6.483640 AGTTTTCAATCGTCTAGCTTTTGAGT 59.516 34.615 0.00 0.00 0.00 3.41
2307 3964 6.892691 AGTTTTCAATCGTCTAGCTTTTGAG 58.107 36.000 0.00 0.00 0.00 3.02
2308 3965 6.861065 AGTTTTCAATCGTCTAGCTTTTGA 57.139 33.333 0.00 0.00 0.00 2.69
2309 3966 8.660373 AGATAGTTTTCAATCGTCTAGCTTTTG 58.340 33.333 0.00 0.00 0.00 2.44
2310 3967 8.779354 AGATAGTTTTCAATCGTCTAGCTTTT 57.221 30.769 0.00 0.00 0.00 2.27
2325 3982 5.643379 TCATGGGTGCAAAGATAGTTTTC 57.357 39.130 0.00 0.00 0.00 2.29
2350 4007 4.992688 CTGTTACAGCAAAACCACAGAAA 58.007 39.130 0.00 0.00 34.74 2.52
2377 4034 4.817318 ACTTGGGAGAAAAACAAAAGCA 57.183 36.364 0.00 0.00 0.00 3.91
2392 4049 7.175104 ACACTGGCCATTTATATATACTTGGG 58.825 38.462 5.51 0.00 0.00 4.12
2400 4057 8.995027 ATTCAAGAACACTGGCCATTTATATA 57.005 30.769 5.51 0.00 0.00 0.86
2401 4058 7.902920 ATTCAAGAACACTGGCCATTTATAT 57.097 32.000 5.51 0.00 0.00 0.86
2402 4059 8.815565 TTATTCAAGAACACTGGCCATTTATA 57.184 30.769 5.51 0.00 0.00 0.98
2403 4060 7.716799 TTATTCAAGAACACTGGCCATTTAT 57.283 32.000 5.51 0.00 0.00 1.40
2424 4243 5.651612 TGGACAGGATGAATGGTGATTAT 57.348 39.130 0.00 0.00 39.69 1.28
2433 4252 2.106166 GAGGCAGATGGACAGGATGAAT 59.894 50.000 0.00 0.00 39.69 2.57
2434 4253 1.487976 GAGGCAGATGGACAGGATGAA 59.512 52.381 0.00 0.00 39.69 2.57
2438 4257 0.252421 ACAGAGGCAGATGGACAGGA 60.252 55.000 0.00 0.00 0.00 3.86
2456 4275 2.656560 ACAAGCCACAGAGACGATAC 57.343 50.000 0.00 0.00 0.00 2.24
2457 4276 2.560981 TCAACAAGCCACAGAGACGATA 59.439 45.455 0.00 0.00 0.00 2.92
2468 4287 2.418368 AGTCTGTGTTCAACAAGCCA 57.582 45.000 0.00 0.00 38.67 4.75
2525 4344 5.365619 CACATTACTAAGATGTGGGGTACC 58.634 45.833 2.17 2.17 46.62 3.34
2536 4355 4.955335 TCCTTCCCCTCACATTACTAAGA 58.045 43.478 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.