Multiple sequence alignment - TraesCS5A01G025600

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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 TraesCS5A01G025600 chr5A 100.000 2633 0 0 1 2633 20793918 20796550 0.000000e+00 4863.0
1 TraesCS5A01G025600 chr5D 88.823 2684 160 46 14 2624 32143729 32146345 0.000000e+00 3166.0
2 TraesCS5A01G025600 chr5D 94.118 51 3 0 1739 1789 32148747 32148797 7.810000e-11 78.7
3 TraesCS5A01G025600 chr5D 87.037 54 5 2 1338 1389 450944682 450944735 2.830000e-05 60.2
4 TraesCS5A01G025600 chr5B 88.117 749 79 5 1888 2633 23876774 23877515 0.000000e+00 881.0
5 TraesCS5A01G025600 chr5B 84.456 772 87 18 1886 2633 23878674 23879436 0.000000e+00 730.0
6 TraesCS5A01G025600 chr5B 85.020 741 64 17 529 1235 23875369 23876096 0.000000e+00 710.0
7 TraesCS5A01G025600 chr5B 87.209 430 25 12 1457 1869 23878212 23878628 1.850000e-126 462.0
8 TraesCS5A01G025600 chr5B 84.567 473 29 22 1326 1787 23876166 23876605 1.870000e-116 429.0
9 TraesCS5A01G025600 chr5B 90.377 239 23 0 305 543 23851916 23852154 5.470000e-82 315.0
10 TraesCS5A01G025600 chr5B 88.942 208 20 2 1 206 23823313 23823519 1.210000e-63 254.0
11 TraesCS5A01G025600 chr5B 88.235 119 8 4 1756 1872 23876612 23876726 1.270000e-28 137.0
12 TraesCS5A01G025600 chr5B 88.889 108 10 2 202 309 23827870 23827975 5.910000e-27 132.0
13 TraesCS5A01G025600 chr7B 81.524 617 100 8 2027 2633 612638449 612637837 1.820000e-136 496.0


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 TraesCS5A01G025600 chr5A 20793918 20796550 2632 False 4863.000000 4863 100.000000 1 2633 1 chr5A.!!$F1 2632
1 TraesCS5A01G025600 chr5D 32143729 32148797 5068 False 1622.350000 3166 91.470500 14 2624 2 chr5D.!!$F2 2610
2 TraesCS5A01G025600 chr5B 23875369 23879436 4067 False 558.166667 881 86.267333 529 2633 6 chr5B.!!$F4 2104
3 TraesCS5A01G025600 chr7B 612637837 612638449 612 True 496.000000 496 81.524000 2027 2633 1 chr7B.!!$R1 606

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
179 182 0.107017 GGTGATGGTGGGAGTGATGG 60.107 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2182 0.108041 GGATCGCTGGTTCCGGTTTA 60.108 55.0 0.0 0.0 0.0 2.01 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
27 28 3.254060 CGGTCAGTTAGTGAACCATCTG 58.746 50.000 0.00 0.00 40.15 2.90
32 33 6.092807 GGTCAGTTAGTGAACCATCTGAATTC 59.907 42.308 0.00 0.00 36.81 2.17
137 140 2.603075 TGGTCTTCTTTGATTGGGGG 57.397 50.000 0.00 0.00 0.00 5.40
158 161 1.000359 GTGGGAGGGATGGGGTTTG 60.000 63.158 0.00 0.00 0.00 2.93
162 165 2.120571 AGGGATGGGGTTTGGGGT 60.121 61.111 0.00 0.00 0.00 4.95
165 168 1.703461 GGATGGGGTTTGGGGTGAT 59.297 57.895 0.00 0.00 0.00 3.06
167 170 0.687427 GATGGGGTTTGGGGTGATGG 60.687 60.000 0.00 0.00 0.00 3.51
168 171 1.451372 ATGGGGTTTGGGGTGATGGT 61.451 55.000 0.00 0.00 0.00 3.55
179 182 0.107017 GGTGATGGTGGGAGTGATGG 60.107 60.000 0.00 0.00 0.00 3.51
183 186 4.408821 GGTGGGAGTGATGGCGCA 62.409 66.667 10.83 0.00 0.00 6.09
185 188 1.971167 GTGGGAGTGATGGCGCAAA 60.971 57.895 10.83 0.00 0.00 3.68
186 189 1.228398 TGGGAGTGATGGCGCAAAA 60.228 52.632 10.83 0.00 0.00 2.44
233 236 1.202818 GCCAGAAAGTGAGACACCCTT 60.203 52.381 0.00 0.00 34.49 3.95
234 237 2.498167 CCAGAAAGTGAGACACCCTTG 58.502 52.381 0.00 0.00 34.49 3.61
271 274 1.628340 CACAACACCATGGGGAGTAGA 59.372 52.381 24.27 0.00 36.95 2.59
287 290 4.247380 GATGCTCCAGCCTCGGGG 62.247 72.222 0.00 0.00 41.18 5.73
288 291 4.804420 ATGCTCCAGCCTCGGGGA 62.804 66.667 4.80 0.00 41.18 4.81
292 295 1.764054 CTCCAGCCTCGGGGATCTT 60.764 63.158 4.80 0.00 31.57 2.40
296 299 1.306141 AGCCTCGGGGATCTTGACA 60.306 57.895 4.80 0.00 33.58 3.58
297 300 0.909610 AGCCTCGGGGATCTTGACAA 60.910 55.000 4.80 0.00 33.58 3.18
309 312 1.337703 TCTTGACAATGCCACACAAGC 59.662 47.619 0.00 0.00 38.13 4.01
312 315 0.670162 GACAATGCCACACAAGCAGT 59.330 50.000 0.00 0.00 44.90 4.40
330 333 0.392193 GTGAGGCATGTGACCCTGAG 60.392 60.000 0.00 0.00 0.00 3.35
353 356 1.934589 TGACAGTGTCACTTGTTCGG 58.065 50.000 22.06 0.00 37.67 4.30
383 386 3.147595 CGATGACGGAGGAGGCCA 61.148 66.667 5.01 0.00 35.72 5.36
384 387 2.502492 CGATGACGGAGGAGGCCAT 61.502 63.158 5.01 0.00 35.72 4.40
425 428 2.993899 GTCGACGATGACAAAACCAGAT 59.006 45.455 0.00 0.00 38.75 2.90
431 434 5.547465 ACGATGACAAAACCAGATGAACTA 58.453 37.500 0.00 0.00 0.00 2.24
438 441 5.009010 ACAAAACCAGATGAACTACTTGCAG 59.991 40.000 0.00 0.00 0.00 4.41
454 457 2.040544 CAGCGGCGGGAAATGAACT 61.041 57.895 9.78 0.00 0.00 3.01
459 462 1.751437 GGCGGGAAATGAACTAGCTT 58.249 50.000 0.00 0.00 0.00 3.74
464 467 4.446371 CGGGAAATGAACTAGCTTGAGAT 58.554 43.478 1.04 0.00 0.00 2.75
483 486 7.181569 TGAGATGAAAGGGAACAAAAACTTT 57.818 32.000 0.00 0.00 35.99 2.66
491 494 2.159156 GGAACAAAAACTTTCACCGGCT 60.159 45.455 0.00 0.00 0.00 5.52
495 498 2.882137 CAAAAACTTTCACCGGCTAGGA 59.118 45.455 0.00 0.00 45.00 2.94
513 516 0.179169 GAGTCGGAAGCCACTACGTC 60.179 60.000 0.00 0.00 0.00 4.34
541 544 6.822676 CCCAAGGCTATTGAATAAAAATTGCA 59.177 34.615 4.09 0.00 37.46 4.08
610 615 8.504005 TGAACTTTCTATGAAAAATTCTCGGAC 58.496 33.333 13.22 0.00 0.00 4.79
615 620 7.553881 TCTATGAAAAATTCTCGGACATTCC 57.446 36.000 0.00 0.00 0.00 3.01
616 621 5.582689 ATGAAAAATTCTCGGACATTCCC 57.417 39.130 0.00 0.00 31.13 3.97
628 633 2.353579 GGACATTCCCGACAATAAACCG 59.646 50.000 0.00 0.00 0.00 4.44
649 654 5.508320 ACCGCTGGTAAAATTCGTTTGAATT 60.508 36.000 0.00 0.00 44.46 2.17
704 709 1.813513 ATATATCAGCCGTGCAAGCC 58.186 50.000 6.37 0.00 0.00 4.35
731 743 4.888326 ACCAGGATCAGAGCATATCTTC 57.112 45.455 0.00 0.00 35.47 2.87
804 816 1.289066 GGCGTTGGGCTTTTTCTCC 59.711 57.895 0.00 0.00 42.94 3.71
937 978 3.375299 CCTCCTTTTCCATTCGACATGTC 59.625 47.826 16.21 16.21 0.00 3.06
992 1033 0.673644 CGTTCCACATCCACCCAGAC 60.674 60.000 0.00 0.00 0.00 3.51
1142 1183 0.178970 GGCATCATCCTGGCCTCATT 60.179 55.000 3.32 0.00 44.32 2.57
1218 1259 1.349627 CGTGTTCATCCATCGCTGC 59.650 57.895 0.00 0.00 0.00 5.25
1235 1276 1.305219 TGCCTTGCAGCATTCGTACC 61.305 55.000 0.00 0.00 38.00 3.34
1247 1288 5.122239 CAGCATTCGTACCAGAAAGAAATCA 59.878 40.000 0.00 0.00 33.43 2.57
1253 1294 7.647907 TCGTACCAGAAAGAAATCAACTTAC 57.352 36.000 0.00 0.00 0.00 2.34
1304 1350 2.593956 GCCCTTCCTCCTTGACCGT 61.594 63.158 0.00 0.00 0.00 4.83
1326 1372 1.322338 GCAACACAATTGATGCGATGC 59.678 47.619 13.59 13.21 41.15 3.91
1327 1373 1.580256 CAACACAATTGATGCGATGCG 59.420 47.619 13.59 0.00 0.00 4.73
1328 1374 1.085893 ACACAATTGATGCGATGCGA 58.914 45.000 13.59 0.00 0.00 5.10
1386 1447 2.509336 CGGACGAGGTGATGGTGC 60.509 66.667 0.00 0.00 0.00 5.01
1401 1462 2.435938 TGCCGAATCCCTTGTCGC 60.436 61.111 0.00 0.00 35.93 5.19
1482 1543 0.104304 GCTGCGTAAGGCCTAGCTAA 59.896 55.000 22.81 8.04 42.61 3.09
1507 1568 4.384940 GGCCTTTTTGCAATTACCTTCAA 58.615 39.130 0.00 0.00 0.00 2.69
1526 1587 7.504911 ACCTTCAATGAATAAATCAGCAGCTAT 59.495 33.333 0.00 0.00 42.53 2.97
1527 1588 7.808381 CCTTCAATGAATAAATCAGCAGCTATG 59.192 37.037 0.00 0.00 42.53 2.23
1559 1629 8.669243 AGACAGTACTAAATAAAGCTGCATTTC 58.331 33.333 1.02 0.00 0.00 2.17
1571 1641 3.840078 AGCTGCATTTCCCCTAAACATTT 59.160 39.130 1.02 0.00 0.00 2.32
1572 1642 5.022787 AGCTGCATTTCCCCTAAACATTTA 58.977 37.500 1.02 0.00 0.00 1.40
1573 1643 5.105351 AGCTGCATTTCCCCTAAACATTTAC 60.105 40.000 1.02 0.00 0.00 2.01
1661 1733 4.357947 ATCTGGTCGCGCGTGTGT 62.358 61.111 30.98 9.45 0.00 3.72
1691 1765 4.579869 AGACGTGCTCCATCAATTAGTTT 58.420 39.130 0.00 0.00 0.00 2.66
1712 1786 2.126618 CGCGCACGTGGAGAACTA 60.127 61.111 18.88 0.00 33.53 2.24
1713 1787 2.152699 CGCGCACGTGGAGAACTAG 61.153 63.158 18.88 0.00 33.53 2.57
1725 1799 0.172352 AGAACTAGCAGCAGCGAGAC 59.828 55.000 17.71 10.67 45.12 3.36
1741 1815 2.735444 CGAGACAATGAGGTGCACGTAT 60.735 50.000 12.81 2.58 0.00 3.06
1794 1907 0.761802 GGGGACTCCATCATCCTGAC 59.238 60.000 0.00 0.00 35.15 3.51
1831 1944 6.641169 AATCTTCAGCAGAGTCGTCATATA 57.359 37.500 0.00 0.00 33.87 0.86
1832 1945 6.832520 ATCTTCAGCAGAGTCGTCATATAT 57.167 37.500 0.00 0.00 33.87 0.86
1833 1946 6.641169 TCTTCAGCAGAGTCGTCATATATT 57.359 37.500 0.00 0.00 0.00 1.28
1834 1947 6.442112 TCTTCAGCAGAGTCGTCATATATTG 58.558 40.000 0.00 0.00 0.00 1.90
1835 1948 5.126396 TCAGCAGAGTCGTCATATATTGG 57.874 43.478 0.00 0.00 0.00 3.16
1836 1949 4.021981 TCAGCAGAGTCGTCATATATTGGG 60.022 45.833 0.00 0.00 0.00 4.12
1838 1951 4.021894 AGCAGAGTCGTCATATATTGGGAC 60.022 45.833 0.00 0.00 32.60 4.46
1839 1952 4.262036 GCAGAGTCGTCATATATTGGGACA 60.262 45.833 8.63 0.00 33.96 4.02
1853 1966 1.213430 TGGGACAAGGTTTCGGTCTTT 59.787 47.619 0.00 0.00 31.92 2.52
1857 1970 3.188667 GGACAAGGTTTCGGTCTTTGATC 59.811 47.826 0.00 0.00 0.00 2.92
1862 1976 5.183014 AGGTTTCGGTCTTTGATCAAAAC 57.817 39.130 20.82 19.03 0.00 2.43
1879 2001 6.918892 TCAAAACATTCTCTCGAGTTTTCA 57.081 33.333 13.13 0.00 40.89 2.69
2011 2157 1.550130 AAGGCGATTTCTCGTGGGGA 61.550 55.000 0.00 0.00 46.71 4.81
2012 2158 1.521681 GGCGATTTCTCGTGGGGAG 60.522 63.158 0.00 0.00 46.71 4.30
2018 2164 3.734293 CGATTTCTCGTGGGGAGTAGTTC 60.734 52.174 0.00 0.00 43.60 3.01
2066 2212 3.080647 AGCGATCCCGATGGTTTTC 57.919 52.632 0.00 0.00 38.22 2.29
2075 2221 0.996462 CGATGGTTTTCTAAGCGCGA 59.004 50.000 12.10 0.00 35.54 5.87
2078 2224 0.318869 TGGTTTTCTAAGCGCGACGA 60.319 50.000 12.10 0.00 34.50 4.20
2103 2249 0.734942 TCGAGCAATCGAACCGGAAC 60.735 55.000 9.46 0.00 39.34 3.62
2109 2255 1.604755 CAATCGAACCGGAACAAACCA 59.395 47.619 9.46 0.00 0.00 3.67
2110 2256 1.970092 ATCGAACCGGAACAAACCAA 58.030 45.000 9.46 0.00 0.00 3.67
2120 2266 0.536460 AACAAACCAACCGAGCCGAT 60.536 50.000 0.00 0.00 0.00 4.18
2135 2281 4.519147 GAGCCGATCGATTTTTCTAAAGC 58.481 43.478 18.66 6.57 0.00 3.51
2141 2287 5.522460 CGATCGATTTTTCTAAAGCCCAGTA 59.478 40.000 10.26 0.00 0.00 2.74
2169 2315 1.963172 GGTTCACAGAAAACCGGACT 58.037 50.000 9.46 0.00 37.06 3.85
2231 2378 2.214376 TTGTATGAACAAGCTGGGGG 57.786 50.000 0.00 0.00 40.69 5.40
2232 2379 1.072266 TGTATGAACAAGCTGGGGGT 58.928 50.000 0.00 0.00 30.91 4.95
2233 2380 2.270858 TGTATGAACAAGCTGGGGGTA 58.729 47.619 0.00 0.00 30.91 3.69
2234 2381 2.238646 TGTATGAACAAGCTGGGGGTAG 59.761 50.000 0.00 0.00 30.91 3.18
2236 2383 1.440618 TGAACAAGCTGGGGGTAGAA 58.559 50.000 0.00 0.00 0.00 2.10
2237 2384 1.992557 TGAACAAGCTGGGGGTAGAAT 59.007 47.619 0.00 0.00 0.00 2.40
2238 2385 2.378547 TGAACAAGCTGGGGGTAGAATT 59.621 45.455 0.00 0.00 0.00 2.17
2268 2415 4.591498 GGAAGAAAACCCCACTTTTGGTAT 59.409 41.667 0.00 0.00 42.10 2.73
2304 2451 6.705863 ACTGGGAGCATTTATCTCAATTTC 57.294 37.500 0.00 0.00 32.38 2.17
2332 2480 4.202161 ACAAACAAACAATATCGGGTGCAA 60.202 37.500 0.00 0.00 0.00 4.08
2368 2516 1.664965 AGCTTTGTCAGGCGTCGTC 60.665 57.895 0.00 0.00 0.00 4.20
2400 2549 3.080121 CCTCTCCCTTGCCGCTCT 61.080 66.667 0.00 0.00 0.00 4.09
2403 2552 4.399395 CTCCCTTGCCGCTCTGCA 62.399 66.667 0.00 0.00 40.07 4.41
2511 2667 3.781307 CGGCCTGGTCGGATTGGA 61.781 66.667 13.97 0.00 33.16 3.53
2569 4647 1.993391 CCAAGCCTCCCTCCGGTTA 60.993 63.158 0.00 0.00 0.00 2.85
2626 4704 2.373707 GCAGGAGGACCAGGATGCT 61.374 63.158 0.00 0.00 38.94 3.79
2627 4705 1.828768 CAGGAGGACCAGGATGCTC 59.171 63.158 0.00 0.00 38.94 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.830444 TCACTAACTGACCGGTGCCT 60.830 55.000 14.63 0.00 0.00 4.75
3 4 1.069513 TGGTTCACTAACTGACCGGTG 59.930 52.381 14.63 0.00 35.81 4.94
4 5 1.416243 TGGTTCACTAACTGACCGGT 58.584 50.000 6.92 6.92 35.81 5.28
7 8 4.537135 TCAGATGGTTCACTAACTGACC 57.463 45.455 0.00 0.00 35.81 4.02
8 9 6.650807 TGAATTCAGATGGTTCACTAACTGAC 59.349 38.462 3.38 0.00 34.79 3.51
9 10 6.768483 TGAATTCAGATGGTTCACTAACTGA 58.232 36.000 3.38 0.00 35.81 3.41
10 11 7.465111 CGATGAATTCAGATGGTTCACTAACTG 60.465 40.741 14.54 0.00 34.98 3.16
11 12 6.536582 CGATGAATTCAGATGGTTCACTAACT 59.463 38.462 14.54 0.00 34.98 2.24
12 13 6.313905 ACGATGAATTCAGATGGTTCACTAAC 59.686 38.462 14.54 0.00 34.98 2.34
27 28 8.450964 TGGAGTTTCAAAGATTACGATGAATTC 58.549 33.333 0.00 0.00 32.35 2.17
32 33 8.883731 AGTAATGGAGTTTCAAAGATTACGATG 58.116 33.333 0.00 0.00 33.46 3.84
79 80 8.895737 GGTAATGTCGGATAAAAATGAAGGTTA 58.104 33.333 0.00 0.00 0.00 2.85
86 87 6.935741 TGGAGGTAATGTCGGATAAAAATG 57.064 37.500 0.00 0.00 0.00 2.32
119 120 2.171003 CACCCCCAATCAAAGAAGACC 58.829 52.381 0.00 0.00 0.00 3.85
137 140 3.420482 CCCCATCCCTCCCACCAC 61.420 72.222 0.00 0.00 0.00 4.16
149 152 1.391729 CCATCACCCCAAACCCCAT 59.608 57.895 0.00 0.00 0.00 4.00
158 161 1.281925 ATCACTCCCACCATCACCCC 61.282 60.000 0.00 0.00 0.00 4.95
162 165 1.609239 GCCATCACTCCCACCATCA 59.391 57.895 0.00 0.00 0.00 3.07
165 168 4.408821 GCGCCATCACTCCCACCA 62.409 66.667 0.00 0.00 0.00 4.17
167 170 1.523154 TTTTGCGCCATCACTCCCAC 61.523 55.000 4.18 0.00 0.00 4.61
168 171 0.825425 TTTTTGCGCCATCACTCCCA 60.825 50.000 4.18 0.00 0.00 4.37
185 188 1.299976 CACCTCCGCCCTAGCTTTT 59.700 57.895 0.00 0.00 36.60 2.27
186 189 1.489560 AACACCTCCGCCCTAGCTTT 61.490 55.000 0.00 0.00 36.60 3.51
233 236 2.225522 TGTGTGGAGAGGATTCTACCCA 60.226 50.000 0.00 0.00 32.87 4.51
234 237 2.467880 TGTGTGGAGAGGATTCTACCC 58.532 52.381 0.00 0.00 32.87 3.69
271 274 4.804420 TCCCCGAGGCTGGAGCAT 62.804 66.667 0.00 0.00 44.36 3.79
277 280 1.144936 GTCAAGATCCCCGAGGCTG 59.855 63.158 0.00 0.00 0.00 4.85
287 290 3.829948 CTTGTGTGGCATTGTCAAGATC 58.170 45.455 14.14 0.00 38.06 2.75
288 291 2.029649 GCTTGTGTGGCATTGTCAAGAT 60.030 45.455 19.71 0.00 38.06 2.40
292 295 0.669619 CTGCTTGTGTGGCATTGTCA 59.330 50.000 0.00 0.00 39.07 3.58
296 299 0.956633 CTCACTGCTTGTGTGGCATT 59.043 50.000 9.53 0.00 46.27 3.56
297 300 2.637521 CTCACTGCTTGTGTGGCAT 58.362 52.632 9.53 0.00 46.27 4.40
309 312 0.675837 CAGGGTCACATGCCTCACTG 60.676 60.000 0.00 0.00 0.00 3.66
312 315 0.545071 TCTCAGGGTCACATGCCTCA 60.545 55.000 0.00 0.00 0.00 3.86
320 323 3.449018 ACACTGTCATATCTCAGGGTCAC 59.551 47.826 5.92 0.00 43.65 3.67
321 324 3.713003 ACACTGTCATATCTCAGGGTCA 58.287 45.455 5.92 0.00 43.65 4.02
330 333 4.327357 CCGAACAAGTGACACTGTCATATC 59.673 45.833 14.95 2.92 44.63 1.63
371 374 2.826777 CTTGCAATGGCCTCCTCCGT 62.827 60.000 3.32 0.00 40.13 4.69
380 383 1.066716 TCATTCCAAGCTTGCAATGGC 60.067 47.619 32.65 7.56 41.68 4.40
383 386 3.243839 ACGTTTCATTCCAAGCTTGCAAT 60.244 39.130 21.43 15.68 0.00 3.56
384 387 2.100584 ACGTTTCATTCCAAGCTTGCAA 59.899 40.909 21.43 13.76 0.00 4.08
425 428 2.027073 CGCCGCTGCAAGTAGTTCA 61.027 57.895 0.00 0.00 37.32 3.18
431 434 4.947147 TTTCCCGCCGCTGCAAGT 62.947 61.111 0.00 0.00 37.32 3.16
438 441 2.014594 CTAGTTCATTTCCCGCCGC 58.985 57.895 0.00 0.00 0.00 6.53
454 457 4.908601 TGTTCCCTTTCATCTCAAGCTA 57.091 40.909 0.00 0.00 0.00 3.32
459 462 6.790232 AAGTTTTTGTTCCCTTTCATCTCA 57.210 33.333 0.00 0.00 0.00 3.27
464 467 5.483811 GGTGAAAGTTTTTGTTCCCTTTCA 58.516 37.500 9.02 9.02 46.22 2.69
483 486 2.439701 CCGACTCCTAGCCGGTGA 60.440 66.667 1.90 0.00 38.55 4.02
491 494 1.760192 GTAGTGGCTTCCGACTCCTA 58.240 55.000 0.00 0.00 0.00 2.94
495 498 4.092343 ACGTAGTGGCTTCCGACT 57.908 55.556 0.00 0.00 42.51 4.18
584 587 8.504005 GTCCGAGAATTTTTCATAGAAAGTTCA 58.496 33.333 15.52 0.00 37.57 3.18
585 588 8.504005 TGTCCGAGAATTTTTCATAGAAAGTTC 58.496 33.333 9.65 9.65 36.23 3.01
587 590 7.979444 TGTCCGAGAATTTTTCATAGAAAGT 57.021 32.000 0.00 0.00 0.00 2.66
588 591 9.495754 GAATGTCCGAGAATTTTTCATAGAAAG 57.504 33.333 0.00 0.00 0.00 2.62
592 597 6.729187 GGGAATGTCCGAGAATTTTTCATAG 58.271 40.000 0.00 0.00 37.43 2.23
594 599 5.582689 GGGAATGTCCGAGAATTTTTCAT 57.417 39.130 0.00 0.00 37.43 2.57
610 615 2.014128 AGCGGTTTATTGTCGGGAATG 58.986 47.619 0.00 0.00 0.00 2.67
615 620 2.012937 TACCAGCGGTTTATTGTCGG 57.987 50.000 5.57 0.00 37.09 4.79
616 621 4.407496 TTTTACCAGCGGTTTATTGTCG 57.593 40.909 5.57 0.00 37.09 4.35
620 625 5.632244 ACGAATTTTACCAGCGGTTTATT 57.368 34.783 5.57 4.20 37.09 1.40
622 627 5.008415 TCAAACGAATTTTACCAGCGGTTTA 59.992 36.000 5.57 0.00 37.09 2.01
626 631 3.546002 TCAAACGAATTTTACCAGCGG 57.454 42.857 0.00 0.00 0.00 5.52
628 633 8.921670 ACATTAATTCAAACGAATTTTACCAGC 58.078 29.630 5.80 0.00 42.00 4.85
704 709 7.166851 AGATATGCTCTGATCCTGGTTTATTG 58.833 38.462 0.00 0.00 31.12 1.90
742 754 0.668535 GTGTTCTGCTCCCGCTTTTT 59.331 50.000 0.00 0.00 36.97 1.94
743 755 1.172812 GGTGTTCTGCTCCCGCTTTT 61.173 55.000 0.00 0.00 36.97 2.27
744 756 1.600916 GGTGTTCTGCTCCCGCTTT 60.601 57.895 0.00 0.00 36.97 3.51
745 757 2.032681 GGTGTTCTGCTCCCGCTT 59.967 61.111 0.00 0.00 36.97 4.68
746 758 2.337879 TTTGGTGTTCTGCTCCCGCT 62.338 55.000 0.00 0.00 36.97 5.52
826 867 6.048732 TCCTACTATCACATGAAAAGCACA 57.951 37.500 0.00 0.00 0.00 4.57
992 1033 1.378119 GCCTCTGTTTTACCCGGGG 60.378 63.158 27.92 12.73 0.00 5.73
1033 1074 1.236628 GATGGATGCAAGCTGCTAGG 58.763 55.000 0.90 0.00 45.31 3.02
1039 1080 2.239400 CATGGATGATGGATGCAAGCT 58.761 47.619 0.00 0.00 35.78 3.74
1040 1081 2.724977 CATGGATGATGGATGCAAGC 57.275 50.000 0.00 0.00 35.78 4.01
1119 1160 2.903855 GCCAGGATGATGCCGGTG 60.904 66.667 1.90 0.00 39.69 4.94
1218 1259 0.729116 CTGGTACGAATGCTGCAAGG 59.271 55.000 6.36 1.08 0.00 3.61
1230 1271 7.653767 AGTAAGTTGATTTCTTTCTGGTACG 57.346 36.000 0.00 0.00 0.00 3.67
1263 1304 8.368668 GGGCAGTCAGTATCTTACAACTTATAT 58.631 37.037 0.00 0.00 0.00 0.86
1264 1305 7.563924 AGGGCAGTCAGTATCTTACAACTTATA 59.436 37.037 0.00 0.00 0.00 0.98
1265 1306 6.384305 AGGGCAGTCAGTATCTTACAACTTAT 59.616 38.462 0.00 0.00 0.00 1.73
1270 1311 4.081087 GGAAGGGCAGTCAGTATCTTACAA 60.081 45.833 0.00 0.00 0.00 2.41
1287 1329 0.321653 CAACGGTCAAGGAGGAAGGG 60.322 60.000 0.00 0.00 0.00 3.95
1304 1350 2.789491 TCGCATCAATTGTGTTGCAA 57.211 40.000 21.62 0.00 46.52 4.08
1338 1384 2.124942 CTTCTTCCTCTGCCGCCC 60.125 66.667 0.00 0.00 0.00 6.13
1386 1447 1.521681 GGAGCGACAAGGGATTCGG 60.522 63.158 0.00 0.00 35.73 4.30
1482 1543 2.831526 AGGTAATTGCAAAAAGGCCGAT 59.168 40.909 1.71 0.00 0.00 4.18
1507 1568 7.677892 TCTCTCATAGCTGCTGATTTATTCAT 58.322 34.615 13.43 0.00 32.72 2.57
1526 1587 9.026121 AGCTTTATTTAGTACTGTCTTCTCTCA 57.974 33.333 5.39 0.00 0.00 3.27
1527 1588 9.296400 CAGCTTTATTTAGTACTGTCTTCTCTC 57.704 37.037 5.39 0.00 0.00 3.20
1559 1629 7.046033 ACTCGAATGTAGTAAATGTTTAGGGG 58.954 38.462 0.00 0.00 0.00 4.79
1634 1706 1.524355 CGCGACCAGATGCTTCATAAG 59.476 52.381 0.00 0.00 0.00 1.73
1635 1707 1.570813 CGCGACCAGATGCTTCATAA 58.429 50.000 0.00 0.00 0.00 1.90
1636 1708 0.875908 GCGCGACCAGATGCTTCATA 60.876 55.000 12.10 0.00 0.00 2.15
1637 1709 2.176273 GCGCGACCAGATGCTTCAT 61.176 57.895 12.10 0.00 0.00 2.57
1661 1733 0.176910 TGGAGCACGTCTCAAACACA 59.823 50.000 14.26 3.38 43.70 3.72
1711 1785 0.532115 TCATTGTCTCGCTGCTGCTA 59.468 50.000 14.03 1.49 36.97 3.49
1712 1786 0.740164 CTCATTGTCTCGCTGCTGCT 60.740 55.000 14.03 0.00 36.97 4.24
1713 1787 1.703438 CCTCATTGTCTCGCTGCTGC 61.703 60.000 5.34 5.34 0.00 5.25
1725 1799 4.433615 ACTCTAATACGTGCACCTCATTG 58.566 43.478 12.15 0.00 0.00 2.82
1741 1815 6.724441 TCCATTCTCAAACACTCCTACTCTAA 59.276 38.462 0.00 0.00 0.00 2.10
1794 1907 5.291858 TGCTGAAGATTCGCTAACAGTTATG 59.708 40.000 0.00 0.00 35.22 1.90
1831 1944 1.423921 AGACCGAAACCTTGTCCCAAT 59.576 47.619 0.00 0.00 0.00 3.16
1832 1945 0.841289 AGACCGAAACCTTGTCCCAA 59.159 50.000 0.00 0.00 0.00 4.12
1833 1946 0.841289 AAGACCGAAACCTTGTCCCA 59.159 50.000 0.00 0.00 0.00 4.37
1834 1947 1.607148 CAAAGACCGAAACCTTGTCCC 59.393 52.381 0.00 0.00 0.00 4.46
1835 1948 2.567985 TCAAAGACCGAAACCTTGTCC 58.432 47.619 0.00 0.00 0.00 4.02
1836 1949 3.813166 TGATCAAAGACCGAAACCTTGTC 59.187 43.478 0.00 0.00 0.00 3.18
1838 1951 4.829064 TTGATCAAAGACCGAAACCTTG 57.171 40.909 5.45 0.00 0.00 3.61
1839 1952 5.126384 TGTTTTGATCAAAGACCGAAACCTT 59.874 36.000 19.64 0.00 34.76 3.50
1840 1953 4.642885 TGTTTTGATCAAAGACCGAAACCT 59.357 37.500 19.64 0.00 34.76 3.50
1842 1955 6.918022 AGAATGTTTTGATCAAAGACCGAAAC 59.082 34.615 19.64 13.84 35.69 2.78
1848 1961 7.095439 ACTCGAGAGAATGTTTTGATCAAAGAC 60.095 37.037 21.68 19.02 41.32 3.01
1853 1966 7.226523 TGAAAACTCGAGAGAATGTTTTGATCA 59.773 33.333 21.68 6.91 43.83 2.92
1857 1970 6.138761 CCTGAAAACTCGAGAGAATGTTTTG 58.861 40.000 21.68 4.43 43.83 2.44
1862 1976 5.578727 CCTAACCTGAAAACTCGAGAGAATG 59.421 44.000 21.68 4.40 41.32 2.67
1989 2135 1.134788 CCCACGAGAAATCGCCTTACT 60.135 52.381 0.00 0.00 36.44 2.24
2033 2179 2.188062 TCGCTGGTTCCGGTTTATTT 57.812 45.000 0.00 0.00 0.00 1.40
2036 2182 0.108041 GGATCGCTGGTTCCGGTTTA 60.108 55.000 0.00 0.00 0.00 2.01
2066 2212 0.362512 GAACAGTTCGTCGCGCTTAG 59.637 55.000 5.56 0.00 0.00 2.18
2103 2249 1.794222 GATCGGCTCGGTTGGTTTG 59.206 57.895 0.00 0.00 0.00 2.93
2120 2266 6.713450 AGTTTACTGGGCTTTAGAAAAATCGA 59.287 34.615 0.00 0.00 0.00 3.59
2141 2287 2.818751 TTCTGTGAACCACCCAGTTT 57.181 45.000 0.00 0.00 32.73 2.66
2169 2315 5.562696 GCTTTTCAGGAAATGACATCGAACA 60.563 40.000 10.71 0.00 37.77 3.18
2231 2378 7.152645 GGGTTTTCTTCCTTTTCCAATTCTAC 58.847 38.462 0.00 0.00 0.00 2.59
2232 2379 6.269077 GGGGTTTTCTTCCTTTTCCAATTCTA 59.731 38.462 0.00 0.00 0.00 2.10
2233 2380 5.071788 GGGGTTTTCTTCCTTTTCCAATTCT 59.928 40.000 0.00 0.00 0.00 2.40
2234 2381 5.163248 TGGGGTTTTCTTCCTTTTCCAATTC 60.163 40.000 0.00 0.00 0.00 2.17
2236 2383 4.102524 GTGGGGTTTTCTTCCTTTTCCAAT 59.897 41.667 0.00 0.00 0.00 3.16
2237 2384 3.452990 GTGGGGTTTTCTTCCTTTTCCAA 59.547 43.478 0.00 0.00 0.00 3.53
2238 2385 3.035363 GTGGGGTTTTCTTCCTTTTCCA 58.965 45.455 0.00 0.00 0.00 3.53
2268 2415 1.830408 CCCAGTTTGGCCGAAACCA 60.830 57.895 20.36 0.00 44.54 3.67
2304 2451 4.155449 CCGATATTGTTTGTTTGTGGACG 58.845 43.478 0.00 0.00 0.00 4.79
2351 2499 2.853914 GACGACGCCTGACAAAGC 59.146 61.111 0.00 0.00 0.00 3.51
2353 2501 1.947146 CACGACGACGCCTGACAAA 60.947 57.895 7.30 0.00 43.96 2.83
2443 2592 0.685458 ATGGCGTAGGACGGTAGGTT 60.685 55.000 0.70 0.00 42.82 3.50
2444 2593 1.076485 ATGGCGTAGGACGGTAGGT 60.076 57.895 0.70 0.00 42.82 3.08
2495 2651 2.124695 GTCCAATCCGACCAGGCC 60.125 66.667 0.00 0.00 40.77 5.19
2511 2667 1.196012 GGAGATCGGAGTTGGAAGGT 58.804 55.000 0.00 0.00 0.00 3.50
2569 4647 2.657143 GACTATGGAACGGAGAGAGGT 58.343 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.