Multiple sequence alignment - TraesCS3B01G114900

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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 TraesCS3B01G114900 chr3B 100.000 2319 0 0 1 2319 81301088 81303406 0.000000e+00 4283
1 TraesCS3B01G114900 chr3B 80.952 714 115 15 639 1344 399502183 399502883 1.570000e-151 545
2 TraesCS3B01G114900 chr3B 95.745 94 4 0 1583 1676 256728028 256728121 3.990000e-33 152
3 TraesCS3B01G114900 chr5B 97.325 1346 34 2 1 1346 401664969 401663626 0.000000e+00 2285
4 TraesCS3B01G114900 chr5B 96.652 1344 41 4 1 1343 686778237 686779577 0.000000e+00 2230
5 TraesCS3B01G114900 chr5B 96.809 94 3 0 1583 1676 107198507 107198414 8.580000e-35 158
6 TraesCS3B01G114900 chr2B 90.416 1346 124 4 1 1345 247562653 247561312 0.000000e+00 1766
7 TraesCS3B01G114900 chr2B 94.175 103 6 0 1575 1677 371564697 371564799 8.580000e-35 158
8 TraesCS3B01G114900 chr2B 95.000 100 5 0 1577 1676 664210409 664210508 8.580000e-35 158
9 TraesCS3B01G114900 chr2B 93.750 96 6 0 1581 1676 708435351 708435256 6.680000e-31 145
10 TraesCS3B01G114900 chr2A 88.327 1345 152 4 4 1345 771799654 771798312 0.000000e+00 1609
11 TraesCS3B01G114900 chr6B 85.577 1352 171 17 1 1346 49987574 49988907 0.000000e+00 1395
12 TraesCS3B01G114900 chr6B 84.384 666 94 10 622 1283 630869140 630868481 0.000000e+00 645
13 TraesCS3B01G114900 chr1D 81.961 1020 173 10 331 1345 335361088 335362101 0.000000e+00 854
14 TraesCS3B01G114900 chr1D 81.273 817 139 11 534 1344 476668269 476669077 0.000000e+00 649
15 TraesCS3B01G114900 chr3D 90.727 550 30 14 1662 2201 50872675 50873213 0.000000e+00 713
16 TraesCS3B01G114900 chr3D 92.000 200 14 2 1368 1565 50872486 50872685 1.750000e-71 279
17 TraesCS3B01G114900 chr3D 89.344 122 11 2 2200 2319 50873182 50873303 3.990000e-33 152
18 TraesCS3B01G114900 chr3A 77.094 585 57 40 1662 2188 63829317 63829882 1.370000e-67 267
19 TraesCS3B01G114900 chr7B 98.947 95 1 0 1580 1674 687432045 687432139 1.100000e-38 171
20 TraesCS3B01G114900 chr4D 95.876 97 3 1 1580 1676 84999369 84999464 3.090000e-34 156
21 TraesCS3B01G114900 chr4B 95.789 95 4 0 1583 1677 104815566 104815660 1.110000e-33 154
22 TraesCS3B01G114900 chr5D 94.000 100 6 0 1575 1674 388860947 388861046 3.990000e-33 152


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 TraesCS3B01G114900 chr3B 81301088 81303406 2318 False 4283.000000 4283 100.000000 1 2319 1 chr3B.!!$F1 2318
1 TraesCS3B01G114900 chr3B 399502183 399502883 700 False 545.000000 545 80.952000 639 1344 1 chr3B.!!$F3 705
2 TraesCS3B01G114900 chr5B 401663626 401664969 1343 True 2285.000000 2285 97.325000 1 1346 1 chr5B.!!$R2 1345
3 TraesCS3B01G114900 chr5B 686778237 686779577 1340 False 2230.000000 2230 96.652000 1 1343 1 chr5B.!!$F1 1342
4 TraesCS3B01G114900 chr2B 247561312 247562653 1341 True 1766.000000 1766 90.416000 1 1345 1 chr2B.!!$R1 1344
5 TraesCS3B01G114900 chr2A 771798312 771799654 1342 True 1609.000000 1609 88.327000 4 1345 1 chr2A.!!$R1 1341
6 TraesCS3B01G114900 chr6B 49987574 49988907 1333 False 1395.000000 1395 85.577000 1 1346 1 chr6B.!!$F1 1345
7 TraesCS3B01G114900 chr6B 630868481 630869140 659 True 645.000000 645 84.384000 622 1283 1 chr6B.!!$R1 661
8 TraesCS3B01G114900 chr1D 335361088 335362101 1013 False 854.000000 854 81.961000 331 1345 1 chr1D.!!$F1 1014
9 TraesCS3B01G114900 chr1D 476668269 476669077 808 False 649.000000 649 81.273000 534 1344 1 chr1D.!!$F2 810
10 TraesCS3B01G114900 chr3D 50872486 50873303 817 False 381.333333 713 90.690333 1368 2319 3 chr3D.!!$F1 951
11 TraesCS3B01G114900 chr3A 63829317 63829882 565 False 267.000000 267 77.094000 1662 2188 1 chr3A.!!$F1 526

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
720 723 0.538584 CAGCTACATGCAGTCCCTCA 59.461 55.0 0.0 0.0 45.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2144 0.394565 GTTGTCTGAGGCCTGTCTGT 59.605 55.0 12.0 0.0 0.0 3.41 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
51 52 3.508845 ATTGCAGACTTAACTGGGTGT 57.491 42.857 0.00 0.00 38.22 4.16
140 141 8.792830 TGGATGTTCGAGAAATTCTTAAGATT 57.207 30.769 5.89 0.00 0.00 2.40
153 154 4.990257 TCTTAAGATTCGTACTTCACCGG 58.010 43.478 0.00 0.00 0.00 5.28
281 282 1.227853 GACCAGCAACAACCCGTCT 60.228 57.895 0.00 0.00 0.00 4.18
720 723 0.538584 CAGCTACATGCAGTCCCTCA 59.461 55.000 0.00 0.00 45.94 3.86
757 760 5.404667 GGTTTTCGACCGAGGATATTATCAC 59.595 44.000 6.04 0.00 39.00 3.06
761 764 3.756963 CGACCGAGGATATTATCACAGGA 59.243 47.826 13.80 0.00 0.00 3.86
1041 1044 1.053835 TCCAACACTGTGAGCTCCCA 61.054 55.000 15.86 4.68 0.00 4.37
1325 1330 9.287818 ACCCTATACCTTTGGAATAAAACTCTA 57.712 33.333 0.00 0.00 0.00 2.43
1334 1339 9.383519 CTTTGGAATAAAACTCTACTATCAGCA 57.616 33.333 0.00 0.00 0.00 4.41
1335 1340 9.733556 TTTGGAATAAAACTCTACTATCAGCAA 57.266 29.630 0.00 0.00 0.00 3.91
1384 1389 9.730420 CTCTTACTGAAAAGAGCTCTTCTATAC 57.270 37.037 28.58 17.22 44.33 1.47
1388 1393 5.103000 TGAAAAGAGCTCTTCTATACGTGC 58.897 41.667 28.58 10.97 34.14 5.34
1432 1437 6.389906 GGCCGCTTTTCTGCATATTTTATAT 58.610 36.000 0.00 0.00 0.00 0.86
1491 1496 7.156000 AGATGTTCATGCATTTCAAACAATGA 58.844 30.769 14.21 0.00 36.39 2.57
1523 1529 9.649024 AACTTGAAAAATGTTTGCGATATTTTG 57.351 25.926 9.12 2.48 38.54 2.44
1524 1530 9.039870 ACTTGAAAAATGTTTGCGATATTTTGA 57.960 25.926 9.12 0.50 38.54 2.69
1525 1531 9.861138 CTTGAAAAATGTTTGCGATATTTTGAA 57.139 25.926 9.12 6.13 38.54 2.69
1531 1537 9.810231 AAATGTTTGCGATATTTTGAAAATGAC 57.190 25.926 13.08 6.21 0.00 3.06
1532 1538 7.344910 TGTTTGCGATATTTTGAAAATGACC 57.655 32.000 13.08 1.95 0.00 4.02
1533 1539 6.925718 TGTTTGCGATATTTTGAAAATGACCA 59.074 30.769 13.08 2.97 0.00 4.02
1534 1540 7.601886 TGTTTGCGATATTTTGAAAATGACCAT 59.398 29.630 13.08 0.00 0.00 3.55
1535 1541 9.081997 GTTTGCGATATTTTGAAAATGACCATA 57.918 29.630 13.08 0.00 0.00 2.74
1536 1542 9.645059 TTTGCGATATTTTGAAAATGACCATAA 57.355 25.926 13.08 0.07 0.00 1.90
1537 1543 9.645059 TTGCGATATTTTGAAAATGACCATAAA 57.355 25.926 13.08 0.00 0.00 1.40
1538 1544 9.814899 TGCGATATTTTGAAAATGACCATAAAT 57.185 25.926 13.08 0.00 0.00 1.40
1607 1613 9.761504 ACAGAATGACTAATTCACATCTAGATG 57.238 33.333 27.63 27.63 46.21 2.90
1608 1614 9.761504 CAGAATGACTAATTCACATCTAGATGT 57.238 33.333 28.95 28.95 46.65 3.06
1634 1640 8.842358 TTTTTAAGGATGTCACACCTAAGTAG 57.158 34.615 0.00 0.00 35.25 2.57
1635 1641 7.549147 TTTAAGGATGTCACACCTAAGTAGT 57.451 36.000 0.00 0.00 35.25 2.73
1636 1642 7.549147 TTAAGGATGTCACACCTAAGTAGTT 57.451 36.000 0.00 0.00 35.25 2.24
1637 1643 5.662674 AGGATGTCACACCTAAGTAGTTC 57.337 43.478 0.00 0.00 34.47 3.01
1638 1644 5.084519 AGGATGTCACACCTAAGTAGTTCA 58.915 41.667 0.00 0.00 34.47 3.18
1639 1645 5.721960 AGGATGTCACACCTAAGTAGTTCAT 59.278 40.000 0.00 0.00 34.47 2.57
1640 1646 6.043411 GGATGTCACACCTAAGTAGTTCATC 58.957 44.000 0.00 0.00 0.00 2.92
1641 1647 6.351033 GGATGTCACACCTAAGTAGTTCATCA 60.351 42.308 0.00 0.00 32.47 3.07
1642 1648 5.779922 TGTCACACCTAAGTAGTTCATCAC 58.220 41.667 0.00 0.00 0.00 3.06
1643 1649 5.303333 TGTCACACCTAAGTAGTTCATCACA 59.697 40.000 0.00 0.00 0.00 3.58
1644 1650 6.014584 TGTCACACCTAAGTAGTTCATCACAT 60.015 38.462 0.00 0.00 0.00 3.21
1645 1651 7.177744 TGTCACACCTAAGTAGTTCATCACATA 59.822 37.037 0.00 0.00 0.00 2.29
1646 1652 8.033038 GTCACACCTAAGTAGTTCATCACATAA 58.967 37.037 0.00 0.00 0.00 1.90
1647 1653 8.758829 TCACACCTAAGTAGTTCATCACATAAT 58.241 33.333 0.00 0.00 0.00 1.28
1648 1654 9.383519 CACACCTAAGTAGTTCATCACATAATT 57.616 33.333 0.00 0.00 0.00 1.40
1652 1658 9.712305 CCTAAGTAGTTCATCACATAATTAGGG 57.288 37.037 1.74 0.00 34.50 3.53
1653 1659 9.712305 CTAAGTAGTTCATCACATAATTAGGGG 57.288 37.037 1.74 0.00 0.00 4.79
1654 1660 6.534634 AGTAGTTCATCACATAATTAGGGGC 58.465 40.000 1.74 0.00 0.00 5.80
1655 1661 5.653255 AGTTCATCACATAATTAGGGGCT 57.347 39.130 1.74 0.00 0.00 5.19
1656 1662 6.018433 AGTTCATCACATAATTAGGGGCTT 57.982 37.500 1.74 0.00 0.00 4.35
1657 1663 6.064717 AGTTCATCACATAATTAGGGGCTTC 58.935 40.000 1.74 0.00 0.00 3.86
1658 1664 5.645056 TCATCACATAATTAGGGGCTTCA 57.355 39.130 1.74 0.00 0.00 3.02
1659 1665 6.012337 TCATCACATAATTAGGGGCTTCAA 57.988 37.500 1.74 0.00 0.00 2.69
1660 1666 6.064060 TCATCACATAATTAGGGGCTTCAAG 58.936 40.000 1.74 0.00 0.00 3.02
1661 1667 5.708736 TCACATAATTAGGGGCTTCAAGA 57.291 39.130 1.74 0.00 0.00 3.02
1662 1668 6.266131 TCACATAATTAGGGGCTTCAAGAT 57.734 37.500 1.74 0.00 0.00 2.40
1663 1669 6.672593 TCACATAATTAGGGGCTTCAAGATT 58.327 36.000 1.74 0.00 0.00 2.40
1664 1670 7.125391 TCACATAATTAGGGGCTTCAAGATTT 58.875 34.615 1.74 0.00 0.00 2.17
1665 1671 7.068593 TCACATAATTAGGGGCTTCAAGATTTG 59.931 37.037 1.74 0.00 0.00 2.32
1666 1672 6.897413 ACATAATTAGGGGCTTCAAGATTTGT 59.103 34.615 1.74 0.00 0.00 2.83
1667 1673 8.058847 ACATAATTAGGGGCTTCAAGATTTGTA 58.941 33.333 1.74 0.00 0.00 2.41
1668 1674 6.775594 AATTAGGGGCTTCAAGATTTGTAC 57.224 37.500 0.00 0.00 0.00 2.90
1676 1682 8.691797 GGGGCTTCAAGATTTGTACAAAATATA 58.308 33.333 23.97 2.05 33.56 0.86
1766 1774 8.592105 AAATACCATGAATGAACAAACAAGTG 57.408 30.769 0.00 0.00 0.00 3.16
1873 1909 9.948964 AAATGGAAGAATGAAATAGGGAAAAAG 57.051 29.630 0.00 0.00 0.00 2.27
1947 1985 7.598493 CGATTGAATAAACAGAAAACCCAACAT 59.402 33.333 0.00 0.00 0.00 2.71
1952 1990 9.974980 GAATAAACAGAAAACCCAACATAGAAA 57.025 29.630 0.00 0.00 0.00 2.52
2004 2056 0.741915 TCCAAAACCACGTGAAAGGC 59.258 50.000 19.30 0.00 0.00 4.35
2113 2181 1.203187 AGACAGGCCTCAGACAACCTA 60.203 52.381 0.00 0.00 0.00 3.08
2158 2226 3.801594 TCCAAAACGTTCGTTACCTGTAC 59.198 43.478 10.89 0.00 0.00 2.90
2167 2235 1.532505 CGTTACCTGTACCATCCGTCG 60.533 57.143 0.00 0.00 0.00 5.12
2168 2236 1.745087 GTTACCTGTACCATCCGTCGA 59.255 52.381 0.00 0.00 0.00 4.20
2169 2237 2.127271 TACCTGTACCATCCGTCGAA 57.873 50.000 0.00 0.00 0.00 3.71
2170 2238 1.259609 ACCTGTACCATCCGTCGAAA 58.740 50.000 0.00 0.00 0.00 3.46
2171 2239 1.829222 ACCTGTACCATCCGTCGAAAT 59.171 47.619 0.00 0.00 0.00 2.17
2172 2240 2.159142 ACCTGTACCATCCGTCGAAATC 60.159 50.000 0.00 0.00 0.00 2.17
2173 2241 2.159156 CCTGTACCATCCGTCGAAATCA 60.159 50.000 0.00 0.00 0.00 2.57
2174 2242 2.858344 CTGTACCATCCGTCGAAATCAC 59.142 50.000 0.00 0.00 0.00 3.06
2175 2243 2.494471 TGTACCATCCGTCGAAATCACT 59.506 45.455 0.00 0.00 0.00 3.41
2176 2244 3.695556 TGTACCATCCGTCGAAATCACTA 59.304 43.478 0.00 0.00 0.00 2.74
2177 2245 3.880047 ACCATCCGTCGAAATCACTAA 57.120 42.857 0.00 0.00 0.00 2.24
2178 2246 4.402056 ACCATCCGTCGAAATCACTAAT 57.598 40.909 0.00 0.00 0.00 1.73
2179 2247 4.766375 ACCATCCGTCGAAATCACTAATT 58.234 39.130 0.00 0.00 0.00 1.40
2180 2248 5.909477 ACCATCCGTCGAAATCACTAATTA 58.091 37.500 0.00 0.00 0.00 1.40
2181 2249 5.983720 ACCATCCGTCGAAATCACTAATTAG 59.016 40.000 11.05 11.05 0.00 1.73
2182 2250 5.405571 CCATCCGTCGAAATCACTAATTAGG 59.594 44.000 16.73 6.10 0.00 2.69
2183 2251 5.840243 TCCGTCGAAATCACTAATTAGGA 57.160 39.130 16.73 10.95 0.00 2.94
2184 2252 6.211587 TCCGTCGAAATCACTAATTAGGAA 57.788 37.500 16.73 4.64 0.00 3.36
2185 2253 6.270815 TCCGTCGAAATCACTAATTAGGAAG 58.729 40.000 16.73 6.49 0.00 3.46
2186 2254 6.040878 CCGTCGAAATCACTAATTAGGAAGT 58.959 40.000 16.73 0.88 0.00 3.01
2187 2255 7.067372 TCCGTCGAAATCACTAATTAGGAAGTA 59.933 37.037 16.73 0.00 0.00 2.24
2188 2256 7.167136 CCGTCGAAATCACTAATTAGGAAGTAC 59.833 40.741 16.73 3.77 0.00 2.73
2189 2257 7.914346 CGTCGAAATCACTAATTAGGAAGTACT 59.086 37.037 16.73 0.00 0.00 2.73
2292 2361 1.662517 ATGTGCGTCACTTGTCACAA 58.337 45.000 10.54 0.00 41.92 3.33
2295 2364 1.279840 GCGTCACTTGTCACAAGCC 59.720 57.895 17.93 5.01 0.00 4.35
2296 2365 1.564622 CGTCACTTGTCACAAGCCG 59.435 57.895 17.93 13.14 0.00 5.52
2305 2374 1.673920 TGTCACAAGCCGGAAGTTTTC 59.326 47.619 5.05 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 0.533491 CATTCCCCGGTGAAGTACGA 59.467 55.000 5.39 0.00 0.00 3.43
153 154 3.570125 GCTATAAAGTCTTGGCCATTCCC 59.430 47.826 6.09 0.00 0.00 3.97
685 686 4.824537 TGTAGCTGCACAAAAAGGATACAA 59.175 37.500 0.00 0.00 41.41 2.41
720 723 1.535462 CGAAAACCGCCTTGACAGATT 59.465 47.619 0.00 0.00 0.00 2.40
1231 1235 0.108329 GCCATACAGCAGTGGTACGT 60.108 55.000 0.00 0.00 37.81 3.57
1359 1364 8.399425 CGTATAGAAGAGCTCTTTTCAGTAAGA 58.601 37.037 29.02 8.03 36.11 2.10
1360 1365 8.185505 ACGTATAGAAGAGCTCTTTTCAGTAAG 58.814 37.037 29.02 19.03 36.11 2.34
1361 1366 7.968956 CACGTATAGAAGAGCTCTTTTCAGTAA 59.031 37.037 29.02 9.47 36.11 2.24
1362 1367 7.473366 CACGTATAGAAGAGCTCTTTTCAGTA 58.527 38.462 29.02 15.66 36.11 2.74
1363 1368 6.326375 CACGTATAGAAGAGCTCTTTTCAGT 58.674 40.000 29.02 19.89 36.11 3.41
1364 1369 5.231147 GCACGTATAGAAGAGCTCTTTTCAG 59.769 44.000 29.02 19.33 36.11 3.02
1365 1370 5.103000 GCACGTATAGAAGAGCTCTTTTCA 58.897 41.667 29.02 17.30 36.11 2.69
1366 1371 4.205385 CGCACGTATAGAAGAGCTCTTTTC 59.795 45.833 29.02 18.00 36.11 2.29
1384 1389 0.948141 TAAAAACGTACCCCCGCACG 60.948 55.000 0.00 0.00 43.63 5.34
1388 1393 2.095692 CCGAAATAAAAACGTACCCCCG 59.904 50.000 0.00 0.00 0.00 5.73
1491 1496 5.276963 CGCAAACATTTTTCAAGTTGCTGAT 60.277 36.000 0.00 0.00 0.00 2.90
1581 1587 9.761504 CATCTAGATGTGAATTAGTCATTCTGT 57.238 33.333 22.42 0.00 41.91 3.41
1609 1615 8.434392 ACTACTTAGGTGTGACATCCTTAAAAA 58.566 33.333 11.02 1.25 35.51 1.94
1610 1616 7.970102 ACTACTTAGGTGTGACATCCTTAAAA 58.030 34.615 11.02 1.54 35.51 1.52
1611 1617 7.549147 ACTACTTAGGTGTGACATCCTTAAA 57.451 36.000 11.02 2.10 35.51 1.52
1612 1618 7.233962 TGAACTACTTAGGTGTGACATCCTTAA 59.766 37.037 11.02 0.00 35.51 1.85
1613 1619 6.722590 TGAACTACTTAGGTGTGACATCCTTA 59.277 38.462 11.02 3.25 35.51 2.69
1614 1620 5.542635 TGAACTACTTAGGTGTGACATCCTT 59.457 40.000 11.02 0.00 35.51 3.36
1615 1621 5.084519 TGAACTACTTAGGTGTGACATCCT 58.915 41.667 10.67 10.67 37.80 3.24
1616 1622 5.401531 TGAACTACTTAGGTGTGACATCC 57.598 43.478 0.00 0.00 0.00 3.51
1617 1623 6.531948 GTGATGAACTACTTAGGTGTGACATC 59.468 42.308 0.00 0.00 0.00 3.06
1618 1624 6.014584 TGTGATGAACTACTTAGGTGTGACAT 60.015 38.462 0.00 0.00 0.00 3.06
1619 1625 5.303333 TGTGATGAACTACTTAGGTGTGACA 59.697 40.000 0.00 0.00 0.00 3.58
1620 1626 5.779922 TGTGATGAACTACTTAGGTGTGAC 58.220 41.667 0.00 0.00 0.00 3.67
1621 1627 6.605471 ATGTGATGAACTACTTAGGTGTGA 57.395 37.500 0.00 0.00 0.00 3.58
1622 1628 8.948631 ATTATGTGATGAACTACTTAGGTGTG 57.051 34.615 0.00 0.00 0.00 3.82
1626 1632 9.712305 CCCTAATTATGTGATGAACTACTTAGG 57.288 37.037 0.00 0.00 32.27 2.69
1627 1633 9.712305 CCCCTAATTATGTGATGAACTACTTAG 57.288 37.037 0.00 0.00 0.00 2.18
1628 1634 8.154856 GCCCCTAATTATGTGATGAACTACTTA 58.845 37.037 0.00 0.00 0.00 2.24
1629 1635 6.998673 GCCCCTAATTATGTGATGAACTACTT 59.001 38.462 0.00 0.00 0.00 2.24
1630 1636 6.330250 AGCCCCTAATTATGTGATGAACTACT 59.670 38.462 0.00 0.00 0.00 2.57
1631 1637 6.534634 AGCCCCTAATTATGTGATGAACTAC 58.465 40.000 0.00 0.00 0.00 2.73
1632 1638 6.763715 AGCCCCTAATTATGTGATGAACTA 57.236 37.500 0.00 0.00 0.00 2.24
1633 1639 5.653255 AGCCCCTAATTATGTGATGAACT 57.347 39.130 0.00 0.00 0.00 3.01
1634 1640 5.827797 TGAAGCCCCTAATTATGTGATGAAC 59.172 40.000 0.00 0.00 0.00 3.18
1635 1641 6.012337 TGAAGCCCCTAATTATGTGATGAA 57.988 37.500 0.00 0.00 0.00 2.57
1636 1642 5.645056 TGAAGCCCCTAATTATGTGATGA 57.355 39.130 0.00 0.00 0.00 2.92
1637 1643 6.064060 TCTTGAAGCCCCTAATTATGTGATG 58.936 40.000 0.00 0.00 0.00 3.07
1638 1644 6.266131 TCTTGAAGCCCCTAATTATGTGAT 57.734 37.500 0.00 0.00 0.00 3.06
1639 1645 5.708736 TCTTGAAGCCCCTAATTATGTGA 57.291 39.130 0.00 0.00 0.00 3.58
1640 1646 6.966534 AATCTTGAAGCCCCTAATTATGTG 57.033 37.500 0.00 0.00 0.00 3.21
1641 1647 6.897413 ACAAATCTTGAAGCCCCTAATTATGT 59.103 34.615 0.00 0.00 0.00 2.29
1642 1648 7.352079 ACAAATCTTGAAGCCCCTAATTATG 57.648 36.000 0.00 0.00 0.00 1.90
1643 1649 8.058847 TGTACAAATCTTGAAGCCCCTAATTAT 58.941 33.333 0.00 0.00 0.00 1.28
1644 1650 7.406916 TGTACAAATCTTGAAGCCCCTAATTA 58.593 34.615 0.00 0.00 0.00 1.40
1645 1651 6.252995 TGTACAAATCTTGAAGCCCCTAATT 58.747 36.000 0.00 0.00 0.00 1.40
1646 1652 5.826643 TGTACAAATCTTGAAGCCCCTAAT 58.173 37.500 0.00 0.00 0.00 1.73
1647 1653 5.249780 TGTACAAATCTTGAAGCCCCTAA 57.750 39.130 0.00 0.00 0.00 2.69
1648 1654 4.919774 TGTACAAATCTTGAAGCCCCTA 57.080 40.909 0.00 0.00 0.00 3.53
1649 1655 3.806949 TGTACAAATCTTGAAGCCCCT 57.193 42.857 0.00 0.00 0.00 4.79
1650 1656 4.864704 TTTGTACAAATCTTGAAGCCCC 57.135 40.909 17.01 0.00 0.00 5.80
1859 1895 9.607988 TCCTTTTTGTTTCTTTTTCCCTATTTC 57.392 29.630 0.00 0.00 0.00 2.17
1917 1955 7.013846 TGGGTTTTCTGTTTATTCAATCGTCTT 59.986 33.333 0.00 0.00 0.00 3.01
1962 2000 9.961264 TGGAAAGGTTTTTGTAGGTTTTTATTT 57.039 25.926 0.00 0.00 0.00 1.40
1965 2003 9.788889 TTTTGGAAAGGTTTTTGTAGGTTTTTA 57.211 25.926 0.00 0.00 0.00 1.52
1976 2028 3.997681 CACGTGGTTTTGGAAAGGTTTTT 59.002 39.130 7.95 0.00 0.00 1.94
2004 2056 6.335777 CCAATCTTAGCTTTGATTTTGGGAG 58.664 40.000 10.08 1.31 31.35 4.30
2091 2144 0.394565 GTTGTCTGAGGCCTGTCTGT 59.605 55.000 12.00 0.00 0.00 3.41
2158 2226 5.405571 CCTAATTAGTGATTTCGACGGATGG 59.594 44.000 11.50 0.00 0.00 3.51
2231 2299 6.015603 TCGCAATCTGAGAATATGAGAGTGAT 60.016 38.462 0.00 0.00 34.50 3.06
2241 2310 4.820897 ACACTTGTCGCAATCTGAGAATA 58.179 39.130 0.00 0.00 0.00 1.75
2276 2345 1.436195 GGCTTGTGACAAGTGACGCA 61.436 55.000 24.51 0.00 0.00 5.24
2278 2347 1.564622 CGGCTTGTGACAAGTGACG 59.435 57.895 24.51 21.19 0.00 4.35


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

AutoCloner maintained by Alex Coulton.