Multiple sequence alignment - TraesCS5D01G157100

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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 TraesCS5D01G157100 chr5D 100.000 3359 0 0 1 3359 244704111 244707469 0.000000e+00 6204.0
1 TraesCS5D01G157100 chr5D 91.379 58 0 1 1679 1731 459929350 459929293 1.290000e-09 75.0
2 TraesCS5D01G157100 chr5A 94.471 1646 68 12 1726 3359 328944987 328946621 0.000000e+00 2514.0
3 TraesCS5D01G157100 chr5A 92.851 1217 45 14 1 1204 328943357 328944544 0.000000e+00 1727.0
4 TraesCS5D01G157100 chr5A 91.772 474 31 4 1200 1667 328944498 328944969 0.000000e+00 652.0
5 TraesCS5D01G157100 chr5B 94.706 1209 45 8 1 1204 278227442 278228636 0.000000e+00 1860.0
6 TraesCS5D01G157100 chr5B 95.819 861 34 2 2499 3359 278229792 278230650 0.000000e+00 1389.0
7 TraesCS5D01G157100 chr5B 92.966 725 38 6 1727 2439 278229067 278229790 0.000000e+00 1044.0
8 TraesCS5D01G157100 chr5B 96.480 483 15 2 1200 1682 278228590 278229070 0.000000e+00 797.0
9 TraesCS5D01G157100 chr5B 89.937 159 14 2 2463 2620 671295926 671295769 1.580000e-48 204.0
10 TraesCS5D01G157100 chr5B 88.889 54 3 2 1678 1728 574906742 574906689 2.800000e-06 63.9
11 TraesCS5D01G157100 chr4A 92.308 156 9 3 2463 2617 460230648 460230801 5.640000e-53 219.0
12 TraesCS5D01G157100 chr4D 91.613 155 11 2 2464 2617 74079351 74079504 2.630000e-51 213.0
13 TraesCS5D01G157100 chr1D 90.566 159 12 3 2464 2620 156133492 156133335 1.220000e-49 207.0
14 TraesCS5D01G157100 chr1D 89.937 159 13 3 2464 2621 305226295 305226451 5.680000e-48 202.0
15 TraesCS5D01G157100 chr2A 90.909 154 13 1 2464 2617 141506470 141506318 4.390000e-49 206.0
16 TraesCS5D01G157100 chr3A 89.937 159 12 2 2463 2618 310692089 310691932 5.680000e-48 202.0
17 TraesCS5D01G157100 chr6D 93.478 46 1 2 1674 1719 100935848 100935805 2.160000e-07 67.6
18 TraesCS5D01G157100 chr6D 97.368 38 1 0 1674 1711 200436516 200436479 7.780000e-07 65.8
19 TraesCS5D01G157100 chr3B 93.182 44 3 0 1668 1711 754970348 754970305 7.780000e-07 65.8
20 TraesCS5D01G157100 chr7D 89.796 49 5 0 1663 1711 155295697 155295745 2.800000e-06 63.9
21 TraesCS5D01G157100 chr1A 90.000 50 4 1 1663 1711 223997788 223997739 2.800000e-06 63.9
22 TraesCS5D01G157100 chr1A 86.207 58 5 2 1679 1733 442560201 442560258 3.620000e-05 60.2
23 TraesCS5D01G157100 chr7B 84.615 65 3 3 1679 1736 552029574 552029510 1.300000e-04 58.4


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 TraesCS5D01G157100 chr5D 244704111 244707469 3358 False 6204.0 6204 100.000000 1 3359 1 chr5D.!!$F1 3358
1 TraesCS5D01G157100 chr5A 328943357 328946621 3264 False 1631.0 2514 93.031333 1 3359 3 chr5A.!!$F1 3358
2 TraesCS5D01G157100 chr5B 278227442 278230650 3208 False 1272.5 1860 94.992750 1 3359 4 chr5B.!!$F1 3358

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
529 536 0.249322 CGGCCTTGTACCATAGTCCG 60.249 60.0 0.0 0.0 0.0 4.79 F
1693 1723 0.107312 CTTCTACTCCCTCCGTCCGA 60.107 60.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1741 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.0 0.00 0.0 0.00 4.30 R
3290 3334 0.678684 TGTCCGTGACATCCGAGCTA 60.679 55.0 3.02 0.0 37.67 3.32 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
101 102 4.754372 CTGCTCAGCAACAAAAGATGTA 57.246 40.909 0.00 0.00 42.99 2.29
366 368 4.095334 TGCAGATTGACTACACATGAATGC 59.905 41.667 0.00 0.00 0.00 3.56
399 401 7.083858 TCGGAATTTCTAGCACAAAATCTTTG 58.916 34.615 0.00 0.00 0.00 2.77
529 536 0.249322 CGGCCTTGTACCATAGTCCG 60.249 60.000 0.00 0.00 0.00 4.79
710 717 4.155733 CATCCCGGCAGCGTACCA 62.156 66.667 0.00 0.00 0.00 3.25
734 744 1.069978 GCAGTCATAGCTTCCTCCTCC 59.930 57.143 0.00 0.00 0.00 4.30
735 745 2.676748 CAGTCATAGCTTCCTCCTCCT 58.323 52.381 0.00 0.00 0.00 3.69
736 746 2.627699 CAGTCATAGCTTCCTCCTCCTC 59.372 54.545 0.00 0.00 0.00 3.71
749 759 0.915364 CCTCCTCCTTCCTTTCAGGG 59.085 60.000 0.00 0.00 35.59 4.45
752 762 0.250513 CCTCCTTCCTTTCAGGGTCG 59.749 60.000 0.00 0.00 35.59 4.79
966 976 4.819761 TCGCCGCCATGAGTCTGC 62.820 66.667 0.00 0.00 0.00 4.26
1095 1109 0.323178 ACCCGCTACCTCTTCTTCGA 60.323 55.000 0.00 0.00 0.00 3.71
1204 1221 0.875728 CAGGTACCGGCTATCTCTCG 59.124 60.000 6.18 0.00 0.00 4.04
1206 1223 1.580437 GTACCGGCTATCTCTCGGC 59.420 63.158 0.00 0.00 46.87 5.54
1207 1224 1.602888 TACCGGCTATCTCTCGGCC 60.603 63.158 0.00 0.00 46.87 6.13
1210 1227 2.646143 GGCTATCTCTCGGCCGAC 59.354 66.667 27.28 12.88 36.37 4.79
1211 1228 2.646143 GCTATCTCTCGGCCGACC 59.354 66.667 27.28 2.67 0.00 4.79
1222 1239 3.760035 GCCGACCGCTCCTCTGAA 61.760 66.667 0.00 0.00 0.00 3.02
1223 1240 2.182030 CCGACCGCTCCTCTGAAC 59.818 66.667 0.00 0.00 0.00 3.18
1224 1241 2.182030 CGACCGCTCCTCTGAACC 59.818 66.667 0.00 0.00 0.00 3.62
1225 1242 2.579738 GACCGCTCCTCTGAACCC 59.420 66.667 0.00 0.00 0.00 4.11
1226 1243 1.985116 GACCGCTCCTCTGAACCCT 60.985 63.158 0.00 0.00 0.00 4.34
1227 1244 2.232298 GACCGCTCCTCTGAACCCTG 62.232 65.000 0.00 0.00 0.00 4.45
1228 1245 1.984570 CCGCTCCTCTGAACCCTGA 60.985 63.158 0.00 0.00 0.00 3.86
1229 1246 1.333636 CCGCTCCTCTGAACCCTGAT 61.334 60.000 0.00 0.00 0.00 2.90
1230 1247 1.403814 CGCTCCTCTGAACCCTGATA 58.596 55.000 0.00 0.00 0.00 2.15
1231 1248 1.339610 CGCTCCTCTGAACCCTGATAG 59.660 57.143 0.00 0.00 0.00 2.08
1232 1249 1.691434 GCTCCTCTGAACCCTGATAGG 59.309 57.143 0.00 0.00 34.30 2.57
1233 1250 2.957312 GCTCCTCTGAACCCTGATAGGT 60.957 54.545 0.00 0.00 44.00 3.08
1234 1251 2.697751 CTCCTCTGAACCCTGATAGGTG 59.302 54.545 0.00 0.00 40.05 4.00
1235 1252 1.139853 CCTCTGAACCCTGATAGGTGC 59.860 57.143 0.00 0.00 40.05 5.01
1236 1253 1.139853 CTCTGAACCCTGATAGGTGCC 59.860 57.143 0.00 0.00 40.05 5.01
1237 1254 0.179073 CTGAACCCTGATAGGTGCCG 60.179 60.000 0.00 0.00 40.05 5.69
1238 1255 1.146263 GAACCCTGATAGGTGCCGG 59.854 63.158 0.00 0.00 40.05 6.13
1239 1256 2.942648 GAACCCTGATAGGTGCCGGC 62.943 65.000 22.73 22.73 40.05 6.13
1240 1257 4.609018 CCCTGATAGGTGCCGGCG 62.609 72.222 23.90 0.00 31.93 6.46
1241 1258 3.536917 CCTGATAGGTGCCGGCGA 61.537 66.667 23.90 8.37 0.00 5.54
1242 1259 2.737180 CTGATAGGTGCCGGCGAT 59.263 61.111 23.90 12.42 0.00 4.58
1243 1260 1.373497 CTGATAGGTGCCGGCGATC 60.373 63.158 23.90 20.54 0.00 3.69
1244 1261 1.810606 CTGATAGGTGCCGGCGATCT 61.811 60.000 23.90 20.24 0.00 2.75
1245 1262 1.080434 GATAGGTGCCGGCGATCTC 60.080 63.158 23.90 10.93 0.00 2.75
1246 1263 1.528292 GATAGGTGCCGGCGATCTCT 61.528 60.000 23.90 15.92 0.00 3.10
1247 1264 1.528292 ATAGGTGCCGGCGATCTCTC 61.528 60.000 23.90 5.66 0.00 3.20
1302 1319 0.824595 TTGTGGATGCAGCAGCTTGT 60.825 50.000 11.16 0.00 42.74 3.16
1305 1322 1.975407 GGATGCAGCAGCTTGTGGT 60.975 57.895 11.16 0.00 42.74 4.16
1443 1460 1.745087 CCTCCATTCAACATCCAACCG 59.255 52.381 0.00 0.00 0.00 4.44
1528 1550 4.776743 CGTGTCAAGTCTCCTCAAAATTG 58.223 43.478 0.00 0.00 0.00 2.32
1682 1712 8.651588 CATCAGTAACATCACAAACTTCTACTC 58.348 37.037 0.00 0.00 0.00 2.59
1683 1713 7.152645 TCAGTAACATCACAAACTTCTACTCC 58.847 38.462 0.00 0.00 0.00 3.85
1684 1714 6.369065 CAGTAACATCACAAACTTCTACTCCC 59.631 42.308 0.00 0.00 0.00 4.30
1685 1715 5.568620 AACATCACAAACTTCTACTCCCT 57.431 39.130 0.00 0.00 0.00 4.20
1686 1716 5.153950 ACATCACAAACTTCTACTCCCTC 57.846 43.478 0.00 0.00 0.00 4.30
1687 1717 4.020128 ACATCACAAACTTCTACTCCCTCC 60.020 45.833 0.00 0.00 0.00 4.30
1688 1718 2.561419 TCACAAACTTCTACTCCCTCCG 59.439 50.000 0.00 0.00 0.00 4.63
1689 1719 2.299297 CACAAACTTCTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
1690 1720 2.561858 ACAAACTTCTACTCCCTCCGTC 59.438 50.000 0.00 0.00 0.00 4.79
1691 1721 1.849977 AACTTCTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
1692 1722 0.394080 ACTTCTACTCCCTCCGTCCG 60.394 60.000 0.00 0.00 0.00 4.79
1693 1723 0.107312 CTTCTACTCCCTCCGTCCGA 60.107 60.000 0.00 0.00 0.00 4.55
1694 1724 0.329261 TTCTACTCCCTCCGTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
1695 1725 0.329261 TCTACTCCCTCCGTCCGAAA 59.671 55.000 0.00 0.00 0.00 3.46
1696 1726 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
1697 1727 1.547372 CTACTCCCTCCGTCCGAAAAA 59.453 52.381 0.00 0.00 0.00 1.94
1698 1728 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
1699 1729 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
1700 1730 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
1701 1731 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
1702 1732 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
1703 1733 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
1704 1734 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
1705 1735 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
1706 1736 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
1707 1737 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
1708 1738 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
1709 1739 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
1710 1740 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
1711 1741 2.558359 CCGAAAAAGCTTGTCCCTCAAT 59.442 45.455 0.00 0.00 35.35 2.57
1712 1742 3.005791 CCGAAAAAGCTTGTCCCTCAATT 59.994 43.478 0.00 0.00 35.35 2.32
1713 1743 4.229876 CGAAAAAGCTTGTCCCTCAATTC 58.770 43.478 0.00 0.00 35.35 2.17
1714 1744 3.923017 AAAAGCTTGTCCCTCAATTCG 57.077 42.857 0.00 0.00 35.35 3.34
1715 1745 1.826385 AAGCTTGTCCCTCAATTCGG 58.174 50.000 0.00 0.00 35.35 4.30
1716 1746 0.984230 AGCTTGTCCCTCAATTCGGA 59.016 50.000 0.00 0.00 35.35 4.55
1719 1749 4.515404 GTCCCTCAATTCGGACGG 57.485 61.111 1.20 0.00 39.29 4.79
1720 1750 1.895238 GTCCCTCAATTCGGACGGA 59.105 57.895 1.20 0.00 39.29 4.69
1721 1751 0.179108 GTCCCTCAATTCGGACGGAG 60.179 60.000 1.20 0.00 39.29 4.63
1722 1752 1.144057 CCCTCAATTCGGACGGAGG 59.856 63.158 5.64 5.64 45.20 4.30
1723 1753 1.144057 CCTCAATTCGGACGGAGGG 59.856 63.158 4.81 0.00 42.55 4.30
1724 1754 1.327690 CCTCAATTCGGACGGAGGGA 61.328 60.000 4.81 0.00 42.55 4.20
1725 1755 0.103208 CTCAATTCGGACGGAGGGAG 59.897 60.000 0.00 0.00 0.00 4.30
1726 1756 0.613853 TCAATTCGGACGGAGGGAGT 60.614 55.000 0.00 0.00 0.00 3.85
1727 1757 1.108776 CAATTCGGACGGAGGGAGTA 58.891 55.000 0.00 0.00 0.00 2.59
1728 1758 1.109609 AATTCGGACGGAGGGAGTAC 58.890 55.000 0.00 0.00 0.00 2.73
1729 1759 0.258194 ATTCGGACGGAGGGAGTACT 59.742 55.000 0.00 0.00 0.00 2.73
1762 1792 6.038825 TGCCCATAGAAATTTACATTGTACCG 59.961 38.462 0.00 0.00 0.00 4.02
1806 1836 4.040217 TCTTTGGCTTGTTTGGTGCATAAT 59.960 37.500 0.00 0.00 0.00 1.28
1862 1892 2.895242 AGGTAACGGTACTGGAGTCT 57.105 50.000 11.05 0.00 46.39 3.24
1880 1910 2.224314 GTCTGAAAAACGAGCTTGGGAG 59.776 50.000 5.79 0.00 0.00 4.30
1901 1931 1.860484 GCAGTCCAGAAGCACAAGCC 61.860 60.000 0.00 0.00 43.56 4.35
1940 1970 2.667874 TGGCACAAGCGCGATGAA 60.668 55.556 20.68 2.51 43.41 2.57
1943 1973 1.082169 GCACAAGCGCGATGAACAA 60.082 52.632 20.68 0.00 0.00 2.83
1976 2006 1.806623 GCAACGATAGGCTCATCGGTT 60.807 52.381 21.66 14.21 45.80 4.44
1977 2007 1.860950 CAACGATAGGCTCATCGGTTG 59.139 52.381 21.66 18.75 45.80 3.77
2002 2032 5.721000 TCCTTTCAAGTAATTGCATTCCCAT 59.279 36.000 0.00 0.00 0.00 4.00
2016 2046 4.590222 GCATTCCCATCCTTCCATTGTATT 59.410 41.667 0.00 0.00 0.00 1.89
2017 2047 5.279156 GCATTCCCATCCTTCCATTGTATTC 60.279 44.000 0.00 0.00 0.00 1.75
2050 2080 0.251922 AAGGTAGTAGGGACGTGGCA 60.252 55.000 0.00 0.00 0.00 4.92
2063 2093 2.724174 GACGTGGCATTTTTGTAGTTGC 59.276 45.455 0.00 0.00 0.00 4.17
2142 2175 7.886970 AGTTATGCCCATATCATATCCATATGC 59.113 37.037 0.00 0.00 39.90 3.14
2283 2323 7.578310 ACCAATCTATGTCTTCCATTCATTG 57.422 36.000 0.00 0.00 34.32 2.82
2358 2398 4.442454 GGTACCCCAGCTTGCCCC 62.442 72.222 0.00 0.00 0.00 5.80
2441 2483 5.238432 TGTTTGCTGTGTCATGTAGGTAAAG 59.762 40.000 0.00 0.00 0.00 1.85
2450 2492 7.936847 TGTGTCATGTAGGTAAAGAACTGAAAT 59.063 33.333 0.00 0.00 0.00 2.17
2547 2589 5.806286 CACGTTTTAGTGTGTTTGATCACT 58.194 37.500 0.00 0.00 45.21 3.41
2592 2634 8.405531 AGTCCATATTCAAATATCCAAAACGTG 58.594 33.333 0.00 0.00 29.35 4.49
2606 2648 6.375377 TCCAAAACGTGCTATATTTGTGAAC 58.625 36.000 7.22 0.00 32.29 3.18
2607 2649 6.017026 TCCAAAACGTGCTATATTTGTGAACA 60.017 34.615 7.22 0.00 32.29 3.18
2668 2710 5.476599 TCCAATTTCAACTCCACCATACTTG 59.523 40.000 0.00 0.00 0.00 3.16
2683 2725 6.003950 ACCATACTTGAAGTAGCAAACATGT 58.996 36.000 11.09 0.00 33.66 3.21
2718 2760 5.303971 AGTTCATGTGAGGTCAGAAAGAAG 58.696 41.667 0.00 0.00 0.00 2.85
2955 2999 3.947834 AGAACAGTGAGGAACAAACAAGG 59.052 43.478 0.00 0.00 0.00 3.61
3170 3214 1.971357 CCAGTGAGGTTGTCCAGTACT 59.029 52.381 0.00 0.00 35.89 2.73
3188 3232 6.043411 CAGTACTGTACTCTTTAGGCCATTC 58.957 44.000 17.22 0.00 36.76 2.67
3290 3334 3.381272 CACCGATGCTATTTGGTCCAAAT 59.619 43.478 28.49 28.49 44.74 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 2.159014 TGTTCCACTGCTTAACGTGACT 60.159 45.455 0.00 0.00 33.04 3.41
134 135 4.661993 TTCGATCTTCAATTTGGTGTCG 57.338 40.909 0.00 3.01 0.00 4.35
366 368 2.356069 GCTAGAAATTCCGAGCCTTTGG 59.644 50.000 6.29 0.00 0.00 3.28
399 401 0.681175 AGCATTGCAACCCAGAAACC 59.319 50.000 11.91 0.00 0.00 3.27
425 428 9.935682 CAACCAAATTATGCTACACTAGTATTG 57.064 33.333 0.00 0.00 33.13 1.90
710 717 1.407258 GAGGAAGCTATGACTGCGACT 59.593 52.381 0.00 0.00 35.28 4.18
752 762 4.144703 GACGCTTCCCGGGAGTCC 62.145 72.222 25.26 14.68 42.52 3.85
838 848 4.711949 CCTGCCGCACTTCTGCCT 62.712 66.667 0.00 0.00 40.73 4.75
1062 1076 2.329614 CGGGTTGTTACGGCCCAAG 61.330 63.158 12.98 0.00 42.44 3.61
1063 1077 2.281622 CGGGTTGTTACGGCCCAA 60.282 61.111 12.98 0.00 42.44 4.12
1205 1222 3.760035 TTCAGAGGAGCGGTCGGC 61.760 66.667 8.77 2.81 44.05 5.54
1206 1223 2.182030 GTTCAGAGGAGCGGTCGG 59.818 66.667 8.77 0.00 0.00 4.79
1207 1224 2.182030 GGTTCAGAGGAGCGGTCG 59.818 66.667 8.77 0.00 0.00 4.79
1208 1225 1.985116 AGGGTTCAGAGGAGCGGTC 60.985 63.158 5.93 5.93 0.00 4.79
1209 1226 2.120718 AGGGTTCAGAGGAGCGGT 59.879 61.111 0.00 0.00 0.00 5.68
1210 1227 1.333636 ATCAGGGTTCAGAGGAGCGG 61.334 60.000 0.00 0.00 0.00 5.52
1211 1228 1.339610 CTATCAGGGTTCAGAGGAGCG 59.660 57.143 0.00 0.00 0.00 5.03
1212 1229 1.691434 CCTATCAGGGTTCAGAGGAGC 59.309 57.143 0.00 0.00 0.00 4.70
1213 1230 2.697751 CACCTATCAGGGTTCAGAGGAG 59.302 54.545 0.00 0.00 40.58 3.69
1214 1231 2.752030 CACCTATCAGGGTTCAGAGGA 58.248 52.381 0.00 0.00 40.58 3.71
1215 1232 1.139853 GCACCTATCAGGGTTCAGAGG 59.860 57.143 0.00 0.00 40.58 3.69
1216 1233 1.139853 GGCACCTATCAGGGTTCAGAG 59.860 57.143 0.00 0.00 40.58 3.35
1217 1234 1.204146 GGCACCTATCAGGGTTCAGA 58.796 55.000 0.00 0.00 40.58 3.27
1218 1235 0.179073 CGGCACCTATCAGGGTTCAG 60.179 60.000 0.00 0.00 40.58 3.02
1219 1236 1.622607 CCGGCACCTATCAGGGTTCA 61.623 60.000 0.00 0.00 40.58 3.18
1220 1237 1.146263 CCGGCACCTATCAGGGTTC 59.854 63.158 0.00 0.00 40.58 3.62
1221 1238 3.043999 GCCGGCACCTATCAGGGTT 62.044 63.158 24.80 0.00 40.58 4.11
1222 1239 3.480133 GCCGGCACCTATCAGGGT 61.480 66.667 24.80 0.00 40.58 4.34
1223 1240 4.609018 CGCCGGCACCTATCAGGG 62.609 72.222 28.98 0.98 40.58 4.45
1224 1241 2.771763 GATCGCCGGCACCTATCAGG 62.772 65.000 28.98 6.54 42.49 3.86
1225 1242 1.373497 GATCGCCGGCACCTATCAG 60.373 63.158 28.98 7.38 0.00 2.90
1226 1243 1.806461 GAGATCGCCGGCACCTATCA 61.806 60.000 28.98 0.08 0.00 2.15
1227 1244 1.080434 GAGATCGCCGGCACCTATC 60.080 63.158 28.98 21.36 0.00 2.08
1228 1245 1.528292 GAGAGATCGCCGGCACCTAT 61.528 60.000 28.98 16.64 0.00 2.57
1229 1246 2.123854 AGAGATCGCCGGCACCTA 60.124 61.111 28.98 8.91 0.00 3.08
1230 1247 3.532155 GAGAGATCGCCGGCACCT 61.532 66.667 28.98 19.38 0.00 4.00
1231 1248 4.593864 GGAGAGATCGCCGGCACC 62.594 72.222 28.98 14.50 0.00 5.01
1232 1249 4.593864 GGGAGAGATCGCCGGCAC 62.594 72.222 28.98 16.94 36.62 5.01
1235 1252 2.370647 GAAAGGGGAGAGATCGCCGG 62.371 65.000 0.00 0.00 45.99 6.13
1236 1253 1.068250 GAAAGGGGAGAGATCGCCG 59.932 63.158 5.79 0.00 45.99 6.46
1237 1254 0.761802 ATGAAAGGGGAGAGATCGCC 59.238 55.000 3.30 3.30 42.33 5.54
1238 1255 2.158900 TGAATGAAAGGGGAGAGATCGC 60.159 50.000 0.00 0.00 0.00 4.58
1239 1256 3.827008 TGAATGAAAGGGGAGAGATCG 57.173 47.619 0.00 0.00 0.00 3.69
1240 1257 6.125029 TCAATTGAATGAAAGGGGAGAGATC 58.875 40.000 5.45 0.00 0.00 2.75
1241 1258 6.083487 TCAATTGAATGAAAGGGGAGAGAT 57.917 37.500 5.45 0.00 0.00 2.75
1242 1259 5.519183 TCAATTGAATGAAAGGGGAGAGA 57.481 39.130 5.45 0.00 0.00 3.10
1243 1260 5.655532 ACATCAATTGAATGAAAGGGGAGAG 59.344 40.000 13.09 0.00 32.06 3.20
1244 1261 5.582953 ACATCAATTGAATGAAAGGGGAGA 58.417 37.500 13.09 0.00 32.06 3.71
1245 1262 5.927281 ACATCAATTGAATGAAAGGGGAG 57.073 39.130 13.09 0.00 32.06 4.30
1246 1263 5.356751 CGTACATCAATTGAATGAAAGGGGA 59.643 40.000 13.09 0.00 32.06 4.81
1247 1264 5.450412 CCGTACATCAATTGAATGAAAGGGG 60.450 44.000 13.09 3.33 32.06 4.79
1302 1319 1.079197 CATACGGCACTGCTGACCA 60.079 57.895 17.08 1.79 38.46 4.02
1305 1322 1.257750 ACCTCATACGGCACTGCTGA 61.258 55.000 17.08 3.80 38.46 4.26
1443 1460 5.569059 CGATTTCAACCAGCTGATTACAAAC 59.431 40.000 17.39 0.00 0.00 2.93
1528 1550 4.335037 ACTTAACGCTAGAGCTAGGTGTAC 59.665 45.833 0.00 0.00 39.32 2.90
1682 1712 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
1683 1713 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
1684 1714 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
1685 1715 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
1686 1716 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
1687 1717 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
1688 1718 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
1689 1719 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
1690 1720 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
1691 1721 3.923017 ATTGAGGGACAAGCTTTTTCG 57.077 42.857 0.00 0.00 42.02 3.46
1692 1722 4.229876 CGAATTGAGGGACAAGCTTTTTC 58.770 43.478 0.00 0.00 42.02 2.29
1693 1723 3.005791 CCGAATTGAGGGACAAGCTTTTT 59.994 43.478 0.00 0.00 42.02 1.94
1694 1724 2.558359 CCGAATTGAGGGACAAGCTTTT 59.442 45.455 0.00 0.00 42.02 2.27
1695 1725 2.162681 CCGAATTGAGGGACAAGCTTT 58.837 47.619 0.00 0.00 42.02 3.51
1696 1726 1.351017 TCCGAATTGAGGGACAAGCTT 59.649 47.619 0.00 0.00 42.02 3.74
1697 1727 0.984230 TCCGAATTGAGGGACAAGCT 59.016 50.000 0.00 0.00 42.02 3.74
1698 1728 3.551259 TCCGAATTGAGGGACAAGC 57.449 52.632 0.00 0.00 42.02 4.01
1703 1733 1.327690 CCTCCGTCCGAATTGAGGGA 61.328 60.000 6.94 6.94 44.68 4.20
1704 1734 1.144057 CCTCCGTCCGAATTGAGGG 59.856 63.158 0.00 0.00 40.59 4.30
1705 1735 1.144057 CCCTCCGTCCGAATTGAGG 59.856 63.158 0.00 0.00 43.29 3.86
1706 1736 0.103208 CTCCCTCCGTCCGAATTGAG 59.897 60.000 0.00 0.00 0.00 3.02
1707 1737 0.613853 ACTCCCTCCGTCCGAATTGA 60.614 55.000 0.00 0.00 0.00 2.57
1708 1738 1.108776 TACTCCCTCCGTCCGAATTG 58.891 55.000 0.00 0.00 0.00 2.32
1709 1739 1.109609 GTACTCCCTCCGTCCGAATT 58.890 55.000 0.00 0.00 0.00 2.17
1710 1740 0.258194 AGTACTCCCTCCGTCCGAAT 59.742 55.000 0.00 0.00 0.00 3.34
1711 1741 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
1712 1742 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
1713 1743 0.893447 AAAAGTACTCCCTCCGTCCG 59.107 55.000 0.00 0.00 0.00 4.79
1714 1744 3.118847 CCTAAAAAGTACTCCCTCCGTCC 60.119 52.174 0.00 0.00 0.00 4.79
1715 1745 3.513119 ACCTAAAAAGTACTCCCTCCGTC 59.487 47.826 0.00 0.00 0.00 4.79
1716 1746 3.260128 CACCTAAAAAGTACTCCCTCCGT 59.740 47.826 0.00 0.00 0.00 4.69
1717 1747 3.858247 CACCTAAAAAGTACTCCCTCCG 58.142 50.000 0.00 0.00 0.00 4.63
1718 1748 3.607741 GCACCTAAAAAGTACTCCCTCC 58.392 50.000 0.00 0.00 0.00 4.30
1719 1749 3.607741 GGCACCTAAAAAGTACTCCCTC 58.392 50.000 0.00 0.00 0.00 4.30
1720 1750 3.715638 GGCACCTAAAAAGTACTCCCT 57.284 47.619 0.00 0.00 0.00 4.20
1762 1792 7.992180 AAGAACTTGACAAAATGAATGACAC 57.008 32.000 0.00 0.00 0.00 3.67
1806 1836 6.494893 AAACAGAAAGCATCATTAACGCTA 57.505 33.333 0.00 0.00 34.11 4.26
1862 1892 2.494059 CTCTCCCAAGCTCGTTTTTCA 58.506 47.619 0.00 0.00 0.00 2.69
1880 1910 1.155042 CTTGTGCTTCTGGACTGCTC 58.845 55.000 0.00 0.00 35.45 4.26
1901 1931 3.882444 TGGATTCAAGGCTTCTCTCATG 58.118 45.455 0.00 0.00 0.00 3.07
1976 2006 5.047377 GGGAATGCAATTACTTGAAAGGACA 60.047 40.000 0.00 0.00 37.31 4.02
1977 2007 5.047377 TGGGAATGCAATTACTTGAAAGGAC 60.047 40.000 0.00 0.00 37.31 3.85
2002 2032 5.043762 AGGGGTTAGAATACAATGGAAGGA 58.956 41.667 0.00 0.00 0.00 3.36
2016 2046 4.237018 ACTACCTTGTTCAAGGGGTTAGA 58.763 43.478 28.01 10.63 44.27 2.10
2017 2047 4.635699 ACTACCTTGTTCAAGGGGTTAG 57.364 45.455 28.01 22.56 44.27 2.34
2037 2067 1.883926 ACAAAAATGCCACGTCCCTAC 59.116 47.619 0.00 0.00 0.00 3.18
2044 2074 2.736978 TGCAACTACAAAAATGCCACG 58.263 42.857 0.00 0.00 38.00 4.94
2050 2080 5.594317 AGAGACAGGTTGCAACTACAAAAAT 59.406 36.000 27.64 7.94 0.00 1.82
2063 2093 1.059913 AACCCCAGAGAGACAGGTTG 58.940 55.000 0.00 0.00 39.32 3.77
2192 2225 9.319143 ACATAGCAGATACTGAGTTTATTCAAC 57.681 33.333 0.00 0.00 32.44 3.18
2227 2267 7.771183 TCTGCAAGTCTAAAATTCTTTGTTGT 58.229 30.769 0.00 0.00 33.76 3.32
2228 2268 7.380602 CCTCTGCAAGTCTAAAATTCTTTGTTG 59.619 37.037 0.00 0.00 33.76 3.33
2283 2323 4.054671 CACAGAAAAGACAGTCCTCACTC 58.945 47.826 0.00 0.00 0.00 3.51
2450 2492 6.012745 ACGGAGGGAGTAAGAAAGTAGTTTA 58.987 40.000 0.00 0.00 0.00 2.01
2547 2589 7.591421 TGGACTATATACGGACTGAAATGAA 57.409 36.000 0.00 0.00 0.00 2.57
2576 2618 9.515020 ACAAATATAGCACGTTTTGGATATTTG 57.485 29.630 21.86 21.86 44.84 2.32
2590 2632 5.428253 TCCCTCTGTTCACAAATATAGCAC 58.572 41.667 0.00 0.00 0.00 4.40
2592 2634 5.675538 ACTCCCTCTGTTCACAAATATAGC 58.324 41.667 0.00 0.00 0.00 2.97
2668 2710 8.853345 CATCAATTTGTACATGTTTGCTACTTC 58.147 33.333 2.30 0.00 0.00 3.01
2683 2725 6.942005 ACCTCACATGAACTCATCAATTTGTA 59.058 34.615 0.00 0.00 42.54 2.41
2718 2760 5.064834 GGTTGCCTTAACTTACTACTGATGC 59.935 44.000 0.00 0.00 39.31 3.91
2756 2798 3.059352 ACAGGGCACTAATGTCAACTC 57.941 47.619 0.00 0.00 29.15 3.01
2796 2838 3.934457 TTAGCAGCCCTTTGTAAAAGC 57.066 42.857 0.00 0.00 0.00 3.51
2955 2999 6.685527 AGTTTTGAGTTGAGAAAGGAACTC 57.314 37.500 0.00 0.00 45.60 3.01
3060 3104 2.072874 ATCACAGTGCTGGGCTTGGT 62.073 55.000 4.11 0.00 33.05 3.67
3170 3214 2.235155 TGCGAATGGCCTAAAGAGTACA 59.765 45.455 3.32 0.00 42.61 2.90
3188 3232 0.740868 CCGCCCTGGTATATGATGCG 60.741 60.000 3.25 3.25 40.17 4.73
3290 3334 0.678684 TGTCCGTGACATCCGAGCTA 60.679 55.000 3.02 0.00 37.67 3.32


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

AutoCloner maintained by Alex Coulton.