Multiple sequence alignment - TraesCS1B01G143300

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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 TraesCS1B01G143300 chr1B 100.000 2291 0 0 1 2291 194358865 194356575 0.000000e+00 4231.0
1 TraesCS1B01G143300 chr1B 87.037 162 18 3 1561 1720 33837195 33837355 1.810000e-41 180.0
2 TraesCS1B01G143300 chr1D 96.440 1573 43 8 1 1564 144678905 144677337 0.000000e+00 2582.0
3 TraesCS1B01G143300 chr1D 96.546 608 12 7 1686 2286 144677340 144676735 0.000000e+00 998.0
4 TraesCS1B01G143300 chr1A 88.833 1585 124 25 1 1564 144551736 144553288 0.000000e+00 1897.0
5 TraesCS1B01G143300 chr1A 93.172 454 24 3 1686 2138 144553285 144553732 0.000000e+00 660.0
6 TraesCS1B01G143300 chr1A 93.571 140 8 1 1551 1690 486045908 486045770 8.290000e-50 207.0
7 TraesCS1B01G143300 chr1A 94.118 85 4 1 2207 2291 144563728 144563811 6.640000e-26 128.0
8 TraesCS1B01G143300 chr6A 87.084 751 73 15 706 1442 98605857 98605117 0.000000e+00 828.0
9 TraesCS1B01G143300 chr6B 86.093 755 75 15 706 1442 156932746 156932004 0.000000e+00 785.0
10 TraesCS1B01G143300 chr6B 94.074 135 8 0 1556 1690 207510896 207511030 2.980000e-49 206.0
11 TraesCS1B01G143300 chr6B 91.837 49 3 1 1783 1830 224867902 224867950 1.470000e-07 67.6
12 TraesCS1B01G143300 chr6D 84.106 755 84 25 706 1442 82092993 82092257 0.000000e+00 697.0
13 TraesCS1B01G143300 chr6D 82.031 128 19 4 504 630 224621 224497 3.110000e-19 106.0
14 TraesCS1B01G143300 chr6D 93.617 47 3 0 1784 1830 345735800 345735846 1.140000e-08 71.3
15 TraesCS1B01G143300 chr6D 91.667 48 3 1 1784 1830 83933304 83933257 5.280000e-07 65.8
16 TraesCS1B01G143300 chr7B 95.349 129 6 0 1561 1689 126893247 126893119 2.980000e-49 206.0
17 TraesCS1B01G143300 chr4D 94.656 131 7 0 1557 1687 306860273 306860403 1.070000e-48 204.0
18 TraesCS1B01G143300 chr3A 93.478 138 8 1 1561 1698 726020425 726020289 1.070000e-48 204.0
19 TraesCS1B01G143300 chr3A 85.000 160 18 4 1559 1718 193932249 193932096 8.470000e-35 158.0
20 TraesCS1B01G143300 chr5B 92.254 142 10 1 1557 1698 46633387 46633247 1.390000e-47 200.0
21 TraesCS1B01G143300 chr5B 93.617 47 2 1 1785 1830 56846443 56846489 4.080000e-08 69.4
22 TraesCS1B01G143300 chr4B 92.143 140 10 1 1548 1687 63765684 63765822 1.800000e-46 196.0
23 TraesCS1B01G143300 chr2B 90.066 151 11 4 1560 1710 281881472 281881618 2.320000e-45 193.0
24 TraesCS1B01G143300 chr3D 84.293 191 20 9 1524 1712 236672587 236672405 6.500000e-41 178.0
25 TraesCS1B01G143300 chr3D 81.538 130 20 4 504 632 27888615 27888489 1.120000e-18 104.0
26 TraesCS1B01G143300 chr7D 83.077 130 18 4 504 632 14255338 14255464 5.170000e-22 115.0
27 TraesCS1B01G143300 chr7D 82.031 128 19 4 504 630 575743261 575743385 3.110000e-19 106.0
28 TraesCS1B01G143300 chr5D 81.159 138 22 4 504 640 434565459 434565325 8.650000e-20 108.0
29 TraesCS1B01G143300 chr2D 81.538 130 19 5 504 631 534124408 534124534 4.030000e-18 102.0
30 TraesCS1B01G143300 chr2D 95.745 47 2 0 1784 1830 312629969 312630015 2.440000e-10 76.8
31 TraesCS1B01G143300 chr3B 80.292 137 22 5 504 639 83543310 83543442 5.210000e-17 99.0
32 TraesCS1B01G143300 chr2A 95.833 48 1 1 1784 1830 334155439 334155486 2.440000e-10 76.8
33 TraesCS1B01G143300 chr4A 93.478 46 2 1 1789 1833 59329565 59329520 1.470000e-07 67.6


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 TraesCS1B01G143300 chr1B 194356575 194358865 2290 True 4231.0 4231 100.0000 1 2291 1 chr1B.!!$R1 2290
1 TraesCS1B01G143300 chr1D 144676735 144678905 2170 True 1790.0 2582 96.4930 1 2286 2 chr1D.!!$R1 2285
2 TraesCS1B01G143300 chr1A 144551736 144553732 1996 False 1278.5 1897 91.0025 1 2138 2 chr1A.!!$F2 2137
3 TraesCS1B01G143300 chr6A 98605117 98605857 740 True 828.0 828 87.0840 706 1442 1 chr6A.!!$R1 736
4 TraesCS1B01G143300 chr6B 156932004 156932746 742 True 785.0 785 86.0930 706 1442 1 chr6B.!!$R1 736
5 TraesCS1B01G143300 chr6D 82092257 82092993 736 True 697.0 697 84.1060 706 1442 1 chr6D.!!$R2 736

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
319 337 0.593128 CTTTGCCGAGGACCAAACTG 59.407 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1634 1.47973 GTATTTTCGGACGGAGGGAGT 59.52 52.381 0.0 0.0 0.0 3.85 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
152 157 2.093500 TGTCACACTCACTCAGCAAAGT 60.093 45.455 0.00 0.00 0.00 2.66
155 160 4.009675 TCACACTCACTCAGCAAAGTTTT 58.990 39.130 0.00 0.00 0.00 2.43
156 161 4.458989 TCACACTCACTCAGCAAAGTTTTT 59.541 37.500 0.00 0.00 0.00 1.94
293 311 8.499403 AAGAAAGTAAAAGAGCACTATCATCC 57.501 34.615 0.00 0.00 0.00 3.51
319 337 0.593128 CTTTGCCGAGGACCAAACTG 59.407 55.000 0.00 0.00 0.00 3.16
516 548 1.172180 GCCGGCCTATTAGCAATGCA 61.172 55.000 18.11 0.00 0.00 3.96
558 590 6.038936 TGCTATTAGCGAGACATTGTACACTA 59.961 38.462 10.94 0.00 46.26 2.74
617 649 7.840342 GCATTGCTATTAGTGATGCTATAGT 57.160 36.000 18.24 0.00 39.84 2.12
619 651 7.332926 GCATTGCTATTAGTGATGCTATAGTGT 59.667 37.037 18.24 0.00 39.84 3.55
654 686 4.634004 CGATGGTTTTTGCCTATGTACTCA 59.366 41.667 0.00 0.00 0.00 3.41
701 733 5.572896 GCCCGATAAAATGAACTTGACAAAG 59.427 40.000 0.00 0.00 39.49 2.77
731 763 2.875933 TGATTTGTGTCGGTCCAAAGAC 59.124 45.455 0.00 0.00 42.73 3.01
1110 1161 2.887568 CCACAGATGCTCGCCGAC 60.888 66.667 0.00 0.00 0.00 4.79
1476 1548 4.272018 GCATCATGCTCTTCAATCGTACTT 59.728 41.667 1.02 0.00 40.96 2.24
1535 1608 5.172687 TGTCATGAAAGGCATACCAGTTA 57.827 39.130 0.00 0.00 39.06 2.24
1570 1643 8.145767 TGTAACAAAACATATATACTCCCTCCG 58.854 37.037 0.00 0.00 0.00 4.63
1571 1644 6.742559 ACAAAACATATATACTCCCTCCGT 57.257 37.500 0.00 0.00 0.00 4.69
1572 1645 6.756221 ACAAAACATATATACTCCCTCCGTC 58.244 40.000 0.00 0.00 0.00 4.79
1573 1646 5.997384 AAACATATATACTCCCTCCGTCC 57.003 43.478 0.00 0.00 0.00 4.79
1574 1647 3.618351 ACATATATACTCCCTCCGTCCG 58.382 50.000 0.00 0.00 0.00 4.79
1575 1648 3.265221 ACATATATACTCCCTCCGTCCGA 59.735 47.826 0.00 0.00 0.00 4.55
1576 1649 2.965671 ATATACTCCCTCCGTCCGAA 57.034 50.000 0.00 0.00 0.00 4.30
1577 1650 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
1578 1651 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
1579 1652 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
1580 1653 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1581 1654 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1582 1655 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1583 1656 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1584 1657 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1585 1658 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1586 1659 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1587 1660 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1588 1661 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1589 1662 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1590 1663 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1591 1664 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1592 1665 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1593 1666 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1594 1667 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1595 1668 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1596 1669 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1597 1670 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1598 1671 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1606 1679 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
1619 1692 8.964476 TGGATAAAAAGAGATGTATCTGGAAC 57.036 34.615 0.00 0.00 37.25 3.62
1620 1693 8.772250 TGGATAAAAAGAGATGTATCTGGAACT 58.228 33.333 0.00 0.00 37.25 3.01
1628 1701 9.751542 AAGAGATGTATCTGGAACTAAAATACG 57.248 33.333 0.00 0.00 37.25 3.06
1629 1702 8.915036 AGAGATGTATCTGGAACTAAAATACGT 58.085 33.333 0.00 0.00 37.25 3.57
1630 1703 9.182933 GAGATGTATCTGGAACTAAAATACGTC 57.817 37.037 0.00 0.00 38.35 4.34
1631 1704 8.915036 AGATGTATCTGGAACTAAAATACGTCT 58.085 33.333 0.00 8.87 41.19 4.18
1634 1707 9.399797 TGTATCTGGAACTAAAATACGTCTAGA 57.600 33.333 0.00 0.00 0.00 2.43
1649 1722 8.896722 ATACGTCTAGATATATCCCCTTTTGT 57.103 34.615 9.18 3.17 0.00 2.83
1650 1723 7.229581 ACGTCTAGATATATCCCCTTTTGTC 57.770 40.000 9.18 0.00 0.00 3.18
1651 1724 6.072064 ACGTCTAGATATATCCCCTTTTGTCG 60.072 42.308 9.18 4.36 0.00 4.35
1652 1725 6.150641 CGTCTAGATATATCCCCTTTTGTCGA 59.849 42.308 9.18 0.00 0.00 4.20
1653 1726 7.148052 CGTCTAGATATATCCCCTTTTGTCGAT 60.148 40.741 9.18 0.00 0.00 3.59
1654 1727 8.532819 GTCTAGATATATCCCCTTTTGTCGATT 58.467 37.037 9.18 0.00 0.00 3.34
1655 1728 9.101325 TCTAGATATATCCCCTTTTGTCGATTT 57.899 33.333 9.18 0.00 0.00 2.17
1656 1729 9.726438 CTAGATATATCCCCTTTTGTCGATTTT 57.274 33.333 9.18 0.00 0.00 1.82
1657 1730 8.396272 AGATATATCCCCTTTTGTCGATTTTG 57.604 34.615 9.18 0.00 0.00 2.44
1658 1731 8.217799 AGATATATCCCCTTTTGTCGATTTTGA 58.782 33.333 9.18 0.00 0.00 2.69
1659 1732 8.940397 ATATATCCCCTTTTGTCGATTTTGAT 57.060 30.769 0.00 0.00 0.00 2.57
1660 1733 4.782019 TCCCCTTTTGTCGATTTTGATG 57.218 40.909 0.00 0.00 0.00 3.07
1661 1734 4.402829 TCCCCTTTTGTCGATTTTGATGA 58.597 39.130 0.00 0.00 0.00 2.92
1662 1735 4.217550 TCCCCTTTTGTCGATTTTGATGAC 59.782 41.667 0.00 0.00 0.00 3.06
1663 1736 4.022416 CCCCTTTTGTCGATTTTGATGACA 60.022 41.667 0.00 0.00 40.62 3.58
1672 1745 8.909708 TGTCGATTTTGATGACAAATATTTCC 57.090 30.769 0.00 0.00 43.99 3.13
1673 1746 7.696035 TGTCGATTTTGATGACAAATATTTCCG 59.304 33.333 0.00 0.00 43.99 4.30
1674 1747 7.165812 GTCGATTTTGATGACAAATATTTCCGG 59.834 37.037 0.00 0.00 43.99 5.14
1675 1748 7.066404 TCGATTTTGATGACAAATATTTCCGGA 59.934 33.333 0.00 0.00 43.99 5.14
1676 1749 7.165812 CGATTTTGATGACAAATATTTCCGGAC 59.834 37.037 1.83 0.00 43.99 4.79
1677 1750 5.478233 TTGATGACAAATATTTCCGGACG 57.522 39.130 1.83 0.00 32.73 4.79
1678 1751 4.760878 TGATGACAAATATTTCCGGACGA 58.239 39.130 1.83 0.00 0.00 4.20
1679 1752 5.179533 TGATGACAAATATTTCCGGACGAA 58.820 37.500 1.83 0.00 0.00 3.85
1680 1753 5.293324 TGATGACAAATATTTCCGGACGAAG 59.707 40.000 1.83 0.00 0.00 3.79
1681 1754 3.936453 TGACAAATATTTCCGGACGAAGG 59.064 43.478 1.83 0.00 0.00 3.46
1682 1755 4.186159 GACAAATATTTCCGGACGAAGGA 58.814 43.478 1.83 0.00 35.69 3.36
1683 1756 4.581868 ACAAATATTTCCGGACGAAGGAA 58.418 39.130 1.83 0.00 45.19 3.36
1752 1825 4.044336 TGCTGTCAGTTTGGATTGTTTG 57.956 40.909 0.93 0.00 0.00 2.93
1763 1836 8.517878 CAGTTTGGATTGTTTGATCACTTCTAT 58.482 33.333 0.00 0.00 0.00 1.98
1764 1837 9.082313 AGTTTGGATTGTTTGATCACTTCTATT 57.918 29.630 0.00 0.00 0.00 1.73
1957 2030 7.811117 TTAGCAGGTTACAAACTAAACATGT 57.189 32.000 0.00 0.00 39.06 3.21
2024 2103 6.821160 TCAATTGCTGTCTTGGAATTACGATA 59.179 34.615 0.00 0.00 36.16 2.92
2025 2104 7.335673 TCAATTGCTGTCTTGGAATTACGATAA 59.664 33.333 0.00 0.00 36.16 1.75
2027 2106 5.730550 TGCTGTCTTGGAATTACGATAACT 58.269 37.500 0.00 0.00 0.00 2.24
2183 2263 7.801547 TCCGTAGAAAAGTAAGAAATGTACG 57.198 36.000 0.00 0.00 34.31 3.67
2217 2297 7.863877 CGGATTCTTTTTATCATGCAATCATCA 59.136 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 230 3.201290 CGAGCGGAGTAAGTACTAGGAA 58.799 50.000 0.00 0.00 36.50 3.36
214 231 2.484417 CCGAGCGGAGTAAGTACTAGGA 60.484 54.545 2.00 0.00 36.50 2.94
215 232 1.872313 CCGAGCGGAGTAAGTACTAGG 59.128 57.143 2.00 0.00 36.50 3.02
216 233 1.263752 GCCGAGCGGAGTAAGTACTAG 59.736 57.143 13.94 0.00 36.50 2.57
217 234 1.303309 GCCGAGCGGAGTAAGTACTA 58.697 55.000 13.94 0.00 36.50 1.82
218 235 0.679002 TGCCGAGCGGAGTAAGTACT 60.679 55.000 13.94 0.00 39.71 2.73
219 236 0.171903 TTGCCGAGCGGAGTAAGTAC 59.828 55.000 13.94 0.00 37.50 2.73
220 237 0.889994 TTTGCCGAGCGGAGTAAGTA 59.110 50.000 13.94 0.00 37.50 2.24
221 238 0.249398 ATTTGCCGAGCGGAGTAAGT 59.751 50.000 13.94 0.00 37.50 2.24
222 239 2.128035 CTATTTGCCGAGCGGAGTAAG 58.872 52.381 13.94 0.00 37.50 2.34
223 240 1.752498 TCTATTTGCCGAGCGGAGTAA 59.248 47.619 13.94 3.36 37.50 2.24
224 241 1.395635 TCTATTTGCCGAGCGGAGTA 58.604 50.000 13.94 0.00 37.50 2.59
265 283 9.732130 ATGATAGTGCTCTTTTACTTTCTTTCT 57.268 29.630 0.00 0.00 0.00 2.52
293 311 1.202348 GGTCCTCGGCAAAGATTTTGG 59.798 52.381 3.97 0.00 0.00 3.28
319 337 3.249799 TGACGTTGTCATGGTGTTTGATC 59.750 43.478 0.00 0.00 37.67 2.92
389 414 6.745116 ACACTATGCAAAAACCTAAAACTCC 58.255 36.000 0.00 0.00 0.00 3.85
488 520 2.554370 AATAGGCCGGCGCTATTTTA 57.446 45.000 29.50 13.06 34.44 1.52
516 548 1.134580 AGCACGCTCTAGCATGATGTT 60.135 47.619 1.61 0.00 36.14 2.71
558 590 5.822519 TGAGAAATGGCTCGCTAAATAATGT 59.177 36.000 0.00 0.00 37.73 2.71
633 665 4.399303 GCTGAGTACATAGGCAAAAACCAT 59.601 41.667 0.00 0.00 0.00 3.55
672 704 5.941058 TCAAGTTCATTTTATCGGGCACTTA 59.059 36.000 0.00 0.00 0.00 2.24
701 733 4.184629 ACCGACACAAATCATAGAGCTTC 58.815 43.478 0.00 0.00 0.00 3.86
731 763 5.845953 GTGAAAACACATCACTATCACGTTG 59.154 40.000 0.00 0.00 43.03 4.10
1110 1161 2.159156 TGGAGGTGAACCGATCGTATTG 60.159 50.000 15.09 0.49 42.08 1.90
1123 1174 3.215151 GAGATGACGAGTATGGAGGTGA 58.785 50.000 0.00 0.00 0.00 4.02
1247 1298 2.047560 GAACGGACCCCTGAACGG 60.048 66.667 0.00 0.00 0.00 4.44
1560 1633 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1561 1634 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1562 1635 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1563 1636 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1564 1637 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1565 1638 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1566 1639 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1567 1640 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1568 1641 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1569 1642 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1570 1643 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1571 1644 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1572 1645 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1573 1646 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1580 1653 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1593 1666 9.566432 GTTCCAGATACATCTCTTTTTATCCAT 57.434 33.333 0.00 0.00 34.22 3.41
1594 1667 8.772250 AGTTCCAGATACATCTCTTTTTATCCA 58.228 33.333 0.00 0.00 34.22 3.41
1602 1675 9.751542 CGTATTTTAGTTCCAGATACATCTCTT 57.248 33.333 0.00 0.00 34.22 2.85
1603 1676 8.915036 ACGTATTTTAGTTCCAGATACATCTCT 58.085 33.333 0.00 0.00 34.22 3.10
1604 1677 9.182933 GACGTATTTTAGTTCCAGATACATCTC 57.817 37.037 0.00 0.00 34.22 2.75
1605 1678 8.915036 AGACGTATTTTAGTTCCAGATACATCT 58.085 33.333 0.00 0.00 37.72 2.90
1608 1681 9.399797 TCTAGACGTATTTTAGTTCCAGATACA 57.600 33.333 0.00 0.00 0.00 2.29
1623 1696 9.322769 ACAAAAGGGGATATATCTAGACGTATT 57.677 33.333 12.42 0.00 0.00 1.89
1624 1697 8.896722 ACAAAAGGGGATATATCTAGACGTAT 57.103 34.615 12.42 0.00 0.00 3.06
1625 1698 7.120285 CGACAAAAGGGGATATATCTAGACGTA 59.880 40.741 12.42 0.00 0.00 3.57
1626 1699 6.072064 CGACAAAAGGGGATATATCTAGACGT 60.072 42.308 12.42 0.00 0.00 4.34
1627 1700 6.150641 TCGACAAAAGGGGATATATCTAGACG 59.849 42.308 12.42 7.16 0.00 4.18
1628 1701 7.463961 TCGACAAAAGGGGATATATCTAGAC 57.536 40.000 12.42 1.59 0.00 2.59
1629 1702 8.666129 AATCGACAAAAGGGGATATATCTAGA 57.334 34.615 12.42 0.00 0.00 2.43
1630 1703 9.726438 AAAATCGACAAAAGGGGATATATCTAG 57.274 33.333 12.42 0.00 0.00 2.43
1631 1704 9.502091 CAAAATCGACAAAAGGGGATATATCTA 57.498 33.333 12.42 0.00 0.00 1.98
1632 1705 8.217799 TCAAAATCGACAAAAGGGGATATATCT 58.782 33.333 12.42 0.00 0.00 1.98
1633 1706 8.391075 TCAAAATCGACAAAAGGGGATATATC 57.609 34.615 3.96 3.96 0.00 1.63
1634 1707 8.796475 CATCAAAATCGACAAAAGGGGATATAT 58.204 33.333 0.00 0.00 0.00 0.86
1635 1708 7.996066 TCATCAAAATCGACAAAAGGGGATATA 59.004 33.333 0.00 0.00 0.00 0.86
1636 1709 6.833416 TCATCAAAATCGACAAAAGGGGATAT 59.167 34.615 0.00 0.00 0.00 1.63
1637 1710 6.094881 GTCATCAAAATCGACAAAAGGGGATA 59.905 38.462 0.00 0.00 0.00 2.59
1638 1711 5.016173 TCATCAAAATCGACAAAAGGGGAT 58.984 37.500 0.00 0.00 0.00 3.85
1639 1712 4.217550 GTCATCAAAATCGACAAAAGGGGA 59.782 41.667 0.00 0.00 0.00 4.81
1640 1713 4.022416 TGTCATCAAAATCGACAAAAGGGG 60.022 41.667 0.00 0.00 36.75 4.79
1641 1714 5.119931 TGTCATCAAAATCGACAAAAGGG 57.880 39.130 0.00 0.00 36.75 3.95
1646 1719 9.352784 GGAAATATTTGTCATCAAAATCGACAA 57.647 29.630 5.17 0.00 45.34 3.18
1647 1720 7.696035 CGGAAATATTTGTCATCAAAATCGACA 59.304 33.333 5.17 0.00 44.97 4.35
1648 1721 7.165812 CCGGAAATATTTGTCATCAAAATCGAC 59.834 37.037 5.17 0.00 44.97 4.20
1649 1722 7.066404 TCCGGAAATATTTGTCATCAAAATCGA 59.934 33.333 0.00 0.00 44.97 3.59
1650 1723 7.165812 GTCCGGAAATATTTGTCATCAAAATCG 59.834 37.037 5.23 0.00 44.97 3.34
1651 1724 7.165812 CGTCCGGAAATATTTGTCATCAAAATC 59.834 37.037 5.23 0.00 44.97 2.17
1652 1725 6.972328 CGTCCGGAAATATTTGTCATCAAAAT 59.028 34.615 5.23 0.00 44.97 1.82
1653 1726 6.149640 TCGTCCGGAAATATTTGTCATCAAAA 59.850 34.615 5.23 0.00 44.97 2.44
1654 1727 5.644206 TCGTCCGGAAATATTTGTCATCAAA 59.356 36.000 5.23 0.00 45.71 2.69
1655 1728 5.179533 TCGTCCGGAAATATTTGTCATCAA 58.820 37.500 5.23 0.00 0.00 2.57
1656 1729 4.760878 TCGTCCGGAAATATTTGTCATCA 58.239 39.130 5.23 0.00 0.00 3.07
1657 1730 5.277345 CCTTCGTCCGGAAATATTTGTCATC 60.277 44.000 5.23 0.00 33.34 2.92
1658 1731 4.574828 CCTTCGTCCGGAAATATTTGTCAT 59.425 41.667 5.23 0.00 33.34 3.06
1659 1732 3.936453 CCTTCGTCCGGAAATATTTGTCA 59.064 43.478 5.23 0.00 33.34 3.58
1660 1733 4.186159 TCCTTCGTCCGGAAATATTTGTC 58.814 43.478 5.23 0.00 33.34 3.18
1661 1734 4.210724 TCCTTCGTCCGGAAATATTTGT 57.789 40.909 5.23 0.00 33.34 2.83
1662 1735 4.634443 ACTTCCTTCGTCCGGAAATATTTG 59.366 41.667 5.23 0.00 39.86 2.32
1663 1736 4.840271 ACTTCCTTCGTCCGGAAATATTT 58.160 39.130 5.23 0.00 39.86 1.40
1664 1737 4.482952 ACTTCCTTCGTCCGGAAATATT 57.517 40.909 5.23 0.00 39.86 1.28
1665 1738 4.648307 AGTACTTCCTTCGTCCGGAAATAT 59.352 41.667 5.23 0.00 39.86 1.28
1666 1739 4.019174 AGTACTTCCTTCGTCCGGAAATA 58.981 43.478 5.23 0.00 39.86 1.40
1667 1740 2.830321 AGTACTTCCTTCGTCCGGAAAT 59.170 45.455 5.23 0.00 39.86 2.17
1668 1741 2.242043 AGTACTTCCTTCGTCCGGAAA 58.758 47.619 5.23 0.00 39.86 3.13
1669 1742 1.915141 AGTACTTCCTTCGTCCGGAA 58.085 50.000 5.23 0.00 38.18 4.30
1670 1743 2.787473 TAGTACTTCCTTCGTCCGGA 57.213 50.000 0.00 0.00 0.00 5.14
1671 1744 2.947652 TGATAGTACTTCCTTCGTCCGG 59.052 50.000 0.00 0.00 0.00 5.14
1672 1745 4.275196 TCATGATAGTACTTCCTTCGTCCG 59.725 45.833 0.00 0.00 0.00 4.79
1673 1746 5.769484 TCATGATAGTACTTCCTTCGTCC 57.231 43.478 0.00 0.00 0.00 4.79
1674 1747 9.745880 TTTATTCATGATAGTACTTCCTTCGTC 57.254 33.333 0.00 0.00 0.00 4.20
1886 1959 2.555199 GCGCCAGATAAGTCTTGATGT 58.445 47.619 0.00 0.00 30.42 3.06
2024 2103 4.900635 AGAGAAATGCACGAAACAAGTT 57.099 36.364 0.00 0.00 0.00 2.66
2025 2104 4.335315 TCAAGAGAAATGCACGAAACAAGT 59.665 37.500 0.00 0.00 0.00 3.16
2027 2106 4.891627 TCAAGAGAAATGCACGAAACAA 57.108 36.364 0.00 0.00 0.00 2.83
2192 2272 9.537192 TTGATGATTGCATGATAAAAAGAATCC 57.463 29.630 0.00 0.00 34.11 3.01
2217 2297 5.014860 ACCACCTTAGGCCACTTATTTAGTT 59.985 40.000 5.01 0.00 33.85 2.24


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

AutoCloner maintained by Alex Coulton.