Multiple sequence alignment - TraesCS7D01G245300

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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 TraesCS7D01G245300 chr7D 100.000 2456 0 0 1 2456 214325215 214322760 0.000000e+00 4536.0
1 TraesCS7D01G245300 chr7B 94.535 1720 51 22 1 1694 186974802 186976504 0.000000e+00 2615.0
2 TraesCS7D01G245300 chr7B 75.954 603 132 11 1862 2456 688058175 688057578 5.130000e-77 298.0
3 TraesCS7D01G245300 chr7A 94.074 1080 41 9 624 1694 226624551 226623486 0.000000e+00 1618.0
4 TraesCS7D01G245300 chr7A 89.573 585 17 10 1 581 226625089 226624545 0.000000e+00 702.0
5 TraesCS7D01G245300 chr2D 88.782 624 67 3 1836 2456 76804032 76804655 0.000000e+00 761.0
6 TraesCS7D01G245300 chr3B 84.229 558 82 6 1847 2401 227672854 227672300 2.780000e-149 538.0
7 TraesCS7D01G245300 chr3B 93.103 58 4 0 2399 2456 227670768 227670711 4.350000e-13 86.1
8 TraesCS7D01G245300 chr1B 82.353 612 104 3 1848 2456 343308261 343308871 1.670000e-146 529.0
9 TraesCS7D01G245300 chr4D 75.763 524 120 7 1848 2367 110032645 110033165 8.710000e-65 257.0


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 TraesCS7D01G245300 chr7D 214322760 214325215 2455 True 4536.00 4536 100.0000 1 2456 1 chr7D.!!$R1 2455
1 TraesCS7D01G245300 chr7B 186974802 186976504 1702 False 2615.00 2615 94.5350 1 1694 1 chr7B.!!$F1 1693
2 TraesCS7D01G245300 chr7B 688057578 688058175 597 True 298.00 298 75.9540 1862 2456 1 chr7B.!!$R1 594
3 TraesCS7D01G245300 chr7A 226623486 226625089 1603 True 1160.00 1618 91.8235 1 1694 2 chr7A.!!$R1 1693
4 TraesCS7D01G245300 chr2D 76804032 76804655 623 False 761.00 761 88.7820 1836 2456 1 chr2D.!!$F1 620
5 TraesCS7D01G245300 chr3B 227670711 227672854 2143 True 312.05 538 88.6660 1847 2456 2 chr3B.!!$R1 609
6 TraesCS7D01G245300 chr1B 343308261 343308871 610 False 529.00 529 82.3530 1848 2456 1 chr1B.!!$F1 608
7 TraesCS7D01G245300 chr4D 110032645 110033165 520 False 257.00 257 75.7630 1848 2367 1 chr4D.!!$F1 519

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
801 806 0.03779 GCTCCACTTTCAGCTCTCGT 60.038 55.0 0.0 0.0 32.48 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1934 0.101219 GATGAATGCGAACTTGGGCC 59.899 55.0 0.0 0.0 0.0 5.8 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
87 88 2.654912 CGTGTGTCGGAAGCGAACC 61.655 63.158 0.00 0.00 35.71 3.62
88 89 2.029964 TGTGTCGGAAGCGAACCC 59.970 61.111 0.00 0.00 0.00 4.11
89 90 2.342648 GTGTCGGAAGCGAACCCT 59.657 61.111 0.00 0.00 0.00 4.34
90 91 2.027625 GTGTCGGAAGCGAACCCTG 61.028 63.158 0.00 0.00 0.00 4.45
91 92 2.204461 TGTCGGAAGCGAACCCTGA 61.204 57.895 0.00 0.00 0.00 3.86
92 93 1.005394 GTCGGAAGCGAACCCTGAA 60.005 57.895 0.00 0.00 0.00 3.02
93 94 1.005394 TCGGAAGCGAACCCTGAAC 60.005 57.895 0.00 0.00 0.00 3.18
94 95 2.033194 CGGAAGCGAACCCTGAACC 61.033 63.158 0.00 0.00 0.00 3.62
133 134 0.170561 GTGTGAGTGATCGGCGTACT 59.829 55.000 6.85 10.31 0.00 2.73
443 448 2.747177 CACCATCTCCCACTGGTACTA 58.253 52.381 0.00 0.00 43.91 1.82
472 477 2.202570 CCCCGTCTTCGTGTAGCG 60.203 66.667 0.00 0.00 43.01 4.26
478 483 2.261671 CTTCGTGTAGCGGTGCCT 59.738 61.111 0.00 0.00 41.72 4.75
479 484 0.961857 TCTTCGTGTAGCGGTGCCTA 60.962 55.000 0.00 0.00 41.72 3.93
503 508 0.400213 AGATTGTTTCGGAGCCACCA 59.600 50.000 0.00 0.00 38.90 4.17
621 626 5.940470 GGTTATGGAGTGATTGATATGGGAC 59.060 44.000 0.00 0.00 0.00 4.46
718 723 3.430565 TACATGCCCTCGCGCTCTG 62.431 63.158 5.56 0.00 38.08 3.35
801 806 0.037790 GCTCCACTTTCAGCTCTCGT 60.038 55.000 0.00 0.00 32.48 4.18
1044 1052 0.543277 AGAAATCGGCTGAGGATGCA 59.457 50.000 0.00 0.00 0.00 3.96
1139 1147 2.045242 TCTGAGGGACGACGGAGG 60.045 66.667 0.00 0.00 0.00 4.30
1179 1187 4.699522 GCCAAGGTCGCGGAGGTT 62.700 66.667 6.13 0.00 0.00 3.50
1329 1337 2.504244 GTTGAGGACGTCGGCGAG 60.504 66.667 20.03 7.37 42.00 5.03
1341 1349 1.153823 CGGCGAGAAAGACGGTGAT 60.154 57.895 0.00 0.00 39.34 3.06
1685 1731 3.005367 CGTTTTGGATAACAAGGTGGCTT 59.995 43.478 0.00 0.00 40.82 4.35
1686 1732 4.306600 GTTTTGGATAACAAGGTGGCTTG 58.693 43.478 0.00 0.00 40.82 4.01
1688 1734 0.817654 GGATAACAAGGTGGCTTGGC 59.182 55.000 0.00 0.00 38.55 4.52
1698 1744 2.188731 GGCTTGGCCGTAGTACCC 59.811 66.667 0.00 0.00 39.62 3.69
1699 1745 2.188731 GCTTGGCCGTAGTACCCC 59.811 66.667 0.00 0.00 0.00 4.95
1700 1746 2.364780 GCTTGGCCGTAGTACCCCT 61.365 63.158 0.00 0.00 0.00 4.79
1701 1747 1.821258 CTTGGCCGTAGTACCCCTC 59.179 63.158 0.00 0.00 0.00 4.30
1702 1748 2.012902 CTTGGCCGTAGTACCCCTCG 62.013 65.000 0.00 0.00 0.00 4.63
1703 1749 2.440980 GGCCGTAGTACCCCTCGT 60.441 66.667 0.00 0.00 0.00 4.18
1704 1750 1.152963 GGCCGTAGTACCCCTCGTA 60.153 63.158 0.00 0.00 0.00 3.43
1705 1751 1.448119 GGCCGTAGTACCCCTCGTAC 61.448 65.000 0.00 0.00 46.69 3.67
1710 1756 2.803479 GTACCCCTCGTACGGCAG 59.197 66.667 16.52 6.19 38.17 4.85
1711 1757 2.048603 GTACCCCTCGTACGGCAGT 61.049 63.158 16.52 10.47 38.17 4.40
1712 1758 1.750399 TACCCCTCGTACGGCAGTC 60.750 63.158 16.52 0.00 0.00 3.51
1713 1759 2.202236 TACCCCTCGTACGGCAGTCT 62.202 60.000 16.52 0.00 0.00 3.24
1714 1760 2.490217 CCCTCGTACGGCAGTCTG 59.510 66.667 16.52 0.00 0.00 3.51
1715 1761 2.490217 CCTCGTACGGCAGTCTGG 59.510 66.667 16.52 3.18 0.00 3.86
1716 1762 2.341101 CCTCGTACGGCAGTCTGGT 61.341 63.158 16.52 0.00 0.00 4.00
1717 1763 1.585006 CTCGTACGGCAGTCTGGTT 59.415 57.895 16.52 0.00 0.00 3.67
1718 1764 0.456312 CTCGTACGGCAGTCTGGTTC 60.456 60.000 16.52 0.00 0.00 3.62
1719 1765 1.800315 CGTACGGCAGTCTGGTTCG 60.800 63.158 7.57 0.00 0.00 3.95
1720 1766 2.092882 GTACGGCAGTCTGGTTCGC 61.093 63.158 1.14 0.00 0.00 4.70
1721 1767 2.566570 TACGGCAGTCTGGTTCGCA 61.567 57.895 1.14 0.00 0.00 5.10
1722 1768 2.089887 TACGGCAGTCTGGTTCGCAA 62.090 55.000 1.14 0.00 0.00 4.85
1723 1769 2.671177 CGGCAGTCTGGTTCGCAAG 61.671 63.158 1.14 0.00 0.00 4.01
1735 1781 4.394712 CGCAAGAGGGCCGGACTT 62.395 66.667 7.57 0.00 43.02 3.01
1736 1782 2.034221 GCAAGAGGGCCGGACTTT 59.966 61.111 7.57 0.00 0.00 2.66
1737 1783 1.603739 GCAAGAGGGCCGGACTTTT 60.604 57.895 7.57 1.38 0.00 2.27
1738 1784 1.179174 GCAAGAGGGCCGGACTTTTT 61.179 55.000 7.57 0.00 0.00 1.94
1763 1809 9.921637 TTTGTAAATTTGGTTATGCCTAAGAAG 57.078 29.630 0.00 0.00 35.56 2.85
1764 1810 7.543756 TGTAAATTTGGTTATGCCTAAGAAGC 58.456 34.615 0.00 0.00 35.56 3.86
1765 1811 5.598416 AATTTGGTTATGCCTAAGAAGCC 57.402 39.130 0.00 0.00 35.56 4.35
1766 1812 4.316025 TTTGGTTATGCCTAAGAAGCCT 57.684 40.909 0.00 0.00 38.35 4.58
1767 1813 3.560636 TGGTTATGCCTAAGAAGCCTC 57.439 47.619 0.00 0.00 38.35 4.70
1768 1814 2.172717 TGGTTATGCCTAAGAAGCCTCC 59.827 50.000 0.00 0.00 38.35 4.30
1769 1815 2.439880 GGTTATGCCTAAGAAGCCTCCT 59.560 50.000 0.00 0.00 0.00 3.69
1770 1816 3.117851 GGTTATGCCTAAGAAGCCTCCTT 60.118 47.826 0.00 0.00 0.00 3.36
1771 1817 4.102681 GGTTATGCCTAAGAAGCCTCCTTA 59.897 45.833 0.00 0.00 0.00 2.69
1772 1818 5.397559 GGTTATGCCTAAGAAGCCTCCTTAA 60.398 44.000 0.00 0.00 0.00 1.85
1773 1819 4.862641 ATGCCTAAGAAGCCTCCTTAAA 57.137 40.909 0.00 0.00 0.00 1.52
1774 1820 4.862641 TGCCTAAGAAGCCTCCTTAAAT 57.137 40.909 0.00 0.00 0.00 1.40
1775 1821 5.968676 TGCCTAAGAAGCCTCCTTAAATA 57.031 39.130 0.00 0.00 0.00 1.40
1776 1822 6.515512 TGCCTAAGAAGCCTCCTTAAATAT 57.484 37.500 0.00 0.00 0.00 1.28
1777 1823 6.911308 TGCCTAAGAAGCCTCCTTAAATATT 58.089 36.000 0.00 0.00 0.00 1.28
1778 1824 6.772716 TGCCTAAGAAGCCTCCTTAAATATTG 59.227 38.462 0.00 0.00 0.00 1.90
1779 1825 6.998673 GCCTAAGAAGCCTCCTTAAATATTGA 59.001 38.462 0.00 0.00 0.00 2.57
1780 1826 7.502561 GCCTAAGAAGCCTCCTTAAATATTGAA 59.497 37.037 0.00 0.00 0.00 2.69
1781 1827 9.579932 CCTAAGAAGCCTCCTTAAATATTGAAT 57.420 33.333 0.00 0.00 0.00 2.57
1783 1829 8.470657 AAGAAGCCTCCTTAAATATTGAATCC 57.529 34.615 0.00 0.00 0.00 3.01
1784 1830 7.007116 AGAAGCCTCCTTAAATATTGAATCCC 58.993 38.462 0.00 0.00 0.00 3.85
1785 1831 5.645201 AGCCTCCTTAAATATTGAATCCCC 58.355 41.667 0.00 0.00 0.00 4.81
1786 1832 4.772624 GCCTCCTTAAATATTGAATCCCCC 59.227 45.833 0.00 0.00 0.00 5.40
1818 1864 3.915437 AAAGATAACAAGGTGGTTGCG 57.085 42.857 0.00 0.00 40.15 4.85
1819 1865 1.821216 AGATAACAAGGTGGTTGCGG 58.179 50.000 0.00 0.00 40.15 5.69
1820 1866 0.170339 GATAACAAGGTGGTTGCGGC 59.830 55.000 0.00 0.00 40.15 6.53
1821 1867 1.248101 ATAACAAGGTGGTTGCGGCC 61.248 55.000 0.00 0.00 40.15 6.13
1822 1868 2.346284 TAACAAGGTGGTTGCGGCCT 62.346 55.000 0.00 0.00 40.15 5.19
1823 1869 2.912025 CAAGGTGGTTGCGGCCTT 60.912 61.111 0.00 0.00 42.77 4.35
1824 1870 1.602323 CAAGGTGGTTGCGGCCTTA 60.602 57.895 0.00 0.00 40.31 2.69
1825 1871 1.303317 AAGGTGGTTGCGGCCTTAG 60.303 57.895 0.00 0.00 40.48 2.18
1826 1872 2.750237 GGTGGTTGCGGCCTTAGG 60.750 66.667 0.00 0.00 0.00 2.69
1827 1873 2.033602 GTGGTTGCGGCCTTAGGT 59.966 61.111 0.00 0.00 0.00 3.08
1828 1874 2.033448 TGGTTGCGGCCTTAGGTG 59.967 61.111 0.00 0.00 0.00 4.00
1829 1875 2.349755 GGTTGCGGCCTTAGGTGA 59.650 61.111 0.00 0.00 0.00 4.02
1830 1876 2.038837 GGTTGCGGCCTTAGGTGAC 61.039 63.158 0.00 0.00 0.00 3.67
1832 1878 0.605589 GTTGCGGCCTTAGGTGACTT 60.606 55.000 0.00 0.00 43.67 3.01
1833 1879 0.978151 TTGCGGCCTTAGGTGACTTA 59.022 50.000 0.00 0.00 43.67 2.24
1834 1880 0.978151 TGCGGCCTTAGGTGACTTAA 59.022 50.000 0.00 0.00 43.67 1.85
1838 1884 2.028385 CGGCCTTAGGTGACTTAACTGT 60.028 50.000 0.00 0.00 43.67 3.55
1845 1891 6.070995 CCTTAGGTGACTTAACTGTATGGTCA 60.071 42.308 0.00 5.84 43.67 4.02
1880 1926 3.118038 AGAAGGGCTGATTTGGCGTATTA 60.118 43.478 0.00 0.00 0.00 0.98
1888 1934 4.641396 TGATTTGGCGTATTAGAGATGGG 58.359 43.478 0.00 0.00 0.00 4.00
1942 1988 0.885879 CAAGGAGCAGCAGCATGAAA 59.114 50.000 3.17 0.00 45.49 2.69
1948 1994 0.730494 GCAGCAGCATGAAACCGTTC 60.730 55.000 0.00 0.00 39.69 3.95
1995 2041 2.363683 GAGAGTTGCCCATCTCCTTTG 58.636 52.381 3.41 0.00 36.72 2.77
2069 2115 4.753610 CGGATGATGTGCAAGATATCAAGT 59.246 41.667 5.32 0.00 35.95 3.16
2103 2149 1.133575 AGGGCCTGGTCATGATGATTG 60.134 52.381 4.50 0.00 0.00 2.67
2206 2252 2.835705 CGGACAGTCGGGATCCTCG 61.836 68.421 12.58 13.65 0.00 4.63
2241 2288 0.462047 CATCGCGGGTTTAGGCTCTT 60.462 55.000 6.13 0.00 0.00 2.85
2381 2430 0.108041 GCGGACGGGAGGAAACAATA 60.108 55.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.951040 GACACACGGAAAGGCAGAGG 60.951 60.000 0.00 0.00 0.00 3.69
85 86 3.971702 GGCAGCTGGGTTCAGGGT 61.972 66.667 17.12 0.00 41.19 4.34
87 88 2.360852 CAGGCAGCTGGGTTCAGG 60.361 66.667 17.12 0.00 41.19 3.86
88 89 1.970114 CACAGGCAGCTGGGTTCAG 60.970 63.158 17.12 0.00 43.64 3.02
89 90 2.113774 CACAGGCAGCTGGGTTCA 59.886 61.111 17.12 0.00 0.00 3.18
90 91 1.673665 CTCACAGGCAGCTGGGTTC 60.674 63.158 17.12 0.00 0.00 3.62
91 92 2.433446 CTCACAGGCAGCTGGGTT 59.567 61.111 17.12 0.00 0.00 4.11
92 93 2.851102 ACTCACAGGCAGCTGGGT 60.851 61.111 17.12 0.00 0.00 4.51
93 94 2.359602 CACTCACAGGCAGCTGGG 60.360 66.667 17.12 0.00 0.00 4.45
94 95 1.964891 CACACTCACAGGCAGCTGG 60.965 63.158 17.12 0.73 0.00 4.85
133 134 0.321830 GTACGCCCCCTTGCTGTTAA 60.322 55.000 0.00 0.00 0.00 2.01
443 448 2.842645 AGACGGGGTGGATACTACTT 57.157 50.000 0.00 0.00 37.61 2.24
472 477 1.668419 AACAATCTCGCATAGGCACC 58.332 50.000 0.00 0.00 41.24 5.01
478 483 2.201732 GCTCCGAAACAATCTCGCATA 58.798 47.619 0.00 0.00 34.95 3.14
479 484 1.009829 GCTCCGAAACAATCTCGCAT 58.990 50.000 0.00 0.00 34.95 4.73
503 508 2.756283 CGAGAAGTCCCCGGCTCT 60.756 66.667 0.00 0.00 0.00 4.09
621 626 1.461127 GAACGCTGAGGTAAGCACAAG 59.539 52.381 0.00 0.00 43.73 3.16
718 723 1.802960 CGGCACATCATCAATCCTAGC 59.197 52.381 0.00 0.00 0.00 3.42
801 806 8.581253 TTTAGCAGAGCATATATACTGAGCTA 57.419 34.615 14.03 12.04 35.36 3.32
1044 1052 3.730761 CCGTCGTCGTCGTCCCTT 61.731 66.667 10.76 0.00 38.33 3.95
1139 1147 0.733223 GTCCTCCACTTCTTCGTCGC 60.733 60.000 0.00 0.00 0.00 5.19
1179 1187 1.159713 CCAGTTTGACGCTGTCTGCA 61.160 55.000 9.49 0.00 43.06 4.41
1232 1240 2.019807 TCCGTCAGGAACTTTACCCT 57.980 50.000 0.00 0.00 45.12 4.34
1329 1337 1.986378 CTCACGTCATCACCGTCTTTC 59.014 52.381 0.00 0.00 36.17 2.62
1341 1349 3.806591 GGATTTCGTCCTCACGTCA 57.193 52.632 0.00 0.00 46.76 4.35
1359 1367 2.973600 TTTCGCCGGAACCCGTTG 60.974 61.111 5.05 0.00 46.80 4.10
1685 1731 1.920734 TACGAGGGGTACTACGGCCA 61.921 60.000 2.24 0.00 0.00 5.36
1686 1732 1.152963 TACGAGGGGTACTACGGCC 60.153 63.158 0.00 0.00 0.00 6.13
1693 1739 1.997928 GACTGCCGTACGAGGGGTAC 61.998 65.000 18.76 0.00 46.54 3.34
1694 1740 1.750399 GACTGCCGTACGAGGGGTA 60.750 63.158 18.76 0.00 0.00 3.69
1695 1741 3.066814 GACTGCCGTACGAGGGGT 61.067 66.667 18.76 9.67 0.00 4.95
1696 1742 2.754658 AGACTGCCGTACGAGGGG 60.755 66.667 18.76 6.40 0.00 4.79
1697 1743 2.490217 CAGACTGCCGTACGAGGG 59.510 66.667 18.76 8.24 0.00 4.30
1698 1744 1.874345 AACCAGACTGCCGTACGAGG 61.874 60.000 18.76 8.60 0.00 4.63
1699 1745 0.456312 GAACCAGACTGCCGTACGAG 60.456 60.000 18.76 9.80 0.00 4.18
1700 1746 1.582968 GAACCAGACTGCCGTACGA 59.417 57.895 18.76 0.00 0.00 3.43
1701 1747 1.800315 CGAACCAGACTGCCGTACG 60.800 63.158 8.69 8.69 0.00 3.67
1702 1748 2.092882 GCGAACCAGACTGCCGTAC 61.093 63.158 0.00 0.00 0.00 3.67
1703 1749 2.089887 TTGCGAACCAGACTGCCGTA 62.090 55.000 0.00 0.00 0.00 4.02
1704 1750 3.454587 TTGCGAACCAGACTGCCGT 62.455 57.895 0.00 0.00 0.00 5.68
1705 1751 2.664851 TTGCGAACCAGACTGCCG 60.665 61.111 0.00 1.55 0.00 5.69
1706 1752 1.294659 CTCTTGCGAACCAGACTGCC 61.295 60.000 0.00 0.00 0.00 4.85
1707 1753 1.294659 CCTCTTGCGAACCAGACTGC 61.295 60.000 0.00 0.00 0.00 4.40
1708 1754 0.671781 CCCTCTTGCGAACCAGACTG 60.672 60.000 0.00 0.00 0.00 3.51
1709 1755 1.674057 CCCTCTTGCGAACCAGACT 59.326 57.895 0.00 0.00 0.00 3.24
1710 1756 2.035442 GCCCTCTTGCGAACCAGAC 61.035 63.158 0.00 0.00 0.00 3.51
1711 1757 2.347490 GCCCTCTTGCGAACCAGA 59.653 61.111 0.00 0.00 0.00 3.86
1712 1758 2.747855 GGCCCTCTTGCGAACCAG 60.748 66.667 0.00 0.00 0.00 4.00
1713 1759 4.697756 CGGCCCTCTTGCGAACCA 62.698 66.667 0.00 0.00 0.00 3.67
1715 1761 4.388499 TCCGGCCCTCTTGCGAAC 62.388 66.667 0.00 0.00 0.00 3.95
1716 1762 4.388499 GTCCGGCCCTCTTGCGAA 62.388 66.667 0.00 0.00 0.00 4.70
1718 1764 3.901797 AAAGTCCGGCCCTCTTGCG 62.902 63.158 0.00 0.00 0.00 4.85
1719 1765 1.179174 AAAAAGTCCGGCCCTCTTGC 61.179 55.000 0.00 0.00 0.00 4.01
1720 1766 3.036431 AAAAAGTCCGGCCCTCTTG 57.964 52.632 0.00 0.00 0.00 3.02
1737 1783 9.921637 CTTCTTAGGCATAACCAAATTTACAAA 57.078 29.630 0.00 0.00 43.14 2.83
1738 1784 8.032451 GCTTCTTAGGCATAACCAAATTTACAA 58.968 33.333 0.00 0.00 43.14 2.41
1739 1785 7.363443 GGCTTCTTAGGCATAACCAAATTTACA 60.363 37.037 0.00 0.00 45.79 2.41
1740 1786 6.978659 GGCTTCTTAGGCATAACCAAATTTAC 59.021 38.462 0.00 0.00 45.79 2.01
1741 1787 7.107639 GGCTTCTTAGGCATAACCAAATTTA 57.892 36.000 0.00 0.00 45.79 1.40
1742 1788 5.977635 GGCTTCTTAGGCATAACCAAATTT 58.022 37.500 0.00 0.00 45.79 1.82
1743 1789 5.598416 GGCTTCTTAGGCATAACCAAATT 57.402 39.130 0.00 0.00 45.79 1.82
1754 1800 6.998673 TCAATATTTAAGGAGGCTTCTTAGGC 59.001 38.462 14.71 0.00 46.82 3.93
1755 1801 8.980481 TTCAATATTTAAGGAGGCTTCTTAGG 57.020 34.615 14.71 3.53 0.00 2.69
1757 1803 9.574516 GGATTCAATATTTAAGGAGGCTTCTTA 57.425 33.333 11.33 11.33 0.00 2.10
1758 1804 7.507277 GGGATTCAATATTTAAGGAGGCTTCTT 59.493 37.037 13.65 13.65 0.00 2.52
1759 1805 7.007116 GGGATTCAATATTTAAGGAGGCTTCT 58.993 38.462 0.00 0.00 0.00 2.85
1760 1806 6.209589 GGGGATTCAATATTTAAGGAGGCTTC 59.790 42.308 0.00 0.00 0.00 3.86
1761 1807 6.077993 GGGGATTCAATATTTAAGGAGGCTT 58.922 40.000 0.00 0.00 0.00 4.35
1762 1808 5.459683 GGGGGATTCAATATTTAAGGAGGCT 60.460 44.000 0.00 0.00 0.00 4.58
1763 1809 4.772624 GGGGGATTCAATATTTAAGGAGGC 59.227 45.833 0.00 0.00 0.00 4.70
1796 1842 4.500716 CCGCAACCACCTTGTTATCTTTTT 60.501 41.667 0.00 0.00 31.73 1.94
1797 1843 3.005367 CCGCAACCACCTTGTTATCTTTT 59.995 43.478 0.00 0.00 31.73 2.27
1798 1844 2.556622 CCGCAACCACCTTGTTATCTTT 59.443 45.455 0.00 0.00 31.73 2.52
1799 1845 2.159382 CCGCAACCACCTTGTTATCTT 58.841 47.619 0.00 0.00 31.73 2.40
1800 1846 1.821216 CCGCAACCACCTTGTTATCT 58.179 50.000 0.00 0.00 31.73 1.98
1801 1847 0.170339 GCCGCAACCACCTTGTTATC 59.830 55.000 0.00 0.00 31.73 1.75
1802 1848 1.248101 GGCCGCAACCACCTTGTTAT 61.248 55.000 0.00 0.00 31.73 1.89
1803 1849 1.899534 GGCCGCAACCACCTTGTTA 60.900 57.895 0.00 0.00 31.73 2.41
1804 1850 3.223589 GGCCGCAACCACCTTGTT 61.224 61.111 0.00 0.00 31.73 2.83
1805 1851 2.346284 TAAGGCCGCAACCACCTTGT 62.346 55.000 0.00 0.00 43.58 3.16
1806 1852 1.586154 CTAAGGCCGCAACCACCTTG 61.586 60.000 0.00 0.00 43.58 3.61
1807 1853 1.303317 CTAAGGCCGCAACCACCTT 60.303 57.895 0.00 0.00 45.62 3.50
1808 1854 2.351276 CTAAGGCCGCAACCACCT 59.649 61.111 0.00 0.00 34.45 4.00
1809 1855 2.750237 CCTAAGGCCGCAACCACC 60.750 66.667 0.00 0.00 0.00 4.61
1810 1856 2.033602 ACCTAAGGCCGCAACCAC 59.966 61.111 0.00 0.00 0.00 4.16
1811 1857 2.033448 CACCTAAGGCCGCAACCA 59.967 61.111 0.00 0.00 0.00 3.67
1812 1858 2.038837 GTCACCTAAGGCCGCAACC 61.039 63.158 0.00 0.00 0.00 3.77
1813 1859 0.605589 AAGTCACCTAAGGCCGCAAC 60.606 55.000 0.00 0.00 0.00 4.17
1814 1860 0.978151 TAAGTCACCTAAGGCCGCAA 59.022 50.000 0.00 0.00 0.00 4.85
1815 1861 0.978151 TTAAGTCACCTAAGGCCGCA 59.022 50.000 0.00 0.00 0.00 5.69
1816 1862 1.066358 AGTTAAGTCACCTAAGGCCGC 60.066 52.381 0.00 0.00 0.00 6.53
1817 1863 2.028385 ACAGTTAAGTCACCTAAGGCCG 60.028 50.000 0.00 0.00 0.00 6.13
1818 1864 3.697619 ACAGTTAAGTCACCTAAGGCC 57.302 47.619 0.00 0.00 0.00 5.19
1819 1865 5.116882 CCATACAGTTAAGTCACCTAAGGC 58.883 45.833 0.00 0.00 0.00 4.35
1820 1866 6.070995 TGACCATACAGTTAAGTCACCTAAGG 60.071 42.308 0.00 0.00 32.75 2.69
1821 1867 6.931838 TGACCATACAGTTAAGTCACCTAAG 58.068 40.000 0.00 0.00 32.75 2.18
1822 1868 6.921486 TGACCATACAGTTAAGTCACCTAA 57.079 37.500 0.00 0.00 32.75 2.69
1823 1869 6.666113 TCATGACCATACAGTTAAGTCACCTA 59.334 38.462 0.00 0.00 40.04 3.08
1824 1870 5.483937 TCATGACCATACAGTTAAGTCACCT 59.516 40.000 0.00 0.00 40.04 4.00
1825 1871 5.730550 TCATGACCATACAGTTAAGTCACC 58.269 41.667 0.00 0.00 40.04 4.02
1826 1872 7.268586 AGATCATGACCATACAGTTAAGTCAC 58.731 38.462 0.00 0.00 40.04 3.67
1827 1873 7.417911 GGAGATCATGACCATACAGTTAAGTCA 60.418 40.741 0.00 0.00 41.35 3.41
1828 1874 6.926272 GGAGATCATGACCATACAGTTAAGTC 59.074 42.308 0.00 0.00 0.00 3.01
1829 1875 6.613271 AGGAGATCATGACCATACAGTTAAGT 59.387 38.462 0.00 0.00 0.00 2.24
1830 1876 7.060383 AGGAGATCATGACCATACAGTTAAG 57.940 40.000 0.00 0.00 0.00 1.85
1831 1877 7.437713 AAGGAGATCATGACCATACAGTTAA 57.562 36.000 0.00 0.00 0.00 2.01
1832 1878 8.004801 TCTAAGGAGATCATGACCATACAGTTA 58.995 37.037 0.00 0.00 0.00 2.24
1833 1879 5.965033 AAGGAGATCATGACCATACAGTT 57.035 39.130 0.00 0.00 0.00 3.16
1834 1880 6.377080 TCTAAGGAGATCATGACCATACAGT 58.623 40.000 0.00 0.00 0.00 3.55
1838 1884 7.773489 CTTCTCTAAGGAGATCATGACCATA 57.227 40.000 0.00 0.00 46.51 2.74
1880 1926 1.915078 CGAACTTGGGCCCCATCTCT 61.915 60.000 22.27 0.00 31.53 3.10
1888 1934 0.101219 GATGAATGCGAACTTGGGCC 59.899 55.000 0.00 0.00 0.00 5.80
1942 1988 1.324740 TGTATAGCTGCCCGAACGGT 61.325 55.000 12.23 0.00 0.00 4.83
1995 2041 3.154827 TCCAACCTTTCCCATCAGAAC 57.845 47.619 0.00 0.00 0.00 3.01
2069 2115 1.379309 GCCCTCCCACCGCAATTTA 60.379 57.895 0.00 0.00 0.00 1.40
2103 2149 2.281484 TGAAGTTCCACGCCAGGC 60.281 61.111 0.00 0.00 0.00 4.85
2206 2252 2.034507 GCGATGCTTAGTGATCGAACAC 60.035 50.000 17.27 17.27 43.36 3.32
2241 2288 0.322098 CCGGCACTTGTGTATCCCAA 60.322 55.000 0.00 0.00 0.00 4.12
2352 2401 2.126888 CCGTCCGCATGCAACAAC 60.127 61.111 19.57 8.46 0.00 3.32
2353 2402 3.361158 CCCGTCCGCATGCAACAA 61.361 61.111 19.57 0.00 0.00 2.83
2381 2430 3.167485 ACATGCCCAAAATCTGTGATGT 58.833 40.909 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.