Multiple sequence alignment - TraesCS7B01G094500

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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 TraesCS7B01G094500 chr7B 100.000 4175 0 0 1 4175 108283083 108287257 0.000000e+00 7710.0
1 TraesCS7B01G094500 chr7D 93.739 1693 82 17 1808 3490 146105414 146107092 0.000000e+00 2518.0
2 TraesCS7B01G094500 chr7D 94.737 1159 48 7 585 1740 146104254 146105402 0.000000e+00 1790.0
3 TraesCS7B01G094500 chr7D 90.210 429 37 3 1 424 146103720 146104148 4.720000e-154 555.0
4 TraesCS7B01G094500 chr7D 79.605 608 76 29 3559 4159 146107094 146107660 3.910000e-105 392.0
5 TraesCS7B01G094500 chr7A 90.895 1889 120 36 1809 3671 146950218 146952080 0.000000e+00 2488.0
6 TraesCS7B01G094500 chr7A 93.624 941 42 7 698 1632 146949236 146950164 0.000000e+00 1389.0
7 TraesCS7B01G094500 chr7A 87.356 696 66 13 1 679 146948562 146949252 0.000000e+00 778.0
8 TraesCS7B01G094500 chr7A 79.630 432 38 21 3762 4175 146952496 146952895 8.900000e-67 265.0
9 TraesCS7B01G094500 chr3B 87.059 85 11 0 2965 3049 798397812 798397896 3.440000e-16 97.1
10 TraesCS7B01G094500 chr3B 85.882 85 12 0 2965 3049 798404347 798404431 1.600000e-14 91.6
11 TraesCS7B01G094500 chr3D 85.882 85 12 0 2965 3049 594955817 594955901 1.600000e-14 91.6
12 TraesCS7B01G094500 chr3A 85.882 85 12 0 2965 3049 725842932 725843016 1.600000e-14 91.6
13 TraesCS7B01G094500 chr3A 85.882 85 12 0 2965 3049 725905356 725905440 1.600000e-14 91.6
14 TraesCS7B01G094500 chr3A 86.420 81 11 0 2965 3045 726714134 726714054 5.750000e-14 89.8


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 TraesCS7B01G094500 chr7B 108283083 108287257 4174 False 7710.00 7710 100.00000 1 4175 1 chr7B.!!$F1 4174
1 TraesCS7B01G094500 chr7D 146103720 146107660 3940 False 1313.75 2518 89.57275 1 4159 4 chr7D.!!$F1 4158
2 TraesCS7B01G094500 chr7A 146948562 146952895 4333 False 1230.00 2488 87.87625 1 4175 4 chr7A.!!$F1 4174

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
917 934 0.677288 TCGTCAACCCATTCGTCTGT 59.323 50.0 0.0 0.0 0.0 3.41 F
1474 1495 0.603065 GCGCCCTGTTTTCATTTCCT 59.397 50.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1750 0.098728 ACGCACACACAGAAAGCAAC 59.901 50.0 0.0 0.0 0.00 4.17 R
3243 3291 0.183014 TAACCACAAGGCACCCGAAA 59.817 50.0 0.0 0.0 39.06 3.46 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
79 80 7.633193 TTATAGTTTGTTGAGTGGTTGTTGT 57.367 32.000 0.00 0.00 0.00 3.32
89 90 4.102524 TGAGTGGTTGTTGTTCCTGATAGT 59.897 41.667 0.00 0.00 0.00 2.12
126 130 2.485814 CTCCTCTTTGCTAGTGTTTGCC 59.514 50.000 0.00 0.00 0.00 4.52
142 146 2.665649 TGCCGTTCTTGATACGTCAT 57.334 45.000 0.00 0.00 37.30 3.06
154 158 6.368791 TCTTGATACGTCATGTTCCTTTTCTG 59.631 38.462 0.00 0.00 33.56 3.02
203 207 7.661536 TCCTGGTATGGTAATATAGATCAGC 57.338 40.000 0.00 0.00 0.00 4.26
205 209 6.321435 CCTGGTATGGTAATATAGATCAGCGA 59.679 42.308 0.00 0.00 0.00 4.93
215 219 9.239002 GTAATATAGATCAGCGATGTAATGGTC 57.761 37.037 0.00 0.00 0.00 4.02
243 247 3.647590 TGCTAGGTTGGAGCATCATGATA 59.352 43.478 8.15 0.00 44.89 2.15
252 256 7.611467 GGTTGGAGCATCATGATATGGTTATAA 59.389 37.037 8.15 0.00 37.69 0.98
301 305 4.794169 CCCTGTAAACAACTCCATTTTCG 58.206 43.478 0.00 0.00 0.00 3.46
325 330 0.893727 GAAAATGGGGTCGTGTGGCT 60.894 55.000 0.00 0.00 0.00 4.75
362 368 5.988865 TGATCTACCACCCTCTTAGACTA 57.011 43.478 0.00 0.00 0.00 2.59
408 415 8.716646 ACTTTGACATAATTGATCGTGATGTA 57.283 30.769 1.87 0.00 31.03 2.29
412 419 9.981114 TTGACATAATTGATCGTGATGTATAGT 57.019 29.630 1.87 0.00 31.03 2.12
413 420 9.410556 TGACATAATTGATCGTGATGTATAGTG 57.589 33.333 1.87 0.00 31.03 2.74
424 431 6.017357 TCGTGATGTATAGTGTGAGTGATACC 60.017 42.308 0.00 0.00 0.00 2.73
426 433 7.142021 GTGATGTATAGTGTGAGTGATACCTG 58.858 42.308 0.00 0.00 0.00 4.00
503 518 7.502226 ACTGTGTTGATGGTTTCTTCTAATGAA 59.498 33.333 0.00 0.00 0.00 2.57
515 530 6.668541 TCTTCTAATGAAAATCGAGGCAAG 57.331 37.500 0.00 0.00 0.00 4.01
558 573 5.967088 TCCAAACTCATTTTTGTTTCCGAA 58.033 33.333 0.00 0.00 35.09 4.30
601 616 5.175859 TGAACAGAGAACAAAACGAACTCT 58.824 37.500 0.00 0.00 38.27 3.24
771 788 8.469200 TCAAATACAAATATTTTGGGAGCTCAG 58.531 33.333 17.19 0.00 38.67 3.35
846 863 2.106683 GGCACCTCCGGAATGTTCG 61.107 63.158 5.23 0.00 0.00 3.95
917 934 0.677288 TCGTCAACCCATTCGTCTGT 59.323 50.000 0.00 0.00 0.00 3.41
945 966 2.249743 ACCCCTCTCCAATCTGAGATCT 59.750 50.000 0.00 0.00 40.47 2.75
1269 1290 1.385206 GGAGAGGAAGGCCAGGGAT 60.385 63.158 5.01 0.00 36.29 3.85
1412 1433 2.419198 CTCGGCGGAGAAGGATGG 59.581 66.667 15.82 0.00 43.27 3.51
1438 1459 1.617263 CGGAGGTGGAGAAGAAGGAGA 60.617 57.143 0.00 0.00 0.00 3.71
1474 1495 0.603065 GCGCCCTGTTTTCATTTCCT 59.397 50.000 0.00 0.00 0.00 3.36
1479 1500 3.250762 GCCCTGTTTTCATTTCCTTTTGC 59.749 43.478 0.00 0.00 0.00 3.68
1489 1510 7.742556 TTCATTTCCTTTTGCCTTTAATTGG 57.257 32.000 0.00 0.00 0.00 3.16
1503 1525 8.703743 TGCCTTTAATTGGTATGATGCTTAATT 58.296 29.630 0.00 0.00 0.00 1.40
1522 1544 7.148590 GCTTAATTTTGGATTGTTGGTGTGATC 60.149 37.037 0.00 0.00 0.00 2.92
1648 1670 2.009051 TGCGTGATAGCTTGGTTGATG 58.991 47.619 0.00 0.00 38.13 3.07
1663 1685 4.222810 TGGTTGATGTAGCGCCATAGATAT 59.777 41.667 2.29 0.00 0.00 1.63
1669 1691 6.323739 TGATGTAGCGCCATAGATATTGGATA 59.676 38.462 2.29 0.00 36.26 2.59
1697 1719 7.872163 TTATGTTGATGCTTTGACAAATCAC 57.128 32.000 6.61 2.94 33.38 3.06
1728 1750 4.878397 AGGAAGTTGTCTGTTTCAGTCAAG 59.122 41.667 8.97 0.00 39.33 3.02
1732 1754 4.098416 GTTGTCTGTTTCAGTCAAGTTGC 58.902 43.478 8.97 0.00 39.33 4.17
1740 1762 4.621068 TTCAGTCAAGTTGCTTTCTGTG 57.379 40.909 0.00 0.00 30.59 3.66
1741 1763 3.609853 TCAGTCAAGTTGCTTTCTGTGT 58.390 40.909 0.00 0.00 30.59 3.72
1742 1764 3.374988 TCAGTCAAGTTGCTTTCTGTGTG 59.625 43.478 0.00 0.00 30.59 3.82
1743 1765 3.127548 CAGTCAAGTTGCTTTCTGTGTGT 59.872 43.478 0.00 0.00 0.00 3.72
1745 1767 2.159393 TCAAGTTGCTTTCTGTGTGTGC 60.159 45.455 0.00 0.00 0.00 4.57
1746 1768 0.378257 AGTTGCTTTCTGTGTGTGCG 59.622 50.000 0.00 0.00 0.00 5.34
1747 1769 0.098728 GTTGCTTTCTGTGTGTGCGT 59.901 50.000 0.00 0.00 0.00 5.24
1748 1770 0.098552 TTGCTTTCTGTGTGTGCGTG 59.901 50.000 0.00 0.00 0.00 5.34
1751 1773 0.732571 CTTTCTGTGTGTGCGTGGTT 59.267 50.000 0.00 0.00 0.00 3.67
1752 1774 1.132262 CTTTCTGTGTGTGCGTGGTTT 59.868 47.619 0.00 0.00 0.00 3.27
1753 1775 0.730265 TTCTGTGTGTGCGTGGTTTC 59.270 50.000 0.00 0.00 0.00 2.78
1754 1776 0.391793 TCTGTGTGTGCGTGGTTTCA 60.392 50.000 0.00 0.00 0.00 2.69
1755 1777 0.027979 CTGTGTGTGCGTGGTTTCAG 59.972 55.000 0.00 0.00 0.00 3.02
1756 1778 0.675208 TGTGTGTGCGTGGTTTCAGT 60.675 50.000 0.00 0.00 0.00 3.41
1757 1779 0.027586 GTGTGTGCGTGGTTTCAGTC 59.972 55.000 0.00 0.00 0.00 3.51
1758 1780 0.391793 TGTGTGCGTGGTTTCAGTCA 60.392 50.000 0.00 0.00 0.00 3.41
1759 1781 0.730265 GTGTGCGTGGTTTCAGTCAA 59.270 50.000 0.00 0.00 0.00 3.18
1760 1782 1.131504 GTGTGCGTGGTTTCAGTCAAA 59.868 47.619 0.00 0.00 0.00 2.69
1761 1783 2.020720 TGTGCGTGGTTTCAGTCAAAT 58.979 42.857 0.00 0.00 0.00 2.32
1762 1784 3.002862 GTGTGCGTGGTTTCAGTCAAATA 59.997 43.478 0.00 0.00 0.00 1.40
1763 1785 3.818210 TGTGCGTGGTTTCAGTCAAATAT 59.182 39.130 0.00 0.00 0.00 1.28
1764 1786 4.158384 GTGCGTGGTTTCAGTCAAATATG 58.842 43.478 0.00 0.00 0.00 1.78
1765 1787 4.068599 TGCGTGGTTTCAGTCAAATATGA 58.931 39.130 0.00 0.00 0.00 2.15
1766 1788 4.154015 TGCGTGGTTTCAGTCAAATATGAG 59.846 41.667 0.00 0.00 35.88 2.90
1767 1789 4.437390 GCGTGGTTTCAGTCAAATATGAGG 60.437 45.833 0.00 0.00 35.88 3.86
1768 1790 4.695455 CGTGGTTTCAGTCAAATATGAGGT 59.305 41.667 0.00 0.00 35.88 3.85
1769 1791 5.390885 CGTGGTTTCAGTCAAATATGAGGTG 60.391 44.000 0.00 0.00 35.88 4.00
1770 1792 5.473504 GTGGTTTCAGTCAAATATGAGGTGT 59.526 40.000 0.00 0.00 35.88 4.16
1771 1793 5.705441 TGGTTTCAGTCAAATATGAGGTGTC 59.295 40.000 0.00 0.00 35.88 3.67
1772 1794 5.705441 GGTTTCAGTCAAATATGAGGTGTCA 59.295 40.000 0.00 0.00 35.88 3.58
1773 1795 6.348540 GGTTTCAGTCAAATATGAGGTGTCAC 60.349 42.308 0.00 0.00 35.88 3.67
1774 1796 5.745312 TCAGTCAAATATGAGGTGTCACT 57.255 39.130 2.35 0.00 35.88 3.41
1775 1797 6.850752 TCAGTCAAATATGAGGTGTCACTA 57.149 37.500 2.35 0.00 35.88 2.74
1776 1798 6.867550 TCAGTCAAATATGAGGTGTCACTAG 58.132 40.000 2.35 0.00 35.88 2.57
1777 1799 6.045318 CAGTCAAATATGAGGTGTCACTAGG 58.955 44.000 2.35 0.00 35.88 3.02
1778 1800 5.721960 AGTCAAATATGAGGTGTCACTAGGT 59.278 40.000 2.35 0.00 35.88 3.08
1779 1801 6.213600 AGTCAAATATGAGGTGTCACTAGGTT 59.786 38.462 2.35 0.00 35.88 3.50
1780 1802 6.879458 GTCAAATATGAGGTGTCACTAGGTTT 59.121 38.462 2.35 0.00 35.88 3.27
1781 1803 6.878923 TCAAATATGAGGTGTCACTAGGTTTG 59.121 38.462 2.35 7.57 34.75 2.93
1782 1804 3.703001 ATGAGGTGTCACTAGGTTTGG 57.297 47.619 2.35 0.00 34.75 3.28
1783 1805 2.404559 TGAGGTGTCACTAGGTTTGGT 58.595 47.619 2.35 0.00 0.00 3.67
1784 1806 2.775384 TGAGGTGTCACTAGGTTTGGTT 59.225 45.455 2.35 0.00 0.00 3.67
1785 1807 3.139077 GAGGTGTCACTAGGTTTGGTTG 58.861 50.000 2.35 0.00 0.00 3.77
1786 1808 2.508300 AGGTGTCACTAGGTTTGGTTGT 59.492 45.455 2.35 0.00 0.00 3.32
1787 1809 3.053917 AGGTGTCACTAGGTTTGGTTGTT 60.054 43.478 2.35 0.00 0.00 2.83
1788 1810 4.164604 AGGTGTCACTAGGTTTGGTTGTTA 59.835 41.667 2.35 0.00 0.00 2.41
1789 1811 4.274214 GGTGTCACTAGGTTTGGTTGTTAC 59.726 45.833 2.35 0.00 0.00 2.50
1790 1812 4.877251 GTGTCACTAGGTTTGGTTGTTACA 59.123 41.667 0.00 0.00 0.00 2.41
1791 1813 5.529800 GTGTCACTAGGTTTGGTTGTTACAT 59.470 40.000 0.00 0.00 0.00 2.29
1792 1814 5.529430 TGTCACTAGGTTTGGTTGTTACATG 59.471 40.000 0.00 0.00 0.00 3.21
1793 1815 5.761234 GTCACTAGGTTTGGTTGTTACATGA 59.239 40.000 0.00 0.00 0.00 3.07
1794 1816 5.761234 TCACTAGGTTTGGTTGTTACATGAC 59.239 40.000 0.00 0.00 0.00 3.06
1795 1817 5.529430 CACTAGGTTTGGTTGTTACATGACA 59.471 40.000 0.00 0.00 0.00 3.58
1796 1818 6.206634 CACTAGGTTTGGTTGTTACATGACAT 59.793 38.462 0.00 0.00 0.00 3.06
1797 1819 5.452078 AGGTTTGGTTGTTACATGACATG 57.548 39.130 14.02 14.02 0.00 3.21
1798 1820 5.136828 AGGTTTGGTTGTTACATGACATGA 58.863 37.500 22.19 3.13 0.00 3.07
1799 1821 5.774690 AGGTTTGGTTGTTACATGACATGAT 59.225 36.000 22.19 8.80 0.00 2.45
1800 1822 5.863397 GGTTTGGTTGTTACATGACATGATG 59.137 40.000 22.19 0.00 0.00 3.07
1801 1823 6.294453 GGTTTGGTTGTTACATGACATGATGA 60.294 38.462 22.19 4.08 0.00 2.92
1802 1824 7.315142 GTTTGGTTGTTACATGACATGATGAT 58.685 34.615 22.19 1.97 0.00 2.45
1803 1825 8.458052 GTTTGGTTGTTACATGACATGATGATA 58.542 33.333 22.19 0.96 0.00 2.15
1804 1826 7.790823 TGGTTGTTACATGACATGATGATAG 57.209 36.000 22.19 0.00 0.00 2.08
1805 1827 7.563906 TGGTTGTTACATGACATGATGATAGA 58.436 34.615 22.19 0.00 0.00 1.98
1806 1828 7.712205 TGGTTGTTACATGACATGATGATAGAG 59.288 37.037 22.19 0.00 0.00 2.43
1821 1843 5.934402 TGATAGAGTTAGGAACTTGGTCC 57.066 43.478 0.00 0.00 43.03 4.46
1917 1939 3.151912 ACTTGCTCTGCTCCTGAAAAT 57.848 42.857 0.00 0.00 0.00 1.82
1965 1993 6.594159 ACTCGGTTAGGATGAAATTACACTTG 59.406 38.462 0.00 0.00 0.00 3.16
2055 2091 1.196012 AAAACTGCCCCAAAACCGAA 58.804 45.000 0.00 0.00 0.00 4.30
2060 2096 1.830847 GCCCCAAAACCGAACCAGT 60.831 57.895 0.00 0.00 0.00 4.00
2121 2157 4.893424 TTGCAGTCAGAAACCAGTTTAC 57.107 40.909 0.00 0.00 32.11 2.01
2127 2163 5.817816 CAGTCAGAAACCAGTTTACAACTCT 59.182 40.000 0.00 0.00 40.46 3.24
2154 2190 3.151554 TGTTCTACAACCGAGTCTGCTA 58.848 45.455 0.00 0.00 0.00 3.49
2169 2205 3.311596 GTCTGCTAAAACACGGTTCTGTT 59.688 43.478 0.00 0.00 35.83 3.16
2219 2255 5.469084 ACTCGATTTGTTAAACCCTGTCTTC 59.531 40.000 0.00 0.00 0.00 2.87
2229 2265 3.806949 ACCCTGTCTTCTTTATGGCAA 57.193 42.857 0.00 0.00 0.00 4.52
2436 2472 4.816385 TCAAGGTTTGTTGTCTGTGAGATC 59.184 41.667 0.00 0.00 0.00 2.75
2522 2558 6.582636 TCAACTAGACAACAGTTCATCTTGT 58.417 36.000 0.00 4.29 33.99 3.16
2528 2564 4.526970 ACAACAGTTCATCTTGTCCTTGT 58.473 39.130 0.00 0.00 0.00 3.16
2529 2565 4.336433 ACAACAGTTCATCTTGTCCTTGTG 59.664 41.667 0.00 0.00 0.00 3.33
2533 2569 3.879295 AGTTCATCTTGTCCTTGTGTGTG 59.121 43.478 0.00 0.00 0.00 3.82
2546 2583 5.592282 TCCTTGTGTGTGAAATCTTTTGCTA 59.408 36.000 0.00 0.00 0.00 3.49
2883 2927 5.965033 ACTGTGGAGAAGATGATGGTAAT 57.035 39.130 0.00 0.00 0.00 1.89
2884 2928 5.923204 ACTGTGGAGAAGATGATGGTAATC 58.077 41.667 0.00 0.00 0.00 1.75
2891 2935 6.166984 AGAAGATGATGGTAATCGATGTGT 57.833 37.500 0.00 0.00 35.37 3.72
2904 2949 3.000041 TCGATGTGTACAACCTGATTGC 59.000 45.455 0.00 0.00 42.62 3.56
2913 2958 2.040813 ACAACCTGATTGCTGGACTGAT 59.959 45.455 0.00 0.00 42.62 2.90
2916 2961 3.878778 ACCTGATTGCTGGACTGATTAC 58.121 45.455 0.00 0.00 36.95 1.89
2917 2962 3.264193 ACCTGATTGCTGGACTGATTACA 59.736 43.478 0.00 0.00 36.95 2.41
2922 2967 1.616374 TGCTGGACTGATTACACGTCA 59.384 47.619 0.00 0.00 0.00 4.35
3063 3109 3.131223 TGTCTCAGGTAAGTAGCAGCATC 59.869 47.826 0.00 0.00 0.00 3.91
3066 3112 4.467795 TCTCAGGTAAGTAGCAGCATCTTT 59.532 41.667 7.28 0.00 0.00 2.52
3086 3133 5.826208 TCTTTATCCTAGTGTATGCGTCTCA 59.174 40.000 0.00 0.00 0.00 3.27
3088 3135 3.277142 TCCTAGTGTATGCGTCTCAGA 57.723 47.619 0.00 0.00 0.00 3.27
3094 3141 4.200092 AGTGTATGCGTCTCAGATGACTA 58.800 43.478 0.00 0.00 35.00 2.59
3096 3143 2.791383 ATGCGTCTCAGATGACTAGC 57.209 50.000 0.00 0.00 35.00 3.42
3214 3262 4.958581 GGGGATGAGAAGTTTTTGATGGAT 59.041 41.667 0.00 0.00 0.00 3.41
3243 3291 6.096987 TCGCATCTATCCTAGTTCTTTTCAGT 59.903 38.462 0.00 0.00 0.00 3.41
3252 3300 2.357952 AGTTCTTTTCAGTTTCGGGTGC 59.642 45.455 0.00 0.00 0.00 5.01
3271 3319 2.171659 TGCCTTGTGGTTAAGTGTCTGA 59.828 45.455 0.00 0.00 35.27 3.27
3324 3372 8.462016 GTGATGCTTTGGAAATATAAGTGAACT 58.538 33.333 0.00 0.00 0.00 3.01
3357 3405 2.290260 TGTTGGAACTGATCGATTGCCT 60.290 45.455 0.00 0.00 0.00 4.75
3367 3415 5.882557 ACTGATCGATTGCCTAATTTTCTGT 59.117 36.000 0.00 0.00 0.00 3.41
3377 3425 7.341445 TGCCTAATTTTCTGTAGTTTGTGTT 57.659 32.000 0.00 0.00 0.00 3.32
3387 3435 4.593157 TGTAGTTTGTGTTTCGTTCATGC 58.407 39.130 0.00 0.00 0.00 4.06
3440 3489 2.171448 AGCTACCTGCATCCCTTTGTAG 59.829 50.000 0.00 0.00 45.94 2.74
3452 3501 6.591935 CATCCCTTTGTAGGCTGTTTATCTA 58.408 40.000 0.00 0.00 40.50 1.98
3453 3502 6.630203 TCCCTTTGTAGGCTGTTTATCTAA 57.370 37.500 0.00 0.00 40.50 2.10
3500 3551 1.594862 GACATGCAACTAGCCGATGAC 59.405 52.381 0.00 0.00 44.83 3.06
3507 3558 1.313091 ACTAGCCGATGACGCTGACA 61.313 55.000 0.00 0.00 38.29 3.58
3537 3590 2.037136 GCGAAGTGATGTGCAGGCT 61.037 57.895 0.00 0.00 0.00 4.58
3568 3621 6.443849 TCCTTCATCACTAATCTAAGGGTTGT 59.556 38.462 0.00 0.00 35.31 3.32
3594 3647 7.646314 AGAAATTTGATCTTGTCACAGAACAG 58.354 34.615 0.00 0.00 36.32 3.16
3597 3650 5.991328 TTGATCTTGTCACAGAACAGAAC 57.009 39.130 0.00 0.00 36.32 3.01
3598 3651 5.022282 TGATCTTGTCACAGAACAGAACA 57.978 39.130 0.00 0.00 0.00 3.18
3601 3654 6.374053 TGATCTTGTCACAGAACAGAACAAAA 59.626 34.615 0.00 0.00 0.00 2.44
3602 3655 6.757897 TCTTGTCACAGAACAGAACAAAAT 57.242 33.333 0.00 0.00 0.00 1.82
3603 3656 6.785191 TCTTGTCACAGAACAGAACAAAATC 58.215 36.000 0.00 0.00 0.00 2.17
3614 3670 4.638421 ACAGAACAAAATCGGTCAAAGTCA 59.362 37.500 0.00 0.00 0.00 3.41
3641 3698 4.263462 TGCTAATGATCACACAAGGGAGTT 60.263 41.667 0.00 0.00 0.00 3.01
3677 3734 1.808945 CACCTTCACCTTGCTGACATC 59.191 52.381 0.00 0.00 0.00 3.06
3691 3748 5.492895 TGCTGACATCGTTAGGGAAATAAA 58.507 37.500 0.00 0.00 0.00 1.40
3708 4130 8.564574 GGGAAATAAAAACCAAAGGAAAACATC 58.435 33.333 0.00 0.00 0.00 3.06
3719 4141 8.579863 ACCAAAGGAAAACATCATCTAGAAAAG 58.420 33.333 0.00 0.00 0.00 2.27
3743 4166 3.588842 TCAAGTGAATGAGATGGGTCCTT 59.411 43.478 0.00 0.00 0.00 3.36
3744 4167 3.641434 AGTGAATGAGATGGGTCCTTG 57.359 47.619 0.00 0.00 0.00 3.61
3745 4168 2.019984 GTGAATGAGATGGGTCCTTGC 58.980 52.381 0.00 0.00 0.00 4.01
3746 4169 1.918262 TGAATGAGATGGGTCCTTGCT 59.082 47.619 0.00 0.00 0.00 3.91
3747 4170 2.092753 TGAATGAGATGGGTCCTTGCTC 60.093 50.000 0.00 0.00 0.00 4.26
3748 4171 1.890552 ATGAGATGGGTCCTTGCTCT 58.109 50.000 0.00 0.00 0.00 4.09
3749 4172 0.907486 TGAGATGGGTCCTTGCTCTG 59.093 55.000 0.00 0.00 0.00 3.35
3750 4173 0.179936 GAGATGGGTCCTTGCTCTGG 59.820 60.000 0.00 0.00 0.00 3.86
3753 4176 1.919600 ATGGGTCCTTGCTCTGGCTC 61.920 60.000 0.00 0.00 39.59 4.70
3760 4183 1.357907 CTTGCTCTGGCTCTTCGAAG 58.642 55.000 19.35 19.35 39.59 3.79
3765 4188 1.821753 CTCTGGCTCTTCGAAGGAGAA 59.178 52.381 24.37 4.72 33.03 2.87
3766 4189 2.430332 CTCTGGCTCTTCGAAGGAGAAT 59.570 50.000 24.37 0.00 33.03 2.40
3830 4255 3.706698 GGTGGAGAGAAACTTTGTTTGC 58.293 45.455 0.10 0.00 0.00 3.68
3858 4283 6.971527 TTTTTGGTGTCTATACGTGTATGG 57.028 37.500 0.00 0.08 0.00 2.74
3859 4284 3.720949 TGGTGTCTATACGTGTATGGC 57.279 47.619 0.00 0.00 0.00 4.40
3860 4285 2.363038 TGGTGTCTATACGTGTATGGCC 59.637 50.000 0.00 0.00 0.00 5.36
3861 4286 2.626743 GGTGTCTATACGTGTATGGCCT 59.373 50.000 3.32 0.00 0.00 5.19
3862 4287 3.069158 GGTGTCTATACGTGTATGGCCTT 59.931 47.826 3.32 0.00 0.00 4.35
3863 4288 4.049186 GTGTCTATACGTGTATGGCCTTG 58.951 47.826 3.32 0.00 0.00 3.61
3878 4303 1.479757 GCCTTGGGGGTGTCTTGTTTA 60.480 52.381 0.00 0.00 37.43 2.01
3881 4306 1.145571 TGGGGGTGTCTTGTTTAGCT 58.854 50.000 0.00 0.00 0.00 3.32
3882 4307 1.202879 TGGGGGTGTCTTGTTTAGCTG 60.203 52.381 0.00 0.00 0.00 4.24
3883 4308 1.073284 GGGGGTGTCTTGTTTAGCTGA 59.927 52.381 0.00 0.00 0.00 4.26
3884 4309 2.427506 GGGGTGTCTTGTTTAGCTGAG 58.572 52.381 0.00 0.00 0.00 3.35
3885 4310 2.224548 GGGGTGTCTTGTTTAGCTGAGT 60.225 50.000 0.00 0.00 0.00 3.41
3886 4311 2.808543 GGGTGTCTTGTTTAGCTGAGTG 59.191 50.000 0.00 0.00 0.00 3.51
3887 4312 3.467803 GGTGTCTTGTTTAGCTGAGTGT 58.532 45.455 0.00 0.00 0.00 3.55
3888 4313 3.248602 GGTGTCTTGTTTAGCTGAGTGTG 59.751 47.826 0.00 0.00 0.00 3.82
3889 4314 4.119862 GTGTCTTGTTTAGCTGAGTGTGA 58.880 43.478 0.00 0.00 0.00 3.58
3890 4315 4.752101 GTGTCTTGTTTAGCTGAGTGTGAT 59.248 41.667 0.00 0.00 0.00 3.06
3891 4316 4.751600 TGTCTTGTTTAGCTGAGTGTGATG 59.248 41.667 0.00 0.00 0.00 3.07
3894 4319 4.335400 TGTTTAGCTGAGTGTGATGTGA 57.665 40.909 0.00 0.00 0.00 3.58
3895 4320 4.702831 TGTTTAGCTGAGTGTGATGTGAA 58.297 39.130 0.00 0.00 0.00 3.18
3896 4321 4.751600 TGTTTAGCTGAGTGTGATGTGAAG 59.248 41.667 0.00 0.00 0.00 3.02
3897 4322 2.469274 AGCTGAGTGTGATGTGAAGG 57.531 50.000 0.00 0.00 0.00 3.46
3898 4323 1.973515 AGCTGAGTGTGATGTGAAGGA 59.026 47.619 0.00 0.00 0.00 3.36
3899 4324 2.072298 GCTGAGTGTGATGTGAAGGAC 58.928 52.381 0.00 0.00 0.00 3.85
3900 4325 2.289320 GCTGAGTGTGATGTGAAGGACT 60.289 50.000 0.00 0.00 0.00 3.85
3923 4358 6.262273 ACTTAGAAGCAATTCTTTGAACCGAA 59.738 34.615 0.00 0.00 34.56 4.30
3924 4359 5.113502 AGAAGCAATTCTTTGAACCGAAG 57.886 39.130 0.00 0.00 34.56 3.79
3925 4360 4.821805 AGAAGCAATTCTTTGAACCGAAGA 59.178 37.500 0.00 0.00 34.56 2.87
3926 4361 5.474876 AGAAGCAATTCTTTGAACCGAAGAT 59.525 36.000 0.00 0.00 34.33 2.40
3927 4362 5.712152 AGCAATTCTTTGAACCGAAGATT 57.288 34.783 0.00 0.00 34.33 2.40
3958 4394 4.155709 TCCATCTCTCCGCTTCAGATATT 58.844 43.478 0.00 0.00 0.00 1.28
3965 4401 8.178313 TCTCTCCGCTTCAGATATTTAACATA 57.822 34.615 0.00 0.00 0.00 2.29
4000 4436 5.293814 TGTTTGCATTGTCATGTTCTTTTGG 59.706 36.000 0.00 0.00 32.28 3.28
4012 4448 6.702723 TCATGTTCTTTTGGAAGATTTTGCAG 59.297 34.615 0.00 0.00 41.35 4.41
4013 4449 6.219417 TGTTCTTTTGGAAGATTTTGCAGA 57.781 33.333 0.00 0.00 41.35 4.26
4015 4451 4.874970 TCTTTTGGAAGATTTTGCAGAGC 58.125 39.130 0.00 0.00 36.99 4.09
4018 4454 5.633830 TTTGGAAGATTTTGCAGAGCTAG 57.366 39.130 0.00 0.00 35.96 3.42
4124 4574 3.072915 TGGGAGTGCATTCTCTTCAGAAA 59.927 43.478 10.76 0.00 42.14 2.52
4140 4590 8.118976 TCTTCAGAAATTTCATTGCAGAAGAT 57.881 30.769 19.99 0.00 35.42 2.40
4148 4598 8.922058 AATTTCATTGCAGAAGATACAATCAC 57.078 30.769 0.00 0.00 31.82 3.06
4151 4601 4.952262 TTGCAGAAGATACAATCACAGC 57.048 40.909 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.529829 GCACGGCATCAAAATTAACATAAAGA 59.470 34.615 0.00 0.00 0.00 2.52
15 16 3.195396 AGGCACGGCATCAAAATTAACAT 59.805 39.130 0.00 0.00 0.00 2.71
25 26 1.539388 CAGTTTAAAGGCACGGCATCA 59.461 47.619 0.00 0.00 0.00 3.07
30 31 3.915437 ATCAACAGTTTAAAGGCACGG 57.085 42.857 0.00 0.00 0.00 4.94
79 80 6.620877 ACATCCAACACTAACTATCAGGAA 57.379 37.500 0.00 0.00 0.00 3.36
89 90 4.353777 AGAGGAGCTACATCCAACACTAA 58.646 43.478 0.00 0.00 42.26 2.24
126 130 4.174009 AGGAACATGACGTATCAAGAACG 58.826 43.478 0.00 0.00 45.64 3.95
142 146 5.420739 AGCAAAACTAACCAGAAAAGGAACA 59.579 36.000 0.00 0.00 0.00 3.18
154 158 4.034163 GCTCCGATCTAAGCAAAACTAACC 59.966 45.833 10.38 0.00 38.42 2.85
203 207 5.178252 CCTAGCAAATCTGACCATTACATCG 59.822 44.000 0.00 0.00 0.00 3.84
205 209 6.006275 ACCTAGCAAATCTGACCATTACAT 57.994 37.500 0.00 0.00 0.00 2.29
211 215 2.642311 TCCAACCTAGCAAATCTGACCA 59.358 45.455 0.00 0.00 0.00 4.02
215 219 2.715046 TGCTCCAACCTAGCAAATCTG 58.285 47.619 0.00 0.00 46.57 2.90
252 256 8.956426 CAACTAACCAACCATACATCACTAATT 58.044 33.333 0.00 0.00 0.00 1.40
261 265 2.377193 AGGGCAACTAACCAACCATACA 59.623 45.455 0.00 0.00 0.00 2.29
301 305 3.119637 CCACACGACCCCATTTTCATTAC 60.120 47.826 0.00 0.00 0.00 1.89
396 403 5.588648 TCACTCACACTATACATCACGATCA 59.411 40.000 0.00 0.00 0.00 2.92
408 415 8.540507 AGTTTATCAGGTATCACTCACACTAT 57.459 34.615 0.00 0.00 0.00 2.12
412 419 9.642343 ACTATAGTTTATCAGGTATCACTCACA 57.358 33.333 0.00 0.00 0.00 3.58
577 592 5.642063 AGAGTTCGTTTTGTTCTCTGTTCAA 59.358 36.000 0.00 0.00 34.74 2.69
579 594 5.720261 AGAGTTCGTTTTGTTCTCTGTTC 57.280 39.130 0.00 0.00 34.74 3.18
580 595 6.496338 AAAGAGTTCGTTTTGTTCTCTGTT 57.504 33.333 0.00 0.00 35.94 3.16
581 596 6.496338 AAAAGAGTTCGTTTTGTTCTCTGT 57.504 33.333 0.00 0.00 35.94 3.41
619 634 6.785191 TCCAACATATGAGCGAATTTCTTTC 58.215 36.000 10.38 0.00 0.00 2.62
623 638 6.555315 AGTTTCCAACATATGAGCGAATTTC 58.445 36.000 10.38 2.53 0.00 2.17
627 642 4.574892 TGAGTTTCCAACATATGAGCGAA 58.425 39.130 10.38 4.53 0.00 4.70
702 719 7.876936 TTCACTTCCACTAGTACTAGGTATG 57.123 40.000 29.05 19.49 37.49 2.39
710 727 6.592994 GGGTTTGTATTCACTTCCACTAGTAC 59.407 42.308 0.00 0.00 0.00 2.73
752 769 6.151648 TGTCTTCTGAGCTCCCAAAATATTTG 59.848 38.462 12.15 0.00 0.00 2.32
766 783 3.321497 ACTCGAATTGTGTCTTCTGAGC 58.679 45.455 0.00 0.00 31.99 4.26
771 788 4.621886 GGTGTCTACTCGAATTGTGTCTTC 59.378 45.833 0.00 0.00 0.00 2.87
818 835 3.570212 GAGGTGCCTGGTGTGGGT 61.570 66.667 0.00 0.00 0.00 4.51
917 934 1.497309 ATTGGAGAGGGGTTTCGGCA 61.497 55.000 0.00 0.00 0.00 5.69
1207 1228 4.592192 CGAGGCCATCGCGGTGAT 62.592 66.667 23.56 6.12 45.98 3.06
1412 1433 3.240134 TTCTCCACCTCCGTGCTGC 62.240 63.158 0.00 0.00 38.79 5.25
1438 1459 1.291877 CGCTTACTGTTCGCCTTGCT 61.292 55.000 0.00 0.00 0.00 3.91
1474 1495 6.945218 AGCATCATACCAATTAAAGGCAAAA 58.055 32.000 0.00 0.00 0.00 2.44
1489 1510 8.819974 CCAACAATCCAAAATTAAGCATCATAC 58.180 33.333 0.00 0.00 0.00 2.39
1503 1525 4.588106 ACATGATCACACCAACAATCCAAA 59.412 37.500 0.00 0.00 0.00 3.28
1522 1544 7.065803 ACCCTATGAACTAACAAATTCGACATG 59.934 37.037 0.00 0.00 0.00 3.21
1648 1670 6.574350 ACTTATCCAATATCTATGGCGCTAC 58.426 40.000 7.64 0.00 37.88 3.58
1663 1685 8.801299 TCAAAGCATCAACATAAACTTATCCAA 58.199 29.630 0.00 0.00 0.00 3.53
1669 1691 8.891671 ATTTGTCAAAGCATCAACATAAACTT 57.108 26.923 4.03 0.00 0.00 2.66
1697 1719 2.064762 CAGACAACTTCCTCTTGCTCG 58.935 52.381 0.00 0.00 0.00 5.03
1728 1750 0.098728 ACGCACACACAGAAAGCAAC 59.901 50.000 0.00 0.00 0.00 4.17
1732 1754 0.732571 AACCACGCACACACAGAAAG 59.267 50.000 0.00 0.00 0.00 2.62
1740 1762 0.730265 TTGACTGAAACCACGCACAC 59.270 50.000 0.00 0.00 0.00 3.82
1741 1763 1.454201 TTTGACTGAAACCACGCACA 58.546 45.000 0.00 0.00 0.00 4.57
1742 1764 2.774439 ATTTGACTGAAACCACGCAC 57.226 45.000 0.00 0.00 0.00 5.34
1743 1765 4.068599 TCATATTTGACTGAAACCACGCA 58.931 39.130 0.00 0.00 0.00 5.24
1745 1767 4.695455 ACCTCATATTTGACTGAAACCACG 59.305 41.667 0.00 0.00 0.00 4.94
1746 1768 5.473504 ACACCTCATATTTGACTGAAACCAC 59.526 40.000 0.00 0.00 0.00 4.16
1747 1769 5.630121 ACACCTCATATTTGACTGAAACCA 58.370 37.500 0.00 0.00 0.00 3.67
1748 1770 5.705441 TGACACCTCATATTTGACTGAAACC 59.295 40.000 0.00 0.00 0.00 3.27
1751 1773 6.114187 AGTGACACCTCATATTTGACTGAA 57.886 37.500 0.84 0.00 0.00 3.02
1752 1774 5.745312 AGTGACACCTCATATTTGACTGA 57.255 39.130 0.84 0.00 0.00 3.41
1753 1775 6.045318 CCTAGTGACACCTCATATTTGACTG 58.955 44.000 0.84 0.00 0.00 3.51
1754 1776 5.721960 ACCTAGTGACACCTCATATTTGACT 59.278 40.000 0.84 0.00 0.00 3.41
1755 1777 5.978814 ACCTAGTGACACCTCATATTTGAC 58.021 41.667 0.84 0.00 0.00 3.18
1756 1778 6.620877 AACCTAGTGACACCTCATATTTGA 57.379 37.500 0.84 0.00 0.00 2.69
1757 1779 6.094048 CCAAACCTAGTGACACCTCATATTTG 59.906 42.308 0.84 6.36 0.00 2.32
1758 1780 6.180472 CCAAACCTAGTGACACCTCATATTT 58.820 40.000 0.84 0.00 0.00 1.40
1759 1781 5.250774 ACCAAACCTAGTGACACCTCATATT 59.749 40.000 0.84 0.00 0.00 1.28
1760 1782 4.783227 ACCAAACCTAGTGACACCTCATAT 59.217 41.667 0.84 0.00 0.00 1.78
1761 1783 4.164981 ACCAAACCTAGTGACACCTCATA 58.835 43.478 0.84 0.00 0.00 2.15
1762 1784 2.979678 ACCAAACCTAGTGACACCTCAT 59.020 45.455 0.84 0.00 0.00 2.90
1763 1785 2.404559 ACCAAACCTAGTGACACCTCA 58.595 47.619 0.84 0.00 0.00 3.86
1764 1786 3.139077 CAACCAAACCTAGTGACACCTC 58.861 50.000 0.84 0.00 0.00 3.85
1765 1787 2.508300 ACAACCAAACCTAGTGACACCT 59.492 45.455 0.84 0.00 0.00 4.00
1766 1788 2.927028 ACAACCAAACCTAGTGACACC 58.073 47.619 0.84 0.00 0.00 4.16
1767 1789 4.877251 TGTAACAACCAAACCTAGTGACAC 59.123 41.667 0.00 0.00 0.00 3.67
1768 1790 5.100344 TGTAACAACCAAACCTAGTGACA 57.900 39.130 0.00 0.00 0.00 3.58
1769 1791 5.761234 TCATGTAACAACCAAACCTAGTGAC 59.239 40.000 0.00 0.00 0.00 3.67
1770 1792 5.761234 GTCATGTAACAACCAAACCTAGTGA 59.239 40.000 0.00 0.00 0.00 3.41
1771 1793 5.529430 TGTCATGTAACAACCAAACCTAGTG 59.471 40.000 0.00 0.00 0.00 2.74
1772 1794 5.686753 TGTCATGTAACAACCAAACCTAGT 58.313 37.500 0.00 0.00 0.00 2.57
1773 1795 6.429692 TCATGTCATGTAACAACCAAACCTAG 59.570 38.462 12.54 0.00 31.81 3.02
1774 1796 6.299922 TCATGTCATGTAACAACCAAACCTA 58.700 36.000 12.54 0.00 31.81 3.08
1775 1797 5.136828 TCATGTCATGTAACAACCAAACCT 58.863 37.500 12.54 0.00 31.81 3.50
1776 1798 5.446143 TCATGTCATGTAACAACCAAACC 57.554 39.130 12.54 0.00 31.81 3.27
1777 1799 6.676950 TCATCATGTCATGTAACAACCAAAC 58.323 36.000 12.54 0.00 31.81 2.93
1778 1800 6.890979 TCATCATGTCATGTAACAACCAAA 57.109 33.333 12.54 0.00 31.81 3.28
1779 1801 8.046107 TCTATCATCATGTCATGTAACAACCAA 58.954 33.333 12.54 0.00 31.81 3.67
1780 1802 7.563906 TCTATCATCATGTCATGTAACAACCA 58.436 34.615 12.54 0.00 31.81 3.67
1781 1803 7.712639 ACTCTATCATCATGTCATGTAACAACC 59.287 37.037 12.54 0.00 31.81 3.77
1782 1804 8.654230 ACTCTATCATCATGTCATGTAACAAC 57.346 34.615 12.54 0.00 31.81 3.32
1784 1806 9.971922 CTAACTCTATCATCATGTCATGTAACA 57.028 33.333 12.54 0.00 0.00 2.41
1785 1807 9.416794 CCTAACTCTATCATCATGTCATGTAAC 57.583 37.037 12.54 0.00 0.00 2.50
1786 1808 9.367160 TCCTAACTCTATCATCATGTCATGTAA 57.633 33.333 12.54 0.54 0.00 2.41
1787 1809 8.940397 TCCTAACTCTATCATCATGTCATGTA 57.060 34.615 12.54 0.56 0.00 2.29
1788 1810 7.846101 TCCTAACTCTATCATCATGTCATGT 57.154 36.000 12.54 0.00 0.00 3.21
1789 1811 8.366401 AGTTCCTAACTCTATCATCATGTCATG 58.634 37.037 6.47 6.47 37.02 3.07
1790 1812 8.489676 AGTTCCTAACTCTATCATCATGTCAT 57.510 34.615 0.00 0.00 37.02 3.06
1791 1813 7.904558 AGTTCCTAACTCTATCATCATGTCA 57.095 36.000 0.00 0.00 37.02 3.58
1792 1814 7.655328 CCAAGTTCCTAACTCTATCATCATGTC 59.345 40.741 0.00 0.00 41.91 3.06
1793 1815 7.126421 ACCAAGTTCCTAACTCTATCATCATGT 59.874 37.037 0.00 0.00 41.91 3.21
1794 1816 7.504403 ACCAAGTTCCTAACTCTATCATCATG 58.496 38.462 0.00 0.00 41.91 3.07
1795 1817 7.202047 GGACCAAGTTCCTAACTCTATCATCAT 60.202 40.741 0.00 0.00 41.91 2.45
1796 1818 6.098409 GGACCAAGTTCCTAACTCTATCATCA 59.902 42.308 0.00 0.00 41.91 3.07
1797 1819 6.098409 TGGACCAAGTTCCTAACTCTATCATC 59.902 42.308 0.00 0.00 41.91 2.92
1798 1820 5.964477 TGGACCAAGTTCCTAACTCTATCAT 59.036 40.000 0.00 0.00 41.91 2.45
1799 1821 5.338632 TGGACCAAGTTCCTAACTCTATCA 58.661 41.667 0.00 0.00 41.91 2.15
1800 1822 5.934402 TGGACCAAGTTCCTAACTCTATC 57.066 43.478 0.00 0.00 41.91 2.08
1801 1823 6.893020 ATTGGACCAAGTTCCTAACTCTAT 57.107 37.500 13.43 0.00 41.91 1.98
1802 1824 6.573680 CGAATTGGACCAAGTTCCTAACTCTA 60.574 42.308 13.43 0.00 41.91 2.43
1803 1825 5.561679 GAATTGGACCAAGTTCCTAACTCT 58.438 41.667 13.43 0.00 41.91 3.24
1804 1826 4.392138 CGAATTGGACCAAGTTCCTAACTC 59.608 45.833 13.43 0.00 41.91 3.01
1805 1827 4.202430 ACGAATTGGACCAAGTTCCTAACT 60.202 41.667 13.43 0.00 45.46 2.24
1806 1828 4.070009 ACGAATTGGACCAAGTTCCTAAC 58.930 43.478 13.43 0.00 36.51 2.34
1821 1843 9.524106 TTGTTACTACATAGTATGGACGAATTG 57.476 33.333 14.59 0.00 38.48 2.32
1878 1900 6.814343 GCAAGTTGCTCAACAAATAAATCAG 58.186 36.000 20.71 0.00 43.47 2.90
1894 1916 0.604780 TCAGGAGCAGAGCAAGTTGC 60.605 55.000 20.44 20.44 45.46 4.17
1917 1939 5.630415 AATTAACCATGCTGCTAGTCCTA 57.370 39.130 0.00 0.00 0.00 2.94
1944 1970 7.175990 TGAACCAAGTGTAATTTCATCCTAACC 59.824 37.037 0.00 0.00 0.00 2.85
2016 2051 7.857885 CAGTTTTACAGATGACAAGGAAAACTC 59.142 37.037 18.57 2.86 41.34 3.01
2121 2157 7.857569 TCGGTTGTAGAACAAATTAAGAGTTG 58.142 34.615 5.00 0.00 40.15 3.16
2127 2163 6.073440 GCAGACTCGGTTGTAGAACAAATTAA 60.073 38.462 5.00 0.00 40.15 1.40
2169 2205 9.571816 TGCAACAATTTCACTATGATATATGGA 57.428 29.630 0.00 0.00 0.00 3.41
2188 2224 5.038033 GGTTTAACAAATCGAGTGCAACAA 58.962 37.500 0.00 0.00 41.43 2.83
2198 2234 5.941948 AGAAGACAGGGTTTAACAAATCG 57.058 39.130 0.00 0.00 0.00 3.34
2229 2265 4.591321 TTCCATAGGCAAATGAAGGAGT 57.409 40.909 1.79 0.00 0.00 3.85
2436 2472 4.639310 CCAACCTTCAGATGATCCTTCTTG 59.361 45.833 0.00 0.00 0.00 3.02
2522 2558 4.402155 AGCAAAAGATTTCACACACAAGGA 59.598 37.500 0.00 0.00 0.00 3.36
2546 2583 4.469657 TGGTAAGAAAGGAACACTGCATT 58.530 39.130 0.00 0.00 0.00 3.56
2584 2621 2.162408 GCAGTCATCCACTTTAACTGGC 59.838 50.000 0.00 0.00 38.19 4.85
2883 2927 3.000041 GCAATCAGGTTGTACACATCGA 59.000 45.455 0.00 0.00 40.07 3.59
2884 2928 3.002791 AGCAATCAGGTTGTACACATCG 58.997 45.455 0.00 0.00 40.07 3.84
2891 2935 2.637382 TCAGTCCAGCAATCAGGTTGTA 59.363 45.455 0.00 0.00 40.07 2.41
2904 2949 4.993905 TGTATGACGTGTAATCAGTCCAG 58.006 43.478 0.00 0.00 34.24 3.86
2913 2958 7.117236 GGTCTGAAGAAATTGTATGACGTGTAA 59.883 37.037 0.00 0.00 0.00 2.41
2916 2961 5.163854 GGGTCTGAAGAAATTGTATGACGTG 60.164 44.000 0.00 0.00 0.00 4.49
2917 2962 4.935808 GGGTCTGAAGAAATTGTATGACGT 59.064 41.667 0.00 0.00 0.00 4.34
3063 3109 6.017026 TCTGAGACGCATACACTAGGATAAAG 60.017 42.308 0.00 0.00 0.00 1.85
3066 3112 4.969484 TCTGAGACGCATACACTAGGATA 58.031 43.478 0.00 0.00 0.00 2.59
3086 3133 2.035632 GCAGGTAGTGGCTAGTCATCT 58.964 52.381 0.00 2.42 0.00 2.90
3088 3135 1.759445 CAGCAGGTAGTGGCTAGTCAT 59.241 52.381 0.00 0.00 38.56 3.06
3094 3141 1.674057 GACACAGCAGGTAGTGGCT 59.326 57.895 0.00 0.00 40.62 4.75
3096 3143 1.067283 CAGAGACACAGCAGGTAGTGG 60.067 57.143 0.00 0.00 39.99 4.00
3196 3243 7.094420 TGCGATTTATCCATCAAAAACTTCTCA 60.094 33.333 0.00 0.00 0.00 3.27
3214 3262 9.477484 GAAAAGAACTAGGATAGATGCGATTTA 57.523 33.333 0.00 0.00 42.77 1.40
3243 3291 0.183014 TAACCACAAGGCACCCGAAA 59.817 50.000 0.00 0.00 39.06 3.46
3252 3300 6.149474 CCTTAATCAGACACTTAACCACAAGG 59.851 42.308 0.00 0.00 42.21 3.61
3271 3319 2.550978 CATGTCCTTCGCGACCTTAAT 58.449 47.619 9.15 0.00 31.35 1.40
3324 3372 7.519809 CGATCAGTTCCAACAACAGAAAACATA 60.520 37.037 0.00 0.00 0.00 2.29
3357 3405 9.493206 GAACGAAACACAAACTACAGAAAATTA 57.507 29.630 0.00 0.00 0.00 1.40
3367 3415 3.846744 GCGCATGAACGAAACACAAACTA 60.847 43.478 0.30 0.00 34.06 2.24
3377 3425 1.569003 CACACAGCGCATGAACGAA 59.431 52.632 17.51 0.00 34.06 3.85
3440 3489 6.431234 CCATGGGTAAGATTAGATAAACAGCC 59.569 42.308 2.85 0.00 0.00 4.85
3500 3551 3.716006 CTTGCACCGGTGTCAGCG 61.716 66.667 33.92 20.93 39.06 5.18
3507 3558 2.357517 CTTCGCTCTTGCACCGGT 60.358 61.111 0.00 0.00 39.64 5.28
3537 3590 7.500227 CCTTAGATTAGTGATGAAGGATTGCAA 59.500 37.037 0.00 0.00 36.37 4.08
3568 3621 8.675705 TGTTCTGTGACAAGATCAAATTTCTA 57.324 30.769 0.00 0.00 39.72 2.10
3575 3628 5.427378 TGTTCTGTTCTGTGACAAGATCAA 58.573 37.500 0.00 0.00 39.72 2.57
3594 3647 4.970003 CAGTGACTTTGACCGATTTTGTTC 59.030 41.667 0.00 0.00 0.00 3.18
3597 3650 4.282068 CACAGTGACTTTGACCGATTTTG 58.718 43.478 0.00 0.00 0.00 2.44
3598 3651 3.243068 GCACAGTGACTTTGACCGATTTT 60.243 43.478 4.15 0.00 0.00 1.82
3601 3654 1.070758 AGCACAGTGACTTTGACCGAT 59.929 47.619 4.15 0.00 0.00 4.18
3602 3655 0.464036 AGCACAGTGACTTTGACCGA 59.536 50.000 4.15 0.00 0.00 4.69
3603 3656 2.148916 TAGCACAGTGACTTTGACCG 57.851 50.000 4.15 0.00 0.00 4.79
3641 3698 1.148273 GTGGGCAATATCTCCGGCA 59.852 57.895 0.00 0.00 0.00 5.69
3677 3734 6.983984 TCCTTTGGTTTTTATTTCCCTAACG 58.016 36.000 0.00 0.00 0.00 3.18
3691 3748 8.477419 TTCTAGATGATGTTTTCCTTTGGTTT 57.523 30.769 0.00 0.00 0.00 3.27
3708 4130 9.597170 TCTCATTCACTTGATCTTTTCTAGATG 57.403 33.333 0.00 0.00 43.75 2.90
3719 4141 4.133078 GGACCCATCTCATTCACTTGATC 58.867 47.826 0.00 0.00 0.00 2.92
3732 4155 1.919600 GCCAGAGCAAGGACCCATCT 61.920 60.000 0.00 0.00 39.53 2.90
3743 4166 0.900182 TCCTTCGAAGAGCCAGAGCA 60.900 55.000 26.61 0.00 43.56 4.26
3744 4167 0.179113 CTCCTTCGAAGAGCCAGAGC 60.179 60.000 26.61 0.00 38.43 4.09
3745 4168 1.468985 TCTCCTTCGAAGAGCCAGAG 58.531 55.000 26.61 21.19 38.43 3.35
3746 4169 1.924731 TTCTCCTTCGAAGAGCCAGA 58.075 50.000 26.61 16.98 38.43 3.86
3747 4170 2.977772 ATTCTCCTTCGAAGAGCCAG 57.022 50.000 26.61 15.12 38.43 4.85
3748 4171 2.695666 CCTATTCTCCTTCGAAGAGCCA 59.304 50.000 26.61 8.04 38.43 4.75
3749 4172 2.036604 CCCTATTCTCCTTCGAAGAGCC 59.963 54.545 26.61 0.00 38.43 4.70
3750 4173 2.036604 CCCCTATTCTCCTTCGAAGAGC 59.963 54.545 26.61 0.00 38.43 4.09
3753 4176 2.365941 GGTCCCCTATTCTCCTTCGAAG 59.634 54.545 18.51 18.51 0.00 3.79
3760 4183 1.896465 CATCTCGGTCCCCTATTCTCC 59.104 57.143 0.00 0.00 0.00 3.71
3849 4274 2.674754 CCCCAAGGCCATACACGT 59.325 61.111 5.01 0.00 0.00 4.49
3850 4275 2.124320 CCCCCAAGGCCATACACG 60.124 66.667 5.01 0.00 0.00 4.49
3854 4279 0.849094 AAGACACCCCCAAGGCCATA 60.849 55.000 5.01 0.00 40.58 2.74
3855 4280 2.169810 AAGACACCCCCAAGGCCAT 61.170 57.895 5.01 0.00 40.58 4.40
3856 4281 2.780924 AAGACACCCCCAAGGCCA 60.781 61.111 5.01 0.00 40.58 5.36
3857 4282 2.283173 CAAGACACCCCCAAGGCC 60.283 66.667 0.00 0.00 40.58 5.19
3858 4283 0.759060 AAACAAGACACCCCCAAGGC 60.759 55.000 0.00 0.00 40.58 4.35
3859 4284 2.514803 CTAAACAAGACACCCCCAAGG 58.485 52.381 0.00 0.00 43.78 3.61
3860 4285 1.886542 GCTAAACAAGACACCCCCAAG 59.113 52.381 0.00 0.00 0.00 3.61
3861 4286 1.497286 AGCTAAACAAGACACCCCCAA 59.503 47.619 0.00 0.00 0.00 4.12
3862 4287 1.145571 AGCTAAACAAGACACCCCCA 58.854 50.000 0.00 0.00 0.00 4.96
3863 4288 1.073284 TCAGCTAAACAAGACACCCCC 59.927 52.381 0.00 0.00 0.00 5.40
3878 4303 1.973515 TCCTTCACATCACACTCAGCT 59.026 47.619 0.00 0.00 0.00 4.24
3881 4306 4.832823 TCTAAGTCCTTCACATCACACTCA 59.167 41.667 0.00 0.00 0.00 3.41
3882 4307 5.392767 TCTAAGTCCTTCACATCACACTC 57.607 43.478 0.00 0.00 0.00 3.51
3883 4308 5.788450 CTTCTAAGTCCTTCACATCACACT 58.212 41.667 0.00 0.00 0.00 3.55
3884 4309 4.390297 GCTTCTAAGTCCTTCACATCACAC 59.610 45.833 0.00 0.00 0.00 3.82
3885 4310 4.040339 TGCTTCTAAGTCCTTCACATCACA 59.960 41.667 0.00 0.00 0.00 3.58
3886 4311 4.569943 TGCTTCTAAGTCCTTCACATCAC 58.430 43.478 0.00 0.00 0.00 3.06
3887 4312 4.890158 TGCTTCTAAGTCCTTCACATCA 57.110 40.909 0.00 0.00 0.00 3.07
3888 4313 6.597280 AGAATTGCTTCTAAGTCCTTCACATC 59.403 38.462 0.00 0.00 40.00 3.06
3889 4314 6.479884 AGAATTGCTTCTAAGTCCTTCACAT 58.520 36.000 0.00 0.00 40.00 3.21
3890 4315 5.869579 AGAATTGCTTCTAAGTCCTTCACA 58.130 37.500 0.00 0.00 40.00 3.58
3891 4316 6.809630 AAGAATTGCTTCTAAGTCCTTCAC 57.190 37.500 0.00 0.00 40.93 3.18
3894 4319 7.255625 GGTTCAAAGAATTGCTTCTAAGTCCTT 60.256 37.037 0.00 0.00 40.93 3.36
3895 4320 6.207614 GGTTCAAAGAATTGCTTCTAAGTCCT 59.792 38.462 0.00 0.00 40.93 3.85
3896 4321 6.382608 GGTTCAAAGAATTGCTTCTAAGTCC 58.617 40.000 0.00 0.00 40.93 3.85
3897 4322 6.073222 TCGGTTCAAAGAATTGCTTCTAAGTC 60.073 38.462 0.00 0.00 40.93 3.01
3898 4323 5.763204 TCGGTTCAAAGAATTGCTTCTAAGT 59.237 36.000 0.00 0.00 40.93 2.24
3899 4324 6.241207 TCGGTTCAAAGAATTGCTTCTAAG 57.759 37.500 0.00 0.00 40.93 2.18
3900 4325 6.485313 TCTTCGGTTCAAAGAATTGCTTCTAA 59.515 34.615 0.00 0.00 40.93 2.10
3934 4369 1.753649 TCTGAAGCGGAGAGATGGAAG 59.246 52.381 0.00 0.00 0.00 3.46
3935 4370 1.852633 TCTGAAGCGGAGAGATGGAA 58.147 50.000 0.00 0.00 0.00 3.53
3936 4371 2.079170 ATCTGAAGCGGAGAGATGGA 57.921 50.000 0.00 0.00 0.00 3.41
3941 4376 8.085296 AGTATGTTAAATATCTGAAGCGGAGAG 58.915 37.037 0.00 0.00 0.00 3.20
3958 4394 8.341892 TGCAAACAACCATCATAGTATGTTAA 57.658 30.769 9.94 0.00 31.33 2.01
3965 4401 5.243507 TGACAATGCAAACAACCATCATAGT 59.756 36.000 0.00 0.00 0.00 2.12
4000 4436 9.054922 AGATTATTCTAGCTCTGCAAAATCTTC 57.945 33.333 0.00 0.00 0.00 2.87
4124 4574 8.058667 TGTGATTGTATCTTCTGCAATGAAAT 57.941 30.769 0.00 0.00 39.88 2.17
4140 4590 4.220163 TGCATTTGGAATGCTGTGATTGTA 59.780 37.500 21.86 1.07 44.79 2.41
4148 4598 2.971660 TCCATGCATTTGGAATGCTG 57.028 45.000 21.86 17.12 42.82 4.41


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

AutoCloner maintained by Alex Coulton.