Multiple sequence alignment - TraesCS4B01G260600

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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 TraesCS4B01G260600 chr4B 100.000 3789 0 0 1 3789 527300191 527296403 0.000000e+00 6998.0
1 TraesCS4B01G260600 chr4A 87.208 3127 242 85 122 3146 37043560 37046630 0.000000e+00 3413.0
2 TraesCS4B01G260600 chr4A 81.625 566 22 32 3271 3789 37046803 37047333 9.870000e-106 394.0
3 TraesCS4B01G260600 chr4D 93.380 1420 64 19 1762 3170 429484585 429483185 0.000000e+00 2074.0
4 TraesCS4B01G260600 chr4D 88.931 1572 113 35 25 1581 429486268 429484743 0.000000e+00 1882.0
5 TraesCS4B01G260600 chr4D 93.377 302 15 4 3491 3789 429482580 429482281 3.470000e-120 442.0
6 TraesCS4B01G260600 chr4D 89.697 165 9 6 3274 3437 429482928 429482771 1.780000e-48 204.0
7 TraesCS4B01G260600 chr5B 82.192 73 10 3 543 614 599691201 599691271 4.090000e-05 60.2
8 TraesCS4B01G260600 chrUn 89.130 46 5 0 3261 3306 79505425 79505470 1.470000e-04 58.4
9 TraesCS4B01G260600 chr7D 90.476 42 4 0 3260 3301 561921878 561921837 5.290000e-04 56.5
10 TraesCS4B01G260600 chr3A 100.000 30 0 0 3274 3303 332556267 332556296 5.290000e-04 56.5
11 TraesCS4B01G260600 chr2A 89.130 46 4 1 3261 3306 567376893 567376937 5.290000e-04 56.5
12 TraesCS4B01G260600 chr7A 90.244 41 4 0 3261 3301 497652182 497652222 2.000000e-03 54.7
13 TraesCS4B01G260600 chr1D 90.244 41 4 0 3261 3301 75109280 75109240 2.000000e-03 54.7
14 TraesCS4B01G260600 chr1B 90.244 41 4 0 3261 3301 118515930 118515890 2.000000e-03 54.7
15 TraesCS4B01G260600 chr1A 94.286 35 2 0 3274 3308 463927843 463927809 2.000000e-03 54.7
16 TraesCS4B01G260600 chr5D 100.000 28 0 0 587 614 487302175 487302202 7.000000e-03 52.8


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 TraesCS4B01G260600 chr4B 527296403 527300191 3788 True 6998.0 6998 100.00000 1 3789 1 chr4B.!!$R1 3788
1 TraesCS4B01G260600 chr4A 37043560 37047333 3773 False 1903.5 3413 84.41650 122 3789 2 chr4A.!!$F1 3667
2 TraesCS4B01G260600 chr4D 429482281 429486268 3987 True 1150.5 2074 91.34625 25 3789 4 chr4D.!!$R1 3764

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
526 534 0.390603 CCGCCAGGATACAAACACGA 60.391 55.000 0.00 0.0 41.02 4.35 F
740 750 0.765510 ACCAAAAGAAGAGACGGGCT 59.234 50.000 0.00 0.0 0.00 5.19 F
1805 1901 1.122323 GCAACGTGTTTAATGCTTGCG 59.878 47.619 0.48 0.0 35.93 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2207 0.397941 TCTGCCACTTCCTCACAAGG 59.602 55.0 0.00 0.0 44.89 3.61 R
2214 2312 1.166531 AAGTGCGCTTCACCTGGTTC 61.167 55.0 9.73 0.0 46.81 3.62 R
3262 3557 0.035439 ATTACTTGTGGCGGAGGTGG 60.035 55.0 0.00 0.0 0.00 4.61 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
20 21 2.969443 AACGCAAATGCTAGTGTGAC 57.031 45.000 3.63 0.00 39.32 3.67
21 22 1.877637 ACGCAAATGCTAGTGTGACA 58.122 45.000 3.63 0.00 39.32 3.58
22 23 2.426522 ACGCAAATGCTAGTGTGACAT 58.573 42.857 3.63 0.00 39.32 3.06
23 24 2.160219 ACGCAAATGCTAGTGTGACATG 59.840 45.455 3.63 0.00 39.32 3.21
30 31 2.009042 GCTAGTGTGACATGAGGCACC 61.009 57.143 0.00 0.00 34.19 5.01
73 74 3.853831 TGCACAAATCTTACATGCCTG 57.146 42.857 0.00 0.00 35.37 4.85
76 77 4.142337 TGCACAAATCTTACATGCCTGATG 60.142 41.667 0.00 0.00 38.15 3.07
97 98 2.147958 GCGTGGTGGACAACTTTGATA 58.852 47.619 0.00 0.00 0.00 2.15
98 99 2.747446 GCGTGGTGGACAACTTTGATAT 59.253 45.455 0.00 0.00 0.00 1.63
99 100 3.426159 GCGTGGTGGACAACTTTGATATG 60.426 47.826 0.00 0.00 0.00 1.78
106 107 6.238484 GGTGGACAACTTTGATATGACATAGC 60.238 42.308 3.70 3.70 0.00 2.97
228 232 9.546428 AACTAATCAATGGGAAAAAGAAACAAG 57.454 29.630 0.00 0.00 0.00 3.16
232 236 7.841915 TCAATGGGAAAAAGAAACAAGAAAC 57.158 32.000 0.00 0.00 0.00 2.78
233 237 6.533367 TCAATGGGAAAAAGAAACAAGAAACG 59.467 34.615 0.00 0.00 0.00 3.60
234 238 4.177783 TGGGAAAAAGAAACAAGAAACGC 58.822 39.130 0.00 0.00 0.00 4.84
235 239 3.554324 GGGAAAAAGAAACAAGAAACGCC 59.446 43.478 0.00 0.00 0.00 5.68
236 240 4.177783 GGAAAAAGAAACAAGAAACGCCA 58.822 39.130 0.00 0.00 0.00 5.69
237 241 4.627900 GGAAAAAGAAACAAGAAACGCCAA 59.372 37.500 0.00 0.00 0.00 4.52
238 242 5.120986 GGAAAAAGAAACAAGAAACGCCAAA 59.879 36.000 0.00 0.00 0.00 3.28
239 243 6.183360 GGAAAAAGAAACAAGAAACGCCAAAT 60.183 34.615 0.00 0.00 0.00 2.32
323 327 3.456380 TGGAAGCTTCTAGCCCAAAAT 57.544 42.857 25.05 0.00 43.77 1.82
326 330 2.789409 AGCTTCTAGCCCAAAATCGT 57.211 45.000 0.00 0.00 43.77 3.73
342 346 1.170442 TCGTTACATGAGAGGTCGCA 58.830 50.000 0.00 0.00 0.00 5.10
345 349 1.204941 GTTACATGAGAGGTCGCAGGT 59.795 52.381 0.00 6.29 42.71 4.00
348 352 0.817654 CATGAGAGGTCGCAGGTACA 59.182 55.000 0.00 0.00 0.00 2.90
363 367 4.163649 GCAGGTACACCTCCTATAAAAGGT 59.836 45.833 0.00 0.74 46.65 3.50
379 383 1.996798 AGGTCCGACTCTTCAGTTCA 58.003 50.000 0.00 0.00 30.63 3.18
384 388 2.557056 TCCGACTCTTCAGTTCATTCGT 59.443 45.455 0.00 0.00 30.63 3.85
398 402 1.282248 ATTCGTCGTGCCACACTTCG 61.282 55.000 0.00 2.17 31.34 3.79
408 412 1.587946 GCCACACTTCGTTGCAAAAAG 59.412 47.619 17.13 17.13 36.30 2.27
414 418 5.783169 CACACTTCGTTGCAAAAAGAAAAAC 59.217 36.000 22.87 0.23 0.00 2.43
415 419 5.107259 ACACTTCGTTGCAAAAAGAAAAACC 60.107 36.000 22.87 0.00 0.00 3.27
429 433 3.580895 AGAAAAACCCACAACAACAAGGT 59.419 39.130 0.00 0.00 0.00 3.50
471 479 7.663493 CCCATATAACCCACAAAACACAAAAAT 59.337 33.333 0.00 0.00 0.00 1.82
526 534 0.390603 CCGCCAGGATACAAACACGA 60.391 55.000 0.00 0.00 41.02 4.35
541 549 4.504916 CGAGCCCGACAGCAGAGG 62.505 72.222 0.00 0.00 38.22 3.69
563 571 3.914364 GCAAACCTTTTGCACGAATCTAG 59.086 43.478 16.79 0.00 44.34 2.43
567 575 3.758554 ACCTTTTGCACGAATCTAGCAAT 59.241 39.130 9.37 0.00 46.32 3.56
695 705 6.697395 ACAAGTATTTATTTTTGTCCAGCCC 58.303 36.000 0.00 0.00 0.00 5.19
696 706 6.268847 ACAAGTATTTATTTTTGTCCAGCCCA 59.731 34.615 0.00 0.00 0.00 5.36
697 707 6.926630 AGTATTTATTTTTGTCCAGCCCAA 57.073 33.333 0.00 0.00 0.00 4.12
698 708 6.935167 AGTATTTATTTTTGTCCAGCCCAAG 58.065 36.000 0.00 0.00 0.00 3.61
709 719 4.785453 GCCCAAGCTCCCCTCGTG 62.785 72.222 0.00 0.00 35.50 4.35
740 750 0.765510 ACCAAAAGAAGAGACGGGCT 59.234 50.000 0.00 0.00 0.00 5.19
776 786 4.699522 GTTGGGCCGAGCGGAGTT 62.700 66.667 13.94 0.00 37.50 3.01
797 807 3.051081 AGAAGCTTCAACGCAATCTCT 57.949 42.857 27.57 0.00 0.00 3.10
902 916 4.335874 CCTCGAAGCGCACTATATATACCT 59.664 45.833 11.47 0.00 0.00 3.08
923 937 1.122632 TCGCCTGTGTAGGGTTTCCA 61.123 55.000 0.00 0.00 44.75 3.53
1088 1102 3.866582 CCCACCCCGCTCATCCTC 61.867 72.222 0.00 0.00 0.00 3.71
1093 1107 2.202987 CCCGCTCATCCTCTGCAC 60.203 66.667 0.00 0.00 0.00 4.57
1105 1119 1.568606 CTCTGCACCATCGTGATCTG 58.431 55.000 0.00 0.00 43.14 2.90
1121 1135 5.495640 GTGATCTGGGATCTGTTTCTTCTT 58.504 41.667 8.66 0.00 0.00 2.52
1125 1139 4.223923 TCTGGGATCTGTTTCTTCTTCTCC 59.776 45.833 0.00 0.00 0.00 3.71
1128 1142 4.223923 GGGATCTGTTTCTTCTTCTCCTCA 59.776 45.833 0.00 0.00 0.00 3.86
1353 1367 3.054875 TCCATTGATGTCTTCTGTCCCAG 60.055 47.826 0.00 0.00 0.00 4.45
1380 1394 2.234908 AGCTGTTTAGTAGTCTGCCTGG 59.765 50.000 0.00 0.00 0.00 4.45
1390 1404 5.898120 AGTAGTCTGCCTGGTCTCATATAT 58.102 41.667 0.00 0.00 0.00 0.86
1414 1428 5.985530 TGCGATTGTGATCTATTTAGTCCTG 59.014 40.000 0.00 0.00 0.00 3.86
1426 1440 7.118723 TCTATTTAGTCCTGTTGGCATGAAAT 58.881 34.615 0.00 0.00 0.00 2.17
1467 1482 3.626930 AGGTTGCCTTGTTGTGTTAAGA 58.373 40.909 0.00 0.00 0.00 2.10
1509 1530 9.360093 AGACTAGAATGCAATCGCTATTATTAC 57.640 33.333 0.00 0.00 39.64 1.89
1510 1531 8.480643 ACTAGAATGCAATCGCTATTATTACC 57.519 34.615 0.00 0.00 39.64 2.85
1511 1532 6.743575 AGAATGCAATCGCTATTATTACCC 57.256 37.500 0.00 0.00 39.64 3.69
1512 1533 6.476378 AGAATGCAATCGCTATTATTACCCT 58.524 36.000 0.00 0.00 39.64 4.34
1513 1534 6.372659 AGAATGCAATCGCTATTATTACCCTG 59.627 38.462 0.00 0.00 39.64 4.45
1530 1573 7.801716 TTACCCTGCTGATAATTGATGTTAC 57.198 36.000 0.00 0.00 0.00 2.50
1534 1577 6.543465 CCCTGCTGATAATTGATGTTACTTCA 59.457 38.462 0.00 0.00 0.00 3.02
1536 1579 7.496920 CCTGCTGATAATTGATGTTACTTCAGA 59.503 37.037 1.40 0.00 32.96 3.27
1537 1580 8.969260 TGCTGATAATTGATGTTACTTCAGAT 57.031 30.769 1.40 0.00 32.96 2.90
1570 1613 6.968131 TTGTCTTACATATGTTCTCAGTGC 57.032 37.500 14.77 4.67 0.00 4.40
1581 1624 8.882736 CATATGTTCTCAGTGCTGTAATTTGTA 58.117 33.333 0.00 0.00 0.00 2.41
1590 1647 8.387354 TCAGTGCTGTAATTTGTATATGAAACG 58.613 33.333 0.00 0.00 0.00 3.60
1592 1649 9.109393 AGTGCTGTAATTTGTATATGAAACGAT 57.891 29.630 0.00 0.00 0.00 3.73
1612 1669 5.819379 ACGATATCATGCATCTTGTTTCACT 59.181 36.000 0.00 0.00 0.00 3.41
1621 1678 4.734402 GCATCTTGTTTCACTCTTGCACAA 60.734 41.667 0.00 0.00 0.00 3.33
1627 1684 7.648908 TCTTGTTTCACTCTTGCACAATTTATG 59.351 33.333 0.00 0.00 29.84 1.90
1651 1714 4.649674 TGTTGTTATGGCCCACTTGTTTTA 59.350 37.500 0.00 0.00 0.00 1.52
1654 1717 5.848406 TGTTATGGCCCACTTGTTTTAAAG 58.152 37.500 0.00 0.00 0.00 1.85
1662 1725 4.278419 CCCACTTGTTTTAAAGCTAGCACT 59.722 41.667 18.83 5.60 0.00 4.40
1663 1726 5.215160 CCACTTGTTTTAAAGCTAGCACTG 58.785 41.667 18.83 5.29 0.00 3.66
1664 1727 4.676924 CACTTGTTTTAAAGCTAGCACTGC 59.323 41.667 18.83 0.00 0.00 4.40
1683 1746 4.867047 ACTGCGTCTGTTGATTAGAATCAG 59.133 41.667 5.18 0.00 45.35 2.90
1684 1747 4.820897 TGCGTCTGTTGATTAGAATCAGT 58.179 39.130 5.18 0.00 45.35 3.41
1686 1749 6.036470 TGCGTCTGTTGATTAGAATCAGTAG 58.964 40.000 5.18 7.86 45.35 2.57
1687 1750 5.051374 GCGTCTGTTGATTAGAATCAGTAGC 60.051 44.000 5.18 4.13 45.35 3.58
1688 1751 6.269315 CGTCTGTTGATTAGAATCAGTAGCT 58.731 40.000 5.18 0.00 45.35 3.32
1689 1752 6.416455 CGTCTGTTGATTAGAATCAGTAGCTC 59.584 42.308 5.18 4.85 45.35 4.09
1699 1764 6.968263 AGAATCAGTAGCTCAGCATAAGTA 57.032 37.500 0.00 0.00 0.00 2.24
1700 1765 6.744112 AGAATCAGTAGCTCAGCATAAGTAC 58.256 40.000 0.00 0.00 0.00 2.73
1704 1769 5.066634 TCAGTAGCTCAGCATAAGTACTGTC 59.933 44.000 17.92 0.00 38.86 3.51
1719 1784 4.933400 AGTACTGTCAGTCGTTTGTGTTTT 59.067 37.500 9.26 0.00 0.00 2.43
1723 1788 3.120130 TGTCAGTCGTTTGTGTTTTGTCC 60.120 43.478 0.00 0.00 0.00 4.02
1729 1794 3.253677 TCGTTTGTGTTTTGTCCAACTGT 59.746 39.130 0.00 0.00 0.00 3.55
1730 1795 3.363426 CGTTTGTGTTTTGTCCAACTGTG 59.637 43.478 0.00 0.00 0.00 3.66
1732 1797 3.567576 TGTGTTTTGTCCAACTGTGTG 57.432 42.857 0.00 0.00 0.00 3.82
1734 1799 3.057876 TGTGTTTTGTCCAACTGTGTGTC 60.058 43.478 0.00 0.00 0.00 3.67
1735 1800 3.190535 GTGTTTTGTCCAACTGTGTGTCT 59.809 43.478 0.00 0.00 0.00 3.41
1736 1801 4.393680 GTGTTTTGTCCAACTGTGTGTCTA 59.606 41.667 0.00 0.00 0.00 2.59
1737 1802 5.065988 GTGTTTTGTCCAACTGTGTGTCTAT 59.934 40.000 0.00 0.00 0.00 1.98
1738 1803 5.065859 TGTTTTGTCCAACTGTGTGTCTATG 59.934 40.000 0.00 0.00 0.00 2.23
1739 1804 4.415881 TTGTCCAACTGTGTGTCTATGT 57.584 40.909 0.00 0.00 0.00 2.29
1743 1808 5.163395 TGTCCAACTGTGTGTCTATGTTGTA 60.163 40.000 0.00 0.00 37.04 2.41
1744 1809 5.405571 GTCCAACTGTGTGTCTATGTTGTAG 59.594 44.000 0.00 0.00 37.04 2.74
1745 1810 4.152402 CCAACTGTGTGTCTATGTTGTAGC 59.848 45.833 0.00 0.00 37.04 3.58
1746 1811 4.873746 ACTGTGTGTCTATGTTGTAGCT 57.126 40.909 0.00 0.00 0.00 3.32
1749 1814 5.011125 ACTGTGTGTCTATGTTGTAGCTCTT 59.989 40.000 0.00 0.00 0.00 2.85
1750 1815 5.230182 TGTGTGTCTATGTTGTAGCTCTTG 58.770 41.667 0.00 0.00 0.00 3.02
1751 1816 5.221441 TGTGTGTCTATGTTGTAGCTCTTGT 60.221 40.000 0.00 0.00 0.00 3.16
1753 1818 6.866770 GTGTGTCTATGTTGTAGCTCTTGTTA 59.133 38.462 0.00 0.00 0.00 2.41
1754 1819 7.545965 GTGTGTCTATGTTGTAGCTCTTGTTAT 59.454 37.037 0.00 0.00 0.00 1.89
1755 1820 7.759886 TGTGTCTATGTTGTAGCTCTTGTTATC 59.240 37.037 0.00 0.00 0.00 1.75
1756 1821 7.222999 GTGTCTATGTTGTAGCTCTTGTTATCC 59.777 40.741 0.00 0.00 0.00 2.59
1757 1822 6.702282 GTCTATGTTGTAGCTCTTGTTATCCC 59.298 42.308 0.00 0.00 0.00 3.85
1758 1823 5.700402 ATGTTGTAGCTCTTGTTATCCCT 57.300 39.130 0.00 0.00 0.00 4.20
1759 1824 6.808321 ATGTTGTAGCTCTTGTTATCCCTA 57.192 37.500 0.00 0.00 0.00 3.53
1761 1826 5.128827 TGTTGTAGCTCTTGTTATCCCTAGG 59.871 44.000 0.06 0.06 0.00 3.02
1762 1827 3.641906 TGTAGCTCTTGTTATCCCTAGGC 59.358 47.826 2.05 0.00 0.00 3.93
1763 1828 2.050918 AGCTCTTGTTATCCCTAGGCC 58.949 52.381 2.05 0.00 0.00 5.19
1764 1829 2.050918 GCTCTTGTTATCCCTAGGCCT 58.949 52.381 11.78 11.78 0.00 5.19
1769 1865 4.538490 TCTTGTTATCCCTAGGCCTTTTGA 59.462 41.667 12.58 5.26 0.00 2.69
1770 1866 5.193728 TCTTGTTATCCCTAGGCCTTTTGAT 59.806 40.000 12.58 13.01 0.00 2.57
1786 1882 8.390354 GGCCTTTTGATTTTACATTCATTTAGC 58.610 33.333 0.00 0.00 0.00 3.09
1800 1896 6.683090 TTCATTTAGCAACGTGTTTAATGC 57.317 33.333 0.00 0.00 39.06 3.56
1804 1900 2.393764 AGCAACGTGTTTAATGCTTGC 58.606 42.857 4.37 0.00 46.36 4.01
1805 1901 1.122323 GCAACGTGTTTAATGCTTGCG 59.878 47.619 0.48 0.00 35.93 4.85
1812 1908 4.086524 CGTGTTTAATGCTTGCGTTTGTAG 59.913 41.667 5.35 0.00 0.00 2.74
1813 1909 5.209240 GTGTTTAATGCTTGCGTTTGTAGA 58.791 37.500 5.35 0.00 0.00 2.59
1814 1910 5.339611 GTGTTTAATGCTTGCGTTTGTAGAG 59.660 40.000 5.35 0.00 0.00 2.43
1816 1912 6.072728 TGTTTAATGCTTGCGTTTGTAGAGAT 60.073 34.615 5.35 0.00 0.00 2.75
1817 1913 6.494893 TTAATGCTTGCGTTTGTAGAGATT 57.505 33.333 5.35 0.00 0.00 2.40
1818 1914 7.603963 TTAATGCTTGCGTTTGTAGAGATTA 57.396 32.000 5.35 0.00 0.00 1.75
1820 1916 7.786178 AATGCTTGCGTTTGTAGAGATTATA 57.214 32.000 0.00 0.00 0.00 0.98
1823 1920 6.592220 TGCTTGCGTTTGTAGAGATTATAACA 59.408 34.615 0.00 0.00 0.00 2.41
1852 1949 4.748102 AGCTGACTGCACATTTCATTTTTG 59.252 37.500 7.11 0.00 45.94 2.44
1891 1988 1.680338 GTCTGAAGCACAGGGTGTTT 58.320 50.000 10.23 0.00 45.76 2.83
1987 2084 2.648059 CAAGGGATGAATGTCCTCACC 58.352 52.381 0.00 0.00 38.38 4.02
2036 2133 7.432869 GGCATTGCCTTTAACATGATGTTATA 58.567 34.615 20.66 12.51 46.69 0.98
2064 2162 3.726291 TTTGCTTTGCTAACCTGTTCC 57.274 42.857 0.00 0.00 0.00 3.62
2160 2258 2.616256 GGCTCATGTGGATGTGAAGACA 60.616 50.000 0.00 0.00 36.22 3.41
2178 2276 4.708177 AGACAACTGACAACTACATGCTT 58.292 39.130 0.00 0.00 0.00 3.91
2214 2312 1.738099 CTTCACCAAGAGACGCCCG 60.738 63.158 0.00 0.00 0.00 6.13
2322 2425 7.147863 TGGATAATGTTTTGGTGATCATTGAGG 60.148 37.037 0.00 0.00 33.48 3.86
2450 2553 3.054802 ACAAGTTCATCCCTGAGGTGATC 60.055 47.826 0.00 0.00 31.68 2.92
2471 2574 2.093235 CGGAAAGGAGATTGAGAAGGCT 60.093 50.000 0.00 0.00 0.00 4.58
2572 2675 4.414337 AGCTCATGGAGGTAATTGTCTC 57.586 45.455 0.00 0.00 38.70 3.36
2573 2676 3.776969 AGCTCATGGAGGTAATTGTCTCA 59.223 43.478 10.61 0.00 38.70 3.27
2596 2699 3.244875 TGGCACAACCATGTCTACTGAAT 60.245 43.478 0.00 0.00 46.36 2.57
2600 2703 6.425114 GGCACAACCATGTCTACTGAATATAG 59.575 42.308 0.00 0.00 37.82 1.31
2602 2705 7.042456 GCACAACCATGTCTACTGAATATAGTG 60.042 40.741 0.00 0.00 37.82 2.74
2616 2719 7.073457 TGAATATAGTGTTAGCTGGGCATTA 57.927 36.000 0.00 0.00 0.00 1.90
2621 2724 5.630415 AGTGTTAGCTGGGCATTAGATAA 57.370 39.130 0.00 0.00 0.00 1.75
2622 2725 6.192970 AGTGTTAGCTGGGCATTAGATAAT 57.807 37.500 0.00 0.00 29.93 1.28
2623 2726 7.316393 AGTGTTAGCTGGGCATTAGATAATA 57.684 36.000 0.00 0.00 29.93 0.98
2624 2727 7.922382 AGTGTTAGCTGGGCATTAGATAATAT 58.078 34.615 0.00 0.00 29.93 1.28
2669 2773 7.284919 TGTCTACTGAAGTTCTAATGTGACA 57.715 36.000 4.17 8.25 0.00 3.58
2743 2847 2.124403 GACAGGCCTGCTGATGGG 60.124 66.667 33.06 6.81 0.00 4.00
2746 2850 3.415087 AGGCCTGCTGATGGGGAC 61.415 66.667 3.11 0.00 0.00 4.46
2752 2856 2.303549 CTGCTGATGGGGACGAGGTC 62.304 65.000 0.00 0.00 0.00 3.85
2844 2948 8.606754 ATCTAGAAGATGATATATGTGCCACT 57.393 34.615 0.00 0.00 32.80 4.00
2896 3001 5.645067 TGATGGCTGATTTCTTGAGTACTTG 59.355 40.000 0.00 0.00 0.00 3.16
3046 3153 7.095695 ACTTATGCTGTGTTGTTTTGTTAGT 57.904 32.000 0.00 0.00 0.00 2.24
3131 3238 5.609104 GCTACAGCTTCTCCTAGCCAAGG 62.609 56.522 0.00 0.00 42.20 3.61
3135 3242 2.112190 GCTTCTCCTAGCCAAGGTAGT 58.888 52.381 2.79 0.00 46.62 2.73
3136 3243 3.052793 AGCTTCTCCTAGCCAAGGTAGTA 60.053 47.826 2.79 0.00 46.62 1.82
3151 3259 5.326200 AGGTAGTACTCCGTCTTGAATTG 57.674 43.478 0.00 0.00 0.00 2.32
3212 3416 0.176680 ATCGAGTCTCATGCGGCTTT 59.823 50.000 0.00 0.00 0.00 3.51
3214 3418 1.424493 CGAGTCTCATGCGGCTTTCC 61.424 60.000 0.00 0.00 0.00 3.13
3215 3419 0.391661 GAGTCTCATGCGGCTTTCCA 60.392 55.000 0.00 0.00 0.00 3.53
3216 3420 0.254178 AGTCTCATGCGGCTTTCCAT 59.746 50.000 0.00 0.00 0.00 3.41
3217 3421 1.486310 AGTCTCATGCGGCTTTCCATA 59.514 47.619 0.00 0.00 0.00 2.74
3221 3425 4.515191 GTCTCATGCGGCTTTCCATATTAA 59.485 41.667 0.00 0.00 0.00 1.40
3222 3426 5.008613 GTCTCATGCGGCTTTCCATATTAAA 59.991 40.000 0.00 0.00 0.00 1.52
3223 3427 5.769662 TCTCATGCGGCTTTCCATATTAAAT 59.230 36.000 0.00 0.00 0.00 1.40
3225 3429 4.582701 TGCGGCTTTCCATATTAAATGG 57.417 40.909 0.00 9.25 40.48 3.16
3226 3430 4.211125 TGCGGCTTTCCATATTAAATGGA 58.789 39.130 12.57 12.57 45.71 3.41
3227 3431 4.832266 TGCGGCTTTCCATATTAAATGGAT 59.168 37.500 15.62 0.00 46.51 3.41
3231 3526 7.870445 GCGGCTTTCCATATTAAATGGATAAAA 59.130 33.333 15.62 9.41 46.51 1.52
3261 3556 3.569701 GCGACATGTAATTTGGGATGGAT 59.430 43.478 0.00 0.00 0.00 3.41
3262 3557 4.320494 GCGACATGTAATTTGGGATGGATC 60.320 45.833 0.00 0.00 0.00 3.36
3263 3558 4.216257 CGACATGTAATTTGGGATGGATCC 59.784 45.833 4.20 4.20 46.41 3.36
3271 3566 2.427753 GGATGGATCCACCTCCGC 59.572 66.667 18.99 2.36 46.38 5.54
3272 3567 2.427753 GATGGATCCACCTCCGCC 59.572 66.667 18.99 0.00 38.21 6.13
3273 3568 2.366837 ATGGATCCACCTCCGCCA 60.367 61.111 18.99 0.00 38.21 5.69
3274 3569 2.666596 GATGGATCCACCTCCGCCAC 62.667 65.000 18.99 0.00 38.21 5.01
3275 3570 3.399181 GGATCCACCTCCGCCACA 61.399 66.667 6.95 0.00 35.41 4.17
3276 3571 2.668632 GATCCACCTCCGCCACAA 59.331 61.111 0.00 0.00 0.00 3.33
3277 3572 1.450312 GATCCACCTCCGCCACAAG 60.450 63.158 0.00 0.00 0.00 3.16
3278 3573 2.185310 GATCCACCTCCGCCACAAGT 62.185 60.000 0.00 0.00 0.00 3.16
3279 3574 0.907704 ATCCACCTCCGCCACAAGTA 60.908 55.000 0.00 0.00 0.00 2.24
3280 3575 1.122632 TCCACCTCCGCCACAAGTAA 61.123 55.000 0.00 0.00 0.00 2.24
3281 3576 0.035439 CCACCTCCGCCACAAGTAAT 60.035 55.000 0.00 0.00 0.00 1.89
3282 3577 1.613255 CCACCTCCGCCACAAGTAATT 60.613 52.381 0.00 0.00 0.00 1.40
3283 3578 2.159382 CACCTCCGCCACAAGTAATTT 58.841 47.619 0.00 0.00 0.00 1.82
3284 3579 2.095263 CACCTCCGCCACAAGTAATTTG 60.095 50.000 0.00 0.00 42.68 2.32
3285 3580 1.472480 CCTCCGCCACAAGTAATTTGG 59.528 52.381 0.00 1.35 41.25 3.28
3286 3581 1.472480 CTCCGCCACAAGTAATTTGGG 59.528 52.381 6.36 0.00 41.25 4.12
3287 3582 1.074084 TCCGCCACAAGTAATTTGGGA 59.926 47.619 6.36 0.00 43.15 4.37
3288 3583 1.201414 CCGCCACAAGTAATTTGGGAC 59.799 52.381 6.36 0.00 43.15 4.46
3289 3584 1.135803 CGCCACAAGTAATTTGGGACG 60.136 52.381 6.36 0.00 43.15 4.79
3290 3585 1.201414 GCCACAAGTAATTTGGGACGG 59.799 52.381 6.36 0.00 43.15 4.79
3291 3586 2.785562 CCACAAGTAATTTGGGACGGA 58.214 47.619 0.00 0.00 43.15 4.69
3386 3687 6.434028 ACTGGTAAGCTGCAATGAAGAAAATA 59.566 34.615 1.02 0.00 0.00 1.40
3395 3696 6.228995 TGCAATGAAGAAAATATTGTTGGCA 58.771 32.000 0.00 0.00 34.98 4.92
3421 3728 4.935702 TCAAAGTTTCAATGAAGTGGCAG 58.064 39.130 0.00 0.00 0.00 4.85
3433 3740 5.284861 TGAAGTGGCAGTACTGACTTAAA 57.715 39.130 28.56 16.12 39.96 1.52
3435 3742 5.069914 TGAAGTGGCAGTACTGACTTAAAGA 59.930 40.000 28.56 5.10 39.96 2.52
3466 3886 5.148502 TCTCTACTCCTTTGAAGGTGAAGT 58.851 41.667 16.38 11.72 46.54 3.01
3471 3891 5.612351 ACTCCTTTGAAGGTGAAGTACTTC 58.388 41.667 25.73 25.73 46.54 3.01
3484 3904 5.865085 TGAAGTACTTCATGTGGCTAGTTT 58.135 37.500 30.07 0.00 43.90 2.66
3490 3910 8.100791 AGTACTTCATGTGGCTAGTTTTGAATA 58.899 33.333 0.00 0.00 0.00 1.75
3493 3913 8.246180 ACTTCATGTGGCTAGTTTTGAATATTG 58.754 33.333 0.00 0.00 0.00 1.90
3536 3979 9.823647 ATACTGATTGTAAACTCTGGTAAGATG 57.176 33.333 0.00 0.00 34.45 2.90
3609 4053 4.584325 GGTGCATATCCTTTGCTTGGATAA 59.416 41.667 13.83 0.42 46.03 1.75
3610 4054 5.244626 GGTGCATATCCTTTGCTTGGATAAT 59.755 40.000 13.83 4.39 46.03 1.28
3615 4059 7.383300 GCATATCCTTTGCTTGGATAATTTCAC 59.617 37.037 13.83 2.03 46.03 3.18
3622 4066 4.701651 TGCTTGGATAATTTCACTCACCAG 59.298 41.667 0.00 0.00 0.00 4.00
3643 4088 5.010516 CCAGTCTATCATGATCGTCTTCCTT 59.989 44.000 12.53 0.00 0.00 3.36
3646 4091 5.010112 GTCTATCATGATCGTCTTCCTTCCA 59.990 44.000 12.53 0.00 0.00 3.53
3653 4098 3.334583 TCGTCTTCCTTCCATTTCCTG 57.665 47.619 0.00 0.00 0.00 3.86
3710 4155 2.551721 CCATCACTTCACAGAGCAGGTT 60.552 50.000 0.00 0.00 0.00 3.50
3749 4196 4.202212 GGGTTAAGTGCAGAAAACCAATGT 60.202 41.667 20.00 0.00 42.61 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.181503 CCTCATGTCACACTAGCATTTGC 60.182 47.826 0.00 0.00 42.49 3.68
5 6 3.181503 GCCTCATGTCACACTAGCATTTG 60.182 47.826 0.00 0.00 0.00 2.32
6 7 3.012518 GCCTCATGTCACACTAGCATTT 58.987 45.455 0.00 0.00 0.00 2.32
7 8 2.026915 TGCCTCATGTCACACTAGCATT 60.027 45.455 0.00 0.00 0.00 3.56
8 9 1.556451 TGCCTCATGTCACACTAGCAT 59.444 47.619 0.00 0.00 0.00 3.79
9 10 0.975887 TGCCTCATGTCACACTAGCA 59.024 50.000 0.00 0.00 0.00 3.49
10 11 1.363744 GTGCCTCATGTCACACTAGC 58.636 55.000 9.46 0.00 33.63 3.42
11 12 1.737029 CGGTGCCTCATGTCACACTAG 60.737 57.143 14.08 0.00 35.04 2.57
12 13 0.246360 CGGTGCCTCATGTCACACTA 59.754 55.000 14.08 0.00 35.04 2.74
13 14 1.004560 CGGTGCCTCATGTCACACT 60.005 57.895 14.08 0.00 35.04 3.55
14 15 1.301716 ACGGTGCCTCATGTCACAC 60.302 57.895 14.08 10.45 35.04 3.82
15 16 1.301637 CACGGTGCCTCATGTCACA 60.302 57.895 14.08 0.00 35.04 3.58
16 17 2.680913 GCACGGTGCCTCATGTCAC 61.681 63.158 22.19 0.00 37.42 3.67
17 18 2.358615 GCACGGTGCCTCATGTCA 60.359 61.111 22.19 0.00 37.42 3.58
18 19 2.358615 TGCACGGTGCCTCATGTC 60.359 61.111 28.57 0.99 44.23 3.06
19 20 2.669569 GTGCACGGTGCCTCATGT 60.670 61.111 28.57 0.00 44.23 3.21
20 21 3.792047 CGTGCACGGTGCCTCATG 61.792 66.667 31.15 13.01 44.23 3.07
30 31 4.415501 GTCTTGCTCGCGTGCACG 62.416 66.667 32.82 34.01 43.20 5.34
73 74 0.889186 AAGTTGTCCACCACGCCATC 60.889 55.000 0.00 0.00 0.00 3.51
76 77 1.098712 TCAAAGTTGTCCACCACGCC 61.099 55.000 0.00 0.00 0.00 5.68
78 79 4.000325 TCATATCAAAGTTGTCCACCACG 59.000 43.478 0.00 0.00 0.00 4.94
215 219 5.771602 TTGGCGTTTCTTGTTTCTTTTTC 57.228 34.783 0.00 0.00 0.00 2.29
299 303 1.705186 TGGGCTAGAAGCTTCCAACTT 59.295 47.619 22.81 6.61 41.99 2.66
323 327 1.132453 CTGCGACCTCTCATGTAACGA 59.868 52.381 0.00 0.00 0.00 3.85
326 330 1.557099 ACCTGCGACCTCTCATGTAA 58.443 50.000 0.00 0.00 0.00 2.41
363 367 2.557056 ACGAATGAACTGAAGAGTCGGA 59.443 45.455 0.00 0.00 33.93 4.55
379 383 1.282248 CGAAGTGTGGCACGACGAAT 61.282 55.000 13.77 4.87 39.64 3.34
384 388 3.712655 CAACGAAGTGTGGCACGA 58.287 55.556 13.77 0.00 45.00 4.35
398 402 5.150683 GTTGTGGGTTTTTCTTTTTGCAAC 58.849 37.500 0.00 0.00 0.00 4.17
408 412 3.682377 CACCTTGTTGTTGTGGGTTTTTC 59.318 43.478 0.00 0.00 0.00 2.29
414 418 0.385390 GCTCACCTTGTTGTTGTGGG 59.615 55.000 0.00 0.00 33.56 4.61
415 419 1.102154 TGCTCACCTTGTTGTTGTGG 58.898 50.000 0.00 0.00 0.00 4.17
440 447 3.458044 TTGTGGGTTATATGGGTTGCA 57.542 42.857 0.00 0.00 0.00 4.08
445 452 5.730296 TTGTGTTTTGTGGGTTATATGGG 57.270 39.130 0.00 0.00 0.00 4.00
451 458 4.636206 GGCATTTTTGTGTTTTGTGGGTTA 59.364 37.500 0.00 0.00 0.00 2.85
471 479 1.026182 GTGTTCATCTCGCATGGGCA 61.026 55.000 4.59 0.00 41.24 5.36
516 524 0.319211 CTGTCGGGCTCGTGTTTGTA 60.319 55.000 5.57 0.00 37.69 2.41
541 549 2.742774 AGATTCGTGCAAAAGGTTTGC 58.257 42.857 16.79 16.79 45.11 3.68
567 575 0.993532 CGTCGCCACGCAATTAGTTA 59.006 50.000 0.00 0.00 39.69 2.24
582 590 4.798907 AGTATTGCACATCTAAGTTCGTCG 59.201 41.667 0.00 0.00 0.00 5.12
669 679 7.309805 GGGCTGGACAAAAATAAATACTTGTCT 60.310 37.037 12.12 0.00 44.52 3.41
670 680 6.811665 GGGCTGGACAAAAATAAATACTTGTC 59.188 38.462 5.44 5.44 44.44 3.18
671 681 6.268847 TGGGCTGGACAAAAATAAATACTTGT 59.731 34.615 0.00 0.00 34.78 3.16
672 682 6.696411 TGGGCTGGACAAAAATAAATACTTG 58.304 36.000 0.00 0.00 0.00 3.16
673 683 6.926630 TGGGCTGGACAAAAATAAATACTT 57.073 33.333 0.00 0.00 0.00 2.24
674 684 6.574269 GCTTGGGCTGGACAAAAATAAATACT 60.574 38.462 0.00 0.00 35.22 2.12
675 685 5.580691 GCTTGGGCTGGACAAAAATAAATAC 59.419 40.000 0.00 0.00 35.22 1.89
677 687 4.578871 GCTTGGGCTGGACAAAAATAAAT 58.421 39.130 0.00 0.00 35.22 1.40
678 688 4.001618 GCTTGGGCTGGACAAAAATAAA 57.998 40.909 0.00 0.00 35.22 1.40
679 689 3.676291 GCTTGGGCTGGACAAAAATAA 57.324 42.857 0.00 0.00 35.22 1.40
693 703 4.785453 GCACGAGGGGAGCTTGGG 62.785 72.222 0.00 0.00 0.00 4.12
695 705 4.379243 ACGCACGAGGGGAGCTTG 62.379 66.667 0.00 0.00 0.00 4.01
696 706 4.379243 CACGCACGAGGGGAGCTT 62.379 66.667 0.00 0.00 0.00 3.74
709 719 3.438017 TTTTGGTTGCCTGCCACGC 62.438 57.895 0.00 0.00 35.46 5.34
751 761 0.177141 GCTCGGCCCAACAGTGTATA 59.823 55.000 0.00 0.00 0.00 1.47
759 769 3.305177 TAACTCCGCTCGGCCCAAC 62.305 63.158 2.96 0.00 34.68 3.77
776 786 4.177026 GAGAGATTGCGTTGAAGCTTCTA 58.823 43.478 26.09 17.01 38.13 2.10
797 807 2.989639 CCATGTGGGCTCTTCGGA 59.010 61.111 0.00 0.00 0.00 4.55
902 916 0.606604 GAAACCCTACACAGGCGAGA 59.393 55.000 0.00 0.00 41.08 4.04
1087 1101 0.176449 CCAGATCACGATGGTGCAGA 59.824 55.000 2.48 0.00 44.03 4.26
1088 1102 0.812811 CCCAGATCACGATGGTGCAG 60.813 60.000 2.48 0.00 44.03 4.41
1093 1107 1.690893 ACAGATCCCAGATCACGATGG 59.309 52.381 7.30 0.00 36.27 3.51
1105 1119 4.223923 TGAGGAGAAGAAGAAACAGATCCC 59.776 45.833 0.00 0.00 0.00 3.85
1121 1135 1.827344 AGCACATGACGAATGAGGAGA 59.173 47.619 0.00 0.00 38.72 3.71
1125 1139 2.286242 GCATCAGCACATGACGAATGAG 60.286 50.000 0.00 3.57 41.91 2.90
1128 1142 0.654160 CGCATCAGCACATGACGAAT 59.346 50.000 0.00 0.00 41.91 3.34
1353 1367 5.051153 GCAGACTACTAAACAGCTAATCCC 58.949 45.833 0.00 0.00 0.00 3.85
1380 1394 9.526713 AATAGATCACAATCGCATATATGAGAC 57.473 33.333 19.70 7.01 39.36 3.36
1390 1404 5.985530 CAGGACTAAATAGATCACAATCGCA 59.014 40.000 0.00 0.00 36.97 5.10
1414 1428 3.934579 GGTTGAATCCATTTCATGCCAAC 59.065 43.478 0.00 0.00 43.73 3.77
1426 1440 5.789643 CCTTGAGAAAAAGGTTGAATCCA 57.210 39.130 0.00 0.00 41.65 3.41
1467 1482 2.729194 AGTCTATCACGTCCTTCAGCT 58.271 47.619 0.00 0.00 0.00 4.24
1508 1529 6.006275 AGTAACATCAATTATCAGCAGGGT 57.994 37.500 0.00 0.00 0.00 4.34
1509 1530 6.543465 TGAAGTAACATCAATTATCAGCAGGG 59.457 38.462 0.00 0.00 0.00 4.45
1510 1531 7.496920 TCTGAAGTAACATCAATTATCAGCAGG 59.503 37.037 0.00 0.00 34.51 4.85
1511 1532 8.429493 TCTGAAGTAACATCAATTATCAGCAG 57.571 34.615 0.00 0.00 34.51 4.24
1512 1533 8.969260 ATCTGAAGTAACATCAATTATCAGCA 57.031 30.769 0.00 0.00 34.51 4.41
1544 1587 8.289618 GCACTGAGAACATATGTAAGACAAAAA 58.710 33.333 9.21 0.00 0.00 1.94
1553 1596 8.882736 CAAATTACAGCACTGAGAACATATGTA 58.117 33.333 9.21 0.00 0.00 2.29
1556 1599 7.928307 ACAAATTACAGCACTGAGAACATAT 57.072 32.000 4.31 0.00 0.00 1.78
1581 1624 8.557592 ACAAGATGCATGATATCGTTTCATAT 57.442 30.769 2.46 4.61 32.63 1.78
1590 1647 7.493743 AGAGTGAAACAAGATGCATGATATC 57.506 36.000 2.46 0.00 41.43 1.63
1592 1649 6.403964 GCAAGAGTGAAACAAGATGCATGATA 60.404 38.462 2.46 0.00 41.43 2.15
1621 1678 5.022787 AGTGGGCCATAACAACACATAAAT 58.977 37.500 10.70 0.00 34.65 1.40
1627 1684 1.960689 ACAAGTGGGCCATAACAACAC 59.039 47.619 10.70 0.72 0.00 3.32
1631 1694 5.740513 GCTTTAAAACAAGTGGGCCATAACA 60.741 40.000 10.70 0.00 0.00 2.41
1637 1700 3.614150 GCTAGCTTTAAAACAAGTGGGCC 60.614 47.826 7.70 0.00 0.00 5.80
1639 1702 4.278419 AGTGCTAGCTTTAAAACAAGTGGG 59.722 41.667 17.23 0.00 0.00 4.61
1662 1725 4.820897 ACTGATTCTAATCAACAGACGCA 58.179 39.130 6.82 0.00 44.20 5.24
1663 1726 5.051374 GCTACTGATTCTAATCAACAGACGC 60.051 44.000 13.48 0.00 44.20 5.19
1664 1727 6.269315 AGCTACTGATTCTAATCAACAGACG 58.731 40.000 13.48 3.04 44.20 4.18
1683 1746 5.163602 ACTGACAGTACTTATGCTGAGCTAC 60.164 44.000 6.24 0.00 40.79 3.58
1684 1747 4.950475 ACTGACAGTACTTATGCTGAGCTA 59.050 41.667 6.24 0.00 40.79 3.32
1686 1749 4.109050 GACTGACAGTACTTATGCTGAGC 58.891 47.826 8.41 0.00 40.79 4.26
1687 1750 4.142578 ACGACTGACAGTACTTATGCTGAG 60.143 45.833 8.41 0.00 40.79 3.35
1688 1751 3.756963 ACGACTGACAGTACTTATGCTGA 59.243 43.478 8.41 0.00 40.79 4.26
1689 1752 4.098055 ACGACTGACAGTACTTATGCTG 57.902 45.455 8.41 0.00 43.70 4.41
1699 1764 3.500680 ACAAAACACAAACGACTGACAGT 59.499 39.130 8.12 8.12 0.00 3.55
1700 1765 4.078363 ACAAAACACAAACGACTGACAG 57.922 40.909 0.00 0.00 0.00 3.51
1704 1769 3.479505 TGGACAAAACACAAACGACTG 57.520 42.857 0.00 0.00 0.00 3.51
1719 1784 4.126437 CAACATAGACACACAGTTGGACA 58.874 43.478 0.00 0.00 36.75 4.02
1723 1788 4.991056 AGCTACAACATAGACACACAGTTG 59.009 41.667 0.00 0.00 43.71 3.16
1729 1794 5.468540 ACAAGAGCTACAACATAGACACA 57.531 39.130 0.00 0.00 0.00 3.72
1730 1795 7.222999 GGATAACAAGAGCTACAACATAGACAC 59.777 40.741 0.00 0.00 0.00 3.67
1732 1797 6.702282 GGGATAACAAGAGCTACAACATAGAC 59.298 42.308 0.00 0.00 0.00 2.59
1734 1799 6.821388 AGGGATAACAAGAGCTACAACATAG 58.179 40.000 0.00 0.00 0.00 2.23
1735 1800 6.808321 AGGGATAACAAGAGCTACAACATA 57.192 37.500 0.00 0.00 0.00 2.29
1736 1801 5.700402 AGGGATAACAAGAGCTACAACAT 57.300 39.130 0.00 0.00 0.00 2.71
1737 1802 5.128827 CCTAGGGATAACAAGAGCTACAACA 59.871 44.000 0.00 0.00 0.00 3.33
1738 1803 5.602628 CCTAGGGATAACAAGAGCTACAAC 58.397 45.833 0.00 0.00 0.00 3.32
1739 1804 4.101119 GCCTAGGGATAACAAGAGCTACAA 59.899 45.833 11.72 0.00 0.00 2.41
1743 1808 2.050918 GGCCTAGGGATAACAAGAGCT 58.949 52.381 11.72 0.00 0.00 4.09
1744 1809 2.050918 AGGCCTAGGGATAACAAGAGC 58.949 52.381 1.29 0.00 0.00 4.09
1745 1810 4.779993 AAAGGCCTAGGGATAACAAGAG 57.220 45.455 5.16 0.00 0.00 2.85
1746 1811 4.538490 TCAAAAGGCCTAGGGATAACAAGA 59.462 41.667 5.16 0.00 0.00 3.02
1749 1814 5.466127 AATCAAAAGGCCTAGGGATAACA 57.534 39.130 5.16 0.00 0.00 2.41
1750 1815 6.791867 AAAATCAAAAGGCCTAGGGATAAC 57.208 37.500 5.16 0.00 0.00 1.89
1751 1816 7.415086 TGTAAAATCAAAAGGCCTAGGGATAA 58.585 34.615 5.16 0.00 0.00 1.75
1753 1818 5.837829 TGTAAAATCAAAAGGCCTAGGGAT 58.162 37.500 5.16 6.40 0.00 3.85
1754 1819 5.263872 TGTAAAATCAAAAGGCCTAGGGA 57.736 39.130 5.16 3.79 0.00 4.20
1755 1820 6.154363 TGAATGTAAAATCAAAAGGCCTAGGG 59.846 38.462 5.16 0.00 0.00 3.53
1756 1821 7.169158 TGAATGTAAAATCAAAAGGCCTAGG 57.831 36.000 5.16 3.67 0.00 3.02
1757 1822 9.657419 AAATGAATGTAAAATCAAAAGGCCTAG 57.343 29.630 5.16 0.00 0.00 3.02
1759 1824 9.657419 CTAAATGAATGTAAAATCAAAAGGCCT 57.343 29.630 0.00 0.00 0.00 5.19
1761 1826 8.934825 TGCTAAATGAATGTAAAATCAAAAGGC 58.065 29.630 0.00 0.00 0.00 4.35
1769 1865 8.810652 AACACGTTGCTAAATGAATGTAAAAT 57.189 26.923 0.00 0.00 0.00 1.82
1770 1866 8.635877 AAACACGTTGCTAAATGAATGTAAAA 57.364 26.923 0.00 0.00 0.00 1.52
1786 1882 2.380660 ACGCAAGCATTAAACACGTTG 58.619 42.857 0.00 0.00 45.62 4.10
1789 1885 2.786578 ACAAACGCAAGCATTAAACACG 59.213 40.909 0.00 0.00 45.62 4.49
1812 1908 9.134734 GCAGTCAGCTAATACTGTTATAATCTC 57.865 37.037 18.83 2.25 44.03 2.75
1813 1909 8.642432 TGCAGTCAGCTAATACTGTTATAATCT 58.358 33.333 18.83 0.00 44.03 2.40
1814 1910 8.704234 GTGCAGTCAGCTAATACTGTTATAATC 58.296 37.037 18.83 6.38 44.03 1.75
1816 1912 7.552459 TGTGCAGTCAGCTAATACTGTTATAA 58.448 34.615 18.83 4.52 44.03 0.98
1817 1913 7.107639 TGTGCAGTCAGCTAATACTGTTATA 57.892 36.000 18.83 8.68 44.03 0.98
1818 1914 5.977635 TGTGCAGTCAGCTAATACTGTTAT 58.022 37.500 18.83 0.00 44.03 1.89
1820 1916 4.271696 TGTGCAGTCAGCTAATACTGTT 57.728 40.909 18.83 0.00 44.03 3.16
1823 1920 5.491070 TGAAATGTGCAGTCAGCTAATACT 58.509 37.500 0.00 0.00 45.94 2.12
1852 1949 3.942115 GACCCTCTGAGGCAATCTAAAAC 59.058 47.826 18.51 0.00 32.73 2.43
1891 1988 7.286313 TCTGAAGATCAGCTAGAGATACTTCA 58.714 38.462 21.69 21.69 43.95 3.02
1921 2018 2.427245 CCTGTAGGCCTGGTCCTCG 61.427 68.421 17.99 0.00 37.66 4.63
1987 2084 6.094603 CCAGAGAAATCATTACCCAGAAGTTG 59.905 42.308 0.00 0.00 0.00 3.16
2036 2133 5.294060 CAGGTTAGCAAAGCAAAAACACAAT 59.706 36.000 0.00 0.00 35.49 2.71
2109 2207 0.397941 TCTGCCACTTCCTCACAAGG 59.602 55.000 0.00 0.00 44.89 3.61
2178 2276 3.050166 GCCAATGGCGAACATGCGA 62.050 57.895 9.14 0.00 39.62 5.10
2214 2312 1.166531 AAGTGCGCTTCACCTGGTTC 61.167 55.000 9.73 0.00 46.81 3.62
2322 2425 8.311650 ACACAGATAGAGTTGTTAACAATCAC 57.688 34.615 23.11 16.35 38.24 3.06
2450 2553 2.093235 AGCCTTCTCAATCTCCTTTCCG 60.093 50.000 0.00 0.00 0.00 4.30
2471 2574 1.213296 GGGGGAAGATGCTTGAGGTA 58.787 55.000 0.00 0.00 0.00 3.08
2596 2699 6.935240 ATCTAATGCCCAGCTAACACTATA 57.065 37.500 0.00 0.00 0.00 1.31
2600 2703 8.454106 CAATATTATCTAATGCCCAGCTAACAC 58.546 37.037 0.00 0.00 0.00 3.32
2602 2705 8.567285 ACAATATTATCTAATGCCCAGCTAAC 57.433 34.615 0.00 0.00 0.00 2.34
2622 2725 9.906660 GACATGGAGAACAAACAATTAACAATA 57.093 29.630 0.00 0.00 0.00 1.90
2623 2726 8.641541 AGACATGGAGAACAAACAATTAACAAT 58.358 29.630 0.00 0.00 0.00 2.71
2624 2727 8.006298 AGACATGGAGAACAAACAATTAACAA 57.994 30.769 0.00 0.00 0.00 2.83
2636 2740 5.540337 AGAACTTCAGTAGACATGGAGAACA 59.460 40.000 0.00 0.00 0.00 3.18
2637 2741 6.031751 AGAACTTCAGTAGACATGGAGAAC 57.968 41.667 0.00 0.00 0.00 3.01
2639 2743 7.397476 ACATTAGAACTTCAGTAGACATGGAGA 59.603 37.037 0.00 0.00 0.00 3.71
2640 2744 7.490725 CACATTAGAACTTCAGTAGACATGGAG 59.509 40.741 0.00 0.00 0.00 3.86
2641 2745 7.178451 TCACATTAGAACTTCAGTAGACATGGA 59.822 37.037 0.00 0.00 0.00 3.41
2643 2747 7.814587 TGTCACATTAGAACTTCAGTAGACATG 59.185 37.037 0.00 0.00 0.00 3.21
2644 2748 7.815068 GTGTCACATTAGAACTTCAGTAGACAT 59.185 37.037 0.00 0.00 34.23 3.06
2645 2749 7.145985 GTGTCACATTAGAACTTCAGTAGACA 58.854 38.462 0.00 0.00 0.00 3.41
2752 2856 1.153289 CTCCTCCGCACCAGGAATG 60.153 63.158 0.00 0.00 39.69 2.67
2761 2865 4.704833 GCAGCAACCTCCTCCGCA 62.705 66.667 0.00 0.00 0.00 5.69
2844 2948 3.864243 ACTACAAAGTTCACGACACCAA 58.136 40.909 0.00 0.00 29.00 3.67
2896 3001 1.927895 CTGGCTAGGAATGTCGACAC 58.072 55.000 22.71 9.19 0.00 3.67
2949 3054 4.361783 TCAACTCATAACCTCCATCCAGA 58.638 43.478 0.00 0.00 0.00 3.86
3031 3138 8.395633 ACTGAGATACAACTAACAAAACAACAC 58.604 33.333 0.00 0.00 0.00 3.32
3046 3153 8.514330 AACAAAAAGTTGGTACTGAGATACAA 57.486 30.769 0.00 0.00 39.49 2.41
3136 3243 9.778426 ACTTCTACAAGCAATTCAAGACGGAGT 62.778 40.741 0.00 0.00 36.75 3.85
3151 3259 2.450609 TTCCCGTCACTTCTACAAGC 57.549 50.000 0.00 0.00 32.09 4.01
3189 3380 1.871408 GCCGCATGAGACTCGATGAAT 60.871 52.381 15.05 0.00 0.00 2.57
3190 3381 0.528466 GCCGCATGAGACTCGATGAA 60.528 55.000 15.05 0.00 0.00 2.57
3193 3384 0.176680 AAAGCCGCATGAGACTCGAT 59.823 50.000 0.00 0.00 0.00 3.59
3195 3386 1.424493 GGAAAGCCGCATGAGACTCG 61.424 60.000 0.00 0.00 0.00 4.18
3221 3425 7.750229 ATGTCGCTACATGATTTTATCCATT 57.250 32.000 2.58 0.00 44.79 3.16
3245 3540 3.531397 AGGTGGATCCATCCCAAATTACA 59.469 43.478 21.88 0.00 46.59 2.41
3261 3556 1.122632 TTACTTGTGGCGGAGGTGGA 61.123 55.000 0.00 0.00 0.00 4.02
3262 3557 0.035439 ATTACTTGTGGCGGAGGTGG 60.035 55.000 0.00 0.00 0.00 4.61
3263 3558 1.821216 AATTACTTGTGGCGGAGGTG 58.179 50.000 0.00 0.00 0.00 4.00
3264 3559 2.159382 CAAATTACTTGTGGCGGAGGT 58.841 47.619 0.00 0.00 0.00 3.85
3265 3560 1.472480 CCAAATTACTTGTGGCGGAGG 59.528 52.381 0.00 0.00 32.65 4.30
3266 3561 1.472480 CCCAAATTACTTGTGGCGGAG 59.528 52.381 0.00 0.00 32.65 4.63
3267 3562 1.074084 TCCCAAATTACTTGTGGCGGA 59.926 47.619 0.00 0.00 32.65 5.54
3268 3563 1.201414 GTCCCAAATTACTTGTGGCGG 59.799 52.381 0.00 0.00 32.65 6.13
3269 3564 1.135803 CGTCCCAAATTACTTGTGGCG 60.136 52.381 0.00 0.00 32.65 5.69
3270 3565 1.201414 CCGTCCCAAATTACTTGTGGC 59.799 52.381 0.00 0.00 32.65 5.01
3271 3566 2.747446 CTCCGTCCCAAATTACTTGTGG 59.253 50.000 0.00 0.00 32.65 4.17
3272 3567 2.747446 CCTCCGTCCCAAATTACTTGTG 59.253 50.000 0.00 0.00 32.65 3.33
3273 3568 2.290705 CCCTCCGTCCCAAATTACTTGT 60.291 50.000 0.00 0.00 32.65 3.16
3274 3569 2.026636 TCCCTCCGTCCCAAATTACTTG 60.027 50.000 0.00 0.00 34.52 3.16
3275 3570 2.238898 CTCCCTCCGTCCCAAATTACTT 59.761 50.000 0.00 0.00 0.00 2.24
3276 3571 1.838077 CTCCCTCCGTCCCAAATTACT 59.162 52.381 0.00 0.00 0.00 2.24
3277 3572 1.558294 ACTCCCTCCGTCCCAAATTAC 59.442 52.381 0.00 0.00 0.00 1.89
3278 3573 1.961133 ACTCCCTCCGTCCCAAATTA 58.039 50.000 0.00 0.00 0.00 1.40
3279 3574 1.961133 TACTCCCTCCGTCCCAAATT 58.039 50.000 0.00 0.00 0.00 1.82
3280 3575 2.191981 ATACTCCCTCCGTCCCAAAT 57.808 50.000 0.00 0.00 0.00 2.32
3281 3576 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3282 3577 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3283 3578 4.687262 ATATAATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
3284 3579 4.776308 ACAATATAATACTCCCTCCGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
3285 3580 5.479375 TCACAATATAATACTCCCTCCGTCC 59.521 44.000 0.00 0.00 0.00 4.79
3286 3581 6.015688 TGTCACAATATAATACTCCCTCCGTC 60.016 42.308 0.00 0.00 0.00 4.79
3287 3582 5.836898 TGTCACAATATAATACTCCCTCCGT 59.163 40.000 0.00 0.00 0.00 4.69
3288 3583 6.340962 TGTCACAATATAATACTCCCTCCG 57.659 41.667 0.00 0.00 0.00 4.63
3289 3584 7.162082 CCTTGTCACAATATAATACTCCCTCC 58.838 42.308 0.00 0.00 0.00 4.30
3290 3585 7.162082 CCCTTGTCACAATATAATACTCCCTC 58.838 42.308 0.00 0.00 0.00 4.30
3291 3586 6.619852 ACCCTTGTCACAATATAATACTCCCT 59.380 38.462 0.00 0.00 0.00 4.20
3386 3687 8.723311 CATTGAAACTTTGATAATGCCAACAAT 58.277 29.630 0.00 0.00 0.00 2.71
3395 3696 7.669427 TGCCACTTCATTGAAACTTTGATAAT 58.331 30.769 0.01 0.00 0.00 1.28
3421 3728 8.308207 AGAGATTTCCACTCTTTAAGTCAGTAC 58.692 37.037 0.00 0.00 41.20 2.73
3433 3740 6.019748 TCAAAGGAGTAGAGATTTCCACTCT 58.980 40.000 10.79 0.00 45.15 3.24
3435 3742 6.688073 TTCAAAGGAGTAGAGATTTCCACT 57.312 37.500 0.00 0.00 33.32 4.00
3466 3886 9.461312 AATATTCAAAACTAGCCACATGAAGTA 57.539 29.630 0.00 0.00 31.14 2.24
3471 3891 7.765307 ACTCAATATTCAAAACTAGCCACATG 58.235 34.615 0.00 0.00 0.00 3.21
3484 3904 6.370442 CCCAGTGACGTTTACTCAATATTCAA 59.630 38.462 3.72 0.00 0.00 2.69
3490 3910 4.553330 ATCCCAGTGACGTTTACTCAAT 57.447 40.909 3.72 0.00 0.00 2.57
3493 3913 4.157289 TCAGTATCCCAGTGACGTTTACTC 59.843 45.833 3.72 0.00 31.34 2.59
3536 3979 5.006386 AGAGAATGTTTTGTGATGTCTCCC 58.994 41.667 0.00 0.00 32.27 4.30
3609 4053 6.550938 TCATGATAGACTGGTGAGTGAAAT 57.449 37.500 0.00 0.00 30.16 2.17
3610 4054 6.550938 ATCATGATAGACTGGTGAGTGAAA 57.449 37.500 6.36 0.00 30.16 2.69
3615 4059 4.518590 AGACGATCATGATAGACTGGTGAG 59.481 45.833 21.00 1.10 0.00 3.51
3622 4066 5.010112 TGGAAGGAAGACGATCATGATAGAC 59.990 44.000 21.00 15.09 0.00 2.59
3643 4088 4.705110 TCTGTTCAGTTCAGGAAATGGA 57.295 40.909 9.29 0.00 37.05 3.41
3646 4091 5.246981 TGGATCTGTTCAGTTCAGGAAAT 57.753 39.130 11.38 0.00 34.15 2.17
3653 4098 3.064900 AGGCTTGGATCTGTTCAGTTC 57.935 47.619 0.00 1.62 0.00 3.01
3710 4155 7.063191 GCACTTAACCCGAAGTTTTAAAACAAA 59.937 33.333 28.03 10.94 41.30 2.83
3749 4196 6.068010 TCCAGCTTTTCTTTGAGGAACATTA 58.932 36.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.