Multiple sequence alignment - TraesCS1A01G175200

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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 TraesCS1A01G175200 chr1A 100.000 2258 0 0 1 2258 313163132 313160875 0.000000e+00 4170.0
1 TraesCS1A01G175200 chr1A 100.000 31 0 0 1899 1929 313161205 313161175 8.710000e-05 58.4
2 TraesCS1A01G175200 chr1A 100.000 31 0 0 1928 1958 313161234 313161204 8.710000e-05 58.4
3 TraesCS1A01G175200 chr1B 88.476 1588 119 27 1 1538 339365667 339364094 0.000000e+00 1860.0
4 TraesCS1A01G175200 chr1B 94.551 312 12 3 1618 1928 339364041 339363734 5.640000e-131 477.0
5 TraesCS1A01G175200 chr1B 94.068 118 7 0 1928 2045 339363763 339363646 1.780000e-41 180.0
6 TraesCS1A01G175200 chr1D 92.866 771 33 13 780 1538 234528167 234528927 0.000000e+00 1099.0
7 TraesCS1A01G175200 chr1D 89.362 799 70 8 3 790 234527353 234528147 0.000000e+00 990.0
8 TraesCS1A01G175200 chr1D 92.683 287 15 4 1611 1896 234528974 234529255 2.090000e-110 409.0
9 TraesCS1A01G175200 chr1D 91.549 213 18 0 2044 2256 28073256 28073044 6.100000e-76 294.0
10 TraesCS1A01G175200 chr1D 91.244 217 18 1 2040 2256 318198229 318198014 6.100000e-76 294.0
11 TraesCS1A01G175200 chr1D 95.699 93 3 1 1953 2045 234529252 234529343 5.020000e-32 148.0
12 TraesCS1A01G175200 chr5A 95.814 215 8 1 2045 2258 591978075 591978289 1.660000e-91 346.0
13 TraesCS1A01G175200 chr2A 95.794 214 8 1 2045 2258 579970743 579970531 5.970000e-91 344.0
14 TraesCS1A01G175200 chr3D 92.019 213 16 1 2045 2256 89921723 89921935 4.710000e-77 298.0
15 TraesCS1A01G175200 chr3D 91.981 212 17 0 2045 2256 136261722 136261933 4.710000e-77 298.0
16 TraesCS1A01G175200 chr3D 98.214 56 1 0 1539 1594 145416344 145416289 5.130000e-17 99.0
17 TraesCS1A01G175200 chr6D 91.549 213 17 1 2045 2256 387808649 387808861 2.190000e-75 292.0
18 TraesCS1A01G175200 chr3B 91.549 213 17 1 2045 2256 466282305 466282093 2.190000e-75 292.0
19 TraesCS1A01G175200 chr7D 90.783 217 19 1 2041 2256 610748650 610748866 2.840000e-74 289.0
20 TraesCS1A01G175200 chr7D 98.214 56 1 0 1539 1594 307074984 307074929 5.130000e-17 99.0
21 TraesCS1A01G175200 chr7D 98.214 56 1 0 1539 1594 382105358 382105413 5.130000e-17 99.0
22 TraesCS1A01G175200 chrUn 98.214 56 1 0 1539 1594 233532298 233532353 5.130000e-17 99.0
23 TraesCS1A01G175200 chrUn 98.214 56 1 0 1539 1594 257937602 257937547 5.130000e-17 99.0
24 TraesCS1A01G175200 chrUn 98.214 56 1 0 1539 1594 409595911 409595966 5.130000e-17 99.0
25 TraesCS1A01G175200 chr4D 98.214 56 1 0 1539 1594 185016102 185016047 5.130000e-17 99.0
26 TraesCS1A01G175200 chr2D 98.214 56 1 0 1539 1594 17977337 17977282 5.130000e-17 99.0
27 TraesCS1A01G175200 chr2D 98.214 56 1 0 1539 1594 53916922 53916977 5.130000e-17 99.0
28 TraesCS1A01G175200 chr2B 100.000 30 0 0 338 367 141251349 141251320 3.130000e-04 56.5


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 TraesCS1A01G175200 chr1A 313160875 313163132 2257 True 1428.933333 4170 100.0000 1 2258 3 chr1A.!!$R1 2257
1 TraesCS1A01G175200 chr1B 339363646 339365667 2021 True 839.000000 1860 92.3650 1 2045 3 chr1B.!!$R1 2044
2 TraesCS1A01G175200 chr1D 234527353 234529343 1990 False 661.500000 1099 92.6525 3 2045 4 chr1D.!!$F1 2042

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
73 74 0.034198 TGACACGGCGAGGAAATGAA 59.966 50.0 16.62 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1644 0.035152 ACATGAGCGGCTGGATGAAA 60.035 50.0 20.1 0.0 0.0 2.69 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
18 19 2.348620 AGCGCATCAACAGCTGGA 59.651 55.556 19.93 6.92 40.07 3.86
36 37 2.803155 GAACATCTCCCACGGCAGCA 62.803 60.000 0.00 0.00 0.00 4.41
49 50 2.757508 CAGCAGAGGAGCTCGGGA 60.758 66.667 7.83 0.00 44.54 5.14
73 74 0.034198 TGACACGGCGAGGAAATGAA 59.966 50.000 16.62 0.00 0.00 2.57
78 79 2.009774 ACGGCGAGGAAATGAATTGAG 58.990 47.619 16.62 0.00 0.00 3.02
211 213 1.506718 GGCGCAACTCCTTAAAGGC 59.493 57.895 10.83 0.00 34.61 4.35
213 215 1.677820 GGCGCAACTCCTTAAAGGCTA 60.678 52.381 10.83 0.00 34.61 3.93
215 217 2.288186 GCGCAACTCCTTAAAGGCTATC 59.712 50.000 0.30 0.00 34.61 2.08
217 219 3.532542 GCAACTCCTTAAAGGCTATCGT 58.467 45.455 0.00 0.00 34.61 3.73
267 270 8.087750 TGTTTTCTTTTCTCATTCTTGTTGTGT 58.912 29.630 0.00 0.00 0.00 3.72
277 280 8.415553 TCTCATTCTTGTTGTGTTTTTCATCAT 58.584 29.630 0.00 0.00 0.00 2.45
289 292 8.256605 TGTGTTTTTCATCATTCTTTTCCTTGA 58.743 29.630 0.00 0.00 0.00 3.02
290 293 9.097257 GTGTTTTTCATCATTCTTTTCCTTGAA 57.903 29.630 0.00 0.00 0.00 2.69
349 352 7.637709 TGCATGTAGTTATACTAAATCAGCG 57.362 36.000 0.00 0.00 31.62 5.18
385 388 5.867174 GGATCGGTGAAAAATAACTTTTGGG 59.133 40.000 0.00 0.00 37.36 4.12
387 390 6.223351 TCGGTGAAAAATAACTTTTGGGTT 57.777 33.333 0.00 0.00 37.36 4.11
399 402 0.260230 TTTGGGTTTGTGAGGCTGGA 59.740 50.000 0.00 0.00 0.00 3.86
428 438 9.097257 GTTTTGACTTCCTTCAAATCATTTCAA 57.903 29.630 0.00 0.00 43.38 2.69
440 450 5.384063 AATCATTTCAACACGGTATTGCA 57.616 34.783 0.00 0.00 0.00 4.08
441 451 4.837896 TCATTTCAACACGGTATTGCAA 57.162 36.364 0.00 0.00 0.00 4.08
445 455 6.703607 TCATTTCAACACGGTATTGCAAAAAT 59.296 30.769 1.71 0.00 0.00 1.82
455 465 1.224965 TTGCAAAAATTCGCAAGGGC 58.775 45.000 0.00 0.00 42.93 5.19
493 503 2.361610 ACCTTTCCGGCCATGCTG 60.362 61.111 2.24 0.00 35.61 4.41
503 513 3.803082 CCATGCTGAACCGCACGG 61.803 66.667 7.71 7.71 43.61 4.94
513 523 2.943653 CCGCACGGTTTCTTGGTC 59.056 61.111 0.00 0.00 0.00 4.02
514 524 2.613506 CCGCACGGTTTCTTGGTCC 61.614 63.158 0.00 0.00 0.00 4.46
515 525 1.890041 CGCACGGTTTCTTGGTCCA 60.890 57.895 0.00 0.00 0.00 4.02
516 526 1.234615 CGCACGGTTTCTTGGTCCAT 61.235 55.000 0.00 0.00 0.00 3.41
521 533 4.794169 CACGGTTTCTTGGTCCATAAAAG 58.206 43.478 0.00 0.00 0.00 2.27
523 535 5.470777 CACGGTTTCTTGGTCCATAAAAGTA 59.529 40.000 0.00 0.00 0.00 2.24
543 555 7.916914 AAGTAGTTGTATTTCGCATAAGGTT 57.083 32.000 0.00 0.00 0.00 3.50
554 566 6.671614 TTCGCATAAGGTTATACCAAGTTG 57.328 37.500 0.00 0.00 41.95 3.16
589 601 2.221517 CCAAAACTTGCTGATTTTGCCG 59.778 45.455 11.87 0.74 42.10 5.69
602 614 6.417930 GCTGATTTTGCCGTTTATTTCTATCC 59.582 38.462 0.00 0.00 0.00 2.59
643 656 6.255950 ACTTGTTGAAGTTCTAAAAACTCGC 58.744 36.000 4.17 0.00 39.56 5.03
660 673 2.799978 CTCGCCAAAACCCATTCAAAAC 59.200 45.455 0.00 0.00 0.00 2.43
663 676 3.739519 CGCCAAAACCCATTCAAAACTCA 60.740 43.478 0.00 0.00 0.00 3.41
727 740 7.319142 TCAAAATCAAAAGCCCAAAGAAAAG 57.681 32.000 0.00 0.00 0.00 2.27
731 744 4.944048 TCAAAAGCCCAAAGAAAAGTAGC 58.056 39.130 0.00 0.00 0.00 3.58
834 877 1.118356 TGCAAAATGTCCGGGGCTTT 61.118 50.000 0.00 0.00 0.00 3.51
835 878 0.670239 GCAAAATGTCCGGGGCTTTG 60.670 55.000 0.00 8.53 0.00 2.77
836 879 0.678950 CAAAATGTCCGGGGCTTTGT 59.321 50.000 0.00 0.00 0.00 2.83
846 889 0.891904 GGGGCTTTGTACTTCCGCAA 60.892 55.000 0.00 0.00 0.00 4.85
918 962 1.196808 CCGTGTACTGCAAACCACATC 59.803 52.381 9.21 0.00 0.00 3.06
919 963 1.870402 CGTGTACTGCAAACCACATCA 59.130 47.619 9.21 0.00 0.00 3.07
1172 1222 3.043713 CTTCTGCCAGTTCGCGCA 61.044 61.111 8.75 0.00 0.00 6.09
1178 1228 4.368808 CCAGTTCGCGCACAACCG 62.369 66.667 12.26 1.57 0.00 4.44
1322 1379 0.031585 CACGCCGCCTATGCTACTAA 59.968 55.000 0.00 0.00 34.43 2.24
1338 1395 7.173863 TGCTACTAATACGTAACGTACTACC 57.826 40.000 0.00 0.00 45.07 3.18
1455 1518 1.989864 TCGTGTGTTCATGTATCGTGC 59.010 47.619 0.00 0.00 32.85 5.34
1481 1544 6.664515 CAAGAATAAAATGGTGTGTACGTGT 58.335 36.000 0.00 0.00 0.00 4.49
1538 1601 5.882553 TGTCAATTTTGATCGATGGATGTG 58.117 37.500 0.54 0.00 39.73 3.21
1539 1602 5.647225 TGTCAATTTTGATCGATGGATGTGA 59.353 36.000 0.54 0.00 39.73 3.58
1540 1603 5.967674 GTCAATTTTGATCGATGGATGTGAC 59.032 40.000 0.54 5.85 39.73 3.67
1541 1604 4.801147 ATTTTGATCGATGGATGTGACG 57.199 40.909 0.54 0.00 31.51 4.35
1542 1605 2.223537 TTGATCGATGGATGTGACGG 57.776 50.000 0.54 0.00 31.51 4.79
1543 1606 1.398692 TGATCGATGGATGTGACGGA 58.601 50.000 0.54 0.00 31.51 4.69
1544 1607 1.067060 TGATCGATGGATGTGACGGAC 59.933 52.381 0.54 0.00 31.51 4.79
1545 1608 1.067060 GATCGATGGATGTGACGGACA 59.933 52.381 0.54 0.00 39.53 4.02
1546 1609 0.892063 TCGATGGATGTGACGGACAA 59.108 50.000 0.00 0.00 38.36 3.18
1547 1610 1.480545 TCGATGGATGTGACGGACAAT 59.519 47.619 0.00 0.00 38.36 2.71
1548 1611 2.691011 TCGATGGATGTGACGGACAATA 59.309 45.455 0.00 0.00 38.36 1.90
1549 1612 2.794910 CGATGGATGTGACGGACAATAC 59.205 50.000 0.00 0.00 38.36 1.89
1550 1613 3.490933 CGATGGATGTGACGGACAATACT 60.491 47.826 0.00 0.00 38.36 2.12
1551 1614 3.973206 TGGATGTGACGGACAATACTT 57.027 42.857 0.00 0.00 38.36 2.24
1552 1615 3.595173 TGGATGTGACGGACAATACTTG 58.405 45.455 0.00 0.00 38.36 3.16
1553 1616 2.351726 GGATGTGACGGACAATACTTGC 59.648 50.000 0.00 0.00 38.36 4.01
1554 1617 2.831685 TGTGACGGACAATACTTGCT 57.168 45.000 0.00 0.00 0.00 3.91
1555 1618 3.120321 TGTGACGGACAATACTTGCTT 57.880 42.857 0.00 0.00 0.00 3.91
1556 1619 4.260139 TGTGACGGACAATACTTGCTTA 57.740 40.909 0.00 0.00 0.00 3.09
1557 1620 4.633175 TGTGACGGACAATACTTGCTTAA 58.367 39.130 0.00 0.00 0.00 1.85
1558 1621 5.057819 TGTGACGGACAATACTTGCTTAAA 58.942 37.500 0.00 0.00 0.00 1.52
1559 1622 5.049954 TGTGACGGACAATACTTGCTTAAAC 60.050 40.000 0.00 0.00 0.00 2.01
1560 1623 4.453136 TGACGGACAATACTTGCTTAAACC 59.547 41.667 0.00 0.00 0.00 3.27
1561 1624 4.648651 ACGGACAATACTTGCTTAAACCT 58.351 39.130 0.00 0.00 0.00 3.50
1562 1625 5.797051 ACGGACAATACTTGCTTAAACCTA 58.203 37.500 0.00 0.00 0.00 3.08
1563 1626 5.873164 ACGGACAATACTTGCTTAAACCTAG 59.127 40.000 0.00 0.00 0.00 3.02
1564 1627 5.220605 CGGACAATACTTGCTTAAACCTAGC 60.221 44.000 0.00 0.00 39.10 3.42
1565 1628 5.646360 GGACAATACTTGCTTAAACCTAGCA 59.354 40.000 0.00 0.00 46.26 3.49
1570 1633 2.489938 TGCTTAAACCTAGCACCCTG 57.510 50.000 0.00 0.00 43.30 4.45
1571 1634 1.702957 TGCTTAAACCTAGCACCCTGT 59.297 47.619 0.00 0.00 43.30 4.00
1572 1635 2.107552 TGCTTAAACCTAGCACCCTGTT 59.892 45.455 0.00 0.00 43.30 3.16
1573 1636 2.488153 GCTTAAACCTAGCACCCTGTTG 59.512 50.000 0.00 0.00 38.51 3.33
1574 1637 2.194201 TAAACCTAGCACCCTGTTGC 57.806 50.000 0.00 0.00 43.34 4.17
1575 1638 0.539669 AAACCTAGCACCCTGTTGCC 60.540 55.000 0.00 0.00 44.14 4.52
1576 1639 1.427072 AACCTAGCACCCTGTTGCCT 61.427 55.000 0.00 0.00 44.14 4.75
1577 1640 1.380302 CCTAGCACCCTGTTGCCTT 59.620 57.895 0.00 0.00 44.14 4.35
1578 1641 0.962356 CCTAGCACCCTGTTGCCTTG 60.962 60.000 0.00 0.00 44.14 3.61
1579 1642 1.589716 CTAGCACCCTGTTGCCTTGC 61.590 60.000 0.00 0.00 44.14 4.01
1580 1643 2.067932 TAGCACCCTGTTGCCTTGCT 62.068 55.000 0.00 0.00 44.14 3.91
1581 1644 2.501602 GCACCCTGTTGCCTTGCTT 61.502 57.895 0.00 0.00 36.42 3.91
1582 1645 2.031674 GCACCCTGTTGCCTTGCTTT 62.032 55.000 0.00 0.00 36.42 3.51
1583 1646 0.465287 CACCCTGTTGCCTTGCTTTT 59.535 50.000 0.00 0.00 0.00 2.27
1584 1647 0.752658 ACCCTGTTGCCTTGCTTTTC 59.247 50.000 0.00 0.00 0.00 2.29
1585 1648 0.752054 CCCTGTTGCCTTGCTTTTCA 59.248 50.000 0.00 0.00 0.00 2.69
1586 1649 1.345415 CCCTGTTGCCTTGCTTTTCAT 59.655 47.619 0.00 0.00 0.00 2.57
1587 1650 2.611224 CCCTGTTGCCTTGCTTTTCATC 60.611 50.000 0.00 0.00 0.00 2.92
1588 1651 2.611224 CCTGTTGCCTTGCTTTTCATCC 60.611 50.000 0.00 0.00 0.00 3.51
1589 1652 2.036217 CTGTTGCCTTGCTTTTCATCCA 59.964 45.455 0.00 0.00 0.00 3.41
1590 1653 2.036217 TGTTGCCTTGCTTTTCATCCAG 59.964 45.455 0.00 0.00 0.00 3.86
1591 1654 0.604578 TGCCTTGCTTTTCATCCAGC 59.395 50.000 0.00 0.00 36.49 4.85
1592 1655 0.108472 GCCTTGCTTTTCATCCAGCC 60.108 55.000 0.00 0.00 34.91 4.85
1593 1656 0.171903 CCTTGCTTTTCATCCAGCCG 59.828 55.000 0.00 0.00 34.91 5.52
1597 1660 1.308069 GCTTTTCATCCAGCCGCTCA 61.308 55.000 0.00 0.00 0.00 4.26
1605 1668 1.667236 TCCAGCCGCTCATGTAATTG 58.333 50.000 0.00 0.00 0.00 2.32
1606 1669 1.209261 TCCAGCCGCTCATGTAATTGA 59.791 47.619 0.00 0.00 0.00 2.57
1614 1677 4.816385 CCGCTCATGTAATTGATGTACCTT 59.184 41.667 0.00 0.00 0.00 3.50
1620 1683 6.533723 TCATGTAATTGATGTACCTTCGACAC 59.466 38.462 0.00 0.00 0.00 3.67
1633 1717 3.059597 CCTTCGACACAAAGTTGCTACTG 60.060 47.826 0.36 0.00 34.01 2.74
1636 1720 4.046462 TCGACACAAAGTTGCTACTGTAC 58.954 43.478 0.36 0.00 34.01 2.90
1660 1744 0.911769 TGGTCATCAGGTCATGGTCC 59.088 55.000 0.00 0.00 0.00 4.46
1671 1755 1.448540 CATGGTCCGCTGGTCACTC 60.449 63.158 0.00 0.00 0.00 3.51
1684 1768 4.623886 GCTGGTCACTCCATCACTAAATGA 60.624 45.833 0.00 0.00 46.12 2.57
1717 1802 3.780925 GCAAACAGATGCCACTCAC 57.219 52.632 0.00 0.00 40.49 3.51
1718 1803 1.242076 GCAAACAGATGCCACTCACT 58.758 50.000 0.00 0.00 40.49 3.41
1719 1804 1.198637 GCAAACAGATGCCACTCACTC 59.801 52.381 0.00 0.00 40.49 3.51
1720 1805 2.497138 CAAACAGATGCCACTCACTCA 58.503 47.619 0.00 0.00 0.00 3.41
1721 1806 2.469274 AACAGATGCCACTCACTCAG 57.531 50.000 0.00 0.00 0.00 3.35
1782 1867 2.691409 TAAGAGCCCATTCAAGACCG 57.309 50.000 0.00 0.00 0.00 4.79
1846 1931 2.480555 CGCGTGGACCTTCAATGC 59.519 61.111 0.00 0.00 0.00 3.56
1903 1988 0.877649 CGCGTGATGGAGCTATGCTT 60.878 55.000 0.00 0.00 39.88 3.91
1904 1989 1.303309 GCGTGATGGAGCTATGCTTT 58.697 50.000 0.00 0.00 39.88 3.51
1905 1990 2.483876 GCGTGATGGAGCTATGCTTTA 58.516 47.619 0.00 0.00 39.88 1.85
1906 1991 2.478134 GCGTGATGGAGCTATGCTTTAG 59.522 50.000 0.00 0.00 39.88 1.85
1907 1992 3.062763 CGTGATGGAGCTATGCTTTAGG 58.937 50.000 0.00 0.00 39.88 2.69
1908 1993 3.243873 CGTGATGGAGCTATGCTTTAGGA 60.244 47.826 0.00 0.00 39.88 2.94
1909 1994 4.562347 CGTGATGGAGCTATGCTTTAGGAT 60.562 45.833 0.00 0.00 39.88 3.24
1910 1995 5.312079 GTGATGGAGCTATGCTTTAGGATT 58.688 41.667 0.00 0.00 39.88 3.01
1911 1996 5.767168 GTGATGGAGCTATGCTTTAGGATTT 59.233 40.000 0.00 0.00 39.88 2.17
1912 1997 6.000219 TGATGGAGCTATGCTTTAGGATTTC 59.000 40.000 0.00 0.00 39.88 2.17
1913 1998 4.380531 TGGAGCTATGCTTTAGGATTTCG 58.619 43.478 0.00 0.00 39.88 3.46
1914 1999 4.141711 TGGAGCTATGCTTTAGGATTTCGT 60.142 41.667 0.00 0.00 39.88 3.85
1915 2000 5.069914 TGGAGCTATGCTTTAGGATTTCGTA 59.930 40.000 0.00 0.00 39.88 3.43
1916 2001 5.635700 GGAGCTATGCTTTAGGATTTCGTAG 59.364 44.000 0.00 0.00 39.88 3.51
1917 2002 6.163135 AGCTATGCTTTAGGATTTCGTAGT 57.837 37.500 0.00 0.00 33.89 2.73
1918 2003 6.217294 AGCTATGCTTTAGGATTTCGTAGTC 58.783 40.000 0.00 0.00 33.89 2.59
1919 2004 5.405873 GCTATGCTTTAGGATTTCGTAGTCC 59.594 44.000 0.00 0.00 34.64 3.85
1920 2005 4.811969 TGCTTTAGGATTTCGTAGTCCA 57.188 40.909 6.37 0.00 36.96 4.02
1921 2006 4.501071 TGCTTTAGGATTTCGTAGTCCAC 58.499 43.478 6.37 0.00 36.96 4.02
1922 2007 4.020928 TGCTTTAGGATTTCGTAGTCCACA 60.021 41.667 6.37 0.00 36.96 4.17
1923 2008 4.567159 GCTTTAGGATTTCGTAGTCCACAG 59.433 45.833 6.37 0.53 36.96 3.66
1924 2009 4.730949 TTAGGATTTCGTAGTCCACAGG 57.269 45.455 6.37 0.00 36.96 4.00
1925 2010 2.816411 AGGATTTCGTAGTCCACAGGA 58.184 47.619 6.37 0.00 36.96 3.86
1926 2011 2.761208 AGGATTTCGTAGTCCACAGGAG 59.239 50.000 6.37 0.00 36.96 3.69
1927 2012 2.758979 GGATTTCGTAGTCCACAGGAGA 59.241 50.000 0.00 0.00 34.57 3.71
1928 2013 3.385111 GGATTTCGTAGTCCACAGGAGAT 59.615 47.826 0.00 0.00 34.57 2.75
1929 2014 3.868757 TTTCGTAGTCCACAGGAGATG 57.131 47.619 0.00 0.00 29.39 2.90
1930 2015 1.103803 TCGTAGTCCACAGGAGATGC 58.896 55.000 0.00 0.00 29.39 3.91
1931 2016 1.107114 CGTAGTCCACAGGAGATGCT 58.893 55.000 0.00 0.00 29.39 3.79
1957 2042 3.385111 GGATTTCGTAGTCCACAGGAGAT 59.615 47.826 0.00 0.00 34.57 2.75
2012 2097 1.234821 GGCGTGGTTTCTCAACATCA 58.765 50.000 0.00 0.00 34.15 3.07
2045 2130 1.344438 TCACAGCTCTCACCGTTCATT 59.656 47.619 0.00 0.00 0.00 2.57
2046 2131 2.146342 CACAGCTCTCACCGTTCATTT 58.854 47.619 0.00 0.00 0.00 2.32
2047 2132 2.549754 CACAGCTCTCACCGTTCATTTT 59.450 45.455 0.00 0.00 0.00 1.82
2048 2133 3.003689 CACAGCTCTCACCGTTCATTTTT 59.996 43.478 0.00 0.00 0.00 1.94
2072 2157 6.606234 TTTTAAAACGGGCAAAAGATTTCC 57.394 33.333 0.00 0.00 0.00 3.13
2073 2158 2.831685 AAACGGGCAAAAGATTTCCC 57.168 45.000 0.00 0.00 38.52 3.97
2074 2159 1.710816 AACGGGCAAAAGATTTCCCA 58.289 45.000 0.00 0.00 41.66 4.37
2075 2160 0.966179 ACGGGCAAAAGATTTCCCAC 59.034 50.000 0.00 0.00 41.66 4.61
2076 2161 0.965439 CGGGCAAAAGATTTCCCACA 59.035 50.000 0.00 0.00 41.66 4.17
2077 2162 1.550072 CGGGCAAAAGATTTCCCACAT 59.450 47.619 0.00 0.00 41.66 3.21
2078 2163 2.757868 CGGGCAAAAGATTTCCCACATA 59.242 45.455 0.00 0.00 41.66 2.29
2079 2164 3.384467 CGGGCAAAAGATTTCCCACATAT 59.616 43.478 0.00 0.00 41.66 1.78
2080 2165 4.582656 CGGGCAAAAGATTTCCCACATATA 59.417 41.667 0.00 0.00 41.66 0.86
2081 2166 5.243730 CGGGCAAAAGATTTCCCACATATAT 59.756 40.000 0.00 0.00 41.66 0.86
2082 2167 6.239289 CGGGCAAAAGATTTCCCACATATATT 60.239 38.462 0.00 0.00 41.66 1.28
2083 2168 7.040062 CGGGCAAAAGATTTCCCACATATATTA 60.040 37.037 0.00 0.00 41.66 0.98
2084 2169 8.646900 GGGCAAAAGATTTCCCACATATATTAA 58.353 33.333 0.00 0.00 41.27 1.40
2113 2198 9.832445 AAGAGAGAATAGAGTTTGTGTTACAAA 57.168 29.630 3.20 3.20 44.91 2.83
2141 2226 8.778059 ACCACTTAATAATACAGGGAAGAATCA 58.222 33.333 0.00 0.00 0.00 2.57
2142 2227 9.057089 CCACTTAATAATACAGGGAAGAATCAC 57.943 37.037 0.00 0.00 0.00 3.06
2143 2228 9.838339 CACTTAATAATACAGGGAAGAATCACT 57.162 33.333 0.00 0.00 41.07 3.41
2147 2232 5.622346 AATACAGGGAAGAATCACTCTCC 57.378 43.478 0.00 0.00 37.13 3.71
2148 2233 2.192263 ACAGGGAAGAATCACTCTCCC 58.808 52.381 0.00 0.00 37.13 4.30
2149 2234 1.137872 CAGGGAAGAATCACTCTCCCG 59.862 57.143 0.41 0.00 43.80 5.14
2150 2235 0.466124 GGGAAGAATCACTCTCCCGG 59.534 60.000 0.00 0.00 36.77 5.73
2151 2236 0.179070 GGAAGAATCACTCTCCCGGC 60.179 60.000 0.00 0.00 31.02 6.13
2152 2237 0.537188 GAAGAATCACTCTCCCGGCA 59.463 55.000 0.00 0.00 31.02 5.69
2153 2238 1.139853 GAAGAATCACTCTCCCGGCAT 59.860 52.381 0.00 0.00 31.02 4.40
2154 2239 0.467384 AGAATCACTCTCCCGGCATG 59.533 55.000 0.00 0.00 0.00 4.06
2155 2240 0.465705 GAATCACTCTCCCGGCATGA 59.534 55.000 0.00 0.00 0.00 3.07
2156 2241 1.071385 GAATCACTCTCCCGGCATGAT 59.929 52.381 0.00 0.00 0.00 2.45
2157 2242 0.395686 ATCACTCTCCCGGCATGATG 59.604 55.000 0.00 0.00 0.00 3.07
2158 2243 1.227764 CACTCTCCCGGCATGATGG 60.228 63.158 0.00 0.00 0.00 3.51
2159 2244 1.383109 ACTCTCCCGGCATGATGGA 60.383 57.895 0.00 0.00 0.00 3.41
2160 2245 1.070445 CTCTCCCGGCATGATGGAC 59.930 63.158 0.00 0.00 0.00 4.02
2161 2246 2.111878 CTCCCGGCATGATGGACC 59.888 66.667 0.00 0.00 0.00 4.46
2162 2247 3.482232 CTCCCGGCATGATGGACCC 62.482 68.421 0.00 0.00 0.00 4.46
2163 2248 3.492353 CCCGGCATGATGGACCCT 61.492 66.667 0.00 0.00 0.00 4.34
2164 2249 2.146724 CCCGGCATGATGGACCCTA 61.147 63.158 0.00 0.00 0.00 3.53
2165 2250 1.372683 CCGGCATGATGGACCCTAG 59.627 63.158 0.00 0.00 0.00 3.02
2166 2251 1.410850 CCGGCATGATGGACCCTAGT 61.411 60.000 0.00 0.00 0.00 2.57
2167 2252 0.469917 CGGCATGATGGACCCTAGTT 59.530 55.000 0.00 0.00 0.00 2.24
2168 2253 1.134098 CGGCATGATGGACCCTAGTTT 60.134 52.381 0.00 0.00 0.00 2.66
2169 2254 2.683742 CGGCATGATGGACCCTAGTTTT 60.684 50.000 0.00 0.00 0.00 2.43
2170 2255 3.365472 GGCATGATGGACCCTAGTTTTT 58.635 45.455 0.00 0.00 0.00 1.94
2184 2269 3.122323 TTTTTAGCTCCGGCGGCG 61.122 61.111 26.12 26.12 44.37 6.46
2185 2270 3.592856 TTTTTAGCTCCGGCGGCGA 62.593 57.895 34.49 17.57 44.37 5.54
2186 2271 4.807039 TTTAGCTCCGGCGGCGAC 62.807 66.667 34.49 20.98 44.37 5.19
2197 2282 2.809601 CGGCGACCCAGAACGAAG 60.810 66.667 0.00 0.00 0.00 3.79
2198 2283 3.119096 GGCGACCCAGAACGAAGC 61.119 66.667 0.00 0.00 0.00 3.86
2199 2284 3.119096 GCGACCCAGAACGAAGCC 61.119 66.667 0.00 0.00 0.00 4.35
2200 2285 2.657237 CGACCCAGAACGAAGCCT 59.343 61.111 0.00 0.00 0.00 4.58
2201 2286 1.446272 CGACCCAGAACGAAGCCTC 60.446 63.158 0.00 0.00 0.00 4.70
2202 2287 1.079057 GACCCAGAACGAAGCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
2203 2288 2.269241 CCCAGAACGAAGCCTCCC 59.731 66.667 0.00 0.00 0.00 4.30
2204 2289 2.294078 CCCAGAACGAAGCCTCCCT 61.294 63.158 0.00 0.00 0.00 4.20
2205 2290 1.679898 CCAGAACGAAGCCTCCCTT 59.320 57.895 0.00 0.00 36.19 3.95
2206 2291 0.036875 CCAGAACGAAGCCTCCCTTT 59.963 55.000 0.00 0.00 32.78 3.11
2207 2292 1.545651 CCAGAACGAAGCCTCCCTTTT 60.546 52.381 0.00 0.00 32.78 2.27
2208 2293 1.537202 CAGAACGAAGCCTCCCTTTTG 59.463 52.381 0.00 0.00 32.78 2.44
2209 2294 1.420138 AGAACGAAGCCTCCCTTTTGA 59.580 47.619 0.00 0.00 32.78 2.69
2210 2295 2.040412 AGAACGAAGCCTCCCTTTTGAT 59.960 45.455 0.00 0.00 32.78 2.57
2211 2296 1.826385 ACGAAGCCTCCCTTTTGATG 58.174 50.000 0.00 0.00 32.78 3.07
2212 2297 1.073923 ACGAAGCCTCCCTTTTGATGT 59.926 47.619 0.00 0.00 32.78 3.06
2213 2298 2.162681 CGAAGCCTCCCTTTTGATGTT 58.837 47.619 0.00 0.00 32.78 2.71
2214 2299 2.095059 CGAAGCCTCCCTTTTGATGTTG 60.095 50.000 0.00 0.00 32.78 3.33
2215 2300 2.683211 AGCCTCCCTTTTGATGTTGT 57.317 45.000 0.00 0.00 0.00 3.32
2216 2301 2.519013 AGCCTCCCTTTTGATGTTGTC 58.481 47.619 0.00 0.00 0.00 3.18
2217 2302 2.158475 AGCCTCCCTTTTGATGTTGTCA 60.158 45.455 0.00 0.00 34.25 3.58
2218 2303 2.627699 GCCTCCCTTTTGATGTTGTCAA 59.372 45.455 0.00 0.00 44.87 3.18
2219 2304 3.305608 GCCTCCCTTTTGATGTTGTCAAG 60.306 47.826 0.00 0.00 46.85 3.02
2220 2305 3.256631 CCTCCCTTTTGATGTTGTCAAGG 59.743 47.826 0.00 0.00 46.85 3.61
2221 2306 4.144297 CTCCCTTTTGATGTTGTCAAGGA 58.856 43.478 0.00 0.00 46.85 3.36
2222 2307 4.144297 TCCCTTTTGATGTTGTCAAGGAG 58.856 43.478 0.00 0.00 46.85 3.69
2223 2308 4.141274 TCCCTTTTGATGTTGTCAAGGAGA 60.141 41.667 0.00 0.00 46.85 3.71
2224 2309 4.584325 CCCTTTTGATGTTGTCAAGGAGAA 59.416 41.667 0.00 0.00 46.85 2.87
2225 2310 5.244626 CCCTTTTGATGTTGTCAAGGAGAAT 59.755 40.000 0.00 0.00 46.85 2.40
2226 2311 6.385033 CCTTTTGATGTTGTCAAGGAGAATC 58.615 40.000 0.00 0.00 46.85 2.52
2227 2312 5.611796 TTTGATGTTGTCAAGGAGAATCG 57.388 39.130 0.00 0.00 46.85 3.34
2228 2313 4.271696 TGATGTTGTCAAGGAGAATCGT 57.728 40.909 0.00 0.00 31.30 3.73
2229 2314 5.400066 TGATGTTGTCAAGGAGAATCGTA 57.600 39.130 0.00 0.00 31.30 3.43
2230 2315 5.410924 TGATGTTGTCAAGGAGAATCGTAG 58.589 41.667 0.00 0.00 31.30 3.51
2231 2316 4.188247 TGTTGTCAAGGAGAATCGTAGG 57.812 45.455 0.00 0.00 34.37 3.18
2232 2317 2.930682 GTTGTCAAGGAGAATCGTAGGC 59.069 50.000 0.00 0.00 34.37 3.93
2233 2318 1.134367 TGTCAAGGAGAATCGTAGGCG 59.866 52.381 0.00 0.00 34.37 5.52
2234 2319 0.744874 TCAAGGAGAATCGTAGGCGG 59.255 55.000 0.00 0.00 38.89 6.13
2235 2320 0.744874 CAAGGAGAATCGTAGGCGGA 59.255 55.000 0.00 0.00 38.89 5.54
2236 2321 1.033574 AAGGAGAATCGTAGGCGGAG 58.966 55.000 0.00 0.00 38.89 4.63
2249 2334 4.093952 CGGAGCAGCCTTGTTGCG 62.094 66.667 0.00 0.00 44.23 4.85
2250 2335 3.741476 GGAGCAGCCTTGTTGCGG 61.741 66.667 0.00 0.00 44.23 5.69
2251 2336 2.669569 GAGCAGCCTTGTTGCGGA 60.670 61.111 0.00 0.00 44.23 5.54
2252 2337 2.203337 AGCAGCCTTGTTGCGGAA 60.203 55.556 0.00 0.00 44.23 4.30
2253 2338 1.589716 GAGCAGCCTTGTTGCGGAAT 61.590 55.000 0.00 0.00 44.23 3.01
2254 2339 0.322456 AGCAGCCTTGTTGCGGAATA 60.322 50.000 0.00 0.00 44.23 1.75
2255 2340 0.179163 GCAGCCTTGTTGCGGAATAC 60.179 55.000 0.00 0.00 36.02 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.996631 GGAGATGTTCCAGCTGTTGAT 58.003 47.619 13.81 0.00 46.01 2.57
18 19 2.045926 GCTGCCGTGGGAGATGTT 60.046 61.111 12.01 0.00 35.50 2.71
36 37 0.754957 CAGTCATCCCGAGCTCCTCT 60.755 60.000 8.47 0.00 0.00 3.69
49 50 1.532604 TTCCTCGCCGTGTCAGTCAT 61.533 55.000 0.00 0.00 0.00 3.06
149 151 5.450818 TCACCCTATAAAAGCAAGGACAT 57.549 39.130 0.00 0.00 31.64 3.06
239 241 8.087750 ACAACAAGAATGAGAAAAGAAAACACA 58.912 29.630 0.00 0.00 0.00 3.72
300 303 7.539034 AGACATTAAGGCCAAAACATTAACT 57.461 32.000 5.01 0.00 0.00 2.24
303 306 6.162777 GCAAGACATTAAGGCCAAAACATTA 58.837 36.000 5.01 0.00 0.00 1.90
307 310 3.988819 TGCAAGACATTAAGGCCAAAAC 58.011 40.909 5.01 0.00 0.00 2.43
385 388 1.692411 AACCTTCCAGCCTCACAAAC 58.308 50.000 0.00 0.00 0.00 2.93
387 390 2.031120 CAAAACCTTCCAGCCTCACAA 58.969 47.619 0.00 0.00 0.00 3.33
428 438 2.983803 GCGAATTTTTGCAATACCGTGT 59.016 40.909 0.00 0.00 37.52 4.49
480 490 2.361104 GGTTCAGCATGGCCGGAA 60.361 61.111 5.05 0.00 36.16 4.30
503 513 7.937649 ACAACTACTTTTATGGACCAAGAAAC 58.062 34.615 0.00 0.00 0.00 2.78
506 516 9.802039 AAATACAACTACTTTTATGGACCAAGA 57.198 29.630 0.00 0.00 0.00 3.02
510 520 7.148373 TGCGAAATACAACTACTTTTATGGACC 60.148 37.037 0.00 0.00 0.00 4.46
512 522 7.908827 TGCGAAATACAACTACTTTTATGGA 57.091 32.000 0.00 0.00 0.00 3.41
516 526 9.439500 ACCTTATGCGAAATACAACTACTTTTA 57.561 29.630 0.00 0.00 0.00 1.52
523 535 7.988599 TGGTATAACCTTATGCGAAATACAACT 59.011 33.333 0.00 0.00 39.58 3.16
547 559 9.810545 TTTTGGAGATTAAAACTTACAACTTGG 57.189 29.630 0.00 0.00 0.00 3.61
589 601 8.045176 AGTGCTGAAACTGGATAGAAATAAAC 57.955 34.615 0.00 0.00 0.00 2.01
632 645 3.719173 TGGGTTTTGGCGAGTTTTTAG 57.281 42.857 0.00 0.00 0.00 1.85
643 656 5.857268 AGATGAGTTTTGAATGGGTTTTGG 58.143 37.500 0.00 0.00 0.00 3.28
673 686 9.844257 TTTGTATCTTTTGAATCAAAAACCCAT 57.156 25.926 19.95 12.47 41.77 4.00
710 723 4.948847 AGCTACTTTTCTTTGGGCTTTTG 58.051 39.130 0.00 0.00 0.00 2.44
748 761 2.560504 ACAAGAGATTTGTGACACGCA 58.439 42.857 0.22 0.00 0.00 5.24
834 877 1.373435 CCACCCTTGCGGAAGTACA 59.627 57.895 15.93 0.00 34.64 2.90
835 878 2.038837 GCCACCCTTGCGGAAGTAC 61.039 63.158 15.93 0.00 34.64 2.73
836 879 1.774894 AAGCCACCCTTGCGGAAGTA 61.775 55.000 15.93 0.00 34.64 2.24
846 889 2.116125 GTCCTTGCAAGCCACCCT 59.884 61.111 21.43 0.00 0.00 4.34
852 895 3.435186 GGAGGCGTCCTTGCAAGC 61.435 66.667 21.43 10.43 40.17 4.01
918 962 0.393673 TGGTGGTGGAAGTGTGTGTG 60.394 55.000 0.00 0.00 0.00 3.82
919 963 0.393808 GTGGTGGTGGAAGTGTGTGT 60.394 55.000 0.00 0.00 0.00 3.72
1172 1222 3.909258 CTGGAGTACGCGCGGTTGT 62.909 63.158 35.22 15.90 0.00 3.32
1178 1228 0.935366 GATGTAGCTGGAGTACGCGC 60.935 60.000 5.73 0.00 0.00 6.86
1315 1365 7.064064 GTGGTAGTACGTTACGTATTAGTAGC 58.936 42.308 20.52 16.14 44.12 3.58
1338 1395 1.022735 ATGGTAGGAGCTCGTACGTG 58.977 55.000 30.16 14.31 37.90 4.49
1429 1492 5.287752 ACGATACATGAACACACGATTGTAC 59.712 40.000 0.00 0.00 33.30 2.90
1455 1518 4.786068 CGTACACACCATTTTATTCTTGCG 59.214 41.667 0.00 0.00 0.00 4.85
1481 1544 0.901827 TACGCAGAGGCTGGATCAAA 59.098 50.000 0.00 0.00 38.10 2.69
1552 1615 2.488153 CAACAGGGTGCTAGGTTTAAGC 59.512 50.000 0.00 0.00 40.50 3.09
1553 1616 2.488153 GCAACAGGGTGCTAGGTTTAAG 59.512 50.000 1.23 0.00 41.51 1.85
1554 1617 2.510613 GCAACAGGGTGCTAGGTTTAA 58.489 47.619 1.23 0.00 41.51 1.52
1555 1618 1.271707 GGCAACAGGGTGCTAGGTTTA 60.272 52.381 9.44 0.00 44.31 2.01
1556 1619 0.539669 GGCAACAGGGTGCTAGGTTT 60.540 55.000 9.44 0.00 44.31 3.27
1557 1620 1.074951 GGCAACAGGGTGCTAGGTT 59.925 57.895 9.44 0.00 44.31 3.50
1558 1621 1.427072 AAGGCAACAGGGTGCTAGGT 61.427 55.000 9.44 0.00 44.31 3.08
1559 1622 0.962356 CAAGGCAACAGGGTGCTAGG 60.962 60.000 9.44 0.00 44.31 3.02
1560 1623 1.589716 GCAAGGCAACAGGGTGCTAG 61.590 60.000 9.44 0.96 44.31 3.42
1561 1624 1.603455 GCAAGGCAACAGGGTGCTA 60.603 57.895 9.44 0.00 44.31 3.49
1562 1625 2.914097 GCAAGGCAACAGGGTGCT 60.914 61.111 9.44 0.00 44.31 4.40
1563 1626 2.031674 AAAGCAAGGCAACAGGGTGC 62.032 55.000 0.00 0.00 44.14 5.01
1564 1627 0.465287 AAAAGCAAGGCAACAGGGTG 59.535 50.000 0.00 0.00 41.41 4.61
1565 1628 0.752658 GAAAAGCAAGGCAACAGGGT 59.247 50.000 0.00 0.00 41.41 4.34
1566 1629 0.752054 TGAAAAGCAAGGCAACAGGG 59.248 50.000 0.00 0.00 41.41 4.45
1567 1630 2.611224 GGATGAAAAGCAAGGCAACAGG 60.611 50.000 0.00 0.00 41.41 4.00
1568 1631 2.036217 TGGATGAAAAGCAAGGCAACAG 59.964 45.455 0.00 0.00 41.41 3.16
1569 1632 2.036217 CTGGATGAAAAGCAAGGCAACA 59.964 45.455 0.00 0.00 41.41 3.33
1570 1633 2.680577 CTGGATGAAAAGCAAGGCAAC 58.319 47.619 0.00 0.00 0.00 4.17
1571 1634 1.001181 GCTGGATGAAAAGCAAGGCAA 59.999 47.619 0.00 0.00 39.31 4.52
1572 1635 0.604578 GCTGGATGAAAAGCAAGGCA 59.395 50.000 0.00 0.00 39.31 4.75
1573 1636 0.108472 GGCTGGATGAAAAGCAAGGC 60.108 55.000 0.00 0.00 41.36 4.35
1574 1637 0.171903 CGGCTGGATGAAAAGCAAGG 59.828 55.000 0.00 0.00 41.36 3.61
1575 1638 0.457337 GCGGCTGGATGAAAAGCAAG 60.457 55.000 0.00 0.00 41.36 4.01
1576 1639 0.895100 AGCGGCTGGATGAAAAGCAA 60.895 50.000 0.00 0.00 41.36 3.91
1577 1640 1.303561 AGCGGCTGGATGAAAAGCA 60.304 52.632 0.00 0.00 41.36 3.91
1578 1641 1.308069 TGAGCGGCTGGATGAAAAGC 61.308 55.000 7.50 0.00 38.76 3.51
1579 1642 1.065102 CATGAGCGGCTGGATGAAAAG 59.935 52.381 7.50 0.00 0.00 2.27
1580 1643 1.097232 CATGAGCGGCTGGATGAAAA 58.903 50.000 7.50 0.00 0.00 2.29
1581 1644 0.035152 ACATGAGCGGCTGGATGAAA 60.035 50.000 20.10 0.00 0.00 2.69
1582 1645 0.829990 TACATGAGCGGCTGGATGAA 59.170 50.000 20.10 0.00 0.00 2.57
1583 1646 0.829990 TTACATGAGCGGCTGGATGA 59.170 50.000 20.10 6.27 0.00 2.92
1584 1647 1.888215 ATTACATGAGCGGCTGGATG 58.112 50.000 7.50 11.96 0.00 3.51
1585 1648 2.158769 TCAATTACATGAGCGGCTGGAT 60.159 45.455 7.50 0.00 0.00 3.41
1586 1649 1.209261 TCAATTACATGAGCGGCTGGA 59.791 47.619 7.50 0.00 0.00 3.86
1587 1650 1.667236 TCAATTACATGAGCGGCTGG 58.333 50.000 7.50 0.00 0.00 4.85
1588 1651 2.615447 ACATCAATTACATGAGCGGCTG 59.385 45.455 7.50 0.00 31.76 4.85
1589 1652 2.923121 ACATCAATTACATGAGCGGCT 58.077 42.857 0.00 0.00 31.76 5.52
1590 1653 3.058914 GGTACATCAATTACATGAGCGGC 60.059 47.826 0.00 0.00 31.76 6.53
1591 1654 4.380531 AGGTACATCAATTACATGAGCGG 58.619 43.478 0.00 0.00 31.76 5.52
1592 1655 5.332581 CGAAGGTACATCAATTACATGAGCG 60.333 44.000 0.00 0.00 31.76 5.03
1593 1656 5.753438 TCGAAGGTACATCAATTACATGAGC 59.247 40.000 0.00 0.00 31.76 4.26
1597 1660 6.403049 TGTGTCGAAGGTACATCAATTACAT 58.597 36.000 0.00 0.00 0.00 2.29
1605 1668 4.610680 GCAACTTTGTGTCGAAGGTACATC 60.611 45.833 0.00 0.00 0.00 3.06
1606 1669 3.250040 GCAACTTTGTGTCGAAGGTACAT 59.750 43.478 0.00 0.00 0.00 2.29
1614 1677 3.173668 ACAGTAGCAACTTTGTGTCGA 57.826 42.857 0.00 0.00 31.97 4.20
1620 1683 4.319766 CCAAGCAGTACAGTAGCAACTTTG 60.320 45.833 0.00 0.00 31.97 2.77
1633 1717 2.028112 TGACCTGATGACCAAGCAGTAC 60.028 50.000 0.00 0.00 0.00 2.73
1636 1720 2.014857 CATGACCTGATGACCAAGCAG 58.985 52.381 0.00 0.00 0.00 4.24
1671 1755 8.820933 CATACAGTACTGTTCATTTAGTGATGG 58.179 37.037 32.15 8.05 41.83 3.51
1684 1768 4.072131 CTGTTTGCCCATACAGTACTGTT 58.928 43.478 32.15 17.44 41.83 3.16
1720 1805 1.948104 TCAACAACAGTGTAAGCGCT 58.052 45.000 2.64 2.64 36.80 5.92
1721 1806 2.032030 ACATCAACAACAGTGTAAGCGC 60.032 45.455 0.00 0.00 36.80 5.92
1755 1840 3.711863 TGAATGGGCTCTTAATTGGCTT 58.288 40.909 0.00 0.00 0.00 4.35
1782 1867 3.179443 TGGCTCGACAGGATTATGTTC 57.821 47.619 0.00 0.00 32.25 3.18
1846 1931 1.153823 GAGTCATGACGGTCACGGG 60.154 63.158 19.85 6.47 46.48 5.28
1903 1988 4.346730 TCCTGTGGACTACGAAATCCTAA 58.653 43.478 0.00 0.00 35.86 2.69
1904 1989 3.952323 CTCCTGTGGACTACGAAATCCTA 59.048 47.826 0.00 0.00 35.86 2.94
1905 1990 2.761208 CTCCTGTGGACTACGAAATCCT 59.239 50.000 0.00 0.00 35.86 3.24
1906 1991 2.758979 TCTCCTGTGGACTACGAAATCC 59.241 50.000 0.00 0.00 35.37 3.01
1907 1992 4.363999 CATCTCCTGTGGACTACGAAATC 58.636 47.826 0.00 0.00 0.00 2.17
1908 1993 3.430929 GCATCTCCTGTGGACTACGAAAT 60.431 47.826 0.00 0.00 0.00 2.17
1909 1994 2.094182 GCATCTCCTGTGGACTACGAAA 60.094 50.000 0.00 0.00 0.00 3.46
1910 1995 1.476891 GCATCTCCTGTGGACTACGAA 59.523 52.381 0.00 0.00 0.00 3.85
1911 1996 1.103803 GCATCTCCTGTGGACTACGA 58.896 55.000 0.00 0.00 0.00 3.43
1912 1997 1.107114 AGCATCTCCTGTGGACTACG 58.893 55.000 0.00 0.00 0.00 3.51
1913 1998 3.618690 AAAGCATCTCCTGTGGACTAC 57.381 47.619 0.00 0.00 0.00 2.73
1914 1999 3.706594 CCTAAAGCATCTCCTGTGGACTA 59.293 47.826 0.00 0.00 0.00 2.59
1915 2000 2.503356 CCTAAAGCATCTCCTGTGGACT 59.497 50.000 0.00 0.00 0.00 3.85
1916 2001 2.501723 TCCTAAAGCATCTCCTGTGGAC 59.498 50.000 0.00 0.00 0.00 4.02
1917 2002 2.832838 TCCTAAAGCATCTCCTGTGGA 58.167 47.619 0.00 0.00 0.00 4.02
1918 2003 3.853355 ATCCTAAAGCATCTCCTGTGG 57.147 47.619 0.00 0.00 0.00 4.17
1919 2004 4.272018 CGAAATCCTAAAGCATCTCCTGTG 59.728 45.833 0.00 0.00 0.00 3.66
1920 2005 4.080863 ACGAAATCCTAAAGCATCTCCTGT 60.081 41.667 0.00 0.00 0.00 4.00
1921 2006 4.446371 ACGAAATCCTAAAGCATCTCCTG 58.554 43.478 0.00 0.00 0.00 3.86
1922 2007 4.762289 ACGAAATCCTAAAGCATCTCCT 57.238 40.909 0.00 0.00 0.00 3.69
1923 2008 5.602628 ACTACGAAATCCTAAAGCATCTCC 58.397 41.667 0.00 0.00 0.00 3.71
1924 2009 5.692654 GGACTACGAAATCCTAAAGCATCTC 59.307 44.000 0.00 0.00 31.75 2.75
1925 2010 5.128827 TGGACTACGAAATCCTAAAGCATCT 59.871 40.000 0.00 0.00 35.86 2.90
1926 2011 5.234543 GTGGACTACGAAATCCTAAAGCATC 59.765 44.000 0.00 0.00 35.86 3.91
1927 2012 5.116882 GTGGACTACGAAATCCTAAAGCAT 58.883 41.667 0.00 0.00 35.86 3.79
1928 2013 4.020928 TGTGGACTACGAAATCCTAAAGCA 60.021 41.667 0.00 0.00 35.86 3.91
1929 2014 4.501071 TGTGGACTACGAAATCCTAAAGC 58.499 43.478 0.00 0.00 35.86 3.51
1930 2015 5.105473 TCCTGTGGACTACGAAATCCTAAAG 60.105 44.000 0.00 0.00 35.86 1.85
1931 2016 4.773674 TCCTGTGGACTACGAAATCCTAAA 59.226 41.667 0.00 0.00 35.86 1.85
1957 2042 1.781025 GCAAAGCCACTGTGCGTGTA 61.781 55.000 1.29 0.00 42.20 2.90
2012 2097 7.308830 GGTGAGAGCTGTGAAAGTTCATATTTT 60.309 37.037 0.00 0.00 38.54 1.82
2048 2133 6.038382 GGGAAATCTTTTGCCCGTTTTAAAAA 59.962 34.615 1.31 0.00 41.15 1.94
2049 2134 5.527951 GGGAAATCTTTTGCCCGTTTTAAAA 59.472 36.000 0.00 0.00 41.15 1.52
2050 2135 5.057819 GGGAAATCTTTTGCCCGTTTTAAA 58.942 37.500 0.00 0.00 41.15 1.52
2051 2136 4.633175 GGGAAATCTTTTGCCCGTTTTAA 58.367 39.130 0.00 0.00 41.15 1.52
2052 2137 4.260139 GGGAAATCTTTTGCCCGTTTTA 57.740 40.909 0.00 0.00 41.15 1.52
2053 2138 3.120321 GGGAAATCTTTTGCCCGTTTT 57.880 42.857 0.00 0.00 41.15 2.43
2054 2139 2.831685 GGGAAATCTTTTGCCCGTTT 57.168 45.000 0.00 0.00 41.15 3.60
2087 2172 9.832445 TTTGTAACACAAACTCTATTCTCTCTT 57.168 29.630 0.45 0.00 42.55 2.85
2115 2200 8.778059 TGATTCTTCCCTGTATTATTAAGTGGT 58.222 33.333 0.00 0.00 0.00 4.16
2116 2201 9.057089 GTGATTCTTCCCTGTATTATTAAGTGG 57.943 37.037 0.00 0.00 0.00 4.00
2117 2202 9.838339 AGTGATTCTTCCCTGTATTATTAAGTG 57.162 33.333 0.00 0.00 0.00 3.16
2121 2206 8.871125 GGAGAGTGATTCTTCCCTGTATTATTA 58.129 37.037 0.00 0.00 35.87 0.98
2122 2207 7.202139 GGGAGAGTGATTCTTCCCTGTATTATT 60.202 40.741 1.18 0.00 44.92 1.40
2123 2208 6.271159 GGGAGAGTGATTCTTCCCTGTATTAT 59.729 42.308 1.18 0.00 44.92 1.28
2124 2209 5.602978 GGGAGAGTGATTCTTCCCTGTATTA 59.397 44.000 1.18 0.00 44.92 0.98
2125 2210 4.410555 GGGAGAGTGATTCTTCCCTGTATT 59.589 45.833 1.18 0.00 44.92 1.89
2126 2211 3.970640 GGGAGAGTGATTCTTCCCTGTAT 59.029 47.826 1.18 0.00 44.92 2.29
2127 2212 3.375699 GGGAGAGTGATTCTTCCCTGTA 58.624 50.000 1.18 0.00 44.92 2.74
2128 2213 2.192263 GGGAGAGTGATTCTTCCCTGT 58.808 52.381 1.18 0.00 44.92 4.00
2129 2214 2.998316 GGGAGAGTGATTCTTCCCTG 57.002 55.000 1.18 0.00 44.92 4.45
2132 2217 0.179070 GCCGGGAGAGTGATTCTTCC 60.179 60.000 2.18 0.00 46.90 3.46
2133 2218 0.537188 TGCCGGGAGAGTGATTCTTC 59.463 55.000 2.18 0.00 35.87 2.87
2134 2219 1.134280 CATGCCGGGAGAGTGATTCTT 60.134 52.381 2.18 0.00 35.87 2.52
2135 2220 0.467384 CATGCCGGGAGAGTGATTCT 59.533 55.000 2.18 0.00 39.43 2.40
2136 2221 0.465705 TCATGCCGGGAGAGTGATTC 59.534 55.000 2.18 0.00 0.00 2.52
2137 2222 1.135094 ATCATGCCGGGAGAGTGATT 58.865 50.000 2.18 0.00 0.00 2.57
2138 2223 0.395686 CATCATGCCGGGAGAGTGAT 59.604 55.000 2.18 3.80 0.00 3.06
2139 2224 1.689243 CCATCATGCCGGGAGAGTGA 61.689 60.000 2.18 0.83 0.00 3.41
2140 2225 1.227764 CCATCATGCCGGGAGAGTG 60.228 63.158 2.18 0.00 0.00 3.51
2141 2226 1.383109 TCCATCATGCCGGGAGAGT 60.383 57.895 2.18 0.00 0.00 3.24
2142 2227 1.070445 GTCCATCATGCCGGGAGAG 59.930 63.158 2.18 0.00 0.00 3.20
2143 2228 2.443394 GGTCCATCATGCCGGGAGA 61.443 63.158 2.18 0.00 0.00 3.71
2144 2229 2.111878 GGTCCATCATGCCGGGAG 59.888 66.667 2.18 0.00 0.00 4.30
2145 2230 2.613576 TAGGGTCCATCATGCCGGGA 62.614 60.000 2.18 0.00 0.00 5.14
2146 2231 2.116983 CTAGGGTCCATCATGCCGGG 62.117 65.000 2.18 0.00 0.00 5.73
2147 2232 1.372683 CTAGGGTCCATCATGCCGG 59.627 63.158 0.00 0.00 0.00 6.13
2148 2233 0.469917 AACTAGGGTCCATCATGCCG 59.530 55.000 0.00 0.00 0.00 5.69
2149 2234 2.736670 AAACTAGGGTCCATCATGCC 57.263 50.000 0.00 0.00 0.00 4.40
2167 2252 3.122323 CGCCGCCGGAGCTAAAAA 61.122 61.111 7.68 0.00 36.60 1.94
2168 2253 4.071875 TCGCCGCCGGAGCTAAAA 62.072 61.111 7.68 0.00 36.60 1.52
2169 2254 4.807039 GTCGCCGCCGGAGCTAAA 62.807 66.667 7.68 0.00 36.60 1.85
2180 2265 2.809601 CTTCGTTCTGGGTCGCCG 60.810 66.667 0.00 0.00 0.00 6.46
2181 2266 3.119096 GCTTCGTTCTGGGTCGCC 61.119 66.667 0.00 0.00 0.00 5.54
2182 2267 3.119096 GGCTTCGTTCTGGGTCGC 61.119 66.667 0.00 0.00 0.00 5.19
2183 2268 1.446272 GAGGCTTCGTTCTGGGTCG 60.446 63.158 0.00 0.00 0.00 4.79
2184 2269 1.079057 GGAGGCTTCGTTCTGGGTC 60.079 63.158 0.00 0.00 0.00 4.46
2185 2270 2.593956 GGGAGGCTTCGTTCTGGGT 61.594 63.158 0.00 0.00 0.00 4.51
2186 2271 1.842381 AAGGGAGGCTTCGTTCTGGG 61.842 60.000 0.00 0.00 0.00 4.45
2187 2272 0.036875 AAAGGGAGGCTTCGTTCTGG 59.963 55.000 0.39 0.00 0.00 3.86
2188 2273 1.537202 CAAAAGGGAGGCTTCGTTCTG 59.463 52.381 0.39 0.00 0.00 3.02
2189 2274 1.420138 TCAAAAGGGAGGCTTCGTTCT 59.580 47.619 0.39 0.00 0.00 3.01
2190 2275 1.892209 TCAAAAGGGAGGCTTCGTTC 58.108 50.000 0.39 0.00 0.00 3.95
2191 2276 2.162681 CATCAAAAGGGAGGCTTCGTT 58.837 47.619 0.00 0.00 0.00 3.85
2192 2277 1.073923 ACATCAAAAGGGAGGCTTCGT 59.926 47.619 0.00 0.00 0.00 3.85
2193 2278 1.826385 ACATCAAAAGGGAGGCTTCG 58.174 50.000 0.00 0.00 0.00 3.79
2194 2279 2.893489 ACAACATCAAAAGGGAGGCTTC 59.107 45.455 0.00 0.00 0.00 3.86
2195 2280 2.893489 GACAACATCAAAAGGGAGGCTT 59.107 45.455 0.00 0.00 0.00 4.35
2196 2281 2.158475 TGACAACATCAAAAGGGAGGCT 60.158 45.455 0.00 0.00 33.02 4.58
2197 2282 2.238521 TGACAACATCAAAAGGGAGGC 58.761 47.619 0.00 0.00 33.02 4.70
2198 2283 3.256631 CCTTGACAACATCAAAAGGGAGG 59.743 47.826 0.00 0.00 46.80 4.30
2199 2284 4.144297 TCCTTGACAACATCAAAAGGGAG 58.856 43.478 0.00 0.00 46.80 4.30
2200 2285 4.141274 TCTCCTTGACAACATCAAAAGGGA 60.141 41.667 0.00 0.00 46.80 4.20
2201 2286 4.144297 TCTCCTTGACAACATCAAAAGGG 58.856 43.478 0.00 0.00 46.80 3.95
2202 2287 5.772825 TTCTCCTTGACAACATCAAAAGG 57.227 39.130 0.00 0.00 46.80 3.11
2203 2288 6.082338 CGATTCTCCTTGACAACATCAAAAG 58.918 40.000 0.00 0.00 46.80 2.27
2204 2289 5.530915 ACGATTCTCCTTGACAACATCAAAA 59.469 36.000 0.00 0.00 46.80 2.44
2205 2290 5.063204 ACGATTCTCCTTGACAACATCAAA 58.937 37.500 0.00 0.00 46.80 2.69
2206 2291 4.641396 ACGATTCTCCTTGACAACATCAA 58.359 39.130 0.00 0.00 45.39 2.57
2207 2292 4.271696 ACGATTCTCCTTGACAACATCA 57.728 40.909 0.00 0.00 34.65 3.07
2208 2293 4.806247 CCTACGATTCTCCTTGACAACATC 59.194 45.833 0.00 0.00 0.00 3.06
2209 2294 4.759782 CCTACGATTCTCCTTGACAACAT 58.240 43.478 0.00 0.00 0.00 2.71
2210 2295 3.616560 GCCTACGATTCTCCTTGACAACA 60.617 47.826 0.00 0.00 0.00 3.33
2211 2296 2.930682 GCCTACGATTCTCCTTGACAAC 59.069 50.000 0.00 0.00 0.00 3.32
2212 2297 2.416836 CGCCTACGATTCTCCTTGACAA 60.417 50.000 0.00 0.00 43.93 3.18
2213 2298 1.134367 CGCCTACGATTCTCCTTGACA 59.866 52.381 0.00 0.00 43.93 3.58
2214 2299 1.536284 CCGCCTACGATTCTCCTTGAC 60.536 57.143 0.00 0.00 43.93 3.18
2215 2300 0.744874 CCGCCTACGATTCTCCTTGA 59.255 55.000 0.00 0.00 43.93 3.02
2216 2301 0.744874 TCCGCCTACGATTCTCCTTG 59.255 55.000 0.00 0.00 43.93 3.61
2217 2302 1.033574 CTCCGCCTACGATTCTCCTT 58.966 55.000 0.00 0.00 43.93 3.36
2218 2303 1.457009 GCTCCGCCTACGATTCTCCT 61.457 60.000 0.00 0.00 43.93 3.69
2219 2304 1.007154 GCTCCGCCTACGATTCTCC 60.007 63.158 0.00 0.00 43.93 3.71
2220 2305 0.318275 CTGCTCCGCCTACGATTCTC 60.318 60.000 0.00 0.00 43.93 2.87
2221 2306 1.736586 CTGCTCCGCCTACGATTCT 59.263 57.895 0.00 0.00 43.93 2.40
2222 2307 1.951631 GCTGCTCCGCCTACGATTC 60.952 63.158 0.00 0.00 43.93 2.52
2223 2308 2.107141 GCTGCTCCGCCTACGATT 59.893 61.111 0.00 0.00 43.93 3.34
2224 2309 3.917760 GGCTGCTCCGCCTACGAT 61.918 66.667 0.00 0.00 46.63 3.73
2231 2316 4.410743 GCAACAAGGCTGCTCCGC 62.411 66.667 0.00 0.00 40.77 5.54
2232 2317 4.093952 CGCAACAAGGCTGCTCCG 62.094 66.667 0.00 0.00 40.77 4.63
2233 2318 3.741476 CCGCAACAAGGCTGCTCC 61.741 66.667 0.00 0.00 37.67 4.70
2234 2319 1.589716 ATTCCGCAACAAGGCTGCTC 61.590 55.000 0.00 0.00 37.67 4.26
2235 2320 0.322456 TATTCCGCAACAAGGCTGCT 60.322 50.000 0.00 0.00 37.67 4.24
2236 2321 0.179163 GTATTCCGCAACAAGGCTGC 60.179 55.000 0.00 0.00 36.41 5.25
2237 2322 0.096976 CGTATTCCGCAACAAGGCTG 59.903 55.000 0.00 0.00 0.00 4.85
2238 2323 2.466867 CGTATTCCGCAACAAGGCT 58.533 52.632 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.