Multiple sequence alignment - TraesCS4A01G065900

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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 TraesCS4A01G065900 chr4A 100.000 4650 0 0 1 4650 63101808 63097159 0.000000e+00 8588
1 TraesCS4A01G065900 chr4D 88.197 3804 178 121 1 3652 405465652 405461968 0.000000e+00 4287
2 TraesCS4A01G065900 chr4D 87.902 529 28 18 3899 4419 405461641 405461141 1.440000e-164 590
3 TraesCS4A01G065900 chr4D 91.765 255 10 4 3644 3898 405461926 405461683 1.240000e-90 344
4 TraesCS4A01G065900 chr4D 87.793 213 2 7 4438 4650 405461074 405460886 1.300000e-55 228
5 TraesCS4A01G065900 chr4B 89.975 1626 78 45 329 1913 504184628 504183047 0.000000e+00 2021
6 TraesCS4A01G065900 chr4B 89.324 1227 56 29 2467 3635 504182387 504181178 0.000000e+00 1471
7 TraesCS4A01G065900 chr4B 85.560 554 27 23 3906 4419 504180821 504180281 8.860000e-147 531
8 TraesCS4A01G065900 chr4B 83.559 590 24 25 1912 2474 504182957 504182414 7.000000e-133 484
9 TraesCS4A01G065900 chr4B 91.018 334 28 2 1 334 504184991 504184660 2.550000e-122 449
10 TraesCS4A01G065900 chr4B 92.045 264 7 8 3644 3907 504181125 504180876 4.420000e-95 359
11 TraesCS4A01G065900 chr4B 79.525 337 62 7 1 334 504236251 504235919 2.800000e-57 233
12 TraesCS4A01G065900 chr4B 86.854 213 3 8 4438 4650 504180214 504180027 1.010000e-51 215


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 TraesCS4A01G065900 chr4A 63097159 63101808 4649 True 8588.00 8588 100.000000 1 4650 1 chr4A.!!$R1 4649
1 TraesCS4A01G065900 chr4D 405460886 405465652 4766 True 1362.25 4287 88.914250 1 4650 4 chr4D.!!$R1 4649
2 TraesCS4A01G065900 chr4B 504180027 504184991 4964 True 790.00 2021 88.333571 1 4650 7 chr4B.!!$R2 4649

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
884 936 0.034380 TCCTCCTCGTCGTCTCCATT 60.034 55.0 0.0 0.0 0.0 3.16 F
2022 2222 0.108615 AGCAATCTCCGTCTCCGTTG 60.109 55.0 0.0 0.0 0.0 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2776 3073 0.097674 GTTGCACCATGATCACGAGC 59.902 55.0 0.0 2.15 0.0 5.03 R
3840 4223 0.405585 TGGGAGCAGAAAGAAAGGGG 59.594 55.0 0.0 0.00 0.0 4.79 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
47 48 8.656806 ACCGGGTCTATCATTAAATGAATAGAA 58.343 33.333 6.32 0.00 43.50 2.10
170 171 3.343421 GTCACCGACCGTTGGCAC 61.343 66.667 4.52 0.00 0.00 5.01
171 172 3.851128 TCACCGACCGTTGGCACA 61.851 61.111 4.52 0.00 0.00 4.57
189 190 5.532779 TGGCACAATCTGTACACAATTAACA 59.467 36.000 0.00 0.00 31.92 2.41
285 286 8.981647 AGAAAATATCGCCATATTTGAAAATGC 58.018 29.630 9.66 0.00 42.20 3.56
324 325 5.740569 CACAATGGTTGCTCATATTTTCTCG 59.259 40.000 0.00 0.00 0.00 4.04
371 407 4.846168 TGTACCCATAAGCCATAACACA 57.154 40.909 0.00 0.00 0.00 3.72
404 440 6.533730 TGAGGTAATTTAGGCACCTATCATG 58.466 40.000 0.00 0.00 42.78 3.07
407 443 7.398024 AGGTAATTTAGGCACCTATCATGATC 58.602 38.462 12.53 0.00 40.93 2.92
408 444 7.017551 AGGTAATTTAGGCACCTATCATGATCA 59.982 37.037 12.53 0.00 40.93 2.92
409 445 7.831193 GGTAATTTAGGCACCTATCATGATCAT 59.169 37.037 12.53 1.18 0.00 2.45
410 446 7.698506 AATTTAGGCACCTATCATGATCATG 57.301 36.000 26.79 26.79 40.09 3.07
463 500 6.239036 GCCAAAAATAGAGCTATAAACCCAGG 60.239 42.308 0.00 0.00 0.00 4.45
467 504 8.520119 AAAATAGAGCTATAAACCCAGGGATA 57.480 34.615 14.54 5.26 0.00 2.59
473 510 4.347000 GCTATAAACCCAGGGATAGACACA 59.653 45.833 14.54 0.00 0.00 3.72
474 511 4.772886 ATAAACCCAGGGATAGACACAC 57.227 45.455 14.54 0.00 0.00 3.82
620 657 5.518487 TGAAAAGCAAAGAAAGGCGTAAAAG 59.482 36.000 0.00 0.00 34.54 2.27
649 686 3.004419 TCCCTAATAATCAGACGCACTCG 59.996 47.826 0.00 0.00 42.43 4.18
651 688 2.961526 AATAATCAGACGCACTCGGT 57.038 45.000 0.00 0.00 40.69 4.69
653 690 4.380841 AATAATCAGACGCACTCGGTAA 57.619 40.909 0.00 0.00 40.69 2.85
654 691 2.279582 AATCAGACGCACTCGGTAAG 57.720 50.000 0.00 0.00 40.69 2.34
659 696 0.666577 GACGCACTCGGTAAGCAGTT 60.667 55.000 0.00 0.00 40.69 3.16
660 697 0.666577 ACGCACTCGGTAAGCAGTTC 60.667 55.000 0.00 0.00 40.69 3.01
663 705 1.337821 CACTCGGTAAGCAGTTCGTC 58.662 55.000 0.00 0.00 0.00 4.20
678 720 3.062042 GTTCGTCCACGGACAGTTATTT 58.938 45.455 16.23 0.00 46.62 1.40
683 725 1.199097 CCACGGACAGTTATTTGGTGC 59.801 52.381 0.00 0.00 0.00 5.01
723 765 1.455786 CGAGCAAAAGTCGACGACAAT 59.544 47.619 28.31 14.80 39.92 2.71
758 800 1.948635 CGGGCAAGCAAACAAACGG 60.949 57.895 0.00 0.00 0.00 4.44
882 934 1.078356 CTCCTCCTCGTCGTCTCCA 60.078 63.158 0.00 0.00 0.00 3.86
883 935 0.464735 CTCCTCCTCGTCGTCTCCAT 60.465 60.000 0.00 0.00 0.00 3.41
884 936 0.034380 TCCTCCTCGTCGTCTCCATT 60.034 55.000 0.00 0.00 0.00 3.16
893 945 1.550976 GTCGTCTCCATTCAGTCCCTT 59.449 52.381 0.00 0.00 0.00 3.95
897 949 2.093235 GTCTCCATTCAGTCCCTTCCTG 60.093 54.545 0.00 0.00 0.00 3.86
900 952 1.005215 CCATTCAGTCCCTTCCTGCTT 59.995 52.381 0.00 0.00 0.00 3.91
901 953 2.363683 CATTCAGTCCCTTCCTGCTTC 58.636 52.381 0.00 0.00 0.00 3.86
902 954 1.734655 TTCAGTCCCTTCCTGCTTCT 58.265 50.000 0.00 0.00 0.00 2.85
904 956 1.203237 TCAGTCCCTTCCTGCTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
946 1013 1.746220 CTGTCCTCTCTCCCGTAGTTG 59.254 57.143 0.00 0.00 0.00 3.16
1114 1189 1.908483 CTCTCCCCCAAGCAGGTAC 59.092 63.158 0.00 0.00 34.66 3.34
1143 1218 1.690633 TGCCCACCTCCATCTCTCC 60.691 63.158 0.00 0.00 0.00 3.71
1165 1244 1.755783 GCCATGCCTCCTTCTTGGG 60.756 63.158 0.00 0.00 36.20 4.12
1166 1245 2.001803 CCATGCCTCCTTCTTGGGA 58.998 57.895 0.00 0.00 36.20 4.37
1167 1246 0.554792 CCATGCCTCCTTCTTGGGAT 59.445 55.000 0.00 0.00 34.68 3.85
1168 1247 1.478288 CCATGCCTCCTTCTTGGGATC 60.478 57.143 0.00 0.00 31.95 3.36
1169 1248 0.471617 ATGCCTCCTTCTTGGGATCG 59.528 55.000 0.00 0.00 34.56 3.69
1185 1264 4.084888 CGTTTCTTGACGCCGGCC 62.085 66.667 23.46 8.57 36.12 6.13
1337 1425 2.345991 CGTTCCGCTTCCCTTCCA 59.654 61.111 0.00 0.00 0.00 3.53
1339 1427 1.072505 GTTCCGCTTCCCTTCCACA 59.927 57.895 0.00 0.00 0.00 4.17
1345 1433 1.482593 CGCTTCCCTTCCACACTCTAT 59.517 52.381 0.00 0.00 0.00 1.98
1351 1439 1.683917 CCTTCCACACTCTATCTCCCG 59.316 57.143 0.00 0.00 0.00 5.14
1353 1441 0.259065 TCCACACTCTATCTCCCGCT 59.741 55.000 0.00 0.00 0.00 5.52
1369 1457 2.903547 GCTTGTTTCCGGCAGCGAA 61.904 57.895 0.00 0.00 0.00 4.70
1404 1493 4.494484 GCCTGCTATTTTTGAAATCCGTT 58.506 39.130 0.00 0.00 0.00 4.44
1406 1495 4.327087 CCTGCTATTTTTGAAATCCGTTGC 59.673 41.667 0.00 0.00 0.00 4.17
1424 1513 1.213537 CACATGCAGAAAAGGGGCG 59.786 57.895 0.00 0.00 0.00 6.13
1438 1527 3.487120 AGGGGCGGTTCATTAATACTC 57.513 47.619 0.00 0.00 0.00 2.59
1477 1566 4.923893 TCTGATGTGCTCTGTTTTTGTTG 58.076 39.130 0.00 0.00 0.00 3.33
1563 1654 2.203480 TGCCGGGCTCTTTGCTTT 60.203 55.556 21.46 0.00 42.39 3.51
1564 1655 2.259511 GCCGGGCTCTTTGCTTTG 59.740 61.111 12.87 0.00 42.39 2.77
1565 1656 2.259511 CCGGGCTCTTTGCTTTGC 59.740 61.111 0.00 0.00 42.39 3.68
1566 1657 2.270986 CCGGGCTCTTTGCTTTGCT 61.271 57.895 0.00 0.00 42.39 3.91
1567 1658 1.662044 CGGGCTCTTTGCTTTGCTT 59.338 52.632 0.00 0.00 42.39 3.91
1568 1659 0.665369 CGGGCTCTTTGCTTTGCTTG 60.665 55.000 0.00 0.00 42.39 4.01
1578 1669 1.213537 CTTTGCTTGGCATCCCGTG 59.786 57.895 0.00 0.00 38.76 4.94
1592 1683 0.531657 CCCGTGTTCCCGTGTATGTA 59.468 55.000 0.00 0.00 0.00 2.29
1596 1687 2.352030 CGTGTTCCCGTGTATGTACAGT 60.352 50.000 0.33 0.00 36.78 3.55
1597 1688 3.119884 CGTGTTCCCGTGTATGTACAGTA 60.120 47.826 0.33 0.00 36.78 2.74
1598 1689 4.168760 GTGTTCCCGTGTATGTACAGTAC 58.831 47.826 0.33 3.49 36.78 2.73
1599 1690 3.119884 TGTTCCCGTGTATGTACAGTACG 60.120 47.826 17.36 17.36 36.78 3.67
1600 1691 2.710377 TCCCGTGTATGTACAGTACGT 58.290 47.619 20.56 10.37 36.78 3.57
1602 1693 2.179589 CCGTGTATGTACAGTACGTGC 58.820 52.381 20.56 13.75 36.78 5.34
1604 1695 3.236005 CGTGTATGTACAGTACGTGCAA 58.764 45.455 21.33 7.04 43.90 4.08
1606 1697 3.060363 GTGTATGTACAGTACGTGCAAGC 59.940 47.826 21.33 9.68 43.90 4.01
1608 1699 0.311477 TGTACAGTACGTGCAAGCGA 59.689 50.000 6.38 0.00 37.28 4.93
1609 1700 0.982673 GTACAGTACGTGCAAGCGAG 59.017 55.000 6.38 0.00 35.59 5.03
1610 1701 0.109458 TACAGTACGTGCAAGCGAGG 60.109 55.000 6.38 0.00 35.59 4.63
1611 1702 1.080772 CAGTACGTGCAAGCGAGGA 60.081 57.895 6.38 0.00 35.59 3.71
1612 1703 1.080705 AGTACGTGCAAGCGAGGAC 60.081 57.895 6.38 0.00 35.59 3.85
1613 1704 1.372499 GTACGTGCAAGCGAGGACA 60.372 57.895 3.48 0.00 35.59 4.02
1614 1705 1.080772 TACGTGCAAGCGAGGACAG 60.081 57.895 3.48 0.38 35.59 3.51
1617 1708 1.498865 CGTGCAAGCGAGGACAGTTT 61.499 55.000 0.00 0.00 0.00 2.66
1627 1718 1.604278 GAGGACAGTTTCAACAGTGCC 59.396 52.381 3.59 1.07 37.44 5.01
1643 1736 0.825840 TGCCCCCTTGTTGTTGCTAC 60.826 55.000 0.00 0.00 0.00 3.58
1652 1745 6.462347 CCCCTTGTTGTTGCTACTATGTTTTT 60.462 38.462 0.00 0.00 0.00 1.94
1653 1746 6.420604 CCCTTGTTGTTGCTACTATGTTTTTG 59.579 38.462 0.00 0.00 0.00 2.44
1654 1747 7.199766 CCTTGTTGTTGCTACTATGTTTTTGA 58.800 34.615 0.00 0.00 0.00 2.69
1655 1748 7.167468 CCTTGTTGTTGCTACTATGTTTTTGAC 59.833 37.037 0.00 0.00 0.00 3.18
1656 1749 7.328277 TGTTGTTGCTACTATGTTTTTGACT 57.672 32.000 0.00 0.00 0.00 3.41
1657 1750 7.192913 TGTTGTTGCTACTATGTTTTTGACTG 58.807 34.615 0.00 0.00 0.00 3.51
1658 1751 6.935741 TGTTGCTACTATGTTTTTGACTGT 57.064 33.333 0.00 0.00 0.00 3.55
1668 1761 5.335827 TGTTTTTGACTGTTTTGTGTTGC 57.664 34.783 0.00 0.00 0.00 4.17
1671 1764 3.932545 TTGACTGTTTTGTGTTGCTGT 57.067 38.095 0.00 0.00 0.00 4.40
1672 1765 3.932545 TGACTGTTTTGTGTTGCTGTT 57.067 38.095 0.00 0.00 0.00 3.16
1674 1767 3.254411 TGACTGTTTTGTGTTGCTGTTGA 59.746 39.130 0.00 0.00 0.00 3.18
1675 1768 3.574614 ACTGTTTTGTGTTGCTGTTGAC 58.425 40.909 0.00 0.00 0.00 3.18
1676 1769 2.590073 TGTTTTGTGTTGCTGTTGACG 58.410 42.857 0.00 0.00 0.00 4.35
1677 1770 1.917303 GTTTTGTGTTGCTGTTGACGG 59.083 47.619 0.00 0.00 0.00 4.79
1695 1788 0.866427 GGCGAGCAGATCACATCATG 59.134 55.000 0.00 0.00 0.00 3.07
1781 1877 3.834799 CCCCGTCCTGGTACGCTC 61.835 72.222 11.53 0.00 41.51 5.03
1782 1878 2.754658 CCCGTCCTGGTACGCTCT 60.755 66.667 11.53 0.00 41.51 4.09
1795 1891 2.031516 CGCTCTCTGCAGTTGGGTG 61.032 63.158 14.67 10.75 43.06 4.61
1812 1908 2.095415 GGGTGTAAATGTTTGGAGCGAC 60.095 50.000 0.00 0.00 0.00 5.19
1827 1923 1.591703 CGACACTGGCTTGGCTCTA 59.408 57.895 0.00 0.00 0.00 2.43
1902 1998 0.912968 ACTACCCCAAGTACCAGCCC 60.913 60.000 0.00 0.00 0.00 5.19
1975 2162 1.736645 ATGAACCGCTTCGTGGACG 60.737 57.895 0.00 0.00 36.58 4.79
2016 2203 2.622436 GCAAGTAAGCAATCTCCGTCT 58.378 47.619 0.00 0.00 0.00 4.18
2022 2222 0.108615 AGCAATCTCCGTCTCCGTTG 60.109 55.000 0.00 0.00 0.00 4.10
2024 2224 0.460284 CAATCTCCGTCTCCGTTGGG 60.460 60.000 0.00 0.00 0.00 4.12
2032 2232 2.104331 CTCCGTTGGGTCGATCGG 59.896 66.667 16.41 0.00 43.65 4.18
2083 2294 1.447140 GGTAGTGGTCGCATCGCAA 60.447 57.895 0.00 0.00 0.00 4.85
2084 2295 0.810031 GGTAGTGGTCGCATCGCAAT 60.810 55.000 0.00 0.00 0.00 3.56
2087 2298 3.563088 TGGTCGCATCGCAATCGC 61.563 61.111 0.00 0.00 35.26 4.58
2088 2299 3.563088 GGTCGCATCGCAATCGCA 61.563 61.111 0.00 0.00 38.40 5.10
2089 2300 2.628106 GTCGCATCGCAATCGCAT 59.372 55.556 0.00 0.00 38.40 4.73
2090 2301 1.437735 GTCGCATCGCAATCGCATC 60.438 57.895 0.00 0.00 38.40 3.91
2091 2302 2.127496 CGCATCGCAATCGCATCC 60.127 61.111 0.00 0.00 38.40 3.51
2092 2303 2.884571 CGCATCGCAATCGCATCCA 61.885 57.895 0.00 0.00 38.40 3.41
2093 2304 1.577922 GCATCGCAATCGCATCCAT 59.422 52.632 0.00 0.00 38.40 3.41
2178 2407 0.248702 GTCAGTACGCTCTGCTAGGC 60.249 60.000 0.00 0.00 35.63 3.93
2196 2425 1.750018 CGCACATGAATCCCTGGCA 60.750 57.895 0.00 0.00 0.00 4.92
2202 2431 2.004408 ATGAATCCCTGGCAGCTCCC 62.004 60.000 9.56 0.00 0.00 4.30
2203 2432 2.614969 AATCCCTGGCAGCTCCCA 60.615 61.111 9.56 0.00 0.00 4.37
2204 2433 2.215451 GAATCCCTGGCAGCTCCCAA 62.215 60.000 9.56 0.00 33.73 4.12
2213 2442 1.845809 GCAGCTCCCAACAACGACAG 61.846 60.000 0.00 0.00 0.00 3.51
2222 2451 1.597663 CAACAACGACAGACACCTTCC 59.402 52.381 0.00 0.00 0.00 3.46
2305 2539 1.364626 CTGCTCGCATTGTCTCCCAC 61.365 60.000 0.00 0.00 0.00 4.61
2310 2544 2.690778 GCATTGTCTCCCACGCACC 61.691 63.158 0.00 0.00 0.00 5.01
2315 2549 1.371558 GTCTCCCACGCACCTTCTT 59.628 57.895 0.00 0.00 0.00 2.52
2316 2550 0.250338 GTCTCCCACGCACCTTCTTT 60.250 55.000 0.00 0.00 0.00 2.52
2317 2551 0.472471 TCTCCCACGCACCTTCTTTT 59.528 50.000 0.00 0.00 0.00 2.27
2318 2552 1.133915 TCTCCCACGCACCTTCTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
2319 2553 2.105134 TCTCCCACGCACCTTCTTTTTA 59.895 45.455 0.00 0.00 0.00 1.52
2320 2554 2.484264 CTCCCACGCACCTTCTTTTTAG 59.516 50.000 0.00 0.00 0.00 1.85
2321 2555 1.539827 CCCACGCACCTTCTTTTTAGG 59.460 52.381 0.00 0.00 38.79 2.69
2349 2583 2.288579 ACTCGTTTGTCTTCCGTATGCA 60.289 45.455 0.00 0.00 0.00 3.96
2460 2694 1.059369 GCGTGCACAGTTATCGCTG 59.941 57.895 18.64 0.00 42.88 5.18
2521 2790 1.665679 CGAGAATGATTGGGTTCCACG 59.334 52.381 0.00 0.00 30.78 4.94
2562 2858 4.093998 CGTGGAAAGCGAAGTAGACTACTA 59.906 45.833 15.51 0.00 38.26 1.82
2588 2885 0.466189 GTGCATGGTGGTATGGGGAG 60.466 60.000 0.00 0.00 0.00 4.30
2666 2963 1.291877 CGTCGGCTTTCCTCAACCTG 61.292 60.000 0.00 0.00 0.00 4.00
2770 3067 2.232941 TCTCCGTCATGTGGAAGGTAAC 59.767 50.000 10.04 0.00 44.56 2.50
2789 3116 1.202417 ACTAACCGCTCGTGATCATGG 60.202 52.381 14.91 7.01 0.00 3.66
2796 3124 1.730501 CTCGTGATCATGGTGCAACT 58.269 50.000 14.91 0.00 36.74 3.16
2799 3127 1.805943 CGTGATCATGGTGCAACTTCA 59.194 47.619 2.04 0.00 36.74 3.02
2812 3140 0.961019 AACTTCATGTGCGTGGCAAT 59.039 45.000 0.00 0.00 41.47 3.56
2813 3141 0.241749 ACTTCATGTGCGTGGCAATG 59.758 50.000 0.00 0.00 41.47 2.82
2815 3143 2.489539 TTCATGTGCGTGGCAATGGC 62.490 55.000 0.00 0.00 41.47 4.40
2818 3146 2.431260 GTGCGTGGCAATGGCAAG 60.431 61.111 17.39 17.39 41.47 4.01
2819 3147 2.911509 TGCGTGGCAATGGCAAGT 60.912 55.556 21.58 0.00 43.71 3.16
2820 3148 2.431260 GCGTGGCAATGGCAAGTG 60.431 61.111 21.58 11.61 43.71 3.16
2821 3149 2.259204 CGTGGCAATGGCAAGTGG 59.741 61.111 12.09 0.00 43.71 4.00
2822 3150 2.267351 CGTGGCAATGGCAAGTGGA 61.267 57.895 12.09 0.00 43.71 4.02
2823 3151 1.804396 CGTGGCAATGGCAAGTGGAA 61.804 55.000 12.09 0.00 43.71 3.53
2824 3152 0.609662 GTGGCAATGGCAAGTGGAAT 59.390 50.000 12.09 0.00 43.71 3.01
2825 3153 1.002315 GTGGCAATGGCAAGTGGAATT 59.998 47.619 12.09 0.00 43.71 2.17
2826 3154 1.698532 TGGCAATGGCAAGTGGAATTT 59.301 42.857 7.14 0.00 43.71 1.82
2827 3155 2.902486 TGGCAATGGCAAGTGGAATTTA 59.098 40.909 7.14 0.00 43.71 1.40
2838 3169 8.811017 TGGCAAGTGGAATTTATATGAAAGAAA 58.189 29.630 0.00 0.00 0.00 2.52
2840 3171 8.798153 GCAAGTGGAATTTATATGAAAGAAACG 58.202 33.333 0.00 0.00 0.00 3.60
2841 3172 9.840427 CAAGTGGAATTTATATGAAAGAAACGT 57.160 29.630 0.00 0.00 0.00 3.99
2863 3194 1.480137 TGTTTTGCTTTGTGACAGGGG 59.520 47.619 0.00 0.00 0.00 4.79
3305 3639 2.679716 CCAAGGGAGGGCAGAAGG 59.320 66.667 0.00 0.00 0.00 3.46
3487 3821 2.638154 CGGCCCTACGACGAGATC 59.362 66.667 0.00 0.00 35.47 2.75
3556 3890 4.821589 GCCGAGGACTTCAGGCCG 62.822 72.222 0.00 0.00 38.63 6.13
3560 3894 1.522580 GAGGACTTCAGGCCGATGC 60.523 63.158 0.00 0.00 0.00 3.91
3692 4075 5.975344 CAGCTTACAACATAATCCAATGCTG 59.025 40.000 0.00 0.00 37.33 4.41
3701 4084 5.183331 ACATAATCCAATGCTGCATCATCTC 59.817 40.000 16.55 0.00 0.00 2.75
3711 4094 3.651206 CTGCATCATCTCGCTAAGTCAT 58.349 45.455 0.00 0.00 0.00 3.06
3768 4151 0.323725 TTTACTCCTACCGACCGCCT 60.324 55.000 0.00 0.00 0.00 5.52
3769 4152 0.546122 TTACTCCTACCGACCGCCTA 59.454 55.000 0.00 0.00 0.00 3.93
3770 4153 0.767375 TACTCCTACCGACCGCCTAT 59.233 55.000 0.00 0.00 0.00 2.57
3771 4154 0.822532 ACTCCTACCGACCGCCTATG 60.823 60.000 0.00 0.00 0.00 2.23
3772 4155 0.536687 CTCCTACCGACCGCCTATGA 60.537 60.000 0.00 0.00 0.00 2.15
3840 4223 6.314784 CCCTGAAATTGTGAGTAAAATCGAC 58.685 40.000 0.00 0.00 0.00 4.20
3861 4244 1.160137 CCTTTCTTTCTGCTCCCACG 58.840 55.000 0.00 0.00 0.00 4.94
3870 4253 1.856265 CTGCTCCCACGGCTTGTTTC 61.856 60.000 0.00 0.00 0.00 2.78
3893 4276 2.952310 TCCTCCGTGTGATGTGATAGAG 59.048 50.000 0.00 0.00 0.00 2.43
3974 4454 4.089636 CCAACTTTCTACTCTTACGTTCGC 59.910 45.833 0.00 0.00 0.00 4.70
3982 4462 2.049248 TTACGTTCGCGGTGGACC 60.049 61.111 6.13 0.00 46.45 4.46
3984 4464 2.752322 TTACGTTCGCGGTGGACCTG 62.752 60.000 6.13 0.00 46.45 4.00
4032 4515 4.262592 GCCAACACATTTGGAGGAAGAAAT 60.263 41.667 7.23 0.00 42.06 2.17
4034 4517 6.518200 GCCAACACATTTGGAGGAAGAAATTA 60.518 38.462 7.23 0.00 42.06 1.40
4035 4518 7.092716 CCAACACATTTGGAGGAAGAAATTAG 58.907 38.462 0.00 0.00 42.06 1.73
4036 4519 7.039784 CCAACACATTTGGAGGAAGAAATTAGA 60.040 37.037 0.00 0.00 42.06 2.10
4037 4520 8.359642 CAACACATTTGGAGGAAGAAATTAGAA 58.640 33.333 0.00 0.00 0.00 2.10
4039 4522 8.579863 ACACATTTGGAGGAAGAAATTAGAAAG 58.420 33.333 0.00 0.00 0.00 2.62
4040 4523 8.579863 CACATTTGGAGGAAGAAATTAGAAAGT 58.420 33.333 0.00 0.00 0.00 2.66
4041 4524 9.807921 ACATTTGGAGGAAGAAATTAGAAAGTA 57.192 29.630 0.00 0.00 0.00 2.24
4070 4573 1.077285 TGAGGCTGTGATGGCATGG 60.077 57.895 3.81 0.00 34.73 3.66
4087 4592 2.568090 GCACCATGGCCGTTGAAG 59.432 61.111 13.04 0.00 0.00 3.02
4105 4610 3.186409 TGAAGATTTTGAAACGGCGAGAG 59.814 43.478 16.62 0.00 0.00 3.20
4153 4658 4.499188 GGGTTCTTCCTTTTCCGTCTTTTG 60.499 45.833 0.00 0.00 36.25 2.44
4157 4662 1.336755 TCCTTTTCCGTCTTTTGCAGC 59.663 47.619 0.00 0.00 0.00 5.25
4190 4695 0.608640 ACCTCGGTAAGCTTCACCAG 59.391 55.000 18.93 15.28 35.67 4.00
4207 4713 3.874543 CACCAGTAAGCACAACACAAGTA 59.125 43.478 0.00 0.00 0.00 2.24
4208 4714 4.515191 CACCAGTAAGCACAACACAAGTAT 59.485 41.667 0.00 0.00 0.00 2.12
4209 4715 4.515191 ACCAGTAAGCACAACACAAGTATG 59.485 41.667 0.00 0.00 0.00 2.39
4232 4738 0.466922 ATTACATGGAGCCTGCCTGC 60.467 55.000 0.00 0.00 0.00 4.85
4244 4750 0.884704 CTGCCTGCCTACACGTTTGT 60.885 55.000 0.00 0.00 40.02 2.83
4320 4841 1.729149 GCTGCATGCGTAAGTTGGTTC 60.729 52.381 14.09 0.00 41.68 3.62
4358 4879 2.340809 CGTACCACGCAGGGTTGA 59.659 61.111 1.11 0.00 43.89 3.18
4359 4880 2.025418 CGTACCACGCAGGGTTGAC 61.025 63.158 1.11 0.00 43.89 3.18
4365 4886 2.805353 CGCAGGGTTGACGACGAG 60.805 66.667 0.00 0.00 0.00 4.18
4377 4898 2.799540 CGACGAGCGCTTTAAGCCC 61.800 63.158 13.26 1.98 38.18 5.19
4382 4903 1.465856 CGAGCGCTTTAAGCCCTTTTC 60.466 52.381 13.26 1.77 38.18 2.29
4383 4904 0.888619 AGCGCTTTAAGCCCTTTTCC 59.111 50.000 2.64 0.00 38.18 3.13
4384 4905 0.108804 GCGCTTTAAGCCCTTTTCCC 60.109 55.000 11.64 0.00 38.18 3.97
4461 5053 8.246908 ACAAACTTTACAAACTTTAAACTGGC 57.753 30.769 0.00 0.00 0.00 4.85
4477 5069 1.603802 CTGGCGGTGGTATAAGCATTG 59.396 52.381 0.00 0.00 0.00 2.82
4478 5070 0.951558 GGCGGTGGTATAAGCATTGG 59.048 55.000 0.00 0.00 0.00 3.16
4479 5071 1.476110 GGCGGTGGTATAAGCATTGGA 60.476 52.381 0.00 0.00 0.00 3.53
4480 5072 1.602377 GCGGTGGTATAAGCATTGGAC 59.398 52.381 0.00 0.00 0.00 4.02
4595 5187 1.227409 CTTTTGCGGCCGGGTTTTT 60.227 52.632 29.38 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.989659 TCATTTAATGATAGACCCGGTCTAC 58.010 40.000 26.50 19.90 46.06 2.59
47 48 6.431198 AAATTGTAGCCGTTCGTCATTTAT 57.569 33.333 0.00 0.00 0.00 1.40
166 167 6.007936 TGTTAATTGTGTACAGATTGTGCC 57.992 37.500 12.44 0.00 31.71 5.01
170 171 6.655003 AGGGACTGTTAATTGTGTACAGATTG 59.345 38.462 12.44 1.91 41.33 2.67
171 172 6.779860 AGGGACTGTTAATTGTGTACAGATT 58.220 36.000 14.66 2.67 41.33 2.40
186 187 0.468226 TTGTCTTGCGAGGGACTGTT 59.532 50.000 0.00 0.00 41.55 3.16
187 188 0.687354 ATTGTCTTGCGAGGGACTGT 59.313 50.000 0.00 0.00 41.55 3.55
268 269 3.188492 TGCTGCATTTTCAAATATGGCG 58.812 40.909 0.00 0.00 0.00 5.69
324 325 2.820728 ATTGCCCTAGTTAACCCACC 57.179 50.000 0.88 0.00 0.00 4.61
463 500 0.457035 TTACGGCCGTGTGTCTATCC 59.543 55.000 40.02 0.00 0.00 2.59
467 504 1.666872 GCTTTACGGCCGTGTGTCT 60.667 57.895 40.02 15.53 0.00 3.41
473 510 1.303091 GGATTGTGCTTTACGGCCGT 61.303 55.000 36.01 36.01 0.00 5.68
474 511 1.427819 GGATTGTGCTTTACGGCCG 59.572 57.895 26.86 26.86 0.00 6.13
597 634 5.051039 CCTTTTACGCCTTTCTTTGCTTTTC 60.051 40.000 0.00 0.00 0.00 2.29
649 686 1.012486 CCGTGGACGAACTGCTTACC 61.012 60.000 0.00 0.00 43.02 2.85
651 688 0.038892 GTCCGTGGACGAACTGCTTA 60.039 55.000 2.78 0.00 43.02 3.09
653 690 2.338984 GTCCGTGGACGAACTGCT 59.661 61.111 2.78 0.00 43.02 4.24
663 705 1.199097 GCACCAAATAACTGTCCGTGG 59.801 52.381 0.00 0.00 0.00 4.94
683 725 1.676006 GTGGTATTCTTGGCCGATTGG 59.324 52.381 0.00 0.00 38.77 3.16
701 743 0.158928 GTCGTCGACTTTTGCTCGTG 59.841 55.000 18.09 0.00 32.77 4.35
815 867 0.521735 GAAGGTGCCGTTTAAGCCAG 59.478 55.000 0.00 0.00 0.00 4.85
845 897 3.119065 GGAGGAGGAGTATTATAAGCCGC 60.119 52.174 0.00 0.00 0.00 6.53
882 934 2.238395 GAGAAGCAGGAAGGGACTGAAT 59.762 50.000 0.00 0.00 40.86 2.57
883 935 1.625818 GAGAAGCAGGAAGGGACTGAA 59.374 52.381 0.00 0.00 40.86 3.02
884 936 1.203237 AGAGAAGCAGGAAGGGACTGA 60.203 52.381 0.00 0.00 40.86 3.41
897 949 0.175531 GTGGCCTGAGAGAGAGAAGC 59.824 60.000 3.32 0.00 0.00 3.86
900 952 1.379176 CGGTGGCCTGAGAGAGAGA 60.379 63.158 3.32 0.00 0.00 3.10
901 953 3.074999 GCGGTGGCCTGAGAGAGAG 62.075 68.421 3.32 0.00 0.00 3.20
902 954 3.071206 GCGGTGGCCTGAGAGAGA 61.071 66.667 3.32 0.00 0.00 3.10
946 1013 2.315386 GGGCGAGTGTGAACGAACC 61.315 63.158 0.00 0.00 0.00 3.62
1122 1197 3.391665 GAGATGGAGGTGGGCACGG 62.392 68.421 0.00 0.00 0.00 4.94
1130 1205 2.835431 CCGCGGAGAGATGGAGGT 60.835 66.667 24.07 0.00 0.00 3.85
1135 1210 2.664185 CATGGCCGCGGAGAGATG 60.664 66.667 33.48 19.41 0.00 2.90
1156 1235 3.437049 GTCAAGAAACGATCCCAAGAAGG 59.563 47.826 0.00 0.00 37.03 3.46
1165 1244 1.708027 CCGGCGTCAAGAAACGATC 59.292 57.895 6.01 0.00 45.37 3.69
1166 1245 2.388232 GCCGGCGTCAAGAAACGAT 61.388 57.895 12.58 0.00 45.37 3.73
1167 1246 3.039588 GCCGGCGTCAAGAAACGA 61.040 61.111 12.58 0.00 45.37 3.85
1168 1247 4.084888 GGCCGGCGTCAAGAAACG 62.085 66.667 22.54 0.00 45.31 3.60
1169 1248 4.084888 CGGCCGGCGTCAAGAAAC 62.085 66.667 22.54 1.28 0.00 2.78
1282 1370 3.522731 CTCCAGGAGAGGACGGCG 61.523 72.222 11.62 4.80 39.13 6.46
1322 1410 1.072505 GTGTGGAAGGGAAGCGGAA 59.927 57.895 0.00 0.00 0.00 4.30
1325 1413 0.895530 TAGAGTGTGGAAGGGAAGCG 59.104 55.000 0.00 0.00 0.00 4.68
1328 1416 3.375699 GGAGATAGAGTGTGGAAGGGAA 58.624 50.000 0.00 0.00 0.00 3.97
1329 1417 2.359355 GGGAGATAGAGTGTGGAAGGGA 60.359 54.545 0.00 0.00 0.00 4.20
1330 1418 2.043227 GGGAGATAGAGTGTGGAAGGG 58.957 57.143 0.00 0.00 0.00 3.95
1333 1421 1.112113 GCGGGAGATAGAGTGTGGAA 58.888 55.000 0.00 0.00 0.00 3.53
1334 1422 0.259065 AGCGGGAGATAGAGTGTGGA 59.741 55.000 0.00 0.00 0.00 4.02
1337 1425 1.853963 ACAAGCGGGAGATAGAGTGT 58.146 50.000 0.00 0.00 0.00 3.55
1339 1427 2.168728 GGAAACAAGCGGGAGATAGAGT 59.831 50.000 0.00 0.00 0.00 3.24
1345 1433 2.345991 CCGGAAACAAGCGGGAGA 59.654 61.111 0.00 0.00 0.00 3.71
1351 1439 2.200170 ATTCGCTGCCGGAAACAAGC 62.200 55.000 5.05 4.42 34.56 4.01
1353 1441 1.169661 ACATTCGCTGCCGGAAACAA 61.170 50.000 5.05 0.00 34.56 2.83
1369 1457 1.153086 GCAGGCCGGAGAATCACAT 60.153 57.895 5.05 0.00 36.25 3.21
1406 1495 1.213537 CGCCCCTTTTCTGCATGTG 59.786 57.895 0.00 0.00 0.00 3.21
1424 1513 9.837525 CGTATGTAGTAGGAGTATTAATGAACC 57.162 37.037 0.00 0.00 0.00 3.62
1438 1527 1.069159 CAGAGCGCCGTATGTAGTAGG 60.069 57.143 2.29 0.00 0.00 3.18
1563 1654 1.971167 GAACACGGGATGCCAAGCA 60.971 57.895 3.39 0.00 44.86 3.91
1564 1655 2.700773 GGAACACGGGATGCCAAGC 61.701 63.158 3.39 0.00 0.00 4.01
1565 1656 2.046285 GGGAACACGGGATGCCAAG 61.046 63.158 0.00 0.00 0.00 3.61
1566 1657 2.034999 GGGAACACGGGATGCCAA 59.965 61.111 0.00 0.00 0.00 4.52
1567 1658 4.402528 CGGGAACACGGGATGCCA 62.403 66.667 6.25 0.00 0.00 4.92
1568 1659 4.404098 ACGGGAACACGGGATGCC 62.404 66.667 0.00 0.00 38.39 4.40
1578 1669 3.119849 ACGTACTGTACATACACGGGAAC 60.120 47.826 20.94 3.41 30.51 3.62
1592 1683 1.372997 CCTCGCTTGCACGTACTGT 60.373 57.895 0.00 0.00 0.00 3.55
1596 1687 1.080772 CTGTCCTCGCTTGCACGTA 60.081 57.895 0.00 0.00 0.00 3.57
1597 1688 2.356313 CTGTCCTCGCTTGCACGT 60.356 61.111 0.00 0.00 0.00 4.49
1598 1689 1.498865 AAACTGTCCTCGCTTGCACG 61.499 55.000 0.00 0.00 0.00 5.34
1599 1690 0.235926 GAAACTGTCCTCGCTTGCAC 59.764 55.000 0.00 0.00 0.00 4.57
1600 1691 0.179059 TGAAACTGTCCTCGCTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
1602 1693 1.939934 TGTTGAAACTGTCCTCGCTTG 59.060 47.619 0.00 0.00 0.00 4.01
1604 1695 1.139058 ACTGTTGAAACTGTCCTCGCT 59.861 47.619 0.38 0.00 36.52 4.93
1606 1697 1.261619 GCACTGTTGAAACTGTCCTCG 59.738 52.381 3.06 0.00 38.76 4.63
1608 1699 1.680338 GGCACTGTTGAAACTGTCCT 58.320 50.000 3.06 0.00 38.76 3.85
1609 1700 0.668535 GGGCACTGTTGAAACTGTCC 59.331 55.000 3.06 7.56 38.76 4.02
1610 1701 0.668535 GGGGCACTGTTGAAACTGTC 59.331 55.000 3.06 0.00 38.76 3.51
1611 1702 0.755327 GGGGGCACTGTTGAAACTGT 60.755 55.000 0.38 0.38 41.00 3.55
1612 1703 0.468029 AGGGGGCACTGTTGAAACTG 60.468 55.000 0.00 0.00 0.00 3.16
1613 1704 0.261696 AAGGGGGCACTGTTGAAACT 59.738 50.000 0.00 0.00 0.00 2.66
1614 1705 0.389025 CAAGGGGGCACTGTTGAAAC 59.611 55.000 0.00 0.00 0.00 2.78
1617 1708 0.754957 CAACAAGGGGGCACTGTTGA 60.755 55.000 14.75 0.00 41.42 3.18
1627 1718 3.686016 ACATAGTAGCAACAACAAGGGG 58.314 45.455 0.00 0.00 0.00 4.79
1643 1736 7.063308 AGCAACACAAAACAGTCAAAAACATAG 59.937 33.333 0.00 0.00 0.00 2.23
1652 1745 3.254411 TCAACAGCAACACAAAACAGTCA 59.746 39.130 0.00 0.00 0.00 3.41
1653 1746 3.608073 GTCAACAGCAACACAAAACAGTC 59.392 43.478 0.00 0.00 0.00 3.51
1654 1747 3.574614 GTCAACAGCAACACAAAACAGT 58.425 40.909 0.00 0.00 0.00 3.55
1655 1748 2.593775 CGTCAACAGCAACACAAAACAG 59.406 45.455 0.00 0.00 0.00 3.16
1656 1749 2.590073 CGTCAACAGCAACACAAAACA 58.410 42.857 0.00 0.00 0.00 2.83
1657 1750 1.917303 CCGTCAACAGCAACACAAAAC 59.083 47.619 0.00 0.00 0.00 2.43
1658 1751 1.734047 GCCGTCAACAGCAACACAAAA 60.734 47.619 0.00 0.00 0.00 2.44
1668 1761 1.416813 GATCTGCTCGCCGTCAACAG 61.417 60.000 0.00 0.00 0.00 3.16
1671 1764 1.446099 GTGATCTGCTCGCCGTCAA 60.446 57.895 0.00 0.00 0.00 3.18
1672 1765 1.948721 ATGTGATCTGCTCGCCGTCA 61.949 55.000 0.00 0.00 33.18 4.35
1674 1767 1.227089 GATGTGATCTGCTCGCCGT 60.227 57.895 0.00 0.00 33.18 5.68
1675 1768 0.599466 ATGATGTGATCTGCTCGCCG 60.599 55.000 0.00 0.00 33.18 6.46
1676 1769 0.866427 CATGATGTGATCTGCTCGCC 59.134 55.000 0.00 0.00 33.18 5.54
1677 1770 0.866427 CCATGATGTGATCTGCTCGC 59.134 55.000 0.00 0.00 34.82 5.03
1678 1771 0.866427 GCCATGATGTGATCTGCTCG 59.134 55.000 0.00 0.00 0.00 5.03
1679 1772 1.236628 GGCCATGATGTGATCTGCTC 58.763 55.000 0.00 0.00 0.00 4.26
1680 1773 0.534427 CGGCCATGATGTGATCTGCT 60.534 55.000 2.24 0.00 0.00 4.24
1695 1788 4.493747 CCGGAGAACTCGTCGGCC 62.494 72.222 0.00 0.00 35.95 6.13
1781 1877 3.149196 ACATTTACACCCAACTGCAGAG 58.851 45.455 23.35 12.34 0.00 3.35
1782 1878 3.222173 ACATTTACACCCAACTGCAGA 57.778 42.857 23.35 0.00 0.00 4.26
1795 1891 3.364964 CCAGTGTCGCTCCAAACATTTAC 60.365 47.826 0.00 0.00 0.00 2.01
1812 1908 1.021390 CGGTTAGAGCCAAGCCAGTG 61.021 60.000 0.00 0.00 0.00 3.66
1827 1923 3.258228 CAAAACAAAAAGCCTCACGGTT 58.742 40.909 0.00 0.00 0.00 4.44
1837 1933 6.896969 TCTGCCAAGAAAACAAAACAAAAAG 58.103 32.000 0.00 0.00 0.00 2.27
1840 1936 5.936956 ACATCTGCCAAGAAAACAAAACAAA 59.063 32.000 0.00 0.00 35.59 2.83
1841 1937 5.486526 ACATCTGCCAAGAAAACAAAACAA 58.513 33.333 0.00 0.00 35.59 2.83
1842 1938 5.083533 ACATCTGCCAAGAAAACAAAACA 57.916 34.783 0.00 0.00 35.59 2.83
1843 1939 5.580297 TGAACATCTGCCAAGAAAACAAAAC 59.420 36.000 0.00 0.00 35.59 2.43
1902 1998 1.289109 ACCGCACGAACGATTTCTGG 61.289 55.000 0.14 0.00 34.06 3.86
1975 2162 0.522180 TCGAAGAGGAGCACGAACTC 59.478 55.000 0.00 0.00 35.86 3.01
2022 2222 0.179081 CTTTCCCTTCCGATCGACCC 60.179 60.000 18.66 0.00 0.00 4.46
2024 2224 0.179081 CCCTTTCCCTTCCGATCGAC 60.179 60.000 18.66 0.00 0.00 4.20
2032 2232 1.340502 CCTCTGCTTCCCTTTCCCTTC 60.341 57.143 0.00 0.00 0.00 3.46
2065 2265 0.810031 ATTGCGATGCGACCACTACC 60.810 55.000 0.00 0.00 0.00 3.18
2083 2294 3.450578 GCATTGTCAAAATGGATGCGAT 58.549 40.909 0.00 0.00 34.50 4.58
2084 2295 2.417107 GGCATTGTCAAAATGGATGCGA 60.417 45.455 0.00 0.00 42.93 5.10
2087 2298 3.527533 CAGGGCATTGTCAAAATGGATG 58.472 45.455 0.00 0.00 0.00 3.51
2088 2299 2.093341 GCAGGGCATTGTCAAAATGGAT 60.093 45.455 0.00 0.00 0.00 3.41
2089 2300 1.275856 GCAGGGCATTGTCAAAATGGA 59.724 47.619 0.00 0.00 0.00 3.41
2090 2301 1.729284 GCAGGGCATTGTCAAAATGG 58.271 50.000 0.00 0.00 0.00 3.16
2091 2302 1.067706 TCGCAGGGCATTGTCAAAATG 60.068 47.619 0.00 0.00 0.00 2.32
2092 2303 1.067635 GTCGCAGGGCATTGTCAAAAT 60.068 47.619 0.00 0.00 0.00 1.82
2093 2304 0.313672 GTCGCAGGGCATTGTCAAAA 59.686 50.000 0.00 0.00 0.00 2.44
2128 2353 1.154282 TCGTCTAAGTCAGTGCGCG 60.154 57.895 0.00 0.00 0.00 6.86
2159 2384 0.248702 GCCTAGCAGAGCGTACTGAC 60.249 60.000 13.41 6.34 39.94 3.51
2173 2402 0.107456 AGGGATTCATGTGCGCCTAG 59.893 55.000 4.18 0.00 0.00 3.02
2174 2403 0.179048 CAGGGATTCATGTGCGCCTA 60.179 55.000 4.18 0.00 0.00 3.93
2178 2407 1.721664 CTGCCAGGGATTCATGTGCG 61.722 60.000 0.00 0.00 0.00 5.34
2196 2425 0.249911 GTCTGTCGTTGTTGGGAGCT 60.250 55.000 0.00 0.00 0.00 4.09
2202 2431 1.597663 GGAAGGTGTCTGTCGTTGTTG 59.402 52.381 0.00 0.00 0.00 3.33
2203 2432 1.474498 GGGAAGGTGTCTGTCGTTGTT 60.474 52.381 0.00 0.00 0.00 2.83
2204 2433 0.106149 GGGAAGGTGTCTGTCGTTGT 59.894 55.000 0.00 0.00 0.00 3.32
2213 2442 1.078426 CCGTCCATGGGAAGGTGTC 60.078 63.158 13.02 0.00 44.42 3.67
2222 2451 4.508128 CCGTCCGTCCGTCCATGG 62.508 72.222 4.97 4.97 0.00 3.66
2243 2472 3.764049 GCAGTTCGTGCGTCCGTC 61.764 66.667 0.00 0.00 43.99 4.79
2292 2521 2.690778 GGTGCGTGGGAGACAATGC 61.691 63.158 0.00 0.00 34.33 3.56
2294 2523 0.321653 GAAGGTGCGTGGGAGACAAT 60.322 55.000 0.00 0.00 0.00 2.71
2305 2539 5.231357 GTGAAAAACCTAAAAAGAAGGTGCG 59.769 40.000 0.00 0.00 46.85 5.34
2310 2544 8.583765 CAAACGAGTGAAAAACCTAAAAAGAAG 58.416 33.333 0.00 0.00 0.00 2.85
2315 2549 7.148355 AGACAAACGAGTGAAAAACCTAAAA 57.852 32.000 0.00 0.00 0.00 1.52
2316 2550 6.746745 AGACAAACGAGTGAAAAACCTAAA 57.253 33.333 0.00 0.00 0.00 1.85
2317 2551 6.183360 GGAAGACAAACGAGTGAAAAACCTAA 60.183 38.462 0.00 0.00 0.00 2.69
2318 2552 5.295045 GGAAGACAAACGAGTGAAAAACCTA 59.705 40.000 0.00 0.00 0.00 3.08
2319 2553 4.095932 GGAAGACAAACGAGTGAAAAACCT 59.904 41.667 0.00 0.00 0.00 3.50
2320 2554 4.348656 GGAAGACAAACGAGTGAAAAACC 58.651 43.478 0.00 0.00 0.00 3.27
2321 2555 4.026407 CGGAAGACAAACGAGTGAAAAAC 58.974 43.478 0.00 0.00 0.00 2.43
2349 2583 1.447838 CGCTTGACCCACGTAGCAT 60.448 57.895 6.56 0.00 33.29 3.79
2386 2620 4.452733 CGAGTCAAGCCCGGGGAC 62.453 72.222 25.28 20.97 0.00 4.46
2562 2858 0.472044 TACCACCATGCACACACAGT 59.528 50.000 0.00 0.00 0.00 3.55
2569 2866 0.466189 CTCCCCATACCACCATGCAC 60.466 60.000 0.00 0.00 0.00 4.57
2572 2869 0.179009 CAGCTCCCCATACCACCATG 60.179 60.000 0.00 0.00 0.00 3.66
2588 2885 2.737376 GTCCCGTCAACGACCAGC 60.737 66.667 3.71 0.00 43.02 4.85
2613 2910 0.179215 CCTGCGAGCATCACGAAAAC 60.179 55.000 0.00 0.00 33.17 2.43
2618 2915 1.915614 AAAAGCCTGCGAGCATCACG 61.916 55.000 0.00 0.00 34.23 4.35
2666 2963 2.747460 TTGAGCGTGCCCATCAGC 60.747 61.111 0.00 0.00 0.00 4.26
2770 3067 1.202417 ACCATGATCACGAGCGGTTAG 60.202 52.381 0.00 0.00 0.00 2.34
2771 3068 0.821517 ACCATGATCACGAGCGGTTA 59.178 50.000 0.00 0.00 0.00 2.85
2773 3070 1.153568 CACCATGATCACGAGCGGT 60.154 57.895 0.00 0.00 0.00 5.68
2774 3071 2.528743 GCACCATGATCACGAGCGG 61.529 63.158 0.00 0.00 0.00 5.52
2775 3072 1.360931 TTGCACCATGATCACGAGCG 61.361 55.000 0.00 0.00 0.00 5.03
2776 3073 0.097674 GTTGCACCATGATCACGAGC 59.902 55.000 0.00 2.15 0.00 5.03
2780 3107 3.192001 ACATGAAGTTGCACCATGATCAC 59.808 43.478 18.54 0.00 39.86 3.06
2782 3109 3.766151 CACATGAAGTTGCACCATGATC 58.234 45.455 18.54 0.00 39.86 2.92
2789 3116 0.661187 CCACGCACATGAAGTTGCAC 60.661 55.000 0.00 0.00 0.00 4.57
2796 3124 1.585517 CCATTGCCACGCACATGAA 59.414 52.632 0.00 0.00 38.71 2.57
2799 3127 2.495366 CTTGCCATTGCCACGCACAT 62.495 55.000 0.00 0.00 38.71 3.21
2812 3140 7.953005 TCTTTCATATAAATTCCACTTGCCA 57.047 32.000 0.00 0.00 0.00 4.92
2813 3141 9.087424 GTTTCTTTCATATAAATTCCACTTGCC 57.913 33.333 0.00 0.00 0.00 4.52
2815 3143 9.840427 ACGTTTCTTTCATATAAATTCCACTTG 57.160 29.630 0.00 0.00 0.00 3.16
2818 3146 9.061610 CACACGTTTCTTTCATATAAATTCCAC 57.938 33.333 0.00 0.00 0.00 4.02
2819 3147 8.788806 ACACACGTTTCTTTCATATAAATTCCA 58.211 29.630 0.00 0.00 0.00 3.53
2820 3148 9.620660 AACACACGTTTCTTTCATATAAATTCC 57.379 29.630 0.00 0.00 28.09 3.01
2824 3152 8.747666 GCAAAACACACGTTTCTTTCATATAAA 58.252 29.630 0.00 0.00 44.65 1.40
2825 3153 8.132362 AGCAAAACACACGTTTCTTTCATATAA 58.868 29.630 0.00 0.00 44.65 0.98
2826 3154 7.644490 AGCAAAACACACGTTTCTTTCATATA 58.356 30.769 0.00 0.00 44.65 0.86
2827 3155 6.503524 AGCAAAACACACGTTTCTTTCATAT 58.496 32.000 0.00 0.00 44.65 1.78
2838 3169 2.030717 TGTCACAAAGCAAAACACACGT 60.031 40.909 0.00 0.00 0.00 4.49
2840 3171 2.923020 CCTGTCACAAAGCAAAACACAC 59.077 45.455 0.00 0.00 0.00 3.82
2841 3172 2.094286 CCCTGTCACAAAGCAAAACACA 60.094 45.455 0.00 0.00 0.00 3.72
3226 3560 3.914579 CTGCTGCTGGAGGGGTGTG 62.915 68.421 4.08 0.00 0.00 3.82
3233 3567 3.128188 CTGCTGCTGCTGCTGGAG 61.128 66.667 27.67 23.82 46.01 3.86
3487 3821 2.108976 ATCATGGCGCGGTAGGTG 59.891 61.111 8.83 0.00 0.00 4.00
3692 4075 6.589523 AGATTAATGACTTAGCGAGATGATGC 59.410 38.462 0.00 0.00 0.00 3.91
3701 4084 5.879237 TGCCAAAAGATTAATGACTTAGCG 58.121 37.500 0.00 0.00 0.00 4.26
3711 4094 6.000840 GGGGAAAATGTTGCCAAAAGATTAA 58.999 36.000 8.63 0.00 46.79 1.40
3796 4179 3.316308 GGGCTGTTATCTTACAATGGCTG 59.684 47.826 0.00 0.00 0.00 4.85
3840 4223 0.405585 TGGGAGCAGAAAGAAAGGGG 59.594 55.000 0.00 0.00 0.00 4.79
3861 4244 0.875059 CACGGAGGAAGAAACAAGCC 59.125 55.000 0.00 0.00 0.00 4.35
3870 4253 2.680312 ATCACATCACACGGAGGAAG 57.320 50.000 0.00 0.00 0.00 3.46
3911 4391 5.522460 CCAAGAACGTAAGAGTGAAAGTTGA 59.478 40.000 0.00 0.00 43.62 3.18
3974 4454 1.373748 CCAACGTACAGGTCCACCG 60.374 63.158 0.00 0.00 42.08 4.94
3982 4462 1.136085 CGCCATTTGACCAACGTACAG 60.136 52.381 0.00 0.00 0.00 2.74
3984 4464 0.453782 GCGCCATTTGACCAACGTAC 60.454 55.000 0.00 0.00 0.00 3.67
4032 4515 8.594550 AGCCTCACTAAGTTCATTACTTTCTAA 58.405 33.333 0.00 0.00 44.73 2.10
4034 4517 6.876257 CAGCCTCACTAAGTTCATTACTTTCT 59.124 38.462 0.00 0.00 44.73 2.52
4035 4518 6.651225 ACAGCCTCACTAAGTTCATTACTTTC 59.349 38.462 0.00 0.00 44.73 2.62
4036 4519 6.428159 CACAGCCTCACTAAGTTCATTACTTT 59.572 38.462 0.00 0.00 44.73 2.66
4039 4522 5.479306 TCACAGCCTCACTAAGTTCATTAC 58.521 41.667 0.00 0.00 0.00 1.89
4040 4523 5.738619 TCACAGCCTCACTAAGTTCATTA 57.261 39.130 0.00 0.00 0.00 1.90
4041 4524 4.623932 TCACAGCCTCACTAAGTTCATT 57.376 40.909 0.00 0.00 0.00 2.57
4042 4525 4.511527 CATCACAGCCTCACTAAGTTCAT 58.488 43.478 0.00 0.00 0.00 2.57
4043 4526 3.306989 CCATCACAGCCTCACTAAGTTCA 60.307 47.826 0.00 0.00 0.00 3.18
4044 4527 3.265791 CCATCACAGCCTCACTAAGTTC 58.734 50.000 0.00 0.00 0.00 3.01
4045 4528 2.616510 GCCATCACAGCCTCACTAAGTT 60.617 50.000 0.00 0.00 0.00 2.66
4046 4529 1.065854 GCCATCACAGCCTCACTAAGT 60.066 52.381 0.00 0.00 0.00 2.24
4053 4556 2.487532 GCCATGCCATCACAGCCTC 61.488 63.158 0.00 0.00 0.00 4.70
4070 4573 1.315257 ATCTTCAACGGCCATGGTGC 61.315 55.000 14.67 0.00 0.00 5.01
4087 4592 2.073816 TCCTCTCGCCGTTTCAAAATC 58.926 47.619 0.00 0.00 0.00 2.17
4099 4604 1.493311 CGTGTTGCTTTCCTCTCGC 59.507 57.895 0.00 0.00 0.00 5.03
4105 4610 0.868406 CACTCTCCGTGTTGCTTTCC 59.132 55.000 0.00 0.00 38.84 3.13
4190 4695 6.480524 TCATCATACTTGTGTTGTGCTTAC 57.519 37.500 0.00 0.00 0.00 2.34
4207 4713 3.418995 GCAGGCTCCATGTAATCATCAT 58.581 45.455 0.00 0.00 31.15 2.45
4208 4714 2.487805 GGCAGGCTCCATGTAATCATCA 60.488 50.000 0.00 0.00 31.15 3.07
4209 4715 2.157738 GGCAGGCTCCATGTAATCATC 58.842 52.381 0.00 0.00 31.15 2.92
4232 4738 7.097449 CGTACGTATGTATAACAAACGTGTAGG 60.097 40.741 7.22 0.00 32.48 3.18
4320 4841 2.733858 GCTGCTCGTCTCCTCAAAGTAG 60.734 54.545 0.00 0.00 0.00 2.57
4346 4867 3.403057 CGTCGTCAACCCTGCGTG 61.403 66.667 0.00 0.00 0.00 5.34
4347 4868 3.553437 CTCGTCGTCAACCCTGCGT 62.553 63.158 0.00 0.00 0.00 5.24
4348 4869 2.805353 CTCGTCGTCAACCCTGCG 60.805 66.667 0.00 0.00 0.00 5.18
4350 4871 2.805353 CGCTCGTCGTCAACCCTG 60.805 66.667 0.00 0.00 0.00 4.45
4351 4872 4.719369 GCGCTCGTCGTCAACCCT 62.719 66.667 0.00 0.00 41.07 4.34
4352 4873 4.719369 AGCGCTCGTCGTCAACCC 62.719 66.667 2.64 0.00 41.07 4.11
4353 4874 1.005294 TAAAGCGCTCGTCGTCAACC 61.005 55.000 12.06 0.00 41.07 3.77
4354 4875 0.780002 TTAAAGCGCTCGTCGTCAAC 59.220 50.000 12.06 0.00 41.07 3.18
4355 4876 1.057636 CTTAAAGCGCTCGTCGTCAA 58.942 50.000 12.06 0.00 41.07 3.18
4356 4877 1.342082 GCTTAAAGCGCTCGTCGTCA 61.342 55.000 12.06 0.00 41.07 4.35
4357 4878 1.340798 GCTTAAAGCGCTCGTCGTC 59.659 57.895 12.06 0.00 41.07 4.20
4358 4879 2.092882 GGCTTAAAGCGCTCGTCGT 61.093 57.895 12.06 0.00 43.62 4.34
4359 4880 2.695646 GGCTTAAAGCGCTCGTCG 59.304 61.111 12.06 0.75 43.62 5.12
4383 4904 0.608035 TTTGTAAGCTCTTGCGGGGG 60.608 55.000 0.00 0.00 45.42 5.40
4384 4905 1.243902 TTTTGTAAGCTCTTGCGGGG 58.756 50.000 0.00 0.00 45.42 5.73
4435 5027 9.356433 GCCAGTTTAAAGTTTGTAAAGTTTGTA 57.644 29.630 16.46 5.70 40.63 2.41
4436 5028 7.062488 CGCCAGTTTAAAGTTTGTAAAGTTTGT 59.938 33.333 16.46 0.00 40.63 2.83
4437 5029 7.387945 CGCCAGTTTAAAGTTTGTAAAGTTTG 58.612 34.615 16.46 4.35 40.63 2.93
4438 5030 6.532302 CCGCCAGTTTAAAGTTTGTAAAGTTT 59.468 34.615 13.02 13.02 42.45 2.66
4439 5031 6.037726 CCGCCAGTTTAAAGTTTGTAAAGTT 58.962 36.000 0.00 0.00 33.16 2.66
4440 5032 5.125900 ACCGCCAGTTTAAAGTTTGTAAAGT 59.874 36.000 0.00 0.00 0.00 2.66
4441 5033 5.457473 CACCGCCAGTTTAAAGTTTGTAAAG 59.543 40.000 0.00 0.00 0.00 1.85
4442 5034 5.341617 CACCGCCAGTTTAAAGTTTGTAAA 58.658 37.500 0.00 0.00 0.00 2.01
4443 5035 4.202030 CCACCGCCAGTTTAAAGTTTGTAA 60.202 41.667 0.00 0.00 0.00 2.41
4444 5036 3.315749 CCACCGCCAGTTTAAAGTTTGTA 59.684 43.478 0.00 0.00 0.00 2.41
4445 5037 2.100087 CCACCGCCAGTTTAAAGTTTGT 59.900 45.455 0.00 0.00 0.00 2.83
4446 5038 2.100087 ACCACCGCCAGTTTAAAGTTTG 59.900 45.455 0.00 0.00 0.00 2.93
4447 5039 2.380941 ACCACCGCCAGTTTAAAGTTT 58.619 42.857 0.00 0.00 0.00 2.66
4448 5040 2.061509 ACCACCGCCAGTTTAAAGTT 57.938 45.000 0.00 0.00 0.00 2.66
4449 5041 2.934886 TACCACCGCCAGTTTAAAGT 57.065 45.000 0.00 0.00 0.00 2.66
4450 5042 4.201881 GCTTATACCACCGCCAGTTTAAAG 60.202 45.833 0.00 0.00 0.00 1.85
4451 5043 3.690628 GCTTATACCACCGCCAGTTTAAA 59.309 43.478 0.00 0.00 0.00 1.52
4452 5044 3.272581 GCTTATACCACCGCCAGTTTAA 58.727 45.455 0.00 0.00 0.00 1.52
4453 5045 2.236644 TGCTTATACCACCGCCAGTTTA 59.763 45.455 0.00 0.00 0.00 2.01
4454 5046 1.003812 TGCTTATACCACCGCCAGTTT 59.996 47.619 0.00 0.00 0.00 2.66
4455 5047 0.616371 TGCTTATACCACCGCCAGTT 59.384 50.000 0.00 0.00 0.00 3.16
4456 5048 0.837272 ATGCTTATACCACCGCCAGT 59.163 50.000 0.00 0.00 0.00 4.00
4457 5049 1.603802 CAATGCTTATACCACCGCCAG 59.396 52.381 0.00 0.00 0.00 4.85
4458 5050 1.674359 CAATGCTTATACCACCGCCA 58.326 50.000 0.00 0.00 0.00 5.69
4459 5051 0.951558 CCAATGCTTATACCACCGCC 59.048 55.000 0.00 0.00 0.00 6.13
4460 5052 1.602377 GTCCAATGCTTATACCACCGC 59.398 52.381 0.00 0.00 0.00 5.68
4461 5053 1.864711 CGTCCAATGCTTATACCACCG 59.135 52.381 0.00 0.00 0.00 4.94
4497 5089 0.393673 GGAAAAGAGAGGGCTGCTCC 60.394 60.000 0.00 0.00 32.82 4.70
4538 5130 0.682209 GATGCATGCCCACTGTTCCT 60.682 55.000 16.68 0.00 0.00 3.36
4539 5131 1.811860 GATGCATGCCCACTGTTCC 59.188 57.895 16.68 0.00 0.00 3.62
4540 5132 1.430632 CGATGCATGCCCACTGTTC 59.569 57.895 16.68 0.05 0.00 3.18
4568 5160 1.365699 GGCCGCAAAAGAAGATCGTA 58.634 50.000 0.00 0.00 0.00 3.43
4569 5161 1.635663 CGGCCGCAAAAGAAGATCGT 61.636 55.000 14.67 0.00 0.00 3.73
4570 5162 1.060937 CGGCCGCAAAAGAAGATCG 59.939 57.895 14.67 0.00 0.00 3.69
4595 5187 3.066621 GGCATATGGATCAACGAAAGCAA 59.933 43.478 4.56 0.00 0.00 3.91
4615 5207 1.612726 GGGACAGATCCTGCATATGGC 60.613 57.143 4.56 0.00 45.46 4.40


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

AutoCloner maintained by Alex Coulton.