Multiple sequence alignment - TraesCS5A01G001300

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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 TraesCS5A01G001300 chr5A 100.000 2366 0 0 1 2366 1202266 1199901 0.000000e+00 4370.0
1 TraesCS5A01G001300 chr5A 87.500 656 60 14 966 1608 1114471 1113825 0.000000e+00 737.0
2 TraesCS5A01G001300 chr5A 79.494 356 52 4 1620 1975 1113596 1113262 1.410000e-57 233.0
3 TraesCS5A01G001300 chr5A 84.800 125 12 5 2246 2365 374918702 374918580 4.130000e-23 119.0
4 TraesCS5A01G001300 chr5D 88.256 1669 86 43 1 1608 2121837 2120218 0.000000e+00 1895.0
5 TraesCS5A01G001300 chr5D 85.922 412 55 3 1617 2027 2119011 2118602 1.000000e-118 436.0
6 TraesCS5A01G001300 chr5D 75.630 357 45 17 2039 2366 94048428 94048771 3.170000e-29 139.0
7 TraesCS5A01G001300 chr5B 87.207 1407 94 39 1 1381 4060126 4061472 0.000000e+00 1522.0
8 TraesCS5A01G001300 chr1D 87.597 129 6 7 2246 2365 490036821 490036948 8.820000e-30 141.0
9 TraesCS5A01G001300 chr6D 86.719 128 8 6 2246 2365 447911159 447911285 1.480000e-27 134.0
10 TraesCS5A01G001300 chr6D 86.260 131 6 8 2246 2365 453944493 453944364 5.310000e-27 132.0
11 TraesCS5A01G001300 chr6D 83.333 126 13 6 2246 2365 82099877 82099754 2.490000e-20 110.0
12 TraesCS5A01G001300 chr7A 85.600 125 11 4 2246 2365 115737697 115737819 8.880000e-25 124.0
13 TraesCS5A01G001300 chr7B 97.727 44 1 0 2041 2084 474126916 474126959 2.520000e-10 76.8
14 TraesCS5A01G001300 chr4D 95.652 46 2 0 2039 2084 233148211 233148256 9.070000e-10 75.0
15 TraesCS5A01G001300 chr3B 95.652 46 2 0 2039 2084 486815454 486815499 9.070000e-10 75.0
16 TraesCS5A01G001300 chr2B 91.837 49 4 0 2042 2090 114505160 114505112 4.220000e-08 69.4
17 TraesCS5A01G001300 chr6B 93.023 43 3 0 2048 2090 346802520 346802478 1.960000e-06 63.9
18 TraesCS5A01G001300 chr1B 91.304 46 4 0 2039 2084 598370050 598370095 1.960000e-06 63.9


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 TraesCS5A01G001300 chr5A 1199901 1202266 2365 True 4370.0 4370 100.000 1 2366 1 chr5A.!!$R1 2365
1 TraesCS5A01G001300 chr5A 1113262 1114471 1209 True 485.0 737 83.497 966 1975 2 chr5A.!!$R3 1009
2 TraesCS5A01G001300 chr5D 2118602 2121837 3235 True 1165.5 1895 87.089 1 2027 2 chr5D.!!$R1 2026
3 TraesCS5A01G001300 chr5B 4060126 4061472 1346 False 1522.0 1522 87.207 1 1381 1 chr5B.!!$F1 1380

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
608 636 0.026544 GAAGACGCCTCTACTCGACG 59.973 60.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 3434 0.029834 GGCGGATGTGCTAATTGCTG 59.97 55.0 0.0 0.0 43.37 4.41 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
30 31 0.033504 ACGACGATGACAAGGTGCTT 59.966 50.000 0.00 0.00 0.00 3.91
45 46 2.203280 CTTGTGGCGGTGGTGGAA 60.203 61.111 0.00 0.00 0.00 3.53
210 220 5.220548 CGATGAAGCCATAACTGTTCTTCTG 60.221 44.000 16.04 6.87 34.13 3.02
231 241 2.824041 CCGGCCCTATGTGTGTGC 60.824 66.667 0.00 0.00 0.00 4.57
233 243 2.046314 GGCCCTATGTGTGTGCGT 60.046 61.111 0.00 0.00 0.00 5.24
270 280 7.596995 GGAAGTATCTCGATCTTATCAAGTTGG 59.403 40.741 2.34 0.00 0.00 3.77
271 281 7.825331 AGTATCTCGATCTTATCAAGTTGGA 57.175 36.000 2.34 0.00 0.00 3.53
272 282 8.239038 AGTATCTCGATCTTATCAAGTTGGAA 57.761 34.615 2.34 0.00 0.00 3.53
273 283 8.138712 AGTATCTCGATCTTATCAAGTTGGAAC 58.861 37.037 2.34 0.00 0.00 3.62
274 284 6.531503 TCTCGATCTTATCAAGTTGGAACT 57.468 37.500 2.34 0.00 42.04 3.01
288 298 5.694995 AGTTGGAACTTGGAAGAGAATTGA 58.305 37.500 0.00 0.00 35.21 2.57
486 514 2.434134 CGCGTACGTGTCCTGCTTC 61.434 63.158 20.36 0.00 33.53 3.86
504 532 2.504681 GCAGCCGCCAACGAAATG 60.505 61.111 0.00 0.00 43.93 2.32
507 535 1.376683 AGCCGCCAACGAAATGCTA 60.377 52.632 0.00 0.00 43.93 3.49
537 565 1.153066 TTCTCGCAACCAACAGCCA 60.153 52.632 0.00 0.00 0.00 4.75
606 634 0.035725 TGGAAGACGCCTCTACTCGA 60.036 55.000 0.00 0.00 0.00 4.04
607 635 0.377905 GGAAGACGCCTCTACTCGAC 59.622 60.000 0.00 0.00 0.00 4.20
608 636 0.026544 GAAGACGCCTCTACTCGACG 59.973 60.000 0.00 0.00 0.00 5.12
609 637 0.390866 AAGACGCCTCTACTCGACGA 60.391 55.000 0.00 0.00 0.00 4.20
611 639 2.320383 CGCCTCTACTCGACGACG 59.680 66.667 0.00 0.00 41.26 5.12
612 640 2.163390 CGCCTCTACTCGACGACGA 61.163 63.158 9.98 9.98 46.56 4.20
628 656 8.176814 TCGACGACGAAAGAATTATTTTATGT 57.823 30.769 7.68 0.00 45.74 2.29
629 657 8.649841 TCGACGACGAAAGAATTATTTTATGTT 58.350 29.630 7.68 0.00 45.74 2.71
630 658 9.257865 CGACGACGAAAGAATTATTTTATGTTT 57.742 29.630 0.00 0.00 42.66 2.83
632 660 9.887406 ACGACGAAAGAATTATTTTATGTTTGT 57.113 25.926 0.00 1.22 0.00 2.83
654 682 5.818336 TGTACACGACCAAAAGAATTTCTCA 59.182 36.000 0.00 0.00 37.28 3.27
817 869 1.301244 CCGGCCATGATCGAGAAGG 60.301 63.158 2.24 0.00 0.00 3.46
819 871 1.449353 GGCCATGATCGAGAAGGCT 59.551 57.895 17.01 0.00 44.60 4.58
995 1065 0.948678 AATCAACCAACCAACCGACG 59.051 50.000 0.00 0.00 0.00 5.12
1483 1565 5.588648 TGAATCAATTGTCTAATTCGGGACC 59.411 40.000 5.13 0.00 34.34 4.46
1489 1571 1.134189 GTCTAATTCGGGACCAAGGGG 60.134 57.143 0.00 0.00 41.29 4.79
1542 1629 1.108776 TATTTGCTCTCCCGTACGCT 58.891 50.000 10.49 0.00 0.00 5.07
1566 1653 5.179368 TCGTTGTCTTGATTGACCATTTCTC 59.821 40.000 0.00 0.00 36.21 2.87
1568 1655 6.606768 GTTGTCTTGATTGACCATTTCTCTC 58.393 40.000 0.00 0.00 36.21 3.20
1572 1660 7.503566 TGTCTTGATTGACCATTTCTCTCTTTT 59.496 33.333 0.00 0.00 36.21 2.27
1631 1719 8.681486 ATTATTTGTAAGATATGCAGTGCTCA 57.319 30.769 17.60 4.03 0.00 4.26
1632 1720 5.801350 TTTGTAAGATATGCAGTGCTCAC 57.199 39.130 17.60 5.45 0.00 3.51
1633 1721 4.470334 TGTAAGATATGCAGTGCTCACA 57.530 40.909 17.60 4.48 0.00 3.58
1635 1723 4.872124 TGTAAGATATGCAGTGCTCACAAG 59.128 41.667 17.60 0.00 0.00 3.16
1636 1724 2.915349 AGATATGCAGTGCTCACAAGG 58.085 47.619 17.60 0.00 0.00 3.61
1638 1726 2.391616 TATGCAGTGCTCACAAGGAG 57.608 50.000 17.60 0.00 46.93 3.69
1647 1735 2.652941 CTCACAAGGAGCTCTCACTC 57.347 55.000 14.64 0.00 36.69 3.51
1649 1737 2.164219 CTCACAAGGAGCTCTCACTCTC 59.836 54.545 14.64 0.00 36.69 3.20
1654 1742 2.428544 GGAGCTCTCACTCTCCTACA 57.571 55.000 14.64 0.00 44.19 2.74
1655 1743 2.944129 GGAGCTCTCACTCTCCTACAT 58.056 52.381 14.64 0.00 44.19 2.29
1657 1745 4.072131 GGAGCTCTCACTCTCCTACATAG 58.928 52.174 14.64 0.00 44.19 2.23
1658 1746 4.445735 GGAGCTCTCACTCTCCTACATAGT 60.446 50.000 14.64 0.00 44.19 2.12
1659 1747 4.714632 AGCTCTCACTCTCCTACATAGTC 58.285 47.826 0.00 0.00 0.00 2.59
1660 1748 4.165180 AGCTCTCACTCTCCTACATAGTCA 59.835 45.833 0.00 0.00 0.00 3.41
1663 1751 5.432645 TCTCACTCTCCTACATAGTCAGTG 58.567 45.833 0.00 0.00 0.00 3.66
1664 1752 5.189934 TCTCACTCTCCTACATAGTCAGTGA 59.810 44.000 0.00 0.00 37.14 3.41
1665 1753 6.007485 TCACTCTCCTACATAGTCAGTGAT 57.993 41.667 0.00 0.00 35.11 3.06
1690 2172 6.611236 TGATATGAATGGAGACCAGTGTAAGA 59.389 38.462 0.00 0.00 36.75 2.10
1698 2180 4.398673 GGAGACCAGTGTAAGACGTATTCT 59.601 45.833 0.00 0.00 35.32 2.40
1699 2181 5.312120 AGACCAGTGTAAGACGTATTCTG 57.688 43.478 0.00 0.65 33.46 3.02
1700 2182 4.765856 AGACCAGTGTAAGACGTATTCTGT 59.234 41.667 0.00 0.00 33.46 3.41
1702 2184 4.096311 CCAGTGTAAGACGTATTCTGTCG 58.904 47.826 0.00 0.00 41.24 4.35
1719 2201 2.239907 TGTCGAGGAGATCAGAGAAGGA 59.760 50.000 0.00 0.00 0.00 3.36
1722 2204 1.963515 GAGGAGATCAGAGAAGGAGCC 59.036 57.143 0.00 0.00 0.00 4.70
1744 2226 3.432326 CCATGAAGGCACTAGGACCTAAC 60.432 52.174 2.08 5.26 38.49 2.34
1767 2249 1.779221 TCCCCGACGCCTTTCTAATA 58.221 50.000 0.00 0.00 0.00 0.98
1775 2257 4.704965 GACGCCTTTCTAATAGACCCATT 58.295 43.478 0.00 0.00 0.00 3.16
1793 2275 6.909909 ACCCATTAGAAACGCTTTTAAAGAG 58.090 36.000 9.10 7.93 0.00 2.85
1801 2283 7.145985 AGAAACGCTTTTAAAGAGGGAATTTC 58.854 34.615 9.10 10.53 32.10 2.17
1803 2285 7.754851 AACGCTTTTAAAGAGGGAATTTCTA 57.245 32.000 9.10 0.00 32.10 2.10
1806 2288 7.229907 ACGCTTTTAAAGAGGGAATTTCTACAA 59.770 33.333 9.10 0.00 32.10 2.41
1825 2307 7.107542 TCTACAATTATTAGCGGTTTCTTGGT 58.892 34.615 0.00 0.00 0.00 3.67
1835 2317 5.145564 AGCGGTTTCTTGGTAGGAGATATA 58.854 41.667 0.00 0.00 0.00 0.86
1839 2321 7.117956 GCGGTTTCTTGGTAGGAGATATAATTC 59.882 40.741 0.00 0.00 0.00 2.17
1841 2323 9.713713 GGTTTCTTGGTAGGAGATATAATTCTC 57.286 37.037 0.00 0.00 41.21 2.87
1851 2333 8.560124 AGGAGATATAATTCTCAAGGAGTTGT 57.440 34.615 5.85 0.00 43.28 3.32
1859 2341 3.223435 TCTCAAGGAGTTGTTCGACTCT 58.777 45.455 16.64 4.14 44.32 3.24
1865 2347 3.833070 AGGAGTTGTTCGACTCTACCATT 59.167 43.478 16.64 0.00 44.32 3.16
1869 2351 4.750098 AGTTGTTCGACTCTACCATTGTTG 59.250 41.667 0.00 0.00 0.00 3.33
1882 3169 2.749076 CCATTGTTGCGATCTCAAAGGA 59.251 45.455 0.00 0.00 33.52 3.36
1883 3170 3.191162 CCATTGTTGCGATCTCAAAGGAA 59.809 43.478 0.00 0.00 33.52 3.36
1887 3174 3.629855 TGTTGCGATCTCAAAGGAAAACA 59.370 39.130 0.00 0.00 0.00 2.83
1891 3179 3.611766 GCGATCTCAAAGGAAAACAACCC 60.612 47.826 0.00 0.00 0.00 4.11
1930 3218 4.460034 ACACACATGTATGCACACATTCAT 59.540 37.500 8.16 0.00 42.91 2.57
1933 3221 5.416639 ACACATGTATGCACACATTCATTCT 59.583 36.000 8.16 0.00 40.26 2.40
1970 3258 4.665451 CCAATGGGATGTTGCCTATATGA 58.335 43.478 0.00 0.00 35.59 2.15
1997 3285 3.441222 CACATGCTTGCAGGTAAGAATCA 59.559 43.478 12.50 0.00 0.00 2.57
2023 3311 6.279123 ACATATCAGACTGACATCATCACAC 58.721 40.000 7.47 0.00 32.37 3.82
2027 3315 5.714047 TCAGACTGACATCATCACACTAAC 58.286 41.667 0.00 0.00 32.37 2.34
2028 3316 5.243730 TCAGACTGACATCATCACACTAACA 59.756 40.000 0.00 0.00 32.37 2.41
2029 3317 5.347093 CAGACTGACATCATCACACTAACAC 59.653 44.000 0.00 0.00 32.37 3.32
2030 3318 5.244851 AGACTGACATCATCACACTAACACT 59.755 40.000 0.00 0.00 32.37 3.55
2031 3319 5.858381 ACTGACATCATCACACTAACACTT 58.142 37.500 0.00 0.00 32.37 3.16
2032 3320 5.928839 ACTGACATCATCACACTAACACTTC 59.071 40.000 0.00 0.00 32.37 3.01
2033 3321 6.101650 TGACATCATCACACTAACACTTCT 57.898 37.500 0.00 0.00 29.99 2.85
2034 3322 5.928264 TGACATCATCACACTAACACTTCTG 59.072 40.000 0.00 0.00 29.99 3.02
2035 3323 4.692625 ACATCATCACACTAACACTTCTGC 59.307 41.667 0.00 0.00 0.00 4.26
2036 3324 4.607293 TCATCACACTAACACTTCTGCT 57.393 40.909 0.00 0.00 0.00 4.24
2037 3325 4.960938 TCATCACACTAACACTTCTGCTT 58.039 39.130 0.00 0.00 0.00 3.91
2038 3326 4.991056 TCATCACACTAACACTTCTGCTTC 59.009 41.667 0.00 0.00 0.00 3.86
2039 3327 4.672587 TCACACTAACACTTCTGCTTCT 57.327 40.909 0.00 0.00 0.00 2.85
2040 3328 5.023533 TCACACTAACACTTCTGCTTCTT 57.976 39.130 0.00 0.00 0.00 2.52
2041 3329 5.428253 TCACACTAACACTTCTGCTTCTTT 58.572 37.500 0.00 0.00 0.00 2.52
2042 3330 5.880332 TCACACTAACACTTCTGCTTCTTTT 59.120 36.000 0.00 0.00 0.00 2.27
2043 3331 6.037172 TCACACTAACACTTCTGCTTCTTTTC 59.963 38.462 0.00 0.00 0.00 2.29
2044 3332 5.880332 ACACTAACACTTCTGCTTCTTTTCA 59.120 36.000 0.00 0.00 0.00 2.69
2045 3333 6.543831 ACACTAACACTTCTGCTTCTTTTCAT 59.456 34.615 0.00 0.00 0.00 2.57
2046 3334 7.715249 ACACTAACACTTCTGCTTCTTTTCATA 59.285 33.333 0.00 0.00 0.00 2.15
2047 3335 8.559536 CACTAACACTTCTGCTTCTTTTCATAA 58.440 33.333 0.00 0.00 0.00 1.90
2048 3336 8.778358 ACTAACACTTCTGCTTCTTTTCATAAG 58.222 33.333 0.00 0.00 0.00 1.73
2049 3337 7.573968 AACACTTCTGCTTCTTTTCATAAGT 57.426 32.000 0.00 0.00 32.25 2.24
2050 3338 8.677148 AACACTTCTGCTTCTTTTCATAAGTA 57.323 30.769 0.00 0.00 31.33 2.24
2051 3339 8.677148 ACACTTCTGCTTCTTTTCATAAGTAA 57.323 30.769 0.00 0.00 31.33 2.24
2052 3340 8.778358 ACACTTCTGCTTCTTTTCATAAGTAAG 58.222 33.333 0.00 0.00 31.33 2.34
2053 3341 8.233190 CACTTCTGCTTCTTTTCATAAGTAAGG 58.767 37.037 0.00 0.00 31.33 2.69
2054 3342 7.391833 ACTTCTGCTTCTTTTCATAAGTAAGGG 59.608 37.037 0.00 0.00 30.93 3.95
2055 3343 6.779860 TCTGCTTCTTTTCATAAGTAAGGGT 58.220 36.000 0.00 0.00 0.00 4.34
2056 3344 7.913789 TCTGCTTCTTTTCATAAGTAAGGGTA 58.086 34.615 0.00 0.00 0.00 3.69
2057 3345 8.548877 TCTGCTTCTTTTCATAAGTAAGGGTAT 58.451 33.333 0.00 0.00 0.00 2.73
2058 3346 8.506168 TGCTTCTTTTCATAAGTAAGGGTATG 57.494 34.615 0.00 0.00 0.00 2.39
2059 3347 8.325787 TGCTTCTTTTCATAAGTAAGGGTATGA 58.674 33.333 0.00 0.00 35.44 2.15
2060 3348 9.343539 GCTTCTTTTCATAAGTAAGGGTATGAT 57.656 33.333 0.00 0.00 36.78 2.45
2100 3388 9.809096 AAACTCTTCATCTATACACTGTACATG 57.191 33.333 0.00 0.00 0.00 3.21
2101 3389 8.753497 ACTCTTCATCTATACACTGTACATGA 57.247 34.615 0.00 0.00 0.00 3.07
2102 3390 9.190317 ACTCTTCATCTATACACTGTACATGAA 57.810 33.333 0.00 14.08 0.00 2.57
2103 3391 9.457110 CTCTTCATCTATACACTGTACATGAAC 57.543 37.037 0.00 0.00 0.00 3.18
2104 3392 8.414003 TCTTCATCTATACACTGTACATGAACC 58.586 37.037 0.00 0.00 0.00 3.62
2105 3393 7.654022 TCATCTATACACTGTACATGAACCA 57.346 36.000 0.00 0.00 0.00 3.67
2106 3394 7.489160 TCATCTATACACTGTACATGAACCAC 58.511 38.462 0.00 0.00 0.00 4.16
2107 3395 6.844097 TCTATACACTGTACATGAACCACA 57.156 37.500 0.00 0.00 0.00 4.17
2108 3396 7.234661 TCTATACACTGTACATGAACCACAA 57.765 36.000 0.00 0.00 0.00 3.33
2109 3397 7.672240 TCTATACACTGTACATGAACCACAAA 58.328 34.615 0.00 0.00 0.00 2.83
2110 3398 8.151596 TCTATACACTGTACATGAACCACAAAA 58.848 33.333 0.00 0.00 0.00 2.44
2111 3399 5.906113 ACACTGTACATGAACCACAAAAA 57.094 34.783 0.00 0.00 0.00 1.94
2135 3423 2.096799 GCATGCTGCAAGATTCGTAC 57.903 50.000 11.37 0.00 44.26 3.67
2136 3424 1.268234 GCATGCTGCAAGATTCGTACC 60.268 52.381 11.37 0.00 44.26 3.34
2137 3425 2.009051 CATGCTGCAAGATTCGTACCA 58.991 47.619 6.36 0.00 34.07 3.25
2138 3426 2.177394 TGCTGCAAGATTCGTACCAA 57.823 45.000 0.00 0.00 34.07 3.67
2139 3427 2.076100 TGCTGCAAGATTCGTACCAAG 58.924 47.619 0.00 0.00 34.07 3.61
2140 3428 2.289382 TGCTGCAAGATTCGTACCAAGA 60.289 45.455 0.00 0.00 34.07 3.02
2141 3429 2.939103 GCTGCAAGATTCGTACCAAGAT 59.061 45.455 0.00 0.00 34.07 2.40
2142 3430 3.001736 GCTGCAAGATTCGTACCAAGATC 59.998 47.826 0.00 0.00 34.07 2.75
2143 3431 3.186909 TGCAAGATTCGTACCAAGATCG 58.813 45.455 0.00 0.00 0.00 3.69
2144 3432 3.187700 GCAAGATTCGTACCAAGATCGT 58.812 45.455 0.00 0.00 0.00 3.73
2145 3433 3.617263 GCAAGATTCGTACCAAGATCGTT 59.383 43.478 0.00 0.00 0.00 3.85
2146 3434 4.259850 GCAAGATTCGTACCAAGATCGTTC 60.260 45.833 0.00 0.00 0.00 3.95
2147 3435 4.713824 AGATTCGTACCAAGATCGTTCA 57.286 40.909 0.00 0.00 0.00 3.18
2148 3436 4.673441 AGATTCGTACCAAGATCGTTCAG 58.327 43.478 0.00 0.00 0.00 3.02
2149 3437 2.273370 TCGTACCAAGATCGTTCAGC 57.727 50.000 0.00 0.00 0.00 4.26
2150 3438 1.542472 TCGTACCAAGATCGTTCAGCA 59.458 47.619 0.00 0.00 0.00 4.41
2151 3439 2.029739 TCGTACCAAGATCGTTCAGCAA 60.030 45.455 0.00 0.00 0.00 3.91
2152 3440 2.930040 CGTACCAAGATCGTTCAGCAAT 59.070 45.455 0.00 0.00 0.00 3.56
2153 3441 3.370978 CGTACCAAGATCGTTCAGCAATT 59.629 43.478 0.00 0.00 0.00 2.32
2154 3442 4.565166 CGTACCAAGATCGTTCAGCAATTA 59.435 41.667 0.00 0.00 0.00 1.40
2155 3443 5.276395 CGTACCAAGATCGTTCAGCAATTAG 60.276 44.000 0.00 0.00 0.00 1.73
2156 3444 3.375299 ACCAAGATCGTTCAGCAATTAGC 59.625 43.478 0.00 0.00 46.19 3.09
2166 3454 2.408333 GCAATTAGCACATCCGCCT 58.592 52.632 0.00 0.00 44.79 5.52
2167 3455 0.740737 GCAATTAGCACATCCGCCTT 59.259 50.000 0.00 0.00 44.79 4.35
2168 3456 1.946768 GCAATTAGCACATCCGCCTTA 59.053 47.619 0.00 0.00 44.79 2.69
2169 3457 2.357637 GCAATTAGCACATCCGCCTTAA 59.642 45.455 0.00 0.00 44.79 1.85
2170 3458 3.792124 GCAATTAGCACATCCGCCTTAAC 60.792 47.826 0.00 0.00 44.79 2.01
2171 3459 2.032680 TTAGCACATCCGCCTTAACC 57.967 50.000 0.00 0.00 0.00 2.85
2172 3460 0.906066 TAGCACATCCGCCTTAACCA 59.094 50.000 0.00 0.00 0.00 3.67
2173 3461 0.037590 AGCACATCCGCCTTAACCAA 59.962 50.000 0.00 0.00 0.00 3.67
2174 3462 1.102978 GCACATCCGCCTTAACCAAT 58.897 50.000 0.00 0.00 0.00 3.16
2175 3463 1.202290 GCACATCCGCCTTAACCAATG 60.202 52.381 0.00 0.00 0.00 2.82
2176 3464 1.405105 CACATCCGCCTTAACCAATGG 59.595 52.381 0.00 0.00 0.00 3.16
2177 3465 1.283613 ACATCCGCCTTAACCAATGGA 59.716 47.619 6.16 0.00 0.00 3.41
2178 3466 1.949525 CATCCGCCTTAACCAATGGAG 59.050 52.381 6.16 0.00 0.00 3.86
2179 3467 0.393808 TCCGCCTTAACCAATGGAGC 60.394 55.000 6.16 0.00 0.00 4.70
2180 3468 0.679640 CCGCCTTAACCAATGGAGCA 60.680 55.000 6.16 0.00 0.00 4.26
2181 3469 1.173043 CGCCTTAACCAATGGAGCAA 58.827 50.000 6.16 0.00 0.00 3.91
2182 3470 1.135402 CGCCTTAACCAATGGAGCAAC 60.135 52.381 6.16 0.00 0.00 4.17
2183 3471 1.204704 GCCTTAACCAATGGAGCAACC 59.795 52.381 6.16 0.00 39.54 3.77
2193 3481 0.984230 TGGAGCAACCAGACCTAAGG 59.016 55.000 0.00 0.00 44.64 2.69
2194 3482 0.984995 GGAGCAACCAGACCTAAGGT 59.015 55.000 0.00 0.00 40.61 3.50
2195 3483 1.339151 GGAGCAACCAGACCTAAGGTG 60.339 57.143 0.00 0.00 38.37 4.00
2196 3484 1.348036 GAGCAACCAGACCTAAGGTGT 59.652 52.381 0.00 0.00 38.37 4.16
2197 3485 1.774856 AGCAACCAGACCTAAGGTGTT 59.225 47.619 0.00 0.00 38.37 3.32
2198 3486 2.976882 AGCAACCAGACCTAAGGTGTTA 59.023 45.455 0.00 0.00 38.37 2.41
2199 3487 3.393278 AGCAACCAGACCTAAGGTGTTAA 59.607 43.478 0.00 0.00 38.37 2.01
2200 3488 3.751698 GCAACCAGACCTAAGGTGTTAAG 59.248 47.826 0.00 0.00 38.37 1.85
2201 3489 4.745783 GCAACCAGACCTAAGGTGTTAAGT 60.746 45.833 0.00 0.00 38.37 2.24
2202 3490 5.511888 GCAACCAGACCTAAGGTGTTAAGTA 60.512 44.000 0.00 0.00 38.37 2.24
2203 3491 6.708285 CAACCAGACCTAAGGTGTTAAGTAT 58.292 40.000 0.00 0.00 38.37 2.12
2204 3492 6.295719 ACCAGACCTAAGGTGTTAAGTATG 57.704 41.667 0.00 0.00 35.25 2.39
2205 3493 5.783875 ACCAGACCTAAGGTGTTAAGTATGT 59.216 40.000 0.00 0.00 35.25 2.29
2206 3494 6.271624 ACCAGACCTAAGGTGTTAAGTATGTT 59.728 38.462 0.00 0.00 35.25 2.71
2207 3495 7.166167 CCAGACCTAAGGTGTTAAGTATGTTT 58.834 38.462 0.00 0.00 35.25 2.83
2208 3496 7.664318 CCAGACCTAAGGTGTTAAGTATGTTTT 59.336 37.037 0.00 0.00 35.25 2.43
2209 3497 8.718734 CAGACCTAAGGTGTTAAGTATGTTTTC 58.281 37.037 0.00 0.00 35.25 2.29
2210 3498 8.657712 AGACCTAAGGTGTTAAGTATGTTTTCT 58.342 33.333 0.00 0.00 35.25 2.52
2211 3499 9.281371 GACCTAAGGTGTTAAGTATGTTTTCTT 57.719 33.333 0.00 0.00 35.25 2.52
2239 3527 7.193595 ACTTGAAATAGAACACTGGAAAAACG 58.806 34.615 0.00 0.00 0.00 3.60
2240 3528 5.516090 TGAAATAGAACACTGGAAAAACGC 58.484 37.500 0.00 0.00 0.00 4.84
2241 3529 5.066634 TGAAATAGAACACTGGAAAAACGCA 59.933 36.000 0.00 0.00 0.00 5.24
2242 3530 5.508200 AATAGAACACTGGAAAAACGCAA 57.492 34.783 0.00 0.00 0.00 4.85
2243 3531 3.145212 AGAACACTGGAAAAACGCAAC 57.855 42.857 0.00 0.00 0.00 4.17
2244 3532 2.490115 AGAACACTGGAAAAACGCAACA 59.510 40.909 0.00 0.00 0.00 3.33
2245 3533 3.130340 AGAACACTGGAAAAACGCAACAT 59.870 39.130 0.00 0.00 0.00 2.71
2246 3534 3.518634 ACACTGGAAAAACGCAACATT 57.481 38.095 0.00 0.00 0.00 2.71
2247 3535 3.855858 ACACTGGAAAAACGCAACATTT 58.144 36.364 0.00 0.00 0.00 2.32
2248 3536 4.249661 ACACTGGAAAAACGCAACATTTT 58.750 34.783 0.00 0.00 0.00 1.82
2249 3537 4.328712 ACACTGGAAAAACGCAACATTTTC 59.671 37.500 0.00 0.00 42.19 2.29
2250 3538 4.566360 CACTGGAAAAACGCAACATTTTCT 59.434 37.500 9.90 0.00 42.43 2.52
2251 3539 5.063312 CACTGGAAAAACGCAACATTTTCTT 59.937 36.000 9.90 0.00 42.43 2.52
2252 3540 5.641636 ACTGGAAAAACGCAACATTTTCTTT 59.358 32.000 9.90 0.00 42.43 2.52
2253 3541 6.148645 ACTGGAAAAACGCAACATTTTCTTTT 59.851 30.769 9.90 0.00 42.43 2.27
2254 3542 6.903419 TGGAAAAACGCAACATTTTCTTTTT 58.097 28.000 9.90 0.00 42.43 1.94
2255 3543 6.798959 TGGAAAAACGCAACATTTTCTTTTTG 59.201 30.769 9.90 0.00 42.43 2.44
2256 3544 6.799441 GGAAAAACGCAACATTTTCTTTTTGT 59.201 30.769 9.90 0.00 42.43 2.83
2257 3545 7.324856 GGAAAAACGCAACATTTTCTTTTTGTT 59.675 29.630 9.90 0.00 42.43 2.83
2258 3546 8.567369 AAAAACGCAACATTTTCTTTTTGTTT 57.433 23.077 0.00 0.00 31.48 2.83
2259 3547 7.774224 AAACGCAACATTTTCTTTTTGTTTC 57.226 28.000 0.00 0.00 31.48 2.78
2260 3548 6.720012 ACGCAACATTTTCTTTTTGTTTCT 57.280 29.167 0.00 0.00 31.48 2.52
2261 3549 7.127917 ACGCAACATTTTCTTTTTGTTTCTT 57.872 28.000 0.00 0.00 31.48 2.52
2262 3550 8.245701 ACGCAACATTTTCTTTTTGTTTCTTA 57.754 26.923 0.00 0.00 31.48 2.10
2263 3551 8.713271 ACGCAACATTTTCTTTTTGTTTCTTAA 58.287 25.926 0.00 0.00 31.48 1.85
2264 3552 9.535270 CGCAACATTTTCTTTTTGTTTCTTAAA 57.465 25.926 0.00 0.00 31.48 1.52
2268 3556 9.701355 ACATTTTCTTTTTGTTTCTTAAATGCG 57.299 25.926 0.00 0.00 35.98 4.73
2269 3557 9.701355 CATTTTCTTTTTGTTTCTTAAATGCGT 57.299 25.926 0.00 0.00 0.00 5.24
2270 3558 9.701355 ATTTTCTTTTTGTTTCTTAAATGCGTG 57.299 25.926 0.00 0.00 0.00 5.34
2271 3559 8.467402 TTTCTTTTTGTTTCTTAAATGCGTGA 57.533 26.923 0.00 0.00 0.00 4.35
2272 3560 8.467402 TTCTTTTTGTTTCTTAAATGCGTGAA 57.533 26.923 0.00 0.00 0.00 3.18
2273 3561 7.890763 TCTTTTTGTTTCTTAAATGCGTGAAC 58.109 30.769 0.00 0.00 0.00 3.18
2274 3562 7.757624 TCTTTTTGTTTCTTAAATGCGTGAACT 59.242 29.630 0.00 0.00 0.00 3.01
2275 3563 7.820044 TTTTGTTTCTTAAATGCGTGAACTT 57.180 28.000 0.00 0.00 0.00 2.66
2276 3564 7.820044 TTTGTTTCTTAAATGCGTGAACTTT 57.180 28.000 0.00 0.00 0.00 2.66
2277 3565 7.820044 TTGTTTCTTAAATGCGTGAACTTTT 57.180 28.000 0.00 0.00 0.00 2.27
2278 3566 7.820044 TGTTTCTTAAATGCGTGAACTTTTT 57.180 28.000 0.00 0.00 0.00 1.94
2279 3567 8.912787 TGTTTCTTAAATGCGTGAACTTTTTA 57.087 26.923 0.00 0.00 0.00 1.52
2280 3568 9.522804 TGTTTCTTAAATGCGTGAACTTTTTAT 57.477 25.926 0.00 0.00 0.00 1.40
2289 3577 9.638239 AATGCGTGAACTTTTTATAATTCATGT 57.362 25.926 15.29 1.02 39.32 3.21
2290 3578 9.638239 ATGCGTGAACTTTTTATAATTCATGTT 57.362 25.926 15.29 6.01 39.32 2.71
2291 3579 9.469807 TGCGTGAACTTTTTATAATTCATGTTT 57.530 25.926 15.29 0.00 39.32 2.83
2321 3609 8.661352 AAATGACGACAAAATTTCAAATTCCT 57.339 26.923 0.00 0.00 0.00 3.36
2322 3610 7.642071 ATGACGACAAAATTTCAAATTCCTG 57.358 32.000 0.00 0.05 0.00 3.86
2323 3611 6.800543 TGACGACAAAATTTCAAATTCCTGA 58.199 32.000 10.47 0.00 0.00 3.86
2324 3612 7.432869 TGACGACAAAATTTCAAATTCCTGAT 58.567 30.769 10.47 0.00 0.00 2.90
2325 3613 7.925483 TGACGACAAAATTTCAAATTCCTGATT 59.075 29.630 10.47 0.00 0.00 2.57
2326 3614 8.661352 ACGACAAAATTTCAAATTCCTGATTT 57.339 26.923 10.47 0.00 38.49 2.17
2327 3615 9.108284 ACGACAAAATTTCAAATTCCTGATTTT 57.892 25.926 10.47 0.00 35.79 1.82
2328 3616 9.934190 CGACAAAATTTCAAATTCCTGATTTTT 57.066 25.926 10.47 0.00 35.79 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.954970 CCACCGCCACAAGCACCT 62.955 66.667 0.00 0.00 44.04 4.00
30 31 3.164977 TCTTCCACCACCGCCACA 61.165 61.111 0.00 0.00 0.00 4.17
80 87 2.624717 ACCTGGTGGTGGGGTACT 59.375 61.111 0.00 0.00 46.51 2.73
210 220 1.144057 CACACATAGGGCCGGAGAC 59.856 63.158 5.05 0.00 0.00 3.36
233 243 0.457853 GATACTTCCAGACACGCGCA 60.458 55.000 5.73 0.00 0.00 6.09
270 280 5.647225 AGCAGATCAATTCTCTTCCAAGTTC 59.353 40.000 0.00 0.00 29.93 3.01
271 281 5.568392 AGCAGATCAATTCTCTTCCAAGTT 58.432 37.500 0.00 0.00 29.93 2.66
272 282 5.176741 AGCAGATCAATTCTCTTCCAAGT 57.823 39.130 0.00 0.00 29.93 3.16
273 283 6.145858 CGATAGCAGATCAATTCTCTTCCAAG 59.854 42.308 0.00 0.00 29.93 3.61
274 284 5.987953 CGATAGCAGATCAATTCTCTTCCAA 59.012 40.000 0.00 0.00 29.93 3.53
275 285 5.302823 TCGATAGCAGATCAATTCTCTTCCA 59.697 40.000 0.00 0.00 29.93 3.53
276 286 5.777802 TCGATAGCAGATCAATTCTCTTCC 58.222 41.667 0.00 0.00 29.93 3.46
277 287 7.510428 GATCGATAGCAGATCAATTCTCTTC 57.490 40.000 0.00 0.00 42.86 2.87
288 298 4.038402 TGTGTCACATGATCGATAGCAGAT 59.962 41.667 0.18 0.00 0.00 2.90
430 444 2.437537 ACCGCCGTTGCATGCATA 60.438 55.556 23.37 9.86 37.32 3.14
450 464 2.360852 AGCACCTCAGGCATGCAC 60.361 61.111 21.36 9.10 41.97 4.57
458 472 2.577112 CGTACGCGAGCACCTCAG 60.577 66.667 15.93 0.00 41.33 3.35
486 514 4.101790 ATTTCGTTGGCGGCTGCG 62.102 61.111 12.29 14.60 44.10 5.18
504 532 1.467713 CGAGAAGGAACGTGGAGTAGC 60.468 57.143 0.00 0.00 0.00 3.58
507 535 1.289380 GCGAGAAGGAACGTGGAGT 59.711 57.895 0.00 0.00 0.00 3.85
595 623 0.445436 TTTCGTCGTCGAGTAGAGGC 59.555 55.000 4.73 0.00 46.81 4.70
606 634 9.887406 ACAAACATAAAATAATTCTTTCGTCGT 57.113 25.926 0.00 0.00 0.00 4.34
619 647 9.666626 CTTTTGGTCGTGTACAAACATAAAATA 57.333 29.630 0.00 0.00 38.08 1.40
620 648 8.407064 TCTTTTGGTCGTGTACAAACATAAAAT 58.593 29.630 0.00 0.00 38.08 1.82
621 649 7.759465 TCTTTTGGTCGTGTACAAACATAAAA 58.241 30.769 0.00 9.60 38.08 1.52
622 650 7.317842 TCTTTTGGTCGTGTACAAACATAAA 57.682 32.000 0.00 2.75 38.08 1.40
623 651 6.922247 TCTTTTGGTCGTGTACAAACATAA 57.078 33.333 0.00 0.00 38.08 1.90
624 652 6.922247 TTCTTTTGGTCGTGTACAAACATA 57.078 33.333 0.00 0.00 38.08 2.29
625 653 5.821516 TTCTTTTGGTCGTGTACAAACAT 57.178 34.783 0.00 0.00 38.08 2.71
626 654 5.821516 ATTCTTTTGGTCGTGTACAAACA 57.178 34.783 0.00 0.00 36.42 2.83
627 655 6.970613 AGAAATTCTTTTGGTCGTGTACAAAC 59.029 34.615 0.00 0.00 36.42 2.93
628 656 7.090953 AGAAATTCTTTTGGTCGTGTACAAA 57.909 32.000 0.00 0.00 35.01 2.83
629 657 6.316640 TGAGAAATTCTTTTGGTCGTGTACAA 59.683 34.615 0.00 0.00 0.00 2.41
630 658 5.818336 TGAGAAATTCTTTTGGTCGTGTACA 59.182 36.000 0.00 0.00 0.00 2.90
631 659 6.134061 GTGAGAAATTCTTTTGGTCGTGTAC 58.866 40.000 0.00 0.00 0.00 2.90
632 660 5.818336 TGTGAGAAATTCTTTTGGTCGTGTA 59.182 36.000 0.00 0.00 0.00 2.90
654 682 2.202440 CGGCTTCGTCGTCGATGT 60.202 61.111 13.91 0.00 45.65 3.06
670 714 2.049985 GGACGATCGAGATGGCCG 60.050 66.667 24.34 0.00 0.00 6.13
671 715 2.049985 CGGACGATCGAGATGGCC 60.050 66.667 24.34 11.26 0.00 5.36
809 861 1.599606 GACCAGCTCAGCCTTCTCGA 61.600 60.000 0.00 0.00 0.00 4.04
817 869 1.078848 ATGAACGGACCAGCTCAGC 60.079 57.895 0.00 0.00 0.00 4.26
819 871 1.375908 GCATGAACGGACCAGCTCA 60.376 57.895 0.00 0.00 0.00 4.26
925 977 1.133790 GGATTGTGAGCTTGTGATGGC 59.866 52.381 0.00 0.00 0.00 4.40
995 1065 0.602372 GCTCGATGAAGCCATCTCCC 60.602 60.000 0.00 0.00 45.37 4.30
1483 1565 2.777692 TGCTTCTCCTATTACCCCCTTG 59.222 50.000 0.00 0.00 0.00 3.61
1489 1571 2.210961 GCCGTTGCTTCTCCTATTACC 58.789 52.381 0.00 0.00 33.53 2.85
1493 1580 1.144057 CGGCCGTTGCTTCTCCTAT 59.856 57.895 19.50 0.00 37.74 2.57
1542 1629 5.063204 AGAAATGGTCAATCAAGACAACGA 58.937 37.500 0.00 0.00 40.29 3.85
1608 1696 7.047271 TGTGAGCACTGCATATCTTACAAATA 58.953 34.615 3.30 0.00 0.00 1.40
1609 1697 5.882000 TGTGAGCACTGCATATCTTACAAAT 59.118 36.000 3.30 0.00 0.00 2.32
1613 1701 4.272018 CCTTGTGAGCACTGCATATCTTAC 59.728 45.833 3.30 0.00 0.00 2.34
1614 1702 4.162131 TCCTTGTGAGCACTGCATATCTTA 59.838 41.667 3.30 0.00 0.00 2.10
1616 1704 2.502947 TCCTTGTGAGCACTGCATATCT 59.497 45.455 3.30 0.00 0.00 1.98
1617 1705 2.871022 CTCCTTGTGAGCACTGCATATC 59.129 50.000 3.30 0.00 33.47 1.63
1618 1706 2.915349 CTCCTTGTGAGCACTGCATAT 58.085 47.619 3.30 0.00 33.47 1.78
1619 1707 2.391616 CTCCTTGTGAGCACTGCATA 57.608 50.000 3.30 0.00 33.47 3.14
1620 1708 3.244764 CTCCTTGTGAGCACTGCAT 57.755 52.632 3.30 0.00 33.47 3.96
1621 1709 4.785767 CTCCTTGTGAGCACTGCA 57.214 55.556 3.30 0.00 33.47 4.41
1628 1716 2.164219 GAGAGTGAGAGCTCCTTGTGAG 59.836 54.545 10.93 0.00 44.47 3.51
1630 1718 1.204467 GGAGAGTGAGAGCTCCTTGTG 59.796 57.143 10.93 0.00 45.72 3.33
1631 1719 1.555967 GGAGAGTGAGAGCTCCTTGT 58.444 55.000 10.93 0.00 45.72 3.16
1636 1724 4.714632 ACTATGTAGGAGAGTGAGAGCTC 58.285 47.826 5.27 5.27 35.82 4.09
1638 1726 4.456535 TGACTATGTAGGAGAGTGAGAGC 58.543 47.826 0.00 0.00 0.00 4.09
1643 1731 5.825151 TCATCACTGACTATGTAGGAGAGTG 59.175 44.000 0.00 0.00 33.14 3.51
1644 1732 6.007485 TCATCACTGACTATGTAGGAGAGT 57.993 41.667 0.00 0.00 0.00 3.24
1645 1733 8.676401 CATATCATCACTGACTATGTAGGAGAG 58.324 40.741 0.00 0.00 33.22 3.20
1647 1735 8.572855 TCATATCATCACTGACTATGTAGGAG 57.427 38.462 0.00 0.00 33.22 3.69
1649 1737 9.583765 CATTCATATCATCACTGACTATGTAGG 57.416 37.037 0.00 0.00 33.22 3.18
1653 1741 8.529476 TCTCCATTCATATCATCACTGACTATG 58.471 37.037 0.00 0.00 33.22 2.23
1654 1742 8.530311 GTCTCCATTCATATCATCACTGACTAT 58.470 37.037 0.00 0.00 33.22 2.12
1655 1743 7.039434 GGTCTCCATTCATATCATCACTGACTA 60.039 40.741 0.00 0.00 33.22 2.59
1657 1745 5.931146 GGTCTCCATTCATATCATCACTGAC 59.069 44.000 0.00 0.00 33.22 3.51
1658 1746 5.603813 TGGTCTCCATTCATATCATCACTGA 59.396 40.000 0.00 0.00 35.41 3.41
1659 1747 5.861727 TGGTCTCCATTCATATCATCACTG 58.138 41.667 0.00 0.00 0.00 3.66
1660 1748 5.605908 ACTGGTCTCCATTCATATCATCACT 59.394 40.000 0.00 0.00 30.82 3.41
1663 1751 5.862845 ACACTGGTCTCCATTCATATCATC 58.137 41.667 0.00 0.00 30.82 2.92
1664 1752 5.901413 ACACTGGTCTCCATTCATATCAT 57.099 39.130 0.00 0.00 30.82 2.45
1665 1753 6.611236 TCTTACACTGGTCTCCATTCATATCA 59.389 38.462 0.00 0.00 30.82 2.15
1690 2172 3.542648 TGATCTCCTCGACAGAATACGT 58.457 45.455 0.00 0.00 0.00 3.57
1698 2180 2.239907 TCCTTCTCTGATCTCCTCGACA 59.760 50.000 0.00 0.00 0.00 4.35
1699 2181 2.878406 CTCCTTCTCTGATCTCCTCGAC 59.122 54.545 0.00 0.00 0.00 4.20
1700 2182 2.748132 GCTCCTTCTCTGATCTCCTCGA 60.748 54.545 0.00 0.00 0.00 4.04
1702 2184 1.963515 GGCTCCTTCTCTGATCTCCTC 59.036 57.143 0.00 0.00 0.00 3.71
1722 2204 1.207791 AGGTCCTAGTGCCTTCATGG 58.792 55.000 0.00 0.00 39.35 3.66
1767 2249 6.713450 TCTTTAAAAGCGTTTCTAATGGGTCT 59.287 34.615 0.00 0.00 0.00 3.85
1775 2257 7.754851 AATTCCCTCTTTAAAAGCGTTTCTA 57.245 32.000 0.00 0.00 0.00 2.10
1793 2275 7.506328 ACCGCTAATAATTGTAGAAATTCCC 57.494 36.000 2.95 0.00 0.00 3.97
1801 2283 7.316544 ACCAAGAAACCGCTAATAATTGTAG 57.683 36.000 0.00 0.00 0.00 2.74
1803 2285 6.317893 CCTACCAAGAAACCGCTAATAATTGT 59.682 38.462 0.00 0.00 0.00 2.71
1806 2288 6.099269 TCTCCTACCAAGAAACCGCTAATAAT 59.901 38.462 0.00 0.00 0.00 1.28
1809 2291 3.773119 TCTCCTACCAAGAAACCGCTAAT 59.227 43.478 0.00 0.00 0.00 1.73
1825 2307 9.661954 ACAACTCCTTGAGAATTATATCTCCTA 57.338 33.333 0.00 0.00 44.27 2.94
1835 2317 4.962155 AGTCGAACAACTCCTTGAGAATT 58.038 39.130 0.00 0.00 33.32 2.17
1839 2321 3.651803 AGAGTCGAACAACTCCTTGAG 57.348 47.619 0.61 0.00 45.61 3.02
1841 2323 3.005472 TGGTAGAGTCGAACAACTCCTTG 59.995 47.826 0.61 0.00 45.61 3.61
1842 2324 3.228453 TGGTAGAGTCGAACAACTCCTT 58.772 45.455 0.61 0.00 45.61 3.36
1851 2333 2.029739 TCGCAACAATGGTAGAGTCGAA 60.030 45.455 0.00 0.00 0.00 3.71
1859 2341 3.689161 CCTTTGAGATCGCAACAATGGTA 59.311 43.478 11.72 0.00 35.53 3.25
1865 2347 3.629855 TGTTTTCCTTTGAGATCGCAACA 59.370 39.130 11.72 2.66 0.00 3.33
1869 2351 3.565516 GGTTGTTTTCCTTTGAGATCGC 58.434 45.455 0.00 0.00 0.00 4.58
1882 3169 9.900710 GTTTTTCTTTATTGTTTGGGTTGTTTT 57.099 25.926 0.00 0.00 0.00 2.43
1883 3170 9.067986 TGTTTTTCTTTATTGTTTGGGTTGTTT 57.932 25.926 0.00 0.00 0.00 2.83
1887 3174 7.661847 TGTGTGTTTTTCTTTATTGTTTGGGTT 59.338 29.630 0.00 0.00 0.00 4.11
1930 3218 2.359850 GATGCCGCACCACCAGAA 60.360 61.111 0.00 0.00 0.00 3.02
1958 3246 4.320057 GCATGTGCTCTTCATATAGGCAAC 60.320 45.833 0.00 0.00 38.21 4.17
1985 3273 9.636879 CAGTCTGATATGTATGATTCTTACCTG 57.363 37.037 0.00 2.37 0.00 4.00
1987 3275 9.632807 GTCAGTCTGATATGTATGATTCTTACC 57.367 37.037 5.68 0.00 0.00 2.85
1997 3285 8.087136 GTGTGATGATGTCAGTCTGATATGTAT 58.913 37.037 16.05 10.27 37.56 2.29
2023 3311 8.778358 ACTTATGAAAAGAAGCAGAAGTGTTAG 58.222 33.333 0.00 0.00 42.81 2.34
2027 3315 8.233190 CCTTACTTATGAAAAGAAGCAGAAGTG 58.767 37.037 11.68 0.00 43.79 3.16
2028 3316 7.391833 CCCTTACTTATGAAAAGAAGCAGAAGT 59.608 37.037 0.00 0.00 45.32 3.01
2029 3317 7.391833 ACCCTTACTTATGAAAAGAAGCAGAAG 59.608 37.037 0.00 0.00 38.80 2.85
2030 3318 7.231467 ACCCTTACTTATGAAAAGAAGCAGAA 58.769 34.615 0.00 0.00 0.00 3.02
2031 3319 6.779860 ACCCTTACTTATGAAAAGAAGCAGA 58.220 36.000 0.00 0.00 0.00 4.26
2032 3320 8.616076 CATACCCTTACTTATGAAAAGAAGCAG 58.384 37.037 0.00 0.00 0.00 4.24
2033 3321 8.325787 TCATACCCTTACTTATGAAAAGAAGCA 58.674 33.333 0.00 0.00 32.84 3.91
2034 3322 8.732746 TCATACCCTTACTTATGAAAAGAAGC 57.267 34.615 0.00 0.00 32.84 3.86
2074 3362 9.809096 CATGTACAGTGTATAGATGAAGAGTTT 57.191 33.333 6.21 0.00 0.00 2.66
2075 3363 9.190317 TCATGTACAGTGTATAGATGAAGAGTT 57.810 33.333 6.21 0.00 31.41 3.01
2076 3364 8.753497 TCATGTACAGTGTATAGATGAAGAGT 57.247 34.615 6.21 0.00 31.41 3.24
2077 3365 9.457110 GTTCATGTACAGTGTATAGATGAAGAG 57.543 37.037 22.83 3.51 40.79 2.85
2078 3366 8.414003 GGTTCATGTACAGTGTATAGATGAAGA 58.586 37.037 22.83 10.38 40.79 2.87
2079 3367 8.197439 TGGTTCATGTACAGTGTATAGATGAAG 58.803 37.037 22.83 6.10 40.79 3.02
2080 3368 7.979537 GTGGTTCATGTACAGTGTATAGATGAA 59.020 37.037 20.54 20.54 38.99 2.57
2081 3369 7.123547 TGTGGTTCATGTACAGTGTATAGATGA 59.876 37.037 6.21 11.35 32.21 2.92
2082 3370 7.264947 TGTGGTTCATGTACAGTGTATAGATG 58.735 38.462 6.21 9.37 0.00 2.90
2083 3371 7.418337 TGTGGTTCATGTACAGTGTATAGAT 57.582 36.000 6.21 0.00 0.00 1.98
2084 3372 6.844097 TGTGGTTCATGTACAGTGTATAGA 57.156 37.500 6.21 2.49 0.00 1.98
2085 3373 7.899178 TTTGTGGTTCATGTACAGTGTATAG 57.101 36.000 6.21 0.04 0.00 1.31
2086 3374 8.678593 TTTTTGTGGTTCATGTACAGTGTATA 57.321 30.769 6.21 3.96 0.00 1.47
2087 3375 7.575414 TTTTTGTGGTTCATGTACAGTGTAT 57.425 32.000 6.21 0.00 0.00 2.29
2089 3377 5.906113 TTTTTGTGGTTCATGTACAGTGT 57.094 34.783 0.33 0.00 0.00 3.55
2117 3405 2.009051 TGGTACGAATCTTGCAGCATG 58.991 47.619 0.00 0.00 40.87 4.06
2118 3406 2.401583 TGGTACGAATCTTGCAGCAT 57.598 45.000 0.00 0.00 0.00 3.79
2119 3407 2.076100 CTTGGTACGAATCTTGCAGCA 58.924 47.619 0.00 0.00 0.00 4.41
2120 3408 2.346803 TCTTGGTACGAATCTTGCAGC 58.653 47.619 0.00 0.00 0.00 5.25
2121 3409 3.243877 CGATCTTGGTACGAATCTTGCAG 59.756 47.826 0.00 0.00 0.00 4.41
2122 3410 3.186909 CGATCTTGGTACGAATCTTGCA 58.813 45.455 0.00 0.00 0.00 4.08
2123 3411 3.187700 ACGATCTTGGTACGAATCTTGC 58.812 45.455 0.00 0.00 0.00 4.01
2124 3412 4.862574 TGAACGATCTTGGTACGAATCTTG 59.137 41.667 0.00 0.00 0.00 3.02
2125 3413 5.068234 TGAACGATCTTGGTACGAATCTT 57.932 39.130 0.00 0.00 0.00 2.40
2126 3414 4.673441 CTGAACGATCTTGGTACGAATCT 58.327 43.478 0.00 0.00 0.00 2.40
2127 3415 3.243177 GCTGAACGATCTTGGTACGAATC 59.757 47.826 0.00 0.00 0.00 2.52
2128 3416 3.187700 GCTGAACGATCTTGGTACGAAT 58.812 45.455 0.00 0.00 0.00 3.34
2129 3417 2.029739 TGCTGAACGATCTTGGTACGAA 60.030 45.455 0.00 0.00 0.00 3.85
2130 3418 1.542472 TGCTGAACGATCTTGGTACGA 59.458 47.619 0.00 0.00 0.00 3.43
2131 3419 1.990799 TGCTGAACGATCTTGGTACG 58.009 50.000 0.00 0.00 0.00 3.67
2132 3420 4.946784 AATTGCTGAACGATCTTGGTAC 57.053 40.909 0.00 0.00 0.00 3.34
2133 3421 4.570772 GCTAATTGCTGAACGATCTTGGTA 59.429 41.667 0.00 0.00 38.95 3.25
2134 3422 3.375299 GCTAATTGCTGAACGATCTTGGT 59.625 43.478 0.00 0.00 38.95 3.67
2135 3423 3.374988 TGCTAATTGCTGAACGATCTTGG 59.625 43.478 0.00 0.00 43.37 3.61
2136 3424 4.142838 TGTGCTAATTGCTGAACGATCTTG 60.143 41.667 0.00 0.00 43.37 3.02
2137 3425 4.002982 TGTGCTAATTGCTGAACGATCTT 58.997 39.130 0.00 0.00 43.37 2.40
2138 3426 3.599343 TGTGCTAATTGCTGAACGATCT 58.401 40.909 0.00 0.00 43.37 2.75
2139 3427 4.521943 GATGTGCTAATTGCTGAACGATC 58.478 43.478 0.00 0.00 43.37 3.69
2140 3428 3.313526 GGATGTGCTAATTGCTGAACGAT 59.686 43.478 0.00 0.00 43.37 3.73
2141 3429 2.677836 GGATGTGCTAATTGCTGAACGA 59.322 45.455 0.00 0.00 43.37 3.85
2142 3430 2.537529 CGGATGTGCTAATTGCTGAACG 60.538 50.000 0.00 0.00 43.37 3.95
2143 3431 2.792542 GCGGATGTGCTAATTGCTGAAC 60.793 50.000 0.00 0.00 43.37 3.18
2144 3432 1.401552 GCGGATGTGCTAATTGCTGAA 59.598 47.619 0.00 0.00 43.37 3.02
2145 3433 1.016627 GCGGATGTGCTAATTGCTGA 58.983 50.000 0.00 0.00 43.37 4.26
2146 3434 0.029834 GGCGGATGTGCTAATTGCTG 59.970 55.000 0.00 0.00 43.37 4.41
2147 3435 0.107017 AGGCGGATGTGCTAATTGCT 60.107 50.000 0.00 0.00 43.37 3.91
2148 3436 0.740737 AAGGCGGATGTGCTAATTGC 59.259 50.000 0.00 0.00 43.25 3.56
2149 3437 3.243068 GGTTAAGGCGGATGTGCTAATTG 60.243 47.826 0.00 0.00 34.52 2.32
2150 3438 2.949644 GGTTAAGGCGGATGTGCTAATT 59.050 45.455 0.00 0.00 34.52 1.40
2151 3439 2.092646 TGGTTAAGGCGGATGTGCTAAT 60.093 45.455 0.00 0.00 34.52 1.73
2152 3440 1.279558 TGGTTAAGGCGGATGTGCTAA 59.720 47.619 0.00 0.00 34.52 3.09
2153 3441 0.906066 TGGTTAAGGCGGATGTGCTA 59.094 50.000 0.00 0.00 34.52 3.49
2154 3442 0.037590 TTGGTTAAGGCGGATGTGCT 59.962 50.000 0.00 0.00 34.52 4.40
2155 3443 1.102978 ATTGGTTAAGGCGGATGTGC 58.897 50.000 0.00 0.00 0.00 4.57
2156 3444 1.405105 CCATTGGTTAAGGCGGATGTG 59.595 52.381 0.00 0.00 0.00 3.21
2157 3445 1.283613 TCCATTGGTTAAGGCGGATGT 59.716 47.619 1.86 0.00 0.00 3.06
2158 3446 1.949525 CTCCATTGGTTAAGGCGGATG 59.050 52.381 1.86 0.00 0.00 3.51
2159 3447 1.750682 GCTCCATTGGTTAAGGCGGAT 60.751 52.381 1.86 0.00 0.00 4.18
2160 3448 0.393808 GCTCCATTGGTTAAGGCGGA 60.394 55.000 1.86 0.00 0.00 5.54
2161 3449 0.679640 TGCTCCATTGGTTAAGGCGG 60.680 55.000 1.86 0.00 0.00 6.13
2162 3450 1.135402 GTTGCTCCATTGGTTAAGGCG 60.135 52.381 1.86 0.00 0.00 5.52
2163 3451 1.204704 GGTTGCTCCATTGGTTAAGGC 59.795 52.381 1.86 2.20 35.97 4.35
2164 3452 2.493278 CTGGTTGCTCCATTGGTTAAGG 59.507 50.000 1.86 0.00 46.12 2.69
2165 3453 3.191371 GTCTGGTTGCTCCATTGGTTAAG 59.809 47.826 1.86 0.00 46.12 1.85
2166 3454 3.153919 GTCTGGTTGCTCCATTGGTTAA 58.846 45.455 1.86 0.00 46.12 2.01
2167 3455 2.554344 GGTCTGGTTGCTCCATTGGTTA 60.554 50.000 1.86 0.00 46.12 2.85
2168 3456 1.620822 GTCTGGTTGCTCCATTGGTT 58.379 50.000 1.86 0.00 46.12 3.67
2169 3457 0.251341 GGTCTGGTTGCTCCATTGGT 60.251 55.000 1.86 0.00 46.12 3.67
2170 3458 0.038744 AGGTCTGGTTGCTCCATTGG 59.961 55.000 0.00 0.00 46.12 3.16
2171 3459 2.787473 TAGGTCTGGTTGCTCCATTG 57.213 50.000 2.00 0.00 46.12 2.82
2172 3460 2.025887 CCTTAGGTCTGGTTGCTCCATT 60.026 50.000 2.00 0.00 46.12 3.16
2173 3461 1.561542 CCTTAGGTCTGGTTGCTCCAT 59.438 52.381 2.00 0.00 46.12 3.41
2174 3462 0.984230 CCTTAGGTCTGGTTGCTCCA 59.016 55.000 0.00 1.68 45.01 3.86
2175 3463 0.984995 ACCTTAGGTCTGGTTGCTCC 59.015 55.000 0.00 0.00 31.62 4.70
2176 3464 1.348036 ACACCTTAGGTCTGGTTGCTC 59.652 52.381 0.00 0.00 31.02 4.26
2177 3465 1.435256 ACACCTTAGGTCTGGTTGCT 58.565 50.000 0.00 0.00 31.02 3.91
2178 3466 2.271944 AACACCTTAGGTCTGGTTGC 57.728 50.000 0.00 0.00 31.02 4.17
2179 3467 4.969484 ACTTAACACCTTAGGTCTGGTTG 58.031 43.478 13.68 0.10 31.02 3.77
2180 3468 6.271624 ACATACTTAACACCTTAGGTCTGGTT 59.728 38.462 0.00 5.88 31.02 3.67
2181 3469 5.783875 ACATACTTAACACCTTAGGTCTGGT 59.216 40.000 0.00 0.00 31.02 4.00
2182 3470 6.295719 ACATACTTAACACCTTAGGTCTGG 57.704 41.667 0.00 0.00 31.02 3.86
2183 3471 8.617290 AAAACATACTTAACACCTTAGGTCTG 57.383 34.615 0.00 0.00 31.02 3.51
2184 3472 8.657712 AGAAAACATACTTAACACCTTAGGTCT 58.342 33.333 0.00 0.00 31.02 3.85
2185 3473 8.843885 AGAAAACATACTTAACACCTTAGGTC 57.156 34.615 0.00 0.00 31.02 3.85
2213 3501 8.339714 CGTTTTTCCAGTGTTCTATTTCAAGTA 58.660 33.333 0.00 0.00 0.00 2.24
2214 3502 7.193595 CGTTTTTCCAGTGTTCTATTTCAAGT 58.806 34.615 0.00 0.00 0.00 3.16
2215 3503 6.142320 GCGTTTTTCCAGTGTTCTATTTCAAG 59.858 38.462 0.00 0.00 0.00 3.02
2216 3504 5.974751 GCGTTTTTCCAGTGTTCTATTTCAA 59.025 36.000 0.00 0.00 0.00 2.69
2217 3505 5.066634 TGCGTTTTTCCAGTGTTCTATTTCA 59.933 36.000 0.00 0.00 0.00 2.69
2218 3506 5.516090 TGCGTTTTTCCAGTGTTCTATTTC 58.484 37.500 0.00 0.00 0.00 2.17
2219 3507 5.508200 TGCGTTTTTCCAGTGTTCTATTT 57.492 34.783 0.00 0.00 0.00 1.40
2220 3508 5.163602 TGTTGCGTTTTTCCAGTGTTCTATT 60.164 36.000 0.00 0.00 0.00 1.73
2221 3509 4.336993 TGTTGCGTTTTTCCAGTGTTCTAT 59.663 37.500 0.00 0.00 0.00 1.98
2222 3510 3.690139 TGTTGCGTTTTTCCAGTGTTCTA 59.310 39.130 0.00 0.00 0.00 2.10
2223 3511 2.490115 TGTTGCGTTTTTCCAGTGTTCT 59.510 40.909 0.00 0.00 0.00 3.01
2224 3512 2.869897 TGTTGCGTTTTTCCAGTGTTC 58.130 42.857 0.00 0.00 0.00 3.18
2225 3513 3.518634 ATGTTGCGTTTTTCCAGTGTT 57.481 38.095 0.00 0.00 0.00 3.32
2226 3514 3.518634 AATGTTGCGTTTTTCCAGTGT 57.481 38.095 0.00 0.00 0.00 3.55
2227 3515 4.566360 AGAAAATGTTGCGTTTTTCCAGTG 59.434 37.500 4.91 0.00 40.88 3.66
2228 3516 4.754322 AGAAAATGTTGCGTTTTTCCAGT 58.246 34.783 4.91 0.00 40.88 4.00
2229 3517 5.717038 AAGAAAATGTTGCGTTTTTCCAG 57.283 34.783 4.91 0.00 40.88 3.86
2230 3518 6.487689 AAAAGAAAATGTTGCGTTTTTCCA 57.512 29.167 4.91 0.00 40.88 3.53
2231 3519 6.799441 ACAAAAAGAAAATGTTGCGTTTTTCC 59.201 30.769 4.91 0.00 40.88 3.13
2232 3520 7.774224 ACAAAAAGAAAATGTTGCGTTTTTC 57.226 28.000 1.34 0.00 40.49 2.29
2233 3521 8.567369 AAACAAAAAGAAAATGTTGCGTTTTT 57.433 23.077 1.34 0.00 37.36 1.94
2234 3522 8.073167 AGAAACAAAAAGAAAATGTTGCGTTTT 58.927 25.926 0.00 0.00 37.62 2.43
2235 3523 7.580600 AGAAACAAAAAGAAAATGTTGCGTTT 58.419 26.923 0.00 0.00 37.62 3.60
2236 3524 7.127917 AGAAACAAAAAGAAAATGTTGCGTT 57.872 28.000 0.00 0.00 37.62 4.84
2237 3525 6.720012 AGAAACAAAAAGAAAATGTTGCGT 57.280 29.167 0.00 0.00 37.62 5.24
2238 3526 9.535270 TTTAAGAAACAAAAAGAAAATGTTGCG 57.465 25.926 0.00 0.00 37.62 4.85
2242 3530 9.701355 CGCATTTAAGAAACAAAAAGAAAATGT 57.299 25.926 0.00 0.00 36.15 2.71
2243 3531 9.701355 ACGCATTTAAGAAACAAAAAGAAAATG 57.299 25.926 0.00 0.00 36.58 2.32
2244 3532 9.701355 CACGCATTTAAGAAACAAAAAGAAAAT 57.299 25.926 0.00 0.00 0.00 1.82
2245 3533 8.926710 TCACGCATTTAAGAAACAAAAAGAAAA 58.073 25.926 0.00 0.00 0.00 2.29
2246 3534 8.467402 TCACGCATTTAAGAAACAAAAAGAAA 57.533 26.923 0.00 0.00 0.00 2.52
2247 3535 8.376942 GTTCACGCATTTAAGAAACAAAAAGAA 58.623 29.630 0.00 0.00 0.00 2.52
2248 3536 7.757624 AGTTCACGCATTTAAGAAACAAAAAGA 59.242 29.630 0.00 0.00 0.00 2.52
2249 3537 7.894847 AGTTCACGCATTTAAGAAACAAAAAG 58.105 30.769 0.00 0.00 0.00 2.27
2250 3538 7.820044 AGTTCACGCATTTAAGAAACAAAAA 57.180 28.000 0.00 0.00 0.00 1.94
2251 3539 7.820044 AAGTTCACGCATTTAAGAAACAAAA 57.180 28.000 0.00 0.00 0.00 2.44
2252 3540 7.820044 AAAGTTCACGCATTTAAGAAACAAA 57.180 28.000 0.00 0.00 0.00 2.83
2253 3541 7.820044 AAAAGTTCACGCATTTAAGAAACAA 57.180 28.000 0.00 0.00 0.00 2.83
2254 3542 7.820044 AAAAAGTTCACGCATTTAAGAAACA 57.180 28.000 0.00 0.00 0.00 2.83
2263 3551 9.638239 ACATGAATTATAAAAAGTTCACGCATT 57.362 25.926 0.00 0.00 33.85 3.56
2264 3552 9.638239 AACATGAATTATAAAAAGTTCACGCAT 57.362 25.926 0.00 0.00 33.85 4.73
2265 3553 9.469807 AAACATGAATTATAAAAAGTTCACGCA 57.530 25.926 0.00 0.00 33.85 5.24
2295 3583 9.757227 AGGAATTTGAAATTTTGTCGTCATTTA 57.243 25.926 4.46 0.00 0.00 1.40
2296 3584 8.550376 CAGGAATTTGAAATTTTGTCGTCATTT 58.450 29.630 4.46 0.00 0.00 2.32
2297 3585 7.925483 TCAGGAATTTGAAATTTTGTCGTCATT 59.075 29.630 4.46 0.00 0.00 2.57
2298 3586 7.432869 TCAGGAATTTGAAATTTTGTCGTCAT 58.567 30.769 4.46 0.00 0.00 3.06
2299 3587 6.800543 TCAGGAATTTGAAATTTTGTCGTCA 58.199 32.000 4.46 0.00 0.00 4.35
2300 3588 7.873739 ATCAGGAATTTGAAATTTTGTCGTC 57.126 32.000 4.46 0.00 0.00 4.20
2301 3589 8.661352 AAATCAGGAATTTGAAATTTTGTCGT 57.339 26.923 4.46 0.00 36.20 4.34
2302 3590 9.934190 AAAAATCAGGAATTTGAAATTTTGTCG 57.066 25.926 4.46 0.00 37.64 4.35


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

AutoCloner maintained by Alex Coulton.