Multiple sequence alignment - TraesCS5B01G072400

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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 TraesCS5B01G072400 chr5B 100.000 3291 0 0 1 3291 84659017 84655727 0.000000e+00 6078.0
1 TraesCS5B01G072400 chr5B 99.000 200 2 0 1457 1656 558456926 558456727 3.120000e-95 359.0
2 TraesCS5B01G072400 chr5B 93.401 197 12 1 3081 3277 638855689 638855494 1.160000e-74 291.0
3 TraesCS5B01G072400 chr5B 91.549 71 4 2 15 84 20630660 20630729 2.700000e-16 97.1
4 TraesCS5B01G072400 chr5B 74.874 199 42 6 1716 1910 460492527 460492333 2.100000e-12 84.2
5 TraesCS5B01G072400 chr5D 95.135 1336 52 10 1655 2982 75997887 75996557 0.000000e+00 2095.0
6 TraesCS5B01G072400 chr5D 91.757 1480 79 14 1 1447 75999378 75997909 0.000000e+00 2017.0
7 TraesCS5B01G072400 chr5D 95.536 112 5 0 2967 3078 75994607 75994496 2.610000e-41 180.0
8 TraesCS5B01G072400 chr5D 72.159 352 73 21 1716 2052 384016805 384016464 2.100000e-12 84.2
9 TraesCS5B01G072400 chr5D 75.796 157 28 5 2918 3064 75920592 75920436 1.640000e-08 71.3
10 TraesCS5B01G072400 chr5A 93.842 1364 59 12 84 1440 71455048 71453703 0.000000e+00 2030.0
11 TraesCS5B01G072400 chr5A 96.023 704 24 3 1664 2365 71453675 71452974 0.000000e+00 1142.0
12 TraesCS5B01G072400 chr5A 91.197 727 45 14 2362 3079 71452774 71452058 0.000000e+00 970.0
13 TraesCS5B01G072400 chr5A 99.479 192 1 0 1457 1648 422876875 422876684 1.880000e-92 350.0
14 TraesCS5B01G072400 chr5A 72.080 351 75 19 1716 2052 484436363 484436022 2.100000e-12 84.2
15 TraesCS5B01G072400 chr2A 90.568 774 56 11 1673 2439 23949036 23949799 0.000000e+00 1009.0
16 TraesCS5B01G072400 chr2A 91.509 318 24 1 972 1289 23940775 23941089 5.040000e-118 435.0
17 TraesCS5B01G072400 chr2A 91.304 207 16 2 3075 3280 360730682 360730887 6.950000e-72 281.0
18 TraesCS5B01G072400 chr2A 86.466 266 16 5 294 540 23939888 23940152 1.160000e-69 274.0
19 TraesCS5B01G072400 chr2A 86.228 167 22 1 2901 3066 32459178 32459012 2.610000e-41 180.0
20 TraesCS5B01G072400 chr6D 84.359 601 82 5 1704 2292 114848141 114847541 2.200000e-161 579.0
21 TraesCS5B01G072400 chr6D 77.623 648 116 22 813 1439 114844351 114843712 1.870000e-97 366.0
22 TraesCS5B01G072400 chr6D 76.945 694 124 22 767 1439 114849222 114848544 2.410000e-96 363.0
23 TraesCS5B01G072400 chr6B 84.359 601 82 5 1704 2292 204124520 204123920 2.200000e-161 579.0
24 TraesCS5B01G072400 chr6B 84.132 605 76 10 1704 2292 204114948 204114348 4.770000e-158 568.0
25 TraesCS5B01G072400 chr6B 97.970 197 4 0 1457 1653 124654427 124654623 3.140000e-90 342.0
26 TraesCS5B01G072400 chr6B 97.970 197 4 0 1458 1654 676881236 676881040 3.140000e-90 342.0
27 TraesCS5B01G072400 chr6B 97.475 198 5 0 1457 1654 78590676 78590873 4.070000e-89 339.0
28 TraesCS5B01G072400 chr6B 77.855 578 107 14 876 1439 204115868 204115298 4.070000e-89 339.0
29 TraesCS5B01G072400 chr6B 82.812 384 60 6 1073 1453 204125290 204124910 4.070000e-89 339.0
30 TraesCS5B01G072400 chr6B 95.477 199 7 2 1457 1655 696118211 696118407 1.910000e-82 316.0
31 TraesCS5B01G072400 chr6B 91.304 207 15 3 3081 3287 165923234 165923031 2.500000e-71 279.0
32 TraesCS5B01G072400 chr6B 77.064 218 31 14 114 324 439434279 439434074 1.250000e-19 108.0
33 TraesCS5B01G072400 chr6A 84.385 602 76 10 1704 2290 143066176 143065578 2.850000e-160 575.0
34 TraesCS5B01G072400 chr6A 84.498 458 62 5 1841 2292 143071375 143070921 8.380000e-121 444.0
35 TraesCS5B01G072400 chr6A 77.163 578 108 16 876 1439 143067101 143066534 6.860000e-82 315.0
36 TraesCS5B01G072400 chr6A 75.823 699 123 25 767 1439 143072716 143072038 2.470000e-81 313.0
37 TraesCS5B01G072400 chr2D 92.787 305 19 1 1041 1345 21913097 21913398 3.900000e-119 438.0
38 TraesCS5B01G072400 chr2D 76.437 174 31 5 2901 3064 22109394 22109567 5.850000e-13 86.1
39 TraesCS5B01G072400 chr3A 98.958 192 1 1 1454 1645 704965985 704966175 3.140000e-90 342.0
40 TraesCS5B01G072400 chr2B 94.737 209 10 1 1457 1665 335806313 335806520 1.140000e-84 324.0
41 TraesCS5B01G072400 chr2B 92.893 197 14 0 3080 3276 508193856 508193660 1.490000e-73 287.0
42 TraesCS5B01G072400 chr2B 84.375 64 7 3 325 386 34546899 34546837 3.550000e-05 60.2
43 TraesCS5B01G072400 chr2B 75.912 137 21 8 2935 3061 35125564 35125430 3.550000e-05 60.2
44 TraesCS5B01G072400 chr2B 97.143 35 1 0 501 535 50193457 50193491 3.550000e-05 60.2
45 TraesCS5B01G072400 chr2B 94.286 35 2 0 501 535 49910793 49910759 2.000000e-03 54.7
46 TraesCS5B01G072400 chr3B 95.980 199 6 2 1457 1655 528652233 528652429 4.100000e-84 322.0
47 TraesCS5B01G072400 chr3B 76.098 205 34 10 1785 1977 39581236 39581035 3.500000e-15 93.5
48 TraesCS5B01G072400 chr1B 91.943 211 15 2 3074 3283 476168313 476168104 8.930000e-76 294.0
49 TraesCS5B01G072400 chr7B 93.367 196 13 0 3078 3273 531116863 531116668 1.160000e-74 291.0
50 TraesCS5B01G072400 chr4B 93.401 197 12 1 3081 3277 253987123 253986928 1.160000e-74 291.0
51 TraesCS5B01G072400 chr4B 93.000 200 12 2 3082 3281 428054381 428054578 1.160000e-74 291.0
52 TraesCS5B01G072400 chrUn 92.079 202 14 2 3080 3281 168302903 168302704 1.930000e-72 283.0


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 TraesCS5B01G072400 chr5B 84655727 84659017 3290 True 6078.000000 6078 100.000000 1 3291 1 chr5B.!!$R1 3290
1 TraesCS5B01G072400 chr5D 75994496 75999378 4882 True 1430.666667 2095 94.142667 1 3078 3 chr5D.!!$R3 3077
2 TraesCS5B01G072400 chr5A 71452058 71455048 2990 True 1380.666667 2030 93.687333 84 3079 3 chr5A.!!$R3 2995
3 TraesCS5B01G072400 chr2A 23949036 23949799 763 False 1009.000000 1009 90.568000 1673 2439 1 chr2A.!!$F1 766
4 TraesCS5B01G072400 chr2A 23939888 23941089 1201 False 354.500000 435 88.987500 294 1289 2 chr2A.!!$F3 995
5 TraesCS5B01G072400 chr6D 114843712 114849222 5510 True 436.000000 579 79.642333 767 2292 3 chr6D.!!$R1 1525
6 TraesCS5B01G072400 chr6B 204123920 204125290 1370 True 459.000000 579 83.585500 1073 2292 2 chr6B.!!$R5 1219
7 TraesCS5B01G072400 chr6B 204114348 204115868 1520 True 453.500000 568 80.993500 876 2292 2 chr6B.!!$R4 1416
8 TraesCS5B01G072400 chr6A 143065578 143072716 7138 True 411.750000 575 80.467250 767 2292 4 chr6A.!!$R1 1525

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
584 774 0.667993 TTTGCTTCTTCCGTGCCTTG 59.332 50.0 0.0 0.0 0.00 3.61 F
1456 1927 0.028770 GCACTACGCAGCACAAACAA 59.971 50.0 0.0 0.0 41.79 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 2030 0.817654 GGCTACCATGTTTCCTTGCC 59.182 55.0 0.00 0.00 0.00 4.52 R
3200 14291 0.395448 GTAGGGTCACCGAGTAGCCT 60.395 60.0 6.78 6.78 45.33 4.58 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
115 143 5.530915 TCTGCGCCTTTTTATTATATGCACT 59.469 36.000 4.18 0.00 0.00 4.40
165 194 6.920758 TGTTTTTATTTGTACAGCTCGCATTT 59.079 30.769 0.00 0.00 0.00 2.32
308 340 1.305623 CTCCATGGAGGCCAAGCTT 59.694 57.895 31.14 0.00 36.95 3.74
363 410 2.362736 ACATGTGGCACTCTTAGCATG 58.637 47.619 19.83 13.97 39.43 4.06
548 599 7.663081 ACTTTGCATATATTATGTGGGTCTGAG 59.337 37.037 3.04 0.00 0.00 3.35
579 769 3.312421 TCTTGAGTTTTGCTTCTTCCGTG 59.688 43.478 0.00 0.00 0.00 4.94
580 770 1.333619 TGAGTTTTGCTTCTTCCGTGC 59.666 47.619 0.00 0.00 0.00 5.34
581 771 0.668535 AGTTTTGCTTCTTCCGTGCC 59.331 50.000 0.00 0.00 0.00 5.01
582 772 0.668535 GTTTTGCTTCTTCCGTGCCT 59.331 50.000 0.00 0.00 0.00 4.75
583 773 1.067060 GTTTTGCTTCTTCCGTGCCTT 59.933 47.619 0.00 0.00 0.00 4.35
584 774 0.667993 TTTGCTTCTTCCGTGCCTTG 59.332 50.000 0.00 0.00 0.00 3.61
723 1140 7.351981 TGTAACAAGATGTTCAACATTCTTCG 58.648 34.615 4.04 7.28 40.22 3.79
735 1152 7.459394 TCAACATTCTTCGGTCGAATAATAC 57.541 36.000 13.59 0.00 31.90 1.89
738 1155 8.691727 CAACATTCTTCGGTCGAATAATACTAG 58.308 37.037 13.59 6.91 31.90 2.57
739 1156 7.938715 ACATTCTTCGGTCGAATAATACTAGT 58.061 34.615 13.59 0.00 31.90 2.57
740 1157 9.060347 ACATTCTTCGGTCGAATAATACTAGTA 57.940 33.333 4.77 4.77 31.90 1.82
909 1336 4.981054 CAGACGAACCATCTCATGTCATAG 59.019 45.833 0.00 0.00 0.00 2.23
1322 1786 3.466836 CAGTTGCTGTGACTAACAAGGA 58.533 45.455 0.00 0.00 38.67 3.36
1456 1927 0.028770 GCACTACGCAGCACAAACAA 59.971 50.000 0.00 0.00 41.79 2.83
1461 1932 0.950836 ACGCAGCACAAACAAGCATA 59.049 45.000 0.00 0.00 0.00 3.14
1464 1935 2.988493 CGCAGCACAAACAAGCATAATT 59.012 40.909 0.00 0.00 0.00 1.40
1465 1936 3.181538 CGCAGCACAAACAAGCATAATTG 60.182 43.478 0.00 0.00 36.22 2.32
1466 1937 3.123959 GCAGCACAAACAAGCATAATTGG 59.876 43.478 0.00 0.00 34.36 3.16
1467 1938 4.309099 CAGCACAAACAAGCATAATTGGT 58.691 39.130 0.00 0.00 34.36 3.67
1468 1939 4.751098 CAGCACAAACAAGCATAATTGGTT 59.249 37.500 0.00 0.00 44.12 3.67
1471 1942 5.236047 GCACAAACAAGCATAATTGGTTTGA 59.764 36.000 18.85 0.00 41.48 2.69
1472 1943 6.073112 GCACAAACAAGCATAATTGGTTTGAT 60.073 34.615 18.85 4.43 41.48 2.57
1473 1944 7.292292 CACAAACAAGCATAATTGGTTTGATG 58.708 34.615 18.85 11.07 41.48 3.07
1474 1945 6.073112 ACAAACAAGCATAATTGGTTTGATGC 60.073 34.615 18.85 10.76 41.48 3.91
1475 1946 4.506758 ACAAGCATAATTGGTTTGATGCC 58.493 39.130 12.96 0.00 44.65 4.40
1476 1947 4.020396 ACAAGCATAATTGGTTTGATGCCA 60.020 37.500 12.96 0.00 44.65 4.92
1529 2000 7.437793 CCAACAATTGGCAATATCAAAAGTT 57.562 32.000 14.05 7.18 45.17 2.66
1530 2001 7.299586 CCAACAATTGGCAATATCAAAAGTTG 58.700 34.615 14.05 16.55 45.17 3.16
1531 2002 6.484818 ACAATTGGCAATATCAAAAGTTGC 57.515 33.333 14.05 0.97 45.54 4.17
1539 2010 7.832503 GCAATATCAAAAGTTGCCAATAGTT 57.167 32.000 0.00 0.00 41.67 2.24
1540 2011 7.678226 GCAATATCAAAAGTTGCCAATAGTTG 58.322 34.615 0.00 0.00 41.67 3.16
1555 2026 5.463061 CCAATAGTTGGCAACTTTTTGTGAG 59.537 40.000 35.13 20.18 45.17 3.51
1556 2027 3.525268 AGTTGGCAACTTTTTGTGAGG 57.475 42.857 26.54 0.00 39.04 3.86
1557 2028 2.831526 AGTTGGCAACTTTTTGTGAGGT 59.168 40.909 26.54 0.60 39.04 3.85
1559 2030 3.244033 TGGCAACTTTTTGTGAGGTTG 57.756 42.857 0.00 0.00 41.07 3.77
1561 2032 1.933181 GCAACTTTTTGTGAGGTTGGC 59.067 47.619 0.00 0.00 39.28 4.52
1562 2033 2.676463 GCAACTTTTTGTGAGGTTGGCA 60.676 45.455 0.00 0.00 39.28 4.92
1566 2143 2.151502 TTTTGTGAGGTTGGCAAGGA 57.848 45.000 0.00 0.00 0.00 3.36
1569 2146 1.398692 TGTGAGGTTGGCAAGGAAAC 58.601 50.000 0.00 0.00 0.00 2.78
1570 2147 1.341482 TGTGAGGTTGGCAAGGAAACA 60.341 47.619 0.00 0.64 0.00 2.83
1573 2150 1.273327 GAGGTTGGCAAGGAAACATGG 59.727 52.381 0.00 0.00 0.00 3.66
1574 2151 1.047801 GGTTGGCAAGGAAACATGGT 58.952 50.000 0.00 0.00 0.00 3.55
1576 2153 2.231235 GGTTGGCAAGGAAACATGGTAG 59.769 50.000 0.00 0.00 0.00 3.18
1603 2180 2.531522 AGCACTGGACAAAATTTGGC 57.468 45.000 10.71 6.87 38.21 4.52
1605 2182 2.369532 AGCACTGGACAAAATTTGGCAT 59.630 40.909 14.12 0.00 41.76 4.40
1606 2183 3.140623 GCACTGGACAAAATTTGGCATT 58.859 40.909 14.12 0.00 41.76 3.56
1607 2184 3.565063 GCACTGGACAAAATTTGGCATTT 59.435 39.130 14.12 0.00 41.76 2.32
1608 2185 4.555116 GCACTGGACAAAATTTGGCATTTG 60.555 41.667 14.12 9.81 41.76 2.32
1609 2186 3.565063 ACTGGACAAAATTTGGCATTTGC 59.435 39.130 14.12 0.00 41.76 3.68
1646 2305 5.708877 CCAATTTTTGGCATCAAACCAAT 57.291 34.783 0.00 0.00 46.25 3.16
1647 2306 6.086785 CCAATTTTTGGCATCAAACCAATT 57.913 33.333 0.00 0.00 46.25 2.32
1649 2308 7.828712 CCAATTTTTGGCATCAAACCAATTAT 58.171 30.769 0.00 0.00 46.25 1.28
1650 2309 7.755822 CCAATTTTTGGCATCAAACCAATTATG 59.244 33.333 0.00 0.00 46.25 1.90
1651 2310 5.876612 TTTTGGCATCAAACCAATTATGC 57.123 34.783 0.00 0.00 46.25 3.14
1652 2311 4.822685 TTGGCATCAAACCAATTATGCT 57.177 36.364 8.17 0.00 42.23 3.79
1653 2312 4.389890 TGGCATCAAACCAATTATGCTC 57.610 40.909 8.17 1.21 43.33 4.26
1654 2313 4.025360 TGGCATCAAACCAATTATGCTCT 58.975 39.130 8.17 0.00 43.33 4.09
1657 2316 7.003482 TGGCATCAAACCAATTATGCTCTATA 58.997 34.615 8.17 0.00 43.33 1.31
1854 8076 2.819595 CGGGCTCATGGACAACGG 60.820 66.667 0.00 0.00 0.00 4.44
1921 8143 2.579201 CCCTACACCGGTGCAGAG 59.421 66.667 32.36 25.56 0.00 3.35
2365 8597 6.765403 AGCGTTTGTGGTGTATATATATGGT 58.235 36.000 5.44 0.00 0.00 3.55
2366 8598 7.898918 AGCGTTTGTGGTGTATATATATGGTA 58.101 34.615 5.44 0.00 0.00 3.25
2367 8599 7.816031 AGCGTTTGTGGTGTATATATATGGTAC 59.184 37.037 5.44 2.18 0.00 3.34
2368 8600 7.201376 GCGTTTGTGGTGTATATATATGGTACG 60.201 40.741 5.44 0.00 0.00 3.67
2370 8602 9.132521 GTTTGTGGTGTATATATATGGTACGAC 57.867 37.037 5.44 8.96 0.00 4.34
2371 8603 7.395190 TGTGGTGTATATATATGGTACGACC 57.605 40.000 5.44 15.35 39.22 4.79
2372 8604 7.177184 TGTGGTGTATATATATGGTACGACCT 58.823 38.462 5.44 0.00 39.58 3.85
2373 8605 7.121611 TGTGGTGTATATATATGGTACGACCTG 59.878 40.741 5.44 0.00 39.58 4.00
2374 8606 6.095860 TGGTGTATATATATGGTACGACCTGC 59.904 42.308 5.44 0.00 39.58 4.85
2412 8849 6.677913 TCACCCTTTTCGAAAAATGATTCTC 58.322 36.000 22.67 0.00 0.00 2.87
2442 8879 6.758886 CAGAAATCTACTATTCACACACCTCC 59.241 42.308 0.00 0.00 0.00 4.30
2557 8997 8.397906 CAACAAAAGAGACTCAAATGTTCAGTA 58.602 33.333 13.58 0.00 0.00 2.74
2587 9030 9.103861 GCTTAGCAACTTAGAATTGTCTCTAAT 57.896 33.333 0.00 0.00 37.30 1.73
2624 9068 6.494666 AATTTGATATACTCCCTTCGTCCA 57.505 37.500 0.00 0.00 0.00 4.02
2688 9133 9.526286 GTTTTCTAAGTTTGAGAAAGCGTATAC 57.474 33.333 2.04 0.00 42.35 1.47
2715 9160 8.455682 ACAAATATGTGAAGGTAAACAATACCG 58.544 33.333 0.00 0.00 39.37 4.02
2915 10217 5.395546 GGGATCAATTTGGCTGCAAAATCTA 60.396 40.000 14.99 7.22 0.00 1.98
3079 14170 3.767230 CTCGACGTGCGCACAAGG 61.767 66.667 37.03 24.38 40.61 3.61
3082 14173 3.726517 GACGTGCGCACAAGGCAT 61.727 61.111 37.03 16.48 45.17 4.40
3097 14188 4.549458 CAAGGCATTGTTGAGAAAATCGT 58.451 39.130 2.19 0.00 0.00 3.73
3098 14189 4.853924 AGGCATTGTTGAGAAAATCGTT 57.146 36.364 0.00 0.00 0.00 3.85
3099 14190 5.957842 AGGCATTGTTGAGAAAATCGTTA 57.042 34.783 0.00 0.00 0.00 3.18
3100 14191 6.325919 AGGCATTGTTGAGAAAATCGTTAA 57.674 33.333 0.00 0.00 0.00 2.01
3101 14192 6.149633 AGGCATTGTTGAGAAAATCGTTAAC 58.850 36.000 0.00 0.00 0.00 2.01
3102 14193 6.016276 AGGCATTGTTGAGAAAATCGTTAACT 60.016 34.615 3.71 0.00 0.00 2.24
3103 14194 6.088085 GGCATTGTTGAGAAAATCGTTAACTG 59.912 38.462 3.71 0.00 0.00 3.16
3104 14195 6.088085 GCATTGTTGAGAAAATCGTTAACTGG 59.912 38.462 3.71 0.00 0.00 4.00
3105 14196 6.687081 TTGTTGAGAAAATCGTTAACTGGT 57.313 33.333 3.71 0.00 0.00 4.00
3106 14197 7.789273 TTGTTGAGAAAATCGTTAACTGGTA 57.211 32.000 3.71 0.00 0.00 3.25
3107 14198 7.789273 TGTTGAGAAAATCGTTAACTGGTAA 57.211 32.000 3.71 0.00 0.00 2.85
3108 14199 7.632721 TGTTGAGAAAATCGTTAACTGGTAAC 58.367 34.615 5.52 5.52 39.05 2.50
3109 14200 7.496591 TGTTGAGAAAATCGTTAACTGGTAACT 59.503 33.333 13.27 0.00 40.10 2.24
3110 14201 7.416154 TGAGAAAATCGTTAACTGGTAACTG 57.584 36.000 13.27 7.40 40.10 3.16
3112 14203 5.995897 AGAAAATCGTTAACTGGTAACTGCT 59.004 36.000 13.27 0.00 40.10 4.24
3113 14204 5.857822 AAATCGTTAACTGGTAACTGCTC 57.142 39.130 13.27 0.00 40.10 4.26
3115 14206 2.553602 TCGTTAACTGGTAACTGCTCGA 59.446 45.455 13.27 2.92 40.10 4.04
3117 14208 3.924686 CGTTAACTGGTAACTGCTCGATT 59.075 43.478 13.27 0.00 40.10 3.34
3121 14212 2.563179 ACTGGTAACTGCTCGATTGAGT 59.437 45.455 11.71 0.00 40.49 3.41
3122 14213 2.926200 CTGGTAACTGCTCGATTGAGTG 59.074 50.000 11.71 7.54 40.49 3.51
3125 14216 1.800805 AACTGCTCGATTGAGTGGTG 58.199 50.000 11.71 2.71 44.48 4.17
3126 14217 0.969149 ACTGCTCGATTGAGTGGTGA 59.031 50.000 11.71 0.00 44.48 4.02
3127 14218 1.067283 ACTGCTCGATTGAGTGGTGAG 60.067 52.381 11.71 3.42 44.48 3.51
3128 14219 0.969149 TGCTCGATTGAGTGGTGAGT 59.031 50.000 11.71 0.00 44.48 3.41
3129 14220 2.164422 CTGCTCGATTGAGTGGTGAGTA 59.836 50.000 11.71 0.00 44.48 2.59
3131 14222 2.480416 GCTCGATTGAGTGGTGAGTAGG 60.480 54.545 11.71 0.00 44.48 3.18
3132 14223 2.099921 CTCGATTGAGTGGTGAGTAGGG 59.900 54.545 1.30 0.00 37.46 3.53
3133 14224 1.137086 CGATTGAGTGGTGAGTAGGGG 59.863 57.143 0.00 0.00 0.00 4.79
3136 14227 2.642171 TGAGTGGTGAGTAGGGGATT 57.358 50.000 0.00 0.00 0.00 3.01
3137 14228 3.769189 TGAGTGGTGAGTAGGGGATTA 57.231 47.619 0.00 0.00 0.00 1.75
3138 14229 4.069312 TGAGTGGTGAGTAGGGGATTAA 57.931 45.455 0.00 0.00 0.00 1.40
3139 14230 4.631234 TGAGTGGTGAGTAGGGGATTAAT 58.369 43.478 0.00 0.00 0.00 1.40
3142 14233 2.969950 TGGTGAGTAGGGGATTAATCGG 59.030 50.000 9.32 0.00 0.00 4.18
3143 14234 2.289506 GGTGAGTAGGGGATTAATCGGC 60.290 54.545 9.32 0.00 0.00 5.54
3144 14235 2.633481 GTGAGTAGGGGATTAATCGGCT 59.367 50.000 9.32 3.11 0.00 5.52
3146 14237 4.282703 GTGAGTAGGGGATTAATCGGCTAA 59.717 45.833 9.32 0.00 0.00 3.09
3147 14238 5.046520 GTGAGTAGGGGATTAATCGGCTAAT 60.047 44.000 9.32 0.00 0.00 1.73
3148 14239 5.187186 TGAGTAGGGGATTAATCGGCTAATC 59.813 44.000 9.32 8.21 37.50 1.75
3149 14240 3.611766 AGGGGATTAATCGGCTAATCG 57.388 47.619 9.32 0.00 38.61 3.34
3150 14241 3.170717 AGGGGATTAATCGGCTAATCGA 58.829 45.455 9.32 0.00 43.61 3.59
3151 14242 3.056035 AGGGGATTAATCGGCTAATCGAC 60.056 47.826 9.32 6.70 42.21 4.20
3152 14243 3.306502 GGGGATTAATCGGCTAATCGACA 60.307 47.826 9.32 0.00 42.21 4.35
3153 14244 4.312443 GGGATTAATCGGCTAATCGACAA 58.688 43.478 9.32 0.00 42.21 3.18
3156 14247 5.465724 GGATTAATCGGCTAATCGACAAGTT 59.534 40.000 9.32 0.00 42.21 2.66
3160 14251 6.526566 AATCGGCTAATCGACAAGTTAATC 57.473 37.500 0.00 0.00 42.21 1.75
3161 14252 4.039703 TCGGCTAATCGACAAGTTAATCG 58.960 43.478 0.00 2.96 39.72 3.34
3171 14262 7.837202 TCGACAAGTTAATCGACCATTTAAT 57.163 32.000 7.19 0.00 42.18 1.40
3172 14263 7.902032 TCGACAAGTTAATCGACCATTTAATC 58.098 34.615 7.19 0.00 42.18 1.75
3174 14265 8.172484 CGACAAGTTAATCGACCATTTAATCAA 58.828 33.333 3.21 0.00 40.86 2.57
3183 14274 8.615878 ATCGACCATTTAATCAATTAATCGGA 57.384 30.769 13.53 0.00 34.43 4.55
3184 14275 8.615878 TCGACCATTTAATCAATTAATCGGAT 57.384 30.769 13.53 0.00 34.43 4.18
3206 14297 9.962783 CGGATAATTTATAGGTGTATAGGCTAC 57.037 37.037 0.00 0.00 0.00 3.58
3210 14301 7.642082 ATTTATAGGTGTATAGGCTACTCGG 57.358 40.000 0.00 0.00 0.00 4.63
3211 14302 4.654389 ATAGGTGTATAGGCTACTCGGT 57.346 45.455 0.00 0.00 0.00 4.69
3212 14303 2.584236 AGGTGTATAGGCTACTCGGTG 58.416 52.381 0.00 0.00 0.00 4.94
3213 14304 2.174210 AGGTGTATAGGCTACTCGGTGA 59.826 50.000 0.00 0.00 0.00 4.02
3214 14305 2.292845 GGTGTATAGGCTACTCGGTGAC 59.707 54.545 0.00 0.00 0.00 3.67
3215 14306 2.292845 GTGTATAGGCTACTCGGTGACC 59.707 54.545 0.00 0.00 0.00 4.02
3216 14307 1.885233 GTATAGGCTACTCGGTGACCC 59.115 57.143 0.00 0.00 0.00 4.46
3217 14308 0.556747 ATAGGCTACTCGGTGACCCT 59.443 55.000 0.00 0.00 0.00 4.34
3219 14310 0.395448 AGGCTACTCGGTGACCCTAC 60.395 60.000 0.00 0.00 0.00 3.18
3221 14312 1.133976 GGCTACTCGGTGACCCTACTA 60.134 57.143 0.00 0.00 0.00 1.82
3222 14313 2.220313 GCTACTCGGTGACCCTACTAG 58.780 57.143 0.00 0.00 0.00 2.57
3223 14314 2.421248 GCTACTCGGTGACCCTACTAGT 60.421 54.545 0.00 0.00 0.00 2.57
3237 14328 5.579564 CCTACTAGTAGGGATTAATCGGC 57.420 47.826 33.34 0.00 46.96 5.54
3238 14329 5.014858 CCTACTAGTAGGGATTAATCGGCA 58.985 45.833 33.34 0.00 46.96 5.69
3239 14330 5.479375 CCTACTAGTAGGGATTAATCGGCAA 59.521 44.000 33.34 0.00 46.96 4.52
3242 14333 4.772886 AGTAGGGATTAATCGGCAAGTT 57.227 40.909 9.32 0.00 0.00 2.66
3243 14334 5.881923 AGTAGGGATTAATCGGCAAGTTA 57.118 39.130 9.32 0.00 0.00 2.24
3245 14336 6.053650 AGTAGGGATTAATCGGCAAGTTAAC 58.946 40.000 9.32 0.00 0.00 2.01
3246 14337 5.112129 AGGGATTAATCGGCAAGTTAACT 57.888 39.130 9.32 1.12 0.00 2.24
3248 14339 4.036380 GGGATTAATCGGCAAGTTAACTGG 59.964 45.833 9.34 7.35 0.00 4.00
3249 14340 4.638865 GGATTAATCGGCAAGTTAACTGGT 59.361 41.667 9.34 0.00 0.00 4.00
3250 14341 5.124936 GGATTAATCGGCAAGTTAACTGGTT 59.875 40.000 9.34 1.66 0.00 3.67
3251 14342 6.316890 GGATTAATCGGCAAGTTAACTGGTTA 59.683 38.462 9.34 0.65 0.00 2.85
3252 14343 7.148205 GGATTAATCGGCAAGTTAACTGGTTAA 60.148 37.037 9.34 9.79 33.48 2.01
3253 14344 7.690952 TTAATCGGCAAGTTAACTGGTTAAT 57.309 32.000 9.34 0.00 37.37 1.40
3254 14345 5.813080 ATCGGCAAGTTAACTGGTTAATC 57.187 39.130 9.34 0.00 37.37 1.75
3257 14348 4.004982 GGCAAGTTAACTGGTTAATCGGA 58.995 43.478 9.34 0.00 37.37 4.55
3260 14351 5.353123 GCAAGTTAACTGGTTAATCGGATGA 59.647 40.000 9.34 0.00 37.37 2.92
3261 14352 6.128117 GCAAGTTAACTGGTTAATCGGATGAA 60.128 38.462 9.34 0.00 37.37 2.57
3262 14353 7.415206 GCAAGTTAACTGGTTAATCGGATGAAT 60.415 37.037 9.34 0.00 37.37 2.57
3263 14354 8.458843 CAAGTTAACTGGTTAATCGGATGAATT 58.541 33.333 9.34 0.00 37.37 2.17
3265 14356 8.047310 AGTTAACTGGTTAATCGGATGAATTCT 58.953 33.333 7.48 0.00 37.37 2.40
3266 14357 8.674607 GTTAACTGGTTAATCGGATGAATTCTT 58.325 33.333 7.05 0.00 37.37 2.52
3268 14359 6.414732 ACTGGTTAATCGGATGAATTCTTGA 58.585 36.000 7.05 0.00 0.00 3.02
3269 14360 6.884295 ACTGGTTAATCGGATGAATTCTTGAA 59.116 34.615 7.05 0.00 0.00 2.69
3273 14364 7.065803 GGTTAATCGGATGAATTCTTGAACAGA 59.934 37.037 7.05 1.15 0.00 3.41
3274 14365 6.674694 AATCGGATGAATTCTTGAACAGAG 57.325 37.500 7.05 0.00 31.12 3.35
3275 14366 4.507710 TCGGATGAATTCTTGAACAGAGG 58.492 43.478 7.05 0.00 31.12 3.69
3276 14367 3.064545 CGGATGAATTCTTGAACAGAGGC 59.935 47.826 7.05 0.00 31.12 4.70
3279 14370 3.819368 TGAATTCTTGAACAGAGGCACA 58.181 40.909 7.05 0.00 31.12 4.57
3280 14371 4.206375 TGAATTCTTGAACAGAGGCACAA 58.794 39.130 7.05 0.00 31.12 3.33
3282 14373 1.597742 TCTTGAACAGAGGCACAAGC 58.402 50.000 0.00 0.00 39.33 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 118 6.207417 AGTGCATATAATAAAAAGGCGCAGAT 59.793 34.615 10.83 0.00 33.10 2.90
92 120 5.762045 AGTGCATATAATAAAAAGGCGCAG 58.238 37.500 10.83 0.00 33.10 5.18
231 260 9.657419 ATCAGTTTCAAAACAATCTGAAGTTTT 57.343 25.926 14.63 14.63 45.77 2.43
234 263 9.956720 CTTATCAGTTTCAAAACAATCTGAAGT 57.043 29.630 8.23 0.00 41.30 3.01
235 264 9.956720 ACTTATCAGTTTCAAAACAATCTGAAG 57.043 29.630 8.23 6.12 41.30 3.02
276 308 2.429610 CCATGGAGGCTGAATTTTCTGG 59.570 50.000 5.56 0.00 0.00 3.86
308 340 3.764237 AAGAAGAGTAGGGCGTTTTGA 57.236 42.857 0.00 0.00 0.00 2.69
363 410 5.050159 CCAAAGTTTTCTAGCCAAATGTTGC 60.050 40.000 0.00 0.00 0.00 4.17
441 488 2.281761 ACTTTGTGCGAGGCCTGG 60.282 61.111 12.00 11.42 0.00 4.45
544 595 5.356291 AAACTCAAGATCATCCTCCTCAG 57.644 43.478 0.00 0.00 0.00 3.35
548 599 4.268359 AGCAAAACTCAAGATCATCCTCC 58.732 43.478 0.00 0.00 0.00 4.30
579 769 4.273724 GCACTTAGTTATAGAAGGCAAGGC 59.726 45.833 0.00 0.00 0.00 4.35
580 770 5.428253 TGCACTTAGTTATAGAAGGCAAGG 58.572 41.667 0.00 0.00 30.78 3.61
581 771 7.497249 AGAATGCACTTAGTTATAGAAGGCAAG 59.503 37.037 0.00 0.00 34.64 4.01
582 772 7.338710 AGAATGCACTTAGTTATAGAAGGCAA 58.661 34.615 0.00 0.00 34.64 4.52
583 773 6.889198 AGAATGCACTTAGTTATAGAAGGCA 58.111 36.000 0.00 0.00 35.10 4.75
584 774 7.793927 AAGAATGCACTTAGTTATAGAAGGC 57.206 36.000 0.00 0.00 0.00 4.35
649 1065 2.719426 AGCTGTACACGACCTGTAAC 57.281 50.000 0.00 0.00 37.09 2.50
738 1155 8.597662 TTGGTGAGAACAACACTAGTTAATAC 57.402 34.615 0.00 0.00 43.86 1.89
739 1156 7.386848 GCTTGGTGAGAACAACACTAGTTAATA 59.613 37.037 0.00 0.00 43.86 0.98
740 1157 6.204882 GCTTGGTGAGAACAACACTAGTTAAT 59.795 38.462 0.00 0.00 43.86 1.40
741 1158 5.526111 GCTTGGTGAGAACAACACTAGTTAA 59.474 40.000 0.00 0.00 43.86 2.01
742 1159 5.054477 GCTTGGTGAGAACAACACTAGTTA 58.946 41.667 0.00 0.00 43.86 2.24
743 1160 3.877508 GCTTGGTGAGAACAACACTAGTT 59.122 43.478 0.00 0.00 43.86 2.24
1456 1927 4.822685 TTGGCATCAAACCAATTATGCT 57.177 36.364 8.17 0.00 42.23 3.79
1464 1935 3.123157 CCAAATGTTGGCATCAAACCA 57.877 42.857 1.83 0.00 45.17 3.67
1491 1962 6.817515 CCAATTGTTGGCTTGCCAAGTATTG 61.818 44.000 30.21 30.21 45.00 1.90
1492 1963 4.317488 CAATTGTTGGCTTGCCAAGTATT 58.683 39.130 25.26 21.82 0.00 1.89
1493 1964 3.306919 CCAATTGTTGGCTTGCCAAGTAT 60.307 43.478 25.26 18.02 45.17 2.12
1494 1965 2.036992 CCAATTGTTGGCTTGCCAAGTA 59.963 45.455 25.26 16.72 45.17 2.24
1495 1966 1.202675 CCAATTGTTGGCTTGCCAAGT 60.203 47.619 25.26 12.86 45.17 3.16
1496 1967 1.515081 CCAATTGTTGGCTTGCCAAG 58.485 50.000 25.26 13.96 45.17 3.61
1497 1968 3.702147 CCAATTGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
1506 1977 6.797995 GCAACTTTTGATATTGCCAATTGTTG 59.202 34.615 4.43 0.16 42.32 3.33
1507 1978 6.901265 GCAACTTTTGATATTGCCAATTGTT 58.099 32.000 4.43 0.00 42.32 2.83
1508 1979 6.484818 GCAACTTTTGATATTGCCAATTGT 57.515 33.333 4.43 0.00 42.32 2.71
1515 1986 7.201548 CCAACTATTGGCAACTTTTGATATTGC 60.202 37.037 0.00 0.00 45.17 3.56
1516 1987 8.188531 CCAACTATTGGCAACTTTTGATATTG 57.811 34.615 0.00 0.00 45.17 1.90
1532 2003 5.463061 CCTCACAAAAAGTTGCCAACTATTG 59.537 40.000 23.68 23.68 41.91 1.90
1533 2004 5.128663 ACCTCACAAAAAGTTGCCAACTATT 59.871 36.000 11.10 6.62 41.91 1.73
1534 2005 4.649218 ACCTCACAAAAAGTTGCCAACTAT 59.351 37.500 11.10 0.00 41.91 2.12
1535 2006 4.020543 ACCTCACAAAAAGTTGCCAACTA 58.979 39.130 11.10 0.00 41.91 2.24
1536 2007 2.831526 ACCTCACAAAAAGTTGCCAACT 59.168 40.909 3.74 3.74 45.46 3.16
1537 2008 3.245518 ACCTCACAAAAAGTTGCCAAC 57.754 42.857 0.00 0.00 38.39 3.77
1538 2009 3.594134 CAACCTCACAAAAAGTTGCCAA 58.406 40.909 0.00 0.00 38.39 4.52
1539 2010 2.093764 CCAACCTCACAAAAAGTTGCCA 60.094 45.455 0.00 0.00 38.58 4.92
1540 2011 2.549926 CCAACCTCACAAAAAGTTGCC 58.450 47.619 0.00 0.00 38.58 4.52
1541 2012 1.933181 GCCAACCTCACAAAAAGTTGC 59.067 47.619 0.00 0.00 38.58 4.17
1545 2016 2.430332 TCCTTGCCAACCTCACAAAAAG 59.570 45.455 0.00 0.00 0.00 2.27
1547 2018 2.151502 TCCTTGCCAACCTCACAAAA 57.848 45.000 0.00 0.00 0.00 2.44
1555 2026 1.047801 ACCATGTTTCCTTGCCAACC 58.952 50.000 0.00 0.00 0.00 3.77
1556 2027 2.352715 GCTACCATGTTTCCTTGCCAAC 60.353 50.000 0.00 0.00 0.00 3.77
1557 2028 1.892474 GCTACCATGTTTCCTTGCCAA 59.108 47.619 0.00 0.00 0.00 4.52
1559 2030 0.817654 GGCTACCATGTTTCCTTGCC 59.182 55.000 0.00 0.00 0.00 4.52
1561 2032 2.231235 GGTTGGCTACCATGTTTCCTTG 59.769 50.000 13.41 0.00 46.92 3.61
1562 2033 2.525368 GGTTGGCTACCATGTTTCCTT 58.475 47.619 13.41 0.00 46.92 3.36
1573 2150 2.257353 CCAGTGCTTGGTTGGCTAC 58.743 57.895 0.21 0.00 42.41 3.58
1574 2151 4.819783 CCAGTGCTTGGTTGGCTA 57.180 55.556 0.21 0.00 42.41 3.93
1585 2162 2.237393 TGCCAAATTTTGTCCAGTGC 57.763 45.000 8.26 4.08 0.00 4.40
1586 2163 4.555116 GCAAATGCCAAATTTTGTCCAGTG 60.555 41.667 8.26 8.10 35.69 3.66
1587 2164 3.565063 GCAAATGCCAAATTTTGTCCAGT 59.435 39.130 8.26 2.11 35.69 4.00
1588 2165 4.149910 GCAAATGCCAAATTTTGTCCAG 57.850 40.909 8.26 0.00 35.69 3.86
1634 2293 9.918630 AAATATAGAGCATAATTGGTTTGATGC 57.081 29.630 1.15 1.15 44.05 3.91
1636 2295 9.918630 GCAAATATAGAGCATAATTGGTTTGAT 57.081 29.630 0.00 0.00 32.65 2.57
1637 2296 8.911965 TGCAAATATAGAGCATAATTGGTTTGA 58.088 29.630 0.00 0.00 32.65 2.69
1638 2297 9.701098 ATGCAAATATAGAGCATAATTGGTTTG 57.299 29.630 7.45 0.00 46.27 2.93
1641 2300 8.640063 TCATGCAAATATAGAGCATAATTGGT 57.360 30.769 8.55 0.00 46.39 3.67
1642 2301 9.350357 GTTCATGCAAATATAGAGCATAATTGG 57.650 33.333 8.55 0.00 46.39 3.16
1643 2302 9.350357 GGTTCATGCAAATATAGAGCATAATTG 57.650 33.333 8.55 0.97 46.39 2.32
1644 2303 9.305555 AGGTTCATGCAAATATAGAGCATAATT 57.694 29.630 8.55 0.00 46.39 1.40
1646 2305 9.964354 ATAGGTTCATGCAAATATAGAGCATAA 57.036 29.630 8.55 0.00 46.39 1.90
1647 2306 9.387257 CATAGGTTCATGCAAATATAGAGCATA 57.613 33.333 8.55 0.00 46.39 3.14
1649 2308 6.656270 CCATAGGTTCATGCAAATATAGAGCA 59.344 38.462 0.00 0.00 43.14 4.26
1650 2309 6.656693 ACCATAGGTTCATGCAAATATAGAGC 59.343 38.462 0.00 0.00 27.29 4.09
1651 2310 7.879677 TGACCATAGGTTCATGCAAATATAGAG 59.120 37.037 0.00 0.00 35.25 2.43
1652 2311 7.661437 GTGACCATAGGTTCATGCAAATATAGA 59.339 37.037 0.00 0.00 35.25 1.98
1653 2312 7.663081 AGTGACCATAGGTTCATGCAAATATAG 59.337 37.037 0.00 0.00 35.25 1.31
1654 2313 7.445096 CAGTGACCATAGGTTCATGCAAATATA 59.555 37.037 0.00 0.00 35.25 0.86
1657 2316 4.400251 CAGTGACCATAGGTTCATGCAAAT 59.600 41.667 0.00 0.00 35.25 2.32
1854 8076 1.126079 TTTGACGACGAACTCGAAGC 58.874 50.000 6.05 0.00 46.14 3.86
2367 8599 5.795939 GTGATATAGAAGAATACGCAGGTCG 59.204 44.000 0.00 0.00 45.38 4.79
2368 8600 6.094061 GGTGATATAGAAGAATACGCAGGTC 58.906 44.000 0.00 0.00 0.00 3.85
2370 8602 5.186021 AGGGTGATATAGAAGAATACGCAGG 59.814 44.000 0.00 0.00 0.00 4.85
2371 8603 6.274157 AGGGTGATATAGAAGAATACGCAG 57.726 41.667 0.00 0.00 0.00 5.18
2372 8604 6.665992 AAGGGTGATATAGAAGAATACGCA 57.334 37.500 0.00 0.00 0.00 5.24
2373 8605 7.148787 CGAAAAGGGTGATATAGAAGAATACGC 60.149 40.741 0.00 0.00 0.00 4.42
2374 8606 8.080417 TCGAAAAGGGTGATATAGAAGAATACG 58.920 37.037 0.00 0.00 0.00 3.06
2377 8609 9.681062 TTTTCGAAAAGGGTGATATAGAAGAAT 57.319 29.630 19.08 0.00 0.00 2.40
2378 8610 9.509956 TTTTTCGAAAAGGGTGATATAGAAGAA 57.490 29.630 21.53 0.05 0.00 2.52
2379 8611 9.681062 ATTTTTCGAAAAGGGTGATATAGAAGA 57.319 29.630 21.53 3.54 0.00 2.87
2380 8612 9.722056 CATTTTTCGAAAAGGGTGATATAGAAG 57.278 33.333 21.53 0.00 0.00 2.85
2381 8613 9.456147 TCATTTTTCGAAAAGGGTGATATAGAA 57.544 29.630 21.53 4.57 0.00 2.10
2382 8614 9.627123 ATCATTTTTCGAAAAGGGTGATATAGA 57.373 29.630 28.00 16.88 31.10 1.98
2412 8849 8.607459 GTGTGTGAATAGTAGATTTCTGATTGG 58.393 37.037 0.00 0.00 0.00 3.16
2557 8997 7.569240 AGACAATTCTAAGTTGCTAAGCCTAT 58.431 34.615 0.00 0.00 0.00 2.57
2624 9068 5.117584 TCGGTTTGTACGCCATGTATTTAT 58.882 37.500 0.00 0.00 35.02 1.40
2663 9108 9.263538 TGTATACGCTTTCTCAAACTTAGAAAA 57.736 29.630 0.00 0.00 41.21 2.29
2688 9133 9.567848 GGTATTGTTTACCTTCACATATTTGTG 57.432 33.333 9.76 9.76 42.78 3.33
2866 10168 7.821359 CCTCTATCCCGAAATATATGGCATATG 59.179 40.741 26.37 11.55 0.00 1.78
2870 10172 4.408921 CCCTCTATCCCGAAATATATGGCA 59.591 45.833 0.00 0.00 0.00 4.92
2882 10184 3.679389 CCAAATTGATCCCTCTATCCCG 58.321 50.000 0.00 0.00 0.00 5.14
2915 10217 6.380079 AGGGAACTCTCACAAGAACATTAT 57.620 37.500 0.00 0.00 32.90 1.28
3079 14170 6.088085 CCAGTTAACGATTTTCTCAACAATGC 59.912 38.462 0.00 0.00 0.00 3.56
3080 14171 7.138736 ACCAGTTAACGATTTTCTCAACAATG 58.861 34.615 0.00 0.00 0.00 2.82
3081 14172 7.272037 ACCAGTTAACGATTTTCTCAACAAT 57.728 32.000 0.00 0.00 0.00 2.71
3082 14173 6.687081 ACCAGTTAACGATTTTCTCAACAA 57.313 33.333 0.00 0.00 0.00 2.83
3086 14177 6.073440 GCAGTTACCAGTTAACGATTTTCTCA 60.073 38.462 0.00 0.00 44.39 3.27
3087 14178 6.147328 AGCAGTTACCAGTTAACGATTTTCTC 59.853 38.462 0.00 0.00 44.39 2.87
3090 14181 5.107220 CGAGCAGTTACCAGTTAACGATTTT 60.107 40.000 0.00 0.00 44.39 1.82
3091 14182 4.387862 CGAGCAGTTACCAGTTAACGATTT 59.612 41.667 0.00 0.00 44.39 2.17
3093 14184 3.192001 TCGAGCAGTTACCAGTTAACGAT 59.808 43.478 0.00 0.00 44.39 3.73
3094 14185 2.553602 TCGAGCAGTTACCAGTTAACGA 59.446 45.455 0.00 0.00 44.39 3.85
3096 14187 4.927425 TCAATCGAGCAGTTACCAGTTAAC 59.073 41.667 0.00 0.00 40.57 2.01
3097 14188 5.142061 TCAATCGAGCAGTTACCAGTTAA 57.858 39.130 0.00 0.00 0.00 2.01
3098 14189 4.219944 ACTCAATCGAGCAGTTACCAGTTA 59.780 41.667 0.00 0.00 43.66 2.24
3099 14190 3.006967 ACTCAATCGAGCAGTTACCAGTT 59.993 43.478 0.00 0.00 43.66 3.16
3100 14191 2.563179 ACTCAATCGAGCAGTTACCAGT 59.437 45.455 0.00 0.00 43.66 4.00
3101 14192 2.926200 CACTCAATCGAGCAGTTACCAG 59.074 50.000 0.00 0.00 43.66 4.00
3102 14193 2.353704 CCACTCAATCGAGCAGTTACCA 60.354 50.000 0.00 0.00 43.66 3.25
3103 14194 2.271800 CCACTCAATCGAGCAGTTACC 58.728 52.381 0.00 0.00 43.66 2.85
3104 14195 2.668457 CACCACTCAATCGAGCAGTTAC 59.332 50.000 0.00 0.00 43.66 2.50
3105 14196 2.560981 TCACCACTCAATCGAGCAGTTA 59.439 45.455 0.00 0.00 43.66 2.24
3106 14197 1.344438 TCACCACTCAATCGAGCAGTT 59.656 47.619 0.00 0.00 43.66 3.16
3107 14198 0.969149 TCACCACTCAATCGAGCAGT 59.031 50.000 0.00 0.00 43.66 4.40
3108 14199 1.067283 ACTCACCACTCAATCGAGCAG 60.067 52.381 0.00 0.00 43.66 4.24
3109 14200 0.969149 ACTCACCACTCAATCGAGCA 59.031 50.000 0.00 0.00 43.66 4.26
3110 14201 2.480416 CCTACTCACCACTCAATCGAGC 60.480 54.545 0.00 0.00 43.66 5.03
3112 14203 2.100197 CCCTACTCACCACTCAATCGA 58.900 52.381 0.00 0.00 0.00 3.59
3113 14204 1.137086 CCCCTACTCACCACTCAATCG 59.863 57.143 0.00 0.00 0.00 3.34
3115 14206 2.642171 TCCCCTACTCACCACTCAAT 57.358 50.000 0.00 0.00 0.00 2.57
3117 14208 2.642171 AATCCCCTACTCACCACTCA 57.358 50.000 0.00 0.00 0.00 3.41
3121 14212 2.969950 CCGATTAATCCCCTACTCACCA 59.030 50.000 9.87 0.00 0.00 4.17
3122 14213 2.289506 GCCGATTAATCCCCTACTCACC 60.290 54.545 9.87 0.00 0.00 4.02
3125 14216 5.662456 GATTAGCCGATTAATCCCCTACTC 58.338 45.833 9.87 9.69 35.12 2.59
3126 14217 4.159879 CGATTAGCCGATTAATCCCCTACT 59.840 45.833 9.87 5.08 36.93 2.57
3127 14218 4.159135 TCGATTAGCCGATTAATCCCCTAC 59.841 45.833 9.87 0.48 36.93 3.18
3128 14219 4.159135 GTCGATTAGCCGATTAATCCCCTA 59.841 45.833 9.87 7.57 40.91 3.53
3129 14220 3.056035 GTCGATTAGCCGATTAATCCCCT 60.056 47.826 9.87 8.47 40.91 4.79
3131 14222 3.921677 TGTCGATTAGCCGATTAATCCC 58.078 45.455 9.87 1.65 40.91 3.85
3132 14223 4.989168 ACTTGTCGATTAGCCGATTAATCC 59.011 41.667 9.87 0.00 40.91 3.01
3133 14224 6.526566 AACTTGTCGATTAGCCGATTAATC 57.473 37.500 5.30 5.30 40.91 1.75
3136 14227 6.361481 CGATTAACTTGTCGATTAGCCGATTA 59.639 38.462 0.00 0.00 40.91 1.75
3137 14228 5.175126 CGATTAACTTGTCGATTAGCCGATT 59.825 40.000 0.00 0.00 40.91 3.34
3138 14229 4.680110 CGATTAACTTGTCGATTAGCCGAT 59.320 41.667 0.00 0.00 40.91 4.18
3139 14230 4.039703 CGATTAACTTGTCGATTAGCCGA 58.960 43.478 0.00 0.00 40.11 5.54
3142 14233 4.802039 TGGTCGATTAACTTGTCGATTAGC 59.198 41.667 2.52 0.00 46.91 3.09
3143 14234 7.464830 AATGGTCGATTAACTTGTCGATTAG 57.535 36.000 2.52 0.00 46.91 1.73
3144 14235 7.837202 AAATGGTCGATTAACTTGTCGATTA 57.163 32.000 2.52 0.00 46.91 1.75
3146 14237 7.837202 TTAAATGGTCGATTAACTTGTCGAT 57.163 32.000 2.52 0.00 46.91 3.59
3147 14238 7.546316 TGATTAAATGGTCGATTAACTTGTCGA 59.454 33.333 0.00 0.00 43.79 4.20
3148 14239 7.680982 TGATTAAATGGTCGATTAACTTGTCG 58.319 34.615 0.00 0.00 39.11 4.35
3178 14269 9.435570 AGCCTATACACCTATAAATTATCCGAT 57.564 33.333 0.00 0.00 0.00 4.18
3179 14270 8.834004 AGCCTATACACCTATAAATTATCCGA 57.166 34.615 0.00 0.00 0.00 4.55
3180 14271 9.962783 GTAGCCTATACACCTATAAATTATCCG 57.037 37.037 0.00 0.00 0.00 4.18
3184 14275 9.182214 CCGAGTAGCCTATACACCTATAAATTA 57.818 37.037 0.00 0.00 0.00 1.40
3186 14277 7.122353 CACCGAGTAGCCTATACACCTATAAAT 59.878 40.741 0.00 0.00 0.00 1.40
3187 14278 6.432162 CACCGAGTAGCCTATACACCTATAAA 59.568 42.308 0.00 0.00 0.00 1.40
3188 14279 5.942236 CACCGAGTAGCCTATACACCTATAA 59.058 44.000 0.00 0.00 0.00 0.98
3191 14282 3.392285 TCACCGAGTAGCCTATACACCTA 59.608 47.826 0.00 0.00 0.00 3.08
3192 14283 2.174210 TCACCGAGTAGCCTATACACCT 59.826 50.000 0.00 0.00 0.00 4.00
3193 14284 2.292845 GTCACCGAGTAGCCTATACACC 59.707 54.545 0.00 0.00 0.00 4.16
3194 14285 2.292845 GGTCACCGAGTAGCCTATACAC 59.707 54.545 0.00 0.00 0.00 2.90
3195 14286 2.579873 GGTCACCGAGTAGCCTATACA 58.420 52.381 0.00 0.00 0.00 2.29
3196 14287 1.885233 GGGTCACCGAGTAGCCTATAC 59.115 57.143 0.00 0.00 0.00 1.47
3198 14289 0.556747 AGGGTCACCGAGTAGCCTAT 59.443 55.000 0.00 0.00 41.72 2.57
3199 14290 1.133976 GTAGGGTCACCGAGTAGCCTA 60.134 57.143 0.00 0.00 43.24 3.93
3200 14291 0.395448 GTAGGGTCACCGAGTAGCCT 60.395 60.000 6.78 6.78 45.33 4.58
3203 14294 3.557228 ACTAGTAGGGTCACCGAGTAG 57.443 52.381 1.45 7.43 45.63 2.57
3206 14297 2.848691 CCTACTAGTAGGGTCACCGAG 58.151 57.143 33.34 10.92 46.96 4.63
3216 14307 6.208994 ACTTGCCGATTAATCCCTACTAGTAG 59.791 42.308 21.11 21.11 0.00 2.57
3217 14308 6.073314 ACTTGCCGATTAATCCCTACTAGTA 58.927 40.000 9.87 1.89 0.00 1.82
3219 14310 5.470047 ACTTGCCGATTAATCCCTACTAG 57.530 43.478 9.87 5.92 0.00 2.57
3221 14312 4.772886 AACTTGCCGATTAATCCCTACT 57.227 40.909 9.87 0.00 0.00 2.57
3222 14313 6.018180 CAGTTAACTTGCCGATTAATCCCTAC 60.018 42.308 5.07 0.00 0.00 3.18
3223 14314 6.053005 CAGTTAACTTGCCGATTAATCCCTA 58.947 40.000 5.07 0.00 0.00 3.53
3227 14318 5.813080 ACCAGTTAACTTGCCGATTAATC 57.187 39.130 5.07 5.30 0.00 1.75
3228 14319 7.690952 TTAACCAGTTAACTTGCCGATTAAT 57.309 32.000 5.07 0.00 30.78 1.40
3229 14320 7.413219 CGATTAACCAGTTAACTTGCCGATTAA 60.413 37.037 5.07 4.36 37.80 1.40
3230 14321 6.036300 CGATTAACCAGTTAACTTGCCGATTA 59.964 38.462 5.07 0.00 37.80 1.75
3231 14322 5.163794 CGATTAACCAGTTAACTTGCCGATT 60.164 40.000 5.07 0.00 37.80 3.34
3232 14323 4.331717 CGATTAACCAGTTAACTTGCCGAT 59.668 41.667 5.07 0.00 37.80 4.18
3233 14324 3.680937 CGATTAACCAGTTAACTTGCCGA 59.319 43.478 5.07 0.00 37.80 5.54
3235 14326 4.004982 TCCGATTAACCAGTTAACTTGCC 58.995 43.478 5.07 0.00 37.80 4.52
3236 14327 5.353123 TCATCCGATTAACCAGTTAACTTGC 59.647 40.000 5.07 0.00 37.80 4.01
3237 14328 6.978343 TCATCCGATTAACCAGTTAACTTG 57.022 37.500 5.07 5.14 37.80 3.16
3238 14329 8.575649 AATTCATCCGATTAACCAGTTAACTT 57.424 30.769 5.07 0.00 37.80 2.66
3239 14330 8.047310 AGAATTCATCCGATTAACCAGTTAACT 58.953 33.333 8.44 1.12 37.80 2.24
3242 14333 8.044309 TCAAGAATTCATCCGATTAACCAGTTA 58.956 33.333 8.44 0.00 0.00 2.24
3243 14334 6.884295 TCAAGAATTCATCCGATTAACCAGTT 59.116 34.615 8.44 0.00 0.00 3.16
3245 14336 6.925610 TCAAGAATTCATCCGATTAACCAG 57.074 37.500 8.44 0.00 0.00 4.00
3246 14337 6.657117 TGTTCAAGAATTCATCCGATTAACCA 59.343 34.615 8.44 0.00 0.00 3.67
3248 14339 7.974675 TCTGTTCAAGAATTCATCCGATTAAC 58.025 34.615 8.44 1.74 29.54 2.01
3249 14340 7.280876 CCTCTGTTCAAGAATTCATCCGATTAA 59.719 37.037 8.44 0.00 33.37 1.40
3250 14341 6.763135 CCTCTGTTCAAGAATTCATCCGATTA 59.237 38.462 8.44 0.00 33.37 1.75
3251 14342 5.587844 CCTCTGTTCAAGAATTCATCCGATT 59.412 40.000 8.44 0.00 33.37 3.34
3252 14343 5.121811 CCTCTGTTCAAGAATTCATCCGAT 58.878 41.667 8.44 0.00 33.37 4.18
3253 14344 4.507710 CCTCTGTTCAAGAATTCATCCGA 58.492 43.478 8.44 0.00 33.37 4.55
3254 14345 3.064545 GCCTCTGTTCAAGAATTCATCCG 59.935 47.826 8.44 0.00 33.37 4.18
3257 14348 4.401022 TGTGCCTCTGTTCAAGAATTCAT 58.599 39.130 8.44 0.00 33.37 2.57
3260 14351 3.005155 GCTTGTGCCTCTGTTCAAGAATT 59.995 43.478 7.75 0.00 39.39 2.17
3261 14352 2.555757 GCTTGTGCCTCTGTTCAAGAAT 59.444 45.455 7.75 0.00 39.39 2.40
3262 14353 1.949525 GCTTGTGCCTCTGTTCAAGAA 59.050 47.619 7.75 0.00 39.39 2.52
3263 14354 1.597742 GCTTGTGCCTCTGTTCAAGA 58.402 50.000 7.75 0.00 39.39 3.02


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

AutoCloner maintained by Alex Coulton.