Multiple sequence alignment - TraesCS3D01G059900

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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 TraesCS3D01G059900 chr3D 100.000 4059 0 0 1 4059 26177907 26173849 0.000000e+00 7496.0
1 TraesCS3D01G059900 chr3A 90.621 1770 119 22 1761 3511 36087789 36086048 0.000000e+00 2305.0
2 TraesCS3D01G059900 chr3A 89.270 932 91 7 6 930 36090341 36089412 0.000000e+00 1158.0
3 TraesCS3D01G059900 chr3A 93.429 487 17 5 928 1400 36089058 36088573 0.000000e+00 708.0
4 TraesCS3D01G059900 chr3A 85.531 546 43 9 3543 4059 36085898 36085360 4.620000e-149 538.0
5 TraesCS3D01G059900 chr3A 90.099 101 7 3 1659 1758 36087923 36087825 1.180000e-25 128.0
6 TraesCS3D01G059900 chr3B 89.337 1735 129 26 1835 3545 43557494 43555792 0.000000e+00 2128.0
7 TraesCS3D01G059900 chr3B 88.195 1025 83 24 398 1400 43559500 43558492 0.000000e+00 1188.0
8 TraesCS3D01G059900 chr3B 83.387 933 105 24 398 1305 43571996 43571089 0.000000e+00 819.0
9 TraesCS3D01G059900 chr3B 83.280 933 106 24 398 1305 43565723 43564816 0.000000e+00 813.0
10 TraesCS3D01G059900 chr3B 82.905 778 81 30 528 1278 43583548 43582796 0.000000e+00 652.0
11 TraesCS3D01G059900 chr3B 87.986 283 20 5 2963 3238 536444663 536444938 5.060000e-84 322.0
12 TraesCS3D01G059900 chr3B 81.532 222 14 5 1659 1854 43557724 43557504 1.510000e-34 158.0
13 TraesCS3D01G059900 chr7B 87.633 283 21 4 2963 3238 703377785 703378060 2.350000e-82 316.0
14 TraesCS3D01G059900 chr7B 86.411 287 25 5 2963 3242 591874261 591873982 6.590000e-78 302.0
15 TraesCS3D01G059900 chr7B 84.146 246 27 5 1842 2076 591873141 591872897 1.130000e-55 228.0
16 TraesCS3D01G059900 chr6A 82.540 126 21 1 30 154 182662581 182662456 4.290000e-20 110.0
17 TraesCS3D01G059900 chr5D 85.294 102 13 2 50 150 430169189 430169089 2.000000e-18 104.0
18 TraesCS3D01G059900 chr5D 92.105 38 3 0 576 613 330303932 330303895 2.000000e-03 54.7
19 TraesCS3D01G059900 chr4B 81.890 127 20 3 30 155 141540633 141540509 2.000000e-18 104.0
20 TraesCS3D01G059900 chr6D 81.667 120 21 1 28 146 463789831 463789950 9.280000e-17 99.0
21 TraesCS3D01G059900 chr2A 84.783 92 10 3 66 155 568421179 568421268 5.590000e-14 89.8
22 TraesCS3D01G059900 chr7D 81.731 104 18 1 50 153 483476827 483476929 7.230000e-13 86.1
23 TraesCS3D01G059900 chr6B 78.740 127 25 2 28 153 21356844 21356719 2.600000e-12 84.2
24 TraesCS3D01G059900 chr4A 81.188 101 19 0 55 155 550171792 550171892 9.350000e-12 82.4


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 TraesCS3D01G059900 chr3D 26173849 26177907 4058 True 7496.0 7496 100.000000 1 4059 1 chr3D.!!$R1 4058
1 TraesCS3D01G059900 chr3A 36085360 36090341 4981 True 967.4 2305 89.790000 6 4059 5 chr3A.!!$R1 4053
2 TraesCS3D01G059900 chr3B 43555792 43559500 3708 True 1158.0 2128 86.354667 398 3545 3 chr3B.!!$R4 3147
3 TraesCS3D01G059900 chr3B 43571089 43571996 907 True 819.0 819 83.387000 398 1305 1 chr3B.!!$R2 907
4 TraesCS3D01G059900 chr3B 43564816 43565723 907 True 813.0 813 83.280000 398 1305 1 chr3B.!!$R1 907
5 TraesCS3D01G059900 chr3B 43582796 43583548 752 True 652.0 652 82.905000 528 1278 1 chr3B.!!$R3 750
6 TraesCS3D01G059900 chr7B 591872897 591874261 1364 True 265.0 302 85.278500 1842 3242 2 chr7B.!!$R1 1400

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
116 117 0.179029 AAAGACACCACCAGAACGGG 60.179 55.0 0.00 0.0 40.22 5.28 F
525 531 0.877071 CCTTTGCGTGCTCACTCAAT 59.123 50.0 6.30 0.0 36.14 2.57 F
1446 1888 0.038343 TTACGGTGGTACCTTGCGTC 60.038 55.0 14.36 0.0 35.66 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 1848 0.165944 CCCGCGCAAAAGTTCAGTAG 59.834 55.0 8.75 0.0 0.00 2.57 R
1448 1890 0.176449 CCAGAGTCATCATCCACGCA 59.824 55.0 0.00 0.0 0.00 5.24 R
3371 4440 0.035915 GACCAGGGGAGCAAACTCTC 60.036 60.0 0.00 0.0 43.33 3.20 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
26 27 5.939457 TCTAGACACATAAACACAGACGAG 58.061 41.667 0.00 0.00 0.00 4.18
27 28 3.318017 AGACACATAAACACAGACGAGC 58.682 45.455 0.00 0.00 0.00 5.03
40 41 1.067212 AGACGAGCGAAGACAAACACT 59.933 47.619 0.00 0.00 0.00 3.55
45 46 1.134521 AGCGAAGACAAACACTGACCA 60.135 47.619 0.00 0.00 0.00 4.02
52 53 3.632145 AGACAAACACTGACCAAATCCAC 59.368 43.478 0.00 0.00 0.00 4.02
73 74 0.250513 AGATCGGCCAGAGACAAACC 59.749 55.000 2.24 0.00 0.00 3.27
84 85 2.238646 AGAGACAAACCTTCACACACCA 59.761 45.455 0.00 0.00 0.00 4.17
104 105 5.409643 CCATTCGATGATGGTAAAGACAC 57.590 43.478 7.82 0.00 41.37 3.67
115 116 2.140717 GTAAAGACACCACCAGAACGG 58.859 52.381 0.00 0.00 42.50 4.44
116 117 0.179029 AAAGACACCACCAGAACGGG 60.179 55.000 0.00 0.00 40.22 5.28
156 157 6.647334 TCTTATTCCATCTACAGAGAGCAG 57.353 41.667 0.00 0.00 34.35 4.24
175 176 4.765339 AGCAGGACACAAACCCTAATAAAC 59.235 41.667 0.00 0.00 0.00 2.01
176 177 4.765339 GCAGGACACAAACCCTAATAAACT 59.235 41.667 0.00 0.00 0.00 2.66
214 218 1.228552 GAACCCTCCTGCCTGCAAA 60.229 57.895 0.00 0.00 0.00 3.68
216 220 2.362120 CCCTCCTGCCTGCAAAGG 60.362 66.667 11.47 11.47 34.65 3.11
226 230 1.233019 CCTGCAAAGGCTGATATCCG 58.767 55.000 0.00 0.00 41.06 4.18
250 254 1.546476 CGCCTCTGTGGTCTTAAGACT 59.454 52.381 29.66 0.00 44.20 3.24
269 273 1.686052 CTGCAGGAGATGAGGTAGACC 59.314 57.143 5.57 0.00 0.00 3.85
304 308 2.025887 ACAGGAGGCAATAGAAACCCTG 60.026 50.000 0.00 0.00 43.77 4.45
310 314 3.844211 AGGCAATAGAAACCCTGACACTA 59.156 43.478 0.00 0.00 0.00 2.74
314 318 5.112686 CAATAGAAACCCTGACACTAGCTC 58.887 45.833 0.00 0.00 0.00 4.09
334 338 3.984749 TGGTGCAGCGTACGAGCA 61.985 61.111 25.36 25.36 40.15 4.26
386 390 2.364002 GTCTCAGGCTGTCTCCTTATCC 59.636 54.545 15.27 0.00 33.25 2.59
387 391 1.691434 CTCAGGCTGTCTCCTTATCCC 59.309 57.143 15.27 0.00 33.25 3.85
388 392 1.008327 TCAGGCTGTCTCCTTATCCCA 59.992 52.381 15.27 0.00 33.25 4.37
422 426 1.327764 CGTGCTTATCTTTTCTCCCGC 59.672 52.381 0.00 0.00 0.00 6.13
503 508 2.930019 CCACTGGCCACCTCTGGA 60.930 66.667 0.00 0.00 40.55 3.86
525 531 0.877071 CCTTTGCGTGCTCACTCAAT 59.123 50.000 6.30 0.00 36.14 2.57
619 627 4.292643 ACTATTCCAGGGGTGTTACGTAT 58.707 43.478 0.00 0.00 0.00 3.06
631 648 5.450412 GGGTGTTACGTATGTCCTCGAATTA 60.450 44.000 0.00 0.00 0.00 1.40
632 649 6.211515 GGTGTTACGTATGTCCTCGAATTAT 58.788 40.000 0.00 0.00 0.00 1.28
633 650 7.362662 GGTGTTACGTATGTCCTCGAATTATA 58.637 38.462 0.00 0.00 0.00 0.98
634 651 7.324616 GGTGTTACGTATGTCCTCGAATTATAC 59.675 40.741 0.00 0.00 0.00 1.47
635 652 7.857389 GTGTTACGTATGTCCTCGAATTATACA 59.143 37.037 0.00 0.00 0.00 2.29
636 653 8.404765 TGTTACGTATGTCCTCGAATTATACAA 58.595 33.333 0.00 0.00 0.00 2.41
637 654 9.236691 GTTACGTATGTCCTCGAATTATACAAA 57.763 33.333 0.00 0.00 0.00 2.83
638 655 9.970395 TTACGTATGTCCTCGAATTATACAAAT 57.030 29.630 0.00 0.00 0.00 2.32
753 772 9.197694 CCTAGCATGACACATTTACTATACTTC 57.802 37.037 0.00 0.00 0.00 3.01
764 783 8.407064 ACATTTACTATACTTCGAGGACTTGAG 58.593 37.037 0.00 0.00 0.00 3.02
793 812 8.701895 ACGATTTTCATACTTTGAGGACCTATA 58.298 33.333 0.00 0.00 35.27 1.31
799 818 8.727100 TCATACTTTGAGGACCTATATGACAT 57.273 34.615 0.00 0.00 0.00 3.06
806 825 5.777223 TGAGGACCTATATGACATCCTTGAG 59.223 44.000 0.00 0.00 39.96 3.02
949 1334 4.591498 GTCTTAATCCAAACCCAAAACCCT 59.409 41.667 0.00 0.00 0.00 4.34
1014 1403 2.044946 GCCATGGCCTCCTTCGTT 60.045 61.111 27.24 0.00 34.56 3.85
1335 1756 1.002502 GGTCCCTGCTTTAAGCGGT 60.003 57.895 22.31 0.00 45.98 5.68
1400 1821 3.254093 TGCCGGAATTAGAGAGGGATA 57.746 47.619 5.05 0.00 0.00 2.59
1401 1822 2.897969 TGCCGGAATTAGAGAGGGATAC 59.102 50.000 5.05 0.00 0.00 2.24
1406 1848 4.616373 CGGAATTAGAGAGGGATACGCTTC 60.616 50.000 0.00 0.00 37.60 3.86
1412 1854 3.136809 AGAGAGGGATACGCTTCTACTGA 59.863 47.826 0.00 0.00 37.60 3.41
1414 1856 3.633065 AGAGGGATACGCTTCTACTGAAC 59.367 47.826 0.00 0.00 37.60 3.18
1420 1862 3.879932 ACGCTTCTACTGAACTTTTGC 57.120 42.857 0.00 0.00 0.00 3.68
1421 1863 2.221055 ACGCTTCTACTGAACTTTTGCG 59.779 45.455 0.00 0.00 43.07 4.85
1425 1867 0.165944 CTACTGAACTTTTGCGCGGG 59.834 55.000 8.83 0.00 0.00 6.13
1446 1888 0.038343 TTACGGTGGTACCTTGCGTC 60.038 55.000 14.36 0.00 35.66 5.19
1447 1889 0.895100 TACGGTGGTACCTTGCGTCT 60.895 55.000 14.36 0.00 35.66 4.18
1448 1890 1.005394 CGGTGGTACCTTGCGTCTT 60.005 57.895 14.36 0.00 35.66 3.01
1449 1891 1.289109 CGGTGGTACCTTGCGTCTTG 61.289 60.000 14.36 0.00 35.66 3.02
1450 1892 1.574702 GGTGGTACCTTGCGTCTTGC 61.575 60.000 14.36 0.00 38.74 4.01
1468 1910 0.531532 GCGTGGATGATGACTCTGGG 60.532 60.000 0.00 0.00 0.00 4.45
1470 1912 1.208052 CGTGGATGATGACTCTGGGTT 59.792 52.381 0.00 0.00 0.00 4.11
1475 1917 4.840680 TGGATGATGACTCTGGGTTATAGG 59.159 45.833 0.00 0.00 0.00 2.57
1502 1951 2.904434 AGTTGTTCGGTAGGAATGGACT 59.096 45.455 0.00 0.00 36.92 3.85
1503 1952 3.000727 GTTGTTCGGTAGGAATGGACTG 58.999 50.000 0.00 0.00 36.92 3.51
1507 1956 0.537188 CGGTAGGAATGGACTGTGCT 59.463 55.000 0.00 0.00 0.00 4.40
1509 1958 2.359900 GGTAGGAATGGACTGTGCTTG 58.640 52.381 0.00 0.00 0.00 4.01
1512 1961 0.610232 GGAATGGACTGTGCTTGGCT 60.610 55.000 0.00 0.00 0.00 4.75
1518 1967 4.027674 TGGACTGTGCTTGGCTAATTTA 57.972 40.909 0.00 0.00 0.00 1.40
1523 1972 3.491342 TGTGCTTGGCTAATTTACCACA 58.509 40.909 0.00 0.00 35.10 4.17
1524 1973 4.085733 TGTGCTTGGCTAATTTACCACAT 58.914 39.130 0.00 0.00 35.10 3.21
1532 1981 5.948758 TGGCTAATTTACCACATCATTGACA 59.051 36.000 0.00 0.00 0.00 3.58
1545 1994 5.663106 ACATCATTGACAGTATACCAGGAGT 59.337 40.000 0.00 0.00 0.00 3.85
1547 1996 7.344612 ACATCATTGACAGTATACCAGGAGTTA 59.655 37.037 0.00 0.00 0.00 2.24
1552 2001 4.691238 ACAGTATACCAGGAGTTACCCAA 58.309 43.478 0.00 0.00 40.05 4.12
1569 2018 4.576330 CCCAACTCTAAGGGTGAATTCT 57.424 45.455 7.05 0.00 40.34 2.40
1571 2020 6.062258 CCCAACTCTAAGGGTGAATTCTTA 57.938 41.667 7.05 0.00 40.34 2.10
1574 2023 7.615757 CCCAACTCTAAGGGTGAATTCTTAATT 59.384 37.037 7.05 0.01 40.34 1.40
1575 2024 9.681062 CCAACTCTAAGGGTGAATTCTTAATTA 57.319 33.333 7.05 1.15 0.00 1.40
1585 2034 9.468532 GGGTGAATTCTTAATTATTTGAGATGC 57.531 33.333 7.05 0.00 28.66 3.91
1602 2051 9.716531 TTTGAGATGCTTAGATATGATGGTAAG 57.283 33.333 0.00 0.00 0.00 2.34
1609 2058 6.814146 GCTTAGATATGATGGTAAGTAGGCAC 59.186 42.308 0.00 0.00 0.00 5.01
1613 2062 6.890268 AGATATGATGGTAAGTAGGCACGATA 59.110 38.462 0.00 0.00 0.00 2.92
1638 2097 3.515630 CTTCTGCTGTGATTTAGCTCGA 58.484 45.455 0.00 0.00 41.66 4.04
1657 2116 5.446473 GCTCGATTTCCTGTGTTCTAATGTG 60.446 44.000 0.00 0.00 0.00 3.21
1733 2701 3.355378 TGTTATCGGGGAGACGTTTCTA 58.645 45.455 6.02 0.00 34.94 2.10
2024 3069 3.568093 GTGCGCAACCATCTGTTTT 57.432 47.368 14.00 0.00 34.00 2.43
2061 3106 3.989817 GCTTGGTTTTATGTTGCTTCTGG 59.010 43.478 0.00 0.00 0.00 3.86
2079 3124 6.572314 GCTTCTGGTGGTATTGTGCTAAAAAT 60.572 38.462 0.00 0.00 0.00 1.82
2155 3200 8.087136 GCTGATATGAGTTCACTGATCATTCTA 58.913 37.037 0.00 0.00 35.39 2.10
2189 3234 5.182570 CAGAGCTTGGATTTGAATGAGTGAA 59.817 40.000 0.00 0.00 0.00 3.18
2190 3235 5.771666 AGAGCTTGGATTTGAATGAGTGAAA 59.228 36.000 0.00 0.00 0.00 2.69
2193 3238 5.279156 GCTTGGATTTGAATGAGTGAAACCT 60.279 40.000 0.00 0.00 37.80 3.50
2197 3242 5.241506 GGATTTGAATGAGTGAAACCTGTGA 59.758 40.000 0.00 0.00 37.80 3.58
2203 3248 4.422073 TGAGTGAAACCTGTGATTGAGT 57.578 40.909 0.00 0.00 37.80 3.41
2208 3253 7.338196 TGAGTGAAACCTGTGATTGAGTTTTTA 59.662 33.333 0.00 0.00 37.80 1.52
2213 3258 4.280929 ACCTGTGATTGAGTTTTTAAGGGC 59.719 41.667 0.00 0.00 0.00 5.19
2221 3266 5.017294 TGAGTTTTTAAGGGCTTGGTTTG 57.983 39.130 0.00 0.00 0.00 2.93
2222 3267 3.804036 AGTTTTTAAGGGCTTGGTTTGC 58.196 40.909 0.00 0.00 0.00 3.68
2224 3269 3.467374 TTTTAAGGGCTTGGTTTGCAG 57.533 42.857 0.00 0.00 0.00 4.41
2228 3273 1.203237 AGGGCTTGGTTTGCAGTTTT 58.797 45.000 0.00 0.00 0.00 2.43
2240 3285 7.556844 TGGTTTGCAGTTTTAATTACTTTGGA 58.443 30.769 0.00 0.00 0.00 3.53
2247 3292 9.255304 GCAGTTTTAATTACTTTGGATTCACAA 57.745 29.630 0.00 0.00 0.00 3.33
2253 3298 2.238521 ACTTTGGATTCACAATGGCGT 58.761 42.857 0.00 0.00 31.83 5.68
2256 3301 1.452110 TGGATTCACAATGGCGTGAG 58.548 50.000 0.00 0.00 46.14 3.51
2266 3311 1.233019 ATGGCGTGAGAGCAATATGC 58.767 50.000 0.00 0.00 45.46 3.14
2310 3355 5.134725 AGTTATTGCCTGGAAATCCTGAT 57.865 39.130 2.30 0.00 37.15 2.90
2312 3357 6.856757 AGTTATTGCCTGGAAATCCTGATAT 58.143 36.000 2.30 1.92 37.15 1.63
2318 3363 4.649692 CCTGGAAATCCTGATATGACTGG 58.350 47.826 7.82 0.00 37.15 4.00
2323 3368 6.214208 TGGAAATCCTGATATGACTGGATAGG 59.786 42.308 0.00 0.00 44.05 2.57
2332 3377 4.946478 ATGACTGGATAGGTGCTACTTC 57.054 45.455 0.00 0.00 0.00 3.01
2339 3385 3.133003 GGATAGGTGCTACTTCTGCAAGA 59.867 47.826 0.00 0.00 44.68 3.02
2361 3407 6.409704 AGATGTAGCTGTACAATTCACATGT 58.590 36.000 13.64 0.00 42.54 3.21
2363 3409 6.239908 TGTAGCTGTACAATTCACATGTTG 57.760 37.500 0.00 0.00 36.15 3.33
2365 3411 3.057315 AGCTGTACAATTCACATGTTGGC 60.057 43.478 0.00 0.00 32.27 4.52
2382 3428 6.214191 TGTTGGCTTAACATCAGTTTTTGA 57.786 33.333 3.48 0.00 44.07 2.69
2421 3468 5.446031 GCTGTTTAGCTCAATTCATTTGC 57.554 39.130 0.00 0.00 46.57 3.68
2680 3727 4.061131 TGAAGGTGATAGTCTCCAAGGA 57.939 45.455 1.46 0.00 32.69 3.36
2772 3819 5.226194 AGCAGAGAAAACAGAGTCTGATT 57.774 39.130 26.86 18.14 39.04 2.57
2812 3859 1.019805 GGCCCTGAGTTCACGTAAGC 61.020 60.000 0.00 0.00 45.62 3.09
2819 3866 3.845178 TGAGTTCACGTAAGCATACTGG 58.155 45.455 0.00 0.00 45.62 4.00
2830 3877 3.550437 AGCATACTGGTTCACATCCTC 57.450 47.619 0.00 0.00 0.00 3.71
2838 3885 2.003301 GGTTCACATCCTCGCTCTTTC 58.997 52.381 0.00 0.00 0.00 2.62
2885 3939 1.329906 CATTGCTGATCGCTTCACTCC 59.670 52.381 10.16 0.00 40.11 3.85
3052 4106 1.413118 CCAAGCTCAAGGGTTTGGTT 58.587 50.000 7.34 0.00 40.89 3.67
3062 4116 3.487120 AGGGTTTGGTTCAGTAGTGAC 57.513 47.619 0.00 0.00 30.10 3.67
3101 4155 0.878523 CCCGTGACTCGACAGCAAAA 60.879 55.000 0.00 0.00 42.86 2.44
3110 4164 4.134563 ACTCGACAGCAAAATTTGGTAGT 58.865 39.130 10.23 10.62 39.79 2.73
3122 4176 7.626452 GCAAAATTTGGTAGTGTAGCCTTCTAG 60.626 40.741 7.89 0.00 0.00 2.43
3148 4202 2.924290 CGTAGCAAGAGCACTAAGAACC 59.076 50.000 0.00 0.00 45.49 3.62
3149 4203 2.481289 AGCAAGAGCACTAAGAACCC 57.519 50.000 0.00 0.00 45.49 4.11
3150 4204 1.981495 AGCAAGAGCACTAAGAACCCT 59.019 47.619 0.00 0.00 45.49 4.34
3152 4206 2.079925 CAAGAGCACTAAGAACCCTGC 58.920 52.381 0.00 0.00 0.00 4.85
3187 4248 6.267928 AGTTTGAAGTGTATCTGTAGTCCTGT 59.732 38.462 0.00 0.00 0.00 4.00
3194 4255 5.299531 GTGTATCTGTAGTCCTGTATCAGCA 59.700 44.000 0.00 0.00 0.00 4.41
3195 4256 5.532779 TGTATCTGTAGTCCTGTATCAGCAG 59.467 44.000 0.00 0.00 36.31 4.24
3196 4257 2.690497 TCTGTAGTCCTGTATCAGCAGC 59.310 50.000 0.00 0.00 35.28 5.25
3197 4258 2.692557 CTGTAGTCCTGTATCAGCAGCT 59.307 50.000 0.00 0.00 35.28 4.24
3227 4288 4.555511 GCAGAGTGAGTTCCATTTGTGTTC 60.556 45.833 0.00 0.00 0.00 3.18
3228 4289 4.818546 CAGAGTGAGTTCCATTTGTGTTCT 59.181 41.667 0.00 0.00 0.00 3.01
3229 4290 5.297776 CAGAGTGAGTTCCATTTGTGTTCTT 59.702 40.000 0.00 0.00 0.00 2.52
3230 4291 5.529060 AGAGTGAGTTCCATTTGTGTTCTTC 59.471 40.000 0.00 0.00 0.00 2.87
3258 4319 1.379527 GCCGGTGAAAATCCTGTAGG 58.620 55.000 1.90 0.00 0.00 3.18
3271 4332 4.680278 TCCTGTAGGAAGGTGGTTACTA 57.320 45.455 0.00 0.00 42.18 1.82
3272 4333 4.607239 TCCTGTAGGAAGGTGGTTACTAG 58.393 47.826 0.00 0.00 42.18 2.57
3273 4334 4.045079 TCCTGTAGGAAGGTGGTTACTAGT 59.955 45.833 0.00 0.00 42.18 2.57
3277 4338 3.022406 AGGAAGGTGGTTACTAGTAGCG 58.978 50.000 10.23 0.00 0.00 4.26
3295 4356 3.070018 AGCGATGAAACAAGACTTCCTG 58.930 45.455 0.00 0.00 0.00 3.86
3320 4389 6.241207 GCTTAATACAAGCTGTGTTTCTGA 57.759 37.500 6.82 0.00 41.98 3.27
3321 4390 6.846350 GCTTAATACAAGCTGTGTTTCTGAT 58.154 36.000 6.82 0.00 41.98 2.90
3371 4440 7.621428 AATGACTGTTGTTAGATGATGGAAG 57.379 36.000 0.00 0.00 0.00 3.46
3423 4492 3.492482 GGATGGTGTTGTTGTGGGAAAAG 60.492 47.826 0.00 0.00 0.00 2.27
3436 4505 5.705400 TGTGGGAAAAGGAAAAGAAGAGAT 58.295 37.500 0.00 0.00 0.00 2.75
3437 4506 6.848069 TGTGGGAAAAGGAAAAGAAGAGATA 58.152 36.000 0.00 0.00 0.00 1.98
3438 4507 6.715264 TGTGGGAAAAGGAAAAGAAGAGATAC 59.285 38.462 0.00 0.00 0.00 2.24
3501 4570 2.722094 TGAATTCGGTGGAGGATTTGG 58.278 47.619 0.04 0.00 0.00 3.28
3511 4580 3.191371 GTGGAGGATTTGGTGTAGCAAAG 59.809 47.826 13.68 0.00 0.00 2.77
3512 4581 2.164422 GGAGGATTTGGTGTAGCAAAGC 59.836 50.000 14.32 14.32 0.00 3.51
3513 4582 2.819608 GAGGATTTGGTGTAGCAAAGCA 59.180 45.455 21.38 0.00 0.00 3.91
3514 4583 3.230134 AGGATTTGGTGTAGCAAAGCAA 58.770 40.909 21.38 0.00 33.46 3.91
3515 4584 3.640967 AGGATTTGGTGTAGCAAAGCAAA 59.359 39.130 21.38 5.31 45.80 3.68
3516 4585 4.100808 AGGATTTGGTGTAGCAAAGCAAAA 59.899 37.500 21.38 0.00 45.14 2.44
3517 4586 4.813697 GGATTTGGTGTAGCAAAGCAAAAA 59.186 37.500 21.38 0.00 45.14 1.94
3619 4820 6.407475 AAGTGAGATTGTGTTTGCAAAAAC 57.593 33.333 23.16 23.16 31.63 2.43
3623 4824 6.737750 GTGAGATTGTGTTTGCAAAAACTTTG 59.262 34.615 28.20 0.00 33.95 2.77
3625 4826 3.820777 TGTGTTTGCAAAAACTTTGGC 57.179 38.095 28.20 9.22 37.62 4.52
3626 4827 2.485814 TGTGTTTGCAAAAACTTTGGCC 59.514 40.909 28.20 8.56 36.25 5.36
3631 4833 0.179070 GCAAAAACTTTGGCCCGGAA 60.179 50.000 0.73 0.00 30.77 4.30
3644 4846 1.234615 CCCGGAAAAGAAGCGAGCAA 61.235 55.000 0.73 0.00 0.00 3.91
3647 4849 1.239347 GGAAAAGAAGCGAGCAAGGT 58.761 50.000 0.00 0.00 0.00 3.50
3673 4875 4.796495 GCGGGGGATGGTGTGGTC 62.796 72.222 0.00 0.00 0.00 4.02
3678 4880 1.286248 GGGGATGGTGTGGTCTAGTT 58.714 55.000 0.00 0.00 0.00 2.24
3695 4897 1.202580 AGTTCAGCGATCATAGCCACC 60.203 52.381 0.00 0.00 34.64 4.61
3696 4898 1.123077 TTCAGCGATCATAGCCACCT 58.877 50.000 0.00 0.00 34.64 4.00
3699 4901 0.760567 AGCGATCATAGCCACCTGGA 60.761 55.000 0.00 0.00 37.39 3.86
3702 4904 1.040646 GATCATAGCCACCTGGACGA 58.959 55.000 0.00 0.00 37.39 4.20
3705 4907 1.837439 TCATAGCCACCTGGACGAAAT 59.163 47.619 0.00 0.00 37.39 2.17
3707 4909 2.107950 TAGCCACCTGGACGAAATTG 57.892 50.000 0.00 0.00 37.39 2.32
3708 4910 0.400213 AGCCACCTGGACGAAATTGA 59.600 50.000 0.00 0.00 37.39 2.57
3740 4942 7.202016 TCAAGTGACAAAGGTAAGCTAATTG 57.798 36.000 0.00 0.00 0.00 2.32
3766 4972 9.130312 GTTCTATATTCTACGAACCAGCATAAG 57.870 37.037 0.00 0.00 31.89 1.73
3768 4974 8.512956 TCTATATTCTACGAACCAGCATAAGTC 58.487 37.037 0.00 0.00 0.00 3.01
3771 4977 2.674796 ACGAACCAGCATAAGTCTCC 57.325 50.000 0.00 0.00 0.00 3.71
3775 4981 0.537188 ACCAGCATAAGTCTCCGGTG 59.463 55.000 0.00 0.00 0.00 4.94
3776 4982 0.811616 CCAGCATAAGTCTCCGGTGC 60.812 60.000 0.00 1.25 36.11 5.01
3806 5012 0.472044 GGCCTCCTCCCATTTCTCTC 59.528 60.000 0.00 0.00 0.00 3.20
3812 5018 1.492599 CCTCCCATTTCTCTCCCCTTC 59.507 57.143 0.00 0.00 0.00 3.46
3916 5144 2.429058 CATGGGGCTCATCTCCGG 59.571 66.667 0.00 0.00 32.92 5.14
3957 5185 0.464373 CTCCCCCACCATCATCAACG 60.464 60.000 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.335740 CGTCTGTGTTTATGTGTCTAGAGGT 60.336 44.000 0.00 0.00 0.00 3.85
2 3 5.939457 TCGTCTGTGTTTATGTGTCTAGAG 58.061 41.667 0.00 0.00 0.00 2.43
3 4 5.619309 GCTCGTCTGTGTTTATGTGTCTAGA 60.619 44.000 0.00 0.00 0.00 2.43
4 5 4.559251 GCTCGTCTGTGTTTATGTGTCTAG 59.441 45.833 0.00 0.00 0.00 2.43
22 23 1.202371 TCAGTGTTTGTCTTCGCTCGT 60.202 47.619 0.00 0.00 0.00 4.18
26 27 1.295792 TGGTCAGTGTTTGTCTTCGC 58.704 50.000 0.00 0.00 0.00 4.70
27 28 4.527564 GATTTGGTCAGTGTTTGTCTTCG 58.472 43.478 0.00 0.00 0.00 3.79
40 41 1.134818 CCGATCTCGTGGATTTGGTCA 60.135 52.381 0.00 0.00 37.74 4.02
45 46 0.179073 CTGGCCGATCTCGTGGATTT 60.179 55.000 0.00 0.00 37.74 2.17
52 53 0.173481 TTTGTCTCTGGCCGATCTCG 59.827 55.000 0.00 0.00 39.44 4.04
73 74 3.064408 CCATCATCGAATGGTGTGTGAAG 59.936 47.826 7.82 0.00 39.77 3.02
84 85 5.097742 TGGTGTCTTTACCATCATCGAAT 57.902 39.130 0.00 0.00 45.46 3.34
95 96 2.140717 CCGTTCTGGTGGTGTCTTTAC 58.859 52.381 0.00 0.00 0.00 2.01
104 105 3.006728 TAGCCCCCGTTCTGGTGG 61.007 66.667 0.00 0.00 35.15 4.61
116 117 4.964241 ATCCTCCCCGCCTAGCCC 62.964 72.222 0.00 0.00 0.00 5.19
219 223 4.057428 AGAGGCGCGGCGGATATC 62.057 66.667 27.74 18.44 0.00 1.63
231 235 2.933056 GCAGTCTTAAGACCACAGAGGC 60.933 54.545 28.05 17.22 45.85 4.70
240 244 4.441356 CCTCATCTCCTGCAGTCTTAAGAC 60.441 50.000 25.24 25.24 45.08 3.01
250 254 1.781786 GGTCTACCTCATCTCCTGCA 58.218 55.000 0.00 0.00 0.00 4.41
277 281 3.733344 TATTGCCTCCTGTCGCCGC 62.733 63.158 0.00 0.00 0.00 6.53
281 285 2.280628 GGTTTCTATTGCCTCCTGTCG 58.719 52.381 0.00 0.00 0.00 4.35
304 308 1.446272 GCACCACCGAGCTAGTGTC 60.446 63.158 13.70 1.71 33.20 3.67
314 318 4.710695 TCGTACGCTGCACCACCG 62.711 66.667 11.24 0.00 0.00 4.94
340 344 0.100503 AAAAAGACACCACGCACAGC 59.899 50.000 0.00 0.00 0.00 4.40
422 426 2.343101 TGTGAAATTTCGGAGCCTACG 58.657 47.619 13.34 0.00 0.00 3.51
503 508 1.580845 GAGTGAGCACGCAAAGGCAT 61.581 55.000 0.00 0.00 41.24 4.40
525 531 2.313317 CTGGATAAGTACCGGCCTACA 58.687 52.381 0.00 0.00 0.00 2.74
619 627 9.208022 GATGATGATTTGTATAATTCGAGGACA 57.792 33.333 0.00 0.00 0.00 4.02
670 687 5.191426 ACTGATTCTGGACATGGATGAAAG 58.809 41.667 0.00 0.00 0.00 2.62
753 772 2.638556 AATCGTCACTCAAGTCCTCG 57.361 50.000 0.00 0.00 0.00 4.63
764 783 6.402226 GGTCCTCAAAGTATGAAAATCGTCAC 60.402 42.308 0.00 0.00 37.67 3.67
806 825 5.294552 GTGCACAATAGGTCCTTGAACTATC 59.705 44.000 13.17 0.00 41.14 2.08
914 943 2.877168 GGATTAAGACGAGAGAGCGGTA 59.123 50.000 0.00 0.00 35.12 4.02
949 1334 0.763223 GGAGGGGATAAGGCGAGGAA 60.763 60.000 0.00 0.00 0.00 3.36
1014 1403 3.319198 GTGGTGGAGGAGGCGGAA 61.319 66.667 0.00 0.00 0.00 4.30
1240 1653 3.607661 GGCCTCCCGGATCTCGAC 61.608 72.222 0.73 0.00 42.43 4.20
1335 1756 0.387112 AAATCGACCGTACAACGCGA 60.387 50.000 15.93 5.02 40.91 5.87
1358 1779 2.292794 GATTCCTCTACCGCGCACCA 62.293 60.000 8.75 0.00 0.00 4.17
1359 1780 1.591863 GATTCCTCTACCGCGCACC 60.592 63.158 8.75 0.00 0.00 5.01
1360 1781 1.591863 GGATTCCTCTACCGCGCAC 60.592 63.158 8.75 0.00 0.00 5.34
1400 1821 2.221055 CGCAAAAGTTCAGTAGAAGCGT 59.779 45.455 0.00 0.00 38.11 5.07
1401 1822 2.827555 CGCAAAAGTTCAGTAGAAGCG 58.172 47.619 0.00 0.00 37.18 4.68
1406 1848 0.165944 CCCGCGCAAAAGTTCAGTAG 59.834 55.000 8.75 0.00 0.00 2.57
1412 1854 1.655885 GTAACCCCGCGCAAAAGTT 59.344 52.632 8.75 7.77 0.00 2.66
1414 1856 2.174835 CGTAACCCCGCGCAAAAG 59.825 61.111 8.75 0.00 0.00 2.27
1420 1862 3.757828 TACCACCGTAACCCCGCG 61.758 66.667 0.00 0.00 0.00 6.46
1421 1863 2.125552 GTACCACCGTAACCCCGC 60.126 66.667 0.00 0.00 0.00 6.13
1425 1867 1.015607 CGCAAGGTACCACCGTAACC 61.016 60.000 15.94 0.00 44.90 2.85
1447 1889 1.405933 CCAGAGTCATCATCCACGCAA 60.406 52.381 0.00 0.00 0.00 4.85
1448 1890 0.176449 CCAGAGTCATCATCCACGCA 59.824 55.000 0.00 0.00 0.00 5.24
1449 1891 0.531532 CCCAGAGTCATCATCCACGC 60.532 60.000 0.00 0.00 0.00 5.34
1450 1892 0.826715 ACCCAGAGTCATCATCCACG 59.173 55.000 0.00 0.00 0.00 4.94
1451 1893 4.696479 ATAACCCAGAGTCATCATCCAC 57.304 45.455 0.00 0.00 0.00 4.02
1452 1894 4.840680 CCTATAACCCAGAGTCATCATCCA 59.159 45.833 0.00 0.00 0.00 3.41
1468 1910 7.276438 CCTACCGAACAACTAAACACCTATAAC 59.724 40.741 0.00 0.00 0.00 1.89
1470 1912 6.663093 TCCTACCGAACAACTAAACACCTATA 59.337 38.462 0.00 0.00 0.00 1.31
1475 1917 5.106830 CCATTCCTACCGAACAACTAAACAC 60.107 44.000 0.00 0.00 31.79 3.32
1502 1951 3.491342 TGTGGTAAATTAGCCAAGCACA 58.509 40.909 2.39 2.39 45.16 4.57
1503 1952 4.157656 TGATGTGGTAAATTAGCCAAGCAC 59.842 41.667 0.00 0.00 39.99 4.40
1507 1956 6.435591 TGTCAATGATGTGGTAAATTAGCCAA 59.564 34.615 0.00 0.00 36.41 4.52
1509 1958 6.095440 ACTGTCAATGATGTGGTAAATTAGCC 59.905 38.462 0.00 0.00 0.00 3.93
1518 1967 5.396772 CCTGGTATACTGTCAATGATGTGGT 60.397 44.000 2.25 0.00 0.00 4.16
1523 1972 6.814954 AACTCCTGGTATACTGTCAATGAT 57.185 37.500 2.25 0.00 0.00 2.45
1524 1973 6.097839 GGTAACTCCTGGTATACTGTCAATGA 59.902 42.308 2.25 0.00 0.00 2.57
1532 1981 4.956582 AGTTGGGTAACTCCTGGTATACT 58.043 43.478 2.25 0.00 43.53 2.12
1578 2027 8.427902 ACTTACCATCATATCTAAGCATCTCA 57.572 34.615 0.00 0.00 0.00 3.27
1580 2029 8.976353 CCTACTTACCATCATATCTAAGCATCT 58.024 37.037 0.00 0.00 0.00 2.90
1582 2031 7.180946 TGCCTACTTACCATCATATCTAAGCAT 59.819 37.037 0.00 0.00 0.00 3.79
1584 2033 6.814146 GTGCCTACTTACCATCATATCTAAGC 59.186 42.308 0.00 0.00 0.00 3.09
1585 2034 7.030165 CGTGCCTACTTACCATCATATCTAAG 58.970 42.308 0.00 0.00 0.00 2.18
1586 2035 6.717997 TCGTGCCTACTTACCATCATATCTAA 59.282 38.462 0.00 0.00 0.00 2.10
1587 2036 6.243148 TCGTGCCTACTTACCATCATATCTA 58.757 40.000 0.00 0.00 0.00 1.98
1588 2037 5.077564 TCGTGCCTACTTACCATCATATCT 58.922 41.667 0.00 0.00 0.00 1.98
1589 2038 5.386958 TCGTGCCTACTTACCATCATATC 57.613 43.478 0.00 0.00 0.00 1.63
1590 2039 6.663953 ACTATCGTGCCTACTTACCATCATAT 59.336 38.462 0.00 0.00 0.00 1.78
1591 2040 6.008331 ACTATCGTGCCTACTTACCATCATA 58.992 40.000 0.00 0.00 0.00 2.15
1592 2041 4.833380 ACTATCGTGCCTACTTACCATCAT 59.167 41.667 0.00 0.00 0.00 2.45
1593 2042 4.037565 CACTATCGTGCCTACTTACCATCA 59.962 45.833 0.00 0.00 33.82 3.07
1594 2043 4.547532 CACTATCGTGCCTACTTACCATC 58.452 47.826 0.00 0.00 33.82 3.51
1595 2044 4.585955 CACTATCGTGCCTACTTACCAT 57.414 45.455 0.00 0.00 33.82 3.55
1609 2058 2.284263 TCACAGCAGAAGCACTATCG 57.716 50.000 0.00 0.00 45.49 2.92
1613 2062 2.746362 GCTAAATCACAGCAGAAGCACT 59.254 45.455 0.00 0.00 45.49 4.40
1622 2071 3.873952 AGGAAATCGAGCTAAATCACAGC 59.126 43.478 0.00 0.00 39.41 4.40
1627 2086 5.582665 AGAACACAGGAAATCGAGCTAAATC 59.417 40.000 0.00 0.00 0.00 2.17
1638 2097 8.157476 AGTAGAACACATTAGAACACAGGAAAT 58.843 33.333 0.00 0.00 0.00 2.17
1657 2116 6.038382 TCAGACAGACCGATATTCAGTAGAAC 59.962 42.308 0.00 0.00 36.39 3.01
2061 3106 8.243426 TCAGATTCATTTTTAGCACAATACCAC 58.757 33.333 0.00 0.00 0.00 4.16
2079 3124 4.340097 CAGCAGCCCAAATATTCAGATTCA 59.660 41.667 0.00 0.00 0.00 2.57
2155 3200 8.125978 TCAAATCCAAGCTCTGTAAAATCATT 57.874 30.769 0.00 0.00 0.00 2.57
2171 3216 5.598005 ACAGGTTTCACTCATTCAAATCCAA 59.402 36.000 0.00 0.00 0.00 3.53
2189 3234 5.221441 GCCCTTAAAAACTCAATCACAGGTT 60.221 40.000 0.00 0.00 0.00 3.50
2190 3235 4.280929 GCCCTTAAAAACTCAATCACAGGT 59.719 41.667 0.00 0.00 0.00 4.00
2193 3238 5.221422 CCAAGCCCTTAAAAACTCAATCACA 60.221 40.000 0.00 0.00 0.00 3.58
2197 3242 5.887214 AACCAAGCCCTTAAAAACTCAAT 57.113 34.783 0.00 0.00 0.00 2.57
2203 3248 3.198853 ACTGCAAACCAAGCCCTTAAAAA 59.801 39.130 0.00 0.00 0.00 1.94
2208 3253 1.203237 AAACTGCAAACCAAGCCCTT 58.797 45.000 0.00 0.00 0.00 3.95
2213 3258 8.334632 CCAAAGTAATTAAAACTGCAAACCAAG 58.665 33.333 0.00 0.00 0.00 3.61
2221 3266 8.810652 TGTGAATCCAAAGTAATTAAAACTGC 57.189 30.769 0.00 0.00 0.00 4.40
2228 3273 6.151985 ACGCCATTGTGAATCCAAAGTAATTA 59.848 34.615 0.00 0.00 0.00 1.40
2247 3292 1.233019 GCATATTGCTCTCACGCCAT 58.767 50.000 0.00 0.00 40.96 4.40
2253 3298 5.280654 TGTCAGTATGCATATTGCTCTCA 57.719 39.130 21.06 14.59 45.31 3.27
2280 3325 9.077885 GGATTTCCAGGCAATAACTAATGAATA 57.922 33.333 0.00 0.00 35.64 1.75
2292 3337 5.075493 GTCATATCAGGATTTCCAGGCAAT 58.925 41.667 0.00 0.00 38.89 3.56
2300 3345 7.102346 CACCTATCCAGTCATATCAGGATTTC 58.898 42.308 0.00 0.00 41.03 2.17
2310 3355 5.536538 CAGAAGTAGCACCTATCCAGTCATA 59.463 44.000 0.00 0.00 0.00 2.15
2312 3357 3.701542 CAGAAGTAGCACCTATCCAGTCA 59.298 47.826 0.00 0.00 0.00 3.41
2318 3363 4.392921 TCTTGCAGAAGTAGCACCTATC 57.607 45.455 0.00 0.00 42.54 2.08
2332 3377 5.352293 TGAATTGTACAGCTACATCTTGCAG 59.648 40.000 0.00 0.00 32.70 4.41
2339 3385 6.127925 CCAACATGTGAATTGTACAGCTACAT 60.128 38.462 0.00 3.76 32.70 2.29
2345 3391 4.771590 AGCCAACATGTGAATTGTACAG 57.228 40.909 0.00 0.00 0.00 2.74
2346 3392 6.039829 TGTTAAGCCAACATGTGAATTGTACA 59.960 34.615 0.00 0.00 42.29 2.90
2347 3393 6.442952 TGTTAAGCCAACATGTGAATTGTAC 58.557 36.000 0.00 0.00 42.29 2.90
2361 3407 7.288810 AGATCAAAAACTGATGTTAAGCCAA 57.711 32.000 0.00 0.00 45.23 4.52
2363 3409 6.089954 GCAAGATCAAAAACTGATGTTAAGCC 59.910 38.462 0.00 0.00 44.14 4.35
2365 3411 8.578308 TTGCAAGATCAAAAACTGATGTTAAG 57.422 30.769 0.00 0.00 44.14 1.85
2378 3424 9.656040 AACAGCATAAATATTTGCAAGATCAAA 57.344 25.926 11.05 0.00 41.35 2.69
2382 3428 9.252962 GCTAAACAGCATAAATATTTGCAAGAT 57.747 29.630 11.05 0.00 41.35 2.40
2398 3445 4.925054 GCAAATGAATTGAGCTAAACAGCA 59.075 37.500 0.00 0.00 41.85 4.41
2421 3468 5.316987 AGTAGGTTCCTGTCAAAAGAATGG 58.683 41.667 1.12 0.00 0.00 3.16
2680 3727 1.961180 CTCGAGGTTCGGGCCAGATT 61.961 60.000 6.36 0.00 40.88 2.40
2772 3819 4.307032 CCTCAAAGGGGAATTTCTCTGA 57.693 45.455 0.00 0.00 0.00 3.27
2812 3859 2.159043 AGCGAGGATGTGAACCAGTATG 60.159 50.000 0.00 0.00 0.00 2.39
2819 3866 2.926838 GAGAAAGAGCGAGGATGTGAAC 59.073 50.000 0.00 0.00 0.00 3.18
2830 3877 1.699656 CCATGGTGCGAGAAAGAGCG 61.700 60.000 2.57 0.00 35.87 5.03
2838 3885 1.534163 CATAAGATGCCATGGTGCGAG 59.466 52.381 14.67 0.00 0.00 5.03
2892 3946 2.433838 GAAGCTCGCTGCAGCAGA 60.434 61.111 36.03 29.56 45.94 4.26
2895 3949 3.194308 GAGGAAGCTCGCTGCAGC 61.194 66.667 29.12 29.12 45.94 5.25
2998 4052 1.729586 ACTCCTTGGTCTGCTTGGTA 58.270 50.000 0.00 0.00 0.00 3.25
3052 4106 4.546570 CATCTGTTCAACGTCACTACTGA 58.453 43.478 0.00 0.00 0.00 3.41
3062 4116 0.109597 GCAAGGCCATCTGTTCAACG 60.110 55.000 5.01 0.00 0.00 4.10
3083 4137 1.148310 ATTTTGCTGTCGAGTCACGG 58.852 50.000 0.00 0.00 42.82 4.94
3101 4155 4.469945 TGCTAGAAGGCTACACTACCAAAT 59.530 41.667 0.00 0.00 0.00 2.32
3110 4164 1.138883 CGCGTGCTAGAAGGCTACA 59.861 57.895 13.42 0.00 0.00 2.74
3122 4176 3.112075 TGCTCTTGCTACGCGTGC 61.112 61.111 24.59 22.69 40.48 5.34
3140 4194 3.222603 ACTGGTTTTGCAGGGTTCTTAG 58.777 45.455 0.00 0.00 0.00 2.18
3148 4202 4.097892 ACTTCAAACTACTGGTTTTGCAGG 59.902 41.667 0.00 0.00 44.77 4.85
3149 4203 5.036737 CACTTCAAACTACTGGTTTTGCAG 58.963 41.667 0.00 0.00 44.77 4.41
3150 4204 4.461081 ACACTTCAAACTACTGGTTTTGCA 59.539 37.500 0.00 0.00 44.77 4.08
3152 4206 8.070171 CAGATACACTTCAAACTACTGGTTTTG 58.930 37.037 0.00 0.00 44.77 2.44
3176 4237 2.692557 AGCTGCTGATACAGGACTACAG 59.307 50.000 0.00 0.00 38.16 2.74
3194 4255 1.064017 ACTCACTCTGCCTAGCTAGCT 60.064 52.381 23.12 23.12 0.00 3.32
3195 4256 1.398692 ACTCACTCTGCCTAGCTAGC 58.601 55.000 15.74 6.62 0.00 3.42
3196 4257 2.360801 GGAACTCACTCTGCCTAGCTAG 59.639 54.545 14.20 14.20 0.00 3.42
3197 4258 2.291605 TGGAACTCACTCTGCCTAGCTA 60.292 50.000 0.00 0.00 0.00 3.32
3227 4288 3.710722 ACCGGCCAGCTCCAGAAG 61.711 66.667 0.00 0.00 0.00 2.85
3228 4289 4.020617 CACCGGCCAGCTCCAGAA 62.021 66.667 0.00 0.00 0.00 3.02
3230 4291 3.551496 TTTCACCGGCCAGCTCCAG 62.551 63.158 0.00 0.00 0.00 3.86
3258 4319 4.337555 TCATCGCTACTAGTAACCACCTTC 59.662 45.833 3.76 0.00 0.00 3.46
3271 4332 4.021016 AGGAAGTCTTGTTTCATCGCTACT 60.021 41.667 0.00 0.00 0.00 2.57
3272 4333 4.092091 CAGGAAGTCTTGTTTCATCGCTAC 59.908 45.833 0.00 0.00 0.00 3.58
3273 4334 4.021456 TCAGGAAGTCTTGTTTCATCGCTA 60.021 41.667 0.00 0.00 0.00 4.26
3277 4338 4.322567 AGCTCAGGAAGTCTTGTTTCATC 58.677 43.478 0.00 0.00 0.00 2.92
3371 4440 0.035915 GACCAGGGGAGCAAACTCTC 60.036 60.000 0.00 0.00 43.33 3.20
3423 4492 9.092876 CACACAATCTAGTATCTCTTCTTTTCC 57.907 37.037 0.00 0.00 0.00 3.13
3436 4505 5.820423 AGCAACACAAACACACAATCTAGTA 59.180 36.000 0.00 0.00 0.00 1.82
3437 4506 4.640201 AGCAACACAAACACACAATCTAGT 59.360 37.500 0.00 0.00 0.00 2.57
3438 4507 5.173774 AGCAACACAAACACACAATCTAG 57.826 39.130 0.00 0.00 0.00 2.43
3494 4563 3.658757 TTGCTTTGCTACACCAAATCC 57.341 42.857 0.00 0.00 34.50 3.01
3554 4754 8.777865 TTCATTTCGATCTCACTATTCAAAGT 57.222 30.769 0.00 0.00 0.00 2.66
3598 4799 6.407475 AAGTTTTTGCAAACACAATCTCAC 57.593 33.333 25.75 7.19 44.32 3.51
3599 4800 6.128336 CCAAAGTTTTTGCAAACACAATCTCA 60.128 34.615 25.75 1.05 44.32 3.27
3606 4807 2.159448 GGGCCAAAGTTTTTGCAAACAC 60.159 45.455 18.60 18.60 44.32 3.32
3619 4820 0.038251 GCTTCTTTTCCGGGCCAAAG 60.038 55.000 4.39 5.96 0.00 2.77
3623 4824 2.359478 TCGCTTCTTTTCCGGGCC 60.359 61.111 0.00 0.00 0.00 5.80
3625 4826 1.234615 TTGCTCGCTTCTTTTCCGGG 61.235 55.000 0.00 0.00 0.00 5.73
3626 4827 0.166814 CTTGCTCGCTTCTTTTCCGG 59.833 55.000 0.00 0.00 0.00 5.14
3631 4833 2.079925 GATCACCTTGCTCGCTTCTTT 58.920 47.619 0.00 0.00 0.00 2.52
3661 4863 2.678190 GCTGAACTAGACCACACCATCC 60.678 54.545 0.00 0.00 0.00 3.51
3662 4864 2.622436 GCTGAACTAGACCACACCATC 58.378 52.381 0.00 0.00 0.00 3.51
3667 4869 2.167662 TGATCGCTGAACTAGACCACA 58.832 47.619 0.00 0.00 0.00 4.17
3669 4871 3.004839 GCTATGATCGCTGAACTAGACCA 59.995 47.826 0.00 0.00 0.00 4.02
3672 4874 3.004839 GTGGCTATGATCGCTGAACTAGA 59.995 47.826 0.00 0.00 0.00 2.43
3673 4875 3.312828 GTGGCTATGATCGCTGAACTAG 58.687 50.000 0.00 0.00 0.00 2.57
3678 4880 0.390492 CAGGTGGCTATGATCGCTGA 59.610 55.000 0.00 0.00 0.00 4.26
3695 4897 6.000891 TGAATCAAGTTCAATTTCGTCCAG 57.999 37.500 0.00 0.00 43.64 3.86
3740 4942 9.130312 CTTATGCTGGTTCGTAGAATATAGAAC 57.870 37.037 0.00 0.00 45.90 3.01
3795 5001 0.553333 GGGAAGGGGAGAGAAATGGG 59.447 60.000 0.00 0.00 0.00 4.00
3796 5002 1.492599 GAGGGAAGGGGAGAGAAATGG 59.507 57.143 0.00 0.00 0.00 3.16
3806 5012 2.849646 GGGGATCGAGGGAAGGGG 60.850 72.222 0.00 0.00 0.00 4.79
3812 5018 3.412350 AAGGGGAGGGGATCGAGGG 62.412 68.421 0.00 0.00 0.00 4.30
3942 5170 2.472059 CGGCGTTGATGATGGTGGG 61.472 63.158 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.