Multiple sequence alignment - TraesCS3A01G332300

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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 TraesCS3A01G332300 chr3A 100.000 4172 0 0 1 4172 576694396 576690225 0.000000e+00 7705
1 TraesCS3A01G332300 chr3D 93.951 1306 57 11 2272 3566 438444216 438442922 0.000000e+00 1954
2 TraesCS3A01G332300 chr3D 89.524 1451 89 24 824 2237 438445638 438444214 0.000000e+00 1779
3 TraesCS3A01G332300 chr3D 96.275 510 18 1 3662 4171 438442922 438442414 0.000000e+00 835
4 TraesCS3A01G332300 chr3D 91.176 204 17 1 132 334 438450591 438450388 4.110000e-70 276
5 TraesCS3A01G332300 chr3D 86.885 244 22 8 599 841 438445889 438445655 8.890000e-67 265
6 TraesCS3A01G332300 chr3D 94.444 144 8 0 464 607 438446063 438445920 5.430000e-54 222
7 TraesCS3A01G332300 chr3D 95.489 133 4 1 336 468 438450345 438450215 1.180000e-50 211
8 TraesCS3A01G332300 chr3B 88.291 1469 121 22 2109 3569 573983855 573985280 0.000000e+00 1712
9 TraesCS3A01G332300 chr3B 88.601 1272 92 27 844 2071 573982491 573983753 0.000000e+00 1496
10 TraesCS3A01G332300 chr3B 93.535 495 32 0 3674 4168 573985281 573985775 0.000000e+00 737
11 TraesCS3A01G332300 chr3B 91.078 269 22 2 337 605 573980501 573980767 3.070000e-96 363
12 TraesCS3A01G332300 chr3B 91.667 252 19 2 84 334 573980207 573980457 8.580000e-92 348
13 TraesCS3A01G332300 chr3B 88.021 192 18 4 601 792 573981345 573981531 5.430000e-54 222
14 TraesCS3A01G332300 chr7A 87.671 292 22 7 1581 1859 338086222 338086512 1.120000e-85 327
15 TraesCS3A01G332300 chr7A 95.679 162 6 1 3673 3833 338086696 338086857 4.140000e-65 259
16 TraesCS3A01G332300 chr7A 94.521 73 4 0 3248 3320 338086609 338086681 3.410000e-21 113
17 TraesCS3A01G332300 chr7A 85.455 110 10 4 491 596 689551122 689551229 4.410000e-20 110
18 TraesCS3A01G332300 chr2A 94.595 185 9 1 3650 3833 103914335 103914151 6.830000e-73 285
19 TraesCS3A01G332300 chr2A 95.161 124 5 1 3426 3548 103914470 103914347 1.180000e-45 195
20 TraesCS3A01G332300 chr1A 93.269 104 3 1 3564 3667 430006486 430006387 2.600000e-32 150
21 TraesCS3A01G332300 chr1A 93.137 102 3 2 3566 3667 464800319 464800416 3.360000e-31 147
22 TraesCS3A01G332300 chr6D 92.381 105 4 1 3567 3671 46709508 46709608 3.360000e-31 147
23 TraesCS3A01G332300 chr5D 90.991 111 6 2 3564 3674 180472059 180472165 3.360000e-31 147
24 TraesCS3A01G332300 chr4D 93.137 102 3 2 3567 3668 375381916 375382013 3.360000e-31 147
25 TraesCS3A01G332300 chr6B 91.589 107 5 2 3562 3668 315650309 315650207 1.210000e-30 145
26 TraesCS3A01G332300 chr6A 92.308 104 4 1 3564 3667 37459179 37459080 1.210000e-30 145
27 TraesCS3A01G332300 chr4B 89.474 114 8 2 3560 3673 262872611 262872502 1.560000e-29 141
28 TraesCS3A01G332300 chr1D 87.805 123 8 5 3561 3683 116786107 116786222 2.020000e-28 137


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 TraesCS3A01G332300 chr3A 576690225 576694396 4171 True 7705 7705 100.000000 1 4172 1 chr3A.!!$R1 4171
1 TraesCS3A01G332300 chr3D 438442414 438446063 3649 True 1011 1954 92.215800 464 4171 5 chr3D.!!$R1 3707
2 TraesCS3A01G332300 chr3B 573980207 573985775 5568 False 813 1712 90.198833 84 4168 6 chr3B.!!$F1 4084
3 TraesCS3A01G332300 chr7A 338086222 338086857 635 False 233 327 92.623667 1581 3833 3 chr7A.!!$F2 2252

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
52 53 0.040499 AGGGTTGGTGGTGTTGTTGT 59.960 50.0 0.0 0.0 0.00 3.32 F
1423 2997 0.393448 TGCTGTTGCACAATGCCATT 59.607 45.0 0.0 0.0 45.31 3.16 F
2276 3973 1.600023 TTTGGGGAAGCAACTGTACG 58.400 50.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 3629 0.534203 ACGAAATTGGCGGTCACACT 60.534 50.0 6.03 0.0 0.0 3.55 R
3108 4820 0.603569 TCTTCCTTCCTCTGTCACGC 59.396 55.0 0.00 0.0 0.0 5.34 R
4105 5819 0.542938 TGGAGGAGATATGGGGCGAG 60.543 60.0 0.00 0.0 0.0 5.03 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
28 29 8.822805 ACTGGATGGAATTAAGAAAGTAGTACA 58.177 33.333 2.52 0.00 0.00 2.90
29 30 9.667107 CTGGATGGAATTAAGAAAGTAGTACAA 57.333 33.333 2.52 0.00 0.00 2.41
39 40 7.745620 AAGAAAGTAGTACAAATCAGGGTTG 57.254 36.000 2.52 0.00 0.00 3.77
40 41 6.238648 AGAAAGTAGTACAAATCAGGGTTGG 58.761 40.000 2.52 0.00 0.00 3.77
41 42 5.578157 AAGTAGTACAAATCAGGGTTGGT 57.422 39.130 2.52 0.00 0.00 3.67
42 43 4.906618 AGTAGTACAAATCAGGGTTGGTG 58.093 43.478 2.52 0.00 0.00 4.17
43 44 3.154827 AGTACAAATCAGGGTTGGTGG 57.845 47.619 0.00 0.00 0.00 4.61
44 45 2.445525 AGTACAAATCAGGGTTGGTGGT 59.554 45.455 0.00 0.00 0.00 4.16
45 46 1.703411 ACAAATCAGGGTTGGTGGTG 58.297 50.000 0.00 0.00 0.00 4.17
46 47 1.063266 ACAAATCAGGGTTGGTGGTGT 60.063 47.619 0.00 0.00 0.00 4.16
47 48 2.038659 CAAATCAGGGTTGGTGGTGTT 58.961 47.619 0.00 0.00 0.00 3.32
48 49 1.703411 AATCAGGGTTGGTGGTGTTG 58.297 50.000 0.00 0.00 0.00 3.33
49 50 0.555769 ATCAGGGTTGGTGGTGTTGT 59.444 50.000 0.00 0.00 0.00 3.32
50 51 0.333312 TCAGGGTTGGTGGTGTTGTT 59.667 50.000 0.00 0.00 0.00 2.83
51 52 0.459489 CAGGGTTGGTGGTGTTGTTG 59.541 55.000 0.00 0.00 0.00 3.33
52 53 0.040499 AGGGTTGGTGGTGTTGTTGT 59.960 50.000 0.00 0.00 0.00 3.32
53 54 0.899019 GGGTTGGTGGTGTTGTTGTT 59.101 50.000 0.00 0.00 0.00 2.83
54 55 1.404851 GGGTTGGTGGTGTTGTTGTTG 60.405 52.381 0.00 0.00 0.00 3.33
55 56 1.273886 GGTTGGTGGTGTTGTTGTTGT 59.726 47.619 0.00 0.00 0.00 3.32
56 57 2.289133 GGTTGGTGGTGTTGTTGTTGTT 60.289 45.455 0.00 0.00 0.00 2.83
57 58 2.732412 TGGTGGTGTTGTTGTTGTTG 57.268 45.000 0.00 0.00 0.00 3.33
58 59 1.964223 TGGTGGTGTTGTTGTTGTTGT 59.036 42.857 0.00 0.00 0.00 3.32
59 60 2.365617 TGGTGGTGTTGTTGTTGTTGTT 59.634 40.909 0.00 0.00 0.00 2.83
60 61 3.572682 TGGTGGTGTTGTTGTTGTTGTTA 59.427 39.130 0.00 0.00 0.00 2.41
61 62 4.220821 TGGTGGTGTTGTTGTTGTTGTTAT 59.779 37.500 0.00 0.00 0.00 1.89
62 63 5.172205 GGTGGTGTTGTTGTTGTTGTTATT 58.828 37.500 0.00 0.00 0.00 1.40
63 64 5.062809 GGTGGTGTTGTTGTTGTTGTTATTG 59.937 40.000 0.00 0.00 0.00 1.90
64 65 5.635700 GTGGTGTTGTTGTTGTTGTTATTGT 59.364 36.000 0.00 0.00 0.00 2.71
65 66 6.146347 GTGGTGTTGTTGTTGTTGTTATTGTT 59.854 34.615 0.00 0.00 0.00 2.83
66 67 6.146184 TGGTGTTGTTGTTGTTGTTATTGTTG 59.854 34.615 0.00 0.00 0.00 3.33
67 68 6.146347 GGTGTTGTTGTTGTTGTTATTGTTGT 59.854 34.615 0.00 0.00 0.00 3.32
68 69 7.307455 GGTGTTGTTGTTGTTGTTATTGTTGTT 60.307 33.333 0.00 0.00 0.00 2.83
69 70 7.528850 GTGTTGTTGTTGTTGTTATTGTTGTTG 59.471 33.333 0.00 0.00 0.00 3.33
70 71 7.224753 TGTTGTTGTTGTTGTTATTGTTGTTGT 59.775 29.630 0.00 0.00 0.00 3.32
71 72 7.715265 TGTTGTTGTTGTTATTGTTGTTGTT 57.285 28.000 0.00 0.00 0.00 2.83
72 73 7.567571 TGTTGTTGTTGTTATTGTTGTTGTTG 58.432 30.769 0.00 0.00 0.00 3.33
73 74 7.224753 TGTTGTTGTTGTTATTGTTGTTGTTGT 59.775 29.630 0.00 0.00 0.00 3.32
74 75 7.715265 TGTTGTTGTTATTGTTGTTGTTGTT 57.285 28.000 0.00 0.00 0.00 2.83
75 76 7.567571 TGTTGTTGTTATTGTTGTTGTTGTTG 58.432 30.769 0.00 0.00 0.00 3.33
76 77 7.224753 TGTTGTTGTTATTGTTGTTGTTGTTGT 59.775 29.630 0.00 0.00 0.00 3.32
77 78 7.715265 TGTTGTTATTGTTGTTGTTGTTGTT 57.285 28.000 0.00 0.00 0.00 2.83
78 79 7.567571 TGTTGTTATTGTTGTTGTTGTTGTTG 58.432 30.769 0.00 0.00 0.00 3.33
79 80 7.224753 TGTTGTTATTGTTGTTGTTGTTGTTGT 59.775 29.630 0.00 0.00 0.00 3.32
80 81 7.715265 TGTTATTGTTGTTGTTGTTGTTGTT 57.285 28.000 0.00 0.00 0.00 2.83
81 82 7.567571 TGTTATTGTTGTTGTTGTTGTTGTTG 58.432 30.769 0.00 0.00 0.00 3.33
82 83 7.224753 TGTTATTGTTGTTGTTGTTGTTGTTGT 59.775 29.630 0.00 0.00 0.00 3.32
87 88 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
90 91 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
93 94 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
96 97 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
99 100 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
103 104 7.064134 TGTTGTTGTTGTTGTTGTTGTTGTTAA 59.936 29.630 0.00 0.00 0.00 2.01
146 147 7.037438 AGATGCAACCAAAATATTGATGTGAC 58.963 34.615 0.00 0.00 38.94 3.67
147 148 6.094193 TGCAACCAAAATATTGATGTGACA 57.906 33.333 0.00 0.00 38.94 3.58
163 164 2.100584 GTGACATTTGTTGTTGCCTCCA 59.899 45.455 0.00 0.00 39.18 3.86
175 176 5.452078 TGTTGCCTCCAATTCAACTTTAG 57.548 39.130 8.04 0.00 40.34 1.85
235 236 0.680618 TTTGCAGGCCAACAATGAGG 59.319 50.000 5.01 0.00 31.97 3.86
450 493 8.238631 TGAACCTTTGTTTTACTTGTGTTAGAC 58.761 33.333 0.00 0.00 33.97 2.59
470 513 4.156556 AGACGTGCATTTGTGCTTTATGAT 59.843 37.500 0.00 0.00 35.49 2.45
482 525 5.149273 GTGCTTTATGATATGAACATGGCG 58.851 41.667 0.00 0.00 0.00 5.69
489 532 4.713553 TGATATGAACATGGCGGTTGTAT 58.286 39.130 0.00 0.00 0.00 2.29
524 567 7.894753 TCATATGGATTTGTGCTTTATGGAA 57.105 32.000 2.13 0.00 0.00 3.53
551 594 8.618677 CAGCTTCATATATGAAAGATTGTGTGT 58.381 33.333 24.61 5.22 45.26 3.72
639 1266 3.646650 CCAAAATGGCAGCCATACG 57.353 52.632 27.91 17.46 44.40 3.06
679 1306 9.603921 ATTTCAATTTATAAATCCTTGTGGCAG 57.396 29.630 11.08 0.00 0.00 4.85
742 1369 7.725844 ACCAACTGAAATCCTAACAGAGATTTT 59.274 33.333 0.00 0.00 41.56 1.82
776 1403 4.310022 TGAAATGAAACGAGGGGGTATT 57.690 40.909 0.00 0.00 0.00 1.89
777 1404 4.668636 TGAAATGAAACGAGGGGGTATTT 58.331 39.130 0.00 0.00 0.00 1.40
782 1409 3.268330 GAAACGAGGGGGTATTTCTCAC 58.732 50.000 0.00 0.00 0.00 3.51
792 1419 9.187996 GAGGGGGTATTTCTCACTATATAGTAC 57.812 40.741 15.03 7.92 34.13 2.73
800 1427 6.782298 TCTCACTATATAGTACGCACACTC 57.218 41.667 15.03 0.00 34.13 3.51
801 1428 6.522946 TCTCACTATATAGTACGCACACTCT 58.477 40.000 15.03 0.00 34.13 3.24
803 1430 8.146412 TCTCACTATATAGTACGCACACTCTAA 58.854 37.037 15.03 0.00 34.13 2.10
804 1431 8.081208 TCACTATATAGTACGCACACTCTAAC 57.919 38.462 15.03 0.00 34.13 2.34
805 1432 7.712205 TCACTATATAGTACGCACACTCTAACA 59.288 37.037 15.03 0.00 34.13 2.41
806 1433 7.797587 CACTATATAGTACGCACACTCTAACAC 59.202 40.741 15.03 0.00 34.13 3.32
807 1434 6.939132 ATATAGTACGCACACTCTAACACT 57.061 37.500 0.00 0.00 0.00 3.55
808 1435 3.555917 AGTACGCACACTCTAACACTC 57.444 47.619 0.00 0.00 0.00 3.51
809 1436 3.147629 AGTACGCACACTCTAACACTCT 58.852 45.455 0.00 0.00 0.00 3.24
810 1437 4.321718 AGTACGCACACTCTAACACTCTA 58.678 43.478 0.00 0.00 0.00 2.43
811 1438 4.942483 AGTACGCACACTCTAACACTCTAT 59.058 41.667 0.00 0.00 0.00 1.98
812 1439 4.358494 ACGCACACTCTAACACTCTATC 57.642 45.455 0.00 0.00 0.00 2.08
813 1440 3.128938 ACGCACACTCTAACACTCTATCC 59.871 47.826 0.00 0.00 0.00 2.59
857 2401 5.134202 TCAAACGAGCTGTTAGAGAATCA 57.866 39.130 0.00 0.00 40.84 2.57
858 2402 4.923871 TCAAACGAGCTGTTAGAGAATCAC 59.076 41.667 0.00 0.00 40.84 3.06
859 2403 4.521130 AACGAGCTGTTAGAGAATCACA 57.479 40.909 0.00 0.00 39.61 3.58
871 2415 1.429148 GAATCACAAGCGGGCCTACG 61.429 60.000 0.84 0.00 0.00 3.51
914 2458 0.980423 TGCCCAAAATTAAGGCCCAC 59.020 50.000 0.00 0.00 46.55 4.61
987 2531 0.825840 GAGAGGATAGCCCGCACTCT 60.826 60.000 0.00 0.00 40.93 3.24
989 2533 0.885196 GAGGATAGCCCGCACTCTAG 59.115 60.000 0.00 0.00 40.87 2.43
994 2538 4.457496 GCCCGCACTCTAGCTGCA 62.457 66.667 1.02 0.00 34.00 4.41
1095 2639 3.961414 GGTCTCCGCCCCCACAAA 61.961 66.667 0.00 0.00 0.00 2.83
1152 2696 1.047801 GGAGCTCCTTCATCTCCTCC 58.952 60.000 26.25 0.00 42.31 4.30
1252 2820 2.376855 AGAAACTCCTCCTTCCCTTTGG 59.623 50.000 0.00 0.00 0.00 3.28
1267 2835 2.162681 CTTTGGCACGAGGGAAATTCT 58.837 47.619 0.00 0.00 0.00 2.40
1367 2941 0.965439 TGGAAATGGCGGGTTTGAAG 59.035 50.000 0.00 0.00 0.00 3.02
1421 2995 1.108132 TCTGCTGTTGCACAATGCCA 61.108 50.000 0.00 0.00 45.31 4.92
1423 2997 0.393448 TGCTGTTGCACAATGCCATT 59.607 45.000 0.00 0.00 45.31 3.16
1440 3014 7.587037 ATGCCATTGTGCTGTATAAGTATTT 57.413 32.000 0.00 0.00 0.00 1.40
1574 3159 6.583050 TGTGTTTGTACAAAACTGTAAACAGC 59.417 34.615 22.14 6.44 40.80 4.40
1662 3250 5.767816 ACTTAAACGTCTCCAGCATTTTT 57.232 34.783 0.00 0.00 0.00 1.94
1725 3320 4.646572 TGTTGGTTCATGTACATAGTGCA 58.353 39.130 8.32 0.00 32.05 4.57
1758 3353 2.338577 ATCTACAATGTCTGGCCTGC 57.661 50.000 3.32 0.30 0.00 4.85
1956 3571 1.820519 GAAAATGTGCATGGCTGAGGA 59.179 47.619 0.00 0.00 0.00 3.71
1973 3588 5.484173 TGAGGATTTATTTGTGTCATCGC 57.516 39.130 0.00 0.00 0.00 4.58
1995 3610 3.125316 CGTCCTGCAATTTCTACTGGTTC 59.875 47.826 0.00 0.00 0.00 3.62
2026 3641 2.358615 GATGCAGTGTGACCGCCA 60.359 61.111 0.00 0.00 0.00 5.69
2064 3679 9.787626 CAATCGAAATTTCAAATTCTCACAAAG 57.212 29.630 17.99 0.00 0.00 2.77
2175 3872 7.125391 TGTATCTGAATTTGAGGGCCTAAAAT 58.875 34.615 21.33 21.33 0.00 1.82
2249 3946 7.900782 TGTAGCTCATGTTTTCTTAACTACC 57.099 36.000 0.00 0.00 0.00 3.18
2253 3950 6.651225 AGCTCATGTTTTCTTAACTACCACTC 59.349 38.462 0.00 0.00 0.00 3.51
2260 3957 9.796120 TGTTTTCTTAACTACCACTCAATTTTG 57.204 29.630 0.00 0.00 0.00 2.44
2261 3958 9.244799 GTTTTCTTAACTACCACTCAATTTTGG 57.755 33.333 0.00 0.00 39.00 3.28
2267 3964 1.970640 ACCACTCAATTTTGGGGAAGC 59.029 47.619 2.98 0.00 37.18 3.86
2273 3970 3.037549 TCAATTTTGGGGAAGCAACTGT 58.962 40.909 0.00 0.00 0.00 3.55
2276 3973 1.600023 TTTGGGGAAGCAACTGTACG 58.400 50.000 0.00 0.00 0.00 3.67
2292 3989 2.946329 TGTACGTGGCTGAACAACAAAT 59.054 40.909 0.00 0.00 0.00 2.32
2294 3991 3.078594 ACGTGGCTGAACAACAAATTC 57.921 42.857 0.00 0.00 0.00 2.17
2404 4111 7.020827 TCATTCTCAACCAGTTTATCCTCTT 57.979 36.000 0.00 0.00 0.00 2.85
2439 4146 3.939592 GTGACCCAGTATGCTTCTAAACC 59.060 47.826 0.00 0.00 31.97 3.27
2487 4194 6.721318 TGAACTAGCTAAAGTGGGAATGAAT 58.279 36.000 0.00 0.00 0.00 2.57
2489 4196 5.360591 ACTAGCTAAAGTGGGAATGAATCG 58.639 41.667 0.00 0.00 0.00 3.34
2548 4255 6.299141 AGTAATCTTCAGAGAACAGCCAAAA 58.701 36.000 0.00 0.00 35.07 2.44
2564 4271 4.082026 AGCCAAAAGGCAGCTAATAGTTTG 60.082 41.667 9.42 0.00 34.38 2.93
2590 4297 7.789273 TTTGGAATACGTTTGTCTGAACTTA 57.211 32.000 0.00 0.00 0.00 2.24
2648 4355 2.225091 TGTGGAGACCATCAAGGCATTT 60.225 45.455 0.00 0.00 43.14 2.32
2680 4387 4.202419 ACTGCACAGAGTAATGGGTTAACA 60.202 41.667 8.10 0.00 0.00 2.41
2709 4416 8.129211 GCAAATCACAAGTTCTTAGTTGTAACT 58.871 33.333 2.51 2.51 44.21 2.24
2799 4507 7.713942 ACGTCTTTGTAACAGATAACCTTTTCT 59.286 33.333 0.00 0.00 0.00 2.52
2811 4519 9.595823 CAGATAACCTTTTCTTCCTTAATACGA 57.404 33.333 0.00 0.00 0.00 3.43
3108 4820 3.320673 AGAAAGGTTCTGAAGCGTAGG 57.679 47.619 13.31 0.00 38.91 3.18
3278 4990 3.311106 ACAATTGCTGCACATCTTTTCG 58.689 40.909 0.00 0.00 0.00 3.46
3348 5060 6.947158 ACCGGTACAATTTATCCTTTTTGGTA 59.053 34.615 4.49 0.00 37.07 3.25
3409 5121 1.381928 ATCTTGGGCGCTGCATTCTG 61.382 55.000 7.64 0.00 0.00 3.02
3533 5246 2.987046 GTTGAAAACTTCAGGCAGTCG 58.013 47.619 0.00 0.00 45.32 4.18
3542 5255 0.901827 TCAGGCAGTCGCTGGAATAA 59.098 50.000 8.57 0.00 38.60 1.40
3543 5256 1.134699 TCAGGCAGTCGCTGGAATAAG 60.135 52.381 8.57 0.00 38.60 1.73
3544 5257 0.905357 AGGCAGTCGCTGGAATAAGT 59.095 50.000 8.57 0.00 38.60 2.24
3552 5265 6.183360 GCAGTCGCTGGAATAAGTTTTATCTT 60.183 38.462 8.57 0.00 34.30 2.40
3569 5282 9.680315 GTTTTATCTTCTACGCTATCATGTACT 57.320 33.333 0.00 0.00 0.00 2.73
3570 5283 9.894783 TTTTATCTTCTACGCTATCATGTACTC 57.105 33.333 0.00 0.00 0.00 2.59
3571 5284 5.943706 TCTTCTACGCTATCATGTACTCC 57.056 43.478 0.00 0.00 0.00 3.85
3572 5285 4.760715 TCTTCTACGCTATCATGTACTCCC 59.239 45.833 0.00 0.00 0.00 4.30
3573 5286 3.418995 TCTACGCTATCATGTACTCCCC 58.581 50.000 0.00 0.00 0.00 4.81
3574 5287 1.339097 ACGCTATCATGTACTCCCCC 58.661 55.000 0.00 0.00 0.00 5.40
3589 5302 3.991972 CCCCCGTCCCAAAATAAGT 57.008 52.632 0.00 0.00 0.00 2.24
3590 5303 1.470051 CCCCCGTCCCAAAATAAGTG 58.530 55.000 0.00 0.00 0.00 3.16
3591 5304 1.004979 CCCCCGTCCCAAAATAAGTGA 59.995 52.381 0.00 0.00 0.00 3.41
3592 5305 2.089201 CCCCGTCCCAAAATAAGTGAC 58.911 52.381 0.00 0.00 0.00 3.67
3593 5306 2.290705 CCCCGTCCCAAAATAAGTGACT 60.291 50.000 0.00 0.00 0.00 3.41
3594 5307 3.054948 CCCCGTCCCAAAATAAGTGACTA 60.055 47.826 0.00 0.00 0.00 2.59
3595 5308 4.566070 CCCCGTCCCAAAATAAGTGACTAA 60.566 45.833 0.00 0.00 0.00 2.24
3596 5309 5.005094 CCCGTCCCAAAATAAGTGACTAAA 58.995 41.667 0.00 0.00 0.00 1.85
3597 5310 5.106436 CCCGTCCCAAAATAAGTGACTAAAC 60.106 44.000 0.00 0.00 0.00 2.01
3598 5311 5.704053 CCGTCCCAAAATAAGTGACTAAACT 59.296 40.000 0.00 0.00 0.00 2.66
3599 5312 6.206048 CCGTCCCAAAATAAGTGACTAAACTT 59.794 38.462 0.00 0.00 42.89 2.66
3600 5313 7.255346 CCGTCCCAAAATAAGTGACTAAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
3601 5314 7.589954 CGTCCCAAAATAAGTGACTAAACTTTG 59.410 37.037 0.00 0.00 40.77 2.77
3602 5315 8.410912 GTCCCAAAATAAGTGACTAAACTTTGT 58.589 33.333 0.00 0.00 40.77 2.83
3603 5316 9.629878 TCCCAAAATAAGTGACTAAACTTTGTA 57.370 29.630 0.00 0.00 40.77 2.41
3604 5317 9.893305 CCCAAAATAAGTGACTAAACTTTGTAG 57.107 33.333 0.00 0.00 40.77 2.74
3641 5354 9.662947 ACAAAGTTAGTTAGTGTAAAGTTGAGT 57.337 29.630 0.00 0.00 0.00 3.41
3643 5356 9.880157 AAAGTTAGTTAGTGTAAAGTTGAGTCA 57.120 29.630 0.00 0.00 0.00 3.41
3644 5357 8.868635 AGTTAGTTAGTGTAAAGTTGAGTCAC 57.131 34.615 0.00 0.00 0.00 3.67
3645 5358 8.693625 AGTTAGTTAGTGTAAAGTTGAGTCACT 58.306 33.333 0.00 0.00 41.32 3.41
3646 5359 9.310716 GTTAGTTAGTGTAAAGTTGAGTCACTT 57.689 33.333 0.00 0.00 39.54 3.16
3653 5366 8.621286 AGTGTAAAGTTGAGTCACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3654 5367 7.860872 GTGTAAAGTTGAGTCACTTATTTTGGG 59.139 37.037 0.00 0.00 35.87 4.12
3655 5368 7.776030 TGTAAAGTTGAGTCACTTATTTTGGGA 59.224 33.333 0.00 0.00 35.87 4.37
3656 5369 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3657 5370 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3658 5371 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3659 5372 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3660 5373 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3661 5374 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3778 5491 7.839705 AGAACCTGAATATGTAGGACTAAGACA 59.160 37.037 11.43 0.00 37.52 3.41
3900 5614 1.597663 CAAGGTCACGGAGAACACAAC 59.402 52.381 0.00 0.00 35.97 3.32
3958 5672 2.031012 CTCTCCAACACGCAGGCA 59.969 61.111 0.00 0.00 0.00 4.75
3991 5705 6.326064 ACTTCATCTGTATGTAAGCCATCTCT 59.674 38.462 0.00 0.00 34.86 3.10
4048 5762 2.422832 CGGGTACTTAAACGAGCTCTCT 59.577 50.000 12.85 0.00 0.00 3.10
4078 5792 1.074926 ACCCTCCTCATCGAGCCAT 60.075 57.895 0.00 0.00 0.00 4.40
4105 5819 1.215647 CCGGTACTCTGCACAGTCC 59.784 63.158 0.00 0.00 0.00 3.85
4123 5837 1.261238 CCTCGCCCCATATCTCCTCC 61.261 65.000 0.00 0.00 0.00 4.30
4168 5882 1.742308 AGGAGACCTGCCAACCTTTA 58.258 50.000 0.00 0.00 29.57 1.85
4171 5885 0.036306 AGACCTGCCAACCTTTACCG 59.964 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.822805 TGTACTACTTTCTTAATTCCATCCAGT 58.177 33.333 0.00 0.00 0.00 4.00
3 4 9.667107 TTGTACTACTTTCTTAATTCCATCCAG 57.333 33.333 0.00 0.00 0.00 3.86
13 14 9.280174 CAACCCTGATTTGTACTACTTTCTTAA 57.720 33.333 0.00 0.00 0.00 1.85
14 15 7.881232 CCAACCCTGATTTGTACTACTTTCTTA 59.119 37.037 0.00 0.00 0.00 2.10
15 16 6.715264 CCAACCCTGATTTGTACTACTTTCTT 59.285 38.462 0.00 0.00 0.00 2.52
16 17 6.183361 ACCAACCCTGATTTGTACTACTTTCT 60.183 38.462 0.00 0.00 0.00 2.52
17 18 6.002082 ACCAACCCTGATTTGTACTACTTTC 58.998 40.000 0.00 0.00 0.00 2.62
18 19 5.768164 CACCAACCCTGATTTGTACTACTTT 59.232 40.000 0.00 0.00 0.00 2.66
19 20 5.313712 CACCAACCCTGATTTGTACTACTT 58.686 41.667 0.00 0.00 0.00 2.24
20 21 4.263331 CCACCAACCCTGATTTGTACTACT 60.263 45.833 0.00 0.00 0.00 2.57
21 22 4.007659 CCACCAACCCTGATTTGTACTAC 58.992 47.826 0.00 0.00 0.00 2.73
22 23 3.653836 ACCACCAACCCTGATTTGTACTA 59.346 43.478 0.00 0.00 0.00 1.82
23 24 2.445525 ACCACCAACCCTGATTTGTACT 59.554 45.455 0.00 0.00 0.00 2.73
24 25 2.556622 CACCACCAACCCTGATTTGTAC 59.443 50.000 0.00 0.00 0.00 2.90
25 26 2.175931 ACACCACCAACCCTGATTTGTA 59.824 45.455 0.00 0.00 0.00 2.41
26 27 1.063266 ACACCACCAACCCTGATTTGT 60.063 47.619 0.00 0.00 0.00 2.83
27 28 1.703411 ACACCACCAACCCTGATTTG 58.297 50.000 0.00 0.00 0.00 2.32
28 29 2.038659 CAACACCACCAACCCTGATTT 58.961 47.619 0.00 0.00 0.00 2.17
29 30 1.063266 ACAACACCACCAACCCTGATT 60.063 47.619 0.00 0.00 0.00 2.57
30 31 0.555769 ACAACACCACCAACCCTGAT 59.444 50.000 0.00 0.00 0.00 2.90
31 32 0.333312 AACAACACCACCAACCCTGA 59.667 50.000 0.00 0.00 0.00 3.86
32 33 0.459489 CAACAACACCACCAACCCTG 59.541 55.000 0.00 0.00 0.00 4.45
33 34 0.040499 ACAACAACACCACCAACCCT 59.960 50.000 0.00 0.00 0.00 4.34
34 35 0.899019 AACAACAACACCACCAACCC 59.101 50.000 0.00 0.00 0.00 4.11
35 36 1.273886 ACAACAACAACACCACCAACC 59.726 47.619 0.00 0.00 0.00 3.77
36 37 2.734079 CAACAACAACAACACCACCAAC 59.266 45.455 0.00 0.00 0.00 3.77
37 38 2.365617 ACAACAACAACAACACCACCAA 59.634 40.909 0.00 0.00 0.00 3.67
38 39 1.964223 ACAACAACAACAACACCACCA 59.036 42.857 0.00 0.00 0.00 4.17
39 40 2.734276 ACAACAACAACAACACCACC 57.266 45.000 0.00 0.00 0.00 4.61
40 41 5.635700 ACAATAACAACAACAACAACACCAC 59.364 36.000 0.00 0.00 0.00 4.16
41 42 5.784177 ACAATAACAACAACAACAACACCA 58.216 33.333 0.00 0.00 0.00 4.17
42 43 6.146347 ACAACAATAACAACAACAACAACACC 59.854 34.615 0.00 0.00 0.00 4.16
43 44 7.111353 ACAACAATAACAACAACAACAACAC 57.889 32.000 0.00 0.00 0.00 3.32
44 45 7.224753 ACAACAACAATAACAACAACAACAACA 59.775 29.630 0.00 0.00 0.00 3.33
45 46 7.568433 ACAACAACAATAACAACAACAACAAC 58.432 30.769 0.00 0.00 0.00 3.32
46 47 7.715265 ACAACAACAATAACAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
47 48 7.224753 ACAACAACAACAATAACAACAACAACA 59.775 29.630 0.00 0.00 0.00 3.33
48 49 7.568433 ACAACAACAACAATAACAACAACAAC 58.432 30.769 0.00 0.00 0.00 3.32
49 50 7.715265 ACAACAACAACAATAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
50 51 7.224753 ACAACAACAACAACAATAACAACAACA 59.775 29.630 0.00 0.00 0.00 3.33
51 52 7.568433 ACAACAACAACAACAATAACAACAAC 58.432 30.769 0.00 0.00 0.00 3.32
52 53 7.715265 ACAACAACAACAACAATAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
53 54 7.224753 ACAACAACAACAACAACAATAACAACA 59.775 29.630 0.00 0.00 0.00 3.33
54 55 7.568433 ACAACAACAACAACAACAATAACAAC 58.432 30.769 0.00 0.00 0.00 3.32
55 56 7.715265 ACAACAACAACAACAACAATAACAA 57.285 28.000 0.00 0.00 0.00 2.83
56 57 7.224753 ACAACAACAACAACAACAACAATAACA 59.775 29.630 0.00 0.00 0.00 2.41
57 58 7.568433 ACAACAACAACAACAACAACAATAAC 58.432 30.769 0.00 0.00 0.00 1.89
58 59 7.715265 ACAACAACAACAACAACAACAATAA 57.285 28.000 0.00 0.00 0.00 1.40
59 60 7.224753 ACAACAACAACAACAACAACAACAATA 59.775 29.630 0.00 0.00 0.00 1.90
60 61 6.037610 ACAACAACAACAACAACAACAACAAT 59.962 30.769 0.00 0.00 0.00 2.71
61 62 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
62 63 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
63 64 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
64 65 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
65 66 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
66 67 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
67 68 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
68 69 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
69 70 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
70 71 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
71 72 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
72 73 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
73 74 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
74 75 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
75 76 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
76 77 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
77 78 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
78 79 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
79 80 7.534085 TTAACAACAACAACAACAACAACAA 57.466 28.000 0.00 0.00 0.00 2.83
80 81 7.715265 ATTAACAACAACAACAACAACAACA 57.285 28.000 0.00 0.00 0.00 3.33
115 116 8.669946 TCAATATTTTGGTTGCATCTATCGTA 57.330 30.769 0.00 0.00 33.44 3.43
117 118 8.077991 ACATCAATATTTTGGTTGCATCTATCG 58.922 33.333 0.00 0.00 33.44 2.92
126 127 8.991026 ACAAATGTCACATCAATATTTTGGTTG 58.009 29.630 0.00 0.00 33.44 3.77
146 147 4.378774 TGAATTGGAGGCAACAACAAATG 58.621 39.130 0.00 0.00 37.86 2.32
147 148 4.686191 TGAATTGGAGGCAACAACAAAT 57.314 36.364 0.00 0.00 37.86 2.32
175 176 7.011669 TGTTGGTGAAGTTACTAAAGTAGTTGC 59.988 37.037 0.00 0.00 40.14 4.17
189 190 6.206634 ACGATGATAAACATGTTGGTGAAGTT 59.793 34.615 12.82 0.00 39.56 2.66
191 192 6.182039 ACGATGATAAACATGTTGGTGAAG 57.818 37.500 12.82 4.41 39.56 3.02
194 195 7.044117 GCAAATACGATGATAAACATGTTGGTG 60.044 37.037 12.82 1.15 39.56 4.17
235 236 1.546029 GGGTTGGAGAAATCTTGTGGC 59.454 52.381 0.00 0.00 0.00 5.01
287 288 1.276622 TGAGTTGGAGGAACTAGCCC 58.723 55.000 0.00 0.00 45.48 5.19
290 291 5.422331 TCAAGGTATGAGTTGGAGGAACTAG 59.578 44.000 0.00 0.00 45.48 2.57
291 292 5.338632 TCAAGGTATGAGTTGGAGGAACTA 58.661 41.667 0.00 0.00 45.48 2.24
293 294 4.553330 TCAAGGTATGAGTTGGAGGAAC 57.447 45.455 0.00 0.00 33.04 3.62
294 295 4.626287 GCATCAAGGTATGAGTTGGAGGAA 60.626 45.833 0.00 0.00 42.53 3.36
296 297 3.209410 GCATCAAGGTATGAGTTGGAGG 58.791 50.000 0.00 0.00 42.53 4.30
394 437 6.785076 TGTATTCAACAAGGTATGGAGGAAA 58.215 36.000 0.00 0.00 34.29 3.13
395 438 6.381498 TGTATTCAACAAGGTATGGAGGAA 57.619 37.500 0.00 0.00 34.29 3.36
409 452 6.756542 ACAAAGGTTCAAAGCTTGTATTCAAC 59.243 34.615 0.00 0.00 45.17 3.18
470 513 4.944317 TCAAATACAACCGCCATGTTCATA 59.056 37.500 0.00 0.00 32.27 2.15
489 532 9.100554 GCACAAATCCATATGATCAAATTCAAA 57.899 29.630 3.65 0.00 31.61 2.69
524 567 8.618677 CACACAATCTTTCATATATGAAGCTGT 58.381 33.333 23.61 20.60 46.34 4.40
551 594 5.236655 TGTCAACATTAAACAAGTTGCGA 57.763 34.783 1.81 0.00 41.67 5.10
673 1300 0.249996 AAAACATGCTTGGCTGCCAC 60.250 50.000 23.30 11.88 30.78 5.01
747 1374 5.399013 CCCTCGTTTCATTTCATTTGGTAC 58.601 41.667 0.00 0.00 0.00 3.34
765 1392 6.890814 ACTATATAGTGAGAAATACCCCCTCG 59.109 42.308 14.71 0.00 34.72 4.63
776 1403 6.990939 AGAGTGTGCGTACTATATAGTGAGAA 59.009 38.462 23.09 10.15 37.10 2.87
777 1404 6.522946 AGAGTGTGCGTACTATATAGTGAGA 58.477 40.000 23.09 2.86 37.10 3.27
782 1409 8.085720 AGTGTTAGAGTGTGCGTACTATATAG 57.914 38.462 8.27 8.27 0.00 1.31
792 1419 3.696898 GGATAGAGTGTTAGAGTGTGCG 58.303 50.000 0.00 0.00 0.00 5.34
807 1434 7.290248 ACCCTCATTTTAATTCTCTCGGATAGA 59.710 37.037 0.00 0.00 0.00 1.98
808 1435 7.445945 ACCCTCATTTTAATTCTCTCGGATAG 58.554 38.462 0.00 0.00 0.00 2.08
809 1436 7.374975 ACCCTCATTTTAATTCTCTCGGATA 57.625 36.000 0.00 0.00 0.00 2.59
810 1437 6.253946 ACCCTCATTTTAATTCTCTCGGAT 57.746 37.500 0.00 0.00 0.00 4.18
811 1438 5.693769 ACCCTCATTTTAATTCTCTCGGA 57.306 39.130 0.00 0.00 0.00 4.55
812 1439 7.217200 TGATACCCTCATTTTAATTCTCTCGG 58.783 38.462 0.00 0.00 0.00 4.63
813 1440 8.662781 TTGATACCCTCATTTTAATTCTCTCG 57.337 34.615 0.00 0.00 32.72 4.04
818 1445 7.644157 GCTCGTTTGATACCCTCATTTTAATTC 59.356 37.037 0.00 0.00 32.72 2.17
821 1448 6.093495 CAGCTCGTTTGATACCCTCATTTTAA 59.907 38.462 0.00 0.00 32.72 1.52
871 2415 2.215942 ACCTGTTAACAAGCCCATCC 57.784 50.000 10.03 0.00 0.00 3.51
914 2458 4.142513 GCTGGATGAGAAGTTTAGGCTTTG 60.143 45.833 0.00 0.00 0.00 2.77
921 2465 2.354704 CCACGGCTGGATGAGAAGTTTA 60.355 50.000 0.00 0.00 40.55 2.01
987 2531 1.448365 CGCCATGTCTGTGCAGCTA 60.448 57.895 0.00 0.00 0.00 3.32
989 2533 4.471726 GCGCCATGTCTGTGCAGC 62.472 66.667 0.00 0.00 0.00 5.25
1140 2684 2.038659 GTGGAGGAGGAGGAGATGAAG 58.961 57.143 0.00 0.00 0.00 3.02
1152 2696 2.055042 CGAGGAGGTGGTGGAGGAG 61.055 68.421 0.00 0.00 0.00 3.69
1252 2820 5.560966 TCAATAAAGAATTTCCCTCGTGC 57.439 39.130 0.00 0.00 40.09 5.34
1267 2835 8.735315 ACCAACATATCGAACACATTCAATAAA 58.265 29.630 0.00 0.00 34.14 1.40
1367 2941 2.160417 ACACACTACTACCGTTCTACGC 59.840 50.000 0.00 0.00 40.91 4.42
1381 2955 6.816640 GCAGAACATCCATAGTTTACACACTA 59.183 38.462 0.00 0.00 33.70 2.74
1423 2997 9.938280 AACTAAGACAAATACTTATACAGCACA 57.062 29.630 0.00 0.00 30.96 4.57
1440 3014 3.244345 CACGCGACAGAAAAACTAAGACA 59.756 43.478 15.93 0.00 0.00 3.41
1456 3030 1.227342 TGAATTTGCAGAGCACGCGA 61.227 50.000 15.93 0.00 38.71 5.87
1558 3143 7.431084 CGTAAATTCTGCTGTTTACAGTTTTGT 59.569 33.333 11.23 0.00 45.45 2.83
1574 3159 4.788100 CCAAATCGAAGTGCGTAAATTCTG 59.212 41.667 0.00 0.00 41.80 3.02
1583 3168 2.482721 ACCTAAACCAAATCGAAGTGCG 59.517 45.455 0.00 0.00 42.69 5.34
1683 3278 7.818930 ACCAACATGTCCAACAATAATGAAATC 59.181 33.333 0.00 0.00 0.00 2.17
1725 3320 8.057623 AGACATTGTAGATTCCAAGATTCCATT 58.942 33.333 0.00 0.00 0.00 3.16
1758 3353 2.093816 TGCTCTCAGATAACTGCACCTG 60.094 50.000 0.00 0.00 43.17 4.00
1793 3406 6.037786 TGGGTCTAAGACTACAATGACTTG 57.962 41.667 0.00 0.00 34.20 3.16
1799 3412 8.706322 ACAAAAATTGGGTCTAAGACTACAAT 57.294 30.769 0.00 0.00 39.58 2.71
1924 3538 6.019640 CCATGCACATTTTCCTAATTTTAGCG 60.020 38.462 0.00 0.00 0.00 4.26
1925 3539 6.238184 GCCATGCACATTTTCCTAATTTTAGC 60.238 38.462 0.00 0.00 0.00 3.09
1934 3548 1.822990 CTCAGCCATGCACATTTTCCT 59.177 47.619 0.00 0.00 0.00 3.36
1936 3550 1.820519 TCCTCAGCCATGCACATTTTC 59.179 47.619 0.00 0.00 0.00 2.29
1937 3551 1.927487 TCCTCAGCCATGCACATTTT 58.073 45.000 0.00 0.00 0.00 1.82
1956 3571 3.938963 AGGACGCGATGACACAAATAAAT 59.061 39.130 15.93 0.00 0.00 1.40
1973 3588 2.699954 ACCAGTAGAAATTGCAGGACG 58.300 47.619 0.00 0.00 0.00 4.79
2014 3629 0.534203 ACGAAATTGGCGGTCACACT 60.534 50.000 6.03 0.00 0.00 3.55
2049 3664 7.750229 ATGTAGCTTCTTTGTGAGAATTTGA 57.250 32.000 0.00 0.00 43.23 2.69
2064 3679 9.155975 CCCAGTCATATGTTAATATGTAGCTTC 57.844 37.037 1.90 0.00 44.16 3.86
2078 3693 4.657814 AACAAGAACCCCAGTCATATGT 57.342 40.909 1.90 0.00 0.00 2.29
2175 3872 7.233553 ACTTTCCATCGTCTATATGATTCAGGA 59.766 37.037 0.00 0.00 0.00 3.86
2249 3946 3.070015 AGTTGCTTCCCCAAAATTGAGTG 59.930 43.478 0.00 0.00 0.00 3.51
2253 3950 3.473923 ACAGTTGCTTCCCCAAAATTG 57.526 42.857 0.00 0.00 0.00 2.32
2260 3957 0.953960 CCACGTACAGTTGCTTCCCC 60.954 60.000 0.00 0.00 0.00 4.81
2261 3958 1.574702 GCCACGTACAGTTGCTTCCC 61.575 60.000 0.00 0.00 38.36 3.97
2267 3964 1.577468 TGTTCAGCCACGTACAGTTG 58.423 50.000 0.00 0.00 0.00 3.16
2273 3970 3.628032 TGAATTTGTTGTTCAGCCACGTA 59.372 39.130 0.00 0.00 32.23 3.57
2276 3973 6.646240 ACATTATGAATTTGTTGTTCAGCCAC 59.354 34.615 0.00 0.00 38.81 5.01
2325 4022 8.675504 TCTTGAAGTTATCCGTTTGTTGTTTAA 58.324 29.630 0.00 0.00 0.00 1.52
2326 4023 8.211116 TCTTGAAGTTATCCGTTTGTTGTTTA 57.789 30.769 0.00 0.00 0.00 2.01
2327 4024 7.090953 TCTTGAAGTTATCCGTTTGTTGTTT 57.909 32.000 0.00 0.00 0.00 2.83
2328 4025 6.687081 TCTTGAAGTTATCCGTTTGTTGTT 57.313 33.333 0.00 0.00 0.00 2.83
2376 4080 5.415701 GGATAAACTGGTTGAGAATGAGCAA 59.584 40.000 0.00 0.00 0.00 3.91
2404 4111 7.094118 GCATACTGGGTCACTTTTAACCATTTA 60.094 37.037 0.00 0.00 37.28 1.40
2439 4146 9.800433 TCATTTAATATAACATTGTTGTGCTGG 57.200 29.630 12.30 0.00 35.83 4.85
2548 4255 5.076873 TCCAAAACAAACTATTAGCTGCCT 58.923 37.500 0.00 0.00 0.00 4.75
2564 4271 6.492254 AGTTCAGACAAACGTATTCCAAAAC 58.508 36.000 0.00 0.00 34.27 2.43
2648 4355 7.552687 CCCATTACTCTGTGCAGTTCTAAATTA 59.447 37.037 0.00 0.00 0.00 1.40
2670 4377 3.900601 TGTGATTTGCCTTGTTAACCCAT 59.099 39.130 2.48 0.00 0.00 4.00
2680 4387 6.096846 ACAACTAAGAACTTGTGATTTGCCTT 59.903 34.615 0.00 0.00 0.00 4.35
2709 4416 7.624360 TCAAAAGAGAAGCTCTAAACAACAA 57.376 32.000 0.00 0.00 40.28 2.83
2713 4420 9.950496 AATAGATCAAAAGAGAAGCTCTAAACA 57.050 29.630 0.00 0.00 40.28 2.83
2799 4507 7.069578 AGGTCTAAGCTTGATCGTATTAAGGAA 59.930 37.037 9.86 0.00 0.00 3.36
2811 4519 3.853355 CCCATGAGGTCTAAGCTTGAT 57.147 47.619 9.86 0.00 0.00 2.57
3108 4820 0.603569 TCTTCCTTCCTCTGTCACGC 59.396 55.000 0.00 0.00 0.00 5.34
3278 4990 5.932303 TCAAGTTATCAACCAGAGTAACAGC 59.068 40.000 0.00 0.00 31.24 4.40
3315 5027 3.994204 AAATTGTACCGGTGTTGGAAC 57.006 42.857 19.93 6.68 0.00 3.62
3348 5060 4.848357 ACATAGCATTAAAGACTGCCACT 58.152 39.130 0.00 0.00 39.22 4.00
3409 5121 3.442625 GCATTGGGGTCCTACAAAGTTAC 59.557 47.826 4.11 0.00 0.00 2.50
3533 5246 7.224949 AGCGTAGAAGATAAAACTTATTCCAGC 59.775 37.037 0.00 0.00 0.00 4.85
3542 5255 9.680315 GTACATGATAGCGTAGAAGATAAAACT 57.320 33.333 0.00 0.00 0.00 2.66
3543 5256 9.680315 AGTACATGATAGCGTAGAAGATAAAAC 57.320 33.333 0.00 0.00 0.00 2.43
3544 5257 9.894783 GAGTACATGATAGCGTAGAAGATAAAA 57.105 33.333 0.00 0.00 0.00 1.52
3552 5265 3.418995 GGGGAGTACATGATAGCGTAGA 58.581 50.000 0.00 0.00 0.00 2.59
3571 5284 1.004979 TCACTTATTTTGGGACGGGGG 59.995 52.381 0.00 0.00 0.00 5.40
3572 5285 2.089201 GTCACTTATTTTGGGACGGGG 58.911 52.381 0.00 0.00 0.00 5.73
3573 5286 3.067684 AGTCACTTATTTTGGGACGGG 57.932 47.619 0.00 0.00 33.84 5.28
3574 5287 5.704053 AGTTTAGTCACTTATTTTGGGACGG 59.296 40.000 0.00 0.00 33.84 4.79
3575 5288 6.796705 AGTTTAGTCACTTATTTTGGGACG 57.203 37.500 0.00 0.00 33.84 4.79
3576 5289 8.410912 ACAAAGTTTAGTCACTTATTTTGGGAC 58.589 33.333 10.40 0.00 35.87 4.46
3577 5290 8.528044 ACAAAGTTTAGTCACTTATTTTGGGA 57.472 30.769 10.40 0.00 35.87 4.37
3578 5291 9.893305 CTACAAAGTTTAGTCACTTATTTTGGG 57.107 33.333 10.40 2.84 35.87 4.12
3615 5328 9.662947 ACTCAACTTTACACTAACTAACTTTGT 57.337 29.630 0.00 0.00 0.00 2.83
3617 5330 9.880157 TGACTCAACTTTACACTAACTAACTTT 57.120 29.630 0.00 0.00 0.00 2.66
3618 5331 9.310716 GTGACTCAACTTTACACTAACTAACTT 57.689 33.333 0.00 0.00 0.00 2.66
3619 5332 8.693625 AGTGACTCAACTTTACACTAACTAACT 58.306 33.333 0.00 0.00 39.52 2.24
3620 5333 8.868635 AGTGACTCAACTTTACACTAACTAAC 57.131 34.615 0.00 0.00 39.52 2.34
3627 5340 8.621286 CCAAAATAAGTGACTCAACTTTACACT 58.379 33.333 0.00 0.00 40.77 3.55
3628 5341 7.860872 CCCAAAATAAGTGACTCAACTTTACAC 59.139 37.037 0.00 0.00 40.77 2.90
3629 5342 7.776030 TCCCAAAATAAGTGACTCAACTTTACA 59.224 33.333 0.00 0.00 40.77 2.41
3630 5343 8.074370 GTCCCAAAATAAGTGACTCAACTTTAC 58.926 37.037 0.00 0.00 40.77 2.01
3631 5344 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3632 5345 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3633 5346 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3634 5347 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3635 5348 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3636 5349 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3637 5350 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3638 5351 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3639 5352 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3640 5353 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3641 5354 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3642 5355 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3643 5356 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3644 5357 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3645 5358 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3646 5359 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3647 5360 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3648 5361 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3649 5362 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3650 5363 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3651 5364 2.023695 ACTTAATACTCCCTCCGTCCCA 60.024 50.000 0.00 0.00 0.00 4.37
3652 5365 2.675583 ACTTAATACTCCCTCCGTCCC 58.324 52.381 0.00 0.00 0.00 4.46
3653 5366 3.571828 GGTACTTAATACTCCCTCCGTCC 59.428 52.174 0.00 0.00 33.87 4.79
3654 5367 4.210331 TGGTACTTAATACTCCCTCCGTC 58.790 47.826 0.00 0.00 33.87 4.79
3655 5368 4.213513 CTGGTACTTAATACTCCCTCCGT 58.786 47.826 0.00 0.00 33.87 4.69
3656 5369 4.213513 ACTGGTACTTAATACTCCCTCCG 58.786 47.826 0.00 0.00 33.87 4.63
3657 5370 5.538053 GGTACTGGTACTTAATACTCCCTCC 59.462 48.000 10.19 0.00 36.36 4.30
3658 5371 6.372104 AGGTACTGGTACTTAATACTCCCTC 58.628 44.000 10.19 0.00 37.18 4.30
3659 5372 6.352739 AGGTACTGGTACTTAATACTCCCT 57.647 41.667 10.19 0.00 37.18 4.20
3778 5491 1.757682 CTCCTCTCTCACGCCTACTT 58.242 55.000 0.00 0.00 0.00 2.24
3842 5556 1.396301 GCCGATGCAAGTGAAGAAGAG 59.604 52.381 0.00 0.00 37.47 2.85
3924 5638 2.037772 GAGAGGTTCAGCTTCCAGTTCA 59.962 50.000 0.00 0.00 0.00 3.18
3958 5672 5.108187 ACATACAGATGAAGTCCATTGCT 57.892 39.130 0.00 0.00 36.48 3.91
4027 5741 2.422832 AGAGAGCTCGTTTAAGTACCCG 59.577 50.000 8.37 0.00 34.09 5.28
4078 5792 3.138798 GAGTACCGGCCAGAGCGA 61.139 66.667 0.00 0.00 41.24 4.93
4105 5819 0.542938 TGGAGGAGATATGGGGCGAG 60.543 60.000 0.00 0.00 0.00 5.03
4123 5837 3.208383 TATGCCATGGCGCGGTTG 61.208 61.111 30.87 0.00 45.51 3.77


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

AutoCloner maintained by Alex Coulton.