Multiple sequence alignment - TraesCS4A01G240300

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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 TraesCS4A01G240300 chr4A 100.000 5566 0 0 1 5566 549883741 549878176 0.000000e+00 10279.0
1 TraesCS4A01G240300 chr4A 88.065 620 59 8 1 611 277893693 277893080 0.000000e+00 721.0
2 TraesCS4A01G240300 chr4A 78.035 173 33 5 36 207 190190437 190190269 2.740000e-18 104.0
3 TraesCS4A01G240300 chr4D 94.003 1951 81 13 3261 5183 47852219 47854161 0.000000e+00 2922.0
4 TraesCS4A01G240300 chr4D 92.439 1640 70 28 1568 3181 47850611 47852222 0.000000e+00 2292.0
5 TraesCS4A01G240300 chr4D 94.163 651 30 5 926 1569 47849932 47850581 0.000000e+00 985.0
6 TraesCS4A01G240300 chr4D 77.457 173 34 5 36 207 297786263 297786431 1.280000e-16 99.0
7 TraesCS4A01G240300 chr4B 94.468 1663 67 9 3261 4906 70255213 70256867 0.000000e+00 2538.0
8 TraesCS4A01G240300 chr4B 94.163 1285 47 10 1907 3181 70253950 70255216 0.000000e+00 1932.0
9 TraesCS4A01G240300 chr4B 92.758 649 36 6 926 1567 70252746 70253390 0.000000e+00 928.0
10 TraesCS4A01G240300 chr4B 94.783 345 15 1 1566 1910 70253576 70253917 8.210000e-148 534.0
11 TraesCS4A01G240300 chr4B 96.403 139 4 1 4965 5102 70256864 70257002 1.560000e-55 228.0
12 TraesCS4A01G240300 chr4B 78.035 173 33 5 36 207 368850104 368850272 2.740000e-18 104.0
13 TraesCS4A01G240300 chr4B 92.647 68 4 1 5492 5559 70257533 70257599 4.590000e-16 97.1
14 TraesCS4A01G240300 chr7A 95.754 895 21 3 1 880 520793260 520792368 0.000000e+00 1426.0
15 TraesCS4A01G240300 chr7A 90.000 110 10 1 3177 3285 155147985 155147876 2.090000e-29 141.0
16 TraesCS4A01G240300 chr7A 92.754 69 5 0 796 864 603354771 603354839 3.550000e-17 100.0
17 TraesCS4A01G240300 chr7A 97.619 42 1 0 4686 4727 120981908 120981949 7.730000e-09 73.1
18 TraesCS4A01G240300 chr7A 82.927 82 10 4 799 878 171266455 171266534 2.780000e-08 71.3
19 TraesCS4A01G240300 chr3D 95.909 880 19 3 1 864 608308136 608309014 0.000000e+00 1410.0
20 TraesCS4A01G240300 chr3D 92.000 100 7 1 3178 3276 587947464 587947365 7.520000e-29 139.0
21 TraesCS4A01G240300 chr1A 89.103 624 46 11 1 611 259200599 259201213 0.000000e+00 756.0
22 TraesCS4A01G240300 chr6A 89.971 349 25 8 268 611 507144224 507144567 5.120000e-120 442.0
23 TraesCS4A01G240300 chr6A 86.364 286 24 5 1 275 507140839 507141120 1.170000e-76 298.0
24 TraesCS4A01G240300 chr6A 95.652 92 3 1 3178 3269 169203395 169203305 4.490000e-31 147.0
25 TraesCS4A01G240300 chr7B 95.604 91 4 0 3176 3266 516805198 516805108 4.490000e-31 147.0
26 TraesCS4A01G240300 chr6B 94.737 95 4 1 3175 3269 96970757 96970850 4.490000e-31 147.0
27 TraesCS4A01G240300 chr6B 92.929 99 7 0 3171 3269 468624569 468624667 1.620000e-30 145.0
28 TraesCS4A01G240300 chr6B 92.929 99 7 0 3171 3269 468652662 468652760 1.620000e-30 145.0
29 TraesCS4A01G240300 chr1D 94.565 92 5 0 3175 3266 415987140 415987231 5.810000e-30 143.0
30 TraesCS4A01G240300 chr2A 93.684 95 5 1 3178 3271 404608293 404608199 2.090000e-29 141.0
31 TraesCS4A01G240300 chr2A 97.500 40 1 0 4687 4726 733925427 733925466 1.000000e-07 69.4
32 TraesCS4A01G240300 chr7D 91.304 69 6 0 796 864 523078627 523078559 1.650000e-15 95.3
33 TraesCS4A01G240300 chr7D 94.545 55 2 1 4673 4727 5333458 5333511 3.570000e-12 84.2
34 TraesCS4A01G240300 chr5D 97.778 45 1 0 4685 4729 381914490 381914446 1.660000e-10 78.7
35 TraesCS4A01G240300 chr5D 92.000 50 2 1 4685 4734 56125637 56125684 1.000000e-07 69.4
36 TraesCS4A01G240300 chr5B 95.349 43 2 0 4687 4729 1739568 1739526 1.000000e-07 69.4
37 TraesCS4A01G240300 chr5A 95.349 43 2 0 4687 4729 10906 10864 1.000000e-07 69.4
38 TraesCS4A01G240300 chr2B 97.368 38 0 1 796 832 794385015 794384978 4.660000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G240300 chr4A 549878176 549883741 5565 True 10279.000000 10279 100.000000 1 5566 1 chr4A.!!$R3 5565
1 TraesCS4A01G240300 chr4A 277893080 277893693 613 True 721.000000 721 88.065000 1 611 1 chr4A.!!$R2 610
2 TraesCS4A01G240300 chr4D 47849932 47854161 4229 False 2066.333333 2922 93.535000 926 5183 3 chr4D.!!$F2 4257
3 TraesCS4A01G240300 chr4B 70252746 70257599 4853 False 1042.850000 2538 94.203667 926 5559 6 chr4B.!!$F2 4633
4 TraesCS4A01G240300 chr7A 520792368 520793260 892 True 1426.000000 1426 95.754000 1 880 1 chr7A.!!$R2 879
5 TraesCS4A01G240300 chr3D 608308136 608309014 878 False 1410.000000 1410 95.909000 1 864 1 chr3D.!!$F1 863
6 TraesCS4A01G240300 chr1A 259200599 259201213 614 False 756.000000 756 89.103000 1 611 1 chr1A.!!$F1 610
7 TraesCS4A01G240300 chr6A 507140839 507144567 3728 False 370.000000 442 88.167500 1 611 2 chr6A.!!$F1 610

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
992 4141 0.736325 TCGCTTCGCTTAGCACTTCC 60.736 55.000 4.7 0.0 41.28 3.46 F
2291 5670 0.304705 CGCCCACGAAATAGACATGC 59.695 55.000 0.0 0.0 43.93 4.06 F
2293 5672 1.331756 GCCCACGAAATAGACATGCAG 59.668 52.381 0.0 0.0 0.00 4.41 F
3188 6582 1.569548 TCTCCAATCTACTCCCTCCGT 59.430 52.381 0.0 0.0 0.00 4.69 F
3263 6657 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.0 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 6090 0.038166 ATGACAACCGTGGATGGCTT 59.962 50.0 3.51 0.0 0.0 4.35 R
3244 6638 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.0 0.00 0.0 0.0 2.74 R
3246 6640 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.0 0.00 0.0 0.0 4.37 R
4436 7836 0.535335 CTACACTAAGGGCCGCTTCA 59.465 55.0 9.46 0.0 0.0 3.02 R
5212 8635 0.034337 AGCGCTAAAGTCACCCGAAA 59.966 50.0 8.99 0.0 0.0 3.46 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
503 3634 9.981114 CCAAACTAAGTTCTGTCCATTTTATTT 57.019 29.630 0.00 0.00 0.00 1.40
715 3849 9.268268 CACTTTTGAAGTACCTTTACATGTAGA 57.732 33.333 5.56 0.30 40.46 2.59
866 4015 3.241995 GCACGTGCATGCTTACTAGTAAC 60.242 47.826 34.52 9.21 42.62 2.50
867 4016 4.174009 CACGTGCATGCTTACTAGTAACT 58.826 43.478 20.33 0.00 0.00 2.24
868 4017 5.337554 CACGTGCATGCTTACTAGTAACTA 58.662 41.667 20.33 4.14 0.00 2.24
869 4018 5.977725 CACGTGCATGCTTACTAGTAACTAT 59.022 40.000 20.33 6.21 0.00 2.12
870 4019 7.136772 CACGTGCATGCTTACTAGTAACTATA 58.863 38.462 20.33 0.00 0.00 1.31
871 4020 7.808381 CACGTGCATGCTTACTAGTAACTATAT 59.192 37.037 20.33 1.67 0.00 0.86
872 4021 9.006839 ACGTGCATGCTTACTAGTAACTATATA 57.993 33.333 20.33 0.00 0.00 0.86
873 4022 9.836076 CGTGCATGCTTACTAGTAACTATATAA 57.164 33.333 20.33 0.00 0.00 0.98
992 4141 0.736325 TCGCTTCGCTTAGCACTTCC 60.736 55.000 4.70 0.00 41.28 3.46
1054 4203 3.966543 CCCTCGGCAAACCCACCT 61.967 66.667 0.00 0.00 0.00 4.00
1240 4389 1.132527 TCCCCTCCTTCTTCCAGTTCA 60.133 52.381 0.00 0.00 0.00 3.18
1246 4395 4.561105 CTCCTTCTTCCAGTTCAGTACAC 58.439 47.826 0.00 0.00 0.00 2.90
1382 4531 0.394938 TGACGTGGGCAAAGAAGCTA 59.605 50.000 0.00 0.00 34.17 3.32
1387 4536 3.502572 GGCAAAGAAGCTAGCCCG 58.497 61.111 12.13 0.00 41.25 6.13
1388 4537 2.115291 GGCAAAGAAGCTAGCCCGG 61.115 63.158 12.13 0.00 41.25 5.73
1389 4538 1.078426 GCAAAGAAGCTAGCCCGGA 60.078 57.895 12.13 0.00 0.00 5.14
1390 4539 1.369839 GCAAAGAAGCTAGCCCGGAC 61.370 60.000 12.13 0.00 0.00 4.79
1392 4541 2.854187 AAAGAAGCTAGCCCGGACGC 62.854 60.000 12.13 0.00 0.00 5.19
1430 4586 8.033038 AGATATTTTGATCATGCATTATGTGGC 58.967 33.333 0.00 0.00 38.01 5.01
1437 4593 4.361420 TCATGCATTATGTGGCAATTTCG 58.639 39.130 0.00 0.00 44.20 3.46
1444 4600 5.888691 TTATGTGGCAATTTCGCTTAAGA 57.111 34.783 6.67 0.00 0.00 2.10
1493 4649 7.830739 ACTGGAATTTTACTTAGGAATTGCTG 58.169 34.615 10.10 0.00 36.68 4.41
1633 4974 3.769739 TGCACTCATGTTTCAGTACCT 57.230 42.857 0.00 0.00 0.00 3.08
1642 4983 6.173339 TCATGTTTCAGTACCTCAAGGAATC 58.827 40.000 2.30 0.00 38.94 2.52
1654 4995 6.784031 ACCTCAAGGAATCTGTTGAATTAGT 58.216 36.000 2.30 0.00 38.94 2.24
1730 5071 5.992217 GCATTCCGTTCTAATTGATCCTACT 59.008 40.000 0.00 0.00 0.00 2.57
1733 5074 8.893727 CATTCCGTTCTAATTGATCCTACTTTT 58.106 33.333 0.00 0.00 0.00 2.27
1808 5149 1.064685 GGTCCGAATTTGAGATGGGGT 60.065 52.381 0.00 0.00 0.00 4.95
1883 5224 7.520798 TGATGGTATTTCTGCTAATTCCAGAT 58.479 34.615 8.92 0.44 38.04 2.90
1887 5228 6.995091 GGTATTTCTGCTAATTCCAGATCAGT 59.005 38.462 8.92 0.00 38.95 3.41
1929 5306 6.533730 ACTTAGACCAATGAATGTGACAAGA 58.466 36.000 0.00 0.00 0.00 3.02
1930 5307 6.428159 ACTTAGACCAATGAATGTGACAAGAC 59.572 38.462 0.00 0.00 0.00 3.01
1990 5367 1.997874 CCTGGGGTGGGAGGAAGAG 60.998 68.421 0.00 0.00 0.00 2.85
2028 5405 9.965902 CAGGGATTATATCTTGGCTAGTTTATT 57.034 33.333 0.00 0.00 0.00 1.40
2060 5437 5.440207 TGGATCATCCATATGGGTACATG 57.560 43.478 21.78 16.69 42.67 3.21
2061 5438 4.227982 TGGATCATCCATATGGGTACATGG 59.772 45.833 21.78 2.32 42.67 3.66
2062 5439 4.228210 GGATCATCCATATGGGTACATGGT 59.772 45.833 21.78 13.62 42.07 3.55
2063 5440 4.639078 TCATCCATATGGGTACATGGTG 57.361 45.455 21.78 0.79 42.07 4.17
2064 5441 3.980022 TCATCCATATGGGTACATGGTGT 59.020 43.478 21.78 0.00 42.07 4.16
2065 5442 4.415179 TCATCCATATGGGTACATGGTGTT 59.585 41.667 21.78 0.00 42.07 3.32
2066 5443 5.608860 TCATCCATATGGGTACATGGTGTTA 59.391 40.000 21.78 0.00 42.07 2.41
2067 5444 5.298989 TCCATATGGGTACATGGTGTTAC 57.701 43.478 21.78 0.00 42.07 2.50
2068 5445 4.972568 TCCATATGGGTACATGGTGTTACT 59.027 41.667 21.78 0.00 42.07 2.24
2069 5446 5.430417 TCCATATGGGTACATGGTGTTACTT 59.570 40.000 21.78 0.00 42.07 2.24
2070 5447 6.616137 TCCATATGGGTACATGGTGTTACTTA 59.384 38.462 21.78 0.00 42.07 2.24
2131 5508 4.536765 CACCTTCCCTAGCAAACCATATT 58.463 43.478 0.00 0.00 0.00 1.28
2246 5625 5.755042 GGATGATTCCTAGCTTGGTGCTTG 61.755 50.000 14.12 0.00 43.63 4.01
2278 5657 2.690778 GCATTGACCTGACGCCCAC 61.691 63.158 0.00 0.00 0.00 4.61
2290 5669 1.593006 GACGCCCACGAAATAGACATG 59.407 52.381 0.00 0.00 43.93 3.21
2291 5670 0.304705 CGCCCACGAAATAGACATGC 59.695 55.000 0.00 0.00 43.93 4.06
2292 5671 1.378531 GCCCACGAAATAGACATGCA 58.621 50.000 0.00 0.00 0.00 3.96
2293 5672 1.331756 GCCCACGAAATAGACATGCAG 59.668 52.381 0.00 0.00 0.00 4.41
2294 5673 2.905075 CCCACGAAATAGACATGCAGA 58.095 47.619 0.00 0.00 0.00 4.26
2483 5867 8.959548 TGATATATCTTTGTGCAGTTGATTTGT 58.040 29.630 13.79 0.00 0.00 2.83
2557 5941 8.678593 AGCCCTACTACTTCTTAATTATTTGC 57.321 34.615 0.00 0.00 0.00 3.68
2566 5950 6.378848 ACTTCTTAATTATTTGCGGGGCTTTA 59.621 34.615 0.00 0.00 0.00 1.85
2576 5960 3.275999 TGCGGGGCTTTATTTTAGAGAC 58.724 45.455 0.00 0.00 0.00 3.36
2600 5984 3.452627 TGTGGGGCTTATGTTTGTTTGTT 59.547 39.130 0.00 0.00 0.00 2.83
2701 6085 4.318332 TCATTGCACCTCTAACAACAGAG 58.682 43.478 0.00 0.00 41.54 3.35
2703 6087 3.667497 TGCACCTCTAACAACAGAGAG 57.333 47.619 1.71 0.00 44.11 3.20
2704 6088 3.230976 TGCACCTCTAACAACAGAGAGA 58.769 45.455 1.71 0.00 44.11 3.10
2706 6090 5.016831 TGCACCTCTAACAACAGAGAGATA 58.983 41.667 1.71 0.00 44.11 1.98
2707 6091 5.480422 TGCACCTCTAACAACAGAGAGATAA 59.520 40.000 1.71 0.00 44.11 1.75
2708 6092 6.039616 GCACCTCTAACAACAGAGAGATAAG 58.960 44.000 1.71 0.00 44.11 1.73
2734 6127 2.031157 CCACGGTTGTCATGTTTCTTCC 60.031 50.000 0.00 0.00 0.00 3.46
2745 6138 9.753674 TTGTCATGTTTCTTCCCTCTATATTTT 57.246 29.630 0.00 0.00 0.00 1.82
2789 6182 7.915397 GCGACCAGATGTTAAATATGAACATTT 59.085 33.333 14.37 8.54 45.33 2.32
2833 6226 7.531857 TCTTCTCTTGATACTGTCACTTCTT 57.468 36.000 0.00 0.00 36.32 2.52
2836 6229 7.531857 TCTCTTGATACTGTCACTTCTTCTT 57.468 36.000 0.00 0.00 36.32 2.52
2979 6372 6.441088 ACAGGCTCCCCTTTAAGATTATAG 57.559 41.667 0.00 0.00 40.33 1.31
3005 6398 9.612620 GTAATAAACAAATCACTGTCTTCAAGG 57.387 33.333 0.00 0.00 0.00 3.61
3043 6436 5.217895 TCCTGATTATATCGATCGTCACG 57.782 43.478 15.94 4.63 0.00 4.35
3056 6449 4.026886 CGATCGTCACGAAATTGCTGATAA 60.027 41.667 2.76 0.00 39.99 1.75
3120 6514 3.078837 AGTTTGGTGCCCTTATTGTACG 58.921 45.455 0.00 0.00 0.00 3.67
3127 6521 2.038689 TGCCCTTATTGTACGAACACCA 59.961 45.455 0.00 0.00 34.61 4.17
3172 6566 8.457238 AAAAATAACCTAGCTGATTGATCTCC 57.543 34.615 0.00 0.00 0.00 3.71
3186 6580 3.850752 TGATCTCCAATCTACTCCCTCC 58.149 50.000 0.00 0.00 0.00 4.30
3187 6581 2.366640 TCTCCAATCTACTCCCTCCG 57.633 55.000 0.00 0.00 0.00 4.63
3188 6582 1.569548 TCTCCAATCTACTCCCTCCGT 59.430 52.381 0.00 0.00 0.00 4.69
3189 6583 1.957877 CTCCAATCTACTCCCTCCGTC 59.042 57.143 0.00 0.00 0.00 4.79
3190 6584 1.569548 TCCAATCTACTCCCTCCGTCT 59.430 52.381 0.00 0.00 0.00 4.18
3191 6585 1.957877 CCAATCTACTCCCTCCGTCTC 59.042 57.143 0.00 0.00 0.00 3.36
3192 6586 2.656002 CAATCTACTCCCTCCGTCTCA 58.344 52.381 0.00 0.00 0.00 3.27
3193 6587 3.226777 CAATCTACTCCCTCCGTCTCAT 58.773 50.000 0.00 0.00 0.00 2.90
3194 6588 4.399219 CAATCTACTCCCTCCGTCTCATA 58.601 47.826 0.00 0.00 0.00 2.15
3195 6589 4.726035 ATCTACTCCCTCCGTCTCATAA 57.274 45.455 0.00 0.00 0.00 1.90
3196 6590 4.726035 TCTACTCCCTCCGTCTCATAAT 57.274 45.455 0.00 0.00 0.00 1.28
3197 6591 4.399219 TCTACTCCCTCCGTCTCATAATG 58.601 47.826 0.00 0.00 0.00 1.90
3198 6592 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
3199 6593 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
3200 6594 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
3201 6595 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
3202 6596 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
3203 6597 4.583489 TCCCTCCGTCTCATAATGTAAGAC 59.417 45.833 0.00 0.00 36.82 3.01
3254 6648 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
3255 6649 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
3256 6650 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
3257 6651 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3258 6652 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3259 6653 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3260 6654 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3261 6655 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3262 6656 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3263 6657 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
3358 6752 4.735822 GTGAGAGCATACGAGTATGTTGAC 59.264 45.833 20.33 12.62 43.57 3.18
3440 6834 7.448748 ACAAATTATCCAGTGTGGTAAGTTC 57.551 36.000 0.00 0.00 39.03 3.01
3488 6882 7.147897 ACACAATTACTCGTTCCTCAGATATGA 60.148 37.037 0.00 0.00 0.00 2.15
3536 6930 7.444487 AGGAAAAGTTAAAGCTGTCGAAGTATT 59.556 33.333 0.00 0.00 0.00 1.89
3563 6957 4.149511 TGGACATTCTGTTCTTGTCACA 57.850 40.909 4.85 0.00 41.17 3.58
3565 6959 4.756642 TGGACATTCTGTTCTTGTCACATC 59.243 41.667 4.85 0.00 41.17 3.06
4130 7530 6.430925 TCAGCTAAATAATGAAGCAACACTGT 59.569 34.615 0.00 0.00 38.75 3.55
4200 7600 6.018913 GCATCATAGGCTGAATCTATCGAATG 60.019 42.308 0.00 0.00 37.44 2.67
4215 7615 3.937814 TCGAATGAAAAGGCTGCTTCTA 58.062 40.909 0.00 0.00 0.00 2.10
4436 7836 2.806434 TGCTGCAGGATGGTAAACATT 58.194 42.857 17.12 0.00 40.72 2.71
4662 8062 7.328737 ACTACTCCGTATGTTAAAAGCTTGAT 58.671 34.615 0.00 0.00 0.00 2.57
4664 8064 5.354234 ACTCCGTATGTTAAAAGCTTGATGG 59.646 40.000 0.00 0.00 0.00 3.51
4838 8261 4.911514 TTTGGGAGTTGTGAAAGCTAAC 57.088 40.909 0.00 0.00 0.00 2.34
4840 8263 4.164843 TGGGAGTTGTGAAAGCTAACTT 57.835 40.909 0.54 0.00 34.99 2.66
4852 8275 5.585445 TGAAAGCTAACTTGGTACGTTTTGA 59.415 36.000 0.00 0.00 35.85 2.69
4906 8329 6.622549 TGTTTAACCAAGTTTAAGTGTGGTG 58.377 36.000 6.75 0.00 43.62 4.17
4907 8330 5.838531 TTAACCAAGTTTAAGTGTGGTGG 57.161 39.130 6.75 0.00 43.62 4.61
4908 8331 3.375647 ACCAAGTTTAAGTGTGGTGGT 57.624 42.857 5.50 0.00 42.79 4.16
4910 8333 4.857679 ACCAAGTTTAAGTGTGGTGGTTA 58.142 39.130 5.50 0.00 42.79 2.85
4911 8334 4.885325 ACCAAGTTTAAGTGTGGTGGTTAG 59.115 41.667 5.50 0.00 42.79 2.34
4912 8335 4.885325 CCAAGTTTAAGTGTGGTGGTTAGT 59.115 41.667 0.00 0.00 0.00 2.24
4913 8336 5.358725 CCAAGTTTAAGTGTGGTGGTTAGTT 59.641 40.000 0.00 0.00 0.00 2.24
4926 8349 8.104566 TGTGGTGGTTAGTTGCTTAACTTATAT 58.895 33.333 0.00 0.00 34.65 0.86
4927 8350 8.395633 GTGGTGGTTAGTTGCTTAACTTATATG 58.604 37.037 0.00 0.00 34.65 1.78
4941 8364 4.137543 ACTTATATGCAACTAAGCCAGCC 58.862 43.478 15.06 0.00 0.00 4.85
4952 8375 0.828762 AAGCCAGCCAAACATGAGCA 60.829 50.000 0.00 0.00 0.00 4.26
4953 8376 1.080298 GCCAGCCAAACATGAGCAC 60.080 57.895 0.00 0.00 0.00 4.40
4955 8378 1.236616 CCAGCCAAACATGAGCACGA 61.237 55.000 0.00 0.00 0.00 4.35
4971 8394 2.479730 GCACGACTCGACAATGGTAGAT 60.480 50.000 5.20 0.00 0.00 1.98
5012 8435 8.306313 TCAGTACTTCCATCTATCAAAGCTTA 57.694 34.615 0.00 0.00 0.00 3.09
5118 8541 8.977412 TGTATTCAGATGGTAGTAAATCAGTCA 58.023 33.333 0.00 0.00 0.00 3.41
5132 8555 1.534235 AGTCACGAGGCAGGGTCTT 60.534 57.895 0.00 0.00 0.00 3.01
5143 8566 0.322456 CAGGGTCTTCGCCAATTCCA 60.322 55.000 0.00 0.00 0.00 3.53
5145 8568 1.843851 AGGGTCTTCGCCAATTCCATA 59.156 47.619 0.00 0.00 0.00 2.74
5146 8569 2.241176 AGGGTCTTCGCCAATTCCATAA 59.759 45.455 0.00 0.00 0.00 1.90
5147 8570 3.117512 AGGGTCTTCGCCAATTCCATAAT 60.118 43.478 0.00 0.00 0.00 1.28
5148 8571 3.636764 GGGTCTTCGCCAATTCCATAATT 59.363 43.478 0.00 0.00 35.65 1.40
5149 8572 4.825085 GGGTCTTCGCCAATTCCATAATTA 59.175 41.667 0.00 0.00 33.45 1.40
5150 8573 5.278315 GGGTCTTCGCCAATTCCATAATTAC 60.278 44.000 0.00 0.00 33.45 1.89
5153 8576 6.912591 GTCTTCGCCAATTCCATAATTACTTG 59.087 38.462 0.00 0.00 33.45 3.16
5157 8580 7.607250 TCGCCAATTCCATAATTACTTGTTTT 58.393 30.769 0.00 0.00 33.45 2.43
5175 8598 3.306917 TTTAGTTGATGTCTTCGCCGA 57.693 42.857 0.00 0.00 0.00 5.54
5183 8606 3.824443 TGATGTCTTCGCCGATTCCTATA 59.176 43.478 0.00 0.00 0.00 1.31
5184 8607 3.637998 TGTCTTCGCCGATTCCTATAC 57.362 47.619 0.00 0.00 0.00 1.47
5185 8608 2.953648 TGTCTTCGCCGATTCCTATACA 59.046 45.455 0.00 0.00 0.00 2.29
5186 8609 3.004419 TGTCTTCGCCGATTCCTATACAG 59.996 47.826 0.00 0.00 0.00 2.74
5187 8610 3.004524 GTCTTCGCCGATTCCTATACAGT 59.995 47.826 0.00 0.00 0.00 3.55
5188 8611 3.004419 TCTTCGCCGATTCCTATACAGTG 59.996 47.826 0.00 0.00 0.00 3.66
5189 8612 2.578786 TCGCCGATTCCTATACAGTGA 58.421 47.619 0.00 0.00 0.00 3.41
5190 8613 2.292569 TCGCCGATTCCTATACAGTGAC 59.707 50.000 0.00 0.00 0.00 3.67
5191 8614 2.293677 CGCCGATTCCTATACAGTGACT 59.706 50.000 0.00 0.00 0.00 3.41
5192 8615 3.501062 CGCCGATTCCTATACAGTGACTA 59.499 47.826 0.00 0.00 0.00 2.59
5193 8616 4.156190 CGCCGATTCCTATACAGTGACTAT 59.844 45.833 0.00 0.00 0.00 2.12
5194 8617 5.353400 CGCCGATTCCTATACAGTGACTATA 59.647 44.000 0.00 0.00 0.00 1.31
5195 8618 6.457122 CGCCGATTCCTATACAGTGACTATAG 60.457 46.154 0.00 0.00 0.00 1.31
5196 8619 6.678409 GCCGATTCCTATACAGTGACTATAGC 60.678 46.154 0.00 0.00 0.00 2.97
5197 8620 6.457122 CCGATTCCTATACAGTGACTATAGCG 60.457 46.154 0.00 0.00 0.00 4.26
5198 8621 5.624344 TTCCTATACAGTGACTATAGCGC 57.376 43.478 0.00 0.00 0.00 5.92
5199 8622 4.008330 TCCTATACAGTGACTATAGCGCC 58.992 47.826 2.29 0.00 0.00 6.53
5200 8623 4.011023 CCTATACAGTGACTATAGCGCCT 58.989 47.826 2.29 0.00 0.00 5.52
5201 8624 4.459685 CCTATACAGTGACTATAGCGCCTT 59.540 45.833 2.29 0.00 0.00 4.35
5202 8625 4.939052 ATACAGTGACTATAGCGCCTTT 57.061 40.909 2.29 0.00 0.00 3.11
5203 8626 3.611766 ACAGTGACTATAGCGCCTTTT 57.388 42.857 2.29 0.00 0.00 2.27
5204 8627 3.939066 ACAGTGACTATAGCGCCTTTTT 58.061 40.909 2.29 0.00 0.00 1.94
5205 8628 5.080969 ACAGTGACTATAGCGCCTTTTTA 57.919 39.130 2.29 0.00 0.00 1.52
5206 8629 4.868734 ACAGTGACTATAGCGCCTTTTTAC 59.131 41.667 2.29 0.00 0.00 2.01
5207 8630 4.270325 CAGTGACTATAGCGCCTTTTTACC 59.730 45.833 2.29 0.00 0.00 2.85
5208 8631 4.161754 AGTGACTATAGCGCCTTTTTACCT 59.838 41.667 2.29 0.00 0.00 3.08
5209 8632 4.874396 GTGACTATAGCGCCTTTTTACCTT 59.126 41.667 2.29 0.00 0.00 3.50
5210 8633 5.353400 GTGACTATAGCGCCTTTTTACCTTT 59.647 40.000 2.29 0.00 0.00 3.11
5211 8634 5.941647 TGACTATAGCGCCTTTTTACCTTTT 59.058 36.000 2.29 0.00 0.00 2.27
5212 8635 6.431852 TGACTATAGCGCCTTTTTACCTTTTT 59.568 34.615 2.29 0.00 0.00 1.94
5230 8653 0.869730 TTTTCGGGTGACTTTAGCGC 59.130 50.000 0.00 0.00 0.00 5.92
5231 8654 0.034337 TTTCGGGTGACTTTAGCGCT 59.966 50.000 17.26 17.26 0.00 5.92
5232 8655 0.669318 TTCGGGTGACTTTAGCGCTG 60.669 55.000 22.90 5.81 0.00 5.18
5233 8656 1.374252 CGGGTGACTTTAGCGCTGT 60.374 57.895 22.90 9.85 0.00 4.40
5234 8657 0.949105 CGGGTGACTTTAGCGCTGTT 60.949 55.000 22.90 0.00 0.00 3.16
5235 8658 1.670674 CGGGTGACTTTAGCGCTGTTA 60.671 52.381 22.90 3.02 0.00 2.41
5236 8659 2.419667 GGGTGACTTTAGCGCTGTTAA 58.580 47.619 22.90 10.61 0.00 2.01
5237 8660 2.809696 GGGTGACTTTAGCGCTGTTAAA 59.190 45.455 22.90 12.09 0.00 1.52
5238 8661 3.251487 GGGTGACTTTAGCGCTGTTAAAA 59.749 43.478 22.90 11.69 0.00 1.52
5246 8847 1.136690 GCGCTGTTAAAAGGCAAACC 58.863 50.000 0.00 0.00 0.00 3.27
5250 8851 3.365565 CGCTGTTAAAAGGCAAACCGTAT 60.366 43.478 0.00 0.00 42.76 3.06
5251 8852 4.552355 GCTGTTAAAAGGCAAACCGTATT 58.448 39.130 0.00 0.00 42.76 1.89
5253 8854 6.151004 GCTGTTAAAAGGCAAACCGTATTAA 58.849 36.000 0.00 0.00 42.76 1.40
5258 8859 3.067684 AGGCAAACCGTATTAAGCACT 57.932 42.857 0.00 0.00 42.76 4.40
5263 8864 4.083484 GCAAACCGTATTAAGCACTCAACT 60.083 41.667 0.00 0.00 0.00 3.16
5265 8866 3.508762 ACCGTATTAAGCACTCAACTCG 58.491 45.455 0.00 0.00 0.00 4.18
5282 8883 2.469516 CGTGATAAAGTGGGCCGGC 61.470 63.158 21.18 21.18 0.00 6.13
5293 8894 2.759560 GGCCGGCCCATGAACATT 60.760 61.111 36.64 0.00 0.00 2.71
5299 8900 0.173255 GGCCCATGAACATTGAACCG 59.827 55.000 0.00 0.00 0.00 4.44
5303 8904 3.801983 GCCCATGAACATTGAACCGTTTT 60.802 43.478 0.00 0.00 0.00 2.43
5320 8921 4.380382 CCGTTTTTGGTTTTGTGTATAGCG 59.620 41.667 0.00 0.00 0.00 4.26
5561 9169 8.614469 TTTTCAAATTCACAAACTTGTTTCCT 57.386 26.923 0.00 0.00 39.91 3.36
5562 9170 7.593875 TTCAAATTCACAAACTTGTTTCCTG 57.406 32.000 0.00 0.00 39.91 3.86
5563 9171 6.929625 TCAAATTCACAAACTTGTTTCCTGA 58.070 32.000 0.00 0.00 39.91 3.86
5564 9172 7.382110 TCAAATTCACAAACTTGTTTCCTGAA 58.618 30.769 13.65 13.65 39.91 3.02
5565 9173 7.545265 TCAAATTCACAAACTTGTTTCCTGAAG 59.455 33.333 15.29 0.00 39.91 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
785 3934 9.034544 GTGAGAATTAACATGCAGTTTCTTTTT 57.965 29.630 6.82 0.00 41.64 1.94
829 3978 3.616821 GCACGTGCAAATGTACATCTAGA 59.383 43.478 34.52 0.00 41.59 2.43
911 4060 0.383949 GAAGCGTCTGCCACCAAAAA 59.616 50.000 0.00 0.00 44.31 1.94
912 4061 0.465460 AGAAGCGTCTGCCACCAAAA 60.465 50.000 0.00 0.00 44.31 2.44
913 4062 0.884704 GAGAAGCGTCTGCCACCAAA 60.885 55.000 6.97 0.00 44.31 3.28
914 4063 1.301716 GAGAAGCGTCTGCCACCAA 60.302 57.895 6.97 0.00 44.31 3.67
915 4064 2.210013 AGAGAAGCGTCTGCCACCA 61.210 57.895 6.97 0.00 44.31 4.17
916 4065 1.739562 CAGAGAAGCGTCTGCCACC 60.740 63.158 6.97 0.00 44.31 4.61
917 4066 1.739562 CCAGAGAAGCGTCTGCCAC 60.740 63.158 6.97 0.00 42.40 5.01
918 4067 2.659016 CCAGAGAAGCGTCTGCCA 59.341 61.111 6.97 0.00 42.40 4.92
919 4068 2.817396 GCCAGAGAAGCGTCTGCC 60.817 66.667 6.97 0.00 42.40 4.85
920 4069 2.817396 GGCCAGAGAAGCGTCTGC 60.817 66.667 6.97 4.30 42.40 4.26
921 4070 2.507992 CGGCCAGAGAAGCGTCTG 60.508 66.667 6.97 6.84 43.23 3.51
922 4071 2.992114 ACGGCCAGAGAAGCGTCT 60.992 61.111 0.31 0.31 36.55 4.18
923 4072 2.507324 GACGGCCAGAGAAGCGTC 60.507 66.667 2.24 0.00 0.00 5.19
924 4073 4.421479 CGACGGCCAGAGAAGCGT 62.421 66.667 2.24 0.00 0.00 5.07
992 4141 1.747709 CAAGGAGACCATCAAGGCAG 58.252 55.000 0.00 0.00 43.14 4.85
1062 4211 3.452786 CGCAGCGAGGAGGAGGAA 61.453 66.667 9.98 0.00 0.00 3.36
1066 4215 3.443925 CAGTCGCAGCGAGGAGGA 61.444 66.667 20.23 0.00 36.23 3.71
1240 4389 0.040794 AAGGAGTAGGGGCGTGTACT 59.959 55.000 0.00 0.00 31.97 2.73
1246 4395 1.619332 GAGGAATAAGGAGTAGGGGCG 59.381 57.143 0.00 0.00 0.00 6.13
1322 4471 3.733988 GCATTCCGTCGAACATCTAGTCA 60.734 47.826 0.00 0.00 0.00 3.41
1386 4535 0.111001 CTAAAAACACCACGCGTCCG 60.111 55.000 9.86 4.75 41.14 4.79
1387 4536 1.219646 TCTAAAAACACCACGCGTCC 58.780 50.000 9.86 0.00 0.00 4.79
1388 4537 4.852609 ATATCTAAAAACACCACGCGTC 57.147 40.909 9.86 0.00 0.00 5.19
1389 4538 5.616488 AAATATCTAAAAACACCACGCGT 57.384 34.783 5.58 5.58 0.00 6.01
1390 4539 6.081049 TCAAAATATCTAAAAACACCACGCG 58.919 36.000 3.53 3.53 0.00 6.01
1392 4541 9.787532 ATGATCAAAATATCTAAAAACACCACG 57.212 29.630 0.00 0.00 0.00 4.94
1394 4543 9.585099 GCATGATCAAAATATCTAAAAACACCA 57.415 29.630 0.00 0.00 0.00 4.17
1427 4583 3.673052 GCACATCTTAAGCGAAATTGCCA 60.673 43.478 0.00 0.00 34.65 4.92
1430 4586 4.726416 ACAGCACATCTTAAGCGAAATTG 58.274 39.130 0.00 0.00 0.00 2.32
1437 4593 2.221981 GCGGATACAGCACATCTTAAGC 59.778 50.000 0.00 0.00 36.37 3.09
1444 4600 2.031870 TCAGTAGCGGATACAGCACAT 58.968 47.619 6.16 0.00 36.79 3.21
1544 4700 7.976734 ACACTCTATTCTGCAGTACTGAATAAC 59.023 37.037 27.08 8.71 44.07 1.89
1671 5012 8.528044 AAAGTGGAAACCAACAGACTTAAATA 57.472 30.769 0.00 0.00 34.18 1.40
1672 5013 7.418337 AAAGTGGAAACCAACAGACTTAAAT 57.582 32.000 0.00 0.00 34.18 1.40
1733 5074 7.689299 TCCTTCATGGACATTCTAGAAGAAAA 58.311 34.615 11.53 0.00 40.56 2.29
1737 5078 6.648192 AGTTCCTTCATGGACATTCTAGAAG 58.352 40.000 11.53 5.93 46.14 2.85
1738 5079 6.352222 GGAGTTCCTTCATGGACATTCTAGAA 60.352 42.308 7.82 7.82 46.14 2.10
1739 5080 5.129485 GGAGTTCCTTCATGGACATTCTAGA 59.871 44.000 0.00 0.00 46.14 2.43
1740 5081 5.130145 AGGAGTTCCTTCATGGACATTCTAG 59.870 44.000 0.00 0.00 46.09 2.43
1903 5244 5.863965 TGTCACATTCATTGGTCTAAGTCA 58.136 37.500 0.00 0.00 0.00 3.41
1929 5306 1.003051 CCTAGGCTGTACCCCCAGT 59.997 63.158 0.00 0.00 40.58 4.00
1930 5307 0.326238 TTCCTAGGCTGTACCCCCAG 60.326 60.000 2.96 0.00 40.58 4.45
1960 5337 2.275418 CCCAGGTACCATGGCCAC 59.725 66.667 8.16 10.24 36.43 5.01
1990 5367 0.322546 AATCCCTGTCCGCAACCTTC 60.323 55.000 0.00 0.00 0.00 3.46
2054 5431 9.924650 CTTCCCTATATAAGTAACACCATGTAC 57.075 37.037 0.00 0.00 0.00 2.90
2055 5432 9.886337 TCTTCCCTATATAAGTAACACCATGTA 57.114 33.333 0.00 0.00 0.00 2.29
2056 5433 8.792830 TCTTCCCTATATAAGTAACACCATGT 57.207 34.615 0.00 0.00 0.00 3.21
2059 5436 9.442062 TGAATCTTCCCTATATAAGTAACACCA 57.558 33.333 0.00 0.00 0.00 4.17
2060 5437 9.930693 CTGAATCTTCCCTATATAAGTAACACC 57.069 37.037 0.00 0.00 0.00 4.16
2061 5438 9.425577 GCTGAATCTTCCCTATATAAGTAACAC 57.574 37.037 0.00 0.00 0.00 3.32
2062 5439 9.381038 AGCTGAATCTTCCCTATATAAGTAACA 57.619 33.333 0.00 0.00 0.00 2.41
2065 5442 9.601810 TCAAGCTGAATCTTCCCTATATAAGTA 57.398 33.333 0.00 0.00 0.00 2.24
2066 5443 8.497910 TCAAGCTGAATCTTCCCTATATAAGT 57.502 34.615 0.00 0.00 0.00 2.24
2067 5444 9.381033 CATCAAGCTGAATCTTCCCTATATAAG 57.619 37.037 0.00 0.00 0.00 1.73
2068 5445 7.826252 GCATCAAGCTGAATCTTCCCTATATAA 59.174 37.037 0.00 0.00 41.15 0.98
2069 5446 7.334090 GCATCAAGCTGAATCTTCCCTATATA 58.666 38.462 0.00 0.00 41.15 0.86
2070 5447 6.179040 GCATCAAGCTGAATCTTCCCTATAT 58.821 40.000 0.00 0.00 41.15 0.86
2131 5508 7.577303 AGTGATAGGCTTGAATGGAAGATAAA 58.423 34.615 0.00 0.00 0.00 1.40
2246 5625 4.996434 ATGCCCGATAGCGCAGGC 62.996 66.667 11.47 12.90 42.74 4.85
2278 5657 4.604843 TTTGCTCTGCATGTCTATTTCG 57.395 40.909 0.00 0.00 38.76 3.46
2290 5669 7.273659 CGTTAGTTTTGTTTTATTTGCTCTGC 58.726 34.615 0.00 0.00 0.00 4.26
2291 5670 7.043722 TGCGTTAGTTTTGTTTTATTTGCTCTG 60.044 33.333 0.00 0.00 0.00 3.35
2292 5671 6.975772 TGCGTTAGTTTTGTTTTATTTGCTCT 59.024 30.769 0.00 0.00 0.00 4.09
2293 5672 7.155858 TGCGTTAGTTTTGTTTTATTTGCTC 57.844 32.000 0.00 0.00 0.00 4.26
2294 5673 7.707774 ATGCGTTAGTTTTGTTTTATTTGCT 57.292 28.000 0.00 0.00 0.00 3.91
2483 5867 4.097741 GTGTCCATGCAATGTTATAAGCCA 59.902 41.667 0.00 0.00 44.81 4.75
2543 5927 5.669164 AAAGCCCCGCAAATAATTAAGAA 57.331 34.783 0.00 0.00 0.00 2.52
2552 5936 4.953579 TCTCTAAAATAAAGCCCCGCAAAT 59.046 37.500 0.00 0.00 0.00 2.32
2555 5939 3.054655 AGTCTCTAAAATAAAGCCCCGCA 60.055 43.478 0.00 0.00 0.00 5.69
2556 5940 3.542648 AGTCTCTAAAATAAAGCCCCGC 58.457 45.455 0.00 0.00 0.00 6.13
2557 5941 4.941873 ACAAGTCTCTAAAATAAAGCCCCG 59.058 41.667 0.00 0.00 0.00 5.73
2566 5950 4.388577 AAGCCCCACAAGTCTCTAAAAT 57.611 40.909 0.00 0.00 0.00 1.82
2576 5960 4.057432 CAAACAAACATAAGCCCCACAAG 58.943 43.478 0.00 0.00 0.00 3.16
2600 5984 4.937696 ACATATTGTTTCACGAATGCGA 57.062 36.364 0.00 0.00 41.64 5.10
2638 6022 8.265055 AGCAATTACCTAGTAGCAGTTTCATTA 58.735 33.333 0.00 0.00 0.00 1.90
2701 6085 2.213499 CAACCGTGGATGGCTTATCTC 58.787 52.381 0.00 0.00 36.03 2.75
2703 6087 1.940613 GACAACCGTGGATGGCTTATC 59.059 52.381 1.07 0.00 34.93 1.75
2704 6088 1.280710 TGACAACCGTGGATGGCTTAT 59.719 47.619 3.51 0.00 0.00 1.73
2706 6090 0.038166 ATGACAACCGTGGATGGCTT 59.962 50.000 3.51 0.00 0.00 4.35
2707 6091 0.677731 CATGACAACCGTGGATGGCT 60.678 55.000 3.51 0.00 0.00 4.75
2708 6092 0.960364 ACATGACAACCGTGGATGGC 60.960 55.000 0.00 0.00 36.10 4.40
2745 6138 5.097529 GGTCGCGATTATGACCGATTAATA 58.902 41.667 14.06 0.00 44.68 0.98
2763 6156 6.358118 TGTTCATATTTAACATCTGGTCGC 57.642 37.500 0.00 0.00 32.07 5.19
2812 6205 7.531857 AAGAAGAAGTGACAGTATCAAGAGA 57.468 36.000 0.00 0.00 39.72 3.10
2979 6372 9.612620 CCTTGAAGACAGTGATTTGTTTATTAC 57.387 33.333 0.00 0.00 0.00 1.89
3172 6566 2.656002 TGAGACGGAGGGAGTAGATTG 58.344 52.381 0.00 0.00 0.00 2.67
3181 6575 4.872664 GTCTTACATTATGAGACGGAGGG 58.127 47.826 0.00 0.00 34.53 4.30
3229 6623 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
3230 6624 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
3231 6625 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
3232 6626 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
3233 6627 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
3235 6629 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
3236 6630 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3237 6631 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3238 6632 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3239 6633 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3240 6634 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3241 6635 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3242 6636 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3243 6637 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3244 6638 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3245 6639 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
3246 6640 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
3247 6641 2.378378 AATAGTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
3248 6642 4.405036 AGAAAAATAGTACTCCCTCCGTCC 59.595 45.833 0.00 0.00 0.00 4.79
3249 6643 5.595257 AGAAAAATAGTACTCCCTCCGTC 57.405 43.478 0.00 0.00 0.00 4.79
3250 6644 5.731591 CAAGAAAAATAGTACTCCCTCCGT 58.268 41.667 0.00 0.00 0.00 4.69
3251 6645 4.571176 GCAAGAAAAATAGTACTCCCTCCG 59.429 45.833 0.00 0.00 0.00 4.63
3252 6646 5.746284 AGCAAGAAAAATAGTACTCCCTCC 58.254 41.667 0.00 0.00 0.00 4.30
3253 6647 8.258708 TCTAAGCAAGAAAAATAGTACTCCCTC 58.741 37.037 0.00 0.00 0.00 4.30
3254 6648 8.147244 TCTAAGCAAGAAAAATAGTACTCCCT 57.853 34.615 0.00 0.00 0.00 4.20
3255 6649 8.788325 TTCTAAGCAAGAAAAATAGTACTCCC 57.212 34.615 0.00 0.00 41.35 4.30
3256 6650 9.654663 TCTTCTAAGCAAGAAAAATAGTACTCC 57.345 33.333 0.00 0.00 43.66 3.85
3358 6752 5.106555 ACTGCAAAGAATATCTTCAACACCG 60.107 40.000 0.00 0.00 35.27 4.94
3440 6834 7.495606 TGTGTACATATGTATCAAGAAAGCTGG 59.504 37.037 18.27 0.00 32.54 4.85
3488 6882 7.466804 TCCTCAATCAACTGGTACCTAAAAAT 58.533 34.615 14.36 0.00 0.00 1.82
3563 6957 9.968870 GAAAAACTGAGATAGATTAGTACCGAT 57.031 33.333 0.00 0.00 0.00 4.18
3565 6959 8.414778 AGGAAAAACTGAGATAGATTAGTACCG 58.585 37.037 0.00 0.00 0.00 4.02
3658 7052 8.009622 TGAAGCTATTCATTCCATTGCATAAA 57.990 30.769 0.00 0.00 40.54 1.40
3848 7248 8.709386 ATTAACTAGCTCAACATGTTACTGAG 57.291 34.615 17.95 17.95 39.69 3.35
3882 7282 5.630415 ATGGCTAAACTACTGCCTATCAA 57.370 39.130 0.00 0.00 46.23 2.57
3892 7292 5.644977 AAGCTCCAAAATGGCTAAACTAC 57.355 39.130 0.00 0.00 37.47 2.73
4135 7535 9.331282 GAGAATAACCTAGCATGAAAACATAGT 57.669 33.333 0.00 0.00 0.00 2.12
4200 7600 4.702131 TCCAAGATTAGAAGCAGCCTTTTC 59.298 41.667 0.00 0.00 0.00 2.29
4215 7615 7.020827 TGATAGAAAGTCCAAGTCCAAGATT 57.979 36.000 0.00 0.00 0.00 2.40
4249 7649 2.812011 GTGAAGGTTTGCGTATTCCTGT 59.188 45.455 0.00 0.00 0.00 4.00
4379 7779 8.532977 AAACATGTCAAGTAATTTACATTGCC 57.467 30.769 0.00 2.30 30.32 4.52
4415 7815 2.284754 TGTTTACCATCCTGCAGCAA 57.715 45.000 8.66 0.00 0.00 3.91
4436 7836 0.535335 CTACACTAAGGGCCGCTTCA 59.465 55.000 9.46 0.00 0.00 3.02
4484 7884 4.706476 CACAAATCATTCTTTAGGGCCTCA 59.294 41.667 10.74 0.00 0.00 3.86
4616 8016 9.702253 AGTAGTTCATAAAGAGACAGAAGGATA 57.298 33.333 0.00 0.00 0.00 2.59
4662 8062 9.062524 GTATAATATTGTGACAATAACAGCCCA 57.937 33.333 20.49 0.00 0.00 5.36
4813 8235 2.159114 GCTTTCACAACTCCCAAAAGCA 60.159 45.455 11.95 0.00 46.84 3.91
4838 8261 3.745975 TGAGCTCATCAAAACGTACCAAG 59.254 43.478 13.74 0.00 34.02 3.61
4840 8263 3.394674 TGAGCTCATCAAAACGTACCA 57.605 42.857 13.74 0.00 34.02 3.25
4852 8275 4.515028 TTTCATCCTGGATTGAGCTCAT 57.485 40.909 19.04 7.83 0.00 2.90
4912 8335 7.338196 TGGCTTAGTTGCATATAAGTTAAGCAA 59.662 33.333 15.84 13.49 42.27 3.91
4913 8336 6.826231 TGGCTTAGTTGCATATAAGTTAAGCA 59.174 34.615 15.84 4.50 39.10 3.91
4926 8349 0.673437 GTTTGGCTGGCTTAGTTGCA 59.327 50.000 2.00 0.00 34.04 4.08
4927 8350 0.673437 TGTTTGGCTGGCTTAGTTGC 59.327 50.000 2.00 0.00 0.00 4.17
4941 8364 1.125021 GTCGAGTCGTGCTCATGTTTG 59.875 52.381 13.12 0.00 44.33 2.93
4952 8375 3.014623 TGATCTACCATTGTCGAGTCGT 58.985 45.455 13.12 0.00 0.00 4.34
4953 8376 3.692791 TGATCTACCATTGTCGAGTCG 57.307 47.619 6.09 6.09 0.00 4.18
4955 8378 5.595885 CAGAATGATCTACCATTGTCGAGT 58.404 41.667 0.00 0.00 39.69 4.18
4971 8394 5.798132 AGTACTGAAGTGAATGCAGAATGA 58.202 37.500 0.00 0.00 39.69 2.57
5012 8435 0.682209 ATTGGCGCAAAGGCTCATCT 60.682 50.000 10.83 0.00 46.88 2.90
5118 8541 4.070552 GCGAAGACCCTGCCTCGT 62.071 66.667 0.00 0.00 0.00 4.18
5132 8555 6.767524 AACAAGTAATTATGGAATTGGCGA 57.232 33.333 0.00 0.00 35.96 5.54
5145 8568 9.878599 CGAAGACATCAACTAAAACAAGTAATT 57.121 29.630 0.00 0.00 0.00 1.40
5146 8569 8.015658 GCGAAGACATCAACTAAAACAAGTAAT 58.984 33.333 0.00 0.00 0.00 1.89
5147 8570 7.349711 GCGAAGACATCAACTAAAACAAGTAA 58.650 34.615 0.00 0.00 0.00 2.24
5148 8571 6.073440 GGCGAAGACATCAACTAAAACAAGTA 60.073 38.462 0.00 0.00 31.66 2.24
5149 8572 5.277828 GGCGAAGACATCAACTAAAACAAGT 60.278 40.000 0.00 0.00 31.66 3.16
5150 8573 5.147162 GGCGAAGACATCAACTAAAACAAG 58.853 41.667 0.00 0.00 31.66 3.16
5153 8576 3.430895 TCGGCGAAGACATCAACTAAAAC 59.569 43.478 7.35 0.00 27.25 2.43
5157 8580 3.444916 GAATCGGCGAAGACATCAACTA 58.555 45.455 15.93 0.00 27.25 2.24
5164 8587 2.953648 TGTATAGGAATCGGCGAAGACA 59.046 45.455 15.93 7.89 27.25 3.41
5175 8598 5.125739 GGCGCTATAGTCACTGTATAGGAAT 59.874 44.000 7.64 0.00 32.95 3.01
5183 8606 3.611766 AAAAGGCGCTATAGTCACTGT 57.388 42.857 7.64 0.00 0.00 3.55
5184 8607 4.270325 GGTAAAAAGGCGCTATAGTCACTG 59.730 45.833 7.64 0.00 0.00 3.66
5185 8608 4.161754 AGGTAAAAAGGCGCTATAGTCACT 59.838 41.667 7.64 0.00 0.00 3.41
5186 8609 4.439968 AGGTAAAAAGGCGCTATAGTCAC 58.560 43.478 7.64 0.00 0.00 3.67
5187 8610 4.748277 AGGTAAAAAGGCGCTATAGTCA 57.252 40.909 7.64 0.00 0.00 3.41
5188 8611 6.432607 AAAAGGTAAAAAGGCGCTATAGTC 57.567 37.500 7.64 0.00 0.00 2.59
5189 8612 6.829229 AAAAAGGTAAAAAGGCGCTATAGT 57.171 33.333 7.64 0.00 0.00 2.12
5210 8633 1.264826 GCGCTAAAGTCACCCGAAAAA 59.735 47.619 0.00 0.00 0.00 1.94
5211 8634 0.869730 GCGCTAAAGTCACCCGAAAA 59.130 50.000 0.00 0.00 0.00 2.29
5212 8635 0.034337 AGCGCTAAAGTCACCCGAAA 59.966 50.000 8.99 0.00 0.00 3.46
5213 8636 0.669318 CAGCGCTAAAGTCACCCGAA 60.669 55.000 10.99 0.00 0.00 4.30
5214 8637 1.080093 CAGCGCTAAAGTCACCCGA 60.080 57.895 10.99 0.00 0.00 5.14
5215 8638 0.949105 AACAGCGCTAAAGTCACCCG 60.949 55.000 10.99 0.00 0.00 5.28
5216 8639 2.088950 TAACAGCGCTAAAGTCACCC 57.911 50.000 10.99 0.00 0.00 4.61
5217 8640 4.464112 CTTTTAACAGCGCTAAAGTCACC 58.536 43.478 10.99 0.00 0.00 4.02
5218 8641 4.464112 CCTTTTAACAGCGCTAAAGTCAC 58.536 43.478 22.43 0.00 0.00 3.67
5219 8642 3.058501 GCCTTTTAACAGCGCTAAAGTCA 60.059 43.478 22.43 0.00 0.00 3.41
5220 8643 3.058501 TGCCTTTTAACAGCGCTAAAGTC 60.059 43.478 22.43 14.48 0.00 3.01
5221 8644 2.882137 TGCCTTTTAACAGCGCTAAAGT 59.118 40.909 22.43 10.70 0.00 2.66
5222 8645 3.552604 TGCCTTTTAACAGCGCTAAAG 57.447 42.857 19.10 19.10 0.00 1.85
5223 8646 3.992260 TTGCCTTTTAACAGCGCTAAA 57.008 38.095 10.99 4.29 0.00 1.85
5224 8647 3.551250 GGTTTGCCTTTTAACAGCGCTAA 60.551 43.478 10.99 0.00 0.00 3.09
5225 8648 2.030628 GGTTTGCCTTTTAACAGCGCTA 60.031 45.455 10.99 0.00 0.00 4.26
5226 8649 1.269569 GGTTTGCCTTTTAACAGCGCT 60.270 47.619 2.64 2.64 0.00 5.92
5227 8650 1.136690 GGTTTGCCTTTTAACAGCGC 58.863 50.000 0.00 0.00 0.00 5.92
5228 8651 1.268845 ACGGTTTGCCTTTTAACAGCG 60.269 47.619 0.00 0.00 0.00 5.18
5229 8652 2.502213 ACGGTTTGCCTTTTAACAGC 57.498 45.000 0.00 0.00 0.00 4.40
5230 8653 6.307077 GCTTAATACGGTTTGCCTTTTAACAG 59.693 38.462 0.00 0.00 0.00 3.16
5231 8654 6.151004 GCTTAATACGGTTTGCCTTTTAACA 58.849 36.000 0.00 0.00 0.00 2.41
5232 8655 6.088483 GTGCTTAATACGGTTTGCCTTTTAAC 59.912 38.462 0.00 0.00 0.00 2.01
5233 8656 6.016108 AGTGCTTAATACGGTTTGCCTTTTAA 60.016 34.615 0.00 0.00 0.00 1.52
5234 8657 5.474189 AGTGCTTAATACGGTTTGCCTTTTA 59.526 36.000 0.00 0.00 0.00 1.52
5235 8658 4.279922 AGTGCTTAATACGGTTTGCCTTTT 59.720 37.500 0.00 0.00 0.00 2.27
5236 8659 3.824443 AGTGCTTAATACGGTTTGCCTTT 59.176 39.130 0.00 0.00 0.00 3.11
5237 8660 3.418047 AGTGCTTAATACGGTTTGCCTT 58.582 40.909 0.00 0.00 0.00 4.35
5238 8661 3.007635 GAGTGCTTAATACGGTTTGCCT 58.992 45.455 0.00 0.00 0.00 4.75
5246 8847 4.163552 TCACGAGTTGAGTGCTTAATACG 58.836 43.478 0.00 0.00 39.31 3.06
5250 8851 6.145534 CACTTTATCACGAGTTGAGTGCTTAA 59.854 38.462 0.00 0.00 37.77 1.85
5251 8852 5.633601 CACTTTATCACGAGTTGAGTGCTTA 59.366 40.000 0.00 0.00 37.77 3.09
5253 8854 3.990469 CACTTTATCACGAGTTGAGTGCT 59.010 43.478 0.00 0.00 37.77 4.40
5258 8859 2.614481 GGCCCACTTTATCACGAGTTGA 60.614 50.000 0.00 0.00 39.11 3.18
5263 8864 1.219664 CCGGCCCACTTTATCACGA 59.780 57.895 0.00 0.00 0.00 4.35
5265 8866 2.119029 GGCCGGCCCACTTTATCAC 61.119 63.158 36.64 4.38 0.00 3.06
5282 8883 3.658757 AAACGGTTCAATGTTCATGGG 57.341 42.857 0.00 0.00 0.00 4.00
5299 8900 6.203647 AGACGCTATACACAAAACCAAAAAC 58.796 36.000 0.00 0.00 0.00 2.43
5303 8904 4.628333 GCTAGACGCTATACACAAAACCAA 59.372 41.667 0.00 0.00 35.14 3.67
5308 8909 2.223641 CCCGCTAGACGCTATACACAAA 60.224 50.000 0.00 0.00 41.76 2.83
5315 8916 1.472728 CCAAAACCCGCTAGACGCTAT 60.473 52.381 0.00 0.00 41.76 2.97
5320 8921 1.302993 TGGCCAAAACCCGCTAGAC 60.303 57.895 0.61 0.00 0.00 2.59
5486 9094 9.814899 TCTTGCAGATTTGAAAAATGTTTAAGA 57.185 25.926 0.00 0.00 0.00 2.10
5512 9120 7.552458 AAAGTTTGCGGATTTTCAGAAAAAT 57.448 28.000 12.38 3.76 45.55 1.82


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

AutoCloner maintained by Alex Coulton.