Multiple sequence alignment - TraesCS5D01G300800

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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 TraesCS5D01G300800 chr5D 100.000 6107 0 0 1 6107 398093437 398099543 0.000000e+00 11278.0
1 TraesCS5D01G300800 chr5D 79.422 277 47 9 5481 5751 391780756 391780484 2.910000e-43 187.0
2 TraesCS5D01G300800 chr5B 93.266 2183 92 21 2519 4661 478127256 478129423 0.000000e+00 3166.0
3 TraesCS5D01G300800 chr5B 87.964 1886 130 50 700 2543 478125364 478127194 0.000000e+00 2135.0
4 TraesCS5D01G300800 chr5B 92.532 549 28 6 4739 5282 478129421 478129961 0.000000e+00 774.0
5 TraesCS5D01G300800 chr5B 90.000 350 32 3 1 349 518686558 518686905 3.360000e-122 449.0
6 TraesCS5D01G300800 chr5B 92.857 294 13 4 395 684 518686902 518687191 2.630000e-113 420.0
7 TraesCS5D01G300800 chr5B 80.727 275 47 6 5481 5751 472063018 472062746 6.200000e-50 209.0
8 TraesCS5D01G300800 chr5A 94.791 1747 43 14 2342 4072 503128953 503130667 0.000000e+00 2678.0
9 TraesCS5D01G300800 chr5A 91.382 1671 63 25 705 2344 503125432 503127052 0.000000e+00 2213.0
10 TraesCS5D01G300800 chr5A 95.455 748 18 6 4088 4822 503130757 503131501 0.000000e+00 1179.0
11 TraesCS5D01G300800 chr5A 85.378 807 81 24 5305 6105 503133287 503134062 0.000000e+00 802.0
12 TraesCS5D01G300800 chr5A 93.333 375 9 2 4914 5282 503131499 503131863 1.940000e-149 540.0
13 TraesCS5D01G300800 chr5A 89.565 115 12 0 5748 5862 503133767 503133881 4.930000e-31 147.0
14 TraesCS5D01G300800 chr3D 98.705 695 8 1 3 696 596609079 596609773 0.000000e+00 1232.0
15 TraesCS5D01G300800 chr3D 76.238 202 40 8 5548 5743 339841941 339841742 3.900000e-17 100.0
16 TraesCS5D01G300800 chr3D 75.238 210 44 6 5482 5688 142448780 142448576 6.520000e-15 93.5
17 TraesCS5D01G300800 chr2B 91.445 713 44 9 1 699 776381961 776381252 0.000000e+00 963.0
18 TraesCS5D01G300800 chr2B 91.311 702 47 6 1 699 556477454 556476764 0.000000e+00 946.0
19 TraesCS5D01G300800 chr2B 91.413 559 39 5 1 553 795628259 795628814 0.000000e+00 758.0
20 TraesCS5D01G300800 chr2B 91.429 140 6 3 557 696 795629030 795629163 2.910000e-43 187.0
21 TraesCS5D01G300800 chr2B 79.268 246 41 6 5859 6102 616935958 616936195 4.900000e-36 163.0
22 TraesCS5D01G300800 chr6B 92.166 651 39 6 1 642 34112683 34113330 0.000000e+00 909.0
23 TraesCS5D01G300800 chr6B 84.422 199 29 1 5858 6054 468253734 468253536 1.740000e-45 195.0
24 TraesCS5D01G300800 chr6B 95.161 62 3 0 1133 1194 633910368 633910429 1.400000e-16 99.0
25 TraesCS5D01G300800 chr7D 89.886 702 49 10 1 696 638033528 638034213 0.000000e+00 883.0
26 TraesCS5D01G300800 chr2D 96.078 510 19 1 1 509 13564004 13563495 0.000000e+00 830.0
27 TraesCS5D01G300800 chr2D 94.156 154 7 2 551 704 13563496 13563345 3.680000e-57 233.0
28 TraesCS5D01G300800 chr2D 81.893 243 37 6 5864 6102 352209303 352209542 1.340000e-46 198.0
29 TraesCS5D01G300800 chr2D 80.567 247 39 8 5859 6102 523124086 523124326 1.350000e-41 182.0
30 TraesCS5D01G300800 chr6D 88.011 709 62 12 1 704 85453131 85452441 0.000000e+00 817.0
31 TraesCS5D01G300800 chr6D 84.925 199 28 1 5858 6054 302580119 302579921 3.730000e-47 200.0
32 TraesCS5D01G300800 chr6D 95.312 64 3 0 1133 1196 420743187 420743250 1.080000e-17 102.0
33 TraesCS5D01G300800 chr4B 93.705 413 26 0 1 413 664174690 664175102 2.420000e-173 619.0
34 TraesCS5D01G300800 chr2A 79.284 531 85 17 3481 3994 69222111 69221589 1.260000e-91 348.0
35 TraesCS5D01G300800 chr2A 81.224 245 34 8 5864 6102 470243316 470243554 2.910000e-43 187.0
36 TraesCS5D01G300800 chr2A 80.800 125 21 3 4073 4195 47670140 47670017 1.810000e-15 95.3
37 TraesCS5D01G300800 chr7B 79.668 241 43 3 5864 6102 418733080 418732844 1.050000e-37 169.0
38 TraesCS5D01G300800 chr7B 75.472 212 45 7 5479 5688 232734935 232734729 5.040000e-16 97.1
39 TraesCS5D01G300800 chr7A 79.668 241 40 5 5864 6102 465749161 465748928 1.360000e-36 165.0
40 TraesCS5D01G300800 chr3A 80.882 136 22 4 5615 5747 730924359 730924493 3.010000e-18 104.0
41 TraesCS5D01G300800 chr3A 78.431 153 27 5 5596 5746 737666791 737666643 1.810000e-15 95.3
42 TraesCS5D01G300800 chr3A 77.222 180 27 10 5521 5690 713220334 713220509 6.520000e-15 93.5
43 TraesCS5D01G300800 chr1B 97.059 34 0 1 5479 5511 591119802 591119769 8.550000e-04 56.5
44 TraesCS5D01G300800 chr1B 100.000 30 0 0 5482 5511 591129203 591129174 8.550000e-04 56.5


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 TraesCS5D01G300800 chr5D 398093437 398099543 6106 False 11278.000000 11278 100.000000 1 6107 1 chr5D.!!$F1 6106
1 TraesCS5D01G300800 chr5B 478125364 478129961 4597 False 2025.000000 3166 91.254000 700 5282 3 chr5B.!!$F1 4582
2 TraesCS5D01G300800 chr5B 518686558 518687191 633 False 434.500000 449 91.428500 1 684 2 chr5B.!!$F2 683
3 TraesCS5D01G300800 chr5A 503125432 503134062 8630 False 1259.833333 2678 91.650667 705 6105 6 chr5A.!!$F1 5400
4 TraesCS5D01G300800 chr3D 596609079 596609773 694 False 1232.000000 1232 98.705000 3 696 1 chr3D.!!$F1 693
5 TraesCS5D01G300800 chr2B 776381252 776381961 709 True 963.000000 963 91.445000 1 699 1 chr2B.!!$R2 698
6 TraesCS5D01G300800 chr2B 556476764 556477454 690 True 946.000000 946 91.311000 1 699 1 chr2B.!!$R1 698
7 TraesCS5D01G300800 chr2B 795628259 795629163 904 False 472.500000 758 91.421000 1 696 2 chr2B.!!$F2 695
8 TraesCS5D01G300800 chr6B 34112683 34113330 647 False 909.000000 909 92.166000 1 642 1 chr6B.!!$F1 641
9 TraesCS5D01G300800 chr7D 638033528 638034213 685 False 883.000000 883 89.886000 1 696 1 chr7D.!!$F1 695
10 TraesCS5D01G300800 chr2D 13563345 13564004 659 True 531.500000 830 95.117000 1 704 2 chr2D.!!$R1 703
11 TraesCS5D01G300800 chr6D 85452441 85453131 690 True 817.000000 817 88.011000 1 704 1 chr6D.!!$R1 703
12 TraesCS5D01G300800 chr2A 69221589 69222111 522 True 348.000000 348 79.284000 3481 3994 1 chr2A.!!$R2 513

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
347 354 1.517257 GTGTCCTCGTGATGAGCGG 60.517 63.158 0.00 0.0 43.82 5.52 F
748 983 1.541439 GCGCGCGCACCTTTTTAAAA 61.541 50.000 46.11 0.0 41.49 1.52 F
1269 1538 1.140052 TGCCTCGAAAAAGGTGACAGA 59.860 47.619 0.00 0.0 38.79 3.41 F
1270 1539 1.531578 GCCTCGAAAAAGGTGACAGAC 59.468 52.381 0.00 0.0 38.79 3.51 F
1559 1833 2.107378 TGCACAACATGAAGGGGTTCTA 59.893 45.455 0.00 0.0 0.00 2.10 F
3129 5422 0.674581 TTCCACGCCTCATTGCAGAG 60.675 55.000 0.00 0.0 35.39 3.35 F
3302 5599 0.405585 TCCCTCCAAAGCTTCCCAAG 59.594 55.000 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1532 1.134128 AGGCACACATGTTGTCTGTCA 60.134 47.619 12.39 0.0 35.67 3.58 R
2404 4602 1.821332 GCACCTGCAGTATCCAGCC 60.821 63.158 13.81 0.0 41.59 4.85 R
3093 5386 1.134068 GGAATTCTTCCTCCCTTCCGG 60.134 57.143 5.23 0.0 46.57 5.14 R
3094 5387 2.333688 GGAATTCTTCCTCCCTTCCG 57.666 55.000 5.23 0.0 46.57 4.30 R
3302 5599 1.840635 ACAAGTCCTGAATCCTAGCCC 59.159 52.381 0.00 0.0 0.00 5.19 R
4878 7289 2.843730 TCTGATGCCCCTACTTTGCTTA 59.156 45.455 0.00 0.0 0.00 3.09 R
5170 7591 0.771127 GCTAGCATGGGGTTATGGGA 59.229 55.000 10.63 0.0 0.00 4.37 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
347 354 1.517257 GTGTCCTCGTGATGAGCGG 60.517 63.158 0.00 0.00 43.82 5.52
700 935 1.746615 CCTTGTCTCCGCCCATGTG 60.747 63.158 0.00 0.00 0.00 3.21
746 981 2.427740 GCGCGCGCACCTTTTTAA 60.428 55.556 46.11 0.00 41.49 1.52
747 982 2.011881 GCGCGCGCACCTTTTTAAA 61.012 52.632 46.11 0.00 41.49 1.52
748 983 1.541439 GCGCGCGCACCTTTTTAAAA 61.541 50.000 46.11 0.00 41.49 1.52
780 1015 3.887716 CAGAGAGGAAATGCCCCAAATAG 59.112 47.826 0.00 0.00 37.37 1.73
781 1016 3.117360 AGAGAGGAAATGCCCCAAATAGG 60.117 47.826 0.00 0.00 37.37 2.57
782 1017 2.587307 AGAGGAAATGCCCCAAATAGGT 59.413 45.455 0.00 0.00 37.37 3.08
826 1063 7.148171 CCTTCCGCTCAAATAAAAAGAGAAGAT 60.148 37.037 0.00 0.00 0.00 2.40
859 1096 3.814906 CCCACCACCACCACACCA 61.815 66.667 0.00 0.00 0.00 4.17
886 1123 3.058914 GTGGGCGCTTGTATAAATAGCTG 60.059 47.826 7.64 0.00 32.80 4.24
911 1148 2.594592 AAGCAACCCTCCGTGTGC 60.595 61.111 0.00 0.00 0.00 4.57
1215 1462 2.580783 CCCACCCTCCCTCTTAATTTCA 59.419 50.000 0.00 0.00 0.00 2.69
1216 1463 3.011257 CCCACCCTCCCTCTTAATTTCAA 59.989 47.826 0.00 0.00 0.00 2.69
1217 1464 4.510205 CCCACCCTCCCTCTTAATTTCAAA 60.510 45.833 0.00 0.00 0.00 2.69
1222 1487 5.775195 CCCTCCCTCTTAATTTCAAAAGTGT 59.225 40.000 0.00 0.00 0.00 3.55
1263 1532 1.227853 AGCGTGCCTCGAAAAAGGT 60.228 52.632 2.66 0.00 42.86 3.50
1267 1536 1.305201 GTGCCTCGAAAAAGGTGACA 58.695 50.000 0.00 0.00 38.79 3.58
1268 1537 1.264288 GTGCCTCGAAAAAGGTGACAG 59.736 52.381 0.00 0.00 38.79 3.51
1269 1538 1.140052 TGCCTCGAAAAAGGTGACAGA 59.860 47.619 0.00 0.00 38.79 3.41
1270 1539 1.531578 GCCTCGAAAAAGGTGACAGAC 59.468 52.381 0.00 0.00 38.79 3.51
1271 1540 2.833794 CCTCGAAAAAGGTGACAGACA 58.166 47.619 0.00 0.00 0.00 3.41
1300 1569 3.935828 GTGCCTAAAAGGTGATGAGAGAC 59.064 47.826 0.00 0.00 37.80 3.36
1308 1577 5.350504 AAGGTGATGAGAGACGAATGAAT 57.649 39.130 0.00 0.00 0.00 2.57
1310 1579 6.662865 AGGTGATGAGAGACGAATGAATAT 57.337 37.500 0.00 0.00 0.00 1.28
1311 1580 7.767250 AGGTGATGAGAGACGAATGAATATA 57.233 36.000 0.00 0.00 0.00 0.86
1312 1581 8.183104 AGGTGATGAGAGACGAATGAATATAA 57.817 34.615 0.00 0.00 0.00 0.98
1313 1582 8.303156 AGGTGATGAGAGACGAATGAATATAAG 58.697 37.037 0.00 0.00 0.00 1.73
1380 1654 3.541516 CGACTCGTATCCATTTGCGAAAC 60.542 47.826 0.00 0.00 32.84 2.78
1392 1666 2.990066 TGCGAAACCCCACAAAATTT 57.010 40.000 0.00 0.00 0.00 1.82
1400 1674 6.145371 CGAAACCCCACAAAATTTCATTACTG 59.855 38.462 0.00 0.00 31.81 2.74
1403 1677 3.925913 CCCACAAAATTTCATTACTGCCG 59.074 43.478 0.00 0.00 0.00 5.69
1411 1685 2.380084 TCATTACTGCCGTCTTCCAC 57.620 50.000 0.00 0.00 0.00 4.02
1424 1698 4.537015 CGTCTTCCACAATTCAAAAGGTC 58.463 43.478 0.00 0.00 0.00 3.85
1445 1719 2.608506 CCATGAATGTGGTGCACTGTTG 60.609 50.000 17.98 3.82 35.11 3.33
1491 1765 9.180678 CATTAGGTTTAGTTTACAAAAGCACAG 57.819 33.333 0.00 0.00 35.95 3.66
1551 1825 3.066342 GGATGGATCTGCACAACATGAAG 59.934 47.826 0.00 0.00 34.80 3.02
1559 1833 2.107378 TGCACAACATGAAGGGGTTCTA 59.893 45.455 0.00 0.00 0.00 2.10
1560 1834 2.488153 GCACAACATGAAGGGGTTCTAC 59.512 50.000 0.00 0.00 0.00 2.59
1599 1873 6.361114 CAGATTTTAATGTATCTCAGCAGCG 58.639 40.000 0.00 0.00 0.00 5.18
1600 1874 6.201615 CAGATTTTAATGTATCTCAGCAGCGA 59.798 38.462 0.00 0.00 0.00 4.93
1676 1954 7.815840 TTTCCAAGAATCTTATTGTGTCACA 57.184 32.000 0.18 0.18 0.00 3.58
1677 1955 6.801539 TCCAAGAATCTTATTGTGTCACAC 57.198 37.500 4.80 0.00 34.56 3.82
1843 2129 6.179906 ACTTGTCAGCCATATAGTTATGCT 57.820 37.500 0.00 0.00 34.94 3.79
1851 2137 7.725397 TCAGCCATATAGTTATGCTGGATTTTT 59.275 33.333 9.62 0.00 38.76 1.94
1904 2190 3.371034 ACCCAACTAAACCTTGCAGTTT 58.629 40.909 8.85 8.85 42.47 2.66
2071 2360 2.921634 TTCATCTTCTCTCCGTGTCG 57.078 50.000 0.00 0.00 0.00 4.35
2085 2374 3.059461 TCCGTGTCGTATTGTTTTGCTTC 60.059 43.478 0.00 0.00 0.00 3.86
2347 4543 5.533482 TCTTTAGTCTTGAGTCTCTTGTGC 58.467 41.667 0.65 0.00 0.00 4.57
2404 4602 2.552315 AGTTTTAGTGTGCCGATGTTGG 59.448 45.455 0.00 0.00 0.00 3.77
2704 4989 8.986477 AACATGGTTATCTTTTACTTTCATGC 57.014 30.769 0.00 0.00 34.57 4.06
2708 4993 6.152661 TGGTTATCTTTTACTTTCATGCTGGG 59.847 38.462 0.00 0.00 0.00 4.45
2725 5010 5.636123 TGCTGGGTGGAATTACTTAGAAAA 58.364 37.500 0.00 0.00 0.00 2.29
2895 5180 5.867716 AGAAAATGATCTGTTTGCTCAATGC 59.132 36.000 0.00 0.00 43.25 3.56
2903 5188 5.284079 TCTGTTTGCTCAATGCTTTTCTTC 58.716 37.500 0.00 0.00 43.37 2.87
2909 5194 6.594788 TGCTCAATGCTTTTCTTCCTTTAT 57.405 33.333 0.00 0.00 43.37 1.40
2910 5195 7.701539 TGCTCAATGCTTTTCTTCCTTTATA 57.298 32.000 0.00 0.00 43.37 0.98
2911 5196 7.765307 TGCTCAATGCTTTTCTTCCTTTATAG 58.235 34.615 0.00 0.00 43.37 1.31
2912 5197 7.394359 TGCTCAATGCTTTTCTTCCTTTATAGT 59.606 33.333 0.00 0.00 43.37 2.12
3076 5369 5.062528 TGTATGTTGAATCTCACTGCACAA 58.937 37.500 0.00 0.00 0.00 3.33
3093 5386 3.578688 CACAATTTTTACAGGCTCAGGC 58.421 45.455 0.00 0.00 37.82 4.85
3129 5422 0.674581 TTCCACGCCTCATTGCAGAG 60.675 55.000 0.00 0.00 35.39 3.35
3172 5465 5.104402 TGACATATCTGAAGAGGCCATTGAA 60.104 40.000 5.01 0.00 0.00 2.69
3302 5599 0.405585 TCCCTCCAAAGCTTCCCAAG 59.594 55.000 0.00 0.00 0.00 3.61
3306 5603 1.228988 CCAAAGCTTCCCAAGGGCT 60.229 57.895 0.00 0.00 37.99 5.19
3362 5659 8.803201 ATATATGCGGTCATTGTAAGATATCG 57.197 34.615 0.00 0.00 34.22 2.92
3409 5706 9.451002 TCATTTTAAAATGCCATCATGATTTGT 57.549 25.926 28.54 0.00 44.15 2.83
3410 5707 9.497030 CATTTTAAAATGCCATCATGATTTGTG 57.503 29.630 24.00 0.00 39.29 3.33
3439 5736 8.857098 ACTGAATTTGGGATTTGATCATATGAG 58.143 33.333 11.78 0.00 0.00 2.90
3610 5914 6.103330 TCATCATCATTGTGCCATTCTTTTG 58.897 36.000 0.00 0.00 0.00 2.44
3611 5915 5.725325 TCATCATTGTGCCATTCTTTTGA 57.275 34.783 0.00 0.00 0.00 2.69
3613 5917 6.160684 TCATCATTGTGCCATTCTTTTGAAG 58.839 36.000 0.00 0.00 42.30 3.02
3952 6264 2.224354 ACATTCTTGGGCTGCTTTTTGG 60.224 45.455 0.00 0.00 0.00 3.28
4285 6682 4.654915 TGTTGATCATTCCTGCTTCTGAA 58.345 39.130 0.00 0.00 0.00 3.02
4295 6692 8.150945 TCATTCCTGCTTCTGAAATAGGTATAC 58.849 37.037 15.26 0.00 0.00 1.47
4361 6759 6.459066 TGTCATGTCTGAGGTAAAGAAGAAG 58.541 40.000 0.00 0.00 30.18 2.85
4585 6989 1.021202 TGGCACTAACACAACACTGC 58.979 50.000 0.00 0.00 0.00 4.40
4606 7010 4.581824 TGCAGCTCTTCATTTCAGTTTTCT 59.418 37.500 0.00 0.00 0.00 2.52
4609 7013 6.501781 CAGCTCTTCATTTCAGTTTTCTGTT 58.498 36.000 0.00 0.00 46.98 3.16
4709 7116 9.632807 TTAATTGCTTACTGATTGCGTAATTTT 57.367 25.926 0.00 0.00 0.00 1.82
4722 7129 7.815398 TTGCGTAATTTTAGAACATCTCGTA 57.185 32.000 0.00 0.00 0.00 3.43
4726 7133 6.976925 CGTAATTTTAGAACATCTCGTACCCT 59.023 38.462 0.00 0.00 0.00 4.34
4751 7159 5.751243 TTTTCTTCCAAAAGGAGAGAACG 57.249 39.130 0.00 0.00 33.03 3.95
4837 7248 3.502211 AGGAATTTCAGCCGTTACACTTG 59.498 43.478 0.00 0.00 0.00 3.16
4876 7287 6.481954 AATGAAATTCTCGAACACAGGTAC 57.518 37.500 0.00 0.00 0.00 3.34
4878 7289 5.547465 TGAAATTCTCGAACACAGGTACAT 58.453 37.500 0.00 0.00 0.00 2.29
4908 7319 2.130193 AGGGGCATCAGAAGCAGATTA 58.870 47.619 0.00 0.00 0.00 1.75
4964 7379 6.526526 TGTAGGCAGTTTTGTCACTTACATA 58.473 36.000 0.00 0.00 38.10 2.29
4976 7391 5.422012 TGTCACTTACATATGCTCTCCTTGA 59.578 40.000 1.58 0.00 31.43 3.02
4983 7398 5.609423 ACATATGCTCTCCTTGATGTCTTC 58.391 41.667 1.58 0.00 0.00 2.87
5137 7552 5.223449 AGGATTAACAGAAACGACCAGAA 57.777 39.130 0.00 0.00 0.00 3.02
5170 7591 4.118168 ACATTGACATTTTCCCCACTCT 57.882 40.909 0.00 0.00 0.00 3.24
5282 7703 6.767902 AGCACTGTTCTGTTCTTGAGAAAATA 59.232 34.615 0.00 0.00 35.58 1.40
5283 7704 7.283127 AGCACTGTTCTGTTCTTGAGAAAATAA 59.717 33.333 0.00 0.00 35.58 1.40
5284 7705 7.915397 GCACTGTTCTGTTCTTGAGAAAATAAA 59.085 33.333 0.00 0.00 35.58 1.40
5286 7707 9.956720 ACTGTTCTGTTCTTGAGAAAATAAATG 57.043 29.630 0.00 0.00 35.58 2.32
5288 7709 8.412456 TGTTCTGTTCTTGAGAAAATAAATGCA 58.588 29.630 0.00 0.00 35.58 3.96
5322 9144 1.808945 ACATCTTTTCGCTGCCTTCTG 59.191 47.619 0.00 0.00 0.00 3.02
5364 9186 2.223572 GCTTGGCCTATTGAATCGTTGG 60.224 50.000 3.32 0.00 0.00 3.77
5367 9189 1.597663 GGCCTATTGAATCGTTGGACG 59.402 52.381 0.00 0.00 44.19 4.79
5398 9220 9.976776 TCTAATCTCTACTAAATCGTCCCATAT 57.023 33.333 0.00 0.00 0.00 1.78
5462 9284 3.685139 GGACTCATCCAGTTCACTTCA 57.315 47.619 0.00 0.00 45.47 3.02
5473 9295 3.885297 CAGTTCACTTCAGGGACATTTGT 59.115 43.478 0.00 0.00 0.00 2.83
5489 9311 5.675538 ACATTTGTAGTCTTAGGCATCTCC 58.324 41.667 0.00 0.00 0.00 3.71
5494 9316 3.274095 AGTCTTAGGCATCTCCAAAGC 57.726 47.619 0.00 0.00 37.29 3.51
5510 9332 2.125633 GCGGACCCTCGAACCTTC 60.126 66.667 0.00 0.00 0.00 3.46
5511 9333 2.577593 CGGACCCTCGAACCTTCC 59.422 66.667 0.00 0.00 0.00 3.46
5518 9340 1.667830 CTCGAACCTTCCGCAAGCA 60.668 57.895 0.00 0.00 0.00 3.91
5521 9343 1.803289 GAACCTTCCGCAAGCATCC 59.197 57.895 0.00 0.00 0.00 3.51
5523 9345 3.880846 CCTTCCGCAAGCATCCGC 61.881 66.667 0.00 0.00 38.99 5.54
5525 9347 3.386867 CTTCCGCAAGCATCCGCAC 62.387 63.158 0.00 0.00 42.27 5.34
5568 9390 1.377202 ATCCAACGCGTCCTGCATT 60.377 52.632 14.44 0.00 46.97 3.56
5571 9393 2.281484 AACGCGTCCTGCATTGGT 60.281 55.556 14.44 0.00 46.97 3.67
5572 9394 1.896660 AACGCGTCCTGCATTGGTT 60.897 52.632 14.44 0.00 46.97 3.67
5593 9415 1.959899 GCGAACCAGTGCAGATGTCG 61.960 60.000 0.00 0.00 0.00 4.35
5594 9416 1.354337 CGAACCAGTGCAGATGTCGG 61.354 60.000 0.00 0.00 0.00 4.79
5602 9424 1.197721 GTGCAGATGTCGGTTTTCCTG 59.802 52.381 0.00 0.00 37.95 3.86
5606 9428 2.095567 CAGATGTCGGTTTTCCTGCAAG 60.096 50.000 0.00 0.00 37.95 4.01
5614 9436 1.805428 TTTTCCTGCAAGCCGGAAGC 61.805 55.000 15.78 5.84 40.17 3.86
5633 9455 1.547901 GCAAACTAGGAGGGGCTTTGT 60.548 52.381 0.00 0.00 0.00 2.83
5654 9476 3.591254 GAGTCCGGACACCAGCCAC 62.591 68.421 35.00 6.70 0.00 5.01
5655 9477 3.936203 GTCCGGACACCAGCCACA 61.936 66.667 29.75 0.00 0.00 4.17
5687 9509 2.989253 CCTCGGCCCACCCAAAAC 60.989 66.667 0.00 0.00 0.00 2.43
5690 9512 4.614036 CGGCCCACCCAAAACCCT 62.614 66.667 0.00 0.00 0.00 4.34
5694 9516 2.922503 CCACCCAAAACCCTGCCC 60.923 66.667 0.00 0.00 0.00 5.36
5695 9517 2.123077 CACCCAAAACCCTGCCCA 60.123 61.111 0.00 0.00 0.00 5.36
5700 9522 1.153756 CAAAACCCTGCCCAGACCT 59.846 57.895 0.00 0.00 0.00 3.85
5711 9533 1.043116 CCCAGACCTGCGTCTCCATA 61.043 60.000 0.00 0.00 46.90 2.74
5712 9534 1.043816 CCAGACCTGCGTCTCCATAT 58.956 55.000 0.00 0.00 46.90 1.78
5732 9554 9.973661 TCCATATTTTCTTTTTCTCTACATCCA 57.026 29.630 0.00 0.00 0.00 3.41
5777 9637 4.509737 GGCCTACGCGACCTCCAC 62.510 72.222 15.93 0.00 35.02 4.02
5786 9646 2.181021 GACCTCCACCGCTACACG 59.819 66.667 0.00 0.00 43.15 4.49
5797 9657 2.264124 GCTACACGAGACCTCCACA 58.736 57.895 0.00 0.00 0.00 4.17
5798 9658 0.109226 GCTACACGAGACCTCCACAC 60.109 60.000 0.00 0.00 0.00 3.82
5799 9659 0.526662 CTACACGAGACCTCCACACC 59.473 60.000 0.00 0.00 0.00 4.16
5800 9660 1.239296 TACACGAGACCTCCACACCG 61.239 60.000 0.00 0.00 0.00 4.94
5801 9661 3.681835 ACGAGACCTCCACACCGC 61.682 66.667 0.00 0.00 0.00 5.68
5802 9662 3.374402 CGAGACCTCCACACCGCT 61.374 66.667 0.00 0.00 0.00 5.52
5803 9663 2.932234 CGAGACCTCCACACCGCTT 61.932 63.158 0.00 0.00 0.00 4.68
5804 9664 1.374758 GAGACCTCCACACCGCTTG 60.375 63.158 0.00 0.00 0.00 4.01
5805 9665 2.100879 GAGACCTCCACACCGCTTGT 62.101 60.000 0.00 0.00 39.97 3.16
5806 9666 1.668151 GACCTCCACACCGCTTGTC 60.668 63.158 0.00 0.00 35.67 3.18
5807 9667 2.358737 CCTCCACACCGCTTGTCC 60.359 66.667 0.00 0.00 35.67 4.02
5808 9668 2.743718 CTCCACACCGCTTGTCCT 59.256 61.111 0.00 0.00 35.67 3.85
5809 9669 1.374758 CTCCACACCGCTTGTCCTC 60.375 63.158 0.00 0.00 35.67 3.71
5810 9670 2.358737 CCACACCGCTTGTCCTCC 60.359 66.667 0.00 0.00 35.67 4.30
5811 9671 2.738521 CACACCGCTTGTCCTCCG 60.739 66.667 0.00 0.00 35.67 4.63
5812 9672 3.231736 ACACCGCTTGTCCTCCGT 61.232 61.111 0.00 0.00 29.79 4.69
5813 9673 2.030562 CACCGCTTGTCCTCCGTT 59.969 61.111 0.00 0.00 0.00 4.44
5814 9674 2.030562 ACCGCTTGTCCTCCGTTG 59.969 61.111 0.00 0.00 0.00 4.10
5815 9675 2.030562 CCGCTTGTCCTCCGTTGT 59.969 61.111 0.00 0.00 0.00 3.32
5816 9676 2.027625 CCGCTTGTCCTCCGTTGTC 61.028 63.158 0.00 0.00 0.00 3.18
5817 9677 2.372690 CGCTTGTCCTCCGTTGTCG 61.373 63.158 0.00 0.00 0.00 4.35
5818 9678 1.300697 GCTTGTCCTCCGTTGTCGT 60.301 57.895 0.00 0.00 35.01 4.34
5819 9679 0.878961 GCTTGTCCTCCGTTGTCGTT 60.879 55.000 0.00 0.00 35.01 3.85
5820 9680 1.137513 CTTGTCCTCCGTTGTCGTTC 58.862 55.000 0.00 0.00 35.01 3.95
5821 9681 0.249573 TTGTCCTCCGTTGTCGTTCC 60.250 55.000 0.00 0.00 35.01 3.62
5822 9682 1.364901 GTCCTCCGTTGTCGTTCCA 59.635 57.895 0.00 0.00 35.01 3.53
5823 9683 0.942884 GTCCTCCGTTGTCGTTCCAC 60.943 60.000 0.00 0.00 35.01 4.02
5824 9684 1.068417 CCTCCGTTGTCGTTCCACA 59.932 57.895 0.00 0.00 35.01 4.17
5825 9685 1.219522 CCTCCGTTGTCGTTCCACAC 61.220 60.000 0.00 0.00 35.01 3.82
5826 9686 1.219522 CTCCGTTGTCGTTCCACACC 61.220 60.000 0.00 0.00 35.01 4.16
5827 9687 1.227438 CCGTTGTCGTTCCACACCT 60.227 57.895 0.00 0.00 35.01 4.00
5828 9688 1.219522 CCGTTGTCGTTCCACACCTC 61.220 60.000 0.00 0.00 35.01 3.85
5829 9689 0.249322 CGTTGTCGTTCCACACCTCT 60.249 55.000 0.00 0.00 0.00 3.69
5830 9690 1.499049 GTTGTCGTTCCACACCTCTC 58.501 55.000 0.00 0.00 0.00 3.20
5831 9691 1.116308 TTGTCGTTCCACACCTCTCA 58.884 50.000 0.00 0.00 0.00 3.27
5832 9692 1.338107 TGTCGTTCCACACCTCTCAT 58.662 50.000 0.00 0.00 0.00 2.90
5833 9693 1.272490 TGTCGTTCCACACCTCTCATC 59.728 52.381 0.00 0.00 0.00 2.92
5834 9694 1.546476 GTCGTTCCACACCTCTCATCT 59.454 52.381 0.00 0.00 0.00 2.90
5835 9695 2.753452 GTCGTTCCACACCTCTCATCTA 59.247 50.000 0.00 0.00 0.00 1.98
5836 9696 3.381908 GTCGTTCCACACCTCTCATCTAT 59.618 47.826 0.00 0.00 0.00 1.98
5837 9697 3.632604 TCGTTCCACACCTCTCATCTATC 59.367 47.826 0.00 0.00 0.00 2.08
5838 9698 3.243569 CGTTCCACACCTCTCATCTATCC 60.244 52.174 0.00 0.00 0.00 2.59
5839 9699 2.587522 TCCACACCTCTCATCTATCCG 58.412 52.381 0.00 0.00 0.00 4.18
5840 9700 1.000283 CCACACCTCTCATCTATCCGC 60.000 57.143 0.00 0.00 0.00 5.54
5841 9701 1.000283 CACACCTCTCATCTATCCGCC 60.000 57.143 0.00 0.00 0.00 6.13
5842 9702 0.242286 CACCTCTCATCTATCCGCCG 59.758 60.000 0.00 0.00 0.00 6.46
5843 9703 1.214062 CCTCTCATCTATCCGCCGC 59.786 63.158 0.00 0.00 0.00 6.53
5844 9704 1.527433 CCTCTCATCTATCCGCCGCA 61.527 60.000 0.00 0.00 0.00 5.69
5845 9705 0.109365 CTCTCATCTATCCGCCGCAG 60.109 60.000 0.00 0.00 0.00 5.18
5846 9706 1.735920 CTCATCTATCCGCCGCAGC 60.736 63.158 0.00 0.00 0.00 5.25
5862 9722 2.267642 GCGCAGGTACCATCCACA 59.732 61.111 15.94 0.00 0.00 4.17
5880 9740 4.379243 CCGCTTGTCCTCCGCTGT 62.379 66.667 0.00 0.00 0.00 4.40
5898 9758 1.272490 TGTCGTTCCACACCTCTCATC 59.728 52.381 0.00 0.00 0.00 2.92
5904 9764 0.174389 CCACACCTCTCATCTGTCCG 59.826 60.000 0.00 0.00 0.00 4.79
5907 9767 2.415010 CCTCTCATCTGTCCGCCG 59.585 66.667 0.00 0.00 0.00 6.46
5908 9768 2.279120 CTCTCATCTGTCCGCCGC 60.279 66.667 0.00 0.00 0.00 6.53
5909 9769 3.068064 TCTCATCTGTCCGCCGCA 61.068 61.111 0.00 0.00 0.00 5.69
5956 9818 0.314935 GTCACCATGCCCAACAAGTG 59.685 55.000 0.00 0.00 37.75 3.16
5968 9830 2.472816 CAACAAGTGTGGTGAAATGCC 58.527 47.619 0.00 0.00 46.17 4.40
5972 9834 1.172180 AGTGTGGTGAAATGCCCGTG 61.172 55.000 0.00 0.00 0.00 4.94
5978 9840 1.065551 GGTGAAATGCCCGTGCTAATC 59.934 52.381 0.00 0.00 38.71 1.75
5996 9859 6.549364 TGCTAATCTTTTTGTCCCTTCTTTGA 59.451 34.615 0.00 0.00 0.00 2.69
6005 9868 3.157087 GTCCCTTCTTTGAAGCAATGGA 58.843 45.455 2.08 1.45 0.00 3.41
6021 9884 4.708177 CAATGGATTCGGACAGGAAGTAT 58.292 43.478 0.00 0.00 0.00 2.12
6036 9899 9.843334 GACAGGAAGTATATATACAAGCACTAC 57.157 37.037 22.00 6.30 35.74 2.73
6040 9903 9.125906 GGAAGTATATATACAAGCACTACGTTG 57.874 37.037 22.00 0.00 35.74 4.10
6044 9907 9.327529 GTATATATACAAGCACTACGTTGAGTC 57.672 37.037 16.50 0.00 33.52 3.36
6045 9908 2.882927 ACAAGCACTACGTTGAGTCA 57.117 45.000 3.44 0.00 0.00 3.41
6049 9912 2.596452 AGCACTACGTTGAGTCATTCG 58.404 47.619 3.44 13.97 0.00 3.34
6068 9931 1.375098 GACGAGGAGGACTACACGGG 61.375 65.000 6.35 0.00 0.00 5.28
6090 9953 3.000674 GTGAAACGACTATGATGCAGACG 60.001 47.826 0.00 0.00 37.25 4.18
6105 9968 0.034059 AGACGGTCCTTGCAGAACAG 59.966 55.000 4.14 0.00 0.00 3.16
6106 9969 0.951040 GACGGTCCTTGCAGAACAGG 60.951 60.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
347 354 2.438434 ATTGCGGGTGCTGGCTAC 60.438 61.111 0.00 0.00 43.34 3.58
696 931 9.653287 TCAAACTCGAAATCTCTTTATACACAT 57.347 29.630 0.00 0.00 0.00 3.21
700 935 8.117370 GGCTTCAAACTCGAAATCTCTTTATAC 58.883 37.037 0.00 0.00 0.00 1.47
748 983 7.161404 GGGCATTTCCTCTCTGTTTAATTTTT 58.839 34.615 0.00 0.00 34.39 1.94
780 1015 1.095807 GCGTCAAATAGGGGAGCACC 61.096 60.000 0.00 0.00 39.11 5.01
781 1016 1.095807 GGCGTCAAATAGGGGAGCAC 61.096 60.000 0.00 0.00 0.00 4.40
782 1017 1.223487 GGCGTCAAATAGGGGAGCA 59.777 57.895 0.00 0.00 0.00 4.26
826 1063 5.671463 TGGTGGGCCAATCCTATTAATAA 57.329 39.130 8.40 0.00 42.83 1.40
859 1096 1.890625 TATACAAGCGCCCACGTGGT 61.891 55.000 31.80 14.92 42.83 4.16
886 1123 1.979155 GAGGGTTGCTTCTTGGGGC 60.979 63.158 0.00 0.00 0.00 5.80
925 1162 0.247736 CAGGGAGGAGTCTTGTTCGG 59.752 60.000 0.00 0.00 0.00 4.30
1023 1266 4.530857 GCCCCGGTCCTGACATCG 62.531 72.222 0.00 0.00 0.00 3.84
1074 1317 1.462238 ATCATTCCGGGGGAGGAGG 60.462 63.158 0.00 0.00 41.98 4.30
1131 1374 3.900855 GTGCTGAGCAGGACCATG 58.099 61.111 7.71 0.00 42.95 3.66
1215 1462 7.549488 GGTACATGTCTAGCTGAATACACTTTT 59.451 37.037 0.00 0.00 0.00 2.27
1216 1463 7.042335 GGTACATGTCTAGCTGAATACACTTT 58.958 38.462 0.00 0.00 0.00 2.66
1217 1464 6.154534 TGGTACATGTCTAGCTGAATACACTT 59.845 38.462 0.00 0.00 0.00 3.16
1222 1487 4.649218 TGCTGGTACATGTCTAGCTGAATA 59.351 41.667 23.52 9.34 39.53 1.75
1263 1532 1.134128 AGGCACACATGTTGTCTGTCA 60.134 47.619 12.39 0.00 35.67 3.58
1267 1536 3.569701 CCTTTTAGGCACACATGTTGTCT 59.430 43.478 15.93 15.93 35.67 3.41
1268 1537 3.317993 ACCTTTTAGGCACACATGTTGTC 59.682 43.478 0.00 0.00 39.63 3.18
1269 1538 3.068024 CACCTTTTAGGCACACATGTTGT 59.932 43.478 0.00 0.00 39.63 3.32
1270 1539 3.317711 TCACCTTTTAGGCACACATGTTG 59.682 43.478 0.00 0.00 39.63 3.33
1271 1540 3.561143 TCACCTTTTAGGCACACATGTT 58.439 40.909 0.00 0.00 39.63 2.71
1310 1579 9.199982 GAAGTTGCTGGCGTATATATAAACTTA 57.800 33.333 12.94 0.00 35.95 2.24
1311 1580 7.931948 AGAAGTTGCTGGCGTATATATAAACTT 59.068 33.333 12.87 12.87 37.87 2.66
1312 1581 7.442656 AGAAGTTGCTGGCGTATATATAAACT 58.557 34.615 0.00 0.00 0.00 2.66
1313 1582 7.653767 AGAAGTTGCTGGCGTATATATAAAC 57.346 36.000 0.00 0.00 0.00 2.01
1319 1588 3.871594 GACAAGAAGTTGCTGGCGTATAT 59.128 43.478 0.00 0.00 37.14 0.86
1320 1589 3.259064 GACAAGAAGTTGCTGGCGTATA 58.741 45.455 0.00 0.00 37.14 1.47
1321 1590 2.076863 GACAAGAAGTTGCTGGCGTAT 58.923 47.619 0.00 0.00 37.14 3.06
1380 1654 4.252878 GGCAGTAATGAAATTTTGTGGGG 58.747 43.478 0.00 0.00 37.87 4.96
1392 1666 1.621317 TGTGGAAGACGGCAGTAATGA 59.379 47.619 0.00 0.00 0.00 2.57
1400 1674 3.308530 CTTTTGAATTGTGGAAGACGGC 58.691 45.455 0.00 0.00 0.00 5.68
1403 1677 4.340950 TGGACCTTTTGAATTGTGGAAGAC 59.659 41.667 0.00 0.00 0.00 3.01
1411 1685 5.640357 CCACATTCATGGACCTTTTGAATTG 59.360 40.000 12.41 12.86 43.02 2.32
1424 1698 1.250328 ACAGTGCACCACATTCATGG 58.750 50.000 14.63 0.00 46.10 3.66
1445 1719 1.535896 GCTGACGGAAGAAGGGAAAAC 59.464 52.381 0.00 0.00 0.00 2.43
1551 1825 1.939980 ACTGTCCAGAGTAGAACCCC 58.060 55.000 0.40 0.00 0.00 4.95
1670 1948 7.505585 TCATAGATAGTACCATCATGTGTGACA 59.494 37.037 4.07 0.00 37.14 3.58
1904 2190 3.196469 TCAACACAGACCCAAAAATTGCA 59.804 39.130 0.00 0.00 0.00 4.08
2071 2360 5.008613 TGGTCTGTGAGAAGCAAAACAATAC 59.991 40.000 0.00 0.00 0.00 1.89
2085 2374 1.871408 GCTATCCGCATGGTCTGTGAG 60.871 57.143 0.00 0.00 37.57 3.51
2111 2400 3.798202 AGCCAACCAAAAACGCAAATAA 58.202 36.364 0.00 0.00 0.00 1.40
2347 4543 7.550551 ACATGTACAACTGATACAAGATTGAGG 59.449 37.037 0.00 0.00 36.19 3.86
2404 4602 1.821332 GCACCTGCAGTATCCAGCC 60.821 63.158 13.81 0.00 41.59 4.85
2704 4989 9.423061 CAAAATTTTCTAAGTAATTCCACCCAG 57.577 33.333 0.00 0.00 0.00 4.45
2725 5010 4.082787 GCACTATACCTGCACACACAAAAT 60.083 41.667 0.00 0.00 34.56 1.82
2811 5096 3.924918 TTCTCCGAAGACTCTGAAGTG 57.075 47.619 0.00 0.00 35.28 3.16
3001 5286 6.595716 AGGTCATTTTAGTTCATGAGTACTGC 59.404 38.462 0.00 0.00 29.85 4.40
3093 5386 1.134068 GGAATTCTTCCTCCCTTCCGG 60.134 57.143 5.23 0.00 46.57 5.14
3094 5387 2.333688 GGAATTCTTCCTCCCTTCCG 57.666 55.000 5.23 0.00 46.57 4.30
3129 5422 2.467826 GCATTCTCTCCACGCAGCC 61.468 63.158 0.00 0.00 0.00 4.85
3172 5465 8.870075 ATTAGGACAGAAAGCTAACTTTGATT 57.130 30.769 0.00 0.00 46.20 2.57
3302 5599 1.840635 ACAAGTCCTGAATCCTAGCCC 59.159 52.381 0.00 0.00 0.00 5.19
3306 5603 5.473504 GCTCAAAAACAAGTCCTGAATCCTA 59.526 40.000 0.00 0.00 0.00 2.94
3359 5656 9.121658 TGAAGTAGTAGTCAAAGTGATATCGAT 57.878 33.333 2.16 2.16 0.00 3.59
3360 5657 8.502105 TGAAGTAGTAGTCAAAGTGATATCGA 57.498 34.615 0.00 0.00 0.00 3.59
3361 5658 9.737427 AATGAAGTAGTAGTCAAAGTGATATCG 57.263 33.333 0.00 0.00 0.00 2.92
3409 5706 3.237746 TCAAATCCCAAATTCAGTGCCA 58.762 40.909 0.00 0.00 0.00 4.92
3410 5707 3.959535 TCAAATCCCAAATTCAGTGCC 57.040 42.857 0.00 0.00 0.00 5.01
3439 5736 7.605410 TCCAGGTTACGAATTATGAGAAAAC 57.395 36.000 0.00 0.00 0.00 2.43
3610 5914 5.112220 TCAACACATTTCATGCAGACTTC 57.888 39.130 0.00 0.00 0.00 3.01
3611 5915 5.717078 ATCAACACATTTCATGCAGACTT 57.283 34.783 0.00 0.00 0.00 3.01
3613 5917 5.463286 TGAATCAACACATTTCATGCAGAC 58.537 37.500 0.00 0.00 0.00 3.51
3909 6221 1.942657 CCAGATGCGGAAACCTGTATG 59.057 52.381 0.00 0.00 0.00 2.39
3952 6264 5.927115 CCTTTAGGTAGAACGATATTCCTGC 59.073 44.000 0.00 0.00 0.00 4.85
4021 6334 5.125578 GTCTCCCATATGTTCCCAAAAGTTC 59.874 44.000 1.24 0.00 0.00 3.01
4281 6678 9.587772 GTATGCACCTATGTATACCTATTTCAG 57.412 37.037 0.00 0.00 44.36 3.02
4295 6692 6.294342 CCATTCCAATTGAGTATGCACCTATG 60.294 42.308 7.12 0.00 0.00 2.23
4585 6989 6.069684 ACAGAAAACTGAAATGAAGAGCTG 57.930 37.500 0.00 0.00 0.00 4.24
4609 7013 3.382083 TGTCACTACTGGAGCTATGGA 57.618 47.619 0.00 0.00 0.00 3.41
4750 7158 7.763172 AAAGACTAATCAGAAATCACTAGCG 57.237 36.000 0.00 0.00 0.00 4.26
4779 7187 7.324935 TGGATTGCTTACTTTTCGACATACTA 58.675 34.615 0.00 0.00 0.00 1.82
4780 7188 6.170506 TGGATTGCTTACTTTTCGACATACT 58.829 36.000 0.00 0.00 0.00 2.12
4781 7189 6.417191 TGGATTGCTTACTTTTCGACATAC 57.583 37.500 0.00 0.00 0.00 2.39
4855 7266 4.951254 TGTACCTGTGTTCGAGAATTTCA 58.049 39.130 0.00 0.00 0.00 2.69
4865 7276 5.941948 ACTTTGCTTATGTACCTGTGTTC 57.058 39.130 0.00 0.00 0.00 3.18
4876 7287 3.554934 TGATGCCCCTACTTTGCTTATG 58.445 45.455 0.00 0.00 0.00 1.90
4878 7289 2.843730 TCTGATGCCCCTACTTTGCTTA 59.156 45.455 0.00 0.00 0.00 3.09
4964 7379 3.682155 GCAGAAGACATCAAGGAGAGCAT 60.682 47.826 0.00 0.00 0.00 3.79
5137 7552 6.704289 AAATGTCAATGTATATGTGCTGCT 57.296 33.333 0.00 0.00 0.00 4.24
5170 7591 0.771127 GCTAGCATGGGGTTATGGGA 59.229 55.000 10.63 0.00 0.00 4.37
5293 7714 5.909610 GGCAGCGAAAAGATGTCATTAATAC 59.090 40.000 0.00 0.00 41.17 1.89
5294 7715 5.822519 AGGCAGCGAAAAGATGTCATTAATA 59.177 36.000 0.00 0.00 44.51 0.98
5296 7717 4.009675 AGGCAGCGAAAAGATGTCATTAA 58.990 39.130 0.00 0.00 44.51 1.40
5297 7718 3.609853 AGGCAGCGAAAAGATGTCATTA 58.390 40.909 0.00 0.00 44.51 1.90
5298 7719 2.440409 AGGCAGCGAAAAGATGTCATT 58.560 42.857 0.00 0.00 44.51 2.57
5300 7721 1.806542 GAAGGCAGCGAAAAGATGTCA 59.193 47.619 0.00 0.00 44.51 3.58
5301 7722 2.079925 AGAAGGCAGCGAAAAGATGTC 58.920 47.619 0.00 0.00 41.97 3.06
5302 7723 1.808945 CAGAAGGCAGCGAAAAGATGT 59.191 47.619 0.00 0.00 38.76 3.06
5303 7724 1.808945 ACAGAAGGCAGCGAAAAGATG 59.191 47.619 0.00 0.00 39.70 2.90
5364 9186 9.749490 CGATTTAGTAGAGATTAGAGAATCGTC 57.251 37.037 0.00 0.00 45.34 4.20
5422 9244 3.173965 CCCTCCGTTGAGTATATGGGAT 58.826 50.000 0.00 0.00 36.86 3.85
5462 9284 3.844211 TGCCTAAGACTACAAATGTCCCT 59.156 43.478 0.00 0.00 35.21 4.20
5489 9311 2.033194 GGTTCGAGGGTCCGCTTTG 61.033 63.158 0.00 0.00 0.00 2.77
5494 9316 2.577593 GGAAGGTTCGAGGGTCCG 59.422 66.667 0.00 0.00 0.00 4.79
5537 9359 0.031994 GTTGGATGGCAAACTGCGTT 59.968 50.000 0.00 0.00 46.21 4.84
5571 9393 1.005037 ATCTGCACTGGTTCGCGAA 60.005 52.632 19.38 19.38 0.00 4.70
5572 9394 1.737735 CATCTGCACTGGTTCGCGA 60.738 57.895 3.71 3.71 0.00 5.87
5584 9406 0.169009 GCAGGAAAACCGACATCTGC 59.831 55.000 0.00 0.00 40.30 4.26
5593 9415 1.460273 TTCCGGCTTGCAGGAAAACC 61.460 55.000 21.31 0.00 41.75 3.27
5594 9416 0.039165 CTTCCGGCTTGCAGGAAAAC 60.039 55.000 23.02 0.00 41.75 2.43
5602 9424 0.169009 CTAGTTTGCTTCCGGCTTGC 59.831 55.000 0.00 0.69 42.39 4.01
5606 9428 0.744771 CCTCCTAGTTTGCTTCCGGC 60.745 60.000 0.00 0.00 42.22 6.13
5614 9436 2.162681 CACAAAGCCCCTCCTAGTTTG 58.837 52.381 0.00 0.00 34.85 2.93
5622 9444 0.035915 GGACTCTCACAAAGCCCCTC 60.036 60.000 0.00 0.00 0.00 4.30
5633 9455 2.276116 GCTGGTGTCCGGACTCTCA 61.276 63.158 33.39 25.31 29.82 3.27
5654 9476 1.033574 GAGGGTGTCGGAGTCCTATG 58.966 60.000 7.77 0.00 0.00 2.23
5655 9477 0.465824 CGAGGGTGTCGGAGTCCTAT 60.466 60.000 7.77 0.00 45.58 2.57
5677 9499 2.922503 GGGCAGGGTTTTGGGTGG 60.923 66.667 0.00 0.00 0.00 4.61
5700 9522 6.655003 AGAGAAAAAGAAAATATGGAGACGCA 59.345 34.615 0.00 0.00 0.00 5.24
5712 9534 9.408648 AGAAAGTGGATGTAGAGAAAAAGAAAA 57.591 29.630 0.00 0.00 0.00 2.29
5732 9554 2.574399 GGCGGCGAGAGAGAAAGT 59.426 61.111 12.98 0.00 0.00 2.66
5777 9637 2.044555 TGGAGGTCTCGTGTAGCGG 61.045 63.158 0.00 0.00 41.72 5.52
5786 9646 1.374758 CAAGCGGTGTGGAGGTCTC 60.375 63.158 0.00 0.00 0.00 3.36
5792 9652 2.741092 GAGGACAAGCGGTGTGGA 59.259 61.111 0.39 0.00 41.96 4.02
5793 9653 2.358737 GGAGGACAAGCGGTGTGG 60.359 66.667 0.39 0.00 41.96 4.17
5794 9654 2.738521 CGGAGGACAAGCGGTGTG 60.739 66.667 0.39 0.00 41.96 3.82
5795 9655 2.803817 AACGGAGGACAAGCGGTGT 61.804 57.895 0.00 0.00 45.74 4.16
5796 9656 2.030562 AACGGAGGACAAGCGGTG 59.969 61.111 0.00 0.00 0.00 4.94
5797 9657 2.030562 CAACGGAGGACAAGCGGT 59.969 61.111 0.00 0.00 0.00 5.68
5798 9658 2.027625 GACAACGGAGGACAAGCGG 61.028 63.158 0.00 0.00 0.00 5.52
5799 9659 2.372690 CGACAACGGAGGACAAGCG 61.373 63.158 0.00 0.00 35.72 4.68
5800 9660 0.878961 AACGACAACGGAGGACAAGC 60.879 55.000 0.00 0.00 44.46 4.01
5801 9661 1.137513 GAACGACAACGGAGGACAAG 58.862 55.000 0.00 0.00 44.46 3.16
5802 9662 0.249573 GGAACGACAACGGAGGACAA 60.250 55.000 0.00 0.00 44.46 3.18
5803 9663 1.364901 GGAACGACAACGGAGGACA 59.635 57.895 0.00 0.00 44.46 4.02
5804 9664 0.942884 GTGGAACGACAACGGAGGAC 60.943 60.000 0.00 0.00 44.46 3.85
5805 9665 1.364901 GTGGAACGACAACGGAGGA 59.635 57.895 0.00 0.00 44.46 3.71
5806 9666 1.068417 TGTGGAACGACAACGGAGG 59.932 57.895 0.00 0.00 42.39 4.30
5807 9667 1.219522 GGTGTGGAACGACAACGGAG 61.220 60.000 0.00 0.00 42.39 4.63
5808 9668 1.227321 GGTGTGGAACGACAACGGA 60.227 57.895 0.00 0.00 42.39 4.69
5809 9669 1.219522 GAGGTGTGGAACGACAACGG 61.220 60.000 0.00 0.00 42.39 4.44
5810 9670 0.249322 AGAGGTGTGGAACGACAACG 60.249 55.000 0.00 0.00 42.39 4.10
5811 9671 1.202486 TGAGAGGTGTGGAACGACAAC 60.202 52.381 0.00 0.00 42.39 3.32
5812 9672 1.116308 TGAGAGGTGTGGAACGACAA 58.884 50.000 0.00 0.00 42.39 3.18
5813 9673 1.272490 GATGAGAGGTGTGGAACGACA 59.728 52.381 0.00 0.00 42.39 4.35
5814 9674 1.546476 AGATGAGAGGTGTGGAACGAC 59.454 52.381 0.00 0.00 42.39 4.34
5815 9675 1.924731 AGATGAGAGGTGTGGAACGA 58.075 50.000 0.00 0.00 42.39 3.85
5816 9676 3.243569 GGATAGATGAGAGGTGTGGAACG 60.244 52.174 0.00 0.00 42.39 3.95
5817 9677 3.243569 CGGATAGATGAGAGGTGTGGAAC 60.244 52.174 0.00 0.00 37.35 3.62
5818 9678 2.959030 CGGATAGATGAGAGGTGTGGAA 59.041 50.000 0.00 0.00 0.00 3.53
5819 9679 2.587522 CGGATAGATGAGAGGTGTGGA 58.412 52.381 0.00 0.00 0.00 4.02
5820 9680 1.000283 GCGGATAGATGAGAGGTGTGG 60.000 57.143 0.00 0.00 0.00 4.17
5821 9681 1.000283 GGCGGATAGATGAGAGGTGTG 60.000 57.143 0.00 0.00 0.00 3.82
5822 9682 1.333177 GGCGGATAGATGAGAGGTGT 58.667 55.000 0.00 0.00 0.00 4.16
5823 9683 0.242286 CGGCGGATAGATGAGAGGTG 59.758 60.000 0.00 0.00 0.00 4.00
5824 9684 1.528292 GCGGCGGATAGATGAGAGGT 61.528 60.000 9.78 0.00 0.00 3.85
5825 9685 1.214062 GCGGCGGATAGATGAGAGG 59.786 63.158 9.78 0.00 0.00 3.69
5826 9686 0.109365 CTGCGGCGGATAGATGAGAG 60.109 60.000 9.78 0.00 0.00 3.20
5827 9687 1.959848 CTGCGGCGGATAGATGAGA 59.040 57.895 9.78 0.00 0.00 3.27
5828 9688 1.735920 GCTGCGGCGGATAGATGAG 60.736 63.158 14.15 0.00 0.00 2.90
5829 9689 2.340078 GCTGCGGCGGATAGATGA 59.660 61.111 14.15 0.00 0.00 2.92
5840 9700 4.838152 ATGGTACCTGCGCTGCGG 62.838 66.667 24.61 9.75 34.23 5.69
5841 9701 3.264897 GATGGTACCTGCGCTGCG 61.265 66.667 19.17 19.17 0.00 5.18
5842 9702 2.897350 GGATGGTACCTGCGCTGC 60.897 66.667 14.36 0.00 0.00 5.25
5843 9703 1.815421 GTGGATGGTACCTGCGCTG 60.815 63.158 14.36 8.47 0.00 5.18
5844 9704 2.290287 TGTGGATGGTACCTGCGCT 61.290 57.895 14.36 0.00 0.00 5.92
5845 9705 2.106683 GTGTGGATGGTACCTGCGC 61.107 63.158 14.36 10.92 0.00 6.09
5846 9706 1.449601 GGTGTGGATGGTACCTGCG 60.450 63.158 14.36 0.00 0.00 5.18
5847 9707 1.449601 CGGTGTGGATGGTACCTGC 60.450 63.158 14.36 4.70 32.28 4.85
5848 9708 1.449601 GCGGTGTGGATGGTACCTG 60.450 63.158 14.36 0.00 32.28 4.00
5849 9709 1.198759 AAGCGGTGTGGATGGTACCT 61.199 55.000 14.36 0.00 32.28 3.08
5850 9710 1.024579 CAAGCGGTGTGGATGGTACC 61.025 60.000 4.43 4.43 0.00 3.34
5851 9711 0.321298 ACAAGCGGTGTGGATGGTAC 60.321 55.000 0.00 0.00 39.72 3.34
5852 9712 0.036765 GACAAGCGGTGTGGATGGTA 60.037 55.000 0.39 0.00 41.96 3.25
5853 9713 1.302511 GACAAGCGGTGTGGATGGT 60.303 57.895 0.39 0.00 41.96 3.55
5854 9714 2.040544 GGACAAGCGGTGTGGATGG 61.041 63.158 0.39 0.00 41.96 3.51
5855 9715 1.003355 AGGACAAGCGGTGTGGATG 60.003 57.895 0.39 0.00 41.96 3.51
5856 9716 1.296715 GAGGACAAGCGGTGTGGAT 59.703 57.895 0.39 0.00 41.96 3.41
5862 9722 4.379243 CAGCGGAGGACAAGCGGT 62.379 66.667 0.00 0.00 35.78 5.68
5880 9740 1.546029 CAGATGAGAGGTGTGGAACGA 59.454 52.381 0.00 0.00 42.39 3.85
5907 9767 2.897350 GGATGGTACCTGCGCTGC 60.897 66.667 14.36 0.00 0.00 5.25
5908 9768 1.815421 GTGGATGGTACCTGCGCTG 60.815 63.158 14.36 8.47 0.00 5.18
5909 9769 2.584608 GTGGATGGTACCTGCGCT 59.415 61.111 14.36 0.00 0.00 5.92
5913 9773 1.699634 CATAGGGGTGGATGGTACCTG 59.300 57.143 14.36 0.00 38.30 4.00
5944 9804 0.323816 TTCACCACACTTGTTGGGCA 60.324 50.000 0.00 0.00 0.00 5.36
5949 9809 1.412343 GGGCATTTCACCACACTTGTT 59.588 47.619 0.00 0.00 0.00 2.83
5956 9818 0.958382 TAGCACGGGCATTTCACCAC 60.958 55.000 14.57 0.00 44.61 4.16
5968 9830 3.081804 AGGGACAAAAAGATTAGCACGG 58.918 45.455 0.00 0.00 0.00 4.94
5972 9834 6.981722 TCAAAGAAGGGACAAAAAGATTAGC 58.018 36.000 0.00 0.00 0.00 3.09
5978 9840 5.009854 TGCTTCAAAGAAGGGACAAAAAG 57.990 39.130 8.66 0.00 0.00 2.27
5996 9859 1.281867 TCCTGTCCGAATCCATTGCTT 59.718 47.619 0.00 0.00 0.00 3.91
6005 9868 8.251721 GCTTGTATATATACTTCCTGTCCGAAT 58.748 37.037 20.80 0.00 34.41 3.34
6021 9884 7.324354 TGACTCAACGTAGTGCTTGTATATA 57.676 36.000 0.00 0.00 45.00 0.86
6036 9899 1.135774 TCCTCGTCGAATGACTCAACG 60.136 52.381 0.00 3.56 43.21 4.10
6040 9903 1.064357 GTCCTCCTCGTCGAATGACTC 59.936 57.143 0.00 0.00 43.21 3.36
6044 9907 2.014857 TGTAGTCCTCCTCGTCGAATG 58.985 52.381 0.00 0.00 0.00 2.67
6045 9908 2.015587 GTGTAGTCCTCCTCGTCGAAT 58.984 52.381 0.00 0.00 0.00 3.34
6049 9912 1.375098 CCCGTGTAGTCCTCCTCGTC 61.375 65.000 0.00 0.00 0.00 4.20
6068 9931 3.000674 CGTCTGCATCATAGTCGTTTCAC 60.001 47.826 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.