Multiple sequence alignment - TraesCS7D01G223800

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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 TraesCS7D01G223800 chr7D 100.000 4242 0 0 1 4242 184557887 184562128 0.000000e+00 7834.0
1 TraesCS7D01G223800 chr7D 87.474 1445 142 20 1982 3405 184514698 184516124 0.000000e+00 1629.0
2 TraesCS7D01G223800 chr7D 88.670 406 32 10 772 1172 184513333 184513729 2.290000e-132 483.0
3 TraesCS7D01G223800 chr7D 94.760 229 2 1 4014 4242 588171034 588170816 8.730000e-92 348.0
4 TraesCS7D01G223800 chr7D 82.057 418 48 19 273 666 173154474 173154060 8.790000e-87 331.0
5 TraesCS7D01G223800 chr7D 86.636 217 13 7 1651 1857 184514462 184514672 4.270000e-55 226.0
6 TraesCS7D01G223800 chr7A 94.101 3831 169 23 29 3828 191658485 191662289 0.000000e+00 5770.0
7 TraesCS7D01G223800 chr7A 89.072 1272 128 9 1982 3246 185982611 185981344 0.000000e+00 1568.0
8 TraesCS7D01G223800 chr7A 88.967 426 39 8 757 1175 185983917 185983493 1.750000e-143 520.0
9 TraesCS7D01G223800 chr7A 93.011 186 11 1 3828 4013 191662259 191662442 1.940000e-68 270.0
10 TraesCS7D01G223800 chr7A 85.185 216 16 8 1651 1856 185982847 185982638 1.550000e-49 207.0
11 TraesCS7D01G223800 chr7A 84.795 171 20 6 6 172 309428856 309429024 2.620000e-37 167.0
12 TraesCS7D01G223800 chr7B 93.701 2175 116 9 1241 3403 154143612 154145777 0.000000e+00 3238.0
13 TraesCS7D01G223800 chr7B 87.291 1495 147 22 1979 3455 153594705 153596174 0.000000e+00 1668.0
14 TraesCS7D01G223800 chr7B 87.602 976 70 26 216 1172 154142500 154143443 0.000000e+00 1085.0
15 TraesCS7D01G223800 chr7B 88.263 426 29 6 757 1172 153592880 153593294 1.370000e-134 490.0
16 TraesCS7D01G223800 chr7B 88.218 331 29 4 3480 3810 154145791 154146111 1.850000e-103 387.0
17 TraesCS7D01G223800 chr7B 93.886 229 5 1 4014 4242 716036677 716036458 1.890000e-88 337.0
18 TraesCS7D01G223800 chr7B 79.825 342 26 20 1526 1856 153594372 153594681 4.300000e-50 209.0
19 TraesCS7D01G223800 chr4D 83.550 462 51 14 221 665 50232654 50232201 3.950000e-110 409.0
20 TraesCS7D01G223800 chr4D 87.654 162 18 2 4 163 112728729 112728890 2.010000e-43 187.0
21 TraesCS7D01G223800 chr5D 83.153 463 49 22 226 665 484025007 484025463 3.070000e-106 396.0
22 TraesCS7D01G223800 chr5D 99.419 172 1 0 4011 4182 535145334 535145505 3.180000e-81 313.0
23 TraesCS7D01G223800 chr5D 90.830 229 15 2 4014 4242 442358588 442358810 6.890000e-78 302.0
24 TraesCS7D01G223800 chr5D 79.825 228 16 16 4032 4242 405165823 405165609 5.720000e-29 139.0
25 TraesCS7D01G223800 chr3D 95.259 232 2 1 4011 4242 101559458 101559236 4.030000e-95 359.0
26 TraesCS7D01G223800 chr3D 81.360 456 57 22 227 665 48172470 48172914 3.140000e-91 346.0
27 TraesCS7D01G223800 chr3D 80.769 156 23 5 505 653 570270185 570270340 9.640000e-22 115.0
28 TraesCS7D01G223800 chr2B 94.348 230 4 1 4013 4242 250686610 250686830 1.130000e-90 344.0
29 TraesCS7D01G223800 chr5A 94.323 229 4 1 4014 4242 158188183 158188402 4.060000e-90 342.0
30 TraesCS7D01G223800 chr3A 82.093 430 49 21 250 665 19315149 19314734 4.060000e-90 342.0
31 TraesCS7D01G223800 chr3A 83.051 354 42 14 221 564 603845664 603845319 5.330000e-79 305.0
32 TraesCS7D01G223800 chr1A 93.886 229 4 1 4014 4242 25560960 25561178 1.890000e-88 337.0
33 TraesCS7D01G223800 chr1A 87.143 140 16 2 3659 3797 38634376 38634238 1.580000e-34 158.0
34 TraesCS7D01G223800 chr1B 80.986 426 62 11 222 632 22649709 22650130 1.900000e-83 320.0
35 TraesCS7D01G223800 chr1B 82.533 229 19 13 4032 4242 35490974 35491199 9.370000e-42 182.0
36 TraesCS7D01G223800 chr1B 91.667 48 4 0 12 59 362608028 362607981 2.740000e-07 67.6
37 TraesCS7D01G223800 chr6B 80.851 423 61 17 224 632 688380591 688381007 8.850000e-82 315.0
38 TraesCS7D01G223800 chr5B 92.273 220 14 1 4023 4242 10552471 10552687 4.120000e-80 309.0
39 TraesCS7D01G223800 chr5B 80.488 246 28 12 4012 4242 423214031 423213791 2.030000e-38 171.0
40 TraesCS7D01G223800 chr5B 79.394 165 30 4 3639 3801 43867188 43867026 3.470000e-21 113.0
41 TraesCS7D01G223800 chr3B 79.212 457 72 16 221 658 478563979 478564431 3.210000e-76 296.0
42 TraesCS7D01G223800 chr3B 79.111 225 26 15 4032 4242 710552213 710551996 7.400000e-28 135.0
43 TraesCS7D01G223800 chr2D 78.495 465 70 23 222 665 72451713 72451258 1.160000e-70 278.0
44 TraesCS7D01G223800 chr6A 83.500 200 24 9 1 194 612621084 612621280 1.210000e-40 178.0
45 TraesCS7D01G223800 chr6A 84.375 160 23 2 3639 3797 18928609 18928767 5.680000e-34 156.0
46 TraesCS7D01G223800 chr4A 83.237 173 23 6 4 172 716984300 716984470 2.040000e-33 154.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G223800 chr7D 184557887 184562128 4241 False 7834.000000 7834 100.000000 1 4242 1 chr7D.!!$F1 4241
1 TraesCS7D01G223800 chr7D 184513333 184516124 2791 False 779.333333 1629 87.593333 772 3405 3 chr7D.!!$F2 2633
2 TraesCS7D01G223800 chr7A 191658485 191662442 3957 False 3020.000000 5770 93.556000 29 4013 2 chr7A.!!$F2 3984
3 TraesCS7D01G223800 chr7A 185981344 185983917 2573 True 765.000000 1568 87.741333 757 3246 3 chr7A.!!$R1 2489
4 TraesCS7D01G223800 chr7B 154142500 154146111 3611 False 1570.000000 3238 89.840333 216 3810 3 chr7B.!!$F2 3594
5 TraesCS7D01G223800 chr7B 153592880 153596174 3294 False 789.000000 1668 85.126333 757 3455 3 chr7B.!!$F1 2698

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
650 672 0.179097 GAGGTTGCCGAGAGCCTAAG 60.179 60.0 0.0 0.0 42.71 2.18 F
981 1015 0.464036 TCACCAGTGCGAGACAAAGT 59.536 50.0 0.0 0.0 0.00 2.66 F
2454 3295 0.317479 ACCTGCCTCTACAACGTGAC 59.683 55.0 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
2454 3295 0.034059 GGATGAGCCGTCACCATAGG 59.966 60.0 0.00 0.00 34.75 2.57 R
2797 3638 0.248907 CGTAGCCACCGATGTCGATT 60.249 55.0 3.62 0.00 43.02 3.34 R
3740 4615 0.163788 GCCACGTCTCATTTGACACG 59.836 55.0 6.79 6.79 41.22 4.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.273257 TCGTCCACGAGCAACGCA 62.273 61.111 0.00 0.00 44.22 5.24
27 28 4.059459 CGTCCACGAGCAACGCAC 62.059 66.667 0.00 0.00 46.94 5.34
36 37 1.459209 CGAGCAACGCACAAGTAATGA 59.541 47.619 0.00 0.00 34.51 2.57
49 50 6.051074 CACAAGTAATGATGAGGCACATAGA 58.949 40.000 0.00 0.00 39.56 1.98
50 51 6.709397 CACAAGTAATGATGAGGCACATAGAT 59.291 38.462 0.00 0.00 39.56 1.98
63 64 4.633565 GGCACATAGATTAGCTAGAATGGC 59.366 45.833 0.00 3.50 46.31 4.40
80 81 1.837439 TGGCCACTACCCTAGACATTG 59.163 52.381 0.00 0.00 0.00 2.82
87 88 1.933021 ACCCTAGACATTGGACGACA 58.067 50.000 0.00 0.00 0.00 4.35
93 94 4.984785 CCTAGACATTGGACGACATATGTG 59.015 45.833 14.43 8.31 33.77 3.21
107 108 3.332783 ACATATGTGGCTCATGGATCCAT 59.667 43.478 22.15 22.15 37.91 3.41
143 144 9.707957 TTTGTATTCCCCTAAATGTTGATACAT 57.292 29.630 0.00 0.00 46.85 2.29
148 149 9.936329 ATTCCCCTAAATGTTGATACATAAAGT 57.064 29.630 0.00 0.00 44.14 2.66
159 160 9.953697 TGTTGATACATAAAGTAAAGCGTTTTT 57.046 25.926 1.60 0.00 36.05 1.94
181 182 5.710613 TCTTTAAAACAAAAGGCAAAGCG 57.289 34.783 0.00 0.00 37.13 4.68
184 185 2.223537 AAACAAAAGGCAAAGCGGAG 57.776 45.000 0.00 0.00 0.00 4.63
193 194 0.742635 GCAAAGCGGAGAGGAAGGAG 60.743 60.000 0.00 0.00 0.00 3.69
203 204 1.681486 GAGGAAGGAGAAGGAGGGCG 61.681 65.000 0.00 0.00 0.00 6.13
219 220 2.588596 CGCCACGCATCATAGCCA 60.589 61.111 0.00 0.00 0.00 4.75
256 257 2.105993 AGCTCGGGTTTTTAGACACCTT 59.894 45.455 0.00 0.00 33.09 3.50
264 265 6.349033 CGGGTTTTTAGACACCTTTTATCCTG 60.349 42.308 0.00 0.00 33.09 3.86
285 286 2.627699 GACCCTCCAATGTTGCTTTGAA 59.372 45.455 0.00 0.00 0.00 2.69
296 297 3.505680 TGTTGCTTTGAAATCCGTGCTAT 59.494 39.130 0.00 0.00 0.00 2.97
360 362 9.743057 TTCTTCAAAACGAAACAACATATGAAT 57.257 25.926 10.38 0.00 31.71 2.57
374 376 9.275398 ACAACATATGAATTTCAAACTTTGCAT 57.725 25.926 10.38 0.00 0.00 3.96
385 387 6.981762 TCAAACTTTGCATGACAACAAAAT 57.018 29.167 0.00 0.00 38.23 1.82
391 393 8.086851 ACTTTGCATGACAACAAAATAAATCC 57.913 30.769 0.00 0.00 38.23 3.01
495 504 9.767684 TGTTTTTAGTATTTATGATGCACGAAG 57.232 29.630 0.00 0.00 0.00 3.79
553 568 3.252400 TGTTGTGCTGCAAAGTTTGAAG 58.748 40.909 19.82 18.91 39.03 3.02
565 580 6.200665 TGCAAAGTTTGAAGTTCATATGTTGC 59.799 34.615 24.19 24.19 34.19 4.17
572 587 7.977789 TTGAAGTTCATATGTTGCTCTACAA 57.022 32.000 6.36 5.35 35.33 2.41
598 619 4.546570 AGCGGAAAAGAAAATACTTGCAC 58.453 39.130 0.00 0.00 0.00 4.57
603 624 6.362283 CGGAAAAGAAAATACTTGCACGAATT 59.638 34.615 0.00 0.00 0.00 2.17
618 639 2.419673 ACGAATTGCGATGCAGAATTGA 59.580 40.909 0.00 0.00 44.57 2.57
632 654 6.594744 TGCAGAATTGAATGGCTAGATAAGA 58.405 36.000 0.00 0.00 0.00 2.10
636 658 7.718753 CAGAATTGAATGGCTAGATAAGAGGTT 59.281 37.037 0.00 0.00 0.00 3.50
637 659 7.718753 AGAATTGAATGGCTAGATAAGAGGTTG 59.281 37.037 0.00 0.00 0.00 3.77
639 661 3.778954 ATGGCTAGATAAGAGGTTGCC 57.221 47.619 0.00 0.00 39.33 4.52
644 666 3.305064 GCTAGATAAGAGGTTGCCGAGAG 60.305 52.174 0.00 0.00 0.00 3.20
650 672 0.179097 GAGGTTGCCGAGAGCCTAAG 60.179 60.000 0.00 0.00 42.71 2.18
651 673 1.815840 GGTTGCCGAGAGCCTAAGC 60.816 63.158 0.00 0.00 42.71 3.09
665 687 4.820284 GCCTAAGCTCCACAATATGTTC 57.180 45.455 0.00 0.00 35.50 3.18
667 689 5.611374 GCCTAAGCTCCACAATATGTTCTA 58.389 41.667 0.00 0.00 35.50 2.10
699 721 2.483745 CGGCAAGCTGCTGTGATG 59.516 61.111 1.35 0.00 44.43 3.07
742 764 2.635229 CTTCAGCCGACCCATCCGAG 62.635 65.000 0.00 0.00 0.00 4.63
967 996 1.031571 GCCGCTCCATTCATTCACCA 61.032 55.000 0.00 0.00 0.00 4.17
981 1015 0.464036 TCACCAGTGCGAGACAAAGT 59.536 50.000 0.00 0.00 0.00 2.66
1429 1617 7.222611 CACACTTTGAAACCAGAAAACTAATGG 59.777 37.037 0.00 0.00 40.10 3.16
1573 2401 7.643764 GCACGTATTATAATTTGCTGAACATGT 59.356 33.333 2.68 0.00 0.00 3.21
1602 2430 9.649167 ACGTTTTAATATAGGCACATATAGGTC 57.351 33.333 0.00 0.00 0.00 3.85
1730 2558 1.066858 TGATTGACAGGCGAGACTTCC 60.067 52.381 0.00 0.00 0.00 3.46
1786 2614 3.918220 CGAGCAAGCGCGACATCC 61.918 66.667 12.10 0.00 45.49 3.51
1789 2617 2.815211 GCAAGCGCGACATCCTCA 60.815 61.111 12.10 0.00 0.00 3.86
1790 2618 2.806856 GCAAGCGCGACATCCTCAG 61.807 63.158 12.10 0.00 0.00 3.35
1791 2619 2.510238 AAGCGCGACATCCTCAGC 60.510 61.111 12.10 0.00 0.00 4.26
1924 2762 3.902112 CCACCAAGCCCCACACCT 61.902 66.667 0.00 0.00 0.00 4.00
2116 2954 1.076485 GCCTCCATCACCAGCCATT 60.076 57.895 0.00 0.00 0.00 3.16
2231 3069 2.552768 CGGAGTTCGTCGTCGTCA 59.447 61.111 1.33 0.00 38.33 4.35
2454 3295 0.317479 ACCTGCCTCTACAACGTGAC 59.683 55.000 0.00 0.00 0.00 3.67
2680 3521 2.479566 ATTGTCTGCCGTCTCACAAT 57.520 45.000 0.00 0.00 35.16 2.71
2797 3638 1.285950 CTTCGTGGAGCTCGTGTCA 59.714 57.895 7.83 0.00 0.00 3.58
2950 3791 2.817844 GTTCACCATGAAGGGGTACAAC 59.182 50.000 0.00 0.00 43.37 3.32
3142 3986 2.571757 GCGTCGTCTGATCCCACA 59.428 61.111 0.00 0.00 0.00 4.17
3288 4149 2.203549 TATCGCCACCCAATGTGCCA 62.204 55.000 0.00 0.00 44.01 4.92
3408 4279 3.506108 CCGGCTGATTTGAGCAGG 58.494 61.111 0.00 0.00 46.00 4.85
3504 4379 2.954989 TGAAGAGCTGCTCGTATCTCAT 59.045 45.455 22.77 0.91 35.36 2.90
3531 4406 6.854496 TTTTTATGAGCGTGTGTCTACTTT 57.146 33.333 0.00 0.00 0.00 2.66
3564 4439 8.877779 TCGCAATTTGGGTATTTATTGAAAATG 58.122 29.630 12.54 0.00 31.29 2.32
3599 4474 7.930332 AGGGAACTTAGTACCACTTTCTGGTC 61.930 46.154 8.40 0.00 45.71 4.02
3635 4510 3.317711 CCACACCATCTTTGCACTTAACA 59.682 43.478 0.00 0.00 0.00 2.41
3636 4511 4.202101 CCACACCATCTTTGCACTTAACAA 60.202 41.667 0.00 0.00 0.00 2.83
3700 4575 2.267961 GGTAGGCCCCACTTGTCG 59.732 66.667 0.00 0.00 0.00 4.35
3787 4662 7.821359 CCACCTATCAATAACTAGATGGTCATG 59.179 40.741 0.00 0.00 0.00 3.07
3799 4674 5.432680 AGATGGTCATGTTCTTCACATCT 57.567 39.130 0.00 0.00 43.17 2.90
3800 4675 5.426504 AGATGGTCATGTTCTTCACATCTC 58.573 41.667 0.00 0.00 43.17 2.75
3801 4676 4.897509 TGGTCATGTTCTTCACATCTCT 57.102 40.909 0.00 0.00 43.17 3.10
3802 4677 4.825422 TGGTCATGTTCTTCACATCTCTC 58.175 43.478 0.00 0.00 43.17 3.20
3803 4678 4.529769 TGGTCATGTTCTTCACATCTCTCT 59.470 41.667 0.00 0.00 43.17 3.10
3804 4679 5.108517 GGTCATGTTCTTCACATCTCTCTC 58.891 45.833 0.00 0.00 43.17 3.20
3805 4680 5.105392 GGTCATGTTCTTCACATCTCTCTCT 60.105 44.000 0.00 0.00 43.17 3.10
3806 4681 6.035843 GTCATGTTCTTCACATCTCTCTCTC 58.964 44.000 0.00 0.00 43.17 3.20
3807 4682 5.951148 TCATGTTCTTCACATCTCTCTCTCT 59.049 40.000 0.00 0.00 43.17 3.10
3808 4683 5.895636 TGTTCTTCACATCTCTCTCTCTC 57.104 43.478 0.00 0.00 0.00 3.20
3809 4684 5.569355 TGTTCTTCACATCTCTCTCTCTCT 58.431 41.667 0.00 0.00 0.00 3.10
3810 4685 5.647658 TGTTCTTCACATCTCTCTCTCTCTC 59.352 44.000 0.00 0.00 0.00 3.20
3811 4686 5.698741 TCTTCACATCTCTCTCTCTCTCT 57.301 43.478 0.00 0.00 0.00 3.10
3812 4687 5.674525 TCTTCACATCTCTCTCTCTCTCTC 58.325 45.833 0.00 0.00 0.00 3.20
3813 4688 5.426509 TCTTCACATCTCTCTCTCTCTCTCT 59.573 44.000 0.00 0.00 0.00 3.10
3814 4689 5.282055 TCACATCTCTCTCTCTCTCTCTC 57.718 47.826 0.00 0.00 0.00 3.20
3815 4690 4.964897 TCACATCTCTCTCTCTCTCTCTCT 59.035 45.833 0.00 0.00 0.00 3.10
3816 4691 5.069648 TCACATCTCTCTCTCTCTCTCTCTC 59.930 48.000 0.00 0.00 0.00 3.20
3817 4692 5.070180 CACATCTCTCTCTCTCTCTCTCTCT 59.930 48.000 0.00 0.00 0.00 3.10
3818 4693 5.304101 ACATCTCTCTCTCTCTCTCTCTCTC 59.696 48.000 0.00 0.00 0.00 3.20
3819 4694 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3820 4695 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3821 4696 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3822 4697 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3823 4698 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3824 4699 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3825 4700 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3826 4701 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3827 4702 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3828 4703 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3878 4753 3.145286 TGAGGCATTTCATCGAACAACA 58.855 40.909 0.00 0.00 0.00 3.33
3898 4773 5.400066 ACATTTGGGCGCTAATACTTTTT 57.600 34.783 7.64 0.00 0.00 1.94
3910 4785 6.183360 CGCTAATACTTTTTCTCTTGGTGGAG 60.183 42.308 0.00 0.00 34.88 3.86
3913 4788 3.481453 ACTTTTTCTCTTGGTGGAGAGC 58.519 45.455 0.00 0.00 42.37 4.09
3914 4789 2.169832 TTTTCTCTTGGTGGAGAGCG 57.830 50.000 0.00 0.00 42.37 5.03
3915 4790 1.048601 TTTCTCTTGGTGGAGAGCGT 58.951 50.000 0.00 0.00 42.37 5.07
3941 4816 4.443266 GCAGCTCGTCCGCCTCTT 62.443 66.667 0.00 0.00 0.00 2.85
3950 4825 0.179097 GTCCGCCTCTTCATGGAGTC 60.179 60.000 0.00 0.00 0.00 3.36
3951 4826 1.144936 CCGCCTCTTCATGGAGTCC 59.855 63.158 0.73 0.73 0.00 3.85
3955 4830 1.577736 CCTCTTCATGGAGTCCTGGT 58.422 55.000 11.33 0.00 0.00 4.00
3999 4874 1.887956 GCTTCCCACACCATGTCATGT 60.888 52.381 11.84 0.00 0.00 3.21
4020 4895 2.060050 GCAGTAGCTCCCTGTAGAGA 57.940 55.000 13.21 0.00 35.82 3.10
4021 4896 1.953686 GCAGTAGCTCCCTGTAGAGAG 59.046 57.143 13.21 0.00 35.82 3.20
4022 4897 2.582052 CAGTAGCTCCCTGTAGAGAGG 58.418 57.143 0.00 0.00 35.82 3.69
4023 4898 2.173782 CAGTAGCTCCCTGTAGAGAGGA 59.826 54.545 0.00 0.00 35.82 3.71
4024 4899 3.060611 AGTAGCTCCCTGTAGAGAGGAT 58.939 50.000 0.00 0.00 35.82 3.24
4025 4900 4.042311 CAGTAGCTCCCTGTAGAGAGGATA 59.958 50.000 0.00 0.00 35.82 2.59
4026 4901 4.855599 AGTAGCTCCCTGTAGAGAGGATAT 59.144 45.833 0.00 0.00 35.82 1.63
4027 4902 4.757997 AGCTCCCTGTAGAGAGGATATT 57.242 45.455 0.00 0.00 35.82 1.28
4028 4903 5.086598 AGCTCCCTGTAGAGAGGATATTT 57.913 43.478 0.00 0.00 35.82 1.40
4029 4904 4.837860 AGCTCCCTGTAGAGAGGATATTTG 59.162 45.833 0.00 0.00 35.82 2.32
4030 4905 4.020662 GCTCCCTGTAGAGAGGATATTTGG 60.021 50.000 0.00 0.00 35.82 3.28
4031 4906 5.151454 CTCCCTGTAGAGAGGATATTTGGT 58.849 45.833 0.00 0.00 35.82 3.67
4032 4907 4.901849 TCCCTGTAGAGAGGATATTTGGTG 59.098 45.833 0.00 0.00 34.69 4.17
4033 4908 4.503991 CCCTGTAGAGAGGATATTTGGTGC 60.504 50.000 0.00 0.00 34.69 5.01
4034 4909 4.101585 CCTGTAGAGAGGATATTTGGTGCA 59.898 45.833 0.00 0.00 34.69 4.57
4035 4910 5.396772 CCTGTAGAGAGGATATTTGGTGCAA 60.397 44.000 0.00 0.00 34.69 4.08
4036 4911 5.428253 TGTAGAGAGGATATTTGGTGCAAC 58.572 41.667 0.00 0.00 0.00 4.17
4037 4912 4.851639 AGAGAGGATATTTGGTGCAACT 57.148 40.909 2.04 0.00 36.74 3.16
4038 4913 4.775236 AGAGAGGATATTTGGTGCAACTC 58.225 43.478 2.04 0.00 36.74 3.01
4039 4914 4.225942 AGAGAGGATATTTGGTGCAACTCA 59.774 41.667 2.04 0.00 36.74 3.41
4040 4915 5.104193 AGAGAGGATATTTGGTGCAACTCAT 60.104 40.000 2.04 0.00 36.74 2.90
4041 4916 5.513233 AGAGGATATTTGGTGCAACTCATT 58.487 37.500 2.04 0.00 36.74 2.57
4042 4917 5.359009 AGAGGATATTTGGTGCAACTCATTG 59.641 40.000 2.04 0.00 38.99 2.82
4043 4918 5.018809 AGGATATTTGGTGCAACTCATTGT 58.981 37.500 2.04 0.00 38.17 2.71
4044 4919 6.186957 AGGATATTTGGTGCAACTCATTGTA 58.813 36.000 2.04 0.00 38.17 2.41
4045 4920 6.835488 AGGATATTTGGTGCAACTCATTGTAT 59.165 34.615 2.04 0.00 38.17 2.29
4046 4921 7.342799 AGGATATTTGGTGCAACTCATTGTATT 59.657 33.333 2.04 0.00 38.17 1.89
4047 4922 7.649306 GGATATTTGGTGCAACTCATTGTATTC 59.351 37.037 2.04 0.00 38.17 1.75
4048 4923 4.782019 TTGGTGCAACTCATTGTATTCC 57.218 40.909 2.04 0.00 38.17 3.01
4049 4924 3.760738 TGGTGCAACTCATTGTATTCCA 58.239 40.909 2.04 0.00 38.17 3.53
4050 4925 4.343231 TGGTGCAACTCATTGTATTCCAT 58.657 39.130 2.04 0.00 38.17 3.41
4051 4926 4.158209 TGGTGCAACTCATTGTATTCCATG 59.842 41.667 2.04 0.00 38.17 3.66
4052 4927 4.440525 GGTGCAACTCATTGTATTCCATGG 60.441 45.833 4.97 4.97 38.17 3.66
4053 4928 4.398988 GTGCAACTCATTGTATTCCATGGA 59.601 41.667 11.44 11.44 38.17 3.41
4054 4929 4.641541 TGCAACTCATTGTATTCCATGGAG 59.358 41.667 15.53 1.18 38.17 3.86
4055 4930 4.641989 GCAACTCATTGTATTCCATGGAGT 59.358 41.667 15.53 15.19 38.02 3.85
4056 4931 5.822519 GCAACTCATTGTATTCCATGGAGTA 59.177 40.000 15.53 14.01 36.41 2.59
4057 4932 6.017605 GCAACTCATTGTATTCCATGGAGTAG 60.018 42.308 16.75 8.78 36.41 2.57
4058 4933 6.179906 ACTCATTGTATTCCATGGAGTAGG 57.820 41.667 16.75 7.76 35.96 3.18
4059 4934 5.667626 ACTCATTGTATTCCATGGAGTAGGT 59.332 40.000 16.75 4.07 35.96 3.08
4060 4935 6.158695 ACTCATTGTATTCCATGGAGTAGGTT 59.841 38.462 16.75 2.63 35.96 3.50
4061 4936 7.347222 ACTCATTGTATTCCATGGAGTAGGTTA 59.653 37.037 16.75 0.00 35.96 2.85
4062 4937 7.506114 TCATTGTATTCCATGGAGTAGGTTAC 58.494 38.462 16.75 8.47 0.00 2.50
4063 4938 6.877668 TTGTATTCCATGGAGTAGGTTACA 57.122 37.500 16.75 10.90 0.00 2.41
4064 4939 7.446106 TTGTATTCCATGGAGTAGGTTACAT 57.554 36.000 16.75 6.15 30.58 2.29
4065 4940 7.446106 TGTATTCCATGGAGTAGGTTACATT 57.554 36.000 16.75 0.00 0.00 2.71
4066 4941 8.555896 TGTATTCCATGGAGTAGGTTACATTA 57.444 34.615 16.75 0.00 0.00 1.90
4067 4942 9.166222 TGTATTCCATGGAGTAGGTTACATTAT 57.834 33.333 16.75 4.75 0.00 1.28
4072 4947 9.831682 TCCATGGAGTAGGTTACATTATATACA 57.168 33.333 11.44 0.00 0.00 2.29
4073 4948 9.871238 CCATGGAGTAGGTTACATTATATACAC 57.129 37.037 5.56 0.00 0.00 2.90
4076 4951 9.085645 TGGAGTAGGTTACATTATATACACAGG 57.914 37.037 0.00 0.00 0.00 4.00
4077 4952 9.305555 GGAGTAGGTTACATTATATACACAGGA 57.694 37.037 0.00 0.00 0.00 3.86
4119 4994 9.411189 GGTAACTAATCCTACCATATCTCTAGG 57.589 40.741 0.00 0.00 37.98 3.02
4122 4997 8.471302 ACTAATCCTACCATATCTCTAGGAGT 57.529 38.462 0.00 0.00 39.53 3.85
4123 4998 8.907050 ACTAATCCTACCATATCTCTAGGAGTT 58.093 37.037 5.56 4.10 39.53 3.01
4126 5001 6.723339 TCCTACCATATCTCTAGGAGTTAGC 58.277 44.000 0.00 0.00 32.64 3.09
4127 5002 6.506056 TCCTACCATATCTCTAGGAGTTAGCT 59.494 42.308 0.00 0.00 32.64 3.32
4128 5003 7.683322 TCCTACCATATCTCTAGGAGTTAGCTA 59.317 40.741 0.00 0.00 32.64 3.32
4129 5004 8.499406 CCTACCATATCTCTAGGAGTTAGCTAT 58.501 40.741 0.00 0.00 30.11 2.97
4132 5007 8.837737 ACCATATCTCTAGGAGTTAGCTATACA 58.162 37.037 0.00 0.00 0.00 2.29
4133 5008 9.688091 CCATATCTCTAGGAGTTAGCTATACAA 57.312 37.037 0.00 0.00 0.00 2.41
4135 5010 9.914834 ATATCTCTAGGAGTTAGCTATACAAGG 57.085 37.037 0.00 0.00 0.00 3.61
4136 5011 6.005198 TCTCTAGGAGTTAGCTATACAAGGC 58.995 44.000 0.00 0.00 0.00 4.35
4137 5012 5.954757 TCTAGGAGTTAGCTATACAAGGCT 58.045 41.667 0.00 0.00 41.92 4.58
4138 5013 7.017353 TCTCTAGGAGTTAGCTATACAAGGCTA 59.983 40.741 0.00 0.00 39.65 3.93
4139 5014 7.169591 TCTAGGAGTTAGCTATACAAGGCTAG 58.830 42.308 0.00 0.00 41.24 3.42
4140 5015 5.954757 AGGAGTTAGCTATACAAGGCTAGA 58.045 41.667 0.00 0.00 41.24 2.43
4141 5016 6.007703 AGGAGTTAGCTATACAAGGCTAGAG 58.992 44.000 0.00 0.00 41.24 2.43
4142 5017 6.005198 GGAGTTAGCTATACAAGGCTAGAGA 58.995 44.000 0.00 0.00 41.24 3.10
4143 5018 6.490721 GGAGTTAGCTATACAAGGCTAGAGAA 59.509 42.308 0.00 0.00 41.24 2.87
4144 5019 7.308951 GGAGTTAGCTATACAAGGCTAGAGAAG 60.309 44.444 0.00 0.00 41.24 2.85
4145 5020 7.291566 AGTTAGCTATACAAGGCTAGAGAAGA 58.708 38.462 0.00 0.00 41.24 2.87
4146 5021 7.947890 AGTTAGCTATACAAGGCTAGAGAAGAT 59.052 37.037 0.00 0.00 41.24 2.40
4147 5022 9.233649 GTTAGCTATACAAGGCTAGAGAAGATA 57.766 37.037 0.00 0.00 41.24 1.98
4148 5023 9.809395 TTAGCTATACAAGGCTAGAGAAGATAA 57.191 33.333 0.00 0.00 41.24 1.75
4149 5024 8.348285 AGCTATACAAGGCTAGAGAAGATAAG 57.652 38.462 0.00 0.00 37.00 1.73
4150 5025 8.167392 AGCTATACAAGGCTAGAGAAGATAAGA 58.833 37.037 0.00 0.00 37.00 2.10
4151 5026 8.241367 GCTATACAAGGCTAGAGAAGATAAGAC 58.759 40.741 0.00 0.00 0.00 3.01
4152 5027 9.515226 CTATACAAGGCTAGAGAAGATAAGACT 57.485 37.037 0.00 0.00 0.00 3.24
4154 5029 7.817418 ACAAGGCTAGAGAAGATAAGACTAG 57.183 40.000 0.00 0.00 35.21 2.57
4155 5030 7.579105 ACAAGGCTAGAGAAGATAAGACTAGA 58.421 38.462 0.00 0.00 34.36 2.43
4156 5031 8.056400 ACAAGGCTAGAGAAGATAAGACTAGAA 58.944 37.037 0.00 0.00 34.36 2.10
4157 5032 8.908903 CAAGGCTAGAGAAGATAAGACTAGAAA 58.091 37.037 0.00 0.00 34.36 2.52
4158 5033 9.654919 AAGGCTAGAGAAGATAAGACTAGAAAT 57.345 33.333 0.00 0.00 34.36 2.17
4173 5048 9.737427 AAGACTAGAAATACAAGATATGTCACG 57.263 33.333 0.00 0.00 42.70 4.35
4174 5049 8.904834 AGACTAGAAATACAAGATATGTCACGT 58.095 33.333 0.00 0.00 42.70 4.49
4175 5050 9.517609 GACTAGAAATACAAGATATGTCACGTT 57.482 33.333 0.00 0.00 42.70 3.99
4176 5051 9.517609 ACTAGAAATACAAGATATGTCACGTTC 57.482 33.333 0.00 0.00 42.70 3.95
4177 5052 9.516314 CTAGAAATACAAGATATGTCACGTTCA 57.484 33.333 0.00 0.00 42.70 3.18
4178 5053 8.771920 AGAAATACAAGATATGTCACGTTCAA 57.228 30.769 0.00 0.00 42.70 2.69
4179 5054 8.656849 AGAAATACAAGATATGTCACGTTCAAC 58.343 33.333 0.00 0.00 42.70 3.18
4180 5055 7.899178 AATACAAGATATGTCACGTTCAACA 57.101 32.000 0.00 0.00 42.70 3.33
4181 5056 5.591643 ACAAGATATGTCACGTTCAACAC 57.408 39.130 0.00 0.00 37.96 3.32
4182 5057 4.451096 ACAAGATATGTCACGTTCAACACC 59.549 41.667 0.00 0.00 37.96 4.16
4183 5058 3.596214 AGATATGTCACGTTCAACACCC 58.404 45.455 0.00 0.00 0.00 4.61
4184 5059 2.172851 TATGTCACGTTCAACACCCC 57.827 50.000 0.00 0.00 0.00 4.95
4185 5060 0.536460 ATGTCACGTTCAACACCCCC 60.536 55.000 0.00 0.00 0.00 5.40
4228 5103 4.520846 GCCGTCGGCGATGCAAAG 62.521 66.667 22.50 10.83 39.62 2.77
4229 5104 2.813474 CCGTCGGCGATGCAAAGA 60.813 61.111 23.15 0.00 41.33 2.52
4230 5105 2.395690 CGTCGGCGATGCAAAGAC 59.604 61.111 17.01 0.00 41.33 3.01
4231 5106 2.094659 CGTCGGCGATGCAAAGACT 61.095 57.895 17.01 0.00 41.33 3.24
4232 5107 1.421485 GTCGGCGATGCAAAGACTG 59.579 57.895 14.79 0.00 0.00 3.51
4233 5108 1.741401 TCGGCGATGCAAAGACTGG 60.741 57.895 4.99 0.00 0.00 4.00
4234 5109 1.741401 CGGCGATGCAAAGACTGGA 60.741 57.895 0.00 0.00 0.00 3.86
4235 5110 1.298157 CGGCGATGCAAAGACTGGAA 61.298 55.000 0.00 0.00 0.00 3.53
4236 5111 0.169009 GGCGATGCAAAGACTGGAAC 59.831 55.000 0.00 0.00 0.00 3.62
4237 5112 0.179215 GCGATGCAAAGACTGGAACG 60.179 55.000 0.00 0.00 43.20 3.95
4238 5113 1.428448 CGATGCAAAGACTGGAACGA 58.572 50.000 0.00 0.00 43.03 3.85
4239 5114 1.798223 CGATGCAAAGACTGGAACGAA 59.202 47.619 0.00 0.00 43.03 3.85
4240 5115 2.223144 CGATGCAAAGACTGGAACGAAA 59.777 45.455 0.00 0.00 43.03 3.46
4241 5116 3.555518 GATGCAAAGACTGGAACGAAAC 58.444 45.455 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.059459 GTGCGTTGCTCGTGGACG 62.059 66.667 0.00 0.00 42.13 4.79
11 12 2.430080 CTTGTGCGTTGCTCGTGGAC 62.430 60.000 4.16 0.00 42.13 4.02
12 13 2.202946 TTGTGCGTTGCTCGTGGA 60.203 55.556 4.16 0.00 42.13 4.02
13 14 1.218875 TACTTGTGCGTTGCTCGTGG 61.219 55.000 4.16 0.00 42.13 4.94
14 15 0.579630 TTACTTGTGCGTTGCTCGTG 59.420 50.000 4.16 0.00 42.13 4.35
15 16 1.194547 CATTACTTGTGCGTTGCTCGT 59.805 47.619 4.16 0.00 42.13 4.18
16 17 1.459209 TCATTACTTGTGCGTTGCTCG 59.541 47.619 0.00 0.00 43.12 5.03
17 18 3.125146 TCATCATTACTTGTGCGTTGCTC 59.875 43.478 0.00 0.00 0.00 4.26
18 19 3.073678 TCATCATTACTTGTGCGTTGCT 58.926 40.909 0.00 0.00 0.00 3.91
19 20 3.419915 CTCATCATTACTTGTGCGTTGC 58.580 45.455 0.00 0.00 0.00 4.17
20 21 3.728864 GCCTCATCATTACTTGTGCGTTG 60.729 47.826 0.00 0.00 0.00 4.10
21 22 2.420022 GCCTCATCATTACTTGTGCGTT 59.580 45.455 0.00 0.00 0.00 4.84
22 23 2.009774 GCCTCATCATTACTTGTGCGT 58.990 47.619 0.00 0.00 0.00 5.24
23 24 2.009051 TGCCTCATCATTACTTGTGCG 58.991 47.619 0.00 0.00 0.00 5.34
24 25 2.749076 TGTGCCTCATCATTACTTGTGC 59.251 45.455 0.00 0.00 0.00 4.57
25 26 6.051074 TCTATGTGCCTCATCATTACTTGTG 58.949 40.000 0.00 0.00 37.91 3.33
26 27 6.239217 TCTATGTGCCTCATCATTACTTGT 57.761 37.500 0.00 0.00 37.91 3.16
27 28 7.741027 AATCTATGTGCCTCATCATTACTTG 57.259 36.000 0.00 0.00 37.91 3.16
36 37 6.924913 TTCTAGCTAATCTATGTGCCTCAT 57.075 37.500 0.00 0.00 40.25 2.90
49 50 3.328050 GGGTAGTGGCCATTCTAGCTAAT 59.672 47.826 24.00 0.00 35.71 1.73
50 51 2.704065 GGGTAGTGGCCATTCTAGCTAA 59.296 50.000 24.00 0.00 35.71 3.09
63 64 2.100916 CGTCCAATGTCTAGGGTAGTGG 59.899 54.545 0.00 0.00 0.00 4.00
66 67 3.021695 TGTCGTCCAATGTCTAGGGTAG 58.978 50.000 0.00 0.00 0.00 3.18
80 81 2.138320 CATGAGCCACATATGTCGTCC 58.862 52.381 5.07 0.00 37.46 4.79
93 94 2.988570 GATCTGATGGATCCATGAGCC 58.011 52.381 30.31 21.57 43.65 4.70
107 108 7.690454 TTAGGGGAATACAAAGATGATCTGA 57.310 36.000 0.00 0.00 0.00 3.27
155 156 7.535599 CGCTTTGCCTTTTGTTTTAAAGAAAAA 59.464 29.630 12.55 6.24 37.31 1.94
156 157 7.018235 CGCTTTGCCTTTTGTTTTAAAGAAAA 58.982 30.769 11.31 11.31 37.31 2.29
157 158 6.402658 CCGCTTTGCCTTTTGTTTTAAAGAAA 60.403 34.615 0.00 0.00 37.31 2.52
158 159 5.064071 CCGCTTTGCCTTTTGTTTTAAAGAA 59.936 36.000 0.00 0.00 37.31 2.52
159 160 4.568760 CCGCTTTGCCTTTTGTTTTAAAGA 59.431 37.500 0.00 0.00 37.31 2.52
162 163 4.116238 CTCCGCTTTGCCTTTTGTTTTAA 58.884 39.130 0.00 0.00 0.00 1.52
181 182 1.691163 CCCTCCTTCTCCTTCCTCTCC 60.691 61.905 0.00 0.00 0.00 3.71
184 185 1.681486 CGCCCTCCTTCTCCTTCCTC 61.681 65.000 0.00 0.00 0.00 3.71
203 204 1.227645 TCTGGCTATGATGCGTGGC 60.228 57.895 0.00 0.00 0.00 5.01
246 247 5.098663 AGGGTCAGGATAAAAGGTGTCTAA 58.901 41.667 0.00 0.00 0.00 2.10
248 249 3.519913 GAGGGTCAGGATAAAAGGTGTCT 59.480 47.826 0.00 0.00 0.00 3.41
256 257 4.599041 CAACATTGGAGGGTCAGGATAAA 58.401 43.478 0.00 0.00 0.00 1.40
264 265 2.238521 TCAAAGCAACATTGGAGGGTC 58.761 47.619 0.00 0.00 0.00 4.46
285 286 7.779073 ACTAAGTTAGTTGTATAGCACGGATT 58.221 34.615 9.85 0.00 34.86 3.01
360 362 6.791887 TTTGTTGTCATGCAAAGTTTGAAA 57.208 29.167 19.82 6.83 39.03 2.69
470 479 9.982291 TCTTCGTGCATCATAAATACTAAAAAC 57.018 29.630 0.00 0.00 0.00 2.43
495 504 6.581171 AGAATGTGGGAAAAATCAGACTTC 57.419 37.500 0.00 0.00 0.00 3.01
498 507 7.454260 AACTAGAATGTGGGAAAAATCAGAC 57.546 36.000 0.00 0.00 0.00 3.51
553 568 7.462109 CTCTCTTGTAGAGCAACATATGAAC 57.538 40.000 10.38 0.00 45.22 3.18
572 587 5.106515 GCAAGTATTTTCTTTTCCGCTCTCT 60.107 40.000 0.00 0.00 0.00 3.10
598 619 3.055613 TCAATTCTGCATCGCAATTCG 57.944 42.857 0.00 0.00 38.41 3.34
603 624 1.202325 GCCATTCAATTCTGCATCGCA 60.202 47.619 0.00 0.00 36.92 5.10
618 639 3.495100 CGGCAACCTCTTATCTAGCCATT 60.495 47.826 0.00 0.00 40.58 3.16
632 654 1.901085 CTTAGGCTCTCGGCAACCT 59.099 57.895 0.00 0.00 44.01 3.50
644 666 4.455606 AGAACATATTGTGGAGCTTAGGC 58.544 43.478 0.00 0.00 39.06 3.93
650 672 4.688413 GCTAGCTAGAACATATTGTGGAGC 59.312 45.833 25.15 1.24 33.14 4.70
651 673 5.221521 TGGCTAGCTAGAACATATTGTGGAG 60.222 44.000 25.15 0.00 0.00 3.86
742 764 2.189499 GCTGATGCAACCGATCCCC 61.189 63.158 0.00 0.00 39.41 4.81
866 893 0.246910 AAAACAAAAACGGGCGTGGT 59.753 45.000 0.00 0.00 0.00 4.16
874 901 6.254600 ACATGATCACGAAAAACAAAAACG 57.745 33.333 0.00 0.00 0.00 3.60
967 996 1.412710 TCAAGGACTTTGTCTCGCACT 59.587 47.619 0.00 0.00 38.01 4.40
981 1015 0.466007 TTGCAAGCACAGCTCAAGGA 60.466 50.000 0.00 0.00 38.25 3.36
1093 1137 2.341101 GGTCGAGGCTGACGGAGAA 61.341 63.158 0.00 0.00 39.83 2.87
1456 1645 2.898705 TGCGGTCAAGCAAAATTGTTT 58.101 38.095 0.00 0.00 45.06 2.83
1730 2558 0.240945 GGATGGTGAACTTGTTGCCG 59.759 55.000 0.00 0.00 0.00 5.69
1779 2607 2.202797 CGTGGGCTGAGGATGTCG 60.203 66.667 0.00 0.00 0.00 4.35
1783 2611 1.305297 TCTGTCGTGGGCTGAGGAT 60.305 57.895 0.00 0.00 0.00 3.24
1784 2612 1.979155 CTCTGTCGTGGGCTGAGGA 60.979 63.158 0.00 0.00 0.00 3.71
1786 2614 2.125753 GCTCTGTCGTGGGCTGAG 60.126 66.667 0.44 0.44 35.77 3.35
1924 2762 1.219124 GTCCGCTGATGCTGGAAGA 59.781 57.895 0.00 0.00 41.08 2.87
2116 2954 2.696526 AGTATATCGGAGGGAAGGCA 57.303 50.000 0.00 0.00 0.00 4.75
2454 3295 0.034059 GGATGAGCCGTCACCATAGG 59.966 60.000 0.00 0.00 34.75 2.57
2680 3521 2.364579 AACCCGGGCCTCGTCATA 60.365 61.111 24.08 0.00 37.11 2.15
2797 3638 0.248907 CGTAGCCACCGATGTCGATT 60.249 55.000 3.62 0.00 43.02 3.34
2923 3764 3.181418 ACCCCTTCATGGTGAACTTGAAT 60.181 43.478 0.00 0.00 40.93 2.57
3142 3986 2.036992 GCCGATGATGGAGAACTGATCT 59.963 50.000 0.00 0.00 42.61 2.75
3288 4149 1.262640 AAAGGATACCGACACCCGCT 61.263 55.000 0.00 0.00 36.84 5.52
3408 4279 2.735762 GCTGTGTAGGTGACCGAGAATC 60.736 54.545 0.00 0.00 0.00 2.52
3531 4406 2.198827 ACCCAAATTGCGATCAGACA 57.801 45.000 0.00 0.00 0.00 3.41
3564 4439 9.708092 GTGGTACTAAGTTCCCTAAATATGATC 57.292 37.037 0.00 0.00 0.00 2.92
3599 4474 0.962356 GTGTGGTTCCTCATGCCCTG 60.962 60.000 0.00 0.00 0.00 4.45
3635 4510 5.801947 GCAAATCGTACAATCATTGCTCTTT 59.198 36.000 0.00 0.00 39.87 2.52
3636 4511 5.335127 GCAAATCGTACAATCATTGCTCTT 58.665 37.500 0.00 0.00 39.87 2.85
3700 4575 1.609208 AATATTCGCCATGTCAGCCC 58.391 50.000 0.00 0.00 0.00 5.19
3740 4615 0.163788 GCCACGTCTCATTTGACACG 59.836 55.000 6.79 6.79 41.22 4.49
3758 4633 5.491982 CATCTAGTTATTGATAGGTGGGGC 58.508 45.833 0.00 0.00 0.00 5.80
3787 4662 5.882557 AGAGAGAGAGAGAGATGTGAAGAAC 59.117 44.000 0.00 0.00 0.00 3.01
3799 4674 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3800 4675 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3801 4676 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3802 4677 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3803 4678 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3804 4679 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3805 4680 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3806 4681 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3807 4682 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3808 4683 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3809 4684 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3810 4685 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3811 4686 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3812 4687 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3813 4688 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3814 4689 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3815 4690 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3816 4691 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3817 4692 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3818 4693 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3819 4694 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3820 4695 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3821 4696 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3822 4697 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3823 4698 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3824 4699 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3825 4700 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3826 4701 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3827 4702 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3828 4703 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3878 4753 5.652452 AGAGAAAAAGTATTAGCGCCCAAAT 59.348 36.000 2.29 4.49 0.00 2.32
3898 4773 0.827925 ACACGCTCTCCACCAAGAGA 60.828 55.000 5.13 0.00 44.67 3.10
3934 4809 0.179089 CAGGACTCCATGAAGAGGCG 60.179 60.000 0.00 0.00 43.43 5.52
3941 4816 0.415830 TACCCACCAGGACTCCATGA 59.584 55.000 0.00 0.00 39.89 3.07
3950 4825 2.224450 ACGAGAAAAACTACCCACCAGG 60.224 50.000 0.00 0.00 43.78 4.45
3951 4826 3.121738 ACGAGAAAAACTACCCACCAG 57.878 47.619 0.00 0.00 0.00 4.00
3955 4830 3.243839 ACGCTTACGAGAAAAACTACCCA 60.244 43.478 0.00 0.00 43.93 4.51
4013 4888 5.189736 AGTTGCACCAAATATCCTCTCTACA 59.810 40.000 0.00 0.00 0.00 2.74
4014 4889 5.675538 AGTTGCACCAAATATCCTCTCTAC 58.324 41.667 0.00 0.00 0.00 2.59
4015 4890 5.425217 TGAGTTGCACCAAATATCCTCTCTA 59.575 40.000 0.00 0.00 0.00 2.43
4016 4891 4.225942 TGAGTTGCACCAAATATCCTCTCT 59.774 41.667 0.00 0.00 0.00 3.10
4017 4892 4.517285 TGAGTTGCACCAAATATCCTCTC 58.483 43.478 0.00 0.00 0.00 3.20
4018 4893 4.574674 TGAGTTGCACCAAATATCCTCT 57.425 40.909 0.00 0.00 0.00 3.69
4019 4894 5.126061 ACAATGAGTTGCACCAAATATCCTC 59.874 40.000 0.00 0.00 38.96 3.71
4020 4895 5.018809 ACAATGAGTTGCACCAAATATCCT 58.981 37.500 0.00 0.00 38.96 3.24
4021 4896 5.329035 ACAATGAGTTGCACCAAATATCC 57.671 39.130 0.00 0.00 38.96 2.59
4022 4897 7.649306 GGAATACAATGAGTTGCACCAAATATC 59.351 37.037 0.00 0.00 38.96 1.63
4023 4898 7.123997 TGGAATACAATGAGTTGCACCAAATAT 59.876 33.333 0.00 0.00 38.96 1.28
4024 4899 6.435591 TGGAATACAATGAGTTGCACCAAATA 59.564 34.615 0.00 0.00 38.96 1.40
4025 4900 5.245751 TGGAATACAATGAGTTGCACCAAAT 59.754 36.000 0.00 0.00 38.96 2.32
4026 4901 4.586421 TGGAATACAATGAGTTGCACCAAA 59.414 37.500 0.00 0.00 38.96 3.28
4027 4902 4.148079 TGGAATACAATGAGTTGCACCAA 58.852 39.130 0.00 0.00 38.96 3.67
4028 4903 3.760738 TGGAATACAATGAGTTGCACCA 58.239 40.909 0.00 0.00 38.96 4.17
4029 4904 4.440525 CCATGGAATACAATGAGTTGCACC 60.441 45.833 5.56 0.00 38.96 5.01
4030 4905 4.398988 TCCATGGAATACAATGAGTTGCAC 59.601 41.667 13.46 0.00 38.96 4.57
4031 4906 4.598022 TCCATGGAATACAATGAGTTGCA 58.402 39.130 13.46 0.00 38.96 4.08
4032 4907 4.641989 ACTCCATGGAATACAATGAGTTGC 59.358 41.667 17.00 0.00 39.53 4.17
4033 4908 6.484643 CCTACTCCATGGAATACAATGAGTTG 59.515 42.308 17.00 7.56 41.44 3.16
4034 4909 6.158695 ACCTACTCCATGGAATACAATGAGTT 59.841 38.462 17.00 0.00 41.44 3.01
4035 4910 5.667626 ACCTACTCCATGGAATACAATGAGT 59.332 40.000 17.00 9.19 42.81 3.41
4036 4911 6.179906 ACCTACTCCATGGAATACAATGAG 57.820 41.667 17.00 2.97 37.03 2.90
4037 4912 6.575244 AACCTACTCCATGGAATACAATGA 57.425 37.500 17.00 0.00 0.00 2.57
4038 4913 7.279615 TGTAACCTACTCCATGGAATACAATG 58.720 38.462 17.00 4.55 31.65 2.82
4039 4914 7.446106 TGTAACCTACTCCATGGAATACAAT 57.554 36.000 17.00 4.03 31.65 2.71
4040 4915 6.877668 TGTAACCTACTCCATGGAATACAA 57.122 37.500 17.00 0.00 31.65 2.41
4041 4916 7.446106 AATGTAACCTACTCCATGGAATACA 57.554 36.000 17.00 16.40 35.49 2.29
4046 4921 9.831682 TGTATATAATGTAACCTACTCCATGGA 57.168 33.333 15.27 15.27 0.00 3.41
4047 4922 9.871238 GTGTATATAATGTAACCTACTCCATGG 57.129 37.037 4.97 4.97 0.00 3.66
4050 4925 9.085645 CCTGTGTATATAATGTAACCTACTCCA 57.914 37.037 0.00 0.00 0.00 3.86
4051 4926 9.305555 TCCTGTGTATATAATGTAACCTACTCC 57.694 37.037 0.00 0.00 0.00 3.85
4056 4931 9.381038 AGACATCCTGTGTATATAATGTAACCT 57.619 33.333 0.00 0.00 42.36 3.50
4057 4932 9.998106 AAGACATCCTGTGTATATAATGTAACC 57.002 33.333 0.00 0.00 42.36 2.85
4059 4934 9.489084 GCAAGACATCCTGTGTATATAATGTAA 57.511 33.333 0.00 0.00 42.36 2.41
4060 4935 7.812669 CGCAAGACATCCTGTGTATATAATGTA 59.187 37.037 0.00 0.00 42.36 2.29
4061 4936 6.646653 CGCAAGACATCCTGTGTATATAATGT 59.353 38.462 0.00 0.00 42.36 2.71
4062 4937 6.646653 ACGCAAGACATCCTGTGTATATAATG 59.353 38.462 0.00 0.00 42.36 1.90
4063 4938 6.646653 CACGCAAGACATCCTGTGTATATAAT 59.353 38.462 0.00 0.00 42.36 1.28
4064 4939 5.983118 CACGCAAGACATCCTGTGTATATAA 59.017 40.000 0.00 0.00 42.36 0.98
4065 4940 5.300792 TCACGCAAGACATCCTGTGTATATA 59.699 40.000 0.00 0.00 42.36 0.86
4066 4941 4.099419 TCACGCAAGACATCCTGTGTATAT 59.901 41.667 0.00 0.00 42.36 0.86
4067 4942 3.445805 TCACGCAAGACATCCTGTGTATA 59.554 43.478 0.00 0.00 42.36 1.47
4068 4943 2.233676 TCACGCAAGACATCCTGTGTAT 59.766 45.455 0.00 0.00 42.36 2.29
4069 4944 1.616374 TCACGCAAGACATCCTGTGTA 59.384 47.619 0.00 0.00 42.36 2.90
4070 4945 0.392706 TCACGCAAGACATCCTGTGT 59.607 50.000 0.00 0.00 45.83 3.72
4071 4946 0.792640 GTCACGCAAGACATCCTGTG 59.207 55.000 0.97 0.00 43.62 3.66
4072 4947 0.392706 TGTCACGCAAGACATCCTGT 59.607 50.000 4.26 0.00 43.18 4.00
4073 4948 1.511850 TTGTCACGCAAGACATCCTG 58.488 50.000 8.81 0.00 46.90 3.86
4082 4957 3.998341 GGATTAGTTACCTTGTCACGCAA 59.002 43.478 0.00 0.00 35.50 4.85
4083 4958 3.259876 AGGATTAGTTACCTTGTCACGCA 59.740 43.478 0.00 0.00 31.95 5.24
4084 4959 3.858247 AGGATTAGTTACCTTGTCACGC 58.142 45.455 0.00 0.00 31.95 5.34
4085 4960 5.105635 TGGTAGGATTAGTTACCTTGTCACG 60.106 44.000 0.00 0.00 40.01 4.35
4086 4961 6.290294 TGGTAGGATTAGTTACCTTGTCAC 57.710 41.667 0.00 0.00 40.01 3.67
4087 4962 8.792830 ATATGGTAGGATTAGTTACCTTGTCA 57.207 34.615 0.00 0.00 40.01 3.58
4088 4963 9.091220 AGATATGGTAGGATTAGTTACCTTGTC 57.909 37.037 0.00 4.40 40.01 3.18
4089 4964 9.091220 GAGATATGGTAGGATTAGTTACCTTGT 57.909 37.037 0.00 0.00 40.01 3.16
4090 4965 9.315363 AGAGATATGGTAGGATTAGTTACCTTG 57.685 37.037 0.00 0.00 40.01 3.61
4093 4968 9.411189 CCTAGAGATATGGTAGGATTAGTTACC 57.589 40.741 0.00 0.00 39.81 2.85
4096 4971 8.907050 ACTCCTAGAGATATGGTAGGATTAGTT 58.093 37.037 0.00 0.00 41.22 2.24
4097 4972 8.471302 ACTCCTAGAGATATGGTAGGATTAGT 57.529 38.462 0.00 0.00 41.22 2.24
4100 4975 7.837187 GCTAACTCCTAGAGATATGGTAGGATT 59.163 40.741 0.00 0.00 41.22 3.01
4101 4976 7.185671 AGCTAACTCCTAGAGATATGGTAGGAT 59.814 40.741 0.00 0.00 41.22 3.24
4102 4977 6.506056 AGCTAACTCCTAGAGATATGGTAGGA 59.494 42.308 0.00 0.00 40.08 2.94
4103 4978 6.727394 AGCTAACTCCTAGAGATATGGTAGG 58.273 44.000 0.00 0.00 35.53 3.18
4106 4981 8.837737 TGTATAGCTAACTCCTAGAGATATGGT 58.162 37.037 0.00 0.00 33.32 3.55
4107 4982 9.688091 TTGTATAGCTAACTCCTAGAGATATGG 57.312 37.037 0.00 0.00 33.32 2.74
4109 4984 9.914834 CCTTGTATAGCTAACTCCTAGAGATAT 57.085 37.037 0.00 0.00 33.32 1.63
4110 4985 7.830201 GCCTTGTATAGCTAACTCCTAGAGATA 59.170 40.741 0.00 0.00 33.32 1.98
4111 4986 6.661805 GCCTTGTATAGCTAACTCCTAGAGAT 59.338 42.308 0.00 0.00 33.32 2.75
4112 4987 6.005198 GCCTTGTATAGCTAACTCCTAGAGA 58.995 44.000 0.00 0.00 33.32 3.10
4113 4988 6.007703 AGCCTTGTATAGCTAACTCCTAGAG 58.992 44.000 0.00 0.00 37.64 2.43
4114 4989 5.954757 AGCCTTGTATAGCTAACTCCTAGA 58.045 41.667 0.00 0.00 37.64 2.43
4115 4990 7.169591 TCTAGCCTTGTATAGCTAACTCCTAG 58.830 42.308 0.00 2.72 40.89 3.02
4116 4991 7.017353 TCTCTAGCCTTGTATAGCTAACTCCTA 59.983 40.741 0.00 0.00 40.89 2.94
4117 4992 5.954757 TCTAGCCTTGTATAGCTAACTCCT 58.045 41.667 0.00 0.00 40.89 3.69
4118 4993 6.005198 TCTCTAGCCTTGTATAGCTAACTCC 58.995 44.000 0.00 0.00 40.89 3.85
4119 4994 7.446013 TCTTCTCTAGCCTTGTATAGCTAACTC 59.554 40.741 0.00 0.00 40.89 3.01
4120 4995 7.291566 TCTTCTCTAGCCTTGTATAGCTAACT 58.708 38.462 0.00 0.00 40.89 2.24
4121 4996 7.513371 TCTTCTCTAGCCTTGTATAGCTAAC 57.487 40.000 0.00 0.00 40.89 2.34
4122 4997 9.809395 TTATCTTCTCTAGCCTTGTATAGCTAA 57.191 33.333 0.00 0.00 40.89 3.09
4123 4998 9.456147 CTTATCTTCTCTAGCCTTGTATAGCTA 57.544 37.037 0.00 0.00 40.56 3.32
4124 4999 8.167392 TCTTATCTTCTCTAGCCTTGTATAGCT 58.833 37.037 0.00 0.00 43.20 3.32
4125 5000 8.241367 GTCTTATCTTCTCTAGCCTTGTATAGC 58.759 40.741 0.00 0.00 0.00 2.97
4126 5001 9.515226 AGTCTTATCTTCTCTAGCCTTGTATAG 57.485 37.037 0.00 0.00 0.00 1.31
4128 5003 9.515226 CTAGTCTTATCTTCTCTAGCCTTGTAT 57.485 37.037 0.00 0.00 0.00 2.29
4129 5004 8.715842 TCTAGTCTTATCTTCTCTAGCCTTGTA 58.284 37.037 0.00 0.00 0.00 2.41
4130 5005 7.579105 TCTAGTCTTATCTTCTCTAGCCTTGT 58.421 38.462 0.00 0.00 0.00 3.16
4131 5006 8.458573 TTCTAGTCTTATCTTCTCTAGCCTTG 57.541 38.462 0.00 0.00 0.00 3.61
4132 5007 9.654919 ATTTCTAGTCTTATCTTCTCTAGCCTT 57.345 33.333 0.00 0.00 0.00 4.35
4147 5022 9.737427 CGTGACATATCTTGTATTTCTAGTCTT 57.263 33.333 0.00 0.00 39.18 3.01
4148 5023 8.904834 ACGTGACATATCTTGTATTTCTAGTCT 58.095 33.333 0.00 0.00 39.18 3.24
4149 5024 9.517609 AACGTGACATATCTTGTATTTCTAGTC 57.482 33.333 0.00 0.00 39.18 2.59
4150 5025 9.517609 GAACGTGACATATCTTGTATTTCTAGT 57.482 33.333 0.00 0.00 39.18 2.57
4151 5026 9.516314 TGAACGTGACATATCTTGTATTTCTAG 57.484 33.333 0.00 0.00 39.18 2.43
4152 5027 9.863845 TTGAACGTGACATATCTTGTATTTCTA 57.136 29.630 0.00 0.00 39.18 2.10
4153 5028 8.656849 GTTGAACGTGACATATCTTGTATTTCT 58.343 33.333 0.00 0.00 39.18 2.52
4154 5029 8.440059 TGTTGAACGTGACATATCTTGTATTTC 58.560 33.333 0.00 0.00 39.18 2.17
4155 5030 8.227791 GTGTTGAACGTGACATATCTTGTATTT 58.772 33.333 0.00 0.00 39.18 1.40
4156 5031 7.148474 GGTGTTGAACGTGACATATCTTGTATT 60.148 37.037 0.00 0.00 39.18 1.89
4157 5032 6.312918 GGTGTTGAACGTGACATATCTTGTAT 59.687 38.462 0.00 0.00 39.18 2.29
4158 5033 5.636121 GGTGTTGAACGTGACATATCTTGTA 59.364 40.000 0.00 0.00 39.18 2.41
4159 5034 4.451096 GGTGTTGAACGTGACATATCTTGT 59.549 41.667 0.00 0.00 42.79 3.16
4160 5035 4.142902 GGGTGTTGAACGTGACATATCTTG 60.143 45.833 0.00 0.00 0.00 3.02
4161 5036 4.000988 GGGTGTTGAACGTGACATATCTT 58.999 43.478 0.00 0.00 0.00 2.40
4162 5037 3.596214 GGGTGTTGAACGTGACATATCT 58.404 45.455 0.00 0.00 0.00 1.98
4163 5038 2.676342 GGGGTGTTGAACGTGACATATC 59.324 50.000 0.00 0.00 0.00 1.63
4164 5039 2.617021 GGGGGTGTTGAACGTGACATAT 60.617 50.000 0.00 0.00 0.00 1.78
4165 5040 1.270947 GGGGGTGTTGAACGTGACATA 60.271 52.381 0.00 0.00 0.00 2.29
4166 5041 0.536460 GGGGGTGTTGAACGTGACAT 60.536 55.000 0.00 0.00 0.00 3.06
4167 5042 1.153127 GGGGGTGTTGAACGTGACA 60.153 57.895 0.00 0.00 0.00 3.58
4168 5043 3.740513 GGGGGTGTTGAACGTGAC 58.259 61.111 0.00 0.00 0.00 3.67
4211 5086 4.520846 CTTTGCATCGCCGACGGC 62.521 66.667 29.10 29.10 46.75 5.68
4212 5087 2.813474 TCTTTGCATCGCCGACGG 60.813 61.111 10.29 10.29 40.63 4.79
4213 5088 2.094659 AGTCTTTGCATCGCCGACG 61.095 57.895 0.00 0.00 42.01 5.12
4214 5089 1.421485 CAGTCTTTGCATCGCCGAC 59.579 57.895 0.00 0.00 0.00 4.79
4215 5090 1.741401 CCAGTCTTTGCATCGCCGA 60.741 57.895 0.00 0.00 0.00 5.54
4216 5091 1.298157 TTCCAGTCTTTGCATCGCCG 61.298 55.000 0.00 0.00 0.00 6.46
4217 5092 0.169009 GTTCCAGTCTTTGCATCGCC 59.831 55.000 0.00 0.00 0.00 5.54
4218 5093 0.179215 CGTTCCAGTCTTTGCATCGC 60.179 55.000 0.00 0.00 0.00 4.58
4219 5094 1.428448 TCGTTCCAGTCTTTGCATCG 58.572 50.000 0.00 0.00 0.00 3.84
4220 5095 3.555518 GTTTCGTTCCAGTCTTTGCATC 58.444 45.455 0.00 0.00 0.00 3.91
4221 5096 3.626028 GTTTCGTTCCAGTCTTTGCAT 57.374 42.857 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.