Multiple sequence alignment - TraesCS2B01G172300

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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 TraesCS2B01G172300 chr2B 100.000 3590 0 0 1 3590 146715213 146718802 0.000000e+00 6630.0
1 TraesCS2B01G172300 chr2B 98.198 111 2 0 2797 2907 464021305 464021415 1.020000e-45 195.0
2 TraesCS2B01G172300 chr2D 96.630 2018 61 4 786 2801 94868269 94870281 0.000000e+00 3343.0
3 TraesCS2B01G172300 chr2D 91.777 681 40 7 2906 3586 94870280 94870944 0.000000e+00 933.0
4 TraesCS2B01G172300 chr2D 90.616 682 35 10 53 732 94867616 94868270 0.000000e+00 878.0
5 TraesCS2B01G172300 chr2D 88.161 473 55 1 3058 3529 238099273 238098801 2.420000e-156 562.0
6 TraesCS2B01G172300 chr2D 92.308 65 2 2 731 792 431424291 431424227 4.940000e-14 89.8
7 TraesCS2B01G172300 chr1D 90.942 1921 88 37 907 2801 427704724 427706584 0.000000e+00 2505.0
8 TraesCS2B01G172300 chr1D 90.215 1911 98 34 907 2764 487224202 487222328 0.000000e+00 2410.0
9 TraesCS2B01G172300 chr1D 91.125 1724 111 12 907 2601 482993618 482991908 0.000000e+00 2298.0
10 TraesCS2B01G172300 chr1D 88.021 192 10 5 554 732 482994757 482994566 7.810000e-52 215.0
11 TraesCS2B01G172300 chr1D 83.333 198 9 6 554 732 487224686 487224494 1.030000e-35 161.0
12 TraesCS2B01G172300 chr1D 83.735 166 8 6 554 705 427704098 427704258 4.830000e-29 139.0
13 TraesCS2B01G172300 chr1D 88.043 92 3 4 554 637 482994191 482994100 6.340000e-18 102.0
14 TraesCS2B01G172300 chr1D 97.297 37 0 1 2906 2941 482991795 482991759 1.080000e-05 62.1
15 TraesCS2B01G172300 chr1B 91.396 1848 119 17 788 2601 671258617 671260458 0.000000e+00 2495.0
16 TraesCS2B01G172300 chr1B 91.676 1766 99 27 907 2634 678469833 678471588 0.000000e+00 2403.0
17 TraesCS2B01G172300 chr1B 85.789 190 25 2 365 553 8015079 8014891 2.190000e-47 200.0
18 TraesCS2B01G172300 chr1B 83.663 202 9 6 554 731 671258414 671258615 6.160000e-38 169.0
19 TraesCS2B01G172300 chr1B 93.182 88 6 0 2907 2994 678471715 678471802 2.910000e-26 130.0
20 TraesCS2B01G172300 chr1B 93.443 61 1 2 730 790 664054184 664054127 1.780000e-13 87.9
21 TraesCS2B01G172300 chr1A 91.788 1790 93 18 907 2663 584809221 584807453 0.000000e+00 2442.0
22 TraesCS2B01G172300 chr1A 91.034 1740 109 13 909 2601 579171864 579173603 0.000000e+00 2305.0
23 TraesCS2B01G172300 chr1A 88.960 471 50 2 3061 3529 157643472 157643002 6.680000e-162 580.0
24 TraesCS2B01G172300 chr1A 87.815 476 52 6 3058 3529 569963545 569963072 1.460000e-153 553.0
25 TraesCS2B01G172300 chr1A 86.667 195 6 4 554 732 584809630 584809440 7.860000e-47 198.0
26 TraesCS2B01G172300 chr1A 88.312 154 6 4 554 695 579171527 579171680 1.320000e-39 174.0
27 TraesCS2B01G172300 chr1A 97.222 36 1 0 2906 2941 579173716 579173751 1.080000e-05 62.1
28 TraesCS2B01G172300 chr7B 77.995 1486 296 26 1111 2584 503272434 503273900 0.000000e+00 904.0
29 TraesCS2B01G172300 chr3B 92.000 525 41 1 3055 3579 640081618 640082141 0.000000e+00 736.0
30 TraesCS2B01G172300 chr3B 98.165 109 2 0 2799 2907 373883287 373883179 1.320000e-44 191.0
31 TraesCS2B01G172300 chr3B 89.552 67 2 2 728 789 547125329 547125263 2.970000e-11 80.5
32 TraesCS2B01G172300 chr6D 89.130 460 48 2 3058 3516 145754841 145754383 4.020000e-159 571.0
33 TraesCS2B01G172300 chr6D 88.050 477 44 10 3058 3529 335035786 335035318 1.460000e-153 553.0
34 TraesCS2B01G172300 chr4A 88.025 476 51 6 3058 3529 440196016 440195543 3.130000e-155 558.0
35 TraesCS2B01G172300 chr3A 88.025 476 51 5 3058 3529 365949613 365950086 3.130000e-155 558.0
36 TraesCS2B01G172300 chr3A 98.148 108 2 0 2800 2907 90877949 90878056 4.730000e-44 189.0
37 TraesCS2B01G172300 chr3A 95.726 117 4 1 2800 2915 614759297 614759413 1.700000e-43 187.0
38 TraesCS2B01G172300 chr6B 90.728 151 14 0 398 548 504590232 504590382 6.080000e-48 202.0
39 TraesCS2B01G172300 chr6B 98.165 109 2 0 2800 2908 460906301 460906193 1.320000e-44 191.0
40 TraesCS2B01G172300 chr6B 89.062 64 3 2 725 787 171704318 171704258 3.840000e-10 76.8
41 TraesCS2B01G172300 chr7D 85.714 189 25 2 367 554 29995969 29996156 7.860000e-47 198.0
42 TraesCS2B01G172300 chrUn 90.541 148 14 0 407 554 31787532 31787679 2.830000e-46 196.0
43 TraesCS2B01G172300 chrUn 84.656 189 27 2 367 554 1072542 1072729 1.700000e-43 187.0
44 TraesCS2B01G172300 chrUn 84.656 189 27 2 367 554 300084031 300083844 1.700000e-43 187.0
45 TraesCS2B01G172300 chrUn 84.656 189 27 2 367 554 304179559 304179746 1.700000e-43 187.0
46 TraesCS2B01G172300 chrUn 91.803 61 2 2 730 790 322491441 322491498 8.260000e-12 82.4
47 TraesCS2B01G172300 chr6A 99.083 109 1 0 2799 2907 596198644 596198536 2.830000e-46 196.0
48 TraesCS2B01G172300 chr4B 96.667 120 1 2 2789 2907 621927 621810 2.830000e-46 196.0
49 TraesCS2B01G172300 chr5D 94.915 118 6 0 2799 2916 450216752 450216635 6.120000e-43 185.0
50 TraesCS2B01G172300 chr7A 93.548 124 7 1 2790 2913 10278382 10278504 2.200000e-42 183.0
51 TraesCS2B01G172300 chr7A 93.333 60 2 1 728 787 538579004 538579061 1.780000e-13 87.9
52 TraesCS2B01G172300 chr2A 83.684 190 28 3 358 546 49940654 49940467 3.680000e-40 176.0
53 TraesCS2B01G172300 chr2A 91.045 67 2 2 728 790 27422804 27422738 1.780000e-13 87.9
54 TraesCS2B01G172300 chr4D 93.443 61 0 2 731 787 389209246 389209186 1.780000e-13 87.9
55 TraesCS2B01G172300 chr4D 90.476 63 2 4 731 792 5527969 5527910 2.970000e-11 80.5


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 TraesCS2B01G172300 chr2B 146715213 146718802 3589 False 6630.000000 6630 100.000000 1 3590 1 chr2B.!!$F1 3589
1 TraesCS2B01G172300 chr2D 94867616 94870944 3328 False 1718.000000 3343 93.007667 53 3586 3 chr2D.!!$F1 3533
2 TraesCS2B01G172300 chr1D 427704098 427706584 2486 False 1322.000000 2505 87.338500 554 2801 2 chr1D.!!$F1 2247
3 TraesCS2B01G172300 chr1D 487222328 487224686 2358 True 1285.500000 2410 86.774000 554 2764 2 chr1D.!!$R2 2210
4 TraesCS2B01G172300 chr1D 482991759 482994757 2998 True 669.275000 2298 91.121500 554 2941 4 chr1D.!!$R1 2387
5 TraesCS2B01G172300 chr1B 671258414 671260458 2044 False 1332.000000 2495 87.529500 554 2601 2 chr1B.!!$F1 2047
6 TraesCS2B01G172300 chr1B 678469833 678471802 1969 False 1266.500000 2403 92.429000 907 2994 2 chr1B.!!$F2 2087
7 TraesCS2B01G172300 chr1A 584807453 584809630 2177 True 1320.000000 2442 89.227500 554 2663 2 chr1A.!!$R3 2109
8 TraesCS2B01G172300 chr1A 579171527 579173751 2224 False 847.033333 2305 92.189333 554 2941 3 chr1A.!!$F1 2387
9 TraesCS2B01G172300 chr7B 503272434 503273900 1466 False 904.000000 904 77.995000 1111 2584 1 chr7B.!!$F1 1473
10 TraesCS2B01G172300 chr3B 640081618 640082141 523 False 736.000000 736 92.000000 3055 3579 1 chr3B.!!$F1 524

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
401 402 0.179062 AATCTCAGCTCGGTGCATCC 60.179 55.000 4.74 0.0 45.94 3.51 F
403 404 1.145598 CTCAGCTCGGTGCATCCAT 59.854 57.895 4.74 0.0 45.94 3.41 F
2049 3311 0.109179 CGACGTCCATACCAACGGAA 60.109 55.000 10.58 0.0 42.99 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 3147 0.400594 AACGCCTGGAAAGTAGCCTT 59.599 50.000 0.00 0.0 0.00 4.35 R
2094 3356 1.557443 CTTGCACGTGGTCGGACTTC 61.557 60.000 18.88 0.0 41.85 3.01 R
3018 4342 1.676529 TCGTGGTGTAGATGCTCTAGC 59.323 52.381 0.00 0.0 42.50 3.42 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
21 22 4.439253 GGTAAAATAGCCATCACCTCCT 57.561 45.455 0.00 0.00 0.00 3.69
22 23 4.390264 GGTAAAATAGCCATCACCTCCTC 58.610 47.826 0.00 0.00 0.00 3.71
23 24 2.918712 AAATAGCCATCACCTCCTCG 57.081 50.000 0.00 0.00 0.00 4.63
24 25 2.088104 AATAGCCATCACCTCCTCGA 57.912 50.000 0.00 0.00 0.00 4.04
25 26 2.317371 ATAGCCATCACCTCCTCGAT 57.683 50.000 0.00 0.00 0.00 3.59
26 27 1.621992 TAGCCATCACCTCCTCGATC 58.378 55.000 0.00 0.00 0.00 3.69
27 28 1.006805 GCCATCACCTCCTCGATCG 60.007 63.158 9.36 9.36 0.00 3.69
28 29 1.662608 CCATCACCTCCTCGATCGG 59.337 63.158 16.41 5.93 0.00 4.18
29 30 1.006805 CATCACCTCCTCGATCGGC 60.007 63.158 16.41 0.00 0.00 5.54
30 31 1.152652 ATCACCTCCTCGATCGGCT 60.153 57.895 16.41 0.00 0.00 5.52
31 32 1.175983 ATCACCTCCTCGATCGGCTC 61.176 60.000 16.41 0.00 0.00 4.70
32 33 2.121538 CACCTCCTCGATCGGCTCA 61.122 63.158 16.41 0.00 0.00 4.26
33 34 1.152652 ACCTCCTCGATCGGCTCAT 60.153 57.895 16.41 0.00 0.00 2.90
34 35 1.288439 CCTCCTCGATCGGCTCATG 59.712 63.158 16.41 1.34 0.00 3.07
35 36 1.372748 CTCCTCGATCGGCTCATGC 60.373 63.158 16.41 0.00 38.76 4.06
36 37 2.080222 CTCCTCGATCGGCTCATGCA 62.080 60.000 16.41 0.00 41.91 3.96
37 38 1.953138 CCTCGATCGGCTCATGCAC 60.953 63.158 16.41 0.00 41.91 4.57
38 39 2.278792 TCGATCGGCTCATGCACG 60.279 61.111 16.41 0.00 41.91 5.34
39 40 3.333189 CGATCGGCTCATGCACGG 61.333 66.667 7.38 0.00 41.91 4.94
40 41 2.969238 GATCGGCTCATGCACGGG 60.969 66.667 0.00 0.00 41.91 5.28
41 42 3.445518 GATCGGCTCATGCACGGGA 62.446 63.158 0.00 0.00 41.91 5.14
42 43 2.923426 GATCGGCTCATGCACGGGAA 62.923 60.000 0.00 0.00 41.91 3.97
43 44 2.535485 ATCGGCTCATGCACGGGAAA 62.535 55.000 0.00 0.00 41.91 3.13
44 45 2.331893 CGGCTCATGCACGGGAAAA 61.332 57.895 0.00 0.00 41.91 2.29
45 46 1.861542 CGGCTCATGCACGGGAAAAA 61.862 55.000 0.00 0.00 41.91 1.94
77 78 3.964688 AGATGGGGACGGAAAAAGTTTTT 59.035 39.130 13.35 13.35 0.00 1.94
81 82 3.070446 GGGGACGGAAAAAGTTTTTCCAT 59.930 43.478 39.64 33.28 46.29 3.41
83 84 4.202172 GGGACGGAAAAAGTTTTTCCATCA 60.202 41.667 37.51 0.00 46.29 3.07
146 147 0.613012 GCTTTTCTGTGGGATGCCCT 60.613 55.000 0.00 0.00 45.70 5.19
158 159 3.077359 GGGATGCCCTATCAAAAGATCG 58.923 50.000 0.00 0.00 41.34 3.69
169 170 3.985008 TCAAAAGATCGAAGTCGTGGAA 58.015 40.909 0.00 0.00 40.80 3.53
259 260 3.084786 CAAACCCTTCAAGGATGAGTCC 58.915 50.000 4.43 0.00 45.45 3.85
290 291 7.165460 ACTTTTAAAGGATTTATCGGTTGGG 57.835 36.000 9.64 0.00 40.76 4.12
309 310 1.202746 GGGCCAGAGATCTTTGCCTAG 60.203 57.143 22.65 6.88 39.81 3.02
337 338 4.627467 GCTAGCGAAAGAAGTTGAGATGAA 59.373 41.667 0.00 0.00 0.00 2.57
367 368 0.326927 ACCGTGGGATTGTACAAGGG 59.673 55.000 14.65 7.96 40.01 3.95
369 370 0.616371 CGTGGGATTGTACAAGGGGA 59.384 55.000 14.65 0.00 0.00 4.81
375 376 4.018779 TGGGATTGTACAAGGGGAAAGTAG 60.019 45.833 14.65 0.00 0.00 2.57
376 377 4.018688 GGGATTGTACAAGGGGAAAGTAGT 60.019 45.833 14.65 0.00 0.00 2.73
379 380 3.320129 TGTACAAGGGGAAAGTAGTGGT 58.680 45.455 0.00 0.00 0.00 4.16
384 385 4.141018 ACAAGGGGAAAGTAGTGGTTGAAT 60.141 41.667 0.00 0.00 0.00 2.57
401 402 0.179062 AATCTCAGCTCGGTGCATCC 60.179 55.000 4.74 0.00 45.94 3.51
403 404 1.145598 CTCAGCTCGGTGCATCCAT 59.854 57.895 4.74 0.00 45.94 3.41
404 405 1.153309 TCAGCTCGGTGCATCCATG 60.153 57.895 4.74 0.00 45.94 3.66
414 415 4.270482 CATCCATGCTGCACCCAT 57.730 55.556 3.57 0.00 0.00 4.00
433 434 7.151308 CACCCATGTAAGAAAACATAGCAAAA 58.849 34.615 0.00 0.00 38.01 2.44
434 435 7.116233 CACCCATGTAAGAAAACATAGCAAAAC 59.884 37.037 0.00 0.00 38.01 2.43
435 436 7.151308 CCCATGTAAGAAAACATAGCAAAACA 58.849 34.615 0.00 0.00 38.01 2.83
440 441 9.809096 TGTAAGAAAACATAGCAAAACATTTCA 57.191 25.926 0.00 0.00 0.00 2.69
522 524 7.974675 AGTTTGATGGTCAAATAACATACGAG 58.025 34.615 8.21 0.00 46.55 4.18
523 525 7.822334 AGTTTGATGGTCAAATAACATACGAGA 59.178 33.333 8.21 0.00 46.55 4.04
524 526 8.447833 GTTTGATGGTCAAATAACATACGAGAA 58.552 33.333 8.21 0.00 46.55 2.87
525 527 7.770801 TGATGGTCAAATAACATACGAGAAG 57.229 36.000 0.00 0.00 0.00 2.85
526 528 6.257849 TGATGGTCAAATAACATACGAGAAGC 59.742 38.462 0.00 0.00 0.00 3.86
527 529 5.730550 TGGTCAAATAACATACGAGAAGCT 58.269 37.500 0.00 0.00 0.00 3.74
633 665 3.460857 TTTCCAAAAATGGTTCACCGG 57.539 42.857 0.00 0.00 39.43 5.28
701 749 2.539302 CAATGGGGGTGAAGTGGATTT 58.461 47.619 0.00 0.00 0.00 2.17
710 758 5.123936 GGGTGAAGTGGATTTGTATAGGTC 58.876 45.833 0.00 0.00 0.00 3.85
732 781 9.601217 AGGTCAGATTAGACACAAAACATATAC 57.399 33.333 0.00 0.00 40.29 1.47
735 784 9.817809 TCAGATTAGACACAAAACATATACTCC 57.182 33.333 0.00 0.00 0.00 3.85
736 785 9.046296 CAGATTAGACACAAAACATATACTCCC 57.954 37.037 0.00 0.00 0.00 4.30
737 786 8.993424 AGATTAGACACAAAACATATACTCCCT 58.007 33.333 0.00 0.00 0.00 4.20
738 787 9.262358 GATTAGACACAAAACATATACTCCCTC 57.738 37.037 0.00 0.00 0.00 4.30
739 788 5.990668 AGACACAAAACATATACTCCCTCC 58.009 41.667 0.00 0.00 0.00 4.30
740 789 4.766375 ACACAAAACATATACTCCCTCCG 58.234 43.478 0.00 0.00 0.00 4.63
742 791 4.809426 CACAAAACATATACTCCCTCCGTC 59.191 45.833 0.00 0.00 0.00 4.79
745 794 5.888982 AAACATATACTCCCTCCGTCAAT 57.111 39.130 0.00 0.00 0.00 2.57
746 795 6.989155 AAACATATACTCCCTCCGTCAATA 57.011 37.500 0.00 0.00 0.00 1.90
747 796 6.989155 AACATATACTCCCTCCGTCAATAA 57.011 37.500 0.00 0.00 0.00 1.40
748 797 6.591750 ACATATACTCCCTCCGTCAATAAG 57.408 41.667 0.00 0.00 0.00 1.73
750 799 7.236529 ACATATACTCCCTCCGTCAATAAGTA 58.763 38.462 0.00 0.00 0.00 2.24
751 800 7.176340 ACATATACTCCCTCCGTCAATAAGTAC 59.824 40.741 0.00 0.00 0.00 2.73
752 801 3.705051 ACTCCCTCCGTCAATAAGTACA 58.295 45.455 0.00 0.00 0.00 2.90
755 804 5.080969 TCCCTCCGTCAATAAGTACAAAG 57.919 43.478 0.00 0.00 0.00 2.77
757 806 5.012354 TCCCTCCGTCAATAAGTACAAAGTT 59.988 40.000 0.00 0.00 0.00 2.66
758 807 5.121768 CCCTCCGTCAATAAGTACAAAGTTG 59.878 44.000 0.00 0.00 0.00 3.16
759 808 5.929992 CCTCCGTCAATAAGTACAAAGTTGA 59.070 40.000 0.00 0.00 0.00 3.18
763 812 6.422701 CCGTCAATAAGTACAAAGTTGAGACA 59.577 38.462 0.00 0.00 30.27 3.41
764 813 7.281484 CGTCAATAAGTACAAAGTTGAGACAC 58.719 38.462 0.00 0.00 30.27 3.67
765 814 7.169308 CGTCAATAAGTACAAAGTTGAGACACT 59.831 37.037 0.00 0.00 30.27 3.55
774 910 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
781 917 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
896 1783 2.029380 GGCCAGTTGTGTAACCATTTCC 60.029 50.000 0.00 0.00 37.52 3.13
1062 2300 2.420890 CTCTGCATCCTCTCGGCC 59.579 66.667 0.00 0.00 0.00 6.13
1357 2613 2.442272 GCCTCTCCTACGCCTCCA 60.442 66.667 0.00 0.00 0.00 3.86
1392 2654 4.735132 CCCTTCGCGGTGCTCGAA 62.735 66.667 6.13 4.32 42.74 3.71
1485 2747 1.720301 CGAGCTCTACTACGCCGTT 59.280 57.895 12.85 0.00 0.00 4.44
1747 3009 2.202756 GGAAGGTGCGGCTAGTCG 60.203 66.667 13.55 13.55 0.00 4.18
1885 3147 1.300931 GTGCTCGTGCTGAACCAGA 60.301 57.895 11.19 0.00 40.48 3.86
2049 3311 0.109179 CGACGTCCATACCAACGGAA 60.109 55.000 10.58 0.00 42.99 4.30
2094 3356 1.600663 CCGCACTACTATCTCAAGGCG 60.601 57.143 0.00 0.00 42.56 5.52
2115 3377 1.593209 GTCCGACCACGTGCAAGAA 60.593 57.895 10.91 0.00 37.88 2.52
2235 3497 1.089481 GCATCTCGCCATCGGAAACA 61.089 55.000 0.00 0.00 36.13 2.83
2343 3605 2.284995 AGCTGGGTCAGGGGACTC 60.285 66.667 0.00 0.00 45.22 3.36
2409 3671 3.767673 TGTATGTCAACTACAGGGACCTC 59.232 47.826 0.00 0.00 42.70 3.85
2650 3962 1.154338 GTGCACTGCTCGTGATTGC 60.154 57.895 10.32 0.00 46.81 3.56
2691 4004 6.805271 CGGTTTCGTCTTTGAGACTCTTATTA 59.195 38.462 3.68 0.00 42.92 0.98
2692 4005 7.327761 CGGTTTCGTCTTTGAGACTCTTATTAA 59.672 37.037 3.68 0.00 42.92 1.40
2693 4006 9.152595 GGTTTCGTCTTTGAGACTCTTATTAAT 57.847 33.333 3.68 0.00 42.92 1.40
2720 4040 4.372656 GTCTCTATGGCTAAAATCGTGCT 58.627 43.478 0.00 0.00 0.00 4.40
2729 4049 3.058224 GCTAAAATCGTGCTGTCTTGGTT 60.058 43.478 0.00 0.00 0.00 3.67
2743 4063 4.636648 TGTCTTGGTTATGTGACGTGTTTT 59.363 37.500 0.00 0.00 32.64 2.43
2770 4094 6.985653 TCATGGGTGGAATAAAAAGAAACA 57.014 33.333 0.00 0.00 0.00 2.83
2795 4119 9.051027 CATGTATCGTGTCAAGTTTATGAAAAC 57.949 33.333 0.00 0.00 44.47 2.43
2810 4134 9.668497 GTTTATGAAAACTAATACTCCCTCTGT 57.332 33.333 0.00 0.00 41.52 3.41
2812 4136 9.886132 TTATGAAAACTAATACTCCCTCTGTTC 57.114 33.333 0.00 0.00 0.00 3.18
2813 4137 7.311092 TGAAAACTAATACTCCCTCTGTTCA 57.689 36.000 0.00 0.00 0.00 3.18
2814 4138 7.159372 TGAAAACTAATACTCCCTCTGTTCAC 58.841 38.462 0.00 0.00 0.00 3.18
2815 4139 6.936968 AAACTAATACTCCCTCTGTTCACT 57.063 37.500 0.00 0.00 0.00 3.41
2816 4140 6.936968 AACTAATACTCCCTCTGTTCACTT 57.063 37.500 0.00 0.00 0.00 3.16
2817 4141 6.936968 ACTAATACTCCCTCTGTTCACTTT 57.063 37.500 0.00 0.00 0.00 2.66
2818 4142 7.317722 ACTAATACTCCCTCTGTTCACTTTT 57.682 36.000 0.00 0.00 0.00 2.27
2819 4143 8.431910 ACTAATACTCCCTCTGTTCACTTTTA 57.568 34.615 0.00 0.00 0.00 1.52
2820 4144 9.047947 ACTAATACTCCCTCTGTTCACTTTTAT 57.952 33.333 0.00 0.00 0.00 1.40
2823 4147 9.892130 AATACTCCCTCTGTTCACTTTTATAAG 57.108 33.333 0.00 0.00 37.40 1.73
2824 4148 7.317722 ACTCCCTCTGTTCACTTTTATAAGT 57.682 36.000 0.00 0.00 45.40 2.24
2825 4149 7.387643 ACTCCCTCTGTTCACTTTTATAAGTC 58.612 38.462 0.00 0.00 42.67 3.01
2826 4150 6.708285 TCCCTCTGTTCACTTTTATAAGTCC 58.292 40.000 0.00 0.00 42.67 3.85
2827 4151 6.500751 TCCCTCTGTTCACTTTTATAAGTCCT 59.499 38.462 0.00 0.00 42.67 3.85
2828 4152 7.017254 TCCCTCTGTTCACTTTTATAAGTCCTT 59.983 37.037 0.00 0.00 42.67 3.36
2829 4153 7.119846 CCCTCTGTTCACTTTTATAAGTCCTTG 59.880 40.741 0.00 0.00 42.67 3.61
2830 4154 7.878127 CCTCTGTTCACTTTTATAAGTCCTTGA 59.122 37.037 0.00 0.00 42.67 3.02
2831 4155 9.273016 CTCTGTTCACTTTTATAAGTCCTTGAA 57.727 33.333 0.00 0.00 42.67 2.69
2832 4156 9.273016 TCTGTTCACTTTTATAAGTCCTTGAAG 57.727 33.333 0.00 0.00 42.67 3.02
2833 4157 9.273016 CTGTTCACTTTTATAAGTCCTTGAAGA 57.727 33.333 0.00 0.00 42.67 2.87
2834 4158 9.052759 TGTTCACTTTTATAAGTCCTTGAAGAC 57.947 33.333 0.00 0.00 42.67 3.01
2835 4159 9.052759 GTTCACTTTTATAAGTCCTTGAAGACA 57.947 33.333 0.00 0.00 42.67 3.41
2836 4160 9.793259 TTCACTTTTATAAGTCCTTGAAGACAT 57.207 29.630 0.00 0.00 42.67 3.06
2837 4161 9.793259 TCACTTTTATAAGTCCTTGAAGACATT 57.207 29.630 0.00 0.00 42.67 2.71
2843 4167 7.913674 ATAAGTCCTTGAAGACATTTCAGAC 57.086 36.000 0.00 2.75 39.34 3.51
2844 4168 5.296151 AGTCCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 39.34 3.41
2845 4169 5.684704 AGTCCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 39.34 3.18
2846 4170 5.529060 AGTCCTTGAAGACATTTCAGACAAC 59.471 40.000 0.00 1.46 39.34 3.32
2847 4171 5.296780 GTCCTTGAAGACATTTCAGACAACA 59.703 40.000 0.00 0.00 36.73 3.33
2848 4172 6.016777 GTCCTTGAAGACATTTCAGACAACAT 60.017 38.462 0.00 0.00 36.73 2.71
2849 4173 6.016860 TCCTTGAAGACATTTCAGACAACATG 60.017 38.462 0.00 0.00 0.00 3.21
2850 4174 5.112220 TGAAGACATTTCAGACAACATGC 57.888 39.130 0.00 0.00 0.00 4.06
2851 4175 4.579753 TGAAGACATTTCAGACAACATGCA 59.420 37.500 0.00 0.00 0.00 3.96
2852 4176 5.067544 TGAAGACATTTCAGACAACATGCAA 59.932 36.000 0.00 0.00 0.00 4.08
2853 4177 5.518848 AGACATTTCAGACAACATGCAAA 57.481 34.783 0.00 0.00 0.00 3.68
2854 4178 5.526115 AGACATTTCAGACAACATGCAAAG 58.474 37.500 0.00 0.00 0.00 2.77
2855 4179 4.053295 ACATTTCAGACAACATGCAAAGC 58.947 39.130 0.00 0.00 0.00 3.51
2856 4180 3.797451 TTTCAGACAACATGCAAAGCA 57.203 38.095 0.00 0.00 44.86 3.91
2857 4181 3.358707 TTCAGACAACATGCAAAGCAG 57.641 42.857 0.00 0.00 43.65 4.24
2858 4182 1.001048 TCAGACAACATGCAAAGCAGC 60.001 47.619 0.00 0.00 43.65 5.25
2859 4183 0.316204 AGACAACATGCAAAGCAGCC 59.684 50.000 0.00 0.00 43.65 4.85
2860 4184 0.316204 GACAACATGCAAAGCAGCCT 59.684 50.000 0.00 0.00 43.65 4.58
2861 4185 1.541147 GACAACATGCAAAGCAGCCTA 59.459 47.619 0.00 0.00 43.65 3.93
2862 4186 2.165030 GACAACATGCAAAGCAGCCTAT 59.835 45.455 0.00 0.00 43.65 2.57
2863 4187 2.564062 ACAACATGCAAAGCAGCCTATT 59.436 40.909 0.00 0.00 43.65 1.73
2864 4188 3.007182 ACAACATGCAAAGCAGCCTATTT 59.993 39.130 0.00 0.00 43.65 1.40
2865 4189 3.967332 ACATGCAAAGCAGCCTATTTT 57.033 38.095 0.00 0.00 43.65 1.82
2866 4190 3.853475 ACATGCAAAGCAGCCTATTTTC 58.147 40.909 0.00 0.00 43.65 2.29
2867 4191 3.258872 ACATGCAAAGCAGCCTATTTTCA 59.741 39.130 0.00 0.00 43.65 2.69
2868 4192 3.581024 TGCAAAGCAGCCTATTTTCAG 57.419 42.857 0.00 0.00 33.32 3.02
2869 4193 2.892852 TGCAAAGCAGCCTATTTTCAGT 59.107 40.909 0.00 0.00 33.32 3.41
2870 4194 3.321682 TGCAAAGCAGCCTATTTTCAGTT 59.678 39.130 0.00 0.00 33.32 3.16
2871 4195 3.676646 GCAAAGCAGCCTATTTTCAGTTG 59.323 43.478 0.00 0.00 0.00 3.16
2872 4196 4.797275 GCAAAGCAGCCTATTTTCAGTTGT 60.797 41.667 0.00 0.00 0.00 3.32
2873 4197 4.773323 AAGCAGCCTATTTTCAGTTGTC 57.227 40.909 0.00 0.00 0.00 3.18
2874 4198 4.026356 AGCAGCCTATTTTCAGTTGTCT 57.974 40.909 0.00 0.00 0.00 3.41
2875 4199 3.755378 AGCAGCCTATTTTCAGTTGTCTG 59.245 43.478 0.00 0.00 42.54 3.51
2901 4225 9.503427 GAAATGACTTATAAAAATGAACGGAGG 57.497 33.333 0.00 0.00 0.00 4.30
2902 4226 6.995511 TGACTTATAAAAATGAACGGAGGG 57.004 37.500 0.00 0.00 0.00 4.30
2903 4227 6.713276 TGACTTATAAAAATGAACGGAGGGA 58.287 36.000 0.00 0.00 0.00 4.20
2904 4228 6.821665 TGACTTATAAAAATGAACGGAGGGAG 59.178 38.462 0.00 0.00 0.00 4.30
2905 4229 6.718294 ACTTATAAAAATGAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
2906 4230 7.854337 ACTTATAAAAATGAACGGAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
2937 4261 5.825532 TGGAATGATATTGTCCCTTTGTCA 58.174 37.500 0.00 0.00 0.00 3.58
2950 4274 4.136796 CCCTTTGTCAAATCTGTGACTGA 58.863 43.478 0.00 0.00 46.70 3.41
3018 4342 2.330286 ACACGCAATCAAATGTGCATG 58.670 42.857 0.00 0.00 39.71 4.06
3019 4343 1.059979 CACGCAATCAAATGTGCATGC 59.940 47.619 11.82 11.82 40.94 4.06
3050 4374 3.194005 ACACCACGACTTGACAAATCT 57.806 42.857 0.00 0.00 0.00 2.40
3067 4391 6.831976 ACAAATCTGCCTCCCTATAGTTTAG 58.168 40.000 0.00 0.00 0.00 1.85
3103 4427 0.600255 CCCGACACGATAAGCATCCC 60.600 60.000 0.00 0.00 0.00 3.85
3105 4429 1.603172 CCGACACGATAAGCATCCCTC 60.603 57.143 0.00 0.00 0.00 4.30
3110 4434 3.070018 CACGATAAGCATCCCTCATTCC 58.930 50.000 0.00 0.00 0.00 3.01
3167 4491 7.542477 ACTCTAGTTGAGACAACAATTACATCG 59.458 37.037 15.29 0.00 45.39 3.84
3174 4498 2.477375 ACAACAATTACATCGTCGCGTT 59.523 40.909 5.77 0.00 0.00 4.84
3312 4636 4.529377 TGACCCCCGTAGAAATCCATATAC 59.471 45.833 0.00 0.00 0.00 1.47
3314 4638 4.909088 ACCCCCGTAGAAATCCATATACAA 59.091 41.667 0.00 0.00 0.00 2.41
3563 4887 2.466846 AGTGGGCTTCAAAACCTTTGT 58.533 42.857 0.00 0.00 0.00 2.83
3586 4910 3.397482 CTTGAGGTCCTTTGTGTCTCAG 58.603 50.000 0.00 0.00 36.11 3.35
3587 4911 1.694150 TGAGGTCCTTTGTGTCTCAGG 59.306 52.381 0.00 0.00 31.73 3.86
3588 4912 1.002544 GAGGTCCTTTGTGTCTCAGGG 59.997 57.143 0.00 0.00 0.00 4.45
3589 4913 1.056660 GGTCCTTTGTGTCTCAGGGA 58.943 55.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.390264 GAGGAGGTGATGGCTATTTTACC 58.610 47.826 4.58 4.58 0.00 2.85
1 2 4.058817 CGAGGAGGTGATGGCTATTTTAC 58.941 47.826 0.00 0.00 0.00 2.01
2 3 3.964688 TCGAGGAGGTGATGGCTATTTTA 59.035 43.478 0.00 0.00 0.00 1.52
3 4 2.771943 TCGAGGAGGTGATGGCTATTTT 59.228 45.455 0.00 0.00 0.00 1.82
4 5 2.398588 TCGAGGAGGTGATGGCTATTT 58.601 47.619 0.00 0.00 0.00 1.40
5 6 2.088104 TCGAGGAGGTGATGGCTATT 57.912 50.000 0.00 0.00 0.00 1.73
6 7 2.175202 GATCGAGGAGGTGATGGCTAT 58.825 52.381 0.00 0.00 0.00 2.97
7 8 1.621992 GATCGAGGAGGTGATGGCTA 58.378 55.000 0.00 0.00 0.00 3.93
8 9 1.459455 CGATCGAGGAGGTGATGGCT 61.459 60.000 10.26 0.00 0.00 4.75
9 10 1.006805 CGATCGAGGAGGTGATGGC 60.007 63.158 10.26 0.00 0.00 4.40
10 11 1.662608 CCGATCGAGGAGGTGATGG 59.337 63.158 18.66 0.00 0.00 3.51
11 12 1.006805 GCCGATCGAGGAGGTGATG 60.007 63.158 18.66 0.00 0.00 3.07
12 13 1.152652 AGCCGATCGAGGAGGTGAT 60.153 57.895 18.66 0.00 0.00 3.06
13 14 1.824329 GAGCCGATCGAGGAGGTGA 60.824 63.158 18.66 0.00 0.00 4.02
14 15 1.459455 ATGAGCCGATCGAGGAGGTG 61.459 60.000 18.66 0.00 0.00 4.00
15 16 1.152652 ATGAGCCGATCGAGGAGGT 60.153 57.895 18.66 4.93 0.00 3.85
16 17 1.288439 CATGAGCCGATCGAGGAGG 59.712 63.158 18.66 0.00 0.00 4.30
17 18 1.372748 GCATGAGCCGATCGAGGAG 60.373 63.158 18.66 0.00 33.58 3.69
18 19 2.127232 TGCATGAGCCGATCGAGGA 61.127 57.895 18.66 0.00 41.13 3.71
19 20 1.953138 GTGCATGAGCCGATCGAGG 60.953 63.158 18.66 1.12 41.13 4.63
20 21 2.298629 CGTGCATGAGCCGATCGAG 61.299 63.158 18.66 8.00 41.13 4.04
21 22 2.278792 CGTGCATGAGCCGATCGA 60.279 61.111 18.66 0.00 41.13 3.59
22 23 3.333189 CCGTGCATGAGCCGATCG 61.333 66.667 8.51 8.51 41.13 3.69
23 24 2.923426 TTCCCGTGCATGAGCCGATC 62.923 60.000 7.72 0.00 41.13 3.69
24 25 2.535485 TTTCCCGTGCATGAGCCGAT 62.535 55.000 7.72 0.00 41.13 4.18
25 26 2.739849 TTTTCCCGTGCATGAGCCGA 62.740 55.000 7.72 0.00 41.13 5.54
26 27 1.861542 TTTTTCCCGTGCATGAGCCG 61.862 55.000 7.72 0.00 41.13 5.52
27 28 1.963679 TTTTTCCCGTGCATGAGCC 59.036 52.632 7.72 0.00 41.13 4.70
42 43 6.439058 TCCGTCCCCATCTTTAATGAATTTTT 59.561 34.615 0.00 0.00 0.00 1.94
43 44 5.955355 TCCGTCCCCATCTTTAATGAATTTT 59.045 36.000 0.00 0.00 0.00 1.82
44 45 5.515106 TCCGTCCCCATCTTTAATGAATTT 58.485 37.500 0.00 0.00 0.00 1.82
45 46 5.124036 TCCGTCCCCATCTTTAATGAATT 57.876 39.130 0.00 0.00 0.00 2.17
46 47 4.788925 TCCGTCCCCATCTTTAATGAAT 57.211 40.909 0.00 0.00 0.00 2.57
47 48 4.577988 TTCCGTCCCCATCTTTAATGAA 57.422 40.909 0.00 0.00 0.00 2.57
48 49 4.577988 TTTCCGTCCCCATCTTTAATGA 57.422 40.909 0.00 0.00 0.00 2.57
49 50 5.185056 ACTTTTTCCGTCCCCATCTTTAATG 59.815 40.000 0.00 0.00 0.00 1.90
50 51 5.330233 ACTTTTTCCGTCCCCATCTTTAAT 58.670 37.500 0.00 0.00 0.00 1.40
51 52 4.732065 ACTTTTTCCGTCCCCATCTTTAA 58.268 39.130 0.00 0.00 0.00 1.52
52 53 4.376225 ACTTTTTCCGTCCCCATCTTTA 57.624 40.909 0.00 0.00 0.00 1.85
53 54 3.238788 ACTTTTTCCGTCCCCATCTTT 57.761 42.857 0.00 0.00 0.00 2.52
54 55 2.971901 ACTTTTTCCGTCCCCATCTT 57.028 45.000 0.00 0.00 0.00 2.40
77 78 6.361433 TGACCTCAACTTAAAACTTGATGGA 58.639 36.000 0.00 0.00 0.00 3.41
81 82 6.285224 TCGATGACCTCAACTTAAAACTTGA 58.715 36.000 0.00 0.00 0.00 3.02
83 84 6.202954 CACTCGATGACCTCAACTTAAAACTT 59.797 38.462 0.00 0.00 0.00 2.66
136 137 3.496692 CGATCTTTTGATAGGGCATCCCA 60.497 47.826 4.51 0.00 42.35 4.37
146 147 5.319140 TCCACGACTTCGATCTTTTGATA 57.681 39.130 5.47 0.00 43.02 2.15
158 159 3.500663 GTTTTCGAGTTCCACGACTTC 57.499 47.619 0.00 0.00 39.46 3.01
177 178 1.968493 TGCCTTCCTAGACTTTCACGT 59.032 47.619 0.00 0.00 0.00 4.49
224 225 2.374170 AGGGTTTGGAATTCTACACGGT 59.626 45.455 5.23 0.00 0.00 4.83
259 260 8.345565 CCGATAAATCCTTTAAAAGTCCATCTG 58.654 37.037 0.00 0.00 0.00 2.90
260 261 8.053355 ACCGATAAATCCTTTAAAAGTCCATCT 58.947 33.333 0.00 0.00 0.00 2.90
290 291 1.765314 TCTAGGCAAAGATCTCTGGCC 59.235 52.381 18.30 18.88 43.55 5.36
309 310 3.684788 TCAACTTCTTTCGCTAGCCATTC 59.315 43.478 9.66 0.00 0.00 2.67
337 338 0.333993 TCCCACGGTAGGAGCTAACT 59.666 55.000 0.00 0.00 0.00 2.24
367 368 4.393371 GCTGAGATTCAACCACTACTTTCC 59.607 45.833 0.00 0.00 0.00 3.13
369 370 5.234466 AGCTGAGATTCAACCACTACTTT 57.766 39.130 0.00 0.00 0.00 2.66
375 376 1.338200 ACCGAGCTGAGATTCAACCAC 60.338 52.381 0.00 0.00 0.00 4.16
376 377 0.976641 ACCGAGCTGAGATTCAACCA 59.023 50.000 0.00 0.00 0.00 3.67
379 380 0.321346 TGCACCGAGCTGAGATTCAA 59.679 50.000 0.00 0.00 45.94 2.69
384 385 1.332889 ATGGATGCACCGAGCTGAGA 61.333 55.000 0.00 0.00 45.94 3.27
401 402 1.753930 TCTTACATGGGTGCAGCATG 58.246 50.000 19.06 19.51 40.87 4.06
403 404 2.284754 TTTCTTACATGGGTGCAGCA 57.715 45.000 19.06 4.31 0.00 4.41
404 405 2.295909 TGTTTTCTTACATGGGTGCAGC 59.704 45.455 7.55 7.55 0.00 5.25
405 406 4.789012 ATGTTTTCTTACATGGGTGCAG 57.211 40.909 0.00 0.00 37.36 4.41
406 407 4.157656 GCTATGTTTTCTTACATGGGTGCA 59.842 41.667 0.00 0.00 39.06 4.57
407 408 4.157656 TGCTATGTTTTCTTACATGGGTGC 59.842 41.667 0.00 0.00 39.06 5.01
408 409 5.895636 TGCTATGTTTTCTTACATGGGTG 57.104 39.130 0.00 0.00 39.06 4.61
409 410 6.909550 TTTGCTATGTTTTCTTACATGGGT 57.090 33.333 0.00 0.00 39.06 4.51
410 411 7.151308 TGTTTTGCTATGTTTTCTTACATGGG 58.849 34.615 0.00 0.00 39.06 4.00
411 412 8.761575 ATGTTTTGCTATGTTTTCTTACATGG 57.238 30.769 0.00 0.00 39.06 3.66
414 415 9.809096 TGAAATGTTTTGCTATGTTTTCTTACA 57.191 25.926 0.00 0.00 0.00 2.41
460 461 9.811995 CCATAACATTTGTTCATGATCATTCTT 57.188 29.630 5.16 1.04 39.31 2.52
461 462 8.418662 CCCATAACATTTGTTCATGATCATTCT 58.581 33.333 5.16 0.00 39.31 2.40
463 464 6.987992 GCCCATAACATTTGTTCATGATCATT 59.012 34.615 5.16 2.17 39.31 2.57
633 665 1.336980 GCTATTGCCTACGCCTACCTC 60.337 57.143 0.00 0.00 0.00 3.85
701 749 8.590204 TGTTTTGTGTCTAATCTGACCTATACA 58.410 33.333 0.00 0.00 36.21 2.29
710 758 9.046296 GGGAGTATATGTTTTGTGTCTAATCTG 57.954 37.037 0.00 0.00 0.00 2.90
732 781 4.730949 TTGTACTTATTGACGGAGGGAG 57.269 45.455 0.00 0.00 0.00 4.30
734 783 4.828829 ACTTTGTACTTATTGACGGAGGG 58.171 43.478 0.00 0.00 0.00 4.30
735 784 5.929992 TCAACTTTGTACTTATTGACGGAGG 59.070 40.000 0.00 0.00 0.00 4.30
736 785 6.866770 TCTCAACTTTGTACTTATTGACGGAG 59.133 38.462 0.00 0.00 0.00 4.63
737 786 6.643770 GTCTCAACTTTGTACTTATTGACGGA 59.356 38.462 0.00 0.00 0.00 4.69
738 787 6.422701 TGTCTCAACTTTGTACTTATTGACGG 59.577 38.462 0.00 0.00 0.00 4.79
739 788 7.169308 AGTGTCTCAACTTTGTACTTATTGACG 59.831 37.037 0.00 0.00 0.00 4.35
740 789 8.366671 AGTGTCTCAACTTTGTACTTATTGAC 57.633 34.615 0.00 0.00 0.00 3.18
747 796 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
748 797 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
750 799 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
751 800 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
752 801 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
755 804 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
757 806 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
758 807 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
759 808 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
763 812 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
764 813 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
765 814 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
771 907 2.767960 GTTTAATACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
896 1783 8.333908 GTTTAAGCATCATCTGTCATAGTTGAG 58.666 37.037 0.00 0.00 38.24 3.02
1062 2300 1.068541 GCTAAAGAGGGCGTGTTTTGG 60.069 52.381 7.64 3.52 0.00 3.28
1335 2591 2.442272 GCGTAGGAGAGGCCCTCA 60.442 66.667 14.46 0.00 43.76 3.86
1357 2613 1.296715 GCTCGTTGTGGAGGTGGAT 59.703 57.895 0.00 0.00 34.56 3.41
1717 2979 1.079819 CCTTCCACGACAGCACGAT 60.080 57.895 5.12 0.00 37.03 3.73
1885 3147 0.400594 AACGCCTGGAAAGTAGCCTT 59.599 50.000 0.00 0.00 0.00 4.35
2094 3356 1.557443 CTTGCACGTGGTCGGACTTC 61.557 60.000 18.88 0.00 41.85 3.01
2343 3605 3.243569 CGTAAGGCTCCATCTCCTTGTAG 60.244 52.174 3.95 0.00 42.29 2.74
2409 3671 1.064296 CTCATTCGTCCCGAGGTCG 59.936 63.158 3.87 3.87 37.14 4.79
2650 3962 1.453155 ACCGCTAAGACATGCAAAGG 58.547 50.000 0.00 0.00 0.00 3.11
2691 4004 7.339466 ACGATTTTAGCCATAGAGACCAAAATT 59.661 33.333 0.00 0.00 0.00 1.82
2692 4005 6.828785 ACGATTTTAGCCATAGAGACCAAAAT 59.171 34.615 0.00 0.00 0.00 1.82
2693 4006 6.093495 CACGATTTTAGCCATAGAGACCAAAA 59.907 38.462 0.00 0.00 0.00 2.44
2694 4007 5.584649 CACGATTTTAGCCATAGAGACCAAA 59.415 40.000 0.00 0.00 0.00 3.28
2720 4040 3.462483 ACACGTCACATAACCAAGACA 57.538 42.857 0.00 0.00 0.00 3.41
2729 4049 6.431543 ACCCATGATTAAAAACACGTCACATA 59.568 34.615 0.00 0.00 0.00 2.29
2743 4063 9.936759 GTTTCTTTTTATTCCACCCATGATTAA 57.063 29.630 0.00 0.00 0.00 1.40
2801 4125 6.819146 GGACTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 46.09 4.30
2802 4126 6.500751 AGGACTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 46.09 4.20
2803 4127 6.712276 AGGACTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 46.09 4.30
2804 4128 7.878127 TCAAGGACTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 46.09 3.69
2805 4129 8.833231 TCAAGGACTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 46.09 3.35
2806 4130 9.273016 CTTCAAGGACTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 46.09 3.41
2807 4131 9.273016 TCTTCAAGGACTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 46.09 3.16
2808 4132 9.052759 GTCTTCAAGGACTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 46.09 3.18
2809 4133 9.052759 TGTCTTCAAGGACTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 46.09 3.18
2810 4134 9.793259 ATGTCTTCAAGGACTTATAAAAGTGAA 57.207 29.630 0.00 0.00 46.09 3.18
2811 4135 9.793259 AATGTCTTCAAGGACTTATAAAAGTGA 57.207 29.630 0.00 0.00 46.09 3.41
2817 4141 9.436957 GTCTGAAATGTCTTCAAGGACTTATAA 57.563 33.333 0.00 0.00 37.16 0.98
2818 4142 8.593679 TGTCTGAAATGTCTTCAAGGACTTATA 58.406 33.333 7.80 0.00 37.16 0.98
2819 4143 7.453393 TGTCTGAAATGTCTTCAAGGACTTAT 58.547 34.615 7.80 0.00 37.16 1.73
2820 4144 6.826668 TGTCTGAAATGTCTTCAAGGACTTA 58.173 36.000 7.80 0.00 37.16 2.24
2821 4145 5.684704 TGTCTGAAATGTCTTCAAGGACTT 58.315 37.500 7.80 0.00 37.16 3.01
2822 4146 5.296151 TGTCTGAAATGTCTTCAAGGACT 57.704 39.130 7.80 0.00 37.16 3.85
2823 4147 5.296780 TGTTGTCTGAAATGTCTTCAAGGAC 59.703 40.000 0.00 0.00 36.81 3.85
2824 4148 5.436175 TGTTGTCTGAAATGTCTTCAAGGA 58.564 37.500 0.00 0.00 0.00 3.36
2825 4149 5.756195 TGTTGTCTGAAATGTCTTCAAGG 57.244 39.130 0.00 0.00 0.00 3.61
2826 4150 5.628193 GCATGTTGTCTGAAATGTCTTCAAG 59.372 40.000 0.00 0.00 0.00 3.02
2827 4151 5.067544 TGCATGTTGTCTGAAATGTCTTCAA 59.932 36.000 0.00 0.00 0.00 2.69
2828 4152 4.579753 TGCATGTTGTCTGAAATGTCTTCA 59.420 37.500 0.00 0.00 0.00 3.02
2829 4153 5.112220 TGCATGTTGTCTGAAATGTCTTC 57.888 39.130 0.00 0.00 0.00 2.87
2830 4154 5.518848 TTGCATGTTGTCTGAAATGTCTT 57.481 34.783 0.00 0.00 0.00 3.01
2831 4155 5.518848 TTTGCATGTTGTCTGAAATGTCT 57.481 34.783 0.00 0.00 0.00 3.41
2832 4156 4.149396 GCTTTGCATGTTGTCTGAAATGTC 59.851 41.667 0.00 0.00 0.00 3.06
2833 4157 4.053295 GCTTTGCATGTTGTCTGAAATGT 58.947 39.130 0.00 0.00 0.00 2.71
2834 4158 4.052608 TGCTTTGCATGTTGTCTGAAATG 58.947 39.130 0.00 0.00 31.71 2.32
2835 4159 4.304110 CTGCTTTGCATGTTGTCTGAAAT 58.696 39.130 0.00 0.00 38.13 2.17
2836 4160 3.708890 CTGCTTTGCATGTTGTCTGAAA 58.291 40.909 0.00 0.00 38.13 2.69
2837 4161 2.544277 GCTGCTTTGCATGTTGTCTGAA 60.544 45.455 0.00 0.00 38.13 3.02
2838 4162 1.001048 GCTGCTTTGCATGTTGTCTGA 60.001 47.619 0.00 0.00 38.13 3.27
2839 4163 1.415374 GCTGCTTTGCATGTTGTCTG 58.585 50.000 0.00 0.00 38.13 3.51
2840 4164 0.316204 GGCTGCTTTGCATGTTGTCT 59.684 50.000 0.00 0.00 38.13 3.41
2841 4165 0.316204 AGGCTGCTTTGCATGTTGTC 59.684 50.000 0.00 0.00 38.13 3.18
2842 4166 1.619654 TAGGCTGCTTTGCATGTTGT 58.380 45.000 0.00 0.00 38.13 3.32
2843 4167 2.953466 ATAGGCTGCTTTGCATGTTG 57.047 45.000 0.00 0.00 38.13 3.33
2844 4168 3.967332 AAATAGGCTGCTTTGCATGTT 57.033 38.095 0.00 0.00 38.13 2.71
2845 4169 3.258872 TGAAAATAGGCTGCTTTGCATGT 59.741 39.130 0.00 0.00 38.13 3.21
2846 4170 3.852286 TGAAAATAGGCTGCTTTGCATG 58.148 40.909 0.00 0.00 38.13 4.06
2847 4171 3.512724 ACTGAAAATAGGCTGCTTTGCAT 59.487 39.130 0.00 0.00 38.13 3.96
2848 4172 2.892852 ACTGAAAATAGGCTGCTTTGCA 59.107 40.909 0.00 0.99 36.92 4.08
2849 4173 3.582714 ACTGAAAATAGGCTGCTTTGC 57.417 42.857 0.00 0.00 0.00 3.68
2850 4174 4.874970 ACAACTGAAAATAGGCTGCTTTG 58.125 39.130 0.00 0.00 0.00 2.77
2851 4175 4.829492 AGACAACTGAAAATAGGCTGCTTT 59.171 37.500 0.00 0.00 0.00 3.51
2852 4176 4.217118 CAGACAACTGAAAATAGGCTGCTT 59.783 41.667 0.00 0.00 46.03 3.91
2853 4177 3.755378 CAGACAACTGAAAATAGGCTGCT 59.245 43.478 0.00 0.00 46.03 4.24
2854 4178 4.088823 CAGACAACTGAAAATAGGCTGC 57.911 45.455 0.00 0.00 46.03 5.25
2875 4199 9.503427 CCTCCGTTCATTTTTATAAGTCATTTC 57.497 33.333 0.00 0.00 0.00 2.17
2876 4200 8.466798 CCCTCCGTTCATTTTTATAAGTCATTT 58.533 33.333 0.00 0.00 0.00 2.32
2877 4201 7.832187 TCCCTCCGTTCATTTTTATAAGTCATT 59.168 33.333 0.00 0.00 0.00 2.57
2878 4202 7.343357 TCCCTCCGTTCATTTTTATAAGTCAT 58.657 34.615 0.00 0.00 0.00 3.06
2879 4203 6.713276 TCCCTCCGTTCATTTTTATAAGTCA 58.287 36.000 0.00 0.00 0.00 3.41
2880 4204 6.822170 ACTCCCTCCGTTCATTTTTATAAGTC 59.178 38.462 0.00 0.00 0.00 3.01
2881 4205 6.718294 ACTCCCTCCGTTCATTTTTATAAGT 58.282 36.000 0.00 0.00 0.00 2.24
2882 4206 8.726870 TTACTCCCTCCGTTCATTTTTATAAG 57.273 34.615 0.00 0.00 0.00 1.73
2883 4207 9.689501 ATTTACTCCCTCCGTTCATTTTTATAA 57.310 29.630 0.00 0.00 0.00 0.98
2885 4209 9.689501 TTATTTACTCCCTCCGTTCATTTTTAT 57.310 29.630 0.00 0.00 0.00 1.40
2886 4210 9.517868 TTTATTTACTCCCTCCGTTCATTTTTA 57.482 29.630 0.00 0.00 0.00 1.52
2887 4211 8.411991 TTTATTTACTCCCTCCGTTCATTTTT 57.588 30.769 0.00 0.00 0.00 1.94
2888 4212 8.411991 TTTTATTTACTCCCTCCGTTCATTTT 57.588 30.769 0.00 0.00 0.00 1.82
2889 4213 8.466798 CATTTTATTTACTCCCTCCGTTCATTT 58.533 33.333 0.00 0.00 0.00 2.32
2890 4214 7.068226 CCATTTTATTTACTCCCTCCGTTCATT 59.932 37.037 0.00 0.00 0.00 2.57
2891 4215 6.546034 CCATTTTATTTACTCCCTCCGTTCAT 59.454 38.462 0.00 0.00 0.00 2.57
2892 4216 5.883673 CCATTTTATTTACTCCCTCCGTTCA 59.116 40.000 0.00 0.00 0.00 3.18
2893 4217 6.117488 TCCATTTTATTTACTCCCTCCGTTC 58.883 40.000 0.00 0.00 0.00 3.95
2894 4218 6.069705 TCCATTTTATTTACTCCCTCCGTT 57.930 37.500 0.00 0.00 0.00 4.44
2895 4219 5.703730 TCCATTTTATTTACTCCCTCCGT 57.296 39.130 0.00 0.00 0.00 4.69
2896 4220 6.770785 TCATTCCATTTTATTTACTCCCTCCG 59.229 38.462 0.00 0.00 0.00 4.63
2897 4221 8.712228 ATCATTCCATTTTATTTACTCCCTCC 57.288 34.615 0.00 0.00 0.00 4.30
2937 4261 3.583806 CGAAGAGCTCAGTCACAGATTT 58.416 45.455 17.77 0.00 0.00 2.17
3018 4342 1.676529 TCGTGGTGTAGATGCTCTAGC 59.323 52.381 0.00 0.00 42.50 3.42
3019 4343 2.946329 AGTCGTGGTGTAGATGCTCTAG 59.054 50.000 0.00 0.00 28.01 2.43
3036 4360 1.734465 GGAGGCAGATTTGTCAAGTCG 59.266 52.381 2.74 0.39 0.00 4.18
3103 4427 2.100197 TGGGTACTCGAGTGGAATGAG 58.900 52.381 28.12 0.00 35.85 2.90
3105 4429 3.005897 CCTATGGGTACTCGAGTGGAATG 59.994 52.174 28.12 11.21 0.00 2.67
3110 4434 2.359981 TCCCTATGGGTACTCGAGTG 57.640 55.000 28.12 9.04 44.74 3.51
3145 4469 6.307077 CGACGATGTAATTGTTGTCTCAACTA 59.693 38.462 12.66 6.69 42.24 2.24
3373 4697 5.880054 ATTGTATCAGCACTTTGGTACAC 57.120 39.130 0.00 0.00 42.63 2.90
3553 4877 3.052869 AGGACCTCAAGGACAAAGGTTTT 60.053 43.478 2.30 0.00 43.43 2.43
3563 4887 2.368875 GAGACACAAAGGACCTCAAGGA 59.631 50.000 2.30 0.00 38.94 3.36


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

AutoCloner maintained by Alex Coulton.