Multiple sequence alignment - TraesCS3A01G433000

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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 TraesCS3A01G433000 chr3A 100.000 5474 0 0 1 5474 674398092 674403565 0.000000e+00 10109.0
1 TraesCS3A01G433000 chr3A 91.473 129 8 2 3865 3990 674401905 674402033 2.030000e-39 174.0
2 TraesCS3A01G433000 chr3A 91.473 129 8 2 3814 3942 674401956 674402081 2.030000e-39 174.0
3 TraesCS3A01G433000 chr3A 88.750 80 6 2 3914 3990 674401906 674401985 1.620000e-15 95.3
4 TraesCS3A01G433000 chr3A 88.750 80 6 2 3815 3894 674402005 674402081 1.620000e-15 95.3
5 TraesCS3A01G433000 chr3D 92.567 1426 78 9 2522 3941 539119790 539121193 0.000000e+00 2021.0
6 TraesCS3A01G433000 chr3D 95.434 1117 33 5 759 1874 539117805 539118904 0.000000e+00 1764.0
7 TraesCS3A01G433000 chr3D 94.455 1028 38 9 3865 4881 539121066 539122085 0.000000e+00 1565.0
8 TraesCS3A01G433000 chr3D 93.991 649 37 2 1871 2518 539118985 539119632 0.000000e+00 981.0
9 TraesCS3A01G433000 chr3D 90.107 657 48 8 112 763 539117136 539117780 0.000000e+00 837.0
10 TraesCS3A01G433000 chr3D 85.435 563 57 5 4935 5474 539122482 539123042 3.700000e-156 562.0
11 TraesCS3A01G433000 chr3D 90.000 80 5 2 3914 3990 539121067 539121146 3.490000e-17 100.0
12 TraesCS3A01G433000 chr3D 88.750 80 6 2 3814 3893 539121117 539121193 1.620000e-15 95.3
13 TraesCS3A01G433000 chr3D 89.189 74 8 0 5401 5474 13491072 13490999 5.840000e-15 93.5
14 TraesCS3A01G433000 chr3B 91.591 1427 86 10 2522 3942 714622146 714623544 0.000000e+00 1940.0
15 TraesCS3A01G433000 chr3B 90.372 1423 103 17 759 2164 714620146 714621551 0.000000e+00 1838.0
16 TraesCS3A01G433000 chr3B 90.051 975 68 13 3864 4832 714623418 714624369 0.000000e+00 1236.0
17 TraesCS3A01G433000 chr3B 92.308 364 27 1 2161 2523 714621617 714621980 2.920000e-142 516.0
18 TraesCS3A01G433000 chr3B 83.473 478 56 9 5006 5462 714624860 714625335 1.820000e-114 424.0
19 TraesCS3A01G433000 chr3B 89.474 76 8 0 3915 3990 714623421 714623496 4.510000e-16 97.1
20 TraesCS3A01G433000 chr3B 90.278 72 7 0 5403 5474 19607604 19607533 1.620000e-15 95.3
21 TraesCS3A01G433000 chr3B 92.188 64 2 2 3834 3894 714623481 714623544 2.720000e-13 87.9
22 TraesCS3A01G433000 chr6D 78.505 321 59 4 5074 5387 20363442 20363759 9.300000e-48 202.0
23 TraesCS3A01G433000 chr7D 77.481 262 44 11 3226 3480 613110796 613110543 5.720000e-30 143.0
24 TraesCS3A01G433000 chr7D 100.000 28 0 0 4923 4950 618064689 618064716 1.000000e-02 52.8
25 TraesCS3A01G433000 chr7B 78.302 212 31 8 3284 3486 623758808 623759013 7.450000e-24 122.0
26 TraesCS3A01G433000 chr7B 87.013 77 10 0 5398 5474 496969314 496969390 2.720000e-13 87.9
27 TraesCS3A01G433000 chr7B 75.287 174 40 2 269 440 116397906 116398078 4.550000e-11 80.5
28 TraesCS3A01G433000 chr1D 82.222 135 21 2 3355 3486 462092507 462092641 4.480000e-21 113.0
29 TraesCS3A01G433000 chr1D 90.909 77 7 0 5398 5474 417364978 417364902 2.700000e-18 104.0
30 TraesCS3A01G433000 chr4B 89.189 74 8 0 5401 5474 253186510 253186437 5.840000e-15 93.5
31 TraesCS3A01G433000 chr2B 89.189 74 8 0 5401 5474 510381326 510381253 5.840000e-15 93.5
32 TraesCS3A01G433000 chr2D 87.838 74 9 0 5401 5474 584537450 584537377 2.720000e-13 87.9
33 TraesCS3A01G433000 chr7A 100.000 28 0 0 4923 4950 711797586 711797613 1.000000e-02 52.8


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 TraesCS3A01G433000 chr3A 674398092 674403565 5473 False 2129.5200 10109 92.089200 1 5474 5 chr3A.!!$F1 5473
1 TraesCS3A01G433000 chr3D 539117136 539123042 5906 False 990.6625 2021 91.342375 112 5474 8 chr3D.!!$F1 5362
2 TraesCS3A01G433000 chr3B 714620146 714625335 5189 False 877.0000 1940 89.922429 759 5462 7 chr3B.!!$F1 4703

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
72 73 0.034089 GAGGGGGTTGTATGCTGCTT 60.034 55.0 0.00 0.00 0.00 3.91 F
228 230 0.037326 GATCTGAGTCGCCAACACCA 60.037 55.0 0.00 0.00 0.00 4.17 F
729 735 0.099259 TGTCCGCGTACGTATTGAGG 59.901 55.0 17.90 12.35 37.70 3.86 F
2430 2633 0.108472 TGCAGAGCAGTGATCTTCCG 60.108 55.0 8.51 0.00 33.32 4.30 F
2498 2701 0.391263 GGGGTGAGTTCGACATGACC 60.391 60.0 0.00 0.00 0.00 4.02 F
4021 4399 0.259065 AGAGTCGCCTCCTGATACCA 59.741 55.0 0.00 0.00 38.58 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1652 0.311790 CAAACACATTGCAGGCGTCT 59.688 50.0 0.0 0.0 31.00 4.18 R
1819 1866 0.392193 AATGAGCAGGCGGAGAACAG 60.392 55.0 0.0 0.0 0.00 3.16 R
2466 2669 0.251916 TCACCCCAAATAGCTCACCG 59.748 55.0 0.0 0.0 0.00 4.94 R
3861 4239 0.035317 CTGGTTCTGCTACTGGTGCA 59.965 55.0 0.0 0.0 38.81 4.57 R
4088 4466 0.173708 AGATCGGTCGGCTTCACTTC 59.826 55.0 0.0 0.0 0.00 3.01 R
4887 5278 0.244994 CTCAGAGGAGACAACACGGG 59.755 60.0 0.0 0.0 44.26 5.28 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
23 24 5.142061 TCGAAACTATACCTTGCTTCACA 57.858 39.130 0.00 0.00 0.00 3.58
24 25 5.168569 TCGAAACTATACCTTGCTTCACAG 58.831 41.667 0.00 0.00 0.00 3.66
36 37 3.536158 GCTTCACAGCATAACAAACGA 57.464 42.857 0.00 0.00 46.49 3.85
37 38 3.226347 GCTTCACAGCATAACAAACGAC 58.774 45.455 0.00 0.00 46.49 4.34
38 39 3.810373 CTTCACAGCATAACAAACGACC 58.190 45.455 0.00 0.00 0.00 4.79
39 40 3.120321 TCACAGCATAACAAACGACCT 57.880 42.857 0.00 0.00 0.00 3.85
40 41 4.260139 TCACAGCATAACAAACGACCTA 57.740 40.909 0.00 0.00 0.00 3.08
41 42 4.633175 TCACAGCATAACAAACGACCTAA 58.367 39.130 0.00 0.00 0.00 2.69
42 43 4.449743 TCACAGCATAACAAACGACCTAAC 59.550 41.667 0.00 0.00 0.00 2.34
43 44 4.212425 CACAGCATAACAAACGACCTAACA 59.788 41.667 0.00 0.00 0.00 2.41
44 45 5.001232 ACAGCATAACAAACGACCTAACAT 58.999 37.500 0.00 0.00 0.00 2.71
45 46 6.091577 CACAGCATAACAAACGACCTAACATA 59.908 38.462 0.00 0.00 0.00 2.29
46 47 6.312918 ACAGCATAACAAACGACCTAACATAG 59.687 38.462 0.00 0.00 0.00 2.23
57 58 2.031495 CTAACATAGGAGGGGGAGGG 57.969 60.000 0.00 0.00 0.00 4.30
58 59 0.571236 TAACATAGGAGGGGGAGGGG 59.429 60.000 0.00 0.00 0.00 4.79
59 60 2.208349 CATAGGAGGGGGAGGGGG 59.792 72.222 0.00 0.00 0.00 5.40
60 61 2.290471 ATAGGAGGGGGAGGGGGT 60.290 66.667 0.00 0.00 0.00 4.95
61 62 1.958359 ATAGGAGGGGGAGGGGGTT 60.958 63.158 0.00 0.00 0.00 4.11
62 63 2.285634 ATAGGAGGGGGAGGGGGTTG 62.286 65.000 0.00 0.00 0.00 3.77
63 64 4.695791 GGAGGGGGAGGGGGTTGT 62.696 72.222 0.00 0.00 0.00 3.32
64 65 2.457794 GAGGGGGAGGGGGTTGTA 59.542 66.667 0.00 0.00 0.00 2.41
65 66 1.005690 GAGGGGGAGGGGGTTGTAT 59.994 63.158 0.00 0.00 0.00 2.29
66 67 1.308746 AGGGGGAGGGGGTTGTATG 60.309 63.158 0.00 0.00 0.00 2.39
67 68 2.601299 GGGGAGGGGGTTGTATGC 59.399 66.667 0.00 0.00 0.00 3.14
68 69 2.006991 GGGGAGGGGGTTGTATGCT 61.007 63.158 0.00 0.00 0.00 3.79
69 70 1.227383 GGGAGGGGGTTGTATGCTG 59.773 63.158 0.00 0.00 0.00 4.41
70 71 1.453928 GGAGGGGGTTGTATGCTGC 60.454 63.158 0.00 0.00 0.00 5.25
71 72 1.609783 GAGGGGGTTGTATGCTGCT 59.390 57.895 0.00 0.00 0.00 4.24
72 73 0.034089 GAGGGGGTTGTATGCTGCTT 60.034 55.000 0.00 0.00 0.00 3.91
73 74 0.323725 AGGGGGTTGTATGCTGCTTG 60.324 55.000 0.00 0.00 0.00 4.01
74 75 1.512694 GGGGTTGTATGCTGCTTGC 59.487 57.895 0.00 0.00 43.25 4.01
87 88 2.256461 CTTGCAAGCTTCGGTGCC 59.744 61.111 14.65 0.00 40.14 5.01
88 89 3.599792 CTTGCAAGCTTCGGTGCCG 62.600 63.158 14.65 3.94 40.14 5.69
138 139 0.961358 AGACGAGGAGGACAAGACGG 60.961 60.000 0.00 0.00 0.00 4.79
161 163 4.797743 AGGCCAAAAAGAAGAGAAGAAGT 58.202 39.130 5.01 0.00 0.00 3.01
163 165 6.000840 AGGCCAAAAAGAAGAGAAGAAGTAG 58.999 40.000 5.01 0.00 0.00 2.57
168 170 5.715434 AAAGAAGAGAAGAAGTAGCTCGT 57.285 39.130 0.00 0.00 33.98 4.18
171 173 2.163509 AGAGAAGAAGTAGCTCGTGCA 58.836 47.619 12.58 0.00 42.74 4.57
173 175 1.889829 AGAAGAAGTAGCTCGTGCAGT 59.110 47.619 12.58 0.00 42.74 4.40
195 197 1.471676 GGAGAGTGATGTTGCTACCGG 60.472 57.143 0.00 0.00 0.00 5.28
197 199 1.421410 GAGTGATGTTGCTACCGGCG 61.421 60.000 0.00 0.00 45.43 6.46
223 225 1.153765 CGCAGATCTGAGTCGCCAA 60.154 57.895 27.04 0.00 0.00 4.52
224 226 1.416813 CGCAGATCTGAGTCGCCAAC 61.417 60.000 27.04 4.08 0.00 3.77
225 227 0.390340 GCAGATCTGAGTCGCCAACA 60.390 55.000 27.04 0.00 0.00 3.33
228 230 0.037326 GATCTGAGTCGCCAACACCA 60.037 55.000 0.00 0.00 0.00 4.17
305 311 0.831307 GGGGTGAGGCTAGATTTCGT 59.169 55.000 0.00 0.00 0.00 3.85
320 326 2.125147 CGTGCCATCCCGTGTCAT 60.125 61.111 0.00 0.00 0.00 3.06
345 351 1.207791 TTCCTTCTCCTGCCATCTCC 58.792 55.000 0.00 0.00 0.00 3.71
366 372 0.940126 CTCGATTTCCCCTTGCATCG 59.060 55.000 0.00 0.00 39.92 3.84
373 379 3.853330 CCCTTGCATCGTCGCGTG 61.853 66.667 5.77 0.00 33.35 5.34
402 408 2.680913 CCTTTTGCGCCTGACTCGG 61.681 63.158 4.18 0.00 0.00 4.63
412 418 1.313812 CCTGACTCGGCCTTACTCGT 61.314 60.000 0.00 0.00 0.00 4.18
416 422 0.896940 ACTCGGCCTTACTCGTTGGA 60.897 55.000 0.00 0.00 0.00 3.53
423 429 2.767505 CCTTACTCGTTGGAAACTGCT 58.232 47.619 0.00 0.00 46.99 4.24
431 437 2.159787 CGTTGGAAACTGCTGATTCGAG 60.160 50.000 7.36 0.00 46.99 4.04
432 438 2.099141 TGGAAACTGCTGATTCGAGG 57.901 50.000 7.36 0.00 0.00 4.63
438 444 3.409026 ACTGCTGATTCGAGGTTTTCT 57.591 42.857 0.00 0.00 0.00 2.52
480 486 7.064966 AGGCTGCTTTAAAATTAATGTTGATGC 59.935 33.333 11.84 11.84 0.00 3.91
485 491 7.518731 TTTAAAATTAATGTTGATGCGAGCC 57.481 32.000 0.78 0.00 0.00 4.70
539 545 2.360475 GCCCAACTGAGCCTGGTC 60.360 66.667 0.00 0.00 0.00 4.02
540 546 2.046892 CCCAACTGAGCCTGGTCG 60.047 66.667 0.00 0.00 0.00 4.79
576 582 0.592247 CCAAACACACTCGCAGTTGC 60.592 55.000 0.00 0.00 37.78 4.17
608 614 5.796935 GCGGCTGCATGATAAGTTTATAATG 59.203 40.000 14.08 5.25 42.15 1.90
658 664 7.845037 TGCTAATTGAGGTATCTGGATATGAG 58.155 38.462 0.00 0.00 0.00 2.90
697 703 1.000843 TGATCGGTCACTGTCCTTGTG 59.999 52.381 0.00 0.00 36.82 3.33
723 729 2.474266 GTCGTGTCCGCGTACGTA 59.526 61.111 17.90 0.00 40.87 3.57
729 735 0.099259 TGTCCGCGTACGTATTGAGG 59.901 55.000 17.90 12.35 37.70 3.86
756 762 1.574428 GTGTCATGCTCGCGGTTTT 59.426 52.632 6.13 0.00 0.00 2.43
778 813 7.851822 TTTTAGAAATGACAAACAAGATCGC 57.148 32.000 0.00 0.00 0.00 4.58
918 953 0.413434 TCATCTCCCCACAGTGAGGA 59.587 55.000 8.35 3.37 0.00 3.71
920 955 1.065854 CATCTCCCCACAGTGAGGAAC 60.066 57.143 8.35 0.00 0.00 3.62
922 957 0.838122 CTCCCCACAGTGAGGAACCT 60.838 60.000 8.35 0.00 0.00 3.50
923 958 1.127567 TCCCCACAGTGAGGAACCTG 61.128 60.000 8.35 0.00 0.00 4.00
932 967 3.672295 GAGGAACCTGGCTCCTGCG 62.672 68.421 22.98 0.00 43.65 5.18
1008 1043 2.480610 CGGTAATGCAATGGCCGCT 61.481 57.895 0.00 0.00 37.55 5.52
1023 1058 1.649815 CGCTATCGTCTCTTCCGCT 59.350 57.895 0.00 0.00 0.00 5.52
1134 1169 1.734477 CTTCACCACGCTCGGACTG 60.734 63.158 0.00 0.00 0.00 3.51
1141 1176 2.125552 CGCTCGGACTGAATGGCA 60.126 61.111 0.00 0.00 0.00 4.92
1338 1373 1.830847 GTTGGCCGTTTCCCAGGTT 60.831 57.895 0.00 0.00 33.13 3.50
1609 1644 3.583806 CTTGACAAGTGAGTAGCTGGAG 58.416 50.000 7.05 0.00 0.00 3.86
1617 1652 5.546621 AGTGAGTAGCTGGAGTTTTTGTA 57.453 39.130 0.00 0.00 0.00 2.41
1819 1866 5.690464 ATCCTCATAGATTGTATCCCTGC 57.310 43.478 0.00 0.00 0.00 4.85
1886 2016 8.826710 TCAACACTTAGAAGTTAGAACATTGTG 58.173 33.333 0.00 0.00 37.08 3.33
1934 2068 6.604735 AGTCGATTGTGGTAATTAAGATGC 57.395 37.500 0.00 0.00 0.00 3.91
1959 2093 7.331026 CCACTGATAAATAGTGAGGAGTTCAA 58.669 38.462 6.70 0.00 46.52 2.69
1960 2094 7.278868 CCACTGATAAATAGTGAGGAGTTCAAC 59.721 40.741 6.70 0.00 46.52 3.18
1988 2122 8.462811 CAGTAGAGAAAAGCTGAACAGATAGTA 58.537 37.037 5.97 0.00 0.00 1.82
1998 2132 5.987953 GCTGAACAGATAGTATGCATCTTGA 59.012 40.000 0.19 0.00 30.18 3.02
2015 2149 8.389603 TGCATCTTGAAAAACTTGAAACAATTC 58.610 29.630 0.00 0.00 36.04 2.17
2135 2269 5.964958 CTTCAGGAGGAAACAAGCAATTA 57.035 39.130 0.00 0.00 34.44 1.40
2185 2388 8.188139 CACATGGTTTTATTACATTGTCCCTAC 58.812 37.037 0.00 0.00 0.00 3.18
2221 2424 8.265998 CGTGAATAAATTTGAAACAGGTTTGAC 58.734 33.333 1.52 0.00 32.11 3.18
2293 2496 1.544246 GCTTTTGCGGTAAAGGATGGT 59.456 47.619 4.93 0.00 36.00 3.55
2296 2499 1.302383 TTGCGGTAAAGGATGGTGCG 61.302 55.000 0.00 0.00 0.00 5.34
2320 2523 3.411517 CCTCGGGGATGGCAGGTT 61.412 66.667 0.00 0.00 33.58 3.50
2333 2536 1.340017 GGCAGGTTCTTATGCTCCACA 60.340 52.381 0.00 0.00 42.19 4.17
2335 2538 2.819608 GCAGGTTCTTATGCTCCACAAA 59.180 45.455 0.00 0.00 39.38 2.83
2345 2548 3.163630 TGCTCCACAAAGCTTGTTTTC 57.836 42.857 0.00 0.00 43.23 2.29
2349 2552 4.107622 CTCCACAAAGCTTGTTTTCACTG 58.892 43.478 0.00 0.00 43.23 3.66
2430 2633 0.108472 TGCAGAGCAGTGATCTTCCG 60.108 55.000 8.51 0.00 33.32 4.30
2466 2669 4.657013 AGAAGGGATTCAGTTTGGACTTC 58.343 43.478 0.00 0.00 32.54 3.01
2490 2693 2.280628 GAGCTATTTGGGGTGAGTTCG 58.719 52.381 0.00 0.00 0.00 3.95
2493 2696 2.614481 GCTATTTGGGGTGAGTTCGACA 60.614 50.000 0.00 0.00 0.00 4.35
2498 2701 0.391263 GGGGTGAGTTCGACATGACC 60.391 60.000 0.00 0.00 0.00 4.02
2509 2712 7.012894 TGAGTTCGACATGACCTTTATTTTGTT 59.987 33.333 0.00 0.00 0.00 2.83
2515 2718 7.749126 CGACATGACCTTTATTTTGTTAACCTC 59.251 37.037 0.00 0.00 0.00 3.85
2516 2719 8.472007 ACATGACCTTTATTTTGTTAACCTCA 57.528 30.769 0.00 0.00 0.00 3.86
2517 2720 9.088987 ACATGACCTTTATTTTGTTAACCTCAT 57.911 29.630 0.00 0.00 0.00 2.90
2518 2721 9.927668 CATGACCTTTATTTTGTTAACCTCATT 57.072 29.630 2.48 0.00 0.00 2.57
2520 2723 9.974980 TGACCTTTATTTTGTTAACCTCATTTC 57.025 29.630 2.48 0.00 0.00 2.17
2553 2924 7.639062 ATCTATTTCCCTGTATCATCTGGTT 57.361 36.000 0.00 0.00 0.00 3.67
2554 2925 7.067496 TCTATTTCCCTGTATCATCTGGTTC 57.933 40.000 0.00 0.00 0.00 3.62
2559 2930 3.144506 CCTGTATCATCTGGTTCCATGC 58.855 50.000 0.00 0.00 0.00 4.06
2562 2933 4.858850 TGTATCATCTGGTTCCATGCTTT 58.141 39.130 0.00 0.00 0.00 3.51
2842 3213 2.062361 TTGTGGCAAGCAAGCTCGTG 62.062 55.000 0.00 0.00 34.17 4.35
2860 3231 2.135933 GTGTATGCCGAGGTGCTTATC 58.864 52.381 0.00 0.00 0.00 1.75
2871 3242 6.049149 CCGAGGTGCTTATCTCATTCTTTTA 58.951 40.000 0.00 0.00 0.00 1.52
2875 3246 8.443953 AGGTGCTTATCTCATTCTTTTATCAC 57.556 34.615 0.00 0.00 0.00 3.06
2971 3342 0.773644 ATTTATGCCGCTCCCAGGAT 59.226 50.000 0.00 0.00 0.00 3.24
3058 3429 7.972832 TGTTGATGAAATTAAGGTAGTTCGT 57.027 32.000 0.00 0.00 0.00 3.85
3062 3433 9.878667 TTGATGAAATTAAGGTAGTTCGTCATA 57.121 29.630 8.83 0.78 42.54 2.15
3086 3457 6.543735 ACTCCTGGTTGCTTAGAGTTAAATT 58.456 36.000 0.00 0.00 34.17 1.82
3130 3501 3.328382 ACTTACGCCTGATTTGCACTA 57.672 42.857 0.00 0.00 0.00 2.74
3132 3503 2.309528 TACGCCTGATTTGCACTAGG 57.690 50.000 0.00 0.00 0.00 3.02
3186 3558 5.366477 TCTCATAAGCCAACCATCAGATACA 59.634 40.000 0.00 0.00 0.00 2.29
3187 3559 6.000246 TCATAAGCCAACCATCAGATACAA 58.000 37.500 0.00 0.00 0.00 2.41
3188 3560 6.604171 TCATAAGCCAACCATCAGATACAAT 58.396 36.000 0.00 0.00 0.00 2.71
3189 3561 6.487668 TCATAAGCCAACCATCAGATACAATG 59.512 38.462 0.00 0.00 0.00 2.82
3190 3562 4.240881 AGCCAACCATCAGATACAATGT 57.759 40.909 0.00 0.00 0.00 2.71
3191 3563 5.372343 AGCCAACCATCAGATACAATGTA 57.628 39.130 0.00 0.00 0.00 2.29
3192 3564 5.945310 AGCCAACCATCAGATACAATGTAT 58.055 37.500 5.47 5.47 0.00 2.29
3193 3565 6.000219 AGCCAACCATCAGATACAATGTATC 59.000 40.000 22.14 22.14 0.00 2.24
3194 3566 5.764686 GCCAACCATCAGATACAATGTATCA 59.235 40.000 28.63 14.17 0.00 2.15
3195 3567 6.072838 GCCAACCATCAGATACAATGTATCAG 60.073 42.308 28.63 22.74 0.00 2.90
3196 3568 7.219322 CCAACCATCAGATACAATGTATCAGA 58.781 38.462 28.63 26.31 0.00 3.27
3197 3569 7.881751 CCAACCATCAGATACAATGTATCAGAT 59.118 37.037 28.63 27.10 32.64 2.90
3198 3570 9.933723 CAACCATCAGATACAATGTATCAGATA 57.066 33.333 28.66 15.78 31.70 1.98
3199 3571 9.935241 AACCATCAGATACAATGTATCAGATAC 57.065 33.333 28.66 13.06 31.70 2.24
3254 3626 9.925268 CAATTTCAGTTTCAGAAAAATTTGAGG 57.075 29.630 0.00 0.00 38.36 3.86
3267 3639 6.658188 AAAATTTGAGGACCAACCGAAATA 57.342 33.333 0.00 0.00 44.74 1.40
3270 3642 3.062122 TGAGGACCAACCGAAATAACC 57.938 47.619 0.00 0.00 44.74 2.85
3275 3647 3.365264 GGACCAACCGAAATAACCGAAAC 60.365 47.826 0.00 0.00 0.00 2.78
3279 3651 4.378046 CCAACCGAAATAACCGAAACTCAG 60.378 45.833 0.00 0.00 0.00 3.35
3447 3821 8.567948 TCAGTGTCTTGAAATTACTGAAATTCC 58.432 33.333 0.00 0.00 43.20 3.01
3452 3826 8.237267 GTCTTGAAATTACTGAAATTCCGTGAT 58.763 33.333 0.22 0.00 36.76 3.06
3468 3842 6.816134 TCCGTGATTTTCATTGAAATCTCA 57.184 33.333 12.39 14.28 43.28 3.27
3469 3843 6.845302 TCCGTGATTTTCATTGAAATCTCAG 58.155 36.000 18.12 13.88 43.28 3.35
3520 3894 2.160417 GCTCCCGTGTGAAAAATCTGAG 59.840 50.000 0.00 0.00 0.00 3.35
3561 3937 3.728845 TGTTCAAGTCCTCTAACTGTGC 58.271 45.455 0.00 0.00 0.00 4.57
3564 3940 4.415881 TCAAGTCCTCTAACTGTGCAAA 57.584 40.909 0.00 0.00 0.00 3.68
3570 3946 5.049405 AGTCCTCTAACTGTGCAAATTTTCG 60.049 40.000 0.00 0.00 0.00 3.46
3630 4006 3.071602 ACATTCCACTCTGAATATCCCCG 59.928 47.826 0.00 0.00 33.27 5.73
3634 4010 2.963101 CCACTCTGAATATCCCCGTGTA 59.037 50.000 0.00 0.00 0.00 2.90
3656 4032 3.476552 ACGCCTTTCTTCAGAACATGAA 58.523 40.909 0.00 0.00 45.79 2.57
3717 4095 7.821846 GGGAAACTTGCATTGGTTTTCATATAA 59.178 33.333 15.69 0.00 36.04 0.98
3832 4210 4.400109 CAGCAGCAGCAACAGCGG 62.400 66.667 3.17 0.00 45.49 5.52
3879 4257 2.141312 TGCACCAGTAGCAGAACCA 58.859 52.632 0.00 0.00 37.02 3.67
3885 4263 1.023513 CAGTAGCAGAACCAGCAGCC 61.024 60.000 0.00 0.00 0.00 4.85
4021 4399 0.259065 AGAGTCGCCTCCTGATACCA 59.741 55.000 0.00 0.00 38.58 3.25
4088 4466 8.950961 CAATATTTCGTTGACATTTATCTGCAG 58.049 33.333 7.63 7.63 0.00 4.41
4115 4493 1.822990 AGCCGACCGATCTAACTCAAA 59.177 47.619 0.00 0.00 0.00 2.69
4119 4497 3.367087 CCGACCGATCTAACTCAAACACT 60.367 47.826 0.00 0.00 0.00 3.55
4256 4637 0.601841 AAGTTAACTCGGCACCGGTG 60.602 55.000 30.66 30.66 40.25 4.94
4274 4655 3.773974 GCAGAAGCCGTCGAAGAG 58.226 61.111 0.00 0.00 32.33 2.85
4404 4786 1.953559 ACGCCATGCTCATCGTTATT 58.046 45.000 0.00 0.00 0.00 1.40
4479 4861 1.153449 TTCGCCGCCTTAGTGATGG 60.153 57.895 0.00 0.00 0.00 3.51
4559 4941 0.323178 AGGGCCATTGAGCTGTTCAG 60.323 55.000 6.18 0.00 37.07 3.02
4616 4998 9.486123 AGCAGTACATATATATCTCCAGTGATT 57.514 33.333 0.00 0.00 0.00 2.57
4630 5012 4.278170 TCCAGTGATTGATTCGTTTTGCTT 59.722 37.500 0.00 0.00 0.00 3.91
4679 5061 3.504906 TGAGTTTACGAGTCTGGGTACTG 59.495 47.826 0.00 0.00 0.00 2.74
4680 5062 2.230750 AGTTTACGAGTCTGGGTACTGC 59.769 50.000 0.00 0.00 0.00 4.40
4697 5079 1.270550 CTGCCTTGACATGTTTCACCC 59.729 52.381 0.00 0.00 0.00 4.61
4704 5086 0.949105 ACATGTTTCACCCGCTCGTC 60.949 55.000 0.00 0.00 0.00 4.20
4753 5135 2.469826 CAGTTGTGAAGCGTACTGTCA 58.530 47.619 0.00 0.00 34.68 3.58
4765 5147 3.120199 GCGTACTGTCATTGTTGCAATCT 60.120 43.478 0.59 0.00 0.00 2.40
4872 5263 9.586150 CTACTGCGTGATTGATAATAATTCAAC 57.414 33.333 0.00 0.00 36.02 3.18
4899 5290 2.959275 CGATAGCCCGTGTTGTCTC 58.041 57.895 0.00 0.00 0.00 3.36
4900 5291 0.527817 CGATAGCCCGTGTTGTCTCC 60.528 60.000 0.00 0.00 0.00 3.71
4901 5292 0.824759 GATAGCCCGTGTTGTCTCCT 59.175 55.000 0.00 0.00 0.00 3.69
4902 5293 0.824759 ATAGCCCGTGTTGTCTCCTC 59.175 55.000 0.00 0.00 0.00 3.71
4903 5294 0.251653 TAGCCCGTGTTGTCTCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
4904 5295 1.374758 GCCCGTGTTGTCTCCTCTG 60.375 63.158 0.00 0.00 0.00 3.35
4905 5296 1.816863 GCCCGTGTTGTCTCCTCTGA 61.817 60.000 0.00 0.00 0.00 3.27
4906 5297 0.244994 CCCGTGTTGTCTCCTCTGAG 59.755 60.000 0.00 0.00 40.17 3.35
4907 5298 0.244994 CCGTGTTGTCTCCTCTGAGG 59.755 60.000 17.84 17.84 39.23 3.86
4908 5299 0.389166 CGTGTTGTCTCCTCTGAGGC 60.389 60.000 19.08 5.87 43.79 4.70
4909 5300 0.389166 GTGTTGTCTCCTCTGAGGCG 60.389 60.000 19.08 13.26 46.58 5.52
4910 5301 0.539669 TGTTGTCTCCTCTGAGGCGA 60.540 55.000 19.08 15.60 46.58 5.54
4912 5303 1.251527 TTGTCTCCTCTGAGGCGACC 61.252 60.000 32.73 20.39 46.75 4.79
4913 5304 1.679305 GTCTCCTCTGAGGCGACCA 60.679 63.158 28.40 8.46 42.72 4.02
4914 5305 1.379176 TCTCCTCTGAGGCGACCAG 60.379 63.158 19.08 10.61 39.23 4.00
4915 5306 2.363018 TCCTCTGAGGCGACCAGG 60.363 66.667 19.08 0.00 34.61 4.45
4916 5307 3.465403 CCTCTGAGGCGACCAGGG 61.465 72.222 11.42 3.55 32.73 4.45
4917 5308 3.465403 CTCTGAGGCGACCAGGGG 61.465 72.222 6.88 0.00 32.73 4.79
4928 5319 4.129148 CCAGGGGGTTGCCCTAGC 62.129 72.222 4.02 0.00 44.66 3.42
4929 5320 4.129148 CAGGGGGTTGCCCTAGCC 62.129 72.222 4.02 0.00 44.66 3.93
4975 5709 2.818132 CCGACAGAGATGCCCTCC 59.182 66.667 0.20 0.00 42.97 4.30
4995 5729 1.528076 GCACCCATGTGTGACACCA 60.528 57.895 12.88 1.72 44.65 4.17
4997 5731 0.667993 CACCCATGTGTGACACCAAC 59.332 55.000 13.85 0.00 38.55 3.77
4998 5732 0.467290 ACCCATGTGTGACACCAACC 60.467 55.000 13.85 0.00 32.73 3.77
5002 5736 2.296792 CATGTGTGACACCAACCAAGA 58.703 47.619 13.85 0.00 32.73 3.02
5003 5737 2.036958 TGTGTGACACCAACCAAGAG 57.963 50.000 13.85 0.00 32.73 2.85
5044 5901 0.547553 TGCATGGAGAGCATAGGCAA 59.452 50.000 0.67 0.00 44.61 4.52
5045 5902 1.144298 TGCATGGAGAGCATAGGCAAT 59.856 47.619 0.67 0.00 44.61 3.56
5146 6017 0.815213 ATCGATGGTGAATGCGGTGG 60.815 55.000 0.00 0.00 0.00 4.61
5147 6018 2.472059 CGATGGTGAATGCGGTGGG 61.472 63.158 0.00 0.00 0.00 4.61
5165 6036 0.686769 GGTGGTCGGTGGGATACTCT 60.687 60.000 0.00 0.00 0.00 3.24
5187 6058 2.423947 GGTGGTCCTCCGTCCTTAGATA 60.424 54.545 0.00 0.00 36.30 1.98
5207 6078 1.981256 TGAAGGTTTGCTTCTCCACC 58.019 50.000 0.00 0.00 0.00 4.61
5211 6082 1.777272 AGGTTTGCTTCTCCACCTTCT 59.223 47.619 0.00 0.00 36.09 2.85
5228 6106 3.441572 CCTTCTTCTAGCCAACCATGTTG 59.558 47.826 0.00 0.00 0.00 3.33
5235 6113 1.506262 CCAACCATGTTGTAGCGGC 59.494 57.895 6.25 0.00 0.00 6.53
5247 6125 0.670546 GTAGCGGCAGTGAAGCTTCA 60.671 55.000 25.16 25.16 41.88 3.02
5309 6187 1.280998 CGGTAGAAATCCCTGGTTGGT 59.719 52.381 0.00 0.00 0.00 3.67
5396 6274 2.366972 CTCTACCCCCACCCCCTG 60.367 72.222 0.00 0.00 0.00 4.45
5399 6277 3.543626 TACCCCCACCCCCTGTCA 61.544 66.667 0.00 0.00 0.00 3.58
5420 6298 1.005347 CGTCCGCCTGCTATTTAAACG 60.005 52.381 0.00 0.00 0.00 3.60
5444 6322 3.597728 GACGCCGGGCAAAAACCA 61.598 61.111 20.71 0.00 0.00 3.67
5453 6331 0.247736 GGCAAAAACCACACCACACA 59.752 50.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.730550 TGTGAAGCAAGGTATAGTTTCGAT 58.269 37.500 0.00 0.00 0.00 3.59
1 2 5.142061 TGTGAAGCAAGGTATAGTTTCGA 57.858 39.130 0.00 0.00 0.00 3.71
2 3 4.201724 GCTGTGAAGCAAGGTATAGTTTCG 60.202 45.833 0.00 0.00 34.41 3.46
3 4 4.695455 TGCTGTGAAGCAAGGTATAGTTTC 59.305 41.667 0.00 0.00 42.40 2.78
4 5 4.651778 TGCTGTGAAGCAAGGTATAGTTT 58.348 39.130 0.00 0.00 42.40 2.66
5 6 4.286297 TGCTGTGAAGCAAGGTATAGTT 57.714 40.909 0.00 0.00 42.40 2.24
6 7 3.981071 TGCTGTGAAGCAAGGTATAGT 57.019 42.857 0.00 0.00 42.40 2.12
16 17 3.226347 GTCGTTTGTTATGCTGTGAAGC 58.774 45.455 0.00 0.00 0.00 3.86
17 18 3.498397 AGGTCGTTTGTTATGCTGTGAAG 59.502 43.478 0.00 0.00 0.00 3.02
18 19 3.472652 AGGTCGTTTGTTATGCTGTGAA 58.527 40.909 0.00 0.00 0.00 3.18
19 20 3.120321 AGGTCGTTTGTTATGCTGTGA 57.880 42.857 0.00 0.00 0.00 3.58
20 21 4.212425 TGTTAGGTCGTTTGTTATGCTGTG 59.788 41.667 0.00 0.00 0.00 3.66
21 22 4.382291 TGTTAGGTCGTTTGTTATGCTGT 58.618 39.130 0.00 0.00 0.00 4.40
22 23 5.545658 ATGTTAGGTCGTTTGTTATGCTG 57.454 39.130 0.00 0.00 0.00 4.41
23 24 5.815740 CCTATGTTAGGTCGTTTGTTATGCT 59.184 40.000 0.00 0.00 41.18 3.79
24 25 5.813672 TCCTATGTTAGGTCGTTTGTTATGC 59.186 40.000 0.72 0.00 46.32 3.14
25 26 6.479001 CCTCCTATGTTAGGTCGTTTGTTATG 59.521 42.308 0.72 0.00 46.32 1.90
26 27 6.407752 CCCTCCTATGTTAGGTCGTTTGTTAT 60.408 42.308 0.72 0.00 46.32 1.89
27 28 5.105228 CCCTCCTATGTTAGGTCGTTTGTTA 60.105 44.000 0.72 0.00 46.32 2.41
28 29 4.323257 CCCTCCTATGTTAGGTCGTTTGTT 60.323 45.833 0.72 0.00 46.32 2.83
29 30 3.197116 CCCTCCTATGTTAGGTCGTTTGT 59.803 47.826 0.72 0.00 46.32 2.83
30 31 3.431766 CCCCTCCTATGTTAGGTCGTTTG 60.432 52.174 0.72 0.00 46.32 2.93
31 32 2.770232 CCCCTCCTATGTTAGGTCGTTT 59.230 50.000 0.72 0.00 46.32 3.60
32 33 2.395619 CCCCTCCTATGTTAGGTCGTT 58.604 52.381 0.72 0.00 46.32 3.85
33 34 1.412649 CCCCCTCCTATGTTAGGTCGT 60.413 57.143 0.72 0.00 46.32 4.34
34 35 1.133262 TCCCCCTCCTATGTTAGGTCG 60.133 57.143 0.72 0.00 46.32 4.79
35 36 2.610873 CTCCCCCTCCTATGTTAGGTC 58.389 57.143 0.72 0.00 46.32 3.85
36 37 1.223337 CCTCCCCCTCCTATGTTAGGT 59.777 57.143 0.72 0.00 46.32 3.08
38 39 1.485210 CCCCTCCCCCTCCTATGTTAG 60.485 61.905 0.00 0.00 0.00 2.34
39 40 0.571236 CCCCTCCCCCTCCTATGTTA 59.429 60.000 0.00 0.00 0.00 2.41
40 41 1.321943 CCCCTCCCCCTCCTATGTT 59.678 63.158 0.00 0.00 0.00 2.71
41 42 2.738094 CCCCCTCCCCCTCCTATGT 61.738 68.421 0.00 0.00 0.00 2.29
42 43 2.208349 CCCCCTCCCCCTCCTATG 59.792 72.222 0.00 0.00 0.00 2.23
43 44 1.958359 AACCCCCTCCCCCTCCTAT 60.958 63.158 0.00 0.00 0.00 2.57
44 45 2.545293 AACCCCCTCCCCCTCCTA 60.545 66.667 0.00 0.00 0.00 2.94
45 46 4.371231 CAACCCCCTCCCCCTCCT 62.371 72.222 0.00 0.00 0.00 3.69
46 47 2.579037 ATACAACCCCCTCCCCCTCC 62.579 65.000 0.00 0.00 0.00 4.30
47 48 1.005690 ATACAACCCCCTCCCCCTC 59.994 63.158 0.00 0.00 0.00 4.30
48 49 1.308746 CATACAACCCCCTCCCCCT 60.309 63.158 0.00 0.00 0.00 4.79
49 50 3.069684 GCATACAACCCCCTCCCCC 62.070 68.421 0.00 0.00 0.00 5.40
50 51 2.006991 AGCATACAACCCCCTCCCC 61.007 63.158 0.00 0.00 0.00 4.81
51 52 1.227383 CAGCATACAACCCCCTCCC 59.773 63.158 0.00 0.00 0.00 4.30
52 53 1.453928 GCAGCATACAACCCCCTCC 60.454 63.158 0.00 0.00 0.00 4.30
53 54 0.034089 AAGCAGCATACAACCCCCTC 60.034 55.000 0.00 0.00 0.00 4.30
54 55 0.323725 CAAGCAGCATACAACCCCCT 60.324 55.000 0.00 0.00 0.00 4.79
55 56 1.948721 GCAAGCAGCATACAACCCCC 61.949 60.000 0.00 0.00 44.79 5.40
56 57 1.512694 GCAAGCAGCATACAACCCC 59.487 57.895 0.00 0.00 44.79 4.95
70 71 2.256461 GGCACCGAAGCTTGCAAG 59.744 61.111 22.44 22.44 40.75 4.01
71 72 3.659092 CGGCACCGAAGCTTGCAA 61.659 61.111 2.10 0.00 40.75 4.08
103 104 4.201122 CTCAGCCATGCCTCCCCC 62.201 72.222 0.00 0.00 0.00 5.40
104 105 3.092511 TCTCAGCCATGCCTCCCC 61.093 66.667 0.00 0.00 0.00 4.81
105 106 2.191641 GTCTCAGCCATGCCTCCC 59.808 66.667 0.00 0.00 0.00 4.30
106 107 2.202987 CGTCTCAGCCATGCCTCC 60.203 66.667 0.00 0.00 0.00 4.30
107 108 1.227205 CTCGTCTCAGCCATGCCTC 60.227 63.158 0.00 0.00 0.00 4.70
108 109 2.729479 CCTCGTCTCAGCCATGCCT 61.729 63.158 0.00 0.00 0.00 4.75
109 110 2.202987 CCTCGTCTCAGCCATGCC 60.203 66.667 0.00 0.00 0.00 4.40
110 111 1.227205 CTCCTCGTCTCAGCCATGC 60.227 63.158 0.00 0.00 0.00 4.06
138 139 4.824537 ACTTCTTCTCTTCTTTTTGGCCTC 59.175 41.667 3.32 0.00 0.00 4.70
161 163 1.369839 CTCTCCGACTGCACGAGCTA 61.370 60.000 6.36 0.00 42.74 3.32
163 165 2.202544 CTCTCCGACTGCACGAGC 60.203 66.667 0.00 0.00 42.57 5.03
168 170 0.969149 AACATCACTCTCCGACTGCA 59.031 50.000 0.00 0.00 0.00 4.41
171 173 1.261480 AGCAACATCACTCTCCGACT 58.739 50.000 0.00 0.00 0.00 4.18
173 175 1.476891 GGTAGCAACATCACTCTCCGA 59.523 52.381 0.00 0.00 0.00 4.55
197 199 1.152989 CTCAGATCTGCGCAAGAGGC 61.153 60.000 18.36 7.80 38.67 4.70
225 227 3.008049 CCTTAGTTCTTAGCACCAGTGGT 59.992 47.826 9.70 9.70 44.31 4.16
228 230 4.080863 CCATCCTTAGTTCTTAGCACCAGT 60.081 45.833 0.00 0.00 0.00 4.00
242 244 3.309296 TCTAGGACAAGCCCATCCTTAG 58.691 50.000 5.63 2.97 43.09 2.18
244 246 2.122768 CTCTAGGACAAGCCCATCCTT 58.877 52.381 5.63 0.00 43.09 3.36
320 326 1.710244 TGGCAGGAGAAGGAAATTGGA 59.290 47.619 0.00 0.00 0.00 3.53
345 351 1.097547 ATGCAAGGGGAAATCGAGCG 61.098 55.000 0.00 0.00 0.00 5.03
373 379 2.028925 CAAAAGGGGGCAACGTGC 59.971 61.111 0.00 0.00 44.08 5.34
402 408 1.197036 GCAGTTTCCAACGAGTAAGGC 59.803 52.381 0.00 0.00 36.23 4.35
412 418 2.224523 ACCTCGAATCAGCAGTTTCCAA 60.225 45.455 0.00 0.00 0.00 3.53
416 422 4.137543 AGAAAACCTCGAATCAGCAGTTT 58.862 39.130 0.00 0.00 0.00 2.66
423 429 3.192844 ACTCGCTAGAAAACCTCGAATCA 59.807 43.478 0.00 0.00 0.00 2.57
431 437 1.066787 AGCCTGACTCGCTAGAAAACC 60.067 52.381 0.00 0.00 33.91 3.27
432 438 2.263945 GAGCCTGACTCGCTAGAAAAC 58.736 52.381 0.00 0.00 36.48 2.43
467 473 3.313526 GTCTGGCTCGCATCAACATTAAT 59.686 43.478 0.00 0.00 0.00 1.40
480 486 0.670546 AAACACGGATGTCTGGCTCG 60.671 55.000 0.00 0.00 38.45 5.03
537 543 0.963355 TTGCTTGCATTACCCCCGAC 60.963 55.000 0.00 0.00 0.00 4.79
539 545 1.510844 GTTGCTTGCATTACCCCCG 59.489 57.895 0.00 0.00 0.00 5.73
540 546 0.902516 TGGTTGCTTGCATTACCCCC 60.903 55.000 12.30 1.28 0.00 5.40
544 550 3.245048 GTGTGTTTGGTTGCTTGCATTAC 59.755 43.478 0.00 0.00 0.00 1.89
709 715 1.186030 CTCAATACGTACGCGGACAC 58.814 55.000 23.49 9.97 43.45 3.67
723 729 3.478857 TGACACGTTGGTTACCTCAAT 57.521 42.857 2.07 0.00 0.00 2.57
729 735 1.126113 CGAGCATGACACGTTGGTTAC 59.874 52.381 0.00 0.00 0.00 2.50
756 762 6.552859 TGCGATCTTGTTTGTCATTTCTAA 57.447 33.333 0.00 0.00 0.00 2.10
778 813 4.724303 ACTCGTCGTCAGTTCTTAGAATG 58.276 43.478 0.00 0.00 0.00 2.67
932 967 1.302832 AACTGCTAGTGGCTGGCAC 60.303 57.895 25.03 25.03 42.73 5.01
1008 1043 1.355563 CGCAGCGGAAGAGACGATA 59.644 57.895 7.00 0.00 0.00 2.92
1325 1360 1.524008 GCCAAGAACCTGGGAAACGG 61.524 60.000 0.00 0.00 36.92 4.44
1359 1394 5.999603 CCTTCACGGACACGGTTTCGTAT 63.000 52.174 0.00 0.00 46.48 3.06
1463 1498 3.147595 CCTCCGAGATGTCCGGCA 61.148 66.667 0.00 0.00 46.10 5.69
1609 1644 2.766970 TTGCAGGCGTCTACAAAAAC 57.233 45.000 0.00 0.00 0.00 2.43
1617 1652 0.311790 CAAACACATTGCAGGCGTCT 59.688 50.000 0.00 0.00 31.00 4.18
1646 1681 2.887152 CCTGGCTATAAAGATTGGGCAC 59.113 50.000 0.00 0.00 0.00 5.01
1787 1822 9.799106 ATACAATCTATGAGGATTTTACCCAAG 57.201 33.333 0.00 0.00 34.15 3.61
1819 1866 0.392193 AATGAGCAGGCGGAGAACAG 60.392 55.000 0.00 0.00 0.00 3.16
1934 2068 6.878317 TGAACTCCTCACTATTTATCAGTGG 58.122 40.000 2.90 0.00 42.98 4.00
1959 2093 5.303078 TCTGTTCAGCTTTTCTCTACTGAGT 59.697 40.000 0.00 0.00 40.08 3.41
1960 2094 5.777802 TCTGTTCAGCTTTTCTCTACTGAG 58.222 41.667 0.00 0.00 40.08 3.35
1988 2122 7.846644 TTGTTTCAAGTTTTTCAAGATGCAT 57.153 28.000 0.00 0.00 0.00 3.96
1998 2132 9.788960 GTAGAGTCAGAATTGTTTCAAGTTTTT 57.211 29.630 0.00 0.00 34.08 1.94
2048 2182 6.540914 GGAACCATATACCGTTGATCAAAAGA 59.459 38.462 10.35 0.00 0.00 2.52
2221 2424 2.028930 AGCAACTAGTTCAGAGTTCCCG 60.029 50.000 4.77 0.00 34.90 5.14
2296 2499 2.444256 CCATCCCCGAGGTCCTTCC 61.444 68.421 0.00 0.00 0.00 3.46
2320 2523 3.754965 ACAAGCTTTGTGGAGCATAAGA 58.245 40.909 0.00 0.00 45.12 2.10
2333 2536 5.582689 AGTTAGCAGTGAAAACAAGCTTT 57.417 34.783 0.00 0.00 36.80 3.51
2335 2538 5.237344 CACTAGTTAGCAGTGAAAACAAGCT 59.763 40.000 0.00 0.00 45.10 3.74
2374 2577 0.874390 GGTGACATTTTGCAGAGCGA 59.126 50.000 0.00 0.00 0.00 4.93
2430 2633 0.322008 CCTTCTTGGGAGCAGTCCAC 60.322 60.000 0.00 0.00 46.07 4.02
2466 2669 0.251916 TCACCCCAAATAGCTCACCG 59.748 55.000 0.00 0.00 0.00 4.94
2490 2693 8.573035 TGAGGTTAACAAAATAAAGGTCATGTC 58.427 33.333 8.10 0.00 0.00 3.06
2527 2898 8.050316 ACCAGATGATACAGGGAAATAGATTT 57.950 34.615 0.00 0.00 0.00 2.17
2589 2960 2.758736 AGGCATCACACTCAGAACTC 57.241 50.000 0.00 0.00 0.00 3.01
2593 2964 4.526650 TGTAAGTTAGGCATCACACTCAGA 59.473 41.667 0.00 0.00 0.00 3.27
2638 3009 1.337703 GCAGCAAGACCAATTGTGACA 59.662 47.619 4.43 0.00 32.56 3.58
2759 3130 5.280654 TCTATCTGCAGCATGTCATACAA 57.719 39.130 9.47 0.00 39.31 2.41
2842 3213 2.035961 TGAGATAAGCACCTCGGCATAC 59.964 50.000 0.00 0.00 35.83 2.39
2860 3231 6.327934 CAAAGCCCAGTGATAAAAGAATGAG 58.672 40.000 0.00 0.00 0.00 2.90
2871 3242 3.718434 TCATATCTCCAAAGCCCAGTGAT 59.282 43.478 0.00 0.00 0.00 3.06
2875 3246 2.808202 CGGTCATATCTCCAAAGCCCAG 60.808 54.545 0.00 0.00 0.00 4.45
2971 3342 1.140052 TGTTGCAGGGTCTTCTTTCGA 59.860 47.619 0.00 0.00 0.00 3.71
3022 3393 1.888512 TCATCAACAAGCTCCTTTGGC 59.111 47.619 0.00 0.00 32.32 4.52
3058 3429 4.353777 ACTCTAAGCAACCAGGAGTATGA 58.646 43.478 0.00 0.00 35.79 2.15
3062 3433 5.562298 TTTAACTCTAAGCAACCAGGAGT 57.438 39.130 0.00 0.00 38.66 3.85
3130 3501 3.509442 TGAGGACATGAAAATTTGCCCT 58.491 40.909 0.00 0.00 0.00 5.19
3132 3503 6.212888 ACTATGAGGACATGAAAATTTGCC 57.787 37.500 0.00 0.00 37.87 4.52
3161 3533 5.579753 ATCTGATGGTTGGCTTATGAGAT 57.420 39.130 0.00 0.00 0.00 2.75
3191 3563 8.896744 CCACATTGTATTCAGTTTGTATCTGAT 58.103 33.333 0.00 0.00 40.83 2.90
3192 3564 7.882791 ACCACATTGTATTCAGTTTGTATCTGA 59.117 33.333 0.00 0.00 39.71 3.27
3193 3565 8.044060 ACCACATTGTATTCAGTTTGTATCTG 57.956 34.615 0.00 0.00 0.00 2.90
3194 3566 8.635765 AACCACATTGTATTCAGTTTGTATCT 57.364 30.769 0.00 0.00 0.00 1.98
3195 3567 9.691362 AAAACCACATTGTATTCAGTTTGTATC 57.309 29.630 0.00 0.00 0.00 2.24
3197 3569 9.953697 GTAAAACCACATTGTATTCAGTTTGTA 57.046 29.630 0.00 0.00 0.00 2.41
3198 3570 8.470805 TGTAAAACCACATTGTATTCAGTTTGT 58.529 29.630 0.00 0.00 0.00 2.83
3199 3571 8.864069 TGTAAAACCACATTGTATTCAGTTTG 57.136 30.769 0.00 0.00 0.00 2.93
3251 3623 2.004733 CGGTTATTTCGGTTGGTCCTC 58.995 52.381 0.00 0.00 0.00 3.71
3254 3626 3.499537 AGTTTCGGTTATTTCGGTTGGTC 59.500 43.478 0.00 0.00 0.00 4.02
3267 3639 3.208747 ACCAATCACTGAGTTTCGGTT 57.791 42.857 0.00 0.00 32.75 4.44
3270 3642 3.243035 TGCAAACCAATCACTGAGTTTCG 60.243 43.478 0.00 0.00 30.56 3.46
3275 3647 3.991773 CCAAATGCAAACCAATCACTGAG 59.008 43.478 0.00 0.00 0.00 3.35
3279 3651 1.805943 GCCCAAATGCAAACCAATCAC 59.194 47.619 0.00 0.00 0.00 3.06
3366 3740 9.869757 GGCAATTTAAATAGTACACAGGAATTT 57.130 29.630 0.01 0.00 0.00 1.82
3384 3758 5.734720 TGGCCAAAATATTTCGGCAATTTA 58.265 33.333 27.17 8.75 46.75 1.40
3421 3795 8.567948 GGAATTTCAGTAATTTCAAGACACTGA 58.432 33.333 1.68 1.68 42.78 3.41
3447 3821 7.300320 TCACTGAGATTTCAATGAAAATCACG 58.700 34.615 12.75 13.89 44.51 4.35
3468 3842 4.709397 TCACCAATGGTTTTCACTTTCACT 59.291 37.500 0.16 0.00 31.02 3.41
3469 3843 5.004922 TCACCAATGGTTTTCACTTTCAC 57.995 39.130 0.16 0.00 31.02 3.18
3520 3894 2.307934 TGCCTTGTTGCCAAAGAAAC 57.692 45.000 0.00 0.00 0.00 2.78
3537 3911 4.153117 CACAGTTAGAGGACTTGAACATGC 59.847 45.833 0.00 0.00 0.00 4.06
3550 3924 4.911610 CCACGAAAATTTGCACAGTTAGAG 59.088 41.667 0.00 0.00 0.00 2.43
3570 3946 4.083110 CCATCACACATGTCTTTTCTCCAC 60.083 45.833 0.00 0.00 0.00 4.02
3607 3983 4.283467 CGGGGATATTCAGAGTGGAATGTA 59.717 45.833 0.00 0.00 37.98 2.29
3630 4006 3.558418 TGTTCTGAAGAAAGGCGTTACAC 59.442 43.478 0.00 0.00 35.58 2.90
3634 4010 3.476552 TCATGTTCTGAAGAAAGGCGTT 58.523 40.909 0.00 0.00 35.58 4.84
3717 4095 6.767524 TTGCTGAATAACCAACCGAATTAT 57.232 33.333 0.00 0.00 0.00 1.28
3721 4099 4.920640 TTTTGCTGAATAACCAACCGAA 57.079 36.364 0.00 0.00 0.00 4.30
3746 4124 2.094675 CCTGCCGATGACAAAAGGATT 58.905 47.619 0.00 0.00 0.00 3.01
3747 4125 1.281867 TCCTGCCGATGACAAAAGGAT 59.718 47.619 0.00 0.00 0.00 3.24
3749 4127 1.533625 TTCCTGCCGATGACAAAAGG 58.466 50.000 0.00 0.00 0.00 3.11
3750 4128 3.728864 CGATTTCCTGCCGATGACAAAAG 60.729 47.826 0.00 0.00 0.00 2.27
3854 4232 0.886043 TGCTACTGGTGCAGCAGTTG 60.886 55.000 45.23 41.61 42.68 3.16
3855 4233 1.451504 TGCTACTGGTGCAGCAGTT 59.548 52.632 45.23 31.56 42.68 3.16
3856 4234 3.150949 TGCTACTGGTGCAGCAGT 58.849 55.556 42.72 42.72 42.68 4.40
3861 4239 0.035317 CTGGTTCTGCTACTGGTGCA 59.965 55.000 0.00 0.00 38.81 4.57
3862 4240 1.301677 GCTGGTTCTGCTACTGGTGC 61.302 60.000 0.00 0.00 0.00 5.01
3863 4241 0.035317 TGCTGGTTCTGCTACTGGTG 59.965 55.000 0.00 0.00 0.00 4.17
3864 4242 0.322975 CTGCTGGTTCTGCTACTGGT 59.677 55.000 0.00 0.00 0.00 4.00
3865 4243 1.023513 GCTGCTGGTTCTGCTACTGG 61.024 60.000 0.00 0.00 0.00 4.00
3866 4244 1.023513 GGCTGCTGGTTCTGCTACTG 61.024 60.000 0.00 0.00 0.00 2.74
3867 4245 1.298014 GGCTGCTGGTTCTGCTACT 59.702 57.895 0.00 0.00 0.00 2.57
3868 4246 1.746991 GGGCTGCTGGTTCTGCTAC 60.747 63.158 0.00 0.00 0.00 3.58
3869 4247 2.671070 GGGCTGCTGGTTCTGCTA 59.329 61.111 0.00 0.00 0.00 3.49
3870 4248 4.357279 GGGGCTGCTGGTTCTGCT 62.357 66.667 0.00 0.00 0.00 4.24
3871 4249 4.666253 TGGGGCTGCTGGTTCTGC 62.666 66.667 0.00 0.00 0.00 4.26
3872 4250 2.360852 CTGGGGCTGCTGGTTCTG 60.361 66.667 0.00 0.00 0.00 3.02
3873 4251 4.357279 GCTGGGGCTGCTGGTTCT 62.357 66.667 0.00 0.00 35.22 3.01
3912 4290 0.392193 CTGCTGGTTCTGCTACTGGG 60.392 60.000 0.00 0.00 0.00 4.45
4021 4399 1.208052 CAGGGGTCTCGATGATGTTGT 59.792 52.381 0.00 0.00 0.00 3.32
4088 4466 0.173708 AGATCGGTCGGCTTCACTTC 59.826 55.000 0.00 0.00 0.00 3.01
4115 4493 3.213206 TGAAATGCAGAACCAGAGTGT 57.787 42.857 0.00 0.00 0.00 3.55
4404 4786 1.298264 CACGCACGCAAAAGCAAGA 60.298 52.632 0.00 0.00 0.00 3.02
4479 4861 2.416893 GCTCGATCCTCTCAAAACAACC 59.583 50.000 0.00 0.00 0.00 3.77
4616 4998 7.254252 CCACAATTACAAAAGCAAAACGAATCA 60.254 33.333 0.00 0.00 0.00 2.57
4630 5012 9.268268 CACTTCTAGTAGTTCCACAATTACAAA 57.732 33.333 0.00 0.00 29.14 2.83
4679 5061 0.240945 CGGGTGAAACATGTCAAGGC 59.759 55.000 0.00 0.00 39.98 4.35
4680 5062 0.240945 GCGGGTGAAACATGTCAAGG 59.759 55.000 0.00 0.00 39.98 3.61
4697 5079 3.759418 TCAGTTTCTTCATAGACGAGCG 58.241 45.455 0.00 0.00 0.00 5.03
4704 5086 2.555199 CCGGCCTCAGTTTCTTCATAG 58.445 52.381 0.00 0.00 0.00 2.23
4848 5232 7.066887 TGGTTGAATTATTATCAATCACGCAGT 59.933 33.333 0.00 0.00 41.64 4.40
4869 5260 1.334869 GGGCTATCGCTTCATTGGTTG 59.665 52.381 0.00 0.00 36.09 3.77
4872 5263 0.532862 ACGGGCTATCGCTTCATTGG 60.533 55.000 0.00 0.00 36.09 3.16
4881 5272 0.527817 GGAGACAACACGGGCTATCG 60.528 60.000 0.00 0.00 0.00 2.92
4882 5273 0.824759 AGGAGACAACACGGGCTATC 59.175 55.000 0.00 0.00 0.00 2.08
4883 5274 0.824759 GAGGAGACAACACGGGCTAT 59.175 55.000 0.00 0.00 0.00 2.97
4884 5275 0.251653 AGAGGAGACAACACGGGCTA 60.252 55.000 0.00 0.00 0.00 3.93
4885 5276 1.534235 AGAGGAGACAACACGGGCT 60.534 57.895 0.00 0.00 0.00 5.19
4886 5277 1.374758 CAGAGGAGACAACACGGGC 60.375 63.158 0.00 0.00 0.00 6.13
4887 5278 0.244994 CTCAGAGGAGACAACACGGG 59.755 60.000 0.00 0.00 44.26 5.28
4888 5279 0.244994 CCTCAGAGGAGACAACACGG 59.755 60.000 11.62 0.00 44.26 4.94
4889 5280 0.389166 GCCTCAGAGGAGACAACACG 60.389 60.000 21.89 0.00 44.26 4.49
4890 5281 0.389166 CGCCTCAGAGGAGACAACAC 60.389 60.000 21.89 0.00 44.26 3.32
4891 5282 0.539669 TCGCCTCAGAGGAGACAACA 60.540 55.000 21.89 0.00 44.26 3.33
4892 5283 2.268022 TCGCCTCAGAGGAGACAAC 58.732 57.895 21.89 0.00 44.26 3.32
4893 5284 4.843624 TCGCCTCAGAGGAGACAA 57.156 55.556 21.89 0.00 44.26 3.18
4896 5287 1.379176 CTGGTCGCCTCAGAGGAGA 60.379 63.158 21.89 20.08 44.26 3.71
4897 5288 2.422231 CCTGGTCGCCTCAGAGGAG 61.422 68.421 21.89 17.79 37.67 3.69
4898 5289 2.363018 CCTGGTCGCCTCAGAGGA 60.363 66.667 21.89 0.00 37.67 3.71
4899 5290 3.465403 CCCTGGTCGCCTCAGAGG 61.465 72.222 12.81 12.81 38.80 3.69
4900 5291 3.465403 CCCCTGGTCGCCTCAGAG 61.465 72.222 0.00 0.00 34.36 3.35
4985 5719 1.308998 CCTCTTGGTTGGTGTCACAC 58.691 55.000 0.00 0.00 0.00 3.82
4995 5729 4.699522 GTCGCCGCCCTCTTGGTT 62.700 66.667 0.00 0.00 36.04 3.67
4998 5732 4.514577 ATCGTCGCCGCCCTCTTG 62.515 66.667 0.00 0.00 0.00 3.02
5059 5916 2.260869 GCCGCTTTGCCAACTCTGA 61.261 57.895 0.00 0.00 0.00 3.27
5061 5918 2.203337 TGCCGCTTTGCCAACTCT 60.203 55.556 0.00 0.00 0.00 3.24
5117 5988 2.106131 CCATCGATTCGCCGTCCA 59.894 61.111 0.00 0.00 0.00 4.02
5146 6017 0.686769 AGAGTATCCCACCGACCACC 60.687 60.000 0.00 0.00 33.66 4.61
5147 6018 0.460311 CAGAGTATCCCACCGACCAC 59.540 60.000 0.00 0.00 33.66 4.16
5159 6030 0.335361 ACGGAGGACCACCAGAGTAT 59.665 55.000 8.82 0.00 38.94 2.12
5165 6036 0.613853 CTAAGGACGGAGGACCACCA 60.614 60.000 8.82 0.00 38.94 4.17
5207 6078 4.074970 ACAACATGGTTGGCTAGAAGAAG 58.925 43.478 13.09 0.00 0.00 2.85
5211 6082 3.343617 GCTACAACATGGTTGGCTAGAA 58.656 45.455 13.09 0.00 0.00 2.10
5228 6106 0.670546 TGAAGCTTCACTGCCGCTAC 60.671 55.000 25.16 0.00 32.90 3.58
5247 6125 3.527937 ACCCAACCACTATTAGACCAGT 58.472 45.455 0.00 0.00 0.00 4.00
5250 6128 4.014406 CCAAACCCAACCACTATTAGACC 58.986 47.826 0.00 0.00 0.00 3.85
5258 6136 0.686112 CACCACCAAACCCAACCACT 60.686 55.000 0.00 0.00 0.00 4.00
5396 6274 0.739813 AAATAGCAGGCGGACGTGAC 60.740 55.000 0.00 0.00 33.41 3.67
5399 6277 2.004733 GTTTAAATAGCAGGCGGACGT 58.995 47.619 0.00 0.00 0.00 4.34
5439 6317 1.452145 GCGGATGTGTGGTGTGGTTT 61.452 55.000 0.00 0.00 0.00 3.27
5444 6322 1.301716 GTGAGCGGATGTGTGGTGT 60.302 57.895 0.00 0.00 0.00 4.16
5453 6331 1.118356 GGAGGAGATGGTGAGCGGAT 61.118 60.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.