Multiple sequence alignment - TraesCS2B01G363000

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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 TraesCS2B01G363000 chr2B 100.000 4335 0 0 1000 5334 517384917 517380583 0.000000e+00 8006
1 TraesCS2B01G363000 chr2B 100.000 684 0 0 1 684 517385916 517385233 0.000000e+00 1264
2 TraesCS2B01G363000 chr2B 92.473 93 7 0 2046 2138 517383778 517383686 3.350000e-27 134
3 TraesCS2B01G363000 chr2B 92.473 93 7 0 2139 2231 517383871 517383779 3.350000e-27 134
4 TraesCS2B01G363000 chr2D 92.524 3344 169 39 2046 5334 439442409 439439092 0.000000e+00 4715
5 TraesCS2B01G363000 chr2D 91.077 1244 50 19 1000 2231 439443604 439442410 0.000000e+00 1626
6 TraesCS2B01G363000 chr2D 87.500 616 32 24 33 648 439444456 439443886 0.000000e+00 669
7 TraesCS2B01G363000 chr2D 93.011 186 12 1 2046 2230 439442502 439442317 2.450000e-68 270
8 TraesCS2B01G363000 chr2A 93.032 2569 124 26 2046 4587 549678450 549680990 0.000000e+00 3701
9 TraesCS2B01G363000 chr2A 91.357 1238 60 20 1000 2229 549677249 549678447 0.000000e+00 1650
10 TraesCS2B01G363000 chr2A 88.824 680 28 12 4682 5334 549680996 549681654 0.000000e+00 791
11 TraesCS2B01G363000 chr2A 85.549 692 37 25 4 684 549676521 549677160 0.000000e+00 665
12 TraesCS2B01G363000 chr2A 93.011 186 13 0 2046 2231 549678357 549678542 6.810000e-69 272
13 TraesCS2B01G363000 chr2A 93.548 93 6 0 2046 2138 549678543 549678635 7.200000e-29 139
14 TraesCS2B01G363000 chrUn 84.242 165 14 5 4427 4581 388893924 388893762 3.330000e-32 150
15 TraesCS2B01G363000 chrUn 83.030 165 16 5 4424 4578 385510752 385510914 7.200000e-29 139
16 TraesCS2B01G363000 chr7A 84.242 165 14 5 4427 4581 537847212 537847050 3.330000e-32 150
17 TraesCS2B01G363000 chr6B 84.242 165 14 5 4424 4578 18741456 18741618 3.330000e-32 150
18 TraesCS2B01G363000 chr6B 85.075 134 9 4 4454 4578 406601951 406602082 5.610000e-25 126
19 TraesCS2B01G363000 chr1B 84.242 165 14 5 4427 4581 633713793 633713631 3.330000e-32 150
20 TraesCS2B01G363000 chr1A 84.713 157 13 4 4434 4581 554479057 554478903 4.300000e-31 147
21 TraesCS2B01G363000 chr1D 81.325 166 19 5 4427 4582 243969313 243969150 2.020000e-24 124


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 TraesCS2B01G363000 chr2B 517380583 517385916 5333 True 2384.5 8006 96.236500 1 5334 4 chr2B.!!$R1 5333
1 TraesCS2B01G363000 chr2D 439439092 439444456 5364 True 1820.0 4715 91.028000 33 5334 4 chr2D.!!$R1 5301
2 TraesCS2B01G363000 chr2A 549676521 549681654 5133 False 1203.0 3701 90.886833 4 5334 6 chr2A.!!$F1 5330

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
241 243 0.033796 CATCCATCCAACCCACAGCT 60.034 55.0 0.00 0.0 0.00 4.24 F
1986 2019 0.035317 GCTTTTGAGGGGCCTTTTGG 59.965 55.0 0.84 0.0 44.18 3.28 F
2335 2554 0.107066 TGCATTCATGGATCCGCACT 60.107 50.0 7.39 0.0 0.00 4.40 F
2718 2948 0.321653 CTGACTTAGGTGGTGGTGGC 60.322 60.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2392 0.107312 CACTGCCAGAAGGAGATGGG 60.107 60.0 0.00 0.00 37.05 4.00 R
3974 4222 0.107165 GTAATGCTCCACCCACCTCC 60.107 60.0 0.00 0.00 0.00 4.30 R
4106 4354 0.034756 CACCGACACCAATCTCACCA 59.965 55.0 0.00 0.00 0.00 4.17 R
4508 4758 0.529378 CAGGCAATCTTGACAAGGGC 59.471 55.0 15.13 14.99 39.18 5.19 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
31 32 0.180171 CCATAGCGTGACCATTCCCA 59.820 55.000 0.00 0.00 0.00 4.37
36 37 0.394352 GCGTGACCATTCCCATTCCT 60.394 55.000 0.00 0.00 0.00 3.36
53 54 1.699634 TCCTTTTCACACCCTCTGGAG 59.300 52.381 0.00 0.00 34.81 3.86
66 67 2.683867 CCTCTGGAGTACCTTGTACTCG 59.316 54.545 21.65 12.88 43.53 4.18
74 76 7.739825 TGGAGTACCTTGTACTCGTAGTATAT 58.260 38.462 21.65 0.00 43.53 0.86
75 77 8.870116 TGGAGTACCTTGTACTCGTAGTATATA 58.130 37.037 21.65 3.94 43.53 0.86
76 78 9.145865 GGAGTACCTTGTACTCGTAGTATATAC 57.854 40.741 21.65 4.60 43.53 1.47
77 79 9.145865 GAGTACCTTGTACTCGTAGTATATACC 57.854 40.741 16.15 0.00 35.23 2.73
78 80 8.651389 AGTACCTTGTACTCGTAGTATATACCA 58.349 37.037 9.32 0.00 32.65 3.25
79 81 7.976135 ACCTTGTACTCGTAGTATATACCAG 57.024 40.000 9.32 3.72 32.65 4.00
94 96 1.920610 ACCAGTACTACTGCTCCGTT 58.079 50.000 10.36 0.00 44.63 4.44
102 104 2.233922 ACTACTGCTCCGTTATGCAAGT 59.766 45.455 0.00 0.00 38.81 3.16
113 115 3.789756 CGTTATGCAAGTGTACGACCTAG 59.210 47.826 0.00 0.00 34.36 3.02
114 116 4.673580 CGTTATGCAAGTGTACGACCTAGT 60.674 45.833 0.00 0.00 34.36 2.57
115 117 5.447683 CGTTATGCAAGTGTACGACCTAGTA 60.448 44.000 0.00 0.00 34.36 1.82
118 120 4.801891 TGCAAGTGTACGACCTAGTAAAG 58.198 43.478 0.00 0.00 0.00 1.85
119 121 4.520111 TGCAAGTGTACGACCTAGTAAAGA 59.480 41.667 0.00 0.00 0.00 2.52
120 122 5.009911 TGCAAGTGTACGACCTAGTAAAGAA 59.990 40.000 0.00 0.00 0.00 2.52
121 123 6.098017 GCAAGTGTACGACCTAGTAAAGAAT 58.902 40.000 0.00 0.00 0.00 2.40
131 133 2.420058 AGTAAAGAATTCCAGCCCCG 57.580 50.000 0.65 0.00 0.00 5.73
215 217 4.020543 CGATAAATTCCTTCCCCAAACCA 58.979 43.478 0.00 0.00 0.00 3.67
241 243 0.033796 CATCCATCCAACCCACAGCT 60.034 55.000 0.00 0.00 0.00 4.24
243 245 1.679977 CCATCCAACCCACAGCTGG 60.680 63.158 19.93 6.95 37.29 4.85
313 320 4.514569 CGAAATTCGCACGGCCGG 62.515 66.667 31.76 19.49 31.14 6.13
315 322 3.376914 GAAATTCGCACGGCCGGTC 62.377 63.158 31.76 19.19 0.00 4.79
374 386 2.396590 TTCCCCGGAAAAAGAGATCG 57.603 50.000 0.73 0.00 0.00 3.69
380 392 1.348594 GAAAAAGAGATCGCCCGCG 59.651 57.895 0.00 0.00 41.35 6.46
382 394 3.950794 AAAAGAGATCGCCCGCGCA 62.951 57.895 8.75 0.00 39.59 6.09
410 422 3.834799 GCCACGTACGGGAGGGAG 61.835 72.222 21.47 2.18 0.00 4.30
411 423 3.834799 CCACGTACGGGAGGGAGC 61.835 72.222 21.47 0.00 0.00 4.70
412 424 4.189188 CACGTACGGGAGGGAGCG 62.189 72.222 21.06 0.00 0.00 5.03
413 425 4.415150 ACGTACGGGAGGGAGCGA 62.415 66.667 21.06 0.00 0.00 4.93
414 426 3.584052 CGTACGGGAGGGAGCGAG 61.584 72.222 7.57 0.00 0.00 5.03
415 427 3.217743 GTACGGGAGGGAGCGAGG 61.218 72.222 0.00 0.00 0.00 4.63
416 428 3.414193 TACGGGAGGGAGCGAGGA 61.414 66.667 0.00 0.00 0.00 3.71
417 429 3.417167 TACGGGAGGGAGCGAGGAG 62.417 68.421 0.00 0.00 0.00 3.69
421 433 2.131067 GGAGGGAGCGAGGAGAAGG 61.131 68.421 0.00 0.00 0.00 3.46
426 438 0.108089 GGAGCGAGGAGAAGGGAAAC 60.108 60.000 0.00 0.00 0.00 2.78
438 450 0.178973 AGGGAAACGAAAACCCCCAG 60.179 55.000 0.00 0.00 44.21 4.45
497 510 0.616891 GCCCCGGAAGTAGAAAAGGA 59.383 55.000 0.73 0.00 0.00 3.36
505 518 3.133183 GGAAGTAGAAAAGGAGATCGGCT 59.867 47.826 0.00 0.00 0.00 5.52
611 626 3.148279 CTCCTCCCGTTCCCTCCG 61.148 72.222 0.00 0.00 0.00 4.63
666 681 2.409948 AGGAGCCTTGGAGATTTTCG 57.590 50.000 0.00 0.00 0.00 3.46
1111 1135 3.889044 TCGGCTCGTGGATCTCGC 61.889 66.667 0.00 0.00 0.00 5.03
1114 1138 2.026879 GCTCGTGGATCTCGCCTC 59.973 66.667 0.00 0.00 0.00 4.70
1252 1282 3.070734 CCGGGTCTGATTCTGATTCTGAT 59.929 47.826 10.82 0.00 0.00 2.90
1253 1283 4.444022 CCGGGTCTGATTCTGATTCTGATT 60.444 45.833 10.82 0.00 0.00 2.57
1254 1284 4.749099 CGGGTCTGATTCTGATTCTGATTC 59.251 45.833 10.82 7.93 0.00 2.52
1255 1285 5.453057 CGGGTCTGATTCTGATTCTGATTCT 60.453 44.000 10.82 0.00 0.00 2.40
1256 1286 5.759273 GGGTCTGATTCTGATTCTGATTCTG 59.241 44.000 10.82 12.71 0.00 3.02
1257 1287 5.759273 GGTCTGATTCTGATTCTGATTCTGG 59.241 44.000 10.82 9.94 0.00 3.86
1321 1351 2.356667 CCTGCCCCTGGTTTCTCC 59.643 66.667 0.00 0.00 0.00 3.71
1535 1565 3.036959 GGGGGAGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1539 1569 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1540 1570 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1541 1571 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1542 1572 0.556380 AGGAGGAGGAGGAGGAGGAA 60.556 60.000 0.00 0.00 0.00 3.36
1543 1573 0.565674 GGAGGAGGAGGAGGAGGAAT 59.434 60.000 0.00 0.00 0.00 3.01
1544 1574 1.061735 GGAGGAGGAGGAGGAGGAATT 60.062 57.143 0.00 0.00 0.00 2.17
1600 1630 2.543777 TGGAGGTTATTATGGCGCTC 57.456 50.000 7.64 0.00 0.00 5.03
1606 1636 5.106673 GGAGGTTATTATGGCGCTCAATTAC 60.107 44.000 7.64 8.33 0.00 1.89
1735 1765 1.502163 GCTGGGATGATTTCGAGCCG 61.502 60.000 0.00 0.00 0.00 5.52
1816 1846 3.064324 GCCATCGCCAGTTGCCTT 61.064 61.111 0.00 0.00 36.24 4.35
1851 1881 2.441164 TGGTGCAGGGCGTTTTGT 60.441 55.556 0.00 0.00 0.00 2.83
1852 1882 2.015227 CTGGTGCAGGGCGTTTTGTT 62.015 55.000 0.00 0.00 0.00 2.83
1853 1883 1.591327 GGTGCAGGGCGTTTTGTTG 60.591 57.895 0.00 0.00 0.00 3.33
1867 1897 1.444119 TTGTTGGAAGCAGTGACGGC 61.444 55.000 0.00 0.00 0.00 5.68
1896 1926 1.067364 TGTTCGTGCCGACTTGAGTTA 59.933 47.619 0.00 0.00 34.89 2.24
1899 1929 3.853831 TCGTGCCGACTTGAGTTATTA 57.146 42.857 0.00 0.00 0.00 0.98
1900 1930 3.504863 TCGTGCCGACTTGAGTTATTAC 58.495 45.455 0.00 0.00 0.00 1.89
1901 1931 2.601763 CGTGCCGACTTGAGTTATTACC 59.398 50.000 0.00 0.00 0.00 2.85
1902 1932 3.675228 CGTGCCGACTTGAGTTATTACCT 60.675 47.826 0.00 0.00 0.00 3.08
1903 1933 3.617263 GTGCCGACTTGAGTTATTACCTG 59.383 47.826 0.00 0.00 0.00 4.00
1904 1934 3.195661 GCCGACTTGAGTTATTACCTGG 58.804 50.000 0.00 0.00 0.00 4.45
1924 1954 2.225019 GGACCTGAATCATGCTATTGCG 59.775 50.000 0.00 0.00 43.34 4.85
1925 1955 1.605710 ACCTGAATCATGCTATTGCGC 59.394 47.619 0.00 0.00 43.34 6.09
1931 1961 0.755079 TCATGCTATTGCGCTCTCCT 59.245 50.000 9.73 0.00 43.34 3.69
1935 1965 2.032860 GCTATTGCGCTCTCCTGGGA 62.033 60.000 9.73 0.00 0.00 4.37
1944 1977 1.151810 TCTCCTGGGAGCCACCTTT 60.152 57.895 11.51 0.00 41.71 3.11
1959 1992 3.628646 CTTTCCTCCCGGGTGGCTG 62.629 68.421 32.94 21.26 36.25 4.85
1981 2014 2.282462 CGTGCTTTTGAGGGGCCT 60.282 61.111 0.84 0.00 0.00 5.19
1986 2019 0.035317 GCTTTTGAGGGGCCTTTTGG 59.965 55.000 0.84 0.00 44.18 3.28
2004 2037 0.824109 GGGTTTGGAGGCCTTTATGC 59.176 55.000 6.77 0.00 0.00 3.14
2005 2038 1.619704 GGGTTTGGAGGCCTTTATGCT 60.620 52.381 6.77 0.00 0.00 3.79
2032 2065 1.004560 CGCCAACTGCTCTCAAGGA 60.005 57.895 0.00 0.00 38.05 3.36
2046 2079 1.000866 AAGGATTGCCTCCCCTTGC 59.999 57.895 0.00 0.00 46.28 4.01
2059 2092 3.114616 CTTGCGTCCTGCTCACGG 61.115 66.667 5.10 0.00 46.63 4.94
2173 2392 1.134491 CCAATTGTACCCGGAGAGGAC 60.134 57.143 0.73 0.00 45.00 3.85
2207 2426 2.048877 GTGCTGCATTGGTGTGCC 60.049 61.111 5.27 0.00 44.43 5.01
2222 2441 1.552792 TGTGCCGTGATGGAGTTGATA 59.447 47.619 0.00 0.00 42.00 2.15
2224 2443 1.134521 TGCCGTGATGGAGTTGATACC 60.135 52.381 0.00 0.00 42.00 2.73
2239 2458 2.515996 ATACCGTGGGAAGTGCACCG 62.516 60.000 14.63 8.64 0.00 4.94
2334 2553 0.740149 TTGCATTCATGGATCCGCAC 59.260 50.000 7.39 0.00 0.00 5.34
2335 2554 0.107066 TGCATTCATGGATCCGCACT 60.107 50.000 7.39 0.00 0.00 4.40
2336 2555 0.590195 GCATTCATGGATCCGCACTC 59.410 55.000 7.39 0.00 0.00 3.51
2338 2557 2.501261 CATTCATGGATCCGCACTCAT 58.499 47.619 7.39 0.00 0.00 2.90
2340 2559 2.245159 TCATGGATCCGCACTCATTC 57.755 50.000 7.39 0.00 0.00 2.67
2341 2560 1.202687 TCATGGATCCGCACTCATTCC 60.203 52.381 7.39 0.00 0.00 3.01
2343 2562 0.911769 TGGATCCGCACTCATTCCTT 59.088 50.000 7.39 0.00 0.00 3.36
2344 2563 2.115427 TGGATCCGCACTCATTCCTTA 58.885 47.619 7.39 0.00 0.00 2.69
2345 2564 2.103094 TGGATCCGCACTCATTCCTTAG 59.897 50.000 7.39 0.00 0.00 2.18
2346 2565 2.103263 GGATCCGCACTCATTCCTTAGT 59.897 50.000 0.00 0.00 0.00 2.24
2380 2599 3.008594 TCCATGTTGAACCGGTATTGAGT 59.991 43.478 8.00 0.00 0.00 3.41
2389 2608 2.844348 ACCGGTATTGAGTGGGAAGATT 59.156 45.455 4.49 0.00 0.00 2.40
2390 2609 4.035112 ACCGGTATTGAGTGGGAAGATTA 58.965 43.478 4.49 0.00 0.00 1.75
2408 2627 8.303876 GGAAGATTACTGATCCTGATCTTCTAC 58.696 40.741 21.84 11.42 45.96 2.59
2409 2628 7.447374 AGATTACTGATCCTGATCTTCTACG 57.553 40.000 8.50 0.00 38.60 3.51
2508 2727 2.867624 TGCTGTTCTCCAAAGCAATCT 58.132 42.857 0.00 0.00 43.65 2.40
2511 2730 3.119919 GCTGTTCTCCAAAGCAATCTGAG 60.120 47.826 0.00 0.00 36.91 3.35
2539 2758 7.448748 AACAAAGGTTAGTATGGTCACAATC 57.551 36.000 0.00 0.00 34.87 2.67
2547 2766 7.039993 GGTTAGTATGGTCACAATCCTTTTTGT 60.040 37.037 0.00 0.00 40.39 2.83
2648 2868 9.710900 CATAATTGCACTGATGTACTTCCTATA 57.289 33.333 6.32 0.00 0.00 1.31
2676 2906 8.975663 AGCATACCCTAATAGAAAAAGTAACC 57.024 34.615 0.00 0.00 0.00 2.85
2689 2919 4.766404 AAAGTAACCCAAATTCGAGCTG 57.234 40.909 0.00 0.00 0.00 4.24
2697 2927 4.576463 ACCCAAATTCGAGCTGAATATGAC 59.424 41.667 10.51 0.00 46.65 3.06
2698 2928 4.818546 CCCAAATTCGAGCTGAATATGACT 59.181 41.667 10.51 0.00 46.65 3.41
2718 2948 0.321653 CTGACTTAGGTGGTGGTGGC 60.322 60.000 0.00 0.00 0.00 5.01
2732 2962 2.813200 TGGCGTACGGACACAACA 59.187 55.556 18.39 0.00 0.00 3.33
2756 2986 2.429494 GATGGAGCTAGGGCCAGC 59.571 66.667 16.99 16.99 42.12 4.85
2846 3076 6.808321 TGCTATCTGGGTAGTATTTTCTGT 57.192 37.500 0.00 0.00 0.00 3.41
2851 3081 5.989477 TCTGGGTAGTATTTTCTGTGATGG 58.011 41.667 0.00 0.00 0.00 3.51
2898 3128 8.099364 TGTGATTTCTCCAGTTATTTTCTGTC 57.901 34.615 0.00 0.00 0.00 3.51
2909 3139 9.655769 CCAGTTATTTTCTGTCATGAATATTCG 57.344 33.333 10.80 0.00 0.00 3.34
2950 3180 9.283420 GTACGATTTCTCTAGTAGTTTACAACC 57.717 37.037 0.00 0.00 0.00 3.77
2952 3182 8.362639 ACGATTTCTCTAGTAGTTTACAACCAA 58.637 33.333 0.00 0.00 0.00 3.67
2955 3185 9.841295 ATTTCTCTAGTAGTTTACAACCAACAA 57.159 29.630 0.00 0.00 0.00 2.83
2956 3186 9.669887 TTTCTCTAGTAGTTTACAACCAACAAA 57.330 29.630 0.00 0.00 0.00 2.83
2959 3189 9.931210 CTCTAGTAGTTTACAACCAACAAAAAG 57.069 33.333 0.00 0.00 0.00 2.27
3011 3246 6.985188 TGCTATTCACTTGAGTGTAAATCC 57.015 37.500 10.66 1.87 45.76 3.01
3012 3247 6.472016 TGCTATTCACTTGAGTGTAAATCCA 58.528 36.000 10.66 3.91 45.76 3.41
3020 3255 7.178451 TCACTTGAGTGTAAATCCACTAGATCA 59.822 37.037 10.66 0.00 45.46 2.92
3027 3262 8.200792 AGTGTAAATCCACTAGATCATTGTCTC 58.799 37.037 0.00 0.00 43.71 3.36
3033 3268 3.634448 CACTAGATCATTGTCTCGAGGGT 59.366 47.826 13.56 0.00 0.00 4.34
3091 3327 9.884465 CTTCCTCACAATAGTTTAAAGTTGAAG 57.116 33.333 0.00 5.06 0.00 3.02
3123 3359 9.695526 TGATGAAAAACTTGTCCTATCAATTTG 57.304 29.630 0.00 0.00 0.00 2.32
3159 3395 4.207635 CGTTATGCTGCATATGCTTTTTGG 59.792 41.667 27.13 11.71 42.66 3.28
3166 3402 5.679382 GCTGCATATGCTTTTTGGTCATACA 60.679 40.000 27.13 2.04 42.66 2.29
3221 3457 5.649831 GTGATTGATTCTAACCTGCTCCTTT 59.350 40.000 0.00 0.00 0.00 3.11
3272 3508 1.161843 CGCGGTTAACTTTGGATGGT 58.838 50.000 5.42 0.00 0.00 3.55
3324 3560 3.975168 AAGCAGTGTCGGGTATTAAGT 57.025 42.857 0.00 0.00 0.00 2.24
3541 3777 1.408702 TGTTTTTGACTGCCCTGAAGC 59.591 47.619 0.00 0.00 0.00 3.86
3573 3809 1.072806 ACAAGAGATCTGGCAAGTGCA 59.927 47.619 0.00 0.00 44.36 4.57
3828 4074 9.322773 CATCTTTCTTAGCATTACTGATGAAGA 57.677 33.333 0.00 0.00 38.03 2.87
3974 4222 2.031516 CAGCCTCACCAGCGACAAG 61.032 63.158 0.00 0.00 34.64 3.16
3986 4234 2.214216 CGACAAGGAGGTGGGTGGA 61.214 63.158 0.00 0.00 0.00 4.02
4004 4252 4.379082 GGTGGAGCATTACTTTTGGTAACG 60.379 45.833 0.00 0.00 42.35 3.18
4078 4326 3.333381 TCCAGGGATGTTTCTTCATGGAA 59.667 43.478 0.00 0.00 0.00 3.53
4104 4352 5.962433 TGCAGTTCAAGAGTGTATAGGTAC 58.038 41.667 0.00 0.00 0.00 3.34
4106 4354 6.154534 TGCAGTTCAAGAGTGTATAGGTACAT 59.845 38.462 0.00 0.00 42.43 2.29
4167 4416 4.592485 TCCTGTGAAGAAGACTGAAGAC 57.408 45.455 0.00 0.00 0.00 3.01
4181 4430 7.463961 AGACTGAAGACGAACTTATTCCTTA 57.536 36.000 0.00 0.00 39.13 2.69
4376 4626 6.879993 TCTGTTGTGTTTAGTTGGAGTTTACA 59.120 34.615 0.00 0.00 0.00 2.41
4471 4721 4.016444 ACCTGAGCAGTTTCTTGAAAACA 58.984 39.130 3.75 0.00 32.81 2.83
4487 4737 8.963725 TCTTGAAAACATGCTTCAGATATGAAT 58.036 29.630 2.71 0.00 34.41 2.57
4508 4758 2.460757 TTTTCGGTACTTCGGGGAAG 57.539 50.000 3.92 3.92 44.37 3.46
4580 4830 3.696051 TGCTTGTTCTGCTCCCAATAATC 59.304 43.478 0.00 0.00 0.00 1.75
4587 4837 2.481952 CTGCTCCCAATAATCTAAGCGC 59.518 50.000 0.00 0.00 32.49 5.92
4589 4839 2.481952 GCTCCCAATAATCTAAGCGCTG 59.518 50.000 12.58 0.00 0.00 5.18
4590 4840 2.481952 CTCCCAATAATCTAAGCGCTGC 59.518 50.000 12.58 0.00 0.00 5.25
4607 4857 0.945743 TGCGCAGGCGATCATGATAC 60.946 55.000 18.96 3.85 44.10 2.24
4608 4858 1.630244 GCGCAGGCGATCATGATACC 61.630 60.000 18.96 13.27 42.83 2.73
4610 4860 0.035317 GCAGGCGATCATGATACCCA 59.965 55.000 19.12 0.00 0.00 4.51
4635 4886 4.142730 CGAGAGTATATGGGTTACGTAGCC 60.143 50.000 19.33 19.33 45.01 3.93
4636 4887 4.085009 AGAGTATATGGGTTACGTAGCCC 58.915 47.826 33.88 33.88 45.98 5.19
4680 4931 4.593864 GGCGAGCTCCATCGGTCC 62.594 72.222 8.47 0.00 42.94 4.46
4806 5059 3.785486 TCGAGAGTAGCAATCCACATTG 58.215 45.455 0.00 0.00 42.26 2.82
4863 5116 2.736236 CTGTCGCGTTGCTCTGCT 60.736 61.111 5.77 0.00 0.00 4.24
4923 5176 2.280660 CCATAGCAGCGGCCAGAG 60.281 66.667 4.82 0.00 42.56 3.35
4937 5190 0.914644 CCAGAGGGATCAAGCAAGGA 59.085 55.000 0.00 0.00 35.59 3.36
5005 5258 3.983044 AATCTGGTGGTACCTTGAGTC 57.017 47.619 14.36 0.00 39.58 3.36
5032 5285 4.580580 CCTCTAACCCCTTGTTTCATATGC 59.419 45.833 0.00 0.00 38.42 3.14
5074 5327 0.681175 ACCACTTTGGCCAGAAATGC 59.319 50.000 5.11 0.00 42.67 3.56
5123 5404 4.097892 GGATTCCATTTAAGACACGGCAAT 59.902 41.667 0.00 0.00 0.00 3.56
5124 5405 4.695217 TTCCATTTAAGACACGGCAATC 57.305 40.909 0.00 0.00 0.00 2.67
5165 5446 3.109151 ACGGGTTACATCATCAGGGTAA 58.891 45.455 0.00 0.00 0.00 2.85
5171 5452 6.157211 GGTTACATCATCAGGGTAACTATCG 58.843 44.000 12.06 0.00 43.83 2.92
5179 5460 5.018539 TCAGGGTAACTATCGAACCATTG 57.981 43.478 5.63 3.74 34.83 2.82
5182 5463 3.800506 GGGTAACTATCGAACCATTGACG 59.199 47.826 5.63 0.00 34.83 4.35
5183 5464 4.440525 GGGTAACTATCGAACCATTGACGA 60.441 45.833 5.63 0.00 40.18 4.20
5184 5465 4.501921 GGTAACTATCGAACCATTGACGAC 59.498 45.833 0.00 0.00 38.79 4.34
5185 5466 4.451629 AACTATCGAACCATTGACGACT 57.548 40.909 0.00 0.00 38.79 4.18
5186 5467 4.451629 ACTATCGAACCATTGACGACTT 57.548 40.909 0.00 0.00 38.79 3.01
5187 5468 4.421948 ACTATCGAACCATTGACGACTTC 58.578 43.478 0.00 0.00 38.79 3.01
5188 5469 2.074547 TCGAACCATTGACGACTTCC 57.925 50.000 0.00 0.00 0.00 3.46
5189 5470 0.713883 CGAACCATTGACGACTTCCG 59.286 55.000 0.00 0.00 45.44 4.30
5190 5471 0.442699 GAACCATTGACGACTTCCGC 59.557 55.000 0.00 0.00 43.32 5.54
5191 5472 0.034896 AACCATTGACGACTTCCGCT 59.965 50.000 0.00 0.00 43.32 5.52
5192 5473 0.892755 ACCATTGACGACTTCCGCTA 59.107 50.000 0.00 0.00 43.32 4.26
5193 5474 1.135083 ACCATTGACGACTTCCGCTAG 60.135 52.381 0.00 0.00 43.32 3.42
5194 5475 1.134367 CCATTGACGACTTCCGCTAGA 59.866 52.381 0.00 0.00 43.32 2.43
5212 5493 4.502645 GCTAGAGAGAGAAAAAGATGCGTC 59.497 45.833 0.00 0.00 0.00 5.19
5253 5534 3.738830 AGAAGCAAATTGTGTGTGCAT 57.261 38.095 2.16 0.00 40.83 3.96
5254 5535 3.386486 AGAAGCAAATTGTGTGTGCATG 58.614 40.909 2.16 0.00 40.83 4.06
5283 5565 1.496429 GATGACCCCCACCTGATTCAT 59.504 52.381 0.00 0.00 0.00 2.57
5312 5594 9.543783 CTACCTGTTTTCTAGTTTCACTAGTTT 57.456 33.333 10.12 0.00 46.31 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.585047 GGTCACGCTATGGAAAAGTTATCTT 59.415 40.000 0.00 0.00 35.14 2.40
1 2 5.116882 GGTCACGCTATGGAAAAGTTATCT 58.883 41.667 0.00 0.00 0.00 1.98
2 3 4.873827 TGGTCACGCTATGGAAAAGTTATC 59.126 41.667 0.00 0.00 0.00 1.75
7 8 3.065371 GGAATGGTCACGCTATGGAAAAG 59.935 47.826 0.00 0.00 0.00 2.27
15 16 1.134220 GGAATGGGAATGGTCACGCTA 60.134 52.381 0.00 0.00 0.00 4.26
31 32 2.716424 TCCAGAGGGTGTGAAAAGGAAT 59.284 45.455 0.00 0.00 34.93 3.01
36 37 2.370849 GGTACTCCAGAGGGTGTGAAAA 59.629 50.000 0.00 0.00 40.91 2.29
53 54 8.833231 TGGTATATACTACGAGTACAAGGTAC 57.167 38.462 12.54 0.00 32.84 3.34
76 78 3.795826 GCATAACGGAGCAGTAGTACTGG 60.796 52.174 27.48 15.39 46.01 4.00
78 80 3.021695 TGCATAACGGAGCAGTAGTACT 58.978 45.455 0.00 0.00 35.51 2.73
79 81 3.431922 TGCATAACGGAGCAGTAGTAC 57.568 47.619 0.00 0.00 35.51 2.73
94 96 6.375174 TCTTTACTAGGTCGTACACTTGCATA 59.625 38.462 0.00 0.00 0.00 3.14
102 104 6.626623 GCTGGAATTCTTTACTAGGTCGTACA 60.627 42.308 5.23 0.00 0.00 2.90
113 115 2.413310 TCGGGGCTGGAATTCTTTAC 57.587 50.000 5.23 0.00 0.00 2.01
114 116 2.158667 GGATCGGGGCTGGAATTCTTTA 60.159 50.000 5.23 0.00 0.00 1.85
115 117 1.410224 GGATCGGGGCTGGAATTCTTT 60.410 52.381 5.23 0.00 0.00 2.52
118 120 0.106719 TTGGATCGGGGCTGGAATTC 60.107 55.000 0.00 0.00 0.00 2.17
119 121 0.557729 ATTGGATCGGGGCTGGAATT 59.442 50.000 0.00 0.00 0.00 2.17
120 122 0.557729 AATTGGATCGGGGCTGGAAT 59.442 50.000 0.00 0.00 0.00 3.01
121 123 0.106719 GAATTGGATCGGGGCTGGAA 60.107 55.000 0.00 0.00 0.00 3.53
131 133 6.683974 TCGATTTCCTTCTTGAATTGGATC 57.316 37.500 0.00 0.00 0.00 3.36
215 217 0.394352 GGTTGGATGGATGCCTCGTT 60.394 55.000 0.00 0.00 0.00 3.85
274 276 2.824880 CGGTTGGACTGTTGGGGGA 61.825 63.158 0.00 0.00 0.00 4.81
395 407 4.189188 CGCTCCCTCCCGTACGTG 62.189 72.222 15.21 2.17 0.00 4.49
396 408 4.415150 TCGCTCCCTCCCGTACGT 62.415 66.667 15.21 0.00 0.00 3.57
397 409 3.584052 CTCGCTCCCTCCCGTACG 61.584 72.222 8.69 8.69 0.00 3.67
398 410 3.217743 CCTCGCTCCCTCCCGTAC 61.218 72.222 0.00 0.00 0.00 3.67
399 411 3.414193 TCCTCGCTCCCTCCCGTA 61.414 66.667 0.00 0.00 0.00 4.02
400 412 4.824515 CTCCTCGCTCCCTCCCGT 62.825 72.222 0.00 0.00 0.00 5.28
401 413 4.507916 TCTCCTCGCTCCCTCCCG 62.508 72.222 0.00 0.00 0.00 5.14
402 414 2.042843 TTCTCCTCGCTCCCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
403 415 2.131067 CCTTCTCCTCGCTCCCTCC 61.131 68.421 0.00 0.00 0.00 4.30
404 416 2.131067 CCCTTCTCCTCGCTCCCTC 61.131 68.421 0.00 0.00 0.00 4.30
405 417 2.042435 CCCTTCTCCTCGCTCCCT 60.042 66.667 0.00 0.00 0.00 4.20
406 418 1.265454 TTTCCCTTCTCCTCGCTCCC 61.265 60.000 0.00 0.00 0.00 4.30
407 419 0.108089 GTTTCCCTTCTCCTCGCTCC 60.108 60.000 0.00 0.00 0.00 4.70
408 420 0.458716 CGTTTCCCTTCTCCTCGCTC 60.459 60.000 0.00 0.00 0.00 5.03
409 421 0.898789 TCGTTTCCCTTCTCCTCGCT 60.899 55.000 0.00 0.00 0.00 4.93
410 422 0.037605 TTCGTTTCCCTTCTCCTCGC 60.038 55.000 0.00 0.00 0.00 5.03
411 423 2.450609 TTTCGTTTCCCTTCTCCTCG 57.549 50.000 0.00 0.00 0.00 4.63
412 424 2.812591 GGTTTTCGTTTCCCTTCTCCTC 59.187 50.000 0.00 0.00 0.00 3.71
413 425 2.488528 GGGTTTTCGTTTCCCTTCTCCT 60.489 50.000 0.00 0.00 38.29 3.69
414 426 1.884579 GGGTTTTCGTTTCCCTTCTCC 59.115 52.381 0.00 0.00 38.29 3.71
415 427 1.884579 GGGGTTTTCGTTTCCCTTCTC 59.115 52.381 0.00 0.00 40.88 2.87
416 428 1.479942 GGGGGTTTTCGTTTCCCTTCT 60.480 52.381 0.00 0.00 40.88 2.85
417 429 0.963962 GGGGGTTTTCGTTTCCCTTC 59.036 55.000 0.00 0.00 40.88 3.46
421 433 1.663739 GCTGGGGGTTTTCGTTTCC 59.336 57.895 0.00 0.00 0.00 3.13
426 438 2.281900 TTCCGCTGGGGGTTTTCG 60.282 61.111 11.17 0.00 36.01 3.46
567 581 0.689412 GTTGGAGAGGAGGGAGGGAG 60.689 65.000 0.00 0.00 0.00 4.30
568 582 1.392534 GTTGGAGAGGAGGGAGGGA 59.607 63.158 0.00 0.00 0.00 4.20
569 583 1.690985 GGTTGGAGAGGAGGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
570 584 1.690985 GGGTTGGAGAGGAGGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
1053 1068 2.125512 GATTGGCGACTCTGCGGT 60.126 61.111 0.00 0.00 35.06 5.68
1127 1151 1.077716 GACCGAAATCCCCACCCAG 60.078 63.158 0.00 0.00 0.00 4.45
1140 1167 0.322322 AGCAATAAACACGGGACCGA 59.678 50.000 18.80 0.00 42.83 4.69
1231 1261 3.808466 TCAGAATCAGAATCAGACCCG 57.192 47.619 0.00 0.00 0.00 5.28
1252 1282 2.345991 CTTCCGCCCGAACCAGAA 59.654 61.111 0.00 0.00 0.00 3.02
1253 1283 3.702048 CCTTCCGCCCGAACCAGA 61.702 66.667 0.00 0.00 0.00 3.86
1254 1284 2.573609 CTACCTTCCGCCCGAACCAG 62.574 65.000 0.00 0.00 0.00 4.00
1255 1285 2.604079 TACCTTCCGCCCGAACCA 60.604 61.111 0.00 0.00 0.00 3.67
1256 1286 2.186125 CTACCTTCCGCCCGAACC 59.814 66.667 0.00 0.00 0.00 3.62
1257 1287 1.141234 CTCTACCTTCCGCCCGAAC 59.859 63.158 0.00 0.00 0.00 3.95
1302 1332 3.185203 AGAAACCAGGGGCAGGCA 61.185 61.111 0.00 0.00 0.00 4.75
1303 1333 2.361737 GAGAAACCAGGGGCAGGC 60.362 66.667 0.00 0.00 0.00 4.85
1304 1334 2.356667 GGAGAAACCAGGGGCAGG 59.643 66.667 0.00 0.00 38.79 4.85
1306 1336 4.344865 GCGGAGAAACCAGGGGCA 62.345 66.667 0.00 0.00 38.90 5.36
1308 1338 4.778143 CGGCGGAGAAACCAGGGG 62.778 72.222 0.00 0.00 38.90 4.79
1321 1351 2.605338 CCAAATCAATCCAATAGCGGCG 60.605 50.000 0.51 0.51 0.00 6.46
1534 1564 1.140652 CTCCTGCTCCAATTCCTCCTC 59.859 57.143 0.00 0.00 0.00 3.71
1535 1565 1.211456 CTCCTGCTCCAATTCCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
1539 1569 0.182299 CCTCCTCCTGCTCCAATTCC 59.818 60.000 0.00 0.00 0.00 3.01
1540 1570 1.140652 CTCCTCCTCCTGCTCCAATTC 59.859 57.143 0.00 0.00 0.00 2.17
1541 1571 1.211456 CTCCTCCTCCTGCTCCAATT 58.789 55.000 0.00 0.00 0.00 2.32
1542 1572 0.693767 CCTCCTCCTCCTGCTCCAAT 60.694 60.000 0.00 0.00 0.00 3.16
1543 1573 1.306482 CCTCCTCCTCCTGCTCCAA 60.306 63.158 0.00 0.00 0.00 3.53
1544 1574 1.597905 ATCCTCCTCCTCCTGCTCCA 61.598 60.000 0.00 0.00 0.00 3.86
1600 1630 1.651987 ATGAGCACGACGGGTAATTG 58.348 50.000 0.00 0.00 0.00 2.32
1606 1636 1.361668 CCAAGAATGAGCACGACGGG 61.362 60.000 0.00 0.00 0.00 5.28
1735 1765 0.603975 GCAATAGATCCGCAGGGTCC 60.604 60.000 4.51 0.00 28.78 4.46
1851 1881 2.664851 CGCCGTCACTGCTTCCAA 60.665 61.111 0.00 0.00 0.00 3.53
1852 1882 4.680237 CCGCCGTCACTGCTTCCA 62.680 66.667 0.00 0.00 0.00 3.53
1881 1911 3.617263 CAGGTAATAACTCAAGTCGGCAC 59.383 47.826 0.00 0.00 0.00 5.01
1882 1912 3.369052 CCAGGTAATAACTCAAGTCGGCA 60.369 47.826 0.00 0.00 0.00 5.69
1883 1913 3.118884 TCCAGGTAATAACTCAAGTCGGC 60.119 47.826 0.00 0.00 0.00 5.54
1884 1914 4.430908 GTCCAGGTAATAACTCAAGTCGG 58.569 47.826 0.00 0.00 0.00 4.79
1896 1926 3.461085 AGCATGATTCAGGTCCAGGTAAT 59.539 43.478 0.00 0.00 0.00 1.89
1899 1929 1.293062 AGCATGATTCAGGTCCAGGT 58.707 50.000 0.00 0.00 0.00 4.00
1900 1930 3.784511 ATAGCATGATTCAGGTCCAGG 57.215 47.619 0.00 0.00 0.00 4.45
1901 1931 3.252701 GCAATAGCATGATTCAGGTCCAG 59.747 47.826 0.00 0.00 41.58 3.86
1902 1932 3.216800 GCAATAGCATGATTCAGGTCCA 58.783 45.455 0.00 0.00 41.58 4.02
1903 1933 2.225019 CGCAATAGCATGATTCAGGTCC 59.775 50.000 0.00 0.00 42.27 4.46
1904 1934 2.350197 GCGCAATAGCATGATTCAGGTC 60.350 50.000 0.30 0.00 42.27 3.85
1925 1955 1.204113 AAAGGTGGCTCCCAGGAGAG 61.204 60.000 18.08 9.12 44.53 3.20
1931 1961 2.231380 GGAGGAAAGGTGGCTCCCA 61.231 63.158 1.14 0.00 36.75 4.37
1959 1992 2.256461 CCTCAAAAGCACGCCTGC 59.744 61.111 0.00 0.00 44.63 4.85
1961 1994 2.282462 CCCCTCAAAAGCACGCCT 60.282 61.111 0.00 0.00 0.00 5.52
1981 2014 1.886422 AAAGGCCTCCAAACCCAAAA 58.114 45.000 5.23 0.00 0.00 2.44
1986 2019 1.478105 CAGCATAAAGGCCTCCAAACC 59.522 52.381 5.23 0.00 0.00 3.27
2032 2065 2.044946 GACGCAAGGGGAGGCAAT 60.045 61.111 0.00 0.00 46.39 3.56
2059 2092 3.350219 TCCTCTCCAGGTACAATTTGC 57.650 47.619 0.00 0.00 41.28 3.68
2060 2093 4.455606 GGATCCTCTCCAGGTACAATTTG 58.544 47.826 3.84 0.00 44.26 2.32
2061 2094 4.779993 GGATCCTCTCCAGGTACAATTT 57.220 45.455 3.84 0.00 44.26 1.82
2150 2369 1.202099 TCTCCGGGTACAATTGGCCA 61.202 55.000 18.79 0.00 0.00 5.36
2173 2392 0.107312 CACTGCCAGAAGGAGATGGG 60.107 60.000 0.00 0.00 37.05 4.00
2207 2426 2.193447 CACGGTATCAACTCCATCACG 58.807 52.381 0.00 0.00 0.00 4.35
2222 2441 4.619227 CGGTGCACTTCCCACGGT 62.619 66.667 17.98 0.00 34.08 4.83
2239 2458 1.532868 GCATACTTCATCCCGTCATGC 59.467 52.381 0.00 0.00 0.00 4.06
2253 2472 3.072184 CCCAAGATAGGCAAGAGCATACT 59.928 47.826 0.00 0.00 40.15 2.12
2323 2542 1.135094 AGGAATGAGTGCGGATCCAT 58.865 50.000 13.41 0.00 32.47 3.41
2334 2553 4.899502 ACACTTCCACACTAAGGAATGAG 58.100 43.478 0.00 0.00 43.74 2.90
2335 2554 4.974645 ACACTTCCACACTAAGGAATGA 57.025 40.909 0.00 0.00 43.74 2.57
2336 2555 5.817816 GGATACACTTCCACACTAAGGAATG 59.182 44.000 0.00 0.00 43.74 2.67
2338 2557 4.841813 TGGATACACTTCCACACTAAGGAA 59.158 41.667 0.00 0.00 46.17 3.36
2340 2559 4.819105 TGGATACACTTCCACACTAAGG 57.181 45.455 0.00 0.00 46.17 2.69
2362 2581 2.551287 CCCACTCAATACCGGTTCAACA 60.551 50.000 15.04 0.00 0.00 3.33
2363 2582 2.081462 CCCACTCAATACCGGTTCAAC 58.919 52.381 15.04 0.00 0.00 3.18
2380 2599 5.471424 AGATCAGGATCAGTAATCTTCCCA 58.529 41.667 11.55 0.00 40.22 4.37
2389 2608 5.760743 CAGACGTAGAAGATCAGGATCAGTA 59.239 44.000 11.55 0.00 40.22 2.74
2390 2609 4.578516 CAGACGTAGAAGATCAGGATCAGT 59.421 45.833 11.55 0.00 40.22 3.41
2408 2627 3.249091 CTGGAATCTTCTGTGTCAGACG 58.751 50.000 0.00 0.00 40.46 4.18
2409 2628 3.007398 ACCTGGAATCTTCTGTGTCAGAC 59.993 47.826 0.00 0.00 40.46 3.51
2508 2727 7.081857 ACCATACTAACCTTTGTTAACCTCA 57.918 36.000 2.48 0.00 36.54 3.86
2511 2730 6.711645 TGTGACCATACTAACCTTTGTTAACC 59.288 38.462 2.48 0.00 36.54 2.85
2570 2789 1.216427 GATCCCAGGCCTTCAAGGAAT 59.784 52.381 7.98 0.00 37.67 3.01
2619 2839 7.776969 AGGAAGTACATCAGTGCAATTATGAAT 59.223 33.333 14.72 0.00 32.20 2.57
2633 2853 8.978472 GGGTATGCTAATATAGGAAGTACATCA 58.022 37.037 0.00 0.00 0.00 3.07
2634 2854 9.203163 AGGGTATGCTAATATAGGAAGTACATC 57.797 37.037 0.00 0.00 0.00 3.06
2658 2878 9.783256 CGAATTTGGGTTACTTTTTCTATTAGG 57.217 33.333 0.00 0.00 0.00 2.69
2661 2881 8.027189 GCTCGAATTTGGGTTACTTTTTCTATT 58.973 33.333 0.00 0.00 0.00 1.73
2671 2892 4.965119 ATTCAGCTCGAATTTGGGTTAC 57.035 40.909 5.80 0.00 41.83 2.50
2672 2893 6.260050 GTCATATTCAGCTCGAATTTGGGTTA 59.740 38.462 19.08 6.79 41.83 2.85
2673 2894 5.066505 GTCATATTCAGCTCGAATTTGGGTT 59.933 40.000 19.08 0.00 41.83 4.11
2676 2906 5.757320 AGAGTCATATTCAGCTCGAATTTGG 59.243 40.000 19.08 10.57 41.83 3.28
2689 2919 6.276847 CACCACCTAAGTCAGAGTCATATTC 58.723 44.000 0.00 0.00 0.00 1.75
2697 2927 1.276421 CCACCACCACCTAAGTCAGAG 59.724 57.143 0.00 0.00 0.00 3.35
2698 2928 1.348064 CCACCACCACCTAAGTCAGA 58.652 55.000 0.00 0.00 0.00 3.27
2718 2948 0.665369 GAGGGTGTTGTGTCCGTACG 60.665 60.000 8.69 8.69 0.00 3.67
2756 2986 5.989777 CGAATACCCAAAGTATCCTAAGGTG 59.010 44.000 0.00 0.00 40.98 4.00
2777 3007 7.666623 TGCTCCATATAACATCTACATTCGAA 58.333 34.615 0.00 0.00 0.00 3.71
2814 3044 1.307097 CCCAGATAGCAAGAGCAAGC 58.693 55.000 0.00 0.00 45.49 4.01
2874 3104 8.099364 TGACAGAAAATAACTGGAGAAATCAC 57.901 34.615 0.00 0.00 39.38 3.06
2884 3114 9.162793 GCGAATATTCATGACAGAAAATAACTG 57.837 33.333 15.57 0.00 40.68 3.16
2948 3178 7.672240 TGAAACCTAACTTTCTTTTTGTTGGT 58.328 30.769 0.00 0.00 32.25 3.67
2949 3179 8.716646 ATGAAACCTAACTTTCTTTTTGTTGG 57.283 30.769 0.00 0.00 32.25 3.77
2959 3189 9.967346 AGCTAAAAAGAATGAAACCTAACTTTC 57.033 29.630 0.00 0.00 0.00 2.62
3002 3237 7.168302 CGAGACAATGATCTAGTGGATTTACAC 59.832 40.741 0.00 0.00 41.63 2.90
3011 3246 3.634448 ACCCTCGAGACAATGATCTAGTG 59.366 47.826 15.71 0.00 0.00 2.74
3012 3247 3.904717 ACCCTCGAGACAATGATCTAGT 58.095 45.455 15.71 0.00 0.00 2.57
3020 3255 5.997384 AACTAGTTTACCCTCGAGACAAT 57.003 39.130 15.71 0.00 0.00 2.71
3068 3304 7.648142 TGCTTCAACTTTAAACTATTGTGAGG 58.352 34.615 0.00 0.00 0.00 3.86
3091 3327 3.676646 GGACAAGTTTTTCATCATGCTGC 59.323 43.478 0.00 0.00 0.00 5.25
3135 3371 3.631145 AAAGCATATGCAGCATAACGG 57.369 42.857 28.62 12.36 45.16 4.44
3136 3372 4.207635 CCAAAAAGCATATGCAGCATAACG 59.792 41.667 28.62 13.81 45.16 3.18
3221 3457 6.195868 CGCAATACTCAACTGTTGTAACAAA 58.804 36.000 19.12 0.00 38.66 2.83
3324 3560 5.126869 TGAAGTTTTTGTCAATTCTGAGGCA 59.873 36.000 0.00 0.00 30.14 4.75
3541 3777 0.315251 TCTCTTGTCACTGCACTCCG 59.685 55.000 0.00 0.00 0.00 4.63
3573 3809 2.089980 GATGCAAACCTCACATGCTCT 58.910 47.619 0.00 0.00 40.66 4.09
3765 4001 0.326264 GGACTGTTGCTCCTCCATGT 59.674 55.000 0.00 0.00 0.00 3.21
3974 4222 0.107165 GTAATGCTCCACCCACCTCC 60.107 60.000 0.00 0.00 0.00 4.30
4004 4252 5.763204 TCTCCTCATCACCAAACAACTAAAC 59.237 40.000 0.00 0.00 0.00 2.01
4078 4326 6.476378 ACCTATACACTCTTGAACTGCAAAT 58.524 36.000 0.00 0.00 35.74 2.32
4104 4352 1.339055 ACCGACACCAATCTCACCATG 60.339 52.381 0.00 0.00 0.00 3.66
4106 4354 0.034756 CACCGACACCAATCTCACCA 59.965 55.000 0.00 0.00 0.00 4.17
4167 4416 5.875359 ACTTGGAAGCTAAGGAATAAGTTCG 59.125 40.000 0.05 0.00 35.10 3.95
4334 4584 7.039504 ACACAACAGATGAAAAAGGATGCTTAT 60.040 33.333 0.00 0.00 0.00 1.73
4335 4585 6.265196 ACACAACAGATGAAAAAGGATGCTTA 59.735 34.615 0.00 0.00 0.00 3.09
4376 4626 4.590647 ACGGGATATCATCACAGATTCACT 59.409 41.667 4.83 0.00 31.40 3.41
4492 4742 2.353610 GGCTTCCCCGAAGTACCGA 61.354 63.158 3.52 0.00 41.27 4.69
4493 4743 2.186125 GGCTTCCCCGAAGTACCG 59.814 66.667 3.52 0.00 41.27 4.02
4508 4758 0.529378 CAGGCAATCTTGACAAGGGC 59.471 55.000 15.13 14.99 39.18 5.19
4587 4837 0.668401 TATCATGATCGCCTGCGCAG 60.668 55.000 30.52 30.52 39.59 5.18
4589 4839 1.630244 GGTATCATGATCGCCTGCGC 61.630 60.000 12.53 0.00 39.59 6.09
4590 4840 1.016130 GGGTATCATGATCGCCTGCG 61.016 60.000 12.53 4.92 41.35 5.18
4595 4845 2.061773 CTCGTTGGGTATCATGATCGC 58.938 52.381 12.53 12.37 0.00 4.58
4597 4847 4.592485 ACTCTCGTTGGGTATCATGATC 57.408 45.455 12.53 4.10 0.00 2.92
4608 4858 4.037208 ACGTAACCCATATACTCTCGTTGG 59.963 45.833 0.00 0.00 0.00 3.77
4610 4860 5.049129 GCTACGTAACCCATATACTCTCGTT 60.049 44.000 0.00 0.00 0.00 3.85
4635 4886 0.798776 GTTGCATGACCTCTTCACGG 59.201 55.000 0.00 0.00 36.92 4.94
4636 4887 1.511850 TGTTGCATGACCTCTTCACG 58.488 50.000 0.00 0.00 36.92 4.35
4642 4893 3.366679 CCTCACATTTGTTGCATGACCTC 60.367 47.826 0.00 0.00 0.00 3.85
4680 4931 1.519455 GGAGTCGACATGCTTCCCG 60.519 63.158 19.50 0.00 0.00 5.14
4806 5059 1.605710 CATGGATTCTTGCCGGATGAC 59.394 52.381 5.05 0.00 0.00 3.06
4863 5116 0.869454 CGCACGCAAGGCAAGAAAAA 60.869 50.000 0.00 0.00 46.39 1.94
4923 5176 1.039785 GGGCTTCCTTGCTTGATCCC 61.040 60.000 0.00 0.00 0.00 3.85
4937 5190 0.624500 TTCCCTAGAGGCATGGGCTT 60.625 55.000 0.00 0.00 38.98 4.35
4947 5200 2.167487 GGTGAACTCTGCTTCCCTAGAG 59.833 54.545 0.00 0.00 44.63 2.43
5005 5258 3.010138 TGAAACAAGGGGTTAGAGGGATG 59.990 47.826 0.00 0.00 39.29 3.51
5051 5304 3.806949 TTTCTGGCCAAAGTGGTCTAT 57.193 42.857 7.01 0.00 44.07 1.98
5123 5404 2.235155 TGCGGTAACTGGCAATCTTAGA 59.765 45.455 0.00 0.00 35.98 2.10
5124 5405 2.351726 GTGCGGTAACTGGCAATCTTAG 59.648 50.000 0.00 0.00 41.46 2.18
5165 5446 4.421948 GAAGTCGTCAATGGTTCGATAGT 58.578 43.478 0.00 0.00 36.08 2.12
5171 5452 0.442699 GCGGAAGTCGTCAATGGTTC 59.557 55.000 0.00 0.00 41.72 3.62
5179 5460 1.595794 CTCTCTCTAGCGGAAGTCGTC 59.404 57.143 0.00 0.00 41.72 4.20
5182 5463 4.705337 TTTTCTCTCTCTAGCGGAAGTC 57.295 45.455 0.00 0.00 0.00 3.01
5183 5464 4.767928 TCTTTTTCTCTCTCTAGCGGAAGT 59.232 41.667 0.00 0.00 0.00 3.01
5184 5465 5.317733 TCTTTTTCTCTCTCTAGCGGAAG 57.682 43.478 0.00 0.00 0.00 3.46
5185 5466 5.655488 CATCTTTTTCTCTCTCTAGCGGAA 58.345 41.667 0.00 0.00 0.00 4.30
5186 5467 4.440802 GCATCTTTTTCTCTCTCTAGCGGA 60.441 45.833 0.00 0.00 0.00 5.54
5187 5468 3.801594 GCATCTTTTTCTCTCTCTAGCGG 59.198 47.826 0.00 0.00 0.00 5.52
5188 5469 3.485378 CGCATCTTTTTCTCTCTCTAGCG 59.515 47.826 0.00 0.00 0.00 4.26
5189 5470 4.429108 ACGCATCTTTTTCTCTCTCTAGC 58.571 43.478 0.00 0.00 0.00 3.42
5190 5471 5.645624 TGACGCATCTTTTTCTCTCTCTAG 58.354 41.667 0.00 0.00 0.00 2.43
5191 5472 5.644977 TGACGCATCTTTTTCTCTCTCTA 57.355 39.130 0.00 0.00 0.00 2.43
5192 5473 4.527509 TGACGCATCTTTTTCTCTCTCT 57.472 40.909 0.00 0.00 0.00 3.10
5193 5474 4.033817 CCATGACGCATCTTTTTCTCTCTC 59.966 45.833 0.00 0.00 0.00 3.20
5194 5475 3.937706 CCATGACGCATCTTTTTCTCTCT 59.062 43.478 0.00 0.00 0.00 3.10
5212 5493 7.361542 GCTTCTTACATATGGAATGTAGCCATG 60.362 40.741 7.80 0.00 45.39 3.66
5253 5534 1.501170 TGGGGGTCATCCAAAGAAACA 59.499 47.619 0.00 0.00 37.22 2.83
5254 5535 1.893137 GTGGGGGTCATCCAAAGAAAC 59.107 52.381 0.00 0.00 35.86 2.78
5283 5565 6.613755 GTGAAACTAGAAAACAGGTAGCAA 57.386 37.500 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.