Multiple sequence alignment - TraesCS4D01G339400

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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 TraesCS4D01G339400 chr4D 100.000 4610 0 0 1 4610 497169764 497165155 0.000000e+00 8514.0
1 TraesCS4D01G339400 chr4D 91.525 59 4 1 3964 4021 467755809 467755867 3.820000e-11 80.5
2 TraesCS4D01G339400 chr5A 90.224 3754 154 64 291 3955 676969198 676965569 0.000000e+00 4702.0
3 TraesCS4D01G339400 chr5A 88.689 389 22 11 3651 4026 676964715 676964336 5.440000e-124 455.0
4 TraesCS4D01G339400 chr5A 84.590 305 31 8 4310 4610 676965078 676964786 5.840000e-74 289.0
5 TraesCS4D01G339400 chr5A 81.102 381 33 15 4058 4428 676964376 676964025 7.600000e-68 268.0
6 TraesCS4D01G339400 chr5A 84.337 166 13 9 177 342 676970896 676970744 2.870000e-32 150.0
7 TraesCS4D01G339400 chr5A 86.957 69 7 2 2308 2375 684708894 684708827 4.950000e-10 76.8
8 TraesCS4D01G339400 chr4B 90.875 1874 84 36 1780 3617 637738898 637737076 0.000000e+00 2433.0
9 TraesCS4D01G339400 chr4B 90.021 1453 56 40 143 1585 637740386 637739013 0.000000e+00 1797.0
10 TraesCS4D01G339400 chr4B 87.473 471 36 11 4145 4607 637736550 637736095 5.290000e-144 521.0
11 TraesCS4D01G339400 chr4B 91.711 374 23 6 3658 4026 637736968 637736598 3.180000e-141 512.0
12 TraesCS4D01G339400 chr4B 89.888 89 8 1 3019 3107 456853098 456853011 3.770000e-21 113.0
13 TraesCS4D01G339400 chr4B 89.888 89 8 1 3019 3107 456897012 456896925 3.770000e-21 113.0
14 TraesCS4D01G339400 chr1A 80.462 650 115 11 2827 3468 253728763 253728118 1.930000e-133 486.0
15 TraesCS4D01G339400 chr1A 79.091 660 113 16 2827 3478 254351346 254351988 9.160000e-117 431.0
16 TraesCS4D01G339400 chr1A 79.322 295 49 9 1281 1568 254350469 254350758 3.640000e-46 196.0
17 TraesCS4D01G339400 chr1A 81.111 180 34 0 1288 1467 253731646 253731467 1.340000e-30 145.0
18 TraesCS4D01G339400 chr1B 77.728 669 122 20 2827 3486 288757684 288758334 7.240000e-103 385.0
19 TraesCS4D01G339400 chr1B 79.264 299 42 12 1281 1568 288756808 288757097 1.690000e-44 191.0
20 TraesCS4D01G339400 chr1D 81.761 318 44 8 3170 3486 200869277 200869581 2.130000e-63 254.0
21 TraesCS4D01G339400 chr1D 79.661 295 48 9 1281 1568 200868701 200868990 7.820000e-48 202.0
22 TraesCS4D01G339400 chr6B 85.057 87 9 4 2294 2379 43319515 43319598 8.220000e-13 86.1
23 TraesCS4D01G339400 chr2B 85.542 83 11 1 2297 2379 752824472 752824553 8.220000e-13 86.1
24 TraesCS4D01G339400 chr2B 85.000 80 11 1 2300 2379 624885252 624885174 3.820000e-11 80.5
25 TraesCS4D01G339400 chr7A 84.884 86 10 3 2296 2379 726797163 726797079 2.960000e-12 84.2
26 TraesCS4D01G339400 chr2A 83.750 80 11 2 2297 2375 729830952 729831030 1.780000e-09 75.0
27 TraesCS4D01G339400 chr4A 85.333 75 6 5 2305 2379 739764199 739764268 6.400000e-09 73.1
28 TraesCS4D01G339400 chr3B 82.716 81 9 5 2300 2379 726513140 726513064 2.980000e-07 67.6
29 TraesCS4D01G339400 chr2D 100.000 29 0 0 66 94 404101745 404101717 2.000000e-03 54.7


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 TraesCS4D01G339400 chr4D 497165155 497169764 4609 True 8514.00 8514 100.0000 1 4610 1 chr4D.!!$R1 4609
1 TraesCS4D01G339400 chr5A 676964025 676970896 6871 True 1172.80 4702 85.7884 177 4610 5 chr5A.!!$R2 4433
2 TraesCS4D01G339400 chr4B 637736095 637740386 4291 True 1315.75 2433 90.0200 143 4607 4 chr4B.!!$R3 4464
3 TraesCS4D01G339400 chr1A 253728118 253731646 3528 True 315.50 486 80.7865 1288 3468 2 chr1A.!!$R1 2180
4 TraesCS4D01G339400 chr1A 254350469 254351988 1519 False 313.50 431 79.2065 1281 3478 2 chr1A.!!$F1 2197
5 TraesCS4D01G339400 chr1B 288756808 288758334 1526 False 288.00 385 78.4960 1281 3486 2 chr1B.!!$F1 2205
6 TraesCS4D01G339400 chr1D 200868701 200869581 880 False 228.00 254 80.7110 1281 3486 2 chr1D.!!$F1 2205

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
130 131 0.036765 GGCGTTGACCCATACACTGA 60.037 55.0 0.0 0.0 0.0 3.41 F
1599 4985 0.758123 GCTCCCTCTTCTCCATCCAG 59.242 60.0 0.0 0.0 0.0 3.86 F
2054 5509 0.105224 TTCCCACGCACTTTCTCGAA 59.895 50.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 5110 0.457166 TACTGCACATGTACGCGTCC 60.457 55.0 18.63 4.27 0.0 4.79 R
3015 6763 0.825840 AGGAGCAGGCGGAGAGTATC 60.826 60.0 0.00 0.00 0.0 2.24 R
3663 7479 0.841289 ACGTTTCCTTCCCACCTTCA 59.159 50.0 0.00 0.00 0.0 3.02 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 6.374417 AGCCCTAAAGTTTCTTCATGTAGA 57.626 37.500 0.00 0.00 0.00 2.59
24 25 6.410540 AGCCCTAAAGTTTCTTCATGTAGAG 58.589 40.000 2.09 0.00 0.00 2.43
25 26 6.013293 AGCCCTAAAGTTTCTTCATGTAGAGT 60.013 38.462 2.09 0.00 0.00 3.24
26 27 6.655425 GCCCTAAAGTTTCTTCATGTAGAGTT 59.345 38.462 2.09 0.07 0.00 3.01
28 29 8.097662 CCCTAAAGTTTCTTCATGTAGAGTTCT 58.902 37.037 2.09 0.87 0.00 3.01
29 30 9.495572 CCTAAAGTTTCTTCATGTAGAGTTCTT 57.504 33.333 2.09 6.17 0.00 2.52
44 45 8.248945 TGTAGAGTTCTTCTAAATCTAAACCCG 58.751 37.037 0.00 0.00 40.04 5.28
46 47 4.868734 AGTTCTTCTAAATCTAAACCCGCG 59.131 41.667 0.00 0.00 0.00 6.46
47 48 3.192466 TCTTCTAAATCTAAACCCGCGC 58.808 45.455 0.00 0.00 0.00 6.86
48 49 1.944032 TCTAAATCTAAACCCGCGCC 58.056 50.000 0.00 0.00 0.00 6.53
49 50 1.207570 TCTAAATCTAAACCCGCGCCA 59.792 47.619 0.00 0.00 0.00 5.69
50 51 2.158871 TCTAAATCTAAACCCGCGCCAT 60.159 45.455 0.00 0.00 0.00 4.40
52 53 0.818040 AATCTAAACCCGCGCCATCC 60.818 55.000 0.00 0.00 0.00 3.51
53 54 2.676163 ATCTAAACCCGCGCCATCCC 62.676 60.000 0.00 0.00 0.00 3.85
60 61 4.161295 CGCGCCATCCCCTCTGAA 62.161 66.667 0.00 0.00 0.00 3.02
62 63 1.895707 GCGCCATCCCCTCTGAATG 60.896 63.158 0.00 0.00 0.00 2.67
63 64 1.228063 CGCCATCCCCTCTGAATGG 60.228 63.158 2.38 2.38 35.59 3.16
64 65 4.916358 CCATCCCCTCTGAATGGC 57.084 61.111 0.00 0.00 0.00 4.40
65 66 2.238530 CCATCCCCTCTGAATGGCT 58.761 57.895 0.00 0.00 0.00 4.75
67 68 1.478288 CCATCCCCTCTGAATGGCTTC 60.478 57.143 0.00 0.00 0.00 3.86
86 87 6.246420 GCTTCAGCCACAGTTATAATATGG 57.754 41.667 7.80 7.80 34.31 2.74
87 88 5.765182 GCTTCAGCCACAGTTATAATATGGT 59.235 40.000 11.91 0.00 32.71 3.55
88 89 6.073003 GCTTCAGCCACAGTTATAATATGGTC 60.073 42.308 11.91 6.67 32.71 4.02
92 93 7.498900 TCAGCCACAGTTATAATATGGTCAAAG 59.501 37.037 11.91 2.51 32.71 2.77
93 94 6.263168 AGCCACAGTTATAATATGGTCAAAGC 59.737 38.462 11.91 0.00 32.71 3.51
94 95 6.039270 GCCACAGTTATAATATGGTCAAAGCA 59.961 38.462 11.91 0.00 32.71 3.91
96 97 8.465999 CCACAGTTATAATATGGTCAAAGCAAA 58.534 33.333 5.84 0.00 0.00 3.68
121 122 8.677148 ATATCATATAATAATGGCGTTGACCC 57.323 34.615 1.27 0.00 0.00 4.46
122 123 5.870706 TCATATAATAATGGCGTTGACCCA 58.129 37.500 1.27 0.00 36.66 4.51
123 124 6.480763 TCATATAATAATGGCGTTGACCCAT 58.519 36.000 1.27 0.00 44.75 4.00
126 127 3.569194 ATAATGGCGTTGACCCATACA 57.431 42.857 1.27 0.00 42.10 2.29
127 128 1.459450 AATGGCGTTGACCCATACAC 58.541 50.000 0.00 0.00 42.10 2.90
128 129 0.618458 ATGGCGTTGACCCATACACT 59.382 50.000 0.00 0.00 41.17 3.55
129 130 0.321210 TGGCGTTGACCCATACACTG 60.321 55.000 0.00 0.00 0.00 3.66
130 131 0.036765 GGCGTTGACCCATACACTGA 60.037 55.000 0.00 0.00 0.00 3.41
131 132 1.406887 GGCGTTGACCCATACACTGAT 60.407 52.381 0.00 0.00 0.00 2.90
132 133 1.933853 GCGTTGACCCATACACTGATC 59.066 52.381 0.00 0.00 0.00 2.92
133 134 2.418746 GCGTTGACCCATACACTGATCT 60.419 50.000 0.00 0.00 0.00 2.75
134 135 3.190079 CGTTGACCCATACACTGATCTG 58.810 50.000 0.00 0.00 0.00 2.90
136 137 4.442052 CGTTGACCCATACACTGATCTGAT 60.442 45.833 6.60 0.00 0.00 2.90
137 138 5.221244 CGTTGACCCATACACTGATCTGATA 60.221 44.000 6.60 0.00 0.00 2.15
139 140 5.458595 TGACCCATACACTGATCTGATACT 58.541 41.667 6.60 0.00 0.00 2.12
140 141 5.536538 TGACCCATACACTGATCTGATACTC 59.463 44.000 6.60 0.00 0.00 2.59
141 142 5.458595 ACCCATACACTGATCTGATACTCA 58.541 41.667 6.60 0.00 0.00 3.41
185 186 1.948834 CAGTTGCCAACATCACACTGA 59.051 47.619 10.69 0.00 0.00 3.41
186 187 2.555325 CAGTTGCCAACATCACACTGAT 59.445 45.455 10.69 0.00 37.65 2.90
187 188 2.816087 AGTTGCCAACATCACACTGATC 59.184 45.455 10.69 0.00 34.28 2.92
208 1658 2.629051 GATCACTTTACCTTCACGGGG 58.371 52.381 0.00 0.00 36.97 5.73
257 1707 1.310216 GCCTGCACTGCATCATGTGA 61.310 55.000 3.64 0.00 38.13 3.58
273 1725 1.488527 GTGACTGACACCACGAGAAC 58.511 55.000 0.00 0.00 43.05 3.01
287 1740 5.237344 ACCACGAGAACTCAGAAAAAGATTG 59.763 40.000 0.00 0.00 0.00 2.67
323 1776 1.139095 GACCGACCACGTCTGATCC 59.861 63.158 0.00 0.00 37.88 3.36
400 1862 1.529438 GGTGAACGAGACGCATTTTCA 59.471 47.619 0.00 0.00 0.00 2.69
412 1874 1.081242 ATTTTCAGCGCACGCAAGG 60.081 52.632 18.24 6.42 44.88 3.61
413 1875 1.795170 ATTTTCAGCGCACGCAAGGT 61.795 50.000 18.24 0.00 44.88 3.50
414 1876 1.160946 TTTTCAGCGCACGCAAGGTA 61.161 50.000 18.24 0.00 44.88 3.08
420 1882 1.447838 CGCACGCAAGGTACAGGAT 60.448 57.895 0.00 0.00 46.39 3.24
421 1883 1.695893 CGCACGCAAGGTACAGGATG 61.696 60.000 0.00 0.00 46.39 3.51
422 1884 1.369091 GCACGCAAGGTACAGGATGG 61.369 60.000 0.00 0.00 42.27 3.51
424 1886 1.819632 CGCAAGGTACAGGATGGGC 60.820 63.158 0.00 0.00 43.62 5.36
429 1891 3.873812 GTACAGGATGGGCCGGGG 61.874 72.222 2.18 0.00 43.62 5.73
444 1906 3.948719 GGGACACGGCTGGTTGGA 61.949 66.667 0.00 0.00 0.00 3.53
445 1907 2.668550 GGACACGGCTGGTTGGAC 60.669 66.667 0.00 0.00 0.00 4.02
446 1908 3.041940 GACACGGCTGGTTGGACG 61.042 66.667 0.00 0.00 44.24 4.79
472 1934 2.257371 CGAGAGACCGCCGAAACA 59.743 61.111 0.00 0.00 0.00 2.83
650 2113 4.988598 CACCGCCTCACGTTGCCT 62.989 66.667 0.00 0.00 41.42 4.75
706 2169 4.520846 CGCGCGCCACCTTTCATC 62.521 66.667 27.72 0.00 0.00 2.92
707 2170 4.520846 GCGCGCCACCTTTCATCG 62.521 66.667 23.24 0.00 0.00 3.84
724 2187 1.287217 TCGCCACTATTTAACCCCCA 58.713 50.000 0.00 0.00 0.00 4.96
725 2188 1.847737 TCGCCACTATTTAACCCCCAT 59.152 47.619 0.00 0.00 0.00 4.00
729 2192 2.316108 CACTATTTAACCCCCATGCCC 58.684 52.381 0.00 0.00 0.00 5.36
730 2193 1.133606 ACTATTTAACCCCCATGCCCG 60.134 52.381 0.00 0.00 0.00 6.13
777 2240 1.681327 CCTTCCCTTCGGTCGAGGA 60.681 63.158 4.06 1.02 30.88 3.71
782 2245 2.970639 CTTCGGTCGAGGAAGGCA 59.029 61.111 15.21 0.00 37.76 4.75
821 2286 3.677527 GAGTCGACTCCGTTCCCA 58.322 61.111 31.24 0.00 37.02 4.37
864 2329 2.814919 ACCGGCGAACACATTCAATAAA 59.185 40.909 9.30 0.00 34.14 1.40
866 2333 3.119990 CCGGCGAACACATTCAATAAACT 60.120 43.478 9.30 0.00 34.14 2.66
909 2378 1.947456 CGTCACCGGTGATCTGATCTA 59.053 52.381 38.11 11.80 42.18 1.98
949 2424 1.153997 GTCGTCCAAGCTCTCCGTC 60.154 63.158 0.00 0.00 0.00 4.79
950 2425 2.202492 CGTCCAAGCTCTCCGTCG 60.202 66.667 0.00 0.00 0.00 5.12
951 2426 2.507324 GTCCAAGCTCTCCGTCGC 60.507 66.667 0.00 0.00 0.00 5.19
952 2427 2.989253 TCCAAGCTCTCCGTCGCA 60.989 61.111 0.00 0.00 0.00 5.10
953 2428 2.811317 CCAAGCTCTCCGTCGCAC 60.811 66.667 0.00 0.00 0.00 5.34
954 2429 3.175240 CAAGCTCTCCGTCGCACG 61.175 66.667 0.00 2.27 42.11 5.34
1580 4966 1.069159 AGTCAAGTACGTCGTGCTCTG 60.069 52.381 16.53 15.36 0.00 3.35
1599 4985 0.758123 GCTCCCTCTTCTCCATCCAG 59.242 60.000 0.00 0.00 0.00 3.86
1621 5007 4.951094 AGTCCTCTGTCTATCCAAGTACAC 59.049 45.833 0.00 0.00 0.00 2.90
1641 5036 4.448732 ACACATATACGTACATGCATGCTG 59.551 41.667 26.53 17.75 0.00 4.41
1693 5088 8.006298 TGTATTTTTCCATGATTCCATGTACC 57.994 34.615 0.00 0.00 46.68 3.34
1694 5089 7.617329 TGTATTTTTCCATGATTCCATGTACCA 59.383 33.333 0.00 0.00 46.68 3.25
1697 5092 4.006780 TCCATGATTCCATGTACCATCG 57.993 45.455 0.00 0.00 46.68 3.84
1698 5093 2.485426 CCATGATTCCATGTACCATCGC 59.515 50.000 0.00 0.00 46.68 4.58
1699 5094 2.998316 TGATTCCATGTACCATCGCA 57.002 45.000 0.00 0.00 0.00 5.10
1701 5096 3.402110 TGATTCCATGTACCATCGCATC 58.598 45.455 0.00 0.00 0.00 3.91
1708 5108 0.956633 GTACCATCGCATCTACGGGA 59.043 55.000 0.00 0.00 0.00 5.14
1751 5151 7.712639 CAGTAGAAGCAAAGCCTGAATTAGATA 59.287 37.037 0.00 0.00 0.00 1.98
1753 5153 6.657875 AGAAGCAAAGCCTGAATTAGATAGT 58.342 36.000 0.00 0.00 0.00 2.12
1757 5157 7.338710 AGCAAAGCCTGAATTAGATAGTGTTA 58.661 34.615 0.00 0.00 0.00 2.41
1832 5245 3.485463 AGTTTGTAGCCACTTGCACTA 57.515 42.857 0.00 0.00 44.83 2.74
1951 5406 1.080298 GCGCTCATGGCAAAGCTTT 60.080 52.632 19.13 5.69 41.91 3.51
1993 5448 3.679917 CGGGAAATCGGGATCTCATATGG 60.680 52.174 2.13 0.00 0.00 2.74
2054 5509 0.105224 TTCCCACGCACTTTCTCGAA 59.895 50.000 0.00 0.00 0.00 3.71
2082 5537 2.018515 ACGTGGACGGTCACAAATTTT 58.981 42.857 10.76 0.00 44.95 1.82
2127 5582 3.897239 TGAAAGAAAACTGGCCTCAAGA 58.103 40.909 3.32 0.00 0.00 3.02
2151 5606 1.135373 ACGACACGTAGAGCTTGGATG 60.135 52.381 0.00 0.00 38.73 3.51
2164 5619 2.735134 GCTTGGATGACGAAAAGTACGT 59.265 45.455 0.00 0.00 46.58 3.57
2228 5683 1.588824 CGTACGTGTCCTGCCCACTA 61.589 60.000 7.22 0.00 0.00 2.74
2286 5741 3.006940 TGATGTGAATTGTTACCCTCGC 58.993 45.455 0.00 0.00 0.00 5.03
2287 5742 1.816074 TGTGAATTGTTACCCTCGCC 58.184 50.000 0.00 0.00 0.00 5.54
2288 5743 0.725117 GTGAATTGTTACCCTCGCCG 59.275 55.000 0.00 0.00 0.00 6.46
2297 5752 3.208594 GTTACCCTCGCCGGAAATTATT 58.791 45.455 5.05 0.00 33.16 1.40
2298 5753 1.963172 ACCCTCGCCGGAAATTATTC 58.037 50.000 5.05 0.00 33.16 1.75
2344 5814 9.432077 CTATTCATCTTCGATCATGATAGTACG 57.568 37.037 8.54 8.17 0.00 3.67
2584 6054 1.063166 CGCCGGAACTACGAGTACC 59.937 63.158 5.05 0.00 35.47 3.34
2979 6727 0.687354 ACGGCCAGTTCTTCATGAGT 59.313 50.000 2.24 0.00 0.00 3.41
3018 6766 4.266070 GAGCACGGCGAGCGGATA 62.266 66.667 22.71 0.00 37.01 2.59
3045 6793 1.153939 CTGCTCCTCCGTCTTCACG 60.154 63.158 0.00 0.00 46.29 4.35
3189 6938 4.950062 ATCGCGCGCATGATCGGT 62.950 61.111 32.61 6.63 0.00 4.69
3429 7178 0.834687 TGGTCGCCTTCACCTACCTT 60.835 55.000 0.00 0.00 34.66 3.50
3625 7430 7.552330 TCTGCAACTAATCAACTATGCATTACA 59.448 33.333 3.54 0.00 42.25 2.41
3647 7452 3.263602 ACATACGTACCGTGATGATCG 57.736 47.619 0.00 0.00 41.39 3.69
3788 7613 1.813513 GCTACCTCAAAGCTTGCAGA 58.186 50.000 0.00 0.00 37.01 4.26
3817 7642 7.224362 ACTGATGTACTACTACGTACTAAGCTG 59.776 40.741 0.00 0.00 40.25 4.24
3949 8934 8.715191 ATTTCTTGTTGCTATCTTCTACTCTG 57.285 34.615 0.00 0.00 0.00 3.35
3957 8942 5.648526 TGCTATCTTCTACTCTGTTCGTCTT 59.351 40.000 0.00 0.00 0.00 3.01
4005 9000 5.559227 CAAGTTGTTTTAGCTTGCAAAACC 58.441 37.500 16.81 6.29 42.54 3.27
4012 9007 7.268586 TGTTTTAGCTTGCAAAACCATCTTAA 58.731 30.769 16.81 0.00 42.54 1.85
4013 9008 7.930865 TGTTTTAGCTTGCAAAACCATCTTAAT 59.069 29.630 16.81 0.00 42.54 1.40
4015 9010 9.988815 TTTTAGCTTGCAAAACCATCTTAATTA 57.011 25.926 0.00 0.00 0.00 1.40
4017 9012 9.585099 TTAGCTTGCAAAACCATCTTAATTATG 57.415 29.630 0.00 0.00 0.00 1.90
4019 9014 6.258507 GCTTGCAAAACCATCTTAATTATGGG 59.741 38.462 17.08 2.44 46.89 4.00
4020 9015 7.487822 TTGCAAAACCATCTTAATTATGGGA 57.512 32.000 17.08 0.00 46.89 4.37
4021 9016 7.673641 TGCAAAACCATCTTAATTATGGGAT 57.326 32.000 17.08 6.76 46.89 3.85
4022 9017 7.499292 TGCAAAACCATCTTAATTATGGGATG 58.501 34.615 17.08 11.49 46.89 3.51
4038 9033 3.477210 GGATGGAGTCCACCTCATAAC 57.523 52.381 15.86 0.00 46.96 1.89
4039 9034 2.771943 GGATGGAGTCCACCTCATAACA 59.228 50.000 15.86 0.00 46.96 2.41
4040 9035 3.392616 GGATGGAGTCCACCTCATAACAT 59.607 47.826 15.86 0.00 46.96 2.71
4041 9036 4.141390 GGATGGAGTCCACCTCATAACATT 60.141 45.833 15.86 0.00 46.96 2.71
4042 9037 5.071788 GGATGGAGTCCACCTCATAACATTA 59.928 44.000 15.86 0.00 46.96 1.90
4043 9038 6.409234 GGATGGAGTCCACCTCATAACATTAA 60.409 42.308 15.86 0.00 46.96 1.40
4044 9039 5.989477 TGGAGTCCACCTCATAACATTAAG 58.011 41.667 8.12 0.00 42.40 1.85
4045 9040 5.724370 TGGAGTCCACCTCATAACATTAAGA 59.276 40.000 8.12 0.00 42.40 2.10
4046 9041 6.386927 TGGAGTCCACCTCATAACATTAAGAT 59.613 38.462 8.12 0.00 42.40 2.40
4047 9042 6.931840 GGAGTCCACCTCATAACATTAAGATC 59.068 42.308 3.60 0.00 42.40 2.75
4048 9043 6.516718 AGTCCACCTCATAACATTAAGATCG 58.483 40.000 0.00 0.00 0.00 3.69
4049 9044 5.177696 GTCCACCTCATAACATTAAGATCGC 59.822 44.000 0.00 0.00 0.00 4.58
4050 9045 5.070446 TCCACCTCATAACATTAAGATCGCT 59.930 40.000 0.00 0.00 0.00 4.93
4051 9046 5.760253 CCACCTCATAACATTAAGATCGCTT 59.240 40.000 0.00 0.00 38.15 4.68
4052 9047 6.293081 CCACCTCATAACATTAAGATCGCTTG 60.293 42.308 0.00 0.00 35.56 4.01
4053 9048 5.237344 ACCTCATAACATTAAGATCGCTTGC 59.763 40.000 0.00 0.00 35.56 4.01
4054 9049 5.237127 CCTCATAACATTAAGATCGCTTGCA 59.763 40.000 0.00 0.00 35.56 4.08
4055 9050 6.238456 CCTCATAACATTAAGATCGCTTGCAA 60.238 38.462 0.00 0.00 35.56 4.08
4056 9051 6.718388 TCATAACATTAAGATCGCTTGCAAG 58.282 36.000 22.44 22.44 35.56 4.01
4080 9075 5.229921 TGTTTTAGCTTGCATAACGATCC 57.770 39.130 0.00 0.00 0.00 3.36
4081 9076 4.941263 TGTTTTAGCTTGCATAACGATCCT 59.059 37.500 0.00 0.00 0.00 3.24
4082 9077 6.110033 TGTTTTAGCTTGCATAACGATCCTA 58.890 36.000 0.00 0.00 0.00 2.94
4089 9084 6.372659 AGCTTGCATAACGATCCTAATTATGG 59.627 38.462 12.20 0.00 36.98 2.74
4110 9114 1.139853 GATGAAGGGAGTGAGCGGATT 59.860 52.381 0.00 0.00 0.00 3.01
4111 9115 0.250234 TGAAGGGAGTGAGCGGATTG 59.750 55.000 0.00 0.00 0.00 2.67
4131 9135 1.261619 GTCTGACTTTGAGTTGCCACG 59.738 52.381 0.00 0.00 0.00 4.94
4136 9140 2.290641 GACTTTGAGTTGCCACGTCATT 59.709 45.455 0.00 0.00 0.00 2.57
4138 9142 1.674359 TTGAGTTGCCACGTCATTGT 58.326 45.000 0.00 0.00 0.00 2.71
4140 9144 0.517316 GAGTTGCCACGTCATTGTCC 59.483 55.000 0.00 0.00 0.00 4.02
4141 9145 0.179032 AGTTGCCACGTCATTGTCCA 60.179 50.000 0.00 0.00 0.00 4.02
4143 9147 0.665835 TTGCCACGTCATTGTCCAAC 59.334 50.000 0.00 0.00 0.00 3.77
4163 9167 5.426504 CAACTGACTTAGCCTCTCATCAAT 58.573 41.667 0.00 0.00 0.00 2.57
4177 9182 7.390996 GCCTCTCATCAATCATACAATCTTCAT 59.609 37.037 0.00 0.00 0.00 2.57
4186 9191 7.876936 ATCATACAATCTTCATCATATGGCC 57.123 36.000 2.13 0.00 0.00 5.36
4187 9192 7.024345 TCATACAATCTTCATCATATGGCCT 57.976 36.000 3.32 0.00 0.00 5.19
4188 9193 6.882678 TCATACAATCTTCATCATATGGCCTG 59.117 38.462 3.32 0.00 0.00 4.85
4189 9194 3.825014 ACAATCTTCATCATATGGCCTGC 59.175 43.478 3.32 0.00 0.00 4.85
4190 9195 4.079970 CAATCTTCATCATATGGCCTGCT 58.920 43.478 3.32 0.00 0.00 4.24
4191 9196 3.870538 TCTTCATCATATGGCCTGCTT 57.129 42.857 3.32 0.00 0.00 3.91
4192 9197 4.174704 TCTTCATCATATGGCCTGCTTT 57.825 40.909 3.32 0.00 0.00 3.51
4193 9198 5.308976 TCTTCATCATATGGCCTGCTTTA 57.691 39.130 3.32 0.00 0.00 1.85
4194 9199 5.693961 TCTTCATCATATGGCCTGCTTTAA 58.306 37.500 3.32 0.00 0.00 1.52
4212 9217 5.576128 CTTTAATTACCCCTCACTTCCCAA 58.424 41.667 0.00 0.00 0.00 4.12
4213 9218 3.451402 AATTACCCCTCACTTCCCAAC 57.549 47.619 0.00 0.00 0.00 3.77
4224 9229 1.850345 ACTTCCCAACCCAAGAACTGA 59.150 47.619 0.00 0.00 0.00 3.41
4230 9235 5.459505 TCCCAACCCAAGAACTGAAAATTA 58.540 37.500 0.00 0.00 0.00 1.40
4296 9301 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
4298 9303 4.352893 TCTCTCTCTCTCTCTCTCTCACA 58.647 47.826 0.00 0.00 0.00 3.58
4300 9305 3.837731 TCTCTCTCTCTCTCTCTCACACA 59.162 47.826 0.00 0.00 0.00 3.72
4302 9307 3.326297 TCTCTCTCTCTCTCTCACACACA 59.674 47.826 0.00 0.00 0.00 3.72
4304 9309 3.145286 CTCTCTCTCTCTCACACACACA 58.855 50.000 0.00 0.00 0.00 3.72
4306 9311 2.620585 CTCTCTCTCTCACACACACACA 59.379 50.000 0.00 0.00 0.00 3.72
4308 9313 2.099405 TCTCTCTCACACACACACACA 58.901 47.619 0.00 0.00 0.00 3.72
4310 9315 1.548269 TCTCTCACACACACACACACA 59.452 47.619 0.00 0.00 0.00 3.72
4312 9317 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
4314 9319 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4317 9324 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4563 9584 3.197766 TGCACTACAGTATGGAAGGAAGG 59.802 47.826 0.00 0.00 43.62 3.46
4574 9595 4.844349 TGGAAGGAAGGGAGTATGAAAG 57.156 45.455 0.00 0.00 0.00 2.62
4578 9599 5.372373 GAAGGAAGGGAGTATGAAAGATGG 58.628 45.833 0.00 0.00 0.00 3.51
4587 9608 6.094186 GGGAGTATGAAAGATGGAAAGTGAAC 59.906 42.308 0.00 0.00 0.00 3.18
4601 9622 7.102346 TGGAAAGTGAACACACAAATTTCATT 58.898 30.769 7.68 0.00 37.04 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.495572 AAGAACTCTACATGAAGAAACTTTAGG 57.504 33.333 0.00 0.00 0.00 2.69
19 20 7.222417 GCGGGTTTAGATTTAGAAGAACTCTAC 59.778 40.741 0.00 0.00 36.32 2.59
20 21 7.263496 GCGGGTTTAGATTTAGAAGAACTCTA 58.737 38.462 0.00 0.00 35.41 2.43
21 22 6.107343 GCGGGTTTAGATTTAGAAGAACTCT 58.893 40.000 0.00 0.00 38.28 3.24
22 23 5.005490 CGCGGGTTTAGATTTAGAAGAACTC 59.995 44.000 0.00 0.00 0.00 3.01
23 24 4.868734 CGCGGGTTTAGATTTAGAAGAACT 59.131 41.667 0.00 0.00 0.00 3.01
24 25 4.493708 GCGCGGGTTTAGATTTAGAAGAAC 60.494 45.833 8.83 0.00 0.00 3.01
25 26 3.619929 GCGCGGGTTTAGATTTAGAAGAA 59.380 43.478 8.83 0.00 0.00 2.52
26 27 3.192466 GCGCGGGTTTAGATTTAGAAGA 58.808 45.455 8.83 0.00 0.00 2.87
28 29 2.282407 GGCGCGGGTTTAGATTTAGAA 58.718 47.619 8.83 0.00 0.00 2.10
29 30 1.207570 TGGCGCGGGTTTAGATTTAGA 59.792 47.619 8.83 0.00 0.00 2.10
30 31 1.658994 TGGCGCGGGTTTAGATTTAG 58.341 50.000 8.83 0.00 0.00 1.85
31 32 2.215196 GATGGCGCGGGTTTAGATTTA 58.785 47.619 8.83 0.00 0.00 1.40
32 33 1.021968 GATGGCGCGGGTTTAGATTT 58.978 50.000 8.83 0.00 0.00 2.17
33 34 0.818040 GGATGGCGCGGGTTTAGATT 60.818 55.000 8.83 0.00 0.00 2.40
34 35 1.227853 GGATGGCGCGGGTTTAGAT 60.228 57.895 8.83 0.00 0.00 1.98
35 36 2.188469 GGATGGCGCGGGTTTAGA 59.812 61.111 8.83 0.00 0.00 2.10
36 37 2.900337 GGGATGGCGCGGGTTTAG 60.900 66.667 8.83 0.00 0.00 1.85
37 38 4.493049 GGGGATGGCGCGGGTTTA 62.493 66.667 8.83 0.00 0.00 2.01
43 44 3.466791 ATTCAGAGGGGATGGCGCG 62.467 63.158 0.00 0.00 0.00 6.86
44 45 1.895707 CATTCAGAGGGGATGGCGC 60.896 63.158 0.00 0.00 0.00 6.53
46 47 4.916358 CCATTCAGAGGGGATGGC 57.084 61.111 0.00 0.00 0.00 4.40
47 48 0.554792 AAGCCATTCAGAGGGGATGG 59.445 55.000 0.00 0.00 35.59 3.51
48 49 1.213678 TGAAGCCATTCAGAGGGGATG 59.786 52.381 0.00 0.00 40.54 3.51
49 50 1.600058 TGAAGCCATTCAGAGGGGAT 58.400 50.000 0.00 0.00 40.54 3.85
50 51 3.103236 TGAAGCCATTCAGAGGGGA 57.897 52.632 0.00 0.00 40.54 4.81
63 64 5.765182 ACCATATTATAACTGTGGCTGAAGC 59.235 40.000 10.84 0.00 41.14 3.86
64 65 6.992123 TGACCATATTATAACTGTGGCTGAAG 59.008 38.462 10.84 0.00 33.24 3.02
65 66 6.894682 TGACCATATTATAACTGTGGCTGAA 58.105 36.000 10.84 0.00 33.24 3.02
67 68 7.566760 TTTGACCATATTATAACTGTGGCTG 57.433 36.000 10.84 0.00 33.24 4.85
70 71 7.566760 TGCTTTGACCATATTATAACTGTGG 57.433 36.000 9.80 9.80 36.06 4.17
96 97 8.271458 TGGGTCAACGCCATTATTATATGATAT 58.729 33.333 0.00 0.00 0.00 1.63
98 99 6.480763 TGGGTCAACGCCATTATTATATGAT 58.519 36.000 0.00 0.00 0.00 2.45
99 100 5.870706 TGGGTCAACGCCATTATTATATGA 58.129 37.500 0.00 0.00 0.00 2.15
100 101 6.757897 ATGGGTCAACGCCATTATTATATG 57.242 37.500 0.00 0.00 0.00 1.78
101 102 7.335924 GTGTATGGGTCAACGCCATTATTATAT 59.664 37.037 0.00 0.00 32.03 0.86
102 103 6.651643 GTGTATGGGTCAACGCCATTATTATA 59.348 38.462 0.00 0.00 32.03 0.98
103 104 5.472137 GTGTATGGGTCAACGCCATTATTAT 59.528 40.000 0.00 0.00 32.03 1.28
104 105 4.817464 GTGTATGGGTCAACGCCATTATTA 59.183 41.667 0.00 0.00 32.03 0.98
105 106 3.630312 GTGTATGGGTCAACGCCATTATT 59.370 43.478 0.00 0.00 32.03 1.40
106 107 3.118038 AGTGTATGGGTCAACGCCATTAT 60.118 43.478 0.00 0.00 32.03 1.28
107 108 2.237643 AGTGTATGGGTCAACGCCATTA 59.762 45.455 0.00 0.00 32.03 1.90
108 109 1.004277 AGTGTATGGGTCAACGCCATT 59.996 47.619 0.00 0.00 32.03 3.16
109 110 0.618458 AGTGTATGGGTCAACGCCAT 59.382 50.000 0.00 0.00 33.50 4.40
110 111 0.321210 CAGTGTATGGGTCAACGCCA 60.321 55.000 0.00 0.00 0.00 5.69
112 113 1.933853 GATCAGTGTATGGGTCAACGC 59.066 52.381 0.00 0.00 0.00 4.84
114 115 4.471904 TCAGATCAGTGTATGGGTCAAC 57.528 45.455 0.00 0.00 0.00 3.18
115 116 5.899547 AGTATCAGATCAGTGTATGGGTCAA 59.100 40.000 0.00 0.00 0.00 3.18
116 117 5.458595 AGTATCAGATCAGTGTATGGGTCA 58.541 41.667 0.00 0.00 0.00 4.02
117 118 5.536538 TGAGTATCAGATCAGTGTATGGGTC 59.463 44.000 0.00 0.00 42.56 4.46
118 119 5.458595 TGAGTATCAGATCAGTGTATGGGT 58.541 41.667 0.00 0.00 42.56 4.51
134 135 6.316140 TGTTGATGTTGCATTAGGTGAGTATC 59.684 38.462 0.00 0.00 0.00 2.24
136 137 5.555966 TGTTGATGTTGCATTAGGTGAGTA 58.444 37.500 0.00 0.00 0.00 2.59
137 138 4.397420 TGTTGATGTTGCATTAGGTGAGT 58.603 39.130 0.00 0.00 0.00 3.41
139 140 4.380761 GCATGTTGATGTTGCATTAGGTGA 60.381 41.667 0.00 0.00 36.40 4.02
140 141 3.861113 GCATGTTGATGTTGCATTAGGTG 59.139 43.478 0.00 0.00 36.40 4.00
141 142 3.510753 TGCATGTTGATGTTGCATTAGGT 59.489 39.130 0.00 0.00 41.18 3.08
175 176 5.233050 GGTAAAGTGATCGATCAGTGTGATG 59.767 44.000 31.18 0.00 40.20 3.07
185 186 3.430374 CCCGTGAAGGTAAAGTGATCGAT 60.430 47.826 0.00 0.00 38.74 3.59
186 187 2.094390 CCCGTGAAGGTAAAGTGATCGA 60.094 50.000 0.00 0.00 38.74 3.59
187 188 2.268298 CCCGTGAAGGTAAAGTGATCG 58.732 52.381 0.00 0.00 38.74 3.69
233 1683 3.332493 GATGCAGTGCAGGCGTTGG 62.332 63.158 24.20 0.00 43.65 3.77
234 1684 1.929806 ATGATGCAGTGCAGGCGTTG 61.930 55.000 24.20 0.00 43.65 4.10
235 1685 1.676635 ATGATGCAGTGCAGGCGTT 60.677 52.632 24.20 5.83 43.65 4.84
236 1686 2.045634 ATGATGCAGTGCAGGCGT 60.046 55.556 24.20 15.81 43.65 5.68
237 1687 2.404186 ACATGATGCAGTGCAGGCG 61.404 57.895 24.20 13.66 43.65 5.52
238 1688 1.138883 CACATGATGCAGTGCAGGC 59.861 57.895 24.20 17.68 43.65 4.85
239 1689 0.450583 GTCACATGATGCAGTGCAGG 59.549 55.000 24.20 14.56 43.65 4.85
240 1690 1.130561 CAGTCACATGATGCAGTGCAG 59.869 52.381 24.20 12.15 43.65 4.41
241 1691 1.161843 CAGTCACATGATGCAGTGCA 58.838 50.000 22.22 22.22 44.86 4.57
242 1692 1.129998 GTCAGTCACATGATGCAGTGC 59.870 52.381 8.58 8.58 35.76 4.40
243 1693 2.159037 GTGTCAGTCACATGATGCAGTG 59.841 50.000 0.00 0.00 45.51 3.66
244 1694 2.420642 GTGTCAGTCACATGATGCAGT 58.579 47.619 0.00 0.00 45.51 4.40
257 1707 1.338337 CTGAGTTCTCGTGGTGTCAGT 59.662 52.381 0.00 0.00 0.00 3.41
273 1725 3.572584 GGCTGTGCAATCTTTTTCTGAG 58.427 45.455 0.00 0.00 0.00 3.35
381 1843 2.827555 CTGAAAATGCGTCTCGTTCAC 58.172 47.619 0.00 0.00 0.00 3.18
382 1844 1.194547 GCTGAAAATGCGTCTCGTTCA 59.805 47.619 0.00 0.00 0.00 3.18
383 1845 1.870765 GCTGAAAATGCGTCTCGTTC 58.129 50.000 0.00 0.00 0.00 3.95
400 1862 2.738521 CTGTACCTTGCGTGCGCT 60.739 61.111 17.49 0.00 42.51 5.92
403 1865 1.369091 CCATCCTGTACCTTGCGTGC 61.369 60.000 0.00 0.00 0.00 5.34
408 1870 1.153168 CGGCCCATCCTGTACCTTG 60.153 63.158 0.00 0.00 0.00 3.61
412 1874 3.873812 CCCCGGCCCATCCTGTAC 61.874 72.222 0.00 0.00 0.00 2.90
413 1875 4.096816 TCCCCGGCCCATCCTGTA 62.097 66.667 0.00 0.00 0.00 2.74
429 1891 2.424705 TACGTCCAACCAGCCGTGTC 62.425 60.000 0.00 0.00 34.95 3.67
431 1893 1.736645 CTACGTCCAACCAGCCGTG 60.737 63.158 0.00 0.00 34.95 4.94
432 1894 0.895100 TACTACGTCCAACCAGCCGT 60.895 55.000 0.00 0.00 37.33 5.68
433 1895 0.457337 GTACTACGTCCAACCAGCCG 60.457 60.000 0.00 0.00 0.00 5.52
434 1896 0.604578 TGTACTACGTCCAACCAGCC 59.395 55.000 0.00 0.00 0.00 4.85
435 1897 1.992170 CTGTACTACGTCCAACCAGC 58.008 55.000 0.00 0.00 0.00 4.85
436 1898 1.731424 CGCTGTACTACGTCCAACCAG 60.731 57.143 0.00 0.00 0.00 4.00
437 1899 0.241749 CGCTGTACTACGTCCAACCA 59.758 55.000 0.00 0.00 0.00 3.67
439 1901 1.466167 TCTCGCTGTACTACGTCCAAC 59.534 52.381 0.00 0.00 0.00 3.77
440 1902 1.736126 CTCTCGCTGTACTACGTCCAA 59.264 52.381 0.00 0.00 0.00 3.53
441 1903 1.066645 TCTCTCGCTGTACTACGTCCA 60.067 52.381 0.00 0.00 0.00 4.02
442 1904 1.327156 GTCTCTCGCTGTACTACGTCC 59.673 57.143 0.00 0.00 0.00 4.79
443 1905 1.327156 GGTCTCTCGCTGTACTACGTC 59.673 57.143 0.00 0.00 0.00 4.34
444 1906 1.367659 GGTCTCTCGCTGTACTACGT 58.632 55.000 0.00 0.00 0.00 3.57
445 1907 0.301088 CGGTCTCTCGCTGTACTACG 59.699 60.000 0.00 0.00 0.00 3.51
455 1917 1.801913 CTGTTTCGGCGGTCTCTCG 60.802 63.158 7.21 0.00 0.00 4.04
689 2152 4.520846 GATGAAAGGTGGCGCGCG 62.521 66.667 28.44 28.44 0.00 6.86
690 2153 4.520846 CGATGAAAGGTGGCGCGC 62.521 66.667 25.94 25.94 0.00 6.86
692 2155 4.179579 GGCGATGAAAGGTGGCGC 62.180 66.667 0.00 0.00 46.20 6.53
693 2156 2.745884 TGGCGATGAAAGGTGGCG 60.746 61.111 0.00 0.00 0.00 5.69
694 2157 0.392461 TAGTGGCGATGAAAGGTGGC 60.392 55.000 0.00 0.00 0.00 5.01
697 2160 4.638865 GGTTAAATAGTGGCGATGAAAGGT 59.361 41.667 0.00 0.00 0.00 3.50
699 2162 4.036380 GGGGTTAAATAGTGGCGATGAAAG 59.964 45.833 0.00 0.00 0.00 2.62
700 2163 3.949113 GGGGTTAAATAGTGGCGATGAAA 59.051 43.478 0.00 0.00 0.00 2.69
701 2164 3.547746 GGGGTTAAATAGTGGCGATGAA 58.452 45.455 0.00 0.00 0.00 2.57
702 2165 2.158726 GGGGGTTAAATAGTGGCGATGA 60.159 50.000 0.00 0.00 0.00 2.92
703 2166 2.227194 GGGGGTTAAATAGTGGCGATG 58.773 52.381 0.00 0.00 0.00 3.84
704 2167 1.847737 TGGGGGTTAAATAGTGGCGAT 59.152 47.619 0.00 0.00 0.00 4.58
705 2168 1.287217 TGGGGGTTAAATAGTGGCGA 58.713 50.000 0.00 0.00 0.00 5.54
706 2169 1.953686 CATGGGGGTTAAATAGTGGCG 59.046 52.381 0.00 0.00 0.00 5.69
707 2170 1.686587 GCATGGGGGTTAAATAGTGGC 59.313 52.381 0.00 0.00 0.00 5.01
724 2187 3.099170 AATGGAGGAGGCGGGCAT 61.099 61.111 3.78 0.00 0.00 4.40
725 2188 4.113815 CAATGGAGGAGGCGGGCA 62.114 66.667 3.78 0.00 0.00 5.36
729 2192 1.817099 GCTGACAATGGAGGAGGCG 60.817 63.158 0.00 0.00 0.00 5.52
730 2193 1.452833 GGCTGACAATGGAGGAGGC 60.453 63.158 0.00 0.00 0.00 4.70
733 2196 1.541118 TGGGGCTGACAATGGAGGA 60.541 57.895 0.00 0.00 0.00 3.71
777 2240 3.887716 CCTAGATTTATTGCTGCTGCCTT 59.112 43.478 13.47 2.96 38.71 4.35
782 2245 3.495100 CCGGACCTAGATTTATTGCTGCT 60.495 47.826 0.00 0.00 0.00 4.24
821 2286 1.007118 GGAATGGTTCTGGGAATGGGT 59.993 52.381 0.00 0.00 0.00 4.51
909 2378 1.664965 GACGGACGCTGCTCAACTT 60.665 57.895 0.00 0.00 0.00 2.66
1580 4966 0.758123 CTGGATGGAGAAGAGGGAGC 59.242 60.000 0.00 0.00 0.00 4.70
1599 4985 4.705507 TGTGTACTTGGATAGACAGAGGAC 59.294 45.833 0.00 0.00 0.00 3.85
1621 5007 5.809051 AGATCAGCATGCATGTACGTATATG 59.191 40.000 26.79 23.51 34.76 1.78
1641 5036 4.371786 TGTACGCAAGGATGATCAAGATC 58.628 43.478 0.00 3.12 46.39 2.75
1699 5094 0.535780 TACGCGTCCATCCCGTAGAT 60.536 55.000 18.63 0.00 36.51 1.98
1701 5096 1.009222 GTACGCGTCCATCCCGTAG 60.009 63.158 18.63 0.00 38.02 3.51
1708 5108 1.079474 TGCACATGTACGCGTCCAT 60.079 52.632 18.63 14.83 0.00 3.41
1710 5110 0.457166 TACTGCACATGTACGCGTCC 60.457 55.000 18.63 4.27 0.00 4.79
1714 5114 1.324736 GCTTCTACTGCACATGTACGC 59.675 52.381 0.00 0.00 0.00 4.42
1751 5151 5.600484 TGGAACCACAAAATCCAATAACACT 59.400 36.000 0.00 0.00 40.19 3.55
1753 5153 6.462500 CATGGAACCACAAAATCCAATAACA 58.538 36.000 0.00 0.00 45.75 2.41
1757 5157 3.263937 CCCATGGAACCACAAAATCCAAT 59.736 43.478 15.22 0.00 45.75 3.16
1832 5245 0.905357 GTCTACCACATGACCCTGCT 59.095 55.000 0.00 0.00 0.00 4.24
1837 5250 1.463444 GCGTTTGTCTACCACATGACC 59.537 52.381 0.00 0.00 33.90 4.02
1838 5251 2.413837 AGCGTTTGTCTACCACATGAC 58.586 47.619 0.00 0.00 33.90 3.06
1951 5406 2.610976 CGGGTACTCAAATCACCAACGA 60.611 50.000 0.00 0.00 33.78 3.85
2054 5509 1.228367 ACCGTCCACGTCCTACAGT 60.228 57.895 0.00 0.00 37.74 3.55
2082 5537 1.541379 TTGAAGATCACGAGGTCCGA 58.459 50.000 0.00 0.00 41.76 4.55
2127 5582 1.069159 CAAGCTCTACGTGTCGTCTGT 60.069 52.381 0.00 0.00 41.54 3.41
2164 5619 0.968901 AGGGCGGAGATCACGTACAA 60.969 55.000 10.79 0.00 0.00 2.41
2209 5664 1.588824 TAGTGGGCAGGACACGTACG 61.589 60.000 15.01 15.01 43.41 3.67
2228 5683 1.806542 GTGGTCAGAAATCACGTGCAT 59.193 47.619 11.67 2.50 0.00 3.96
2281 5736 4.095782 TGAAAAGAATAATTTCCGGCGAGG 59.904 41.667 9.30 0.00 42.97 4.63
2329 5787 5.344207 TGTCTGTCGTACTATCATGATCG 57.656 43.478 12.53 8.73 0.00 3.69
2330 5788 9.678941 TTTTATGTCTGTCGTACTATCATGATC 57.321 33.333 12.53 0.00 0.00 2.92
2913 6658 1.545706 GGAAGAAGCCGGTGTCCTCT 61.546 60.000 1.90 0.00 0.00 3.69
3015 6763 0.825840 AGGAGCAGGCGGAGAGTATC 60.826 60.000 0.00 0.00 0.00 2.24
3018 6766 2.757917 GAGGAGCAGGCGGAGAGT 60.758 66.667 0.00 0.00 0.00 3.24
3054 6802 1.911766 GACGGAGACCTTGACCCCA 60.912 63.158 0.00 0.00 0.00 4.96
3327 7076 2.732619 CCTGGGTAGGGCGTTCTCC 61.733 68.421 0.00 0.00 40.63 3.71
3339 7088 2.037136 CGTCTCGTCGTACCTGGGT 61.037 63.158 0.00 0.00 0.00 4.51
3384 7133 3.077556 TCCTCAGCCTTCTCCGCC 61.078 66.667 0.00 0.00 0.00 6.13
3396 7145 2.284625 ACCATGCGGTCCTCCTCA 60.285 61.111 0.00 0.00 44.71 3.86
3647 7452 3.000727 CCTTCATTCGGTACACACCTTC 58.999 50.000 0.00 0.00 43.33 3.46
3663 7479 0.841289 ACGTTTCCTTCCCACCTTCA 59.159 50.000 0.00 0.00 0.00 3.02
3817 7642 2.100991 GCAACATGCTACTGCGGC 59.899 61.111 0.00 0.00 40.96 6.53
3899 8884 1.074752 CTCGCCAAGCTCTGTTCTTC 58.925 55.000 0.00 0.00 0.00 2.87
3927 8912 6.842437 ACAGAGTAGAAGATAGCAACAAGA 57.158 37.500 0.00 0.00 0.00 3.02
3928 8913 6.252441 CGAACAGAGTAGAAGATAGCAACAAG 59.748 42.308 0.00 0.00 0.00 3.16
3929 8914 6.093404 CGAACAGAGTAGAAGATAGCAACAA 58.907 40.000 0.00 0.00 0.00 2.83
3984 8975 4.826556 TGGTTTTGCAAGCTAAAACAACT 58.173 34.783 19.75 0.00 45.28 3.16
4019 9014 4.696479 ATGTTATGAGGTGGACTCCATC 57.304 45.455 0.00 0.00 46.01 3.51
4020 9015 6.386927 TCTTAATGTTATGAGGTGGACTCCAT 59.613 38.462 0.00 0.00 46.01 3.41
4021 9016 5.724370 TCTTAATGTTATGAGGTGGACTCCA 59.276 40.000 0.00 0.00 46.01 3.86
4022 9017 6.235231 TCTTAATGTTATGAGGTGGACTCC 57.765 41.667 0.00 0.00 46.01 3.85
4025 9020 5.177696 GCGATCTTAATGTTATGAGGTGGAC 59.822 44.000 0.00 0.00 0.00 4.02
4026 9021 5.070446 AGCGATCTTAATGTTATGAGGTGGA 59.930 40.000 0.00 0.00 0.00 4.02
4027 9022 5.300752 AGCGATCTTAATGTTATGAGGTGG 58.699 41.667 0.00 0.00 0.00 4.61
4028 9023 6.653183 CAAGCGATCTTAATGTTATGAGGTG 58.347 40.000 0.00 0.00 0.00 4.00
4029 9024 5.237344 GCAAGCGATCTTAATGTTATGAGGT 59.763 40.000 0.00 0.00 0.00 3.85
4030 9025 5.237127 TGCAAGCGATCTTAATGTTATGAGG 59.763 40.000 0.00 0.00 0.00 3.86
4031 9026 6.291067 TGCAAGCGATCTTAATGTTATGAG 57.709 37.500 0.00 0.00 0.00 2.90
4032 9027 6.676237 TTGCAAGCGATCTTAATGTTATGA 57.324 33.333 0.00 0.00 0.00 2.15
4033 9028 5.397534 GCTTGCAAGCGATCTTAATGTTATG 59.602 40.000 33.75 0.32 42.88 1.90
4034 9029 5.514279 GCTTGCAAGCGATCTTAATGTTAT 58.486 37.500 33.75 0.00 42.88 1.89
4035 9030 4.908736 GCTTGCAAGCGATCTTAATGTTA 58.091 39.130 33.75 0.00 42.88 2.41
4036 9031 3.762779 GCTTGCAAGCGATCTTAATGTT 58.237 40.909 33.75 0.00 42.88 2.71
4037 9032 3.411415 GCTTGCAAGCGATCTTAATGT 57.589 42.857 33.75 0.00 42.88 2.71
4057 9052 5.065218 AGGATCGTTATGCAAGCTAAAACAG 59.935 40.000 0.00 0.00 0.00 3.16
4058 9053 4.941263 AGGATCGTTATGCAAGCTAAAACA 59.059 37.500 0.00 0.00 0.00 2.83
4059 9054 5.485662 AGGATCGTTATGCAAGCTAAAAC 57.514 39.130 0.00 0.00 0.00 2.43
4060 9055 7.801716 ATTAGGATCGTTATGCAAGCTAAAA 57.198 32.000 0.00 0.00 0.00 1.52
4061 9056 7.801716 AATTAGGATCGTTATGCAAGCTAAA 57.198 32.000 0.00 0.00 0.00 1.85
4062 9057 8.935844 CATAATTAGGATCGTTATGCAAGCTAA 58.064 33.333 0.00 0.00 31.45 3.09
4063 9058 7.549134 CCATAATTAGGATCGTTATGCAAGCTA 59.451 37.037 0.00 0.00 35.51 3.32
4064 9059 6.372659 CCATAATTAGGATCGTTATGCAAGCT 59.627 38.462 0.00 0.00 35.51 3.74
4065 9060 6.403636 CCCATAATTAGGATCGTTATGCAAGC 60.404 42.308 0.00 0.00 35.51 4.01
4066 9061 6.878923 TCCCATAATTAGGATCGTTATGCAAG 59.121 38.462 0.00 0.00 35.51 4.01
4067 9062 6.774673 TCCCATAATTAGGATCGTTATGCAA 58.225 36.000 0.00 0.00 35.51 4.08
4068 9063 6.367374 TCCCATAATTAGGATCGTTATGCA 57.633 37.500 0.00 0.00 35.51 3.96
4069 9064 7.047891 TCATCCCATAATTAGGATCGTTATGC 58.952 38.462 0.00 0.00 41.05 3.14
4070 9065 9.102757 CTTCATCCCATAATTAGGATCGTTATG 57.897 37.037 0.00 3.08 41.05 1.90
4071 9066 8.267894 CCTTCATCCCATAATTAGGATCGTTAT 58.732 37.037 0.00 0.00 41.05 1.89
4072 9067 7.311046 CCCTTCATCCCATAATTAGGATCGTTA 60.311 40.741 0.00 0.00 41.05 3.18
4073 9068 6.476378 CCTTCATCCCATAATTAGGATCGTT 58.524 40.000 0.00 0.00 41.05 3.85
4074 9069 5.045578 CCCTTCATCCCATAATTAGGATCGT 60.046 44.000 0.00 0.00 41.05 3.73
4075 9070 5.189736 TCCCTTCATCCCATAATTAGGATCG 59.810 44.000 0.00 0.00 41.05 3.69
4076 9071 6.216456 ACTCCCTTCATCCCATAATTAGGATC 59.784 42.308 0.00 0.00 41.05 3.36
4077 9072 6.012157 CACTCCCTTCATCCCATAATTAGGAT 60.012 42.308 0.00 0.00 43.89 3.24
4078 9073 5.310594 CACTCCCTTCATCCCATAATTAGGA 59.689 44.000 0.00 0.00 36.36 2.94
4079 9074 5.310594 TCACTCCCTTCATCCCATAATTAGG 59.689 44.000 0.00 0.00 0.00 2.69
4080 9075 6.439636 TCACTCCCTTCATCCCATAATTAG 57.560 41.667 0.00 0.00 0.00 1.73
4081 9076 5.221925 GCTCACTCCCTTCATCCCATAATTA 60.222 44.000 0.00 0.00 0.00 1.40
4082 9077 4.446889 GCTCACTCCCTTCATCCCATAATT 60.447 45.833 0.00 0.00 0.00 1.40
4089 9084 1.144936 CCGCTCACTCCCTTCATCC 59.855 63.158 0.00 0.00 0.00 3.51
4110 9114 2.288666 GTGGCAACTCAAAGTCAGACA 58.711 47.619 2.66 0.00 37.61 3.41
4111 9115 1.261619 CGTGGCAACTCAAAGTCAGAC 59.738 52.381 0.00 0.00 37.61 3.51
4138 9142 2.889512 TGAGAGGCTAAGTCAGTTGGA 58.110 47.619 0.00 0.00 0.00 3.53
4140 9144 4.462508 TGATGAGAGGCTAAGTCAGTTG 57.537 45.455 0.00 0.00 0.00 3.16
4141 9145 5.188555 TGATTGATGAGAGGCTAAGTCAGTT 59.811 40.000 0.00 0.00 0.00 3.16
4143 9147 5.273674 TGATTGATGAGAGGCTAAGTCAG 57.726 43.478 0.00 0.00 0.00 3.51
4163 9167 6.882678 CAGGCCATATGATGAAGATTGTATGA 59.117 38.462 5.01 0.00 0.00 2.15
4177 9182 5.076873 GGGTAATTAAAGCAGGCCATATGA 58.923 41.667 5.01 0.00 0.00 2.15
4180 9185 3.465588 AGGGGTAATTAAAGCAGGCCATA 59.534 43.478 5.01 0.00 0.00 2.74
4181 9186 2.247372 AGGGGTAATTAAAGCAGGCCAT 59.753 45.455 5.01 0.00 0.00 4.40
4182 9187 1.643811 AGGGGTAATTAAAGCAGGCCA 59.356 47.619 5.01 0.00 0.00 5.36
4184 9189 2.688446 GTGAGGGGTAATTAAAGCAGGC 59.312 50.000 0.00 0.00 0.00 4.85
4186 9191 4.640647 GGAAGTGAGGGGTAATTAAAGCAG 59.359 45.833 0.00 0.00 0.00 4.24
4187 9192 4.569015 GGGAAGTGAGGGGTAATTAAAGCA 60.569 45.833 0.00 0.00 0.00 3.91
4188 9193 3.952323 GGGAAGTGAGGGGTAATTAAAGC 59.048 47.826 0.00 0.00 0.00 3.51
4189 9194 5.187621 TGGGAAGTGAGGGGTAATTAAAG 57.812 43.478 0.00 0.00 0.00 1.85
4190 9195 5.326900 GTTGGGAAGTGAGGGGTAATTAAA 58.673 41.667 0.00 0.00 0.00 1.52
4191 9196 4.264038 GGTTGGGAAGTGAGGGGTAATTAA 60.264 45.833 0.00 0.00 0.00 1.40
4192 9197 3.267551 GGTTGGGAAGTGAGGGGTAATTA 59.732 47.826 0.00 0.00 0.00 1.40
4193 9198 2.042569 GGTTGGGAAGTGAGGGGTAATT 59.957 50.000 0.00 0.00 0.00 1.40
4194 9199 1.639108 GGTTGGGAAGTGAGGGGTAAT 59.361 52.381 0.00 0.00 0.00 1.89
4212 9217 8.893563 TTCCATATAATTTTCAGTTCTTGGGT 57.106 30.769 0.00 0.00 0.00 4.51
4213 9218 9.754382 CATTCCATATAATTTTCAGTTCTTGGG 57.246 33.333 0.00 0.00 0.00 4.12
4296 9301 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4298 9303 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4300 9305 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4302 9307 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4304 9309 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4306 9311 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4308 9313 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4310 9315 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
4312 9317 2.158559 ACATTGTGTGTGTGTGTGTGT 58.841 42.857 0.00 0.00 40.28 3.72
4314 9319 3.373748 CACTACATTGTGTGTGTGTGTGT 59.626 43.478 13.26 0.00 42.24 3.72
4504 9521 7.223387 CCTCACAAACTTTTCAAATCTTTGGAG 59.777 37.037 3.02 7.59 38.66 3.86
4506 9523 6.818142 ACCTCACAAACTTTTCAAATCTTTGG 59.182 34.615 3.02 0.00 38.66 3.28
4556 9577 5.039645 TCCATCTTTCATACTCCCTTCCTT 58.960 41.667 0.00 0.00 0.00 3.36
4558 9579 5.373812 TTCCATCTTTCATACTCCCTTCC 57.626 43.478 0.00 0.00 0.00 3.46
4560 9581 6.012508 TCACTTTCCATCTTTCATACTCCCTT 60.013 38.462 0.00 0.00 0.00 3.95
4563 9584 6.655003 TGTTCACTTTCCATCTTTCATACTCC 59.345 38.462 0.00 0.00 0.00 3.85
4574 9595 6.756074 TGAAATTTGTGTGTTCACTTTCCATC 59.244 34.615 0.00 0.00 44.14 3.51


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

AutoCloner maintained by Alex Coulton.