Multiple sequence alignment - TraesCS6B01G271700

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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 TraesCS6B01G271700 chr6B 100.000 3915 0 0 1 3915 490253333 490257247 0.000000e+00 7230.0
1 TraesCS6B01G271700 chr6A 91.251 3406 181 42 123 3476 469434544 469431204 0.000000e+00 4530.0
2 TraesCS6B01G271700 chr6A 87.309 457 35 7 3478 3913 469431160 469430706 5.840000e-138 501.0
3 TraesCS6B01G271700 chr6A 85.714 77 11 0 2122 2198 570383485 570383409 9.020000e-12 82.4
4 TraesCS6B01G271700 chr6D 92.472 2670 118 31 484 3117 330159454 330156832 0.000000e+00 3740.0
5 TraesCS6B01G271700 chr6D 90.722 388 26 6 3211 3598 330114765 330114388 3.490000e-140 508.0
6 TraesCS6B01G271700 chr6D 91.928 223 18 0 3692 3914 330114337 330114115 2.940000e-81 313.0
7 TraesCS6B01G271700 chr6D 94.444 72 3 1 3144 3215 330115939 330115869 4.140000e-20 110.0
8 TraesCS6B01G271700 chr6D 84.337 83 13 0 2122 2204 425903627 425903545 9.020000e-12 82.4
9 TraesCS6B01G271700 chr2D 86.158 419 52 5 2320 2735 516370452 516370867 7.720000e-122 448.0
10 TraesCS6B01G271700 chr2D 83.217 143 22 2 1806 1947 14106349 14106208 3.170000e-26 130.0
11 TraesCS6B01G271700 chr2B 86.158 419 52 5 2320 2735 607953249 607953664 7.720000e-122 448.0
12 TraesCS6B01G271700 chr2B 83.217 143 22 2 1806 1947 25687528 25687387 3.170000e-26 130.0
13 TraesCS6B01G271700 chr2B 88.776 98 11 0 2104 2201 25687084 25686987 1.910000e-23 121.0
14 TraesCS6B01G271700 chr2A 86.788 386 45 5 2320 2702 660224055 660224437 3.620000e-115 425.0
15 TraesCS6B01G271700 chr2A 83.217 143 22 2 1806 1947 16477998 16477857 3.170000e-26 130.0
16 TraesCS6B01G271700 chr7B 84.937 239 32 4 2321 2557 565577309 565577545 5.060000e-59 239.0
17 TraesCS6B01G271700 chr7B 78.696 230 38 5 1387 1615 730181129 730180910 4.080000e-30 143.0
18 TraesCS6B01G271700 chr7A 84.100 239 34 4 2321 2557 608359403 608359639 1.090000e-55 228.0
19 TraesCS6B01G271700 chr7A 77.391 230 41 3 1387 1615 724137187 724136968 4.110000e-25 126.0
20 TraesCS6B01G271700 chr7A 95.349 43 2 0 2153 2195 465377114 465377156 7.020000e-08 69.4
21 TraesCS6B01G271700 chr7D 83.682 239 35 4 2321 2557 528080135 528080371 5.090000e-54 222.0
22 TraesCS6B01G271700 chrUn 76.547 307 64 7 2439 2741 92744492 92744190 1.130000e-35 161.0
23 TraesCS6B01G271700 chrUn 76.957 230 42 3 1387 1615 92746368 92746149 1.910000e-23 121.0
24 TraesCS6B01G271700 chr4D 76.852 216 42 8 2436 2647 464156698 464156909 8.890000e-22 115.0
25 TraesCS6B01G271700 chr4D 97.674 43 1 0 2151 2193 464280 464238 1.510000e-09 75.0
26 TraesCS6B01G271700 chr4B 97.674 43 1 0 2151 2193 234387 234345 1.510000e-09 75.0
27 TraesCS6B01G271700 chr4A 97.674 43 1 0 2151 2193 193726 193684 1.510000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G271700 chr6B 490253333 490257247 3914 False 7230.000000 7230 100.000000 1 3915 1 chr6B.!!$F1 3914
1 TraesCS6B01G271700 chr6A 469430706 469434544 3838 True 2515.500000 4530 89.280000 123 3913 2 chr6A.!!$R2 3790
2 TraesCS6B01G271700 chr6D 330156832 330159454 2622 True 3740.000000 3740 92.472000 484 3117 1 chr6D.!!$R1 2633
3 TraesCS6B01G271700 chr6D 330114115 330115939 1824 True 310.333333 508 92.364667 3144 3914 3 chr6D.!!$R3 770

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 0.037975 GCGGTTAAACCTCTCGGTGA 60.038 55.0 0.00 0.0 44.73 4.02 F
81 82 0.173708 CCTCTCGGTGAAGGTAGTGC 59.826 60.0 0.00 0.0 0.00 4.40 F
95 96 0.388907 TAGTGCCTTCGTGTAACCGC 60.389 55.0 0.00 0.0 0.00 5.68 F
513 534 0.392461 GTATTGGCCAGGTGCGAGAA 60.392 55.0 5.11 0.0 42.61 2.87 F
640 661 0.455633 CGAAATGCAAGCAGAGGCAC 60.456 55.0 0.00 0.0 43.75 5.01 F
1723 1753 0.662619 CGAAATGTGTGTGTGTGCCT 59.337 50.0 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2004 0.319405 CGGGACTTTTACTCCGTGGT 59.681 55.000 0.0 0.0 37.92 4.16 R
1997 2054 1.833630 CTCAGGTTATCCCAGTCTGCA 59.166 52.381 0.0 0.0 34.66 4.41 R
2011 2068 2.159085 GCTATTCGTGTTAGCCTCAGGT 60.159 50.000 0.0 0.0 36.82 4.00 R
2278 2352 1.076192 GCGGGAGAGGAGGGTTAGA 60.076 63.158 0.0 0.0 0.00 2.10 R
2303 2377 2.126346 GTGGAATTGCTGCGGTGC 60.126 61.111 0.0 0.0 0.00 5.01 R
2967 3042 0.101399 AGAGGATAGACGCAGCAACG 59.899 55.000 0.0 0.0 39.50 4.10 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
20 21 2.973945 CCGTCCTTCTTTAGGTCCTTG 58.026 52.381 0.00 0.00 45.03 3.61
21 22 2.354805 CCGTCCTTCTTTAGGTCCTTGG 60.355 54.545 0.00 0.00 45.03 3.61
22 23 2.712709 GTCCTTCTTTAGGTCCTTGGC 58.287 52.381 0.00 0.00 45.03 4.52
23 24 2.306219 GTCCTTCTTTAGGTCCTTGGCT 59.694 50.000 0.00 0.00 45.03 4.75
24 25 3.518303 GTCCTTCTTTAGGTCCTTGGCTA 59.482 47.826 0.00 0.00 45.03 3.93
25 26 3.775316 TCCTTCTTTAGGTCCTTGGCTAG 59.225 47.826 0.00 0.00 45.03 3.42
26 27 3.118223 CCTTCTTTAGGTCCTTGGCTAGG 60.118 52.174 8.84 8.84 39.25 3.02
27 28 3.200958 TCTTTAGGTCCTTGGCTAGGT 57.799 47.619 14.66 0.00 45.03 3.08
28 29 2.838202 TCTTTAGGTCCTTGGCTAGGTG 59.162 50.000 14.66 0.00 45.03 4.00
29 30 1.580059 TTAGGTCCTTGGCTAGGTGG 58.420 55.000 14.66 0.00 45.03 4.61
30 31 0.326238 TAGGTCCTTGGCTAGGTGGG 60.326 60.000 14.66 0.00 45.03 4.61
31 32 1.923909 GGTCCTTGGCTAGGTGGGT 60.924 63.158 14.66 0.00 45.03 4.51
32 33 1.299976 GTCCTTGGCTAGGTGGGTG 59.700 63.158 14.66 0.00 45.03 4.61
33 34 1.159905 TCCTTGGCTAGGTGGGTGA 59.840 57.895 14.66 0.00 45.03 4.02
34 35 0.253160 TCCTTGGCTAGGTGGGTGAT 60.253 55.000 14.66 0.00 45.03 3.06
35 36 0.107017 CCTTGGCTAGGTGGGTGATG 60.107 60.000 6.84 0.00 39.39 3.07
36 37 0.911769 CTTGGCTAGGTGGGTGATGA 59.088 55.000 0.00 0.00 0.00 2.92
37 38 0.618458 TTGGCTAGGTGGGTGATGAC 59.382 55.000 0.00 0.00 0.00 3.06
38 39 1.144057 GGCTAGGTGGGTGATGACG 59.856 63.158 0.00 0.00 0.00 4.35
39 40 1.327690 GGCTAGGTGGGTGATGACGA 61.328 60.000 0.00 0.00 0.00 4.20
40 41 0.103208 GCTAGGTGGGTGATGACGAG 59.897 60.000 0.00 0.00 0.00 4.18
41 42 1.475403 CTAGGTGGGTGATGACGAGT 58.525 55.000 0.00 0.00 0.00 4.18
42 43 2.651455 CTAGGTGGGTGATGACGAGTA 58.349 52.381 0.00 0.00 0.00 2.59
43 44 1.475403 AGGTGGGTGATGACGAGTAG 58.525 55.000 0.00 0.00 0.00 2.57
44 45 1.183549 GGTGGGTGATGACGAGTAGT 58.816 55.000 0.00 0.00 0.00 2.73
45 46 1.549170 GGTGGGTGATGACGAGTAGTT 59.451 52.381 0.00 0.00 0.00 2.24
46 47 2.756760 GGTGGGTGATGACGAGTAGTTA 59.243 50.000 0.00 0.00 0.00 2.24
47 48 3.181489 GGTGGGTGATGACGAGTAGTTAG 60.181 52.174 0.00 0.00 0.00 2.34
48 49 2.426024 TGGGTGATGACGAGTAGTTAGC 59.574 50.000 0.00 0.00 0.00 3.09
49 50 2.426024 GGGTGATGACGAGTAGTTAGCA 59.574 50.000 0.00 0.00 32.19 3.49
50 51 3.068307 GGGTGATGACGAGTAGTTAGCAT 59.932 47.826 0.00 0.00 37.11 3.79
51 52 4.441634 GGGTGATGACGAGTAGTTAGCATT 60.442 45.833 0.00 0.00 37.11 3.56
52 53 5.109903 GGTGATGACGAGTAGTTAGCATTT 58.890 41.667 0.00 0.00 37.11 2.32
53 54 5.005779 GGTGATGACGAGTAGTTAGCATTTG 59.994 44.000 0.00 0.00 37.11 2.32
54 55 4.566759 TGATGACGAGTAGTTAGCATTTGC 59.433 41.667 0.00 0.00 42.49 3.68
67 68 2.863739 GCATTTGCGGTTAAACCTCTC 58.136 47.619 0.00 0.00 35.66 3.20
68 69 2.727916 GCATTTGCGGTTAAACCTCTCG 60.728 50.000 0.00 0.00 35.66 4.04
69 70 1.515081 TTTGCGGTTAAACCTCTCGG 58.485 50.000 0.00 0.00 35.66 4.63
71 72 0.320073 TGCGGTTAAACCTCTCGGTG 60.320 55.000 0.00 0.00 44.73 4.94
72 73 0.037975 GCGGTTAAACCTCTCGGTGA 60.038 55.000 0.00 0.00 44.73 4.02
73 74 1.606224 GCGGTTAAACCTCTCGGTGAA 60.606 52.381 0.00 0.00 44.73 3.18
74 75 2.334838 CGGTTAAACCTCTCGGTGAAG 58.665 52.381 0.00 0.00 44.73 3.02
75 76 2.696506 GGTTAAACCTCTCGGTGAAGG 58.303 52.381 0.00 0.00 44.73 3.46
76 77 2.038164 GGTTAAACCTCTCGGTGAAGGT 59.962 50.000 0.00 0.00 44.73 3.50
77 78 3.259123 GGTTAAACCTCTCGGTGAAGGTA 59.741 47.826 0.00 0.00 44.73 3.08
78 79 4.492611 GTTAAACCTCTCGGTGAAGGTAG 58.507 47.826 0.00 0.00 44.73 3.18
79 80 2.305858 AACCTCTCGGTGAAGGTAGT 57.694 50.000 0.00 0.00 44.73 2.73
80 81 1.546961 ACCTCTCGGTGAAGGTAGTG 58.453 55.000 0.00 0.00 43.51 2.74
81 82 0.173708 CCTCTCGGTGAAGGTAGTGC 59.826 60.000 0.00 0.00 0.00 4.40
82 83 0.173708 CTCTCGGTGAAGGTAGTGCC 59.826 60.000 0.00 0.00 37.58 5.01
93 94 1.718396 GGTAGTGCCTTCGTGTAACC 58.282 55.000 0.00 0.00 0.00 2.85
94 95 1.343506 GTAGTGCCTTCGTGTAACCG 58.656 55.000 0.00 0.00 0.00 4.44
95 96 0.388907 TAGTGCCTTCGTGTAACCGC 60.389 55.000 0.00 0.00 0.00 5.68
96 97 1.957186 GTGCCTTCGTGTAACCGCA 60.957 57.895 0.00 0.00 0.00 5.69
97 98 1.004320 TGCCTTCGTGTAACCGCAT 60.004 52.632 0.00 0.00 0.00 4.73
98 99 1.295357 TGCCTTCGTGTAACCGCATG 61.295 55.000 0.00 0.00 0.00 4.06
99 100 1.296056 GCCTTCGTGTAACCGCATGT 61.296 55.000 0.00 0.00 0.00 3.21
100 101 1.999048 CCTTCGTGTAACCGCATGTA 58.001 50.000 0.00 0.00 0.00 2.29
101 102 2.339418 CCTTCGTGTAACCGCATGTAA 58.661 47.619 0.00 0.00 0.00 2.41
102 103 2.347452 CCTTCGTGTAACCGCATGTAAG 59.653 50.000 0.00 0.00 0.00 2.34
103 104 3.247442 CTTCGTGTAACCGCATGTAAGA 58.753 45.455 0.00 0.00 0.00 2.10
104 105 2.598589 TCGTGTAACCGCATGTAAGAC 58.401 47.619 0.00 0.00 0.00 3.01
105 106 2.030096 TCGTGTAACCGCATGTAAGACA 60.030 45.455 0.00 0.00 0.00 3.41
106 107 2.091588 CGTGTAACCGCATGTAAGACAC 59.908 50.000 0.00 2.61 34.36 3.67
107 108 3.323243 GTGTAACCGCATGTAAGACACT 58.677 45.455 10.71 0.00 34.64 3.55
108 109 3.367025 GTGTAACCGCATGTAAGACACTC 59.633 47.826 10.71 0.00 34.64 3.51
109 110 1.710013 AACCGCATGTAAGACACTCG 58.290 50.000 0.00 0.00 0.00 4.18
110 111 0.601558 ACCGCATGTAAGACACTCGT 59.398 50.000 0.00 0.00 0.00 4.18
111 112 0.992072 CCGCATGTAAGACACTCGTG 59.008 55.000 0.00 0.00 0.00 4.35
112 113 0.992072 CGCATGTAAGACACTCGTGG 59.008 55.000 1.77 0.00 34.19 4.94
113 114 1.402325 CGCATGTAAGACACTCGTGGA 60.402 52.381 1.77 0.00 34.19 4.02
114 115 1.993370 GCATGTAAGACACTCGTGGAC 59.007 52.381 1.77 0.00 34.19 4.02
115 116 2.251040 CATGTAAGACACTCGTGGACG 58.749 52.381 1.77 0.00 41.45 4.79
116 117 0.594602 TGTAAGACACTCGTGGACGG 59.405 55.000 1.77 0.00 40.29 4.79
118 119 1.870055 TAAGACACTCGTGGACGGGC 61.870 60.000 0.00 0.00 45.27 6.13
119 120 4.736896 GACACTCGTGGACGGGCC 62.737 72.222 0.00 0.00 45.27 5.80
121 122 4.742201 CACTCGTGGACGGGCCTG 62.742 72.222 11.02 11.02 45.27 4.85
137 138 2.163509 GCCTGTTTTCCCCTCTTCTTC 58.836 52.381 0.00 0.00 0.00 2.87
145 146 7.066781 TGTTTTCCCCTCTTCTTCTTTAATGT 58.933 34.615 0.00 0.00 0.00 2.71
195 196 9.535270 CTTAGAGAAAAAGAAACTTAATCTGCG 57.465 33.333 0.00 0.00 0.00 5.18
196 197 6.903419 AGAGAAAAAGAAACTTAATCTGCGG 58.097 36.000 0.00 0.00 0.00 5.69
203 204 0.613260 ACTTAATCTGCGGCCTCACA 59.387 50.000 0.00 0.00 0.00 3.58
204 205 1.210478 ACTTAATCTGCGGCCTCACAT 59.790 47.619 0.00 0.00 0.00 3.21
217 218 2.775890 CCTCACATGAGCATCCCATAC 58.224 52.381 0.00 0.00 40.75 2.39
226 227 7.445096 CACATGAGCATCCCATACTGTAATTTA 59.555 37.037 0.00 0.00 0.00 1.40
244 245 9.581289 TGTAATTTACAGGGATTTCAAAAGAGA 57.419 29.630 5.14 0.00 34.06 3.10
246 247 7.709149 ATTTACAGGGATTTCAAAAGAGAGG 57.291 36.000 0.00 0.00 0.00 3.69
255 257 9.194972 GGGATTTCAAAAGAGAGGATATTTTCT 57.805 33.333 0.00 0.00 29.95 2.52
263 265 9.997172 AAAAGAGAGGATATTTTCTAAACCCAT 57.003 29.630 0.00 0.00 25.62 4.00
288 290 6.268847 TGGTTAGTTTTTGCCTCCATAAATGT 59.731 34.615 0.00 0.00 0.00 2.71
303 305 7.161404 TCCATAAATGTATCAGCACCAGATAC 58.839 38.462 6.43 6.43 45.05 2.24
327 329 0.397957 TATTCCGTAGCAGGGCAGGA 60.398 55.000 0.00 0.00 0.00 3.86
368 370 5.651612 TGGACCATATTGTCTGGAATCAT 57.348 39.130 6.87 0.00 37.22 2.45
391 393 6.257994 TCTTCCAGATGAAAATATGAGCCT 57.742 37.500 0.00 0.00 31.06 4.58
394 396 6.196918 TCCAGATGAAAATATGAGCCTCAT 57.803 37.500 12.62 12.62 40.72 2.90
415 417 6.934056 TCATTTATGTGTGCCTTAATTGCTT 58.066 32.000 0.00 0.00 0.00 3.91
424 426 7.093988 TGTGTGCCTTAATTGCTTTACATGTAT 60.094 33.333 6.36 0.00 0.00 2.29
429 431 9.023967 GCCTTAATTGCTTTACATGTATTTGAG 57.976 33.333 6.36 4.35 0.00 3.02
444 446 9.390795 CATGTATTTGAGAGTGAACTTTGAAAG 57.609 33.333 2.89 2.89 0.00 2.62
452 455 8.356657 TGAGAGTGAACTTTGAAAGAACAAAAA 58.643 29.630 12.53 0.00 38.90 1.94
461 464 4.739195 TGAAAGAACAAAAAGTTGACCCG 58.261 39.130 0.00 0.00 41.51 5.28
475 496 2.329267 TGACCCGATTATGCTCCTGAT 58.671 47.619 0.00 0.00 0.00 2.90
477 498 3.244215 TGACCCGATTATGCTCCTGATTC 60.244 47.826 0.00 0.00 0.00 2.52
513 534 0.392461 GTATTGGCCAGGTGCGAGAA 60.392 55.000 5.11 0.00 42.61 2.87
536 557 2.490270 GAATGGCTGTCCCCTGCAGT 62.490 60.000 13.81 0.00 37.27 4.40
548 569 0.947244 CCTGCAGTCGCTTCAGTTTT 59.053 50.000 13.81 0.00 39.64 2.43
636 657 2.975410 TGTTCGAAATGCAAGCAGAG 57.025 45.000 0.00 0.00 0.00 3.35
640 661 0.455633 CGAAATGCAAGCAGAGGCAC 60.456 55.000 0.00 0.00 43.75 5.01
669 690 5.739161 GCGCTCATTTCTCGTTTGATTATTT 59.261 36.000 0.00 0.00 0.00 1.40
848 869 0.681175 GCCCAAAGTCACATTTGCCT 59.319 50.000 0.00 0.00 38.57 4.75
952 973 4.153835 CAGCCATCAAGTCAGAAGAAAGAC 59.846 45.833 0.00 0.00 35.02 3.01
956 977 3.643763 TCAAGTCAGAAGAAAGACGAGC 58.356 45.455 0.00 0.00 39.67 5.03
1104 1126 4.982916 GCCATGATTCTCAATTGATCTTGC 59.017 41.667 8.96 5.01 0.00 4.01
1114 1136 5.188434 TCAATTGATCTTGCTCTACCTTGG 58.812 41.667 3.38 0.00 0.00 3.61
1132 1154 4.284178 CTTGGTTCCTTGATGGGATTCAT 58.716 43.478 0.00 0.00 39.13 2.57
1144 1166 6.377327 GATGGGATTCATCGTGTATTTTGT 57.623 37.500 0.00 0.00 42.29 2.83
1146 1168 6.582677 TGGGATTCATCGTGTATTTTGTTT 57.417 33.333 0.00 0.00 0.00 2.83
1151 1173 9.221775 GGATTCATCGTGTATTTTGTTTGATAC 57.778 33.333 0.00 0.00 0.00 2.24
1177 1201 2.430465 ACTTCTGACGCATGCAATCTT 58.570 42.857 19.57 0.00 0.00 2.40
1200 1224 2.611292 GCTCATTTTACTCTCGCAGCAT 59.389 45.455 0.00 0.00 0.00 3.79
1654 1684 2.158740 TCAACCCGAACCATGTTCTGAA 60.159 45.455 5.53 0.00 0.00 3.02
1656 1686 3.154827 ACCCGAACCATGTTCTGAATT 57.845 42.857 5.53 0.00 0.00 2.17
1723 1753 0.662619 CGAAATGTGTGTGTGTGCCT 59.337 50.000 0.00 0.00 0.00 4.75
1732 1762 1.200716 GTGTGTGTGCCTTCCATGATG 59.799 52.381 0.00 0.00 0.00 3.07
1742 1772 3.552273 GCCTTCCATGATGATGCATGTTC 60.552 47.826 2.46 0.62 43.16 3.18
1951 2004 3.578716 AGGATCACCTCTTCAGAAACGAA 59.421 43.478 0.00 0.00 44.13 3.85
1963 2016 3.125316 CAGAAACGAACCACGGAGTAAA 58.875 45.455 0.00 0.00 41.61 2.01
1964 2017 3.556775 CAGAAACGAACCACGGAGTAAAA 59.443 43.478 0.00 0.00 41.61 1.52
1985 2038 2.300152 AGTCCCGGCACATACATATCAG 59.700 50.000 0.00 0.00 0.00 2.90
1987 2040 1.270785 CCCGGCACATACATATCAGCA 60.271 52.381 0.00 0.00 0.00 4.41
1993 2050 5.639082 CGGCACATACATATCAGCAGATTAA 59.361 40.000 0.00 0.00 35.67 1.40
1997 2054 8.944029 GCACATACATATCAGCAGATTAAAGAT 58.056 33.333 0.00 0.00 35.67 2.40
2011 2068 6.994496 CAGATTAAAGATGCAGACTGGGATAA 59.006 38.462 4.26 0.00 0.00 1.75
2012 2069 6.995091 AGATTAAAGATGCAGACTGGGATAAC 59.005 38.462 4.26 0.00 0.00 1.89
2013 2070 3.567478 AAGATGCAGACTGGGATAACC 57.433 47.619 4.26 0.00 40.81 2.85
2014 2071 2.769209 AGATGCAGACTGGGATAACCT 58.231 47.619 4.26 0.00 41.11 3.50
2015 2072 2.437281 AGATGCAGACTGGGATAACCTG 59.563 50.000 4.26 0.00 43.37 4.00
2016 2073 1.951209 TGCAGACTGGGATAACCTGA 58.049 50.000 4.26 0.00 40.42 3.86
2017 2074 1.833630 TGCAGACTGGGATAACCTGAG 59.166 52.381 4.26 0.00 40.42 3.35
2278 2352 1.474017 GCGCATCGTACACGTCTAAT 58.526 50.000 0.30 0.00 40.80 1.73
2344 2418 2.802106 CTCTCGGACTTCGGGCTC 59.198 66.667 0.00 0.00 39.67 4.70
2503 2577 3.075005 GAGGTGCTGACGGGCCTA 61.075 66.667 0.84 0.00 0.00 3.93
2714 2788 1.612146 TCCATGAAGGAGGCCGTCA 60.612 57.895 4.64 4.64 45.06 4.35
2745 2819 0.895530 GAGGTCGAGTCCATGTCCAA 59.104 55.000 0.00 0.00 0.00 3.53
2750 2824 1.450312 GAGTCCATGTCCAAGGGCG 60.450 63.158 0.00 0.00 33.85 6.13
2751 2825 3.134127 GTCCATGTCCAAGGGCGC 61.134 66.667 0.00 0.00 0.00 6.53
2752 2826 4.424711 TCCATGTCCAAGGGCGCC 62.425 66.667 21.18 21.18 0.00 6.53
2851 2926 3.069946 CCACGGCCAGGGTACGTA 61.070 66.667 2.24 0.00 39.02 3.57
2921 2996 1.226435 CGAGTGAGGTAGCGACTGC 60.226 63.158 4.60 0.00 43.24 4.40
2928 3003 2.076863 GAGGTAGCGACTGCAATTGTT 58.923 47.619 7.40 0.00 46.23 2.83
2936 3011 1.798725 CTGCAATTGTTCTGCGGCG 60.799 57.895 0.51 0.51 42.97 6.46
2953 3028 1.442520 CGCTTGGATTTGCACGTGG 60.443 57.895 18.88 0.00 0.00 4.94
2967 3042 2.399611 GTGGCGCGTGCTAATGAC 59.600 61.111 21.89 3.07 42.25 3.06
2976 3051 0.519175 GTGCTAATGACGTTGCTGCG 60.519 55.000 0.00 0.00 37.94 5.18
2983 3058 4.496670 ACGTTGCTGCGTCTATCC 57.503 55.556 0.00 0.00 41.71 2.59
2999 3074 5.861251 CGTCTATCCTCTGAGCATGTTATTC 59.139 44.000 0.00 0.00 0.00 1.75
3016 3095 8.501580 CATGTTATTCTCATGTGTCATATGGAC 58.498 37.037 9.43 1.00 39.16 4.02
3033 3112 1.209128 GACGGATGTGCGGTAATCTG 58.791 55.000 0.00 0.00 35.64 2.90
3039 3118 3.319972 GGATGTGCGGTAATCTGTAGGTA 59.680 47.826 0.00 0.00 0.00 3.08
3119 3198 5.096443 TGGAAGCCAGTTCAAATTTTGTT 57.904 34.783 8.89 0.00 36.82 2.83
3127 3206 5.006552 CCAGTTCAAATTTTGTTGCGAATGT 59.993 36.000 8.89 0.00 0.00 2.71
3137 3216 3.865446 TGTTGCGAATGTCAGAGATCAT 58.135 40.909 0.00 0.00 0.00 2.45
3139 3218 5.604565 TGTTGCGAATGTCAGAGATCATAT 58.395 37.500 0.00 0.00 0.00 1.78
3142 3221 3.931468 GCGAATGTCAGAGATCATATGGG 59.069 47.826 2.13 0.00 0.00 4.00
3250 4436 1.662517 TCAGACACTTTTTGCGCAGA 58.337 45.000 11.31 2.14 0.00 4.26
3325 4515 5.188327 TCTCTTCCTTCAGTGCATATACG 57.812 43.478 0.00 0.00 0.00 3.06
3331 4521 5.828747 TCCTTCAGTGCATATACGACTTAC 58.171 41.667 0.00 0.00 0.00 2.34
3388 4579 7.540745 ACTTTTATGTTTTCACCGCATACAATC 59.459 33.333 0.00 0.00 0.00 2.67
3389 4580 3.463533 TGTTTTCACCGCATACAATCG 57.536 42.857 0.00 0.00 0.00 3.34
3390 4581 3.067833 TGTTTTCACCGCATACAATCGA 58.932 40.909 0.00 0.00 0.00 3.59
3391 4582 3.498777 TGTTTTCACCGCATACAATCGAA 59.501 39.130 0.00 0.00 0.00 3.71
3392 4583 4.155099 TGTTTTCACCGCATACAATCGAAT 59.845 37.500 0.00 0.00 0.00 3.34
3395 4586 5.398176 TTCACCGCATACAATCGAATAAC 57.602 39.130 0.00 0.00 0.00 1.89
3412 4603 7.304735 TCGAATAACAACATTTCAAGTCCATG 58.695 34.615 0.00 0.00 0.00 3.66
3419 4610 6.211986 ACAACATTTCAAGTCCATGATTCCAT 59.788 34.615 0.00 0.00 0.00 3.41
3420 4611 6.461110 ACATTTCAAGTCCATGATTCCATC 57.539 37.500 0.00 0.00 0.00 3.51
3421 4612 5.361857 ACATTTCAAGTCCATGATTCCATCC 59.638 40.000 0.00 0.00 0.00 3.51
3422 4613 4.589647 TTCAAGTCCATGATTCCATCCA 57.410 40.909 0.00 0.00 0.00 3.41
3438 4629 9.307121 GATTCCATCCAGTATAACATAGAATCG 57.693 37.037 0.00 0.00 30.20 3.34
3527 4763 5.453762 CCACATATGCTCAACTAGGTCATCA 60.454 44.000 1.58 0.00 0.00 3.07
3649 4905 6.646267 TCTTTGATCTCACATGATGTCATCA 58.354 36.000 17.70 17.70 44.55 3.07
3698 4954 8.883731 CCAAAATCTAGTAGGTACATGAACAAG 58.116 37.037 0.00 0.00 0.00 3.16
3703 4959 1.156736 AGGTACATGAACAAGCGCAC 58.843 50.000 11.47 0.00 0.00 5.34
3705 4961 1.468520 GGTACATGAACAAGCGCACAT 59.531 47.619 11.47 4.20 0.00 3.21
3730 4986 3.067180 ACTTGCAATATCCCAAATGCTCG 59.933 43.478 0.00 0.00 39.49 5.03
3745 5001 1.092345 GCTCGCTCAACATCCTTCCC 61.092 60.000 0.00 0.00 0.00 3.97
3774 5030 8.231692 TGATTGAACCTTGTTGAAATGAACTA 57.768 30.769 0.00 0.00 0.00 2.24
3782 5038 7.118390 ACCTTGTTGAAATGAACTATCTTCTCG 59.882 37.037 0.00 0.00 0.00 4.04
3813 5069 7.926018 GTGGGTTAGAAATTTCTTCACAATTGT 59.074 33.333 25.02 4.92 38.70 2.71
3839 5095 4.106179 ACCACAAGGGATATATGCCATCAA 59.894 41.667 23.67 0.00 41.29 2.57
3844 5100 6.610830 ACAAGGGATATATGCCATCAACAAAA 59.389 34.615 23.67 0.00 41.29 2.44
3858 5114 7.335924 GCCATCAACAAAAATAGTAGTCCACTA 59.664 37.037 0.00 0.00 43.89 2.74
3894 5150 6.655003 ACCATTGACTATAAAGTTCACCACTG 59.345 38.462 0.00 0.00 35.56 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.911769 TCATCACCCACCTAGCCAAG 59.088 55.000 0.00 0.00 0.00 3.61
18 19 0.618458 GTCATCACCCACCTAGCCAA 59.382 55.000 0.00 0.00 0.00 4.52
19 20 1.613317 CGTCATCACCCACCTAGCCA 61.613 60.000 0.00 0.00 0.00 4.75
20 21 1.144057 CGTCATCACCCACCTAGCC 59.856 63.158 0.00 0.00 0.00 3.93
21 22 0.103208 CTCGTCATCACCCACCTAGC 59.897 60.000 0.00 0.00 0.00 3.42
22 23 1.475403 ACTCGTCATCACCCACCTAG 58.525 55.000 0.00 0.00 0.00 3.02
23 24 2.025605 ACTACTCGTCATCACCCACCTA 60.026 50.000 0.00 0.00 0.00 3.08
24 25 1.272536 ACTACTCGTCATCACCCACCT 60.273 52.381 0.00 0.00 0.00 4.00
25 26 1.183549 ACTACTCGTCATCACCCACC 58.816 55.000 0.00 0.00 0.00 4.61
26 27 3.734293 GCTAACTACTCGTCATCACCCAC 60.734 52.174 0.00 0.00 0.00 4.61
27 28 2.426024 GCTAACTACTCGTCATCACCCA 59.574 50.000 0.00 0.00 0.00 4.51
28 29 2.426024 TGCTAACTACTCGTCATCACCC 59.574 50.000 0.00 0.00 0.00 4.61
29 30 3.777465 TGCTAACTACTCGTCATCACC 57.223 47.619 0.00 0.00 0.00 4.02
30 31 5.500931 GCAAATGCTAACTACTCGTCATCAC 60.501 44.000 0.00 0.00 38.21 3.06
31 32 4.566759 GCAAATGCTAACTACTCGTCATCA 59.433 41.667 0.00 0.00 38.21 3.07
32 33 4.317418 CGCAAATGCTAACTACTCGTCATC 60.317 45.833 3.63 0.00 39.32 2.92
33 34 3.551890 CGCAAATGCTAACTACTCGTCAT 59.448 43.478 3.63 0.00 39.32 3.06
34 35 2.921121 CGCAAATGCTAACTACTCGTCA 59.079 45.455 3.63 0.00 39.32 4.35
35 36 2.281762 CCGCAAATGCTAACTACTCGTC 59.718 50.000 3.63 0.00 39.32 4.20
36 37 2.268298 CCGCAAATGCTAACTACTCGT 58.732 47.619 3.63 0.00 39.32 4.18
37 38 2.268298 ACCGCAAATGCTAACTACTCG 58.732 47.619 3.63 0.00 39.32 4.18
38 39 5.789710 TTAACCGCAAATGCTAACTACTC 57.210 39.130 3.63 0.00 39.32 2.59
39 40 5.106436 GGTTTAACCGCAAATGCTAACTACT 60.106 40.000 0.00 0.00 39.32 2.57
40 41 5.090757 GGTTTAACCGCAAATGCTAACTAC 58.909 41.667 0.00 0.00 39.32 2.73
41 42 5.005094 AGGTTTAACCGCAAATGCTAACTA 58.995 37.500 8.63 0.00 44.90 2.24
42 43 3.824443 AGGTTTAACCGCAAATGCTAACT 59.176 39.130 8.63 0.00 44.90 2.24
43 44 4.082949 AGAGGTTTAACCGCAAATGCTAAC 60.083 41.667 19.29 0.99 44.90 2.34
44 45 4.076394 AGAGGTTTAACCGCAAATGCTAA 58.924 39.130 19.29 0.00 44.90 3.09
45 46 3.681593 AGAGGTTTAACCGCAAATGCTA 58.318 40.909 19.29 0.00 44.90 3.49
46 47 2.488153 GAGAGGTTTAACCGCAAATGCT 59.512 45.455 19.29 4.95 44.90 3.79
47 48 2.727916 CGAGAGGTTTAACCGCAAATGC 60.728 50.000 19.29 0.00 44.90 3.56
48 49 3.117434 CGAGAGGTTTAACCGCAAATG 57.883 47.619 19.29 3.00 44.90 2.32
63 64 0.173708 GGCACTACCTTCACCGAGAG 59.826 60.000 0.00 0.00 34.51 3.20
64 65 2.273908 GGCACTACCTTCACCGAGA 58.726 57.895 0.00 0.00 34.51 4.04
65 66 4.913126 GGCACTACCTTCACCGAG 57.087 61.111 0.00 0.00 34.51 4.63
74 75 1.718396 GGTTACACGAAGGCACTACC 58.282 55.000 0.00 0.00 38.49 3.18
75 76 1.343506 CGGTTACACGAAGGCACTAC 58.656 55.000 0.00 0.00 38.49 2.73
76 77 0.388907 GCGGTTACACGAAGGCACTA 60.389 55.000 0.00 0.00 38.49 2.74
78 79 1.296056 ATGCGGTTACACGAAGGCAC 61.296 55.000 0.00 0.00 32.23 5.01
79 80 1.004320 ATGCGGTTACACGAAGGCA 60.004 52.632 0.00 0.00 33.53 4.75
80 81 1.296056 ACATGCGGTTACACGAAGGC 61.296 55.000 0.00 0.00 35.47 4.35
81 82 1.999048 TACATGCGGTTACACGAAGG 58.001 50.000 0.00 0.00 35.47 3.46
82 83 3.060363 GTCTTACATGCGGTTACACGAAG 59.940 47.826 0.00 0.00 35.47 3.79
83 84 2.988493 GTCTTACATGCGGTTACACGAA 59.012 45.455 0.00 0.00 35.47 3.85
84 85 2.030096 TGTCTTACATGCGGTTACACGA 60.030 45.455 0.00 0.00 35.47 4.35
85 86 2.091588 GTGTCTTACATGCGGTTACACG 59.908 50.000 0.00 0.00 31.34 4.49
86 87 3.323243 AGTGTCTTACATGCGGTTACAC 58.677 45.455 9.62 9.62 37.00 2.90
87 88 3.581755 GAGTGTCTTACATGCGGTTACA 58.418 45.455 0.00 0.00 0.00 2.41
88 89 2.597305 CGAGTGTCTTACATGCGGTTAC 59.403 50.000 0.00 0.00 0.00 2.50
89 90 2.229543 ACGAGTGTCTTACATGCGGTTA 59.770 45.455 0.00 0.00 33.75 2.85
90 91 1.000506 ACGAGTGTCTTACATGCGGTT 59.999 47.619 0.00 0.00 33.75 4.44
91 92 0.601558 ACGAGTGTCTTACATGCGGT 59.398 50.000 0.00 0.00 33.75 5.68
92 93 0.992072 CACGAGTGTCTTACATGCGG 59.008 55.000 0.00 0.00 33.75 5.69
93 94 0.992072 CCACGAGTGTCTTACATGCG 59.008 55.000 2.36 0.00 34.96 4.73
94 95 1.993370 GTCCACGAGTGTCTTACATGC 59.007 52.381 2.36 0.00 0.00 4.06
95 96 2.251040 CGTCCACGAGTGTCTTACATG 58.749 52.381 2.36 0.00 43.02 3.21
96 97 1.201647 CCGTCCACGAGTGTCTTACAT 59.798 52.381 0.00 0.00 43.02 2.29
97 98 0.594602 CCGTCCACGAGTGTCTTACA 59.405 55.000 0.00 0.00 43.02 2.41
98 99 0.109412 CCCGTCCACGAGTGTCTTAC 60.109 60.000 0.00 0.00 43.02 2.34
99 100 1.870055 GCCCGTCCACGAGTGTCTTA 61.870 60.000 0.00 0.00 43.02 2.10
100 101 3.048602 CCCGTCCACGAGTGTCTT 58.951 61.111 0.00 0.00 43.02 3.01
101 102 3.681835 GCCCGTCCACGAGTGTCT 61.682 66.667 0.00 0.00 43.02 3.41
102 103 4.736896 GGCCCGTCCACGAGTGTC 62.737 72.222 0.00 0.00 43.02 3.67
104 105 4.742201 CAGGCCCGTCCACGAGTG 62.742 72.222 0.00 0.00 43.02 3.51
106 107 3.530910 AAACAGGCCCGTCCACGAG 62.531 63.158 0.00 0.00 43.02 4.18
107 108 2.999739 GAAAACAGGCCCGTCCACGA 63.000 60.000 0.00 0.00 43.02 4.35
108 109 2.593436 AAAACAGGCCCGTCCACG 60.593 61.111 0.00 0.00 37.29 4.94
109 110 2.265904 GGAAAACAGGCCCGTCCAC 61.266 63.158 0.00 0.00 37.29 4.02
110 111 2.114411 GGAAAACAGGCCCGTCCA 59.886 61.111 0.00 0.00 37.29 4.02
111 112 2.675423 GGGAAAACAGGCCCGTCC 60.675 66.667 0.00 0.00 34.00 4.79
112 113 2.675423 GGGGAAAACAGGCCCGTC 60.675 66.667 0.00 0.00 45.67 4.79
113 114 3.182996 AGGGGAAAACAGGCCCGT 61.183 61.111 0.00 0.00 45.67 5.28
114 115 2.361230 GAGGGGAAAACAGGCCCG 60.361 66.667 0.00 0.00 45.67 6.13
115 116 0.612174 GAAGAGGGGAAAACAGGCCC 60.612 60.000 0.00 0.00 43.91 5.80
116 117 0.405973 AGAAGAGGGGAAAACAGGCC 59.594 55.000 0.00 0.00 0.00 5.19
117 118 2.163509 GAAGAAGAGGGGAAAACAGGC 58.836 52.381 0.00 0.00 0.00 4.85
118 119 3.797559 AGAAGAAGAGGGGAAAACAGG 57.202 47.619 0.00 0.00 0.00 4.00
119 120 7.231519 ACATTAAAGAAGAAGAGGGGAAAACAG 59.768 37.037 0.00 0.00 0.00 3.16
120 121 7.066781 ACATTAAAGAAGAAGAGGGGAAAACA 58.933 34.615 0.00 0.00 0.00 2.83
121 122 7.526142 ACATTAAAGAAGAAGAGGGGAAAAC 57.474 36.000 0.00 0.00 0.00 2.43
156 157 8.761497 TCTTTTTCTCTAAGATACACACAAACG 58.239 33.333 0.00 0.00 0.00 3.60
169 170 9.535270 CGCAGATTAAGTTTCTTTTTCTCTAAG 57.465 33.333 0.00 0.00 0.00 2.18
170 171 8.504005 CCGCAGATTAAGTTTCTTTTTCTCTAA 58.496 33.333 0.00 0.00 0.00 2.10
172 173 6.568653 GCCGCAGATTAAGTTTCTTTTTCTCT 60.569 38.462 0.00 0.00 0.00 3.10
173 174 5.569441 GCCGCAGATTAAGTTTCTTTTTCTC 59.431 40.000 0.00 0.00 0.00 2.87
175 176 4.621460 GGCCGCAGATTAAGTTTCTTTTTC 59.379 41.667 0.00 0.00 0.00 2.29
176 177 4.280929 AGGCCGCAGATTAAGTTTCTTTTT 59.719 37.500 0.00 0.00 0.00 1.94
177 178 3.826729 AGGCCGCAGATTAAGTTTCTTTT 59.173 39.130 0.00 0.00 0.00 2.27
185 186 1.600957 CATGTGAGGCCGCAGATTAAG 59.399 52.381 16.71 2.25 36.09 1.85
195 196 1.527844 GGGATGCTCATGTGAGGCC 60.528 63.158 11.66 0.00 42.29 5.19
196 197 0.178998 ATGGGATGCTCATGTGAGGC 60.179 55.000 11.66 5.14 42.29 4.70
203 204 7.517320 TGTAAATTACAGTATGGGATGCTCAT 58.483 34.615 1.08 0.00 43.62 2.90
204 205 6.894682 TGTAAATTACAGTATGGGATGCTCA 58.105 36.000 1.08 0.00 43.62 4.26
226 227 5.527026 ATCCTCTCTTTTGAAATCCCTGT 57.473 39.130 0.00 0.00 0.00 4.00
242 243 7.226059 ACCATGGGTTTAGAAAATATCCTCT 57.774 36.000 18.09 0.00 27.29 3.69
243 244 7.898014 AACCATGGGTTTAGAAAATATCCTC 57.102 36.000 18.09 0.00 44.33 3.71
244 245 8.566109 ACTAACCATGGGTTTAGAAAATATCCT 58.434 33.333 22.62 1.37 44.33 3.24
245 246 8.762481 ACTAACCATGGGTTTAGAAAATATCC 57.238 34.615 22.62 0.00 44.33 2.59
255 257 4.902448 AGGCAAAAACTAACCATGGGTTTA 59.098 37.500 18.09 5.66 44.33 2.01
263 265 6.268847 ACATTTATGGAGGCAAAAACTAACCA 59.731 34.615 0.00 0.00 0.00 3.67
288 290 7.161404 GGAATACAATGTATCTGGTGCTGATA 58.839 38.462 6.34 0.00 0.00 2.15
303 305 1.873591 GCCCTGCTACGGAATACAATG 59.126 52.381 0.00 0.00 0.00 2.82
305 307 0.906066 TGCCCTGCTACGGAATACAA 59.094 50.000 0.00 0.00 0.00 2.41
309 311 1.271840 TTCCTGCCCTGCTACGGAAT 61.272 55.000 0.00 0.00 30.25 3.01
310 312 1.271840 ATTCCTGCCCTGCTACGGAA 61.272 55.000 0.00 0.00 35.76 4.30
327 329 6.069088 TGGTCCAAATAATCCTCACACCTATT 60.069 38.462 0.00 0.00 0.00 1.73
368 370 7.421030 ATGAGGCTCATATTTTCATCTGGAAGA 60.421 37.037 27.87 0.00 41.12 2.87
391 393 6.528537 AGCAATTAAGGCACACATAAATGA 57.471 33.333 4.90 0.00 0.00 2.57
394 396 7.661968 TGTAAAGCAATTAAGGCACACATAAA 58.338 30.769 4.90 0.00 0.00 1.40
415 417 9.554395 TCAAAGTTCACTCTCAAATACATGTAA 57.446 29.630 10.14 0.00 0.00 2.41
424 426 7.447374 TGTTCTTTCAAAGTTCACTCTCAAA 57.553 32.000 0.00 0.00 0.00 2.69
429 431 8.520835 ACTTTTTGTTCTTTCAAAGTTCACTC 57.479 30.769 0.00 0.00 36.29 3.51
444 446 5.344933 GCATAATCGGGTCAACTTTTTGTTC 59.655 40.000 0.00 0.00 36.63 3.18
452 455 2.119495 AGGAGCATAATCGGGTCAACT 58.881 47.619 0.00 0.00 34.56 3.16
461 464 5.226194 AGTCAGGAATCAGGAGCATAATC 57.774 43.478 0.00 0.00 0.00 1.75
475 496 5.717078 ATACGCGGAAATATAGTCAGGAA 57.283 39.130 12.47 0.00 0.00 3.36
477 498 4.625742 CCAATACGCGGAAATATAGTCAGG 59.374 45.833 12.47 0.00 0.00 3.86
513 534 0.622665 CAGGGGACAGCCATTCTTCT 59.377 55.000 0.00 0.00 35.15 2.85
536 557 4.518590 TGGAATGATCAAAAACTGAAGCGA 59.481 37.500 0.00 0.00 37.67 4.93
548 569 3.503363 GCTGACACTGTTGGAATGATCAA 59.497 43.478 0.00 0.00 0.00 2.57
611 632 3.921630 TGCTTGCATTTCGAACATGATTG 59.078 39.130 18.43 0.00 0.00 2.67
612 633 4.082625 TCTGCTTGCATTTCGAACATGATT 60.083 37.500 18.43 0.00 0.00 2.57
613 634 3.441222 TCTGCTTGCATTTCGAACATGAT 59.559 39.130 18.43 0.00 0.00 2.45
640 661 1.073216 ACGAGAAATGAGCGCGTCAG 61.073 55.000 8.43 0.37 37.18 3.51
952 973 1.586422 CTCTCTCTCTCCTCTGCTCG 58.414 60.000 0.00 0.00 0.00 5.03
956 977 3.470709 CTGTAGCTCTCTCTCTCCTCTG 58.529 54.545 0.00 0.00 0.00 3.35
1032 1054 2.431683 GCCTTGACAGCCTCCACA 59.568 61.111 0.00 0.00 0.00 4.17
1104 1126 3.370953 CCCATCAAGGAACCAAGGTAGAG 60.371 52.174 0.00 0.00 41.22 2.43
1132 1154 9.866936 GTTGTAAGTATCAAACAAAATACACGA 57.133 29.630 0.00 0.00 35.08 4.35
1144 1166 5.986741 TGCGTCAGAAGTTGTAAGTATCAAA 59.013 36.000 0.00 0.00 0.00 2.69
1146 1168 5.128992 TGCGTCAGAAGTTGTAAGTATCA 57.871 39.130 0.00 0.00 0.00 2.15
1151 1173 2.480037 TGCATGCGTCAGAAGTTGTAAG 59.520 45.455 14.09 0.00 0.00 2.34
1177 1201 2.416547 GCTGCGAGAGTAAAATGAGCAA 59.583 45.455 0.00 0.00 32.53 3.91
1674 1704 0.469331 ATGCAATGCTATGCCCAGCT 60.469 50.000 6.82 0.00 45.83 4.24
1679 1709 3.258872 TGGGAATTATGCAATGCTATGCC 59.741 43.478 6.82 5.48 45.83 4.40
1723 1753 4.097286 CACTGAACATGCATCATCATGGAA 59.903 41.667 10.51 0.00 46.02 3.53
1732 1762 2.164827 TGCCAATCACTGAACATGCATC 59.835 45.455 0.00 0.00 0.00 3.91
1742 1772 2.116736 AACGTGCGTGCCAATCACTG 62.117 55.000 0.00 0.00 43.46 3.66
1947 2000 2.546584 GGACTTTTACTCCGTGGTTCGT 60.547 50.000 0.00 0.00 37.94 3.85
1951 2004 0.319405 CGGGACTTTTACTCCGTGGT 59.681 55.000 0.00 0.00 37.92 4.16
1963 2016 2.703536 TGATATGTATGTGCCGGGACTT 59.296 45.455 27.28 22.62 0.00 3.01
1964 2017 2.300152 CTGATATGTATGTGCCGGGACT 59.700 50.000 27.28 14.68 0.00 3.85
1985 2038 3.314635 CCCAGTCTGCATCTTTAATCTGC 59.685 47.826 0.00 0.00 36.45 4.26
1987 2040 5.643421 ATCCCAGTCTGCATCTTTAATCT 57.357 39.130 0.00 0.00 0.00 2.40
1993 2050 3.118112 CAGGTTATCCCAGTCTGCATCTT 60.118 47.826 0.00 0.00 34.66 2.40
1997 2054 1.833630 CTCAGGTTATCCCAGTCTGCA 59.166 52.381 0.00 0.00 34.66 4.41
2011 2068 2.159085 GCTATTCGTGTTAGCCTCAGGT 60.159 50.000 0.00 0.00 36.82 4.00
2012 2069 2.159099 TGCTATTCGTGTTAGCCTCAGG 60.159 50.000 10.11 0.00 41.10 3.86
2013 2070 3.165058 TGCTATTCGTGTTAGCCTCAG 57.835 47.619 10.11 0.00 41.10 3.35
2014 2071 3.819564 ATGCTATTCGTGTTAGCCTCA 57.180 42.857 10.11 0.00 41.10 3.86
2015 2072 3.871594 ACAATGCTATTCGTGTTAGCCTC 59.128 43.478 10.11 0.00 41.10 4.70
2016 2073 3.623060 CACAATGCTATTCGTGTTAGCCT 59.377 43.478 10.11 0.78 41.10 4.58
2017 2074 3.788797 GCACAATGCTATTCGTGTTAGCC 60.789 47.826 10.11 0.00 41.10 3.93
2267 2341 5.104193 AGAGGAGGGTTAGATTAGACGTGTA 60.104 44.000 0.00 0.00 0.00 2.90
2278 2352 1.076192 GCGGGAGAGGAGGGTTAGA 60.076 63.158 0.00 0.00 0.00 2.10
2302 2376 3.736100 TGGAATTGCTGCGGTGCG 61.736 61.111 0.00 0.00 35.36 5.34
2303 2377 2.126346 GTGGAATTGCTGCGGTGC 60.126 61.111 0.00 0.00 0.00 5.01
2304 2378 2.176546 CGTGGAATTGCTGCGGTG 59.823 61.111 0.00 0.00 0.00 4.94
2305 2379 3.737172 GCGTGGAATTGCTGCGGT 61.737 61.111 13.77 0.00 0.00 5.68
2306 2380 4.817063 CGCGTGGAATTGCTGCGG 62.817 66.667 22.41 9.47 44.65 5.69
2714 2788 4.008933 GACCTCCTGCAGCACGGT 62.009 66.667 16.59 16.59 0.00 4.83
2722 2796 1.142748 CATGGACTCGACCTCCTGC 59.857 63.158 6.06 0.00 0.00 4.85
2785 2859 2.281208 TTGTTTGGTCGCGGGGAG 60.281 61.111 6.13 0.00 0.00 4.30
2806 2880 1.291272 GTAACCTTGACCGCTCCGT 59.709 57.895 0.00 0.00 0.00 4.69
2849 2924 2.588034 GCTGGCCCGTTCCGATAC 60.588 66.667 0.00 0.00 0.00 2.24
2921 2996 1.081242 AAGCGCCGCAGAACAATTG 60.081 52.632 13.36 3.24 0.00 2.32
2928 3003 2.359850 AAATCCAAGCGCCGCAGA 60.360 55.556 13.36 5.26 0.00 4.26
2936 3011 1.734117 GCCACGTGCAAATCCAAGC 60.734 57.895 10.91 0.39 40.77 4.01
2953 3028 1.577616 CAACGTCATTAGCACGCGC 60.578 57.895 5.73 0.00 41.10 6.86
2955 3030 0.519175 CAGCAACGTCATTAGCACGC 60.519 55.000 0.00 0.00 41.10 5.34
2967 3042 0.101399 AGAGGATAGACGCAGCAACG 59.899 55.000 0.00 0.00 39.50 4.10
2976 3051 6.991938 AGAATAACATGCTCAGAGGATAGAC 58.008 40.000 3.75 0.00 0.00 2.59
2980 3055 5.883685 TGAGAATAACATGCTCAGAGGAT 57.116 39.130 0.00 0.00 34.02 3.24
2983 3058 5.816258 ACACATGAGAATAACATGCTCAGAG 59.184 40.000 0.00 0.00 41.45 3.35
2999 3074 3.733443 TCCGTCCATATGACACATGAG 57.267 47.619 3.65 0.00 44.71 2.90
3016 3095 2.394708 CTACAGATTACCGCACATCCG 58.605 52.381 0.00 0.00 0.00 4.18
3017 3096 2.102588 ACCTACAGATTACCGCACATCC 59.897 50.000 0.00 0.00 0.00 3.51
3018 3097 3.454371 ACCTACAGATTACCGCACATC 57.546 47.619 0.00 0.00 0.00 3.06
3019 3098 3.321111 CCTACCTACAGATTACCGCACAT 59.679 47.826 0.00 0.00 0.00 3.21
3033 3112 3.562505 CGATACGAACATGCCTACCTAC 58.437 50.000 0.00 0.00 0.00 3.18
3039 3118 1.480954 AGTTCCGATACGAACATGCCT 59.519 47.619 4.46 0.00 43.82 4.75
3119 3198 4.562143 CCCATATGATCTCTGACATTCGCA 60.562 45.833 3.65 0.00 0.00 5.10
3127 3206 1.895798 GCGACCCCATATGATCTCTGA 59.104 52.381 3.65 0.00 0.00 3.27
3250 4436 8.793592 GTGGTTTTAGACAATCTGTTTTAGGAT 58.206 33.333 0.00 0.00 0.00 3.24
3292 4479 4.040755 TGAAGGAAGAGAAATAGGAGGGG 58.959 47.826 0.00 0.00 0.00 4.79
3293 4480 4.719273 ACTGAAGGAAGAGAAATAGGAGGG 59.281 45.833 0.00 0.00 0.00 4.30
3294 4481 5.669477 CACTGAAGGAAGAGAAATAGGAGG 58.331 45.833 0.00 0.00 0.00 4.30
3295 4482 5.115480 GCACTGAAGGAAGAGAAATAGGAG 58.885 45.833 0.00 0.00 0.00 3.69
3325 4515 6.818644 TGATGCAATAGGAGTTCAAGTAAGTC 59.181 38.462 0.00 0.00 36.88 3.01
3331 4521 4.183865 TCGTGATGCAATAGGAGTTCAAG 58.816 43.478 0.00 0.00 0.00 3.02
3378 4569 7.427895 TGAAATGTTGTTATTCGATTGTATGCG 59.572 33.333 0.00 0.00 0.00 4.73
3388 4579 7.304735 TCATGGACTTGAAATGTTGTTATTCG 58.695 34.615 0.00 0.00 0.00 3.34
3389 4580 9.643693 AATCATGGACTTGAAATGTTGTTATTC 57.356 29.630 0.00 0.00 0.00 1.75
3390 4581 9.643693 GAATCATGGACTTGAAATGTTGTTATT 57.356 29.630 0.00 0.00 0.00 1.40
3391 4582 8.253113 GGAATCATGGACTTGAAATGTTGTTAT 58.747 33.333 0.00 0.00 0.00 1.89
3392 4583 7.232330 TGGAATCATGGACTTGAAATGTTGTTA 59.768 33.333 0.00 0.00 0.00 2.41
3395 4586 6.028146 TGGAATCATGGACTTGAAATGTTG 57.972 37.500 0.00 0.00 0.00 3.33
3412 4603 9.307121 CGATTCTATGTTATACTGGATGGAATC 57.693 37.037 0.00 0.00 44.55 2.52
3438 4629 6.436843 ACCTACATCATTCGGTTCATTTTC 57.563 37.500 0.00 0.00 0.00 2.29
3527 4763 3.805207 AGACTAAGCGGAACAACTTTGT 58.195 40.909 0.00 0.00 44.72 2.83
3673 4929 8.391106 GCTTGTTCATGTACCTACTAGATTTTG 58.609 37.037 0.00 0.00 0.00 2.44
3683 4939 2.289133 TGTGCGCTTGTTCATGTACCTA 60.289 45.455 9.73 0.00 0.00 3.08
3685 4941 0.871722 TGTGCGCTTGTTCATGTACC 59.128 50.000 9.73 0.00 0.00 3.34
3698 4954 0.373370 TATTGCAAGTCGATGTGCGC 59.627 50.000 15.80 0.00 43.93 6.09
3703 4959 4.898829 TTTGGGATATTGCAAGTCGATG 57.101 40.909 4.94 0.00 0.00 3.84
3705 4961 3.066621 GCATTTGGGATATTGCAAGTCGA 59.933 43.478 4.94 0.00 35.22 4.20
3730 4986 2.115291 GCCGGGAAGGATGTTGAGC 61.115 63.158 2.18 0.00 45.00 4.26
3745 5001 1.879380 TCAACAAGGTTCAATCAGCCG 59.121 47.619 0.00 0.00 0.00 5.52
3774 5030 4.087182 TCTAACCCACAAGACGAGAAGAT 58.913 43.478 0.00 0.00 0.00 2.40
3782 5038 7.139392 GTGAAGAAATTTCTAACCCACAAGAC 58.861 38.462 20.76 7.31 36.28 3.01
3813 5069 3.461458 TGGCATATATCCCTTGTGGTTCA 59.539 43.478 0.00 0.00 34.77 3.18
3839 5095 9.886132 CAATACCTAGTGGACTACTATTTTTGT 57.114 33.333 0.00 0.00 40.94 2.83
3844 5100 7.287235 GTCACCAATACCTAGTGGACTACTATT 59.713 40.741 5.82 0.00 43.74 1.73
3858 5114 5.975988 ATAGTCAATGGTCACCAATACCT 57.024 39.130 0.00 0.00 36.95 3.08


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

AutoCloner maintained by Alex Coulton.