Multiple sequence alignment - TraesCS5B01G504600

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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 TraesCS5B01G504600 chr5B 100.000 2399 0 0 1 2399 670695685 670693287 0.000000e+00 4431.0
1 TraesCS5B01G504600 chr5B 83.543 796 77 28 611 1368 670717194 670716415 0.000000e+00 695.0
2 TraesCS5B01G504600 chr5B 82.155 594 57 29 839 1420 670798423 670797867 4.670000e-127 464.0
3 TraesCS5B01G504600 chr5B 77.778 387 58 18 114 494 670710419 670710055 1.870000e-51 213.0
4 TraesCS5B01G504600 chr5B 87.288 118 11 3 1299 1415 670707696 670707582 5.380000e-27 132.0
5 TraesCS5B01G504600 chr5B 82.474 97 11 5 615 708 670802047 670801954 1.980000e-11 80.5
6 TraesCS5B01G504600 chr5D 86.126 1629 127 37 440 2018 531412686 531411107 0.000000e+00 1664.0
7 TraesCS5B01G504600 chr5D 82.658 963 77 43 505 1415 531445615 531444691 0.000000e+00 771.0
8 TraesCS5B01G504600 chr5D 80.023 871 95 49 589 1412 531476907 531476069 2.680000e-159 571.0
9 TraesCS5B01G504600 chr5D 79.714 838 97 42 611 1415 531463042 531462245 2.710000e-149 538.0
10 TraesCS5B01G504600 chr5D 84.584 493 29 14 1912 2390 531411102 531410643 1.690000e-121 446.0
11 TraesCS5B01G504600 chr5D 80.238 673 51 31 120 729 531419088 531418435 4.740000e-117 431.0
12 TraesCS5B01G504600 chr5D 82.834 501 23 22 739 1188 531416633 531416145 8.040000e-105 390.0
13 TraesCS5B01G504600 chr5D 83.146 356 25 14 115 436 531413080 531412726 2.330000e-75 292.0
14 TraesCS5B01G504600 chr5D 93.478 46 1 2 393 436 531477070 531477025 1.540000e-07 67.6
15 TraesCS5B01G504600 chr4A 86.212 1349 79 47 467 1748 640999658 641000966 0.000000e+00 1362.0
16 TraesCS5B01G504600 chr4A 82.029 690 77 26 713 1368 640944579 640945255 5.830000e-151 544.0
17 TraesCS5B01G504600 chr4A 82.862 601 45 25 1825 2399 641002465 641003033 9.970000e-134 486.0
18 TraesCS5B01G504600 chr4A 78.495 837 101 52 617 1412 640916106 640916904 2.160000e-130 475.0
19 TraesCS5B01G504600 chr4A 81.622 185 23 9 505 686 640941878 640942054 2.490000e-30 143.0
20 TraesCS5B01G504600 chr4A 88.158 76 9 0 436 511 640903865 640903940 9.130000e-15 91.6
21 TraesCS5B01G504600 chr4A 97.222 36 1 0 625 660 640921631 640921666 7.160000e-06 62.1


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 TraesCS5B01G504600 chr5B 670693287 670695685 2398 True 4431.00 4431 100.0000 1 2399 1 chr5B.!!$R1 2398
1 TraesCS5B01G504600 chr5B 670716415 670717194 779 True 695.00 695 83.5430 611 1368 1 chr5B.!!$R2 757
2 TraesCS5B01G504600 chr5B 670797867 670802047 4180 True 272.25 464 82.3145 615 1420 2 chr5B.!!$R4 805
3 TraesCS5B01G504600 chr5D 531444691 531445615 924 True 771.00 771 82.6580 505 1415 1 chr5D.!!$R1 910
4 TraesCS5B01G504600 chr5D 531410643 531419088 8445 True 644.60 1664 83.3856 115 2390 5 chr5D.!!$R3 2275
5 TraesCS5B01G504600 chr5D 531462245 531463042 797 True 538.00 538 79.7140 611 1415 1 chr5D.!!$R2 804
6 TraesCS5B01G504600 chr5D 531476069 531477070 1001 True 319.30 571 86.7505 393 1412 2 chr5D.!!$R4 1019
7 TraesCS5B01G504600 chr4A 640999658 641003033 3375 False 924.00 1362 84.5370 467 2399 2 chr4A.!!$F5 1932
8 TraesCS5B01G504600 chr4A 640916106 640916904 798 False 475.00 475 78.4950 617 1412 1 chr4A.!!$F2 795
9 TraesCS5B01G504600 chr4A 640941878 640945255 3377 False 343.50 544 81.8255 505 1368 2 chr4A.!!$F4 863

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
93 94 0.035056 CCAATGGCGTTTCCTCCTCT 60.035 55.0 0.0 0.0 35.26 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 14910 0.167908 CACACACACACACACACACC 59.832 55.0 0.0 0.0 0.0 4.16 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
19 20 1.382914 ACCCAGGGCTTATGTTTCCT 58.617 50.000 4.91 0.00 0.00 3.36
20 21 1.716503 ACCCAGGGCTTATGTTTCCTT 59.283 47.619 4.91 0.00 0.00 3.36
21 22 2.111792 ACCCAGGGCTTATGTTTCCTTT 59.888 45.455 4.91 0.00 0.00 3.11
22 23 3.173151 CCCAGGGCTTATGTTTCCTTTT 58.827 45.455 0.00 0.00 0.00 2.27
23 24 4.202738 ACCCAGGGCTTATGTTTCCTTTTA 60.203 41.667 4.91 0.00 0.00 1.52
24 25 4.775253 CCCAGGGCTTATGTTTCCTTTTAA 59.225 41.667 0.00 0.00 0.00 1.52
25 26 5.247337 CCCAGGGCTTATGTTTCCTTTTAAA 59.753 40.000 0.00 0.00 0.00 1.52
26 27 6.239743 CCCAGGGCTTATGTTTCCTTTTAAAA 60.240 38.462 0.00 0.00 0.00 1.52
27 28 6.873605 CCAGGGCTTATGTTTCCTTTTAAAAG 59.126 38.462 19.19 19.19 35.79 2.27
28 29 7.256154 CCAGGGCTTATGTTTCCTTTTAAAAGA 60.256 37.037 26.11 11.62 38.28 2.52
29 30 8.147704 CAGGGCTTATGTTTCCTTTTAAAAGAA 58.852 33.333 26.11 16.06 38.28 2.52
30 31 8.367911 AGGGCTTATGTTTCCTTTTAAAAGAAG 58.632 33.333 26.11 19.40 38.28 2.85
31 32 8.364894 GGGCTTATGTTTCCTTTTAAAAGAAGA 58.635 33.333 26.11 14.47 38.28 2.87
32 33 9.758651 GGCTTATGTTTCCTTTTAAAAGAAGAA 57.241 29.630 26.11 18.75 38.28 2.52
40 41 9.783256 TTTCCTTTTAAAAGAAGAAGAAGAACG 57.217 29.630 26.11 7.42 38.28 3.95
41 42 8.502105 TCCTTTTAAAAGAAGAAGAAGAACGT 57.498 30.769 26.11 0.00 38.28 3.99
42 43 8.610035 TCCTTTTAAAAGAAGAAGAAGAACGTC 58.390 33.333 26.11 0.00 38.28 4.34
43 44 7.583040 CCTTTTAAAAGAAGAAGAAGAACGTCG 59.417 37.037 26.11 2.70 38.28 5.12
44 45 7.529880 TTTAAAAGAAGAAGAAGAACGTCGT 57.470 32.000 0.00 0.00 32.54 4.34
45 46 8.633075 TTTAAAAGAAGAAGAAGAACGTCGTA 57.367 30.769 0.00 0.00 32.54 3.43
46 47 6.507890 AAAAGAAGAAGAAGAACGTCGTAC 57.492 37.500 0.00 0.00 32.54 3.67
48 49 3.496130 AGAAGAAGAAGAACGTCGTACGA 59.504 43.478 15.28 15.28 46.05 3.43
49 50 3.885484 AGAAGAAGAACGTCGTACGAA 57.115 42.857 21.39 0.92 46.05 3.85
50 51 3.808095 AGAAGAAGAACGTCGTACGAAG 58.192 45.455 26.18 26.18 46.05 3.79
51 52 1.961079 AGAAGAACGTCGTACGAAGC 58.039 50.000 27.40 14.43 46.05 3.86
52 53 0.980525 GAAGAACGTCGTACGAAGCC 59.019 55.000 27.40 19.81 46.05 4.35
53 54 0.311790 AAGAACGTCGTACGAAGCCA 59.688 50.000 27.40 0.00 46.05 4.75
54 55 0.386478 AGAACGTCGTACGAAGCCAC 60.386 55.000 27.40 18.84 46.05 5.01
55 56 0.661187 GAACGTCGTACGAAGCCACA 60.661 55.000 27.40 0.00 46.05 4.17
56 57 0.662374 AACGTCGTACGAAGCCACAG 60.662 55.000 27.40 12.30 46.05 3.66
57 58 2.434134 CGTCGTACGAAGCCACAGC 61.434 63.158 21.39 3.75 46.05 4.40
58 59 2.797866 CGTCGTACGAAGCCACAGCT 62.798 60.000 21.39 0.00 46.05 4.24
68 69 3.239861 GCCACAGCTTAGCTTGTCT 57.760 52.632 3.00 0.00 36.40 3.41
69 70 1.082690 GCCACAGCTTAGCTTGTCTC 58.917 55.000 3.00 0.00 36.40 3.36
70 71 1.731720 CCACAGCTTAGCTTGTCTCC 58.268 55.000 3.00 0.00 36.40 3.71
71 72 1.002430 CCACAGCTTAGCTTGTCTCCA 59.998 52.381 3.00 0.00 36.40 3.86
72 73 2.072298 CACAGCTTAGCTTGTCTCCAC 58.928 52.381 3.00 0.00 36.40 4.02
73 74 1.694150 ACAGCTTAGCTTGTCTCCACA 59.306 47.619 3.00 0.00 36.40 4.17
74 75 2.072298 CAGCTTAGCTTGTCTCCACAC 58.928 52.381 3.00 0.00 36.40 3.82
75 76 1.002544 AGCTTAGCTTGTCTCCACACC 59.997 52.381 0.00 0.00 33.89 4.16
76 77 1.270839 GCTTAGCTTGTCTCCACACCA 60.271 52.381 0.00 0.00 29.76 4.17
77 78 2.810400 GCTTAGCTTGTCTCCACACCAA 60.810 50.000 0.00 0.00 29.76 3.67
78 79 3.679389 CTTAGCTTGTCTCCACACCAAT 58.321 45.455 0.00 0.00 29.76 3.16
79 80 1.901591 AGCTTGTCTCCACACCAATG 58.098 50.000 0.00 0.00 29.76 2.82
80 81 0.883833 GCTTGTCTCCACACCAATGG 59.116 55.000 0.00 0.00 41.57 3.16
81 82 0.883833 CTTGTCTCCACACCAATGGC 59.116 55.000 0.00 0.00 39.85 4.40
82 83 0.888736 TTGTCTCCACACCAATGGCG 60.889 55.000 0.00 0.00 39.85 5.69
83 84 1.302511 GTCTCCACACCAATGGCGT 60.303 57.895 0.00 0.00 39.85 5.68
84 85 0.889186 GTCTCCACACCAATGGCGTT 60.889 55.000 0.00 0.00 39.85 4.84
85 86 0.179004 TCTCCACACCAATGGCGTTT 60.179 50.000 0.00 0.00 39.85 3.60
86 87 0.240945 CTCCACACCAATGGCGTTTC 59.759 55.000 0.00 0.00 39.85 2.78
87 88 1.175983 TCCACACCAATGGCGTTTCC 61.176 55.000 0.00 0.00 39.85 3.13
88 89 1.178534 CCACACCAATGGCGTTTCCT 61.179 55.000 0.00 0.00 35.26 3.36
89 90 0.240945 CACACCAATGGCGTTTCCTC 59.759 55.000 0.00 0.00 35.26 3.71
90 91 0.893727 ACACCAATGGCGTTTCCTCC 60.894 55.000 0.00 0.00 35.26 4.30
91 92 0.609131 CACCAATGGCGTTTCCTCCT 60.609 55.000 0.00 0.00 35.26 3.69
92 93 0.322546 ACCAATGGCGTTTCCTCCTC 60.323 55.000 0.00 0.00 35.26 3.71
93 94 0.035056 CCAATGGCGTTTCCTCCTCT 60.035 55.000 0.00 0.00 35.26 3.69
94 95 1.373570 CAATGGCGTTTCCTCCTCTC 58.626 55.000 0.00 0.00 35.26 3.20
95 96 0.108138 AATGGCGTTTCCTCCTCTCG 60.108 55.000 0.00 0.00 35.26 4.04
96 97 1.258445 ATGGCGTTTCCTCCTCTCGT 61.258 55.000 0.00 0.00 35.26 4.18
97 98 1.292541 GGCGTTTCCTCCTCTCGTT 59.707 57.895 0.00 0.00 0.00 3.85
98 99 1.014564 GGCGTTTCCTCCTCTCGTTG 61.015 60.000 0.00 0.00 0.00 4.10
99 100 0.319641 GCGTTTCCTCCTCTCGTTGT 60.320 55.000 0.00 0.00 0.00 3.32
100 101 1.068055 GCGTTTCCTCCTCTCGTTGTA 60.068 52.381 0.00 0.00 0.00 2.41
101 102 2.593257 CGTTTCCTCCTCTCGTTGTAC 58.407 52.381 0.00 0.00 0.00 2.90
102 103 2.228343 CGTTTCCTCCTCTCGTTGTACT 59.772 50.000 0.00 0.00 0.00 2.73
103 104 3.438087 CGTTTCCTCCTCTCGTTGTACTA 59.562 47.826 0.00 0.00 0.00 1.82
104 105 4.671250 CGTTTCCTCCTCTCGTTGTACTAC 60.671 50.000 0.00 0.00 0.00 2.73
105 106 3.996921 TCCTCCTCTCGTTGTACTACT 57.003 47.619 5.91 0.00 0.00 2.57
106 107 3.871485 TCCTCCTCTCGTTGTACTACTC 58.129 50.000 5.91 0.00 0.00 2.59
107 108 3.262660 TCCTCCTCTCGTTGTACTACTCA 59.737 47.826 5.91 0.00 0.00 3.41
108 109 4.080469 TCCTCCTCTCGTTGTACTACTCAT 60.080 45.833 5.91 0.00 0.00 2.90
109 110 4.273969 CCTCCTCTCGTTGTACTACTCATC 59.726 50.000 5.91 0.00 0.00 2.92
110 111 4.840271 TCCTCTCGTTGTACTACTCATCA 58.160 43.478 5.91 0.00 0.00 3.07
111 112 4.876679 TCCTCTCGTTGTACTACTCATCAG 59.123 45.833 5.91 0.00 0.00 2.90
112 113 4.636648 CCTCTCGTTGTACTACTCATCAGT 59.363 45.833 5.91 0.00 36.55 3.41
113 114 5.816258 CCTCTCGTTGTACTACTCATCAGTA 59.184 44.000 5.91 0.00 33.62 2.74
140 141 4.398044 CCTAAACCTGCGTTCCATTTATGT 59.602 41.667 0.00 0.00 0.00 2.29
145 146 1.740585 TGCGTTCCATTTATGTTCGGG 59.259 47.619 0.00 0.00 0.00 5.14
188 193 3.129502 AGCATGCATTCACGCGCT 61.130 55.556 21.98 0.00 36.37 5.92
191 196 1.368493 CATGCATTCACGCGCTAGC 60.368 57.895 5.73 4.06 40.74 3.42
192 197 1.522355 ATGCATTCACGCGCTAGCT 60.522 52.632 13.93 0.00 42.32 3.32
198 203 2.125912 CACGCGCTAGCTTCAGGT 60.126 61.111 13.93 0.24 42.32 4.00
201 206 0.245539 ACGCGCTAGCTTCAGGTTTA 59.754 50.000 13.93 0.00 42.32 2.01
203 208 1.933853 CGCGCTAGCTTCAGGTTTAAT 59.066 47.619 13.93 0.00 42.32 1.40
204 209 2.285834 CGCGCTAGCTTCAGGTTTAATG 60.286 50.000 13.93 0.00 42.32 1.90
206 211 2.285834 CGCTAGCTTCAGGTTTAATGCG 60.286 50.000 13.93 0.00 0.00 4.73
213 218 1.950216 TCAGGTTTAATGCGTGCACAA 59.050 42.857 18.64 4.45 0.00 3.33
214 219 2.031245 TCAGGTTTAATGCGTGCACAAG 60.031 45.455 18.64 2.05 0.00 3.16
216 221 1.668628 GGTTTAATGCGTGCACAAGGG 60.669 52.381 18.64 0.81 0.00 3.95
233 238 6.386654 CACAAGGGCGAAAACAGTAAATAAT 58.613 36.000 0.00 0.00 0.00 1.28
248 253 9.777297 ACAGTAAATAATTGCAAAAAGGTCAAT 57.223 25.926 1.71 0.00 32.36 2.57
279 289 1.079503 GATCCAACGGTCACAAGAGC 58.920 55.000 0.00 0.00 38.87 4.09
309 319 3.680156 CCAAATGGGTCACCGGTG 58.320 61.111 29.26 29.26 40.75 4.94
310 320 1.228429 CCAAATGGGTCACCGGTGT 60.228 57.895 32.74 11.90 40.75 4.16
311 321 0.037017 CCAAATGGGTCACCGGTGTA 59.963 55.000 32.74 17.60 40.75 2.90
313 323 0.766131 AAATGGGTCACCGGTGTACA 59.234 50.000 32.74 27.27 40.75 2.90
314 324 0.988832 AATGGGTCACCGGTGTACAT 59.011 50.000 32.74 28.09 40.75 2.29
321 354 1.003839 ACCGGTGTACATGGCACTG 60.004 57.895 6.12 18.78 41.51 3.66
357 390 4.862574 GCAATAGTTTTTGGGACGGAAATC 59.137 41.667 0.00 0.00 0.00 2.17
436 471 2.223923 GGAAGTGTCGATCCATCCTCAG 60.224 54.545 0.00 0.00 35.71 3.35
463 536 8.255394 CCAATTCCTTGGTGAAAATGATTAAC 57.745 34.615 0.00 0.00 45.90 2.01
545 625 0.790207 CACCACACACGTAGACATGC 59.210 55.000 0.00 0.00 0.00 4.06
567 647 3.618351 CAATTCTCCTCAAGCACCAGAT 58.382 45.455 0.00 0.00 0.00 2.90
604 687 6.164176 ACTACTACTACTGAAACAATGTGGC 58.836 40.000 0.00 0.00 0.00 5.01
608 691 3.815401 ACTACTGAAACAATGTGGCAGAC 59.185 43.478 18.43 0.00 0.00 3.51
609 692 2.936202 ACTGAAACAATGTGGCAGACT 58.064 42.857 18.43 0.00 0.00 3.24
613 699 4.065088 TGAAACAATGTGGCAGACTCTAC 58.935 43.478 0.00 0.00 0.00 2.59
660 746 7.014134 TGTCATTTTCCAATCAAGCAGAAAGTA 59.986 33.333 0.00 0.00 30.49 2.24
949 12111 0.846693 ACCACCTTCTTGCTTCCACT 59.153 50.000 0.00 0.00 0.00 4.00
979 12163 2.415426 GGAGCCGAGCAGAGCTAC 59.585 66.667 0.00 0.00 39.88 3.58
994 12204 2.237392 GAGCTACCCAAGAACCTGTCAT 59.763 50.000 0.00 0.00 0.00 3.06
1040 12269 4.200283 GGCGACGGCAGGAGAGAG 62.200 72.222 17.49 0.00 42.47 3.20
1399 12649 1.174783 GTCCGTCTGCTTCTGGTAGA 58.825 55.000 0.00 0.00 34.37 2.59
1467 12721 1.734465 CTGGCTTCCAAGTTAAGCTCG 59.266 52.381 9.63 0.00 46.81 5.03
1481 12735 3.887621 AAGCTCGTGATTGCTTAGGTA 57.112 42.857 0.00 0.00 46.19 3.08
1485 12739 4.631813 AGCTCGTGATTGCTTAGGTAAAAG 59.368 41.667 0.00 0.00 35.86 2.27
1507 12761 0.179056 TTAGCCGGTGAATGCTAGCC 60.179 55.000 13.29 0.00 40.85 3.93
1628 12891 3.153919 GTTGCTCAAGTGGGATTGGTTA 58.846 45.455 0.00 0.00 0.00 2.85
1692 12955 6.761714 ACTCCGAATGAATTAACTGTGTATCC 59.238 38.462 0.00 0.00 0.00 2.59
1700 12963 9.685276 ATGAATTAACTGTGTATCCATCTGAAA 57.315 29.630 0.00 0.00 0.00 2.69
1712 12975 8.981659 TGTATCCATCTGAAATCTTCTCTGTTA 58.018 33.333 0.00 0.00 0.00 2.41
1713 12976 9.995003 GTATCCATCTGAAATCTTCTCTGTTAT 57.005 33.333 0.00 0.00 0.00 1.89
1715 12978 8.728337 TCCATCTGAAATCTTCTCTGTTATTG 57.272 34.615 0.00 0.00 0.00 1.90
1716 12979 7.281774 TCCATCTGAAATCTTCTCTGTTATTGC 59.718 37.037 0.00 0.00 0.00 3.56
1717 12980 7.282675 CCATCTGAAATCTTCTCTGTTATTGCT 59.717 37.037 0.00 0.00 0.00 3.91
1718 12981 7.606858 TCTGAAATCTTCTCTGTTATTGCTG 57.393 36.000 0.00 0.00 0.00 4.41
1719 12982 6.596888 TCTGAAATCTTCTCTGTTATTGCTGG 59.403 38.462 0.00 0.00 0.00 4.85
1720 12983 5.649395 TGAAATCTTCTCTGTTATTGCTGGG 59.351 40.000 0.00 0.00 0.00 4.45
1721 12984 3.634397 TCTTCTCTGTTATTGCTGGGG 57.366 47.619 0.00 0.00 0.00 4.96
1722 12985 2.912956 TCTTCTCTGTTATTGCTGGGGT 59.087 45.455 0.00 0.00 0.00 4.95
1723 12986 2.787473 TCTCTGTTATTGCTGGGGTG 57.213 50.000 0.00 0.00 0.00 4.61
1733 12996 1.980772 GCTGGGGTGCTTGCTTGAT 60.981 57.895 0.00 0.00 0.00 2.57
1740 13003 0.170561 GTGCTTGCTTGATGCCTCTG 59.829 55.000 0.00 0.00 42.00 3.35
1743 13006 2.015588 GCTTGCTTGATGCCTCTGCTA 61.016 52.381 8.37 2.11 42.00 3.49
1753 13016 5.994250 TGATGCCTCTGCTAATTTCTTACT 58.006 37.500 0.00 0.00 38.71 2.24
1754 13017 7.124573 TGATGCCTCTGCTAATTTCTTACTA 57.875 36.000 0.00 0.00 38.71 1.82
1755 13018 7.212976 TGATGCCTCTGCTAATTTCTTACTAG 58.787 38.462 0.00 0.00 38.71 2.57
1757 13020 5.129485 TGCCTCTGCTAATTTCTTACTAGCT 59.871 40.000 0.00 0.00 39.06 3.32
1758 13021 5.694458 GCCTCTGCTAATTTCTTACTAGCTC 59.306 44.000 0.00 0.00 39.06 4.09
1759 13022 6.220201 CCTCTGCTAATTTCTTACTAGCTCC 58.780 44.000 0.00 0.00 39.06 4.70
1760 13023 6.183360 CCTCTGCTAATTTCTTACTAGCTCCA 60.183 42.308 0.00 0.00 39.06 3.86
1761 13024 7.366847 TCTGCTAATTTCTTACTAGCTCCAT 57.633 36.000 0.00 0.00 39.06 3.41
1762 13025 8.478775 TCTGCTAATTTCTTACTAGCTCCATA 57.521 34.615 0.00 0.00 39.06 2.74
1763 13026 9.094578 TCTGCTAATTTCTTACTAGCTCCATAT 57.905 33.333 0.00 0.00 39.06 1.78
1764 13027 9.149225 CTGCTAATTTCTTACTAGCTCCATATG 57.851 37.037 0.00 0.00 39.06 1.78
1775 13038 7.136822 ACTAGCTCCATATGTGATTGGTAAA 57.863 36.000 1.24 0.00 34.48 2.01
1783 13046 8.902806 TCCATATGTGATTGGTAAATCTGAAAC 58.097 33.333 1.24 0.00 42.40 2.78
1786 13049 4.083003 TGTGATTGGTAAATCTGAAACCGC 60.083 41.667 0.63 0.00 42.40 5.68
1793 13056 2.100605 AATCTGAAACCGCCTCTGTC 57.899 50.000 0.00 0.00 0.00 3.51
1821 13084 0.232303 GGTGTTTGACTTGCGTCTCG 59.768 55.000 0.00 0.00 40.86 4.04
1833 14600 2.780094 CGTCTCGGCCTCTGCTCAT 61.780 63.158 0.00 0.00 37.74 2.90
1856 14623 9.699410 TCATTTTCTTACCTCCATATGTGATTT 57.301 29.630 1.24 0.00 0.00 2.17
1888 14655 7.763172 AGATAAAAGTGAAGAGAACATAGCG 57.237 36.000 0.00 0.00 0.00 4.26
1895 14662 4.691216 GTGAAGAGAACATAGCGGAAAACT 59.309 41.667 0.00 0.00 0.00 2.66
1924 14805 2.031807 AGTAGTAGTATCGTGCGTGCAG 59.968 50.000 0.00 0.00 0.00 4.41
1950 14831 3.054878 GCAGCAATTCAGTGAAACCAAG 58.945 45.455 10.14 1.92 37.80 3.61
1952 14833 2.053627 GCAATTCAGTGAAACCAAGCG 58.946 47.619 10.14 0.00 37.80 4.68
1961 14842 3.105937 GTGAAACCAAGCGACACTTTTC 58.894 45.455 0.00 0.00 36.04 2.29
1963 14844 3.380004 TGAAACCAAGCGACACTTTTCAT 59.620 39.130 0.00 0.00 36.04 2.57
1972 14853 3.248602 GCGACACTTTTCATCTGTCAAGT 59.751 43.478 0.00 0.00 35.06 3.16
2044 14925 1.428370 CCTCGGTGTGTGTGTGTGTG 61.428 60.000 0.00 0.00 0.00 3.82
2045 14926 0.739462 CTCGGTGTGTGTGTGTGTGT 60.739 55.000 0.00 0.00 0.00 3.72
2046 14927 1.016653 TCGGTGTGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
2047 14928 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
2048 14929 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2049 14930 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2050 14931 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2051 14932 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2052 14933 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2053 14934 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2054 14935 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
2086 14967 5.511386 AACAAGATGAGGTGGAGAAAGAT 57.489 39.130 0.00 0.00 0.00 2.40
2103 14984 1.349026 AGATGTGTGGTGTCTCCTTGG 59.651 52.381 0.00 0.00 37.07 3.61
2104 14985 1.347707 GATGTGTGGTGTCTCCTTGGA 59.652 52.381 0.00 0.00 37.07 3.53
2105 14986 0.468226 TGTGTGGTGTCTCCTTGGAC 59.532 55.000 0.00 0.00 37.07 4.02
2106 14987 0.759346 GTGTGGTGTCTCCTTGGACT 59.241 55.000 0.00 0.00 37.16 3.85
2109 14990 1.053835 TGGTGTCTCCTTGGACTGCA 61.054 55.000 0.00 0.00 37.16 4.41
2112 14993 1.131638 TGTCTCCTTGGACTGCAGTT 58.868 50.000 22.65 4.46 37.16 3.16
2114 14995 1.070758 GTCTCCTTGGACTGCAGTTCA 59.929 52.381 24.41 24.41 33.81 3.18
2115 14996 1.070758 TCTCCTTGGACTGCAGTTCAC 59.929 52.381 27.82 17.39 32.26 3.18
2116 14997 0.836606 TCCTTGGACTGCAGTTCACA 59.163 50.000 27.82 19.72 32.26 3.58
2117 14998 1.211703 TCCTTGGACTGCAGTTCACAA 59.788 47.619 27.82 24.63 32.26 3.33
2118 14999 2.158623 TCCTTGGACTGCAGTTCACAAT 60.159 45.455 27.82 0.00 32.26 2.71
2119 15000 2.624838 CCTTGGACTGCAGTTCACAATT 59.375 45.455 27.82 0.00 32.26 2.32
2180 15070 2.143925 GTCTCGGGTCAGTTTTGAAGG 58.856 52.381 0.00 0.00 34.49 3.46
2181 15071 1.071699 TCTCGGGTCAGTTTTGAAGGG 59.928 52.381 0.00 0.00 34.49 3.95
2182 15072 1.071699 CTCGGGTCAGTTTTGAAGGGA 59.928 52.381 0.00 0.00 34.49 4.20
2183 15073 1.491332 TCGGGTCAGTTTTGAAGGGAA 59.509 47.619 0.00 0.00 34.49 3.97
2184 15074 2.092321 TCGGGTCAGTTTTGAAGGGAAA 60.092 45.455 0.00 0.00 34.49 3.13
2185 15075 2.293399 CGGGTCAGTTTTGAAGGGAAAG 59.707 50.000 0.00 0.00 34.49 2.62
2238 15128 1.839424 GTGAACCAGCCCAGCTTTAT 58.161 50.000 0.00 0.00 36.40 1.40
2239 15129 2.171003 GTGAACCAGCCCAGCTTTATT 58.829 47.619 0.00 0.00 36.40 1.40
2240 15130 2.562738 GTGAACCAGCCCAGCTTTATTT 59.437 45.455 0.00 0.00 36.40 1.40
2241 15131 2.825532 TGAACCAGCCCAGCTTTATTTC 59.174 45.455 0.00 0.00 36.40 2.17
2242 15132 2.603075 ACCAGCCCAGCTTTATTTCA 57.397 45.000 0.00 0.00 36.40 2.69
2243 15133 2.888212 ACCAGCCCAGCTTTATTTCAA 58.112 42.857 0.00 0.00 36.40 2.69
2244 15134 3.444029 ACCAGCCCAGCTTTATTTCAAT 58.556 40.909 0.00 0.00 36.40 2.57
2340 15237 4.021192 AGCCTCTGTCTCTCTTTTCTCTTG 60.021 45.833 0.00 0.00 0.00 3.02
2347 15245 3.392616 TCTCTCTTTTCTCTTGGCCTGTT 59.607 43.478 3.32 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.382914 AGGAAACATAAGCCCTGGGT 58.617 50.000 15.56 0.00 0.00 4.51
1 2 2.532250 AAGGAAACATAAGCCCTGGG 57.468 50.000 8.86 8.86 0.00 4.45
2 3 5.993748 TTAAAAGGAAACATAAGCCCTGG 57.006 39.130 0.00 0.00 0.00 4.45
3 4 7.666623 TCTTTTAAAAGGAAACATAAGCCCTG 58.333 34.615 24.20 0.00 36.67 4.45
4 5 7.849322 TCTTTTAAAAGGAAACATAAGCCCT 57.151 32.000 24.20 0.00 36.67 5.19
5 6 8.364894 TCTTCTTTTAAAAGGAAACATAAGCCC 58.635 33.333 24.20 0.00 36.67 5.19
6 7 9.758651 TTCTTCTTTTAAAAGGAAACATAAGCC 57.241 29.630 24.20 0.00 36.67 4.35
14 15 9.783256 CGTTCTTCTTCTTCTTTTAAAAGGAAA 57.217 29.630 24.20 13.25 36.67 3.13
15 16 8.953313 ACGTTCTTCTTCTTCTTTTAAAAGGAA 58.047 29.630 24.20 18.96 36.67 3.36
16 17 8.502105 ACGTTCTTCTTCTTCTTTTAAAAGGA 57.498 30.769 24.20 17.02 36.67 3.36
17 18 7.583040 CGACGTTCTTCTTCTTCTTTTAAAAGG 59.417 37.037 24.20 11.85 36.67 3.11
18 19 8.114905 ACGACGTTCTTCTTCTTCTTTTAAAAG 58.885 33.333 19.91 19.91 37.36 2.27
19 20 7.967178 ACGACGTTCTTCTTCTTCTTTTAAAA 58.033 30.769 0.00 0.00 0.00 1.52
20 21 7.529880 ACGACGTTCTTCTTCTTCTTTTAAA 57.470 32.000 0.00 0.00 0.00 1.52
21 22 7.096885 CGTACGACGTTCTTCTTCTTCTTTTAA 60.097 37.037 10.44 0.00 36.74 1.52
22 23 6.358030 CGTACGACGTTCTTCTTCTTCTTTTA 59.642 38.462 10.44 0.00 36.74 1.52
23 24 5.172771 CGTACGACGTTCTTCTTCTTCTTTT 59.827 40.000 10.44 0.00 36.74 2.27
24 25 4.674211 CGTACGACGTTCTTCTTCTTCTTT 59.326 41.667 10.44 0.00 36.74 2.52
25 26 4.024556 TCGTACGACGTTCTTCTTCTTCTT 60.025 41.667 15.28 0.00 43.14 2.52
26 27 3.496130 TCGTACGACGTTCTTCTTCTTCT 59.504 43.478 15.28 0.00 43.14 2.85
27 28 3.803555 TCGTACGACGTTCTTCTTCTTC 58.196 45.455 15.28 0.00 43.14 2.87
28 29 3.885484 TCGTACGACGTTCTTCTTCTT 57.115 42.857 15.28 0.00 43.14 2.52
29 30 3.808095 CTTCGTACGACGTTCTTCTTCT 58.192 45.455 19.36 0.00 43.14 2.85
30 31 2.337936 GCTTCGTACGACGTTCTTCTTC 59.662 50.000 19.36 0.00 43.14 2.87
31 32 2.314122 GCTTCGTACGACGTTCTTCTT 58.686 47.619 19.36 0.00 43.14 2.52
32 33 1.400759 GGCTTCGTACGACGTTCTTCT 60.401 52.381 19.36 0.00 43.14 2.85
33 34 0.980525 GGCTTCGTACGACGTTCTTC 59.019 55.000 19.36 2.60 43.14 2.87
34 35 0.311790 TGGCTTCGTACGACGTTCTT 59.688 50.000 19.36 0.00 43.14 2.52
35 36 0.386478 GTGGCTTCGTACGACGTTCT 60.386 55.000 19.36 0.00 43.14 3.01
36 37 0.661187 TGTGGCTTCGTACGACGTTC 60.661 55.000 19.36 12.95 43.14 3.95
37 38 0.662374 CTGTGGCTTCGTACGACGTT 60.662 55.000 19.36 0.00 43.14 3.99
38 39 1.081641 CTGTGGCTTCGTACGACGT 60.082 57.895 19.36 5.52 43.14 4.34
39 40 2.434134 GCTGTGGCTTCGTACGACG 61.434 63.158 19.36 17.87 38.03 5.12
40 41 3.460144 GCTGTGGCTTCGTACGAC 58.540 61.111 19.36 7.46 35.22 4.34
50 51 1.082690 GAGACAAGCTAAGCTGTGGC 58.917 55.000 0.00 0.00 39.62 5.01
51 52 1.002430 TGGAGACAAGCTAAGCTGTGG 59.998 52.381 0.00 0.00 39.62 4.17
52 53 2.072298 GTGGAGACAAGCTAAGCTGTG 58.928 52.381 0.00 0.00 46.06 3.66
53 54 1.694150 TGTGGAGACAAGCTAAGCTGT 59.306 47.619 0.00 0.00 46.06 4.40
54 55 2.072298 GTGTGGAGACAAGCTAAGCTG 58.928 52.381 0.00 0.00 46.06 4.24
55 56 1.002544 GGTGTGGAGACAAGCTAAGCT 59.997 52.381 0.00 0.00 46.06 3.74
56 57 1.270839 TGGTGTGGAGACAAGCTAAGC 60.271 52.381 0.00 0.00 46.06 3.09
57 58 2.839486 TGGTGTGGAGACAAGCTAAG 57.161 50.000 0.00 0.00 46.06 2.18
58 59 3.411446 CATTGGTGTGGAGACAAGCTAA 58.589 45.455 0.00 0.00 46.06 3.09
59 60 2.290260 CCATTGGTGTGGAGACAAGCTA 60.290 50.000 0.00 0.00 46.06 3.32
60 61 1.546323 CCATTGGTGTGGAGACAAGCT 60.546 52.381 0.00 0.00 46.06 3.74
61 62 0.883833 CCATTGGTGTGGAGACAAGC 59.116 55.000 0.00 0.00 46.06 4.01
62 63 0.883833 GCCATTGGTGTGGAGACAAG 59.116 55.000 4.26 0.00 46.06 3.16
63 64 0.888736 CGCCATTGGTGTGGAGACAA 60.889 55.000 8.14 0.00 46.06 3.18
64 65 1.302431 CGCCATTGGTGTGGAGACA 60.302 57.895 8.14 0.00 41.02 3.41
65 66 0.889186 AACGCCATTGGTGTGGAGAC 60.889 55.000 22.06 0.00 46.56 3.36
66 67 0.179004 AAACGCCATTGGTGTGGAGA 60.179 50.000 22.06 0.00 46.56 3.71
67 68 0.240945 GAAACGCCATTGGTGTGGAG 59.759 55.000 22.06 0.00 46.56 3.86
68 69 1.175983 GGAAACGCCATTGGTGTGGA 61.176 55.000 22.06 0.00 46.56 4.02
69 70 1.178534 AGGAAACGCCATTGGTGTGG 61.179 55.000 22.06 3.44 46.56 4.17
70 71 0.240945 GAGGAAACGCCATTGGTGTG 59.759 55.000 22.06 6.43 46.56 3.82
80 81 0.319641 ACAACGAGAGGAGGAAACGC 60.320 55.000 0.00 0.00 0.00 4.84
81 82 2.228343 AGTACAACGAGAGGAGGAAACG 59.772 50.000 0.00 0.00 0.00 3.60
82 83 3.938289 AGTACAACGAGAGGAGGAAAC 57.062 47.619 0.00 0.00 0.00 2.78
83 84 4.660168 AGTAGTACAACGAGAGGAGGAAA 58.340 43.478 2.52 0.00 0.00 3.13
84 85 4.260170 GAGTAGTACAACGAGAGGAGGAA 58.740 47.826 2.52 0.00 0.00 3.36
85 86 3.262660 TGAGTAGTACAACGAGAGGAGGA 59.737 47.826 2.52 0.00 0.00 3.71
86 87 3.607741 TGAGTAGTACAACGAGAGGAGG 58.392 50.000 2.52 0.00 0.00 4.30
87 88 4.876679 TGATGAGTAGTACAACGAGAGGAG 59.123 45.833 2.52 0.00 0.00 3.69
88 89 4.840271 TGATGAGTAGTACAACGAGAGGA 58.160 43.478 2.52 0.00 0.00 3.71
89 90 4.636648 ACTGATGAGTAGTACAACGAGAGG 59.363 45.833 2.52 0.00 0.00 3.69
90 91 5.804692 ACTGATGAGTAGTACAACGAGAG 57.195 43.478 2.52 0.00 0.00 3.20
91 92 6.905544 CTACTGATGAGTAGTACAACGAGA 57.094 41.667 10.89 0.00 44.76 4.04
92 93 7.676807 GGTTCTACTGATGAGTAGTACAACGAG 60.677 44.444 23.43 0.14 46.96 4.18
93 94 6.093219 GGTTCTACTGATGAGTAGTACAACGA 59.907 42.308 23.43 2.23 46.96 3.85
94 95 6.093771 AGGTTCTACTGATGAGTAGTACAACG 59.906 42.308 23.43 0.09 46.96 4.10
95 96 7.393841 AGGTTCTACTGATGAGTAGTACAAC 57.606 40.000 23.43 17.49 46.96 3.32
96 97 9.524496 TTTAGGTTCTACTGATGAGTAGTACAA 57.476 33.333 23.43 12.16 46.96 2.41
97 98 8.954350 GTTTAGGTTCTACTGATGAGTAGTACA 58.046 37.037 23.43 7.83 46.96 2.90
102 103 6.127423 GCAGGTTTAGGTTCTACTGATGAGTA 60.127 42.308 0.00 0.00 33.21 2.59
103 104 5.337652 GCAGGTTTAGGTTCTACTGATGAGT 60.338 44.000 0.00 0.00 36.07 3.41
104 105 5.112686 GCAGGTTTAGGTTCTACTGATGAG 58.887 45.833 0.00 0.00 0.00 2.90
105 106 4.381612 CGCAGGTTTAGGTTCTACTGATGA 60.382 45.833 0.00 0.00 0.00 2.92
106 107 3.865745 CGCAGGTTTAGGTTCTACTGATG 59.134 47.826 0.00 0.00 0.00 3.07
107 108 3.514309 ACGCAGGTTTAGGTTCTACTGAT 59.486 43.478 0.00 0.00 0.00 2.90
108 109 2.895404 ACGCAGGTTTAGGTTCTACTGA 59.105 45.455 0.00 0.00 0.00 3.41
109 110 3.314541 ACGCAGGTTTAGGTTCTACTG 57.685 47.619 0.00 0.00 0.00 2.74
110 111 3.306571 GGAACGCAGGTTTAGGTTCTACT 60.307 47.826 3.21 0.00 38.94 2.57
111 112 2.998670 GGAACGCAGGTTTAGGTTCTAC 59.001 50.000 3.21 0.00 38.94 2.59
112 113 2.633967 TGGAACGCAGGTTTAGGTTCTA 59.366 45.455 3.21 0.00 38.94 2.10
113 114 1.418637 TGGAACGCAGGTTTAGGTTCT 59.581 47.619 3.21 0.00 38.94 3.01
114 115 1.886886 TGGAACGCAGGTTTAGGTTC 58.113 50.000 0.00 0.00 36.24 3.62
115 116 2.579410 ATGGAACGCAGGTTTAGGTT 57.421 45.000 0.00 0.00 36.24 3.50
116 117 2.579410 AATGGAACGCAGGTTTAGGT 57.421 45.000 0.00 0.00 36.24 3.08
117 118 4.398044 ACATAAATGGAACGCAGGTTTAGG 59.602 41.667 0.00 0.00 36.24 2.69
118 119 5.560966 ACATAAATGGAACGCAGGTTTAG 57.439 39.130 0.00 0.00 36.24 1.85
119 120 5.391097 CGAACATAAATGGAACGCAGGTTTA 60.391 40.000 0.00 0.00 36.24 2.01
120 121 4.614993 CGAACATAAATGGAACGCAGGTTT 60.615 41.667 0.00 0.00 36.24 3.27
121 122 3.119990 CGAACATAAATGGAACGCAGGTT 60.120 43.478 0.00 0.00 39.63 3.50
122 123 2.418628 CGAACATAAATGGAACGCAGGT 59.581 45.455 0.00 0.00 0.00 4.00
123 124 2.223249 CCGAACATAAATGGAACGCAGG 60.223 50.000 0.00 0.00 0.00 4.85
140 141 2.962786 CGTGCGTGTCAACCCGAA 60.963 61.111 0.00 0.00 0.00 4.30
145 146 4.643385 CCGTGCGTGCGTGTCAAC 62.643 66.667 0.00 0.00 0.00 3.18
158 159 0.247814 GCATGCTGAAATCGTCCGTG 60.248 55.000 11.37 0.00 0.00 4.94
159 160 0.673333 TGCATGCTGAAATCGTCCGT 60.673 50.000 20.33 0.00 0.00 4.69
188 193 2.418628 GCACGCATTAAACCTGAAGCTA 59.581 45.455 0.00 0.00 0.00 3.32
191 196 2.031245 TGTGCACGCATTAAACCTGAAG 60.031 45.455 13.13 0.00 0.00 3.02
192 197 1.950216 TGTGCACGCATTAAACCTGAA 59.050 42.857 13.13 0.00 0.00 3.02
198 203 0.038709 GCCCTTGTGCACGCATTAAA 60.039 50.000 13.13 0.00 0.00 1.52
201 206 4.041917 CGCCCTTGTGCACGCATT 62.042 61.111 13.13 0.00 0.00 3.56
204 209 3.477224 TTTTCGCCCTTGTGCACGC 62.477 57.895 13.13 8.40 0.00 5.34
206 211 0.594796 CTGTTTTCGCCCTTGTGCAC 60.595 55.000 10.75 10.75 0.00 4.57
213 218 5.047660 TGCAATTATTTACTGTTTTCGCCCT 60.048 36.000 0.00 0.00 0.00 5.19
214 219 5.164954 TGCAATTATTTACTGTTTTCGCCC 58.835 37.500 0.00 0.00 0.00 6.13
216 221 8.979817 TTTTTGCAATTATTTACTGTTTTCGC 57.020 26.923 0.00 0.00 0.00 4.70
233 238 2.836262 CAGGCATTGACCTTTTTGCAA 58.164 42.857 0.00 0.00 38.26 4.08
279 289 2.548493 CCCATTTGGTGTGCCTTTTCTG 60.548 50.000 0.00 0.00 35.27 3.02
302 312 1.003839 AGTGCCATGTACACCGGTG 60.004 57.895 32.83 32.83 38.87 4.94
304 314 2.398554 GCAGTGCCATGTACACCGG 61.399 63.158 2.85 0.00 38.87 5.28
305 315 1.361668 GAGCAGTGCCATGTACACCG 61.362 60.000 12.58 4.23 38.87 4.94
306 316 1.026718 GGAGCAGTGCCATGTACACC 61.027 60.000 12.58 0.00 38.87 4.16
308 318 0.036105 CAGGAGCAGTGCCATGTACA 60.036 55.000 12.58 0.00 0.00 2.90
309 319 1.372087 GCAGGAGCAGTGCCATGTAC 61.372 60.000 12.58 0.00 41.58 2.90
310 320 1.078214 GCAGGAGCAGTGCCATGTA 60.078 57.895 12.58 0.00 41.58 2.29
311 321 2.360852 GCAGGAGCAGTGCCATGT 60.361 61.111 12.58 0.00 41.58 3.21
330 363 5.197451 TCCGTCCCAAAAACTATTGCATAT 58.803 37.500 0.00 0.00 0.00 1.78
332 365 3.426615 TCCGTCCCAAAAACTATTGCAT 58.573 40.909 0.00 0.00 0.00 3.96
340 373 2.035321 TGCAGATTTCCGTCCCAAAAAC 59.965 45.455 0.00 0.00 0.00 2.43
348 381 0.955428 TGCCAGTGCAGATTTCCGTC 60.955 55.000 0.00 0.00 44.23 4.79
395 428 6.653740 ACTTCCACTTTGGCACTAATTACTAC 59.346 38.462 0.00 0.00 37.47 2.73
545 625 2.089980 CTGGTGCTTGAGGAGAATTGG 58.910 52.381 0.00 0.00 0.00 3.16
588 671 4.065088 GAGTCTGCCACATTGTTTCAGTA 58.935 43.478 12.25 1.55 0.00 2.74
590 673 3.144506 AGAGTCTGCCACATTGTTTCAG 58.855 45.455 0.00 8.15 0.00 3.02
591 674 3.213206 AGAGTCTGCCACATTGTTTCA 57.787 42.857 0.00 0.00 0.00 2.69
604 687 5.392767 TTGTAGCTTCCTTGTAGAGTCTG 57.607 43.478 1.86 0.00 0.00 3.51
608 691 4.333926 GCCATTTGTAGCTTCCTTGTAGAG 59.666 45.833 0.00 0.00 0.00 2.43
609 692 4.261801 GCCATTTGTAGCTTCCTTGTAGA 58.738 43.478 0.00 0.00 0.00 2.59
613 699 2.821969 ACTGCCATTTGTAGCTTCCTTG 59.178 45.455 0.00 0.00 0.00 3.61
660 746 6.538742 ACTTTTCATCGACAAATCATACGGAT 59.461 34.615 0.00 0.00 38.05 4.18
691 3263 1.031571 TGAGCTTGGCGGGCTAATTG 61.032 55.000 2.38 0.00 40.40 2.32
889 12038 0.393944 TGCGTGAGGAGGACGAGTAT 60.394 55.000 0.00 0.00 39.21 2.12
949 12111 1.684734 GGCTCCCGGTCTCTTGGTA 60.685 63.158 0.00 0.00 0.00 3.25
977 12161 1.066430 GCGATGACAGGTTCTTGGGTA 60.066 52.381 0.00 0.00 0.00 3.69
979 12163 1.026718 GGCGATGACAGGTTCTTGGG 61.027 60.000 0.00 0.00 0.00 4.12
1032 12261 1.383803 GGCCATGGTCCTCTCTCCT 60.384 63.158 14.67 0.00 0.00 3.69
1035 12264 2.362369 CGTGGCCATGGTCCTCTCT 61.362 63.158 17.90 0.00 0.00 3.10
1417 12671 3.737172 CGCGTTGGCCTTCCCTTG 61.737 66.667 3.32 0.00 35.02 3.61
1467 12721 7.915923 GGCTAATTCTTTTACCTAAGCAATCAC 59.084 37.037 0.00 0.00 0.00 3.06
1481 12735 3.763897 AGCATTCACCGGCTAATTCTTTT 59.236 39.130 0.00 0.00 38.90 2.27
1485 12739 2.224314 GCTAGCATTCACCGGCTAATTC 59.776 50.000 10.63 0.00 41.67 2.17
1692 12955 8.123575 CAGCAATAACAGAGAAGATTTCAGATG 58.876 37.037 0.00 0.00 0.00 2.90
1700 12963 3.525199 ACCCCAGCAATAACAGAGAAGAT 59.475 43.478 0.00 0.00 0.00 2.40
1712 12975 1.534717 AAGCAAGCACCCCAGCAAT 60.535 52.632 0.00 0.00 36.85 3.56
1713 12976 2.123338 AAGCAAGCACCCCAGCAA 60.123 55.556 0.00 0.00 36.85 3.91
1714 12977 2.718487 ATCAAGCAAGCACCCCAGCA 62.718 55.000 0.00 0.00 36.85 4.41
1715 12978 1.980772 ATCAAGCAAGCACCCCAGC 60.981 57.895 0.00 0.00 0.00 4.85
1716 12979 1.888018 CATCAAGCAAGCACCCCAG 59.112 57.895 0.00 0.00 0.00 4.45
1717 12980 2.277591 GCATCAAGCAAGCACCCCA 61.278 57.895 0.00 0.00 44.79 4.96
1718 12981 2.575461 GCATCAAGCAAGCACCCC 59.425 61.111 0.00 0.00 44.79 4.95
1733 12996 5.129485 AGCTAGTAAGAAATTAGCAGAGGCA 59.871 40.000 5.64 0.00 44.61 4.75
1740 13003 8.930760 CACATATGGAGCTAGTAAGAAATTAGC 58.069 37.037 7.80 0.00 39.99 3.09
1753 13016 7.879677 CAGATTTACCAATCACATATGGAGCTA 59.120 37.037 7.80 0.00 41.37 3.32
1754 13017 6.713903 CAGATTTACCAATCACATATGGAGCT 59.286 38.462 7.80 0.00 41.37 4.09
1755 13018 6.712095 TCAGATTTACCAATCACATATGGAGC 59.288 38.462 7.80 0.00 41.37 4.70
1757 13020 8.902806 GTTTCAGATTTACCAATCACATATGGA 58.097 33.333 7.80 2.05 41.37 3.41
1758 13021 8.137437 GGTTTCAGATTTACCAATCACATATGG 58.863 37.037 7.80 0.00 41.37 2.74
1759 13022 7.857389 CGGTTTCAGATTTACCAATCACATATG 59.143 37.037 0.00 0.00 41.37 1.78
1760 13023 7.468631 GCGGTTTCAGATTTACCAATCACATAT 60.469 37.037 0.00 0.00 41.37 1.78
1761 13024 6.183360 GCGGTTTCAGATTTACCAATCACATA 60.183 38.462 0.00 0.00 41.37 2.29
1762 13025 5.393027 GCGGTTTCAGATTTACCAATCACAT 60.393 40.000 0.00 0.00 41.37 3.21
1763 13026 4.083003 GCGGTTTCAGATTTACCAATCACA 60.083 41.667 0.00 0.00 41.37 3.58
1764 13027 4.412207 GCGGTTTCAGATTTACCAATCAC 58.588 43.478 0.00 0.00 41.37 3.06
1775 13038 0.250513 GGACAGAGGCGGTTTCAGAT 59.749 55.000 0.00 0.00 0.00 2.90
1783 13046 2.435586 CAGCAAGGACAGAGGCGG 60.436 66.667 0.00 0.00 0.00 6.13
1786 13049 0.604780 CACCACAGCAAGGACAGAGG 60.605 60.000 0.00 0.00 0.00 3.69
1793 13056 1.392589 AGTCAAACACCACAGCAAGG 58.607 50.000 0.00 0.00 0.00 3.61
1821 13084 2.685388 GGTAAGAAAATGAGCAGAGGCC 59.315 50.000 0.00 0.00 42.56 5.19
1877 14644 5.607119 TTTCAGTTTTCCGCTATGTTCTC 57.393 39.130 0.00 0.00 0.00 2.87
1895 14662 6.037500 ACGCACGATACTACTACTGTATTTCA 59.962 38.462 0.00 0.00 31.55 2.69
1905 14672 2.282407 TCTGCACGCACGATACTACTA 58.718 47.619 0.00 0.00 0.00 1.82
1906 14673 1.092348 TCTGCACGCACGATACTACT 58.908 50.000 0.00 0.00 0.00 2.57
1907 14674 2.121116 ATCTGCACGCACGATACTAC 57.879 50.000 0.00 0.00 0.00 2.73
1910 14677 2.077155 CAAATCTGCACGCACGATAC 57.923 50.000 0.00 0.00 0.00 2.24
1924 14805 4.151157 GGTTTCACTGAATTGCTGCAAATC 59.849 41.667 20.06 20.37 0.00 2.17
1950 14831 3.248602 ACTTGACAGATGAAAAGTGTCGC 59.751 43.478 0.00 0.00 42.98 5.19
1952 14833 5.742446 GTCACTTGACAGATGAAAAGTGTC 58.258 41.667 20.92 15.93 46.14 3.67
1972 14853 5.008980 TGATGTAAAATGTGCCATCTGTCA 58.991 37.500 0.00 0.00 35.76 3.58
2009 14890 8.691797 ACACACCGAGGCAAATATTATTATTTT 58.308 29.630 0.82 0.00 36.16 1.82
2029 14910 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
2044 14925 1.147473 TGCATGATCGACACACACAC 58.853 50.000 0.00 0.00 0.00 3.82
2045 14926 1.876322 TTGCATGATCGACACACACA 58.124 45.000 0.00 0.00 0.00 3.72
2046 14927 2.032117 TGTTTGCATGATCGACACACAC 60.032 45.455 0.00 0.00 0.00 3.82
2047 14928 2.216898 TGTTTGCATGATCGACACACA 58.783 42.857 0.00 0.00 0.00 3.72
2048 14929 2.967459 TGTTTGCATGATCGACACAC 57.033 45.000 0.00 0.00 0.00 3.82
2049 14930 3.137533 TCTTGTTTGCATGATCGACACA 58.862 40.909 0.00 0.00 0.00 3.72
2050 14931 3.811722 TCTTGTTTGCATGATCGACAC 57.188 42.857 0.00 0.00 0.00 3.67
2051 14932 4.002316 TCATCTTGTTTGCATGATCGACA 58.998 39.130 0.00 0.00 37.39 4.35
2052 14933 4.495349 CCTCATCTTGTTTGCATGATCGAC 60.495 45.833 0.00 0.00 37.39 4.20
2053 14934 3.624410 CCTCATCTTGTTTGCATGATCGA 59.376 43.478 0.00 0.00 37.39 3.59
2054 14935 3.376234 ACCTCATCTTGTTTGCATGATCG 59.624 43.478 0.00 0.00 37.39 3.69
2086 14967 0.468226 GTCCAAGGAGACACCACACA 59.532 55.000 0.00 0.00 42.04 3.72
2103 14984 2.227388 CCCTGAATTGTGAACTGCAGTC 59.773 50.000 21.95 14.06 0.00 3.51
2104 14985 2.158623 TCCCTGAATTGTGAACTGCAGT 60.159 45.455 15.25 15.25 0.00 4.40
2105 14986 2.227388 GTCCCTGAATTGTGAACTGCAG 59.773 50.000 13.48 13.48 0.00 4.41
2106 14987 2.229792 GTCCCTGAATTGTGAACTGCA 58.770 47.619 0.00 0.00 0.00 4.41
2109 14990 3.117512 ACTTGGTCCCTGAATTGTGAACT 60.118 43.478 0.00 0.00 0.00 3.01
2112 14993 2.224769 GGACTTGGTCCCTGAATTGTGA 60.225 50.000 5.48 0.00 46.19 3.58
2114 14995 2.586648 GGACTTGGTCCCTGAATTGT 57.413 50.000 5.48 0.00 46.19 2.71
2136 15017 7.946207 ACTTTGGAGAATCTTCCTTCTTTTTC 58.054 34.615 0.00 0.00 35.63 2.29
2138 15019 7.293828 AGACTTTGGAGAATCTTCCTTCTTTT 58.706 34.615 0.00 0.00 35.63 2.27
2140 15021 6.446909 AGACTTTGGAGAATCTTCCTTCTT 57.553 37.500 0.00 0.00 35.63 2.52
2141 15022 5.337169 CGAGACTTTGGAGAATCTTCCTTCT 60.337 44.000 0.00 0.00 38.18 2.85
2142 15023 4.867608 CGAGACTTTGGAGAATCTTCCTTC 59.132 45.833 0.00 0.00 38.12 3.46
2180 15070 2.554032 CACACATTCTCACCCACTTTCC 59.446 50.000 0.00 0.00 0.00 3.13
2181 15071 2.554032 CCACACATTCTCACCCACTTTC 59.446 50.000 0.00 0.00 0.00 2.62
2182 15072 2.586425 CCACACATTCTCACCCACTTT 58.414 47.619 0.00 0.00 0.00 2.66
2183 15073 1.819305 GCCACACATTCTCACCCACTT 60.819 52.381 0.00 0.00 0.00 3.16
2184 15074 0.250901 GCCACACATTCTCACCCACT 60.251 55.000 0.00 0.00 0.00 4.00
2185 15075 1.577328 CGCCACACATTCTCACCCAC 61.577 60.000 0.00 0.00 0.00 4.61
2238 15128 3.788694 CGACACGCACTTGAAAATTGAAA 59.211 39.130 0.00 0.00 0.00 2.69
2239 15129 3.358775 CGACACGCACTTGAAAATTGAA 58.641 40.909 0.00 0.00 0.00 2.69
2240 15130 2.980586 CGACACGCACTTGAAAATTGA 58.019 42.857 0.00 0.00 0.00 2.57
2340 15237 0.178961 ACTGGAAAGGGAAACAGGCC 60.179 55.000 0.00 0.00 35.34 5.19
2347 15245 1.003118 CGTCATGGACTGGAAAGGGAA 59.997 52.381 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.