Multiple sequence alignment - TraesCS6B01G225700

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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 TraesCS6B01G225700 chr6B 100.000 4815 0 0 1 4815 347225457 347220643 0.000000e+00 8892.0
1 TraesCS6B01G225700 chr6D 93.040 4138 153 58 195 4236 262776030 262780128 0.000000e+00 5921.0
2 TraesCS6B01G225700 chr6A 94.871 3373 87 34 776 4098 356975770 356979106 0.000000e+00 5192.0
3 TraesCS6B01G225700 chr6A 86.559 558 42 16 182 718 356975212 356975757 6.940000e-163 584.0
4 TraesCS6B01G225700 chr6A 96.142 337 11 2 4087 4423 356987356 356987690 2.530000e-152 549.0
5 TraesCS6B01G225700 chr6A 95.087 346 14 3 4439 4784 356987864 356988206 4.240000e-150 542.0
6 TraesCS6B01G225700 chr6A 82.692 156 23 4 1 155 15805203 15805051 8.410000e-28 135.0
7 TraesCS6B01G225700 chr6A 93.750 64 2 2 4126 4187 356987457 356987520 1.430000e-15 95.3
8 TraesCS6B01G225700 chr6A 87.719 57 7 0 4214 4270 19523254 19523310 3.110000e-07 67.6
9 TraesCS6B01G225700 chr2A 80.683 1522 166 52 979 2419 701485084 701486558 0.000000e+00 1064.0
10 TraesCS6B01G225700 chr2A 85.462 736 85 14 2556 3278 701486585 701487311 0.000000e+00 747.0
11 TraesCS6B01G225700 chr2A 82.335 334 37 13 3664 3986 701487715 701488037 2.210000e-68 270.0
12 TraesCS6B01G225700 chr2A 95.238 42 2 0 4334 4375 758548611 758548570 3.110000e-07 67.6
13 TraesCS6B01G225700 chr2B 80.341 1526 169 56 975 2420 670834476 670835950 0.000000e+00 1035.0
14 TraesCS6B01G225700 chr2B 85.054 736 88 15 2556 3278 670835976 670836702 0.000000e+00 730.0
15 TraesCS6B01G225700 chr2B 86.009 436 47 8 2851 3278 670840100 670840529 5.680000e-124 455.0
16 TraesCS6B01G225700 chr2B 81.675 382 40 20 3593 3963 670841252 670841614 1.700000e-74 291.0
17 TraesCS6B01G225700 chr2B 81.121 339 38 18 3662 3986 670837115 670837441 1.030000e-61 248.0
18 TraesCS6B01G225700 chr2B 86.275 204 20 4 2551 2747 670838672 670838874 1.050000e-51 215.0
19 TraesCS6B01G225700 chr2B 79.487 195 28 12 2250 2435 670838420 670838611 1.410000e-25 128.0
20 TraesCS6B01G225700 chr2B 86.538 52 5 1 4336 4387 668775682 668775633 6.730000e-04 56.5
21 TraesCS6B01G225700 chr2D 80.118 1524 171 55 978 2420 561838830 561840302 0.000000e+00 1014.0
22 TraesCS6B01G225700 chr2D 89.552 536 42 11 2586 3114 561843691 561844219 0.000000e+00 667.0
23 TraesCS6B01G225700 chr2D 86.067 445 46 12 2553 2987 561840327 561840765 9.440000e-127 464.0
24 TraesCS6B01G225700 chr2D 83.383 337 33 16 3663 3986 561844507 561844833 1.700000e-74 291.0
25 TraesCS6B01G225700 chr2D 77.165 508 59 35 3664 4158 561841583 561842046 4.810000e-60 243.0
26 TraesCS6B01G225700 chr2D 79.688 192 31 8 2250 2436 561843001 561843189 1.090000e-26 132.0
27 TraesCS6B01G225700 chr4D 87.037 162 20 1 1 162 8931155 8930995 1.060000e-41 182.0
28 TraesCS6B01G225700 chr7A 85.455 165 18 4 1 162 567345430 567345269 2.980000e-37 167.0
29 TraesCS6B01G225700 chr7B 81.707 164 26 4 1 162 544962176 544962015 3.020000e-27 134.0
30 TraesCS6B01G225700 chr1B 82.166 157 25 3 1 156 121480223 121480069 1.090000e-26 132.0
31 TraesCS6B01G225700 chr1B 81.290 155 26 3 3 156 121708165 121708013 6.540000e-24 122.0
32 TraesCS6B01G225700 chr1B 91.525 59 5 0 4219 4277 378208413 378208471 1.110000e-11 82.4
33 TraesCS6B01G225700 chr7D 82.550 149 22 4 13 159 514087753 514087607 1.410000e-25 128.0
34 TraesCS6B01G225700 chr1A 81.646 158 22 7 1 154 105308323 105308477 1.820000e-24 124.0
35 TraesCS6B01G225700 chr3D 83.582 134 15 7 28 159 437737400 437737272 8.470000e-23 119.0
36 TraesCS6B01G225700 chr1D 89.831 59 6 0 4219 4277 278473257 278473315 5.170000e-10 76.8
37 TraesCS6B01G225700 chr5D 84.416 77 10 2 980 1056 356979307 356979233 1.860000e-09 75.0
38 TraesCS6B01G225700 chr5D 96.875 32 1 0 4336 4367 5117676 5117707 2.000000e-03 54.7
39 TraesCS6B01G225700 chr3A 92.683 41 3 0 4335 4375 431669099 431669139 5.200000e-05 60.2
40 TraesCS6B01G225700 chr3A 87.755 49 6 0 4221 4269 102553693 102553645 1.870000e-04 58.4
41 TraesCS6B01G225700 chr5B 96.875 32 1 0 4336 4367 6660569 6660538 2.000000e-03 54.7
42 TraesCS6B01G225700 chr5B 96.875 32 1 0 4336 4367 24315020 24314989 2.000000e-03 54.7
43 TraesCS6B01G225700 chr5B 96.875 32 1 0 4336 4367 24332280 24332249 2.000000e-03 54.7
44 TraesCS6B01G225700 chr5B 96.875 32 1 0 4336 4367 24357993 24357962 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 TraesCS6B01G225700 chr6B 347220643 347225457 4814 True 8892.000000 8892 100.000000 1 4815 1 chr6B.!!$R1 4814
1 TraesCS6B01G225700 chr6D 262776030 262780128 4098 False 5921.000000 5921 93.040000 195 4236 1 chr6D.!!$F1 4041
2 TraesCS6B01G225700 chr6A 356975212 356979106 3894 False 2888.000000 5192 90.715000 182 4098 2 chr6A.!!$F2 3916
3 TraesCS6B01G225700 chr6A 356987356 356988206 850 False 395.433333 549 94.993000 4087 4784 3 chr6A.!!$F3 697
4 TraesCS6B01G225700 chr2A 701485084 701488037 2953 False 693.666667 1064 82.826667 979 3986 3 chr2A.!!$F1 3007
5 TraesCS6B01G225700 chr2B 670834476 670841614 7138 False 443.142857 1035 82.851714 975 3986 7 chr2B.!!$F1 3011
6 TraesCS6B01G225700 chr2D 561838830 561844833 6003 False 468.500000 1014 82.662167 978 4158 6 chr2D.!!$F1 3180

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
163 164 0.035317 TGTATGCATCGCCCTCATCC 59.965 55.0 0.19 0.0 0.0 3.51 F
172 173 0.253044 CGCCCTCATCCTCCTTTTCA 59.747 55.0 0.00 0.0 0.0 2.69 F
1383 1476 0.320247 CGAGTCCAAGCAGAGCAAGT 60.320 55.0 0.00 0.0 0.0 3.16 F
2165 2326 5.060077 CGTGTTATCAGCAAGCATTTTTGAG 59.940 40.0 0.00 0.0 0.0 3.02 F
3644 8760 0.390603 TGTTCGTGTATGCCTTCCCG 60.391 55.0 0.00 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2218 1.669115 CCAGTGAGGTTGCTGGTCG 60.669 63.158 2.66 0.0 45.28 4.79 R
2432 2600 6.013984 AGGTTTCCGTTAACTTGGATCTCTTA 60.014 38.462 3.71 0.0 33.42 2.10 R
3181 3498 4.164988 CCTTGATGATGGAAGAGGTAACCT 59.835 45.833 0.00 0.0 36.03 3.50 R
3695 8814 1.003696 GTACTTGCCTGCCTTCTTCCT 59.996 52.381 0.00 0.0 0.00 3.36 R
4786 10097 0.837272 TGCTTACTATGGAGGTGGCC 59.163 55.000 0.00 0.0 0.00 5.36 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
17 18 4.767255 GTGAGGTCAGGGCAGGCG 62.767 72.222 0.00 0.00 0.00 5.52
22 23 4.459089 GTCAGGGCAGGCGGTCTC 62.459 72.222 0.00 0.00 0.00 3.36
26 27 4.593864 GGGCAGGCGGTCTCGATC 62.594 72.222 0.00 0.00 39.00 3.69
27 28 3.838271 GGCAGGCGGTCTCGATCA 61.838 66.667 0.00 0.00 39.00 2.92
28 29 2.419198 GCAGGCGGTCTCGATCAT 59.581 61.111 0.00 0.00 39.00 2.45
29 30 1.663074 GCAGGCGGTCTCGATCATC 60.663 63.158 0.00 0.00 39.00 2.92
30 31 2.037053 CAGGCGGTCTCGATCATCT 58.963 57.895 0.00 0.00 39.00 2.90
31 32 0.318529 CAGGCGGTCTCGATCATCTG 60.319 60.000 0.00 0.00 39.00 2.90
32 33 1.663074 GGCGGTCTCGATCATCTGC 60.663 63.158 0.00 0.00 39.00 4.26
33 34 1.066422 GCGGTCTCGATCATCTGCA 59.934 57.895 0.00 0.00 39.00 4.41
34 35 1.211818 GCGGTCTCGATCATCTGCAC 61.212 60.000 0.00 0.00 39.00 4.57
35 36 0.596083 CGGTCTCGATCATCTGCACC 60.596 60.000 0.00 0.00 39.00 5.01
36 37 0.249657 GGTCTCGATCATCTGCACCC 60.250 60.000 0.00 0.00 0.00 4.61
37 38 0.249657 GTCTCGATCATCTGCACCCC 60.250 60.000 0.00 0.00 0.00 4.95
38 39 1.070445 CTCGATCATCTGCACCCCC 59.930 63.158 0.00 0.00 0.00 5.40
39 40 1.383109 TCGATCATCTGCACCCCCT 60.383 57.895 0.00 0.00 0.00 4.79
40 41 0.982852 TCGATCATCTGCACCCCCTT 60.983 55.000 0.00 0.00 0.00 3.95
41 42 0.533755 CGATCATCTGCACCCCCTTC 60.534 60.000 0.00 0.00 0.00 3.46
42 43 0.548031 GATCATCTGCACCCCCTTCA 59.452 55.000 0.00 0.00 0.00 3.02
43 44 1.144503 GATCATCTGCACCCCCTTCAT 59.855 52.381 0.00 0.00 0.00 2.57
44 45 0.548031 TCATCTGCACCCCCTTCATC 59.452 55.000 0.00 0.00 0.00 2.92
45 46 0.256752 CATCTGCACCCCCTTCATCA 59.743 55.000 0.00 0.00 0.00 3.07
46 47 0.257039 ATCTGCACCCCCTTCATCAC 59.743 55.000 0.00 0.00 0.00 3.06
47 48 0.842030 TCTGCACCCCCTTCATCACT 60.842 55.000 0.00 0.00 0.00 3.41
48 49 0.038744 CTGCACCCCCTTCATCACTT 59.961 55.000 0.00 0.00 0.00 3.16
49 50 0.251297 TGCACCCCCTTCATCACTTG 60.251 55.000 0.00 0.00 0.00 3.16
50 51 0.038166 GCACCCCCTTCATCACTTGA 59.962 55.000 0.00 0.00 0.00 3.02
51 52 1.341383 GCACCCCCTTCATCACTTGAT 60.341 52.381 0.00 0.00 33.34 2.57
52 53 2.092429 GCACCCCCTTCATCACTTGATA 60.092 50.000 0.00 0.00 33.34 2.15
53 54 3.813443 CACCCCCTTCATCACTTGATAG 58.187 50.000 0.00 0.00 33.34 2.08
54 55 2.780010 ACCCCCTTCATCACTTGATAGG 59.220 50.000 2.16 2.16 34.76 2.57
55 56 2.780010 CCCCCTTCATCACTTGATAGGT 59.220 50.000 7.11 0.00 33.91 3.08
56 57 3.434167 CCCCCTTCATCACTTGATAGGTG 60.434 52.174 7.11 0.00 33.91 4.00
57 58 3.200825 CCCCTTCATCACTTGATAGGTGT 59.799 47.826 7.11 0.00 33.91 4.16
58 59 4.408921 CCCCTTCATCACTTGATAGGTGTA 59.591 45.833 7.11 0.00 33.91 2.90
59 60 5.453903 CCCCTTCATCACTTGATAGGTGTAG 60.454 48.000 7.11 0.00 33.91 2.74
60 61 5.053145 CCTTCATCACTTGATAGGTGTAGC 58.947 45.833 1.23 0.00 36.25 3.58
61 62 4.307443 TCATCACTTGATAGGTGTAGCG 57.693 45.455 0.00 0.00 36.25 4.26
62 63 3.951680 TCATCACTTGATAGGTGTAGCGA 59.048 43.478 0.00 0.00 36.25 4.93
63 64 3.777465 TCACTTGATAGGTGTAGCGAC 57.223 47.619 0.00 0.00 36.25 5.19
64 65 3.353557 TCACTTGATAGGTGTAGCGACT 58.646 45.455 0.00 0.00 36.25 4.18
65 66 4.520179 TCACTTGATAGGTGTAGCGACTA 58.480 43.478 0.00 0.00 36.25 2.59
66 67 4.334759 TCACTTGATAGGTGTAGCGACTAC 59.665 45.833 9.27 9.27 37.46 2.73
67 68 3.311871 ACTTGATAGGTGTAGCGACTACG 59.688 47.826 10.88 0.00 39.58 3.51
68 69 2.216046 TGATAGGTGTAGCGACTACGG 58.784 52.381 10.88 0.00 39.58 4.02
76 77 3.645286 GCGACTACGGTTGCCAAA 58.355 55.556 0.00 0.00 44.75 3.28
77 78 1.495951 GCGACTACGGTTGCCAAAG 59.504 57.895 0.00 0.00 44.75 2.77
78 79 0.947180 GCGACTACGGTTGCCAAAGA 60.947 55.000 0.00 0.00 44.75 2.52
79 80 1.504359 CGACTACGGTTGCCAAAGAA 58.496 50.000 0.00 0.00 35.72 2.52
80 81 1.459592 CGACTACGGTTGCCAAAGAAG 59.540 52.381 0.00 0.00 35.72 2.85
81 82 1.804748 GACTACGGTTGCCAAAGAAGG 59.195 52.381 0.00 0.00 0.00 3.46
82 83 1.142262 ACTACGGTTGCCAAAGAAGGT 59.858 47.619 0.00 0.00 0.00 3.50
83 84 1.535462 CTACGGTTGCCAAAGAAGGTG 59.465 52.381 0.00 0.00 0.00 4.00
84 85 1.106944 ACGGTTGCCAAAGAAGGTGG 61.107 55.000 0.00 0.00 39.33 4.61
90 91 2.257353 CCAAAGAAGGTGGCTTCGG 58.743 57.895 0.00 0.00 38.31 4.30
91 92 0.250727 CCAAAGAAGGTGGCTTCGGA 60.251 55.000 0.00 0.00 38.31 4.55
92 93 1.604604 CAAAGAAGGTGGCTTCGGAA 58.395 50.000 0.00 0.00 38.31 4.30
93 94 2.162681 CAAAGAAGGTGGCTTCGGAAT 58.837 47.619 0.00 0.00 38.31 3.01
94 95 2.558359 CAAAGAAGGTGGCTTCGGAATT 59.442 45.455 0.00 0.00 38.31 2.17
95 96 2.586648 AGAAGGTGGCTTCGGAATTT 57.413 45.000 0.00 0.00 38.31 1.82
96 97 3.713826 AGAAGGTGGCTTCGGAATTTA 57.286 42.857 0.00 0.00 38.31 1.40
97 98 4.236527 AGAAGGTGGCTTCGGAATTTAT 57.763 40.909 0.00 0.00 38.31 1.40
98 99 3.947834 AGAAGGTGGCTTCGGAATTTATG 59.052 43.478 0.00 0.00 38.31 1.90
99 100 2.654863 AGGTGGCTTCGGAATTTATGG 58.345 47.619 0.00 0.00 0.00 2.74
100 101 2.241176 AGGTGGCTTCGGAATTTATGGA 59.759 45.455 0.00 0.00 0.00 3.41
101 102 3.117512 AGGTGGCTTCGGAATTTATGGAT 60.118 43.478 0.00 0.00 0.00 3.41
102 103 3.004734 GGTGGCTTCGGAATTTATGGATG 59.995 47.826 0.00 0.00 0.00 3.51
103 104 3.632145 GTGGCTTCGGAATTTATGGATGT 59.368 43.478 0.00 0.00 0.00 3.06
104 105 4.819630 GTGGCTTCGGAATTTATGGATGTA 59.180 41.667 0.00 0.00 0.00 2.29
105 106 5.473504 GTGGCTTCGGAATTTATGGATGTAT 59.526 40.000 0.00 0.00 0.00 2.29
106 107 6.016276 GTGGCTTCGGAATTTATGGATGTATT 60.016 38.462 0.00 0.00 0.00 1.89
107 108 6.549364 TGGCTTCGGAATTTATGGATGTATTT 59.451 34.615 0.00 0.00 0.00 1.40
108 109 7.084486 GGCTTCGGAATTTATGGATGTATTTC 58.916 38.462 0.00 0.00 0.00 2.17
109 110 7.040409 GGCTTCGGAATTTATGGATGTATTTCT 60.040 37.037 0.00 0.00 0.00 2.52
110 111 8.352942 GCTTCGGAATTTATGGATGTATTTCTT 58.647 33.333 0.00 0.00 0.00 2.52
111 112 9.884465 CTTCGGAATTTATGGATGTATTTCTTC 57.116 33.333 0.00 0.00 0.00 2.87
112 113 8.083462 TCGGAATTTATGGATGTATTTCTTCG 57.917 34.615 0.00 0.00 0.00 3.79
113 114 7.713507 TCGGAATTTATGGATGTATTTCTTCGT 59.286 33.333 0.00 0.00 0.00 3.85
114 115 8.984764 CGGAATTTATGGATGTATTTCTTCGTA 58.015 33.333 0.00 0.00 0.00 3.43
118 119 9.847224 ATTTATGGATGTATTTCTTCGTAAGGT 57.153 29.630 0.00 0.00 38.47 3.50
119 120 8.882415 TTATGGATGTATTTCTTCGTAAGGTC 57.118 34.615 0.00 0.00 38.47 3.85
120 121 6.540438 TGGATGTATTTCTTCGTAAGGTCT 57.460 37.500 0.00 0.00 38.47 3.85
121 122 6.942976 TGGATGTATTTCTTCGTAAGGTCTT 58.057 36.000 0.00 0.00 38.47 3.01
122 123 6.816640 TGGATGTATTTCTTCGTAAGGTCTTG 59.183 38.462 0.00 0.00 38.47 3.02
123 124 7.039882 GGATGTATTTCTTCGTAAGGTCTTGA 58.960 38.462 0.00 0.00 38.47 3.02
124 125 7.711339 GGATGTATTTCTTCGTAAGGTCTTGAT 59.289 37.037 0.00 0.00 38.47 2.57
125 126 7.827819 TGTATTTCTTCGTAAGGTCTTGATG 57.172 36.000 0.00 0.00 38.47 3.07
126 127 7.608153 TGTATTTCTTCGTAAGGTCTTGATGA 58.392 34.615 0.00 0.00 38.47 2.92
127 128 8.092068 TGTATTTCTTCGTAAGGTCTTGATGAA 58.908 33.333 0.00 0.00 38.47 2.57
128 129 9.099454 GTATTTCTTCGTAAGGTCTTGATGAAT 57.901 33.333 0.00 0.00 38.47 2.57
130 131 9.667107 ATTTCTTCGTAAGGTCTTGATGAATAA 57.333 29.630 0.00 0.00 38.47 1.40
131 132 9.667107 TTTCTTCGTAAGGTCTTGATGAATAAT 57.333 29.630 0.00 0.00 38.47 1.28
132 133 9.667107 TTCTTCGTAAGGTCTTGATGAATAATT 57.333 29.630 0.00 0.00 38.47 1.40
155 156 7.922505 TTAATAAAATGGTTGTATGCATCGC 57.077 32.000 0.19 0.00 0.00 4.58
156 157 2.869233 AAATGGTTGTATGCATCGCC 57.131 45.000 0.19 1.97 0.00 5.54
157 158 1.032014 AATGGTTGTATGCATCGCCC 58.968 50.000 0.19 0.00 0.00 6.13
158 159 0.183492 ATGGTTGTATGCATCGCCCT 59.817 50.000 0.19 0.00 0.00 5.19
159 160 0.463654 TGGTTGTATGCATCGCCCTC 60.464 55.000 0.19 0.00 0.00 4.30
160 161 0.463654 GGTTGTATGCATCGCCCTCA 60.464 55.000 0.19 0.00 0.00 3.86
161 162 1.597742 GTTGTATGCATCGCCCTCAT 58.402 50.000 0.19 0.00 0.00 2.90
162 163 1.532868 GTTGTATGCATCGCCCTCATC 59.467 52.381 0.19 0.00 0.00 2.92
163 164 0.035317 TGTATGCATCGCCCTCATCC 59.965 55.000 0.19 0.00 0.00 3.51
164 165 0.322975 GTATGCATCGCCCTCATCCT 59.677 55.000 0.19 0.00 0.00 3.24
165 166 0.610174 TATGCATCGCCCTCATCCTC 59.390 55.000 0.19 0.00 0.00 3.71
166 167 2.031768 GCATCGCCCTCATCCTCC 59.968 66.667 0.00 0.00 0.00 4.30
167 168 2.515071 GCATCGCCCTCATCCTCCT 61.515 63.158 0.00 0.00 0.00 3.69
168 169 2.049627 GCATCGCCCTCATCCTCCTT 62.050 60.000 0.00 0.00 0.00 3.36
169 170 0.471617 CATCGCCCTCATCCTCCTTT 59.528 55.000 0.00 0.00 0.00 3.11
170 171 1.133976 CATCGCCCTCATCCTCCTTTT 60.134 52.381 0.00 0.00 0.00 2.27
171 172 0.541863 TCGCCCTCATCCTCCTTTTC 59.458 55.000 0.00 0.00 0.00 2.29
172 173 0.253044 CGCCCTCATCCTCCTTTTCA 59.747 55.000 0.00 0.00 0.00 2.69
173 174 1.340017 CGCCCTCATCCTCCTTTTCAA 60.340 52.381 0.00 0.00 0.00 2.69
174 175 2.807676 GCCCTCATCCTCCTTTTCAAA 58.192 47.619 0.00 0.00 0.00 2.69
175 176 3.165071 GCCCTCATCCTCCTTTTCAAAA 58.835 45.455 0.00 0.00 0.00 2.44
176 177 3.578282 GCCCTCATCCTCCTTTTCAAAAA 59.422 43.478 0.00 0.00 0.00 1.94
230 232 6.600427 AGCTTAGAGAGTAGAAGTAACTCACC 59.400 42.308 6.06 0.00 44.77 4.02
232 234 5.163281 AGAGAGTAGAAGTAACTCACCGA 57.837 43.478 6.06 0.00 44.77 4.69
252 254 7.436080 TCACCGATTACCTGATTCGTTAATTAC 59.564 37.037 0.00 0.00 30.58 1.89
258 260 6.753107 ACCTGATTCGTTAATTACTTTGGG 57.247 37.500 0.00 0.00 0.00 4.12
287 289 3.883489 ACCAGAAAGTTGTAGCTTCCAAC 59.117 43.478 16.91 16.91 41.94 3.77
295 297 3.678056 TGTAGCTTCCAACGAGACATT 57.322 42.857 0.00 0.00 0.00 2.71
296 298 3.585862 TGTAGCTTCCAACGAGACATTC 58.414 45.455 0.00 0.00 0.00 2.67
310 312 3.357203 AGACATTCTTCGCCACTCTCTA 58.643 45.455 0.00 0.00 0.00 2.43
319 321 6.100004 TCTTCGCCACTCTCTAAAATGTAAG 58.900 40.000 0.00 0.00 0.00 2.34
361 363 7.576861 AAATCCTAAACTTCCAACGAAAGAA 57.423 32.000 0.00 0.00 0.00 2.52
426 428 6.442952 TGCACAAACATAAACTGGTTCATAC 58.557 36.000 0.00 0.00 30.24 2.39
429 431 7.521423 GCACAAACATAAACTGGTTCATACAGA 60.521 37.037 0.00 0.00 39.24 3.41
431 433 8.908903 ACAAACATAAACTGGTTCATACAGAAA 58.091 29.630 0.00 0.00 38.13 2.52
432 434 9.180678 CAAACATAAACTGGTTCATACAGAAAC 57.819 33.333 0.00 0.00 44.46 2.78
494 502 9.738832 CGGTAAAAGTACAATATTAAAATGGGG 57.261 33.333 0.00 0.00 31.21 4.96
562 582 6.472163 ACAACAAGAACGAAAACTAGCAAATG 59.528 34.615 0.00 0.00 0.00 2.32
567 587 3.638484 ACGAAAACTAGCAAATGCCAAC 58.362 40.909 0.94 0.00 43.38 3.77
612 650 2.289320 ACTAGCACTTGCCTCTGTTCTG 60.289 50.000 0.00 0.00 43.38 3.02
632 670 5.674525 TCTGTTCTCTGTTGTTTCTCATGT 58.325 37.500 0.00 0.00 0.00 3.21
639 677 6.823182 TCTCTGTTGTTTCTCATGTTCTTCAA 59.177 34.615 0.00 0.00 0.00 2.69
681 719 4.819761 GTCTGCGCCGATCTGCCA 62.820 66.667 4.18 2.33 0.00 4.92
780 824 1.985622 TTCCCAGTTCATCATCCCCT 58.014 50.000 0.00 0.00 0.00 4.79
796 840 5.877564 TCATCCCCTTTTGTTTGTTTGTTTC 59.122 36.000 0.00 0.00 0.00 2.78
1173 1235 1.073284 CCCTTCTTCCGGAACAAGGAA 59.927 52.381 38.42 26.74 44.72 3.36
1271 1361 3.214328 ACAGATGCTTTTGTCTTTCGGT 58.786 40.909 0.00 0.00 0.00 4.69
1383 1476 0.320247 CGAGTCCAAGCAGAGCAAGT 60.320 55.000 0.00 0.00 0.00 3.16
1529 1631 5.430089 AGGTTGCCTACTTTGATAGGAGAAT 59.570 40.000 2.94 0.00 44.12 2.40
1568 1670 9.200817 ACATTAAAGGTTGCTAAATCATACCAT 57.799 29.630 0.00 0.00 0.00 3.55
1934 2095 6.801539 ATGCGTGTATTCTTACCATAATGG 57.198 37.500 0.00 0.00 45.02 3.16
2057 2218 8.919661 CCTCTGCTAACATTTTCTTCAAATTTC 58.080 33.333 0.00 0.00 32.24 2.17
2165 2326 5.060077 CGTGTTATCAGCAAGCATTTTTGAG 59.940 40.000 0.00 0.00 0.00 3.02
2554 2722 7.727634 AGGTCATCAGATCAGTATTAGTGATGA 59.272 37.037 16.89 13.17 44.93 2.92
2593 2771 9.502091 CGATAGGGTCAAATTAATTCTATGGAA 57.498 33.333 0.10 0.00 35.78 3.53
3206 3523 5.363939 GTTACCTCTTCCATCATCAAGGAG 58.636 45.833 0.00 0.00 34.91 3.69
3220 3537 9.730705 CATCATCAAGGAGTGGTTATATTATGT 57.269 33.333 0.00 0.00 0.00 2.29
3589 8705 6.058183 GCTCTGTTCACCAGGATTTATGTAT 58.942 40.000 0.00 0.00 41.83 2.29
3590 8706 6.543831 GCTCTGTTCACCAGGATTTATGTATT 59.456 38.462 0.00 0.00 41.83 1.89
3591 8707 7.067494 GCTCTGTTCACCAGGATTTATGTATTT 59.933 37.037 0.00 0.00 41.83 1.40
3644 8760 0.390603 TGTTCGTGTATGCCTTCCCG 60.391 55.000 0.00 0.00 0.00 5.14
3695 8814 1.202710 AGATCCGCGCTCTAGAGAAGA 60.203 52.381 24.24 12.97 0.00 2.87
3964 9099 3.575965 AATGAACAACTGGATTTCGGC 57.424 42.857 0.00 0.00 0.00 5.54
4033 9180 1.588674 CGGCTGTGTGTTTCACCTTA 58.411 50.000 0.00 0.00 45.61 2.69
4082 9229 3.084039 CTCAGTTTTTATGCTGGCCTCA 58.916 45.455 3.32 1.86 33.81 3.86
4107 9254 8.664798 CAGTAAAAACGGTTGATATGATCTCAA 58.335 33.333 0.00 0.00 0.00 3.02
4121 9268 2.890808 TCTCAAGTCGTGTTCTGCTT 57.109 45.000 0.00 0.00 0.00 3.91
4331 9484 9.703892 CCTACAGAGTATTGATTCTTATCCTTG 57.296 37.037 0.00 0.00 0.00 3.61
4332 9485 9.202273 CTACAGAGTATTGATTCTTATCCTTGC 57.798 37.037 0.00 0.00 0.00 4.01
4423 9576 7.339212 TGGAACACATGATAGGAAAAATACAGG 59.661 37.037 0.00 0.00 0.00 4.00
4424 9577 7.556275 GGAACACATGATAGGAAAAATACAGGA 59.444 37.037 0.00 0.00 0.00 3.86
4425 9578 8.877864 AACACATGATAGGAAAAATACAGGAA 57.122 30.769 0.00 0.00 0.00 3.36
4428 9581 8.960591 CACATGATAGGAAAAATACAGGAAAGT 58.039 33.333 0.00 0.00 0.00 2.66
4429 9582 8.960591 ACATGATAGGAAAAATACAGGAAAGTG 58.039 33.333 0.00 0.00 0.00 3.16
4430 9583 7.391148 TGATAGGAAAAATACAGGAAAGTGC 57.609 36.000 0.00 0.00 0.00 4.40
4431 9584 6.945435 TGATAGGAAAAATACAGGAAAGTGCA 59.055 34.615 0.00 0.00 0.00 4.57
4432 9585 5.712152 AGGAAAAATACAGGAAAGTGCAG 57.288 39.130 0.00 0.00 0.00 4.41
4433 9586 4.524328 AGGAAAAATACAGGAAAGTGCAGG 59.476 41.667 0.00 0.00 0.00 4.85
4434 9587 4.280929 GGAAAAATACAGGAAAGTGCAGGT 59.719 41.667 0.00 0.00 0.00 4.00
4435 9588 5.221441 GGAAAAATACAGGAAAGTGCAGGTT 60.221 40.000 0.00 0.00 0.00 3.50
4469 9780 7.391148 TTCTAAAACAGCATAGGGTTTGATC 57.609 36.000 0.00 0.00 37.30 2.92
4481 9792 8.303876 GCATAGGGTTTGATCTGTTTCTAAAAA 58.696 33.333 0.00 0.00 0.00 1.94
4525 9836 9.182214 AGATGAGATGCACATTTATTTAACTGT 57.818 29.630 0.00 0.00 30.46 3.55
4574 9885 5.052693 TGTTGGGAATTGAGCTGCTATAT 57.947 39.130 0.15 0.00 0.00 0.86
4641 9952 9.777297 ATTGTTCTTGCAAAAGGTATAACAATT 57.223 25.926 0.00 0.00 41.17 2.32
4644 9955 9.040939 GTTCTTGCAAAAGGTATAACAATTGTT 57.959 29.630 25.99 25.99 41.73 2.83
4714 10025 2.125773 CCAAGCTGAGGCAAGAATCT 57.874 50.000 0.00 0.00 41.70 2.40
4755 10066 6.642733 TCTGATTTTGGGAGGTCTAGAATT 57.357 37.500 0.00 0.00 0.00 2.17
4784 10095 5.235850 TCACTATCTGTAGCCCAAAACAA 57.764 39.130 0.00 0.00 0.00 2.83
4785 10096 5.626142 TCACTATCTGTAGCCCAAAACAAA 58.374 37.500 0.00 0.00 0.00 2.83
4786 10097 5.705441 TCACTATCTGTAGCCCAAAACAAAG 59.295 40.000 0.00 0.00 0.00 2.77
4787 10098 5.010282 ACTATCTGTAGCCCAAAACAAAGG 58.990 41.667 0.00 0.00 0.00 3.11
4791 10102 4.454948 GCCCAAAACAAAGGCCAC 57.545 55.556 5.01 0.00 41.00 5.01
4792 10103 1.227823 GCCCAAAACAAAGGCCACC 60.228 57.895 5.01 0.00 41.00 4.61
4793 10104 1.695114 GCCCAAAACAAAGGCCACCT 61.695 55.000 5.01 0.00 41.00 4.00
4794 10105 0.392706 CCCAAAACAAAGGCCACCTC 59.607 55.000 5.01 0.00 30.89 3.85
4795 10106 0.392706 CCAAAACAAAGGCCACCTCC 59.607 55.000 5.01 0.00 30.89 4.30
4796 10107 1.118838 CAAAACAAAGGCCACCTCCA 58.881 50.000 5.01 0.00 30.89 3.86
4797 10108 1.693606 CAAAACAAAGGCCACCTCCAT 59.306 47.619 5.01 0.00 30.89 3.41
4798 10109 2.896685 CAAAACAAAGGCCACCTCCATA 59.103 45.455 5.01 0.00 30.89 2.74
4799 10110 2.514458 AACAAAGGCCACCTCCATAG 57.486 50.000 5.01 0.00 30.89 2.23
4800 10111 1.372501 ACAAAGGCCACCTCCATAGT 58.627 50.000 5.01 0.00 30.89 2.12
4801 10112 2.557869 ACAAAGGCCACCTCCATAGTA 58.442 47.619 5.01 0.00 30.89 1.82
4802 10113 2.916934 ACAAAGGCCACCTCCATAGTAA 59.083 45.455 5.01 0.00 30.89 2.24
4803 10114 3.054361 ACAAAGGCCACCTCCATAGTAAG 60.054 47.826 5.01 0.00 30.89 2.34
4804 10115 1.132500 AGGCCACCTCCATAGTAAGC 58.868 55.000 5.01 0.00 0.00 3.09
4805 10116 0.837272 GGCCACCTCCATAGTAAGCA 59.163 55.000 0.00 0.00 0.00 3.91
4806 10117 1.202698 GGCCACCTCCATAGTAAGCAG 60.203 57.143 0.00 0.00 0.00 4.24
4807 10118 1.202698 GCCACCTCCATAGTAAGCAGG 60.203 57.143 0.00 0.00 0.00 4.85
4808 10119 2.398588 CCACCTCCATAGTAAGCAGGA 58.601 52.381 0.00 0.00 0.00 3.86
4809 10120 2.366916 CCACCTCCATAGTAAGCAGGAG 59.633 54.545 0.00 0.00 45.68 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.767255 CGCCTGCCCTGACCTCAC 62.767 72.222 0.00 0.00 0.00 3.51
5 6 4.459089 GAGACCGCCTGCCCTGAC 62.459 72.222 0.00 0.00 0.00 3.51
9 10 4.593864 GATCGAGACCGCCTGCCC 62.594 72.222 0.00 0.00 35.37 5.36
10 11 3.157217 ATGATCGAGACCGCCTGCC 62.157 63.158 0.00 0.00 35.37 4.85
11 12 1.663074 GATGATCGAGACCGCCTGC 60.663 63.158 0.00 0.00 35.37 4.85
12 13 0.318529 CAGATGATCGAGACCGCCTG 60.319 60.000 0.00 0.00 35.37 4.85
13 14 2.037053 CAGATGATCGAGACCGCCT 58.963 57.895 0.00 0.00 35.37 5.52
14 15 1.663074 GCAGATGATCGAGACCGCC 60.663 63.158 0.00 0.00 35.37 6.13
15 16 1.066422 TGCAGATGATCGAGACCGC 59.934 57.895 0.00 0.00 35.37 5.68
16 17 0.596083 GGTGCAGATGATCGAGACCG 60.596 60.000 0.00 0.00 37.07 4.79
17 18 0.249657 GGGTGCAGATGATCGAGACC 60.250 60.000 0.00 2.37 0.00 3.85
18 19 0.249657 GGGGTGCAGATGATCGAGAC 60.250 60.000 0.00 0.00 0.00 3.36
19 20 1.402896 GGGGGTGCAGATGATCGAGA 61.403 60.000 0.00 0.00 0.00 4.04
20 21 1.070445 GGGGGTGCAGATGATCGAG 59.930 63.158 0.00 0.00 0.00 4.04
21 22 0.982852 AAGGGGGTGCAGATGATCGA 60.983 55.000 0.00 0.00 0.00 3.59
22 23 0.533755 GAAGGGGGTGCAGATGATCG 60.534 60.000 0.00 0.00 0.00 3.69
23 24 0.548031 TGAAGGGGGTGCAGATGATC 59.452 55.000 0.00 0.00 0.00 2.92
24 25 1.144503 GATGAAGGGGGTGCAGATGAT 59.855 52.381 0.00 0.00 0.00 2.45
25 26 0.548031 GATGAAGGGGGTGCAGATGA 59.452 55.000 0.00 0.00 0.00 2.92
26 27 0.256752 TGATGAAGGGGGTGCAGATG 59.743 55.000 0.00 0.00 0.00 2.90
27 28 0.257039 GTGATGAAGGGGGTGCAGAT 59.743 55.000 0.00 0.00 0.00 2.90
28 29 0.842030 AGTGATGAAGGGGGTGCAGA 60.842 55.000 0.00 0.00 0.00 4.26
29 30 0.038744 AAGTGATGAAGGGGGTGCAG 59.961 55.000 0.00 0.00 0.00 4.41
30 31 0.251297 CAAGTGATGAAGGGGGTGCA 60.251 55.000 0.00 0.00 0.00 4.57
31 32 0.038166 TCAAGTGATGAAGGGGGTGC 59.962 55.000 0.00 0.00 34.30 5.01
32 33 2.814805 ATCAAGTGATGAAGGGGGTG 57.185 50.000 0.00 0.00 42.54 4.61
33 34 2.780010 CCTATCAAGTGATGAAGGGGGT 59.220 50.000 4.00 0.00 42.54 4.95
34 35 2.780010 ACCTATCAAGTGATGAAGGGGG 59.220 50.000 12.64 5.11 42.54 5.40
35 36 3.200825 ACACCTATCAAGTGATGAAGGGG 59.799 47.826 9.83 9.83 42.54 4.79
36 37 4.494091 ACACCTATCAAGTGATGAAGGG 57.506 45.455 12.64 8.21 42.54 3.95
37 38 5.053145 GCTACACCTATCAAGTGATGAAGG 58.947 45.833 4.00 6.35 42.54 3.46
38 39 4.742167 CGCTACACCTATCAAGTGATGAAG 59.258 45.833 4.00 0.00 42.54 3.02
39 40 4.401202 TCGCTACACCTATCAAGTGATGAA 59.599 41.667 4.00 0.00 42.54 2.57
40 41 3.951680 TCGCTACACCTATCAAGTGATGA 59.048 43.478 4.00 0.00 43.67 2.92
41 42 4.045104 GTCGCTACACCTATCAAGTGATG 58.955 47.826 4.00 0.00 38.63 3.07
42 43 3.954904 AGTCGCTACACCTATCAAGTGAT 59.045 43.478 0.00 0.00 38.63 3.06
43 44 3.353557 AGTCGCTACACCTATCAAGTGA 58.646 45.455 0.00 0.00 38.63 3.41
44 45 3.784701 AGTCGCTACACCTATCAAGTG 57.215 47.619 0.00 0.00 41.15 3.16
45 46 3.311871 CGTAGTCGCTACACCTATCAAGT 59.688 47.826 14.49 0.00 36.83 3.16
46 47 3.303857 CCGTAGTCGCTACACCTATCAAG 60.304 52.174 14.49 0.00 36.83 3.02
47 48 2.615447 CCGTAGTCGCTACACCTATCAA 59.385 50.000 14.49 0.00 36.83 2.57
48 49 2.216046 CCGTAGTCGCTACACCTATCA 58.784 52.381 14.49 0.00 36.83 2.15
49 50 2.216898 ACCGTAGTCGCTACACCTATC 58.783 52.381 14.49 0.00 36.83 2.08
50 51 2.338577 ACCGTAGTCGCTACACCTAT 57.661 50.000 14.49 0.00 36.83 2.57
51 52 1.739466 CAACCGTAGTCGCTACACCTA 59.261 52.381 14.49 0.00 36.83 3.08
52 53 0.524862 CAACCGTAGTCGCTACACCT 59.475 55.000 14.49 0.00 36.83 4.00
53 54 1.074872 GCAACCGTAGTCGCTACACC 61.075 60.000 14.49 0.00 36.83 4.16
54 55 1.074872 GGCAACCGTAGTCGCTACAC 61.075 60.000 14.49 0.00 36.83 2.90
55 56 1.213537 GGCAACCGTAGTCGCTACA 59.786 57.895 14.49 0.00 36.83 2.74
56 57 0.388907 TTGGCAACCGTAGTCGCTAC 60.389 55.000 0.00 6.87 33.99 3.58
57 58 0.317799 TTTGGCAACCGTAGTCGCTA 59.682 50.000 0.00 0.00 35.54 4.26
58 59 0.949105 CTTTGGCAACCGTAGTCGCT 60.949 55.000 0.00 0.00 35.54 4.93
59 60 0.947180 TCTTTGGCAACCGTAGTCGC 60.947 55.000 0.00 0.00 35.54 5.19
60 61 1.459592 CTTCTTTGGCAACCGTAGTCG 59.540 52.381 0.00 0.00 0.00 4.18
61 62 1.804748 CCTTCTTTGGCAACCGTAGTC 59.195 52.381 0.00 0.00 0.00 2.59
62 63 1.142262 ACCTTCTTTGGCAACCGTAGT 59.858 47.619 0.00 0.00 0.00 2.73
63 64 1.535462 CACCTTCTTTGGCAACCGTAG 59.465 52.381 0.00 0.00 0.00 3.51
64 65 1.600023 CACCTTCTTTGGCAACCGTA 58.400 50.000 0.00 0.00 0.00 4.02
65 66 1.106944 CCACCTTCTTTGGCAACCGT 61.107 55.000 0.00 0.00 0.00 4.83
66 67 1.659794 CCACCTTCTTTGGCAACCG 59.340 57.895 0.00 0.00 0.00 4.44
72 73 0.250727 TCCGAAGCCACCTTCTTTGG 60.251 55.000 3.23 3.23 44.24 3.28
73 74 1.604604 TTCCGAAGCCACCTTCTTTG 58.395 50.000 2.44 0.00 44.24 2.77
74 75 2.586648 ATTCCGAAGCCACCTTCTTT 57.413 45.000 2.44 0.00 44.24 2.52
75 76 2.586648 AATTCCGAAGCCACCTTCTT 57.413 45.000 2.44 0.00 44.24 2.52
76 77 2.586648 AAATTCCGAAGCCACCTTCT 57.413 45.000 2.44 0.00 44.24 2.85
77 78 3.066760 CCATAAATTCCGAAGCCACCTTC 59.933 47.826 0.00 0.00 43.23 3.46
78 79 3.023832 CCATAAATTCCGAAGCCACCTT 58.976 45.455 0.00 0.00 0.00 3.50
79 80 2.241176 TCCATAAATTCCGAAGCCACCT 59.759 45.455 0.00 0.00 0.00 4.00
80 81 2.650322 TCCATAAATTCCGAAGCCACC 58.350 47.619 0.00 0.00 0.00 4.61
81 82 3.632145 ACATCCATAAATTCCGAAGCCAC 59.368 43.478 0.00 0.00 0.00 5.01
82 83 3.897239 ACATCCATAAATTCCGAAGCCA 58.103 40.909 0.00 0.00 0.00 4.75
83 84 6.575162 AATACATCCATAAATTCCGAAGCC 57.425 37.500 0.00 0.00 0.00 4.35
84 85 7.875971 AGAAATACATCCATAAATTCCGAAGC 58.124 34.615 0.00 0.00 0.00 3.86
85 86 9.884465 GAAGAAATACATCCATAAATTCCGAAG 57.116 33.333 0.00 0.00 0.00 3.79
86 87 8.556194 CGAAGAAATACATCCATAAATTCCGAA 58.444 33.333 0.00 0.00 0.00 4.30
87 88 7.713507 ACGAAGAAATACATCCATAAATTCCGA 59.286 33.333 0.00 0.00 0.00 4.55
88 89 7.861630 ACGAAGAAATACATCCATAAATTCCG 58.138 34.615 0.00 0.00 0.00 4.30
92 93 9.847224 ACCTTACGAAGAAATACATCCATAAAT 57.153 29.630 0.00 0.00 0.00 1.40
93 94 9.321562 GACCTTACGAAGAAATACATCCATAAA 57.678 33.333 0.00 0.00 0.00 1.40
94 95 8.701895 AGACCTTACGAAGAAATACATCCATAA 58.298 33.333 0.00 0.00 0.00 1.90
95 96 8.246430 AGACCTTACGAAGAAATACATCCATA 57.754 34.615 0.00 0.00 0.00 2.74
96 97 7.125792 AGACCTTACGAAGAAATACATCCAT 57.874 36.000 0.00 0.00 0.00 3.41
97 98 6.540438 AGACCTTACGAAGAAATACATCCA 57.460 37.500 0.00 0.00 0.00 3.41
98 99 7.039882 TCAAGACCTTACGAAGAAATACATCC 58.960 38.462 0.00 0.00 0.00 3.51
99 100 8.543774 CATCAAGACCTTACGAAGAAATACATC 58.456 37.037 0.00 0.00 0.00 3.06
100 101 8.258007 TCATCAAGACCTTACGAAGAAATACAT 58.742 33.333 0.00 0.00 0.00 2.29
101 102 7.608153 TCATCAAGACCTTACGAAGAAATACA 58.392 34.615 0.00 0.00 0.00 2.29
102 103 8.475331 TTCATCAAGACCTTACGAAGAAATAC 57.525 34.615 0.00 0.00 0.00 1.89
104 105 9.667107 TTATTCATCAAGACCTTACGAAGAAAT 57.333 29.630 0.00 0.00 0.00 2.17
105 106 9.667107 ATTATTCATCAAGACCTTACGAAGAAA 57.333 29.630 0.00 0.00 0.00 2.52
106 107 9.667107 AATTATTCATCAAGACCTTACGAAGAA 57.333 29.630 0.00 0.00 0.00 2.52
129 130 8.977505 GCGATGCATACAACCATTTTATTAATT 58.022 29.630 0.00 0.00 0.00 1.40
130 131 7.598493 GGCGATGCATACAACCATTTTATTAAT 59.402 33.333 0.00 0.00 0.00 1.40
131 132 6.920758 GGCGATGCATACAACCATTTTATTAA 59.079 34.615 0.00 0.00 0.00 1.40
132 133 6.442952 GGCGATGCATACAACCATTTTATTA 58.557 36.000 0.00 0.00 0.00 0.98
133 134 5.288804 GGCGATGCATACAACCATTTTATT 58.711 37.500 0.00 0.00 0.00 1.40
134 135 4.261994 GGGCGATGCATACAACCATTTTAT 60.262 41.667 0.00 0.00 0.00 1.40
135 136 3.067461 GGGCGATGCATACAACCATTTTA 59.933 43.478 0.00 0.00 0.00 1.52
136 137 2.159114 GGGCGATGCATACAACCATTTT 60.159 45.455 0.00 0.00 0.00 1.82
137 138 1.408702 GGGCGATGCATACAACCATTT 59.591 47.619 0.00 0.00 0.00 2.32
138 139 1.032014 GGGCGATGCATACAACCATT 58.968 50.000 0.00 0.00 0.00 3.16
139 140 0.183492 AGGGCGATGCATACAACCAT 59.817 50.000 0.00 0.00 0.00 3.55
140 141 0.463654 GAGGGCGATGCATACAACCA 60.464 55.000 0.00 0.00 0.00 3.67
141 142 0.463654 TGAGGGCGATGCATACAACC 60.464 55.000 0.00 0.00 0.00 3.77
142 143 1.532868 GATGAGGGCGATGCATACAAC 59.467 52.381 0.00 0.00 0.00 3.32
143 144 1.543208 GGATGAGGGCGATGCATACAA 60.543 52.381 0.00 0.00 0.00 2.41
144 145 0.035317 GGATGAGGGCGATGCATACA 59.965 55.000 0.00 0.00 0.00 2.29
145 146 0.322975 AGGATGAGGGCGATGCATAC 59.677 55.000 0.00 0.00 0.00 2.39
146 147 0.610174 GAGGATGAGGGCGATGCATA 59.390 55.000 0.00 0.00 0.00 3.14
147 148 1.374190 GAGGATGAGGGCGATGCAT 59.626 57.895 0.00 0.00 0.00 3.96
148 149 2.811514 GGAGGATGAGGGCGATGCA 61.812 63.158 0.00 0.00 0.00 3.96
149 150 2.031768 GGAGGATGAGGGCGATGC 59.968 66.667 0.00 0.00 0.00 3.91
150 151 0.471617 AAAGGAGGATGAGGGCGATG 59.528 55.000 0.00 0.00 0.00 3.84
151 152 1.141858 GAAAAGGAGGATGAGGGCGAT 59.858 52.381 0.00 0.00 0.00 4.58
152 153 0.541863 GAAAAGGAGGATGAGGGCGA 59.458 55.000 0.00 0.00 0.00 5.54
153 154 0.253044 TGAAAAGGAGGATGAGGGCG 59.747 55.000 0.00 0.00 0.00 6.13
154 155 2.514458 TTGAAAAGGAGGATGAGGGC 57.486 50.000 0.00 0.00 0.00 5.19
192 193 7.948034 ACTCTCTAAGCTATTCAGTACAGTT 57.052 36.000 0.00 0.00 0.00 3.16
230 232 9.632969 CAAAGTAATTAACGAATCAGGTAATCG 57.367 33.333 0.00 0.00 42.05 3.34
232 234 8.899771 CCCAAAGTAATTAACGAATCAGGTAAT 58.100 33.333 0.00 0.00 35.69 1.89
287 289 1.135257 AGAGTGGCGAAGAATGTCTCG 60.135 52.381 0.00 0.00 0.00 4.04
295 297 4.537135 ACATTTTAGAGAGTGGCGAAGA 57.463 40.909 0.00 0.00 0.00 2.87
296 298 5.220491 GCTTACATTTTAGAGAGTGGCGAAG 60.220 44.000 0.00 0.00 0.00 3.79
365 367 7.968014 AGATATTTTGCCAATCTTCTCCTTT 57.032 32.000 0.00 0.00 0.00 3.11
366 368 7.968014 AAGATATTTTGCCAATCTTCTCCTT 57.032 32.000 0.00 0.00 35.55 3.36
367 369 7.230309 GCTAAGATATTTTGCCAATCTTCTCCT 59.770 37.037 0.36 0.00 39.85 3.69
368 370 7.230309 AGCTAAGATATTTTGCCAATCTTCTCC 59.770 37.037 0.36 0.00 39.85 3.71
369 371 8.164058 AGCTAAGATATTTTGCCAATCTTCTC 57.836 34.615 0.36 0.00 39.85 2.87
378 380 7.596621 GCATTCCTAAAGCTAAGATATTTTGCC 59.403 37.037 0.00 0.00 0.00 4.52
426 428 1.549203 CCCCCATGGTTCTGTTTCTG 58.451 55.000 11.73 0.00 0.00 3.02
438 440 4.365514 TGTATAATGCACTACCCCCATG 57.634 45.455 0.00 0.00 0.00 3.66
446 448 5.063691 CCGTTCGGTTTTGTATAATGCACTA 59.936 40.000 2.82 0.00 0.00 2.74
457 459 4.633565 TGTACTTTTACCGTTCGGTTTTGT 59.366 37.500 21.64 16.26 39.52 2.83
494 502 7.039714 ACAGATGAAAGGAATTGGGTTTAAGTC 60.040 37.037 0.00 0.00 0.00 3.01
562 582 2.669391 CGGCTCTTCTGAAATTGTTGGC 60.669 50.000 0.00 0.00 0.00 4.52
567 587 1.135575 GTGGCGGCTCTTCTGAAATTG 60.136 52.381 11.43 0.00 0.00 2.32
593 613 1.694150 ACAGAACAGAGGCAAGTGCTA 59.306 47.619 2.85 0.00 41.70 3.49
596 616 2.805099 GAGAACAGAACAGAGGCAAGTG 59.195 50.000 0.00 0.00 0.00 3.16
597 617 2.703007 AGAGAACAGAACAGAGGCAAGT 59.297 45.455 0.00 0.00 0.00 3.16
612 650 6.610741 AGAACATGAGAAACAACAGAGAAC 57.389 37.500 0.00 0.00 0.00 3.01
632 670 1.078709 CTGCGGCTCGATTTGAAGAA 58.921 50.000 0.00 0.00 0.00 2.52
671 709 1.117749 TGGAGAGGATGGCAGATCGG 61.118 60.000 0.00 0.00 0.00 4.18
681 719 0.189822 GGGAGCTAGGTGGAGAGGAT 59.810 60.000 0.00 0.00 0.00 3.24
752 796 3.563808 TGATGAACTGGGAAAAGACAACG 59.436 43.478 0.00 0.00 0.00 4.10
753 797 5.335976 GGATGATGAACTGGGAAAAGACAAC 60.336 44.000 0.00 0.00 0.00 3.32
754 798 4.766891 GGATGATGAACTGGGAAAAGACAA 59.233 41.667 0.00 0.00 0.00 3.18
780 824 5.163913 CCATGAGCGAAACAAACAAACAAAA 60.164 36.000 0.00 0.00 0.00 2.44
824 868 5.582950 TCCTTTTCTTTTCTGATGAGGGA 57.417 39.130 0.00 0.00 0.00 4.20
897 942 2.189784 GGGGCGAGAGGGCTTAAC 59.810 66.667 0.00 0.00 41.87 2.01
898 943 3.467226 CGGGGCGAGAGGGCTTAA 61.467 66.667 0.00 0.00 41.87 1.85
899 944 4.452251 TCGGGGCGAGAGGGCTTA 62.452 66.667 0.00 0.00 41.87 3.09
997 1059 1.208052 CTTCCTCTTCTTCGCCATGGA 59.792 52.381 18.40 0.00 0.00 3.41
1045 1107 2.110967 CGTCGGGCTTCTCTACGGA 61.111 63.158 0.00 0.00 0.00 4.69
1173 1235 2.076863 GAGCACGTAATGAGCACCTTT 58.923 47.619 0.00 0.00 36.53 3.11
1241 1314 2.172483 AAAGCATCTGTCCGGCGACT 62.172 55.000 9.30 0.00 39.94 4.18
1271 1361 1.900981 CACGCATCAACCCAACCCA 60.901 57.895 0.00 0.00 0.00 4.51
1930 2091 5.387113 TGGGCATTAGTAGATGAACCATT 57.613 39.130 0.00 0.00 33.50 3.16
1934 2095 4.523083 TGGTTGGGCATTAGTAGATGAAC 58.477 43.478 0.00 0.00 0.00 3.18
2057 2218 1.669115 CCAGTGAGGTTGCTGGTCG 60.669 63.158 2.66 0.00 45.28 4.79
2432 2600 6.013984 AGGTTTCCGTTAACTTGGATCTCTTA 60.014 38.462 3.71 0.00 33.42 2.10
2449 2617 5.699097 TTTTAACATCCAGAAGGTTTCCG 57.301 39.130 0.00 0.00 35.89 4.30
2554 2722 7.792364 TTGACCCTATCGGAATGTATTATCT 57.208 36.000 0.00 0.00 34.64 1.98
3042 3354 8.368668 CCACCAAAACTACCACCAAATATTTTA 58.631 33.333 0.00 0.00 0.00 1.52
3181 3498 4.164988 CCTTGATGATGGAAGAGGTAACCT 59.835 45.833 0.00 0.00 36.03 3.50
3325 8051 6.982141 TGGTTGTACCATAACTGATATCGAAC 59.018 38.462 0.00 0.00 44.79 3.95
3590 8706 7.369803 TGCTTTGTTGCAACTGAATTAAAAA 57.630 28.000 28.61 16.78 40.29 1.94
3591 8707 6.974932 TGCTTTGTTGCAACTGAATTAAAA 57.025 29.167 28.61 17.42 40.29 1.52
3695 8814 1.003696 GTACTTGCCTGCCTTCTTCCT 59.996 52.381 0.00 0.00 0.00 3.36
4033 9180 4.535781 TGCAATTATATCAGGCACAAGGT 58.464 39.130 0.00 0.00 0.00 3.50
4082 9229 8.786826 TTGAGATCATATCAACCGTTTTTACT 57.213 30.769 0.00 0.00 31.86 2.24
4107 9254 1.620819 AGATCCAAGCAGAACACGACT 59.379 47.619 0.00 0.00 0.00 4.18
4121 9268 6.343703 CAAGTATCACTCATCAACAGATCCA 58.656 40.000 0.00 0.00 0.00 3.41
4274 9427 3.826157 TCCATTCCTGCAAACCAAAGTAG 59.174 43.478 0.00 0.00 0.00 2.57
4281 9434 5.859205 ATAGAAATCCATTCCTGCAAACC 57.141 39.130 0.00 0.00 38.94 3.27
4309 9462 6.347240 GCGCAAGGATAAGAATCAATACTCTG 60.347 42.308 0.30 0.00 33.41 3.35
4310 9463 5.698545 GCGCAAGGATAAGAATCAATACTCT 59.301 40.000 0.30 0.00 33.41 3.24
4331 9484 2.227865 TCTTGTAAACCAAATGAGGCGC 59.772 45.455 0.00 0.00 31.20 6.53
4332 9485 4.497473 TTCTTGTAAACCAAATGAGGCG 57.503 40.909 0.00 0.00 31.20 5.52
4423 9576 5.886960 ATCATGTAGAAACCTGCACTTTC 57.113 39.130 4.54 4.54 0.00 2.62
4424 9577 6.006449 AGAATCATGTAGAAACCTGCACTTT 58.994 36.000 0.00 0.00 0.00 2.66
4425 9578 5.564550 AGAATCATGTAGAAACCTGCACTT 58.435 37.500 0.00 0.00 0.00 3.16
4428 9581 7.446931 TGTTTTAGAATCATGTAGAAACCTGCA 59.553 33.333 0.00 0.00 0.00 4.41
4429 9582 7.816640 TGTTTTAGAATCATGTAGAAACCTGC 58.183 34.615 0.00 0.00 0.00 4.85
4430 9583 7.965107 GCTGTTTTAGAATCATGTAGAAACCTG 59.035 37.037 0.00 0.00 0.00 4.00
4431 9584 7.665559 TGCTGTTTTAGAATCATGTAGAAACCT 59.334 33.333 0.00 0.00 0.00 3.50
4432 9585 7.816640 TGCTGTTTTAGAATCATGTAGAAACC 58.183 34.615 0.00 0.00 0.00 3.27
4435 9588 9.330063 CCTATGCTGTTTTAGAATCATGTAGAA 57.670 33.333 0.00 0.00 0.00 2.10
4483 9794 7.930865 GCATCTCATCTACAAAAGAATACCTCT 59.069 37.037 0.00 0.00 37.89 3.69
4485 9796 7.497249 GTGCATCTCATCTACAAAAGAATACCT 59.503 37.037 0.00 0.00 37.89 3.08
4574 9885 7.380536 TGAAGTGTTTTACTATCGGCTTCTTA 58.619 34.615 0.00 0.00 39.18 2.10
4641 9952 1.423541 ACAGGCCAGGTGTCATTAACA 59.576 47.619 5.01 0.00 34.78 2.41
4644 9955 2.500098 GTCTACAGGCCAGGTGTCATTA 59.500 50.000 5.01 0.00 0.00 1.90
4696 10007 2.708051 TCAGATTCTTGCCTCAGCTTG 58.292 47.619 0.00 0.00 40.80 4.01
4711 10022 7.944061 TCAGATTGTCAAACAAACATTCAGAT 58.056 30.769 0.00 0.00 41.96 2.90
4714 10025 8.945481 AAATCAGATTGTCAAACAAACATTCA 57.055 26.923 0.00 0.00 41.96 2.57
4755 10066 4.962362 TGGGCTACAGATAGTGATTCTCAA 59.038 41.667 0.00 0.00 0.00 3.02
4771 10082 1.270094 GTGGCCTTTGTTTTGGGCTAC 60.270 52.381 3.32 4.16 46.75 3.58
4784 10095 1.490910 GCTTACTATGGAGGTGGCCTT 59.509 52.381 3.32 0.00 31.76 4.35
4785 10096 1.132500 GCTTACTATGGAGGTGGCCT 58.868 55.000 3.32 0.00 36.03 5.19
4786 10097 0.837272 TGCTTACTATGGAGGTGGCC 59.163 55.000 0.00 0.00 0.00 5.36
4787 10098 1.202698 CCTGCTTACTATGGAGGTGGC 60.203 57.143 2.27 0.00 38.09 5.01
4788 10099 2.366916 CTCCTGCTTACTATGGAGGTGG 59.633 54.545 8.75 2.05 42.58 4.61
4789 10100 3.300388 TCTCCTGCTTACTATGGAGGTG 58.700 50.000 7.86 7.13 44.43 4.00
4790 10101 3.205507 TCTCTCCTGCTTACTATGGAGGT 59.794 47.826 7.86 0.00 44.43 3.85
4791 10102 3.838565 TCTCTCCTGCTTACTATGGAGG 58.161 50.000 7.86 3.73 44.43 4.30


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

AutoCloner maintained by Alex Coulton.