Multiple sequence alignment - TraesCS5D01G362400

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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 TraesCS5D01G362400 chr5D 100.000 4016 0 0 1 4016 441026908 441022893 0.000000e+00 7417.0
1 TraesCS5D01G362400 chr5D 92.214 411 30 2 358 768 190649144 190649552 7.480000e-162 580.0
2 TraesCS5D01G362400 chr5D 91.469 422 34 2 358 779 239964234 239963815 2.690000e-161 579.0
3 TraesCS5D01G362400 chr5D 91.667 420 31 4 350 768 266177365 266177781 2.690000e-161 579.0
4 TraesCS5D01G362400 chr5D 94.805 77 4 0 1924 2000 441024701 441024625 1.960000e-23 121.0
5 TraesCS5D01G362400 chr5D 94.805 77 4 0 2208 2284 441024985 441024909 1.960000e-23 121.0
6 TraesCS5D01G362400 chr5B 92.390 1498 75 13 1896 3372 536592190 536590711 0.000000e+00 2098.0
7 TraesCS5D01G362400 chr5B 91.771 802 39 13 769 1550 536593143 536592349 0.000000e+00 1090.0
8 TraesCS5D01G362400 chr5B 92.473 651 30 6 3380 4016 536590193 536589548 0.000000e+00 913.0
9 TraesCS5D01G362400 chr5B 94.020 301 13 3 879 1175 536596053 536595754 6.120000e-123 451.0
10 TraesCS5D01G362400 chr5B 91.192 193 16 1 1549 1741 656171512 656171703 1.110000e-65 261.0
11 TraesCS5D01G362400 chr5B 92.308 182 13 1 1548 1729 528368549 528368729 1.430000e-64 257.0
12 TraesCS5D01G362400 chr5B 95.690 116 3 2 769 883 536596204 536596090 6.850000e-43 185.0
13 TraesCS5D01G362400 chr5B 92.969 128 7 2 227 353 701685997 701686123 6.850000e-43 185.0
14 TraesCS5D01G362400 chr5B 91.603 131 10 1 1739 1869 528368852 528368981 3.190000e-41 180.0
15 TraesCS5D01G362400 chr5B 87.387 111 11 2 2209 2319 536592161 536592054 1.520000e-24 124.0
16 TraesCS5D01G362400 chr5A 90.625 1216 82 12 1866 3075 557131703 557130514 0.000000e+00 1585.0
17 TraesCS5D01G362400 chr5A 90.437 732 42 13 3306 4016 557130217 557129493 0.000000e+00 939.0
18 TraesCS5D01G362400 chr5A 89.655 609 40 8 936 1535 557132316 557131722 0.000000e+00 754.0
19 TraesCS5D01G362400 chr5A 91.667 132 10 1 222 353 682708258 682708388 8.870000e-42 182.0
20 TraesCS5D01G362400 chr5A 85.124 121 15 1 2209 2329 557131644 557131527 1.960000e-23 121.0
21 TraesCS5D01G362400 chr5A 87.179 78 10 0 1923 2000 557131375 557131298 5.530000e-14 89.8
22 TraesCS5D01G362400 chr4D 92.736 413 27 3 358 769 67421728 67422138 9.610000e-166 593.0
23 TraesCS5D01G362400 chr4D 91.489 423 35 1 349 770 67421709 67421287 7.480000e-162 580.0
24 TraesCS5D01G362400 chr4D 95.122 123 5 1 231 353 67422137 67422016 4.100000e-45 193.0
25 TraesCS5D01G362400 chr4D 92.366 131 8 2 224 353 92767124 92767253 6.850000e-43 185.0
26 TraesCS5D01G362400 chr2D 92.233 412 30 2 358 768 64993432 64993022 2.080000e-162 582.0
27 TraesCS5D01G362400 chr2D 94.330 194 11 0 1549 1742 98660558 98660751 8.440000e-77 298.0
28 TraesCS5D01G362400 chr2D 93.525 139 8 1 1739 1877 98660833 98660970 5.260000e-49 206.0
29 TraesCS5D01G362400 chr2D 94.488 127 4 3 228 353 322946897 322946773 4.100000e-45 193.0
30 TraesCS5D01G362400 chr7D 91.866 418 31 2 358 772 354133954 354133537 7.480000e-162 580.0
31 TraesCS5D01G362400 chr7D 90.487 431 40 1 349 778 244723506 244723936 5.820000e-158 568.0
32 TraesCS5D01G362400 chr7D 92.818 181 13 0 1549 1729 626481366 626481546 3.080000e-66 263.0
33 TraesCS5D01G362400 chr7D 93.182 132 6 3 222 352 211659191 211659320 1.470000e-44 191.0
34 TraesCS5D01G362400 chr7D 91.667 132 9 2 222 353 87744039 87744168 8.870000e-42 182.0
35 TraesCS5D01G362400 chr7D 87.786 131 15 1 1739 1869 535656636 535656765 6.950000e-33 152.0
36 TraesCS5D01G362400 chr4B 92.233 412 29 3 358 768 407730416 407730007 7.480000e-162 580.0
37 TraesCS5D01G362400 chr1A 94.845 194 10 0 1549 1742 397416148 397416341 1.810000e-78 303.0
38 TraesCS5D01G362400 chr1A 93.893 131 8 0 1739 1869 397416440 397416570 8.800000e-47 198.0
39 TraesCS5D01G362400 chr4A 93.814 194 12 0 1549 1742 508934404 508934211 3.930000e-75 292.0
40 TraesCS5D01G362400 chr4A 95.420 131 6 0 1739 1869 508934112 508933982 4.070000e-50 209.0
41 TraesCS5D01G362400 chr2B 91.667 180 14 1 1549 1728 83174557 83174379 8.620000e-62 248.0
42 TraesCS5D01G362400 chr2B 87.234 141 16 2 1739 1879 83172493 83172355 4.150000e-35 159.0
43 TraesCS5D01G362400 chr6A 93.373 166 11 0 1577 1742 467574827 467574662 3.100000e-61 246.0
44 TraesCS5D01G362400 chr6A 93.130 131 9 0 1739 1869 467574563 467574433 4.100000e-45 193.0
45 TraesCS5D01G362400 chr3A 92.500 160 12 0 1570 1729 94568666 94568825 3.120000e-56 230.0
46 TraesCS5D01G362400 chr3A 95.495 111 4 1 1739 1848 94569847 94569957 4.130000e-40 176.0
47 TraesCS5D01G362400 chr6B 93.651 126 7 1 228 353 309757652 309757776 1.910000e-43 187.0
48 TraesCS5D01G362400 chr3D 92.366 131 6 4 224 353 538691242 538691369 2.470000e-42 183.0
49 TraesCS5D01G362400 chr7A 85.714 112 16 0 1758 1869 546432480 546432369 7.050000e-23 119.0
50 TraesCS5D01G362400 chr3B 93.333 45 2 1 1540 1583 433572937 433572893 9.320000e-07 65.8
51 TraesCS5D01G362400 chr3B 80.769 78 11 4 1532 1606 709513625 709513701 1.560000e-04 58.4


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 TraesCS5D01G362400 chr5D 441022893 441026908 4015 True 2553.000000 7417 96.536667 1 4016 3 chr5D.!!$R2 4015
1 TraesCS5D01G362400 chr5B 536589548 536596204 6656 True 810.166667 2098 92.288500 769 4016 6 chr5B.!!$R1 3247
2 TraesCS5D01G362400 chr5A 557129493 557132316 2823 True 697.760000 1585 88.604000 936 4016 5 chr5A.!!$R1 3080
3 TraesCS5D01G362400 chr4D 67421287 67422137 850 True 386.500000 580 93.305500 231 770 2 chr4D.!!$R1 539
4 TraesCS5D01G362400 chr2B 83172355 83174557 2202 True 203.500000 248 89.450500 1549 1879 2 chr2B.!!$R1 330
5 TraesCS5D01G362400 chr3A 94568666 94569957 1291 False 203.000000 230 93.997500 1570 1848 2 chr3A.!!$F1 278

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
217 218 0.034283 TGCCCAGATGCATTGCAGTA 60.034 50.0 17.52 0.00 43.65 2.74 F
708 1021 0.316689 GGCAAGACCACGTGTTTTCG 60.317 55.0 15.65 0.51 38.86 3.46 F
1319 4706 0.034476 GTTCCGGTCCGAGGTTTCTT 59.966 55.0 14.39 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 4706 0.698238 CCCACCAGATCCAGGAAACA 59.302 55.0 8.69 0.0 0.00 2.83 R
2697 8111 0.248012 TTATCGAGCCTTGCCGACAA 59.752 50.0 0.00 0.0 35.11 3.18 R
3137 8598 0.920664 GTGCAGTGCGTTTCCAAAAC 59.079 50.0 11.20 0.0 0.00 2.43 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
24 25 7.921041 TTGTATCCTCTTCCACAATCTATCT 57.079 36.000 0.00 0.00 0.00 1.98
25 26 7.921041 TGTATCCTCTTCCACAATCTATCTT 57.079 36.000 0.00 0.00 0.00 2.40
26 27 8.324191 TGTATCCTCTTCCACAATCTATCTTT 57.676 34.615 0.00 0.00 0.00 2.52
27 28 8.772250 TGTATCCTCTTCCACAATCTATCTTTT 58.228 33.333 0.00 0.00 0.00 2.27
59 60 7.589958 TGAATACTCCACTCTTAGATCTTCC 57.410 40.000 0.00 0.00 0.00 3.46
60 61 6.551601 TGAATACTCCACTCTTAGATCTTCCC 59.448 42.308 0.00 0.00 0.00 3.97
61 62 4.338795 ACTCCACTCTTAGATCTTCCCA 57.661 45.455 0.00 0.00 0.00 4.37
62 63 4.027437 ACTCCACTCTTAGATCTTCCCAC 58.973 47.826 0.00 0.00 0.00 4.61
63 64 4.026744 CTCCACTCTTAGATCTTCCCACA 58.973 47.826 0.00 0.00 0.00 4.17
64 65 4.624913 TCCACTCTTAGATCTTCCCACAT 58.375 43.478 0.00 0.00 0.00 3.21
65 66 4.406972 TCCACTCTTAGATCTTCCCACATG 59.593 45.833 0.00 0.00 0.00 3.21
66 67 4.406972 CCACTCTTAGATCTTCCCACATGA 59.593 45.833 0.00 0.00 0.00 3.07
67 68 5.453057 CCACTCTTAGATCTTCCCACATGAG 60.453 48.000 0.00 1.53 0.00 2.90
68 69 5.128499 CACTCTTAGATCTTCCCACATGAGT 59.872 44.000 0.00 2.18 0.00 3.41
69 70 6.322456 CACTCTTAGATCTTCCCACATGAGTA 59.678 42.308 0.00 0.00 31.09 2.59
70 71 6.549364 ACTCTTAGATCTTCCCACATGAGTAG 59.451 42.308 0.00 0.00 30.59 2.57
71 72 5.835819 TCTTAGATCTTCCCACATGAGTAGG 59.164 44.000 0.00 0.00 0.00 3.18
72 73 2.703007 AGATCTTCCCACATGAGTAGGC 59.297 50.000 0.00 0.00 0.00 3.93
73 74 1.951209 TCTTCCCACATGAGTAGGCA 58.049 50.000 0.00 0.00 0.00 4.75
74 75 2.265367 TCTTCCCACATGAGTAGGCAA 58.735 47.619 0.00 0.00 0.00 4.52
75 76 2.846206 TCTTCCCACATGAGTAGGCAAT 59.154 45.455 0.00 0.00 0.00 3.56
76 77 3.118261 TCTTCCCACATGAGTAGGCAATC 60.118 47.826 0.00 0.00 0.00 2.67
77 78 1.490490 TCCCACATGAGTAGGCAATCC 59.510 52.381 0.00 0.00 0.00 3.01
78 79 1.492176 CCCACATGAGTAGGCAATCCT 59.508 52.381 0.00 0.00 46.57 3.24
79 80 2.705658 CCCACATGAGTAGGCAATCCTA 59.294 50.000 0.00 0.00 43.91 2.94
80 81 3.244353 CCCACATGAGTAGGCAATCCTAG 60.244 52.174 0.00 0.00 45.23 3.02
81 82 3.643320 CCACATGAGTAGGCAATCCTAGA 59.357 47.826 0.00 0.00 45.23 2.43
82 83 4.285517 CCACATGAGTAGGCAATCCTAGAT 59.714 45.833 0.00 0.00 45.23 1.98
83 84 5.236282 CACATGAGTAGGCAATCCTAGATG 58.764 45.833 0.00 0.00 45.23 2.90
84 85 4.252073 CATGAGTAGGCAATCCTAGATGC 58.748 47.826 6.59 6.59 45.23 3.91
85 86 3.581101 TGAGTAGGCAATCCTAGATGCT 58.419 45.455 12.72 4.65 45.23 3.79
86 87 3.969976 TGAGTAGGCAATCCTAGATGCTT 59.030 43.478 12.72 9.12 45.23 3.91
87 88 4.039730 TGAGTAGGCAATCCTAGATGCTTC 59.960 45.833 12.72 0.00 45.23 3.86
88 89 4.230455 AGTAGGCAATCCTAGATGCTTCT 58.770 43.478 7.35 7.35 45.23 2.85
89 90 3.767902 AGGCAATCCTAGATGCTTCTC 57.232 47.619 5.22 0.00 42.06 2.87
90 91 3.316501 AGGCAATCCTAGATGCTTCTCT 58.683 45.455 5.22 0.00 42.06 3.10
91 92 3.071312 AGGCAATCCTAGATGCTTCTCTG 59.929 47.826 5.22 0.96 42.06 3.35
92 93 3.070734 GGCAATCCTAGATGCTTCTCTGA 59.929 47.826 5.22 4.61 42.20 3.27
93 94 4.262981 GGCAATCCTAGATGCTTCTCTGAT 60.263 45.833 5.22 6.67 42.20 2.90
94 95 5.046735 GGCAATCCTAGATGCTTCTCTGATA 60.047 44.000 5.22 0.00 42.20 2.15
95 96 6.101332 GCAATCCTAGATGCTTCTCTGATAG 58.899 44.000 5.22 0.00 39.46 2.08
96 97 6.295236 GCAATCCTAGATGCTTCTCTGATAGT 60.295 42.308 5.22 0.00 39.46 2.12
97 98 6.839124 ATCCTAGATGCTTCTCTGATAGTG 57.161 41.667 5.22 0.00 33.17 2.74
98 99 4.522405 TCCTAGATGCTTCTCTGATAGTGC 59.478 45.833 5.22 0.00 33.17 4.40
99 100 4.523943 CCTAGATGCTTCTCTGATAGTGCT 59.476 45.833 5.22 0.00 33.17 4.40
100 101 5.010922 CCTAGATGCTTCTCTGATAGTGCTT 59.989 44.000 5.22 0.00 33.17 3.91
101 102 4.947645 AGATGCTTCTCTGATAGTGCTTC 58.052 43.478 0.00 0.00 34.04 3.86
102 103 4.650588 AGATGCTTCTCTGATAGTGCTTCT 59.349 41.667 0.00 0.00 36.50 2.85
103 104 4.120792 TGCTTCTCTGATAGTGCTTCTG 57.879 45.455 0.00 0.00 0.00 3.02
104 105 3.766051 TGCTTCTCTGATAGTGCTTCTGA 59.234 43.478 0.00 0.00 0.00 3.27
105 106 4.142204 TGCTTCTCTGATAGTGCTTCTGAG 60.142 45.833 0.00 0.00 39.31 3.35
133 134 5.209818 CCCCCAAAAACTTCTTTAACCTC 57.790 43.478 0.00 0.00 0.00 3.85
134 135 4.651962 CCCCCAAAAACTTCTTTAACCTCA 59.348 41.667 0.00 0.00 0.00 3.86
135 136 5.306937 CCCCCAAAAACTTCTTTAACCTCAT 59.693 40.000 0.00 0.00 0.00 2.90
136 137 6.455647 CCCCAAAAACTTCTTTAACCTCATC 58.544 40.000 0.00 0.00 0.00 2.92
137 138 6.267699 CCCCAAAAACTTCTTTAACCTCATCT 59.732 38.462 0.00 0.00 0.00 2.90
138 139 7.202001 CCCCAAAAACTTCTTTAACCTCATCTT 60.202 37.037 0.00 0.00 0.00 2.40
139 140 7.867909 CCCAAAAACTTCTTTAACCTCATCTTC 59.132 37.037 0.00 0.00 0.00 2.87
140 141 7.867909 CCAAAAACTTCTTTAACCTCATCTTCC 59.132 37.037 0.00 0.00 0.00 3.46
141 142 8.413229 CAAAAACTTCTTTAACCTCATCTTCCA 58.587 33.333 0.00 0.00 0.00 3.53
142 143 7.751768 AAACTTCTTTAACCTCATCTTCCAG 57.248 36.000 0.00 0.00 0.00 3.86
143 144 5.249420 ACTTCTTTAACCTCATCTTCCAGC 58.751 41.667 0.00 0.00 0.00 4.85
144 145 5.013599 ACTTCTTTAACCTCATCTTCCAGCT 59.986 40.000 0.00 0.00 0.00 4.24
145 146 5.091261 TCTTTAACCTCATCTTCCAGCTC 57.909 43.478 0.00 0.00 0.00 4.09
146 147 4.532126 TCTTTAACCTCATCTTCCAGCTCA 59.468 41.667 0.00 0.00 0.00 4.26
147 148 5.190528 TCTTTAACCTCATCTTCCAGCTCAT 59.809 40.000 0.00 0.00 0.00 2.90
148 149 5.441718 TTAACCTCATCTTCCAGCTCATT 57.558 39.130 0.00 0.00 0.00 2.57
149 150 6.560003 TTAACCTCATCTTCCAGCTCATTA 57.440 37.500 0.00 0.00 0.00 1.90
150 151 4.686191 ACCTCATCTTCCAGCTCATTAG 57.314 45.455 0.00 0.00 0.00 1.73
151 152 3.390639 ACCTCATCTTCCAGCTCATTAGG 59.609 47.826 0.00 0.00 0.00 2.69
152 153 3.645212 CCTCATCTTCCAGCTCATTAGGA 59.355 47.826 0.00 0.00 0.00 2.94
153 154 4.502950 CCTCATCTTCCAGCTCATTAGGAC 60.503 50.000 0.00 0.00 0.00 3.85
154 155 4.033009 TCATCTTCCAGCTCATTAGGACA 58.967 43.478 0.00 0.00 0.00 4.02
155 156 4.657504 TCATCTTCCAGCTCATTAGGACAT 59.342 41.667 0.00 0.00 0.00 3.06
156 157 5.131642 TCATCTTCCAGCTCATTAGGACATT 59.868 40.000 0.00 0.00 0.00 2.71
157 158 5.441718 TCTTCCAGCTCATTAGGACATTT 57.558 39.130 0.00 0.00 0.00 2.32
158 159 5.819991 TCTTCCAGCTCATTAGGACATTTT 58.180 37.500 0.00 0.00 0.00 1.82
159 160 6.248433 TCTTCCAGCTCATTAGGACATTTTT 58.752 36.000 0.00 0.00 0.00 1.94
198 199 6.971932 AGGACTTCTCCTAATTTACCCTTT 57.028 37.500 0.00 0.00 46.16 3.11
199 200 6.722328 AGGACTTCTCCTAATTTACCCTTTG 58.278 40.000 0.00 0.00 46.16 2.77
200 201 5.357314 GGACTTCTCCTAATTTACCCTTTGC 59.643 44.000 0.00 0.00 33.07 3.68
201 202 5.262009 ACTTCTCCTAATTTACCCTTTGCC 58.738 41.667 0.00 0.00 0.00 4.52
202 203 4.245251 TCTCCTAATTTACCCTTTGCCC 57.755 45.455 0.00 0.00 0.00 5.36
203 204 3.594232 TCTCCTAATTTACCCTTTGCCCA 59.406 43.478 0.00 0.00 0.00 5.36
204 205 3.954258 CTCCTAATTTACCCTTTGCCCAG 59.046 47.826 0.00 0.00 0.00 4.45
205 206 3.594232 TCCTAATTTACCCTTTGCCCAGA 59.406 43.478 0.00 0.00 0.00 3.86
206 207 4.231890 TCCTAATTTACCCTTTGCCCAGAT 59.768 41.667 0.00 0.00 0.00 2.90
207 208 4.342092 CCTAATTTACCCTTTGCCCAGATG 59.658 45.833 0.00 0.00 0.00 2.90
208 209 1.555967 TTTACCCTTTGCCCAGATGC 58.444 50.000 0.00 0.00 0.00 3.91
209 210 0.407528 TTACCCTTTGCCCAGATGCA 59.592 50.000 0.00 0.00 40.07 3.96
210 211 0.630673 TACCCTTTGCCCAGATGCAT 59.369 50.000 0.00 0.00 41.70 3.96
211 212 0.252375 ACCCTTTGCCCAGATGCATT 60.252 50.000 0.00 0.00 41.70 3.56
212 213 0.177141 CCCTTTGCCCAGATGCATTG 59.823 55.000 0.00 1.14 41.70 2.82
213 214 0.461339 CCTTTGCCCAGATGCATTGC 60.461 55.000 0.00 0.46 41.70 3.56
214 215 0.248012 CTTTGCCCAGATGCATTGCA 59.752 50.000 14.72 14.72 44.86 4.08
215 216 0.248012 TTTGCCCAGATGCATTGCAG 59.752 50.000 17.52 4.02 43.65 4.41
216 217 0.901114 TTGCCCAGATGCATTGCAGT 60.901 50.000 17.52 3.96 43.65 4.40
217 218 0.034283 TGCCCAGATGCATTGCAGTA 60.034 50.000 17.52 0.00 43.65 2.74
218 219 0.383231 GCCCAGATGCATTGCAGTAC 59.617 55.000 17.52 10.67 43.65 2.73
219 220 1.753930 CCCAGATGCATTGCAGTACA 58.246 50.000 17.52 0.00 43.65 2.90
220 221 1.674441 CCCAGATGCATTGCAGTACAG 59.326 52.381 17.52 7.83 43.65 2.74
221 222 2.635714 CCAGATGCATTGCAGTACAGA 58.364 47.619 17.52 0.00 43.65 3.41
222 223 3.211865 CCAGATGCATTGCAGTACAGAT 58.788 45.455 17.52 0.00 43.65 2.90
223 224 4.383173 CCAGATGCATTGCAGTACAGATA 58.617 43.478 17.52 0.00 43.65 1.98
224 225 4.818005 CCAGATGCATTGCAGTACAGATAA 59.182 41.667 17.52 0.00 43.65 1.75
225 226 5.297527 CCAGATGCATTGCAGTACAGATAAA 59.702 40.000 17.52 0.00 43.65 1.40
226 227 6.427974 CAGATGCATTGCAGTACAGATAAAG 58.572 40.000 17.52 0.00 43.65 1.85
227 228 6.259387 CAGATGCATTGCAGTACAGATAAAGA 59.741 38.462 17.52 0.00 43.65 2.52
228 229 6.825213 AGATGCATTGCAGTACAGATAAAGAA 59.175 34.615 17.52 0.00 43.65 2.52
229 230 6.816134 TGCATTGCAGTACAGATAAAGAAA 57.184 33.333 7.38 0.00 33.32 2.52
279 280 1.080354 TCCCCCTCGTCAGGATTGT 59.920 57.895 0.00 0.00 43.65 2.71
281 282 1.264749 CCCCCTCGTCAGGATTGTCA 61.265 60.000 0.00 0.00 43.65 3.58
356 668 1.611491 TGCCCTTTGACCGATTGTTTC 59.389 47.619 0.00 0.00 0.00 2.78
391 703 2.691409 TCCACGAATGTCATTCCCTC 57.309 50.000 17.95 0.00 35.89 4.30
392 704 1.134818 TCCACGAATGTCATTCCCTCG 60.135 52.381 17.95 10.79 35.89 4.63
422 734 3.559242 TGGCAAGCACTTAAAACATTTGC 59.441 39.130 0.00 0.00 38.85 3.68
440 752 0.681175 GCCATTCTTTGCCACCAACT 59.319 50.000 0.00 0.00 0.00 3.16
441 753 1.070601 GCCATTCTTTGCCACCAACTT 59.929 47.619 0.00 0.00 0.00 2.66
445 757 4.273235 CCATTCTTTGCCACCAACTTTTTC 59.727 41.667 0.00 0.00 0.00 2.29
447 759 4.817318 TCTTTGCCACCAACTTTTTCTT 57.183 36.364 0.00 0.00 0.00 2.52
448 760 4.502962 TCTTTGCCACCAACTTTTTCTTG 58.497 39.130 0.00 0.00 0.00 3.02
452 764 5.096443 TGCCACCAACTTTTTCTTGAATT 57.904 34.783 0.00 0.00 0.00 2.17
453 765 5.115480 TGCCACCAACTTTTTCTTGAATTC 58.885 37.500 0.00 0.00 0.00 2.17
459 771 9.101655 CACCAACTTTTTCTTGAATTCTTTGAT 57.898 29.630 7.05 0.00 0.00 2.57
460 772 9.101655 ACCAACTTTTTCTTGAATTCTTTGATG 57.898 29.630 7.05 0.00 0.00 3.07
491 804 7.402054 AGATTTTACTGTTCATGGTGGTATGA 58.598 34.615 0.00 0.00 35.38 2.15
531 844 2.428890 TGGGCACTTACCAACACTTTTG 59.571 45.455 0.00 0.00 34.44 2.44
559 872 4.604843 ATGCAAGTGACATTGACATACG 57.395 40.909 0.00 0.00 30.44 3.06
560 873 2.741517 TGCAAGTGACATTGACATACGG 59.258 45.455 0.00 0.00 31.55 4.02
573 886 4.647611 TGACATACGGGTGATGTTTTTCT 58.352 39.130 0.00 0.00 37.65 2.52
651 964 4.477780 GTTTTCAAAGTGACGGTCAAACA 58.522 39.130 13.23 0.00 28.17 2.83
660 973 1.602377 GACGGTCAAACAGTCAAAGGG 59.398 52.381 2.62 0.00 41.82 3.95
708 1021 0.316689 GGCAAGACCACGTGTTTTCG 60.317 55.000 15.65 0.51 38.86 3.46
709 1022 0.375803 GCAAGACCACGTGTTTTCGT 59.624 50.000 15.65 4.27 45.10 3.85
756 1069 4.387098 GGGGGCACAACTAAGGGTATAAAT 60.387 45.833 0.00 0.00 0.00 1.40
757 1070 4.583073 GGGGCACAACTAAGGGTATAAATG 59.417 45.833 0.00 0.00 0.00 2.32
760 1073 5.126384 GGCACAACTAAGGGTATAAATGCAA 59.874 40.000 0.00 0.00 0.00 4.08
856 1170 1.006832 CGTTCGTGGGCTTAAGATGG 58.993 55.000 6.67 0.00 0.00 3.51
957 4329 1.531602 AAGCCCAACAAGGACTGGC 60.532 57.895 0.00 0.00 41.22 4.85
1026 4401 1.217001 GGAAAGCAAAACCAAAGCCG 58.783 50.000 0.00 0.00 0.00 5.52
1048 4427 3.492102 AGTATCCATCCAATCCAACCG 57.508 47.619 0.00 0.00 0.00 4.44
1089 4468 1.381928 CCGGAGAAGAATCCCGTCGA 61.382 60.000 0.00 0.00 37.56 4.20
1100 4479 3.611766 ATCCCGTCGAGAAATCAAACT 57.388 42.857 0.00 0.00 0.00 2.66
1234 4617 1.655329 GATCTCGATTCCTCGCCGT 59.345 57.895 0.00 0.00 44.65 5.68
1315 4702 0.533531 GTTTGTTCCGGTCCGAGGTT 60.534 55.000 14.39 0.00 0.00 3.50
1319 4706 0.034476 GTTCCGGTCCGAGGTTTCTT 59.966 55.000 14.39 0.00 0.00 2.52
1535 4931 6.994496 TGATTTGCAAGACAGAATAGGATAGG 59.006 38.462 0.00 0.00 0.00 2.57
1558 4961 2.700897 AGAATCATTGGTACTCCCTCCG 59.299 50.000 0.00 0.00 0.00 4.63
1605 5008 3.449227 CAGCGCGACCTAGGTGGA 61.449 66.667 26.51 0.00 39.71 4.02
1616 5019 4.344102 CGACCTAGGTGGATTTAGATTGGA 59.656 45.833 22.10 0.00 39.71 3.53
1620 5023 4.837093 AGGTGGATTTAGATTGGACGAA 57.163 40.909 0.00 0.00 0.00 3.85
1629 5032 1.205893 AGATTGGACGAAGAGGAGCAC 59.794 52.381 0.00 0.00 0.00 4.40
1635 5038 2.427245 CGAAGAGGAGCACCGGGAT 61.427 63.158 6.32 0.00 41.83 3.85
1655 5058 4.034510 GGATGAGCTAAACTTCCAATCACG 59.965 45.833 0.00 0.00 33.58 4.35
1661 5064 0.893727 AACTTCCAATCACGGCACCC 60.894 55.000 0.00 0.00 0.00 4.61
1810 7090 5.046910 AGAATTCAATGTTACACGCCTTG 57.953 39.130 8.44 0.00 0.00 3.61
1839 7120 7.475137 TTTGGGAAAATCTGGATTTCGTAAT 57.525 32.000 8.71 0.00 39.88 1.89
1850 7131 7.383687 TCTGGATTTCGTAATGTGACTTACTT 58.616 34.615 0.00 0.00 30.88 2.24
1858 7139 7.978982 TCGTAATGTGACTTACTTACCTAGAC 58.021 38.462 0.00 0.00 30.88 2.59
1859 7140 7.607607 TCGTAATGTGACTTACTTACCTAGACA 59.392 37.037 0.00 0.00 30.88 3.41
1883 7164 2.599659 GGAGTAGCTGTTTTGCATTGC 58.400 47.619 0.46 0.46 34.99 3.56
1917 7330 7.506328 AACTTAGCGAATATTATGGGTTTCC 57.494 36.000 0.00 0.00 0.00 3.13
1977 7390 5.278610 GCTGTATCTGAATATTGGCAATGCA 60.279 40.000 22.57 15.48 0.00 3.96
2003 7416 5.055642 CATGTGATGCTTTGTCTCAATGT 57.944 39.130 0.00 0.00 0.00 2.71
2004 7417 4.754372 TGTGATGCTTTGTCTCAATGTC 57.246 40.909 0.00 0.00 0.00 3.06
2005 7418 4.392047 TGTGATGCTTTGTCTCAATGTCT 58.608 39.130 0.00 0.00 0.00 3.41
2006 7419 4.453478 TGTGATGCTTTGTCTCAATGTCTC 59.547 41.667 0.00 0.00 0.00 3.36
2007 7420 4.453478 GTGATGCTTTGTCTCAATGTCTCA 59.547 41.667 0.00 0.00 0.00 3.27
2008 7421 5.123502 GTGATGCTTTGTCTCAATGTCTCAT 59.876 40.000 0.00 0.00 0.00 2.90
2009 7422 6.314648 GTGATGCTTTGTCTCAATGTCTCATA 59.685 38.462 0.00 0.00 0.00 2.15
2010 7423 6.314648 TGATGCTTTGTCTCAATGTCTCATAC 59.685 38.462 0.00 0.00 0.00 2.39
2011 7424 4.937620 TGCTTTGTCTCAATGTCTCATACC 59.062 41.667 0.00 0.00 0.00 2.73
2012 7425 4.333926 GCTTTGTCTCAATGTCTCATACCC 59.666 45.833 0.00 0.00 0.00 3.69
2045 7458 6.114187 ACCAGTTCATTGATGTTGTCTCTA 57.886 37.500 0.00 0.00 0.00 2.43
2047 7460 7.170965 ACCAGTTCATTGATGTTGTCTCTATT 58.829 34.615 0.00 0.00 0.00 1.73
2145 7558 8.213518 TCAGACAATTCAGCCTTGTATATTTC 57.786 34.615 0.00 0.00 36.98 2.17
2146 7559 7.828717 TCAGACAATTCAGCCTTGTATATTTCA 59.171 33.333 0.00 0.00 36.98 2.69
2206 7619 8.041323 ACTCTTGAGTATAATTACCTTGGTGTG 58.959 37.037 0.89 0.00 0.00 3.82
2328 7742 9.788960 TTCATCAATATTATCTCCTACGATTCG 57.211 33.333 4.14 4.14 0.00 3.34
2393 7807 6.435277 AGCCTGTATATTTTCCATGGCAATAG 59.565 38.462 6.96 2.47 41.33 1.73
2401 7815 2.580962 TCCATGGCAATAGCGCATTTA 58.419 42.857 11.47 0.00 43.41 1.40
2418 7832 5.351458 GCATTTATCTTTTGGTGATGGACC 58.649 41.667 0.00 0.00 46.37 4.46
2675 8089 6.015856 TGGTTCAACTCTCTCTTCAGTTAGAG 60.016 42.308 0.00 0.00 42.46 2.43
2697 8111 3.699894 CCGCAGAGCTGGACAGGT 61.700 66.667 3.35 3.35 42.58 4.00
2929 8343 0.746063 CTTTGTGCCAGCCTTGTTCA 59.254 50.000 0.00 0.00 0.00 3.18
2944 8358 3.096489 TGTTCAGCATTTTCCTTGCAC 57.904 42.857 0.00 0.00 42.62 4.57
3010 8429 9.316859 GCAATAACAGAAAATAAAAACACATGC 57.683 29.630 0.00 0.00 0.00 4.06
3081 8501 1.080298 GCCAAGCATTGTGTCTGGC 60.080 57.895 8.11 8.11 46.99 4.85
3093 8513 0.545309 TGTCTGGCTGCTAGTTCCCT 60.545 55.000 12.90 0.00 0.00 4.20
3097 8558 2.087646 CTGGCTGCTAGTTCCCTTTTC 58.912 52.381 4.68 0.00 0.00 2.29
3098 8559 1.705186 TGGCTGCTAGTTCCCTTTTCT 59.295 47.619 0.00 0.00 0.00 2.52
3099 8560 2.290323 TGGCTGCTAGTTCCCTTTTCTC 60.290 50.000 0.00 0.00 0.00 2.87
3100 8561 2.360844 GCTGCTAGTTCCCTTTTCTCC 58.639 52.381 0.00 0.00 0.00 3.71
3121 8582 2.099592 CCTTCAGTTTCAAAGCTGCACA 59.900 45.455 1.02 0.00 37.20 4.57
3137 8598 1.493772 CACATGCACTGCCAAGTTTG 58.506 50.000 0.00 0.00 32.98 2.93
3147 8608 4.000325 ACTGCCAAGTTTGTTTTGGAAAC 59.000 39.130 8.13 0.00 46.42 2.78
3151 8612 3.181525 CCAAGTTTGTTTTGGAAACGCAC 60.182 43.478 0.00 0.00 46.42 5.34
3186 8648 6.655078 TGTAGCATGTAGAGATCATAAGCA 57.345 37.500 0.00 0.00 0.00 3.91
3187 8649 6.685657 TGTAGCATGTAGAGATCATAAGCAG 58.314 40.000 0.00 0.00 0.00 4.24
3189 8651 5.782047 AGCATGTAGAGATCATAAGCAGTC 58.218 41.667 0.00 0.00 0.00 3.51
3220 8682 3.320541 TCATTTGCCACTTTGGTTTCGAT 59.679 39.130 0.00 0.00 40.46 3.59
3234 8696 8.850454 TTTGGTTTCGATGAACTTTTTAGAAG 57.150 30.769 0.35 0.00 0.00 2.85
3315 8810 8.635765 TCCACAGTAGCTAATTCAAATTTTCT 57.364 30.769 0.00 0.00 0.00 2.52
3316 8811 8.514594 TCCACAGTAGCTAATTCAAATTTTCTG 58.485 33.333 0.00 0.00 0.00 3.02
3318 8813 9.897744 CACAGTAGCTAATTCAAATTTTCTGAA 57.102 29.630 0.00 0.00 37.22 3.02
3321 8816 9.578439 AGTAGCTAATTCAAATTTTCTGAATGC 57.422 29.630 0.00 5.48 41.56 3.56
3322 8817 9.578439 GTAGCTAATTCAAATTTTCTGAATGCT 57.422 29.630 15.16 15.16 41.56 3.79
3324 8819 9.578439 AGCTAATTCAAATTTTCTGAATGCTAC 57.422 29.630 11.57 2.41 41.56 3.58
3325 8820 9.578439 GCTAATTCAAATTTTCTGAATGCTACT 57.422 29.630 4.93 0.00 41.56 2.57
3330 8825 8.268850 TCAAATTTTCTGAATGCTACTAGGTC 57.731 34.615 0.00 0.00 0.00 3.85
3331 8826 7.336931 TCAAATTTTCTGAATGCTACTAGGTCC 59.663 37.037 0.00 0.00 0.00 4.46
3332 8827 5.755409 TTTTCTGAATGCTACTAGGTCCA 57.245 39.130 0.00 0.00 0.00 4.02
3338 8833 2.781681 TGCTACTAGGTCCAAAAGGC 57.218 50.000 0.00 0.00 0.00 4.35
3341 8837 1.553704 CTACTAGGTCCAAAAGGCGGT 59.446 52.381 0.00 0.00 0.00 5.68
3366 8862 0.322546 ACGGGGCAATCTGGTCTTTC 60.323 55.000 0.00 0.00 0.00 2.62
3369 8865 2.421388 CGGGGCAATCTGGTCTTTCATA 60.421 50.000 0.00 0.00 0.00 2.15
3370 8866 3.748668 CGGGGCAATCTGGTCTTTCATAT 60.749 47.826 0.00 0.00 0.00 1.78
3399 9406 9.283768 TGTTTCAGAATAATAAAGAGACAAGCA 57.716 29.630 0.00 0.00 0.00 3.91
3422 9430 8.207521 GCATAGAGCATTATCCTCTAAAATCC 57.792 38.462 0.00 0.00 43.10 3.01
3423 9432 7.826252 GCATAGAGCATTATCCTCTAAAATCCA 59.174 37.037 0.00 0.00 43.10 3.41
3455 9464 1.016627 AATCACATGATCCGTTGGCG 58.983 50.000 0.00 0.00 32.75 5.69
3598 9619 1.618888 CCTCCCGAGTACCTCCAAAGA 60.619 57.143 0.00 0.00 0.00 2.52
3661 9682 2.614057 CACACACTTCACCTTCTTGTCC 59.386 50.000 0.00 0.00 0.00 4.02
3664 9685 1.129058 ACTTCACCTTCTTGTCCCGT 58.871 50.000 0.00 0.00 0.00 5.28
3679 9700 2.496470 GTCCCGTCTTATCCACACTCTT 59.504 50.000 0.00 0.00 0.00 2.85
3680 9701 2.496070 TCCCGTCTTATCCACACTCTTG 59.504 50.000 0.00 0.00 0.00 3.02
4008 10029 2.261361 CGCCTGTCCATGACGTCA 59.739 61.111 22.48 22.48 34.95 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.921041 AGATAGATTGTGGAAGAGGATACAA 57.079 36.000 0.00 0.00 37.43 2.41
1 2 7.921041 AAGATAGATTGTGGAAGAGGATACA 57.079 36.000 0.00 0.00 41.41 2.29
33 34 8.478877 GGAAGATCTAAGAGTGGAGTATTCAAA 58.521 37.037 0.00 0.00 0.00 2.69
34 35 7.070074 GGGAAGATCTAAGAGTGGAGTATTCAA 59.930 40.741 0.00 0.00 0.00 2.69
35 36 6.551601 GGGAAGATCTAAGAGTGGAGTATTCA 59.448 42.308 0.00 0.00 0.00 2.57
36 37 6.551601 TGGGAAGATCTAAGAGTGGAGTATTC 59.448 42.308 0.00 0.00 0.00 1.75
37 38 6.325286 GTGGGAAGATCTAAGAGTGGAGTATT 59.675 42.308 0.00 0.00 0.00 1.89
38 39 5.836358 GTGGGAAGATCTAAGAGTGGAGTAT 59.164 44.000 0.00 0.00 0.00 2.12
39 40 5.202004 GTGGGAAGATCTAAGAGTGGAGTA 58.798 45.833 0.00 0.00 0.00 2.59
40 41 4.027437 GTGGGAAGATCTAAGAGTGGAGT 58.973 47.826 0.00 0.00 0.00 3.85
41 42 4.026744 TGTGGGAAGATCTAAGAGTGGAG 58.973 47.826 0.00 0.00 0.00 3.86
42 43 4.061131 TGTGGGAAGATCTAAGAGTGGA 57.939 45.455 0.00 0.00 0.00 4.02
43 44 4.406972 TCATGTGGGAAGATCTAAGAGTGG 59.593 45.833 0.00 0.00 0.00 4.00
44 45 5.128499 ACTCATGTGGGAAGATCTAAGAGTG 59.872 44.000 0.00 0.00 32.03 3.51
45 46 5.276440 ACTCATGTGGGAAGATCTAAGAGT 58.724 41.667 0.00 0.00 0.00 3.24
46 47 5.867903 ACTCATGTGGGAAGATCTAAGAG 57.132 43.478 0.00 0.00 0.00 2.85
47 48 5.835819 CCTACTCATGTGGGAAGATCTAAGA 59.164 44.000 0.00 0.00 46.33 2.10
48 49 5.510520 GCCTACTCATGTGGGAAGATCTAAG 60.511 48.000 0.00 0.00 46.33 2.18
49 50 4.345257 GCCTACTCATGTGGGAAGATCTAA 59.655 45.833 0.00 0.00 46.33 2.10
50 51 3.898123 GCCTACTCATGTGGGAAGATCTA 59.102 47.826 0.00 0.00 46.33 1.98
51 52 2.703007 GCCTACTCATGTGGGAAGATCT 59.297 50.000 2.75 0.00 46.33 2.75
52 53 2.435805 TGCCTACTCATGTGGGAAGATC 59.564 50.000 2.75 0.00 46.33 2.75
53 54 2.481441 TGCCTACTCATGTGGGAAGAT 58.519 47.619 2.75 0.00 46.33 2.40
54 55 1.951209 TGCCTACTCATGTGGGAAGA 58.049 50.000 2.75 0.00 46.33 2.87
55 56 2.787473 TTGCCTACTCATGTGGGAAG 57.213 50.000 2.75 0.00 46.33 3.46
56 57 2.092429 GGATTGCCTACTCATGTGGGAA 60.092 50.000 2.75 3.47 46.33 3.97
57 58 1.490490 GGATTGCCTACTCATGTGGGA 59.510 52.381 2.75 0.00 46.33 4.37
58 59 1.492176 AGGATTGCCTACTCATGTGGG 59.508 52.381 0.00 0.00 44.74 4.61
59 60 3.643320 TCTAGGATTGCCTACTCATGTGG 59.357 47.826 0.00 0.00 44.74 4.17
60 61 4.944619 TCTAGGATTGCCTACTCATGTG 57.055 45.455 0.00 0.00 44.74 3.21
61 62 4.262808 GCATCTAGGATTGCCTACTCATGT 60.263 45.833 0.00 0.00 44.74 3.21
62 63 4.020396 AGCATCTAGGATTGCCTACTCATG 60.020 45.833 8.88 0.00 44.74 3.07
63 64 4.166539 AGCATCTAGGATTGCCTACTCAT 58.833 43.478 8.88 0.00 44.74 2.90
64 65 3.581101 AGCATCTAGGATTGCCTACTCA 58.419 45.455 8.88 0.00 44.74 3.41
65 66 4.283212 AGAAGCATCTAGGATTGCCTACTC 59.717 45.833 8.88 3.45 44.74 2.59
66 67 4.230455 AGAAGCATCTAGGATTGCCTACT 58.770 43.478 8.88 4.93 44.74 2.57
67 68 4.283212 AGAGAAGCATCTAGGATTGCCTAC 59.717 45.833 8.88 3.28 45.98 3.18
68 69 4.282957 CAGAGAAGCATCTAGGATTGCCTA 59.717 45.833 8.88 0.00 45.98 3.93
70 71 3.070734 TCAGAGAAGCATCTAGGATTGCC 59.929 47.826 8.88 0.00 39.72 4.52
71 72 4.333913 TCAGAGAAGCATCTAGGATTGC 57.666 45.455 0.00 5.43 35.54 3.56
72 73 7.092079 CACTATCAGAGAAGCATCTAGGATTG 58.908 42.308 9.31 9.77 35.54 2.67
73 74 6.295236 GCACTATCAGAGAAGCATCTAGGATT 60.295 42.308 9.31 0.00 35.54 3.01
74 75 5.185635 GCACTATCAGAGAAGCATCTAGGAT 59.814 44.000 9.08 9.08 35.54 3.24
75 76 4.522405 GCACTATCAGAGAAGCATCTAGGA 59.478 45.833 0.00 0.00 35.54 2.94
76 77 4.523943 AGCACTATCAGAGAAGCATCTAGG 59.476 45.833 0.00 0.00 35.54 3.02
77 78 5.710513 AGCACTATCAGAGAAGCATCTAG 57.289 43.478 0.00 0.00 35.54 2.43
78 79 5.832595 AGAAGCACTATCAGAGAAGCATCTA 59.167 40.000 0.00 0.00 36.64 1.98
79 80 4.650588 AGAAGCACTATCAGAGAAGCATCT 59.349 41.667 0.00 0.00 39.10 2.90
80 81 4.746115 CAGAAGCACTATCAGAGAAGCATC 59.254 45.833 0.00 0.00 33.85 3.91
81 82 4.405036 TCAGAAGCACTATCAGAGAAGCAT 59.595 41.667 0.00 0.00 33.85 3.79
82 83 3.766051 TCAGAAGCACTATCAGAGAAGCA 59.234 43.478 0.00 0.00 33.85 3.91
83 84 4.362279 CTCAGAAGCACTATCAGAGAAGC 58.638 47.826 0.00 0.00 33.63 3.86
111 112 4.651962 TGAGGTTAAAGAAGTTTTTGGGGG 59.348 41.667 0.00 0.00 0.00 5.40
112 113 5.862678 TGAGGTTAAAGAAGTTTTTGGGG 57.137 39.130 0.00 0.00 0.00 4.96
113 114 7.290110 AGATGAGGTTAAAGAAGTTTTTGGG 57.710 36.000 0.00 0.00 0.00 4.12
114 115 7.867909 GGAAGATGAGGTTAAAGAAGTTTTTGG 59.132 37.037 0.00 0.00 0.00 3.28
115 116 8.413229 TGGAAGATGAGGTTAAAGAAGTTTTTG 58.587 33.333 0.00 0.00 0.00 2.44
116 117 8.533569 TGGAAGATGAGGTTAAAGAAGTTTTT 57.466 30.769 0.00 0.00 0.00 1.94
117 118 7.255625 GCTGGAAGATGAGGTTAAAGAAGTTTT 60.256 37.037 0.00 0.00 34.07 2.43
118 119 6.207614 GCTGGAAGATGAGGTTAAAGAAGTTT 59.792 38.462 0.00 0.00 34.07 2.66
119 120 5.707764 GCTGGAAGATGAGGTTAAAGAAGTT 59.292 40.000 0.00 0.00 34.07 2.66
120 121 5.013599 AGCTGGAAGATGAGGTTAAAGAAGT 59.986 40.000 0.00 0.00 34.07 3.01
121 122 5.495640 AGCTGGAAGATGAGGTTAAAGAAG 58.504 41.667 0.00 0.00 34.07 2.85
122 123 5.013079 TGAGCTGGAAGATGAGGTTAAAGAA 59.987 40.000 0.00 0.00 34.07 2.52
123 124 4.532126 TGAGCTGGAAGATGAGGTTAAAGA 59.468 41.667 0.00 0.00 34.07 2.52
124 125 4.836825 TGAGCTGGAAGATGAGGTTAAAG 58.163 43.478 0.00 0.00 34.07 1.85
125 126 4.908601 TGAGCTGGAAGATGAGGTTAAA 57.091 40.909 0.00 0.00 34.07 1.52
126 127 5.441718 AATGAGCTGGAAGATGAGGTTAA 57.558 39.130 0.00 0.00 34.07 2.01
127 128 5.070981 CCTAATGAGCTGGAAGATGAGGTTA 59.929 44.000 0.00 0.00 34.07 2.85
128 129 4.141528 CCTAATGAGCTGGAAGATGAGGTT 60.142 45.833 0.00 0.00 34.07 3.50
129 130 3.390639 CCTAATGAGCTGGAAGATGAGGT 59.609 47.826 0.00 0.00 34.07 3.85
130 131 3.645212 TCCTAATGAGCTGGAAGATGAGG 59.355 47.826 0.00 0.00 34.07 3.86
131 132 4.100653 TGTCCTAATGAGCTGGAAGATGAG 59.899 45.833 0.00 0.00 34.07 2.90
132 133 4.033009 TGTCCTAATGAGCTGGAAGATGA 58.967 43.478 0.00 0.00 34.07 2.92
133 134 4.412796 TGTCCTAATGAGCTGGAAGATG 57.587 45.455 0.00 0.00 34.07 2.90
134 135 5.643421 AATGTCCTAATGAGCTGGAAGAT 57.357 39.130 0.00 0.00 34.07 2.40
135 136 5.441718 AAATGTCCTAATGAGCTGGAAGA 57.558 39.130 0.00 0.00 34.07 2.87
136 137 6.521151 AAAAATGTCCTAATGAGCTGGAAG 57.479 37.500 0.00 0.00 0.00 3.46
176 177 5.357314 GCAAAGGGTAAATTAGGAGAAGTCC 59.643 44.000 0.00 0.00 44.33 3.85
177 178 5.357314 GGCAAAGGGTAAATTAGGAGAAGTC 59.643 44.000 0.00 0.00 0.00 3.01
178 179 5.262009 GGCAAAGGGTAAATTAGGAGAAGT 58.738 41.667 0.00 0.00 0.00 3.01
179 180 4.645136 GGGCAAAGGGTAAATTAGGAGAAG 59.355 45.833 0.00 0.00 0.00 2.85
180 181 4.044825 TGGGCAAAGGGTAAATTAGGAGAA 59.955 41.667 0.00 0.00 0.00 2.87
181 182 3.594232 TGGGCAAAGGGTAAATTAGGAGA 59.406 43.478 0.00 0.00 0.00 3.71
182 183 3.954258 CTGGGCAAAGGGTAAATTAGGAG 59.046 47.826 0.00 0.00 0.00 3.69
183 184 3.594232 TCTGGGCAAAGGGTAAATTAGGA 59.406 43.478 0.00 0.00 0.00 2.94
184 185 3.976015 TCTGGGCAAAGGGTAAATTAGG 58.024 45.455 0.00 0.00 0.00 2.69
185 186 4.202151 GCATCTGGGCAAAGGGTAAATTAG 60.202 45.833 0.00 0.00 0.00 1.73
186 187 3.704061 GCATCTGGGCAAAGGGTAAATTA 59.296 43.478 0.00 0.00 0.00 1.40
187 188 2.501316 GCATCTGGGCAAAGGGTAAATT 59.499 45.455 0.00 0.00 0.00 1.82
188 189 2.110578 GCATCTGGGCAAAGGGTAAAT 58.889 47.619 0.00 0.00 0.00 1.40
189 190 1.203112 TGCATCTGGGCAAAGGGTAAA 60.203 47.619 0.00 0.00 41.65 2.01
190 191 0.407528 TGCATCTGGGCAAAGGGTAA 59.592 50.000 0.00 0.00 41.65 2.85
191 192 2.082834 TGCATCTGGGCAAAGGGTA 58.917 52.632 0.00 0.00 41.65 3.69
192 193 2.853316 TGCATCTGGGCAAAGGGT 59.147 55.556 0.00 0.00 41.65 4.34
199 200 0.383231 GTACTGCAATGCATCTGGGC 59.617 55.000 8.91 2.51 38.13 5.36
200 201 1.674441 CTGTACTGCAATGCATCTGGG 59.326 52.381 8.91 0.00 38.13 4.45
201 202 2.635714 TCTGTACTGCAATGCATCTGG 58.364 47.619 8.91 0.00 38.13 3.86
202 203 5.996669 TTATCTGTACTGCAATGCATCTG 57.003 39.130 8.91 0.00 38.13 2.90
203 204 6.351711 TCTTTATCTGTACTGCAATGCATCT 58.648 36.000 8.91 0.00 38.13 2.90
204 205 6.609237 TCTTTATCTGTACTGCAATGCATC 57.391 37.500 8.91 3.34 38.13 3.91
205 206 7.395190 TTTCTTTATCTGTACTGCAATGCAT 57.605 32.000 8.91 0.00 38.13 3.96
206 207 6.127925 CCTTTCTTTATCTGTACTGCAATGCA 60.128 38.462 7.99 7.99 36.92 3.96
207 208 6.261118 CCTTTCTTTATCTGTACTGCAATGC 58.739 40.000 0.00 0.00 0.00 3.56
208 209 6.599244 TCCCTTTCTTTATCTGTACTGCAATG 59.401 38.462 0.00 0.00 0.00 2.82
209 210 6.721318 TCCCTTTCTTTATCTGTACTGCAAT 58.279 36.000 0.00 0.00 0.00 3.56
210 211 6.121776 TCCCTTTCTTTATCTGTACTGCAA 57.878 37.500 0.00 0.00 0.00 4.08
211 212 5.755409 TCCCTTTCTTTATCTGTACTGCA 57.245 39.130 0.00 0.00 0.00 4.41
212 213 8.910351 ATTATCCCTTTCTTTATCTGTACTGC 57.090 34.615 0.00 0.00 0.00 4.40
240 241 7.366732 GGGGGACACAACTAAAGGGTATAAATA 60.367 40.741 0.00 0.00 0.00 1.40
241 242 6.429151 GGGGACACAACTAAAGGGTATAAAT 58.571 40.000 0.00 0.00 0.00 1.40
251 252 1.345415 GACGAGGGGGACACAACTAAA 59.655 52.381 0.00 0.00 0.00 1.85
279 280 4.569162 CCACGTGTTTTCAGAAACTAGTGA 59.431 41.667 15.65 0.00 45.45 3.41
281 282 4.510571 ACCACGTGTTTTCAGAAACTAGT 58.489 39.130 15.65 0.00 44.33 2.57
376 688 2.293677 TCACGAGGGAATGACATTCG 57.706 50.000 19.43 12.69 40.17 3.34
391 703 0.381801 AGTGCTTGCCAAGTTTCACG 59.618 50.000 6.28 0.00 0.00 4.35
392 704 2.584492 AAGTGCTTGCCAAGTTTCAC 57.416 45.000 6.28 5.99 0.00 3.18
422 734 3.473923 AAAGTTGGTGGCAAAGAATGG 57.526 42.857 0.00 0.00 0.00 3.16
459 771 9.743057 CACCATGAACAGTAAAATCTAAAAACA 57.257 29.630 0.00 0.00 0.00 2.83
460 772 9.191995 CCACCATGAACAGTAAAATCTAAAAAC 57.808 33.333 0.00 0.00 0.00 2.43
491 804 4.743955 GCCCATCCGAGTTTTAGCTCTTAT 60.744 45.833 0.00 0.00 33.55 1.73
531 844 4.855388 GTCAATGTCACTTGCATTCATGAC 59.145 41.667 0.00 11.27 41.51 3.06
559 872 6.760770 TCAAAATGTTCAGAAAAACATCACCC 59.239 34.615 3.00 0.00 46.49 4.61
560 873 7.769272 TCAAAATGTTCAGAAAAACATCACC 57.231 32.000 3.00 0.00 46.49 4.02
619 932 6.425721 CCGTCACTTTGAAAACCTCATAACTA 59.574 38.462 0.00 0.00 32.78 2.24
628 941 3.768468 TTGACCGTCACTTTGAAAACC 57.232 42.857 0.00 0.00 0.00 3.27
642 955 0.310854 GCCCTTTGACTGTTTGACCG 59.689 55.000 0.00 0.00 0.00 4.79
651 964 1.484038 TGTGCTTTTGCCCTTTGACT 58.516 45.000 0.00 0.00 46.87 3.41
756 1069 8.316497 TGGATTTTCTTTATGGGATAATTGCA 57.684 30.769 0.00 0.00 0.00 4.08
757 1070 9.783081 ATTGGATTTTCTTTATGGGATAATTGC 57.217 29.630 0.00 0.00 0.00 3.56
809 1123 7.855784 ACCTCAACCTTTTTCCTTTATTGAT 57.144 32.000 0.00 0.00 0.00 2.57
810 1124 8.950007 ATACCTCAACCTTTTTCCTTTATTGA 57.050 30.769 0.00 0.00 0.00 2.57
889 4261 5.721232 CTTGGTACATCGGAGAGTAAAGTT 58.279 41.667 0.00 0.00 43.63 2.66
908 4280 0.971386 AGCAGAATTGTTGGGCTTGG 59.029 50.000 0.00 0.00 0.00 3.61
957 4329 0.610687 GGAGTTCTGGACTGACTGGG 59.389 60.000 0.00 0.00 39.19 4.45
1026 4401 3.815401 CGGTTGGATTGGATGGATACTTC 59.185 47.826 0.00 0.00 39.93 3.01
1089 4468 4.407296 AGCTCCTCCGATAGTTTGATTTCT 59.593 41.667 0.00 0.00 0.00 2.52
1100 4479 1.609072 CATCGTGAAGCTCCTCCGATA 59.391 52.381 9.31 0.00 36.58 2.92
1315 4702 3.498481 CCACCAGATCCAGGAAACAAGAA 60.498 47.826 8.69 0.00 0.00 2.52
1319 4706 0.698238 CCCACCAGATCCAGGAAACA 59.302 55.000 8.69 0.00 0.00 2.83
1363 4750 6.317088 CAATGTCAACGATTGTAAGCAGAAT 58.683 36.000 0.00 0.00 0.00 2.40
1535 4931 3.471680 GAGGGAGTACCAATGATTCTGC 58.528 50.000 0.00 0.00 43.89 4.26
1605 5008 4.162320 TGCTCCTCTTCGTCCAATCTAAAT 59.838 41.667 0.00 0.00 0.00 1.40
1616 5019 3.382832 CCCGGTGCTCCTCTTCGT 61.383 66.667 0.00 0.00 0.00 3.85
1620 5023 1.760086 CTCATCCCGGTGCTCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
1629 5032 1.209504 TGGAAGTTTAGCTCATCCCGG 59.790 52.381 0.00 0.00 0.00 5.73
1635 5038 3.334691 CCGTGATTGGAAGTTTAGCTCA 58.665 45.455 0.00 0.00 0.00 4.26
1655 5058 3.501040 TTCCCTTTGTCCGGGTGCC 62.501 63.158 0.00 0.00 42.56 5.01
1661 5064 2.295909 TGATTTTGCTTCCCTTTGTCCG 59.704 45.455 0.00 0.00 0.00 4.79
1810 7090 4.890158 ATCCAGATTTTCCCAAAACCAC 57.110 40.909 0.00 0.00 32.37 4.16
1839 7120 5.944599 CCTCTGTCTAGGTAAGTAAGTCACA 59.055 44.000 0.00 0.00 31.46 3.58
1850 7131 3.136809 CAGCTACTCCCTCTGTCTAGGTA 59.863 52.174 0.00 0.00 34.56 3.08
1858 7139 2.079925 GCAAAACAGCTACTCCCTCTG 58.920 52.381 0.00 0.00 0.00 3.35
1859 7140 1.699634 TGCAAAACAGCTACTCCCTCT 59.300 47.619 0.00 0.00 34.99 3.69
1982 7395 5.008331 AGACATTGAGACAAAGCATCACAT 58.992 37.500 0.00 0.00 0.00 3.21
2000 7413 6.787458 TGGTATACAGATTGGGTATGAGACAT 59.213 38.462 5.01 0.00 33.68 3.06
2001 7414 6.140377 TGGTATACAGATTGGGTATGAGACA 58.860 40.000 5.01 0.00 33.68 3.41
2002 7415 6.665992 TGGTATACAGATTGGGTATGAGAC 57.334 41.667 5.01 0.00 33.68 3.36
2045 7458 5.065859 TCGCATAACAAATGTCCGAATCAAT 59.934 36.000 0.00 0.00 0.00 2.57
2047 7460 3.935828 TCGCATAACAAATGTCCGAATCA 59.064 39.130 0.00 0.00 0.00 2.57
2145 7558 0.810648 AAATGCGGTACTGCCATGTG 59.189 50.000 23.70 0.00 36.97 3.21
2146 7559 0.810648 CAAATGCGGTACTGCCATGT 59.189 50.000 23.70 9.68 36.97 3.21
2175 7588 9.838339 CAAGGTAATTATACTCAAGAGTCCATT 57.162 33.333 5.91 6.39 42.54 3.16
2206 7619 1.400737 AGTAGGGTAGATGCACGGAC 58.599 55.000 0.00 0.00 0.00 4.79
2314 7728 1.883275 CTGAGGCGAATCGTAGGAGAT 59.117 52.381 4.07 0.00 0.00 2.75
2393 7807 3.798337 CCATCACCAAAAGATAAATGCGC 59.202 43.478 0.00 0.00 0.00 6.09
2586 8000 1.556911 AGCAGGATGTGGTGGTAAGAG 59.443 52.381 0.00 0.00 39.31 2.85
2652 8066 7.209471 TCTCTAACTGAAGAGAGAGTTGAAC 57.791 40.000 9.40 0.00 45.54 3.18
2675 8089 1.300542 GTCCAGCTCTGCGGCTATC 60.301 63.158 0.00 0.00 41.00 2.08
2697 8111 0.248012 TTATCGAGCCTTGCCGACAA 59.752 50.000 0.00 0.00 35.11 3.18
2929 8343 1.609208 ACTCGTGCAAGGAAAATGCT 58.391 45.000 0.00 0.00 44.14 3.79
3039 8459 6.456988 GCAGACTTTTATTACCTCAACCATCG 60.457 42.308 0.00 0.00 0.00 3.84
3081 8501 2.573915 AGGGAGAAAAGGGAACTAGCAG 59.426 50.000 0.00 0.00 42.68 4.24
3093 8513 4.956075 AGCTTTGAAACTGAAGGGAGAAAA 59.044 37.500 0.00 0.00 0.00 2.29
3097 8558 2.030451 GCAGCTTTGAAACTGAAGGGAG 60.030 50.000 10.31 0.00 35.90 4.30
3098 8559 1.956477 GCAGCTTTGAAACTGAAGGGA 59.044 47.619 10.31 0.00 35.90 4.20
3099 8560 1.682854 TGCAGCTTTGAAACTGAAGGG 59.317 47.619 10.31 0.00 35.90 3.95
3100 8561 2.099592 TGTGCAGCTTTGAAACTGAAGG 59.900 45.455 10.31 0.00 35.90 3.46
3121 8582 2.937799 CAAAACAAACTTGGCAGTGCAT 59.062 40.909 18.61 0.00 31.60 3.96
3137 8598 0.920664 GTGCAGTGCGTTTCCAAAAC 59.079 50.000 11.20 0.00 0.00 2.43
3147 8608 1.157257 TACAACCACAGTGCAGTGCG 61.157 55.000 21.57 12.15 38.18 5.34
3151 8612 1.198408 CATGCTACAACCACAGTGCAG 59.802 52.381 0.00 0.00 33.87 4.41
3186 8648 1.970640 GGCAAATGAACCCCAAAGACT 59.029 47.619 0.00 0.00 0.00 3.24
3187 8649 1.691434 TGGCAAATGAACCCCAAAGAC 59.309 47.619 0.00 0.00 0.00 3.01
3189 8651 1.693606 AGTGGCAAATGAACCCCAAAG 59.306 47.619 0.00 0.00 0.00 2.77
3220 8682 9.131791 GGCCAATATATCCTTCTAAAAAGTTCA 57.868 33.333 0.00 0.00 0.00 3.18
3234 8696 3.758554 ACATTCTTGCGGCCAATATATCC 59.241 43.478 2.24 0.00 0.00 2.59
3315 8810 4.843728 CCTTTTGGACCTAGTAGCATTCA 58.156 43.478 0.00 0.00 44.07 2.57
3316 8811 3.628032 GCCTTTTGGACCTAGTAGCATTC 59.372 47.826 0.00 0.00 44.07 2.67
3318 8813 2.420129 CGCCTTTTGGACCTAGTAGCAT 60.420 50.000 0.00 0.00 44.07 3.79
3320 8815 1.653151 CGCCTTTTGGACCTAGTAGC 58.347 55.000 0.00 0.00 44.07 3.58
3321 8816 1.553704 ACCGCCTTTTGGACCTAGTAG 59.446 52.381 0.00 0.00 44.07 2.57
3322 8817 1.276989 CACCGCCTTTTGGACCTAGTA 59.723 52.381 0.00 0.00 44.07 1.82
3323 8818 0.036306 CACCGCCTTTTGGACCTAGT 59.964 55.000 0.00 0.00 44.07 2.57
3324 8819 1.305930 GCACCGCCTTTTGGACCTAG 61.306 60.000 0.00 0.00 44.07 3.02
3325 8820 1.302993 GCACCGCCTTTTGGACCTA 60.303 57.895 0.00 0.00 44.07 3.08
3344 8840 2.046314 ACCAGATTGCCCCGTTCG 60.046 61.111 0.00 0.00 0.00 3.95
3389 8885 5.543405 AGGATAATGCTCTATGCTTGTCTCT 59.457 40.000 0.00 0.00 43.37 3.10
3399 9406 9.902684 CATGGATTTTAGAGGATAATGCTCTAT 57.097 33.333 0.00 0.00 44.92 1.98
3422 9430 8.188799 GGATCATGTGATTGGATAAATAGCATG 58.811 37.037 0.00 0.00 39.44 4.06
3423 9432 7.066645 CGGATCATGTGATTGGATAAATAGCAT 59.933 37.037 0.00 0.00 34.37 3.79
3574 9595 3.529412 AGGTACTCGGGAGGGGAA 58.471 61.111 0.00 0.00 31.41 3.97
3598 9619 4.119363 ATGGCTGGCTGGCGACAT 62.119 61.111 13.03 8.20 45.14 3.06
3661 9682 2.093973 AGCAAGAGTGTGGATAAGACGG 60.094 50.000 0.00 0.00 0.00 4.79
3664 9685 4.026744 AGCTAGCAAGAGTGTGGATAAGA 58.973 43.478 18.83 0.00 0.00 2.10
3680 9701 0.037326 TGTAGTGTGGTGCAGCTAGC 60.037 55.000 18.08 6.62 45.96 3.42
3726 9747 2.866028 GCAAGCAGCTCGTGAAGG 59.134 61.111 0.00 0.00 41.15 3.46
3873 9894 2.668212 TTGCTGTGCGCCTGGTAC 60.668 61.111 4.18 0.00 38.05 3.34


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

AutoCloner maintained by Alex Coulton.