Multiple sequence alignment - TraesCS5B01G136100

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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 TraesCS5B01G136100 chr5B 100.000 3267 0 0 488 3754 255683364 255680098 0.000000e+00 6034.0
1 TraesCS5B01G136100 chr5B 91.272 1203 91 9 2559 3754 148503660 148502465 0.000000e+00 1628.0
2 TraesCS5B01G136100 chr5B 82.748 626 82 15 1071 1687 6535963 6536571 5.520000e-148 534.0
3 TraesCS5B01G136100 chr5B 100.000 232 0 0 1 232 255683851 255683620 2.680000e-116 429.0
4 TraesCS5B01G136100 chr5B 85.890 326 43 3 1859 2183 6536602 6536925 9.980000e-91 344.0
5 TraesCS5B01G136100 chr5B 88.085 235 18 5 3530 3754 672544429 672544195 1.720000e-68 270.0
6 TraesCS5B01G136100 chr5B 79.570 186 24 6 3044 3219 396491610 396491429 1.830000e-23 121.0
7 TraesCS5B01G136100 chr5A 93.885 2077 76 17 529 2560 309313500 309311430 0.000000e+00 3085.0
8 TraesCS5B01G136100 chr5A 85.021 1442 180 15 1128 2560 3432834 3431420 0.000000e+00 1434.0
9 TraesCS5B01G136100 chr5D 95.771 1608 50 7 959 2560 242847463 242849058 0.000000e+00 2577.0
10 TraesCS5B01G136100 chr5D 84.446 1498 205 15 1077 2560 5632330 5630847 0.000000e+00 1450.0
11 TraesCS5B01G136100 chr5D 88.011 367 23 9 528 874 242845289 242845654 7.500000e-112 414.0
12 TraesCS5B01G136100 chr5D 81.818 99 14 3 869 965 242846804 242846900 3.110000e-11 80.5
13 TraesCS5B01G136100 chr2B 99.249 1198 9 0 2557 3754 132280862 132282059 0.000000e+00 2163.0
14 TraesCS5B01G136100 chr2B 86.809 235 21 5 3530 3754 183538104 183537870 1.730000e-63 254.0
15 TraesCS5B01G136100 chr2B 77.528 178 35 5 1304 1479 596075702 596075528 6.630000e-18 102.0
16 TraesCS5B01G136100 chr7B 96.833 1200 35 3 2558 3754 590950516 590951715 0.000000e+00 2002.0
17 TraesCS5B01G136100 chr3B 91.286 1205 88 11 2557 3754 603624730 603625924 0.000000e+00 1628.0
18 TraesCS5B01G136100 chr3B 91.346 104 8 1 2672 2775 75346188 75346086 1.410000e-29 141.0
19 TraesCS5B01G136100 chr7A 90.864 1204 95 10 2559 3754 220547093 220545897 0.000000e+00 1600.0
20 TraesCS5B01G136100 chr6B 89.185 1202 95 14 2558 3753 123198254 123197082 0.000000e+00 1467.0
21 TraesCS5B01G136100 chr6B 88.189 127 14 1 3530 3655 599818206 599818332 2.340000e-32 150.0
22 TraesCS5B01G136100 chr6B 88.060 67 5 3 3044 3108 349462878 349462813 4.020000e-10 76.8
23 TraesCS5B01G136100 chr3D 95.050 707 27 5 2554 3258 141380802 141381502 0.000000e+00 1105.0
24 TraesCS5B01G136100 chr3D 97.410 502 11 2 3254 3754 141386640 141387140 0.000000e+00 854.0
25 TraesCS5B01G136100 chr3D 91.346 104 9 0 2672 2775 549730658 549730761 3.910000e-30 143.0
26 TraesCS5B01G136100 chr3D 88.608 79 9 0 2559 2637 549730579 549730657 3.090000e-16 97.1
27 TraesCS5B01G136100 chr4B 72.995 611 127 28 1879 2463 500080012 500080610 2.980000e-41 180.0
28 TraesCS5B01G136100 chr3A 79.570 186 24 6 3044 3219 265258509 265258328 1.830000e-23 121.0
29 TraesCS5B01G136100 chr2D 78.652 178 33 5 1304 1479 507434410 507434236 3.060000e-21 113.0
30 TraesCS5B01G136100 chr4D 88.608 79 9 0 2559 2637 443717369 443717447 3.090000e-16 97.1
31 TraesCS5B01G136100 chr4D 78.906 128 22 4 1291 1417 494877397 494877520 8.640000e-12 82.4


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 TraesCS5B01G136100 chr5B 255680098 255683851 3753 True 3231.500000 6034 100.000000 1 3754 2 chr5B.!!$R4 3753
1 TraesCS5B01G136100 chr5B 148502465 148503660 1195 True 1628.000000 1628 91.272000 2559 3754 1 chr5B.!!$R1 1195
2 TraesCS5B01G136100 chr5B 6535963 6536925 962 False 439.000000 534 84.319000 1071 2183 2 chr5B.!!$F1 1112
3 TraesCS5B01G136100 chr5A 309311430 309313500 2070 True 3085.000000 3085 93.885000 529 2560 1 chr5A.!!$R2 2031
4 TraesCS5B01G136100 chr5A 3431420 3432834 1414 True 1434.000000 1434 85.021000 1128 2560 1 chr5A.!!$R1 1432
5 TraesCS5B01G136100 chr5D 5630847 5632330 1483 True 1450.000000 1450 84.446000 1077 2560 1 chr5D.!!$R1 1483
6 TraesCS5B01G136100 chr5D 242845289 242849058 3769 False 1023.833333 2577 88.533333 528 2560 3 chr5D.!!$F1 2032
7 TraesCS5B01G136100 chr2B 132280862 132282059 1197 False 2163.000000 2163 99.249000 2557 3754 1 chr2B.!!$F1 1197
8 TraesCS5B01G136100 chr7B 590950516 590951715 1199 False 2002.000000 2002 96.833000 2558 3754 1 chr7B.!!$F1 1196
9 TraesCS5B01G136100 chr3B 603624730 603625924 1194 False 1628.000000 1628 91.286000 2557 3754 1 chr3B.!!$F1 1197
10 TraesCS5B01G136100 chr7A 220545897 220547093 1196 True 1600.000000 1600 90.864000 2559 3754 1 chr7A.!!$R1 1195
11 TraesCS5B01G136100 chr6B 123197082 123198254 1172 True 1467.000000 1467 89.185000 2558 3753 1 chr6B.!!$R1 1195
12 TraesCS5B01G136100 chr3D 141380802 141381502 700 False 1105.000000 1105 95.050000 2554 3258 1 chr3D.!!$F1 704
13 TraesCS5B01G136100 chr3D 141386640 141387140 500 False 854.000000 854 97.410000 3254 3754 1 chr3D.!!$F2 500

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
64 65 0.035152 ATGAGCCGTTGGATGCAAGA 60.035 50.0 0.0 0.0 0.0 3.02 F
197 198 0.105039 CTCGCCACCCATCCTCTAAC 59.895 60.0 0.0 0.0 0.0 2.34 F
200 201 0.470341 GCCACCCATCCTCTAACCTC 59.530 60.0 0.0 0.0 0.0 3.85 F
1338 3105 0.606401 CACATCCTCCGCACCAACTT 60.606 55.0 0.0 0.0 0.0 2.66 F
2011 3805 0.670854 GGTTCTTCTGGCTCGTGTCC 60.671 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 3102 0.036306 CTTGGGGTAGTTGGCGAAGT 59.964 55.000 0.00 0.00 0.00 3.01 R
1855 3649 0.181587 TGTTTTCTTCCCCAGACGCA 59.818 50.000 0.00 0.00 0.00 5.24 R
2230 4027 3.134127 GTGATGTTCCAGCCGGCC 61.134 66.667 26.15 7.94 0.00 6.13 R
2572 4369 0.842635 GGACGGGTACTCTAGGAGGA 59.157 60.000 0.00 0.00 33.35 3.71 R
2908 4708 3.077556 GAAGGAGAGGAGGCGGCA 61.078 66.667 13.08 0.00 0.00 5.69 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
30 31 4.832823 AGGTGACTGAAAACCCAATTTAGG 59.167 41.667 0.00 0.00 41.13 2.69
31 32 4.556233 GTGACTGAAAACCCAATTTAGGC 58.444 43.478 0.00 0.00 0.00 3.93
32 33 3.576550 TGACTGAAAACCCAATTTAGGCC 59.423 43.478 0.00 0.00 0.00 5.19
33 34 3.576550 GACTGAAAACCCAATTTAGGCCA 59.423 43.478 5.01 0.00 0.00 5.36
34 35 3.578282 ACTGAAAACCCAATTTAGGCCAG 59.422 43.478 5.01 0.00 0.00 4.85
35 36 3.578282 CTGAAAACCCAATTTAGGCCAGT 59.422 43.478 5.01 0.00 0.00 4.00
36 37 3.576550 TGAAAACCCAATTTAGGCCAGTC 59.423 43.478 5.01 0.00 0.00 3.51
37 38 2.990740 AACCCAATTTAGGCCAGTCA 57.009 45.000 5.01 0.00 0.00 3.41
38 39 2.990740 ACCCAATTTAGGCCAGTCAA 57.009 45.000 5.01 0.00 0.00 3.18
39 40 3.473113 ACCCAATTTAGGCCAGTCAAT 57.527 42.857 5.01 0.00 0.00 2.57
40 41 3.790126 ACCCAATTTAGGCCAGTCAATT 58.210 40.909 5.01 0.23 0.00 2.32
41 42 3.769300 ACCCAATTTAGGCCAGTCAATTC 59.231 43.478 5.01 0.00 0.00 2.17
42 43 3.181487 CCCAATTTAGGCCAGTCAATTCG 60.181 47.826 5.01 0.00 0.00 3.34
43 44 3.443681 CCAATTTAGGCCAGTCAATTCGT 59.556 43.478 5.01 0.00 0.00 3.85
44 45 4.082245 CCAATTTAGGCCAGTCAATTCGTT 60.082 41.667 5.01 0.00 0.00 3.85
45 46 5.124776 CCAATTTAGGCCAGTCAATTCGTTA 59.875 40.000 5.01 0.00 0.00 3.18
46 47 6.183360 CCAATTTAGGCCAGTCAATTCGTTAT 60.183 38.462 5.01 0.00 0.00 1.89
47 48 5.811399 TTTAGGCCAGTCAATTCGTTATG 57.189 39.130 5.01 0.00 0.00 1.90
48 49 3.627395 AGGCCAGTCAATTCGTTATGA 57.373 42.857 5.01 0.00 0.00 2.15
49 50 3.535561 AGGCCAGTCAATTCGTTATGAG 58.464 45.455 5.01 0.00 0.00 2.90
50 51 2.032178 GGCCAGTCAATTCGTTATGAGC 59.968 50.000 0.00 0.00 0.00 4.26
51 52 2.032178 GCCAGTCAATTCGTTATGAGCC 59.968 50.000 0.00 0.00 0.00 4.70
52 53 2.285220 CCAGTCAATTCGTTATGAGCCG 59.715 50.000 0.00 0.00 0.00 5.52
53 54 2.930040 CAGTCAATTCGTTATGAGCCGT 59.070 45.455 0.00 0.00 0.00 5.68
54 55 3.370978 CAGTCAATTCGTTATGAGCCGTT 59.629 43.478 0.00 0.00 0.00 4.44
55 56 3.370978 AGTCAATTCGTTATGAGCCGTTG 59.629 43.478 0.00 0.00 0.00 4.10
56 57 2.675844 TCAATTCGTTATGAGCCGTTGG 59.324 45.455 0.00 0.00 0.00 3.77
57 58 2.675844 CAATTCGTTATGAGCCGTTGGA 59.324 45.455 0.00 0.00 0.00 3.53
58 59 2.684001 TTCGTTATGAGCCGTTGGAT 57.316 45.000 0.00 0.00 0.00 3.41
59 60 1.934589 TCGTTATGAGCCGTTGGATG 58.065 50.000 0.00 0.00 0.00 3.51
60 61 0.304705 CGTTATGAGCCGTTGGATGC 59.695 55.000 0.00 0.00 0.00 3.91
61 62 1.378531 GTTATGAGCCGTTGGATGCA 58.621 50.000 0.00 0.00 0.00 3.96
62 63 1.742831 GTTATGAGCCGTTGGATGCAA 59.257 47.619 0.00 0.00 0.00 4.08
63 64 1.667236 TATGAGCCGTTGGATGCAAG 58.333 50.000 0.00 0.00 0.00 4.01
64 65 0.035152 ATGAGCCGTTGGATGCAAGA 60.035 50.000 0.00 0.00 0.00 3.02
65 66 0.035152 TGAGCCGTTGGATGCAAGAT 60.035 50.000 0.00 0.00 0.00 2.40
66 67 0.379669 GAGCCGTTGGATGCAAGATG 59.620 55.000 0.00 0.00 0.00 2.90
67 68 1.033746 AGCCGTTGGATGCAAGATGG 61.034 55.000 0.00 4.17 0.00 3.51
68 69 1.031571 GCCGTTGGATGCAAGATGGA 61.032 55.000 14.55 0.00 0.00 3.41
69 70 1.683943 CCGTTGGATGCAAGATGGAT 58.316 50.000 0.00 0.00 0.00 3.41
70 71 1.335810 CCGTTGGATGCAAGATGGATG 59.664 52.381 0.00 0.00 0.00 3.51
71 72 1.335810 CGTTGGATGCAAGATGGATGG 59.664 52.381 0.00 0.00 0.00 3.51
72 73 2.381911 GTTGGATGCAAGATGGATGGT 58.618 47.619 0.00 0.00 0.00 3.55
73 74 2.353357 TGGATGCAAGATGGATGGTC 57.647 50.000 0.00 0.00 0.00 4.02
74 75 1.565288 TGGATGCAAGATGGATGGTCA 59.435 47.619 0.00 0.00 0.00 4.02
75 76 2.228059 GGATGCAAGATGGATGGTCAG 58.772 52.381 0.00 0.00 0.00 3.51
76 77 2.158711 GGATGCAAGATGGATGGTCAGA 60.159 50.000 0.00 0.00 0.00 3.27
77 78 3.498121 GGATGCAAGATGGATGGTCAGAT 60.498 47.826 0.00 0.00 0.00 2.90
78 79 4.263199 GGATGCAAGATGGATGGTCAGATA 60.263 45.833 0.00 0.00 0.00 1.98
79 80 4.776435 TGCAAGATGGATGGTCAGATAA 57.224 40.909 0.00 0.00 0.00 1.75
80 81 4.711399 TGCAAGATGGATGGTCAGATAAG 58.289 43.478 0.00 0.00 0.00 1.73
81 82 4.164796 TGCAAGATGGATGGTCAGATAAGT 59.835 41.667 0.00 0.00 0.00 2.24
82 83 5.128919 GCAAGATGGATGGTCAGATAAGTT 58.871 41.667 0.00 0.00 0.00 2.66
83 84 5.591877 GCAAGATGGATGGTCAGATAAGTTT 59.408 40.000 0.00 0.00 0.00 2.66
84 85 6.238593 GCAAGATGGATGGTCAGATAAGTTTC 60.239 42.308 0.00 0.00 0.00 2.78
85 86 6.821616 AGATGGATGGTCAGATAAGTTTCT 57.178 37.500 0.00 0.00 0.00 2.52
86 87 7.205515 AGATGGATGGTCAGATAAGTTTCTT 57.794 36.000 0.00 0.00 0.00 2.52
87 88 7.278875 AGATGGATGGTCAGATAAGTTTCTTC 58.721 38.462 0.00 0.00 0.00 2.87
88 89 6.373005 TGGATGGTCAGATAAGTTTCTTCA 57.627 37.500 0.00 0.00 0.00 3.02
89 90 6.778821 TGGATGGTCAGATAAGTTTCTTCAA 58.221 36.000 0.00 0.00 0.00 2.69
90 91 6.655003 TGGATGGTCAGATAAGTTTCTTCAAC 59.345 38.462 0.00 0.00 35.32 3.18
91 92 6.655003 GGATGGTCAGATAAGTTTCTTCAACA 59.345 38.462 0.00 0.00 37.93 3.33
92 93 7.337942 GGATGGTCAGATAAGTTTCTTCAACAT 59.662 37.037 0.00 0.00 37.93 2.71
93 94 7.672983 TGGTCAGATAAGTTTCTTCAACATC 57.327 36.000 0.00 0.00 37.93 3.06
94 95 6.655003 TGGTCAGATAAGTTTCTTCAACATCC 59.345 38.462 0.00 0.00 37.93 3.51
95 96 6.655003 GGTCAGATAAGTTTCTTCAACATCCA 59.345 38.462 0.00 0.00 37.93 3.41
96 97 7.174946 GGTCAGATAAGTTTCTTCAACATCCAA 59.825 37.037 0.00 0.00 37.93 3.53
97 98 8.017946 GTCAGATAAGTTTCTTCAACATCCAAC 58.982 37.037 0.00 0.00 37.93 3.77
98 99 7.174946 TCAGATAAGTTTCTTCAACATCCAACC 59.825 37.037 0.00 0.00 37.93 3.77
99 100 4.937201 AAGTTTCTTCAACATCCAACCC 57.063 40.909 0.00 0.00 37.93 4.11
100 101 4.184649 AGTTTCTTCAACATCCAACCCT 57.815 40.909 0.00 0.00 37.93 4.34
101 102 4.546674 AGTTTCTTCAACATCCAACCCTT 58.453 39.130 0.00 0.00 37.93 3.95
102 103 5.701224 AGTTTCTTCAACATCCAACCCTTA 58.299 37.500 0.00 0.00 37.93 2.69
103 104 6.314917 AGTTTCTTCAACATCCAACCCTTAT 58.685 36.000 0.00 0.00 37.93 1.73
104 105 6.209391 AGTTTCTTCAACATCCAACCCTTATG 59.791 38.462 0.00 0.00 37.93 1.90
105 106 5.255397 TCTTCAACATCCAACCCTTATGT 57.745 39.130 0.00 0.00 35.40 2.29
106 107 5.253330 TCTTCAACATCCAACCCTTATGTC 58.747 41.667 0.00 0.00 32.80 3.06
107 108 3.963129 TCAACATCCAACCCTTATGTCC 58.037 45.455 0.00 0.00 32.80 4.02
108 109 3.332187 TCAACATCCAACCCTTATGTCCA 59.668 43.478 0.00 0.00 32.80 4.02
109 110 4.017591 TCAACATCCAACCCTTATGTCCAT 60.018 41.667 0.00 0.00 32.80 3.41
110 111 4.170468 ACATCCAACCCTTATGTCCATC 57.830 45.455 0.00 0.00 0.00 3.51
111 112 3.788142 ACATCCAACCCTTATGTCCATCT 59.212 43.478 0.00 0.00 0.00 2.90
112 113 4.141390 ACATCCAACCCTTATGTCCATCTC 60.141 45.833 0.00 0.00 0.00 2.75
113 114 2.777692 TCCAACCCTTATGTCCATCTCC 59.222 50.000 0.00 0.00 0.00 3.71
114 115 2.780010 CCAACCCTTATGTCCATCTCCT 59.220 50.000 0.00 0.00 0.00 3.69
115 116 3.203040 CCAACCCTTATGTCCATCTCCTT 59.797 47.826 0.00 0.00 0.00 3.36
116 117 4.455606 CAACCCTTATGTCCATCTCCTTC 58.544 47.826 0.00 0.00 0.00 3.46
117 118 3.049344 ACCCTTATGTCCATCTCCTTCC 58.951 50.000 0.00 0.00 0.00 3.46
118 119 2.373502 CCCTTATGTCCATCTCCTTCCC 59.626 54.545 0.00 0.00 0.00 3.97
119 120 3.048600 CCTTATGTCCATCTCCTTCCCA 58.951 50.000 0.00 0.00 0.00 4.37
120 121 3.459598 CCTTATGTCCATCTCCTTCCCAA 59.540 47.826 0.00 0.00 0.00 4.12
121 122 4.105377 CCTTATGTCCATCTCCTTCCCAAT 59.895 45.833 0.00 0.00 0.00 3.16
122 123 3.872459 ATGTCCATCTCCTTCCCAATC 57.128 47.619 0.00 0.00 0.00 2.67
123 124 1.486310 TGTCCATCTCCTTCCCAATCG 59.514 52.381 0.00 0.00 0.00 3.34
124 125 0.469917 TCCATCTCCTTCCCAATCGC 59.530 55.000 0.00 0.00 0.00 4.58
125 126 0.536006 CCATCTCCTTCCCAATCGCC 60.536 60.000 0.00 0.00 0.00 5.54
126 127 0.536006 CATCTCCTTCCCAATCGCCC 60.536 60.000 0.00 0.00 0.00 6.13
127 128 1.709994 ATCTCCTTCCCAATCGCCCC 61.710 60.000 0.00 0.00 0.00 5.80
128 129 2.612430 TCCTTCCCAATCGCCCCA 60.612 61.111 0.00 0.00 0.00 4.96
129 130 2.440247 CCTTCCCAATCGCCCCAC 60.440 66.667 0.00 0.00 0.00 4.61
130 131 2.824041 CTTCCCAATCGCCCCACG 60.824 66.667 0.00 0.00 45.62 4.94
141 142 4.410400 CCCCACGAACTCCCAGCC 62.410 72.222 0.00 0.00 0.00 4.85
142 143 3.636231 CCCACGAACTCCCAGCCA 61.636 66.667 0.00 0.00 0.00 4.75
143 144 2.358737 CCACGAACTCCCAGCCAC 60.359 66.667 0.00 0.00 0.00 5.01
144 145 2.358737 CACGAACTCCCAGCCACC 60.359 66.667 0.00 0.00 0.00 4.61
145 146 2.847234 ACGAACTCCCAGCCACCA 60.847 61.111 0.00 0.00 0.00 4.17
146 147 2.224159 ACGAACTCCCAGCCACCAT 61.224 57.895 0.00 0.00 0.00 3.55
147 148 1.450312 CGAACTCCCAGCCACCATC 60.450 63.158 0.00 0.00 0.00 3.51
148 149 1.450312 GAACTCCCAGCCACCATCG 60.450 63.158 0.00 0.00 0.00 3.84
149 150 3.628646 AACTCCCAGCCACCATCGC 62.629 63.158 0.00 0.00 0.00 4.58
150 151 3.790437 CTCCCAGCCACCATCGCT 61.790 66.667 0.00 0.00 36.91 4.93
151 152 2.364973 TCCCAGCCACCATCGCTA 60.365 61.111 0.00 0.00 33.91 4.26
152 153 2.109799 CCCAGCCACCATCGCTAG 59.890 66.667 0.00 0.00 33.91 3.42
153 154 2.590007 CCAGCCACCATCGCTAGC 60.590 66.667 4.06 4.06 33.91 3.42
154 155 2.963854 CAGCCACCATCGCTAGCG 60.964 66.667 30.91 30.91 41.35 4.26
155 156 4.227134 AGCCACCATCGCTAGCGG 62.227 66.667 34.76 22.04 40.25 5.52
189 190 3.866582 GCTAGCCTCGCCACCCAT 61.867 66.667 2.29 0.00 0.00 4.00
190 191 2.423446 CTAGCCTCGCCACCCATC 59.577 66.667 0.00 0.00 0.00 3.51
191 192 3.161450 TAGCCTCGCCACCCATCC 61.161 66.667 0.00 0.00 0.00 3.51
192 193 3.696518 TAGCCTCGCCACCCATCCT 62.697 63.158 0.00 0.00 0.00 3.24
193 194 4.554036 GCCTCGCCACCCATCCTC 62.554 72.222 0.00 0.00 0.00 3.71
194 195 2.765807 CCTCGCCACCCATCCTCT 60.766 66.667 0.00 0.00 0.00 3.69
195 196 1.457643 CCTCGCCACCCATCCTCTA 60.458 63.158 0.00 0.00 0.00 2.43
196 197 1.048724 CCTCGCCACCCATCCTCTAA 61.049 60.000 0.00 0.00 0.00 2.10
197 198 0.105039 CTCGCCACCCATCCTCTAAC 59.895 60.000 0.00 0.00 0.00 2.34
198 199 1.146263 CGCCACCCATCCTCTAACC 59.854 63.158 0.00 0.00 0.00 2.85
199 200 1.338136 CGCCACCCATCCTCTAACCT 61.338 60.000 0.00 0.00 0.00 3.50
200 201 0.470341 GCCACCCATCCTCTAACCTC 59.530 60.000 0.00 0.00 0.00 3.85
201 202 0.753262 CCACCCATCCTCTAACCTCG 59.247 60.000 0.00 0.00 0.00 4.63
202 203 1.688311 CCACCCATCCTCTAACCTCGA 60.688 57.143 0.00 0.00 0.00 4.04
203 204 1.409427 CACCCATCCTCTAACCTCGAC 59.591 57.143 0.00 0.00 0.00 4.20
204 205 0.669077 CCCATCCTCTAACCTCGACG 59.331 60.000 0.00 0.00 0.00 5.12
205 206 1.676746 CCATCCTCTAACCTCGACGA 58.323 55.000 0.00 0.00 0.00 4.20
206 207 2.231529 CCATCCTCTAACCTCGACGAT 58.768 52.381 0.00 0.00 0.00 3.73
207 208 2.030717 CCATCCTCTAACCTCGACGATG 60.031 54.545 0.00 0.00 0.00 3.84
208 209 2.704464 TCCTCTAACCTCGACGATGA 57.296 50.000 7.16 0.00 0.00 2.92
209 210 3.210232 TCCTCTAACCTCGACGATGAT 57.790 47.619 7.16 0.00 0.00 2.45
210 211 3.139850 TCCTCTAACCTCGACGATGATC 58.860 50.000 7.16 0.00 0.00 2.92
211 212 2.879026 CCTCTAACCTCGACGATGATCA 59.121 50.000 7.16 0.00 0.00 2.92
212 213 3.058570 CCTCTAACCTCGACGATGATCAG 60.059 52.174 7.16 1.59 0.00 2.90
213 214 3.542648 TCTAACCTCGACGATGATCAGT 58.457 45.455 7.16 0.00 0.00 3.41
214 215 3.945921 TCTAACCTCGACGATGATCAGTT 59.054 43.478 7.16 0.00 0.00 3.16
215 216 3.594603 AACCTCGACGATGATCAGTTT 57.405 42.857 7.16 0.00 0.00 2.66
216 217 3.594603 ACCTCGACGATGATCAGTTTT 57.405 42.857 7.16 0.00 0.00 2.43
217 218 3.512680 ACCTCGACGATGATCAGTTTTC 58.487 45.455 7.16 0.00 0.00 2.29
218 219 3.193691 ACCTCGACGATGATCAGTTTTCT 59.806 43.478 7.16 0.00 0.00 2.52
219 220 3.794028 CCTCGACGATGATCAGTTTTCTC 59.206 47.826 0.09 0.00 0.00 2.87
220 221 4.439426 CCTCGACGATGATCAGTTTTCTCT 60.439 45.833 0.09 0.00 0.00 3.10
221 222 4.415735 TCGACGATGATCAGTTTTCTCTG 58.584 43.478 0.09 0.00 36.85 3.35
222 223 4.156008 TCGACGATGATCAGTTTTCTCTGA 59.844 41.667 0.09 0.00 46.39 3.27
223 224 4.264145 CGACGATGATCAGTTTTCTCTGAC 59.736 45.833 0.09 0.00 45.40 3.51
224 225 5.139435 ACGATGATCAGTTTTCTCTGACA 57.861 39.130 0.09 1.30 45.40 3.58
225 226 5.541845 ACGATGATCAGTTTTCTCTGACAA 58.458 37.500 0.09 0.00 45.40 3.18
226 227 5.991606 ACGATGATCAGTTTTCTCTGACAAA 59.008 36.000 0.09 0.00 45.40 2.83
227 228 6.073548 ACGATGATCAGTTTTCTCTGACAAAC 60.074 38.462 0.09 1.18 45.40 2.93
228 229 6.566197 ATGATCAGTTTTCTCTGACAAACC 57.434 37.500 0.09 0.00 45.40 3.27
229 230 4.821805 TGATCAGTTTTCTCTGACAAACCC 59.178 41.667 0.00 0.00 45.40 4.11
230 231 3.551846 TCAGTTTTCTCTGACAAACCCC 58.448 45.455 4.75 0.00 39.20 4.95
231 232 2.623416 CAGTTTTCTCTGACAAACCCCC 59.377 50.000 4.75 0.00 37.61 5.40
507 508 0.912486 AGATAGATAATGGGGCCGGC 59.088 55.000 21.18 21.18 0.00 6.13
508 509 0.912486 GATAGATAATGGGGCCGGCT 59.088 55.000 28.56 8.66 0.00 5.52
509 510 0.620556 ATAGATAATGGGGCCGGCTG 59.379 55.000 28.56 0.00 0.00 4.85
510 511 2.124507 TAGATAATGGGGCCGGCTGC 62.125 60.000 28.56 10.77 40.16 5.25
521 522 4.408821 CGGCTGCCACCCTAAGCA 62.409 66.667 20.29 0.00 38.73 3.91
522 523 2.035626 GGCTGCCACCCTAAGCAA 59.964 61.111 15.17 0.00 38.82 3.91
523 524 1.606313 GGCTGCCACCCTAAGCAAA 60.606 57.895 15.17 0.00 38.82 3.68
524 525 1.184970 GGCTGCCACCCTAAGCAAAA 61.185 55.000 15.17 0.00 38.82 2.44
525 526 0.678950 GCTGCCACCCTAAGCAAAAA 59.321 50.000 0.00 0.00 38.82 1.94
555 556 8.134895 GTGATCCAAATATTATTTTCAGGCGAA 58.865 33.333 0.00 0.00 0.00 4.70
674 695 0.957888 GAAGAAGCAGGGCAGGACAC 60.958 60.000 0.00 0.00 0.00 3.67
719 741 2.096958 GTGCGCAATTAAAAACAGCACC 60.097 45.455 14.00 0.00 45.16 5.01
726 748 6.155827 GCAATTAAAAACAGCACCACTATGA 58.844 36.000 0.00 0.00 0.00 2.15
728 750 7.359181 GCAATTAAAAACAGCACCACTATGAAC 60.359 37.037 0.00 0.00 0.00 3.18
749 771 2.799126 AGCCCATCCGTTCATTTACA 57.201 45.000 0.00 0.00 0.00 2.41
817 844 1.617018 CCTCCATCGCAAGGTCCTGA 61.617 60.000 0.00 0.00 38.47 3.86
899 2083 9.305925 CTCATCTTTGGAACCATATTTAAAAGC 57.694 33.333 0.00 0.00 0.00 3.51
901 2085 7.455641 TCTTTGGAACCATATTTAAAAGCGA 57.544 32.000 0.00 0.00 0.00 4.93
902 2086 7.887381 TCTTTGGAACCATATTTAAAAGCGAA 58.113 30.769 0.00 0.00 0.00 4.70
904 2088 8.527567 TTTGGAACCATATTTAAAAGCGAAAG 57.472 30.769 0.00 0.00 0.00 2.62
906 2090 7.887381 TGGAACCATATTTAAAAGCGAAAGAA 58.113 30.769 0.00 0.00 0.00 2.52
914 2106 9.827411 ATATTTAAAAGCGAAAGAACTCTTCAC 57.173 29.630 0.00 0.00 34.61 3.18
986 2747 6.527023 CGCGTATATATAAACCAAGAGGACAG 59.473 42.308 0.00 0.00 38.69 3.51
1026 2789 3.005155 AGTTCAACAGCAAAGCCAAGATC 59.995 43.478 0.00 0.00 0.00 2.75
1067 2831 1.152271 TCCCCTCTTCTTCTTCCCTGT 59.848 52.381 0.00 0.00 0.00 4.00
1246 3013 3.842923 CTCATCGTCGCCAGCCCT 61.843 66.667 0.00 0.00 0.00 5.19
1298 3065 4.386951 CCACCGGCATCGTCACCA 62.387 66.667 0.00 0.00 33.95 4.17
1327 3094 1.583967 CGACGTCGAGCACATCCTC 60.584 63.158 33.35 0.00 43.02 3.71
1330 3097 2.583593 GTCGAGCACATCCTCCGC 60.584 66.667 0.00 0.00 0.00 5.54
1331 3098 3.068064 TCGAGCACATCCTCCGCA 61.068 61.111 0.00 0.00 0.00 5.69
1332 3099 2.887568 CGAGCACATCCTCCGCAC 60.888 66.667 0.00 0.00 0.00 5.34
1333 3100 2.512515 GAGCACATCCTCCGCACC 60.513 66.667 0.00 0.00 0.00 5.01
1334 3101 3.315142 GAGCACATCCTCCGCACCA 62.315 63.158 0.00 0.00 0.00 4.17
1335 3102 2.359850 GCACATCCTCCGCACCAA 60.360 61.111 0.00 0.00 0.00 3.67
1336 3103 2.690778 GCACATCCTCCGCACCAAC 61.691 63.158 0.00 0.00 0.00 3.77
1337 3104 1.003355 CACATCCTCCGCACCAACT 60.003 57.895 0.00 0.00 0.00 3.16
1338 3105 0.606401 CACATCCTCCGCACCAACTT 60.606 55.000 0.00 0.00 0.00 2.66
1729 3523 1.519455 CATCGTCAGCCGGTTCCTC 60.519 63.158 1.90 0.00 37.11 3.71
2011 3805 0.670854 GGTTCTTCTGGCTCGTGTCC 60.671 60.000 0.00 0.00 0.00 4.02
2443 4240 1.930100 GATGAAGTCCATCGCTGCG 59.070 57.895 17.25 17.25 41.88 5.18
2488 4285 2.733593 GTCGTCCGCAAGAACGCT 60.734 61.111 0.00 0.00 43.02 5.07
2490 4287 3.777925 CGTCCGCAAGAACGCTGG 61.778 66.667 0.00 0.00 43.02 4.85
2491 4288 4.090057 GTCCGCAAGAACGCTGGC 62.090 66.667 0.00 0.00 37.74 4.85
2492 4289 4.617520 TCCGCAAGAACGCTGGCA 62.618 61.111 0.00 0.00 41.40 4.92
2572 4369 8.995027 TGCCTGTCCAAATCTAACATATAAAT 57.005 30.769 0.00 0.00 0.00 1.40
2595 4392 1.144503 TCCTAGAGTACCCGTCCATCC 59.855 57.143 0.00 0.00 0.00 3.51
2647 4444 0.395686 ACCCGATCGATCTCCTACGA 59.604 55.000 22.43 0.00 42.49 3.43
2908 4708 4.150454 CGAGCCCCTCTCCCCTCT 62.150 72.222 0.00 0.00 38.62 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.593442 ATTGGGTTTTCAGTCACCTGA 57.407 42.857 0.00 0.00 45.95 3.86
6 7 4.670896 AAATTGGGTTTTCAGTCACCTG 57.329 40.909 0.00 0.00 40.25 4.00
7 8 4.832823 CCTAAATTGGGTTTTCAGTCACCT 59.167 41.667 0.00 0.00 33.09 4.00
8 9 4.560716 GCCTAAATTGGGTTTTCAGTCACC 60.561 45.833 0.00 0.00 0.00 4.02
9 10 4.556233 GCCTAAATTGGGTTTTCAGTCAC 58.444 43.478 0.00 0.00 0.00 3.67
10 11 3.576550 GGCCTAAATTGGGTTTTCAGTCA 59.423 43.478 0.00 0.00 0.00 3.41
11 12 3.576550 TGGCCTAAATTGGGTTTTCAGTC 59.423 43.478 3.32 0.00 0.00 3.51
12 13 3.578282 CTGGCCTAAATTGGGTTTTCAGT 59.422 43.478 3.32 0.00 0.00 3.41
13 14 3.578282 ACTGGCCTAAATTGGGTTTTCAG 59.422 43.478 3.32 3.56 0.00 3.02
14 15 3.576550 GACTGGCCTAAATTGGGTTTTCA 59.423 43.478 3.32 0.00 0.00 2.69
15 16 3.576550 TGACTGGCCTAAATTGGGTTTTC 59.423 43.478 3.32 0.00 0.00 2.29
16 17 3.582164 TGACTGGCCTAAATTGGGTTTT 58.418 40.909 3.32 0.00 0.00 2.43
17 18 3.252554 TGACTGGCCTAAATTGGGTTT 57.747 42.857 3.32 0.00 0.00 3.27
18 19 2.990740 TGACTGGCCTAAATTGGGTT 57.009 45.000 3.32 0.00 0.00 4.11
19 20 2.990740 TTGACTGGCCTAAATTGGGT 57.009 45.000 3.32 0.00 0.00 4.51
20 21 3.181487 CGAATTGACTGGCCTAAATTGGG 60.181 47.826 3.32 0.00 0.00 4.12
21 22 3.443681 ACGAATTGACTGGCCTAAATTGG 59.556 43.478 3.32 8.58 0.00 3.16
22 23 4.701956 ACGAATTGACTGGCCTAAATTG 57.298 40.909 3.32 3.42 0.00 2.32
23 24 6.601613 TCATAACGAATTGACTGGCCTAAATT 59.398 34.615 3.32 4.77 0.00 1.82
24 25 6.119536 TCATAACGAATTGACTGGCCTAAAT 58.880 36.000 3.32 0.00 0.00 1.40
25 26 5.492895 TCATAACGAATTGACTGGCCTAAA 58.507 37.500 3.32 0.00 0.00 1.85
26 27 5.092554 TCATAACGAATTGACTGGCCTAA 57.907 39.130 3.32 0.00 0.00 2.69
27 28 4.693283 CTCATAACGAATTGACTGGCCTA 58.307 43.478 3.32 0.00 0.00 3.93
28 29 3.535561 CTCATAACGAATTGACTGGCCT 58.464 45.455 3.32 0.00 0.00 5.19
29 30 2.032178 GCTCATAACGAATTGACTGGCC 59.968 50.000 0.00 0.00 0.00 5.36
30 31 2.032178 GGCTCATAACGAATTGACTGGC 59.968 50.000 0.00 0.00 0.00 4.85
31 32 2.285220 CGGCTCATAACGAATTGACTGG 59.715 50.000 0.00 0.00 0.00 4.00
32 33 2.930040 ACGGCTCATAACGAATTGACTG 59.070 45.455 0.00 0.00 0.00 3.51
33 34 3.247006 ACGGCTCATAACGAATTGACT 57.753 42.857 0.00 0.00 0.00 3.41
34 35 3.485216 CCAACGGCTCATAACGAATTGAC 60.485 47.826 0.00 0.00 0.00 3.18
35 36 2.675844 CCAACGGCTCATAACGAATTGA 59.324 45.455 0.00 0.00 0.00 2.57
36 37 2.675844 TCCAACGGCTCATAACGAATTG 59.324 45.455 0.00 0.00 0.00 2.32
37 38 2.980568 TCCAACGGCTCATAACGAATT 58.019 42.857 0.00 0.00 0.00 2.17
38 39 2.684001 TCCAACGGCTCATAACGAAT 57.316 45.000 0.00 0.00 0.00 3.34
39 40 2.276201 CATCCAACGGCTCATAACGAA 58.724 47.619 0.00 0.00 0.00 3.85
40 41 1.934589 CATCCAACGGCTCATAACGA 58.065 50.000 0.00 0.00 0.00 3.85
41 42 0.304705 GCATCCAACGGCTCATAACG 59.695 55.000 0.00 0.00 0.00 3.18
42 43 1.378531 TGCATCCAACGGCTCATAAC 58.621 50.000 0.00 0.00 0.00 1.89
43 44 2.016318 CTTGCATCCAACGGCTCATAA 58.984 47.619 0.00 0.00 0.00 1.90
44 45 1.209261 TCTTGCATCCAACGGCTCATA 59.791 47.619 0.00 0.00 0.00 2.15
45 46 0.035152 TCTTGCATCCAACGGCTCAT 60.035 50.000 0.00 0.00 0.00 2.90
46 47 0.035152 ATCTTGCATCCAACGGCTCA 60.035 50.000 0.00 0.00 0.00 4.26
47 48 0.379669 CATCTTGCATCCAACGGCTC 59.620 55.000 0.00 0.00 0.00 4.70
48 49 1.033746 CCATCTTGCATCCAACGGCT 61.034 55.000 0.00 0.00 0.00 5.52
49 50 1.031571 TCCATCTTGCATCCAACGGC 61.032 55.000 0.00 0.00 0.00 5.68
50 51 1.335810 CATCCATCTTGCATCCAACGG 59.664 52.381 0.00 0.00 0.00 4.44
51 52 1.335810 CCATCCATCTTGCATCCAACG 59.664 52.381 0.00 0.00 0.00 4.10
52 53 2.360165 GACCATCCATCTTGCATCCAAC 59.640 50.000 0.00 0.00 0.00 3.77
53 54 2.025131 TGACCATCCATCTTGCATCCAA 60.025 45.455 0.00 0.00 0.00 3.53
54 55 1.565288 TGACCATCCATCTTGCATCCA 59.435 47.619 0.00 0.00 0.00 3.41
55 56 2.158711 TCTGACCATCCATCTTGCATCC 60.159 50.000 0.00 0.00 0.00 3.51
56 57 3.204306 TCTGACCATCCATCTTGCATC 57.796 47.619 0.00 0.00 0.00 3.91
57 58 3.878237 ATCTGACCATCCATCTTGCAT 57.122 42.857 0.00 0.00 0.00 3.96
58 59 4.164796 ACTTATCTGACCATCCATCTTGCA 59.835 41.667 0.00 0.00 0.00 4.08
59 60 4.712476 ACTTATCTGACCATCCATCTTGC 58.288 43.478 0.00 0.00 0.00 4.01
60 61 7.052873 AGAAACTTATCTGACCATCCATCTTG 58.947 38.462 0.00 0.00 0.00 3.02
61 62 7.205515 AGAAACTTATCTGACCATCCATCTT 57.794 36.000 0.00 0.00 0.00 2.40
62 63 6.821616 AGAAACTTATCTGACCATCCATCT 57.178 37.500 0.00 0.00 0.00 2.90
63 64 7.050377 TGAAGAAACTTATCTGACCATCCATC 58.950 38.462 0.00 0.00 0.00 3.51
64 65 6.962182 TGAAGAAACTTATCTGACCATCCAT 58.038 36.000 0.00 0.00 0.00 3.41
65 66 6.373005 TGAAGAAACTTATCTGACCATCCA 57.627 37.500 0.00 0.00 0.00 3.41
66 67 6.655003 TGTTGAAGAAACTTATCTGACCATCC 59.345 38.462 0.00 0.00 39.70 3.51
67 68 7.672983 TGTTGAAGAAACTTATCTGACCATC 57.327 36.000 0.00 0.00 39.70 3.51
68 69 7.337942 GGATGTTGAAGAAACTTATCTGACCAT 59.662 37.037 0.00 0.00 39.70 3.55
69 70 6.655003 GGATGTTGAAGAAACTTATCTGACCA 59.345 38.462 0.00 0.00 39.70 4.02
70 71 6.655003 TGGATGTTGAAGAAACTTATCTGACC 59.345 38.462 0.00 0.00 39.70 4.02
71 72 7.672983 TGGATGTTGAAGAAACTTATCTGAC 57.327 36.000 0.00 0.00 39.70 3.51
72 73 7.174946 GGTTGGATGTTGAAGAAACTTATCTGA 59.825 37.037 0.00 0.00 39.70 3.27
73 74 7.308435 GGTTGGATGTTGAAGAAACTTATCTG 58.692 38.462 0.00 0.00 39.70 2.90
74 75 6.434340 GGGTTGGATGTTGAAGAAACTTATCT 59.566 38.462 0.00 0.00 39.70 1.98
75 76 6.434340 AGGGTTGGATGTTGAAGAAACTTATC 59.566 38.462 0.00 0.00 39.70 1.75
76 77 6.314917 AGGGTTGGATGTTGAAGAAACTTAT 58.685 36.000 0.00 0.00 39.70 1.73
77 78 5.701224 AGGGTTGGATGTTGAAGAAACTTA 58.299 37.500 0.00 0.00 39.70 2.24
78 79 4.546674 AGGGTTGGATGTTGAAGAAACTT 58.453 39.130 0.00 0.00 39.70 2.66
79 80 4.184649 AGGGTTGGATGTTGAAGAAACT 57.815 40.909 0.00 0.00 39.70 2.66
80 81 4.937201 AAGGGTTGGATGTTGAAGAAAC 57.063 40.909 0.00 0.00 39.41 2.78
81 82 6.074648 ACATAAGGGTTGGATGTTGAAGAAA 58.925 36.000 0.00 0.00 29.46 2.52
82 83 5.640147 ACATAAGGGTTGGATGTTGAAGAA 58.360 37.500 0.00 0.00 29.46 2.52
83 84 5.253330 GACATAAGGGTTGGATGTTGAAGA 58.747 41.667 0.00 0.00 33.99 2.87
84 85 4.399303 GGACATAAGGGTTGGATGTTGAAG 59.601 45.833 0.00 0.00 33.99 3.02
85 86 4.202620 TGGACATAAGGGTTGGATGTTGAA 60.203 41.667 0.00 0.00 33.99 2.69
86 87 3.332187 TGGACATAAGGGTTGGATGTTGA 59.668 43.478 0.00 0.00 33.99 3.18
87 88 3.696045 TGGACATAAGGGTTGGATGTTG 58.304 45.455 0.00 0.00 33.99 3.33
88 89 4.230502 AGATGGACATAAGGGTTGGATGTT 59.769 41.667 0.00 0.00 33.99 2.71
89 90 3.788142 AGATGGACATAAGGGTTGGATGT 59.212 43.478 0.00 0.00 36.52 3.06
90 91 4.392940 GAGATGGACATAAGGGTTGGATG 58.607 47.826 0.00 0.00 0.00 3.51
91 92 3.395941 GGAGATGGACATAAGGGTTGGAT 59.604 47.826 0.00 0.00 0.00 3.41
92 93 2.777692 GGAGATGGACATAAGGGTTGGA 59.222 50.000 0.00 0.00 0.00 3.53
93 94 2.780010 AGGAGATGGACATAAGGGTTGG 59.220 50.000 0.00 0.00 0.00 3.77
94 95 4.455606 GAAGGAGATGGACATAAGGGTTG 58.544 47.826 0.00 0.00 0.00 3.77
95 96 3.459969 GGAAGGAGATGGACATAAGGGTT 59.540 47.826 0.00 0.00 0.00 4.11
96 97 3.049344 GGAAGGAGATGGACATAAGGGT 58.951 50.000 0.00 0.00 0.00 4.34
97 98 2.373502 GGGAAGGAGATGGACATAAGGG 59.626 54.545 0.00 0.00 0.00 3.95
98 99 3.048600 TGGGAAGGAGATGGACATAAGG 58.951 50.000 0.00 0.00 0.00 2.69
99 100 4.778213 TTGGGAAGGAGATGGACATAAG 57.222 45.455 0.00 0.00 0.00 1.73
100 101 4.202357 CGATTGGGAAGGAGATGGACATAA 60.202 45.833 0.00 0.00 0.00 1.90
101 102 3.324846 CGATTGGGAAGGAGATGGACATA 59.675 47.826 0.00 0.00 0.00 2.29
102 103 2.105477 CGATTGGGAAGGAGATGGACAT 59.895 50.000 0.00 0.00 0.00 3.06
103 104 1.486310 CGATTGGGAAGGAGATGGACA 59.514 52.381 0.00 0.00 0.00 4.02
104 105 1.811941 GCGATTGGGAAGGAGATGGAC 60.812 57.143 0.00 0.00 0.00 4.02
105 106 0.469917 GCGATTGGGAAGGAGATGGA 59.530 55.000 0.00 0.00 0.00 3.41
106 107 0.536006 GGCGATTGGGAAGGAGATGG 60.536 60.000 0.00 0.00 0.00 3.51
107 108 0.536006 GGGCGATTGGGAAGGAGATG 60.536 60.000 0.00 0.00 0.00 2.90
108 109 1.709994 GGGGCGATTGGGAAGGAGAT 61.710 60.000 0.00 0.00 0.00 2.75
109 110 2.375345 GGGGCGATTGGGAAGGAGA 61.375 63.158 0.00 0.00 0.00 3.71
110 111 2.193248 GGGGCGATTGGGAAGGAG 59.807 66.667 0.00 0.00 0.00 3.69
111 112 2.612430 TGGGGCGATTGGGAAGGA 60.612 61.111 0.00 0.00 0.00 3.36
112 113 2.440247 GTGGGGCGATTGGGAAGG 60.440 66.667 0.00 0.00 0.00 3.46
113 114 2.824041 CGTGGGGCGATTGGGAAG 60.824 66.667 0.00 0.00 44.77 3.46
114 115 3.323286 TCGTGGGGCGATTGGGAA 61.323 61.111 0.00 0.00 45.68 3.97
122 123 4.760047 CTGGGAGTTCGTGGGGCG 62.760 72.222 0.00 0.00 43.01 6.13
124 125 4.410400 GGCTGGGAGTTCGTGGGG 62.410 72.222 0.00 0.00 0.00 4.96
125 126 3.636231 TGGCTGGGAGTTCGTGGG 61.636 66.667 0.00 0.00 0.00 4.61
126 127 2.358737 GTGGCTGGGAGTTCGTGG 60.359 66.667 0.00 0.00 0.00 4.94
127 128 2.358737 GGTGGCTGGGAGTTCGTG 60.359 66.667 0.00 0.00 0.00 4.35
128 129 2.185310 GATGGTGGCTGGGAGTTCGT 62.185 60.000 0.00 0.00 0.00 3.85
129 130 1.450312 GATGGTGGCTGGGAGTTCG 60.450 63.158 0.00 0.00 0.00 3.95
130 131 1.450312 CGATGGTGGCTGGGAGTTC 60.450 63.158 0.00 0.00 0.00 3.01
131 132 2.671070 CGATGGTGGCTGGGAGTT 59.329 61.111 0.00 0.00 0.00 3.01
132 133 4.101448 GCGATGGTGGCTGGGAGT 62.101 66.667 0.00 0.00 0.00 3.85
133 134 2.374830 CTAGCGATGGTGGCTGGGAG 62.375 65.000 0.00 0.00 41.69 4.30
134 135 2.364973 TAGCGATGGTGGCTGGGA 60.365 61.111 0.00 0.00 41.69 4.37
135 136 2.109799 CTAGCGATGGTGGCTGGG 59.890 66.667 0.00 0.00 41.69 4.45
136 137 2.590007 GCTAGCGATGGTGGCTGG 60.590 66.667 0.00 0.00 41.69 4.85
137 138 2.963854 CGCTAGCGATGGTGGCTG 60.964 66.667 32.98 0.00 41.69 4.85
138 139 4.227134 CCGCTAGCGATGGTGGCT 62.227 66.667 37.39 0.00 44.35 4.75
172 173 3.816367 GATGGGTGGCGAGGCTAGC 62.816 68.421 11.48 11.48 36.82 3.42
173 174 2.423446 GATGGGTGGCGAGGCTAG 59.577 66.667 0.00 0.00 0.00 3.42
174 175 3.161450 GGATGGGTGGCGAGGCTA 61.161 66.667 0.00 0.00 0.00 3.93
176 177 4.554036 GAGGATGGGTGGCGAGGC 62.554 72.222 0.00 0.00 0.00 4.70
177 178 1.048724 TTAGAGGATGGGTGGCGAGG 61.049 60.000 0.00 0.00 0.00 4.63
178 179 0.105039 GTTAGAGGATGGGTGGCGAG 59.895 60.000 0.00 0.00 0.00 5.03
179 180 1.335132 GGTTAGAGGATGGGTGGCGA 61.335 60.000 0.00 0.00 0.00 5.54
180 181 1.146263 GGTTAGAGGATGGGTGGCG 59.854 63.158 0.00 0.00 0.00 5.69
181 182 0.470341 GAGGTTAGAGGATGGGTGGC 59.530 60.000 0.00 0.00 0.00 5.01
182 183 0.753262 CGAGGTTAGAGGATGGGTGG 59.247 60.000 0.00 0.00 0.00 4.61
183 184 1.409427 GTCGAGGTTAGAGGATGGGTG 59.591 57.143 0.00 0.00 0.00 4.61
184 185 1.777941 GTCGAGGTTAGAGGATGGGT 58.222 55.000 0.00 0.00 0.00 4.51
185 186 0.669077 CGTCGAGGTTAGAGGATGGG 59.331 60.000 0.00 0.00 0.00 4.00
186 187 1.676746 TCGTCGAGGTTAGAGGATGG 58.323 55.000 4.85 0.00 0.00 3.51
187 188 3.275400 CATCGTCGAGGTTAGAGGATG 57.725 52.381 12.39 12.39 46.98 3.51
188 189 3.210232 TCATCGTCGAGGTTAGAGGAT 57.790 47.619 6.80 0.00 41.96 3.24
189 190 2.704464 TCATCGTCGAGGTTAGAGGA 57.296 50.000 6.80 0.00 37.01 3.71
190 191 2.879026 TGATCATCGTCGAGGTTAGAGG 59.121 50.000 6.80 0.00 0.00 3.69
191 192 3.562141 ACTGATCATCGTCGAGGTTAGAG 59.438 47.826 6.80 1.64 0.00 2.43
192 193 3.542648 ACTGATCATCGTCGAGGTTAGA 58.457 45.455 6.80 2.60 0.00 2.10
193 194 3.972950 ACTGATCATCGTCGAGGTTAG 57.027 47.619 6.80 6.54 0.00 2.34
194 195 4.713824 AAACTGATCATCGTCGAGGTTA 57.286 40.909 6.80 0.00 0.00 2.85
195 196 3.594603 AAACTGATCATCGTCGAGGTT 57.405 42.857 6.80 0.00 0.00 3.50
196 197 3.193691 AGAAAACTGATCATCGTCGAGGT 59.806 43.478 6.80 0.00 0.00 3.85
197 198 3.775202 AGAAAACTGATCATCGTCGAGG 58.225 45.455 0.00 0.00 0.00 4.63
198 199 4.498681 CAGAGAAAACTGATCATCGTCGAG 59.501 45.833 0.00 0.00 39.94 4.04
199 200 4.156008 TCAGAGAAAACTGATCATCGTCGA 59.844 41.667 0.00 0.00 41.21 4.20
200 201 4.264145 GTCAGAGAAAACTGATCATCGTCG 59.736 45.833 0.00 0.00 46.36 5.12
201 202 5.164233 TGTCAGAGAAAACTGATCATCGTC 58.836 41.667 0.00 0.00 46.36 4.20
202 203 5.139435 TGTCAGAGAAAACTGATCATCGT 57.861 39.130 0.00 0.00 46.36 3.73
203 204 6.302615 GTTTGTCAGAGAAAACTGATCATCG 58.697 40.000 0.00 0.00 46.36 3.84
204 205 6.348868 GGGTTTGTCAGAGAAAACTGATCATC 60.349 42.308 7.94 0.00 46.36 2.92
205 206 5.474876 GGGTTTGTCAGAGAAAACTGATCAT 59.525 40.000 7.94 0.00 46.36 2.45
206 207 4.821805 GGGTTTGTCAGAGAAAACTGATCA 59.178 41.667 7.94 0.00 46.36 2.92
207 208 4.216472 GGGGTTTGTCAGAGAAAACTGATC 59.784 45.833 7.94 0.00 46.36 2.92
208 209 4.145052 GGGGTTTGTCAGAGAAAACTGAT 58.855 43.478 7.94 0.00 46.36 2.90
209 210 3.551846 GGGGTTTGTCAGAGAAAACTGA 58.448 45.455 7.94 0.00 43.39 3.41
210 211 2.623416 GGGGGTTTGTCAGAGAAAACTG 59.377 50.000 7.94 0.00 36.68 3.16
211 212 2.945456 GGGGGTTTGTCAGAGAAAACT 58.055 47.619 7.94 0.00 36.68 2.66
487 488 1.282157 GCCGGCCCCATTATCTATCTT 59.718 52.381 18.11 0.00 0.00 2.40
488 489 0.912486 GCCGGCCCCATTATCTATCT 59.088 55.000 18.11 0.00 0.00 1.98
489 490 0.912486 AGCCGGCCCCATTATCTATC 59.088 55.000 26.15 0.00 0.00 2.08
490 491 0.620556 CAGCCGGCCCCATTATCTAT 59.379 55.000 26.15 0.00 0.00 1.98
491 492 2.066340 CAGCCGGCCCCATTATCTA 58.934 57.895 26.15 0.00 0.00 1.98
492 493 2.839098 CAGCCGGCCCCATTATCT 59.161 61.111 26.15 0.00 0.00 1.98
493 494 2.985847 GCAGCCGGCCCCATTATC 60.986 66.667 26.15 0.00 36.11 1.75
504 505 3.918253 TTGCTTAGGGTGGCAGCCG 62.918 63.158 28.36 16.45 41.56 5.52
505 506 1.184970 TTTTGCTTAGGGTGGCAGCC 61.185 55.000 27.81 27.81 39.68 4.85
506 507 0.678950 TTTTTGCTTAGGGTGGCAGC 59.321 50.000 8.47 8.47 39.68 5.25
526 527 8.854117 GCCTGAAAATAATATTTGGATCACTCT 58.146 33.333 0.00 0.00 0.00 3.24
545 546 5.001232 AGCTACTTTGTAATTCGCCTGAAA 58.999 37.500 0.00 0.00 37.71 2.69
551 552 9.503427 AATCATTTTAGCTACTTTGTAATTCGC 57.497 29.630 0.00 0.00 0.00 4.70
578 579 7.944729 AGGCTATGATGTTTCTTTGTATGTT 57.055 32.000 0.00 0.00 0.00 2.71
584 585 4.082081 TGCCAAGGCTATGATGTTTCTTTG 60.082 41.667 12.96 0.00 42.51 2.77
674 695 0.324285 ACTTTCAGCAGCTCCTCCTG 59.676 55.000 0.00 0.00 35.93 3.86
719 741 2.365617 ACGGATGGGCTAGTTCATAGTG 59.634 50.000 0.00 0.00 33.65 2.74
726 748 3.366052 AAATGAACGGATGGGCTAGTT 57.634 42.857 0.00 0.00 0.00 2.24
728 750 3.560068 GTGTAAATGAACGGATGGGCTAG 59.440 47.826 0.00 0.00 0.00 3.42
749 771 7.065803 CGGATTAGAATAACAAATGTGTCCTGT 59.934 37.037 0.00 0.00 36.80 4.00
914 2106 4.583489 ACTGTCCAACCCATACTCTATACG 59.417 45.833 0.00 0.00 0.00 3.06
986 2747 8.081633 TGTTGAACTGTGAATATTTTGATGGAC 58.918 33.333 0.00 0.00 0.00 4.02
1026 2789 5.105997 GGGAACTCCATTGATTCTGACTTTG 60.106 44.000 0.00 0.00 37.91 2.77
1067 2831 2.119495 GGGAGGAAGCAGGATGAGTAA 58.881 52.381 0.00 0.00 39.69 2.24
1246 3013 0.252881 AGAAGCCCATCCTGAGGTCA 60.253 55.000 0.00 0.00 0.00 4.02
1327 3094 3.283684 TTGGCGAAGTTGGTGCGG 61.284 61.111 0.00 0.00 0.00 5.69
1330 3097 0.872388 GGTAGTTGGCGAAGTTGGTG 59.128 55.000 0.00 0.00 0.00 4.17
1331 3098 0.250597 GGGTAGTTGGCGAAGTTGGT 60.251 55.000 0.00 0.00 0.00 3.67
1332 3099 0.958876 GGGGTAGTTGGCGAAGTTGG 60.959 60.000 0.00 0.00 0.00 3.77
1333 3100 0.250553 TGGGGTAGTTGGCGAAGTTG 60.251 55.000 0.00 0.00 0.00 3.16
1334 3101 0.475044 TTGGGGTAGTTGGCGAAGTT 59.525 50.000 0.00 0.00 0.00 2.66
1335 3102 0.036306 CTTGGGGTAGTTGGCGAAGT 59.964 55.000 0.00 0.00 0.00 3.01
1336 3103 0.676782 CCTTGGGGTAGTTGGCGAAG 60.677 60.000 0.00 0.00 0.00 3.79
1337 3104 1.377229 CCTTGGGGTAGTTGGCGAA 59.623 57.895 0.00 0.00 0.00 4.70
1338 3105 2.598787 CCCTTGGGGTAGTTGGCGA 61.599 63.158 0.00 0.00 38.25 5.54
1855 3649 0.181587 TGTTTTCTTCCCCAGACGCA 59.818 50.000 0.00 0.00 0.00 5.24
2230 4027 3.134127 GTGATGTTCCAGCCGGCC 61.134 66.667 26.15 7.94 0.00 6.13
2572 4369 0.842635 GGACGGGTACTCTAGGAGGA 59.157 60.000 0.00 0.00 33.35 3.71
2908 4708 3.077556 GAAGGAGAGGAGGCGGCA 61.078 66.667 13.08 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.