Multiple sequence alignment - TraesCS5A01G125600

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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 TraesCS5A01G125600 chr5A 100.000 1803 0 0 1 1803 276110788 276112590 0.000000e+00 3330.0
1 TraesCS5A01G125600 chr5A 89.139 801 47 14 775 1535 276981097 276980297 0.000000e+00 961.0
2 TraesCS5A01G125600 chr5A 100.000 498 0 0 2175 2672 276112962 276113459 0.000000e+00 920.0
3 TraesCS5A01G125600 chr5A 93.519 216 12 2 1536 1751 276113896 276113683 1.190000e-83 320.0
4 TraesCS5A01G125600 chr5A 91.781 219 18 0 2 220 538101399 538101181 3.340000e-79 305.0
5 TraesCS5A01G125600 chr5D 94.495 1308 35 20 232 1535 212626516 212627790 0.000000e+00 1982.0
6 TraesCS5A01G125600 chr5D 89.737 799 55 11 763 1535 213128945 213129742 0.000000e+00 996.0
7 TraesCS5A01G125600 chr5D 73.805 481 97 17 1067 1535 528230578 528230115 2.130000e-36 163.0
8 TraesCS5A01G125600 chr5D 94.643 56 1 2 664 718 213128373 213128427 4.740000e-13 86.1
9 TraesCS5A01G125600 chr5B 95.656 1105 47 1 431 1535 226758715 226759818 0.000000e+00 1773.0
10 TraesCS5A01G125600 chr5B 89.693 815 54 11 750 1535 227120701 227121514 0.000000e+00 1013.0
11 TraesCS5A01G125600 chr5B 97.701 174 4 0 1536 1709 696405426 696405599 1.550000e-77 300.0
12 TraesCS5A01G125600 chr5B 97.222 72 2 0 325 396 226756892 226756963 3.610000e-24 122.0
13 TraesCS5A01G125600 chr7B 98.384 495 7 1 2178 2672 675009115 675008622 0.000000e+00 869.0
14 TraesCS5A01G125600 chr7B 97.992 498 10 0 2175 2672 425884749 425884252 0.000000e+00 865.0
15 TraesCS5A01G125600 chr7B 97.388 268 5 1 1536 1803 425885120 425884855 3.140000e-124 455.0
16 TraesCS5A01G125600 chr7B 96.283 269 3 2 1535 1803 675009485 675009224 4.090000e-118 435.0
17 TraesCS5A01G125600 chr7B 95.896 268 7 1 1536 1803 425876356 425876619 5.280000e-117 431.0
18 TraesCS5A01G125600 chr7B 95.522 268 10 1 1536 1803 675008056 675008321 6.840000e-116 427.0
19 TraesCS5A01G125600 chr2B 95.783 498 11 3 2175 2672 51143880 51143393 0.000000e+00 795.0
20 TraesCS5A01G125600 chr2B 74.057 212 38 13 1069 1270 785208592 785208796 1.330000e-08 71.3
21 TraesCS5A01G125600 chr2D 94.779 498 16 3 2175 2672 31027756 31028243 0.000000e+00 767.0
22 TraesCS5A01G125600 chr2D 73.408 267 54 15 1098 1354 649338500 649338759 1.700000e-12 84.2
23 TraesCS5A01G125600 chr4A 82.944 557 72 12 998 1535 487868994 487868442 5.170000e-132 481.0
24 TraesCS5A01G125600 chr4A 97.701 174 4 0 1536 1709 36323509 36323336 1.550000e-77 300.0
25 TraesCS5A01G125600 chr4A 91.324 219 19 0 2 220 631371489 631371707 1.550000e-77 300.0
26 TraesCS5A01G125600 chr4A 97.126 174 5 0 1536 1709 590267730 590267557 7.230000e-76 294.0
27 TraesCS5A01G125600 chr4D 82.406 557 75 13 998 1535 93841194 93841746 5.210000e-127 464.0
28 TraesCS5A01G125600 chr4B 82.226 557 76 13 998 1535 132331565 132332117 2.420000e-125 459.0
29 TraesCS5A01G125600 chr6A 92.694 219 16 0 2 220 80803302 80803084 1.540000e-82 316.0
30 TraesCS5A01G125600 chr6A 91.781 219 18 0 2 220 46548931 46549149 3.340000e-79 305.0
31 TraesCS5A01G125600 chr6A 91.364 220 19 0 2 221 547740678 547740459 4.320000e-78 302.0
32 TraesCS5A01G125600 chr6A 91.667 216 18 0 5 220 422776173 422775958 1.550000e-77 300.0
33 TraesCS5A01G125600 chr3A 92.273 220 15 2 2 220 111840024 111839806 7.180000e-81 311.0
34 TraesCS5A01G125600 chr3A 92.273 220 15 2 2 220 726339027 726338809 7.180000e-81 311.0
35 TraesCS5A01G125600 chr3A 92.202 218 17 0 2 219 670674128 670673911 2.580000e-80 309.0
36 TraesCS5A01G125600 chr7A 97.701 174 4 0 1536 1709 701581458 701581285 1.550000e-77 300.0
37 TraesCS5A01G125600 chr2A 96.907 97 3 0 2175 2271 33316339 33316435 2.130000e-36 163.0
38 TraesCS5A01G125600 chr2A 73.308 266 56 13 1098 1354 775379045 775378786 1.700000e-12 84.2


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 TraesCS5A01G125600 chr5A 276110788 276113459 2671 False 2125.00 3330 100.0000 1 2672 2 chr5A.!!$F1 2671
1 TraesCS5A01G125600 chr5A 276980297 276981097 800 True 961.00 961 89.1390 775 1535 1 chr5A.!!$R2 760
2 TraesCS5A01G125600 chr5D 212626516 212627790 1274 False 1982.00 1982 94.4950 232 1535 1 chr5D.!!$F1 1303
3 TraesCS5A01G125600 chr5D 213128373 213129742 1369 False 541.05 996 92.1900 664 1535 2 chr5D.!!$F2 871
4 TraesCS5A01G125600 chr5B 227120701 227121514 813 False 1013.00 1013 89.6930 750 1535 1 chr5B.!!$F1 785
5 TraesCS5A01G125600 chr5B 226756892 226759818 2926 False 947.50 1773 96.4390 325 1535 2 chr5B.!!$F3 1210
6 TraesCS5A01G125600 chr7B 425884252 425885120 868 True 660.00 865 97.6900 1536 2672 2 chr7B.!!$R1 1136
7 TraesCS5A01G125600 chr7B 675008622 675009485 863 True 652.00 869 97.3335 1535 2672 2 chr7B.!!$R2 1137
8 TraesCS5A01G125600 chr4A 487868442 487868994 552 True 481.00 481 82.9440 998 1535 1 chr4A.!!$R2 537
9 TraesCS5A01G125600 chr4D 93841194 93841746 552 False 464.00 464 82.4060 998 1535 1 chr4D.!!$F1 537
10 TraesCS5A01G125600 chr4B 132331565 132332117 552 False 459.00 459 82.2260 998 1535 1 chr4B.!!$F1 537

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
109 110 0.037232 GGGAACGTCTCCTTCCACTG 60.037 60.0 13.94 0.0 44.68 3.66 F
1158 3392 0.034089 CGGGCTTTTTCCTCCAGGAT 60.034 55.0 0.00 0.0 44.98 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 3734 0.687757 AGATCCAGCTGCCGACCTTA 60.688 55.000 8.66 0.0 0.0 2.69 R
2288 4543 2.757099 GTACGGGAGCGGGGAAGA 60.757 66.667 0.00 0.0 0.0 2.87 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.414158 GCACCCTACCTCTATGAGCA 58.586 55.000 0.00 0.00 0.00 4.26
20 21 1.069358 GCACCCTACCTCTATGAGCAC 59.931 57.143 0.00 0.00 0.00 4.40
21 22 1.689273 CACCCTACCTCTATGAGCACC 59.311 57.143 0.00 0.00 0.00 5.01
22 23 1.576272 ACCCTACCTCTATGAGCACCT 59.424 52.381 0.00 0.00 0.00 4.00
23 24 2.022918 ACCCTACCTCTATGAGCACCTT 60.023 50.000 0.00 0.00 0.00 3.50
24 25 2.630580 CCCTACCTCTATGAGCACCTTC 59.369 54.545 0.00 0.00 0.00 3.46
25 26 2.294791 CCTACCTCTATGAGCACCTTCG 59.705 54.545 0.00 0.00 0.00 3.79
26 27 2.145397 ACCTCTATGAGCACCTTCGA 57.855 50.000 0.00 0.00 0.00 3.71
27 28 2.028130 ACCTCTATGAGCACCTTCGAG 58.972 52.381 0.00 0.00 0.00 4.04
28 29 2.302260 CCTCTATGAGCACCTTCGAGA 58.698 52.381 0.00 0.00 0.00 4.04
29 30 2.293122 CCTCTATGAGCACCTTCGAGAG 59.707 54.545 0.00 0.00 33.13 3.20
30 31 3.210227 CTCTATGAGCACCTTCGAGAGA 58.790 50.000 0.00 0.00 34.28 3.10
31 32 2.946329 TCTATGAGCACCTTCGAGAGAC 59.054 50.000 0.00 0.00 41.84 3.36
32 33 1.846007 ATGAGCACCTTCGAGAGACT 58.154 50.000 0.00 0.00 41.84 3.24
33 34 0.884514 TGAGCACCTTCGAGAGACTG 59.115 55.000 0.00 0.00 41.84 3.51
34 35 1.169577 GAGCACCTTCGAGAGACTGA 58.830 55.000 0.00 0.00 41.84 3.41
35 36 1.132262 GAGCACCTTCGAGAGACTGAG 59.868 57.143 0.00 0.00 41.84 3.35
36 37 0.457681 GCACCTTCGAGAGACTGAGC 60.458 60.000 0.00 0.00 41.84 4.26
37 38 0.884514 CACCTTCGAGAGACTGAGCA 59.115 55.000 0.00 0.00 41.84 4.26
38 39 1.135431 CACCTTCGAGAGACTGAGCAG 60.135 57.143 0.00 0.00 41.84 4.24
39 40 0.455410 CCTTCGAGAGACTGAGCAGG 59.545 60.000 2.20 0.00 41.84 4.85
40 41 0.179140 CTTCGAGAGACTGAGCAGGC 60.179 60.000 2.20 0.00 41.84 4.85
41 42 0.895559 TTCGAGAGACTGAGCAGGCA 60.896 55.000 6.06 0.00 39.50 4.75
42 43 0.682532 TCGAGAGACTGAGCAGGCAT 60.683 55.000 6.06 0.00 39.50 4.40
43 44 1.028130 CGAGAGACTGAGCAGGCATA 58.972 55.000 6.06 0.00 39.50 3.14
44 45 1.612950 CGAGAGACTGAGCAGGCATAT 59.387 52.381 6.06 0.00 39.50 1.78
45 46 2.351641 CGAGAGACTGAGCAGGCATATC 60.352 54.545 6.06 0.00 39.50 1.63
46 47 2.627221 GAGAGACTGAGCAGGCATATCA 59.373 50.000 6.06 0.00 39.50 2.15
47 48 3.241156 AGAGACTGAGCAGGCATATCAT 58.759 45.455 6.06 0.00 39.50 2.45
48 49 3.258872 AGAGACTGAGCAGGCATATCATC 59.741 47.826 6.06 0.00 39.50 2.92
49 50 3.241156 AGACTGAGCAGGCATATCATCT 58.759 45.455 6.06 0.00 39.50 2.90
50 51 3.647113 AGACTGAGCAGGCATATCATCTT 59.353 43.478 6.06 0.00 39.50 2.40
51 52 3.741249 ACTGAGCAGGCATATCATCTTG 58.259 45.455 2.20 0.00 0.00 3.02
52 53 3.390311 ACTGAGCAGGCATATCATCTTGA 59.610 43.478 2.20 0.00 0.00 3.02
53 54 3.997681 CTGAGCAGGCATATCATCTTGAG 59.002 47.826 0.00 0.00 0.00 3.02
54 55 3.644738 TGAGCAGGCATATCATCTTGAGA 59.355 43.478 0.00 0.00 0.00 3.27
55 56 4.286291 TGAGCAGGCATATCATCTTGAGAT 59.714 41.667 0.00 0.00 34.56 2.75
56 57 5.221864 TGAGCAGGCATATCATCTTGAGATT 60.222 40.000 0.00 0.00 31.21 2.40
57 58 5.632118 AGCAGGCATATCATCTTGAGATTT 58.368 37.500 0.00 0.00 31.21 2.17
58 59 6.069331 AGCAGGCATATCATCTTGAGATTTT 58.931 36.000 0.00 0.00 31.21 1.82
59 60 7.229308 AGCAGGCATATCATCTTGAGATTTTA 58.771 34.615 0.00 0.00 31.21 1.52
60 61 7.174599 AGCAGGCATATCATCTTGAGATTTTAC 59.825 37.037 0.00 0.00 31.21 2.01
61 62 7.516481 CAGGCATATCATCTTGAGATTTTACG 58.484 38.462 0.00 0.00 31.21 3.18
62 63 7.386025 CAGGCATATCATCTTGAGATTTTACGA 59.614 37.037 0.00 0.00 31.21 3.43
63 64 7.933577 AGGCATATCATCTTGAGATTTTACGAA 59.066 33.333 0.00 0.00 31.21 3.85
64 65 8.226448 GGCATATCATCTTGAGATTTTACGAAG 58.774 37.037 0.00 0.00 31.21 3.79
65 66 8.768955 GCATATCATCTTGAGATTTTACGAAGT 58.231 33.333 0.00 0.00 37.29 3.01
68 69 7.582435 TCATCTTGAGATTTTACGAAGTCAC 57.418 36.000 0.00 0.00 35.39 3.67
69 70 6.590292 TCATCTTGAGATTTTACGAAGTCACC 59.410 38.462 0.00 0.00 35.39 4.02
70 71 4.921515 TCTTGAGATTTTACGAAGTCACCG 59.078 41.667 0.00 0.00 43.93 4.94
71 72 4.247267 TGAGATTTTACGAAGTCACCGT 57.753 40.909 0.00 0.00 43.93 4.83
72 73 5.375417 TGAGATTTTACGAAGTCACCGTA 57.625 39.130 0.00 0.00 43.93 4.02
73 74 5.396484 TGAGATTTTACGAAGTCACCGTAG 58.604 41.667 0.00 0.00 43.93 3.51
74 75 5.181811 TGAGATTTTACGAAGTCACCGTAGA 59.818 40.000 0.00 0.00 43.93 2.59
75 76 5.397326 AGATTTTACGAAGTCACCGTAGAC 58.603 41.667 0.00 0.00 43.93 2.59
76 77 2.880822 TTACGAAGTCACCGTAGACG 57.119 50.000 0.00 0.00 43.93 4.18
77 78 0.443869 TACGAAGTCACCGTAGACGC 59.556 55.000 0.00 0.00 43.93 5.19
78 79 1.513586 CGAAGTCACCGTAGACGCC 60.514 63.158 0.00 0.00 43.24 5.68
79 80 1.881602 GAAGTCACCGTAGACGCCT 59.118 57.895 0.00 0.00 43.24 5.52
80 81 0.179169 GAAGTCACCGTAGACGCCTC 60.179 60.000 0.00 0.00 43.24 4.70
81 82 1.919956 AAGTCACCGTAGACGCCTCG 61.920 60.000 0.00 0.00 43.24 4.63
82 83 2.359107 TCACCGTAGACGCCTCGT 60.359 61.111 0.00 0.00 45.10 4.18
83 84 1.079197 TCACCGTAGACGCCTCGTA 60.079 57.895 0.00 0.00 41.37 3.43
84 85 1.086067 TCACCGTAGACGCCTCGTAG 61.086 60.000 0.00 0.00 41.37 3.51
85 86 1.078848 ACCGTAGACGCCTCGTAGT 60.079 57.895 0.00 0.00 41.37 2.73
86 87 1.086634 ACCGTAGACGCCTCGTAGTC 61.087 60.000 0.00 0.00 41.37 2.59
87 88 1.272131 CGTAGACGCCTCGTAGTCG 59.728 63.158 0.00 0.00 41.37 4.18
88 89 1.142185 CGTAGACGCCTCGTAGTCGA 61.142 60.000 0.00 0.00 41.37 4.20
89 90 0.300193 GTAGACGCCTCGTAGTCGAC 59.700 60.000 7.70 7.70 41.37 4.20
108 109 2.363297 GGGAACGTCTCCTTCCACT 58.637 57.895 13.94 0.00 44.68 4.00
109 110 0.037232 GGGAACGTCTCCTTCCACTG 60.037 60.000 13.94 0.00 44.68 3.66
110 111 0.966920 GGAACGTCTCCTTCCACTGA 59.033 55.000 8.87 0.00 41.61 3.41
111 112 1.343465 GGAACGTCTCCTTCCACTGAA 59.657 52.381 8.87 0.00 41.61 3.02
112 113 2.224209 GGAACGTCTCCTTCCACTGAAA 60.224 50.000 8.87 0.00 41.61 2.69
113 114 2.821991 ACGTCTCCTTCCACTGAAAG 57.178 50.000 0.00 0.00 42.29 2.62
114 115 1.270358 ACGTCTCCTTCCACTGAAAGC 60.270 52.381 0.00 0.00 37.60 3.51
115 116 1.270305 CGTCTCCTTCCACTGAAAGCA 60.270 52.381 0.00 0.00 37.60 3.91
116 117 2.613977 CGTCTCCTTCCACTGAAAGCAT 60.614 50.000 0.00 0.00 37.60 3.79
117 118 3.368427 CGTCTCCTTCCACTGAAAGCATA 60.368 47.826 0.00 0.00 37.60 3.14
118 119 4.681781 CGTCTCCTTCCACTGAAAGCATAT 60.682 45.833 0.00 0.00 37.60 1.78
119 120 4.813697 GTCTCCTTCCACTGAAAGCATATC 59.186 45.833 0.00 0.00 37.60 1.63
120 121 4.471025 TCTCCTTCCACTGAAAGCATATCA 59.529 41.667 0.00 0.00 37.60 2.15
121 122 5.131642 TCTCCTTCCACTGAAAGCATATCAT 59.868 40.000 0.00 0.00 37.60 2.45
122 123 5.371526 TCCTTCCACTGAAAGCATATCATC 58.628 41.667 0.00 0.00 37.60 2.92
123 124 4.212847 CCTTCCACTGAAAGCATATCATCG 59.787 45.833 0.00 0.00 37.60 3.84
124 125 3.732212 TCCACTGAAAGCATATCATCGG 58.268 45.455 0.00 0.00 37.60 4.18
125 126 3.387699 TCCACTGAAAGCATATCATCGGA 59.612 43.478 0.00 0.00 37.60 4.55
126 127 4.129380 CCACTGAAAGCATATCATCGGAA 58.871 43.478 0.00 0.00 37.60 4.30
127 128 4.758674 CCACTGAAAGCATATCATCGGAAT 59.241 41.667 0.00 0.00 37.60 3.01
128 129 5.240183 CCACTGAAAGCATATCATCGGAATT 59.760 40.000 0.00 0.00 37.60 2.17
129 130 6.369005 CACTGAAAGCATATCATCGGAATTC 58.631 40.000 0.00 0.00 37.60 2.17
130 131 5.471456 ACTGAAAGCATATCATCGGAATTCC 59.529 40.000 15.01 15.01 37.60 3.01
131 132 5.624159 TGAAAGCATATCATCGGAATTCCT 58.376 37.500 22.05 5.68 0.00 3.36
132 133 5.471116 TGAAAGCATATCATCGGAATTCCTG 59.529 40.000 22.05 14.38 0.00 3.86
133 134 4.897509 AGCATATCATCGGAATTCCTGA 57.102 40.909 22.05 18.99 0.00 3.86
134 135 5.233083 AGCATATCATCGGAATTCCTGAA 57.767 39.130 22.05 8.11 0.00 3.02
135 136 5.624159 AGCATATCATCGGAATTCCTGAAA 58.376 37.500 22.05 12.99 0.00 2.69
136 137 6.243900 AGCATATCATCGGAATTCCTGAAAT 58.756 36.000 22.05 17.67 0.00 2.17
137 138 7.397221 AGCATATCATCGGAATTCCTGAAATA 58.603 34.615 22.05 18.84 0.00 1.40
138 139 7.884877 AGCATATCATCGGAATTCCTGAAATAA 59.115 33.333 22.05 8.01 0.00 1.40
139 140 8.514594 GCATATCATCGGAATTCCTGAAATAAA 58.485 33.333 22.05 8.06 0.00 1.40
145 146 9.683069 CATCGGAATTCCTGAAATAAATTTAGG 57.317 33.333 22.05 0.94 0.00 2.69
146 147 9.640952 ATCGGAATTCCTGAAATAAATTTAGGA 57.359 29.630 22.05 6.49 32.66 2.94
147 148 9.640952 TCGGAATTCCTGAAATAAATTTAGGAT 57.359 29.630 22.05 0.00 33.61 3.24
157 158 9.677567 TGAAATAAATTTAGGATAAATGCGAGC 57.322 29.630 3.94 0.00 0.00 5.03
158 159 9.677567 GAAATAAATTTAGGATAAATGCGAGCA 57.322 29.630 3.94 0.00 0.00 4.26
159 160 9.463443 AAATAAATTTAGGATAAATGCGAGCAC 57.537 29.630 0.00 0.00 0.00 4.40
160 161 5.438761 AATTTAGGATAAATGCGAGCACC 57.561 39.130 0.00 0.00 0.00 5.01
161 162 3.552132 TTAGGATAAATGCGAGCACCA 57.448 42.857 0.00 0.00 0.00 4.17
162 163 1.959042 AGGATAAATGCGAGCACCAG 58.041 50.000 0.00 0.00 0.00 4.00
163 164 0.947244 GGATAAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
164 165 1.475034 GGATAAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
165 166 2.498167 GATAAATGCGAGCACCAGGAT 58.502 47.619 0.00 0.00 0.00 3.24
166 167 2.418368 TAAATGCGAGCACCAGGATT 57.582 45.000 0.00 0.00 0.00 3.01
167 168 1.549203 AAATGCGAGCACCAGGATTT 58.451 45.000 0.00 0.00 34.37 2.17
168 169 2.418368 AATGCGAGCACCAGGATTTA 57.582 45.000 0.00 0.00 0.00 1.40
169 170 2.418368 ATGCGAGCACCAGGATTTAA 57.582 45.000 0.00 0.00 0.00 1.52
170 171 2.192664 TGCGAGCACCAGGATTTAAA 57.807 45.000 0.00 0.00 0.00 1.52
171 172 1.810151 TGCGAGCACCAGGATTTAAAC 59.190 47.619 0.00 0.00 0.00 2.01
172 173 1.132453 GCGAGCACCAGGATTTAAACC 59.868 52.381 0.00 0.00 0.00 3.27
173 174 1.743394 CGAGCACCAGGATTTAAACCC 59.257 52.381 0.00 0.00 0.00 4.11
174 175 2.618045 CGAGCACCAGGATTTAAACCCT 60.618 50.000 0.00 0.00 0.00 4.34
193 194 3.744660 CCTGATGGGTTAGGAATAGCAC 58.255 50.000 0.00 0.00 36.11 4.40
194 195 3.392616 CCTGATGGGTTAGGAATAGCACT 59.607 47.826 0.00 0.00 36.11 4.40
195 196 4.384056 CTGATGGGTTAGGAATAGCACTG 58.616 47.826 0.00 0.00 0.00 3.66
196 197 3.780294 TGATGGGTTAGGAATAGCACTGT 59.220 43.478 0.00 0.00 0.00 3.55
197 198 3.906720 TGGGTTAGGAATAGCACTGTC 57.093 47.619 0.00 0.00 0.00 3.51
198 199 2.504175 TGGGTTAGGAATAGCACTGTCC 59.496 50.000 0.00 0.00 0.00 4.02
199 200 2.504175 GGGTTAGGAATAGCACTGTCCA 59.496 50.000 5.35 0.00 33.57 4.02
200 201 3.532542 GGTTAGGAATAGCACTGTCCAC 58.467 50.000 5.35 0.00 33.57 4.02
201 202 3.197983 GGTTAGGAATAGCACTGTCCACT 59.802 47.826 5.35 0.00 33.57 4.00
202 203 4.323562 GGTTAGGAATAGCACTGTCCACTT 60.324 45.833 5.35 0.00 33.57 3.16
203 204 5.105064 GGTTAGGAATAGCACTGTCCACTTA 60.105 44.000 5.35 0.00 33.57 2.24
204 205 6.403878 GTTAGGAATAGCACTGTCCACTTAA 58.596 40.000 5.35 0.00 33.57 1.85
205 206 4.833390 AGGAATAGCACTGTCCACTTAAC 58.167 43.478 5.35 0.00 33.57 2.01
206 207 3.939592 GGAATAGCACTGTCCACTTAACC 59.060 47.826 0.00 0.00 0.00 2.85
207 208 4.564821 GGAATAGCACTGTCCACTTAACCA 60.565 45.833 0.00 0.00 0.00 3.67
208 209 4.844349 ATAGCACTGTCCACTTAACCAT 57.156 40.909 0.00 0.00 0.00 3.55
209 210 3.059352 AGCACTGTCCACTTAACCATC 57.941 47.619 0.00 0.00 0.00 3.51
210 211 2.639839 AGCACTGTCCACTTAACCATCT 59.360 45.455 0.00 0.00 0.00 2.90
211 212 3.003480 GCACTGTCCACTTAACCATCTC 58.997 50.000 0.00 0.00 0.00 2.75
212 213 3.557054 GCACTGTCCACTTAACCATCTCA 60.557 47.826 0.00 0.00 0.00 3.27
213 214 4.641396 CACTGTCCACTTAACCATCTCAA 58.359 43.478 0.00 0.00 0.00 3.02
214 215 4.452455 CACTGTCCACTTAACCATCTCAAC 59.548 45.833 0.00 0.00 0.00 3.18
215 216 4.003648 CTGTCCACTTAACCATCTCAACC 58.996 47.826 0.00 0.00 0.00 3.77
216 217 3.392947 TGTCCACTTAACCATCTCAACCA 59.607 43.478 0.00 0.00 0.00 3.67
217 218 4.003648 GTCCACTTAACCATCTCAACCAG 58.996 47.826 0.00 0.00 0.00 4.00
218 219 3.907474 TCCACTTAACCATCTCAACCAGA 59.093 43.478 0.00 0.00 34.78 3.86
219 220 4.020218 TCCACTTAACCATCTCAACCAGAG 60.020 45.833 0.00 0.00 46.14 3.35
230 231 3.468071 TCAACCAGAGAGCCTACCTAA 57.532 47.619 0.00 0.00 0.00 2.69
231 232 3.995636 TCAACCAGAGAGCCTACCTAAT 58.004 45.455 0.00 0.00 0.00 1.73
232 233 4.362677 TCAACCAGAGAGCCTACCTAATT 58.637 43.478 0.00 0.00 0.00 1.40
233 234 4.783227 TCAACCAGAGAGCCTACCTAATTT 59.217 41.667 0.00 0.00 0.00 1.82
234 235 5.250774 TCAACCAGAGAGCCTACCTAATTTT 59.749 40.000 0.00 0.00 0.00 1.82
235 236 5.780958 ACCAGAGAGCCTACCTAATTTTT 57.219 39.130 0.00 0.00 0.00 1.94
236 237 6.886178 ACCAGAGAGCCTACCTAATTTTTA 57.114 37.500 0.00 0.00 0.00 1.52
267 268 4.092968 GGCGAGAACGTTTATGATTCTTGT 59.907 41.667 0.46 0.00 41.98 3.16
274 275 5.699839 ACGTTTATGATTCTTGTTTCTGCC 58.300 37.500 0.00 0.00 0.00 4.85
299 300 1.202675 AGATCCTCCCGACTCGAGTAC 60.203 57.143 20.09 11.22 0.00 2.73
300 301 0.838608 ATCCTCCCGACTCGAGTACT 59.161 55.000 20.09 0.00 0.00 2.73
301 302 0.177604 TCCTCCCGACTCGAGTACTC 59.822 60.000 20.09 13.18 0.00 2.59
321 322 8.068733 AGTACTCCTATCTCCCTTTTATCTGTT 58.931 37.037 0.00 0.00 0.00 3.16
322 323 7.757242 ACTCCTATCTCCCTTTTATCTGTTT 57.243 36.000 0.00 0.00 0.00 2.83
323 324 8.855804 ACTCCTATCTCCCTTTTATCTGTTTA 57.144 34.615 0.00 0.00 0.00 2.01
345 346 2.685850 ATTACTCACCGTTACCAGGC 57.314 50.000 0.00 0.00 0.00 4.85
399 400 0.745845 ATTGACCACCTGCTGCGATC 60.746 55.000 0.00 0.00 0.00 3.69
400 401 2.110757 TTGACCACCTGCTGCGATCA 62.111 55.000 0.00 0.00 0.00 2.92
406 410 0.671781 ACCTGCTGCGATCAAGACAC 60.672 55.000 0.00 0.00 0.00 3.67
425 2037 6.677913 AGACACATCAAACCCGAAAATAAAG 58.322 36.000 0.00 0.00 0.00 1.85
476 2194 0.588252 GAATCGGCGACATGATTGGG 59.412 55.000 13.76 0.00 35.06 4.12
502 2220 3.899726 TCTACCACTCCTACTTGCCTAG 58.100 50.000 0.00 0.00 0.00 3.02
587 2305 1.214589 CAACGAATCGAGTCCCCGT 59.785 57.895 10.55 0.00 34.74 5.28
656 2374 1.878953 TTCTCTTCTCCAACGCAACC 58.121 50.000 0.00 0.00 0.00 3.77
756 2942 3.480470 CTCCAAAGAGGTTCAAGAAGCA 58.520 45.455 13.70 0.00 40.96 3.91
761 2947 5.394553 CCAAAGAGGTTCAAGAAGCAAAGTT 60.395 40.000 13.70 0.96 40.96 2.66
860 3050 1.283613 GTGGGACTCAGAGGAGAGAGA 59.716 57.143 1.53 0.00 44.26 3.10
922 3134 1.152777 CCAGCACCACACCTTTCCA 60.153 57.895 0.00 0.00 0.00 3.53
1158 3392 0.034089 CGGGCTTTTTCCTCCAGGAT 60.034 55.000 0.00 0.00 44.98 3.24
1219 3468 1.700368 CTCTCCACCTCCCTCCAGA 59.300 63.158 0.00 0.00 0.00 3.86
1635 3884 0.237235 CATGTTTGGACCGAACCGTG 59.763 55.000 20.05 14.99 0.00 4.94
1686 3935 0.396435 ATTGACGCTGGAACTGACCA 59.604 50.000 0.00 0.00 38.33 4.02
1687 3936 0.531974 TTGACGCTGGAACTGACCAC 60.532 55.000 0.00 0.00 35.91 4.16
1688 3937 1.668151 GACGCTGGAACTGACCACC 60.668 63.158 0.00 0.00 35.91 4.61
1689 3938 2.358737 CGCTGGAACTGACCACCC 60.359 66.667 0.00 0.00 35.91 4.61
1690 3939 2.358737 GCTGGAACTGACCACCCG 60.359 66.667 0.00 0.00 35.91 5.28
1691 3940 2.347490 CTGGAACTGACCACCCGG 59.653 66.667 0.00 0.00 35.91 5.73
2367 4622 4.069232 CGTCGAAGGGAGGCAGCA 62.069 66.667 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.069358 GTGCTCATAGAGGTAGGGTGC 59.931 57.143 0.00 0.00 0.00 5.01
1 2 1.689273 GGTGCTCATAGAGGTAGGGTG 59.311 57.143 0.00 0.00 0.00 4.61
4 5 2.294791 CGAAGGTGCTCATAGAGGTAGG 59.705 54.545 0.00 0.00 0.00 3.18
6 7 3.118000 TCTCGAAGGTGCTCATAGAGGTA 60.118 47.826 6.17 0.00 0.00 3.08
7 8 2.028130 CTCGAAGGTGCTCATAGAGGT 58.972 52.381 0.00 0.00 0.00 3.85
8 9 2.293122 CTCTCGAAGGTGCTCATAGAGG 59.707 54.545 6.17 0.00 0.00 3.69
9 10 3.003275 GTCTCTCGAAGGTGCTCATAGAG 59.997 52.174 0.00 0.00 31.13 2.43
10 11 2.946329 GTCTCTCGAAGGTGCTCATAGA 59.054 50.000 0.00 0.00 0.00 1.98
11 12 2.948979 AGTCTCTCGAAGGTGCTCATAG 59.051 50.000 0.00 0.00 0.00 2.23
12 13 2.685388 CAGTCTCTCGAAGGTGCTCATA 59.315 50.000 0.00 0.00 0.00 2.15
13 14 1.476085 CAGTCTCTCGAAGGTGCTCAT 59.524 52.381 0.00 0.00 0.00 2.90
14 15 0.884514 CAGTCTCTCGAAGGTGCTCA 59.115 55.000 0.00 0.00 0.00 4.26
15 16 1.132262 CTCAGTCTCTCGAAGGTGCTC 59.868 57.143 0.00 0.00 0.00 4.26
16 17 1.173043 CTCAGTCTCTCGAAGGTGCT 58.827 55.000 0.00 0.00 0.00 4.40
17 18 0.457681 GCTCAGTCTCTCGAAGGTGC 60.458 60.000 0.00 0.00 0.00 5.01
18 19 0.884514 TGCTCAGTCTCTCGAAGGTG 59.115 55.000 0.00 0.00 0.00 4.00
19 20 1.173043 CTGCTCAGTCTCTCGAAGGT 58.827 55.000 0.00 0.00 0.00 3.50
20 21 0.455410 CCTGCTCAGTCTCTCGAAGG 59.545 60.000 0.00 0.00 0.00 3.46
21 22 0.179140 GCCTGCTCAGTCTCTCGAAG 60.179 60.000 0.00 0.00 0.00 3.79
22 23 0.895559 TGCCTGCTCAGTCTCTCGAA 60.896 55.000 0.00 0.00 0.00 3.71
23 24 0.682532 ATGCCTGCTCAGTCTCTCGA 60.683 55.000 0.00 0.00 0.00 4.04
24 25 1.028130 TATGCCTGCTCAGTCTCTCG 58.972 55.000 0.00 0.00 0.00 4.04
25 26 2.627221 TGATATGCCTGCTCAGTCTCTC 59.373 50.000 0.00 0.00 0.00 3.20
26 27 2.675583 TGATATGCCTGCTCAGTCTCT 58.324 47.619 0.00 0.00 0.00 3.10
27 28 3.258872 AGATGATATGCCTGCTCAGTCTC 59.741 47.826 0.00 0.00 0.00 3.36
28 29 3.241156 AGATGATATGCCTGCTCAGTCT 58.759 45.455 0.00 0.00 0.00 3.24
29 30 3.681593 AGATGATATGCCTGCTCAGTC 57.318 47.619 0.00 0.00 0.00 3.51
30 31 3.390311 TCAAGATGATATGCCTGCTCAGT 59.610 43.478 0.00 0.00 0.00 3.41
31 32 3.997681 CTCAAGATGATATGCCTGCTCAG 59.002 47.826 0.00 0.00 0.00 3.35
32 33 3.644738 TCTCAAGATGATATGCCTGCTCA 59.355 43.478 0.00 0.00 0.00 4.26
33 34 4.268797 TCTCAAGATGATATGCCTGCTC 57.731 45.455 0.00 0.00 0.00 4.26
34 35 4.912317 ATCTCAAGATGATATGCCTGCT 57.088 40.909 0.00 0.00 32.68 4.24
35 36 5.961396 AAATCTCAAGATGATATGCCTGC 57.039 39.130 0.00 0.00 34.49 4.85
36 37 7.386025 TCGTAAAATCTCAAGATGATATGCCTG 59.614 37.037 0.00 0.00 34.49 4.85
37 38 7.445121 TCGTAAAATCTCAAGATGATATGCCT 58.555 34.615 0.00 0.00 34.49 4.75
38 39 7.658179 TCGTAAAATCTCAAGATGATATGCC 57.342 36.000 0.00 0.00 34.49 4.40
39 40 8.768955 ACTTCGTAAAATCTCAAGATGATATGC 58.231 33.333 0.00 0.00 34.49 3.14
42 43 9.302345 GTGACTTCGTAAAATCTCAAGATGATA 57.698 33.333 0.00 0.00 34.49 2.15
43 44 7.278868 GGTGACTTCGTAAAATCTCAAGATGAT 59.721 37.037 0.00 0.00 34.49 2.45
44 45 6.590292 GGTGACTTCGTAAAATCTCAAGATGA 59.410 38.462 0.00 0.00 34.49 2.92
45 46 6.454318 CGGTGACTTCGTAAAATCTCAAGATG 60.454 42.308 0.00 0.00 34.49 2.90
46 47 5.577164 CGGTGACTTCGTAAAATCTCAAGAT 59.423 40.000 0.00 0.00 36.07 2.40
47 48 4.921515 CGGTGACTTCGTAAAATCTCAAGA 59.078 41.667 0.00 0.00 0.00 3.02
48 49 4.684703 ACGGTGACTTCGTAAAATCTCAAG 59.315 41.667 0.00 0.00 39.22 3.02
49 50 4.624015 ACGGTGACTTCGTAAAATCTCAA 58.376 39.130 0.00 0.00 39.22 3.02
50 51 4.247267 ACGGTGACTTCGTAAAATCTCA 57.753 40.909 0.00 0.00 39.22 3.27
51 52 5.511025 GTCTACGGTGACTTCGTAAAATCTC 59.489 44.000 0.00 0.00 41.62 2.75
52 53 5.397326 GTCTACGGTGACTTCGTAAAATCT 58.603 41.667 0.00 0.00 41.62 2.40
53 54 4.261581 CGTCTACGGTGACTTCGTAAAATC 59.738 45.833 8.11 0.00 41.62 2.17
54 55 4.161333 CGTCTACGGTGACTTCGTAAAAT 58.839 43.478 8.11 0.00 41.62 1.82
55 56 3.554524 CGTCTACGGTGACTTCGTAAAA 58.445 45.455 8.11 0.00 41.62 1.52
56 57 2.665519 GCGTCTACGGTGACTTCGTAAA 60.666 50.000 4.49 0.00 41.62 2.01
57 58 1.135972 GCGTCTACGGTGACTTCGTAA 60.136 52.381 4.49 0.00 41.62 3.18
58 59 0.443869 GCGTCTACGGTGACTTCGTA 59.556 55.000 4.49 0.00 41.38 3.43
59 60 1.208614 GCGTCTACGGTGACTTCGT 59.791 57.895 4.49 0.00 43.64 3.85
60 61 1.513586 GGCGTCTACGGTGACTTCG 60.514 63.158 4.49 0.00 40.23 3.79
61 62 0.179169 GAGGCGTCTACGGTGACTTC 60.179 60.000 4.49 0.00 40.23 3.01
62 63 1.881602 GAGGCGTCTACGGTGACTT 59.118 57.895 4.49 0.00 40.23 3.01
63 64 2.396955 CGAGGCGTCTACGGTGACT 61.397 63.158 4.69 0.00 40.23 3.41
64 65 1.361668 TACGAGGCGTCTACGGTGAC 61.362 60.000 12.25 0.00 41.54 3.67
65 66 1.079197 TACGAGGCGTCTACGGTGA 60.079 57.895 12.25 0.00 41.54 4.02
66 67 1.351012 CTACGAGGCGTCTACGGTG 59.649 63.158 12.25 2.70 41.54 4.94
67 68 1.078848 ACTACGAGGCGTCTACGGT 60.079 57.895 12.25 3.90 41.54 4.83
68 69 1.640604 GACTACGAGGCGTCTACGG 59.359 63.158 12.25 0.00 41.54 4.02
69 70 1.272131 CGACTACGAGGCGTCTACG 59.728 63.158 4.69 0.00 42.99 3.51
80 81 2.863153 ACGTTCCCGTCGACTACG 59.137 61.111 14.70 18.15 46.28 3.51
92 93 2.814280 TTCAGTGGAAGGAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
93 94 2.807108 GCTTTCAGTGGAAGGAGACGTT 60.807 50.000 13.22 0.00 32.18 3.99
94 95 1.270358 GCTTTCAGTGGAAGGAGACGT 60.270 52.381 13.22 0.00 32.18 4.34
95 96 1.270305 TGCTTTCAGTGGAAGGAGACG 60.270 52.381 13.22 0.00 32.18 4.18
96 97 2.550830 TGCTTTCAGTGGAAGGAGAC 57.449 50.000 13.22 0.00 32.18 3.36
97 98 4.471025 TGATATGCTTTCAGTGGAAGGAGA 59.529 41.667 13.22 7.91 32.18 3.71
98 99 4.774124 TGATATGCTTTCAGTGGAAGGAG 58.226 43.478 13.22 0.00 32.18 3.69
99 100 4.842531 TGATATGCTTTCAGTGGAAGGA 57.157 40.909 13.22 10.72 32.18 3.36
100 101 4.212847 CGATGATATGCTTTCAGTGGAAGG 59.787 45.833 13.22 0.00 33.82 3.46
101 102 4.212847 CCGATGATATGCTTTCAGTGGAAG 59.787 45.833 6.82 6.82 33.82 3.46
102 103 4.129380 CCGATGATATGCTTTCAGTGGAA 58.871 43.478 0.00 0.00 0.00 3.53
103 104 3.387699 TCCGATGATATGCTTTCAGTGGA 59.612 43.478 0.00 0.00 31.56 4.02
104 105 3.732212 TCCGATGATATGCTTTCAGTGG 58.268 45.455 0.00 0.00 0.00 4.00
105 106 5.936686 ATTCCGATGATATGCTTTCAGTG 57.063 39.130 0.00 0.00 0.00 3.66
106 107 5.471456 GGAATTCCGATGATATGCTTTCAGT 59.529 40.000 9.17 0.00 0.00 3.41
107 108 5.704515 AGGAATTCCGATGATATGCTTTCAG 59.295 40.000 18.82 0.00 42.08 3.02
108 109 5.471116 CAGGAATTCCGATGATATGCTTTCA 59.529 40.000 18.82 0.00 42.08 2.69
109 110 5.702670 TCAGGAATTCCGATGATATGCTTTC 59.297 40.000 18.82 0.00 42.08 2.62
110 111 5.624159 TCAGGAATTCCGATGATATGCTTT 58.376 37.500 18.82 0.00 42.08 3.51
111 112 5.233083 TCAGGAATTCCGATGATATGCTT 57.767 39.130 18.82 0.00 42.08 3.91
112 113 4.897509 TCAGGAATTCCGATGATATGCT 57.102 40.909 18.82 0.00 42.08 3.79
113 114 5.947228 TTTCAGGAATTCCGATGATATGC 57.053 39.130 18.82 0.00 42.08 3.14
119 120 9.683069 CCTAAATTTATTTCAGGAATTCCGATG 57.317 33.333 18.82 12.67 42.08 3.84
120 121 9.640952 TCCTAAATTTATTTCAGGAATTCCGAT 57.359 29.630 18.82 13.30 42.08 4.18
121 122 9.640952 ATCCTAAATTTATTTCAGGAATTCCGA 57.359 29.630 18.82 15.51 42.08 4.55
131 132 9.677567 GCTCGCATTTATCCTAAATTTATTTCA 57.322 29.630 0.00 0.00 0.00 2.69
132 133 9.677567 TGCTCGCATTTATCCTAAATTTATTTC 57.322 29.630 0.00 0.00 0.00 2.17
133 134 9.463443 GTGCTCGCATTTATCCTAAATTTATTT 57.537 29.630 0.00 0.00 0.00 1.40
134 135 8.082242 GGTGCTCGCATTTATCCTAAATTTATT 58.918 33.333 0.00 0.00 0.00 1.40
135 136 7.230510 TGGTGCTCGCATTTATCCTAAATTTAT 59.769 33.333 0.00 0.00 0.00 1.40
136 137 6.544197 TGGTGCTCGCATTTATCCTAAATTTA 59.456 34.615 0.00 0.00 0.00 1.40
137 138 5.359576 TGGTGCTCGCATTTATCCTAAATTT 59.640 36.000 0.00 0.00 0.00 1.82
138 139 4.887071 TGGTGCTCGCATTTATCCTAAATT 59.113 37.500 0.00 0.00 0.00 1.82
139 140 4.460263 TGGTGCTCGCATTTATCCTAAAT 58.540 39.130 0.00 0.00 0.00 1.40
140 141 3.876914 CTGGTGCTCGCATTTATCCTAAA 59.123 43.478 0.00 0.00 0.00 1.85
141 142 3.466836 CTGGTGCTCGCATTTATCCTAA 58.533 45.455 0.00 0.00 0.00 2.69
142 143 2.224281 CCTGGTGCTCGCATTTATCCTA 60.224 50.000 0.00 0.00 0.00 2.94
143 144 1.475751 CCTGGTGCTCGCATTTATCCT 60.476 52.381 0.00 0.00 0.00 3.24
144 145 0.947244 CCTGGTGCTCGCATTTATCC 59.053 55.000 0.00 0.00 0.00 2.59
145 146 1.953559 TCCTGGTGCTCGCATTTATC 58.046 50.000 0.00 0.00 0.00 1.75
146 147 2.645838 ATCCTGGTGCTCGCATTTAT 57.354 45.000 0.00 0.00 0.00 1.40
147 148 2.418368 AATCCTGGTGCTCGCATTTA 57.582 45.000 0.00 0.00 0.00 1.40
148 149 1.549203 AAATCCTGGTGCTCGCATTT 58.451 45.000 0.00 0.00 0.00 2.32
149 150 2.418368 TAAATCCTGGTGCTCGCATT 57.582 45.000 0.00 0.00 0.00 3.56
150 151 2.418368 TTAAATCCTGGTGCTCGCAT 57.582 45.000 0.00 0.00 0.00 4.73
151 152 1.810151 GTTTAAATCCTGGTGCTCGCA 59.190 47.619 0.00 0.00 0.00 5.10
152 153 1.132453 GGTTTAAATCCTGGTGCTCGC 59.868 52.381 0.00 0.00 0.00 5.03
153 154 1.743394 GGGTTTAAATCCTGGTGCTCG 59.257 52.381 10.45 0.00 0.00 5.03
154 155 3.087370 AGGGTTTAAATCCTGGTGCTC 57.913 47.619 19.53 0.00 38.36 4.26
172 173 3.392616 AGTGCTATTCCTAACCCATCAGG 59.607 47.826 0.00 0.00 43.78 3.86
173 174 4.141620 ACAGTGCTATTCCTAACCCATCAG 60.142 45.833 0.00 0.00 0.00 2.90
174 175 3.780294 ACAGTGCTATTCCTAACCCATCA 59.220 43.478 0.00 0.00 0.00 3.07
175 176 4.381411 GACAGTGCTATTCCTAACCCATC 58.619 47.826 0.00 0.00 0.00 3.51
176 177 3.136626 GGACAGTGCTATTCCTAACCCAT 59.863 47.826 0.00 0.00 0.00 4.00
177 178 2.504175 GGACAGTGCTATTCCTAACCCA 59.496 50.000 0.00 0.00 0.00 4.51
178 179 2.504175 TGGACAGTGCTATTCCTAACCC 59.496 50.000 0.00 0.00 0.00 4.11
179 180 3.197983 AGTGGACAGTGCTATTCCTAACC 59.802 47.826 0.00 0.00 0.00 2.85
180 181 4.473477 AGTGGACAGTGCTATTCCTAAC 57.527 45.455 0.00 0.00 0.00 2.34
181 182 6.403878 GTTAAGTGGACAGTGCTATTCCTAA 58.596 40.000 0.00 0.00 0.00 2.69
182 183 5.105064 GGTTAAGTGGACAGTGCTATTCCTA 60.105 44.000 0.00 0.00 0.00 2.94
183 184 4.323562 GGTTAAGTGGACAGTGCTATTCCT 60.324 45.833 0.00 0.00 0.00 3.36
184 185 3.939592 GGTTAAGTGGACAGTGCTATTCC 59.060 47.826 0.00 0.00 0.00 3.01
185 186 4.575885 TGGTTAAGTGGACAGTGCTATTC 58.424 43.478 0.00 0.00 0.00 1.75
186 187 4.634012 TGGTTAAGTGGACAGTGCTATT 57.366 40.909 0.00 0.00 0.00 1.73
187 188 4.471386 AGATGGTTAAGTGGACAGTGCTAT 59.529 41.667 0.00 0.00 0.00 2.97
188 189 3.838317 AGATGGTTAAGTGGACAGTGCTA 59.162 43.478 0.00 0.00 0.00 3.49
189 190 2.639839 AGATGGTTAAGTGGACAGTGCT 59.360 45.455 0.00 0.00 0.00 4.40
190 191 3.003480 GAGATGGTTAAGTGGACAGTGC 58.997 50.000 0.00 0.00 0.00 4.40
191 192 4.271696 TGAGATGGTTAAGTGGACAGTG 57.728 45.455 0.00 0.00 0.00 3.66
192 193 4.505039 GGTTGAGATGGTTAAGTGGACAGT 60.505 45.833 0.00 0.00 0.00 3.55
193 194 4.003648 GGTTGAGATGGTTAAGTGGACAG 58.996 47.826 0.00 0.00 0.00 3.51
194 195 3.392947 TGGTTGAGATGGTTAAGTGGACA 59.607 43.478 0.00 0.00 0.00 4.02
195 196 4.003648 CTGGTTGAGATGGTTAAGTGGAC 58.996 47.826 0.00 0.00 0.00 4.02
196 197 3.907474 TCTGGTTGAGATGGTTAAGTGGA 59.093 43.478 0.00 0.00 0.00 4.02
197 198 4.020218 TCTCTGGTTGAGATGGTTAAGTGG 60.020 45.833 0.00 0.00 46.03 4.00
198 199 5.152623 TCTCTGGTTGAGATGGTTAAGTG 57.847 43.478 0.00 0.00 46.03 3.16
209 210 1.859302 AGGTAGGCTCTCTGGTTGAG 58.141 55.000 0.00 0.00 43.96 3.02
210 211 3.468071 TTAGGTAGGCTCTCTGGTTGA 57.532 47.619 0.00 0.00 0.00 3.18
211 212 4.762289 AATTAGGTAGGCTCTCTGGTTG 57.238 45.455 0.00 0.00 0.00 3.77
212 213 5.780958 AAAATTAGGTAGGCTCTCTGGTT 57.219 39.130 0.00 0.00 0.00 3.67
213 214 5.780958 AAAAATTAGGTAGGCTCTCTGGT 57.219 39.130 0.00 0.00 0.00 4.00
214 215 7.993183 TCAATAAAAATTAGGTAGGCTCTCTGG 59.007 37.037 0.00 0.00 0.00 3.86
215 216 8.964476 TCAATAAAAATTAGGTAGGCTCTCTG 57.036 34.615 0.00 0.00 0.00 3.35
219 220 9.750125 CCAAATCAATAAAAATTAGGTAGGCTC 57.250 33.333 0.00 0.00 0.00 4.70
220 221 8.204160 GCCAAATCAATAAAAATTAGGTAGGCT 58.796 33.333 0.00 0.00 0.00 4.58
221 222 7.169140 CGCCAAATCAATAAAAATTAGGTAGGC 59.831 37.037 0.00 0.00 0.00 3.93
222 223 8.410141 TCGCCAAATCAATAAAAATTAGGTAGG 58.590 33.333 0.00 0.00 0.00 3.18
223 224 9.450807 CTCGCCAAATCAATAAAAATTAGGTAG 57.549 33.333 0.00 0.00 0.00 3.18
224 225 9.179909 TCTCGCCAAATCAATAAAAATTAGGTA 57.820 29.630 0.00 0.00 0.00 3.08
225 226 8.062065 TCTCGCCAAATCAATAAAAATTAGGT 57.938 30.769 0.00 0.00 0.00 3.08
226 227 8.807581 GTTCTCGCCAAATCAATAAAAATTAGG 58.192 33.333 0.00 0.00 0.00 2.69
227 228 8.523464 CGTTCTCGCCAAATCAATAAAAATTAG 58.477 33.333 0.00 0.00 0.00 1.73
228 229 8.024285 ACGTTCTCGCCAAATCAATAAAAATTA 58.976 29.630 0.00 0.00 41.18 1.40
229 230 6.866248 ACGTTCTCGCCAAATCAATAAAAATT 59.134 30.769 0.00 0.00 41.18 1.82
230 231 6.386654 ACGTTCTCGCCAAATCAATAAAAAT 58.613 32.000 0.00 0.00 41.18 1.82
231 232 5.764131 ACGTTCTCGCCAAATCAATAAAAA 58.236 33.333 0.00 0.00 41.18 1.94
232 233 5.365403 ACGTTCTCGCCAAATCAATAAAA 57.635 34.783 0.00 0.00 41.18 1.52
233 234 5.365403 AACGTTCTCGCCAAATCAATAAA 57.635 34.783 0.00 0.00 41.18 1.40
234 235 5.365403 AAACGTTCTCGCCAAATCAATAA 57.635 34.783 0.00 0.00 41.18 1.40
235 236 6.314152 TCATAAACGTTCTCGCCAAATCAATA 59.686 34.615 0.00 0.00 41.18 1.90
236 237 3.915437 AAACGTTCTCGCCAAATCAAT 57.085 38.095 0.00 0.00 41.18 2.57
244 245 4.092968 ACAAGAATCATAAACGTTCTCGCC 59.907 41.667 0.00 0.00 41.18 5.54
291 292 4.360951 AAGGGAGATAGGAGTACTCGAG 57.639 50.000 16.56 11.84 0.00 4.04
321 322 6.127111 TGCCTGGTAACGGTGAGTAATAATAA 60.127 38.462 0.00 0.00 43.49 1.40
322 323 5.363292 TGCCTGGTAACGGTGAGTAATAATA 59.637 40.000 0.00 0.00 43.49 0.98
323 324 4.162698 TGCCTGGTAACGGTGAGTAATAAT 59.837 41.667 0.00 0.00 43.49 1.28
336 337 0.109723 TGGTCAAGGTGCCTGGTAAC 59.890 55.000 0.00 0.00 0.00 2.50
399 400 3.980646 TTTCGGGTTTGATGTGTCTTG 57.019 42.857 0.00 0.00 0.00 3.02
400 401 6.642707 TTATTTTCGGGTTTGATGTGTCTT 57.357 33.333 0.00 0.00 0.00 3.01
406 410 6.677913 ACTGTCTTTATTTTCGGGTTTGATG 58.322 36.000 0.00 0.00 0.00 3.07
425 2037 3.181523 GGAACGGCGATTTCTTTACTGTC 60.182 47.826 16.62 0.00 0.00 3.51
476 2194 3.119065 GCAAGTAGGAGTGGTAGAAGGTC 60.119 52.174 0.00 0.00 0.00 3.85
502 2220 2.031682 GCATGTGTTTGTCTGTCTGGTC 60.032 50.000 0.00 0.00 0.00 4.02
533 2251 1.078709 CACCGCCAGATGTGTACTTG 58.921 55.000 0.00 0.00 0.00 3.16
534 2252 0.036388 CCACCGCCAGATGTGTACTT 60.036 55.000 0.00 0.00 0.00 2.24
587 2305 2.225491 GTGCAGAATCTTTGGCACGTAA 59.775 45.455 8.16 0.00 45.84 3.18
656 2374 6.326064 TGGGTTGATGGATGGGTTATAAAATG 59.674 38.462 0.00 0.00 0.00 2.32
829 3019 1.535444 AGTCCCACGGTCATGGTGA 60.535 57.895 2.52 0.00 38.16 4.02
860 3050 2.420967 GCCGGGTCACACCATTAATAGT 60.421 50.000 2.18 0.00 41.02 2.12
922 3134 4.871871 TTCTCTGTAGTGAGAGGAGGAT 57.128 45.455 0.00 0.00 43.05 3.24
1219 3468 3.537874 GCGGGAGGCTACGGTGAT 61.538 66.667 12.18 0.00 39.11 3.06
1485 3734 0.687757 AGATCCAGCTGCCGACCTTA 60.688 55.000 8.66 0.00 0.00 2.69
1606 3855 3.686016 GGTCCAAACATGGTACTGACAT 58.314 45.455 0.00 0.00 0.00 3.06
1635 3884 2.029380 ACAAAGTTTAGCCCGATTTGCC 60.029 45.455 0.00 0.00 34.90 4.52
2288 4543 2.757099 GTACGGGAGCGGGGAAGA 60.757 66.667 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.