Multiple sequence alignment - TraesCS2D01G480400

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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 TraesCS2D01G480400 chr2D 100.000 3179 0 0 1 3179 582488023 582491201 0.000000e+00 5871
1 TraesCS2D01G480400 chr2D 75.087 1148 243 33 979 2115 588162269 588163384 2.200000e-136 496
2 TraesCS2D01G480400 chr2D 82.927 369 45 11 223 581 582185667 582186027 1.840000e-82 316
3 TraesCS2D01G480400 chr2B 91.400 3035 172 51 223 3179 701483227 701486250 0.000000e+00 4076
4 TraesCS2D01G480400 chr2B 87.407 945 93 10 1339 2272 701197478 701198407 0.000000e+00 1062
5 TraesCS2D01G480400 chr2B 96.311 515 16 3 2302 2815 701198400 701198912 0.000000e+00 843
6 TraesCS2D01G480400 chr2B 76.040 1106 233 22 1036 2134 711161459 711162539 2.160000e-151 545
7 TraesCS2D01G480400 chr2B 92.353 340 25 1 2840 3179 701198906 701199244 1.710000e-132 483
8 TraesCS2D01G480400 chr2B 79.502 522 49 23 564 1049 701196124 701196623 5.120000e-83 318
9 TraesCS2D01G480400 chr2B 89.593 221 23 0 1 221 11081319 11081099 6.710000e-72 281
10 TraesCS2D01G480400 chr2B 80.473 338 44 14 223 545 701185946 701186276 4.100000e-59 239
11 TraesCS2D01G480400 chr5D 90.895 626 46 4 2555 3179 375873367 375873982 0.000000e+00 830
12 TraesCS2D01G480400 chr5D 75.924 1217 240 41 979 2168 27985504 27984314 2.750000e-160 575
13 TraesCS2D01G480400 chr6B 77.298 1088 220 22 1050 2130 39326206 39327273 1.620000e-172 616
14 TraesCS2D01G480400 chr6B 76.740 1135 231 25 1037 2156 16429040 16430156 1.260000e-168 603
15 TraesCS2D01G480400 chr6B 76.774 1085 214 32 1086 2154 90939429 90940491 9.890000e-160 573
16 TraesCS2D01G480400 chr6B 76.039 1131 238 23 1050 2168 39311141 39312250 9.960000e-155 556
17 TraesCS2D01G480400 chr6B 75.823 1154 236 34 1037 2166 53077108 53075974 2.160000e-151 545
18 TraesCS2D01G480400 chr6B 75.875 1086 243 15 1071 2154 15397870 15396802 1.300000e-148 536
19 TraesCS2D01G480400 chr6B 75.523 1148 242 31 1036 2168 15744029 15742906 7.810000e-146 527
20 TraesCS2D01G480400 chr6B 75.940 1064 215 27 1117 2169 15216735 15215702 2.830000e-140 508
21 TraesCS2D01G480400 chr6D 77.007 1096 215 30 1086 2165 8967670 8968744 7.590000e-166 593
22 TraesCS2D01G480400 chr6D 75.249 1204 250 38 985 2166 8894042 8895219 2.170000e-146 529
23 TraesCS2D01G480400 chr6D 79.495 634 116 12 1050 1673 9056925 9057554 3.760000e-119 438
24 TraesCS2D01G480400 chr6D 77.358 583 126 6 1575 2154 8915627 8916206 1.090000e-89 340
25 TraesCS2D01G480400 chr6D 89.732 224 19 4 1 221 141592856 141593078 1.870000e-72 283
26 TraesCS2D01G480400 chr6A 76.825 1096 224 21 1050 2138 9364664 9365736 9.820000e-165 590
27 TraesCS2D01G480400 chr6A 74.603 1197 267 32 986 2168 10511162 10509989 2.850000e-135 492
28 TraesCS2D01G480400 chr1B 75.351 1067 238 21 1107 2163 27678006 27676955 1.020000e-134 490
29 TraesCS2D01G480400 chr1B 74.617 1044 214 32 1132 2154 662037456 662038469 2.280000e-111 412
30 TraesCS2D01G480400 chr1B 75.942 823 149 36 999 1803 48102399 48101608 8.320000e-101 377
31 TraesCS2D01G480400 chr5A 91.403 221 19 0 1 221 436355653 436355433 1.430000e-78 303
32 TraesCS2D01G480400 chr3A 90.991 222 19 1 1 222 716129944 716129724 6.670000e-77 298
33 TraesCS2D01G480400 chr4D 90.625 224 20 1 1 224 500007004 500007226 2.400000e-76 296
34 TraesCS2D01G480400 chr4D 90.222 225 20 2 1 224 298111696 298111919 3.100000e-75 292
35 TraesCS2D01G480400 chr4D 90.498 221 19 2 1 221 505966754 505966972 1.120000e-74 291
36 TraesCS2D01G480400 chr3D 91.827 208 16 1 16 223 532236535 532236741 4.010000e-74 289
37 TraesCS2D01G480400 chr1D 89.686 223 20 2 1 221 469388417 469388638 6.710000e-72 281


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 TraesCS2D01G480400 chr2D 582488023 582491201 3178 False 5871.0 5871 100.00000 1 3179 1 chr2D.!!$F2 3178
1 TraesCS2D01G480400 chr2D 588162269 588163384 1115 False 496.0 496 75.08700 979 2115 1 chr2D.!!$F3 1136
2 TraesCS2D01G480400 chr2B 701483227 701486250 3023 False 4076.0 4076 91.40000 223 3179 1 chr2B.!!$F2 2956
3 TraesCS2D01G480400 chr2B 701196124 701199244 3120 False 676.5 1062 88.89325 564 3179 4 chr2B.!!$F4 2615
4 TraesCS2D01G480400 chr2B 711161459 711162539 1080 False 545.0 545 76.04000 1036 2134 1 chr2B.!!$F3 1098
5 TraesCS2D01G480400 chr5D 375873367 375873982 615 False 830.0 830 90.89500 2555 3179 1 chr5D.!!$F1 624
6 TraesCS2D01G480400 chr5D 27984314 27985504 1190 True 575.0 575 75.92400 979 2168 1 chr5D.!!$R1 1189
7 TraesCS2D01G480400 chr6B 39326206 39327273 1067 False 616.0 616 77.29800 1050 2130 1 chr6B.!!$F3 1080
8 TraesCS2D01G480400 chr6B 16429040 16430156 1116 False 603.0 603 76.74000 1037 2156 1 chr6B.!!$F1 1119
9 TraesCS2D01G480400 chr6B 90939429 90940491 1062 False 573.0 573 76.77400 1086 2154 1 chr6B.!!$F4 1068
10 TraesCS2D01G480400 chr6B 39311141 39312250 1109 False 556.0 556 76.03900 1050 2168 1 chr6B.!!$F2 1118
11 TraesCS2D01G480400 chr6B 53075974 53077108 1134 True 545.0 545 75.82300 1037 2166 1 chr6B.!!$R4 1129
12 TraesCS2D01G480400 chr6B 15396802 15397870 1068 True 536.0 536 75.87500 1071 2154 1 chr6B.!!$R2 1083
13 TraesCS2D01G480400 chr6B 15742906 15744029 1123 True 527.0 527 75.52300 1036 2168 1 chr6B.!!$R3 1132
14 TraesCS2D01G480400 chr6B 15215702 15216735 1033 True 508.0 508 75.94000 1117 2169 1 chr6B.!!$R1 1052
15 TraesCS2D01G480400 chr6D 8967670 8968744 1074 False 593.0 593 77.00700 1086 2165 1 chr6D.!!$F3 1079
16 TraesCS2D01G480400 chr6D 8894042 8895219 1177 False 529.0 529 75.24900 985 2166 1 chr6D.!!$F1 1181
17 TraesCS2D01G480400 chr6D 9056925 9057554 629 False 438.0 438 79.49500 1050 1673 1 chr6D.!!$F4 623
18 TraesCS2D01G480400 chr6D 8915627 8916206 579 False 340.0 340 77.35800 1575 2154 1 chr6D.!!$F2 579
19 TraesCS2D01G480400 chr6A 9364664 9365736 1072 False 590.0 590 76.82500 1050 2138 1 chr6A.!!$F1 1088
20 TraesCS2D01G480400 chr6A 10509989 10511162 1173 True 492.0 492 74.60300 986 2168 1 chr6A.!!$R1 1182
21 TraesCS2D01G480400 chr1B 27676955 27678006 1051 True 490.0 490 75.35100 1107 2163 1 chr1B.!!$R1 1056
22 TraesCS2D01G480400 chr1B 662037456 662038469 1013 False 412.0 412 74.61700 1132 2154 1 chr1B.!!$F1 1022
23 TraesCS2D01G480400 chr1B 48101608 48102399 791 True 377.0 377 75.94200 999 1803 1 chr1B.!!$R2 804

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
215 216 0.106149 GTCCGGGCGTAGAATTGGAT 59.894 55.0 0.0 0.0 0.0 3.41 F
452 469 0.106708 GTTGTGGTGTCAGCTCTCCA 59.893 55.0 3.3 0.0 0.0 3.86 F
1643 2430 0.179048 CTCACCACCAACACAGAGCA 60.179 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 2188 1.442769 CACCCTGGAGACGACAAATG 58.557 55.000 0.0 0.0 0.00 2.32 R
1837 2639 2.009774 CAGCCTGTCCTTTGAATACCG 58.990 52.381 0.0 0.0 0.00 4.02 R
2835 3674 1.400242 GCTTCGGCACAAACATGACTC 60.400 52.381 0.0 0.0 41.33 3.36 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.933215 ATTTGGGGTCTGTTAAATAGTGTAC 57.067 36.000 0.00 0.00 0.00 2.90
26 27 6.691255 TTGGGGTCTGTTAAATAGTGTACT 57.309 37.500 0.00 0.00 0.00 2.73
27 28 6.045072 TGGGGTCTGTTAAATAGTGTACTG 57.955 41.667 0.00 0.00 0.00 2.74
28 29 5.544948 TGGGGTCTGTTAAATAGTGTACTGT 59.455 40.000 0.00 0.00 0.00 3.55
29 30 6.725369 TGGGGTCTGTTAAATAGTGTACTGTA 59.275 38.462 0.00 0.00 0.00 2.74
30 31 7.038048 GGGGTCTGTTAAATAGTGTACTGTAC 58.962 42.308 10.98 10.98 0.00 2.90
31 32 6.749118 GGGTCTGTTAAATAGTGTACTGTACG 59.251 42.308 12.87 0.00 0.00 3.67
32 33 7.308435 GGTCTGTTAAATAGTGTACTGTACGT 58.692 38.462 12.87 5.79 0.00 3.57
33 34 8.450964 GGTCTGTTAAATAGTGTACTGTACGTA 58.549 37.037 12.87 7.69 0.00 3.57
34 35 9.994432 GTCTGTTAAATAGTGTACTGTACGTAT 57.006 33.333 12.87 9.46 0.00 3.06
41 42 9.994432 AAATAGTGTACTGTACGTATACTGTTC 57.006 33.333 23.75 0.00 44.66 3.18
42 43 8.954950 ATAGTGTACTGTACGTATACTGTTCT 57.045 34.615 23.75 11.89 46.16 3.01
43 44 7.069852 AGTGTACTGTACGTATACTGTTCTG 57.930 40.000 18.77 5.80 45.35 3.02
44 45 6.875726 AGTGTACTGTACGTATACTGTTCTGA 59.124 38.462 18.77 0.00 45.35 3.27
45 46 6.958193 GTGTACTGTACGTATACTGTTCTGAC 59.042 42.308 12.87 0.00 41.92 3.51
46 47 5.557891 ACTGTACGTATACTGTTCTGACC 57.442 43.478 0.00 0.00 39.66 4.02
47 48 4.397417 ACTGTACGTATACTGTTCTGACCC 59.603 45.833 0.00 0.00 39.66 4.46
48 49 4.334552 TGTACGTATACTGTTCTGACCCA 58.665 43.478 0.00 0.00 32.00 4.51
49 50 4.766373 TGTACGTATACTGTTCTGACCCAA 59.234 41.667 0.00 0.00 32.00 4.12
50 51 5.419788 TGTACGTATACTGTTCTGACCCAAT 59.580 40.000 0.00 0.00 32.00 3.16
51 52 5.416271 ACGTATACTGTTCTGACCCAATT 57.584 39.130 0.56 0.00 0.00 2.32
52 53 5.801380 ACGTATACTGTTCTGACCCAATTT 58.199 37.500 0.56 0.00 0.00 1.82
53 54 6.938507 ACGTATACTGTTCTGACCCAATTTA 58.061 36.000 0.56 0.00 0.00 1.40
54 55 7.562135 ACGTATACTGTTCTGACCCAATTTAT 58.438 34.615 0.56 0.00 0.00 1.40
55 56 7.709613 ACGTATACTGTTCTGACCCAATTTATC 59.290 37.037 0.56 0.00 0.00 1.75
56 57 7.926555 CGTATACTGTTCTGACCCAATTTATCT 59.073 37.037 0.56 0.00 0.00 1.98
57 58 9.614792 GTATACTGTTCTGACCCAATTTATCTT 57.385 33.333 0.00 0.00 0.00 2.40
58 59 6.824305 ACTGTTCTGACCCAATTTATCTTG 57.176 37.500 0.00 0.00 0.00 3.02
59 60 6.306987 ACTGTTCTGACCCAATTTATCTTGT 58.693 36.000 0.00 0.00 0.00 3.16
60 61 6.777580 ACTGTTCTGACCCAATTTATCTTGTT 59.222 34.615 0.00 0.00 0.00 2.83
61 62 7.287696 ACTGTTCTGACCCAATTTATCTTGTTT 59.712 33.333 0.00 0.00 0.00 2.83
62 63 7.432869 TGTTCTGACCCAATTTATCTTGTTTG 58.567 34.615 0.00 0.00 0.00 2.93
63 64 6.024552 TCTGACCCAATTTATCTTGTTTGC 57.975 37.500 0.00 0.00 0.00 3.68
64 65 5.774690 TCTGACCCAATTTATCTTGTTTGCT 59.225 36.000 0.00 0.00 0.00 3.91
65 66 5.782047 TGACCCAATTTATCTTGTTTGCTG 58.218 37.500 0.00 0.00 0.00 4.41
66 67 5.538053 TGACCCAATTTATCTTGTTTGCTGA 59.462 36.000 0.00 0.00 0.00 4.26
67 68 6.029346 ACCCAATTTATCTTGTTTGCTGAG 57.971 37.500 0.00 0.00 0.00 3.35
68 69 5.774690 ACCCAATTTATCTTGTTTGCTGAGA 59.225 36.000 0.00 0.00 0.00 3.27
69 70 6.071728 ACCCAATTTATCTTGTTTGCTGAGAG 60.072 38.462 0.00 0.00 0.00 3.20
70 71 5.803967 CCAATTTATCTTGTTTGCTGAGAGC 59.196 40.000 0.00 0.00 42.82 4.09
71 72 6.349944 CCAATTTATCTTGTTTGCTGAGAGCT 60.350 38.462 0.00 0.00 42.97 4.09
72 73 7.148188 CCAATTTATCTTGTTTGCTGAGAGCTA 60.148 37.037 0.00 0.00 42.97 3.32
73 74 6.727824 TTTATCTTGTTTGCTGAGAGCTAC 57.272 37.500 0.00 0.00 42.97 3.58
74 75 4.550076 ATCTTGTTTGCTGAGAGCTACT 57.450 40.909 0.00 0.00 42.97 2.57
75 76 3.919216 TCTTGTTTGCTGAGAGCTACTC 58.081 45.455 6.31 6.31 42.97 2.59
88 89 6.116680 GAGAGCTACTCAAATGTCCAAATG 57.883 41.667 7.93 0.00 44.36 2.32
89 90 4.397417 AGAGCTACTCAAATGTCCAAATGC 59.603 41.667 0.00 0.00 32.06 3.56
90 91 4.338879 AGCTACTCAAATGTCCAAATGCT 58.661 39.130 0.00 0.00 0.00 3.79
91 92 4.397417 AGCTACTCAAATGTCCAAATGCTC 59.603 41.667 0.00 0.00 0.00 4.26
92 93 4.397417 GCTACTCAAATGTCCAAATGCTCT 59.603 41.667 0.00 0.00 0.00 4.09
93 94 4.778534 ACTCAAATGTCCAAATGCTCTG 57.221 40.909 0.00 0.00 0.00 3.35
94 95 4.401022 ACTCAAATGTCCAAATGCTCTGA 58.599 39.130 0.00 0.00 0.00 3.27
95 96 4.828939 ACTCAAATGTCCAAATGCTCTGAA 59.171 37.500 0.00 0.00 0.00 3.02
96 97 5.302568 ACTCAAATGTCCAAATGCTCTGAAA 59.697 36.000 0.00 0.00 0.00 2.69
97 98 6.014840 ACTCAAATGTCCAAATGCTCTGAAAT 60.015 34.615 0.00 0.00 0.00 2.17
98 99 6.761312 TCAAATGTCCAAATGCTCTGAAATT 58.239 32.000 0.00 0.00 0.00 1.82
99 100 7.218614 TCAAATGTCCAAATGCTCTGAAATTT 58.781 30.769 0.00 0.00 0.00 1.82
100 101 7.171848 TCAAATGTCCAAATGCTCTGAAATTTG 59.828 33.333 14.21 14.21 41.41 2.32
106 107 3.319245 GCTCTGAAATTTGGAGCGC 57.681 52.632 19.96 0.00 42.03 5.92
107 108 0.523072 GCTCTGAAATTTGGAGCGCA 59.477 50.000 19.96 2.00 42.03 6.09
108 109 1.730446 GCTCTGAAATTTGGAGCGCAC 60.730 52.381 19.96 1.97 42.03 5.34
109 110 0.881118 TCTGAAATTTGGAGCGCACC 59.119 50.000 17.78 17.78 0.00 5.01
110 111 0.883833 CTGAAATTTGGAGCGCACCT 59.116 50.000 24.52 3.63 0.00 4.00
111 112 0.881118 TGAAATTTGGAGCGCACCTC 59.119 50.000 24.52 13.56 39.98 3.85
112 113 0.881118 GAAATTTGGAGCGCACCTCA 59.119 50.000 24.52 11.44 42.62 3.86
113 114 1.474077 GAAATTTGGAGCGCACCTCAT 59.526 47.619 24.52 13.21 42.62 2.90
114 115 0.813184 AATTTGGAGCGCACCTCATG 59.187 50.000 24.52 0.00 42.62 3.07
129 130 6.064846 CACCTCATGCACCAAATTATCTAC 57.935 41.667 0.00 0.00 0.00 2.59
130 131 5.009010 CACCTCATGCACCAAATTATCTACC 59.991 44.000 0.00 0.00 0.00 3.18
131 132 5.132502 CCTCATGCACCAAATTATCTACCA 58.867 41.667 0.00 0.00 0.00 3.25
132 133 5.771666 CCTCATGCACCAAATTATCTACCAT 59.228 40.000 0.00 0.00 0.00 3.55
133 134 6.294342 CCTCATGCACCAAATTATCTACCATG 60.294 42.308 0.00 0.00 0.00 3.66
134 135 4.916983 TGCACCAAATTATCTACCATGC 57.083 40.909 0.00 0.00 0.00 4.06
135 136 4.276642 TGCACCAAATTATCTACCATGCA 58.723 39.130 0.00 0.00 38.17 3.96
136 137 4.097741 TGCACCAAATTATCTACCATGCAC 59.902 41.667 0.00 0.00 35.74 4.57
137 138 4.097741 GCACCAAATTATCTACCATGCACA 59.902 41.667 0.00 0.00 0.00 4.57
138 139 5.394005 GCACCAAATTATCTACCATGCACAA 60.394 40.000 0.00 0.00 0.00 3.33
139 140 6.629128 CACCAAATTATCTACCATGCACAAA 58.371 36.000 0.00 0.00 0.00 2.83
140 141 7.095910 CACCAAATTATCTACCATGCACAAAA 58.904 34.615 0.00 0.00 0.00 2.44
141 142 7.601886 CACCAAATTATCTACCATGCACAAAAA 59.398 33.333 0.00 0.00 0.00 1.94
142 143 8.320617 ACCAAATTATCTACCATGCACAAAAAT 58.679 29.630 0.00 0.00 0.00 1.82
143 144 9.165035 CCAAATTATCTACCATGCACAAAAATT 57.835 29.630 0.00 0.00 0.00 1.82
147 148 8.545229 TTATCTACCATGCACAAAAATTTTGG 57.455 30.769 20.79 3.67 0.00 3.28
148 149 6.166984 TCTACCATGCACAAAAATTTTGGA 57.833 33.333 20.79 6.50 0.00 3.53
149 150 5.988561 TCTACCATGCACAAAAATTTTGGAC 59.011 36.000 20.79 13.08 0.00 4.02
150 151 3.882288 ACCATGCACAAAAATTTTGGACC 59.118 39.130 20.79 9.94 0.00 4.46
151 152 4.136051 CCATGCACAAAAATTTTGGACCT 58.864 39.130 20.79 4.60 0.00 3.85
152 153 4.579753 CCATGCACAAAAATTTTGGACCTT 59.420 37.500 20.79 5.85 0.00 3.50
153 154 5.067544 CCATGCACAAAAATTTTGGACCTTT 59.932 36.000 20.79 0.00 0.00 3.11
154 155 6.405619 CCATGCACAAAAATTTTGGACCTTTT 60.406 34.615 20.79 0.00 0.00 2.27
155 156 6.581171 TGCACAAAAATTTTGGACCTTTTT 57.419 29.167 20.79 0.00 33.57 1.94
186 187 8.764524 TTTTTATGAATTATTTGTTGACCGGG 57.235 30.769 6.32 0.00 0.00 5.73
187 188 7.469537 TTTATGAATTATTTGTTGACCGGGT 57.530 32.000 6.32 0.00 0.00 5.28
188 189 4.775058 TGAATTATTTGTTGACCGGGTG 57.225 40.909 3.30 0.00 0.00 4.61
189 190 3.057174 TGAATTATTTGTTGACCGGGTGC 60.057 43.478 3.30 0.00 0.00 5.01
190 191 1.982660 TTATTTGTTGACCGGGTGCA 58.017 45.000 3.30 0.00 0.00 4.57
191 192 1.529226 TATTTGTTGACCGGGTGCAG 58.471 50.000 3.30 0.00 0.00 4.41
192 193 0.179004 ATTTGTTGACCGGGTGCAGA 60.179 50.000 3.30 0.00 0.00 4.26
193 194 1.098712 TTTGTTGACCGGGTGCAGAC 61.099 55.000 3.30 0.00 0.00 3.51
194 195 3.041940 GTTGACCGGGTGCAGACG 61.042 66.667 3.30 3.14 0.00 4.18
195 196 3.228017 TTGACCGGGTGCAGACGA 61.228 61.111 3.30 0.00 0.00 4.20
196 197 3.220999 TTGACCGGGTGCAGACGAG 62.221 63.158 3.30 4.65 0.00 4.18
197 198 3.681835 GACCGGGTGCAGACGAGT 61.682 66.667 3.30 7.47 0.00 4.18
198 199 3.628280 GACCGGGTGCAGACGAGTC 62.628 68.421 3.30 11.88 0.00 3.36
199 200 4.436998 CCGGGTGCAGACGAGTCC 62.437 72.222 11.19 0.00 0.00 3.85
200 201 4.778415 CGGGTGCAGACGAGTCCG 62.778 72.222 4.04 0.00 42.50 4.79
201 202 4.436998 GGGTGCAGACGAGTCCGG 62.437 72.222 0.00 0.00 40.78 5.14
202 203 4.436998 GGTGCAGACGAGTCCGGG 62.437 72.222 0.00 0.00 40.78 5.73
206 207 3.129502 CAGACGAGTCCGGGCGTA 61.130 66.667 15.79 0.00 41.34 4.42
207 208 2.823147 AGACGAGTCCGGGCGTAG 60.823 66.667 15.79 7.32 41.34 3.51
208 209 2.821366 GACGAGTCCGGGCGTAGA 60.821 66.667 15.79 0.00 41.34 2.59
209 210 2.360350 ACGAGTCCGGGCGTAGAA 60.360 61.111 14.56 0.00 39.21 2.10
210 211 1.722636 GACGAGTCCGGGCGTAGAAT 61.723 60.000 15.79 0.00 41.34 2.40
211 212 1.318158 ACGAGTCCGGGCGTAGAATT 61.318 55.000 14.56 0.00 39.21 2.17
212 213 0.870307 CGAGTCCGGGCGTAGAATTG 60.870 60.000 0.00 0.00 0.00 2.32
213 214 0.529992 GAGTCCGGGCGTAGAATTGG 60.530 60.000 0.00 0.00 0.00 3.16
214 215 0.974010 AGTCCGGGCGTAGAATTGGA 60.974 55.000 0.00 0.00 0.00 3.53
215 216 0.106149 GTCCGGGCGTAGAATTGGAT 59.894 55.000 0.00 0.00 0.00 3.41
216 217 1.342174 GTCCGGGCGTAGAATTGGATA 59.658 52.381 0.00 0.00 0.00 2.59
217 218 2.028385 GTCCGGGCGTAGAATTGGATAT 60.028 50.000 0.00 0.00 0.00 1.63
218 219 2.635915 TCCGGGCGTAGAATTGGATATT 59.364 45.455 0.00 0.00 0.00 1.28
219 220 3.000727 CCGGGCGTAGAATTGGATATTC 58.999 50.000 0.00 0.00 0.00 1.75
220 221 2.666508 CGGGCGTAGAATTGGATATTCG 59.333 50.000 0.00 0.00 33.51 3.34
221 222 3.613193 CGGGCGTAGAATTGGATATTCGA 60.613 47.826 0.00 0.00 33.51 3.71
242 243 9.862371 ATTCGAATGTCCATACACTTATCTATC 57.138 33.333 10.50 0.00 38.78 2.08
243 244 8.637196 TCGAATGTCCATACACTTATCTATCT 57.363 34.615 0.00 0.00 38.78 1.98
244 245 8.731605 TCGAATGTCCATACACTTATCTATCTC 58.268 37.037 0.00 0.00 38.78 2.75
245 246 7.694367 CGAATGTCCATACACTTATCTATCTCG 59.306 40.741 0.00 0.00 38.78 4.04
246 247 8.410673 AATGTCCATACACTTATCTATCTCGT 57.589 34.615 0.00 0.00 38.78 4.18
247 248 9.516546 AATGTCCATACACTTATCTATCTCGTA 57.483 33.333 0.00 0.00 38.78 3.43
248 249 9.688091 ATGTCCATACACTTATCTATCTCGTAT 57.312 33.333 0.00 0.00 38.78 3.06
249 250 9.516546 TGTCCATACACTTATCTATCTCGTATT 57.483 33.333 0.00 0.00 0.00 1.89
297 298 5.297776 AGGACAATGTCTTTCTCAACAAGTG 59.702 40.000 13.53 0.00 32.47 3.16
299 300 6.016777 GGACAATGTCTTTCTCAACAAGTGAT 60.017 38.462 13.53 0.00 32.14 3.06
300 301 6.732154 ACAATGTCTTTCTCAACAAGTGATG 58.268 36.000 0.00 0.00 35.07 3.07
301 302 6.543465 ACAATGTCTTTCTCAACAAGTGATGA 59.457 34.615 0.00 0.00 35.07 2.92
302 303 6.798315 ATGTCTTTCTCAACAAGTGATGAG 57.202 37.500 11.28 11.28 43.62 2.90
311 321 4.020751 TCAACAAGTGATGAGGAGGAAGAG 60.021 45.833 0.00 0.00 0.00 2.85
343 353 0.178953 ATGCCCATGGATAAGTGGCC 60.179 55.000 15.22 0.00 41.46 5.36
348 358 1.410648 CCATGGATAAGTGGCCAAGCT 60.411 52.381 7.24 0.00 37.78 3.74
357 367 2.193248 GGCCAAGCTAGCCGGAAT 59.807 61.111 21.98 0.00 41.41 3.01
367 377 2.037251 GCTAGCCGGAATAATCTGTGGA 59.963 50.000 5.05 0.00 0.00 4.02
448 465 4.893424 TTTTAAGTTGTGGTGTCAGCTC 57.107 40.909 3.30 0.07 0.00 4.09
449 466 3.838244 TTAAGTTGTGGTGTCAGCTCT 57.162 42.857 3.30 0.00 0.00 4.09
452 469 0.106708 GTTGTGGTGTCAGCTCTCCA 59.893 55.000 3.30 0.00 0.00 3.86
455 472 0.320247 GTGGTGTCAGCTCTCCACAG 60.320 60.000 17.35 0.00 45.55 3.66
456 473 1.375268 GGTGTCAGCTCTCCACAGC 60.375 63.158 8.66 4.29 39.99 4.40
463 480 2.743195 GCTCTCCACAGCTTGTACG 58.257 57.895 0.00 0.00 36.38 3.67
464 481 1.355066 GCTCTCCACAGCTTGTACGC 61.355 60.000 0.00 0.00 36.38 4.42
474 493 1.067846 AGCTTGTACGCAGAATCGTCA 60.068 47.619 0.00 0.00 43.15 4.35
475 494 1.927174 GCTTGTACGCAGAATCGTCAT 59.073 47.619 0.00 0.00 43.15 3.06
478 497 2.954316 TGTACGCAGAATCGTCATTGT 58.046 42.857 0.00 0.00 43.15 2.71
483 502 2.472886 CGCAGAATCGTCATTGTCACAC 60.473 50.000 0.00 0.00 0.00 3.82
486 505 4.329801 GCAGAATCGTCATTGTCACACATA 59.670 41.667 0.00 0.00 0.00 2.29
488 507 6.472680 CAGAATCGTCATTGTCACACATAAG 58.527 40.000 0.00 0.00 0.00 1.73
492 511 5.402398 TCGTCATTGTCACACATAAGAGAG 58.598 41.667 0.00 0.00 0.00 3.20
496 515 7.378194 CGTCATTGTCACACATAAGAGAGATAG 59.622 40.741 0.00 0.00 0.00 2.08
500 519 5.360999 TGTCACACATAAGAGAGATAGGTGG 59.639 44.000 3.81 0.00 38.87 4.61
502 521 4.895889 CACACATAAGAGAGATAGGTGGGA 59.104 45.833 3.81 0.00 40.02 4.37
503 522 5.541868 CACACATAAGAGAGATAGGTGGGAT 59.458 44.000 3.81 0.00 40.02 3.85
505 524 5.046735 CACATAAGAGAGATAGGTGGGATGG 60.047 48.000 0.00 0.00 32.87 3.51
508 527 3.855668 AGAGAGATAGGTGGGATGGAAG 58.144 50.000 0.00 0.00 0.00 3.46
509 528 3.469006 AGAGAGATAGGTGGGATGGAAGA 59.531 47.826 0.00 0.00 0.00 2.87
510 529 4.078336 AGAGAGATAGGTGGGATGGAAGAA 60.078 45.833 0.00 0.00 0.00 2.52
514 533 0.328258 AGGTGGGATGGAAGAAACGG 59.672 55.000 0.00 0.00 0.00 4.44
516 535 1.165270 GTGGGATGGAAGAAACGGTG 58.835 55.000 0.00 0.00 0.00 4.94
525 544 4.503910 TGGAAGAAACGGTGATAGACATG 58.496 43.478 0.00 0.00 0.00 3.21
527 546 5.175859 GGAAGAAACGGTGATAGACATGAA 58.824 41.667 0.00 0.00 0.00 2.57
531 550 7.133891 AGAAACGGTGATAGACATGAAAAAG 57.866 36.000 0.00 0.00 0.00 2.27
535 554 6.698380 ACGGTGATAGACATGAAAAAGTAGT 58.302 36.000 0.00 0.00 0.00 2.73
541 560 5.695851 AGACATGAAAAAGTAGTTGGCTG 57.304 39.130 0.00 0.00 0.00 4.85
549 568 5.552870 AAAAGTAGTTGGCTGAGAAGAGA 57.447 39.130 0.00 0.00 0.00 3.10
552 571 4.093011 AGTAGTTGGCTGAGAAGAGACAT 58.907 43.478 0.00 0.00 28.45 3.06
557 576 2.169978 TGGCTGAGAAGAGACATGGATG 59.830 50.000 0.00 0.00 0.00 3.51
559 578 2.836262 CTGAGAAGAGACATGGATGCC 58.164 52.381 0.00 0.00 0.00 4.40
562 581 4.229639 TGAGAAGAGACATGGATGCCTAT 58.770 43.478 0.00 0.00 0.00 2.57
567 586 3.078153 AGAGACATGGATGCCTATAGGGA 59.922 47.826 20.58 18.48 40.76 4.20
568 587 3.448934 AGACATGGATGCCTATAGGGAG 58.551 50.000 20.58 7.85 39.50 4.30
570 589 3.448934 ACATGGATGCCTATAGGGAGAG 58.551 50.000 20.58 9.28 39.50 3.20
571 590 3.078153 ACATGGATGCCTATAGGGAGAGA 59.922 47.826 20.58 5.71 39.50 3.10
578 627 2.025321 GCCTATAGGGAGAGAGGGAGAG 60.025 59.091 20.58 0.00 37.23 3.20
582 631 1.152546 GGGAGAGAGGGAGAGAGCC 60.153 68.421 0.00 0.00 0.00 4.70
687 741 6.826893 AATTTCTTTGTGTCAAATCCGTTG 57.173 33.333 0.00 0.00 38.71 4.10
699 759 6.494893 TCAAATCCGTTGAAGACCATTTAG 57.505 37.500 0.00 0.00 43.43 1.85
706 766 1.339631 TGAAGACCATTTAGGCCGTGG 60.340 52.381 15.18 15.18 43.14 4.94
708 768 1.205460 AGACCATTTAGGCCGTGGGT 61.205 55.000 19.18 13.84 43.14 4.51
713 773 3.028130 CCATTTAGGCCGTGGGTAAAAT 58.972 45.455 10.54 2.01 0.00 1.82
716 776 3.724732 TTAGGCCGTGGGTAAAATTCT 57.275 42.857 0.00 0.00 0.00 2.40
724 784 5.124936 GCCGTGGGTAAAATTCTAAAGATGT 59.875 40.000 0.00 0.00 0.00 3.06
767 827 6.216801 ACTTAGCGACTATGGATGTGTTTA 57.783 37.500 0.00 0.00 0.00 2.01
787 847 7.115236 GTGTTTATAACCAAAATTCACGGGTTC 59.885 37.037 0.00 0.00 42.37 3.62
798 880 6.894339 AATTCACGGGTTCAAATTTCTACT 57.106 33.333 0.00 0.00 0.00 2.57
808 890 7.362660 GGGTTCAAATTTCTACTGGATGTAACC 60.363 40.741 0.00 0.00 0.00 2.85
811 893 8.506168 TCAAATTTCTACTGGATGTAACCATC 57.494 34.615 0.00 0.00 45.65 3.51
816 898 3.526931 ACTGGATGTAACCATCTGTCG 57.473 47.619 3.01 0.00 45.66 4.35
836 919 9.372369 TCTGTCGAAATTATTTTTGGTGTTTTT 57.628 25.926 0.00 0.00 0.00 1.94
875 958 7.367159 TCATTGCTGCAAATTAAGGAAAATG 57.633 32.000 20.06 8.38 0.00 2.32
877 960 5.226194 TGCTGCAAATTAAGGAAAATGGT 57.774 34.783 0.00 0.00 0.00 3.55
907 992 0.764271 CAAAATTGCCAACCTGGGGT 59.236 50.000 0.00 0.00 38.19 4.95
957 1043 3.614390 CGACAGAGAGTTCCAAACCTACC 60.614 52.174 0.00 0.00 0.00 3.18
977 1064 2.556559 CCGGAAATTTCTCCCCTTTCCA 60.557 50.000 17.42 0.00 45.33 3.53
981 1068 0.331616 ATTTCTCCCCTTTCCACCGG 59.668 55.000 0.00 0.00 0.00 5.28
1079 1182 4.154347 CCACCGCTGCCTCCTCTC 62.154 72.222 0.00 0.00 0.00 3.20
1427 2188 3.174573 CGGCCGTTTCCGTCGTAC 61.175 66.667 19.50 0.00 44.18 3.67
1643 2430 0.179048 CTCACCACCAACACAGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
1827 2629 1.337118 TTGCTGTGTCCAAATTCCCC 58.663 50.000 0.00 0.00 0.00 4.81
1837 2639 1.406903 CAAATTCCCCCATCTCCTGC 58.593 55.000 0.00 0.00 0.00 4.85
1840 2642 3.943137 TTCCCCCATCTCCTGCGGT 62.943 63.158 0.00 0.00 0.00 5.68
1853 2655 2.009774 CCTGCGGTATTCAAAGGACAG 58.990 52.381 0.00 0.00 0.00 3.51
1861 2663 0.183492 TTCAAAGGACAGGCTGCAGT 59.817 50.000 15.89 0.00 0.00 4.40
2202 3009 5.221501 ACCTTGAAAATGCTTGCTGTAACAT 60.222 36.000 0.00 0.00 0.00 2.71
2585 3392 7.781324 TTTGATTTCTTTGCCCTTATTCTCT 57.219 32.000 0.00 0.00 0.00 3.10
2592 3399 6.415573 TCTTTGCCCTTATTCTCTTAAGGTC 58.584 40.000 1.85 0.00 44.57 3.85
2733 3540 0.099436 GGATTTGTCACGGATGCTGC 59.901 55.000 0.00 0.00 0.00 5.25
3030 3869 3.563390 TCGTGTGAATTTTGATGTGCTCA 59.437 39.130 0.00 0.00 0.00 4.26
3153 3993 7.293073 AGGTGGCATGAATTAGTCTTCATAAT 58.707 34.615 0.00 0.00 42.52 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.610305 CAGTACACTATTTAACAGACCCCAAAT 59.390 37.037 0.00 0.00 0.00 2.32
6 7 6.749118 CGTACAGTACACTATTTAACAGACCC 59.251 42.308 11.37 0.00 0.00 4.46
15 16 9.994432 GAACAGTATACGTACAGTACACTATTT 57.006 33.333 11.37 3.86 40.81 1.40
16 17 9.388506 AGAACAGTATACGTACAGTACACTATT 57.611 33.333 11.37 2.28 40.81 1.73
17 18 8.824781 CAGAACAGTATACGTACAGTACACTAT 58.175 37.037 11.37 7.20 40.81 2.12
18 19 8.034804 TCAGAACAGTATACGTACAGTACACTA 58.965 37.037 11.37 0.11 40.81 2.74
19 20 6.875726 TCAGAACAGTATACGTACAGTACACT 59.124 38.462 11.37 3.82 43.33 3.55
20 21 6.958193 GTCAGAACAGTATACGTACAGTACAC 59.042 42.308 11.37 1.52 38.29 2.90
21 22 6.092670 GGTCAGAACAGTATACGTACAGTACA 59.907 42.308 11.37 0.00 38.29 2.90
22 23 6.457528 GGGTCAGAACAGTATACGTACAGTAC 60.458 46.154 0.00 0.00 38.29 2.73
23 24 5.586243 GGGTCAGAACAGTATACGTACAGTA 59.414 44.000 0.00 0.00 40.03 2.74
24 25 4.397417 GGGTCAGAACAGTATACGTACAGT 59.603 45.833 0.00 0.00 32.61 3.55
25 26 4.397103 TGGGTCAGAACAGTATACGTACAG 59.603 45.833 0.00 0.00 33.09 2.74
26 27 4.334552 TGGGTCAGAACAGTATACGTACA 58.665 43.478 0.00 0.00 33.09 2.90
27 28 4.970662 TGGGTCAGAACAGTATACGTAC 57.029 45.455 0.00 0.00 0.00 3.67
28 29 6.534475 AATTGGGTCAGAACAGTATACGTA 57.466 37.500 0.00 0.00 0.00 3.57
29 30 5.416271 AATTGGGTCAGAACAGTATACGT 57.584 39.130 0.00 0.00 0.00 3.57
30 31 7.926555 AGATAAATTGGGTCAGAACAGTATACG 59.073 37.037 0.00 0.00 0.00 3.06
31 32 9.614792 AAGATAAATTGGGTCAGAACAGTATAC 57.385 33.333 0.00 0.00 0.00 1.47
32 33 9.613428 CAAGATAAATTGGGTCAGAACAGTATA 57.387 33.333 0.00 0.00 0.00 1.47
33 34 8.109634 ACAAGATAAATTGGGTCAGAACAGTAT 58.890 33.333 0.00 0.00 34.36 2.12
34 35 7.458397 ACAAGATAAATTGGGTCAGAACAGTA 58.542 34.615 0.00 0.00 34.36 2.74
35 36 6.306987 ACAAGATAAATTGGGTCAGAACAGT 58.693 36.000 0.00 0.00 34.36 3.55
36 37 6.824305 ACAAGATAAATTGGGTCAGAACAG 57.176 37.500 0.00 0.00 34.36 3.16
37 38 7.432869 CAAACAAGATAAATTGGGTCAGAACA 58.567 34.615 0.00 0.00 34.36 3.18
38 39 6.366061 GCAAACAAGATAAATTGGGTCAGAAC 59.634 38.462 0.00 0.00 34.36 3.01
39 40 6.267471 AGCAAACAAGATAAATTGGGTCAGAA 59.733 34.615 0.00 0.00 34.36 3.02
40 41 5.774690 AGCAAACAAGATAAATTGGGTCAGA 59.225 36.000 0.00 0.00 34.36 3.27
41 42 5.865552 CAGCAAACAAGATAAATTGGGTCAG 59.134 40.000 0.00 0.00 34.36 3.51
42 43 5.538053 TCAGCAAACAAGATAAATTGGGTCA 59.462 36.000 0.00 0.00 34.36 4.02
43 44 6.024552 TCAGCAAACAAGATAAATTGGGTC 57.975 37.500 0.00 0.00 34.36 4.46
44 45 5.774690 TCTCAGCAAACAAGATAAATTGGGT 59.225 36.000 0.00 0.00 34.36 4.51
45 46 6.271488 TCTCAGCAAACAAGATAAATTGGG 57.729 37.500 0.00 0.00 34.36 4.12
46 47 5.803967 GCTCTCAGCAAACAAGATAAATTGG 59.196 40.000 0.00 0.00 41.89 3.16
47 48 6.618811 AGCTCTCAGCAAACAAGATAAATTG 58.381 36.000 0.00 0.00 45.56 2.32
48 49 6.830873 AGCTCTCAGCAAACAAGATAAATT 57.169 33.333 0.00 0.00 45.56 1.82
49 50 7.108847 AGTAGCTCTCAGCAAACAAGATAAAT 58.891 34.615 0.00 0.00 45.56 1.40
50 51 6.467677 AGTAGCTCTCAGCAAACAAGATAAA 58.532 36.000 0.00 0.00 45.56 1.40
51 52 6.042638 AGTAGCTCTCAGCAAACAAGATAA 57.957 37.500 0.00 0.00 45.56 1.75
52 53 5.185828 TGAGTAGCTCTCAGCAAACAAGATA 59.814 40.000 10.62 0.00 46.77 1.98
53 54 4.020751 TGAGTAGCTCTCAGCAAACAAGAT 60.021 41.667 10.62 0.00 46.77 2.40
54 55 3.321968 TGAGTAGCTCTCAGCAAACAAGA 59.678 43.478 10.62 0.00 46.77 3.02
55 56 3.657634 TGAGTAGCTCTCAGCAAACAAG 58.342 45.455 10.62 0.00 46.77 3.16
56 57 3.751479 TGAGTAGCTCTCAGCAAACAA 57.249 42.857 10.62 0.00 46.77 2.83
65 66 5.448360 GCATTTGGACATTTGAGTAGCTCTC 60.448 44.000 0.00 0.00 43.03 3.20
66 67 4.397417 GCATTTGGACATTTGAGTAGCTCT 59.603 41.667 0.00 0.00 0.00 4.09
67 68 4.397417 AGCATTTGGACATTTGAGTAGCTC 59.603 41.667 0.00 0.00 0.00 4.09
68 69 4.338879 AGCATTTGGACATTTGAGTAGCT 58.661 39.130 0.00 0.00 0.00 3.32
69 70 4.397417 AGAGCATTTGGACATTTGAGTAGC 59.603 41.667 0.00 0.00 0.00 3.58
70 71 5.645067 TCAGAGCATTTGGACATTTGAGTAG 59.355 40.000 0.00 0.00 0.00 2.57
71 72 5.559770 TCAGAGCATTTGGACATTTGAGTA 58.440 37.500 0.00 0.00 0.00 2.59
72 73 4.401022 TCAGAGCATTTGGACATTTGAGT 58.599 39.130 0.00 0.00 0.00 3.41
73 74 5.381174 TTCAGAGCATTTGGACATTTGAG 57.619 39.130 0.00 0.00 0.00 3.02
74 75 5.787953 TTTCAGAGCATTTGGACATTTGA 57.212 34.783 0.00 0.00 0.00 2.69
75 76 7.295201 CAAATTTCAGAGCATTTGGACATTTG 58.705 34.615 8.42 0.00 36.93 2.32
76 77 7.429636 CAAATTTCAGAGCATTTGGACATTT 57.570 32.000 8.42 0.00 36.93 2.32
89 90 1.135575 GGTGCGCTCCAAATTTCAGAG 60.136 52.381 23.09 9.49 0.00 3.35
90 91 0.881118 GGTGCGCTCCAAATTTCAGA 59.119 50.000 23.09 0.00 0.00 3.27
91 92 0.883833 AGGTGCGCTCCAAATTTCAG 59.116 50.000 28.68 0.00 0.00 3.02
92 93 0.881118 GAGGTGCGCTCCAAATTTCA 59.119 50.000 28.68 0.00 0.00 2.69
93 94 0.881118 TGAGGTGCGCTCCAAATTTC 59.119 50.000 28.68 17.55 0.00 2.17
94 95 1.203052 CATGAGGTGCGCTCCAAATTT 59.797 47.619 28.68 9.09 0.00 1.82
95 96 0.813184 CATGAGGTGCGCTCCAAATT 59.187 50.000 28.68 9.48 0.00 1.82
96 97 1.660560 GCATGAGGTGCGCTCCAAAT 61.661 55.000 28.68 18.48 45.23 2.32
97 98 2.334946 GCATGAGGTGCGCTCCAAA 61.335 57.895 28.68 17.08 45.23 3.28
98 99 2.747460 GCATGAGGTGCGCTCCAA 60.747 61.111 28.68 17.43 45.23 3.53
106 107 5.009010 GGTAGATAATTTGGTGCATGAGGTG 59.991 44.000 0.00 0.00 0.00 4.00
107 108 5.133221 GGTAGATAATTTGGTGCATGAGGT 58.867 41.667 0.00 0.00 0.00 3.85
108 109 5.132502 TGGTAGATAATTTGGTGCATGAGG 58.867 41.667 0.00 0.00 0.00 3.86
109 110 6.675026 CATGGTAGATAATTTGGTGCATGAG 58.325 40.000 0.00 0.00 0.00 2.90
110 111 5.009911 GCATGGTAGATAATTTGGTGCATGA 59.990 40.000 0.00 0.00 0.00 3.07
111 112 5.221283 TGCATGGTAGATAATTTGGTGCATG 60.221 40.000 0.00 0.00 35.41 4.06
112 113 4.894705 TGCATGGTAGATAATTTGGTGCAT 59.105 37.500 0.00 0.00 35.41 3.96
113 114 4.097741 GTGCATGGTAGATAATTTGGTGCA 59.902 41.667 0.00 0.00 37.69 4.57
114 115 4.097741 TGTGCATGGTAGATAATTTGGTGC 59.902 41.667 0.00 0.00 0.00 5.01
115 116 5.833406 TGTGCATGGTAGATAATTTGGTG 57.167 39.130 0.00 0.00 0.00 4.17
116 117 6.849085 TTTGTGCATGGTAGATAATTTGGT 57.151 33.333 0.00 0.00 0.00 3.67
117 118 8.721019 ATTTTTGTGCATGGTAGATAATTTGG 57.279 30.769 0.00 0.00 0.00 3.28
121 122 9.165035 CCAAAATTTTTGTGCATGGTAGATAAT 57.835 29.630 18.05 0.00 0.00 1.28
122 123 8.370940 TCCAAAATTTTTGTGCATGGTAGATAA 58.629 29.630 18.05 0.00 0.00 1.75
123 124 7.816995 GTCCAAAATTTTTGTGCATGGTAGATA 59.183 33.333 18.05 0.00 0.00 1.98
124 125 6.650390 GTCCAAAATTTTTGTGCATGGTAGAT 59.350 34.615 18.05 0.00 0.00 1.98
125 126 5.988561 GTCCAAAATTTTTGTGCATGGTAGA 59.011 36.000 18.05 4.85 0.00 2.59
126 127 5.179182 GGTCCAAAATTTTTGTGCATGGTAG 59.821 40.000 18.05 2.87 0.00 3.18
127 128 5.059833 GGTCCAAAATTTTTGTGCATGGTA 58.940 37.500 18.05 0.00 0.00 3.25
128 129 3.882288 GGTCCAAAATTTTTGTGCATGGT 59.118 39.130 18.05 0.00 0.00 3.55
129 130 4.136051 AGGTCCAAAATTTTTGTGCATGG 58.864 39.130 18.05 5.28 0.00 3.66
130 131 5.754543 AAGGTCCAAAATTTTTGTGCATG 57.245 34.783 18.05 5.27 0.00 4.06
131 132 6.772360 AAAAGGTCCAAAATTTTTGTGCAT 57.228 29.167 18.05 7.44 0.00 3.96
132 133 6.581171 AAAAAGGTCCAAAATTTTTGTGCA 57.419 29.167 18.05 2.22 35.43 4.57
161 162 8.368668 ACCCGGTCAACAAATAATTCATAAAAA 58.631 29.630 0.00 0.00 0.00 1.94
162 163 7.815068 CACCCGGTCAACAAATAATTCATAAAA 59.185 33.333 0.00 0.00 0.00 1.52
163 164 7.316640 CACCCGGTCAACAAATAATTCATAAA 58.683 34.615 0.00 0.00 0.00 1.40
164 165 6.626181 GCACCCGGTCAACAAATAATTCATAA 60.626 38.462 0.00 0.00 0.00 1.90
165 166 5.163602 GCACCCGGTCAACAAATAATTCATA 60.164 40.000 0.00 0.00 0.00 2.15
166 167 4.381505 GCACCCGGTCAACAAATAATTCAT 60.382 41.667 0.00 0.00 0.00 2.57
167 168 3.057174 GCACCCGGTCAACAAATAATTCA 60.057 43.478 0.00 0.00 0.00 2.57
168 169 3.057174 TGCACCCGGTCAACAAATAATTC 60.057 43.478 0.00 0.00 0.00 2.17
169 170 2.894126 TGCACCCGGTCAACAAATAATT 59.106 40.909 0.00 0.00 0.00 1.40
170 171 2.491693 CTGCACCCGGTCAACAAATAAT 59.508 45.455 0.00 0.00 0.00 1.28
171 172 1.883275 CTGCACCCGGTCAACAAATAA 59.117 47.619 0.00 0.00 0.00 1.40
172 173 1.072489 TCTGCACCCGGTCAACAAATA 59.928 47.619 0.00 0.00 0.00 1.40
173 174 0.179004 TCTGCACCCGGTCAACAAAT 60.179 50.000 0.00 0.00 0.00 2.32
174 175 1.098712 GTCTGCACCCGGTCAACAAA 61.099 55.000 0.00 0.00 0.00 2.83
175 176 1.525077 GTCTGCACCCGGTCAACAA 60.525 57.895 0.00 0.00 0.00 2.83
176 177 2.110213 GTCTGCACCCGGTCAACA 59.890 61.111 0.00 0.00 0.00 3.33
177 178 3.041940 CGTCTGCACCCGGTCAAC 61.042 66.667 0.00 0.00 0.00 3.18
178 179 3.220999 CTCGTCTGCACCCGGTCAA 62.221 63.158 0.00 0.00 0.00 3.18
179 180 3.680786 CTCGTCTGCACCCGGTCA 61.681 66.667 0.00 0.00 0.00 4.02
180 181 3.628280 GACTCGTCTGCACCCGGTC 62.628 68.421 0.00 4.09 0.00 4.79
181 182 3.681835 GACTCGTCTGCACCCGGT 61.682 66.667 0.00 0.00 0.00 5.28
182 183 4.436998 GGACTCGTCTGCACCCGG 62.437 72.222 0.00 0.00 0.00 5.73
183 184 4.778415 CGGACTCGTCTGCACCCG 62.778 72.222 0.00 0.00 0.00 5.28
184 185 4.436998 CCGGACTCGTCTGCACCC 62.437 72.222 0.00 0.00 34.69 4.61
185 186 4.436998 CCCGGACTCGTCTGCACC 62.437 72.222 0.73 0.00 34.69 5.01
189 190 3.109612 CTACGCCCGGACTCGTCTG 62.110 68.421 17.14 9.77 39.79 3.51
190 191 2.809861 TTCTACGCCCGGACTCGTCT 62.810 60.000 17.14 0.65 39.79 4.18
191 192 1.722636 ATTCTACGCCCGGACTCGTC 61.723 60.000 17.14 0.00 39.79 4.20
192 193 1.318158 AATTCTACGCCCGGACTCGT 61.318 55.000 17.60 17.60 42.09 4.18
193 194 0.870307 CAATTCTACGCCCGGACTCG 60.870 60.000 0.73 6.05 0.00 4.18
194 195 0.529992 CCAATTCTACGCCCGGACTC 60.530 60.000 0.73 0.00 0.00 3.36
195 196 0.974010 TCCAATTCTACGCCCGGACT 60.974 55.000 0.73 0.00 0.00 3.85
196 197 0.106149 ATCCAATTCTACGCCCGGAC 59.894 55.000 0.73 0.00 0.00 4.79
197 198 1.707106 TATCCAATTCTACGCCCGGA 58.293 50.000 0.73 0.00 0.00 5.14
198 199 2.762535 ATATCCAATTCTACGCCCGG 57.237 50.000 0.00 0.00 0.00 5.73
199 200 2.666508 CGAATATCCAATTCTACGCCCG 59.333 50.000 0.00 0.00 0.00 6.13
200 201 3.921677 TCGAATATCCAATTCTACGCCC 58.078 45.455 0.00 0.00 0.00 6.13
201 202 5.408604 ACATTCGAATATCCAATTCTACGCC 59.591 40.000 10.97 0.00 0.00 5.68
202 203 6.401153 GGACATTCGAATATCCAATTCTACGC 60.401 42.308 26.87 0.00 32.18 4.42
203 204 6.645003 TGGACATTCGAATATCCAATTCTACG 59.355 38.462 30.99 8.46 38.95 3.51
204 205 7.962964 TGGACATTCGAATATCCAATTCTAC 57.037 36.000 30.99 6.86 38.95 2.59
205 206 9.653287 GTATGGACATTCGAATATCCAATTCTA 57.347 33.333 34.96 22.53 44.51 2.10
206 207 8.156820 TGTATGGACATTCGAATATCCAATTCT 58.843 33.333 34.96 23.45 44.51 2.40
207 208 8.230486 GTGTATGGACATTCGAATATCCAATTC 58.770 37.037 34.96 26.71 44.51 2.17
208 209 7.939039 AGTGTATGGACATTCGAATATCCAATT 59.061 33.333 34.96 24.39 44.51 2.32
209 210 7.453393 AGTGTATGGACATTCGAATATCCAAT 58.547 34.615 34.96 25.47 44.51 3.16
210 211 6.826668 AGTGTATGGACATTCGAATATCCAA 58.173 36.000 34.96 23.11 44.51 3.53
211 212 6.419484 AGTGTATGGACATTCGAATATCCA 57.581 37.500 33.87 33.87 45.33 3.41
212 213 9.088512 GATAAGTGTATGGACATTCGAATATCC 57.911 37.037 25.48 25.48 38.04 2.59
213 214 9.862371 AGATAAGTGTATGGACATTCGAATATC 57.138 33.333 10.97 9.36 38.04 1.63
216 217 9.862371 GATAGATAAGTGTATGGACATTCGAAT 57.138 33.333 4.39 4.39 38.04 3.34
217 218 9.078990 AGATAGATAAGTGTATGGACATTCGAA 57.921 33.333 0.00 0.00 38.04 3.71
218 219 8.637196 AGATAGATAAGTGTATGGACATTCGA 57.363 34.615 0.00 0.00 38.04 3.71
219 220 7.694367 CGAGATAGATAAGTGTATGGACATTCG 59.306 40.741 0.00 0.00 38.04 3.34
220 221 8.516234 ACGAGATAGATAAGTGTATGGACATTC 58.484 37.037 0.00 0.00 38.04 2.67
221 222 8.410673 ACGAGATAGATAAGTGTATGGACATT 57.589 34.615 0.00 0.00 38.04 2.71
274 275 5.296780 TCACTTGTTGAGAAAGACATTGTCC 59.703 40.000 13.14 0.00 32.18 4.02
290 291 3.307339 GCTCTTCCTCCTCATCACTTGTT 60.307 47.826 0.00 0.00 0.00 2.83
293 294 2.235898 GTGCTCTTCCTCCTCATCACTT 59.764 50.000 0.00 0.00 0.00 3.16
297 298 2.627699 CCTAGTGCTCTTCCTCCTCATC 59.372 54.545 0.00 0.00 0.00 2.92
299 300 1.962402 GCCTAGTGCTCTTCCTCCTCA 60.962 57.143 0.00 0.00 36.87 3.86
300 301 0.750249 GCCTAGTGCTCTTCCTCCTC 59.250 60.000 0.00 0.00 36.87 3.71
301 302 1.040339 CGCCTAGTGCTCTTCCTCCT 61.040 60.000 0.00 0.00 38.05 3.69
302 303 1.439644 CGCCTAGTGCTCTTCCTCC 59.560 63.158 0.00 0.00 38.05 4.30
321 331 1.342174 CCACTTATCCATGGGCATTGC 59.658 52.381 13.02 0.00 31.83 3.56
331 341 1.134098 GCTAGCTTGGCCACTTATCCA 60.134 52.381 3.88 0.00 0.00 3.41
343 353 3.496130 CACAGATTATTCCGGCTAGCTTG 59.504 47.826 15.72 7.61 0.00 4.01
348 358 4.346709 TGAATCCACAGATTATTCCGGCTA 59.653 41.667 0.00 0.00 42.93 3.93
429 446 3.494398 GGAGAGCTGACACCACAACTTAA 60.494 47.826 0.00 0.00 0.00 1.85
430 447 2.037251 GGAGAGCTGACACCACAACTTA 59.963 50.000 0.00 0.00 0.00 2.24
436 453 0.320247 CTGTGGAGAGCTGACACCAC 60.320 60.000 13.11 13.11 46.39 4.16
445 462 1.355066 GCGTACAAGCTGTGGAGAGC 61.355 60.000 0.00 0.00 39.46 4.09
448 465 0.038251 TCTGCGTACAAGCTGTGGAG 60.038 55.000 0.00 0.00 37.36 3.86
449 466 0.391228 TTCTGCGTACAAGCTGTGGA 59.609 50.000 0.00 0.00 37.36 4.02
452 469 1.336887 ACGATTCTGCGTACAAGCTGT 60.337 47.619 0.00 0.00 43.61 4.40
455 472 1.346365 TGACGATTCTGCGTACAAGC 58.654 50.000 0.00 0.00 45.72 4.01
456 473 3.367932 ACAATGACGATTCTGCGTACAAG 59.632 43.478 0.00 0.00 45.72 3.16
457 474 3.322369 ACAATGACGATTCTGCGTACAA 58.678 40.909 0.00 0.00 45.72 2.41
458 475 2.921121 GACAATGACGATTCTGCGTACA 59.079 45.455 0.00 0.00 45.72 2.90
459 476 2.921121 TGACAATGACGATTCTGCGTAC 59.079 45.455 0.00 0.00 45.72 3.67
463 480 2.480037 TGTGTGACAATGACGATTCTGC 59.520 45.455 0.00 0.00 0.00 4.26
464 481 4.934075 ATGTGTGACAATGACGATTCTG 57.066 40.909 0.00 0.00 0.00 3.02
474 493 7.418368 CCACCTATCTCTCTTATGTGTGACAAT 60.418 40.741 0.00 0.00 0.00 2.71
475 494 6.127338 CCACCTATCTCTCTTATGTGTGACAA 60.127 42.308 0.00 0.00 0.00 3.18
478 497 4.895889 CCCACCTATCTCTCTTATGTGTGA 59.104 45.833 0.00 0.00 0.00 3.58
483 502 5.336945 TCCATCCCACCTATCTCTCTTATG 58.663 45.833 0.00 0.00 0.00 1.90
486 505 4.078336 TCTTCCATCCCACCTATCTCTCTT 60.078 45.833 0.00 0.00 0.00 2.85
488 507 3.850752 TCTTCCATCCCACCTATCTCTC 58.149 50.000 0.00 0.00 0.00 3.20
492 511 3.467803 CGTTTCTTCCATCCCACCTATC 58.532 50.000 0.00 0.00 0.00 2.08
496 515 0.037734 ACCGTTTCTTCCATCCCACC 59.962 55.000 0.00 0.00 0.00 4.61
500 519 4.120589 GTCTATCACCGTTTCTTCCATCC 58.879 47.826 0.00 0.00 0.00 3.51
502 521 4.819105 TGTCTATCACCGTTTCTTCCAT 57.181 40.909 0.00 0.00 0.00 3.41
503 522 4.221924 TCATGTCTATCACCGTTTCTTCCA 59.778 41.667 0.00 0.00 0.00 3.53
505 524 6.721571 TTTCATGTCTATCACCGTTTCTTC 57.278 37.500 0.00 0.00 0.00 2.87
508 527 6.899114 ACTTTTTCATGTCTATCACCGTTTC 58.101 36.000 0.00 0.00 0.00 2.78
509 528 6.877611 ACTTTTTCATGTCTATCACCGTTT 57.122 33.333 0.00 0.00 0.00 3.60
510 529 7.159372 ACTACTTTTTCATGTCTATCACCGTT 58.841 34.615 0.00 0.00 0.00 4.44
514 533 7.119846 AGCCAACTACTTTTTCATGTCTATCAC 59.880 37.037 0.00 0.00 0.00 3.06
516 535 7.334421 TCAGCCAACTACTTTTTCATGTCTATC 59.666 37.037 0.00 0.00 0.00 2.08
525 544 5.992217 TCTCTTCTCAGCCAACTACTTTTTC 59.008 40.000 0.00 0.00 0.00 2.29
527 546 5.163301 TGTCTCTTCTCAGCCAACTACTTTT 60.163 40.000 0.00 0.00 0.00 2.27
531 550 3.944055 TGTCTCTTCTCAGCCAACTAC 57.056 47.619 0.00 0.00 0.00 2.73
535 554 2.259917 TCCATGTCTCTTCTCAGCCAA 58.740 47.619 0.00 0.00 0.00 4.52
541 560 4.888326 ATAGGCATCCATGTCTCTTCTC 57.112 45.455 0.00 0.00 42.67 2.87
549 568 3.078153 TCTCTCCCTATAGGCATCCATGT 59.922 47.826 13.85 0.00 34.51 3.21
552 571 2.043664 CCTCTCTCCCTATAGGCATCCA 59.956 54.545 13.85 0.00 34.51 3.41
557 576 1.997040 TCTCCCTCTCTCCCTATAGGC 59.003 57.143 13.85 0.00 34.51 3.93
559 578 3.054361 GCTCTCTCCCTCTCTCCCTATAG 60.054 56.522 0.00 0.00 0.00 1.31
562 581 1.145571 GCTCTCTCCCTCTCTCCCTA 58.854 60.000 0.00 0.00 0.00 3.53
567 586 1.938596 TGGGGCTCTCTCCCTCTCT 60.939 63.158 0.00 0.00 45.80 3.10
568 587 1.760480 GTGGGGCTCTCTCCCTCTC 60.760 68.421 0.00 0.00 45.80 3.20
570 589 0.105453 TATGTGGGGCTCTCTCCCTC 60.105 60.000 0.00 0.00 45.80 4.30
571 590 0.570218 ATATGTGGGGCTCTCTCCCT 59.430 55.000 0.00 0.00 45.80 4.20
578 627 5.796424 AATCAAAATCATATGTGGGGCTC 57.204 39.130 1.90 0.00 0.00 4.70
582 631 8.392612 GCTTCAAAAATCAAAATCATATGTGGG 58.607 33.333 1.90 0.00 0.00 4.61
671 725 3.314080 GGTCTTCAACGGATTTGACACAA 59.686 43.478 0.00 0.00 44.28 3.33
687 741 1.379527 CCACGGCCTAAATGGTCTTC 58.620 55.000 0.00 0.00 38.58 2.87
699 759 4.011698 TCTTTAGAATTTTACCCACGGCC 58.988 43.478 0.00 0.00 0.00 6.13
742 802 3.243101 ACACATCCATAGTCGCTAAGTCG 60.243 47.826 0.00 0.00 0.00 4.18
749 809 5.756347 TGGTTATAAACACATCCATAGTCGC 59.244 40.000 0.00 0.00 0.00 5.19
767 827 5.793030 TTGAACCCGTGAATTTTGGTTAT 57.207 34.783 0.00 0.00 41.03 1.89
808 890 8.519492 AACACCAAAAATAATTTCGACAGATG 57.481 30.769 0.00 0.00 0.00 2.90
836 919 6.183360 TGCAGCAATGAAAAGTCAAGTTAGAA 60.183 34.615 0.00 0.00 37.30 2.10
839 922 5.512753 TGCAGCAATGAAAAGTCAAGTTA 57.487 34.783 0.00 0.00 37.30 2.24
852 935 6.149807 ACCATTTTCCTTAATTTGCAGCAATG 59.850 34.615 9.12 0.00 0.00 2.82
900 985 1.692042 ATCCAGCTCTGACCCCAGG 60.692 63.158 0.00 0.00 40.76 4.45
907 992 1.045350 CGAAGGGGATCCAGCTCTGA 61.045 60.000 15.23 0.00 34.83 3.27
942 1027 2.845363 TTCCGGTAGGTTTGGAACTC 57.155 50.000 0.00 0.00 36.87 3.01
1427 2188 1.442769 CACCCTGGAGACGACAAATG 58.557 55.000 0.00 0.00 0.00 2.32
1837 2639 2.009774 CAGCCTGTCCTTTGAATACCG 58.990 52.381 0.00 0.00 0.00 4.02
1840 2642 2.040278 ACTGCAGCCTGTCCTTTGAATA 59.960 45.455 15.27 0.00 0.00 1.75
1853 2655 3.807538 CGGACATGCACTGCAGCC 61.808 66.667 15.27 5.76 43.65 4.85
1861 2663 2.234661 AGATGAAGAACTCGGACATGCA 59.765 45.455 0.00 0.00 0.00 3.96
2202 3009 5.010719 CCAGCTTAATACGGAGAGTAATCCA 59.989 44.000 0.00 0.00 39.53 3.41
2835 3674 1.400242 GCTTCGGCACAAACATGACTC 60.400 52.381 0.00 0.00 41.33 3.36
2932 3771 2.963371 ACGTCTCGTGCCCTCTTC 59.037 61.111 0.00 0.00 39.18 2.87
3153 3993 5.952347 TGCAAGGACTGAAGAGTAAGAGATA 59.048 40.000 0.00 0.00 30.16 1.98


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

AutoCloner maintained by Alex Coulton.