Multiple sequence alignment - TraesCS3B01G210400

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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 TraesCS3B01G210400 chr3B 100.000 2779 0 0 1 2779 246502659 246505437 0.000000e+00 5132.0
1 TraesCS3B01G210400 chr3B 97.436 39 1 0 1240 1278 259702050 259702012 1.790000e-07 67.6
2 TraesCS3B01G210400 chr3B 90.000 50 5 0 47 96 5899556 5899507 6.420000e-07 65.8
3 TraesCS3B01G210400 chr3B 100.000 30 0 0 878 907 707270167 707270196 3.870000e-04 56.5
4 TraesCS3B01G210400 chr3A 88.491 1173 61 30 362 1501 208454401 208455532 0.000000e+00 1351.0
5 TraesCS3B01G210400 chr3A 88.612 922 77 11 1536 2443 208455540 208456447 0.000000e+00 1096.0
6 TraesCS3B01G210400 chr3A 90.154 325 30 1 2457 2779 208456431 208456755 3.310000e-114 422.0
7 TraesCS3B01G210400 chr3A 89.068 311 28 4 2471 2778 600067117 600066810 5.620000e-102 381.0
8 TraesCS3B01G210400 chr3D 86.525 1269 103 19 1539 2778 170931109 170932338 0.000000e+00 1334.0
9 TraesCS3B01G210400 chr3D 87.244 878 72 26 100 957 170929707 170930564 0.000000e+00 965.0
10 TraesCS3B01G210400 chr3D 86.257 553 37 22 955 1501 170930593 170931112 5.200000e-157 564.0
11 TraesCS3B01G210400 chr3D 83.146 89 7 2 1190 1278 212868911 212868991 1.070000e-09 75.0
12 TraesCS3B01G210400 chr5D 90.728 302 23 3 2480 2779 522481257 522481555 5.580000e-107 398.0
13 TraesCS3B01G210400 chr2D 88.580 324 29 6 2457 2778 293714939 293715256 1.210000e-103 387.0
14 TraesCS3B01G210400 chr2D 83.544 79 5 2 1199 1277 291911397 291911467 1.790000e-07 67.6
15 TraesCS3B01G210400 chr7D 88.218 331 24 8 2457 2779 140800357 140800034 5.620000e-102 381.0
16 TraesCS3B01G210400 chr4B 87.915 331 24 10 2457 2779 529352858 529352536 2.610000e-100 375.0
17 TraesCS3B01G210400 chr5A 87.613 331 26 9 2457 2779 649235977 649235654 1.220000e-98 370.0
18 TraesCS3B01G210400 chr5A 89.109 303 22 5 2485 2779 521195350 521195649 1.570000e-97 366.0
19 TraesCS3B01G210400 chr4D 87.311 331 28 8 2457 2779 300795282 300795606 1.570000e-97 366.0
20 TraesCS3B01G210400 chr6B 87.009 331 29 7 2457 2779 132429241 132428917 7.320000e-96 361.0
21 TraesCS3B01G210400 chr6B 100.000 39 0 0 1240 1278 471136077 471136115 3.840000e-09 73.1
22 TraesCS3B01G210400 chr2A 88.040 301 31 3 2480 2778 360779572 360779869 4.400000e-93 351.0
23 TraesCS3B01G210400 chr7A 97.436 39 1 0 1240 1278 238551311 238551273 1.790000e-07 67.6
24 TraesCS3B01G210400 chr7A 97.368 38 1 0 1241 1278 327312285 327312322 6.420000e-07 65.8
25 TraesCS3B01G210400 chr1D 97.436 39 1 0 60 98 225696071 225696109 1.790000e-07 67.6
26 TraesCS3B01G210400 chrUn 88.679 53 6 0 44 96 34299125 34299177 6.420000e-07 65.8
27 TraesCS3B01G210400 chrUn 88.679 53 6 0 44 96 372848289 372848341 6.420000e-07 65.8
28 TraesCS3B01G210400 chr6A 97.368 38 1 0 1241 1278 155935681 155935718 6.420000e-07 65.8
29 TraesCS3B01G210400 chr4A 81.333 75 12 2 266 339 659820286 659820213 2.990000e-05 60.2


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 TraesCS3B01G210400 chr3B 246502659 246505437 2778 False 5132.000000 5132 100.000000 1 2779 1 chr3B.!!$F1 2778
1 TraesCS3B01G210400 chr3A 208454401 208456755 2354 False 956.333333 1351 89.085667 362 2779 3 chr3A.!!$F1 2417
2 TraesCS3B01G210400 chr3D 170929707 170932338 2631 False 954.333333 1334 86.675333 100 2778 3 chr3D.!!$F2 2678

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
857 875 0.303493 CCGTGTGAACAGTGTTTCGG 59.697 55.0 10.45 16.57 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 2240 0.107654 AGAATCCCGCCCGAAAAGAG 60.108 55.0 0.0 0.0 0.0 2.85 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
34 35 4.946255 CGTTAATGACGCTGCTATTATGG 58.054 43.478 0.00 0.00 45.86 2.74
35 36 4.666655 CGTTAATGACGCTGCTATTATGGC 60.667 45.833 0.00 0.00 45.86 4.40
40 41 1.502231 CGCTGCTATTATGGCGTTCT 58.498 50.000 0.00 0.00 42.23 3.01
41 42 1.457303 CGCTGCTATTATGGCGTTCTC 59.543 52.381 0.00 0.00 42.23 2.87
42 43 2.483876 GCTGCTATTATGGCGTTCTCA 58.516 47.619 0.00 0.00 0.00 3.27
43 44 2.221981 GCTGCTATTATGGCGTTCTCAC 59.778 50.000 0.00 0.00 0.00 3.51
44 45 3.457234 CTGCTATTATGGCGTTCTCACA 58.543 45.455 0.00 0.00 0.00 3.58
45 46 4.060900 CTGCTATTATGGCGTTCTCACAT 58.939 43.478 0.00 0.00 0.00 3.21
46 47 5.208463 TGCTATTATGGCGTTCTCACATA 57.792 39.130 0.00 0.00 0.00 2.29
47 48 5.606505 TGCTATTATGGCGTTCTCACATAA 58.393 37.500 0.00 0.00 40.23 1.90
48 49 5.696270 TGCTATTATGGCGTTCTCACATAAG 59.304 40.000 0.00 0.00 39.56 1.73
49 50 5.696724 GCTATTATGGCGTTCTCACATAAGT 59.303 40.000 0.00 0.00 39.56 2.24
51 52 2.831685 TGGCGTTCTCACATAAGTGT 57.168 45.000 0.00 0.00 46.01 3.55
52 53 2.683968 TGGCGTTCTCACATAAGTGTC 58.316 47.619 0.00 0.00 46.01 3.67
53 54 2.000447 GGCGTTCTCACATAAGTGTCC 59.000 52.381 0.00 0.00 46.01 4.02
54 55 2.353803 GGCGTTCTCACATAAGTGTCCT 60.354 50.000 0.00 0.00 46.01 3.85
55 56 3.326747 GCGTTCTCACATAAGTGTCCTT 58.673 45.455 0.00 0.00 46.01 3.36
56 57 3.746492 GCGTTCTCACATAAGTGTCCTTT 59.254 43.478 0.00 0.00 46.01 3.11
57 58 4.213482 GCGTTCTCACATAAGTGTCCTTTT 59.787 41.667 0.00 0.00 46.01 2.27
58 59 5.277828 GCGTTCTCACATAAGTGTCCTTTTT 60.278 40.000 0.00 0.00 46.01 1.94
59 60 6.073440 GCGTTCTCACATAAGTGTCCTTTTTA 60.073 38.462 0.00 0.00 46.01 1.52
60 61 7.510630 CGTTCTCACATAAGTGTCCTTTTTAG 58.489 38.462 0.00 0.00 46.01 1.85
61 62 7.170998 CGTTCTCACATAAGTGTCCTTTTTAGT 59.829 37.037 0.00 0.00 46.01 2.24
62 63 8.837389 GTTCTCACATAAGTGTCCTTTTTAGTT 58.163 33.333 0.00 0.00 46.01 2.24
63 64 8.603242 TCTCACATAAGTGTCCTTTTTAGTTC 57.397 34.615 0.00 0.00 46.01 3.01
64 65 7.384115 TCTCACATAAGTGTCCTTTTTAGTTCG 59.616 37.037 0.00 0.00 46.01 3.95
65 66 7.211573 TCACATAAGTGTCCTTTTTAGTTCGA 58.788 34.615 0.00 0.00 46.01 3.71
66 67 7.384115 TCACATAAGTGTCCTTTTTAGTTCGAG 59.616 37.037 0.00 0.00 46.01 4.04
67 68 6.147328 ACATAAGTGTCCTTTTTAGTTCGAGC 59.853 38.462 0.00 0.00 31.41 5.03
68 69 4.338379 AGTGTCCTTTTTAGTTCGAGCT 57.662 40.909 7.07 7.07 0.00 4.09
69 70 4.308265 AGTGTCCTTTTTAGTTCGAGCTC 58.692 43.478 4.56 2.73 0.00 4.09
70 71 4.056050 GTGTCCTTTTTAGTTCGAGCTCA 58.944 43.478 15.40 0.00 0.00 4.26
71 72 4.691216 GTGTCCTTTTTAGTTCGAGCTCAT 59.309 41.667 15.40 0.00 0.00 2.90
72 73 5.867716 GTGTCCTTTTTAGTTCGAGCTCATA 59.132 40.000 15.40 0.00 0.00 2.15
73 74 6.535508 GTGTCCTTTTTAGTTCGAGCTCATAT 59.464 38.462 15.40 0.00 0.00 1.78
74 75 6.535150 TGTCCTTTTTAGTTCGAGCTCATATG 59.465 38.462 15.40 0.00 0.00 1.78
75 76 6.757010 GTCCTTTTTAGTTCGAGCTCATATGA 59.243 38.462 15.40 5.07 0.00 2.15
76 77 6.980978 TCCTTTTTAGTTCGAGCTCATATGAG 59.019 38.462 25.64 25.64 44.75 2.90
90 91 6.922247 CTCATATGAGCTTGAGTGAACAAT 57.078 37.500 19.47 0.00 35.66 2.71
92 93 8.429493 CTCATATGAGCTTGAGTGAACAATAA 57.571 34.615 19.47 0.00 35.66 1.40
93 94 8.791327 TCATATGAGCTTGAGTGAACAATAAA 57.209 30.769 0.00 0.00 0.00 1.40
94 95 9.230122 TCATATGAGCTTGAGTGAACAATAAAA 57.770 29.630 0.00 0.00 0.00 1.52
97 98 6.913170 TGAGCTTGAGTGAACAATAAAATCC 58.087 36.000 0.00 0.00 0.00 3.01
98 99 6.071952 TGAGCTTGAGTGAACAATAAAATCCC 60.072 38.462 0.00 0.00 0.00 3.85
99 100 5.185828 AGCTTGAGTGAACAATAAAATCCCC 59.814 40.000 0.00 0.00 0.00 4.81
100 101 5.624509 GCTTGAGTGAACAATAAAATCCCCC 60.625 44.000 0.00 0.00 0.00 5.40
101 102 5.004361 TGAGTGAACAATAAAATCCCCCA 57.996 39.130 0.00 0.00 0.00 4.96
102 103 5.398236 TGAGTGAACAATAAAATCCCCCAA 58.602 37.500 0.00 0.00 0.00 4.12
103 104 5.841237 TGAGTGAACAATAAAATCCCCCAAA 59.159 36.000 0.00 0.00 0.00 3.28
104 105 6.327626 TGAGTGAACAATAAAATCCCCCAAAA 59.672 34.615 0.00 0.00 0.00 2.44
105 106 7.142995 AGTGAACAATAAAATCCCCCAAAAA 57.857 32.000 0.00 0.00 0.00 1.94
167 168 8.245701 TGTGACAAAGTTTGGTAAATGTTTTC 57.754 30.769 19.45 4.84 34.12 2.29
169 170 8.379902 GTGACAAAGTTTGGTAAATGTTTTCAG 58.620 33.333 19.45 0.00 34.12 3.02
172 173 6.902224 AAGTTTGGTAAATGTTTTCAGTGC 57.098 33.333 0.00 0.00 0.00 4.40
180 181 3.756933 ATGTTTTCAGTGCCTTGCAAT 57.243 38.095 0.00 0.00 41.47 3.56
190 191 2.028748 GTGCCTTGCAATGTTTCATCCT 60.029 45.455 0.00 0.00 41.47 3.24
194 195 4.800249 GCCTTGCAATGTTTCATCCTGAAA 60.800 41.667 0.00 0.00 43.37 2.69
195 196 5.484715 CCTTGCAATGTTTCATCCTGAAAT 58.515 37.500 0.00 0.00 46.55 2.17
197 198 5.725325 TGCAATGTTTCATCCTGAAATGA 57.275 34.783 5.67 0.00 46.55 2.57
198 199 5.472148 TGCAATGTTTCATCCTGAAATGAC 58.528 37.500 5.67 0.00 46.55 3.06
199 200 5.010820 TGCAATGTTTCATCCTGAAATGACA 59.989 36.000 5.67 1.36 46.55 3.58
201 202 7.093858 TGCAATGTTTCATCCTGAAATGACATA 60.094 33.333 5.67 0.00 46.55 2.29
202 203 7.221452 GCAATGTTTCATCCTGAAATGACATAC 59.779 37.037 5.67 0.28 46.55 2.39
203 204 6.757897 TGTTTCATCCTGAAATGACATACC 57.242 37.500 5.67 0.00 46.55 2.73
204 205 6.484288 TGTTTCATCCTGAAATGACATACCT 58.516 36.000 5.67 0.00 46.55 3.08
206 207 7.770433 TGTTTCATCCTGAAATGACATACCTAG 59.230 37.037 5.67 0.00 46.55 3.02
211 212 7.113658 TCCTGAAATGACATACCTAGAAGTC 57.886 40.000 0.00 0.00 0.00 3.01
218 219 2.165845 ACATACCTAGAAGTCGTGGCAC 59.834 50.000 7.79 7.79 0.00 5.01
225 226 2.365582 AGAAGTCGTGGCACAAAAACT 58.634 42.857 19.09 11.72 44.16 2.66
226 227 2.097466 AGAAGTCGTGGCACAAAAACTG 59.903 45.455 19.09 0.00 44.16 3.16
227 228 0.738389 AGTCGTGGCACAAAAACTGG 59.262 50.000 19.09 0.00 44.16 4.00
275 276 8.568732 AGTGTTGATTTTGTATTTTTACCACG 57.431 30.769 0.00 0.00 0.00 4.94
280 281 9.453325 TTGATTTTGTATTTTTACCACGACTTC 57.547 29.630 0.00 0.00 0.00 3.01
299 300 6.313658 CGACTTCCACAAATGTCATTCTATGA 59.686 38.462 0.00 0.00 36.84 2.15
318 319 8.619146 TCTATGACGAAATTTTGCAATCATTC 57.381 30.769 13.09 10.39 0.00 2.67
329 331 9.976255 AATTTTGCAATCATTCGAAACATTATG 57.024 25.926 0.00 0.00 0.00 1.90
395 402 9.840427 AATATTTTCAGATTTTACTGTTCACCG 57.160 29.630 0.00 0.00 38.79 4.94
399 406 3.125316 CAGATTTTACTGTTCACCGGCTC 59.875 47.826 0.00 0.00 33.73 4.70
408 415 3.753434 CACCGGCTCGAGCTCAGT 61.753 66.667 34.46 25.25 41.70 3.41
414 421 1.066303 CGGCTCGAGCTCAGTTAATCT 59.934 52.381 34.46 0.00 41.70 2.40
416 423 2.468831 GCTCGAGCTCAGTTAATCTGG 58.531 52.381 29.88 0.00 43.76 3.86
534 542 4.893608 TCGAATCATGAGACCTGACAAAA 58.106 39.130 0.09 0.00 0.00 2.44
535 543 5.304778 TCGAATCATGAGACCTGACAAAAA 58.695 37.500 0.09 0.00 0.00 1.94
561 571 1.728971 GGTTTCTCTGTGTGATCTGCG 59.271 52.381 0.00 0.00 0.00 5.18
563 573 1.256812 TTCTCTGTGTGATCTGCGGA 58.743 50.000 0.00 0.00 0.00 5.54
570 580 1.224592 GTGATCTGCGGAACCCCAT 59.775 57.895 0.00 0.00 0.00 4.00
634 650 0.758123 AGCAGATCCTAAGCTGGAGC 59.242 55.000 0.11 0.11 42.38 4.70
806 824 4.384247 CAGAGCGAAAGAGGCGATAAATAG 59.616 45.833 0.00 0.00 35.00 1.73
812 830 1.687123 AGAGGCGATAAATAGTGCGGT 59.313 47.619 0.00 0.00 0.00 5.68
821 839 0.398696 AATAGTGCGGTGGTTGACCA 59.601 50.000 0.00 0.00 46.55 4.02
853 871 1.151777 CGCTCCGTGTGAACAGTGTT 61.152 55.000 8.61 8.61 0.00 3.32
856 874 1.257936 CTCCGTGTGAACAGTGTTTCG 59.742 52.381 10.45 12.13 0.00 3.46
857 875 0.303493 CCGTGTGAACAGTGTTTCGG 59.697 55.000 10.45 16.57 0.00 4.30
895 920 4.030178 CGTTTGTACGTCGTTTGTTTGTTC 60.030 41.667 1.78 0.00 42.72 3.18
992 1054 1.136984 CACTCCTACTCGTCGCACC 59.863 63.158 0.00 0.00 0.00 5.01
1083 1147 1.927710 GCCAAGCAAAGAACGAAGCAG 60.928 52.381 0.00 0.00 0.00 4.24
1144 1214 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1145 1215 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1146 1216 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1147 1217 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1148 1218 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1149 1219 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1150 1220 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1151 1221 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1152 1222 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1153 1223 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1154 1224 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
1155 1225 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1156 1226 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1157 1227 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
1158 1228 3.036959 GGGAGGGAGGGAGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1159 1229 2.612251 GGAGGGAGGGAGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
1160 1230 2.015726 GGAGGGAGGGAGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
1161 1231 1.541672 GAGGGAGGGAGGGAGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
1162 1232 0.996762 GAGGGAGGGAGGGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
1163 1233 0.998945 AGGGAGGGAGGGAGAGAGAG 60.999 65.000 0.00 0.00 0.00 3.20
1164 1234 0.996762 GGGAGGGAGGGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
1165 1235 0.478507 GGAGGGAGGGAGAGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
1166 1236 0.478507 GAGGGAGGGAGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1167 1237 0.047176 AGGGAGGGAGAGAGAGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
1168 1238 1.158007 GGGAGGGAGAGAGAGAGGAT 58.842 60.000 0.00 0.00 0.00 3.24
1169 1239 1.503347 GGGAGGGAGAGAGAGAGGATT 59.497 57.143 0.00 0.00 0.00 3.01
1170 1240 2.490902 GGGAGGGAGAGAGAGAGGATTC 60.491 59.091 0.00 0.00 0.00 2.52
1178 1248 3.111484 GAGAGAGAGGATTCCCTGGTTT 58.889 50.000 0.00 0.00 44.53 3.27
1474 1544 2.523902 CAGGTTTGCCTTGCCCCA 60.524 61.111 0.00 0.00 44.18 4.96
1501 1571 3.403038 CATCCCCACCGATTGATTAGTC 58.597 50.000 0.00 0.00 0.00 2.59
1503 1573 3.918566 TCCCCACCGATTGATTAGTCTA 58.081 45.455 0.00 0.00 0.00 2.59
1504 1574 3.895656 TCCCCACCGATTGATTAGTCTAG 59.104 47.826 0.00 0.00 0.00 2.43
1505 1575 3.006967 CCCCACCGATTGATTAGTCTAGG 59.993 52.174 0.00 0.00 0.00 3.02
1508 1578 4.827835 CCACCGATTGATTAGTCTAGGAGA 59.172 45.833 0.00 0.00 0.00 3.71
1509 1579 5.302059 CCACCGATTGATTAGTCTAGGAGAA 59.698 44.000 0.00 0.00 0.00 2.87
1510 1580 6.442952 CACCGATTGATTAGTCTAGGAGAAG 58.557 44.000 0.00 0.00 0.00 2.85
1511 1581 6.263392 CACCGATTGATTAGTCTAGGAGAAGA 59.737 42.308 0.00 0.00 0.00 2.87
1512 1582 6.488683 ACCGATTGATTAGTCTAGGAGAAGAG 59.511 42.308 0.00 0.00 0.00 2.85
1513 1583 6.712998 CCGATTGATTAGTCTAGGAGAAGAGA 59.287 42.308 0.00 0.00 0.00 3.10
1514 1584 7.229707 CCGATTGATTAGTCTAGGAGAAGAGAA 59.770 40.741 0.00 0.00 0.00 2.87
1515 1585 8.625651 CGATTGATTAGTCTAGGAGAAGAGAAA 58.374 37.037 0.00 0.00 0.00 2.52
1518 1588 7.763356 TGATTAGTCTAGGAGAAGAGAAAACG 58.237 38.462 0.00 0.00 0.00 3.60
1519 1589 4.443913 AGTCTAGGAGAAGAGAAAACGC 57.556 45.455 0.00 0.00 0.00 4.84
1520 1590 4.083565 AGTCTAGGAGAAGAGAAAACGCT 58.916 43.478 0.00 0.00 0.00 5.07
1521 1591 4.157105 AGTCTAGGAGAAGAGAAAACGCTC 59.843 45.833 0.00 0.00 35.11 5.03
1522 1592 4.157105 GTCTAGGAGAAGAGAAAACGCTCT 59.843 45.833 0.00 0.00 46.81 4.09
1523 1593 5.354792 GTCTAGGAGAAGAGAAAACGCTCTA 59.645 44.000 0.00 0.00 44.18 2.43
1524 1594 4.443913 AGGAGAAGAGAAAACGCTCTAC 57.556 45.455 0.00 0.00 44.18 2.59
1525 1595 3.119779 AGGAGAAGAGAAAACGCTCTACG 60.120 47.826 0.00 0.00 44.18 3.51
1536 1606 1.868469 CGCTCTACGCTACTCCTAGT 58.132 55.000 0.00 0.00 36.13 2.57
1537 1607 3.023946 CGCTCTACGCTACTCCTAGTA 57.976 52.381 0.00 0.00 36.13 1.82
1546 1616 3.190953 CGCTACTCCTAGTATACTTGCCC 59.809 52.174 11.40 0.00 29.08 5.36
1600 1670 3.754965 TGGAGTGGAGATCAACCTTTTG 58.245 45.455 9.71 0.00 0.00 2.44
1613 1683 3.982576 ACCTTTTGTGTTTCATCCGTC 57.017 42.857 0.00 0.00 0.00 4.79
1628 1698 4.887655 TCATCCGTCGTATATATGCAGGAT 59.112 41.667 17.89 17.89 37.70 3.24
1700 1770 2.044650 CGAGGACCGGTGAGGGTA 60.045 66.667 14.63 0.00 46.96 3.69
1712 1782 2.188817 GTGAGGGTAGTGATGGAGGTT 58.811 52.381 0.00 0.00 0.00 3.50
1983 2064 2.661979 CGTAGCTTCGCTTTTCGCTTTT 60.662 45.455 0.00 0.00 40.44 2.27
1985 2066 1.053048 GCTTCGCTTTTCGCTTTTCC 58.947 50.000 0.00 0.00 38.27 3.13
1986 2067 1.686464 CTTCGCTTTTCGCTTTTCCC 58.314 50.000 0.00 0.00 38.27 3.97
1987 2068 1.266989 CTTCGCTTTTCGCTTTTCCCT 59.733 47.619 0.00 0.00 38.27 4.20
1988 2069 1.314730 TCGCTTTTCGCTTTTCCCTT 58.685 45.000 0.00 0.00 38.27 3.95
1990 2071 2.051423 CGCTTTTCGCTTTTCCCTTTC 58.949 47.619 0.00 0.00 36.13 2.62
1991 2072 2.404215 GCTTTTCGCTTTTCCCTTTCC 58.596 47.619 0.00 0.00 35.14 3.13
1992 2073 2.035961 GCTTTTCGCTTTTCCCTTTCCT 59.964 45.455 0.00 0.00 35.14 3.36
1993 2074 3.254903 GCTTTTCGCTTTTCCCTTTCCTA 59.745 43.478 0.00 0.00 35.14 2.94
1994 2075 4.795268 CTTTTCGCTTTTCCCTTTCCTAC 58.205 43.478 0.00 0.00 0.00 3.18
1995 2076 2.088950 TCGCTTTTCCCTTTCCTACG 57.911 50.000 0.00 0.00 0.00 3.51
1996 2077 1.345415 TCGCTTTTCCCTTTCCTACGT 59.655 47.619 0.00 0.00 0.00 3.57
1997 2078 2.148768 CGCTTTTCCCTTTCCTACGTT 58.851 47.619 0.00 0.00 0.00 3.99
1998 2079 2.095919 CGCTTTTCCCTTTCCTACGTTG 60.096 50.000 0.00 0.00 0.00 4.10
1999 2080 3.143728 GCTTTTCCCTTTCCTACGTTGA 58.856 45.455 0.00 0.00 0.00 3.18
2000 2081 3.756963 GCTTTTCCCTTTCCTACGTTGAT 59.243 43.478 0.00 0.00 0.00 2.57
2076 2172 1.537202 GCTGGACCTGAACATTGTGAC 59.463 52.381 1.91 0.00 0.00 3.67
2144 2240 1.009675 CGCATGTTTATGGCCGAGC 60.010 57.895 0.00 0.00 34.79 5.03
2152 2248 1.651987 TTATGGCCGAGCTCTTTTCG 58.348 50.000 12.85 0.00 37.78 3.46
2176 2279 3.378427 GCGGGATTCTGCAGAACTAAAAT 59.622 43.478 30.66 14.43 44.43 1.82
2177 2280 4.142381 GCGGGATTCTGCAGAACTAAAATT 60.142 41.667 30.66 13.65 44.43 1.82
2178 2281 5.622233 GCGGGATTCTGCAGAACTAAAATTT 60.622 40.000 30.66 12.88 44.43 1.82
2181 2284 8.026607 CGGGATTCTGCAGAACTAAAATTTTTA 58.973 33.333 30.66 4.74 36.80 1.52
2211 2314 3.954200 TCTGCTTTCCACATAATCTGCA 58.046 40.909 0.00 0.00 0.00 4.41
2217 2320 3.165058 TCCACATAATCTGCAGTCGAC 57.835 47.619 14.67 7.70 0.00 4.20
2234 2337 5.347364 CAGTCGACTTCTTTTCTGAGATTCC 59.653 44.000 17.26 0.00 0.00 3.01
2258 2361 8.160765 TCCAGTTTAAGATTGTGGATTCAGTTA 58.839 33.333 0.00 0.00 32.21 2.24
2271 2374 4.500477 GGATTCAGTTATGCGTTGAAATGC 59.500 41.667 0.14 0.14 41.27 3.56
2272 2375 3.485947 TCAGTTATGCGTTGAAATGCC 57.514 42.857 4.85 0.00 40.18 4.40
2275 2378 1.919918 GTTATGCGTTGAAATGCCTGC 59.080 47.619 4.85 0.00 40.18 4.85
2281 2385 2.584791 CGTTGAAATGCCTGCAAGTAC 58.415 47.619 0.00 0.00 0.00 2.73
2300 2404 7.573283 GCAAGTACCCTTAGACAGAAATTGTTC 60.573 40.741 0.00 0.00 41.05 3.18
2305 2409 5.065218 CCCTTAGACAGAAATTGTTCGATGG 59.935 44.000 0.00 0.00 41.05 3.51
2307 2411 6.183360 CCTTAGACAGAAATTGTTCGATGGAC 60.183 42.308 0.00 0.00 41.05 4.02
2352 2456 9.000486 TCGAATAGTATCTTGTCGAATATGAGT 58.000 33.333 2.85 0.00 37.75 3.41
2353 2457 9.056306 CGAATAGTATCTTGTCGAATATGAGTG 57.944 37.037 0.00 0.00 33.63 3.51
2368 2472 7.464045 CGAATATGAGTGCGAAAGTGATTTACA 60.464 37.037 0.00 0.00 0.00 2.41
2433 2541 3.677596 AGTTTTGTTCGTTGCAAAAGTGG 59.322 39.130 0.00 0.00 43.59 4.00
2435 2543 0.179124 TGTTCGTTGCAAAAGTGGGC 60.179 50.000 0.00 0.00 0.00 5.36
2437 2545 1.377366 TTCGTTGCAAAAGTGGGCGA 61.377 50.000 0.00 0.58 0.00 5.54
2438 2546 1.064946 CGTTGCAAAAGTGGGCGAA 59.935 52.632 0.00 0.00 0.00 4.70
2439 2547 1.206115 CGTTGCAAAAGTGGGCGAAC 61.206 55.000 0.00 0.00 0.00 3.95
2440 2548 0.102300 GTTGCAAAAGTGGGCGAACT 59.898 50.000 0.00 0.00 0.00 3.01
2441 2549 1.335496 GTTGCAAAAGTGGGCGAACTA 59.665 47.619 0.00 0.00 0.00 2.24
2442 2550 1.681538 TGCAAAAGTGGGCGAACTAA 58.318 45.000 0.00 0.00 0.00 2.24
2443 2551 1.606668 TGCAAAAGTGGGCGAACTAAG 59.393 47.619 0.00 0.00 0.00 2.18
2444 2552 1.607148 GCAAAAGTGGGCGAACTAAGT 59.393 47.619 0.00 0.00 0.00 2.24
2445 2553 2.034179 GCAAAAGTGGGCGAACTAAGTT 59.966 45.455 0.00 0.00 0.00 2.66
2446 2554 3.852205 GCAAAAGTGGGCGAACTAAGTTC 60.852 47.826 0.00 0.00 38.97 3.01
2447 2555 2.922740 AAGTGGGCGAACTAAGTTCA 57.077 45.000 0.00 0.00 42.05 3.18
2448 2556 2.922740 AGTGGGCGAACTAAGTTCAA 57.077 45.000 0.00 0.00 42.05 2.69
2449 2557 3.202829 AGTGGGCGAACTAAGTTCAAA 57.797 42.857 0.00 0.00 42.05 2.69
2450 2558 3.547746 AGTGGGCGAACTAAGTTCAAAA 58.452 40.909 0.00 0.00 42.05 2.44
2451 2559 3.949113 AGTGGGCGAACTAAGTTCAAAAA 59.051 39.130 0.00 0.00 42.05 1.94
2474 2582 6.838198 AAAAGAAAAATGGGCGAACTAAAC 57.162 33.333 0.00 0.00 0.00 2.01
2536 2646 1.424403 CTCGCGTGTTGTTCATGGTA 58.576 50.000 5.77 0.00 33.96 3.25
2550 2660 7.135591 TGTTCATGGTACCATCATCATCTTA 57.864 36.000 24.99 0.00 33.90 2.10
2580 2690 1.134340 AGTGTTGGCACCTGTAAACGA 60.134 47.619 0.00 0.00 46.35 3.85
2644 2754 2.068519 TGCTCATCACGTAACTTGCTG 58.931 47.619 0.00 0.00 0.00 4.41
2648 2758 3.925379 TCATCACGTAACTTGCTGTCAT 58.075 40.909 0.00 0.00 0.00 3.06
2723 2833 4.560919 CGAGTTTATACCCAGGTATGCCTC 60.561 50.000 17.85 16.36 44.97 4.70
2761 2871 1.305201 TCTTGAGAACACCAAACGCC 58.695 50.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.666655 CGCCATAATAGCAGCGTCATTAAC 60.667 45.833 0.00 0.00 43.45 2.01
14 15 3.431912 CGCCATAATAGCAGCGTCATTAA 59.568 43.478 0.00 0.00 43.45 1.40
15 16 2.993220 CGCCATAATAGCAGCGTCATTA 59.007 45.455 0.00 0.00 43.45 1.90
16 17 1.800586 CGCCATAATAGCAGCGTCATT 59.199 47.619 0.00 0.00 43.45 2.57
17 18 1.432514 CGCCATAATAGCAGCGTCAT 58.567 50.000 0.00 0.00 43.45 3.06
18 19 2.899153 CGCCATAATAGCAGCGTCA 58.101 52.632 0.00 0.00 43.45 4.35
22 23 2.221981 GTGAGAACGCCATAATAGCAGC 59.778 50.000 0.00 0.00 0.00 5.25
23 24 3.457234 TGTGAGAACGCCATAATAGCAG 58.543 45.455 0.00 0.00 0.00 4.24
24 25 3.535280 TGTGAGAACGCCATAATAGCA 57.465 42.857 0.00 0.00 0.00 3.49
25 26 5.696724 ACTTATGTGAGAACGCCATAATAGC 59.303 40.000 0.00 0.00 0.00 2.97
26 27 6.701841 ACACTTATGTGAGAACGCCATAATAG 59.298 38.462 15.13 0.00 46.55 1.73
27 28 6.578944 ACACTTATGTGAGAACGCCATAATA 58.421 36.000 15.13 0.00 46.55 0.98
28 29 5.428253 ACACTTATGTGAGAACGCCATAAT 58.572 37.500 15.13 0.00 46.55 1.28
29 30 4.827692 ACACTTATGTGAGAACGCCATAA 58.172 39.130 15.13 0.00 46.55 1.90
30 31 4.430007 GACACTTATGTGAGAACGCCATA 58.570 43.478 15.13 0.00 46.55 2.74
31 32 3.262420 GACACTTATGTGAGAACGCCAT 58.738 45.455 15.13 0.00 46.55 4.40
32 33 2.611971 GGACACTTATGTGAGAACGCCA 60.612 50.000 15.13 0.00 46.55 5.69
33 34 2.000447 GGACACTTATGTGAGAACGCC 59.000 52.381 15.13 3.65 46.55 5.68
34 35 2.960819 AGGACACTTATGTGAGAACGC 58.039 47.619 15.13 0.00 46.55 4.84
35 36 5.924475 AAAAGGACACTTATGTGAGAACG 57.076 39.130 15.13 0.00 46.55 3.95
36 37 8.379457 ACTAAAAAGGACACTTATGTGAGAAC 57.621 34.615 15.13 3.05 46.55 3.01
37 38 8.974060 AACTAAAAAGGACACTTATGTGAGAA 57.026 30.769 15.13 0.00 46.55 2.87
38 39 7.384115 CGAACTAAAAAGGACACTTATGTGAGA 59.616 37.037 15.13 0.00 46.55 3.27
39 40 7.384115 TCGAACTAAAAAGGACACTTATGTGAG 59.616 37.037 15.13 2.70 46.55 3.51
40 41 7.211573 TCGAACTAAAAAGGACACTTATGTGA 58.788 34.615 15.13 0.00 46.55 3.58
42 43 6.147328 GCTCGAACTAAAAAGGACACTTATGT 59.853 38.462 0.00 0.00 43.71 2.29
43 44 6.369065 AGCTCGAACTAAAAAGGACACTTATG 59.631 38.462 0.00 0.00 35.41 1.90
44 45 6.465084 AGCTCGAACTAAAAAGGACACTTAT 58.535 36.000 0.00 0.00 35.41 1.73
45 46 5.850614 AGCTCGAACTAAAAAGGACACTTA 58.149 37.500 0.00 0.00 35.41 2.24
46 47 4.704965 AGCTCGAACTAAAAAGGACACTT 58.295 39.130 0.00 0.00 38.99 3.16
47 48 4.202223 TGAGCTCGAACTAAAAAGGACACT 60.202 41.667 9.64 0.00 0.00 3.55
48 49 4.056050 TGAGCTCGAACTAAAAAGGACAC 58.944 43.478 9.64 0.00 0.00 3.67
49 50 4.330944 TGAGCTCGAACTAAAAAGGACA 57.669 40.909 9.64 0.00 0.00 4.02
50 51 6.757010 TCATATGAGCTCGAACTAAAAAGGAC 59.243 38.462 9.64 0.00 0.00 3.85
51 52 6.873997 TCATATGAGCTCGAACTAAAAAGGA 58.126 36.000 9.64 0.00 0.00 3.36
52 53 7.171447 CTCATATGAGCTCGAACTAAAAAGG 57.829 40.000 19.47 0.00 35.13 3.11
67 68 6.922247 ATTGTTCACTCAAGCTCATATGAG 57.078 37.500 25.64 25.64 46.69 2.90
68 69 8.791327 TTTATTGTTCACTCAAGCTCATATGA 57.209 30.769 5.07 5.07 0.00 2.15
71 72 8.677300 GGATTTTATTGTTCACTCAAGCTCATA 58.323 33.333 0.00 0.00 0.00 2.15
72 73 7.363268 GGGATTTTATTGTTCACTCAAGCTCAT 60.363 37.037 0.00 0.00 0.00 2.90
73 74 6.071952 GGGATTTTATTGTTCACTCAAGCTCA 60.072 38.462 0.00 0.00 0.00 4.26
74 75 6.325596 GGGATTTTATTGTTCACTCAAGCTC 58.674 40.000 0.00 0.00 0.00 4.09
75 76 5.185828 GGGGATTTTATTGTTCACTCAAGCT 59.814 40.000 0.00 0.00 0.00 3.74
76 77 5.410924 GGGGATTTTATTGTTCACTCAAGC 58.589 41.667 0.00 0.00 0.00 4.01
77 78 5.480073 TGGGGGATTTTATTGTTCACTCAAG 59.520 40.000 0.00 0.00 0.00 3.02
78 79 5.398236 TGGGGGATTTTATTGTTCACTCAA 58.602 37.500 0.00 0.00 0.00 3.02
79 80 5.004361 TGGGGGATTTTATTGTTCACTCA 57.996 39.130 0.00 0.00 0.00 3.41
80 81 5.993748 TTGGGGGATTTTATTGTTCACTC 57.006 39.130 0.00 0.00 0.00 3.51
81 82 6.755542 TTTTGGGGGATTTTATTGTTCACT 57.244 33.333 0.00 0.00 0.00 3.41
139 140 6.692486 ACATTTACCAAACTTTGTCACAACA 58.308 32.000 0.00 0.00 0.00 3.33
140 141 7.589574 AACATTTACCAAACTTTGTCACAAC 57.410 32.000 0.00 0.00 0.00 3.32
142 143 7.872993 TGAAAACATTTACCAAACTTTGTCACA 59.127 29.630 0.88 0.00 0.00 3.58
143 144 8.245701 TGAAAACATTTACCAAACTTTGTCAC 57.754 30.769 0.88 0.00 0.00 3.67
145 146 8.379902 CACTGAAAACATTTACCAAACTTTGTC 58.620 33.333 0.88 0.00 0.00 3.18
157 158 4.662468 TGCAAGGCACTGAAAACATTTA 57.338 36.364 0.00 0.00 40.86 1.40
167 168 2.512485 TGAAACATTGCAAGGCACTG 57.488 45.000 11.69 2.98 43.30 3.66
169 170 2.028748 AGGATGAAACATTGCAAGGCAC 60.029 45.455 11.69 3.53 38.71 5.01
190 191 6.330278 CACGACTTCTAGGTATGTCATTTCA 58.670 40.000 0.00 0.00 0.00 2.69
194 195 3.068307 GCCACGACTTCTAGGTATGTCAT 59.932 47.826 0.00 0.00 0.00 3.06
195 196 2.426024 GCCACGACTTCTAGGTATGTCA 59.574 50.000 0.00 0.00 0.00 3.58
197 198 2.165845 GTGCCACGACTTCTAGGTATGT 59.834 50.000 0.00 0.00 0.00 2.29
198 199 2.165641 TGTGCCACGACTTCTAGGTATG 59.834 50.000 0.00 0.00 0.00 2.39
199 200 2.453521 TGTGCCACGACTTCTAGGTAT 58.546 47.619 0.00 0.00 0.00 2.73
201 202 1.045407 TTGTGCCACGACTTCTAGGT 58.955 50.000 0.00 0.00 0.00 3.08
202 203 2.163818 TTTGTGCCACGACTTCTAGG 57.836 50.000 0.00 0.00 0.00 3.02
203 204 3.560068 AGTTTTTGTGCCACGACTTCTAG 59.440 43.478 0.00 0.00 0.00 2.43
204 205 3.311322 CAGTTTTTGTGCCACGACTTCTA 59.689 43.478 0.00 0.00 0.00 2.10
206 207 2.450160 CAGTTTTTGTGCCACGACTTC 58.550 47.619 0.00 0.00 0.00 3.01
211 212 2.956469 CACCAGTTTTTGTGCCACG 58.044 52.632 0.00 0.00 0.00 4.94
251 252 8.473796 GTCGTGGTAAAAATACAAAATCAACAC 58.526 33.333 0.00 0.00 0.00 3.32
252 253 8.407064 AGTCGTGGTAAAAATACAAAATCAACA 58.593 29.630 0.00 0.00 0.00 3.33
254 255 9.453325 GAAGTCGTGGTAAAAATACAAAATCAA 57.547 29.630 0.00 0.00 0.00 2.57
264 265 5.838531 TTTGTGGAAGTCGTGGTAAAAAT 57.161 34.783 0.00 0.00 0.00 1.82
265 266 5.125739 ACATTTGTGGAAGTCGTGGTAAAAA 59.874 36.000 0.00 0.00 0.00 1.94
270 271 2.218603 GACATTTGTGGAAGTCGTGGT 58.781 47.619 0.00 0.00 0.00 4.16
275 276 7.615582 TCATAGAATGACATTTGTGGAAGTC 57.384 36.000 1.39 0.00 33.59 3.01
299 300 6.199908 TGTTTCGAATGATTGCAAAATTTCGT 59.800 30.769 26.21 11.90 37.06 3.85
300 301 6.579583 TGTTTCGAATGATTGCAAAATTTCG 58.420 32.000 23.74 23.74 37.07 3.46
305 306 8.754230 TCATAATGTTTCGAATGATTGCAAAA 57.246 26.923 1.71 0.00 0.00 2.44
395 402 2.880963 AGATTAACTGAGCTCGAGCC 57.119 50.000 32.94 23.66 43.38 4.70
408 415 3.681594 GCACGAATCAGGACCCAGATTAA 60.682 47.826 9.17 0.00 33.35 1.40
414 421 0.327924 AATGCACGAATCAGGACCCA 59.672 50.000 0.00 0.00 0.00 4.51
416 423 3.689649 AGTAAAATGCACGAATCAGGACC 59.310 43.478 0.00 0.00 0.00 4.46
534 542 5.835280 AGATCACACAGAGAAACCCAATTTT 59.165 36.000 0.00 0.00 0.00 1.82
535 543 5.242393 CAGATCACACAGAGAAACCCAATTT 59.758 40.000 0.00 0.00 0.00 1.82
570 580 0.808125 ATAAATCGCGCCACAGCAAA 59.192 45.000 0.00 0.00 39.83 3.68
634 650 4.534794 AAGCGTTTGAAAAATTGGCAAG 57.465 36.364 5.96 0.00 0.00 4.01
812 830 2.513259 GGGTCCGTCTGGTCAACCA 61.513 63.158 1.20 1.20 45.30 3.67
821 839 3.069318 GAGCGAAGGGGTCCGTCT 61.069 66.667 0.00 0.00 37.18 4.18
853 871 1.599171 CGCAAATGTTTGACTGCCGAA 60.599 47.619 9.53 0.00 40.55 4.30
856 874 1.851658 AACGCAAATGTTTGACTGCC 58.148 45.000 9.53 0.00 40.55 4.85
877 902 2.022080 GCGAACAAACAAACGACGTAC 58.978 47.619 0.00 0.00 0.00 3.67
878 903 1.657594 TGCGAACAAACAAACGACGTA 59.342 42.857 0.00 0.00 0.00 3.57
879 904 0.443088 TGCGAACAAACAAACGACGT 59.557 45.000 0.00 0.00 0.00 4.34
880 905 0.828959 GTGCGAACAAACAAACGACG 59.171 50.000 0.00 0.00 0.00 5.12
881 906 1.185189 GGTGCGAACAAACAAACGAC 58.815 50.000 0.00 0.00 0.00 4.34
883 908 2.741122 TAGGTGCGAACAAACAAACG 57.259 45.000 0.00 0.00 0.00 3.60
885 910 5.353123 GGATAGATAGGTGCGAACAAACAAA 59.647 40.000 0.00 0.00 0.00 2.83
886 911 4.873827 GGATAGATAGGTGCGAACAAACAA 59.126 41.667 0.00 0.00 0.00 2.83
887 912 4.081365 TGGATAGATAGGTGCGAACAAACA 60.081 41.667 0.00 0.00 0.00 2.83
895 920 1.200252 CCGTCTGGATAGATAGGTGCG 59.800 57.143 0.00 0.00 37.49 5.34
928 958 3.626542 GTTACCGACGAAAACGCAG 57.373 52.632 0.00 0.00 0.00 5.18
1083 1147 4.264460 AGGAAGACAGACAGATGTGTTC 57.736 45.455 0.00 7.90 47.00 3.18
1127 1191 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
1130 1194 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1138 1208 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1144 1214 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
1145 1215 0.996762 TCTCTCTCTCCCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
1146 1216 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
1147 1217 0.478507 CCTCTCTCTCTCCCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
1148 1218 0.047176 TCCTCTCTCTCTCCCTCCCT 59.953 60.000 0.00 0.00 0.00 4.20
1149 1219 1.158007 ATCCTCTCTCTCTCCCTCCC 58.842 60.000 0.00 0.00 0.00 4.30
1150 1220 2.490902 GGAATCCTCTCTCTCTCCCTCC 60.491 59.091 0.00 0.00 0.00 4.30
1151 1221 2.490902 GGGAATCCTCTCTCTCTCCCTC 60.491 59.091 0.00 0.00 39.61 4.30
1152 1222 1.503347 GGGAATCCTCTCTCTCTCCCT 59.497 57.143 0.00 0.00 39.61 4.20
1153 1223 1.503347 AGGGAATCCTCTCTCTCTCCC 59.497 57.143 0.00 0.00 39.80 4.30
1154 1224 2.597455 CAGGGAATCCTCTCTCTCTCC 58.403 57.143 0.00 0.00 42.67 3.71
1155 1225 2.091333 ACCAGGGAATCCTCTCTCTCTC 60.091 54.545 0.00 0.00 42.67 3.20
1156 1226 1.936631 ACCAGGGAATCCTCTCTCTCT 59.063 52.381 0.00 0.00 42.67 3.10
1157 1227 2.470057 ACCAGGGAATCCTCTCTCTC 57.530 55.000 0.00 0.00 42.67 3.20
1158 1228 2.843113 CAAACCAGGGAATCCTCTCTCT 59.157 50.000 0.00 0.00 42.67 3.10
1159 1229 2.092699 CCAAACCAGGGAATCCTCTCTC 60.093 54.545 0.00 0.00 42.67 3.20
1160 1230 1.918957 CCAAACCAGGGAATCCTCTCT 59.081 52.381 0.00 0.00 42.67 3.10
1161 1231 1.636003 ACCAAACCAGGGAATCCTCTC 59.364 52.381 0.00 0.00 42.67 3.20
1162 1232 1.355720 CACCAAACCAGGGAATCCTCT 59.644 52.381 0.00 0.00 42.67 3.69
1163 1233 1.616994 CCACCAAACCAGGGAATCCTC 60.617 57.143 0.00 0.00 42.67 3.71
1164 1234 0.409484 CCACCAAACCAGGGAATCCT 59.591 55.000 0.00 0.00 46.26 3.24
1165 1235 1.257750 GCCACCAAACCAGGGAATCC 61.258 60.000 0.00 0.00 0.00 3.01
1166 1236 1.595093 CGCCACCAAACCAGGGAATC 61.595 60.000 0.00 0.00 0.00 2.52
1167 1237 1.606313 CGCCACCAAACCAGGGAAT 60.606 57.895 0.00 0.00 0.00 3.01
1168 1238 2.203422 CGCCACCAAACCAGGGAA 60.203 61.111 0.00 0.00 0.00 3.97
1169 1239 4.966787 GCGCCACCAAACCAGGGA 62.967 66.667 0.00 0.00 0.00 4.20
1170 1240 4.974721 AGCGCCACCAAACCAGGG 62.975 66.667 2.29 0.00 0.00 4.45
1211 1281 3.969802 GTTGCCGTTGCTGCTGCT 61.970 61.111 17.00 0.00 40.48 4.24
1323 1393 3.764218 AGAACAAGAAGAGAGACGGGTA 58.236 45.455 0.00 0.00 0.00 3.69
1474 1544 0.326618 AATCGGTGGGGATGGAGAGT 60.327 55.000 0.00 0.00 0.00 3.24
1501 1571 4.712122 AGAGCGTTTTCTCTTCTCCTAG 57.288 45.455 0.00 0.00 40.32 3.02
1503 1573 3.119779 CGTAGAGCGTTTTCTCTTCTCCT 60.120 47.826 0.00 0.00 42.88 3.69
1504 1574 3.172824 CGTAGAGCGTTTTCTCTTCTCC 58.827 50.000 0.00 0.00 42.88 3.71
1505 1575 2.595095 GCGTAGAGCGTTTTCTCTTCTC 59.405 50.000 0.00 0.00 42.88 2.87
1519 1589 6.091169 GCAAGTATACTAGGAGTAGCGTAGAG 59.909 46.154 5.65 0.00 38.14 2.43
1520 1590 5.931146 GCAAGTATACTAGGAGTAGCGTAGA 59.069 44.000 5.65 0.00 38.14 2.59
1521 1591 5.122082 GGCAAGTATACTAGGAGTAGCGTAG 59.878 48.000 5.65 0.00 40.07 3.51
1522 1592 4.999950 GGCAAGTATACTAGGAGTAGCGTA 59.000 45.833 5.65 0.00 33.66 4.42
1523 1593 3.819902 GGCAAGTATACTAGGAGTAGCGT 59.180 47.826 5.65 0.00 33.66 5.07
1524 1594 3.190953 GGGCAAGTATACTAGGAGTAGCG 59.809 52.174 5.65 0.00 33.66 4.26
1525 1595 4.409187 AGGGCAAGTATACTAGGAGTAGC 58.591 47.826 5.65 2.51 33.66 3.58
1526 1596 6.980416 AAAGGGCAAGTATACTAGGAGTAG 57.020 41.667 5.65 0.00 33.66 2.57
1527 1597 8.284435 TCTAAAAGGGCAAGTATACTAGGAGTA 58.716 37.037 5.65 0.00 34.82 2.59
1528 1598 7.130775 TCTAAAAGGGCAAGTATACTAGGAGT 58.869 38.462 5.65 0.00 0.00 3.85
1529 1599 7.598759 TCTAAAAGGGCAAGTATACTAGGAG 57.401 40.000 5.65 0.00 0.00 3.69
1530 1600 9.310449 CTATCTAAAAGGGCAAGTATACTAGGA 57.690 37.037 5.65 0.00 0.00 2.94
1531 1601 9.091220 ACTATCTAAAAGGGCAAGTATACTAGG 57.909 37.037 5.65 2.99 0.00 3.02
1534 1604 7.715686 GCAACTATCTAAAAGGGCAAGTATACT 59.284 37.037 0.00 0.00 0.00 2.12
1535 1605 7.715686 AGCAACTATCTAAAAGGGCAAGTATAC 59.284 37.037 0.00 0.00 0.00 1.47
1536 1606 7.715249 CAGCAACTATCTAAAAGGGCAAGTATA 59.285 37.037 0.00 0.00 0.00 1.47
1537 1607 6.543831 CAGCAACTATCTAAAAGGGCAAGTAT 59.456 38.462 0.00 0.00 0.00 2.12
1600 1670 5.631929 TGCATATATACGACGGATGAAACAC 59.368 40.000 1.83 0.00 0.00 3.32
1613 1683 4.500545 GCCTCCTCATCCTGCATATATACG 60.501 50.000 0.00 0.00 0.00 3.06
1654 1724 4.065281 GGTCCTCCACGGTGGTCG 62.065 72.222 25.53 17.32 45.88 4.79
1700 1770 2.167281 CTCGATGTCAACCTCCATCACT 59.833 50.000 0.00 0.00 37.84 3.41
1712 1782 1.996798 GGGGATAGTCCTCGATGTCA 58.003 55.000 0.00 0.00 36.57 3.58
1954 2035 3.203442 CGAAGCTACGGGCCTACA 58.797 61.111 0.84 0.00 43.05 2.74
1983 2064 4.721132 ACAAAATCAACGTAGGAAAGGGA 58.279 39.130 0.00 0.00 0.00 4.20
1985 2066 5.941948 AGACAAAATCAACGTAGGAAAGG 57.058 39.130 0.00 0.00 0.00 3.11
1986 2067 6.371389 GGAAGACAAAATCAACGTAGGAAAG 58.629 40.000 0.00 0.00 0.00 2.62
1987 2068 5.049954 CGGAAGACAAAATCAACGTAGGAAA 60.050 40.000 0.00 0.00 0.00 3.13
1988 2069 4.449743 CGGAAGACAAAATCAACGTAGGAA 59.550 41.667 0.00 0.00 0.00 3.36
1990 2071 3.424433 GCGGAAGACAAAATCAACGTAGG 60.424 47.826 0.00 0.00 0.00 3.18
1991 2072 3.432252 AGCGGAAGACAAAATCAACGTAG 59.568 43.478 0.00 0.00 0.00 3.51
1992 2073 3.395639 AGCGGAAGACAAAATCAACGTA 58.604 40.909 0.00 0.00 0.00 3.57
1993 2074 2.218603 AGCGGAAGACAAAATCAACGT 58.781 42.857 0.00 0.00 0.00 3.99
1994 2075 2.969443 AGCGGAAGACAAAATCAACG 57.031 45.000 0.00 0.00 0.00 4.10
1995 2076 4.712763 CAGTAGCGGAAGACAAAATCAAC 58.287 43.478 0.00 0.00 0.00 3.18
1996 2077 3.188460 GCAGTAGCGGAAGACAAAATCAA 59.812 43.478 0.00 0.00 0.00 2.57
1997 2078 2.742053 GCAGTAGCGGAAGACAAAATCA 59.258 45.455 0.00 0.00 0.00 2.57
1998 2079 3.391227 GCAGTAGCGGAAGACAAAATC 57.609 47.619 0.00 0.00 0.00 2.17
2097 2193 2.095059 AGGACGAACACACGTACCATAC 60.095 50.000 0.00 0.00 46.76 2.39
2098 2194 2.161855 AGGACGAACACACGTACCATA 58.838 47.619 0.00 0.00 46.76 2.74
2099 2195 0.963962 AGGACGAACACACGTACCAT 59.036 50.000 0.00 0.00 46.76 3.55
2144 2240 0.107654 AGAATCCCGCCCGAAAAGAG 60.108 55.000 0.00 0.00 0.00 2.85
2152 2248 2.115291 GTTCTGCAGAATCCCGCCC 61.115 63.158 30.65 13.24 36.33 6.13
2187 2290 6.121590 TGCAGATTATGTGGAAAGCAGATTA 58.878 36.000 0.00 0.00 0.00 1.75
2211 2314 5.011125 TGGAATCTCAGAAAAGAAGTCGACT 59.989 40.000 13.58 13.58 0.00 4.18
2217 2320 9.277783 TCTTAAACTGGAATCTCAGAAAAGAAG 57.722 33.333 5.89 3.30 38.11 2.85
2234 2337 9.778993 CATAACTGAATCCACAATCTTAAACTG 57.221 33.333 0.00 0.00 0.00 3.16
2258 2361 0.317799 TTGCAGGCATTTCAACGCAT 59.682 45.000 0.00 0.00 0.00 4.73
2271 2374 2.832129 TCTGTCTAAGGGTACTTGCAGG 59.168 50.000 0.00 0.00 37.53 4.85
2272 2375 4.537135 TTCTGTCTAAGGGTACTTGCAG 57.463 45.455 0.00 0.00 37.53 4.41
2275 2378 7.360101 CGAACAATTTCTGTCTAAGGGTACTTG 60.360 40.741 0.00 0.00 37.23 3.16
2281 2385 5.065218 CCATCGAACAATTTCTGTCTAAGGG 59.935 44.000 0.00 0.00 37.23 3.95
2328 2432 8.855279 GCACTCATATTCGACAAGATACTATTC 58.145 37.037 0.00 0.00 0.00 1.75
2331 2435 6.204108 TCGCACTCATATTCGACAAGATACTA 59.796 38.462 0.00 0.00 0.00 1.82
2404 2512 9.323963 CTTTTGCAACGAACAAAACTTTAAAAT 57.676 25.926 0.00 0.00 40.94 1.82
2424 2532 1.607148 ACTTAGTTCGCCCACTTTTGC 59.393 47.619 0.00 0.00 0.00 3.68
2429 2537 2.922740 TTGAACTTAGTTCGCCCACT 57.077 45.000 18.64 0.00 44.55 4.00
2450 2558 6.819146 TGTTTAGTTCGCCCATTTTTCTTTTT 59.181 30.769 0.00 0.00 0.00 1.94
2451 2559 6.342111 TGTTTAGTTCGCCCATTTTTCTTTT 58.658 32.000 0.00 0.00 0.00 2.27
2452 2560 5.908341 TGTTTAGTTCGCCCATTTTTCTTT 58.092 33.333 0.00 0.00 0.00 2.52
2453 2561 5.523438 TGTTTAGTTCGCCCATTTTTCTT 57.477 34.783 0.00 0.00 0.00 2.52
2454 2562 5.722021 ATGTTTAGTTCGCCCATTTTTCT 57.278 34.783 0.00 0.00 0.00 2.52
2455 2563 6.848451 TCTATGTTTAGTTCGCCCATTTTTC 58.152 36.000 0.00 0.00 0.00 2.29
2460 2568 3.869246 CGTTCTATGTTTAGTTCGCCCAT 59.131 43.478 0.00 0.00 0.00 4.00
2474 2582 9.914131 TCATACCTTGAGATTATTCGTTCTATG 57.086 33.333 0.00 0.00 0.00 2.23
2550 2660 1.064003 TGCCAACACTCTACCACCAT 58.936 50.000 0.00 0.00 0.00 3.55
2694 2804 3.297736 CCTGGGTATAAACTCGAGACCT 58.702 50.000 21.68 5.16 0.00 3.85
2723 2833 2.874701 AGATGAAATGGCGAATTCTCGG 59.125 45.455 3.52 0.00 45.55 4.63


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

AutoCloner maintained by Alex Coulton.