Multiple sequence alignment - TraesCS3A01G095900

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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 TraesCS3A01G095900 chr3A 100.000 1363 0 0 1 1363 61307087 61308449 0.000000e+00 2518
1 TraesCS3A01G095900 chr3A 100.000 1233 0 0 1715 2947 61308801 61310033 0.000000e+00 2278
2 TraesCS3A01G095900 chr3A 93.636 220 14 0 1727 1946 61308220 61308439 2.190000e-86 329
3 TraesCS3A01G095900 chr3A 93.636 220 14 0 1134 1353 61308813 61309032 2.190000e-86 329
4 TraesCS3A01G095900 chr3A 98.844 173 2 0 1715 1887 61308277 61308449 2.850000e-80 309
5 TraesCS3A01G095900 chr3A 98.844 173 2 0 1191 1363 61308801 61308973 2.850000e-80 309
6 TraesCS3A01G095900 chr3A 94.413 179 7 3 1186 1363 61308204 61308380 3.740000e-69 272
7 TraesCS3A01G095900 chr3A 94.413 179 7 3 1118 1294 61308272 61308449 3.740000e-69 272
8 TraesCS3A01G095900 chr3A 94.444 162 9 0 1785 1946 61308802 61308963 1.750000e-62 250
9 TraesCS3A01G095900 chr3A 94.444 162 9 0 1716 1877 61308871 61309032 1.750000e-62 250
10 TraesCS3A01G095900 chr3A 100.000 103 0 0 1261 1363 61308802 61308904 1.080000e-44 191
11 TraesCS3A01G095900 chr3A 91.489 94 8 0 1853 1946 61308801 61308894 2.380000e-26 130
12 TraesCS3A01G095900 chr3D 92.998 914 53 6 1715 2621 48820760 48821669 0.000000e+00 1323
13 TraesCS3A01G095900 chr3D 88.899 1090 71 19 2 1084 48819036 48820082 0.000000e+00 1297
14 TraesCS3A01G095900 chr3D 88.742 302 16 2 1078 1361 48820560 48820861 1.300000e-93 353
15 TraesCS3A01G095900 chr3D 94.222 225 13 0 1716 1940 48820623 48820847 7.820000e-91 344
16 TraesCS3A01G095900 chr3D 92.760 221 16 0 1143 1363 48820712 48820932 1.320000e-83 320
17 TraesCS3A01G095900 chr3D 90.517 232 22 0 1715 1946 48820691 48820922 1.030000e-79 307
18 TraesCS3A01G095900 chr3D 89.076 238 23 3 1118 1353 48820755 48820991 2.870000e-75 292
19 TraesCS3A01G095900 chr3D 95.930 172 7 0 1192 1363 48820623 48820794 2.240000e-71 279
20 TraesCS3A01G095900 chr3D 93.902 164 10 0 1783 1946 48820621 48820784 6.310000e-62 248
21 TraesCS3A01G095900 chr3D 89.571 163 17 0 1715 1877 48820829 48820991 1.070000e-49 207
22 TraesCS3A01G095900 chr3D 93.617 94 6 0 1715 1808 48820898 48820991 1.100000e-29 141
23 TraesCS3A01G095900 chr3D 95.833 72 3 0 2765 2836 48821665 48821736 1.860000e-22 117
24 TraesCS3A01G095900 chr3D 88.000 100 9 3 1118 1215 48820893 48820991 6.670000e-22 115
25 TraesCS3A01G095900 chr3B 86.469 909 95 19 1727 2621 77852094 77852988 0.000000e+00 972
26 TraesCS3A01G095900 chr3B 83.756 671 84 16 688 1353 77851663 77852313 1.940000e-171 612
27 TraesCS3A01G095900 chr3B 82.709 347 54 5 1 346 818995301 818994960 1.330000e-78 303
28 TraesCS3A01G095900 chr3B 94.030 134 8 0 2620 2753 201487966 201488099 1.380000e-48 204
29 TraesCS3A01G095900 chr3B 93.284 134 9 0 2620 2753 201484693 201484826 6.440000e-47 198
30 TraesCS3A01G095900 chr7D 82.609 345 53 5 2 343 503923396 503923736 6.170000e-77 298
31 TraesCS3A01G095900 chr7D 86.873 259 33 1 3 260 232489041 232489299 3.720000e-74 289
32 TraesCS3A01G095900 chr2B 82.609 322 47 6 5 324 20031893 20031579 2.890000e-70 276
33 TraesCS3A01G095900 chr2B 80.966 352 56 8 2 346 704289375 704289722 4.840000e-68 268
34 TraesCS3A01G095900 chr2B 94.030 134 8 0 2620 2753 683740693 683740826 1.380000e-48 204
35 TraesCS3A01G095900 chr7B 80.857 350 59 6 4 349 409172128 409172473 4.840000e-68 268
36 TraesCS3A01G095900 chr7B 93.284 134 9 0 2620 2753 662742776 662742643 6.440000e-47 198
37 TraesCS3A01G095900 chr4B 80.692 347 60 6 2 346 510564040 510563699 2.250000e-66 263
38 TraesCS3A01G095900 chr5D 80.172 348 65 4 2 346 401391393 401391047 1.050000e-64 257
39 TraesCS3A01G095900 chr4A 80.290 345 62 6 5 345 109862631 109862289 3.770000e-64 255
40 TraesCS3A01G095900 chrUn 94.030 134 8 0 2620 2753 423004191 423004324 1.380000e-48 204
41 TraesCS3A01G095900 chr6B 94.030 134 8 0 2620 2753 22428365 22428232 1.380000e-48 204
42 TraesCS3A01G095900 chr1A 94.030 134 8 0 2620 2753 554453491 554453358 1.380000e-48 204
43 TraesCS3A01G095900 chr7A 93.284 134 9 0 2620 2753 12217636 12217503 6.440000e-47 198
44 TraesCS3A01G095900 chr1D 93.333 135 8 1 2620 2753 244763348 244763482 6.440000e-47 198


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 TraesCS3A01G095900 chr3A 61307087 61310033 2946 False 619.75 2518 96.180250 1 2947 12 chr3A.!!$F1 2946
1 TraesCS3A01G095900 chr3D 48819036 48821736 2700 False 411.00 1323 91.851308 2 2836 13 chr3D.!!$F1 2834
2 TraesCS3A01G095900 chr3B 77851663 77852988 1325 False 792.00 972 85.112500 688 2621 2 chr3B.!!$F1 1933
3 TraesCS3A01G095900 chr3B 201484693 201488099 3406 False 201.00 204 93.657000 2620 2753 2 chr3B.!!$F2 133

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
259 262 0.105039 GCTCTCCGGACCAATACAGG 59.895 60.0 0.0 0.0 0.00 4.0 F
1180 1679 0.037590 TACATGGTGGTGTTGCCCTC 59.962 55.0 0.0 0.0 36.04 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1660 0.037590 GAGGGCAACACCACCATGTA 59.962 55.0 0.0 0.0 42.05 2.29 R
2890 4174 0.037326 GTGGTTCAGAGTCGGCATGA 60.037 55.0 0.0 0.0 0.00 3.07 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
28 29 0.749649 AATAGCGGAGGCAGTGAGAG 59.250 55.000 0.00 0.00 43.41 3.20
30 31 2.500815 TAGCGGAGGCAGTGAGAGGT 62.501 60.000 0.00 0.00 43.41 3.85
39 40 3.735029 GTGAGAGGTCGCGTCCGT 61.735 66.667 16.59 8.32 35.54 4.69
55 56 0.250234 CCGTCCTGAGCCATCTTCAA 59.750 55.000 0.00 0.00 0.00 2.69
139 140 1.132849 AGGAGGGGGAAAGGGTTTTTG 60.133 52.381 0.00 0.00 0.00 2.44
140 141 1.132977 GGAGGGGGAAAGGGTTTTTGA 60.133 52.381 0.00 0.00 0.00 2.69
141 142 2.494627 GGAGGGGGAAAGGGTTTTTGAT 60.495 50.000 0.00 0.00 0.00 2.57
142 143 2.567169 GAGGGGGAAAGGGTTTTTGATG 59.433 50.000 0.00 0.00 0.00 3.07
144 145 2.615391 GGGGAAAGGGTTTTTGATGGA 58.385 47.619 0.00 0.00 0.00 3.41
145 146 3.181329 GGGGAAAGGGTTTTTGATGGAT 58.819 45.455 0.00 0.00 0.00 3.41
147 148 3.837731 GGGAAAGGGTTTTTGATGGATCA 59.162 43.478 0.00 0.00 34.44 2.92
148 149 4.081476 GGGAAAGGGTTTTTGATGGATCAG 60.081 45.833 0.00 0.00 38.19 2.90
151 152 1.482182 GGGTTTTTGATGGATCAGGGC 59.518 52.381 0.00 0.00 38.19 5.19
170 172 2.747855 GTCAGAAGCGGGCTTGGG 60.748 66.667 11.17 2.77 36.26 4.12
171 173 2.927856 TCAGAAGCGGGCTTGGGA 60.928 61.111 11.17 5.17 36.26 4.37
204 207 0.105709 CCACAAACCTCCCCCACTTT 60.106 55.000 0.00 0.00 0.00 2.66
211 214 1.068121 CCTCCCCCACTTTTGTCTCT 58.932 55.000 0.00 0.00 0.00 3.10
213 216 1.699634 CTCCCCCACTTTTGTCTCTGA 59.300 52.381 0.00 0.00 0.00 3.27
220 223 4.339247 CCCACTTTTGTCTCTGATTTGTGT 59.661 41.667 0.00 0.00 0.00 3.72
221 224 5.530915 CCCACTTTTGTCTCTGATTTGTGTA 59.469 40.000 0.00 0.00 0.00 2.90
234 237 5.893143 GATTTGTGTAAGAAATCGCGTTC 57.107 39.130 5.77 3.24 44.92 3.95
235 238 3.427516 TTGTGTAAGAAATCGCGTTCG 57.572 42.857 5.77 0.00 32.50 3.95
236 239 1.722464 TGTGTAAGAAATCGCGTTCGG 59.278 47.619 5.77 0.00 36.13 4.30
237 240 1.987770 GTGTAAGAAATCGCGTTCGGA 59.012 47.619 5.77 0.00 36.13 4.55
238 241 1.987770 TGTAAGAAATCGCGTTCGGAC 59.012 47.619 5.77 7.78 36.13 4.79
239 242 1.322637 GTAAGAAATCGCGTTCGGACC 59.677 52.381 5.77 0.00 36.13 4.46
240 243 1.349259 AAGAAATCGCGTTCGGACCG 61.349 55.000 7.84 7.84 36.13 4.79
259 262 0.105039 GCTCTCCGGACCAATACAGG 59.895 60.000 0.00 0.00 0.00 4.00
264 267 2.995547 GGACCAATACAGGCCGGT 59.004 61.111 14.55 14.55 0.00 5.28
277 280 0.893727 GGCCGGTGTTGGATGACTTT 60.894 55.000 1.90 0.00 0.00 2.66
282 285 0.165944 GTGTTGGATGACTTTCGCGG 59.834 55.000 6.13 0.00 0.00 6.46
289 292 2.808321 GACTTTCGCGGTCCGGAC 60.808 66.667 27.04 27.04 37.59 4.79
305 308 1.592669 GACAGCATGATCCGGACGG 60.593 63.158 6.12 3.96 39.69 4.79
309 312 2.823829 GCATGATCCGGACGGTTGC 61.824 63.158 6.12 10.65 36.47 4.17
310 313 1.449423 CATGATCCGGACGGTTGCA 60.449 57.895 6.12 7.85 36.47 4.08
332 335 4.362476 GTTTGCAGGCCCGCCTTG 62.362 66.667 8.88 3.26 45.70 3.61
341 344 4.883354 CCCGCCTTGGAGATGCCC 62.883 72.222 0.00 0.00 42.00 5.36
398 401 7.407393 AGGATAGAAGTAGGTGTTTGAGTAC 57.593 40.000 0.00 0.00 0.00 2.73
405 408 5.997843 AGTAGGTGTTTGAGTACTTTGGTT 58.002 37.500 0.00 0.00 0.00 3.67
467 470 6.652205 TCAGGGGTTCTTTAGGTCATATTT 57.348 37.500 0.00 0.00 0.00 1.40
514 517 9.787435 AAGTTAGAATTATGTGTGTCACCTAAA 57.213 29.630 0.00 0.00 30.84 1.85
515 518 9.436957 AGTTAGAATTATGTGTGTCACCTAAAG 57.563 33.333 0.00 0.00 30.84 1.85
582 585 9.685828 GTTATAGTGCACAAAACCTTTTTATCA 57.314 29.630 21.04 0.00 0.00 2.15
613 616 9.941664 AATTTATGATATTTTCAAGCGTCTGAG 57.058 29.630 0.00 0.00 38.03 3.35
637 640 6.441924 AGTCAATATGAAGACTCTGAAAGGGA 59.558 38.462 0.00 0.00 35.24 4.20
638 641 7.127032 AGTCAATATGAAGACTCTGAAAGGGAT 59.873 37.037 0.00 0.00 35.24 3.85
669 672 5.818136 TCTGTATAAAATGAGGCACTTGC 57.182 39.130 0.00 0.00 41.55 4.01
670 673 4.332543 TCTGTATAAAATGAGGCACTTGCG 59.667 41.667 0.00 0.00 41.55 4.85
722 728 0.321996 TAACCCACGTGCATGCACTA 59.678 50.000 39.46 25.18 44.16 2.74
760 771 4.763793 AGTCAAATGGTGATTGGACAAGAG 59.236 41.667 5.35 0.00 42.90 2.85
761 772 4.761739 GTCAAATGGTGATTGGACAAGAGA 59.238 41.667 0.00 0.00 40.89 3.10
806 817 1.298859 GAGCTTTGGCACGTACAGGG 61.299 60.000 0.00 0.00 41.70 4.45
813 825 1.599797 GCACGTACAGGGCCAAACT 60.600 57.895 6.18 0.00 45.50 2.66
910 925 5.604650 AGGAGATGTCTATAAAAGGGAGTGG 59.395 44.000 0.00 0.00 0.00 4.00
928 943 5.805994 GGAGTGGAGTTTTAGTAACATCTCG 59.194 44.000 0.00 0.00 0.00 4.04
1001 1016 8.894768 ACAATCTTATCGAGCTTTTTAGCTAT 57.105 30.769 0.00 0.00 46.36 2.97
1100 1599 1.226575 TTACTGATGCGTCGGCTCG 60.227 57.895 14.91 0.00 40.82 5.03
1105 1604 4.760047 ATGCGTCGGCTCGGCTTT 62.760 61.111 0.00 0.00 40.82 3.51
1141 1640 0.320771 GGAGCGCTCAACCTCTGAAA 60.321 55.000 36.27 0.00 32.17 2.69
1142 1641 1.512926 GAGCGCTCAACCTCTGAAAA 58.487 50.000 31.91 0.00 32.17 2.29
1143 1642 2.079925 GAGCGCTCAACCTCTGAAAAT 58.920 47.619 31.91 0.00 32.17 1.82
1144 1643 2.485814 GAGCGCTCAACCTCTGAAAATT 59.514 45.455 31.91 0.00 32.17 1.82
1145 1644 2.227388 AGCGCTCAACCTCTGAAAATTG 59.773 45.455 2.64 0.00 32.17 2.32
1146 1645 2.030805 GCGCTCAACCTCTGAAAATTGT 60.031 45.455 0.00 0.00 32.17 2.71
1147 1646 3.814945 CGCTCAACCTCTGAAAATTGTC 58.185 45.455 0.00 0.00 32.17 3.18
1148 1647 3.499918 CGCTCAACCTCTGAAAATTGTCT 59.500 43.478 0.00 0.00 32.17 3.41
1149 1648 4.377841 CGCTCAACCTCTGAAAATTGTCTC 60.378 45.833 0.00 0.00 32.17 3.36
1150 1649 4.759183 GCTCAACCTCTGAAAATTGTCTCT 59.241 41.667 0.00 0.00 32.17 3.10
1151 1650 5.334724 GCTCAACCTCTGAAAATTGTCTCTG 60.335 44.000 0.00 0.00 32.17 3.35
1152 1651 4.516698 TCAACCTCTGAAAATTGTCTCTGC 59.483 41.667 0.00 0.00 0.00 4.26
1153 1652 4.090761 ACCTCTGAAAATTGTCTCTGCA 57.909 40.909 0.00 0.00 0.00 4.41
1154 1653 4.070716 ACCTCTGAAAATTGTCTCTGCAG 58.929 43.478 7.63 7.63 0.00 4.41
1155 1654 3.119919 CCTCTGAAAATTGTCTCTGCAGC 60.120 47.826 9.47 0.00 0.00 5.25
1156 1655 2.816087 TCTGAAAATTGTCTCTGCAGCC 59.184 45.455 9.47 0.00 0.00 4.85
1157 1656 1.888512 TGAAAATTGTCTCTGCAGCCC 59.111 47.619 9.47 0.00 0.00 5.19
1158 1657 2.165998 GAAAATTGTCTCTGCAGCCCT 58.834 47.619 9.47 0.00 0.00 5.19
1159 1658 1.542492 AAATTGTCTCTGCAGCCCTG 58.458 50.000 9.47 0.00 0.00 4.45
1169 1668 4.230603 CAGCCCTGCTACATGGTG 57.769 61.111 0.00 0.00 36.40 4.17
1170 1669 1.452651 CAGCCCTGCTACATGGTGG 60.453 63.158 0.00 0.00 36.40 4.61
1171 1670 1.925455 AGCCCTGCTACATGGTGGT 60.925 57.895 0.00 0.00 36.99 4.16
1172 1671 1.750399 GCCCTGCTACATGGTGGTG 60.750 63.158 0.00 0.00 0.00 4.17
1173 1672 1.685224 CCCTGCTACATGGTGGTGT 59.315 57.895 0.00 0.00 36.13 4.16
1174 1673 0.038166 CCCTGCTACATGGTGGTGTT 59.962 55.000 0.00 0.00 33.62 3.32
1175 1674 1.167851 CCTGCTACATGGTGGTGTTG 58.832 55.000 0.00 0.00 33.62 3.33
1176 1675 0.523072 CTGCTACATGGTGGTGTTGC 59.477 55.000 0.00 6.53 46.34 4.17
1177 1676 0.893270 TGCTACATGGTGGTGTTGCC 60.893 55.000 10.07 0.00 45.84 4.52
1178 1677 1.595093 GCTACATGGTGGTGTTGCCC 61.595 60.000 0.00 0.00 42.41 5.36
1179 1678 0.038166 CTACATGGTGGTGTTGCCCT 59.962 55.000 0.00 0.00 36.04 5.19
1180 1679 0.037590 TACATGGTGGTGTTGCCCTC 59.962 55.000 0.00 0.00 36.04 4.30
1181 1680 1.978617 CATGGTGGTGTTGCCCTCC 60.979 63.158 0.00 0.00 36.04 4.30
1182 1681 2.468868 ATGGTGGTGTTGCCCTCCA 61.469 57.895 3.70 3.70 41.77 3.86
1183 1682 2.282462 GGTGGTGTTGCCCTCCAG 60.282 66.667 0.00 0.00 37.39 3.86
1184 1683 2.985847 GTGGTGTTGCCCTCCAGC 60.986 66.667 0.00 0.00 37.39 4.85
1185 1684 3.497115 TGGTGTTGCCCTCCAGCA 61.497 61.111 0.00 0.00 42.17 4.41
1195 1694 2.507992 CTCCAGCAAGCGGAGTCG 60.508 66.667 18.41 0.00 44.35 4.18
1276 1775 1.866925 GAAGTCGCAAAACCCTCCG 59.133 57.895 0.00 0.00 0.00 4.63
1329 1828 3.952508 TGCCCTCCAGCAAGCGAA 61.953 61.111 0.00 0.00 40.56 4.70
1330 1829 3.130160 GCCCTCCAGCAAGCGAAG 61.130 66.667 0.00 0.00 0.00 3.79
1331 1830 2.348998 CCCTCCAGCAAGCGAAGT 59.651 61.111 0.00 0.00 0.00 3.01
1332 1831 1.743252 CCCTCCAGCAAGCGAAGTC 60.743 63.158 0.00 0.00 0.00 3.01
1333 1832 2.097038 CCTCCAGCAAGCGAAGTCG 61.097 63.158 0.00 0.00 43.27 4.18
1344 1843 1.866925 CGAAGTCGCAAAACCCTCC 59.133 57.895 0.00 0.00 0.00 4.30
1345 1844 1.866925 GAAGTCGCAAAACCCTCCG 59.133 57.895 0.00 0.00 0.00 4.63
1346 1845 0.601841 GAAGTCGCAAAACCCTCCGA 60.602 55.000 0.00 0.00 0.00 4.55
1347 1846 0.602905 AAGTCGCAAAACCCTCCGAG 60.603 55.000 0.00 0.00 0.00 4.63
1348 1847 2.033194 GTCGCAAAACCCTCCGAGG 61.033 63.158 7.56 7.56 34.30 4.63
1349 1848 2.211410 TCGCAAAACCCTCCGAGGA 61.211 57.895 16.69 0.00 37.67 3.71
1350 1849 1.078426 CGCAAAACCCTCCGAGGAT 60.078 57.895 16.69 0.00 37.67 3.24
1351 1850 0.676782 CGCAAAACCCTCCGAGGATT 60.677 55.000 16.69 1.07 37.67 3.01
1352 1851 0.811281 GCAAAACCCTCCGAGGATTG 59.189 55.000 16.69 16.85 37.67 2.67
1353 1852 0.811281 CAAAACCCTCCGAGGATTGC 59.189 55.000 16.69 0.00 37.67 3.56
1354 1853 0.323451 AAAACCCTCCGAGGATTGCC 60.323 55.000 16.69 0.00 37.67 4.52
1803 2302 2.033194 GTCGCAAAACCCTCCGAGG 61.033 63.158 7.56 7.56 34.30 4.63
1804 2303 2.211410 TCGCAAAACCCTCCGAGGA 61.211 57.895 16.69 0.00 37.67 3.71
1809 2308 0.323451 AAAACCCTCCGAGGATTGCC 60.323 55.000 16.69 0.00 37.67 4.52
1845 2344 2.282462 GGTGGTGTTGCCCTCCAG 60.282 66.667 0.00 0.00 37.39 3.86
1846 2345 2.985847 GTGGTGTTGCCCTCCAGC 60.986 66.667 0.00 0.00 37.39 4.85
1940 2439 0.601841 GAGTCGCAAAACCCTCCGAA 60.602 55.000 0.00 0.00 0.00 4.30
1985 2484 1.072965 GGGGCAGATGGTAAGAGATGG 59.927 57.143 0.00 0.00 0.00 3.51
1995 2494 7.333921 CAGATGGTAAGAGATGGATCATTAAGC 59.666 40.741 0.00 0.00 0.00 3.09
2019 2518 1.001633 ACGTACGGCCTGAACTTGAAT 59.998 47.619 21.06 0.00 0.00 2.57
2074 2573 7.949903 ACGTCTTTTGTGTGTATTGTATGTA 57.050 32.000 0.00 0.00 0.00 2.29
2080 2584 9.261318 CTTTTGTGTGTATTGTATGTAATGTCG 57.739 33.333 0.00 0.00 0.00 4.35
2084 2588 5.869888 TGTGTATTGTATGTAATGTCGTGCA 59.130 36.000 0.00 0.00 0.00 4.57
2146 2650 8.077836 GACATATAATTGTCTTGGAGTGCTAC 57.922 38.462 0.10 0.00 42.22 3.58
2150 2654 4.530710 ATTGTCTTGGAGTGCTACGTAA 57.469 40.909 0.00 0.00 0.00 3.18
2180 2684 2.558359 GGGGATGCATATGCCAGTTTAC 59.442 50.000 24.54 8.45 45.91 2.01
2199 2703 6.603997 AGTTTACTGTTGGGTTGATGTTGTAA 59.396 34.615 0.00 0.00 0.00 2.41
2371 2877 2.956333 TGTGACAGACGGAGAGAGAAAA 59.044 45.455 0.00 0.00 0.00 2.29
2372 2878 3.004839 TGTGACAGACGGAGAGAGAAAAG 59.995 47.826 0.00 0.00 0.00 2.27
2447 2953 0.617413 AGCCATCAGACACAAGAGGG 59.383 55.000 0.00 0.00 38.66 4.30
2474 2981 0.828343 GAGCCCTAGGGTGCGTAGAT 60.828 60.000 28.96 0.00 37.65 1.98
2562 3069 2.037847 GGGCCTTGGCTCCAATGT 59.962 61.111 11.71 0.00 35.20 2.71
2570 3077 2.479566 TGGCTCCAATGTCTCTTCAC 57.520 50.000 0.00 0.00 0.00 3.18
2583 3090 2.497675 TCTCTTCACGCATCCTAAGCTT 59.502 45.455 3.48 3.48 0.00 3.74
2616 3129 2.422803 CGGAATCTTTTGAGGCCCCATA 60.423 50.000 0.00 0.00 0.00 2.74
2617 3130 3.642141 GGAATCTTTTGAGGCCCCATAA 58.358 45.455 0.00 0.00 0.00 1.90
2618 3131 4.226384 GGAATCTTTTGAGGCCCCATAAT 58.774 43.478 0.00 0.00 0.00 1.28
2635 3148 9.590451 GCCCCATAATATGTATCAAATCAAATG 57.410 33.333 0.00 0.00 0.00 2.32
2854 4138 6.597832 ACTAGAGTTGTGCAGAAGATTACT 57.402 37.500 0.00 0.00 0.00 2.24
2856 4140 5.474578 AGAGTTGTGCAGAAGATTACTCA 57.525 39.130 13.31 0.00 34.48 3.41
2857 4141 5.477510 AGAGTTGTGCAGAAGATTACTCAG 58.522 41.667 13.31 0.00 34.48 3.35
2858 4142 4.573900 AGTTGTGCAGAAGATTACTCAGG 58.426 43.478 0.00 0.00 0.00 3.86
2860 4144 4.890158 TGTGCAGAAGATTACTCAGGAA 57.110 40.909 0.00 0.00 0.00 3.36
2861 4145 4.569943 TGTGCAGAAGATTACTCAGGAAC 58.430 43.478 0.00 0.00 0.00 3.62
2862 4146 4.284490 TGTGCAGAAGATTACTCAGGAACT 59.716 41.667 0.00 0.00 43.88 3.01
2863 4147 5.480422 TGTGCAGAAGATTACTCAGGAACTA 59.520 40.000 0.00 0.00 36.02 2.24
2864 4148 6.039616 GTGCAGAAGATTACTCAGGAACTAG 58.960 44.000 0.00 0.00 36.02 2.57
2865 4149 5.717178 TGCAGAAGATTACTCAGGAACTAGT 59.283 40.000 0.00 0.00 36.02 2.57
2866 4150 6.890268 TGCAGAAGATTACTCAGGAACTAGTA 59.110 38.462 0.00 0.00 36.02 1.82
2867 4151 7.067615 TGCAGAAGATTACTCAGGAACTAGTAG 59.932 40.741 0.00 0.00 36.02 2.57
2869 4153 8.617809 CAGAAGATTACTCAGGAACTAGTAGAC 58.382 40.741 3.59 0.00 36.02 2.59
2870 4154 7.776500 AGAAGATTACTCAGGAACTAGTAGACC 59.224 40.741 3.59 7.07 36.02 3.85
2871 4155 6.056884 AGATTACTCAGGAACTAGTAGACCG 58.943 44.000 3.59 4.48 36.02 4.79
2872 4156 3.002038 ACTCAGGAACTAGTAGACCGG 57.998 52.381 3.59 0.00 36.02 5.28
2873 4157 2.299521 CTCAGGAACTAGTAGACCGGG 58.700 57.143 6.32 0.00 36.02 5.73
2875 4159 1.064166 CAGGAACTAGTAGACCGGGGA 60.064 57.143 6.32 0.00 36.02 4.81
2876 4160 1.064091 AGGAACTAGTAGACCGGGGAC 60.064 57.143 6.32 0.00 36.02 4.46
2878 4162 2.022934 GAACTAGTAGACCGGGGACAG 58.977 57.143 6.32 3.85 0.00 3.51
2879 4163 0.395448 ACTAGTAGACCGGGGACAGC 60.395 60.000 6.32 0.00 0.00 4.40
2880 4164 0.395311 CTAGTAGACCGGGGACAGCA 60.395 60.000 6.32 0.00 0.00 4.41
2881 4165 0.260816 TAGTAGACCGGGGACAGCAT 59.739 55.000 6.32 0.00 0.00 3.79
2883 4167 1.117150 GTAGACCGGGGACAGCATAA 58.883 55.000 6.32 0.00 0.00 1.90
2884 4168 1.068741 GTAGACCGGGGACAGCATAAG 59.931 57.143 6.32 0.00 0.00 1.73
2885 4169 1.523938 GACCGGGGACAGCATAAGC 60.524 63.158 6.32 0.00 42.56 3.09
2886 4170 2.203209 CCGGGGACAGCATAAGCC 60.203 66.667 0.00 0.00 43.56 4.35
2888 4172 1.149174 CGGGGACAGCATAAGCCAT 59.851 57.895 0.00 0.00 43.56 4.40
2890 4174 1.780503 GGGGACAGCATAAGCCATTT 58.219 50.000 0.00 0.00 43.56 2.32
2891 4175 1.683385 GGGGACAGCATAAGCCATTTC 59.317 52.381 0.00 0.00 43.56 2.17
2892 4176 2.378038 GGGACAGCATAAGCCATTTCA 58.622 47.619 0.00 0.00 43.56 2.69
2894 4178 3.243636 GGGACAGCATAAGCCATTTCATG 60.244 47.826 0.00 0.00 43.56 3.07
2895 4179 3.378339 GACAGCATAAGCCATTTCATGC 58.622 45.455 0.00 0.00 43.56 4.06
2896 4180 2.101917 ACAGCATAAGCCATTTCATGCC 59.898 45.455 2.00 0.00 43.81 4.40
2897 4181 1.338973 AGCATAAGCCATTTCATGCCG 59.661 47.619 2.00 0.00 43.81 5.69
2898 4182 1.337703 GCATAAGCCATTTCATGCCGA 59.662 47.619 0.00 0.00 38.24 5.54
2899 4183 2.859806 GCATAAGCCATTTCATGCCGAC 60.860 50.000 0.00 0.00 38.24 4.79
2901 4185 1.098050 AAGCCATTTCATGCCGACTC 58.902 50.000 0.00 0.00 0.00 3.36
2902 4186 0.254178 AGCCATTTCATGCCGACTCT 59.746 50.000 0.00 0.00 0.00 3.24
2903 4187 0.379669 GCCATTTCATGCCGACTCTG 59.620 55.000 0.00 0.00 0.00 3.35
2905 4189 2.358957 CCATTTCATGCCGACTCTGAA 58.641 47.619 0.00 0.00 0.00 3.02
2906 4190 2.096496 CCATTTCATGCCGACTCTGAAC 59.904 50.000 0.00 0.00 0.00 3.18
2907 4191 1.808411 TTTCATGCCGACTCTGAACC 58.192 50.000 0.00 0.00 0.00 3.62
2909 4193 0.037326 TCATGCCGACTCTGAACCAC 60.037 55.000 0.00 0.00 0.00 4.16
2910 4194 1.021390 CATGCCGACTCTGAACCACC 61.021 60.000 0.00 0.00 0.00 4.61
2912 4196 1.374758 GCCGACTCTGAACCACCAG 60.375 63.158 0.00 0.00 35.55 4.00
2913 4197 1.374758 CCGACTCTGAACCACCAGC 60.375 63.158 0.00 0.00 34.28 4.85
2914 4198 1.367471 CGACTCTGAACCACCAGCA 59.633 57.895 0.00 0.00 34.28 4.41
2916 4200 1.230324 GACTCTGAACCACCAGCAAC 58.770 55.000 0.00 0.00 34.28 4.17
2918 4202 1.202698 ACTCTGAACCACCAGCAACTC 60.203 52.381 0.00 0.00 34.28 3.01
2919 4203 0.108585 TCTGAACCACCAGCAACTCC 59.891 55.000 0.00 0.00 34.28 3.85
2920 4204 0.179020 CTGAACCACCAGCAACTCCA 60.179 55.000 0.00 0.00 0.00 3.86
2921 4205 0.465460 TGAACCACCAGCAACTCCAC 60.465 55.000 0.00 0.00 0.00 4.02
2923 4207 1.071699 GAACCACCAGCAACTCCACTA 59.928 52.381 0.00 0.00 0.00 2.74
2924 4208 0.396811 ACCACCAGCAACTCCACTAC 59.603 55.000 0.00 0.00 0.00 2.73
2925 4209 0.321653 CCACCAGCAACTCCACTACC 60.322 60.000 0.00 0.00 0.00 3.18
2926 4210 0.396435 CACCAGCAACTCCACTACCA 59.604 55.000 0.00 0.00 0.00 3.25
2928 4212 2.236146 CACCAGCAACTCCACTACCATA 59.764 50.000 0.00 0.00 0.00 2.74
2929 4213 2.910319 ACCAGCAACTCCACTACCATAA 59.090 45.455 0.00 0.00 0.00 1.90
2930 4214 3.055094 ACCAGCAACTCCACTACCATAAG 60.055 47.826 0.00 0.00 0.00 1.73
2931 4215 2.939103 CAGCAACTCCACTACCATAAGC 59.061 50.000 0.00 0.00 0.00 3.09
2932 4216 2.571653 AGCAACTCCACTACCATAAGCA 59.428 45.455 0.00 0.00 0.00 3.91
2933 4217 2.939103 GCAACTCCACTACCATAAGCAG 59.061 50.000 0.00 0.00 0.00 4.24
2934 4218 3.619979 GCAACTCCACTACCATAAGCAGT 60.620 47.826 0.00 0.00 0.00 4.40
2935 4219 4.184629 CAACTCCACTACCATAAGCAGTC 58.815 47.826 0.00 0.00 0.00 3.51
2937 4221 2.103263 CTCCACTACCATAAGCAGTCCC 59.897 54.545 0.00 0.00 0.00 4.46
2938 4222 1.141053 CCACTACCATAAGCAGTCCCC 59.859 57.143 0.00 0.00 0.00 4.81
2939 4223 1.120530 ACTACCATAAGCAGTCCCCG 58.879 55.000 0.00 0.00 0.00 5.73
2940 4224 0.393077 CTACCATAAGCAGTCCCCGG 59.607 60.000 0.00 0.00 0.00 5.73
2944 4228 0.251916 CATAAGCAGTCCCCGGTTGA 59.748 55.000 0.00 0.00 0.00 3.18
2945 4229 0.252197 ATAAGCAGTCCCCGGTTGAC 59.748 55.000 12.25 12.25 0.00 3.18
2946 4230 2.162338 TAAGCAGTCCCCGGTTGACG 62.162 60.000 13.80 10.62 43.80 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.073735 CCTCTCACTGCCTCCGCT 61.074 66.667 0.00 0.00 35.36 5.52
28 29 4.477975 CTCAGGACGGACGCGACC 62.478 72.222 15.93 17.09 0.00 4.79
39 40 1.744798 CGCATTGAAGATGGCTCAGGA 60.745 52.381 0.00 0.00 0.00 3.86
43 44 0.942962 CTCCGCATTGAAGATGGCTC 59.057 55.000 0.00 0.00 0.00 4.70
68 69 3.189429 GCATTCATGCCGCTATAGAGCA 61.189 50.000 17.19 17.19 46.92 4.26
112 113 3.643595 TTTCCCCCTCCTGCATGCG 62.644 63.158 14.09 7.87 0.00 4.73
113 114 1.755783 CTTTCCCCCTCCTGCATGC 60.756 63.158 11.82 11.82 0.00 4.06
114 115 1.076485 CCTTTCCCCCTCCTGCATG 60.076 63.158 0.00 0.00 0.00 4.06
115 116 2.319762 CCCTTTCCCCCTCCTGCAT 61.320 63.158 0.00 0.00 0.00 3.96
116 117 2.941025 CCCTTTCCCCCTCCTGCA 60.941 66.667 0.00 0.00 0.00 4.41
123 124 1.628340 CCATCAAAAACCCTTTCCCCC 59.372 52.381 0.00 0.00 0.00 5.40
139 140 1.070445 CTGACCGCCCTGATCCATC 59.930 63.158 0.00 0.00 0.00 3.51
140 141 0.982852 TTCTGACCGCCCTGATCCAT 60.983 55.000 0.00 0.00 0.00 3.41
141 142 1.612146 TTCTGACCGCCCTGATCCA 60.612 57.895 0.00 0.00 0.00 3.41
142 143 1.144936 CTTCTGACCGCCCTGATCC 59.855 63.158 0.00 0.00 0.00 3.36
144 145 2.586792 GCTTCTGACCGCCCTGAT 59.413 61.111 0.00 0.00 0.00 2.90
145 146 4.069232 CGCTTCTGACCGCCCTGA 62.069 66.667 0.00 0.00 0.00 3.86
151 152 3.121030 CAAGCCCGCTTCTGACCG 61.121 66.667 0.00 0.00 33.42 4.79
204 207 7.571244 GCGATTTCTTACACAAATCAGAGACAA 60.571 37.037 6.09 0.00 39.34 3.18
211 214 5.351233 AACGCGATTTCTTACACAAATCA 57.649 34.783 15.93 0.00 39.34 2.57
213 216 4.391358 CGAACGCGATTTCTTACACAAAT 58.609 39.130 15.93 0.00 40.82 2.32
220 223 1.632422 GGTCCGAACGCGATTTCTTA 58.368 50.000 15.93 0.00 40.82 2.10
221 224 1.349259 CGGTCCGAACGCGATTTCTT 61.349 55.000 15.93 0.00 40.82 2.52
236 239 1.389609 TATTGGTCCGGAGAGCGGTC 61.390 60.000 3.06 6.48 43.71 4.79
237 240 1.380785 TATTGGTCCGGAGAGCGGT 60.381 57.895 3.06 0.00 43.71 5.68
238 241 1.067582 GTATTGGTCCGGAGAGCGG 59.932 63.158 3.06 0.00 43.71 5.52
239 242 0.249073 CTGTATTGGTCCGGAGAGCG 60.249 60.000 3.06 0.00 43.71 5.03
240 243 0.105039 CCTGTATTGGTCCGGAGAGC 59.895 60.000 3.06 0.00 41.06 4.09
241 244 0.105039 GCCTGTATTGGTCCGGAGAG 59.895 60.000 3.06 0.00 0.00 3.20
242 245 1.335132 GGCCTGTATTGGTCCGGAGA 61.335 60.000 3.06 0.00 0.00 3.71
243 246 1.146263 GGCCTGTATTGGTCCGGAG 59.854 63.158 3.06 0.00 0.00 4.63
252 255 0.623723 ATCCAACACCGGCCTGTATT 59.376 50.000 0.00 0.00 0.00 1.89
259 262 0.521735 GAAAGTCATCCAACACCGGC 59.478 55.000 0.00 0.00 0.00 6.13
264 267 0.250124 ACCGCGAAAGTCATCCAACA 60.250 50.000 8.23 0.00 0.00 3.33
282 285 4.445699 GGATCATGCTGTCCGGAC 57.554 61.111 28.17 28.17 0.00 4.79
289 292 1.153369 AACCGTCCGGATCATGCTG 60.153 57.895 7.81 0.00 38.96 4.41
293 296 1.153369 CTGCAACCGTCCGGATCAT 60.153 57.895 7.81 0.00 38.96 2.45
309 312 2.677875 GGGCCTGCAAACCTCCTG 60.678 66.667 0.84 0.00 0.00 3.86
310 313 4.351054 CGGGCCTGCAAACCTCCT 62.351 66.667 0.84 0.00 0.00 3.69
373 376 8.334734 AGTACTCAAACACCTACTTCTATCCTA 58.665 37.037 0.00 0.00 0.00 2.94
375 378 7.407393 AGTACTCAAACACCTACTTCTATCC 57.593 40.000 0.00 0.00 0.00 2.59
507 510 8.498054 AGATCACACATATTTCACTTTAGGTG 57.502 34.615 0.00 0.00 46.60 4.00
548 551 6.531240 GGTTTTGTGCACTATAACCATCATTG 59.469 38.462 28.01 0.00 38.46 2.82
598 601 5.931724 TCATATTGACTCAGACGCTTGAAAA 59.068 36.000 0.00 0.00 0.00 2.29
605 608 4.677584 AGTCTTCATATTGACTCAGACGC 58.322 43.478 0.00 0.00 39.04 5.19
613 616 6.644347 TCCCTTTCAGAGTCTTCATATTGAC 58.356 40.000 0.00 0.00 0.00 3.18
648 651 4.591202 CGCAAGTGCCTCATTTTATACAG 58.409 43.478 0.00 0.00 37.91 2.74
665 668 3.781926 TTCGTGCACGCAACGCAAG 62.782 57.895 33.63 5.25 41.97 4.01
666 669 3.865830 TTCGTGCACGCAACGCAA 61.866 55.556 33.63 18.81 41.97 4.85
667 670 4.583254 GTTCGTGCACGCAACGCA 62.583 61.111 33.63 13.42 39.60 5.24
669 672 4.273951 ACGTTCGTGCACGCAACG 62.274 61.111 41.25 41.25 46.88 4.10
670 673 2.424576 ATCACGTTCGTGCACGCAAC 62.425 55.000 33.63 30.62 44.37 4.17
786 797 1.298859 CCTGTACGTGCCAAAGCTCC 61.299 60.000 0.00 0.00 40.80 4.70
806 817 0.663153 AGCGAACTGTTCAGTTTGGC 59.337 50.000 25.05 23.78 34.58 4.52
860 875 0.101759 GCACGACCCGAGCTTACATA 59.898 55.000 0.00 0.00 40.03 2.29
883 898 5.788430 TCCCTTTTATAGACATCTCCTGGA 58.212 41.667 0.00 0.00 0.00 3.86
884 899 5.604650 ACTCCCTTTTATAGACATCTCCTGG 59.395 44.000 0.00 0.00 0.00 4.45
887 902 5.602978 TCCACTCCCTTTTATAGACATCTCC 59.397 44.000 0.00 0.00 0.00 3.71
910 925 5.169295 AGGTGCGAGATGTTACTAAAACTC 58.831 41.667 0.00 0.00 0.00 3.01
928 943 1.719600 GAGATGTGTGAGTGAGGTGC 58.280 55.000 0.00 0.00 0.00 5.01
991 1006 2.948979 CCATGACGGCCATAGCTAAAAA 59.051 45.455 2.24 0.00 39.73 1.94
1141 1640 3.261250 CAGGGCTGCAGAGACAATT 57.739 52.632 20.43 0.00 0.00 2.32
1152 1651 1.452651 CCACCATGTAGCAGGGCTG 60.453 63.158 0.07 0.00 39.09 4.85
1153 1652 1.925455 ACCACCATGTAGCAGGGCT 60.925 57.895 0.00 0.00 39.09 5.19
1154 1653 1.750399 CACCACCATGTAGCAGGGC 60.750 63.158 0.00 0.00 39.09 5.19
1155 1654 0.038166 AACACCACCATGTAGCAGGG 59.962 55.000 0.00 0.00 41.50 4.45
1156 1655 1.167851 CAACACCACCATGTAGCAGG 58.832 55.000 0.00 0.00 30.75 4.85
1157 1656 0.523072 GCAACACCACCATGTAGCAG 59.477 55.000 0.00 0.00 30.75 4.24
1158 1657 0.893270 GGCAACACCACCATGTAGCA 60.893 55.000 0.00 0.00 38.86 3.49
1159 1658 1.595093 GGGCAACACCACCATGTAGC 61.595 60.000 0.00 0.00 42.05 3.58
1160 1659 0.038166 AGGGCAACACCACCATGTAG 59.962 55.000 0.00 0.00 42.05 2.74
1161 1660 0.037590 GAGGGCAACACCACCATGTA 59.962 55.000 0.00 0.00 42.05 2.29
1162 1661 1.228552 GAGGGCAACACCACCATGT 60.229 57.895 0.00 0.00 42.05 3.21
1163 1662 1.978617 GGAGGGCAACACCACCATG 60.979 63.158 0.00 0.00 42.05 3.66
1164 1663 2.430704 CTGGAGGGCAACACCACCAT 62.431 60.000 1.92 0.00 42.73 3.55
1165 1664 3.099841 TGGAGGGCAACACCACCA 61.100 61.111 0.00 0.00 41.89 4.17
1166 1665 2.282462 CTGGAGGGCAACACCACC 60.282 66.667 0.00 0.00 42.05 4.61
1167 1666 2.985847 GCTGGAGGGCAACACCAC 60.986 66.667 0.00 0.00 42.05 4.16
1168 1667 2.981914 CTTGCTGGAGGGCAACACCA 62.982 60.000 0.00 0.00 45.64 4.17
1169 1668 2.203480 TTGCTGGAGGGCAACACC 60.203 61.111 0.00 0.00 45.64 4.16
1170 1669 2.924105 GCTTGCTGGAGGGCAACAC 61.924 63.158 0.00 0.00 45.64 3.32
1171 1670 2.598394 GCTTGCTGGAGGGCAACA 60.598 61.111 0.00 0.00 45.64 3.33
1172 1671 3.741476 CGCTTGCTGGAGGGCAAC 61.741 66.667 0.00 0.00 45.64 4.17
1188 1687 2.033194 GGAGGGTTTTGCGACTCCG 61.033 63.158 0.00 0.00 40.01 4.63
1189 1688 2.033194 CGGAGGGTTTTGCGACTCC 61.033 63.158 0.00 0.00 44.71 3.85
1190 1689 1.005394 TCGGAGGGTTTTGCGACTC 60.005 57.895 0.00 0.00 35.97 3.36
1191 1690 1.004918 CTCGGAGGGTTTTGCGACT 60.005 57.895 0.00 0.00 35.97 4.18
1195 1694 0.811281 CAATCCTCGGAGGGTTTTGC 59.189 55.000 19.88 0.00 34.28 3.68
1227 1726 0.893270 GGCAACACCACCATGTAGCA 60.893 55.000 0.00 0.00 38.86 3.49
1259 1758 0.602905 CTCGGAGGGTTTTGCGACTT 60.603 55.000 0.00 0.00 35.97 3.01
1328 1827 0.602905 CTCGGAGGGTTTTGCGACTT 60.603 55.000 0.00 0.00 35.97 3.01
1329 1828 1.004918 CTCGGAGGGTTTTGCGACT 60.005 57.895 0.00 0.00 35.97 4.18
1330 1829 2.033194 CCTCGGAGGGTTTTGCGAC 61.033 63.158 16.59 0.00 35.97 5.19
1331 1830 1.550130 ATCCTCGGAGGGTTTTGCGA 61.550 55.000 23.39 2.17 38.62 5.10
1332 1831 0.676782 AATCCTCGGAGGGTTTTGCG 60.677 55.000 23.39 0.00 34.28 4.85
1333 1832 0.811281 CAATCCTCGGAGGGTTTTGC 59.189 55.000 19.88 0.00 34.28 3.68
1334 1833 0.811281 GCAATCCTCGGAGGGTTTTG 59.189 55.000 19.88 20.63 34.28 2.44
1335 1834 0.323451 GGCAATCCTCGGAGGGTTTT 60.323 55.000 19.88 10.34 34.28 2.43
1336 1835 1.208165 AGGCAATCCTCGGAGGGTTT 61.208 55.000 19.88 12.71 34.28 3.27
1337 1836 1.616628 AGGCAATCCTCGGAGGGTT 60.617 57.895 23.39 20.24 39.91 4.11
1338 1837 2.041265 AGGCAATCCTCGGAGGGT 59.959 61.111 23.39 14.75 38.72 4.34
1754 2253 0.037590 GAGGGCAACACCACCATGTA 59.962 55.000 0.00 0.00 42.05 2.29
1783 2282 0.602905 CTCGGAGGGTTTTGCGACTT 60.603 55.000 0.00 0.00 35.97 3.01
1816 2315 1.750399 CACCACCATGTAGCAGGGC 60.750 63.158 0.00 0.00 39.09 5.19
1822 2321 0.038166 AGGGCAACACCACCATGTAG 59.962 55.000 0.00 0.00 42.05 2.74
1823 2322 0.037590 GAGGGCAACACCACCATGTA 59.962 55.000 0.00 0.00 42.05 2.29
1825 2324 1.978617 GGAGGGCAACACCACCATG 60.979 63.158 0.00 0.00 42.05 3.66
1919 2418 1.072505 GGAGGGTTTTGCGACTCCA 59.927 57.895 4.78 0.00 46.81 3.86
1940 2439 7.559170 CCCCTCATGAAGATTTTAGTTCAATCT 59.441 37.037 0.00 0.00 41.84 2.40
2039 2538 4.188462 CACAAAAGACGTAGGCATGGATA 58.812 43.478 0.00 0.00 0.00 2.59
2074 2573 1.502231 GAGACACACTGCACGACATT 58.498 50.000 0.00 0.00 0.00 2.71
2080 2584 3.575630 TCTTTATCGAGACACACTGCAC 58.424 45.455 0.00 0.00 0.00 4.57
2084 2588 8.873830 CATATTTGTTCTTTATCGAGACACACT 58.126 33.333 0.00 0.00 0.00 3.55
2142 2646 0.457337 CCCACACGGACTTACGTAGC 60.457 60.000 0.00 0.00 46.75 3.58
2146 2650 0.459585 CATCCCCACACGGACTTACG 60.460 60.000 0.00 0.00 33.77 3.18
2150 2654 0.980754 TATGCATCCCCACACGGACT 60.981 55.000 0.19 0.00 33.77 3.85
2180 2684 3.634448 TGGTTACAACATCAACCCAACAG 59.366 43.478 1.30 0.00 43.01 3.16
2199 2703 6.872920 ACACTTGAAAACAACATACAATGGT 58.127 32.000 0.00 0.00 33.60 3.55
2262 2766 2.008268 GACAAATCCATGGGGCAGCG 62.008 60.000 13.02 0.00 0.00 5.18
2355 2860 1.205893 CCCCTTTTCTCTCTCCGTCTG 59.794 57.143 0.00 0.00 0.00 3.51
2541 3048 4.659172 TGGAGCCAAGGCCCAACG 62.659 66.667 15.92 0.00 43.17 4.10
2562 3069 2.103373 AGCTTAGGATGCGTGAAGAGA 58.897 47.619 0.00 0.00 35.28 3.10
2570 3077 1.463674 AACCCAAAGCTTAGGATGCG 58.536 50.000 19.61 1.22 35.28 4.73
2595 3108 0.323360 TGGGGCCTCAAAAGATTCCG 60.323 55.000 0.25 0.00 0.00 4.30
2712 3225 9.699703 GTGTATTTTACATACCACACCAATTTT 57.300 29.630 0.00 0.00 41.34 1.82
2718 3231 8.951787 TCTATGTGTATTTTACATACCACACC 57.048 34.615 0.00 0.00 41.34 4.16
2719 3232 9.042008 CCTCTATGTGTATTTTACATACCACAC 57.958 37.037 0.00 0.00 41.34 3.82
2720 3233 8.983789 TCCTCTATGTGTATTTTACATACCACA 58.016 33.333 0.00 0.00 41.34 4.17
2793 3920 5.334414 GCTCACTACCAGTTCATGTTTTCTG 60.334 44.000 0.00 0.00 0.00 3.02
2837 4121 4.569943 TCCTGAGTAATCTTCTGCACAAC 58.430 43.478 0.00 0.00 0.00 3.32
2838 4122 4.890158 TCCTGAGTAATCTTCTGCACAA 57.110 40.909 0.00 0.00 0.00 3.33
2839 4123 4.284490 AGTTCCTGAGTAATCTTCTGCACA 59.716 41.667 0.00 0.00 0.00 4.57
2840 4124 4.826556 AGTTCCTGAGTAATCTTCTGCAC 58.173 43.478 0.00 0.00 0.00 4.57
2841 4125 5.717178 ACTAGTTCCTGAGTAATCTTCTGCA 59.283 40.000 0.00 0.00 0.00 4.41
2842 4126 6.215495 ACTAGTTCCTGAGTAATCTTCTGC 57.785 41.667 0.00 0.00 0.00 4.26
2843 4127 8.617809 GTCTACTAGTTCCTGAGTAATCTTCTG 58.382 40.741 0.00 0.00 0.00 3.02
2846 4130 6.543100 CGGTCTACTAGTTCCTGAGTAATCTT 59.457 42.308 0.00 0.00 0.00 2.40
2848 4132 5.239087 CCGGTCTACTAGTTCCTGAGTAATC 59.761 48.000 0.00 0.00 0.00 1.75
2850 4134 4.521146 CCGGTCTACTAGTTCCTGAGTAA 58.479 47.826 0.00 0.00 0.00 2.24
2852 4136 2.356947 CCCGGTCTACTAGTTCCTGAGT 60.357 54.545 0.00 0.00 0.00 3.41
2853 4137 2.299521 CCCGGTCTACTAGTTCCTGAG 58.700 57.143 0.00 0.00 0.00 3.35
2854 4138 1.064166 CCCCGGTCTACTAGTTCCTGA 60.064 57.143 0.00 0.00 0.00 3.86
2856 4140 1.064091 GTCCCCGGTCTACTAGTTCCT 60.064 57.143 0.00 0.00 0.00 3.36
2857 4141 1.341383 TGTCCCCGGTCTACTAGTTCC 60.341 57.143 0.00 0.96 0.00 3.62
2858 4142 2.022934 CTGTCCCCGGTCTACTAGTTC 58.977 57.143 0.00 0.00 0.00 3.01
2860 4144 0.395448 GCTGTCCCCGGTCTACTAGT 60.395 60.000 0.00 0.00 0.00 2.57
2861 4145 0.395311 TGCTGTCCCCGGTCTACTAG 60.395 60.000 0.00 0.00 0.00 2.57
2862 4146 0.260816 ATGCTGTCCCCGGTCTACTA 59.739 55.000 0.00 0.00 0.00 1.82
2863 4147 0.260816 TATGCTGTCCCCGGTCTACT 59.739 55.000 0.00 0.00 0.00 2.57
2864 4148 1.068741 CTTATGCTGTCCCCGGTCTAC 59.931 57.143 0.00 0.00 0.00 2.59
2865 4149 1.410004 CTTATGCTGTCCCCGGTCTA 58.590 55.000 0.00 0.00 0.00 2.59
2866 4150 1.972660 GCTTATGCTGTCCCCGGTCT 61.973 60.000 0.00 0.00 36.03 3.85
2867 4151 1.523938 GCTTATGCTGTCCCCGGTC 60.524 63.158 0.00 0.00 36.03 4.79
2869 4153 2.203209 GGCTTATGCTGTCCCCGG 60.203 66.667 0.00 0.00 39.59 5.73
2870 4154 0.466189 AATGGCTTATGCTGTCCCCG 60.466 55.000 0.13 0.00 39.59 5.73
2871 4155 1.683385 GAAATGGCTTATGCTGTCCCC 59.317 52.381 0.13 0.00 39.59 4.81
2872 4156 2.378038 TGAAATGGCTTATGCTGTCCC 58.622 47.619 0.13 0.00 39.59 4.46
2873 4157 3.797865 GCATGAAATGGCTTATGCTGTCC 60.798 47.826 0.00 0.00 46.86 4.02
2875 4159 3.447918 GCATGAAATGGCTTATGCTGT 57.552 42.857 0.00 0.00 46.86 4.40
2885 4169 2.028420 TCAGAGTCGGCATGAAATGG 57.972 50.000 0.00 0.00 46.86 3.16
2888 4172 1.071542 TGGTTCAGAGTCGGCATGAAA 59.928 47.619 8.97 0.00 34.91 2.69
2890 4174 0.037326 GTGGTTCAGAGTCGGCATGA 60.037 55.000 0.00 0.00 0.00 3.07
2891 4175 1.021390 GGTGGTTCAGAGTCGGCATG 61.021 60.000 0.00 0.00 0.00 4.06
2892 4176 1.296715 GGTGGTTCAGAGTCGGCAT 59.703 57.895 0.00 0.00 0.00 4.40
2894 4178 1.374758 CTGGTGGTTCAGAGTCGGC 60.375 63.158 0.00 0.00 36.93 5.54
2895 4179 1.374758 GCTGGTGGTTCAGAGTCGG 60.375 63.158 0.00 0.00 36.93 4.79
2896 4180 0.249868 TTGCTGGTGGTTCAGAGTCG 60.250 55.000 0.00 0.00 36.93 4.18
2897 4181 1.202698 AGTTGCTGGTGGTTCAGAGTC 60.203 52.381 0.00 0.00 36.93 3.36
2898 4182 0.839946 AGTTGCTGGTGGTTCAGAGT 59.160 50.000 0.00 0.00 36.93 3.24
2899 4183 1.517242 GAGTTGCTGGTGGTTCAGAG 58.483 55.000 0.00 0.00 36.93 3.35
2901 4185 0.179020 TGGAGTTGCTGGTGGTTCAG 60.179 55.000 0.00 0.00 37.79 3.02
2902 4186 0.465460 GTGGAGTTGCTGGTGGTTCA 60.465 55.000 0.00 0.00 0.00 3.18
2903 4187 0.179018 AGTGGAGTTGCTGGTGGTTC 60.179 55.000 0.00 0.00 0.00 3.62
2905 4189 0.396811 GTAGTGGAGTTGCTGGTGGT 59.603 55.000 0.00 0.00 0.00 4.16
2906 4190 0.321653 GGTAGTGGAGTTGCTGGTGG 60.322 60.000 0.00 0.00 0.00 4.61
2907 4191 0.396435 TGGTAGTGGAGTTGCTGGTG 59.604 55.000 0.00 0.00 0.00 4.17
2909 4193 3.535561 CTTATGGTAGTGGAGTTGCTGG 58.464 50.000 0.00 0.00 0.00 4.85
2910 4194 2.939103 GCTTATGGTAGTGGAGTTGCTG 59.061 50.000 0.00 0.00 0.00 4.41
2912 4196 2.939103 CTGCTTATGGTAGTGGAGTTGC 59.061 50.000 0.00 0.00 0.00 4.17
2913 4197 4.184629 GACTGCTTATGGTAGTGGAGTTG 58.815 47.826 0.00 0.00 40.86 3.16
2914 4198 3.197983 GGACTGCTTATGGTAGTGGAGTT 59.802 47.826 0.00 0.00 40.86 3.01
2916 4200 2.103263 GGGACTGCTTATGGTAGTGGAG 59.897 54.545 0.00 0.00 40.86 3.86
2918 4202 1.141053 GGGGACTGCTTATGGTAGTGG 59.859 57.143 0.00 0.00 40.86 4.00
2919 4203 1.202533 CGGGGACTGCTTATGGTAGTG 60.203 57.143 0.00 0.00 40.86 2.74
2920 4204 1.120530 CGGGGACTGCTTATGGTAGT 58.879 55.000 0.00 0.00 43.38 2.73
2921 4205 0.393077 CCGGGGACTGCTTATGGTAG 59.607 60.000 0.00 0.00 0.00 3.18
2923 4207 1.205460 AACCGGGGACTGCTTATGGT 61.205 55.000 6.32 0.00 0.00 3.55
2924 4208 0.748005 CAACCGGGGACTGCTTATGG 60.748 60.000 6.32 0.00 0.00 2.74
2925 4209 0.251916 TCAACCGGGGACTGCTTATG 59.748 55.000 6.32 0.00 0.00 1.90
2926 4210 0.252197 GTCAACCGGGGACTGCTTAT 59.748 55.000 18.20 0.00 32.54 1.73
2928 4212 2.430367 GTCAACCGGGGACTGCTT 59.570 61.111 18.20 0.00 32.54 3.91
2929 4213 4.003788 CGTCAACCGGGGACTGCT 62.004 66.667 21.51 0.00 33.11 4.24


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

AutoCloner maintained by Alex Coulton.