Multiple sequence alignment - TraesCS4A01G013300

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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 TraesCS4A01G013300 chr4A 100.000 2201 0 0 1 2201 7598163 7600363 0.000000e+00 4065
1 TraesCS4A01G013300 chr4D 85.775 703 57 18 130 804 460710874 460710187 0.000000e+00 704
2 TraesCS4A01G013300 chr4D 87.631 477 18 18 798 1268 460710135 460709694 1.170000e-142 516
3 TraesCS4A01G013300 chr4D 77.864 899 67 59 1379 2201 460709596 460708754 9.330000e-119 436
4 TraesCS4A01G013300 chr4B 83.644 697 65 20 135 804 575607795 575608469 5.200000e-171 610
5 TraesCS4A01G013300 chr4B 80.730 877 64 43 1376 2201 575609046 575609868 8.760000e-164 586
6 TraesCS4A01G013300 chr4B 88.075 478 25 21 798 1268 575608506 575608958 2.490000e-149 538
7 TraesCS4A01G013300 chr5A 92.982 114 8 0 4 117 564386365 564386252 1.350000e-37 167
8 TraesCS4A01G013300 chr7D 92.982 114 7 1 1 114 136489503 136489615 4.860000e-37 165
9 TraesCS4A01G013300 chr7D 90.678 118 10 1 1 117 511139147 511139030 2.930000e-34 156
10 TraesCS4A01G013300 chr7A 91.453 117 10 0 1 117 276144677 276144561 6.290000e-36 161
11 TraesCS4A01G013300 chr6A 92.105 114 9 0 4 117 30376615 30376502 6.290000e-36 161
12 TraesCS4A01G013300 chr6A 91.453 117 9 1 1 117 578665538 578665423 2.260000e-35 159
13 TraesCS4A01G013300 chr6A 91.228 114 9 1 1 114 463527508 463527620 1.050000e-33 154
14 TraesCS4A01G013300 chr6B 91.379 116 7 2 1 114 536006687 536006801 2.930000e-34 156
15 TraesCS4A01G013300 chr1A 91.228 114 9 1 1 114 133174314 133174426 1.050000e-33 154


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 TraesCS4A01G013300 chr4A 7598163 7600363 2200 False 4065 4065 100.000000 1 2201 1 chr4A.!!$F1 2200
1 TraesCS4A01G013300 chr4D 460708754 460710874 2120 True 552 704 83.756667 130 2201 3 chr4D.!!$R1 2071
2 TraesCS4A01G013300 chr4B 575607795 575609868 2073 False 578 610 84.149667 135 2201 3 chr4B.!!$F1 2066

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
107 108 0.033366 ATTTTTGCCGCAAGTCCCAC 59.967 50.0 5.83 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2310 0.027979 CTTTGTGACACCTGTGCGTG 59.972 55.0 2.45 0.0 39.75 5.34 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
48 49 6.541969 TCTTAATATGTGTTGTGAACATGCG 58.458 36.000 0.00 0.00 44.35 4.73
49 50 4.764679 AATATGTGTTGTGAACATGCGT 57.235 36.364 0.00 0.00 44.35 5.24
50 51 2.404265 ATGTGTTGTGAACATGCGTG 57.596 45.000 3.82 3.82 44.35 5.34
51 52 1.373570 TGTGTTGTGAACATGCGTGA 58.626 45.000 14.17 0.00 44.35 4.35
52 53 1.946081 TGTGTTGTGAACATGCGTGAT 59.054 42.857 14.17 0.00 44.35 3.06
53 54 2.357323 TGTGTTGTGAACATGCGTGATT 59.643 40.909 14.17 3.09 44.35 2.57
54 55 3.181492 TGTGTTGTGAACATGCGTGATTT 60.181 39.130 14.17 0.00 44.35 2.17
55 56 3.796178 GTGTTGTGAACATGCGTGATTTT 59.204 39.130 14.17 0.00 44.35 1.82
56 57 4.267452 GTGTTGTGAACATGCGTGATTTTT 59.733 37.500 14.17 0.00 44.35 1.94
96 97 9.837525 TGCAATGTTTAAATATGAATTTTTGCC 57.162 25.926 11.94 0.52 40.17 4.52
97 98 8.997960 GCAATGTTTAAATATGAATTTTTGCCG 58.002 29.630 0.00 0.00 37.60 5.69
98 99 8.997960 CAATGTTTAAATATGAATTTTTGCCGC 58.002 29.630 0.00 0.00 36.67 6.53
99 100 7.658179 TGTTTAAATATGAATTTTTGCCGCA 57.342 28.000 0.00 0.00 36.67 5.69
100 101 8.087982 TGTTTAAATATGAATTTTTGCCGCAA 57.912 26.923 0.38 0.38 36.67 4.85
101 102 8.226448 TGTTTAAATATGAATTTTTGCCGCAAG 58.774 29.630 5.83 0.00 36.67 4.01
102 103 7.897575 TTAAATATGAATTTTTGCCGCAAGT 57.102 28.000 5.83 0.00 36.67 3.16
103 104 6.407475 AAATATGAATTTTTGCCGCAAGTC 57.593 33.333 5.83 3.97 30.98 3.01
104 105 2.147436 TGAATTTTTGCCGCAAGTCC 57.853 45.000 5.83 0.00 0.00 3.85
105 106 1.270041 TGAATTTTTGCCGCAAGTCCC 60.270 47.619 5.83 0.00 0.00 4.46
106 107 0.755686 AATTTTTGCCGCAAGTCCCA 59.244 45.000 5.83 0.00 0.00 4.37
107 108 0.033366 ATTTTTGCCGCAAGTCCCAC 59.967 50.000 5.83 0.00 0.00 4.61
108 109 2.343163 TTTTTGCCGCAAGTCCCACG 62.343 55.000 5.83 0.00 0.00 4.94
112 113 4.308458 CCGCAAGTCCCACGGTGA 62.308 66.667 10.28 0.00 42.01 4.02
113 114 3.041940 CGCAAGTCCCACGGTGAC 61.042 66.667 10.28 0.32 0.00 3.67
125 126 3.388841 GGTGACGTGATCCCCTGT 58.611 61.111 0.00 0.00 0.00 4.00
126 127 1.218316 GGTGACGTGATCCCCTGTC 59.782 63.158 0.00 0.00 0.00 3.51
127 128 1.218316 GTGACGTGATCCCCTGTCC 59.782 63.158 0.00 0.00 0.00 4.02
128 129 1.229051 TGACGTGATCCCCTGTCCA 60.229 57.895 0.00 0.00 0.00 4.02
136 137 0.842635 ATCCCCTGTCCATCTTGCTC 59.157 55.000 0.00 0.00 0.00 4.26
147 148 1.903877 ATCTTGCTCGGGGTCAGGTG 61.904 60.000 0.00 0.00 0.00 4.00
148 149 4.329545 TTGCTCGGGGTCAGGTGC 62.330 66.667 0.00 0.00 0.00 5.01
164 165 2.042162 AGGTGCAGAAATTCCACAGGAT 59.958 45.455 5.11 0.00 0.00 3.24
179 180 2.499289 ACAGGATCTGCTGAGTGGTTAG 59.501 50.000 5.66 0.00 34.37 2.34
181 182 2.499289 AGGATCTGCTGAGTGGTTAGTG 59.501 50.000 0.00 0.00 0.00 2.74
190 191 4.024809 GCTGAGTGGTTAGTGTCTTGTTTC 60.025 45.833 0.00 0.00 0.00 2.78
191 192 4.448210 TGAGTGGTTAGTGTCTTGTTTCC 58.552 43.478 0.00 0.00 0.00 3.13
192 193 3.813724 GAGTGGTTAGTGTCTTGTTTCCC 59.186 47.826 0.00 0.00 0.00 3.97
193 194 3.458487 AGTGGTTAGTGTCTTGTTTCCCT 59.542 43.478 0.00 0.00 0.00 4.20
194 195 4.657039 AGTGGTTAGTGTCTTGTTTCCCTA 59.343 41.667 0.00 0.00 0.00 3.53
195 196 5.131475 AGTGGTTAGTGTCTTGTTTCCCTAA 59.869 40.000 0.00 0.00 0.00 2.69
196 197 5.469084 GTGGTTAGTGTCTTGTTTCCCTAAG 59.531 44.000 0.00 0.00 0.00 2.18
197 198 4.454847 GGTTAGTGTCTTGTTTCCCTAAGC 59.545 45.833 0.00 0.00 0.00 3.09
198 199 5.306394 GTTAGTGTCTTGTTTCCCTAAGCT 58.694 41.667 0.00 0.00 0.00 3.74
200 201 5.562298 AGTGTCTTGTTTCCCTAAGCTAA 57.438 39.130 0.00 0.00 0.00 3.09
221 228 6.073222 GCTAACCTTGAAGAGATCGTTTCAAA 60.073 38.462 20.60 10.63 41.30 2.69
227 234 4.755123 TGAAGAGATCGTTTCAAACTTCCC 59.245 41.667 11.10 0.00 33.97 3.97
244 251 3.507597 CCTTTTTAAGGGCCGTTGC 57.492 52.632 20.82 0.00 45.27 4.17
245 252 0.676736 CCTTTTTAAGGGCCGTTGCA 59.323 50.000 20.82 4.39 45.27 4.08
246 253 1.069358 CCTTTTTAAGGGCCGTTGCAA 59.931 47.619 20.82 10.34 45.27 4.08
249 256 1.917872 TTTAAGGGCCGTTGCAATCT 58.082 45.000 20.82 0.00 40.13 2.40
250 257 1.917872 TTAAGGGCCGTTGCAATCTT 58.082 45.000 20.82 6.41 40.13 2.40
251 258 1.459450 TAAGGGCCGTTGCAATCTTC 58.541 50.000 20.82 0.00 40.13 2.87
252 259 1.586154 AAGGGCCGTTGCAATCTTCG 61.586 55.000 10.51 0.55 40.13 3.79
272 282 4.805768 TAACGGGCGGCCATTGGG 62.806 66.667 29.19 13.68 37.18 4.12
284 294 1.138036 CATTGGGTGCGCATGTCAG 59.862 57.895 15.91 0.00 0.00 3.51
285 295 1.303561 ATTGGGTGCGCATGTCAGT 60.304 52.632 15.91 6.57 0.00 3.41
286 296 0.035534 ATTGGGTGCGCATGTCAGTA 60.036 50.000 15.91 0.00 0.00 2.74
287 297 0.035534 TTGGGTGCGCATGTCAGTAT 60.036 50.000 15.91 0.00 0.00 2.12
288 298 0.744057 TGGGTGCGCATGTCAGTATG 60.744 55.000 15.91 0.00 37.54 2.39
289 299 0.744414 GGGTGCGCATGTCAGTATGT 60.744 55.000 15.91 0.00 37.40 2.29
290 300 0.652592 GGTGCGCATGTCAGTATGTC 59.347 55.000 15.91 0.00 37.40 3.06
291 301 1.358877 GTGCGCATGTCAGTATGTCA 58.641 50.000 15.91 0.00 38.75 3.58
295 305 1.290203 GCATGTCAGTATGTCACGGG 58.710 55.000 0.00 0.00 36.88 5.28
306 316 2.827604 GTCACGGGACACAGACATG 58.172 57.895 14.30 0.00 43.73 3.21
307 317 1.005037 TCACGGGACACAGACATGC 60.005 57.895 0.00 0.00 0.00 4.06
372 385 4.200283 CGTCCCCTCTCAGCTCGC 62.200 72.222 0.00 0.00 0.00 5.03
391 404 4.348656 TCGCGCTACTAATCAAACTAGTG 58.651 43.478 5.56 0.00 31.98 2.74
393 406 3.245519 GCGCTACTAATCAAACTAGTGGC 59.754 47.826 0.00 7.94 45.41 5.01
424 437 0.307453 TTGCTTGCACACGCTACAAG 59.693 50.000 0.00 0.00 42.90 3.16
447 460 1.908619 ACCCGGTCCCGTAAATTTACT 59.091 47.619 22.57 1.69 37.81 2.24
460 473 6.539464 CCGTAAATTTACTGTAACCATGGCTA 59.461 38.462 22.57 0.00 0.00 3.93
482 495 8.292448 GGCTATCATCCACATATTTAACTGTTG 58.708 37.037 2.69 0.00 0.00 3.33
617 642 2.025418 GTGAACTGGCACGTACCCG 61.025 63.158 1.39 0.00 40.83 5.28
663 688 3.870606 CCGCCGGGCTATAAATCG 58.129 61.111 18.34 0.00 0.00 3.34
668 693 0.608640 CCGGGCTATAAATCGGAGCT 59.391 55.000 0.00 0.00 44.69 4.09
684 709 1.448717 GCTCGAGAAGGACAAGGCC 60.449 63.158 18.75 0.00 0.00 5.19
839 943 4.248842 CGCCACCACCACCTCACA 62.249 66.667 0.00 0.00 0.00 3.58
840 944 2.281761 GCCACCACCACCTCACAG 60.282 66.667 0.00 0.00 0.00 3.66
841 945 2.818169 GCCACCACCACCTCACAGA 61.818 63.158 0.00 0.00 0.00 3.41
842 946 1.071471 CCACCACCACCTCACAGAC 59.929 63.158 0.00 0.00 0.00 3.51
843 947 1.410850 CCACCACCACCTCACAGACT 61.411 60.000 0.00 0.00 0.00 3.24
845 949 1.290324 CCACCACCTCACAGACTCG 59.710 63.158 0.00 0.00 0.00 4.18
846 950 1.373497 CACCACCTCACAGACTCGC 60.373 63.158 0.00 0.00 0.00 5.03
878 983 3.611766 ATAACCCTCGTCTTCTTGGTG 57.388 47.619 0.00 0.00 0.00 4.17
881 986 1.376037 CCTCGTCTTCTTGGTGGCC 60.376 63.158 0.00 0.00 0.00 5.36
895 1000 4.654412 GGCCGCTGCTCGATCGAT 62.654 66.667 19.78 0.00 41.67 3.59
917 1022 1.172812 ACCGGGCAAGAAGAAGCAAC 61.173 55.000 6.32 0.00 0.00 4.17
934 1039 1.188219 AACAAGCGGCAGGAGAGAGA 61.188 55.000 1.45 0.00 0.00 3.10
935 1040 1.141449 CAAGCGGCAGGAGAGAGAG 59.859 63.158 1.45 0.00 0.00 3.20
936 1041 1.000270 AAGCGGCAGGAGAGAGAGA 60.000 57.895 1.45 0.00 0.00 3.10
937 1042 1.037030 AAGCGGCAGGAGAGAGAGAG 61.037 60.000 1.45 0.00 0.00 3.20
938 1043 1.453015 GCGGCAGGAGAGAGAGAGA 60.453 63.158 0.00 0.00 0.00 3.10
939 1044 1.447317 GCGGCAGGAGAGAGAGAGAG 61.447 65.000 0.00 0.00 0.00 3.20
940 1045 0.180171 CGGCAGGAGAGAGAGAGAGA 59.820 60.000 0.00 0.00 0.00 3.10
941 1046 1.811558 CGGCAGGAGAGAGAGAGAGAG 60.812 61.905 0.00 0.00 0.00 3.20
942 1047 1.477558 GGCAGGAGAGAGAGAGAGAGG 60.478 61.905 0.00 0.00 0.00 3.69
943 1048 1.477558 GCAGGAGAGAGAGAGAGAGGG 60.478 61.905 0.00 0.00 0.00 4.30
944 1049 2.126882 CAGGAGAGAGAGAGAGAGGGA 58.873 57.143 0.00 0.00 0.00 4.20
945 1050 2.105477 CAGGAGAGAGAGAGAGAGGGAG 59.895 59.091 0.00 0.00 0.00 4.30
946 1051 1.421646 GGAGAGAGAGAGAGAGGGAGG 59.578 61.905 0.00 0.00 0.00 4.30
952 1057 0.478507 GAGAGAGAGGGAGGGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
1213 1323 3.255379 GCTAAGGCGGACGAAGCG 61.255 66.667 0.00 0.00 35.00 4.68
1234 1344 2.573869 CGGTGACACGCAGATCCT 59.426 61.111 0.00 0.00 0.00 3.24
1235 1345 1.079819 CGGTGACACGCAGATCCTT 60.080 57.895 0.00 0.00 0.00 3.36
1236 1346 1.078759 CGGTGACACGCAGATCCTTC 61.079 60.000 0.00 0.00 0.00 3.46
1237 1347 0.247736 GGTGACACGCAGATCCTTCT 59.752 55.000 0.00 0.00 0.00 2.85
1238 1348 1.338200 GGTGACACGCAGATCCTTCTT 60.338 52.381 0.00 0.00 0.00 2.52
1243 1356 2.275318 CACGCAGATCCTTCTTCTTCC 58.725 52.381 0.00 0.00 0.00 3.46
1249 1362 4.683129 GCAGATCCTTCTTCTTCCTCTTCC 60.683 50.000 0.00 0.00 0.00 3.46
1253 1366 4.757692 TCCTTCTTCTTCCTCTTCCTCTT 58.242 43.478 0.00 0.00 0.00 2.85
1257 1370 2.030027 TCTTCCTCTTCCTCTTGCCA 57.970 50.000 0.00 0.00 0.00 4.92
1268 1381 1.571919 CTCTTGCCATAGGTACACGC 58.428 55.000 0.00 0.00 0.00 5.34
1269 1382 0.177141 TCTTGCCATAGGTACACGCC 59.823 55.000 0.00 0.00 0.00 5.68
1271 1384 2.110420 GCCATAGGTACACGCCCC 59.890 66.667 0.00 0.00 0.00 5.80
1272 1385 2.737881 GCCATAGGTACACGCCCCA 61.738 63.158 0.00 0.00 0.00 4.96
1274 1387 0.250295 CCATAGGTACACGCCCCATG 60.250 60.000 0.00 0.00 0.00 3.66
1276 1389 2.052047 ATAGGTACACGCCCCATGCC 62.052 60.000 0.00 0.00 36.24 4.40
1324 1459 1.344438 TGTGCTCGTCTTGGATCTTGT 59.656 47.619 0.00 0.00 0.00 3.16
1325 1460 1.996191 GTGCTCGTCTTGGATCTTGTC 59.004 52.381 0.00 0.00 0.00 3.18
1327 1462 2.266554 GCTCGTCTTGGATCTTGTCTG 58.733 52.381 0.00 0.00 0.00 3.51
1330 1465 2.094494 TCGTCTTGGATCTTGTCTGCTC 60.094 50.000 0.00 0.00 0.00 4.26
1331 1466 2.094286 CGTCTTGGATCTTGTCTGCTCT 60.094 50.000 0.00 0.00 0.00 4.09
1332 1467 3.616076 CGTCTTGGATCTTGTCTGCTCTT 60.616 47.826 0.00 0.00 0.00 2.85
1333 1468 3.932089 GTCTTGGATCTTGTCTGCTCTTC 59.068 47.826 0.00 0.00 0.00 2.87
1334 1469 3.837146 TCTTGGATCTTGTCTGCTCTTCT 59.163 43.478 0.00 0.00 0.00 2.85
1335 1470 4.285517 TCTTGGATCTTGTCTGCTCTTCTT 59.714 41.667 0.00 0.00 0.00 2.52
1336 1471 4.199432 TGGATCTTGTCTGCTCTTCTTC 57.801 45.455 0.00 0.00 0.00 2.87
1337 1472 3.837146 TGGATCTTGTCTGCTCTTCTTCT 59.163 43.478 0.00 0.00 0.00 2.85
1338 1473 4.285517 TGGATCTTGTCTGCTCTTCTTCTT 59.714 41.667 0.00 0.00 0.00 2.52
1339 1474 4.869861 GGATCTTGTCTGCTCTTCTTCTTC 59.130 45.833 0.00 0.00 0.00 2.87
1340 1475 5.337491 GGATCTTGTCTGCTCTTCTTCTTCT 60.337 44.000 0.00 0.00 0.00 2.85
1341 1476 5.543507 TCTTGTCTGCTCTTCTTCTTCTT 57.456 39.130 0.00 0.00 0.00 2.52
1342 1477 5.537188 TCTTGTCTGCTCTTCTTCTTCTTC 58.463 41.667 0.00 0.00 0.00 2.87
1343 1478 5.304101 TCTTGTCTGCTCTTCTTCTTCTTCT 59.696 40.000 0.00 0.00 0.00 2.85
1344 1479 4.880759 TGTCTGCTCTTCTTCTTCTTCTG 58.119 43.478 0.00 0.00 0.00 3.02
1345 1480 3.679502 GTCTGCTCTTCTTCTTCTTCTGC 59.320 47.826 0.00 0.00 0.00 4.26
1346 1481 3.002102 CTGCTCTTCTTCTTCTTCTGCC 58.998 50.000 0.00 0.00 0.00 4.85
1347 1482 2.289945 TGCTCTTCTTCTTCTTCTGCCC 60.290 50.000 0.00 0.00 0.00 5.36
1348 1483 2.027285 GCTCTTCTTCTTCTTCTGCCCT 60.027 50.000 0.00 0.00 0.00 5.19
1349 1484 3.860641 CTCTTCTTCTTCTTCTGCCCTC 58.139 50.000 0.00 0.00 0.00 4.30
1350 1485 3.515104 CTCTTCTTCTTCTTCTGCCCTCT 59.485 47.826 0.00 0.00 0.00 3.69
1351 1486 3.513515 TCTTCTTCTTCTTCTGCCCTCTC 59.486 47.826 0.00 0.00 0.00 3.20
1352 1487 2.894731 TCTTCTTCTTCTGCCCTCTCA 58.105 47.619 0.00 0.00 0.00 3.27
1353 1488 3.448934 TCTTCTTCTTCTGCCCTCTCAT 58.551 45.455 0.00 0.00 0.00 2.90
1354 1489 4.614475 TCTTCTTCTTCTGCCCTCTCATA 58.386 43.478 0.00 0.00 0.00 2.15
1355 1490 4.648762 TCTTCTTCTTCTGCCCTCTCATAG 59.351 45.833 0.00 0.00 0.00 2.23
1356 1491 4.256983 TCTTCTTCTGCCCTCTCATAGA 57.743 45.455 0.00 0.00 0.00 1.98
1357 1492 4.813809 TCTTCTTCTGCCCTCTCATAGAT 58.186 43.478 0.00 0.00 0.00 1.98
1358 1493 5.215069 TCTTCTTCTGCCCTCTCATAGATT 58.785 41.667 0.00 0.00 0.00 2.40
1381 1516 9.976255 GATTCTTCATATAGTACTGCTACTACG 57.024 37.037 5.39 0.00 38.12 3.51
1428 1563 9.818796 GTTTTGAGTAGCATTTAGAGAAGAAAG 57.181 33.333 0.00 0.00 0.00 2.62
1461 1598 2.816672 CTCTGCCCAAAGAGGAGTTTTC 59.183 50.000 0.00 0.00 40.11 2.29
1469 1606 3.669251 AAGAGGAGTTTTCGTGAGAGG 57.331 47.619 0.00 0.00 43.69 3.69
1482 1619 2.600731 GTGAGAGGTCGTGACAAGATG 58.399 52.381 2.00 0.00 0.00 2.90
1509 1646 3.686016 GGTGTTCTTATGTGGTGGATGT 58.314 45.455 0.00 0.00 0.00 3.06
1536 1673 4.393371 GCAAGGTAGTCCATGAGAAAGTTC 59.607 45.833 0.00 0.00 34.72 3.01
1569 1710 9.920133 ATCTGTACATAAATCATACTGCTACTG 57.080 33.333 0.00 0.00 0.00 2.74
1603 1744 6.150976 AGTTTGTGTGTTCTTGAGATGTTCAA 59.849 34.615 0.00 0.00 43.40 2.69
1604 1745 6.507958 TTGTGTGTTCTTGAGATGTTCAAA 57.492 33.333 0.00 0.00 44.84 2.69
1605 1746 5.879237 TGTGTGTTCTTGAGATGTTCAAAC 58.121 37.500 0.00 0.00 44.84 2.93
1606 1747 5.647658 TGTGTGTTCTTGAGATGTTCAAACT 59.352 36.000 0.00 0.00 44.84 2.66
1609 1750 7.218963 GTGTGTTCTTGAGATGTTCAAACTTTC 59.781 37.037 0.00 0.00 44.84 2.62
1615 1759 7.770433 TCTTGAGATGTTCAAACTTTCTTGAGA 59.230 33.333 0.00 3.05 44.84 3.27
1659 1815 1.952102 GATTCGGTCAGTGCCCCGTA 61.952 60.000 17.21 10.68 44.51 4.02
1678 1834 5.157067 CCGTATCTGTATCTGTATGTGCAG 58.843 45.833 0.00 0.00 37.81 4.41
1686 1842 2.382882 TCTGTATGTGCAGAGGAGAGG 58.617 52.381 0.00 0.00 40.23 3.69
1687 1843 2.024941 TCTGTATGTGCAGAGGAGAGGA 60.025 50.000 0.00 0.00 40.23 3.71
1688 1844 2.762887 CTGTATGTGCAGAGGAGAGGAA 59.237 50.000 0.00 0.00 38.70 3.36
1689 1845 3.173151 TGTATGTGCAGAGGAGAGGAAA 58.827 45.455 0.00 0.00 0.00 3.13
1691 1847 2.775911 TGTGCAGAGGAGAGGAAATG 57.224 50.000 0.00 0.00 0.00 2.32
1692 1848 1.339438 TGTGCAGAGGAGAGGAAATGC 60.339 52.381 0.00 0.00 0.00 3.56
1693 1849 0.986527 TGCAGAGGAGAGGAAATGCA 59.013 50.000 0.00 0.00 41.05 3.96
1694 1850 1.352017 TGCAGAGGAGAGGAAATGCAA 59.648 47.619 0.00 0.00 40.43 4.08
1695 1851 2.224843 TGCAGAGGAGAGGAAATGCAAA 60.225 45.455 0.00 0.00 40.43 3.68
1696 1852 2.821969 GCAGAGGAGAGGAAATGCAAAA 59.178 45.455 0.00 0.00 33.92 2.44
1697 1853 3.256631 GCAGAGGAGAGGAAATGCAAAAA 59.743 43.478 0.00 0.00 33.92 1.94
1728 1912 2.034053 TCAATTTCCTGTTGGTGCGAAC 59.966 45.455 0.00 0.00 34.23 3.95
1751 1935 1.000274 GAATGCCAACAACTCCCACAC 60.000 52.381 0.00 0.00 0.00 3.82
1754 1938 1.172812 GCCAACAACTCCCACACTCC 61.173 60.000 0.00 0.00 0.00 3.85
1774 1963 0.040425 ATTTTCTGTTCGTGCGCACC 60.040 50.000 33.23 20.44 0.00 5.01
1800 1989 4.395231 GGAGGAAATGCTAGTGTAACAACC 59.605 45.833 0.00 0.00 41.43 3.77
1827 2016 2.717580 TTTCTTTCTCGAGCGCACTA 57.282 45.000 11.47 0.00 0.00 2.74
1828 2017 2.717580 TTCTTTCTCGAGCGCACTAA 57.282 45.000 11.47 0.00 0.00 2.24
1829 2018 2.264109 TCTTTCTCGAGCGCACTAAG 57.736 50.000 11.47 3.81 0.00 2.18
1830 2019 1.810755 TCTTTCTCGAGCGCACTAAGA 59.189 47.619 11.47 6.43 0.00 2.10
1831 2020 2.228103 TCTTTCTCGAGCGCACTAAGAA 59.772 45.455 11.47 12.43 0.00 2.52
1832 2021 2.717580 TTCTCGAGCGCACTAAGAAA 57.282 45.000 11.47 0.00 29.36 2.52
1833 2022 2.941453 TCTCGAGCGCACTAAGAAAT 57.059 45.000 11.47 0.00 0.00 2.17
1905 2094 3.058160 CAGCAGTTCCCGGCCTTG 61.058 66.667 0.00 0.00 31.47 3.61
1939 2154 0.863144 GCACAACCGCGTTCTCTAAA 59.137 50.000 4.92 0.00 0.00 1.85
1940 2155 1.262151 GCACAACCGCGTTCTCTAAAA 59.738 47.619 4.92 0.00 0.00 1.52
1948 2163 3.063997 CCGCGTTCTCTAAAATGCAGAAT 59.936 43.478 4.92 0.00 40.45 2.40
1953 2168 6.457392 GCGTTCTCTAAAATGCAGAATGATCA 60.457 38.462 0.00 0.00 39.69 2.92
1969 2184 2.912987 ATCACGACCTCTCCCTCCCG 62.913 65.000 0.00 0.00 0.00 5.14
1984 2202 4.973055 CCGGACGCGGTGGTTCAA 62.973 66.667 12.47 0.00 0.00 2.69
2025 2243 8.969121 TCAATGTTAATGTCAATGTCAATGTC 57.031 30.769 0.00 0.00 0.00 3.06
2085 2308 4.643385 CCGTTCACACGCACGCAC 62.643 66.667 0.00 0.00 45.72 5.34
2086 2309 4.968164 CGTTCACACGCACGCACG 62.968 66.667 0.00 0.00 40.18 5.34
2105 2328 1.987704 GCACGCACAGGTGTCACAAA 61.988 55.000 5.12 0.00 40.08 2.83
2106 2329 0.027979 CACGCACAGGTGTCACAAAG 59.972 55.000 5.12 0.00 35.01 2.77
2115 2338 2.936498 AGGTGTCACAAAGAACTGTTCG 59.064 45.455 14.35 3.90 34.02 3.95
2135 2358 3.785859 TCACATCCGGCCAGCTCC 61.786 66.667 2.24 0.00 0.00 4.70
2174 2402 0.237498 GCCGACACTTGTAACAAGCC 59.763 55.000 0.00 0.00 0.00 4.35
2176 2404 1.588674 CGACACTTGTAACAAGCCCA 58.411 50.000 0.00 0.00 0.00 5.36
2181 2409 1.414919 ACTTGTAACAAGCCCAGACGA 59.585 47.619 0.00 0.00 0.00 4.20
2190 2418 2.184322 CCCAGACGATGTCACGGG 59.816 66.667 9.28 9.28 39.80 5.28
2191 2419 2.348104 CCCAGACGATGTCACGGGA 61.348 63.158 15.64 0.00 44.93 5.14
2192 2420 1.676678 CCCAGACGATGTCACGGGAT 61.677 60.000 15.64 0.00 44.93 3.85
2193 2421 0.249073 CCAGACGATGTCACGGGATC 60.249 60.000 0.00 0.00 34.60 3.36
2194 2422 0.455815 CAGACGATGTCACGGGATCA 59.544 55.000 0.00 0.00 34.60 2.92
2195 2423 0.456221 AGACGATGTCACGGGATCAC 59.544 55.000 0.00 0.00 34.60 3.06
2196 2424 0.172578 GACGATGTCACGGGATCACA 59.827 55.000 0.00 0.00 37.61 3.58
2197 2425 0.824109 ACGATGTCACGGGATCACAT 59.176 50.000 0.00 0.00 37.61 3.21
2198 2426 1.202417 ACGATGTCACGGGATCACATC 60.202 52.381 7.69 7.69 42.02 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.334632 CGCATGTTCACAACACATATTAAGATA 58.665 33.333 0.00 0.00 45.50 1.98
23 24 7.148255 ACGCATGTTCACAACACATATTAAGAT 60.148 33.333 0.00 0.00 45.50 2.40
24 25 6.148645 ACGCATGTTCACAACACATATTAAGA 59.851 34.615 0.00 0.00 45.50 2.10
25 26 6.249050 CACGCATGTTCACAACACATATTAAG 59.751 38.462 0.00 0.00 45.50 1.85
26 27 6.073003 TCACGCATGTTCACAACACATATTAA 60.073 34.615 0.00 0.00 45.50 1.40
27 28 5.409826 TCACGCATGTTCACAACACATATTA 59.590 36.000 0.00 0.00 45.50 0.98
28 29 4.215185 TCACGCATGTTCACAACACATATT 59.785 37.500 0.00 0.00 45.50 1.28
29 30 3.750652 TCACGCATGTTCACAACACATAT 59.249 39.130 0.00 0.00 45.50 1.78
30 31 3.134458 TCACGCATGTTCACAACACATA 58.866 40.909 0.00 0.00 45.50 2.29
31 32 1.946081 TCACGCATGTTCACAACACAT 59.054 42.857 0.00 0.00 45.50 3.21
32 33 1.373570 TCACGCATGTTCACAACACA 58.626 45.000 0.00 0.00 45.50 3.72
33 34 2.686558 ATCACGCATGTTCACAACAC 57.313 45.000 0.00 0.00 45.50 3.32
34 35 3.706802 AAATCACGCATGTTCACAACA 57.293 38.095 0.00 0.00 46.94 3.33
70 71 9.837525 GGCAAAAATTCATATTTAAACATTGCA 57.162 25.926 14.06 0.00 40.67 4.08
71 72 8.997960 CGGCAAAAATTCATATTTAAACATTGC 58.002 29.630 0.00 0.00 39.47 3.56
72 73 8.997960 GCGGCAAAAATTCATATTTAAACATTG 58.002 29.630 0.00 0.00 32.85 2.82
73 74 8.725148 TGCGGCAAAAATTCATATTTAAACATT 58.275 25.926 0.00 0.00 32.85 2.71
74 75 8.261492 TGCGGCAAAAATTCATATTTAAACAT 57.739 26.923 0.00 0.00 32.85 2.71
75 76 7.658179 TGCGGCAAAAATTCATATTTAAACA 57.342 28.000 0.00 0.00 32.85 2.83
76 77 8.227119 ACTTGCGGCAAAAATTCATATTTAAAC 58.773 29.630 17.13 0.00 32.85 2.01
77 78 8.316640 ACTTGCGGCAAAAATTCATATTTAAA 57.683 26.923 17.13 0.00 32.85 1.52
78 79 7.064016 GGACTTGCGGCAAAAATTCATATTTAA 59.936 33.333 17.13 0.00 32.85 1.52
79 80 6.533367 GGACTTGCGGCAAAAATTCATATTTA 59.467 34.615 17.13 0.00 32.85 1.40
80 81 5.351189 GGACTTGCGGCAAAAATTCATATTT 59.649 36.000 17.13 0.00 35.49 1.40
81 82 4.869861 GGACTTGCGGCAAAAATTCATATT 59.130 37.500 17.13 0.00 0.00 1.28
82 83 4.432712 GGACTTGCGGCAAAAATTCATAT 58.567 39.130 17.13 0.00 0.00 1.78
83 84 3.367910 GGGACTTGCGGCAAAAATTCATA 60.368 43.478 17.13 0.00 0.00 2.15
84 85 2.612721 GGGACTTGCGGCAAAAATTCAT 60.613 45.455 17.13 0.00 0.00 2.57
85 86 1.270041 GGGACTTGCGGCAAAAATTCA 60.270 47.619 17.13 0.00 0.00 2.57
86 87 1.270041 TGGGACTTGCGGCAAAAATTC 60.270 47.619 17.13 10.16 0.00 2.17
87 88 0.755686 TGGGACTTGCGGCAAAAATT 59.244 45.000 17.13 1.27 0.00 1.82
88 89 0.033366 GTGGGACTTGCGGCAAAAAT 59.967 50.000 17.13 5.21 0.00 1.82
89 90 1.439644 GTGGGACTTGCGGCAAAAA 59.560 52.632 17.13 0.00 0.00 1.94
90 91 2.840066 CGTGGGACTTGCGGCAAAA 61.840 57.895 17.13 0.00 0.00 2.44
91 92 3.283684 CGTGGGACTTGCGGCAAA 61.284 61.111 17.13 0.00 0.00 3.68
96 97 3.041940 GTCACCGTGGGACTTGCG 61.042 66.667 0.00 0.00 32.54 4.85
97 98 3.041940 CGTCACCGTGGGACTTGC 61.042 66.667 0.00 0.00 33.11 4.01
109 110 1.218316 GGACAGGGGATCACGTCAC 59.782 63.158 5.51 0.00 0.00 3.67
110 111 0.617535 ATGGACAGGGGATCACGTCA 60.618 55.000 5.51 0.00 0.00 4.35
111 112 0.105039 GATGGACAGGGGATCACGTC 59.895 60.000 0.00 0.00 0.00 4.34
112 113 0.325671 AGATGGACAGGGGATCACGT 60.326 55.000 0.00 0.00 0.00 4.49
113 114 0.833287 AAGATGGACAGGGGATCACG 59.167 55.000 0.00 0.00 0.00 4.35
114 115 1.748591 GCAAGATGGACAGGGGATCAC 60.749 57.143 0.00 0.00 0.00 3.06
115 116 0.548031 GCAAGATGGACAGGGGATCA 59.452 55.000 0.00 0.00 0.00 2.92
116 117 0.842635 AGCAAGATGGACAGGGGATC 59.157 55.000 0.00 0.00 0.00 3.36
117 118 0.842635 GAGCAAGATGGACAGGGGAT 59.157 55.000 0.00 0.00 0.00 3.85
118 119 1.617018 CGAGCAAGATGGACAGGGGA 61.617 60.000 0.00 0.00 0.00 4.81
119 120 1.153289 CGAGCAAGATGGACAGGGG 60.153 63.158 0.00 0.00 0.00 4.79
120 121 1.153289 CCGAGCAAGATGGACAGGG 60.153 63.158 0.00 0.00 0.00 4.45
121 122 1.153289 CCCGAGCAAGATGGACAGG 60.153 63.158 0.00 0.00 0.00 4.00
122 123 1.153289 CCCCGAGCAAGATGGACAG 60.153 63.158 0.00 0.00 0.00 3.51
123 124 1.899437 GACCCCGAGCAAGATGGACA 61.899 60.000 0.00 0.00 0.00 4.02
124 125 1.153349 GACCCCGAGCAAGATGGAC 60.153 63.158 0.00 0.00 0.00 4.02
125 126 1.612146 TGACCCCGAGCAAGATGGA 60.612 57.895 0.00 0.00 0.00 3.41
126 127 1.153289 CTGACCCCGAGCAAGATGG 60.153 63.158 0.00 0.00 0.00 3.51
127 128 1.153289 CCTGACCCCGAGCAAGATG 60.153 63.158 0.00 0.00 0.00 2.90
128 129 1.613630 ACCTGACCCCGAGCAAGAT 60.614 57.895 0.00 0.00 0.00 2.40
136 137 0.609131 AATTTCTGCACCTGACCCCG 60.609 55.000 0.00 0.00 0.00 5.73
148 149 3.377485 CAGCAGATCCTGTGGAATTTCTG 59.623 47.826 9.94 9.94 38.60 3.02
164 165 2.598565 AGACACTAACCACTCAGCAGA 58.401 47.619 0.00 0.00 0.00 4.26
179 180 4.454847 GGTTAGCTTAGGGAAACAAGACAC 59.545 45.833 0.00 0.00 0.00 3.67
181 182 4.907809 AGGTTAGCTTAGGGAAACAAGAC 58.092 43.478 0.00 0.00 0.00 3.01
190 191 5.606505 GATCTCTTCAAGGTTAGCTTAGGG 58.393 45.833 0.00 0.00 0.00 3.53
191 192 5.163499 ACGATCTCTTCAAGGTTAGCTTAGG 60.163 44.000 0.00 0.00 0.00 2.69
192 193 5.897050 ACGATCTCTTCAAGGTTAGCTTAG 58.103 41.667 0.00 0.00 0.00 2.18
193 194 5.916661 ACGATCTCTTCAAGGTTAGCTTA 57.083 39.130 0.00 0.00 0.00 3.09
194 195 4.810191 ACGATCTCTTCAAGGTTAGCTT 57.190 40.909 0.00 0.00 0.00 3.74
195 196 4.810191 AACGATCTCTTCAAGGTTAGCT 57.190 40.909 0.00 0.00 0.00 3.32
196 197 4.929808 TGAAACGATCTCTTCAAGGTTAGC 59.070 41.667 4.37 0.00 0.00 3.09
197 198 7.171678 AGTTTGAAACGATCTCTTCAAGGTTAG 59.828 37.037 14.86 0.00 41.30 2.34
198 199 6.990349 AGTTTGAAACGATCTCTTCAAGGTTA 59.010 34.615 14.86 3.29 41.30 2.85
200 201 5.368989 AGTTTGAAACGATCTCTTCAAGGT 58.631 37.500 14.86 7.47 41.30 3.50
227 234 2.517650 TTGCAACGGCCCTTAAAAAG 57.482 45.000 0.00 0.00 40.13 2.27
238 245 1.129811 GTTACCCGAAGATTGCAACGG 59.870 52.381 16.90 16.90 44.16 4.44
243 250 1.712018 GCCCGTTACCCGAAGATTGC 61.712 60.000 0.00 0.00 39.56 3.56
244 251 1.426041 CGCCCGTTACCCGAAGATTG 61.426 60.000 0.00 0.00 39.56 2.67
245 252 1.153509 CGCCCGTTACCCGAAGATT 60.154 57.895 0.00 0.00 39.56 2.40
246 253 2.497770 CGCCCGTTACCCGAAGAT 59.502 61.111 0.00 0.00 39.56 2.40
252 259 4.807631 AATGGCCGCCCGTTACCC 62.808 66.667 7.03 0.00 38.58 3.69
272 282 1.061131 GTGACATACTGACATGCGCAC 59.939 52.381 14.90 0.00 31.60 5.34
288 298 1.291877 GCATGTCTGTGTCCCGTGAC 61.292 60.000 0.00 0.00 42.12 3.67
289 299 1.005037 GCATGTCTGTGTCCCGTGA 60.005 57.895 0.00 0.00 0.00 4.35
290 300 2.382746 CGCATGTCTGTGTCCCGTG 61.383 63.158 0.00 0.00 0.00 4.94
291 301 2.048222 CGCATGTCTGTGTCCCGT 60.048 61.111 0.00 0.00 0.00 5.28
295 305 1.002366 GTGATCCGCATGTCTGTGTC 58.998 55.000 0.00 0.00 0.00 3.67
306 316 1.883084 GTGACATCCCGTGATCCGC 60.883 63.158 0.00 0.00 34.38 5.54
307 317 1.588932 CGTGACATCCCGTGATCCG 60.589 63.158 0.00 0.00 0.00 4.18
355 368 4.200283 GCGAGCTGAGAGGGGACG 62.200 72.222 0.00 0.00 0.00 4.79
356 369 4.200283 CGCGAGCTGAGAGGGGAC 62.200 72.222 0.00 0.00 0.00 4.46
372 385 4.267928 GTGCCACTAGTTTGATTAGTAGCG 59.732 45.833 0.00 0.00 38.20 4.26
391 404 1.515521 AAGCAAGCCAAGTACGTGCC 61.516 55.000 2.94 0.00 42.51 5.01
393 406 0.385974 GCAAGCAAGCCAAGTACGTG 60.386 55.000 0.00 1.33 0.00 4.49
424 437 2.857575 AATTTACGGGACCGGGTCGC 62.858 60.000 28.77 28.77 44.69 5.19
437 450 9.116067 TGATAGCCATGGTTACAGTAAATTTAC 57.884 33.333 18.77 18.77 0.00 2.01
447 460 3.457749 TGTGGATGATAGCCATGGTTACA 59.542 43.478 14.67 12.57 37.81 2.41
460 473 7.467267 GCGACAACAGTTAAATATGTGGATGAT 60.467 37.037 7.05 0.00 0.00 2.45
482 495 0.601841 TCCGGTTTTTCAGAGGCGAC 60.602 55.000 0.00 0.00 0.00 5.19
588 613 0.105964 CCAGTTCACTTGACGTGGGA 59.894 55.000 0.00 0.00 43.94 4.37
632 657 4.620937 GCGGCGGAGGGGATAACC 62.621 72.222 9.78 0.00 39.11 2.85
663 688 0.174617 CCTTGTCCTTCTCGAGCTCC 59.825 60.000 7.81 0.00 0.00 4.70
668 693 2.646175 CGGGCCTTGTCCTTCTCGA 61.646 63.158 0.84 0.00 0.00 4.04
684 709 3.365265 GGCTGGGTTTGTGAGCGG 61.365 66.667 0.00 0.00 33.26 5.52
790 836 2.571653 CTCCTCTTGTGGTGGATTGGTA 59.428 50.000 0.00 0.00 37.04 3.25
823 927 2.281761 CTGTGAGGTGGTGGTGGC 60.282 66.667 0.00 0.00 0.00 5.01
832 936 1.528292 GGACTGCGAGTCTGTGAGGT 61.528 60.000 13.59 0.00 44.46 3.85
834 938 1.154131 CGGACTGCGAGTCTGTGAG 60.154 63.158 13.77 0.00 44.56 3.51
835 939 2.954611 CGGACTGCGAGTCTGTGA 59.045 61.111 13.77 0.00 44.56 3.58
839 943 0.393944 TATGGACGGACTGCGAGTCT 60.394 55.000 13.59 0.00 44.46 3.24
840 944 0.669077 ATATGGACGGACTGCGAGTC 59.331 55.000 0.00 7.52 44.32 3.36
841 945 1.977056 TATATGGACGGACTGCGAGT 58.023 50.000 0.00 0.00 0.00 4.18
842 946 2.607282 GGTTATATGGACGGACTGCGAG 60.607 54.545 0.00 0.00 0.00 5.03
843 947 1.338973 GGTTATATGGACGGACTGCGA 59.661 52.381 0.00 0.00 0.00 5.10
845 949 1.692519 AGGGTTATATGGACGGACTGC 59.307 52.381 0.00 0.00 0.00 4.40
846 950 2.030185 CGAGGGTTATATGGACGGACTG 60.030 54.545 0.00 0.00 0.00 3.51
878 983 4.654412 ATCGATCGAGCAGCGGCC 62.654 66.667 23.84 0.00 42.56 6.13
895 1000 1.292223 CTTCTTCTTGCCCGGTCGA 59.708 57.895 0.00 0.00 0.00 4.20
917 1022 1.141449 CTCTCTCTCCTGCCGCTTG 59.859 63.158 0.00 0.00 0.00 4.01
934 1039 0.254107 ACCTCTCCCTCCCTCTCTCT 60.254 60.000 0.00 0.00 0.00 3.10
935 1040 1.423921 CTACCTCTCCCTCCCTCTCTC 59.576 61.905 0.00 0.00 0.00 3.20
936 1041 1.529744 CTACCTCTCCCTCCCTCTCT 58.470 60.000 0.00 0.00 0.00 3.10
937 1042 0.178973 GCTACCTCTCCCTCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
938 1043 0.629270 AGCTACCTCTCCCTCCCTCT 60.629 60.000 0.00 0.00 0.00 3.69
939 1044 0.469144 CAGCTACCTCTCCCTCCCTC 60.469 65.000 0.00 0.00 0.00 4.30
940 1045 1.623625 CAGCTACCTCTCCCTCCCT 59.376 63.158 0.00 0.00 0.00 4.20
941 1046 1.458588 CCAGCTACCTCTCCCTCCC 60.459 68.421 0.00 0.00 0.00 4.30
942 1047 0.189822 ATCCAGCTACCTCTCCCTCC 59.810 60.000 0.00 0.00 0.00 4.30
943 1048 1.146982 AGATCCAGCTACCTCTCCCTC 59.853 57.143 0.00 0.00 0.00 4.30
944 1049 1.133199 CAGATCCAGCTACCTCTCCCT 60.133 57.143 0.00 0.00 0.00 4.20
945 1050 1.337118 CAGATCCAGCTACCTCTCCC 58.663 60.000 0.00 0.00 0.00 4.30
946 1051 0.678950 GCAGATCCAGCTACCTCTCC 59.321 60.000 0.75 0.00 0.00 3.71
952 1057 0.249238 CCACGAGCAGATCCAGCTAC 60.249 60.000 9.98 4.35 43.58 3.58
977 1082 3.119096 GCGCTCCCCTTGTTCGAC 61.119 66.667 0.00 0.00 0.00 4.20
1217 1327 1.078759 GAAGGATCTGCGTGTCACCG 61.079 60.000 0.00 0.00 0.00 4.94
1218 1328 0.247736 AGAAGGATCTGCGTGTCACC 59.752 55.000 0.00 0.00 33.59 4.02
1220 1330 1.895798 AGAAGAAGGATCTGCGTGTCA 59.104 47.619 0.00 0.00 36.21 3.58
1221 1331 2.663826 AGAAGAAGGATCTGCGTGTC 57.336 50.000 0.00 0.00 36.21 3.67
1222 1332 2.354203 GGAAGAAGAAGGATCTGCGTGT 60.354 50.000 0.00 0.00 36.21 4.49
1223 1333 2.093764 AGGAAGAAGAAGGATCTGCGTG 60.094 50.000 0.00 0.00 36.21 5.34
1224 1334 2.167487 GAGGAAGAAGAAGGATCTGCGT 59.833 50.000 0.00 0.00 36.21 5.24
1227 1337 4.716287 AGGAAGAGGAAGAAGAAGGATCTG 59.284 45.833 0.00 0.00 35.59 2.90
1228 1338 4.959080 AGGAAGAGGAAGAAGAAGGATCT 58.041 43.478 0.00 0.00 37.57 2.75
1229 1339 4.962362 AGAGGAAGAGGAAGAAGAAGGATC 59.038 45.833 0.00 0.00 0.00 3.36
1230 1340 4.959080 AGAGGAAGAGGAAGAAGAAGGAT 58.041 43.478 0.00 0.00 0.00 3.24
1231 1341 4.412060 AGAGGAAGAGGAAGAAGAAGGA 57.588 45.455 0.00 0.00 0.00 3.36
1232 1342 4.831107 CAAGAGGAAGAGGAAGAAGAAGG 58.169 47.826 0.00 0.00 0.00 3.46
1233 1343 4.252878 GCAAGAGGAAGAGGAAGAAGAAG 58.747 47.826 0.00 0.00 0.00 2.85
1234 1344 3.008485 GGCAAGAGGAAGAGGAAGAAGAA 59.992 47.826 0.00 0.00 0.00 2.52
1235 1345 2.569404 GGCAAGAGGAAGAGGAAGAAGA 59.431 50.000 0.00 0.00 0.00 2.87
1236 1346 2.304180 TGGCAAGAGGAAGAGGAAGAAG 59.696 50.000 0.00 0.00 0.00 2.85
1237 1347 2.338809 TGGCAAGAGGAAGAGGAAGAA 58.661 47.619 0.00 0.00 0.00 2.52
1238 1348 2.030027 TGGCAAGAGGAAGAGGAAGA 57.970 50.000 0.00 0.00 0.00 2.87
1243 1356 3.706594 TGTACCTATGGCAAGAGGAAGAG 59.293 47.826 21.91 0.00 36.88 2.85
1249 1362 1.571919 GCGTGTACCTATGGCAAGAG 58.428 55.000 0.00 0.00 0.00 2.85
1253 1366 2.737881 GGGGCGTGTACCTATGGCA 61.738 63.158 0.00 0.00 34.11 4.92
1257 1370 1.450211 GCATGGGGCGTGTACCTAT 59.550 57.895 0.00 0.00 0.00 2.57
1304 1430 1.344438 ACAAGATCCAAGACGAGCACA 59.656 47.619 0.00 0.00 0.00 4.57
1324 1459 3.306641 GGCAGAAGAAGAAGAAGAGCAGA 60.307 47.826 0.00 0.00 0.00 4.26
1325 1460 3.002102 GGCAGAAGAAGAAGAAGAGCAG 58.998 50.000 0.00 0.00 0.00 4.24
1327 1462 2.027285 AGGGCAGAAGAAGAAGAAGAGC 60.027 50.000 0.00 0.00 0.00 4.09
1330 1465 3.260380 TGAGAGGGCAGAAGAAGAAGAAG 59.740 47.826 0.00 0.00 0.00 2.85
1331 1466 3.242867 TGAGAGGGCAGAAGAAGAAGAA 58.757 45.455 0.00 0.00 0.00 2.52
1332 1467 2.894731 TGAGAGGGCAGAAGAAGAAGA 58.105 47.619 0.00 0.00 0.00 2.87
1333 1468 3.910568 ATGAGAGGGCAGAAGAAGAAG 57.089 47.619 0.00 0.00 0.00 2.85
1334 1469 4.614475 TCTATGAGAGGGCAGAAGAAGAA 58.386 43.478 0.00 0.00 0.00 2.52
1335 1470 4.256983 TCTATGAGAGGGCAGAAGAAGA 57.743 45.455 0.00 0.00 0.00 2.87
1336 1471 5.305128 AGAATCTATGAGAGGGCAGAAGAAG 59.695 44.000 0.00 0.00 0.00 2.85
1337 1472 5.215069 AGAATCTATGAGAGGGCAGAAGAA 58.785 41.667 0.00 0.00 0.00 2.52
1338 1473 4.813809 AGAATCTATGAGAGGGCAGAAGA 58.186 43.478 0.00 0.00 0.00 2.87
1339 1474 5.070180 TGAAGAATCTATGAGAGGGCAGAAG 59.930 44.000 0.00 0.00 0.00 2.85
1340 1475 4.964897 TGAAGAATCTATGAGAGGGCAGAA 59.035 41.667 0.00 0.00 0.00 3.02
1341 1476 4.550669 TGAAGAATCTATGAGAGGGCAGA 58.449 43.478 0.00 0.00 0.00 4.26
1342 1477 4.952071 TGAAGAATCTATGAGAGGGCAG 57.048 45.455 0.00 0.00 0.00 4.85
1343 1478 7.898100 ACTATATGAAGAATCTATGAGAGGGCA 59.102 37.037 0.00 0.00 0.00 5.36
1344 1479 8.305046 ACTATATGAAGAATCTATGAGAGGGC 57.695 38.462 0.00 0.00 0.00 5.19
1355 1490 9.976255 CGTAGTAGCAGTACTATATGAAGAATC 57.024 37.037 0.00 0.00 42.51 2.52
1356 1491 9.504708 ACGTAGTAGCAGTACTATATGAAGAAT 57.495 33.333 0.00 0.00 42.51 2.40
1357 1492 8.899427 ACGTAGTAGCAGTACTATATGAAGAA 57.101 34.615 0.00 0.00 42.51 2.52
1375 1510 3.058016 ACAAAGCTCGCAACTACGTAGTA 60.058 43.478 27.59 11.85 45.11 1.82
1377 1512 2.325761 ACAAAGCTCGCAACTACGTAG 58.674 47.619 20.97 20.97 0.00 3.51
1378 1513 2.427232 ACAAAGCTCGCAACTACGTA 57.573 45.000 0.00 0.00 0.00 3.57
1379 1514 1.525619 GAACAAAGCTCGCAACTACGT 59.474 47.619 0.00 0.00 0.00 3.57
1380 1515 1.792949 AGAACAAAGCTCGCAACTACG 59.207 47.619 0.00 0.00 0.00 3.51
1381 1516 3.441492 GAGAACAAAGCTCGCAACTAC 57.559 47.619 0.00 0.00 0.00 2.73
1389 1524 4.537936 ACTCAAAACGAGAACAAAGCTC 57.462 40.909 0.00 0.00 45.45 4.09
1428 1563 3.857157 TGGGCAGAGATTATTACCCAC 57.143 47.619 0.00 0.00 42.38 4.61
1461 1598 0.591659 TCTTGTCACGACCTCTCACG 59.408 55.000 0.00 0.00 0.00 4.35
1469 1606 1.588404 CCGTATGCATCTTGTCACGAC 59.412 52.381 16.80 0.24 0.00 4.34
1482 1619 3.063452 CACCACATAAGAACACCGTATGC 59.937 47.826 0.00 0.00 39.73 3.14
1509 1646 3.106827 TCTCATGGACTACCTTGCATCA 58.893 45.455 0.00 0.00 39.99 3.07
1536 1673 9.249457 AGTATGATTTATGTACAGATCACAACG 57.751 33.333 16.80 0.00 31.94 4.10
1568 1709 2.530701 ACACACAAACTTTCCCAACCA 58.469 42.857 0.00 0.00 0.00 3.67
1569 1710 3.194755 AGAACACACAAACTTTCCCAACC 59.805 43.478 0.00 0.00 0.00 3.77
1603 1744 7.391833 GGTCTTCCATTACATCTCAAGAAAGTT 59.608 37.037 0.00 0.00 0.00 2.66
1604 1745 6.881602 GGTCTTCCATTACATCTCAAGAAAGT 59.118 38.462 0.00 0.00 0.00 2.66
1605 1746 7.108847 AGGTCTTCCATTACATCTCAAGAAAG 58.891 38.462 0.00 0.00 35.89 2.62
1606 1747 7.020827 AGGTCTTCCATTACATCTCAAGAAA 57.979 36.000 0.00 0.00 35.89 2.52
1609 1750 6.314896 GTCAAGGTCTTCCATTACATCTCAAG 59.685 42.308 0.00 0.00 35.89 3.02
1615 1759 5.880901 ACAAGTCAAGGTCTTCCATTACAT 58.119 37.500 0.00 0.00 35.89 2.29
1659 1815 5.143369 TCCTCTGCACATACAGATACAGAT 58.857 41.667 0.00 0.00 45.34 2.90
1696 1852 6.290605 CAACAGGAAATTGATGGGAGTTTTT 58.709 36.000 0.00 0.00 0.00 1.94
1697 1853 5.221702 CCAACAGGAAATTGATGGGAGTTTT 60.222 40.000 0.00 0.00 37.36 2.43
1698 1854 4.284234 CCAACAGGAAATTGATGGGAGTTT 59.716 41.667 0.00 0.00 37.36 2.66
1699 1855 3.834231 CCAACAGGAAATTGATGGGAGTT 59.166 43.478 0.00 0.00 37.36 3.01
1700 1856 3.181418 ACCAACAGGAAATTGATGGGAGT 60.181 43.478 7.15 0.00 43.21 3.85
1702 1858 3.164268 CACCAACAGGAAATTGATGGGA 58.836 45.455 7.15 0.00 43.21 4.37
1704 1860 2.671914 CGCACCAACAGGAAATTGATGG 60.672 50.000 1.36 1.36 44.15 3.51
1705 1861 2.228582 TCGCACCAACAGGAAATTGATG 59.771 45.455 0.00 0.00 0.00 3.07
1706 1862 2.513753 TCGCACCAACAGGAAATTGAT 58.486 42.857 0.00 0.00 0.00 2.57
1707 1863 1.974265 TCGCACCAACAGGAAATTGA 58.026 45.000 0.00 0.00 0.00 2.57
1728 1912 1.154225 GGAGTTGTTGGCATTCGCG 60.154 57.895 0.00 0.00 39.92 5.87
1751 1935 1.725931 GCGCACGAACAGAAAATGGAG 60.726 52.381 0.30 0.00 0.00 3.86
1754 1938 1.044725 GTGCGCACGAACAGAAAATG 58.955 50.000 26.77 0.00 0.00 2.32
1774 1963 0.460284 ACACTAGCATTTCCTCCGCG 60.460 55.000 0.00 0.00 0.00 6.46
1800 1989 2.094417 GCTCGAGAAAGAAATTGGACGG 59.906 50.000 18.75 0.00 0.00 4.79
1833 2022 9.840427 GTTTTGTCTATTGCTGCTAAATTCTTA 57.160 29.630 0.00 0.00 0.00 2.10
1939 2154 3.118482 AGAGGTCGTGATCATTCTGCATT 60.118 43.478 0.00 0.00 0.00 3.56
1940 2155 2.433604 AGAGGTCGTGATCATTCTGCAT 59.566 45.455 0.00 0.00 0.00 3.96
1948 2163 0.395862 GGAGGGAGAGGTCGTGATCA 60.396 60.000 0.00 0.00 0.00 2.92
1969 2184 1.231958 TTGATTGAACCACCGCGTCC 61.232 55.000 4.92 0.00 0.00 4.79
2010 2228 8.720562 CAACTAGTATTGACATTGACATTGACA 58.279 33.333 0.00 1.81 0.00 3.58
2011 2229 8.721478 ACAACTAGTATTGACATTGACATTGAC 58.279 33.333 0.00 0.00 33.57 3.18
2012 2230 8.846943 ACAACTAGTATTGACATTGACATTGA 57.153 30.769 0.00 0.00 33.57 2.57
2014 2232 9.944376 ACTACAACTAGTATTGACATTGACATT 57.056 29.630 0.00 0.00 30.81 2.71
2015 2233 9.944376 AACTACAACTAGTATTGACATTGACAT 57.056 29.630 0.00 0.00 32.46 3.06
2016 2234 9.772973 AAACTACAACTAGTATTGACATTGACA 57.227 29.630 0.00 0.00 32.46 3.58
2018 2236 9.772973 ACAAACTACAACTAGTATTGACATTGA 57.227 29.630 0.00 0.00 32.46 2.57
2025 2243 5.670341 GCCGCACAAACTACAACTAGTATTG 60.670 44.000 0.00 0.00 32.46 1.90
2085 2308 4.000557 GTGACACCTGTGCGTGCG 62.001 66.667 0.00 0.00 37.25 5.34
2086 2309 1.987704 TTTGTGACACCTGTGCGTGC 61.988 55.000 2.45 0.00 37.25 5.34
2087 2310 0.027979 CTTTGTGACACCTGTGCGTG 59.972 55.000 2.45 0.00 39.75 5.34
2088 2311 0.107897 TCTTTGTGACACCTGTGCGT 60.108 50.000 2.45 0.00 0.00 5.24
2089 2312 1.013596 TTCTTTGTGACACCTGTGCG 58.986 50.000 2.45 0.00 0.00 5.34
2090 2313 2.017049 AGTTCTTTGTGACACCTGTGC 58.983 47.619 2.45 0.00 0.00 4.57
2091 2314 3.009723 ACAGTTCTTTGTGACACCTGTG 58.990 45.455 10.83 0.00 0.00 3.66
2092 2315 3.350219 ACAGTTCTTTGTGACACCTGT 57.650 42.857 2.45 5.19 0.00 4.00
2093 2316 3.242413 CGAACAGTTCTTTGTGACACCTG 60.242 47.826 11.60 4.55 0.00 4.00
2094 2317 2.936498 CGAACAGTTCTTTGTGACACCT 59.064 45.455 11.60 0.00 0.00 4.00
2105 2328 2.755650 GGATGTGACACGAACAGTTCT 58.244 47.619 11.60 0.00 0.00 3.01
2106 2329 1.455786 CGGATGTGACACGAACAGTTC 59.544 52.381 2.85 2.85 0.00 3.01
2115 2338 3.127533 GCTGGCCGGATGTGACAC 61.128 66.667 18.31 0.00 0.00 3.67
2174 2402 0.249073 GATCCCGTGACATCGTCTGG 60.249 60.000 0.00 0.00 33.15 3.86
2176 2404 0.456221 GTGATCCCGTGACATCGTCT 59.544 55.000 0.00 0.00 33.15 4.18


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

AutoCloner maintained by Alex Coulton.