Multiple sequence alignment - TraesCS5D01G422700

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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 TraesCS5D01G422700 chr5D 100.000 6210 0 0 1 6210 482586630 482592839 0.000000e+00 11468.0
1 TraesCS5D01G422700 chr5D 84.509 581 68 12 2006 2570 482244523 482245097 7.030000e-154 555.0
2 TraesCS5D01G422700 chr5D 83.175 630 82 12 2006 2619 482410218 482410839 7.030000e-154 555.0
3 TraesCS5D01G422700 chr5D 85.448 536 70 6 3371 3903 482246184 482246714 9.100000e-153 551.0
4 TraesCS5D01G422700 chr5D 90.588 85 8 0 2485 2569 482294447 482294531 5.090000e-21 113.0
5 TraesCS5D01G422700 chr5D 94.872 39 2 0 11 49 8502182 8502220 1.870000e-05 62.1
6 TraesCS5D01G422700 chr5B 92.243 4164 242 42 1743 5881 591828454 591832561 0.000000e+00 5825.0
7 TraesCS5D01G422700 chr5B 89.564 1102 68 17 76 1142 591826733 591827822 0.000000e+00 1354.0
8 TraesCS5D01G422700 chr5B 80.693 953 137 28 2974 3903 591555652 591556580 0.000000e+00 697.0
9 TraesCS5D01G422700 chr5B 90.244 492 30 7 1267 1745 591827910 591828396 1.470000e-175 627.0
10 TraesCS5D01G422700 chr5B 84.337 581 69 9 2006 2570 591554443 591555017 3.270000e-152 549.0
11 TraesCS5D01G422700 chr5B 80.827 266 6 15 5950 6196 591832887 591833126 3.850000e-37 167.0
12 TraesCS5D01G422700 chr5B 93.023 43 2 1 8 49 364085960 364085918 1.870000e-05 62.1
13 TraesCS5D01G422700 chr5A 92.305 2664 158 26 2659 5296 602344149 602346791 0.000000e+00 3740.0
14 TraesCS5D01G422700 chr5A 94.045 890 34 6 1773 2662 602342968 602343838 0.000000e+00 1332.0
15 TraesCS5D01G422700 chr5A 80.693 953 137 29 2974 3903 601728481 601729409 0.000000e+00 697.0
16 TraesCS5D01G422700 chr5A 83.633 611 73 15 1975 2570 601727282 601727880 3.270000e-152 549.0
17 TraesCS5D01G422700 chr5A 87.438 406 27 13 5280 5674 602346807 602347199 4.420000e-121 446.0
18 TraesCS5D01G422700 chr5A 94.030 134 7 1 889 1021 602341980 602342113 1.060000e-47 202.0
19 TraesCS5D01G422700 chr5A 82.072 251 28 12 1330 1571 602342527 602342769 1.370000e-46 198.0
20 TraesCS5D01G422700 chr5A 96.078 102 4 0 1629 1730 602342784 602342885 3.850000e-37 167.0
21 TraesCS5D01G422700 chr5A 85.246 183 4 9 5950 6110 602352158 602352339 3.850000e-37 167.0
22 TraesCS5D01G422700 chr5A 100.000 45 0 0 1225 1269 546897827 546897783 3.990000e-12 84.2
23 TraesCS5D01G422700 chr5A 92.982 57 4 0 5803 5859 602347456 602347512 3.990000e-12 84.2
24 TraesCS5D01G422700 chr5A 97.368 38 1 0 6127 6164 602352528 602352565 1.440000e-06 65.8
25 TraesCS5D01G422700 chr3B 82.541 905 124 19 3013 3912 821094052 821093177 0.000000e+00 765.0
26 TraesCS5D01G422700 chr3B 97.872 47 1 0 1226 1272 187335723 187335769 1.430000e-11 82.4
27 TraesCS5D01G422700 chr3D 81.818 902 114 23 3013 3899 609933388 609932522 0.000000e+00 712.0
28 TraesCS5D01G422700 chr2A 100.000 45 0 0 1226 1270 753776409 753776365 3.990000e-12 84.2
29 TraesCS5D01G422700 chr7B 97.872 47 1 0 1226 1272 460584997 460585043 1.430000e-11 82.4
30 TraesCS5D01G422700 chr4B 96.000 50 2 0 1223 1272 178078856 178078905 1.430000e-11 82.4
31 TraesCS5D01G422700 chr2D 97.872 47 1 0 1221 1267 526157424 526157378 1.430000e-11 82.4
32 TraesCS5D01G422700 chrUn 94.231 52 2 1 1225 1276 119047585 119047535 1.860000e-10 78.7
33 TraesCS5D01G422700 chr2B 100.000 42 0 0 1226 1267 41129536 41129577 1.860000e-10 78.7
34 TraesCS5D01G422700 chr2B 97.561 41 1 0 1227 1267 771233667 771233627 3.110000e-08 71.3
35 TraesCS5D01G422700 chr2B 94.595 37 2 0 13 49 106155764 106155728 2.420000e-04 58.4
36 TraesCS5D01G422700 chr6D 97.368 38 0 1 17 54 435298542 435298506 5.200000e-06 63.9
37 TraesCS5D01G422700 chr7D 93.023 43 2 1 8 49 579194980 579194938 1.870000e-05 62.1
38 TraesCS5D01G422700 chr1D 100.000 30 0 0 5804 5833 408937483 408937454 8.700000e-04 56.5


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 TraesCS5D01G422700 chr5D 482586630 482592839 6209 False 11468.000000 11468 100.000000 1 6210 1 chr5D.!!$F4 6209
1 TraesCS5D01G422700 chr5D 482410218 482410839 621 False 555.000000 555 83.175000 2006 2619 1 chr5D.!!$F3 613
2 TraesCS5D01G422700 chr5D 482244523 482246714 2191 False 553.000000 555 84.978500 2006 3903 2 chr5D.!!$F5 1897
3 TraesCS5D01G422700 chr5B 591826733 591833126 6393 False 1993.250000 5825 88.219500 76 6196 4 chr5B.!!$F2 6120
4 TraesCS5D01G422700 chr5B 591554443 591556580 2137 False 623.000000 697 82.515000 2006 3903 2 chr5B.!!$F1 1897
5 TraesCS5D01G422700 chr5A 602341980 602347512 5532 False 881.314286 3740 91.278571 889 5859 7 chr5A.!!$F2 4970
6 TraesCS5D01G422700 chr5A 601727282 601729409 2127 False 623.000000 697 82.163000 1975 3903 2 chr5A.!!$F1 1928
7 TraesCS5D01G422700 chr3B 821093177 821094052 875 True 765.000000 765 82.541000 3013 3912 1 chr3B.!!$R1 899
8 TraesCS5D01G422700 chr3D 609932522 609933388 866 True 712.000000 712 81.818000 3013 3899 1 chr3D.!!$R1 886

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
309 317 1.079612 TGATGAGGTCAGCACTGCG 60.080 57.895 0.00 0.00 37.34 5.18 F
1059 1246 0.259065 ACTCGGTCATGGAGAGGCTA 59.741 55.000 14.32 0.00 36.40 3.93 F
1265 1476 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85 F
2137 2438 0.389166 CTGGAAGCGACACTGGAGTC 60.389 60.000 0.00 0.00 35.19 3.36 F
3879 4946 2.148052 TAACGGCCACCTTGTCCCA 61.148 57.895 2.24 0.00 0.00 4.37 F
5000 6073 0.630673 ATCACAGGGCCTGGCAATTA 59.369 50.000 35.34 15.06 35.51 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 1461 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.0 0.0 0.00 4.00 R
2127 2428 1.269998 GTAGCTTGACGACTCCAGTGT 59.730 52.381 0.0 0.0 0.00 3.55 R
2379 2692 1.798813 GACTAACAGTTGCCAAGACCG 59.201 52.381 0.0 0.0 0.00 4.79 R
4043 5110 0.941542 TGCAACCTGTTCGTAACTGC 59.058 50.000 0.0 0.0 31.69 4.40 R
5193 6275 0.599558 CAATCACCAGTTGCCACCAG 59.400 55.000 0.0 0.0 0.00 4.00 R
5988 7503 0.924090 CTCGCTGCTTAACGTCCATC 59.076 55.000 0.0 0.0 0.00 3.51 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
60 61 2.933495 GGAGCGGGTCCAAAATAAAC 57.067 50.000 20.82 0.00 46.10 2.01
61 62 2.443416 GGAGCGGGTCCAAAATAAACT 58.557 47.619 20.82 0.00 46.10 2.66
62 63 2.422479 GGAGCGGGTCCAAAATAAACTC 59.578 50.000 20.82 0.00 46.10 3.01
63 64 2.081462 AGCGGGTCCAAAATAAACTCG 58.919 47.619 0.00 0.00 39.83 4.18
64 65 2.537639 CGGGTCCAAAATAAACTCGC 57.462 50.000 0.00 0.00 29.12 5.03
65 66 1.807742 CGGGTCCAAAATAAACTCGCA 59.192 47.619 0.00 0.00 29.12 5.10
66 67 2.159572 CGGGTCCAAAATAAACTCGCAG 60.160 50.000 0.00 0.00 29.12 5.18
67 68 2.415491 GGGTCCAAAATAAACTCGCAGC 60.415 50.000 0.00 0.00 0.00 5.25
68 69 2.415491 GGTCCAAAATAAACTCGCAGCC 60.415 50.000 0.00 0.00 0.00 4.85
69 70 1.466950 TCCAAAATAAACTCGCAGCCG 59.533 47.619 0.00 0.00 0.00 5.52
70 71 1.199097 CCAAAATAAACTCGCAGCCGT 59.801 47.619 0.00 0.00 35.54 5.68
71 72 2.351350 CCAAAATAAACTCGCAGCCGTT 60.351 45.455 0.00 0.00 35.54 4.44
72 73 2.894307 AAATAAACTCGCAGCCGTTC 57.106 45.000 0.00 0.00 35.54 3.95
73 74 1.803334 AATAAACTCGCAGCCGTTCA 58.197 45.000 0.00 0.00 35.54 3.18
74 75 2.024176 ATAAACTCGCAGCCGTTCAT 57.976 45.000 0.00 0.00 35.54 2.57
89 90 4.475944 CCGTTCATTTGGATGAGTGTTTC 58.524 43.478 0.00 0.00 42.90 2.78
91 92 4.475944 GTTCATTTGGATGAGTGTTTCCG 58.524 43.478 0.00 0.00 42.90 4.30
93 94 3.751175 TCATTTGGATGAGTGTTTCCGTC 59.249 43.478 0.00 0.00 37.37 4.79
132 134 9.906660 GTTTATTTTACTCAATGTCAACCATCA 57.093 29.630 0.00 0.00 31.75 3.07
157 159 9.787532 CAAGAACTTCTTACAAATTCAAAGTGA 57.212 29.630 3.64 0.00 33.78 3.41
167 169 6.945072 ACAAATTCAAAGTGACGAGTAGTTC 58.055 36.000 0.00 0.00 0.00 3.01
168 170 6.018180 ACAAATTCAAAGTGACGAGTAGTTCC 60.018 38.462 0.00 0.00 0.00 3.62
192 194 2.176546 CAAGTGCCGTTGCCATCG 59.823 61.111 0.00 0.00 36.33 3.84
200 202 2.931512 CCGTTGCCATCGGTTAAATT 57.068 45.000 6.04 0.00 42.62 1.82
202 204 3.947626 CCGTTGCCATCGGTTAAATTAG 58.052 45.455 6.04 0.00 42.62 1.73
224 231 1.755179 AGAATGGACGCCAAATGAGG 58.245 50.000 2.68 0.00 36.95 3.86
256 263 5.966636 AAAGGCATTCGAACTTGTTTTTC 57.033 34.783 0.00 0.00 0.00 2.29
257 264 3.977427 AGGCATTCGAACTTGTTTTTCC 58.023 40.909 0.00 0.00 0.00 3.13
258 265 3.636764 AGGCATTCGAACTTGTTTTTCCT 59.363 39.130 0.00 0.00 0.00 3.36
262 269 3.007473 TCGAACTTGTTTTTCCTGGGT 57.993 42.857 0.00 0.00 0.00 4.51
263 270 4.153673 TCGAACTTGTTTTTCCTGGGTA 57.846 40.909 0.00 0.00 0.00 3.69
268 275 6.200097 CGAACTTGTTTTTCCTGGGTAAATTG 59.800 38.462 0.00 0.00 0.00 2.32
271 278 3.385111 TGTTTTTCCTGGGTAAATTGCGT 59.615 39.130 0.00 0.00 0.00 5.24
277 284 1.801771 CTGGGTAAATTGCGTCGAACA 59.198 47.619 0.00 0.00 0.00 3.18
294 302 1.678635 CATGTTGTGCGGGGGTGAT 60.679 57.895 0.00 0.00 0.00 3.06
297 305 2.040544 GTTGTGCGGGGGTGATGAG 61.041 63.158 0.00 0.00 0.00 2.90
298 306 3.266686 TTGTGCGGGGGTGATGAGG 62.267 63.158 0.00 0.00 0.00 3.86
309 317 1.079612 TGATGAGGTCAGCACTGCG 60.080 57.895 0.00 0.00 37.34 5.18
582 612 2.192979 CCCACCATCCCCATCACG 59.807 66.667 0.00 0.00 0.00 4.35
586 616 2.203252 CCATCCCCATCACGGCAG 60.203 66.667 0.00 0.00 0.00 4.85
588 618 3.410628 ATCCCCATCACGGCAGCA 61.411 61.111 0.00 0.00 0.00 4.41
589 619 2.760378 ATCCCCATCACGGCAGCAT 61.760 57.895 0.00 0.00 0.00 3.79
591 621 3.274586 CCCATCACGGCAGCATCG 61.275 66.667 0.00 0.00 0.00 3.84
600 630 3.567797 GCAGCATCGCCGTTCCTC 61.568 66.667 0.00 0.00 0.00 3.71
601 631 2.125552 CAGCATCGCCGTTCCTCA 60.126 61.111 0.00 0.00 0.00 3.86
602 632 1.522355 CAGCATCGCCGTTCCTCAT 60.522 57.895 0.00 0.00 0.00 2.90
603 633 1.227380 AGCATCGCCGTTCCTCATC 60.227 57.895 0.00 0.00 0.00 2.92
604 634 2.247437 GCATCGCCGTTCCTCATCC 61.247 63.158 0.00 0.00 0.00 3.51
605 635 1.951130 CATCGCCGTTCCTCATCCG 60.951 63.158 0.00 0.00 0.00 4.18
809 850 2.359169 GGGGCTCCTCGTCATGTGA 61.359 63.158 0.00 0.00 0.00 3.58
841 882 2.691252 CCCCTGACCCCCACCTAC 60.691 72.222 0.00 0.00 0.00 3.18
899 940 1.358877 GGTTTCGCCATTCAATTGCC 58.641 50.000 0.00 0.00 37.17 4.52
1059 1246 0.259065 ACTCGGTCATGGAGAGGCTA 59.741 55.000 14.32 0.00 36.40 3.93
1063 1250 1.742768 GTCATGGAGAGGCTACCCG 59.257 63.158 7.58 0.58 35.76 5.28
1118 1305 2.660236 GTGCTTTCAAGAGGTACGTACG 59.340 50.000 18.98 15.01 0.00 3.67
1119 1306 2.294233 TGCTTTCAAGAGGTACGTACGT 59.706 45.455 25.98 25.98 0.00 3.57
1120 1307 3.501828 TGCTTTCAAGAGGTACGTACGTA 59.498 43.478 23.60 23.60 0.00 3.57
1142 1329 5.266733 ACACATGTTTTTCTCAAGCACAT 57.733 34.783 0.00 0.00 0.00 3.21
1147 1334 9.229784 CACATGTTTTTCTCAAGCACATATATC 57.770 33.333 0.00 0.00 0.00 1.63
1149 1336 9.447040 CATGTTTTTCTCAAGCACATATATCTG 57.553 33.333 0.00 0.00 0.00 2.90
1150 1337 8.791327 TGTTTTTCTCAAGCACATATATCTGA 57.209 30.769 0.00 0.00 0.00 3.27
1151 1338 9.399797 TGTTTTTCTCAAGCACATATATCTGAT 57.600 29.630 0.00 0.00 0.00 2.90
1152 1339 9.875675 GTTTTTCTCAAGCACATATATCTGATC 57.124 33.333 0.00 0.00 0.00 2.92
1153 1340 8.613060 TTTTCTCAAGCACATATATCTGATCC 57.387 34.615 0.00 0.00 0.00 3.36
1154 1341 5.958955 TCTCAAGCACATATATCTGATCCG 58.041 41.667 0.00 0.00 0.00 4.18
1155 1342 5.077134 TCAAGCACATATATCTGATCCGG 57.923 43.478 0.00 0.00 0.00 5.14
1160 1347 5.012046 AGCACATATATCTGATCCGGTTGAA 59.988 40.000 0.00 0.00 0.00 2.69
1162 1349 6.347725 GCACATATATCTGATCCGGTTGAAAC 60.348 42.308 0.00 0.00 0.00 2.78
1175 1362 5.047802 TCCGGTTGAAACGTTCTACTTAGAT 60.048 40.000 0.00 0.00 36.02 1.98
1176 1363 5.061808 CCGGTTGAAACGTTCTACTTAGATG 59.938 44.000 0.00 0.00 36.02 2.90
1177 1364 5.061808 CGGTTGAAACGTTCTACTTAGATGG 59.938 44.000 0.00 0.00 36.02 3.51
1178 1365 6.161381 GGTTGAAACGTTCTACTTAGATGGA 58.839 40.000 0.00 0.00 36.02 3.41
1179 1366 6.817140 GGTTGAAACGTTCTACTTAGATGGAT 59.183 38.462 0.00 0.00 36.02 3.41
1181 1368 6.263344 TGAAACGTTCTACTTAGATGGATCG 58.737 40.000 0.00 0.00 31.40 3.69
1182 1369 4.832590 ACGTTCTACTTAGATGGATCGG 57.167 45.455 0.00 0.00 31.40 4.18
1183 1370 3.004524 ACGTTCTACTTAGATGGATCGGC 59.995 47.826 0.00 0.00 31.40 5.54
1184 1371 3.253677 CGTTCTACTTAGATGGATCGGCT 59.746 47.826 0.00 0.00 31.40 5.52
1185 1372 4.261656 CGTTCTACTTAGATGGATCGGCTT 60.262 45.833 0.00 0.00 31.40 4.35
1187 1374 6.514541 CGTTCTACTTAGATGGATCGGCTTAA 60.515 42.308 0.00 0.00 31.40 1.85
1189 1376 7.159322 TCTACTTAGATGGATCGGCTTAATC 57.841 40.000 0.00 0.00 0.00 1.75
1190 1377 5.808366 ACTTAGATGGATCGGCTTAATCA 57.192 39.130 0.00 0.00 0.00 2.57
1191 1378 6.174720 ACTTAGATGGATCGGCTTAATCAA 57.825 37.500 0.00 0.00 0.00 2.57
1192 1379 5.992217 ACTTAGATGGATCGGCTTAATCAAC 59.008 40.000 0.00 0.00 0.00 3.18
1194 1381 4.780815 AGATGGATCGGCTTAATCAACAA 58.219 39.130 0.00 0.00 0.00 2.83
1196 1383 3.950397 TGGATCGGCTTAATCAACAACT 58.050 40.909 0.00 0.00 0.00 3.16
1197 1384 4.331968 TGGATCGGCTTAATCAACAACTT 58.668 39.130 0.00 0.00 0.00 2.66
1198 1385 4.394920 TGGATCGGCTTAATCAACAACTTC 59.605 41.667 0.00 0.00 0.00 3.01
1202 1389 4.933400 TCGGCTTAATCAACAACTTCCTAC 59.067 41.667 0.00 0.00 0.00 3.18
1203 1390 4.935808 CGGCTTAATCAACAACTTCCTACT 59.064 41.667 0.00 0.00 0.00 2.57
1207 1394 7.822822 GGCTTAATCAACAACTTCCTACTTAGA 59.177 37.037 0.00 0.00 0.00 2.10
1213 1424 9.965902 ATCAACAACTTCCTACTTAGATGAATT 57.034 29.630 0.00 0.00 0.00 2.17
1215 1426 8.454106 CAACAACTTCCTACTTAGATGAATTGG 58.546 37.037 0.00 0.00 0.00 3.16
1236 1447 5.482686 GGTTACAAACCGTAGTGTCAAAA 57.517 39.130 0.00 0.00 42.62 2.44
1237 1448 5.878133 GGTTACAAACCGTAGTGTCAAAAA 58.122 37.500 0.00 0.00 42.62 1.94
1259 1470 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1260 1471 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1261 1472 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
1262 1473 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
1263 1474 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
1264 1475 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1265 1476 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
1268 1479 2.077687 TATGGGACGGAGGGAGTAAC 57.922 55.000 0.00 0.00 0.00 2.50
1336 1552 1.518903 GCTTGTGGGAACTGCCAGTC 61.519 60.000 0.00 0.00 38.95 3.51
1344 1560 2.026262 GGGAACTGCCAGTCTTTATCCA 60.026 50.000 13.14 0.00 38.95 3.41
1346 1562 2.789409 ACTGCCAGTCTTTATCCACC 57.211 50.000 0.00 0.00 0.00 4.61
1353 1569 4.069304 CCAGTCTTTATCCACCGAAAACA 58.931 43.478 0.00 0.00 0.00 2.83
1359 1575 1.956297 ATCCACCGAAAACAACACGA 58.044 45.000 0.00 0.00 0.00 4.35
1360 1576 1.735386 TCCACCGAAAACAACACGAA 58.265 45.000 0.00 0.00 0.00 3.85
1367 1583 6.199342 CCACCGAAAACAACACGAATATTTTT 59.801 34.615 0.00 0.00 0.00 1.94
1417 1633 2.230025 AGCGCACGAGCTCATATAGAAT 59.770 45.455 15.40 0.00 45.67 2.40
1439 1662 7.337942 AGAATGGAAAACTGGACAATCATACTC 59.662 37.037 0.00 0.00 0.00 2.59
1442 1665 5.586643 GGAAAACTGGACAATCATACTCCTC 59.413 44.000 0.00 0.00 0.00 3.71
1530 1755 7.962964 TTCAGTAACCATAGCTGCATAATAC 57.037 36.000 1.02 0.00 0.00 1.89
1613 1838 5.005740 TGTGATGGATAATGCTTCCTATGC 58.994 41.667 0.00 0.00 34.17 3.14
1620 1845 7.290061 TGGATAATGCTTCCTATGCTTAGTTT 58.710 34.615 5.95 0.00 34.17 2.66
1621 1846 7.779798 TGGATAATGCTTCCTATGCTTAGTTTT 59.220 33.333 5.95 0.00 34.17 2.43
1622 1847 8.078596 GGATAATGCTTCCTATGCTTAGTTTTG 58.921 37.037 5.95 0.00 0.00 2.44
1623 1848 8.752005 ATAATGCTTCCTATGCTTAGTTTTGA 57.248 30.769 5.95 0.00 0.00 2.69
1624 1849 6.690194 ATGCTTCCTATGCTTAGTTTTGAG 57.310 37.500 5.95 0.00 0.00 3.02
1698 1929 6.126507 TGGGATGCATAGAAGATAAGGTTCAA 60.127 38.462 0.00 0.00 0.00 2.69
1737 1968 8.522830 ACAAAGGTTAGTATCCATGAAACAATG 58.477 33.333 0.00 0.00 0.00 2.82
1740 1971 8.281212 AGGTTAGTATCCATGAAACAATGTTC 57.719 34.615 0.00 0.00 0.00 3.18
1770 2061 3.753272 TCTCTTTTATTGTGCTCCTGTGC 59.247 43.478 0.00 0.00 0.00 4.57
1785 2080 2.820197 CCTGTGCCCTAACTCCTTTTTC 59.180 50.000 0.00 0.00 0.00 2.29
1792 2087 8.113462 TGTGCCCTAACTCCTTTTTCTTATATT 58.887 33.333 0.00 0.00 0.00 1.28
1859 2154 3.310193 GTTTATGAGCCTCCTCCTAGGT 58.690 50.000 9.08 0.00 39.02 3.08
1860 2155 4.481072 GTTTATGAGCCTCCTCCTAGGTA 58.519 47.826 9.08 0.00 39.02 3.08
1861 2156 2.687003 ATGAGCCTCCTCCTAGGTAC 57.313 55.000 9.08 0.00 39.02 3.34
1956 2251 2.840038 TGGACATGCATAGTTCCTCTGT 59.160 45.455 17.67 3.55 0.00 3.41
2021 2319 4.202212 ACAAAACCTGCCAAACCAAGTATC 60.202 41.667 0.00 0.00 0.00 2.24
2104 2405 9.233232 GTTTTAAATTTTAGGCATGTATCGGAG 57.767 33.333 0.00 0.00 0.00 4.63
2127 2428 2.494059 CTTTCCTGAAACTGGAAGCGA 58.506 47.619 9.33 0.00 41.25 4.93
2137 2438 0.389166 CTGGAAGCGACACTGGAGTC 60.389 60.000 0.00 0.00 35.19 3.36
2572 2885 6.425114 GCCGAAGTGAATGTGAGTATATTCAT 59.575 38.462 0.83 0.00 43.38 2.57
2648 3029 5.243954 ACTGTGTAGTCAGCTGAAGAACATA 59.756 40.000 20.19 18.21 38.84 2.29
2680 3375 6.942532 TTAAGTGTCTGACAAGCTGATTTT 57.057 33.333 12.81 0.82 0.00 1.82
2681 3376 5.841957 AAGTGTCTGACAAGCTGATTTTT 57.158 34.783 12.81 0.00 0.00 1.94
2687 3382 6.017934 TGTCTGACAAGCTGATTTTTGAGTAC 60.018 38.462 8.27 0.00 0.00 2.73
2743 3438 8.740123 TTTCAAAGAACGATTATGGCCTTATA 57.260 30.769 3.32 0.00 0.00 0.98
2751 3446 5.412594 ACGATTATGGCCTTATACATGCAAG 59.587 40.000 3.32 0.00 0.00 4.01
2814 3615 4.648762 TGTTCTGCTTTTTGAAGGGAATGA 59.351 37.500 0.00 0.00 0.00 2.57
3002 3967 8.311109 ACCATGACATTAATCCTTTGGTAAAAC 58.689 33.333 0.00 0.00 0.00 2.43
3377 4434 5.022787 AGATATCCAGCATCTCTTAGGACC 58.977 45.833 0.00 0.00 0.00 4.46
3655 4712 2.683968 TCCTTACAGTGTCAATGACGC 58.316 47.619 18.29 18.29 42.60 5.19
3706 4763 6.365970 AACACTCTTCCACTTCTATCACAT 57.634 37.500 0.00 0.00 0.00 3.21
3710 4767 7.819900 ACACTCTTCCACTTCTATCACATTTAC 59.180 37.037 0.00 0.00 0.00 2.01
3726 4783 5.120053 CACATTTACGCAGTTGATAGTCACA 59.880 40.000 0.00 0.00 37.78 3.58
3869 4936 3.985019 TTATTTCCTGAGTAACGGCCA 57.015 42.857 2.24 0.00 0.00 5.36
3879 4946 2.148052 TAACGGCCACCTTGTCCCA 61.148 57.895 2.24 0.00 0.00 4.37
4024 5091 2.351111 GCTGCTCCTTCGAATCAAGAAG 59.649 50.000 0.00 1.84 43.35 2.85
4036 5103 4.941263 CGAATCAAGAAGGACCACCATTTA 59.059 41.667 0.00 0.00 38.94 1.40
4043 5110 3.140325 AGGACCACCATTTACACAGTG 57.860 47.619 0.00 0.00 38.94 3.66
4060 5127 2.032894 CAGTGCAGTTACGAACAGGTTG 60.033 50.000 0.00 0.00 0.00 3.77
4062 5129 0.941542 GCAGTTACGAACAGGTTGCA 59.058 50.000 0.00 0.00 31.46 4.08
4208 5275 6.603940 AGAACTATATCAGCAGGATCCTTC 57.396 41.667 13.00 7.60 37.44 3.46
4212 5279 9.415008 GAACTATATCAGCAGGATCCTTCTATA 57.585 37.037 13.99 11.84 37.44 1.31
4214 5281 8.565239 ACTATATCAGCAGGATCCTTCTATACT 58.435 37.037 13.99 2.77 37.44 2.12
4231 5298 9.482627 CTTCTATACTGTGTAATGGAATTCCTC 57.517 37.037 24.73 12.83 37.87 3.71
4237 5304 6.160459 ACTGTGTAATGGAATTCCTCCCTATT 59.840 38.462 24.73 16.95 44.69 1.73
4245 5312 4.140924 GGAATTCCTCCCTATTTGACCCAT 60.141 45.833 17.73 0.00 38.44 4.00
4273 5340 4.167502 ACATCAATGGTCAGGGATCATTCT 59.832 41.667 1.87 0.00 40.85 2.40
4278 5345 1.202746 GGTCAGGGATCATTCTCAGCC 60.203 57.143 0.00 0.00 0.00 4.85
4371 5438 2.988493 CCAACAATTCATTGCCAACTCG 59.012 45.455 0.00 0.00 41.38 4.18
4482 5549 2.284190 GACTGCTGCTCCTGGTAATTC 58.716 52.381 0.00 0.00 0.00 2.17
4509 5576 1.207593 GTAACAGGCGTGCTTGCTG 59.792 57.895 6.26 0.00 34.52 4.41
4705 5777 8.490355 CCAATTGAAGTATGTGCTTTTCTTTTC 58.510 33.333 7.12 0.00 0.00 2.29
4944 6017 6.655078 ATTTTCTATGCCCATGATAACCAC 57.345 37.500 0.00 0.00 0.00 4.16
4988 6061 1.669779 GCTCAGCTGCTAAATCACAGG 59.330 52.381 9.47 0.00 34.38 4.00
5000 6073 0.630673 ATCACAGGGCCTGGCAATTA 59.369 50.000 35.34 15.06 35.51 1.40
5055 6129 6.554334 TGTTTACCTTCACAATAAGCAGAC 57.446 37.500 0.00 0.00 0.00 3.51
5099 6181 3.111484 ACCAAAATGTTGAAACCCTGGT 58.889 40.909 0.00 0.00 36.83 4.00
5177 6259 4.155826 TGCCGAATTCTAACAACCAATCTG 59.844 41.667 3.52 0.00 0.00 2.90
5233 6315 2.645838 ACTTGAGACCACAGCAACAT 57.354 45.000 0.00 0.00 0.00 2.71
5237 6319 3.319137 TGAGACCACAGCAACATACTC 57.681 47.619 0.00 0.00 0.00 2.59
5248 6330 4.343526 CAGCAACATACTCTCCTCTACCAT 59.656 45.833 0.00 0.00 0.00 3.55
5260 6342 7.285858 ACTCTCCTCTACCATAGTAAACATGAC 59.714 40.741 0.00 0.00 0.00 3.06
5266 6348 3.202906 CCATAGTAAACATGACGGTGGG 58.797 50.000 0.00 0.00 0.00 4.61
5283 6397 2.464459 GGAGCCGGCGATTCAAGTG 61.464 63.158 23.20 0.00 0.00 3.16
5344 6459 5.687730 CAGTGTTGTGAGTAGTAACAGACAG 59.312 44.000 0.00 0.00 35.24 3.51
5438 6561 7.603180 ATCTTTTAGAAAAAGAGGGCACTTT 57.397 32.000 17.10 3.68 39.36 2.66
5452 6575 5.236655 GGGCACTTTGCTCTTCTTAATAC 57.763 43.478 0.00 0.00 41.63 1.89
5478 6604 3.699067 GCAAATATTCGCATTGCTGACT 58.301 40.909 7.12 3.32 44.54 3.41
5534 6660 7.715249 TGCTAAGGTGAATTTCCTATGTATGTC 59.285 37.037 4.02 0.00 34.56 3.06
5548 6674 6.312672 CCTATGTATGTCGACACATTTTCACA 59.687 38.462 22.71 15.24 40.66 3.58
5549 6675 6.741992 ATGTATGTCGACACATTTTCACAT 57.258 33.333 22.71 16.64 40.66 3.21
5550 6676 6.552859 TGTATGTCGACACATTTTCACATT 57.447 33.333 22.71 2.47 40.66 2.71
5551 6677 6.598525 TGTATGTCGACACATTTTCACATTC 58.401 36.000 22.71 0.00 40.66 2.67
5552 6678 5.947228 ATGTCGACACATTTTCACATTCT 57.053 34.783 22.71 0.00 40.66 2.40
5640 6768 1.878953 GACATTCGGTCAGTTGGTGT 58.121 50.000 0.00 0.00 46.19 4.16
5642 6770 1.416401 ACATTCGGTCAGTTGGTGTCT 59.584 47.619 0.00 0.00 0.00 3.41
5656 6784 6.656693 CAGTTGGTGTCTCCTAATTGAAAGAT 59.343 38.462 0.00 0.00 37.07 2.40
5674 6802 8.243961 TGAAAGATTTCCTTCCACATTTTACA 57.756 30.769 3.00 0.00 36.36 2.41
5692 6889 2.639065 ACAGCTGGTTCTCGTTTTGAA 58.361 42.857 19.93 0.00 0.00 2.69
5694 6891 3.632145 ACAGCTGGTTCTCGTTTTGAATT 59.368 39.130 19.93 0.00 0.00 2.17
5695 6892 4.097892 ACAGCTGGTTCTCGTTTTGAATTT 59.902 37.500 19.93 0.00 0.00 1.82
5761 6958 1.228124 TCAAACAGGTTGAGGGCGG 60.228 57.895 0.00 0.00 41.47 6.13
5848 7107 0.671163 CCGCGGTTTAGTTAGCACCA 60.671 55.000 19.50 0.00 0.00 4.17
5864 7123 1.080569 CCAGCGATTTGTGCCCAAC 60.081 57.895 0.00 0.00 0.00 3.77
5883 7158 4.796231 CGCCTCGGACTTGGTCGG 62.796 72.222 0.00 0.00 34.82 4.79
5921 7392 2.665603 GAGGGCCACTCCAGACAC 59.334 66.667 6.18 0.00 40.49 3.67
5922 7393 2.930562 AGGGCCACTCCAGACACC 60.931 66.667 6.18 0.00 36.21 4.16
5935 7437 2.034066 ACACCATGCCGTCAAGGG 59.966 61.111 0.00 0.00 41.48 3.95
5947 7449 4.988598 CAAGGGTGCGTCGGTGCT 62.989 66.667 0.00 0.00 35.36 4.40
5948 7450 4.681978 AAGGGTGCGTCGGTGCTC 62.682 66.667 0.00 0.00 35.36 4.26
5979 7494 0.104120 GGCCTTTGTTTCCTGCGTTT 59.896 50.000 0.00 0.00 0.00 3.60
5983 7498 2.035832 CCTTTGTTTCCTGCGTTTGGAT 59.964 45.455 0.00 0.00 33.09 3.41
5988 7503 3.814268 CCTGCGTTTGGATGGCGG 61.814 66.667 0.00 0.00 0.00 6.13
6002 7517 1.448893 GGCGGATGGACGTTAAGCA 60.449 57.895 0.00 0.00 35.98 3.91
6044 7575 2.128507 GCGTAGGAGGGAGGGTGAG 61.129 68.421 0.00 0.00 0.00 3.51
6079 7610 4.100084 CAGTGGGCATGGCGGAGA 62.100 66.667 13.76 0.00 0.00 3.71
6080 7611 4.101448 AGTGGGCATGGCGGAGAC 62.101 66.667 13.76 7.16 0.00 3.36
6092 7623 3.878519 GGAGACGGACGAGCTCGG 61.879 72.222 36.93 22.99 44.95 4.63
6093 7624 2.818714 GAGACGGACGAGCTCGGA 60.819 66.667 36.93 0.00 44.95 4.55
6094 7625 2.815298 GAGACGGACGAGCTCGGAG 61.815 68.421 36.93 27.98 44.95 4.63
6095 7626 4.539881 GACGGACGAGCTCGGAGC 62.540 72.222 36.93 25.16 44.95 4.70
6126 7657 4.101448 GTGGGGCATGCTCGGAGT 62.101 66.667 18.92 0.00 0.00 3.85
6127 7658 3.785859 TGGGGCATGCTCGGAGTC 61.786 66.667 18.92 0.00 0.00 3.36
6128 7659 4.899239 GGGGCATGCTCGGAGTCG 62.899 72.222 18.92 0.00 37.82 4.18
6129 7660 4.899239 GGGCATGCTCGGAGTCGG 62.899 72.222 18.92 0.00 36.95 4.79
6130 7661 3.838271 GGCATGCTCGGAGTCGGA 61.838 66.667 18.92 0.00 36.95 4.55
6131 7662 2.279120 GCATGCTCGGAGTCGGAG 60.279 66.667 20.38 20.38 36.95 4.63
6196 7730 0.533755 GTTATCGCTGCAGCTGGGAT 60.534 55.000 34.22 28.80 38.22 3.85
6197 7731 0.250038 TTATCGCTGCAGCTGGGATC 60.250 55.000 34.22 6.15 36.65 3.36
6198 7732 1.117749 TATCGCTGCAGCTGGGATCT 61.118 55.000 34.22 14.00 36.65 2.75
6199 7733 2.661840 ATCGCTGCAGCTGGGATCTG 62.662 60.000 34.22 17.37 39.32 2.90
6200 7734 2.516460 GCTGCAGCTGGGATCTGG 60.516 66.667 31.33 0.00 38.21 3.86
6201 7735 2.516460 CTGCAGCTGGGATCTGGC 60.516 66.667 17.12 0.00 32.41 4.85
6202 7736 4.478371 TGCAGCTGGGATCTGGCG 62.478 66.667 17.12 0.00 32.41 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.928714 TATTTTGGACCCGCTCCCCC 61.929 60.000 0.00 0.00 38.49 5.40
39 40 0.033894 TTATTTTGGACCCGCTCCCC 60.034 55.000 0.00 0.00 38.49 4.81
40 41 1.475280 GTTTATTTTGGACCCGCTCCC 59.525 52.381 0.00 0.00 38.49 4.30
41 42 2.422479 GAGTTTATTTTGGACCCGCTCC 59.578 50.000 0.00 0.00 39.97 4.70
42 43 2.095372 CGAGTTTATTTTGGACCCGCTC 59.905 50.000 0.00 0.00 0.00 5.03
43 44 2.081462 CGAGTTTATTTTGGACCCGCT 58.919 47.619 0.00 0.00 0.00 5.52
44 45 1.466866 GCGAGTTTATTTTGGACCCGC 60.467 52.381 0.00 0.00 0.00 6.13
45 46 1.807742 TGCGAGTTTATTTTGGACCCG 59.192 47.619 0.00 0.00 0.00 5.28
46 47 2.415491 GCTGCGAGTTTATTTTGGACCC 60.415 50.000 0.00 0.00 0.00 4.46
47 48 2.415491 GGCTGCGAGTTTATTTTGGACC 60.415 50.000 0.00 0.00 0.00 4.46
48 49 2.727916 CGGCTGCGAGTTTATTTTGGAC 60.728 50.000 0.00 0.00 0.00 4.02
49 50 1.466950 CGGCTGCGAGTTTATTTTGGA 59.533 47.619 0.00 0.00 0.00 3.53
50 51 1.199097 ACGGCTGCGAGTTTATTTTGG 59.801 47.619 0.00 0.00 0.00 3.28
51 52 2.611974 ACGGCTGCGAGTTTATTTTG 57.388 45.000 0.00 0.00 0.00 2.44
52 53 2.550606 TGAACGGCTGCGAGTTTATTTT 59.449 40.909 12.17 0.00 0.00 1.82
53 54 2.147958 TGAACGGCTGCGAGTTTATTT 58.852 42.857 12.17 0.00 0.00 1.40
54 55 1.803334 TGAACGGCTGCGAGTTTATT 58.197 45.000 12.17 0.00 0.00 1.40
55 56 2.024176 ATGAACGGCTGCGAGTTTAT 57.976 45.000 12.17 10.89 0.00 1.40
56 57 1.803334 AATGAACGGCTGCGAGTTTA 58.197 45.000 12.17 9.32 0.00 2.01
57 58 0.951558 AAATGAACGGCTGCGAGTTT 59.048 45.000 12.17 0.00 0.00 2.66
58 59 0.238289 CAAATGAACGGCTGCGAGTT 59.762 50.000 11.02 11.02 0.00 3.01
59 60 1.577328 CCAAATGAACGGCTGCGAGT 61.577 55.000 0.00 0.00 0.00 4.18
60 61 1.135315 CCAAATGAACGGCTGCGAG 59.865 57.895 0.00 0.00 0.00 5.03
61 62 0.676466 ATCCAAATGAACGGCTGCGA 60.676 50.000 0.00 0.00 0.00 5.10
62 63 0.523968 CATCCAAATGAACGGCTGCG 60.524 55.000 0.00 0.00 34.61 5.18
63 64 0.810648 TCATCCAAATGAACGGCTGC 59.189 50.000 0.00 0.00 38.97 5.25
64 65 2.086869 ACTCATCCAAATGAACGGCTG 58.913 47.619 0.00 0.00 41.33 4.85
65 66 2.086869 CACTCATCCAAATGAACGGCT 58.913 47.619 0.00 0.00 41.33 5.52
66 67 1.812571 ACACTCATCCAAATGAACGGC 59.187 47.619 0.00 0.00 41.33 5.68
67 68 4.475944 GAAACACTCATCCAAATGAACGG 58.524 43.478 0.00 0.00 41.33 4.44
68 69 4.475944 GGAAACACTCATCCAAATGAACG 58.524 43.478 0.00 0.00 41.33 3.95
69 70 4.023193 ACGGAAACACTCATCCAAATGAAC 60.023 41.667 0.00 0.00 41.33 3.18
70 71 4.141287 ACGGAAACACTCATCCAAATGAA 58.859 39.130 0.00 0.00 41.33 2.57
71 72 3.750371 ACGGAAACACTCATCCAAATGA 58.250 40.909 0.00 0.00 39.63 2.57
72 73 3.424829 CGACGGAAACACTCATCCAAATG 60.425 47.826 0.00 0.00 35.34 2.32
73 74 2.742053 CGACGGAAACACTCATCCAAAT 59.258 45.455 0.00 0.00 35.34 2.32
74 75 2.139917 CGACGGAAACACTCATCCAAA 58.860 47.619 0.00 0.00 35.34 3.28
89 90 1.833860 AACAAAACATTGCACGACGG 58.166 45.000 0.00 0.00 0.00 4.79
91 92 8.536407 AGTAAAATAAACAAAACATTGCACGAC 58.464 29.630 0.00 0.00 0.00 4.34
93 94 8.535592 TGAGTAAAATAAACAAAACATTGCACG 58.464 29.630 0.00 0.00 0.00 5.34
132 134 9.788960 GTCACTTTGAATTTGTAAGAAGTTCTT 57.211 29.630 21.35 21.35 40.35 2.52
133 135 8.122952 CGTCACTTTGAATTTGTAAGAAGTTCT 58.877 33.333 0.00 0.00 0.00 3.01
157 159 0.322277 TGCCTCTCGGAACTACTCGT 60.322 55.000 0.00 0.00 0.00 4.18
187 189 8.129211 GTCCATTCTTTCTAATTTAACCGATGG 58.871 37.037 0.00 0.00 0.00 3.51
192 194 6.127842 TGGCGTCCATTCTTTCTAATTTAACC 60.128 38.462 0.00 0.00 0.00 2.85
197 199 5.975693 TTTGGCGTCCATTCTTTCTAATT 57.024 34.783 0.00 0.00 31.53 1.40
198 200 5.652014 TCATTTGGCGTCCATTCTTTCTAAT 59.348 36.000 0.00 0.00 31.53 1.73
199 201 5.007034 TCATTTGGCGTCCATTCTTTCTAA 58.993 37.500 0.00 0.00 31.53 2.10
200 202 4.584874 TCATTTGGCGTCCATTCTTTCTA 58.415 39.130 0.00 0.00 31.53 2.10
202 204 3.428045 CCTCATTTGGCGTCCATTCTTTC 60.428 47.826 0.00 0.00 31.53 2.62
238 245 3.735746 CCAGGAAAAACAAGTTCGAATGC 59.264 43.478 0.00 0.00 0.00 3.56
242 249 3.007473 ACCCAGGAAAAACAAGTTCGA 57.993 42.857 0.00 0.00 0.00 3.71
256 263 1.129811 GTTCGACGCAATTTACCCAGG 59.870 52.381 0.00 0.00 0.00 4.45
257 264 1.801771 TGTTCGACGCAATTTACCCAG 59.198 47.619 0.00 0.00 0.00 4.45
258 265 1.880271 TGTTCGACGCAATTTACCCA 58.120 45.000 0.00 0.00 0.00 4.51
262 269 4.215201 CACAACATGTTCGACGCAATTTA 58.785 39.130 8.48 0.00 0.00 1.40
263 270 3.042189 CACAACATGTTCGACGCAATTT 58.958 40.909 8.48 0.00 0.00 1.82
268 275 1.788203 CGCACAACATGTTCGACGC 60.788 57.895 8.48 7.93 39.26 5.19
271 278 1.963855 CCCCGCACAACATGTTCGA 60.964 57.895 17.01 0.00 39.26 3.71
277 284 1.678635 CATCACCCCCGCACAACAT 60.679 57.895 0.00 0.00 0.00 2.71
421 429 4.934942 TCACGCACACACGGACGG 62.935 66.667 0.00 0.00 37.37 4.79
456 464 0.329596 GGCCAAGTGAAGGTGGAGAT 59.670 55.000 0.00 0.00 37.03 2.75
540 548 2.034066 TTTGAGGGGCGAGCTTGG 59.966 61.111 2.37 0.00 0.00 3.61
586 616 2.247437 GGATGAGGAACGGCGATGC 61.247 63.158 16.62 7.41 0.00 3.91
588 618 2.417516 CGGATGAGGAACGGCGAT 59.582 61.111 16.62 0.00 0.00 4.58
589 619 4.508128 GCGGATGAGGAACGGCGA 62.508 66.667 16.62 0.00 0.00 5.54
850 891 1.517242 CACAAGAGGAGACCAACTGC 58.483 55.000 0.00 0.00 37.22 4.40
853 894 0.951040 CGGCACAAGAGGAGACCAAC 60.951 60.000 0.00 0.00 0.00 3.77
899 940 1.468224 CGGTGAGTTCAGATCGTGGAG 60.468 57.143 0.00 0.00 0.00 3.86
1080 1267 0.609662 CACCAAAATGCTCCCCCAAG 59.390 55.000 0.00 0.00 0.00 3.61
1118 1305 5.577835 TGTGCTTGAGAAAAACATGTGTAC 58.422 37.500 0.00 0.00 0.00 2.90
1119 1306 5.826601 TGTGCTTGAGAAAAACATGTGTA 57.173 34.783 0.00 0.00 0.00 2.90
1120 1307 4.717233 TGTGCTTGAGAAAAACATGTGT 57.283 36.364 0.00 0.00 0.00 3.72
1121 1308 9.229784 GATATATGTGCTTGAGAAAAACATGTG 57.770 33.333 0.00 0.00 33.67 3.21
1142 1329 5.524971 ACGTTTCAACCGGATCAGATATA 57.475 39.130 9.46 0.00 0.00 0.86
1147 1334 2.413837 AGAACGTTTCAACCGGATCAG 58.586 47.619 9.46 0.00 0.00 2.90
1149 1336 3.582780 AGTAGAACGTTTCAACCGGATC 58.417 45.455 9.46 0.00 0.00 3.36
1150 1337 3.672767 AGTAGAACGTTTCAACCGGAT 57.327 42.857 9.46 0.00 0.00 4.18
1151 1338 3.457610 AAGTAGAACGTTTCAACCGGA 57.542 42.857 9.46 0.00 0.00 5.14
1152 1339 4.549458 TCTAAGTAGAACGTTTCAACCGG 58.451 43.478 0.46 0.00 0.00 5.28
1153 1340 5.061808 CCATCTAAGTAGAACGTTTCAACCG 59.938 44.000 0.46 0.00 35.69 4.44
1154 1341 6.161381 TCCATCTAAGTAGAACGTTTCAACC 58.839 40.000 0.46 0.00 35.69 3.77
1155 1342 7.253684 CGATCCATCTAAGTAGAACGTTTCAAC 60.254 40.741 0.46 1.20 35.69 3.18
1160 1347 4.499357 GCCGATCCATCTAAGTAGAACGTT 60.499 45.833 0.00 0.00 35.69 3.99
1162 1349 3.253677 AGCCGATCCATCTAAGTAGAACG 59.746 47.826 0.00 0.00 35.69 3.95
1175 1362 3.950397 AGTTGTTGATTAAGCCGATCCA 58.050 40.909 0.00 0.00 0.00 3.41
1176 1363 4.201920 GGAAGTTGTTGATTAAGCCGATCC 60.202 45.833 0.00 0.00 0.00 3.36
1177 1364 4.636206 AGGAAGTTGTTGATTAAGCCGATC 59.364 41.667 0.00 0.00 0.00 3.69
1178 1365 4.589908 AGGAAGTTGTTGATTAAGCCGAT 58.410 39.130 0.00 0.00 0.00 4.18
1179 1366 4.015872 AGGAAGTTGTTGATTAAGCCGA 57.984 40.909 0.00 0.00 0.00 5.54
1181 1368 6.819397 AAGTAGGAAGTTGTTGATTAAGCC 57.181 37.500 0.00 0.00 0.00 4.35
1182 1369 8.773404 TCTAAGTAGGAAGTTGTTGATTAAGC 57.227 34.615 0.00 0.00 0.00 3.09
1187 1374 9.965902 AATTCATCTAAGTAGGAAGTTGTTGAT 57.034 29.630 0.00 0.00 0.00 2.57
1189 1376 8.454106 CCAATTCATCTAAGTAGGAAGTTGTTG 58.546 37.037 0.00 0.00 0.00 3.33
1190 1377 8.164070 ACCAATTCATCTAAGTAGGAAGTTGTT 58.836 33.333 0.00 0.00 0.00 2.83
1191 1378 7.690256 ACCAATTCATCTAAGTAGGAAGTTGT 58.310 34.615 0.00 0.00 0.00 3.32
1192 1379 8.567285 AACCAATTCATCTAAGTAGGAAGTTG 57.433 34.615 0.00 0.00 0.00 3.16
1194 1381 8.822805 TGTAACCAATTCATCTAAGTAGGAAGT 58.177 33.333 0.00 0.00 0.00 3.01
1197 1384 9.444600 GTTTGTAACCAATTCATCTAAGTAGGA 57.555 33.333 0.00 0.00 0.00 2.94
1234 1445 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1235 1446 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1236 1447 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1237 1448 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1238 1449 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1240 1451 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
1241 1452 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1242 1453 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
1243 1454 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
1244 1455 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1245 1456 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1246 1457 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1247 1458 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
1248 1459 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
1249 1460 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
1250 1461 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
1251 1462 0.613853 CTGTTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
1252 1463 0.324091 TCTGTTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
1253 1464 1.104630 CTCTGTTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
1254 1465 1.104630 CCTCTGTTACTCCCTCCGTC 58.895 60.000 0.00 0.00 0.00 4.79
1255 1466 0.702902 TCCTCTGTTACTCCCTCCGT 59.297 55.000 0.00 0.00 0.00 4.69
1256 1467 1.848652 TTCCTCTGTTACTCCCTCCG 58.151 55.000 0.00 0.00 0.00 4.63
1257 1468 3.682999 GCATTTCCTCTGTTACTCCCTCC 60.683 52.174 0.00 0.00 0.00 4.30
1258 1469 3.055094 TGCATTTCCTCTGTTACTCCCTC 60.055 47.826 0.00 0.00 0.00 4.30
1259 1470 2.912956 TGCATTTCCTCTGTTACTCCCT 59.087 45.455 0.00 0.00 0.00 4.20
1260 1471 3.010420 GTGCATTTCCTCTGTTACTCCC 58.990 50.000 0.00 0.00 0.00 4.30
1261 1472 3.674997 TGTGCATTTCCTCTGTTACTCC 58.325 45.455 0.00 0.00 0.00 3.85
1262 1473 5.886960 AATGTGCATTTCCTCTGTTACTC 57.113 39.130 0.00 0.00 0.00 2.59
1263 1474 6.259550 GAAATGTGCATTTCCTCTGTTACT 57.740 37.500 20.87 0.00 46.68 2.24
1296 1507 2.970324 TCGGCACACTTCAACCGC 60.970 61.111 0.00 0.00 45.23 5.68
1336 1552 4.024725 TCGTGTTGTTTTCGGTGGATAAAG 60.025 41.667 0.00 0.00 0.00 1.85
1417 1633 5.014123 AGGAGTATGATTGTCCAGTTTTCCA 59.986 40.000 0.00 0.00 32.23 3.53
1439 1662 8.970859 ATAACTTGATTATCTGAACTTGGAGG 57.029 34.615 0.00 0.00 0.00 4.30
1530 1755 7.950512 AGACTCACAGAGACCATTTCTATATG 58.049 38.462 0.31 0.00 33.22 1.78
1620 1845 9.627123 CAAGAGATACAATTAATTACCCCTCAA 57.373 33.333 0.00 0.00 0.00 3.02
1621 1846 8.778059 ACAAGAGATACAATTAATTACCCCTCA 58.222 33.333 0.00 0.00 0.00 3.86
1622 1847 9.628500 AACAAGAGATACAATTAATTACCCCTC 57.372 33.333 0.00 6.15 0.00 4.30
1623 1848 9.408648 CAACAAGAGATACAATTAATTACCCCT 57.591 33.333 0.00 0.00 0.00 4.79
1624 1849 9.185680 ACAACAAGAGATACAATTAATTACCCC 57.814 33.333 0.00 0.00 0.00 4.95
1698 1929 9.959721 ATACTAACCTTTGTCTGTACAATTGAT 57.040 29.630 13.59 0.00 44.85 2.57
1737 1968 9.372369 AGCACAATAAAAGAGATACTACAGAAC 57.628 33.333 0.00 0.00 0.00 3.01
1740 1971 8.200792 AGGAGCACAATAAAAGAGATACTACAG 58.799 37.037 0.00 0.00 0.00 2.74
1980 2275 9.466497 AGGTTTTGTAGTATCATGACATGAATT 57.534 29.630 21.52 9.29 43.50 2.17
1999 2295 2.689553 ACTTGGTTTGGCAGGTTTTG 57.310 45.000 0.00 0.00 0.00 2.44
2003 2299 2.795329 CAGATACTTGGTTTGGCAGGT 58.205 47.619 0.00 0.00 0.00 4.00
2004 2300 1.474077 GCAGATACTTGGTTTGGCAGG 59.526 52.381 0.00 0.00 0.00 4.85
2021 2319 7.840342 ACTTCACAGATTATGTAGAAAGCAG 57.160 36.000 0.00 0.00 41.41 4.24
2104 2405 1.889170 CTTCCAGTTTCAGGAAAGCCC 59.111 52.381 0.00 0.00 44.07 5.19
2127 2428 1.269998 GTAGCTTGACGACTCCAGTGT 59.730 52.381 0.00 0.00 0.00 3.55
2155 2459 2.811431 TGTATCTTTTGGTCCTGCAACG 59.189 45.455 0.00 0.00 0.00 4.10
2379 2692 1.798813 GACTAACAGTTGCCAAGACCG 59.201 52.381 0.00 0.00 0.00 4.79
2572 2885 6.855763 AAATTGGTGCTCAGAATGGATAAA 57.144 33.333 0.00 0.00 36.16 1.40
2601 2972 6.835488 AGTGTACCTCCAATTCGGTATAGTTA 59.165 38.462 0.00 0.00 38.01 2.24
2609 2980 2.289444 ACACAGTGTACCTCCAATTCGG 60.289 50.000 3.69 0.00 0.00 4.30
2648 3029 5.871396 TGTCAGACACTTAAAGGAGAAGT 57.129 39.130 0.00 0.00 37.64 3.01
2680 3375 9.772973 TGCTGTAAGATTTTCTTTAGTACTCAA 57.227 29.630 0.00 0.00 37.89 3.02
2681 3376 9.204570 GTGCTGTAAGATTTTCTTTAGTACTCA 57.795 33.333 0.00 0.00 37.89 3.41
2743 3438 6.663093 TGAGGTAAAATAATGTCCTTGCATGT 59.337 34.615 0.00 0.00 0.00 3.21
2833 3634 4.506886 GTGAAGTCACAGTACTGCTACT 57.493 45.455 22.90 21.09 45.75 2.57
3039 4004 6.541641 AGAGTTCAGACAAGATTGCCAATATC 59.458 38.462 0.00 0.00 0.00 1.63
3243 4208 5.547465 TGCATATATACCTTTTGGAGACCG 58.453 41.667 0.00 0.00 44.07 4.79
3353 4403 6.011185 AGGTCCTAAGAGATGCTGGATATCTA 60.011 42.308 6.73 0.00 31.01 1.98
3377 4434 5.565592 TTTAGCAGTGCATGTCCAAATAG 57.434 39.130 19.20 0.00 0.00 1.73
3466 4523 2.725637 TCATGCCAGCAAGCTAATTGA 58.274 42.857 0.00 0.00 41.83 2.57
3655 4712 1.001974 TCACCTGTGGAAACTGATCGG 59.998 52.381 0.00 0.00 0.00 4.18
3706 4763 6.606234 TTTTGTGACTATCAACTGCGTAAA 57.394 33.333 0.00 0.00 0.00 2.01
3710 4767 9.425893 CTATTATTTTTGTGACTATCAACTGCG 57.574 33.333 0.00 0.00 0.00 5.18
3763 4824 7.255104 CCAGTTCTTCACTTTATGCTGTAACAA 60.255 37.037 0.00 0.00 30.92 2.83
3879 4946 3.574074 ATTGTTGGGAGGCGCTGCT 62.574 57.895 7.64 0.00 0.00 4.24
3891 4958 2.228822 GGAAGTACTGGCACCATTGTTG 59.771 50.000 0.00 0.00 0.00 3.33
3996 5063 1.896220 TCGAAGGAGCAGCAACATTT 58.104 45.000 0.00 0.00 0.00 2.32
4024 5091 1.539827 GCACTGTGTAAATGGTGGTCC 59.460 52.381 9.86 0.00 0.00 4.46
4036 5103 2.201732 CTGTTCGTAACTGCACTGTGT 58.798 47.619 9.86 0.00 0.00 3.72
4043 5110 0.941542 TGCAACCTGTTCGTAACTGC 59.058 50.000 0.00 0.00 31.69 4.40
4060 5127 6.072728 TGTGTTCAGTATTTACCTTGATGTGC 60.073 38.462 0.00 0.00 0.00 4.57
4062 5129 7.362056 GCATGTGTTCAGTATTTACCTTGATGT 60.362 37.037 0.00 0.00 0.00 3.06
4190 5257 8.340002 ACAGTATAGAAGGATCCTGCTGATATA 58.660 37.037 30.27 17.74 33.21 0.86
4231 5298 3.707316 TGTTTCCATGGGTCAAATAGGG 58.293 45.455 13.02 0.00 0.00 3.53
4237 5304 3.514706 CCATTGATGTTTCCATGGGTCAA 59.485 43.478 13.02 14.26 40.10 3.18
4245 5312 2.378208 TCCCTGACCATTGATGTTTCCA 59.622 45.455 0.00 0.00 0.00 3.53
4254 5321 4.135306 CTGAGAATGATCCCTGACCATTG 58.865 47.826 0.00 0.00 31.40 2.82
4255 5322 3.434739 GCTGAGAATGATCCCTGACCATT 60.435 47.826 0.00 0.00 33.66 3.16
4261 5328 1.202782 CCAGGCTGAGAATGATCCCTG 60.203 57.143 17.94 4.01 39.56 4.45
4262 5329 1.138568 CCAGGCTGAGAATGATCCCT 58.861 55.000 17.94 0.00 0.00 4.20
4371 5438 6.299141 TCAGCCTACATCCAGGAAATATTTC 58.701 40.000 18.22 18.22 38.00 2.17
4482 5549 1.531149 CACGCCTGTTACAAGACAAGG 59.469 52.381 0.00 0.00 0.00 3.61
4565 5633 3.033184 ACCCAACAATGCATAATGGAGG 58.967 45.455 20.95 13.03 32.82 4.30
4944 6017 8.725148 AGCTTAAATCAACAGAAGTTATCACTG 58.275 33.333 0.00 0.00 35.85 3.66
5055 6129 6.641314 GGTAGTTATCAGTCAATCATACACGG 59.359 42.308 0.00 0.00 0.00 4.94
5099 6181 5.070313 AGGGCAAATTTCAACTTCTAAGCAA 59.930 36.000 0.00 0.00 0.00 3.91
5177 6259 4.082571 GCCACCAGCATATTCATAACCATC 60.083 45.833 0.00 0.00 42.97 3.51
5193 6275 0.599558 CAATCACCAGTTGCCACCAG 59.400 55.000 0.00 0.00 0.00 4.00
5202 6284 3.136443 TGGTCTCAAGTTCAATCACCAGT 59.864 43.478 0.00 0.00 0.00 4.00
5233 6315 8.500238 TCATGTTTACTATGGTAGAGGAGAGTA 58.500 37.037 0.00 0.00 0.00 2.59
5237 6319 6.439599 CGTCATGTTTACTATGGTAGAGGAG 58.560 44.000 0.00 0.00 0.00 3.69
5248 6330 2.093869 GCTCCCACCGTCATGTTTACTA 60.094 50.000 0.00 0.00 0.00 1.82
5266 6348 1.298859 AACACTTGAATCGCCGGCTC 61.299 55.000 26.68 16.37 0.00 4.70
5273 6355 4.997905 ATCACACAGAACACTTGAATCG 57.002 40.909 0.00 0.00 0.00 3.34
5283 6397 8.905702 CAAACTAAATGCTTAATCACACAGAAC 58.094 33.333 0.00 0.00 0.00 3.01
5448 6571 6.441274 CAATGCGAATATTTGCTCCTGTATT 58.559 36.000 24.73 13.83 38.42 1.89
5450 6573 4.261155 GCAATGCGAATATTTGCTCCTGTA 60.261 41.667 24.73 7.31 38.42 2.74
5451 6574 3.489738 GCAATGCGAATATTTGCTCCTGT 60.490 43.478 24.73 6.35 38.42 4.00
5452 6575 3.047796 GCAATGCGAATATTTGCTCCTG 58.952 45.455 24.73 19.11 38.42 3.86
5512 6638 6.761714 GTCGACATACATAGGAAATTCACCTT 59.238 38.462 11.55 0.00 38.76 3.50
5593 6721 4.016444 GGGGATAAAATCTGTCACAAGCA 58.984 43.478 0.00 0.00 0.00 3.91
5611 6739 0.616371 ACCGAATGTCGATTTGGGGA 59.384 50.000 13.88 0.00 44.86 4.81
5633 6761 7.454260 AATCTTTCAATTAGGAGACACCAAC 57.546 36.000 0.00 0.00 42.04 3.77
5640 6768 7.611855 GTGGAAGGAAATCTTTCAATTAGGAGA 59.388 37.037 7.46 0.00 42.27 3.71
5642 6770 7.237982 TGTGGAAGGAAATCTTTCAATTAGGA 58.762 34.615 7.46 0.00 42.27 2.94
5656 6784 4.280677 CCAGCTGTAAAATGTGGAAGGAAA 59.719 41.667 13.81 0.00 0.00 3.13
5674 6802 4.918810 AAATTCAAAACGAGAACCAGCT 57.081 36.364 0.00 0.00 0.00 4.24
5702 6899 2.963101 TCTGAACCGGTTTCTGAAGAGA 59.037 45.455 23.22 10.98 38.76 3.10
5710 6907 2.607038 GCCAAACATCTGAACCGGTTTC 60.607 50.000 23.22 14.88 31.57 2.78
5761 6958 2.782615 CCACCGGAATTTCGACGC 59.217 61.111 9.46 0.00 0.00 5.19
5848 7107 2.257353 GAGTTGGGCACAAATCGCT 58.743 52.632 14.05 0.59 41.14 4.93
5864 7123 2.182030 GACCAAGTCCGAGGCGAG 59.818 66.667 0.00 0.00 0.00 5.03
5921 7392 3.443045 GCACCCTTGACGGCATGG 61.443 66.667 16.28 16.28 38.66 3.66
5922 7393 3.803082 CGCACCCTTGACGGCATG 61.803 66.667 0.00 0.00 0.00 4.06
5935 7437 2.505118 GAGAGAGCACCGACGCAC 60.505 66.667 0.00 0.00 0.00 5.34
5947 7449 1.349026 CAAAGGCCCAAGACAGAGAGA 59.651 52.381 0.00 0.00 0.00 3.10
5948 7450 1.072965 ACAAAGGCCCAAGACAGAGAG 59.927 52.381 0.00 0.00 0.00 3.20
5979 7494 1.331399 TAACGTCCATCCGCCATCCA 61.331 55.000 0.00 0.00 0.00 3.41
5983 7498 1.448893 GCTTAACGTCCATCCGCCA 60.449 57.895 0.00 0.00 0.00 5.69
5988 7503 0.924090 CTCGCTGCTTAACGTCCATC 59.076 55.000 0.00 0.00 0.00 3.51
6082 7613 4.560856 ATGCGCTCCGAGCTCGTC 62.561 66.667 32.41 20.02 39.60 4.20
6083 7614 4.862092 CATGCGCTCCGAGCTCGT 62.862 66.667 32.41 11.35 39.60 4.18
6097 7628 3.072468 CCCCACCCAAGCAGCATG 61.072 66.667 0.00 0.00 40.87 4.06
6101 7632 3.072468 CATGCCCCACCCAAGCAG 61.072 66.667 0.00 0.00 40.40 4.24
6104 7635 2.757099 GAGCATGCCCCACCCAAG 60.757 66.667 15.66 0.00 0.00 3.61
6105 7636 4.738998 CGAGCATGCCCCACCCAA 62.739 66.667 15.66 0.00 0.00 4.12
6145 7676 2.125512 GTGCCCACTACCTGCTCG 60.126 66.667 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.