Multiple sequence alignment - TraesCS3B01G212400

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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 TraesCS3B01G212400 chr3B 100.000 2249 0 0 1 2249 252342793 252345041 0.000000e+00 4154
1 TraesCS3B01G212400 chr3D 90.360 1805 85 30 381 2162 173595719 173597457 0.000000e+00 2287
2 TraesCS3B01G212400 chr3A 88.599 1842 107 36 84 1890 211953063 211954836 0.000000e+00 2143
3 TraesCS3B01G212400 chr3A 93.617 94 6 0 1 94 211901352 211901445 8.370000e-30 141
4 TraesCS3B01G212400 chr2A 98.876 89 1 0 2161 2249 766707001 766707089 2.310000e-35 159
5 TraesCS3B01G212400 chr6B 97.778 90 2 0 2160 2249 716638360 716638271 2.990000e-34 156
6 TraesCS3B01G212400 chr6B 94.444 90 5 0 2160 2249 703802093 703802004 3.010000e-29 139
7 TraesCS3B01G212400 chr2D 97.778 90 2 0 2160 2249 203457361 203457272 2.990000e-34 156
8 TraesCS3B01G212400 chr5A 94.898 98 3 1 2152 2249 555280763 555280858 3.870000e-33 152
9 TraesCS3B01G212400 chr5D 94.845 97 3 1 2153 2249 25039974 25040068 1.390000e-32 150
10 TraesCS3B01G212400 chr5D 91.667 108 5 3 2144 2249 422020146 422020251 1.800000e-31 147
11 TraesCS3B01G212400 chr7B 91.589 107 7 2 2145 2249 186868800 186868906 1.800000e-31 147
12 TraesCS3B01G212400 chr4B 93.000 100 6 1 2150 2249 671654096 671653998 6.470000e-31 145


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 TraesCS3B01G212400 chr3B 252342793 252345041 2248 False 4154 4154 100.000 1 2249 1 chr3B.!!$F1 2248
1 TraesCS3B01G212400 chr3D 173595719 173597457 1738 False 2287 2287 90.360 381 2162 1 chr3D.!!$F1 1781
2 TraesCS3B01G212400 chr3A 211953063 211954836 1773 False 2143 2143 88.599 84 1890 1 chr3A.!!$F2 1806

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
252 256 0.031994 GGTGGTTGGTTGTGTGCATC 59.968 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1352 0.026544 TCGTCGTCGGCAACAAAAAC 59.973 50.0 1.55 0.0 37.69 2.43 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
37 38 9.898152 TTATTTTACACCATAGACATGACATCA 57.102 29.630 0.00 0.00 33.67 3.07
38 39 8.806429 ATTTTACACCATAGACATGACATCAA 57.194 30.769 0.00 0.00 33.67 2.57
39 40 7.609760 TTTACACCATAGACATGACATCAAC 57.390 36.000 0.00 0.00 33.67 3.18
40 41 5.426689 ACACCATAGACATGACATCAACT 57.573 39.130 0.00 0.00 33.67 3.16
41 42 5.809001 ACACCATAGACATGACATCAACTT 58.191 37.500 0.00 0.00 33.67 2.66
42 43 5.877012 ACACCATAGACATGACATCAACTTC 59.123 40.000 0.00 0.00 33.67 3.01
43 44 5.295292 CACCATAGACATGACATCAACTTCC 59.705 44.000 0.00 0.00 33.67 3.46
44 45 4.818546 CCATAGACATGACATCAACTTCCC 59.181 45.833 0.00 0.00 33.67 3.97
45 46 5.430886 CATAGACATGACATCAACTTCCCA 58.569 41.667 0.00 0.00 33.67 4.37
46 47 4.371624 AGACATGACATCAACTTCCCAA 57.628 40.909 0.00 0.00 0.00 4.12
47 48 4.074970 AGACATGACATCAACTTCCCAAC 58.925 43.478 0.00 0.00 0.00 3.77
48 49 3.157087 ACATGACATCAACTTCCCAACC 58.843 45.455 0.00 0.00 0.00 3.77
49 50 1.890876 TGACATCAACTTCCCAACCG 58.109 50.000 0.00 0.00 0.00 4.44
50 51 0.521735 GACATCAACTTCCCAACCGC 59.478 55.000 0.00 0.00 0.00 5.68
51 52 0.893727 ACATCAACTTCCCAACCGCC 60.894 55.000 0.00 0.00 0.00 6.13
52 53 0.893270 CATCAACTTCCCAACCGCCA 60.893 55.000 0.00 0.00 0.00 5.69
53 54 0.893727 ATCAACTTCCCAACCGCCAC 60.894 55.000 0.00 0.00 0.00 5.01
54 55 1.528309 CAACTTCCCAACCGCCACT 60.528 57.895 0.00 0.00 0.00 4.00
55 56 1.228154 AACTTCCCAACCGCCACTC 60.228 57.895 0.00 0.00 0.00 3.51
56 57 1.705997 AACTTCCCAACCGCCACTCT 61.706 55.000 0.00 0.00 0.00 3.24
57 58 1.376037 CTTCCCAACCGCCACTCTC 60.376 63.158 0.00 0.00 0.00 3.20
58 59 1.831652 CTTCCCAACCGCCACTCTCT 61.832 60.000 0.00 0.00 0.00 3.10
59 60 1.415672 TTCCCAACCGCCACTCTCTT 61.416 55.000 0.00 0.00 0.00 2.85
60 61 1.376037 CCCAACCGCCACTCTCTTC 60.376 63.158 0.00 0.00 0.00 2.87
61 62 1.376037 CCAACCGCCACTCTCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
62 63 1.674057 CAACCGCCACTCTCTTCCT 59.326 57.895 0.00 0.00 0.00 3.36
63 64 0.390472 CAACCGCCACTCTCTTCCTC 60.390 60.000 0.00 0.00 0.00 3.71
64 65 1.545706 AACCGCCACTCTCTTCCTCC 61.546 60.000 0.00 0.00 0.00 4.30
65 66 2.726351 CCGCCACTCTCTTCCTCCC 61.726 68.421 0.00 0.00 0.00 4.30
66 67 2.726351 CGCCACTCTCTTCCTCCCC 61.726 68.421 0.00 0.00 0.00 4.81
67 68 1.306568 GCCACTCTCTTCCTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
68 69 1.334384 GCCACTCTCTTCCTCCCCTC 61.334 65.000 0.00 0.00 0.00 4.30
69 70 0.689412 CCACTCTCTTCCTCCCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
70 71 0.689412 CACTCTCTTCCTCCCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
71 72 1.074850 CTCTCTTCCTCCCCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
72 73 1.550374 TCTCTTCCTCCCCTCCCCT 60.550 63.158 0.00 0.00 0.00 4.79
73 74 1.162951 TCTCTTCCTCCCCTCCCCTT 61.163 60.000 0.00 0.00 0.00 3.95
74 75 0.985490 CTCTTCCTCCCCTCCCCTTG 60.985 65.000 0.00 0.00 0.00 3.61
75 76 2.614013 TTCCTCCCCTCCCCTTGC 60.614 66.667 0.00 0.00 0.00 4.01
76 77 3.515383 TTCCTCCCCTCCCCTTGCA 62.515 63.158 0.00 0.00 0.00 4.08
77 78 3.732849 CCTCCCCTCCCCTTGCAC 61.733 72.222 0.00 0.00 0.00 4.57
78 79 2.612115 CTCCCCTCCCCTTGCACT 60.612 66.667 0.00 0.00 0.00 4.40
79 80 2.935481 TCCCCTCCCCTTGCACTG 60.935 66.667 0.00 0.00 0.00 3.66
80 81 4.748144 CCCCTCCCCTTGCACTGC 62.748 72.222 0.00 0.00 0.00 4.40
81 82 3.655211 CCCTCCCCTTGCACTGCT 61.655 66.667 1.98 0.00 0.00 4.24
82 83 2.360852 CCTCCCCTTGCACTGCTG 60.361 66.667 1.98 0.00 0.00 4.41
94 95 0.976641 CACTGCTGTCAGGACCCTAA 59.023 55.000 1.14 0.00 44.54 2.69
96 97 2.054799 ACTGCTGTCAGGACCCTAAAA 58.945 47.619 1.14 0.00 44.54 1.52
98 99 1.073284 TGCTGTCAGGACCCTAAAACC 59.927 52.381 1.14 0.00 0.00 3.27
118 119 0.995024 AGGCTAACTTGGATGGCAGT 59.005 50.000 0.00 0.00 0.00 4.40
129 130 4.356405 TGGATGGCAGTATAATCACCAG 57.644 45.455 0.00 0.00 33.03 4.00
131 132 4.598807 TGGATGGCAGTATAATCACCAGAT 59.401 41.667 0.00 0.00 33.03 2.90
151 155 0.325671 TGGTCCATCACCTCCTCTCC 60.326 60.000 0.00 0.00 46.98 3.71
152 156 1.395826 GGTCCATCACCTCCTCTCCG 61.396 65.000 0.00 0.00 42.84 4.63
160 164 1.834378 CCTCCTCTCCGCATAGGCA 60.834 63.158 0.00 0.00 41.24 4.75
163 167 1.895798 CTCCTCTCCGCATAGGCATAA 59.104 52.381 0.00 0.00 41.24 1.90
168 172 1.995484 CTCCGCATAGGCATAATGTCG 59.005 52.381 0.00 0.00 41.24 4.35
188 192 9.444600 AATGTCGGTTTTATATGACTTTACTGT 57.555 29.630 0.00 0.00 32.64 3.55
191 195 8.715088 GTCGGTTTTATATGACTTTACTGTTGT 58.285 33.333 0.00 0.00 0.00 3.32
192 196 9.275398 TCGGTTTTATATGACTTTACTGTTGTT 57.725 29.630 0.00 0.00 0.00 2.83
201 205 5.924254 TGACTTTACTGTTGTTGATAGGTCG 59.076 40.000 0.00 0.00 0.00 4.79
206 210 4.457466 ACTGTTGTTGATAGGTCGGTTTT 58.543 39.130 0.00 0.00 0.00 2.43
213 217 7.989416 TGTTGATAGGTCGGTTTTTATCTTT 57.011 32.000 0.00 0.00 0.00 2.52
216 220 9.338291 GTTGATAGGTCGGTTTTTATCTTTTTC 57.662 33.333 0.00 0.00 0.00 2.29
252 256 0.031994 GGTGGTTGGTTGTGTGCATC 59.968 55.000 0.00 0.00 0.00 3.91
257 261 2.351738 GGTTGGTTGTGTGCATCTTAGC 60.352 50.000 0.00 0.00 0.00 3.09
265 269 1.297664 GTGCATCTTAGCTCTGCAGG 58.702 55.000 15.13 5.82 45.77 4.85
295 299 5.494632 TGTTGCTCATCATGCTTTCTATG 57.505 39.130 0.00 0.00 0.00 2.23
296 300 4.201980 TGTTGCTCATCATGCTTTCTATGC 60.202 41.667 0.00 0.00 0.00 3.14
297 301 3.547746 TGCTCATCATGCTTTCTATGCA 58.452 40.909 0.00 0.00 44.95 3.96
372 379 7.779754 TCCCTCTTTTCATTTTCATCATGAA 57.220 32.000 0.00 0.00 38.59 2.57
423 430 3.801983 GCCACGTGGAAAATGGAAAATGT 60.802 43.478 38.30 0.00 35.33 2.71
488 495 2.008329 CGTCGGTAGAGTAGAGCAAGT 58.992 52.381 0.00 0.00 0.00 3.16
489 496 2.223066 CGTCGGTAGAGTAGAGCAAGTG 60.223 54.545 0.00 0.00 0.00 3.16
495 502 4.322049 GGTAGAGTAGAGCAAGTGAGCAAA 60.322 45.833 0.00 0.00 36.85 3.68
531 538 0.674895 GGACACACACAGGATCAGCC 60.675 60.000 0.00 0.00 0.00 4.85
542 549 4.286320 ATCAGCCGATCCGTCCGC 62.286 66.667 0.00 0.00 0.00 5.54
547 554 3.911698 CCGATCCGTCCGCCATCA 61.912 66.667 0.00 0.00 0.00 3.07
549 556 2.280186 GATCCGTCCGCCATCACC 60.280 66.667 0.00 0.00 0.00 4.02
550 557 4.221422 ATCCGTCCGCCATCACCG 62.221 66.667 0.00 0.00 0.00 4.94
573 594 1.872237 CGGGACACGGCATAATACCAG 60.872 57.143 0.00 0.00 39.42 4.00
604 625 1.900498 GCCAGCTGCACTCCAAAGT 60.900 57.895 8.66 0.00 40.77 2.66
605 626 1.458639 GCCAGCTGCACTCCAAAGTT 61.459 55.000 8.66 0.00 40.77 2.66
606 627 0.313043 CCAGCTGCACTCCAAAGTTG 59.687 55.000 8.66 0.00 31.71 3.16
613 634 4.354587 CTGCACTCCAAAGTTGAGAAAAC 58.645 43.478 0.00 0.00 31.71 2.43
674 695 1.071814 GACAACACAAGGGGCCGTA 59.928 57.895 0.00 0.00 0.00 4.02
841 866 1.332904 GCGCGCATATAAAGACCACAC 60.333 52.381 29.10 0.00 0.00 3.82
842 867 1.930503 CGCGCATATAAAGACCACACA 59.069 47.619 8.75 0.00 0.00 3.72
918 944 3.838244 TCAACAGTTCAGGCTTACAGT 57.162 42.857 0.00 0.00 0.00 3.55
919 945 4.948341 TCAACAGTTCAGGCTTACAGTA 57.052 40.909 0.00 0.00 0.00 2.74
920 946 4.628074 TCAACAGTTCAGGCTTACAGTAC 58.372 43.478 0.00 0.00 0.00 2.73
921 947 4.100344 TCAACAGTTCAGGCTTACAGTACA 59.900 41.667 0.00 0.00 0.00 2.90
922 948 4.258702 ACAGTTCAGGCTTACAGTACAG 57.741 45.455 0.00 0.00 0.00 2.74
939 965 1.336887 ACAGCTAGTTGCAGTACCACG 60.337 52.381 6.48 0.00 45.94 4.94
979 1005 0.173708 CGCCCAACAGAGAGGTAGTC 59.826 60.000 0.00 0.00 0.00 2.59
986 1012 0.171455 CAGAGAGGTAGTCGTGCCAC 59.829 60.000 0.00 0.00 0.00 5.01
987 1013 0.038455 AGAGAGGTAGTCGTGCCACT 59.962 55.000 0.00 0.00 32.00 4.00
988 1014 0.171455 GAGAGGTAGTCGTGCCACTG 59.829 60.000 0.00 0.00 29.45 3.66
989 1015 1.215647 GAGGTAGTCGTGCCACTGG 59.784 63.158 0.00 0.00 0.00 4.00
990 1016 2.227089 GAGGTAGTCGTGCCACTGGG 62.227 65.000 0.00 0.00 37.18 4.45
991 1017 2.580601 GGTAGTCGTGCCACTGGGT 61.581 63.158 0.00 0.00 36.17 4.51
992 1018 1.080025 GTAGTCGTGCCACTGGGTC 60.080 63.158 0.00 0.00 36.17 4.46
1167 1205 3.959991 GAAGCTGTCCACGGAGGCC 62.960 68.421 0.00 0.00 37.29 5.19
1281 1328 3.827898 CCGCTGACTCGGGAGGTC 61.828 72.222 0.00 0.00 45.38 3.85
1282 1329 3.827898 CGCTGACTCGGGAGGTCC 61.828 72.222 0.00 0.00 33.22 4.46
1283 1330 2.680352 GCTGACTCGGGAGGTCCA 60.680 66.667 0.00 0.00 37.91 4.02
1285 1332 1.617947 GCTGACTCGGGAGGTCCATT 61.618 60.000 0.00 0.00 37.91 3.16
1286 1333 0.461961 CTGACTCGGGAGGTCCATTC 59.538 60.000 0.00 0.00 37.91 2.67
1288 1335 2.107141 CTCGGGAGGTCCATTCGC 59.893 66.667 0.00 0.00 37.91 4.70
1289 1336 3.447025 CTCGGGAGGTCCATTCGCC 62.447 68.421 0.00 0.00 37.91 5.54
1290 1337 3.470888 CGGGAGGTCCATTCGCCT 61.471 66.667 0.00 0.00 37.91 5.52
1293 1340 3.207354 GAGGTCCATTCGCCTCGA 58.793 61.111 0.00 0.00 41.40 4.04
1294 1341 1.066587 GAGGTCCATTCGCCTCGAG 59.933 63.158 5.13 5.13 41.40 4.04
1295 1342 2.107141 GGTCCATTCGCCTCGAGG 59.893 66.667 27.83 27.83 37.14 4.63
1296 1343 2.722201 GGTCCATTCGCCTCGAGGT 61.722 63.158 31.43 10.08 37.14 3.85
1297 1344 1.218316 GTCCATTCGCCTCGAGGTT 59.782 57.895 31.43 12.37 37.14 3.50
1298 1345 0.806492 GTCCATTCGCCTCGAGGTTC 60.806 60.000 31.43 15.68 37.14 3.62
1299 1346 1.521681 CCATTCGCCTCGAGGTTCC 60.522 63.158 31.43 14.94 37.14 3.62
1300 1347 1.517832 CATTCGCCTCGAGGTTCCT 59.482 57.895 31.43 12.56 37.14 3.36
1301 1348 0.528684 CATTCGCCTCGAGGTTCCTC 60.529 60.000 31.43 14.19 37.14 3.71
1302 1349 0.684805 ATTCGCCTCGAGGTTCCTCT 60.685 55.000 31.43 10.09 37.14 3.69
1303 1350 1.595993 TTCGCCTCGAGGTTCCTCTG 61.596 60.000 31.43 13.20 37.14 3.35
1304 1351 2.344203 CGCCTCGAGGTTCCTCTGT 61.344 63.158 31.43 0.00 37.57 3.41
1305 1352 1.216710 GCCTCGAGGTTCCTCTGTG 59.783 63.158 31.43 3.47 37.57 3.66
1306 1353 1.536943 GCCTCGAGGTTCCTCTGTGT 61.537 60.000 31.43 0.00 37.57 3.72
1319 1366 2.450160 CTCTGTGTTTTTGTTGCCGAC 58.550 47.619 0.00 0.00 0.00 4.79
1333 1380 0.793853 GCCGACGACGAAGAAGAGAC 60.794 60.000 9.28 0.00 42.66 3.36
1372 1419 3.797039 TGCCTCGAGTTCTATGAAATGG 58.203 45.455 12.31 0.00 0.00 3.16
1410 1457 0.537188 CCACCGCTGAATGTACTCCT 59.463 55.000 0.00 0.00 0.00 3.69
1412 1459 2.615493 CCACCGCTGAATGTACTCCTTT 60.615 50.000 0.00 0.00 0.00 3.11
1421 1468 6.568653 GCTGAATGTACTCCTTTTGTTCCTTC 60.569 42.308 0.00 0.00 0.00 3.46
1427 1474 4.207955 ACTCCTTTTGTTCCTTCTTGTCC 58.792 43.478 0.00 0.00 0.00 4.02
1429 1476 3.053245 TCCTTTTGTTCCTTCTTGTCCCA 60.053 43.478 0.00 0.00 0.00 4.37
1438 1485 4.398319 TCCTTCTTGTCCCATGACTTTTC 58.602 43.478 0.00 0.00 42.28 2.29
1439 1486 3.507622 CCTTCTTGTCCCATGACTTTTCC 59.492 47.826 0.00 0.00 42.28 3.13
1440 1487 4.401925 CTTCTTGTCCCATGACTTTTCCT 58.598 43.478 0.00 0.00 42.28 3.36
1441 1488 5.514834 CCTTCTTGTCCCATGACTTTTCCTA 60.515 44.000 0.00 0.00 42.28 2.94
1442 1489 4.906618 TCTTGTCCCATGACTTTTCCTAC 58.093 43.478 0.00 0.00 42.28 3.18
1443 1490 4.349636 TCTTGTCCCATGACTTTTCCTACA 59.650 41.667 0.00 0.00 42.28 2.74
1444 1491 4.015872 TGTCCCATGACTTTTCCTACAC 57.984 45.455 0.00 0.00 42.28 2.90
1445 1492 3.392947 TGTCCCATGACTTTTCCTACACA 59.607 43.478 0.00 0.00 42.28 3.72
1446 1493 3.751698 GTCCCATGACTTTTCCTACACAC 59.248 47.826 0.00 0.00 38.53 3.82
1447 1494 3.392947 TCCCATGACTTTTCCTACACACA 59.607 43.478 0.00 0.00 0.00 3.72
1448 1495 3.753272 CCCATGACTTTTCCTACACACAG 59.247 47.826 0.00 0.00 0.00 3.66
1449 1496 4.389374 CCATGACTTTTCCTACACACAGT 58.611 43.478 0.00 0.00 0.00 3.55
1450 1497 4.821805 CCATGACTTTTCCTACACACAGTT 59.178 41.667 0.00 0.00 0.00 3.16
1451 1498 5.049405 CCATGACTTTTCCTACACACAGTTC 60.049 44.000 0.00 0.00 0.00 3.01
1479 1526 3.452474 GGATTCAACCGTCTGATCAGAG 58.548 50.000 25.76 17.00 38.27 3.35
1480 1527 3.131223 GGATTCAACCGTCTGATCAGAGA 59.869 47.826 25.76 15.67 38.27 3.10
1499 1550 2.297912 ACGACCGAACTCGTTTGCG 61.298 57.895 0.00 0.00 44.51 4.85
1502 1553 0.938168 GACCGAACTCGTTTGCGACT 60.938 55.000 0.00 0.00 42.81 4.18
1504 1555 1.269206 ACCGAACTCGTTTGCGACTTA 60.269 47.619 0.00 0.00 42.81 2.24
1539 1590 0.528924 TCGACCGGGTACTGACAATG 59.471 55.000 6.32 0.00 36.31 2.82
1625 1678 0.841961 GGTATACCCACCCACCTTCC 59.158 60.000 11.17 0.00 31.91 3.46
1658 1711 4.116747 ACAGAAAACAACGCATTTTCCA 57.883 36.364 12.99 0.00 43.92 3.53
1671 1724 6.919721 ACGCATTTTCCATATACAAACTTGT 58.080 32.000 0.07 0.07 44.86 3.16
1706 1759 8.256611 TGAGATATTGCTGTAACTGAACTTTC 57.743 34.615 0.00 0.00 0.00 2.62
1721 1774 7.694886 ACTGAACTTTCTGTACTTTTAACAGC 58.305 34.615 0.03 0.00 43.30 4.40
1780 1833 2.706190 AGGTAAACCACAAGAGCTCTGT 59.294 45.455 19.06 14.51 38.89 3.41
1809 1862 9.680315 TTTTTAAGTCCCACATTACAAATAACG 57.320 29.630 0.00 0.00 0.00 3.18
1839 1892 9.846248 AACAGAATTGCAAATAGTATCAAAGAC 57.154 29.630 1.71 0.00 0.00 3.01
1846 1899 8.437360 TGCAAATAGTATCAAAGACCATACTG 57.563 34.615 2.48 0.00 36.64 2.74
1856 1909 0.536006 GACCATACTGCTCCATGGGC 60.536 60.000 13.02 14.76 45.08 5.36
1872 1925 3.047877 GCGGTGGGTTGTCTTCGG 61.048 66.667 0.00 0.00 0.00 4.30
2024 2077 1.250154 TATTGGTGGCCTTGCACAGC 61.250 55.000 3.32 0.00 35.77 4.40
2125 2178 7.309177 CCCACAACGATTGTTCATATTACAAA 58.691 34.615 0.00 0.00 43.23 2.83
2132 2185 5.883503 TTGTTCATATTACAAACCCGACC 57.116 39.130 0.00 0.00 32.89 4.79
2153 2206 3.443681 CCGTGATTTCCCTACAAAGCAAT 59.556 43.478 0.00 0.00 33.63 3.56
2169 2222 2.557920 CAATCATGCCTACTCCCTCC 57.442 55.000 0.00 0.00 0.00 4.30
2170 2223 1.051812 AATCATGCCTACTCCCTCCG 58.948 55.000 0.00 0.00 0.00 4.63
2171 2224 0.188587 ATCATGCCTACTCCCTCCGA 59.811 55.000 0.00 0.00 0.00 4.55
2172 2225 0.188587 TCATGCCTACTCCCTCCGAT 59.811 55.000 0.00 0.00 0.00 4.18
2173 2226 0.605589 CATGCCTACTCCCTCCGATC 59.394 60.000 0.00 0.00 0.00 3.69
2174 2227 0.543174 ATGCCTACTCCCTCCGATCC 60.543 60.000 0.00 0.00 0.00 3.36
2175 2228 1.154221 GCCTACTCCCTCCGATCCT 59.846 63.158 0.00 0.00 0.00 3.24
2176 2229 0.404812 GCCTACTCCCTCCGATCCTA 59.595 60.000 0.00 0.00 0.00 2.94
2177 2230 1.203025 GCCTACTCCCTCCGATCCTAA 60.203 57.143 0.00 0.00 0.00 2.69
2178 2231 2.755549 GCCTACTCCCTCCGATCCTAAA 60.756 54.545 0.00 0.00 0.00 1.85
2179 2232 3.780626 CCTACTCCCTCCGATCCTAAAT 58.219 50.000 0.00 0.00 0.00 1.40
2180 2233 4.813479 GCCTACTCCCTCCGATCCTAAATA 60.813 50.000 0.00 0.00 0.00 1.40
2181 2234 5.331069 CCTACTCCCTCCGATCCTAAATAA 58.669 45.833 0.00 0.00 0.00 1.40
2182 2235 5.958987 CCTACTCCCTCCGATCCTAAATAAT 59.041 44.000 0.00 0.00 0.00 1.28
2183 2236 6.440965 CCTACTCCCTCCGATCCTAAATAATT 59.559 42.308 0.00 0.00 0.00 1.40
2184 2237 6.115448 ACTCCCTCCGATCCTAAATAATTG 57.885 41.667 0.00 0.00 0.00 2.32
2185 2238 5.607171 ACTCCCTCCGATCCTAAATAATTGT 59.393 40.000 0.00 0.00 0.00 2.71
2186 2239 6.110411 TCCCTCCGATCCTAAATAATTGTC 57.890 41.667 0.00 0.00 0.00 3.18
2187 2240 5.844516 TCCCTCCGATCCTAAATAATTGTCT 59.155 40.000 0.00 0.00 0.00 3.41
2188 2241 6.329197 TCCCTCCGATCCTAAATAATTGTCTT 59.671 38.462 0.00 0.00 0.00 3.01
2189 2242 6.998673 CCCTCCGATCCTAAATAATTGTCTTT 59.001 38.462 0.00 0.00 0.00 2.52
2190 2243 7.173390 CCCTCCGATCCTAAATAATTGTCTTTC 59.827 40.741 0.00 0.00 0.00 2.62
2191 2244 7.934120 CCTCCGATCCTAAATAATTGTCTTTCT 59.066 37.037 0.00 0.00 0.00 2.52
2192 2245 9.982651 CTCCGATCCTAAATAATTGTCTTTCTA 57.017 33.333 0.00 0.00 0.00 2.10
2193 2246 9.982651 TCCGATCCTAAATAATTGTCTTTCTAG 57.017 33.333 0.00 0.00 0.00 2.43
2194 2247 9.982651 CCGATCCTAAATAATTGTCTTTCTAGA 57.017 33.333 0.00 0.00 0.00 2.43
2207 2260 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2208 2261 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2209 2262 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2210 2263 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2211 2264 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2212 2265 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2213 2266 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2214 2267 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2215 2268 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2217 2270 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2218 2271 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2219 2272 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
2220 2273 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
2221 2274 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
2222 2275 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
2223 2276 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
2224 2277 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
2225 2278 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
2226 2279 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
2227 2280 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
2228 2281 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
2229 2282 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
2230 2283 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
2231 2284 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
2232 2285 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
2233 2286 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2234 2287 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2235 2288 5.689819 ACATACGAAGCAAAATGAGTGAAC 58.310 37.500 0.00 0.00 0.00 3.18
2236 2289 3.626028 ACGAAGCAAAATGAGTGAACC 57.374 42.857 0.00 0.00 0.00 3.62
2237 2290 3.214328 ACGAAGCAAAATGAGTGAACCT 58.786 40.909 0.00 0.00 0.00 3.50
2238 2291 4.385825 ACGAAGCAAAATGAGTGAACCTA 58.614 39.130 0.00 0.00 0.00 3.08
2239 2292 4.213482 ACGAAGCAAAATGAGTGAACCTAC 59.787 41.667 0.00 0.00 0.00 3.18
2240 2293 4.213270 CGAAGCAAAATGAGTGAACCTACA 59.787 41.667 0.00 0.00 0.00 2.74
2241 2294 5.438761 AAGCAAAATGAGTGAACCTACAC 57.561 39.130 0.00 0.00 40.60 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.898152 TGATGTCATGTCTATGGTGTAAAATAA 57.102 29.630 0.00 0.00 34.97 1.40
12 13 9.898152 TTGATGTCATGTCTATGGTGTAAAATA 57.102 29.630 0.00 0.00 34.97 1.40
13 14 8.677300 GTTGATGTCATGTCTATGGTGTAAAAT 58.323 33.333 0.00 0.00 34.97 1.82
14 15 7.882791 AGTTGATGTCATGTCTATGGTGTAAAA 59.117 33.333 0.00 0.00 34.97 1.52
15 16 7.394016 AGTTGATGTCATGTCTATGGTGTAAA 58.606 34.615 0.00 0.00 34.97 2.01
16 17 6.946340 AGTTGATGTCATGTCTATGGTGTAA 58.054 36.000 0.00 0.00 34.97 2.41
17 18 6.544928 AGTTGATGTCATGTCTATGGTGTA 57.455 37.500 0.00 0.00 34.97 2.90
18 19 5.426689 AGTTGATGTCATGTCTATGGTGT 57.573 39.130 0.00 0.00 34.97 4.16
19 20 5.295292 GGAAGTTGATGTCATGTCTATGGTG 59.705 44.000 0.00 0.00 34.97 4.17
20 21 5.431765 GGAAGTTGATGTCATGTCTATGGT 58.568 41.667 0.00 0.00 34.97 3.55
21 22 4.818546 GGGAAGTTGATGTCATGTCTATGG 59.181 45.833 0.00 0.00 34.97 2.74
22 23 5.430886 TGGGAAGTTGATGTCATGTCTATG 58.569 41.667 0.00 0.00 35.57 2.23
23 24 5.698741 TGGGAAGTTGATGTCATGTCTAT 57.301 39.130 0.00 0.00 0.00 1.98
24 25 5.245531 GTTGGGAAGTTGATGTCATGTCTA 58.754 41.667 0.00 0.00 0.00 2.59
25 26 4.074970 GTTGGGAAGTTGATGTCATGTCT 58.925 43.478 0.00 0.00 0.00 3.41
26 27 3.191371 GGTTGGGAAGTTGATGTCATGTC 59.809 47.826 0.00 0.00 0.00 3.06
27 28 3.157087 GGTTGGGAAGTTGATGTCATGT 58.843 45.455 0.00 0.00 0.00 3.21
28 29 2.162208 CGGTTGGGAAGTTGATGTCATG 59.838 50.000 0.00 0.00 0.00 3.07
29 30 2.436417 CGGTTGGGAAGTTGATGTCAT 58.564 47.619 0.00 0.00 0.00 3.06
30 31 1.890876 CGGTTGGGAAGTTGATGTCA 58.109 50.000 0.00 0.00 0.00 3.58
31 32 0.521735 GCGGTTGGGAAGTTGATGTC 59.478 55.000 0.00 0.00 0.00 3.06
32 33 0.893727 GGCGGTTGGGAAGTTGATGT 60.894 55.000 0.00 0.00 0.00 3.06
33 34 0.893270 TGGCGGTTGGGAAGTTGATG 60.893 55.000 0.00 0.00 0.00 3.07
34 35 0.893727 GTGGCGGTTGGGAAGTTGAT 60.894 55.000 0.00 0.00 0.00 2.57
35 36 1.527380 GTGGCGGTTGGGAAGTTGA 60.527 57.895 0.00 0.00 0.00 3.18
36 37 1.515521 GAGTGGCGGTTGGGAAGTTG 61.516 60.000 0.00 0.00 0.00 3.16
37 38 1.228154 GAGTGGCGGTTGGGAAGTT 60.228 57.895 0.00 0.00 0.00 2.66
38 39 2.113243 GAGAGTGGCGGTTGGGAAGT 62.113 60.000 0.00 0.00 0.00 3.01
39 40 1.376037 GAGAGTGGCGGTTGGGAAG 60.376 63.158 0.00 0.00 0.00 3.46
40 41 1.415672 AAGAGAGTGGCGGTTGGGAA 61.416 55.000 0.00 0.00 0.00 3.97
41 42 1.827399 GAAGAGAGTGGCGGTTGGGA 61.827 60.000 0.00 0.00 0.00 4.37
42 43 1.376037 GAAGAGAGTGGCGGTTGGG 60.376 63.158 0.00 0.00 0.00 4.12
43 44 1.376037 GGAAGAGAGTGGCGGTTGG 60.376 63.158 0.00 0.00 0.00 3.77
44 45 0.390472 GAGGAAGAGAGTGGCGGTTG 60.390 60.000 0.00 0.00 0.00 3.77
45 46 1.545706 GGAGGAAGAGAGTGGCGGTT 61.546 60.000 0.00 0.00 0.00 4.44
46 47 1.985116 GGAGGAAGAGAGTGGCGGT 60.985 63.158 0.00 0.00 0.00 5.68
47 48 2.726351 GGGAGGAAGAGAGTGGCGG 61.726 68.421 0.00 0.00 0.00 6.13
48 49 2.726351 GGGGAGGAAGAGAGTGGCG 61.726 68.421 0.00 0.00 0.00 5.69
49 50 1.306568 AGGGGAGGAAGAGAGTGGC 60.307 63.158 0.00 0.00 0.00 5.01
50 51 0.689412 GGAGGGGAGGAAGAGAGTGG 60.689 65.000 0.00 0.00 0.00 4.00
51 52 0.689412 GGGAGGGGAGGAAGAGAGTG 60.689 65.000 0.00 0.00 0.00 3.51
52 53 1.707200 GGGAGGGGAGGAAGAGAGT 59.293 63.158 0.00 0.00 0.00 3.24
53 54 1.074850 GGGGAGGGGAGGAAGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
54 55 1.162951 AAGGGGAGGGGAGGAAGAGA 61.163 60.000 0.00 0.00 0.00 3.10
55 56 0.985490 CAAGGGGAGGGGAGGAAGAG 60.985 65.000 0.00 0.00 0.00 2.85
56 57 1.082954 CAAGGGGAGGGGAGGAAGA 59.917 63.158 0.00 0.00 0.00 2.87
57 58 2.684499 GCAAGGGGAGGGGAGGAAG 61.684 68.421 0.00 0.00 0.00 3.46
58 59 2.614013 GCAAGGGGAGGGGAGGAA 60.614 66.667 0.00 0.00 0.00 3.36
59 60 3.953652 TGCAAGGGGAGGGGAGGA 61.954 66.667 0.00 0.00 0.00 3.71
60 61 3.732849 GTGCAAGGGGAGGGGAGG 61.733 72.222 0.00 0.00 0.00 4.30
61 62 2.612115 AGTGCAAGGGGAGGGGAG 60.612 66.667 0.00 0.00 0.00 4.30
62 63 2.935481 CAGTGCAAGGGGAGGGGA 60.935 66.667 0.00 0.00 0.00 4.81
63 64 4.748144 GCAGTGCAAGGGGAGGGG 62.748 72.222 11.09 0.00 0.00 4.79
64 65 3.655211 AGCAGTGCAAGGGGAGGG 61.655 66.667 19.20 0.00 0.00 4.30
65 66 2.360852 CAGCAGTGCAAGGGGAGG 60.361 66.667 19.20 0.00 0.00 4.30
66 67 1.673665 GACAGCAGTGCAAGGGGAG 60.674 63.158 19.20 0.36 0.00 4.30
67 68 2.401699 CTGACAGCAGTGCAAGGGGA 62.402 60.000 19.20 0.00 37.37 4.81
68 69 1.970114 CTGACAGCAGTGCAAGGGG 60.970 63.158 19.20 3.61 37.37 4.79
69 70 1.970114 CCTGACAGCAGTGCAAGGG 60.970 63.158 19.20 7.96 40.63 3.95
70 71 1.071987 TCCTGACAGCAGTGCAAGG 59.928 57.895 19.20 17.28 40.63 3.61
71 72 1.233285 GGTCCTGACAGCAGTGCAAG 61.233 60.000 19.20 11.98 40.63 4.01
72 73 1.227943 GGTCCTGACAGCAGTGCAA 60.228 57.895 19.20 0.00 40.63 4.08
73 74 2.427320 GGTCCTGACAGCAGTGCA 59.573 61.111 19.20 0.00 40.63 4.57
74 75 1.544825 TAGGGTCCTGACAGCAGTGC 61.545 60.000 7.13 7.13 40.63 4.40
75 76 0.976641 TTAGGGTCCTGACAGCAGTG 59.023 55.000 0.00 0.00 40.63 3.66
76 77 1.729586 TTTAGGGTCCTGACAGCAGT 58.270 50.000 0.00 0.00 40.63 4.40
77 78 2.427506 GTTTTAGGGTCCTGACAGCAG 58.572 52.381 0.00 0.00 41.93 4.24
78 79 1.073284 GGTTTTAGGGTCCTGACAGCA 59.927 52.381 0.00 0.00 0.00 4.41
79 80 1.073284 TGGTTTTAGGGTCCTGACAGC 59.927 52.381 0.00 0.00 0.00 4.40
80 81 2.290323 CCTGGTTTTAGGGTCCTGACAG 60.290 54.545 0.00 0.00 34.06 3.51
81 82 1.702957 CCTGGTTTTAGGGTCCTGACA 59.297 52.381 0.00 0.00 34.06 3.58
82 83 1.613520 GCCTGGTTTTAGGGTCCTGAC 60.614 57.143 0.00 0.00 38.32 3.51
94 95 2.807676 CCATCCAAGTTAGCCTGGTTT 58.192 47.619 0.00 0.00 0.00 3.27
96 97 0.034089 GCCATCCAAGTTAGCCTGGT 60.034 55.000 0.00 0.00 0.00 4.00
98 99 1.340405 ACTGCCATCCAAGTTAGCCTG 60.340 52.381 0.00 0.00 0.00 4.85
151 155 1.795768 ACCGACATTATGCCTATGCG 58.204 50.000 0.00 0.00 41.78 4.73
152 156 4.568152 AAAACCGACATTATGCCTATGC 57.432 40.909 0.00 0.00 38.26 3.14
163 167 9.444600 AACAGTAAAGTCATATAAAACCGACAT 57.555 29.630 0.00 0.00 0.00 3.06
188 192 7.989416 AAGATAAAAACCGACCTATCAACAA 57.011 32.000 0.00 0.00 0.00 2.83
191 195 9.292195 AGAAAAAGATAAAAACCGACCTATCAA 57.708 29.630 0.00 0.00 0.00 2.57
192 196 8.857694 AGAAAAAGATAAAAACCGACCTATCA 57.142 30.769 0.00 0.00 0.00 2.15
197 201 7.849026 GCAAAAAGAAAAAGATAAAAACCGACC 59.151 33.333 0.00 0.00 0.00 4.79
213 217 6.127196 ACCACCAACATTCTAGCAAAAAGAAA 60.127 34.615 0.00 0.00 36.60 2.52
216 220 5.200368 ACCACCAACATTCTAGCAAAAAG 57.800 39.130 0.00 0.00 0.00 2.27
230 234 0.459411 GCACACAACCAACCACCAAC 60.459 55.000 0.00 0.00 0.00 3.77
252 256 0.177604 CTGACCCCTGCAGAGCTAAG 59.822 60.000 17.39 3.22 35.39 2.18
257 261 0.617413 AACATCTGACCCCTGCAGAG 59.383 55.000 17.39 8.86 44.75 3.35
347 354 7.966339 TCATGATGAAAATGAAAAGAGGGAT 57.034 32.000 0.00 0.00 31.17 3.85
348 355 7.575532 CGTTCATGATGAAAATGAAAAGAGGGA 60.576 37.037 9.78 0.00 43.66 4.20
372 379 8.223330 ACCCGGTAATAGAGAATATATATCCGT 58.777 37.037 0.00 0.00 32.27 4.69
423 430 4.163427 CCTGATGGATAGAAAGGCTAGGA 58.837 47.826 0.00 0.00 34.57 2.94
488 495 0.178992 CCAGGTTCCTGGTTTGCTCA 60.179 55.000 25.10 0.00 46.22 4.26
489 496 2.646121 CCAGGTTCCTGGTTTGCTC 58.354 57.895 25.10 0.00 46.22 4.26
531 538 2.658593 GTGATGGCGGACGGATCG 60.659 66.667 0.00 0.00 0.00 3.69
542 549 4.386951 TGTCCCGTGCGGTGATGG 62.387 66.667 9.90 0.00 0.00 3.51
543 550 3.118454 GTGTCCCGTGCGGTGATG 61.118 66.667 9.90 0.00 0.00 3.07
544 551 4.735132 CGTGTCCCGTGCGGTGAT 62.735 66.667 9.90 0.00 0.00 3.06
549 556 4.805231 TATGCCGTGTCCCGTGCG 62.805 66.667 0.00 0.00 36.09 5.34
550 557 0.531090 TATTATGCCGTGTCCCGTGC 60.531 55.000 0.00 0.00 34.58 5.34
551 558 1.214367 GTATTATGCCGTGTCCCGTG 58.786 55.000 0.00 0.00 33.66 4.94
552 559 0.105408 GGTATTATGCCGTGTCCCGT 59.895 55.000 0.00 0.00 33.66 5.28
553 560 0.105224 TGGTATTATGCCGTGTCCCG 59.895 55.000 0.00 0.00 0.00 5.14
554 561 1.542547 CCTGGTATTATGCCGTGTCCC 60.543 57.143 0.00 0.00 0.00 4.46
555 562 1.878953 CCTGGTATTATGCCGTGTCC 58.121 55.000 0.00 0.00 0.00 4.02
556 563 1.226746 GCCTGGTATTATGCCGTGTC 58.773 55.000 0.00 0.00 0.00 3.67
557 564 0.544223 TGCCTGGTATTATGCCGTGT 59.456 50.000 0.00 0.00 0.00 4.49
604 625 1.202722 GGGAGACGTGGGTTTTCTCAA 60.203 52.381 0.00 0.00 38.02 3.02
605 626 0.395312 GGGAGACGTGGGTTTTCTCA 59.605 55.000 0.00 0.00 38.02 3.27
606 627 0.395312 TGGGAGACGTGGGTTTTCTC 59.605 55.000 0.00 0.00 35.92 2.87
613 634 3.717842 TTTTTCTGGGAGACGTGGG 57.282 52.632 0.00 0.00 0.00 4.61
637 658 2.788786 GTCGTTGTCAACTTGCCATTTG 59.211 45.455 13.67 0.00 0.00 2.32
638 659 2.425312 TGTCGTTGTCAACTTGCCATTT 59.575 40.909 13.67 0.00 0.00 2.32
639 660 2.020720 TGTCGTTGTCAACTTGCCATT 58.979 42.857 13.67 0.00 0.00 3.16
674 695 3.775654 CGGAGGGCGGAGAAAGCT 61.776 66.667 0.00 0.00 34.52 3.74
841 866 1.002624 TGCGGCTAAAGGAAGGGTG 60.003 57.895 0.00 0.00 0.00 4.61
842 867 1.299976 CTGCGGCTAAAGGAAGGGT 59.700 57.895 0.00 0.00 0.00 4.34
920 946 1.350193 CGTGGTACTGCAACTAGCTG 58.650 55.000 0.00 0.00 45.94 4.24
921 947 0.389948 GCGTGGTACTGCAACTAGCT 60.390 55.000 0.00 0.00 45.94 3.32
922 948 1.683790 CGCGTGGTACTGCAACTAGC 61.684 60.000 0.00 0.00 45.96 3.42
936 962 1.282248 CTTGGTGGTGTACTCGCGTG 61.282 60.000 5.77 6.24 0.00 5.34
939 965 2.033194 GGCTTGGTGGTGTACTCGC 61.033 63.158 0.00 0.00 0.00 5.03
979 1005 4.704833 CCCAGACCCAGTGGCACG 62.705 72.222 12.71 7.23 33.24 5.34
986 1012 2.750657 GCCATCCTCCCAGACCCAG 61.751 68.421 0.00 0.00 0.00 4.45
987 1013 2.692368 GCCATCCTCCCAGACCCA 60.692 66.667 0.00 0.00 0.00 4.51
988 1014 1.988982 GAAGCCATCCTCCCAGACCC 61.989 65.000 0.00 0.00 0.00 4.46
989 1015 1.529309 GAAGCCATCCTCCCAGACC 59.471 63.158 0.00 0.00 0.00 3.85
990 1016 1.144936 CGAAGCCATCCTCCCAGAC 59.855 63.158 0.00 0.00 0.00 3.51
991 1017 0.399091 ATCGAAGCCATCCTCCCAGA 60.399 55.000 0.00 0.00 0.00 3.86
992 1018 0.034616 GATCGAAGCCATCCTCCCAG 59.965 60.000 0.00 0.00 0.00 4.45
1158 1196 1.153289 CTCATCCTTGGCCTCCGTG 60.153 63.158 3.32 0.00 0.00 4.94
1167 1205 1.227089 CGACGGCTCCTCATCCTTG 60.227 63.158 0.00 0.00 0.00 3.61
1210 1251 0.396695 ACCGATATCCTGGACACGGT 60.397 55.000 26.45 26.45 46.69 4.83
1281 1328 1.521681 GGAACCTCGAGGCGAATGG 60.522 63.158 31.56 7.27 39.32 3.16
1282 1329 0.528684 GAGGAACCTCGAGGCGAATG 60.529 60.000 31.56 6.99 39.32 2.67
1283 1330 0.684805 AGAGGAACCTCGAGGCGAAT 60.685 55.000 31.56 15.28 46.90 3.34
1285 1332 2.046864 CAGAGGAACCTCGAGGCGA 61.047 63.158 31.56 0.00 46.90 5.54
1286 1333 2.344203 ACAGAGGAACCTCGAGGCG 61.344 63.158 31.56 9.41 46.90 5.52
1288 1335 0.969894 AACACAGAGGAACCTCGAGG 59.030 55.000 30.11 30.11 46.90 4.63
1289 1336 2.821991 AAACACAGAGGAACCTCGAG 57.178 50.000 14.13 5.13 46.90 4.04
1290 1337 3.202906 CAAAAACACAGAGGAACCTCGA 58.797 45.455 14.13 0.00 46.90 4.04
1291 1338 2.943033 ACAAAAACACAGAGGAACCTCG 59.057 45.455 14.13 11.66 46.90 4.63
1292 1339 4.672409 CAACAAAAACACAGAGGAACCTC 58.328 43.478 12.42 12.42 43.03 3.85
1293 1340 3.119137 GCAACAAAAACACAGAGGAACCT 60.119 43.478 0.00 0.00 0.00 3.50
1294 1341 3.186909 GCAACAAAAACACAGAGGAACC 58.813 45.455 0.00 0.00 0.00 3.62
1295 1342 3.186909 GGCAACAAAAACACAGAGGAAC 58.813 45.455 0.00 0.00 0.00 3.62
1296 1343 2.159310 CGGCAACAAAAACACAGAGGAA 60.159 45.455 0.00 0.00 0.00 3.36
1297 1344 1.403679 CGGCAACAAAAACACAGAGGA 59.596 47.619 0.00 0.00 0.00 3.71
1298 1345 1.403679 TCGGCAACAAAAACACAGAGG 59.596 47.619 0.00 0.00 0.00 3.69
1299 1346 2.450160 GTCGGCAACAAAAACACAGAG 58.550 47.619 0.00 0.00 0.00 3.35
1300 1347 1.202087 CGTCGGCAACAAAAACACAGA 60.202 47.619 0.00 0.00 0.00 3.41
1301 1348 1.187715 CGTCGGCAACAAAAACACAG 58.812 50.000 0.00 0.00 0.00 3.66
1302 1349 0.803117 TCGTCGGCAACAAAAACACA 59.197 45.000 0.00 0.00 0.00 3.72
1303 1350 1.185189 GTCGTCGGCAACAAAAACAC 58.815 50.000 0.00 0.00 0.00 3.32
1304 1351 0.247735 CGTCGTCGGCAACAAAAACA 60.248 50.000 0.00 0.00 0.00 2.83
1305 1352 0.026544 TCGTCGTCGGCAACAAAAAC 59.973 50.000 1.55 0.00 37.69 2.43
1306 1353 0.725686 TTCGTCGTCGGCAACAAAAA 59.274 45.000 1.55 0.00 37.69 1.94
1333 1380 1.061131 GCAACGAGGAATCACATGACG 59.939 52.381 0.00 0.00 0.00 4.35
1372 1419 5.523369 GGTGGCTTTGCATATTTACATCTC 58.477 41.667 0.00 0.00 0.00 2.75
1405 1452 4.207955 GGACAAGAAGGAACAAAAGGAGT 58.792 43.478 0.00 0.00 0.00 3.85
1427 1474 4.389374 ACTGTGTGTAGGAAAAGTCATGG 58.611 43.478 0.00 0.00 0.00 3.66
1429 1476 5.063880 GGAACTGTGTGTAGGAAAAGTCAT 58.936 41.667 0.00 0.00 0.00 3.06
1468 1515 1.738350 TCGGTCGTTCTCTGATCAGAC 59.262 52.381 21.67 11.77 33.22 3.51
1499 1550 8.697960 GGTCGATTATTACGAGGAAAATAAGTC 58.302 37.037 0.00 0.00 40.37 3.01
1502 1553 6.642131 CCGGTCGATTATTACGAGGAAAATAA 59.358 38.462 0.00 0.00 40.37 1.40
1504 1555 4.986659 CCGGTCGATTATTACGAGGAAAAT 59.013 41.667 0.00 0.00 40.37 1.82
1563 1614 1.001048 CGCCCGATTACGAGAACCATA 60.001 52.381 0.00 0.00 42.66 2.74
1625 1678 1.798813 GTTTTCTGTAGTCCACGCAGG 59.201 52.381 0.00 0.00 39.47 4.85
1671 1724 9.494271 GTTACAGCAATATCTCAGAATGGATTA 57.506 33.333 0.00 0.00 36.16 1.75
1706 1759 6.747659 AAAAATGCGCTGTTAAAAGTACAG 57.252 33.333 9.73 0.00 44.55 2.74
1809 1862 9.624697 TTGATACTATTTGCAATTCTGTTTGAC 57.375 29.630 0.00 0.00 0.00 3.18
1839 1892 1.598962 CGCCCATGGAGCAGTATGG 60.599 63.158 15.22 6.24 42.77 2.74
1856 1909 0.389426 CTACCGAAGACAACCCACCG 60.389 60.000 0.00 0.00 0.00 4.94
1872 1925 5.107298 GCAGATATGCTTGGAATCGAACTAC 60.107 44.000 4.74 0.00 0.00 2.73
1972 2025 9.448587 AGTAACCTCTTCCCACATAGTTATATT 57.551 33.333 0.00 0.00 0.00 1.28
2024 2077 1.226974 CACTCCGCCGGTGTATGAG 60.227 63.158 15.14 15.41 0.00 2.90
2125 2178 0.615544 TAGGGAAATCACGGTCGGGT 60.616 55.000 0.00 0.00 0.00 5.28
2132 2185 4.155826 TGATTGCTTTGTAGGGAAATCACG 59.844 41.667 0.00 0.00 0.00 4.35
2153 2206 0.188587 ATCGGAGGGAGTAGGCATGA 59.811 55.000 0.00 0.00 0.00 3.07
2162 2215 6.014156 AGACAATTATTTAGGATCGGAGGGAG 60.014 42.308 0.00 0.00 0.00 4.30
2163 2216 5.844516 AGACAATTATTTAGGATCGGAGGGA 59.155 40.000 0.00 0.00 0.00 4.20
2164 2217 6.115448 AGACAATTATTTAGGATCGGAGGG 57.885 41.667 0.00 0.00 0.00 4.30
2165 2218 7.934120 AGAAAGACAATTATTTAGGATCGGAGG 59.066 37.037 0.00 0.00 0.00 4.30
2166 2219 8.894768 AGAAAGACAATTATTTAGGATCGGAG 57.105 34.615 0.00 0.00 0.00 4.63
2167 2220 9.982651 CTAGAAAGACAATTATTTAGGATCGGA 57.017 33.333 0.00 0.00 0.00 4.55
2168 2221 9.982651 TCTAGAAAGACAATTATTTAGGATCGG 57.017 33.333 0.00 0.00 0.00 4.18
2181 2234 9.566432 ACTTGTTGAAATCTCTAGAAAGACAAT 57.434 29.630 0.00 0.00 0.00 2.71
2182 2235 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2183 2236 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2184 2237 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2185 2238 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
2186 2239 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2187 2240 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2188 2241 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
2189 2242 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2190 2243 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
2191 2244 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2192 2245 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2193 2246 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
2194 2247 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
2195 2248 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
2196 2249 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
2197 2250 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
2198 2251 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
2199 2252 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
2200 2253 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
2201 2254 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
2202 2255 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
2203 2256 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
2204 2257 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
2205 2258 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
2206 2259 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
2207 2260 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
2208 2261 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
2209 2262 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2210 2263 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2211 2264 6.128391 GGTTCACTCATTTTGCTTCGTATGTA 60.128 38.462 0.00 0.00 0.00 2.29
2212 2265 5.334879 GGTTCACTCATTTTGCTTCGTATGT 60.335 40.000 0.00 0.00 0.00 2.29
2213 2266 5.088739 GGTTCACTCATTTTGCTTCGTATG 58.911 41.667 0.00 0.00 0.00 2.39
2214 2267 5.003804 AGGTTCACTCATTTTGCTTCGTAT 58.996 37.500 0.00 0.00 0.00 3.06
2215 2268 4.385825 AGGTTCACTCATTTTGCTTCGTA 58.614 39.130 0.00 0.00 0.00 3.43
2216 2269 3.214328 AGGTTCACTCATTTTGCTTCGT 58.786 40.909 0.00 0.00 0.00 3.85
2217 2270 3.904136 AGGTTCACTCATTTTGCTTCG 57.096 42.857 0.00 0.00 0.00 3.79
2218 2271 5.239525 AGTGTAGGTTCACTCATTTTGCTTC 59.760 40.000 0.00 0.00 44.07 3.86
2219 2272 5.133221 AGTGTAGGTTCACTCATTTTGCTT 58.867 37.500 0.00 0.00 44.07 3.91
2220 2273 4.718961 AGTGTAGGTTCACTCATTTTGCT 58.281 39.130 0.00 0.00 44.07 3.91


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

AutoCloner maintained by Alex Coulton.