Multiple sequence alignment - TraesCS7D01G311400

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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 TraesCS7D01G311400 chr7D 100.000 2507 0 0 1 2507 394831141 394833647 0.000000e+00 4630.0
1 TraesCS7D01G311400 chr7D 98.026 608 12 0 1777 2384 170955282 170954675 0.000000e+00 1057.0
2 TraesCS7D01G311400 chr7D 89.147 516 55 1 1070 1584 166514227 166513712 2.100000e-180 641.0
3 TraesCS7D01G311400 chr7D 99.206 126 1 0 2382 2507 170954043 170953918 6.980000e-56 228.0
4 TraesCS7D01G311400 chr7D 75.000 192 46 2 1391 1581 53809061 53809251 1.240000e-13 87.9
5 TraesCS7D01G311400 chr7B 94.952 931 30 9 1 923 394402549 394403470 0.000000e+00 1443.0
6 TraesCS7D01G311400 chr7B 92.969 128 9 0 416 543 394402733 394402860 1.180000e-43 187.0
7 TraesCS7D01G311400 chr7A 96.010 827 28 5 4 827 448100133 448100957 0.000000e+00 1339.0
8 TraesCS7D01G311400 chr7A 86.254 582 77 3 1033 1613 448101431 448102010 1.640000e-176 628.0
9 TraesCS7D01G311400 chr7A 92.969 128 9 0 416 543 448100314 448100441 1.180000e-43 187.0
10 TraesCS7D01G311400 chr7A 91.304 138 10 2 176 312 448100536 448100672 1.180000e-43 187.0
11 TraesCS7D01G311400 chr4D 97.876 612 13 0 1773 2384 469323637 469323026 0.000000e+00 1059.0
12 TraesCS7D01G311400 chr4D 98.413 126 2 0 2382 2507 87949605 87949480 3.250000e-54 222.0
13 TraesCS7D01G311400 chr5D 97.565 616 14 1 1770 2384 274779760 274780375 0.000000e+00 1053.0
14 TraesCS7D01G311400 chr5D 97.553 613 15 0 1772 2384 362187881 362188493 0.000000e+00 1050.0
15 TraesCS7D01G311400 chr5D 97.705 610 13 1 1775 2384 233733828 233733220 0.000000e+00 1048.0
16 TraesCS7D01G311400 chr5D 98.413 126 2 0 2382 2507 424077549 424077424 3.250000e-54 222.0
17 TraesCS7D01G311400 chr3D 97.705 610 14 0 1775 2384 520593371 520592762 0.000000e+00 1050.0
18 TraesCS7D01G311400 chr3D 97.541 610 15 0 1775 2384 484115423 484116032 0.000000e+00 1044.0
19 TraesCS7D01G311400 chr3D 97.541 610 15 0 1775 2384 560890274 560889665 0.000000e+00 1044.0
20 TraesCS7D01G311400 chr3D 97.386 612 16 0 1773 2384 378043973 378043362 0.000000e+00 1042.0
21 TraesCS7D01G311400 chr3D 98.413 126 2 0 2382 2507 69792266 69792391 3.250000e-54 222.0
22 TraesCS7D01G311400 chr3D 98.413 126 2 0 2382 2507 170560270 170560395 3.250000e-54 222.0
23 TraesCS7D01G311400 chr3D 98.413 126 2 0 2382 2507 484116664 484116789 3.250000e-54 222.0
24 TraesCS7D01G311400 chr3D 98.413 126 2 0 2382 2507 520592131 520592006 3.250000e-54 222.0
25 TraesCS7D01G311400 chrUn 98.413 126 2 0 2382 2507 467865261 467865136 3.250000e-54 222.0
26 TraesCS7D01G311400 chr2D 98.413 126 2 0 2382 2507 589195816 589195941 3.250000e-54 222.0
27 TraesCS7D01G311400 chr3B 86.466 133 14 2 1640 1771 52788323 52788452 2.600000e-30 143.0
28 TraesCS7D01G311400 chr6A 90.000 70 7 0 1070 1139 608403387 608403456 9.550000e-15 91.6
29 TraesCS7D01G311400 chr1A 74.479 192 47 2 1391 1581 13879819 13880009 5.750000e-12 82.4
30 TraesCS7D01G311400 chr2B 85.484 62 9 0 911 972 636708846 636708785 5.790000e-07 65.8


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 TraesCS7D01G311400 chr7D 394831141 394833647 2506 False 4630.00 4630 100.00000 1 2507 1 chr7D.!!$F2 2506
1 TraesCS7D01G311400 chr7D 170953918 170955282 1364 True 642.50 1057 98.61600 1777 2507 2 chr7D.!!$R2 730
2 TraesCS7D01G311400 chr7D 166513712 166514227 515 True 641.00 641 89.14700 1070 1584 1 chr7D.!!$R1 514
3 TraesCS7D01G311400 chr7B 394402549 394403470 921 False 815.00 1443 93.96050 1 923 2 chr7B.!!$F1 922
4 TraesCS7D01G311400 chr7A 448100133 448102010 1877 False 585.25 1339 91.63425 4 1613 4 chr7A.!!$F1 1609
5 TraesCS7D01G311400 chr4D 469323026 469323637 611 True 1059.00 1059 97.87600 1773 2384 1 chr4D.!!$R2 611
6 TraesCS7D01G311400 chr5D 274779760 274780375 615 False 1053.00 1053 97.56500 1770 2384 1 chr5D.!!$F1 614
7 TraesCS7D01G311400 chr5D 362187881 362188493 612 False 1050.00 1050 97.55300 1772 2384 1 chr5D.!!$F2 612
8 TraesCS7D01G311400 chr5D 233733220 233733828 608 True 1048.00 1048 97.70500 1775 2384 1 chr5D.!!$R1 609
9 TraesCS7D01G311400 chr3D 560889665 560890274 609 True 1044.00 1044 97.54100 1775 2384 1 chr3D.!!$R2 609
10 TraesCS7D01G311400 chr3D 378043362 378043973 611 True 1042.00 1042 97.38600 1773 2384 1 chr3D.!!$R1 611
11 TraesCS7D01G311400 chr3D 520592006 520593371 1365 True 636.00 1050 98.05900 1775 2507 2 chr3D.!!$R3 732
12 TraesCS7D01G311400 chr3D 484115423 484116789 1366 False 633.00 1044 97.97700 1775 2507 2 chr3D.!!$F3 732

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
966 1319 0.110373 GGTGACCACATCGAAAACGC 60.11 55.0 0.0 0.0 0.0 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2444 0.107703 GGTGATGGTGCCGATGAGAA 60.108 55.0 0.0 0.0 0.0 2.87 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
539 540 1.317613 ACCAGCTCAACAAAATGCGA 58.682 45.000 0.00 0.00 0.00 5.10
554 555 3.918220 CGATCCAACTGAGCGCGC 61.918 66.667 26.66 26.66 46.85 6.86
555 556 3.918220 GATCCAACTGAGCGCGCG 61.918 66.667 28.44 28.44 0.00 6.86
556 557 4.742201 ATCCAACTGAGCGCGCGT 62.742 61.111 32.35 18.26 0.00 6.01
557 558 3.350909 ATCCAACTGAGCGCGCGTA 62.351 57.895 32.35 17.73 0.00 4.42
861 1210 5.682943 TTTTACTTCAGATTTGACCGGTG 57.317 39.130 14.63 0.00 31.71 4.94
909 1262 8.655970 ACGAGTAAAGTTACTTTTTGTTTACGT 58.344 29.630 15.83 13.70 43.64 3.57
938 1291 2.584791 GAACATTTGTCATGCGTGTCC 58.415 47.619 5.68 0.00 0.00 4.02
939 1292 0.516877 ACATTTGTCATGCGTGTCCG 59.483 50.000 5.68 0.00 37.07 4.79
951 1304 1.153647 GTGTCCGCGATGATGGTGA 60.154 57.895 8.23 0.00 0.00 4.02
952 1305 1.153647 TGTCCGCGATGATGGTGAC 60.154 57.895 8.23 4.04 0.00 3.67
953 1306 1.883084 GTCCGCGATGATGGTGACC 60.883 63.158 8.23 0.00 0.00 4.02
954 1307 2.186644 CCGCGATGATGGTGACCA 59.813 61.111 6.84 6.84 38.19 4.02
955 1308 2.173669 CCGCGATGATGGTGACCAC 61.174 63.158 6.40 1.42 35.80 4.16
956 1309 1.447663 CGCGATGATGGTGACCACA 60.448 57.895 6.40 7.96 35.80 4.17
957 1310 0.811219 CGCGATGATGGTGACCACAT 60.811 55.000 6.40 12.79 35.80 3.21
958 1311 0.940126 GCGATGATGGTGACCACATC 59.060 55.000 24.63 24.63 43.82 3.06
959 1312 1.211743 CGATGATGGTGACCACATCG 58.788 55.000 33.18 33.18 46.78 3.84
960 1313 2.602257 GATGATGGTGACCACATCGA 57.398 50.000 22.20 5.90 45.90 3.59
961 1314 2.905075 GATGATGGTGACCACATCGAA 58.095 47.619 22.20 0.99 45.90 3.71
962 1315 2.849294 TGATGGTGACCACATCGAAA 57.151 45.000 6.40 0.00 45.90 3.46
963 1316 3.133141 TGATGGTGACCACATCGAAAA 57.867 42.857 6.40 0.00 45.90 2.29
964 1317 2.811431 TGATGGTGACCACATCGAAAAC 59.189 45.455 6.40 0.00 45.90 2.43
965 1318 1.222300 TGGTGACCACATCGAAAACG 58.778 50.000 0.00 0.00 0.00 3.60
966 1319 0.110373 GGTGACCACATCGAAAACGC 60.110 55.000 0.00 0.00 0.00 4.84
967 1320 0.865769 GTGACCACATCGAAAACGCT 59.134 50.000 0.00 0.00 0.00 5.07
968 1321 0.865111 TGACCACATCGAAAACGCTG 59.135 50.000 0.00 0.00 0.00 5.18
969 1322 0.165944 GACCACATCGAAAACGCTGG 59.834 55.000 0.00 0.00 0.00 4.85
970 1323 1.154225 CCACATCGAAAACGCTGGC 60.154 57.895 0.00 0.00 0.00 4.85
971 1324 1.509787 CACATCGAAAACGCTGGCG 60.510 57.895 13.56 13.56 46.03 5.69
986 1339 3.330853 GCGTCCGCCATCGTGATC 61.331 66.667 0.00 0.00 34.56 2.92
987 1340 3.024609 CGTCCGCCATCGTGATCG 61.025 66.667 0.00 0.00 38.55 3.69
988 1341 2.104331 GTCCGCCATCGTGATCGT 59.896 61.111 0.00 0.00 38.33 3.73
989 1342 2.104132 TCCGCCATCGTGATCGTG 59.896 61.111 0.00 0.00 38.33 4.35
990 1343 3.630148 CCGCCATCGTGATCGTGC 61.630 66.667 0.00 0.00 38.33 5.34
991 1344 2.583319 CGCCATCGTGATCGTGCT 60.583 61.111 0.00 0.00 38.33 4.40
992 1345 2.580470 CGCCATCGTGATCGTGCTC 61.580 63.158 0.00 0.00 38.33 4.26
993 1346 2.580470 GCCATCGTGATCGTGCTCG 61.580 63.158 0.81 0.81 38.33 5.03
994 1347 1.946156 CCATCGTGATCGTGCTCGG 60.946 63.158 8.49 0.00 38.33 4.63
995 1348 2.278857 ATCGTGATCGTGCTCGGC 60.279 61.111 8.49 1.89 38.33 5.54
996 1349 4.829518 TCGTGATCGTGCTCGGCG 62.830 66.667 8.49 0.00 38.33 6.46
997 1350 4.829518 CGTGATCGTGCTCGGCGA 62.830 66.667 10.14 10.14 42.75 5.54
998 1351 2.951745 GTGATCGTGCTCGGCGAG 60.952 66.667 31.40 31.40 41.83 5.03
999 1352 4.193334 TGATCGTGCTCGGCGAGG 62.193 66.667 35.03 20.44 41.83 4.63
1000 1353 3.889044 GATCGTGCTCGGCGAGGA 61.889 66.667 35.03 31.54 41.83 3.71
1001 1354 3.200887 GATCGTGCTCGGCGAGGAT 62.201 63.158 35.03 27.80 41.83 3.24
1002 1355 3.490793 ATCGTGCTCGGCGAGGATG 62.491 63.158 35.51 35.51 41.83 3.51
1004 1357 3.838271 GTGCTCGGCGAGGATGGA 61.838 66.667 35.03 11.58 31.72 3.41
1005 1358 3.074369 TGCTCGGCGAGGATGGAA 61.074 61.111 35.03 4.13 0.00 3.53
1006 1359 2.279784 GCTCGGCGAGGATGGAAG 60.280 66.667 35.03 11.46 0.00 3.46
1007 1360 2.419198 CTCGGCGAGGATGGAAGG 59.581 66.667 28.52 0.25 0.00 3.46
1008 1361 3.798954 CTCGGCGAGGATGGAAGGC 62.799 68.421 28.52 0.00 0.00 4.35
1010 1363 4.918201 GGCGAGGATGGAAGGCGG 62.918 72.222 0.00 0.00 0.00 6.13
1013 1366 4.162690 GAGGATGGAAGGCGGCGT 62.163 66.667 9.37 0.00 0.00 5.68
1014 1367 3.682292 GAGGATGGAAGGCGGCGTT 62.682 63.158 9.37 7.76 0.00 4.84
1015 1368 3.508840 GGATGGAAGGCGGCGTTG 61.509 66.667 13.20 0.00 0.00 4.10
1016 1369 3.508840 GATGGAAGGCGGCGTTGG 61.509 66.667 13.20 0.00 0.00 3.77
1025 1378 4.003788 CGGCGTTGGGGTCACTCT 62.004 66.667 0.00 0.00 0.00 3.24
1026 1379 2.642254 CGGCGTTGGGGTCACTCTA 61.642 63.158 0.00 0.00 0.00 2.43
1027 1380 1.218316 GGCGTTGGGGTCACTCTAG 59.782 63.158 0.00 0.00 0.00 2.43
1028 1381 1.255667 GGCGTTGGGGTCACTCTAGA 61.256 60.000 0.00 0.00 0.00 2.43
1029 1382 0.173708 GCGTTGGGGTCACTCTAGAG 59.826 60.000 18.49 18.49 0.00 2.43
1030 1383 0.173708 CGTTGGGGTCACTCTAGAGC 59.826 60.000 19.97 3.47 35.36 4.09
1036 1389 1.668101 GGTCACTCTAGAGCCACCCG 61.668 65.000 22.48 6.52 30.80 5.28
1038 1391 0.965866 TCACTCTAGAGCCACCCGTG 60.966 60.000 19.97 9.45 0.00 4.94
1068 1421 2.835431 CGTCTCCCTCGGCCATCT 60.835 66.667 2.24 0.00 0.00 2.90
1090 1443 3.555324 TGCACGTCTTCCTGGCCA 61.555 61.111 4.71 4.71 0.00 5.36
1138 1491 2.431454 TACCTCATGATGCGGCCGT 61.431 57.895 28.70 7.71 0.00 5.68
1143 1496 4.166888 ATGATGCGGCCGTGCTCT 62.167 61.111 28.70 6.90 35.36 4.09
1152 1505 1.446272 GCCGTGCTCTGTGTACCTC 60.446 63.158 0.00 0.00 0.00 3.85
1156 1509 0.596577 GTGCTCTGTGTACCTCGTCA 59.403 55.000 0.00 0.00 0.00 4.35
1162 1515 3.748083 TCTGTGTACCTCGTCAACTACT 58.252 45.455 0.00 0.00 0.00 2.57
1172 1525 1.272490 CGTCAACTACTCCTGCTTCCA 59.728 52.381 0.00 0.00 0.00 3.53
1179 1532 0.179018 ACTCCTGCTTCCACACCAAC 60.179 55.000 0.00 0.00 0.00 3.77
1232 1585 3.121030 GCACGCCAAGCTCGTCAT 61.121 61.111 0.00 0.00 38.19 3.06
1250 1603 0.695803 ATCTTCATCGAGGGGGCCTT 60.696 55.000 0.84 0.00 31.76 4.35
1265 1618 1.911293 GCCTTCATTGACGAGCGCAA 61.911 55.000 11.47 0.00 0.00 4.85
1321 1674 3.685214 CTCGGGAAGGAGACGTGCG 62.685 68.421 0.00 0.00 36.08 5.34
1371 1724 2.592993 CCGGAACTTGGAGGCCTCA 61.593 63.158 33.29 17.15 0.00 3.86
1372 1725 1.078848 CGGAACTTGGAGGCCTCAG 60.079 63.158 33.29 24.52 0.00 3.35
1373 1726 1.831652 CGGAACTTGGAGGCCTCAGT 61.832 60.000 33.29 25.19 0.00 3.41
1386 1740 3.372557 CTCAGTGAGGAGGTGGAGT 57.627 57.895 12.67 0.00 0.00 3.85
1389 1743 1.133167 TCAGTGAGGAGGTGGAGTTCA 60.133 52.381 0.00 0.00 0.00 3.18
1395 1749 2.103941 GAGGAGGTGGAGTTCATCATCC 59.896 54.545 0.00 0.00 36.05 3.51
1397 1751 2.507471 GGAGGTGGAGTTCATCATCCTT 59.493 50.000 0.00 0.00 36.50 3.36
1412 1766 0.251916 TCCTTTCCGCCATTGACGAT 59.748 50.000 0.00 0.00 0.00 3.73
1415 1769 2.009774 CTTTCCGCCATTGACGATCTT 58.990 47.619 0.00 0.00 0.00 2.40
1526 1880 6.765036 ACATGATCATCCACAAGTACAAGATC 59.235 38.462 4.86 0.00 33.19 2.75
1531 1885 2.037902 TCCACAAGTACAAGATCCGCAA 59.962 45.455 0.00 0.00 0.00 4.85
1542 1896 0.807667 GATCCGCAACGACATCTGCT 60.808 55.000 0.00 0.00 36.38 4.24
1544 1898 0.459899 TCCGCAACGACATCTGCTAT 59.540 50.000 0.00 0.00 36.38 2.97
1591 1945 2.586293 CGGGGGTGGTCGTTAGGTT 61.586 63.158 0.00 0.00 0.00 3.50
1592 1946 1.002990 GGGGGTGGTCGTTAGGTTG 60.003 63.158 0.00 0.00 0.00 3.77
1596 1950 1.071228 GGGTGGTCGTTAGGTTGAGTT 59.929 52.381 0.00 0.00 0.00 3.01
1597 1951 2.410939 GGTGGTCGTTAGGTTGAGTTC 58.589 52.381 0.00 0.00 0.00 3.01
1598 1952 2.036862 GGTGGTCGTTAGGTTGAGTTCT 59.963 50.000 0.00 0.00 0.00 3.01
1599 1953 3.493873 GGTGGTCGTTAGGTTGAGTTCTT 60.494 47.826 0.00 0.00 0.00 2.52
1600 1954 3.739810 GTGGTCGTTAGGTTGAGTTCTTC 59.260 47.826 0.00 0.00 0.00 2.87
1601 1955 2.985139 GGTCGTTAGGTTGAGTTCTTCG 59.015 50.000 0.00 0.00 0.00 3.79
1602 1956 3.551659 GGTCGTTAGGTTGAGTTCTTCGT 60.552 47.826 0.00 0.00 0.00 3.85
1603 1957 3.667726 GTCGTTAGGTTGAGTTCTTCGTC 59.332 47.826 0.00 0.00 0.00 4.20
1604 1958 3.567164 TCGTTAGGTTGAGTTCTTCGTCT 59.433 43.478 0.00 0.00 0.00 4.18
1605 1959 4.756642 TCGTTAGGTTGAGTTCTTCGTCTA 59.243 41.667 0.00 0.00 0.00 2.59
1606 1960 4.850470 CGTTAGGTTGAGTTCTTCGTCTAC 59.150 45.833 0.00 0.00 0.00 2.59
1607 1961 3.555917 AGGTTGAGTTCTTCGTCTACG 57.444 47.619 0.00 0.00 41.45 3.51
1617 1971 2.850439 TCGTCTACGAGGTCACCAG 58.150 57.895 0.00 0.00 44.22 4.00
1618 1972 0.675837 TCGTCTACGAGGTCACCAGG 60.676 60.000 0.00 0.00 44.22 4.45
1619 1973 0.675837 CGTCTACGAGGTCACCAGGA 60.676 60.000 0.00 0.00 43.02 3.86
1620 1974 1.096416 GTCTACGAGGTCACCAGGAG 58.904 60.000 0.00 0.00 0.00 3.69
1621 1975 0.034380 TCTACGAGGTCACCAGGAGG 60.034 60.000 0.00 0.00 42.21 4.30
1631 1985 2.675423 CCAGGAGGTCACCGTCGA 60.675 66.667 0.00 0.00 34.73 4.20
1632 1986 2.701780 CCAGGAGGTCACCGTCGAG 61.702 68.421 0.00 0.00 34.73 4.04
1643 1997 4.394078 CGTCGAGGTCGTTGGCGA 62.394 66.667 0.36 0.00 45.79 5.54
1670 2024 4.812476 TCGCCGCCATCGACAAGG 62.812 66.667 0.00 0.00 38.10 3.61
1671 2025 4.812476 CGCCGCCATCGACAAGGA 62.812 66.667 4.68 0.00 38.10 3.36
1672 2026 2.892425 GCCGCCATCGACAAGGAG 60.892 66.667 4.68 1.38 38.10 3.69
1673 2027 2.892425 CCGCCATCGACAAGGAGC 60.892 66.667 4.68 0.00 38.10 4.70
1674 2028 2.185350 CGCCATCGACAAGGAGCT 59.815 61.111 4.68 0.00 38.10 4.09
1675 2029 1.448540 CGCCATCGACAAGGAGCTT 60.449 57.895 4.68 0.00 38.10 3.74
1676 2030 1.424493 CGCCATCGACAAGGAGCTTC 61.424 60.000 4.68 0.00 38.10 3.86
1677 2031 0.391661 GCCATCGACAAGGAGCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
1678 2032 1.363744 CCATCGACAAGGAGCTTCAC 58.636 55.000 0.00 0.00 0.00 3.18
1679 2033 0.994995 CATCGACAAGGAGCTTCACG 59.005 55.000 0.00 0.00 0.00 4.35
1680 2034 0.737715 ATCGACAAGGAGCTTCACGC 60.738 55.000 0.00 0.00 39.57 5.34
1681 2035 1.664649 CGACAAGGAGCTTCACGCA 60.665 57.895 0.00 0.00 42.61 5.24
1682 2036 1.221466 CGACAAGGAGCTTCACGCAA 61.221 55.000 0.00 0.00 42.61 4.85
1683 2037 0.944386 GACAAGGAGCTTCACGCAAA 59.056 50.000 0.00 0.00 42.61 3.68
1684 2038 1.537202 GACAAGGAGCTTCACGCAAAT 59.463 47.619 0.00 0.00 42.61 2.32
1685 2039 1.537202 ACAAGGAGCTTCACGCAAATC 59.463 47.619 0.00 0.00 42.61 2.17
1686 2040 0.798776 AAGGAGCTTCACGCAAATCG 59.201 50.000 0.00 0.00 42.61 3.34
1687 2041 1.226128 GGAGCTTCACGCAAATCGC 60.226 57.895 0.00 0.00 43.23 4.58
1688 2042 1.226128 GAGCTTCACGCAAATCGCC 60.226 57.895 0.00 0.00 43.23 5.54
1689 2043 2.574212 GCTTCACGCAAATCGCCG 60.574 61.111 0.00 0.00 43.23 6.46
1690 2044 2.098298 CTTCACGCAAATCGCCGG 59.902 61.111 0.00 0.00 43.23 6.13
1691 2045 4.096558 TTCACGCAAATCGCCGGC 62.097 61.111 19.07 19.07 43.23 6.13
1704 2058 3.058160 CCGGCCAGCCACAAGAAG 61.058 66.667 9.78 0.00 35.37 2.85
1705 2059 3.058160 CGGCCAGCCACAAGAAGG 61.058 66.667 9.78 0.00 35.37 3.46
1712 2066 1.005748 GCCACAAGAAGGCCTTTGC 60.006 57.895 21.54 7.89 46.50 3.68
1713 2067 1.286880 CCACAAGAAGGCCTTTGCG 59.713 57.895 21.54 13.12 38.85 4.85
1714 2068 1.455383 CCACAAGAAGGCCTTTGCGT 61.455 55.000 21.54 13.80 38.85 5.24
1715 2069 0.318107 CACAAGAAGGCCTTTGCGTG 60.318 55.000 21.54 21.08 38.85 5.34
1716 2070 0.465460 ACAAGAAGGCCTTTGCGTGA 60.465 50.000 21.54 0.00 38.85 4.35
1717 2071 0.667993 CAAGAAGGCCTTTGCGTGAA 59.332 50.000 21.54 0.00 38.85 3.18
1718 2072 0.954452 AAGAAGGCCTTTGCGTGAAG 59.046 50.000 21.54 0.00 38.85 3.02
1719 2073 0.108585 AGAAGGCCTTTGCGTGAAGA 59.891 50.000 21.54 0.00 38.85 2.87
1720 2074 0.238553 GAAGGCCTTTGCGTGAAGAC 59.761 55.000 21.54 0.00 38.85 3.01
1721 2075 0.465460 AAGGCCTTTGCGTGAAGACA 60.465 50.000 13.78 0.00 38.85 3.41
1722 2076 0.465460 AGGCCTTTGCGTGAAGACAA 60.465 50.000 0.00 0.00 38.85 3.18
1723 2077 0.598065 GGCCTTTGCGTGAAGACAAT 59.402 50.000 0.00 0.00 38.85 2.71
1724 2078 1.000274 GGCCTTTGCGTGAAGACAATT 60.000 47.619 0.00 0.00 38.85 2.32
1725 2079 2.545742 GGCCTTTGCGTGAAGACAATTT 60.546 45.455 0.00 0.00 38.85 1.82
1726 2080 3.305064 GGCCTTTGCGTGAAGACAATTTA 60.305 43.478 0.00 0.00 38.85 1.40
1727 2081 4.485163 GCCTTTGCGTGAAGACAATTTAT 58.515 39.130 2.10 0.00 0.00 1.40
1728 2082 4.558860 GCCTTTGCGTGAAGACAATTTATC 59.441 41.667 2.10 0.00 0.00 1.75
1729 2083 5.095490 CCTTTGCGTGAAGACAATTTATCC 58.905 41.667 2.10 0.00 0.00 2.59
1730 2084 5.106157 CCTTTGCGTGAAGACAATTTATCCT 60.106 40.000 2.10 0.00 0.00 3.24
1731 2085 5.545658 TTGCGTGAAGACAATTTATCCTC 57.454 39.130 0.00 0.00 0.00 3.71
1732 2086 3.616821 TGCGTGAAGACAATTTATCCTCG 59.383 43.478 0.00 0.00 0.00 4.63
1733 2087 3.001330 GCGTGAAGACAATTTATCCTCGG 59.999 47.826 0.00 0.00 0.00 4.63
1734 2088 3.001330 CGTGAAGACAATTTATCCTCGGC 59.999 47.826 0.00 0.00 0.00 5.54
1735 2089 3.312697 GTGAAGACAATTTATCCTCGGCC 59.687 47.826 0.00 0.00 0.00 6.13
1736 2090 2.240493 AGACAATTTATCCTCGGCCG 57.760 50.000 22.12 22.12 0.00 6.13
1737 2091 0.586802 GACAATTTATCCTCGGCCGC 59.413 55.000 23.51 0.00 0.00 6.53
1738 2092 0.818040 ACAATTTATCCTCGGCCGCC 60.818 55.000 23.51 0.00 0.00 6.13
1739 2093 0.817634 CAATTTATCCTCGGCCGCCA 60.818 55.000 23.51 6.62 0.00 5.69
1740 2094 0.110486 AATTTATCCTCGGCCGCCAT 59.890 50.000 23.51 14.25 0.00 4.40
1741 2095 0.321653 ATTTATCCTCGGCCGCCATC 60.322 55.000 23.51 0.00 0.00 3.51
1742 2096 1.691195 TTTATCCTCGGCCGCCATCA 61.691 55.000 23.51 0.55 0.00 3.07
1743 2097 2.099652 TTATCCTCGGCCGCCATCAG 62.100 60.000 23.51 12.55 0.00 2.90
1744 2098 2.994643 TATCCTCGGCCGCCATCAGA 62.995 60.000 23.51 10.59 0.00 3.27
1745 2099 4.899239 CCTCGGCCGCCATCAGAC 62.899 72.222 23.51 0.00 0.00 3.51
1788 2142 6.149640 TCGATAGGCTAAGAGCATTACTAGTG 59.850 42.308 5.39 0.00 44.75 2.74
1797 2151 2.431057 AGCATTACTAGTGGAACCCTCG 59.569 50.000 5.39 0.00 37.80 4.63
1852 2206 3.953612 TGAGAAGTGCCACTTTTTGACAT 59.046 39.130 12.09 0.00 38.80 3.06
1859 2213 7.913674 AGTGCCACTTTTTGACATTTTTAAA 57.086 28.000 0.00 0.00 0.00 1.52
1933 2288 7.633789 ACTGCTTTAAGGATTAGATTTGAGGA 58.366 34.615 0.00 0.00 0.00 3.71
2089 2444 7.117397 ACATCACAAAATCATCATCTTCCTCT 58.883 34.615 0.00 0.00 0.00 3.69
2149 2504 1.751351 CATCTCCTAGACCACAAGCGA 59.249 52.381 0.00 0.00 0.00 4.93
2230 2585 1.177401 CTCATCGGAGTGTCACCTCA 58.823 55.000 0.00 0.00 36.36 3.86
2296 2651 1.192146 TCCTCCTTGGTGTCCTTCCG 61.192 60.000 0.00 0.00 37.07 4.30
2323 2678 3.833650 TGCAATTGGTCTTGATCCATGTT 59.166 39.130 7.72 0.00 34.75 2.71
2372 2727 4.645535 TCTCTTCCACCATGAGTTCTTTG 58.354 43.478 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 225 2.743928 GCCACCACGAAGAGCAGG 60.744 66.667 0.00 0.00 0.00 4.85
485 486 1.556911 AGGATGTTGTAGAGCACCCAG 59.443 52.381 0.00 0.00 0.00 4.45
539 540 3.350909 TACGCGCGCTCAGTTGGAT 62.351 57.895 32.58 8.80 0.00 3.41
822 825 8.020819 TGAAGTAAAAACATTTGCTAAGGATCG 58.979 33.333 0.00 0.00 0.00 3.69
833 1065 7.651704 CCGGTCAAATCTGAAGTAAAAACATTT 59.348 33.333 0.00 0.00 31.88 2.32
836 1068 5.591067 ACCGGTCAAATCTGAAGTAAAAACA 59.409 36.000 0.00 0.00 31.88 2.83
837 1069 5.912955 CACCGGTCAAATCTGAAGTAAAAAC 59.087 40.000 2.59 0.00 31.88 2.43
861 1210 5.459107 CGTTATATATTGTGGATCGGCTAGC 59.541 44.000 6.04 6.04 0.00 3.42
909 1262 5.320723 GCATGACAAATGTTCGACGAAATA 58.679 37.500 12.67 5.05 0.00 1.40
938 1291 0.811219 ATGTGGTCACCATCATCGCG 60.811 55.000 0.00 0.00 35.28 5.87
939 1292 0.940126 GATGTGGTCACCATCATCGC 59.060 55.000 18.09 0.00 34.81 4.58
940 1293 1.211743 CGATGTGGTCACCATCATCG 58.788 55.000 30.33 30.33 46.78 3.84
943 1296 2.811431 GTTTTCGATGTGGTCACCATCA 59.189 45.455 0.00 0.00 35.28 3.07
969 1322 3.330853 GATCACGATGGCGGACGC 61.331 66.667 8.39 8.39 43.17 5.19
970 1323 3.024609 CGATCACGATGGCGGACG 61.025 66.667 0.00 0.00 43.17 4.79
971 1324 2.104331 ACGATCACGATGGCGGAC 59.896 61.111 0.00 0.00 43.17 4.79
972 1325 2.104132 CACGATCACGATGGCGGA 59.896 61.111 0.00 0.00 43.17 5.54
973 1326 3.630148 GCACGATCACGATGGCGG 61.630 66.667 0.00 0.00 43.17 6.13
974 1327 2.580470 GAGCACGATCACGATGGCG 61.580 63.158 0.00 0.00 42.66 5.69
975 1328 2.580470 CGAGCACGATCACGATGGC 61.580 63.158 0.00 0.00 42.66 4.40
976 1329 1.946156 CCGAGCACGATCACGATGG 60.946 63.158 4.70 0.00 42.66 3.51
977 1330 2.580470 GCCGAGCACGATCACGATG 61.580 63.158 4.70 0.00 42.66 3.84
978 1331 2.278857 GCCGAGCACGATCACGAT 60.279 61.111 4.70 0.00 42.66 3.73
979 1332 4.829518 CGCCGAGCACGATCACGA 62.830 66.667 4.70 0.00 42.66 4.35
980 1333 4.829518 TCGCCGAGCACGATCACG 62.830 66.667 4.70 3.61 42.66 4.35
981 1334 2.951745 CTCGCCGAGCACGATCAC 60.952 66.667 4.70 0.00 42.66 3.06
982 1335 4.193334 CCTCGCCGAGCACGATCA 62.193 66.667 9.01 0.00 42.66 2.92
983 1336 3.200887 ATCCTCGCCGAGCACGATC 62.201 63.158 9.01 0.00 42.66 3.69
984 1337 3.219928 ATCCTCGCCGAGCACGAT 61.220 61.111 9.01 3.48 42.66 3.73
985 1338 4.193334 CATCCTCGCCGAGCACGA 62.193 66.667 9.01 0.83 42.66 4.35
987 1340 3.371097 TTCCATCCTCGCCGAGCAC 62.371 63.158 9.01 0.00 0.00 4.40
988 1341 3.074369 TTCCATCCTCGCCGAGCA 61.074 61.111 9.01 0.00 0.00 4.26
989 1342 2.279784 CTTCCATCCTCGCCGAGC 60.280 66.667 9.01 0.00 0.00 5.03
990 1343 2.419198 CCTTCCATCCTCGCCGAG 59.581 66.667 7.25 7.25 0.00 4.63
991 1344 3.849951 GCCTTCCATCCTCGCCGA 61.850 66.667 0.00 0.00 0.00 5.54
993 1346 4.918201 CCGCCTTCCATCCTCGCC 62.918 72.222 0.00 0.00 0.00 5.54
996 1349 3.682292 AACGCCGCCTTCCATCCTC 62.682 63.158 0.00 0.00 0.00 3.71
997 1350 3.717294 AACGCCGCCTTCCATCCT 61.717 61.111 0.00 0.00 0.00 3.24
998 1351 3.508840 CAACGCCGCCTTCCATCC 61.509 66.667 0.00 0.00 0.00 3.51
999 1352 3.508840 CCAACGCCGCCTTCCATC 61.509 66.667 0.00 0.00 0.00 3.51
1008 1361 2.558554 CTAGAGTGACCCCAACGCCG 62.559 65.000 0.00 0.00 0.00 6.46
1009 1362 1.218316 CTAGAGTGACCCCAACGCC 59.782 63.158 0.00 0.00 0.00 5.68
1010 1363 0.173708 CTCTAGAGTGACCCCAACGC 59.826 60.000 11.89 0.00 0.00 4.84
1011 1364 0.173708 GCTCTAGAGTGACCCCAACG 59.826 60.000 20.75 0.00 0.00 4.10
1012 1365 0.537653 GGCTCTAGAGTGACCCCAAC 59.462 60.000 20.75 0.94 0.00 3.77
1013 1366 0.116342 TGGCTCTAGAGTGACCCCAA 59.884 55.000 20.75 2.37 0.00 4.12
1014 1367 0.614979 GTGGCTCTAGAGTGACCCCA 60.615 60.000 20.75 15.45 0.00 4.96
1015 1368 1.331399 GGTGGCTCTAGAGTGACCCC 61.331 65.000 22.62 15.44 0.00 4.95
1016 1369 1.331399 GGGTGGCTCTAGAGTGACCC 61.331 65.000 30.41 30.41 41.52 4.46
1017 1370 1.668101 CGGGTGGCTCTAGAGTGACC 61.668 65.000 24.06 24.06 33.62 4.02
1018 1371 0.966370 ACGGGTGGCTCTAGAGTGAC 60.966 60.000 20.75 16.08 0.00 3.67
1019 1372 0.965866 CACGGGTGGCTCTAGAGTGA 60.966 60.000 20.75 5.25 0.00 3.41
1020 1373 1.513158 CACGGGTGGCTCTAGAGTG 59.487 63.158 20.75 6.63 0.00 3.51
1021 1374 1.682684 CCACGGGTGGCTCTAGAGT 60.683 63.158 20.75 0.00 44.73 3.24
1022 1375 3.211288 CCACGGGTGGCTCTAGAG 58.789 66.667 15.85 15.85 44.73 2.43
1031 1384 4.760047 CGAGGGCTTCCACGGGTG 62.760 72.222 0.00 0.00 40.22 4.61
1036 1389 3.644399 GACGGTCGAGGGCTTCCAC 62.644 68.421 0.00 0.00 0.00 4.02
1038 1391 3.066233 GAGACGGTCGAGGGCTTCC 62.066 68.421 1.89 0.00 0.00 3.46
1052 1405 2.503382 GGAGATGGCCGAGGGAGAC 61.503 68.421 0.00 0.00 0.00 3.36
1063 1416 2.507110 AAGACGTGCACGGGAGATGG 62.507 60.000 39.21 13.10 44.95 3.51
1068 1421 2.915659 AGGAAGACGTGCACGGGA 60.916 61.111 39.21 0.00 44.95 5.14
1106 1459 4.424566 GGTACAGAACGGCCGCGA 62.425 66.667 28.58 0.29 0.00 5.87
1112 1465 2.205074 GCATCATGAGGTACAGAACGG 58.795 52.381 9.42 0.00 0.00 4.44
1138 1491 1.000607 GTTGACGAGGTACACAGAGCA 60.001 52.381 0.00 0.00 0.00 4.26
1143 1496 2.816087 GGAGTAGTTGACGAGGTACACA 59.184 50.000 0.00 0.00 0.00 3.72
1152 1505 1.272490 TGGAAGCAGGAGTAGTTGACG 59.728 52.381 0.00 0.00 0.00 4.35
1156 1509 1.348036 GGTGTGGAAGCAGGAGTAGTT 59.652 52.381 0.00 0.00 0.00 2.24
1162 1515 1.150536 GGTTGGTGTGGAAGCAGGA 59.849 57.895 0.00 0.00 37.63 3.86
1172 1525 4.218686 GGTGGCTGGGGTTGGTGT 62.219 66.667 0.00 0.00 0.00 4.16
1195 1548 0.323087 TCGAGGAATGTGTCGAGGGA 60.323 55.000 0.00 0.00 40.19 4.20
1202 1555 1.738099 GCGTGCTCGAGGAATGTGT 60.738 57.895 15.58 0.00 39.71 3.72
1227 1580 0.032678 CCCCCTCGATGAAGATGACG 59.967 60.000 0.00 0.00 0.00 4.35
1232 1585 1.306997 AAGGCCCCCTCGATGAAGA 60.307 57.895 0.00 0.00 30.89 2.87
1250 1603 1.663388 ACGTTGCGCTCGTCAATGA 60.663 52.632 21.00 0.00 36.85 2.57
1273 1626 3.561213 CAGCAGCCGCGTCATGAG 61.561 66.667 4.92 0.00 45.49 2.90
1298 1651 4.056584 TCTCCTTCCCGAGCCCGA 62.057 66.667 0.00 0.00 38.22 5.14
1371 1724 2.183679 GATGAACTCCACCTCCTCACT 58.816 52.381 0.00 0.00 0.00 3.41
1372 1725 1.902508 TGATGAACTCCACCTCCTCAC 59.097 52.381 0.00 0.00 0.00 3.51
1373 1726 2.325661 TGATGAACTCCACCTCCTCA 57.674 50.000 0.00 0.00 0.00 3.86
1386 1740 2.689471 CAATGGCGGAAAGGATGATGAA 59.311 45.455 0.00 0.00 0.00 2.57
1389 1743 2.301346 GTCAATGGCGGAAAGGATGAT 58.699 47.619 0.00 0.00 0.00 2.45
1395 1749 1.656652 AGATCGTCAATGGCGGAAAG 58.343 50.000 7.59 0.00 0.00 2.62
1397 1751 1.207089 AGAAGATCGTCAATGGCGGAA 59.793 47.619 7.59 0.00 0.00 4.30
1526 1880 0.578683 CATAGCAGATGTCGTTGCGG 59.421 55.000 0.00 0.00 44.80 5.69
1542 1896 0.980754 ATCCCGGACAGGTGCACATA 60.981 55.000 20.43 0.00 38.74 2.29
1544 1898 2.927856 ATCCCGGACAGGTGCACA 60.928 61.111 20.43 0.00 38.74 4.57
1553 1907 4.489771 CTGCACCCCATCCCGGAC 62.490 72.222 0.73 0.00 36.56 4.79
1578 1932 3.382048 AGAACTCAACCTAACGACCAC 57.618 47.619 0.00 0.00 0.00 4.16
1600 1954 0.675837 TCCTGGTGACCTCGTAGACG 60.676 60.000 2.11 0.00 41.45 4.18
1601 1955 1.096416 CTCCTGGTGACCTCGTAGAC 58.904 60.000 2.11 0.00 0.00 2.59
1602 1956 0.034380 CCTCCTGGTGACCTCGTAGA 60.034 60.000 2.11 0.00 0.00 2.59
1603 1957 0.323542 ACCTCCTGGTGACCTCGTAG 60.324 60.000 2.11 0.00 46.51 3.51
1604 1958 1.772308 ACCTCCTGGTGACCTCGTA 59.228 57.895 2.11 0.00 46.51 3.43
1605 1959 2.526628 ACCTCCTGGTGACCTCGT 59.473 61.111 2.11 0.00 46.51 4.18
1614 1968 2.675423 TCGACGGTGACCTCCTGG 60.675 66.667 0.00 0.00 39.83 4.45
1615 1969 2.701780 CCTCGACGGTGACCTCCTG 61.702 68.421 0.00 0.00 0.00 3.86
1616 1970 2.361357 CCTCGACGGTGACCTCCT 60.361 66.667 0.00 0.00 0.00 3.69
1617 1971 2.675772 ACCTCGACGGTGACCTCC 60.676 66.667 0.00 0.00 46.80 4.30
1626 1980 4.394078 TCGCCAACGACCTCGACG 62.394 66.667 0.78 0.00 45.12 5.12
1627 1981 2.504244 CTCGCCAACGACCTCGAC 60.504 66.667 0.78 0.00 45.12 4.20
1628 1982 3.744719 CCTCGCCAACGACCTCGA 61.745 66.667 0.78 0.00 45.12 4.04
1655 2009 2.892425 CTCCTTGTCGATGGCGGC 60.892 66.667 0.00 0.00 43.78 6.53
1656 2010 2.859273 AAGCTCCTTGTCGATGGCGG 62.859 60.000 0.00 0.00 38.28 6.13
1657 2011 1.424493 GAAGCTCCTTGTCGATGGCG 61.424 60.000 0.00 0.00 39.35 5.69
1658 2012 0.391661 TGAAGCTCCTTGTCGATGGC 60.392 55.000 0.00 0.00 0.00 4.40
1659 2013 1.363744 GTGAAGCTCCTTGTCGATGG 58.636 55.000 0.00 0.00 0.00 3.51
1660 2014 0.994995 CGTGAAGCTCCTTGTCGATG 59.005 55.000 0.00 0.00 0.00 3.84
1661 2015 0.737715 GCGTGAAGCTCCTTGTCGAT 60.738 55.000 0.00 0.00 44.04 3.59
1662 2016 1.372997 GCGTGAAGCTCCTTGTCGA 60.373 57.895 0.00 0.00 44.04 4.20
1663 2017 3.159984 GCGTGAAGCTCCTTGTCG 58.840 61.111 0.00 0.00 44.04 4.35
1687 2041 3.058160 CTTCTTGTGGCTGGCCGG 61.058 66.667 7.41 7.41 39.42 6.13
1688 2042 3.058160 CCTTCTTGTGGCTGGCCG 61.058 66.667 7.14 0.00 39.42 6.13
1689 2043 3.376918 GCCTTCTTGTGGCTGGCC 61.377 66.667 4.43 4.43 46.38 5.36
1695 2049 1.286880 CGCAAAGGCCTTCTTGTGG 59.713 57.895 20.79 7.18 35.55 4.17
1696 2050 0.318107 CACGCAAAGGCCTTCTTGTG 60.318 55.000 23.27 23.27 35.55 3.33
1697 2051 0.465460 TCACGCAAAGGCCTTCTTGT 60.465 50.000 20.79 14.28 35.55 3.16
1698 2052 0.667993 TTCACGCAAAGGCCTTCTTG 59.332 50.000 20.79 15.84 35.55 3.02
1699 2053 0.954452 CTTCACGCAAAGGCCTTCTT 59.046 50.000 20.79 0.00 37.28 2.52
1700 2054 0.108585 TCTTCACGCAAAGGCCTTCT 59.891 50.000 20.79 6.40 36.38 2.85
1701 2055 0.238553 GTCTTCACGCAAAGGCCTTC 59.761 55.000 20.79 6.25 36.38 3.46
1702 2056 0.465460 TGTCTTCACGCAAAGGCCTT 60.465 50.000 13.78 13.78 36.38 4.35
1703 2057 0.465460 TTGTCTTCACGCAAAGGCCT 60.465 50.000 0.00 0.00 36.38 5.19
1704 2058 0.598065 ATTGTCTTCACGCAAAGGCC 59.402 50.000 0.00 0.00 36.38 5.19
1705 2059 2.422276 AATTGTCTTCACGCAAAGGC 57.578 45.000 0.00 0.00 0.00 4.35
1706 2060 5.095490 GGATAAATTGTCTTCACGCAAAGG 58.905 41.667 0.00 0.00 0.00 3.11
1707 2061 5.942872 AGGATAAATTGTCTTCACGCAAAG 58.057 37.500 0.00 0.00 0.00 2.77
1708 2062 5.390461 CGAGGATAAATTGTCTTCACGCAAA 60.390 40.000 3.16 0.00 0.00 3.68
1709 2063 4.092821 CGAGGATAAATTGTCTTCACGCAA 59.907 41.667 3.16 0.00 0.00 4.85
1710 2064 3.616821 CGAGGATAAATTGTCTTCACGCA 59.383 43.478 3.16 0.00 0.00 5.24
1711 2065 3.001330 CCGAGGATAAATTGTCTTCACGC 59.999 47.826 3.16 0.00 0.00 5.34
1712 2066 3.001330 GCCGAGGATAAATTGTCTTCACG 59.999 47.826 3.16 0.00 0.00 4.35
1713 2067 3.312697 GGCCGAGGATAAATTGTCTTCAC 59.687 47.826 3.16 0.00 0.00 3.18
1714 2068 3.541632 GGCCGAGGATAAATTGTCTTCA 58.458 45.455 3.16 0.00 0.00 3.02
1715 2069 2.544267 CGGCCGAGGATAAATTGTCTTC 59.456 50.000 24.07 0.00 0.00 2.87
1716 2070 2.561569 CGGCCGAGGATAAATTGTCTT 58.438 47.619 24.07 0.00 0.00 3.01
1717 2071 1.810412 GCGGCCGAGGATAAATTGTCT 60.810 52.381 33.48 0.00 0.00 3.41
1718 2072 0.586802 GCGGCCGAGGATAAATTGTC 59.413 55.000 33.48 1.16 0.00 3.18
1719 2073 0.818040 GGCGGCCGAGGATAAATTGT 60.818 55.000 33.48 0.00 0.00 2.71
1720 2074 0.817634 TGGCGGCCGAGGATAAATTG 60.818 55.000 33.48 0.00 0.00 2.32
1721 2075 0.110486 ATGGCGGCCGAGGATAAATT 59.890 50.000 33.48 0.00 0.00 1.82
1722 2076 0.321653 GATGGCGGCCGAGGATAAAT 60.322 55.000 33.48 10.32 0.00 1.40
1723 2077 1.070786 GATGGCGGCCGAGGATAAA 59.929 57.895 33.48 5.20 0.00 1.40
1724 2078 2.099652 CTGATGGCGGCCGAGGATAA 62.100 60.000 33.48 8.90 0.00 1.75
1725 2079 2.523168 TGATGGCGGCCGAGGATA 60.523 61.111 33.48 8.74 0.00 2.59
1726 2080 3.933722 CTGATGGCGGCCGAGGAT 61.934 66.667 33.48 16.96 0.00 3.24
1728 2082 4.899239 GTCTGATGGCGGCCGAGG 62.899 72.222 33.48 11.10 0.00 4.63
1732 2086 4.899239 CTCCGTCTGATGGCGGCC 62.899 72.222 13.32 13.32 46.79 6.13
1733 2087 2.088674 ATACTCCGTCTGATGGCGGC 62.089 60.000 11.17 0.00 46.79 6.53
1735 2089 3.577649 AATATACTCCGTCTGATGGCG 57.422 47.619 11.17 7.70 0.00 5.69
1736 2090 5.411781 CCTAAATATACTCCGTCTGATGGC 58.588 45.833 11.17 0.00 0.00 4.40
1737 2091 5.715279 TCCCTAAATATACTCCGTCTGATGG 59.285 44.000 9.73 9.73 0.00 3.51
1738 2092 6.835819 TCCCTAAATATACTCCGTCTGATG 57.164 41.667 0.00 0.00 0.00 3.07
1739 2093 7.148052 CGAATCCCTAAATATACTCCGTCTGAT 60.148 40.741 0.00 0.00 0.00 2.90
1740 2094 6.150641 CGAATCCCTAAATATACTCCGTCTGA 59.849 42.308 0.00 0.00 0.00 3.27
1741 2095 6.150641 TCGAATCCCTAAATATACTCCGTCTG 59.849 42.308 0.00 0.00 0.00 3.51
1742 2096 6.243900 TCGAATCCCTAAATATACTCCGTCT 58.756 40.000 0.00 0.00 0.00 4.18
1743 2097 6.506500 TCGAATCCCTAAATATACTCCGTC 57.493 41.667 0.00 0.00 0.00 4.79
1744 2098 7.284944 CCTATCGAATCCCTAAATATACTCCGT 59.715 40.741 0.00 0.00 0.00 4.69
1745 2099 7.649973 CCTATCGAATCCCTAAATATACTCCG 58.350 42.308 0.00 0.00 0.00 4.63
1746 2100 7.288158 AGCCTATCGAATCCCTAAATATACTCC 59.712 40.741 0.00 0.00 0.00 3.85
1747 2101 8.240267 AGCCTATCGAATCCCTAAATATACTC 57.760 38.462 0.00 0.00 0.00 2.59
1748 2102 9.710818 TTAGCCTATCGAATCCCTAAATATACT 57.289 33.333 0.00 0.00 0.00 2.12
1749 2103 9.968870 CTTAGCCTATCGAATCCCTAAATATAC 57.031 37.037 0.00 0.00 0.00 1.47
1750 2104 9.931698 TCTTAGCCTATCGAATCCCTAAATATA 57.068 33.333 0.00 0.00 0.00 0.86
1751 2105 8.840200 TCTTAGCCTATCGAATCCCTAAATAT 57.160 34.615 0.00 0.00 0.00 1.28
1752 2106 7.147880 GCTCTTAGCCTATCGAATCCCTAAATA 60.148 40.741 0.00 0.00 34.48 1.40
1753 2107 6.351456 GCTCTTAGCCTATCGAATCCCTAAAT 60.351 42.308 0.00 0.00 34.48 1.40
1754 2108 5.047235 GCTCTTAGCCTATCGAATCCCTAAA 60.047 44.000 0.00 0.00 34.48 1.85
1755 2109 4.463186 GCTCTTAGCCTATCGAATCCCTAA 59.537 45.833 0.00 0.00 34.48 2.69
1756 2110 4.017808 GCTCTTAGCCTATCGAATCCCTA 58.982 47.826 0.00 0.00 34.48 3.53
1757 2111 2.829120 GCTCTTAGCCTATCGAATCCCT 59.171 50.000 0.00 0.00 34.48 4.20
1758 2112 2.563179 TGCTCTTAGCCTATCGAATCCC 59.437 50.000 0.00 0.00 41.51 3.85
1759 2113 3.944055 TGCTCTTAGCCTATCGAATCC 57.056 47.619 0.00 0.00 41.51 3.01
1760 2114 6.626302 AGTAATGCTCTTAGCCTATCGAATC 58.374 40.000 0.00 0.00 41.51 2.52
1761 2115 6.597832 AGTAATGCTCTTAGCCTATCGAAT 57.402 37.500 0.00 0.00 41.51 3.34
1762 2116 6.715718 ACTAGTAATGCTCTTAGCCTATCGAA 59.284 38.462 0.00 0.00 41.51 3.71
1763 2117 6.149640 CACTAGTAATGCTCTTAGCCTATCGA 59.850 42.308 0.00 0.00 41.51 3.59
1764 2118 6.318628 CACTAGTAATGCTCTTAGCCTATCG 58.681 44.000 0.00 0.00 41.51 2.92
1765 2119 6.434652 TCCACTAGTAATGCTCTTAGCCTATC 59.565 42.308 0.00 0.00 41.51 2.08
1766 2120 6.315714 TCCACTAGTAATGCTCTTAGCCTAT 58.684 40.000 0.00 0.00 41.51 2.57
1767 2121 5.702266 TCCACTAGTAATGCTCTTAGCCTA 58.298 41.667 0.00 0.00 41.51 3.93
1768 2122 4.547671 TCCACTAGTAATGCTCTTAGCCT 58.452 43.478 0.00 0.00 41.51 4.58
1788 2142 0.399075 TTTGAGGGTTCGAGGGTTCC 59.601 55.000 0.00 0.00 0.00 3.62
1797 2151 4.767409 ACTGCTTTAAGGATTTGAGGGTTC 59.233 41.667 0.00 0.00 0.00 3.62
1852 2206 5.648526 GCCCCTGTTTTTCAACCTTTAAAAA 59.351 36.000 0.00 0.00 33.41 1.94
1859 2213 1.872773 TTGCCCCTGTTTTTCAACCT 58.127 45.000 0.00 0.00 31.02 3.50
1933 2288 2.168728 GGGTCGAGGCAAAGACTAGAAT 59.831 50.000 0.00 0.00 37.52 2.40
2089 2444 0.107703 GGTGATGGTGCCGATGAGAA 60.108 55.000 0.00 0.00 0.00 2.87
2149 2504 1.210538 TGGAGATGCTTGATGGAGCT 58.789 50.000 0.00 0.00 43.11 4.09
2230 2585 2.542595 CGTGTTGCGTCCTCTACTTTTT 59.457 45.455 0.00 0.00 35.54 1.94
2296 2651 2.747396 TCAAGACCAATTGCAATGGC 57.253 45.000 13.82 3.26 41.89 4.40
2323 2678 5.748402 AGCACATTATGATGTCCAAGAAGA 58.252 37.500 0.00 0.00 44.55 2.87
2372 2727 2.221169 TCATCCATCGCAAAGGTATGC 58.779 47.619 0.00 0.00 42.94 3.14
2459 3448 0.320421 AACCACCGACACCGATCAAG 60.320 55.000 0.00 0.00 38.22 3.02


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

AutoCloner maintained by Alex Coulton.