Multiple sequence alignment - TraesCS3B01G517600

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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 TraesCS3B01G517600 chr3B 100.000 3826 0 0 1 3826 760581086 760577261 0.000000e+00 7066.0
1 TraesCS3B01G517600 chr3B 86.339 2628 225 57 1095 3663 760607680 760605128 0.000000e+00 2741.0
2 TraesCS3B01G517600 chr3B 87.696 2227 199 34 1096 3279 760598998 760596804 0.000000e+00 2525.0
3 TraesCS3B01G517600 chr3B 84.169 758 102 12 2088 2831 760590558 760589805 0.000000e+00 719.0
4 TraesCS3B01G517600 chr3B 78.983 1042 163 34 1834 2838 760549090 760548068 0.000000e+00 660.0
5 TraesCS3B01G517600 chr3B 90.057 352 19 7 3311 3661 760596805 760596469 3.510000e-120 442.0
6 TraesCS3B01G517600 chr3B 81.237 469 79 8 2858 3323 760589651 760589189 1.680000e-98 370.0
7 TraesCS3B01G517600 chr3B 79.641 501 88 13 2364 2855 761761916 761762411 7.870000e-92 348.0
8 TraesCS3B01G517600 chr3B 88.406 276 27 4 440 714 760608535 760608264 1.020000e-85 327.0
9 TraesCS3B01G517600 chr3B 78.333 480 84 19 2389 2855 761494682 761495154 3.740000e-75 292.0
10 TraesCS3B01G517600 chr3B 86.897 145 18 1 267 410 760671033 760670889 1.100000e-35 161.0
11 TraesCS3B01G517600 chr3B 88.636 132 8 2 814 938 760607984 760607853 1.840000e-33 154.0
12 TraesCS3B01G517600 chr3B 93.103 87 5 1 347 433 760608784 760608699 4.010000e-25 126.0
13 TraesCS3B01G517600 chr3B 88.421 95 11 0 1329 1423 761036311 761036405 8.690000e-22 115.0
14 TraesCS3B01G517600 chr3B 85.263 95 14 0 1329 1423 761006975 761007069 8.750000e-17 99.0
15 TraesCS3B01G517600 chr3B 85.263 95 14 0 1329 1423 761135354 761135448 8.750000e-17 99.0
16 TraesCS3B01G517600 chr3B 87.209 86 10 1 1342 1427 761794814 761794898 3.150000e-16 97.1
17 TraesCS3B01G517600 chr3B 84.946 93 14 0 1331 1423 761063579 761063671 1.130000e-15 95.3
18 TraesCS3B01G517600 chr3B 83.158 95 16 0 1329 1423 761105165 761105259 1.890000e-13 87.9
19 TraesCS3B01G517600 chr3D 88.965 1903 159 10 1100 2955 572791049 572792947 0.000000e+00 2303.0
20 TraesCS3B01G517600 chr3D 78.343 1062 174 34 1812 2845 572830672 572831705 1.500000e-178 636.0
21 TraesCS3B01G517600 chr3D 94.531 384 19 1 3028 3411 572792942 572793323 3.290000e-165 592.0
22 TraesCS3B01G517600 chr3D 87.810 443 35 10 205 647 572790211 572790634 5.710000e-138 501.0
23 TraesCS3B01G517600 chr3D 93.893 262 9 5 809 1067 572790718 572790975 4.640000e-104 388.0
24 TraesCS3B01G517600 chr3D 80.000 480 78 15 2388 2855 572426069 572425596 4.730000e-89 339.0
25 TraesCS3B01G517600 chr3D 91.617 167 11 1 1 164 572789561 572789727 1.070000e-55 228.0
26 TraesCS3B01G517600 chr3D 83.824 136 20 2 27 161 572813915 572814049 1.120000e-25 128.0
27 TraesCS3B01G517600 chr3D 86.585 82 11 0 1342 1423 572552914 572552833 1.460000e-14 91.6
28 TraesCS3B01G517600 chr3D 92.157 51 2 2 1530 1579 572586999 572586950 1.910000e-08 71.3
29 TraesCS3B01G517600 chrUn 74.746 887 164 43 1802 2650 132014629 132015493 3.660000e-90 342.0
30 TraesCS3B01G517600 chrUn 89.024 82 7 2 1342 1423 132018783 132018862 2.430000e-17 100.0
31 TraesCS3B01G517600 chrUn 84.694 98 9 3 69 165 131963260 131963352 4.070000e-15 93.5


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 TraesCS3B01G517600 chr3B 760577261 760581086 3825 True 7066.0 7066 100.0000 1 3826 1 chr3B.!!$R2 3825
1 TraesCS3B01G517600 chr3B 760596469 760598998 2529 True 1483.5 2525 88.8765 1096 3661 2 chr3B.!!$R5 2565
2 TraesCS3B01G517600 chr3B 760605128 760608784 3656 True 837.0 2741 89.1210 347 3663 4 chr3B.!!$R6 3316
3 TraesCS3B01G517600 chr3B 760548068 760549090 1022 True 660.0 660 78.9830 1834 2838 1 chr3B.!!$R1 1004
4 TraesCS3B01G517600 chr3B 760589189 760590558 1369 True 544.5 719 82.7030 2088 3323 2 chr3B.!!$R4 1235
5 TraesCS3B01G517600 chr3D 572789561 572793323 3762 False 802.4 2303 91.3632 1 3411 5 chr3D.!!$F3 3410
6 TraesCS3B01G517600 chr3D 572830672 572831705 1033 False 636.0 636 78.3430 1812 2845 1 chr3D.!!$F2 1033
7 TraesCS3B01G517600 chrUn 132014629 132018862 4233 False 221.0 342 81.8850 1342 2650 2 chrUn.!!$F2 1308

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
164 168 0.037326 TGGAGACGCAAGATGACACC 60.037 55.0 0.0 0.0 43.62 4.16 F
166 170 0.109272 GAGACGCAAGATGACACCGA 60.109 55.0 0.0 0.0 43.62 4.69 F
1196 2101 0.168788 AATTTGTGCATGTCGCTCCG 59.831 50.0 0.0 0.0 43.06 4.63 F
1498 2403 0.110056 GTGTCTGTCATGCTTTGGCG 60.110 55.0 0.0 0.0 42.25 5.69 F
2003 2944 0.179145 GCTCATGTGGCAGCACAATC 60.179 55.0 0.0 0.0 38.69 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 2030 0.107017 AAGACCCGGATCAATGCCTG 60.107 55.000 0.73 0.0 0.00 4.85 R
1485 2390 0.110056 CACAGACGCCAAAGCATGAC 60.110 55.000 0.00 0.0 39.83 3.06 R
2507 3501 1.134907 CCTGTCATTTTGGATGGCAGC 60.135 52.381 13.58 0.0 46.99 5.25 R
2646 3649 1.547449 TGGCAGCAGGCATGTAGAAAA 60.547 47.619 0.00 0.0 46.46 2.29 R
3587 4731 0.106519 GATGACCATGGTCCCTTGGG 60.107 60.000 36.27 0.0 43.97 4.12 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
50 54 1.880340 GAACAGATCGCGGCTGAGG 60.880 63.158 28.11 9.61 36.86 3.86
51 55 4.521062 ACAGATCGCGGCTGAGGC 62.521 66.667 28.11 0.00 36.86 4.70
54 58 2.355244 GATCGCGGCTGAGGCTAC 60.355 66.667 6.13 0.00 38.73 3.58
60 64 4.840005 GGCTGAGGCTACGGTGGC 62.840 72.222 8.09 8.09 38.73 5.01
72 76 2.595095 GGTGGCGGGGAATGATGA 59.405 61.111 0.00 0.00 0.00 2.92
85 89 3.252215 GGAATGATGAACACGACACCAAA 59.748 43.478 0.00 0.00 0.00 3.28
152 156 4.269603 GTCAATGATTCAGACATGGAGACG 59.730 45.833 0.00 0.00 29.71 4.18
160 164 1.827344 AGACATGGAGACGCAAGATGA 59.173 47.619 0.00 0.00 43.62 2.92
164 168 0.037326 TGGAGACGCAAGATGACACC 60.037 55.000 0.00 0.00 43.62 4.16
166 170 0.109272 GAGACGCAAGATGACACCGA 60.109 55.000 0.00 0.00 43.62 4.69
167 171 0.317160 AGACGCAAGATGACACCGAA 59.683 50.000 0.00 0.00 43.62 4.30
168 172 1.144969 GACGCAAGATGACACCGAAA 58.855 50.000 0.00 0.00 43.62 3.46
169 173 1.529438 GACGCAAGATGACACCGAAAA 59.471 47.619 0.00 0.00 43.62 2.29
170 174 1.944024 ACGCAAGATGACACCGAAAAA 59.056 42.857 0.00 0.00 43.62 1.94
171 175 2.286772 ACGCAAGATGACACCGAAAAAC 60.287 45.455 0.00 0.00 43.62 2.43
172 176 2.286713 CGCAAGATGACACCGAAAAACA 60.287 45.455 0.00 0.00 43.02 2.83
173 177 3.701241 GCAAGATGACACCGAAAAACAA 58.299 40.909 0.00 0.00 0.00 2.83
178 182 4.821805 AGATGACACCGAAAAACAAGATGT 59.178 37.500 0.00 0.00 0.00 3.06
179 183 4.974368 TGACACCGAAAAACAAGATGTT 57.026 36.364 0.00 0.00 43.41 2.71
192 196 7.169158 AAACAAGATGTTTCTTCTTGAACCA 57.831 32.000 22.74 0.00 46.61 3.67
193 197 7.260603 AAACAAGATGTTTCTTCTTGAACCAG 58.739 34.615 22.74 5.20 46.61 4.00
194 198 7.093771 AAACAAGATGTTTCTTCTTGAACCAGT 60.094 33.333 22.74 5.70 46.61 4.00
196 200 7.410120 AAGATGTTTCTTCTTGAACCAGTTT 57.590 32.000 0.00 0.00 37.69 2.66
197 201 6.799512 AGATGTTTCTTCTTGAACCAGTTTG 58.200 36.000 0.00 0.00 30.71 2.93
199 203 4.219507 TGTTTCTTCTTGAACCAGTTTGCA 59.780 37.500 0.00 0.00 33.88 4.08
200 204 5.105392 TGTTTCTTCTTGAACCAGTTTGCAT 60.105 36.000 0.00 0.00 33.88 3.96
201 205 4.836125 TCTTCTTGAACCAGTTTGCATC 57.164 40.909 0.00 0.00 0.00 3.91
202 206 4.206375 TCTTCTTGAACCAGTTTGCATCA 58.794 39.130 0.00 0.00 0.00 3.07
203 207 4.828939 TCTTCTTGAACCAGTTTGCATCAT 59.171 37.500 0.00 0.00 0.00 2.45
213 660 7.713764 ACCAGTTTGCATCATTTAACTTTTC 57.286 32.000 0.00 0.00 0.00 2.29
214 661 7.271511 ACCAGTTTGCATCATTTAACTTTTCA 58.728 30.769 0.00 0.00 0.00 2.69
221 668 8.129161 TGCATCATTTAACTTTTCAACTTGTG 57.871 30.769 0.00 0.00 0.00 3.33
232 679 6.964934 ACTTTTCAACTTGTGAACGATGTTAC 59.035 34.615 0.00 0.00 46.09 2.50
235 682 4.025229 TCAACTTGTGAACGATGTTACAGC 60.025 41.667 0.00 0.00 31.51 4.40
246 693 2.185004 TGTTACAGCCTTCTTGAGCC 57.815 50.000 0.00 0.00 0.00 4.70
257 704 3.251972 CCTTCTTGAGCCAGTTTGAAGAC 59.748 47.826 0.00 0.00 34.57 3.01
287 734 4.141390 ACGGATCAAAAGGATAGCTTGGAT 60.141 41.667 0.00 0.00 36.00 3.41
302 749 9.189723 GATAGCTTGGATGATTTTATTTTGAGC 57.810 33.333 0.00 0.00 0.00 4.26
303 750 6.938507 AGCTTGGATGATTTTATTTTGAGCA 58.061 32.000 0.00 0.00 0.00 4.26
328 775 7.276438 CACGAATCTTCACATCACTCTCAATAA 59.724 37.037 0.00 0.00 0.00 1.40
473 1080 4.220602 GGCAACATATCTGGTGAAAACCTT 59.779 41.667 0.00 0.00 43.13 3.50
477 1084 7.702348 GCAACATATCTGGTGAAAACCTTATTC 59.298 37.037 0.00 0.00 43.13 1.75
486 1093 5.095490 GTGAAAACCTTATTCCGATGCAAG 58.905 41.667 0.00 0.00 0.00 4.01
516 1123 4.614946 ACTTACGCTATAAACCATCCGAC 58.385 43.478 0.00 0.00 0.00 4.79
522 1129 4.642429 GCTATAAACCATCCGACCTCAAT 58.358 43.478 0.00 0.00 0.00 2.57
546 1153 2.086610 AGAAACAAGGTGGGTGCATT 57.913 45.000 0.00 0.00 0.00 3.56
563 1170 2.540361 GCATTTGCAGCCACTTAGATCG 60.540 50.000 0.00 0.00 41.59 3.69
597 1204 6.882678 AGATGAGAAATCATGTGACATTGTCA 59.117 34.615 15.41 15.41 40.50 3.58
664 1271 7.229707 TGCTTTCCTGCTAAGTTGTAAATTGTA 59.770 33.333 0.00 0.00 0.00 2.41
665 1272 7.537649 GCTTTCCTGCTAAGTTGTAAATTGTAC 59.462 37.037 0.00 0.00 0.00 2.90
667 1274 7.900782 TCCTGCTAAGTTGTAAATTGTACTC 57.099 36.000 0.00 0.00 0.00 2.59
684 1292 6.007936 TGTACTCCCGTCATTTTCATTTTG 57.992 37.500 0.00 0.00 0.00 2.44
697 1305 7.434897 TCATTTTCATTTTGCTGTGAAGTGTAC 59.565 33.333 0.00 0.00 35.91 2.90
701 1309 5.468746 TCATTTTGCTGTGAAGTGTACTACC 59.531 40.000 0.00 0.00 0.00 3.18
709 1317 3.079578 TGAAGTGTACTACCGGAGACAG 58.920 50.000 9.46 1.58 0.00 3.51
714 1322 2.836372 TGTACTACCGGAGACAGAGAGA 59.164 50.000 9.46 0.00 0.00 3.10
715 1323 3.455177 TGTACTACCGGAGACAGAGAGAT 59.545 47.826 9.46 0.00 0.00 2.75
716 1324 4.652881 TGTACTACCGGAGACAGAGAGATA 59.347 45.833 9.46 0.00 0.00 1.98
717 1325 4.774660 ACTACCGGAGACAGAGAGATAA 57.225 45.455 9.46 0.00 0.00 1.75
718 1326 5.313280 ACTACCGGAGACAGAGAGATAAT 57.687 43.478 9.46 0.00 0.00 1.28
719 1327 5.310451 ACTACCGGAGACAGAGAGATAATC 58.690 45.833 9.46 0.00 0.00 1.75
720 1328 4.171878 ACCGGAGACAGAGAGATAATCA 57.828 45.455 9.46 0.00 0.00 2.57
721 1329 3.886505 ACCGGAGACAGAGAGATAATCAC 59.113 47.826 9.46 0.00 0.00 3.06
722 1330 3.254657 CCGGAGACAGAGAGATAATCACC 59.745 52.174 0.00 0.00 0.00 4.02
723 1331 3.254657 CGGAGACAGAGAGATAATCACCC 59.745 52.174 0.00 0.00 0.00 4.61
724 1332 3.254657 GGAGACAGAGAGATAATCACCCG 59.745 52.174 0.00 0.00 0.00 5.28
725 1333 2.625790 AGACAGAGAGATAATCACCCGC 59.374 50.000 0.00 0.00 0.00 6.13
726 1334 2.362397 GACAGAGAGATAATCACCCGCA 59.638 50.000 0.00 0.00 0.00 5.69
727 1335 2.766263 ACAGAGAGATAATCACCCGCAA 59.234 45.455 0.00 0.00 0.00 4.85
728 1336 3.197766 ACAGAGAGATAATCACCCGCAAA 59.802 43.478 0.00 0.00 0.00 3.68
729 1337 4.191544 CAGAGAGATAATCACCCGCAAAA 58.808 43.478 0.00 0.00 0.00 2.44
730 1338 4.635765 CAGAGAGATAATCACCCGCAAAAA 59.364 41.667 0.00 0.00 0.00 1.94
781 1587 1.325355 AGATTGTGCTGCTTGCTGTT 58.675 45.000 0.00 0.00 43.37 3.16
784 1590 3.318839 AGATTGTGCTGCTTGCTGTTAAA 59.681 39.130 0.00 0.00 43.37 1.52
785 1591 2.780065 TGTGCTGCTTGCTGTTAAAG 57.220 45.000 0.00 0.00 43.37 1.85
786 1592 2.023673 TGTGCTGCTTGCTGTTAAAGT 58.976 42.857 0.00 0.00 43.37 2.66
787 1593 2.223548 TGTGCTGCTTGCTGTTAAAGTG 60.224 45.455 0.00 0.00 43.37 3.16
788 1594 2.023673 TGCTGCTTGCTGTTAAAGTGT 58.976 42.857 0.00 0.00 43.37 3.55
789 1595 3.003275 GTGCTGCTTGCTGTTAAAGTGTA 59.997 43.478 0.00 0.00 43.37 2.90
790 1596 3.003275 TGCTGCTTGCTGTTAAAGTGTAC 59.997 43.478 0.00 0.00 43.37 2.90
792 1598 4.261197 GCTGCTTGCTGTTAAAGTGTACTT 60.261 41.667 0.00 0.00 38.95 2.24
793 1599 5.418310 TGCTTGCTGTTAAAGTGTACTTC 57.582 39.130 0.00 0.00 34.61 3.01
794 1600 4.274950 TGCTTGCTGTTAAAGTGTACTTCC 59.725 41.667 0.00 0.00 34.61 3.46
978 1803 3.188786 CGCAGTTGGTAGGAGCGC 61.189 66.667 0.00 0.00 41.95 5.92
994 1819 3.338676 GCCATCGATTCCGGCGAC 61.339 66.667 9.30 0.00 40.94 5.19
1039 1866 2.188947 TACCCTCCCCAAGTCCCCT 61.189 63.158 0.00 0.00 0.00 4.79
1042 1869 1.229984 CCTCCCCAAGTCCCCTTCT 60.230 63.158 0.00 0.00 0.00 2.85
1047 1874 1.541368 CCAAGTCCCCTTCTCCCCA 60.541 63.158 0.00 0.00 0.00 4.96
1053 1880 1.076485 CCCCTTCTCCCCATTGCTG 60.076 63.158 0.00 0.00 0.00 4.41
1075 1964 8.629158 TGCTGATGTACTGTAAAAATCTTGTTT 58.371 29.630 0.00 0.00 0.00 2.83
1084 1973 9.120538 ACTGTAAAAATCTTGTTTCTGCTTCTA 57.879 29.630 0.00 0.00 0.00 2.10
1091 1980 5.858381 TCTTGTTTCTGCTTCTAGATGTGT 58.142 37.500 7.41 0.00 0.00 3.72
1098 1999 5.204292 TCTGCTTCTAGATGTGTACCTCAT 58.796 41.667 7.41 0.00 0.00 2.90
1118 2019 0.548510 GAGGAGATTCAGGGGGTTGG 59.451 60.000 0.00 0.00 0.00 3.77
1155 2059 4.683400 GCATTGATCCGGGTCTTAGAAAGA 60.683 45.833 17.40 0.00 34.51 2.52
1169 2073 7.608376 GGTCTTAGAAAGAGAAATTACTTGCCT 59.392 37.037 0.00 0.00 38.41 4.75
1170 2074 8.447053 GTCTTAGAAAGAGAAATTACTTGCCTG 58.553 37.037 0.00 0.00 38.41 4.85
1171 2075 8.157476 TCTTAGAAAGAGAAATTACTTGCCTGT 58.843 33.333 0.00 0.00 32.71 4.00
1173 2077 6.299141 AGAAAGAGAAATTACTTGCCTGTCA 58.701 36.000 0.00 0.00 0.00 3.58
1178 2083 6.716628 AGAGAAATTACTTGCCTGTCATTCAA 59.283 34.615 0.00 0.00 0.00 2.69
1180 2085 7.899973 AGAAATTACTTGCCTGTCATTCAATT 58.100 30.769 0.00 0.00 0.00 2.32
1186 2091 2.364647 TGCCTGTCATTCAATTTGTGCA 59.635 40.909 0.00 0.00 0.00 4.57
1194 2099 2.617250 TCAATTTGTGCATGTCGCTC 57.383 45.000 0.00 0.00 43.06 5.03
1196 2101 0.168788 AATTTGTGCATGTCGCTCCG 59.831 50.000 0.00 0.00 43.06 4.63
1197 2102 0.673333 ATTTGTGCATGTCGCTCCGA 60.673 50.000 0.00 0.00 43.06 4.55
1199 2104 2.125912 GTGCATGTCGCTCCGAGT 60.126 61.111 0.00 0.00 43.06 4.18
1200 2105 2.161486 GTGCATGTCGCTCCGAGTC 61.161 63.158 0.00 0.00 43.06 3.36
1205 2110 3.063084 GTCGCTCCGAGTCCCTGT 61.063 66.667 0.00 0.00 36.23 4.00
1207 2112 1.102222 GTCGCTCCGAGTCCCTGTAT 61.102 60.000 0.00 0.00 36.23 2.29
1208 2113 0.818445 TCGCTCCGAGTCCCTGTATC 60.818 60.000 0.00 0.00 0.00 2.24
1216 2121 3.056107 CCGAGTCCCTGTATCACTTTCAA 60.056 47.826 0.00 0.00 0.00 2.69
1227 2132 7.984050 CCTGTATCACTTTCAACAGATCTGTAT 59.016 37.037 28.10 16.93 44.13 2.29
1237 2142 7.895975 TCAACAGATCTGTATTGTCTTCTTG 57.104 36.000 28.10 17.63 44.13 3.02
1247 2152 5.810587 TGTATTGTCTTCTTGTTATCTCGGC 59.189 40.000 0.00 0.00 0.00 5.54
1249 2154 4.111375 TGTCTTCTTGTTATCTCGGCTC 57.889 45.455 0.00 0.00 0.00 4.70
1287 2192 2.922503 TGTCGCTGCCTTCCCTCA 60.923 61.111 0.00 0.00 0.00 3.86
1290 2195 1.092345 GTCGCTGCCTTCCCTCATTC 61.092 60.000 0.00 0.00 0.00 2.67
1294 2199 1.467920 CTGCCTTCCCTCATTCCAAC 58.532 55.000 0.00 0.00 0.00 3.77
1299 2204 3.682999 GCCTTCCCTCATTCCAACTAGTC 60.683 52.174 0.00 0.00 0.00 2.59
1315 2220 8.529476 TCCAACTAGTCTAATCTTACTTTGTCC 58.471 37.037 0.00 0.00 0.00 4.02
1322 2227 7.178628 AGTCTAATCTTACTTTGTCCTACAGCA 59.821 37.037 0.00 0.00 0.00 4.41
1325 2230 4.883083 TCTTACTTTGTCCTACAGCACTG 58.117 43.478 0.00 0.00 0.00 3.66
1326 2231 1.884235 ACTTTGTCCTACAGCACTGC 58.116 50.000 0.00 0.00 0.00 4.40
1327 2232 1.140852 ACTTTGTCCTACAGCACTGCA 59.859 47.619 3.30 0.00 0.00 4.41
1335 2240 2.277969 CTACAGCACTGCAGATTCCTG 58.722 52.381 23.35 20.30 43.22 3.86
1338 2243 0.917533 AGCACTGCAGATTCCTGGAT 59.082 50.000 23.35 0.00 40.04 3.41
1343 2248 2.968574 ACTGCAGATTCCTGGATACGAT 59.031 45.455 23.35 0.00 40.04 3.73
1344 2249 3.244009 ACTGCAGATTCCTGGATACGATG 60.244 47.826 23.35 0.00 40.04 3.84
1364 2269 2.244510 TGTGTTTCCATATGCCTCCCAT 59.755 45.455 0.00 0.00 37.97 4.00
1374 2279 5.953548 CCATATGCCTCCCATTCATATTTCA 59.046 40.000 0.00 0.00 32.75 2.69
1379 2284 4.095483 GCCTCCCATTCATATTTCATAGCG 59.905 45.833 0.00 0.00 0.00 4.26
1409 2314 3.685756 TCGGTTCAACCCATCGTTTATTC 59.314 43.478 0.00 0.00 33.75 1.75
1423 2328 4.109050 CGTTTATTCTCACTGCTCTCTCC 58.891 47.826 0.00 0.00 0.00 3.71
1434 2339 5.893824 TCACTGCTCTCTCCTGATAACATAA 59.106 40.000 0.00 0.00 0.00 1.90
1443 2348 7.952930 TCTCTCCTGATAACATAATTAGAGGCT 59.047 37.037 0.00 0.00 31.13 4.58
1451 2356 8.958060 ATAACATAATTAGAGGCTACAGGAGA 57.042 34.615 0.00 0.00 0.00 3.71
1497 2402 1.242076 AGTGTCTGTCATGCTTTGGC 58.758 50.000 0.00 0.00 39.26 4.52
1498 2403 0.110056 GTGTCTGTCATGCTTTGGCG 60.110 55.000 0.00 0.00 42.25 5.69
1499 2404 0.534877 TGTCTGTCATGCTTTGGCGT 60.535 50.000 0.00 0.00 42.25 5.68
1526 2431 4.218200 TGAATGGTTGGTGAGCACATTAAG 59.782 41.667 2.75 0.00 38.83 1.85
1545 2450 6.824958 TTAAGTATTCATCCCTGCTAGGTT 57.175 37.500 0.00 0.00 31.93 3.50
1566 2473 6.552350 AGGTTGTAAATCTTATCCCTAGCGTA 59.448 38.462 0.00 0.00 28.40 4.42
1576 2483 7.365741 TCTTATCCCTAGCGTAAATTAACTCG 58.634 38.462 0.00 0.00 0.00 4.18
1582 2489 4.572950 AGCGTAAATTAACTCGAAACCG 57.427 40.909 0.00 0.00 0.00 4.44
1603 2510 4.439057 CGCACACCTTGGTATTACACTAT 58.561 43.478 0.00 0.00 0.00 2.12
1680 2587 5.104776 ACAGCCATATAGAGTGTGACATGTT 60.105 40.000 0.00 0.00 0.00 2.71
1690 2597 6.291377 AGAGTGTGACATGTTATGTGTTTCT 58.709 36.000 0.00 0.00 45.03 2.52
1725 2632 6.073058 CCATTCATAATGTACTGCAGCGTAAT 60.073 38.462 15.27 0.00 37.18 1.89
1730 2637 3.596310 TGTACTGCAGCGTAATAACCA 57.404 42.857 15.27 0.00 0.00 3.67
1758 2674 5.753716 TGATTGTCATCTCTCTCTCTCTCA 58.246 41.667 0.00 0.00 0.00 3.27
1772 2708 0.378257 CTCTCACTCTCTCTCTGCGC 59.622 60.000 0.00 0.00 0.00 6.09
2002 2943 0.896479 TGCTCATGTGGCAGCACAAT 60.896 50.000 10.92 0.00 40.80 2.71
2003 2944 0.179145 GCTCATGTGGCAGCACAATC 60.179 55.000 0.00 0.00 38.69 2.67
2080 3045 1.745087 CAAGCAATCACCCAACGCTAT 59.255 47.619 0.00 0.00 31.36 2.97
2134 3100 6.072230 TGCATTCATTATTCGACTGGTTCAAA 60.072 34.615 0.00 0.00 0.00 2.69
2161 3128 6.468000 ACTTCAACGTCTTTTTGAAATCGAAC 59.532 34.615 1.65 0.00 41.32 3.95
2162 3129 5.870444 TCAACGTCTTTTTGAAATCGAACA 58.130 33.333 0.00 0.00 29.89 3.18
2210 3202 9.638300 CTATTTGCTTAGTATAGTTTTGCGAAG 57.362 33.333 0.00 0.00 0.00 3.79
2227 3219 7.724305 TTGCGAAGTTTATCTAAACAAGAGT 57.276 32.000 13.65 0.00 45.97 3.24
2360 3354 0.456221 ATCGAAGCTACAGTCCGTGG 59.544 55.000 0.00 0.00 0.00 4.94
2369 3363 0.180406 ACAGTCCGTGGCAAAGAAGT 59.820 50.000 0.00 0.00 0.00 3.01
2507 3501 4.376146 GCCTTATGAGAACTGGCTTCTAG 58.624 47.826 0.00 0.00 39.53 2.43
2627 3630 8.794553 TGGACTTTTCACTTAGTTTTGTAAACA 58.205 29.630 5.23 0.00 0.00 2.83
2666 3670 0.038021 TTTCTACATGCCTGCTGCCA 59.962 50.000 0.00 0.00 40.16 4.92
3129 4269 8.743085 AGATTTCTATGTGTCTTGTGCATATT 57.257 30.769 0.00 0.00 0.00 1.28
3151 4291 7.568128 ATTCTTATGCCCTGTGTACCATATA 57.432 36.000 0.00 0.00 0.00 0.86
3389 4530 9.562583 GCTAACTCGGTTCTCTATTTCTATATG 57.437 37.037 0.00 0.00 0.00 1.78
3438 4579 2.277247 GCGTGTGTGTGTGTGTGC 60.277 61.111 0.00 0.00 0.00 4.57
3529 4673 5.975693 CCTTAGGGAGAGTAGATGATGAC 57.024 47.826 0.00 0.00 33.58 3.06
3535 4679 4.520874 GGGAGAGTAGATGATGACGATGAA 59.479 45.833 0.00 0.00 0.00 2.57
3540 4684 6.714356 AGAGTAGATGATGACGATGAAGATGA 59.286 38.462 0.00 0.00 0.00 2.92
3587 4731 7.870445 TGAATGTTATTTTTCTTGGGCAGTTAC 59.130 33.333 0.00 0.00 0.00 2.50
3602 4776 0.702316 GTTACCCAAGGGACCATGGT 59.298 55.000 19.89 19.89 38.96 3.55
3642 4816 2.727123 AATATGCCATTGTCCGACCA 57.273 45.000 0.00 0.00 0.00 4.02
3663 4837 8.223769 CGACCAAAGCTTACTATATATTTGCTG 58.776 37.037 0.00 0.00 0.00 4.41
3664 4838 7.875971 ACCAAAGCTTACTATATATTTGCTGC 58.124 34.615 0.00 0.00 0.00 5.25
3665 4839 7.502226 ACCAAAGCTTACTATATATTTGCTGCA 59.498 33.333 0.00 0.00 0.00 4.41
3666 4840 8.517878 CCAAAGCTTACTATATATTTGCTGCAT 58.482 33.333 1.84 0.00 0.00 3.96
3669 4843 6.536582 AGCTTACTATATATTTGCTGCATCGG 59.463 38.462 1.84 0.00 0.00 4.18
3671 4845 7.464710 GCTTACTATATATTTGCTGCATCGGTC 60.465 40.741 1.84 0.00 0.00 4.79
3672 4846 5.793817 ACTATATATTTGCTGCATCGGTCA 58.206 37.500 1.84 0.00 0.00 4.02
3678 4852 0.036105 TGCTGCATCGGTCAATCAGT 60.036 50.000 0.00 0.00 0.00 3.41
3679 4853 0.654683 GCTGCATCGGTCAATCAGTC 59.345 55.000 0.00 0.00 0.00 3.51
3682 4856 3.005554 CTGCATCGGTCAATCAGTCTTT 58.994 45.455 0.00 0.00 0.00 2.52
3686 4860 4.095483 GCATCGGTCAATCAGTCTTTCATT 59.905 41.667 0.00 0.00 0.00 2.57
3710 4884 4.835284 TTTAGCATGTCCACCTCATGTA 57.165 40.909 7.55 0.00 42.94 2.29
3711 4885 4.835284 TTAGCATGTCCACCTCATGTAA 57.165 40.909 7.55 3.61 42.94 2.41
3719 6191 6.325919 TGTCCACCTCATGTAACATTTTTC 57.674 37.500 0.00 0.00 0.00 2.29
3722 6194 7.174253 TGTCCACCTCATGTAACATTTTTCTAC 59.826 37.037 0.00 0.00 0.00 2.59
3727 6199 8.357402 ACCTCATGTAACATTTTTCTACCAAAC 58.643 33.333 0.00 0.00 0.00 2.93
3753 6225 7.824704 AATCATATAGCATCTTTCACTAGCG 57.175 36.000 0.00 0.00 0.00 4.26
3755 6227 6.382608 TCATATAGCATCTTTCACTAGCGAC 58.617 40.000 0.00 0.00 0.00 5.19
3756 6228 2.301577 AGCATCTTTCACTAGCGACC 57.698 50.000 0.00 0.00 0.00 4.79
3757 6229 0.924090 GCATCTTTCACTAGCGACCG 59.076 55.000 0.00 0.00 0.00 4.79
3760 6232 0.388134 TCTTTCACTAGCGACCGTGC 60.388 55.000 0.00 0.00 0.00 5.34
3761 6233 0.666274 CTTTCACTAGCGACCGTGCA 60.666 55.000 0.00 0.00 37.31 4.57
3762 6234 0.666274 TTTCACTAGCGACCGTGCAG 60.666 55.000 0.00 0.00 37.31 4.41
3765 6237 2.432456 CTAGCGACCGTGCAGCAA 60.432 61.111 0.00 0.00 37.31 3.91
3769 6241 1.060937 GCGACCGTGCAGCAATAAG 59.939 57.895 0.00 0.00 34.15 1.73
3786 6258 6.974965 GCAATAAGCTATTGGAACTTATGCT 58.025 36.000 14.00 0.00 44.36 3.79
3790 6262 5.559148 AGCTATTGGAACTTATGCTAGCT 57.441 39.130 17.23 4.07 34.04 3.32
3796 6268 2.436173 GGAACTTATGCTAGCTGGAGGT 59.564 50.000 17.23 9.09 0.00 3.85
3811 6283 1.264295 GAGGTTCTCCCGTTACTGGT 58.736 55.000 0.00 0.00 38.74 4.00
3812 6284 1.204231 GAGGTTCTCCCGTTACTGGTC 59.796 57.143 0.00 0.00 38.74 4.02
3813 6285 1.203149 AGGTTCTCCCGTTACTGGTCT 60.203 52.381 0.00 0.00 38.74 3.85
3814 6286 2.042162 AGGTTCTCCCGTTACTGGTCTA 59.958 50.000 0.00 0.00 38.74 2.59
3815 6287 2.165234 GGTTCTCCCGTTACTGGTCTAC 59.835 54.545 0.00 0.00 0.00 2.59
3818 6290 1.749634 CTCCCGTTACTGGTCTACTGG 59.250 57.143 0.00 0.00 0.00 4.00
3819 6291 1.076024 TCCCGTTACTGGTCTACTGGT 59.924 52.381 0.00 0.00 0.00 4.00
3820 6292 2.308570 TCCCGTTACTGGTCTACTGGTA 59.691 50.000 0.00 0.00 0.00 3.25
3821 6293 3.091545 CCCGTTACTGGTCTACTGGTAA 58.908 50.000 0.00 0.00 0.00 2.85
3822 6294 3.703052 CCCGTTACTGGTCTACTGGTAAT 59.297 47.826 0.00 0.00 0.00 1.89
3823 6295 4.202090 CCCGTTACTGGTCTACTGGTAATC 60.202 50.000 0.00 0.00 0.00 1.75
3825 6297 5.126707 CCGTTACTGGTCTACTGGTAATCTT 59.873 44.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.205655 TCTCTGCCATGACACTAGTGC 59.794 52.381 22.90 15.35 0.00 4.40
17 18 3.668447 TCTGTTCTTTGATGGTCTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
27 28 0.037326 AGCCGCGATCTGTTCTTTGA 60.037 50.000 8.23 0.00 0.00 2.69
50 54 4.171103 ATTCCCCGCCACCGTAGC 62.171 66.667 0.00 0.00 0.00 3.58
51 55 2.040009 ATCATTCCCCGCCACCGTAG 62.040 60.000 0.00 0.00 0.00 3.51
54 58 2.884997 TTCATCATTCCCCGCCACCG 62.885 60.000 0.00 0.00 0.00 4.94
60 64 1.006832 GTCGTGTTCATCATTCCCCG 58.993 55.000 0.00 0.00 0.00 5.73
72 76 2.702592 TCTTCCTTTGGTGTCGTGTT 57.297 45.000 0.00 0.00 0.00 3.32
85 89 1.833630 TGTCGAATGAGGCATCTTCCT 59.166 47.619 0.00 0.00 39.67 3.36
152 156 3.347958 TGTTTTTCGGTGTCATCTTGC 57.652 42.857 0.00 0.00 0.00 4.01
178 182 5.126869 TGATGCAAACTGGTTCAAGAAGAAA 59.873 36.000 0.00 0.00 38.13 2.52
179 183 4.644234 TGATGCAAACTGGTTCAAGAAGAA 59.356 37.500 0.00 0.00 0.00 2.52
181 185 4.572985 TGATGCAAACTGGTTCAAGAAG 57.427 40.909 0.00 0.00 0.00 2.85
182 186 5.534207 AATGATGCAAACTGGTTCAAGAA 57.466 34.783 0.00 0.00 0.00 2.52
183 187 5.534207 AAATGATGCAAACTGGTTCAAGA 57.466 34.783 0.00 0.00 0.00 3.02
184 188 6.925165 AGTTAAATGATGCAAACTGGTTCAAG 59.075 34.615 0.00 0.00 31.20 3.02
185 189 6.815089 AGTTAAATGATGCAAACTGGTTCAA 58.185 32.000 0.00 0.00 31.20 2.69
186 190 6.403866 AGTTAAATGATGCAAACTGGTTCA 57.596 33.333 0.00 0.00 31.20 3.18
187 191 7.713764 AAAGTTAAATGATGCAAACTGGTTC 57.286 32.000 0.16 0.00 32.69 3.62
188 192 7.768120 TGAAAAGTTAAATGATGCAAACTGGTT 59.232 29.630 0.16 0.00 32.69 3.67
190 194 7.712264 TGAAAAGTTAAATGATGCAAACTGG 57.288 32.000 0.16 0.00 32.69 4.00
191 195 8.819974 AGTTGAAAAGTTAAATGATGCAAACTG 58.180 29.630 0.16 0.00 32.69 3.16
192 196 8.947055 AGTTGAAAAGTTAAATGATGCAAACT 57.053 26.923 0.00 0.00 33.72 2.66
193 197 9.424659 CAAGTTGAAAAGTTAAATGATGCAAAC 57.575 29.630 0.00 0.00 37.37 2.93
194 198 9.160496 ACAAGTTGAAAAGTTAAATGATGCAAA 57.840 25.926 10.54 0.00 37.37 3.68
195 199 8.602328 CACAAGTTGAAAAGTTAAATGATGCAA 58.398 29.630 10.54 0.00 37.37 4.08
196 200 7.978414 TCACAAGTTGAAAAGTTAAATGATGCA 59.022 29.630 10.54 0.00 37.37 3.96
197 201 8.351495 TCACAAGTTGAAAAGTTAAATGATGC 57.649 30.769 10.54 0.00 37.37 3.91
199 203 9.019764 CGTTCACAAGTTGAAAAGTTAAATGAT 57.980 29.630 10.54 0.00 46.09 2.45
200 204 8.237949 TCGTTCACAAGTTGAAAAGTTAAATGA 58.762 29.630 10.54 0.00 46.09 2.57
201 205 8.388319 TCGTTCACAAGTTGAAAAGTTAAATG 57.612 30.769 10.54 0.00 46.09 2.32
202 206 9.019764 CATCGTTCACAAGTTGAAAAGTTAAAT 57.980 29.630 10.54 0.00 46.09 1.40
203 207 8.024285 ACATCGTTCACAAGTTGAAAAGTTAAA 58.976 29.630 10.54 0.00 46.09 1.52
213 660 4.211389 GCTGTAACATCGTTCACAAGTTG 58.789 43.478 0.00 0.00 0.00 3.16
214 661 3.250040 GGCTGTAACATCGTTCACAAGTT 59.750 43.478 0.00 0.00 0.00 2.66
221 668 3.994392 TCAAGAAGGCTGTAACATCGTTC 59.006 43.478 0.00 0.00 0.00 3.95
235 682 3.251972 GTCTTCAAACTGGCTCAAGAAGG 59.748 47.826 0.00 0.00 34.70 3.46
246 693 2.345641 CCGTAGCATCGTCTTCAAACTG 59.654 50.000 0.00 0.00 0.00 3.16
257 704 2.821546 TCCTTTTGATCCGTAGCATCG 58.178 47.619 0.00 0.00 0.00 3.84
287 734 8.296000 TGAAGATTCGTGCTCAAAATAAAATCA 58.704 29.630 0.00 0.00 0.00 2.57
302 749 4.488879 TGAGAGTGATGTGAAGATTCGTG 58.511 43.478 0.00 0.00 0.00 4.35
303 750 4.790765 TGAGAGTGATGTGAAGATTCGT 57.209 40.909 0.00 0.00 0.00 3.85
437 1044 8.587608 CCAGATATGTTGCCCATAAACATTATT 58.412 33.333 7.06 0.00 43.94 1.40
438 1045 7.729881 ACCAGATATGTTGCCCATAAACATTAT 59.270 33.333 7.06 0.75 43.94 1.28
473 1080 7.624360 AAGTTTTCATACTTGCATCGGAATA 57.376 32.000 0.00 0.00 37.00 1.75
477 1084 5.255596 CGTAAGTTTTCATACTTGCATCGG 58.744 41.667 0.00 0.00 39.71 4.18
486 1093 9.859692 GATGGTTTATAGCGTAAGTTTTCATAC 57.140 33.333 0.00 0.00 41.68 2.39
516 1123 5.126061 CCCACCTTGTTTCTTCATATTGAGG 59.874 44.000 0.00 0.00 0.00 3.86
522 1129 3.153919 GCACCCACCTTGTTTCTTCATA 58.846 45.455 0.00 0.00 0.00 2.15
546 1153 0.036483 TGCGATCTAAGTGGCTGCAA 60.036 50.000 0.50 0.00 0.00 4.08
550 1157 2.482142 GCTAAGTGCGATCTAAGTGGCT 60.482 50.000 0.00 0.00 0.00 4.75
563 1170 5.296283 ACATGATTTCTCATCTGCTAAGTGC 59.704 40.000 0.00 0.00 40.20 4.40
665 1272 3.922240 CAGCAAAATGAAAATGACGGGAG 59.078 43.478 0.00 0.00 0.00 4.30
667 1274 3.429543 CACAGCAAAATGAAAATGACGGG 59.570 43.478 0.00 0.00 0.00 5.28
684 1292 1.542915 TCCGGTAGTACACTTCACAGC 59.457 52.381 0.00 0.00 0.00 4.40
697 1305 5.180492 GTGATTATCTCTCTGTCTCCGGTAG 59.820 48.000 0.00 0.00 0.00 3.18
701 1309 3.254657 GGGTGATTATCTCTCTGTCTCCG 59.745 52.174 0.00 0.00 0.00 4.63
746 1354 9.688592 CAGCACAATCTAAATTTCTCTTCTTTT 57.311 29.630 0.00 0.00 0.00 2.27
747 1355 7.811713 GCAGCACAATCTAAATTTCTCTTCTTT 59.188 33.333 0.00 0.00 0.00 2.52
748 1356 7.176340 AGCAGCACAATCTAAATTTCTCTTCTT 59.824 33.333 0.00 0.00 0.00 2.52
749 1357 6.658391 AGCAGCACAATCTAAATTTCTCTTCT 59.342 34.615 0.00 0.00 0.00 2.85
750 1358 6.850555 AGCAGCACAATCTAAATTTCTCTTC 58.149 36.000 0.00 0.00 0.00 2.87
751 1359 6.830873 AGCAGCACAATCTAAATTTCTCTT 57.169 33.333 0.00 0.00 0.00 2.85
752 1360 6.618811 CAAGCAGCACAATCTAAATTTCTCT 58.381 36.000 0.00 0.00 0.00 3.10
753 1361 5.287992 GCAAGCAGCACAATCTAAATTTCTC 59.712 40.000 0.00 0.00 44.79 2.87
781 1587 5.359009 CGTATGGAGGAGGAAGTACACTTTA 59.641 44.000 0.00 0.00 36.11 1.85
784 1590 3.053842 TCGTATGGAGGAGGAAGTACACT 60.054 47.826 0.00 0.00 0.00 3.55
785 1591 3.285484 TCGTATGGAGGAGGAAGTACAC 58.715 50.000 0.00 0.00 0.00 2.90
786 1592 3.552875 CTCGTATGGAGGAGGAAGTACA 58.447 50.000 0.00 0.00 39.22 2.90
787 1593 2.293955 GCTCGTATGGAGGAGGAAGTAC 59.706 54.545 0.00 0.00 43.36 2.73
788 1594 2.584236 GCTCGTATGGAGGAGGAAGTA 58.416 52.381 0.00 0.00 43.36 2.24
789 1595 1.404843 GCTCGTATGGAGGAGGAAGT 58.595 55.000 0.00 0.00 43.36 3.01
790 1596 0.312416 CGCTCGTATGGAGGAGGAAG 59.688 60.000 0.00 0.00 43.36 3.46
792 1598 0.535328 CTCGCTCGTATGGAGGAGGA 60.535 60.000 0.00 0.00 43.36 3.71
793 1599 0.535328 TCTCGCTCGTATGGAGGAGG 60.535 60.000 10.95 0.00 43.36 4.30
794 1600 0.871722 CTCTCGCTCGTATGGAGGAG 59.128 60.000 0.00 3.85 43.36 3.69
821 1627 1.227586 GCTAACTTAGCCGAGGCCC 60.228 63.158 10.95 0.00 45.95 5.80
978 1803 2.661866 GGTCGCCGGAATCGATGG 60.662 66.667 5.05 0.00 38.29 3.51
1039 1866 2.846206 AGTACATCAGCAATGGGGAGAA 59.154 45.455 0.00 0.00 39.90 2.87
1042 1869 1.915489 ACAGTACATCAGCAATGGGGA 59.085 47.619 0.00 0.00 39.90 4.81
1047 1874 8.796475 ACAAGATTTTTACAGTACATCAGCAAT 58.204 29.630 0.00 0.00 0.00 3.56
1053 1880 9.118236 GCAGAAACAAGATTTTTACAGTACATC 57.882 33.333 0.00 0.00 0.00 3.06
1075 1964 4.600062 TGAGGTACACATCTAGAAGCAGA 58.400 43.478 0.00 0.00 0.00 4.26
1098 1999 1.289160 CAACCCCCTGAATCTCCTCA 58.711 55.000 0.00 0.00 0.00 3.86
1107 2008 3.547737 TCCTCCCCAACCCCCTGA 61.548 66.667 0.00 0.00 0.00 3.86
1108 2009 3.017581 CTCCTCCCCAACCCCCTG 61.018 72.222 0.00 0.00 0.00 4.45
1127 2028 2.908940 CCCGGATCAATGCCTGCC 60.909 66.667 0.73 0.00 0.00 4.85
1129 2030 0.107017 AAGACCCGGATCAATGCCTG 60.107 55.000 0.73 0.00 0.00 4.85
1130 2031 1.417890 CTAAGACCCGGATCAATGCCT 59.582 52.381 0.73 0.00 0.00 4.75
1133 2037 5.023533 TCTTTCTAAGACCCGGATCAATG 57.976 43.478 0.73 0.00 31.20 2.82
1155 2059 6.899393 TTGAATGACAGGCAAGTAATTTCT 57.101 33.333 0.00 0.00 0.00 2.52
1169 2073 4.228317 CGACATGCACAAATTGAATGACA 58.772 39.130 0.00 0.00 43.57 3.58
1170 2074 3.059834 GCGACATGCACAAATTGAATGAC 59.940 43.478 0.00 1.06 43.57 3.06
1171 2075 3.057386 AGCGACATGCACAAATTGAATGA 60.057 39.130 0.00 0.00 43.57 2.57
1186 2091 2.043852 AGGGACTCGGAGCGACAT 60.044 61.111 4.58 0.00 0.00 3.06
1194 2099 2.496070 TGAAAGTGATACAGGGACTCGG 59.504 50.000 0.00 0.00 34.60 4.63
1196 2101 4.894784 TGTTGAAAGTGATACAGGGACTC 58.105 43.478 0.00 0.00 34.60 3.36
1197 2102 4.593206 TCTGTTGAAAGTGATACAGGGACT 59.407 41.667 0.00 0.00 38.75 3.85
1199 2104 5.485353 AGATCTGTTGAAAGTGATACAGGGA 59.515 40.000 0.00 0.00 38.75 4.20
1200 2105 5.583854 CAGATCTGTTGAAAGTGATACAGGG 59.416 44.000 14.95 0.00 38.75 4.45
1205 2110 9.371136 GACAATACAGATCTGTTGAAAGTGATA 57.629 33.333 32.14 11.61 41.83 2.15
1207 2112 7.445121 AGACAATACAGATCTGTTGAAAGTGA 58.555 34.615 32.14 13.10 41.83 3.41
1208 2113 7.664082 AGACAATACAGATCTGTTGAAAGTG 57.336 36.000 32.14 23.96 41.83 3.16
1216 2121 9.593134 GATAACAAGAAGACAATACAGATCTGT 57.407 33.333 30.11 30.11 46.87 3.41
1227 2132 4.495422 GAGCCGAGATAACAAGAAGACAA 58.505 43.478 0.00 0.00 0.00 3.18
1269 2174 2.125350 GAGGGAAGGCAGCGACAG 60.125 66.667 0.00 0.00 0.00 3.51
1270 2175 1.841302 AATGAGGGAAGGCAGCGACA 61.841 55.000 0.00 0.00 0.00 4.35
1273 2178 1.821332 GGAATGAGGGAAGGCAGCG 60.821 63.158 0.00 0.00 0.00 5.18
1290 2195 8.532819 AGGACAAAGTAAGATTAGACTAGTTGG 58.467 37.037 0.00 0.00 0.00 3.77
1299 2204 7.276658 CAGTGCTGTAGGACAAAGTAAGATTAG 59.723 40.741 6.32 0.00 38.96 1.73
1315 2220 2.277969 CAGGAATCTGCAGTGCTGTAG 58.722 52.381 17.60 10.40 43.36 2.74
1320 2225 2.216898 GTATCCAGGAATCTGCAGTGC 58.783 52.381 14.67 8.58 39.61 4.40
1322 2227 2.388735 TCGTATCCAGGAATCTGCAGT 58.611 47.619 14.67 0.00 39.61 4.40
1325 2230 3.062763 CACATCGTATCCAGGAATCTGC 58.937 50.000 0.00 0.00 39.61 4.26
1326 2231 4.327982 ACACATCGTATCCAGGAATCTG 57.672 45.455 0.00 0.00 40.59 2.90
1327 2232 5.359194 AAACACATCGTATCCAGGAATCT 57.641 39.130 0.00 0.00 0.00 2.40
1364 2269 6.402442 CGATGCAATCCGCTATGAAATATGAA 60.402 38.462 0.00 0.00 41.39 2.57
1374 2279 1.202639 TGAACCGATGCAATCCGCTAT 60.203 47.619 0.00 0.00 41.39 2.97
1379 2284 0.455815 GGGTTGAACCGATGCAATCC 59.544 55.000 8.47 0.00 41.39 3.01
1388 2293 3.687698 AGAATAAACGATGGGTTGAACCG 59.312 43.478 8.47 0.00 39.83 4.44
1409 2314 3.698539 TGTTATCAGGAGAGAGCAGTGAG 59.301 47.826 0.00 0.00 0.00 3.51
1423 2328 8.807118 TCCTGTAGCCTCTAATTATGTTATCAG 58.193 37.037 0.00 0.00 0.00 2.90
1434 2339 2.962421 GCAGTCTCCTGTAGCCTCTAAT 59.038 50.000 0.00 0.00 41.02 1.73
1443 2348 1.468985 GCTCTCTGCAGTCTCCTGTA 58.531 55.000 14.67 0.00 41.02 2.74
1484 2389 0.534877 ACAGACGCCAAAGCATGACA 60.535 50.000 0.00 0.00 39.83 3.58
1485 2390 0.110056 CACAGACGCCAAAGCATGAC 60.110 55.000 0.00 0.00 39.83 3.06
1497 2402 1.800586 CTCACCAACCATTCACAGACG 59.199 52.381 0.00 0.00 0.00 4.18
1498 2403 1.537202 GCTCACCAACCATTCACAGAC 59.463 52.381 0.00 0.00 0.00 3.51
1499 2404 1.142667 TGCTCACCAACCATTCACAGA 59.857 47.619 0.00 0.00 0.00 3.41
1526 2431 4.423625 ACAACCTAGCAGGGATGAATAC 57.576 45.455 11.07 0.00 40.58 1.89
1566 2473 3.304190 GGTGTGCGGTTTCGAGTTAATTT 60.304 43.478 0.00 0.00 39.00 1.82
1576 2483 1.530323 ATACCAAGGTGTGCGGTTTC 58.470 50.000 1.07 0.00 34.12 2.78
1582 2489 7.519970 GCAATATAGTGTAATACCAAGGTGTGC 60.520 40.741 1.07 0.00 0.00 4.57
1603 2510 4.383118 GCAGAAGAAGGGACAGTAGCAATA 60.383 45.833 0.00 0.00 0.00 1.90
1680 2587 7.395772 TGAATGGGAAGCATAAAGAAACACATA 59.604 33.333 0.00 0.00 0.00 2.29
1690 2597 8.849168 CAGTACATTATGAATGGGAAGCATAAA 58.151 33.333 0.00 0.00 43.21 1.40
1730 2637 7.507956 AGAGAGAGAGAGATGACAATCATGATT 59.492 37.037 15.36 15.36 37.20 2.57
1758 2674 1.134753 CATCAAGCGCAGAGAGAGAGT 59.865 52.381 11.47 0.00 0.00 3.24
1772 2708 3.191371 GGCCTTTCAACTGTACCATCAAG 59.809 47.826 0.00 0.00 0.00 3.02
1786 2722 6.432403 AATTGTTTTAGATTGGGCCTTTCA 57.568 33.333 4.53 0.00 0.00 2.69
1868 2809 5.559770 TCTGTTTTCATTAGATGCAGGACA 58.440 37.500 0.00 0.00 0.00 4.02
1871 2812 5.188434 TCCTCTGTTTTCATTAGATGCAGG 58.812 41.667 0.00 0.00 0.00 4.85
2002 2943 3.754965 AGCATTTAACCTCTGCACAAGA 58.245 40.909 0.00 0.00 38.37 3.02
2003 2944 4.437930 GCTAGCATTTAACCTCTGCACAAG 60.438 45.833 10.63 0.00 38.37 3.16
2080 3045 4.335315 CAGTTTGGTACTTCAGCAACTGAA 59.665 41.667 9.51 9.51 46.50 3.02
2218 3210 9.220767 GAACAGGACTTGATATAACTCTTGTTT 57.779 33.333 0.00 0.00 37.59 2.83
2360 3354 5.893897 ATCATCTCTTTGGACTTCTTTGC 57.106 39.130 0.00 0.00 0.00 3.68
2369 3363 9.035890 TCTAGAAAAGTGTATCATCTCTTTGGA 57.964 33.333 0.00 0.00 33.43 3.53
2507 3501 1.134907 CCTGTCATTTTGGATGGCAGC 60.135 52.381 13.58 0.00 46.99 5.25
2573 3570 9.458374 AATTAAACATCAACTACAAAGGAAACG 57.542 29.630 0.00 0.00 0.00 3.60
2646 3649 1.547449 TGGCAGCAGGCATGTAGAAAA 60.547 47.619 0.00 0.00 46.46 2.29
2855 3859 6.148948 CCATCAATTTACGCTTGAAAACTGA 58.851 36.000 0.00 0.00 36.30 3.41
3151 4291 6.122277 CACATTTGTAGGGTCAATACAGGAT 58.878 40.000 0.00 0.00 34.76 3.24
3422 4563 2.021243 CGCACACACACACACACG 59.979 61.111 0.00 0.00 0.00 4.49
3454 4595 2.084546 GCAAAAGAAGGTACGCAGGAT 58.915 47.619 0.00 0.00 0.00 3.24
3519 4663 8.985805 CATTTTCATCTTCATCGTCATCATCTA 58.014 33.333 0.00 0.00 0.00 1.98
3529 4673 6.659361 ACAGAGACATTTTCATCTTCATCG 57.341 37.500 0.00 0.00 0.00 3.84
3580 4724 0.331616 ATGGTCCCTTGGGTAACTGC 59.668 55.000 5.51 0.00 0.00 4.40
3587 4731 0.106519 GATGACCATGGTCCCTTGGG 60.107 60.000 36.27 0.00 43.97 4.12
3642 4816 8.446273 CGATGCAGCAAATATATAGTAAGCTTT 58.554 33.333 3.20 0.00 0.00 3.51
3663 4837 3.002791 TGAAAGACTGATTGACCGATGC 58.997 45.455 0.00 0.00 0.00 3.91
3664 4838 5.808042 AATGAAAGACTGATTGACCGATG 57.192 39.130 0.00 0.00 0.00 3.84
3665 4839 6.824305 AAAATGAAAGACTGATTGACCGAT 57.176 33.333 0.00 0.00 0.00 4.18
3666 4840 6.633500 AAAAATGAAAGACTGATTGACCGA 57.367 33.333 0.00 0.00 0.00 4.69
3691 4865 3.517500 TGTTACATGAGGTGGACATGCTA 59.482 43.478 0.00 0.00 45.95 3.49
3692 4866 2.305635 TGTTACATGAGGTGGACATGCT 59.694 45.455 0.00 0.00 45.95 3.79
3694 4868 5.902613 AAATGTTACATGAGGTGGACATG 57.097 39.130 0.00 0.00 46.96 3.21
3697 4871 6.575162 AGAAAAATGTTACATGAGGTGGAC 57.425 37.500 0.00 0.00 0.00 4.02
3699 4873 6.432783 TGGTAGAAAAATGTTACATGAGGTGG 59.567 38.462 0.00 0.00 0.00 4.61
3701 4875 8.357402 GTTTGGTAGAAAAATGTTACATGAGGT 58.643 33.333 0.00 0.00 0.00 3.85
3722 6194 9.241317 GTGAAAGATGCTATATGATTTGTTTGG 57.759 33.333 0.00 0.00 0.00 3.28
3727 6199 8.167345 CGCTAGTGAAAGATGCTATATGATTTG 58.833 37.037 0.00 0.00 0.00 2.32
3735 6207 3.551046 CGGTCGCTAGTGAAAGATGCTAT 60.551 47.826 7.75 0.00 0.00 2.97
3737 6209 1.469940 CGGTCGCTAGTGAAAGATGCT 60.470 52.381 7.75 0.00 0.00 3.79
3738 6210 0.924090 CGGTCGCTAGTGAAAGATGC 59.076 55.000 7.75 0.00 0.00 3.91
3739 6211 1.920574 CACGGTCGCTAGTGAAAGATG 59.079 52.381 7.75 0.92 40.56 2.90
3751 6223 1.060937 CTTATTGCTGCACGGTCGC 59.939 57.895 0.00 0.00 0.00 5.19
3762 6234 6.974965 AGCATAAGTTCCAATAGCTTATTGC 58.025 36.000 0.00 0.00 43.19 3.56
3765 6237 7.605691 CAGCTAGCATAAGTTCCAATAGCTTAT 59.394 37.037 18.83 0.00 41.78 1.73
3769 6241 4.453819 CCAGCTAGCATAAGTTCCAATAGC 59.546 45.833 18.83 0.00 35.52 2.97
3776 6248 3.828875 ACCTCCAGCTAGCATAAGTTC 57.171 47.619 18.83 0.00 0.00 3.01
3778 6250 3.379452 AGAACCTCCAGCTAGCATAAGT 58.621 45.455 18.83 4.53 0.00 2.24
3796 6268 3.087031 CAGTAGACCAGTAACGGGAGAA 58.913 50.000 0.00 0.00 0.00 2.87
3802 6274 5.831702 AGATTACCAGTAGACCAGTAACG 57.168 43.478 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.