Multiple sequence alignment - TraesCS6D01G331400

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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 TraesCS6D01G331400 chr6D 100.000 6040 0 0 1 6040 434258781 434252742 0.000000e+00 11154.0
1 TraesCS6D01G331400 chr6D 87.004 2901 256 65 3174 6035 434171949 434169131 0.000000e+00 3157.0
2 TraesCS6D01G331400 chr6D 100.000 698 0 0 6254 6951 434252528 434251831 0.000000e+00 1290.0
3 TraesCS6D01G331400 chr6D 85.400 637 83 10 2025 2657 434173188 434172558 0.000000e+00 652.0
4 TraesCS6D01G331400 chr6D 95.238 63 3 0 6345 6407 434169104 434169042 4.440000e-17 100.0
5 TraesCS6D01G331400 chr6B 94.327 3314 134 29 2759 6040 656999841 656996550 0.000000e+00 5029.0
6 TraesCS6D01G331400 chr6B 87.158 2811 217 72 4 2746 657002556 656999822 0.000000e+00 3059.0
7 TraesCS6D01G331400 chr6B 85.224 1137 136 27 3169 4299 656547070 656545960 0.000000e+00 1140.0
8 TraesCS6D01G331400 chr6B 88.605 509 41 11 6450 6951 656996295 656995797 2.770000e-168 603.0
9 TraesCS6D01G331400 chr6B 85.222 406 49 6 4299 4693 656544617 656544212 2.330000e-109 407.0
10 TraesCS6D01G331400 chr6B 79.321 619 68 31 2034 2651 656548267 656547708 5.090000e-101 379.0
11 TraesCS6D01G331400 chr6B 94.262 122 7 0 6341 6462 656996433 656996312 3.310000e-43 187.0
12 TraesCS6D01G331400 chr6B 76.418 335 58 17 64 391 173576576 173576896 2.010000e-35 161.0
13 TraesCS6D01G331400 chr6A 95.288 2780 107 15 2759 5531 580536346 580533584 0.000000e+00 4386.0
14 TraesCS6D01G331400 chr6A 86.441 2891 282 59 3175 6035 580319023 580316213 0.000000e+00 3066.0
15 TraesCS6D01G331400 chr6A 89.768 1251 61 22 1551 2746 580537564 580536326 0.000000e+00 1539.0
16 TraesCS6D01G331400 chr6A 91.180 771 41 11 458 1225 580538478 580537732 0.000000e+00 1022.0
17 TraesCS6D01G331400 chr6A 92.075 530 29 7 5521 6040 580533561 580533035 0.000000e+00 734.0
18 TraesCS6D01G331400 chr6A 94.421 466 23 2 6341 6806 580532901 580532439 0.000000e+00 713.0
19 TraesCS6D01G331400 chr6A 86.808 614 72 9 2044 2654 580320246 580319639 0.000000e+00 676.0
20 TraesCS6D01G331400 chr6A 87.957 465 40 7 8 461 580539289 580538830 1.030000e-147 534.0
21 TraesCS6D01G331400 chr6A 82.262 451 36 22 6538 6951 580315741 580315298 3.990000e-92 350.0
22 TraesCS6D01G331400 chr6A 92.517 147 9 2 1325 1471 580537731 580537587 7.060000e-50 209.0
23 TraesCS6D01G331400 chr6A 84.868 152 11 9 6806 6950 580532171 580532025 7.270000e-30 143.0
24 TraesCS6D01G331400 chr6A 97.561 41 1 0 1485 1525 580537602 580537562 3.480000e-08 71.3
25 TraesCS6D01G331400 chr7D 99.437 2310 10 2 2319 4625 86841634 86843943 0.000000e+00 4191.0
26 TraesCS6D01G331400 chr3B 81.114 413 59 17 58 460 253631713 253632116 5.230000e-81 313.0
27 TraesCS6D01G331400 chr3B 78.191 188 32 7 45 230 183544956 183544776 2.050000e-20 111.0
28 TraesCS6D01G331400 chr3A 86.301 219 24 5 50 266 214120936 214121150 4.190000e-57 233.0
29 TraesCS6D01G331400 chr3A 81.111 180 28 5 46 225 729436414 729436587 9.400000e-29 139.0
30 TraesCS6D01G331400 chr2A 86.301 146 14 6 90 230 762860966 762860822 3.360000e-33 154.0
31 TraesCS6D01G331400 chr2B 74.286 315 67 12 47 358 776660865 776661168 3.410000e-23 121.0
32 TraesCS6D01G331400 chr7A 78.022 182 32 5 49 228 717466873 717467048 2.650000e-19 108.0
33 TraesCS6D01G331400 chr7A 73.817 317 62 15 63 377 547526444 547526147 9.540000e-19 106.0
34 TraesCS6D01G331400 chr3D 73.487 347 66 20 73 411 548731437 548731109 2.650000e-19 108.0
35 TraesCS6D01G331400 chr1A 74.419 301 48 21 72 363 20096973 20097253 1.230000e-17 102.0
36 TraesCS6D01G331400 chr4B 77.987 159 20 10 6781 6933 272067250 272067101 1.240000e-12 86.1
37 TraesCS6D01G331400 chr5D 85.915 71 6 4 294 363 408212850 408212917 9.670000e-09 73.1
38 TraesCS6D01G331400 chr4A 97.059 34 1 0 6640 6673 547310973 547311006 2.710000e-04 58.4
39 TraesCS6D01G331400 chr1B 94.444 36 1 1 6623 6657 403585979 403585944 4.000000e-03 54.7


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 TraesCS6D01G331400 chr6D 434251831 434258781 6950 True 6222.000000 11154 100.000000 1 6951 2 chr6D.!!$R2 6950
1 TraesCS6D01G331400 chr6D 434169042 434173188 4146 True 1303.000000 3157 89.214000 2025 6407 3 chr6D.!!$R1 4382
2 TraesCS6D01G331400 chr6B 656995797 657002556 6759 True 2219.500000 5029 91.088000 4 6951 4 chr6B.!!$R2 6947
3 TraesCS6D01G331400 chr6B 656544212 656548267 4055 True 642.000000 1140 83.255667 2034 4693 3 chr6B.!!$R1 2659
4 TraesCS6D01G331400 chr6A 580315298 580320246 4948 True 1364.000000 3066 85.170333 2044 6951 3 chr6A.!!$R1 4907
5 TraesCS6D01G331400 chr6A 580532025 580539289 7264 True 1039.033333 4386 91.737222 8 6950 9 chr6A.!!$R2 6942
6 TraesCS6D01G331400 chr7D 86841634 86843943 2309 False 4191.000000 4191 99.437000 2319 4625 1 chr7D.!!$F1 2306

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
913 1285 0.378962 TTGCTCGTCCAAAAACCACG 59.621 50.000 0.00 0.00 34.78 4.94 F
1302 1701 0.241749 TAAGTGTTCGATCGCGGTGT 59.758 50.000 11.09 0.00 38.28 4.16 F
1474 1876 0.331616 ACATCCGGGGCTAGCTTTTT 59.668 50.000 15.72 0.00 0.00 1.94 F
2052 2514 1.390123 CATGATCACGACGTGGTGTTC 59.610 52.381 26.72 26.23 39.00 3.18 F
2451 2917 1.986882 CTGGTGTTGGCCTTCTTTCT 58.013 50.000 3.32 0.00 0.00 2.52 F
4660 6705 3.119173 CCTTGGTTTTGTTGTCTTCTGCA 60.119 43.478 0.00 0.00 0.00 4.41 F
5064 7110 0.892755 TGTAGGCTCCGTTACAGGTG 59.107 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2166 0.391263 GCCAGGTGTACAGGTAGTGC 60.391 60.000 0.00 0.00 0.00 4.40 R
2451 2917 2.777094 TCATGAATTGTGAACGGAGCA 58.223 42.857 0.00 0.00 0.00 4.26 R
2749 3306 3.508793 ACCGTCCTAGAAAACATTCTCGA 59.491 43.478 0.00 0.00 32.72 4.04 R
3741 4414 0.238289 GAGTTGCAATCACACCACCG 59.762 55.000 0.59 0.00 0.00 4.94 R
4718 6763 8.826710 GGAAATTTACTGGGTTTTCAAGAAAAG 58.173 33.333 8.14 0.16 40.53 2.27 R
5761 7865 0.679321 GAGGAGTACGTTCCGAGGGT 60.679 60.000 0.00 0.00 42.29 4.34 R
6530 8914 1.326852 CAGAATGATCTGCACGACTGC 59.673 52.381 0.00 0.00 46.11 4.40 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
55 56 1.138859 CCCATGTATGTTGGAGAGCGA 59.861 52.381 0.00 0.00 36.26 4.93
56 57 2.224378 CCCATGTATGTTGGAGAGCGAT 60.224 50.000 0.00 0.00 36.26 4.58
69 70 3.006672 AGCGATTAAATGGCTCCCG 57.993 52.632 0.00 0.00 40.48 5.14
323 324 0.379669 GCAGCTCGGATGTCCAAATG 59.620 55.000 0.00 0.00 35.14 2.32
342 343 4.519540 ATGAGTTGAAATTTTGGACGGG 57.480 40.909 0.00 0.00 0.00 5.28
361 362 4.162698 ACGGGCCTCACACACTAAAATATA 59.837 41.667 0.84 0.00 0.00 0.86
424 435 9.788960 GTTAGATTTTATTGTTCACCAAGATCC 57.211 33.333 0.00 0.00 36.25 3.36
435 446 1.686052 ACCAAGATCCGATGAGCTCTC 59.314 52.381 16.19 9.01 35.85 3.20
438 449 2.198827 AGATCCGATGAGCTCTCGAT 57.801 50.000 26.66 19.82 38.38 3.59
487 853 9.529823 AATGATGAATATACGGTACTTCTCCTA 57.470 33.333 11.41 0.00 0.00 2.94
533 903 0.811219 TCATGCACGTGATAGGCAGC 60.811 55.000 22.23 0.67 41.40 5.25
598 968 1.643286 TCCCACAGGTCAGAGAGAGAT 59.357 52.381 0.00 0.00 0.00 2.75
603 973 3.378112 CACAGGTCAGAGAGAGATGAGAC 59.622 52.174 0.00 0.00 0.00 3.36
604 974 2.613595 CAGGTCAGAGAGAGATGAGACG 59.386 54.545 0.00 0.00 0.00 4.18
605 975 2.238646 AGGTCAGAGAGAGATGAGACGT 59.761 50.000 0.00 0.00 0.00 4.34
606 976 2.354510 GGTCAGAGAGAGATGAGACGTG 59.645 54.545 0.00 0.00 0.00 4.49
697 1067 2.107366 TGACAGACAGACAGGACACAA 58.893 47.619 0.00 0.00 0.00 3.33
709 1079 1.276421 AGGACACAACCTCCAATCGAG 59.724 52.381 0.00 0.00 34.98 4.04
715 1085 2.154462 CAACCTCCAATCGAGCAACTT 58.846 47.619 0.00 0.00 37.27 2.66
750 1120 4.394712 CCTCCCCTCACACGTGGC 62.395 72.222 21.57 0.00 0.00 5.01
775 1145 2.734723 CCCACACGTCAGCGACAG 60.735 66.667 8.91 3.93 42.00 3.51
895 1267 2.282462 CTTCCAACCCCGCTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
907 1279 1.654220 GCTGCTTGCTCGTCCAAAA 59.346 52.632 0.00 0.00 38.95 2.44
909 1281 1.758783 CTGCTTGCTCGTCCAAAAAC 58.241 50.000 0.00 0.00 0.00 2.43
910 1282 0.383949 TGCTTGCTCGTCCAAAAACC 59.616 50.000 0.00 0.00 0.00 3.27
911 1283 0.383949 GCTTGCTCGTCCAAAAACCA 59.616 50.000 0.00 0.00 0.00 3.67
912 1284 1.864029 GCTTGCTCGTCCAAAAACCAC 60.864 52.381 0.00 0.00 0.00 4.16
913 1285 0.378962 TTGCTCGTCCAAAAACCACG 59.621 50.000 0.00 0.00 34.78 4.94
914 1286 1.370051 GCTCGTCCAAAAACCACGC 60.370 57.895 0.00 0.00 33.46 5.34
915 1287 1.281656 CTCGTCCAAAAACCACGCC 59.718 57.895 0.00 0.00 33.46 5.68
916 1288 2.125202 CTCGTCCAAAAACCACGCCC 62.125 60.000 0.00 0.00 33.46 6.13
917 1289 2.482333 CGTCCAAAAACCACGCCCA 61.482 57.895 0.00 0.00 0.00 5.36
918 1290 1.817209 GTCCAAAAACCACGCCCAA 59.183 52.632 0.00 0.00 0.00 4.12
919 1291 0.391228 GTCCAAAAACCACGCCCAAT 59.609 50.000 0.00 0.00 0.00 3.16
920 1292 1.614413 GTCCAAAAACCACGCCCAATA 59.386 47.619 0.00 0.00 0.00 1.90
921 1293 2.036089 GTCCAAAAACCACGCCCAATAA 59.964 45.455 0.00 0.00 0.00 1.40
922 1294 2.900546 TCCAAAAACCACGCCCAATAAT 59.099 40.909 0.00 0.00 0.00 1.28
948 1320 0.934302 TCCCTCCCCTACCATCTCCA 60.934 60.000 0.00 0.00 0.00 3.86
1131 1506 3.862402 CGACTCCGACGACGAGGG 61.862 72.222 9.28 1.79 42.66 4.30
1229 1620 1.519719 GTGCGCATTCTCTCTCCCT 59.480 57.895 15.91 0.00 0.00 4.20
1234 1625 1.122227 GCATTCTCTCTCCCTGCTCT 58.878 55.000 0.00 0.00 0.00 4.09
1235 1626 2.315176 GCATTCTCTCTCCCTGCTCTA 58.685 52.381 0.00 0.00 0.00 2.43
1243 1634 0.825425 CTCCCTGCTCTATCGCCTCA 60.825 60.000 0.00 0.00 0.00 3.86
1247 1638 1.202114 CCTGCTCTATCGCCTCATCTC 59.798 57.143 0.00 0.00 0.00 2.75
1248 1639 1.885233 CTGCTCTATCGCCTCATCTCA 59.115 52.381 0.00 0.00 0.00 3.27
1251 1642 3.252400 GCTCTATCGCCTCATCTCAATG 58.748 50.000 0.00 0.00 0.00 2.82
1252 1643 3.056962 GCTCTATCGCCTCATCTCAATGA 60.057 47.826 0.00 0.00 39.63 2.57
1254 1645 4.148079 TCTATCGCCTCATCTCAATGACT 58.852 43.478 0.00 0.00 36.98 3.41
1256 1647 1.410517 TCGCCTCATCTCAATGACTCC 59.589 52.381 0.00 0.00 36.98 3.85
1258 1649 1.137872 GCCTCATCTCAATGACTCCGT 59.862 52.381 0.00 0.00 36.98 4.69
1259 1650 2.819115 CCTCATCTCAATGACTCCGTG 58.181 52.381 0.00 0.00 36.98 4.94
1261 1652 1.550072 TCATCTCAATGACTCCGTGCA 59.450 47.619 0.00 0.00 36.98 4.57
1262 1653 1.662629 CATCTCAATGACTCCGTGCAC 59.337 52.381 6.82 6.82 34.61 4.57
1263 1654 0.969149 TCTCAATGACTCCGTGCACT 59.031 50.000 16.19 0.00 0.00 4.40
1264 1655 1.067565 TCTCAATGACTCCGTGCACTC 60.068 52.381 16.19 6.05 0.00 3.51
1265 1656 0.969149 TCAATGACTCCGTGCACTCT 59.031 50.000 16.19 0.00 0.00 3.24
1266 1657 1.073964 CAATGACTCCGTGCACTCTG 58.926 55.000 16.19 6.78 0.00 3.35
1267 1658 0.671781 AATGACTCCGTGCACTCTGC 60.672 55.000 16.19 1.04 45.29 4.26
1268 1659 1.539560 ATGACTCCGTGCACTCTGCT 61.540 55.000 16.19 0.00 45.31 4.24
1269 1660 1.735920 GACTCCGTGCACTCTGCTG 60.736 63.158 16.19 0.00 45.31 4.41
1270 1661 2.341543 CTCCGTGCACTCTGCTGT 59.658 61.111 16.19 0.00 45.31 4.40
1271 1662 2.025969 CTCCGTGCACTCTGCTGTG 61.026 63.158 16.19 0.00 45.31 3.66
1272 1663 2.280389 CCGTGCACTCTGCTGTGT 60.280 61.111 16.19 0.39 45.31 3.72
1278 1677 3.181530 CGTGCACTCTGCTGTGTTATTAC 60.182 47.826 16.19 0.00 45.31 1.89
1293 1692 7.208777 TGTGTTATTACTGGTTAAGTGTTCGA 58.791 34.615 0.00 0.00 40.26 3.71
1294 1693 7.874016 TGTGTTATTACTGGTTAAGTGTTCGAT 59.126 33.333 0.00 0.00 40.26 3.59
1295 1694 8.378421 GTGTTATTACTGGTTAAGTGTTCGATC 58.622 37.037 0.00 0.00 40.26 3.69
1296 1695 7.274033 TGTTATTACTGGTTAAGTGTTCGATCG 59.726 37.037 9.36 9.36 40.26 3.69
1297 1696 2.334838 ACTGGTTAAGTGTTCGATCGC 58.665 47.619 11.09 0.00 37.88 4.58
1298 1697 1.320555 CTGGTTAAGTGTTCGATCGCG 59.679 52.381 11.09 0.00 39.35 5.87
1300 1699 1.343506 GTTAAGTGTTCGATCGCGGT 58.656 50.000 11.09 0.00 38.28 5.68
1301 1700 1.058695 GTTAAGTGTTCGATCGCGGTG 59.941 52.381 11.09 0.00 38.28 4.94
1302 1701 0.241749 TAAGTGTTCGATCGCGGTGT 59.758 50.000 11.09 0.00 38.28 4.16
1303 1702 1.282248 AAGTGTTCGATCGCGGTGTG 61.282 55.000 11.09 0.00 38.28 3.82
1304 1703 2.431771 TGTTCGATCGCGGTGTGG 60.432 61.111 11.09 0.00 38.28 4.17
1305 1704 2.431942 GTTCGATCGCGGTGTGGT 60.432 61.111 11.09 0.00 38.28 4.16
1306 1705 2.126228 TTCGATCGCGGTGTGGTC 60.126 61.111 11.09 0.00 38.28 4.02
1316 1715 2.427320 GTGTGGTCTGCTCTGCCA 59.573 61.111 0.00 0.00 0.00 4.92
1321 1720 1.615392 GTGGTCTGCTCTGCCAATTTT 59.385 47.619 0.00 0.00 33.66 1.82
1322 1721 1.614903 TGGTCTGCTCTGCCAATTTTG 59.385 47.619 0.00 0.00 0.00 2.44
1333 1732 1.838913 CCAATTTTGGCCGCTATTCG 58.161 50.000 0.00 0.00 42.21 3.34
1348 1747 3.248602 GCTATTCGGTTAGATTGCTGTGG 59.751 47.826 0.00 0.00 0.00 4.17
1353 1755 2.352651 CGGTTAGATTGCTGTGGTGATG 59.647 50.000 0.00 0.00 0.00 3.07
1370 1772 3.441572 GTGATGAGAGTGGATTTGGTTGG 59.558 47.826 0.00 0.00 0.00 3.77
1407 1809 0.815734 GGCCGACAGAGCACTAGTTA 59.184 55.000 0.00 0.00 0.00 2.24
1461 1863 1.354337 CGAGTCTGGTTGCACATCCG 61.354 60.000 0.00 0.00 0.00 4.18
1462 1864 1.003355 AGTCTGGTTGCACATCCGG 60.003 57.895 0.00 0.00 0.00 5.14
1463 1865 2.040544 GTCTGGTTGCACATCCGGG 61.041 63.158 0.00 0.00 0.00 5.73
1464 1866 2.751436 CTGGTTGCACATCCGGGG 60.751 66.667 0.00 0.00 0.00 5.73
1466 1868 4.740822 GGTTGCACATCCGGGGCT 62.741 66.667 0.00 0.00 0.00 5.19
1468 1870 1.819632 GTTGCACATCCGGGGCTAG 60.820 63.158 0.00 0.00 0.00 3.42
1470 1872 3.866582 GCACATCCGGGGCTAGCT 61.867 66.667 15.72 0.00 0.00 3.32
1472 1874 1.224592 CACATCCGGGGCTAGCTTT 59.775 57.895 15.72 0.00 0.00 3.51
1474 1876 0.331616 ACATCCGGGGCTAGCTTTTT 59.668 50.000 15.72 0.00 0.00 1.94
1525 1927 5.648526 TCCATGTTTAATCGATTTTCGGGAA 59.351 36.000 17.19 0.00 40.88 3.97
1526 1928 6.151312 TCCATGTTTAATCGATTTTCGGGAAA 59.849 34.615 17.19 6.69 40.88 3.13
1527 1929 6.252655 CCATGTTTAATCGATTTTCGGGAAAC 59.747 38.462 17.19 18.03 40.88 2.78
1528 1930 6.315091 TGTTTAATCGATTTTCGGGAAACA 57.685 33.333 21.87 21.87 40.30 2.83
1529 1931 6.144175 TGTTTAATCGATTTTCGGGAAACAC 58.856 36.000 21.87 6.59 39.11 3.32
1530 1932 5.943706 TTAATCGATTTTCGGGAAACACA 57.056 34.783 17.19 0.00 40.88 3.72
1531 1933 3.824414 ATCGATTTTCGGGAAACACAC 57.176 42.857 0.00 0.00 40.88 3.82
1532 1934 2.562635 TCGATTTTCGGGAAACACACA 58.437 42.857 0.00 0.00 40.88 3.72
1533 1935 3.142951 TCGATTTTCGGGAAACACACAT 58.857 40.909 0.00 0.00 40.88 3.21
1534 1936 3.058570 TCGATTTTCGGGAAACACACATG 60.059 43.478 0.00 0.00 40.88 3.21
1535 1937 3.304391 CGATTTTCGGGAAACACACATGT 60.304 43.478 0.00 0.00 37.08 3.21
1542 1944 2.749621 GGGAAACACACATGTCCTGATC 59.250 50.000 0.00 0.00 38.45 2.92
1546 1948 3.726557 ACACACATGTCCTGATCCAAT 57.273 42.857 0.00 0.00 31.55 3.16
1600 2002 3.190874 GGAATGGTCTGATCTGTTCGAC 58.809 50.000 0.00 0.00 0.00 4.20
1708 2111 5.959527 GCATCAGTACGACAATGTTGTAATG 59.040 40.000 26.45 26.45 44.71 1.90
1756 2166 3.441496 AGTGCAGTGTTCAATGTTTGG 57.559 42.857 0.00 0.00 0.00 3.28
1858 2300 1.534163 GGCTCCCGTTTTTGTACTGAC 59.466 52.381 0.00 0.00 0.00 3.51
1960 2413 1.808945 AGCAGCTTGTACAGATTGCAC 59.191 47.619 21.69 11.15 37.19 4.57
1965 2418 5.284079 CAGCTTGTACAGATTGCACTTTTT 58.716 37.500 12.37 0.00 0.00 1.94
2005 2459 2.887152 ACAGATGGCAGTTTTCCTGTTC 59.113 45.455 0.00 0.00 43.55 3.18
2012 2466 2.610374 GCAGTTTTCCTGTTCGTGTACA 59.390 45.455 0.00 0.00 43.55 2.90
2013 2467 3.303132 GCAGTTTTCCTGTTCGTGTACAG 60.303 47.826 0.00 7.72 43.55 2.74
2015 2469 4.750098 CAGTTTTCCTGTTCGTGTACAGAT 59.250 41.667 13.85 0.00 46.72 2.90
2016 2470 5.924254 CAGTTTTCCTGTTCGTGTACAGATA 59.076 40.000 13.85 2.90 46.72 1.98
2017 2471 6.089551 CAGTTTTCCTGTTCGTGTACAGATAG 59.910 42.308 13.85 0.00 46.72 2.08
2018 2472 5.970317 TTTCCTGTTCGTGTACAGATAGA 57.030 39.130 13.85 0.00 46.72 1.98
2019 2473 5.562506 TTCCTGTTCGTGTACAGATAGAG 57.437 43.478 13.85 0.00 46.72 2.43
2020 2474 4.586884 TCCTGTTCGTGTACAGATAGAGT 58.413 43.478 13.85 0.00 46.72 3.24
2021 2475 4.634883 TCCTGTTCGTGTACAGATAGAGTC 59.365 45.833 13.85 0.00 46.72 3.36
2052 2514 1.390123 CATGATCACGACGTGGTGTTC 59.610 52.381 26.72 26.23 39.00 3.18
2089 2551 2.504367 ACTGACACCTACACAATTGCC 58.496 47.619 5.05 0.00 0.00 4.52
2113 2575 2.500504 GTCTCCCATCTTCGGTTACCTT 59.499 50.000 0.00 0.00 0.00 3.50
2451 2917 1.986882 CTGGTGTTGGCCTTCTTTCT 58.013 50.000 3.32 0.00 0.00 2.52
2740 3297 5.979993 TGCATACATTTTTCTAGGTCGGTA 58.020 37.500 0.00 0.00 0.00 4.02
2741 3298 6.588204 TGCATACATTTTTCTAGGTCGGTAT 58.412 36.000 0.00 0.00 0.00 2.73
2742 3299 7.051623 TGCATACATTTTTCTAGGTCGGTATT 58.948 34.615 0.00 0.00 0.00 1.89
2743 3300 7.554835 TGCATACATTTTTCTAGGTCGGTATTT 59.445 33.333 0.00 0.00 0.00 1.40
2744 3301 8.403236 GCATACATTTTTCTAGGTCGGTATTTT 58.597 33.333 0.00 0.00 0.00 1.82
2769 3326 6.462073 TTTTCGAGAATGTTTTCTAGGACG 57.538 37.500 0.00 0.00 42.34 4.79
4660 6705 3.119173 CCTTGGTTTTGTTGTCTTCTGCA 60.119 43.478 0.00 0.00 0.00 4.41
4718 6763 9.405587 TCTTGTAGTATGTTTTATTTGCTTTGC 57.594 29.630 0.00 0.00 0.00 3.68
4754 6799 4.574828 CCCAGTAAATTTCCTATGGACACG 59.425 45.833 10.75 0.00 0.00 4.49
4793 6838 6.606796 TGATGGATGGTGCATAAACTTTACAT 59.393 34.615 0.00 0.00 0.00 2.29
4848 6893 6.237915 GCAAAGTGGCTCATTACAAATAATGC 60.238 38.462 2.74 0.00 45.07 3.56
4900 6946 7.552687 AGCATCTTGATTCATTGCATTTTCAAT 59.447 29.630 15.06 0.00 37.16 2.57
5061 7107 1.471119 TCCTGTAGGCTCCGTTACAG 58.529 55.000 7.28 7.28 43.97 2.74
5064 7110 0.892755 TGTAGGCTCCGTTACAGGTG 59.107 55.000 0.00 0.00 0.00 4.00
5375 7424 8.737168 AGCTGCACATAATAAGAAAATCTGTA 57.263 30.769 1.02 0.00 0.00 2.74
5426 7475 6.900568 TTTTTGGTGTGCTAAAATTGACTG 57.099 33.333 0.00 0.00 35.51 3.51
5460 7509 5.703130 GGGCTGTTCATGAGAATAATAGTCC 59.297 44.000 0.00 0.00 35.92 3.85
5468 7517 6.441924 TCATGAGAATAATAGTCCCATCCTCC 59.558 42.308 0.00 0.00 0.00 4.30
5536 7624 2.554032 CGGATGTGCTCCTTTTGACTTT 59.446 45.455 0.00 0.00 42.47 2.66
5537 7625 3.365364 CGGATGTGCTCCTTTTGACTTTC 60.365 47.826 0.00 0.00 42.47 2.62
5539 7627 4.279420 GGATGTGCTCCTTTTGACTTTCTT 59.721 41.667 0.00 0.00 41.29 2.52
5544 7632 4.099881 TGCTCCTTTTGACTTTCTTTGCAT 59.900 37.500 0.00 0.00 0.00 3.96
5695 7792 7.060383 TCTGAACACTCAAGATTTCTCTCTT 57.940 36.000 0.00 0.00 35.88 2.85
5705 7802 6.765036 TCAAGATTTCTCTCTTCATACCATGC 59.235 38.462 0.00 0.00 33.18 4.06
5732 7836 1.301716 AGGTGATTGCAAGCGTCGT 60.302 52.632 10.55 4.77 0.00 4.34
5761 7865 0.036732 GGTTGGAGTCATCAGTGCCA 59.963 55.000 0.00 0.00 0.00 4.92
5805 7909 3.774766 TGGCCAGCATAATCGGATACTAT 59.225 43.478 0.00 0.00 0.00 2.12
5899 8003 5.597806 TCATCGAATTTTACCGTGCTCTAT 58.402 37.500 0.00 0.00 0.00 1.98
5900 8004 5.462068 TCATCGAATTTTACCGTGCTCTATG 59.538 40.000 0.00 0.00 0.00 2.23
5918 8022 3.526931 ATGTGTACATCCTTCGACCTG 57.473 47.619 0.00 0.00 28.78 4.00
6036 8155 3.132111 CCCTGCGGTTTAAATATTGCCTT 59.868 43.478 0.00 0.00 0.00 4.35
6296 8415 4.584327 ATTAACCCGAAATATTGCCTGC 57.416 40.909 0.00 0.00 0.00 4.85
6305 8425 2.335092 ATATTGCCTGCTGCTCCGCT 62.335 55.000 0.00 0.00 42.00 5.52
6397 8750 4.217550 CGAAATGGACACAGTAAAATGGGT 59.782 41.667 0.00 0.00 40.30 4.51
6408 8761 1.560505 AAAATGGGTCAGGATGCACC 58.439 50.000 0.00 0.00 36.14 5.01
6459 8812 0.258774 TGGGCTGGAATTTAGGGCTC 59.741 55.000 0.00 0.00 0.00 4.70
6497 8879 1.969589 GTACGTGGGTTGGGCCTTG 60.970 63.158 4.53 0.00 37.43 3.61
6530 8914 2.033801 CCTCCTGTGCACTTTGAACAAG 59.966 50.000 19.41 3.91 0.00 3.16
6574 8991 8.450578 TGATTTCTGAGTTTCTAAAAAGCTGA 57.549 30.769 0.00 0.00 0.00 4.26
6575 8992 8.902806 TGATTTCTGAGTTTCTAAAAAGCTGAA 58.097 29.630 0.00 0.00 0.00 3.02
6576 8993 9.736023 GATTTCTGAGTTTCTAAAAAGCTGAAA 57.264 29.630 0.00 0.00 35.19 2.69
6617 9035 7.384439 TCTCATAAAAATACGACCATTTGCA 57.616 32.000 0.00 0.00 0.00 4.08
6625 9043 7.801716 AAATACGACCATTTGCAGTATGTAT 57.198 32.000 9.27 3.81 39.31 2.29
6687 9106 6.552859 GCTTCTATCCCTCTAAGCAAATTC 57.447 41.667 0.00 0.00 43.00 2.17
6742 9162 2.421751 TTTTCAAACCGACTCCACCA 57.578 45.000 0.00 0.00 0.00 4.17
6783 9204 5.960202 AGAAATCCCTTGTAAGGCAATCAAT 59.040 36.000 5.11 0.00 45.10 2.57
6803 9224 6.491394 TCAATAGAAATCAAATAAACCGCCG 58.509 36.000 0.00 0.00 0.00 6.46
6817 9506 3.261981 ACCGCCGATAACAAGAAATCT 57.738 42.857 0.00 0.00 0.00 2.40
6878 9600 6.904498 AGTTCTATGTATACAGTCTCATCGC 58.096 40.000 11.91 0.00 0.00 4.58
6901 9623 8.234546 TCGCATTTTTCCTTATCTTTTGACTAC 58.765 33.333 0.00 0.00 0.00 2.73
6910 9636 7.048512 CCTTATCTTTTGACTACGGATTCCTT 58.951 38.462 0.30 0.00 0.00 3.36
6912 9638 5.740290 TCTTTTGACTACGGATTCCTTCT 57.260 39.130 0.30 0.00 0.00 2.85
6913 9639 5.721232 TCTTTTGACTACGGATTCCTTCTC 58.279 41.667 0.30 0.00 0.00 2.87
6914 9640 5.480772 TCTTTTGACTACGGATTCCTTCTCT 59.519 40.000 0.30 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.754965 TGGGTTCTCTTTGGAACATCTG 58.245 45.455 9.12 0.00 45.07 2.90
18 19 4.202609 ACATGGGTTCTCTTTGGAACATCT 60.203 41.667 0.00 0.00 45.07 2.90
132 133 7.804843 TCTTCCATGCAAAAACAATTTGAAT 57.195 28.000 2.79 0.00 0.00 2.57
134 135 6.205076 CCATCTTCCATGCAAAAACAATTTGA 59.795 34.615 2.79 0.00 0.00 2.69
141 142 4.525912 AGACCATCTTCCATGCAAAAAC 57.474 40.909 0.00 0.00 0.00 2.43
323 324 2.609491 GGCCCGTCCAAAATTTCAACTC 60.609 50.000 0.00 0.00 34.01 3.01
342 343 8.673711 TGTGAAATATATTTTAGTGTGTGAGGC 58.326 33.333 11.92 0.00 0.00 4.70
409 420 3.599343 CTCATCGGATCTTGGTGAACAA 58.401 45.455 3.62 0.00 37.55 2.83
418 429 1.974265 TCGAGAGCTCATCGGATCTT 58.026 50.000 25.15 1.51 40.54 2.40
424 435 0.588737 TTCGGATCGAGAGCTCATCG 59.411 55.000 21.94 21.94 41.50 3.84
453 464 9.634163 GTACCGTATATTCATCATTCATACACA 57.366 33.333 0.00 0.00 0.00 3.72
574 944 1.536418 CTCTGACCTGTGGGACCCA 60.536 63.158 9.95 9.95 36.25 4.51
575 945 1.229209 TCTCTGACCTGTGGGACCC 60.229 63.158 2.45 2.45 36.25 4.46
697 1067 1.339151 GGAAGTTGCTCGATTGGAGGT 60.339 52.381 0.00 0.00 43.36 3.85
709 1079 2.035783 GGGGGTGGAGGAAGTTGC 59.964 66.667 0.00 0.00 0.00 4.17
715 1085 3.864983 GAGTGGTGGGGGTGGAGGA 62.865 68.421 0.00 0.00 0.00 3.71
803 1173 4.818835 GCTGCGCTTGCTTACGGC 62.819 66.667 9.73 0.00 40.12 5.68
854 1226 4.401925 GGGGATGAAATAGTTGGAGATGG 58.598 47.826 0.00 0.00 0.00 3.51
891 1263 0.383949 GGTTTTTGGACGAGCAAGCA 59.616 50.000 0.00 0.00 0.00 3.91
895 1267 2.018544 CGTGGTTTTTGGACGAGCA 58.981 52.632 0.00 0.00 35.05 4.26
907 1279 4.090819 AGGTAAAATTATTGGGCGTGGTT 58.909 39.130 0.00 0.00 0.00 3.67
909 1281 3.067601 GGAGGTAAAATTATTGGGCGTGG 59.932 47.826 0.00 0.00 0.00 4.94
910 1282 3.067601 GGGAGGTAAAATTATTGGGCGTG 59.932 47.826 0.00 0.00 0.00 5.34
911 1283 3.053170 AGGGAGGTAAAATTATTGGGCGT 60.053 43.478 0.00 0.00 0.00 5.68
912 1284 3.562182 AGGGAGGTAAAATTATTGGGCG 58.438 45.455 0.00 0.00 0.00 6.13
913 1285 3.895656 GGAGGGAGGTAAAATTATTGGGC 59.104 47.826 0.00 0.00 0.00 5.36
914 1286 4.480115 GGGAGGGAGGTAAAATTATTGGG 58.520 47.826 0.00 0.00 0.00 4.12
915 1287 4.170053 AGGGGAGGGAGGTAAAATTATTGG 59.830 45.833 0.00 0.00 0.00 3.16
916 1288 5.403558 AGGGGAGGGAGGTAAAATTATTG 57.596 43.478 0.00 0.00 0.00 1.90
917 1289 5.374753 GGTAGGGGAGGGAGGTAAAATTATT 59.625 44.000 0.00 0.00 0.00 1.40
918 1290 4.918273 GGTAGGGGAGGGAGGTAAAATTAT 59.082 45.833 0.00 0.00 0.00 1.28
919 1291 4.265864 TGGTAGGGGAGGGAGGTAAAATTA 60.266 45.833 0.00 0.00 0.00 1.40
920 1292 3.128848 GGTAGGGGAGGGAGGTAAAATT 58.871 50.000 0.00 0.00 0.00 1.82
921 1293 2.048150 TGGTAGGGGAGGGAGGTAAAAT 59.952 50.000 0.00 0.00 0.00 1.82
922 1294 1.441956 TGGTAGGGGAGGGAGGTAAAA 59.558 52.381 0.00 0.00 0.00 1.52
948 1320 2.010582 GCGACGCTTCCAGAGGAGAT 62.011 60.000 13.73 0.00 31.21 2.75
1035 1407 4.521062 CCTCCTTCCGCTGCCTCG 62.521 72.222 0.00 0.00 0.00 4.63
1037 1409 3.080121 CTCCTCCTTCCGCTGCCT 61.080 66.667 0.00 0.00 0.00 4.75
1038 1410 4.168291 CCTCCTCCTTCCGCTGCC 62.168 72.222 0.00 0.00 0.00 4.85
1039 1411 3.077556 TCCTCCTCCTTCCGCTGC 61.078 66.667 0.00 0.00 0.00 5.25
1040 1412 2.430610 CCTCCTCCTCCTTCCGCTG 61.431 68.421 0.00 0.00 0.00 5.18
1041 1413 2.042435 CCTCCTCCTCCTTCCGCT 60.042 66.667 0.00 0.00 0.00 5.52
1042 1414 2.042843 TCCTCCTCCTCCTTCCGC 60.043 66.667 0.00 0.00 0.00 5.54
1229 1620 1.986882 TGAGATGAGGCGATAGAGCA 58.013 50.000 0.00 0.00 39.27 4.26
1234 1625 3.256879 GGAGTCATTGAGATGAGGCGATA 59.743 47.826 0.00 0.00 42.73 2.92
1235 1626 2.036992 GGAGTCATTGAGATGAGGCGAT 59.963 50.000 0.00 0.00 42.73 4.58
1243 1634 1.552337 AGTGCACGGAGTCATTGAGAT 59.448 47.619 12.01 0.00 41.61 2.75
1247 1638 1.073964 CAGAGTGCACGGAGTCATTG 58.926 55.000 12.01 0.00 41.61 2.82
1248 1639 0.671781 GCAGAGTGCACGGAGTCATT 60.672 55.000 12.01 0.00 41.61 2.57
1259 1650 3.372206 CCAGTAATAACACAGCAGAGTGC 59.628 47.826 4.18 0.00 45.46 4.40
1261 1652 4.891992 ACCAGTAATAACACAGCAGAGT 57.108 40.909 0.00 0.00 0.00 3.24
1262 1653 6.874134 ACTTAACCAGTAATAACACAGCAGAG 59.126 38.462 0.00 0.00 31.97 3.35
1263 1654 6.649141 CACTTAACCAGTAATAACACAGCAGA 59.351 38.462 0.00 0.00 32.76 4.26
1264 1655 6.426937 ACACTTAACCAGTAATAACACAGCAG 59.573 38.462 0.00 0.00 32.76 4.24
1265 1656 6.292923 ACACTTAACCAGTAATAACACAGCA 58.707 36.000 0.00 0.00 32.76 4.41
1266 1657 6.796705 ACACTTAACCAGTAATAACACAGC 57.203 37.500 0.00 0.00 32.76 4.40
1267 1658 7.383029 TCGAACACTTAACCAGTAATAACACAG 59.617 37.037 0.00 0.00 32.76 3.66
1268 1659 7.208777 TCGAACACTTAACCAGTAATAACACA 58.791 34.615 0.00 0.00 32.76 3.72
1269 1660 7.642071 TCGAACACTTAACCAGTAATAACAC 57.358 36.000 0.00 0.00 32.76 3.32
1270 1661 7.274033 CGATCGAACACTTAACCAGTAATAACA 59.726 37.037 10.26 0.00 32.76 2.41
1271 1662 7.607005 CGATCGAACACTTAACCAGTAATAAC 58.393 38.462 10.26 0.00 32.76 1.89
1272 1663 6.254157 GCGATCGAACACTTAACCAGTAATAA 59.746 38.462 21.57 0.00 32.76 1.40
1278 1677 1.320555 CGCGATCGAACACTTAACCAG 59.679 52.381 21.57 0.00 38.10 4.00
1293 1692 3.649277 GAGCAGACCACACCGCGAT 62.649 63.158 8.23 0.00 0.00 4.58
1294 1693 4.357947 GAGCAGACCACACCGCGA 62.358 66.667 8.23 0.00 0.00 5.87
1295 1694 4.363990 AGAGCAGACCACACCGCG 62.364 66.667 0.00 0.00 0.00 6.46
1296 1695 2.740055 CAGAGCAGACCACACCGC 60.740 66.667 0.00 0.00 0.00 5.68
1297 1696 2.740055 GCAGAGCAGACCACACCG 60.740 66.667 0.00 0.00 0.00 4.94
1298 1697 2.359230 GGCAGAGCAGACCACACC 60.359 66.667 0.00 0.00 0.00 4.16
1300 1699 0.111061 AATTGGCAGAGCAGACCACA 59.889 50.000 0.00 0.00 31.83 4.17
1301 1700 1.251251 AAATTGGCAGAGCAGACCAC 58.749 50.000 0.00 0.00 31.83 4.16
1302 1701 1.614903 CAAAATTGGCAGAGCAGACCA 59.385 47.619 0.00 0.00 0.00 4.02
1303 1702 1.067354 CCAAAATTGGCAGAGCAGACC 60.067 52.381 0.00 0.00 42.21 3.85
1304 1703 2.358939 CCAAAATTGGCAGAGCAGAC 57.641 50.000 0.00 0.00 42.21 3.51
1333 1732 3.609853 TCATCACCACAGCAATCTAACC 58.390 45.455 0.00 0.00 0.00 2.85
1336 1735 3.771479 ACTCTCATCACCACAGCAATCTA 59.229 43.478 0.00 0.00 0.00 1.98
1341 1740 0.322648 CCACTCTCATCACCACAGCA 59.677 55.000 0.00 0.00 0.00 4.41
1348 1747 3.441572 CCAACCAAATCCACTCTCATCAC 59.558 47.826 0.00 0.00 0.00 3.06
1353 1755 2.206576 AGCCAACCAAATCCACTCTC 57.793 50.000 0.00 0.00 0.00 3.20
1370 1772 0.740737 CCATTCCCAATCACCGAAGC 59.259 55.000 0.00 0.00 0.00 3.86
1407 1809 3.079578 CAGTGAATCCACATGCAGAACT 58.920 45.455 0.00 0.00 45.54 3.01
1477 1879 1.001406 CTAGCCCCGGATGTCTTCATC 59.999 57.143 0.73 0.22 46.82 2.92
1478 1880 1.051812 CTAGCCCCGGATGTCTTCAT 58.948 55.000 0.73 0.00 36.95 2.57
1479 1881 1.686325 GCTAGCCCCGGATGTCTTCA 61.686 60.000 0.73 0.00 0.00 3.02
1480 1882 1.069935 GCTAGCCCCGGATGTCTTC 59.930 63.158 0.73 0.00 0.00 2.87
1481 1883 1.383248 AGCTAGCCCCGGATGTCTT 60.383 57.895 12.13 0.00 0.00 3.01
1482 1884 2.136878 CAGCTAGCCCCGGATGTCT 61.137 63.158 12.13 0.00 0.00 3.41
1483 1885 2.370647 GACAGCTAGCCCCGGATGTC 62.371 65.000 12.13 13.56 40.67 3.06
1484 1886 2.365635 ACAGCTAGCCCCGGATGT 60.366 61.111 12.13 5.05 0.00 3.06
1485 1887 2.423446 GACAGCTAGCCCCGGATG 59.577 66.667 12.13 4.32 0.00 3.51
1486 1888 2.844839 GGACAGCTAGCCCCGGAT 60.845 66.667 12.13 0.00 0.00 4.18
1487 1889 3.696518 ATGGACAGCTAGCCCCGGA 62.697 63.158 12.13 0.00 0.00 5.14
1488 1890 3.164269 ATGGACAGCTAGCCCCGG 61.164 66.667 12.13 0.00 0.00 5.73
1489 1891 2.109799 CATGGACAGCTAGCCCCG 59.890 66.667 12.13 2.68 0.00 5.73
1525 1927 3.507162 TTGGATCAGGACATGTGTGTT 57.493 42.857 1.15 0.00 39.09 3.32
1526 1928 3.265221 AGATTGGATCAGGACATGTGTGT 59.735 43.478 1.15 0.00 42.49 3.72
1527 1929 3.875727 GAGATTGGATCAGGACATGTGTG 59.124 47.826 1.15 0.00 0.00 3.82
1528 1930 3.431346 CGAGATTGGATCAGGACATGTGT 60.431 47.826 1.15 0.00 0.00 3.72
1529 1931 3.129109 CGAGATTGGATCAGGACATGTG 58.871 50.000 1.15 0.00 0.00 3.21
1530 1932 2.103771 CCGAGATTGGATCAGGACATGT 59.896 50.000 0.00 0.00 33.10 3.21
1531 1933 2.366590 TCCGAGATTGGATCAGGACATG 59.633 50.000 0.00 0.00 34.78 3.21
1532 1934 2.632028 CTCCGAGATTGGATCAGGACAT 59.368 50.000 0.00 0.00 37.41 3.06
1533 1935 2.034878 CTCCGAGATTGGATCAGGACA 58.965 52.381 0.00 0.00 37.41 4.02
1534 1936 2.035632 ACTCCGAGATTGGATCAGGAC 58.964 52.381 1.33 0.00 37.41 3.85
1535 1937 2.034878 CACTCCGAGATTGGATCAGGA 58.965 52.381 1.33 5.48 37.41 3.86
1542 1944 0.390860 CTAGGCCACTCCGAGATTGG 59.609 60.000 5.01 1.37 39.66 3.16
1546 1948 0.331954 AACTCTAGGCCACTCCGAGA 59.668 55.000 5.01 0.00 43.18 4.04
1600 2002 2.038952 TCAGTCAACCTTGGTCATCTGG 59.961 50.000 13.54 0.00 0.00 3.86
1756 2166 0.391263 GCCAGGTGTACAGGTAGTGC 60.391 60.000 0.00 0.00 0.00 4.40
1809 2224 9.811995 TGATGAAGCAAAATAATACTACGTACT 57.188 29.630 0.00 0.00 0.00 2.73
1812 2227 9.935682 CATTGATGAAGCAAAATAATACTACGT 57.064 29.630 0.00 0.00 0.00 3.57
1813 2228 9.385902 CCATTGATGAAGCAAAATAATACTACG 57.614 33.333 0.00 0.00 0.00 3.51
1858 2300 7.592938 TGATGCTTTATTTCTTGTTACACCAG 58.407 34.615 0.00 0.00 0.00 4.00
2005 2459 6.562455 CGTCTGTATGACTCTATCTGTACACG 60.562 46.154 0.00 0.00 43.25 4.49
2012 2466 3.821748 TGCCGTCTGTATGACTCTATCT 58.178 45.455 0.00 0.00 43.25 1.98
2013 2467 4.216472 TCATGCCGTCTGTATGACTCTATC 59.784 45.833 0.00 0.00 40.61 2.08
2015 2469 3.551846 TCATGCCGTCTGTATGACTCTA 58.448 45.455 0.00 0.00 40.61 2.43
2016 2470 2.379005 TCATGCCGTCTGTATGACTCT 58.621 47.619 0.00 0.00 40.61 3.24
2017 2471 2.871182 TCATGCCGTCTGTATGACTC 57.129 50.000 0.00 0.00 40.61 3.36
2018 2472 2.695147 TGATCATGCCGTCTGTATGACT 59.305 45.455 0.00 0.00 46.84 3.41
2019 2473 2.797156 GTGATCATGCCGTCTGTATGAC 59.203 50.000 0.00 0.00 46.84 3.06
2021 2475 1.788886 CGTGATCATGCCGTCTGTATG 59.211 52.381 1.07 0.00 38.32 2.39
2052 2514 3.803778 GTCAGTTGTTTCCCTGCAAAATG 59.196 43.478 0.00 0.00 0.00 2.32
2089 2551 2.278857 CCGAAGATGGGAGACGCG 60.279 66.667 3.53 3.53 0.00 6.01
2451 2917 2.777094 TCATGAATTGTGAACGGAGCA 58.223 42.857 0.00 0.00 0.00 4.26
2745 3302 6.073440 CCGTCCTAGAAAACATTCTCGAAAAA 60.073 38.462 0.00 0.00 32.72 1.94
2746 3303 5.407387 CCGTCCTAGAAAACATTCTCGAAAA 59.593 40.000 0.00 0.00 32.72 2.29
2747 3304 4.927425 CCGTCCTAGAAAACATTCTCGAAA 59.073 41.667 0.00 0.00 32.72 3.46
2748 3305 4.021719 ACCGTCCTAGAAAACATTCTCGAA 60.022 41.667 0.00 0.00 32.72 3.71
2749 3306 3.508793 ACCGTCCTAGAAAACATTCTCGA 59.491 43.478 0.00 0.00 32.72 4.04
2750 3307 3.846360 ACCGTCCTAGAAAACATTCTCG 58.154 45.455 0.00 0.00 32.72 4.04
2751 3308 9.543783 AATAATACCGTCCTAGAAAACATTCTC 57.456 33.333 0.00 0.00 32.72 2.87
2752 3309 9.543783 GAATAATACCGTCCTAGAAAACATTCT 57.456 33.333 0.00 0.00 35.17 2.40
2753 3310 8.485591 CGAATAATACCGTCCTAGAAAACATTC 58.514 37.037 0.00 0.00 0.00 2.67
2754 3311 7.042254 GCGAATAATACCGTCCTAGAAAACATT 60.042 37.037 0.00 0.00 0.00 2.71
2755 3312 6.423001 GCGAATAATACCGTCCTAGAAAACAT 59.577 38.462 0.00 0.00 0.00 2.71
2756 3313 5.750067 GCGAATAATACCGTCCTAGAAAACA 59.250 40.000 0.00 0.00 0.00 2.83
2757 3314 5.981915 AGCGAATAATACCGTCCTAGAAAAC 59.018 40.000 0.00 0.00 0.00 2.43
2758 3315 6.152932 AGCGAATAATACCGTCCTAGAAAA 57.847 37.500 0.00 0.00 0.00 2.29
2759 3316 5.779529 AGCGAATAATACCGTCCTAGAAA 57.220 39.130 0.00 0.00 0.00 2.52
2760 3317 5.779529 AAGCGAATAATACCGTCCTAGAA 57.220 39.130 0.00 0.00 0.00 2.10
2761 3318 5.068198 ACAAAGCGAATAATACCGTCCTAGA 59.932 40.000 0.00 0.00 0.00 2.43
2762 3319 5.287226 ACAAAGCGAATAATACCGTCCTAG 58.713 41.667 0.00 0.00 0.00 3.02
2763 3320 5.266733 ACAAAGCGAATAATACCGTCCTA 57.733 39.130 0.00 0.00 0.00 2.94
2764 3321 4.133013 ACAAAGCGAATAATACCGTCCT 57.867 40.909 0.00 0.00 0.00 3.85
2765 3322 4.495184 CCAACAAAGCGAATAATACCGTCC 60.495 45.833 0.00 0.00 0.00 4.79
2766 3323 4.093850 ACCAACAAAGCGAATAATACCGTC 59.906 41.667 0.00 0.00 0.00 4.79
2767 3324 4.004982 ACCAACAAAGCGAATAATACCGT 58.995 39.130 0.00 0.00 0.00 4.83
2768 3325 4.609691 ACCAACAAAGCGAATAATACCG 57.390 40.909 0.00 0.00 0.00 4.02
2769 3326 9.442033 GTTTATACCAACAAAGCGAATAATACC 57.558 33.333 0.00 0.00 0.00 2.73
3741 4414 0.238289 GAGTTGCAATCACACCACCG 59.762 55.000 0.59 0.00 0.00 4.94
4718 6763 8.826710 GGAAATTTACTGGGTTTTCAAGAAAAG 58.173 33.333 8.14 0.16 40.53 2.27
4754 6799 5.069516 ACCATCCATCATTCCAAAGTAATGC 59.930 40.000 0.00 0.00 34.89 3.56
4793 6838 1.988293 TTCCGAGGGAAACAATTGCA 58.012 45.000 5.05 0.00 38.93 4.08
4848 6893 9.268268 TGTTTTCAACTACTAATCTTGGTACTG 57.732 33.333 0.00 0.00 0.00 2.74
5042 7088 1.471119 CTGTAACGGAGCCTACAGGA 58.529 55.000 0.00 0.00 41.04 3.86
5061 7107 6.811665 GGAAGTGTTTTAGGAATATTTGCACC 59.188 38.462 0.00 0.00 0.00 5.01
5062 7108 7.602753 AGGAAGTGTTTTAGGAATATTTGCAC 58.397 34.615 0.00 0.00 0.00 4.57
5064 7110 8.523658 AGAAGGAAGTGTTTTAGGAATATTTGC 58.476 33.333 0.00 0.00 0.00 3.68
5155 7202 7.376866 CGCCAATAATAAAGTACAAAGCAGATG 59.623 37.037 0.00 0.00 0.00 2.90
5474 7524 4.062677 TCTTACGCAACTGTAGGTTTGT 57.937 40.909 0.00 0.00 35.74 2.83
5556 7644 1.321474 CACAAGGCGGGCATTATGAT 58.679 50.000 3.78 0.00 0.00 2.45
5705 7802 3.731867 GCTTGCAATCACCTGAATAACCG 60.732 47.826 0.00 0.00 0.00 4.44
5732 7836 8.204160 CACTGATGACTCCAACCACTATTATAA 58.796 37.037 0.00 0.00 0.00 0.98
5761 7865 0.679321 GAGGAGTACGTTCCGAGGGT 60.679 60.000 0.00 0.00 42.29 4.34
5805 7909 4.927049 AGAGATTGCCTTGGAAGAATCAA 58.073 39.130 0.00 0.00 0.00 2.57
5899 8003 1.548719 CCAGGTCGAAGGATGTACACA 59.451 52.381 0.00 0.00 0.00 3.72
5900 8004 1.549170 ACCAGGTCGAAGGATGTACAC 59.451 52.381 0.00 0.00 0.00 2.90
5918 8022 9.640963 ATGCAGTCTTTATAAATCGACTATACC 57.359 33.333 15.82 8.56 35.15 2.73
5970 8082 7.503566 ACACCAAATGATATAGCAGCTAAATGT 59.496 33.333 6.13 0.00 0.00 2.71
6328 8448 4.133820 TCGACTCAGAATTGCCTCAAAAA 58.866 39.130 0.00 0.00 0.00 1.94
6329 8449 3.738982 TCGACTCAGAATTGCCTCAAAA 58.261 40.909 0.00 0.00 0.00 2.44
6330 8450 3.401033 TCGACTCAGAATTGCCTCAAA 57.599 42.857 0.00 0.00 0.00 2.69
6331 8451 3.244215 ACTTCGACTCAGAATTGCCTCAA 60.244 43.478 0.00 0.00 0.00 3.02
6332 8452 2.300152 ACTTCGACTCAGAATTGCCTCA 59.700 45.455 0.00 0.00 0.00 3.86
6333 8453 2.966050 ACTTCGACTCAGAATTGCCTC 58.034 47.619 0.00 0.00 0.00 4.70
6334 8454 3.070018 CAACTTCGACTCAGAATTGCCT 58.930 45.455 0.00 0.00 0.00 4.75
6335 8455 2.413371 GCAACTTCGACTCAGAATTGCC 60.413 50.000 11.82 0.00 37.92 4.52
6336 8456 2.481952 AGCAACTTCGACTCAGAATTGC 59.518 45.455 13.57 13.57 40.56 3.56
6337 8457 3.124297 GGAGCAACTTCGACTCAGAATTG 59.876 47.826 2.83 0.00 31.88 2.32
6338 8458 3.244215 TGGAGCAACTTCGACTCAGAATT 60.244 43.478 2.83 0.00 31.88 2.17
6339 8459 2.300152 TGGAGCAACTTCGACTCAGAAT 59.700 45.455 2.83 0.00 31.88 2.40
6397 8750 2.615465 CCCTTGGGGTGCATCCTGA 61.615 63.158 17.44 3.68 38.25 3.86
6408 8761 1.456331 CCTGCCATAAGCCCTTGGG 60.456 63.158 0.32 0.32 42.71 4.12
6422 8775 1.523758 CACCTACTGAAACCACCTGC 58.476 55.000 0.00 0.00 0.00 4.85
6459 8812 2.280389 ATATCACCAGCTGGCGCG 60.280 61.111 33.06 20.83 42.32 6.86
6497 8879 2.799562 GCACAGGAGGCAGAAACAAAAC 60.800 50.000 0.00 0.00 0.00 2.43
6530 8914 1.326852 CAGAATGATCTGCACGACTGC 59.673 52.381 0.00 0.00 46.11 4.40
6684 9103 7.378181 AGTTATCGCATGGTTTGAAAAAGAAT 58.622 30.769 0.00 0.00 0.00 2.40
6687 9106 6.089417 GGAAGTTATCGCATGGTTTGAAAAAG 59.911 38.462 0.00 0.00 0.00 2.27
6742 9162 3.825908 TTCTTGCCCCAGAAATAAGGT 57.174 42.857 0.00 0.00 29.41 3.50
6783 9204 7.280428 TGTTATCGGCGGTTTATTTGATTTCTA 59.720 33.333 7.21 0.00 0.00 2.10
6817 9506 6.974932 TTATTTTGTTGTTTGCTTGCAAGA 57.025 29.167 30.39 12.25 0.00 3.02
6858 9574 8.526218 AAAATGCGATGAGACTGTATACATAG 57.474 34.615 5.91 0.00 0.00 2.23
6869 9585 6.610741 AGATAAGGAAAAATGCGATGAGAC 57.389 37.500 0.00 0.00 0.00 3.36
6878 9600 8.726988 TCCGTAGTCAAAAGATAAGGAAAAATG 58.273 33.333 0.00 0.00 0.00 2.32
6901 9623 3.664107 TGTTGTGAAGAGAAGGAATCCG 58.336 45.455 0.00 0.00 0.00 4.18
6910 9636 8.071177 TGAGATTGAGATATGTTGTGAAGAGA 57.929 34.615 0.00 0.00 0.00 3.10
6912 9638 7.845037 ACTGAGATTGAGATATGTTGTGAAGA 58.155 34.615 0.00 0.00 0.00 2.87
6913 9639 7.980662 AGACTGAGATTGAGATATGTTGTGAAG 59.019 37.037 0.00 0.00 0.00 3.02
6914 9640 7.845037 AGACTGAGATTGAGATATGTTGTGAA 58.155 34.615 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.