Multiple sequence alignment - TraesCS5D01G286200

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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 TraesCS5D01G286200 chr5D 100.000 3607 0 0 1 3607 386644893 386648499 0.000000e+00 6661.0
1 TraesCS5D01G286200 chr5D 83.218 721 68 26 1925 2608 386687783 386687079 2.380000e-171 612.0
2 TraesCS5D01G286200 chr5D 88.838 439 44 4 128 561 566042817 566043255 5.300000e-148 534.0
3 TraesCS5D01G286200 chr5A 91.347 913 42 18 2128 3032 488255863 488256746 0.000000e+00 1214.0
4 TraesCS5D01G286200 chr5A 88.584 911 56 29 711 1582 488254522 488255423 0.000000e+00 1062.0
5 TraesCS5D01G286200 chr5A 92.342 444 29 4 1606 2046 488255418 488255859 8.500000e-176 627.0
6 TraesCS5D01G286200 chr5A 82.182 724 77 30 1925 2608 488316605 488315894 3.120000e-160 575.0
7 TraesCS5D01G286200 chr5A 78.691 596 57 35 978 1531 676106599 676107166 2.080000e-87 333.0
8 TraesCS5D01G286200 chr5A 95.135 185 9 0 3204 3388 488256922 488257106 3.520000e-75 292.0
9 TraesCS5D01G286200 chr5A 88.824 170 3 8 3432 3591 488257310 488257473 1.020000e-45 195.0
10 TraesCS5D01G286200 chr5A 99.065 107 0 1 1 106 488253152 488253258 1.320000e-44 191.0
11 TraesCS5D01G286200 chr5B 88.235 1037 74 22 111 1118 464319811 464320828 0.000000e+00 1195.0
12 TraesCS5D01G286200 chr5B 92.565 807 48 9 1974 2776 464321963 464322761 0.000000e+00 1147.0
13 TraesCS5D01G286200 chr5B 86.490 829 68 19 111 915 464315772 464316580 0.000000e+00 870.0
14 TraesCS5D01G286200 chr5B 86.369 829 71 18 111 915 464318464 464319274 0.000000e+00 867.0
15 TraesCS5D01G286200 chr5B 86.128 829 73 20 111 915 464317117 464317927 0.000000e+00 856.0
16 TraesCS5D01G286200 chr5B 86.145 830 70 20 111 915 464314426 464315235 0.000000e+00 854.0
17 TraesCS5D01G286200 chr5B 82.030 729 70 32 1925 2608 464364980 464364268 6.760000e-157 564.0
18 TraesCS5D01G286200 chr5B 96.178 157 5 1 2801 2957 464322755 464322910 4.620000e-64 255.0
19 TraesCS5D01G286200 chr5B 94.194 155 5 2 3442 3592 464323274 464323428 2.170000e-57 233.0
20 TraesCS5D01G286200 chr5B 77.681 457 40 29 1100 1531 464320839 464321258 4.690000e-54 222.0
21 TraesCS5D01G286200 chr5B 96.226 106 4 0 1 106 464239840 464239945 1.330000e-39 174.0
22 TraesCS5D01G286200 chr5B 97.059 102 3 0 991 1092 464365810 464365709 4.790000e-39 172.0
23 TraesCS5D01G286200 chr5B 96.117 103 4 0 1 103 464230750 464230852 6.190000e-38 169.0
24 TraesCS5D01G286200 chr5B 94.186 86 5 0 3249 3334 464322960 464323045 8.130000e-27 132.0
25 TraesCS5D01G286200 chr1D 88.147 464 50 4 103 561 106292623 106293086 6.810000e-152 547.0
26 TraesCS5D01G286200 chr1B 87.742 465 50 6 100 558 678205127 678205590 1.470000e-148 536.0
27 TraesCS5D01G286200 chr2B 88.262 443 46 5 128 564 688429582 688430024 3.190000e-145 525.0
28 TraesCS5D01G286200 chr2B 93.617 94 6 0 9 102 183266184 183266091 1.350000e-29 141.0
29 TraesCS5D01G286200 chr7D 80.570 597 46 29 977 1531 597714893 597714325 2.610000e-106 396.0
30 TraesCS5D01G286200 chr7D 79.899 597 49 30 977 1531 597736539 597735972 4.400000e-99 372.0
31 TraesCS5D01G286200 chr7D 92.553 188 14 0 2170 2357 232497317 232497130 1.650000e-68 270.0
32 TraesCS5D01G286200 chr7D 92.308 182 14 0 2176 2357 230994998 230995179 3.570000e-65 259.0
33 TraesCS5D01G286200 chr7D 88.889 144 13 3 2465 2606 232497058 232496916 1.330000e-39 174.0
34 TraesCS5D01G286200 chr7A 79.062 597 55 37 977 1531 98531256 98530688 2.670000e-91 346.0
35 TraesCS5D01G286200 chr7A 93.617 188 12 0 2170 2357 244670920 244670733 7.620000e-72 281.0
36 TraesCS5D01G286200 chr7A 90.972 144 10 3 2465 2606 244670661 244670519 1.320000e-44 191.0
37 TraesCS5D01G286200 chr1A 78.859 596 58 38 977 1531 413415082 413414514 1.240000e-89 340.0
38 TraesCS5D01G286200 chr3D 78.224 597 55 31 977 1530 558114045 558113481 2.700000e-81 313.0
39 TraesCS5D01G286200 chr7B 93.617 188 12 0 2170 2357 203280557 203280370 7.620000e-72 281.0
40 TraesCS5D01G286200 chr7B 89.583 144 12 3 2465 2606 203280113 203279971 2.860000e-41 180.0
41 TraesCS5D01G286200 chr6A 77.437 554 50 36 976 1480 507829490 507830017 9.930000e-66 261.0
42 TraesCS5D01G286200 chr3A 81.197 117 15 4 2921 3030 58689468 58689584 1.780000e-13 87.9


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 TraesCS5D01G286200 chr5D 386644893 386648499 3606 False 6661.000000 6661 100.0000 1 3607 1 chr5D.!!$F1 3606
1 TraesCS5D01G286200 chr5D 386687079 386687783 704 True 612.000000 612 83.2180 1925 2608 1 chr5D.!!$R1 683
2 TraesCS5D01G286200 chr5A 488253152 488257473 4321 False 596.833333 1214 92.5495 1 3591 6 chr5A.!!$F2 3590
3 TraesCS5D01G286200 chr5A 488315894 488316605 711 True 575.000000 575 82.1820 1925 2608 1 chr5A.!!$R1 683
4 TraesCS5D01G286200 chr5A 676106599 676107166 567 False 333.000000 333 78.6910 978 1531 1 chr5A.!!$F1 553
5 TraesCS5D01G286200 chr5B 464314426 464323428 9002 False 663.100000 1195 88.8171 111 3592 10 chr5B.!!$F3 3481
6 TraesCS5D01G286200 chr5B 464364268 464365810 1542 True 368.000000 564 89.5445 991 2608 2 chr5B.!!$R1 1617
7 TraesCS5D01G286200 chr7D 597714325 597714893 568 True 396.000000 396 80.5700 977 1531 1 chr7D.!!$R1 554
8 TraesCS5D01G286200 chr7D 597735972 597736539 567 True 372.000000 372 79.8990 977 1531 1 chr7D.!!$R2 554
9 TraesCS5D01G286200 chr7A 98530688 98531256 568 True 346.000000 346 79.0620 977 1531 1 chr7A.!!$R1 554
10 TraesCS5D01G286200 chr1A 413414514 413415082 568 True 340.000000 340 78.8590 977 1531 1 chr1A.!!$R1 554
11 TraesCS5D01G286200 chr3D 558113481 558114045 564 True 313.000000 313 78.2240 977 1530 1 chr3D.!!$R1 553
12 TraesCS5D01G286200 chr7B 203279971 203280557 586 True 230.500000 281 91.6000 2170 2606 2 chr7B.!!$R1 436
13 TraesCS5D01G286200 chr6A 507829490 507830017 527 False 261.000000 261 77.4370 976 1480 1 chr6A.!!$F1 504

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
305 307 0.249868 TTCACGAGTGCTCAGGTTGG 60.250 55.0 0.00 0.0 0.0 3.77 F
1599 7149 0.107703 TGGAAGAATGGGTGCTAGCG 60.108 55.0 10.77 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 7155 0.251073 GCCCATGATTTTGCCTTGCT 59.749 50.0 0.00 0.0 0.0 3.91 R
3045 9171 0.175989 GCTAGAGGTTAAGCTGGCGT 59.824 55.0 12.82 0.0 35.8 5.68 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
106 108 6.913170 TGTTTTATTCTTCTTGCTCATGTCC 58.087 36.000 0.00 0.00 0.00 4.02
107 109 6.716628 TGTTTTATTCTTCTTGCTCATGTCCT 59.283 34.615 0.00 0.00 0.00 3.85
108 110 7.882791 TGTTTTATTCTTCTTGCTCATGTCCTA 59.117 33.333 0.00 0.00 0.00 2.94
109 111 8.897752 GTTTTATTCTTCTTGCTCATGTCCTAT 58.102 33.333 0.00 0.00 0.00 2.57
180 182 3.616721 CCTAGCCCCGTCCCGATG 61.617 72.222 0.00 0.00 0.00 3.84
182 184 4.468769 TAGCCCCGTCCCGATGGT 62.469 66.667 2.35 0.00 35.70 3.55
233 235 2.693591 GGTGTATCTCCAACGGATCTCA 59.306 50.000 0.00 0.00 0.00 3.27
234 236 3.322254 GGTGTATCTCCAACGGATCTCAT 59.678 47.826 0.00 0.00 0.00 2.90
237 239 1.123077 TCTCCAACGGATCTCATGGG 58.877 55.000 10.08 0.00 33.66 4.00
242 244 3.714280 TCCAACGGATCTCATGGGATTTA 59.286 43.478 10.06 0.00 33.66 1.40
249 251 4.527038 GGATCTCATGGGATTTAGTCGGTA 59.473 45.833 10.06 0.00 0.00 4.02
269 271 1.079503 GTTGTCTTCGGTGGATCTGC 58.920 55.000 0.00 0.00 0.00 4.26
276 278 1.006805 CGGTGGATCTGCTCGGATC 60.007 63.158 9.62 9.62 40.78 3.36
290 292 2.996621 CTCGGATCCAGTCTTTGTTCAC 59.003 50.000 13.41 0.00 0.00 3.18
292 294 2.609491 CGGATCCAGTCTTTGTTCACGA 60.609 50.000 13.41 0.00 0.00 4.35
305 307 0.249868 TTCACGAGTGCTCAGGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
334 336 7.043722 CCTTTCGATCTAAACTTCTCTTCATCG 60.044 40.741 0.00 0.00 34.55 3.84
356 358 2.186826 GCGGTTGCTGTTCTGGTGT 61.187 57.895 0.00 0.00 38.39 4.16
357 359 0.882927 GCGGTTGCTGTTCTGGTGTA 60.883 55.000 0.00 0.00 38.39 2.90
371 373 2.106511 CTGGTGTATTGGTCCTATGGGG 59.893 54.545 0.00 0.00 0.00 4.96
372 374 1.202891 GGTGTATTGGTCCTATGGGGC 60.203 57.143 0.00 0.00 36.26 5.80
383 385 0.687354 CTATGGGGCCTTAGCACGAT 59.313 55.000 0.84 0.00 46.55 3.73
386 388 1.344953 TGGGGCCTTAGCACGATGAT 61.345 55.000 0.84 0.00 46.55 2.45
389 391 1.604278 GGGCCTTAGCACGATGATTTC 59.396 52.381 0.84 0.00 42.56 2.17
390 392 2.565841 GGCCTTAGCACGATGATTTCT 58.434 47.619 0.00 0.00 42.56 2.52
395 397 1.927895 AGCACGATGATTTCTCGACC 58.072 50.000 0.00 0.00 39.38 4.79
410 413 3.439476 TCTCGACCTCTACTACAACAAGC 59.561 47.826 0.00 0.00 0.00 4.01
415 418 2.996621 CCTCTACTACAACAAGCTGTGC 59.003 50.000 0.00 0.00 0.00 4.57
472 475 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
484 487 2.862530 GCTTCAGTGCTTGTAGTCGTCA 60.863 50.000 0.00 0.00 0.00 4.35
602 3333 8.876275 AAAAATACACCATCATCATGTTATGC 57.124 30.769 0.00 0.00 0.00 3.14
679 3410 2.673368 AGAAATAAAAGTCTCGCAGCCG 59.327 45.455 0.00 0.00 0.00 5.52
691 3422 4.785453 CAGCCGGGCCCAAGAGAC 62.785 72.222 24.92 3.37 0.00 3.36
696 4796 2.035783 GGGCCCAAGAGACAACCC 59.964 66.667 19.95 0.00 0.00 4.11
708 4808 2.342279 CAACCCTCCGTCTCGCAA 59.658 61.111 0.00 0.00 0.00 4.85
750 4861 3.083997 GGGTCACTGGGCCGAGAT 61.084 66.667 23.01 2.74 0.00 2.75
783 4894 4.626081 CGCCGATCCCATCCCACC 62.626 72.222 0.00 0.00 0.00 4.61
784 4895 3.171388 GCCGATCCCATCCCACCT 61.171 66.667 0.00 0.00 0.00 4.00
807 4918 4.388499 GGTTTCTCCTCGCCCGCA 62.388 66.667 0.00 0.00 0.00 5.69
989 6440 2.297597 CTCACCTCGAGTTTCCTCTGTT 59.702 50.000 12.31 0.00 36.94 3.16
1092 6551 0.750850 GCTACATCGGCCTCAAGGTA 59.249 55.000 0.00 0.00 37.57 3.08
1173 6684 1.688197 CTTGGCTTTGTTCATGTGGGT 59.312 47.619 0.00 0.00 0.00 4.51
1174 6685 1.327303 TGGCTTTGTTCATGTGGGTC 58.673 50.000 0.00 0.00 0.00 4.46
1209 6721 2.895680 CCTCCTCTGCTTGCGCTA 59.104 61.111 9.73 0.00 36.97 4.26
1227 6739 2.035961 GCTAGATGCGTGGATCTGGTTA 59.964 50.000 13.38 0.00 34.32 2.85
1229 6741 3.845781 AGATGCGTGGATCTGGTTAAT 57.154 42.857 2.86 0.00 31.14 1.40
1230 6742 3.733337 AGATGCGTGGATCTGGTTAATC 58.267 45.455 2.86 0.00 31.14 1.75
1233 6745 4.054780 TGCGTGGATCTGGTTAATCTAC 57.945 45.455 0.00 0.00 32.89 2.59
1234 6746 3.704566 TGCGTGGATCTGGTTAATCTACT 59.295 43.478 0.00 0.00 33.75 2.57
1235 6747 4.891168 TGCGTGGATCTGGTTAATCTACTA 59.109 41.667 0.00 0.00 33.75 1.82
1237 6749 5.009811 GCGTGGATCTGGTTAATCTACTACT 59.990 44.000 0.00 0.00 33.75 2.57
1238 6750 6.439599 CGTGGATCTGGTTAATCTACTACTG 58.560 44.000 0.00 0.00 33.75 2.74
1246 6771 4.337555 GGTTAATCTACTACTGGCGTCTGA 59.662 45.833 0.00 0.00 0.00 3.27
1248 6773 2.039818 TCTACTACTGGCGTCTGAGG 57.960 55.000 0.00 0.00 0.00 3.86
1305 6847 1.848652 TAGTGAGCACAGTAGGGGAC 58.151 55.000 3.19 0.00 0.00 4.46
1344 6886 5.555966 TGAACTGTAGTATTGCATTGTGGA 58.444 37.500 0.00 0.00 0.00 4.02
1345 6887 6.179756 TGAACTGTAGTATTGCATTGTGGAT 58.820 36.000 0.00 0.00 0.00 3.41
1346 6888 6.658816 TGAACTGTAGTATTGCATTGTGGATT 59.341 34.615 0.00 0.00 0.00 3.01
1347 6889 6.683974 ACTGTAGTATTGCATTGTGGATTC 57.316 37.500 0.00 0.00 0.00 2.52
1348 6890 6.179756 ACTGTAGTATTGCATTGTGGATTCA 58.820 36.000 0.00 0.00 0.00 2.57
1349 6891 6.658816 ACTGTAGTATTGCATTGTGGATTCAA 59.341 34.615 0.00 0.00 0.00 2.69
1350 6892 7.340232 ACTGTAGTATTGCATTGTGGATTCAAT 59.660 33.333 0.00 0.00 36.00 2.57
1373 6920 6.286240 TGTCTTATCATTGCTGTAGACACT 57.714 37.500 0.00 0.00 37.62 3.55
1416 6963 6.558909 CCTGTGATGCTAGAAATTTCCTTTC 58.441 40.000 14.61 6.03 43.07 2.62
1426 6976 8.084684 GCTAGAAATTTCCTTTCAAGATGTGTT 58.915 33.333 14.61 0.00 44.82 3.32
1540 7090 2.481449 GGTTGAGCCTAGACATACCACG 60.481 54.545 0.00 0.00 0.00 4.94
1544 7094 2.012902 GCCTAGACATACCACGCCGT 62.013 60.000 0.00 0.00 0.00 5.68
1547 7097 0.452987 TAGACATACCACGCCGTGAC 59.547 55.000 20.57 2.92 35.23 3.67
1568 7118 2.032528 AGGCACATGTGACCGGTG 59.967 61.111 28.23 0.00 40.19 4.94
1576 7126 0.955428 ATGTGACCGGTGATGTGCAC 60.955 55.000 14.63 13.84 46.98 4.57
1583 7133 3.577229 GTGATGTGCACGCATGGA 58.423 55.556 13.13 0.00 37.83 3.41
1584 7134 1.875262 GTGATGTGCACGCATGGAA 59.125 52.632 13.13 0.00 37.83 3.53
1585 7135 0.179181 GTGATGTGCACGCATGGAAG 60.179 55.000 13.13 0.00 37.83 3.46
1586 7136 0.321475 TGATGTGCACGCATGGAAGA 60.321 50.000 13.13 0.00 0.00 2.87
1587 7137 0.804364 GATGTGCACGCATGGAAGAA 59.196 50.000 13.13 0.00 0.00 2.52
1588 7138 1.402968 GATGTGCACGCATGGAAGAAT 59.597 47.619 13.13 0.00 0.00 2.40
1589 7139 0.522626 TGTGCACGCATGGAAGAATG 59.477 50.000 13.13 0.00 0.00 2.67
1590 7140 0.179156 GTGCACGCATGGAAGAATGG 60.179 55.000 0.00 0.00 0.00 3.16
1591 7141 1.314534 TGCACGCATGGAAGAATGGG 61.315 55.000 0.00 0.27 43.95 4.00
1594 7144 1.434696 CGCATGGAAGAATGGGTGC 59.565 57.895 0.00 0.00 36.15 5.01
1595 7145 1.033746 CGCATGGAAGAATGGGTGCT 61.034 55.000 0.00 0.00 36.15 4.40
1596 7146 1.746861 CGCATGGAAGAATGGGTGCTA 60.747 52.381 0.00 0.00 36.15 3.49
1597 7147 1.952296 GCATGGAAGAATGGGTGCTAG 59.048 52.381 0.00 0.00 0.00 3.42
1598 7148 1.952296 CATGGAAGAATGGGTGCTAGC 59.048 52.381 8.10 8.10 0.00 3.42
1599 7149 0.107703 TGGAAGAATGGGTGCTAGCG 60.108 55.000 10.77 0.00 0.00 4.26
1600 7150 1.440145 GGAAGAATGGGTGCTAGCGC 61.440 60.000 20.17 20.17 0.00 5.92
1601 7151 1.440145 GAAGAATGGGTGCTAGCGCC 61.440 60.000 34.77 34.77 45.29 6.53
1602 7152 3.272334 GAATGGGTGCTAGCGCCG 61.272 66.667 34.75 0.00 46.85 6.46
1603 7153 4.856801 AATGGGTGCTAGCGCCGG 62.857 66.667 34.75 0.00 46.85 6.13
1609 7159 4.386951 TGCTAGCGCCGGAAGCAA 62.387 61.111 21.62 5.99 42.96 3.91
1619 7169 0.602562 CCGGAAGCAAGGCAAAATCA 59.397 50.000 0.00 0.00 0.00 2.57
1624 7174 0.251073 AGCAAGGCAAAATCATGGGC 59.749 50.000 0.00 0.00 0.00 5.36
1634 7184 4.095782 GCAAAATCATGGGCGTTAGACTTA 59.904 41.667 0.00 0.00 0.00 2.24
1635 7185 5.392595 GCAAAATCATGGGCGTTAGACTTAA 60.393 40.000 0.00 0.00 0.00 1.85
1638 7188 4.119442 TCATGGGCGTTAGACTTAAGAC 57.881 45.455 10.09 2.62 0.00 3.01
1639 7189 3.767673 TCATGGGCGTTAGACTTAAGACT 59.232 43.478 10.09 11.23 0.00 3.24
1640 7190 4.222145 TCATGGGCGTTAGACTTAAGACTT 59.778 41.667 12.62 0.00 0.00 3.01
1642 7192 3.575256 TGGGCGTTAGACTTAAGACTTGA 59.425 43.478 12.62 0.41 0.00 3.02
1643 7193 4.222145 TGGGCGTTAGACTTAAGACTTGAT 59.778 41.667 12.62 0.00 0.00 2.57
1644 7194 4.567159 GGGCGTTAGACTTAAGACTTGATG 59.433 45.833 12.62 8.71 0.00 3.07
1645 7195 4.033014 GGCGTTAGACTTAAGACTTGATGC 59.967 45.833 12.62 16.08 0.00 3.91
1646 7196 4.865365 GCGTTAGACTTAAGACTTGATGCT 59.135 41.667 12.62 0.00 0.00 3.79
1647 7197 5.220303 GCGTTAGACTTAAGACTTGATGCTG 60.220 44.000 12.62 0.00 0.00 4.41
1650 7200 4.573900 AGACTTAAGACTTGATGCTGTGG 58.426 43.478 10.09 0.00 0.00 4.17
1651 7201 3.077359 ACTTAAGACTTGATGCTGTGGC 58.923 45.455 10.09 0.00 39.26 5.01
1799 7373 4.876107 TCAGTTTCTTCAAGTGTCTTGGAC 59.124 41.667 9.18 0.00 37.15 4.02
1851 7429 5.733373 GCGATGTTTCTGGAAAACAAAGTCT 60.733 40.000 7.36 0.00 42.57 3.24
1943 7603 8.739972 GTTGGTGTTATTCAGTTATTCCTTCAT 58.260 33.333 0.00 0.00 0.00 2.57
1978 7725 6.699895 TGCTTATGTAATAAATAGTCGCCG 57.300 37.500 0.00 0.00 38.53 6.46
2076 7954 8.662781 TTATAATACAGTGAATGCTTGGAGAC 57.337 34.615 0.00 0.00 0.00 3.36
2122 8012 6.767524 TTTTCCTTTCTGTAGTTGCTGAAA 57.232 33.333 3.23 3.23 35.82 2.69
2426 8533 4.883585 TGCAGTTATCATCTTCCATGTTCC 59.116 41.667 0.00 0.00 0.00 3.62
2469 8579 6.974932 TTGCTAATGACTGTCATCTTTCTC 57.025 37.500 22.47 10.05 35.76 2.87
2470 8580 6.291648 TGCTAATGACTGTCATCTTTCTCT 57.708 37.500 22.47 8.67 35.76 3.10
2471 8581 6.104665 TGCTAATGACTGTCATCTTTCTCTG 58.895 40.000 22.47 8.65 35.76 3.35
2835 8945 2.014128 AGACCTGTGTGTTGGTTTTCG 58.986 47.619 0.00 0.00 36.59 3.46
2884 8994 5.212532 TGCATTTGCTGTTATTGTTCCTT 57.787 34.783 3.94 0.00 42.66 3.36
2947 9057 3.074538 AGAAGTTTGGGAATGGCTACACT 59.925 43.478 0.00 0.00 0.00 3.55
2978 9088 5.742838 GCCTGATTTTCAAATTTGGGTCAGT 60.743 40.000 24.43 9.91 0.00 3.41
2980 9090 5.527951 TGATTTTCAAATTTGGGTCAGTCG 58.472 37.500 17.90 0.00 0.00 4.18
2986 9096 3.880047 AATTTGGGTCAGTCGATCGTA 57.120 42.857 15.94 0.00 0.00 3.43
2994 9109 0.448990 CAGTCGATCGTACCGTTGGA 59.551 55.000 15.94 0.00 0.00 3.53
2999 9114 0.928229 GATCGTACCGTTGGATGCAC 59.072 55.000 0.00 0.00 0.00 4.57
3002 9117 0.650512 CGTACCGTTGGATGCACATC 59.349 55.000 1.86 1.86 37.11 3.06
3006 9121 1.016627 CCGTTGGATGCACATCGAAT 58.983 50.000 10.63 0.00 37.74 3.34
3018 9133 2.982643 ATCGAATGGTGGGCAGCCA 61.983 57.895 15.19 1.79 40.68 4.75
3055 9181 2.124736 GCATGGGACGCCAGCTTA 60.125 61.111 0.00 0.00 0.00 3.09
3056 9182 1.748879 GCATGGGACGCCAGCTTAA 60.749 57.895 0.00 0.00 0.00 1.85
3057 9183 1.993369 GCATGGGACGCCAGCTTAAC 61.993 60.000 0.00 0.00 0.00 2.01
3058 9184 1.077716 ATGGGACGCCAGCTTAACC 60.078 57.895 0.00 0.00 0.00 2.85
3059 9185 1.562672 ATGGGACGCCAGCTTAACCT 61.563 55.000 0.00 0.00 0.00 3.50
3060 9186 1.449778 GGGACGCCAGCTTAACCTC 60.450 63.158 0.00 0.00 0.00 3.85
3061 9187 1.597461 GGACGCCAGCTTAACCTCT 59.403 57.895 0.00 0.00 0.00 3.69
3062 9188 0.822164 GGACGCCAGCTTAACCTCTA 59.178 55.000 0.00 0.00 0.00 2.43
3063 9189 1.202428 GGACGCCAGCTTAACCTCTAG 60.202 57.143 0.00 0.00 0.00 2.43
3064 9190 0.175989 ACGCCAGCTTAACCTCTAGC 59.824 55.000 0.00 0.00 37.66 3.42
3065 9191 0.872021 CGCCAGCTTAACCTCTAGCG 60.872 60.000 0.00 0.00 42.18 4.26
3066 9192 0.460311 GCCAGCTTAACCTCTAGCGA 59.540 55.000 0.00 0.00 42.18 4.93
3067 9193 1.803252 GCCAGCTTAACCTCTAGCGAC 60.803 57.143 0.00 0.00 42.18 5.19
3068 9194 1.202428 CCAGCTTAACCTCTAGCGACC 60.202 57.143 0.00 0.00 42.18 4.79
3069 9195 1.476891 CAGCTTAACCTCTAGCGACCA 59.523 52.381 0.00 0.00 42.18 4.02
3070 9196 1.477295 AGCTTAACCTCTAGCGACCAC 59.523 52.381 0.00 0.00 42.18 4.16
3071 9197 1.471153 GCTTAACCTCTAGCGACCACC 60.471 57.143 0.00 0.00 0.00 4.61
3072 9198 1.822990 CTTAACCTCTAGCGACCACCA 59.177 52.381 0.00 0.00 0.00 4.17
3073 9199 1.180029 TAACCTCTAGCGACCACCAC 58.820 55.000 0.00 0.00 0.00 4.16
3074 9200 1.542187 AACCTCTAGCGACCACCACC 61.542 60.000 0.00 0.00 0.00 4.61
3075 9201 2.722201 CCTCTAGCGACCACCACCC 61.722 68.421 0.00 0.00 0.00 4.61
3076 9202 3.064987 CTCTAGCGACCACCACCCG 62.065 68.421 0.00 0.00 0.00 5.28
3109 9235 4.426313 CCCCGCCCTCCTTGGAAC 62.426 72.222 0.00 0.00 38.35 3.62
3110 9236 4.426313 CCCGCCCTCCTTGGAACC 62.426 72.222 0.00 0.00 38.35 3.62
3111 9237 4.778143 CCGCCCTCCTTGGAACCG 62.778 72.222 0.00 0.00 38.35 4.44
3113 9239 4.344865 GCCCTCCTTGGAACCGCA 62.345 66.667 0.00 0.00 38.35 5.69
3114 9240 2.359975 CCCTCCTTGGAACCGCAC 60.360 66.667 0.00 0.00 38.35 5.34
3115 9241 2.359975 CCTCCTTGGAACCGCACC 60.360 66.667 0.00 0.00 38.35 5.01
3116 9242 2.359975 CTCCTTGGAACCGCACCC 60.360 66.667 0.00 0.00 0.00 4.61
3117 9243 3.920093 CTCCTTGGAACCGCACCCC 62.920 68.421 0.00 0.00 0.00 4.95
3118 9244 4.278513 CCTTGGAACCGCACCCCA 62.279 66.667 0.00 0.00 0.00 4.96
3119 9245 2.983592 CTTGGAACCGCACCCCAC 60.984 66.667 0.00 0.00 0.00 4.61
3120 9246 4.589675 TTGGAACCGCACCCCACC 62.590 66.667 0.00 0.00 0.00 4.61
3142 9268 2.279073 CCTCCAGCCGTCCCTCTA 59.721 66.667 0.00 0.00 0.00 2.43
3143 9269 1.830408 CCTCCAGCCGTCCCTCTAG 60.830 68.421 0.00 0.00 0.00 2.43
3144 9270 2.442272 TCCAGCCGTCCCTCTAGC 60.442 66.667 0.00 0.00 0.00 3.42
3145 9271 3.541713 CCAGCCGTCCCTCTAGCC 61.542 72.222 0.00 0.00 0.00 3.93
3146 9272 3.541713 CAGCCGTCCCTCTAGCCC 61.542 72.222 0.00 0.00 0.00 5.19
3147 9273 4.862823 AGCCGTCCCTCTAGCCCC 62.863 72.222 0.00 0.00 0.00 5.80
3217 9436 4.722279 ACCCTAGGGAACTCTCAAAATAGG 59.278 45.833 35.38 1.21 43.67 2.57
3220 9439 4.227864 AGGGAACTCTCAAAATAGGCTG 57.772 45.455 0.00 0.00 32.90 4.85
3221 9440 3.054065 AGGGAACTCTCAAAATAGGCTGG 60.054 47.826 0.00 0.00 32.90 4.85
3223 9442 3.347216 GAACTCTCAAAATAGGCTGGCA 58.653 45.455 3.38 0.00 0.00 4.92
3232 9451 3.615224 AATAGGCTGGCACCAAATTTG 57.385 42.857 11.40 11.40 0.00 2.32
3410 9667 2.292267 CTGGTCTGGAATATGGTGCAC 58.708 52.381 8.80 8.80 0.00 4.57
3432 9689 3.357203 TGGCACTTGTCAGTTTTGGTTA 58.643 40.909 0.00 0.00 0.00 2.85
3435 9692 4.546570 GCACTTGTCAGTTTTGGTTATCC 58.453 43.478 0.00 0.00 0.00 2.59
3436 9693 4.037446 GCACTTGTCAGTTTTGGTTATCCA 59.963 41.667 0.00 0.00 42.66 3.41
3437 9694 5.762045 CACTTGTCAGTTTTGGTTATCCAG 58.238 41.667 0.00 0.00 45.22 3.86
3585 9999 0.529833 ACTCGACATGGAGCAGTCAG 59.470 55.000 0.00 0.00 37.57 3.51
3592 10006 0.108424 ATGGAGCAGTCAGTCGCTTC 60.108 55.000 0.00 0.00 38.99 3.86
3593 10007 1.446966 GGAGCAGTCAGTCGCTTCC 60.447 63.158 0.00 0.00 38.99 3.46
3594 10008 1.290324 GAGCAGTCAGTCGCTTCCA 59.710 57.895 0.00 0.00 38.99 3.53
3595 10009 1.005630 AGCAGTCAGTCGCTTCCAC 60.006 57.895 0.00 0.00 33.81 4.02
3596 10010 2.029844 GCAGTCAGTCGCTTCCACC 61.030 63.158 0.00 0.00 0.00 4.61
3597 10011 1.367471 CAGTCAGTCGCTTCCACCA 59.633 57.895 0.00 0.00 0.00 4.17
3598 10012 0.946221 CAGTCAGTCGCTTCCACCAC 60.946 60.000 0.00 0.00 0.00 4.16
3599 10013 1.115930 AGTCAGTCGCTTCCACCACT 61.116 55.000 0.00 0.00 0.00 4.00
3600 10014 0.946221 GTCAGTCGCTTCCACCACTG 60.946 60.000 0.00 0.00 38.09 3.66
3601 10015 1.112916 TCAGTCGCTTCCACCACTGA 61.113 55.000 0.00 0.00 42.34 3.41
3602 10016 0.036952 CAGTCGCTTCCACCACTGAT 60.037 55.000 0.00 0.00 38.90 2.90
3603 10017 0.247736 AGTCGCTTCCACCACTGATC 59.752 55.000 0.00 0.00 0.00 2.92
3604 10018 1.078759 GTCGCTTCCACCACTGATCG 61.079 60.000 0.00 0.00 0.00 3.69
3605 10019 1.811266 CGCTTCCACCACTGATCGG 60.811 63.158 0.00 0.00 0.00 4.18
3606 10020 2.109126 GCTTCCACCACTGATCGGC 61.109 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 6.148948 GTCGTCATCTCATCTTCCTGAATAG 58.851 44.000 0.00 0.00 0.00 1.73
107 109 5.278022 CGTCGTCATCTCATCTTCCTGAATA 60.278 44.000 0.00 0.00 0.00 1.75
108 110 4.498850 CGTCGTCATCTCATCTTCCTGAAT 60.499 45.833 0.00 0.00 0.00 2.57
109 111 3.181496 CGTCGTCATCTCATCTTCCTGAA 60.181 47.826 0.00 0.00 0.00 3.02
119 121 0.888619 AAGAAGCCGTCGTCATCTCA 59.111 50.000 0.00 0.00 0.00 3.27
125 127 1.656095 CATCTTCAAGAAGCCGTCGTC 59.344 52.381 4.95 0.00 38.28 4.20
126 128 1.673033 CCATCTTCAAGAAGCCGTCGT 60.673 52.381 4.95 0.00 38.28 4.34
127 129 1.002366 CCATCTTCAAGAAGCCGTCG 58.998 55.000 4.95 0.00 38.28 5.12
172 174 1.065928 CTAGACGCACCATCGGGAC 59.934 63.158 0.00 0.00 38.05 4.46
173 175 2.782222 GCTAGACGCACCATCGGGA 61.782 63.158 0.00 0.00 38.92 5.14
177 179 0.179134 ACGAAGCTAGACGCACCATC 60.179 55.000 0.00 0.00 42.61 3.51
179 181 1.211969 GACGAAGCTAGACGCACCA 59.788 57.895 0.00 0.00 42.61 4.17
180 182 1.868251 CGACGAAGCTAGACGCACC 60.868 63.158 0.00 0.00 42.61 5.01
182 184 1.978712 CTCCGACGAAGCTAGACGCA 61.979 60.000 0.00 0.00 42.61 5.24
183 185 1.297745 CTCCGACGAAGCTAGACGC 60.298 63.158 0.00 0.00 39.57 5.19
184 186 1.352404 CCTCCGACGAAGCTAGACG 59.648 63.158 0.00 6.92 0.00 4.18
185 187 1.728672 CCCTCCGACGAAGCTAGAC 59.271 63.158 0.00 0.00 0.00 2.59
186 188 2.119655 GCCCTCCGACGAAGCTAGA 61.120 63.158 0.00 0.00 0.00 2.43
195 197 4.436998 CTCCACACGCCCTCCGAC 62.437 72.222 0.00 0.00 41.02 4.79
223 225 4.501571 CGACTAAATCCCATGAGATCCGTT 60.502 45.833 0.00 0.00 0.00 4.44
226 228 3.325135 ACCGACTAAATCCCATGAGATCC 59.675 47.826 0.00 0.00 0.00 3.36
233 235 4.715297 AGACAACTACCGACTAAATCCCAT 59.285 41.667 0.00 0.00 0.00 4.00
234 236 4.091549 AGACAACTACCGACTAAATCCCA 58.908 43.478 0.00 0.00 0.00 4.37
237 239 4.797349 CCGAAGACAACTACCGACTAAATC 59.203 45.833 0.00 0.00 0.00 2.17
242 244 1.268899 CACCGAAGACAACTACCGACT 59.731 52.381 0.00 0.00 0.00 4.18
249 251 1.338200 GCAGATCCACCGAAGACAACT 60.338 52.381 0.00 0.00 0.00 3.16
269 271 2.996621 GTGAACAAAGACTGGATCCGAG 59.003 50.000 7.39 8.36 0.00 4.63
276 278 1.261619 GCACTCGTGAACAAAGACTGG 59.738 52.381 0.39 0.00 0.00 4.00
290 292 0.460987 GGATCCAACCTGAGCACTCG 60.461 60.000 6.95 0.00 0.00 4.18
292 294 1.366319 AAGGATCCAACCTGAGCACT 58.634 50.000 15.82 0.00 40.49 4.40
347 349 4.451900 CCATAGGACCAATACACCAGAAC 58.548 47.826 0.00 0.00 0.00 3.01
371 373 2.219674 CGAGAAATCATCGTGCTAAGGC 59.780 50.000 0.00 0.00 35.48 4.35
372 374 3.487574 GTCGAGAAATCATCGTGCTAAGG 59.512 47.826 0.00 0.00 40.95 2.69
373 375 3.487574 GGTCGAGAAATCATCGTGCTAAG 59.512 47.826 0.00 0.00 40.95 2.18
383 385 5.708697 TGTTGTAGTAGAGGTCGAGAAATCA 59.291 40.000 0.00 0.00 0.00 2.57
386 388 5.564259 GCTTGTTGTAGTAGAGGTCGAGAAA 60.564 44.000 0.00 0.00 0.00 2.52
389 391 3.440872 AGCTTGTTGTAGTAGAGGTCGAG 59.559 47.826 0.00 0.00 0.00 4.04
390 392 3.190744 CAGCTTGTTGTAGTAGAGGTCGA 59.809 47.826 0.00 0.00 0.00 4.20
395 397 2.996621 GGCACAGCTTGTTGTAGTAGAG 59.003 50.000 0.00 0.00 0.00 2.43
425 428 2.123251 TCATCGCCCCTCCCTCTC 60.123 66.667 0.00 0.00 0.00 3.20
426 429 2.444895 GTCATCGCCCCTCCCTCT 60.445 66.667 0.00 0.00 0.00 3.69
463 466 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
472 475 2.818432 ACCACCTAGTGACGACTACAAG 59.182 50.000 0.00 0.00 35.23 3.16
484 487 3.053842 TCCAGATTCGTAGACCACCTAGT 60.054 47.826 0.00 0.00 34.32 2.57
581 3312 4.154737 GCGCATAACATGATGATGGTGTAT 59.845 41.667 0.30 0.00 33.39 2.29
632 3363 4.756642 TCGATTTCTCAAAGACAGTGCATT 59.243 37.500 0.00 0.00 0.00 3.56
638 3369 6.957984 TTCTCATCGATTTCTCAAAGACAG 57.042 37.500 0.00 0.00 0.00 3.51
679 3410 2.035783 GGGTTGTCTCTTGGGCCC 59.964 66.667 17.59 17.59 0.00 5.80
691 3422 2.027625 GTTGCGAGACGGAGGGTTG 61.028 63.158 0.00 0.00 0.00 3.77
726 4837 2.584608 CCCAGTGACCCGCTTAGG 59.415 66.667 0.00 0.00 40.63 2.69
783 4894 0.747852 GCGAGGAGAAACCCTAGGAG 59.252 60.000 11.48 2.69 40.05 3.69
784 4895 0.686769 GGCGAGGAGAAACCCTAGGA 60.687 60.000 11.48 0.00 40.05 2.94
950 6401 1.749634 GAGAAGATCCGGAACCGAGAA 59.250 52.381 9.01 0.43 42.83 2.87
1206 6718 0.390860 ACCAGATCCACGCATCTAGC 59.609 55.000 0.00 0.00 40.87 3.42
1209 6721 3.389329 AGATTAACCAGATCCACGCATCT 59.611 43.478 0.00 0.00 33.00 2.90
1227 6739 2.952978 CCTCAGACGCCAGTAGTAGATT 59.047 50.000 0.00 0.00 0.00 2.40
1229 6741 1.558294 TCCTCAGACGCCAGTAGTAGA 59.442 52.381 0.00 0.00 0.00 2.59
1230 6742 2.039818 TCCTCAGACGCCAGTAGTAG 57.960 55.000 0.00 0.00 0.00 2.57
1233 6745 1.268794 CGATTCCTCAGACGCCAGTAG 60.269 57.143 0.00 0.00 0.00 2.57
1234 6746 0.738975 CGATTCCTCAGACGCCAGTA 59.261 55.000 0.00 0.00 0.00 2.74
1235 6747 1.251527 ACGATTCCTCAGACGCCAGT 61.252 55.000 0.00 0.00 0.00 4.00
1237 6749 1.215382 CACGATTCCTCAGACGCCA 59.785 57.895 0.00 0.00 0.00 5.69
1238 6750 1.519455 CCACGATTCCTCAGACGCC 60.519 63.158 0.00 0.00 0.00 5.68
1246 6771 3.443681 CCAATTTTGTAGCCACGATTCCT 59.556 43.478 0.00 0.00 0.00 3.36
1248 6773 3.769536 CCCAATTTTGTAGCCACGATTC 58.230 45.455 0.00 0.00 0.00 2.52
1305 6847 3.723764 CAGTTCATCGAACAACAAAACCG 59.276 43.478 9.36 0.00 44.11 4.44
1348 6890 7.334090 AGTGTCTACAGCAATGATAAGACATT 58.666 34.615 15.60 10.67 43.55 2.71
1349 6891 6.882656 AGTGTCTACAGCAATGATAAGACAT 58.117 36.000 15.60 6.01 43.55 3.06
1350 6892 6.286240 AGTGTCTACAGCAATGATAAGACA 57.714 37.500 10.54 10.54 40.60 3.41
1354 6896 7.404671 TCAGTAGTGTCTACAGCAATGATAA 57.595 36.000 9.16 0.00 0.00 1.75
1359 6906 5.105716 ACGAATCAGTAGTGTCTACAGCAAT 60.106 40.000 9.16 0.00 0.00 3.56
1362 6909 4.358494 ACGAATCAGTAGTGTCTACAGC 57.642 45.455 9.16 0.00 0.00 4.40
1392 6939 6.151648 TGAAAGGAAATTTCTAGCATCACAGG 59.848 38.462 17.42 0.00 46.34 4.00
1416 6963 7.020010 GCTCTCAAGAACATAAACACATCTTG 58.980 38.462 7.34 7.34 45.18 3.02
1426 6976 4.686091 CACAACGAGCTCTCAAGAACATAA 59.314 41.667 12.85 0.00 0.00 1.90
1428 6978 3.062763 CACAACGAGCTCTCAAGAACAT 58.937 45.455 12.85 0.00 0.00 2.71
1544 7094 2.669229 CACATGTGCCTGGCGTCA 60.669 61.111 13.94 15.75 0.00 4.35
1547 7097 3.434319 GGTCACATGTGCCTGGCG 61.434 66.667 21.38 1.58 0.00 5.69
1568 7118 0.804364 TTCTTCCATGCGTGCACATC 59.196 50.000 18.64 8.42 0.00 3.06
1576 7126 1.033746 AGCACCCATTCTTCCATGCG 61.034 55.000 0.00 0.00 38.12 4.73
1577 7127 1.952296 CTAGCACCCATTCTTCCATGC 59.048 52.381 0.00 0.00 0.00 4.06
1578 7128 1.952296 GCTAGCACCCATTCTTCCATG 59.048 52.381 10.63 0.00 0.00 3.66
1579 7129 1.475751 CGCTAGCACCCATTCTTCCAT 60.476 52.381 16.45 0.00 0.00 3.41
1582 7132 2.017752 GCGCTAGCACCCATTCTTC 58.982 57.895 16.45 0.00 44.35 2.87
1583 7133 4.225497 GCGCTAGCACCCATTCTT 57.775 55.556 16.45 0.00 44.35 2.52
1593 7143 3.567797 CTTGCTTCCGGCGCTAGC 61.568 66.667 20.06 20.06 45.43 3.42
1594 7144 2.892425 CCTTGCTTCCGGCGCTAG 60.892 66.667 7.64 16.00 45.43 3.42
1599 7149 0.737367 GATTTTGCCTTGCTTCCGGC 60.737 55.000 0.00 0.00 46.46 6.13
1600 7150 0.602562 TGATTTTGCCTTGCTTCCGG 59.397 50.000 0.00 0.00 0.00 5.14
1601 7151 2.264813 CATGATTTTGCCTTGCTTCCG 58.735 47.619 0.00 0.00 0.00 4.30
1602 7152 2.624636 CCATGATTTTGCCTTGCTTCC 58.375 47.619 0.00 0.00 0.00 3.46
1603 7153 2.624636 CCCATGATTTTGCCTTGCTTC 58.375 47.619 0.00 0.00 0.00 3.86
1605 7155 0.251073 GCCCATGATTTTGCCTTGCT 59.749 50.000 0.00 0.00 0.00 3.91
1609 7159 1.750778 CTAACGCCCATGATTTTGCCT 59.249 47.619 0.00 0.00 0.00 4.75
1619 7169 4.222145 TCAAGTCTTAAGTCTAACGCCCAT 59.778 41.667 2.56 0.00 0.00 4.00
1624 7174 5.864474 ACAGCATCAAGTCTTAAGTCTAACG 59.136 40.000 2.56 0.00 0.00 3.18
1634 7184 0.957395 CCGCCACAGCATCAAGTCTT 60.957 55.000 0.00 0.00 39.83 3.01
1635 7185 1.376424 CCGCCACAGCATCAAGTCT 60.376 57.895 0.00 0.00 39.83 3.24
1638 7188 4.170062 CGCCGCCACAGCATCAAG 62.170 66.667 0.00 0.00 39.83 3.02
1647 7197 3.090219 ATAGTCCTTCCGCCGCCAC 62.090 63.158 0.00 0.00 0.00 5.01
1650 7200 2.967615 GCATAGTCCTTCCGCCGC 60.968 66.667 0.00 0.00 0.00 6.53
1651 7201 1.153449 TTGCATAGTCCTTCCGCCG 60.153 57.895 0.00 0.00 0.00 6.46
1799 7373 2.095059 GCTGTGCACACCAGGATAAAAG 60.095 50.000 17.42 2.44 0.00 2.27
1851 7429 4.341235 AGTCGTCCAAATTCGAGGATATCA 59.659 41.667 4.83 0.00 36.11 2.15
2053 7931 6.765036 CAGTCTCCAAGCATTCACTGTATTAT 59.235 38.462 0.00 0.00 0.00 1.28
2061 7939 2.479566 TCCAGTCTCCAAGCATTCAC 57.520 50.000 0.00 0.00 0.00 3.18
2076 7954 5.665916 AAAAACAAAGAGGGCATATCCAG 57.334 39.130 0.00 0.00 36.21 3.86
2102 7992 5.278463 GCAATTTCAGCAACTACAGAAAGGA 60.278 40.000 0.00 0.00 33.96 3.36
2426 8533 1.225936 CGCTGCAAGATCAAGCACG 60.226 57.895 7.87 11.89 36.62 5.34
2458 8568 4.020662 AGGTCCTGTTCAGAGAAAGATGAC 60.021 45.833 1.00 0.00 0.00 3.06
2469 8579 1.620819 AGCACAGTAGGTCCTGTTCAG 59.379 52.381 0.00 0.00 42.99 3.02
2470 8580 1.344438 CAGCACAGTAGGTCCTGTTCA 59.656 52.381 0.00 0.00 42.99 3.18
2471 8581 1.618837 TCAGCACAGTAGGTCCTGTTC 59.381 52.381 0.00 0.00 42.99 3.18
2835 8945 2.979813 CAAAACGTTATGAGGCACAAGC 59.020 45.455 0.00 0.00 41.10 4.01
2884 8994 3.519579 CAACAGCACCACAAAACATTCA 58.480 40.909 0.00 0.00 0.00 2.57
2980 9090 4.881886 GATGTGCATCCAACGGTACGATC 61.882 52.174 0.00 0.00 42.97 3.69
2986 9096 0.321210 TTCGATGTGCATCCAACGGT 60.321 50.000 7.05 0.00 34.40 4.83
2994 9109 1.386525 GCCCACCATTCGATGTGCAT 61.387 55.000 0.00 0.00 0.00 3.96
2999 9114 2.484062 GGCTGCCCACCATTCGATG 61.484 63.158 7.66 0.00 0.00 3.84
3002 9117 2.440796 ATGGCTGCCCACCATTCG 60.441 61.111 17.53 0.00 45.86 3.34
3006 9121 1.792757 AAGAAGATGGCTGCCCACCA 61.793 55.000 17.53 0.00 45.77 4.17
3018 9133 3.049080 GCGGCCTGGGGAAGAAGAT 62.049 63.158 0.00 0.00 0.00 2.40
3038 9164 1.748879 TTAAGCTGGCGTCCCATGC 60.749 57.895 0.00 0.00 41.21 4.06
3040 9166 1.077716 GGTTAAGCTGGCGTCCCAT 60.078 57.895 0.00 0.00 41.21 4.00
3041 9167 2.180159 GAGGTTAAGCTGGCGTCCCA 62.180 60.000 12.82 0.00 39.32 4.37
3043 9169 0.822164 TAGAGGTTAAGCTGGCGTCC 59.178 55.000 12.82 0.00 0.00 4.79
3044 9170 1.803252 GCTAGAGGTTAAGCTGGCGTC 60.803 57.143 12.82 0.00 35.80 5.19
3045 9171 0.175989 GCTAGAGGTTAAGCTGGCGT 59.824 55.000 12.82 0.00 35.80 5.68
3046 9172 2.979130 GCTAGAGGTTAAGCTGGCG 58.021 57.895 12.82 0.84 35.80 5.69
3050 9176 1.477295 GTGGTCGCTAGAGGTTAAGCT 59.523 52.381 6.94 6.94 36.56 3.74
3052 9178 1.822990 TGGTGGTCGCTAGAGGTTAAG 59.177 52.381 0.00 0.00 0.00 1.85
3053 9179 1.547372 GTGGTGGTCGCTAGAGGTTAA 59.453 52.381 0.00 0.00 0.00 2.01
3054 9180 1.180029 GTGGTGGTCGCTAGAGGTTA 58.820 55.000 0.00 0.00 0.00 2.85
3055 9181 1.542187 GGTGGTGGTCGCTAGAGGTT 61.542 60.000 0.00 0.00 0.00 3.50
3056 9182 1.982938 GGTGGTGGTCGCTAGAGGT 60.983 63.158 0.00 0.00 0.00 3.85
3057 9183 2.722201 GGGTGGTGGTCGCTAGAGG 61.722 68.421 0.00 0.00 0.00 3.69
3058 9184 2.893398 GGGTGGTGGTCGCTAGAG 59.107 66.667 0.00 0.00 0.00 2.43
3059 9185 3.066190 CGGGTGGTGGTCGCTAGA 61.066 66.667 0.00 0.00 0.00 2.43
3060 9186 4.814294 GCGGGTGGTGGTCGCTAG 62.814 72.222 0.00 0.00 45.16 3.42
3092 9218 4.426313 GTTCCAAGGAGGGCGGGG 62.426 72.222 0.00 0.00 38.24 5.73
3093 9219 4.426313 GGTTCCAAGGAGGGCGGG 62.426 72.222 0.00 0.00 38.24 6.13
3094 9220 4.778143 CGGTTCCAAGGAGGGCGG 62.778 72.222 0.00 0.00 38.24 6.13
3096 9222 4.344865 TGCGGTTCCAAGGAGGGC 62.345 66.667 0.00 0.00 38.24 5.19
3097 9223 2.359975 GTGCGGTTCCAAGGAGGG 60.360 66.667 0.00 0.00 38.24 4.30
3098 9224 2.359975 GGTGCGGTTCCAAGGAGG 60.360 66.667 0.00 0.00 39.47 4.30
3099 9225 2.359975 GGGTGCGGTTCCAAGGAG 60.360 66.667 0.00 0.00 0.00 3.69
3100 9226 3.961414 GGGGTGCGGTTCCAAGGA 61.961 66.667 0.00 0.00 0.00 3.36
3101 9227 4.278513 TGGGGTGCGGTTCCAAGG 62.279 66.667 0.00 0.00 0.00 3.61
3102 9228 2.983592 GTGGGGTGCGGTTCCAAG 60.984 66.667 0.00 0.00 31.73 3.61
3103 9229 4.589675 GGTGGGGTGCGGTTCCAA 62.590 66.667 0.00 0.00 31.73 3.53
3125 9251 1.830408 CTAGAGGGACGGCTGGAGG 60.830 68.421 0.00 0.00 0.00 4.30
3126 9252 2.494530 GCTAGAGGGACGGCTGGAG 61.495 68.421 0.00 0.00 0.00 3.86
3127 9253 2.442272 GCTAGAGGGACGGCTGGA 60.442 66.667 0.00 0.00 0.00 3.86
3128 9254 3.541713 GGCTAGAGGGACGGCTGG 61.542 72.222 0.00 0.00 0.00 4.85
3129 9255 3.541713 GGGCTAGAGGGACGGCTG 61.542 72.222 0.00 0.00 0.00 4.85
3130 9256 4.862823 GGGGCTAGAGGGACGGCT 62.863 72.222 0.00 0.00 0.00 5.52
3144 9270 3.546714 AAAGAAGACACGGGCGGGG 62.547 63.158 0.00 0.00 0.00 5.73
3145 9271 1.170290 AAAAAGAAGACACGGGCGGG 61.170 55.000 0.00 0.00 0.00 6.13
3146 9272 2.327228 AAAAAGAAGACACGGGCGG 58.673 52.632 0.00 0.00 0.00 6.13
3194 9320 4.722279 CCTATTTTGAGAGTTCCCTAGGGT 59.278 45.833 27.58 8.62 36.47 4.34
3195 9321 4.445019 GCCTATTTTGAGAGTTCCCTAGGG 60.445 50.000 23.22 23.22 0.00 3.53
3200 9326 3.282885 CCAGCCTATTTTGAGAGTTCCC 58.717 50.000 0.00 0.00 0.00 3.97
3201 9327 2.685388 GCCAGCCTATTTTGAGAGTTCC 59.315 50.000 0.00 0.00 0.00 3.62
3202 9328 3.127721 GTGCCAGCCTATTTTGAGAGTTC 59.872 47.826 0.00 0.00 0.00 3.01
3217 9436 2.802247 GACTTTCAAATTTGGTGCCAGC 59.198 45.455 17.90 0.00 0.00 4.85
3220 9439 3.392882 CCTGACTTTCAAATTTGGTGCC 58.607 45.455 17.90 5.23 0.00 5.01
3221 9440 2.802247 GCCTGACTTTCAAATTTGGTGC 59.198 45.455 17.90 5.05 0.00 5.01
3223 9442 2.955660 TCGCCTGACTTTCAAATTTGGT 59.044 40.909 17.90 8.20 0.00 3.67
3363 9602 7.495606 TGCATCGATTCAAACATTAGTACAGAT 59.504 33.333 0.00 0.00 0.00 2.90
3410 9667 1.750778 ACCAAAACTGACAAGTGCCAG 59.249 47.619 0.00 0.00 36.51 4.85
3432 9689 6.737720 TGAACTGAATGAGTATAGCTGGAT 57.262 37.500 0.00 0.00 33.09 3.41
3435 9692 6.519382 TGGATGAACTGAATGAGTATAGCTG 58.481 40.000 0.00 0.00 33.09 4.24
3436 9693 6.737720 TGGATGAACTGAATGAGTATAGCT 57.262 37.500 0.00 0.00 33.09 3.32
3437 9694 6.989169 ACTTGGATGAACTGAATGAGTATAGC 59.011 38.462 0.00 0.00 33.09 2.97
3585 9999 1.078759 CGATCAGTGGTGGAAGCGAC 61.079 60.000 0.00 0.00 36.92 5.19


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

AutoCloner maintained by Alex Coulton.