Multiple sequence alignment - TraesCS2B01G441100

Loading Multiple Alignment...

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 TraesCS2B01G441100 chr2B 100.000 6176 0 0 1 6176 632915578 632921753 0.000000e+00 11406.0
1 TraesCS2B01G441100 chr2B 81.644 888 120 20 2778 3647 769597246 769596384 0.000000e+00 697.0
2 TraesCS2B01G441100 chr2B 81.752 274 30 11 4877 5147 769596373 769596117 1.740000e-50 211.0
3 TraesCS2B01G441100 chr2B 90.789 76 0 3 6073 6141 782533404 782533479 1.830000e-15 95.3
4 TraesCS2B01G441100 chr2A 92.872 5668 226 64 1 5555 677524794 677530396 0.000000e+00 8065.0
5 TraesCS2B01G441100 chr2A 90.968 310 25 2 5553 5861 65743622 65743929 1.240000e-111 414.0
6 TraesCS2B01G441100 chr2A 90.385 312 27 2 5559 5869 597848116 597847807 2.070000e-109 407.0
7 TraesCS2B01G441100 chr2A 85.446 213 19 3 5862 6074 677530397 677530597 1.740000e-50 211.0
8 TraesCS2B01G441100 chr2D 96.138 2356 74 10 3323 5669 533135416 533137763 0.000000e+00 3831.0
9 TraesCS2B01G441100 chr2D 90.316 2819 159 53 1 2743 533132011 533134791 0.000000e+00 3589.0
10 TraesCS2B01G441100 chr2D 95.146 515 24 1 2740 3253 533134911 533135425 0.000000e+00 811.0
11 TraesCS2B01G441100 chr2D 89.516 372 27 10 5706 6074 533137757 533138119 1.570000e-125 460.0
12 TraesCS2B01G441100 chr6B 81.109 884 132 19 2778 3647 376338534 376339396 0.000000e+00 675.0
13 TraesCS2B01G441100 chr6B 83.841 328 32 13 4871 5195 376339400 376339709 6.060000e-75 292.0
14 TraesCS2B01G441100 chr6B 84.013 319 30 12 4880 5195 201998805 201998505 2.820000e-73 287.0
15 TraesCS2B01G441100 chr5A 91.234 308 23 3 5556 5861 366030499 366030804 3.440000e-112 416.0
16 TraesCS2B01G441100 chr5A 90.221 317 25 5 5548 5861 151066924 151067237 5.760000e-110 409.0
17 TraesCS2B01G441100 chr7A 91.419 303 23 2 5560 5861 620420379 620420679 4.450000e-111 412.0
18 TraesCS2B01G441100 chr4A 91.419 303 23 2 5560 5861 58521756 58522056 4.450000e-111 412.0
19 TraesCS2B01G441100 chr6D 91.118 304 23 3 5559 5861 353638201 353637901 5.760000e-110 409.0
20 TraesCS2B01G441100 chr1A 91.118 304 24 2 5559 5861 350489892 350489591 5.760000e-110 409.0
21 TraesCS2B01G441100 chr3A 90.461 304 26 2 5559 5861 140004584 140004283 1.250000e-106 398.0
22 TraesCS2B01G441100 chr3A 92.537 67 1 2 6076 6141 64772922 64772859 6.590000e-15 93.5
23 TraesCS2B01G441100 chr7B 94.444 72 1 2 6073 6141 508830644 508830715 2.350000e-19 108.0
24 TraesCS2B01G441100 chr5B 91.250 80 2 2 6072 6146 644352390 644352469 3.050000e-18 104.0
25 TraesCS2B01G441100 chr5B 90.361 83 1 3 6073 6148 650345377 650345295 1.100000e-17 102.0
26 TraesCS2B01G441100 chr5B 90.667 75 6 1 6072 6145 448441343 448441417 1.420000e-16 99.0
27 TraesCS2B01G441100 chr5D 87.952 83 3 4 6068 6143 169535163 169535245 2.370000e-14 91.6
28 TraesCS2B01G441100 chr1B 88.000 75 6 3 6073 6144 657169185 657169259 1.100000e-12 86.1
29 TraesCS2B01G441100 chr1D 87.179 78 4 5 6073 6148 30517879 30517806 3.970000e-12 84.2


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 TraesCS2B01G441100 chr2B 632915578 632921753 6175 False 11406.00 11406 100.000 1 6176 1 chr2B.!!$F1 6175
1 TraesCS2B01G441100 chr2B 769596117 769597246 1129 True 454.00 697 81.698 2778 5147 2 chr2B.!!$R1 2369
2 TraesCS2B01G441100 chr2A 677524794 677530597 5803 False 4138.00 8065 89.159 1 6074 2 chr2A.!!$F2 6073
3 TraesCS2B01G441100 chr2D 533132011 533138119 6108 False 2172.75 3831 92.779 1 6074 4 chr2D.!!$F1 6073
4 TraesCS2B01G441100 chr6B 376338534 376339709 1175 False 483.50 675 82.475 2778 5195 2 chr6B.!!$F1 2417

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
945 1031 0.036875 GTGGAGGACTTGTCCCTTGG 59.963 60.000 15.44 0.0 33.36 3.61 F
1128 1214 0.319641 ACCGAGAAAAGGTCTGACGC 60.320 55.000 1.07 0.0 37.44 5.19 F
1486 1579 0.373716 CGCGCTTCTGGGTGTTATTC 59.626 55.000 5.56 0.0 32.85 1.75 F
1489 1582 1.393539 CGCTTCTGGGTGTTATTCGTG 59.606 52.381 0.00 0.0 0.00 4.35 F
3112 3351 2.431419 TCACAGGTCAGTCCGTTTTACA 59.569 45.455 0.00 0.0 41.99 2.41 F
3522 3803 1.081242 CCAGCACATCACGTTTGCC 60.081 57.895 4.94 0.0 36.91 4.52 F
3523 3804 1.440850 CAGCACATCACGTTTGCCG 60.441 57.895 4.94 0.0 44.03 5.69 F
4794 5078 1.903183 AGTTTACCAGAGCAGAGGACC 59.097 52.381 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2870 3105 2.168106 ACCAAAGTGTTGCATGCTGAAA 59.832 40.909 20.33 1.44 33.01 2.69 R
2957 3196 3.181455 ACTTGTGTATGTTCAGTGCTCCA 60.181 43.478 0.00 0.00 0.00 3.86 R
3017 3256 4.090930 CGCCTTCGGAAATAACGGTATATG 59.909 45.833 0.00 0.00 0.00 1.78 R
3455 3729 4.649692 AGTCAATAGGATGCCAAGCTATG 58.350 43.478 0.00 0.00 0.00 2.23 R
4776 5060 0.895530 CGGTCCTCTGCTCTGGTAAA 59.104 55.000 0.00 0.00 0.00 2.01 R
4794 5078 1.667724 GCAGTGTTGATGGATCCTTCG 59.332 52.381 19.69 8.00 0.00 3.79 R
4803 5087 2.029739 TGCCAGAAATGCAGTGTTGATG 60.030 45.455 0.00 0.00 34.05 3.07 R
6133 6429 0.031716 TCAGCTGCCATCTACTCCCT 60.032 55.000 9.47 0.00 0.00 4.20 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
64 72 0.251297 CATGAGGGCAACAACCTGGA 60.251 55.000 0.00 0.00 38.79 3.86
75 83 5.010213 GGCAACAACCTGGATTTGTTTAGTA 59.990 40.000 11.48 0.00 43.16 1.82
81 89 7.994334 ACAACCTGGATTTGTTTAGTAACACTA 59.006 33.333 0.00 0.00 43.66 2.74
303 325 0.968393 GCTCCGTCCAGTCTCCTCTT 60.968 60.000 0.00 0.00 0.00 2.85
325 347 8.110860 TCTTCTCTTCTCTTCTTCTTCTTCTC 57.889 38.462 0.00 0.00 0.00 2.87
327 349 5.714806 TCTCTTCTCTTCTTCTTCTTCTCCC 59.285 44.000 0.00 0.00 0.00 4.30
330 352 4.013728 TCTCTTCTTCTTCTTCTCCCTCG 58.986 47.826 0.00 0.00 0.00 4.63
331 353 3.761752 CTCTTCTTCTTCTTCTCCCTCGT 59.238 47.826 0.00 0.00 0.00 4.18
333 355 3.156288 TCTTCTTCTTCTCCCTCGTCA 57.844 47.619 0.00 0.00 0.00 4.35
334 356 3.702792 TCTTCTTCTTCTCCCTCGTCAT 58.297 45.455 0.00 0.00 0.00 3.06
335 357 4.090090 TCTTCTTCTTCTCCCTCGTCATT 58.910 43.478 0.00 0.00 0.00 2.57
412 459 4.135153 CACCAGCGTCCTCCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
466 518 3.465403 CCGTCCTCCTCCTGCCAG 61.465 72.222 0.00 0.00 0.00 4.85
467 519 2.681778 CGTCCTCCTCCTGCCAGT 60.682 66.667 0.00 0.00 0.00 4.00
488 540 5.068329 CAGTTTCTTCCTTTCCTTGCTTCTT 59.932 40.000 0.00 0.00 0.00 2.52
491 543 4.792068 TCTTCCTTTCCTTGCTTCTTTCA 58.208 39.130 0.00 0.00 0.00 2.69
502 554 1.888215 CTTCTTTCACTCTGCCAGCA 58.112 50.000 0.00 0.00 0.00 4.41
507 559 1.708993 TTCACTCTGCCAGCACCCTT 61.709 55.000 0.00 0.00 0.00 3.95
649 713 1.416030 GCTGGTTGGTTGGGATTTTGT 59.584 47.619 0.00 0.00 0.00 2.83
652 716 4.522114 CTGGTTGGTTGGGATTTTGTTTT 58.478 39.130 0.00 0.00 0.00 2.43
778 842 1.541310 AATTCAGACCGGTCGAGGCA 61.541 55.000 28.26 13.24 33.69 4.75
917 1003 3.624326 TTTCAGATTGGTTGTTGCGAG 57.376 42.857 0.00 0.00 0.00 5.03
935 1021 2.753029 GGCTGCAAGTGGAGGACT 59.247 61.111 0.50 0.00 35.94 3.85
936 1022 1.073897 GGCTGCAAGTGGAGGACTT 59.926 57.895 0.50 0.00 46.52 3.01
942 1028 3.579496 AAGTGGAGGACTTGTCCCT 57.421 52.632 15.44 3.68 43.71 4.20
943 1029 1.821088 AAGTGGAGGACTTGTCCCTT 58.179 50.000 15.44 9.15 43.71 3.95
944 1030 1.059913 AGTGGAGGACTTGTCCCTTG 58.940 55.000 15.44 0.00 33.36 3.61
945 1031 0.036875 GTGGAGGACTTGTCCCTTGG 59.963 60.000 15.44 0.00 33.36 3.61
959 1045 1.607148 CCCTTGGGACTGTCGTTTTTC 59.393 52.381 0.00 0.00 0.00 2.29
1113 1199 4.954202 ACCAGACTCAAGAATATGTACCGA 59.046 41.667 0.00 0.00 0.00 4.69
1128 1214 0.319641 ACCGAGAAAAGGTCTGACGC 60.320 55.000 1.07 0.00 37.44 5.19
1142 1228 2.887783 TCTGACGCTTCTCTTCTTCAGT 59.112 45.455 0.00 0.00 33.63 3.41
1319 1407 8.432013 AGATGTGCTACTTTGATATGGATTGTA 58.568 33.333 0.00 0.00 0.00 2.41
1350 1438 7.751732 TGAACATATTGTTTGTCATCTGTAGC 58.248 34.615 0.00 0.00 41.28 3.58
1384 1472 4.358214 TCTGGTGTAGTTGGTATGATGGA 58.642 43.478 0.00 0.00 0.00 3.41
1415 1508 9.678260 CCATTTTAATTTTGATGGTGGGATTAA 57.322 29.630 5.81 0.00 35.43 1.40
1429 1522 5.823045 GGTGGGATTAATGAGTAACTGAAGG 59.177 44.000 0.00 0.00 0.00 3.46
1435 1528 8.994170 GGATTAATGAGTAACTGAAGGAATAGC 58.006 37.037 0.00 0.00 0.00 2.97
1437 1530 5.854010 ATGAGTAACTGAAGGAATAGCGA 57.146 39.130 0.00 0.00 0.00 4.93
1466 1559 5.049405 AGTGCTTTCTTCGTAGTGAAAATGG 60.049 40.000 0.00 0.00 35.79 3.16
1475 1568 1.210155 GTGAAAATGGCGCGCTTCT 59.790 52.632 32.29 13.04 0.00 2.85
1476 1569 1.067199 GTGAAAATGGCGCGCTTCTG 61.067 55.000 32.29 0.00 0.00 3.02
1483 1576 2.740826 GCGCGCTTCTGGGTGTTA 60.741 61.111 26.67 0.00 38.63 2.41
1484 1577 2.106683 GCGCGCTTCTGGGTGTTAT 61.107 57.895 26.67 0.00 38.63 1.89
1485 1578 1.644786 GCGCGCTTCTGGGTGTTATT 61.645 55.000 26.67 0.00 38.63 1.40
1486 1579 0.373716 CGCGCTTCTGGGTGTTATTC 59.626 55.000 5.56 0.00 32.85 1.75
1488 1581 1.722011 CGCTTCTGGGTGTTATTCGT 58.278 50.000 0.00 0.00 0.00 3.85
1489 1582 1.393539 CGCTTCTGGGTGTTATTCGTG 59.606 52.381 0.00 0.00 0.00 4.35
1493 1586 4.023536 GCTTCTGGGTGTTATTCGTGAAAA 60.024 41.667 0.00 0.00 0.00 2.29
1541 1634 4.305989 TCAAGTTCTTTGTGCATTCCAC 57.694 40.909 0.00 0.00 44.90 4.02
1545 1638 3.953612 AGTTCTTTGTGCATTCCACTTCA 59.046 39.130 0.00 0.00 44.92 3.02
1546 1639 4.037208 AGTTCTTTGTGCATTCCACTTCAG 59.963 41.667 0.00 0.00 44.92 3.02
1578 1671 9.770097 CAATTAGCAGAAGAATCATTAGTCCTA 57.230 33.333 0.00 0.00 0.00 2.94
1661 1767 8.932791 AGTTGTTAAGAGTTTATATTGACGGTG 58.067 33.333 0.00 0.00 0.00 4.94
1797 1903 3.568853 CCTTTCCTCACGGAGTATACGAT 59.431 47.826 0.00 0.00 41.61 3.73
2068 2176 2.549754 CCAACACCAAGCACAGTAGAAG 59.450 50.000 0.00 0.00 0.00 2.85
2071 2179 3.886123 ACACCAAGCACAGTAGAAGTTT 58.114 40.909 0.00 0.00 0.00 2.66
2096 2204 3.955471 AGTGGCAACTATAACAGTGCAT 58.045 40.909 0.00 0.00 37.63 3.96
2097 2205 4.335416 AGTGGCAACTATAACAGTGCATT 58.665 39.130 0.00 0.00 37.63 3.56
2225 2334 4.948341 TCACTTTACTGTTGCCTCAGTA 57.052 40.909 12.13 12.13 45.31 2.74
2294 2404 7.261325 TGATAACTTTGCTTGCAGTTTTACAA 58.739 30.769 5.74 0.00 34.92 2.41
2295 2405 5.778161 AACTTTGCTTGCAGTTTTACAAC 57.222 34.783 0.00 0.00 28.27 3.32
2296 2406 4.815269 ACTTTGCTTGCAGTTTTACAACA 58.185 34.783 0.00 0.00 35.05 3.33
2643 2753 6.001460 TGAGTAAATTGAACGTTTCCAGGAT 58.999 36.000 0.46 0.00 0.00 3.24
2661 2771 5.107133 CAGGATCCTGATTTGTGATTTTGC 58.893 41.667 34.54 0.00 46.30 3.68
2870 3105 4.194640 CCGTGATCATCTTGATTGGAGTT 58.805 43.478 0.00 0.00 37.20 3.01
2957 3196 8.017418 TCTGGTTCATTTTAATTGGAAGTGTT 57.983 30.769 0.00 0.00 0.00 3.32
3017 3256 6.956299 TTAAAAGCGTACAATCCAGTCTAC 57.044 37.500 0.00 0.00 0.00 2.59
3112 3351 2.431419 TCACAGGTCAGTCCGTTTTACA 59.569 45.455 0.00 0.00 41.99 2.41
3455 3729 1.218196 TCCAGGTCCTCCTCAGATACC 59.782 57.143 0.00 0.00 43.07 2.73
3522 3803 1.081242 CCAGCACATCACGTTTGCC 60.081 57.895 4.94 0.00 36.91 4.52
3523 3804 1.440850 CAGCACATCACGTTTGCCG 60.441 57.895 4.94 0.00 44.03 5.69
3649 3930 2.710096 TATACTGGCCAGCCTTTGTC 57.290 50.000 33.06 0.00 36.94 3.18
3877 4158 5.498393 CAGAGCCAGATAGGAAATGCATAT 58.502 41.667 0.00 0.00 41.22 1.78
3920 4201 3.937778 TGGATTCTGATGAGCATTCCA 57.062 42.857 0.00 0.00 31.41 3.53
3946 4227 8.203937 TGTTTGCAACACCATGTAGTATATAC 57.796 34.615 0.00 4.60 36.25 1.47
4051 4335 9.793259 ACTGAAATTGTCCTGAAATAAGAACTA 57.207 29.630 0.00 0.00 0.00 2.24
4079 4363 7.192232 GCAGAATTTTCATGACATAGTCTTCC 58.808 38.462 0.00 0.00 33.15 3.46
4377 4661 4.094294 TGCACTGTAAAGCGGTATGAATTC 59.906 41.667 0.00 0.00 34.32 2.17
4419 4703 4.772678 GCCTGGATTCTTGGCCTT 57.227 55.556 3.32 0.00 40.71 4.35
4644 4928 6.479001 CGAAGAACTTCCATATATTCCGTTGT 59.521 38.462 8.66 0.00 36.27 3.32
4651 4935 6.795098 TCCATATATTCCGTTGTATTGCAC 57.205 37.500 0.00 0.00 0.00 4.57
4656 4940 2.676632 TCCGTTGTATTGCACGGTAT 57.323 45.000 10.53 0.00 40.29 2.73
4764 5048 6.622245 GCATGATGGATGGTTATTCAGATTCG 60.622 42.308 0.00 0.00 31.99 3.34
4776 5060 2.160205 TCAGATTCGGACGAGTTCAGT 58.840 47.619 0.00 0.00 0.00 3.41
4794 5078 1.903183 AGTTTACCAGAGCAGAGGACC 59.097 52.381 0.00 0.00 0.00 4.46
4863 5147 0.250858 TGTGCTCCAATGGTGACCTG 60.251 55.000 2.11 0.00 0.00 4.00
5022 5309 1.279271 GTGCACATCCTAGGGAACACT 59.721 52.381 13.17 0.00 34.34 3.55
5213 5500 5.560722 TTGGTTTGTACTGGATTCTGAGA 57.439 39.130 0.00 0.00 0.00 3.27
5288 5578 9.603921 TTAAACTGTAAATAGGGAACTTATCGG 57.396 33.333 0.00 0.00 43.67 4.18
5346 5636 2.475466 CGCGCCCTGCATCTTTCAT 61.475 57.895 0.00 0.00 46.97 2.57
5348 5638 1.660560 GCGCCCTGCATCTTTCATGT 61.661 55.000 0.00 0.00 45.45 3.21
5384 5674 2.422276 ATGTTCGCCTTTTGTCTTGC 57.578 45.000 0.00 0.00 0.00 4.01
5462 5752 6.546428 TGTCTAGGAAAATCTCTAACTGGG 57.454 41.667 0.00 0.00 0.00 4.45
5542 5835 9.252962 GTTGAAAAATCATCATCTTTGTGTCTT 57.747 29.630 0.00 0.00 0.00 3.01
5583 5876 5.076873 CCTTTGGTTTGGAGGAAGTTCATA 58.923 41.667 5.01 0.00 32.11 2.15
5692 5985 8.341892 GGATTGGTTCCTATCCTTCATATTTC 57.658 38.462 19.71 0.00 41.78 2.17
5693 5986 7.944554 GGATTGGTTCCTATCCTTCATATTTCA 59.055 37.037 19.71 0.00 41.78 2.69
5694 5987 9.354673 GATTGGTTCCTATCCTTCATATTTCAA 57.645 33.333 2.68 0.00 0.00 2.69
5695 5988 9.713684 ATTGGTTCCTATCCTTCATATTTCAAA 57.286 29.630 0.00 0.00 0.00 2.69
5696 5989 8.752005 TGGTTCCTATCCTTCATATTTCAAAG 57.248 34.615 0.00 0.00 0.00 2.77
5697 5990 7.779798 TGGTTCCTATCCTTCATATTTCAAAGG 59.220 37.037 0.00 0.00 40.80 3.11
5716 6009 8.055279 TCAAAGGAAAATAAACATGAGCCTAG 57.945 34.615 0.00 0.00 0.00 3.02
5763 6056 9.426837 CAATGTGAACCAAATGACATATCTTTT 57.573 29.630 0.00 0.00 33.61 2.27
5855 6149 9.813826 ATAATCCTAAATCCTATGAACCAAAGG 57.186 33.333 0.00 0.00 0.00 3.11
5857 6151 6.900194 TCCTAAATCCTATGAACCAAAGGAG 58.100 40.000 0.00 0.00 42.53 3.69
5858 6152 6.064717 CCTAAATCCTATGAACCAAAGGAGG 58.935 44.000 0.00 0.00 42.53 4.30
5859 6153 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
5860 6154 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
5910 6204 5.474825 TGCGACAGTCAGATAAATGTACAA 58.525 37.500 0.00 0.00 0.00 2.41
6020 6316 9.144747 CATAGTTTCAGGGTAATCATATTCTCG 57.855 37.037 0.00 0.00 0.00 4.04
6048 6344 3.228188 TCAGCAACAAAGGAGTTCCAT 57.772 42.857 0.28 0.00 38.89 3.41
6065 6361 7.364585 GGAGTTCCATGATAGCTAGCAGATAAT 60.365 40.741 17.82 5.59 35.64 1.28
6074 6370 9.616156 TGATAGCTAGCAGATAATACTACCTAC 57.384 37.037 18.83 0.00 0.00 3.18
6075 6371 9.841295 GATAGCTAGCAGATAATACTACCTACT 57.159 37.037 18.83 0.00 0.00 2.57
6076 6372 9.841295 ATAGCTAGCAGATAATACTACCTACTC 57.159 37.037 18.83 0.00 0.00 2.59
6077 6373 7.114095 AGCTAGCAGATAATACTACCTACTCC 58.886 42.308 18.83 0.00 0.00 3.85
6078 6374 6.319405 GCTAGCAGATAATACTACCTACTCCC 59.681 46.154 10.63 0.00 0.00 4.30
6079 6375 6.471942 AGCAGATAATACTACCTACTCCCT 57.528 41.667 0.00 0.00 0.00 4.20
6080 6376 6.486941 AGCAGATAATACTACCTACTCCCTC 58.513 44.000 0.00 0.00 0.00 4.30
6081 6377 5.653330 GCAGATAATACTACCTACTCCCTCC 59.347 48.000 0.00 0.00 0.00 4.30
6082 6378 5.881443 CAGATAATACTACCTACTCCCTCCG 59.119 48.000 0.00 0.00 0.00 4.63
6083 6379 5.551189 AGATAATACTACCTACTCCCTCCGT 59.449 44.000 0.00 0.00 0.00 4.69
6084 6380 3.786368 ATACTACCTACTCCCTCCGTC 57.214 52.381 0.00 0.00 0.00 4.79
6085 6381 0.550432 ACTACCTACTCCCTCCGTCC 59.450 60.000 0.00 0.00 0.00 4.79
6086 6382 0.534652 CTACCTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 0.00 4.79
6087 6383 0.982852 TACCTACTCCCTCCGTCCGA 60.983 60.000 0.00 0.00 0.00 4.55
6088 6384 1.150992 CCTACTCCCTCCGTCCGAT 59.849 63.158 0.00 0.00 0.00 4.18
6089 6385 0.467659 CCTACTCCCTCCGTCCGATT 60.468 60.000 0.00 0.00 0.00 3.34
6090 6386 1.400737 CTACTCCCTCCGTCCGATTT 58.599 55.000 0.00 0.00 0.00 2.17
6091 6387 2.579873 CTACTCCCTCCGTCCGATTTA 58.420 52.381 0.00 0.00 0.00 1.40
6092 6388 1.109609 ACTCCCTCCGTCCGATTTAC 58.890 55.000 0.00 0.00 0.00 2.01
6093 6389 1.341778 ACTCCCTCCGTCCGATTTACT 60.342 52.381 0.00 0.00 0.00 2.24
6094 6390 1.337387 CTCCCTCCGTCCGATTTACTC 59.663 57.143 0.00 0.00 0.00 2.59
6096 6392 0.737219 CCTCCGTCCGATTTACTCGT 59.263 55.000 0.00 0.00 46.18 4.18
6097 6393 1.268437 CCTCCGTCCGATTTACTCGTC 60.268 57.143 0.00 0.00 46.18 4.20
6098 6394 1.399440 CTCCGTCCGATTTACTCGTCA 59.601 52.381 0.00 0.00 46.18 4.35
6099 6395 2.019249 TCCGTCCGATTTACTCGTCAT 58.981 47.619 0.00 0.00 46.18 3.06
6100 6396 2.117137 CCGTCCGATTTACTCGTCATG 58.883 52.381 0.00 0.00 46.18 3.07
6101 6397 2.117137 CGTCCGATTTACTCGTCATGG 58.883 52.381 0.00 0.00 46.18 3.66
6102 6398 2.479049 CGTCCGATTTACTCGTCATGGT 60.479 50.000 0.00 0.00 46.18 3.55
6103 6399 3.518590 GTCCGATTTACTCGTCATGGTT 58.481 45.455 0.00 0.00 46.18 3.67
6104 6400 3.930848 GTCCGATTTACTCGTCATGGTTT 59.069 43.478 0.00 0.00 46.18 3.27
6105 6401 4.390909 GTCCGATTTACTCGTCATGGTTTT 59.609 41.667 0.00 0.00 46.18 2.43
6106 6402 5.577945 GTCCGATTTACTCGTCATGGTTTTA 59.422 40.000 0.00 0.00 46.18 1.52
6107 6403 5.808540 TCCGATTTACTCGTCATGGTTTTAG 59.191 40.000 0.00 0.00 46.18 1.85
6108 6404 5.579511 CCGATTTACTCGTCATGGTTTTAGT 59.420 40.000 0.00 0.00 46.18 2.24
6109 6405 6.091713 CCGATTTACTCGTCATGGTTTTAGTT 59.908 38.462 0.00 0.00 46.18 2.24
6110 6406 7.171434 CGATTTACTCGTCATGGTTTTAGTTC 58.829 38.462 0.00 0.00 42.56 3.01
6111 6407 7.148705 CGATTTACTCGTCATGGTTTTAGTTCA 60.149 37.037 0.00 0.00 42.56 3.18
6112 6408 7.789273 TTTACTCGTCATGGTTTTAGTTCAA 57.211 32.000 0.00 0.00 0.00 2.69
6113 6409 5.668558 ACTCGTCATGGTTTTAGTTCAAC 57.331 39.130 0.00 0.00 0.00 3.18
6114 6410 5.120399 ACTCGTCATGGTTTTAGTTCAACA 58.880 37.500 0.00 0.00 0.00 3.33
6115 6411 5.587043 ACTCGTCATGGTTTTAGTTCAACAA 59.413 36.000 0.00 0.00 0.00 2.83
6116 6412 5.812652 TCGTCATGGTTTTAGTTCAACAAC 58.187 37.500 0.00 0.00 0.00 3.32
6117 6413 4.668837 CGTCATGGTTTTAGTTCAACAACG 59.331 41.667 0.00 0.00 37.61 4.10
6118 6414 5.502706 CGTCATGGTTTTAGTTCAACAACGA 60.503 40.000 0.00 0.00 37.61 3.85
6119 6415 5.907391 GTCATGGTTTTAGTTCAACAACGAG 59.093 40.000 0.00 0.00 37.61 4.18
6120 6416 5.587043 TCATGGTTTTAGTTCAACAACGAGT 59.413 36.000 0.00 0.00 37.61 4.18
6121 6417 6.762187 TCATGGTTTTAGTTCAACAACGAGTA 59.238 34.615 0.00 0.00 37.61 2.59
6122 6418 6.981762 TGGTTTTAGTTCAACAACGAGTAA 57.018 33.333 0.00 0.00 37.61 2.24
6123 6419 7.375106 TGGTTTTAGTTCAACAACGAGTAAA 57.625 32.000 0.00 0.00 37.61 2.01
6124 6420 7.987649 TGGTTTTAGTTCAACAACGAGTAAAT 58.012 30.769 0.00 0.00 37.61 1.40
6125 6421 8.124199 TGGTTTTAGTTCAACAACGAGTAAATC 58.876 33.333 0.00 0.00 37.61 2.17
6145 6441 1.041437 GGAACGGAGGGAGTAGATGG 58.959 60.000 0.00 0.00 0.00 3.51
6146 6442 0.389757 GAACGGAGGGAGTAGATGGC 59.610 60.000 0.00 0.00 0.00 4.40
6147 6443 0.325296 AACGGAGGGAGTAGATGGCA 60.325 55.000 0.00 0.00 0.00 4.92
6148 6444 0.757188 ACGGAGGGAGTAGATGGCAG 60.757 60.000 0.00 0.00 0.00 4.85
6149 6445 1.751563 GGAGGGAGTAGATGGCAGC 59.248 63.158 0.00 0.00 0.00 5.25
6150 6446 0.762461 GGAGGGAGTAGATGGCAGCT 60.762 60.000 11.24 11.24 0.00 4.24
6151 6447 0.392336 GAGGGAGTAGATGGCAGCTG 59.608 60.000 16.84 10.11 0.00 4.24
6152 6448 0.031716 AGGGAGTAGATGGCAGCTGA 60.032 55.000 20.43 0.00 0.00 4.26
6153 6449 1.055040 GGGAGTAGATGGCAGCTGAT 58.945 55.000 20.43 1.92 0.00 2.90
6154 6450 1.001860 GGGAGTAGATGGCAGCTGATC 59.998 57.143 20.43 12.70 0.00 2.92
6155 6451 1.690893 GGAGTAGATGGCAGCTGATCA 59.309 52.381 20.43 15.21 0.00 2.92
6156 6452 2.547642 GGAGTAGATGGCAGCTGATCAC 60.548 54.545 20.43 12.51 0.00 3.06
6157 6453 2.102084 GAGTAGATGGCAGCTGATCACA 59.898 50.000 20.43 10.57 0.00 3.58
6158 6454 2.704596 AGTAGATGGCAGCTGATCACAT 59.295 45.455 20.43 15.02 0.00 3.21
6159 6455 2.730934 AGATGGCAGCTGATCACATT 57.269 45.000 20.43 0.00 0.00 2.71
6160 6456 3.014304 AGATGGCAGCTGATCACATTT 57.986 42.857 20.43 8.00 0.00 2.32
6161 6457 2.688446 AGATGGCAGCTGATCACATTTG 59.312 45.455 20.43 0.00 0.00 2.32
6162 6458 0.528924 TGGCAGCTGATCACATTTGC 59.471 50.000 20.43 0.00 35.77 3.68
6163 6459 0.524816 GGCAGCTGATCACATTTGCG 60.525 55.000 20.43 0.00 36.67 4.85
6164 6460 0.524816 GCAGCTGATCACATTTGCGG 60.525 55.000 20.43 0.00 0.00 5.69
6165 6461 0.099968 CAGCTGATCACATTTGCGGG 59.900 55.000 8.42 0.00 0.00 6.13
6166 6462 0.322816 AGCTGATCACATTTGCGGGT 60.323 50.000 0.00 0.00 0.00 5.28
6167 6463 0.099436 GCTGATCACATTTGCGGGTC 59.901 55.000 0.00 0.00 0.00 4.46
6168 6464 0.374758 CTGATCACATTTGCGGGTCG 59.625 55.000 0.00 0.00 0.00 4.79
6169 6465 0.321210 TGATCACATTTGCGGGTCGT 60.321 50.000 0.00 0.00 0.00 4.34
6170 6466 0.096976 GATCACATTTGCGGGTCGTG 59.903 55.000 0.00 0.00 0.00 4.35
6171 6467 0.321210 ATCACATTTGCGGGTCGTGA 60.321 50.000 0.00 0.00 40.59 4.35
6172 6468 0.321210 TCACATTTGCGGGTCGTGAT 60.321 50.000 0.00 0.00 31.92 3.06
6173 6469 0.179192 CACATTTGCGGGTCGTGATG 60.179 55.000 0.00 0.00 0.00 3.07
6174 6470 1.305219 ACATTTGCGGGTCGTGATGG 61.305 55.000 0.00 0.00 0.00 3.51
6175 6471 1.002624 ATTTGCGGGTCGTGATGGT 60.003 52.632 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 72 8.992073 CCGGTTAACTAGTGTTACTAAACAAAT 58.008 33.333 5.42 0.00 46.84 2.32
75 83 2.105306 ACTTGGCCGGTTAACTAGTGTT 59.895 45.455 1.90 0.00 39.98 3.32
81 89 4.813346 CCACTTGGCCGGTTAACT 57.187 55.556 1.90 0.00 0.00 2.24
253 272 3.001514 CTGACCCATCACCCCCTG 58.998 66.667 0.00 0.00 0.00 4.45
303 325 5.714806 GGGAGAAGAAGAAGAAGAGAAGAGA 59.285 44.000 0.00 0.00 0.00 3.10
325 347 2.758089 GCAGCAGCAATGACGAGGG 61.758 63.158 0.00 0.00 41.58 4.30
327 349 1.424240 CAGCAGCAGCAATGACGAG 59.576 57.895 3.17 0.00 45.49 4.18
330 352 0.098376 GTAGCAGCAGCAGCAATGAC 59.902 55.000 12.92 0.83 45.49 3.06
331 353 1.028330 GGTAGCAGCAGCAGCAATGA 61.028 55.000 12.92 0.00 45.49 2.57
333 355 0.395311 ATGGTAGCAGCAGCAGCAAT 60.395 50.000 12.92 0.00 45.49 3.56
334 356 1.001764 ATGGTAGCAGCAGCAGCAA 60.002 52.632 12.92 0.00 45.49 3.91
335 357 1.450848 GATGGTAGCAGCAGCAGCA 60.451 57.895 12.92 5.91 45.49 4.41
403 450 4.144727 GAGAGGGGCGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
466 518 5.521906 AAGAAGCAAGGAAAGGAAGAAAC 57.478 39.130 0.00 0.00 0.00 2.78
467 519 5.656416 TGAAAGAAGCAAGGAAAGGAAGAAA 59.344 36.000 0.00 0.00 0.00 2.52
488 540 1.708993 AAGGGTGCTGGCAGAGTGAA 61.709 55.000 20.86 0.00 0.00 3.18
491 543 1.835927 GAGAAGGGTGCTGGCAGAGT 61.836 60.000 20.86 0.00 0.00 3.24
502 554 1.684049 CAGCGAGGAGGAGAAGGGT 60.684 63.158 0.00 0.00 0.00 4.34
507 559 1.214175 AGAGATTCAGCGAGGAGGAGA 59.786 52.381 0.00 0.00 0.00 3.71
652 716 3.505680 CCGAAATCACCACTGGAATCAAA 59.494 43.478 0.71 0.00 0.00 2.69
659 723 0.881118 CCAACCGAAATCACCACTGG 59.119 55.000 0.00 0.00 0.00 4.00
660 724 1.604604 ACCAACCGAAATCACCACTG 58.395 50.000 0.00 0.00 0.00 3.66
663 727 3.067461 CAGAAAACCAACCGAAATCACCA 59.933 43.478 0.00 0.00 0.00 4.17
666 730 2.287308 CGCAGAAAACCAACCGAAATCA 60.287 45.455 0.00 0.00 0.00 2.57
767 831 1.446272 GAAGAACTGCCTCGACCGG 60.446 63.158 0.00 0.00 0.00 5.28
771 835 1.213013 GAGCGAAGAACTGCCTCGA 59.787 57.895 0.00 0.00 0.00 4.04
778 842 4.083862 GGCCCGGAGCGAAGAACT 62.084 66.667 0.73 0.00 45.17 3.01
867 953 4.823157 TCACGGATAAAAATCGACCTTCA 58.177 39.130 0.00 0.00 0.00 3.02
917 1003 2.360475 GTCCTCCACTTGCAGCCC 60.360 66.667 0.00 0.00 0.00 5.19
938 1024 0.841289 AAAACGACAGTCCCAAGGGA 59.159 50.000 3.04 3.04 42.90 4.20
939 1025 1.607148 GAAAAACGACAGTCCCAAGGG 59.393 52.381 0.00 0.00 0.00 3.95
940 1026 1.263217 CGAAAAACGACAGTCCCAAGG 59.737 52.381 0.00 0.00 45.77 3.61
941 1027 1.333791 GCGAAAAACGACAGTCCCAAG 60.334 52.381 0.00 0.00 45.77 3.61
942 1028 0.658897 GCGAAAAACGACAGTCCCAA 59.341 50.000 0.00 0.00 45.77 4.12
943 1029 1.492319 CGCGAAAAACGACAGTCCCA 61.492 55.000 0.00 0.00 45.77 4.37
944 1030 1.203313 CGCGAAAAACGACAGTCCC 59.797 57.895 0.00 0.00 45.77 4.46
945 1031 0.161024 CTCGCGAAAAACGACAGTCC 59.839 55.000 11.33 0.00 45.77 3.85
959 1045 0.459237 ACAGCTCTCAAATCCTCGCG 60.459 55.000 0.00 0.00 0.00 5.87
1113 1199 2.630580 AGAGAAGCGTCAGACCTTTTCT 59.369 45.455 14.23 14.23 30.39 2.52
1178 1264 3.382227 TGGCAGCCAAATACAGATGAATG 59.618 43.478 13.33 0.00 0.00 2.67
1233 1321 2.104622 TGAACTGGTCACATGCAGAGAA 59.895 45.455 5.23 0.00 0.00 2.87
1300 1388 8.554528 CAAGCAGTACAATCCATATCAAAGTAG 58.445 37.037 0.00 0.00 0.00 2.57
1319 1407 6.389830 TGACAAACAATATGTTCAAGCAGT 57.610 33.333 0.00 0.00 40.14 4.40
1350 1438 1.076533 ACACCAGATTACTTCGCGCG 61.077 55.000 26.76 26.76 0.00 6.86
1397 1485 8.695456 GTTACTCATTAATCCCACCATCAAAAT 58.305 33.333 0.00 0.00 0.00 1.82
1398 1486 7.893302 AGTTACTCATTAATCCCACCATCAAAA 59.107 33.333 0.00 0.00 0.00 2.44
1415 1508 5.854010 TCGCTATTCCTTCAGTTACTCAT 57.146 39.130 0.00 0.00 0.00 2.90
1429 1522 6.625310 CGAAGAAAGCACTAAAATCGCTATTC 59.375 38.462 0.00 0.00 34.11 1.75
1435 1528 6.089016 TCACTACGAAGAAAGCACTAAAATCG 59.911 38.462 0.00 0.00 35.36 3.34
1437 1530 7.724305 TTCACTACGAAGAAAGCACTAAAAT 57.276 32.000 0.00 0.00 0.00 1.82
1466 1559 1.644786 AATAACACCCAGAAGCGCGC 61.645 55.000 26.66 26.66 0.00 6.86
1513 1606 8.992073 GGAATGCACAAAGAACTTGAATAAAAT 58.008 29.630 0.00 0.00 38.50 1.82
1514 1607 7.984050 TGGAATGCACAAAGAACTTGAATAAAA 59.016 29.630 0.00 0.00 38.50 1.52
1520 1613 3.953612 AGTGGAATGCACAAAGAACTTGA 59.046 39.130 7.79 0.00 38.50 3.02
1527 1620 3.316029 TCACTGAAGTGGAATGCACAAAG 59.684 43.478 7.79 4.00 45.65 2.77
1541 1634 7.194607 TCTTCTGCTAATTGTTTCACTGAAG 57.805 36.000 0.00 0.00 35.60 3.02
1545 1638 7.750229 TGATTCTTCTGCTAATTGTTTCACT 57.250 32.000 0.00 0.00 0.00 3.41
1546 1639 8.976986 AATGATTCTTCTGCTAATTGTTTCAC 57.023 30.769 0.00 0.00 0.00 3.18
1578 1671 8.674263 TCAAAAATACACAGGCATCAAATTTT 57.326 26.923 0.00 0.00 0.00 1.82
1633 1726 9.755064 CCGTCAATATAAACTCTTAACAACTTG 57.245 33.333 0.00 0.00 0.00 3.16
1658 1764 2.726821 TCTGCATCAAGGGAAATCACC 58.273 47.619 0.00 0.00 0.00 4.02
1661 1767 6.127535 TGAGAATTTCTGCATCAAGGGAAATC 60.128 38.462 3.03 4.84 37.40 2.17
1797 1903 4.160439 AGAGCTCCAATAACATCTTCGTCA 59.840 41.667 10.93 0.00 0.00 4.35
1966 2074 5.982516 CCAAGTACAGAGCAGATCATAAGAC 59.017 44.000 0.00 0.00 0.00 3.01
1998 2106 8.043113 TGAGATGTATTGCAGTCAGTATTTTCT 58.957 33.333 0.00 0.00 0.00 2.52
2068 2176 7.908601 GCACTGTTATAGTTGCCACTTATAAAC 59.091 37.037 0.00 0.00 37.60 2.01
2071 2179 6.645306 TGCACTGTTATAGTTGCCACTTATA 58.355 36.000 0.00 0.00 37.60 0.98
2643 2753 6.424509 GTGAAATGCAAAATCACAAATCAGGA 59.575 34.615 19.18 0.00 42.31 3.86
2661 2771 5.765176 TGATGCAGAAAGAACTGTGAAATG 58.235 37.500 0.00 0.00 39.73 2.32
2870 3105 2.168106 ACCAAAGTGTTGCATGCTGAAA 59.832 40.909 20.33 1.44 33.01 2.69
2957 3196 3.181455 ACTTGTGTATGTTCAGTGCTCCA 60.181 43.478 0.00 0.00 0.00 3.86
3017 3256 4.090930 CGCCTTCGGAAATAACGGTATATG 59.909 45.833 0.00 0.00 0.00 1.78
3209 3475 4.813161 ACAGGAAAATGACATAGATCTGCG 59.187 41.667 5.18 0.00 0.00 5.18
3455 3729 4.649692 AGTCAATAGGATGCCAAGCTATG 58.350 43.478 0.00 0.00 0.00 2.23
3523 3804 0.439985 CACTATGACAGCGTGCACAC 59.560 55.000 18.64 7.31 0.00 3.82
3524 3805 0.033366 ACACTATGACAGCGTGCACA 59.967 50.000 18.64 0.00 32.07 4.57
3525 3806 0.439985 CACACTATGACAGCGTGCAC 59.560 55.000 6.82 6.82 30.93 4.57
3526 3807 0.033366 ACACACTATGACAGCGTGCA 59.967 50.000 6.77 0.00 40.35 4.57
3527 3808 1.920574 CTACACACTATGACAGCGTGC 59.079 52.381 6.77 0.00 40.35 5.34
3528 3809 1.920574 GCTACACACTATGACAGCGTG 59.079 52.381 5.60 5.60 42.06 5.34
3531 3812 2.672961 TGGCTACACACTATGACAGC 57.327 50.000 0.00 0.00 38.44 4.40
3543 3824 3.949132 TGCACTGTCAATAATGGCTACA 58.051 40.909 0.00 0.00 30.51 2.74
4051 4335 6.765036 AGACTATGTCATGAAAATTCTGCGAT 59.235 34.615 0.00 0.00 34.60 4.58
4079 4363 4.669206 AGAGTTGTCTGAGATATGCAGG 57.331 45.455 0.00 0.00 34.20 4.85
4114 4398 3.243367 GCAGTGCCTGTTCACACAAATAA 60.243 43.478 2.85 0.00 39.30 1.40
4116 4400 1.067516 GCAGTGCCTGTTCACACAAAT 59.932 47.619 2.85 0.00 39.30 2.32
4377 4661 0.952497 ACACCTTGCTGTGCATCTCG 60.952 55.000 0.00 0.00 38.76 4.04
4419 4703 0.970937 CTAGACCAAGGCTCGGACCA 60.971 60.000 0.00 0.00 0.00 4.02
4644 4928 7.038587 AGGTCTTTATATCCATACCGTGCAATA 60.039 37.037 0.00 0.00 32.18 1.90
4651 4935 5.245301 TGTGGAGGTCTTTATATCCATACCG 59.755 44.000 0.00 0.00 43.42 4.02
4656 4940 6.884472 TTCTTGTGGAGGTCTTTATATCCA 57.116 37.500 0.00 0.00 39.50 3.41
4764 5048 3.576648 CTCTGGTAAACTGAACTCGTCC 58.423 50.000 0.00 0.00 0.00 4.79
4776 5060 0.895530 CGGTCCTCTGCTCTGGTAAA 59.104 55.000 0.00 0.00 0.00 2.01
4794 5078 1.667724 GCAGTGTTGATGGATCCTTCG 59.332 52.381 19.69 8.00 0.00 3.79
4803 5087 2.029739 TGCCAGAAATGCAGTGTTGATG 60.030 45.455 0.00 0.00 34.05 3.07
4835 5119 2.610976 CCATTGGAGCACATTGTGTTGG 60.611 50.000 17.64 11.09 35.75 3.77
4863 5147 4.935352 AGAATCCTGTGATGAGTAGCTC 57.065 45.455 0.00 0.00 0.00 4.09
5022 5309 2.582226 CTCCGAGCGCGCACAATA 60.582 61.111 35.10 13.75 35.83 1.90
5127 5414 3.842007 AGAAGGCTCTCATGAGGAATG 57.158 47.619 22.42 11.28 40.53 2.67
5306 5596 5.225949 GCGAAACAAAATCTGAAGCTATTCG 59.774 40.000 0.00 0.00 38.34 3.34
5346 5636 4.397420 ACATTTCTAGCATGAACACCACA 58.603 39.130 0.00 0.00 0.00 4.17
5348 5638 4.154015 CGAACATTTCTAGCATGAACACCA 59.846 41.667 0.00 0.00 0.00 4.17
5384 5674 6.259608 AGGAAGCATCTGAATCTTACGAATTG 59.740 38.462 0.00 0.00 0.00 2.32
5462 5752 7.814107 TGCAAATACTTTTGAATCCATGAGTTC 59.186 33.333 0.00 0.00 44.11 3.01
5542 5835 0.110486 GGAGTCCAACCTTTCCAGCA 59.890 55.000 3.60 0.00 0.00 4.41
5624 5917 3.731431 TCCTATGAACCAAAGGGCTCTA 58.269 45.455 0.00 0.00 37.90 2.43
5668 5961 8.924511 TGAAATATGAAGGATAGGAACCAATC 57.075 34.615 0.00 0.00 0.00 2.67
5669 5962 9.713684 TTTGAAATATGAAGGATAGGAACCAAT 57.286 29.630 0.00 0.00 0.00 3.16
5670 5963 9.189156 CTTTGAAATATGAAGGATAGGAACCAA 57.811 33.333 0.00 0.00 0.00 3.67
5671 5964 7.779798 CCTTTGAAATATGAAGGATAGGAACCA 59.220 37.037 0.00 0.00 41.97 3.67
5672 5965 7.998964 TCCTTTGAAATATGAAGGATAGGAACC 59.001 37.037 0.15 0.00 42.90 3.62
5673 5966 8.980481 TCCTTTGAAATATGAAGGATAGGAAC 57.020 34.615 0.15 0.00 42.90 3.62
5674 5967 9.989296 TTTCCTTTGAAATATGAAGGATAGGAA 57.011 29.630 5.03 0.00 45.99 3.36
5675 5968 9.989296 TTTTCCTTTGAAATATGAAGGATAGGA 57.011 29.630 5.03 0.00 45.99 2.94
5687 5980 9.651913 GGCTCATGTTTATTTTCCTTTGAAATA 57.348 29.630 0.00 0.00 40.08 1.40
5688 5981 8.377799 AGGCTCATGTTTATTTTCCTTTGAAAT 58.622 29.630 0.00 0.00 40.08 2.17
5689 5982 7.734942 AGGCTCATGTTTATTTTCCTTTGAAA 58.265 30.769 0.00 0.00 38.69 2.69
5690 5983 7.301868 AGGCTCATGTTTATTTTCCTTTGAA 57.698 32.000 0.00 0.00 0.00 2.69
5691 5984 6.916360 AGGCTCATGTTTATTTTCCTTTGA 57.084 33.333 0.00 0.00 0.00 2.69
5692 5985 7.970614 GTCTAGGCTCATGTTTATTTTCCTTTG 59.029 37.037 0.00 0.00 0.00 2.77
5693 5986 7.890655 AGTCTAGGCTCATGTTTATTTTCCTTT 59.109 33.333 0.00 0.00 0.00 3.11
5694 5987 7.406104 AGTCTAGGCTCATGTTTATTTTCCTT 58.594 34.615 0.00 0.00 0.00 3.36
5695 5988 6.963322 AGTCTAGGCTCATGTTTATTTTCCT 58.037 36.000 0.00 0.00 0.00 3.36
5696 5989 6.823689 TGAGTCTAGGCTCATGTTTATTTTCC 59.176 38.462 23.07 0.00 40.23 3.13
5697 5990 7.849804 TGAGTCTAGGCTCATGTTTATTTTC 57.150 36.000 23.07 0.00 40.23 2.29
5698 5991 8.680903 CATTGAGTCTAGGCTCATGTTTATTTT 58.319 33.333 26.91 2.41 43.99 1.82
5699 5992 8.049117 TCATTGAGTCTAGGCTCATGTTTATTT 58.951 33.333 26.91 3.37 43.99 1.40
5700 5993 7.568349 TCATTGAGTCTAGGCTCATGTTTATT 58.432 34.615 26.91 4.66 43.99 1.40
5701 5994 7.129457 TCATTGAGTCTAGGCTCATGTTTAT 57.871 36.000 26.91 14.49 43.99 1.40
5702 5995 6.544928 TCATTGAGTCTAGGCTCATGTTTA 57.455 37.500 26.91 12.75 43.99 2.01
5703 5996 5.426689 TCATTGAGTCTAGGCTCATGTTT 57.573 39.130 26.91 10.30 43.99 2.83
5704 5997 5.426689 TTCATTGAGTCTAGGCTCATGTT 57.573 39.130 26.91 12.69 43.99 2.71
5705 5998 5.426689 TTTCATTGAGTCTAGGCTCATGT 57.573 39.130 26.91 16.10 43.99 3.21
5706 5999 6.748333 TTTTTCATTGAGTCTAGGCTCATG 57.252 37.500 26.91 23.46 43.99 3.07
5730 6023 6.493115 TGTCATTTGGTTCACATTGTAGGAAT 59.507 34.615 0.00 0.00 0.00 3.01
5732 6025 5.380900 TGTCATTTGGTTCACATTGTAGGA 58.619 37.500 0.00 0.00 0.00 2.94
5734 6027 8.896744 AGATATGTCATTTGGTTCACATTGTAG 58.103 33.333 0.00 0.00 31.83 2.74
5735 6028 8.806429 AGATATGTCATTTGGTTCACATTGTA 57.194 30.769 0.00 0.00 31.83 2.41
5736 6029 7.707624 AGATATGTCATTTGGTTCACATTGT 57.292 32.000 0.00 0.00 31.83 2.71
5737 6030 8.991243 AAAGATATGTCATTTGGTTCACATTG 57.009 30.769 0.00 0.00 31.83 2.82
5738 6031 9.643693 GAAAAGATATGTCATTTGGTTCACATT 57.356 29.630 0.00 0.00 31.83 2.71
5791 6084 6.715280 ACTTGTAGGAAATGAGATGACATGT 58.285 36.000 0.00 0.00 0.00 3.21
5838 6132 3.373110 GGCCTCCTTTGGTTCATAGGATT 60.373 47.826 0.00 0.00 39.94 3.01
5839 6133 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
5840 6134 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
5841 6135 1.410224 GGGCCTCCTTTGGTTCATAGG 60.410 57.143 0.84 0.00 34.61 2.57
5842 6136 1.284785 TGGGCCTCCTTTGGTTCATAG 59.715 52.381 4.53 0.00 0.00 2.23
5844 6138 0.040204 CTGGGCCTCCTTTGGTTCAT 59.960 55.000 4.53 0.00 0.00 2.57
5845 6139 1.460255 CTGGGCCTCCTTTGGTTCA 59.540 57.895 4.53 0.00 0.00 3.18
5848 6142 1.664956 AAACCTGGGCCTCCTTTGGT 61.665 55.000 4.53 0.56 34.93 3.67
5849 6143 0.471780 AAAACCTGGGCCTCCTTTGG 60.472 55.000 4.53 0.00 0.00 3.28
5852 6146 0.113190 CTGAAAACCTGGGCCTCCTT 59.887 55.000 4.53 0.00 0.00 3.36
5853 6147 1.068352 ACTGAAAACCTGGGCCTCCT 61.068 55.000 4.53 0.00 0.00 3.69
5854 6148 0.696501 TACTGAAAACCTGGGCCTCC 59.303 55.000 4.53 0.00 0.00 4.30
5855 6149 2.369394 CATACTGAAAACCTGGGCCTC 58.631 52.381 4.53 0.00 0.00 4.70
5857 6151 1.474330 CCATACTGAAAACCTGGGCC 58.526 55.000 0.00 0.00 0.00 5.80
5858 6152 0.817654 GCCATACTGAAAACCTGGGC 59.182 55.000 0.00 0.00 0.00 5.36
5859 6153 2.514458 AGCCATACTGAAAACCTGGG 57.486 50.000 0.00 0.00 0.00 4.45
5889 6183 7.963981 ACATTTGTACATTTATCTGACTGTCG 58.036 34.615 0.00 0.00 0.00 4.35
5958 6254 8.413229 ACATGCACTGTTTAATTAGTTTGACTT 58.587 29.630 0.00 0.00 32.90 3.01
6020 6316 4.276926 ACTCCTTTGTTGCTGAATTCAGAC 59.723 41.667 34.43 24.86 46.59 3.51
6065 6361 1.771255 GGACGGAGGGAGTAGGTAGTA 59.229 57.143 0.00 0.00 0.00 1.82
6074 6370 1.337387 GAGTAAATCGGACGGAGGGAG 59.663 57.143 0.00 0.00 0.00 4.30
6075 6371 1.396653 GAGTAAATCGGACGGAGGGA 58.603 55.000 0.00 0.00 0.00 4.20
6076 6372 3.961576 GAGTAAATCGGACGGAGGG 57.038 57.895 0.00 0.00 0.00 4.30
6086 6382 8.025243 TGAACTAAAACCATGACGAGTAAATC 57.975 34.615 0.00 0.00 0.00 2.17
6087 6383 7.972832 TGAACTAAAACCATGACGAGTAAAT 57.027 32.000 0.00 0.00 0.00 1.40
6088 6384 7.280428 TGTTGAACTAAAACCATGACGAGTAAA 59.720 33.333 0.00 0.00 0.00 2.01
6089 6385 6.762187 TGTTGAACTAAAACCATGACGAGTAA 59.238 34.615 0.00 0.00 0.00 2.24
6090 6386 6.282167 TGTTGAACTAAAACCATGACGAGTA 58.718 36.000 0.00 0.00 0.00 2.59
6091 6387 5.120399 TGTTGAACTAAAACCATGACGAGT 58.880 37.500 0.00 0.00 0.00 4.18
6092 6388 5.666969 TGTTGAACTAAAACCATGACGAG 57.333 39.130 0.00 0.00 0.00 4.18
6093 6389 5.502706 CGTTGTTGAACTAAAACCATGACGA 60.503 40.000 0.00 0.00 0.00 4.20
6094 6390 4.668837 CGTTGTTGAACTAAAACCATGACG 59.331 41.667 0.00 0.00 0.00 4.35
6095 6391 5.812652 TCGTTGTTGAACTAAAACCATGAC 58.187 37.500 0.00 0.00 0.00 3.06
6096 6392 5.587043 ACTCGTTGTTGAACTAAAACCATGA 59.413 36.000 0.00 0.00 0.00 3.07
6097 6393 5.816919 ACTCGTTGTTGAACTAAAACCATG 58.183 37.500 0.00 0.00 0.00 3.66
6098 6394 7.556733 TTACTCGTTGTTGAACTAAAACCAT 57.443 32.000 0.00 0.00 0.00 3.55
6099 6395 6.981762 TTACTCGTTGTTGAACTAAAACCA 57.018 33.333 0.00 0.00 0.00 3.67
6100 6396 7.319615 CGATTTACTCGTTGTTGAACTAAAACC 59.680 37.037 0.00 0.00 42.56 3.27
6101 6397 7.319615 CCGATTTACTCGTTGTTGAACTAAAAC 59.680 37.037 0.00 0.00 46.18 2.43
6102 6398 7.224362 TCCGATTTACTCGTTGTTGAACTAAAA 59.776 33.333 0.00 0.00 46.18 1.52
6103 6399 6.700960 TCCGATTTACTCGTTGTTGAACTAAA 59.299 34.615 0.00 0.00 46.18 1.85
6104 6400 6.215121 TCCGATTTACTCGTTGTTGAACTAA 58.785 36.000 0.00 0.00 46.18 2.24
6105 6401 5.771469 TCCGATTTACTCGTTGTTGAACTA 58.229 37.500 0.00 0.00 46.18 2.24
6106 6402 4.624015 TCCGATTTACTCGTTGTTGAACT 58.376 39.130 0.00 0.00 46.18 3.01
6107 6403 4.977741 TCCGATTTACTCGTTGTTGAAC 57.022 40.909 0.00 0.00 46.18 3.18
6108 6404 4.084952 CGTTCCGATTTACTCGTTGTTGAA 60.085 41.667 0.00 0.00 46.18 2.69
6109 6405 3.426191 CGTTCCGATTTACTCGTTGTTGA 59.574 43.478 0.00 0.00 46.18 3.18
6110 6406 3.422603 CCGTTCCGATTTACTCGTTGTTG 60.423 47.826 0.00 0.00 46.18 3.33
6111 6407 2.733026 CCGTTCCGATTTACTCGTTGTT 59.267 45.455 0.00 0.00 46.18 2.83
6112 6408 2.030007 TCCGTTCCGATTTACTCGTTGT 60.030 45.455 0.00 0.00 46.18 3.32
6113 6409 2.597305 CTCCGTTCCGATTTACTCGTTG 59.403 50.000 0.00 0.00 46.18 4.10
6114 6410 2.416431 CCTCCGTTCCGATTTACTCGTT 60.416 50.000 0.00 0.00 46.18 3.85
6115 6411 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
6117 6413 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
6118 6414 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
6119 6415 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
6120 6416 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
6121 6417 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
6122 6418 1.064166 TCTACTCCCTCCGTTCCGATT 60.064 52.381 0.00 0.00 0.00 3.34
6123 6419 0.549950 TCTACTCCCTCCGTTCCGAT 59.450 55.000 0.00 0.00 0.00 4.18
6124 6420 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
6125 6421 0.669077 CATCTACTCCCTCCGTTCCG 59.331 60.000 0.00 0.00 0.00 4.30
6126 6422 1.041437 CCATCTACTCCCTCCGTTCC 58.959 60.000 0.00 0.00 0.00 3.62
6127 6423 0.389757 GCCATCTACTCCCTCCGTTC 59.610 60.000 0.00 0.00 0.00 3.95
6128 6424 0.325296 TGCCATCTACTCCCTCCGTT 60.325 55.000 0.00 0.00 0.00 4.44
6129 6425 0.757188 CTGCCATCTACTCCCTCCGT 60.757 60.000 0.00 0.00 0.00 4.69
6130 6426 2.045280 CTGCCATCTACTCCCTCCG 58.955 63.158 0.00 0.00 0.00 4.63
6131 6427 0.762461 AGCTGCCATCTACTCCCTCC 60.762 60.000 0.00 0.00 0.00 4.30
6132 6428 0.392336 CAGCTGCCATCTACTCCCTC 59.608 60.000 0.00 0.00 0.00 4.30
6133 6429 0.031716 TCAGCTGCCATCTACTCCCT 60.032 55.000 9.47 0.00 0.00 4.20
6134 6430 1.001860 GATCAGCTGCCATCTACTCCC 59.998 57.143 9.47 0.00 0.00 4.30
6135 6431 1.690893 TGATCAGCTGCCATCTACTCC 59.309 52.381 9.47 0.00 0.00 3.85
6136 6432 2.102084 TGTGATCAGCTGCCATCTACTC 59.898 50.000 9.47 2.13 0.00 2.59
6137 6433 2.113807 TGTGATCAGCTGCCATCTACT 58.886 47.619 9.47 0.00 0.00 2.57
6138 6434 2.609427 TGTGATCAGCTGCCATCTAC 57.391 50.000 9.47 9.31 0.00 2.59
6139 6435 3.851458 AATGTGATCAGCTGCCATCTA 57.149 42.857 9.47 2.49 0.00 1.98
6140 6436 2.688446 CAAATGTGATCAGCTGCCATCT 59.312 45.455 9.47 0.00 0.00 2.90
6141 6437 2.798499 GCAAATGTGATCAGCTGCCATC 60.798 50.000 9.47 8.69 32.43 3.51
6142 6438 1.136305 GCAAATGTGATCAGCTGCCAT 59.864 47.619 9.47 5.56 32.43 4.40
6143 6439 0.528924 GCAAATGTGATCAGCTGCCA 59.471 50.000 9.47 6.69 32.43 4.92
6144 6440 0.524816 CGCAAATGTGATCAGCTGCC 60.525 55.000 9.47 3.77 33.97 4.85
6145 6441 0.524816 CCGCAAATGTGATCAGCTGC 60.525 55.000 9.47 1.87 34.09 5.25
6146 6442 0.099968 CCCGCAAATGTGATCAGCTG 59.900 55.000 7.63 7.63 0.00 4.24
6147 6443 0.322816 ACCCGCAAATGTGATCAGCT 60.323 50.000 0.00 0.00 0.00 4.24
6148 6444 0.099436 GACCCGCAAATGTGATCAGC 59.901 55.000 0.00 0.00 0.00 4.26
6149 6445 0.374758 CGACCCGCAAATGTGATCAG 59.625 55.000 0.00 0.00 0.00 2.90
6150 6446 0.321210 ACGACCCGCAAATGTGATCA 60.321 50.000 0.00 0.00 0.00 2.92
6151 6447 0.096976 CACGACCCGCAAATGTGATC 59.903 55.000 0.00 0.00 32.39 2.92
6152 6448 0.321210 TCACGACCCGCAAATGTGAT 60.321 50.000 0.00 0.00 34.85 3.06
6153 6449 0.321210 ATCACGACCCGCAAATGTGA 60.321 50.000 0.00 0.00 43.02 3.58
6154 6450 0.179192 CATCACGACCCGCAAATGTG 60.179 55.000 0.00 0.00 0.00 3.21
6155 6451 1.305219 CCATCACGACCCGCAAATGT 61.305 55.000 0.00 0.00 0.00 2.71
6156 6452 1.305219 ACCATCACGACCCGCAAATG 61.305 55.000 0.00 0.00 0.00 2.32
6157 6453 1.002624 ACCATCACGACCCGCAAAT 60.003 52.632 0.00 0.00 0.00 2.32
6158 6454 2.428187 ACCATCACGACCCGCAAA 59.572 55.556 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.