Multiple sequence alignment - TraesCS3D01G152500

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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 TraesCS3D01G152500 chr3D 100.000 2621 0 0 1 2621 116406907 116409527 0.000000e+00 4841
1 TraesCS3D01G152500 chr3A 86.405 2420 126 90 285 2621 125495316 125497615 0.000000e+00 2459
2 TraesCS3D01G152500 chr3A 89.714 175 11 3 112 283 125495093 125495263 1.580000e-52 217
3 TraesCS3D01G152500 chr3B 88.409 1691 73 55 988 2621 171600250 171601874 0.000000e+00 1923
4 TraesCS3D01G152500 chr3B 89.851 808 44 14 200 978 171597363 171598161 0.000000e+00 1003


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 TraesCS3D01G152500 chr3D 116406907 116409527 2620 False 4841 4841 100.0000 1 2621 1 chr3D.!!$F1 2620
1 TraesCS3D01G152500 chr3A 125495093 125497615 2522 False 1338 2459 88.0595 112 2621 2 chr3A.!!$F1 2509
2 TraesCS3D01G152500 chr3B 171597363 171601874 4511 False 1463 1923 89.1300 200 2621 2 chr3B.!!$F1 2421

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
463 525 0.337773 TCCTCTCCATGGTCTCTGCT 59.662 55.0 12.58 0.0 0.0 4.24 F
1113 3301 0.381801 AAAGCACAGCCACAAGTTCG 59.618 50.0 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 3513 0.107945 GCCAGCTCCACCTACTTCAG 60.108 60.000 0.0 0.0 0.0 3.02 R
2349 4578 1.380380 CCAATCAAGCTCCCCACCC 60.380 63.158 0.0 0.0 0.0 4.61 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
21 22 0.957362 AGCAACCTGAAAGCAGAAGC 59.043 50.000 0.00 0.00 45.17 3.86
22 23 0.670162 GCAACCTGAAAGCAGAAGCA 59.330 50.000 0.00 0.00 45.17 3.91
23 24 1.335689 GCAACCTGAAAGCAGAAGCAG 60.336 52.381 0.00 0.00 45.17 4.24
24 25 0.957362 AACCTGAAAGCAGAAGCAGC 59.043 50.000 0.00 0.00 45.17 5.25
25 26 1.233285 ACCTGAAAGCAGAAGCAGCG 61.233 55.000 0.00 0.00 45.17 5.18
26 27 1.154263 CTGAAAGCAGAAGCAGCGC 60.154 57.895 0.00 0.00 45.17 5.92
27 28 1.848932 CTGAAAGCAGAAGCAGCGCA 61.849 55.000 11.47 0.00 45.17 6.09
28 29 1.154263 GAAAGCAGAAGCAGCGCAG 60.154 57.895 11.47 1.31 45.49 5.18
29 30 1.572085 GAAAGCAGAAGCAGCGCAGA 61.572 55.000 11.47 0.00 45.49 4.26
30 31 1.849976 AAAGCAGAAGCAGCGCAGAC 61.850 55.000 11.47 0.00 45.49 3.51
31 32 4.144681 GCAGAAGCAGCGCAGACG 62.145 66.667 11.47 0.00 41.58 4.18
32 33 2.736236 CAGAAGCAGCGCAGACGT 60.736 61.111 11.47 0.00 42.83 4.34
33 34 2.736236 AGAAGCAGCGCAGACGTG 60.736 61.111 11.47 0.00 42.83 4.49
34 35 3.782244 GAAGCAGCGCAGACGTGG 61.782 66.667 11.47 0.00 42.83 4.94
35 36 4.609018 AAGCAGCGCAGACGTGGT 62.609 61.111 11.47 0.15 42.83 4.16
42 43 3.279116 GCAGACGTGGTGCAGCAA 61.279 61.111 22.04 1.63 40.86 3.91
43 44 2.941333 CAGACGTGGTGCAGCAAG 59.059 61.111 26.65 26.65 0.00 4.01
44 45 2.281070 AGACGTGGTGCAGCAAGG 60.281 61.111 30.25 22.45 0.00 3.61
45 46 2.280797 GACGTGGTGCAGCAAGGA 60.281 61.111 30.25 3.09 0.00 3.36
46 47 1.672356 GACGTGGTGCAGCAAGGAT 60.672 57.895 30.25 14.55 0.00 3.24
47 48 1.639298 GACGTGGTGCAGCAAGGATC 61.639 60.000 30.25 18.55 0.00 3.36
48 49 1.672030 CGTGGTGCAGCAAGGATCA 60.672 57.895 22.04 0.00 0.00 2.92
49 50 1.878775 GTGGTGCAGCAAGGATCAC 59.121 57.895 22.04 2.01 42.62 3.06
50 51 0.607489 GTGGTGCAGCAAGGATCACT 60.607 55.000 22.04 0.00 45.31 3.41
51 52 0.607217 TGGTGCAGCAAGGATCACTG 60.607 55.000 17.80 0.00 34.48 3.66
52 53 1.310933 GGTGCAGCAAGGATCACTGG 61.311 60.000 11.86 0.00 31.94 4.00
53 54 0.607489 GTGCAGCAAGGATCACTGGT 60.607 55.000 0.00 0.00 31.94 4.00
54 55 0.983467 TGCAGCAAGGATCACTGGTA 59.017 50.000 0.00 0.00 31.94 3.25
55 56 1.350684 TGCAGCAAGGATCACTGGTAA 59.649 47.619 0.00 0.00 31.94 2.85
56 57 2.025981 TGCAGCAAGGATCACTGGTAAT 60.026 45.455 0.00 0.00 31.94 1.89
57 58 3.019564 GCAGCAAGGATCACTGGTAATT 58.980 45.455 0.00 0.00 31.94 1.40
58 59 3.445096 GCAGCAAGGATCACTGGTAATTT 59.555 43.478 0.00 0.00 31.94 1.82
59 60 4.082026 GCAGCAAGGATCACTGGTAATTTT 60.082 41.667 0.00 0.00 31.94 1.82
60 61 5.567423 GCAGCAAGGATCACTGGTAATTTTT 60.567 40.000 0.00 0.00 31.94 1.94
61 62 6.095377 CAGCAAGGATCACTGGTAATTTTTC 58.905 40.000 0.00 0.00 0.00 2.29
62 63 6.012745 AGCAAGGATCACTGGTAATTTTTCT 58.987 36.000 0.00 0.00 0.00 2.52
63 64 6.494835 AGCAAGGATCACTGGTAATTTTTCTT 59.505 34.615 0.00 0.00 0.00 2.52
64 65 6.808704 GCAAGGATCACTGGTAATTTTTCTTC 59.191 38.462 0.00 0.00 0.00 2.87
65 66 7.315890 CAAGGATCACTGGTAATTTTTCTTCC 58.684 38.462 0.00 0.00 0.00 3.46
66 67 6.794534 AGGATCACTGGTAATTTTTCTTCCT 58.205 36.000 0.00 0.00 0.00 3.36
67 68 7.241628 AGGATCACTGGTAATTTTTCTTCCTT 58.758 34.615 0.00 0.00 0.00 3.36
68 69 7.177392 AGGATCACTGGTAATTTTTCTTCCTTG 59.823 37.037 0.00 0.00 0.00 3.61
69 70 6.648879 TCACTGGTAATTTTTCTTCCTTGG 57.351 37.500 0.00 0.00 0.00 3.61
70 71 6.369629 TCACTGGTAATTTTTCTTCCTTGGA 58.630 36.000 0.00 0.00 0.00 3.53
71 72 7.010160 TCACTGGTAATTTTTCTTCCTTGGAT 58.990 34.615 0.00 0.00 0.00 3.41
72 73 7.039784 TCACTGGTAATTTTTCTTCCTTGGATG 60.040 37.037 0.00 0.00 0.00 3.51
73 74 6.211384 ACTGGTAATTTTTCTTCCTTGGATGG 59.789 38.462 3.24 0.00 0.00 3.51
74 75 6.318913 TGGTAATTTTTCTTCCTTGGATGGA 58.681 36.000 3.24 0.00 0.00 3.41
75 76 6.784969 TGGTAATTTTTCTTCCTTGGATGGAA 59.215 34.615 3.24 0.00 43.16 3.53
76 77 7.291182 TGGTAATTTTTCTTCCTTGGATGGAAA 59.709 33.333 5.27 5.27 44.49 3.13
77 78 7.819415 GGTAATTTTTCTTCCTTGGATGGAAAG 59.181 37.037 8.42 0.00 44.49 2.62
78 79 5.806654 TTTTTCTTCCTTGGATGGAAAGG 57.193 39.130 8.42 0.00 44.49 3.11
79 80 2.514458 TCTTCCTTGGATGGAAAGGC 57.486 50.000 0.00 0.00 44.49 4.35
80 81 1.098050 CTTCCTTGGATGGAAAGGCG 58.902 55.000 0.00 0.00 44.49 5.52
81 82 0.965363 TTCCTTGGATGGAAAGGCGC 60.965 55.000 0.00 0.00 43.38 6.53
82 83 1.678635 CCTTGGATGGAAAGGCGCA 60.679 57.895 10.83 0.00 37.96 6.09
83 84 1.508088 CTTGGATGGAAAGGCGCAC 59.492 57.895 10.83 0.00 0.00 5.34
84 85 1.228398 TTGGATGGAAAGGCGCACA 60.228 52.632 10.83 0.00 0.00 4.57
85 86 1.523154 TTGGATGGAAAGGCGCACAC 61.523 55.000 10.83 0.00 0.00 3.82
86 87 1.675641 GGATGGAAAGGCGCACACT 60.676 57.895 10.83 0.00 0.00 3.55
87 88 0.392461 GGATGGAAAGGCGCACACTA 60.392 55.000 10.83 0.00 0.00 2.74
88 89 1.009829 GATGGAAAGGCGCACACTAG 58.990 55.000 10.83 0.00 0.00 2.57
89 90 0.613260 ATGGAAAGGCGCACACTAGA 59.387 50.000 10.83 0.00 0.00 2.43
90 91 0.394938 TGGAAAGGCGCACACTAGAA 59.605 50.000 10.83 0.00 0.00 2.10
91 92 1.003118 TGGAAAGGCGCACACTAGAAT 59.997 47.619 10.83 0.00 0.00 2.40
92 93 1.666189 GGAAAGGCGCACACTAGAATC 59.334 52.381 10.83 0.00 0.00 2.52
93 94 1.324736 GAAAGGCGCACACTAGAATCG 59.675 52.381 10.83 0.00 0.00 3.34
94 95 0.530744 AAGGCGCACACTAGAATCGA 59.469 50.000 10.83 0.00 0.00 3.59
95 96 0.747255 AGGCGCACACTAGAATCGAT 59.253 50.000 10.83 0.00 0.00 3.59
96 97 1.132588 GGCGCACACTAGAATCGATC 58.867 55.000 10.83 0.00 0.00 3.69
97 98 1.269309 GGCGCACACTAGAATCGATCT 60.269 52.381 10.83 0.28 42.48 2.75
98 99 2.047769 GCGCACACTAGAATCGATCTC 58.952 52.381 0.30 0.00 39.71 2.75
99 100 2.656085 CGCACACTAGAATCGATCTCC 58.344 52.381 0.00 0.00 39.71 3.71
100 101 2.292016 CGCACACTAGAATCGATCTCCT 59.708 50.000 0.00 0.00 39.71 3.69
101 102 3.637432 GCACACTAGAATCGATCTCCTG 58.363 50.000 0.00 0.30 39.71 3.86
102 103 3.637432 CACACTAGAATCGATCTCCTGC 58.363 50.000 0.00 0.00 39.71 4.85
103 104 2.625790 ACACTAGAATCGATCTCCTGCC 59.374 50.000 0.00 0.00 39.71 4.85
104 105 2.625314 CACTAGAATCGATCTCCTGCCA 59.375 50.000 0.00 0.00 39.71 4.92
105 106 3.257873 CACTAGAATCGATCTCCTGCCAT 59.742 47.826 0.00 0.00 39.71 4.40
106 107 3.900601 ACTAGAATCGATCTCCTGCCATT 59.099 43.478 0.00 0.00 39.71 3.16
107 108 3.399440 AGAATCGATCTCCTGCCATTC 57.601 47.619 0.00 0.00 30.46 2.67
108 109 2.702478 AGAATCGATCTCCTGCCATTCA 59.298 45.455 0.00 0.00 30.46 2.57
109 110 3.327172 AGAATCGATCTCCTGCCATTCAT 59.673 43.478 0.00 0.00 30.46 2.57
110 111 4.529769 AGAATCGATCTCCTGCCATTCATA 59.470 41.667 0.00 0.00 30.46 2.15
123 124 1.863454 CATTCATACGCAGTGGAGCTC 59.137 52.381 4.71 4.71 45.73 4.09
159 160 3.495100 GGGTTGAGAGCTTCAAGTTCTGA 60.495 47.826 8.75 0.00 46.09 3.27
190 191 2.125229 CAGCTGCAGACTGCCGAT 60.125 61.111 24.33 14.53 44.23 4.18
191 192 2.125229 AGCTGCAGACTGCCGATG 60.125 61.111 24.33 12.64 44.23 3.84
192 193 2.435586 GCTGCAGACTGCCGATGT 60.436 61.111 24.33 0.00 44.23 3.06
194 195 1.217511 CTGCAGACTGCCGATGTCT 59.782 57.895 24.33 0.00 44.23 3.41
195 196 0.805322 CTGCAGACTGCCGATGTCTC 60.805 60.000 24.33 0.00 44.23 3.36
198 199 0.463204 CAGACTGCCGATGTCTCCAT 59.537 55.000 0.00 0.00 42.21 3.41
350 402 2.164219 CGTGGTTAGGCAAATCAGCAAT 59.836 45.455 0.00 0.00 35.83 3.56
400 453 1.333636 GCTTAGAGGCCAGGCTCAGA 61.334 60.000 21.66 7.73 0.00 3.27
453 513 1.063183 GCCAGCCTAATCCTCTCCAT 58.937 55.000 0.00 0.00 0.00 3.41
459 521 2.301583 GCCTAATCCTCTCCATGGTCTC 59.698 54.545 12.58 0.00 0.00 3.36
460 522 3.855668 CCTAATCCTCTCCATGGTCTCT 58.144 50.000 12.58 0.00 0.00 3.10
461 523 3.577848 CCTAATCCTCTCCATGGTCTCTG 59.422 52.174 12.58 0.00 0.00 3.35
462 524 1.422531 ATCCTCTCCATGGTCTCTGC 58.577 55.000 12.58 0.00 0.00 4.26
463 525 0.337773 TCCTCTCCATGGTCTCTGCT 59.662 55.000 12.58 0.00 0.00 4.24
464 526 1.570979 TCCTCTCCATGGTCTCTGCTA 59.429 52.381 12.58 0.00 0.00 3.49
480 542 5.104067 TCTCTGCTACTCCATTGGACTAGTA 60.104 44.000 16.25 12.65 0.00 1.82
542 604 6.037610 GGTCCAAGCTCAAGTACAAGATAATG 59.962 42.308 0.00 0.00 0.00 1.90
553 615 7.623999 AGTACAAGATAATGATCCTGGTCAT 57.376 36.000 0.00 6.10 40.44 3.06
696 777 0.883153 TGAAGTGCCATCACACATGC 59.117 50.000 0.00 0.00 45.49 4.06
710 791 4.070716 CACACATGCTCCTCTCTTTTCTT 58.929 43.478 0.00 0.00 0.00 2.52
711 792 4.518211 CACACATGCTCCTCTCTTTTCTTT 59.482 41.667 0.00 0.00 0.00 2.52
712 793 4.759183 ACACATGCTCCTCTCTTTTCTTTC 59.241 41.667 0.00 0.00 0.00 2.62
714 795 5.002516 ACATGCTCCTCTCTTTTCTTTCTG 58.997 41.667 0.00 0.00 0.00 3.02
755 836 3.704061 AGTACAAATGTTGGCCAAGTTGT 59.296 39.130 30.26 30.26 38.33 3.32
756 837 4.890581 AGTACAAATGTTGGCCAAGTTGTA 59.109 37.500 28.81 28.81 36.94 2.41
757 838 4.320608 ACAAATGTTGGCCAAGTTGTAG 57.679 40.909 28.22 17.03 35.03 2.74
810 895 6.446318 TGCTTTGATGTGATTAGTTTTGGTC 58.554 36.000 0.00 0.00 0.00 4.02
823 908 2.685897 GTTTTGGTCTGTGCAGTGGTAA 59.314 45.455 0.00 0.00 0.00 2.85
887 981 3.876309 TTTTGACCCCTAAGCTCTTGT 57.124 42.857 0.00 0.00 0.00 3.16
956 1054 9.193806 ACTATATTCTAGTTACGTTTCCTTCCA 57.806 33.333 0.00 0.00 0.00 3.53
968 1066 1.529744 TCCTTCCAACCCTTGTCCTT 58.470 50.000 0.00 0.00 0.00 3.36
1009 3186 0.679505 TATAGACGCCATGGCTGTCC 59.320 55.000 36.31 25.94 41.68 4.02
1047 3224 3.323115 TGGCACTGCTCATCTATTCTAGG 59.677 47.826 0.00 0.00 0.00 3.02
1048 3225 3.323403 GGCACTGCTCATCTATTCTAGGT 59.677 47.826 0.00 0.00 0.00 3.08
1049 3226 4.202305 GGCACTGCTCATCTATTCTAGGTT 60.202 45.833 0.00 0.00 0.00 3.50
1050 3227 5.363939 GCACTGCTCATCTATTCTAGGTTT 58.636 41.667 0.00 0.00 0.00 3.27
1051 3228 5.465056 GCACTGCTCATCTATTCTAGGTTTC 59.535 44.000 0.00 0.00 0.00 2.78
1052 3229 6.685116 GCACTGCTCATCTATTCTAGGTTTCT 60.685 42.308 0.00 0.00 0.00 2.52
1053 3230 7.470702 GCACTGCTCATCTATTCTAGGTTTCTA 60.471 40.741 0.00 0.00 0.00 2.10
1054 3231 8.081633 CACTGCTCATCTATTCTAGGTTTCTAG 58.918 40.741 0.00 0.00 43.27 2.43
1064 3243 1.770294 AGGTTTCTAGCCCTCTCTCG 58.230 55.000 0.00 0.00 0.00 4.04
1092 3271 4.463879 CCCCAGCTCTGCTCACGG 62.464 72.222 0.00 0.00 36.40 4.94
1113 3301 0.381801 AAAGCACAGCCACAAGTTCG 59.618 50.000 0.00 0.00 0.00 3.95
1253 3441 2.195096 CTCGCTCAAGCTTCTCATGAG 58.805 52.381 17.07 17.07 41.95 2.90
1311 3499 1.078143 GATTGGCGGCAAGTCCTCT 60.078 57.895 28.83 11.81 0.00 3.69
1320 3508 0.827368 GCAAGTCCTCTCCGGAATCT 59.173 55.000 5.23 0.00 45.32 2.40
1321 3509 1.472376 GCAAGTCCTCTCCGGAATCTG 60.472 57.143 5.23 0.00 45.32 2.90
1322 3510 2.103373 CAAGTCCTCTCCGGAATCTGA 58.897 52.381 5.23 0.00 45.32 3.27
1323 3511 2.697751 CAAGTCCTCTCCGGAATCTGAT 59.302 50.000 5.23 0.00 45.32 2.90
1324 3512 3.039252 AGTCCTCTCCGGAATCTGATT 57.961 47.619 5.23 1.81 45.32 2.57
1325 3513 2.962421 AGTCCTCTCCGGAATCTGATTC 59.038 50.000 19.67 19.67 45.32 2.52
1326 3514 2.962421 GTCCTCTCCGGAATCTGATTCT 59.038 50.000 24.96 0.00 45.32 2.40
1338 3526 5.129485 GGAATCTGATTCTGAAGTAGGTGGA 59.871 44.000 24.96 0.00 39.24 4.02
1341 3529 3.445008 TGATTCTGAAGTAGGTGGAGCT 58.555 45.455 0.00 0.00 0.00 4.09
1353 3541 2.210013 TGGAGCTGGCGTGAAGAGT 61.210 57.895 0.00 0.00 0.00 3.24
1354 3542 1.739562 GGAGCTGGCGTGAAGAGTG 60.740 63.158 0.00 0.00 0.00 3.51
1356 3544 1.005630 AGCTGGCGTGAAGAGTGTC 60.006 57.895 0.00 0.00 0.00 3.67
1357 3545 1.300931 GCTGGCGTGAAGAGTGTCA 60.301 57.895 0.00 0.00 0.00 3.58
1358 3546 0.880278 GCTGGCGTGAAGAGTGTCAA 60.880 55.000 0.00 0.00 0.00 3.18
1359 3547 1.143305 CTGGCGTGAAGAGTGTCAAG 58.857 55.000 0.00 0.00 0.00 3.02
1360 3548 0.249868 TGGCGTGAAGAGTGTCAAGG 60.250 55.000 0.00 0.00 0.00 3.61
1361 3549 1.569479 GGCGTGAAGAGTGTCAAGGC 61.569 60.000 0.00 0.00 43.15 4.35
1362 3550 1.569479 GCGTGAAGAGTGTCAAGGCC 61.569 60.000 0.00 0.00 0.00 5.19
1363 3551 0.249868 CGTGAAGAGTGTCAAGGCCA 60.250 55.000 5.01 0.00 0.00 5.36
1364 3552 1.517242 GTGAAGAGTGTCAAGGCCAG 58.483 55.000 5.01 0.00 0.00 4.85
1365 3553 0.250467 TGAAGAGTGTCAAGGCCAGC 60.250 55.000 5.01 0.00 0.00 4.85
1366 3554 0.957888 GAAGAGTGTCAAGGCCAGCC 60.958 60.000 5.01 0.00 0.00 4.85
1367 3555 1.708993 AAGAGTGTCAAGGCCAGCCA 61.709 55.000 12.03 0.00 38.92 4.75
1368 3556 1.968540 GAGTGTCAAGGCCAGCCAC 60.969 63.158 12.03 2.93 38.92 5.01
1369 3557 3.357079 GTGTCAAGGCCAGCCACG 61.357 66.667 12.03 0.93 38.92 4.94
1370 3558 4.641645 TGTCAAGGCCAGCCACGG 62.642 66.667 12.03 0.00 38.92 4.94
1623 3820 0.170561 CCGAGGAGTTGTCGTAGGTG 59.829 60.000 0.00 0.00 35.59 4.00
1624 3821 0.456312 CGAGGAGTTGTCGTAGGTGC 60.456 60.000 0.00 0.00 32.62 5.01
1625 3822 0.601558 GAGGAGTTGTCGTAGGTGCA 59.398 55.000 0.00 0.00 0.00 4.57
1626 3823 0.317479 AGGAGTTGTCGTAGGTGCAC 59.683 55.000 8.80 8.80 0.00 4.57
1627 3824 0.669625 GGAGTTGTCGTAGGTGCACC 60.670 60.000 29.22 29.22 0.00 5.01
1628 3825 1.006571 AGTTGTCGTAGGTGCACCG 60.007 57.895 29.68 18.24 42.08 4.94
1629 3826 2.025418 GTTGTCGTAGGTGCACCGG 61.025 63.158 29.68 21.96 42.08 5.28
1654 3851 1.201619 CGTGCACGTACGTGTGTTATG 60.202 52.381 39.56 26.53 46.90 1.90
1655 3852 1.788308 GTGCACGTACGTGTGTTATGT 59.212 47.619 39.56 6.84 46.90 2.29
1656 3853 2.979151 GTGCACGTACGTGTGTTATGTA 59.021 45.455 39.56 16.66 46.90 2.29
1658 3855 2.027214 GCACGTACGTGTGTTATGTAGC 59.973 50.000 39.56 23.14 46.90 3.58
1659 3856 3.495193 CACGTACGTGTGTTATGTAGCT 58.505 45.455 34.48 0.00 40.91 3.32
1660 3857 3.916172 CACGTACGTGTGTTATGTAGCTT 59.084 43.478 34.48 0.00 40.91 3.74
1661 3858 4.029861 CACGTACGTGTGTTATGTAGCTTC 59.970 45.833 34.48 0.00 40.91 3.86
1662 3859 3.236754 CGTACGTGTGTTATGTAGCTTCG 59.763 47.826 7.22 0.00 31.59 3.79
1663 3860 1.990563 ACGTGTGTTATGTAGCTTCGC 59.009 47.619 0.00 0.00 0.00 4.70
1664 3861 1.007422 CGTGTGTTATGTAGCTTCGCG 60.007 52.381 0.00 0.00 0.00 5.87
1665 3862 1.990563 GTGTGTTATGTAGCTTCGCGT 59.009 47.619 5.77 0.00 0.00 6.01
1666 3863 1.989864 TGTGTTATGTAGCTTCGCGTG 59.010 47.619 5.77 1.17 0.00 5.34
1667 3864 1.990563 GTGTTATGTAGCTTCGCGTGT 59.009 47.619 5.77 0.00 0.00 4.49
1668 3865 2.027688 GTGTTATGTAGCTTCGCGTGTC 59.972 50.000 5.77 0.00 0.00 3.67
1669 3866 1.587034 GTTATGTAGCTTCGCGTGTCC 59.413 52.381 5.77 0.00 0.00 4.02
1671 3868 1.929806 ATGTAGCTTCGCGTGTCCGA 61.930 55.000 5.77 0.00 35.63 4.55
1678 3877 1.636570 TTCGCGTGTCCGAGAGAGAG 61.637 60.000 5.77 0.00 43.70 3.20
1694 3893 0.106719 AGAGGGAGAGAGCGAGAAGG 60.107 60.000 0.00 0.00 0.00 3.46
1695 3894 1.076339 AGGGAGAGAGCGAGAAGGG 60.076 63.158 0.00 0.00 0.00 3.95
1696 3895 1.076632 GGGAGAGAGCGAGAAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
1712 3920 0.624795 GGGAGGAGGGAGATTTGGGT 60.625 60.000 0.00 0.00 0.00 4.51
1765 3973 1.609061 CCTCCCATGCATCATCCGTAC 60.609 57.143 0.00 0.00 0.00 3.67
1827 4045 0.617935 AAGCTTCTCTTCTGCTCCCC 59.382 55.000 0.00 0.00 35.85 4.81
1907 4128 8.885494 AATGGAATGAAATTTCGTTTTCTTCA 57.115 26.923 23.11 16.62 37.80 3.02
1934 4155 3.871006 TCATTCGTGCTAATCCATGTGTC 59.129 43.478 0.00 0.00 0.00 3.67
1941 4162 5.106555 CGTGCTAATCCATGTGTCTTTTCTT 60.107 40.000 0.00 0.00 0.00 2.52
1942 4163 6.317857 GTGCTAATCCATGTGTCTTTTCTTC 58.682 40.000 0.00 0.00 0.00 2.87
1943 4164 6.150140 GTGCTAATCCATGTGTCTTTTCTTCT 59.850 38.462 0.00 0.00 0.00 2.85
1944 4165 6.716628 TGCTAATCCATGTGTCTTTTCTTCTT 59.283 34.615 0.00 0.00 0.00 2.52
1977 4198 6.509418 AGTTGTGTGTTTTCTTCTAGCAAA 57.491 33.333 0.00 0.00 0.00 3.68
2009 4230 6.985188 TGGACATTGTTTCAGATAACTAGC 57.015 37.500 0.00 0.00 0.00 3.42
2070 4295 2.852413 CTGACAGAATTGGCTACGTACG 59.148 50.000 15.01 15.01 31.73 3.67
2071 4296 2.229543 TGACAGAATTGGCTACGTACGT 59.770 45.455 25.98 25.98 31.73 3.57
2072 4297 3.439825 TGACAGAATTGGCTACGTACGTA 59.560 43.478 25.41 25.41 31.73 3.57
2073 4298 3.762779 ACAGAATTGGCTACGTACGTAC 58.237 45.455 23.60 18.69 0.00 3.67
2074 4299 3.441572 ACAGAATTGGCTACGTACGTACT 59.558 43.478 23.60 14.26 0.00 2.73
2075 4300 3.789756 CAGAATTGGCTACGTACGTACTG 59.210 47.826 23.60 20.94 0.00 2.74
2076 4301 2.857592 ATTGGCTACGTACGTACTGG 57.142 50.000 23.60 15.29 0.00 4.00
2077 4302 1.819928 TTGGCTACGTACGTACTGGA 58.180 50.000 23.60 12.26 0.00 3.86
2163 4388 4.098349 ACACATTTTGTTCACATCTGCACT 59.902 37.500 0.00 0.00 33.09 4.40
2273 4502 4.559153 GAAGGTGGATCATTTGTTGGTTG 58.441 43.478 0.00 0.00 0.00 3.77
2348 4577 1.736645 CTCGTGCGACGGATTGGTT 60.737 57.895 8.46 0.00 42.81 3.67
2349 4578 1.955529 CTCGTGCGACGGATTGGTTG 61.956 60.000 8.46 0.00 42.81 3.77
2350 4579 2.867472 GTGCGACGGATTGGTTGG 59.133 61.111 0.00 0.00 0.00 3.77
2351 4580 2.359354 TGCGACGGATTGGTTGGG 60.359 61.111 0.00 0.00 0.00 4.12
2394 4624 0.314935 CCCATGTGCAGTGGTTGTTC 59.685 55.000 15.03 0.00 34.87 3.18
2456 4706 4.122046 TGATGACTGAATCGGTTGCATAG 58.878 43.478 0.00 0.00 0.00 2.23
2474 4724 5.047377 TGCATAGAAAACCCAACAAATCCTC 60.047 40.000 0.00 0.00 0.00 3.71
2476 4726 6.625960 GCATAGAAAACCCAACAAATCCTCTC 60.626 42.308 0.00 0.00 0.00 3.20
2525 4781 6.712547 TCAACCAATCCTTTCTTCTTCTTCTC 59.287 38.462 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.161211 GCTTCTGCTTTCAGGTTGCTAG 59.839 50.000 0.00 0.00 40.69 3.42
1 2 2.154462 GCTTCTGCTTTCAGGTTGCTA 58.846 47.619 0.00 0.00 40.69 3.49
2 3 0.957362 GCTTCTGCTTTCAGGTTGCT 59.043 50.000 0.00 0.00 40.69 3.91
3 4 0.670162 TGCTTCTGCTTTCAGGTTGC 59.330 50.000 0.00 0.00 40.69 4.17
4 5 1.335689 GCTGCTTCTGCTTTCAGGTTG 60.336 52.381 0.00 0.00 40.69 3.77
5 6 0.957362 GCTGCTTCTGCTTTCAGGTT 59.043 50.000 0.00 0.00 40.69 3.50
6 7 1.233285 CGCTGCTTCTGCTTTCAGGT 61.233 55.000 0.00 0.00 40.69 4.00
7 8 1.500844 CGCTGCTTCTGCTTTCAGG 59.499 57.895 0.00 0.00 40.69 3.86
8 9 1.154263 GCGCTGCTTCTGCTTTCAG 60.154 57.895 0.00 0.00 41.67 3.02
9 10 1.848932 CTGCGCTGCTTCTGCTTTCA 61.849 55.000 9.73 0.00 40.48 2.69
10 11 1.154263 CTGCGCTGCTTCTGCTTTC 60.154 57.895 9.73 0.00 40.48 2.62
11 12 1.598962 TCTGCGCTGCTTCTGCTTT 60.599 52.632 9.73 0.00 40.48 3.51
12 13 2.031616 TCTGCGCTGCTTCTGCTT 59.968 55.556 9.73 0.00 40.48 3.91
13 14 2.741598 GTCTGCGCTGCTTCTGCT 60.742 61.111 9.73 0.00 40.48 4.24
14 15 4.144681 CGTCTGCGCTGCTTCTGC 62.145 66.667 9.73 0.00 40.20 4.26
15 16 2.736236 ACGTCTGCGCTGCTTCTG 60.736 61.111 9.73 0.00 42.83 3.02
16 17 2.736236 CACGTCTGCGCTGCTTCT 60.736 61.111 9.73 0.00 42.83 2.85
17 18 3.782244 CCACGTCTGCGCTGCTTC 61.782 66.667 9.73 1.54 42.83 3.86
18 19 4.609018 ACCACGTCTGCGCTGCTT 62.609 61.111 9.73 0.00 42.83 3.91
25 26 3.245948 CTTGCTGCACCACGTCTGC 62.246 63.158 0.00 7.65 35.03 4.26
26 27 2.610694 CCTTGCTGCACCACGTCTG 61.611 63.158 0.00 0.00 0.00 3.51
27 28 2.116983 ATCCTTGCTGCACCACGTCT 62.117 55.000 0.00 0.00 0.00 4.18
28 29 1.639298 GATCCTTGCTGCACCACGTC 61.639 60.000 0.00 0.00 0.00 4.34
29 30 1.672356 GATCCTTGCTGCACCACGT 60.672 57.895 0.00 0.00 0.00 4.49
30 31 1.672030 TGATCCTTGCTGCACCACG 60.672 57.895 0.00 0.00 0.00 4.94
31 32 0.607489 AGTGATCCTTGCTGCACCAC 60.607 55.000 0.00 6.06 31.85 4.16
32 33 0.607217 CAGTGATCCTTGCTGCACCA 60.607 55.000 0.00 0.00 31.85 4.17
33 34 1.310933 CCAGTGATCCTTGCTGCACC 61.311 60.000 0.00 0.00 31.85 5.01
34 35 0.607489 ACCAGTGATCCTTGCTGCAC 60.607 55.000 0.00 0.00 0.00 4.57
35 36 0.983467 TACCAGTGATCCTTGCTGCA 59.017 50.000 0.00 0.00 0.00 4.41
36 37 2.113860 TTACCAGTGATCCTTGCTGC 57.886 50.000 0.00 0.00 0.00 5.25
37 38 5.649782 AAAATTACCAGTGATCCTTGCTG 57.350 39.130 0.00 0.00 0.00 4.41
38 39 6.012745 AGAAAAATTACCAGTGATCCTTGCT 58.987 36.000 0.00 0.00 0.00 3.91
39 40 6.272822 AGAAAAATTACCAGTGATCCTTGC 57.727 37.500 0.00 0.00 0.00 4.01
40 41 7.177392 AGGAAGAAAAATTACCAGTGATCCTTG 59.823 37.037 0.00 0.00 0.00 3.61
41 42 7.241628 AGGAAGAAAAATTACCAGTGATCCTT 58.758 34.615 0.00 0.00 0.00 3.36
42 43 6.794534 AGGAAGAAAAATTACCAGTGATCCT 58.205 36.000 0.00 0.00 0.00 3.24
43 44 7.315890 CAAGGAAGAAAAATTACCAGTGATCC 58.684 38.462 0.00 0.00 0.00 3.36
44 45 7.176690 TCCAAGGAAGAAAAATTACCAGTGATC 59.823 37.037 0.00 0.00 0.00 2.92
45 46 7.010160 TCCAAGGAAGAAAAATTACCAGTGAT 58.990 34.615 0.00 0.00 0.00 3.06
46 47 6.369629 TCCAAGGAAGAAAAATTACCAGTGA 58.630 36.000 0.00 0.00 0.00 3.41
47 48 6.648879 TCCAAGGAAGAAAAATTACCAGTG 57.351 37.500 0.00 0.00 0.00 3.66
48 49 6.211384 CCATCCAAGGAAGAAAAATTACCAGT 59.789 38.462 0.00 0.00 0.00 4.00
49 50 6.437162 TCCATCCAAGGAAGAAAAATTACCAG 59.563 38.462 0.00 0.00 33.93 4.00
50 51 6.318913 TCCATCCAAGGAAGAAAAATTACCA 58.681 36.000 0.00 0.00 33.93 3.25
51 52 6.850752 TCCATCCAAGGAAGAAAAATTACC 57.149 37.500 0.00 0.00 33.93 2.85
62 63 0.965363 GCGCCTTTCCATCCAAGGAA 60.965 55.000 0.00 0.00 43.32 3.36
63 64 1.378514 GCGCCTTTCCATCCAAGGA 60.379 57.895 0.00 0.00 43.32 3.36
64 65 1.678635 TGCGCCTTTCCATCCAAGG 60.679 57.895 4.18 0.00 43.47 3.61
65 66 1.243342 TGTGCGCCTTTCCATCCAAG 61.243 55.000 4.18 0.00 0.00 3.61
66 67 1.228398 TGTGCGCCTTTCCATCCAA 60.228 52.632 4.18 0.00 0.00 3.53
67 68 1.971167 GTGTGCGCCTTTCCATCCA 60.971 57.895 4.18 0.00 0.00 3.41
68 69 0.392461 TAGTGTGCGCCTTTCCATCC 60.392 55.000 4.18 0.00 0.00 3.51
69 70 1.009829 CTAGTGTGCGCCTTTCCATC 58.990 55.000 4.18 0.00 0.00 3.51
70 71 0.613260 TCTAGTGTGCGCCTTTCCAT 59.387 50.000 4.18 0.00 0.00 3.41
71 72 0.394938 TTCTAGTGTGCGCCTTTCCA 59.605 50.000 4.18 0.00 0.00 3.53
72 73 1.666189 GATTCTAGTGTGCGCCTTTCC 59.334 52.381 4.18 0.00 0.00 3.13
73 74 1.324736 CGATTCTAGTGTGCGCCTTTC 59.675 52.381 4.18 0.00 0.00 2.62
74 75 1.067142 TCGATTCTAGTGTGCGCCTTT 60.067 47.619 4.18 0.00 0.00 3.11
75 76 0.530744 TCGATTCTAGTGTGCGCCTT 59.469 50.000 4.18 0.00 0.00 4.35
76 77 0.747255 ATCGATTCTAGTGTGCGCCT 59.253 50.000 4.18 0.00 0.00 5.52
77 78 1.132588 GATCGATTCTAGTGTGCGCC 58.867 55.000 4.18 0.00 0.00 6.53
78 79 2.047769 GAGATCGATTCTAGTGTGCGC 58.952 52.381 0.00 0.00 33.74 6.09
79 80 2.292016 AGGAGATCGATTCTAGTGTGCG 59.708 50.000 0.00 0.00 33.74 5.34
80 81 3.637432 CAGGAGATCGATTCTAGTGTGC 58.363 50.000 0.00 0.00 33.74 4.57
81 82 3.551863 GGCAGGAGATCGATTCTAGTGTG 60.552 52.174 0.00 0.00 33.74 3.82
82 83 2.625790 GGCAGGAGATCGATTCTAGTGT 59.374 50.000 0.00 0.00 33.74 3.55
83 84 2.625314 TGGCAGGAGATCGATTCTAGTG 59.375 50.000 0.00 1.32 33.74 2.74
84 85 2.950781 TGGCAGGAGATCGATTCTAGT 58.049 47.619 0.00 0.00 33.74 2.57
85 86 4.021632 TGAATGGCAGGAGATCGATTCTAG 60.022 45.833 0.00 0.00 33.74 2.43
86 87 3.897505 TGAATGGCAGGAGATCGATTCTA 59.102 43.478 0.00 0.00 33.74 2.10
87 88 2.702478 TGAATGGCAGGAGATCGATTCT 59.298 45.455 0.00 0.00 37.41 2.40
88 89 3.117491 TGAATGGCAGGAGATCGATTC 57.883 47.619 0.00 0.00 0.00 2.52
89 90 3.784511 ATGAATGGCAGGAGATCGATT 57.215 42.857 0.00 0.00 0.00 3.34
90 91 3.367806 CGTATGAATGGCAGGAGATCGAT 60.368 47.826 0.00 0.00 0.00 3.59
91 92 2.029918 CGTATGAATGGCAGGAGATCGA 60.030 50.000 0.00 0.00 0.00 3.59
92 93 2.332104 CGTATGAATGGCAGGAGATCG 58.668 52.381 0.00 0.00 0.00 3.69
93 94 2.072298 GCGTATGAATGGCAGGAGATC 58.928 52.381 0.00 0.00 0.00 2.75
94 95 1.417517 TGCGTATGAATGGCAGGAGAT 59.582 47.619 0.00 0.00 32.07 2.75
95 96 0.829990 TGCGTATGAATGGCAGGAGA 59.170 50.000 0.00 0.00 32.07 3.71
96 97 3.384816 TGCGTATGAATGGCAGGAG 57.615 52.632 0.00 0.00 32.07 3.69
100 101 0.251634 TCCACTGCGTATGAATGGCA 59.748 50.000 0.00 0.00 35.07 4.92
101 102 0.940126 CTCCACTGCGTATGAATGGC 59.060 55.000 0.00 0.00 0.00 4.40
102 103 0.940126 GCTCCACTGCGTATGAATGG 59.060 55.000 0.00 0.00 0.00 3.16
103 104 1.863454 GAGCTCCACTGCGTATGAATG 59.137 52.381 0.87 0.00 38.13 2.67
104 105 1.759445 AGAGCTCCACTGCGTATGAAT 59.241 47.619 10.93 0.00 38.13 2.57
105 106 1.186200 AGAGCTCCACTGCGTATGAA 58.814 50.000 10.93 0.00 38.13 2.57
106 107 2.052782 TAGAGCTCCACTGCGTATGA 57.947 50.000 10.93 0.00 38.13 2.15
107 108 2.736978 CTTAGAGCTCCACTGCGTATG 58.263 52.381 10.93 0.00 38.13 2.39
108 109 1.067821 GCTTAGAGCTCCACTGCGTAT 59.932 52.381 10.93 0.00 38.45 3.06
109 110 0.456221 GCTTAGAGCTCCACTGCGTA 59.544 55.000 10.93 0.00 38.45 4.42
110 111 1.216710 GCTTAGAGCTCCACTGCGT 59.783 57.895 10.93 0.00 38.45 5.24
123 124 2.554032 CTCAACCCAACAACCAGCTTAG 59.446 50.000 0.00 0.00 0.00 2.18
138 139 3.733337 TCAGAACTTGAAGCTCTCAACC 58.267 45.455 0.00 2.19 39.20 3.77
159 160 1.506493 CAGCTGCGAGTTCAGACTTT 58.494 50.000 0.00 0.00 35.88 2.66
191 192 1.452833 GCCAAGCCCAGATGGAGAC 60.453 63.158 0.00 0.00 39.12 3.36
192 193 1.499913 TTGCCAAGCCCAGATGGAGA 61.500 55.000 0.00 0.00 39.12 3.71
194 195 0.041535 AATTGCCAAGCCCAGATGGA 59.958 50.000 0.00 0.00 39.12 3.41
195 196 0.462789 GAATTGCCAAGCCCAGATGG 59.537 55.000 0.00 0.00 39.80 3.51
198 199 1.678635 CGGAATTGCCAAGCCCAGA 60.679 57.895 0.00 0.00 35.94 3.86
350 402 1.544825 GCAGACAGAGGTGGGTGCTA 61.545 60.000 0.00 0.00 34.93 3.49
400 453 6.350612 GGAACAAGTAGATCACAGCTACTCTT 60.351 42.308 2.07 0.00 45.72 2.85
453 513 1.833630 CCAATGGAGTAGCAGAGACCA 59.166 52.381 0.00 0.00 35.09 4.02
463 525 6.075984 GGATTCCTACTAGTCCAATGGAGTA 58.924 44.000 15.46 15.46 36.65 2.59
464 526 4.902448 GGATTCCTACTAGTCCAATGGAGT 59.098 45.833 14.78 14.78 39.02 3.85
480 542 0.820891 GCATCATGTGCGGGATTCCT 60.821 55.000 2.01 0.00 45.23 3.36
542 604 4.073293 ACGGTTTATCATGACCAGGATC 57.927 45.455 0.00 0.00 35.63 3.36
553 615 6.108015 AGGCGACTAAAAATACGGTTTATCA 58.892 36.000 0.00 0.00 40.61 2.15
696 777 8.839310 TGTTATTCAGAAAGAAAAGAGAGGAG 57.161 34.615 0.00 0.00 40.22 3.69
810 895 7.280876 ACACAGATTATTATTACCACTGCACAG 59.719 37.037 0.00 0.00 0.00 3.66
823 908 8.239314 CACTTGCAAGTTGACACAGATTATTAT 58.761 33.333 29.23 0.00 37.08 1.28
956 1054 2.978010 CGCGCAAGGACAAGGGTT 60.978 61.111 8.75 0.00 38.28 4.11
978 1076 1.719780 GCGTCTATATAACGGCACAGC 59.280 52.381 14.81 0.00 40.41 4.40
1047 3224 1.066454 GAGCGAGAGAGGGCTAGAAAC 59.934 57.143 0.00 0.00 40.16 2.78
1048 3225 1.064314 AGAGCGAGAGAGGGCTAGAAA 60.064 52.381 0.00 0.00 40.16 2.52
1049 3226 0.548989 AGAGCGAGAGAGGGCTAGAA 59.451 55.000 0.00 0.00 40.16 2.10
1050 3227 0.107831 GAGAGCGAGAGAGGGCTAGA 59.892 60.000 0.00 0.00 40.16 2.43
1051 3228 0.108585 AGAGAGCGAGAGAGGGCTAG 59.891 60.000 0.00 0.00 40.16 3.42
1052 3229 0.107831 GAGAGAGCGAGAGAGGGCTA 59.892 60.000 0.00 0.00 40.16 3.93
1053 3230 1.152963 GAGAGAGCGAGAGAGGGCT 60.153 63.158 0.00 0.00 43.42 5.19
1054 3231 0.751643 AAGAGAGAGCGAGAGAGGGC 60.752 60.000 0.00 0.00 0.00 5.19
1064 3243 0.177836 GAGCTGGGGAAAGAGAGAGC 59.822 60.000 0.00 0.00 0.00 4.09
1092 3271 0.179103 AACTTGTGGCTGTGCTTTGC 60.179 50.000 0.00 0.00 0.00 3.68
1093 3272 1.843992 GAACTTGTGGCTGTGCTTTG 58.156 50.000 0.00 0.00 0.00 2.77
1094 3273 0.381801 CGAACTTGTGGCTGTGCTTT 59.618 50.000 0.00 0.00 0.00 3.51
1095 3274 2.024918 CGAACTTGTGGCTGTGCTT 58.975 52.632 0.00 0.00 0.00 3.91
1096 3275 2.546494 GCGAACTTGTGGCTGTGCT 61.546 57.895 0.00 0.00 0.00 4.40
1097 3276 2.050985 GCGAACTTGTGGCTGTGC 60.051 61.111 0.00 0.00 0.00 4.57
1311 3499 4.342378 CCTACTTCAGAATCAGATTCCGGA 59.658 45.833 18.11 13.63 40.13 5.14
1320 3508 3.196469 CAGCTCCACCTACTTCAGAATCA 59.804 47.826 0.00 0.00 0.00 2.57
1321 3509 3.431486 CCAGCTCCACCTACTTCAGAATC 60.431 52.174 0.00 0.00 0.00 2.52
1322 3510 2.503356 CCAGCTCCACCTACTTCAGAAT 59.497 50.000 0.00 0.00 0.00 2.40
1323 3511 1.902508 CCAGCTCCACCTACTTCAGAA 59.097 52.381 0.00 0.00 0.00 3.02
1324 3512 1.561643 CCAGCTCCACCTACTTCAGA 58.438 55.000 0.00 0.00 0.00 3.27
1325 3513 0.107945 GCCAGCTCCACCTACTTCAG 60.108 60.000 0.00 0.00 0.00 3.02
1326 3514 1.888436 CGCCAGCTCCACCTACTTCA 61.888 60.000 0.00 0.00 0.00 3.02
1338 3526 1.005630 GACACTCTTCACGCCAGCT 60.006 57.895 0.00 0.00 0.00 4.24
1341 3529 0.249868 CCTTGACACTCTTCACGCCA 60.250 55.000 0.00 0.00 0.00 5.69
1353 3541 4.641645 CCGTGGCTGGCCTTGACA 62.642 66.667 13.05 1.74 36.94 3.58
1370 3558 4.475135 GTCTCGGGGAGGCCTTGC 62.475 72.222 6.77 0.00 0.00 4.01
1613 3810 3.687102 CCCGGTGCACCTACGACA 61.687 66.667 32.28 0.00 0.00 4.35
1658 3855 1.226156 CTCTCTCGGACACGCGAAG 60.226 63.158 15.93 7.57 40.69 3.79
1659 3856 1.636570 CTCTCTCTCGGACACGCGAA 61.637 60.000 15.93 0.00 40.69 4.70
1660 3857 2.047560 TCTCTCTCGGACACGCGA 60.048 61.111 15.93 0.00 40.69 5.87
1661 3858 2.401592 CTCTCTCTCGGACACGCG 59.598 66.667 3.53 3.53 40.69 6.01
1662 3859 2.766400 CCCTCTCTCTCGGACACGC 61.766 68.421 0.00 0.00 40.69 5.34
1663 3860 1.078356 TCCCTCTCTCTCGGACACG 60.078 63.158 0.00 0.00 42.74 4.49
1664 3861 0.253610 TCTCCCTCTCTCTCGGACAC 59.746 60.000 0.00 0.00 0.00 3.67
1665 3862 0.544223 CTCTCCCTCTCTCTCGGACA 59.456 60.000 0.00 0.00 0.00 4.02
1666 3863 0.834612 TCTCTCCCTCTCTCTCGGAC 59.165 60.000 0.00 0.00 0.00 4.79
1667 3864 1.128200 CTCTCTCCCTCTCTCTCGGA 58.872 60.000 0.00 0.00 0.00 4.55
1668 3865 0.535102 GCTCTCTCCCTCTCTCTCGG 60.535 65.000 0.00 0.00 0.00 4.63
1669 3866 0.880278 CGCTCTCTCCCTCTCTCTCG 60.880 65.000 0.00 0.00 0.00 4.04
1671 3868 0.469917 CTCGCTCTCTCCCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
1678 3877 1.076632 TCCCTTCTCGCTCTCTCCC 60.077 63.158 0.00 0.00 0.00 4.30
1694 3893 1.064389 CAACCCAAATCTCCCTCCTCC 60.064 57.143 0.00 0.00 0.00 4.30
1695 3894 1.916181 TCAACCCAAATCTCCCTCCTC 59.084 52.381 0.00 0.00 0.00 3.71
1696 3895 1.918957 CTCAACCCAAATCTCCCTCCT 59.081 52.381 0.00 0.00 0.00 3.69
1712 3920 4.441695 CGCCTGCTCGCCTCTCAA 62.442 66.667 0.00 0.00 0.00 3.02
1737 3945 4.201122 GCATGGGAGGGGGAGCTG 62.201 72.222 0.00 0.00 0.00 4.24
1827 4045 0.179009 ATCGGGATGAACAGCATGGG 60.179 55.000 0.00 0.00 43.62 4.00
1907 4128 7.229306 ACACATGGATTAGCACGAATGATTTAT 59.771 33.333 0.00 0.00 0.00 1.40
1949 4170 7.982919 TGCTAGAAGAAAACACACAACTAACTA 59.017 33.333 0.00 0.00 0.00 2.24
1954 4175 6.374333 TCTTTGCTAGAAGAAAACACACAACT 59.626 34.615 0.00 0.00 32.95 3.16
1956 4177 6.751514 TCTTTGCTAGAAGAAAACACACAA 57.248 33.333 0.00 0.00 32.95 3.33
1984 4205 7.831193 AGCTAGTTATCTGAAACAATGTCCATT 59.169 33.333 0.00 0.00 0.00 3.16
1986 4207 6.711277 AGCTAGTTATCTGAAACAATGTCCA 58.289 36.000 0.00 0.00 0.00 4.02
1988 4209 7.492669 TGCTAGCTAGTTATCTGAAACAATGTC 59.507 37.037 21.62 0.00 0.00 3.06
2006 4227 6.043243 AGGCCAGATAGTTAATTTGCTAGCTA 59.957 38.462 17.23 5.31 32.90 3.32
2009 4230 7.500559 AGAAAGGCCAGATAGTTAATTTGCTAG 59.499 37.037 5.01 0.00 0.00 3.42
2163 4388 2.363795 AGCGATGGGAGTTCGGGA 60.364 61.111 0.00 0.00 37.10 5.14
2200 4425 5.702670 CAGCTTCCTCTACATTGTTTTCTGA 59.297 40.000 0.00 0.00 0.00 3.27
2273 4502 7.061094 GCTGCATTATTAAGTTTTCCATATCGC 59.939 37.037 0.00 0.00 0.00 4.58
2348 4577 1.383799 CAATCAAGCTCCCCACCCA 59.616 57.895 0.00 0.00 0.00 4.51
2349 4578 1.380380 CCAATCAAGCTCCCCACCC 60.380 63.158 0.00 0.00 0.00 4.61
2350 4579 2.054453 GCCAATCAAGCTCCCCACC 61.054 63.158 0.00 0.00 0.00 4.61
2351 4580 2.409870 CGCCAATCAAGCTCCCCAC 61.410 63.158 0.00 0.00 0.00 4.61
2394 4624 2.071778 AGGCCTAGCAGAGAGAGAAG 57.928 55.000 1.29 0.00 0.00 2.85
2425 4673 3.119849 CGATTCAGTCATCAAAACCCACC 60.120 47.826 0.00 0.00 0.00 4.61
2434 4682 2.470983 TGCAACCGATTCAGTCATCA 57.529 45.000 0.00 0.00 0.00 3.07
2456 4706 5.791336 AAGAGAGGATTTGTTGGGTTTTC 57.209 39.130 0.00 0.00 0.00 2.29
2493 4743 7.795047 AGAAGAAAGGATTGGTTGATTGTTTT 58.205 30.769 0.00 0.00 0.00 2.43
2497 4747 7.224522 AGAAGAAGAAAGGATTGGTTGATTG 57.775 36.000 0.00 0.00 0.00 2.67
2500 4750 6.605119 AGAAGAAGAAGAAAGGATTGGTTGA 58.395 36.000 0.00 0.00 0.00 3.18
2507 4757 5.549619 TGGAAGGAGAAGAAGAAGAAAGGAT 59.450 40.000 0.00 0.00 0.00 3.24
2525 4781 5.412286 CCCTTGTTTATTGCAATTTGGAAGG 59.588 40.000 18.75 20.73 29.36 3.46


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

AutoCloner maintained by Alex Coulton.