Multiple sequence alignment - TraesCS2D01G531600

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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 TraesCS2D01G531600 chr2D 100.000 7132 0 0 1 7132 617397264 617390133 0.000000e+00 13171.0
1 TraesCS2D01G531600 chr2B 90.630 3874 180 93 1 3800 753098177 753094413 0.000000e+00 4974.0
2 TraesCS2D01G531600 chr2B 94.697 2376 98 13 3791 6158 753094388 753092033 0.000000e+00 3664.0
3 TraesCS2D01G531600 chr2B 92.790 319 21 2 6740 7057 753091255 753090938 1.810000e-125 460.0
4 TraesCS2D01G531600 chr2B 91.525 295 25 0 6577 6871 753091457 753091163 2.400000e-109 407.0
5 TraesCS2D01G531600 chr2B 81.992 261 31 6 6194 6439 753092029 753091770 2.610000e-49 207.0
6 TraesCS2D01G531600 chr2B 84.103 195 15 2 6439 6617 753091650 753091456 2.640000e-39 174.0
7 TraesCS2D01G531600 chr2A 94.337 2419 94 16 3791 6196 747612951 747610563 0.000000e+00 3668.0
8 TraesCS2D01G531600 chr2A 87.948 2622 153 77 1 2545 747616740 747614205 0.000000e+00 2940.0
9 TraesCS2D01G531600 chr2A 95.543 1234 42 7 2575 3800 747614204 747612976 0.000000e+00 1962.0
10 TraesCS2D01G531600 chr2A 94.095 525 31 0 6577 7101 747609788 747609264 0.000000e+00 798.0
11 TraesCS2D01G531600 chr2A 88.690 168 17 2 6215 6381 747610398 747610232 3.370000e-48 204.0
12 TraesCS2D01G531600 chr2A 85.567 194 12 2 6440 6617 747609980 747609787 9.440000e-44 189.0
13 TraesCS2D01G531600 chr2A 96.364 55 2 0 6385 6439 747610166 747610112 2.740000e-14 91.6
14 TraesCS2D01G531600 chr3B 92.846 629 43 1 1712 2340 152226288 152225662 0.000000e+00 911.0
15 TraesCS2D01G531600 chr3B 84.028 983 119 18 602 1562 152227574 152226608 0.000000e+00 911.0
16 TraesCS2D01G531600 chr3B 80.123 488 67 18 3016 3496 616087135 616086671 3.190000e-88 337.0
17 TraesCS2D01G531600 chr3B 93.056 144 7 3 1573 1714 152226516 152226374 2.610000e-49 207.0
18 TraesCS2D01G531600 chr3B 83.333 138 16 4 2732 2866 616087430 616087297 3.490000e-23 121.0
19 TraesCS2D01G531600 chr4B 90.302 629 59 1 1712 2340 157289496 157288870 0.000000e+00 822.0
20 TraesCS2D01G531600 chr4B 82.562 843 106 19 904 1714 157290415 157289582 0.000000e+00 704.0
21 TraesCS2D01G531600 chr1B 89.209 417 24 5 5969 6379 577179068 577179469 1.070000e-137 501.0
22 TraesCS2D01G531600 chr1B 77.911 584 106 9 2736 3307 591393895 591394467 6.850000e-90 342.0
23 TraesCS2D01G531600 chr1B 90.411 73 3 4 1 72 651391960 651391891 7.620000e-15 93.5
24 TraesCS2D01G531600 chr7A 78.020 596 89 27 2998 3580 126087870 126087304 3.190000e-88 337.0
25 TraesCS2D01G531600 chr4A 91.045 134 10 2 3 135 108192265 108192397 5.680000e-41 180.0
26 TraesCS2D01G531600 chr4D 90.977 133 10 2 4 135 289493989 289493858 2.040000e-40 178.0
27 TraesCS2D01G531600 chr4D 91.379 116 9 1 3 117 150649812 150649927 2.660000e-34 158.0
28 TraesCS2D01G531600 chr4D 88.136 118 10 2 1 117 166138113 166137999 3.470000e-28 137.0
29 TraesCS2D01G531600 chr1D 82.326 215 18 9 3019 3232 463164512 463164707 1.230000e-37 169.0
30 TraesCS2D01G531600 chr1D 95.312 64 1 2 1 63 42524095 42524157 4.550000e-17 100.0
31 TraesCS2D01G531600 chr7B 92.373 118 8 1 1 117 709578717 709578834 4.430000e-37 167.0
32 TraesCS2D01G531600 chr7B 89.831 118 5 4 1 117 597764246 597764135 2.070000e-30 145.0
33 TraesCS2D01G531600 chr7B 79.581 191 24 11 128 314 653341649 653341470 9.720000e-24 122.0
34 TraesCS2D01G531600 chr1A 82.110 218 18 10 3017 3232 555075841 555076039 4.430000e-37 167.0


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 TraesCS2D01G531600 chr2D 617390133 617397264 7131 True 13171.000000 13171 100.000000 1 7132 1 chr2D.!!$R1 7131
1 TraesCS2D01G531600 chr2B 753090938 753098177 7239 True 1647.666667 4974 89.289500 1 7057 6 chr2B.!!$R1 7056
2 TraesCS2D01G531600 chr2A 747609264 747616740 7476 True 1407.514286 3668 91.792000 1 7101 7 chr2A.!!$R1 7100
3 TraesCS2D01G531600 chr3B 152225662 152227574 1912 True 676.333333 911 89.976667 602 2340 3 chr3B.!!$R1 1738
4 TraesCS2D01G531600 chr3B 616086671 616087430 759 True 229.000000 337 81.728000 2732 3496 2 chr3B.!!$R2 764
5 TraesCS2D01G531600 chr4B 157288870 157290415 1545 True 763.000000 822 86.432000 904 2340 2 chr4B.!!$R1 1436
6 TraesCS2D01G531600 chr1B 591393895 591394467 572 False 342.000000 342 77.911000 2736 3307 1 chr1B.!!$F2 571
7 TraesCS2D01G531600 chr7A 126087304 126087870 566 True 337.000000 337 78.020000 2998 3580 1 chr7A.!!$R1 582

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
424 468 0.036306 GCGACCCAGAAAGGAAAGGA 59.964 55.000 0.00 0.00 41.22 3.36 F
1009 1085 0.720027 CAGCAGAGCAATGTGAGTCG 59.280 55.000 0.00 0.00 0.00 4.18 F
2236 2541 1.202268 GCTGTCAGATGCCAAATCTGC 60.202 52.381 3.32 6.63 43.79 4.26 F
2903 3214 1.541588 GTTGCAACCTCCCTGATTGAC 59.458 52.381 19.15 0.00 0.00 3.18 F
4262 4687 1.666872 GGCTATTCGGCCGCGTTAT 60.667 57.895 23.51 13.29 42.82 1.89 F
5853 6285 0.914551 CTCGTAATTGTCGCGTGAGG 59.085 55.000 5.77 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1683 0.175760 GGTCATTCAGGCAGTAGCGA 59.824 55.000 0.0 0.0 43.41 4.93 R
2903 3214 1.208259 GCTTTGGTTTTGCTTCACCG 58.792 50.000 0.0 0.0 35.60 4.94 R
3148 3525 3.951037 AGCACAACCTACACATTCAACAA 59.049 39.130 0.0 0.0 0.00 2.83 R
4581 5007 1.556911 ACTTCTCAGGAATCATGCGGT 59.443 47.619 0.0 0.0 0.00 5.68 R
5925 6357 0.755686 ATCATCTCCTCTTGACGGCC 59.244 55.000 0.0 0.0 0.00 6.13 R
6865 7740 0.039346 GCTACCCGAATCCGAGCTAC 60.039 60.000 0.0 0.0 38.22 3.58 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
54 55 4.056125 GCCCCGCCTGAGCAAAAC 62.056 66.667 0.00 0.00 39.83 2.43
55 56 2.597217 CCCCGCCTGAGCAAAACA 60.597 61.111 0.00 0.00 39.83 2.83
56 57 2.199652 CCCCGCCTGAGCAAAACAA 61.200 57.895 0.00 0.00 39.83 2.83
58 59 0.597377 CCCGCCTGAGCAAAACAAAC 60.597 55.000 0.00 0.00 39.83 2.93
59 60 0.102120 CCGCCTGAGCAAAACAAACA 59.898 50.000 0.00 0.00 39.83 2.83
61 62 1.587946 CGCCTGAGCAAAACAAACAAC 59.412 47.619 0.00 0.00 39.83 3.32
62 63 2.615869 GCCTGAGCAAAACAAACAACA 58.384 42.857 0.00 0.00 39.53 3.33
64 65 3.181521 GCCTGAGCAAAACAAACAACAAC 60.182 43.478 0.00 0.00 39.53 3.32
66 67 4.143137 CCTGAGCAAAACAAACAACAACAC 60.143 41.667 0.00 0.00 0.00 3.32
67 68 4.371786 TGAGCAAAACAAACAACAACACA 58.628 34.783 0.00 0.00 0.00 3.72
69 70 5.050499 TGAGCAAAACAAACAACAACACAAG 60.050 36.000 0.00 0.00 0.00 3.16
70 71 5.053145 AGCAAAACAAACAACAACACAAGA 58.947 33.333 0.00 0.00 0.00 3.02
71 72 5.050431 AGCAAAACAAACAACAACACAAGAC 60.050 36.000 0.00 0.00 0.00 3.01
72 73 5.050431 GCAAAACAAACAACAACACAAGACT 60.050 36.000 0.00 0.00 0.00 3.24
75 76 2.825086 AACAACAACACAAGACTCGC 57.175 45.000 0.00 0.00 0.00 5.03
76 77 1.732941 ACAACAACACAAGACTCGCA 58.267 45.000 0.00 0.00 0.00 5.10
77 78 2.288666 ACAACAACACAAGACTCGCAT 58.711 42.857 0.00 0.00 0.00 4.73
91 102 1.854743 CTCGCATCACACGAATCGAAT 59.145 47.619 10.55 0.00 39.39 3.34
94 105 2.347016 CGCATCACACGAATCGAATCAG 60.347 50.000 10.55 0.00 0.00 2.90
99 110 2.092055 CACACGAATCGAATCAGCGAAA 59.908 45.455 10.55 0.00 44.22 3.46
101 112 1.659098 ACGAATCGAATCAGCGAAACC 59.341 47.619 10.55 0.00 44.22 3.27
102 113 1.658596 CGAATCGAATCAGCGAAACCA 59.341 47.619 0.00 0.00 44.22 3.67
104 115 0.999406 ATCGAATCAGCGAAACCACG 59.001 50.000 0.00 0.00 44.22 4.94
105 116 1.011968 TCGAATCAGCGAAACCACGG 61.012 55.000 0.00 0.00 37.35 4.94
107 118 1.644786 GAATCAGCGAAACCACGGGG 61.645 60.000 0.00 0.00 41.29 5.73
112 123 4.323477 CGAAACCACGGGGCCAGA 62.323 66.667 11.67 0.00 37.90 3.86
113 124 2.671963 GAAACCACGGGGCCAGAC 60.672 66.667 11.67 0.00 37.90 3.51
114 125 4.636435 AAACCACGGGGCCAGACG 62.636 66.667 11.67 8.82 37.90 4.18
133 151 1.873903 CGAAGCTTACCATCCCGGATG 60.874 57.143 19.26 19.26 39.52 3.51
212 230 3.118592 AGGAGTTTGCCCTAGAAATCGAG 60.119 47.826 0.00 0.00 30.92 4.04
213 231 3.118738 GGAGTTTGCCCTAGAAATCGAGA 60.119 47.826 0.00 0.00 0.00 4.04
214 232 4.504858 GAGTTTGCCCTAGAAATCGAGAA 58.495 43.478 0.00 0.00 0.00 2.87
217 235 2.467880 TGCCCTAGAAATCGAGAACCT 58.532 47.619 0.00 0.00 0.00 3.50
219 237 2.696187 GCCCTAGAAATCGAGAACCTCT 59.304 50.000 0.00 0.00 0.00 3.69
222 240 2.682155 AGAAATCGAGAACCTCTGCC 57.318 50.000 0.00 0.00 0.00 4.85
223 241 1.134965 AGAAATCGAGAACCTCTGCCG 60.135 52.381 0.00 0.00 0.00 5.69
224 242 0.741221 AAATCGAGAACCTCTGCCGC 60.741 55.000 0.00 0.00 0.00 6.53
225 243 2.579684 AATCGAGAACCTCTGCCGCC 62.580 60.000 0.00 0.00 0.00 6.13
257 279 0.322277 AGGAACACTCTCGCGTAGGA 60.322 55.000 5.77 2.40 0.00 2.94
264 286 0.248702 CTCTCGCGTAGGAAGGAAGC 60.249 60.000 5.77 0.00 0.00 3.86
266 288 0.526524 CTCGCGTAGGAAGGAAGCAG 60.527 60.000 5.77 0.00 0.00 4.24
268 290 1.898154 GCGTAGGAAGGAAGCAGGA 59.102 57.895 0.00 0.00 0.00 3.86
269 291 0.179097 GCGTAGGAAGGAAGCAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
271 293 0.179234 GTAGGAAGGAAGCAGGAGGC 59.821 60.000 0.00 0.00 45.30 4.70
316 338 2.338984 CTATGGGCTACGGACGGC 59.661 66.667 0.00 0.00 0.00 5.68
317 339 3.553437 CTATGGGCTACGGACGGCG 62.553 68.421 4.80 4.80 0.00 6.46
321 343 4.440127 GGCTACGGACGGCGGAAA 62.440 66.667 13.24 0.00 0.00 3.13
322 344 2.432972 GCTACGGACGGCGGAAAA 60.433 61.111 13.24 0.00 0.00 2.29
323 345 2.450345 GCTACGGACGGCGGAAAAG 61.450 63.158 13.24 2.90 0.00 2.27
324 346 1.213537 CTACGGACGGCGGAAAAGA 59.786 57.895 13.24 0.00 0.00 2.52
327 353 1.373748 CGGACGGCGGAAAAGAAGA 60.374 57.895 13.24 0.00 0.00 2.87
328 354 0.947180 CGGACGGCGGAAAAGAAGAA 60.947 55.000 13.24 0.00 0.00 2.52
362 388 3.290776 CCAGCTAGGGTCGTATTGC 57.709 57.895 0.00 0.00 0.00 3.56
363 389 0.464036 CCAGCTAGGGTCGTATTGCA 59.536 55.000 0.00 0.00 0.00 4.08
364 390 1.539065 CCAGCTAGGGTCGTATTGCAG 60.539 57.143 0.00 0.00 0.00 4.41
365 391 0.753262 AGCTAGGGTCGTATTGCAGG 59.247 55.000 0.00 0.00 0.00 4.85
367 393 0.249911 CTAGGGTCGTATTGCAGGCC 60.250 60.000 0.00 0.00 0.00 5.19
421 465 1.840598 TGGCGACCCAGAAAGGAAA 59.159 52.632 0.00 0.00 41.22 3.13
422 466 0.250727 TGGCGACCCAGAAAGGAAAG 60.251 55.000 0.00 0.00 41.22 2.62
423 467 0.960861 GGCGACCCAGAAAGGAAAGG 60.961 60.000 0.00 0.00 41.22 3.11
424 468 0.036306 GCGACCCAGAAAGGAAAGGA 59.964 55.000 0.00 0.00 41.22 3.36
425 469 1.544759 GCGACCCAGAAAGGAAAGGAA 60.545 52.381 0.00 0.00 41.22 3.36
569 637 3.319198 TGCAGGGGAGGGTTCGAC 61.319 66.667 0.00 0.00 0.00 4.20
599 667 4.121669 TGGCTGACGCTCGAGCTC 62.122 66.667 32.88 26.81 39.32 4.09
600 668 4.863925 GGCTGACGCTCGAGCTCC 62.864 72.222 32.88 23.75 39.32 4.70
709 778 2.093973 TCAGGAGAAGCGAAGGTGATTC 60.094 50.000 0.00 0.00 39.47 2.52
890 959 4.459089 GTGCTCCCGCCACTCTCC 62.459 72.222 0.00 0.00 34.43 3.71
893 962 3.151022 CTCCCGCCACTCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
934 1009 2.484264 GCTAACCATGGTTGTGTGTCTC 59.516 50.000 35.49 13.62 38.92 3.36
985 1060 1.334869 CGAGTGCTTTGGCTCAAGTTT 59.665 47.619 0.00 0.00 39.59 2.66
1009 1085 0.720027 CAGCAGAGCAATGTGAGTCG 59.280 55.000 0.00 0.00 0.00 4.18
1022 1114 2.164422 TGTGAGTCGTCCTGATCATCAC 59.836 50.000 13.86 13.86 37.66 3.06
1038 1137 4.009675 TCATCACAATGCCTTAGTGGAAC 58.990 43.478 0.00 0.00 38.35 3.62
1051 1150 6.295123 GCCTTAGTGGAACGATAATCTGGATA 60.295 42.308 0.00 0.00 45.86 2.59
1052 1151 7.667557 CCTTAGTGGAACGATAATCTGGATAA 58.332 38.462 0.00 0.00 45.86 1.75
1053 1152 8.314751 CCTTAGTGGAACGATAATCTGGATAAT 58.685 37.037 0.00 0.00 45.86 1.28
1095 1198 3.911964 CGTATTGTTTGCAAGTAACTGCC 59.088 43.478 0.00 0.00 41.90 4.85
1132 1259 1.276989 CAATCTTTGTGCATTGGGGCT 59.723 47.619 0.00 0.00 34.04 5.19
1227 1360 3.499406 TGCCACTGCAGGGAAGAT 58.501 55.556 20.22 0.00 44.23 2.40
1396 1529 6.344624 CGTTTTGTGTGTGGTTATTTTGATCG 60.345 38.462 0.00 0.00 0.00 3.69
1404 1537 5.533154 TGTGGTTATTTTGATCGACCTGTTT 59.467 36.000 0.00 0.00 0.00 2.83
1419 1552 2.615493 CCTGTTTATCTTGTCGTGGGCT 60.615 50.000 0.00 0.00 0.00 5.19
1436 1569 3.483235 CTGCCCGTTGTTGGTGTGC 62.483 63.158 0.00 0.00 0.00 4.57
1443 1576 2.389998 CGTTGTTGGTGTGCAATAACC 58.610 47.619 7.39 7.39 32.45 2.85
1456 1589 3.262420 GCAATAACCGTGATGAGACTGT 58.738 45.455 0.00 0.00 0.00 3.55
1550 1683 5.411781 GTGAAGACCATTGAGATTCTACGT 58.588 41.667 0.00 0.00 0.00 3.57
1745 2050 5.947228 TCATGAGAAAGCCTGTTACTTTG 57.053 39.130 0.00 0.00 37.47 2.77
1754 2059 5.607119 AGCCTGTTACTTTGAACGTATTG 57.393 39.130 0.00 0.00 31.59 1.90
1821 2126 9.448438 AAAGATGTGTGCAGTTATATTCTTGTA 57.552 29.630 0.00 0.00 0.00 2.41
1822 2127 9.618890 AAGATGTGTGCAGTTATATTCTTGTAT 57.381 29.630 0.00 0.00 0.00 2.29
2043 2348 6.873605 TCTCTCGACTTTCTTTTATGCATTCA 59.126 34.615 3.54 0.00 0.00 2.57
2236 2541 1.202268 GCTGTCAGATGCCAAATCTGC 60.202 52.381 3.32 6.63 43.79 4.26
2333 2638 3.318839 CAGAATGTTTCAGGTGCCTTTCA 59.681 43.478 0.00 0.00 0.00 2.69
2401 2707 9.979578 TTTTTGTATCTTTGTACATCTGCAATT 57.020 25.926 0.00 0.00 34.76 2.32
2402 2708 8.969121 TTTGTATCTTTGTACATCTGCAATTG 57.031 30.769 0.00 0.00 34.76 2.32
2442 2748 9.034544 TGATTTCATATTCTGTATCTCAACACG 57.965 33.333 0.00 0.00 0.00 4.49
2497 2803 2.368875 TGAAAGTCAAGAGGGTCTGTCC 59.631 50.000 0.00 0.00 0.00 4.02
2573 2879 6.437928 CAAGTGAACAGCAGCAAAGTAAATA 58.562 36.000 0.00 0.00 0.00 1.40
2608 2914 8.593945 ATTTATTTCAGTCCTTAATCCTGCAA 57.406 30.769 0.00 0.00 0.00 4.08
2617 2923 3.703052 CCTTAATCCTGCAAGCTGGAAAT 59.297 43.478 21.88 16.37 45.02 2.17
2666 2972 5.064707 CACATACAGGATAAAGACAAACCCG 59.935 44.000 0.00 0.00 0.00 5.28
2814 3122 3.391296 TCAAGGAGGAAACTTACTGTGCT 59.609 43.478 0.00 0.00 44.43 4.40
2815 3123 3.409026 AGGAGGAAACTTACTGTGCTG 57.591 47.619 0.00 0.00 44.43 4.41
2816 3124 2.972713 AGGAGGAAACTTACTGTGCTGA 59.027 45.455 0.00 0.00 44.43 4.26
2903 3214 1.541588 GTTGCAACCTCCCTGATTGAC 59.458 52.381 19.15 0.00 0.00 3.18
2936 3247 5.799681 AACCAAAGCATGTTCTTTTGTTG 57.200 34.783 11.78 0.26 39.16 3.33
2989 3344 9.973450 TTTATGTTAAGCATTATGTTGTTGTGT 57.027 25.926 0.00 0.00 38.94 3.72
3006 3361 6.148948 TGTTGTGTTGTTCAGAGTTTTCTTG 58.851 36.000 0.00 0.00 0.00 3.02
3148 3525 7.675062 AGTAAGTGATTCTCAGTTTCTCATGT 58.325 34.615 2.79 0.00 40.28 3.21
3169 3546 3.980646 TGTTGAATGTGTAGGTTGTGC 57.019 42.857 0.00 0.00 0.00 4.57
3365 3752 4.618920 TCTTTAGTCTGGTGAAACTCCC 57.381 45.455 0.00 0.00 36.74 4.30
3375 3762 6.040504 GTCTGGTGAAACTCCCTTGTTAAATT 59.959 38.462 0.00 0.00 36.74 1.82
3437 3824 4.423625 AAAGAGTAGTCAACCAACAGCT 57.576 40.909 0.00 0.00 0.00 4.24
3500 3889 7.621796 AGGTAAAATATCAAGAGAAGTTCCGT 58.378 34.615 0.00 0.00 0.00 4.69
3789 4179 6.016276 ACAGGAGGTATTTTGCTGTGTTTAAG 60.016 38.462 0.00 0.00 44.16 1.85
3966 4391 9.146984 TCTTGAAACTACACCTATTACATTTCG 57.853 33.333 0.00 0.00 0.00 3.46
4074 4499 9.330063 CAGGAAAACAATCTACTAAGCATCATA 57.670 33.333 0.00 0.00 0.00 2.15
4076 4501 8.276325 GGAAAACAATCTACTAAGCATCATACG 58.724 37.037 0.00 0.00 0.00 3.06
4111 4536 6.801539 TCAAATGCTCACTGTTAGTTTAGG 57.198 37.500 0.00 0.00 0.00 2.69
4262 4687 1.666872 GGCTATTCGGCCGCGTTAT 60.667 57.895 23.51 13.29 42.82 1.89
4358 4783 9.528018 TCCAAATTTTGTTCTACAGATTTGAAC 57.472 29.630 20.34 0.00 41.14 3.18
4365 4790 7.202016 TGTTCTACAGATTTGAACACATTCC 57.798 36.000 0.00 0.00 43.15 3.01
4530 4956 6.095440 CGAAATCTGGATGAAACAAGGGTATT 59.905 38.462 0.00 0.00 0.00 1.89
4564 4990 6.430308 CCGTTCTGTAGTCTTAGGCATATAGA 59.570 42.308 0.00 0.00 0.00 1.98
4581 5007 7.201920 GGCATATAGAGTTAGTCCTCAACTTGA 60.202 40.741 0.00 0.00 39.55 3.02
4591 5017 2.086869 CCTCAACTTGACCGCATGATT 58.913 47.619 0.00 0.00 0.00 2.57
4720 5146 1.524621 GGCGAGTGCATGCAGGTAT 60.525 57.895 23.41 7.55 45.35 2.73
4874 5301 5.697633 GCACTCAAAATTTGGTGATCACATT 59.302 36.000 26.47 14.94 35.32 2.71
4974 5401 4.225942 TCTGATGGTACTCAAAGCAGGATT 59.774 41.667 0.00 0.00 0.00 3.01
4978 5405 5.086104 TGGTACTCAAAGCAGGATTCTAC 57.914 43.478 0.00 0.00 0.00 2.59
5060 5487 1.002087 AGGGAGTTGCTTCTTGGTACG 59.998 52.381 0.00 0.00 0.00 3.67
5070 5497 3.522553 CTTCTTGGTACGAGATCAACCC 58.477 50.000 0.00 0.00 31.97 4.11
5235 5662 5.163468 TGCCATTTTTGTCTTTTCAGCACTA 60.163 36.000 0.00 0.00 0.00 2.74
5265 5695 7.956328 TTCTAGTCTGGTGTGAACTATATGT 57.044 36.000 0.00 0.00 0.00 2.29
5280 5710 9.832445 TGAACTATATGTTACCTTGGAGAAATC 57.168 33.333 0.00 0.00 39.30 2.17
5298 5728 7.308830 GGAGAAATCTATGGATTAACACCATGC 60.309 40.741 19.89 7.61 46.05 4.06
5299 5729 7.062322 AGAAATCTATGGATTAACACCATGCA 58.938 34.615 19.89 10.48 46.05 3.96
5350 5780 3.500448 TCAGTTGTCTGCCATTTACCA 57.500 42.857 0.00 0.00 41.10 3.25
5356 5786 5.070313 AGTTGTCTGCCATTTACCAATGTTT 59.930 36.000 0.00 0.00 38.58 2.83
5357 5787 5.543507 TGTCTGCCATTTACCAATGTTTT 57.456 34.783 0.00 0.00 38.58 2.43
5420 5850 4.154737 ACATTGATCTGACCGAACAACATG 59.845 41.667 0.00 0.00 37.26 3.21
5491 5921 2.127232 GGACGCAGCAAACGAAGC 60.127 61.111 0.00 0.00 0.00 3.86
5581 6011 1.271871 ACAAATCGGCAATCTGGACCA 60.272 47.619 0.00 0.00 0.00 4.02
5853 6285 0.914551 CTCGTAATTGTCGCGTGAGG 59.085 55.000 5.77 0.00 0.00 3.86
5925 6357 0.964358 AGGTCACGAGGAACTACGGG 60.964 60.000 0.00 0.00 43.43 5.28
5982 6414 1.943340 GATTCGGAGAATCAAGGGCAC 59.057 52.381 15.48 0.00 45.90 5.01
6009 6444 4.458397 AGAATAGCTGATGTGTTCCCATG 58.542 43.478 0.00 0.00 0.00 3.66
6147 6587 9.936329 AGTTTACCATTGGGAACTATTATCATT 57.064 29.630 19.29 0.35 33.60 2.57
6172 6614 4.278669 ACATATAGTGTTCCAGGCTAGTCG 59.721 45.833 0.00 0.00 38.01 4.18
6182 6624 0.680280 AGGCTAGTCGGTCGTGTGAT 60.680 55.000 0.00 0.00 0.00 3.06
6183 6625 0.525668 GGCTAGTCGGTCGTGTGATG 60.526 60.000 0.00 0.00 0.00 3.07
6184 6626 1.140407 GCTAGTCGGTCGTGTGATGC 61.140 60.000 0.00 0.00 0.00 3.91
6185 6627 0.525668 CTAGTCGGTCGTGTGATGCC 60.526 60.000 0.00 0.00 0.00 4.40
6186 6628 0.963856 TAGTCGGTCGTGTGATGCCT 60.964 55.000 0.00 0.00 0.00 4.75
6187 6629 0.963856 AGTCGGTCGTGTGATGCCTA 60.964 55.000 0.00 0.00 0.00 3.93
6188 6630 0.102481 GTCGGTCGTGTGATGCCTAT 59.898 55.000 0.00 0.00 0.00 2.57
6190 6632 0.875908 CGGTCGTGTGATGCCTATGG 60.876 60.000 0.00 0.00 0.00 2.74
6232 6819 3.005155 AGCAAGGCATTGAACTGAAACTC 59.995 43.478 16.56 0.00 38.83 3.01
6234 6821 4.560108 GCAAGGCATTGAACTGAAACTCAT 60.560 41.667 16.56 0.00 38.83 2.90
6264 6851 5.818136 TCATTTTTCTCGAGCAATTAGGG 57.182 39.130 7.81 0.00 0.00 3.53
6281 6868 7.170320 GCAATTAGGGAAACAATGCTGATAATG 59.830 37.037 0.00 0.00 0.00 1.90
6381 6969 6.208402 TCAAAAGCAAATTACAGAGGCATGTA 59.792 34.615 0.00 0.00 34.56 2.29
6382 6970 5.824904 AAGCAAATTACAGAGGCATGTAG 57.175 39.130 0.00 0.00 37.01 2.74
6383 6971 4.848357 AGCAAATTACAGAGGCATGTAGT 58.152 39.130 0.00 0.00 37.01 2.73
6397 7047 1.814169 GTAGTAACGGCCTGGCTGC 60.814 63.158 27.03 11.30 38.71 5.25
6466 7249 7.913789 TCAACTTGGGTGTATGTAATAGAGTT 58.086 34.615 0.00 0.00 0.00 3.01
6525 7308 1.142465 CCAAGAGGCTGCTGTCCATAT 59.858 52.381 0.00 0.00 0.00 1.78
6531 7314 0.181114 GCTGCTGTCCATATGGTCCA 59.819 55.000 21.28 16.90 36.34 4.02
6595 7431 3.731728 GGCTGGGCATGGACTGGA 61.732 66.667 0.00 0.00 0.00 3.86
6597 7433 2.976490 GCTGGGCATGGACTGGAGT 61.976 63.158 0.00 0.00 0.00 3.85
6632 7468 0.396695 GGATCCCACGTAGTCTCCCA 60.397 60.000 0.00 0.00 41.61 4.37
6741 7577 1.418908 CCATATCCAGGAAGCGGGGT 61.419 60.000 0.00 0.00 0.00 4.95
6865 7740 2.203280 TGGTCTGCGGTGTTTGGG 60.203 61.111 0.00 0.00 0.00 4.12
6939 7814 4.619973 GAGTAGCTTGACTGGATCTGATG 58.380 47.826 0.00 0.00 0.00 3.07
6947 7822 1.209019 ACTGGATCTGATGTGGAGCAC 59.791 52.381 0.00 0.00 34.56 4.40
6960 7835 0.898320 GGAGCACTTGAGTAGCCAGA 59.102 55.000 0.00 0.00 0.00 3.86
7020 7895 3.299503 AGTTCATTGGTGGTTCAAAGCT 58.700 40.909 0.00 0.00 0.00 3.74
7043 7918 3.432051 GACGGAGATGGTCCTGCCG 62.432 68.421 0.00 0.00 44.35 5.69
7052 7927 2.617274 GGTCCTGCCGCAGAAACAC 61.617 63.158 22.35 11.65 32.44 3.32
7072 7947 2.225041 ACTCCCGGTATATGCTGAGCTA 60.225 50.000 5.83 0.00 0.00 3.32
7078 7953 3.615110 CGGTATATGCTGAGCTAACCTGG 60.615 52.174 5.83 0.00 0.00 4.45
7101 7976 5.411053 GGAAAACAATCTCAGAGAAGTCAGG 59.589 44.000 3.63 0.00 0.00 3.86
7102 7977 4.550076 AACAATCTCAGAGAAGTCAGGG 57.450 45.455 3.63 0.00 0.00 4.45
7103 7978 2.235898 ACAATCTCAGAGAAGTCAGGGC 59.764 50.000 3.63 0.00 0.00 5.19
7104 7979 2.235650 CAATCTCAGAGAAGTCAGGGCA 59.764 50.000 3.63 0.00 0.00 5.36
7105 7980 2.244486 TCTCAGAGAAGTCAGGGCAT 57.756 50.000 0.00 0.00 0.00 4.40
7106 7981 2.544721 TCTCAGAGAAGTCAGGGCATT 58.455 47.619 0.00 0.00 0.00 3.56
7107 7982 2.235650 TCTCAGAGAAGTCAGGGCATTG 59.764 50.000 0.00 0.00 0.00 2.82
7108 7983 1.093159 CAGAGAAGTCAGGGCATTGC 58.907 55.000 0.00 0.00 0.00 3.56
7109 7984 0.990374 AGAGAAGTCAGGGCATTGCT 59.010 50.000 8.82 0.00 0.00 3.91
7110 7985 1.093159 GAGAAGTCAGGGCATTGCTG 58.907 55.000 8.82 0.00 0.00 4.41
7111 7986 0.403271 AGAAGTCAGGGCATTGCTGT 59.597 50.000 8.82 0.00 0.00 4.40
7112 7987 1.202976 AGAAGTCAGGGCATTGCTGTT 60.203 47.619 8.82 0.00 0.00 3.16
7113 7988 0.963962 AAGTCAGGGCATTGCTGTTG 59.036 50.000 8.82 5.09 0.00 3.33
7114 7989 0.178981 AGTCAGGGCATTGCTGTTGT 60.179 50.000 8.82 0.00 0.00 3.32
7115 7990 0.242017 GTCAGGGCATTGCTGTTGTC 59.758 55.000 8.82 0.00 0.00 3.18
7116 7991 0.178995 TCAGGGCATTGCTGTTGTCA 60.179 50.000 8.82 0.00 0.00 3.58
7117 7992 0.038892 CAGGGCATTGCTGTTGTCAC 60.039 55.000 8.82 0.00 0.00 3.67
7118 7993 0.178981 AGGGCATTGCTGTTGTCACT 60.179 50.000 8.82 0.00 0.00 3.41
7119 7994 0.675633 GGGCATTGCTGTTGTCACTT 59.324 50.000 8.82 0.00 0.00 3.16
7120 7995 1.885887 GGGCATTGCTGTTGTCACTTA 59.114 47.619 8.82 0.00 0.00 2.24
7121 7996 2.095059 GGGCATTGCTGTTGTCACTTAG 60.095 50.000 8.82 0.00 0.00 2.18
7122 7997 2.095059 GGCATTGCTGTTGTCACTTAGG 60.095 50.000 8.82 0.00 0.00 2.69
7123 7998 2.813754 GCATTGCTGTTGTCACTTAGGA 59.186 45.455 0.16 0.00 0.00 2.94
7124 7999 3.441572 GCATTGCTGTTGTCACTTAGGAT 59.558 43.478 0.16 0.00 0.00 3.24
7125 8000 4.437930 GCATTGCTGTTGTCACTTAGGATC 60.438 45.833 0.16 0.00 0.00 3.36
7126 8001 2.959516 TGCTGTTGTCACTTAGGATCG 58.040 47.619 0.00 0.00 0.00 3.69
7127 8002 2.299013 TGCTGTTGTCACTTAGGATCGT 59.701 45.455 0.00 0.00 0.00 3.73
7128 8003 3.244078 TGCTGTTGTCACTTAGGATCGTT 60.244 43.478 0.00 0.00 0.00 3.85
7129 8004 4.021807 TGCTGTTGTCACTTAGGATCGTTA 60.022 41.667 0.00 0.00 0.00 3.18
7130 8005 5.109903 GCTGTTGTCACTTAGGATCGTTAT 58.890 41.667 0.00 0.00 0.00 1.89
7131 8006 6.127563 TGCTGTTGTCACTTAGGATCGTTATA 60.128 38.462 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.915085 CGAGTCTTGTGTTGTTGTTTGTTT 59.085 37.500 0.00 0.00 0.00 2.83
54 55 2.845967 GCGAGTCTTGTGTTGTTGTTTG 59.154 45.455 0.00 0.00 0.00 2.93
55 56 2.486203 TGCGAGTCTTGTGTTGTTGTTT 59.514 40.909 0.00 0.00 0.00 2.83
56 57 2.080693 TGCGAGTCTTGTGTTGTTGTT 58.919 42.857 0.00 0.00 0.00 2.83
58 59 2.287644 TGATGCGAGTCTTGTGTTGTTG 59.712 45.455 0.00 0.00 0.00 3.33
59 60 2.287915 GTGATGCGAGTCTTGTGTTGTT 59.712 45.455 0.00 0.00 0.00 2.83
61 62 1.866601 TGTGATGCGAGTCTTGTGTTG 59.133 47.619 0.00 0.00 0.00 3.33
62 63 1.867233 GTGTGATGCGAGTCTTGTGTT 59.133 47.619 0.00 0.00 0.00 3.32
64 65 0.436150 CGTGTGATGCGAGTCTTGTG 59.564 55.000 0.00 0.00 0.00 3.33
66 67 1.418373 TTCGTGTGATGCGAGTCTTG 58.582 50.000 0.00 0.00 39.61 3.02
67 68 2.263077 GATTCGTGTGATGCGAGTCTT 58.737 47.619 0.00 0.00 40.38 3.01
69 70 0.567968 CGATTCGTGTGATGCGAGTC 59.432 55.000 0.00 0.00 40.22 3.36
70 71 0.170339 TCGATTCGTGTGATGCGAGT 59.830 50.000 5.89 0.00 39.61 4.18
71 72 1.268265 TTCGATTCGTGTGATGCGAG 58.732 50.000 5.89 0.00 39.61 5.03
72 73 1.852280 GATTCGATTCGTGTGATGCGA 59.148 47.619 5.89 0.00 36.51 5.10
75 76 2.347016 CGCTGATTCGATTCGTGTGATG 60.347 50.000 5.89 0.00 0.00 3.07
76 77 1.854743 CGCTGATTCGATTCGTGTGAT 59.145 47.619 5.89 0.00 0.00 3.06
77 78 1.135517 TCGCTGATTCGATTCGTGTGA 60.136 47.619 5.89 10.30 33.02 3.58
104 115 1.449778 GTAAGCTTCGTCTGGCCCC 60.450 63.158 0.00 0.00 0.00 5.80
105 116 1.449778 GGTAAGCTTCGTCTGGCCC 60.450 63.158 0.00 0.00 0.00 5.80
107 118 1.291132 GATGGTAAGCTTCGTCTGGC 58.709 55.000 0.00 0.00 0.00 4.85
108 119 1.473434 GGGATGGTAAGCTTCGTCTGG 60.473 57.143 0.00 0.00 0.00 3.86
111 122 0.529992 CCGGGATGGTAAGCTTCGTC 60.530 60.000 0.00 0.00 0.00 4.20
112 123 0.974010 TCCGGGATGGTAAGCTTCGT 60.974 55.000 0.00 0.00 39.52 3.85
113 124 0.393077 ATCCGGGATGGTAAGCTTCG 59.607 55.000 9.17 0.00 39.52 3.79
114 125 1.884235 CATCCGGGATGGTAAGCTTC 58.116 55.000 26.20 0.00 36.51 3.86
115 126 0.179018 GCATCCGGGATGGTAAGCTT 60.179 55.000 32.28 3.48 40.10 3.74
133 151 4.500116 GCAGGTCGTCGGAGGAGC 62.500 72.222 19.07 19.07 0.00 4.70
178 196 2.168666 AAACTCCTCGCTCGGGTTCC 62.169 60.000 0.00 0.00 0.00 3.62
179 197 1.014564 CAAACTCCTCGCTCGGGTTC 61.015 60.000 0.00 0.00 0.00 3.62
180 198 1.004918 CAAACTCCTCGCTCGGGTT 60.005 57.895 0.00 0.00 0.00 4.11
181 199 2.657237 CAAACTCCTCGCTCGGGT 59.343 61.111 0.00 0.00 0.00 5.28
182 200 2.815647 GCAAACTCCTCGCTCGGG 60.816 66.667 0.00 0.00 0.00 5.14
183 201 2.815647 GGCAAACTCCTCGCTCGG 60.816 66.667 0.00 0.00 0.00 4.63
184 202 1.945354 TAGGGCAAACTCCTCGCTCG 61.945 60.000 0.00 0.00 35.92 5.03
185 203 0.179097 CTAGGGCAAACTCCTCGCTC 60.179 60.000 0.00 0.00 35.92 5.03
186 204 0.614979 TCTAGGGCAAACTCCTCGCT 60.615 55.000 0.00 0.00 35.92 4.93
223 241 3.130160 CCTTCCTGAGCTTGCGGC 61.130 66.667 0.00 0.00 42.19 6.53
224 242 1.003355 TTCCTTCCTGAGCTTGCGG 60.003 57.895 0.00 0.00 0.00 5.69
225 243 0.603707 TGTTCCTTCCTGAGCTTGCG 60.604 55.000 0.00 0.00 0.00 4.85
226 244 0.877743 GTGTTCCTTCCTGAGCTTGC 59.122 55.000 0.00 0.00 0.00 4.01
227 245 2.038295 AGAGTGTTCCTTCCTGAGCTTG 59.962 50.000 0.00 0.00 0.00 4.01
228 246 2.301583 GAGAGTGTTCCTTCCTGAGCTT 59.698 50.000 0.00 0.00 0.00 3.74
234 252 1.587054 CGCGAGAGTGTTCCTTCCT 59.413 57.895 0.00 0.00 36.71 3.36
257 279 4.416738 GCCGCCTCCTGCTTCCTT 62.417 66.667 0.00 0.00 38.05 3.36
278 300 4.394712 CAGCCCACAGGTCCCGAC 62.395 72.222 0.00 0.00 34.57 4.79
283 305 1.915078 ATAGCCACAGCCCACAGGTC 61.915 60.000 0.00 0.00 41.25 3.85
284 306 1.925455 ATAGCCACAGCCCACAGGT 60.925 57.895 0.00 0.00 41.25 4.00
285 307 1.452651 CATAGCCACAGCCCACAGG 60.453 63.158 0.00 0.00 41.25 4.00
286 308 1.452651 CCATAGCCACAGCCCACAG 60.453 63.158 0.00 0.00 41.25 3.66
287 309 2.676608 CCATAGCCACAGCCCACA 59.323 61.111 0.00 0.00 41.25 4.17
288 310 2.124151 CCCATAGCCACAGCCCAC 60.124 66.667 0.00 0.00 41.25 4.61
289 311 4.127744 GCCCATAGCCACAGCCCA 62.128 66.667 0.00 0.00 41.25 5.36
290 312 2.452064 TAGCCCATAGCCACAGCCC 61.452 63.158 0.00 0.00 45.47 5.19
316 338 4.985409 CCTCGGATAGATTCTTCTTTTCCG 59.015 45.833 15.40 15.40 46.97 4.30
317 339 4.752604 GCCTCGGATAGATTCTTCTTTTCC 59.247 45.833 0.00 0.00 33.11 3.13
318 340 4.446051 CGCCTCGGATAGATTCTTCTTTTC 59.554 45.833 0.00 0.00 33.17 2.29
319 341 4.372656 CGCCTCGGATAGATTCTTCTTTT 58.627 43.478 0.00 0.00 33.17 2.27
320 342 3.983741 CGCCTCGGATAGATTCTTCTTT 58.016 45.455 0.00 0.00 33.17 2.52
321 343 3.651803 CGCCTCGGATAGATTCTTCTT 57.348 47.619 0.00 0.00 33.17 2.52
348 374 0.249911 GGCCTGCAATACGACCCTAG 60.250 60.000 0.00 0.00 0.00 3.02
350 376 2.590092 GGCCTGCAATACGACCCT 59.410 61.111 0.00 0.00 0.00 4.34
352 378 2.895372 CCGGCCTGCAATACGACC 60.895 66.667 0.00 0.00 0.00 4.79
354 380 4.849310 GCCCGGCCTGCAATACGA 62.849 66.667 0.00 0.00 0.00 3.43
375 402 2.357760 GCCCGCAACTACCGAACA 60.358 61.111 0.00 0.00 0.00 3.18
380 407 0.321830 TAAACAGGCCCGCAACTACC 60.322 55.000 0.00 0.00 0.00 3.18
383 410 1.971695 GCTAAACAGGCCCGCAACT 60.972 57.895 0.00 0.00 0.00 3.16
384 411 2.566529 GCTAAACAGGCCCGCAAC 59.433 61.111 0.00 0.00 0.00 4.17
421 465 1.218316 CCTCGCGGCTTTACTTCCT 59.782 57.895 6.13 0.00 0.00 3.36
422 466 1.814169 CCCTCGCGGCTTTACTTCC 60.814 63.158 6.13 0.00 0.00 3.46
423 467 1.079336 ACCCTCGCGGCTTTACTTC 60.079 57.895 6.13 0.00 33.26 3.01
424 468 1.079336 GACCCTCGCGGCTTTACTT 60.079 57.895 6.13 0.00 33.26 2.24
425 469 2.577593 GACCCTCGCGGCTTTACT 59.422 61.111 6.13 0.00 33.26 2.24
558 626 3.767806 GGACCGGTCGAACCCTCC 61.768 72.222 27.68 8.80 33.75 4.30
688 757 1.561643 ATCACCTTCGCTTCTCCTGA 58.438 50.000 0.00 0.00 0.00 3.86
709 778 0.109272 TACGGCGAGAGAAGCACAAG 60.109 55.000 16.62 0.00 36.08 3.16
760 829 1.370051 GCCGCCACGAAACAAGAAC 60.370 57.895 0.00 0.00 0.00 3.01
890 959 2.673368 GACAAGCGACAATACCAAGGAG 59.327 50.000 0.00 0.00 0.00 3.69
893 962 2.159653 GCTGACAAGCGACAATACCAAG 60.160 50.000 0.00 0.00 40.27 3.61
934 1009 1.571460 GGCTCACTGCAACGACAAG 59.429 57.895 0.00 0.00 45.15 3.16
985 1060 1.202794 TCACATTGCTCTGCTGGTTCA 60.203 47.619 0.00 0.00 0.00 3.18
1009 1085 2.928334 AGGCATTGTGATGATCAGGAC 58.072 47.619 0.09 0.51 35.16 3.85
1022 1114 5.760253 AGATTATCGTTCCACTAAGGCATTG 59.240 40.000 0.00 0.00 37.29 2.82
1051 1150 9.944376 ATACGGATTGAGTGCTATGTATTTATT 57.056 29.630 0.00 0.00 0.00 1.40
1052 1151 9.944376 AATACGGATTGAGTGCTATGTATTTAT 57.056 29.630 0.00 0.00 29.62 1.40
1053 1152 9.203421 CAATACGGATTGAGTGCTATGTATTTA 57.797 33.333 15.69 0.00 44.59 1.40
1064 1167 4.418013 TGCAAACAATACGGATTGAGTG 57.582 40.909 27.03 21.72 44.59 3.51
1066 1169 5.046910 ACTTGCAAACAATACGGATTGAG 57.953 39.130 27.03 14.29 44.59 3.02
1095 1198 4.437239 AGATTGTTCTCTCTATGCAACGG 58.563 43.478 0.00 0.00 0.00 4.44
1132 1259 1.522668 CAGGTGGCAGTCAATCGAAA 58.477 50.000 0.00 0.00 0.00 3.46
1227 1360 2.626780 CCGGAGCGTGTCTCTGTCA 61.627 63.158 0.00 0.00 44.91 3.58
1396 1529 3.000727 CCCACGACAAGATAAACAGGTC 58.999 50.000 0.00 0.00 0.00 3.85
1404 1537 1.220749 GGCAGCCCACGACAAGATA 59.779 57.895 0.00 0.00 0.00 1.98
1419 1552 3.522731 GCACACCAACAACGGGCA 61.523 61.111 0.00 0.00 0.00 5.36
1436 1569 5.444613 CGAAACAGTCTCATCACGGTTATTG 60.445 44.000 0.00 0.00 34.11 1.90
1443 1576 1.388093 CTGCGAAACAGTCTCATCACG 59.612 52.381 0.00 0.00 41.86 4.35
1456 1589 1.871039 GCACAAAGTCTACCTGCGAAA 59.129 47.619 0.00 0.00 0.00 3.46
1550 1683 0.175760 GGTCATTCAGGCAGTAGCGA 59.824 55.000 0.00 0.00 43.41 4.93
1822 2127 9.436957 GGAAAGTTTATCTGAGAACATGAAGTA 57.563 33.333 0.00 0.00 0.00 2.24
2236 2541 9.520204 GTTGTACCCTGAAATGATATGAAATTG 57.480 33.333 0.00 0.00 0.00 2.32
2333 2638 4.021981 GCTCCAAACCAAACTAGCAGAATT 60.022 41.667 0.00 0.00 0.00 2.17
2400 2706 5.886609 TGAAATCATTAAGGGGTGACTCAA 58.113 37.500 0.00 0.00 0.00 3.02
2401 2707 5.512942 TGAAATCATTAAGGGGTGACTCA 57.487 39.130 0.00 0.00 0.00 3.41
2402 2708 8.697507 AATATGAAATCATTAAGGGGTGACTC 57.302 34.615 0.55 0.00 37.76 3.36
2442 2748 3.990092 TGTACTGAATGTGGTGTCTGAC 58.010 45.455 0.00 0.00 0.00 3.51
2608 2914 7.707624 TCAGATGTAAAATTGATTTCCAGCT 57.292 32.000 0.00 0.00 31.68 4.24
2617 2923 9.119418 TGTTCAGAACTTCAGATGTAAAATTGA 57.881 29.630 14.51 0.00 0.00 2.57
2666 2972 3.581024 TGCTCATTGATGGCACTTTTC 57.419 42.857 0.00 0.00 31.96 2.29
2799 3107 4.212214 CAGAAGTCAGCACAGTAAGTTTCC 59.788 45.833 0.00 0.00 0.00 3.13
2800 3108 5.050490 TCAGAAGTCAGCACAGTAAGTTTC 58.950 41.667 0.00 0.00 0.00 2.78
2814 3122 4.025040 ACAGGCAATTGATCAGAAGTCA 57.975 40.909 10.34 0.00 0.00 3.41
2815 3123 4.574013 CCTACAGGCAATTGATCAGAAGTC 59.426 45.833 10.34 0.00 0.00 3.01
2816 3124 4.225942 TCCTACAGGCAATTGATCAGAAGT 59.774 41.667 10.34 0.00 34.44 3.01
2903 3214 1.208259 GCTTTGGTTTTGCTTCACCG 58.792 50.000 0.00 0.00 35.60 4.94
2936 3247 8.363390 AGAAGAAGAAAATTGACCTTGATTTCC 58.637 33.333 0.00 0.00 31.91 3.13
2973 3328 5.976534 TCTGAACAACACAACAACATAATGC 59.023 36.000 0.00 0.00 0.00 3.56
2989 3344 6.834168 AAGGAACAAGAAAACTCTGAACAA 57.166 33.333 0.00 0.00 0.00 2.83
3148 3525 3.951037 AGCACAACCTACACATTCAACAA 59.049 39.130 0.00 0.00 0.00 2.83
3169 3546 4.032672 GTCGACATCTGCTTCATCTTTCAG 59.967 45.833 11.55 0.00 0.00 3.02
3365 3752 9.672086 TGAGGTAAATCGTTTCAATTTAACAAG 57.328 29.630 6.46 0.00 38.28 3.16
3375 3762 6.488683 ACCTGAAATTGAGGTAAATCGTTTCA 59.511 34.615 1.32 0.00 42.35 2.69
3789 4179 8.801715 TCAAAATTTCTCATAGCACTGTTTTC 57.198 30.769 0.00 0.00 0.00 2.29
3797 4222 8.094798 ACGTTTACTCAAAATTTCTCATAGCA 57.905 30.769 0.00 0.00 0.00 3.49
3966 4391 8.844287 TATGTATCCCATCCCCTTCTGAAAGAC 61.844 44.444 0.00 0.00 37.61 3.01
4063 4488 4.807304 ACGGGTTTAACGTATGATGCTTAG 59.193 41.667 0.00 0.00 43.60 2.18
4076 4501 4.443063 GTGAGCATTTGAAACGGGTTTAAC 59.557 41.667 0.00 0.00 32.11 2.01
4262 4687 8.621532 ATCAACTTTCAGCTCATGTAAAGTTA 57.378 30.769 16.95 10.90 41.75 2.24
4530 4956 5.909621 AGACTACAGAACGGTAGCAAATA 57.090 39.130 10.89 0.00 43.61 1.40
4564 4990 2.288886 GCGGTCAAGTTGAGGACTAACT 60.289 50.000 5.62 0.00 37.72 2.24
4581 5007 1.556911 ACTTCTCAGGAATCATGCGGT 59.443 47.619 0.00 0.00 0.00 5.68
4591 5017 5.361285 GGAGCTTAGACATAACTTCTCAGGA 59.639 44.000 0.00 0.00 0.00 3.86
4720 5146 8.102676 GTCCCAAAACTATAGTACAAGGGTTTA 58.897 37.037 22.14 9.08 35.31 2.01
4874 5301 3.384467 GCAGATGGCAAGGGCTTAAATAA 59.616 43.478 0.00 0.00 43.97 1.40
4974 5401 6.487331 GCTGCTACAGATTTACCTCTAGTAGA 59.513 42.308 0.00 0.00 33.46 2.59
4978 5405 5.300539 TCAGCTGCTACAGATTTACCTCTAG 59.699 44.000 9.47 0.00 32.44 2.43
5070 5497 6.375377 GTCTAGTAAATCCAGCTGTAGATCG 58.625 44.000 13.81 0.00 0.00 3.69
5235 5662 7.881775 AGTTCACACCAGACTAGAAATTTTT 57.118 32.000 0.00 0.00 0.00 1.94
5265 5695 9.847224 GTTAATCCATAGATTTCTCCAAGGTAA 57.153 33.333 0.00 0.00 39.83 2.85
5280 5710 5.278610 CCACATGCATGGTGTTAATCCATAG 60.279 44.000 29.41 0.00 42.92 2.23
5298 5728 2.118313 TTGTCCATGAGCTCCACATG 57.882 50.000 12.15 9.06 42.99 3.21
5299 5729 2.619849 CCTTTGTCCATGAGCTCCACAT 60.620 50.000 12.15 0.00 0.00 3.21
5356 5786 8.885722 ACAAGTTCTACGACATTCAAAAACTAA 58.114 29.630 0.00 0.00 0.00 2.24
5357 5787 8.332464 CACAAGTTCTACGACATTCAAAAACTA 58.668 33.333 0.00 0.00 0.00 2.24
5420 5850 2.169832 TAGCAGCACTTGACCTGAAC 57.830 50.000 0.00 0.00 0.00 3.18
5581 6011 4.196193 TCATGAAGTCGTTTGTCAAAGGT 58.804 39.130 15.60 0.00 0.00 3.50
5853 6285 6.749578 TCATGTAACACAACACAAACAACATC 59.250 34.615 0.00 0.00 30.75 3.06
5894 6326 1.400142 TCGTGACCTGCAAAACAACAG 59.600 47.619 0.00 0.00 0.00 3.16
5897 6329 1.021202 CCTCGTGACCTGCAAAACAA 58.979 50.000 0.00 0.00 0.00 2.83
5925 6357 0.755686 ATCATCTCCTCTTGACGGCC 59.244 55.000 0.00 0.00 0.00 6.13
5982 6414 4.508124 GGAACACATCAGCTATTCTAACCG 59.492 45.833 0.00 0.00 0.00 4.44
6147 6587 5.208890 ACTAGCCTGGAACACTATATGTCA 58.791 41.667 0.00 0.00 42.31 3.58
6161 6603 2.341101 ACACGACCGACTAGCCTGG 61.341 63.158 0.00 0.00 0.00 4.45
6172 6614 2.992089 CCATAGGCATCACACGACC 58.008 57.895 0.00 0.00 0.00 4.79
6184 6626 2.437281 AGACTTCTGTGGATGCCATAGG 59.563 50.000 9.83 0.00 42.00 2.57
6185 6627 3.464907 CAGACTTCTGTGGATGCCATAG 58.535 50.000 4.06 4.06 42.88 2.23
6186 6628 3.548745 CAGACTTCTGTGGATGCCATA 57.451 47.619 0.00 0.00 39.09 2.74
6187 6629 2.414994 CAGACTTCTGTGGATGCCAT 57.585 50.000 0.00 0.00 39.09 4.40
6188 6630 3.942351 CAGACTTCTGTGGATGCCA 57.058 52.632 0.00 0.00 39.09 4.92
6264 6851 5.252969 TCCTGCATTATCAGCATTGTTTC 57.747 39.130 0.00 0.00 41.82 2.78
6281 6868 1.340405 TGAGAAGATGGCCTTTCCTGC 60.340 52.381 3.32 0.00 34.68 4.85
6381 6969 4.760047 CGCAGCCAGGCCGTTACT 62.760 66.667 8.22 0.00 0.00 2.24
6397 7047 2.628178 TCCTCCCTACTACATGAATGCG 59.372 50.000 0.00 0.00 0.00 4.73
6430 7080 0.811281 CCAAGTTGATTCCGCCTTCC 59.189 55.000 3.87 0.00 0.00 3.46
6466 7249 3.131755 GCCCGAGGCTCTTACTTTAGTTA 59.868 47.826 13.50 0.00 46.69 2.24
6525 7308 0.253044 GCTCTGGCAGTTATGGACCA 59.747 55.000 15.27 0.00 38.54 4.02
6531 7314 1.871418 TGAGGAGCTCTGGCAGTTAT 58.129 50.000 15.27 0.83 41.70 1.89
6595 7431 1.221840 CGGCTATGGACCTGCAACT 59.778 57.895 0.00 0.00 0.00 3.16
6597 7433 1.344953 ATCCGGCTATGGACCTGCAA 61.345 55.000 0.00 0.00 41.85 4.08
6632 7468 0.409876 TACCAGACTCCTGAGCCAGT 59.590 55.000 0.00 0.00 43.02 4.00
6716 7552 2.037641 CGCTTCCTGGATATGGATCACA 59.962 50.000 0.00 0.00 33.27 3.58
6747 7583 0.822164 TCAAGCCTACGGAAGCTACC 59.178 55.000 0.00 0.00 38.74 3.18
6865 7740 0.039346 GCTACCCGAATCCGAGCTAC 60.039 60.000 0.00 0.00 38.22 3.58
6939 7814 0.321671 TGGCTACTCAAGTGCTCCAC 59.678 55.000 0.00 0.00 34.10 4.02
6982 7857 5.023533 TGAACTACTCATATGGACAAGGC 57.976 43.478 2.13 0.00 0.00 4.35
7020 7895 0.611062 AGGACCATCTCCGTCGTCAA 60.611 55.000 0.00 0.00 45.10 3.18
7043 7918 2.973694 TATACCGGGAGTGTTTCTGC 57.026 50.000 6.32 0.00 0.00 4.26
7052 7927 1.261480 AGCTCAGCATATACCGGGAG 58.739 55.000 6.32 0.41 0.00 4.30
7072 7947 5.310409 TCTCTGAGATTGTTTTCCAGGTT 57.690 39.130 2.58 0.00 0.00 3.50
7078 7953 5.411053 CCCTGACTTCTCTGAGATTGTTTTC 59.589 44.000 8.42 0.45 0.00 2.29
7101 7976 2.095059 CCTAAGTGACAACAGCAATGCC 60.095 50.000 0.00 0.00 0.00 4.40
7102 7977 2.813754 TCCTAAGTGACAACAGCAATGC 59.186 45.455 0.00 0.00 0.00 3.56
7103 7978 4.201753 CGATCCTAAGTGACAACAGCAATG 60.202 45.833 0.00 0.00 0.00 2.82
7104 7979 3.935203 CGATCCTAAGTGACAACAGCAAT 59.065 43.478 0.00 0.00 0.00 3.56
7105 7980 3.244078 ACGATCCTAAGTGACAACAGCAA 60.244 43.478 0.00 0.00 0.00 3.91
7106 7981 2.299013 ACGATCCTAAGTGACAACAGCA 59.701 45.455 0.00 0.00 0.00 4.41
7107 7982 2.960819 ACGATCCTAAGTGACAACAGC 58.039 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.