Multiple sequence alignment - TraesCS3D01G055300

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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 TraesCS3D01G055300 chr3D 100.000 4569 0 0 1 4569 23053124 23057692 0.000000e+00 8438.0
1 TraesCS3D01G055300 chr3D 95.459 991 36 4 2402 3384 22376870 22377859 0.000000e+00 1572.0
2 TraesCS3D01G055300 chr3D 85.681 1278 94 51 1084 2278 22375600 22376871 0.000000e+00 1264.0
3 TraesCS3D01G055300 chr3D 83.882 1123 96 25 1188 2259 22384079 22385167 0.000000e+00 992.0
4 TraesCS3D01G055300 chr3D 91.396 709 36 13 3418 4120 22377810 22378499 0.000000e+00 948.0
5 TraesCS3D01G055300 chr3D 83.766 770 83 26 1516 2266 22726231 22725485 0.000000e+00 691.0
6 TraesCS3D01G055300 chr3D 86.422 545 55 14 2791 3321 22386073 22386612 3.060000e-161 579.0
7 TraesCS3D01G055300 chr3D 95.000 40 1 1 902 941 562514718 562514756 1.370000e-05 62.1
8 TraesCS3D01G055300 chr3B 91.916 1472 68 21 834 2278 40231350 40232797 0.000000e+00 2012.0
9 TraesCS3D01G055300 chr3B 92.150 828 43 12 2402 3213 40233218 40234039 0.000000e+00 1149.0
10 TraesCS3D01G055300 chr3B 88.935 958 62 22 3447 4379 40234360 40235298 0.000000e+00 1142.0
11 TraesCS3D01G055300 chr3B 93.232 591 33 7 1 589 40227246 40227831 0.000000e+00 863.0
12 TraesCS3D01G055300 chr3B 81.572 776 96 33 1516 2266 40165043 40165796 8.460000e-167 597.0
13 TraesCS3D01G055300 chr3B 84.237 590 63 16 2757 3321 39806777 39806193 8.640000e-152 547.0
14 TraesCS3D01G055300 chr3B 89.790 333 33 1 1342 1673 95900222 95900554 4.220000e-115 425.0
15 TraesCS3D01G055300 chr3B 96.498 257 8 1 579 834 40228011 40228267 1.520000e-114 424.0
16 TraesCS3D01G055300 chr3B 93.208 265 4 6 2402 2666 40232796 40233046 1.200000e-100 377.0
17 TraesCS3D01G055300 chr3B 93.956 182 8 3 3206 3385 40234207 40234387 5.820000e-69 272.0
18 TraesCS3D01G055300 chr3B 86.022 93 2 3 4440 4531 40235602 40235684 6.300000e-14 89.8
19 TraesCS3D01G055300 chr3A 89.086 678 43 9 3447 4113 32144727 32145384 0.000000e+00 813.0
20 TraesCS3D01G055300 chr3A 90.635 598 48 7 2791 3382 32144155 32144750 0.000000e+00 787.0
21 TraesCS3D01G055300 chr3A 89.268 615 49 12 1133 1735 32142393 32143002 0.000000e+00 754.0
22 TraesCS3D01G055300 chr3A 85.122 531 40 8 1727 2229 32143253 32143772 1.470000e-139 507.0
23 TraesCS3D01G055300 chr3A 86.585 328 23 9 2402 2727 32143807 32144115 4.380000e-90 342.0
24 TraesCS3D01G055300 chr3A 89.147 129 9 4 4441 4569 32145942 32146065 6.120000e-34 156.0
25 TraesCS3D01G055300 chr3A 80.795 151 17 8 4231 4377 32145480 32145622 1.740000e-19 108.0
26 TraesCS3D01G055300 chr4D 82.397 534 82 9 279 807 96133370 96132844 5.390000e-124 455.0
27 TraesCS3D01G055300 chr4D 96.241 133 5 0 2272 2404 306860408 306860276 7.700000e-53 219.0
28 TraesCS3D01G055300 chr4D 100.000 34 0 0 909 942 165592377 165592344 3.820000e-06 63.9
29 TraesCS3D01G055300 chr1A 89.189 333 35 1 1342 1673 427395680 427396012 9.150000e-112 414.0
30 TraesCS3D01G055300 chr1A 88.589 333 37 1 1342 1673 529310523 529310855 1.980000e-108 403.0
31 TraesCS3D01G055300 chr1A 90.164 183 13 3 1972 2152 526135451 526135272 2.750000e-57 233.0
32 TraesCS3D01G055300 chr5D 83.455 411 63 3 266 672 539965926 539966335 1.200000e-100 377.0
33 TraesCS3D01G055300 chr5D 100.000 32 0 0 909 940 10986528 10986497 4.940000e-05 60.2
34 TraesCS3D01G055300 chr6B 86.486 333 42 2 1342 1673 125201405 125201075 3.360000e-96 363.0
35 TraesCS3D01G055300 chr6B 92.683 41 3 0 902 942 662911138 662911178 4.940000e-05 60.2
36 TraesCS3D01G055300 chr7A 89.617 183 17 2 1972 2152 17964129 17963947 9.890000e-57 231.0
37 TraesCS3D01G055300 chr7A 97.692 130 3 0 2276 2405 78506264 78506135 1.650000e-54 224.0
38 TraesCS3D01G055300 chr7A 97.368 38 1 0 910 947 19390315 19390278 1.060000e-06 65.8
39 TraesCS3D01G055300 chr5A 89.130 184 17 3 1972 2152 500029979 500029796 4.600000e-55 226.0
40 TraesCS3D01G055300 chr5B 96.992 133 4 0 2276 2408 257529893 257529761 1.650000e-54 224.0
41 TraesCS3D01G055300 chr7B 97.674 129 3 0 2276 2404 140609404 140609532 5.950000e-54 222.0
42 TraesCS3D01G055300 chr2B 97.674 129 3 0 2276 2404 545760387 545760515 5.950000e-54 222.0
43 TraesCS3D01G055300 chr2B 88.710 124 13 1 1344 1466 73073248 73073125 2.850000e-32 150.0
44 TraesCS3D01G055300 chr6D 95.620 137 5 1 2277 2412 9360022 9360158 7.700000e-53 219.0
45 TraesCS3D01G055300 chr4B 94.964 139 7 0 2270 2408 660689362 660689500 7.700000e-53 219.0
46 TraesCS3D01G055300 chr4B 90.968 155 11 3 2250 2403 652259655 652259503 5.990000e-49 206.0
47 TraesCS3D01G055300 chr4B 95.000 40 1 1 909 947 416541479 416541440 1.370000e-05 62.1
48 TraesCS3D01G055300 chr1B 91.391 151 10 3 2254 2403 499688418 499688566 2.160000e-48 204.0
49 TraesCS3D01G055300 chr2D 97.297 37 1 0 906 942 524945578 524945614 3.820000e-06 63.9
50 TraesCS3D01G055300 chr2D 95.000 40 0 2 901 940 36768668 36768705 1.370000e-05 62.1


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 TraesCS3D01G055300 chr3D 23053124 23057692 4568 False 8438.000000 8438 100.000000 1 4569 1 chr3D.!!$F1 4568
1 TraesCS3D01G055300 chr3D 22375600 22378499 2899 False 1261.333333 1572 90.845333 1084 4120 3 chr3D.!!$F3 3036
2 TraesCS3D01G055300 chr3D 22384079 22386612 2533 False 785.500000 992 85.152000 1188 3321 2 chr3D.!!$F4 2133
3 TraesCS3D01G055300 chr3D 22725485 22726231 746 True 691.000000 691 83.766000 1516 2266 1 chr3D.!!$R1 750
4 TraesCS3D01G055300 chr3B 40227246 40235684 8438 False 791.100000 2012 91.989625 1 4531 8 chr3B.!!$F3 4530
5 TraesCS3D01G055300 chr3B 40165043 40165796 753 False 597.000000 597 81.572000 1516 2266 1 chr3B.!!$F1 750
6 TraesCS3D01G055300 chr3B 39806193 39806777 584 True 547.000000 547 84.237000 2757 3321 1 chr3B.!!$R1 564
7 TraesCS3D01G055300 chr3A 32142393 32146065 3672 False 495.285714 813 87.234000 1133 4569 7 chr3A.!!$F1 3436
8 TraesCS3D01G055300 chr4D 96132844 96133370 526 True 455.000000 455 82.397000 279 807 1 chr4D.!!$R1 528

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
247 249 0.036388 TGGAAATCTCGTCCCACTGC 60.036 55.0 0.00 0.0 33.89 4.40 F
486 489 0.332632 ATTGCACTGCATACCTGGGT 59.667 50.0 4.10 0.0 38.76 4.51 F
1833 5425 0.534412 CAGAGTCCCTGAAGCGATGT 59.466 55.0 0.00 0.0 45.78 3.06 F
2294 5934 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 5492 0.482446 AAGGGGTGCATCCTGAACAA 59.518 50.0 17.44 0.0 34.34 2.83 R
2276 5916 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 R
3218 8073 0.469705 TTGAAACACCCTGCTGCCAT 60.470 50.0 0.00 0.0 0.00 4.40 R
4160 9052 0.817013 TTCTGAAATCCGCATTGCCC 59.183 50.0 2.41 0.0 0.00 5.36 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
36 37 6.911250 AACAAAGAAATACCGAGGGAAAAT 57.089 33.333 0.00 0.00 0.00 1.82
43 44 7.514721 AGAAATACCGAGGGAAAATATAAGCA 58.485 34.615 0.00 0.00 0.00 3.91
65 66 6.482973 AGCAAAAACGGATGAAAAACATGAAT 59.517 30.769 0.00 0.00 39.56 2.57
81 82 8.519492 AAACATGAATGAAAGAAACAATACCG 57.481 30.769 0.00 0.00 0.00 4.02
98 99 9.810545 AACAATACCGAAGAAAAATGAAAGAAA 57.189 25.926 0.00 0.00 0.00 2.52
201 203 8.314021 AGAAAGAAAAGAACAGGTGAAAACAAT 58.686 29.630 0.00 0.00 0.00 2.71
247 249 0.036388 TGGAAATCTCGTCCCACTGC 60.036 55.000 0.00 0.00 33.89 4.40
276 278 2.548057 CAGCTGAAAAGTTGCGGACTAA 59.452 45.455 8.42 0.00 37.72 2.24
315 317 3.007831 GCTATAGCTGGCTCCAGAAGATT 59.992 47.826 19.45 2.13 46.30 2.40
359 361 5.343249 GCTGAACAAGCGATAAAATTGGAT 58.657 37.500 0.00 0.00 43.45 3.41
409 411 9.573133 CAATTGTATGACCAAATAAAAGTCTCC 57.427 33.333 0.00 0.00 0.00 3.71
429 431 3.048600 CCTGTCCAATCCCTATCCTTCA 58.951 50.000 0.00 0.00 0.00 3.02
475 478 3.891366 CCCTCCCCTAAAATATTGCACTG 59.109 47.826 0.00 0.00 0.00 3.66
482 485 5.536161 CCCTAAAATATTGCACTGCATACCT 59.464 40.000 4.10 0.00 38.76 3.08
486 489 0.332632 ATTGCACTGCATACCTGGGT 59.667 50.000 4.10 0.00 38.76 4.51
505 508 1.480545 GTGGGTTTTGTGCCAAGTTCT 59.519 47.619 0.00 0.00 0.00 3.01
512 515 4.662468 TTTGTGCCAAGTTCTGCATTAA 57.338 36.364 0.29 0.00 40.07 1.40
515 518 3.503363 TGTGCCAAGTTCTGCATTAAGAG 59.497 43.478 0.29 0.00 40.07 2.85
528 531 8.908786 TCTGCATTAAGAGTTTTATCCTATGG 57.091 34.615 0.00 0.00 0.00 2.74
559 562 4.574599 AGCTTTCAAAATTCTCGCACTT 57.425 36.364 0.00 0.00 0.00 3.16
589 592 3.606972 AGGCTCCTGAATAATCCTCCAT 58.393 45.455 0.00 0.00 0.00 3.41
590 593 3.330110 AGGCTCCTGAATAATCCTCCATG 59.670 47.826 0.00 0.00 0.00 3.66
672 865 5.465724 CCTATTTAGGCCGTGTCATAACTTC 59.534 44.000 0.00 0.00 36.53 3.01
679 873 3.560068 GCCGTGTCATAACTTCCCAATAG 59.440 47.826 0.00 0.00 0.00 1.73
708 902 0.962855 GGCTTCCTTTGTCCCTCTGC 60.963 60.000 0.00 0.00 0.00 4.26
765 959 7.857734 TTAAATGTTCACACAGTTCTCTTGA 57.142 32.000 0.00 0.00 40.35 3.02
865 4142 3.763360 CACAAATTGAGGGATGGCTTACA 59.237 43.478 0.00 0.00 0.00 2.41
866 4143 4.403432 CACAAATTGAGGGATGGCTTACAT 59.597 41.667 0.00 0.00 44.18 2.29
867 4144 5.025453 ACAAATTGAGGGATGGCTTACATT 58.975 37.500 0.00 0.00 40.72 2.71
895 4172 7.865706 ACTCTTTTTCTTTGAGACAAGCTTA 57.134 32.000 0.00 0.00 0.00 3.09
920 4197 7.355778 ACTGTCTTGCTTCTTTTTCGATAAAG 58.644 34.615 18.81 18.81 36.64 1.85
964 4249 5.443230 AAAAGCCTACTTCTTGCTCCTAT 57.557 39.130 0.00 0.00 34.05 2.57
1021 4313 2.980233 AGTGTGAAAGGCCAGCGC 60.980 61.111 5.01 0.00 0.00 5.92
1193 4494 2.567985 GGAAGAAACCAAACCTCGTCA 58.432 47.619 0.00 0.00 0.00 4.35
1224 4526 1.339438 GCATGAAGAGCTTCCCTGTGA 60.339 52.381 7.69 0.00 38.77 3.58
1471 4783 1.966451 GCTGGTACTGTGCCACACC 60.966 63.158 13.90 1.43 32.73 4.16
1518 4835 1.667236 TGCTGCAATTGAGGATACCG 58.333 50.000 10.34 0.00 37.17 4.02
1521 4838 3.070878 TGCTGCAATTGAGGATACCGATA 59.929 43.478 10.34 0.00 37.17 2.92
1632 4952 2.743718 CACGAGGACCCTGCACTT 59.256 61.111 0.00 0.00 0.00 3.16
1761 5344 8.043113 TGATCTTATATTACATGAGGATGGCAC 58.957 37.037 0.00 0.00 33.39 5.01
1833 5425 0.534412 CAGAGTCCCTGAAGCGATGT 59.466 55.000 0.00 0.00 45.78 3.06
2112 5738 3.243704 TGCTTTGGACATTTAGTGTTGGC 60.244 43.478 0.00 0.00 42.36 4.52
2216 5855 5.476599 TCATTCTGGTTCCTGTTACCAATTG 59.523 40.000 0.00 0.00 44.63 2.32
2274 5914 4.886579 ACCAAAATTCTCATGGCAAACTC 58.113 39.130 0.00 0.00 37.77 3.01
2276 5916 5.012354 ACCAAAATTCTCATGGCAAACTCAT 59.988 36.000 0.00 0.00 37.77 2.90
2277 5917 6.211184 ACCAAAATTCTCATGGCAAACTCATA 59.789 34.615 0.00 0.00 37.77 2.15
2278 5918 6.532657 CCAAAATTCTCATGGCAAACTCATAC 59.467 38.462 0.00 0.00 0.00 2.39
2279 5919 7.318141 CAAAATTCTCATGGCAAACTCATACT 58.682 34.615 0.00 0.00 0.00 2.12
2280 5920 6.690194 AATTCTCATGGCAAACTCATACTC 57.310 37.500 0.00 0.00 0.00 2.59
2281 5921 4.142609 TCTCATGGCAAACTCATACTCC 57.857 45.455 0.00 0.00 0.00 3.85
2282 5922 3.118261 TCTCATGGCAAACTCATACTCCC 60.118 47.826 0.00 0.00 0.00 4.30
2283 5923 2.846206 TCATGGCAAACTCATACTCCCT 59.154 45.455 0.00 0.00 0.00 4.20
2284 5924 3.118261 TCATGGCAAACTCATACTCCCTC 60.118 47.826 0.00 0.00 0.00 4.30
2285 5925 1.559682 TGGCAAACTCATACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
2286 5926 1.473434 GGCAAACTCATACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
2287 5927 1.207329 GCAAACTCATACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
2288 5928 2.738964 GCAAACTCATACTCCCTCCGTC 60.739 54.545 0.00 0.00 0.00 4.79
2289 5929 1.777941 AACTCATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2290 5930 0.465824 ACTCATACTCCCTCCGTCCG 60.466 60.000 0.00 0.00 0.00 4.79
2291 5931 1.152819 TCATACTCCCTCCGTCCGG 60.153 63.158 0.00 0.00 0.00 5.14
2292 5932 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
2293 5933 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
2294 5934 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2295 5935 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2296 5936 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2297 5937 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2298 5938 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2299 5939 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2300 5940 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2301 5941 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2302 5942 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2303 5943 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2304 5944 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2305 5945 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2306 5946 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2307 5947 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2308 5948 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2309 5949 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2310 5950 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2311 5951 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2312 5952 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2313 5953 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2314 5954 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2315 5955 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2321 5961 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
2322 5962 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
2323 5963 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
2324 5964 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
2325 5965 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
2326 5966 6.327104 TCATCAAAATGGATAAAAGGGGATGG 59.673 38.462 0.00 0.00 33.42 3.51
2327 5967 5.848004 TCAAAATGGATAAAAGGGGATGGA 58.152 37.500 0.00 0.00 0.00 3.41
2328 5968 6.451714 TCAAAATGGATAAAAGGGGATGGAT 58.548 36.000 0.00 0.00 0.00 3.41
2329 5969 6.554605 TCAAAATGGATAAAAGGGGATGGATC 59.445 38.462 0.00 0.00 0.00 3.36
2330 5970 5.955850 AATGGATAAAAGGGGATGGATCT 57.044 39.130 0.00 0.00 0.00 2.75
2331 5971 7.420624 AAATGGATAAAAGGGGATGGATCTA 57.579 36.000 0.00 0.00 0.00 1.98
2332 5972 6.649041 ATGGATAAAAGGGGATGGATCTAG 57.351 41.667 0.00 0.00 0.00 2.43
2333 5973 5.737318 TGGATAAAAGGGGATGGATCTAGA 58.263 41.667 0.00 0.00 0.00 2.43
2334 5974 5.548056 TGGATAAAAGGGGATGGATCTAGAC 59.452 44.000 0.00 0.00 0.00 2.59
2335 5975 5.337652 GGATAAAAGGGGATGGATCTAGACG 60.338 48.000 0.00 0.00 0.00 4.18
2336 5976 2.777459 AAGGGGATGGATCTAGACGT 57.223 50.000 0.00 0.00 0.00 4.34
2337 5977 3.897657 AAGGGGATGGATCTAGACGTA 57.102 47.619 0.00 0.00 0.00 3.57
2338 5978 4.405756 AAGGGGATGGATCTAGACGTAT 57.594 45.455 0.00 0.00 0.00 3.06
2339 5979 4.405756 AGGGGATGGATCTAGACGTATT 57.594 45.455 0.00 0.00 0.00 1.89
2340 5980 4.753186 AGGGGATGGATCTAGACGTATTT 58.247 43.478 0.00 0.00 0.00 1.40
2341 5981 5.155905 AGGGGATGGATCTAGACGTATTTT 58.844 41.667 0.00 0.00 0.00 1.82
2342 5982 6.320518 AGGGGATGGATCTAGACGTATTTTA 58.679 40.000 0.00 0.00 0.00 1.52
2343 5983 6.437793 AGGGGATGGATCTAGACGTATTTTAG 59.562 42.308 0.00 0.00 0.00 1.85
2344 5984 6.210984 GGGGATGGATCTAGACGTATTTTAGT 59.789 42.308 0.00 0.00 0.00 2.24
2345 5985 7.256225 GGGGATGGATCTAGACGTATTTTAGTT 60.256 40.741 0.00 0.00 0.00 2.24
2346 5986 7.813627 GGGATGGATCTAGACGTATTTTAGTTC 59.186 40.741 0.00 0.00 0.00 3.01
2347 5987 8.578151 GGATGGATCTAGACGTATTTTAGTTCT 58.422 37.037 0.00 0.00 0.00 3.01
2350 5990 9.842775 TGGATCTAGACGTATTTTAGTTCTAGA 57.157 33.333 8.64 8.64 38.94 2.43
2391 6031 9.443323 TCTATTTTGATGACAAGTATTTTCGGA 57.557 29.630 0.00 0.00 37.32 4.55
2392 6032 9.490663 CTATTTTGATGACAAGTATTTTCGGAC 57.509 33.333 0.00 0.00 37.32 4.79
2393 6033 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2394 6034 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2395 6035 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2396 6036 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2397 6037 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2398 6038 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2399 6039 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2400 6040 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2494 6570 6.443934 TTCGAAAGGAACAGTTTGAAATGA 57.556 33.333 0.00 0.00 29.08 2.57
2613 7275 7.652909 TGCAAACATTTTCTGAAGAACCAATAG 59.347 33.333 0.00 0.00 33.13 1.73
3021 7700 4.324267 TCCTTTCCTTGACCGATTCTTTC 58.676 43.478 0.00 0.00 0.00 2.62
3051 7730 4.142491 TGGCAGCAATACAAAATAACTCCG 60.142 41.667 0.00 0.00 0.00 4.63
3063 7742 5.968387 AAATAACTCCGCAAGAACTATCG 57.032 39.130 0.00 0.00 43.02 2.92
3181 7861 4.399978 GTGTTGAATTATTGGGACGAACG 58.600 43.478 0.00 0.00 0.00 3.95
3218 8073 3.318839 CCTTTTGTCATGGTCAAAGCTCA 59.681 43.478 13.49 0.00 36.40 4.26
3394 8252 9.927081 AACCTTCAGTTGATATCAAGGATATTT 57.073 29.630 21.95 11.71 35.64 1.40
3395 8253 9.347240 ACCTTCAGTTGATATCAAGGATATTTG 57.653 33.333 21.95 11.35 35.64 2.32
3396 8254 9.347240 CCTTCAGTTGATATCAAGGATATTTGT 57.653 33.333 18.47 0.00 35.64 2.83
3460 8318 8.980143 TTAGATTTAACTTAATGCAAGCAACC 57.020 30.769 0.00 0.00 37.83 3.77
3461 8319 7.232118 AGATTTAACTTAATGCAAGCAACCT 57.768 32.000 0.00 0.00 37.83 3.50
3462 8320 7.092716 AGATTTAACTTAATGCAAGCAACCTG 58.907 34.615 0.00 0.00 37.83 4.00
3463 8321 2.730550 ACTTAATGCAAGCAACCTGC 57.269 45.000 0.00 0.00 45.46 4.85
3480 8338 2.222678 CCTGCAGTGATATTGCGATGTC 59.777 50.000 13.81 3.78 44.40 3.06
3539 8399 7.134815 ACATGAGTAAAATCAGCGAAATATGC 58.865 34.615 0.00 0.00 31.44 3.14
3551 8411 0.324275 AAATATGCGTGGCCTGGGTT 60.324 50.000 3.32 0.00 0.00 4.11
3599 8459 7.790823 TCATGAACATAATGATGTGGTACTG 57.209 36.000 0.00 0.00 45.93 2.74
3640 8507 2.907634 TGTAATGGTTCACGTGTGTGT 58.092 42.857 16.51 0.16 46.49 3.72
3641 8508 2.609916 TGTAATGGTTCACGTGTGTGTG 59.390 45.455 16.51 0.00 46.49 3.82
3642 8509 1.745232 AATGGTTCACGTGTGTGTGT 58.255 45.000 16.51 0.00 46.49 3.72
3643 8510 1.013596 ATGGTTCACGTGTGTGTGTG 58.986 50.000 16.51 0.00 46.49 3.82
3644 8511 0.320858 TGGTTCACGTGTGTGTGTGT 60.321 50.000 16.51 0.00 46.49 3.72
3645 8512 0.096281 GGTTCACGTGTGTGTGTGTG 59.904 55.000 16.51 0.00 46.49 3.82
3852 8728 1.446792 CCACTAGCAGCTCACCACG 60.447 63.158 0.00 0.00 0.00 4.94
3904 8780 9.595357 GTAGCAGTTATTGTCAGTTAGTTTTTC 57.405 33.333 0.00 0.00 0.00 2.29
3983 8864 3.753272 AGCACAACAATCATAGACCACAC 59.247 43.478 0.00 0.00 0.00 3.82
4028 8909 0.877743 GAGCTCTCAGCCAAACCAAC 59.122 55.000 6.43 0.00 43.77 3.77
4123 9013 3.057969 ACATGCAAGATTCGGACTTCA 57.942 42.857 0.00 0.00 0.00 3.02
4135 9025 1.852895 CGGACTTCACGAATTCGGATC 59.147 52.381 29.79 18.23 44.95 3.36
4157 9049 4.158025 TCTTGTTGTGCTCTAGTAGTAGGC 59.842 45.833 4.74 7.71 0.00 3.93
4158 9050 3.427573 TGTTGTGCTCTAGTAGTAGGCA 58.572 45.455 13.58 13.58 32.94 4.75
4160 9052 2.656002 TGTGCTCTAGTAGTAGGCAGG 58.344 52.381 16.46 3.49 34.83 4.85
4162 9054 1.133450 TGCTCTAGTAGTAGGCAGGGG 60.133 57.143 13.58 0.00 32.16 4.79
4163 9055 1.623163 CTCTAGTAGTAGGCAGGGGC 58.377 60.000 4.74 0.00 40.13 5.80
4164 9056 0.931468 TCTAGTAGTAGGCAGGGGCA 59.069 55.000 4.74 0.00 43.71 5.36
4165 9057 1.289830 TCTAGTAGTAGGCAGGGGCAA 59.710 52.381 4.74 0.00 43.71 4.52
4167 9059 0.839946 AGTAGTAGGCAGGGGCAATG 59.160 55.000 0.00 0.00 43.71 2.82
4168 9060 0.819666 GTAGTAGGCAGGGGCAATGC 60.820 60.000 0.00 0.00 43.71 3.56
4169 9061 2.324014 TAGTAGGCAGGGGCAATGCG 62.324 60.000 0.00 0.00 44.80 4.73
4170 9062 4.504596 TAGGCAGGGGCAATGCGG 62.505 66.667 0.00 0.00 44.80 5.69
4191 9083 6.485313 TGCGGATTTCAGAAAAAGAAAGTAGA 59.515 34.615 0.00 0.00 38.27 2.59
4196 9088 4.315803 TCAGAAAAAGAAAGTAGAGGCCG 58.684 43.478 0.00 0.00 0.00 6.13
4197 9089 4.039973 TCAGAAAAAGAAAGTAGAGGCCGA 59.960 41.667 0.00 0.00 0.00 5.54
4268 9162 4.018779 TCCATTGTTCTTAACCCTACCCTG 60.019 45.833 0.00 0.00 0.00 4.45
4274 9168 5.829391 TGTTCTTAACCCTACCCTGTTTTTC 59.171 40.000 0.00 0.00 0.00 2.29
4278 9172 6.492087 TCTTAACCCTACCCTGTTTTTCATTG 59.508 38.462 0.00 0.00 0.00 2.82
4281 9175 4.966168 ACCCTACCCTGTTTTTCATTGTTT 59.034 37.500 0.00 0.00 0.00 2.83
4286 9180 4.635324 ACCCTGTTTTTCATTGTTTTGCAG 59.365 37.500 0.00 0.00 0.00 4.41
4304 9199 5.465532 TGCAGGCACAATTATTTTCTTGA 57.534 34.783 0.00 0.00 0.00 3.02
4305 9200 6.040209 TGCAGGCACAATTATTTTCTTGAT 57.960 33.333 0.00 0.00 0.00 2.57
4325 9220 8.811017 TCTTGATTCACTCTCTTCAGTCTTATT 58.189 33.333 0.00 0.00 0.00 1.40
4326 9221 8.994429 TTGATTCACTCTCTTCAGTCTTATTC 57.006 34.615 0.00 0.00 0.00 1.75
4333 9228 8.191446 CACTCTCTTCAGTCTTATTCCGAAATA 58.809 37.037 0.00 0.00 0.00 1.40
4334 9229 8.919145 ACTCTCTTCAGTCTTATTCCGAAATAT 58.081 33.333 0.00 0.00 0.00 1.28
4373 9268 2.032549 CACTGCACTGAAAGCACACTAC 60.033 50.000 0.00 0.00 37.60 2.73
4379 9274 4.378459 GCACTGAAAGCACACTACCATTAC 60.378 45.833 0.00 0.00 37.60 1.89
4381 9276 6.163476 CACTGAAAGCACACTACCATTACTA 58.837 40.000 0.00 0.00 37.60 1.82
4384 9279 8.537016 ACTGAAAGCACACTACCATTACTATTA 58.463 33.333 0.00 0.00 37.60 0.98
4388 9312 9.774413 AAAGCACACTACCATTACTATTATACC 57.226 33.333 0.00 0.00 0.00 2.73
4393 9317 8.654094 ACACTACCATTACTATTATACCCCAAC 58.346 37.037 0.00 0.00 0.00 3.77
4423 9347 5.590530 TTTTGGGGTCCAATCATTAATCG 57.409 39.130 0.00 0.00 43.55 3.34
4424 9348 2.582052 TGGGGTCCAATCATTAATCGC 58.418 47.619 0.00 0.00 0.00 4.58
4425 9349 2.092158 TGGGGTCCAATCATTAATCGCA 60.092 45.455 0.00 0.00 0.00 5.10
4426 9350 2.554032 GGGGTCCAATCATTAATCGCAG 59.446 50.000 0.00 0.00 0.00 5.18
4427 9351 3.476552 GGGTCCAATCATTAATCGCAGA 58.523 45.455 0.00 0.00 45.75 4.26
4428 9352 3.882888 GGGTCCAATCATTAATCGCAGAA 59.117 43.478 0.00 0.00 43.58 3.02
4429 9353 4.023707 GGGTCCAATCATTAATCGCAGAAG 60.024 45.833 0.00 0.00 43.58 2.85
4431 9355 5.296780 GGTCCAATCATTAATCGCAGAAGAA 59.703 40.000 0.00 0.00 43.58 2.52
4432 9356 6.016777 GGTCCAATCATTAATCGCAGAAGAAT 60.017 38.462 0.00 0.00 43.58 2.40
4433 9357 7.173218 GGTCCAATCATTAATCGCAGAAGAATA 59.827 37.037 0.00 0.00 43.58 1.75
4434 9358 8.559536 GTCCAATCATTAATCGCAGAAGAATAA 58.440 33.333 0.00 0.00 43.58 1.40
4436 9360 9.903682 CCAATCATTAATCGCAGAAGAATAATT 57.096 29.630 0.00 0.00 43.58 1.40
4473 9722 3.269381 TGCAAAGTTCCCTCCAATATCCT 59.731 43.478 0.00 0.00 0.00 3.24
4484 9733 3.976654 CTCCAATATCCTCTTCTTCCCCA 59.023 47.826 0.00 0.00 0.00 4.96
4513 9762 1.527370 CCCCTCGAATTCTCCCACC 59.473 63.158 3.52 0.00 0.00 4.61
4515 9764 0.179000 CCCTCGAATTCTCCCACCTG 59.821 60.000 3.52 0.00 0.00 4.00
4519 9768 1.825474 TCGAATTCTCCCACCTGTCTC 59.175 52.381 3.52 0.00 0.00 3.36
4530 9779 2.239654 CCACCTGTCTCTCTCTCTCTCT 59.760 54.545 0.00 0.00 0.00 3.10
4531 9780 3.273434 CACCTGTCTCTCTCTCTCTCTG 58.727 54.545 0.00 0.00 0.00 3.35
4532 9781 2.912956 ACCTGTCTCTCTCTCTCTCTGT 59.087 50.000 0.00 0.00 0.00 3.41
4533 9782 3.273434 CCTGTCTCTCTCTCTCTCTGTG 58.727 54.545 0.00 0.00 0.00 3.66
4539 9788 7.625469 TGTCTCTCTCTCTCTCTGTGTTATAA 58.375 38.462 0.00 0.00 0.00 0.98
4544 9793 7.279090 TCTCTCTCTCTCTGTGTTATAAACTCG 59.721 40.741 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.718522 TTCCCTCGGTATTTCTTTGTTTTT 57.281 33.333 0.00 0.00 0.00 1.94
27 28 6.859017 TCCGTTTTTGCTTATATTTTCCCTC 58.141 36.000 0.00 0.00 0.00 4.30
36 37 8.920665 CATGTTTTTCATCCGTTTTTGCTTATA 58.079 29.630 0.00 0.00 34.09 0.98
43 44 8.430801 TTCATTCATGTTTTTCATCCGTTTTT 57.569 26.923 0.00 0.00 34.09 1.94
65 66 9.243637 CATTTTTCTTCGGTATTGTTTCTTTCA 57.756 29.630 0.00 0.00 0.00 2.69
98 99 9.942850 TCTTGGTTTTCAATTTTTCTTCTTCTT 57.057 25.926 0.00 0.00 34.45 2.52
173 174 7.176690 TGTTTTCACCTGTTCTTTTCTTTCTCT 59.823 33.333 0.00 0.00 0.00 3.10
208 210 4.020662 TCCACTGCTTTTCAAGGTTTTTGT 60.021 37.500 0.00 0.00 0.00 2.83
209 211 4.502962 TCCACTGCTTTTCAAGGTTTTTG 58.497 39.130 0.00 0.00 0.00 2.44
247 249 4.259530 CGCAACTTTTCAGCTGTTTTTCAG 60.260 41.667 14.67 5.23 46.12 3.02
258 260 3.914364 GCATTTAGTCCGCAACTTTTCAG 59.086 43.478 0.00 0.00 39.55 3.02
276 278 6.572519 GCTATAGCTAGCTAGAATGAGCATT 58.427 40.000 27.42 10.85 45.78 3.56
315 317 1.814429 TCCACCAGAGAGGGTTTCAA 58.186 50.000 0.00 0.00 43.89 2.69
390 392 5.946377 GGACAGGAGACTTTTATTTGGTCAT 59.054 40.000 0.00 0.00 40.21 3.06
409 411 3.969976 TCTGAAGGATAGGGATTGGACAG 59.030 47.826 0.00 0.00 0.00 3.51
429 431 3.795688 TCCTGAAGCAAGGTTTGATCT 57.204 42.857 0.00 0.00 38.58 2.75
475 478 0.894835 CAAAACCCACCCAGGTATGC 59.105 55.000 0.00 0.00 40.05 3.14
482 485 2.364560 TGGCACAAAACCCACCCA 59.635 55.556 0.00 0.00 31.92 4.51
505 508 7.811282 TCCCATAGGATAAAACTCTTAATGCA 58.189 34.615 0.00 0.00 37.19 3.96
515 518 9.740710 AGCTATGTATTTCCCATAGGATAAAAC 57.259 33.333 8.91 0.00 43.54 2.43
528 531 9.226345 CGAGAATTTTGAAAGCTATGTATTTCC 57.774 33.333 0.00 0.00 35.08 3.13
537 540 5.689383 AAGTGCGAGAATTTTGAAAGCTA 57.311 34.783 0.00 0.00 0.00 3.32
539 542 5.689819 TCTAAGTGCGAGAATTTTGAAAGC 58.310 37.500 0.00 0.00 0.00 3.51
559 562 6.722129 GGATTATTCAGGAGCCTAACTCTCTA 59.278 42.308 0.00 0.00 45.48 2.43
660 853 5.123936 GGGTCTATTGGGAAGTTATGACAC 58.876 45.833 0.00 0.00 0.00 3.67
745 939 6.763355 ACTATCAAGAGAACTGTGTGAACAT 58.237 36.000 0.00 0.00 0.00 2.71
758 952 9.436957 GATGGTCTGTTTTAAACTATCAAGAGA 57.563 33.333 9.33 0.00 32.84 3.10
866 4143 8.398665 GCTTGTCTCAAAGAAAAAGAGTAAGAA 58.601 33.333 0.00 0.00 32.15 2.52
867 4144 7.770897 AGCTTGTCTCAAAGAAAAAGAGTAAGA 59.229 33.333 0.00 0.00 32.15 2.10
895 4172 6.861065 TTATCGAAAAAGAAGCAAGACAGT 57.139 33.333 0.00 0.00 0.00 3.55
948 4225 7.335422 ACAAACATCAATAGGAGCAAGAAGTAG 59.665 37.037 0.00 0.00 0.00 2.57
953 4238 5.335897 GCAACAAACATCAATAGGAGCAAGA 60.336 40.000 0.00 0.00 0.00 3.02
964 4249 0.392336 GGCCCAGCAACAAACATCAA 59.608 50.000 0.00 0.00 0.00 2.57
1021 4313 2.433994 GGAGCAGAGGAGAGCCAGG 61.434 68.421 0.00 0.00 36.29 4.45
1029 4321 0.105760 GGATGAGGAGGAGCAGAGGA 60.106 60.000 0.00 0.00 0.00 3.71
1030 4322 1.120795 GGGATGAGGAGGAGCAGAGG 61.121 65.000 0.00 0.00 0.00 3.69
1471 4783 7.441836 TGGTGTGATTTAGCATATACAGTAGG 58.558 38.462 0.00 0.00 0.00 3.18
1518 4835 5.753438 TGACATTGCATCGACCTAACTTATC 59.247 40.000 0.00 0.00 0.00 1.75
1521 4838 3.935203 CTGACATTGCATCGACCTAACTT 59.065 43.478 0.00 0.00 0.00 2.66
1632 4952 1.550524 AGCAATTGTAGACGAGCTCCA 59.449 47.619 8.47 0.00 0.00 3.86
1743 5326 5.130975 AGAACAGTGCCATCCTCATGTAATA 59.869 40.000 0.00 0.00 0.00 0.98
1753 5336 2.682893 CGCTAGAACAGTGCCATCC 58.317 57.895 0.00 0.00 0.00 3.51
1761 5344 2.094659 CCACACCGCGCTAGAACAG 61.095 63.158 5.56 0.00 0.00 3.16
1833 5425 1.020861 GTGTGTCATCAGCGATGCCA 61.021 55.000 11.98 6.06 39.63 4.92
1900 5492 0.482446 AAGGGGTGCATCCTGAACAA 59.518 50.000 17.44 0.00 34.34 2.83
2112 5738 6.064060 TGATTCAAGGCCCATAATTAGAGTG 58.936 40.000 0.00 0.00 0.00 3.51
2180 5817 6.381994 AGGAACCAGAATGATGCACATAAAAT 59.618 34.615 0.00 0.00 39.69 1.82
2240 5879 9.241317 CATGAGAATTTTGGTTCTGTATAATGC 57.759 33.333 0.00 0.00 38.51 3.56
2249 5888 5.070847 AGTTTGCCATGAGAATTTTGGTTCT 59.929 36.000 0.00 0.00 40.99 3.01
2250 5889 5.299949 AGTTTGCCATGAGAATTTTGGTTC 58.700 37.500 0.00 0.00 32.90 3.62
2274 5914 0.754217 TTCCGGACGGAGGGAGTATG 60.754 60.000 13.64 0.00 46.06 2.39
2276 5916 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2277 5917 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2278 5918 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2279 5919 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2280 5920 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2281 5921 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2282 5922 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2283 5923 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2284 5924 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2285 5925 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2286 5926 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2287 5927 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2288 5928 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2289 5929 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2295 5935 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2296 5936 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
2297 5937 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
2298 5938 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
2299 5939 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
2300 5940 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
2301 5941 6.327104 CCATCCCCTTTTATCCATTTTGATGA 59.673 38.462 0.00 0.00 0.00 2.92
2302 5942 6.327104 TCCATCCCCTTTTATCCATTTTGATG 59.673 38.462 0.00 0.00 0.00 3.07
2303 5943 6.451714 TCCATCCCCTTTTATCCATTTTGAT 58.548 36.000 0.00 0.00 0.00 2.57
2304 5944 5.848004 TCCATCCCCTTTTATCCATTTTGA 58.152 37.500 0.00 0.00 0.00 2.69
2305 5945 6.556116 AGATCCATCCCCTTTTATCCATTTTG 59.444 38.462 0.00 0.00 0.00 2.44
2306 5946 6.696638 AGATCCATCCCCTTTTATCCATTTT 58.303 36.000 0.00 0.00 0.00 1.82
2307 5947 6.299227 AGATCCATCCCCTTTTATCCATTT 57.701 37.500 0.00 0.00 0.00 2.32
2308 5948 5.955850 AGATCCATCCCCTTTTATCCATT 57.044 39.130 0.00 0.00 0.00 3.16
2309 5949 6.216456 GTCTAGATCCATCCCCTTTTATCCAT 59.784 42.308 0.00 0.00 0.00 3.41
2310 5950 5.548056 GTCTAGATCCATCCCCTTTTATCCA 59.452 44.000 0.00 0.00 0.00 3.41
2311 5951 5.337652 CGTCTAGATCCATCCCCTTTTATCC 60.338 48.000 0.00 0.00 0.00 2.59
2312 5952 5.246429 ACGTCTAGATCCATCCCCTTTTATC 59.754 44.000 0.00 0.00 0.00 1.75
2313 5953 5.155905 ACGTCTAGATCCATCCCCTTTTAT 58.844 41.667 0.00 0.00 0.00 1.40
2314 5954 4.553678 ACGTCTAGATCCATCCCCTTTTA 58.446 43.478 0.00 0.00 0.00 1.52
2315 5955 3.385115 ACGTCTAGATCCATCCCCTTTT 58.615 45.455 0.00 0.00 0.00 2.27
2316 5956 3.047695 ACGTCTAGATCCATCCCCTTT 57.952 47.619 0.00 0.00 0.00 3.11
2317 5957 2.777459 ACGTCTAGATCCATCCCCTT 57.223 50.000 0.00 0.00 0.00 3.95
2318 5958 4.405756 AATACGTCTAGATCCATCCCCT 57.594 45.455 0.00 0.00 0.00 4.79
2319 5959 5.485209 AAAATACGTCTAGATCCATCCCC 57.515 43.478 0.00 0.00 0.00 4.81
2320 5960 7.229581 ACTAAAATACGTCTAGATCCATCCC 57.770 40.000 0.00 0.00 0.00 3.85
2321 5961 8.578151 AGAACTAAAATACGTCTAGATCCATCC 58.422 37.037 0.00 0.00 0.00 3.51
2324 5964 9.842775 TCTAGAACTAAAATACGTCTAGATCCA 57.157 33.333 0.00 0.00 32.48 3.41
2365 6005 9.443323 TCCGAAAATACTTGTCATCAAAATAGA 57.557 29.630 0.00 0.00 32.87 1.98
2366 6006 9.490663 GTCCGAAAATACTTGTCATCAAAATAG 57.509 33.333 0.00 0.00 32.87 1.73
2367 6007 8.172484 CGTCCGAAAATACTTGTCATCAAAATA 58.828 33.333 0.00 0.00 32.87 1.40
2368 6008 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2369 6009 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2370 6010 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2371 6011 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2372 6012 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2373 6013 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2374 6014 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2375 6015 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2376 6016 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2377 6017 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2378 6018 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2379 6019 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2380 6020 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2381 6021 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2382 6022 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2383 6023 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2384 6024 1.753073 GATACTCCCTCCGTCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
2385 6025 1.064166 AGATACTCCCTCCGTCCGAAA 60.064 52.381 0.00 0.00 0.00 3.46
2386 6026 0.549950 AGATACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
2387 6027 0.549950 AAGATACTCCCTCCGTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
2388 6028 1.067212 CAAAGATACTCCCTCCGTCCG 59.933 57.143 0.00 0.00 0.00 4.79
2389 6029 2.385803 TCAAAGATACTCCCTCCGTCC 58.614 52.381 0.00 0.00 0.00 4.79
2390 6030 4.501743 GGAATCAAAGATACTCCCTCCGTC 60.502 50.000 0.00 0.00 0.00 4.79
2391 6031 3.388350 GGAATCAAAGATACTCCCTCCGT 59.612 47.826 0.00 0.00 0.00 4.69
2392 6032 3.388024 TGGAATCAAAGATACTCCCTCCG 59.612 47.826 0.00 0.00 0.00 4.63
2393 6033 5.574970 ATGGAATCAAAGATACTCCCTCC 57.425 43.478 0.00 0.00 0.00 4.30
2394 6034 8.040132 CAGATATGGAATCAAAGATACTCCCTC 58.960 40.741 0.00 0.00 0.00 4.30
2395 6035 7.037730 CCAGATATGGAATCAAAGATACTCCCT 60.038 40.741 0.00 0.00 0.00 4.20
2396 6036 7.108847 CCAGATATGGAATCAAAGATACTCCC 58.891 42.308 0.00 0.00 0.00 4.30
2397 6037 7.108847 CCCAGATATGGAATCAAAGATACTCC 58.891 42.308 8.28 0.00 0.00 3.85
2398 6038 7.684529 ACCCAGATATGGAATCAAAGATACTC 58.315 38.462 8.28 0.00 0.00 2.59
2399 6039 7.639062 ACCCAGATATGGAATCAAAGATACT 57.361 36.000 8.28 0.00 0.00 2.12
2400 6040 9.793259 TTTACCCAGATATGGAATCAAAGATAC 57.207 33.333 8.28 0.00 0.00 2.24
2474 6121 7.545615 ACACTTTCATTTCAAACTGTTCCTTTC 59.454 33.333 0.00 0.00 0.00 2.62
2661 7323 7.386059 TCATAGTGCTTCTGACACATTTAGAA 58.614 34.615 1.90 0.00 40.59 2.10
2998 7672 3.618690 AGAATCGGTCAAGGAAAGGAG 57.381 47.619 0.00 0.00 0.00 3.69
3021 7700 0.546122 TGTATTGCTGCCAGTAGGGG 59.454 55.000 0.00 0.00 37.04 4.79
3051 7730 6.306837 GCAGTGTAGATATCGATAGTTCTTGC 59.693 42.308 12.55 12.07 37.40 4.01
3218 8073 0.469705 TTGAAACACCCTGCTGCCAT 60.470 50.000 0.00 0.00 0.00 4.40
3434 8292 9.418045 GGTTGCTTGCATTAAGTTAAATCTAAA 57.582 29.630 0.00 0.00 38.70 1.85
3435 8293 8.802267 AGGTTGCTTGCATTAAGTTAAATCTAA 58.198 29.630 0.00 0.00 38.70 2.10
3436 8294 8.243426 CAGGTTGCTTGCATTAAGTTAAATCTA 58.757 33.333 0.00 0.00 38.70 1.98
3437 8295 7.092716 CAGGTTGCTTGCATTAAGTTAAATCT 58.907 34.615 0.00 0.00 38.70 2.40
3438 8296 6.183360 GCAGGTTGCTTGCATTAAGTTAAATC 60.183 38.462 0.00 0.00 40.96 2.17
3439 8297 5.639082 GCAGGTTGCTTGCATTAAGTTAAAT 59.361 36.000 0.00 0.00 40.96 1.40
3440 8298 4.987912 GCAGGTTGCTTGCATTAAGTTAAA 59.012 37.500 0.00 0.00 40.96 1.52
3441 8299 4.038522 TGCAGGTTGCTTGCATTAAGTTAA 59.961 37.500 1.79 0.00 45.89 2.01
3442 8300 3.571828 TGCAGGTTGCTTGCATTAAGTTA 59.428 39.130 1.79 0.00 45.89 2.24
3443 8301 2.364970 TGCAGGTTGCTTGCATTAAGTT 59.635 40.909 1.79 0.00 45.89 2.66
3444 8302 1.962807 TGCAGGTTGCTTGCATTAAGT 59.037 42.857 1.79 0.00 45.89 2.24
3445 8303 2.728690 TGCAGGTTGCTTGCATTAAG 57.271 45.000 1.79 0.00 45.89 1.85
3451 8309 1.167851 TATCACTGCAGGTTGCTTGC 58.832 50.000 19.93 0.00 45.31 4.01
3452 8310 3.766151 CAATATCACTGCAGGTTGCTTG 58.234 45.455 19.93 11.78 45.31 4.01
3453 8311 2.165030 GCAATATCACTGCAGGTTGCTT 59.835 45.455 19.93 2.96 45.31 3.91
3454 8312 1.747355 GCAATATCACTGCAGGTTGCT 59.253 47.619 19.93 2.10 45.31 3.91
3455 8313 1.532505 CGCAATATCACTGCAGGTTGC 60.533 52.381 19.93 21.33 45.29 4.17
3456 8314 2.009051 TCGCAATATCACTGCAGGTTG 58.991 47.619 19.93 14.53 39.91 3.77
3457 8315 2.401583 TCGCAATATCACTGCAGGTT 57.598 45.000 19.93 4.56 39.91 3.50
3458 8316 2.216046 CATCGCAATATCACTGCAGGT 58.784 47.619 19.93 6.21 39.91 4.00
3459 8317 2.216046 ACATCGCAATATCACTGCAGG 58.784 47.619 19.93 7.28 39.91 4.85
3460 8318 2.097056 CGACATCGCAATATCACTGCAG 60.097 50.000 13.48 13.48 39.91 4.41
3461 8319 1.860326 CGACATCGCAATATCACTGCA 59.140 47.619 0.00 0.00 39.91 4.41
3462 8320 2.097202 GTCGACATCGCAATATCACTGC 60.097 50.000 11.55 0.00 39.60 4.40
3463 8321 3.375642 AGTCGACATCGCAATATCACTG 58.624 45.455 19.50 0.00 39.60 3.66
3464 8322 3.066760 TGAGTCGACATCGCAATATCACT 59.933 43.478 19.50 0.00 39.60 3.41
3465 8323 3.372060 TGAGTCGACATCGCAATATCAC 58.628 45.455 19.50 0.00 39.60 3.06
3466 8324 3.315191 TCTGAGTCGACATCGCAATATCA 59.685 43.478 19.50 8.18 39.60 2.15
3467 8325 3.890128 TCTGAGTCGACATCGCAATATC 58.110 45.455 19.50 3.46 39.60 1.63
3468 8326 3.990318 TCTGAGTCGACATCGCAATAT 57.010 42.857 19.50 0.00 39.60 1.28
3469 8327 3.565902 AGATCTGAGTCGACATCGCAATA 59.434 43.478 19.50 2.29 39.60 1.90
3480 8338 2.663602 CCGAAACAACAGATCTGAGTCG 59.336 50.000 29.27 23.79 0.00 4.18
3506 8366 5.570589 GCTGATTTTACTCATGTTCTGCAAC 59.429 40.000 0.00 0.00 30.05 4.17
3539 8399 2.342650 CCAATGAACCCAGGCCACG 61.343 63.158 5.01 0.00 0.00 4.94
3599 8459 1.598701 GGAGGCAACAACATCCCAGC 61.599 60.000 0.00 0.00 41.41 4.85
3640 8507 3.274095 TCATTGGACAGAACACACACA 57.726 42.857 0.00 0.00 0.00 3.72
3641 8508 3.814842 TCATCATTGGACAGAACACACAC 59.185 43.478 0.00 0.00 0.00 3.82
3642 8509 4.084011 TCATCATTGGACAGAACACACA 57.916 40.909 0.00 0.00 0.00 3.72
3643 8510 4.456911 ACATCATCATTGGACAGAACACAC 59.543 41.667 0.00 0.00 0.00 3.82
3644 8511 4.654915 ACATCATCATTGGACAGAACACA 58.345 39.130 0.00 0.00 0.00 3.72
3645 8512 5.392380 GGAACATCATCATTGGACAGAACAC 60.392 44.000 0.00 0.00 0.00 3.32
3852 8728 2.095008 GCCTACAAAGAAGCCTGAAAGC 60.095 50.000 0.00 0.00 0.00 3.51
3983 8864 6.540189 AGATCTGAGTCATTTTTACCCATTCG 59.460 38.462 0.00 0.00 0.00 3.34
4080 8967 6.945435 TGTAAAAATGGATTTAGCTGGTCAGA 59.055 34.615 0.00 0.00 0.00 3.27
4115 9005 1.852895 GATCCGAATTCGTGAAGTCCG 59.147 52.381 25.10 8.43 37.74 4.79
4123 9013 2.159627 GCACAACAAGATCCGAATTCGT 59.840 45.455 25.10 8.91 37.74 3.85
4131 9021 5.331876 ACTACTAGAGCACAACAAGATCC 57.668 43.478 0.00 0.00 0.00 3.36
4135 9025 4.082190 TGCCTACTACTAGAGCACAACAAG 60.082 45.833 0.00 0.00 0.00 3.16
4157 9049 1.321805 TGAAATCCGCATTGCCCCTG 61.322 55.000 2.41 0.00 0.00 4.45
4158 9050 1.000233 TGAAATCCGCATTGCCCCT 60.000 52.632 2.41 0.00 0.00 4.79
4160 9052 0.817013 TTCTGAAATCCGCATTGCCC 59.183 50.000 2.41 0.00 0.00 5.36
4162 9054 4.236935 TCTTTTTCTGAAATCCGCATTGC 58.763 39.130 3.31 0.00 0.00 3.56
4163 9055 6.421801 ACTTTCTTTTTCTGAAATCCGCATTG 59.578 34.615 3.31 0.00 33.65 2.82
4164 9056 6.515832 ACTTTCTTTTTCTGAAATCCGCATT 58.484 32.000 3.31 0.00 33.65 3.56
4165 9057 6.089249 ACTTTCTTTTTCTGAAATCCGCAT 57.911 33.333 3.31 0.00 33.65 4.73
4167 9059 6.899114 TCTACTTTCTTTTTCTGAAATCCGC 58.101 36.000 3.31 0.00 33.65 5.54
4168 9060 7.522374 CCTCTACTTTCTTTTTCTGAAATCCG 58.478 38.462 3.31 0.00 33.65 4.18
4169 9061 7.309177 GCCTCTACTTTCTTTTTCTGAAATCC 58.691 38.462 3.31 0.00 33.65 3.01
4170 9062 7.309177 GGCCTCTACTTTCTTTTTCTGAAATC 58.691 38.462 3.31 0.00 33.65 2.17
4223 9117 7.240897 TGGATTATATTTTAGCTCTGGGCATT 58.759 34.615 0.74 0.00 44.79 3.56
4268 9162 4.142730 TGTGCCTGCAAAACAATGAAAAAC 60.143 37.500 0.00 0.00 0.00 2.43
4274 9168 5.866335 ATAATTGTGCCTGCAAAACAATG 57.134 34.783 17.32 0.00 42.24 2.82
4278 9172 6.544038 AGAAAATAATTGTGCCTGCAAAAC 57.456 33.333 0.00 0.00 31.63 2.43
4281 9175 5.851720 TCAAGAAAATAATTGTGCCTGCAA 58.148 33.333 0.00 0.00 0.00 4.08
4286 9180 8.031277 AGAGTGAATCAAGAAAATAATTGTGCC 58.969 33.333 0.00 0.00 0.00 5.01
4304 9199 6.378564 TCGGAATAAGACTGAAGAGAGTGAAT 59.621 38.462 0.00 0.00 0.00 2.57
4305 9200 5.710567 TCGGAATAAGACTGAAGAGAGTGAA 59.289 40.000 0.00 0.00 0.00 3.18
4316 9211 5.692204 AGCGACATATTTCGGAATAAGACTG 59.308 40.000 12.84 0.00 39.50 3.51
4325 9220 3.863424 GTGAGAAAGCGACATATTTCGGA 59.137 43.478 12.84 0.00 39.78 4.55
4326 9221 3.865745 AGTGAGAAAGCGACATATTTCGG 59.134 43.478 12.84 0.00 39.78 4.30
4333 9228 4.867047 CAGTGATAAGTGAGAAAGCGACAT 59.133 41.667 0.00 0.00 0.00 3.06
4334 9229 4.237724 CAGTGATAAGTGAGAAAGCGACA 58.762 43.478 0.00 0.00 0.00 4.35
4373 9268 8.950007 AAATGGTTGGGGTATAATAGTAATGG 57.050 34.615 0.00 0.00 0.00 3.16
4405 9329 2.554032 CTGCGATTAATGATTGGACCCC 59.446 50.000 0.00 0.00 0.00 4.95
4406 9330 3.476552 TCTGCGATTAATGATTGGACCC 58.523 45.455 0.00 0.00 0.00 4.46
4407 9331 4.816385 TCTTCTGCGATTAATGATTGGACC 59.184 41.667 0.00 0.00 0.00 4.46
4408 9332 5.991328 TCTTCTGCGATTAATGATTGGAC 57.009 39.130 0.00 0.00 0.00 4.02
4409 9333 8.675705 TTATTCTTCTGCGATTAATGATTGGA 57.324 30.769 0.00 0.00 0.00 3.53
4410 9334 9.903682 AATTATTCTTCTGCGATTAATGATTGG 57.096 29.630 0.00 0.00 0.00 3.16
4421 9345 9.882996 CATATGCTTTTAATTATTCTTCTGCGA 57.117 29.630 0.00 0.00 0.00 5.10
4484 9733 1.797320 TTCGAGGGGGATATTCCGTT 58.203 50.000 0.00 0.00 37.43 4.44
4513 9762 3.942829 ACACAGAGAGAGAGAGAGACAG 58.057 50.000 0.00 0.00 0.00 3.51
4515 9764 8.395633 GTTTATAACACAGAGAGAGAGAGAGAC 58.604 40.741 0.00 0.00 0.00 3.36
4519 9768 7.406553 CGAGTTTATAACACAGAGAGAGAGAG 58.593 42.308 0.00 0.00 0.00 3.20
4530 9779 1.405797 CGGGGCCGAGTTTATAACACA 60.406 52.381 0.00 0.00 42.83 3.72
4531 9780 1.134729 TCGGGGCCGAGTTTATAACAC 60.135 52.381 0.00 0.00 44.01 3.32
4532 9781 1.193323 TCGGGGCCGAGTTTATAACA 58.807 50.000 0.00 0.00 44.01 2.41


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

AutoCloner maintained by Alex Coulton.