Multiple sequence alignment - TraesCS6A01G110000

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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 TraesCS6A01G110000 chr6A 100.000 6299 0 0 1 6299 79258643 79264941 0.000000e+00 11633
1 TraesCS6A01G110000 chr6D 94.305 5057 184 36 638 5607 62104699 62109738 0.000000e+00 7648
2 TraesCS6A01G110000 chr6D 89.201 676 34 14 5643 6299 62109828 62110483 0.000000e+00 808
3 TraesCS6A01G110000 chr6D 86.918 558 43 20 82 615 62104080 62104631 3.250000e-167 599
4 TraesCS6A01G110000 chr6B 92.310 3173 150 47 638 3763 135842372 135845497 0.000000e+00 4421
5 TraesCS6A01G110000 chr6B 97.095 1790 39 6 3818 5607 135845494 135847270 0.000000e+00 3005
6 TraesCS6A01G110000 chr6B 91.183 431 22 6 5643 6064 135847352 135847775 7.080000e-159 571
7 TraesCS6A01G110000 chr6B 80.787 635 41 37 57 612 135841665 135842297 7.550000e-114 422
8 TraesCS6A01G110000 chr6B 90.456 241 17 6 6061 6298 135847849 135848086 4.740000e-81 313
9 TraesCS6A01G110000 chr6B 88.172 93 8 3 2366 2455 649800537 649800629 2.400000e-19 108
10 TraesCS6A01G110000 chr3A 88.000 175 6 2 2365 2524 528529311 528529485 6.440000e-45 193
11 TraesCS6A01G110000 chr5A 85.057 174 12 6 2366 2525 401760747 401760920 1.400000e-36 165
12 TraesCS6A01G110000 chr5A 80.500 200 39 0 1106 1305 457789097 457789296 3.040000e-33 154
13 TraesCS6A01G110000 chr5D 84.571 175 11 6 2366 2525 297309719 297309546 6.540000e-35 159
14 TraesCS6A01G110000 chr5D 91.000 100 8 1 2428 2526 155844990 155845089 3.960000e-27 134
15 TraesCS6A01G110000 chr5B 80.500 200 39 0 1106 1305 420984907 420984708 3.040000e-33 154
16 TraesCS6A01G110000 chrUn 91.919 99 7 1 2428 2525 67785026 67784928 3.060000e-28 137
17 TraesCS6A01G110000 chr2A 90.909 99 8 1 2428 2525 601333267 601333169 1.420000e-26 132
18 TraesCS6A01G110000 chr2A 89.247 93 7 3 2366 2455 595288231 595288323 5.160000e-21 113
19 TraesCS6A01G110000 chr2B 89.320 103 10 1 2428 2529 502123808 502123706 1.840000e-25 128
20 TraesCS6A01G110000 chr7D 80.000 190 13 11 2366 2530 114770994 114771183 3.990000e-22 117
21 TraesCS6A01G110000 chr1A 89.247 93 7 3 2366 2455 105728016 105728108 5.160000e-21 113
22 TraesCS6A01G110000 chr4B 88.172 93 8 3 2366 2455 625435750 625435658 2.400000e-19 108
23 TraesCS6A01G110000 chr3B 88.172 93 8 3 2366 2455 424648440 424648532 2.400000e-19 108
24 TraesCS6A01G110000 chr2D 88.172 93 8 3 2366 2455 387311271 387311179 2.400000e-19 108


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 TraesCS6A01G110000 chr6A 79258643 79264941 6298 False 11633.000000 11633 100.000000 1 6299 1 chr6A.!!$F1 6298
1 TraesCS6A01G110000 chr6D 62104080 62110483 6403 False 3018.333333 7648 90.141333 82 6299 3 chr6D.!!$F1 6217
2 TraesCS6A01G110000 chr6B 135841665 135848086 6421 False 1746.400000 4421 90.366200 57 6298 5 chr6B.!!$F2 6241

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
47 48 0.029834 GCCACCGATGCAAATGCTAG 59.970 55.0 6.97 0.00 42.66 3.42 F
244 258 0.036483 TCATGGCAGTGAAAGCGCTA 60.036 50.0 12.05 0.00 32.56 4.26 F
466 514 0.036875 CTCTTCTCCAACCCCACACC 59.963 60.0 0.00 0.00 0.00 4.16 F
1011 1142 0.108138 GTCTGTCCATGGGTTCTCGG 60.108 60.0 13.02 3.42 0.00 4.63 F
2227 2381 0.251916 CGCCCCACCTCTTATTCACA 59.748 55.0 0.00 0.00 0.00 3.58 F
3129 3320 0.824759 TTCCCTTCGAAGCTCCTAGC 59.175 55.0 19.99 0.00 42.84 3.42 F
4632 4857 1.499049 GGAACCTGCCGATCGTTATC 58.501 55.0 15.09 3.50 0.00 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1854 0.179000 CAAGAAGGGGGTCTCCGATG 59.821 60.000 0.0 0.0 36.01 3.84 R
2208 2362 0.251916 TGTGAATAAGAGGTGGGGCG 59.748 55.000 0.0 0.0 0.00 6.13 R
2443 2618 2.762535 AACGCCTAGTGCATAACTGT 57.237 45.000 0.0 0.0 40.26 3.55 R
2928 3118 1.271163 ACCCCACATGTTAGAACCGTG 60.271 52.381 0.0 5.5 33.54 4.94 R
3227 3418 0.043334 TCAAGGGAGAGGGAAGAGGG 59.957 60.000 0.0 0.0 0.00 4.30 R
4848 5073 0.947244 GCTGATACTTTGGGATGCCG 59.053 55.000 0.0 0.0 0.00 5.69 R
5718 6029 0.105778 GCAGATGTCTACAGGCTCCC 59.894 60.000 0.0 0.0 0.00 4.30 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
24 25 3.052082 GCGCAGTGCAGTGACCAT 61.052 61.111 25.76 0.00 45.45 3.55
25 26 2.865308 CGCAGTGCAGTGACCATG 59.135 61.111 25.76 4.89 0.00 3.66
26 27 2.564975 GCAGTGCAGTGACCATGC 59.435 61.111 25.76 4.52 44.11 4.06
27 28 1.970114 GCAGTGCAGTGACCATGCT 60.970 57.895 25.76 0.00 44.17 3.79
28 29 1.873863 CAGTGCAGTGACCATGCTG 59.126 57.895 16.94 0.00 44.17 4.41
32 33 3.271014 CAGTGACCATGCTGCCAC 58.729 61.111 0.00 0.00 0.00 5.01
33 34 2.034687 AGTGACCATGCTGCCACC 59.965 61.111 0.00 0.00 0.00 4.61
34 35 3.434319 GTGACCATGCTGCCACCG 61.434 66.667 0.00 0.00 0.00 4.94
35 36 3.635191 TGACCATGCTGCCACCGA 61.635 61.111 0.00 0.00 0.00 4.69
36 37 2.124570 GACCATGCTGCCACCGAT 60.125 61.111 0.00 0.00 0.00 4.18
37 38 2.438975 ACCATGCTGCCACCGATG 60.439 61.111 0.00 0.00 0.00 3.84
38 39 3.896133 CCATGCTGCCACCGATGC 61.896 66.667 0.00 0.00 0.00 3.91
39 40 3.135457 CATGCTGCCACCGATGCA 61.135 61.111 0.00 0.00 39.83 3.96
40 41 2.361483 ATGCTGCCACCGATGCAA 60.361 55.556 0.00 0.00 38.46 4.08
41 42 1.978080 ATGCTGCCACCGATGCAAA 60.978 52.632 0.00 0.00 38.46 3.68
42 43 1.324740 ATGCTGCCACCGATGCAAAT 61.325 50.000 0.00 0.00 38.46 2.32
43 44 1.517694 GCTGCCACCGATGCAAATG 60.518 57.895 0.00 0.00 38.46 2.32
44 45 1.517694 CTGCCACCGATGCAAATGC 60.518 57.895 0.00 0.00 38.46 3.56
45 46 1.940883 CTGCCACCGATGCAAATGCT 61.941 55.000 6.97 0.00 42.66 3.79
46 47 0.679321 TGCCACCGATGCAAATGCTA 60.679 50.000 6.97 0.00 42.66 3.49
47 48 0.029834 GCCACCGATGCAAATGCTAG 59.970 55.000 6.97 0.00 42.66 3.42
48 49 1.382522 CCACCGATGCAAATGCTAGT 58.617 50.000 6.97 0.00 42.66 2.57
49 50 2.560504 CCACCGATGCAAATGCTAGTA 58.439 47.619 6.97 0.00 42.66 1.82
50 51 2.545526 CCACCGATGCAAATGCTAGTAG 59.454 50.000 6.97 0.00 42.66 2.57
51 52 3.198068 CACCGATGCAAATGCTAGTAGT 58.802 45.455 6.97 0.00 42.66 2.73
52 53 4.368315 CACCGATGCAAATGCTAGTAGTA 58.632 43.478 6.97 0.00 42.66 1.82
53 54 4.445718 CACCGATGCAAATGCTAGTAGTAG 59.554 45.833 6.97 0.00 42.66 2.57
54 55 4.099573 ACCGATGCAAATGCTAGTAGTAGT 59.900 41.667 6.97 0.00 42.66 2.73
55 56 5.301045 ACCGATGCAAATGCTAGTAGTAGTA 59.699 40.000 6.97 2.09 42.66 1.82
113 114 3.515502 CCTTTCCCCCAAATCTTTTCCTC 59.484 47.826 0.00 0.00 0.00 3.71
118 119 2.042979 CCCCAAATCTTTTCCTCCCTCA 59.957 50.000 0.00 0.00 0.00 3.86
144 145 0.901124 TGCCCAAACAGTGCAAAACT 59.099 45.000 0.00 0.00 40.93 2.66
159 160 3.963665 CAAAACTGTCCTCGATTTGCAA 58.036 40.909 0.00 0.00 0.00 4.08
193 196 5.163301 TGCAGGTGATAGGAATCTTTCTACC 60.163 44.000 0.00 0.00 32.93 3.18
195 198 6.465035 GCAGGTGATAGGAATCTTTCTACCAT 60.465 42.308 0.00 0.00 31.53 3.55
196 199 6.933521 CAGGTGATAGGAATCTTTCTACCATG 59.066 42.308 0.00 0.00 31.53 3.66
197 200 6.617371 AGGTGATAGGAATCTTTCTACCATGT 59.383 38.462 0.00 0.00 31.53 3.21
199 202 7.775561 GGTGATAGGAATCTTTCTACCATGTTT 59.224 37.037 0.00 0.00 32.93 2.83
200 203 9.832445 GTGATAGGAATCTTTCTACCATGTTTA 57.168 33.333 0.00 0.00 32.93 2.01
201 204 9.832445 TGATAGGAATCTTTCTACCATGTTTAC 57.168 33.333 0.00 0.00 32.93 2.01
202 205 9.832445 GATAGGAATCTTTCTACCATGTTTACA 57.168 33.333 0.00 0.00 0.00 2.41
203 206 9.838339 ATAGGAATCTTTCTACCATGTTTACAG 57.162 33.333 0.00 0.00 0.00 2.74
204 207 7.690256 AGGAATCTTTCTACCATGTTTACAGT 58.310 34.615 0.00 0.00 0.00 3.55
215 227 7.739498 ACCATGTTTACAGTAAGTAACCAAG 57.261 36.000 0.00 0.00 42.19 3.61
230 242 2.528564 ACCAAGAAACCACCATCATGG 58.471 47.619 0.54 0.54 46.10 3.66
239 253 1.475280 CCACCATCATGGCAGTGAAAG 59.525 52.381 2.52 2.89 42.67 2.62
240 254 1.135199 CACCATCATGGCAGTGAAAGC 60.135 52.381 2.52 0.00 42.67 3.51
241 255 0.099968 CCATCATGGCAGTGAAAGCG 59.900 55.000 0.00 0.00 0.00 4.68
242 256 0.524816 CATCATGGCAGTGAAAGCGC 60.525 55.000 0.00 0.00 0.00 5.92
244 258 0.036483 TCATGGCAGTGAAAGCGCTA 60.036 50.000 12.05 0.00 32.56 4.26
245 259 0.376152 CATGGCAGTGAAAGCGCTAG 59.624 55.000 12.05 0.00 32.56 3.42
268 284 1.895707 CCATGCTGCTCCGATTCCC 60.896 63.158 0.00 0.00 0.00 3.97
278 294 1.137404 CCGATTCCCTTTGCTTGCG 59.863 57.895 0.00 0.00 0.00 4.85
327 343 2.661866 AAGCGTGTGAGGCGTGAC 60.662 61.111 0.00 0.00 33.62 3.67
329 345 3.406361 GCGTGTGAGGCGTGACTG 61.406 66.667 0.00 0.00 0.00 3.51
330 346 3.406361 CGTGTGAGGCGTGACTGC 61.406 66.667 0.00 0.00 0.00 4.40
340 356 2.494918 GTGACTGCCGCCGTATCT 59.505 61.111 0.00 0.00 0.00 1.98
345 361 1.202582 GACTGCCGCCGTATCTCATAT 59.797 52.381 0.00 0.00 0.00 1.78
363 397 2.568003 TCGATAGAGCCATAGCCCG 58.432 57.895 0.00 0.00 42.67 6.13
375 409 0.979665 ATAGCCCGTCCATCCATCAG 59.020 55.000 0.00 0.00 0.00 2.90
392 426 4.301628 CATCAGCAACTTTTGAGGTTTCC 58.698 43.478 0.00 0.00 0.00 3.13
393 427 3.360867 TCAGCAACTTTTGAGGTTTCCA 58.639 40.909 0.00 0.00 0.00 3.53
435 483 3.493877 CCGCTTTGCTAGATGAGATCAAG 59.506 47.826 0.00 0.00 0.00 3.02
438 486 4.024725 GCTTTGCTAGATGAGATCAAGCAG 60.025 45.833 7.52 0.80 35.00 4.24
445 493 1.817099 GAGATCAAGCAGCACCCCG 60.817 63.158 0.00 0.00 0.00 5.73
466 514 0.036875 CTCTTCTCCAACCCCACACC 59.963 60.000 0.00 0.00 0.00 4.16
493 541 2.310052 CACAATCTTCCTTTCCCCCTCT 59.690 50.000 0.00 0.00 0.00 3.69
494 542 2.578480 ACAATCTTCCTTTCCCCCTCTC 59.422 50.000 0.00 0.00 0.00 3.20
538 615 2.697431 TTCCGTTTTGCTTTGATCCG 57.303 45.000 0.00 0.00 0.00 4.18
639 770 3.055719 CCGTCAATGCCCGCACTT 61.056 61.111 0.00 0.00 0.00 3.16
711 842 2.223572 CGCCAGGGCTTCATTTATTGTC 60.224 50.000 8.91 0.00 39.32 3.18
712 843 2.760092 GCCAGGGCTTCATTTATTGTCA 59.240 45.455 2.30 0.00 38.26 3.58
726 857 5.993748 TTATTGTCACCCCAAAAGATTCC 57.006 39.130 0.00 0.00 0.00 3.01
774 905 1.884926 GCTCGGGGATTTGAGAGCG 60.885 63.158 0.43 0.00 45.08 5.03
782 913 2.933260 GGGATTTGAGAGCGTTCTTCTC 59.067 50.000 2.39 2.60 32.53 2.87
793 924 2.329379 CGTTCTTCTCGAGTTCTTGGG 58.671 52.381 13.13 0.00 0.00 4.12
802 933 1.464198 AGTTCTTGGGGCCTCTGGT 60.464 57.895 3.07 0.00 0.00 4.00
881 1012 0.685660 GTTCTTGGAGGTTCCCGACT 59.314 55.000 0.00 0.00 35.03 4.18
900 1031 4.021894 CGACTAGATCCCCTCTTGTATTGG 60.022 50.000 0.00 0.00 39.60 3.16
1011 1142 0.108138 GTCTGTCCATGGGTTCTCGG 60.108 60.000 13.02 3.42 0.00 4.63
1012 1143 1.221840 CTGTCCATGGGTTCTCGGG 59.778 63.158 13.02 0.00 0.00 5.14
1076 1213 0.693049 GTGATGGTGGTCTCCTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
1329 1466 1.166989 GGGTCGAGAAGAACGTCTCT 58.833 55.000 13.68 0.00 41.69 3.10
1413 1550 5.185442 TCTCATTTGTTGCCATGCTTGATTA 59.815 36.000 0.22 0.00 0.00 1.75
1425 1562 7.771361 TGCCATGCTTGATTAATTGATTGATTT 59.229 29.630 0.22 0.00 0.00 2.17
1426 1563 8.067784 GCCATGCTTGATTAATTGATTGATTTG 58.932 33.333 0.22 0.00 0.00 2.32
1441 1578 8.969260 TGATTGATTTGTACTTGATGCTATCT 57.031 30.769 0.00 0.00 0.00 1.98
1448 1585 9.650539 ATTTGTACTTGATGCTATCTATGCTAG 57.349 33.333 0.00 0.00 0.00 3.42
1472 1609 4.326826 TGGAGTGTGGTCTCATTTGATTC 58.673 43.478 0.00 0.00 36.30 2.52
1477 1617 6.169094 AGTGTGGTCTCATTTGATTCTACTG 58.831 40.000 0.00 0.00 0.00 2.74
1478 1618 5.934625 GTGTGGTCTCATTTGATTCTACTGT 59.065 40.000 0.00 0.00 0.00 3.55
1522 1662 4.846040 TGAGTCTAGAGTTAGTGAGGGAC 58.154 47.826 0.56 0.00 0.00 4.46
1523 1663 4.288887 TGAGTCTAGAGTTAGTGAGGGACA 59.711 45.833 0.56 0.00 0.00 4.02
1636 1777 1.866496 CTGCTTCATTTGCGCTCGC 60.866 57.895 9.73 7.38 42.35 5.03
1682 1823 7.836183 ACAAATCTAGAATTAGCAGGGAAATGT 59.164 33.333 0.00 0.00 0.00 2.71
1713 1854 3.557595 CGCATTACCTTCAATCTGTCTCC 59.442 47.826 0.00 0.00 0.00 3.71
1731 1872 0.983378 CCATCGGAGACCCCCTTCTT 60.983 60.000 0.00 0.00 42.51 2.52
1735 1876 2.231380 GGAGACCCCCTTCTTGGCA 61.231 63.158 0.00 0.00 0.00 4.92
1777 1919 2.353610 CCCCCTGCTTGGTTGCATC 61.354 63.158 0.00 0.00 42.48 3.91
1787 1929 2.481289 TGGTTGCATCGGTTACATGA 57.519 45.000 0.00 0.00 0.00 3.07
1877 2023 3.992943 TGGTGGTATCGGTTTGAAGAT 57.007 42.857 0.00 0.00 0.00 2.40
1907 2053 7.811236 ACTTTGCTCATCAATTCATACTGTTTG 59.189 33.333 0.00 0.00 34.12 2.93
1909 2055 7.920160 TGCTCATCAATTCATACTGTTTGTA 57.080 32.000 0.00 0.00 35.37 2.41
1945 2098 2.030805 GCAAGAAGTTCACCATGTCCAC 60.031 50.000 5.50 0.00 0.00 4.02
2208 2362 0.536460 TCCTGAAAACCGCTTCACCC 60.536 55.000 0.00 0.00 32.00 4.61
2227 2381 0.251916 CGCCCCACCTCTTATTCACA 59.748 55.000 0.00 0.00 0.00 3.58
2378 2553 4.433283 GCAATGCACGCATAGTTCAAAAAG 60.433 41.667 4.68 0.00 35.31 2.27
2405 2580 4.379339 AGGCGTTAATTGTGTGTTTTGT 57.621 36.364 0.00 0.00 0.00 2.83
2443 2618 3.993920 TCTGATATGCGCAGATTAAGCA 58.006 40.909 19.93 11.20 45.46 3.91
2496 2671 0.984230 AGCCTAGGCACACTTAAGCA 59.016 50.000 34.70 0.00 44.88 3.91
2722 2912 4.202274 TGGGCCTTTTTACAAGGTAAAAGC 60.202 41.667 4.53 12.85 39.09 3.51
2816 3006 4.210331 AGTTCCCTTGATCCATTATGTGC 58.790 43.478 0.00 0.00 0.00 4.57
2928 3118 3.418684 ACACAGTGTAAAGGACCATCC 57.581 47.619 3.69 0.00 36.58 3.51
2999 3189 2.202260 CAATGCTCACAGCGTGCG 60.202 61.111 4.15 0.01 46.26 5.34
3065 3256 5.121768 ACTTATGAGTTGTGCGTACCATTTC 59.878 40.000 0.00 0.00 29.87 2.17
3072 3263 1.264826 GTGCGTACCATTTCCAAACGT 59.735 47.619 0.00 0.00 36.03 3.99
3105 3296 4.582869 TCAAGTTGAGCAGTAGCATTCAT 58.417 39.130 0.08 0.00 45.49 2.57
3129 3320 0.824759 TTCCCTTCGAAGCTCCTAGC 59.175 55.000 19.99 0.00 42.84 3.42
3201 3392 6.183361 TGTCCAGTCCTCTTTATTTCTGTTGA 60.183 38.462 0.00 0.00 0.00 3.18
3227 3418 8.677148 TTCTTTGAGGGTGATATAATAGTTGC 57.323 34.615 0.00 0.00 0.00 4.17
3428 3619 5.631096 GCTTCAACCTTTTTAGCACATTCTC 59.369 40.000 0.00 0.00 0.00 2.87
3438 3629 9.696917 CTTTTTAGCACATTCTCAAAACCTATT 57.303 29.630 0.00 0.00 0.00 1.73
3492 3693 8.908786 AACATCTTTCTGTTCTTTCTATGACA 57.091 30.769 0.00 0.00 34.26 3.58
3509 3712 8.158169 TCTATGACATGTTCAATTTATGGCTC 57.842 34.615 0.00 0.00 37.92 4.70
3600 3805 8.383175 ACTCAGATTACTATTCAACCTGGAAAA 58.617 33.333 0.00 0.00 0.00 2.29
3604 3809 6.995511 TTACTATTCAACCTGGAAAATCCG 57.004 37.500 0.00 0.00 40.17 4.18
3674 3879 7.433425 GCACATTTCCAGCTTTTGATATACTTC 59.567 37.037 0.00 0.00 0.00 3.01
3808 4032 1.792026 TCTAGCTCCATCCCTCCATCT 59.208 52.381 0.00 0.00 0.00 2.90
3853 4077 9.525409 GCATTTATTTTGATGAAACAGCTCTAT 57.475 29.630 0.00 0.00 0.00 1.98
3855 4079 8.915871 TTTATTTTGATGAAACAGCTCTATGC 57.084 30.769 0.00 0.00 43.29 3.14
4166 4391 3.441222 TCATTGTCGCATCTTGATTTGCT 59.559 39.130 0.00 0.00 36.71 3.91
4392 4617 6.138761 GGATTTTCGCACAGATATTCATGAC 58.861 40.000 0.00 0.00 0.00 3.06
4584 4809 2.052237 GCAAACCACGACACGCTG 60.052 61.111 0.00 0.00 0.00 5.18
4632 4857 1.499049 GGAACCTGCCGATCGTTATC 58.501 55.000 15.09 3.50 0.00 1.75
4848 5073 2.296471 CTGGGGGATCTACACATACGAC 59.704 54.545 0.00 0.00 0.00 4.34
4881 5106 3.762288 AGTATCAGCTGAACTTCGGTGTA 59.238 43.478 22.50 1.82 0.00 2.90
5088 5313 1.527034 TCTCGTACGCCTACAACAGT 58.473 50.000 11.24 0.00 0.00 3.55
5283 5508 1.002033 CTTGCACTTGTTCACCTCTGC 60.002 52.381 0.00 0.00 0.00 4.26
5303 5528 2.418746 GCGTGTCATCCTCATAGGTGTT 60.419 50.000 0.00 0.00 36.53 3.32
5384 5612 0.106015 AGGGGTATTTGATGCCTGCC 60.106 55.000 0.00 0.00 35.15 4.85
5420 5648 4.034048 CCATGTAGGAACCTTTTTCGATCG 59.966 45.833 9.36 9.36 41.22 3.69
5607 5840 3.259374 TGGTGAGTCCAGATCAGTCTTTC 59.741 47.826 0.00 0.00 41.93 2.62
5609 5842 4.381505 GGTGAGTCCAGATCAGTCTTTCTC 60.382 50.000 0.00 0.00 35.97 2.87
5613 5846 4.466015 AGTCCAGATCAGTCTTTCTCTTCC 59.534 45.833 0.00 0.00 30.42 3.46
5614 5847 4.221703 GTCCAGATCAGTCTTTCTCTTCCA 59.778 45.833 0.00 0.00 30.42 3.53
5615 5848 4.465660 TCCAGATCAGTCTTTCTCTTCCAG 59.534 45.833 0.00 0.00 30.42 3.86
5618 5851 6.229733 CAGATCAGTCTTTCTCTTCCAGTTT 58.770 40.000 0.00 0.00 30.42 2.66
5619 5852 7.382110 CAGATCAGTCTTTCTCTTCCAGTTTA 58.618 38.462 0.00 0.00 30.42 2.01
5621 5854 8.040132 AGATCAGTCTTTCTCTTCCAGTTTATG 58.960 37.037 0.00 0.00 0.00 1.90
5622 5855 5.934625 TCAGTCTTTCTCTTCCAGTTTATGC 59.065 40.000 0.00 0.00 0.00 3.14
5623 5856 5.702670 CAGTCTTTCTCTTCCAGTTTATGCA 59.297 40.000 0.00 0.00 0.00 3.96
5625 5858 6.944862 AGTCTTTCTCTTCCAGTTTATGCATT 59.055 34.615 3.54 0.00 0.00 3.56
5626 5859 8.103305 AGTCTTTCTCTTCCAGTTTATGCATTA 58.897 33.333 3.54 0.00 0.00 1.90
5627 5860 8.897752 GTCTTTCTCTTCCAGTTTATGCATTAT 58.102 33.333 3.54 0.00 0.00 1.28
5677 5983 5.460416 TGGTAACTACCTATGCACCATAGA 58.540 41.667 12.53 0.00 46.58 1.98
5683 5989 3.317406 ACCTATGCACCATAGACCATCA 58.683 45.455 12.53 0.00 44.55 3.07
5684 5990 3.071602 ACCTATGCACCATAGACCATCAC 59.928 47.826 12.53 0.00 44.55 3.06
5694 6000 4.528206 CCATAGACCATCACAGTAGCCATA 59.472 45.833 0.00 0.00 0.00 2.74
5810 6121 1.466167 CACTTGGGAGCAGTCATTTCG 59.534 52.381 0.00 0.00 0.00 3.46
5837 6148 1.471676 GGATCTAGTGCCAGACAACCG 60.472 57.143 0.00 0.00 0.00 4.44
5960 6280 7.362920 CCCCATCATCGTCTTCTTAAATTTTGT 60.363 37.037 0.00 0.00 0.00 2.83
5961 6281 8.673711 CCCATCATCGTCTTCTTAAATTTTGTA 58.326 33.333 0.00 0.00 0.00 2.41
5962 6282 9.490663 CCATCATCGTCTTCTTAAATTTTGTAC 57.509 33.333 0.00 0.00 0.00 2.90
5974 6294 8.372459 TCTTAAATTTTGTACTAGCTCTGGACA 58.628 33.333 0.00 0.00 0.00 4.02
6057 6377 8.876275 TCACCATCCGTATATAACAACTTAAC 57.124 34.615 0.00 0.00 0.00 2.01
6078 6475 6.737254 AACGAAGTAACCACCATGATAAAG 57.263 37.500 0.00 0.00 45.00 1.85
6152 6549 1.068748 CAGCTCATCCAAGCACAACAC 60.069 52.381 0.00 0.00 45.00 3.32
6156 6553 0.038892 CATCCAAGCACAACACAGGC 60.039 55.000 0.00 0.00 0.00 4.85
6159 6556 0.461135 CCAAGCACAACACAGGCTTT 59.539 50.000 0.00 0.00 44.93 3.51
6162 6559 3.243839 CCAAGCACAACACAGGCTTTTAT 60.244 43.478 0.00 0.00 44.93 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.385093 CTGCACTGCGCTGCACTG 62.385 66.667 19.17 9.33 42.36 3.66
1 2 4.923942 ACTGCACTGCGCTGCACT 62.924 61.111 19.17 8.82 42.36 4.40
2 3 4.678269 CACTGCACTGCGCTGCAC 62.678 66.667 19.17 9.87 42.36 4.57
3 4 4.914388 TCACTGCACTGCGCTGCA 62.914 61.111 21.30 21.30 45.06 4.41
4 5 4.380628 GTCACTGCACTGCGCTGC 62.381 66.667 14.80 14.49 43.01 5.25
5 6 3.720193 GGTCACTGCACTGCGCTG 61.720 66.667 13.23 13.23 44.66 5.18
6 7 3.541950 ATGGTCACTGCACTGCGCT 62.542 57.895 9.73 0.00 43.06 5.92
7 8 3.052082 ATGGTCACTGCACTGCGC 61.052 61.111 0.00 0.00 42.89 6.09
8 9 2.865308 CATGGTCACTGCACTGCG 59.135 61.111 0.00 0.00 0.00 5.18
9 10 1.970114 AGCATGGTCACTGCACTGC 60.970 57.895 0.00 0.00 42.15 4.40
10 11 1.873863 CAGCATGGTCACTGCACTG 59.126 57.895 0.00 0.00 42.15 3.66
11 12 4.391869 CAGCATGGTCACTGCACT 57.608 55.556 0.00 0.00 42.15 4.40
15 16 2.338015 GGTGGCAGCATGGTCACTG 61.338 63.158 12.58 5.42 42.86 3.66
16 17 2.034687 GGTGGCAGCATGGTCACT 59.965 61.111 12.58 0.00 42.86 3.41
17 18 3.434319 CGGTGGCAGCATGGTCAC 61.434 66.667 17.80 7.93 42.56 3.67
18 19 2.970379 ATCGGTGGCAGCATGGTCA 61.970 57.895 17.80 0.00 35.86 4.02
19 20 2.124570 ATCGGTGGCAGCATGGTC 60.125 61.111 17.80 0.00 35.86 4.02
20 21 2.438975 CATCGGTGGCAGCATGGT 60.439 61.111 17.80 0.00 35.86 3.55
21 22 3.896133 GCATCGGTGGCAGCATGG 61.896 66.667 17.80 5.83 35.86 3.66
22 23 2.215465 TTTGCATCGGTGGCAGCATG 62.215 55.000 17.80 18.19 43.05 4.06
23 24 1.324740 ATTTGCATCGGTGGCAGCAT 61.325 50.000 17.80 6.65 43.05 3.79
24 25 1.978080 ATTTGCATCGGTGGCAGCA 60.978 52.632 17.80 5.83 43.05 4.41
25 26 1.517694 CATTTGCATCGGTGGCAGC 60.518 57.895 6.62 6.62 43.05 5.25
26 27 1.517694 GCATTTGCATCGGTGGCAG 60.518 57.895 0.00 0.00 43.05 4.85
27 28 0.679321 TAGCATTTGCATCGGTGGCA 60.679 50.000 5.20 0.00 45.16 4.92
28 29 0.029834 CTAGCATTTGCATCGGTGGC 59.970 55.000 5.20 0.00 45.16 5.01
29 30 1.382522 ACTAGCATTTGCATCGGTGG 58.617 50.000 5.20 0.00 45.16 4.61
30 31 3.198068 ACTACTAGCATTTGCATCGGTG 58.802 45.455 5.20 0.00 45.16 4.94
31 32 3.543680 ACTACTAGCATTTGCATCGGT 57.456 42.857 5.20 1.01 45.16 4.69
32 33 4.621991 ACTACTACTAGCATTTGCATCGG 58.378 43.478 5.20 0.00 45.16 4.18
33 34 6.439599 AGTACTACTACTAGCATTTGCATCG 58.560 40.000 5.20 0.00 45.16 3.84
34 35 8.784994 TCTAGTACTACTACTAGCATTTGCATC 58.215 37.037 5.20 0.00 46.89 3.91
35 36 8.693120 TCTAGTACTACTACTAGCATTTGCAT 57.307 34.615 5.20 0.00 46.89 3.96
36 37 7.228906 CCTCTAGTACTACTACTAGCATTTGCA 59.771 40.741 5.20 0.00 46.89 4.08
37 38 7.229106 ACCTCTAGTACTACTACTAGCATTTGC 59.771 40.741 0.00 0.00 46.89 3.68
38 39 8.680039 ACCTCTAGTACTACTACTAGCATTTG 57.320 38.462 0.00 0.00 46.89 2.32
41 42 9.158097 ACTAACCTCTAGTACTACTACTAGCAT 57.842 37.037 0.00 2.43 46.89 3.79
42 43 8.420222 CACTAACCTCTAGTACTACTACTAGCA 58.580 40.741 0.00 2.35 46.89 3.49
43 44 7.872483 CCACTAACCTCTAGTACTACTACTAGC 59.128 44.444 0.00 0.00 46.89 3.42
45 46 7.470702 CGCCACTAACCTCTAGTACTACTACTA 60.471 44.444 0.00 0.00 34.79 1.82
46 47 6.591001 GCCACTAACCTCTAGTACTACTACT 58.409 44.000 0.00 0.00 37.04 2.57
47 48 5.465056 CGCCACTAACCTCTAGTACTACTAC 59.535 48.000 0.00 0.00 0.00 2.73
48 49 5.129485 ACGCCACTAACCTCTAGTACTACTA 59.871 44.000 0.00 0.00 0.00 1.82
49 50 4.080638 ACGCCACTAACCTCTAGTACTACT 60.081 45.833 0.00 0.00 0.00 2.57
50 51 4.195416 ACGCCACTAACCTCTAGTACTAC 58.805 47.826 0.00 0.00 0.00 2.73
51 52 4.494091 ACGCCACTAACCTCTAGTACTA 57.506 45.455 1.89 1.89 0.00 1.82
52 53 3.362870 ACGCCACTAACCTCTAGTACT 57.637 47.619 0.00 0.00 0.00 2.73
53 54 4.034975 CACTACGCCACTAACCTCTAGTAC 59.965 50.000 0.00 0.00 0.00 2.73
54 55 4.194640 CACTACGCCACTAACCTCTAGTA 58.805 47.826 0.00 0.00 0.00 1.82
55 56 3.015327 CACTACGCCACTAACCTCTAGT 58.985 50.000 0.00 0.00 0.00 2.57
66 67 1.692519 AGATATTCCCCACTACGCCAC 59.307 52.381 0.00 0.00 0.00 5.01
165 166 2.440627 AGATTCCTATCACCTGCATGCA 59.559 45.455 21.29 21.29 32.95 3.96
166 167 3.137446 AGATTCCTATCACCTGCATGC 57.863 47.619 11.82 11.82 32.95 4.06
167 168 5.374921 AGAAAGATTCCTATCACCTGCATG 58.625 41.667 0.00 0.00 32.95 4.06
168 169 5.643421 AGAAAGATTCCTATCACCTGCAT 57.357 39.130 0.00 0.00 32.95 3.96
169 170 5.163301 GGTAGAAAGATTCCTATCACCTGCA 60.163 44.000 0.00 0.00 32.95 4.41
170 171 5.163301 TGGTAGAAAGATTCCTATCACCTGC 60.163 44.000 0.00 0.00 32.95 4.85
171 172 6.485830 TGGTAGAAAGATTCCTATCACCTG 57.514 41.667 0.00 0.00 32.95 4.00
173 174 6.831976 ACATGGTAGAAAGATTCCTATCACC 58.168 40.000 0.00 0.00 29.77 4.02
174 175 8.738645 AAACATGGTAGAAAGATTCCTATCAC 57.261 34.615 0.00 0.00 29.77 3.06
175 176 9.832445 GTAAACATGGTAGAAAGATTCCTATCA 57.168 33.333 0.00 0.00 32.95 2.15
176 177 9.832445 TGTAAACATGGTAGAAAGATTCCTATC 57.168 33.333 0.00 0.00 0.00 2.08
177 178 9.838339 CTGTAAACATGGTAGAAAGATTCCTAT 57.162 33.333 0.00 0.00 0.00 2.57
178 179 8.822805 ACTGTAAACATGGTAGAAAGATTCCTA 58.177 33.333 0.00 0.00 0.00 2.94
196 199 8.124823 GTGGTTTCTTGGTTACTTACTGTAAAC 58.875 37.037 1.46 0.00 46.22 2.01
197 200 7.282901 GGTGGTTTCTTGGTTACTTACTGTAAA 59.717 37.037 1.46 0.00 42.12 2.01
199 202 6.126825 TGGTGGTTTCTTGGTTACTTACTGTA 60.127 38.462 0.00 0.00 0.00 2.74
200 203 5.128205 GGTGGTTTCTTGGTTACTTACTGT 58.872 41.667 0.00 0.00 0.00 3.55
201 204 5.127491 TGGTGGTTTCTTGGTTACTTACTG 58.873 41.667 0.00 0.00 0.00 2.74
202 205 5.376756 TGGTGGTTTCTTGGTTACTTACT 57.623 39.130 0.00 0.00 0.00 2.24
203 206 5.766174 TGATGGTGGTTTCTTGGTTACTTAC 59.234 40.000 0.00 0.00 0.00 2.34
204 207 5.942961 TGATGGTGGTTTCTTGGTTACTTA 58.057 37.500 0.00 0.00 0.00 2.24
215 227 1.203052 CACTGCCATGATGGTGGTTTC 59.797 52.381 13.84 0.00 40.46 2.78
230 242 0.238289 TTTGCTAGCGCTTTCACTGC 59.762 50.000 18.68 11.44 36.97 4.40
298 314 2.032681 ACGCTTGGAGGTTGGAGC 59.967 61.111 0.00 0.00 0.00 4.70
327 343 1.795525 CGATATGAGATACGGCGGCAG 60.796 57.143 13.24 0.00 0.00 4.85
329 345 0.450583 TCGATATGAGATACGGCGGC 59.549 55.000 13.24 0.00 0.00 6.53
330 346 3.808174 TCTATCGATATGAGATACGGCGG 59.192 47.826 13.24 0.00 0.00 6.13
331 347 4.609559 GCTCTATCGATATGAGATACGGCG 60.610 50.000 24.20 4.80 0.00 6.46
340 356 3.891977 GGGCTATGGCTCTATCGATATGA 59.108 47.826 5.40 5.17 35.73 2.15
345 361 0.251209 ACGGGCTATGGCTCTATCGA 60.251 55.000 0.00 0.00 36.65 3.59
363 397 3.507233 TCAAAAGTTGCTGATGGATGGAC 59.493 43.478 0.00 0.00 0.00 4.02
375 409 3.243535 CCTCTGGAAACCTCAAAAGTTGC 60.244 47.826 0.00 0.00 0.00 4.17
392 426 1.953138 GCATGATCGGTCGCCTCTG 60.953 63.158 0.00 0.00 0.00 3.35
393 427 2.419198 GCATGATCGGTCGCCTCT 59.581 61.111 0.00 0.00 0.00 3.69
435 483 2.435059 GAAGAGACGGGGTGCTGC 60.435 66.667 0.00 0.00 0.00 5.25
438 486 1.827399 TTGGAGAAGAGACGGGGTGC 61.827 60.000 0.00 0.00 0.00 5.01
445 493 1.056660 TGTGGGGTTGGAGAAGAGAC 58.943 55.000 0.00 0.00 0.00 3.36
466 514 4.081476 GGGGAAAGGAAGATTGTGATTTGG 60.081 45.833 0.00 0.00 0.00 3.28
493 541 2.489938 AGCCTTTCCAAGTAATGCGA 57.510 45.000 0.00 0.00 0.00 5.10
494 542 4.576463 AGATTAGCCTTTCCAAGTAATGCG 59.424 41.667 0.00 0.00 0.00 4.73
538 615 2.493973 CGAGCAGAGCAGAGGGAC 59.506 66.667 0.00 0.00 0.00 4.46
616 698 4.778143 GGGCATTGACGGCGAGGT 62.778 66.667 16.62 0.00 0.00 3.85
711 842 1.821136 GAGCTGGAATCTTTTGGGGTG 59.179 52.381 0.00 0.00 0.00 4.61
712 843 1.272704 GGAGCTGGAATCTTTTGGGGT 60.273 52.381 0.00 0.00 0.00 4.95
774 905 2.689646 CCCCAAGAACTCGAGAAGAAC 58.310 52.381 21.68 5.30 0.00 3.01
782 913 1.078848 CAGAGGCCCCAAGAACTCG 60.079 63.158 0.00 0.00 35.22 4.18
810 941 1.990614 ACCGGAAAGAGAGGGGAGC 60.991 63.158 9.46 0.00 0.00 4.70
881 1012 3.904339 GAGCCAATACAAGAGGGGATCTA 59.096 47.826 0.00 0.00 37.23 1.98
900 1031 1.776034 GATGAACCAATCCGGCGAGC 61.776 60.000 9.30 0.00 39.03 5.03
1060 1197 2.078452 CCAACCAGGAGACCACCAT 58.922 57.895 0.00 0.00 41.22 3.55
1277 1414 1.000646 TTCATGCTGCTGGCCATGA 60.001 52.632 5.51 2.33 40.92 3.07
1329 1466 3.181449 TGCAGCCTTTGTTGAGGTAGTTA 60.181 43.478 0.00 0.00 39.11 2.24
1425 1562 6.625362 GCTAGCATAGATAGCATCAAGTACA 58.375 40.000 10.63 0.00 45.44 2.90
1435 1572 3.509575 ACACTCCAGCTAGCATAGATAGC 59.490 47.826 18.83 6.19 46.33 2.97
1436 1573 4.082300 CCACACTCCAGCTAGCATAGATAG 60.082 50.000 18.83 7.64 42.77 2.08
1437 1574 3.829026 CCACACTCCAGCTAGCATAGATA 59.171 47.826 18.83 0.00 42.77 1.98
1438 1575 2.632028 CCACACTCCAGCTAGCATAGAT 59.368 50.000 18.83 0.00 42.77 1.98
1441 1578 1.757118 GACCACACTCCAGCTAGCATA 59.243 52.381 18.83 0.09 0.00 3.14
1448 1585 1.808945 CAAATGAGACCACACTCCAGC 59.191 52.381 0.00 0.00 36.22 4.85
1636 1777 5.027293 TGTCACTGTCCATCCATATGAAG 57.973 43.478 3.65 0.00 34.84 3.02
1682 1823 5.713792 TTGAAGGTAATGCGGAAATTTCA 57.286 34.783 19.49 0.42 0.00 2.69
1713 1854 0.179000 CAAGAAGGGGGTCTCCGATG 59.821 60.000 0.00 0.00 36.01 3.84
1725 1866 1.547372 CCATGGAAAGTGCCAAGAAGG 59.453 52.381 5.56 0.00 42.16 3.46
1735 1876 1.145738 ACCAGAAGCACCATGGAAAGT 59.854 47.619 21.47 0.00 37.54 2.66
1777 1919 3.616219 TCCCAAGGAATTCATGTAACCG 58.384 45.455 7.93 0.00 0.00 4.44
1787 1929 6.041637 GGTAACTTTTCTGTTCCCAAGGAATT 59.958 38.462 0.00 0.00 44.04 2.17
1877 2023 9.844790 CAGTATGAATTGATGAGCAAAGTAAAA 57.155 29.630 0.00 0.00 38.17 1.52
1907 2053 5.728351 TCTTGCTGCCGTGTAATTTATAC 57.272 39.130 0.00 0.00 0.00 1.47
1909 2055 4.700213 ACTTCTTGCTGCCGTGTAATTTAT 59.300 37.500 0.00 0.00 0.00 1.40
1960 2113 3.827008 TGATGAGAATCCAGTAGTGCC 57.173 47.619 0.00 0.00 0.00 5.01
2045 2198 8.763984 ATAGGAGAGAAGATTTAACCTAACGA 57.236 34.615 0.00 0.00 33.30 3.85
2078 2232 0.318784 GACGACAGAACCTTGCGTCT 60.319 55.000 0.00 0.00 40.75 4.18
2153 2307 6.581171 AAAAACTAGAGATGGGAGCAAAAG 57.419 37.500 0.00 0.00 0.00 2.27
2208 2362 0.251916 TGTGAATAAGAGGTGGGGCG 59.748 55.000 0.00 0.00 0.00 6.13
2443 2618 2.762535 AACGCCTAGTGCATAACTGT 57.237 45.000 0.00 0.00 40.26 3.55
2626 2808 4.511826 GGTACAGTTTTTGTGAGAGACAGG 59.488 45.833 0.00 0.00 41.10 4.00
2722 2912 9.076596 GGTTTCTGCTTGCTAAATAATTTGTAG 57.923 33.333 0.00 0.00 0.00 2.74
2878 3068 4.218635 TGGTTTCACAACTTGCTGTTTACA 59.781 37.500 0.00 0.00 36.63 2.41
2909 3099 3.074412 GTGGATGGTCCTTTACACTGTG 58.926 50.000 6.19 6.19 37.46 3.66
2928 3118 1.271163 ACCCCACATGTTAGAACCGTG 60.271 52.381 0.00 5.50 33.54 4.94
2999 3189 8.500773 TCTCATTTAAAACATGAACCTCGTAAC 58.499 33.333 0.00 0.00 30.12 2.50
3065 3256 4.210537 ACTTGATCGTTCAGTTACGTTTGG 59.789 41.667 0.00 0.00 42.01 3.28
3072 3263 4.627058 TGCTCAACTTGATCGTTCAGTTA 58.373 39.130 9.48 0.00 32.27 2.24
3144 3335 3.842925 TTCCTCCACGGTGCAAGGC 62.843 63.158 18.05 0.00 0.00 4.35
3149 3340 1.315257 ATGCATTTCCTCCACGGTGC 61.315 55.000 1.68 0.00 33.96 5.01
3154 3345 4.541973 AAAAAGGATGCATTTCCTCCAC 57.458 40.909 9.32 0.00 45.63 4.02
3201 3392 9.289782 GCAACTATTATATCACCCTCAAAGAAT 57.710 33.333 0.00 0.00 0.00 2.40
3227 3418 0.043334 TCAAGGGAGAGGGAAGAGGG 59.957 60.000 0.00 0.00 0.00 4.30
3282 3473 6.492007 AAACATAGTCATTGCAAGACAGAG 57.508 37.500 22.54 15.95 38.46 3.35
3283 3474 9.098355 GTATAAACATAGTCATTGCAAGACAGA 57.902 33.333 22.54 14.39 38.46 3.41
3428 3619 4.923281 GCTTGGTAGTGCAAATAGGTTTTG 59.077 41.667 0.00 0.00 0.00 2.44
3438 3629 2.102084 TGCAAAATGCTTGGTAGTGCAA 59.898 40.909 3.78 0.00 45.31 4.08
3439 3630 1.685517 TGCAAAATGCTTGGTAGTGCA 59.314 42.857 3.78 0.00 45.31 4.57
3491 3692 6.369340 TGCAAAAGAGCCATAAATTGAACATG 59.631 34.615 0.00 0.00 0.00 3.21
3492 3693 6.369615 GTGCAAAAGAGCCATAAATTGAACAT 59.630 34.615 0.00 0.00 0.00 2.71
3584 3789 4.941263 TCACGGATTTTCCAGGTTGAATAG 59.059 41.667 0.00 0.00 35.91 1.73
3600 3805 4.640201 CCACCAATGAAATAGTTCACGGAT 59.360 41.667 23.04 9.83 46.40 4.18
3604 3809 6.073819 GCAAAACCACCAATGAAATAGTTCAC 60.074 38.462 7.92 0.00 46.40 3.18
3674 3879 3.441572 AGAGACATGAAAATTGCGGAAGG 59.558 43.478 0.00 0.00 0.00 3.46
3789 4013 2.323999 AGATGGAGGGATGGAGCTAG 57.676 55.000 0.00 0.00 0.00 3.42
3794 4018 5.307976 CAGTGTTATAAGATGGAGGGATGGA 59.692 44.000 0.00 0.00 0.00 3.41
3795 4019 5.072329 ACAGTGTTATAAGATGGAGGGATGG 59.928 44.000 0.00 0.00 0.00 3.51
3796 4020 6.179906 ACAGTGTTATAAGATGGAGGGATG 57.820 41.667 0.00 0.00 0.00 3.51
3853 4077 1.207089 GGGACAGTGCATGTACTAGCA 59.793 52.381 16.53 8.42 44.17 3.49
3855 4079 2.760650 TCAGGGACAGTGCATGTACTAG 59.239 50.000 16.53 12.81 44.17 2.57
3988 4212 9.512435 CAGTAAAGACCATTTCATTTCATCATC 57.488 33.333 0.00 0.00 0.00 2.92
4166 4391 6.183360 CGCAACATACCTAGCAAAATAACAGA 60.183 38.462 0.00 0.00 0.00 3.41
4392 4617 8.543071 GAAATTTTACAATTTCGAGTATCCGG 57.457 34.615 10.47 0.00 45.23 5.14
4440 4665 6.212589 TGATGAAAGGGTAGATGTTGACAGTA 59.787 38.462 0.00 0.00 0.00 2.74
4584 4809 3.902881 TTCTTCTTCAGAGCCCAGATC 57.097 47.619 0.00 0.00 31.12 2.75
4632 4857 3.631046 GGCCAGCCTATCTCCCCG 61.631 72.222 0.00 0.00 0.00 5.73
4848 5073 0.947244 GCTGATACTTTGGGATGCCG 59.053 55.000 0.00 0.00 0.00 5.69
4881 5106 5.705441 TGCTCTTTTAATCTGTGAATTCGGT 59.295 36.000 0.04 0.00 0.00 4.69
5088 5313 4.342951 TCTTGGTCGTTCTTCTGGTAGAAA 59.657 41.667 0.00 0.00 36.01 2.52
5283 5508 3.526931 AACACCTATGAGGATGACACG 57.473 47.619 0.00 0.00 37.67 4.49
5303 5528 6.257630 CCATCTTCCGCAAAGAAAAAGAAAAA 59.742 34.615 2.92 0.00 46.85 1.94
5384 5612 3.119137 TCCTACATGGATGAACACTGACG 60.119 47.826 0.00 0.00 40.56 4.35
5416 5644 7.688578 CACCGAAATTAGAAGAAGAAAACGATC 59.311 37.037 0.00 0.00 0.00 3.69
5420 5648 7.198306 TCCACCGAAATTAGAAGAAGAAAAC 57.802 36.000 0.00 0.00 0.00 2.43
5465 5693 4.091509 AGCTACGCTAACAAGAATTCAACG 59.908 41.667 8.44 3.13 36.99 4.10
5607 5840 6.769822 AGACCATAATGCATAAACTGGAAGAG 59.230 38.462 18.36 0.00 37.43 2.85
5609 5842 6.769822 AGAGACCATAATGCATAAACTGGAAG 59.230 38.462 18.36 0.00 42.29 3.46
5613 5846 8.147058 AGTCTAGAGACCATAATGCATAAACTG 58.853 37.037 0.00 0.00 45.85 3.16
5614 5847 8.256356 AGTCTAGAGACCATAATGCATAAACT 57.744 34.615 0.00 0.00 45.85 2.66
5615 5848 8.894768 AAGTCTAGAGACCATAATGCATAAAC 57.105 34.615 0.00 0.00 45.85 2.01
5618 5851 9.760926 ATCTAAGTCTAGAGACCATAATGCATA 57.239 33.333 0.00 0.00 45.85 3.14
5619 5852 8.530311 CATCTAAGTCTAGAGACCATAATGCAT 58.470 37.037 6.05 0.00 45.85 3.96
5621 5854 7.177568 TCCATCTAAGTCTAGAGACCATAATGC 59.822 40.741 6.05 0.00 45.85 3.56
5622 5855 8.642935 TCCATCTAAGTCTAGAGACCATAATG 57.357 38.462 6.05 6.05 45.85 1.90
5623 5856 9.084533 GTTCCATCTAAGTCTAGAGACCATAAT 57.915 37.037 6.05 0.00 45.85 1.28
5625 5858 7.502895 GTGTTCCATCTAAGTCTAGAGACCATA 59.497 40.741 6.05 0.25 45.85 2.74
5626 5859 6.322712 GTGTTCCATCTAAGTCTAGAGACCAT 59.677 42.308 6.05 0.00 45.85 3.55
5627 5860 5.652891 GTGTTCCATCTAAGTCTAGAGACCA 59.347 44.000 6.05 0.00 45.85 4.02
5661 5963 4.283467 GTGATGGTCTATGGTGCATAGGTA 59.717 45.833 0.00 0.00 42.71 3.08
5662 5964 3.071602 GTGATGGTCTATGGTGCATAGGT 59.928 47.826 0.00 0.00 42.71 3.08
5663 5965 3.071457 TGTGATGGTCTATGGTGCATAGG 59.929 47.826 0.00 0.00 42.71 2.57
5677 5983 1.417890 GGCTATGGCTACTGTGATGGT 59.582 52.381 0.00 0.00 38.73 3.55
5683 5989 3.511934 GCTAGTATGGCTATGGCTACTGT 59.488 47.826 11.71 0.00 40.65 3.55
5684 5990 3.511540 TGCTAGTATGGCTATGGCTACTG 59.488 47.826 11.71 5.08 46.01 2.74
5718 6029 0.105778 GCAGATGTCTACAGGCTCCC 59.894 60.000 0.00 0.00 0.00 4.30
5810 6121 2.902486 TCTGGCACTAGATCCATGATCC 59.098 50.000 0.00 0.00 39.66 3.36
5837 6148 2.229543 TGCAACATGGATTCAAGCAGAC 59.770 45.455 0.00 0.00 0.00 3.51
5960 6280 3.365472 TCATTGCTGTCCAGAGCTAGTA 58.635 45.455 0.00 0.00 39.90 1.82
5961 6281 2.182827 TCATTGCTGTCCAGAGCTAGT 58.817 47.619 0.00 0.00 39.90 2.57
5962 6282 2.975732 TCATTGCTGTCCAGAGCTAG 57.024 50.000 0.00 0.00 39.90 3.42
5974 6294 1.822990 CCACATTGCCTCTTCATTGCT 59.177 47.619 0.00 0.00 0.00 3.91
6023 6343 8.483758 GTTATATACGGATGGTGAGGGAAATAT 58.516 37.037 0.00 0.00 0.00 1.28
6029 6349 5.011738 AGTTGTTATATACGGATGGTGAGGG 59.988 44.000 0.00 0.00 0.00 4.30
6057 6377 6.511767 GCATCTTTATCATGGTGGTTACTTCG 60.512 42.308 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.