Multiple sequence alignment - TraesCS6B01G137100

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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 TraesCS6B01G137100 chr6B 100.000 4954 0 0 1 4954 134816433 134821386 0.000000e+00 9149.0
1 TraesCS6B01G137100 chr6B 91.489 94 7 1 22 114 49950693 49950600 1.450000e-25 128.0
2 TraesCS6B01G137100 chr6B 100.000 28 0 0 1 28 3643593 3643566 9.000000e-03 52.8
3 TraesCS6B01G137100 chr6A 95.021 3314 127 12 760 4063 77511328 77514613 0.000000e+00 5171.0
4 TraesCS6B01G137100 chr6A 88.721 727 32 17 4071 4763 77532591 77533301 0.000000e+00 843.0
5 TraesCS6B01G137100 chr6A 88.856 341 36 2 115 454 77509981 77510320 7.670000e-113 418.0
6 TraesCS6B01G137100 chr6A 90.850 153 13 1 520 672 77510826 77510977 2.340000e-48 204.0
7 TraesCS6B01G137100 chr6A 89.796 147 6 4 4766 4905 77533381 77533525 3.940000e-41 180.0
8 TraesCS6B01G137100 chr6A 86.957 69 8 1 658 725 77510935 77511003 5.320000e-10 76.8
9 TraesCS6B01G137100 chr6D 93.855 3287 134 21 812 4064 60537834 60541086 0.000000e+00 4889.0
10 TraesCS6B01G137100 chr6D 88.618 615 26 14 4064 4675 60542054 60542627 0.000000e+00 708.0
11 TraesCS6B01G137100 chr6D 92.241 232 16 1 4674 4905 60542672 60542901 1.330000e-85 327.0
12 TraesCS6B01G137100 chr6D 90.588 85 8 0 30 114 269967343 269967259 4.050000e-21 113.0
13 TraesCS6B01G137100 chr2A 81.301 246 40 3 115 354 335820956 335821201 1.410000e-45 195.0
14 TraesCS6B01G137100 chr2A 92.553 94 7 0 21 114 385442859 385442766 8.650000e-28 135.0
15 TraesCS6B01G137100 chr3A 92.632 95 7 0 21 115 715553553 715553459 2.410000e-28 137.0
16 TraesCS6B01G137100 chr5A 92.553 94 7 0 21 114 8499525 8499432 8.650000e-28 135.0
17 TraesCS6B01G137100 chr5A 91.667 84 7 0 31 114 512824732 512824815 3.130000e-22 117.0
18 TraesCS6B01G137100 chr4B 91.489 94 8 0 21 114 30593788 30593881 4.020000e-26 130.0
19 TraesCS6B01G137100 chr5D 91.489 94 7 1 21 114 446512390 446512298 1.450000e-25 128.0
20 TraesCS6B01G137100 chr4D 88.421 95 11 0 21 115 43263126 43263032 1.130000e-21 115.0
21 TraesCS6B01G137100 chr7A 81.679 131 23 1 216 346 460433493 460433622 1.890000e-19 108.0


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 TraesCS6B01G137100 chr6B 134816433 134821386 4953 False 9149.000000 9149 100.000000 1 4954 1 chr6B.!!$F1 4953
1 TraesCS6B01G137100 chr6A 77509981 77514613 4632 False 1467.450000 5171 90.421000 115 4063 4 chr6A.!!$F1 3948
2 TraesCS6B01G137100 chr6A 77532591 77533525 934 False 511.500000 843 89.258500 4071 4905 2 chr6A.!!$F2 834
3 TraesCS6B01G137100 chr6D 60537834 60542901 5067 False 1974.666667 4889 91.571333 812 4905 3 chr6D.!!$F1 4093

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
266 267 0.107066 TAGGGTGCGGTACTCGATCA 60.107 55.0 7.77 0.0 42.43 2.92 F
493 911 0.465705 TGGTCCAAATTGCGCCAAAA 59.534 45.0 4.18 0.0 0.00 2.44 F
1365 2121 0.178068 GAGCGCCTTTGGTGGAGATA 59.822 55.0 2.29 0.0 33.18 1.98 F
2827 3595 0.460311 ATTAGGACGAGCGGTTCAGG 59.540 55.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 2096 0.099436 CACCAAAGGCGCTCATTAGC 59.901 55.0 7.64 0.00 45.86 3.09 R
1566 2322 0.179171 CATTTCTTGAGCAGCTGCCG 60.179 55.0 34.39 19.98 43.38 5.69 R
3147 3918 0.035458 CTGAGTCCACACAGAACCCC 59.965 60.0 0.00 0.00 36.82 4.95 R
4064 4838 0.677842 GCGACCCTCCGTATAACCAT 59.322 55.0 0.00 0.00 0.00 3.55 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
18 19 3.978876 AGAATTTTGGGACGGAGGG 57.021 52.632 0.00 0.00 0.00 4.30
19 20 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
20 21 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
21 22 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
22 23 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
23 24 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
24 25 1.252904 TTTGGGACGGAGGGAGTACG 61.253 60.000 0.00 0.00 0.00 3.67
25 26 2.044551 GGGACGGAGGGAGTACGT 60.045 66.667 0.00 0.00 44.35 3.57
26 27 1.224592 GGGACGGAGGGAGTACGTA 59.775 63.158 0.00 0.00 41.40 3.57
27 28 1.098129 GGGACGGAGGGAGTACGTAC 61.098 65.000 18.10 18.10 41.40 3.67
28 29 0.107459 GGACGGAGGGAGTACGTACT 60.107 60.000 27.71 27.71 41.40 2.73
29 30 1.139058 GGACGGAGGGAGTACGTACTA 59.861 57.143 27.44 0.00 41.40 1.82
30 31 2.420129 GGACGGAGGGAGTACGTACTAA 60.420 54.545 27.44 0.00 41.40 2.24
31 32 2.609916 GACGGAGGGAGTACGTACTAAC 59.390 54.545 27.44 21.61 41.40 2.34
46 47 5.931532 CGTACTAACGTACATATACCTGGG 58.068 45.833 0.00 0.00 44.97 4.45
47 48 5.700832 CGTACTAACGTACATATACCTGGGA 59.299 44.000 0.00 0.00 44.97 4.37
48 49 6.128445 CGTACTAACGTACATATACCTGGGAG 60.128 46.154 0.00 0.00 44.97 4.30
49 50 5.075493 ACTAACGTACATATACCTGGGAGG 58.925 45.833 0.00 0.00 42.49 4.30
50 51 2.885616 ACGTACATATACCTGGGAGGG 58.114 52.381 0.00 0.00 40.58 4.30
51 52 2.176889 CGTACATATACCTGGGAGGGG 58.823 57.143 0.00 0.00 40.58 4.79
52 53 2.547990 GTACATATACCTGGGAGGGGG 58.452 57.143 0.00 0.00 40.58 5.40
53 54 0.475828 ACATATACCTGGGAGGGGGC 60.476 60.000 0.00 0.00 40.58 5.80
54 55 1.163555 ATATACCTGGGAGGGGGCC 59.836 63.158 0.00 0.00 40.58 5.80
64 65 3.181282 AGGGGGCCCTTGACTTTC 58.819 61.111 24.38 2.24 45.70 2.62
65 66 2.361230 GGGGGCCCTTGACTTTCG 60.361 66.667 24.38 0.00 0.00 3.46
66 67 2.361230 GGGGCCCTTGACTTTCGG 60.361 66.667 24.38 0.00 0.00 4.30
67 68 2.361230 GGGCCCTTGACTTTCGGG 60.361 66.667 17.04 0.00 41.06 5.14
68 69 2.361230 GGCCCTTGACTTTCGGGG 60.361 66.667 0.00 0.00 41.64 5.73
69 70 2.361230 GCCCTTGACTTTCGGGGG 60.361 66.667 0.00 0.00 39.27 5.40
70 71 2.361230 CCCTTGACTTTCGGGGGC 60.361 66.667 0.00 0.00 35.49 5.80
71 72 2.361230 CCTTGACTTTCGGGGGCC 60.361 66.667 0.00 0.00 0.00 5.80
72 73 2.361230 CTTGACTTTCGGGGGCCC 60.361 66.667 15.76 15.76 0.00 5.80
102 103 4.157120 CCGTTCGCCCTACCCCAG 62.157 72.222 0.00 0.00 0.00 4.45
103 104 4.157120 CGTTCGCCCTACCCCAGG 62.157 72.222 0.00 0.00 45.07 4.45
111 112 3.242291 CTACCCCAGGATCGGCCC 61.242 72.222 0.00 0.00 37.37 5.80
112 113 3.774336 TACCCCAGGATCGGCCCT 61.774 66.667 0.00 0.00 37.37 5.19
126 127 1.583054 GGCCCTGTACTTTGCTATCG 58.417 55.000 0.00 0.00 0.00 2.92
133 134 1.134491 GTACTTTGCTATCGCCACCCT 60.134 52.381 0.00 0.00 34.43 4.34
178 179 6.042777 GTGATCCTTGTTGATTCATACGAGA 58.957 40.000 13.46 0.51 0.00 4.04
180 181 6.925718 TGATCCTTGTTGATTCATACGAGATC 59.074 38.462 13.46 10.99 0.00 2.75
181 182 5.601662 TCCTTGTTGATTCATACGAGATCC 58.398 41.667 13.46 0.00 0.00 3.36
182 183 4.752101 CCTTGTTGATTCATACGAGATCCC 59.248 45.833 13.46 0.00 0.00 3.85
189 190 2.319844 TCATACGAGATCCCATGTGCT 58.680 47.619 0.00 0.00 0.00 4.40
205 206 0.744874 TGCTACATGCTACTCGGGTC 59.255 55.000 0.00 0.00 43.37 4.46
209 210 1.107114 ACATGCTACTCGGGTCAGAG 58.893 55.000 0.00 0.00 43.56 3.35
231 232 3.062234 GTGTAAGTGATGCTTTCGGCTAC 59.938 47.826 0.00 0.00 42.39 3.58
261 262 0.674534 CCATCTAGGGTGCGGTACTC 59.325 60.000 0.00 0.00 0.00 2.59
262 263 0.311165 CATCTAGGGTGCGGTACTCG 59.689 60.000 0.00 0.00 42.76 4.18
265 266 0.592148 CTAGGGTGCGGTACTCGATC 59.408 60.000 7.77 0.00 42.43 3.69
266 267 0.107066 TAGGGTGCGGTACTCGATCA 60.107 55.000 7.77 0.00 42.43 2.92
285 286 4.955925 TCATTTCGTTTGACAACACACT 57.044 36.364 0.00 0.00 32.54 3.55
312 313 5.603596 TGTATTGTTCTTACACAACCTCGT 58.396 37.500 0.00 0.00 39.48 4.18
318 319 5.411977 TGTTCTTACACAACCTCGTTTTCAA 59.588 36.000 0.00 0.00 0.00 2.69
332 333 2.561419 GTTTTCAAGGTTTAGGCCCCTC 59.439 50.000 0.00 0.00 0.00 4.30
338 339 2.419686 AGGTTTAGGCCCCTCCTATTC 58.580 52.381 0.00 0.00 46.40 1.75
344 345 1.052617 GGCCCCTCCTATTCTCTCAC 58.947 60.000 0.00 0.00 0.00 3.51
345 346 1.052617 GCCCCTCCTATTCTCTCACC 58.947 60.000 0.00 0.00 0.00 4.02
350 351 3.318557 CCCTCCTATTCTCTCACCGTTAC 59.681 52.174 0.00 0.00 0.00 2.50
363 364 6.558009 TCTCACCGTTACTACATGATTACAC 58.442 40.000 0.00 0.00 0.00 2.90
369 370 8.190122 ACCGTTACTACATGATTACACGAATAA 58.810 33.333 0.00 0.00 0.00 1.40
386 387 7.116819 CACGAATAACTTTTGCTTTGTTTTCC 58.883 34.615 0.00 0.00 0.00 3.13
396 397 3.004315 TGCTTTGTTTTCCTCCACGATTC 59.996 43.478 0.00 0.00 0.00 2.52
406 407 0.961857 TCCACGATTCCGGTCTTCGA 60.962 55.000 23.22 5.28 42.43 3.71
421 422 2.164491 TCGATAGACGACGTGTGCA 58.836 52.632 4.58 0.00 46.45 4.57
424 425 1.728179 CGATAGACGACGTGTGCAAGT 60.728 52.381 4.58 0.00 45.77 3.16
430 431 3.181169 GACGTGTGCAAGTGGTGGC 62.181 63.158 0.00 0.00 0.00 5.01
436 437 1.176527 GTGCAAGTGGTGGCATACAT 58.823 50.000 7.45 0.00 42.75 2.29
454 455 7.492669 GGCATACATGACACATCTATATGTACC 59.507 40.741 0.00 0.00 44.70 3.34
455 456 8.253810 GCATACATGACACATCTATATGTACCT 58.746 37.037 0.00 0.00 44.70 3.08
459 874 6.650427 TGACACATCTATATGTACCTGGTC 57.350 41.667 0.63 0.00 44.70 4.02
473 888 7.712204 TGTACCTGGTCTTTTCTTTTCTTTT 57.288 32.000 0.63 0.00 0.00 2.27
483 901 8.946085 GTCTTTTCTTTTCTTTTTGGTCCAAAT 58.054 29.630 17.79 0.00 33.19 2.32
484 902 9.513906 TCTTTTCTTTTCTTTTTGGTCCAAATT 57.486 25.926 17.79 0.00 33.19 1.82
493 911 0.465705 TGGTCCAAATTGCGCCAAAA 59.534 45.000 4.18 0.00 0.00 2.44
494 912 1.071385 TGGTCCAAATTGCGCCAAAAT 59.929 42.857 4.18 0.00 0.00 1.82
495 913 2.300152 TGGTCCAAATTGCGCCAAAATA 59.700 40.909 4.18 0.00 0.00 1.40
496 914 2.929398 GGTCCAAATTGCGCCAAAATAG 59.071 45.455 4.18 0.00 0.00 1.73
497 915 2.348362 GTCCAAATTGCGCCAAAATAGC 59.652 45.455 4.18 0.00 0.00 2.97
498 916 2.028658 TCCAAATTGCGCCAAAATAGCA 60.029 40.909 4.18 0.00 39.33 3.49
555 996 9.872757 CTTTTCATTTGAGAAACATGAAAATGG 57.127 29.630 15.88 5.90 41.92 3.16
615 1056 6.076981 ACACATGAAAAATGGTCTCTCAAC 57.923 37.500 0.00 0.00 0.00 3.18
666 1107 9.713713 TTTTAAGAAAATAGGGCAATAACAACC 57.286 29.630 0.00 0.00 0.00 3.77
667 1108 8.658840 TTAAGAAAATAGGGCAATAACAACCT 57.341 30.769 0.00 0.00 37.13 3.50
668 1109 7.553504 AAGAAAATAGGGCAATAACAACCTT 57.446 32.000 0.00 0.00 34.59 3.50
669 1110 7.553504 AGAAAATAGGGCAATAACAACCTTT 57.446 32.000 0.00 0.00 34.59 3.11
670 1111 7.973402 AGAAAATAGGGCAATAACAACCTTTT 58.027 30.769 0.00 0.00 34.59 2.27
671 1112 8.436778 AGAAAATAGGGCAATAACAACCTTTTT 58.563 29.630 0.00 0.00 36.33 1.94
725 1166 6.369629 TGGAAAAATGGTCTCTCAACCTTAA 58.630 36.000 0.00 0.00 40.20 1.85
726 1167 6.836527 TGGAAAAATGGTCTCTCAACCTTAAA 59.163 34.615 0.00 0.00 40.20 1.52
727 1168 7.343316 TGGAAAAATGGTCTCTCAACCTTAAAA 59.657 33.333 0.00 0.00 40.20 1.52
728 1169 7.652105 GGAAAAATGGTCTCTCAACCTTAAAAC 59.348 37.037 0.00 0.00 40.20 2.43
729 1170 6.650427 AAATGGTCTCTCAACCTTAAAACC 57.350 37.500 0.00 0.00 40.20 3.27
730 1171 3.735591 TGGTCTCTCAACCTTAAAACCG 58.264 45.455 0.00 0.00 40.20 4.44
731 1172 3.135167 TGGTCTCTCAACCTTAAAACCGT 59.865 43.478 0.00 0.00 40.20 4.83
732 1173 4.132336 GGTCTCTCAACCTTAAAACCGTT 58.868 43.478 0.00 0.00 36.32 4.44
733 1174 4.212847 GGTCTCTCAACCTTAAAACCGTTC 59.787 45.833 0.00 0.00 36.32 3.95
734 1175 4.812626 GTCTCTCAACCTTAAAACCGTTCA 59.187 41.667 0.00 0.00 0.00 3.18
735 1176 5.050295 GTCTCTCAACCTTAAAACCGTTCAG 60.050 44.000 0.00 0.00 0.00 3.02
736 1177 4.773013 TCTCAACCTTAAAACCGTTCAGT 58.227 39.130 0.00 0.00 0.00 3.41
737 1178 5.187687 TCTCAACCTTAAAACCGTTCAGTT 58.812 37.500 0.00 0.00 0.00 3.16
738 1179 5.648960 TCTCAACCTTAAAACCGTTCAGTTT 59.351 36.000 0.00 0.00 41.67 2.66
740 1181 6.689554 TCAACCTTAAAACCGTTCAGTTTTT 58.310 32.000 7.61 0.00 45.34 1.94
901 1633 4.320456 CAGCCACCGACCACAGCT 62.320 66.667 0.00 0.00 0.00 4.24
1100 1832 1.085893 TCACCACGCGTCTATTCGTA 58.914 50.000 9.86 0.00 37.14 3.43
1276 2008 3.261951 CACCGTAAGCATCCGCCG 61.262 66.667 0.00 0.00 39.83 6.46
1301 2057 4.202441 CCATCCAACCATCTCCTTGTTAG 58.798 47.826 0.00 0.00 0.00 2.34
1340 2096 4.765281 TTGTTAATTCTATCCGTTCGCG 57.235 40.909 0.00 0.00 40.93 5.87
1365 2121 0.178068 GAGCGCCTTTGGTGGAGATA 59.822 55.000 2.29 0.00 33.18 1.98
1381 2137 4.200092 GGAGATAAACGAGATTTTGGCCT 58.800 43.478 3.32 0.00 0.00 5.19
1486 2242 3.877735 GCAAATGGAAAGGAGGGAAGCTA 60.878 47.826 0.00 0.00 0.00 3.32
1599 2355 2.843701 AGAAATGCCTGCGGAAGATAG 58.156 47.619 0.00 0.00 0.00 2.08
1730 2492 5.048083 TCTGTGTTGCATAATTCTTTGGTCC 60.048 40.000 0.00 0.00 0.00 4.46
1740 2502 7.574217 GCATAATTCTTTGGTCCGACTGTTTTA 60.574 37.037 0.00 0.00 0.00 1.52
1758 2520 8.495148 ACTGTTTTAATGAATTTTCCAAATCGC 58.505 29.630 0.00 0.00 0.00 4.58
1760 2522 5.694674 TTAATGAATTTTCCAAATCGCGC 57.305 34.783 0.00 0.00 0.00 6.86
1773 2535 1.425412 ATCGCGCGTTCTGTAGTTTT 58.575 45.000 30.98 0.00 0.00 2.43
1916 2680 7.087409 TGCTCGAATCATGTTCATTTTGTAT 57.913 32.000 0.00 0.00 0.00 2.29
1917 2681 7.537715 TGCTCGAATCATGTTCATTTTGTATT 58.462 30.769 0.00 0.00 0.00 1.89
1947 2711 5.676552 TGAGACAAACTTAGCAGGTGTAAA 58.323 37.500 0.00 0.00 0.00 2.01
2028 2793 5.886960 AATATCTTGTTGAGACTGGTTGC 57.113 39.130 0.00 0.00 37.17 4.17
2060 2825 4.932200 CAGCAAGGGTAAAAGAGTAGTCTG 59.068 45.833 0.00 0.00 31.37 3.51
2074 2839 7.447374 AGAGTAGTCTGTCATGCAGTATATC 57.553 40.000 14.21 9.06 45.23 1.63
2170 2935 9.177608 CATTCTCCTAACCAATGATCTGTTTTA 57.822 33.333 0.00 0.00 30.31 1.52
2242 3007 8.166726 AGTTTCAGAAATATTGAAGTCCCTTCT 58.833 33.333 0.00 0.00 40.73 2.85
2260 3025 5.394553 CCCTTCTTACCCAATTCATTTCTGC 60.395 44.000 0.00 0.00 0.00 4.26
2347 3112 2.168313 TGTTGCATATGAGAAGGAGCGA 59.832 45.455 6.97 0.00 0.00 4.93
2488 3256 3.030291 ACCCTCTAATGCTGAGACAGAG 58.970 50.000 2.81 0.00 32.44 3.35
2527 3295 2.028020 AGAACCCTCTGATTCCGACAAC 60.028 50.000 0.00 0.00 0.00 3.32
2528 3296 1.348064 ACCCTCTGATTCCGACAACA 58.652 50.000 0.00 0.00 0.00 3.33
2599 3367 5.003096 ACCTCCAAATGGAAGAAACAGAT 57.997 39.130 5.08 0.00 44.91 2.90
2717 3485 3.002656 CCAAGCAGTGAATAAGGTATGCG 59.997 47.826 0.00 0.00 38.65 4.73
2744 3512 7.695480 TTGCAGTTACTTGCCTGAATAATTA 57.305 32.000 4.82 0.00 43.43 1.40
2827 3595 0.460311 ATTAGGACGAGCGGTTCAGG 59.540 55.000 0.00 0.00 0.00 3.86
2876 3644 6.595682 TCTCCACAAAAGAAGAGACAGAAAT 58.404 36.000 0.00 0.00 30.56 2.17
2903 3671 8.260818 CAGAGGATTTATCTGAACCTAGAAACA 58.739 37.037 0.00 0.00 45.80 2.83
2933 3701 5.640783 CAGTCTACTTCAATGAATGCAGACA 59.359 40.000 22.34 0.00 34.89 3.41
2934 3702 5.873712 AGTCTACTTCAATGAATGCAGACAG 59.126 40.000 22.34 4.38 34.89 3.51
2935 3703 5.064452 GTCTACTTCAATGAATGCAGACAGG 59.936 44.000 18.61 1.02 33.13 4.00
3034 3805 2.039084 AGGAACGCATGGTTTCTCTTCT 59.961 45.455 0.00 0.00 40.66 2.85
3079 3850 2.158623 TGCTGGTCTTCAAGGTGTTGAT 60.159 45.455 0.00 0.00 42.41 2.57
3142 3913 3.774734 TGAGCTTCCTACTACTGAACCA 58.225 45.455 0.00 0.00 0.00 3.67
3147 3918 5.998363 AGCTTCCTACTACTGAACCAAAAAG 59.002 40.000 0.00 0.00 0.00 2.27
3381 4152 1.153667 CCTCGGCTGAGCAGAACTC 60.154 63.158 17.68 0.00 46.45 3.01
3448 4219 0.613260 CTGGTCATGAAACCCGAGGA 59.387 55.000 0.00 0.00 38.65 3.71
3449 4220 1.210478 CTGGTCATGAAACCCGAGGAT 59.790 52.381 0.00 0.00 38.65 3.24
3450 4221 1.065491 TGGTCATGAAACCCGAGGATG 60.065 52.381 0.00 0.00 38.65 3.51
3456 4227 2.830704 GAAACCCGAGGATGCGACGT 62.831 60.000 0.00 0.00 0.00 4.34
3605 4376 0.037605 GAGGGGCGACGAGAAGAAAA 60.038 55.000 0.00 0.00 0.00 2.29
3616 4387 2.010497 GAGAAGAAAACCGGATCCAGC 58.990 52.381 9.46 0.00 0.00 4.85
3683 4454 0.038166 TCTTGGGGTCACATCTTGCC 59.962 55.000 0.00 0.00 0.00 4.52
3709 4480 1.278127 ACCTCGTACCATCACCAAAGG 59.722 52.381 0.00 0.00 0.00 3.11
3761 4532 3.151912 AGCTTGACTCCTGCAAATTCT 57.848 42.857 0.00 0.00 0.00 2.40
3881 4652 1.495878 GCTCCGATGTATCTGCAGTG 58.504 55.000 14.67 0.00 0.00 3.66
3970 4741 9.330063 TCTTGCAATATGTTTAATCTCCTAGTG 57.670 33.333 0.00 0.00 0.00 2.74
4018 4792 1.134228 TAATACCGGGGGCTCCTTTC 58.866 55.000 6.32 0.00 0.00 2.62
4020 4794 2.850851 ATACCGGGGGCTCCTTTCCA 62.851 60.000 6.32 0.00 0.00 3.53
4021 4795 3.657350 CCGGGGGCTCCTTTCCAA 61.657 66.667 0.52 0.00 0.00 3.53
4022 4796 2.438795 CGGGGGCTCCTTTCCAAA 59.561 61.111 0.52 0.00 0.00 3.28
4023 4797 1.228737 CGGGGGCTCCTTTCCAAAA 60.229 57.895 0.52 0.00 0.00 2.44
4024 4798 0.830023 CGGGGGCTCCTTTCCAAAAA 60.830 55.000 0.52 0.00 0.00 1.94
4064 4838 1.486310 ACTGCTGTGTTCTTCCACTCA 59.514 47.619 0.00 0.00 36.30 3.41
4066 4840 2.483106 CTGCTGTGTTCTTCCACTCATG 59.517 50.000 0.00 0.00 36.30 3.07
4148 5892 5.652014 TCAACCGATTGAAAATATTCAGGCT 59.348 36.000 0.00 0.00 45.82 4.58
4165 5909 1.740025 GGCTATGAATGAATAGGCGCC 59.260 52.381 21.89 21.89 43.31 6.53
4231 5975 3.296854 AGACGCTCTCTCTCTCTCTCTA 58.703 50.000 0.00 0.00 0.00 2.43
4245 5989 6.268617 TCTCTCTCTCTATCTCTCTCTTCCAG 59.731 46.154 0.00 0.00 0.00 3.86
4261 6005 1.621814 TCCAGACCACGACCTAAAAGG 59.378 52.381 0.00 0.00 42.49 3.11
4267 6011 2.224450 ACCACGACCTAAAAGGAACCTG 60.224 50.000 0.00 0.00 37.67 4.00
4268 6012 2.038033 CCACGACCTAAAAGGAACCTGA 59.962 50.000 0.00 0.00 37.67 3.86
4269 6013 3.326747 CACGACCTAAAAGGAACCTGAG 58.673 50.000 0.00 0.00 37.67 3.35
4270 6014 3.006537 CACGACCTAAAAGGAACCTGAGA 59.993 47.826 0.00 0.00 37.67 3.27
4332 6076 1.755380 CCCGTCTCTAACCTAACCTGG 59.245 57.143 0.00 0.00 0.00 4.45
4348 6092 3.945434 GGCCATGCACGCATCTCG 61.945 66.667 0.44 0.00 45.38 4.04
4422 6166 5.222278 ACTAGGATCAGGTTTTAGGAGGA 57.778 43.478 0.00 0.00 0.00 3.71
4424 6168 4.354208 AGGATCAGGTTTTAGGAGGAGA 57.646 45.455 0.00 0.00 0.00 3.71
4426 6170 6.044411 AGGATCAGGTTTTAGGAGGAGATA 57.956 41.667 0.00 0.00 0.00 1.98
4427 6171 6.638953 AGGATCAGGTTTTAGGAGGAGATAT 58.361 40.000 0.00 0.00 0.00 1.63
4428 6172 7.780822 AGGATCAGGTTTTAGGAGGAGATATA 58.219 38.462 0.00 0.00 0.00 0.86
4465 6209 6.911250 TTTCGCAGGAGATCAGGTAATATA 57.089 37.500 0.00 0.00 0.00 0.86
4466 6210 6.911250 TTCGCAGGAGATCAGGTAATATAA 57.089 37.500 0.00 0.00 0.00 0.98
4467 6211 7.482169 TTCGCAGGAGATCAGGTAATATAAT 57.518 36.000 0.00 0.00 0.00 1.28
4468 6212 8.589701 TTCGCAGGAGATCAGGTAATATAATA 57.410 34.615 0.00 0.00 0.00 0.98
4469 6213 8.768501 TCGCAGGAGATCAGGTAATATAATAT 57.231 34.615 0.00 0.00 0.00 1.28
4470 6214 9.201989 TCGCAGGAGATCAGGTAATATAATATT 57.798 33.333 0.00 0.00 0.00 1.28
4503 6253 4.261994 CCGATCATCTCCCTCTTCTTCTTC 60.262 50.000 0.00 0.00 0.00 2.87
4504 6254 4.584325 CGATCATCTCCCTCTTCTTCTTCT 59.416 45.833 0.00 0.00 0.00 2.85
4505 6255 5.068987 CGATCATCTCCCTCTTCTTCTTCTT 59.931 44.000 0.00 0.00 0.00 2.52
4506 6256 5.930837 TCATCTCCCTCTTCTTCTTCTTC 57.069 43.478 0.00 0.00 0.00 2.87
4507 6257 4.714308 TCATCTCCCTCTTCTTCTTCTTCC 59.286 45.833 0.00 0.00 0.00 3.46
4508 6258 3.093057 TCTCCCTCTTCTTCTTCTTCCG 58.907 50.000 0.00 0.00 0.00 4.30
4509 6259 3.093057 CTCCCTCTTCTTCTTCTTCCGA 58.907 50.000 0.00 0.00 0.00 4.55
4510 6260 3.704061 CTCCCTCTTCTTCTTCTTCCGAT 59.296 47.826 0.00 0.00 0.00 4.18
4511 6261 4.097418 TCCCTCTTCTTCTTCTTCCGATT 58.903 43.478 0.00 0.00 0.00 3.34
4512 6262 4.160626 TCCCTCTTCTTCTTCTTCCGATTC 59.839 45.833 0.00 0.00 0.00 2.52
4513 6263 4.081420 CCCTCTTCTTCTTCTTCCGATTCA 60.081 45.833 0.00 0.00 0.00 2.57
4648 6402 1.469940 CCCATCAGGTTCGTTCTCTCG 60.470 57.143 0.00 0.00 0.00 4.04
4652 6406 0.109226 CAGGTTCGTTCTCTCGTCCC 60.109 60.000 0.00 0.00 0.00 4.46
4675 6430 2.751806 CTCCTTTCCTGTTCTGCATTCC 59.248 50.000 0.00 0.00 0.00 3.01
4687 6488 3.237746 TCTGCATTCCACCCAAATCAAA 58.762 40.909 0.00 0.00 0.00 2.69
4697 6498 6.188407 TCCACCCAAATCAAACCGATAATTA 58.812 36.000 0.00 0.00 32.51 1.40
4703 6504 9.593134 CCCAAATCAAACCGATAATTAATTGAA 57.407 29.630 11.05 0.00 32.51 2.69
4863 6743 5.185454 AGTGAGTGATCACAACAGTTTTCA 58.815 37.500 27.02 15.86 42.68 2.69
4864 6744 5.065218 AGTGAGTGATCACAACAGTTTTCAC 59.935 40.000 27.02 24.63 42.68 3.18
4868 6748 5.036737 GTGATCACAACAGTTTTCACCTTG 58.963 41.667 21.07 0.00 0.00 3.61
4870 6750 3.088532 TCACAACAGTTTTCACCTTGCT 58.911 40.909 0.00 0.00 0.00 3.91
4905 6790 7.407393 TTCATCATACATTCCTCATTTGCAA 57.593 32.000 0.00 0.00 0.00 4.08
4906 6791 7.407393 TCATCATACATTCCTCATTTGCAAA 57.593 32.000 15.44 15.44 0.00 3.68
4907 6792 7.259882 TCATCATACATTCCTCATTTGCAAAC 58.740 34.615 15.41 0.00 0.00 2.93
4908 6793 6.839124 TCATACATTCCTCATTTGCAAACT 57.161 33.333 15.41 0.99 0.00 2.66
4909 6794 6.623486 TCATACATTCCTCATTTGCAAACTG 58.377 36.000 15.41 13.63 0.00 3.16
4910 6795 3.656559 ACATTCCTCATTTGCAAACTGC 58.343 40.909 15.41 0.00 45.29 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1 2 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2 3 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3 4 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4 5 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5 6 1.252904 CGTACTCCCTCCGTCCCAAA 61.253 60.000 0.00 0.00 0.00 3.28
6 7 1.679977 CGTACTCCCTCCGTCCCAA 60.680 63.158 0.00 0.00 0.00 4.12
7 8 1.561769 TACGTACTCCCTCCGTCCCA 61.562 60.000 0.00 0.00 36.12 4.37
8 9 1.098129 GTACGTACTCCCTCCGTCCC 61.098 65.000 18.47 0.00 36.12 4.46
9 10 0.107459 AGTACGTACTCCCTCCGTCC 60.107 60.000 22.45 0.00 36.12 4.79
10 11 2.604046 TAGTACGTACTCCCTCCGTC 57.396 55.000 30.53 0.00 37.73 4.79
11 12 2.633488 GTTAGTACGTACTCCCTCCGT 58.367 52.381 30.53 8.23 37.73 4.69
12 13 1.594862 CGTTAGTACGTACTCCCTCCG 59.405 57.143 30.53 20.53 42.72 4.63
24 25 8.706547 CCCTCCCAGGTATATGTACGTTAGTAC 61.707 48.148 0.00 2.18 42.63 2.73
25 26 6.240894 CCTCCCAGGTATATGTACGTTAGTA 58.759 44.000 0.00 0.00 0.00 1.82
26 27 5.075493 CCTCCCAGGTATATGTACGTTAGT 58.925 45.833 0.00 0.00 0.00 2.24
27 28 4.461781 CCCTCCCAGGTATATGTACGTTAG 59.538 50.000 0.00 0.00 31.93 2.34
28 29 4.410099 CCCTCCCAGGTATATGTACGTTA 58.590 47.826 0.00 0.00 31.93 3.18
29 30 3.236896 CCCTCCCAGGTATATGTACGTT 58.763 50.000 0.00 0.00 31.93 3.99
30 31 2.492196 CCCCTCCCAGGTATATGTACGT 60.492 54.545 0.00 0.00 31.93 3.57
31 32 2.176889 CCCCTCCCAGGTATATGTACG 58.823 57.143 0.00 0.00 31.93 3.67
32 33 2.547990 CCCCCTCCCAGGTATATGTAC 58.452 57.143 0.00 0.00 31.93 2.90
33 34 1.203389 GCCCCCTCCCAGGTATATGTA 60.203 57.143 0.00 0.00 31.93 2.29
34 35 0.475828 GCCCCCTCCCAGGTATATGT 60.476 60.000 0.00 0.00 31.93 2.29
35 36 1.208165 GGCCCCCTCCCAGGTATATG 61.208 65.000 0.00 0.00 31.93 1.78
36 37 1.163555 GGCCCCCTCCCAGGTATAT 59.836 63.158 0.00 0.00 31.93 0.86
37 38 2.624717 GGCCCCCTCCCAGGTATA 59.375 66.667 0.00 0.00 31.93 1.47
38 39 4.533794 GGGCCCCCTCCCAGGTAT 62.534 72.222 12.23 0.00 45.82 2.73
48 49 2.361230 CGAAAGTCAAGGGCCCCC 60.361 66.667 21.43 3.87 0.00 5.40
49 50 2.361230 CCGAAAGTCAAGGGCCCC 60.361 66.667 21.43 1.95 0.00 5.80
50 51 2.361230 CCCGAAAGTCAAGGGCCC 60.361 66.667 16.46 16.46 38.51 5.80
51 52 2.361230 CCCCGAAAGTCAAGGGCC 60.361 66.667 0.00 0.00 43.74 5.80
52 53 2.361230 CCCCCGAAAGTCAAGGGC 60.361 66.667 0.00 0.00 43.74 5.19
53 54 2.361230 GCCCCCGAAAGTCAAGGG 60.361 66.667 0.00 0.00 44.67 3.95
54 55 2.361230 GGCCCCCGAAAGTCAAGG 60.361 66.667 0.00 0.00 0.00 3.61
55 56 2.361230 GGGCCCCCGAAAGTCAAG 60.361 66.667 12.23 0.00 0.00 3.02
85 86 4.157120 CTGGGGTAGGGCGAACGG 62.157 72.222 0.00 0.00 0.00 4.44
86 87 4.157120 CCTGGGGTAGGGCGAACG 62.157 72.222 0.00 0.00 43.33 3.95
94 95 3.242291 GGGCCGATCCTGGGGTAG 61.242 72.222 0.00 0.00 34.39 3.18
95 96 3.774336 AGGGCCGATCCTGGGGTA 61.774 66.667 0.00 0.00 35.47 3.69
101 102 0.541863 CAAAGTACAGGGCCGATCCT 59.458 55.000 0.00 0.00 37.71 3.24
102 103 1.095807 GCAAAGTACAGGGCCGATCC 61.096 60.000 0.00 0.00 0.00 3.36
103 104 0.107654 AGCAAAGTACAGGGCCGATC 60.108 55.000 0.00 0.00 0.00 3.69
104 105 1.200519 TAGCAAAGTACAGGGCCGAT 58.799 50.000 0.00 0.00 0.00 4.18
105 106 1.138266 GATAGCAAAGTACAGGGCCGA 59.862 52.381 0.00 0.00 0.00 5.54
106 107 1.583054 GATAGCAAAGTACAGGGCCG 58.417 55.000 0.00 0.00 0.00 6.13
107 108 1.583054 CGATAGCAAAGTACAGGGCC 58.417 55.000 0.00 0.00 0.00 5.80
126 127 4.489306 AGTCTAAATACTCAAGGGTGGC 57.511 45.455 0.00 0.00 0.00 5.01
133 134 6.530120 TCACCTTGCAAGTCTAAATACTCAA 58.470 36.000 24.35 0.00 0.00 3.02
189 190 2.298610 CTCTGACCCGAGTAGCATGTA 58.701 52.381 0.00 0.00 0.00 2.29
205 206 3.369147 CCGAAAGCATCACTTACACTCTG 59.631 47.826 0.00 0.00 37.75 3.35
209 210 2.527442 GCCGAAAGCATCACTTACAC 57.473 50.000 0.00 0.00 42.97 2.90
231 232 4.262249 GCACCCTAGATGGCTAAAGTCTAG 60.262 50.000 0.00 0.45 40.57 2.43
262 263 5.396362 CAGTGTGTTGTCAAACGAAATGATC 59.604 40.000 0.00 0.00 39.30 2.92
265 266 4.411327 ACAGTGTGTTGTCAAACGAAATG 58.589 39.130 0.00 0.00 39.30 2.32
266 267 4.695217 ACAGTGTGTTGTCAAACGAAAT 57.305 36.364 0.00 0.00 39.30 2.17
282 283 7.431084 GGTTGTGTAAGAACAATACAAACAGTG 59.569 37.037 0.00 0.00 42.75 3.66
285 286 7.466185 CGAGGTTGTGTAAGAACAATACAAACA 60.466 37.037 0.00 0.00 42.75 2.83
312 313 2.492010 GGAGGGGCCTAAACCTTGAAAA 60.492 50.000 0.84 0.00 37.18 2.29
332 333 6.262496 TCATGTAGTAACGGTGAGAGAATAGG 59.738 42.308 0.00 0.00 0.00 2.57
338 339 6.691818 GTGTAATCATGTAGTAACGGTGAGAG 59.308 42.308 0.00 0.00 0.00 3.20
344 345 8.474577 GTTATTCGTGTAATCATGTAGTAACGG 58.525 37.037 11.12 0.00 32.85 4.44
345 346 9.229784 AGTTATTCGTGTAATCATGTAGTAACG 57.770 33.333 0.00 0.00 33.63 3.18
350 351 9.210426 GCAAAAGTTATTCGTGTAATCATGTAG 57.790 33.333 0.00 0.00 32.85 2.74
363 364 7.306574 GGAGGAAAACAAAGCAAAAGTTATTCG 60.307 37.037 0.00 0.00 0.00 3.34
369 370 4.503910 GTGGAGGAAAACAAAGCAAAAGT 58.496 39.130 0.00 0.00 0.00 2.66
386 387 0.525668 CGAAGACCGGAATCGTGGAG 60.526 60.000 9.46 0.00 33.95 3.86
406 407 1.668919 CCACTTGCACACGTCGTCTAT 60.669 52.381 0.00 0.00 0.00 1.98
412 413 3.022287 CCACCACTTGCACACGTC 58.978 61.111 0.00 0.00 0.00 4.34
413 414 3.209097 GCCACCACTTGCACACGT 61.209 61.111 0.00 0.00 0.00 4.49
414 415 1.233950 TATGCCACCACTTGCACACG 61.234 55.000 0.00 0.00 40.88 4.49
415 416 0.240945 GTATGCCACCACTTGCACAC 59.759 55.000 0.00 0.00 40.88 3.82
421 422 2.224744 TGTGTCATGTATGCCACCACTT 60.225 45.455 3.88 0.00 35.94 3.16
424 425 2.239402 AGATGTGTCATGTATGCCACCA 59.761 45.455 3.88 0.00 35.94 4.17
430 431 9.578439 CAGGTACATATAGATGTGTCATGTATG 57.422 37.037 13.22 7.02 46.11 2.39
436 437 6.373759 AGACCAGGTACATATAGATGTGTCA 58.626 40.000 13.22 0.00 46.11 3.58
444 445 9.892130 AGAAAAGAAAAGACCAGGTACATATAG 57.108 33.333 0.00 0.00 0.00 1.31
454 455 6.535150 GGACCAAAAAGAAAAGAAAAGACCAG 59.465 38.462 0.00 0.00 0.00 4.00
455 456 6.014156 TGGACCAAAAAGAAAAGAAAAGACCA 60.014 34.615 0.00 0.00 0.00 4.02
459 874 9.558648 CAATTTGGACCAAAAAGAAAAGAAAAG 57.441 29.630 23.11 0.00 36.90 2.27
473 888 0.465705 TTTGGCGCAATTTGGACCAA 59.534 45.000 10.83 1.69 38.58 3.67
483 901 6.083098 ACATATAATGCTATTTTGGCGCAA 57.917 33.333 10.83 0.00 37.20 4.85
484 902 5.703978 ACATATAATGCTATTTTGGCGCA 57.296 34.783 10.83 0.00 38.14 6.09
522 941 8.912658 CATGTTTCTCAAATGAAAAGAGATGTG 58.087 33.333 0.00 0.00 38.14 3.21
524 943 9.687210 TTCATGTTTCTCAAATGAAAAGAGATG 57.313 29.630 0.00 0.00 37.37 2.90
587 1028 6.064060 AGAGACCATTTTTCATGTGTTCTGA 58.936 36.000 0.00 0.00 0.00 3.27
588 1029 6.016860 TGAGAGACCATTTTTCATGTGTTCTG 60.017 38.462 0.00 0.00 0.00 3.02
593 1034 6.323203 AGTTGAGAGACCATTTTTCATGTG 57.677 37.500 0.00 0.00 0.00 3.21
607 1048 7.461182 TTTTCTCCAAACAAAAGTTGAGAGA 57.539 32.000 0.00 0.00 33.89 3.10
643 1084 8.658840 AAGGTTGTTATTGCCCTATTTTCTTA 57.341 30.769 0.00 0.00 0.00 2.10
646 1087 8.615878 AAAAAGGTTGTTATTGCCCTATTTTC 57.384 30.769 0.00 0.00 0.00 2.29
670 1111 8.678593 AAGGTTGTTTTTGTCCAAGTTAAAAA 57.321 26.923 0.00 0.00 32.64 1.94
671 1112 8.678593 AAAGGTTGTTTTTGTCCAAGTTAAAA 57.321 26.923 0.00 0.00 0.00 1.52
672 1113 8.678593 AAAAGGTTGTTTTTGTCCAAGTTAAA 57.321 26.923 0.00 0.00 0.00 1.52
673 1114 8.678593 AAAAAGGTTGTTTTTGTCCAAGTTAA 57.321 26.923 0.00 0.00 31.05 2.01
674 1115 9.774413 TTAAAAAGGTTGTTTTTGTCCAAGTTA 57.226 25.926 5.86 0.00 34.01 2.24
675 1116 8.678593 TTAAAAAGGTTGTTTTTGTCCAAGTT 57.321 26.923 5.86 0.00 34.01 2.66
676 1117 8.726068 CATTAAAAAGGTTGTTTTTGTCCAAGT 58.274 29.630 5.86 0.00 34.01 3.16
677 1118 8.180920 CCATTAAAAAGGTTGTTTTTGTCCAAG 58.819 33.333 5.86 0.00 34.01 3.61
678 1119 7.883311 TCCATTAAAAAGGTTGTTTTTGTCCAA 59.117 29.630 5.86 0.00 34.01 3.53
679 1120 7.394816 TCCATTAAAAAGGTTGTTTTTGTCCA 58.605 30.769 5.86 0.00 34.01 4.02
680 1121 7.851387 TCCATTAAAAAGGTTGTTTTTGTCC 57.149 32.000 5.86 0.00 34.01 4.02
745 1186 2.593026 AGCCTGAACGATTCCCAAAAA 58.407 42.857 0.00 0.00 0.00 1.94
746 1187 2.286365 AGCCTGAACGATTCCCAAAA 57.714 45.000 0.00 0.00 0.00 2.44
747 1188 3.078837 GTTAGCCTGAACGATTCCCAAA 58.921 45.455 0.00 0.00 0.00 3.28
748 1189 2.304761 AGTTAGCCTGAACGATTCCCAA 59.695 45.455 0.00 0.00 34.36 4.12
749 1190 1.906574 AGTTAGCCTGAACGATTCCCA 59.093 47.619 0.00 0.00 34.36 4.37
750 1191 2.168728 AGAGTTAGCCTGAACGATTCCC 59.831 50.000 0.00 0.00 34.36 3.97
751 1192 3.528597 AGAGTTAGCCTGAACGATTCC 57.471 47.619 0.00 0.00 34.36 3.01
752 1193 5.044558 CCTAAGAGTTAGCCTGAACGATTC 58.955 45.833 0.00 0.00 34.36 2.52
753 1194 4.141914 CCCTAAGAGTTAGCCTGAACGATT 60.142 45.833 0.00 0.00 34.36 3.34
754 1195 3.385111 CCCTAAGAGTTAGCCTGAACGAT 59.615 47.826 0.00 0.00 34.36 3.73
755 1196 2.758979 CCCTAAGAGTTAGCCTGAACGA 59.241 50.000 0.00 0.00 34.36 3.85
756 1197 2.738964 GCCCTAAGAGTTAGCCTGAACG 60.739 54.545 0.00 0.00 34.36 3.95
757 1198 2.502130 AGCCCTAAGAGTTAGCCTGAAC 59.498 50.000 0.00 0.00 31.81 3.18
758 1199 2.834113 AGCCCTAAGAGTTAGCCTGAA 58.166 47.619 0.00 0.00 31.81 3.02
759 1200 2.552093 AGCCCTAAGAGTTAGCCTGA 57.448 50.000 0.00 0.00 31.81 3.86
760 1201 2.365941 GGTAGCCCTAAGAGTTAGCCTG 59.634 54.545 0.00 0.00 31.81 4.85
761 1202 2.023307 TGGTAGCCCTAAGAGTTAGCCT 60.023 50.000 0.00 0.00 31.81 4.58
762 1203 2.395619 TGGTAGCCCTAAGAGTTAGCC 58.604 52.381 0.00 0.00 31.81 3.93
805 1536 2.228545 TGGGCCAAATTGTATGCTCA 57.771 45.000 2.13 0.00 0.00 4.26
901 1633 2.660802 GGGTTCCTTTCTCGCGGA 59.339 61.111 6.13 0.00 0.00 5.54
939 1671 1.348594 GCTGTAAGATTCGTGCGGC 59.651 57.895 5.83 5.83 34.07 6.53
1091 1823 1.461091 CCAGCCCGCCTACGAATAGA 61.461 60.000 0.00 0.00 43.93 1.98
1276 2008 1.152673 GGAGATGGTTGGATGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
1301 2057 3.951663 ACAAACCCCAATCTGCTACTAC 58.048 45.455 0.00 0.00 0.00 2.73
1340 2096 0.099436 CACCAAAGGCGCTCATTAGC 59.901 55.000 7.64 0.00 45.86 3.09
1365 2121 2.876581 AGGAAGGCCAAAATCTCGTTT 58.123 42.857 5.01 0.00 36.29 3.60
1381 2137 5.466728 GCGAGATATCAAACAGCAATAGGAA 59.533 40.000 5.32 0.00 0.00 3.36
1434 2190 4.390603 TGTACTACACGCAAATTGACATCC 59.609 41.667 0.00 0.00 0.00 3.51
1440 2196 4.083003 ACCCATTGTACTACACGCAAATTG 60.083 41.667 0.00 0.00 0.00 2.32
1486 2242 1.499007 TCCTTGGCCTTCTCCAGTTTT 59.501 47.619 3.32 0.00 37.44 2.43
1565 2321 1.930908 ATTTCTTGAGCAGCTGCCGC 61.931 55.000 34.39 26.07 43.38 6.53
1566 2322 0.179171 CATTTCTTGAGCAGCTGCCG 60.179 55.000 34.39 19.98 43.38 5.69
1599 2355 0.321122 CTCCTCCTGCTTGTCCACAC 60.321 60.000 0.00 0.00 0.00 3.82
1740 2502 2.598192 CGCGCGATTTGGAAAATTCATT 59.402 40.909 28.94 0.00 0.00 2.57
1773 2535 6.017440 GTCACACCTATTTGCACAGACTAAAA 60.017 38.462 0.00 0.00 0.00 1.52
1916 2680 6.599244 CCTGCTAAGTTTGTCTCATATTCCAA 59.401 38.462 0.00 0.00 0.00 3.53
1917 2681 6.115446 CCTGCTAAGTTTGTCTCATATTCCA 58.885 40.000 0.00 0.00 0.00 3.53
2028 2793 4.647424 TTTACCCTTGCTGTTTCTGTTG 57.353 40.909 0.00 0.00 0.00 3.33
2060 2825 8.113062 GCTATTTTGATCGATATACTGCATGAC 58.887 37.037 0.00 0.00 0.00 3.06
2074 2839 2.096335 TGCACAGCTGCTATTTTGATCG 59.904 45.455 15.27 0.00 44.57 3.69
2138 2903 5.263599 TCATTGGTTAGGAGAATGCATGTT 58.736 37.500 0.00 0.00 0.00 2.71
2170 2935 1.780503 AAGGCAAAGGTTTCAGCTGT 58.219 45.000 14.67 0.00 0.00 4.40
2242 3007 4.155826 CAGTCGCAGAAATGAATTGGGTAA 59.844 41.667 0.00 0.00 39.69 2.85
2347 3112 7.698506 ACTCATCACAGAATTCATGATGTTT 57.301 32.000 31.48 23.31 46.45 2.83
2488 3256 0.671251 CTGTCTCCGTATCAGAGGGC 59.329 60.000 0.00 0.00 32.71 5.19
2527 3295 5.296283 TGTTGTTTCTTCCATTGGCAAATTG 59.704 36.000 3.01 0.00 0.00 2.32
2528 3296 5.435291 TGTTGTTTCTTCCATTGGCAAATT 58.565 33.333 3.01 0.00 0.00 1.82
2599 3367 6.378661 TCCAATTCTTCTTCAGAAGGATCA 57.621 37.500 15.17 0.00 46.78 2.92
2621 3389 5.587443 TGTTGATCACAAGGTCATCATCATC 59.413 40.000 0.00 0.00 36.64 2.92
2622 3390 5.503002 TGTTGATCACAAGGTCATCATCAT 58.497 37.500 0.00 0.00 36.64 2.45
2623 3391 4.909001 TGTTGATCACAAGGTCATCATCA 58.091 39.130 0.00 0.00 36.64 3.07
2717 3485 5.567138 ATTCAGGCAAGTAACTGCAATAC 57.433 39.130 1.92 1.92 44.52 1.89
2765 3533 8.190122 GGAGTGTTATTGCACATAATTGAATGA 58.810 33.333 0.00 0.00 41.52 2.57
2827 3595 5.034554 TCTCATCAAAATGCTGACGTTTC 57.965 39.130 0.00 0.00 33.82 2.78
2876 3644 8.478877 GTTTCTAGGTTCAGATAAATCCTCTGA 58.521 37.037 0.00 0.00 45.58 3.27
2903 3671 6.128063 GCATTCATTGAAGTAGACTGCTTCTT 60.128 38.462 26.99 15.69 41.94 2.52
2933 3701 2.004589 AGACTTCCCTGTAGTCCTCCT 58.995 52.381 0.00 0.00 42.35 3.69
2934 3702 2.535836 AGACTTCCCTGTAGTCCTCC 57.464 55.000 0.00 0.00 42.35 4.30
2935 3703 3.617775 GCAAAGACTTCCCTGTAGTCCTC 60.618 52.174 0.00 0.00 42.35 3.71
3034 3805 7.545965 GCAGAACTTTTAGCTCTATCAAGTACA 59.454 37.037 0.00 0.00 0.00 2.90
3079 3850 1.000506 GTGGAACGACCTGTTAGAGCA 59.999 52.381 0.00 0.00 42.09 4.26
3142 3913 2.024369 AGTCCACACAGAACCCCTTTTT 60.024 45.455 0.00 0.00 0.00 1.94
3147 3918 0.035458 CTGAGTCCACACAGAACCCC 59.965 60.000 0.00 0.00 36.82 4.95
3208 3979 7.670916 GCAATATCTGCGATATACTGAAAGAC 58.329 38.462 10.19 0.00 42.37 3.01
3289 4060 2.892425 CTCCTGGATTCGGTGCGC 60.892 66.667 0.00 0.00 0.00 6.09
3448 4219 1.568612 CCTTGTTGCTCACGTCGCAT 61.569 55.000 9.58 0.00 37.22 4.73
3449 4220 2.243957 CCTTGTTGCTCACGTCGCA 61.244 57.895 5.02 5.02 35.22 5.10
3450 4221 0.942410 TACCTTGTTGCTCACGTCGC 60.942 55.000 0.00 0.00 0.00 5.19
3456 4227 3.740115 GGTTCTTCTACCTTGTTGCTCA 58.260 45.455 0.00 0.00 35.23 4.26
3605 4376 1.903877 CTGGAGTTGCTGGATCCGGT 61.904 60.000 21.88 1.34 35.18 5.28
3616 4387 1.339535 GGCTTTCCTCTCCTGGAGTTG 60.340 57.143 22.50 15.89 40.30 3.16
3660 4431 2.554032 CAAGATGTGACCCCAAGAACAC 59.446 50.000 0.00 0.00 0.00 3.32
3709 4480 2.968655 GCGTGATTGTTCGTTTGGTAAC 59.031 45.455 0.00 0.00 0.00 2.50
3761 4532 8.715191 ATGTAAAACAAAATTTGCAAGACTCA 57.285 26.923 5.52 0.00 38.19 3.41
3881 4652 5.572126 GTGATTTACTGAGGTCTCACGTAAC 59.428 44.000 15.63 10.19 35.28 2.50
4064 4838 0.677842 GCGACCCTCCGTATAACCAT 59.322 55.000 0.00 0.00 0.00 3.55
4066 4840 1.008079 CGCGACCCTCCGTATAACC 60.008 63.158 0.00 0.00 0.00 2.85
4068 4842 1.168407 CCTCGCGACCCTCCGTATAA 61.168 60.000 3.71 0.00 0.00 0.98
4069 4843 1.598962 CCTCGCGACCCTCCGTATA 60.599 63.158 3.71 0.00 0.00 1.47
4148 5892 1.004277 GGGGGCGCCTATTCATTCATA 59.996 52.381 28.56 0.00 0.00 2.15
4165 5909 3.072211 GAGAACGTCAGTTTTAAGGGGG 58.928 50.000 0.00 0.00 41.34 5.40
4245 5989 2.038164 AGGTTCCTTTTAGGTCGTGGTC 59.962 50.000 0.00 0.00 36.53 4.02
4261 6005 2.491693 CACCTCTGTCTCTCTCAGGTTC 59.508 54.545 0.00 0.00 34.15 3.62
4267 6011 4.502962 CAAAATCCACCTCTGTCTCTCTC 58.497 47.826 0.00 0.00 0.00 3.20
4268 6012 3.262915 CCAAAATCCACCTCTGTCTCTCT 59.737 47.826 0.00 0.00 0.00 3.10
4269 6013 3.008485 ACCAAAATCCACCTCTGTCTCTC 59.992 47.826 0.00 0.00 0.00 3.20
4270 6014 2.982488 ACCAAAATCCACCTCTGTCTCT 59.018 45.455 0.00 0.00 0.00 3.10
4332 6076 4.602696 GCGAGATGCGTGCATGGC 62.603 66.667 12.81 8.96 43.41 4.40
4348 6092 1.826487 GAGGAGGAGGACGAGAGGC 60.826 68.421 0.00 0.00 39.70 4.70
4465 6209 9.454859 GGAGATGATCGGGAGAAATTAAATATT 57.545 33.333 0.00 0.00 45.37 1.28
4466 6210 8.049721 GGGAGATGATCGGGAGAAATTAAATAT 58.950 37.037 0.00 0.00 45.37 1.28
4467 6211 7.237679 AGGGAGATGATCGGGAGAAATTAAATA 59.762 37.037 0.00 0.00 45.37 1.40
4468 6212 6.044871 AGGGAGATGATCGGGAGAAATTAAAT 59.955 38.462 0.00 0.00 45.37 1.40
4469 6213 5.369699 AGGGAGATGATCGGGAGAAATTAAA 59.630 40.000 0.00 0.00 45.37 1.52
4470 6214 4.907875 AGGGAGATGATCGGGAGAAATTAA 59.092 41.667 0.00 0.00 45.37 1.40
4503 6253 5.798132 TCCTCATGGATAATGAATCGGAAG 58.202 41.667 0.00 0.00 44.77 3.46
4504 6254 5.823861 TCCTCATGGATAATGAATCGGAA 57.176 39.130 0.00 0.00 44.77 4.30
4551 6301 1.068083 CATCGTCCTGATCCACGGG 59.932 63.158 8.57 0.00 45.93 5.28
4648 6402 2.027653 CAGAACAGGAAAGGAGAGGGAC 60.028 54.545 0.00 0.00 0.00 4.46
4652 6406 2.847327 TGCAGAACAGGAAAGGAGAG 57.153 50.000 0.00 0.00 0.00 3.20
4675 6430 8.816144 CAATTAATTATCGGTTTGATTTGGGTG 58.184 33.333 0.00 0.00 38.57 4.61
4703 6504 8.967664 ATTGCCATGTTAATTATTGCAATCTT 57.032 26.923 16.86 13.13 40.67 2.40
4778 6658 5.990386 CCATCTGTGAATCAATAGAGACCAG 59.010 44.000 5.05 0.00 0.00 4.00
4783 6663 5.990386 CCTGTCCATCTGTGAATCAATAGAG 59.010 44.000 5.05 0.00 0.00 2.43
4868 6748 1.575244 TGATGAATGCGCTAGACAGC 58.425 50.000 9.73 7.33 44.90 4.40
4870 6750 4.320608 TGTATGATGAATGCGCTAGACA 57.679 40.909 9.73 4.21 0.00 3.41
4877 6762 5.874895 ATGAGGAATGTATGATGAATGCG 57.125 39.130 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.