Multiple sequence alignment - TraesCS6D01G310300

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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 TraesCS6D01G310300 chr6D 100.000 5254 0 0 1 5254 420390065 420395318 0.000000e+00 9703
1 TraesCS6D01G310300 chr6B 84.200 1924 174 68 1494 3345 633533681 633535546 0.000000e+00 1749
2 TraesCS6D01G310300 chr6B 93.367 1191 47 17 3575 4745 633535649 633536827 0.000000e+00 1733
3 TraesCS6D01G310300 chr6B 89.583 1008 57 14 529 1501 633532659 633533653 0.000000e+00 1236
4 TraesCS6D01G310300 chr6B 88.566 516 37 12 4735 5235 633537321 633537829 1.620000e-169 606
5 TraesCS6D01G310300 chr6B 86.557 424 13 16 1 416 633532213 633532600 1.350000e-115 427
6 TraesCS6D01G310300 chr6B 93.333 105 7 0 1680 1784 633533942 633534046 7.040000e-34 156
7 TraesCS6D01G310300 chr6A 93.059 1167 42 18 3575 4722 563377450 563378596 0.000000e+00 1670
8 TraesCS6D01G310300 chr6A 89.238 1338 75 28 531 1808 563374235 563375563 0.000000e+00 1609
9 TraesCS6D01G310300 chr6A 84.975 1411 128 46 2156 3529 563376096 563377459 0.000000e+00 1354
10 TraesCS6D01G310300 chr6A 91.022 802 51 6 992 1780 549489394 549488601 0.000000e+00 1062
11 TraesCS6D01G310300 chr6A 80.590 407 41 24 4707 5104 563379304 563379681 4.010000e-71 279
12 TraesCS6D01G310300 chr6A 78.356 365 33 27 113 444 563373848 563374199 1.490000e-45 195
13 TraesCS6D01G310300 chr3B 91.035 792 61 3 992 1780 712415582 712414798 0.000000e+00 1061
14 TraesCS6D01G310300 chr3B 87.399 865 81 15 2156 3014 532209841 532208999 0.000000e+00 968
15 TraesCS6D01G310300 chr3B 80.180 333 40 14 989 1320 31992325 31992632 5.290000e-55 226
16 TraesCS6D01G310300 chr7A 90.762 801 55 4 992 1780 576476179 576476972 0.000000e+00 1051
17 TraesCS6D01G310300 chr7A 90.000 800 61 6 993 1780 528227311 528226519 0.000000e+00 1016
18 TraesCS6D01G310300 chr7A 87.847 864 78 21 2156 3014 401560989 401560148 0.000000e+00 989
19 TraesCS6D01G310300 chr7A 83.090 479 51 19 2541 3014 393333383 393332930 4.900000e-110 409
20 TraesCS6D01G310300 chr5B 88.760 863 72 16 2156 3014 237818303 237817462 0.000000e+00 1033
21 TraesCS6D01G310300 chr5B 87.168 865 83 15 2156 3014 480307994 480307152 0.000000e+00 957
22 TraesCS6D01G310300 chr5B 81.279 219 38 2 4324 4542 578848442 578848227 1.940000e-39 174
23 TraesCS6D01G310300 chr1B 88.065 863 78 18 2156 3014 646747345 646748186 0.000000e+00 1000
24 TraesCS6D01G310300 chr2B 89.263 801 67 8 992 1780 98484934 98484141 0.000000e+00 985
25 TraesCS6D01G310300 chr3A 87.283 865 82 15 2156 3014 35852007 35852849 0.000000e+00 963
26 TraesCS6D01G310300 chr2A 85.791 936 95 17 2156 3085 92975846 92974943 0.000000e+00 957
27 TraesCS6D01G310300 chr1A 85.684 936 96 17 2156 3085 458922529 458921626 0.000000e+00 952
28 TraesCS6D01G310300 chr2D 90.244 123 12 0 1201 1323 404380002 404380124 1.510000e-35 161


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 TraesCS6D01G310300 chr6D 420390065 420395318 5253 False 9703.0 9703 100.000000 1 5254 1 chr6D.!!$F1 5253
1 TraesCS6D01G310300 chr6B 633532213 633537829 5616 False 984.5 1749 89.267667 1 5235 6 chr6B.!!$F1 5234
2 TraesCS6D01G310300 chr6A 549488601 549489394 793 True 1062.0 1062 91.022000 992 1780 1 chr6A.!!$R1 788
3 TraesCS6D01G310300 chr6A 563373848 563379681 5833 False 1021.4 1670 85.243600 113 5104 5 chr6A.!!$F1 4991
4 TraesCS6D01G310300 chr3B 712414798 712415582 784 True 1061.0 1061 91.035000 992 1780 1 chr3B.!!$R2 788
5 TraesCS6D01G310300 chr3B 532208999 532209841 842 True 968.0 968 87.399000 2156 3014 1 chr3B.!!$R1 858
6 TraesCS6D01G310300 chr7A 576476179 576476972 793 False 1051.0 1051 90.762000 992 1780 1 chr7A.!!$F1 788
7 TraesCS6D01G310300 chr7A 528226519 528227311 792 True 1016.0 1016 90.000000 993 1780 1 chr7A.!!$R3 787
8 TraesCS6D01G310300 chr7A 401560148 401560989 841 True 989.0 989 87.847000 2156 3014 1 chr7A.!!$R2 858
9 TraesCS6D01G310300 chr5B 237817462 237818303 841 True 1033.0 1033 88.760000 2156 3014 1 chr5B.!!$R1 858
10 TraesCS6D01G310300 chr5B 480307152 480307994 842 True 957.0 957 87.168000 2156 3014 1 chr5B.!!$R2 858
11 TraesCS6D01G310300 chr1B 646747345 646748186 841 False 1000.0 1000 88.065000 2156 3014 1 chr1B.!!$F1 858
12 TraesCS6D01G310300 chr2B 98484141 98484934 793 True 985.0 985 89.263000 992 1780 1 chr2B.!!$R1 788
13 TraesCS6D01G310300 chr3A 35852007 35852849 842 False 963.0 963 87.283000 2156 3014 1 chr3A.!!$F1 858
14 TraesCS6D01G310300 chr2A 92974943 92975846 903 True 957.0 957 85.791000 2156 3085 1 chr2A.!!$R1 929
15 TraesCS6D01G310300 chr1A 458921626 458922529 903 True 952.0 952 85.684000 2156 3085 1 chr1A.!!$R1 929

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
779 859 0.104671 CCAACCAACCACAAGCCAAG 59.895 55.000 0.00 0.0 0.00 3.61 F
1918 2279 1.003580 CAGTCCCAACTGTATGGCTGT 59.996 52.381 0.00 0.0 46.52 4.40 F
2790 3241 0.249996 ACAAATGTGGCCTGCTTTGC 60.250 50.000 18.38 0.0 33.03 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2647 0.251916 TCGCGGGGTCAATCTGAAAT 59.748 50.0 6.13 0.0 0.00 2.17 R
3394 3878 0.960364 TGGAAGCGGATTCTGGCAAC 60.960 55.0 5.91 0.0 38.07 4.17 R
4668 5187 0.383949 TGCCCGAACAAAACAAGAGC 59.616 50.0 0.00 0.0 0.00 4.09 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
53 55 4.710695 TGTCAGCGGCGTGTACGG 62.711 66.667 9.37 0.00 40.23 4.02
94 96 6.436843 AACAACGTCTTGAGACTTTTTCAT 57.563 33.333 9.28 0.00 42.66 2.57
95 97 6.049263 ACAACGTCTTGAGACTTTTTCATC 57.951 37.500 9.28 0.00 42.66 2.92
96 98 5.584649 ACAACGTCTTGAGACTTTTTCATCA 59.415 36.000 9.28 0.00 42.66 3.07
100 102 7.535139 ACGTCTTGAGACTTTTTCATCAAAAA 58.465 30.769 9.28 0.00 42.66 1.94
190 199 3.071023 CCGGCTTGAGGTAGATTTCCATA 59.929 47.826 0.00 0.00 0.00 2.74
231 243 0.944386 CAAACCGTCCCAACAGACAG 59.056 55.000 0.00 0.00 36.52 3.51
254 266 1.228215 AAGCTCCTCTCCCTCTCCCT 61.228 60.000 0.00 0.00 0.00 4.20
290 302 6.183360 TGCTTTCATTTGACTTGTGCTTTTTC 60.183 34.615 0.00 0.00 0.00 2.29
304 321 9.657419 CTTGTGCTTTTTCCTTGGAAATAATAT 57.343 29.630 14.66 0.00 0.00 1.28
315 341 8.429641 TCCTTGGAAATAATATTCGTAGCTCTT 58.570 33.333 0.00 0.00 0.00 2.85
318 344 8.589335 TGGAAATAATATTCGTAGCTCTTCAC 57.411 34.615 0.00 0.00 0.00 3.18
326 352 2.273179 TAGCTCTTCACGTGCCGGT 61.273 57.895 11.67 6.89 32.66 5.28
335 361 2.030562 CGTGCCGGTCTTGAAGGT 59.969 61.111 1.90 0.00 0.00 3.50
337 363 2.281484 TGCCGGTCTTGAAGGTGC 60.281 61.111 1.90 0.00 0.00 5.01
338 364 2.281484 GCCGGTCTTGAAGGTGCA 60.281 61.111 1.90 0.00 0.00 4.57
339 365 2.617274 GCCGGTCTTGAAGGTGCAC 61.617 63.158 8.80 8.80 0.00 4.57
341 367 2.317609 CGGTCTTGAAGGTGCACCG 61.318 63.158 29.68 15.52 43.71 4.94
342 368 1.070786 GGTCTTGAAGGTGCACCGA 59.929 57.895 29.68 17.69 42.08 4.69
345 371 0.531974 TCTTGAAGGTGCACCGACAC 60.532 55.000 29.68 20.74 42.08 3.67
347 373 1.092921 TTGAAGGTGCACCGACACAC 61.093 55.000 29.68 17.51 42.55 3.82
465 514 3.760035 GCGGAGAACTCGGCCAGA 61.760 66.667 18.94 0.00 46.21 3.86
466 515 2.182030 CGGAGAACTCGGCCAGAC 59.818 66.667 2.24 0.46 0.00 3.51
467 516 2.579738 GGAGAACTCGGCCAGACC 59.420 66.667 2.24 0.00 0.00 3.85
468 517 2.579738 GAGAACTCGGCCAGACCC 59.420 66.667 2.24 0.00 33.26 4.46
709 771 7.011389 CCAAAGTTTTCTTCACTTCCCATTTTC 59.989 37.037 0.00 0.00 39.48 2.29
711 773 7.423844 AGTTTTCTTCACTTCCCATTTTCTT 57.576 32.000 0.00 0.00 0.00 2.52
716 778 5.470098 TCTTCACTTCCCATTTTCTTTCTCG 59.530 40.000 0.00 0.00 0.00 4.04
720 782 4.278419 ACTTCCCATTTTCTTTCTCGTTGG 59.722 41.667 0.00 0.00 0.00 3.77
752 832 1.407656 TACCATCCACGCCCCAGATC 61.408 60.000 0.00 0.00 0.00 2.75
762 842 3.016971 CCCAGATCCCAGGCACCA 61.017 66.667 0.00 0.00 0.00 4.17
763 843 2.615465 CCCAGATCCCAGGCACCAA 61.615 63.158 0.00 0.00 0.00 3.67
764 844 1.379044 CCAGATCCCAGGCACCAAC 60.379 63.158 0.00 0.00 0.00 3.77
765 845 1.379044 CAGATCCCAGGCACCAACC 60.379 63.158 0.00 0.00 0.00 3.77
766 846 1.852157 AGATCCCAGGCACCAACCA 60.852 57.895 0.00 0.00 0.00 3.67
767 847 1.076549 GATCCCAGGCACCAACCAA 59.923 57.895 0.00 0.00 0.00 3.67
768 848 1.228862 ATCCCAGGCACCAACCAAC 60.229 57.895 0.00 0.00 0.00 3.77
769 849 2.730129 ATCCCAGGCACCAACCAACC 62.730 60.000 0.00 0.00 0.00 3.77
770 850 2.123511 CCAGGCACCAACCAACCA 60.124 61.111 0.00 0.00 0.00 3.67
771 851 2.498056 CCAGGCACCAACCAACCAC 61.498 63.158 0.00 0.00 0.00 4.16
772 852 1.756172 CAGGCACCAACCAACCACA 60.756 57.895 0.00 0.00 0.00 4.17
773 853 1.000993 AGGCACCAACCAACCACAA 59.999 52.632 0.00 0.00 0.00 3.33
774 854 1.042559 AGGCACCAACCAACCACAAG 61.043 55.000 0.00 0.00 0.00 3.16
775 855 1.227234 GCACCAACCAACCACAAGC 60.227 57.895 0.00 0.00 0.00 4.01
776 856 1.441311 CACCAACCAACCACAAGCC 59.559 57.895 0.00 0.00 0.00 4.35
779 859 0.104671 CCAACCAACCACAAGCCAAG 59.895 55.000 0.00 0.00 0.00 3.61
782 862 1.364901 CCAACCACAAGCCAAGCAG 59.635 57.895 0.00 0.00 0.00 4.24
802 891 3.550431 ACACTGGACACTGCCGCT 61.550 61.111 0.00 0.00 0.00 5.52
850 949 6.068140 ACCACCAATACCCTAATAATTTGGGA 60.068 38.462 14.88 0.00 43.47 4.37
1424 1534 1.270305 GGATGCGGATTTCGATCTCCA 60.270 52.381 12.70 0.00 42.43 3.86
1588 1760 3.114616 CGCTCGCAGTTGAGTGGG 61.115 66.667 0.00 0.00 41.65 4.61
1607 1779 3.197766 TGGGTTGCAGTTCCAGTAGATAG 59.802 47.826 6.91 0.00 0.00 2.08
1608 1780 3.451178 GGGTTGCAGTTCCAGTAGATAGA 59.549 47.826 6.91 0.00 0.00 1.98
1609 1781 4.101741 GGGTTGCAGTTCCAGTAGATAGAT 59.898 45.833 6.91 0.00 0.00 1.98
1610 1782 5.304614 GGGTTGCAGTTCCAGTAGATAGATA 59.695 44.000 6.91 0.00 0.00 1.98
1696 1894 7.557724 TCATCGGAGTGGTACAAATTATGTTA 58.442 34.615 0.00 0.00 44.16 2.41
1739 1938 6.016276 AGGCTTTTACTTGGTTCTGTATTGTG 60.016 38.462 0.00 0.00 0.00 3.33
1784 2041 6.677913 TGTGCAATTCTTAGGCTTTTACTTC 58.322 36.000 0.00 0.00 0.00 3.01
1785 2042 6.490040 TGTGCAATTCTTAGGCTTTTACTTCT 59.510 34.615 0.00 0.00 0.00 2.85
1786 2043 6.803807 GTGCAATTCTTAGGCTTTTACTTCTG 59.196 38.462 0.00 0.00 0.00 3.02
1787 2044 6.490040 TGCAATTCTTAGGCTTTTACTTCTGT 59.510 34.615 0.00 0.00 0.00 3.41
1791 2048 8.691661 ATTCTTAGGCTTTTACTTCTGTTCAA 57.308 30.769 0.00 0.00 0.00 2.69
1814 2071 9.904198 TCAATATAAATTCATGTCTGAACCTGA 57.096 29.630 0.00 0.00 43.92 3.86
1819 2076 9.911788 ATAAATTCATGTCTGAACCTGAACTAT 57.088 29.630 0.00 0.00 43.92 2.12
1839 2121 9.092876 GAACTATATAATCAAGTCTATGCCTGC 57.907 37.037 0.00 0.00 0.00 4.85
1876 2158 8.698210 AGTTACCCGTGATCACTTTATATGTAA 58.302 33.333 22.95 14.72 0.00 2.41
1918 2279 1.003580 CAGTCCCAACTGTATGGCTGT 59.996 52.381 0.00 0.00 46.52 4.40
1986 2378 7.856145 AATGTTGTTTATTTGAAAAGTGGCA 57.144 28.000 0.00 0.00 0.00 4.92
1993 2385 7.116090 TGTTTATTTGAAAAGTGGCATTGATCG 59.884 33.333 0.00 0.00 0.00 3.69
1995 2387 4.424061 TTGAAAAGTGGCATTGATCGAG 57.576 40.909 0.00 0.00 0.00 4.04
2083 2477 9.162764 CAGTTAGCATTGTACATTTAAGTACCT 57.837 33.333 0.00 0.00 42.84 3.08
2109 2503 5.982890 ACTTTGATTTGGGATTACTGTGG 57.017 39.130 0.00 0.00 0.00 4.17
2119 2513 3.545703 GGATTACTGTGGGAGATGGTTG 58.454 50.000 0.00 0.00 0.00 3.77
2347 2795 2.562738 GGCTTGCAAGTTTGGGTTCTAT 59.437 45.455 26.55 0.00 0.00 1.98
2416 2866 3.512680 CGTGAAGTACAAGACCCTGATC 58.487 50.000 0.00 0.00 0.00 2.92
2560 3010 3.415212 CAAGTTCATCAAAGCTGAGGGA 58.585 45.455 0.00 0.00 34.07 4.20
2579 3029 2.945668 GGAGCTGCTGGGTAAGTAAATG 59.054 50.000 7.01 0.00 0.00 2.32
2587 3037 2.916934 TGGGTAAGTAAATGTCCCAGCT 59.083 45.455 0.00 0.00 42.52 4.24
2593 3043 3.679389 AGTAAATGTCCCAGCTGACTTG 58.321 45.455 17.39 0.00 36.21 3.16
2601 3051 2.951642 TCCCAGCTGACTTGAAAACTTG 59.048 45.455 17.39 0.00 0.00 3.16
2604 3054 3.629398 CCAGCTGACTTGAAAACTTGACT 59.371 43.478 17.39 0.00 0.00 3.41
2646 3097 7.208064 TGATCCTAGCCCTAACTTTTATTGT 57.792 36.000 0.00 0.00 0.00 2.71
2727 3178 7.849804 TGTAAGTGCTTTCTCTTATCATTCC 57.150 36.000 0.00 0.00 32.81 3.01
2790 3241 0.249996 ACAAATGTGGCCTGCTTTGC 60.250 50.000 18.38 0.00 33.03 3.68
2826 3280 2.551270 AGCTGGTCCTCCTGTTTCATA 58.449 47.619 0.00 0.00 35.49 2.15
2829 3283 4.101741 AGCTGGTCCTCCTGTTTCATATAC 59.898 45.833 0.00 0.00 35.49 1.47
2833 3287 5.724370 TGGTCCTCCTGTTTCATATACTTGA 59.276 40.000 0.00 0.00 34.23 3.02
2835 3291 6.351881 GGTCCTCCTGTTTCATATACTTGACA 60.352 42.308 0.00 0.00 0.00 3.58
2836 3292 6.535508 GTCCTCCTGTTTCATATACTTGACAC 59.464 42.308 0.00 0.00 0.00 3.67
2837 3293 6.440647 TCCTCCTGTTTCATATACTTGACACT 59.559 38.462 0.00 0.00 29.64 3.55
2838 3294 6.536582 CCTCCTGTTTCATATACTTGACACTG 59.463 42.308 0.00 0.00 29.64 3.66
2854 3310 7.872483 ACTTGACACTGTTTGTTTTCTTTGATT 59.128 29.630 0.00 0.00 39.17 2.57
2855 3313 7.579589 TGACACTGTTTGTTTTCTTTGATTG 57.420 32.000 0.00 0.00 39.17 2.67
2856 3314 7.151308 TGACACTGTTTGTTTTCTTTGATTGT 58.849 30.769 0.00 0.00 39.17 2.71
2857 3315 7.655328 TGACACTGTTTGTTTTCTTTGATTGTT 59.345 29.630 0.00 0.00 39.17 2.83
2886 3349 8.275015 TGTGATGTTTTGTTACTTTCTCTTCA 57.725 30.769 0.00 0.00 0.00 3.02
2892 3355 6.677781 TTTGTTACTTTCTCTTCACCTGTG 57.322 37.500 0.00 0.00 0.00 3.66
2893 3356 5.607939 TGTTACTTTCTCTTCACCTGTGA 57.392 39.130 0.00 0.00 37.91 3.58
2894 3357 5.357257 TGTTACTTTCTCTTCACCTGTGAC 58.643 41.667 0.00 0.00 39.66 3.67
2895 3358 3.477210 ACTTTCTCTTCACCTGTGACC 57.523 47.619 0.00 0.00 39.66 4.02
2896 3359 3.041946 ACTTTCTCTTCACCTGTGACCT 58.958 45.455 0.00 0.00 39.66 3.85
2897 3360 3.456277 ACTTTCTCTTCACCTGTGACCTT 59.544 43.478 0.00 0.00 39.66 3.50
2898 3361 3.475566 TTCTCTTCACCTGTGACCTTG 57.524 47.619 0.00 0.00 39.66 3.61
2899 3362 1.070758 TCTCTTCACCTGTGACCTTGC 59.929 52.381 0.00 0.00 39.66 4.01
2900 3363 1.071385 CTCTTCACCTGTGACCTTGCT 59.929 52.381 0.00 0.00 39.66 3.91
2901 3364 1.202687 TCTTCACCTGTGACCTTGCTG 60.203 52.381 0.00 0.00 39.66 4.41
2902 3365 0.546122 TTCACCTGTGACCTTGCTGT 59.454 50.000 0.00 0.00 39.66 4.40
2925 3388 9.973450 CTGTATGAGCAAACTACTAGTATCATT 57.027 33.333 15.90 4.64 0.00 2.57
3014 3477 8.757982 AGCTTATGGACATTATTCATTGACTT 57.242 30.769 0.00 0.00 0.00 3.01
3015 3478 9.851686 AGCTTATGGACATTATTCATTGACTTA 57.148 29.630 0.00 0.00 0.00 2.24
3062 3525 6.147821 ACTCGATAGTTGTGATGGAAGTTTTG 59.852 38.462 0.00 0.00 29.00 2.44
3066 3529 7.117812 CGATAGTTGTGATGGAAGTTTTGTAGT 59.882 37.037 0.00 0.00 0.00 2.73
3093 3556 4.843728 ACTTCAAGTTTCACCTCTCACAA 58.156 39.130 0.00 0.00 0.00 3.33
3096 3559 5.560966 TCAAGTTTCACCTCTCACAAAAC 57.439 39.130 0.00 0.00 0.00 2.43
3098 3561 5.652014 TCAAGTTTCACCTCTCACAAAACAT 59.348 36.000 0.00 0.00 33.37 2.71
3102 3565 8.237811 AGTTTCACCTCTCACAAAACATAAAT 57.762 30.769 0.00 0.00 33.37 1.40
3107 3570 9.109393 TCACCTCTCACAAAACATAAATATAGC 57.891 33.333 0.00 0.00 0.00 2.97
3108 3571 8.345565 CACCTCTCACAAAACATAAATATAGCC 58.654 37.037 0.00 0.00 0.00 3.93
3109 3572 8.052748 ACCTCTCACAAAACATAAATATAGCCA 58.947 33.333 0.00 0.00 0.00 4.75
3111 3574 9.888878 CTCTCACAAAACATAAATATAGCCATG 57.111 33.333 0.00 0.00 0.00 3.66
3112 3575 8.352201 TCTCACAAAACATAAATATAGCCATGC 58.648 33.333 0.00 0.00 0.00 4.06
3136 3602 5.610398 TGGACATTACTGTATGCCTGTATG 58.390 41.667 0.00 0.00 35.14 2.39
3143 3609 8.793592 CATTACTGTATGCCTGTATGTAGTCTA 58.206 37.037 0.00 0.00 0.00 2.59
3152 3618 8.577048 TGCCTGTATGTAGTCTAATATCTACC 57.423 38.462 0.00 0.00 36.63 3.18
3167 3650 4.553330 ATCTACCGAACTTGACAATGGT 57.447 40.909 6.73 6.73 0.00 3.55
3173 3656 5.067273 ACCGAACTTGACAATGGTTTATGA 58.933 37.500 0.00 0.00 0.00 2.15
3176 3659 6.434596 CGAACTTGACAATGGTTTATGACAA 58.565 36.000 0.00 0.00 32.09 3.18
3203 3686 3.889196 TTGAAACCGCATGTCTGTTAC 57.111 42.857 0.00 0.00 0.00 2.50
3221 3704 6.478344 TCTGTTACATGTTTGGCAATTTTGTC 59.522 34.615 2.30 0.00 0.00 3.18
3282 3765 8.742125 TCCTATCAATCTCATTACCATACCTT 57.258 34.615 0.00 0.00 0.00 3.50
3283 3766 8.597167 TCCTATCAATCTCATTACCATACCTTG 58.403 37.037 0.00 0.00 0.00 3.61
3289 3772 7.691993 ATCTCATTACCATACCTTGTACCTT 57.308 36.000 0.00 0.00 0.00 3.50
3335 3819 2.889200 CCTCTCGTAAGGGCTCTGT 58.111 57.895 0.00 0.00 38.17 3.41
3345 3829 3.306472 AAGGGCTCTGTTTGGTTACAA 57.694 42.857 0.00 0.00 34.07 2.41
3348 3832 3.826729 AGGGCTCTGTTTGGTTACAATTC 59.173 43.478 0.00 0.00 36.29 2.17
3350 3834 3.365969 GGCTCTGTTTGGTTACAATTCGG 60.366 47.826 0.00 0.00 36.29 4.30
3351 3835 3.252458 GCTCTGTTTGGTTACAATTCGGT 59.748 43.478 0.00 0.00 36.29 4.69
3352 3836 4.783242 CTCTGTTTGGTTACAATTCGGTG 58.217 43.478 0.00 0.00 36.29 4.94
3353 3837 4.200874 TCTGTTTGGTTACAATTCGGTGT 58.799 39.130 0.00 0.00 36.29 4.16
3360 3844 4.992319 TGGTTACAATTCGGTGTAAGTCTG 59.008 41.667 7.29 0.00 42.99 3.51
3369 3853 5.733620 TCGGTGTAAGTCTGGAAGTTTAT 57.266 39.130 0.00 0.00 33.76 1.40
3370 3854 6.839124 TCGGTGTAAGTCTGGAAGTTTATA 57.161 37.500 0.00 0.00 33.76 0.98
3384 3868 9.226606 CTGGAAGTTTATACAGACCAATGTTAA 57.773 33.333 0.00 0.00 34.56 2.01
3385 3869 9.226606 TGGAAGTTTATACAGACCAATGTTAAG 57.773 33.333 0.00 0.00 34.56 1.85
3394 3878 5.415701 ACAGACCAATGTTAAGTAATGCAGG 59.584 40.000 0.00 0.00 0.00 4.85
3399 3883 4.718940 ATGTTAAGTAATGCAGGTTGCC 57.281 40.909 0.00 0.00 44.23 4.52
3402 3886 2.584835 AAGTAATGCAGGTTGCCAGA 57.415 45.000 0.00 0.00 44.23 3.86
3403 3887 2.584835 AGTAATGCAGGTTGCCAGAA 57.415 45.000 0.00 0.00 44.23 3.02
3406 3890 1.188863 AATGCAGGTTGCCAGAATCC 58.811 50.000 0.00 0.00 44.23 3.01
3407 3891 1.033746 ATGCAGGTTGCCAGAATCCG 61.034 55.000 0.00 0.00 44.23 4.18
3421 3905 3.131223 CAGAATCCGCTTCCACTTCTAGA 59.869 47.826 0.00 0.00 34.11 2.43
3428 3912 2.352960 GCTTCCACTTCTAGAATTGGCG 59.647 50.000 28.55 22.98 39.94 5.69
3429 3913 2.691409 TCCACTTCTAGAATTGGCGG 57.309 50.000 28.55 15.04 39.94 6.13
3433 3917 2.289002 CACTTCTAGAATTGGCGGATGC 59.711 50.000 13.60 0.00 41.71 3.91
3436 3920 3.667497 TCTAGAATTGGCGGATGCTAG 57.333 47.619 8.65 8.65 42.25 3.42
3441 3925 2.645838 ATTGGCGGATGCTAGTTGAT 57.354 45.000 0.00 0.00 42.25 2.57
3447 3931 4.256920 GGCGGATGCTAGTTGATTATGAT 58.743 43.478 0.00 0.00 42.25 2.45
3448 3932 4.093998 GGCGGATGCTAGTTGATTATGATG 59.906 45.833 0.00 0.00 42.25 3.07
3453 3937 9.586435 CGGATGCTAGTTGATTATGATGTAATA 57.414 33.333 0.00 0.00 0.00 0.98
3487 3979 4.959210 AGCACTTCTAGGTATCACATGTCT 59.041 41.667 0.00 0.00 0.00 3.41
3489 3981 5.521735 GCACTTCTAGGTATCACATGTCTTG 59.478 44.000 0.00 0.00 0.00 3.02
3490 3982 5.521735 CACTTCTAGGTATCACATGTCTTGC 59.478 44.000 0.00 0.00 0.00 4.01
3503 3995 7.212976 TCACATGTCTTGCCTAGATAGAATTC 58.787 38.462 0.00 0.00 34.79 2.17
3504 3996 6.988580 CACATGTCTTGCCTAGATAGAATTCA 59.011 38.462 8.44 0.00 34.79 2.57
3524 4016 9.107177 GAATTCAATATAGAGGCTGGATGTATG 57.893 37.037 0.00 0.00 0.00 2.39
3525 4017 7.797121 TTCAATATAGAGGCTGGATGTATGA 57.203 36.000 0.00 0.00 0.00 2.15
3526 4018 7.984859 TCAATATAGAGGCTGGATGTATGAT 57.015 36.000 0.00 0.00 0.00 2.45
3527 4019 7.789026 TCAATATAGAGGCTGGATGTATGATG 58.211 38.462 0.00 0.00 0.00 3.07
3528 4020 2.855209 AGAGGCTGGATGTATGATGC 57.145 50.000 0.00 0.00 0.00 3.91
3529 4021 1.001746 AGAGGCTGGATGTATGATGCG 59.998 52.381 0.00 0.00 0.00 4.73
3530 4022 0.761187 AGGCTGGATGTATGATGCGT 59.239 50.000 0.00 0.00 0.00 5.24
3531 4023 1.970640 AGGCTGGATGTATGATGCGTA 59.029 47.619 0.00 0.00 0.00 4.42
3532 4024 2.368548 AGGCTGGATGTATGATGCGTAA 59.631 45.455 0.00 0.00 0.00 3.18
3533 4025 3.008375 AGGCTGGATGTATGATGCGTAAT 59.992 43.478 0.00 0.00 0.00 1.89
3534 4026 4.222810 AGGCTGGATGTATGATGCGTAATA 59.777 41.667 0.00 0.00 0.00 0.98
3535 4027 5.104776 AGGCTGGATGTATGATGCGTAATAT 60.105 40.000 0.00 0.00 0.00 1.28
3536 4028 5.586243 GGCTGGATGTATGATGCGTAATATT 59.414 40.000 0.00 0.00 0.00 1.28
3537 4029 6.457392 GGCTGGATGTATGATGCGTAATATTG 60.457 42.308 0.00 0.00 0.00 1.90
3538 4030 6.421377 TGGATGTATGATGCGTAATATTGC 57.579 37.500 0.00 0.00 0.00 3.56
3539 4031 6.172630 TGGATGTATGATGCGTAATATTGCT 58.827 36.000 0.00 0.00 0.00 3.91
3540 4032 6.654582 TGGATGTATGATGCGTAATATTGCTT 59.345 34.615 0.00 0.00 0.00 3.91
3541 4033 6.963242 GGATGTATGATGCGTAATATTGCTTG 59.037 38.462 0.00 0.00 0.00 4.01
3542 4034 6.859420 TGTATGATGCGTAATATTGCTTGT 57.141 33.333 0.00 0.00 0.00 3.16
3543 4035 6.657888 TGTATGATGCGTAATATTGCTTGTG 58.342 36.000 0.00 0.00 0.00 3.33
3544 4036 4.550577 TGATGCGTAATATTGCTTGTGG 57.449 40.909 0.00 0.00 0.00 4.17
3545 4037 4.195416 TGATGCGTAATATTGCTTGTGGA 58.805 39.130 0.00 0.00 0.00 4.02
3546 4038 4.821260 TGATGCGTAATATTGCTTGTGGAT 59.179 37.500 0.00 0.00 0.00 3.41
3547 4039 4.550577 TGCGTAATATTGCTTGTGGATG 57.449 40.909 0.00 0.00 0.00 3.51
3548 4040 3.944650 TGCGTAATATTGCTTGTGGATGT 59.055 39.130 0.00 0.00 0.00 3.06
3549 4041 5.119694 TGCGTAATATTGCTTGTGGATGTA 58.880 37.500 0.00 0.00 0.00 2.29
3550 4042 5.586643 TGCGTAATATTGCTTGTGGATGTAA 59.413 36.000 0.00 0.00 0.00 2.41
3551 4043 6.262049 TGCGTAATATTGCTTGTGGATGTAAT 59.738 34.615 0.00 0.00 0.00 1.89
3552 4044 6.578545 GCGTAATATTGCTTGTGGATGTAATG 59.421 38.462 0.00 0.00 0.00 1.90
3553 4045 7.519809 GCGTAATATTGCTTGTGGATGTAATGA 60.520 37.037 0.00 0.00 0.00 2.57
3554 4046 8.341903 CGTAATATTGCTTGTGGATGTAATGAA 58.658 33.333 0.00 0.00 0.00 2.57
3560 4052 7.275888 TGCTTGTGGATGTAATGAATATTCC 57.724 36.000 12.90 0.00 0.00 3.01
3561 4053 7.062322 TGCTTGTGGATGTAATGAATATTCCT 58.938 34.615 12.90 0.00 0.00 3.36
3562 4054 7.560991 TGCTTGTGGATGTAATGAATATTCCTT 59.439 33.333 12.90 11.49 0.00 3.36
3563 4055 9.066892 GCTTGTGGATGTAATGAATATTCCTTA 57.933 33.333 12.90 10.52 0.00 2.69
3576 4068 9.975218 ATGAATATTCCTTAACTTGGTAGTTGT 57.025 29.630 12.90 0.00 44.22 3.32
3719 4211 5.449177 GCTTATCTACAAACATGCTGTTCCC 60.449 44.000 6.37 0.00 40.14 3.97
3951 4443 3.691118 TGGACTATTTGCTGACTGAATGC 59.309 43.478 0.00 0.00 0.00 3.56
3993 4485 3.442100 GCTGTTAAGAAGATTGGCATGC 58.558 45.455 9.90 9.90 0.00 4.06
4091 4583 0.321653 ACGCCTTCAAGGTCATGGTC 60.322 55.000 5.03 0.00 37.80 4.02
4123 4615 6.019779 AGTATCTCATCCTCTACGCAAATC 57.980 41.667 0.00 0.00 0.00 2.17
4137 4629 5.734855 ACGCAAATCCATCACTATGTAAC 57.265 39.130 0.00 0.00 0.00 2.50
4172 4664 5.488341 TCTGAGGAAGTACTAACAATTGGC 58.512 41.667 10.83 0.00 0.00 4.52
4266 4758 4.802039 CCATCGCTTGATTGATTTTTCCTG 59.198 41.667 0.00 0.00 0.00 3.86
4290 4782 2.287427 ACGACGATGACGATGTATTCCC 60.287 50.000 0.00 0.00 42.66 3.97
4320 4812 1.143073 GGTATTGGTGGATGGGGACTC 59.857 57.143 0.00 0.00 0.00 3.36
4533 5029 7.674348 CCTGTACTGAGGAATTCCCATATACTA 59.326 40.741 21.22 11.94 34.69 1.82
4563 5059 3.881688 CCTCCAATTCTCTATGCTGTTGG 59.118 47.826 0.00 0.00 37.91 3.77
4600 5096 4.578516 TGTGTGTTAGTTTCTGAATGGGTG 59.421 41.667 0.00 0.00 0.00 4.61
4601 5097 4.578928 GTGTGTTAGTTTCTGAATGGGTGT 59.421 41.667 0.00 0.00 0.00 4.16
4611 5130 5.818678 TCTGAATGGGTGTGTAGTAGTTT 57.181 39.130 0.00 0.00 0.00 2.66
4616 5135 7.057894 TGAATGGGTGTGTAGTAGTTTTCTTT 58.942 34.615 0.00 0.00 0.00 2.52
4645 5164 2.417586 GCTTGCAAAATCATTCCTTGGC 59.582 45.455 0.00 0.00 0.00 4.52
4668 5187 4.809958 CCTTCTGAGATAAGTCATGCAGTG 59.190 45.833 0.00 0.00 0.00 3.66
4688 5207 1.864029 GCTCTTGTTTTGTTCGGGCAC 60.864 52.381 0.00 0.00 0.00 5.01
4718 5958 4.571372 GCTAGAGTATTAGCGACAGGTT 57.429 45.455 0.00 0.00 36.97 3.50
4757 6502 5.720371 ATTGCTGTTTGTGTAATGCCTTA 57.280 34.783 0.00 0.00 0.00 2.69
4765 6510 6.547880 TGTTTGTGTAATGCCTTAAGGAAGAA 59.452 34.615 26.21 3.94 37.39 2.52
4779 6526 5.876651 AAGGAAGAAACCAGCTGATTTTT 57.123 34.783 17.39 11.31 0.00 1.94
4798 6545 8.559536 TGATTTTTAATTCATATCTCGGCAGTC 58.440 33.333 0.00 0.00 0.00 3.51
4801 6548 3.567576 ATTCATATCTCGGCAGTCTCG 57.432 47.619 0.00 0.00 0.00 4.04
4846 6593 6.017109 CACCAGGTTATATTGCCAACATACTC 60.017 42.308 0.00 0.00 0.00 2.59
4852 6599 7.095607 GGTTATATTGCCAACATACTCTTCTCG 60.096 40.741 0.00 0.00 0.00 4.04
4857 6604 3.589988 CCAACATACTCTTCTCGCAAGT 58.410 45.455 0.00 0.00 39.48 3.16
4865 6612 7.916450 ACATACTCTTCTCGCAAGTAATTCTAC 59.084 37.037 0.00 0.00 39.48 2.59
4871 6618 6.268825 TCTCGCAAGTAATTCTACAAGTCT 57.731 37.500 0.00 0.00 39.48 3.24
4906 6653 9.965902 ATGTATGATTATCTTTAGCCTTTAGGG 57.034 33.333 0.00 0.00 35.18 3.53
4979 6737 7.396540 ACATAGAAAAATTCTAGGGTTGCAG 57.603 36.000 14.12 0.00 45.57 4.41
5052 6811 2.096248 GTGTGTGGGTTTCAACAGGAA 58.904 47.619 0.00 0.00 0.00 3.36
5080 6842 8.271458 TCTATTCCATAGTAAGGCAACATTTCA 58.729 33.333 0.00 0.00 34.69 2.69
5140 6902 8.746052 AATGGATAGTCAAATTGAATACGGAA 57.254 30.769 5.24 0.00 29.22 4.30
5157 6919 5.900865 ACGGAAAACACAAGAAACCTAAA 57.099 34.783 0.00 0.00 0.00 1.85
5227 6990 2.488820 GTCCTAGTGGCGTCCGAC 59.511 66.667 0.00 0.00 0.00 4.79
5235 6998 2.025727 GGCGTCCGACCTACATCG 59.974 66.667 0.00 0.00 41.89 3.84
5236 6999 2.475466 GGCGTCCGACCTACATCGA 61.475 63.158 0.00 0.00 45.13 3.59
5237 7000 1.009900 GCGTCCGACCTACATCGAG 60.010 63.158 0.00 0.00 45.13 4.04
5238 7001 1.712977 GCGTCCGACCTACATCGAGT 61.713 60.000 0.00 0.00 45.13 4.18
5239 7002 0.027716 CGTCCGACCTACATCGAGTG 59.972 60.000 0.00 0.00 45.13 3.51
5240 7003 0.248539 GTCCGACCTACATCGAGTGC 60.249 60.000 0.00 0.00 45.13 4.40
5241 7004 0.678684 TCCGACCTACATCGAGTGCA 60.679 55.000 0.00 0.00 45.13 4.57
5242 7005 0.248661 CCGACCTACATCGAGTGCAG 60.249 60.000 0.00 0.00 45.13 4.41
5243 7006 0.867753 CGACCTACATCGAGTGCAGC 60.868 60.000 0.00 0.00 45.13 5.25
5244 7007 0.457851 GACCTACATCGAGTGCAGCT 59.542 55.000 0.00 0.00 0.00 4.24
5245 7008 1.676529 GACCTACATCGAGTGCAGCTA 59.323 52.381 0.00 0.00 0.00 3.32
5246 7009 2.294791 GACCTACATCGAGTGCAGCTAT 59.705 50.000 0.00 0.00 0.00 2.97
5247 7010 2.035193 ACCTACATCGAGTGCAGCTATG 59.965 50.000 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.634444 TCCGATTGTCTTTTGGAAAATAAGAAA 58.366 29.630 0.00 0.00 32.40 2.52
9 10 8.986477 AATCCGATTGTCTTTTGGAAAATAAG 57.014 30.769 0.00 0.00 32.40 1.73
10 11 9.771534 AAAATCCGATTGTCTTTTGGAAAATAA 57.228 25.926 0.00 0.00 32.40 1.40
53 55 2.217750 GTTTGTTGGGAAACATTGCCC 58.782 47.619 0.00 0.00 44.93 5.36
55 57 3.242252 CGTTGTTTGTTGGGAAACATTGC 60.242 43.478 0.00 0.00 43.56 3.56
100 102 4.215613 GGCCGTCTCAAGTGTTTCTTTATT 59.784 41.667 0.00 0.00 33.63 1.40
102 104 3.135994 GGCCGTCTCAAGTGTTTCTTTA 58.864 45.455 0.00 0.00 33.63 1.85
106 113 0.599204 TCGGCCGTCTCAAGTGTTTC 60.599 55.000 27.15 0.00 0.00 2.78
149 158 2.282745 GCCAAGGGCTGCTTGACT 60.283 61.111 0.00 0.00 46.69 3.41
231 243 2.762043 AGGGAGAGGAGCTTCGCC 60.762 66.667 0.00 0.00 36.43 5.54
290 302 8.608844 AAGAGCTACGAATATTATTTCCAAGG 57.391 34.615 0.00 0.00 0.00 3.61
304 321 0.388134 GGCACGTGAAGAGCTACGAA 60.388 55.000 22.23 0.00 42.54 3.85
326 352 0.531974 GTGTCGGTGCACCTTCAAGA 60.532 55.000 32.28 19.29 33.53 3.02
335 361 2.103647 GTGTGTGTGTGTCGGTGCA 61.104 57.895 0.00 0.00 0.00 4.57
337 363 1.016653 TGTGTGTGTGTGTGTCGGTG 61.017 55.000 0.00 0.00 0.00 4.94
338 364 1.017177 GTGTGTGTGTGTGTGTCGGT 61.017 55.000 0.00 0.00 0.00 4.69
339 365 1.016653 TGTGTGTGTGTGTGTGTCGG 61.017 55.000 0.00 0.00 0.00 4.79
341 367 0.094558 CGTGTGTGTGTGTGTGTGTC 59.905 55.000 0.00 0.00 0.00 3.67
342 368 1.295357 CCGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
345 371 1.428370 CTCCCGTGTGTGTGTGTGTG 61.428 60.000 0.00 0.00 0.00 3.82
347 373 0.461163 TTCTCCCGTGTGTGTGTGTG 60.461 55.000 0.00 0.00 0.00 3.82
448 497 3.760035 TCTGGCCGAGTTCTCCGC 61.760 66.667 0.00 4.96 0.00 5.54
449 498 2.182030 GTCTGGCCGAGTTCTCCG 59.818 66.667 0.00 0.00 0.00 4.63
452 501 3.382832 CGGGTCTGGCCGAGTTCT 61.383 66.667 0.00 0.00 38.44 3.01
454 503 3.692406 GACGGGTCTGGCCGAGTT 61.692 66.667 0.00 0.00 38.44 3.01
473 522 2.125673 CCCATGTGGTCGACCGAC 60.126 66.667 28.70 25.14 43.87 4.79
474 523 4.077184 GCCCATGTGGTCGACCGA 62.077 66.667 28.70 18.57 39.43 4.69
531 580 2.996470 TATTCCGAGGGAGAGGGGCG 62.996 65.000 0.00 0.00 31.21 6.13
532 581 0.545548 ATATTCCGAGGGAGAGGGGC 60.546 60.000 0.00 0.00 31.21 5.80
533 582 1.903183 GAATATTCCGAGGGAGAGGGG 59.097 57.143 3.92 0.00 31.21 4.79
534 583 2.564947 CTGAATATTCCGAGGGAGAGGG 59.435 54.545 12.90 0.00 31.21 4.30
539 588 1.070758 GCAGCTGAATATTCCGAGGGA 59.929 52.381 20.43 0.00 0.00 4.20
709 771 3.724257 GCGTTCTTTTTCCAACGAGAAAG 59.276 43.478 8.31 0.00 46.70 2.62
711 773 2.285950 CGCGTTCTTTTTCCAACGAGAA 60.286 45.455 8.31 0.00 46.70 2.87
716 778 2.031930 TGGTACGCGTTCTTTTTCCAAC 59.968 45.455 20.78 4.76 0.00 3.77
720 782 2.481185 TGGATGGTACGCGTTCTTTTTC 59.519 45.455 20.78 7.55 0.00 2.29
752 832 2.917227 GGTTGGTTGGTGCCTGGG 60.917 66.667 0.00 0.00 0.00 4.45
762 842 0.975040 TGCTTGGCTTGTGGTTGGTT 60.975 50.000 0.00 0.00 0.00 3.67
763 843 1.381056 TGCTTGGCTTGTGGTTGGT 60.381 52.632 0.00 0.00 0.00 3.67
764 844 1.364901 CTGCTTGGCTTGTGGTTGG 59.635 57.895 0.00 0.00 0.00 3.77
765 845 1.300388 GCTGCTTGGCTTGTGGTTG 60.300 57.895 0.00 0.00 0.00 3.77
766 846 2.501602 GGCTGCTTGGCTTGTGGTT 61.502 57.895 0.00 0.00 38.32 3.67
767 847 2.914097 GGCTGCTTGGCTTGTGGT 60.914 61.111 0.00 0.00 38.32 4.16
768 848 2.913578 TGGCTGCTTGGCTTGTGG 60.914 61.111 0.00 0.00 42.34 4.17
769 849 2.337532 GTGGCTGCTTGGCTTGTG 59.662 61.111 0.00 0.00 42.34 3.33
770 850 2.123769 TGTGGCTGCTTGGCTTGT 60.124 55.556 0.00 0.00 42.34 3.16
771 851 2.198287 AGTGTGGCTGCTTGGCTTG 61.198 57.895 0.00 0.00 42.34 4.01
772 852 2.196776 AGTGTGGCTGCTTGGCTT 59.803 55.556 0.00 0.00 42.34 4.35
773 853 2.596631 CAGTGTGGCTGCTTGGCT 60.597 61.111 0.00 0.00 42.34 4.75
774 854 3.677648 CCAGTGTGGCTGCTTGGC 61.678 66.667 0.00 0.00 43.71 4.52
775 855 2.113774 TCCAGTGTGGCTGCTTGG 59.886 61.111 0.00 0.84 43.71 3.61
776 856 1.526686 TGTCCAGTGTGGCTGCTTG 60.527 57.895 0.00 0.00 43.71 4.01
779 859 2.111878 AGTGTCCAGTGTGGCTGC 59.888 61.111 0.00 0.00 43.71 5.25
782 862 2.980233 GGCAGTGTCCAGTGTGGC 60.980 66.667 4.19 0.00 37.47 5.01
1396 1506 1.224069 AAATCCGCATCCGCATCGAG 61.224 55.000 0.00 0.00 38.40 4.04
1424 1534 1.475751 CGAAATGCCTGCCTAGATGGT 60.476 52.381 0.00 0.00 38.35 3.55
1540 1712 9.280174 CTAGTAGTCACCAATTCCTAACAAAAA 57.720 33.333 0.00 0.00 0.00 1.94
1541 1713 8.434392 ACTAGTAGTCACCAATTCCTAACAAAA 58.566 33.333 0.00 0.00 0.00 2.44
1588 1760 6.806751 TGTATCTATCTACTGGAACTGCAAC 58.193 40.000 0.00 0.00 0.00 4.17
1739 1938 6.455913 GCACATTCATCAACATAATTTGCACC 60.456 38.462 0.00 0.00 36.67 5.01
1814 2071 8.597167 TGCAGGCATAGACTTGATTATATAGTT 58.403 33.333 0.00 0.00 0.00 2.24
1815 2072 8.138928 TGCAGGCATAGACTTGATTATATAGT 57.861 34.615 0.00 0.00 0.00 2.12
1816 2073 9.043079 CATGCAGGCATAGACTTGATTATATAG 57.957 37.037 6.42 0.00 34.91 1.31
1819 2076 6.175471 CCATGCAGGCATAGACTTGATTATA 58.825 40.000 6.42 0.00 34.91 0.98
1820 2077 5.008331 CCATGCAGGCATAGACTTGATTAT 58.992 41.667 6.42 0.00 34.91 1.28
1822 2079 3.220110 CCATGCAGGCATAGACTTGATT 58.780 45.455 6.42 0.00 34.91 2.57
1823 2080 2.488528 CCCATGCAGGCATAGACTTGAT 60.489 50.000 6.42 0.00 34.91 2.57
1876 2158 6.207417 ACTGAATTGAACGGACAGAAATGAAT 59.793 34.615 0.00 0.00 33.53 2.57
1912 2273 1.578897 TGACCAATAGCCTACAGCCA 58.421 50.000 0.00 0.00 45.47 4.75
1918 2279 8.700439 AAACTTTAGTTTTGACCAATAGCCTA 57.300 30.769 2.10 0.00 45.07 3.93
1972 2364 5.389859 TCGATCAATGCCACTTTTCAAAT 57.610 34.783 0.00 0.00 0.00 2.32
1977 2369 2.440409 AGCTCGATCAATGCCACTTTT 58.560 42.857 0.00 0.00 0.00 2.27
1979 2371 2.119801 AAGCTCGATCAATGCCACTT 57.880 45.000 0.00 0.00 0.00 3.16
1980 2372 2.988010 TAAGCTCGATCAATGCCACT 57.012 45.000 0.00 0.00 0.00 4.00
1981 2373 4.752101 AGTATTAAGCTCGATCAATGCCAC 59.248 41.667 0.00 0.00 0.00 5.01
1983 2375 5.931441 AAGTATTAAGCTCGATCAATGCC 57.069 39.130 0.00 0.00 0.00 4.40
1986 2378 9.593134 GATGGATAAGTATTAAGCTCGATCAAT 57.407 33.333 0.00 0.00 32.17 2.57
2083 2477 7.040062 CCACAGTAATCCCAAATCAAAGTACAA 60.040 37.037 0.00 0.00 0.00 2.41
2109 2503 0.332972 AAGGAAGCCCAACCATCTCC 59.667 55.000 0.00 0.00 33.88 3.71
2119 2513 4.380973 GCTTCTAATGTCAAAAGGAAGCCC 60.381 45.833 12.61 0.00 45.38 5.19
2200 2647 0.251916 TCGCGGGGTCAATCTGAAAT 59.748 50.000 6.13 0.00 0.00 2.17
2560 3010 3.610911 GACATTTACTTACCCAGCAGCT 58.389 45.455 0.00 0.00 0.00 4.24
2579 3029 2.576615 AGTTTTCAAGTCAGCTGGGAC 58.423 47.619 15.13 5.57 38.08 4.46
2601 3051 8.894731 GGATCAGGGTAAGAAAAGAAAATAGTC 58.105 37.037 0.00 0.00 0.00 2.59
2646 3097 5.827797 CCTTGTAGAGCCTGGCATTATTAAA 59.172 40.000 22.65 5.37 0.00 1.52
2790 3241 2.803956 CCAGCTTTTGAGCATTTGGTTG 59.196 45.455 0.88 0.00 37.25 3.77
2815 3269 7.004555 ACAGTGTCAAGTATATGAAACAGGA 57.995 36.000 0.00 0.00 39.57 3.86
2826 3280 8.519526 TCAAAGAAAACAAACAGTGTCAAGTAT 58.480 29.630 0.00 0.00 40.60 2.12
2829 3283 7.816945 ATCAAAGAAAACAAACAGTGTCAAG 57.183 32.000 0.00 0.00 40.60 3.02
2833 3287 7.961325 AACAATCAAAGAAAACAAACAGTGT 57.039 28.000 0.00 0.00 44.64 3.55
2861 3319 8.181573 GTGAAGAGAAAGTAACAAAACATCACA 58.818 33.333 0.00 0.00 33.15 3.58
2886 3349 1.977854 TCATACAGCAAGGTCACAGGT 59.022 47.619 0.00 0.00 0.00 4.00
2899 3362 9.973450 AATGATACTAGTAGTTTGCTCATACAG 57.027 33.333 8.40 0.00 0.00 2.74
2916 3379 5.514169 TGGTTGGCCATCAAAATGATACTA 58.486 37.500 6.09 0.00 40.46 1.82
2917 3380 4.352009 TGGTTGGCCATCAAAATGATACT 58.648 39.130 6.09 0.00 40.46 2.12
2918 3381 4.734398 TGGTTGGCCATCAAAATGATAC 57.266 40.909 6.09 0.00 40.46 2.24
2964 3427 7.872113 AGGCAACAAATTGAAATGGTAAAAA 57.128 28.000 0.00 0.00 38.15 1.94
2977 3440 5.016173 TGTCCATAAGCTAGGCAACAAATT 58.984 37.500 0.00 0.00 41.41 1.82
3041 3504 8.324163 ACTACAAAACTTCCATCACAACTATC 57.676 34.615 0.00 0.00 0.00 2.08
3043 3506 7.771361 TCAACTACAAAACTTCCATCACAACTA 59.229 33.333 0.00 0.00 0.00 2.24
3074 3537 5.007034 TGTTTTGTGAGAGGTGAAACTTGA 58.993 37.500 0.00 0.00 36.74 3.02
3085 3548 9.888878 CATGGCTATATTTATGTTTTGTGAGAG 57.111 33.333 0.00 0.00 0.00 3.20
3108 3571 3.251729 GGCATACAGTAATGTCCAGCATG 59.748 47.826 0.00 0.00 37.96 4.06
3109 3572 3.137176 AGGCATACAGTAATGTCCAGCAT 59.863 43.478 0.00 0.00 40.03 3.79
3111 3574 2.874701 CAGGCATACAGTAATGTCCAGC 59.125 50.000 0.00 2.49 31.61 4.85
3112 3575 4.142609 ACAGGCATACAGTAATGTCCAG 57.857 45.455 0.00 0.00 31.61 3.86
3136 3602 8.834465 TGTCAAGTTCGGTAGATATTAGACTAC 58.166 37.037 0.00 0.00 38.44 2.73
3143 3609 6.650120 ACCATTGTCAAGTTCGGTAGATATT 58.350 36.000 0.00 0.00 0.00 1.28
3152 3618 5.996219 TGTCATAAACCATTGTCAAGTTCG 58.004 37.500 0.00 0.00 0.00 3.95
3167 3650 7.064609 TGCGGTTTCAAAATGTTTTGTCATAAA 59.935 29.630 15.51 7.92 45.77 1.40
3173 3656 4.633565 ACATGCGGTTTCAAAATGTTTTGT 59.366 33.333 15.51 0.00 45.77 2.83
3176 3659 4.507388 CAGACATGCGGTTTCAAAATGTTT 59.493 37.500 0.00 0.00 31.82 2.83
3203 3686 3.499157 CCCAGACAAAATTGCCAAACATG 59.501 43.478 0.00 0.00 0.00 3.21
3221 3704 7.864108 TGTCATTTATGAACAGAATACCCAG 57.136 36.000 0.00 0.00 38.75 4.45
3295 3778 4.064388 GGGAACAAAAACATTCACCATGG 58.936 43.478 11.19 11.19 37.17 3.66
3300 3783 4.556699 CGAGAGGGGAACAAAAACATTCAC 60.557 45.833 0.00 0.00 0.00 3.18
3303 3786 3.562182 ACGAGAGGGGAACAAAAACATT 58.438 40.909 0.00 0.00 0.00 2.71
3330 3813 4.274950 ACACCGAATTGTAACCAAACAGAG 59.725 41.667 0.00 0.00 33.44 3.35
3332 3815 4.561735 ACACCGAATTGTAACCAAACAG 57.438 40.909 0.00 0.00 33.44 3.16
3335 3819 6.017770 CAGACTTACACCGAATTGTAACCAAA 60.018 38.462 0.00 0.00 37.10 3.28
3345 3829 4.618920 AACTTCCAGACTTACACCGAAT 57.381 40.909 0.00 0.00 0.00 3.34
3348 3832 6.392354 TGTATAAACTTCCAGACTTACACCG 58.608 40.000 0.00 0.00 0.00 4.94
3350 3834 8.463456 GTCTGTATAAACTTCCAGACTTACAC 57.537 38.462 10.52 0.00 46.46 2.90
3360 3844 9.227777 ACTTAACATTGGTCTGTATAAACTTCC 57.772 33.333 0.00 0.00 0.00 3.46
3369 3853 6.597672 CCTGCATTACTTAACATTGGTCTGTA 59.402 38.462 0.00 0.00 0.00 2.74
3370 3854 5.415701 CCTGCATTACTTAACATTGGTCTGT 59.584 40.000 0.00 0.00 0.00 3.41
3394 3878 0.960364 TGGAAGCGGATTCTGGCAAC 60.960 55.000 5.91 0.00 38.07 4.17
3399 3883 2.393271 AGAAGTGGAAGCGGATTCTG 57.607 50.000 5.91 0.00 38.07 3.02
3402 3886 4.762289 ATTCTAGAAGTGGAAGCGGATT 57.238 40.909 11.53 0.00 0.00 3.01
3403 3887 4.446371 CAATTCTAGAAGTGGAAGCGGAT 58.554 43.478 22.23 0.00 33.25 4.18
3421 3905 2.418368 TCAACTAGCATCCGCCAATT 57.582 45.000 0.00 0.00 39.83 2.32
3457 3941 8.534954 TGTGATACCTAGAAGTGCTAGTATTT 57.465 34.615 4.37 0.00 44.24 1.40
3461 3945 5.894393 ACATGTGATACCTAGAAGTGCTAGT 59.106 40.000 0.00 0.00 44.24 2.57
3462 3946 6.264292 AGACATGTGATACCTAGAAGTGCTAG 59.736 42.308 1.15 0.00 45.12 3.42
3465 3949 5.269505 AGACATGTGATACCTAGAAGTGC 57.730 43.478 1.15 0.00 0.00 4.40
3466 3950 5.521735 GCAAGACATGTGATACCTAGAAGTG 59.478 44.000 1.15 0.00 0.00 3.16
3489 3981 8.923270 AGCCTCTATATTGAATTCTATCTAGGC 58.077 37.037 22.49 22.49 0.00 3.93
3503 3995 6.482641 GCATCATACATCCAGCCTCTATATTG 59.517 42.308 0.00 0.00 0.00 1.90
3504 3996 6.590068 GCATCATACATCCAGCCTCTATATT 58.410 40.000 0.00 0.00 0.00 1.28
3508 4000 2.232208 CGCATCATACATCCAGCCTCTA 59.768 50.000 0.00 0.00 0.00 2.43
3509 4001 1.001746 CGCATCATACATCCAGCCTCT 59.998 52.381 0.00 0.00 0.00 3.69
3512 4004 2.455674 TACGCATCATACATCCAGCC 57.544 50.000 0.00 0.00 0.00 4.85
3517 4009 7.479603 CACAAGCAATATTACGCATCATACATC 59.520 37.037 1.12 0.00 0.00 3.06
3524 4016 4.811555 TCCACAAGCAATATTACGCATC 57.188 40.909 1.12 0.00 0.00 3.91
3525 4017 4.580167 ACATCCACAAGCAATATTACGCAT 59.420 37.500 1.12 0.00 0.00 4.73
3526 4018 3.944650 ACATCCACAAGCAATATTACGCA 59.055 39.130 1.12 0.00 0.00 5.24
3527 4019 4.552166 ACATCCACAAGCAATATTACGC 57.448 40.909 0.00 0.00 0.00 4.42
3528 4020 7.860613 TCATTACATCCACAAGCAATATTACG 58.139 34.615 0.00 0.00 0.00 3.18
3534 4026 8.362639 GGAATATTCATTACATCCACAAGCAAT 58.637 33.333 17.07 0.00 0.00 3.56
3535 4027 7.560991 AGGAATATTCATTACATCCACAAGCAA 59.439 33.333 17.07 0.00 0.00 3.91
3536 4028 7.062322 AGGAATATTCATTACATCCACAAGCA 58.938 34.615 17.07 0.00 0.00 3.91
3537 4029 7.516198 AGGAATATTCATTACATCCACAAGC 57.484 36.000 17.07 0.00 0.00 4.01
3550 4042 9.975218 ACAACTACCAAGTTAAGGAATATTCAT 57.025 29.630 17.07 7.33 44.28 2.57
3558 4050 9.661563 CATGTAATACAACTACCAAGTTAAGGA 57.338 33.333 0.00 0.00 44.28 3.36
3559 4051 8.395633 GCATGTAATACAACTACCAAGTTAAGG 58.604 37.037 0.00 0.00 44.28 2.69
3560 4052 9.162764 AGCATGTAATACAACTACCAAGTTAAG 57.837 33.333 0.00 0.00 44.28 1.85
3561 4053 9.509956 AAGCATGTAATACAACTACCAAGTTAA 57.490 29.630 0.00 0.00 44.28 2.01
3562 4054 9.509956 AAAGCATGTAATACAACTACCAAGTTA 57.490 29.630 0.00 0.00 44.28 2.24
3564 4056 7.663905 TCAAAGCATGTAATACAACTACCAAGT 59.336 33.333 0.00 0.00 37.65 3.16
3565 4057 8.039603 TCAAAGCATGTAATACAACTACCAAG 57.960 34.615 0.00 0.00 0.00 3.61
3566 4058 7.987750 TCAAAGCATGTAATACAACTACCAA 57.012 32.000 0.00 0.00 0.00 3.67
3567 4059 7.663905 AGTTCAAAGCATGTAATACAACTACCA 59.336 33.333 0.00 0.00 0.00 3.25
3568 4060 8.040716 AGTTCAAAGCATGTAATACAACTACC 57.959 34.615 0.00 0.00 0.00 3.18
3569 4061 9.543018 GAAGTTCAAAGCATGTAATACAACTAC 57.457 33.333 0.00 0.00 0.00 2.73
3570 4062 9.502091 AGAAGTTCAAAGCATGTAATACAACTA 57.498 29.630 5.50 0.00 0.00 2.24
3571 4063 8.292448 CAGAAGTTCAAAGCATGTAATACAACT 58.708 33.333 5.50 0.00 0.00 3.16
3572 4064 8.076178 ACAGAAGTTCAAAGCATGTAATACAAC 58.924 33.333 5.50 0.00 0.00 3.32
3573 4065 8.165239 ACAGAAGTTCAAAGCATGTAATACAA 57.835 30.769 5.50 0.00 0.00 2.41
3574 4066 7.744087 ACAGAAGTTCAAAGCATGTAATACA 57.256 32.000 5.50 0.00 0.00 2.29
3575 4067 8.076178 ACAACAGAAGTTCAAAGCATGTAATAC 58.924 33.333 5.50 0.00 35.28 1.89
3576 4068 8.165239 ACAACAGAAGTTCAAAGCATGTAATA 57.835 30.769 5.50 0.00 35.28 0.98
3577 4069 7.042797 ACAACAGAAGTTCAAAGCATGTAAT 57.957 32.000 5.50 0.00 35.28 1.89
3578 4070 6.449635 ACAACAGAAGTTCAAAGCATGTAA 57.550 33.333 5.50 0.00 35.28 2.41
3579 4071 6.127758 ACAACAACAGAAGTTCAAAGCATGTA 60.128 34.615 5.50 0.00 35.28 2.29
3580 4072 4.989279 ACAACAGAAGTTCAAAGCATGT 57.011 36.364 5.50 0.00 35.28 3.21
3581 4073 5.104374 ACAACAACAGAAGTTCAAAGCATG 58.896 37.500 5.50 0.00 35.28 4.06
3710 4202 1.228124 CTTGGGAACGGGAACAGCA 60.228 57.895 0.00 0.00 0.00 4.41
3719 4211 2.742372 CACTCGGCCTTGGGAACG 60.742 66.667 0.00 0.00 0.00 3.95
3962 4454 7.337942 CCAATCTTCTTAACAGCCTACAAAGAT 59.662 37.037 0.00 0.00 34.58 2.40
3963 4455 6.655003 CCAATCTTCTTAACAGCCTACAAAGA 59.345 38.462 0.00 0.00 0.00 2.52
3993 4485 0.610232 CCTCTGGTGAAAAGGCCCAG 60.610 60.000 0.00 0.00 45.81 4.45
4091 4583 5.067273 AGAGGATGAGATACTTACAGTCCG 58.933 45.833 0.00 0.00 0.00 4.79
4123 4615 5.006358 GCTGTTTACCGTTACATAGTGATGG 59.994 44.000 0.00 0.00 37.39 3.51
4137 4629 2.743636 TCCTCAGAAGCTGTTTACCG 57.256 50.000 0.00 0.00 32.61 4.02
4172 4664 2.159198 CGGGCTGGAAGAAAATGGATTG 60.159 50.000 0.00 0.00 34.07 2.67
4266 4758 2.657960 TACATCGTCATCGTCGTAGC 57.342 50.000 0.00 0.00 38.33 3.58
4290 4782 1.545428 CCACCAATACCCCATCATCCG 60.545 57.143 0.00 0.00 0.00 4.18
4320 4812 8.116753 CGGTTGCTAAACTCAAGTAATTGATAG 58.883 37.037 6.00 6.84 36.48 2.08
4533 5029 6.069963 AGCATAGAGAATTGGAGGTAAACAGT 60.070 38.462 0.00 0.00 0.00 3.55
4551 5047 2.483013 GCCACGATACCAACAGCATAGA 60.483 50.000 0.00 0.00 0.00 1.98
4552 5048 1.867233 GCCACGATACCAACAGCATAG 59.133 52.381 0.00 0.00 0.00 2.23
4563 5059 1.804151 ACACACAACATGCCACGATAC 59.196 47.619 0.00 0.00 0.00 2.24
4600 5096 6.844779 GCACGAAGAAAAGAAAACTACTACAC 59.155 38.462 0.00 0.00 0.00 2.90
4601 5097 6.759827 AGCACGAAGAAAAGAAAACTACTACA 59.240 34.615 0.00 0.00 0.00 2.74
4611 5130 3.773860 TTGCAAGCACGAAGAAAAGAA 57.226 38.095 0.00 0.00 0.00 2.52
4616 5135 3.706802 TGATTTTGCAAGCACGAAGAA 57.293 38.095 0.00 0.00 0.00 2.52
4645 5164 4.809958 CACTGCATGACTTATCTCAGAAGG 59.190 45.833 0.00 0.00 0.00 3.46
4668 5187 0.383949 TGCCCGAACAAAACAAGAGC 59.616 50.000 0.00 0.00 0.00 4.09
4688 5207 4.555708 CGCTAATACTCTAGCTGACCTGTG 60.556 50.000 0.00 0.00 41.86 3.66
4718 5958 4.210328 CAGCAATAACTGTTGACGTGTACA 59.790 41.667 2.69 0.00 38.47 2.90
4757 6502 5.876651 AAAAATCAGCTGGTTTCTTCCTT 57.123 34.783 24.67 12.39 0.00 3.36
4779 6526 4.082733 CCGAGACTGCCGAGATATGAATTA 60.083 45.833 0.00 0.00 0.00 1.40
4798 6545 2.403252 AGAATACCAGTTTGGCCGAG 57.597 50.000 0.00 0.00 42.67 4.63
4801 6548 4.082408 GGTGTAAAGAATACCAGTTTGGCC 60.082 45.833 0.00 0.00 42.67 5.36
4846 6593 6.809196 AGACTTGTAGAATTACTTGCGAGAAG 59.191 38.462 8.31 0.00 0.00 2.85
4852 6599 8.958043 CAAACAAAGACTTGTAGAATTACTTGC 58.042 33.333 0.00 0.00 45.25 4.01
4964 6722 1.839424 GCACCTGCAACCCTAGAATT 58.161 50.000 0.00 0.00 41.59 2.17
4979 6737 3.131046 CCACCAATCCTCTATTTTGCACC 59.869 47.826 0.00 0.00 0.00 5.01
5131 6893 6.068473 AGGTTTCTTGTGTTTTCCGTATTC 57.932 37.500 0.00 0.00 0.00 1.75
5205 6967 1.513586 GACGCCACTAGGACGTTCG 60.514 63.158 8.12 0.00 43.98 3.95
5227 6990 2.670479 CATAGCTGCACTCGATGTAGG 58.330 52.381 1.02 0.00 41.13 3.18


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

AutoCloner maintained by Alex Coulton.