Multiple sequence alignment - TraesCS2A01G233500

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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 TraesCS2A01G233500 chr2A 100.000 4895 0 0 1 4895 278907836 278902942 0.000000e+00 9040.0
1 TraesCS2A01G233500 chr2A 92.683 41 0 3 4144 4183 423175084 423175046 6.840000e-04 56.5
2 TraesCS2A01G233500 chr2D 94.724 3620 121 23 6 3616 204505768 204509326 0.000000e+00 5563.0
3 TraesCS2A01G233500 chr2D 93.142 452 30 1 4284 4735 204550152 204550602 0.000000e+00 662.0
4 TraesCS2A01G233500 chr2D 94.148 393 17 4 3614 4002 204509357 204509747 1.170000e-165 593.0
5 TraesCS2A01G233500 chr2D 96.226 106 4 0 4003 4108 204509802 204509907 1.810000e-39 174.0
6 TraesCS2A01G233500 chr2D 96.923 65 2 0 4769 4833 204550670 204550734 5.180000e-20 110.0
7 TraesCS2A01G233500 chr2D 97.674 43 1 0 4114 4156 204509936 204509978 1.890000e-09 75.0
8 TraesCS2A01G233500 chr2D 87.755 49 6 0 3903 3951 614813198 614813246 1.900000e-04 58.4
9 TraesCS2A01G233500 chr2B 93.562 3184 119 32 449 3616 258663679 258666792 0.000000e+00 4665.0
10 TraesCS2A01G233500 chr2B 82.940 1143 112 45 3614 4734 258666823 258667904 0.000000e+00 953.0
11 TraesCS2A01G233500 chr2B 90.888 428 22 4 17 443 258663211 258663622 4.280000e-155 558.0
12 TraesCS2A01G233500 chr2B 97.059 68 2 0 4828 4895 722371749 722371682 1.110000e-21 115.0
13 TraesCS2A01G233500 chr2B 100.000 40 0 0 4119 4158 258667347 258667386 1.890000e-09 75.0
14 TraesCS2A01G233500 chr2B 97.222 36 0 1 4152 4187 131332144 131332178 5.290000e-05 60.2
15 TraesCS2A01G233500 chr7A 98.529 68 1 0 4828 4895 368394109 368394042 2.390000e-23 121.0
16 TraesCS2A01G233500 chr7A 95.000 40 2 0 3912 3951 696849830 696849869 4.090000e-06 63.9
17 TraesCS2A01G233500 chr4D 98.529 68 1 0 4828 4895 310531272 310531205 2.390000e-23 121.0
18 TraesCS2A01G233500 chr4D 97.101 69 1 1 4828 4895 310570891 310570823 1.110000e-21 115.0
19 TraesCS2A01G233500 chr4D 96.552 58 2 0 4776 4833 310531262 310531205 4.030000e-16 97.1
20 TraesCS2A01G233500 chr3A 98.529 68 1 0 4828 4895 218259066 218259133 2.390000e-23 121.0
21 TraesCS2A01G233500 chr3A 98.529 68 1 0 4828 4895 218308480 218308547 2.390000e-23 121.0
22 TraesCS2A01G233500 chr5A 87.879 99 11 1 4735 4833 469518472 469518569 1.110000e-21 115.0
23 TraesCS2A01G233500 chr5A 85.859 99 6 5 4735 4833 394533552 394533462 1.120000e-16 99.0
24 TraesCS2A01G233500 chr3D 97.101 69 1 1 4828 4895 177641705 177641773 1.110000e-21 115.0
25 TraesCS2A01G233500 chr3D 97.059 68 2 0 4828 4895 312733181 312733248 1.110000e-21 115.0
26 TraesCS2A01G233500 chr3D 93.939 66 2 2 4768 4833 177641710 177641773 1.120000e-16 99.0
27 TraesCS2A01G233500 chr3D 93.182 44 3 0 3907 3950 611474370 611474327 1.140000e-06 65.8
28 TraesCS2A01G233500 chr6A 97.059 68 1 1 4828 4895 478111201 478111267 4.000000e-21 113.0
29 TraesCS2A01G233500 chr5D 85.859 99 8 5 4735 4833 56443609 56443517 3.120000e-17 100.0
30 TraesCS2A01G233500 chr5D 86.813 91 6 4 4735 4825 315675847 315675763 4.030000e-16 97.1
31 TraesCS2A01G233500 chr5D 95.000 40 2 0 3912 3951 66745476 66745437 4.090000e-06 63.9
32 TraesCS2A01G233500 chrUn 93.846 65 2 2 4769 4833 276929261 276929323 4.030000e-16 97.1
33 TraesCS2A01G233500 chr1B 84.694 98 9 5 4736 4833 495752549 495752458 5.220000e-15 93.5
34 TraesCS2A01G233500 chr4A 97.222 36 0 1 4152 4187 636525925 636525959 5.290000e-05 60.2
35 TraesCS2A01G233500 chr4A 97.222 36 0 1 4152 4187 636560494 636560528 5.290000e-05 60.2
36 TraesCS2A01G233500 chr4A 96.970 33 0 1 4155 4187 590337436 590337467 2.000000e-03 54.7
37 TraesCS2A01G233500 chr3B 90.000 50 0 4 4152 4197 677612921 677612873 5.290000e-05 60.2
38 TraesCS2A01G233500 chr7B 92.683 41 1 2 4148 4187 245206094 245206133 1.900000e-04 58.4
39 TraesCS2A01G233500 chr7B 92.683 41 1 2 4147 4187 635750346 635750384 1.900000e-04 58.4
40 TraesCS2A01G233500 chr7D 92.500 40 2 1 3912 3951 18804154 18804116 6.840000e-04 56.5
41 TraesCS2A01G233500 chr7D 88.636 44 5 0 3907 3950 157241080 157241123 2.000000e-03 54.7
42 TraesCS2A01G233500 chr4B 97.059 34 0 1 4154 4187 667852770 667852802 6.840000e-04 56.5
43 TraesCS2A01G233500 chr5B 94.118 34 2 0 3917 3950 401142084 401142117 9.000000e-03 52.8


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 TraesCS2A01G233500 chr2A 278902942 278907836 4894 True 9040.00 9040 100.0000 1 4895 1 chr2A.!!$R1 4894
1 TraesCS2A01G233500 chr2D 204505768 204509978 4210 False 1601.25 5563 95.6930 6 4156 4 chr2D.!!$F2 4150
2 TraesCS2A01G233500 chr2D 204550152 204550734 582 False 386.00 662 95.0325 4284 4833 2 chr2D.!!$F3 549
3 TraesCS2A01G233500 chr2B 258663211 258667904 4693 False 1562.75 4665 91.8475 17 4734 4 chr2B.!!$F2 4717

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
281 282 0.472471 TGGCCTTCTTTCCAACTCGT 59.528 50.000 3.32 0.00 0.0 4.18 F
399 402 1.070786 GCCTGTCAACCGGTCTGAA 59.929 57.895 8.04 4.85 0.0 3.02 F
1271 1334 1.078497 CTGGCCATCAACCGCACTA 60.078 57.895 5.51 0.00 0.0 2.74 F
1990 2054 1.483415 AGCACCCATGGCATTTTGATC 59.517 47.619 6.09 0.00 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2030 1.037030 AAATGCCATGGGTGCTACCG 61.037 55.000 15.13 0.00 39.83 4.02 R
1995 2059 1.076485 GGTGAGGCTTGCCATCCAT 60.076 57.895 14.54 0.00 0.00 3.41 R
2461 2535 0.801251 GTGTCAACCATGAGCAGCTC 59.199 55.000 16.21 16.21 35.88 4.09 R
3956 4119 0.398948 GGTACTCCCCCGTCCCATAA 60.399 60.000 0.00 0.00 0.00 1.90 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
20 21 3.953874 CATCTTCGCTCTACTCGAGAA 57.046 47.619 21.68 2.99 42.62 2.87
208 209 9.245962 CGGTGTATAGTCAATTTAAAGGAGTAG 57.754 37.037 10.95 0.00 0.00 2.57
280 281 1.826385 ATGGCCTTCTTTCCAACTCG 58.174 50.000 3.32 0.00 35.75 4.18
281 282 0.472471 TGGCCTTCTTTCCAACTCGT 59.528 50.000 3.32 0.00 0.00 4.18
292 293 7.575332 TCTTTCCAACTCGTTTTTCAAAAAG 57.425 32.000 0.00 0.00 0.00 2.27
293 294 7.371936 TCTTTCCAACTCGTTTTTCAAAAAGA 58.628 30.769 0.00 0.00 35.61 2.52
302 303 7.644986 TCGTTTTTCAAAAAGAGAGCAAAAA 57.355 28.000 0.00 0.00 32.77 1.94
350 351 5.981174 TGGCTGGTTGGTTAGTAATAGTAC 58.019 41.667 0.00 0.00 0.00 2.73
386 388 2.383245 CTTGGGTGTCTGTCGCCTGT 62.383 60.000 4.58 0.00 45.32 4.00
399 402 1.070786 GCCTGTCAACCGGTCTGAA 59.929 57.895 8.04 4.85 0.00 3.02
466 520 6.814644 ACACACCATCATGAATAATTTTGCTG 59.185 34.615 0.00 0.00 0.00 4.41
493 547 4.389077 CCGTATTTCAAGGAGTTGACTCAC 59.611 45.833 12.76 3.14 42.60 3.51
535 589 2.178580 GGAATTCTGGTTTCCATGCCA 58.821 47.619 5.23 0.00 41.91 4.92
601 655 4.479158 TGCCCTTTTACCATTCAAACTCT 58.521 39.130 0.00 0.00 0.00 3.24
653 707 7.361894 CAATTTAAAGGCCAAACCATTGAAAG 58.638 34.615 5.01 0.00 43.14 2.62
1086 1149 2.765699 AGTGACACCAATTTGCCAAACT 59.234 40.909 0.84 0.00 0.00 2.66
1151 1214 4.523382 GCAGGAAGCTCGTGAACTATCAC 61.523 52.174 9.18 0.00 45.38 3.06
1192 1255 5.113446 AGCTCAAGACATGGAATCTGAAT 57.887 39.130 0.00 0.00 0.00 2.57
1271 1334 1.078497 CTGGCCATCAACCGCACTA 60.078 57.895 5.51 0.00 0.00 2.74
1370 1433 2.604046 CAGGGACACTGCCTACATAC 57.396 55.000 0.00 0.00 35.31 2.39
1603 1666 4.072131 TCTTGTACTTGATTGGAGCAACC 58.928 43.478 0.00 0.00 39.54 3.77
1730 1793 5.336150 TCATCTTTACAAGGCTCTCTCTG 57.664 43.478 0.00 0.00 0.00 3.35
1732 1795 2.899900 TCTTTACAAGGCTCTCTCTGCA 59.100 45.455 0.00 0.00 0.00 4.41
1818 1881 5.762179 TGTGAACTCTCATTTATCAGGGT 57.238 39.130 0.00 0.00 33.05 4.34
1835 1898 3.933332 CAGGGTCAAATCTTACTTCGGTC 59.067 47.826 0.00 0.00 0.00 4.79
1849 1913 4.461198 ACTTCGGTCATTTTCTTCCAGTT 58.539 39.130 0.00 0.00 0.00 3.16
1897 1961 8.760569 TCTTCTTTGTTGAATAAAATTTTCGCC 58.239 29.630 6.72 0.00 0.00 5.54
1909 1973 4.929819 AATTTTCGCCTTAGGTTTGTGT 57.070 36.364 0.00 0.00 0.00 3.72
1961 2025 9.218440 CTAATTTATTTTCAAACAATGGGCACT 57.782 29.630 0.00 0.00 0.00 4.40
1963 2027 8.776376 ATTTATTTTCAAACAATGGGCACTAG 57.224 30.769 0.00 0.00 0.00 2.57
1964 2028 3.658757 TTTCAAACAATGGGCACTAGC 57.341 42.857 0.00 0.00 41.10 3.42
1965 2029 2.284754 TCAAACAATGGGCACTAGCA 57.715 45.000 0.00 0.00 44.61 3.49
1990 2054 1.483415 AGCACCCATGGCATTTTGATC 59.517 47.619 6.09 0.00 0.00 2.92
1992 2056 2.158871 GCACCCATGGCATTTTGATCAT 60.159 45.455 6.09 0.00 0.00 2.45
1995 2059 5.672503 CACCCATGGCATTTTGATCATTAA 58.327 37.500 6.09 0.00 0.00 1.40
1996 2060 6.292923 CACCCATGGCATTTTGATCATTAAT 58.707 36.000 6.09 0.00 0.00 1.40
1997 2061 6.203915 CACCCATGGCATTTTGATCATTAATG 59.796 38.462 19.33 19.33 33.49 1.90
2011 2076 2.824689 TTAATGGATGGCAAGCCTCA 57.175 45.000 12.96 8.49 36.94 3.86
2047 2112 3.941188 CTGCACCCCACACCGAGT 61.941 66.667 0.00 0.00 0.00 4.18
2138 2203 3.817084 CTGAAAAGGCACAAGTGAGATGA 59.183 43.478 4.04 0.00 0.00 2.92
2395 2469 9.093458 ACAGGAAAAGGAAAATGTGATCTAATT 57.907 29.630 0.00 0.00 0.00 1.40
2627 2701 4.513442 TGTTCTAAGTTGTGACACTGCTT 58.487 39.130 7.20 12.53 0.00 3.91
2843 2917 5.613577 GCTTCGAGTTTCAGATGTGAGTTTC 60.614 44.000 0.00 0.00 32.98 2.78
3116 3190 1.648467 GGTCAAGAACAGCATCCGGC 61.648 60.000 0.00 0.00 45.30 6.13
3174 3248 0.742281 CGTCAGTGGATTGGAGCCTG 60.742 60.000 0.00 0.00 0.00 4.85
3361 3435 6.998074 TGGTCCATAAAGGTAATGCTTATGAG 59.002 38.462 0.00 0.00 35.82 2.90
3401 3475 7.984050 CACAGTCTAAGTGACCTATCATTCATT 59.016 37.037 0.00 0.00 46.46 2.57
3402 3476 8.200792 ACAGTCTAAGTGACCTATCATTCATTC 58.799 37.037 0.00 0.00 46.46 2.67
3403 3477 8.200120 CAGTCTAAGTGACCTATCATTCATTCA 58.800 37.037 0.00 0.00 46.46 2.57
3404 3478 8.932610 AGTCTAAGTGACCTATCATTCATTCAT 58.067 33.333 0.00 0.00 46.46 2.57
3459 3533 1.202065 CCAACCATCACGCGATTTCTG 60.202 52.381 15.93 0.00 0.00 3.02
3708 3850 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
3709 3851 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
3710 3852 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
3711 3853 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
3712 3854 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
3713 3855 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
3714 3856 2.015726 GGAGGAGGAGGAGGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
3715 3857 1.541672 GAGGAGGAGGAGGAGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
3716 3858 0.996762 GAGGAGGAGGAGGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
3717 3859 1.231928 GGAGGAGGAGGAGGGAGAC 59.768 68.421 0.00 0.00 0.00 3.36
3718 3860 1.152839 GAGGAGGAGGAGGGAGACG 60.153 68.421 0.00 0.00 0.00 4.18
3719 3861 2.123640 GGAGGAGGAGGGAGACGG 60.124 72.222 0.00 0.00 0.00 4.79
3720 3862 2.835895 GAGGAGGAGGGAGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
3721 3863 3.663815 GAGGAGGAGGGAGACGGCA 62.664 68.421 0.00 0.00 0.00 5.69
3722 3864 2.683933 GGAGGAGGGAGACGGCAA 60.684 66.667 0.00 0.00 0.00 4.52
3723 3865 2.726351 GGAGGAGGGAGACGGCAAG 61.726 68.421 0.00 0.00 0.00 4.01
3724 3866 2.685380 AGGAGGGAGACGGCAAGG 60.685 66.667 0.00 0.00 0.00 3.61
3725 3867 4.475135 GGAGGGAGACGGCAAGGC 62.475 72.222 0.00 0.00 0.00 4.35
3911 4074 1.092348 TGACTGCTGCATTCATCTGC 58.908 50.000 17.36 0.00 42.62 4.26
3918 4081 1.941294 CTGCATTCATCTGCTCACTCC 59.059 52.381 0.00 0.00 42.75 3.85
3921 4084 1.931841 CATTCATCTGCTCACTCCGTG 59.068 52.381 0.00 0.00 34.45 4.94
3932 4095 4.039852 TGCTCACTCCGTGCCATAATATAA 59.960 41.667 0.00 0.00 32.98 0.98
3935 4098 6.025749 TCACTCCGTGCCATAATATAAGAG 57.974 41.667 0.00 0.00 32.98 2.85
3938 4101 3.257375 TCCGTGCCATAATATAAGAGCGT 59.743 43.478 0.00 0.00 0.00 5.07
3942 4105 6.071463 CGTGCCATAATATAAGAGCGTTTTC 58.929 40.000 0.00 0.00 0.00 2.29
3943 4106 6.292649 CGTGCCATAATATAAGAGCGTTTTCA 60.293 38.462 0.00 0.00 0.00 2.69
3955 4118 9.865321 ATAAGAGCGTTTTCAACACTACTTATA 57.135 29.630 0.00 0.00 30.83 0.98
3956 4119 8.773404 AAGAGCGTTTTCAACACTACTTATAT 57.227 30.769 0.00 0.00 0.00 0.86
3958 4121 9.865321 AGAGCGTTTTCAACACTACTTATATTA 57.135 29.630 0.00 0.00 0.00 0.98
3961 4124 9.646336 GCGTTTTCAACACTACTTATATTATGG 57.354 33.333 0.00 0.00 0.00 2.74
4017 4234 3.536158 TTGCAGTGATTTGTTACGCTC 57.464 42.857 0.00 0.00 0.00 5.03
4026 4243 8.817100 CAGTGATTTGTTACGCTCAGATTTATA 58.183 33.333 0.00 0.00 0.00 0.98
4108 4325 4.026356 ACTAGTGAGATTTGCTTTGGCT 57.974 40.909 0.00 0.00 39.59 4.75
4109 4326 3.755378 ACTAGTGAGATTTGCTTTGGCTG 59.245 43.478 0.00 0.00 39.59 4.85
4110 4327 2.867624 AGTGAGATTTGCTTTGGCTGA 58.132 42.857 0.00 0.00 39.59 4.26
4111 4328 3.225104 AGTGAGATTTGCTTTGGCTGAA 58.775 40.909 0.00 0.00 39.59 3.02
4112 4329 3.830755 AGTGAGATTTGCTTTGGCTGAAT 59.169 39.130 0.00 0.00 39.59 2.57
4158 4422 3.128068 TGTGAGCGAAACGAGCTATTAGA 59.872 43.478 0.00 0.00 46.13 2.10
4159 4423 3.726730 GTGAGCGAAACGAGCTATTAGAG 59.273 47.826 0.00 0.00 46.13 2.43
4179 4443 6.935240 AGAGCATGGTTAATAGTATAGCCA 57.065 37.500 0.00 3.65 39.96 4.75
4180 4444 7.316393 AGAGCATGGTTAATAGTATAGCCAA 57.684 36.000 0.00 0.00 39.25 4.52
4181 4445 7.162082 AGAGCATGGTTAATAGTATAGCCAAC 58.838 38.462 0.00 2.18 39.25 3.77
4182 4446 7.016661 AGAGCATGGTTAATAGTATAGCCAACT 59.983 37.037 0.00 5.70 39.25 3.16
4183 4447 7.518188 AGCATGGTTAATAGTATAGCCAACTT 58.482 34.615 0.00 0.00 39.25 2.66
4184 4448 7.445402 AGCATGGTTAATAGTATAGCCAACTTG 59.555 37.037 0.00 1.96 39.25 3.16
4185 4449 7.584987 CATGGTTAATAGTATAGCCAACTTGC 58.415 38.462 4.90 0.00 39.25 4.01
4186 4450 6.895782 TGGTTAATAGTATAGCCAACTTGCT 58.104 36.000 0.00 0.00 45.38 3.91
4187 4451 6.990349 TGGTTAATAGTATAGCCAACTTGCTC 59.010 38.462 0.00 0.00 41.68 4.26
4188 4452 7.147549 TGGTTAATAGTATAGCCAACTTGCTCT 60.148 37.037 0.00 0.00 41.68 4.09
4189 4453 7.715686 GGTTAATAGTATAGCCAACTTGCTCTT 59.284 37.037 0.00 0.00 41.68 2.85
4190 4454 9.760077 GTTAATAGTATAGCCAACTTGCTCTTA 57.240 33.333 0.00 0.00 41.68 2.10
4191 4455 9.982651 TTAATAGTATAGCCAACTTGCTCTTAG 57.017 33.333 0.00 0.00 41.68 2.18
4192 4456 5.941555 AGTATAGCCAACTTGCTCTTAGT 57.058 39.130 0.00 0.00 41.68 2.24
4193 4457 5.908341 AGTATAGCCAACTTGCTCTTAGTC 58.092 41.667 0.00 0.00 41.68 2.59
4194 4458 4.826274 ATAGCCAACTTGCTCTTAGTCA 57.174 40.909 0.00 0.00 41.68 3.41
4195 4459 3.710209 AGCCAACTTGCTCTTAGTCAT 57.290 42.857 0.00 0.00 36.75 3.06
4196 4460 4.026356 AGCCAACTTGCTCTTAGTCATT 57.974 40.909 0.00 0.00 36.75 2.57
4197 4461 5.165961 AGCCAACTTGCTCTTAGTCATTA 57.834 39.130 0.00 0.00 36.75 1.90
4198 4462 5.560724 AGCCAACTTGCTCTTAGTCATTAA 58.439 37.500 0.00 0.00 36.75 1.40
4199 4463 5.412904 AGCCAACTTGCTCTTAGTCATTAAC 59.587 40.000 0.00 0.00 36.75 2.01
4200 4464 5.412904 GCCAACTTGCTCTTAGTCATTAACT 59.587 40.000 0.00 0.00 42.33 2.24
4201 4465 6.072452 GCCAACTTGCTCTTAGTCATTAACTT 60.072 38.462 0.00 0.00 39.55 2.66
4202 4466 7.522374 CCAACTTGCTCTTAGTCATTAACTTC 58.478 38.462 0.00 0.00 39.55 3.01
4203 4467 7.389053 CCAACTTGCTCTTAGTCATTAACTTCT 59.611 37.037 0.00 0.00 39.55 2.85
4204 4468 8.778358 CAACTTGCTCTTAGTCATTAACTTCTT 58.222 33.333 0.00 0.00 39.55 2.52
4205 4469 8.910351 ACTTGCTCTTAGTCATTAACTTCTTT 57.090 30.769 0.00 0.00 39.55 2.52
4206 4470 9.343539 ACTTGCTCTTAGTCATTAACTTCTTTT 57.656 29.630 0.00 0.00 39.55 2.27
4227 4491 3.452755 TTCGAGATATGCCAATGACGT 57.547 42.857 0.00 0.00 0.00 4.34
4229 4493 4.783764 TCGAGATATGCCAATGACGTAT 57.216 40.909 0.00 0.00 0.00 3.06
4272 4536 9.267084 GAAGAAAGCATTGTTTATAAAAACCCA 57.733 29.630 0.00 0.00 43.66 4.51
4273 4537 9.791801 AAGAAAGCATTGTTTATAAAAACCCAT 57.208 25.926 0.00 0.00 43.66 4.00
4303 4567 2.095263 GCAAACATCGCAACAGGTACAT 60.095 45.455 0.00 0.00 0.00 2.29
4340 4604 1.909986 AGAAAAGGCCTACTCTCCCAC 59.090 52.381 5.16 0.00 0.00 4.61
4356 4620 2.767960 TCCCACGAATCTAGTTAACCCC 59.232 50.000 0.88 0.00 0.00 4.95
4364 4628 3.659183 TCTAGTTAACCCCGCTACTCT 57.341 47.619 0.88 0.00 0.00 3.24
4376 4640 1.067212 CGCTACTCTAACTCCGGCAAT 59.933 52.381 0.00 0.00 0.00 3.56
4380 4644 4.395231 GCTACTCTAACTCCGGCAATTTTT 59.605 41.667 0.00 0.00 0.00 1.94
4394 4658 8.690884 TCCGGCAATTTTTCATATTTTGATCTA 58.309 29.630 0.00 0.00 33.34 1.98
4445 4709 4.127171 GGTGTTCTAACTTGCTCAACTCA 58.873 43.478 0.00 0.00 0.00 3.41
4470 4734 2.614829 ACACTCTTGCGTACCTTTGT 57.385 45.000 0.00 0.00 0.00 2.83
4545 4809 1.438710 CTCGCGAAAGTTTGCACGG 60.439 57.895 11.33 0.00 37.43 4.94
4583 4847 4.107072 TCCATGAAGGAGTCATCTTCCTT 58.893 43.478 6.25 6.25 44.01 3.36
4587 4851 1.490574 AGGAGTCATCTTCCTTCGGG 58.509 55.000 0.00 0.00 0.00 5.14
4633 4897 0.467804 AAAACAACCATGCCACACCC 59.532 50.000 0.00 0.00 0.00 4.61
4674 4938 5.312895 TGTGCCAATATATGTATGGTCCAC 58.687 41.667 0.00 5.28 0.00 4.02
4693 4957 0.612174 CGGTGTCCTCCTCCTGAAGA 60.612 60.000 0.00 0.00 0.00 2.87
4740 5048 1.398390 CGGAAGTACATGCCTGAAAGC 59.602 52.381 0.00 0.00 0.00 3.51
4744 5052 0.179189 GTACATGCCTGAAAGCGCAC 60.179 55.000 11.47 0.51 41.64 5.34
4746 5054 2.669569 ATGCCTGAAAGCGCACGT 60.670 55.556 11.47 0.00 41.64 4.49
4753 5061 1.324736 CTGAAAGCGCACGTTATCTCC 59.675 52.381 11.47 0.00 0.00 3.71
4754 5062 0.651031 GAAAGCGCACGTTATCTCCC 59.349 55.000 11.47 0.00 0.00 4.30
4758 5066 0.249489 GCGCACGTTATCTCCCAGAT 60.249 55.000 0.30 0.00 38.70 2.90
4759 5067 1.491670 CGCACGTTATCTCCCAGATG 58.508 55.000 0.00 0.00 35.37 2.90
4760 5068 1.869754 CGCACGTTATCTCCCAGATGG 60.870 57.143 0.00 0.00 35.37 3.51
4774 5082 4.301662 ATGGGAGGGTGGGGTGGT 62.302 66.667 0.00 0.00 0.00 4.16
4782 5090 1.458486 GGTGGGGTGGTGTGAATGA 59.542 57.895 0.00 0.00 0.00 2.57
4833 5141 3.931578 AGAATTTGACGAAGACCAGAGG 58.068 45.455 0.00 0.00 0.00 3.69
4834 5142 2.770164 ATTTGACGAAGACCAGAGGG 57.230 50.000 0.00 0.00 41.29 4.30
4835 5143 0.685097 TTTGACGAAGACCAGAGGGG 59.315 55.000 0.00 0.00 44.81 4.79
4836 5144 1.192146 TTGACGAAGACCAGAGGGGG 61.192 60.000 0.00 0.00 42.91 5.40
4852 5160 2.550277 GGGGGTGAATGGGAGATTTT 57.450 50.000 0.00 0.00 0.00 1.82
4853 5161 2.832838 GGGGGTGAATGGGAGATTTTT 58.167 47.619 0.00 0.00 0.00 1.94
4854 5162 3.989056 GGGGGTGAATGGGAGATTTTTA 58.011 45.455 0.00 0.00 0.00 1.52
4855 5163 3.960755 GGGGGTGAATGGGAGATTTTTAG 59.039 47.826 0.00 0.00 0.00 1.85
4856 5164 4.325816 GGGGGTGAATGGGAGATTTTTAGA 60.326 45.833 0.00 0.00 0.00 2.10
4857 5165 5.269189 GGGGTGAATGGGAGATTTTTAGAA 58.731 41.667 0.00 0.00 0.00 2.10
4858 5166 5.719563 GGGGTGAATGGGAGATTTTTAGAAA 59.280 40.000 0.00 0.00 0.00 2.52
4859 5167 6.384015 GGGGTGAATGGGAGATTTTTAGAAAT 59.616 38.462 0.00 0.00 38.16 2.17
4860 5168 7.092891 GGGGTGAATGGGAGATTTTTAGAAATT 60.093 37.037 0.00 0.00 35.65 1.82
4861 5169 7.981789 GGGTGAATGGGAGATTTTTAGAAATTC 59.018 37.037 0.00 0.00 35.65 2.17
4862 5170 7.702348 GGTGAATGGGAGATTTTTAGAAATTCG 59.298 37.037 0.00 0.00 35.65 3.34
4863 5171 8.244113 GTGAATGGGAGATTTTTAGAAATTCGT 58.756 33.333 0.00 0.00 35.65 3.85
4864 5172 8.458843 TGAATGGGAGATTTTTAGAAATTCGTC 58.541 33.333 0.00 0.00 35.65 4.20
4865 5173 7.938140 ATGGGAGATTTTTAGAAATTCGTCA 57.062 32.000 0.00 0.00 35.65 4.35
4866 5174 7.753309 TGGGAGATTTTTAGAAATTCGTCAA 57.247 32.000 0.00 0.00 35.65 3.18
4867 5175 8.172352 TGGGAGATTTTTAGAAATTCGTCAAA 57.828 30.769 0.00 0.00 35.65 2.69
4868 5176 8.079809 TGGGAGATTTTTAGAAATTCGTCAAAC 58.920 33.333 0.00 0.00 35.65 2.93
4869 5177 8.297426 GGGAGATTTTTAGAAATTCGTCAAACT 58.703 33.333 0.00 0.00 35.65 2.66
4870 5178 9.331106 GGAGATTTTTAGAAATTCGTCAAACTC 57.669 33.333 0.00 0.00 35.65 3.01
4888 5196 8.657074 TCAAACTCTAAAGAATTTGACGAAGA 57.343 30.769 11.43 0.00 42.85 2.87
4889 5197 9.273016 TCAAACTCTAAAGAATTTGACGAAGAT 57.727 29.630 11.43 0.00 42.85 2.40
4890 5198 9.535270 CAAACTCTAAAGAATTTGACGAAGATC 57.465 33.333 7.91 0.00 42.01 2.75
4891 5199 8.833231 AACTCTAAAGAATTTGACGAAGATCA 57.167 30.769 0.00 0.00 39.63 2.92
4892 5200 8.472683 ACTCTAAAGAATTTGACGAAGATCAG 57.527 34.615 0.00 0.00 39.63 2.90
4893 5201 8.307483 ACTCTAAAGAATTTGACGAAGATCAGA 58.693 33.333 0.00 0.00 39.63 3.27
4894 5202 8.694975 TCTAAAGAATTTGACGAAGATCAGAG 57.305 34.615 0.00 0.00 39.63 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.953874 TTCTCGAGTAGAGCGAAGATG 57.046 47.619 13.13 0.00 46.44 2.90
1 2 4.966965 TTTTCTCGAGTAGAGCGAAGAT 57.033 40.909 13.13 0.00 46.44 2.40
29 30 1.202143 CGGATTTCGCCTTGTAAAGCC 60.202 52.381 0.00 0.00 44.44 4.35
253 254 4.735369 TGGAAAGAAGGCCATAGTTGAAA 58.265 39.130 5.01 0.00 0.00 2.69
350 351 3.057526 CCCAAGGTAAAAGAAAAGGAGCG 60.058 47.826 0.00 0.00 0.00 5.03
386 388 5.677319 AGAATAAGATTCAGACCGGTTGA 57.323 39.130 9.42 11.98 0.00 3.18
466 520 2.005971 ACTCCTTGAAATACGGCGTC 57.994 50.000 19.21 1.76 0.00 5.19
493 547 5.030295 CCATAAAAGCATAAACGACTGCAG 58.970 41.667 13.48 13.48 40.88 4.41
535 589 6.543465 TCAACAAGAATGTGAGACAAGACAAT 59.457 34.615 0.00 0.00 40.46 2.71
653 707 6.881602 AGTTGGGAAGAATGTAGATTTCAGAC 59.118 38.462 0.00 0.00 0.00 3.51
747 807 9.399797 TGTATGCAAAATAAGAATCAGAGACAT 57.600 29.630 0.00 0.00 0.00 3.06
806 866 8.553696 ACGACAAAACTACAGTAAATGTTTAGG 58.446 33.333 0.00 0.00 39.96 2.69
980 1041 5.129320 TCCATTTAGTTCTGCTGCATAGAGA 59.871 40.000 1.31 0.00 0.00 3.10
981 1042 5.363101 TCCATTTAGTTCTGCTGCATAGAG 58.637 41.667 1.31 0.00 0.00 2.43
1086 1149 7.014711 TGTTATACATGCAAGAACCAAAGGAAA 59.985 33.333 0.00 0.00 0.00 3.13
1115 1178 1.667236 TCCTGCATGATTAAGCACCG 58.333 50.000 0.00 0.00 36.62 4.94
1192 1255 1.225855 CTAACTGTTGCTGCCGTTCA 58.774 50.000 2.69 0.00 0.00 3.18
1231 1294 7.002879 CCAGATCTCCCATGTATTTCAGATTT 58.997 38.462 0.00 0.00 0.00 2.17
1271 1334 2.292267 CTCGCAAAATACCCTGAGCAT 58.708 47.619 0.00 0.00 0.00 3.79
1309 1372 2.362077 GTCATGGAACCTTGCTGTGTTT 59.638 45.455 0.00 0.00 0.00 2.83
1370 1433 2.616510 GGCCTATGATCGGAATTCCCAG 60.617 54.545 19.01 5.97 34.14 4.45
1543 1606 4.475028 TGCACGCAATTTCTTTATCAGTG 58.525 39.130 0.00 0.00 0.00 3.66
1603 1666 4.202050 CCCTTGTCTTTGTCTGAAAACAGG 60.202 45.833 0.00 0.00 0.00 4.00
1730 1793 3.157932 AGAGTGAGAAGACGCTAATGC 57.842 47.619 0.00 0.00 0.00 3.56
1732 1795 5.285651 GCAATAGAGTGAGAAGACGCTAAT 58.714 41.667 0.00 0.00 32.81 1.73
1818 1881 7.979444 AGAAAATGACCGAAGTAAGATTTGA 57.021 32.000 0.00 0.00 0.00 2.69
1849 1913 6.235664 AGAAGGGTTTGCGAAGTTAAATAGA 58.764 36.000 0.00 0.00 0.00 1.98
1897 1961 5.811399 TCACTGTTTCACACAAACCTAAG 57.189 39.130 0.00 0.00 33.87 2.18
1954 2018 3.014085 GCTACCGTGCTAGTGCCCA 62.014 63.158 0.00 0.00 38.71 5.36
1961 2025 1.520192 CATGGGTGCTACCGTGCTA 59.480 57.895 6.54 0.00 40.38 3.49
1962 2026 2.268920 CATGGGTGCTACCGTGCT 59.731 61.111 6.54 0.00 40.38 4.40
1963 2027 2.824041 CCATGGGTGCTACCGTGC 60.824 66.667 2.85 0.00 44.48 5.34
1964 2028 2.824041 GCCATGGGTGCTACCGTG 60.824 66.667 15.13 11.19 45.24 4.94
1965 2029 2.210144 AATGCCATGGGTGCTACCGT 62.210 55.000 15.13 0.00 39.83 4.83
1966 2030 1.037030 AAATGCCATGGGTGCTACCG 61.037 55.000 15.13 0.00 39.83 4.02
1967 2031 1.134729 CAAAATGCCATGGGTGCTACC 60.135 52.381 15.13 0.00 37.60 3.18
1968 2032 1.824230 TCAAAATGCCATGGGTGCTAC 59.176 47.619 15.13 0.00 0.00 3.58
1990 2054 2.960384 TGAGGCTTGCCATCCATTAATG 59.040 45.455 14.54 8.58 0.00 1.90
1992 2056 2.378038 GTGAGGCTTGCCATCCATTAA 58.622 47.619 14.54 0.00 0.00 1.40
1995 2059 1.076485 GGTGAGGCTTGCCATCCAT 60.076 57.895 14.54 0.00 0.00 3.41
1996 2060 2.356278 GGTGAGGCTTGCCATCCA 59.644 61.111 14.54 5.93 0.00 3.41
1997 2061 1.751927 CTGGTGAGGCTTGCCATCC 60.752 63.158 14.54 12.39 0.00 3.51
2030 2095 3.941188 ACTCGGTGTGGGGTGCAG 61.941 66.667 0.00 0.00 0.00 4.41
2047 2112 4.471904 AACATTAGAGAACCGAGCATCA 57.528 40.909 0.00 0.00 33.17 3.07
2091 2156 4.576053 TCTTATTCCACTGTGCATGCATAC 59.424 41.667 25.64 12.77 0.00 2.39
2229 2302 1.374947 CGAGAACCCAGAAGGCCAA 59.625 57.895 5.01 0.00 40.58 4.52
2395 2469 9.341078 ACATGTTCTGTATATCAAATACATGCA 57.659 29.630 0.00 0.00 39.71 3.96
2461 2535 0.801251 GTGTCAACCATGAGCAGCTC 59.199 55.000 16.21 16.21 35.88 4.09
2627 2701 9.201989 AGATACATTAGAACACTTCCATACTGA 57.798 33.333 0.00 0.00 0.00 3.41
2711 2785 2.133520 AGTGCTGGATCATCCTCCATT 58.866 47.619 4.96 0.00 44.23 3.16
2771 2845 1.928868 CTTCCTTTGCTGGTTGGGAT 58.071 50.000 0.00 0.00 0.00 3.85
2843 2917 8.624956 AGTATGGCTACGAATTACCGAAAGGG 62.625 46.154 0.00 0.00 43.89 3.95
2973 3047 4.437967 TGGGAATAGATGCAGGATCCATA 58.562 43.478 15.82 0.00 0.00 2.74
3116 3190 4.715523 ACCCACCAACATCGCCGG 62.716 66.667 0.00 0.00 0.00 6.13
3174 3248 5.363101 TGTTTGATCTCTGATGCATACTCC 58.637 41.667 0.00 0.00 0.00 3.85
3361 3435 1.109323 ACTGTGGACAAAGCTTGCCC 61.109 55.000 0.00 2.17 33.27 5.36
3401 3475 8.217111 TGATGCTTTCCACCTACAATTATATGA 58.783 33.333 0.00 0.00 0.00 2.15
3402 3476 8.394971 TGATGCTTTCCACCTACAATTATATG 57.605 34.615 0.00 0.00 0.00 1.78
3403 3477 8.995027 TTGATGCTTTCCACCTACAATTATAT 57.005 30.769 0.00 0.00 0.00 0.86
3404 3478 8.271458 TCTTGATGCTTTCCACCTACAATTATA 58.729 33.333 0.00 0.00 0.00 0.98
3420 3494 1.064832 GGGAGCTCCTTCTTGATGCTT 60.065 52.381 31.36 0.00 33.83 3.91
3459 3533 1.671379 GGGAAGTGACCGTTGCTCC 60.671 63.158 0.00 0.00 0.00 4.70
3708 3850 4.475135 GCCTTGCCGTCTCCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
3709 3851 4.821589 CGCCTTGCCGTCTCCCTC 62.822 72.222 0.00 0.00 0.00 4.30
3718 3860 4.803908 CTCTTCCCCCGCCTTGCC 62.804 72.222 0.00 0.00 0.00 4.52
3719 3861 4.803908 CCTCTTCCCCCGCCTTGC 62.804 72.222 0.00 0.00 0.00 4.01
3720 3862 3.009115 TCCTCTTCCCCCGCCTTG 61.009 66.667 0.00 0.00 0.00 3.61
3721 3863 2.689034 CTCCTCTTCCCCCGCCTT 60.689 66.667 0.00 0.00 0.00 4.35
3722 3864 4.806339 CCTCCTCTTCCCCCGCCT 62.806 72.222 0.00 0.00 0.00 5.52
3725 3867 2.770048 ATGCCTCCTCTTCCCCCG 60.770 66.667 0.00 0.00 0.00 5.73
3918 4081 5.591643 AAACGCTCTTATATTATGGCACG 57.408 39.130 0.00 0.00 0.00 5.34
3921 4084 7.837898 GTTGAAAACGCTCTTATATTATGGC 57.162 36.000 0.00 0.00 36.92 4.40
3942 4105 6.872020 CCCGTCCCATAATATAAGTAGTGTTG 59.128 42.308 0.00 0.00 0.00 3.33
3943 4106 6.013984 CCCCGTCCCATAATATAAGTAGTGTT 60.014 42.308 0.00 0.00 0.00 3.32
3955 4118 1.725803 GTACTCCCCCGTCCCATAAT 58.274 55.000 0.00 0.00 0.00 1.28
3956 4119 0.398948 GGTACTCCCCCGTCCCATAA 60.399 60.000 0.00 0.00 0.00 1.90
3958 4121 2.041197 GGTACTCCCCCGTCCCAT 60.041 66.667 0.00 0.00 0.00 4.00
3959 4122 2.480255 AATGGTACTCCCCCGTCCCA 62.480 60.000 0.00 0.00 0.00 4.37
3961 4124 0.622136 AAAATGGTACTCCCCCGTCC 59.378 55.000 0.00 0.00 0.00 4.79
3962 4125 3.851458 ATAAAATGGTACTCCCCCGTC 57.149 47.619 0.00 0.00 0.00 4.79
3964 4127 2.621526 GCAATAAAATGGTACTCCCCCG 59.378 50.000 0.00 0.00 0.00 5.73
4017 4234 2.291465 TCGACGTCCCGGTATAAATCTG 59.709 50.000 10.58 0.00 0.00 2.90
4036 4253 0.030369 GTGTGGGTATCTAGCCGTCG 59.970 60.000 1.32 0.00 46.56 5.12
4108 4325 4.887655 TCAGCTACCGATGACTCTTATTCA 59.112 41.667 0.00 0.00 29.10 2.57
4109 4326 5.440234 TCAGCTACCGATGACTCTTATTC 57.560 43.478 0.00 0.00 29.10 1.75
4110 4327 5.854010 TTCAGCTACCGATGACTCTTATT 57.146 39.130 0.00 0.00 34.88 1.40
4111 4328 7.526142 TTATTCAGCTACCGATGACTCTTAT 57.474 36.000 0.00 0.00 34.88 1.73
4112 4329 6.954487 TTATTCAGCTACCGATGACTCTTA 57.046 37.500 0.00 0.00 34.88 2.10
4158 4422 7.079451 AGTTGGCTATACTATTAACCATGCT 57.921 36.000 0.00 0.00 0.00 3.79
4159 4423 7.584987 CAAGTTGGCTATACTATTAACCATGC 58.415 38.462 0.00 0.00 0.00 4.06
4160 4424 7.445402 AGCAAGTTGGCTATACTATTAACCATG 59.555 37.037 4.75 0.00 43.70 3.66
4161 4425 7.518188 AGCAAGTTGGCTATACTATTAACCAT 58.482 34.615 4.75 0.00 43.70 3.55
4163 4427 7.217906 AGAGCAAGTTGGCTATACTATTAACC 58.782 38.462 4.75 0.00 45.99 2.85
4164 4428 8.664211 AAGAGCAAGTTGGCTATACTATTAAC 57.336 34.615 4.75 0.00 45.99 2.01
4167 4431 8.024145 ACTAAGAGCAAGTTGGCTATACTATT 57.976 34.615 4.75 0.00 45.99 1.73
4168 4432 7.287927 TGACTAAGAGCAAGTTGGCTATACTAT 59.712 37.037 4.75 0.00 45.99 2.12
4170 4434 5.422331 TGACTAAGAGCAAGTTGGCTATACT 59.578 40.000 4.75 0.00 45.99 2.12
4172 4436 5.932619 TGACTAAGAGCAAGTTGGCTATA 57.067 39.130 4.75 0.09 45.99 1.31
4173 4437 4.826274 TGACTAAGAGCAAGTTGGCTAT 57.174 40.909 4.75 0.00 45.99 2.97
4175 4439 6.745474 AGTTAATGACTAAGAGCAAGTTGGCT 60.745 38.462 4.75 2.21 41.50 4.75
4176 4440 5.412904 AGTTAATGACTAAGAGCAAGTTGGC 59.587 40.000 4.75 0.00 36.65 4.52
4177 4441 7.389053 AGAAGTTAATGACTAAGAGCAAGTTGG 59.611 37.037 4.75 0.00 37.72 3.77
4178 4442 8.316640 AGAAGTTAATGACTAAGAGCAAGTTG 57.683 34.615 0.00 0.00 37.72 3.16
4179 4443 8.910351 AAGAAGTTAATGACTAAGAGCAAGTT 57.090 30.769 0.00 0.00 37.72 2.66
4180 4444 8.910351 AAAGAAGTTAATGACTAAGAGCAAGT 57.090 30.769 0.00 0.00 37.72 3.16
4204 4468 4.634004 ACGTCATTGGCATATCTCGAAAAA 59.366 37.500 0.00 0.00 0.00 1.94
4205 4469 4.188462 ACGTCATTGGCATATCTCGAAAA 58.812 39.130 0.00 0.00 0.00 2.29
4206 4470 3.792401 ACGTCATTGGCATATCTCGAAA 58.208 40.909 0.00 0.00 0.00 3.46
4207 4471 3.452755 ACGTCATTGGCATATCTCGAA 57.547 42.857 0.00 0.00 0.00 3.71
4208 4472 4.671766 CGATACGTCATTGGCATATCTCGA 60.672 45.833 3.21 0.00 0.00 4.04
4209 4473 3.543889 CGATACGTCATTGGCATATCTCG 59.456 47.826 3.21 0.00 0.00 4.04
4210 4474 4.486090 ACGATACGTCATTGGCATATCTC 58.514 43.478 3.21 0.00 33.69 2.75
4211 4475 4.521130 ACGATACGTCATTGGCATATCT 57.479 40.909 3.21 0.00 33.69 1.98
4212 4476 6.887376 AATACGATACGTCATTGGCATATC 57.113 37.500 0.00 0.00 41.54 1.63
4213 4477 7.667043 AAAATACGATACGTCATTGGCATAT 57.333 32.000 0.00 0.00 41.54 1.78
4214 4478 7.485418 AAAAATACGATACGTCATTGGCATA 57.515 32.000 0.00 0.00 41.54 3.14
4215 4479 6.371809 AAAAATACGATACGTCATTGGCAT 57.628 33.333 0.00 0.00 41.54 4.40
4216 4480 5.804692 AAAAATACGATACGTCATTGGCA 57.195 34.783 0.00 0.00 41.54 4.92
4245 4509 9.489084 GGGTTTTTATAAACAATGCTTTCTTCT 57.511 29.630 10.38 0.00 44.37 2.85
4255 4519 8.903059 TCCTACCATGGGTTTTTATAAACAAT 57.097 30.769 18.09 1.94 44.37 2.71
4263 4527 4.323569 TGCATCCTACCATGGGTTTTTA 57.676 40.909 18.09 0.00 37.09 1.52
4266 4530 2.831526 GTTTGCATCCTACCATGGGTTT 59.168 45.455 18.09 0.00 37.09 3.27
4272 4536 1.949525 GCGATGTTTGCATCCTACCAT 59.050 47.619 0.00 0.00 46.56 3.55
4273 4537 1.339535 TGCGATGTTTGCATCCTACCA 60.340 47.619 0.00 0.00 46.56 3.25
4296 4560 3.586470 TTGGTTGGTGTTGATGTACCT 57.414 42.857 0.00 0.00 37.84 3.08
4337 4601 2.817901 CGGGGTTAACTAGATTCGTGG 58.182 52.381 5.42 0.00 0.00 4.94
4340 4604 2.884894 AGCGGGGTTAACTAGATTCG 57.115 50.000 5.42 2.69 0.00 3.34
4356 4620 0.454600 TTGCCGGAGTTAGAGTAGCG 59.545 55.000 5.05 0.00 0.00 4.26
4364 4628 8.307483 TCAAAATATGAAAAATTGCCGGAGTTA 58.693 29.630 5.05 0.00 34.30 2.24
4394 4658 3.488778 TGGTGCAGCAAATTTTGGAAT 57.511 38.095 17.80 0.00 0.00 3.01
4445 4709 3.740115 AGGTACGCAAGAGTGTTCAATT 58.260 40.909 0.00 0.00 39.61 2.32
4470 4734 0.677731 CCGCTTGGCATCTCTGGAAA 60.678 55.000 0.00 0.00 0.00 3.13
4545 4809 0.914417 TGGAATGGTGGGAGAGGACC 60.914 60.000 0.00 0.00 0.00 4.46
4583 4847 3.547054 GGGTTAACATACACATCCCGA 57.453 47.619 8.10 0.00 0.00 5.14
4587 4851 3.486875 GCTTGCGGGTTAACATACACATC 60.487 47.826 8.10 0.00 0.00 3.06
4674 4938 0.612174 TCTTCAGGAGGAGGACACCG 60.612 60.000 0.00 0.00 34.73 4.94
4693 4957 4.130118 CTCCTTCTGCTTGTTACACTTGT 58.870 43.478 0.00 0.00 0.00 3.16
4721 4985 1.398390 CGCTTTCAGGCATGTACTTCC 59.602 52.381 0.00 0.00 0.00 3.46
4727 4991 2.956987 GTGCGCTTTCAGGCATGT 59.043 55.556 9.73 0.00 41.83 3.21
4740 5048 1.491670 CATCTGGGAGATAACGTGCG 58.508 55.000 0.00 0.00 32.12 5.34
4753 5061 3.099170 CCCCACCCTCCCATCTGG 61.099 72.222 0.00 0.00 0.00 3.86
4754 5062 2.286425 ACCCCACCCTCCCATCTG 60.286 66.667 0.00 0.00 0.00 2.90
4760 5068 3.966543 CACACCACCCCACCCTCC 61.967 72.222 0.00 0.00 0.00 4.30
4761 5069 1.789576 ATTCACACCACCCCACCCTC 61.790 60.000 0.00 0.00 0.00 4.30
4762 5070 1.778383 ATTCACACCACCCCACCCT 60.778 57.895 0.00 0.00 0.00 4.34
4763 5071 1.606313 CATTCACACCACCCCACCC 60.606 63.158 0.00 0.00 0.00 4.61
4764 5072 0.609131 CTCATTCACACCACCCCACC 60.609 60.000 0.00 0.00 0.00 4.61
4765 5073 0.400213 TCTCATTCACACCACCCCAC 59.600 55.000 0.00 0.00 0.00 4.61
4766 5074 0.692476 CTCTCATTCACACCACCCCA 59.308 55.000 0.00 0.00 0.00 4.96
4767 5075 0.984230 TCTCTCATTCACACCACCCC 59.016 55.000 0.00 0.00 0.00 4.95
4833 5141 2.550277 AAAATCTCCCATTCACCCCC 57.450 50.000 0.00 0.00 0.00 5.40
4834 5142 4.867086 TCTAAAAATCTCCCATTCACCCC 58.133 43.478 0.00 0.00 0.00 4.95
4835 5143 6.850752 TTTCTAAAAATCTCCCATTCACCC 57.149 37.500 0.00 0.00 0.00 4.61
4836 5144 7.702348 CGAATTTCTAAAAATCTCCCATTCACC 59.298 37.037 0.00 0.00 33.93 4.02
4837 5145 8.244113 ACGAATTTCTAAAAATCTCCCATTCAC 58.756 33.333 0.00 0.00 33.93 3.18
4838 5146 8.348285 ACGAATTTCTAAAAATCTCCCATTCA 57.652 30.769 0.00 0.00 33.93 2.57
4839 5147 8.458843 TGACGAATTTCTAAAAATCTCCCATTC 58.541 33.333 0.00 0.00 33.93 2.67
4840 5148 8.348285 TGACGAATTTCTAAAAATCTCCCATT 57.652 30.769 0.00 0.00 33.93 3.16
4841 5149 7.938140 TGACGAATTTCTAAAAATCTCCCAT 57.062 32.000 0.00 0.00 33.93 4.00
4842 5150 7.753309 TTGACGAATTTCTAAAAATCTCCCA 57.247 32.000 0.00 0.00 33.93 4.37
4843 5151 8.297426 AGTTTGACGAATTTCTAAAAATCTCCC 58.703 33.333 0.00 0.00 33.93 4.30
4844 5152 9.331106 GAGTTTGACGAATTTCTAAAAATCTCC 57.669 33.333 0.00 0.00 33.93 3.71
4864 5172 9.535270 GATCTTCGTCAAATTCTTTAGAGTTTG 57.465 33.333 16.96 16.96 46.52 2.93
4865 5173 9.273016 TGATCTTCGTCAAATTCTTTAGAGTTT 57.727 29.630 0.00 0.00 34.87 2.66
4866 5174 8.833231 TGATCTTCGTCAAATTCTTTAGAGTT 57.167 30.769 0.00 0.00 0.00 3.01
4867 5175 8.307483 TCTGATCTTCGTCAAATTCTTTAGAGT 58.693 33.333 0.00 0.00 0.00 3.24
4868 5176 8.694975 TCTGATCTTCGTCAAATTCTTTAGAG 57.305 34.615 0.00 0.00 0.00 2.43
4869 5177 8.694975 CTCTGATCTTCGTCAAATTCTTTAGA 57.305 34.615 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.