Multiple sequence alignment - TraesCS3A01G177300

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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 TraesCS3A01G177300 chr3A 100.000 3180 0 0 1 3180 199687875 199691054 0.000000e+00 5873.0
1 TraesCS3A01G177300 chr3D 95.374 1643 49 10 93 1715 168291873 168290238 0.000000e+00 2588.0
2 TraesCS3A01G177300 chr3D 97.476 515 7 2 1974 2488 168289646 168289138 0.000000e+00 874.0
3 TraesCS3A01G177300 chr3D 95.511 401 17 1 2477 2876 168289116 168288716 9.620000e-180 640.0
4 TraesCS3A01G177300 chr3D 93.114 334 13 2 2681 3013 168288716 168288392 6.170000e-132 481.0
5 TraesCS3A01G177300 chr3D 96.838 253 8 0 1720 1972 168290200 168289948 1.050000e-114 424.0
6 TraesCS3A01G177300 chr3D 91.818 110 8 1 3000 3109 75350868 75350976 5.490000e-33 152.0
7 TraesCS3A01G177300 chr3D 96.078 51 2 0 1974 2024 168289703 168289653 2.030000e-12 84.2
8 TraesCS3A01G177300 chr3B 95.018 1646 43 13 93 1700 243252489 243250845 0.000000e+00 2549.0
9 TraesCS3A01G177300 chr3B 96.355 631 12 4 1927 2552 243250307 243249683 0.000000e+00 1027.0
10 TraesCS3A01G177300 chr3B 94.725 436 20 3 2551 2986 243249589 243249157 0.000000e+00 675.0
11 TraesCS3A01G177300 chr3B 93.103 232 11 2 1699 1929 243250777 243250550 5.080000e-88 335.0
12 TraesCS3A01G177300 chr2B 87.791 172 15 4 3014 3180 178860185 178860355 2.500000e-46 196.0
13 TraesCS3A01G177300 chr2B 97.260 73 2 0 3108 3180 551106598 551106670 1.200000e-24 124.0
14 TraesCS3A01G177300 chr7B 97.917 96 2 0 3014 3109 141165831 141165926 1.960000e-37 167.0
15 TraesCS3A01G177300 chr7B 96.939 98 3 0 3012 3109 600023877 600023974 7.060000e-37 165.0
16 TraesCS3A01G177300 chr7B 83.117 154 22 3 3015 3165 194788123 194788275 1.540000e-28 137.0
17 TraesCS3A01G177300 chr7D 96.907 97 3 0 3013 3109 45132422 45132518 2.540000e-36 163.0
18 TraesCS3A01G177300 chr7D 97.260 73 2 0 3108 3180 494452259 494452331 1.200000e-24 124.0
19 TraesCS3A01G177300 chr4A 96.000 100 4 0 3013 3112 695017804 695017705 2.540000e-36 163.0
20 TraesCS3A01G177300 chr6B 95.146 103 4 1 3011 3112 40713527 40713425 9.130000e-36 161.0
21 TraesCS3A01G177300 chr4B 96.875 96 3 0 3014 3109 483761691 483761786 9.130000e-36 161.0
22 TraesCS3A01G177300 chr4B 97.260 73 2 0 3108 3180 63511367 63511295 1.200000e-24 124.0
23 TraesCS3A01G177300 chr6D 97.260 73 2 0 3108 3180 414926946 414927018 1.200000e-24 124.0
24 TraesCS3A01G177300 chr1D 97.260 73 2 0 3108 3180 482768388 482768316 1.200000e-24 124.0
25 TraesCS3A01G177300 chr1B 97.260 73 2 0 3108 3180 66377744 66377672 1.200000e-24 124.0
26 TraesCS3A01G177300 chr1B 95.946 74 3 0 3107 3180 522613865 522613938 1.550000e-23 121.0


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 TraesCS3A01G177300 chr3A 199687875 199691054 3179 False 5873.000000 5873 100.000000 1 3180 1 chr3A.!!$F1 3179
1 TraesCS3A01G177300 chr3D 168288392 168291873 3481 True 848.533333 2588 95.731833 93 3013 6 chr3D.!!$R1 2920
2 TraesCS3A01G177300 chr3B 243249157 243252489 3332 True 1146.500000 2549 94.800250 93 2986 4 chr3B.!!$R1 2893

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
140 144 0.034896 CAAAGGGACCACTACGTGCT 59.965 55.000 0.0 0.0 31.34 4.40 F
143 147 1.112113 AGGGACCACTACGTGCTATG 58.888 55.000 0.0 0.0 31.34 2.23 F
1255 1275 2.008329 GCAGAGGAAGTTGCTGATGAG 58.992 52.381 0.0 0.0 37.35 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1666 2.028876 TCGGGAGAAACTGCATCGATA 58.971 47.619 0.00 0.00 34.75 2.92 R
1794 1940 2.549754 TCTTGCTGCTTGTGCTAGTTTC 59.450 45.455 0.00 0.00 40.48 2.78 R
3066 4082 0.030369 GTGCATGCTCTAGCCAATGC 59.970 55.000 20.33 16.33 45.25 3.56 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
22 23 4.320456 CCACGGAGGCAGTGCAGT 62.320 66.667 18.61 8.15 38.22 4.40
23 24 2.740055 CACGGAGGCAGTGCAGTC 60.740 66.667 18.61 12.62 32.52 3.51
24 25 4.363990 ACGGAGGCAGTGCAGTCG 62.364 66.667 18.61 17.88 0.00 4.18
35 36 2.918571 TGCAGTCGCAGGAGAAAAG 58.081 52.632 0.00 0.00 45.36 2.27
36 37 0.603707 TGCAGTCGCAGGAGAAAAGG 60.604 55.000 0.00 0.00 45.36 3.11
37 38 0.320771 GCAGTCGCAGGAGAAAAGGA 60.321 55.000 0.00 0.00 38.36 3.36
38 39 1.878102 GCAGTCGCAGGAGAAAAGGAA 60.878 52.381 0.00 0.00 38.36 3.36
39 40 2.072298 CAGTCGCAGGAGAAAAGGAAG 58.928 52.381 0.00 0.00 0.00 3.46
40 41 1.971357 AGTCGCAGGAGAAAAGGAAGA 59.029 47.619 0.00 0.00 0.00 2.87
41 42 2.028567 AGTCGCAGGAGAAAAGGAAGAG 60.029 50.000 0.00 0.00 0.00 2.85
42 43 1.276421 TCGCAGGAGAAAAGGAAGAGG 59.724 52.381 0.00 0.00 0.00 3.69
43 44 1.002544 CGCAGGAGAAAAGGAAGAGGT 59.997 52.381 0.00 0.00 0.00 3.85
44 45 2.431454 GCAGGAGAAAAGGAAGAGGTG 58.569 52.381 0.00 0.00 0.00 4.00
45 46 2.224646 GCAGGAGAAAAGGAAGAGGTGT 60.225 50.000 0.00 0.00 0.00 4.16
46 47 3.669536 CAGGAGAAAAGGAAGAGGTGTC 58.330 50.000 0.00 0.00 0.00 3.67
47 48 2.300437 AGGAGAAAAGGAAGAGGTGTCG 59.700 50.000 0.00 0.00 0.00 4.35
48 49 2.070028 GAGAAAAGGAAGAGGTGTCGC 58.930 52.381 0.00 0.00 0.00 5.19
49 50 0.790814 GAAAAGGAAGAGGTGTCGCG 59.209 55.000 0.00 0.00 0.00 5.87
50 51 1.228657 AAAAGGAAGAGGTGTCGCGC 61.229 55.000 0.00 0.00 0.00 6.86
51 52 2.100879 AAAGGAAGAGGTGTCGCGCT 62.101 55.000 5.56 0.00 0.00 5.92
52 53 2.048127 GGAAGAGGTGTCGCGCTT 60.048 61.111 5.56 0.00 0.00 4.68
53 54 2.095252 GGAAGAGGTGTCGCGCTTC 61.095 63.158 5.56 7.32 36.81 3.86
54 55 2.430921 AAGAGGTGTCGCGCTTCG 60.431 61.111 5.56 0.00 40.15 3.79
71 72 2.395690 GCGCCGTCGTGATTTCAG 59.604 61.111 0.00 0.00 38.14 3.02
72 73 2.092291 GCGCCGTCGTGATTTCAGA 61.092 57.895 0.00 0.00 38.14 3.27
73 74 1.421410 GCGCCGTCGTGATTTCAGAT 61.421 55.000 0.00 0.00 38.14 2.90
74 75 1.835121 CGCCGTCGTGATTTCAGATA 58.165 50.000 0.00 0.00 0.00 1.98
75 76 1.517276 CGCCGTCGTGATTTCAGATAC 59.483 52.381 0.00 0.00 0.00 2.24
76 77 2.536365 GCCGTCGTGATTTCAGATACA 58.464 47.619 0.00 0.00 0.00 2.29
77 78 2.281762 GCCGTCGTGATTTCAGATACAC 59.718 50.000 0.00 0.00 0.00 2.90
78 79 3.507786 CCGTCGTGATTTCAGATACACA 58.492 45.455 0.00 0.00 33.56 3.72
79 80 3.303495 CCGTCGTGATTTCAGATACACAC 59.697 47.826 0.00 0.00 33.56 3.82
80 81 3.917985 CGTCGTGATTTCAGATACACACA 59.082 43.478 0.00 0.00 33.56 3.72
81 82 4.562789 CGTCGTGATTTCAGATACACACAT 59.437 41.667 0.00 0.00 33.56 3.21
82 83 5.062183 CGTCGTGATTTCAGATACACACATT 59.938 40.000 0.00 0.00 33.56 2.71
83 84 6.470160 GTCGTGATTTCAGATACACACATTC 58.530 40.000 0.00 0.00 33.56 2.67
84 85 5.580691 TCGTGATTTCAGATACACACATTCC 59.419 40.000 0.00 0.00 33.56 3.01
85 86 5.351189 CGTGATTTCAGATACACACATTCCA 59.649 40.000 0.00 0.00 33.56 3.53
86 87 6.128309 CGTGATTTCAGATACACACATTCCAA 60.128 38.462 0.00 0.00 33.56 3.53
87 88 7.414429 CGTGATTTCAGATACACACATTCCAAT 60.414 37.037 0.00 0.00 33.56 3.16
88 89 7.699391 GTGATTTCAGATACACACATTCCAATG 59.301 37.037 0.00 0.00 42.10 2.82
89 90 7.611079 TGATTTCAGATACACACATTCCAATGA 59.389 33.333 6.29 0.00 39.67 2.57
90 91 6.741992 TTCAGATACACACATTCCAATGAC 57.258 37.500 6.29 0.00 39.67 3.06
91 92 5.803552 TCAGATACACACATTCCAATGACA 58.196 37.500 6.29 0.00 39.67 3.58
99 100 4.516698 ACACATTCCAATGACAGTCAAGAC 59.483 41.667 7.50 0.00 39.67 3.01
106 107 5.485353 TCCAATGACAGTCAAGACCTAAGAT 59.515 40.000 7.50 0.00 0.00 2.40
136 140 2.546789 GTCAAACAAAGGGACCACTACG 59.453 50.000 0.00 0.00 0.00 3.51
137 141 2.171027 TCAAACAAAGGGACCACTACGT 59.829 45.455 0.00 0.00 0.00 3.57
138 142 2.249844 AACAAAGGGACCACTACGTG 57.750 50.000 0.00 0.00 0.00 4.49
139 143 0.250166 ACAAAGGGACCACTACGTGC 60.250 55.000 0.00 0.00 31.34 5.34
140 144 0.034896 CAAAGGGACCACTACGTGCT 59.965 55.000 0.00 0.00 31.34 4.40
141 145 1.274167 CAAAGGGACCACTACGTGCTA 59.726 52.381 0.00 0.00 31.34 3.49
143 147 1.112113 AGGGACCACTACGTGCTATG 58.888 55.000 0.00 0.00 31.34 2.23
145 149 2.026641 GGGACCACTACGTGCTATGTA 58.973 52.381 0.00 0.00 31.34 2.29
146 150 2.034305 GGGACCACTACGTGCTATGTAG 59.966 54.545 0.00 11.61 42.07 2.74
354 364 3.560636 ATGGCATCTAACACCACTACC 57.439 47.619 0.00 0.00 35.99 3.18
507 517 2.285083 CCGAACAACAACCAGTCTCAA 58.715 47.619 0.00 0.00 0.00 3.02
508 518 2.878406 CCGAACAACAACCAGTCTCAAT 59.122 45.455 0.00 0.00 0.00 2.57
587 597 4.142534 CGTCATTGCACTCCAAGAATGAAT 60.143 41.667 0.00 0.00 36.76 2.57
1096 1116 2.071688 GCTATAGCTCCACATGGTCG 57.928 55.000 17.75 0.00 38.21 4.79
1143 1163 6.711277 AGGTCATGTATGTGCTTTTCTCTTA 58.289 36.000 0.00 0.00 0.00 2.10
1188 1208 4.576463 GCATCCGAGAATGTTGGTTCTATT 59.424 41.667 0.00 0.00 38.51 1.73
1195 1215 6.568462 CGAGAATGTTGGTTCTATTGCTTTGT 60.568 38.462 0.00 0.00 38.51 2.83
1255 1275 2.008329 GCAGAGGAAGTTGCTGATGAG 58.992 52.381 0.00 0.00 37.35 2.90
1276 1296 3.058450 GTGAAGATGATGCAGGATCGAG 58.942 50.000 0.00 0.00 33.17 4.04
1438 1479 7.079182 AGTTGTTAACACGTGAGAAATTTGA 57.921 32.000 25.01 0.00 0.00 2.69
1451 1492 8.973378 CGTGAGAAATTTGAAGAGATATACTCC 58.027 37.037 0.00 0.00 45.96 3.85
1572 1615 2.406559 CCATCTCCTCTTGGTCTGGAT 58.593 52.381 0.00 0.00 32.77 3.41
1623 1666 5.659079 AGTTGACTAGCTAGGCATAAGACTT 59.341 40.000 29.70 11.59 41.82 3.01
1718 1864 4.937201 ATATATGACGAACTGCAGACCA 57.063 40.909 23.35 10.39 0.00 4.02
1789 1935 8.749499 GGATCGAATCAAAATCACAAATCATTC 58.251 33.333 0.00 0.00 0.00 2.67
1794 1940 9.895894 GAATCAAAATCACAAATCATTCGAATG 57.104 29.630 28.48 28.48 37.75 2.67
1874 2020 7.169813 TCAAATTAGCACTAGCATATCACTTCG 59.830 37.037 0.00 0.00 45.49 3.79
2338 3034 5.825679 GTGTGCTACATATTATTTGTCCCCA 59.174 40.000 0.00 0.00 0.00 4.96
2395 3091 5.220381 CGCGTGTGGAACTTATATATGTCT 58.780 41.667 0.00 0.00 38.04 3.41
2396 3092 6.016860 ACGCGTGTGGAACTTATATATGTCTA 60.017 38.462 12.93 0.00 38.04 2.59
2466 3162 3.428045 GCATCCTTGTTTGGTACTCATGC 60.428 47.826 0.00 0.00 0.00 4.06
2467 3163 3.500448 TCCTTGTTTGGTACTCATGCA 57.500 42.857 0.00 0.00 0.00 3.96
2468 3164 4.032960 TCCTTGTTTGGTACTCATGCAT 57.967 40.909 0.00 0.00 0.00 3.96
2488 3213 3.394674 TGTTCGTTGATTACTCCTGCA 57.605 42.857 0.00 0.00 0.00 4.41
2489 3214 3.937814 TGTTCGTTGATTACTCCTGCAT 58.062 40.909 0.00 0.00 0.00 3.96
2505 3230 7.753630 ACTCCTGCATATTTGATTATCTCCTT 58.246 34.615 0.00 0.00 0.00 3.36
2596 3416 3.628032 TGAAATTGTGTCGTGGCTAACAA 59.372 39.130 0.00 0.00 36.98 2.83
2733 3553 3.462982 TGCAACAACACTACTCAACGAT 58.537 40.909 0.00 0.00 0.00 3.73
2746 3566 1.529438 TCAACGATCGCAAACTGAACC 59.471 47.619 16.60 0.00 0.00 3.62
2806 3821 2.027073 GCGGATGCACGTCTGTTCA 61.027 57.895 0.00 0.00 42.15 3.18
2810 3825 2.616960 GGATGCACGTCTGTTCATGTA 58.383 47.619 0.00 0.00 31.88 2.29
2859 3874 1.661112 GCACGCTTGAGGATTGTAGTC 59.339 52.381 0.00 0.00 0.00 2.59
2912 3927 4.678256 AGAATGAGACTGTAAGGACTCCA 58.322 43.478 0.00 0.00 39.50 3.86
3003 4019 8.673711 TCTTAAAAATGATCATACGGACTTTGG 58.326 33.333 9.04 0.61 0.00 3.28
3013 4029 5.650266 TCATACGGACTTTGGTTGCATAATT 59.350 36.000 0.00 0.00 0.00 1.40
3014 4030 4.173036 ACGGACTTTGGTTGCATAATTG 57.827 40.909 0.00 0.00 0.00 2.32
3015 4031 3.572255 ACGGACTTTGGTTGCATAATTGT 59.428 39.130 0.00 0.00 0.00 2.71
3016 4032 4.038642 ACGGACTTTGGTTGCATAATTGTT 59.961 37.500 0.00 0.00 0.00 2.83
3017 4033 4.385447 CGGACTTTGGTTGCATAATTGTTG 59.615 41.667 0.00 0.00 0.00 3.33
3018 4034 5.537188 GGACTTTGGTTGCATAATTGTTGA 58.463 37.500 0.00 0.00 0.00 3.18
3019 4035 5.405269 GGACTTTGGTTGCATAATTGTTGAC 59.595 40.000 0.00 0.00 0.00 3.18
3020 4036 4.981674 ACTTTGGTTGCATAATTGTTGACG 59.018 37.500 0.00 0.00 0.00 4.35
3021 4037 4.576216 TTGGTTGCATAATTGTTGACGT 57.424 36.364 0.00 0.00 0.00 4.34
3022 4038 5.690997 TTGGTTGCATAATTGTTGACGTA 57.309 34.783 0.00 0.00 0.00 3.57
3023 4039 5.888691 TGGTTGCATAATTGTTGACGTAT 57.111 34.783 0.00 0.00 0.00 3.06
3024 4040 6.986904 TGGTTGCATAATTGTTGACGTATA 57.013 33.333 0.00 0.00 0.00 1.47
3025 4041 7.379098 TGGTTGCATAATTGTTGACGTATAA 57.621 32.000 0.00 0.00 0.00 0.98
3026 4042 7.990917 TGGTTGCATAATTGTTGACGTATAAT 58.009 30.769 0.00 0.00 0.00 1.28
3027 4043 7.912773 TGGTTGCATAATTGTTGACGTATAATG 59.087 33.333 0.00 0.00 0.00 1.90
3028 4044 7.913297 GGTTGCATAATTGTTGACGTATAATGT 59.087 33.333 0.00 0.00 0.00 2.71
3029 4045 8.733128 GTTGCATAATTGTTGACGTATAATGTG 58.267 33.333 0.00 0.00 0.00 3.21
3030 4046 6.909895 TGCATAATTGTTGACGTATAATGTGC 59.090 34.615 0.00 0.24 0.00 4.57
3031 4047 7.132213 GCATAATTGTTGACGTATAATGTGCT 58.868 34.615 0.00 0.00 0.00 4.40
3032 4048 7.112009 GCATAATTGTTGACGTATAATGTGCTG 59.888 37.037 0.00 0.00 0.00 4.41
3033 4049 4.335082 TTGTTGACGTATAATGTGCTGC 57.665 40.909 0.00 0.00 0.00 5.25
3034 4050 2.675844 TGTTGACGTATAATGTGCTGCC 59.324 45.455 0.00 0.00 0.00 4.85
3035 4051 2.936498 GTTGACGTATAATGTGCTGCCT 59.064 45.455 0.00 0.00 0.00 4.75
3036 4052 4.116961 GTTGACGTATAATGTGCTGCCTA 58.883 43.478 0.00 0.00 0.00 3.93
3037 4053 3.977427 TGACGTATAATGTGCTGCCTAG 58.023 45.455 0.00 0.00 0.00 3.02
3038 4054 3.383505 TGACGTATAATGTGCTGCCTAGT 59.616 43.478 0.00 0.00 0.00 2.57
3039 4055 3.978687 ACGTATAATGTGCTGCCTAGTC 58.021 45.455 0.00 0.00 0.00 2.59
3040 4056 3.637229 ACGTATAATGTGCTGCCTAGTCT 59.363 43.478 0.00 0.00 0.00 3.24
3041 4057 4.099573 ACGTATAATGTGCTGCCTAGTCTT 59.900 41.667 0.00 0.00 0.00 3.01
3042 4058 5.050490 CGTATAATGTGCTGCCTAGTCTTT 58.950 41.667 0.00 0.00 0.00 2.52
3043 4059 5.523916 CGTATAATGTGCTGCCTAGTCTTTT 59.476 40.000 0.00 0.00 0.00 2.27
3044 4060 6.292381 CGTATAATGTGCTGCCTAGTCTTTTC 60.292 42.308 0.00 0.00 0.00 2.29
3045 4061 2.185004 TGTGCTGCCTAGTCTTTTCC 57.815 50.000 0.00 0.00 0.00 3.13
3046 4062 1.419762 TGTGCTGCCTAGTCTTTTCCA 59.580 47.619 0.00 0.00 0.00 3.53
3047 4063 2.040278 TGTGCTGCCTAGTCTTTTCCAT 59.960 45.455 0.00 0.00 0.00 3.41
3048 4064 2.680339 GTGCTGCCTAGTCTTTTCCATC 59.320 50.000 0.00 0.00 0.00 3.51
3049 4065 2.305635 TGCTGCCTAGTCTTTTCCATCA 59.694 45.455 0.00 0.00 0.00 3.07
3050 4066 2.941720 GCTGCCTAGTCTTTTCCATCAG 59.058 50.000 0.00 0.00 0.00 2.90
3051 4067 3.369892 GCTGCCTAGTCTTTTCCATCAGA 60.370 47.826 0.00 0.00 0.00 3.27
3052 4068 4.685575 GCTGCCTAGTCTTTTCCATCAGAT 60.686 45.833 0.00 0.00 0.00 2.90
3053 4069 5.028549 TGCCTAGTCTTTTCCATCAGATC 57.971 43.478 0.00 0.00 0.00 2.75
3054 4070 4.054671 GCCTAGTCTTTTCCATCAGATCG 58.945 47.826 0.00 0.00 0.00 3.69
3055 4071 4.626042 CCTAGTCTTTTCCATCAGATCGG 58.374 47.826 0.00 0.00 0.00 4.18
3056 4072 4.100189 CCTAGTCTTTTCCATCAGATCGGT 59.900 45.833 0.00 0.00 0.00 4.69
3057 4073 4.559862 AGTCTTTTCCATCAGATCGGTT 57.440 40.909 0.00 0.00 0.00 4.44
3058 4074 4.911390 AGTCTTTTCCATCAGATCGGTTT 58.089 39.130 0.00 0.00 0.00 3.27
3059 4075 5.316987 AGTCTTTTCCATCAGATCGGTTTT 58.683 37.500 0.00 0.00 0.00 2.43
3060 4076 5.770162 AGTCTTTTCCATCAGATCGGTTTTT 59.230 36.000 0.00 0.00 0.00 1.94
3078 4094 3.940209 TTTTGGTTGCATTGGCTAGAG 57.060 42.857 0.00 0.00 41.91 2.43
3079 4095 1.176527 TTGGTTGCATTGGCTAGAGC 58.823 50.000 0.00 0.00 41.91 4.09
3080 4096 0.038021 TGGTTGCATTGGCTAGAGCA 59.962 50.000 3.54 0.00 44.36 4.26
3081 4097 1.341285 TGGTTGCATTGGCTAGAGCAT 60.341 47.619 3.54 0.00 44.36 3.79
3082 4098 1.066605 GGTTGCATTGGCTAGAGCATG 59.933 52.381 3.54 0.90 44.36 4.06
3083 4099 0.742505 TTGCATTGGCTAGAGCATGC 59.257 50.000 10.51 10.51 45.25 4.06
3084 4100 2.411535 GCATTGGCTAGAGCATGCA 58.588 52.632 21.98 0.00 44.74 3.96
3085 4101 0.030369 GCATTGGCTAGAGCATGCAC 59.970 55.000 21.98 14.59 44.74 4.57
3086 4102 1.676746 CATTGGCTAGAGCATGCACT 58.323 50.000 21.45 21.45 44.36 4.40
3087 4103 2.022195 CATTGGCTAGAGCATGCACTT 58.978 47.619 22.83 8.33 44.36 3.16
3088 4104 1.742761 TTGGCTAGAGCATGCACTTC 58.257 50.000 22.83 14.30 44.36 3.01
3089 4105 0.907486 TGGCTAGAGCATGCACTTCT 59.093 50.000 22.83 17.00 44.36 2.85
3090 4106 2.110578 TGGCTAGAGCATGCACTTCTA 58.889 47.619 22.83 17.21 44.36 2.10
3091 4107 2.159043 TGGCTAGAGCATGCACTTCTAC 60.159 50.000 22.83 12.67 44.36 2.59
3092 4108 2.159043 GGCTAGAGCATGCACTTCTACA 60.159 50.000 22.83 3.70 44.36 2.74
3093 4109 3.494048 GGCTAGAGCATGCACTTCTACAT 60.494 47.826 22.83 0.00 44.36 2.29
3094 4110 3.493877 GCTAGAGCATGCACTTCTACATG 59.506 47.826 22.83 8.90 45.19 3.21
3095 4111 2.915349 AGAGCATGCACTTCTACATGG 58.085 47.619 21.98 0.00 43.13 3.66
3096 4112 2.795231 AGCATGCACTTCTACATGGT 57.205 45.000 21.98 2.10 46.94 3.55
3099 4115 4.739046 GCATGCACTTCTACATGGTATC 57.261 45.455 14.21 0.00 43.13 2.24
3100 4116 3.185188 GCATGCACTTCTACATGGTATCG 59.815 47.826 14.21 0.00 43.13 2.92
3101 4117 3.452755 TGCACTTCTACATGGTATCGG 57.547 47.619 0.00 0.00 0.00 4.18
3102 4118 3.028130 TGCACTTCTACATGGTATCGGA 58.972 45.455 0.00 0.00 0.00 4.55
3103 4119 3.068165 TGCACTTCTACATGGTATCGGAG 59.932 47.826 0.00 0.00 0.00 4.63
3104 4120 3.068307 GCACTTCTACATGGTATCGGAGT 59.932 47.826 0.00 0.00 0.00 3.85
3105 4121 4.793353 GCACTTCTACATGGTATCGGAGTC 60.793 50.000 0.00 0.00 0.00 3.36
3106 4122 4.338400 CACTTCTACATGGTATCGGAGTCA 59.662 45.833 0.00 0.00 0.00 3.41
3107 4123 4.954202 ACTTCTACATGGTATCGGAGTCAA 59.046 41.667 0.00 0.00 0.00 3.18
3108 4124 5.067936 ACTTCTACATGGTATCGGAGTCAAG 59.932 44.000 0.00 0.00 0.00 3.02
3109 4125 3.889538 TCTACATGGTATCGGAGTCAAGG 59.110 47.826 0.00 0.00 0.00 3.61
3110 4126 1.762957 ACATGGTATCGGAGTCAAGGG 59.237 52.381 0.00 0.00 0.00 3.95
3111 4127 1.070758 CATGGTATCGGAGTCAAGGGG 59.929 57.143 0.00 0.00 0.00 4.79
3112 4128 0.689745 TGGTATCGGAGTCAAGGGGG 60.690 60.000 0.00 0.00 0.00 5.40
3113 4129 0.398098 GGTATCGGAGTCAAGGGGGA 60.398 60.000 0.00 0.00 0.00 4.81
3114 4130 1.041437 GTATCGGAGTCAAGGGGGAG 58.959 60.000 0.00 0.00 0.00 4.30
3115 4131 0.635009 TATCGGAGTCAAGGGGGAGT 59.365 55.000 0.00 0.00 0.00 3.85
3116 4132 0.978146 ATCGGAGTCAAGGGGGAGTG 60.978 60.000 0.00 0.00 0.00 3.51
3117 4133 1.913762 CGGAGTCAAGGGGGAGTGT 60.914 63.158 0.00 0.00 0.00 3.55
3118 4134 1.481056 CGGAGTCAAGGGGGAGTGTT 61.481 60.000 0.00 0.00 0.00 3.32
3119 4135 0.036875 GGAGTCAAGGGGGAGTGTTG 59.963 60.000 0.00 0.00 0.00 3.33
3120 4136 1.056660 GAGTCAAGGGGGAGTGTTGA 58.943 55.000 0.00 0.00 0.00 3.18
3121 4137 0.765510 AGTCAAGGGGGAGTGTTGAC 59.234 55.000 6.36 6.36 46.93 3.18
3122 4138 0.602905 GTCAAGGGGGAGTGTTGACG 60.603 60.000 0.00 0.00 40.38 4.35
3123 4139 1.052124 TCAAGGGGGAGTGTTGACGT 61.052 55.000 0.00 0.00 0.00 4.34
3124 4140 0.682852 CAAGGGGGAGTGTTGACGTA 59.317 55.000 0.00 0.00 0.00 3.57
3125 4141 1.278127 CAAGGGGGAGTGTTGACGTAT 59.722 52.381 0.00 0.00 0.00 3.06
3126 4142 2.498481 CAAGGGGGAGTGTTGACGTATA 59.502 50.000 0.00 0.00 0.00 1.47
3127 4143 2.823959 AGGGGGAGTGTTGACGTATAA 58.176 47.619 0.00 0.00 0.00 0.98
3128 4144 3.381335 AGGGGGAGTGTTGACGTATAAT 58.619 45.455 0.00 0.00 0.00 1.28
3129 4145 3.134081 AGGGGGAGTGTTGACGTATAATG 59.866 47.826 0.00 0.00 0.00 1.90
3130 4146 3.118519 GGGGGAGTGTTGACGTATAATGT 60.119 47.826 0.00 0.00 0.00 2.71
3131 4147 3.869246 GGGGAGTGTTGACGTATAATGTG 59.131 47.826 0.00 0.00 0.00 3.21
3132 4148 4.501071 GGGAGTGTTGACGTATAATGTGT 58.499 43.478 0.00 0.00 0.00 3.72
3133 4149 4.933400 GGGAGTGTTGACGTATAATGTGTT 59.067 41.667 0.00 0.00 0.00 3.32
3134 4150 5.163893 GGGAGTGTTGACGTATAATGTGTTG 60.164 44.000 0.00 0.00 0.00 3.33
3135 4151 5.277601 AGTGTTGACGTATAATGTGTTGC 57.722 39.130 0.00 0.00 0.00 4.17
3136 4152 4.153475 AGTGTTGACGTATAATGTGTTGCC 59.847 41.667 0.00 0.00 0.00 4.52
3137 4153 4.153475 GTGTTGACGTATAATGTGTTGCCT 59.847 41.667 0.00 0.00 0.00 4.75
3138 4154 5.349270 GTGTTGACGTATAATGTGTTGCCTA 59.651 40.000 0.00 0.00 0.00 3.93
3139 4155 5.579119 TGTTGACGTATAATGTGTTGCCTAG 59.421 40.000 0.00 0.00 0.00 3.02
3140 4156 5.333299 TGACGTATAATGTGTTGCCTAGT 57.667 39.130 0.00 0.00 0.00 2.57
3141 4157 5.345702 TGACGTATAATGTGTTGCCTAGTC 58.654 41.667 0.00 0.00 0.00 2.59
3142 4158 5.126545 TGACGTATAATGTGTTGCCTAGTCT 59.873 40.000 0.00 0.00 0.00 3.24
3143 4159 5.589192 ACGTATAATGTGTTGCCTAGTCTC 58.411 41.667 0.00 0.00 0.00 3.36
3144 4160 5.360144 ACGTATAATGTGTTGCCTAGTCTCT 59.640 40.000 0.00 0.00 0.00 3.10
3145 4161 6.127423 ACGTATAATGTGTTGCCTAGTCTCTT 60.127 38.462 0.00 0.00 0.00 2.85
3146 4162 6.418226 CGTATAATGTGTTGCCTAGTCTCTTC 59.582 42.308 0.00 0.00 0.00 2.87
3147 4163 3.618690 ATGTGTTGCCTAGTCTCTTCC 57.381 47.619 0.00 0.00 0.00 3.46
3148 4164 2.609747 TGTGTTGCCTAGTCTCTTCCT 58.390 47.619 0.00 0.00 0.00 3.36
3149 4165 2.972713 TGTGTTGCCTAGTCTCTTCCTT 59.027 45.455 0.00 0.00 0.00 3.36
3150 4166 3.006967 TGTGTTGCCTAGTCTCTTCCTTC 59.993 47.826 0.00 0.00 0.00 3.46
3151 4167 3.006967 GTGTTGCCTAGTCTCTTCCTTCA 59.993 47.826 0.00 0.00 0.00 3.02
3152 4168 3.259374 TGTTGCCTAGTCTCTTCCTTCAG 59.741 47.826 0.00 0.00 0.00 3.02
3153 4169 3.458044 TGCCTAGTCTCTTCCTTCAGA 57.542 47.619 0.00 0.00 0.00 3.27
3154 4170 3.987745 TGCCTAGTCTCTTCCTTCAGAT 58.012 45.455 0.00 0.00 0.00 2.90
3155 4171 3.957497 TGCCTAGTCTCTTCCTTCAGATC 59.043 47.826 0.00 0.00 0.00 2.75
3156 4172 3.004315 GCCTAGTCTCTTCCTTCAGATCG 59.996 52.174 0.00 0.00 0.00 3.69
3157 4173 3.568007 CCTAGTCTCTTCCTTCAGATCGG 59.432 52.174 0.00 0.00 0.00 4.18
3158 4174 3.094484 AGTCTCTTCCTTCAGATCGGT 57.906 47.619 0.00 0.00 0.00 4.69
3159 4175 3.020984 AGTCTCTTCCTTCAGATCGGTC 58.979 50.000 0.00 0.00 0.00 4.79
3160 4176 3.020984 GTCTCTTCCTTCAGATCGGTCT 58.979 50.000 0.00 0.00 34.14 3.85
3161 4177 3.445805 GTCTCTTCCTTCAGATCGGTCTT 59.554 47.826 0.00 0.00 30.42 3.01
3162 4178 4.081917 GTCTCTTCCTTCAGATCGGTCTTT 60.082 45.833 0.00 0.00 30.42 2.52
3163 4179 4.528596 TCTCTTCCTTCAGATCGGTCTTTT 59.471 41.667 0.00 0.00 30.42 2.27
3164 4180 4.569943 TCTTCCTTCAGATCGGTCTTTTG 58.430 43.478 0.00 0.00 30.42 2.44
3165 4181 4.040461 TCTTCCTTCAGATCGGTCTTTTGT 59.960 41.667 0.00 0.00 30.42 2.83
3166 4182 4.351874 TCCTTCAGATCGGTCTTTTGTT 57.648 40.909 0.00 0.00 30.42 2.83
3167 4183 4.714632 TCCTTCAGATCGGTCTTTTGTTT 58.285 39.130 0.00 0.00 30.42 2.83
3168 4184 4.515191 TCCTTCAGATCGGTCTTTTGTTTG 59.485 41.667 0.00 0.00 30.42 2.93
3169 4185 3.896648 TCAGATCGGTCTTTTGTTTGC 57.103 42.857 0.00 0.00 30.42 3.68
3170 4186 3.210227 TCAGATCGGTCTTTTGTTTGCA 58.790 40.909 0.00 0.00 30.42 4.08
3171 4187 3.820467 TCAGATCGGTCTTTTGTTTGCAT 59.180 39.130 0.00 0.00 30.42 3.96
3172 4188 4.278170 TCAGATCGGTCTTTTGTTTGCATT 59.722 37.500 0.00 0.00 30.42 3.56
3173 4189 4.383649 CAGATCGGTCTTTTGTTTGCATTG 59.616 41.667 0.00 0.00 30.42 2.82
3174 4190 3.090952 TCGGTCTTTTGTTTGCATTGG 57.909 42.857 0.00 0.00 0.00 3.16
3175 4191 1.526464 CGGTCTTTTGTTTGCATTGGC 59.474 47.619 0.00 0.00 41.68 4.52
3176 4192 2.802774 CGGTCTTTTGTTTGCATTGGCT 60.803 45.455 0.00 0.00 41.91 4.75
3177 4193 3.551863 CGGTCTTTTGTTTGCATTGGCTA 60.552 43.478 0.00 0.00 41.91 3.93
3178 4194 3.989817 GGTCTTTTGTTTGCATTGGCTAG 59.010 43.478 0.00 0.00 41.91 3.42
3179 4195 4.261994 GGTCTTTTGTTTGCATTGGCTAGA 60.262 41.667 0.00 0.00 41.91 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.320456 ACTGCACTGCCTCCGTGG 62.320 66.667 0.00 0.00 39.35 4.94
6 7 2.740055 GACTGCACTGCCTCCGTG 60.740 66.667 0.00 0.00 35.53 4.94
7 8 4.363990 CGACTGCACTGCCTCCGT 62.364 66.667 0.00 0.00 0.00 4.69
18 19 0.320771 TCCTTTTCTCCTGCGACTGC 60.321 55.000 0.00 0.00 43.20 4.40
19 20 2.072298 CTTCCTTTTCTCCTGCGACTG 58.928 52.381 0.00 0.00 0.00 3.51
20 21 1.971357 TCTTCCTTTTCTCCTGCGACT 59.029 47.619 0.00 0.00 0.00 4.18
21 22 2.342179 CTCTTCCTTTTCTCCTGCGAC 58.658 52.381 0.00 0.00 0.00 5.19
22 23 1.276421 CCTCTTCCTTTTCTCCTGCGA 59.724 52.381 0.00 0.00 0.00 5.10
23 24 1.002544 ACCTCTTCCTTTTCTCCTGCG 59.997 52.381 0.00 0.00 0.00 5.18
24 25 2.224646 ACACCTCTTCCTTTTCTCCTGC 60.225 50.000 0.00 0.00 0.00 4.85
25 26 3.669536 GACACCTCTTCCTTTTCTCCTG 58.330 50.000 0.00 0.00 0.00 3.86
26 27 2.300437 CGACACCTCTTCCTTTTCTCCT 59.700 50.000 0.00 0.00 0.00 3.69
27 28 2.689646 CGACACCTCTTCCTTTTCTCC 58.310 52.381 0.00 0.00 0.00 3.71
28 29 2.070028 GCGACACCTCTTCCTTTTCTC 58.930 52.381 0.00 0.00 0.00 2.87
29 30 1.605712 CGCGACACCTCTTCCTTTTCT 60.606 52.381 0.00 0.00 0.00 2.52
30 31 0.790814 CGCGACACCTCTTCCTTTTC 59.209 55.000 0.00 0.00 0.00 2.29
31 32 1.228657 GCGCGACACCTCTTCCTTTT 61.229 55.000 12.10 0.00 0.00 2.27
32 33 1.668151 GCGCGACACCTCTTCCTTT 60.668 57.895 12.10 0.00 0.00 3.11
33 34 2.048127 GCGCGACACCTCTTCCTT 60.048 61.111 12.10 0.00 0.00 3.36
34 35 2.493907 GAAGCGCGACACCTCTTCCT 62.494 60.000 12.10 0.00 31.33 3.36
35 36 2.048127 AAGCGCGACACCTCTTCC 60.048 61.111 12.10 0.00 0.00 3.46
36 37 2.437343 CGAAGCGCGACACCTCTTC 61.437 63.158 12.10 11.14 44.57 2.87
37 38 2.430921 CGAAGCGCGACACCTCTT 60.431 61.111 12.10 1.19 44.57 2.85
50 51 2.597650 GAAATCACGACGGCGCGAAG 62.598 60.000 25.37 17.80 42.48 3.79
51 52 2.722731 GAAATCACGACGGCGCGAA 61.723 57.895 25.37 15.17 42.48 4.70
52 53 3.176578 GAAATCACGACGGCGCGA 61.177 61.111 25.37 7.47 42.48 5.87
53 54 3.406060 CTGAAATCACGACGGCGCG 62.406 63.158 12.58 19.04 42.48 6.86
54 55 1.421410 ATCTGAAATCACGACGGCGC 61.421 55.000 12.58 0.00 42.48 6.53
55 56 1.517276 GTATCTGAAATCACGACGGCG 59.483 52.381 10.39 10.39 44.79 6.46
56 57 2.281762 GTGTATCTGAAATCACGACGGC 59.718 50.000 0.00 0.00 0.00 5.68
57 58 3.303495 GTGTGTATCTGAAATCACGACGG 59.697 47.826 0.00 0.00 34.08 4.79
58 59 3.917985 TGTGTGTATCTGAAATCACGACG 59.082 43.478 0.00 0.00 34.08 5.12
59 60 6.408858 AATGTGTGTATCTGAAATCACGAC 57.591 37.500 0.00 0.00 34.08 4.34
60 61 5.580691 GGAATGTGTGTATCTGAAATCACGA 59.419 40.000 0.00 0.00 34.08 4.35
61 62 5.351189 TGGAATGTGTGTATCTGAAATCACG 59.649 40.000 0.00 0.00 34.08 4.35
62 63 6.741992 TGGAATGTGTGTATCTGAAATCAC 57.258 37.500 0.00 0.00 0.00 3.06
63 64 7.611079 TCATTGGAATGTGTGTATCTGAAATCA 59.389 33.333 0.00 0.00 37.65 2.57
64 65 7.912250 GTCATTGGAATGTGTGTATCTGAAATC 59.088 37.037 0.00 0.00 37.65 2.17
65 66 7.394077 TGTCATTGGAATGTGTGTATCTGAAAT 59.606 33.333 0.00 0.00 37.65 2.17
66 67 6.714356 TGTCATTGGAATGTGTGTATCTGAAA 59.286 34.615 0.00 0.00 37.65 2.69
67 68 6.237154 TGTCATTGGAATGTGTGTATCTGAA 58.763 36.000 0.00 0.00 37.65 3.02
68 69 5.803552 TGTCATTGGAATGTGTGTATCTGA 58.196 37.500 0.00 0.00 37.65 3.27
69 70 5.645067 ACTGTCATTGGAATGTGTGTATCTG 59.355 40.000 0.00 0.00 37.65 2.90
70 71 5.809001 ACTGTCATTGGAATGTGTGTATCT 58.191 37.500 0.00 0.00 37.65 1.98
71 72 5.643348 TGACTGTCATTGGAATGTGTGTATC 59.357 40.000 6.36 0.00 37.65 2.24
72 73 5.559770 TGACTGTCATTGGAATGTGTGTAT 58.440 37.500 6.36 0.00 37.65 2.29
73 74 4.967036 TGACTGTCATTGGAATGTGTGTA 58.033 39.130 6.36 0.00 37.65 2.90
74 75 3.819368 TGACTGTCATTGGAATGTGTGT 58.181 40.909 6.36 0.00 37.65 3.72
75 76 4.516321 TCTTGACTGTCATTGGAATGTGTG 59.484 41.667 11.86 0.00 37.65 3.82
76 77 4.516698 GTCTTGACTGTCATTGGAATGTGT 59.483 41.667 11.86 0.00 37.65 3.72
77 78 4.083110 GGTCTTGACTGTCATTGGAATGTG 60.083 45.833 11.86 0.00 37.65 3.21
78 79 4.074970 GGTCTTGACTGTCATTGGAATGT 58.925 43.478 11.86 0.00 37.65 2.71
79 80 4.330250 AGGTCTTGACTGTCATTGGAATG 58.670 43.478 11.86 0.00 37.75 2.67
80 81 4.647564 AGGTCTTGACTGTCATTGGAAT 57.352 40.909 11.86 1.40 0.00 3.01
81 82 5.306937 TCTTAGGTCTTGACTGTCATTGGAA 59.693 40.000 11.86 0.00 0.00 3.53
82 83 4.838423 TCTTAGGTCTTGACTGTCATTGGA 59.162 41.667 11.86 7.77 0.00 3.53
83 84 5.152623 TCTTAGGTCTTGACTGTCATTGG 57.847 43.478 11.86 5.58 0.00 3.16
84 85 6.312426 GTCATCTTAGGTCTTGACTGTCATTG 59.688 42.308 11.86 8.02 36.43 2.82
85 86 6.014242 TGTCATCTTAGGTCTTGACTGTCATT 60.014 38.462 11.86 0.00 39.33 2.57
86 87 5.481824 TGTCATCTTAGGTCTTGACTGTCAT 59.518 40.000 11.86 0.00 39.33 3.06
87 88 4.832823 TGTCATCTTAGGTCTTGACTGTCA 59.167 41.667 6.36 6.36 39.33 3.58
88 89 5.184096 TCTGTCATCTTAGGTCTTGACTGTC 59.816 44.000 0.00 0.00 39.33 3.51
89 90 5.047660 GTCTGTCATCTTAGGTCTTGACTGT 60.048 44.000 0.61 0.00 39.33 3.55
90 91 5.184864 AGTCTGTCATCTTAGGTCTTGACTG 59.815 44.000 0.61 0.00 39.33 3.51
91 92 5.184864 CAGTCTGTCATCTTAGGTCTTGACT 59.815 44.000 0.61 0.00 39.33 3.41
139 143 8.102800 TCATATCCTTGCATTTTGCTACATAG 57.897 34.615 0.75 0.00 45.31 2.23
140 144 7.720957 ACTCATATCCTTGCATTTTGCTACATA 59.279 33.333 0.75 0.00 45.31 2.29
141 145 6.548622 ACTCATATCCTTGCATTTTGCTACAT 59.451 34.615 0.75 0.00 45.31 2.29
143 147 6.382869 ACTCATATCCTTGCATTTTGCTAC 57.617 37.500 0.75 0.00 45.31 3.58
145 149 6.039047 CACTACTCATATCCTTGCATTTTGCT 59.961 38.462 0.75 0.00 45.31 3.91
146 150 6.038603 TCACTACTCATATCCTTGCATTTTGC 59.961 38.462 0.00 0.00 45.29 3.68
147 151 7.558161 TCACTACTCATATCCTTGCATTTTG 57.442 36.000 0.00 0.00 0.00 2.44
354 364 1.728971 GACATTGGTCAGAGTTCTGCG 59.271 52.381 4.25 0.00 43.73 5.18
452 462 2.812011 CTGGTAGGTGCCACAAGTTAAC 59.188 50.000 0.00 0.00 34.36 2.01
491 501 3.897239 TCCAATTGAGACTGGTTGTTGT 58.103 40.909 7.12 0.00 34.11 3.32
507 517 4.286297 TCCTGTGAAAACGAGATCCAAT 57.714 40.909 0.00 0.00 0.00 3.16
508 518 3.762407 TCCTGTGAAAACGAGATCCAA 57.238 42.857 0.00 0.00 0.00 3.53
612 622 2.806608 AAAGCAACTGACCATGCAAG 57.193 45.000 0.00 0.00 44.95 4.01
829 849 5.694910 GTGAGTTGTCCGAAAGAACAGAATA 59.305 40.000 0.00 0.00 0.00 1.75
1096 1116 8.251026 ACCTAGCTAAAAGGAAATAAATGCAAC 58.749 33.333 8.06 0.00 37.57 4.17
1143 1163 4.499696 GCACAAGAACTAACAAAGGCACAT 60.500 41.667 0.00 0.00 0.00 3.21
1188 1208 4.647424 AAATCAGAACCGAAACAAAGCA 57.353 36.364 0.00 0.00 0.00 3.91
1221 1241 2.818714 CTGCGCTCCTGCCTCAAG 60.819 66.667 9.73 0.00 35.36 3.02
1255 1275 3.058450 CTCGATCCTGCATCATCTTCAC 58.942 50.000 0.00 0.00 0.00 3.18
1276 1296 6.067217 AGCTGGGTCATTTATATACCATCC 57.933 41.667 0.00 0.00 34.83 3.51
1376 1416 7.891183 TTACTAAGAACTTCTTGCTAGCTTG 57.109 36.000 17.23 8.68 37.29 4.01
1377 1417 7.931948 TGTTTACTAAGAACTTCTTGCTAGCTT 59.068 33.333 17.23 0.00 37.29 3.74
1378 1418 7.442656 TGTTTACTAAGAACTTCTTGCTAGCT 58.557 34.615 17.23 0.00 37.29 3.32
1379 1419 7.653767 TGTTTACTAAGAACTTCTTGCTAGC 57.346 36.000 8.10 8.10 37.29 3.42
1415 1455 7.694784 TCTTCAAATTTCTCACGTGTTAACAAC 59.305 33.333 16.51 4.11 0.00 3.32
1572 1615 6.038161 GTGTTGCATGTCCTATTTATGTGCTA 59.962 38.462 0.00 0.00 32.67 3.49
1623 1666 2.028876 TCGGGAGAAACTGCATCGATA 58.971 47.619 0.00 0.00 34.75 2.92
1694 1738 6.112734 TGGTCTGCAGTTCGTCATATATTTT 58.887 36.000 14.67 0.00 0.00 1.82
1716 1829 3.641437 ATCGTTTTGTTCACCACATGG 57.359 42.857 0.00 0.00 42.17 3.66
1718 1864 3.562141 TCGAATCGTTTTGTTCACCACAT 59.438 39.130 1.52 0.00 34.43 3.21
1768 1914 9.895894 CATTCGAATGATTTGTGATTTTGATTC 57.104 29.630 30.12 0.00 38.70 2.52
1789 1935 3.740590 CTGCTTGTGCTAGTTTCATTCG 58.259 45.455 0.00 0.00 40.48 3.34
1794 1940 2.549754 TCTTGCTGCTTGTGCTAGTTTC 59.450 45.455 0.00 0.00 40.48 2.78
2466 3162 3.684305 TGCAGGAGTAATCAACGAACATG 59.316 43.478 0.00 0.00 0.00 3.21
2467 3163 3.937814 TGCAGGAGTAATCAACGAACAT 58.062 40.909 0.00 0.00 0.00 2.71
2468 3164 3.394674 TGCAGGAGTAATCAACGAACA 57.605 42.857 0.00 0.00 0.00 3.18
2521 3246 4.844349 AGAGCATACAACCACTACCAAT 57.156 40.909 0.00 0.00 0.00 3.16
2566 3386 4.267452 CCACGACACAATTTCAAGGTTTTG 59.733 41.667 0.00 0.00 35.57 2.44
2733 3553 2.623878 TGTTAGGGTTCAGTTTGCGA 57.376 45.000 0.00 0.00 0.00 5.10
2859 3874 6.201044 CCACGTGCCTACTTTCTTTCTATATG 59.799 42.308 10.91 0.00 0.00 1.78
3003 4019 8.733128 CACATTATACGTCAACAATTATGCAAC 58.267 33.333 0.00 0.00 0.00 4.17
3013 4029 2.675844 GGCAGCACATTATACGTCAACA 59.324 45.455 0.00 0.00 0.00 3.33
3014 4030 2.936498 AGGCAGCACATTATACGTCAAC 59.064 45.455 0.00 0.00 0.00 3.18
3015 4031 3.260475 AGGCAGCACATTATACGTCAA 57.740 42.857 0.00 0.00 0.00 3.18
3016 4032 2.979814 AGGCAGCACATTATACGTCA 57.020 45.000 0.00 0.00 0.00 4.35
3017 4033 3.978687 ACTAGGCAGCACATTATACGTC 58.021 45.455 0.00 0.00 0.00 4.34
3018 4034 3.637229 AGACTAGGCAGCACATTATACGT 59.363 43.478 0.00 0.00 0.00 3.57
3019 4035 4.244425 AGACTAGGCAGCACATTATACG 57.756 45.455 0.00 0.00 0.00 3.06
3020 4036 6.017852 GGAAAAGACTAGGCAGCACATTATAC 60.018 42.308 0.00 0.00 0.00 1.47
3021 4037 6.055588 GGAAAAGACTAGGCAGCACATTATA 58.944 40.000 0.00 0.00 0.00 0.98
3022 4038 4.884164 GGAAAAGACTAGGCAGCACATTAT 59.116 41.667 0.00 0.00 0.00 1.28
3023 4039 4.261801 GGAAAAGACTAGGCAGCACATTA 58.738 43.478 0.00 0.00 0.00 1.90
3024 4040 3.084786 GGAAAAGACTAGGCAGCACATT 58.915 45.455 0.00 0.00 0.00 2.71
3025 4041 2.040278 TGGAAAAGACTAGGCAGCACAT 59.960 45.455 0.00 0.00 0.00 3.21
3026 4042 1.419762 TGGAAAAGACTAGGCAGCACA 59.580 47.619 0.00 0.00 0.00 4.57
3027 4043 2.185004 TGGAAAAGACTAGGCAGCAC 57.815 50.000 0.00 0.00 0.00 4.40
3028 4044 2.305635 TGATGGAAAAGACTAGGCAGCA 59.694 45.455 0.00 0.00 0.00 4.41
3029 4045 2.941720 CTGATGGAAAAGACTAGGCAGC 59.058 50.000 0.00 0.00 0.00 5.25
3030 4046 4.478206 TCTGATGGAAAAGACTAGGCAG 57.522 45.455 0.00 0.00 0.00 4.85
3031 4047 4.442052 CGATCTGATGGAAAAGACTAGGCA 60.442 45.833 0.00 0.00 0.00 4.75
3032 4048 4.054671 CGATCTGATGGAAAAGACTAGGC 58.945 47.826 0.00 0.00 0.00 3.93
3033 4049 4.100189 ACCGATCTGATGGAAAAGACTAGG 59.900 45.833 11.46 0.00 0.00 3.02
3034 4050 5.269505 ACCGATCTGATGGAAAAGACTAG 57.730 43.478 11.46 0.00 0.00 2.57
3035 4051 5.677319 AACCGATCTGATGGAAAAGACTA 57.323 39.130 11.46 0.00 0.00 2.59
3036 4052 4.559862 AACCGATCTGATGGAAAAGACT 57.440 40.909 11.46 0.00 0.00 3.24
3037 4053 5.629079 AAAACCGATCTGATGGAAAAGAC 57.371 39.130 11.46 0.00 0.00 3.01
3057 4073 3.554752 GCTCTAGCCAATGCAACCAAAAA 60.555 43.478 0.00 0.00 41.13 1.94
3058 4074 2.029110 GCTCTAGCCAATGCAACCAAAA 60.029 45.455 0.00 0.00 41.13 2.44
3059 4075 1.545582 GCTCTAGCCAATGCAACCAAA 59.454 47.619 0.00 0.00 41.13 3.28
3060 4076 1.176527 GCTCTAGCCAATGCAACCAA 58.823 50.000 0.00 0.00 41.13 3.67
3061 4077 0.038021 TGCTCTAGCCAATGCAACCA 59.962 50.000 0.00 0.00 41.13 3.67
3062 4078 1.066605 CATGCTCTAGCCAATGCAACC 59.933 52.381 0.00 0.00 41.13 3.77
3063 4079 1.535437 GCATGCTCTAGCCAATGCAAC 60.535 52.381 11.37 2.38 44.74 4.17
3064 4080 0.742505 GCATGCTCTAGCCAATGCAA 59.257 50.000 11.37 0.00 44.74 4.08
3065 4081 2.411535 GCATGCTCTAGCCAATGCA 58.588 52.632 11.37 0.00 44.74 3.96
3066 4082 0.030369 GTGCATGCTCTAGCCAATGC 59.970 55.000 20.33 16.33 45.25 3.56
3067 4083 1.676746 AGTGCATGCTCTAGCCAATG 58.323 50.000 20.22 0.00 41.18 2.82
3068 4084 2.092538 AGAAGTGCATGCTCTAGCCAAT 60.093 45.455 21.70 5.92 41.18 3.16
3069 4085 1.280133 AGAAGTGCATGCTCTAGCCAA 59.720 47.619 21.70 0.00 41.18 4.52
3070 4086 0.907486 AGAAGTGCATGCTCTAGCCA 59.093 50.000 21.70 0.00 41.18 4.75
3071 4087 2.159043 TGTAGAAGTGCATGCTCTAGCC 60.159 50.000 21.70 13.81 41.18 3.93
3072 4088 3.170791 TGTAGAAGTGCATGCTCTAGC 57.829 47.619 21.70 16.29 42.50 3.42
3073 4089 4.056740 CCATGTAGAAGTGCATGCTCTAG 58.943 47.826 21.70 7.70 43.45 2.43
3074 4090 3.452264 ACCATGTAGAAGTGCATGCTCTA 59.548 43.478 21.70 15.62 43.45 2.43
3075 4091 2.238144 ACCATGTAGAAGTGCATGCTCT 59.762 45.455 20.33 18.23 43.45 4.09
3076 4092 2.636830 ACCATGTAGAAGTGCATGCTC 58.363 47.619 20.33 15.94 43.45 4.26
3077 4093 2.795231 ACCATGTAGAAGTGCATGCT 57.205 45.000 20.33 0.00 43.45 3.79
3078 4094 3.185188 CGATACCATGTAGAAGTGCATGC 59.815 47.826 11.82 11.82 43.45 4.06
3079 4095 3.742882 CCGATACCATGTAGAAGTGCATG 59.257 47.826 0.00 0.00 44.17 4.06
3080 4096 3.641436 TCCGATACCATGTAGAAGTGCAT 59.359 43.478 0.00 0.00 0.00 3.96
3081 4097 3.028130 TCCGATACCATGTAGAAGTGCA 58.972 45.455 0.00 0.00 0.00 4.57
3082 4098 3.068307 ACTCCGATACCATGTAGAAGTGC 59.932 47.826 0.00 0.00 0.00 4.40
3083 4099 4.338400 TGACTCCGATACCATGTAGAAGTG 59.662 45.833 0.00 0.00 0.00 3.16
3084 4100 4.533815 TGACTCCGATACCATGTAGAAGT 58.466 43.478 0.00 0.00 0.00 3.01
3085 4101 5.508153 CCTTGACTCCGATACCATGTAGAAG 60.508 48.000 0.00 0.00 0.00 2.85
3086 4102 4.341235 CCTTGACTCCGATACCATGTAGAA 59.659 45.833 0.00 0.00 0.00 2.10
3087 4103 3.889538 CCTTGACTCCGATACCATGTAGA 59.110 47.826 0.00 0.00 0.00 2.59
3088 4104 3.005897 CCCTTGACTCCGATACCATGTAG 59.994 52.174 0.00 0.00 0.00 2.74
3089 4105 2.963101 CCCTTGACTCCGATACCATGTA 59.037 50.000 0.00 0.00 0.00 2.29
3090 4106 1.762957 CCCTTGACTCCGATACCATGT 59.237 52.381 0.00 0.00 0.00 3.21
3091 4107 1.070758 CCCCTTGACTCCGATACCATG 59.929 57.143 0.00 0.00 0.00 3.66
3092 4108 1.424638 CCCCTTGACTCCGATACCAT 58.575 55.000 0.00 0.00 0.00 3.55
3093 4109 0.689745 CCCCCTTGACTCCGATACCA 60.690 60.000 0.00 0.00 0.00 3.25
3094 4110 0.398098 TCCCCCTTGACTCCGATACC 60.398 60.000 0.00 0.00 0.00 2.73
3095 4111 1.041437 CTCCCCCTTGACTCCGATAC 58.959 60.000 0.00 0.00 0.00 2.24
3096 4112 0.635009 ACTCCCCCTTGACTCCGATA 59.365 55.000 0.00 0.00 0.00 2.92
3097 4113 0.978146 CACTCCCCCTTGACTCCGAT 60.978 60.000 0.00 0.00 0.00 4.18
3098 4114 1.609501 CACTCCCCCTTGACTCCGA 60.610 63.158 0.00 0.00 0.00 4.55
3099 4115 1.481056 AACACTCCCCCTTGACTCCG 61.481 60.000 0.00 0.00 0.00 4.63
3100 4116 0.036875 CAACACTCCCCCTTGACTCC 59.963 60.000 0.00 0.00 0.00 3.85
3101 4117 1.056660 TCAACACTCCCCCTTGACTC 58.943 55.000 0.00 0.00 0.00 3.36
3102 4118 0.765510 GTCAACACTCCCCCTTGACT 59.234 55.000 0.00 0.00 40.37 3.41
3103 4119 0.602905 CGTCAACACTCCCCCTTGAC 60.603 60.000 0.00 0.00 40.20 3.18
3104 4120 1.052124 ACGTCAACACTCCCCCTTGA 61.052 55.000 0.00 0.00 0.00 3.02
3105 4121 0.682852 TACGTCAACACTCCCCCTTG 59.317 55.000 0.00 0.00 0.00 3.61
3106 4122 1.652947 ATACGTCAACACTCCCCCTT 58.347 50.000 0.00 0.00 0.00 3.95
3107 4123 2.537633 TATACGTCAACACTCCCCCT 57.462 50.000 0.00 0.00 0.00 4.79
3108 4124 3.118519 ACATTATACGTCAACACTCCCCC 60.119 47.826 0.00 0.00 0.00 5.40
3109 4125 3.869246 CACATTATACGTCAACACTCCCC 59.131 47.826 0.00 0.00 0.00 4.81
3110 4126 4.501071 ACACATTATACGTCAACACTCCC 58.499 43.478 0.00 0.00 0.00 4.30
3111 4127 5.670341 GCAACACATTATACGTCAACACTCC 60.670 44.000 0.00 0.00 0.00 3.85
3112 4128 5.313623 GCAACACATTATACGTCAACACTC 58.686 41.667 0.00 0.00 0.00 3.51
3113 4129 4.153475 GGCAACACATTATACGTCAACACT 59.847 41.667 0.00 0.00 0.00 3.55
3114 4130 4.153475 AGGCAACACATTATACGTCAACAC 59.847 41.667 0.00 0.00 41.41 3.32
3115 4131 4.320023 AGGCAACACATTATACGTCAACA 58.680 39.130 0.00 0.00 41.41 3.33
3116 4132 4.939509 AGGCAACACATTATACGTCAAC 57.060 40.909 0.00 0.00 41.41 3.18
3117 4133 5.726397 ACTAGGCAACACATTATACGTCAA 58.274 37.500 0.00 0.00 41.41 3.18
3118 4134 5.126545 AGACTAGGCAACACATTATACGTCA 59.873 40.000 0.00 0.00 41.41 4.35
3119 4135 5.589192 AGACTAGGCAACACATTATACGTC 58.411 41.667 0.00 0.00 41.41 4.34
3120 4136 5.360144 AGAGACTAGGCAACACATTATACGT 59.640 40.000 0.00 0.00 41.41 3.57
3121 4137 5.833082 AGAGACTAGGCAACACATTATACG 58.167 41.667 0.00 0.00 41.41 3.06
3122 4138 6.702282 GGAAGAGACTAGGCAACACATTATAC 59.298 42.308 0.00 0.00 41.41 1.47
3123 4139 6.611642 AGGAAGAGACTAGGCAACACATTATA 59.388 38.462 0.00 0.00 41.41 0.98
3124 4140 5.426833 AGGAAGAGACTAGGCAACACATTAT 59.573 40.000 0.00 0.00 41.41 1.28
3125 4141 4.777896 AGGAAGAGACTAGGCAACACATTA 59.222 41.667 0.00 0.00 41.41 1.90
3126 4142 3.584848 AGGAAGAGACTAGGCAACACATT 59.415 43.478 0.00 0.00 41.41 2.71
3127 4143 3.177228 AGGAAGAGACTAGGCAACACAT 58.823 45.455 0.00 0.00 41.41 3.21
3128 4144 2.609747 AGGAAGAGACTAGGCAACACA 58.390 47.619 0.00 0.00 41.41 3.72
3129 4145 3.006967 TGAAGGAAGAGACTAGGCAACAC 59.993 47.826 0.00 0.00 41.41 3.32
3130 4146 3.239449 TGAAGGAAGAGACTAGGCAACA 58.761 45.455 0.00 0.00 41.41 3.33
3131 4147 3.511934 TCTGAAGGAAGAGACTAGGCAAC 59.488 47.826 0.00 0.00 0.00 4.17
3132 4148 3.779444 TCTGAAGGAAGAGACTAGGCAA 58.221 45.455 0.00 0.00 0.00 4.52
3133 4149 3.458044 TCTGAAGGAAGAGACTAGGCA 57.542 47.619 0.00 0.00 0.00 4.75
3134 4150 3.004315 CGATCTGAAGGAAGAGACTAGGC 59.996 52.174 0.00 0.00 0.00 3.93
3135 4151 3.568007 CCGATCTGAAGGAAGAGACTAGG 59.432 52.174 0.00 0.00 0.00 3.02
3136 4152 4.204012 ACCGATCTGAAGGAAGAGACTAG 58.796 47.826 9.14 0.00 0.00 2.57
3137 4153 4.080243 AGACCGATCTGAAGGAAGAGACTA 60.080 45.833 9.14 0.00 32.29 2.59
3138 4154 3.020984 GACCGATCTGAAGGAAGAGACT 58.979 50.000 9.14 0.00 0.00 3.24
3139 4155 3.020984 AGACCGATCTGAAGGAAGAGAC 58.979 50.000 9.14 0.00 32.29 3.36
3140 4156 3.374042 AGACCGATCTGAAGGAAGAGA 57.626 47.619 9.14 0.00 32.29 3.10
3141 4157 4.464069 AAAGACCGATCTGAAGGAAGAG 57.536 45.455 9.14 0.00 34.48 2.85
3142 4158 4.040461 ACAAAAGACCGATCTGAAGGAAGA 59.960 41.667 9.14 0.00 34.48 2.87
3143 4159 4.319177 ACAAAAGACCGATCTGAAGGAAG 58.681 43.478 9.14 0.00 34.48 3.46
3144 4160 4.351874 ACAAAAGACCGATCTGAAGGAA 57.648 40.909 9.14 0.00 34.48 3.36
3145 4161 4.351874 AACAAAAGACCGATCTGAAGGA 57.648 40.909 9.14 0.00 34.48 3.36
3146 4162 4.787598 CAAACAAAAGACCGATCTGAAGG 58.212 43.478 0.00 1.62 34.48 3.46
3147 4163 4.222114 GCAAACAAAAGACCGATCTGAAG 58.778 43.478 0.00 0.00 34.48 3.02
3148 4164 3.629855 TGCAAACAAAAGACCGATCTGAA 59.370 39.130 0.00 0.00 34.48 3.02
3149 4165 3.210227 TGCAAACAAAAGACCGATCTGA 58.790 40.909 0.00 0.00 34.48 3.27
3150 4166 3.624326 TGCAAACAAAAGACCGATCTG 57.376 42.857 0.00 0.00 34.48 2.90
3151 4167 4.549458 CAATGCAAACAAAAGACCGATCT 58.451 39.130 0.00 0.00 36.42 2.75
3152 4168 3.674753 CCAATGCAAACAAAAGACCGATC 59.325 43.478 0.00 0.00 0.00 3.69
3153 4169 3.652274 CCAATGCAAACAAAAGACCGAT 58.348 40.909 0.00 0.00 0.00 4.18
3154 4170 2.801342 GCCAATGCAAACAAAAGACCGA 60.801 45.455 0.00 0.00 37.47 4.69
3155 4171 1.526464 GCCAATGCAAACAAAAGACCG 59.474 47.619 0.00 0.00 37.47 4.79
3156 4172 2.837498 AGCCAATGCAAACAAAAGACC 58.163 42.857 0.00 0.00 41.13 3.85
3157 4173 4.870363 TCTAGCCAATGCAAACAAAAGAC 58.130 39.130 0.00 0.00 41.13 3.01


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

AutoCloner maintained by Alex Coulton.