Multiple sequence alignment - TraesCS6D01G387700

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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 TraesCS6D01G387700 chr6D 100.000 3737 0 0 1 3737 464498009 464494273 0.000000e+00 6902.0
1 TraesCS6D01G387700 chr6D 97.872 47 1 0 21 67 464497943 464497897 8.600000e-12 82.4
2 TraesCS6D01G387700 chr6D 97.872 47 1 0 67 113 464497989 464497943 8.600000e-12 82.4
3 TraesCS6D01G387700 chr6D 100.000 28 0 0 2471 2498 163135298 163135271 7.000000e-03 52.8
4 TraesCS6D01G387700 chr6A 90.030 3350 184 71 67 3331 611080451 611077167 0.000000e+00 4198.0
5 TraesCS6D01G387700 chr6A 92.683 82 4 2 3328 3409 611076885 611076806 2.360000e-22 117.0
6 TraesCS6D01G387700 chr6A 100.000 28 0 0 2471 2498 223414105 223414078 7.000000e-03 52.8
7 TraesCS6D01G387700 chr6B 93.099 2246 107 29 983 3203 708273120 708270898 0.000000e+00 3245.0
8 TraesCS6D01G387700 chr6B 89.575 518 26 13 434 942 708273622 708273124 1.890000e-177 632.0
9 TraesCS6D01G387700 chr6B 85.142 424 29 13 67 479 708274010 708273610 1.620000e-108 403.0
10 TraesCS6D01G387700 chr6B 96.364 55 2 0 13 67 708274018 708273964 1.430000e-14 91.6
11 TraesCS6D01G387700 chr6B 93.750 48 3 0 3685 3732 708270707 708270660 5.180000e-09 73.1
12 TraesCS6D01G387700 chr5D 76.847 203 26 9 3465 3665 439260044 439260227 1.100000e-15 95.3


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 TraesCS6D01G387700 chr6D 464494273 464498009 3736 True 2355.60 6902 98.581333 1 3737 3 chr6D.!!$R2 3736
1 TraesCS6D01G387700 chr6A 611076806 611080451 3645 True 2157.50 4198 91.356500 67 3409 2 chr6A.!!$R2 3342
2 TraesCS6D01G387700 chr6B 708270660 708274018 3358 True 888.94 3245 91.586000 13 3732 5 chr6B.!!$R1 3719

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
20 21 0.178990 AAGGTTCCTTCTGGTGCACC 60.179 55.0 29.67 29.67 34.23 5.01 F
25 26 0.250858 TCCTTCTGGTGCACCACATG 60.251 55.0 34.74 24.71 42.01 3.21 F
956 1045 0.396060 TTCCCTTTGCCAATTGCCAC 59.604 50.0 0.00 0.00 40.16 5.01 F
1633 1761 2.285602 GCGCACTGACATTTACGTATGG 60.286 50.0 0.30 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1738 0.320421 ACGTAAATGTCAGTGCGCCT 60.320 50.000 4.18 0.0 0.00 5.52 R
1628 1756 1.003118 TGTCCTGCAGTTCACCCATAC 59.997 52.381 13.81 0.0 0.00 2.39 R
2274 2402 0.323178 CCATCTTGGTGAGCTTGCCT 60.323 55.000 8.64 0.0 31.35 4.75 R
3042 3196 0.246360 TACTGGACACACCTCATGCG 59.754 55.000 0.00 0.0 39.86 4.73 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
19 20 1.692411 AAAGGTTCCTTCTGGTGCAC 58.308 50.000 8.80 8.80 34.23 4.57
20 21 0.178990 AAGGTTCCTTCTGGTGCACC 60.179 55.000 29.67 29.67 34.23 5.01
21 22 1.150536 GGTTCCTTCTGGTGCACCA 59.849 57.895 35.49 35.49 45.30 4.17
22 23 1.172812 GGTTCCTTCTGGTGCACCAC 61.173 60.000 34.74 21.79 42.01 4.16
23 24 0.465460 GTTCCTTCTGGTGCACCACA 60.465 55.000 34.74 23.05 42.01 4.17
24 25 0.478072 TTCCTTCTGGTGCACCACAT 59.522 50.000 34.74 0.00 42.01 3.21
25 26 0.250858 TCCTTCTGGTGCACCACATG 60.251 55.000 34.74 24.71 42.01 3.21
26 27 1.246056 CCTTCTGGTGCACCACATGG 61.246 60.000 34.74 29.14 42.01 3.66
47 48 4.730966 GGTCTATATGGTGACCTCTCTCA 58.269 47.826 2.11 0.00 46.65 3.27
48 49 5.141182 GGTCTATATGGTGACCTCTCTCAA 58.859 45.833 2.11 0.00 46.65 3.02
49 50 5.598830 GGTCTATATGGTGACCTCTCTCAAA 59.401 44.000 2.11 0.00 46.65 2.69
50 51 6.098409 GGTCTATATGGTGACCTCTCTCAAAA 59.902 42.308 2.11 0.00 46.65 2.44
51 52 7.364762 GGTCTATATGGTGACCTCTCTCAAAAA 60.365 40.741 2.11 0.00 46.65 1.94
52 53 7.708752 GTCTATATGGTGACCTCTCTCAAAAAG 59.291 40.741 2.11 0.00 0.00 2.27
53 54 4.982241 ATGGTGACCTCTCTCAAAAAGA 57.018 40.909 2.11 0.00 0.00 2.52
54 55 4.771114 TGGTGACCTCTCTCAAAAAGAA 57.229 40.909 2.11 0.00 32.23 2.52
55 56 5.310409 TGGTGACCTCTCTCAAAAAGAAT 57.690 39.130 2.11 0.00 32.23 2.40
56 57 6.433847 TGGTGACCTCTCTCAAAAAGAATA 57.566 37.500 2.11 0.00 32.23 1.75
57 58 6.467677 TGGTGACCTCTCTCAAAAAGAATAG 58.532 40.000 2.11 0.00 32.23 1.73
58 59 6.270000 TGGTGACCTCTCTCAAAAAGAATAGA 59.730 38.462 2.11 0.00 32.23 1.98
59 60 6.816140 GGTGACCTCTCTCAAAAAGAATAGAG 59.184 42.308 0.00 0.00 36.71 2.43
60 61 7.310113 GGTGACCTCTCTCAAAAAGAATAGAGA 60.310 40.741 0.00 0.00 41.58 3.10
61 62 8.091449 GTGACCTCTCTCAAAAAGAATAGAGAA 58.909 37.037 0.00 0.00 42.81 2.87
62 63 8.651389 TGACCTCTCTCAAAAAGAATAGAGAAA 58.349 33.333 0.00 0.00 42.81 2.52
63 64 9.495572 GACCTCTCTCAAAAAGAATAGAGAAAA 57.504 33.333 0.00 0.00 42.81 2.29
64 65 9.500785 ACCTCTCTCAAAAAGAATAGAGAAAAG 57.499 33.333 0.00 0.00 42.81 2.27
65 66 9.500785 CCTCTCTCAAAAAGAATAGAGAAAAGT 57.499 33.333 0.00 0.00 42.81 2.66
169 170 6.817140 CGAGCCCTACAGTTTAGTTAAATTCT 59.183 38.462 0.00 0.00 0.00 2.40
225 232 7.179966 ACTAAAAATGGTTAGTTTCCTAGGGG 58.820 38.462 9.46 0.00 40.63 4.79
246 253 4.287326 GGGCATCTAGCTAGGGAATTTAGT 59.713 45.833 20.58 0.00 44.79 2.24
251 258 3.847671 AGCTAGGGAATTTAGTCAGCC 57.152 47.619 0.00 0.00 0.00 4.85
253 260 3.135530 AGCTAGGGAATTTAGTCAGCCAG 59.864 47.826 0.00 0.00 0.00 4.85
370 389 1.485032 CGCCCGCGGTGAGTATAAAC 61.485 60.000 26.12 0.00 34.74 2.01
374 393 2.199236 CCGCGGTGAGTATAAACCTTC 58.801 52.381 19.50 0.00 34.06 3.46
449 476 5.163405 CGGGAATGAGAATCTGGACTTCTTA 60.163 44.000 0.00 0.00 33.18 2.10
490 550 9.739276 TGAGAATCTGGACTTAAACATGTAATT 57.261 29.630 0.00 0.00 34.92 1.40
531 591 6.346477 ACATGTAGTAGCAGAGAAAACTCA 57.654 37.500 0.00 0.00 0.00 3.41
631 700 2.809601 CCCGCGTTTGACCGAGAG 60.810 66.667 4.92 0.00 0.00 3.20
666 735 0.575390 CGCAAGTGAAAACGAGACGT 59.425 50.000 0.00 0.00 43.97 4.34
813 897 1.279271 CAAACCCACCTACTCCCTCAG 59.721 57.143 0.00 0.00 0.00 3.35
861 945 6.188407 TCATCTCCTCCCCTCTATATAAACG 58.812 44.000 0.00 0.00 0.00 3.60
908 992 2.739932 CGAACCATCTCTCATCACACCC 60.740 54.545 0.00 0.00 0.00 4.61
910 994 2.269023 ACCATCTCTCATCACACCCAA 58.731 47.619 0.00 0.00 0.00 4.12
943 1027 4.335416 TCTTCGCTTCATTGAATTCCCTT 58.665 39.130 2.27 0.00 0.00 3.95
945 1029 4.439305 TCGCTTCATTGAATTCCCTTTG 57.561 40.909 2.27 0.00 0.00 2.77
946 1030 2.925563 CGCTTCATTGAATTCCCTTTGC 59.074 45.455 2.27 0.20 0.00 3.68
951 1040 5.502089 TCATTGAATTCCCTTTGCCAATT 57.498 34.783 2.27 0.00 0.00 2.32
956 1045 0.396060 TTCCCTTTGCCAATTGCCAC 59.604 50.000 0.00 0.00 40.16 5.01
964 1053 5.486526 CTTTGCCAATTGCCACCTTAATTA 58.513 37.500 0.00 0.00 40.16 1.40
967 1056 4.530161 TGCCAATTGCCACCTTAATTACTT 59.470 37.500 0.00 0.00 40.16 2.24
968 1057 5.012561 TGCCAATTGCCACCTTAATTACTTT 59.987 36.000 0.00 0.00 40.16 2.66
969 1058 5.580691 GCCAATTGCCACCTTAATTACTTTC 59.419 40.000 0.00 0.00 0.00 2.62
973 1062 3.687698 TGCCACCTTAATTACTTTCTCGC 59.312 43.478 0.00 0.00 0.00 5.03
974 1063 3.939592 GCCACCTTAATTACTTTCTCGCT 59.060 43.478 0.00 0.00 0.00 4.93
975 1064 4.395231 GCCACCTTAATTACTTTCTCGCTT 59.605 41.667 0.00 0.00 0.00 4.68
976 1065 5.673818 GCCACCTTAATTACTTTCTCGCTTG 60.674 44.000 0.00 0.00 0.00 4.01
977 1066 5.642063 CCACCTTAATTACTTTCTCGCTTGA 59.358 40.000 0.00 0.00 0.00 3.02
978 1067 6.183360 CCACCTTAATTACTTTCTCGCTTGAG 60.183 42.308 0.00 0.00 41.33 3.02
979 1068 5.351740 ACCTTAATTACTTTCTCGCTTGAGC 59.648 40.000 0.00 0.00 39.70 4.26
980 1069 5.351465 CCTTAATTACTTTCTCGCTTGAGCA 59.649 40.000 3.65 0.00 42.21 4.26
981 1070 4.670227 AATTACTTTCTCGCTTGAGCAC 57.330 40.909 3.65 0.00 42.21 4.40
1011 1120 4.802051 GCCCCAATGGAGCTCGCA 62.802 66.667 7.83 7.50 35.39 5.10
1027 1136 3.385384 CAGCGGCTCTCCTGGTGA 61.385 66.667 0.00 0.00 36.90 4.02
1030 1139 3.062466 CGGCTCTCCTGGTGACGA 61.062 66.667 6.53 0.00 41.88 4.20
1090 1199 2.890602 GCCACCTTCCTCTACTTCCTCT 60.891 54.545 0.00 0.00 0.00 3.69
1260 1369 4.082523 ACCAGCGACATCCACGGG 62.083 66.667 0.00 0.00 0.00 5.28
1538 1647 2.353011 CCACCAACCTCAACGTACGTAT 60.353 50.000 23.12 9.26 0.00 3.06
1568 1677 4.888038 ATTACACGTGTAGCGATCTGTA 57.112 40.909 26.04 10.56 44.77 2.74
1573 1701 3.973135 CACGTGTAGCGATCTGTAATACC 59.027 47.826 7.58 0.00 44.77 2.73
1602 1730 2.693762 ATGCATGCACGCACTCACC 61.694 57.895 25.37 0.00 46.56 4.02
1611 1739 3.349006 GCACTCACCCACGCACAG 61.349 66.667 0.00 0.00 0.00 3.66
1612 1740 2.666190 CACTCACCCACGCACAGG 60.666 66.667 0.00 0.00 0.00 4.00
1628 1756 2.456000 AGGCGCACTGACATTTACG 58.544 52.632 10.83 0.00 0.00 3.18
1633 1761 2.285602 GCGCACTGACATTTACGTATGG 60.286 50.000 0.30 0.00 0.00 2.74
2037 2165 2.557920 AGAAGAACAAGGACCTGCTG 57.442 50.000 0.00 0.00 0.00 4.41
2085 2213 2.440599 GGGGAAGCAGCAGGGAAA 59.559 61.111 0.00 0.00 0.00 3.13
2373 2501 2.733671 CCTGCACGATGTCGCTGTG 61.734 63.158 1.77 0.00 44.43 3.66
2749 2880 1.325355 CAAATAGATGGCCAGCTGGG 58.675 55.000 33.38 15.33 40.85 4.45
2962 3113 8.567948 ACAAAACAAATATACCAAGTGAGACTG 58.432 33.333 0.00 0.00 0.00 3.51
2963 3114 6.743575 AACAAATATACCAAGTGAGACTGC 57.256 37.500 0.00 0.00 0.00 4.40
2990 3141 0.312729 CATGCAACTGAGCTGTGCAA 59.687 50.000 13.16 0.91 39.04 4.08
3127 3281 0.248990 GTTGACCGTACACGTGGTGA 60.249 55.000 21.57 0.00 38.99 4.02
3248 3402 1.081556 AGATCGTGCGCGCATGTAAA 61.082 50.000 42.21 29.30 38.14 2.01
3260 3414 2.483877 CGCATGTAAAGCTTGGAAGTCA 59.516 45.455 0.00 0.00 0.00 3.41
3261 3415 3.127548 CGCATGTAAAGCTTGGAAGTCAT 59.872 43.478 0.00 0.00 0.00 3.06
3262 3416 4.379813 CGCATGTAAAGCTTGGAAGTCATT 60.380 41.667 0.00 0.00 0.00 2.57
3263 3417 5.163764 CGCATGTAAAGCTTGGAAGTCATTA 60.164 40.000 0.00 0.00 0.00 1.90
3270 3424 9.914131 GTAAAGCTTGGAAGTCATTAATTTCTT 57.086 29.630 0.00 2.66 0.00 2.52
3272 3426 6.846350 AGCTTGGAAGTCATTAATTTCTTCG 58.154 36.000 16.50 9.10 37.67 3.79
3279 3433 4.580580 AGTCATTAATTTCTTCGGGCATCC 59.419 41.667 0.00 0.00 0.00 3.51
3292 3446 2.945668 CGGGCATCCTTCTTTTTCTAGG 59.054 50.000 0.00 0.00 0.00 3.02
3294 3448 2.356069 GGCATCCTTCTTTTTCTAGGCG 59.644 50.000 0.00 0.00 0.00 5.52
3302 3456 2.084546 CTTTTTCTAGGCGGTTCCTGG 58.915 52.381 0.00 0.00 46.98 4.45
3308 3462 1.003233 CTAGGCGGTTCCTGGAACTTT 59.997 52.381 32.12 19.68 45.56 2.66
3309 3463 1.061546 AGGCGGTTCCTGGAACTTTA 58.938 50.000 32.12 0.00 45.54 1.85
3333 3487 5.422666 TGATCGGCAGCATTAATAAGTTG 57.577 39.130 0.00 0.00 0.00 3.16
3334 3488 4.275689 TGATCGGCAGCATTAATAAGTTGG 59.724 41.667 0.00 0.00 0.00 3.77
3380 3827 6.910536 TCATCGGCTCTAAATCTTTCTTTC 57.089 37.500 0.00 0.00 0.00 2.62
3381 3828 6.644347 TCATCGGCTCTAAATCTTTCTTTCT 58.356 36.000 0.00 0.00 0.00 2.52
3394 3841 8.681486 AATCTTTCTTTCTTTTTGAAATGGGG 57.319 30.769 0.00 0.00 42.96 4.96
3395 3842 7.430760 TCTTTCTTTCTTTTTGAAATGGGGA 57.569 32.000 0.00 0.00 42.96 4.81
3396 3843 8.033178 TCTTTCTTTCTTTTTGAAATGGGGAT 57.967 30.769 0.00 0.00 42.96 3.85
3397 3844 8.150296 TCTTTCTTTCTTTTTGAAATGGGGATC 58.850 33.333 0.00 0.00 42.96 3.36
3398 3845 6.024552 TCTTTCTTTTTGAAATGGGGATCG 57.975 37.500 0.00 0.00 42.96 3.69
3399 3846 5.538433 TCTTTCTTTTTGAAATGGGGATCGT 59.462 36.000 0.00 0.00 42.96 3.73
3400 3847 5.385509 TTCTTTTTGAAATGGGGATCGTC 57.614 39.130 0.00 0.00 0.00 4.20
3401 3848 3.438781 TCTTTTTGAAATGGGGATCGTCG 59.561 43.478 0.00 0.00 0.00 5.12
3402 3849 1.745232 TTTGAAATGGGGATCGTCGG 58.255 50.000 0.00 0.00 0.00 4.79
3403 3850 0.746563 TTGAAATGGGGATCGTCGGC 60.747 55.000 0.00 0.00 0.00 5.54
3404 3851 1.146263 GAAATGGGGATCGTCGGCT 59.854 57.895 0.00 0.00 0.00 5.52
3405 3852 0.880718 GAAATGGGGATCGTCGGCTC 60.881 60.000 0.00 0.00 0.00 4.70
3406 3853 1.338136 AAATGGGGATCGTCGGCTCT 61.338 55.000 0.00 0.00 0.00 4.09
3407 3854 0.469331 AATGGGGATCGTCGGCTCTA 60.469 55.000 0.00 0.00 0.00 2.43
3408 3855 0.469331 ATGGGGATCGTCGGCTCTAA 60.469 55.000 0.00 0.00 0.00 2.10
3409 3856 1.107538 TGGGGATCGTCGGCTCTAAG 61.108 60.000 0.00 0.00 0.00 2.18
3410 3857 1.660917 GGGATCGTCGGCTCTAAGG 59.339 63.158 0.00 0.00 0.00 2.69
3411 3858 1.007154 GGATCGTCGGCTCTAAGGC 60.007 63.158 0.00 0.00 37.44 4.35
3419 3866 2.873797 GGCTCTAAGGCCCTGTTTG 58.126 57.895 0.00 0.00 45.92 2.93
3420 3867 0.038310 GGCTCTAAGGCCCTGTTTGT 59.962 55.000 0.00 0.00 45.92 2.83
3421 3868 1.547901 GGCTCTAAGGCCCTGTTTGTT 60.548 52.381 0.00 0.00 45.92 2.83
3422 3869 2.239400 GCTCTAAGGCCCTGTTTGTTT 58.761 47.619 0.00 0.00 0.00 2.83
3423 3870 2.029918 GCTCTAAGGCCCTGTTTGTTTG 60.030 50.000 0.00 0.00 0.00 2.93
3424 3871 3.486383 CTCTAAGGCCCTGTTTGTTTGA 58.514 45.455 0.00 0.00 0.00 2.69
3425 3872 3.486383 TCTAAGGCCCTGTTTGTTTGAG 58.514 45.455 0.00 0.00 0.00 3.02
3426 3873 0.752658 AAGGCCCTGTTTGTTTGAGC 59.247 50.000 0.00 0.00 0.00 4.26
3427 3874 0.396974 AGGCCCTGTTTGTTTGAGCA 60.397 50.000 0.00 0.00 0.00 4.26
3428 3875 0.681175 GGCCCTGTTTGTTTGAGCAT 59.319 50.000 0.00 0.00 0.00 3.79
3429 3876 1.070601 GGCCCTGTTTGTTTGAGCATT 59.929 47.619 0.00 0.00 0.00 3.56
3430 3877 2.485302 GGCCCTGTTTGTTTGAGCATTT 60.485 45.455 0.00 0.00 0.00 2.32
3431 3878 2.545106 GCCCTGTTTGTTTGAGCATTTG 59.455 45.455 0.00 0.00 0.00 2.32
3432 3879 2.545106 CCCTGTTTGTTTGAGCATTTGC 59.455 45.455 0.00 0.00 42.49 3.68
3446 3893 4.317804 GCATTTGCTTCTGCTTTTTAGC 57.682 40.909 0.00 0.00 40.48 3.09
3447 3894 3.992427 GCATTTGCTTCTGCTTTTTAGCT 59.008 39.130 0.00 0.00 40.48 3.32
3448 3895 4.450080 GCATTTGCTTCTGCTTTTTAGCTT 59.550 37.500 0.00 0.00 40.48 3.74
3449 3896 5.049886 GCATTTGCTTCTGCTTTTTAGCTTT 60.050 36.000 0.00 0.00 40.48 3.51
3450 3897 6.512253 GCATTTGCTTCTGCTTTTTAGCTTTT 60.512 34.615 0.00 0.00 40.48 2.27
3451 3898 6.983474 TTTGCTTCTGCTTTTTAGCTTTTT 57.017 29.167 0.00 0.00 40.48 1.94
3452 3899 6.588348 TTGCTTCTGCTTTTTAGCTTTTTC 57.412 33.333 0.00 0.00 40.48 2.29
3453 3900 5.659463 TGCTTCTGCTTTTTAGCTTTTTCA 58.341 33.333 0.00 0.00 40.48 2.69
3454 3901 6.282930 TGCTTCTGCTTTTTAGCTTTTTCAT 58.717 32.000 0.00 0.00 40.48 2.57
3455 3902 6.762661 TGCTTCTGCTTTTTAGCTTTTTCATT 59.237 30.769 0.00 0.00 40.48 2.57
3456 3903 7.280652 TGCTTCTGCTTTTTAGCTTTTTCATTT 59.719 29.630 0.00 0.00 40.48 2.32
3457 3904 8.124823 GCTTCTGCTTTTTAGCTTTTTCATTTT 58.875 29.630 0.00 0.00 36.03 1.82
3458 3905 9.429600 CTTCTGCTTTTTAGCTTTTTCATTTTG 57.570 29.630 0.00 0.00 35.49 2.44
3459 3906 8.715191 TCTGCTTTTTAGCTTTTTCATTTTGA 57.285 26.923 0.00 0.00 35.49 2.69
3460 3907 8.603181 TCTGCTTTTTAGCTTTTTCATTTTGAC 58.397 29.630 0.00 0.00 35.49 3.18
3461 3908 8.491331 TGCTTTTTAGCTTTTTCATTTTGACT 57.509 26.923 0.00 0.00 35.49 3.41
3462 3909 9.593134 TGCTTTTTAGCTTTTTCATTTTGACTA 57.407 25.926 0.00 0.00 35.49 2.59
3500 3947 6.148264 GCTTCTAAATAGATGCATTTGGAGC 58.852 40.000 18.29 0.00 46.64 4.70
3501 3948 6.016443 GCTTCTAAATAGATGCATTTGGAGCT 60.016 38.462 18.29 0.00 46.64 4.09
3502 3949 7.469732 GCTTCTAAATAGATGCATTTGGAGCTT 60.470 37.037 18.29 0.00 46.64 3.74
3503 3950 7.886629 TCTAAATAGATGCATTTGGAGCTTT 57.113 32.000 0.00 0.00 32.43 3.51
3504 3951 8.297470 TCTAAATAGATGCATTTGGAGCTTTT 57.703 30.769 0.00 0.33 32.43 2.27
3505 3952 9.407380 TCTAAATAGATGCATTTGGAGCTTTTA 57.593 29.630 0.00 1.34 32.43 1.52
3557 4004 9.208022 AGATTTGACTTTAAAAGCCATAAAAGC 57.792 29.630 0.00 0.00 33.25 3.51
3558 4005 9.208022 GATTTGACTTTAAAAGCCATAAAAGCT 57.792 29.630 0.00 0.00 44.19 3.74
3581 4028 9.844257 AGCTTTAAAATCATCTATGTAGAAGCT 57.156 29.630 0.00 0.00 35.69 3.74
3596 4043 7.899178 TGTAGAAGCTTTTATCGAAATCACA 57.101 32.000 0.00 0.00 0.00 3.58
3597 4044 7.963981 TGTAGAAGCTTTTATCGAAATCACAG 58.036 34.615 0.00 0.00 0.00 3.66
3598 4045 5.873732 AGAAGCTTTTATCGAAATCACAGC 58.126 37.500 0.00 0.00 0.00 4.40
3599 4046 5.645497 AGAAGCTTTTATCGAAATCACAGCT 59.355 36.000 0.00 0.00 36.85 4.24
3600 4047 5.886960 AGCTTTTATCGAAATCACAGCTT 57.113 34.783 0.00 0.00 33.26 3.74
3601 4048 6.259550 AGCTTTTATCGAAATCACAGCTTT 57.740 33.333 0.00 0.00 33.26 3.51
3602 4049 6.681777 AGCTTTTATCGAAATCACAGCTTTT 58.318 32.000 0.00 0.00 33.26 2.27
3603 4050 7.816640 AGCTTTTATCGAAATCACAGCTTTTA 58.183 30.769 0.00 0.00 33.26 1.52
3604 4051 8.462016 AGCTTTTATCGAAATCACAGCTTTTAT 58.538 29.630 0.00 0.00 33.26 1.40
3605 4052 8.526681 GCTTTTATCGAAATCACAGCTTTTATG 58.473 33.333 0.00 0.00 0.00 1.90
3606 4053 8.909708 TTTTATCGAAATCACAGCTTTTATGG 57.090 30.769 0.00 0.00 0.00 2.74
3607 4054 7.624360 TTATCGAAATCACAGCTTTTATGGT 57.376 32.000 0.00 0.00 0.00 3.55
3608 4055 5.957842 TCGAAATCACAGCTTTTATGGTT 57.042 34.783 0.00 0.00 0.00 3.67
3609 4056 6.325919 TCGAAATCACAGCTTTTATGGTTT 57.674 33.333 0.00 0.00 0.00 3.27
3610 4057 6.744112 TCGAAATCACAGCTTTTATGGTTTT 58.256 32.000 0.00 0.00 0.00 2.43
3611 4058 7.206687 TCGAAATCACAGCTTTTATGGTTTTT 58.793 30.769 0.00 0.00 0.00 1.94
3632 4079 5.809719 TTTGGTCAAAGTGGAAAAATTGC 57.190 34.783 0.00 0.00 0.00 3.56
3633 4080 4.478206 TGGTCAAAGTGGAAAAATTGCA 57.522 36.364 0.00 0.00 0.00 4.08
3634 4081 4.836825 TGGTCAAAGTGGAAAAATTGCAA 58.163 34.783 0.00 0.00 30.97 4.08
3635 4082 4.874966 TGGTCAAAGTGGAAAAATTGCAAG 59.125 37.500 4.94 0.00 30.97 4.01
3636 4083 5.115480 GGTCAAAGTGGAAAAATTGCAAGA 58.885 37.500 4.94 0.00 30.97 3.02
3637 4084 5.234972 GGTCAAAGTGGAAAAATTGCAAGAG 59.765 40.000 4.94 0.00 30.97 2.85
3638 4085 5.812127 GTCAAAGTGGAAAAATTGCAAGAGT 59.188 36.000 4.94 0.00 30.97 3.24
3639 4086 6.978080 GTCAAAGTGGAAAAATTGCAAGAGTA 59.022 34.615 4.94 0.00 30.97 2.59
3640 4087 7.168135 GTCAAAGTGGAAAAATTGCAAGAGTAG 59.832 37.037 4.94 0.00 30.97 2.57
3641 4088 6.959639 AAGTGGAAAAATTGCAAGAGTAGA 57.040 33.333 4.94 0.00 30.97 2.59
3642 4089 6.959639 AGTGGAAAAATTGCAAGAGTAGAA 57.040 33.333 4.94 0.00 30.97 2.10
3643 4090 6.974965 AGTGGAAAAATTGCAAGAGTAGAAG 58.025 36.000 4.94 0.00 30.97 2.85
3644 4091 5.631096 GTGGAAAAATTGCAAGAGTAGAAGC 59.369 40.000 4.94 0.00 30.97 3.86
3645 4092 5.301551 TGGAAAAATTGCAAGAGTAGAAGCA 59.698 36.000 4.94 0.00 34.79 3.91
3646 4093 5.860716 GGAAAAATTGCAAGAGTAGAAGCAG 59.139 40.000 4.94 0.00 38.35 4.24
3647 4094 6.294176 GGAAAAATTGCAAGAGTAGAAGCAGA 60.294 38.462 4.94 0.00 38.35 4.26
3648 4095 6.639632 AAAATTGCAAGAGTAGAAGCAGAA 57.360 33.333 4.94 0.00 38.35 3.02
3649 4096 5.876612 AATTGCAAGAGTAGAAGCAGAAG 57.123 39.130 4.94 0.00 38.35 2.85
3650 4097 2.693069 TGCAAGAGTAGAAGCAGAAGC 58.307 47.619 0.00 0.00 42.56 3.86
3651 4098 2.006169 GCAAGAGTAGAAGCAGAAGCC 58.994 52.381 0.00 0.00 43.56 4.35
3652 4099 2.626840 CAAGAGTAGAAGCAGAAGCCC 58.373 52.381 0.00 0.00 43.56 5.19
3653 4100 1.944177 AGAGTAGAAGCAGAAGCCCA 58.056 50.000 0.00 0.00 43.56 5.36
3654 4101 2.260822 AGAGTAGAAGCAGAAGCCCAA 58.739 47.619 0.00 0.00 43.56 4.12
3655 4102 2.639839 AGAGTAGAAGCAGAAGCCCAAA 59.360 45.455 0.00 0.00 43.56 3.28
3656 4103 2.744741 GAGTAGAAGCAGAAGCCCAAAC 59.255 50.000 0.00 0.00 43.56 2.93
3657 4104 2.106511 AGTAGAAGCAGAAGCCCAAACA 59.893 45.455 0.00 0.00 43.56 2.83
3658 4105 2.071778 AGAAGCAGAAGCCCAAACAA 57.928 45.000 0.00 0.00 43.56 2.83
3659 4106 2.387757 AGAAGCAGAAGCCCAAACAAA 58.612 42.857 0.00 0.00 43.56 2.83
3660 4107 2.101415 AGAAGCAGAAGCCCAAACAAAC 59.899 45.455 0.00 0.00 43.56 2.93
3661 4108 1.484038 AGCAGAAGCCCAAACAAACA 58.516 45.000 0.00 0.00 43.56 2.83
3662 4109 1.410153 AGCAGAAGCCCAAACAAACAG 59.590 47.619 0.00 0.00 43.56 3.16
3663 4110 1.538849 GCAGAAGCCCAAACAAACAGG 60.539 52.381 0.00 0.00 33.58 4.00
3664 4111 1.069049 CAGAAGCCCAAACAAACAGGG 59.931 52.381 0.00 0.00 45.68 4.45
3665 4112 1.119684 GAAGCCCAAACAAACAGGGT 58.880 50.000 0.00 0.00 44.69 4.34
3666 4113 1.068588 GAAGCCCAAACAAACAGGGTC 59.931 52.381 0.00 0.00 44.69 4.46
3667 4114 0.261696 AGCCCAAACAAACAGGGTCT 59.738 50.000 0.00 0.00 44.69 3.85
3668 4115 1.497286 AGCCCAAACAAACAGGGTCTA 59.503 47.619 0.00 0.00 44.69 2.59
3669 4116 2.091555 AGCCCAAACAAACAGGGTCTAA 60.092 45.455 0.00 0.00 44.69 2.10
3670 4117 2.696187 GCCCAAACAAACAGGGTCTAAA 59.304 45.455 0.00 0.00 44.69 1.85
3671 4118 3.323691 GCCCAAACAAACAGGGTCTAAAT 59.676 43.478 0.00 0.00 44.69 1.40
3672 4119 4.560716 GCCCAAACAAACAGGGTCTAAATC 60.561 45.833 0.00 0.00 44.69 2.17
3673 4120 4.832823 CCCAAACAAACAGGGTCTAAATCT 59.167 41.667 0.00 0.00 37.81 2.40
3674 4121 5.304357 CCCAAACAAACAGGGTCTAAATCTT 59.696 40.000 0.00 0.00 37.81 2.40
3675 4122 6.183360 CCCAAACAAACAGGGTCTAAATCTTT 60.183 38.462 0.00 0.00 37.81 2.52
3676 4123 7.272244 CCAAACAAACAGGGTCTAAATCTTTT 58.728 34.615 0.00 0.00 0.00 2.27
3677 4124 7.768582 CCAAACAAACAGGGTCTAAATCTTTTT 59.231 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.692411 GTGCACCAGAAGGAACCTTT 58.308 50.000 5.22 0.00 36.26 3.11
1 2 0.178990 GGTGCACCAGAAGGAACCTT 60.179 55.000 31.23 5.74 38.69 3.50
2 3 1.352622 TGGTGCACCAGAAGGAACCT 61.353 55.000 34.74 0.00 42.01 3.50
3 4 1.150536 TGGTGCACCAGAAGGAACC 59.849 57.895 34.74 4.95 42.01 3.62
26 27 6.716934 TTTGAGAGAGGTCACCATATAGAC 57.283 41.667 0.00 0.00 0.00 2.59
27 28 7.619698 TCTTTTTGAGAGAGGTCACCATATAGA 59.380 37.037 0.00 0.00 0.00 1.98
28 29 7.786030 TCTTTTTGAGAGAGGTCACCATATAG 58.214 38.462 0.00 0.00 0.00 1.31
29 30 7.733773 TCTTTTTGAGAGAGGTCACCATATA 57.266 36.000 0.00 0.00 0.00 0.86
30 31 6.627087 TCTTTTTGAGAGAGGTCACCATAT 57.373 37.500 0.00 0.00 0.00 1.78
31 32 6.433847 TTCTTTTTGAGAGAGGTCACCATA 57.566 37.500 0.00 0.00 35.37 2.74
32 33 4.982241 TCTTTTTGAGAGAGGTCACCAT 57.018 40.909 0.00 0.00 0.00 3.55
33 34 4.771114 TTCTTTTTGAGAGAGGTCACCA 57.229 40.909 0.00 0.00 35.37 4.17
34 35 6.702329 TCTATTCTTTTTGAGAGAGGTCACC 58.298 40.000 0.00 0.00 35.37 4.02
35 36 7.607250 TCTCTATTCTTTTTGAGAGAGGTCAC 58.393 38.462 0.00 0.00 39.56 3.67
36 37 7.782897 TCTCTATTCTTTTTGAGAGAGGTCA 57.217 36.000 0.00 0.00 39.56 4.02
37 38 9.495572 TTTTCTCTATTCTTTTTGAGAGAGGTC 57.504 33.333 0.00 0.00 43.90 3.85
38 39 9.500785 CTTTTCTCTATTCTTTTTGAGAGAGGT 57.499 33.333 0.00 0.00 43.90 3.85
39 40 9.500785 ACTTTTCTCTATTCTTTTTGAGAGAGG 57.499 33.333 0.00 0.00 43.90 3.69
43 44 9.613428 TGTGACTTTTCTCTATTCTTTTTGAGA 57.387 29.630 0.00 0.00 34.25 3.27
46 47 9.403110 CCATGTGACTTTTCTCTATTCTTTTTG 57.597 33.333 0.00 0.00 0.00 2.44
47 48 9.136323 ACCATGTGACTTTTCTCTATTCTTTTT 57.864 29.630 0.00 0.00 0.00 1.94
48 49 8.697507 ACCATGTGACTTTTCTCTATTCTTTT 57.302 30.769 0.00 0.00 0.00 2.27
49 50 8.160106 AGACCATGTGACTTTTCTCTATTCTTT 58.840 33.333 0.00 0.00 0.00 2.52
50 51 7.684529 AGACCATGTGACTTTTCTCTATTCTT 58.315 34.615 0.00 0.00 0.00 2.52
51 52 7.251321 AGACCATGTGACTTTTCTCTATTCT 57.749 36.000 0.00 0.00 0.00 2.40
54 55 8.353684 CGTATAGACCATGTGACTTTTCTCTAT 58.646 37.037 0.00 0.00 0.00 1.98
55 56 7.201794 CCGTATAGACCATGTGACTTTTCTCTA 60.202 40.741 0.00 0.00 0.00 2.43
56 57 6.405953 CCGTATAGACCATGTGACTTTTCTCT 60.406 42.308 0.00 0.00 0.00 3.10
57 58 5.749109 CCGTATAGACCATGTGACTTTTCTC 59.251 44.000 0.00 0.00 0.00 2.87
58 59 5.187186 ACCGTATAGACCATGTGACTTTTCT 59.813 40.000 0.00 0.00 0.00 2.52
59 60 5.291128 CACCGTATAGACCATGTGACTTTTC 59.709 44.000 0.00 0.00 0.00 2.29
60 61 5.046878 TCACCGTATAGACCATGTGACTTTT 60.047 40.000 0.00 0.00 0.00 2.27
61 62 4.464951 TCACCGTATAGACCATGTGACTTT 59.535 41.667 0.00 0.00 0.00 2.66
62 63 4.021229 TCACCGTATAGACCATGTGACTT 58.979 43.478 0.00 0.00 0.00 3.01
63 64 3.380637 GTCACCGTATAGACCATGTGACT 59.619 47.826 18.14 0.00 45.52 3.41
64 65 3.703420 GTCACCGTATAGACCATGTGAC 58.297 50.000 13.44 13.44 43.73 3.67
147 148 7.498239 CCCTAGAATTTAACTAAACTGTAGGGC 59.502 40.741 15.80 0.00 37.34 5.19
219 226 1.359474 TCCCTAGCTAGATGCCCCTAG 59.641 57.143 22.70 1.70 44.23 3.02
225 232 6.102897 TGACTAAATTCCCTAGCTAGATGC 57.897 41.667 22.70 0.55 43.29 3.91
246 253 0.178995 TTCCACACATTGCTGGCTGA 60.179 50.000 0.00 0.00 0.00 4.26
251 258 7.331440 TGCTTAATTAAATTCCACACATTGCTG 59.669 33.333 0.00 0.00 0.00 4.41
253 260 7.593875 TGCTTAATTAAATTCCACACATTGC 57.406 32.000 0.00 0.00 0.00 3.56
449 476 9.745018 TCCAGATTCTCATTAAGTTCAGAAAAT 57.255 29.630 0.00 0.00 0.00 1.82
454 514 9.658799 TTAAGTCCAGATTCTCATTAAGTTCAG 57.341 33.333 0.00 0.00 0.00 3.02
508 568 6.159988 GTGAGTTTTCTCTGCTACTACATGT 58.840 40.000 2.69 2.69 46.30 3.21
509 569 6.159293 TGTGAGTTTTCTCTGCTACTACATG 58.841 40.000 0.00 0.00 46.30 3.21
510 570 6.346477 TGTGAGTTTTCTCTGCTACTACAT 57.654 37.500 0.00 0.00 46.30 2.29
511 571 5.784578 TGTGAGTTTTCTCTGCTACTACA 57.215 39.130 0.00 0.00 46.30 2.74
512 572 6.868864 TGATTGTGAGTTTTCTCTGCTACTAC 59.131 38.462 0.00 0.00 46.30 2.73
513 573 6.993079 TGATTGTGAGTTTTCTCTGCTACTA 58.007 36.000 0.00 0.00 46.30 1.82
514 574 5.858381 TGATTGTGAGTTTTCTCTGCTACT 58.142 37.500 0.00 0.00 46.30 2.57
561 629 1.153353 GGCGAACGATTTTCAGACCA 58.847 50.000 0.00 0.00 0.00 4.02
631 700 3.367025 ACTTGCGTACGTAGCTTCAAATC 59.633 43.478 17.90 0.00 35.28 2.17
666 735 2.903784 TCGTCCCATTCTTCTCCTTCAA 59.096 45.455 0.00 0.00 0.00 2.69
667 736 2.497675 CTCGTCCCATTCTTCTCCTTCA 59.502 50.000 0.00 0.00 0.00 3.02
669 738 1.208293 GCTCGTCCCATTCTTCTCCTT 59.792 52.381 0.00 0.00 0.00 3.36
823 907 1.960250 GATGAGCAGAGCGGCCATC 60.960 63.158 2.24 0.00 35.70 3.51
908 992 3.575297 CGAAGAATGTCGCTGCTTG 57.425 52.632 0.00 0.00 33.66 4.01
945 1029 4.736126 AGTAATTAAGGTGGCAATTGGC 57.264 40.909 24.20 24.20 43.74 4.52
946 1030 6.935167 AGAAAGTAATTAAGGTGGCAATTGG 58.065 36.000 7.72 0.00 0.00 3.16
951 1040 3.687698 GCGAGAAAGTAATTAAGGTGGCA 59.312 43.478 0.00 0.00 0.00 4.92
956 1045 5.351465 TGCTCAAGCGAGAAAGTAATTAAGG 59.649 40.000 0.00 0.00 45.83 2.69
964 1053 2.928731 GCTAGTGCTCAAGCGAGAAAGT 60.929 50.000 0.00 0.00 45.83 2.66
967 1056 3.425578 GCTAGTGCTCAAGCGAGAA 57.574 52.632 0.00 0.00 45.83 2.87
1011 1120 3.386237 GTCACCAGGAGAGCCGCT 61.386 66.667 0.00 0.00 39.96 5.52
1068 1177 1.203313 AGGAAGTAGAGGAAGGTGGCA 60.203 52.381 0.00 0.00 0.00 4.92
1260 1369 1.153686 GAAGTACGGGAAGACGGCC 60.154 63.158 0.00 0.00 38.39 6.13
1293 1402 3.249973 GAACACCTTGCCGAACGCC 62.250 63.158 0.00 0.00 36.24 5.68
1538 1647 5.021389 CGCTACACGTGTAATAAGTACGAA 58.979 41.667 27.16 4.61 40.01 3.85
1546 1655 4.888038 ACAGATCGCTACACGTGTAATA 57.112 40.909 27.16 16.29 44.19 0.98
1547 1656 3.777465 ACAGATCGCTACACGTGTAAT 57.223 42.857 27.16 18.62 44.19 1.89
1568 1677 3.311167 TGCATGCATAACCAGGGTATT 57.689 42.857 18.46 0.00 0.00 1.89
1610 1738 0.320421 ACGTAAATGTCAGTGCGCCT 60.320 50.000 4.18 0.00 0.00 5.52
1611 1739 1.352114 TACGTAAATGTCAGTGCGCC 58.648 50.000 4.18 0.00 0.00 6.53
1612 1740 2.285602 CCATACGTAAATGTCAGTGCGC 60.286 50.000 0.00 0.00 0.00 6.09
1614 1742 3.063452 CACCCATACGTAAATGTCAGTGC 59.937 47.826 0.00 0.00 0.00 4.40
1615 1743 4.500127 TCACCCATACGTAAATGTCAGTG 58.500 43.478 0.00 3.58 0.00 3.66
1618 1746 4.932799 CAGTTCACCCATACGTAAATGTCA 59.067 41.667 0.00 0.00 0.00 3.58
1620 1748 3.687698 GCAGTTCACCCATACGTAAATGT 59.312 43.478 0.00 0.00 0.00 2.71
1621 1749 3.687212 TGCAGTTCACCCATACGTAAATG 59.313 43.478 0.00 0.00 0.00 2.32
1622 1750 3.938963 CTGCAGTTCACCCATACGTAAAT 59.061 43.478 5.25 0.00 0.00 1.40
1628 1756 1.003118 TGTCCTGCAGTTCACCCATAC 59.997 52.381 13.81 0.00 0.00 2.39
1633 1761 2.012673 GATCATGTCCTGCAGTTCACC 58.987 52.381 13.81 0.00 0.00 4.02
2085 2213 3.450028 GCTCGTCATCAGCCTCTTT 57.550 52.632 0.00 0.00 0.00 2.52
2274 2402 0.323178 CCATCTTGGTGAGCTTGCCT 60.323 55.000 8.64 0.00 31.35 4.75
2275 2403 1.318158 CCCATCTTGGTGAGCTTGCC 61.318 60.000 0.00 0.00 35.17 4.52
2276 2404 1.318158 CCCCATCTTGGTGAGCTTGC 61.318 60.000 0.00 0.00 35.17 4.01
2553 2681 2.892425 CTTCCCACGCAGATCCGC 60.892 66.667 0.00 0.00 0.00 5.54
2749 2880 2.050985 GGCTTGCTCACGTGCAAC 60.051 61.111 11.67 7.51 46.43 4.17
2765 2896 0.332632 ATAATCATCATGCCCCGGGG 59.667 55.000 37.09 37.09 38.57 5.73
3039 3193 1.301716 GGACACACCTCATGCGTGT 60.302 57.895 11.37 11.37 46.16 4.49
3042 3196 0.246360 TACTGGACACACCTCATGCG 59.754 55.000 0.00 0.00 39.86 4.73
3222 3376 3.121030 GCGCACGATCTTGCAGGT 61.121 61.111 22.36 0.00 43.15 4.00
3224 3378 4.858200 GCGCGCACGATCTTGCAG 62.858 66.667 29.10 16.26 43.15 4.41
3248 3402 6.127897 CCGAAGAAATTAATGACTTCCAAGCT 60.128 38.462 19.80 0.00 36.43 3.74
3260 3414 5.449553 AGAAGGATGCCCGAAGAAATTAAT 58.550 37.500 0.00 0.00 37.58 1.40
3261 3415 4.855340 AGAAGGATGCCCGAAGAAATTAA 58.145 39.130 0.00 0.00 37.58 1.40
3262 3416 4.503714 AGAAGGATGCCCGAAGAAATTA 57.496 40.909 0.00 0.00 37.58 1.40
3263 3417 3.372440 AGAAGGATGCCCGAAGAAATT 57.628 42.857 0.00 0.00 37.58 1.82
3270 3424 2.879103 AGAAAAAGAAGGATGCCCGA 57.121 45.000 0.00 0.00 37.58 5.14
3272 3426 2.690497 GCCTAGAAAAAGAAGGATGCCC 59.310 50.000 0.00 0.00 31.64 5.36
3292 3446 3.078837 TCAATAAAGTTCCAGGAACCGC 58.921 45.455 26.34 4.46 42.85 5.68
3294 3448 4.335594 CCGATCAATAAAGTTCCAGGAACC 59.664 45.833 26.34 10.61 42.85 3.62
3300 3454 2.682856 GCTGCCGATCAATAAAGTTCCA 59.317 45.455 0.00 0.00 0.00 3.53
3302 3456 4.558538 ATGCTGCCGATCAATAAAGTTC 57.441 40.909 0.00 0.00 0.00 3.01
3308 3462 7.308529 CCAACTTATTAATGCTGCCGATCAATA 60.309 37.037 0.00 0.00 0.00 1.90
3309 3463 6.441274 CAACTTATTAATGCTGCCGATCAAT 58.559 36.000 0.00 0.00 0.00 2.57
3333 3487 3.859386 CCGCAAAATCAATTTACTCAGCC 59.141 43.478 0.00 0.00 0.00 4.85
3334 3488 4.732784 TCCGCAAAATCAATTTACTCAGC 58.267 39.130 0.00 0.00 0.00 4.26
3380 3827 3.427503 CCGACGATCCCCATTTCAAAAAG 60.428 47.826 0.00 0.00 0.00 2.27
3381 3828 2.490115 CCGACGATCCCCATTTCAAAAA 59.510 45.455 0.00 0.00 0.00 1.94
3394 3841 1.007154 GGCCTTAGAGCCGACGATC 60.007 63.158 0.00 0.00 44.57 3.69
3395 3842 3.130227 GGCCTTAGAGCCGACGAT 58.870 61.111 0.00 0.00 44.57 3.73
3402 3849 1.911057 AACAAACAGGGCCTTAGAGC 58.089 50.000 1.32 0.00 0.00 4.09
3403 3850 3.486383 TCAAACAAACAGGGCCTTAGAG 58.514 45.455 1.32 0.00 0.00 2.43
3404 3851 3.486383 CTCAAACAAACAGGGCCTTAGA 58.514 45.455 1.32 0.00 0.00 2.10
3405 3852 2.029918 GCTCAAACAAACAGGGCCTTAG 60.030 50.000 1.32 0.00 0.00 2.18
3406 3853 1.960689 GCTCAAACAAACAGGGCCTTA 59.039 47.619 1.32 0.00 0.00 2.69
3407 3854 0.752658 GCTCAAACAAACAGGGCCTT 59.247 50.000 1.32 0.00 0.00 4.35
3408 3855 0.396974 TGCTCAAACAAACAGGGCCT 60.397 50.000 0.00 0.00 0.00 5.19
3409 3856 0.681175 ATGCTCAAACAAACAGGGCC 59.319 50.000 0.00 0.00 0.00 5.80
3410 3857 2.531522 AATGCTCAAACAAACAGGGC 57.468 45.000 0.00 0.00 0.00 5.19
3411 3858 2.545106 GCAAATGCTCAAACAAACAGGG 59.455 45.455 0.00 0.00 38.21 4.45
3412 3859 3.865224 GCAAATGCTCAAACAAACAGG 57.135 42.857 0.00 0.00 38.21 4.00
3425 3872 3.992427 AGCTAAAAAGCAGAAGCAAATGC 59.008 39.130 0.00 0.00 45.49 3.56
3426 3873 6.535274 AAAGCTAAAAAGCAGAAGCAAATG 57.465 33.333 0.00 0.00 45.49 2.32
3427 3874 7.280652 TGAAAAAGCTAAAAAGCAGAAGCAAAT 59.719 29.630 0.00 0.00 45.49 2.32
3428 3875 6.593382 TGAAAAAGCTAAAAAGCAGAAGCAAA 59.407 30.769 0.00 0.00 45.49 3.68
3429 3876 6.105333 TGAAAAAGCTAAAAAGCAGAAGCAA 58.895 32.000 0.00 0.00 45.49 3.91
3430 3877 5.659463 TGAAAAAGCTAAAAAGCAGAAGCA 58.341 33.333 0.00 0.00 45.49 3.91
3431 3878 6.775939 ATGAAAAAGCTAAAAAGCAGAAGC 57.224 33.333 0.00 0.00 42.56 3.86
3432 3879 9.429600 CAAAATGAAAAAGCTAAAAAGCAGAAG 57.570 29.630 0.00 0.00 37.25 2.85
3433 3880 9.160496 TCAAAATGAAAAAGCTAAAAAGCAGAA 57.840 25.926 0.00 0.00 37.25 3.02
3434 3881 8.603181 GTCAAAATGAAAAAGCTAAAAAGCAGA 58.397 29.630 0.00 0.00 37.25 4.26
3435 3882 8.606602 AGTCAAAATGAAAAAGCTAAAAAGCAG 58.393 29.630 0.00 0.00 37.25 4.24
3436 3883 8.491331 AGTCAAAATGAAAAAGCTAAAAAGCA 57.509 26.923 0.00 0.00 37.25 3.91
3466 3913 9.189156 TGCATCTATTTAGAAGCTTTTATGGTT 57.811 29.630 13.94 0.00 44.72 3.67
3467 3914 8.752005 TGCATCTATTTAGAAGCTTTTATGGT 57.248 30.769 13.94 0.00 44.72 3.55
3472 3919 8.752187 TCCAAATGCATCTATTTAGAAGCTTTT 58.248 29.630 16.48 16.48 46.10 2.27
3473 3920 8.297470 TCCAAATGCATCTATTTAGAAGCTTT 57.703 30.769 13.94 11.38 44.72 3.51
3474 3921 7.469732 GCTCCAAATGCATCTATTTAGAAGCTT 60.470 37.037 13.94 0.00 44.72 3.74
3475 3922 6.016443 GCTCCAAATGCATCTATTTAGAAGCT 60.016 38.462 13.94 0.00 44.72 3.74
3476 3923 6.016443 AGCTCCAAATGCATCTATTTAGAAGC 60.016 38.462 0.00 7.65 44.69 3.86
3477 3924 7.507733 AGCTCCAAATGCATCTATTTAGAAG 57.492 36.000 0.00 0.00 35.69 2.85
3478 3925 7.886629 AAGCTCCAAATGCATCTATTTAGAA 57.113 32.000 0.00 0.00 35.69 2.10
3479 3926 7.886629 AAAGCTCCAAATGCATCTATTTAGA 57.113 32.000 0.00 0.00 36.65 2.10
3555 4002 9.844257 AGCTTCTACATAGATGATTTTAAAGCT 57.156 29.630 6.10 0.00 30.86 3.74
3570 4017 9.594478 TGTGATTTCGATAAAAGCTTCTACATA 57.406 29.630 0.00 0.00 34.32 2.29
3571 4018 8.492673 TGTGATTTCGATAAAAGCTTCTACAT 57.507 30.769 0.00 0.00 34.32 2.29
3572 4019 7.413000 GCTGTGATTTCGATAAAAGCTTCTACA 60.413 37.037 0.00 0.00 34.32 2.74
3573 4020 6.902417 GCTGTGATTTCGATAAAAGCTTCTAC 59.098 38.462 0.00 0.00 34.32 2.59
3574 4021 6.818644 AGCTGTGATTTCGATAAAAGCTTCTA 59.181 34.615 0.00 0.00 33.35 2.10
3575 4022 5.645497 AGCTGTGATTTCGATAAAAGCTTCT 59.355 36.000 0.00 0.00 33.35 2.85
3576 4023 5.873732 AGCTGTGATTTCGATAAAAGCTTC 58.126 37.500 0.00 0.00 33.35 3.86
3577 4024 5.886960 AGCTGTGATTTCGATAAAAGCTT 57.113 34.783 0.00 0.00 33.35 3.74
3578 4025 5.886960 AAGCTGTGATTTCGATAAAAGCT 57.113 34.783 0.00 0.00 36.89 3.74
3579 4026 6.934561 AAAAGCTGTGATTTCGATAAAAGC 57.065 33.333 0.00 0.00 33.79 3.51
3580 4027 9.013490 CCATAAAAGCTGTGATTTCGATAAAAG 57.987 33.333 0.00 0.00 0.00 2.27
3581 4028 8.519526 ACCATAAAAGCTGTGATTTCGATAAAA 58.480 29.630 0.00 0.00 0.00 1.52
3582 4029 8.050778 ACCATAAAAGCTGTGATTTCGATAAA 57.949 30.769 0.00 0.00 0.00 1.40
3583 4030 7.624360 ACCATAAAAGCTGTGATTTCGATAA 57.376 32.000 0.00 0.00 0.00 1.75
3584 4031 7.624360 AACCATAAAAGCTGTGATTTCGATA 57.376 32.000 0.00 0.00 0.00 2.92
3585 4032 6.515272 AACCATAAAAGCTGTGATTTCGAT 57.485 33.333 0.00 0.00 0.00 3.59
3586 4033 5.957842 AACCATAAAAGCTGTGATTTCGA 57.042 34.783 0.00 0.00 0.00 3.71
3587 4034 7.406799 AAAAACCATAAAAGCTGTGATTTCG 57.593 32.000 0.00 0.00 0.00 3.46
3608 4055 6.207417 TGCAATTTTTCCACTTTGACCAAAAA 59.793 30.769 0.00 0.00 32.16 1.94
3609 4056 5.707298 TGCAATTTTTCCACTTTGACCAAAA 59.293 32.000 0.00 0.00 0.00 2.44
3610 4057 5.248640 TGCAATTTTTCCACTTTGACCAAA 58.751 33.333 0.00 0.00 0.00 3.28
3611 4058 4.836825 TGCAATTTTTCCACTTTGACCAA 58.163 34.783 0.00 0.00 0.00 3.67
3612 4059 4.478206 TGCAATTTTTCCACTTTGACCA 57.522 36.364 0.00 0.00 0.00 4.02
3613 4060 5.115480 TCTTGCAATTTTTCCACTTTGACC 58.885 37.500 0.00 0.00 0.00 4.02
3614 4061 5.812127 ACTCTTGCAATTTTTCCACTTTGAC 59.188 36.000 0.00 0.00 0.00 3.18
3615 4062 5.976458 ACTCTTGCAATTTTTCCACTTTGA 58.024 33.333 0.00 0.00 0.00 2.69
3616 4063 7.202526 TCTACTCTTGCAATTTTTCCACTTTG 58.797 34.615 0.00 0.00 0.00 2.77
3617 4064 7.346751 TCTACTCTTGCAATTTTTCCACTTT 57.653 32.000 0.00 0.00 0.00 2.66
3618 4065 6.959639 TCTACTCTTGCAATTTTTCCACTT 57.040 33.333 0.00 0.00 0.00 3.16
3619 4066 6.515696 GCTTCTACTCTTGCAATTTTTCCACT 60.516 38.462 0.00 0.00 0.00 4.00
3620 4067 5.631096 GCTTCTACTCTTGCAATTTTTCCAC 59.369 40.000 0.00 0.00 0.00 4.02
3621 4068 5.301551 TGCTTCTACTCTTGCAATTTTTCCA 59.698 36.000 0.00 0.00 32.12 3.53
3622 4069 5.772521 TGCTTCTACTCTTGCAATTTTTCC 58.227 37.500 0.00 0.00 32.12 3.13
3623 4070 6.672147 TCTGCTTCTACTCTTGCAATTTTTC 58.328 36.000 0.00 0.00 34.90 2.29
3624 4071 6.639632 TCTGCTTCTACTCTTGCAATTTTT 57.360 33.333 0.00 0.00 34.90 1.94
3625 4072 6.639632 TTCTGCTTCTACTCTTGCAATTTT 57.360 33.333 0.00 0.00 34.90 1.82
3626 4073 5.335504 GCTTCTGCTTCTACTCTTGCAATTT 60.336 40.000 0.00 0.00 34.90 1.82
3627 4074 4.155644 GCTTCTGCTTCTACTCTTGCAATT 59.844 41.667 0.00 0.00 34.90 2.32
3628 4075 3.688673 GCTTCTGCTTCTACTCTTGCAAT 59.311 43.478 0.00 0.00 34.90 3.56
3629 4076 3.070018 GCTTCTGCTTCTACTCTTGCAA 58.930 45.455 0.00 0.00 34.90 4.08
3630 4077 2.613977 GGCTTCTGCTTCTACTCTTGCA 60.614 50.000 0.00 0.00 39.59 4.08
3631 4078 2.006169 GGCTTCTGCTTCTACTCTTGC 58.994 52.381 0.00 0.00 39.59 4.01
3632 4079 2.027745 TGGGCTTCTGCTTCTACTCTTG 60.028 50.000 0.00 0.00 39.59 3.02
3633 4080 2.260822 TGGGCTTCTGCTTCTACTCTT 58.739 47.619 0.00 0.00 39.59 2.85
3634 4081 1.944177 TGGGCTTCTGCTTCTACTCT 58.056 50.000 0.00 0.00 39.59 3.24
3635 4082 2.744741 GTTTGGGCTTCTGCTTCTACTC 59.255 50.000 0.00 0.00 39.59 2.59
3636 4083 2.106511 TGTTTGGGCTTCTGCTTCTACT 59.893 45.455 0.00 0.00 39.59 2.57
3637 4084 2.504367 TGTTTGGGCTTCTGCTTCTAC 58.496 47.619 0.00 0.00 39.59 2.59
3638 4085 2.949177 TGTTTGGGCTTCTGCTTCTA 57.051 45.000 0.00 0.00 39.59 2.10
3639 4086 2.071778 TTGTTTGGGCTTCTGCTTCT 57.928 45.000 0.00 0.00 39.59 2.85
3640 4087 2.159114 TGTTTGTTTGGGCTTCTGCTTC 60.159 45.455 0.00 0.00 39.59 3.86
3641 4088 1.830477 TGTTTGTTTGGGCTTCTGCTT 59.170 42.857 0.00 0.00 39.59 3.91
3642 4089 1.410153 CTGTTTGTTTGGGCTTCTGCT 59.590 47.619 0.00 0.00 39.59 4.24
3643 4090 1.538849 CCTGTTTGTTTGGGCTTCTGC 60.539 52.381 0.00 0.00 38.76 4.26
3644 4091 1.069049 CCCTGTTTGTTTGGGCTTCTG 59.931 52.381 0.00 0.00 33.88 3.02
3645 4092 1.342975 ACCCTGTTTGTTTGGGCTTCT 60.343 47.619 0.00 0.00 44.56 2.85
3646 4093 1.068588 GACCCTGTTTGTTTGGGCTTC 59.931 52.381 0.00 0.00 44.56 3.86
3647 4094 1.119684 GACCCTGTTTGTTTGGGCTT 58.880 50.000 0.00 0.00 44.56 4.35
3648 4095 0.261696 AGACCCTGTTTGTTTGGGCT 59.738 50.000 0.00 0.00 44.56 5.19
3649 4096 1.989706 TAGACCCTGTTTGTTTGGGC 58.010 50.000 0.00 0.00 44.56 5.36
3650 4097 4.832823 AGATTTAGACCCTGTTTGTTTGGG 59.167 41.667 0.00 0.00 46.07 4.12
3651 4098 6.405278 AAGATTTAGACCCTGTTTGTTTGG 57.595 37.500 0.00 0.00 0.00 3.28
3652 4099 8.716646 AAAAAGATTTAGACCCTGTTTGTTTG 57.283 30.769 0.00 0.00 0.00 2.93
3674 4121 6.038997 TCCCCGTTTCAAAAGAAAGAAAAA 57.961 33.333 0.00 0.00 35.71 1.94
3675 4122 5.662674 TCCCCGTTTCAAAAGAAAGAAAA 57.337 34.783 0.00 0.00 35.71 2.29
3676 4123 5.361285 TGATCCCCGTTTCAAAAGAAAGAAA 59.639 36.000 0.00 0.00 0.00 2.52
3677 4124 4.890581 TGATCCCCGTTTCAAAAGAAAGAA 59.109 37.500 0.00 0.00 0.00 2.52
3678 4125 4.465886 TGATCCCCGTTTCAAAAGAAAGA 58.534 39.130 0.00 0.00 0.00 2.52
3679 4126 4.846779 TGATCCCCGTTTCAAAAGAAAG 57.153 40.909 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.