Multiple sequence alignment - TraesCS3D01G417100

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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 TraesCS3D01G417100 chr3D 100.000 7235 0 0 1 7235 528607193 528614427 0.000000e+00 13361.0
1 TraesCS3D01G417100 chr3D 100.000 48 0 0 6139 6186 602232033 602231986 1.000000e-13 89.8
2 TraesCS3D01G417100 chr3D 90.323 62 4 2 6122 6183 81200903 81200962 6.020000e-11 80.5
3 TraesCS3D01G417100 chr3A 91.433 3385 206 44 179 3536 662954392 662951065 0.000000e+00 4567.0
4 TraesCS3D01G417100 chr3A 87.821 1675 108 28 4501 6145 662950187 662948579 0.000000e+00 1875.0
5 TraesCS3D01G417100 chr3A 93.137 816 44 11 3524 4335 662951000 662950193 0.000000e+00 1186.0
6 TraesCS3D01G417100 chr3A 91.800 561 35 9 6595 7147 28392485 28393042 0.000000e+00 771.0
7 TraesCS3D01G417100 chr3A 91.429 560 37 10 6595 7145 724577330 724576773 0.000000e+00 758.0
8 TraesCS3D01G417100 chr3A 95.000 60 3 0 6140 6199 32635226 32635285 2.150000e-15 95.3
9 TraesCS3D01G417100 chr3A 91.176 68 6 0 7147 7214 662947913 662947846 7.730000e-15 93.5
10 TraesCS3D01G417100 chr3B 96.332 2399 63 12 843 3235 698607460 698609839 0.000000e+00 3919.0
11 TraesCS3D01G417100 chr3B 96.508 1718 49 6 3221 4936 698610247 698611955 0.000000e+00 2830.0
12 TraesCS3D01G417100 chr3B 95.346 752 20 3 4935 5671 698612109 698612860 0.000000e+00 1181.0
13 TraesCS3D01G417100 chr3B 96.384 636 20 3 179 812 698606828 698607462 0.000000e+00 1044.0
14 TraesCS3D01G417100 chr3B 95.807 477 12 3 5672 6145 698612943 698613414 0.000000e+00 763.0
15 TraesCS3D01G417100 chr3B 93.725 255 11 4 6341 6593 698613590 698613841 1.910000e-100 377.0
16 TraesCS3D01G417100 chr3B 90.667 150 8 2 6202 6345 698613416 698613565 2.060000e-45 195.0
17 TraesCS3D01G417100 chr3B 96.429 112 4 0 3232 3343 698610147 698610258 1.240000e-42 185.0
18 TraesCS3D01G417100 chr3B 93.182 88 6 0 7147 7234 698613832 698613919 5.890000e-26 130.0
19 TraesCS3D01G417100 chr3B 88.660 97 11 0 1 97 698605382 698605478 1.280000e-22 119.0
20 TraesCS3D01G417100 chr3B 94.545 55 3 0 6132 6186 549759057 549759111 1.290000e-12 86.1
21 TraesCS3D01G417100 chr5D 92.527 562 31 10 6592 7147 560487102 560486546 0.000000e+00 795.0
22 TraesCS3D01G417100 chr6D 92.349 562 31 10 6593 7147 81778173 81778729 0.000000e+00 789.0
23 TraesCS3D01G417100 chr4D 92.335 561 33 9 6594 7147 97440269 97440826 0.000000e+00 789.0
24 TraesCS3D01G417100 chr4D 93.827 162 10 0 4334 4495 21147732 21147893 2.020000e-60 244.0
25 TraesCS3D01G417100 chr4D 93.293 164 11 0 4334 4497 465125310 465125473 7.250000e-60 243.0
26 TraesCS3D01G417100 chr2B 91.921 557 37 4 6595 7145 776235651 776236205 0.000000e+00 773.0
27 TraesCS3D01G417100 chr2B 91.756 558 37 7 6597 7147 63843336 63842781 0.000000e+00 767.0
28 TraesCS3D01G417100 chr2B 92.857 168 12 0 4334 4501 76912299 76912132 2.020000e-60 244.0
29 TraesCS3D01G417100 chr2A 92.072 555 33 5 6600 7147 743092673 743092123 0.000000e+00 771.0
30 TraesCS3D01G417100 chr2A 93.252 163 11 0 4333 4495 249754458 249754620 2.610000e-59 241.0
31 TraesCS3D01G417100 chr5A 91.771 559 36 9 6595 7145 608872793 608872237 0.000000e+00 769.0
32 TraesCS3D01G417100 chr4B 92.941 170 11 1 4326 4495 28724311 28724143 5.610000e-61 246.0
33 TraesCS3D01G417100 chr6A 90.449 178 13 4 4320 4495 504487243 504487068 1.570000e-56 231.0
34 TraesCS3D01G417100 chr2D 90.395 177 16 1 4319 4495 299891540 299891715 1.570000e-56 231.0
35 TraesCS3D01G417100 chr2D 95.000 60 3 0 6139 6198 126125698 126125757 2.150000e-15 95.3
36 TraesCS3D01G417100 chr1D 90.449 178 14 3 4327 4502 30365554 30365730 1.570000e-56 231.0
37 TraesCS3D01G417100 chrUn 91.209 91 8 0 4 94 46179862 46179772 2.740000e-24 124.0
38 TraesCS3D01G417100 chr7A 94.737 57 3 0 6143 6199 360611198 360611254 1.000000e-13 89.8
39 TraesCS3D01G417100 chr1B 93.103 58 2 2 6129 6186 402103414 402103359 4.650000e-12 84.2
40 TraesCS3D01G417100 chr7D 91.667 60 4 1 6141 6199 568014372 568014431 1.670000e-11 82.4
41 TraesCS3D01G417100 chr7B 100.000 44 0 0 6143 6186 412543761 412543718 1.670000e-11 82.4


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 TraesCS3D01G417100 chr3D 528607193 528614427 7234 False 13361.000 13361 100.00000 1 7235 1 chr3D.!!$F2 7234
1 TraesCS3D01G417100 chr3A 662947846 662954392 6546 True 1930.375 4567 90.89175 179 7214 4 chr3A.!!$R2 7035
2 TraesCS3D01G417100 chr3A 28392485 28393042 557 False 771.000 771 91.80000 6595 7147 1 chr3A.!!$F1 552
3 TraesCS3D01G417100 chr3A 724576773 724577330 557 True 758.000 758 91.42900 6595 7145 1 chr3A.!!$R1 550
4 TraesCS3D01G417100 chr3B 698605382 698613919 8537 False 1074.300 3919 94.30400 1 7234 10 chr3B.!!$F2 7233
5 TraesCS3D01G417100 chr5D 560486546 560487102 556 True 795.000 795 92.52700 6592 7147 1 chr5D.!!$R1 555
6 TraesCS3D01G417100 chr6D 81778173 81778729 556 False 789.000 789 92.34900 6593 7147 1 chr6D.!!$F1 554
7 TraesCS3D01G417100 chr4D 97440269 97440826 557 False 789.000 789 92.33500 6594 7147 1 chr4D.!!$F2 553
8 TraesCS3D01G417100 chr2B 776235651 776236205 554 False 773.000 773 91.92100 6595 7145 1 chr2B.!!$F1 550
9 TraesCS3D01G417100 chr2B 63842781 63843336 555 True 767.000 767 91.75600 6597 7147 1 chr2B.!!$R1 550
10 TraesCS3D01G417100 chr2A 743092123 743092673 550 True 771.000 771 92.07200 6600 7147 1 chr2A.!!$R1 547
11 TraesCS3D01G417100 chr5A 608872237 608872793 556 True 769.000 769 91.77100 6595 7145 1 chr5A.!!$R1 550

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
84 85 1.135746 CGTGGACCAGTCGTAGTCTTC 60.136 57.143 0.00 0.0 33.39 2.87 F
425 1698 1.447314 GACCGGTGGGAATCGTGTC 60.447 63.158 14.63 0.0 36.97 3.67 F
966 2275 2.024176 TAAGCTGGTGGAGATTTCGC 57.976 50.000 0.00 0.0 31.11 4.70 F
2463 3787 0.320374 AAGCGAAAGGTGATGACGGA 59.680 50.000 0.00 0.0 43.76 4.69 F
4039 5873 3.708210 TGGGAGCCACCTACTTCG 58.292 61.111 0.00 0.0 38.98 3.79 F
4343 6179 3.127030 GCATTTTCAAACTACTCCCTCCG 59.873 47.826 0.00 0.0 0.00 4.63 F
5385 7393 1.153628 ACGAGCAGCGGATACAACC 60.154 57.895 4.06 0.0 46.49 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 2434 0.463654 GATAAGCATGTGGGCGTGGA 60.464 55.000 0.00 0.0 39.27 4.02 R
1336 2645 1.004440 GAGCACTTTGAGCGGGAGT 60.004 57.895 0.00 0.0 37.01 3.85 R
2715 4041 0.250295 CACAGACCCCACACGACATT 60.250 55.000 0.00 0.0 0.00 2.71 R
4067 5901 0.754957 TGAACTGCAACAAGGGTGGG 60.755 55.000 0.00 0.0 0.00 4.61 R
5246 7254 1.572085 CCAAGCCAGACTGAAGCACG 61.572 60.000 3.32 0.0 0.00 5.34 R
6187 8305 0.175989 GCTCCTTTGTACTCCCTCCG 59.824 60.000 0.00 0.0 0.00 4.63 R
6603 9082 0.392706 TCTGCTTGAGCCTTCGTTCA 59.607 50.000 0.00 0.0 41.18 3.18 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
24 25 6.660887 TTGGAGTGTCTTTTGCAAAATTTC 57.339 33.333 24.06 16.65 0.00 2.17
31 32 5.585445 TGTCTTTTGCAAAATTTCAGCACAT 59.415 32.000 24.06 0.00 38.11 3.21
32 33 6.760298 TGTCTTTTGCAAAATTTCAGCACATA 59.240 30.769 24.06 0.00 38.11 2.29
38 39 7.990541 TGCAAAATTTCAGCACATATGTATC 57.009 32.000 8.32 3.65 32.55 2.24
68 69 3.254060 CTCTCTTGTTGTATCCACGTGG 58.746 50.000 29.26 29.26 0.00 4.94
80 81 1.521450 CCACGTGGACCAGTCGTAGT 61.521 60.000 31.31 0.00 37.39 2.73
84 85 1.135746 CGTGGACCAGTCGTAGTCTTC 60.136 57.143 0.00 0.00 33.39 2.87
90 91 2.628657 ACCAGTCGTAGTCTTCTTGCTT 59.371 45.455 0.00 0.00 0.00 3.91
97 98 9.171701 CAGTCGTAGTCTTCTTGCTTTATATAC 57.828 37.037 0.00 0.00 0.00 1.47
98 99 9.122779 AGTCGTAGTCTTCTTGCTTTATATACT 57.877 33.333 0.00 0.00 0.00 2.12
99 100 9.171701 GTCGTAGTCTTCTTGCTTTATATACTG 57.828 37.037 0.00 0.00 0.00 2.74
100 101 8.900781 TCGTAGTCTTCTTGCTTTATATACTGT 58.099 33.333 0.00 0.00 0.00 3.55
101 102 9.171701 CGTAGTCTTCTTGCTTTATATACTGTC 57.828 37.037 0.00 0.00 0.00 3.51
102 103 9.465985 GTAGTCTTCTTGCTTTATATACTGTCC 57.534 37.037 0.00 0.00 0.00 4.02
103 104 8.312669 AGTCTTCTTGCTTTATATACTGTCCT 57.687 34.615 0.00 0.00 0.00 3.85
122 123 8.867097 ACTGTCCTAAATGAATATATACGTGGT 58.133 33.333 0.00 0.00 0.00 4.16
123 124 9.706691 CTGTCCTAAATGAATATATACGTGGTT 57.293 33.333 0.00 0.00 0.00 3.67
169 1431 2.981859 AGATCTTACCGCCGTTGAAT 57.018 45.000 0.00 0.00 0.00 2.57
375 1648 4.493747 CCTCCTCGCCCGTTCGAC 62.494 72.222 0.00 0.00 34.46 4.20
425 1698 1.447314 GACCGGTGGGAATCGTGTC 60.447 63.158 14.63 0.00 36.97 3.67
427 1700 3.186047 CGGTGGGAATCGTGTCGC 61.186 66.667 0.00 0.00 0.00 5.19
618 1892 5.279758 GGTGTTAGGGTTTATGTTTTGGCAT 60.280 40.000 0.00 0.00 0.00 4.40
682 1956 3.996825 GCAGGTGCGGTTTCTATTG 57.003 52.632 0.00 0.00 0.00 1.90
690 1964 5.129815 AGGTGCGGTTTCTATTGATAGGTTA 59.870 40.000 0.00 0.00 0.00 2.85
691 1965 5.995897 GGTGCGGTTTCTATTGATAGGTTAT 59.004 40.000 0.00 0.00 0.00 1.89
717 1991 6.154203 TGTGCATGGACAAAAAGTAAATCA 57.846 33.333 18.56 0.00 0.00 2.57
796 2072 3.703001 ACATGAACTGAACACCCCTAG 57.297 47.619 0.00 0.00 0.00 3.02
810 2086 4.102681 ACACCCCTAGTTGCATATTCCTAC 59.897 45.833 0.00 0.00 0.00 3.18
811 2087 4.102524 CACCCCTAGTTGCATATTCCTACA 59.897 45.833 0.00 0.00 0.00 2.74
812 2088 4.913968 ACCCCTAGTTGCATATTCCTACAT 59.086 41.667 0.00 0.00 0.00 2.29
813 2089 5.372661 ACCCCTAGTTGCATATTCCTACATT 59.627 40.000 0.00 0.00 0.00 2.71
814 2090 6.126185 ACCCCTAGTTGCATATTCCTACATTT 60.126 38.462 0.00 0.00 0.00 2.32
815 2091 7.073215 ACCCCTAGTTGCATATTCCTACATTTA 59.927 37.037 0.00 0.00 0.00 1.40
816 2092 7.390718 CCCCTAGTTGCATATTCCTACATTTAC 59.609 40.741 0.00 0.00 0.00 2.01
817 2093 7.936847 CCCTAGTTGCATATTCCTACATTTACA 59.063 37.037 0.00 0.00 0.00 2.41
818 2094 9.507329 CCTAGTTGCATATTCCTACATTTACAT 57.493 33.333 0.00 0.00 0.00 2.29
841 2117 9.659135 ACATTAGGATTTTATGGATTCATGGAA 57.341 29.630 0.00 0.00 34.96 3.53
867 2176 6.147581 CACATGAGTTTGATTTCAAGACCAG 58.852 40.000 0.00 0.00 37.15 4.00
870 2179 7.884877 ACATGAGTTTGATTTCAAGACCAGATA 59.115 33.333 0.00 0.00 37.15 1.98
922 2231 4.852134 TGTTGCTACACTGATTGCATTT 57.148 36.364 0.00 0.00 35.27 2.32
927 2236 4.277921 TGCTACACTGATTGCATTTTGTCA 59.722 37.500 0.00 0.00 0.00 3.58
966 2275 2.024176 TAAGCTGGTGGAGATTTCGC 57.976 50.000 0.00 0.00 31.11 4.70
996 2305 2.584791 GTCAAATTTACCTGCTGCGTG 58.415 47.619 0.00 0.00 0.00 5.34
1122 2431 2.094026 GCATCCCTCACAATTTCAACCC 60.094 50.000 0.00 0.00 0.00 4.11
1125 2434 2.176798 TCCCTCACAATTTCAACCCACT 59.823 45.455 0.00 0.00 0.00 4.00
1305 2614 5.046910 ACAATCAAAATACAGCAGGAACG 57.953 39.130 0.00 0.00 0.00 3.95
1335 2644 2.162681 ACACAACCTAGCATGCCTTTC 58.837 47.619 15.66 0.00 0.00 2.62
1336 2645 2.161855 CACAACCTAGCATGCCTTTCA 58.838 47.619 15.66 0.00 0.00 2.69
1351 2660 1.532868 CTTTCACTCCCGCTCAAAGTG 59.467 52.381 0.00 0.00 41.38 3.16
1360 2669 1.476891 CCGCTCAAAGTGCTCCTAGTA 59.523 52.381 0.00 0.00 0.00 1.82
1412 2721 0.907486 CTCAAGGCCCATCAGACTGA 59.093 55.000 7.80 7.80 0.00 3.41
1642 2961 1.597854 CTTCTGTGCCGCTTGTCCA 60.598 57.895 0.00 0.00 0.00 4.02
1711 3030 3.886505 AGCAAAATCAACAAACGACCCTA 59.113 39.130 0.00 0.00 0.00 3.53
2069 3390 8.996651 ATCCGGTGATTAGGATTTTTAATTCT 57.003 30.769 0.00 0.00 44.26 2.40
2104 3425 7.780271 AGAATTAGTCTCAGGGTGTTTCTTTTT 59.220 33.333 0.00 0.00 0.00 1.94
2145 3466 7.874016 TGTCATTTTCTTATGTTACGTACCTGT 59.126 33.333 0.00 0.00 0.00 4.00
2146 3467 8.715088 GTCATTTTCTTATGTTACGTACCTGTT 58.285 33.333 0.00 0.00 0.00 3.16
2147 3468 8.714179 TCATTTTCTTATGTTACGTACCTGTTG 58.286 33.333 0.00 0.00 0.00 3.33
2148 3469 8.714179 CATTTTCTTATGTTACGTACCTGTTGA 58.286 33.333 0.00 0.00 0.00 3.18
2149 3470 7.642071 TTTCTTATGTTACGTACCTGTTGAC 57.358 36.000 0.00 0.00 0.00 3.18
2150 3471 6.579666 TCTTATGTTACGTACCTGTTGACT 57.420 37.500 0.00 0.00 0.00 3.41
2151 3472 6.384224 TCTTATGTTACGTACCTGTTGACTG 58.616 40.000 0.00 0.00 0.00 3.51
2164 3485 6.296026 ACCTGTTGACTGTTGTGTTATACAT 58.704 36.000 0.00 0.00 39.48 2.29
2197 3518 1.311859 TTGTCAAAGTGAGGCAGCTG 58.688 50.000 10.11 10.11 0.00 4.24
2300 3621 7.545265 TGCTTATTATGCTGGAAATTTGTCAAC 59.455 33.333 0.00 0.00 0.00 3.18
2305 3626 3.054878 GCTGGAAATTTGTCAACTGCTG 58.945 45.455 0.00 0.00 0.00 4.41
2320 3641 3.012518 ACTGCTGAAATGAGTATGCCAC 58.987 45.455 0.00 0.00 0.00 5.01
2463 3787 0.320374 AAGCGAAAGGTGATGACGGA 59.680 50.000 0.00 0.00 43.76 4.69
2641 3965 6.343716 TGCATGGATGTTACAAACTGAATT 57.656 33.333 0.00 0.00 0.00 2.17
2766 4092 4.400884 TGACTTAGCTGGAGAGAAGATGTC 59.599 45.833 0.00 0.00 0.00 3.06
3185 4517 8.243961 TCCTGATTTTCTTGGTCAATTTACAA 57.756 30.769 0.00 0.00 0.00 2.41
3269 5023 5.755409 ACCTTGACATGGAAGTGTATGTA 57.245 39.130 14.05 0.00 37.63 2.29
3599 5432 6.758416 GGAATATTCCAAAACAATCTTCTGCC 59.242 38.462 26.61 0.00 46.76 4.85
3628 5462 4.277476 AGGATGAAAACAAGTTGGACACA 58.723 39.130 7.96 2.99 0.00 3.72
3928 5762 8.893563 TTCTAAAACCCCACATATTTCTCAAT 57.106 30.769 0.00 0.00 0.00 2.57
3932 5766 5.408079 ACCCCACATATTTCTCAATGGAT 57.592 39.130 0.00 0.00 0.00 3.41
4039 5873 3.708210 TGGGAGCCACCTACTTCG 58.292 61.111 0.00 0.00 38.98 3.79
4130 5964 4.394729 TCTTTGGAACCCTCACATACAAC 58.605 43.478 0.00 0.00 0.00 3.32
4283 6117 7.238486 GAGTTATCTCTATCATGTGGATGGT 57.762 40.000 0.00 0.00 36.72 3.55
4292 6126 3.613030 TCATGTGGATGGTGTGATCTTG 58.387 45.455 0.00 0.00 0.00 3.02
4313 6148 4.702831 TGTCTGAAAGCACACATACTTGA 58.297 39.130 0.00 0.00 0.00 3.02
4343 6179 3.127030 GCATTTTCAAACTACTCCCTCCG 59.873 47.826 0.00 0.00 0.00 4.63
4356 6192 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
4363 6199 7.284716 CCCTCCGTTTCTAAATATAAGCCTTTT 59.715 37.037 0.00 0.00 0.00 2.27
4460 6296 7.383687 TCCGTATGTAGTCCATATTGAAATCC 58.616 38.462 0.00 0.00 38.29 3.01
4577 6413 7.731882 TTTCTGTGTATATTTTGACGGTGAA 57.268 32.000 0.00 0.00 0.00 3.18
4583 6419 7.771361 TGTGTATATTTTGACGGTGAATATGGT 59.229 33.333 9.49 0.00 30.80 3.55
4643 6480 4.938080 AGATAGAAGGCGATACAACACAG 58.062 43.478 0.00 0.00 0.00 3.66
4709 6546 6.578020 AACAACGAATACACATATGTACGG 57.422 37.500 8.32 0.00 44.11 4.02
4761 6598 7.938140 TCTAGCTAATGTTGGCTTGTTATTT 57.062 32.000 8.90 0.00 42.75 1.40
4802 6639 4.365514 TCTGCCTTTTCAACAGTATCCA 57.634 40.909 0.00 0.00 33.12 3.41
5050 7043 3.935172 TCAAAACCCCCTTCAGGAAAAT 58.065 40.909 0.00 0.00 38.24 1.82
5152 7145 3.319198 CACGGGGTGGCTGGTACT 61.319 66.667 0.00 0.00 0.00 2.73
5243 7251 7.336931 AGAATGGCATTTGTAGTTACTAGTTGG 59.663 37.037 14.93 0.00 0.00 3.77
5246 7254 5.353400 GGCATTTGTAGTTACTAGTTGGGAC 59.647 44.000 0.00 0.00 0.00 4.46
5385 7393 1.153628 ACGAGCAGCGGATACAACC 60.154 57.895 4.06 0.00 46.49 3.77
5398 7406 2.728690 TACAACCGCATCTGTACGTT 57.271 45.000 0.00 0.00 0.00 3.99
5431 7439 8.650143 TTGCAACTTCCCTTTATCTAATCTTT 57.350 30.769 0.00 0.00 0.00 2.52
5551 7560 1.183549 ACCTTACTGCCTGGTCTACG 58.816 55.000 0.00 0.00 0.00 3.51
5589 7610 4.102681 TGATGTAGGACTGATCTAGGACGA 59.897 45.833 0.00 0.00 0.00 4.20
5680 7784 9.931210 GCGCTTGTTAATTACTATATCAGTTTT 57.069 29.630 0.00 0.00 38.80 2.43
5920 8031 1.269517 GCCGTGTTGAGGAAAAATGCA 60.270 47.619 0.00 0.00 0.00 3.96
6009 8123 2.418083 GGCTTGGGGAAGCGGATTG 61.418 63.158 0.00 0.00 46.38 2.67
6032 8146 8.594881 TTGAGTTTCTTAGTAAGCTTTCTCTG 57.405 34.615 9.07 4.19 0.00 3.35
6033 8147 6.647067 TGAGTTTCTTAGTAAGCTTTCTCTGC 59.353 38.462 9.07 0.00 0.00 4.26
6034 8148 6.525629 AGTTTCTTAGTAAGCTTTCTCTGCA 58.474 36.000 9.07 0.00 0.00 4.41
6035 8149 6.992715 AGTTTCTTAGTAAGCTTTCTCTGCAA 59.007 34.615 9.07 0.00 0.00 4.08
6051 8165 1.630369 TGCAAGCAACCAGTAGATCCT 59.370 47.619 0.00 0.00 0.00 3.24
6150 8268 9.998106 TTATCAGCTGTAAATTATTACTCCCTC 57.002 33.333 14.67 0.00 41.65 4.30
6151 8269 7.676683 TCAGCTGTAAATTATTACTCCCTCT 57.323 36.000 14.67 0.00 41.65 3.69
6152 8270 7.500992 TCAGCTGTAAATTATTACTCCCTCTG 58.499 38.462 14.67 0.00 41.65 3.35
6153 8271 7.125811 TCAGCTGTAAATTATTACTCCCTCTGT 59.874 37.037 14.67 0.00 41.65 3.41
6154 8272 8.421784 CAGCTGTAAATTATTACTCCCTCTGTA 58.578 37.037 5.25 0.00 41.65 2.74
6155 8273 8.989131 AGCTGTAAATTATTACTCCCTCTGTAA 58.011 33.333 0.00 0.00 41.65 2.41
6156 8274 9.609346 GCTGTAAATTATTACTCCCTCTGTAAA 57.391 33.333 1.02 0.00 41.65 2.01
6169 8287 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
6171 8289 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
6189 8307 7.086230 AGAGTGTTTAGATCACTACTTACGG 57.914 40.000 0.00 0.00 44.68 4.02
6190 8308 6.883217 AGAGTGTTTAGATCACTACTTACGGA 59.117 38.462 0.00 0.00 44.68 4.69
6191 8309 7.066043 AGAGTGTTTAGATCACTACTTACGGAG 59.934 40.741 0.00 0.00 44.68 4.63
6192 8310 6.095160 AGTGTTTAGATCACTACTTACGGAGG 59.905 42.308 0.00 0.00 43.17 4.30
6193 8311 5.359009 TGTTTAGATCACTACTTACGGAGGG 59.641 44.000 0.00 0.00 0.00 4.30
6194 8312 3.947612 AGATCACTACTTACGGAGGGA 57.052 47.619 0.00 0.00 0.00 4.20
6195 8313 3.822940 AGATCACTACTTACGGAGGGAG 58.177 50.000 0.00 0.00 0.00 4.30
6196 8314 3.202595 AGATCACTACTTACGGAGGGAGT 59.797 47.826 0.00 0.00 0.00 3.85
6197 8315 4.411540 AGATCACTACTTACGGAGGGAGTA 59.588 45.833 0.00 0.00 0.00 2.59
6198 8316 3.878778 TCACTACTTACGGAGGGAGTAC 58.121 50.000 0.00 0.00 0.00 2.73
6199 8317 3.264193 TCACTACTTACGGAGGGAGTACA 59.736 47.826 0.00 0.00 0.00 2.90
6200 8318 4.012374 CACTACTTACGGAGGGAGTACAA 58.988 47.826 0.00 0.00 0.00 2.41
6250 8368 1.993542 CTAGTGCAGTGTGAGCTCAG 58.006 55.000 18.89 6.48 0.00 3.35
6263 8382 1.599047 GCTCAGCTGAGGTGCCTTA 59.401 57.895 37.86 5.84 42.29 2.69
6264 8383 0.179936 GCTCAGCTGAGGTGCCTTAT 59.820 55.000 37.86 0.00 42.29 1.73
6266 8385 0.461548 TCAGCTGAGGTGCCTTATCG 59.538 55.000 13.74 0.00 0.00 2.92
6267 8386 0.531532 CAGCTGAGGTGCCTTATCGG 60.532 60.000 8.42 0.00 0.00 4.18
6296 8421 5.248380 AGCTAATATCATGGGGGAGTTTC 57.752 43.478 0.00 0.00 0.00 2.78
6391 8545 8.983702 AATTTTGTACTGGAAACTGTAAGGTA 57.016 30.769 0.00 0.00 44.87 3.08
6396 8550 7.383687 TGTACTGGAAACTGTAAGGTAGAATG 58.616 38.462 0.00 0.00 44.87 2.67
6416 8570 7.613585 AGAATGTTTTGGTCATGCAATATGAA 58.386 30.769 0.00 0.00 0.00 2.57
6417 8571 7.546667 AGAATGTTTTGGTCATGCAATATGAAC 59.453 33.333 0.00 0.00 36.34 3.18
6418 8572 6.094193 TGTTTTGGTCATGCAATATGAACA 57.906 33.333 2.36 2.36 43.27 3.18
6419 8573 5.925397 TGTTTTGGTCATGCAATATGAACAC 59.075 36.000 6.02 0.00 44.48 3.32
6458 8612 4.790861 GCGAACGAGGGTCGGACC 62.791 72.222 19.06 19.06 45.59 4.46
6563 9042 6.442952 GTGATAATACAGTGACTAGAGCTGG 58.557 44.000 0.00 0.00 34.79 4.85
6590 9069 0.897621 CCACTTGGCCATTTTCTCCC 59.102 55.000 6.09 0.00 0.00 4.30
6591 9070 0.897621 CACTTGGCCATTTTCTCCCC 59.102 55.000 6.09 0.00 0.00 4.81
6592 9071 0.786435 ACTTGGCCATTTTCTCCCCT 59.214 50.000 6.09 0.00 0.00 4.79
6593 9072 2.000048 ACTTGGCCATTTTCTCCCCTA 59.000 47.619 6.09 0.00 0.00 3.53
6821 9307 1.065491 TGCCATTATCCTCTTGCACGT 60.065 47.619 0.00 0.00 0.00 4.49
6822 9308 2.017049 GCCATTATCCTCTTGCACGTT 58.983 47.619 0.00 0.00 0.00 3.99
6840 9327 2.478879 CGTTGAAAACCAAGGCGAAAGT 60.479 45.455 0.00 0.00 46.28 2.66
6870 9357 3.374402 AGGAGAGTGCACCGACGG 61.374 66.667 14.63 13.61 0.00 4.79
6911 9401 1.110442 CACAACACCTGGGCTTGAAA 58.890 50.000 11.36 0.00 0.00 2.69
6922 9417 3.565307 TGGGCTTGAAAAAGACACATCT 58.435 40.909 0.00 0.00 36.42 2.90
6931 9426 8.868522 TTGAAAAAGACACATCTAGATCCATT 57.131 30.769 1.03 0.00 33.57 3.16
6996 9491 0.740868 CCGTTGAGCGATGGACATGT 60.741 55.000 0.00 0.00 44.77 3.21
6998 9493 2.267426 CGTTGAGCGATGGACATGTTA 58.733 47.619 0.00 0.00 44.77 2.41
7121 9618 3.274288 GCCATAGTTCTGACTTGGAAGG 58.726 50.000 10.09 0.00 36.76 3.46
7188 9692 2.623416 ACAAGTAACTTTCTGGCTTGCC 59.377 45.455 4.43 4.43 39.86 4.52
7223 9727 3.935828 GACAACCCTATGTCTTCTGCTTC 59.064 47.826 0.38 0.00 44.98 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.233005 CACGAGAGGATACATATGTGCTG 58.767 47.826 18.81 2.51 41.41 4.41
31 32 4.359434 AGAGAGCACGAGAGGATACATA 57.641 45.455 0.00 0.00 41.41 2.29
32 33 3.222173 AGAGAGCACGAGAGGATACAT 57.778 47.619 0.00 0.00 41.41 2.29
38 39 1.000283 ACAACAAGAGAGCACGAGAGG 60.000 52.381 0.00 0.00 0.00 3.69
68 69 2.229302 AGCAAGAAGACTACGACTGGTC 59.771 50.000 0.00 0.00 0.00 4.02
70 71 3.305398 AAGCAAGAAGACTACGACTGG 57.695 47.619 0.00 0.00 0.00 4.00
75 76 9.171701 GACAGTATATAAAGCAAGAAGACTACG 57.828 37.037 0.00 0.00 0.00 3.51
97 98 9.706691 AACCACGTATATATTCATTTAGGACAG 57.293 33.333 0.00 0.00 0.00 3.51
137 1363 6.127952 GGCGGTAAGATCTAGTATAACTCTGG 60.128 46.154 0.00 0.00 0.00 3.86
138 1364 6.402334 CGGCGGTAAGATCTAGTATAACTCTG 60.402 46.154 0.00 0.00 0.00 3.35
149 1375 3.549423 CGATTCAACGGCGGTAAGATCTA 60.549 47.826 13.24 0.00 0.00 1.98
150 1376 2.798499 CGATTCAACGGCGGTAAGATCT 60.798 50.000 13.24 0.00 0.00 2.75
155 1381 1.079875 GCTCGATTCAACGGCGGTAA 61.080 55.000 13.24 2.15 0.00 2.85
156 1382 1.517694 GCTCGATTCAACGGCGGTA 60.518 57.895 13.24 0.00 0.00 4.02
157 1383 2.813908 GCTCGATTCAACGGCGGT 60.814 61.111 13.24 0.00 0.00 5.68
158 1384 2.802667 CTGCTCGATTCAACGGCGG 61.803 63.158 13.24 0.00 34.24 6.13
159 1385 2.697425 CTGCTCGATTCAACGGCG 59.303 61.111 4.80 4.80 34.24 6.46
169 1431 2.491621 CCGTCAGATGCTGCTCGA 59.508 61.111 0.00 0.00 33.41 4.04
375 1648 1.271656 AGGTTCGAGTAAACACGGAGG 59.728 52.381 0.27 0.00 0.00 4.30
427 1700 2.333225 CTCGTAGCTAGGGCGCAG 59.667 66.667 10.83 0.00 44.37 5.18
618 1892 2.434336 ACTATTAATCTGTCCCGCAGCA 59.566 45.455 0.00 0.00 44.66 4.41
679 1953 7.944000 TGTCCATGCACATTATAACCTATCAAT 59.056 33.333 0.00 0.00 0.00 2.57
682 1956 7.744087 TTGTCCATGCACATTATAACCTATC 57.256 36.000 0.00 0.00 0.00 2.08
690 1964 9.369904 GATTTACTTTTTGTCCATGCACATTAT 57.630 29.630 0.00 0.00 0.00 1.28
691 1965 8.363390 TGATTTACTTTTTGTCCATGCACATTA 58.637 29.630 0.00 0.00 0.00 1.90
815 2091 9.659135 TTCCATGAATCCATAAAATCCTAATGT 57.341 29.630 0.00 0.00 0.00 2.71
818 2094 9.486123 TGTTTCCATGAATCCATAAAATCCTAA 57.514 29.630 0.00 0.00 0.00 2.69
819 2095 8.912988 GTGTTTCCATGAATCCATAAAATCCTA 58.087 33.333 0.00 0.00 0.00 2.94
820 2096 7.399765 TGTGTTTCCATGAATCCATAAAATCCT 59.600 33.333 0.00 0.00 0.00 3.24
821 2097 7.555087 TGTGTTTCCATGAATCCATAAAATCC 58.445 34.615 0.00 0.00 0.00 3.01
822 2098 9.037737 CATGTGTTTCCATGAATCCATAAAATC 57.962 33.333 0.00 0.00 43.99 2.17
823 2099 8.760735 TCATGTGTTTCCATGAATCCATAAAAT 58.239 29.630 0.00 0.00 46.12 1.82
824 2100 8.131847 TCATGTGTTTCCATGAATCCATAAAA 57.868 30.769 0.00 0.00 46.12 1.52
825 2101 7.715266 TCATGTGTTTCCATGAATCCATAAA 57.285 32.000 0.00 0.00 46.12 1.40
834 2110 6.653526 AATCAAACTCATGTGTTTCCATGA 57.346 33.333 20.08 16.01 46.74 3.07
835 2111 6.924612 TGAAATCAAACTCATGTGTTTCCATG 59.075 34.615 20.08 11.89 42.89 3.66
836 2112 7.053316 TGAAATCAAACTCATGTGTTTCCAT 57.947 32.000 20.08 13.33 37.98 3.41
837 2113 6.462552 TGAAATCAAACTCATGTGTTTCCA 57.537 33.333 20.08 11.89 37.98 3.53
838 2114 7.168135 GTCTTGAAATCAAACTCATGTGTTTCC 59.832 37.037 20.08 9.74 37.98 3.13
839 2115 7.168135 GGTCTTGAAATCAAACTCATGTGTTTC 59.832 37.037 20.08 11.30 37.98 2.78
840 2116 6.980397 GGTCTTGAAATCAAACTCATGTGTTT 59.020 34.615 17.83 17.83 40.34 2.83
841 2117 6.096705 TGGTCTTGAAATCAAACTCATGTGTT 59.903 34.615 7.33 7.33 35.15 3.32
842 2118 5.593909 TGGTCTTGAAATCAAACTCATGTGT 59.406 36.000 0.00 0.00 35.15 3.72
867 2176 7.589221 GCAATTAGCTTCACAGTTATTGCTATC 59.411 37.037 0.00 0.00 41.15 2.08
870 2179 5.644644 GCAATTAGCTTCACAGTTATTGCT 58.355 37.500 0.00 0.00 41.15 3.91
922 2231 4.251543 TCGCTAAACAGATCTGTGACAA 57.748 40.909 28.52 13.15 44.13 3.18
927 2236 6.794675 AGCTTAAGTTCGCTAAACAGATCTGT 60.795 38.462 22.89 22.89 40.56 3.41
966 2275 2.471749 GGTAAATTTGACGCGTGACTCG 60.472 50.000 20.70 0.00 43.12 4.18
996 2305 0.532573 TCTGAGAGTTGTCCATCGGC 59.467 55.000 0.00 0.00 0.00 5.54
1122 2431 3.434319 GCATGTGGGCGTGGAGTG 61.434 66.667 0.00 0.00 32.43 3.51
1125 2434 0.463654 GATAAGCATGTGGGCGTGGA 60.464 55.000 0.00 0.00 39.27 4.02
1305 2614 4.755411 TGCTAGGTTGTGTAGCATAGAAC 58.245 43.478 0.67 0.00 46.29 3.01
1335 2644 1.294659 GAGCACTTTGAGCGGGAGTG 61.295 60.000 7.80 7.80 42.75 3.51
1336 2645 1.004440 GAGCACTTTGAGCGGGAGT 60.004 57.895 0.00 0.00 37.01 3.85
1351 2660 3.491792 GCTTCTGTGGTGATACTAGGAGC 60.492 52.174 0.00 0.00 0.00 4.70
1360 2669 1.067295 TTCCCAGCTTCTGTGGTGAT 58.933 50.000 0.00 0.00 37.61 3.06
1579 2898 6.867816 CCTTTGATTTTGTATTACTTGCTGCA 59.132 34.615 0.00 0.00 0.00 4.41
1711 3030 6.831664 AAGTATGTCTTCCCCATATTCTGT 57.168 37.500 0.00 0.00 0.00 3.41
1830 3150 9.609346 AACAAAGCTGAACTAACTAAAGAAGTA 57.391 29.630 0.00 0.00 37.50 2.24
2029 3350 6.415206 TCACCGGATTAAAGGGATACTTAG 57.585 41.667 9.46 0.00 38.85 2.18
2036 3357 4.300345 TCCTAATCACCGGATTAAAGGGA 58.700 43.478 9.46 3.43 43.50 4.20
2099 3420 7.301068 TGACAGCCAAAATGTTAACAAAAAG 57.699 32.000 13.23 3.64 0.00 2.27
2104 3425 7.271511 AGAAAATGACAGCCAAAATGTTAACA 58.728 30.769 11.41 11.41 0.00 2.41
2146 3467 8.726068 CCAACAATATGTATAACACAACAGTCA 58.274 33.333 0.00 0.00 41.55 3.41
2147 3468 8.726988 ACCAACAATATGTATAACACAACAGTC 58.273 33.333 0.00 0.00 41.55 3.51
2148 3469 8.630054 ACCAACAATATGTATAACACAACAGT 57.370 30.769 0.00 0.00 41.55 3.55
2164 3485 8.226819 TCACTTTGACAATGTAACCAACAATA 57.773 30.769 6.41 0.00 42.70 1.90
2197 3518 6.324819 TGCTTAATCATCAGCTTTAGCAAAC 58.675 36.000 4.33 0.00 45.16 2.93
2300 3621 2.357009 GGTGGCATACTCATTTCAGCAG 59.643 50.000 0.00 0.00 0.00 4.24
2305 3626 5.189180 AGAAAGAGGTGGCATACTCATTTC 58.811 41.667 19.78 21.02 36.20 2.17
2320 3641 5.971763 AGCAGTGAGTAACATAGAAAGAGG 58.028 41.667 0.00 0.00 0.00 3.69
2463 3787 0.321996 GCTTCAGAAACTCGGGGAGT 59.678 55.000 0.00 0.00 45.64 3.85
2641 3965 3.835978 TCGAGGTTTTTCCATCTACCAGA 59.164 43.478 0.00 0.00 39.02 3.86
2715 4041 0.250295 CACAGACCCCACACGACATT 60.250 55.000 0.00 0.00 0.00 2.71
2766 4092 7.798596 ACAGCTTTGATATTTCTATGTCCTG 57.201 36.000 0.00 0.00 0.00 3.86
2811 4137 7.725818 TCTATTGTAGGTATCAGTGTACTCG 57.274 40.000 0.00 0.00 0.00 4.18
2875 4201 6.878923 ACACCAATCAGAGAAAAATATCACGA 59.121 34.615 0.00 0.00 0.00 4.35
2968 4298 4.569966 GTGAGATAAGGATCAACTGTGCAG 59.430 45.833 0.00 0.00 34.17 4.41
3269 5023 6.314896 GCACATAAGAGCTGTTGAAAGATACT 59.685 38.462 6.33 0.00 0.00 2.12
3599 5432 5.697633 CCAACTTGTTTTCATCCTTGGAATG 59.302 40.000 0.00 0.00 33.47 2.67
3928 5762 3.907474 TCACCAAGAAAGTACTCCATCCA 59.093 43.478 0.00 0.00 0.00 3.41
3932 5766 3.452990 TGTGTCACCAAGAAAGTACTCCA 59.547 43.478 0.00 0.00 0.00 3.86
4039 5873 1.544246 GGCACAATAACTGGGTTCACC 59.456 52.381 0.00 0.00 40.81 4.02
4067 5901 0.754957 TGAACTGCAACAAGGGTGGG 60.755 55.000 0.00 0.00 0.00 4.61
4130 5964 1.300971 CCACCACAGCCTGAACATCG 61.301 60.000 0.00 0.00 0.00 3.84
4241 6075 3.707793 ACTCTCACAAGAACTTCACGAC 58.292 45.455 0.00 0.00 0.00 4.34
4273 6107 3.265221 AGACAAGATCACACCATCCACAT 59.735 43.478 0.00 0.00 0.00 3.21
4283 6117 3.561310 GTGTGCTTTCAGACAAGATCACA 59.439 43.478 0.00 0.00 36.58 3.58
4292 6126 5.673337 TTCAAGTATGTGTGCTTTCAGAC 57.327 39.130 0.00 0.00 37.04 3.51
4313 6148 8.416329 GGGAGTAGTTTGAAAATGCATATGATT 58.584 33.333 6.97 0.91 0.00 2.57
4416 6252 5.245531 ACGGAGCAAAATGAGTGAATCTAA 58.754 37.500 0.00 0.00 0.00 2.10
4460 6296 8.990163 TGTTCCTAAATATAAGCCCTTTTAGG 57.010 34.615 12.11 12.11 46.30 2.69
4485 6321 6.071278 GCGAGGATATAAACATTACTCCCTCT 60.071 42.308 0.00 0.00 36.45 3.69
4643 6480 5.687285 CAGAAAATGGAAATTATGTAGCCGC 59.313 40.000 0.00 0.00 0.00 6.53
4692 6529 9.251792 TGTTACATTCCGTACATATGTGTATTC 57.748 33.333 18.81 7.18 42.43 1.75
4802 6639 4.982916 GGCACGATATTGTTCGAGTAAGAT 59.017 41.667 0.31 0.00 41.62 2.40
5016 7009 3.259123 GGGGTTTTGAACTTGATCTGCAT 59.741 43.478 0.00 0.00 0.00 3.96
5152 7145 3.450457 GCTTCCAGGAAGAGAGAGATCAA 59.550 47.826 30.67 0.00 41.71 2.57
5212 7206 8.177119 AGTAACTACAAATGCCATTCTCAAAA 57.823 30.769 0.00 0.00 0.00 2.44
5231 7239 2.245582 AGCACGTCCCAACTAGTAACT 58.754 47.619 0.00 0.00 0.00 2.24
5243 7251 2.029844 GCCAGACTGAAGCACGTCC 61.030 63.158 3.32 0.00 0.00 4.79
5246 7254 1.572085 CCAAGCCAGACTGAAGCACG 61.572 60.000 3.32 0.00 0.00 5.34
5385 7393 5.660391 CAAATCAGATAACGTACAGATGCG 58.340 41.667 0.00 0.00 40.17 4.73
5398 7406 8.055181 AGATAAAGGGAAGTTGCAAATCAGATA 58.945 33.333 0.00 0.00 0.00 1.98
5431 7439 5.658198 TCAGAGGGTAGGCAAGTATAGTA 57.342 43.478 0.00 0.00 0.00 1.82
5551 7560 3.492421 ACATCATTTGGCACGATGAAC 57.508 42.857 21.23 0.00 39.09 3.18
5589 7610 5.587844 GCCTGATTCAACATCTCACATAAGT 59.412 40.000 0.00 0.00 0.00 2.24
5680 7784 2.805295 CGGGAAGTGTGCACTGAAGTAA 60.805 50.000 19.41 0.00 41.58 2.24
5830 7941 4.627467 TCAAAGCATAGAAAGAAGACTCGC 59.373 41.667 0.00 0.00 0.00 5.03
6009 8123 6.647067 TGCAGAGAAAGCTTACTAAGAAACTC 59.353 38.462 0.00 0.00 0.00 3.01
6032 8146 2.012673 CAGGATCTACTGGTTGCTTGC 58.987 52.381 0.00 0.00 34.84 4.01
6145 8263 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
6163 8281 8.671921 CCGTAAGTAGTGATCTAAACACTCTTA 58.328 37.037 0.00 0.00 45.58 2.10
6164 8282 7.392673 TCCGTAAGTAGTGATCTAAACACTCTT 59.607 37.037 0.00 0.98 45.58 2.85
6165 8283 6.883217 TCCGTAAGTAGTGATCTAAACACTCT 59.117 38.462 0.00 0.00 45.58 3.24
6166 8284 7.081526 TCCGTAAGTAGTGATCTAAACACTC 57.918 40.000 0.00 0.00 45.58 3.51
6168 8286 6.264088 CCTCCGTAAGTAGTGATCTAAACAC 58.736 44.000 0.00 0.00 38.38 3.32
6169 8287 5.359009 CCCTCCGTAAGTAGTGATCTAAACA 59.641 44.000 0.00 0.00 0.00 2.83
6170 8288 5.591877 TCCCTCCGTAAGTAGTGATCTAAAC 59.408 44.000 0.00 0.00 0.00 2.01
6171 8289 5.759059 TCCCTCCGTAAGTAGTGATCTAAA 58.241 41.667 0.00 0.00 0.00 1.85
6172 8290 5.104193 ACTCCCTCCGTAAGTAGTGATCTAA 60.104 44.000 0.00 0.00 0.00 2.10
6173 8291 4.411540 ACTCCCTCCGTAAGTAGTGATCTA 59.588 45.833 0.00 0.00 0.00 1.98
6174 8292 3.202595 ACTCCCTCCGTAAGTAGTGATCT 59.797 47.826 0.00 0.00 0.00 2.75
6175 8293 3.553904 ACTCCCTCCGTAAGTAGTGATC 58.446 50.000 0.00 0.00 0.00 2.92
6176 8294 3.666345 ACTCCCTCCGTAAGTAGTGAT 57.334 47.619 0.00 0.00 0.00 3.06
6177 8295 3.264193 TGTACTCCCTCCGTAAGTAGTGA 59.736 47.826 0.00 0.00 0.00 3.41
6178 8296 3.614092 TGTACTCCCTCCGTAAGTAGTG 58.386 50.000 0.00 0.00 0.00 2.74
6179 8297 4.307032 TTGTACTCCCTCCGTAAGTAGT 57.693 45.455 0.00 0.00 0.00 2.73
6180 8298 4.097589 CCTTTGTACTCCCTCCGTAAGTAG 59.902 50.000 0.00 0.00 0.00 2.57
6181 8299 4.019174 CCTTTGTACTCCCTCCGTAAGTA 58.981 47.826 0.00 0.00 0.00 2.24
6182 8300 2.830321 CCTTTGTACTCCCTCCGTAAGT 59.170 50.000 0.00 0.00 0.00 2.24
6183 8301 3.094572 TCCTTTGTACTCCCTCCGTAAG 58.905 50.000 0.00 0.00 0.00 2.34
6184 8302 3.094572 CTCCTTTGTACTCCCTCCGTAA 58.905 50.000 0.00 0.00 0.00 3.18
6185 8303 2.731572 CTCCTTTGTACTCCCTCCGTA 58.268 52.381 0.00 0.00 0.00 4.02
6186 8304 1.558233 CTCCTTTGTACTCCCTCCGT 58.442 55.000 0.00 0.00 0.00 4.69
6187 8305 0.175989 GCTCCTTTGTACTCCCTCCG 59.824 60.000 0.00 0.00 0.00 4.63
6188 8306 1.276622 TGCTCCTTTGTACTCCCTCC 58.723 55.000 0.00 0.00 0.00 4.30
6189 8307 2.303311 ACTTGCTCCTTTGTACTCCCTC 59.697 50.000 0.00 0.00 0.00 4.30
6190 8308 2.303311 GACTTGCTCCTTTGTACTCCCT 59.697 50.000 0.00 0.00 0.00 4.20
6191 8309 2.615747 GGACTTGCTCCTTTGTACTCCC 60.616 54.545 0.00 0.00 35.89 4.30
6192 8310 2.038557 TGGACTTGCTCCTTTGTACTCC 59.961 50.000 0.00 0.00 40.26 3.85
6193 8311 3.244249 ACTGGACTTGCTCCTTTGTACTC 60.244 47.826 0.00 0.00 40.26 2.59
6194 8312 2.706190 ACTGGACTTGCTCCTTTGTACT 59.294 45.455 0.00 0.00 40.26 2.73
6195 8313 2.808543 CACTGGACTTGCTCCTTTGTAC 59.191 50.000 0.00 0.00 40.26 2.90
6196 8314 2.810400 GCACTGGACTTGCTCCTTTGTA 60.810 50.000 0.00 0.00 40.26 2.41
6197 8315 1.972872 CACTGGACTTGCTCCTTTGT 58.027 50.000 0.00 0.00 40.26 2.83
6198 8316 0.595095 GCACTGGACTTGCTCCTTTG 59.405 55.000 0.00 0.00 40.26 2.77
6199 8317 0.538287 GGCACTGGACTTGCTCCTTT 60.538 55.000 0.00 0.00 40.26 3.11
6200 8318 1.073897 GGCACTGGACTTGCTCCTT 59.926 57.895 0.00 0.00 40.26 3.36
6250 8368 4.445699 CCGATAAGGCACCTCAGC 57.554 61.111 0.00 0.00 0.00 4.26
6259 8378 6.978659 TGATATTAGCTTTATCGCCGATAAGG 59.021 38.462 20.70 20.70 44.97 2.69
6260 8379 7.987268 TGATATTAGCTTTATCGCCGATAAG 57.013 36.000 17.95 13.53 36.15 1.73
6261 8380 7.438160 CCATGATATTAGCTTTATCGCCGATAA 59.562 37.037 15.16 15.16 33.38 1.75
6263 8382 5.755375 CCATGATATTAGCTTTATCGCCGAT 59.245 40.000 4.45 4.45 0.00 4.18
6264 8383 5.109210 CCATGATATTAGCTTTATCGCCGA 58.891 41.667 0.00 0.00 0.00 5.54
6266 8385 4.576463 CCCCATGATATTAGCTTTATCGCC 59.424 45.833 0.00 0.00 0.00 5.54
6267 8386 4.576463 CCCCCATGATATTAGCTTTATCGC 59.424 45.833 0.00 0.00 0.00 4.58
6323 8448 6.607600 TCATACCATAGTGAGCTACTGAACTT 59.392 38.462 0.00 0.00 40.65 2.66
6391 8545 7.172868 TCATATTGCATGACCAAAACATTCT 57.827 32.000 0.00 0.00 0.00 2.40
6396 8550 6.158598 AGTGTTCATATTGCATGACCAAAAC 58.841 36.000 0.00 0.00 0.00 2.43
6416 8570 6.147821 CCGTGTCAATCTAGAAAATCAAGTGT 59.852 38.462 0.00 0.00 0.00 3.55
6417 8571 6.537566 CCGTGTCAATCTAGAAAATCAAGTG 58.462 40.000 0.00 0.00 0.00 3.16
6418 8572 5.122396 GCCGTGTCAATCTAGAAAATCAAGT 59.878 40.000 0.00 0.00 0.00 3.16
6419 8573 5.563842 GCCGTGTCAATCTAGAAAATCAAG 58.436 41.667 0.00 0.00 0.00 3.02
6458 8612 5.469760 TGAATTATCATACATCAAGCACCCG 59.530 40.000 0.00 0.00 0.00 5.28
6516 8672 9.098355 TCACGAATGAATACCTAATCTCAAAAG 57.902 33.333 0.00 0.00 0.00 2.27
6603 9082 0.392706 TCTGCTTGAGCCTTCGTTCA 59.607 50.000 0.00 0.00 41.18 3.18
6646 9128 2.120312 TGTAATCCTGGCCGGTTGATA 58.880 47.619 11.58 0.00 0.00 2.15
6821 9307 2.755655 TCACTTTCGCCTTGGTTTTCAA 59.244 40.909 0.00 0.00 0.00 2.69
6822 9308 2.370349 TCACTTTCGCCTTGGTTTTCA 58.630 42.857 0.00 0.00 0.00 2.69
6894 9381 2.430332 TCTTTTTCAAGCCCAGGTGTTG 59.570 45.455 0.00 0.00 0.00 3.33
6895 9382 2.430694 GTCTTTTTCAAGCCCAGGTGTT 59.569 45.455 0.00 0.00 0.00 3.32
6911 9401 6.950842 TGACAATGGATCTAGATGTGTCTTT 58.049 36.000 22.97 9.91 35.92 2.52
6922 9417 4.526970 GGCCTTCTTTGACAATGGATCTA 58.473 43.478 0.00 0.00 0.00 1.98
6931 9426 1.228552 GCAGGGGCCTTCTTTGACA 60.229 57.895 0.84 0.00 0.00 3.58
6996 9491 5.087323 CCATCCATCTAGGCTCTAGGTTAA 58.913 45.833 0.00 0.00 37.29 2.01
6998 9493 3.515562 CCATCCATCTAGGCTCTAGGTT 58.484 50.000 0.00 0.00 37.29 3.50
7121 9618 4.162690 ATTCTGACCGCTCGCCCC 62.163 66.667 0.00 0.00 0.00 5.80
7202 9706 3.584848 AGAAGCAGAAGACATAGGGTTGT 59.415 43.478 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.