Multiple sequence alignment - TraesCS2D01G394800

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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 TraesCS2D01G394800 chr2D 100.000 5263 0 0 1 5263 506151859 506146597 0.000000e+00 9720.0
1 TraesCS2D01G394800 chr2B 95.035 4431 139 38 291 4681 593662260 593657871 0.000000e+00 6889.0
2 TraesCS2D01G394800 chr2B 91.618 513 18 11 4754 5250 593657869 593657366 0.000000e+00 686.0
3 TraesCS2D01G394800 chr2B 88.485 165 11 2 90 254 593663414 593663258 5.380000e-45 193.0
4 TraesCS2D01G394800 chr2A 93.291 4248 189 49 494 4681 650633440 650629229 0.000000e+00 6178.0
5 TraesCS2D01G394800 chr2A 87.798 377 12 7 123 497 650634144 650633800 1.360000e-110 411.0
6 TraesCS2D01G394800 chr2A 81.034 290 19 21 4754 5021 650629227 650628952 1.160000e-46 198.0
7 TraesCS2D01G394800 chr6D 83.333 252 42 0 3352 3603 339972927 339973178 3.170000e-57 233.0
8 TraesCS2D01G394800 chr5D 89.041 73 7 1 4686 4758 219645671 219645742 7.260000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G394800 chr2D 506146597 506151859 5262 True 9720.000000 9720 100.000000 1 5263 1 chr2D.!!$R1 5262
1 TraesCS2D01G394800 chr2B 593657366 593663414 6048 True 2589.333333 6889 91.712667 90 5250 3 chr2B.!!$R1 5160
2 TraesCS2D01G394800 chr2A 650628952 650634144 5192 True 2262.333333 6178 87.374333 123 5021 3 chr2A.!!$R1 4898

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
50 51 0.029300 GCACACGCACACAAACATCT 59.971 50.0 0.00 0.0 38.36 2.90 F
718 2061 0.042188 CCAAAGATAATCGCGTGCCG 60.042 55.0 5.77 0.0 38.61 5.69 F
1078 2432 0.105709 GGAGGAGGAGGAGGAGGAAG 60.106 65.0 0.00 0.0 0.00 3.46 F
2593 3967 0.034756 TGTCATACTGCTGCCGTTGT 59.965 50.0 1.15 0.0 0.00 3.32 F
3302 4694 1.026718 GCTTGTCGGCAATGGCTACT 61.027 55.0 1.35 0.0 40.87 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 2961 1.416030 TGTGCTGACAAGTGCCTAGAA 59.584 47.619 0.00 0.0 0.00 2.10 R
1606 2963 1.532868 GTTGTGCTGACAAGTGCCTAG 59.467 52.381 0.00 0.0 42.87 3.02 R
2922 4298 1.210478 TGAAGGCCTGAAGCTGGTATC 59.790 52.381 5.69 0.0 43.05 2.24 R
3878 5276 0.454452 GAATTGGACAAGCGAACGGC 60.454 55.000 0.00 0.0 44.05 5.68 R
4712 6124 0.036164 ACTTTACTGCCCGATGTGCA 59.964 50.000 0.00 0.0 37.17 4.57 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
17 18 4.347096 TTAACACACACGCGAGGG 57.653 55.556 15.93 9.40 43.28 4.30
18 19 1.740905 TTAACACACACGCGAGGGA 59.259 52.632 15.93 0.00 38.45 4.20
19 20 0.104487 TTAACACACACGCGAGGGAA 59.896 50.000 15.93 0.00 38.45 3.97
20 21 0.104487 TAACACACACGCGAGGGAAA 59.896 50.000 15.93 0.00 38.45 3.13
21 22 0.745128 AACACACACGCGAGGGAAAA 60.745 50.000 15.93 0.00 38.45 2.29
22 23 0.745128 ACACACACGCGAGGGAAAAA 60.745 50.000 15.93 0.00 38.45 1.94
23 24 0.041312 CACACACGCGAGGGAAAAAG 60.041 55.000 15.93 0.00 38.45 2.27
24 25 1.082104 CACACGCGAGGGAAAAAGC 60.082 57.895 15.93 0.00 38.45 3.51
29 30 4.794241 CGAGGGAAAAAGCGCGCG 62.794 66.667 28.44 28.44 37.62 6.86
47 48 2.099254 CGCACACGCACACAAACA 59.901 55.556 0.00 0.00 38.40 2.83
48 49 1.298264 CGCACACGCACACAAACAT 60.298 52.632 0.00 0.00 38.40 2.71
49 50 1.261510 CGCACACGCACACAAACATC 61.262 55.000 0.00 0.00 38.40 3.06
50 51 0.029300 GCACACGCACACAAACATCT 59.971 50.000 0.00 0.00 38.36 2.90
51 52 1.533756 GCACACGCACACAAACATCTT 60.534 47.619 0.00 0.00 38.36 2.40
52 53 2.375110 CACACGCACACAAACATCTTC 58.625 47.619 0.00 0.00 0.00 2.87
53 54 2.032054 CACACGCACACAAACATCTTCT 59.968 45.455 0.00 0.00 0.00 2.85
54 55 2.682856 ACACGCACACAAACATCTTCTT 59.317 40.909 0.00 0.00 0.00 2.52
55 56 3.242739 ACACGCACACAAACATCTTCTTC 60.243 43.478 0.00 0.00 0.00 2.87
56 57 2.290641 ACGCACACAAACATCTTCTTCC 59.709 45.455 0.00 0.00 0.00 3.46
57 58 2.290367 CGCACACAAACATCTTCTTCCA 59.710 45.455 0.00 0.00 0.00 3.53
58 59 3.607775 CGCACACAAACATCTTCTTCCAG 60.608 47.826 0.00 0.00 0.00 3.86
59 60 3.854784 GCACACAAACATCTTCTTCCAGC 60.855 47.826 0.00 0.00 0.00 4.85
60 61 2.887152 ACACAAACATCTTCTTCCAGCC 59.113 45.455 0.00 0.00 0.00 4.85
61 62 2.886523 CACAAACATCTTCTTCCAGCCA 59.113 45.455 0.00 0.00 0.00 4.75
62 63 3.057736 CACAAACATCTTCTTCCAGCCAG 60.058 47.826 0.00 0.00 0.00 4.85
63 64 3.181440 ACAAACATCTTCTTCCAGCCAGA 60.181 43.478 0.00 0.00 0.00 3.86
64 65 4.015084 CAAACATCTTCTTCCAGCCAGAT 58.985 43.478 0.00 0.00 0.00 2.90
65 66 5.188434 CAAACATCTTCTTCCAGCCAGATA 58.812 41.667 0.00 0.00 0.00 1.98
66 67 5.441718 AACATCTTCTTCCAGCCAGATAA 57.558 39.130 0.00 0.00 0.00 1.75
67 68 5.643421 ACATCTTCTTCCAGCCAGATAAT 57.357 39.130 0.00 0.00 0.00 1.28
68 69 6.011122 ACATCTTCTTCCAGCCAGATAATT 57.989 37.500 0.00 0.00 0.00 1.40
69 70 5.826737 ACATCTTCTTCCAGCCAGATAATTG 59.173 40.000 0.00 0.00 0.00 2.32
70 71 5.441718 TCTTCTTCCAGCCAGATAATTGT 57.558 39.130 0.00 0.00 0.00 2.71
71 72 6.560003 TCTTCTTCCAGCCAGATAATTGTA 57.440 37.500 0.00 0.00 0.00 2.41
72 73 6.349300 TCTTCTTCCAGCCAGATAATTGTAC 58.651 40.000 0.00 0.00 0.00 2.90
73 74 5.692115 TCTTCCAGCCAGATAATTGTACA 57.308 39.130 0.00 0.00 0.00 2.90
74 75 5.428253 TCTTCCAGCCAGATAATTGTACAC 58.572 41.667 0.00 0.00 0.00 2.90
75 76 3.792401 TCCAGCCAGATAATTGTACACG 58.208 45.455 0.00 0.00 0.00 4.49
76 77 2.287915 CCAGCCAGATAATTGTACACGC 59.712 50.000 0.00 0.00 0.00 5.34
77 78 3.198068 CAGCCAGATAATTGTACACGCT 58.802 45.455 0.00 0.00 0.00 5.07
78 79 3.246226 CAGCCAGATAATTGTACACGCTC 59.754 47.826 0.00 0.00 0.00 5.03
79 80 2.544267 GCCAGATAATTGTACACGCTCC 59.456 50.000 0.00 0.00 0.00 4.70
80 81 3.792401 CCAGATAATTGTACACGCTCCA 58.208 45.455 0.00 0.00 0.00 3.86
81 82 3.555956 CCAGATAATTGTACACGCTCCAC 59.444 47.826 0.00 0.00 0.00 4.02
82 83 4.180817 CAGATAATTGTACACGCTCCACA 58.819 43.478 0.00 0.00 0.00 4.17
83 84 4.811024 CAGATAATTGTACACGCTCCACAT 59.189 41.667 0.00 0.00 0.00 3.21
84 85 5.983118 CAGATAATTGTACACGCTCCACATA 59.017 40.000 0.00 0.00 0.00 2.29
85 86 5.983720 AGATAATTGTACACGCTCCACATAC 59.016 40.000 0.00 0.00 0.00 2.39
86 87 1.985334 TTGTACACGCTCCACATACG 58.015 50.000 0.00 0.00 0.00 3.06
87 88 1.166989 TGTACACGCTCCACATACGA 58.833 50.000 0.00 0.00 0.00 3.43
88 89 1.135603 TGTACACGCTCCACATACGAC 60.136 52.381 0.00 0.00 0.00 4.34
142 143 0.818296 ATCTGGTCTGGTGAGCGTAC 59.182 55.000 0.00 0.00 43.09 3.67
143 144 1.154016 CTGGTCTGGTGAGCGTACG 60.154 63.158 11.84 11.84 43.09 3.67
144 145 1.863662 CTGGTCTGGTGAGCGTACGT 61.864 60.000 17.90 3.43 43.09 3.57
145 146 1.443872 GGTCTGGTGAGCGTACGTG 60.444 63.158 17.90 0.00 0.00 4.49
185 186 1.028330 ACGTCGCGATTACTGAGGGA 61.028 55.000 14.06 0.00 0.00 4.20
186 187 0.317103 CGTCGCGATTACTGAGGGAG 60.317 60.000 14.06 0.00 0.00 4.30
187 188 0.595310 GTCGCGATTACTGAGGGAGC 60.595 60.000 14.06 0.00 0.00 4.70
188 189 1.035385 TCGCGATTACTGAGGGAGCA 61.035 55.000 3.71 0.00 0.00 4.26
254 255 2.281761 ACTGCACTTGCCCTTCCG 60.282 61.111 0.00 0.00 41.18 4.30
255 256 3.058160 CTGCACTTGCCCTTCCGG 61.058 66.667 0.00 0.00 41.18 5.14
271 272 2.202899 GGCCTTCCCCCAACCAAA 59.797 61.111 0.00 0.00 0.00 3.28
548 1883 2.438434 CCGCCCAGGCTGTAAAGG 60.438 66.667 14.43 8.46 39.32 3.11
670 2013 2.652348 ACCATAATCCAACCACTTCCCA 59.348 45.455 0.00 0.00 0.00 4.37
671 2014 3.023832 CCATAATCCAACCACTTCCCAC 58.976 50.000 0.00 0.00 0.00 4.61
718 2061 0.042188 CCAAAGATAATCGCGTGCCG 60.042 55.000 5.77 0.00 38.61 5.69
794 2139 2.486951 GTAATCACGAGCGGCTAAGA 57.513 50.000 0.60 1.31 0.00 2.10
1074 2428 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1077 2431 0.556380 AGGAGGAGGAGGAGGAGGAA 60.556 60.000 0.00 0.00 0.00 3.36
1078 2432 0.105709 GGAGGAGGAGGAGGAGGAAG 60.106 65.000 0.00 0.00 0.00 3.46
1079 2433 0.930726 GAGGAGGAGGAGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
1080 2434 0.634465 AGGAGGAGGAGGAGGAAGAC 59.366 60.000 0.00 0.00 0.00 3.01
1081 2435 0.753848 GGAGGAGGAGGAGGAAGACG 60.754 65.000 0.00 0.00 0.00 4.18
1082 2436 0.256464 GAGGAGGAGGAGGAAGACGA 59.744 60.000 0.00 0.00 0.00 4.20
1083 2437 0.705253 AGGAGGAGGAGGAAGACGAA 59.295 55.000 0.00 0.00 0.00 3.85
1086 2440 2.448453 GAGGAGGAGGAAGACGAAGAA 58.552 52.381 0.00 0.00 0.00 2.52
1089 2443 2.826725 GGAGGAGGAAGACGAAGAAGAA 59.173 50.000 0.00 0.00 0.00 2.52
1446 2800 2.436292 CTCTGCCAGCCACTCTGC 60.436 66.667 0.00 0.00 41.50 4.26
1454 2808 2.113986 GCCACTCTGCACCTGGTT 59.886 61.111 0.00 0.00 0.00 3.67
1455 2809 1.529244 GCCACTCTGCACCTGGTTT 60.529 57.895 0.00 0.00 0.00 3.27
1456 2810 1.799258 GCCACTCTGCACCTGGTTTG 61.799 60.000 0.00 0.00 0.00 2.93
1459 2813 1.750778 CACTCTGCACCTGGTTTGTTT 59.249 47.619 0.00 0.00 0.00 2.83
1602 2959 1.414919 TGCTAGTTTCTGGACCGTGTT 59.585 47.619 0.00 0.00 0.00 3.32
1604 2961 2.876550 GCTAGTTTCTGGACCGTGTTTT 59.123 45.455 0.00 0.00 0.00 2.43
1606 2963 4.554134 GCTAGTTTCTGGACCGTGTTTTTC 60.554 45.833 0.00 0.00 0.00 2.29
1666 3026 8.119226 GGTGATCAGAAATTTTAGACTTCGATG 58.881 37.037 0.00 0.00 0.00 3.84
1834 3203 9.787435 TTTAACAACACATGAAACTCTAGGTAT 57.213 29.630 0.00 0.00 0.00 2.73
1838 3207 5.651530 ACACATGAAACTCTAGGTATGACG 58.348 41.667 0.00 0.00 0.00 4.35
1854 3223 0.169009 GACGATTGTTGCCAGGAAGC 59.831 55.000 0.00 0.00 0.00 3.86
2157 3531 3.173151 TGATTTAGTGGTCTGCTCCTGA 58.827 45.455 0.00 0.00 0.00 3.86
2264 3638 0.323302 TCTGTTGCATGGCTAACGGA 59.677 50.000 0.00 9.44 39.24 4.69
2593 3967 0.034756 TGTCATACTGCTGCCGTTGT 59.965 50.000 1.15 0.00 0.00 3.32
2602 3976 1.345089 TGCTGCCGTTGTTTCCTAGTA 59.655 47.619 0.00 0.00 0.00 1.82
2758 4132 6.893020 AACCTGTCCTAGTCATATTTTCCT 57.107 37.500 0.00 0.00 0.00 3.36
2848 4222 2.484264 GTGTGCCCACAATACTCTTGAC 59.516 50.000 2.19 0.00 43.77 3.18
2922 4298 9.661187 CTGTAAGCTAATAAATCAGCAAATGAG 57.339 33.333 0.00 0.00 42.53 2.90
2935 4311 4.035324 CAGCAAATGAGATACCAGCTTCAG 59.965 45.833 0.00 0.00 0.00 3.02
2939 4315 1.127343 GAGATACCAGCTTCAGGCCT 58.873 55.000 0.00 0.00 43.05 5.19
2962 4338 7.967303 GCCTTCAGAATGCTTATTTATATCTGC 59.033 37.037 3.30 0.00 34.33 4.26
3129 4505 3.921021 CCGCAGTAACACTAACTCTCTTG 59.079 47.826 0.00 0.00 0.00 3.02
3234 4615 3.710209 AAGATCAACACTCAGGAAGGG 57.290 47.619 0.00 0.00 0.00 3.95
3289 4681 7.437862 TGAAACTAAAAATGAATGTGGCTTGTC 59.562 33.333 0.00 0.00 0.00 3.18
3302 4694 1.026718 GCTTGTCGGCAATGGCTACT 61.027 55.000 1.35 0.00 40.87 2.57
3305 4697 1.164411 TGTCGGCAATGGCTACTTTG 58.836 50.000 12.29 0.00 40.87 2.77
3307 4699 2.017049 GTCGGCAATGGCTACTTTGAT 58.983 47.619 5.02 0.00 40.87 2.57
3326 4724 9.405587 ACTTTGATATACACAAACCATTTTTCG 57.594 29.630 0.00 0.00 34.30 3.46
3336 4734 6.142161 CACAAACCATTTTTCGTGTACATCAG 59.858 38.462 0.00 0.00 0.00 2.90
3556 4954 7.487484 TGAAAACTACAACAAGATGAATGCAA 58.513 30.769 0.00 0.00 0.00 4.08
3567 4965 2.634982 TGAATGCAAGAAACATCGCC 57.365 45.000 0.00 0.00 0.00 5.54
3764 5162 6.950041 TGATGAATTTCCTCAGGACTTTGATT 59.050 34.615 0.00 0.00 0.00 2.57
3773 5171 5.280215 CCTCAGGACTTTGATTGTAAGGACT 60.280 44.000 0.00 0.00 0.00 3.85
3792 5190 1.840635 CTGTAAGGGAAAGGGAGGAGG 59.159 57.143 0.00 0.00 0.00 4.30
3818 5216 1.134936 GCAGCATCCATGACATTGCAA 60.135 47.619 0.00 0.00 37.56 4.08
3878 5276 1.709147 CGCCGGAGCATTTGGAGAAG 61.709 60.000 5.05 0.00 39.83 2.85
3885 5283 0.179189 GCATTTGGAGAAGCCGTTCG 60.179 55.000 0.00 0.00 40.66 3.95
3907 5305 0.620556 TGTCCAATTCAGGAGAGGGC 59.379 55.000 0.00 0.00 38.64 5.19
4112 5510 6.389906 CGGAAAAGAATTTGGTAGCAGAAAT 58.610 36.000 0.00 0.00 39.02 2.17
4247 5645 0.255318 ATGCTCCCAGAGAAGCAAGG 59.745 55.000 0.69 0.00 40.82 3.61
4267 5665 2.821969 GGCAAGCTTGGGTATGATATGG 59.178 50.000 27.10 0.00 0.00 2.74
4281 5679 7.501559 GGGTATGATATGGTAGCGAGATAGTAA 59.498 40.741 0.00 0.00 0.00 2.24
4282 5680 9.069082 GGTATGATATGGTAGCGAGATAGTAAT 57.931 37.037 0.00 0.00 0.00 1.89
4615 6027 7.955750 AGTATATATTCCATTTTTCCAAGGGGG 59.044 37.037 0.00 0.00 38.37 5.40
4670 6082 0.170339 GCATTTGCCTTGGTACGGAC 59.830 55.000 0.00 0.00 34.31 4.79
4681 6093 1.447140 GTACGGACGCATCTGCCAA 60.447 57.895 0.00 0.00 37.91 4.52
4682 6094 0.810031 GTACGGACGCATCTGCCAAT 60.810 55.000 0.00 0.00 37.91 3.16
4683 6095 0.809636 TACGGACGCATCTGCCAATG 60.810 55.000 0.00 0.00 37.91 2.82
4684 6096 2.827051 CGGACGCATCTGCCAATGG 61.827 63.158 0.00 0.00 37.91 3.16
4694 6106 3.776158 GCCAATGGCTCACAACCA 58.224 55.556 18.47 0.00 46.69 3.67
4703 6115 2.754552 TGGCTCACAACCATTGATTAGC 59.245 45.455 0.00 1.67 34.71 3.09
4704 6116 2.223340 GGCTCACAACCATTGATTAGCG 60.223 50.000 0.00 0.00 35.57 4.26
4705 6117 2.420022 GCTCACAACCATTGATTAGCGT 59.580 45.455 0.00 0.00 0.00 5.07
4706 6118 3.728864 GCTCACAACCATTGATTAGCGTG 60.729 47.826 0.00 0.00 0.00 5.34
4707 6119 3.407698 TCACAACCATTGATTAGCGTGT 58.592 40.909 0.00 0.00 0.00 4.49
4708 6120 3.435327 TCACAACCATTGATTAGCGTGTC 59.565 43.478 0.00 0.00 0.00 3.67
4709 6121 2.415168 ACAACCATTGATTAGCGTGTCG 59.585 45.455 0.00 0.00 0.00 4.35
4710 6122 2.380084 ACCATTGATTAGCGTGTCGT 57.620 45.000 0.00 0.00 0.00 4.34
4711 6123 1.999735 ACCATTGATTAGCGTGTCGTG 59.000 47.619 0.00 0.00 0.00 4.35
4712 6124 1.999735 CCATTGATTAGCGTGTCGTGT 59.000 47.619 0.00 0.00 0.00 4.49
4713 6125 2.222796 CCATTGATTAGCGTGTCGTGTG 60.223 50.000 0.00 0.00 0.00 3.82
4714 6126 0.787787 TTGATTAGCGTGTCGTGTGC 59.212 50.000 0.00 0.00 0.00 4.57
4715 6127 0.319125 TGATTAGCGTGTCGTGTGCA 60.319 50.000 0.00 0.00 0.00 4.57
4716 6128 0.093026 GATTAGCGTGTCGTGTGCAC 59.907 55.000 10.75 10.75 0.00 4.57
4717 6129 0.598942 ATTAGCGTGTCGTGTGCACA 60.599 50.000 17.42 17.42 36.71 4.57
4718 6130 0.598942 TTAGCGTGTCGTGTGCACAT 60.599 50.000 24.69 6.69 36.71 3.21
4719 6131 1.006825 TAGCGTGTCGTGTGCACATC 61.007 55.000 24.69 16.44 36.71 3.06
4720 6132 2.465486 CGTGTCGTGTGCACATCG 59.535 61.111 24.69 25.36 36.71 3.84
4721 6133 2.853210 GTGTCGTGTGCACATCGG 59.147 61.111 28.68 19.92 36.88 4.18
4722 6134 2.356913 TGTCGTGTGCACATCGGG 60.357 61.111 28.68 17.96 0.00 5.14
4723 6135 3.788766 GTCGTGTGCACATCGGGC 61.789 66.667 28.68 21.45 0.00 6.13
4724 6136 4.306967 TCGTGTGCACATCGGGCA 62.307 61.111 28.68 15.42 39.32 5.36
4725 6137 3.792047 CGTGTGCACATCGGGCAG 61.792 66.667 24.69 5.13 42.85 4.85
4726 6138 2.669569 GTGTGCACATCGGGCAGT 60.670 61.111 24.69 0.00 42.85 4.40
4727 6139 1.375396 GTGTGCACATCGGGCAGTA 60.375 57.895 24.69 0.00 42.85 2.74
4728 6140 0.953471 GTGTGCACATCGGGCAGTAA 60.953 55.000 24.69 0.00 42.85 2.24
4729 6141 0.250510 TGTGCACATCGGGCAGTAAA 60.251 50.000 17.42 0.00 42.85 2.01
4730 6142 0.447801 GTGCACATCGGGCAGTAAAG 59.552 55.000 13.17 0.00 42.85 1.85
4731 6143 0.036164 TGCACATCGGGCAGTAAAGT 59.964 50.000 0.00 0.00 36.11 2.66
4732 6144 0.447801 GCACATCGGGCAGTAAAGTG 59.552 55.000 0.00 0.00 0.00 3.16
4733 6145 1.808411 CACATCGGGCAGTAAAGTGT 58.192 50.000 0.00 0.00 0.00 3.55
4734 6146 1.732259 CACATCGGGCAGTAAAGTGTC 59.268 52.381 0.00 0.00 0.00 3.67
4735 6147 0.999406 CATCGGGCAGTAAAGTGTCG 59.001 55.000 0.00 0.00 0.00 4.35
4736 6148 0.606604 ATCGGGCAGTAAAGTGTCGT 59.393 50.000 0.00 0.00 0.00 4.34
4737 6149 0.038892 TCGGGCAGTAAAGTGTCGTC 60.039 55.000 0.00 0.00 0.00 4.20
4738 6150 0.038526 CGGGCAGTAAAGTGTCGTCT 60.039 55.000 0.00 0.00 0.00 4.18
4739 6151 1.429463 GGGCAGTAAAGTGTCGTCTG 58.571 55.000 0.00 0.00 0.00 3.51
4740 6152 1.270147 GGGCAGTAAAGTGTCGTCTGT 60.270 52.381 0.00 0.00 0.00 3.41
4741 6153 2.029649 GGGCAGTAAAGTGTCGTCTGTA 60.030 50.000 0.00 0.00 0.00 2.74
4742 6154 2.985139 GGCAGTAAAGTGTCGTCTGTAC 59.015 50.000 0.00 0.00 0.00 2.90
4743 6155 3.551454 GGCAGTAAAGTGTCGTCTGTACA 60.551 47.826 0.00 0.00 32.31 2.90
4744 6156 3.669122 GCAGTAAAGTGTCGTCTGTACAG 59.331 47.826 17.17 17.17 32.31 2.74
4745 6157 4.792057 GCAGTAAAGTGTCGTCTGTACAGT 60.792 45.833 21.99 2.56 32.31 3.55
4746 6158 4.910456 CAGTAAAGTGTCGTCTGTACAGTC 59.090 45.833 21.99 15.74 32.31 3.51
4747 6159 4.577693 AGTAAAGTGTCGTCTGTACAGTCA 59.422 41.667 21.99 13.81 32.31 3.41
4748 6160 4.585955 AAAGTGTCGTCTGTACAGTCAT 57.414 40.909 21.99 0.90 30.21 3.06
4749 6161 4.585955 AAGTGTCGTCTGTACAGTCATT 57.414 40.909 21.99 11.16 30.21 2.57
4750 6162 4.585955 AGTGTCGTCTGTACAGTCATTT 57.414 40.909 21.99 7.98 0.00 2.32
4751 6163 4.547532 AGTGTCGTCTGTACAGTCATTTC 58.452 43.478 21.99 10.33 0.00 2.17
4752 6164 3.361053 GTGTCGTCTGTACAGTCATTTCG 59.639 47.826 21.99 16.23 0.00 3.46
4781 6193 1.159713 TCAGTGCAGCTGTGGAAACG 61.160 55.000 16.64 0.00 45.23 3.60
4783 6195 1.009675 GTGCAGCTGTGGAAACGTG 60.010 57.895 16.64 0.00 0.00 4.49
4784 6196 1.451207 TGCAGCTGTGGAAACGTGT 60.451 52.632 16.64 0.00 0.00 4.49
4792 6206 5.173131 CAGCTGTGGAAACGTGTTTTATTTC 59.827 40.000 5.25 0.00 32.11 2.17
4794 6208 5.746721 GCTGTGGAAACGTGTTTTATTTCTT 59.253 36.000 0.00 0.00 33.68 2.52
4795 6209 6.291585 GCTGTGGAAACGTGTTTTATTTCTTG 60.292 38.462 0.00 0.00 33.68 3.02
4812 6226 5.356882 TTCTTGTTTTTAGGACAGATGCG 57.643 39.130 0.00 0.00 0.00 4.73
4822 6236 2.819595 CAGATGCGTTCCCCCGTG 60.820 66.667 0.00 0.00 0.00 4.94
4830 6245 1.971695 GTTCCCCCGTGAGCCAAAG 60.972 63.158 0.00 0.00 0.00 2.77
4896 6321 1.126488 TCATCTCATCCAGGTCCAGC 58.874 55.000 0.00 0.00 0.00 4.85
4916 6341 2.879103 TGGGACAGTTCAAATCTCCC 57.121 50.000 0.00 0.00 36.52 4.30
5068 6504 2.677848 GCCTCCCCTTCCCAAGTC 59.322 66.667 0.00 0.00 0.00 3.01
5069 6505 2.231380 GCCTCCCCTTCCCAAGTCA 61.231 63.158 0.00 0.00 0.00 3.41
5070 6506 1.789576 GCCTCCCCTTCCCAAGTCAA 61.790 60.000 0.00 0.00 0.00 3.18
5071 6507 0.329596 CCTCCCCTTCCCAAGTCAAG 59.670 60.000 0.00 0.00 0.00 3.02
5072 6508 1.068121 CTCCCCTTCCCAAGTCAAGT 58.932 55.000 0.00 0.00 0.00 3.16
5108 6544 2.183046 GTCGAGCTGCTCCTGGTC 59.817 66.667 22.97 4.52 0.00 4.02
5117 6557 2.970639 CTCCTGGTCGCGAGGAAA 59.029 61.111 10.24 0.00 37.88 3.13
5151 6591 0.535797 GTTACTCCCGGTGGAAGGAG 59.464 60.000 0.00 4.52 41.17 3.69
5152 6592 0.616679 TTACTCCCGGTGGAAGGAGG 60.617 60.000 10.61 0.00 41.17 4.30
5153 6593 3.787001 CTCCCGGTGGAAGGAGGC 61.787 72.222 0.00 0.00 41.17 4.70
5219 6659 0.802494 GTGGTGGTAATTGCAGGTCG 59.198 55.000 0.00 0.00 0.00 4.79
5221 6661 1.338674 TGGTGGTAATTGCAGGTCGAG 60.339 52.381 0.00 0.00 0.00 4.04
5250 6690 0.247460 CTCCGCAGAGTCCATGTTCA 59.753 55.000 0.00 0.00 35.21 3.18
5251 6691 0.247460 TCCGCAGAGTCCATGTTCAG 59.753 55.000 0.00 0.00 0.00 3.02
5252 6692 0.036952 CCGCAGAGTCCATGTTCAGT 60.037 55.000 0.00 0.00 0.00 3.41
5253 6693 1.073964 CGCAGAGTCCATGTTCAGTG 58.926 55.000 0.00 0.00 0.00 3.66
5254 6694 1.446907 GCAGAGTCCATGTTCAGTGG 58.553 55.000 0.00 0.00 38.11 4.00
5255 6695 1.446907 CAGAGTCCATGTTCAGTGGC 58.553 55.000 0.00 0.00 36.66 5.01
5256 6696 0.326264 AGAGTCCATGTTCAGTGGCC 59.674 55.000 0.00 0.00 36.66 5.36
5257 6697 1.003355 AGTCCATGTTCAGTGGCCG 60.003 57.895 0.00 0.00 36.66 6.13
5258 6698 2.040544 GTCCATGTTCAGTGGCCGG 61.041 63.158 0.00 0.00 36.66 6.13
5259 6699 3.443045 CCATGTTCAGTGGCCGGC 61.443 66.667 21.18 21.18 0.00 6.13
5260 6700 2.360350 CATGTTCAGTGGCCGGCT 60.360 61.111 28.56 2.77 0.00 5.52
5261 6701 2.360350 ATGTTCAGTGGCCGGCTG 60.360 61.111 28.56 17.63 35.43 4.85
5262 6702 2.894257 ATGTTCAGTGGCCGGCTGA 61.894 57.895 28.56 19.92 40.76 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104487 TTCCCTCGCGTGTGTGTTAA 59.896 50.000 5.77 0.00 0.00 2.01
1 2 0.104487 TTTCCCTCGCGTGTGTGTTA 59.896 50.000 5.77 0.00 0.00 2.41
2 3 0.745128 TTTTCCCTCGCGTGTGTGTT 60.745 50.000 5.77 0.00 0.00 3.32
3 4 0.745128 TTTTTCCCTCGCGTGTGTGT 60.745 50.000 5.77 0.00 0.00 3.72
4 5 0.041312 CTTTTTCCCTCGCGTGTGTG 60.041 55.000 5.77 0.00 0.00 3.82
5 6 1.782028 GCTTTTTCCCTCGCGTGTGT 61.782 55.000 5.77 0.00 0.00 3.72
6 7 1.082104 GCTTTTTCCCTCGCGTGTG 60.082 57.895 5.77 0.00 0.00 3.82
7 8 2.604174 CGCTTTTTCCCTCGCGTGT 61.604 57.895 5.77 0.00 40.64 4.49
8 9 2.173382 CGCTTTTTCCCTCGCGTG 59.827 61.111 5.77 2.75 40.64 5.34
9 10 3.723348 GCGCTTTTTCCCTCGCGT 61.723 61.111 5.77 0.00 46.56 6.01
12 13 4.794241 CGCGCGCTTTTTCCCTCG 62.794 66.667 30.48 5.07 0.00 4.63
31 32 0.029300 AGATGTTTGTGTGCGTGTGC 59.971 50.000 0.00 0.00 43.20 4.57
32 33 2.032054 AGAAGATGTTTGTGTGCGTGTG 59.968 45.455 0.00 0.00 0.00 3.82
33 34 2.288666 AGAAGATGTTTGTGTGCGTGT 58.711 42.857 0.00 0.00 0.00 4.49
34 35 3.291585 GAAGAAGATGTTTGTGTGCGTG 58.708 45.455 0.00 0.00 0.00 5.34
35 36 2.290641 GGAAGAAGATGTTTGTGTGCGT 59.709 45.455 0.00 0.00 0.00 5.24
36 37 2.290367 TGGAAGAAGATGTTTGTGTGCG 59.710 45.455 0.00 0.00 0.00 5.34
37 38 3.854784 GCTGGAAGAAGATGTTTGTGTGC 60.855 47.826 0.00 0.00 34.07 4.57
38 39 3.304928 GGCTGGAAGAAGATGTTTGTGTG 60.305 47.826 0.00 0.00 34.07 3.82
39 40 2.887152 GGCTGGAAGAAGATGTTTGTGT 59.113 45.455 0.00 0.00 34.07 3.72
40 41 2.886523 TGGCTGGAAGAAGATGTTTGTG 59.113 45.455 0.00 0.00 34.07 3.33
41 42 3.152341 CTGGCTGGAAGAAGATGTTTGT 58.848 45.455 0.00 0.00 34.07 2.83
42 43 3.415212 TCTGGCTGGAAGAAGATGTTTG 58.585 45.455 0.00 0.00 34.07 2.93
43 44 3.795688 TCTGGCTGGAAGAAGATGTTT 57.204 42.857 0.00 0.00 34.07 2.83
44 45 5.441718 TTATCTGGCTGGAAGAAGATGTT 57.558 39.130 0.00 0.00 38.73 2.71
45 46 5.643421 ATTATCTGGCTGGAAGAAGATGT 57.357 39.130 0.00 0.00 38.73 3.06
46 47 5.826737 ACAATTATCTGGCTGGAAGAAGATG 59.173 40.000 0.00 0.00 38.73 2.90
47 48 6.011122 ACAATTATCTGGCTGGAAGAAGAT 57.989 37.500 0.00 0.00 40.57 2.40
48 49 5.441718 ACAATTATCTGGCTGGAAGAAGA 57.558 39.130 0.00 0.00 34.07 2.87
49 50 6.037610 GTGTACAATTATCTGGCTGGAAGAAG 59.962 42.308 0.00 0.00 34.07 2.85
50 51 5.880332 GTGTACAATTATCTGGCTGGAAGAA 59.120 40.000 0.00 0.00 34.07 2.52
51 52 5.428253 GTGTACAATTATCTGGCTGGAAGA 58.572 41.667 0.00 0.00 34.07 2.87
52 53 4.271049 CGTGTACAATTATCTGGCTGGAAG 59.729 45.833 0.00 0.00 0.00 3.46
53 54 4.188462 CGTGTACAATTATCTGGCTGGAA 58.812 43.478 0.00 0.00 0.00 3.53
54 55 3.792401 CGTGTACAATTATCTGGCTGGA 58.208 45.455 0.00 0.00 0.00 3.86
55 56 2.287915 GCGTGTACAATTATCTGGCTGG 59.712 50.000 0.00 0.00 0.00 4.85
56 57 3.198068 AGCGTGTACAATTATCTGGCTG 58.802 45.455 0.00 0.00 0.00 4.85
57 58 3.458189 GAGCGTGTACAATTATCTGGCT 58.542 45.455 0.00 0.00 0.00 4.75
58 59 2.544267 GGAGCGTGTACAATTATCTGGC 59.456 50.000 0.00 0.00 0.00 4.85
59 60 3.555956 GTGGAGCGTGTACAATTATCTGG 59.444 47.826 0.00 0.00 0.00 3.86
60 61 4.180817 TGTGGAGCGTGTACAATTATCTG 58.819 43.478 0.00 0.00 0.00 2.90
61 62 4.465632 TGTGGAGCGTGTACAATTATCT 57.534 40.909 0.00 0.00 0.00 1.98
62 63 5.107989 CGTATGTGGAGCGTGTACAATTATC 60.108 44.000 0.00 0.00 0.00 1.75
63 64 4.743151 CGTATGTGGAGCGTGTACAATTAT 59.257 41.667 0.00 0.00 0.00 1.28
64 65 4.106909 CGTATGTGGAGCGTGTACAATTA 58.893 43.478 0.00 0.00 0.00 1.40
65 66 2.927477 CGTATGTGGAGCGTGTACAATT 59.073 45.455 0.00 0.00 0.00 2.32
66 67 2.164827 TCGTATGTGGAGCGTGTACAAT 59.835 45.455 0.00 0.00 0.00 2.71
67 68 1.540707 TCGTATGTGGAGCGTGTACAA 59.459 47.619 0.00 0.00 0.00 2.41
68 69 1.135603 GTCGTATGTGGAGCGTGTACA 60.136 52.381 0.00 0.00 0.00 2.90
69 70 1.135603 TGTCGTATGTGGAGCGTGTAC 60.136 52.381 0.00 0.00 0.00 2.90
70 71 1.135603 GTGTCGTATGTGGAGCGTGTA 60.136 52.381 0.00 0.00 0.00 2.90
71 72 0.388134 GTGTCGTATGTGGAGCGTGT 60.388 55.000 0.00 0.00 0.00 4.49
72 73 0.388006 TGTGTCGTATGTGGAGCGTG 60.388 55.000 0.00 0.00 0.00 5.34
73 74 0.388134 GTGTGTCGTATGTGGAGCGT 60.388 55.000 0.00 0.00 0.00 5.07
74 75 1.403225 CGTGTGTCGTATGTGGAGCG 61.403 60.000 0.00 0.00 34.52 5.03
75 76 2.359792 CGTGTGTCGTATGTGGAGC 58.640 57.895 0.00 0.00 34.52 4.70
85 86 1.403225 CGATGGTAGCACGTGTGTCG 61.403 60.000 18.38 13.29 46.00 4.35
86 87 1.076533 CCGATGGTAGCACGTGTGTC 61.077 60.000 18.38 7.38 0.00 3.67
87 88 1.080093 CCGATGGTAGCACGTGTGT 60.080 57.895 18.38 7.62 0.00 3.72
88 89 2.452813 GCCGATGGTAGCACGTGTG 61.453 63.158 18.38 0.00 0.00 3.82
114 115 3.005554 CACCAGACCAGATGTTCATGTC 58.994 50.000 0.00 0.00 0.00 3.06
115 116 2.639347 TCACCAGACCAGATGTTCATGT 59.361 45.455 0.00 0.00 0.00 3.21
117 118 2.355513 GCTCACCAGACCAGATGTTCAT 60.356 50.000 0.00 0.00 0.00 2.57
125 126 1.154016 CGTACGCTCACCAGACCAG 60.154 63.158 0.52 0.00 0.00 4.00
154 155 2.954753 GCGACGTGACAAGCCAAGG 61.955 63.158 0.00 0.00 0.00 3.61
185 186 0.472471 TCCGTGAAAAGACCCTTGCT 59.528 50.000 0.00 0.00 0.00 3.91
186 187 0.875059 CTCCGTGAAAAGACCCTTGC 59.125 55.000 0.00 0.00 0.00 4.01
187 188 1.523758 CCTCCGTGAAAAGACCCTTG 58.476 55.000 0.00 0.00 0.00 3.61
188 189 0.250770 GCCTCCGTGAAAAGACCCTT 60.251 55.000 0.00 0.00 0.00 3.95
236 237 2.620112 CGGAAGGGCAAGTGCAGTG 61.620 63.158 5.52 0.00 44.36 3.66
254 255 0.041982 TATTTGGTTGGGGGAAGGCC 59.958 55.000 0.00 0.00 0.00 5.19
255 256 1.191535 GTATTTGGTTGGGGGAAGGC 58.808 55.000 0.00 0.00 0.00 4.35
256 257 2.225267 ACAGTATTTGGTTGGGGGAAGG 60.225 50.000 0.00 0.00 0.00 3.46
257 258 3.169512 ACAGTATTTGGTTGGGGGAAG 57.830 47.619 0.00 0.00 0.00 3.46
258 259 3.245336 GGTACAGTATTTGGTTGGGGGAA 60.245 47.826 0.00 0.00 0.00 3.97
259 260 2.309458 GGTACAGTATTTGGTTGGGGGA 59.691 50.000 0.00 0.00 0.00 4.81
260 261 2.041891 TGGTACAGTATTTGGTTGGGGG 59.958 50.000 0.00 0.00 0.00 5.40
261 262 3.443145 TGGTACAGTATTTGGTTGGGG 57.557 47.619 0.00 0.00 0.00 4.96
271 272 1.105457 TACGCGGCTTGGTACAGTAT 58.895 50.000 12.47 0.00 42.39 2.12
345 1315 3.670377 GGTTTGGTGCCCAGCGAC 61.670 66.667 0.00 0.00 33.81 5.19
670 2013 4.699522 GCGGGACAAAGCGGAGGT 62.700 66.667 0.00 0.00 44.60 3.85
718 2061 0.095417 GATCGTGTTCGCTTTGGCTC 59.905 55.000 0.00 0.00 36.96 4.70
719 2062 1.626654 CGATCGTGTTCGCTTTGGCT 61.627 55.000 7.03 0.00 36.96 4.75
787 2132 4.493747 ACCGCGCTCGTCTTAGCC 62.494 66.667 5.56 0.00 39.43 3.93
802 2147 3.366052 AATCTGATTACCACCACCACC 57.634 47.619 0.00 0.00 0.00 4.61
986 2340 4.247380 CCATGGCGGCTCTCCTCC 62.247 72.222 11.43 0.00 37.75 4.30
1074 2428 4.218852 TCCTCTTCTTCTTCTTCGTCTTCC 59.781 45.833 0.00 0.00 0.00 3.46
1077 2431 5.074115 TCTTCCTCTTCTTCTTCTTCGTCT 58.926 41.667 0.00 0.00 0.00 4.18
1078 2432 5.048294 ACTCTTCCTCTTCTTCTTCTTCGTC 60.048 44.000 0.00 0.00 0.00 4.20
1079 2433 4.830600 ACTCTTCCTCTTCTTCTTCTTCGT 59.169 41.667 0.00 0.00 0.00 3.85
1080 2434 5.385509 ACTCTTCCTCTTCTTCTTCTTCG 57.614 43.478 0.00 0.00 0.00 3.79
1081 2435 5.861787 CGAACTCTTCCTCTTCTTCTTCTTC 59.138 44.000 0.00 0.00 0.00 2.87
1082 2436 5.536916 TCGAACTCTTCCTCTTCTTCTTCTT 59.463 40.000 0.00 0.00 0.00 2.52
1083 2437 5.074115 TCGAACTCTTCCTCTTCTTCTTCT 58.926 41.667 0.00 0.00 0.00 2.85
1086 2440 3.761752 CCTCGAACTCTTCCTCTTCTTCT 59.238 47.826 0.00 0.00 0.00 2.85
1089 2443 3.352648 CTCCTCGAACTCTTCCTCTTCT 58.647 50.000 0.00 0.00 0.00 2.85
1335 2689 2.430244 CGGTCGAAGGTGACGTGG 60.430 66.667 0.00 0.00 39.83 4.94
1459 2813 8.547069 GCACAATTAATACTGCAACAAAGAAAA 58.453 29.630 10.88 0.00 0.00 2.29
1529 2883 7.957484 CACAAATTCACGAAAACTATACTCAGG 59.043 37.037 0.00 0.00 0.00 3.86
1602 2959 2.878406 GTGCTGACAAGTGCCTAGAAAA 59.122 45.455 0.00 0.00 0.00 2.29
1604 2961 1.416030 TGTGCTGACAAGTGCCTAGAA 59.584 47.619 0.00 0.00 0.00 2.10
1606 2963 1.532868 GTTGTGCTGACAAGTGCCTAG 59.467 52.381 0.00 0.00 42.87 3.02
1854 3223 3.616956 TGCATCAACTTAGTCAGGAGG 57.383 47.619 0.00 0.00 0.00 4.30
2004 3374 3.421844 AGGCACCACTTGTCCTATTTTC 58.578 45.455 0.00 0.00 31.97 2.29
2071 3441 3.763360 CACTCCTTGGCATGGATTAACAA 59.237 43.478 21.04 0.00 32.56 2.83
2157 3531 5.748402 TCTTCAGAATCATGGCAACTATGT 58.252 37.500 0.00 0.00 37.61 2.29
2264 3638 6.203723 GCTACGAAATCCAATAAAGAGCTCAT 59.796 38.462 17.77 0.00 0.00 2.90
2620 3994 6.471146 AGCAGAAAACATACAATCTGAGACT 58.529 36.000 5.85 0.00 41.38 3.24
2622 3996 6.531594 CGTAGCAGAAAACATACAATCTGAGA 59.468 38.462 5.85 0.00 41.38 3.27
2758 4132 2.034432 CCAAATACACTTGCACTGCACA 59.966 45.455 2.26 0.00 38.71 4.57
2848 4222 4.052159 AGATACAACTTCCTCTGCATCG 57.948 45.455 0.00 0.00 0.00 3.84
2918 4294 1.419387 GGCCTGAAGCTGGTATCTCAT 59.581 52.381 0.00 0.00 43.05 2.90
2922 4298 1.210478 TGAAGGCCTGAAGCTGGTATC 59.790 52.381 5.69 0.00 43.05 2.24
2935 4311 8.457261 CAGATATAAATAAGCATTCTGAAGGCC 58.543 37.037 21.81 0.00 39.39 5.19
2939 4315 9.565090 ACAGCAGATATAAATAAGCATTCTGAA 57.435 29.630 0.00 0.00 0.00 3.02
2962 4338 6.648192 AGATCCCTTCAATCTAAGAACACAG 58.352 40.000 0.00 0.00 31.71 3.66
3129 4505 6.635755 AGGTATCTCTTGAAGCTGAAAGTAC 58.364 40.000 8.16 4.71 35.30 2.73
3176 4556 1.270094 TGGTTCGCAGAGAAATCACGT 60.270 47.619 0.00 0.00 41.10 4.49
3234 4615 5.309323 TGCTCAAACTTAATGTGTATGGC 57.691 39.130 0.00 0.00 0.00 4.40
3289 4681 4.754618 TGTATATCAAAGTAGCCATTGCCG 59.245 41.667 0.00 0.00 38.69 5.69
3302 4694 9.186323 CACGAAAAATGGTTTGTGTATATCAAA 57.814 29.630 0.00 3.14 37.88 2.69
3326 4724 3.299340 AGGTCACGAACTGATGTACAC 57.701 47.619 0.00 0.00 0.00 2.90
3336 4734 1.132643 AGAGCACGATAGGTCACGAAC 59.867 52.381 0.00 0.00 43.77 3.95
3556 4954 3.652274 CAAAAACCATGGCGATGTTTCT 58.348 40.909 13.04 0.00 0.00 2.52
3567 4965 1.293924 TGTTTGGCGCAAAAACCATG 58.706 45.000 25.83 0.00 36.82 3.66
3764 5162 3.585732 CCCTTTCCCTTACAGTCCTTACA 59.414 47.826 0.00 0.00 0.00 2.41
3773 5171 1.966845 CCTCCTCCCTTTCCCTTACA 58.033 55.000 0.00 0.00 0.00 2.41
3792 5190 2.119029 TCATGGATGCTGCAGCTGC 61.119 57.895 36.61 31.89 42.66 5.25
3878 5276 0.454452 GAATTGGACAAGCGAACGGC 60.454 55.000 0.00 0.00 44.05 5.68
3885 5283 2.363683 CCTCTCCTGAATTGGACAAGC 58.636 52.381 0.00 0.00 31.94 4.01
3891 5289 1.153086 CGGCCCTCTCCTGAATTGG 60.153 63.158 0.00 0.00 0.00 3.16
3907 5305 2.462456 ATCAATCATCGGGTGATCGG 57.538 50.000 3.85 0.59 46.80 4.18
4112 5510 3.621805 TCGAACAAGCCCTCCGCA 61.622 61.111 0.00 0.00 41.38 5.69
4247 5645 3.490348 ACCATATCATACCCAAGCTTGC 58.510 45.455 21.43 0.00 0.00 4.01
4267 5665 6.456501 ACAATCCCAATTACTATCTCGCTAC 58.543 40.000 0.00 0.00 0.00 3.58
4281 5679 8.231007 TCCATTACCATTACATACAATCCCAAT 58.769 33.333 0.00 0.00 0.00 3.16
4282 5680 7.587258 TCCATTACCATTACATACAATCCCAA 58.413 34.615 0.00 0.00 0.00 4.12
4447 5846 2.617250 TGATGCAATCTTTCACACGC 57.383 45.000 0.00 0.00 45.81 5.34
4615 6027 1.094785 ACTGGCAATACCGAATGCAC 58.905 50.000 0.00 0.00 44.32 4.57
4646 6058 2.667481 CGTACCAAGGCAAATGCATTTG 59.333 45.455 36.80 36.80 42.92 2.32
4682 6094 2.754552 GCTAATCAATGGTTGTGAGCCA 59.245 45.455 0.00 0.00 40.68 4.75
4683 6095 2.223340 CGCTAATCAATGGTTGTGAGCC 60.223 50.000 0.00 0.00 31.66 4.70
4684 6096 2.420022 ACGCTAATCAATGGTTGTGAGC 59.580 45.455 0.00 0.00 0.00 4.26
4685 6097 3.436704 ACACGCTAATCAATGGTTGTGAG 59.563 43.478 2.77 0.00 0.00 3.51
4686 6098 3.407698 ACACGCTAATCAATGGTTGTGA 58.592 40.909 2.77 0.00 0.00 3.58
4687 6099 3.724716 CGACACGCTAATCAATGGTTGTG 60.725 47.826 0.00 0.00 0.00 3.33
4688 6100 2.415168 CGACACGCTAATCAATGGTTGT 59.585 45.455 0.00 0.00 0.00 3.32
4689 6101 2.415168 ACGACACGCTAATCAATGGTTG 59.585 45.455 0.00 0.00 0.00 3.77
4690 6102 2.415168 CACGACACGCTAATCAATGGTT 59.585 45.455 0.00 0.00 0.00 3.67
4691 6103 1.999735 CACGACACGCTAATCAATGGT 59.000 47.619 0.00 0.00 0.00 3.55
4692 6104 1.999735 ACACGACACGCTAATCAATGG 59.000 47.619 0.00 0.00 0.00 3.16
4693 6105 2.784327 GCACACGACACGCTAATCAATG 60.784 50.000 0.00 0.00 0.00 2.82
4694 6106 1.393539 GCACACGACACGCTAATCAAT 59.606 47.619 0.00 0.00 0.00 2.57
4695 6107 0.787787 GCACACGACACGCTAATCAA 59.212 50.000 0.00 0.00 0.00 2.57
4696 6108 0.319125 TGCACACGACACGCTAATCA 60.319 50.000 0.00 0.00 0.00 2.57
4697 6109 0.093026 GTGCACACGACACGCTAATC 59.907 55.000 13.17 0.00 0.00 1.75
4698 6110 0.598942 TGTGCACACGACACGCTAAT 60.599 50.000 17.42 0.00 41.03 1.73
4699 6111 0.598942 ATGTGCACACGACACGCTAA 60.599 50.000 24.37 0.00 41.03 3.09
4700 6112 1.006688 ATGTGCACACGACACGCTA 60.007 52.632 24.37 0.00 41.03 4.26
4701 6113 2.280119 ATGTGCACACGACACGCT 60.280 55.556 24.37 0.00 41.03 5.07
4702 6114 2.170985 GATGTGCACACGACACGC 59.829 61.111 24.37 1.97 41.03 5.34
4703 6115 2.465486 CGATGTGCACACGACACG 59.535 61.111 24.37 17.84 41.03 4.49
4704 6116 2.667318 CCCGATGTGCACACGACAC 61.667 63.158 30.26 16.88 38.55 3.67
4705 6117 2.356913 CCCGATGTGCACACGACA 60.357 61.111 30.26 9.50 0.00 4.35
4706 6118 3.788766 GCCCGATGTGCACACGAC 61.789 66.667 30.26 21.76 0.00 4.34
4707 6119 4.306967 TGCCCGATGTGCACACGA 62.307 61.111 30.26 16.04 32.85 4.35
4708 6120 3.792047 CTGCCCGATGTGCACACG 61.792 66.667 24.37 24.87 34.46 4.49
4709 6121 0.953471 TTACTGCCCGATGTGCACAC 60.953 55.000 24.37 14.98 34.46 3.82
4710 6122 0.250510 TTTACTGCCCGATGTGCACA 60.251 50.000 24.08 24.08 34.46 4.57
4711 6123 0.447801 CTTTACTGCCCGATGTGCAC 59.552 55.000 10.75 10.75 34.46 4.57
4712 6124 0.036164 ACTTTACTGCCCGATGTGCA 59.964 50.000 0.00 0.00 37.17 4.57
4713 6125 0.447801 CACTTTACTGCCCGATGTGC 59.552 55.000 0.00 0.00 0.00 4.57
4714 6126 1.732259 GACACTTTACTGCCCGATGTG 59.268 52.381 0.00 0.00 0.00 3.21
4715 6127 1.671850 CGACACTTTACTGCCCGATGT 60.672 52.381 0.00 0.00 0.00 3.06
4716 6128 0.999406 CGACACTTTACTGCCCGATG 59.001 55.000 0.00 0.00 0.00 3.84
4717 6129 0.606604 ACGACACTTTACTGCCCGAT 59.393 50.000 0.00 0.00 0.00 4.18
4718 6130 0.038892 GACGACACTTTACTGCCCGA 60.039 55.000 0.00 0.00 0.00 5.14
4719 6131 0.038526 AGACGACACTTTACTGCCCG 60.039 55.000 0.00 0.00 0.00 6.13
4720 6132 1.270147 ACAGACGACACTTTACTGCCC 60.270 52.381 0.00 0.00 32.67 5.36
4721 6133 2.150397 ACAGACGACACTTTACTGCC 57.850 50.000 0.00 0.00 32.67 4.85
4722 6134 3.635331 TGTACAGACGACACTTTACTGC 58.365 45.455 0.00 0.00 32.67 4.40
4723 6135 4.856664 ACTGTACAGACGACACTTTACTG 58.143 43.478 29.30 0.00 32.39 2.74
4724 6136 4.577693 TGACTGTACAGACGACACTTTACT 59.422 41.667 29.30 1.42 0.00 2.24
4725 6137 4.852138 TGACTGTACAGACGACACTTTAC 58.148 43.478 29.30 6.08 0.00 2.01
4726 6138 5.700722 ATGACTGTACAGACGACACTTTA 57.299 39.130 29.30 5.12 0.00 1.85
4727 6139 4.585955 ATGACTGTACAGACGACACTTT 57.414 40.909 29.30 3.01 0.00 2.66
4728 6140 4.585955 AATGACTGTACAGACGACACTT 57.414 40.909 29.30 3.81 0.00 3.16
4729 6141 4.547532 GAAATGACTGTACAGACGACACT 58.452 43.478 29.30 10.36 0.00 3.55
4730 6142 3.361053 CGAAATGACTGTACAGACGACAC 59.639 47.826 29.30 14.06 0.00 3.67
4731 6143 3.004002 ACGAAATGACTGTACAGACGACA 59.996 43.478 29.30 20.44 0.00 4.35
4732 6144 3.562505 ACGAAATGACTGTACAGACGAC 58.437 45.455 29.30 16.10 0.00 4.34
4733 6145 3.501062 AGACGAAATGACTGTACAGACGA 59.499 43.478 29.30 13.65 0.00 4.20
4734 6146 3.822996 AGACGAAATGACTGTACAGACG 58.177 45.455 29.30 21.73 0.00 4.18
4735 6147 5.049398 AGAGACGAAATGACTGTACAGAC 57.951 43.478 29.30 22.83 0.00 3.51
4736 6148 7.094334 ACAATAGAGACGAAATGACTGTACAGA 60.094 37.037 29.30 8.39 0.00 3.41
4737 6149 7.030165 ACAATAGAGACGAAATGACTGTACAG 58.970 38.462 21.44 21.44 0.00 2.74
4738 6150 6.920817 ACAATAGAGACGAAATGACTGTACA 58.079 36.000 0.00 0.00 0.00 2.90
4739 6151 7.027760 TGACAATAGAGACGAAATGACTGTAC 58.972 38.462 0.00 0.00 0.00 2.90
4740 6152 7.094334 ACTGACAATAGAGACGAAATGACTGTA 60.094 37.037 0.00 0.00 0.00 2.74
4741 6153 6.025749 TGACAATAGAGACGAAATGACTGT 57.974 37.500 0.00 0.00 0.00 3.55
4742 6154 6.034363 CACTGACAATAGAGACGAAATGACTG 59.966 42.308 0.00 0.00 0.00 3.51
4743 6155 6.096036 CACTGACAATAGAGACGAAATGACT 58.904 40.000 0.00 0.00 0.00 3.41
4744 6156 5.220303 GCACTGACAATAGAGACGAAATGAC 60.220 44.000 0.00 0.00 0.00 3.06
4745 6157 4.864806 GCACTGACAATAGAGACGAAATGA 59.135 41.667 0.00 0.00 0.00 2.57
4746 6158 4.627035 TGCACTGACAATAGAGACGAAATG 59.373 41.667 0.00 0.00 0.00 2.32
4747 6159 4.820897 TGCACTGACAATAGAGACGAAAT 58.179 39.130 0.00 0.00 0.00 2.17
4748 6160 4.237724 CTGCACTGACAATAGAGACGAAA 58.762 43.478 0.00 0.00 0.00 3.46
4749 6161 3.838120 CTGCACTGACAATAGAGACGAA 58.162 45.455 0.00 0.00 0.00 3.85
4750 6162 2.416027 GCTGCACTGACAATAGAGACGA 60.416 50.000 0.00 0.00 0.00 4.20
4751 6163 1.923204 GCTGCACTGACAATAGAGACG 59.077 52.381 0.00 0.00 0.00 4.18
4752 6164 3.244033 AGCTGCACTGACAATAGAGAC 57.756 47.619 1.02 0.00 0.00 3.36
4792 6206 4.749245 ACGCATCTGTCCTAAAAACAAG 57.251 40.909 0.00 0.00 0.00 3.16
4794 6208 3.500680 GGAACGCATCTGTCCTAAAAACA 59.499 43.478 0.00 0.00 0.00 2.83
4795 6209 3.119955 GGGAACGCATCTGTCCTAAAAAC 60.120 47.826 0.00 0.00 0.00 2.43
4802 6216 2.124695 GGGGGAACGCATCTGTCC 60.125 66.667 0.00 0.00 45.96 4.02
4812 6226 1.971695 CTTTGGCTCACGGGGGAAC 60.972 63.158 0.00 0.00 0.00 3.62
4822 6236 2.354199 GACATGCTAGCTTCTTTGGCTC 59.646 50.000 17.23 0.00 40.74 4.70
4826 6240 3.999001 TGTCAGACATGCTAGCTTCTTTG 59.001 43.478 17.23 9.23 0.00 2.77
4827 6242 4.252073 CTGTCAGACATGCTAGCTTCTTT 58.748 43.478 17.23 0.00 0.00 2.52
4830 6245 1.932511 GCTGTCAGACATGCTAGCTTC 59.067 52.381 17.23 9.66 34.34 3.86
4865 6290 5.818887 TGGATGAGATGATTTTCTGTTGGA 58.181 37.500 0.00 0.00 0.00 3.53
4896 6321 2.716217 GGGAGATTTGAACTGTCCCAG 58.284 52.381 12.12 0.00 45.58 4.45
4916 6341 2.740981 GTCATGTCTGACTGCTTCAAGG 59.259 50.000 9.51 0.00 46.84 3.61
4994 6430 5.679894 GCATATATCCCATCCTCGTACACTG 60.680 48.000 0.00 0.00 0.00 3.66
5068 6504 2.880890 CAAGGAGGAGGACAACAACTTG 59.119 50.000 0.00 0.00 0.00 3.16
5069 6505 2.158608 CCAAGGAGGAGGACAACAACTT 60.159 50.000 0.00 0.00 41.22 2.66
5070 6506 1.421646 CCAAGGAGGAGGACAACAACT 59.578 52.381 0.00 0.00 41.22 3.16
5071 6507 1.545651 CCCAAGGAGGAGGACAACAAC 60.546 57.143 0.00 0.00 41.22 3.32
5072 6508 0.771127 CCCAAGGAGGAGGACAACAA 59.229 55.000 0.00 0.00 41.22 2.83
5108 6544 1.437986 CTACCCCTCTTTCCTCGCG 59.562 63.158 0.00 0.00 0.00 5.87
5117 6557 3.367321 GAGTAACTTCAGCTACCCCTCT 58.633 50.000 0.00 0.00 0.00 3.69
5221 6661 2.232298 CTCTGCGGAGAGGTTGGACC 62.232 65.000 24.95 0.00 42.03 4.46


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

AutoCloner maintained by Alex Coulton.