Multiple sequence alignment - TraesCS7D01G534000

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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 TraesCS7D01G534000 chr7D 100.000 3775 0 0 1 3775 626907866 626911640 0.000000e+00 6972.0
1 TraesCS7D01G534000 chr7D 84.059 1079 134 17 1090 2146 626946358 626947420 0.000000e+00 1005.0
2 TraesCS7D01G534000 chr7D 85.380 855 109 11 1149 1991 627059172 627060022 0.000000e+00 872.0
3 TraesCS7D01G534000 chr7D 85.444 845 91 14 1149 1983 627071307 627072129 0.000000e+00 850.0
4 TraesCS7D01G534000 chr7D 81.343 938 123 28 1250 2172 626922876 626923776 0.000000e+00 715.0
5 TraesCS7D01G534000 chr7D 78.672 497 74 19 3298 3774 627074663 627075147 6.130000e-78 302.0
6 TraesCS7D01G534000 chr7D 76.179 424 60 20 3291 3682 627079717 627080131 6.440000e-43 185.0
7 TraesCS7D01G534000 chr7D 89.231 65 3 1 2537 2597 626902269 626902333 1.120000e-10 78.7
8 TraesCS7D01G534000 chr7D 88.462 52 6 0 3075 3126 191470783 191470834 3.150000e-06 63.9
9 TraesCS7D01G534000 chr7B 89.190 2692 196 40 1126 3774 727186293 727183654 0.000000e+00 3271.0
10 TraesCS7D01G534000 chr7B 87.611 1461 109 24 2172 3606 727326707 727325293 0.000000e+00 1629.0
11 TraesCS7D01G534000 chr7B 91.531 921 59 9 1114 2028 727392054 727392961 0.000000e+00 1251.0
12 TraesCS7D01G534000 chr7B 89.399 849 64 8 2885 3717 727393879 727394717 0.000000e+00 1046.0
13 TraesCS7D01G534000 chr7B 82.188 1106 157 18 1090 2179 727381764 727380683 0.000000e+00 915.0
14 TraesCS7D01G534000 chr7B 85.699 937 54 30 141 1053 727391166 727392046 0.000000e+00 915.0
15 TraesCS7D01G534000 chr7B 84.752 846 113 11 1149 1983 727654097 727653257 0.000000e+00 833.0
16 TraesCS7D01G534000 chr7B 80.528 1099 156 26 1090 2165 727397680 727398743 0.000000e+00 791.0
17 TraesCS7D01G534000 chr7B 85.714 749 77 12 1128 1866 727328251 727327523 0.000000e+00 763.0
18 TraesCS7D01G534000 chr7B 85.441 522 42 12 140 651 727186993 727186496 2.600000e-141 512.0
19 TraesCS7D01G534000 chr7B 84.861 502 46 13 2086 2584 727392978 727393452 2.640000e-131 479.0
20 TraesCS7D01G534000 chr7B 86.849 403 25 6 1862 2263 727327052 727326677 3.490000e-115 425.0
21 TraesCS7D01G534000 chr7B 79.441 501 75 14 3291 3774 727645807 727645318 2.810000e-86 329.0
22 TraesCS7D01G534000 chr7B 76.223 736 104 32 2170 2897 727409502 727410174 1.310000e-84 324.0
23 TraesCS7D01G534000 chr7B 84.277 318 39 7 2652 2960 727393475 727393790 2.200000e-77 300.0
24 TraesCS7D01G534000 chr7B 81.370 365 40 15 1825 2167 727683475 727683117 4.800000e-69 272.0
25 TraesCS7D01G534000 chr7B 78.886 431 66 12 3332 3745 727650397 727649975 6.220000e-68 268.0
26 TraesCS7D01G534000 chr7B 85.417 192 9 4 904 1081 727186474 727186288 8.330000e-42 182.0
27 TraesCS7D01G534000 chr7B 88.462 156 7 2 904 1048 727328414 727328259 1.080000e-40 178.0
28 TraesCS7D01G534000 chr7B 100.000 55 0 0 3720 3774 727394984 727395038 6.670000e-18 102.0
29 TraesCS7D01G534000 chr7B 97.619 42 1 0 4 45 283661961 283662002 5.230000e-09 73.1
30 TraesCS7D01G534000 chrUn 90.578 1072 65 14 1100 2167 83608218 83609257 0.000000e+00 1387.0
31 TraesCS7D01G534000 chrUn 83.078 981 129 13 1090 2051 83627391 83628353 0.000000e+00 857.0
32 TraesCS7D01G534000 chrUn 85.749 821 77 15 2978 3774 83610002 83610806 0.000000e+00 832.0
33 TraesCS7D01G534000 chrUn 88.950 543 48 12 129 662 83607321 83607860 0.000000e+00 660.0
34 TraesCS7D01G534000 chrUn 86.517 356 26 10 709 1053 83607864 83608208 4.610000e-99 372.0
35 TraesCS7D01G534000 chrUn 83.088 136 17 5 923 1053 83627258 83627392 6.620000e-23 119.0
36 TraesCS7D01G534000 chrUn 95.556 45 2 0 6 50 227963034 227963078 5.230000e-09 73.1
37 TraesCS7D01G534000 chr7A 79.129 1653 250 53 2170 3774 722415806 722417411 0.000000e+00 1053.0
38 TraesCS7D01G534000 chr7A 85.442 838 115 6 1149 1983 722482162 722482995 0.000000e+00 865.0
39 TraesCS7D01G534000 chr7A 82.231 1013 125 32 1167 2167 722414384 722415353 0.000000e+00 822.0
40 TraesCS7D01G534000 chr7A 83.502 691 97 9 1149 1828 722451455 722452139 2.470000e-176 628.0
41 TraesCS7D01G534000 chr7A 77.440 461 78 15 3299 3742 722580142 722580593 6.260000e-63 252.0
42 TraesCS7D01G534000 chr7A 77.698 139 17 12 3340 3470 722591067 722591199 5.230000e-09 73.1
43 TraesCS7D01G534000 chr6B 97.619 42 1 0 4 45 69552852 69552811 5.230000e-09 73.1
44 TraesCS7D01G534000 chr6B 95.455 44 2 0 4 47 450801885 450801928 1.880000e-08 71.3
45 TraesCS7D01G534000 chr3B 95.556 45 2 0 1 45 805611211 805611167 5.230000e-09 73.1
46 TraesCS7D01G534000 chr1D 90.909 55 4 1 1 54 481715009 481715063 5.230000e-09 73.1
47 TraesCS7D01G534000 chr1A 93.750 48 3 0 1 48 255846676 255846723 5.230000e-09 73.1
48 TraesCS7D01G534000 chr2B 93.617 47 3 0 3 49 61584615 61584569 1.880000e-08 71.3
49 TraesCS7D01G534000 chr1B 95.455 44 2 0 2 45 108556747 108556790 1.880000e-08 71.3


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 TraesCS7D01G534000 chr7D 626907866 626911640 3774 False 6972.000000 6972 100.000000 1 3775 1 chr7D.!!$F3 3774
1 TraesCS7D01G534000 chr7D 626946358 626947420 1062 False 1005.000000 1005 84.059000 1090 2146 1 chr7D.!!$F5 1056
2 TraesCS7D01G534000 chr7D 627059172 627060022 850 False 872.000000 872 85.380000 1149 1991 1 chr7D.!!$F6 842
3 TraesCS7D01G534000 chr7D 626922876 626923776 900 False 715.000000 715 81.343000 1250 2172 1 chr7D.!!$F4 922
4 TraesCS7D01G534000 chr7D 627071307 627075147 3840 False 576.000000 850 82.058000 1149 3774 2 chr7D.!!$F8 2625
5 TraesCS7D01G534000 chr7B 727183654 727186993 3339 True 1321.666667 3271 86.682667 140 3774 3 chr7B.!!$R4 3634
6 TraesCS7D01G534000 chr7B 727380683 727381764 1081 True 915.000000 915 82.188000 1090 2179 1 chr7B.!!$R1 1089
7 TraesCS7D01G534000 chr7B 727325293 727328414 3121 True 748.750000 1629 87.159000 904 3606 4 chr7B.!!$R5 2702
8 TraesCS7D01G534000 chr7B 727391166 727398743 7577 False 697.714286 1251 88.042143 141 3774 7 chr7B.!!$F3 3633
9 TraesCS7D01G534000 chr7B 727649975 727654097 4122 True 550.500000 833 81.819000 1149 3745 2 chr7B.!!$R6 2596
10 TraesCS7D01G534000 chr7B 727409502 727410174 672 False 324.000000 324 76.223000 2170 2897 1 chr7B.!!$F2 727
11 TraesCS7D01G534000 chrUn 83607321 83610806 3485 False 812.750000 1387 87.948500 129 3774 4 chrUn.!!$F2 3645
12 TraesCS7D01G534000 chrUn 83627258 83628353 1095 False 488.000000 857 83.083000 923 2051 2 chrUn.!!$F3 1128
13 TraesCS7D01G534000 chr7A 722414384 722417411 3027 False 937.500000 1053 80.680000 1167 3774 2 chr7A.!!$F5 2607
14 TraesCS7D01G534000 chr7A 722482162 722482995 833 False 865.000000 865 85.442000 1149 1983 1 chr7A.!!$F2 834
15 TraesCS7D01G534000 chr7A 722451455 722452139 684 False 628.000000 628 83.502000 1149 1828 1 chr7A.!!$F1 679

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
706 728 0.037697 GCGTCACACCACAGGTCATA 60.038 55.0 0.0 0.0 31.02 2.15 F
1081 1139 0.516877 TTTTCTCACGCATCTTGCCG 59.483 50.0 0.0 0.0 41.12 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2641 1.194547 CGCGCTGTGTAGTGACAAATT 59.805 47.619 5.56 0.0 37.31 1.82 R
2960 4979 0.388659 TGTGGCATGTGTTTTGGCTC 59.611 50.000 0.00 0.0 40.12 4.70 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
18 19 1.789116 TGTAAAAATCGACGGGCGC 59.211 52.632 0.00 0.00 40.61 6.53
19 20 1.296360 GTAAAAATCGACGGGCGCG 60.296 57.895 22.69 22.69 40.61 6.86
20 21 2.454464 TAAAAATCGACGGGCGCGG 61.454 57.895 27.52 10.61 40.61 6.46
38 39 4.892379 CAACGCGCGCCATCATGG 62.892 66.667 32.58 12.27 41.55 3.66
42 43 2.280119 GCGCGCCATCATGGTCTA 60.280 61.111 23.24 0.00 40.46 2.59
43 44 2.313172 GCGCGCCATCATGGTCTAG 61.313 63.158 23.24 0.00 40.46 2.43
44 45 1.068083 CGCGCCATCATGGTCTAGT 59.932 57.895 5.31 0.00 40.46 2.57
45 46 1.217585 CGCGCCATCATGGTCTAGTG 61.218 60.000 5.31 0.00 40.46 2.74
46 47 0.179073 GCGCCATCATGGTCTAGTGT 60.179 55.000 5.31 0.00 40.46 3.55
47 48 1.743772 GCGCCATCATGGTCTAGTGTT 60.744 52.381 5.31 0.00 40.46 3.32
48 49 2.205074 CGCCATCATGGTCTAGTGTTC 58.795 52.381 5.31 0.00 40.46 3.18
49 50 2.159043 CGCCATCATGGTCTAGTGTTCT 60.159 50.000 5.31 0.00 40.46 3.01
50 51 3.462021 GCCATCATGGTCTAGTGTTCTC 58.538 50.000 5.31 0.00 40.46 2.87
51 52 3.133721 GCCATCATGGTCTAGTGTTCTCT 59.866 47.826 5.31 0.00 40.46 3.10
52 53 4.342378 GCCATCATGGTCTAGTGTTCTCTA 59.658 45.833 5.31 0.00 40.46 2.43
53 54 5.163405 GCCATCATGGTCTAGTGTTCTCTAA 60.163 44.000 5.31 0.00 40.46 2.10
54 55 6.511416 CCATCATGGTCTAGTGTTCTCTAAG 58.489 44.000 0.00 0.00 31.35 2.18
55 56 6.322456 CCATCATGGTCTAGTGTTCTCTAAGA 59.678 42.308 0.00 0.00 31.35 2.10
56 57 6.761099 TCATGGTCTAGTGTTCTCTAAGAC 57.239 41.667 0.00 0.00 0.00 3.01
57 58 5.652891 TCATGGTCTAGTGTTCTCTAAGACC 59.347 44.000 11.91 11.91 37.94 3.85
58 59 4.008330 TGGTCTAGTGTTCTCTAAGACCG 58.992 47.826 13.49 0.00 38.93 4.79
59 60 3.181498 GGTCTAGTGTTCTCTAAGACCGC 60.181 52.174 4.21 0.00 33.38 5.68
60 61 2.676839 TCTAGTGTTCTCTAAGACCGCG 59.323 50.000 0.00 0.00 29.18 6.46
61 62 0.109226 AGTGTTCTCTAAGACCGCGC 60.109 55.000 0.00 0.00 29.18 6.86
62 63 0.388134 GTGTTCTCTAAGACCGCGCA 60.388 55.000 8.75 0.00 0.00 6.09
63 64 0.388134 TGTTCTCTAAGACCGCGCAC 60.388 55.000 8.75 0.00 0.00 5.34
64 65 1.077089 GTTCTCTAAGACCGCGCACC 61.077 60.000 8.75 0.00 0.00 5.01
65 66 1.248785 TTCTCTAAGACCGCGCACCT 61.249 55.000 8.75 0.00 0.00 4.00
66 67 1.226717 CTCTAAGACCGCGCACCTC 60.227 63.158 8.75 0.00 0.00 3.85
67 68 2.202756 CTAAGACCGCGCACCTCC 60.203 66.667 8.75 0.00 0.00 4.30
68 69 2.992689 TAAGACCGCGCACCTCCA 60.993 61.111 8.75 0.00 0.00 3.86
69 70 2.501223 CTAAGACCGCGCACCTCCAA 62.501 60.000 8.75 0.00 0.00 3.53
70 71 2.775032 TAAGACCGCGCACCTCCAAC 62.775 60.000 8.75 0.00 0.00 3.77
76 77 3.357079 CGCACCTCCAACCTGCAC 61.357 66.667 0.00 0.00 0.00 4.57
77 78 2.985847 GCACCTCCAACCTGCACC 60.986 66.667 0.00 0.00 0.00 5.01
78 79 2.515398 CACCTCCAACCTGCACCA 59.485 61.111 0.00 0.00 0.00 4.17
79 80 1.152777 CACCTCCAACCTGCACCAA 60.153 57.895 0.00 0.00 0.00 3.67
80 81 0.540365 CACCTCCAACCTGCACCAAT 60.540 55.000 0.00 0.00 0.00 3.16
81 82 0.251341 ACCTCCAACCTGCACCAATC 60.251 55.000 0.00 0.00 0.00 2.67
82 83 0.251297 CCTCCAACCTGCACCAATCA 60.251 55.000 0.00 0.00 0.00 2.57
83 84 1.619654 CTCCAACCTGCACCAATCAA 58.380 50.000 0.00 0.00 0.00 2.57
84 85 1.270550 CTCCAACCTGCACCAATCAAC 59.729 52.381 0.00 0.00 0.00 3.18
85 86 0.318120 CCAACCTGCACCAATCAACC 59.682 55.000 0.00 0.00 0.00 3.77
86 87 0.318120 CAACCTGCACCAATCAACCC 59.682 55.000 0.00 0.00 0.00 4.11
87 88 0.188342 AACCTGCACCAATCAACCCT 59.812 50.000 0.00 0.00 0.00 4.34
88 89 0.251341 ACCTGCACCAATCAACCCTC 60.251 55.000 0.00 0.00 0.00 4.30
89 90 0.038744 CCTGCACCAATCAACCCTCT 59.961 55.000 0.00 0.00 0.00 3.69
90 91 1.548582 CCTGCACCAATCAACCCTCTT 60.549 52.381 0.00 0.00 0.00 2.85
91 92 1.815003 CTGCACCAATCAACCCTCTTC 59.185 52.381 0.00 0.00 0.00 2.87
92 93 1.177401 GCACCAATCAACCCTCTTCC 58.823 55.000 0.00 0.00 0.00 3.46
93 94 1.272147 GCACCAATCAACCCTCTTCCT 60.272 52.381 0.00 0.00 0.00 3.36
94 95 2.716217 CACCAATCAACCCTCTTCCTC 58.284 52.381 0.00 0.00 0.00 3.71
95 96 1.279271 ACCAATCAACCCTCTTCCTCG 59.721 52.381 0.00 0.00 0.00 4.63
96 97 1.373570 CAATCAACCCTCTTCCTCGC 58.626 55.000 0.00 0.00 0.00 5.03
97 98 0.253327 AATCAACCCTCTTCCTCGCC 59.747 55.000 0.00 0.00 0.00 5.54
98 99 0.618968 ATCAACCCTCTTCCTCGCCT 60.619 55.000 0.00 0.00 0.00 5.52
99 100 1.219393 CAACCCTCTTCCTCGCCTC 59.781 63.158 0.00 0.00 0.00 4.70
100 101 1.990614 AACCCTCTTCCTCGCCTCC 60.991 63.158 0.00 0.00 0.00 4.30
101 102 3.532155 CCCTCTTCCTCGCCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
102 103 4.214327 CCTCTTCCTCGCCTCCGC 62.214 72.222 0.00 0.00 0.00 5.54
112 113 3.130227 GCCTCCGCGGTTCTATCT 58.870 61.111 27.15 0.00 34.25 1.98
113 114 2.338381 GCCTCCGCGGTTCTATCTA 58.662 57.895 27.15 1.04 34.25 1.98
114 115 0.672342 GCCTCCGCGGTTCTATCTAA 59.328 55.000 27.15 0.17 34.25 2.10
115 116 1.336056 GCCTCCGCGGTTCTATCTAAG 60.336 57.143 27.15 11.53 34.25 2.18
116 117 2.228059 CCTCCGCGGTTCTATCTAAGA 58.772 52.381 27.15 0.00 0.00 2.10
117 118 2.030981 CCTCCGCGGTTCTATCTAAGAC 60.031 54.545 27.15 0.00 32.51 3.01
118 119 1.600957 TCCGCGGTTCTATCTAAGACG 59.399 52.381 27.15 0.00 32.51 4.18
119 120 1.332997 CCGCGGTTCTATCTAAGACGT 59.667 52.381 19.50 0.00 32.51 4.34
120 121 2.601741 CCGCGGTTCTATCTAAGACGTC 60.602 54.545 19.50 7.70 32.51 4.34
121 122 2.637595 GCGGTTCTATCTAAGACGTCG 58.362 52.381 10.46 0.00 32.51 5.12
122 123 2.031437 GCGGTTCTATCTAAGACGTCGT 59.969 50.000 10.46 9.92 32.51 4.34
123 124 3.246226 GCGGTTCTATCTAAGACGTCGTA 59.754 47.826 10.46 10.64 32.51 3.43
124 125 4.608000 GCGGTTCTATCTAAGACGTCGTAG 60.608 50.000 26.54 26.54 32.51 3.51
125 126 4.608000 CGGTTCTATCTAAGACGTCGTAGC 60.608 50.000 27.32 15.33 32.51 3.58
126 127 4.511082 GGTTCTATCTAAGACGTCGTAGCT 59.489 45.833 27.32 22.08 32.51 3.32
127 128 5.333263 GGTTCTATCTAAGACGTCGTAGCTC 60.333 48.000 27.32 15.23 32.51 4.09
135 136 1.648756 CGTCGTAGCTCTCTTCGCG 60.649 63.158 0.00 0.00 33.83 5.87
143 144 3.916392 CTCTCTTCGCGGGCGTTGT 62.916 63.158 13.21 0.00 40.74 3.32
154 156 2.188161 GGCGTTGTTCCCGTTTCCA 61.188 57.895 0.00 0.00 0.00 3.53
184 186 4.408182 AATAATCAAGTGACGGGAGAGG 57.592 45.455 0.00 0.00 0.00 3.69
197 199 1.073923 GGGAGAGGAACTTTCAGCCAA 59.926 52.381 0.00 0.00 41.85 4.52
218 221 5.508825 CCAACTAGGTTTAGCAAACATGCAA 60.509 40.000 11.93 0.00 43.15 4.08
239 247 1.171549 TCATGCATGTGGTGTGCGTT 61.172 50.000 25.43 0.00 45.37 4.84
262 272 0.389948 CCTCTCCCTGAACGAAACGG 60.390 60.000 0.00 0.00 0.00 4.44
267 277 0.317519 CCCTGAACGAAACGGCAAAC 60.318 55.000 0.00 0.00 0.00 2.93
358 368 1.524482 GAGTGCTCATCCCTCCCAC 59.476 63.158 0.00 0.00 0.00 4.61
420 433 3.063045 GTGCCTACGTACACCAAAATAGC 59.937 47.826 5.27 0.00 0.00 2.97
557 579 2.359848 CCAACGGTAGATCGTGGATGTA 59.640 50.000 0.00 0.00 43.07 2.29
586 608 0.899720 CTGCATTGTCCTGCCCAATT 59.100 50.000 0.00 0.00 41.58 2.32
616 638 8.727910 CATCTTCCATTACTCCAATCATATGTG 58.272 37.037 1.90 0.00 0.00 3.21
682 704 2.888513 TCGAGTACGAGCTGTTGTAC 57.111 50.000 10.90 10.90 43.81 2.90
683 705 1.127397 TCGAGTACGAGCTGTTGTACG 59.873 52.381 12.35 2.46 45.23 3.67
684 706 1.136141 CGAGTACGAGCTGTTGTACGT 60.136 52.381 12.35 7.72 45.23 3.57
706 728 0.037697 GCGTCACACCACAGGTCATA 60.038 55.000 0.00 0.00 31.02 2.15
723 749 8.144478 ACAGGTCATATATACACACATCTTGAC 58.856 37.037 0.00 0.00 0.00 3.18
730 756 0.943835 CACACATCTTGACCGTGCGA 60.944 55.000 0.00 0.00 33.89 5.10
769 795 1.758514 CCTGGGCTAGCTCCTCGAA 60.759 63.158 13.26 0.00 0.00 3.71
796 822 5.487433 CAACATGACACCTAATCCACACTA 58.513 41.667 0.00 0.00 0.00 2.74
798 824 3.861276 TGACACCTAATCCACACTACG 57.139 47.619 0.00 0.00 0.00 3.51
828 860 2.124570 ATGCACGGAGATGGTGGC 60.125 61.111 0.00 0.00 35.94 5.01
835 867 2.894387 GAGATGGTGGCTCGCTGC 60.894 66.667 0.00 0.00 41.94 5.25
846 878 3.599792 CTCGCTGCCGTTGCTTTGG 62.600 63.158 0.00 0.00 38.71 3.28
872 904 5.521010 ACGTACGTTGAGATTTGACTTTGAA 59.479 36.000 16.72 0.00 0.00 2.69
878 910 5.437289 TGAGATTTGACTTTGAACGCATT 57.563 34.783 0.00 0.00 0.00 3.56
879 911 5.214417 TGAGATTTGACTTTGAACGCATTG 58.786 37.500 0.00 0.00 0.00 2.82
902 941 4.475135 GCGGCAACCTCCTCCTCC 62.475 72.222 0.00 0.00 0.00 4.30
1053 1111 6.551975 AGTTCTCACATCTCATCTCATCTCAT 59.448 38.462 0.00 0.00 0.00 2.90
1054 1112 6.578163 TCTCACATCTCATCTCATCTCATC 57.422 41.667 0.00 0.00 0.00 2.92
1055 1113 6.308566 TCTCACATCTCATCTCATCTCATCT 58.691 40.000 0.00 0.00 0.00 2.90
1056 1114 6.431852 TCTCACATCTCATCTCATCTCATCTC 59.568 42.308 0.00 0.00 0.00 2.75
1057 1115 6.069331 TCACATCTCATCTCATCTCATCTCA 58.931 40.000 0.00 0.00 0.00 3.27
1063 1121 6.834969 TCTCATCTCATCTCATCTCAGTTCTT 59.165 38.462 0.00 0.00 0.00 2.52
1069 1127 7.178097 TCTCATCTCATCTCAGTTCTTTTCTCA 59.822 37.037 0.00 0.00 0.00 3.27
1075 1133 3.990469 TCTCAGTTCTTTTCTCACGCATC 59.010 43.478 0.00 0.00 0.00 3.91
1076 1134 3.993081 CTCAGTTCTTTTCTCACGCATCT 59.007 43.478 0.00 0.00 0.00 2.90
1077 1135 4.380531 TCAGTTCTTTTCTCACGCATCTT 58.619 39.130 0.00 0.00 0.00 2.40
1078 1136 4.212004 TCAGTTCTTTTCTCACGCATCTTG 59.788 41.667 0.00 0.00 0.00 3.02
1079 1137 3.058639 AGTTCTTTTCTCACGCATCTTGC 60.059 43.478 0.00 0.00 40.69 4.01
1080 1138 1.806542 TCTTTTCTCACGCATCTTGCC 59.193 47.619 0.00 0.00 41.12 4.52
1081 1139 0.516877 TTTTCTCACGCATCTTGCCG 59.483 50.000 0.00 0.00 41.12 5.69
1082 1140 1.911293 TTTCTCACGCATCTTGCCGC 61.911 55.000 0.00 0.00 41.12 6.53
1083 1141 3.120385 CTCACGCATCTTGCCGCA 61.120 61.111 0.00 0.00 41.12 5.69
1084 1142 3.372676 CTCACGCATCTTGCCGCAC 62.373 63.158 0.00 0.00 41.12 5.34
1085 1143 4.465512 CACGCATCTTGCCGCACC 62.466 66.667 0.00 0.00 41.12 5.01
1086 1144 4.704833 ACGCATCTTGCCGCACCT 62.705 61.111 0.00 0.00 41.12 4.00
1087 1145 2.511373 CGCATCTTGCCGCACCTA 60.511 61.111 0.00 0.00 41.12 3.08
1088 1146 2.813179 CGCATCTTGCCGCACCTAC 61.813 63.158 0.00 0.00 41.12 3.18
1469 1541 4.214327 GCCTTCCTCCTCCTCGCG 62.214 72.222 0.00 0.00 0.00 5.87
1610 1683 2.202676 GCAGAGAAGGACCTCGCG 60.203 66.667 0.00 0.00 38.19 5.87
1780 1853 2.261671 GTCCATGTCGTCTGCGGT 59.738 61.111 0.00 0.00 38.89 5.68
2065 2641 7.973388 GCTAAACCATGTATGTTTTGCTGATTA 59.027 33.333 18.04 0.00 36.46 1.75
2082 2659 6.024049 GCTGATTAATTTGTCACTACACAGC 58.976 40.000 0.00 0.00 38.07 4.40
2084 2661 2.969443 AATTTGTCACTACACAGCGC 57.031 45.000 0.00 0.00 34.61 5.92
2187 3330 8.874156 TGAATAATACTCAGAGCAATATGTCCT 58.126 33.333 0.00 0.00 0.00 3.85
2312 3517 6.524101 ACCATAATCGCCAAATTAACAAGT 57.476 33.333 0.00 0.00 0.00 3.16
2320 3531 8.880878 ATCGCCAAATTAACAAGTTTACTTTT 57.119 26.923 0.00 0.00 33.11 2.27
2321 3532 8.121167 TCGCCAAATTAACAAGTTTACTTTTG 57.879 30.769 0.00 0.00 33.11 2.44
2362 3574 3.592059 GATCCTAACTTACGCACACCAA 58.408 45.455 0.00 0.00 0.00 3.67
2364 3576 4.010667 TCCTAACTTACGCACACCAATT 57.989 40.909 0.00 0.00 0.00 2.32
2378 3597 5.408299 GCACACCAATTTTCTCCCATAAAAC 59.592 40.000 0.00 0.00 0.00 2.43
2597 3830 0.807496 CCAAAGCAAGCCAGTCTAGC 59.193 55.000 0.00 0.00 0.00 3.42
2600 3833 0.676151 AAGCAAGCCAGTCTAGCAGC 60.676 55.000 0.00 0.00 34.82 5.25
2602 3835 0.176680 GCAAGCCAGTCTAGCAGCTA 59.823 55.000 1.13 1.13 34.49 3.32
2603 3836 1.805871 GCAAGCCAGTCTAGCAGCTAG 60.806 57.143 21.97 21.97 34.49 3.42
2630 3863 5.625656 GCTCTAGTCATGCTAGGTTTCTTGT 60.626 44.000 18.22 0.00 45.55 3.16
2650 3883 7.441017 TCTTGTTTTTGTATGGAGGGAAATTG 58.559 34.615 0.00 0.00 0.00 2.32
2724 4330 6.697455 ACTGATCATATTGTACGTGTGATGAC 59.303 38.462 12.77 3.63 29.14 3.06
2762 4606 9.345517 CATTGTCCATAACACAACTGAAATTAG 57.654 33.333 0.00 0.00 37.70 1.73
2776 4620 6.314917 ACTGAAATTAGGACAAGGTTCCAAT 58.685 36.000 0.00 0.00 38.25 3.16
2777 4628 7.466804 ACTGAAATTAGGACAAGGTTCCAATA 58.533 34.615 0.00 0.00 38.25 1.90
2831 4683 0.952010 TTGCCCGACTTTAGCGAACC 60.952 55.000 0.00 0.00 0.00 3.62
2832 4684 2.104859 GCCCGACTTTAGCGAACCC 61.105 63.158 0.00 0.00 0.00 4.11
2840 4692 0.529378 TTTAGCGAACCCGAGACCTC 59.471 55.000 0.00 0.00 38.22 3.85
2848 4700 5.174120 CGAACCCGAGACCTCAAGGTTTA 62.174 52.174 17.39 0.00 42.48 2.01
2909 4764 6.603201 ACTTGAAACAAATTCTCAGAAGGACA 59.397 34.615 0.00 0.00 38.92 4.02
2930 4949 1.462731 GCTCAATGCCAACACACCCA 61.463 55.000 0.00 0.00 35.15 4.51
2941 4960 1.611519 ACACACCCAATACAAACCCG 58.388 50.000 0.00 0.00 0.00 5.28
2960 4979 2.421424 CCGAAAAGATCCTTGGCTCAAG 59.579 50.000 7.69 7.69 40.75 3.02
3069 5353 0.462047 CGCCGGAGCTTTTGGTAGAT 60.462 55.000 5.05 0.00 36.60 1.98
3117 5401 4.397417 GGTCTTGCTGAGTTGCTTGAATAT 59.603 41.667 0.00 0.00 0.00 1.28
3145 5429 8.531982 TGTAAGAACATAGTCATCTTGTAGCTT 58.468 33.333 0.00 0.00 35.22 3.74
3167 5451 3.753272 TGTCCAGCAGCAGAATTCTTAAC 59.247 43.478 4.86 0.00 0.00 2.01
3199 6150 6.097554 TCTCTAGTTGATGAGTGAAGATTCCC 59.902 42.308 0.00 0.00 0.00 3.97
3200 6151 4.916041 AGTTGATGAGTGAAGATTCCCA 57.084 40.909 0.00 0.00 0.00 4.37
3255 6214 4.141274 CCACCCATCACATAATACCTCCAA 60.141 45.833 0.00 0.00 0.00 3.53
3283 6242 4.624452 GGATAGAACTTTAGTTGCGTCGTT 59.376 41.667 0.00 0.00 38.56 3.85
3293 6271 2.202440 GCGTCGTTGCTAGCGAGA 60.202 61.111 10.77 6.37 39.14 4.04
3301 6279 3.057736 TCGTTGCTAGCGAGAACTAAGTT 60.058 43.478 10.77 0.00 34.11 2.66
3408 6398 4.913335 TCTATTGACTGTCCATACGTCC 57.087 45.455 5.17 0.00 32.02 4.79
3431 6421 0.109723 TGCCCTAATATTGTCGGCCC 59.890 55.000 15.62 0.00 38.92 5.80
3606 6619 1.804601 AGCGTTTTAGTGGCAGTACC 58.195 50.000 0.44 0.00 39.84 3.34
3608 6621 1.463444 GCGTTTTAGTGGCAGTACCTG 59.537 52.381 0.44 0.00 40.22 4.00
3774 7080 7.989741 ACTTGATCAAGCTAAGCATGTACTATT 59.010 33.333 30.95 6.43 41.99 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.789116 GCGCCCGTCGATTTTTACA 59.211 52.632 0.00 0.00 41.67 2.41
1 2 1.296360 CGCGCCCGTCGATTTTTAC 60.296 57.895 0.00 0.00 41.67 2.01
2 3 2.454464 CCGCGCCCGTCGATTTTTA 61.454 57.895 0.00 0.00 41.67 1.52
3 4 3.795342 CCGCGCCCGTCGATTTTT 61.795 61.111 0.00 0.00 41.67 1.94
21 22 4.892379 CCATGATGGCGCGCGTTG 62.892 66.667 32.35 16.50 0.00 4.10
25 26 2.280119 TAGACCATGATGGCGCGC 60.280 61.111 25.94 25.94 42.67 6.86
26 27 1.068083 ACTAGACCATGATGGCGCG 59.932 57.895 12.25 0.00 42.67 6.86
27 28 0.179073 ACACTAGACCATGATGGCGC 60.179 55.000 12.25 0.00 42.67 6.53
28 29 2.159043 AGAACACTAGACCATGATGGCG 60.159 50.000 12.25 0.18 42.67 5.69
29 30 3.133721 AGAGAACACTAGACCATGATGGC 59.866 47.826 12.25 4.53 42.67 4.40
30 31 6.322456 TCTTAGAGAACACTAGACCATGATGG 59.678 42.308 10.53 10.53 45.02 3.51
31 32 7.199766 GTCTTAGAGAACACTAGACCATGATG 58.800 42.308 0.00 0.00 0.00 3.07
32 33 6.322712 GGTCTTAGAGAACACTAGACCATGAT 59.677 42.308 13.22 0.00 38.69 2.45
33 34 5.652891 GGTCTTAGAGAACACTAGACCATGA 59.347 44.000 13.22 0.00 38.69 3.07
34 35 5.449314 CGGTCTTAGAGAACACTAGACCATG 60.449 48.000 17.01 1.51 38.72 3.66
35 36 4.641094 CGGTCTTAGAGAACACTAGACCAT 59.359 45.833 17.01 0.00 38.72 3.55
36 37 4.008330 CGGTCTTAGAGAACACTAGACCA 58.992 47.826 17.01 0.00 38.72 4.02
37 38 3.181498 GCGGTCTTAGAGAACACTAGACC 60.181 52.174 9.06 9.06 37.34 3.85
38 39 3.485546 CGCGGTCTTAGAGAACACTAGAC 60.486 52.174 0.00 0.00 29.18 2.59
39 40 2.676839 CGCGGTCTTAGAGAACACTAGA 59.323 50.000 0.00 0.00 29.18 2.43
40 41 2.791849 GCGCGGTCTTAGAGAACACTAG 60.792 54.545 8.83 0.00 29.18 2.57
41 42 1.131883 GCGCGGTCTTAGAGAACACTA 59.868 52.381 8.83 0.00 29.18 2.74
42 43 0.109226 GCGCGGTCTTAGAGAACACT 60.109 55.000 8.83 0.00 29.18 3.55
43 44 0.388134 TGCGCGGTCTTAGAGAACAC 60.388 55.000 8.83 0.00 29.18 3.32
44 45 0.388134 GTGCGCGGTCTTAGAGAACA 60.388 55.000 8.83 0.00 29.18 3.18
45 46 1.077089 GGTGCGCGGTCTTAGAGAAC 61.077 60.000 8.83 0.00 0.00 3.01
46 47 1.214589 GGTGCGCGGTCTTAGAGAA 59.785 57.895 8.83 0.00 0.00 2.87
47 48 1.654954 GAGGTGCGCGGTCTTAGAGA 61.655 60.000 8.83 0.00 0.00 3.10
48 49 1.226717 GAGGTGCGCGGTCTTAGAG 60.227 63.158 8.83 0.00 0.00 2.43
49 50 2.707849 GGAGGTGCGCGGTCTTAGA 61.708 63.158 8.83 0.00 0.00 2.10
50 51 2.202756 GGAGGTGCGCGGTCTTAG 60.203 66.667 8.83 0.00 0.00 2.18
51 52 2.575893 TTGGAGGTGCGCGGTCTTA 61.576 57.895 8.83 0.00 0.00 2.10
52 53 3.936203 TTGGAGGTGCGCGGTCTT 61.936 61.111 8.83 0.00 0.00 3.01
53 54 4.681978 GTTGGAGGTGCGCGGTCT 62.682 66.667 8.83 0.00 0.00 3.85
59 60 3.357079 GTGCAGGTTGGAGGTGCG 61.357 66.667 0.00 0.00 40.23 5.34
60 61 2.985847 GGTGCAGGTTGGAGGTGC 60.986 66.667 0.00 0.00 37.73 5.01
61 62 0.540365 ATTGGTGCAGGTTGGAGGTG 60.540 55.000 0.00 0.00 0.00 4.00
62 63 0.251341 GATTGGTGCAGGTTGGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
63 64 0.251297 TGATTGGTGCAGGTTGGAGG 60.251 55.000 0.00 0.00 0.00 4.30
64 65 1.270550 GTTGATTGGTGCAGGTTGGAG 59.729 52.381 0.00 0.00 0.00 3.86
65 66 1.327303 GTTGATTGGTGCAGGTTGGA 58.673 50.000 0.00 0.00 0.00 3.53
66 67 0.318120 GGTTGATTGGTGCAGGTTGG 59.682 55.000 0.00 0.00 0.00 3.77
67 68 0.318120 GGGTTGATTGGTGCAGGTTG 59.682 55.000 0.00 0.00 0.00 3.77
68 69 0.188342 AGGGTTGATTGGTGCAGGTT 59.812 50.000 0.00 0.00 0.00 3.50
69 70 0.251341 GAGGGTTGATTGGTGCAGGT 60.251 55.000 0.00 0.00 0.00 4.00
70 71 0.038744 AGAGGGTTGATTGGTGCAGG 59.961 55.000 0.00 0.00 0.00 4.85
71 72 1.815003 GAAGAGGGTTGATTGGTGCAG 59.185 52.381 0.00 0.00 0.00 4.41
72 73 1.547675 GGAAGAGGGTTGATTGGTGCA 60.548 52.381 0.00 0.00 0.00 4.57
73 74 1.177401 GGAAGAGGGTTGATTGGTGC 58.823 55.000 0.00 0.00 0.00 5.01
74 75 2.716217 GAGGAAGAGGGTTGATTGGTG 58.284 52.381 0.00 0.00 0.00 4.17
75 76 1.279271 CGAGGAAGAGGGTTGATTGGT 59.721 52.381 0.00 0.00 0.00 3.67
76 77 2.014068 GCGAGGAAGAGGGTTGATTGG 61.014 57.143 0.00 0.00 0.00 3.16
77 78 1.373570 GCGAGGAAGAGGGTTGATTG 58.626 55.000 0.00 0.00 0.00 2.67
78 79 0.253327 GGCGAGGAAGAGGGTTGATT 59.747 55.000 0.00 0.00 0.00 2.57
79 80 0.618968 AGGCGAGGAAGAGGGTTGAT 60.619 55.000 0.00 0.00 0.00 2.57
80 81 1.229209 AGGCGAGGAAGAGGGTTGA 60.229 57.895 0.00 0.00 0.00 3.18
81 82 1.219393 GAGGCGAGGAAGAGGGTTG 59.781 63.158 0.00 0.00 0.00 3.77
82 83 1.990614 GGAGGCGAGGAAGAGGGTT 60.991 63.158 0.00 0.00 0.00 4.11
83 84 2.364448 GGAGGCGAGGAAGAGGGT 60.364 66.667 0.00 0.00 0.00 4.34
84 85 3.532155 CGGAGGCGAGGAAGAGGG 61.532 72.222 0.00 0.00 0.00 4.30
85 86 4.214327 GCGGAGGCGAGGAAGAGG 62.214 72.222 0.00 0.00 0.00 3.69
95 96 0.672342 TTAGATAGAACCGCGGAGGC 59.328 55.000 35.90 19.96 46.52 4.70
97 98 2.349627 CGTCTTAGATAGAACCGCGGAG 60.350 54.545 35.90 15.71 33.81 4.63
98 99 1.600957 CGTCTTAGATAGAACCGCGGA 59.399 52.381 35.90 10.13 33.81 5.54
99 100 1.332997 ACGTCTTAGATAGAACCGCGG 59.667 52.381 26.86 26.86 33.81 6.46
100 101 2.637595 GACGTCTTAGATAGAACCGCG 58.362 52.381 8.70 0.00 33.81 6.46
101 102 2.031437 ACGACGTCTTAGATAGAACCGC 59.969 50.000 14.70 0.00 33.81 5.68
102 103 3.940657 ACGACGTCTTAGATAGAACCG 57.059 47.619 14.70 0.00 33.81 4.44
103 104 4.511082 AGCTACGACGTCTTAGATAGAACC 59.489 45.833 27.74 11.51 33.81 3.62
104 105 5.463061 AGAGCTACGACGTCTTAGATAGAAC 59.537 44.000 27.74 12.83 33.81 3.01
105 106 5.599732 AGAGCTACGACGTCTTAGATAGAA 58.400 41.667 27.74 0.00 33.81 2.10
106 107 5.009911 AGAGAGCTACGACGTCTTAGATAGA 59.990 44.000 27.74 0.00 0.00 1.98
107 108 5.224888 AGAGAGCTACGACGTCTTAGATAG 58.775 45.833 27.74 15.21 0.00 2.08
108 109 5.199024 AGAGAGCTACGACGTCTTAGATA 57.801 43.478 27.74 6.70 0.00 1.98
109 110 4.062677 AGAGAGCTACGACGTCTTAGAT 57.937 45.455 27.74 23.39 0.00 1.98
110 111 3.523606 AGAGAGCTACGACGTCTTAGA 57.476 47.619 27.74 4.60 0.00 2.10
111 112 3.301963 CGAAGAGAGCTACGACGTCTTAG 60.302 52.174 21.35 21.35 0.00 2.18
112 113 2.602211 CGAAGAGAGCTACGACGTCTTA 59.398 50.000 14.70 7.86 0.00 2.10
113 114 1.394227 CGAAGAGAGCTACGACGTCTT 59.606 52.381 14.70 6.93 0.00 3.01
114 115 1.000884 CGAAGAGAGCTACGACGTCT 58.999 55.000 14.70 0.00 0.00 4.18
115 116 0.586995 GCGAAGAGAGCTACGACGTC 60.587 60.000 2.43 5.18 0.00 4.34
116 117 1.424635 GCGAAGAGAGCTACGACGT 59.575 57.895 5.52 5.52 0.00 4.34
117 118 1.648756 CGCGAAGAGAGCTACGACG 60.649 63.158 0.00 0.00 0.00 5.12
118 119 1.297745 CCGCGAAGAGAGCTACGAC 60.298 63.158 8.23 0.00 0.00 4.34
119 120 2.470362 CCCGCGAAGAGAGCTACGA 61.470 63.158 8.23 0.00 0.00 3.43
120 121 2.024871 CCCGCGAAGAGAGCTACG 59.975 66.667 8.23 0.00 0.00 3.51
121 122 2.278923 GCCCGCGAAGAGAGCTAC 60.279 66.667 8.23 0.00 0.00 3.58
122 123 3.889044 CGCCCGCGAAGAGAGCTA 61.889 66.667 8.23 0.00 42.83 3.32
125 126 3.181967 CAACGCCCGCGAAGAGAG 61.182 66.667 17.16 0.00 42.83 3.20
126 127 3.509137 AACAACGCCCGCGAAGAGA 62.509 57.895 17.16 0.00 42.83 3.10
127 128 3.011760 GAACAACGCCCGCGAAGAG 62.012 63.158 17.16 2.40 42.83 2.85
135 136 2.640989 GAAACGGGAACAACGCCC 59.359 61.111 0.00 0.00 42.41 6.13
143 144 0.250553 AACGATGCTGGAAACGGGAA 60.251 50.000 0.00 0.00 41.93 3.97
154 156 5.234329 CCGTCACTTGATTATTAACGATGCT 59.766 40.000 0.00 0.00 0.00 3.79
184 186 5.334957 GCTAAACCTAGTTGGCTGAAAGTTC 60.335 44.000 0.00 0.00 40.22 3.01
218 221 1.579964 CGCACACCACATGCATGAGT 61.580 55.000 32.75 24.21 43.57 3.41
239 247 3.473625 GTTTCGTTCAGGGAGAGGAAAA 58.526 45.455 0.00 0.00 34.44 2.29
262 272 5.743872 GGGAGACATGAAATATTTCGTTTGC 59.256 40.000 18.33 12.76 40.01 3.68
267 277 6.683974 AGTTGGGAGACATGAAATATTTCG 57.316 37.500 20.45 11.43 40.01 3.46
269 279 6.211184 TGCAAGTTGGGAGACATGAAATATTT 59.789 34.615 4.75 0.00 0.00 1.40
273 283 3.499338 TGCAAGTTGGGAGACATGAAAT 58.501 40.909 4.75 0.00 0.00 2.17
275 285 2.622942 GTTGCAAGTTGGGAGACATGAA 59.377 45.455 0.00 0.00 0.00 2.57
557 579 1.841663 GACAATGCAGCGGAACACGT 61.842 55.000 0.00 0.00 46.52 4.49
586 608 7.675161 TGATTGGAGTAATGGAAGATGACTA 57.325 36.000 0.00 0.00 0.00 2.59
643 665 1.827969 AGCTAGACTGGCACTGTTAGG 59.172 52.381 13.78 0.00 41.64 2.69
647 669 0.609406 TCGAGCTAGACTGGCACTGT 60.609 55.000 13.78 0.00 45.09 3.55
695 717 6.997655 AGATGTGTGTATATATGACCTGTGG 58.002 40.000 0.00 0.00 0.00 4.17
706 728 4.119862 GCACGGTCAAGATGTGTGTATAT 58.880 43.478 7.09 0.00 36.04 0.86
730 756 1.898094 TTGGACATGCTTGCACGCT 60.898 52.632 16.80 0.00 0.00 5.07
755 781 2.798364 GGGGTTCGAGGAGCTAGCC 61.798 68.421 12.13 2.59 0.00 3.93
769 795 2.025321 GGATTAGGTGTCATGTTGGGGT 60.025 50.000 0.00 0.00 0.00 4.95
828 860 2.127118 CAAAGCAACGGCAGCGAG 60.127 61.111 0.00 0.00 44.61 5.03
846 878 2.729882 AGTCAAATCTCAACGTACGTGC 59.270 45.455 23.57 0.00 0.00 5.34
847 879 4.966850 AAGTCAAATCTCAACGTACGTG 57.033 40.909 23.57 15.75 0.00 4.49
848 880 5.045215 TCAAAGTCAAATCTCAACGTACGT 58.955 37.500 16.72 16.72 0.00 3.57
849 881 5.570262 TCAAAGTCAAATCTCAACGTACG 57.430 39.130 15.01 15.01 0.00 3.67
884 916 4.821589 GAGGAGGAGGTTGCCGCG 62.822 72.222 0.00 0.00 0.00 6.46
885 917 4.475135 GGAGGAGGAGGTTGCCGC 62.475 72.222 0.00 0.00 0.00 6.53
985 1031 3.589951 ATATGCAATGCAAGGAGGAGT 57.410 42.857 13.45 0.00 43.62 3.85
1053 1111 3.452755 TGCGTGAGAAAAGAACTGAGA 57.547 42.857 0.00 0.00 0.00 3.27
1054 1112 3.993081 AGATGCGTGAGAAAAGAACTGAG 59.007 43.478 0.00 0.00 0.00 3.35
1055 1113 3.995199 AGATGCGTGAGAAAAGAACTGA 58.005 40.909 0.00 0.00 0.00 3.41
1056 1114 4.461405 CAAGATGCGTGAGAAAAGAACTG 58.539 43.478 0.00 0.00 0.00 3.16
1057 1115 3.058639 GCAAGATGCGTGAGAAAAGAACT 60.059 43.478 0.00 0.00 31.71 3.01
1063 1121 1.911293 GCGGCAAGATGCGTGAGAAA 61.911 55.000 0.00 0.00 46.21 2.52
1069 1127 3.309436 TAGGTGCGGCAAGATGCGT 62.309 57.895 3.23 0.00 46.21 5.24
1075 1133 3.127533 GCTGGTAGGTGCGGCAAG 61.128 66.667 3.23 0.00 0.00 4.01
1076 1134 3.483788 TTGCTGGTAGGTGCGGCAA 62.484 57.895 3.23 0.00 39.99 4.52
1077 1135 3.947459 TTGCTGGTAGGTGCGGCA 61.947 61.111 0.00 0.00 0.00 5.69
1078 1136 3.431725 GTTGCTGGTAGGTGCGGC 61.432 66.667 0.00 0.00 0.00 6.53
1079 1137 1.169661 TTTGTTGCTGGTAGGTGCGG 61.170 55.000 0.00 0.00 0.00 5.69
1080 1138 0.040425 GTTTGTTGCTGGTAGGTGCG 60.040 55.000 0.00 0.00 0.00 5.34
1081 1139 1.028905 TGTTTGTTGCTGGTAGGTGC 58.971 50.000 0.00 0.00 0.00 5.01
1082 1140 2.020720 TGTGTTTGTTGCTGGTAGGTG 58.979 47.619 0.00 0.00 0.00 4.00
1083 1141 2.428544 TGTGTTTGTTGCTGGTAGGT 57.571 45.000 0.00 0.00 0.00 3.08
1084 1142 3.380004 TCTTTGTGTTTGTTGCTGGTAGG 59.620 43.478 0.00 0.00 0.00 3.18
1085 1143 4.498009 CCTCTTTGTGTTTGTTGCTGGTAG 60.498 45.833 0.00 0.00 0.00 3.18
1086 1144 3.380004 CCTCTTTGTGTTTGTTGCTGGTA 59.620 43.478 0.00 0.00 0.00 3.25
1087 1145 2.166254 CCTCTTTGTGTTTGTTGCTGGT 59.834 45.455 0.00 0.00 0.00 4.00
1088 1146 2.426738 TCCTCTTTGTGTTTGTTGCTGG 59.573 45.455 0.00 0.00 0.00 4.85
1154 1213 4.324991 GACCGGCCGAAGTTGGGT 62.325 66.667 30.73 14.54 0.00 4.51
1580 1653 3.306595 CTCTGCTCTGCGCTGGGAA 62.307 63.158 19.39 6.49 40.21 3.97
2043 2615 9.723601 AAATTAATCAGCAAAACATACATGGTT 57.276 25.926 0.00 0.00 39.91 3.67
2053 2625 8.690840 GTGTAGTGACAAATTAATCAGCAAAAC 58.309 33.333 0.00 0.00 37.31 2.43
2065 2641 1.194547 CGCGCTGTGTAGTGACAAATT 59.805 47.619 5.56 0.00 37.31 1.82
2123 2701 5.009010 AGGTCTGAACAAGTGTAGCAAAATG 59.991 40.000 0.00 0.00 0.00 2.32
2187 3330 2.146342 GCAAGTGCTTCACAAGAGCTA 58.854 47.619 0.00 0.00 36.74 3.32
2290 3495 7.826260 AAACTTGTTAATTTGGCGATTATGG 57.174 32.000 0.00 0.00 0.00 2.74
2312 3517 8.842358 AACGACTGAATAGATCCAAAAGTAAA 57.158 30.769 0.00 0.00 0.00 2.01
2349 3561 3.365969 GGGAGAAAATTGGTGTGCGTAAG 60.366 47.826 0.00 0.00 43.44 2.34
2362 3574 5.773176 ACTGTTCGGTTTTATGGGAGAAAAT 59.227 36.000 0.00 0.00 0.00 1.82
2364 3576 4.721132 ACTGTTCGGTTTTATGGGAGAAA 58.279 39.130 0.00 0.00 0.00 2.52
2378 3597 6.307800 CCAAGTTGCATATTTTAACTGTTCGG 59.692 38.462 0.00 0.00 35.06 4.30
2630 3863 5.604650 ACCACAATTTCCCTCCATACAAAAA 59.395 36.000 0.00 0.00 0.00 1.94
2724 4330 1.247567 GGACAATGTTCACCACAGGG 58.752 55.000 0.00 0.00 39.40 4.45
2840 4692 6.400568 TCGAACTAGGGTATGTTAAACCTTG 58.599 40.000 0.00 0.00 37.18 3.61
2848 4700 6.732896 ATTCTCATCGAACTAGGGTATGTT 57.267 37.500 0.00 0.00 33.72 2.71
2897 4752 2.015456 TTGAGCCTGTCCTTCTGAGA 57.985 50.000 0.00 0.00 0.00 3.27
2930 4949 5.185056 CCAAGGATCTTTTCGGGTTTGTATT 59.815 40.000 0.00 0.00 0.00 1.89
2941 4960 3.128415 GCTCTTGAGCCAAGGATCTTTTC 59.872 47.826 11.24 0.00 41.33 2.29
2960 4979 0.388659 TGTGGCATGTGTTTTGGCTC 59.611 50.000 0.00 0.00 40.12 4.70
3034 5318 4.251760 CGACACGCTTCAGCTCTT 57.748 55.556 0.00 0.00 39.32 2.85
3051 5335 1.017387 CATCTACCAAAAGCTCCGGC 58.983 55.000 0.00 0.00 39.06 6.13
3052 5336 2.691409 TCATCTACCAAAAGCTCCGG 57.309 50.000 0.00 0.00 0.00 5.14
3069 5353 6.168389 CAGGAATCATCGACCATTGATATCA 58.832 40.000 0.00 0.00 32.40 2.15
3117 5401 9.151471 GCTACAAGATGACTATGTTCTTACAAA 57.849 33.333 0.00 0.00 37.91 2.83
3145 5429 2.574006 AAGAATTCTGCTGCTGGACA 57.426 45.000 9.17 0.00 0.00 4.02
3167 5451 9.823098 CTTCACTCATCAACTAGAGAATTTTTG 57.177 33.333 0.00 0.00 35.83 2.44
3199 6150 2.823829 GCGTTGGGAGCGGCTATTG 61.824 63.158 0.60 0.00 0.00 1.90
3200 6151 2.513897 GCGTTGGGAGCGGCTATT 60.514 61.111 0.60 0.00 0.00 1.73
3229 6187 4.307259 AGGTATTATGTGATGGGTGGTCT 58.693 43.478 0.00 0.00 0.00 3.85
3230 6188 4.505039 GGAGGTATTATGTGATGGGTGGTC 60.505 50.000 0.00 0.00 0.00 4.02
3231 6189 3.394606 GGAGGTATTATGTGATGGGTGGT 59.605 47.826 0.00 0.00 0.00 4.16
3233 6192 4.705110 TGGAGGTATTATGTGATGGGTG 57.295 45.455 0.00 0.00 0.00 4.61
3255 6214 4.677250 CGCAACTAAAGTTCTATCCCTCGT 60.677 45.833 0.00 0.00 35.83 4.18
3265 6224 2.033151 AGCAACGACGCAACTAAAGTTC 60.033 45.455 0.00 0.00 35.83 3.01
3283 6242 2.745821 TCGAACTTAGTTCTCGCTAGCA 59.254 45.455 20.87 0.92 40.05 3.49
3293 6271 4.514066 GTGTGGAAACCATCGAACTTAGTT 59.486 41.667 0.00 0.00 35.28 2.24
3355 6336 4.090090 CAAGTCTTCTCTTCACCCCTCTA 58.910 47.826 0.00 0.00 0.00 2.43
3408 6398 3.243401 GGCCGACAATATTAGGGCAAAAG 60.243 47.826 19.36 0.00 46.93 2.27
3431 6421 3.520290 TGATTAGCTGTAAGACCCACG 57.480 47.619 0.00 0.00 34.07 4.94
3608 6621 8.070769 GTTCATTAACTAGCTTAATTAGCCAGC 58.929 37.037 0.00 0.17 41.68 4.85
3609 6622 9.331282 AGTTCATTAACTAGCTTAATTAGCCAG 57.669 33.333 0.00 0.00 44.26 4.85
3617 6630 8.504005 GCAACTTGAGTTCATTAACTAGCTTAA 58.496 33.333 0.00 0.00 46.09 1.85
3618 6631 7.148639 CGCAACTTGAGTTCATTAACTAGCTTA 60.149 37.037 0.00 0.00 46.09 3.09
3619 6632 6.347725 CGCAACTTGAGTTCATTAACTAGCTT 60.348 38.462 0.00 0.00 46.09 3.74
3620 6633 5.120830 CGCAACTTGAGTTCATTAACTAGCT 59.879 40.000 0.00 0.00 46.09 3.32


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

AutoCloner maintained by Alex Coulton.