Multiple sequence alignment - TraesCS1A01G239500

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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 TraesCS1A01G239500 chr1A 100.000 4696 0 0 1 4696 426877445 426872750 0.000000e+00 8672
1 TraesCS1A01G239500 chr1D 87.076 2476 201 52 2283 4696 329668062 329665644 0.000000e+00 2689
2 TraesCS1A01G239500 chr1D 94.638 1492 61 7 677 2160 329669940 329668460 0.000000e+00 2294
3 TraesCS1A01G239500 chr1D 90.433 554 26 4 122 661 329671411 329670871 0.000000e+00 704
4 TraesCS1A01G239500 chr1B 92.975 1580 75 10 677 2232 444671277 444669710 0.000000e+00 2270
5 TraesCS1A01G239500 chr1B 87.882 1634 121 30 2287 3865 444669627 444668016 0.000000e+00 1849
6 TraesCS1A01G239500 chr1B 88.221 832 78 9 3869 4696 444667930 444667115 0.000000e+00 976
7 TraesCS1A01G239500 chr1B 90.391 562 27 4 124 671 444673064 444672516 0.000000e+00 713
8 TraesCS1A01G239500 chr2A 87.104 1295 148 14 810 2094 19949092 19947807 0.000000e+00 1448
9 TraesCS1A01G239500 chr2A 81.900 884 109 26 2983 3830 19944852 19943984 0.000000e+00 699
10 TraesCS1A01G239500 chr2D 86.692 1300 153 14 801 2094 19045668 19046953 0.000000e+00 1424
11 TraesCS1A01G239500 chr2D 86.057 1291 168 8 812 2094 18763315 18762029 0.000000e+00 1376
12 TraesCS1A01G239500 chr2D 79.094 861 125 23 2984 3804 18756602 18755757 4.130000e-150 542
13 TraesCS1A01G239500 chr2D 79.665 418 75 5 4113 4528 18755673 18755264 4.600000e-75 292
14 TraesCS1A01G239500 chr2D 83.240 179 28 2 2642 2820 18757403 18757227 3.760000e-36 163
15 TraesCS1A01G239500 chr4A 84.103 1277 166 20 813 2085 589787466 589788709 0.000000e+00 1199
16 TraesCS1A01G239500 chr4A 84.073 766 112 5 1324 2088 589781454 589780698 0.000000e+00 730
17 TraesCS1A01G239500 chr4A 80.272 882 122 28 2986 3832 589790120 589790984 6.680000e-173 617
18 TraesCS1A01G239500 chr4A 79.887 885 119 34 2986 3832 589845187 589846050 1.130000e-165 593
19 TraesCS1A01G239500 chr4A 77.597 616 89 25 3250 3832 589778858 589778259 1.260000e-85 327
20 TraesCS1A01G239500 chr4A 74.194 527 80 39 2314 2820 589844575 589845065 8.080000e-38 169
21 TraesCS1A01G239500 chr4D 83.346 1285 181 17 809 2088 12662113 12660857 0.000000e+00 1157
22 TraesCS1A01G239500 chr4D 80.616 877 117 31 2986 3827 12659807 12658949 3.080000e-176 628
23 TraesCS1A01G239500 chr4D 79.271 878 137 26 2986 3832 12655778 12656641 5.270000e-159 571
24 TraesCS1A01G239500 chr4D 74.667 525 83 34 2314 2820 12660421 12659929 2.230000e-43 187
25 TraesCS1A01G239500 chr4B 83.204 1286 184 17 806 2088 23354408 23355664 0.000000e+00 1149
26 TraesCS1A01G239500 chr4B 80.995 884 110 28 2986 3832 23356824 23357686 0.000000e+00 649
27 TraesCS1A01G239500 chrUn 82.506 886 99 25 2983 3830 314646101 314646968 0.000000e+00 726
28 TraesCS1A01G239500 chrUn 86.014 429 48 6 801 1229 322648384 322647968 2.580000e-122 449


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 TraesCS1A01G239500 chr1A 426872750 426877445 4695 True 8672.000000 8672 100.000000 1 4696 1 chr1A.!!$R1 4695
1 TraesCS1A01G239500 chr1D 329665644 329671411 5767 True 1895.666667 2689 90.715667 122 4696 3 chr1D.!!$R1 4574
2 TraesCS1A01G239500 chr1B 444667115 444673064 5949 True 1452.000000 2270 89.867250 124 4696 4 chr1B.!!$R1 4572
3 TraesCS1A01G239500 chr2A 19943984 19949092 5108 True 1073.500000 1448 84.502000 810 3830 2 chr2A.!!$R1 3020
4 TraesCS1A01G239500 chr2D 19045668 19046953 1285 False 1424.000000 1424 86.692000 801 2094 1 chr2D.!!$F1 1293
5 TraesCS1A01G239500 chr2D 18762029 18763315 1286 True 1376.000000 1376 86.057000 812 2094 1 chr2D.!!$R1 1282
6 TraesCS1A01G239500 chr2D 18755264 18757403 2139 True 332.333333 542 80.666333 2642 4528 3 chr2D.!!$R2 1886
7 TraesCS1A01G239500 chr4A 589787466 589790984 3518 False 908.000000 1199 82.187500 813 3832 2 chr4A.!!$F1 3019
8 TraesCS1A01G239500 chr4A 589778259 589781454 3195 True 528.500000 730 80.835000 1324 3832 2 chr4A.!!$R1 2508
9 TraesCS1A01G239500 chr4A 589844575 589846050 1475 False 381.000000 593 77.040500 2314 3832 2 chr4A.!!$F2 1518
10 TraesCS1A01G239500 chr4D 12658949 12662113 3164 True 657.333333 1157 79.543000 809 3827 3 chr4D.!!$R1 3018
11 TraesCS1A01G239500 chr4D 12655778 12656641 863 False 571.000000 571 79.271000 2986 3832 1 chr4D.!!$F1 846
12 TraesCS1A01G239500 chr4B 23354408 23357686 3278 False 899.000000 1149 82.099500 806 3832 2 chr4B.!!$F1 3026
13 TraesCS1A01G239500 chrUn 314646101 314646968 867 False 726.000000 726 82.506000 2983 3830 1 chrUn.!!$F1 847

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
79 80 0.034337 GGTGTACAAGTGCGGAGGAA 59.966 55.0 0.00 0.00 0.00 3.36 F
81 82 0.034337 TGTACAAGTGCGGAGGAACC 59.966 55.0 0.00 0.00 0.00 3.62 F
1484 2807 0.034059 GGCATACCGGAGATGACCAG 59.966 60.0 20.66 0.00 0.00 4.00 F
2230 6163 0.537188 TCTCCCGGCTGAATTCAGTC 59.463 55.0 30.88 28.93 45.45 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 2807 1.272781 CTCGAACATGTCCTCGAAGC 58.727 55.000 19.93 0.0 43.03 3.86 R
1947 3285 2.790231 CGCGTACGCCGTGCAATTA 61.790 57.895 32.64 0.0 40.62 1.40 R
2891 7145 0.249155 GCGTACTGCTATACGGCCAA 60.249 55.000 17.99 0.0 46.39 4.52 R
4213 9373 0.248296 GACTTGCTCTAGCTCCGTCG 60.248 60.000 3.26 0.0 42.66 5.12 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
33 34 2.132740 CTCTGATAGAGCTTCACGGC 57.867 55.000 0.00 0.00 35.30 5.68
34 35 1.406898 CTCTGATAGAGCTTCACGGCA 59.593 52.381 0.00 0.00 35.30 5.69
35 36 1.824852 TCTGATAGAGCTTCACGGCAA 59.175 47.619 0.00 0.00 34.17 4.52
36 37 2.159184 TCTGATAGAGCTTCACGGCAAG 60.159 50.000 0.00 0.00 34.17 4.01
37 38 1.550524 TGATAGAGCTTCACGGCAAGT 59.449 47.619 0.00 0.00 34.17 3.16
49 50 2.113986 GCAAGTGTGGCAGGGTCT 59.886 61.111 0.00 0.00 0.00 3.85
50 51 2.263741 GCAAGTGTGGCAGGGTCTG 61.264 63.158 0.00 0.00 34.12 3.51
51 52 1.149174 CAAGTGTGGCAGGGTCTGT 59.851 57.895 0.00 0.00 33.43 3.41
52 53 0.886490 CAAGTGTGGCAGGGTCTGTC 60.886 60.000 0.00 0.00 36.52 3.51
53 54 1.344953 AAGTGTGGCAGGGTCTGTCA 61.345 55.000 0.00 0.00 44.22 3.58
56 57 4.898607 TGGCAGGGTCTGTCAAAC 57.101 55.556 0.00 0.00 43.43 2.93
57 58 1.150536 TGGCAGGGTCTGTCAAACC 59.849 57.895 0.00 0.00 43.43 3.27
58 59 1.352622 TGGCAGGGTCTGTCAAACCT 61.353 55.000 0.00 0.00 43.43 3.50
59 60 0.178990 GGCAGGGTCTGTCAAACCTT 60.179 55.000 0.00 0.00 35.96 3.50
60 61 0.954452 GCAGGGTCTGTCAAACCTTG 59.046 55.000 3.07 3.07 44.42 3.61
61 62 1.609208 CAGGGTCTGTCAAACCTTGG 58.391 55.000 0.00 0.00 39.52 3.61
62 63 1.133792 CAGGGTCTGTCAAACCTTGGT 60.134 52.381 0.00 0.00 39.52 3.67
63 64 1.133792 AGGGTCTGTCAAACCTTGGTG 60.134 52.381 0.00 0.00 36.97 4.17
64 65 1.409661 GGGTCTGTCAAACCTTGGTGT 60.410 52.381 0.00 0.00 36.97 4.16
65 66 2.158726 GGGTCTGTCAAACCTTGGTGTA 60.159 50.000 0.00 0.00 36.97 2.90
66 67 2.876550 GGTCTGTCAAACCTTGGTGTAC 59.123 50.000 0.00 0.00 33.78 2.90
67 68 3.537580 GTCTGTCAAACCTTGGTGTACA 58.462 45.455 0.00 0.00 0.00 2.90
68 69 3.942748 GTCTGTCAAACCTTGGTGTACAA 59.057 43.478 0.00 0.00 37.55 2.41
76 77 3.299050 TTGGTGTACAAGTGCGGAG 57.701 52.632 0.00 0.00 33.18 4.63
77 78 0.250124 TTGGTGTACAAGTGCGGAGG 60.250 55.000 0.00 0.00 33.18 4.30
78 79 1.116536 TGGTGTACAAGTGCGGAGGA 61.117 55.000 0.00 0.00 0.00 3.71
79 80 0.034337 GGTGTACAAGTGCGGAGGAA 59.966 55.000 0.00 0.00 0.00 3.36
80 81 1.145803 GTGTACAAGTGCGGAGGAAC 58.854 55.000 0.00 0.00 0.00 3.62
81 82 0.034337 TGTACAAGTGCGGAGGAACC 59.966 55.000 0.00 0.00 0.00 3.62
82 83 0.672711 GTACAAGTGCGGAGGAACCC 60.673 60.000 0.00 0.00 34.64 4.11
83 84 1.122632 TACAAGTGCGGAGGAACCCA 61.123 55.000 0.00 0.00 34.64 4.51
84 85 1.002134 CAAGTGCGGAGGAACCCAT 60.002 57.895 0.00 0.00 34.64 4.00
85 86 0.251916 CAAGTGCGGAGGAACCCATA 59.748 55.000 0.00 0.00 34.64 2.74
86 87 1.134098 CAAGTGCGGAGGAACCCATAT 60.134 52.381 0.00 0.00 34.64 1.78
87 88 2.097110 AGTGCGGAGGAACCCATATA 57.903 50.000 0.00 0.00 34.64 0.86
88 89 2.621070 AGTGCGGAGGAACCCATATAT 58.379 47.619 0.00 0.00 34.64 0.86
89 90 3.786553 AGTGCGGAGGAACCCATATATA 58.213 45.455 0.00 0.00 34.64 0.86
90 91 4.164981 AGTGCGGAGGAACCCATATATAA 58.835 43.478 0.00 0.00 34.64 0.98
91 92 4.223032 AGTGCGGAGGAACCCATATATAAG 59.777 45.833 0.00 0.00 34.64 1.73
92 93 3.055385 TGCGGAGGAACCCATATATAAGC 60.055 47.826 0.00 0.00 34.64 3.09
93 94 3.681874 GCGGAGGAACCCATATATAAGCC 60.682 52.174 0.00 0.00 34.64 4.35
94 95 3.775316 CGGAGGAACCCATATATAAGCCT 59.225 47.826 0.00 0.00 34.64 4.58
95 96 4.383118 CGGAGGAACCCATATATAAGCCTG 60.383 50.000 0.00 0.00 34.64 4.85
96 97 4.518249 GAGGAACCCATATATAAGCCTGC 58.482 47.826 0.00 0.00 0.00 4.85
97 98 3.916349 AGGAACCCATATATAAGCCTGCA 59.084 43.478 0.00 0.00 0.00 4.41
98 99 4.541714 AGGAACCCATATATAAGCCTGCAT 59.458 41.667 0.00 0.00 0.00 3.96
99 100 4.884164 GGAACCCATATATAAGCCTGCATC 59.116 45.833 0.00 0.00 0.00 3.91
100 101 5.500234 GAACCCATATATAAGCCTGCATCA 58.500 41.667 0.00 0.00 0.00 3.07
101 102 5.722172 ACCCATATATAAGCCTGCATCAT 57.278 39.130 0.00 0.00 0.00 2.45
102 103 5.688807 ACCCATATATAAGCCTGCATCATC 58.311 41.667 0.00 0.00 0.00 2.92
103 104 5.192321 ACCCATATATAAGCCTGCATCATCA 59.808 40.000 0.00 0.00 0.00 3.07
104 105 5.530171 CCCATATATAAGCCTGCATCATCAC 59.470 44.000 0.00 0.00 0.00 3.06
105 106 5.235831 CCATATATAAGCCTGCATCATCACG 59.764 44.000 0.00 0.00 0.00 4.35
106 107 1.888215 ATAAGCCTGCATCATCACGG 58.112 50.000 0.00 0.00 0.00 4.94
107 108 0.815213 TAAGCCTGCATCATCACGGC 60.815 55.000 2.78 2.78 40.99 5.68
108 109 2.825075 AAGCCTGCATCATCACGGCA 62.825 55.000 12.78 0.00 43.07 5.69
109 110 2.409055 GCCTGCATCATCACGGCAA 61.409 57.895 6.04 0.00 40.41 4.52
110 111 1.936436 GCCTGCATCATCACGGCAAA 61.936 55.000 6.04 0.00 40.41 3.68
111 112 0.179156 CCTGCATCATCACGGCAAAC 60.179 55.000 0.00 0.00 37.06 2.93
112 113 0.806868 CTGCATCATCACGGCAAACT 59.193 50.000 0.00 0.00 37.06 2.66
113 114 0.522626 TGCATCATCACGGCAAACTG 59.477 50.000 0.00 0.00 34.05 3.16
114 115 0.799534 GCATCATCACGGCAAACTGC 60.800 55.000 0.00 0.00 44.08 4.40
212 227 0.599558 TCTCATGTTTGGCTTGCTGC 59.400 50.000 0.00 0.00 41.94 5.25
241 256 5.163258 ACTGGAGATCGGATAAAAATCTGCT 60.163 40.000 5.02 0.00 38.33 4.24
261 276 1.129326 AACGAACGAAAGCGAGTCTG 58.871 50.000 0.14 0.00 41.64 3.51
307 322 9.482627 CCTTGACCATGAATAGTAAGAGAATAC 57.517 37.037 0.00 0.00 0.00 1.89
414 429 1.359848 CCCGCACTGATACTGACAAC 58.640 55.000 0.00 0.00 0.00 3.32
415 430 1.066858 CCCGCACTGATACTGACAACT 60.067 52.381 0.00 0.00 0.00 3.16
416 431 2.165641 CCCGCACTGATACTGACAACTA 59.834 50.000 0.00 0.00 0.00 2.24
417 432 3.179830 CCGCACTGATACTGACAACTAC 58.820 50.000 0.00 0.00 0.00 2.73
418 433 3.119459 CCGCACTGATACTGACAACTACT 60.119 47.826 0.00 0.00 0.00 2.57
419 434 4.099120 CGCACTGATACTGACAACTACTC 58.901 47.826 0.00 0.00 0.00 2.59
420 435 4.425520 GCACTGATACTGACAACTACTCC 58.574 47.826 0.00 0.00 0.00 3.85
421 436 4.082190 GCACTGATACTGACAACTACTCCA 60.082 45.833 0.00 0.00 0.00 3.86
422 437 5.645624 CACTGATACTGACAACTACTCCAG 58.354 45.833 0.00 0.00 0.00 3.86
625 640 0.591741 CGCTTACCGTCGATCTGTCC 60.592 60.000 0.00 0.00 0.00 4.02
631 646 2.202756 GTCGATCTGTCCCCGCAC 60.203 66.667 0.00 0.00 0.00 5.34
662 677 1.977188 CAATTTCGTTCCTTTCGGGC 58.023 50.000 0.00 0.00 34.39 6.13
702 2001 1.806542 GACAACATTCCGTGACATGCT 59.193 47.619 0.00 0.00 0.00 3.79
737 2040 3.933332 GCCATCGGTATATAGAACTTGGC 59.067 47.826 9.58 9.58 40.16 4.52
782 2089 3.832615 ACATTCCCCGTACTTCCATAC 57.167 47.619 0.00 0.00 0.00 2.39
862 2169 1.667191 CGTGCTGCTTCTCACTGCT 60.667 57.895 0.00 0.00 33.58 4.24
863 2170 1.867615 GTGCTGCTTCTCACTGCTG 59.132 57.895 0.00 0.00 33.58 4.41
864 2171 2.868920 GCTGCTTCTCACTGCTGC 59.131 61.111 0.00 0.00 44.21 5.25
1159 2478 0.178973 TCTGGTCGTCCAACTCCTCA 60.179 55.000 2.32 0.00 43.81 3.86
1213 2532 1.599518 CAACGGCAACCTGGTGCTA 60.600 57.895 16.88 0.00 44.31 3.49
1384 2707 2.954868 GCTACGACATGGACGCGG 60.955 66.667 12.47 0.00 0.00 6.46
1484 2807 0.034059 GGCATACCGGAGATGACCAG 59.966 60.000 20.66 0.00 0.00 4.00
1947 3285 1.451936 GAGGTGCCTGTCCAACTGT 59.548 57.895 0.00 0.00 31.67 3.55
2094 3436 2.416972 GGCGTTGTCTGACCTAGGTAAG 60.417 54.545 19.47 19.47 0.00 2.34
2095 3437 2.490903 GCGTTGTCTGACCTAGGTAAGA 59.509 50.000 23.54 23.54 33.43 2.10
2096 3438 3.057033 GCGTTGTCTGACCTAGGTAAGAA 60.057 47.826 28.05 16.37 37.36 2.52
2097 3439 4.483311 CGTTGTCTGACCTAGGTAAGAAC 58.517 47.826 28.05 21.84 37.36 3.01
2098 3440 4.483311 GTTGTCTGACCTAGGTAAGAACG 58.517 47.826 28.05 3.74 37.36 3.95
2131 5813 8.571461 TGCAATTCTCTCTTATTCAAATCACT 57.429 30.769 0.00 0.00 0.00 3.41
2229 6162 1.207791 ATCTCCCGGCTGAATTCAGT 58.792 50.000 30.88 10.63 45.45 3.41
2230 6163 0.537188 TCTCCCGGCTGAATTCAGTC 59.463 55.000 30.88 28.93 45.45 3.51
2256 6189 3.565905 GACTTTTTGTCCATGCAGAGG 57.434 47.619 1.59 1.59 39.69 3.69
2281 6217 9.950496 GGATGATATTTCCAATCACTAGTATGT 57.050 33.333 0.00 0.00 36.24 2.29
2329 6311 2.361757 TGTGCAAGGACCTTGTCAAATG 59.638 45.455 30.34 9.19 42.77 2.32
2352 6334 3.338249 CCTACCAGGACAAACATGTCAG 58.662 50.000 0.00 0.00 37.67 3.51
2364 6346 3.928727 ACATGTCAGGCTCAAACAATG 57.071 42.857 0.00 0.00 0.00 2.82
2405 6629 2.143925 GTAACACACTGGCTTGAGGAC 58.856 52.381 0.00 0.00 0.00 3.85
2416 6642 2.225467 GCTTGAGGACTGCAGTTTTCT 58.775 47.619 22.65 18.13 0.00 2.52
2451 6688 3.178267 GACGCTGACATTCTTCAGAGAG 58.822 50.000 10.33 1.27 45.19 3.20
2575 6820 1.904990 GCCAGGAAGGTCAGAGTCCC 61.905 65.000 0.00 0.00 40.61 4.46
2657 6903 4.944619 TCCTACTATTGCTCATGTCAGG 57.055 45.455 0.00 0.00 0.00 3.86
2710 6958 5.240183 CACCATGTTTGAAGACATCTTGAGT 59.760 40.000 0.00 0.00 38.15 3.41
2820 7068 5.123186 TCGGCATTGTTTACAAGGTGATAAG 59.877 40.000 8.77 0.00 39.56 1.73
2821 7069 5.123186 CGGCATTGTTTACAAGGTGATAAGA 59.877 40.000 8.77 0.00 39.56 2.10
2822 7070 6.555315 GGCATTGTTTACAAGGTGATAAGAG 58.445 40.000 8.77 0.00 39.56 2.85
2823 7071 6.151144 GGCATTGTTTACAAGGTGATAAGAGT 59.849 38.462 8.77 0.00 39.56 3.24
2825 7073 8.726988 GCATTGTTTACAAGGTGATAAGAGTAA 58.273 33.333 8.77 0.00 39.56 2.24
2828 7076 8.263940 TGTTTACAAGGTGATAAGAGTAATGC 57.736 34.615 0.00 0.00 0.00 3.56
2830 7078 8.947115 GTTTACAAGGTGATAAGAGTAATGCTT 58.053 33.333 0.00 0.00 0.00 3.91
2831 7079 9.515226 TTTACAAGGTGATAAGAGTAATGCTTT 57.485 29.630 0.00 0.00 0.00 3.51
2832 7080 9.515226 TTACAAGGTGATAAGAGTAATGCTTTT 57.485 29.630 0.00 0.00 0.00 2.27
2834 7082 8.947115 ACAAGGTGATAAGAGTAATGCTTTTAC 58.053 33.333 0.00 0.00 0.00 2.01
2835 7083 8.946085 CAAGGTGATAAGAGTAATGCTTTTACA 58.054 33.333 11.16 0.00 0.00 2.41
2836 7084 8.494016 AGGTGATAAGAGTAATGCTTTTACAC 57.506 34.615 11.16 0.00 32.21 2.90
2837 7085 8.100791 AGGTGATAAGAGTAATGCTTTTACACA 58.899 33.333 11.16 3.39 33.23 3.72
2838 7086 8.726988 GGTGATAAGAGTAATGCTTTTACACAA 58.273 33.333 11.16 1.39 33.23 3.33
2859 7107 8.183536 ACACAATACACATTGCAATACTACATG 58.816 33.333 12.53 10.19 44.62 3.21
2890 7144 7.093814 CCATGTAAATCAGGACTGAAATTTCCA 60.094 37.037 15.48 1.76 43.58 3.53
2891 7145 8.472413 CATGTAAATCAGGACTGAAATTTCCAT 58.528 33.333 15.48 3.42 43.58 3.41
2903 7157 4.037446 TGAAATTTCCATTGGCCGTATAGC 59.963 41.667 15.48 0.00 0.00 2.97
2904 7158 2.719531 TTTCCATTGGCCGTATAGCA 57.280 45.000 0.00 0.00 0.00 3.49
2905 7159 2.254546 TTCCATTGGCCGTATAGCAG 57.745 50.000 0.00 0.00 0.00 4.24
2906 7160 1.128200 TCCATTGGCCGTATAGCAGT 58.872 50.000 0.00 0.00 0.00 4.40
2907 7161 2.321719 TCCATTGGCCGTATAGCAGTA 58.678 47.619 0.00 0.00 0.00 2.74
2908 7162 2.036733 TCCATTGGCCGTATAGCAGTAC 59.963 50.000 0.00 0.00 0.00 2.73
2922 7196 1.203994 GCAGTACGCCTTCCTTGTAGA 59.796 52.381 0.00 0.00 32.94 2.59
2928 7202 2.158726 ACGCCTTCCTTGTAGAACCAAA 60.159 45.455 0.00 0.00 0.00 3.28
2929 7203 3.081804 CGCCTTCCTTGTAGAACCAAAT 58.918 45.455 0.00 0.00 0.00 2.32
2933 7207 5.572885 GCCTTCCTTGTAGAACCAAATAGGA 60.573 44.000 0.00 0.00 41.22 2.94
2981 7713 1.425066 AGGACCAAAATCTGACCAGCA 59.575 47.619 0.00 0.00 0.00 4.41
3031 7763 1.946768 CAGGAAGTTGCGGTGAAGAAA 59.053 47.619 0.00 0.00 0.00 2.52
3063 7795 0.109342 AACAGGGTGCAAGGACTGAG 59.891 55.000 13.13 0.00 35.08 3.35
3177 7913 5.049543 GGATACTGGTCTACGAGTACATGAC 60.050 48.000 0.00 0.00 39.40 3.06
3196 7932 1.064758 ACCAACAAGAGCTTGGACACA 60.065 47.619 14.14 0.00 44.45 3.72
3205 7941 5.382618 AGAGCTTGGACACATTCATTTTC 57.617 39.130 0.00 0.00 0.00 2.29
3212 7948 4.083003 TGGACACATTCATTTTCGGTTAGC 60.083 41.667 0.00 0.00 0.00 3.09
3233 7970 2.555325 CACGTGTCACTCACCCTAACTA 59.445 50.000 7.58 0.00 43.51 2.24
3248 7986 5.187576 ACCCTAACTACGGCAAATAGTTACA 59.812 40.000 8.75 0.00 41.84 2.41
3256 8233 6.091718 ACGGCAAATAGTTACAACCATTTT 57.908 33.333 0.00 0.00 29.79 1.82
3272 8264 4.749598 ACCATTTTTGCCGAGAAATTCAAC 59.250 37.500 0.00 0.00 0.00 3.18
3479 8471 2.210116 GATTTCGGAATCGCCAAGCTA 58.790 47.619 0.00 0.00 35.94 3.32
3524 8519 1.266175 GACTCGACCGTCACAGAAAGA 59.734 52.381 0.00 0.00 34.11 2.52
3615 8628 3.322828 AGTTTCTTTGCGAGTGTACCCTA 59.677 43.478 0.00 0.00 0.00 3.53
3636 8650 3.420893 AGCCGGATTTTCTGATTGTTGA 58.579 40.909 5.05 0.00 0.00 3.18
3705 8735 5.105877 CCATGGATGGCTTGATATCATTCAC 60.106 44.000 5.56 0.00 41.75 3.18
3720 8750 8.846943 ATATCATTCACGCAGGATGTTTATAA 57.153 30.769 0.00 0.00 39.31 0.98
3868 9024 3.808728 AGATGTGCCTTACGTATTGCAT 58.191 40.909 18.74 9.56 35.96 3.96
3872 9028 5.416862 TGTGCCTTACGTATTGCATATTG 57.583 39.130 18.74 0.00 35.96 1.90
3873 9029 4.219033 GTGCCTTACGTATTGCATATTGC 58.781 43.478 18.74 5.95 45.29 3.56
3886 9042 4.756084 GCATATTGCACATCTAACTCCC 57.244 45.455 0.00 0.00 44.26 4.30
3905 9061 8.415950 AACTCCCATGTCATTAATTTTACACA 57.584 30.769 0.00 0.00 0.00 3.72
3918 9074 8.851541 TTAATTTTACACAGGGATTCTTACGT 57.148 30.769 0.00 0.00 0.00 3.57
3993 9153 4.759693 CACACCTAGATGTGCCTTAAACAA 59.240 41.667 3.75 0.00 43.29 2.83
4049 9209 1.956802 GTGCCTACACAACCCAAGC 59.043 57.895 0.00 0.00 46.61 4.01
4059 9219 1.780911 AACCCAAGCCCCAACCCTA 60.781 57.895 0.00 0.00 0.00 3.53
4093 9253 4.338879 CAAGAAACTCACCCTGATGGAAT 58.661 43.478 0.00 0.00 38.00 3.01
4229 9389 2.415608 CCCGACGGAGCTAGAGCAA 61.416 63.158 17.49 0.00 45.16 3.91
4231 9391 1.658686 CCGACGGAGCTAGAGCAAGT 61.659 60.000 8.64 0.43 45.16 3.16
4316 9480 2.422803 GGCTGCTGTAATCCCCATGTTA 60.423 50.000 0.00 0.00 0.00 2.41
4358 9522 3.697747 CCACTTCGGCCGGTGGTA 61.698 66.667 33.23 12.04 45.52 3.25
4385 9549 1.610673 AGTGAGCACTCCGGTGGAT 60.611 57.895 8.63 0.00 43.18 3.41
4403 9567 2.159226 GGATCTTCTCGACGTGTTGGAT 60.159 50.000 0.00 0.00 0.00 3.41
4427 9591 3.193479 ACACATCTGACAATGTCGAGCTA 59.807 43.478 9.00 0.00 37.78 3.32
4433 9597 4.401202 TCTGACAATGTCGAGCTAACCATA 59.599 41.667 9.00 0.00 34.95 2.74
4547 9711 8.694394 CACGACTAATTGATAGACATGTGTATG 58.306 37.037 19.40 7.14 36.42 2.39
4562 9726 8.574251 ACATGTGTATGCCTCTTAATAAACAA 57.426 30.769 0.00 0.00 37.85 2.83
4583 9747 6.650120 ACAAACCTATGTAAATCACGGAGAT 58.350 36.000 0.00 0.00 39.09 2.75
4592 9756 8.731275 ATGTAAATCACGGAGATTGATAACAA 57.269 30.769 6.19 0.00 46.09 2.83
4604 9768 8.072567 GGAGATTGATAACAAATTCAAGATCCG 58.927 37.037 0.00 0.00 39.54 4.18
4664 9829 7.521529 CAGATGGTAGGCAATGATTTAATACG 58.478 38.462 0.00 0.00 0.00 3.06
4673 9838 5.393678 GCAATGATTTAATACGTGGTGGGTT 60.394 40.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.406898 TGCCGTGAAGCTCTATCAGAG 59.593 52.381 0.00 0.00 45.04 3.35
15 16 1.474330 TGCCGTGAAGCTCTATCAGA 58.526 50.000 0.00 0.00 0.00 3.27
16 17 2.200067 CTTGCCGTGAAGCTCTATCAG 58.800 52.381 0.00 0.00 0.00 2.90
17 18 1.550524 ACTTGCCGTGAAGCTCTATCA 59.449 47.619 0.00 0.00 0.00 2.15
18 19 1.929836 CACTTGCCGTGAAGCTCTATC 59.070 52.381 0.00 0.00 46.81 2.08
19 20 1.276421 ACACTTGCCGTGAAGCTCTAT 59.724 47.619 9.87 0.00 46.81 1.98
20 21 0.679505 ACACTTGCCGTGAAGCTCTA 59.320 50.000 9.87 0.00 46.81 2.43
21 22 0.882042 CACACTTGCCGTGAAGCTCT 60.882 55.000 9.87 0.00 46.81 4.09
22 23 1.571460 CACACTTGCCGTGAAGCTC 59.429 57.895 9.87 0.00 46.81 4.09
23 24 1.893808 CCACACTTGCCGTGAAGCT 60.894 57.895 9.87 0.00 46.81 3.74
24 25 2.639286 CCACACTTGCCGTGAAGC 59.361 61.111 9.87 0.00 46.81 3.86
25 26 2.121564 CTGCCACACTTGCCGTGAAG 62.122 60.000 9.87 0.00 46.81 3.02
26 27 2.124529 TGCCACACTTGCCGTGAA 60.125 55.556 9.87 0.00 46.81 3.18
27 28 2.591429 CTGCCACACTTGCCGTGA 60.591 61.111 9.87 0.00 46.81 4.35
29 30 4.954970 CCCTGCCACACTTGCCGT 62.955 66.667 0.00 0.00 0.00 5.68
30 31 4.954970 ACCCTGCCACACTTGCCG 62.955 66.667 0.00 0.00 0.00 5.69
31 32 2.985847 GACCCTGCCACACTTGCC 60.986 66.667 0.00 0.00 0.00 4.52
32 33 2.113986 AGACCCTGCCACACTTGC 59.886 61.111 0.00 0.00 0.00 4.01
33 34 0.886490 GACAGACCCTGCCACACTTG 60.886 60.000 0.00 0.00 34.37 3.16
34 35 1.344953 TGACAGACCCTGCCACACTT 61.345 55.000 0.00 0.00 34.37 3.16
35 36 1.344953 TTGACAGACCCTGCCACACT 61.345 55.000 0.00 0.00 34.37 3.55
36 37 0.465460 TTTGACAGACCCTGCCACAC 60.465 55.000 0.00 0.00 34.37 3.82
37 38 0.465460 GTTTGACAGACCCTGCCACA 60.465 55.000 0.00 0.00 34.37 4.17
38 39 1.172812 GGTTTGACAGACCCTGCCAC 61.173 60.000 3.71 0.00 34.37 5.01
39 40 1.150536 GGTTTGACAGACCCTGCCA 59.849 57.895 3.71 0.00 34.37 4.92
40 41 0.178990 AAGGTTTGACAGACCCTGCC 60.179 55.000 11.43 0.00 37.93 4.85
41 42 0.954452 CAAGGTTTGACAGACCCTGC 59.046 55.000 11.43 0.00 37.93 4.85
42 43 1.133792 ACCAAGGTTTGACAGACCCTG 60.134 52.381 11.43 8.96 37.93 4.45
43 44 1.133792 CACCAAGGTTTGACAGACCCT 60.134 52.381 11.43 0.00 37.93 4.34
44 45 1.318576 CACCAAGGTTTGACAGACCC 58.681 55.000 11.43 0.00 37.93 4.46
45 46 2.052782 ACACCAAGGTTTGACAGACC 57.947 50.000 7.07 7.07 37.44 3.85
46 47 3.537580 TGTACACCAAGGTTTGACAGAC 58.462 45.455 0.00 0.00 0.00 3.51
47 48 3.916359 TGTACACCAAGGTTTGACAGA 57.084 42.857 0.00 0.00 0.00 3.41
48 49 4.552166 CTTGTACACCAAGGTTTGACAG 57.448 45.455 0.00 0.00 45.70 3.51
58 59 0.250124 CCTCCGCACTTGTACACCAA 60.250 55.000 0.00 0.00 0.00 3.67
59 60 1.116536 TCCTCCGCACTTGTACACCA 61.117 55.000 0.00 0.00 0.00 4.17
60 61 0.034337 TTCCTCCGCACTTGTACACC 59.966 55.000 0.00 0.00 0.00 4.16
61 62 1.145803 GTTCCTCCGCACTTGTACAC 58.854 55.000 0.00 0.00 0.00 2.90
62 63 0.034337 GGTTCCTCCGCACTTGTACA 59.966 55.000 0.00 0.00 0.00 2.90
63 64 0.672711 GGGTTCCTCCGCACTTGTAC 60.673 60.000 0.00 0.00 37.00 2.90
64 65 1.122632 TGGGTTCCTCCGCACTTGTA 61.123 55.000 0.00 0.00 37.00 2.41
65 66 1.779061 ATGGGTTCCTCCGCACTTGT 61.779 55.000 0.00 0.00 37.00 3.16
66 67 0.251916 TATGGGTTCCTCCGCACTTG 59.748 55.000 0.00 0.00 37.00 3.16
67 68 1.213296 ATATGGGTTCCTCCGCACTT 58.787 50.000 0.00 0.00 37.00 3.16
68 69 2.097110 TATATGGGTTCCTCCGCACT 57.903 50.000 0.00 0.00 37.00 4.40
69 70 4.504858 CTTATATATGGGTTCCTCCGCAC 58.495 47.826 0.00 0.00 37.00 5.34
70 71 3.055385 GCTTATATATGGGTTCCTCCGCA 60.055 47.826 0.00 0.00 37.00 5.69
71 72 3.532542 GCTTATATATGGGTTCCTCCGC 58.467 50.000 0.00 0.00 37.00 5.54
72 73 3.775316 AGGCTTATATATGGGTTCCTCCG 59.225 47.826 0.00 0.00 37.00 4.63
73 74 4.626529 GCAGGCTTATATATGGGTTCCTCC 60.627 50.000 0.00 0.00 0.00 4.30
74 75 4.019321 TGCAGGCTTATATATGGGTTCCTC 60.019 45.833 0.00 0.00 0.00 3.71
75 76 3.916349 TGCAGGCTTATATATGGGTTCCT 59.084 43.478 0.00 0.00 0.00 3.36
76 77 4.301072 TGCAGGCTTATATATGGGTTCC 57.699 45.455 0.00 0.00 0.00 3.62
77 78 5.500234 TGATGCAGGCTTATATATGGGTTC 58.500 41.667 0.00 0.00 0.00 3.62
78 79 5.519183 TGATGCAGGCTTATATATGGGTT 57.481 39.130 0.00 0.00 0.00 4.11
79 80 5.192321 TGATGATGCAGGCTTATATATGGGT 59.808 40.000 0.00 0.00 0.00 4.51
80 81 5.530171 GTGATGATGCAGGCTTATATATGGG 59.470 44.000 0.00 0.00 0.00 4.00
81 82 5.235831 CGTGATGATGCAGGCTTATATATGG 59.764 44.000 0.00 0.00 0.00 2.74
82 83 5.235831 CCGTGATGATGCAGGCTTATATATG 59.764 44.000 0.00 0.00 0.00 1.78
83 84 5.363101 CCGTGATGATGCAGGCTTATATAT 58.637 41.667 0.00 0.00 0.00 0.86
84 85 4.758688 CCGTGATGATGCAGGCTTATATA 58.241 43.478 0.00 0.00 0.00 0.86
85 86 3.603532 CCGTGATGATGCAGGCTTATAT 58.396 45.455 0.00 0.00 0.00 0.86
86 87 2.871637 GCCGTGATGATGCAGGCTTATA 60.872 50.000 3.76 0.00 44.06 0.98
87 88 1.888215 CCGTGATGATGCAGGCTTAT 58.112 50.000 0.00 0.00 0.00 1.73
88 89 0.815213 GCCGTGATGATGCAGGCTTA 60.815 55.000 3.76 0.00 44.06 3.09
89 90 2.117156 GCCGTGATGATGCAGGCTT 61.117 57.895 3.76 0.00 44.06 4.35
90 91 2.515523 GCCGTGATGATGCAGGCT 60.516 61.111 3.76 0.00 44.06 4.58
92 93 0.179156 GTTTGCCGTGATGATGCAGG 60.179 55.000 0.00 0.00 36.21 4.85
93 94 0.806868 AGTTTGCCGTGATGATGCAG 59.193 50.000 0.00 0.00 36.21 4.41
94 95 0.522626 CAGTTTGCCGTGATGATGCA 59.477 50.000 0.00 0.00 0.00 3.96
95 96 0.799534 GCAGTTTGCCGTGATGATGC 60.800 55.000 0.00 0.00 37.42 3.91
96 97 0.522626 TGCAGTTTGCCGTGATGATG 59.477 50.000 0.00 0.00 44.23 3.07
97 98 0.523072 GTGCAGTTTGCCGTGATGAT 59.477 50.000 0.00 0.00 44.23 2.45
98 99 0.534877 AGTGCAGTTTGCCGTGATGA 60.535 50.000 0.00 0.00 44.23 2.92
99 100 0.386352 CAGTGCAGTTTGCCGTGATG 60.386 55.000 0.00 0.00 44.23 3.07
100 101 0.534877 TCAGTGCAGTTTGCCGTGAT 60.535 50.000 0.00 0.00 44.23 3.06
101 102 0.534877 ATCAGTGCAGTTTGCCGTGA 60.535 50.000 0.00 2.22 44.23 4.35
102 103 1.129251 CTATCAGTGCAGTTTGCCGTG 59.871 52.381 0.00 0.00 44.23 4.94
103 104 1.442769 CTATCAGTGCAGTTTGCCGT 58.557 50.000 0.00 0.00 44.23 5.68
104 105 0.097674 GCTATCAGTGCAGTTTGCCG 59.902 55.000 0.00 0.00 44.23 5.69
105 106 1.399791 GAGCTATCAGTGCAGTTTGCC 59.600 52.381 0.00 0.00 44.23 4.52
106 107 1.399791 GGAGCTATCAGTGCAGTTTGC 59.600 52.381 0.00 0.00 45.29 3.68
107 108 1.662629 CGGAGCTATCAGTGCAGTTTG 59.337 52.381 0.00 0.00 0.00 2.93
108 109 1.276421 ACGGAGCTATCAGTGCAGTTT 59.724 47.619 0.00 0.00 32.21 2.66
109 110 0.898320 ACGGAGCTATCAGTGCAGTT 59.102 50.000 0.00 0.00 32.21 3.16
110 111 0.457851 GACGGAGCTATCAGTGCAGT 59.542 55.000 0.00 0.00 33.70 4.40
111 112 0.457443 TGACGGAGCTATCAGTGCAG 59.543 55.000 0.00 0.00 33.70 4.41
112 113 0.894835 TTGACGGAGCTATCAGTGCA 59.105 50.000 0.00 0.00 33.70 4.57
113 114 1.134965 AGTTGACGGAGCTATCAGTGC 60.135 52.381 0.00 0.00 33.70 4.40
114 115 2.949451 AGTTGACGGAGCTATCAGTG 57.051 50.000 0.00 0.00 33.70 3.66
115 116 3.963428 AAAGTTGACGGAGCTATCAGT 57.037 42.857 0.00 0.00 36.49 3.41
116 117 6.276847 AGATAAAAGTTGACGGAGCTATCAG 58.723 40.000 0.00 0.00 0.00 2.90
117 118 6.222038 AGATAAAAGTTGACGGAGCTATCA 57.778 37.500 0.00 0.00 0.00 2.15
118 119 6.018669 CCAAGATAAAAGTTGACGGAGCTATC 60.019 42.308 0.00 0.00 0.00 2.08
119 120 5.817816 CCAAGATAAAAGTTGACGGAGCTAT 59.182 40.000 0.00 0.00 0.00 2.97
120 121 5.175859 CCAAGATAAAAGTTGACGGAGCTA 58.824 41.667 0.00 0.00 0.00 3.32
212 227 7.815068 AGATTTTTATCCGATCTCCAGTTATCG 59.185 37.037 0.00 0.00 43.53 2.92
241 256 2.287188 ACAGACTCGCTTTCGTTCGTTA 60.287 45.455 0.00 0.00 36.96 3.18
332 347 3.181533 GCCAGTGAAGACGAATCGTAAAC 60.182 47.826 8.77 4.96 41.37 2.01
396 411 2.370281 AGTTGTCAGTATCAGTGCGG 57.630 50.000 0.00 0.00 0.00 5.69
414 429 3.551046 CCATACGTTGCTAGCTGGAGTAG 60.551 52.174 17.23 8.69 0.00 2.57
415 430 2.361119 CCATACGTTGCTAGCTGGAGTA 59.639 50.000 17.23 14.36 0.00 2.59
416 431 1.137086 CCATACGTTGCTAGCTGGAGT 59.863 52.381 17.23 12.70 0.00 3.85
417 432 1.409064 TCCATACGTTGCTAGCTGGAG 59.591 52.381 17.23 7.35 0.00 3.86
418 433 1.480789 TCCATACGTTGCTAGCTGGA 58.519 50.000 17.23 16.05 0.00 3.86
419 434 2.309528 TTCCATACGTTGCTAGCTGG 57.690 50.000 17.23 13.88 0.00 4.85
420 435 3.871006 TGATTTCCATACGTTGCTAGCTG 59.129 43.478 17.23 8.41 0.00 4.24
421 436 4.137116 TGATTTCCATACGTTGCTAGCT 57.863 40.909 17.23 0.00 0.00 3.32
422 437 4.875544 TTGATTTCCATACGTTGCTAGC 57.124 40.909 8.10 8.10 0.00 3.42
453 468 2.365293 ACCATTTCAAACCAGTTCTGGC 59.635 45.455 17.55 0.00 0.00 4.85
584 599 2.136728 GATCGCTGACTCGTCTAGCTA 58.863 52.381 14.73 0.00 34.15 3.32
585 600 0.941542 GATCGCTGACTCGTCTAGCT 59.058 55.000 14.73 0.00 34.15 3.32
586 601 0.941542 AGATCGCTGACTCGTCTAGC 59.058 55.000 9.79 9.79 33.49 3.42
587 602 1.191425 CGAGATCGCTGACTCGTCTAG 59.809 57.143 0.00 0.00 46.90 2.43
614 629 2.202756 GTGCGGGGACAGATCGAC 60.203 66.667 0.00 0.00 0.00 4.20
672 687 0.320073 GAATGTTGTCACGGACGGGA 60.320 55.000 0.00 0.00 34.95 5.14
675 1974 0.942410 ACGGAATGTTGTCACGGACG 60.942 55.000 0.00 0.00 34.95 4.79
681 1980 1.535028 GCATGTCACGGAATGTTGTCA 59.465 47.619 0.00 0.00 0.00 3.58
682 1981 1.806542 AGCATGTCACGGAATGTTGTC 59.193 47.619 0.00 0.00 0.00 3.18
702 2001 0.179076 CGATGGCTGGCAGATGTACA 60.179 55.000 20.86 8.61 0.00 2.90
737 2040 2.076863 GTGGAGTCGGTGGATTTCTTG 58.923 52.381 0.00 0.00 0.00 3.02
782 2089 3.267860 GATCTTGCGCCGGCTCAG 61.268 66.667 26.68 16.99 40.82 3.35
880 2187 3.326981 CGCGTCAACGTGCTGTCA 61.327 61.111 0.00 0.00 43.06 3.58
994 2313 1.139058 GAGACGGTGAACCATATGCCT 59.861 52.381 0.00 0.00 35.14 4.75
1236 2555 2.431430 TGCTCGAAGCTCTGCACG 60.431 61.111 8.07 0.00 42.97 5.34
1313 2633 2.361357 ACGAGGAGAGGGACCACG 60.361 66.667 0.00 0.00 44.40 4.94
1484 2807 1.272781 CTCGAACATGTCCTCGAAGC 58.727 55.000 19.93 0.00 43.03 3.86
1581 2904 4.719369 ACGCCGGACTCGTTCAGC 62.719 66.667 5.05 0.00 36.72 4.26
1668 2991 3.691342 AGGCCGTAGCTGTCGCAA 61.691 61.111 0.00 0.00 39.73 4.85
1926 3264 4.329545 TTGGACAGGCACCTCCGC 62.330 66.667 0.00 0.00 40.77 5.54
1947 3285 2.790231 CGCGTACGCCGTGCAATTA 61.790 57.895 32.64 0.00 40.62 1.40
2076 3418 4.483311 CGTTCTTACCTAGGTCAGACAAC 58.517 47.826 22.86 18.09 29.31 3.32
2094 3436 5.986135 AGAGAGAATTGCATATGTACCGTTC 59.014 40.000 4.29 4.90 0.00 3.95
2095 3437 5.918608 AGAGAGAATTGCATATGTACCGTT 58.081 37.500 4.29 0.00 0.00 4.44
2096 3438 5.537300 AGAGAGAATTGCATATGTACCGT 57.463 39.130 4.29 0.00 0.00 4.83
2097 3439 8.539770 AATAAGAGAGAATTGCATATGTACCG 57.460 34.615 4.29 0.00 0.00 4.02
2098 3440 9.494271 TGAATAAGAGAGAATTGCATATGTACC 57.506 33.333 4.29 0.00 0.00 3.34
2329 6311 1.271926 ACATGTTTGTCCTGGTAGGCC 60.272 52.381 0.00 0.00 34.61 5.19
2352 6334 4.534168 CATCGATCATCATTGTTTGAGCC 58.466 43.478 0.00 0.00 37.89 4.70
2405 6629 5.284079 AGTTAAATGCACAGAAAACTGCAG 58.716 37.500 13.48 13.48 46.26 4.41
2416 6642 1.459209 CAGCGTCGAGTTAAATGCACA 59.541 47.619 0.00 0.00 0.00 4.57
2451 6688 2.031944 GCGAACTTCTTGGTCTTGGTTC 60.032 50.000 0.00 0.00 0.00 3.62
2497 6734 1.229975 GCACAAGCAATGCAAACCCC 61.230 55.000 8.35 0.00 42.88 4.95
2575 6820 0.592637 TCTGAAAACGCATGCACCAG 59.407 50.000 19.57 15.28 0.00 4.00
2710 6958 1.153978 GTACGTCGGACATTCGCCA 60.154 57.895 9.10 0.00 0.00 5.69
2820 7068 9.840427 AATGTGTATTGTGTAAAAGCATTACTC 57.160 29.630 12.02 9.57 0.00 2.59
2821 7069 9.624697 CAATGTGTATTGTGTAAAAGCATTACT 57.375 29.630 12.02 0.00 39.05 2.24
2822 7070 8.372521 GCAATGTGTATTGTGTAAAAGCATTAC 58.627 33.333 5.69 5.69 44.41 1.89
2823 7071 8.084684 TGCAATGTGTATTGTGTAAAAGCATTA 58.915 29.630 0.00 0.00 44.41 1.90
2825 7073 6.453943 TGCAATGTGTATTGTGTAAAAGCAT 58.546 32.000 0.00 0.00 44.41 3.79
2827 7075 6.761731 TTGCAATGTGTATTGTGTAAAAGC 57.238 33.333 0.00 0.00 44.41 3.51
2828 7076 9.624697 AGTATTGCAATGTGTATTGTGTAAAAG 57.375 29.630 22.27 0.00 44.41 2.27
2831 7079 9.220767 TGTAGTATTGCAATGTGTATTGTGTAA 57.779 29.630 22.27 0.00 44.41 2.41
2832 7080 8.779354 TGTAGTATTGCAATGTGTATTGTGTA 57.221 30.769 22.27 0.00 44.41 2.90
2833 7081 7.680442 TGTAGTATTGCAATGTGTATTGTGT 57.320 32.000 22.27 0.00 44.41 3.72
2834 7082 7.644945 CCATGTAGTATTGCAATGTGTATTGTG 59.355 37.037 22.27 10.43 44.41 3.33
2835 7083 7.555914 TCCATGTAGTATTGCAATGTGTATTGT 59.444 33.333 22.27 0.00 44.41 2.71
2836 7084 7.929159 TCCATGTAGTATTGCAATGTGTATTG 58.071 34.615 22.27 12.01 45.17 1.90
2837 7085 8.518430 TTCCATGTAGTATTGCAATGTGTATT 57.482 30.769 22.27 1.20 0.00 1.89
2838 7086 8.696043 ATTCCATGTAGTATTGCAATGTGTAT 57.304 30.769 22.27 7.12 0.00 2.29
2859 7107 5.684704 TCAGTCCTGATTTACATGGATTCC 58.315 41.667 0.00 0.00 34.14 3.01
2890 7144 1.604693 GCGTACTGCTATACGGCCAAT 60.605 52.381 17.99 0.00 46.39 3.16
2891 7145 0.249155 GCGTACTGCTATACGGCCAA 60.249 55.000 17.99 0.00 46.39 4.52
2903 7157 3.251571 GTTCTACAAGGAAGGCGTACTG 58.748 50.000 0.00 0.00 0.00 2.74
2904 7158 2.233186 GGTTCTACAAGGAAGGCGTACT 59.767 50.000 0.00 0.00 0.00 2.73
2905 7159 2.028748 TGGTTCTACAAGGAAGGCGTAC 60.029 50.000 0.00 0.00 0.00 3.67
2906 7160 2.250031 TGGTTCTACAAGGAAGGCGTA 58.750 47.619 0.00 0.00 0.00 4.42
2907 7161 1.053424 TGGTTCTACAAGGAAGGCGT 58.947 50.000 0.00 0.00 0.00 5.68
2908 7162 2.178912 TTGGTTCTACAAGGAAGGCG 57.821 50.000 0.00 0.00 0.00 5.52
2922 7196 5.305139 CGAAATTTCGGTCCTATTTGGTT 57.695 39.130 28.73 0.00 46.30 3.67
2933 7207 5.683020 ACTGGCCAGTACGAAATTTCGGT 62.683 47.826 37.12 25.46 43.63 4.69
2951 7225 4.697352 CAGATTTTGGTCCTGACTAACTGG 59.303 45.833 0.00 0.00 38.68 4.00
2981 7713 5.271598 TGGCATTTCACCCTGATAAATTCT 58.728 37.500 0.00 0.00 0.00 2.40
3031 7763 1.524863 CCCTGTTCTCCGTCGACAGT 61.525 60.000 17.16 0.00 39.23 3.55
3063 7795 2.296471 TCCACCTCGTTCTTGAACTCTC 59.704 50.000 11.11 0.00 0.00 3.20
3177 7913 1.679139 TGTGTCCAAGCTCTTGTTGG 58.321 50.000 8.60 0.00 45.18 3.77
3196 7932 3.500680 ACACGTGCTAACCGAAAATGAAT 59.499 39.130 17.22 0.00 0.00 2.57
3205 7941 0.318360 TGAGTGACACGTGCTAACCG 60.318 55.000 17.22 0.00 0.00 4.44
3233 7970 5.715434 AAATGGTTGTAACTATTTGCCGT 57.285 34.783 15.36 0.00 44.82 5.68
3248 7986 4.954875 TGAATTTCTCGGCAAAAATGGTT 58.045 34.783 0.00 0.00 0.00 3.67
3256 8233 5.000591 TCACATAGTTGAATTTCTCGGCAA 58.999 37.500 0.00 0.00 0.00 4.52
3272 8264 5.125900 TGGATCTGTTGGCAAATTCACATAG 59.874 40.000 0.00 0.00 0.00 2.23
3479 8471 2.176273 GTCGCCGATGCTGCTGAAT 61.176 57.895 0.00 0.00 34.43 2.57
3524 8519 7.230510 TGCAGTTCTTACTATGTTCCAACAATT 59.769 33.333 0.00 0.00 35.90 2.32
3562 8560 2.806244 AGTACTTGAACATTGCCGTGTC 59.194 45.455 0.00 0.00 0.00 3.67
3593 8604 2.104281 AGGGTACACTCGCAAAGAAACT 59.896 45.455 0.00 0.00 0.00 2.66
3602 8615 2.412112 CGGCTAGGGTACACTCGC 59.588 66.667 13.07 13.07 0.00 5.03
3615 8628 3.420893 TCAACAATCAGAAAATCCGGCT 58.579 40.909 0.00 0.00 0.00 5.52
3636 8650 1.000717 GCCAGCACACCGTACAAAAAT 60.001 47.619 0.00 0.00 0.00 1.82
3695 8725 8.721478 GTTATAAACATCCTGCGTGAATGATAT 58.279 33.333 0.00 0.00 0.00 1.63
3705 8735 2.800544 CCGAGGTTATAAACATCCTGCG 59.199 50.000 2.78 4.57 38.90 5.18
3720 8750 1.095228 CAGCAACAACACACCGAGGT 61.095 55.000 0.00 0.00 0.00 3.85
3753 8796 3.003480 AGCTATGAGGTTGAAACTTCGC 58.997 45.455 0.00 0.00 37.79 4.70
3845 8912 4.760878 TGCAATACGTAAGGCACATCTAA 58.239 39.130 17.40 0.00 46.39 2.10
3868 9024 5.104569 TGACATGGGAGTTAGATGTGCAATA 60.105 40.000 0.00 0.00 30.39 1.90
3872 9028 3.266510 TGACATGGGAGTTAGATGTGC 57.733 47.619 0.00 0.00 30.39 4.57
3873 9029 8.455903 AATTAATGACATGGGAGTTAGATGTG 57.544 34.615 0.00 0.00 30.39 3.21
3874 9030 9.479549 AAAATTAATGACATGGGAGTTAGATGT 57.520 29.630 0.00 0.00 32.95 3.06
3877 9033 9.967451 TGTAAAATTAATGACATGGGAGTTAGA 57.033 29.630 0.00 0.00 0.00 2.10
3886 9042 9.520204 GAATCCCTGTGTAAAATTAATGACATG 57.480 33.333 0.00 0.00 0.00 3.21
3945 9105 8.186163 TGCTCTTCTTATTGCACATCTAAATTG 58.814 33.333 0.00 0.00 0.00 2.32
3974 9134 4.764823 TGGTTTGTTTAAGGCACATCTAGG 59.235 41.667 0.00 0.00 0.00 3.02
4008 9168 5.631929 ACGAACTTTCTTGGTTCAAACAAAC 59.368 36.000 0.00 0.00 41.99 2.93
4012 9172 3.546271 GCACGAACTTTCTTGGTTCAAAC 59.454 43.478 7.24 0.00 41.99 2.93
4042 9202 1.153041 AATAGGGTTGGGGCTTGGGT 61.153 55.000 0.00 0.00 0.00 4.51
4049 9209 3.007506 GGTTCAAACAAATAGGGTTGGGG 59.992 47.826 0.00 0.00 32.50 4.96
4059 9219 6.106003 GGTGAGTTTCTTGGTTCAAACAAAT 58.894 36.000 0.00 0.00 35.33 2.32
4200 9360 4.473520 CGTCGGGGAGCAGCCATT 62.474 66.667 0.00 0.00 38.95 3.16
4213 9373 0.248296 GACTTGCTCTAGCTCCGTCG 60.248 60.000 3.26 0.00 42.66 5.12
4215 9375 0.961358 ACGACTTGCTCTAGCTCCGT 60.961 55.000 3.26 4.92 42.66 4.69
4229 9389 0.667487 CCTGAATGCACGTCACGACT 60.667 55.000 2.91 0.00 0.00 4.18
4231 9391 0.599060 TACCTGAATGCACGTCACGA 59.401 50.000 2.91 0.00 0.00 4.35
4241 9401 3.615110 CGCATAGTAGCCCTACCTGAATG 60.615 52.174 1.98 3.57 36.75 2.67
4242 9402 2.563179 CGCATAGTAGCCCTACCTGAAT 59.437 50.000 1.98 0.00 36.75 2.57
4243 9403 1.961394 CGCATAGTAGCCCTACCTGAA 59.039 52.381 1.98 0.00 36.75 3.02
4244 9404 1.133575 ACGCATAGTAGCCCTACCTGA 60.134 52.381 1.98 0.00 36.75 3.86
4316 9480 2.672996 GGTGCCTGTTGGTGCGAT 60.673 61.111 0.00 0.00 35.27 4.58
4358 9522 1.001269 AGTGCTCACTGGCATGCAT 60.001 52.632 21.36 0.55 44.34 3.96
4385 9549 1.883926 TCATCCAACACGTCGAGAAGA 59.116 47.619 0.00 0.00 0.00 2.87
4403 9567 3.578688 CTCGACATTGTCAGATGTGTCA 58.421 45.455 16.61 0.00 40.21 3.58
4412 9576 3.610040 ATGGTTAGCTCGACATTGTCA 57.390 42.857 16.61 3.66 32.09 3.58
4427 9591 2.676342 GCCTTCGATGTTCGTTATGGTT 59.324 45.455 0.00 0.00 41.35 3.67
4433 9597 0.034896 ACCTGCCTTCGATGTTCGTT 59.965 50.000 0.00 0.00 41.35 3.85
4562 9726 6.884832 TCAATCTCCGTGATTTACATAGGTT 58.115 36.000 0.00 0.00 43.00 3.50
4577 9741 8.072567 GGATCTTGAATTTGTTATCAATCTCCG 58.927 37.037 0.00 0.00 35.20 4.63
4583 9747 7.680442 TGTCGGATCTTGAATTTGTTATCAA 57.320 32.000 0.00 0.00 34.57 2.57
4592 9756 9.981114 AGTTAAAATTTTGTCGGATCTTGAATT 57.019 25.926 13.76 0.00 0.00 2.17
4604 9768 9.424659 CAAATGCAGTTCAGTTAAAATTTTGTC 57.575 29.630 13.76 6.41 30.99 3.18
4664 9829 3.694566 GGACTCAATCATTAACCCACCAC 59.305 47.826 0.00 0.00 0.00 4.16
4673 9838 5.201713 GAGATCGTGGGACTCAATCATTA 57.798 43.478 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.