Multiple sequence alignment - TraesCS5A01G026200

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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 TraesCS5A01G026200 chr5A 100.000 3371 0 0 1 3371 21417791 21421161 0.000000e+00 6226
1 TraesCS5A01G026200 chr5A 87.296 1535 152 23 851 2371 21415076 21413571 0.000000e+00 1714
2 TraesCS5A01G026200 chr5D 92.301 2143 107 37 670 2786 32809958 32812068 0.000000e+00 2990
3 TraesCS5A01G026200 chr5D 86.101 849 98 7 1522 2360 32699373 32698535 0.000000e+00 896
4 TraesCS5A01G026200 chr5D 91.203 557 26 6 2818 3370 32812068 32812605 0.000000e+00 736
5 TraesCS5A01G026200 chr5D 91.667 432 32 3 993 1421 239492846 239493276 2.240000e-166 595
6 TraesCS5A01G026200 chr5D 86.580 462 38 10 207 658 32809528 32809975 3.910000e-134 488
7 TraesCS5A01G026200 chr5D 92.982 114 8 0 3258 3371 133635641 133635754 2.080000e-37 167
8 TraesCS5A01G026200 chr6B 89.577 1583 102 25 852 2404 683371500 683373049 0.000000e+00 1951
9 TraesCS5A01G026200 chr6B 88.100 521 42 9 1897 2404 683317379 683317892 4.810000e-168 601
10 TraesCS5A01G026200 chr6B 91.435 432 30 3 993 1421 705881150 705880723 1.350000e-163 586
11 TraesCS5A01G026200 chr6B 83.251 203 17 10 670 862 683316661 683316856 1.610000e-38 171
12 TraesCS5A01G026200 chr2A 86.930 1798 113 37 670 2404 38614865 38613127 0.000000e+00 1906
13 TraesCS5A01G026200 chr2A 95.109 184 9 0 1 184 74892256 74892439 1.180000e-74 291
14 TraesCS5A01G026200 chr2A 93.299 194 13 0 1 194 205003811 205004004 1.530000e-73 287
15 TraesCS5A01G026200 chr2D 88.742 906 68 12 1511 2404 605386712 605385829 0.000000e+00 1077
16 TraesCS5A01G026200 chr2D 90.909 682 39 12 852 1517 605387620 605386946 0.000000e+00 894
17 TraesCS5A01G026200 chr7D 94.700 434 18 4 993 1421 500956168 500956601 0.000000e+00 669
18 TraesCS5A01G026200 chr7D 95.628 183 8 0 1 183 11437528 11437346 9.150000e-76 294
19 TraesCS5A01G026200 chr3D 76.267 1361 263 49 1081 2404 80478666 80477329 0.000000e+00 669
20 TraesCS5A01G026200 chr3D 85.510 628 52 16 2577 3183 491175054 491174445 1.330000e-173 619
21 TraesCS5A01G026200 chr3D 75.567 1322 246 55 1078 2361 80568922 80567640 6.270000e-162 580
22 TraesCS5A01G026200 chr3D 84.466 206 19 6 364 556 474459432 474459637 1.230000e-44 191
23 TraesCS5A01G026200 chr3D 90.083 121 11 1 3252 3371 571465536 571465416 4.500000e-34 156
24 TraesCS5A01G026200 chr3B 76.568 1323 232 54 1078 2361 126310682 126309399 0.000000e+00 654
25 TraesCS5A01G026200 chr3B 75.749 1336 260 50 1081 2378 126302781 126301472 6.180000e-172 614
26 TraesCS5A01G026200 chr3B 90.152 132 10 3 3241 3371 410043906 410043777 5.780000e-38 169
27 TraesCS5A01G026200 chr3B 90.164 122 12 0 3250 3371 507505543 507505664 3.480000e-35 159
28 TraesCS5A01G026200 chr3B 80.000 200 31 5 364 556 228640112 228639915 4.540000e-29 139
29 TraesCS5A01G026200 chr2B 84.873 628 56 18 2577 3183 690932394 690933003 6.230000e-167 597
30 TraesCS5A01G026200 chr2B 84.738 629 56 17 2577 3183 672021230 672020620 8.050000e-166 593
31 TraesCS5A01G026200 chr2B 86.667 135 18 0 2553 2687 748333943 748333809 2.100000e-32 150
32 TraesCS5A01G026200 chr2B 86.667 135 18 0 2553 2687 748420261 748420127 2.100000e-32 150
33 TraesCS5A01G026200 chr6A 84.640 625 53 19 2577 3183 553938284 553938883 1.740000e-162 582
34 TraesCS5A01G026200 chr6A 96.739 184 6 0 1 184 91414173 91414356 1.170000e-79 307
35 TraesCS5A01G026200 chr6A 95.652 184 8 0 1 184 569393502 569393685 2.540000e-76 296
36 TraesCS5A01G026200 chr6A 95.628 183 6 2 1 183 91419787 91419967 3.290000e-75 292
37 TraesCS5A01G026200 chr6A 95.109 184 9 0 1 184 559284989 559284806 1.180000e-74 291
38 TraesCS5A01G026200 chr6A 92.982 114 8 0 3258 3371 140050597 140050710 2.080000e-37 167
39 TraesCS5A01G026200 chr6A 92.982 114 8 0 3258 3371 140070980 140071093 2.080000e-37 167
40 TraesCS5A01G026200 chr4A 91.827 416 30 3 1001 1413 275447605 275448019 8.110000e-161 577
41 TraesCS5A01G026200 chr4A 81.720 651 63 22 2554 3183 174726257 174725642 3.020000e-135 492
42 TraesCS5A01G026200 chr5B 88.046 435 45 6 1547 1978 24104702 24104272 3.000000e-140 508
43 TraesCS5A01G026200 chr5B 90.751 173 16 0 2188 2360 24104276 24104104 7.270000e-57 231
44 TraesCS5A01G026200 chr3A 95.604 182 7 1 3 184 688531866 688532046 1.180000e-74 291
45 TraesCS5A01G026200 chr3A 95.109 184 9 0 1 184 688561382 688561565 1.180000e-74 291
46 TraesCS5A01G026200 chr4B 92.105 114 9 0 3258 3371 483266378 483266491 9.680000e-36 161
47 TraesCS5A01G026200 chr7B 90.756 119 11 0 3253 3371 20046720 20046838 3.480000e-35 159


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 TraesCS5A01G026200 chr5A 21417791 21421161 3370 False 6226.000000 6226 100.0000 1 3371 1 chr5A.!!$F1 3370
1 TraesCS5A01G026200 chr5A 21413571 21415076 1505 True 1714.000000 1714 87.2960 851 2371 1 chr5A.!!$R1 1520
2 TraesCS5A01G026200 chr5D 32809528 32812605 3077 False 1404.666667 2990 90.0280 207 3370 3 chr5D.!!$F3 3163
3 TraesCS5A01G026200 chr5D 32698535 32699373 838 True 896.000000 896 86.1010 1522 2360 1 chr5D.!!$R1 838
4 TraesCS5A01G026200 chr6B 683371500 683373049 1549 False 1951.000000 1951 89.5770 852 2404 1 chr6B.!!$F1 1552
5 TraesCS5A01G026200 chr6B 683316661 683317892 1231 False 386.000000 601 85.6755 670 2404 2 chr6B.!!$F2 1734
6 TraesCS5A01G026200 chr2A 38613127 38614865 1738 True 1906.000000 1906 86.9300 670 2404 1 chr2A.!!$R1 1734
7 TraesCS5A01G026200 chr2D 605385829 605387620 1791 True 985.500000 1077 89.8255 852 2404 2 chr2D.!!$R1 1552
8 TraesCS5A01G026200 chr3D 80477329 80478666 1337 True 669.000000 669 76.2670 1081 2404 1 chr3D.!!$R1 1323
9 TraesCS5A01G026200 chr3D 491174445 491175054 609 True 619.000000 619 85.5100 2577 3183 1 chr3D.!!$R3 606
10 TraesCS5A01G026200 chr3D 80567640 80568922 1282 True 580.000000 580 75.5670 1078 2361 1 chr3D.!!$R2 1283
11 TraesCS5A01G026200 chr3B 126309399 126310682 1283 True 654.000000 654 76.5680 1078 2361 1 chr3B.!!$R2 1283
12 TraesCS5A01G026200 chr3B 126301472 126302781 1309 True 614.000000 614 75.7490 1081 2378 1 chr3B.!!$R1 1297
13 TraesCS5A01G026200 chr2B 690932394 690933003 609 False 597.000000 597 84.8730 2577 3183 1 chr2B.!!$F1 606
14 TraesCS5A01G026200 chr2B 672020620 672021230 610 True 593.000000 593 84.7380 2577 3183 1 chr2B.!!$R1 606
15 TraesCS5A01G026200 chr6A 553938284 553938883 599 False 582.000000 582 84.6400 2577 3183 1 chr6A.!!$F5 606
16 TraesCS5A01G026200 chr4A 174725642 174726257 615 True 492.000000 492 81.7200 2554 3183 1 chr4A.!!$R1 629
17 TraesCS5A01G026200 chr5B 24104104 24104702 598 True 369.500000 508 89.3985 1547 2360 2 chr5B.!!$R1 813

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
316 317 0.038310 AGCAAGGAAACTAGGCCCAC 59.962 55.0 0.00 0.0 42.68 4.61 F
317 318 0.251165 GCAAGGAAACTAGGCCCACA 60.251 55.0 0.00 0.0 42.68 4.17 F
758 783 0.394216 TCAATTGATCACCTGCCCCG 60.394 55.0 3.38 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 1923 1.212229 GTCGACGGTGAAGGTCTCC 59.788 63.158 0.00 0.0 32.24 3.71 R
2115 2527 1.373748 CAACGTCACGTCCGGGAAT 60.374 57.895 1.67 0.0 39.99 3.01 R
2641 3074 0.949397 GGGACAGGAACAAAACGGAC 59.051 55.000 0.00 0.0 0.00 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.561478 ACATTTACACCGCTCCTGTT 57.439 45.000 0.00 0.00 0.00 3.16
20 21 2.858745 ACATTTACACCGCTCCTGTTT 58.141 42.857 0.00 0.00 0.00 2.83
21 22 4.010667 ACATTTACACCGCTCCTGTTTA 57.989 40.909 0.00 0.00 0.00 2.01
22 23 3.749609 ACATTTACACCGCTCCTGTTTAC 59.250 43.478 0.00 0.00 0.00 2.01
23 24 3.756933 TTTACACCGCTCCTGTTTACT 57.243 42.857 0.00 0.00 0.00 2.24
24 25 3.756933 TTACACCGCTCCTGTTTACTT 57.243 42.857 0.00 0.00 0.00 2.24
25 26 2.632987 ACACCGCTCCTGTTTACTTT 57.367 45.000 0.00 0.00 0.00 2.66
26 27 2.490991 ACACCGCTCCTGTTTACTTTC 58.509 47.619 0.00 0.00 0.00 2.62
27 28 2.158871 ACACCGCTCCTGTTTACTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
28 29 3.074412 CACCGCTCCTGTTTACTTTCAT 58.926 45.455 0.00 0.00 0.00 2.57
29 30 3.074412 ACCGCTCCTGTTTACTTTCATG 58.926 45.455 0.00 0.00 0.00 3.07
30 31 3.074412 CCGCTCCTGTTTACTTTCATGT 58.926 45.455 0.00 0.00 0.00 3.21
31 32 3.120199 CCGCTCCTGTTTACTTTCATGTG 60.120 47.826 0.00 0.00 0.00 3.21
32 33 3.498397 CGCTCCTGTTTACTTTCATGTGT 59.502 43.478 0.00 0.00 0.00 3.72
33 34 4.611355 CGCTCCTGTTTACTTTCATGTGTG 60.611 45.833 0.00 0.00 0.00 3.82
34 35 4.787598 CTCCTGTTTACTTTCATGTGTGC 58.212 43.478 0.00 0.00 0.00 4.57
35 36 4.203226 TCCTGTTTACTTTCATGTGTGCA 58.797 39.130 0.00 0.00 0.00 4.57
36 37 4.275689 TCCTGTTTACTTTCATGTGTGCAG 59.724 41.667 0.00 0.00 0.00 4.41
37 38 4.036734 CCTGTTTACTTTCATGTGTGCAGT 59.963 41.667 0.00 0.00 0.00 4.40
38 39 5.238432 CCTGTTTACTTTCATGTGTGCAGTA 59.762 40.000 0.00 0.00 0.00 2.74
39 40 6.055231 TGTTTACTTTCATGTGTGCAGTAC 57.945 37.500 0.00 0.00 0.00 2.73
40 41 5.820423 TGTTTACTTTCATGTGTGCAGTACT 59.180 36.000 0.00 0.00 0.00 2.73
41 42 6.987404 TGTTTACTTTCATGTGTGCAGTACTA 59.013 34.615 0.00 0.00 0.00 1.82
42 43 7.170828 TGTTTACTTTCATGTGTGCAGTACTAG 59.829 37.037 0.00 0.00 0.00 2.57
43 44 5.215252 ACTTTCATGTGTGCAGTACTAGT 57.785 39.130 0.00 0.00 0.00 2.57
44 45 6.340962 ACTTTCATGTGTGCAGTACTAGTA 57.659 37.500 0.00 0.00 0.00 1.82
45 46 6.390721 ACTTTCATGTGTGCAGTACTAGTAG 58.609 40.000 1.87 0.00 0.00 2.57
46 47 5.977489 TTCATGTGTGCAGTACTAGTAGT 57.023 39.130 8.14 8.14 0.00 2.73
47 48 5.977489 TCATGTGTGCAGTACTAGTAGTT 57.023 39.130 8.40 0.00 0.00 2.24
48 49 6.340962 TCATGTGTGCAGTACTAGTAGTTT 57.659 37.500 8.40 0.00 0.00 2.66
49 50 6.156519 TCATGTGTGCAGTACTAGTAGTTTG 58.843 40.000 8.40 8.86 0.00 2.93
50 51 4.304110 TGTGTGCAGTACTAGTAGTTTGC 58.696 43.478 22.78 22.78 37.79 3.68
51 52 4.202172 TGTGTGCAGTACTAGTAGTTTGCA 60.202 41.667 25.96 25.96 41.79 4.08
52 53 4.929808 GTGTGCAGTACTAGTAGTTTGCAT 59.070 41.667 29.38 3.87 43.94 3.96
53 54 6.097356 GTGTGCAGTACTAGTAGTTTGCATA 58.903 40.000 29.38 26.21 43.94 3.14
54 55 6.253727 GTGTGCAGTACTAGTAGTTTGCATAG 59.746 42.308 29.38 10.59 43.94 2.23
55 56 6.152154 TGTGCAGTACTAGTAGTTTGCATAGA 59.848 38.462 29.38 19.82 43.94 1.98
56 57 7.147897 TGTGCAGTACTAGTAGTTTGCATAGAT 60.148 37.037 29.38 1.46 43.94 1.98
57 58 8.350722 GTGCAGTACTAGTAGTTTGCATAGATA 58.649 37.037 29.38 13.87 43.94 1.98
58 59 9.078990 TGCAGTACTAGTAGTTTGCATAGATAT 57.921 33.333 25.96 0.00 40.33 1.63
59 60 9.915629 GCAGTACTAGTAGTTTGCATAGATATT 57.084 33.333 23.83 0.00 37.47 1.28
82 83 6.841443 TTCTACTATCTGTCTAGTACGTGC 57.159 41.667 0.00 0.00 33.96 5.34
83 84 4.981054 TCTACTATCTGTCTAGTACGTGCG 59.019 45.833 0.00 0.00 33.96 5.34
84 85 3.529533 ACTATCTGTCTAGTACGTGCGT 58.470 45.455 0.00 2.05 30.16 5.24
85 86 4.686972 ACTATCTGTCTAGTACGTGCGTA 58.313 43.478 0.00 0.00 30.16 4.42
98 99 4.678509 ACGTGCGTACATCATCAAAATT 57.321 36.364 4.09 0.00 0.00 1.82
99 100 4.647964 ACGTGCGTACATCATCAAAATTC 58.352 39.130 4.09 0.00 0.00 2.17
100 101 4.153296 ACGTGCGTACATCATCAAAATTCA 59.847 37.500 4.09 0.00 0.00 2.57
101 102 4.725280 CGTGCGTACATCATCAAAATTCAG 59.275 41.667 4.09 0.00 0.00 3.02
102 103 5.631026 GTGCGTACATCATCAAAATTCAGT 58.369 37.500 0.00 0.00 0.00 3.41
103 104 6.454981 CGTGCGTACATCATCAAAATTCAGTA 60.455 38.462 4.09 0.00 0.00 2.74
104 105 7.409697 GTGCGTACATCATCAAAATTCAGTAT 58.590 34.615 0.00 0.00 0.00 2.12
105 106 7.374228 GTGCGTACATCATCAAAATTCAGTATG 59.626 37.037 0.00 0.00 37.54 2.39
106 107 7.065683 TGCGTACATCATCAAAATTCAGTATGT 59.934 33.333 0.00 0.00 37.40 2.29
107 108 7.584123 GCGTACATCATCAAAATTCAGTATGTC 59.416 37.037 0.00 0.00 37.40 3.06
108 109 8.603181 CGTACATCATCAAAATTCAGTATGTCA 58.397 33.333 0.00 0.00 37.40 3.58
114 115 9.176460 TCATCAAAATTCAGTATGTCATTAGCA 57.824 29.630 0.00 0.00 37.40 3.49
115 116 9.229784 CATCAAAATTCAGTATGTCATTAGCAC 57.770 33.333 0.00 0.00 37.40 4.40
116 117 8.565896 TCAAAATTCAGTATGTCATTAGCACT 57.434 30.769 0.00 0.00 37.40 4.40
117 118 8.453320 TCAAAATTCAGTATGTCATTAGCACTG 58.547 33.333 7.02 7.02 38.34 3.66
118 119 5.998454 ATTCAGTATGTCATTAGCACTGC 57.002 39.130 8.14 0.00 37.20 4.40
119 120 3.797039 TCAGTATGTCATTAGCACTGCC 58.203 45.455 8.14 0.00 37.20 4.85
120 121 3.452264 TCAGTATGTCATTAGCACTGCCT 59.548 43.478 8.14 0.00 37.20 4.75
121 122 4.649218 TCAGTATGTCATTAGCACTGCCTA 59.351 41.667 8.14 0.00 37.20 3.93
122 123 5.305386 TCAGTATGTCATTAGCACTGCCTAT 59.695 40.000 8.14 0.00 37.20 2.57
123 124 6.493458 TCAGTATGTCATTAGCACTGCCTATA 59.507 38.462 8.14 0.00 37.20 1.31
124 125 7.179160 TCAGTATGTCATTAGCACTGCCTATAT 59.821 37.037 8.14 0.00 37.20 0.86
125 126 7.490725 CAGTATGTCATTAGCACTGCCTATATC 59.509 40.741 0.00 0.00 31.14 1.63
126 127 5.806654 TGTCATTAGCACTGCCTATATCA 57.193 39.130 0.00 0.00 0.00 2.15
127 128 6.364568 TGTCATTAGCACTGCCTATATCAT 57.635 37.500 0.00 0.00 0.00 2.45
128 129 6.168389 TGTCATTAGCACTGCCTATATCATG 58.832 40.000 0.00 0.00 0.00 3.07
129 130 6.169094 GTCATTAGCACTGCCTATATCATGT 58.831 40.000 0.00 0.00 0.00 3.21
130 131 6.652481 GTCATTAGCACTGCCTATATCATGTT 59.348 38.462 0.00 0.00 0.00 2.71
131 132 6.875726 TCATTAGCACTGCCTATATCATGTTC 59.124 38.462 0.00 0.00 0.00 3.18
132 133 4.694760 AGCACTGCCTATATCATGTTCA 57.305 40.909 0.00 0.00 0.00 3.18
133 134 5.238624 AGCACTGCCTATATCATGTTCAT 57.761 39.130 0.00 0.00 0.00 2.57
134 135 5.001874 AGCACTGCCTATATCATGTTCATG 58.998 41.667 6.46 6.46 0.00 3.07
135 136 4.999311 GCACTGCCTATATCATGTTCATGA 59.001 41.667 16.19 16.19 34.73 3.07
136 137 5.646793 GCACTGCCTATATCATGTTCATGAT 59.353 40.000 24.96 24.96 43.17 2.45
137 138 6.150641 GCACTGCCTATATCATGTTCATGATT 59.849 38.462 26.19 18.07 41.20 2.57
138 139 7.309012 GCACTGCCTATATCATGTTCATGATTT 60.309 37.037 26.19 21.62 41.20 2.17
139 140 9.223099 CACTGCCTATATCATGTTCATGATTTA 57.777 33.333 26.19 21.59 41.20 1.40
140 141 9.970553 ACTGCCTATATCATGTTCATGATTTAT 57.029 29.630 26.19 18.86 41.20 1.40
181 182 7.851822 TCGAACAATTGCTTAATTTCTCAAC 57.148 32.000 5.05 0.00 0.00 3.18
182 183 7.421599 TCGAACAATTGCTTAATTTCTCAACA 58.578 30.769 5.05 0.00 0.00 3.33
183 184 7.918033 TCGAACAATTGCTTAATTTCTCAACAA 59.082 29.630 5.05 0.00 0.00 2.83
184 185 8.209869 CGAACAATTGCTTAATTTCTCAACAAG 58.790 33.333 5.05 0.00 0.00 3.16
185 186 7.412137 ACAATTGCTTAATTTCTCAACAAGC 57.588 32.000 5.05 0.82 41.51 4.01
188 189 5.772825 TGCTTAATTTCTCAACAAGCAGT 57.227 34.783 5.63 0.00 44.79 4.40
189 190 6.875948 TGCTTAATTTCTCAACAAGCAGTA 57.124 33.333 5.63 0.00 44.79 2.74
190 191 6.902341 TGCTTAATTTCTCAACAAGCAGTAG 58.098 36.000 5.63 0.00 44.79 2.57
191 192 5.797434 GCTTAATTTCTCAACAAGCAGTAGC 59.203 40.000 2.69 0.00 40.96 3.58
242 243 1.022735 CGACAGGCTAGGTACACGAT 58.977 55.000 0.00 0.00 0.00 3.73
251 252 2.068834 AGGTACACGATCCAGGTAGG 57.931 55.000 0.00 0.00 39.47 3.18
255 256 0.824759 ACACGATCCAGGTAGGCTTC 59.175 55.000 0.00 0.00 37.29 3.86
256 257 0.824109 CACGATCCAGGTAGGCTTCA 59.176 55.000 0.00 0.00 37.29 3.02
269 270 1.902508 AGGCTTCAAGCACTGTAGCTA 59.097 47.619 12.53 0.00 45.89 3.32
270 271 2.003301 GGCTTCAAGCACTGTAGCTAC 58.997 52.381 17.30 17.30 45.89 3.58
271 272 2.612972 GGCTTCAAGCACTGTAGCTACA 60.613 50.000 24.63 24.63 45.89 2.74
272 273 3.067106 GCTTCAAGCACTGTAGCTACAA 58.933 45.455 25.95 7.99 45.89 2.41
273 274 3.498397 GCTTCAAGCACTGTAGCTACAAA 59.502 43.478 25.95 14.79 45.89 2.83
274 275 4.154918 GCTTCAAGCACTGTAGCTACAAAT 59.845 41.667 25.95 15.14 45.89 2.32
275 276 5.611796 TTCAAGCACTGTAGCTACAAATG 57.388 39.130 25.95 24.90 45.89 2.32
276 277 3.436704 TCAAGCACTGTAGCTACAAATGC 59.563 43.478 34.73 34.73 45.89 3.56
277 278 3.340814 AGCACTGTAGCTACAAATGCT 57.659 42.857 36.83 36.83 45.95 3.79
286 287 3.254060 AGCTACAAATGCTACAGTGACG 58.746 45.455 0.00 0.00 39.21 4.35
293 294 0.526211 TGCTACAGTGACGGCTACAG 59.474 55.000 0.00 0.00 0.00 2.74
294 295 0.802607 GCTACAGTGACGGCTACAGC 60.803 60.000 0.00 0.00 41.14 4.40
316 317 0.038310 AGCAAGGAAACTAGGCCCAC 59.962 55.000 0.00 0.00 42.68 4.61
317 318 0.251165 GCAAGGAAACTAGGCCCACA 60.251 55.000 0.00 0.00 42.68 4.17
323 324 2.076597 AAACTAGGCCCACACCCCAC 62.077 60.000 0.00 0.00 0.00 4.61
393 394 7.288672 AGTTTCTATTCTTTAAACTGTTCGCG 58.711 34.615 0.00 0.00 40.85 5.87
422 423 6.538742 TGAATATTCACTAGCAGTTAACTGGC 59.461 38.462 31.42 23.80 37.06 4.85
450 451 1.595993 TAGCCTCTCTGTGTGGACGC 61.596 60.000 2.28 0.00 0.00 5.19
472 473 4.933064 GGGCGCGAGATCCAGTCG 62.933 72.222 12.10 0.00 40.50 4.18
476 477 2.473760 CGCGAGATCCAGTCGAGGT 61.474 63.158 0.00 0.00 39.92 3.85
505 506 1.154654 CGGTCTCTTTTCGCGTTGC 60.155 57.895 5.77 0.00 0.00 4.17
556 557 2.043980 CGGGCGCCAATTACCTTGT 61.044 57.895 30.85 0.00 32.61 3.16
557 558 1.510844 GGGCGCCAATTACCTTGTG 59.489 57.895 30.85 0.00 32.61 3.33
577 587 2.815308 CCGCGCAATAGGAGGTCT 59.185 61.111 8.75 0.00 0.00 3.85
578 588 1.144057 CCGCGCAATAGGAGGTCTT 59.856 57.895 8.75 0.00 0.00 3.01
641 652 8.729805 ACAGAGGAGAAATATCAAATCAGTTC 57.270 34.615 0.00 0.00 0.00 3.01
642 653 8.324306 ACAGAGGAGAAATATCAAATCAGTTCA 58.676 33.333 0.00 0.00 0.00 3.18
643 654 9.170734 CAGAGGAGAAATATCAAATCAGTTCAA 57.829 33.333 0.00 0.00 0.00 2.69
644 655 9.917887 AGAGGAGAAATATCAAATCAGTTCAAT 57.082 29.630 0.00 0.00 0.00 2.57
646 657 8.834465 AGGAGAAATATCAAATCAGTTCAATCG 58.166 33.333 0.00 0.00 0.00 3.34
647 658 8.616076 GGAGAAATATCAAATCAGTTCAATCGT 58.384 33.333 0.00 0.00 0.00 3.73
648 659 9.994432 GAGAAATATCAAATCAGTTCAATCGTT 57.006 29.630 0.00 0.00 0.00 3.85
651 662 9.573133 AAATATCAAATCAGTTCAATCGTTTCC 57.427 29.630 0.00 0.00 0.00 3.13
652 663 6.573664 ATCAAATCAGTTCAATCGTTTCCA 57.426 33.333 0.00 0.00 0.00 3.53
653 664 6.573664 TCAAATCAGTTCAATCGTTTCCAT 57.426 33.333 0.00 0.00 0.00 3.41
654 665 6.980593 TCAAATCAGTTCAATCGTTTCCATT 58.019 32.000 0.00 0.00 0.00 3.16
655 666 7.432869 TCAAATCAGTTCAATCGTTTCCATTT 58.567 30.769 0.00 0.00 0.00 2.32
656 667 7.594758 TCAAATCAGTTCAATCGTTTCCATTTC 59.405 33.333 0.00 0.00 0.00 2.17
657 668 6.824305 ATCAGTTCAATCGTTTCCATTTCT 57.176 33.333 0.00 0.00 0.00 2.52
658 669 6.633500 TCAGTTCAATCGTTTCCATTTCTT 57.367 33.333 0.00 0.00 0.00 2.52
659 670 7.038154 TCAGTTCAATCGTTTCCATTTCTTT 57.962 32.000 0.00 0.00 0.00 2.52
660 671 7.488322 TCAGTTCAATCGTTTCCATTTCTTTT 58.512 30.769 0.00 0.00 0.00 2.27
661 672 7.978975 TCAGTTCAATCGTTTCCATTTCTTTTT 59.021 29.630 0.00 0.00 0.00 1.94
698 709 6.768861 TCGTTTCCATTTCTGAAAGGTCTAAA 59.231 34.615 13.03 8.08 38.25 1.85
708 719 4.985538 TGAAAGGTCTAAAGTTGATGCCT 58.014 39.130 0.00 0.00 0.00 4.75
758 783 0.394216 TCAATTGATCACCTGCCCCG 60.394 55.000 3.38 0.00 0.00 5.73
768 793 2.721167 CCTGCCCCGACTCGAATGA 61.721 63.158 0.00 0.00 0.00 2.57
799 830 8.359642 TCCTAAATTCCTAATTAACATGCATGC 58.640 33.333 26.53 11.82 0.00 4.06
800 831 8.143193 CCTAAATTCCTAATTAACATGCATGCA 58.857 33.333 26.53 25.04 0.00 3.96
801 832 7.775397 AAATTCCTAATTAACATGCATGCAC 57.225 32.000 25.37 0.00 0.00 4.57
802 833 6.720112 ATTCCTAATTAACATGCATGCACT 57.280 33.333 25.37 13.20 0.00 4.40
803 834 6.528537 TTCCTAATTAACATGCATGCACTT 57.471 33.333 25.37 19.07 0.00 3.16
804 835 7.637631 TTCCTAATTAACATGCATGCACTTA 57.362 32.000 25.37 18.00 0.00 2.24
805 836 7.026631 TCCTAATTAACATGCATGCACTTAC 57.973 36.000 25.37 0.00 0.00 2.34
837 869 6.575572 TCATTTGTTGCGTCAACTTAATTACG 59.424 34.615 18.81 0.00 43.85 3.18
842 874 2.030091 GCGTCAACTTAATTACGGCCTC 59.970 50.000 0.00 0.00 35.93 4.70
855 887 3.309600 ACGGCCTCCAAGTATAGTAGT 57.690 47.619 0.00 0.00 0.00 2.73
856 888 4.443978 ACGGCCTCCAAGTATAGTAGTA 57.556 45.455 0.00 0.00 0.00 1.82
956 1031 4.489810 CGCTATTAATACTGCCCTGAGAG 58.510 47.826 0.00 0.00 0.00 3.20
979 1057 4.434520 GAAGATCGAGTTAGGAACTTGGG 58.565 47.826 6.73 0.00 43.03 4.12
988 1082 5.701224 AGTTAGGAACTTGGGAAACAATCA 58.299 37.500 0.00 0.00 39.04 2.57
989 1083 6.133356 AGTTAGGAACTTGGGAAACAATCAA 58.867 36.000 0.00 0.00 39.04 2.57
992 1086 5.917462 AGGAACTTGGGAAACAATCAAAAG 58.083 37.500 0.00 0.00 38.65 2.27
997 1091 5.585844 ACTTGGGAAACAATCAAAAGCAAAG 59.414 36.000 0.00 0.00 38.65 2.77
1473 1605 4.293648 CACTCGGTCCACGGCACA 62.294 66.667 0.00 0.00 44.45 4.57
1999 2396 1.000896 AAGGAATTGCTGGACCCCG 60.001 57.895 0.00 0.00 0.00 5.73
2115 2527 0.902984 TGAAGGCGCTGGAGAAGGTA 60.903 55.000 7.64 0.00 0.00 3.08
2263 2675 2.026734 CGACGATCGGCAGCATCT 59.973 61.111 23.01 0.00 36.00 2.90
2361 2774 4.465446 CCCTCTCCTCCCGCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
2362 2775 2.123077 CCTCTCCTCCCGCCTCAT 60.123 66.667 0.00 0.00 0.00 2.90
2363 2776 2.206536 CCTCTCCTCCCGCCTCATC 61.207 68.421 0.00 0.00 0.00 2.92
2415 2844 7.341256 AGGAGTAATAATCACCGTGTCTTCTAA 59.659 37.037 0.00 0.00 0.00 2.10
2419 2848 3.870633 ATCACCGTGTCTTCTAAGGTC 57.129 47.619 0.00 0.00 32.04 3.85
2424 2853 6.182627 TCACCGTGTCTTCTAAGGTCTTATA 58.817 40.000 0.00 0.00 32.04 0.98
2425 2854 6.832384 TCACCGTGTCTTCTAAGGTCTTATAT 59.168 38.462 0.00 0.00 32.04 0.86
2426 2855 7.994911 TCACCGTGTCTTCTAAGGTCTTATATA 59.005 37.037 0.00 0.00 32.04 0.86
2427 2856 8.794553 CACCGTGTCTTCTAAGGTCTTATATAT 58.205 37.037 0.00 0.00 32.04 0.86
2477 2906 9.981114 AAAAAGAAAGAAAGAAACTCTTCAACA 57.019 25.926 0.00 0.00 35.27 3.33
2491 2920 5.036117 TCTTCAACAAAGTAGTCCAGCTT 57.964 39.130 0.00 0.00 36.31 3.74
2508 2937 2.357637 AGCTTTTGTACGCACATGTGTT 59.642 40.909 26.01 16.06 39.74 3.32
2528 2957 4.532521 TGTTTGGAAGGGAAAAGAACCAAA 59.467 37.500 0.00 0.00 42.46 3.28
2533 2962 3.680777 AGGGAAAAGAACCAAACCAGA 57.319 42.857 0.00 0.00 0.00 3.86
2547 2976 7.648039 ACCAAACCAGAGTAATAACAAACAA 57.352 32.000 0.00 0.00 0.00 2.83
2549 2978 8.700973 ACCAAACCAGAGTAATAACAAACAAAT 58.299 29.630 0.00 0.00 0.00 2.32
2550 2979 9.191995 CCAAACCAGAGTAATAACAAACAAATC 57.808 33.333 0.00 0.00 0.00 2.17
2552 2981 8.706322 AACCAGAGTAATAACAAACAAATCCT 57.294 30.769 0.00 0.00 0.00 3.24
2557 2989 7.947890 AGAGTAATAACAAACAAATCCTGGGAA 59.052 33.333 0.00 0.00 0.00 3.97
2591 3023 3.740044 TTCGACTGAAATCCAATTCGC 57.260 42.857 0.00 0.00 32.99 4.70
2612 3045 3.910767 GCTTTCAGTCAGATTTTTCAGCG 59.089 43.478 0.00 0.00 0.00 5.18
2617 3050 3.496130 CAGTCAGATTTTTCAGCGACACT 59.504 43.478 0.00 0.00 0.00 3.55
2641 3074 5.006261 TGAGTTTAACAAGTGTCACATGTCG 59.994 40.000 13.83 0.00 27.55 4.35
2710 3145 1.104577 TCAAACAAGGAACCACGGGC 61.105 55.000 0.00 0.00 0.00 6.13
2761 3196 3.702548 CCTGGAGAAAATCATGGATGCAA 59.297 43.478 0.00 0.00 0.00 4.08
2766 3201 5.080969 AGAAAATCATGGATGCAAAGGTG 57.919 39.130 0.00 0.00 0.00 4.00
2786 3221 2.493099 AGAGATCCTCTCCTGGCAAT 57.507 50.000 0.60 0.00 44.42 3.56
2787 3222 2.328319 AGAGATCCTCTCCTGGCAATC 58.672 52.381 0.60 0.00 44.42 2.67
2788 3223 2.090606 AGAGATCCTCTCCTGGCAATCT 60.091 50.000 0.60 0.00 44.42 2.40
2789 3224 2.705127 GAGATCCTCTCCTGGCAATCTT 59.295 50.000 0.00 0.00 37.55 2.40
2790 3225 2.705127 AGATCCTCTCCTGGCAATCTTC 59.295 50.000 0.00 0.00 0.00 2.87
2791 3226 2.260639 TCCTCTCCTGGCAATCTTCT 57.739 50.000 0.00 0.00 0.00 2.85
2792 3227 2.555664 TCCTCTCCTGGCAATCTTCTT 58.444 47.619 0.00 0.00 0.00 2.52
2793 3228 2.915604 TCCTCTCCTGGCAATCTTCTTT 59.084 45.455 0.00 0.00 0.00 2.52
2794 3229 3.015327 CCTCTCCTGGCAATCTTCTTTG 58.985 50.000 0.00 0.00 0.00 2.77
2848 3286 7.827787 TCCCTCTCCTACTTTAGAATCTACAT 58.172 38.462 0.00 0.00 0.00 2.29
2932 3370 9.082313 AGAAAAGCAGATTTGAAAAGGAGAATA 57.918 29.630 0.00 0.00 0.00 1.75
2993 3431 5.786457 TCAAACTCCCCCTTTACATAGTACA 59.214 40.000 0.00 0.00 0.00 2.90
3045 3485 7.615403 AGATTAGTCAAATTACTGTGAGCAGA 58.385 34.615 1.30 0.00 45.28 4.26
3046 3486 8.263640 AGATTAGTCAAATTACTGTGAGCAGAT 58.736 33.333 1.30 0.00 45.28 2.90
3114 3570 9.654663 AGTATTCACAGTAGAATTCCTGTAAAC 57.345 33.333 14.59 10.98 39.83 2.01
3125 3581 8.045176 AGAATTCCTGTAAACTTACAATGCTC 57.955 34.615 0.65 0.00 42.55 4.26
3131 3587 9.461312 TCCTGTAAACTTACAATGCTCATTTAT 57.539 29.630 4.01 0.00 42.55 1.40
3155 3611 6.919721 TGGTAGAATTACAATGAAAAGCCAC 58.080 36.000 0.00 0.00 0.00 5.01
3338 3794 7.889469 ACAAAGCAAAATGAGTGAATCTACAT 58.111 30.769 0.00 0.00 0.00 2.29
3370 3826 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.281898 AGTAAACAGGAGCGGTGTAAAT 57.718 40.909 0.00 0.00 0.00 1.40
3 4 3.756933 AGTAAACAGGAGCGGTGTAAA 57.243 42.857 0.00 0.00 0.00 2.01
4 5 3.756933 AAGTAAACAGGAGCGGTGTAA 57.243 42.857 0.00 0.00 0.00 2.41
6 7 2.158871 TGAAAGTAAACAGGAGCGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
7 8 2.489971 TGAAAGTAAACAGGAGCGGTG 58.510 47.619 0.00 0.00 0.00 4.94
8 9 2.922740 TGAAAGTAAACAGGAGCGGT 57.077 45.000 0.00 0.00 0.00 5.68
9 10 3.074412 ACATGAAAGTAAACAGGAGCGG 58.926 45.455 0.00 0.00 0.00 5.52
10 11 3.498397 ACACATGAAAGTAAACAGGAGCG 59.502 43.478 0.00 0.00 0.00 5.03
11 12 4.787598 CACACATGAAAGTAAACAGGAGC 58.212 43.478 0.00 0.00 0.00 4.70
12 13 4.275689 TGCACACATGAAAGTAAACAGGAG 59.724 41.667 0.00 0.00 0.00 3.69
13 14 4.203226 TGCACACATGAAAGTAAACAGGA 58.797 39.130 0.00 0.00 0.00 3.86
14 15 4.036734 ACTGCACACATGAAAGTAAACAGG 59.963 41.667 0.00 0.00 0.00 4.00
15 16 5.173774 ACTGCACACATGAAAGTAAACAG 57.826 39.130 0.00 6.41 0.00 3.16
16 17 5.820423 AGTACTGCACACATGAAAGTAAACA 59.180 36.000 0.00 0.00 31.83 2.83
17 18 6.300354 AGTACTGCACACATGAAAGTAAAC 57.700 37.500 0.00 0.00 31.83 2.01
18 19 7.214381 ACTAGTACTGCACACATGAAAGTAAA 58.786 34.615 5.39 0.00 31.83 2.01
19 20 6.755206 ACTAGTACTGCACACATGAAAGTAA 58.245 36.000 5.39 0.00 31.83 2.24
20 21 6.340962 ACTAGTACTGCACACATGAAAGTA 57.659 37.500 5.39 0.00 0.00 2.24
21 22 5.215252 ACTAGTACTGCACACATGAAAGT 57.785 39.130 5.39 0.00 0.00 2.66
22 23 6.390721 ACTACTAGTACTGCACACATGAAAG 58.609 40.000 5.39 0.00 0.00 2.62
23 24 6.340962 ACTACTAGTACTGCACACATGAAA 57.659 37.500 5.39 0.00 0.00 2.69
24 25 5.977489 ACTACTAGTACTGCACACATGAA 57.023 39.130 5.39 0.00 0.00 2.57
25 26 5.977489 AACTACTAGTACTGCACACATGA 57.023 39.130 5.39 0.00 0.00 3.07
26 27 5.163953 GCAAACTACTAGTACTGCACACATG 60.164 44.000 16.57 0.00 37.23 3.21
27 28 4.929808 GCAAACTACTAGTACTGCACACAT 59.070 41.667 16.57 0.00 37.23 3.21
28 29 4.202172 TGCAAACTACTAGTACTGCACACA 60.202 41.667 18.82 3.49 40.24 3.72
29 30 4.304110 TGCAAACTACTAGTACTGCACAC 58.696 43.478 18.82 1.43 40.24 3.82
30 31 4.594123 TGCAAACTACTAGTACTGCACA 57.406 40.909 18.82 5.99 40.24 4.57
31 32 6.561614 TCTATGCAAACTACTAGTACTGCAC 58.438 40.000 22.54 6.25 44.59 4.57
32 33 6.769134 TCTATGCAAACTACTAGTACTGCA 57.231 37.500 22.41 22.41 45.32 4.41
33 34 9.915629 AATATCTATGCAAACTACTAGTACTGC 57.084 33.333 5.39 15.36 37.56 4.40
56 57 8.986847 GCACGTACTAGACAGATAGTAGAAATA 58.013 37.037 0.00 0.00 38.58 1.40
57 58 7.307278 CGCACGTACTAGACAGATAGTAGAAAT 60.307 40.741 0.00 0.00 38.58 2.17
58 59 6.019237 CGCACGTACTAGACAGATAGTAGAAA 60.019 42.308 0.00 0.00 38.58 2.52
59 60 5.461407 CGCACGTACTAGACAGATAGTAGAA 59.539 44.000 0.00 0.00 38.58 2.10
60 61 4.981054 CGCACGTACTAGACAGATAGTAGA 59.019 45.833 0.00 0.00 38.58 2.59
61 62 4.744137 ACGCACGTACTAGACAGATAGTAG 59.256 45.833 0.00 0.00 38.58 2.57
62 63 4.686972 ACGCACGTACTAGACAGATAGTA 58.313 43.478 0.00 0.00 37.24 1.82
63 64 3.529533 ACGCACGTACTAGACAGATAGT 58.470 45.455 0.00 0.00 39.35 2.12
64 65 5.004255 GTACGCACGTACTAGACAGATAG 57.996 47.826 22.45 0.00 45.30 2.08
66 67 3.940657 GTACGCACGTACTAGACAGAT 57.059 47.619 22.45 0.00 45.30 2.90
76 77 5.348997 TGAATTTTGATGATGTACGCACGTA 59.651 36.000 0.00 0.00 0.00 3.57
77 78 4.153296 TGAATTTTGATGATGTACGCACGT 59.847 37.500 0.00 0.00 0.00 4.49
78 79 4.646960 TGAATTTTGATGATGTACGCACG 58.353 39.130 0.00 0.00 0.00 5.34
79 80 5.631026 ACTGAATTTTGATGATGTACGCAC 58.369 37.500 0.00 0.00 0.00 5.34
80 81 5.878332 ACTGAATTTTGATGATGTACGCA 57.122 34.783 0.00 0.00 0.00 5.24
81 82 7.409697 ACATACTGAATTTTGATGATGTACGC 58.590 34.615 0.00 0.00 0.00 4.42
82 83 8.603181 TGACATACTGAATTTTGATGATGTACG 58.397 33.333 0.00 0.00 0.00 3.67
88 89 9.176460 TGCTAATGACATACTGAATTTTGATGA 57.824 29.630 0.00 0.00 0.00 2.92
89 90 9.229784 GTGCTAATGACATACTGAATTTTGATG 57.770 33.333 0.00 0.00 0.00 3.07
90 91 9.182214 AGTGCTAATGACATACTGAATTTTGAT 57.818 29.630 0.00 0.00 0.00 2.57
91 92 8.453320 CAGTGCTAATGACATACTGAATTTTGA 58.547 33.333 9.57 0.00 40.80 2.69
92 93 7.219535 GCAGTGCTAATGACATACTGAATTTTG 59.780 37.037 16.76 0.00 40.80 2.44
93 94 7.253422 GCAGTGCTAATGACATACTGAATTTT 58.747 34.615 16.76 0.00 40.80 1.82
94 95 6.183360 GGCAGTGCTAATGACATACTGAATTT 60.183 38.462 16.11 0.00 40.80 1.82
95 96 5.297776 GGCAGTGCTAATGACATACTGAATT 59.702 40.000 16.11 0.00 40.80 2.17
96 97 4.818546 GGCAGTGCTAATGACATACTGAAT 59.181 41.667 16.11 0.00 40.80 2.57
97 98 4.080919 AGGCAGTGCTAATGACATACTGAA 60.081 41.667 16.11 0.00 40.80 3.02
98 99 3.452264 AGGCAGTGCTAATGACATACTGA 59.548 43.478 16.11 0.00 40.80 3.41
99 100 3.801698 AGGCAGTGCTAATGACATACTG 58.198 45.455 16.11 10.50 41.15 2.74
100 101 5.815233 ATAGGCAGTGCTAATGACATACT 57.185 39.130 16.11 1.70 0.00 2.12
101 102 7.323420 TGATATAGGCAGTGCTAATGACATAC 58.677 38.462 16.11 0.00 0.00 2.39
102 103 7.480760 TGATATAGGCAGTGCTAATGACATA 57.519 36.000 16.11 3.21 0.00 2.29
103 104 6.364568 TGATATAGGCAGTGCTAATGACAT 57.635 37.500 16.11 0.00 0.00 3.06
104 105 5.806654 TGATATAGGCAGTGCTAATGACA 57.193 39.130 16.11 10.07 0.00 3.58
105 106 6.169094 ACATGATATAGGCAGTGCTAATGAC 58.831 40.000 16.11 7.94 0.00 3.06
106 107 6.364568 ACATGATATAGGCAGTGCTAATGA 57.635 37.500 16.11 0.00 0.00 2.57
107 108 6.652062 TGAACATGATATAGGCAGTGCTAATG 59.348 38.462 16.11 6.10 0.00 1.90
108 109 6.772605 TGAACATGATATAGGCAGTGCTAAT 58.227 36.000 16.11 11.14 0.00 1.73
109 110 6.173427 TGAACATGATATAGGCAGTGCTAA 57.827 37.500 16.11 3.56 0.00 3.09
110 111 5.806654 TGAACATGATATAGGCAGTGCTA 57.193 39.130 16.11 5.93 0.00 3.49
111 112 4.694760 TGAACATGATATAGGCAGTGCT 57.305 40.909 16.11 3.64 0.00 4.40
112 113 4.999311 TCATGAACATGATATAGGCAGTGC 59.001 41.667 6.55 6.55 42.42 4.40
155 156 8.915654 GTTGAGAAATTAAGCAATTGTTCGATT 58.084 29.630 7.40 2.70 34.53 3.34
156 157 8.081633 TGTTGAGAAATTAAGCAATTGTTCGAT 58.918 29.630 7.40 0.00 34.53 3.59
157 158 7.421599 TGTTGAGAAATTAAGCAATTGTTCGA 58.578 30.769 7.40 0.00 34.53 3.71
158 159 7.621832 TGTTGAGAAATTAAGCAATTGTTCG 57.378 32.000 7.40 0.00 34.53 3.95
159 160 8.006027 GCTTGTTGAGAAATTAAGCAATTGTTC 58.994 33.333 7.40 1.86 42.35 3.18
160 161 7.854534 GCTTGTTGAGAAATTAAGCAATTGTT 58.145 30.769 7.40 0.00 42.35 2.83
161 162 7.412137 GCTTGTTGAGAAATTAAGCAATTGT 57.588 32.000 7.40 0.00 42.35 2.71
167 168 5.797434 GCTACTGCTTGTTGAGAAATTAAGC 59.203 40.000 0.00 0.00 42.92 3.09
197 198 4.202010 GCTACTGCTTGTTGGACTCAAAAA 60.202 41.667 0.00 0.00 33.67 1.94
198 199 3.315191 GCTACTGCTTGTTGGACTCAAAA 59.685 43.478 0.00 0.00 33.67 2.44
199 200 2.878406 GCTACTGCTTGTTGGACTCAAA 59.122 45.455 0.00 0.00 33.67 2.69
200 201 2.494059 GCTACTGCTTGTTGGACTCAA 58.506 47.619 0.00 0.00 36.03 3.02
201 202 2.169832 GCTACTGCTTGTTGGACTCA 57.830 50.000 0.00 0.00 36.03 3.41
216 217 1.677942 ACCTAGCCTGTCGTAGCTAC 58.322 55.000 14.19 14.19 40.56 3.58
242 243 0.324943 GTGCTTGAAGCCTACCTGGA 59.675 55.000 15.43 0.00 41.51 3.86
251 252 2.688507 TGTAGCTACAGTGCTTGAAGC 58.311 47.619 22.67 10.84 43.74 3.86
255 256 3.751621 GCATTTGTAGCTACAGTGCTTG 58.248 45.455 35.14 25.28 43.74 4.01
268 269 2.028476 AGCCGTCACTGTAGCATTTGTA 60.028 45.455 0.00 0.00 0.00 2.41
269 270 1.156736 GCCGTCACTGTAGCATTTGT 58.843 50.000 0.00 0.00 0.00 2.83
270 271 1.442769 AGCCGTCACTGTAGCATTTG 58.557 50.000 0.00 0.00 0.00 2.32
271 272 2.028476 TGTAGCCGTCACTGTAGCATTT 60.028 45.455 0.00 0.00 0.00 2.32
272 273 1.548719 TGTAGCCGTCACTGTAGCATT 59.451 47.619 0.00 0.00 0.00 3.56
273 274 1.135139 CTGTAGCCGTCACTGTAGCAT 59.865 52.381 0.00 0.00 0.00 3.79
274 275 0.526211 CTGTAGCCGTCACTGTAGCA 59.474 55.000 0.00 0.00 0.00 3.49
275 276 0.802607 GCTGTAGCCGTCACTGTAGC 60.803 60.000 0.00 0.00 34.31 3.58
276 277 3.330766 GCTGTAGCCGTCACTGTAG 57.669 57.895 0.00 0.00 34.31 2.74
293 294 0.528017 GCCTAGTTTCCTTGCTTGGC 59.472 55.000 0.00 0.00 43.72 4.52
294 295 1.177401 GGCCTAGTTTCCTTGCTTGG 58.823 55.000 0.00 0.00 0.00 3.61
295 296 1.177401 GGGCCTAGTTTCCTTGCTTG 58.823 55.000 0.84 0.00 0.00 4.01
351 352 3.480225 CTTAGACGTAGGGGCGGCG 62.480 68.421 0.51 0.51 45.96 6.46
408 409 2.620367 CCATTGGGCCAGTTAACTGCTA 60.620 50.000 27.05 11.85 42.47 3.49
413 414 2.165641 GCTAACCATTGGGCCAGTTAAC 59.834 50.000 15.25 9.22 37.90 2.01
417 418 1.000359 GGCTAACCATTGGGCCAGT 60.000 57.895 6.23 0.00 43.59 4.00
422 423 1.561542 ACAGAGAGGCTAACCATTGGG 59.438 52.381 7.78 0.00 39.06 4.12
472 473 2.937149 GAGACCGCCAAAAATAGACCTC 59.063 50.000 0.00 0.00 0.00 3.85
476 477 4.153475 CGAAAAGAGACCGCCAAAAATAGA 59.847 41.667 0.00 0.00 0.00 1.98
533 534 1.588667 GTAATTGGCGCCCGCAATG 60.589 57.895 26.77 0.00 44.11 2.82
547 548 3.496131 CGCGGCGCACAAGGTAAT 61.496 61.111 32.61 0.00 0.00 1.89
577 587 6.662865 TTTTCATCTGGCCATGTTTTAGAA 57.337 33.333 5.51 1.22 0.00 2.10
578 588 6.662865 TTTTTCATCTGGCCATGTTTTAGA 57.337 33.333 5.51 0.00 0.00 2.10
602 612 6.704056 TCTCCTCTGTTATTTTCTTCCCTT 57.296 37.500 0.00 0.00 0.00 3.95
622 633 9.994432 AACGATTGAACTGATTTGATATTTCTC 57.006 29.630 0.00 0.00 0.00 2.87
659 670 6.588719 ATGGAAACGATTGATCCTCAAAAA 57.411 33.333 9.85 0.00 40.12 1.94
660 671 6.588719 AATGGAAACGATTGATCCTCAAAA 57.411 33.333 9.85 0.00 40.12 2.44
661 672 6.434028 AGAAATGGAAACGATTGATCCTCAAA 59.566 34.615 9.85 0.00 40.12 2.69
662 673 5.945784 AGAAATGGAAACGATTGATCCTCAA 59.054 36.000 9.85 0.00 41.09 3.02
663 674 5.355071 CAGAAATGGAAACGATTGATCCTCA 59.645 40.000 9.85 0.00 34.24 3.86
664 675 5.586243 TCAGAAATGGAAACGATTGATCCTC 59.414 40.000 9.85 2.05 34.24 3.71
665 676 5.500234 TCAGAAATGGAAACGATTGATCCT 58.500 37.500 9.85 0.00 34.24 3.24
666 677 5.818136 TCAGAAATGGAAACGATTGATCC 57.182 39.130 0.00 3.42 0.00 3.36
667 678 6.749118 CCTTTCAGAAATGGAAACGATTGATC 59.251 38.462 0.00 0.00 32.63 2.92
668 679 6.209391 ACCTTTCAGAAATGGAAACGATTGAT 59.791 34.615 14.78 0.00 34.54 2.57
715 734 3.612247 TTTCTCCGCCAGCCTCAGC 62.612 63.158 0.00 0.00 40.32 4.26
716 735 0.606401 TTTTTCTCCGCCAGCCTCAG 60.606 55.000 0.00 0.00 0.00 3.35
717 736 0.606401 CTTTTTCTCCGCCAGCCTCA 60.606 55.000 0.00 0.00 0.00 3.86
718 737 0.321653 TCTTTTTCTCCGCCAGCCTC 60.322 55.000 0.00 0.00 0.00 4.70
719 738 0.110486 TTCTTTTTCTCCGCCAGCCT 59.890 50.000 0.00 0.00 0.00 4.58
758 783 7.659390 AGGAATTTAGGATGAATCATTCGAGTC 59.341 37.037 0.00 0.00 36.77 3.36
797 828 6.676950 CAACAAATGATTAGTGGTAAGTGCA 58.323 36.000 0.00 0.00 0.00 4.57
798 829 5.572896 GCAACAAATGATTAGTGGTAAGTGC 59.427 40.000 0.00 0.00 0.00 4.40
799 830 5.794945 CGCAACAAATGATTAGTGGTAAGTG 59.205 40.000 0.00 0.00 0.00 3.16
800 831 5.472137 ACGCAACAAATGATTAGTGGTAAGT 59.528 36.000 0.00 0.00 0.00 2.24
801 832 5.938322 ACGCAACAAATGATTAGTGGTAAG 58.062 37.500 0.00 0.00 0.00 2.34
802 833 5.470437 TGACGCAACAAATGATTAGTGGTAA 59.530 36.000 0.00 0.00 0.00 2.85
803 834 4.998033 TGACGCAACAAATGATTAGTGGTA 59.002 37.500 0.00 0.00 0.00 3.25
804 835 3.818210 TGACGCAACAAATGATTAGTGGT 59.182 39.130 0.00 0.00 0.00 4.16
805 836 4.418013 TGACGCAACAAATGATTAGTGG 57.582 40.909 0.00 0.00 0.00 4.00
837 869 4.280425 GTGGTACTACTATACTTGGAGGCC 59.720 50.000 1.48 0.00 0.00 5.19
842 874 7.940137 AGAGATCAGTGGTACTACTATACTTGG 59.060 40.741 11.97 0.00 0.00 3.61
855 887 4.461198 TGATTAGCGAGAGATCAGTGGTA 58.539 43.478 0.00 0.00 0.00 3.25
856 888 3.291584 TGATTAGCGAGAGATCAGTGGT 58.708 45.455 0.00 0.00 0.00 4.16
909 983 3.367630 CAGTGTGTTTCAAAAGTGGCAAC 59.632 43.478 0.00 0.00 0.00 4.17
912 986 1.926510 GCAGTGTGTTTCAAAAGTGGC 59.073 47.619 0.00 0.00 0.00 5.01
956 1031 4.434520 CCAAGTTCCTAACTCGATCTTCC 58.565 47.826 0.00 0.00 41.91 3.46
979 1057 5.910723 CCATTGCTTTGCTTTTGATTGTTTC 59.089 36.000 0.00 0.00 0.00 2.78
988 1082 1.219646 CACGCCATTGCTTTGCTTTT 58.780 45.000 0.00 0.00 34.43 2.27
989 1083 1.223417 GCACGCCATTGCTTTGCTTT 61.223 50.000 5.32 0.00 39.68 3.51
992 1086 2.356075 TGCACGCCATTGCTTTGC 60.356 55.556 5.55 5.55 43.41 3.68
997 1091 2.507547 CATGGTGCACGCCATTGC 60.508 61.111 12.98 0.00 46.33 3.56
1473 1605 2.507944 GAGGTGGCATCGCAGGAT 59.492 61.111 0.00 0.00 0.00 3.24
1482 1614 2.853542 TGGCAGAAGGAGGTGGCA 60.854 61.111 0.00 0.00 46.10 4.92
1551 1923 1.212229 GTCGACGGTGAAGGTCTCC 59.788 63.158 0.00 0.00 32.24 3.71
1839 2223 3.399181 GGGGAGTGCACCATCGGA 61.399 66.667 14.63 0.00 37.60 4.55
1986 2383 3.319198 ACGACGGGGTCCAGCAAT 61.319 61.111 0.00 0.00 0.00 3.56
1987 2384 4.308458 CACGACGGGGTCCAGCAA 62.308 66.667 0.00 0.00 0.00 3.91
1999 2396 4.736896 GGTGACCGCCTCCACGAC 62.737 72.222 0.00 0.00 34.30 4.34
2011 2408 2.109126 GCTTGATGCTCCCGGTGAC 61.109 63.158 0.00 0.00 38.95 3.67
2054 2457 1.400500 CCGAAAACATTTCCGGGTTCG 60.400 52.381 0.00 6.12 38.42 3.95
2055 2458 1.610038 ACCGAAAACATTTCCGGGTTC 59.390 47.619 6.97 0.00 45.63 3.62
2064 2467 2.478894 CTCGTAGCACACCGAAAACATT 59.521 45.455 0.00 0.00 31.92 2.71
2065 2468 2.066262 CTCGTAGCACACCGAAAACAT 58.934 47.619 0.00 0.00 31.92 2.71
2115 2527 1.373748 CAACGTCACGTCCGGGAAT 60.374 57.895 1.67 0.00 39.99 3.01
2382 2798 8.193438 ACACGGTGATTATTACTCCTACTTAAC 58.807 37.037 16.29 0.00 0.00 2.01
2391 2820 7.648510 CCTTAGAAGACACGGTGATTATTACTC 59.351 40.741 16.29 0.00 0.00 2.59
2460 2889 8.123575 GGACTACTTTGTTGAAGAGTTTCTTTC 58.876 37.037 0.00 0.00 36.73 2.62
2462 2891 7.110155 TGGACTACTTTGTTGAAGAGTTTCTT 58.890 34.615 0.00 0.00 39.87 2.52
2463 2892 6.650120 TGGACTACTTTGTTGAAGAGTTTCT 58.350 36.000 0.00 0.00 38.77 2.52
2464 2893 6.511929 GCTGGACTACTTTGTTGAAGAGTTTC 60.512 42.308 0.00 0.00 38.77 2.78
2465 2894 5.297029 GCTGGACTACTTTGTTGAAGAGTTT 59.703 40.000 0.00 0.00 38.77 2.66
2466 2895 4.816925 GCTGGACTACTTTGTTGAAGAGTT 59.183 41.667 0.00 0.00 38.77 3.01
2477 2906 3.497262 GCGTACAAAAGCTGGACTACTTT 59.503 43.478 0.00 0.00 36.62 2.66
2491 2920 2.683362 TCCAAACACATGTGCGTACAAA 59.317 40.909 25.68 2.96 40.84 2.83
2508 2937 3.452990 GGTTTGGTTCTTTTCCCTTCCAA 59.547 43.478 0.00 0.00 33.90 3.53
2528 2957 7.176690 CCAGGATTTGTTTGTTATTACTCTGGT 59.823 37.037 0.00 0.00 33.10 4.00
2533 2962 8.531146 CATTCCCAGGATTTGTTTGTTATTACT 58.469 33.333 0.00 0.00 0.00 2.24
2547 2976 5.640147 TGTAAAACAGACATTCCCAGGATT 58.360 37.500 0.00 0.00 0.00 3.01
2549 2978 4.715534 TGTAAAACAGACATTCCCAGGA 57.284 40.909 0.00 0.00 0.00 3.86
2550 2979 5.982890 AATGTAAAACAGACATTCCCAGG 57.017 39.130 0.00 0.00 42.51 4.45
2557 2989 7.490962 TTTCAGTCGAATGTAAAACAGACAT 57.509 32.000 13.18 0.00 39.22 3.06
2591 3023 5.142962 GTCGCTGAAAAATCTGACTGAAAG 58.857 41.667 0.00 0.00 42.29 2.62
2617 3050 5.006261 CGACATGTGACACTTGTTAAACTCA 59.994 40.000 23.43 0.00 36.73 3.41
2641 3074 0.949397 GGGACAGGAACAAAACGGAC 59.051 55.000 0.00 0.00 0.00 4.79
2785 3220 6.956497 AGGTAGAGAAGATTGCAAAGAAGAT 58.044 36.000 1.71 0.00 0.00 2.40
2786 3221 6.365970 AGGTAGAGAAGATTGCAAAGAAGA 57.634 37.500 1.71 0.00 0.00 2.87
2787 3222 5.584251 GGAGGTAGAGAAGATTGCAAAGAAG 59.416 44.000 1.71 0.00 0.00 2.85
2788 3223 5.491982 GGAGGTAGAGAAGATTGCAAAGAA 58.508 41.667 1.71 0.00 0.00 2.52
2789 3224 4.080863 GGGAGGTAGAGAAGATTGCAAAGA 60.081 45.833 1.71 0.00 0.00 2.52
2790 3225 4.080638 AGGGAGGTAGAGAAGATTGCAAAG 60.081 45.833 1.71 0.00 0.00 2.77
2791 3226 3.846588 AGGGAGGTAGAGAAGATTGCAAA 59.153 43.478 1.71 0.00 0.00 3.68
2792 3227 3.198635 CAGGGAGGTAGAGAAGATTGCAA 59.801 47.826 0.00 0.00 0.00 4.08
2793 3228 2.768527 CAGGGAGGTAGAGAAGATTGCA 59.231 50.000 0.00 0.00 0.00 4.08
2794 3229 2.769095 ACAGGGAGGTAGAGAAGATTGC 59.231 50.000 0.00 0.00 0.00 3.56
2875 3313 9.627123 TTCCTGCAAAGTAATGCTAGTATTATT 57.373 29.630 15.19 9.25 46.54 1.40
2876 3314 9.627123 TTTCCTGCAAAGTAATGCTAGTATTAT 57.373 29.630 15.19 0.00 46.54 1.28
2877 3315 9.627123 ATTTCCTGCAAAGTAATGCTAGTATTA 57.373 29.630 8.99 8.99 46.54 0.98
2932 3370 4.019174 GTCAATGTTGATCCCATGACCTT 58.981 43.478 0.00 0.00 39.73 3.50
2993 3431 7.746703 AGTAGAGTTCCTGTTTTATGTTTCCT 58.253 34.615 0.00 0.00 0.00 3.36
3131 3587 6.719370 AGTGGCTTTTCATTGTAATTCTACCA 59.281 34.615 0.00 0.00 0.00 3.25
3247 3703 9.449719 AGGAACGAAAGAAGTATAAAATGTCAT 57.550 29.630 0.00 0.00 0.00 3.06
3310 3766 9.282247 GTAGATTCACTCATTTTGCTTTGTATG 57.718 33.333 0.00 0.00 0.00 2.39
3315 3771 8.800332 AGAATGTAGATTCACTCATTTTGCTTT 58.200 29.630 14.46 0.00 40.59 3.51
3316 3772 8.345724 AGAATGTAGATTCACTCATTTTGCTT 57.654 30.769 14.46 0.00 40.59 3.91


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

AutoCloner maintained by Alex Coulton.