Multiple sequence alignment - TraesCS5B01G558100

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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 TraesCS5B01G558100 chr5B 100.000 3015 0 0 1 3015 705616100 705619114 0.000000e+00 5568.0
1 TraesCS5B01G558100 chr5B 100.000 2609 0 0 4330 6938 705620429 705623037 0.000000e+00 4819.0
2 TraesCS5B01G558100 chr5B 100.000 790 0 0 3264 4053 705619363 705620152 0.000000e+00 1459.0
3 TraesCS5B01G558100 chr5B 80.864 324 40 5 3522 3825 119120491 119120812 1.160000e-57 235.0
4 TraesCS5B01G558100 chr5B 81.287 171 29 2 5960 6128 354289971 354290140 1.210000e-27 135.0
5 TraesCS5B01G558100 chr4A 93.681 2532 120 19 4417 6922 609081589 609079072 0.000000e+00 3753.0
6 TraesCS5B01G558100 chr4A 92.061 1121 38 24 727 1829 609085006 609083919 0.000000e+00 1530.0
7 TraesCS5B01G558100 chr4A 93.804 1033 33 10 1972 3004 609083610 609082609 0.000000e+00 1524.0
8 TraesCS5B01G558100 chr4A 89.849 729 43 8 1 703 609086565 609085842 0.000000e+00 907.0
9 TraesCS5B01G558100 chr4A 89.951 617 53 4 3296 3904 609082283 609081668 0.000000e+00 787.0
10 TraesCS5B01G558100 chr4A 98.039 51 0 1 3956 4006 609081668 609081619 3.450000e-13 87.9
11 TraesCS5B01G558100 chr5D 92.383 2639 141 32 4330 6938 563401544 563404152 0.000000e+00 3705.0
12 TraesCS5B01G558100 chr5D 88.842 1174 87 18 1 1140 563397647 563398810 0.000000e+00 1402.0
13 TraesCS5B01G558100 chr5D 91.249 937 44 14 1200 2134 563398819 563399719 0.000000e+00 1242.0
14 TraesCS5B01G558100 chr5D 94.080 777 30 7 2229 3004 563400036 563400797 0.000000e+00 1166.0
15 TraesCS5B01G558100 chr5D 86.676 713 53 9 3290 3971 563400822 563401523 0.000000e+00 752.0
16 TraesCS5B01G558100 chr3A 80.580 345 45 12 3520 3842 423974016 423974360 5.370000e-61 246.0
17 TraesCS5B01G558100 chr1D 80.645 341 39 15 3523 3842 110656485 110656151 8.990000e-59 239.0
18 TraesCS5B01G558100 chr7A 80.805 323 39 18 3538 3847 733258867 733258555 1.500000e-56 231.0
19 TraesCS5B01G558100 chr7A 90.226 133 12 1 4393 4525 147928079 147927948 9.250000e-39 172.0
20 TraesCS5B01G558100 chr2D 79.310 348 41 18 3523 3842 108690217 108690561 1.520000e-51 215.0
21 TraesCS5B01G558100 chr2D 83.929 168 24 3 4340 4506 15127648 15127813 2.590000e-34 158.0
22 TraesCS5B01G558100 chr2D 82.840 169 23 5 5972 6137 478820895 478820730 5.610000e-31 147.0
23 TraesCS5B01G558100 chr5A 79.464 336 41 15 3520 3835 407123278 407123605 5.450000e-51 213.0
24 TraesCS5B01G558100 chr5A 84.977 213 22 9 3522 3731 164200882 164201087 2.540000e-49 207.0
25 TraesCS5B01G558100 chr2B 79.104 335 47 16 3522 3842 770106346 770106671 7.050000e-50 209.0
26 TraesCS5B01G558100 chr2B 90.179 112 10 1 3731 3842 26750398 26750508 2.020000e-30 145.0
27 TraesCS5B01G558100 chr4B 78.533 368 34 20 3522 3846 387336991 387337356 4.240000e-47 200.0
28 TraesCS5B01G558100 chr4B 80.693 202 38 1 4330 4530 489674524 489674725 9.320000e-34 156.0
29 TraesCS5B01G558100 chr1A 86.339 183 23 2 4340 4522 493208691 493208871 1.530000e-46 198.0
30 TraesCS5B01G558100 chr1A 79.545 176 25 8 4330 4503 44982974 44983140 1.580000e-21 115.0
31 TraesCS5B01G558100 chr1A 78.488 172 28 6 4333 4503 31564023 31563860 3.420000e-18 104.0
32 TraesCS5B01G558100 chr6D 83.482 224 13 7 3640 3842 399041631 399041411 3.300000e-43 187.0
33 TraesCS5B01G558100 chr7D 87.898 157 19 0 4343 4499 13688636 13688480 1.190000e-42 185.0
34 TraesCS5B01G558100 chr7D 88.722 133 14 1 4393 4525 146631598 146631467 2.000000e-35 161.0
35 TraesCS5B01G558100 chr4D 77.746 346 42 12 3522 3842 459265033 459264698 5.530000e-41 180.0
36 TraesCS5B01G558100 chr7B 90.977 133 11 1 4393 4525 109186433 109186302 1.990000e-40 178.0
37 TraesCS5B01G558100 chr7B 84.049 163 24 2 5973 6134 676414515 676414354 9.320000e-34 156.0
38 TraesCS5B01G558100 chr7B 88.991 109 10 2 3513 3620 296347594 296347487 4.370000e-27 134.0
39 TraesCS5B01G558100 chrUn 80.242 248 23 9 3621 3845 399318106 399317862 5.570000e-36 163.0
40 TraesCS5B01G558100 chrUn 80.162 247 25 7 3621 3845 400072956 400072712 5.570000e-36 163.0
41 TraesCS5B01G558100 chr2A 84.118 170 26 1 5965 6133 127198485 127198316 5.570000e-36 163.0
42 TraesCS5B01G558100 chr2A 80.337 178 31 3 5954 6128 755772909 755772733 1.570000e-26 132.0
43 TraesCS5B01G558100 chr6B 80.342 234 21 11 3631 3842 666225091 666224861 3.350000e-33 154.0
44 TraesCS5B01G558100 chr1B 82.840 169 26 3 5969 6135 470935685 470935518 1.560000e-31 148.0
45 TraesCS5B01G558100 chr1B 82.317 164 21 6 5972 6129 626226582 626226743 1.210000e-27 135.0


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 TraesCS5B01G558100 chr5B 705616100 705623037 6937 False 3948.666667 5568 100.0000 1 6938 3 chr5B.!!$F3 6937
1 TraesCS5B01G558100 chr4A 609079072 609086565 7493 True 1431.483333 3753 92.8975 1 6922 6 chr4A.!!$R1 6921
2 TraesCS5B01G558100 chr5D 563397647 563404152 6505 False 1653.400000 3705 90.6460 1 6938 5 chr5D.!!$F1 6937

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
710 1576 0.107459 CTTGCCAAGCCCTACTCCTC 60.107 60.000 0.00 0.0 0.00 3.71 F
711 1577 0.547712 TTGCCAAGCCCTACTCCTCT 60.548 55.000 0.00 0.0 0.00 3.69 F
713 1579 0.689412 GCCAAGCCCTACTCCTCTCT 60.689 60.000 0.00 0.0 0.00 3.10 F
1180 2093 0.753262 GGAGGACAGTGTGAGTGTGT 59.247 55.000 0.00 0.0 30.64 3.72 F
1195 2108 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1197 2110 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1199 2112 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1203 2116 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 F
1204 2117 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.0 0.00 3.72 F
2616 3956 1.542492 TTAGGTCGACTGGTCTGGTC 58.458 55.000 16.46 0.0 0.00 4.02 F
3283 4624 0.196631 TAGTGGGTAGGGTTGGGGTT 59.803 55.000 0.00 0.0 0.00 4.11 F
3802 5200 0.036388 TCGTGTCCCCTGATTGCTTC 60.036 55.000 0.00 0.0 0.00 3.86 F
4040 5445 1.003812 CCCCGTGTCCCAAATAGTTGA 59.996 52.381 4.10 0.0 36.83 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 2465 0.323451 GGGGCCTCAAAGGTAACCTG 60.323 60.000 0.84 0.00 37.80 4.00 R
1904 2823 1.272985 TGCAATTGTAAGGGAAGGGGG 60.273 52.381 7.40 0.00 0.00 5.40 R
2535 3875 3.194861 TGTGAGGCATGTACTTATTCGC 58.805 45.455 0.00 0.00 0.00 4.70 R
2995 4336 3.782443 CCCGCCCCGCTCTAAACT 61.782 66.667 0.00 0.00 0.00 2.66 R
3264 4605 0.196631 AACCCCAACCCTACCCACTA 59.803 55.000 0.00 0.00 0.00 2.74 R
3267 4608 0.196631 AGTAACCCCAACCCTACCCA 59.803 55.000 0.00 0.00 0.00 4.51 R
3268 4609 0.914644 GAGTAACCCCAACCCTACCC 59.085 60.000 0.00 0.00 0.00 3.69 R
3269 4610 1.962558 AGAGTAACCCCAACCCTACC 58.037 55.000 0.00 0.00 0.00 3.18 R
3272 4613 3.878086 TCTTAAGAGTAACCCCAACCCT 58.122 45.455 0.00 0.00 0.00 4.34 R
3597 4977 0.257039 CTTCAGCCCAAGCCTACCAT 59.743 55.000 0.00 0.00 41.25 3.55 R
4981 6390 0.802494 AATTTGGTGTGGTCGATCGC 59.198 50.000 11.09 1.22 0.00 4.58 R
5183 6596 1.065491 TGTAGTAACCCCTGCATGCAG 60.065 52.381 35.88 35.88 43.26 4.41 R
5963 7378 0.396811 AGGAACGGAGGAAGTGGTTG 59.603 55.000 0.00 0.00 0.00 3.77 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
89 98 9.562408 TTGACTAGGTTGTCATGTGTATAAAAA 57.438 29.630 0.00 0.00 45.03 1.94
92 101 9.787435 ACTAGGTTGTCATGTGTATAAAAAGAA 57.213 29.630 0.00 0.00 0.00 2.52
94 103 7.593825 AGGTTGTCATGTGTATAAAAAGAAGC 58.406 34.615 0.00 0.00 0.00 3.86
96 105 6.176975 TGTCATGTGTATAAAAAGAAGCCG 57.823 37.500 0.00 0.00 0.00 5.52
105 115 2.130073 AAAAGAAGCCGCACCTTCGC 62.130 55.000 7.47 0.00 44.56 4.70
189 204 2.631062 TGGTGATGTAATAGGCTACCCG 59.369 50.000 0.00 0.00 35.76 5.28
197 212 1.348064 ATAGGCTACCCGCATTGCTA 58.652 50.000 7.12 0.00 41.67 3.49
215 230 7.223387 GCATTGCTACTTTTATTTCTTCCATGG 59.777 37.037 4.97 4.97 0.00 3.66
239 254 8.171400 TGGTTTACCATAAAATCTTCCTGGTAA 58.829 33.333 8.08 8.08 45.80 2.85
240 255 9.197306 GGTTTACCATAAAATCTTCCTGGTAAT 57.803 33.333 11.93 0.00 46.35 1.89
291 306 1.174783 ATAGCACGTTGAGACCGTCT 58.825 50.000 0.00 0.00 36.17 4.18
390 405 5.997384 TCTTCCTCTTTAACCTAGACACC 57.003 43.478 0.00 0.00 0.00 4.16
402 417 3.596956 ACCTAGACACCTCTCTTCCCTTA 59.403 47.826 0.00 0.00 0.00 2.69
477 493 6.774673 TCATACTTTGACCAACACCTTGATA 58.225 36.000 0.00 0.00 0.00 2.15
505 531 0.543277 TGTCCAGCCAAGCCATCTAG 59.457 55.000 0.00 0.00 0.00 2.43
510 536 1.889573 GCCAAGCCATCTAGGTCGC 60.890 63.158 0.00 0.00 40.61 5.19
580 611 1.671054 AACACGCGACCAGATTGGG 60.671 57.895 15.93 0.00 43.37 4.12
581 612 2.107041 AACACGCGACCAGATTGGGA 62.107 55.000 15.93 0.00 43.37 4.37
677 709 1.882623 GGTGAAAAGAAGCTGGTGAGG 59.117 52.381 0.00 0.00 0.00 3.86
688 720 1.850755 TGGTGAGGGGGAAAGGACC 60.851 63.158 0.00 0.00 0.00 4.46
708 1574 4.645809 CTTGCCAAGCCCTACTCC 57.354 61.111 0.00 0.00 0.00 3.85
709 1575 1.994463 CTTGCCAAGCCCTACTCCT 59.006 57.895 0.00 0.00 0.00 3.69
710 1576 0.107459 CTTGCCAAGCCCTACTCCTC 60.107 60.000 0.00 0.00 0.00 3.71
711 1577 0.547712 TTGCCAAGCCCTACTCCTCT 60.548 55.000 0.00 0.00 0.00 3.69
712 1578 0.978146 TGCCAAGCCCTACTCCTCTC 60.978 60.000 0.00 0.00 0.00 3.20
713 1579 0.689412 GCCAAGCCCTACTCCTCTCT 60.689 60.000 0.00 0.00 0.00 3.10
714 1580 1.408969 CCAAGCCCTACTCCTCTCTC 58.591 60.000 0.00 0.00 0.00 3.20
715 1581 1.063266 CCAAGCCCTACTCCTCTCTCT 60.063 57.143 0.00 0.00 0.00 3.10
716 1582 2.306847 CAAGCCCTACTCCTCTCTCTC 58.693 57.143 0.00 0.00 0.00 3.20
717 1583 1.907240 AGCCCTACTCCTCTCTCTCT 58.093 55.000 0.00 0.00 0.00 3.10
718 1584 1.774856 AGCCCTACTCCTCTCTCTCTC 59.225 57.143 0.00 0.00 0.00 3.20
719 1585 1.774856 GCCCTACTCCTCTCTCTCTCT 59.225 57.143 0.00 0.00 0.00 3.10
720 1586 2.224548 GCCCTACTCCTCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
721 1587 3.318313 CCCTACTCCTCTCTCTCTCTCT 58.682 54.545 0.00 0.00 0.00 3.10
722 1588 3.325135 CCCTACTCCTCTCTCTCTCTCTC 59.675 56.522 0.00 0.00 0.00 3.20
723 1589 4.227197 CCTACTCCTCTCTCTCTCTCTCT 58.773 52.174 0.00 0.00 0.00 3.10
724 1590 4.282195 CCTACTCCTCTCTCTCTCTCTCTC 59.718 54.167 0.00 0.00 0.00 3.20
725 1591 4.000928 ACTCCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
774 1670 2.268920 CACCATGTCCCTGTCCCG 59.731 66.667 0.00 0.00 0.00 5.14
888 1784 1.171308 CTGTGGTGCAATAAGCTGCT 58.829 50.000 0.00 0.00 45.94 4.24
984 1882 1.878522 GCCTCACGCTCACCATACG 60.879 63.158 0.00 0.00 0.00 3.06
1054 1952 4.084013 GGTTAGTCCATGAAAAGACACACG 60.084 45.833 0.00 0.00 35.38 4.49
1065 1963 2.663852 ACACACGCGCACTTACCC 60.664 61.111 5.73 0.00 0.00 3.69
1066 1964 3.773630 CACACGCGCACTTACCCG 61.774 66.667 5.73 0.00 0.00 5.28
1072 1970 3.047280 CGCACTTACCCGCTTGCA 61.047 61.111 0.00 0.00 34.49 4.08
1074 1972 2.978018 GCACTTACCCGCTTGCACC 61.978 63.158 0.00 0.00 34.97 5.01
1075 1973 1.599518 CACTTACCCGCTTGCACCA 60.600 57.895 0.00 0.00 0.00 4.17
1154 2067 9.913310 TGAATCAGAGATAGAGAGAGAGTTTTA 57.087 33.333 0.00 0.00 0.00 1.52
1175 2088 2.091541 GAGAGAGGAGGACAGTGTGAG 58.908 57.143 0.00 0.00 0.00 3.51
1176 2089 1.427368 AGAGAGGAGGACAGTGTGAGT 59.573 52.381 0.00 0.00 0.00 3.41
1177 2090 1.543802 GAGAGGAGGACAGTGTGAGTG 59.456 57.143 0.00 0.00 0.00 3.51
1178 2091 1.133325 AGAGGAGGACAGTGTGAGTGT 60.133 52.381 0.00 0.00 33.77 3.55
1179 2092 1.000283 GAGGAGGACAGTGTGAGTGTG 60.000 57.143 0.00 0.00 30.64 3.82
1180 2093 0.753262 GGAGGACAGTGTGAGTGTGT 59.247 55.000 0.00 0.00 30.64 3.72
1181 2094 1.539065 GGAGGACAGTGTGAGTGTGTG 60.539 57.143 0.00 0.00 30.64 3.82
1182 2095 1.137086 GAGGACAGTGTGAGTGTGTGT 59.863 52.381 0.00 0.00 30.64 3.72
1183 2096 1.134699 AGGACAGTGTGAGTGTGTGTG 60.135 52.381 0.00 0.00 30.64 3.82
1184 2097 1.405526 GGACAGTGTGAGTGTGTGTGT 60.406 52.381 0.00 0.00 30.64 3.72
1185 2098 1.660607 GACAGTGTGAGTGTGTGTGTG 59.339 52.381 0.00 0.00 30.64 3.82
1186 2099 1.001974 ACAGTGTGAGTGTGTGTGTGT 59.998 47.619 0.00 0.00 29.04 3.72
1187 2100 1.394572 CAGTGTGAGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
1188 2101 1.001974 AGTGTGAGTGTGTGTGTGTGT 59.998 47.619 0.00 0.00 0.00 3.72
1189 2102 1.128507 GTGTGAGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1190 2103 1.270571 TGTGAGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1191 2104 1.128507 GTGAGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1192 2105 1.270571 TGAGTGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
1193 2106 1.128507 GAGTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
1194 2107 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1195 2108 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1196 2109 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1197 2110 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1198 2111 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1199 2112 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1200 2113 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1201 2114 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1202 2115 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1203 2116 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1204 2117 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1787 2706 6.708054 CAGATGATCACCAGGTTATTAACTCC 59.292 42.308 0.00 0.00 0.00 3.85
1829 2748 5.611374 TCCATCCTAATTTCTTTCCTAGCG 58.389 41.667 0.00 0.00 0.00 4.26
1830 2749 4.757149 CCATCCTAATTTCTTTCCTAGCGG 59.243 45.833 0.00 0.00 0.00 5.52
1845 2764 1.846007 AGCGGAGAGACTTGATCTGT 58.154 50.000 0.00 0.00 38.00 3.41
1885 2804 9.143631 GCTTCAGTATTTTATTTGTCATTTGCT 57.856 29.630 0.00 0.00 0.00 3.91
1887 2806 9.638239 TTCAGTATTTTATTTGTCATTTGCTCC 57.362 29.630 0.00 0.00 0.00 4.70
1888 2807 9.023962 TCAGTATTTTATTTGTCATTTGCTCCT 57.976 29.630 0.00 0.00 0.00 3.69
1926 2845 3.106827 CCCCTTCCCTTACAATTGCATT 58.893 45.455 5.05 0.00 0.00 3.56
1956 2875 8.839343 TCATGCATGTACCTATGTAATTTTCTG 58.161 33.333 25.43 0.00 0.00 3.02
2027 3112 6.647481 TGGTTCATTTCAGCATCATTTTTCAG 59.353 34.615 0.00 0.00 0.00 3.02
2032 3117 8.963725 TCATTTCAGCATCATTTTTCAGTAGAT 58.036 29.630 0.00 0.00 0.00 1.98
2079 3164 7.281040 ACATCTGTGAAATTGTCATTCTGTT 57.719 32.000 0.00 0.00 38.90 3.16
2127 3214 8.641498 ACAGTTCATAGTTTTGAATTCCTGAT 57.359 30.769 2.27 0.00 37.88 2.90
2174 3514 9.506018 CATGTTTCTCCCCTTTCAAATTAAATT 57.494 29.630 0.00 0.00 0.00 1.82
2272 3612 2.012673 CTAACTGCTCTGCCATTCACC 58.987 52.381 0.00 0.00 0.00 4.02
2535 3875 8.251026 TCTGATGTCTTAGTTTGGTACTGTATG 58.749 37.037 0.00 0.00 37.73 2.39
2573 3913 7.324935 TGCCTCACATTAGTTATTCTCGTTTA 58.675 34.615 0.00 0.00 0.00 2.01
2612 3952 2.816411 TCCAATTAGGTCGACTGGTCT 58.184 47.619 16.46 6.40 39.02 3.85
2613 3953 2.496070 TCCAATTAGGTCGACTGGTCTG 59.504 50.000 16.46 7.87 39.02 3.51
2614 3954 2.418746 CCAATTAGGTCGACTGGTCTGG 60.419 54.545 16.46 12.90 0.00 3.86
2615 3955 2.233305 ATTAGGTCGACTGGTCTGGT 57.767 50.000 16.46 0.00 0.00 4.00
2616 3956 1.542492 TTAGGTCGACTGGTCTGGTC 58.458 55.000 16.46 0.00 0.00 4.02
2663 4003 6.397272 TGTTTTGCTGTCAACTCAAATTTCT 58.603 32.000 0.00 0.00 30.89 2.52
2668 4008 4.978580 GCTGTCAACTCAAATTTCTCCAAC 59.021 41.667 0.00 0.00 0.00 3.77
2696 4036 5.066375 TCCACATTTGATCGACATGGAAATC 59.934 40.000 0.00 0.00 32.92 2.17
2765 4105 2.359531 TGGATTTGGACGGAAAACACAC 59.640 45.455 0.00 0.00 0.00 3.82
2928 4269 3.649277 GAAAGCTGCGGCGGAGAGA 62.649 63.158 32.74 0.00 44.37 3.10
2995 4336 2.281484 GCGAGGGTGGAACTGCAA 60.281 61.111 0.00 0.00 36.74 4.08
3008 4349 2.471255 CTGCAAGTTTAGAGCGGGG 58.529 57.895 0.00 0.00 0.00 5.73
3009 4350 1.648467 CTGCAAGTTTAGAGCGGGGC 61.648 60.000 0.00 0.00 0.00 5.80
3012 4353 3.325201 AAGTTTAGAGCGGGGCGGG 62.325 63.158 0.00 0.00 0.00 6.13
3013 4354 4.851179 GTTTAGAGCGGGGCGGGG 62.851 72.222 0.00 0.00 0.00 5.73
3281 4622 2.304069 GTAGTGGGTAGGGTTGGGG 58.696 63.158 0.00 0.00 0.00 4.96
3282 4623 0.548439 GTAGTGGGTAGGGTTGGGGT 60.548 60.000 0.00 0.00 0.00 4.95
3283 4624 0.196631 TAGTGGGTAGGGTTGGGGTT 59.803 55.000 0.00 0.00 0.00 4.11
3284 4625 0.196631 AGTGGGTAGGGTTGGGGTTA 59.803 55.000 0.00 0.00 0.00 2.85
3285 4626 0.329261 GTGGGTAGGGTTGGGGTTAC 59.671 60.000 0.00 0.00 0.00 2.50
3286 4627 0.196631 TGGGTAGGGTTGGGGTTACT 59.803 55.000 0.00 0.00 0.00 2.24
3287 4628 0.914644 GGGTAGGGTTGGGGTTACTC 59.085 60.000 0.00 0.00 0.00 2.59
3288 4629 1.556475 GGGTAGGGTTGGGGTTACTCT 60.556 57.143 0.00 0.00 0.00 3.24
3384 4759 1.601419 CCGTCCGGTTAGAGAGCCAA 61.601 60.000 0.00 0.00 0.00 4.52
3407 4782 1.134965 AGACGGAGCAATAGAGTGTGC 60.135 52.381 0.00 0.00 41.22 4.57
3436 4811 4.587262 TGTGACATAGGGCGTGAGTATAAT 59.413 41.667 0.00 0.00 0.00 1.28
3629 5009 1.405526 GGCTGAAGCGGTACAGATCAA 60.406 52.381 0.00 0.00 43.26 2.57
3637 5017 4.579869 AGCGGTACAGATCAATTTTGACT 58.420 39.130 0.00 0.00 40.49 3.41
3638 5018 4.393062 AGCGGTACAGATCAATTTTGACTG 59.607 41.667 15.27 15.27 40.49 3.51
3679 5059 2.406616 CCTTTGTAAGCCGCCGCAT 61.407 57.895 0.00 0.00 37.52 4.73
3693 5073 1.956477 GCCGCATGGGATAAGTTGATT 59.044 47.619 12.02 0.00 38.47 2.57
3713 5093 2.052782 AGTTGTAATCCCCGGCATTC 57.947 50.000 0.00 0.00 0.00 2.67
3802 5200 0.036388 TCGTGTCCCCTGATTGCTTC 60.036 55.000 0.00 0.00 0.00 3.86
3814 5212 1.996191 GATTGCTTCTCGTTCTTCGCT 59.004 47.619 0.00 0.00 39.67 4.93
3825 5223 3.311322 TCGTTCTTCGCTGTGTTGATTTT 59.689 39.130 0.00 0.00 39.67 1.82
3830 5228 1.266718 TCGCTGTGTTGATTTTCCTGC 59.733 47.619 0.00 0.00 0.00 4.85
3850 5248 7.208080 TCCTGCCGTATCTCTAAAATAAGTTC 58.792 38.462 0.00 0.00 0.00 3.01
3888 5293 8.469200 TGGAAAATTGAGATTGGTGCTATTTAG 58.531 33.333 0.00 0.00 0.00 1.85
3914 5319 1.750778 ACACACAGGTTTGGCTCTTTG 59.249 47.619 0.00 0.00 0.00 2.77
3916 5321 2.024414 ACACAGGTTTGGCTCTTTGTC 58.976 47.619 0.00 0.00 0.00 3.18
4005 5410 9.588096 AATTAGATTCAATCTTATAACACCCCC 57.412 33.333 4.90 0.00 40.76 5.40
4040 5445 1.003812 CCCCGTGTCCCAAATAGTTGA 59.996 52.381 4.10 0.00 36.83 3.18
4042 5447 3.352648 CCCGTGTCCCAAATAGTTGATT 58.647 45.455 4.10 0.00 36.83 2.57
4527 5933 7.908827 TTTTTAGTCAGTTTATACGCCATCA 57.091 32.000 0.00 0.00 0.00 3.07
4633 6039 8.928733 GTTCATGAGTTGTTTCATTATGCAATT 58.071 29.630 0.00 0.00 35.67 2.32
4642 6048 7.259882 TGTTTCATTATGCAATTGGCTCTAAG 58.740 34.615 7.72 0.00 45.15 2.18
4790 6199 9.185680 CTAAACTGCAGGGGTAATTAACTAAAT 57.814 33.333 19.93 0.00 0.00 1.40
4795 6204 6.543100 TGCAGGGGTAATTAACTAAATAACCG 59.457 38.462 0.00 0.00 0.00 4.44
4815 6224 5.794894 ACCGAAACACAATCATTCTAGACT 58.205 37.500 0.00 0.00 0.00 3.24
4818 6227 6.183360 CCGAAACACAATCATTCTAGACTCAC 60.183 42.308 0.00 0.00 0.00 3.51
4820 6229 7.426929 AAACACAATCATTCTAGACTCACAC 57.573 36.000 0.00 0.00 0.00 3.82
4822 6231 6.162079 ACACAATCATTCTAGACTCACACAG 58.838 40.000 0.00 0.00 0.00 3.66
4981 6390 1.668793 TGCATCTGTCACCTGCACG 60.669 57.895 1.32 0.00 40.75 5.34
4985 6394 2.230994 ATCTGTCACCTGCACGCGAT 62.231 55.000 15.93 0.00 0.00 4.58
5012 6421 8.818057 CGACCACACCAAATTAAATTTAAACAA 58.182 29.630 14.35 0.00 0.00 2.83
5062 6473 3.367630 CACACAAAAAGGACAGTTTGCAC 59.632 43.478 0.00 0.00 38.10 4.57
5065 6476 3.189285 CAAAAAGGACAGTTTGCACCTG 58.811 45.455 10.32 10.32 36.01 4.00
5093 6504 9.113838 AGGATTATGCTGTGTAATTAACTTGAG 57.886 33.333 0.00 0.00 0.00 3.02
5183 6596 2.693074 ACGATGGGATATTTTTGGTGCC 59.307 45.455 0.00 0.00 0.00 5.01
5583 6996 1.059098 TCTTTGCAGAGCTGGAGGAA 58.941 50.000 0.00 0.00 31.08 3.36
5604 7017 7.390027 AGGAATTGGAGACTGATAATAATCCG 58.610 38.462 0.00 0.00 0.00 4.18
5990 7405 6.557633 ACCACTTCCTCCGTTCCTAAATATAT 59.442 38.462 0.00 0.00 0.00 0.86
5991 7406 7.731688 ACCACTTCCTCCGTTCCTAAATATATA 59.268 37.037 0.00 0.00 0.00 0.86
6034 7453 7.672983 ATAGATTACATACGGAGCAAAATGG 57.327 36.000 0.00 0.00 0.00 3.16
6203 7625 3.139077 GTCCCAACTAACACCAAGTCAG 58.861 50.000 0.00 0.00 0.00 3.51
6216 7638 4.022329 CACCAAGTCAGTTATTTTGGGACC 60.022 45.833 7.00 0.00 43.38 4.46
6217 7639 4.141018 ACCAAGTCAGTTATTTTGGGACCT 60.141 41.667 7.00 0.00 43.38 3.85
6244 7666 7.939588 AGGGAGTAGTAATTATTTCTTCATGGC 59.060 37.037 0.00 0.00 0.00 4.40
6380 7821 3.430453 CCTGACTGCCCTTTTAATTCCA 58.570 45.455 0.00 0.00 0.00 3.53
6521 7962 9.005777 TGTTCATGTAGTTAAAATCCTTGTACC 57.994 33.333 0.00 0.00 0.00 3.34
6614 8055 8.479313 TCAACTTTAGAGTGTGCACTAATATG 57.521 34.615 19.41 7.63 42.66 1.78
6626 8068 7.657354 GTGTGCACTAATATGGTCATAATCTCA 59.343 37.037 19.41 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 98 3.825160 TTGCGAAGGTGCGGCTTCT 62.825 57.895 0.00 0.00 37.81 2.85
92 101 2.485795 TTTTTGCGAAGGTGCGGCT 61.486 52.632 0.00 0.00 37.81 5.52
93 102 2.026879 TTTTTGCGAAGGTGCGGC 59.973 55.556 0.00 0.00 37.81 6.53
94 103 0.934436 CAGTTTTTGCGAAGGTGCGG 60.934 55.000 0.00 0.00 37.81 5.69
96 105 1.921243 AACAGTTTTTGCGAAGGTGC 58.079 45.000 0.00 0.00 0.00 5.01
189 204 7.223387 CCATGGAAGAAATAAAAGTAGCAATGC 59.777 37.037 5.56 0.00 0.00 3.56
197 212 8.485578 TGGTAAACCATGGAAGAAATAAAAGT 57.514 30.769 21.47 0.00 42.01 2.66
239 254 6.718294 AGAGACGGTTGAATAGGGTTTTAAT 58.282 36.000 0.00 0.00 0.00 1.40
240 255 6.117975 AGAGACGGTTGAATAGGGTTTTAA 57.882 37.500 0.00 0.00 0.00 1.52
241 256 5.750352 AGAGACGGTTGAATAGGGTTTTA 57.250 39.130 0.00 0.00 0.00 1.52
242 257 4.635699 AGAGACGGTTGAATAGGGTTTT 57.364 40.909 0.00 0.00 0.00 2.43
291 306 7.609097 AGAAGCATCCTTAGATACATCTCAA 57.391 36.000 0.00 0.00 38.32 3.02
390 405 3.491792 GCGTGAGGAATAAGGGAAGAGAG 60.492 52.174 0.00 0.00 0.00 3.20
402 417 0.250513 GAGGAGTTGGCGTGAGGAAT 59.749 55.000 0.00 0.00 0.00 3.01
510 536 4.540735 AATTACGCCCCCTCGCCG 62.541 66.667 0.00 0.00 0.00 6.46
581 612 2.510238 GAGAGCACATTCCGCGCT 60.510 61.111 5.56 0.00 42.55 5.92
654 686 2.023673 CACCAGCTTCTTTTCACCACA 58.976 47.619 0.00 0.00 0.00 4.17
677 709 1.979155 GCAAGCTGGTCCTTTCCCC 60.979 63.158 0.00 0.00 0.00 4.81
705 1571 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
706 1572 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
707 1573 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
708 1574 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
709 1575 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
710 1576 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
711 1577 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
712 1578 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
713 1579 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
714 1580 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
715 1581 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
716 1582 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
717 1583 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
718 1584 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
719 1585 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
720 1586 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
721 1587 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
722 1588 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
723 1589 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
724 1590 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
725 1591 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
774 1670 8.530269 TTATTTAGAGAGAGGAAAACGACAAC 57.470 34.615 0.00 0.00 0.00 3.32
973 1871 4.128643 AGTCTAGTCTACGTATGGTGAGC 58.871 47.826 0.00 0.00 0.00 4.26
984 1882 3.504520 GGCTGGCTATGAGTCTAGTCTAC 59.495 52.174 0.00 0.00 0.00 2.59
1054 1952 4.460873 GCAAGCGGGTAAGTGCGC 62.461 66.667 0.00 0.00 35.87 6.09
1066 1964 3.677648 CAGGGCTGTGGTGCAAGC 61.678 66.667 0.00 0.00 34.04 4.01
1067 1965 3.677648 GCAGGGCTGTGGTGCAAG 61.678 66.667 0.00 0.00 37.16 4.01
1072 1970 1.152269 AATTTGGCAGGGCTGTGGT 60.152 52.632 0.00 0.00 0.00 4.16
1074 1972 0.320073 CACAATTTGGCAGGGCTGTG 60.320 55.000 0.78 6.67 0.00 3.66
1075 1973 2.051941 CACAATTTGGCAGGGCTGT 58.948 52.632 0.78 0.00 0.00 4.40
1154 2067 1.707989 TCACACTGTCCTCCTCTCTCT 59.292 52.381 0.00 0.00 0.00 3.10
1155 2068 2.091541 CTCACACTGTCCTCCTCTCTC 58.908 57.143 0.00 0.00 0.00 3.20
1156 2069 1.427368 ACTCACACTGTCCTCCTCTCT 59.573 52.381 0.00 0.00 0.00 3.10
1175 2088 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1176 2089 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1177 2090 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1178 2091 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1179 2092 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1180 2093 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1181 2094 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1182 2095 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1183 2096 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1184 2097 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1185 2098 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1186 2099 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1187 2100 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1188 2101 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1189 2102 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1190 2103 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1191 2104 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1192 2105 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1193 2106 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1194 2107 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1195 2108 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1196 2109 2.070028 GTACACACACACACACACACA 58.930 47.619 0.00 0.00 0.00 3.72
1197 2110 2.070028 TGTACACACACACACACACAC 58.930 47.619 0.00 0.00 0.00 3.82
1198 2111 2.342179 CTGTACACACACACACACACA 58.658 47.619 0.00 0.00 0.00 3.72
1199 2112 1.062002 GCTGTACACACACACACACAC 59.938 52.381 0.00 0.00 0.00 3.82
1200 2113 1.066502 AGCTGTACACACACACACACA 60.067 47.619 0.00 0.00 0.00 3.72
1201 2114 1.593006 GAGCTGTACACACACACACAC 59.407 52.381 0.00 0.00 0.00 3.82
1202 2115 1.472552 GGAGCTGTACACACACACACA 60.473 52.381 0.00 0.00 0.00 3.72
1203 2116 1.202533 AGGAGCTGTACACACACACAC 60.203 52.381 0.00 0.00 0.00 3.82
1204 2117 1.119684 AGGAGCTGTACACACACACA 58.880 50.000 0.00 0.00 0.00 3.72
1546 2465 0.323451 GGGGCCTCAAAGGTAACCTG 60.323 60.000 0.84 0.00 37.80 4.00
1787 2706 6.665248 GGATGGATGGAAGGGGAATTAATTAG 59.335 42.308 0.00 0.00 0.00 1.73
1804 2723 6.148480 CGCTAGGAAAGAAATTAGGATGGATG 59.852 42.308 0.00 0.00 0.00 3.51
1829 2748 5.833131 AGAATAGGACAGATCAAGTCTCTCC 59.167 44.000 15.24 3.02 41.09 3.71
1830 2749 6.959639 AGAATAGGACAGATCAAGTCTCTC 57.040 41.667 15.24 8.69 34.00 3.20
1845 2764 8.635765 AAATACTGAAGCAACAAAGAATAGGA 57.364 30.769 0.00 0.00 0.00 2.94
1904 2823 1.272985 TGCAATTGTAAGGGAAGGGGG 60.273 52.381 7.40 0.00 0.00 5.40
1926 2845 9.845740 AAATTACATAGGTACATGCATGAACTA 57.154 29.630 32.75 26.27 0.00 2.24
1940 2859 9.975218 AATAGAACCACAGAAAATTACATAGGT 57.025 29.630 0.00 0.00 0.00 3.08
2127 3214 4.400120 TGCAGCTATCCATGCATCAAATA 58.600 39.130 0.00 0.00 46.97 1.40
2174 3514 8.055181 ACATCATGAAAGGAATAAAGAAGCCTA 58.945 33.333 0.00 0.00 0.00 3.93
2272 3612 4.043750 CCATGCCGCAATAACTTAATGTG 58.956 43.478 0.00 0.00 0.00 3.21
2359 3699 3.499737 CGGTTGCTCATCACCGGC 61.500 66.667 0.00 0.00 41.55 6.13
2535 3875 3.194861 TGTGAGGCATGTACTTATTCGC 58.805 45.455 0.00 0.00 0.00 4.70
2612 3952 7.624360 AAGCTCGTTCAAATTTATATGACCA 57.376 32.000 0.00 0.00 0.00 4.02
2613 3953 8.827677 AGTAAGCTCGTTCAAATTTATATGACC 58.172 33.333 0.00 0.00 0.00 4.02
2614 3954 9.638300 CAGTAAGCTCGTTCAAATTTATATGAC 57.362 33.333 0.00 0.00 0.00 3.06
2615 3955 9.378551 ACAGTAAGCTCGTTCAAATTTATATGA 57.621 29.630 0.00 0.00 0.00 2.15
2616 3956 9.988350 AACAGTAAGCTCGTTCAAATTTATATG 57.012 29.630 0.00 0.00 0.00 1.78
2663 4003 4.824537 TCGATCAAATGTGGAAAAGTTGGA 59.175 37.500 0.00 0.00 0.00 3.53
2668 4008 5.097529 CCATGTCGATCAAATGTGGAAAAG 58.902 41.667 0.00 0.00 0.00 2.27
2696 4036 7.116805 GCTGTTTTTCCTTTGGTCAAATCATAG 59.883 37.037 0.00 0.00 0.00 2.23
2765 4105 5.516090 ACGCAACAAACACCAGTTTAATAG 58.484 37.500 0.00 0.00 45.80 1.73
2995 4336 3.782443 CCCGCCCCGCTCTAAACT 61.782 66.667 0.00 0.00 0.00 2.66
3263 4604 0.548439 ACCCCAACCCTACCCACTAC 60.548 60.000 0.00 0.00 0.00 2.73
3264 4605 0.196631 AACCCCAACCCTACCCACTA 59.803 55.000 0.00 0.00 0.00 2.74
3265 4606 0.196631 TAACCCCAACCCTACCCACT 59.803 55.000 0.00 0.00 0.00 4.00
3266 4607 0.329261 GTAACCCCAACCCTACCCAC 59.671 60.000 0.00 0.00 0.00 4.61
3267 4608 0.196631 AGTAACCCCAACCCTACCCA 59.803 55.000 0.00 0.00 0.00 4.51
3268 4609 0.914644 GAGTAACCCCAACCCTACCC 59.085 60.000 0.00 0.00 0.00 3.69
3269 4610 1.962558 AGAGTAACCCCAACCCTACC 58.037 55.000 0.00 0.00 0.00 3.18
3270 4611 4.779489 TCTTAAGAGTAACCCCAACCCTAC 59.221 45.833 0.00 0.00 0.00 3.18
3271 4612 5.027385 TCTTAAGAGTAACCCCAACCCTA 57.973 43.478 0.00 0.00 0.00 3.53
3272 4613 3.878086 TCTTAAGAGTAACCCCAACCCT 58.122 45.455 0.00 0.00 0.00 4.34
3273 4614 4.524053 CATCTTAAGAGTAACCCCAACCC 58.476 47.826 11.53 0.00 0.00 4.11
3274 4615 4.524053 CCATCTTAAGAGTAACCCCAACC 58.476 47.826 11.53 0.00 0.00 3.77
3275 4616 4.018688 ACCCATCTTAAGAGTAACCCCAAC 60.019 45.833 11.53 0.00 0.00 3.77
3276 4617 4.180723 ACCCATCTTAAGAGTAACCCCAA 58.819 43.478 11.53 0.00 0.00 4.12
3277 4618 3.810623 ACCCATCTTAAGAGTAACCCCA 58.189 45.455 11.53 0.00 0.00 4.96
3278 4619 4.524053 CAACCCATCTTAAGAGTAACCCC 58.476 47.826 11.53 0.00 0.00 4.95
3279 4620 4.524053 CCAACCCATCTTAAGAGTAACCC 58.476 47.826 11.53 0.00 0.00 4.11
3280 4621 4.524053 CCCAACCCATCTTAAGAGTAACC 58.476 47.826 11.53 0.00 0.00 2.85
3281 4622 4.018688 ACCCCAACCCATCTTAAGAGTAAC 60.019 45.833 11.53 0.00 0.00 2.50
3282 4623 4.180723 ACCCCAACCCATCTTAAGAGTAA 58.819 43.478 11.53 0.00 0.00 2.24
3283 4624 3.810623 ACCCCAACCCATCTTAAGAGTA 58.189 45.455 11.53 0.00 0.00 2.59
3284 4625 2.644151 ACCCCAACCCATCTTAAGAGT 58.356 47.619 11.53 0.58 0.00 3.24
3285 4626 3.739401 AACCCCAACCCATCTTAAGAG 57.261 47.619 11.53 0.00 0.00 2.85
3286 4627 3.917629 TGTAACCCCAACCCATCTTAAGA 59.082 43.478 7.82 7.82 0.00 2.10
3287 4628 4.310022 TGTAACCCCAACCCATCTTAAG 57.690 45.455 0.00 0.00 0.00 1.85
3288 4629 4.140994 TGTTGTAACCCCAACCCATCTTAA 60.141 41.667 0.00 0.00 43.22 1.85
3384 4759 1.402259 CACTCTATTGCTCCGTCTCGT 59.598 52.381 0.00 0.00 0.00 4.18
3407 4782 0.806102 CGCCCTATGTCACACTTCCG 60.806 60.000 0.00 0.00 0.00 4.30
3436 4811 2.763448 CCACCTCCCACAAAAGTCAAAA 59.237 45.455 0.00 0.00 0.00 2.44
3553 4933 4.561105 CTCGTCAGAAGTTAGCCTTTCTT 58.439 43.478 0.00 0.00 32.03 2.52
3587 4967 4.540153 CCTACCATTGACAGGCCG 57.460 61.111 0.00 0.00 0.00 6.13
3592 4972 0.323360 GCCCAAGCCTACCATTGACA 60.323 55.000 0.00 0.00 0.00 3.58
3596 4976 0.704076 TTCAGCCCAAGCCTACCATT 59.296 50.000 0.00 0.00 41.25 3.16
3597 4977 0.257039 CTTCAGCCCAAGCCTACCAT 59.743 55.000 0.00 0.00 41.25 3.55
3598 4978 1.685224 CTTCAGCCCAAGCCTACCA 59.315 57.895 0.00 0.00 41.25 3.25
3637 5017 8.129001 AGGATATATATAACCCATGTGACCTCA 58.871 37.037 13.88 0.00 0.00 3.86
3638 5018 8.554490 AGGATATATATAACCCATGTGACCTC 57.446 38.462 13.88 0.00 0.00 3.85
3649 5029 7.226128 GGCGGCTTACAAAGGATATATATAACC 59.774 40.741 10.37 10.37 0.00 2.85
3679 5059 7.996644 GGGATTACAACTAATCAACTTATCCCA 59.003 37.037 0.00 0.00 44.39 4.37
3693 5073 2.484065 CGAATGCCGGGGATTACAACTA 60.484 50.000 14.16 0.00 33.91 2.24
3713 5093 0.606604 CCATATCGGGGGAGGTTACG 59.393 60.000 0.00 0.00 0.00 3.18
3802 5200 1.487482 TCAACACAGCGAAGAACGAG 58.513 50.000 0.00 0.00 45.77 4.18
3814 5212 1.686355 ACGGCAGGAAAATCAACACA 58.314 45.000 0.00 0.00 0.00 3.72
3825 5223 6.726490 ACTTATTTTAGAGATACGGCAGGA 57.274 37.500 0.00 0.00 0.00 3.86
3888 5293 0.385390 CCAAACCTGTGTGTTCCAGC 59.615 55.000 0.00 0.00 0.00 4.85
3897 5302 1.338020 GGACAAAGAGCCAAACCTGTG 59.662 52.381 0.00 0.00 0.00 3.66
3898 5303 1.064017 TGGACAAAGAGCCAAACCTGT 60.064 47.619 0.00 0.00 0.00 4.00
3914 5319 4.822896 TGTACATACTTGTTGGGTTTGGAC 59.177 41.667 0.00 0.00 37.28 4.02
3916 5321 5.776173 TTGTACATACTTGTTGGGTTTGG 57.224 39.130 0.00 0.00 37.28 3.28
4016 5421 1.276140 TATTTGGGACACGGGGAGGG 61.276 60.000 0.00 0.00 39.29 4.30
4019 5424 1.003812 CAACTATTTGGGACACGGGGA 59.996 52.381 0.00 0.00 39.29 4.81
4461 5867 8.806146 AGTTTGACCAAGCAGATATACAAAAAT 58.194 29.630 0.00 0.00 0.00 1.82
4507 5913 6.700081 GTCAATGATGGCGTATAAACTGACTA 59.300 38.462 0.00 0.00 0.00 2.59
4512 5918 6.767902 AGAATGTCAATGATGGCGTATAAACT 59.232 34.615 0.00 0.00 32.34 2.66
4556 5962 8.801299 TGCCTCTTGTTGAATTATATGAAACAA 58.199 29.630 0.00 0.00 38.15 2.83
4558 5964 9.455847 GATGCCTCTTGTTGAATTATATGAAAC 57.544 33.333 0.00 0.00 0.00 2.78
4577 5983 9.252962 CCAATATTTGAATACAAAAGATGCCTC 57.747 33.333 0.00 0.00 46.77 4.70
4633 6039 1.571955 TCATCCTGTGCTTAGAGCCA 58.428 50.000 0.00 0.00 41.51 4.75
4790 6199 7.383687 AGTCTAGAATGATTGTGTTTCGGTTA 58.616 34.615 0.00 0.00 0.00 2.85
4795 6204 7.171508 TGTGTGAGTCTAGAATGATTGTGTTTC 59.828 37.037 0.00 0.00 0.00 2.78
4981 6390 0.802494 AATTTGGTGTGGTCGATCGC 59.198 50.000 11.09 1.22 0.00 4.58
4985 6394 8.195436 TGTTTAAATTTAATTTGGTGTGGTCGA 58.805 29.630 11.33 0.00 33.82 4.20
5039 6450 3.006323 TGCAAACTGTCCTTTTTGTGTGT 59.994 39.130 0.00 0.00 35.51 3.72
5045 6456 3.096092 TCAGGTGCAAACTGTCCTTTTT 58.904 40.909 16.56 0.00 37.25 1.94
5062 6473 6.949352 AATTACACAGCATAATCCTTCAGG 57.051 37.500 0.00 0.00 0.00 3.86
5065 6476 9.722056 CAAGTTAATTACACAGCATAATCCTTC 57.278 33.333 0.00 0.00 0.00 3.46
5169 6582 2.867975 GCATGCAGGCACCAAAAATATC 59.132 45.455 20.11 0.00 0.00 1.63
5183 6596 1.065491 TGTAGTAACCCCTGCATGCAG 60.065 52.381 35.88 35.88 43.26 4.41
5313 6726 1.375396 AAGGACGTTGCGCTGCATA 60.375 52.632 9.73 0.00 38.76 3.14
5583 6996 8.138928 TCATCGGATTATTATCAGTCTCCAAT 57.861 34.615 0.00 0.00 32.09 3.16
5604 7017 3.187227 AGACGTTTGCACTTGTCATCATC 59.813 43.478 12.37 0.00 33.83 2.92
5963 7378 0.396811 AGGAACGGAGGAAGTGGTTG 59.603 55.000 0.00 0.00 0.00 3.77
6100 7519 7.876068 ACTCATTCCGTTTCTAAATGTTAGACA 59.124 33.333 0.00 0.00 33.22 3.41
6105 7524 9.886132 ATAGTACTCATTCCGTTTCTAAATGTT 57.114 29.630 0.00 0.00 33.22 2.71
6203 7625 4.857130 ACTCCCTAGGTCCCAAAATAAC 57.143 45.455 8.29 0.00 0.00 1.89
6239 7661 2.802816 GTTGTAAGCTAGATCCGCCATG 59.197 50.000 0.00 0.00 0.00 3.66
6244 7666 5.592054 TCATCTTGTTGTAAGCTAGATCCG 58.408 41.667 0.00 0.00 0.00 4.18
6280 7705 8.648557 TGAATATATGCACACAGTTCTAGAAC 57.351 34.615 25.24 25.24 41.45 3.01
6285 7710 7.389884 GGATCATGAATATATGCACACAGTTCT 59.610 37.037 0.00 0.00 0.00 3.01
6288 7713 5.640783 CGGATCATGAATATATGCACACAGT 59.359 40.000 0.00 0.00 0.00 3.55
6626 8068 8.612619 CGTGCTAAGATGTACAAATAGGAAAAT 58.387 33.333 0.00 0.00 0.00 1.82
6809 8254 0.168128 ATTTTGCTAGCAACGACGGC 59.832 50.000 29.33 0.00 35.46 5.68


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

AutoCloner maintained by Alex Coulton.