Multiple sequence alignment - TraesCS4D01G351200

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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 TraesCS4D01G351200 chr4D 100.000 2870 0 0 1 2870 503171715 503168846 0.000000e+00 5301
1 TraesCS4D01G351200 chr4D 96.891 579 13 5 2294 2870 385503236 385502661 0.000000e+00 965
2 TraesCS4D01G351200 chr4D 96.886 578 14 4 2291 2867 421068511 421069085 0.000000e+00 965
3 TraesCS4D01G351200 chr4D 76.522 230 29 16 1122 1333 509171491 509171269 5.060000e-18 102
4 TraesCS4D01G351200 chr5A 90.214 1124 81 17 875 1977 687643588 687642473 0.000000e+00 1439
5 TraesCS4D01G351200 chr5A 92.675 628 14 5 144 749 687646988 687646371 0.000000e+00 876
6 TraesCS4D01G351200 chr5A 92.079 101 8 0 759 859 687644462 687644362 2.980000e-30 143
7 TraesCS4D01G351200 chr5A 77.528 267 34 17 1123 1372 328551315 328551058 1.390000e-28 137
8 TraesCS4D01G351200 chr3D 97.436 585 12 3 2286 2869 11987266 11987848 0.000000e+00 994
9 TraesCS4D01G351200 chr5D 97.079 582 14 3 2290 2870 462329622 462329043 0.000000e+00 977
10 TraesCS4D01G351200 chr5D 89.933 149 11 4 1224 1369 8964225 8964372 3.770000e-44 189
11 TraesCS4D01G351200 chr5D 79.310 174 14 13 1123 1282 244107730 244107565 5.060000e-18 102
12 TraesCS4D01G351200 chr2D 97.074 581 14 3 2291 2870 524062895 524063473 0.000000e+00 976
13 TraesCS4D01G351200 chr2D 97.391 575 12 3 2294 2867 529039329 529038757 0.000000e+00 976
14 TraesCS4D01G351200 chr2D 78.868 265 37 12 1122 1379 635871584 635871332 8.230000e-36 161
15 TraesCS4D01G351200 chr1D 97.074 581 14 3 2291 2870 481043424 481044002 0.000000e+00 976
16 TraesCS4D01G351200 chr7D 96.392 582 17 4 2286 2866 21626737 21627315 0.000000e+00 955
17 TraesCS4D01G351200 chr7D 82.642 265 22 15 1120 1370 57880417 57880671 2.240000e-51 213
18 TraesCS4D01G351200 chr6D 96.082 587 18 5 2283 2867 443234027 443233444 0.000000e+00 952
19 TraesCS4D01G351200 chr6D 80.273 512 77 15 1537 2039 7517799 7517303 5.840000e-97 364
20 TraesCS4D01G351200 chr6D 83.025 324 48 5 383 705 7518787 7518470 1.300000e-73 287
21 TraesCS4D01G351200 chr4B 91.553 367 18 4 1 363 647702938 647703295 7.140000e-136 494
22 TraesCS4D01G351200 chr4B 87.654 405 31 9 708 1105 648206419 648206027 1.210000e-123 453
23 TraesCS4D01G351200 chr4B 87.654 405 31 9 708 1105 648229912 648229520 1.210000e-123 453
24 TraesCS4D01G351200 chr4B 87.654 405 31 9 708 1105 648256133 648255741 1.210000e-123 453
25 TraesCS4D01G351200 chr4B 87.407 405 32 7 708 1105 648185553 648185161 5.640000e-122 448
26 TraesCS4D01G351200 chr4B 88.623 334 23 9 778 1108 647703642 647703963 2.680000e-105 392
27 TraesCS4D01G351200 chr4B 87.625 299 33 4 1402 1698 647704224 647704520 7.610000e-91 344
28 TraesCS4D01G351200 chr4B 94.083 169 6 1 141 309 648207179 648207015 1.320000e-63 254
29 TraesCS4D01G351200 chr4B 94.083 169 6 1 141 309 648230675 648230511 1.320000e-63 254
30 TraesCS4D01G351200 chr4B 94.083 169 6 1 141 309 648256896 648256732 1.320000e-63 254
31 TraesCS4D01G351200 chr4B 93.491 169 7 1 141 309 648186316 648186152 6.140000e-62 248
32 TraesCS4D01G351200 chr4B 86.818 220 15 7 492 711 648256536 648256331 1.720000e-57 233
33 TraesCS4D01G351200 chr4B 86.364 220 16 7 492 711 648185956 648185751 8.000000e-56 228
34 TraesCS4D01G351200 chr4B 86.364 220 16 7 492 711 648206819 648206614 8.000000e-56 228
35 TraesCS4D01G351200 chr4B 86.364 220 16 7 492 711 648230315 648230110 8.000000e-56 228
36 TraesCS4D01G351200 chr4B 96.241 133 3 2 1 131 648186495 648186363 1.730000e-52 217
37 TraesCS4D01G351200 chr4B 93.878 147 3 3 1 145 648207358 648207216 1.730000e-52 217
38 TraesCS4D01G351200 chr4B 93.878 147 3 3 1 145 648230854 648230712 1.730000e-52 217
39 TraesCS4D01G351200 chr4B 93.878 147 3 3 1 145 648257075 648256933 1.730000e-52 217
40 TraesCS4D01G351200 chr6A 87.037 270 31 3 437 705 7596986 7596720 4.650000e-78 302
41 TraesCS4D01G351200 chr6A 83.492 315 45 6 1563 1872 7596007 7595695 1.300000e-73 287
42 TraesCS4D01G351200 chr6A 85.778 225 22 6 1151 1369 554512565 554512785 2.220000e-56 230
43 TraesCS4D01G351200 chr6B 85.609 271 33 5 437 705 14095026 14094760 2.180000e-71 279
44 TraesCS4D01G351200 chr6B 83.983 231 16 14 1153 1369 718336262 718336039 4.850000e-48 202
45 TraesCS4D01G351200 chrUn 94.083 169 6 1 141 309 331155567 331155731 1.320000e-63 254
46 TraesCS4D01G351200 chrUn 86.364 220 16 7 492 711 331155927 331156132 8.000000e-56 228
47 TraesCS4D01G351200 chrUn 96.241 133 3 2 1 131 331155388 331155520 1.730000e-52 217
48 TraesCS4D01G351200 chr2B 87.195 164 16 3 1218 1379 458248422 458248582 6.320000e-42 182
49 TraesCS4D01G351200 chr2A 87.195 164 16 3 1218 1379 523869060 523869220 6.320000e-42 182
50 TraesCS4D01G351200 chr4A 79.537 259 36 12 1123 1379 632174839 632175082 4.920000e-38 169
51 TraesCS4D01G351200 chr1B 81.166 223 26 12 1123 1342 623394018 623393809 6.360000e-37 165


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 TraesCS4D01G351200 chr4D 503168846 503171715 2869 True 5301.000000 5301 100.000000 1 2870 1 chr4D.!!$R2 2869
1 TraesCS4D01G351200 chr4D 385502661 385503236 575 True 965.000000 965 96.891000 2294 2870 1 chr4D.!!$R1 576
2 TraesCS4D01G351200 chr4D 421068511 421069085 574 False 965.000000 965 96.886000 2291 2867 1 chr4D.!!$F1 576
3 TraesCS4D01G351200 chr5A 687642473 687646988 4515 True 819.333333 1439 91.656000 144 1977 3 chr5A.!!$R2 1833
4 TraesCS4D01G351200 chr3D 11987266 11987848 582 False 994.000000 994 97.436000 2286 2869 1 chr3D.!!$F1 583
5 TraesCS4D01G351200 chr5D 462329043 462329622 579 True 977.000000 977 97.079000 2290 2870 1 chr5D.!!$R2 580
6 TraesCS4D01G351200 chr2D 524062895 524063473 578 False 976.000000 976 97.074000 2291 2870 1 chr2D.!!$F1 579
7 TraesCS4D01G351200 chr2D 529038757 529039329 572 True 976.000000 976 97.391000 2294 2867 1 chr2D.!!$R1 573
8 TraesCS4D01G351200 chr1D 481043424 481044002 578 False 976.000000 976 97.074000 2291 2870 1 chr1D.!!$F1 579
9 TraesCS4D01G351200 chr7D 21626737 21627315 578 False 955.000000 955 96.392000 2286 2866 1 chr7D.!!$F1 580
10 TraesCS4D01G351200 chr6D 443233444 443234027 583 True 952.000000 952 96.082000 2283 2867 1 chr6D.!!$R1 584
11 TraesCS4D01G351200 chr6D 7517303 7518787 1484 True 325.500000 364 81.649000 383 2039 2 chr6D.!!$R2 1656
12 TraesCS4D01G351200 chr4B 647702938 647704520 1582 False 410.000000 494 89.267000 1 1698 3 chr4B.!!$F1 1697
13 TraesCS4D01G351200 chr4B 648255741 648257075 1334 True 289.250000 453 90.608250 1 1105 4 chr4B.!!$R4 1104
14 TraesCS4D01G351200 chr4B 648206027 648207358 1331 True 288.000000 453 90.494750 1 1105 4 chr4B.!!$R2 1104
15 TraesCS4D01G351200 chr4B 648229520 648230854 1334 True 288.000000 453 90.494750 1 1105 4 chr4B.!!$R3 1104
16 TraesCS4D01G351200 chr4B 648185161 648186495 1334 True 285.250000 448 90.875750 1 1105 4 chr4B.!!$R1 1104
17 TraesCS4D01G351200 chr6A 7595695 7596986 1291 True 294.500000 302 85.264500 437 1872 2 chr6A.!!$R1 1435
18 TraesCS4D01G351200 chrUn 331155388 331156132 744 False 233.000000 254 92.229333 1 711 3 chrUn.!!$F1 710

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
42 45 0.043907 CGTGCGTCGCATCTTGTATG 60.044 55.0 24.65 0.00 41.91 2.39 F
1522 4603 0.107945 CCTCTTCCGCTAAGCTGCTT 60.108 55.0 19.93 19.93 34.97 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 4867 0.539669 TCCTCTTCCACTCACGCTCA 60.540 55.000 0.00 0.0 0.0 4.26 R
2633 5737 2.613691 CTTATAAACCGGTGTGAGCGT 58.386 47.619 8.52 0.0 37.4 5.07 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
42 45 0.043907 CGTGCGTCGCATCTTGTATG 60.044 55.000 24.65 0.00 41.91 2.39
72 76 2.655090 TGGCCATCTGTTGTTGAAGA 57.345 45.000 0.00 0.00 0.00 2.87
111 117 8.078060 TGGAACAACAGATGATCATAAGACTA 57.922 34.615 8.54 0.00 32.74 2.59
196 239 2.353704 CCACCTTACTCATGCGACTCAA 60.354 50.000 0.00 0.00 0.00 3.02
217 260 8.859090 ACTCAATTCATCAATTTGTTTGACCTA 58.141 29.630 0.00 0.00 46.80 3.08
232 275 7.771183 TGTTTGACCTAATTAAATGATGGAGC 58.229 34.615 0.00 0.00 0.00 4.70
310 361 6.455360 AATCTGCTGTTAGAGAGAGAAGAG 57.545 41.667 0.00 0.00 36.79 2.85
311 362 4.917385 TCTGCTGTTAGAGAGAGAAGAGT 58.083 43.478 0.00 0.00 28.46 3.24
312 363 6.056090 TCTGCTGTTAGAGAGAGAAGAGTA 57.944 41.667 0.00 0.00 28.46 2.59
314 365 6.056090 TGCTGTTAGAGAGAGAAGAGTAGA 57.944 41.667 0.00 0.00 0.00 2.59
315 366 6.477253 TGCTGTTAGAGAGAGAAGAGTAGAA 58.523 40.000 0.00 0.00 0.00 2.10
317 368 6.821665 GCTGTTAGAGAGAGAAGAGTAGAAGA 59.178 42.308 0.00 0.00 0.00 2.87
363 442 3.105283 GTTGGTAGGAAGAGCTAGGGAA 58.895 50.000 0.00 0.00 0.00 3.97
364 443 3.708236 TGGTAGGAAGAGCTAGGGAAT 57.292 47.619 0.00 0.00 0.00 3.01
368 447 5.088026 GGTAGGAAGAGCTAGGGAATACAT 58.912 45.833 0.00 0.00 0.00 2.29
749 1093 3.837570 AAGGACGCCGGGTTCAACC 62.838 63.158 2.18 0.00 37.60 3.77
801 3044 2.573920 AGCTCTTCCTCGAGGTCAC 58.426 57.895 30.17 16.19 37.16 3.67
920 3922 2.433145 CATCGAGTGCACCGTGCT 60.433 61.111 23.52 4.95 45.31 4.40
921 3923 2.433145 ATCGAGTGCACCGTGCTG 60.433 61.111 23.52 11.27 45.31 4.41
922 3924 3.939837 ATCGAGTGCACCGTGCTGG 62.940 63.158 23.52 10.44 45.31 4.85
923 3925 4.662961 CGAGTGCACCGTGCTGGA 62.663 66.667 23.52 1.26 45.31 3.86
924 3926 2.740055 GAGTGCACCGTGCTGGAG 60.740 66.667 23.52 0.00 45.31 3.86
931 3933 4.767255 CCGTGCTGGAGCCTGGAC 62.767 72.222 0.00 7.78 42.00 4.02
1034 4051 0.955428 CCACCCACGGATGTTGTCTG 60.955 60.000 0.00 0.00 39.25 3.51
1124 4151 4.747218 TTGGCGGGTCCCAAATAC 57.253 55.556 9.12 0.00 41.69 1.89
1132 4159 1.214673 GGGTCCCAAATACTCCCTTCC 59.785 57.143 1.78 0.00 35.63 3.46
1176 4203 9.453572 AGTGCATATAGATTTTCTGAAAAGTCA 57.546 29.630 19.14 8.21 34.49 3.41
1392 4434 6.663953 ACAGATGCAGTAGTCTAAGACCTTTA 59.336 38.462 0.00 0.00 32.18 1.85
1495 4576 8.800370 TGGTTCTTATAGTGCAATCAATGTTA 57.200 30.769 0.00 0.00 0.00 2.41
1516 4597 2.955614 TCGTTTTCCTCTTCCGCTAAG 58.044 47.619 0.00 0.00 36.45 2.18
1522 4603 0.107945 CCTCTTCCGCTAAGCTGCTT 60.108 55.000 19.93 19.93 34.97 3.91
1603 4700 1.355381 ACTGGGGTCATGAAGATTGCA 59.645 47.619 0.00 0.00 0.00 4.08
1619 4716 8.358895 TGAAGATTGCATCAAAATACTTCAACA 58.641 29.630 0.00 0.00 39.19 3.33
1636 4733 1.033746 ACATTGCAAGGAGGCCATCG 61.034 55.000 19.41 0.00 0.00 3.84
1726 4824 0.391661 GATCAGCGAGTGGAAGCCAA 60.392 55.000 0.00 0.00 34.18 4.52
1757 4855 0.804364 TCTCAATGTGCATCAACGGC 59.196 50.000 0.00 0.00 0.00 5.68
1808 4906 6.770746 AGGATCTTTTCTGATGTTGGATTG 57.229 37.500 0.00 0.00 0.00 2.67
1890 4990 4.022935 TGAAAGCTTTGCATGGTGAACTAG 60.023 41.667 18.30 0.00 0.00 2.57
1928 5028 3.484649 ACACAATATGTCGAACGCGTATC 59.515 43.478 14.46 11.71 36.54 2.24
1935 5035 2.094803 TGTCGAACGCGTATCCCTAAAA 60.095 45.455 14.46 0.00 38.98 1.52
1937 5037 1.253545 CGAACGCGTATCCCTAAAACG 59.746 52.381 14.46 2.31 39.55 3.60
1957 5061 1.945207 CAACACGTTCGTTGGTATGC 58.055 50.000 10.16 0.00 42.10 3.14
1958 5062 0.869730 AACACGTTCGTTGGTATGCC 59.130 50.000 0.00 0.00 0.00 4.40
1978 5082 1.596260 CTGCGCATGAATCTAGTGTGG 59.404 52.381 12.24 0.00 0.00 4.17
1984 5088 4.268644 CGCATGAATCTAGTGTGGTGTTAG 59.731 45.833 0.00 0.00 0.00 2.34
1991 5095 5.995565 TCTAGTGTGGTGTTAGTAAGCAT 57.004 39.130 0.00 0.00 0.00 3.79
1993 5097 4.351874 AGTGTGGTGTTAGTAAGCATGT 57.648 40.909 0.00 0.00 0.00 3.21
2002 5106 6.348213 GGTGTTAGTAAGCATGTTACCTTGTG 60.348 42.308 11.94 0.00 0.00 3.33
2012 5116 5.689383 ATGTTACCTTGTGAACATGTGTC 57.311 39.130 0.00 0.00 43.07 3.67
2014 5118 4.574421 TGTTACCTTGTGAACATGTGTCTG 59.426 41.667 0.00 0.00 30.72 3.51
2015 5119 1.949525 ACCTTGTGAACATGTGTCTGC 59.050 47.619 0.00 0.00 0.00 4.26
2016 5120 1.948834 CCTTGTGAACATGTGTCTGCA 59.051 47.619 0.00 1.31 0.00 4.41
2018 5122 2.330440 TGTGAACATGTGTCTGCAGT 57.670 45.000 14.67 0.00 0.00 4.40
2019 5123 1.941975 TGTGAACATGTGTCTGCAGTG 59.058 47.619 14.67 6.67 0.00 3.66
2020 5124 1.942657 GTGAACATGTGTCTGCAGTGT 59.057 47.619 14.67 7.38 0.00 3.55
2021 5125 2.355756 GTGAACATGTGTCTGCAGTGTT 59.644 45.455 16.85 16.85 37.35 3.32
2022 5126 2.355444 TGAACATGTGTCTGCAGTGTTG 59.645 45.455 20.54 12.04 35.85 3.33
2023 5127 2.042686 ACATGTGTCTGCAGTGTTGT 57.957 45.000 14.67 8.87 0.00 3.32
2024 5128 1.942657 ACATGTGTCTGCAGTGTTGTC 59.057 47.619 14.67 0.87 0.00 3.18
2025 5129 1.941975 CATGTGTCTGCAGTGTTGTCA 59.058 47.619 14.67 6.45 0.00 3.58
2026 5130 2.330440 TGTGTCTGCAGTGTTGTCAT 57.670 45.000 14.67 0.00 0.00 3.06
2027 5131 2.642427 TGTGTCTGCAGTGTTGTCATT 58.358 42.857 14.67 0.00 0.00 2.57
2028 5132 3.016031 TGTGTCTGCAGTGTTGTCATTT 58.984 40.909 14.67 0.00 0.00 2.32
2029 5133 3.443329 TGTGTCTGCAGTGTTGTCATTTT 59.557 39.130 14.67 0.00 0.00 1.82
2030 5134 4.637977 TGTGTCTGCAGTGTTGTCATTTTA 59.362 37.500 14.67 0.00 0.00 1.52
2031 5135 5.299028 TGTGTCTGCAGTGTTGTCATTTTAT 59.701 36.000 14.67 0.00 0.00 1.40
2032 5136 6.484977 TGTGTCTGCAGTGTTGTCATTTTATA 59.515 34.615 14.67 0.00 0.00 0.98
2033 5137 7.174772 TGTGTCTGCAGTGTTGTCATTTTATAT 59.825 33.333 14.67 0.00 0.00 0.86
2034 5138 7.693951 GTGTCTGCAGTGTTGTCATTTTATATC 59.306 37.037 14.67 0.00 0.00 1.63
2035 5139 7.607607 TGTCTGCAGTGTTGTCATTTTATATCT 59.392 33.333 14.67 0.00 0.00 1.98
2036 5140 8.454106 GTCTGCAGTGTTGTCATTTTATATCTT 58.546 33.333 14.67 0.00 0.00 2.40
2037 5141 8.668353 TCTGCAGTGTTGTCATTTTATATCTTC 58.332 33.333 14.67 0.00 0.00 2.87
2038 5142 8.565896 TGCAGTGTTGTCATTTTATATCTTCT 57.434 30.769 0.00 0.00 0.00 2.85
2039 5143 9.665719 TGCAGTGTTGTCATTTTATATCTTCTA 57.334 29.630 0.00 0.00 0.00 2.10
2070 5174 9.890629 TTGTAATCATAGATGCTAGAGTTTGTT 57.109 29.630 0.00 0.00 0.00 2.83
2087 5191 9.448438 AGAGTTTGTTACTATTGTATTGATGCA 57.552 29.630 0.00 0.00 37.17 3.96
2089 5193 9.840427 AGTTTGTTACTATTGTATTGATGCAAC 57.160 29.630 0.00 0.00 35.28 4.17
2090 5194 9.840427 GTTTGTTACTATTGTATTGATGCAACT 57.160 29.630 0.00 0.00 35.28 3.16
2108 5212 8.743085 ATGCAACTATGTATCATTTTGAGAGT 57.257 30.769 0.00 0.00 0.00 3.24
2109 5213 7.977904 TGCAACTATGTATCATTTTGAGAGTG 58.022 34.615 0.00 0.00 0.00 3.51
2110 5214 7.607607 TGCAACTATGTATCATTTTGAGAGTGT 59.392 33.333 0.00 0.00 0.00 3.55
2111 5215 9.098355 GCAACTATGTATCATTTTGAGAGTGTA 57.902 33.333 7.49 0.00 0.00 2.90
2134 5238 9.477484 TGTAGATTAGATTTTATTTCTCCGAGC 57.523 33.333 0.00 0.00 0.00 5.03
2135 5239 9.477484 GTAGATTAGATTTTATTTCTCCGAGCA 57.523 33.333 0.00 0.00 0.00 4.26
2136 5240 8.964476 AGATTAGATTTTATTTCTCCGAGCAA 57.036 30.769 0.00 0.00 0.00 3.91
2137 5241 9.050601 AGATTAGATTTTATTTCTCCGAGCAAG 57.949 33.333 0.00 0.00 0.00 4.01
2138 5242 7.553881 TTAGATTTTATTTCTCCGAGCAAGG 57.446 36.000 0.00 0.00 0.00 3.61
2139 5243 5.501156 AGATTTTATTTCTCCGAGCAAGGT 58.499 37.500 0.00 0.00 0.00 3.50
2140 5244 5.355350 AGATTTTATTTCTCCGAGCAAGGTG 59.645 40.000 0.00 0.00 0.00 4.00
2141 5245 3.973206 TTATTTCTCCGAGCAAGGTGA 57.027 42.857 0.00 0.00 32.58 4.02
2142 5246 2.100605 ATTTCTCCGAGCAAGGTGAC 57.899 50.000 2.35 0.00 34.00 3.67
2143 5247 0.756294 TTTCTCCGAGCAAGGTGACA 59.244 50.000 2.35 0.00 34.00 3.58
2144 5248 0.756294 TTCTCCGAGCAAGGTGACAA 59.244 50.000 2.35 0.00 34.00 3.18
2145 5249 0.976641 TCTCCGAGCAAGGTGACAAT 59.023 50.000 0.00 0.00 0.00 2.71
2146 5250 1.347707 TCTCCGAGCAAGGTGACAATT 59.652 47.619 0.00 0.00 0.00 2.32
2147 5251 2.154462 CTCCGAGCAAGGTGACAATTT 58.846 47.619 0.00 0.00 0.00 1.82
2148 5252 2.554032 CTCCGAGCAAGGTGACAATTTT 59.446 45.455 0.00 0.00 0.00 1.82
2149 5253 2.293122 TCCGAGCAAGGTGACAATTTTG 59.707 45.455 0.00 0.00 0.00 2.44
2150 5254 2.034558 CCGAGCAAGGTGACAATTTTGT 59.965 45.455 0.00 0.00 45.65 2.83
2151 5255 3.252215 CCGAGCAAGGTGACAATTTTGTA 59.748 43.478 0.00 0.00 42.43 2.41
2152 5256 4.082787 CCGAGCAAGGTGACAATTTTGTAT 60.083 41.667 0.00 0.00 42.43 2.29
2153 5257 4.853196 CGAGCAAGGTGACAATTTTGTATG 59.147 41.667 0.00 0.00 42.43 2.39
2154 5258 5.138125 AGCAAGGTGACAATTTTGTATGG 57.862 39.130 0.00 0.00 42.43 2.74
2155 5259 4.588528 AGCAAGGTGACAATTTTGTATGGT 59.411 37.500 0.00 0.00 42.43 3.55
2156 5260 5.772672 AGCAAGGTGACAATTTTGTATGGTA 59.227 36.000 0.00 0.00 42.43 3.25
2157 5261 6.437162 AGCAAGGTGACAATTTTGTATGGTAT 59.563 34.615 0.00 0.00 42.43 2.73
2158 5262 7.039082 AGCAAGGTGACAATTTTGTATGGTATT 60.039 33.333 0.00 0.00 42.43 1.89
2159 5263 7.602265 GCAAGGTGACAATTTTGTATGGTATTT 59.398 33.333 0.00 0.00 42.43 1.40
2160 5264 9.139174 CAAGGTGACAATTTTGTATGGTATTTC 57.861 33.333 0.00 0.00 42.43 2.17
2161 5265 7.535139 AGGTGACAATTTTGTATGGTATTTCG 58.465 34.615 0.00 0.00 42.43 3.46
2162 5266 7.392113 AGGTGACAATTTTGTATGGTATTTCGA 59.608 33.333 0.00 0.00 42.43 3.71
2163 5267 8.024285 GGTGACAATTTTGTATGGTATTTCGAA 58.976 33.333 0.00 0.00 42.43 3.71
2164 5268 9.400638 GTGACAATTTTGTATGGTATTTCGAAA 57.599 29.630 13.91 13.91 42.43 3.46
2165 5269 9.967346 TGACAATTTTGTATGGTATTTCGAAAA 57.033 25.926 15.66 0.00 42.43 2.29
2171 5275 9.967346 TTTTGTATGGTATTTCGAAAAATGTCA 57.033 25.926 15.66 9.49 35.84 3.58
2174 5278 9.566530 TGTATGGTATTTCGAAAAATGTCATTG 57.433 29.630 15.66 0.00 35.84 2.82
2175 5279 9.567848 GTATGGTATTTCGAAAAATGTCATTGT 57.432 29.630 15.66 0.00 35.84 2.71
2177 5281 8.514136 TGGTATTTCGAAAAATGTCATTGTTC 57.486 30.769 15.66 15.88 35.84 3.18
2178 5282 8.356657 TGGTATTTCGAAAAATGTCATTGTTCT 58.643 29.630 21.11 9.14 34.92 3.01
2179 5283 9.191995 GGTATTTCGAAAAATGTCATTGTTCTT 57.808 29.630 21.11 9.65 34.92 2.52
2182 5286 8.694975 TTTCGAAAAATGTCATTGTTCTTTCA 57.305 26.923 21.11 5.19 34.92 2.69
2183 5287 7.678194 TCGAAAAATGTCATTGTTCTTTCAC 57.322 32.000 21.11 1.14 34.92 3.18
2184 5288 6.695278 TCGAAAAATGTCATTGTTCTTTCACC 59.305 34.615 21.11 0.55 34.92 4.02
2185 5289 6.697019 CGAAAAATGTCATTGTTCTTTCACCT 59.303 34.615 21.11 0.00 34.92 4.00
2186 5290 7.222611 CGAAAAATGTCATTGTTCTTTCACCTT 59.777 33.333 21.11 0.00 34.92 3.50
2187 5291 7.775397 AAAATGTCATTGTTCTTTCACCTTG 57.225 32.000 0.00 0.00 0.00 3.61
2188 5292 6.469782 AATGTCATTGTTCTTTCACCTTGT 57.530 33.333 0.00 0.00 0.00 3.16
2189 5293 5.913137 TGTCATTGTTCTTTCACCTTGTT 57.087 34.783 0.00 0.00 0.00 2.83
2190 5294 5.649557 TGTCATTGTTCTTTCACCTTGTTG 58.350 37.500 0.00 0.00 0.00 3.33
2191 5295 5.417266 TGTCATTGTTCTTTCACCTTGTTGA 59.583 36.000 0.00 0.00 0.00 3.18
2192 5296 6.071672 TGTCATTGTTCTTTCACCTTGTTGAA 60.072 34.615 0.00 0.00 33.55 2.69
2193 5297 6.473455 GTCATTGTTCTTTCACCTTGTTGAAG 59.527 38.462 0.00 0.00 36.84 3.02
2207 5311 6.875926 CTTGTTGAAGGAAAAACACTTCTG 57.124 37.500 0.00 0.00 42.67 3.02
2208 5312 5.323371 TGTTGAAGGAAAAACACTTCTGG 57.677 39.130 0.00 0.00 42.67 3.86
2209 5313 4.770010 TGTTGAAGGAAAAACACTTCTGGT 59.230 37.500 0.00 0.00 42.67 4.00
2218 5322 3.040965 CACTTCTGGTGGCAATGGT 57.959 52.632 0.00 0.00 41.90 3.55
2219 5323 0.883833 CACTTCTGGTGGCAATGGTC 59.116 55.000 0.00 0.00 41.90 4.02
2220 5324 0.478072 ACTTCTGGTGGCAATGGTCA 59.522 50.000 0.00 0.00 0.00 4.02
2221 5325 1.133513 ACTTCTGGTGGCAATGGTCAA 60.134 47.619 0.00 0.00 0.00 3.18
2222 5326 1.542915 CTTCTGGTGGCAATGGTCAAG 59.457 52.381 0.00 0.00 0.00 3.02
2223 5327 0.770499 TCTGGTGGCAATGGTCAAGA 59.230 50.000 0.00 0.00 0.00 3.02
2224 5328 0.883833 CTGGTGGCAATGGTCAAGAC 59.116 55.000 0.00 0.00 0.00 3.01
2225 5329 0.888736 TGGTGGCAATGGTCAAGACG 60.889 55.000 0.00 0.00 0.00 4.18
2226 5330 0.605319 GGTGGCAATGGTCAAGACGA 60.605 55.000 0.00 0.00 0.00 4.20
2227 5331 0.798776 GTGGCAATGGTCAAGACGAG 59.201 55.000 0.00 0.00 0.00 4.18
2228 5332 0.321564 TGGCAATGGTCAAGACGAGG 60.322 55.000 0.00 0.00 0.00 4.63
2229 5333 1.648467 GGCAATGGTCAAGACGAGGC 61.648 60.000 0.00 4.02 0.00 4.70
2230 5334 0.674895 GCAATGGTCAAGACGAGGCT 60.675 55.000 0.00 0.00 0.00 4.58
2231 5335 1.405526 GCAATGGTCAAGACGAGGCTA 60.406 52.381 0.00 0.00 0.00 3.93
2232 5336 2.544685 CAATGGTCAAGACGAGGCTAG 58.455 52.381 0.00 0.00 0.00 3.42
2233 5337 2.145397 ATGGTCAAGACGAGGCTAGA 57.855 50.000 0.28 0.00 0.00 2.43
2234 5338 2.145397 TGGTCAAGACGAGGCTAGAT 57.855 50.000 0.28 0.00 0.00 1.98
2235 5339 2.025155 TGGTCAAGACGAGGCTAGATC 58.975 52.381 0.28 0.00 0.00 2.75
2236 5340 2.303175 GGTCAAGACGAGGCTAGATCT 58.697 52.381 0.28 0.00 0.00 2.75
2237 5341 2.034053 GGTCAAGACGAGGCTAGATCTG 59.966 54.545 5.18 0.00 0.00 2.90
2238 5342 1.678627 TCAAGACGAGGCTAGATCTGC 59.321 52.381 5.18 7.04 0.00 4.26
2239 5343 0.665835 AAGACGAGGCTAGATCTGCG 59.334 55.000 5.18 4.05 0.00 5.18
2240 5344 1.371145 GACGAGGCTAGATCTGCGC 60.371 63.158 5.18 0.00 0.00 6.09
2241 5345 2.049618 CGAGGCTAGATCTGCGCC 60.050 66.667 23.20 23.20 44.09 6.53
2244 5348 2.653702 GGCTAGATCTGCGCCGAT 59.346 61.111 14.58 14.58 33.64 4.18
2245 5349 1.735920 GGCTAGATCTGCGCCGATG 60.736 63.158 19.55 6.17 33.64 3.84
2246 5350 1.287191 GCTAGATCTGCGCCGATGA 59.713 57.895 19.55 5.99 0.00 2.92
2247 5351 0.108898 GCTAGATCTGCGCCGATGAT 60.109 55.000 19.55 10.26 0.00 2.45
2248 5352 1.626747 CTAGATCTGCGCCGATGATG 58.373 55.000 19.55 4.80 0.00 3.07
2249 5353 0.389037 TAGATCTGCGCCGATGATGC 60.389 55.000 19.55 4.64 0.00 3.91
2250 5354 1.957695 GATCTGCGCCGATGATGCA 60.958 57.895 19.55 0.00 37.07 3.96
2251 5355 1.501337 GATCTGCGCCGATGATGCAA 61.501 55.000 19.55 0.00 38.30 4.08
2252 5356 1.779025 ATCTGCGCCGATGATGCAAC 61.779 55.000 13.90 0.00 38.30 4.17
2253 5357 3.459378 CTGCGCCGATGATGCAACC 62.459 63.158 4.18 0.00 38.30 3.77
2254 5358 3.204827 GCGCCGATGATGCAACCT 61.205 61.111 0.00 0.00 0.00 3.50
2255 5359 2.711311 CGCCGATGATGCAACCTG 59.289 61.111 0.00 0.00 0.00 4.00
2256 5360 1.815003 CGCCGATGATGCAACCTGA 60.815 57.895 0.00 0.00 0.00 3.86
2257 5361 1.723870 GCCGATGATGCAACCTGAC 59.276 57.895 0.00 0.00 0.00 3.51
2258 5362 2.009108 CCGATGATGCAACCTGACG 58.991 57.895 0.00 0.00 0.00 4.35
2259 5363 1.349627 CGATGATGCAACCTGACGC 59.650 57.895 0.00 0.00 0.00 5.19
2260 5364 1.723870 GATGATGCAACCTGACGCC 59.276 57.895 0.00 0.00 0.00 5.68
2261 5365 1.718757 GATGATGCAACCTGACGCCC 61.719 60.000 0.00 0.00 0.00 6.13
2262 5366 2.045926 GATGCAACCTGACGCCCT 60.046 61.111 0.00 0.00 0.00 5.19
2263 5367 2.045926 ATGCAACCTGACGCCCTC 60.046 61.111 0.00 0.00 0.00 4.30
2264 5368 3.628646 ATGCAACCTGACGCCCTCC 62.629 63.158 0.00 0.00 0.00 4.30
2265 5369 4.329545 GCAACCTGACGCCCTCCA 62.330 66.667 0.00 0.00 0.00 3.86
2266 5370 2.429930 CAACCTGACGCCCTCCAA 59.570 61.111 0.00 0.00 0.00 3.53
2267 5371 1.672356 CAACCTGACGCCCTCCAAG 60.672 63.158 0.00 0.00 0.00 3.61
2268 5372 2.895424 AACCTGACGCCCTCCAAGG 61.895 63.158 0.00 0.00 34.30 3.61
2277 5381 3.255032 CCTCCAAGGGCTATGGGG 58.745 66.667 8.82 5.76 38.23 4.96
2278 5382 3.255032 CTCCAAGGGCTATGGGGG 58.745 66.667 8.82 0.00 38.54 5.40
2279 5383 3.103213 TCCAAGGGCTATGGGGGC 61.103 66.667 8.82 0.00 38.54 5.80
2292 5396 3.813724 GGGGCCACCAGCTAGCAT 61.814 66.667 18.83 0.00 43.05 3.79
2506 5610 2.120274 CCTGGCCCACCACCATTT 59.880 61.111 0.00 0.00 42.67 2.32
2518 5622 0.538516 CACCATTTGTCCCGGTTGGA 60.539 55.000 0.00 0.00 42.41 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 45 2.299867 ACAGATGGCCATGTTTGGAAAC 59.700 45.455 26.56 4.89 46.92 2.78
90 96 7.358770 AGCTAGTCTTATGATCATCTGTTGT 57.641 36.000 12.53 0.00 0.00 3.32
111 117 6.240118 CCTTAATTTGATGAGGATAGGGAGCT 60.240 42.308 0.00 0.00 0.00 4.09
269 316 9.784680 CAGCAGATTTTGATTATCCAATATAGC 57.215 33.333 0.00 0.00 0.00 2.97
310 361 3.619929 ACACAAACAACCGTGTCTTCTAC 59.380 43.478 0.00 0.00 42.61 2.59
311 362 3.864243 ACACAAACAACCGTGTCTTCTA 58.136 40.909 0.00 0.00 42.61 2.10
312 363 2.706890 ACACAAACAACCGTGTCTTCT 58.293 42.857 0.00 0.00 42.61 2.85
314 365 6.680874 TTTATACACAAACAACCGTGTCTT 57.319 33.333 0.00 0.00 44.93 3.01
315 366 6.680874 TTTTATACACAAACAACCGTGTCT 57.319 33.333 0.00 0.00 44.93 3.41
920 3922 2.607750 GGTCCAGTCCAGGCTCCA 60.608 66.667 0.00 0.00 0.00 3.86
921 3923 2.284995 AGGTCCAGTCCAGGCTCC 60.285 66.667 0.00 0.00 0.00 4.70
922 3924 2.363172 GGAGGTCCAGTCCAGGCTC 61.363 68.421 0.00 0.00 33.84 4.70
923 3925 2.284995 GGAGGTCCAGTCCAGGCT 60.285 66.667 0.00 0.00 33.84 4.58
924 3926 3.403558 GGGAGGTCCAGTCCAGGC 61.404 72.222 0.00 0.00 35.57 4.85
925 3927 1.687493 GAGGGAGGTCCAGTCCAGG 60.687 68.421 0.00 0.00 38.24 4.45
926 3928 1.079256 TGAGGGAGGTCCAGTCCAG 59.921 63.158 0.00 0.00 38.24 3.86
927 3929 1.229209 GTGAGGGAGGTCCAGTCCA 60.229 63.158 0.00 0.00 38.24 4.02
928 3930 2.352032 CGTGAGGGAGGTCCAGTCC 61.352 68.421 0.00 0.00 38.24 3.85
929 3931 1.186267 AACGTGAGGGAGGTCCAGTC 61.186 60.000 0.00 0.00 38.24 3.51
930 3932 1.152312 AACGTGAGGGAGGTCCAGT 60.152 57.895 0.00 0.00 38.24 4.00
931 3933 1.293498 CAACGTGAGGGAGGTCCAG 59.707 63.158 0.00 0.00 38.24 3.86
1034 4051 4.262506 GGGTACATAGACATACCTTGAGCC 60.263 50.000 0.00 0.00 40.71 4.70
1124 4151 8.651389 TCTACTACATTATGAAATGGAAGGGAG 58.349 37.037 0.00 3.33 45.72 4.30
1176 4203 8.766000 AACTCGGTCAAAATTTGTTTAGTTTT 57.234 26.923 5.56 0.00 0.00 2.43
1342 4384 9.250624 GTTCCATAATGTAGTGTGTAGAGATTC 57.749 37.037 0.00 0.00 0.00 2.52
1468 4548 8.297470 ACATTGATTGCACTATAAGAACCAAT 57.703 30.769 0.00 0.00 0.00 3.16
1472 4552 9.586150 CGATAACATTGATTGCACTATAAGAAC 57.414 33.333 0.00 0.00 0.00 3.01
1495 4576 3.522553 CTTAGCGGAAGAGGAAAACGAT 58.477 45.455 0.00 0.00 37.33 3.73
1516 4597 3.978718 AAGAAGAAGACAACAAGCAGC 57.021 42.857 0.00 0.00 0.00 5.25
1603 4700 7.669427 TCCTTGCAATGTTGAAGTATTTTGAT 58.331 30.769 0.00 0.00 0.00 2.57
1619 4716 2.123428 GCGATGGCCTCCTTGCAAT 61.123 57.895 3.32 0.00 0.00 3.56
1639 4736 4.016706 CCCTCCGGCGTTCTTGGT 62.017 66.667 6.01 0.00 0.00 3.67
1740 4838 1.233950 ACGCCGTTGATGCACATTGA 61.234 50.000 0.00 0.00 0.00 2.57
1757 4855 2.885644 CGCTCATCCCGTTCCACG 60.886 66.667 0.00 0.00 42.11 4.94
1769 4867 0.539669 TCCTCTTCCACTCACGCTCA 60.540 55.000 0.00 0.00 0.00 4.26
1773 4871 3.601443 AAAGATCCTCTTCCACTCACG 57.399 47.619 0.00 0.00 35.27 4.35
1801 4899 4.715534 TCTTGTAAGTCACCCAATCCAA 57.284 40.909 0.00 0.00 0.00 3.53
1808 4906 2.945668 GGCATGATCTTGTAAGTCACCC 59.054 50.000 10.05 0.00 0.00 4.61
1890 4990 9.998106 ACATATTGTGTCCATTAGTATAAGGTC 57.002 33.333 0.00 0.00 35.77 3.85
1917 5017 1.253545 CGTTTTAGGGATACGCGTTCG 59.746 52.381 20.78 3.62 42.43 3.95
1937 5037 1.945207 CATACCAACGAACGTGTTGC 58.055 50.000 12.08 0.00 46.14 4.17
1938 5038 1.399215 GGCATACCAACGAACGTGTTG 60.399 52.381 10.88 10.88 46.86 3.33
1957 5061 1.596260 CACACTAGATTCATGCGCAGG 59.404 52.381 17.42 17.42 0.00 4.85
1958 5062 1.596260 CCACACTAGATTCATGCGCAG 59.404 52.381 18.32 8.46 0.00 5.18
1971 5075 5.477607 ACATGCTTACTAACACCACACTA 57.522 39.130 0.00 0.00 0.00 2.74
1972 5076 4.351874 ACATGCTTACTAACACCACACT 57.648 40.909 0.00 0.00 0.00 3.55
1978 5082 6.425721 TCACAAGGTAACATGCTTACTAACAC 59.574 38.462 13.98 2.79 39.40 3.32
1984 5088 5.682943 TGTTCACAAGGTAACATGCTTAC 57.317 39.130 0.00 1.26 39.40 2.34
1991 5095 4.574421 CAGACACATGTTCACAAGGTAACA 59.426 41.667 0.00 0.00 39.73 2.41
1993 5097 3.563808 GCAGACACATGTTCACAAGGTAA 59.436 43.478 0.00 0.00 0.00 2.85
2002 5106 2.355756 ACAACACTGCAGACACATGTTC 59.644 45.455 23.35 0.00 31.25 3.18
2009 5113 7.607607 AGATATAAAATGACAACACTGCAGACA 59.392 33.333 23.35 10.33 0.00 3.41
2010 5114 7.978982 AGATATAAAATGACAACACTGCAGAC 58.021 34.615 23.35 4.93 0.00 3.51
2012 5116 8.671921 AGAAGATATAAAATGACAACACTGCAG 58.328 33.333 13.48 13.48 0.00 4.41
2044 5148 9.890629 AACAAACTCTAGCATCTATGATTACAA 57.109 29.630 0.00 0.00 0.00 2.41
2061 5165 9.448438 TGCATCAATACAATAGTAACAAACTCT 57.552 29.630 0.00 0.00 39.80 3.24
2063 5167 9.840427 GTTGCATCAATACAATAGTAACAAACT 57.160 29.630 0.00 0.00 42.62 2.66
2064 5168 9.840427 AGTTGCATCAATACAATAGTAACAAAC 57.160 29.630 0.00 0.00 33.13 2.93
2079 5183 9.961265 CTCAAAATGATACATAGTTGCATCAAT 57.039 29.630 0.00 0.00 38.73 2.57
2080 5184 9.176460 TCTCAAAATGATACATAGTTGCATCAA 57.824 29.630 0.00 0.00 38.73 2.57
2081 5185 8.735692 TCTCAAAATGATACATAGTTGCATCA 57.264 30.769 0.00 0.00 39.40 3.07
2082 5186 8.834465 ACTCTCAAAATGATACATAGTTGCATC 58.166 33.333 0.00 0.00 0.00 3.91
2083 5187 8.618677 CACTCTCAAAATGATACATAGTTGCAT 58.381 33.333 0.00 0.00 0.00 3.96
2084 5188 7.607607 ACACTCTCAAAATGATACATAGTTGCA 59.392 33.333 0.00 0.00 0.00 4.08
2085 5189 7.978982 ACACTCTCAAAATGATACATAGTTGC 58.021 34.615 0.00 0.00 0.00 4.17
2108 5212 9.477484 GCTCGGAGAAATAAAATCTAATCTACA 57.523 33.333 9.69 0.00 34.09 2.74
2109 5213 9.477484 TGCTCGGAGAAATAAAATCTAATCTAC 57.523 33.333 9.69 0.00 34.09 2.59
2111 5215 8.964476 TTGCTCGGAGAAATAAAATCTAATCT 57.036 30.769 9.69 0.00 34.09 2.40
2112 5216 8.286097 CCTTGCTCGGAGAAATAAAATCTAATC 58.714 37.037 9.69 0.00 34.09 1.75
2113 5217 7.775561 ACCTTGCTCGGAGAAATAAAATCTAAT 59.224 33.333 9.69 0.00 34.09 1.73
2114 5218 7.065803 CACCTTGCTCGGAGAAATAAAATCTAA 59.934 37.037 9.69 0.00 34.09 2.10
2115 5219 6.538742 CACCTTGCTCGGAGAAATAAAATCTA 59.461 38.462 9.69 0.00 34.09 1.98
2116 5220 5.355350 CACCTTGCTCGGAGAAATAAAATCT 59.645 40.000 9.69 0.00 34.09 2.40
2117 5221 5.354234 TCACCTTGCTCGGAGAAATAAAATC 59.646 40.000 9.69 0.00 34.09 2.17
2118 5222 5.123979 GTCACCTTGCTCGGAGAAATAAAAT 59.876 40.000 9.69 0.00 34.09 1.82
2119 5223 4.454504 GTCACCTTGCTCGGAGAAATAAAA 59.545 41.667 9.69 0.00 34.09 1.52
2120 5224 4.000988 GTCACCTTGCTCGGAGAAATAAA 58.999 43.478 9.69 0.00 34.09 1.40
2121 5225 3.007506 TGTCACCTTGCTCGGAGAAATAA 59.992 43.478 9.69 0.00 34.09 1.40
2122 5226 2.565391 TGTCACCTTGCTCGGAGAAATA 59.435 45.455 9.69 0.00 34.09 1.40
2123 5227 1.347707 TGTCACCTTGCTCGGAGAAAT 59.652 47.619 9.69 0.00 34.09 2.17
2124 5228 0.756294 TGTCACCTTGCTCGGAGAAA 59.244 50.000 9.69 3.26 34.09 2.52
2125 5229 0.756294 TTGTCACCTTGCTCGGAGAA 59.244 50.000 9.69 0.00 34.09 2.87
2126 5230 0.976641 ATTGTCACCTTGCTCGGAGA 59.023 50.000 9.69 0.00 0.00 3.71
2127 5231 1.813513 AATTGTCACCTTGCTCGGAG 58.186 50.000 0.00 0.00 0.00 4.63
2128 5232 2.270352 AAATTGTCACCTTGCTCGGA 57.730 45.000 0.00 0.00 0.00 4.55
2129 5233 2.034558 ACAAAATTGTCACCTTGCTCGG 59.965 45.455 0.00 0.00 36.50 4.63
2130 5234 3.354089 ACAAAATTGTCACCTTGCTCG 57.646 42.857 0.00 0.00 36.50 5.03
2131 5235 5.163513 CCATACAAAATTGTCACCTTGCTC 58.836 41.667 1.37 0.00 42.35 4.26
2132 5236 4.588528 ACCATACAAAATTGTCACCTTGCT 59.411 37.500 1.37 0.00 42.35 3.91
2133 5237 4.881920 ACCATACAAAATTGTCACCTTGC 58.118 39.130 1.37 0.00 42.35 4.01
2134 5238 9.139174 GAAATACCATACAAAATTGTCACCTTG 57.861 33.333 1.37 0.00 42.35 3.61
2135 5239 8.026607 CGAAATACCATACAAAATTGTCACCTT 58.973 33.333 1.37 0.00 42.35 3.50
2136 5240 7.392113 TCGAAATACCATACAAAATTGTCACCT 59.608 33.333 1.37 0.00 42.35 4.00
2137 5241 7.531716 TCGAAATACCATACAAAATTGTCACC 58.468 34.615 1.37 0.00 42.35 4.02
2138 5242 8.958175 TTCGAAATACCATACAAAATTGTCAC 57.042 30.769 1.37 0.00 42.35 3.67
2139 5243 9.967346 TTTTCGAAATACCATACAAAATTGTCA 57.033 25.926 12.12 0.00 42.35 3.58
2145 5249 9.967346 TGACATTTTTCGAAATACCATACAAAA 57.033 25.926 12.12 0.00 0.00 2.44
2148 5252 9.566530 CAATGACATTTTTCGAAATACCATACA 57.433 29.630 12.12 7.19 0.00 2.29
2149 5253 9.567848 ACAATGACATTTTTCGAAATACCATAC 57.432 29.630 12.12 1.90 0.00 2.39
2151 5255 9.139174 GAACAATGACATTTTTCGAAATACCAT 57.861 29.630 12.12 8.69 0.00 3.55
2152 5256 8.356657 AGAACAATGACATTTTTCGAAATACCA 58.643 29.630 12.12 6.85 34.89 3.25
2153 5257 8.742554 AGAACAATGACATTTTTCGAAATACC 57.257 30.769 12.12 1.48 34.89 2.73
2156 5260 9.311916 TGAAAGAACAATGACATTTTTCGAAAT 57.688 25.926 12.12 0.00 34.89 2.17
2157 5261 8.591312 GTGAAAGAACAATGACATTTTTCGAAA 58.409 29.630 17.25 6.47 34.89 3.46
2158 5262 7.221838 GGTGAAAGAACAATGACATTTTTCGAA 59.778 33.333 17.25 0.00 34.89 3.71
2159 5263 6.695278 GGTGAAAGAACAATGACATTTTTCGA 59.305 34.615 17.25 6.38 34.89 3.71
2160 5264 6.697019 AGGTGAAAGAACAATGACATTTTTCG 59.303 34.615 17.25 2.40 34.89 3.46
2161 5265 8.330302 CAAGGTGAAAGAACAATGACATTTTTC 58.670 33.333 16.08 16.08 30.96 2.29
2162 5266 7.823799 ACAAGGTGAAAGAACAATGACATTTTT 59.176 29.630 0.00 0.00 0.00 1.94
2163 5267 7.330262 ACAAGGTGAAAGAACAATGACATTTT 58.670 30.769 0.00 0.00 0.00 1.82
2164 5268 6.877236 ACAAGGTGAAAGAACAATGACATTT 58.123 32.000 0.00 0.00 0.00 2.32
2165 5269 6.469782 ACAAGGTGAAAGAACAATGACATT 57.530 33.333 0.00 0.00 0.00 2.71
2166 5270 6.096705 TCAACAAGGTGAAAGAACAATGACAT 59.903 34.615 0.00 0.00 0.00 3.06
2167 5271 5.417266 TCAACAAGGTGAAAGAACAATGACA 59.583 36.000 0.00 0.00 0.00 3.58
2168 5272 5.890334 TCAACAAGGTGAAAGAACAATGAC 58.110 37.500 0.00 0.00 0.00 3.06
2169 5273 6.405731 CCTTCAACAAGGTGAAAGAACAATGA 60.406 38.462 1.83 0.00 44.11 2.57
2170 5274 5.750067 CCTTCAACAAGGTGAAAGAACAATG 59.250 40.000 1.83 0.00 44.11 2.82
2171 5275 5.906073 CCTTCAACAAGGTGAAAGAACAAT 58.094 37.500 1.83 0.00 44.11 2.71
2172 5276 5.323371 CCTTCAACAAGGTGAAAGAACAA 57.677 39.130 1.83 0.00 44.11 2.83
2173 5277 4.981806 CCTTCAACAAGGTGAAAGAACA 57.018 40.909 1.83 0.00 44.11 3.18
2184 5288 5.807011 CCAGAAGTGTTTTTCCTTCAACAAG 59.193 40.000 0.00 0.00 39.61 3.16
2185 5289 5.245075 ACCAGAAGTGTTTTTCCTTCAACAA 59.755 36.000 0.00 0.00 39.61 2.83
2186 5290 4.770010 ACCAGAAGTGTTTTTCCTTCAACA 59.230 37.500 0.00 0.00 39.61 3.33
2187 5291 5.102313 CACCAGAAGTGTTTTTCCTTCAAC 58.898 41.667 0.00 0.00 41.93 3.18
2188 5292 4.159506 CCACCAGAAGTGTTTTTCCTTCAA 59.840 41.667 0.00 0.00 45.74 2.69
2189 5293 3.699038 CCACCAGAAGTGTTTTTCCTTCA 59.301 43.478 0.00 0.00 45.74 3.02
2190 5294 3.490933 GCCACCAGAAGTGTTTTTCCTTC 60.491 47.826 0.00 0.00 45.74 3.46
2191 5295 2.430694 GCCACCAGAAGTGTTTTTCCTT 59.569 45.455 0.00 0.00 45.74 3.36
2192 5296 2.031870 GCCACCAGAAGTGTTTTTCCT 58.968 47.619 0.00 0.00 45.74 3.36
2193 5297 1.754226 TGCCACCAGAAGTGTTTTTCC 59.246 47.619 0.00 0.00 45.74 3.13
2194 5298 3.518634 TTGCCACCAGAAGTGTTTTTC 57.481 42.857 0.00 0.00 45.74 2.29
2195 5299 3.432046 CCATTGCCACCAGAAGTGTTTTT 60.432 43.478 0.00 0.00 45.74 1.94
2196 5300 2.102925 CCATTGCCACCAGAAGTGTTTT 59.897 45.455 0.00 0.00 45.74 2.43
2197 5301 1.688197 CCATTGCCACCAGAAGTGTTT 59.312 47.619 0.00 0.00 45.74 2.83
2198 5302 1.331214 CCATTGCCACCAGAAGTGTT 58.669 50.000 0.00 0.00 45.74 3.32
2199 5303 0.185901 ACCATTGCCACCAGAAGTGT 59.814 50.000 0.00 0.00 45.74 3.55
2200 5304 0.883833 GACCATTGCCACCAGAAGTG 59.116 55.000 0.00 0.00 46.83 3.16
2201 5305 0.478072 TGACCATTGCCACCAGAAGT 59.522 50.000 0.00 0.00 0.00 3.01
2202 5306 1.542915 CTTGACCATTGCCACCAGAAG 59.457 52.381 0.00 0.00 0.00 2.85
2203 5307 1.144708 TCTTGACCATTGCCACCAGAA 59.855 47.619 0.00 0.00 0.00 3.02
2204 5308 0.770499 TCTTGACCATTGCCACCAGA 59.230 50.000 0.00 0.00 0.00 3.86
2205 5309 0.883833 GTCTTGACCATTGCCACCAG 59.116 55.000 0.00 0.00 0.00 4.00
2206 5310 0.888736 CGTCTTGACCATTGCCACCA 60.889 55.000 0.00 0.00 0.00 4.17
2207 5311 0.605319 TCGTCTTGACCATTGCCACC 60.605 55.000 0.00 0.00 0.00 4.61
2208 5312 0.798776 CTCGTCTTGACCATTGCCAC 59.201 55.000 0.00 0.00 0.00 5.01
2209 5313 0.321564 CCTCGTCTTGACCATTGCCA 60.322 55.000 0.00 0.00 0.00 4.92
2210 5314 1.648467 GCCTCGTCTTGACCATTGCC 61.648 60.000 0.00 0.00 0.00 4.52
2211 5315 0.674895 AGCCTCGTCTTGACCATTGC 60.675 55.000 0.00 0.00 0.00 3.56
2212 5316 2.166459 TCTAGCCTCGTCTTGACCATTG 59.834 50.000 0.00 0.00 0.00 2.82
2213 5317 2.457598 TCTAGCCTCGTCTTGACCATT 58.542 47.619 0.00 0.00 0.00 3.16
2214 5318 2.145397 TCTAGCCTCGTCTTGACCAT 57.855 50.000 0.00 0.00 0.00 3.55
2215 5319 2.025155 GATCTAGCCTCGTCTTGACCA 58.975 52.381 0.00 0.00 0.00 4.02
2216 5320 2.034053 CAGATCTAGCCTCGTCTTGACC 59.966 54.545 0.00 0.00 0.00 4.02
2217 5321 2.542824 GCAGATCTAGCCTCGTCTTGAC 60.543 54.545 0.00 0.00 0.00 3.18
2218 5322 1.678627 GCAGATCTAGCCTCGTCTTGA 59.321 52.381 0.00 0.00 0.00 3.02
2219 5323 1.599171 CGCAGATCTAGCCTCGTCTTG 60.599 57.143 0.00 0.00 0.00 3.02
2220 5324 0.665835 CGCAGATCTAGCCTCGTCTT 59.334 55.000 0.00 0.00 0.00 3.01
2221 5325 1.791103 GCGCAGATCTAGCCTCGTCT 61.791 60.000 0.30 0.00 0.00 4.18
2222 5326 1.371145 GCGCAGATCTAGCCTCGTC 60.371 63.158 0.30 0.00 0.00 4.20
2223 5327 2.725008 GCGCAGATCTAGCCTCGT 59.275 61.111 0.30 0.00 0.00 4.18
2224 5328 2.049618 GGCGCAGATCTAGCCTCG 60.050 66.667 25.73 12.79 46.83 4.63
2227 5331 1.735920 CATCGGCGCAGATCTAGCC 60.736 63.158 20.49 24.09 46.88 3.93
2228 5332 0.108898 ATCATCGGCGCAGATCTAGC 60.109 55.000 20.49 12.46 0.00 3.42
2229 5333 1.626747 CATCATCGGCGCAGATCTAG 58.373 55.000 20.49 9.86 0.00 2.43
2230 5334 0.389037 GCATCATCGGCGCAGATCTA 60.389 55.000 20.49 11.90 0.00 1.98
2231 5335 1.667191 GCATCATCGGCGCAGATCT 60.667 57.895 20.49 8.12 0.00 2.75
2232 5336 1.501337 TTGCATCATCGGCGCAGATC 61.501 55.000 20.49 9.81 36.91 2.75
2233 5337 1.524393 TTGCATCATCGGCGCAGAT 60.524 52.632 17.67 17.67 36.91 2.90
2234 5338 2.125188 TTGCATCATCGGCGCAGA 60.125 55.556 13.82 13.82 36.91 4.26
2235 5339 2.023741 GTTGCATCATCGGCGCAG 59.976 61.111 10.83 5.07 36.91 5.18
2236 5340 3.507924 GGTTGCATCATCGGCGCA 61.508 61.111 10.83 0.00 0.00 6.09
2237 5341 3.204827 AGGTTGCATCATCGGCGC 61.205 61.111 0.00 0.00 0.00 6.53
2238 5342 1.815003 TCAGGTTGCATCATCGGCG 60.815 57.895 0.00 0.00 0.00 6.46
2239 5343 1.723870 GTCAGGTTGCATCATCGGC 59.276 57.895 0.00 0.00 0.00 5.54
2240 5344 2.009108 CGTCAGGTTGCATCATCGG 58.991 57.895 0.00 0.00 0.00 4.18
2241 5345 1.349627 GCGTCAGGTTGCATCATCG 59.650 57.895 0.00 0.00 0.00 3.84
2242 5346 1.718757 GGGCGTCAGGTTGCATCATC 61.719 60.000 0.00 0.00 0.00 2.92
2243 5347 1.750399 GGGCGTCAGGTTGCATCAT 60.750 57.895 0.00 0.00 0.00 2.45
2244 5348 2.359850 GGGCGTCAGGTTGCATCA 60.360 61.111 0.00 0.00 0.00 3.07
2245 5349 2.045926 AGGGCGTCAGGTTGCATC 60.046 61.111 0.00 0.00 0.00 3.91
2246 5350 2.045926 GAGGGCGTCAGGTTGCAT 60.046 61.111 1.64 0.00 0.00 3.96
2247 5351 4.329545 GGAGGGCGTCAGGTTGCA 62.330 66.667 9.66 0.00 0.00 4.08
2248 5352 3.842925 TTGGAGGGCGTCAGGTTGC 62.843 63.158 9.66 0.00 0.00 4.17
2249 5353 1.672356 CTTGGAGGGCGTCAGGTTG 60.672 63.158 9.66 0.00 0.00 3.77
2250 5354 2.750350 CTTGGAGGGCGTCAGGTT 59.250 61.111 9.66 0.00 0.00 3.50
2251 5355 3.322466 CCTTGGAGGGCGTCAGGT 61.322 66.667 9.66 0.00 0.00 4.00
2260 5364 2.464403 CCCCCATAGCCCTTGGAGG 61.464 68.421 0.00 0.00 36.26 4.30
2261 5365 3.138728 GCCCCCATAGCCCTTGGAG 62.139 68.421 0.00 0.00 36.26 3.86
2262 5366 3.103213 GCCCCCATAGCCCTTGGA 61.103 66.667 0.00 0.00 36.26 3.53
2263 5367 4.224609 GGCCCCCATAGCCCTTGG 62.225 72.222 0.00 0.00 45.16 3.61
2269 5373 4.902645 GCTGGTGGCCCCCATAGC 62.903 72.222 7.67 4.85 38.60 2.97
2270 5374 1.770110 TAGCTGGTGGCCCCCATAG 60.770 63.158 7.67 0.00 43.05 2.23
2271 5375 1.770110 CTAGCTGGTGGCCCCCATA 60.770 63.158 7.67 0.00 43.05 2.74
2272 5376 3.099170 CTAGCTGGTGGCCCCCAT 61.099 66.667 7.67 0.00 43.05 4.00
2275 5379 1.994885 TAATGCTAGCTGGTGGCCCC 61.995 60.000 17.23 0.85 43.05 5.80
2276 5380 0.536006 CTAATGCTAGCTGGTGGCCC 60.536 60.000 17.23 0.00 43.05 5.80
2277 5381 0.181350 ACTAATGCTAGCTGGTGGCC 59.819 55.000 17.23 0.00 43.05 5.36
2278 5382 2.365617 TCTACTAATGCTAGCTGGTGGC 59.634 50.000 17.23 8.34 42.19 5.01
2279 5383 4.672587 TTCTACTAATGCTAGCTGGTGG 57.327 45.455 17.23 6.88 0.00 4.61
2280 5384 6.036517 CAGTTTTCTACTAATGCTAGCTGGTG 59.963 42.308 17.23 6.55 34.56 4.17
2281 5385 6.109359 CAGTTTTCTACTAATGCTAGCTGGT 58.891 40.000 17.23 7.25 34.56 4.00
2292 5396 5.056553 ACCAAAGCCCAGTTTTCTACTAA 57.943 39.130 0.00 0.00 34.56 2.24
2429 5533 3.246880 AAAGGGGCCGGACGAACT 61.247 61.111 5.05 0.00 0.00 3.01
2506 5610 2.852075 AAGCCTCCAACCGGGACA 60.852 61.111 6.32 0.00 42.15 4.02
2518 5622 2.852075 TGGTCCCGGTTCAAGCCT 60.852 61.111 0.00 0.00 0.00 4.58
2633 5737 2.613691 CTTATAAACCGGTGTGAGCGT 58.386 47.619 8.52 0.00 37.40 5.07


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

AutoCloner maintained by Alex Coulton.