Multiple sequence alignment - TraesCS2B01G236000

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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 TraesCS2B01G236000 chr2B 100.000 4600 0 0 1 4600 236170350 236165751 0.000000e+00 8495.0
1 TraesCS2B01G236000 chr2A 92.510 1976 107 19 1 1942 193878904 193876936 0.000000e+00 2791.0
2 TraesCS2B01G236000 chr2A 92.275 932 38 8 2403 3316 193876467 193875552 0.000000e+00 1291.0
3 TraesCS2B01G236000 chr2A 90.203 541 27 12 3313 3849 193875586 193875068 0.000000e+00 682.0
4 TraesCS2B01G236000 chr2A 81.688 628 78 26 3996 4600 193874876 193874263 5.350000e-134 488.0
5 TraesCS2B01G236000 chr2A 93.831 308 16 2 2101 2406 193876854 193876548 1.170000e-125 460.0
6 TraesCS2B01G236000 chr2D 87.500 720 50 5 2209 2895 179353768 179353056 0.000000e+00 795.0
7 TraesCS2B01G236000 chr2D 86.408 721 68 17 641 1344 179355477 179354770 0.000000e+00 761.0
8 TraesCS2B01G236000 chr2D 90.641 577 31 13 3313 3880 179352740 179352178 0.000000e+00 745.0
9 TraesCS2B01G236000 chr2D 84.640 625 51 23 1603 2213 179354471 179353878 8.580000e-162 580.0
10 TraesCS2B01G236000 chr2D 82.985 335 37 10 2984 3318 179353015 179352701 7.530000e-73 285.0
11 TraesCS2B01G236000 chr2D 83.390 295 22 14 3996 4285 179334933 179334661 9.880000e-62 248.0
12 TraesCS2B01G236000 chr7D 77.702 583 98 25 4019 4589 185689006 185689568 1.230000e-85 327.0
13 TraesCS2B01G236000 chr7D 79.798 297 39 15 2605 2897 5379367 5379088 3.630000e-46 196.0
14 TraesCS2B01G236000 chr7D 90.769 65 6 0 1000 1064 5308750 5308814 2.280000e-13 87.9
15 TraesCS2B01G236000 chr7D 92.593 54 4 0 1008 1061 5381137 5381084 1.370000e-10 78.7
16 TraesCS2B01G236000 chr7D 73.869 199 42 9 4400 4595 104641569 104641760 2.300000e-08 71.3
17 TraesCS2B01G236000 chr7A 80.645 310 41 14 2593 2893 6597638 6597937 5.990000e-54 222.0
18 TraesCS2B01G236000 chr7A 92.593 54 4 0 1008 1061 6848516 6848463 1.370000e-10 78.7
19 TraesCS2B01G236000 chr7A 95.349 43 1 1 4523 4565 166990811 166990770 2.970000e-07 67.6
20 TraesCS2B01G236000 chr4A 81.315 289 38 12 2605 2893 737096787 737097059 2.150000e-53 220.0
21 TraesCS2B01G236000 chr4A 92.593 54 4 0 1008 1061 737094890 737094943 1.370000e-10 78.7
22 TraesCS2B01G236000 chr4D 81.013 158 20 7 4407 4563 495910768 495910916 2.910000e-22 117.0
23 TraesCS2B01G236000 chr3D 84.211 76 11 1 4288 4363 533682395 533682321 6.380000e-09 73.1
24 TraesCS2B01G236000 chr1B 82.716 81 11 2 4465 4544 666820894 666820972 8.260000e-08 69.4
25 TraesCS2B01G236000 chr5B 83.562 73 8 4 4496 4565 66989449 66989520 1.070000e-06 65.8
26 TraesCS2B01G236000 chr5B 83.562 73 8 4 4496 4565 66990186 66990257 1.070000e-06 65.8
27 TraesCS2B01G236000 chr5B 83.562 73 8 4 4496 4565 66992016 66992087 1.070000e-06 65.8
28 TraesCS2B01G236000 chr5A 89.362 47 4 1 4196 4241 378707195 378707149 1.790000e-04 58.4
29 TraesCS2B01G236000 chr6B 96.970 33 0 1 1031 1062 620909321 620909289 2.000000e-03 54.7


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 TraesCS2B01G236000 chr2B 236165751 236170350 4599 True 8495.0 8495 100.0000 1 4600 1 chr2B.!!$R1 4599
1 TraesCS2B01G236000 chr2A 193874263 193878904 4641 True 1142.4 2791 90.1014 1 4600 5 chr2A.!!$R1 4599
2 TraesCS2B01G236000 chr2D 179352178 179355477 3299 True 633.2 795 86.4348 641 3880 5 chr2D.!!$R2 3239
3 TraesCS2B01G236000 chr7D 185689006 185689568 562 False 327.0 327 77.7020 4019 4589 1 chr7D.!!$F3 570

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
566 572 0.316204 GTTTGGCAGCAGCTCAACAT 59.684 50.0 0.00 0.0 41.70 2.71 F
1755 1902 0.615331 GATCCTTCCTGCAGACACCA 59.385 55.0 17.39 0.0 0.00 4.17 F
3237 3640 0.179089 GCGGCATCAGAGACATGAGT 60.179 55.0 0.00 0.0 31.44 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2171 1.379044 CATGGCAGGGAGTTCCACC 60.379 63.158 0.00 0.0 38.24 4.61 R
3423 3826 0.677731 GCTGATACAAGCCTGTGCCA 60.678 55.000 0.00 0.0 37.20 4.92 R
4049 4538 2.610479 CGCTGAAGGACTTTAGTCTGCA 60.610 50.000 9.56 5.2 44.20 4.41 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
31 35 2.856089 TTTTTGTACGTTTGGCGCG 58.144 47.368 0.00 0.00 46.11 6.86
34 38 0.933097 TTTGTACGTTTGGCGCGTTA 59.067 45.000 8.43 0.00 46.11 3.18
48 52 2.530700 GCGCGTTAGATGTAGTTCTGTC 59.469 50.000 8.43 0.00 0.00 3.51
52 56 4.096311 CGTTAGATGTAGTTCTGTCCACG 58.904 47.826 0.00 0.00 0.00 4.94
53 57 4.421948 GTTAGATGTAGTTCTGTCCACGG 58.578 47.826 0.00 0.00 0.00 4.94
107 111 6.069088 TGGGTGGTAGGTATTCTGAATTGATT 60.069 38.462 8.38 0.00 0.00 2.57
123 127 7.199766 TGAATTGATTAAACGGATTGGTATGC 58.800 34.615 0.00 0.00 0.00 3.14
149 153 9.575783 CTAGTTCAATACTCTTGTAGAAGGAAC 57.424 37.037 0.00 4.76 38.33 3.62
216 220 9.856488 ATATTTCATGAATGCTATTCATCTTGC 57.144 29.630 9.40 0.00 37.06 4.01
237 241 2.095110 CGACATGCTCTTCAATTTGGCA 60.095 45.455 0.00 0.00 37.32 4.92
238 242 3.428452 CGACATGCTCTTCAATTTGGCAT 60.428 43.478 5.38 5.38 43.19 4.40
247 251 6.349280 GCTCTTCAATTTGGCATACTGTTGTA 60.349 38.462 0.00 0.00 0.00 2.41
343 349 4.511454 TCTTCCATTGAAAGTTGTGACTCG 59.489 41.667 0.00 0.00 34.21 4.18
366 372 6.239092 TCGGTGTACGGTATGAACATTCATAT 60.239 38.462 15.53 4.96 44.80 1.78
419 425 4.887748 AGAGGCAATTCTACATGATACCG 58.112 43.478 0.00 0.00 0.00 4.02
472 478 4.620723 TCCTAGCTCAAGGAATGTAAGGA 58.379 43.478 2.51 0.00 42.83 3.36
479 485 6.376581 AGCTCAAGGAATGTAAGGAGAATTTG 59.623 38.462 0.00 0.00 0.00 2.32
481 487 5.123820 TCAAGGAATGTAAGGAGAATTTGCG 59.876 40.000 0.00 0.00 0.00 4.85
493 499 4.261614 GGAGAATTTGCGTTGTTTCTTCCT 60.262 41.667 0.00 0.00 0.00 3.36
503 509 8.568732 TGCGTTGTTTCTTCCTAATTTAAAAG 57.431 30.769 0.00 0.00 0.00 2.27
505 511 7.168469 GCGTTGTTTCTTCCTAATTTAAAAGCA 59.832 33.333 0.00 0.00 0.00 3.91
515 521 9.528018 TTCCTAATTTAAAAGCAAACTTGACAG 57.472 29.630 0.00 0.00 35.85 3.51
535 541 6.072064 TGACAGACTAACAGTTCCTAAGCTAC 60.072 42.308 0.00 0.00 0.00 3.58
553 559 3.493524 GCTACCTCCATCTCTAGTTTGGC 60.494 52.174 0.00 0.00 0.00 4.52
566 572 0.316204 GTTTGGCAGCAGCTCAACAT 59.684 50.000 0.00 0.00 41.70 2.71
568 574 2.133281 TTGGCAGCAGCTCAACATAT 57.867 45.000 0.00 0.00 41.70 1.78
607 613 6.414987 GCCAAATGCGTCTCTATGTTTATTTC 59.585 38.462 0.00 0.00 0.00 2.17
608 614 6.912591 CCAAATGCGTCTCTATGTTTATTTCC 59.087 38.462 0.00 0.00 0.00 3.13
632 638 1.315257 CGGAGGCAAATGGACCCTTG 61.315 60.000 0.00 0.00 0.00 3.61
651 657 4.498682 CCTTGCATAGCCTATCAAGTTTGC 60.499 45.833 16.08 4.50 35.42 3.68
659 665 4.511826 AGCCTATCAAGTTTGCGTTATAGC 59.488 41.667 0.00 0.00 37.71 2.97
663 669 4.413495 TCAAGTTTGCGTTATAGCCAAC 57.587 40.909 0.00 0.00 41.37 3.77
679 685 3.135414 CCAACGGCACAAATCACTATG 57.865 47.619 0.00 0.00 0.00 2.23
689 695 7.547227 GGCACAAATCACTATGATAAGGTTTT 58.453 34.615 0.00 0.00 35.76 2.43
881 895 7.044798 AGGCATATTCTGACTGAGTTTTACTC 58.955 38.462 0.00 0.00 43.63 2.59
896 910 9.290988 TGAGTTTTACTCTTGTATTATGCCAAA 57.709 29.630 8.18 0.00 45.27 3.28
970 991 2.093658 AGTGAGTGAAACAAGGTCGTGT 60.094 45.455 0.00 0.00 41.43 4.49
1067 1090 5.889289 GCCCCAAAACCAGTTAGTGATATTA 59.111 40.000 0.00 0.00 0.00 0.98
1068 1091 6.549736 GCCCCAAAACCAGTTAGTGATATTAT 59.450 38.462 0.00 0.00 0.00 1.28
1069 1092 7.722285 GCCCCAAAACCAGTTAGTGATATTATA 59.278 37.037 0.00 0.00 0.00 0.98
1121 1150 4.629200 TCTGTTTTGTTTGTCAATTGCCAC 59.371 37.500 0.00 0.00 35.84 5.01
1194 1223 4.277672 GGACATCAAGATAGCATGCACATT 59.722 41.667 21.98 6.05 0.00 2.71
1245 1274 3.745480 GCATTGCTTAGGAGTGATAGCCA 60.745 47.826 0.16 0.00 32.73 4.75
1258 1287 4.080356 AGTGATAGCCAATTGCCAGACTAA 60.080 41.667 0.00 0.00 42.71 2.24
1281 1310 6.882768 AAGAATTTAGGAGGAGAGTGATGT 57.117 37.500 0.00 0.00 0.00 3.06
1314 1344 8.909708 TCTTTGTTCAGTTCAAAACAGTAATG 57.090 30.769 0.00 0.00 36.78 1.90
1332 1366 1.616159 TGGAAAAGTAGCAACCAGGC 58.384 50.000 0.00 0.00 0.00 4.85
1353 1387 0.674895 GCCAGCTTTGTCGACCAGAT 60.675 55.000 14.12 4.85 0.00 2.90
1361 1395 1.946984 TGTCGACCAGATACCCCTTT 58.053 50.000 14.12 0.00 0.00 3.11
1367 1401 3.371595 CGACCAGATACCCCTTTTGGAAT 60.372 47.826 0.00 0.00 44.07 3.01
1414 1448 2.223377 CAGTTGTCCTAAGAACGGTTGC 59.777 50.000 0.00 0.00 34.00 4.17
1440 1482 3.565307 TCTGGTTCTGAATTGGTTGCTT 58.435 40.909 0.00 0.00 0.00 3.91
1487 1529 1.798223 CCTGTCGATGAGCGTTTTGAA 59.202 47.619 0.00 0.00 41.80 2.69
1492 1534 5.277825 TGTCGATGAGCGTTTTGAATTTTT 58.722 33.333 0.00 0.00 41.80 1.94
1573 1615 3.084039 TGACATCCCTTGAATGCAGAAC 58.916 45.455 0.00 0.00 0.00 3.01
1617 1754 3.397618 TCATTAAATGGGACCGGGATGAT 59.602 43.478 6.32 0.00 0.00 2.45
1645 1785 9.793259 ACTTCCTTGTATTGAAAAATGACTAGA 57.207 29.630 0.00 0.00 0.00 2.43
1675 1822 4.881019 AGTCAGCGAGAATAATAGCCAT 57.119 40.909 0.00 0.00 0.00 4.40
1706 1853 7.648142 TGACATCACAGATAAAACCTGAAAAC 58.352 34.615 0.00 0.00 35.69 2.43
1755 1902 0.615331 GATCCTTCCTGCAGACACCA 59.385 55.000 17.39 0.00 0.00 4.17
1832 1979 4.658901 AGTTTCACCTTCTCCTTACCTTCA 59.341 41.667 0.00 0.00 0.00 3.02
1870 2022 3.255642 ACATTGCTGCGTGGAAGTAAAAT 59.744 39.130 9.22 0.00 0.00 1.82
1872 2024 5.125417 ACATTGCTGCGTGGAAGTAAAATAT 59.875 36.000 9.22 0.00 0.00 1.28
1915 2069 6.410540 AGTTAGCCAAGAACTTATTCCTCAG 58.589 40.000 0.00 0.00 33.25 3.35
1963 2117 5.913946 AGTGGCTAGGGCTAGATATTTTT 57.086 39.130 0.00 0.00 38.73 1.94
1964 2118 8.540388 CATAGTGGCTAGGGCTAGATATTTTTA 58.460 37.037 0.00 0.00 38.73 1.52
1965 2119 7.010339 AGTGGCTAGGGCTAGATATTTTTAG 57.990 40.000 0.00 0.00 38.73 1.85
1966 2120 5.644206 GTGGCTAGGGCTAGATATTTTTAGC 59.356 44.000 0.00 0.00 41.16 3.09
1968 2122 6.183361 TGGCTAGGGCTAGATATTTTTAGCAA 60.183 38.462 7.77 0.00 43.14 3.91
1969 2123 6.372937 GGCTAGGGCTAGATATTTTTAGCAAG 59.627 42.308 7.77 3.89 43.14 4.01
1970 2124 6.372937 GCTAGGGCTAGATATTTTTAGCAAGG 59.627 42.308 7.77 0.00 43.14 3.61
1971 2125 6.267492 AGGGCTAGATATTTTTAGCAAGGT 57.733 37.500 7.77 0.00 43.14 3.50
1977 2131 9.454859 GCTAGATATTTTTAGCAAGGTCCATAT 57.545 33.333 0.00 0.00 41.45 1.78
2010 2164 1.388547 TGTCCCTCACAAAGTGCAAC 58.611 50.000 0.00 0.00 32.98 4.17
2017 2171 0.670162 CACAAAGTGCAACAGGGAGG 59.330 55.000 0.00 0.00 41.43 4.30
2037 2191 0.251341 GTGGAACTCCCTGCCATGTT 60.251 55.000 0.00 0.00 33.66 2.71
2044 2198 0.550914 TCCCTGCCATGTTCCATACC 59.449 55.000 0.00 0.00 0.00 2.73
2045 2199 0.258484 CCCTGCCATGTTCCATACCA 59.742 55.000 0.00 0.00 0.00 3.25
2136 2290 4.288626 TCCTTTAGCTAACCATGGAACTGT 59.711 41.667 21.47 2.14 0.00 3.55
2143 2297 6.010219 AGCTAACCATGGAACTGTAATGTTT 58.990 36.000 21.47 0.00 0.00 2.83
2192 2346 7.935338 TTCATTTGCTCTTGTTTCTGAATTC 57.065 32.000 0.00 0.00 0.00 2.17
2216 2484 4.324022 CCCCCTGGTAAACTTGTACTAAGG 60.324 50.000 9.05 0.00 32.22 2.69
2307 2583 2.376518 TCTCAAGCCCCAAAGAGACAAT 59.623 45.455 0.00 0.00 32.57 2.71
2308 2584 3.160269 CTCAAGCCCCAAAGAGACAATT 58.840 45.455 0.00 0.00 0.00 2.32
2314 2590 3.573967 GCCCCAAAGAGACAATTTCTTCA 59.426 43.478 0.00 0.00 33.92 3.02
2387 2688 6.940739 AGCTACATTCTTGGCTATTCGATAT 58.059 36.000 0.00 0.00 32.94 1.63
2396 2697 9.607988 TTCTTGGCTATTCGATATTGAACTTAA 57.392 29.630 7.58 0.06 0.00 1.85
2441 2826 5.761234 TGGTAAATGTGTTCTTGGTCAGTAC 59.239 40.000 0.00 0.00 0.00 2.73
2459 2844 4.393062 CAGTACTGTGAATCATGGACCAAC 59.607 45.833 15.06 0.00 0.00 3.77
2750 3135 4.247267 CAATTCTGCACTTGTGTTCCAT 57.753 40.909 2.61 0.00 0.00 3.41
2755 3140 4.203226 TCTGCACTTGTGTTCCATACAAA 58.797 39.130 2.61 0.00 38.80 2.83
2756 3141 4.826733 TCTGCACTTGTGTTCCATACAAAT 59.173 37.500 2.61 0.00 38.80 2.32
2895 3280 2.290641 CCGGTAAGCCATTGATACTTGC 59.709 50.000 0.00 0.00 34.09 4.01
2896 3281 3.206150 CGGTAAGCCATTGATACTTGCT 58.794 45.455 0.00 0.00 34.09 3.91
2897 3282 3.627577 CGGTAAGCCATTGATACTTGCTT 59.372 43.478 0.00 0.00 43.97 3.91
2898 3283 4.496341 CGGTAAGCCATTGATACTTGCTTG 60.496 45.833 5.38 0.00 41.92 4.01
2952 3337 4.130118 GCACTAAGGAGGTGTGGATTATG 58.870 47.826 0.00 0.00 37.07 1.90
2954 3339 5.360591 CACTAAGGAGGTGTGGATTATGTC 58.639 45.833 0.00 0.00 0.00 3.06
3095 3498 2.821991 AATATTCCGGAGCCTTCTCG 57.178 50.000 3.34 0.00 40.26 4.04
3200 3603 8.911918 TTCTTATTTACCTTGTGCTGAAAGTA 57.088 30.769 0.00 0.00 35.30 2.24
3236 3639 0.879400 GGCGGCATCAGAGACATGAG 60.879 60.000 3.07 0.00 31.44 2.90
3237 3640 0.179089 GCGGCATCAGAGACATGAGT 60.179 55.000 0.00 0.00 31.44 3.41
3255 3658 8.891671 ACATGAGTTCTTTATTTTGCATGTTT 57.108 26.923 0.00 0.00 41.38 2.83
3297 3700 4.766891 CCCATTGTTCTTATTCTGTGGTGT 59.233 41.667 0.00 0.00 0.00 4.16
3299 3702 6.381801 CCATTGTTCTTATTCTGTGGTGTTC 58.618 40.000 0.00 0.00 0.00 3.18
3300 3703 6.207417 CCATTGTTCTTATTCTGTGGTGTTCT 59.793 38.462 0.00 0.00 0.00 3.01
3301 3704 6.861065 TTGTTCTTATTCTGTGGTGTTCTC 57.139 37.500 0.00 0.00 0.00 2.87
3302 3705 5.924356 TGTTCTTATTCTGTGGTGTTCTCA 58.076 37.500 0.00 0.00 0.00 3.27
3303 3706 6.533730 TGTTCTTATTCTGTGGTGTTCTCAT 58.466 36.000 0.00 0.00 0.00 2.90
3304 3707 6.998074 TGTTCTTATTCTGTGGTGTTCTCATT 59.002 34.615 0.00 0.00 0.00 2.57
3305 3708 7.502226 TGTTCTTATTCTGTGGTGTTCTCATTT 59.498 33.333 0.00 0.00 0.00 2.32
3306 3709 8.352942 GTTCTTATTCTGTGGTGTTCTCATTTT 58.647 33.333 0.00 0.00 0.00 1.82
3307 3710 8.463930 TCTTATTCTGTGGTGTTCTCATTTTT 57.536 30.769 0.00 0.00 0.00 1.94
3308 3711 9.567776 TCTTATTCTGTGGTGTTCTCATTTTTA 57.432 29.630 0.00 0.00 0.00 1.52
3310 3713 9.959749 TTATTCTGTGGTGTTCTCATTTTTAAC 57.040 29.630 0.00 0.00 0.00 2.01
3311 3714 6.055231 TCTGTGGTGTTCTCATTTTTAACG 57.945 37.500 0.00 0.00 0.00 3.18
3312 3715 5.587043 TCTGTGGTGTTCTCATTTTTAACGT 59.413 36.000 0.00 0.00 0.00 3.99
3313 3716 6.094325 TCTGTGGTGTTCTCATTTTTAACGTT 59.906 34.615 5.88 5.88 0.00 3.99
3314 3717 6.030849 TGTGGTGTTCTCATTTTTAACGTTG 58.969 36.000 11.99 0.00 0.00 4.10
3315 3718 5.038033 TGGTGTTCTCATTTTTAACGTTGC 58.962 37.500 11.99 0.00 0.00 4.17
3316 3719 5.163602 TGGTGTTCTCATTTTTAACGTTGCT 60.164 36.000 11.99 0.00 0.00 3.91
3317 3720 5.746721 GGTGTTCTCATTTTTAACGTTGCTT 59.253 36.000 11.99 0.00 0.00 3.91
3318 3721 6.075046 GGTGTTCTCATTTTTAACGTTGCTTC 60.075 38.462 11.99 0.00 0.00 3.86
3319 3722 6.691388 GTGTTCTCATTTTTAACGTTGCTTCT 59.309 34.615 11.99 0.00 0.00 2.85
3320 3723 7.220108 GTGTTCTCATTTTTAACGTTGCTTCTT 59.780 33.333 11.99 0.00 0.00 2.52
3321 3724 8.399425 TGTTCTCATTTTTAACGTTGCTTCTTA 58.601 29.630 11.99 0.00 0.00 2.10
3322 3725 9.394477 GTTCTCATTTTTAACGTTGCTTCTTAT 57.606 29.630 11.99 0.00 0.00 1.73
3323 3726 9.959749 TTCTCATTTTTAACGTTGCTTCTTATT 57.040 25.926 11.99 0.00 0.00 1.40
3324 3727 9.607285 TCTCATTTTTAACGTTGCTTCTTATTC 57.393 29.630 11.99 0.00 0.00 1.75
3325 3728 9.612620 CTCATTTTTAACGTTGCTTCTTATTCT 57.387 29.630 11.99 0.00 0.00 2.40
3326 3729 9.393249 TCATTTTTAACGTTGCTTCTTATTCTG 57.607 29.630 11.99 0.00 0.00 3.02
3327 3730 9.180678 CATTTTTAACGTTGCTTCTTATTCTGT 57.819 29.630 11.99 0.00 0.00 3.41
3328 3731 8.555166 TTTTTAACGTTGCTTCTTATTCTGTG 57.445 30.769 11.99 0.00 0.00 3.66
3329 3732 4.749245 AACGTTGCTTCTTATTCTGTGG 57.251 40.909 0.00 0.00 0.00 4.17
3330 3733 3.740115 ACGTTGCTTCTTATTCTGTGGT 58.260 40.909 0.00 0.00 0.00 4.16
3331 3734 4.890088 ACGTTGCTTCTTATTCTGTGGTA 58.110 39.130 0.00 0.00 0.00 3.25
3423 3826 1.953686 AGTGTAAACGTTGCAATGGCT 59.046 42.857 22.20 11.15 41.91 4.75
3500 3903 2.545106 GTGTTTTCCCATTTGCTGCTTG 59.455 45.455 0.00 0.00 0.00 4.01
3516 3919 4.613167 GCTGCTTGATGTCTCAGAAAAGTG 60.613 45.833 0.00 0.00 31.68 3.16
3518 3921 5.311265 TGCTTGATGTCTCAGAAAAGTGAT 58.689 37.500 0.00 0.00 31.68 3.06
3519 3922 5.766670 TGCTTGATGTCTCAGAAAAGTGATT 59.233 36.000 0.00 0.00 31.68 2.57
3524 3929 8.900195 TTGATGTCTCAGAAAAGTGATTCCACG 61.900 40.741 0.00 0.00 39.33 4.94
3587 3992 1.021390 AGAAAGAGGTTGCCGCATCG 61.021 55.000 0.00 0.00 0.00 3.84
3603 4008 2.289320 GCATCGCTGGAAGGATAGTGAT 60.289 50.000 0.00 0.00 42.97 3.06
3630 4035 3.541632 GATTAATCGACTGAAAGCCCCA 58.458 45.455 0.00 0.00 37.60 4.96
3637 4042 1.676967 CTGAAAGCCCCACTGCCTC 60.677 63.158 0.00 0.00 0.00 4.70
3656 4061 1.005294 CAAATTCAGTGTGCCGCAGC 61.005 55.000 0.00 0.00 40.48 5.25
3689 4094 4.952071 TCATCTGAGACAGGAATCCATC 57.048 45.455 0.61 0.00 31.51 3.51
3690 4095 4.292643 TCATCTGAGACAGGAATCCATCA 58.707 43.478 0.61 0.00 31.51 3.07
3740 4145 0.961019 GCTCAGTTGCACCCATGAAA 59.039 50.000 0.00 0.00 0.00 2.69
3741 4146 1.068055 GCTCAGTTGCACCCATGAAAG 60.068 52.381 0.00 0.00 0.00 2.62
3742 4147 2.507484 CTCAGTTGCACCCATGAAAGA 58.493 47.619 0.00 0.00 0.00 2.52
3747 4152 1.927487 TGCACCCATGAAAGAAGCAT 58.073 45.000 0.00 0.00 0.00 3.79
3775 4181 8.997960 GTGAAAATTTACACAAACAAGCAAATG 58.002 29.630 0.00 0.00 37.05 2.32
3787 4193 5.671742 ACAAGCAAATGTTTGTTTATGGC 57.328 34.783 9.46 0.00 45.08 4.40
3788 4194 5.367302 ACAAGCAAATGTTTGTTTATGGCT 58.633 33.333 9.46 0.00 45.08 4.75
3789 4195 5.821995 ACAAGCAAATGTTTGTTTATGGCTT 59.178 32.000 9.46 0.00 45.08 4.35
3790 4196 6.318396 ACAAGCAAATGTTTGTTTATGGCTTT 59.682 30.769 9.46 0.00 45.08 3.51
3791 4197 7.497249 ACAAGCAAATGTTTGTTTATGGCTTTA 59.503 29.630 9.46 0.00 45.08 1.85
3792 4198 8.505625 CAAGCAAATGTTTGTTTATGGCTTTAT 58.494 29.630 7.15 0.00 39.15 1.40
3793 4199 8.031848 AGCAAATGTTTGTTTATGGCTTTATG 57.968 30.769 7.26 0.00 40.24 1.90
3796 4202 6.966435 ATGTTTGTTTATGGCTTTATGCAC 57.034 33.333 0.00 0.00 45.15 4.57
3846 4252 8.553459 AATACATCAATCGATCCCTTGTATTC 57.447 34.615 19.59 0.00 27.57 1.75
3851 4257 5.128663 TCAATCGATCCCTTGTATTCTGTCA 59.871 40.000 0.00 0.00 0.00 3.58
3854 4260 4.405680 TCGATCCCTTGTATTCTGTCATGT 59.594 41.667 0.00 0.00 0.00 3.21
3856 4262 4.123497 TCCCTTGTATTCTGTCATGTCG 57.877 45.455 0.00 0.00 0.00 4.35
3860 4266 4.031765 CCTTGTATTCTGTCATGTCGTTCG 59.968 45.833 0.00 0.00 0.00 3.95
3863 4269 1.778334 TTCTGTCATGTCGTTCGGTG 58.222 50.000 0.00 0.00 0.00 4.94
3864 4270 0.666274 TCTGTCATGTCGTTCGGTGC 60.666 55.000 0.00 0.00 0.00 5.01
3866 4272 0.599060 TGTCATGTCGTTCGGTGCTA 59.401 50.000 0.00 0.00 0.00 3.49
3867 4273 0.989890 GTCATGTCGTTCGGTGCTAC 59.010 55.000 0.00 0.00 0.00 3.58
3868 4274 0.599060 TCATGTCGTTCGGTGCTACA 59.401 50.000 0.00 0.00 0.00 2.74
3870 4276 2.424246 TCATGTCGTTCGGTGCTACATA 59.576 45.455 0.00 0.00 0.00 2.29
3871 4277 2.554806 TGTCGTTCGGTGCTACATAG 57.445 50.000 0.00 0.00 0.00 2.23
3872 4278 2.086094 TGTCGTTCGGTGCTACATAGA 58.914 47.619 0.00 0.00 0.00 1.98
3873 4279 2.159476 TGTCGTTCGGTGCTACATAGAC 60.159 50.000 0.00 0.00 0.00 2.59
3874 4280 1.402968 TCGTTCGGTGCTACATAGACC 59.597 52.381 0.00 0.00 0.00 3.85
3875 4281 1.133598 CGTTCGGTGCTACATAGACCA 59.866 52.381 0.00 0.00 0.00 4.02
3876 4282 2.223735 CGTTCGGTGCTACATAGACCAT 60.224 50.000 0.00 0.00 0.00 3.55
3886 4322 0.947244 CATAGACCATTGCCGCCTTC 59.053 55.000 0.00 0.00 0.00 3.46
3905 4341 3.512516 GCACGAGCAAGGGCCATC 61.513 66.667 6.18 0.00 42.56 3.51
3937 4426 3.805267 GCATGAAGCGTCCTGAGG 58.195 61.111 8.96 0.00 0.00 3.86
3942 4431 3.708220 GAAGCGTCCTGAGGCGGAG 62.708 68.421 15.09 0.00 45.87 4.63
3949 4438 2.202987 CTGAGGCGGAGATGGTGC 60.203 66.667 0.00 0.00 0.00 5.01
3950 4439 2.685017 TGAGGCGGAGATGGTGCT 60.685 61.111 0.00 0.00 0.00 4.40
3964 4453 3.902881 TGGTGCTCCATGTTTGTTTTT 57.097 38.095 2.64 0.00 39.03 1.94
3966 4455 4.688021 TGGTGCTCCATGTTTGTTTTTAC 58.312 39.130 2.64 0.00 39.03 2.01
3967 4456 4.160439 TGGTGCTCCATGTTTGTTTTTACA 59.840 37.500 2.64 0.00 39.03 2.41
3968 4457 4.744631 GGTGCTCCATGTTTGTTTTTACAG 59.255 41.667 0.00 0.00 0.00 2.74
3969 4458 4.744631 GTGCTCCATGTTTGTTTTTACAGG 59.255 41.667 0.00 0.00 0.00 4.00
3970 4459 3.740832 GCTCCATGTTTGTTTTTACAGGC 59.259 43.478 0.00 0.00 0.00 4.85
3971 4460 3.971150 TCCATGTTTGTTTTTACAGGCG 58.029 40.909 0.00 0.00 0.00 5.52
3972 4461 3.381908 TCCATGTTTGTTTTTACAGGCGT 59.618 39.130 0.00 0.00 0.00 5.68
3973 4462 3.489047 CCATGTTTGTTTTTACAGGCGTG 59.511 43.478 4.53 4.53 0.00 5.34
3974 4463 4.355437 CATGTTTGTTTTTACAGGCGTGA 58.645 39.130 14.38 0.00 0.00 4.35
3975 4464 3.760537 TGTTTGTTTTTACAGGCGTGAC 58.239 40.909 14.38 0.58 0.00 3.67
3976 4465 3.440872 TGTTTGTTTTTACAGGCGTGACT 59.559 39.130 14.38 0.00 0.00 3.41
3977 4466 4.082679 TGTTTGTTTTTACAGGCGTGACTT 60.083 37.500 14.38 0.00 0.00 3.01
3978 4467 4.705337 TTGTTTTTACAGGCGTGACTTT 57.295 36.364 14.38 0.00 0.00 2.66
3979 4468 4.705337 TGTTTTTACAGGCGTGACTTTT 57.295 36.364 14.38 0.00 0.00 2.27
3980 4469 5.061920 TGTTTTTACAGGCGTGACTTTTT 57.938 34.783 14.38 0.00 0.00 1.94
4031 4520 1.503542 CTCATGTCAAGCAACCGCC 59.496 57.895 0.00 0.00 39.83 6.13
4058 4547 2.047655 CGGCCCGTTGCAGACTAA 60.048 61.111 0.00 0.00 43.89 2.24
4124 4614 8.873242 TTTTGCATTCGTTTTTCTTTCTTTTC 57.127 26.923 0.00 0.00 0.00 2.29
4127 4617 8.918961 TGCATTCGTTTTTCTTTCTTTTCTTA 57.081 26.923 0.00 0.00 0.00 2.10
4128 4618 8.803799 TGCATTCGTTTTTCTTTCTTTTCTTAC 58.196 29.630 0.00 0.00 0.00 2.34
4132 4622 9.769093 TTCGTTTTTCTTTCTTTTCTTACTCTG 57.231 29.630 0.00 0.00 0.00 3.35
4186 4680 9.844790 TCTATTAGAAAAATCACTTTGTGCATG 57.155 29.630 0.00 0.00 32.98 4.06
4193 4687 6.548441 AAATCACTTTGTGCATGAAAATGG 57.452 33.333 0.00 0.00 32.98 3.16
4206 4700 7.899330 GTGCATGAAAATGGAAAATGTTAATCG 59.101 33.333 0.00 0.00 0.00 3.34
4224 4718 7.114953 TGTTAATCGCGCATTTGAAAAATGTTA 59.885 29.630 8.75 2.89 0.00 2.41
4227 4721 4.615121 TCGCGCATTTGAAAAATGTTAGAC 59.385 37.500 8.75 0.00 0.00 2.59
4305 4828 5.659440 AGGGTTAATCGTGCATTTGAAAT 57.341 34.783 0.00 0.00 0.00 2.17
4377 4900 8.192110 TGTAAAATGTGTTTGGGAAAAGTAGAC 58.808 33.333 0.00 0.00 0.00 2.59
4378 4901 5.784578 AATGTGTTTGGGAAAAGTAGACC 57.215 39.130 0.00 0.00 0.00 3.85
4385 4908 3.568443 TGGGAAAAGTAGACCCCAAAAC 58.432 45.455 0.00 0.00 45.19 2.43
4387 4910 3.572682 GGGAAAAGTAGACCCCAAAACAG 59.427 47.826 0.00 0.00 38.69 3.16
4394 4917 8.980481 AAAGTAGACCCCAAAACAGATATATG 57.020 34.615 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.098376 ACGCGCCAAACGTACAAAAA 59.902 45.000 5.73 0.00 46.11 1.94
18 22 0.994263 ATCTAACGCGCCAAACGTAC 59.006 50.000 5.73 0.00 44.30 3.67
30 34 4.096311 CGTGGACAGAACTACATCTAACG 58.904 47.826 0.00 0.00 0.00 3.18
31 35 4.082354 ACCGTGGACAGAACTACATCTAAC 60.082 45.833 0.00 0.00 0.00 2.34
34 38 2.526432 ACCGTGGACAGAACTACATCT 58.474 47.619 0.00 0.00 0.00 2.90
107 111 5.979993 TGAACTAGCATACCAATCCGTTTA 58.020 37.500 0.00 0.00 0.00 2.01
123 127 9.575783 GTTCCTTCTACAAGAGTATTGAACTAG 57.424 37.037 4.13 0.00 39.07 2.57
173 177 9.308318 CATGAAATATGCTTTGAATGTCATTCA 57.692 29.630 21.80 21.80 46.77 2.57
216 220 2.095110 TGCCAAATTGAAGAGCATGTCG 60.095 45.455 0.00 0.00 0.00 4.35
366 372 4.999469 ATATGTGGCATCCTGGTCATAA 57.001 40.909 0.00 0.00 0.00 1.90
444 450 6.168270 ACATTCCTTGAGCTAGGACTTATC 57.832 41.667 4.62 0.00 43.91 1.75
465 471 5.298276 AGAAACAACGCAAATTCTCCTTACA 59.702 36.000 0.00 0.00 0.00 2.41
472 478 4.918810 AGGAAGAAACAACGCAAATTCT 57.081 36.364 0.00 0.00 33.73 2.40
479 485 7.168469 TGCTTTTAAATTAGGAAGAAACAACGC 59.832 33.333 0.00 0.00 0.00 4.84
503 509 5.485662 AACTGTTAGTCTGTCAAGTTTGC 57.514 39.130 0.00 0.00 0.00 3.68
505 511 5.990668 AGGAACTGTTAGTCTGTCAAGTTT 58.009 37.500 0.00 0.00 37.18 2.66
512 518 5.185442 GGTAGCTTAGGAACTGTTAGTCTGT 59.815 44.000 0.00 0.00 41.52 3.41
515 521 5.163530 GGAGGTAGCTTAGGAACTGTTAGTC 60.164 48.000 0.00 0.00 41.52 2.59
535 541 2.744494 GCTGCCAAACTAGAGATGGAGG 60.744 54.545 14.55 8.47 36.27 4.30
566 572 0.264657 TGGCCCTGCTCCTACTCATA 59.735 55.000 0.00 0.00 0.00 2.15
568 574 0.840288 TTTGGCCCTGCTCCTACTCA 60.840 55.000 0.00 0.00 0.00 3.41
632 638 2.614057 ACGCAAACTTGATAGGCTATGC 59.386 45.455 12.68 7.83 0.00 3.14
659 665 2.746904 TCATAGTGATTTGTGCCGTTGG 59.253 45.455 0.00 0.00 0.00 3.77
663 669 4.816385 ACCTTATCATAGTGATTTGTGCCG 59.184 41.667 0.00 0.00 38.26 5.69
701 707 9.277783 GCCAATAAACTCTCTACATACATTCAT 57.722 33.333 0.00 0.00 0.00 2.57
782 791 7.338800 AGTTCATGCAATATAAGAACCAAGG 57.661 36.000 0.00 0.00 39.39 3.61
783 792 8.461222 TCAAGTTCATGCAATATAAGAACCAAG 58.539 33.333 0.00 0.00 39.39 3.61
909 930 5.337169 GCCCCTACAAGCAAACATAAAATCA 60.337 40.000 0.00 0.00 0.00 2.57
1107 1136 8.424918 TCTAAAATAAAGGTGGCAATTGACAAA 58.575 29.630 17.49 0.00 32.99 2.83
1245 1274 7.340487 CCTCCTAAATTCTTTAGTCTGGCAATT 59.660 37.037 6.04 0.00 40.76 2.32
1258 1287 6.882768 ACATCACTCTCCTCCTAAATTCTT 57.117 37.500 0.00 0.00 0.00 2.52
1281 1310 4.541705 TGAACTGAACAAAGAATCCCCAA 58.458 39.130 0.00 0.00 0.00 4.12
1313 1343 1.133637 TGCCTGGTTGCTACTTTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
1314 1344 1.541588 CTGCCTGGTTGCTACTTTTCC 59.458 52.381 0.00 0.00 0.00 3.13
1332 1366 1.572085 CTGGTCGACAAAGCTGGCTG 61.572 60.000 18.91 0.00 0.00 4.85
1392 1426 3.724374 CAACCGTTCTTAGGACAACTGA 58.276 45.455 0.00 0.00 0.00 3.41
1414 1448 5.291971 CAACCAATTCAGAACCAGAAAAGG 58.708 41.667 0.00 0.00 32.51 3.11
1492 1534 7.093068 ACAAGGGAAAAAGCTAAAAGGAGAAAA 60.093 33.333 0.00 0.00 0.00 2.29
1617 1754 8.463930 AGTCATTTTTCAATACAAGGAAGTCA 57.536 30.769 0.00 0.00 0.00 3.41
1668 1808 7.012661 TCTGTGATGTCATCAATATGGCTAT 57.987 36.000 17.11 0.00 41.69 2.97
1669 1809 6.423776 TCTGTGATGTCATCAATATGGCTA 57.576 37.500 17.11 0.00 41.69 3.93
1675 1822 9.112725 CAGGTTTTATCTGTGATGTCATCAATA 57.887 33.333 17.11 8.99 41.69 1.90
1706 1853 1.401905 GCCGCCTCTAGGTTCATTTTG 59.598 52.381 0.00 0.00 37.57 2.44
1755 1902 4.219944 AGAATTGCATCATGAAGCACAGTT 59.780 37.500 24.21 18.16 41.05 3.16
1769 1916 3.657398 TGGGTCATCAGAGAATTGCAT 57.343 42.857 0.00 0.00 0.00 3.96
1832 1979 3.619979 GCAATGTAGGTGCCTACTTCAGT 60.620 47.826 23.91 5.89 46.53 3.41
1870 2022 9.305925 CTAACTCGCTGATGCATCATAATAATA 57.694 33.333 28.81 16.52 39.64 0.98
1872 2024 6.091305 GCTAACTCGCTGATGCATCATAATAA 59.909 38.462 28.81 12.34 39.64 1.40
1915 2069 4.201822 GGCTAATCAGAACACAACGGAATC 60.202 45.833 0.00 0.00 0.00 2.52
1949 2103 5.473846 GGACCTTGCTAAAAATATCTAGCCC 59.526 44.000 8.27 1.05 39.89 5.19
1963 2117 6.899089 TCAAATCAAGATATGGACCTTGCTA 58.101 36.000 0.00 0.00 39.53 3.49
1964 2118 5.759059 TCAAATCAAGATATGGACCTTGCT 58.241 37.500 0.00 0.00 39.53 3.91
1965 2119 6.455360 TTCAAATCAAGATATGGACCTTGC 57.545 37.500 0.00 0.00 39.53 4.01
1968 2122 9.512588 GACATATTCAAATCAAGATATGGACCT 57.487 33.333 0.00 0.00 0.00 3.85
1969 2123 8.734386 GGACATATTCAAATCAAGATATGGACC 58.266 37.037 0.00 0.00 0.00 4.46
1970 2124 8.734386 GGGACATATTCAAATCAAGATATGGAC 58.266 37.037 0.00 0.00 0.00 4.02
1971 2125 8.672329 AGGGACATATTCAAATCAAGATATGGA 58.328 33.333 0.00 0.00 0.00 3.41
1977 2131 6.720309 TGTGAGGGACATATTCAAATCAAGA 58.280 36.000 0.00 0.00 0.00 3.02
2010 2164 3.404773 GGAGTTCCACCCTCCCTG 58.595 66.667 0.00 0.00 42.29 4.45
2017 2171 1.379044 CATGGCAGGGAGTTCCACC 60.379 63.158 0.00 0.00 38.24 4.61
2037 2191 4.297768 TGAGAGATGGATTGTGGTATGGA 58.702 43.478 0.00 0.00 0.00 3.41
2044 2198 4.958509 AGCTGTATGAGAGATGGATTGTG 58.041 43.478 0.00 0.00 0.00 3.33
2045 2199 4.040217 GGAGCTGTATGAGAGATGGATTGT 59.960 45.833 0.00 0.00 0.00 2.71
2136 2290 6.632909 CAATTGGCAAGAGGATGAAACATTA 58.367 36.000 5.96 0.00 0.00 1.90
2216 2484 3.669023 CGCAAGATCTTTGCAGGTCTTTC 60.669 47.826 21.68 0.00 46.87 2.62
2262 2530 6.992063 AAACATCAGCCACTATCACTTTAG 57.008 37.500 0.00 0.00 0.00 1.85
2307 2583 6.467677 CATCTAACTCTCCAAGGTGAAGAAA 58.532 40.000 0.00 0.00 0.00 2.52
2308 2584 5.046304 CCATCTAACTCTCCAAGGTGAAGAA 60.046 44.000 0.00 0.00 0.00 2.52
2314 2590 4.027437 GAGACCATCTAACTCTCCAAGGT 58.973 47.826 0.00 0.00 0.00 3.50
2414 2799 4.578516 TGACCAAGAACACATTTACCACAG 59.421 41.667 0.00 0.00 0.00 3.66
2441 2826 3.678289 TGAGTTGGTCCATGATTCACAG 58.322 45.455 0.00 0.00 0.00 3.66
2459 2844 3.795877 ACCACAAAGTTTGGCATTTGAG 58.204 40.909 19.45 9.88 38.42 3.02
2583 2968 6.761242 TGCAATGTAGGTATATTGTGTCAGTC 59.239 38.462 7.91 0.00 37.20 3.51
2750 3135 6.293516 CGTAGTAAACAAGTGGGCAATTTGTA 60.294 38.462 2.92 0.00 34.18 2.41
2755 3140 3.746940 ACGTAGTAAACAAGTGGGCAAT 58.253 40.909 0.00 0.00 41.94 3.56
2756 3141 3.196939 ACGTAGTAAACAAGTGGGCAA 57.803 42.857 0.00 0.00 41.94 4.52
2816 3201 0.816373 TGCAAGCAACAGCTGAACAA 59.184 45.000 23.35 0.00 38.93 2.83
2895 3280 4.174009 CCTGATGGTACGTACTGAACAAG 58.826 47.826 24.07 13.93 0.00 3.16
2896 3281 3.575256 ACCTGATGGTACGTACTGAACAA 59.425 43.478 24.07 6.04 46.43 2.83
2897 3282 3.159472 ACCTGATGGTACGTACTGAACA 58.841 45.455 24.07 14.26 46.43 3.18
2898 3283 3.863142 ACCTGATGGTACGTACTGAAC 57.137 47.619 24.07 13.71 46.43 3.18
2922 3307 3.583086 ACACCTCCTTAGTGCATAACAGT 59.417 43.478 0.00 0.00 38.87 3.55
3040 3443 6.817641 TCAAAAACAAGCTGAACATTGACAAT 59.182 30.769 0.00 0.00 0.00 2.71
3041 3444 6.162079 TCAAAAACAAGCTGAACATTGACAA 58.838 32.000 0.00 0.00 0.00 3.18
3225 3628 7.587629 TGCAAAATAAAGAACTCATGTCTCTG 58.412 34.615 0.00 0.00 0.00 3.35
3255 3658 2.306847 GGTGCTCCAACAGAAAAAGGA 58.693 47.619 0.00 0.00 0.00 3.36
3297 3700 9.959749 AATAAGAAGCAACGTTAAAAATGAGAA 57.040 25.926 0.00 0.00 0.00 2.87
3299 3702 9.612620 AGAATAAGAAGCAACGTTAAAAATGAG 57.387 29.630 0.00 0.00 0.00 2.90
3300 3703 9.393249 CAGAATAAGAAGCAACGTTAAAAATGA 57.607 29.630 0.00 0.00 0.00 2.57
3301 3704 9.180678 ACAGAATAAGAAGCAACGTTAAAAATG 57.819 29.630 0.00 0.00 0.00 2.32
3302 3705 9.180678 CACAGAATAAGAAGCAACGTTAAAAAT 57.819 29.630 0.00 0.00 0.00 1.82
3303 3706 7.646130 CCACAGAATAAGAAGCAACGTTAAAAA 59.354 33.333 0.00 0.00 0.00 1.94
3304 3707 7.136119 CCACAGAATAAGAAGCAACGTTAAAA 58.864 34.615 0.00 0.00 0.00 1.52
3305 3708 6.261381 ACCACAGAATAAGAAGCAACGTTAAA 59.739 34.615 0.00 0.00 0.00 1.52
3306 3709 5.761234 ACCACAGAATAAGAAGCAACGTTAA 59.239 36.000 0.00 0.00 0.00 2.01
3307 3710 5.302360 ACCACAGAATAAGAAGCAACGTTA 58.698 37.500 0.00 0.00 0.00 3.18
3308 3711 4.134563 ACCACAGAATAAGAAGCAACGTT 58.865 39.130 0.00 0.00 0.00 3.99
3309 3712 3.740115 ACCACAGAATAAGAAGCAACGT 58.260 40.909 0.00 0.00 0.00 3.99
3310 3713 6.313905 AGAATACCACAGAATAAGAAGCAACG 59.686 38.462 0.00 0.00 0.00 4.10
3311 3714 7.201652 GGAGAATACCACAGAATAAGAAGCAAC 60.202 40.741 0.00 0.00 0.00 4.17
3312 3715 6.823689 GGAGAATACCACAGAATAAGAAGCAA 59.176 38.462 0.00 0.00 0.00 3.91
3313 3716 6.070251 TGGAGAATACCACAGAATAAGAAGCA 60.070 38.462 0.00 0.00 34.77 3.91
3314 3717 6.349300 TGGAGAATACCACAGAATAAGAAGC 58.651 40.000 0.00 0.00 34.77 3.86
3315 3718 8.970859 AATGGAGAATACCACAGAATAAGAAG 57.029 34.615 0.00 0.00 43.03 2.85
3316 3719 9.753674 AAAATGGAGAATACCACAGAATAAGAA 57.246 29.630 0.00 0.00 43.03 2.52
3320 3723 9.104965 CGTTAAAATGGAGAATACCACAGAATA 57.895 33.333 0.00 0.00 43.03 1.75
3321 3724 7.610305 ACGTTAAAATGGAGAATACCACAGAAT 59.390 33.333 0.00 0.00 43.03 2.40
3322 3725 6.938030 ACGTTAAAATGGAGAATACCACAGAA 59.062 34.615 0.00 0.00 43.03 3.02
3323 3726 6.469410 ACGTTAAAATGGAGAATACCACAGA 58.531 36.000 0.00 0.00 43.03 3.41
3324 3727 6.737254 ACGTTAAAATGGAGAATACCACAG 57.263 37.500 0.00 0.00 43.03 3.66
3325 3728 6.568844 GCAACGTTAAAATGGAGAATACCACA 60.569 38.462 0.00 0.00 43.03 4.17
3326 3729 5.798434 GCAACGTTAAAATGGAGAATACCAC 59.202 40.000 0.00 0.00 43.03 4.16
3327 3730 5.708230 AGCAACGTTAAAATGGAGAATACCA 59.292 36.000 0.00 0.00 44.41 3.25
3328 3731 6.128117 TGAGCAACGTTAAAATGGAGAATACC 60.128 38.462 0.00 0.00 0.00 2.73
3329 3732 6.837992 TGAGCAACGTTAAAATGGAGAATAC 58.162 36.000 0.00 0.00 0.00 1.89
3330 3733 7.552687 AGATGAGCAACGTTAAAATGGAGAATA 59.447 33.333 0.00 0.00 0.00 1.75
3331 3734 5.957842 TGAGCAACGTTAAAATGGAGAAT 57.042 34.783 0.00 0.00 0.00 2.40
3423 3826 0.677731 GCTGATACAAGCCTGTGCCA 60.678 55.000 0.00 0.00 37.20 4.92
3500 3903 5.163913 CGTGGAATCACTTTTCTGAGACATC 60.164 44.000 0.00 0.00 41.53 3.06
3524 3929 5.220643 CCTGCAAAGAAAATCAACACAAACC 60.221 40.000 0.00 0.00 0.00 3.27
3562 3967 2.005451 CGGCAACCTCTTTCTCATCTG 58.995 52.381 0.00 0.00 0.00 2.90
3587 3992 3.126831 CGTTCATCACTATCCTTCCAGC 58.873 50.000 0.00 0.00 0.00 4.85
3603 4008 4.328983 GCTTTCAGTCGATTAATCCGTTCA 59.671 41.667 9.87 0.00 0.00 3.18
3630 4035 1.610522 GCACACTGAATTTGAGGCAGT 59.389 47.619 0.00 0.00 43.16 4.40
3637 4042 1.005294 GCTGCGGCACACTGAATTTG 61.005 55.000 14.08 0.00 38.54 2.32
3656 4061 6.896111 CTGTCTCAGATGAAACGACACATCG 61.896 48.000 0.00 0.00 44.92 3.84
3689 4094 5.104374 CCAATTCGGACATGGAAAGAAATG 58.896 41.667 0.00 1.17 36.27 2.32
3690 4095 4.772100 ACCAATTCGGACATGGAAAGAAAT 59.228 37.500 13.59 0.00 37.66 2.17
3775 4181 5.925969 ACAGTGCATAAAGCCATAAACAAAC 59.074 36.000 0.00 0.00 44.83 2.93
3812 4218 7.255590 GGGATCGATTGATGTATTTGGATGTTT 60.256 37.037 0.00 0.00 34.09 2.83
3813 4219 6.207417 GGGATCGATTGATGTATTTGGATGTT 59.793 38.462 0.00 0.00 34.09 2.71
3814 4220 5.707298 GGGATCGATTGATGTATTTGGATGT 59.293 40.000 0.00 0.00 34.09 3.06
3818 4224 5.532406 ACAAGGGATCGATTGATGTATTTGG 59.468 40.000 13.66 0.00 34.09 3.28
3831 4237 4.405680 ACATGACAGAATACAAGGGATCGA 59.594 41.667 0.00 0.00 0.00 3.59
3846 4252 0.667487 AGCACCGAACGACATGACAG 60.667 55.000 0.00 0.00 0.00 3.51
3851 4257 2.686405 TCTATGTAGCACCGAACGACAT 59.314 45.455 0.00 0.29 37.22 3.06
3854 4260 1.402968 GGTCTATGTAGCACCGAACGA 59.597 52.381 0.00 0.00 0.00 3.85
3856 4262 2.953466 TGGTCTATGTAGCACCGAAC 57.047 50.000 0.00 0.00 32.27 3.95
3860 4266 2.222027 GGCAATGGTCTATGTAGCACC 58.778 52.381 0.00 0.00 0.00 5.01
3863 4269 0.868406 GCGGCAATGGTCTATGTAGC 59.132 55.000 0.00 0.00 0.00 3.58
3864 4270 1.070758 AGGCGGCAATGGTCTATGTAG 59.929 52.381 13.08 0.00 0.00 2.74
3866 4272 0.255890 AAGGCGGCAATGGTCTATGT 59.744 50.000 13.08 0.00 0.00 2.29
3867 4273 0.947244 GAAGGCGGCAATGGTCTATG 59.053 55.000 13.08 0.00 0.00 2.23
3868 4274 0.839946 AGAAGGCGGCAATGGTCTAT 59.160 50.000 13.08 0.00 0.00 1.98
3870 4276 1.377725 CAGAAGGCGGCAATGGTCT 60.378 57.895 13.08 2.47 0.00 3.85
3871 4277 3.056313 GCAGAAGGCGGCAATGGTC 62.056 63.158 13.08 0.00 35.17 4.02
3872 4278 3.064324 GCAGAAGGCGGCAATGGT 61.064 61.111 13.08 0.00 35.17 3.55
3873 4279 3.346631 GTGCAGAAGGCGGCAATGG 62.347 63.158 13.08 0.00 46.46 3.16
3874 4280 2.180017 GTGCAGAAGGCGGCAATG 59.820 61.111 13.08 7.77 46.46 2.82
3875 4281 3.434319 CGTGCAGAAGGCGGCAAT 61.434 61.111 13.08 0.00 46.46 3.56
3876 4282 4.617520 TCGTGCAGAAGGCGGCAA 62.618 61.111 13.08 0.00 46.46 4.52
3910 4346 2.672651 CTTCATGCACACCCCGCA 60.673 61.111 0.00 0.00 44.94 5.69
3923 4412 4.069232 CCGCCTCAGGACGCTTCA 62.069 66.667 0.00 0.00 0.00 3.02
3929 4418 2.060980 ACCATCTCCGCCTCAGGAC 61.061 63.158 0.00 0.00 36.14 3.85
3949 4438 3.980775 CGCCTGTAAAAACAAACATGGAG 59.019 43.478 0.00 0.00 0.00 3.86
3950 4439 3.381908 ACGCCTGTAAAAACAAACATGGA 59.618 39.130 0.00 0.00 0.00 3.41
3952 4441 4.206200 GTCACGCCTGTAAAAACAAACATG 59.794 41.667 0.00 0.00 0.00 3.21
3953 4442 4.097286 AGTCACGCCTGTAAAAACAAACAT 59.903 37.500 0.00 0.00 0.00 2.71
3954 4443 3.440872 AGTCACGCCTGTAAAAACAAACA 59.559 39.130 0.00 0.00 0.00 2.83
3955 4444 4.023739 AGTCACGCCTGTAAAAACAAAC 57.976 40.909 0.00 0.00 0.00 2.93
3957 4446 4.705337 AAAGTCACGCCTGTAAAAACAA 57.295 36.364 0.00 0.00 0.00 2.83
3958 4447 4.705337 AAAAGTCACGCCTGTAAAAACA 57.295 36.364 0.00 0.00 0.00 2.83
3980 4469 4.314121 GCCCATAATGTTGCTCACAAAAA 58.686 39.130 0.00 0.00 39.50 1.94
3981 4470 3.613671 CGCCCATAATGTTGCTCACAAAA 60.614 43.478 0.00 0.00 39.50 2.44
3982 4471 2.094803 CGCCCATAATGTTGCTCACAAA 60.095 45.455 0.00 0.00 39.50 2.83
3983 4472 1.472082 CGCCCATAATGTTGCTCACAA 59.528 47.619 0.00 0.00 39.50 3.33
3984 4473 1.093972 CGCCCATAATGTTGCTCACA 58.906 50.000 0.00 0.00 40.71 3.58
3985 4474 1.094785 ACGCCCATAATGTTGCTCAC 58.905 50.000 0.00 0.00 0.00 3.51
3986 4475 1.093972 CACGCCCATAATGTTGCTCA 58.906 50.000 0.00 0.00 0.00 4.26
3987 4476 1.064060 GTCACGCCCATAATGTTGCTC 59.936 52.381 0.00 0.00 0.00 4.26
3988 4477 1.094785 GTCACGCCCATAATGTTGCT 58.905 50.000 0.00 0.00 0.00 3.91
3989 4478 1.094785 AGTCACGCCCATAATGTTGC 58.905 50.000 0.00 0.00 0.00 4.17
3990 4479 3.303990 GCATAGTCACGCCCATAATGTTG 60.304 47.826 0.00 0.00 0.00 3.33
3991 4480 2.878406 GCATAGTCACGCCCATAATGTT 59.122 45.455 0.00 0.00 0.00 2.71
3992 4481 2.494059 GCATAGTCACGCCCATAATGT 58.506 47.619 0.00 0.00 0.00 2.71
3993 4482 1.806542 GGCATAGTCACGCCCATAATG 59.193 52.381 0.00 0.00 42.82 1.90
3994 4483 2.185004 GGCATAGTCACGCCCATAAT 57.815 50.000 0.00 0.00 42.82 1.28
4016 4505 2.796483 TAGCGGCGGTTGCTTGACAT 62.796 55.000 19.60 0.00 43.71 3.06
4017 4506 2.796483 ATAGCGGCGGTTGCTTGACA 62.796 55.000 19.60 0.00 43.71 3.58
4048 4537 3.403038 GCTGAAGGACTTTAGTCTGCAA 58.597 45.455 9.56 0.00 44.20 4.08
4049 4538 2.610479 CGCTGAAGGACTTTAGTCTGCA 60.610 50.000 9.56 5.20 44.20 4.41
4180 4674 7.899330 CGATTAACATTTTCCATTTTCATGCAC 59.101 33.333 0.00 0.00 0.00 4.57
4182 4676 6.901357 GCGATTAACATTTTCCATTTTCATGC 59.099 34.615 0.00 0.00 0.00 4.06
4186 4680 5.061560 TGCGCGATTAACATTTTCCATTTTC 59.938 36.000 12.10 0.00 0.00 2.29
4193 4687 5.678910 TCAAATGCGCGATTAACATTTTC 57.321 34.783 12.10 0.00 40.94 2.29
4206 4700 4.923281 AGGTCTAACATTTTTCAAATGCGC 59.077 37.500 0.00 0.00 0.00 6.09
4285 4808 7.985634 ACATATTTCAAATGCACGATTAACC 57.014 32.000 0.00 0.00 0.00 2.85
4293 4816 6.307800 ACACGCTTAACATATTTCAAATGCAC 59.692 34.615 0.00 0.00 0.00 4.57
4313 4836 7.298507 TCAGGAACACTTTTTATATACACGC 57.701 36.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.