Multiple sequence alignment - TraesCS1A01G203600

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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 TraesCS1A01G203600 chr1A 100.000 3147 0 0 1 3147 365491282 365494428 0.000000e+00 5812.0
1 TraesCS1A01G203600 chr1A 85.578 1366 122 34 855 2152 365507343 365508701 0.000000e+00 1362.0
2 TraesCS1A01G203600 chr1A 100.000 30 0 0 210 239 365491457 365491486 4.380000e-04 56.5
3 TraesCS1A01G203600 chr1A 100.000 30 0 0 176 205 365491491 365491520 4.380000e-04 56.5
4 TraesCS1A01G203600 chr1D 88.183 2361 215 37 743 3068 293458522 293460853 0.000000e+00 2756.0
5 TraesCS1A01G203600 chr1D 85.830 1355 112 39 865 2152 293523911 293525252 0.000000e+00 1365.0
6 TraesCS1A01G203600 chr1D 91.944 360 20 5 210 561 293457980 293458338 2.180000e-136 496.0
7 TraesCS1A01G203600 chr1D 96.045 177 3 1 554 726 293458362 293458538 5.140000e-73 285.0
8 TraesCS1A01G203600 chr1D 96.000 100 4 0 108 207 293457912 293458011 2.510000e-36 163.0
9 TraesCS1A01G203600 chr1B 89.881 1423 95 23 743 2152 394507690 394509076 0.000000e+00 1784.0
10 TraesCS1A01G203600 chr1B 85.017 1475 122 54 746 2152 394637389 394638832 0.000000e+00 1408.0
11 TraesCS1A01G203600 chr1B 86.555 476 32 20 5 480 394506779 394507222 2.180000e-136 496.0
12 TraesCS1A01G203600 chr1B 94.220 173 8 1 554 726 394507536 394507706 2.410000e-66 263.0
13 TraesCS1A01G203600 chr1B 92.857 84 4 2 3064 3145 394634333 394634416 1.530000e-23 121.0
14 TraesCS1A01G203600 chr5D 85.065 462 59 6 1688 2142 472803478 472803936 2.210000e-126 462.0
15 TraesCS1A01G203600 chr5D 76.429 980 121 57 743 1623 472802503 472803471 2.240000e-116 429.0
16 TraesCS1A01G203600 chr5D 81.614 223 29 10 2468 2684 67044711 67044495 1.160000e-39 174.0
17 TraesCS1A01G203600 chr5D 78.467 274 48 11 2450 2715 496276344 496276614 5.400000e-38 169.0
18 TraesCS1A01G203600 chr5B 85.071 422 55 4 1727 2142 580165865 580166284 1.040000e-114 424.0
19 TraesCS1A01G203600 chr5B 84.375 384 52 3 1765 2142 580174876 580175257 1.380000e-98 370.0
20 TraesCS1A01G203600 chr5B 80.517 503 72 20 1015 1501 580165074 580165566 2.310000e-96 363.0
21 TraesCS1A01G203600 chr3A 79.245 318 49 15 2422 2735 451155064 451154760 4.110000e-49 206.0
22 TraesCS1A01G203600 chr3A 78.049 287 56 6 2448 2729 691295159 691295443 1.160000e-39 174.0
23 TraesCS1A01G203600 chr5A 80.071 281 42 7 2407 2684 315263370 315263639 2.480000e-46 196.0
24 TraesCS1A01G203600 chrUn 78.694 291 47 14 2448 2729 99878698 99878982 2.490000e-41 180.0
25 TraesCS1A01G203600 chr3B 80.426 235 41 5 2499 2729 623667350 623667583 1.160000e-39 174.0
26 TraesCS1A01G203600 chr4A 80.085 236 41 6 2499 2730 12206842 12206609 1.500000e-38 171.0
27 TraesCS1A01G203600 chr4A 79.310 116 13 6 2413 2528 599340490 599340386 1.570000e-08 71.3
28 TraesCS1A01G203600 chr7A 86.207 145 16 4 1133 1275 722767986 722768128 1.510000e-33 154.0
29 TraesCS1A01G203600 chr7B 73.514 370 87 10 1781 2144 727536608 727536244 2.550000e-26 130.0


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 TraesCS1A01G203600 chr1A 365491282 365494428 3146 False 1975.000000 5812 100.000000 1 3147 3 chr1A.!!$F2 3146
1 TraesCS1A01G203600 chr1A 365507343 365508701 1358 False 1362.000000 1362 85.578000 855 2152 1 chr1A.!!$F1 1297
2 TraesCS1A01G203600 chr1D 293523911 293525252 1341 False 1365.000000 1365 85.830000 865 2152 1 chr1D.!!$F1 1287
3 TraesCS1A01G203600 chr1D 293457912 293460853 2941 False 925.000000 2756 93.043000 108 3068 4 chr1D.!!$F2 2960
4 TraesCS1A01G203600 chr1B 394506779 394509076 2297 False 847.666667 1784 90.218667 5 2152 3 chr1B.!!$F1 2147
5 TraesCS1A01G203600 chr1B 394634333 394638832 4499 False 764.500000 1408 88.937000 746 3145 2 chr1B.!!$F2 2399
6 TraesCS1A01G203600 chr5D 472802503 472803936 1433 False 445.500000 462 80.747000 743 2142 2 chr5D.!!$F2 1399
7 TraesCS1A01G203600 chr5B 580165074 580166284 1210 False 393.500000 424 82.794000 1015 2142 2 chr5B.!!$F2 1127

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
733 982 0.036164 TACGCCACATGCCTCTTGTT 59.964 50.0 0.0 0.0 36.24 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 5200 0.31716 TCTCGCAGTTGACCGAATGT 59.683 50.0 0.0 0.0 32.56 2.71 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
66 67 3.603532 AGGTGTACGACTCGTTAGATGA 58.396 45.455 9.84 0.00 41.54 2.92
67 68 3.373439 AGGTGTACGACTCGTTAGATGAC 59.627 47.826 9.84 1.20 41.54 3.06
79 80 1.688772 TAGATGACCGGCTCCTGTAC 58.311 55.000 0.00 0.00 0.00 2.90
80 81 1.043673 AGATGACCGGCTCCTGTACC 61.044 60.000 0.00 0.00 0.00 3.34
89 90 2.553172 CGGCTCCTGTACCACTATCTAC 59.447 54.545 0.00 0.00 0.00 2.59
154 155 2.430694 ACTGGCAAGCGAGATGTACATA 59.569 45.455 8.71 0.00 0.00 2.29
164 165 4.026062 GCGAGATGTACATATTTTGCGTCA 60.026 41.667 8.71 0.00 0.00 4.35
206 207 5.971202 CAGTCTAGTTTGTTCAACGCAAATT 59.029 36.000 0.00 0.00 40.75 1.82
207 208 5.971202 AGTCTAGTTTGTTCAACGCAAATTG 59.029 36.000 0.00 0.00 40.75 2.32
210 211 4.489810 AGTTTGTTCAACGCAAATTGTCA 58.510 34.783 0.00 0.00 40.75 3.58
213 214 6.091986 AGTTTGTTCAACGCAAATTGTCATTT 59.908 30.769 0.00 0.00 40.75 2.32
214 215 7.883177 AGTTTGTTCAACGCAAATTGTCATTTG 60.883 33.333 3.71 3.71 41.36 2.32
224 225 6.017400 CAAATTGTCATTTGCCAGTCTAGT 57.983 37.500 0.00 0.00 42.20 2.57
225 226 6.449698 CAAATTGTCATTTGCCAGTCTAGTT 58.550 36.000 0.00 0.00 42.20 2.24
227 228 5.437289 TTGTCATTTGCCAGTCTAGTTTG 57.563 39.130 0.00 0.00 0.00 2.93
228 229 4.460263 TGTCATTTGCCAGTCTAGTTTGT 58.540 39.130 0.00 0.00 0.00 2.83
229 230 4.887071 TGTCATTTGCCAGTCTAGTTTGTT 59.113 37.500 0.00 0.00 0.00 2.83
231 232 5.008613 GTCATTTGCCAGTCTAGTTTGTTCA 59.991 40.000 0.00 0.00 0.00 3.18
233 234 4.893424 TTGCCAGTCTAGTTTGTTCAAC 57.107 40.909 0.00 0.00 35.32 3.18
234 235 2.869801 TGCCAGTCTAGTTTGTTCAACG 59.130 45.455 0.00 0.00 40.75 4.10
235 236 2.349532 GCCAGTCTAGTTTGTTCAACGC 60.350 50.000 0.00 0.00 40.75 4.84
237 238 3.311322 CCAGTCTAGTTTGTTCAACGCAA 59.689 43.478 0.00 0.00 40.75 4.85
238 239 4.201871 CCAGTCTAGTTTGTTCAACGCAAA 60.202 41.667 0.00 0.00 40.75 3.68
270 271 9.754382 GTCCGATTACTACCATGTTTTATCTAA 57.246 33.333 0.00 0.00 0.00 2.10
418 423 1.762222 GATTCGACCATTGGACGCCG 61.762 60.000 20.40 12.29 40.30 6.46
423 428 3.197790 CCATTGGACGCCGAGCTG 61.198 66.667 0.00 0.00 0.00 4.24
470 475 2.494073 CGTAGAAGCTTCTTCCAGTCCT 59.506 50.000 32.70 9.18 38.70 3.85
476 481 1.283321 GCTTCTTCCAGTCCTCCCATT 59.717 52.381 0.00 0.00 0.00 3.16
492 497 1.064505 CCATTCATGCGCTGTACAAGG 59.935 52.381 9.73 0.00 0.00 3.61
601 846 0.567968 CAAGAAGTCTGCGCGTATCG 59.432 55.000 8.43 0.00 42.12 2.92
710 959 1.226974 GCGGCTGCGAGAGTGATAA 60.227 57.895 0.00 0.00 0.00 1.75
711 960 1.483424 GCGGCTGCGAGAGTGATAAC 61.483 60.000 0.00 0.00 0.00 1.89
714 963 1.269309 GGCTGCGAGAGTGATAACGAT 60.269 52.381 0.00 0.00 0.00 3.73
715 964 2.031069 GGCTGCGAGAGTGATAACGATA 60.031 50.000 0.00 0.00 0.00 2.92
716 965 2.974536 GCTGCGAGAGTGATAACGATAC 59.025 50.000 0.00 0.00 0.00 2.24
717 966 3.219189 CTGCGAGAGTGATAACGATACG 58.781 50.000 0.00 0.00 0.00 3.06
719 968 2.572243 CGAGAGTGATAACGATACGCC 58.428 52.381 0.00 0.00 0.00 5.68
720 969 2.032290 CGAGAGTGATAACGATACGCCA 60.032 50.000 0.00 0.00 0.00 5.69
721 970 3.298317 GAGAGTGATAACGATACGCCAC 58.702 50.000 0.00 0.00 0.00 5.01
722 971 2.686405 AGAGTGATAACGATACGCCACA 59.314 45.455 0.00 0.00 0.00 4.17
723 972 3.318275 AGAGTGATAACGATACGCCACAT 59.682 43.478 0.00 0.00 0.00 3.21
724 973 3.381045 AGTGATAACGATACGCCACATG 58.619 45.455 0.00 0.00 0.00 3.21
725 974 2.096909 GTGATAACGATACGCCACATGC 60.097 50.000 0.00 0.00 0.00 4.06
726 975 1.459592 GATAACGATACGCCACATGCC 59.540 52.381 0.00 0.00 36.24 4.40
728 977 0.810031 AACGATACGCCACATGCCTC 60.810 55.000 0.00 0.00 36.24 4.70
729 978 1.068083 CGATACGCCACATGCCTCT 59.932 57.895 0.00 0.00 36.24 3.69
730 979 0.530650 CGATACGCCACATGCCTCTT 60.531 55.000 0.00 0.00 36.24 2.85
731 980 0.940126 GATACGCCACATGCCTCTTG 59.060 55.000 0.00 0.00 36.24 3.02
732 981 0.253044 ATACGCCACATGCCTCTTGT 59.747 50.000 0.00 0.00 36.24 3.16
733 982 0.036164 TACGCCACATGCCTCTTGTT 59.964 50.000 0.00 0.00 36.24 2.83
734 983 0.823356 ACGCCACATGCCTCTTGTTT 60.823 50.000 0.00 0.00 36.24 2.83
735 984 1.164411 CGCCACATGCCTCTTGTTTA 58.836 50.000 0.00 0.00 36.24 2.01
737 986 2.030363 CGCCACATGCCTCTTGTTTAAA 60.030 45.455 0.00 0.00 36.24 1.52
738 987 3.551863 CGCCACATGCCTCTTGTTTAAAA 60.552 43.478 0.00 0.00 36.24 1.52
739 988 4.376146 GCCACATGCCTCTTGTTTAAAAA 58.624 39.130 0.00 0.00 0.00 1.94
772 3085 0.977627 ACATGCCTCCATCGTCCTGA 60.978 55.000 0.00 0.00 0.00 3.86
795 3108 1.799916 GCGGCCCGTCAAATTTTCG 60.800 57.895 4.45 5.79 0.00 3.46
833 3156 2.475022 GCAACGTGGAAAAGTATACGCC 60.475 50.000 0.00 0.00 39.94 5.68
851 3197 2.877113 CGCGACGAACCGTGCATA 60.877 61.111 0.00 0.00 41.37 3.14
852 3198 2.438148 CGCGACGAACCGTGCATAA 61.438 57.895 0.00 0.00 41.37 1.90
863 3209 0.924777 CGTGCATAATCACCGCGTTA 59.075 50.000 4.92 0.00 33.57 3.18
868 3223 2.073816 CATAATCACCGCGTTATCCCC 58.926 52.381 4.92 0.00 0.00 4.81
908 3263 2.398498 CTGCTATAAGTACCGCTGCAG 58.602 52.381 10.11 10.11 39.98 4.41
922 3285 3.123620 GCAGACCCAGCAGCTTCG 61.124 66.667 0.00 0.00 0.00 3.79
937 3300 0.389166 CTTCGTCACACAGGCCTCTC 60.389 60.000 0.00 0.00 0.00 3.20
938 3301 0.827925 TTCGTCACACAGGCCTCTCT 60.828 55.000 0.00 0.00 0.00 3.10
940 3303 1.594310 GTCACACAGGCCTCTCTCC 59.406 63.158 0.00 0.00 0.00 3.71
959 3330 4.167113 TCTCCACTCTCCTTGAGCTATACT 59.833 45.833 0.00 0.00 46.41 2.12
960 3331 5.369993 TCTCCACTCTCCTTGAGCTATACTA 59.630 44.000 0.00 0.00 46.41 1.82
975 3351 5.048643 AGCTATACTACATTACACGAGCTGG 60.049 44.000 0.00 0.00 36.44 4.85
1277 3670 0.609957 TCACACGAGACCACCGGTAT 60.610 55.000 6.87 0.00 35.25 2.73
1284 3679 1.549170 GAGACCACCGGTATGTCAGTT 59.451 52.381 28.37 14.72 35.25 3.16
1312 3731 8.327429 GTGTTGATTTCGATTGTTGTTTTCAAT 58.673 29.630 0.00 0.00 42.08 2.57
1338 3763 1.003118 TCGTGGCTGCCTTGATTAACT 59.997 47.619 21.03 0.00 0.00 2.24
1548 4159 5.461078 GCATCTTCCACATGCAAAATGATAC 59.539 40.000 0.00 0.00 45.19 2.24
1558 4170 5.132897 TGCAAAATGATACTTGGTCAACC 57.867 39.130 0.00 0.00 0.00 3.77
1597 4214 9.727627 GCTCAAATAATCTGTAGAAAAATCTGG 57.272 33.333 0.00 0.00 0.00 3.86
1679 4299 0.492737 CTTTCGTTTTCGCGTGCAAC 59.507 50.000 5.77 6.87 43.73 4.17
1694 4315 5.441356 CGCGTGCAACAATTGTTAATAACAG 60.441 40.000 22.87 10.37 38.93 3.16
1843 4473 1.913762 CAACCCGGACCTGGTCTCT 60.914 63.158 25.01 3.84 34.15 3.10
2029 4659 2.045926 GGGCTCGAGTGTGGCATT 60.046 61.111 15.13 0.00 36.01 3.56
2156 4786 6.121613 ACTTCGCTAGTTAGACAGTGTATC 57.878 41.667 0.00 0.00 31.29 2.24
2157 4787 5.066246 ACTTCGCTAGTTAGACAGTGTATCC 59.934 44.000 0.00 0.00 31.29 2.59
2162 4792 2.165845 AGTTAGACAGTGTATCCACGCC 59.834 50.000 0.00 0.00 46.56 5.68
2170 4800 4.141711 ACAGTGTATCCACGCCTTATGAAT 60.142 41.667 0.00 0.00 46.56 2.57
2240 4870 8.700644 GTGATCAGTTGATTCGTATGGTAATAC 58.299 37.037 0.00 0.00 34.37 1.89
2254 4884 6.657836 ATGGTAATACGACTAAGTTGTTGC 57.342 37.500 0.00 0.00 31.92 4.17
2306 4945 9.883142 TCAGATGATATTGTTATGTTGTGTACA 57.117 29.630 0.00 0.00 41.97 2.90
2334 4973 1.855295 TGTATAACAGGCCGACCAGA 58.145 50.000 0.00 0.00 39.06 3.86
2338 4977 0.541063 TAACAGGCCGACCAGAGTGA 60.541 55.000 0.00 0.00 39.06 3.41
2348 4987 2.733542 CGACCAGAGTGATAGCTGTGTG 60.734 54.545 0.00 0.00 0.00 3.82
2381 5020 4.576463 GGGGAAAGTATGATAGCTGTGTTG 59.424 45.833 0.00 0.00 0.00 3.33
2389 5028 2.224499 TGATAGCTGTGTTGCTTGTCCA 60.224 45.455 0.00 0.00 43.74 4.02
2391 5030 1.696063 AGCTGTGTTGCTTGTCCAAT 58.304 45.000 0.00 0.00 40.93 3.16
2394 5033 2.606308 GCTGTGTTGCTTGTCCAATCAG 60.606 50.000 0.00 0.00 35.12 2.90
2395 5034 2.620115 CTGTGTTGCTTGTCCAATCAGT 59.380 45.455 0.00 0.00 31.44 3.41
2400 5039 2.426522 TGCTTGTCCAATCAGTAGTGC 58.573 47.619 0.00 0.00 0.00 4.40
2404 5043 1.555075 TGTCCAATCAGTAGTGCCCTC 59.445 52.381 0.00 0.00 0.00 4.30
2406 5045 2.171448 GTCCAATCAGTAGTGCCCTCAT 59.829 50.000 0.00 0.00 0.00 2.90
2410 5049 0.817654 TCAGTAGTGCCCTCATGTCG 59.182 55.000 0.00 0.00 0.00 4.35
2415 5054 2.434185 TGCCCTCATGTCGCGAAC 60.434 61.111 12.06 6.01 0.00 3.95
2420 5059 1.086696 CCTCATGTCGCGAACCAATT 58.913 50.000 12.06 0.00 0.00 2.32
2421 5060 1.468520 CCTCATGTCGCGAACCAATTT 59.531 47.619 12.06 0.00 0.00 1.82
2422 5061 2.508867 CTCATGTCGCGAACCAATTTG 58.491 47.619 12.06 1.13 0.00 2.32
2425 5064 1.300481 TGTCGCGAACCAATTTGTGA 58.700 45.000 12.06 0.00 36.55 3.58
2428 5067 3.498777 TGTCGCGAACCAATTTGTGATTA 59.501 39.130 12.06 0.00 40.17 1.75
2436 5075 7.627513 GCGAACCAATTTGTGATTAGATGGTTA 60.628 37.037 7.22 0.00 46.52 2.85
2448 5087 7.278868 GTGATTAGATGGTTAGAAGGACACAAG 59.721 40.741 0.00 0.00 0.00 3.16
2453 5092 5.677319 TGGTTAGAAGGACACAAGGATAG 57.323 43.478 0.00 0.00 0.00 2.08
2479 5120 1.280133 TCCAGCTCATCAGGGTTCAAG 59.720 52.381 0.00 0.00 0.00 3.02
2481 5122 2.553904 CCAGCTCATCAGGGTTCAAGTT 60.554 50.000 0.00 0.00 0.00 2.66
2482 5123 2.746362 CAGCTCATCAGGGTTCAAGTTC 59.254 50.000 0.00 0.00 0.00 3.01
2483 5124 2.087646 GCTCATCAGGGTTCAAGTTCC 58.912 52.381 0.00 0.00 0.00 3.62
2485 5126 3.875369 GCTCATCAGGGTTCAAGTTCCAT 60.875 47.826 0.00 0.00 0.00 3.41
2515 5156 5.574055 ACATTTTGTGCTCGCATTATTTCTG 59.426 36.000 0.00 0.00 0.00 3.02
2516 5157 3.763097 TTGTGCTCGCATTATTTCTGG 57.237 42.857 0.00 0.00 0.00 3.86
2528 5169 8.902806 TCGCATTATTTCTGGATTTATTTCAGT 58.097 29.630 0.00 0.00 0.00 3.41
2536 5177 3.945285 TGGATTTATTTCAGTTCTCCGGC 59.055 43.478 0.00 0.00 0.00 6.13
2543 5184 0.108804 TCAGTTCTCCGGCGATGTTC 60.109 55.000 9.30 0.00 0.00 3.18
2556 5197 1.067846 CGATGTTCGTTCAGTGGGAGA 60.068 52.381 0.00 0.00 34.72 3.71
2559 5200 2.036387 TGTTCGTTCAGTGGGAGAAGA 58.964 47.619 0.00 0.00 0.00 2.87
2561 5202 1.699730 TCGTTCAGTGGGAGAAGACA 58.300 50.000 0.00 0.00 0.00 3.41
2565 5206 2.996621 GTTCAGTGGGAGAAGACATTCG 59.003 50.000 0.00 0.00 40.58 3.34
2566 5207 1.550524 TCAGTGGGAGAAGACATTCGG 59.449 52.381 0.00 0.00 40.58 4.30
2567 5208 1.276421 CAGTGGGAGAAGACATTCGGT 59.724 52.381 0.00 0.00 40.58 4.69
2576 5217 2.822306 GACATTCGGTCAACTGCGA 58.178 52.632 0.00 0.00 46.19 5.10
2577 5218 0.716108 GACATTCGGTCAACTGCGAG 59.284 55.000 0.00 0.00 46.19 5.03
2578 5219 0.317160 ACATTCGGTCAACTGCGAGA 59.683 50.000 0.00 0.00 0.00 4.04
2579 5220 0.716108 CATTCGGTCAACTGCGAGAC 59.284 55.000 0.00 0.00 0.00 3.36
2580 5221 0.732880 ATTCGGTCAACTGCGAGACG 60.733 55.000 0.00 0.00 35.63 4.18
2581 5222 2.050351 CGGTCAACTGCGAGACGT 60.050 61.111 0.00 0.00 35.63 4.34
2583 5224 1.286260 GGTCAACTGCGAGACGTCT 59.714 57.895 20.18 20.18 35.63 4.18
2584 5225 0.520404 GGTCAACTGCGAGACGTCTA 59.480 55.000 20.09 1.55 35.63 2.59
2585 5226 1.132643 GGTCAACTGCGAGACGTCTAT 59.867 52.381 20.09 0.00 35.63 1.98
2586 5227 2.177977 GTCAACTGCGAGACGTCTATG 58.822 52.381 20.09 15.26 0.00 2.23
2588 5229 1.135373 CAACTGCGAGACGTCTATGGT 60.135 52.381 20.09 12.07 0.00 3.55
2589 5230 0.452184 ACTGCGAGACGTCTATGGTG 59.548 55.000 20.09 10.42 0.00 4.17
2591 5232 0.450583 TGCGAGACGTCTATGGTGAC 59.549 55.000 20.09 2.83 0.00 3.67
2593 5234 1.132643 GCGAGACGTCTATGGTGACTT 59.867 52.381 20.09 0.00 35.00 3.01
2594 5235 2.415625 GCGAGACGTCTATGGTGACTTT 60.416 50.000 20.09 0.00 35.00 2.66
2595 5236 3.181503 GCGAGACGTCTATGGTGACTTTA 60.182 47.826 20.09 0.00 35.00 1.85
2610 5251 9.739276 ATGGTGACTTTATAAAATCTCAAGACA 57.261 29.630 8.05 5.92 0.00 3.41
2632 5273 4.035792 CACTATACCAACTCAGTCTCTCGG 59.964 50.000 0.00 0.00 0.00 4.63
2634 5275 1.540267 ACCAACTCAGTCTCTCGGAG 58.460 55.000 0.00 0.00 42.53 4.63
2636 5277 1.540267 CAACTCAGTCTCTCGGAGGT 58.460 55.000 4.96 0.00 41.46 3.85
2640 5281 0.251386 TCAGTCTCTCGGAGGTGCTT 60.251 55.000 4.96 0.00 0.00 3.91
2647 5288 0.969894 CTCGGAGGTGCTTATAGGGG 59.030 60.000 0.00 0.00 0.00 4.79
2652 5293 2.158204 GGAGGTGCTTATAGGGGTAGGA 60.158 54.545 0.00 0.00 0.00 2.94
2660 5301 1.048601 ATAGGGGTAGGATGTGCGTG 58.951 55.000 0.00 0.00 0.00 5.34
2661 5302 0.324923 TAGGGGTAGGATGTGCGTGT 60.325 55.000 0.00 0.00 0.00 4.49
2672 5314 3.058570 GGATGTGCGTGTTGTGTTCATAA 60.059 43.478 0.00 0.00 0.00 1.90
2675 5317 1.876799 TGCGTGTTGTGTTCATAAGGG 59.123 47.619 0.00 0.00 0.00 3.95
2677 5319 3.068560 GCGTGTTGTGTTCATAAGGGTA 58.931 45.455 0.00 0.00 0.00 3.69
2685 5327 6.675413 TGTGTTCATAAGGGTAAGTGTACT 57.325 37.500 0.00 0.00 0.00 2.73
2686 5328 7.069877 TGTGTTCATAAGGGTAAGTGTACTT 57.930 36.000 2.51 2.51 39.85 2.24
2688 5330 8.649591 TGTGTTCATAAGGGTAAGTGTACTTTA 58.350 33.333 2.20 0.00 37.40 1.85
2697 5339 7.609056 AGGGTAAGTGTACTTTAGTGTATGTG 58.391 38.462 2.20 0.00 37.40 3.21
2707 5349 6.163476 ACTTTAGTGTATGTGAGCGATTTCA 58.837 36.000 0.00 0.00 0.00 2.69
2716 5358 5.281693 TGTGAGCGATTTCAATTGTACTG 57.718 39.130 5.13 0.00 0.00 2.74
2720 5362 5.238432 TGAGCGATTTCAATTGTACTGTGTT 59.762 36.000 5.13 0.00 0.00 3.32
2724 5366 7.803189 AGCGATTTCAATTGTACTGTGTTAAAG 59.197 33.333 5.13 0.00 0.00 1.85
2726 5368 9.658475 CGATTTCAATTGTACTGTGTTAAAGAA 57.342 29.630 5.13 0.00 0.00 2.52
2745 5387 4.844884 AGAAAAGCAGTACCCTTATGTCC 58.155 43.478 0.00 0.00 0.00 4.02
2746 5388 2.981859 AAGCAGTACCCTTATGTCCG 57.018 50.000 0.00 0.00 0.00 4.79
2772 5414 4.116878 GCAGCCTCGCCTAAAGAG 57.883 61.111 0.00 0.00 35.60 2.85
2781 5423 1.429463 CGCCTAAAGAGAGCGTTGTT 58.571 50.000 0.00 0.00 44.65 2.83
2782 5424 1.126846 CGCCTAAAGAGAGCGTTGTTG 59.873 52.381 0.00 0.00 44.65 3.33
2785 5427 3.123116 GCCTAAAGAGAGCGTTGTTGTAC 59.877 47.826 0.00 0.00 0.00 2.90
2786 5428 4.557205 CCTAAAGAGAGCGTTGTTGTACT 58.443 43.478 0.00 0.00 0.00 2.73
2787 5429 4.386049 CCTAAAGAGAGCGTTGTTGTACTG 59.614 45.833 0.00 0.00 0.00 2.74
2788 5430 1.784525 AGAGAGCGTTGTTGTACTGC 58.215 50.000 0.00 0.00 0.00 4.40
2789 5431 1.068588 AGAGAGCGTTGTTGTACTGCA 59.931 47.619 0.00 0.00 0.00 4.41
2792 5434 0.790207 AGCGTTGTTGTACTGCATCG 59.210 50.000 12.81 12.81 0.00 3.84
2795 5437 1.790043 CGTTGTTGTACTGCATCGTCA 59.210 47.619 0.00 0.00 0.00 4.35
2799 5441 3.398406 TGTTGTACTGCATCGTCACAAT 58.602 40.909 0.00 0.00 32.27 2.71
2800 5442 3.186205 TGTTGTACTGCATCGTCACAATG 59.814 43.478 0.00 0.00 32.27 2.82
2804 5446 0.519792 CTGCATCGTCACAATGTGCG 60.520 55.000 18.87 18.87 38.58 5.34
2807 5449 1.003839 ATCGTCACAATGTGCGGGT 60.004 52.632 22.42 13.23 35.24 5.28
2811 5453 1.302431 TCACAATGTGCGGGTGGAG 60.302 57.895 8.78 0.00 32.98 3.86
2812 5454 1.302431 CACAATGTGCGGGTGGAGA 60.302 57.895 0.00 0.00 0.00 3.71
2813 5455 0.677731 CACAATGTGCGGGTGGAGAT 60.678 55.000 0.00 0.00 0.00 2.75
2814 5456 0.677731 ACAATGTGCGGGTGGAGATG 60.678 55.000 0.00 0.00 0.00 2.90
2815 5457 0.392863 CAATGTGCGGGTGGAGATGA 60.393 55.000 0.00 0.00 0.00 2.92
2816 5458 0.548031 AATGTGCGGGTGGAGATGAT 59.452 50.000 0.00 0.00 0.00 2.45
2945 5587 8.560576 AAAACACTCTCACATAAAACATTTCG 57.439 30.769 0.00 0.00 0.00 3.46
3001 5643 8.673626 AAATGTGTATAGAAAAATGTTGCTCG 57.326 30.769 0.00 0.00 0.00 5.03
3010 5652 6.785191 AGAAAAATGTTGCTCGTGTATATGG 58.215 36.000 0.00 0.00 0.00 2.74
3016 5658 6.117911 TGTTGCTCGTGTATATGGAAAATG 57.882 37.500 0.00 0.00 0.00 2.32
3023 5665 8.648097 GCTCGTGTATATGGAAAATGTATACAG 58.352 37.037 11.91 0.00 40.19 2.74
3073 5715 9.480053 AAAGTTGATCATGTATTCAAACTTTGG 57.520 29.630 13.03 0.00 35.01 3.28
3074 5716 7.092716 AGTTGATCATGTATTCAAACTTTGGC 58.907 34.615 0.00 0.00 33.90 4.52
3075 5717 6.587206 TGATCATGTATTCAAACTTTGGCA 57.413 33.333 1.62 0.00 0.00 4.92
3076 5718 6.389091 TGATCATGTATTCAAACTTTGGCAC 58.611 36.000 1.62 0.00 0.00 5.01
3077 5719 5.132897 TCATGTATTCAAACTTTGGCACC 57.867 39.130 1.62 0.00 0.00 5.01
3078 5720 4.832266 TCATGTATTCAAACTTTGGCACCT 59.168 37.500 1.62 0.00 0.00 4.00
3079 5721 5.304101 TCATGTATTCAAACTTTGGCACCTT 59.696 36.000 1.62 0.00 0.00 3.50
3080 5722 5.606348 TGTATTCAAACTTTGGCACCTTT 57.394 34.783 1.62 0.00 0.00 3.11
3081 5723 5.983540 TGTATTCAAACTTTGGCACCTTTT 58.016 33.333 1.62 0.00 0.00 2.27
3082 5724 5.814705 TGTATTCAAACTTTGGCACCTTTTG 59.185 36.000 1.62 7.30 0.00 2.44
3084 5726 2.093235 TCAAACTTTGGCACCTTTTGGG 60.093 45.455 11.77 0.00 46.08 4.12
3099 5741 6.544928 CCTTTTGGGTTCCTTTGCTATATT 57.455 37.500 0.00 0.00 35.46 1.28
3100 5742 6.946340 CCTTTTGGGTTCCTTTGCTATATTT 58.054 36.000 0.00 0.00 35.46 1.40
3101 5743 8.073467 CCTTTTGGGTTCCTTTGCTATATTTA 57.927 34.615 0.00 0.00 35.46 1.40
3102 5744 8.197439 CCTTTTGGGTTCCTTTGCTATATTTAG 58.803 37.037 0.00 0.00 35.46 1.85
3103 5745 8.887264 TTTTGGGTTCCTTTGCTATATTTAGA 57.113 30.769 0.00 0.00 0.00 2.10
3104 5746 8.519799 TTTGGGTTCCTTTGCTATATTTAGAG 57.480 34.615 0.00 0.00 0.00 2.43
3105 5747 7.446106 TGGGTTCCTTTGCTATATTTAGAGA 57.554 36.000 0.00 0.00 0.00 3.10
3106 5748 7.867921 TGGGTTCCTTTGCTATATTTAGAGAA 58.132 34.615 0.00 0.00 0.00 2.87
3107 5749 8.502738 TGGGTTCCTTTGCTATATTTAGAGAAT 58.497 33.333 0.00 0.00 0.00 2.40
3108 5750 9.355916 GGGTTCCTTTGCTATATTTAGAGAATT 57.644 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.404096 TCGTTCGCAATACAGACAGATTTA 58.596 37.500 0.00 0.00 0.00 1.40
30 31 2.066262 ACACCTTCGTTCGCAATACAG 58.934 47.619 0.00 0.00 0.00 2.74
38 39 1.599992 GAGTCGTACACCTTCGTTCG 58.400 55.000 0.00 0.00 0.00 3.95
66 67 0.032416 ATAGTGGTACAGGAGCCGGT 60.032 55.000 1.90 0.00 41.80 5.28
67 68 0.674534 GATAGTGGTACAGGAGCCGG 59.325 60.000 0.00 0.00 41.80 6.13
79 80 4.916412 CGCGGACGTAGATAGTGG 57.084 61.111 0.00 0.00 33.53 4.00
99 100 3.698263 AACCCCGCCCCCAAAAACA 62.698 57.895 0.00 0.00 0.00 2.83
154 155 6.985188 ATGTGTAGATAAGTGACGCAAAAT 57.015 33.333 0.00 0.00 37.17 1.82
164 165 6.054860 AGACTGGCAAATGTGTAGATAAGT 57.945 37.500 0.00 0.00 0.00 2.24
206 207 4.460263 ACAAACTAGACTGGCAAATGACA 58.540 39.130 0.00 0.00 0.00 3.58
207 208 5.008613 TGAACAAACTAGACTGGCAAATGAC 59.991 40.000 0.00 0.00 0.00 3.06
210 211 5.505654 CGTTGAACAAACTAGACTGGCAAAT 60.506 40.000 0.00 0.00 36.56 2.32
213 214 2.869801 CGTTGAACAAACTAGACTGGCA 59.130 45.455 0.00 0.00 36.56 4.92
214 215 2.349532 GCGTTGAACAAACTAGACTGGC 60.350 50.000 0.00 0.00 36.56 4.85
215 216 2.869801 TGCGTTGAACAAACTAGACTGG 59.130 45.455 0.00 0.00 36.56 4.00
216 217 4.530094 TTGCGTTGAACAAACTAGACTG 57.470 40.909 0.00 0.00 36.56 3.51
218 219 6.806120 AATTTTGCGTTGAACAAACTAGAC 57.194 33.333 0.00 0.00 36.77 2.59
220 221 6.035542 ACCAAATTTTGCGTTGAACAAACTAG 59.964 34.615 3.50 0.00 36.77 2.57
221 222 5.869888 ACCAAATTTTGCGTTGAACAAACTA 59.130 32.000 3.50 0.00 36.77 2.24
224 225 4.093556 GGACCAAATTTTGCGTTGAACAAA 59.906 37.500 3.50 0.00 35.30 2.83
225 226 3.619038 GGACCAAATTTTGCGTTGAACAA 59.381 39.130 3.50 0.00 0.00 2.83
227 228 2.217620 CGGACCAAATTTTGCGTTGAAC 59.782 45.455 3.50 0.00 0.00 3.18
228 229 2.099263 TCGGACCAAATTTTGCGTTGAA 59.901 40.909 3.50 0.00 0.00 2.69
229 230 1.676529 TCGGACCAAATTTTGCGTTGA 59.323 42.857 3.50 3.99 0.00 3.18
231 232 3.378911 AATCGGACCAAATTTTGCGTT 57.621 38.095 3.50 0.00 0.00 4.84
233 234 4.091453 AGTAATCGGACCAAATTTTGCG 57.909 40.909 3.50 2.90 0.00 4.85
234 235 5.106078 TGGTAGTAATCGGACCAAATTTTGC 60.106 40.000 3.50 0.00 40.29 3.68
235 236 6.503589 TGGTAGTAATCGGACCAAATTTTG 57.496 37.500 1.99 1.99 40.29 2.44
237 238 6.184789 ACATGGTAGTAATCGGACCAAATTT 58.815 36.000 0.00 0.00 46.03 1.82
238 239 5.751586 ACATGGTAGTAATCGGACCAAATT 58.248 37.500 0.00 0.00 46.03 1.82
423 428 0.883370 ACGGCTCGTGGAAAAACTCC 60.883 55.000 0.00 0.00 45.64 3.85
470 475 0.251634 TGTACAGCGCATGAATGGGA 59.748 50.000 11.47 0.00 42.66 4.37
476 481 1.020861 CAGCCTTGTACAGCGCATGA 61.021 55.000 11.47 0.00 0.00 3.07
526 534 3.323691 TCATGTGGTTGTACTGCTACTGT 59.676 43.478 0.00 0.00 0.00 3.55
532 540 3.501828 TGAACATCATGTGGTTGTACTGC 59.498 43.478 8.99 0.00 0.00 4.40
533 541 4.378770 GCTGAACATCATGTGGTTGTACTG 60.379 45.833 8.99 2.47 0.00 2.74
601 846 0.318699 GTTCTTTTCAGGGCGTTGGC 60.319 55.000 0.00 0.00 38.90 4.52
704 953 2.096909 GCATGTGGCGTATCGTTATCAC 60.097 50.000 0.00 0.00 0.00 3.06
706 955 1.459592 GGCATGTGGCGTATCGTTATC 59.540 52.381 0.00 0.00 46.16 1.75
707 956 1.070134 AGGCATGTGGCGTATCGTTAT 59.930 47.619 0.64 0.00 46.16 1.89
708 957 0.462375 AGGCATGTGGCGTATCGTTA 59.538 50.000 0.64 0.00 46.16 3.18
710 959 1.227263 GAGGCATGTGGCGTATCGT 60.227 57.895 0.64 0.00 46.16 3.73
711 960 0.530650 AAGAGGCATGTGGCGTATCG 60.531 55.000 0.64 0.00 46.16 2.92
714 963 0.036164 AACAAGAGGCATGTGGCGTA 59.964 50.000 0.64 0.00 46.16 4.42
715 964 0.823356 AAACAAGAGGCATGTGGCGT 60.823 50.000 0.64 0.00 46.16 5.68
716 965 1.164411 TAAACAAGAGGCATGTGGCG 58.836 50.000 0.64 0.00 46.16 5.69
717 966 3.658757 TTTAAACAAGAGGCATGTGGC 57.341 42.857 0.00 0.00 43.74 5.01
740 989 2.423538 GAGGCATGTGGCGTATCTTTTT 59.576 45.455 0.64 0.00 46.16 1.94
741 990 2.017049 GAGGCATGTGGCGTATCTTTT 58.983 47.619 0.64 0.00 46.16 2.27
743 992 0.179045 GGAGGCATGTGGCGTATCTT 60.179 55.000 0.64 0.00 46.16 2.40
744 993 1.337384 TGGAGGCATGTGGCGTATCT 61.337 55.000 0.64 0.00 46.16 1.98
745 994 0.250467 ATGGAGGCATGTGGCGTATC 60.250 55.000 0.64 0.00 46.16 2.24
746 995 0.250467 GATGGAGGCATGTGGCGTAT 60.250 55.000 0.64 0.00 46.16 3.06
747 996 1.146041 GATGGAGGCATGTGGCGTA 59.854 57.895 0.64 0.00 46.16 4.42
748 997 2.124570 GATGGAGGCATGTGGCGT 60.125 61.111 0.64 0.00 46.16 5.68
749 998 3.274586 CGATGGAGGCATGTGGCG 61.275 66.667 0.64 0.00 46.16 5.69
851 3197 4.870190 GGGGATAACGCGGTGATT 57.130 55.556 7.07 0.00 0.00 2.57
889 3244 2.028876 TCTGCAGCGGTACTTATAGCA 58.971 47.619 9.47 0.00 0.00 3.49
908 3263 2.029844 GTGACGAAGCTGCTGGGTC 61.030 63.158 20.26 20.26 0.00 4.46
922 3285 1.188219 TGGAGAGAGGCCTGTGTGAC 61.188 60.000 12.00 0.00 0.00 3.67
937 3300 4.469657 AGTATAGCTCAAGGAGAGTGGAG 58.530 47.826 0.00 0.00 46.47 3.86
938 3301 4.528076 AGTATAGCTCAAGGAGAGTGGA 57.472 45.455 0.00 0.00 46.47 4.02
940 3303 6.892658 ATGTAGTATAGCTCAAGGAGAGTG 57.107 41.667 0.00 0.00 46.47 3.51
959 3330 3.503827 CTGACCAGCTCGTGTAATGTA 57.496 47.619 0.00 0.00 0.00 2.29
960 3331 2.370281 CTGACCAGCTCGTGTAATGT 57.630 50.000 0.00 0.00 0.00 2.71
975 3351 2.096248 ACTAGCTCACCTACAGCTGAC 58.904 52.381 23.35 0.00 46.99 3.51
1277 3670 6.481976 ACAATCGAAATCAACACTAACTGACA 59.518 34.615 0.00 0.00 0.00 3.58
1284 3679 8.184848 TGAAAACAACAATCGAAATCAACACTA 58.815 29.630 0.00 0.00 0.00 2.74
1312 3731 1.074775 AAGGCAGCCACGAATTCCA 59.925 52.632 15.80 0.00 0.00 3.53
1338 3763 2.286713 GCATGCACAAACACGTACTTCA 60.287 45.455 14.21 0.00 0.00 3.02
1558 4170 8.080417 CAGATTATTTGAGCCTGTGATATTTGG 58.920 37.037 0.00 0.00 0.00 3.28
1597 4214 5.028375 GTCAACACTGCTGTACTTTTCAAC 58.972 41.667 0.00 0.00 0.00 3.18
1679 4299 8.994429 TGGGTATTTGCTGTTATTAACAATTG 57.006 30.769 10.32 3.24 41.61 2.32
1843 4473 4.041917 GACACCACCGCGTCCGTA 62.042 66.667 4.92 0.00 0.00 4.02
1861 4491 2.100631 CCACATCGCCGTCCTGAAC 61.101 63.158 0.00 0.00 0.00 3.18
2156 4786 4.442706 AGACACTTATTCATAAGGCGTGG 58.557 43.478 10.63 0.00 43.07 4.94
2157 4787 8.082852 AGTATAGACACTTATTCATAAGGCGTG 58.917 37.037 10.63 4.36 43.07 5.34
2170 4800 7.931407 CCACAATGGCATAAGTATAGACACTTA 59.069 37.037 0.00 0.00 43.31 2.24
2302 4941 7.095774 CGGCCTGTTATACATTATCTTGTGTAC 60.096 40.741 0.00 0.00 34.00 2.90
2306 4945 5.989777 GTCGGCCTGTTATACATTATCTTGT 59.010 40.000 0.00 0.00 0.00 3.16
2313 4952 2.769663 TCTGGTCGGCCTGTTATACATT 59.230 45.455 7.97 0.00 35.49 2.71
2315 4954 1.754803 CTCTGGTCGGCCTGTTATACA 59.245 52.381 7.97 0.00 35.49 2.29
2355 4994 2.632996 CAGCTATCATACTTTCCCCGGA 59.367 50.000 0.73 0.00 0.00 5.14
2367 5006 3.012518 GGACAAGCAACACAGCTATCAT 58.987 45.455 0.00 0.00 45.89 2.45
2381 5020 1.740025 GGCACTACTGATTGGACAAGC 59.260 52.381 0.00 0.00 0.00 4.01
2389 5028 2.159043 CGACATGAGGGCACTACTGATT 60.159 50.000 0.00 0.00 0.00 2.57
2391 5030 0.817654 CGACATGAGGGCACTACTGA 59.182 55.000 0.00 0.00 0.00 3.41
2394 5033 1.878522 CGCGACATGAGGGCACTAC 60.879 63.158 0.00 0.00 0.00 2.73
2395 5034 1.600511 TTCGCGACATGAGGGCACTA 61.601 55.000 9.15 0.00 0.00 2.74
2400 5039 0.744414 ATTGGTTCGCGACATGAGGG 60.744 55.000 9.15 1.41 0.00 4.30
2404 5043 1.978097 CACAAATTGGTTCGCGACATG 59.022 47.619 9.15 2.63 0.00 3.21
2406 5045 1.300481 TCACAAATTGGTTCGCGACA 58.700 45.000 9.15 0.42 0.00 4.35
2410 5049 5.036737 CCATCTAATCACAAATTGGTTCGC 58.963 41.667 0.00 0.00 28.69 4.70
2415 5054 8.408601 CCTTCTAACCATCTAATCACAAATTGG 58.591 37.037 0.00 0.00 0.00 3.16
2420 5059 7.103641 GTGTCCTTCTAACCATCTAATCACAA 58.896 38.462 0.00 0.00 0.00 3.33
2421 5060 6.212589 TGTGTCCTTCTAACCATCTAATCACA 59.787 38.462 0.00 0.00 0.00 3.58
2422 5061 6.640518 TGTGTCCTTCTAACCATCTAATCAC 58.359 40.000 0.00 0.00 0.00 3.06
2425 5064 6.443849 TCCTTGTGTCCTTCTAACCATCTAAT 59.556 38.462 0.00 0.00 0.00 1.73
2428 5067 4.168101 TCCTTGTGTCCTTCTAACCATCT 58.832 43.478 0.00 0.00 0.00 2.90
2436 5075 3.521727 ACCACTATCCTTGTGTCCTTCT 58.478 45.455 0.00 0.00 33.92 2.85
2448 5087 3.834813 TGATGAGCTGGATACCACTATCC 59.165 47.826 0.00 0.43 46.49 2.59
2453 5092 1.071385 CCCTGATGAGCTGGATACCAC 59.929 57.143 0.00 0.00 37.79 4.16
2468 5109 4.993705 AAGTATGGAACTTGAACCCTGA 57.006 40.909 0.00 0.00 46.90 3.86
2479 5120 5.772521 AGCACAAAATGTCAAGTATGGAAC 58.227 37.500 0.00 0.00 0.00 3.62
2481 5122 4.154015 CGAGCACAAAATGTCAAGTATGGA 59.846 41.667 0.00 0.00 0.00 3.41
2482 5123 4.406069 CGAGCACAAAATGTCAAGTATGG 58.594 43.478 0.00 0.00 0.00 2.74
2483 5124 3.848019 GCGAGCACAAAATGTCAAGTATG 59.152 43.478 0.00 0.00 0.00 2.39
2485 5126 2.875317 TGCGAGCACAAAATGTCAAGTA 59.125 40.909 0.00 0.00 0.00 2.24
2497 5138 2.984562 TCCAGAAATAATGCGAGCACA 58.015 42.857 0.00 0.00 0.00 4.57
2498 5139 4.558538 AATCCAGAAATAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
2515 5156 3.002348 CGCCGGAGAACTGAAATAAATCC 59.998 47.826 5.05 0.00 0.00 3.01
2516 5157 3.869246 TCGCCGGAGAACTGAAATAAATC 59.131 43.478 5.05 0.00 0.00 2.17
2528 5169 0.734942 GAACGAACATCGCCGGAGAA 60.735 55.000 13.28 0.00 45.12 2.87
2530 5171 1.413767 CTGAACGAACATCGCCGGAG 61.414 60.000 5.05 0.00 45.12 4.63
2532 5173 1.736645 ACTGAACGAACATCGCCGG 60.737 57.895 0.00 0.00 45.12 6.13
2536 5177 1.067846 TCTCCCACTGAACGAACATCG 60.068 52.381 0.00 0.00 46.93 3.84
2543 5184 2.751166 ATGTCTTCTCCCACTGAACG 57.249 50.000 0.00 0.00 0.00 3.95
2556 5197 1.148310 CGCAGTTGACCGAATGTCTT 58.852 50.000 0.00 0.00 44.75 3.01
2559 5200 0.317160 TCTCGCAGTTGACCGAATGT 59.683 50.000 0.00 0.00 32.56 2.71
2561 5202 0.732880 CGTCTCGCAGTTGACCGAAT 60.733 55.000 0.00 0.00 32.56 3.34
2565 5206 0.520404 TAGACGTCTCGCAGTTGACC 59.480 55.000 23.89 0.00 0.00 4.02
2566 5207 2.177977 CATAGACGTCTCGCAGTTGAC 58.822 52.381 23.89 0.00 0.00 3.18
2567 5208 1.132453 CCATAGACGTCTCGCAGTTGA 59.868 52.381 23.89 1.38 0.00 3.18
2568 5209 1.135373 ACCATAGACGTCTCGCAGTTG 60.135 52.381 23.89 10.81 0.00 3.16
2569 5210 1.135373 CACCATAGACGTCTCGCAGTT 60.135 52.381 23.89 0.00 0.00 3.16
2570 5211 0.452184 CACCATAGACGTCTCGCAGT 59.548 55.000 23.89 12.68 0.00 4.40
2571 5212 0.733150 TCACCATAGACGTCTCGCAG 59.267 55.000 23.89 12.01 0.00 5.18
2573 5214 0.733729 AGTCACCATAGACGTCTCGC 59.266 55.000 23.89 5.65 43.24 5.03
2574 5215 3.489180 AAAGTCACCATAGACGTCTCG 57.511 47.619 23.89 14.51 43.24 4.04
2575 5216 8.922058 TTTTATAAAGTCACCATAGACGTCTC 57.078 34.615 23.89 5.63 43.24 3.36
2576 5217 9.530633 GATTTTATAAAGTCACCATAGACGTCT 57.469 33.333 23.66 23.66 43.24 4.18
2577 5218 9.530633 AGATTTTATAAAGTCACCATAGACGTC 57.469 33.333 19.33 7.70 43.24 4.34
2578 5219 9.530633 GAGATTTTATAAAGTCACCATAGACGT 57.469 33.333 19.33 0.00 43.24 4.34
2579 5220 9.529325 TGAGATTTTATAAAGTCACCATAGACG 57.471 33.333 19.33 0.00 43.24 4.18
2584 5225 9.739276 TGTCTTGAGATTTTATAAAGTCACCAT 57.261 29.630 19.33 2.55 0.00 3.55
2585 5226 8.999431 GTGTCTTGAGATTTTATAAAGTCACCA 58.001 33.333 19.33 14.25 33.60 4.17
2586 5227 9.220767 AGTGTCTTGAGATTTTATAAAGTCACC 57.779 33.333 19.33 12.37 37.51 4.02
2609 5250 4.035792 CCGAGAGACTGAGTTGGTATAGTG 59.964 50.000 0.00 0.00 0.00 2.74
2610 5251 4.080469 TCCGAGAGACTGAGTTGGTATAGT 60.080 45.833 0.00 0.00 0.00 2.12
2617 5258 1.201181 CACCTCCGAGAGACTGAGTTG 59.799 57.143 0.00 0.00 0.00 3.16
2618 5259 1.540267 CACCTCCGAGAGACTGAGTT 58.460 55.000 0.00 0.00 0.00 3.01
2619 5260 0.963355 GCACCTCCGAGAGACTGAGT 60.963 60.000 0.00 0.00 0.00 3.41
2620 5261 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
2632 5273 3.255634 TCCTACCCCTATAAGCACCTC 57.744 52.381 0.00 0.00 0.00 3.85
2634 5275 3.008049 CACATCCTACCCCTATAAGCACC 59.992 52.174 0.00 0.00 0.00 5.01
2636 5277 2.637872 GCACATCCTACCCCTATAAGCA 59.362 50.000 0.00 0.00 0.00 3.91
2640 5281 2.244695 CACGCACATCCTACCCCTATA 58.755 52.381 0.00 0.00 0.00 1.31
2647 5288 1.508632 ACACAACACGCACATCCTAC 58.491 50.000 0.00 0.00 0.00 3.18
2652 5293 3.058293 CCTTATGAACACAACACGCACAT 60.058 43.478 0.00 0.00 0.00 3.21
2660 5301 6.932960 AGTACACTTACCCTTATGAACACAAC 59.067 38.462 0.00 0.00 0.00 3.32
2661 5302 7.069877 AGTACACTTACCCTTATGAACACAA 57.930 36.000 0.00 0.00 0.00 3.33
2672 5314 7.452501 TCACATACACTAAAGTACACTTACCCT 59.547 37.037 0.00 0.00 34.61 4.34
2675 5317 7.008086 CGCTCACATACACTAAAGTACACTTAC 59.992 40.741 0.00 0.00 34.61 2.34
2677 5319 5.862323 CGCTCACATACACTAAAGTACACTT 59.138 40.000 0.00 0.00 37.91 3.16
2685 5327 7.609760 ATTGAAATCGCTCACATACACTAAA 57.390 32.000 0.00 0.00 0.00 1.85
2686 5328 7.119116 ACAATTGAAATCGCTCACATACACTAA 59.881 33.333 13.59 0.00 0.00 2.24
2688 5330 5.412594 ACAATTGAAATCGCTCACATACACT 59.587 36.000 13.59 0.00 0.00 3.55
2697 5339 5.283060 ACACAGTACAATTGAAATCGCTC 57.717 39.130 13.59 0.00 0.00 5.03
2707 5349 8.466798 ACTGCTTTTCTTTAACACAGTACAATT 58.533 29.630 0.00 0.00 32.90 2.32
2716 5358 6.387041 AAGGGTACTGCTTTTCTTTAACAC 57.613 37.500 0.00 0.00 0.00 3.32
2720 5362 6.882678 GGACATAAGGGTACTGCTTTTCTTTA 59.117 38.462 0.00 0.00 0.00 1.85
2724 5366 3.621715 CGGACATAAGGGTACTGCTTTTC 59.378 47.826 0.00 0.00 0.00 2.29
2726 5368 2.093128 CCGGACATAAGGGTACTGCTTT 60.093 50.000 0.00 0.00 0.00 3.51
2767 5409 2.544267 GCAGTACAACAACGCTCTCTTT 59.456 45.455 0.00 0.00 0.00 2.52
2772 5414 1.201812 CGATGCAGTACAACAACGCTC 60.202 52.381 0.00 0.00 0.00 5.03
2781 5423 2.736192 CACATTGTGACGATGCAGTACA 59.264 45.455 11.45 0.00 35.23 2.90
2782 5424 2.474526 GCACATTGTGACGATGCAGTAC 60.475 50.000 20.77 0.00 35.23 2.73
2785 5427 0.519792 CGCACATTGTGACGATGCAG 60.520 55.000 20.77 7.05 36.03 4.41
2786 5428 1.496835 CGCACATTGTGACGATGCA 59.503 52.632 20.77 0.00 36.03 3.96
2787 5429 1.226101 CCGCACATTGTGACGATGC 60.226 57.895 24.92 9.16 36.03 3.91
2788 5430 1.298157 ACCCGCACATTGTGACGATG 61.298 55.000 24.92 11.19 36.03 3.84
2789 5431 1.003839 ACCCGCACATTGTGACGAT 60.004 52.632 24.92 14.96 36.03 3.73
2792 5434 1.577328 CTCCACCCGCACATTGTGAC 61.577 60.000 20.77 10.48 35.23 3.67
2795 5437 0.677731 CATCTCCACCCGCACATTGT 60.678 55.000 0.00 0.00 0.00 2.71
2799 5441 0.327924 AAATCATCTCCACCCGCACA 59.672 50.000 0.00 0.00 0.00 4.57
2800 5442 1.463674 AAAATCATCTCCACCCGCAC 58.536 50.000 0.00 0.00 0.00 5.34
2980 5622 6.599437 ACACGAGCAACATTTTTCTATACAC 58.401 36.000 0.00 0.00 0.00 2.90
2998 5640 9.908152 TCTGTATACATTTTCCATATACACGAG 57.092 33.333 5.91 0.00 37.04 4.18
3050 5692 6.867816 TGCCAAAGTTTGAATACATGATCAAC 59.132 34.615 17.33 3.20 35.42 3.18
3076 5718 6.544928 AATATAGCAAAGGAACCCAAAAGG 57.455 37.500 0.00 0.00 43.78 3.11
3077 5719 8.966868 TCTAAATATAGCAAAGGAACCCAAAAG 58.033 33.333 0.00 0.00 0.00 2.27
3078 5720 8.887264 TCTAAATATAGCAAAGGAACCCAAAA 57.113 30.769 0.00 0.00 0.00 2.44
3079 5721 8.333235 TCTCTAAATATAGCAAAGGAACCCAAA 58.667 33.333 0.00 0.00 0.00 3.28
3080 5722 7.867921 TCTCTAAATATAGCAAAGGAACCCAA 58.132 34.615 0.00 0.00 0.00 4.12
3081 5723 7.446106 TCTCTAAATATAGCAAAGGAACCCA 57.554 36.000 0.00 0.00 0.00 4.51
3082 5724 8.926092 ATTCTCTAAATATAGCAAAGGAACCC 57.074 34.615 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.