Multiple sequence alignment - TraesCS3A01G096100

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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 TraesCS3A01G096100 chr3A 100.000 5217 0 0 1 5217 61321331 61316115 0.000000e+00 9635.0
1 TraesCS3A01G096100 chr3A 84.420 276 43 0 4934 5209 396015227 396015502 6.660000e-69 272.0
2 TraesCS3A01G096100 chr3A 84.756 164 17 3 4692 4848 396013561 396013723 1.940000e-34 158.0
3 TraesCS3A01G096100 chr3A 84.252 127 13 7 5082 5206 714423298 714423177 3.300000e-22 117.0
4 TraesCS3A01G096100 chr3A 75.093 269 56 11 4943 5207 714419888 714419627 1.190000e-21 115.0
5 TraesCS3A01G096100 chr3A 86.598 97 9 4 2762 2856 518640178 518640272 2.570000e-18 104.0
6 TraesCS3A01G096100 chrUn 91.356 2869 139 42 743 3564 39579924 39577118 0.000000e+00 3823.0
7 TraesCS3A01G096100 chrUn 84.743 662 56 25 1 622 39580591 39579935 5.740000e-174 621.0
8 TraesCS3A01G096100 chrUn 87.613 444 42 9 3733 4170 39576784 39576348 2.170000e-138 503.0
9 TraesCS3A01G096100 chrUn 97.491 279 7 0 4931 5209 39538418 39538140 1.310000e-130 477.0
10 TraesCS3A01G096100 chrUn 86.260 393 33 8 4468 4845 39538929 39538543 1.750000e-109 407.0
11 TraesCS3A01G096100 chrUn 87.442 215 19 2 3555 3761 39576997 39576783 1.880000e-59 241.0
12 TraesCS3A01G096100 chr3B 90.144 2567 159 46 253 2774 78234069 78231552 0.000000e+00 3253.0
13 TraesCS3A01G096100 chr3B 86.763 1390 108 32 2842 4170 78231233 78229859 0.000000e+00 1478.0
14 TraesCS3A01G096100 chr3B 88.768 276 31 0 4934 5209 393325265 393325540 6.470000e-89 339.0
15 TraesCS3A01G096100 chr3B 87.209 258 26 6 1 253 78234350 78234095 2.380000e-73 287.0
16 TraesCS3A01G096100 chr3B 82.731 249 22 15 4473 4710 78227227 78226989 8.860000e-48 202.0
17 TraesCS3A01G096100 chr3B 83.537 164 18 4 4692 4849 393316291 393316451 1.510000e-30 145.0
18 TraesCS3A01G096100 chr3D 92.677 1584 85 14 522 2095 48853252 48851690 0.000000e+00 2254.0
19 TraesCS3A01G096100 chr3D 91.912 1051 51 11 2134 3176 48851693 48850669 0.000000e+00 1439.0
20 TraesCS3A01G096100 chr3D 88.825 1047 65 15 3170 4170 48844997 48843957 0.000000e+00 1238.0
21 TraesCS3A01G096100 chr3D 86.082 776 44 26 4465 5215 48842479 48841743 0.000000e+00 776.0
22 TraesCS3A01G096100 chr3D 89.170 277 30 0 4933 5209 298354897 298355173 3.870000e-91 346.0
23 TraesCS3A01G096100 chr3D 82.609 184 24 3 4672 4848 298353026 298353208 6.990000e-34 156.0
24 TraesCS3A01G096100 chr3D 83.448 145 16 8 5065 5206 578926159 578926298 1.520000e-25 128.0
25 TraesCS3A01G096100 chr7B 78.689 427 51 18 273 665 59074758 59075178 1.120000e-61 248.0
26 TraesCS3A01G096100 chr6A 92.045 88 7 0 2763 2850 64260791 64260704 1.970000e-24 124.0
27 TraesCS3A01G096100 chr6B 91.954 87 7 0 2764 2850 512188590 512188504 7.090000e-24 122.0
28 TraesCS3A01G096100 chr2B 93.827 81 5 0 4468 4548 598810152 598810232 7.090000e-24 122.0
29 TraesCS3A01G096100 chr2B 89.412 85 9 0 2766 2850 754008534 754008450 1.990000e-19 108.0
30 TraesCS3A01G096100 chr2B 83.099 71 8 2 662 730 450746557 450746489 1.570000e-05 62.1
31 TraesCS3A01G096100 chr1D 89.535 86 9 0 2761 2846 311756220 311756135 5.520000e-20 110.0
32 TraesCS3A01G096100 chr1D 87.778 90 11 0 2761 2850 320589942 320590031 7.140000e-19 106.0
33 TraesCS3A01G096100 chr1A 88.043 92 9 2 2761 2850 287311436 287311527 1.990000e-19 108.0
34 TraesCS3A01G096100 chr5A 77.387 199 29 12 256 445 42693246 42693055 2.570000e-18 104.0
35 TraesCS3A01G096100 chr5A 77.966 177 29 9 273 445 43252026 43251856 9.240000e-18 102.0


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 TraesCS3A01G096100 chr3A 61316115 61321331 5216 True 9635.0 9635 100.00000 1 5217 1 chr3A.!!$R1 5216
1 TraesCS3A01G096100 chr3A 396013561 396015502 1941 False 215.0 272 84.58800 4692 5209 2 chr3A.!!$F2 517
2 TraesCS3A01G096100 chrUn 39576348 39580591 4243 True 1297.0 3823 87.78850 1 4170 4 chrUn.!!$R2 4169
3 TraesCS3A01G096100 chrUn 39538140 39538929 789 True 442.0 477 91.87550 4468 5209 2 chrUn.!!$R1 741
4 TraesCS3A01G096100 chr3B 78226989 78234350 7361 True 1305.0 3253 86.71175 1 4710 4 chr3B.!!$R1 4709
5 TraesCS3A01G096100 chr3D 48850669 48853252 2583 True 1846.5 2254 92.29450 522 3176 2 chr3D.!!$R2 2654
6 TraesCS3A01G096100 chr3D 48841743 48844997 3254 True 1007.0 1238 87.45350 3170 5215 2 chr3D.!!$R1 2045
7 TraesCS3A01G096100 chr3D 298353026 298355173 2147 False 251.0 346 85.88950 4672 5209 2 chr3D.!!$F2 537

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
214 216 1.064017 ACCCATGCATTGTAACGGGAT 60.064 47.619 21.19 5.86 37.13 3.85 F
1029 1093 0.336737 ACAACCCCAACCTCCAAACA 59.663 50.000 0.00 0.00 0.00 2.83 F
2105 2179 0.467804 GAGCTGTGGGGATTCTCTCC 59.532 60.000 0.00 0.00 44.11 3.71 F
3927 4489 0.442310 TCGCGTGCTGCTAATTTGTC 59.558 50.000 5.77 0.00 43.27 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1239 0.679505 AAACAGCACCACGAGAGCTA 59.320 50.000 0.00 0.00 36.73 3.32 R
2304 2378 1.144057 CCTGTAGCAGCCCCGTTAG 59.856 63.158 0.00 0.00 0.00 2.34 R
4033 4603 0.036732 AGGACATTGTCACGCATGGT 59.963 50.000 18.09 0.00 33.68 3.55 R
5036 10868 1.153369 CCAGCCGTAGACCATGGTG 60.153 63.158 25.52 8.65 35.49 4.17 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
26 27 7.472945 GCTCTAACTTAGCCCATATTGAAGGTA 60.473 40.741 0.00 0.00 33.73 3.08
198 200 1.145571 ACCACTAGCAAAAGGACCCA 58.854 50.000 0.00 0.00 0.00 4.51
202 204 1.075374 ACTAGCAAAAGGACCCATGCA 59.925 47.619 14.16 0.00 41.18 3.96
214 216 1.064017 ACCCATGCATTGTAACGGGAT 60.064 47.619 21.19 5.86 37.13 3.85
215 217 2.031120 CCCATGCATTGTAACGGGATT 58.969 47.619 11.29 0.00 35.57 3.01
216 218 2.430332 CCCATGCATTGTAACGGGATTT 59.570 45.455 11.29 0.00 35.57 2.17
217 219 3.118811 CCCATGCATTGTAACGGGATTTT 60.119 43.478 11.29 0.00 35.57 1.82
218 220 4.502962 CCATGCATTGTAACGGGATTTTT 58.497 39.130 0.00 0.00 0.00 1.94
445 480 2.352651 TGAATCAGCGCACATTTCTAGC 59.647 45.455 11.47 0.00 0.00 3.42
446 481 1.303309 ATCAGCGCACATTTCTAGCC 58.697 50.000 11.47 0.00 0.00 3.93
447 482 1.083806 TCAGCGCACATTTCTAGCCG 61.084 55.000 11.47 0.00 0.00 5.52
448 483 1.079127 AGCGCACATTTCTAGCCGT 60.079 52.632 11.47 0.00 0.00 5.68
451 486 1.075542 CGCACATTTCTAGCCGTGAA 58.924 50.000 0.00 0.00 0.00 3.18
452 487 1.201921 CGCACATTTCTAGCCGTGAAC 60.202 52.381 0.00 0.00 0.00 3.18
454 489 2.420022 GCACATTTCTAGCCGTGAACAT 59.580 45.455 0.00 0.00 0.00 2.71
455 490 3.119849 GCACATTTCTAGCCGTGAACATT 60.120 43.478 0.00 0.00 0.00 2.71
456 491 4.615912 GCACATTTCTAGCCGTGAACATTT 60.616 41.667 0.00 0.00 0.00 2.32
459 494 6.088085 CACATTTCTAGCCGTGAACATTTTTC 59.912 38.462 0.00 0.00 0.00 2.29
561 612 9.821662 AAATAAACTATTTTGTAAGTCACGAGC 57.178 29.630 0.00 0.00 34.91 5.03
562 613 5.857822 AACTATTTTGTAAGTCACGAGCC 57.142 39.130 0.00 0.00 0.00 4.70
563 614 3.924686 ACTATTTTGTAAGTCACGAGCCG 59.075 43.478 0.00 0.00 0.00 5.52
568 619 2.553086 TGTAAGTCACGAGCCGTTTTT 58.447 42.857 0.00 0.00 38.32 1.94
578 630 6.634035 GTCACGAGCCGTTTTTAATTTTTAGT 59.366 34.615 0.00 0.00 38.32 2.24
657 709 9.907576 CATGAATCTCTTTTAATACACGAACTC 57.092 33.333 0.00 0.00 0.00 3.01
783 839 8.600449 TTTCAACCCACAAACATTTTATGATC 57.400 30.769 0.00 0.00 0.00 2.92
846 904 1.809684 GGACCTTTTCGAAGTCCCAG 58.190 55.000 19.43 4.26 43.60 4.45
1029 1093 0.336737 ACAACCCCAACCTCCAAACA 59.663 50.000 0.00 0.00 0.00 2.83
1118 1183 0.671781 CGCCCTGGTTCTCACTCTTG 60.672 60.000 0.00 0.00 0.00 3.02
1121 1186 1.338579 CCCTGGTTCTCACTCTTGCTC 60.339 57.143 0.00 0.00 0.00 4.26
1155 1220 4.409570 CTTCATTTGAGCTCACCATTTCG 58.590 43.478 18.03 1.02 0.00 3.46
1157 1222 3.189080 TCATTTGAGCTCACCATTTCGTG 59.811 43.478 18.03 6.70 34.93 4.35
1174 1239 4.801330 TCGTGGTCACATTACTCAGATT 57.199 40.909 1.90 0.00 0.00 2.40
1209 1274 3.128242 GCTGTTTGCAGATCTAGCATTGT 59.872 43.478 16.96 0.00 45.28 2.71
1500 1568 2.364186 TGGATCTGCTCTCCGGCA 60.364 61.111 0.00 0.00 40.15 5.69
1652 1720 0.733909 CTGTCATCAGCTCGTCGCAA 60.734 55.000 0.00 0.00 42.61 4.85
1654 1722 0.734253 GTCATCAGCTCGTCGCAAGT 60.734 55.000 0.00 0.00 42.61 3.16
1673 1741 5.366460 CAAGTCATCTCCATGAAGTATGCT 58.634 41.667 0.00 0.00 40.90 3.79
1688 1756 1.251251 ATGCTGGTTTGCTGAAGACC 58.749 50.000 0.00 0.00 0.00 3.85
1699 1767 1.742268 GCTGAAGACCAGAAAGGCATC 59.258 52.381 0.00 0.00 45.78 3.91
1796 1864 1.811679 GGTTAGTCCGCAGCAGCTC 60.812 63.158 0.00 0.00 39.10 4.09
1934 2002 8.020819 GTCGTGTATTTCTTGATGGATTTTTCA 58.979 33.333 0.00 0.00 0.00 2.69
2105 2179 0.467804 GAGCTGTGGGGATTCTCTCC 59.532 60.000 0.00 0.00 44.11 3.71
2155 2229 1.599542 GGCGCAGGTTCATCATAGTTC 59.400 52.381 10.83 0.00 0.00 3.01
2224 2298 4.577283 TGTCTGGGTTAAAAAGTACAGCAC 59.423 41.667 0.00 0.00 0.00 4.40
2304 2378 4.217118 AGAGGATTGTCTTTGTGATGCAAC 59.783 41.667 0.00 0.00 36.72 4.17
2430 2507 1.609072 GTCAAGAGGCTGGTTTTCACC 59.391 52.381 0.00 0.00 44.56 4.02
2484 2562 3.961480 TTACCATGTGTCAGAGTGAGG 57.039 47.619 0.00 0.00 0.00 3.86
2528 2606 6.199908 CCAGTTCTAAGCGTCATTCTCAATAG 59.800 42.308 0.00 0.00 0.00 1.73
2529 2607 6.754209 CAGTTCTAAGCGTCATTCTCAATAGT 59.246 38.462 0.00 0.00 0.00 2.12
2534 2612 8.630037 TCTAAGCGTCATTCTCAATAGTCAATA 58.370 33.333 0.00 0.00 0.00 1.90
2535 2613 7.470289 AAGCGTCATTCTCAATAGTCAATAC 57.530 36.000 0.00 0.00 0.00 1.89
2536 2614 5.986135 AGCGTCATTCTCAATAGTCAATACC 59.014 40.000 0.00 0.00 0.00 2.73
2537 2615 5.177696 GCGTCATTCTCAATAGTCAATACCC 59.822 44.000 0.00 0.00 0.00 3.69
2538 2616 6.280643 CGTCATTCTCAATAGTCAATACCCA 58.719 40.000 0.00 0.00 0.00 4.51
2539 2617 6.761242 CGTCATTCTCAATAGTCAATACCCAA 59.239 38.462 0.00 0.00 0.00 4.12
2540 2618 7.442364 CGTCATTCTCAATAGTCAATACCCAAT 59.558 37.037 0.00 0.00 0.00 3.16
2541 2619 8.778358 GTCATTCTCAATAGTCAATACCCAATC 58.222 37.037 0.00 0.00 0.00 2.67
2542 2620 8.493607 TCATTCTCAATAGTCAATACCCAATCA 58.506 33.333 0.00 0.00 0.00 2.57
2543 2621 9.293404 CATTCTCAATAGTCAATACCCAATCAT 57.707 33.333 0.00 0.00 0.00 2.45
2602 2681 4.337274 TCGCTTGCAGTTATGTAGCTAGTA 59.663 41.667 0.00 0.00 35.41 1.82
2721 2808 3.694072 CACTGGAGTTTTGTGAAGAACCA 59.306 43.478 0.00 0.00 33.95 3.67
2774 2862 5.753721 AGAAACTGGCAAATACTCTCTCT 57.246 39.130 0.00 0.00 0.00 3.10
2840 2928 2.785713 ACGTGTTACATTTTGGTGCC 57.214 45.000 0.00 0.00 0.00 5.01
2946 3285 8.311109 TGATTCTTAAGGCCTTTTTGGTTATTC 58.689 33.333 26.08 9.87 38.35 1.75
2950 3289 9.020731 TCTTAAGGCCTTTTTGGTTATTCTTAG 57.979 33.333 26.08 0.00 38.35 2.18
2966 3305 4.963276 TCTTAGACGCCAAATTGGATTG 57.037 40.909 17.47 6.99 40.96 2.67
3079 3420 2.793831 GCCCAACGATTAGCATGGT 58.206 52.632 1.62 1.62 0.00 3.55
3150 3499 8.196771 TGCATAGATTTTTACCATTTGGATGTC 58.803 33.333 3.01 0.00 38.94 3.06
3197 3555 3.585289 TCCCAATCAACCTAAGTAGCACA 59.415 43.478 0.00 0.00 0.00 4.57
3278 3636 2.222027 GTTTACTGACACAAGCTGGCT 58.778 47.619 0.00 0.00 0.00 4.75
3300 3658 0.963962 CAGGCAAGCTGGTCAACAAT 59.036 50.000 0.00 0.00 0.00 2.71
3316 3674 6.824557 GTCAACAATGAGCATTTCAATTTCC 58.175 36.000 0.00 0.00 39.77 3.13
3318 3676 7.172019 GTCAACAATGAGCATTTCAATTTCCTT 59.828 33.333 0.00 0.00 39.77 3.36
3319 3677 7.716123 TCAACAATGAGCATTTCAATTTCCTTT 59.284 29.630 0.00 0.00 39.77 3.11
3321 3679 8.091385 ACAATGAGCATTTCAATTTCCTTTTC 57.909 30.769 0.00 0.00 39.77 2.29
3342 3703 7.713764 TTTCCTTTTTGCTCATTTAAGCTTC 57.286 32.000 0.00 0.00 42.94 3.86
3468 3835 2.472816 GTGTGTTTTAGACCCGACGAA 58.527 47.619 0.00 0.00 0.00 3.85
3518 3905 5.323371 TGCCTTGAATTATCCTTTTTCGG 57.677 39.130 0.00 0.00 0.00 4.30
3519 3906 4.770010 TGCCTTGAATTATCCTTTTTCGGT 59.230 37.500 0.00 0.00 0.00 4.69
3564 4081 7.903145 ACACTGTCTTATTAGTTGATACACCA 58.097 34.615 0.00 0.00 0.00 4.17
3570 4087 8.656849 GTCTTATTAGTTGATACACCAAGTGTG 58.343 37.037 10.55 0.00 46.84 3.82
3714 4233 4.637574 TTGCGTTTGGAATTTTTATGCG 57.362 36.364 0.00 0.00 0.00 4.73
3722 4241 8.217778 CGTTTGGAATTTTTATGCGTTGTAATT 58.782 29.630 0.00 0.00 0.00 1.40
3737 4264 6.586082 GCGTTGTAATTGTCAATGATCCTTTT 59.414 34.615 16.29 0.00 34.80 2.27
3746 4300 5.045872 GTCAATGATCCTTTTTATGCTGCC 58.954 41.667 0.00 0.00 0.00 4.85
3752 4306 4.799564 TCCTTTTTATGCTGCCGAATTT 57.200 36.364 0.00 0.00 0.00 1.82
3812 4370 2.031333 GCTTCACTCTCTGTTTGCTTGG 60.031 50.000 0.00 0.00 0.00 3.61
3825 4386 6.371548 TCTGTTTGCTTGGTGTCTAATGTATC 59.628 38.462 0.00 0.00 0.00 2.24
3826 4387 6.237901 TGTTTGCTTGGTGTCTAATGTATCT 58.762 36.000 0.00 0.00 0.00 1.98
3827 4388 6.149308 TGTTTGCTTGGTGTCTAATGTATCTG 59.851 38.462 0.00 0.00 0.00 2.90
3863 4424 2.162681 ACAGGCCAAGCATTCTACAAC 58.837 47.619 5.01 0.00 0.00 3.32
3927 4489 0.442310 TCGCGTGCTGCTAATTTGTC 59.558 50.000 5.77 0.00 43.27 3.18
3951 4521 1.949525 GAAGCCAGTTTGCTCAGTTGA 59.050 47.619 0.00 0.00 41.80 3.18
3952 4522 2.057137 AGCCAGTTTGCTCAGTTGAA 57.943 45.000 0.00 0.00 36.75 2.69
3958 4528 3.488310 CAGTTTGCTCAGTTGAATTGTGC 59.512 43.478 7.63 7.63 36.04 4.57
4033 4603 1.307355 CGCTTGCATGTGTGGATGGA 61.307 55.000 5.04 0.00 0.00 3.41
4046 4616 0.676466 GGATGGACCATGCGTGACAA 60.676 55.000 12.99 0.00 38.79 3.18
4080 4650 5.349817 GGACTCTTAATCATGTATGCATCGG 59.650 44.000 0.19 0.00 31.99 4.18
4089 4659 4.692155 TCATGTATGCATCGGATTGTCATC 59.308 41.667 0.19 0.00 31.99 2.92
4101 4671 5.363868 TCGGATTGTCATCTATCCTTTGTCT 59.636 40.000 0.00 0.00 41.48 3.41
4115 4685 5.410067 TCCTTTGTCTTTTTGTGAAAGCAG 58.590 37.500 0.00 0.00 0.00 4.24
4151 4721 7.106439 TGGCTTTGTGACTCTAATTTCAAAA 57.894 32.000 0.00 0.00 0.00 2.44
4164 4734 8.894409 TCTAATTTCAAAATACATTGTCTGCG 57.106 30.769 0.00 0.00 0.00 5.18
4170 4740 5.348724 TCAAAATACATTGTCTGCGAGTCTC 59.651 40.000 0.00 0.00 0.00 3.36
4172 4742 2.645730 ACATTGTCTGCGAGTCTCTC 57.354 50.000 0.00 0.00 0.00 3.20
4174 4744 2.560542 ACATTGTCTGCGAGTCTCTCTT 59.439 45.455 0.00 0.00 0.00 2.85
4175 4745 3.759086 ACATTGTCTGCGAGTCTCTCTTA 59.241 43.478 0.00 0.00 0.00 2.10
4176 4746 4.142491 ACATTGTCTGCGAGTCTCTCTTAG 60.142 45.833 0.00 0.00 0.00 2.18
4177 4747 2.360844 TGTCTGCGAGTCTCTCTTAGG 58.639 52.381 0.00 0.00 0.00 2.69
4178 4748 2.027100 TGTCTGCGAGTCTCTCTTAGGA 60.027 50.000 0.00 0.00 0.00 2.94
4180 4750 2.502130 TCTGCGAGTCTCTCTTAGGAGA 59.498 50.000 4.29 4.29 45.30 3.71
4191 4761 4.703379 CTCTTAGGAGAGGCCATGAATT 57.297 45.455 5.01 0.00 44.69 2.17
4192 4762 5.046288 CTCTTAGGAGAGGCCATGAATTT 57.954 43.478 5.01 0.00 44.69 1.82
4193 4763 4.785301 TCTTAGGAGAGGCCATGAATTTG 58.215 43.478 5.01 0.00 40.02 2.32
4194 4764 2.449137 AGGAGAGGCCATGAATTTGG 57.551 50.000 5.01 0.00 40.02 3.28
4195 4765 1.925255 AGGAGAGGCCATGAATTTGGA 59.075 47.619 5.01 0.00 39.25 3.53
4196 4766 2.312741 AGGAGAGGCCATGAATTTGGAA 59.687 45.455 5.01 0.00 39.25 3.53
4197 4767 3.099141 GGAGAGGCCATGAATTTGGAAA 58.901 45.455 5.01 0.00 39.25 3.13
4199 4769 4.382362 GGAGAGGCCATGAATTTGGAAAAG 60.382 45.833 5.01 0.00 39.25 2.27
4203 4774 5.939447 AGGCCATGAATTTGGAAAAGAAAA 58.061 33.333 5.01 0.00 39.25 2.29
4207 4778 8.236586 GGCCATGAATTTGGAAAAGAAAATTAC 58.763 33.333 0.00 0.00 39.25 1.89
4219 4790 9.541143 GGAAAAGAAAATTACAACTTCATGGAA 57.459 29.630 0.00 0.00 0.00 3.53
4235 4806 8.917088 ACTTCATGGAATAATTGTTATCTTGGG 58.083 33.333 0.00 0.00 0.00 4.12
4237 4808 8.696043 TCATGGAATAATTGTTATCTTGGGAG 57.304 34.615 0.00 0.00 0.00 4.30
4238 4809 6.959639 TGGAATAATTGTTATCTTGGGAGC 57.040 37.500 0.00 0.00 0.00 4.70
4240 4811 6.547141 TGGAATAATTGTTATCTTGGGAGCTG 59.453 38.462 0.00 0.00 0.00 4.24
4243 4814 1.965414 TGTTATCTTGGGAGCTGGGA 58.035 50.000 0.00 0.00 0.00 4.37
4244 4815 2.274542 TGTTATCTTGGGAGCTGGGAA 58.725 47.619 0.00 0.00 0.00 3.97
4245 4816 2.647299 TGTTATCTTGGGAGCTGGGAAA 59.353 45.455 0.00 0.00 0.00 3.13
4246 4817 3.075283 TGTTATCTTGGGAGCTGGGAAAA 59.925 43.478 0.00 0.00 0.00 2.29
4247 4818 2.999185 ATCTTGGGAGCTGGGAAAAA 57.001 45.000 0.00 0.00 0.00 1.94
4277 4849 7.590279 TCTTAAAACCATGAAAATTCGAGACC 58.410 34.615 0.00 0.00 0.00 3.85
4279 4851 2.356135 ACCATGAAAATTCGAGACCGG 58.644 47.619 0.00 0.00 36.24 5.28
4287 4859 0.981943 ATTCGAGACCGGTCCCTTTT 59.018 50.000 30.82 12.40 36.24 2.27
4288 4860 0.760572 TTCGAGACCGGTCCCTTTTT 59.239 50.000 30.82 11.57 36.24 1.94
4318 4890 6.713450 TCTTTCTGTTGTAACCCTATTGGAAC 59.287 38.462 0.00 0.00 38.00 3.62
4320 4892 4.040706 TCTGTTGTAACCCTATTGGAACGT 59.959 41.667 0.00 0.00 38.00 3.99
4321 4893 4.066490 TGTTGTAACCCTATTGGAACGTG 58.934 43.478 0.00 0.00 38.00 4.49
4324 4916 3.837146 TGTAACCCTATTGGAACGTGGTA 59.163 43.478 0.00 0.00 38.00 3.25
4329 4921 3.937079 CCCTATTGGAACGTGGTAGAAAC 59.063 47.826 0.00 0.00 35.39 2.78
4332 4924 5.704053 CCTATTGGAACGTGGTAGAAACTTT 59.296 40.000 0.00 0.00 34.57 2.66
4334 4926 5.989551 TTGGAACGTGGTAGAAACTTTAC 57.010 39.130 0.00 0.00 0.00 2.01
4335 4927 5.021033 TGGAACGTGGTAGAAACTTTACA 57.979 39.130 0.00 0.00 0.00 2.41
4343 4935 6.346598 CGTGGTAGAAACTTTACACTGTCATG 60.347 42.308 0.00 0.00 0.00 3.07
4344 4936 5.995282 TGGTAGAAACTTTACACTGTCATGG 59.005 40.000 0.00 0.00 0.00 3.66
4347 4939 7.012989 GGTAGAAACTTTACACTGTCATGGTTT 59.987 37.037 0.00 0.00 0.00 3.27
4349 4941 7.480810 AGAAACTTTACACTGTCATGGTTTTC 58.519 34.615 0.00 0.00 0.00 2.29
4351 4961 6.377327 ACTTTACACTGTCATGGTTTTCTG 57.623 37.500 0.00 0.00 0.00 3.02
4356 4966 4.826733 ACACTGTCATGGTTTTCTGCATTA 59.173 37.500 0.00 0.00 0.00 1.90
4357 4967 5.156355 CACTGTCATGGTTTTCTGCATTAC 58.844 41.667 0.00 0.00 0.00 1.89
4365 4975 4.336993 TGGTTTTCTGCATTACTGAAACGT 59.663 37.500 0.00 0.00 43.42 3.99
4366 4976 4.675114 GGTTTTCTGCATTACTGAAACGTG 59.325 41.667 0.00 0.00 43.42 4.49
4367 4977 5.270853 GTTTTCTGCATTACTGAAACGTGT 58.729 37.500 0.00 0.00 43.42 4.49
4380 5000 5.608676 TGAAACGTGTCAGTTTTGTGTTA 57.391 34.783 3.71 0.00 43.54 2.41
4383 5003 5.616488 AACGTGTCAGTTTTGTGTTAACT 57.384 34.783 7.22 0.00 36.31 2.24
4384 5004 5.616488 ACGTGTCAGTTTTGTGTTAACTT 57.384 34.783 7.22 0.00 33.73 2.66
4385 5005 5.387279 ACGTGTCAGTTTTGTGTTAACTTG 58.613 37.500 7.22 0.00 33.73 3.16
4386 5006 5.179742 ACGTGTCAGTTTTGTGTTAACTTGA 59.820 36.000 7.22 0.00 33.73 3.02
4388 5008 6.032042 CGTGTCAGTTTTGTGTTAACTTGAAC 59.968 38.462 7.22 6.84 33.73 3.18
4389 5009 6.032042 GTGTCAGTTTTGTGTTAACTTGAACG 59.968 38.462 7.22 4.49 33.73 3.95
4390 5010 6.073167 TGTCAGTTTTGTGTTAACTTGAACGA 60.073 34.615 7.22 6.29 33.73 3.85
4391 5011 6.464834 GTCAGTTTTGTGTTAACTTGAACGAG 59.535 38.462 7.22 5.81 33.73 4.18
4392 5012 5.227184 CAGTTTTGTGTTAACTTGAACGAGC 59.773 40.000 7.22 0.00 33.73 5.03
4393 5013 3.955771 TTGTGTTAACTTGAACGAGCC 57.044 42.857 7.22 0.00 31.59 4.70
4395 5015 3.537580 TGTGTTAACTTGAACGAGCCTT 58.462 40.909 7.22 0.00 31.59 4.35
4396 5016 3.558418 TGTGTTAACTTGAACGAGCCTTC 59.442 43.478 7.22 0.00 31.59 3.46
4397 5017 3.808174 GTGTTAACTTGAACGAGCCTTCT 59.192 43.478 7.22 0.00 31.59 2.85
4398 5018 4.272748 GTGTTAACTTGAACGAGCCTTCTT 59.727 41.667 7.22 0.00 31.59 2.52
4399 5019 4.272504 TGTTAACTTGAACGAGCCTTCTTG 59.727 41.667 7.22 0.00 31.59 3.02
4400 5020 2.622064 ACTTGAACGAGCCTTCTTGT 57.378 45.000 0.00 0.00 38.58 3.16
4401 5021 3.746045 ACTTGAACGAGCCTTCTTGTA 57.254 42.857 0.00 0.00 35.92 2.41
4402 5022 4.273148 ACTTGAACGAGCCTTCTTGTAT 57.727 40.909 0.00 0.00 35.92 2.29
4403 5023 4.642429 ACTTGAACGAGCCTTCTTGTATT 58.358 39.130 0.00 0.00 35.92 1.89
4404 5024 4.691216 ACTTGAACGAGCCTTCTTGTATTC 59.309 41.667 0.00 0.00 35.92 1.75
4405 5025 3.596214 TGAACGAGCCTTCTTGTATTCC 58.404 45.455 0.00 0.00 35.92 3.01
4413 5075 4.962995 AGCCTTCTTGTATTCCAGTAGCTA 59.037 41.667 0.00 0.00 0.00 3.32
4429 5091 2.104170 AGCTAGTCAGGCTGTAGAACC 58.896 52.381 15.27 0.37 38.73 3.62
4430 5092 1.825474 GCTAGTCAGGCTGTAGAACCA 59.175 52.381 15.27 0.00 0.00 3.67
4434 5096 2.639839 AGTCAGGCTGTAGAACCATGTT 59.360 45.455 15.27 0.00 0.00 2.71
4439 5101 1.885887 GCTGTAGAACCATGTTGGCAA 59.114 47.619 0.00 0.00 42.67 4.52
4440 5102 2.295909 GCTGTAGAACCATGTTGGCAAA 59.704 45.455 0.00 0.00 42.67 3.68
4442 5104 4.739137 GCTGTAGAACCATGTTGGCAAAAA 60.739 41.667 0.00 0.00 42.67 1.94
4444 5106 5.537188 TGTAGAACCATGTTGGCAAAAATC 58.463 37.500 0.00 0.00 42.67 2.17
4445 5107 4.006780 AGAACCATGTTGGCAAAAATCC 57.993 40.909 0.00 0.00 42.67 3.01
4446 5108 2.857186 ACCATGTTGGCAAAAATCCC 57.143 45.000 0.00 0.00 42.67 3.85
4447 5109 2.337849 ACCATGTTGGCAAAAATCCCT 58.662 42.857 0.00 0.00 42.67 4.20
4449 5111 3.075884 CCATGTTGGCAAAAATCCCTTG 58.924 45.455 0.00 0.00 0.00 3.61
4450 5112 2.926778 TGTTGGCAAAAATCCCTTGG 57.073 45.000 0.00 0.00 0.00 3.61
4453 5115 3.007831 TGTTGGCAAAAATCCCTTGGATC 59.992 43.478 0.00 0.00 42.27 3.36
4454 5116 1.824230 TGGCAAAAATCCCTTGGATCG 59.176 47.619 0.00 0.00 42.27 3.69
4458 5120 3.836949 CAAAAATCCCTTGGATCGTGTG 58.163 45.455 0.00 0.00 42.27 3.82
4463 5125 2.187958 TCCCTTGGATCGTGTGAAGAT 58.812 47.619 0.00 0.00 0.00 2.40
4464 5126 2.093500 TCCCTTGGATCGTGTGAAGATG 60.093 50.000 0.00 0.00 0.00 2.90
4466 5128 1.325640 CTTGGATCGTGTGAAGATGCG 59.674 52.381 0.00 0.00 38.96 4.73
4477 8487 1.486310 TGAAGATGCGTGGGCTAATCT 59.514 47.619 0.00 0.00 40.82 2.40
4483 8493 3.111853 TGCGTGGGCTAATCTAATCAG 57.888 47.619 0.00 0.00 40.82 2.90
4515 8525 2.582498 GGAGATCGTCGCCCAACG 60.582 66.667 0.00 0.00 43.92 4.10
4548 8558 0.258484 TTTCACATGGCCGGATGGAT 59.742 50.000 5.05 0.00 37.49 3.41
4589 8610 2.446036 AGGCGGGCCCTACCTTAG 60.446 66.667 24.19 6.81 44.08 2.18
4598 8619 2.165301 CCTACCTTAGCGCACGCAC 61.165 63.158 18.24 0.00 44.88 5.34
4626 8647 3.003897 GTCCCTCTCTATAAGCTCGTGTG 59.996 52.174 0.00 0.00 0.00 3.82
4641 8662 1.661341 GTGTGATGAGCCATCTGGAC 58.339 55.000 13.94 6.85 41.06 4.02
4683 8713 6.435277 TCGGACTGGTAGTTGTTATTAGTCTT 59.565 38.462 0.00 0.00 34.89 3.01
4702 8732 2.175878 TCAGGCAACAGAAAGAGAGC 57.824 50.000 0.00 0.00 41.41 4.09
4854 8891 0.938713 CTCGTACGTGCTCCTCCTAG 59.061 60.000 16.05 0.00 0.00 3.02
4855 8892 0.251354 TCGTACGTGCTCCTCCTAGT 59.749 55.000 16.05 0.00 0.00 2.57
4861 8898 1.134037 CGTGCTCCTCCTAGTCCTACT 60.134 57.143 0.00 0.00 0.00 2.57
4880 8917 5.121768 CCTACTCCACATTAACTTTTCACCG 59.878 44.000 0.00 0.00 0.00 4.94
4885 8922 4.083484 CCACATTAACTTTTCACCGTCTCC 60.083 45.833 0.00 0.00 0.00 3.71
4886 8923 4.513692 CACATTAACTTTTCACCGTCTCCA 59.486 41.667 0.00 0.00 0.00 3.86
4887 8924 5.181245 CACATTAACTTTTCACCGTCTCCAT 59.819 40.000 0.00 0.00 0.00 3.41
4888 8925 5.768164 ACATTAACTTTTCACCGTCTCCATT 59.232 36.000 0.00 0.00 0.00 3.16
4889 8926 6.264518 ACATTAACTTTTCACCGTCTCCATTT 59.735 34.615 0.00 0.00 0.00 2.32
5045 10877 4.796495 GGGCCGGTCACCATGGTC 62.796 72.222 16.53 4.44 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.379428 AGGAATAAAGTTTATCCAAAGGCAAT 57.621 30.769 18.43 0.09 34.30 3.56
77 78 7.181569 TGGTCAAGACATGATTATACAGTCA 57.818 36.000 0.00 0.00 40.97 3.41
90 91 7.568349 TCAAAGAGCTATATTGGTCAAGACAT 58.432 34.615 16.71 0.00 36.97 3.06
91 92 6.946340 TCAAAGAGCTATATTGGTCAAGACA 58.054 36.000 16.71 0.00 36.97 3.41
180 182 2.094675 CATGGGTCCTTTTGCTAGTGG 58.905 52.381 0.00 0.00 0.00 4.00
194 196 0.329931 TCCCGTTACAATGCATGGGT 59.670 50.000 15.22 12.19 39.93 4.51
245 250 9.720667 CATTATTTCACGAGATTGAGCAAAATA 57.279 29.630 0.00 0.00 0.00 1.40
278 312 9.791820 CAAGATTGCAAATATGTTCATGAGTTA 57.208 29.630 1.71 0.00 0.00 2.24
343 377 9.783081 AAAATATTCTTGGCTTCTGAAAATGTT 57.217 25.926 0.00 0.00 0.00 2.71
445 480 4.300189 TGTTCCAGAAAAATGTTCACGG 57.700 40.909 0.00 0.00 0.00 4.94
446 481 6.826893 AATTGTTCCAGAAAAATGTTCACG 57.173 33.333 0.00 0.00 29.19 4.35
447 482 9.276397 CAAAAATTGTTCCAGAAAAATGTTCAC 57.724 29.630 0.19 0.00 26.93 3.18
448 483 9.224267 TCAAAAATTGTTCCAGAAAAATGTTCA 57.776 25.926 0.19 0.00 26.93 3.18
456 491 8.812329 CGTGTATTTCAAAAATTGTTCCAGAAA 58.188 29.630 0.00 0.00 0.00 2.52
459 494 7.922505 TCGTGTATTTCAAAAATTGTTCCAG 57.077 32.000 0.00 0.00 0.00 3.86
665 717 9.393249 GTTCAGAAAATCATAAAATGTTCACGA 57.607 29.630 0.00 0.00 0.00 4.35
666 718 9.179552 TGTTCAGAAAATCATAAAATGTTCACG 57.820 29.630 0.00 0.00 0.00 4.35
678 732 8.870160 TTGAAAACGAATGTTCAGAAAATCAT 57.130 26.923 0.00 0.00 37.31 2.45
761 815 9.874205 AATAGATCATAAAATGTTTGTGGGTTG 57.126 29.630 0.00 0.00 0.00 3.77
818 875 7.204604 GGACTTCGAAAAGGTCCAAAAATTTA 58.795 34.615 23.24 0.00 36.78 1.40
822 879 3.382227 GGGACTTCGAAAAGGTCCAAAAA 59.618 43.478 26.99 0.00 35.81 1.94
826 884 1.071699 CTGGGACTTCGAAAAGGTCCA 59.928 52.381 26.99 16.61 36.78 4.02
830 888 3.334583 TGATCTGGGACTTCGAAAAGG 57.665 47.619 0.00 0.00 36.78 3.11
836 894 7.265673 TCTACTTTAAATGATCTGGGACTTCG 58.734 38.462 0.00 0.00 0.00 3.79
906 965 6.526325 GCATAACAATTAATTGACGCACTTCA 59.474 34.615 30.18 8.03 40.14 3.02
1029 1093 0.790993 TCAGGGTTCCAGAGGTAGGT 59.209 55.000 0.00 0.00 0.00 3.08
1140 1205 3.231734 CCACGAAATGGTGAGCTCA 57.768 52.632 13.74 13.74 44.46 4.26
1155 1220 5.665459 AGCTAATCTGAGTAATGTGACCAC 58.335 41.667 0.00 0.00 0.00 4.16
1157 1222 6.155475 AGAGCTAATCTGAGTAATGTGACC 57.845 41.667 0.00 0.00 36.69 4.02
1174 1239 0.679505 AAACAGCACCACGAGAGCTA 59.320 50.000 0.00 0.00 36.73 3.32
1209 1274 4.193334 CGCCATCGCTGAGGTCGA 62.193 66.667 0.00 0.00 40.45 4.20
1238 1303 4.452733 CCCCGCTTGTCCGAGTCC 62.453 72.222 0.00 0.00 0.00 3.85
1500 1568 1.556564 CGTATCCGCTTGATGACGTT 58.443 50.000 0.00 0.00 34.76 3.99
1652 1720 4.202336 CCAGCATACTTCATGGAGATGACT 60.202 45.833 8.39 6.35 38.38 3.41
1654 1722 3.713248 ACCAGCATACTTCATGGAGATGA 59.287 43.478 8.39 0.00 36.78 2.92
1673 1741 2.727123 TTCTGGTCTTCAGCAAACCA 57.273 45.000 0.00 0.00 43.06 3.67
1688 1756 2.295885 GAGTCCATGGATGCCTTTCTG 58.704 52.381 19.62 0.00 0.00 3.02
1699 1767 2.598589 CAAAAATGCACGAGTCCATGG 58.401 47.619 4.97 4.97 0.00 3.66
1767 1835 0.831307 GGACTAACCAGAGGGCGAAT 59.169 55.000 0.00 0.00 37.90 3.34
1796 1864 0.813821 TGAGAGTCATGACCTCGCAG 59.186 55.000 25.94 0.00 33.91 5.18
1934 2002 4.929808 GTCACCTTCGACTGATACATGTTT 59.070 41.667 2.30 0.00 32.92 2.83
2105 2179 5.937975 AGGACCCATTCAAATTGGTTATG 57.062 39.130 0.51 0.00 34.83 1.90
2155 2229 3.555795 CCATAGGTCCATCGATTGAGGTG 60.556 52.174 0.00 0.00 0.00 4.00
2224 2298 2.424601 TCCTCACGTCGGTAATAACCTG 59.575 50.000 0.00 0.00 44.35 4.00
2304 2378 1.144057 CCTGTAGCAGCCCCGTTAG 59.856 63.158 0.00 0.00 0.00 2.34
2430 2507 3.784701 AATACAGTACTCACCTCAGCG 57.215 47.619 0.00 0.00 0.00 5.18
2472 2550 6.946340 TCATTTTTATAGCCTCACTCTGACA 58.054 36.000 0.00 0.00 0.00 3.58
2475 2553 7.856145 AACTCATTTTTATAGCCTCACTCTG 57.144 36.000 0.00 0.00 0.00 3.35
2484 2562 8.678199 AGAACTGGCTTAACTCATTTTTATAGC 58.322 33.333 0.00 0.00 0.00 2.97
2573 2651 5.220586 GCTACATAACTGCAAGCGACATTAA 60.221 40.000 0.00 0.00 37.60 1.40
2579 2658 2.672961 AGCTACATAACTGCAAGCGA 57.327 45.000 0.00 0.00 38.86 4.93
2730 2817 5.721960 TCTTCCTAAGATGGCAGTATATCCC 59.278 44.000 0.00 0.00 31.20 3.85
2840 2928 5.786264 ACCTACAAATACATACTCCCTCG 57.214 43.478 0.00 0.00 0.00 4.63
2935 3274 6.636562 TTTGGCGTCTAAGAATAACCAAAA 57.363 33.333 0.00 0.00 41.38 2.44
2946 3285 3.119531 TGCAATCCAATTTGGCGTCTAAG 60.120 43.478 10.76 0.00 37.47 2.18
2950 3289 1.202114 TCTGCAATCCAATTTGGCGTC 59.798 47.619 10.76 0.98 37.47 5.19
2966 3305 1.490910 ACTAGGCCCCAGTAAATCTGC 59.509 52.381 5.81 0.00 42.38 4.26
3061 3402 0.663153 GACCATGCTAATCGTTGGGC 59.337 55.000 0.00 0.00 0.00 5.36
3110 3451 5.700722 ATCTATGCATGCATGTTGTTAGG 57.299 39.130 37.43 18.32 37.82 2.69
3150 3499 2.060050 TACCACCAAAACCCACACTG 57.940 50.000 0.00 0.00 0.00 3.66
3197 3555 1.896220 TGGCTGAAGAAACATTCGCT 58.104 45.000 0.00 0.00 32.80 4.93
3278 3636 1.133945 TGTTGACCAGCTTGCCTGTTA 60.134 47.619 0.00 0.00 40.06 2.41
3300 3658 6.423776 AGGAAAAGGAAATTGAAATGCTCA 57.576 33.333 0.00 0.00 0.00 4.26
3305 3663 8.523915 AGCAAAAAGGAAAAGGAAATTGAAAT 57.476 26.923 0.00 0.00 0.00 2.17
3315 3673 6.707608 AGCTTAAATGAGCAAAAAGGAAAAGG 59.292 34.615 0.00 0.00 45.12 3.11
3316 3674 7.719778 AGCTTAAATGAGCAAAAAGGAAAAG 57.280 32.000 0.00 0.00 45.12 2.27
3318 3676 7.271511 TGAAGCTTAAATGAGCAAAAAGGAAA 58.728 30.769 0.00 0.00 45.12 3.13
3319 3677 6.815089 TGAAGCTTAAATGAGCAAAAAGGAA 58.185 32.000 0.00 0.00 45.12 3.36
3321 3679 5.636543 CCTGAAGCTTAAATGAGCAAAAAGG 59.363 40.000 0.00 0.00 45.12 3.11
3342 3703 8.862325 TTATCATAATAACTATGTTGCCCCTG 57.138 34.615 0.00 0.00 38.87 4.45
3415 3782 0.181114 TGGTGAAACTGCTGCACTCT 59.819 50.000 0.00 0.00 36.74 3.24
3416 3783 0.590195 CTGGTGAAACTGCTGCACTC 59.410 55.000 0.00 0.00 36.74 3.51
3417 3784 0.820891 CCTGGTGAAACTGCTGCACT 60.821 55.000 0.00 0.00 36.74 4.40
3418 3785 1.656441 CCTGGTGAAACTGCTGCAC 59.344 57.895 0.00 0.00 36.74 4.57
3419 3786 2.195567 GCCTGGTGAAACTGCTGCA 61.196 57.895 0.88 0.88 36.74 4.41
3420 3787 2.647297 GCCTGGTGAAACTGCTGC 59.353 61.111 0.00 0.00 36.74 5.25
3468 3835 7.624360 TTTGCTCGTTTCAATAGAATACCAT 57.376 32.000 0.00 0.00 32.89 3.55
3564 4081 2.552315 CACGGCCTTAATCAACACACTT 59.448 45.455 0.00 0.00 0.00 3.16
3570 4087 2.941428 CCAAACACGGCCTTAATCAAC 58.059 47.619 0.00 0.00 0.00 3.18
3596 4113 8.230848 ACCAAATAGGATATCATAATCCACCA 57.769 34.615 4.83 0.00 46.81 4.17
3722 4241 5.394443 GGCAGCATAAAAAGGATCATTGACA 60.394 40.000 0.00 0.00 0.00 3.58
3737 4264 4.038642 GGGGATAAAAATTCGGCAGCATAA 59.961 41.667 0.00 0.00 0.00 1.90
3746 4300 3.492482 GCCATGGTGGGGATAAAAATTCG 60.492 47.826 14.67 0.00 38.19 3.34
3777 4331 2.297597 AGTGAAGCCAGCGATATACTCC 59.702 50.000 0.00 0.00 0.00 3.85
3778 4332 3.254657 AGAGTGAAGCCAGCGATATACTC 59.745 47.826 0.00 0.00 34.92 2.59
3812 4370 4.942852 AGAGCAGCAGATACATTAGACAC 58.057 43.478 0.00 0.00 0.00 3.67
3825 4386 0.179205 GTAAGCGCAAAGAGCAGCAG 60.179 55.000 11.47 0.00 46.13 4.24
3826 4387 0.884259 TGTAAGCGCAAAGAGCAGCA 60.884 50.000 11.47 0.00 46.13 4.41
3827 4388 0.179205 CTGTAAGCGCAAAGAGCAGC 60.179 55.000 11.47 0.00 46.13 5.25
3863 4424 0.379669 GCCTCTTTGGATGATGCACG 59.620 55.000 0.00 0.00 38.35 5.34
3927 4489 1.129998 CTGAGCAAACTGGCTTCATCG 59.870 52.381 0.00 0.00 45.99 3.84
3970 4540 8.311836 AGATTCTACAGACGGTAAAAAGATTCA 58.688 33.333 0.00 0.00 0.00 2.57
4033 4603 0.036732 AGGACATTGTCACGCATGGT 59.963 50.000 18.09 0.00 33.68 3.55
4039 4609 0.608130 TCCTCCAGGACATTGTCACG 59.392 55.000 18.09 8.19 39.78 4.35
4080 4650 9.565213 CAAAAAGACAAAGGATAGATGACAATC 57.435 33.333 0.00 0.00 0.00 2.67
4089 4659 7.202526 TGCTTTCACAAAAAGACAAAGGATAG 58.797 34.615 1.85 0.00 0.00 2.08
4101 4671 3.761218 TGTCAGTCCTGCTTTCACAAAAA 59.239 39.130 0.00 0.00 0.00 1.94
4115 4685 2.024414 ACAAAGCCAAACTGTCAGTCC 58.976 47.619 5.82 0.00 0.00 3.85
4151 4721 3.951037 AGAGAGACTCGCAGACAATGTAT 59.049 43.478 9.00 0.00 35.36 2.29
4157 4727 2.027100 TCCTAAGAGAGACTCGCAGACA 60.027 50.000 9.00 0.00 35.36 3.41
4158 4728 2.612212 CTCCTAAGAGAGACTCGCAGAC 59.388 54.545 9.00 0.00 43.39 3.51
4170 4740 8.328436 TCCAAATTCATGGCCTCTCCTAAGAG 62.328 46.154 3.32 0.00 42.61 2.85
4172 4742 3.887716 CCAAATTCATGGCCTCTCCTAAG 59.112 47.826 3.32 0.00 32.78 2.18
4174 4744 3.122480 TCCAAATTCATGGCCTCTCCTA 58.878 45.455 3.32 0.00 40.46 2.94
4175 4745 1.925255 TCCAAATTCATGGCCTCTCCT 59.075 47.619 3.32 0.00 40.46 3.69
4176 4746 2.442236 TCCAAATTCATGGCCTCTCC 57.558 50.000 3.32 0.00 40.46 3.71
4177 4747 4.463891 TCTTTTCCAAATTCATGGCCTCTC 59.536 41.667 3.32 0.00 40.46 3.20
4178 4748 4.419282 TCTTTTCCAAATTCATGGCCTCT 58.581 39.130 3.32 0.00 40.46 3.69
4180 4750 5.565455 TTTCTTTTCCAAATTCATGGCCT 57.435 34.783 3.32 0.00 40.46 5.19
4181 4751 6.822667 ATTTTCTTTTCCAAATTCATGGCC 57.177 33.333 0.00 0.00 40.46 5.36
4182 4752 8.782144 TGTAATTTTCTTTTCCAAATTCATGGC 58.218 29.630 0.00 0.00 40.46 4.40
4191 4761 9.323985 CCATGAAGTTGTAATTTTCTTTTCCAA 57.676 29.630 0.00 0.00 0.00 3.53
4192 4762 8.700051 TCCATGAAGTTGTAATTTTCTTTTCCA 58.300 29.630 0.00 0.00 0.00 3.53
4193 4763 9.541143 TTCCATGAAGTTGTAATTTTCTTTTCC 57.459 29.630 0.00 0.00 0.00 3.13
4213 4784 7.232127 AGCTCCCAAGATAACAATTATTCCATG 59.768 37.037 0.00 0.00 0.00 3.66
4214 4785 7.232127 CAGCTCCCAAGATAACAATTATTCCAT 59.768 37.037 0.00 0.00 0.00 3.41
4219 4790 5.134339 TCCCAGCTCCCAAGATAACAATTAT 59.866 40.000 0.00 0.00 0.00 1.28
4222 4793 2.852449 TCCCAGCTCCCAAGATAACAAT 59.148 45.455 0.00 0.00 0.00 2.71
4225 4796 3.366052 TTTCCCAGCTCCCAAGATAAC 57.634 47.619 0.00 0.00 0.00 1.89
4226 4797 4.396357 TTTTTCCCAGCTCCCAAGATAA 57.604 40.909 0.00 0.00 0.00 1.75
4250 4821 9.626045 GTCTCGAATTTTCATGGTTTTAAGATT 57.374 29.630 0.00 0.00 0.00 2.40
4252 4823 7.572353 CGGTCTCGAATTTTCATGGTTTTAAGA 60.572 37.037 0.00 0.00 39.00 2.10
4253 4824 6.523201 CGGTCTCGAATTTTCATGGTTTTAAG 59.477 38.462 0.00 0.00 39.00 1.85
4258 4830 2.747446 CCGGTCTCGAATTTTCATGGTT 59.253 45.455 0.00 0.00 39.00 3.67
4289 4861 8.417884 CCAATAGGGTTACAACAGAAAGAAAAA 58.582 33.333 0.00 0.00 0.00 1.94
4291 4863 7.291566 TCCAATAGGGTTACAACAGAAAGAAA 58.708 34.615 0.00 0.00 38.11 2.52
4292 4864 6.843752 TCCAATAGGGTTACAACAGAAAGAA 58.156 36.000 0.00 0.00 38.11 2.52
4293 4865 6.442541 TCCAATAGGGTTACAACAGAAAGA 57.557 37.500 0.00 0.00 38.11 2.52
4294 4866 6.348213 CGTTCCAATAGGGTTACAACAGAAAG 60.348 42.308 0.00 0.00 38.11 2.62
4295 4867 5.470777 CGTTCCAATAGGGTTACAACAGAAA 59.529 40.000 0.00 0.00 38.11 2.52
4297 4869 4.040706 ACGTTCCAATAGGGTTACAACAGA 59.959 41.667 0.00 0.00 38.11 3.41
4299 4871 4.066490 CACGTTCCAATAGGGTTACAACA 58.934 43.478 0.00 0.00 38.11 3.33
4300 4872 3.437741 CCACGTTCCAATAGGGTTACAAC 59.562 47.826 0.00 0.00 38.11 3.32
4302 4874 2.638855 ACCACGTTCCAATAGGGTTACA 59.361 45.455 0.00 0.00 38.11 2.41
4303 4875 3.339253 ACCACGTTCCAATAGGGTTAC 57.661 47.619 0.00 0.00 38.11 2.50
4304 4876 4.352009 TCTACCACGTTCCAATAGGGTTA 58.648 43.478 0.00 0.00 38.11 2.85
4306 4878 2.823959 TCTACCACGTTCCAATAGGGT 58.176 47.619 0.00 0.00 38.11 4.34
4308 4880 4.828829 AGTTTCTACCACGTTCCAATAGG 58.171 43.478 0.00 0.00 0.00 2.57
4318 4890 5.045215 TGACAGTGTAAAGTTTCTACCACG 58.955 41.667 0.00 0.00 0.00 4.94
4320 4892 5.995282 CCATGACAGTGTAAAGTTTCTACCA 59.005 40.000 0.00 0.00 0.00 3.25
4321 4893 5.995897 ACCATGACAGTGTAAAGTTTCTACC 59.004 40.000 0.00 0.00 0.00 3.18
4324 4916 7.339466 AGAAAACCATGACAGTGTAAAGTTTCT 59.661 33.333 10.91 10.86 0.00 2.52
4329 4921 5.215160 GCAGAAAACCATGACAGTGTAAAG 58.785 41.667 0.00 0.00 0.00 1.85
4332 4924 3.814625 TGCAGAAAACCATGACAGTGTA 58.185 40.909 0.00 0.00 0.00 2.90
4334 4926 3.928727 ATGCAGAAAACCATGACAGTG 57.071 42.857 0.00 0.00 0.00 3.66
4335 4927 5.048504 CAGTAATGCAGAAAACCATGACAGT 60.049 40.000 0.00 0.00 0.00 3.55
4343 4935 4.675114 CACGTTTCAGTAATGCAGAAAACC 59.325 41.667 0.00 0.00 34.99 3.27
4344 4936 5.270853 ACACGTTTCAGTAATGCAGAAAAC 58.729 37.500 0.00 0.00 34.99 2.43
4347 4939 4.123506 TGACACGTTTCAGTAATGCAGAA 58.876 39.130 0.00 0.00 0.00 3.02
4349 4941 4.057730 CTGACACGTTTCAGTAATGCAG 57.942 45.455 21.03 0.61 38.61 4.41
4365 4975 6.073167 TCGTTCAAGTTAACACAAAACTGACA 60.073 34.615 8.61 0.00 37.26 3.58
4366 4976 6.308675 TCGTTCAAGTTAACACAAAACTGAC 58.691 36.000 8.61 0.00 37.26 3.51
4367 4977 6.483385 TCGTTCAAGTTAACACAAAACTGA 57.517 33.333 8.61 6.16 37.26 3.41
4371 4981 4.396790 AGGCTCGTTCAAGTTAACACAAAA 59.603 37.500 8.61 0.00 0.00 2.44
4373 4993 3.537580 AGGCTCGTTCAAGTTAACACAA 58.462 40.909 8.61 0.00 0.00 3.33
4377 4997 4.272748 ACAAGAAGGCTCGTTCAAGTTAAC 59.727 41.667 0.00 0.00 0.00 2.01
4380 5000 2.919228 ACAAGAAGGCTCGTTCAAGTT 58.081 42.857 5.31 0.00 0.00 2.66
4383 5003 4.000988 GGAATACAAGAAGGCTCGTTCAA 58.999 43.478 5.31 0.00 0.00 2.69
4384 5004 3.007506 TGGAATACAAGAAGGCTCGTTCA 59.992 43.478 5.31 0.00 0.00 3.18
4385 5005 3.596214 TGGAATACAAGAAGGCTCGTTC 58.404 45.455 0.00 0.00 0.00 3.95
4386 5006 3.008049 ACTGGAATACAAGAAGGCTCGTT 59.992 43.478 0.00 0.00 0.00 3.85
4388 5008 3.252974 ACTGGAATACAAGAAGGCTCG 57.747 47.619 0.00 0.00 0.00 5.03
4389 5009 4.123506 GCTACTGGAATACAAGAAGGCTC 58.876 47.826 0.00 0.00 0.00 4.70
4390 5010 3.777522 AGCTACTGGAATACAAGAAGGCT 59.222 43.478 0.00 0.00 0.00 4.58
4391 5011 4.143986 AGCTACTGGAATACAAGAAGGC 57.856 45.455 0.00 0.00 0.00 4.35
4392 5012 6.096987 TGACTAGCTACTGGAATACAAGAAGG 59.903 42.308 0.00 0.00 0.00 3.46
4393 5013 7.101652 TGACTAGCTACTGGAATACAAGAAG 57.898 40.000 0.00 0.00 0.00 2.85
4395 5015 5.594725 CCTGACTAGCTACTGGAATACAAGA 59.405 44.000 2.15 0.00 0.00 3.02
4396 5016 5.737635 GCCTGACTAGCTACTGGAATACAAG 60.738 48.000 10.40 0.00 0.00 3.16
4397 5017 4.099573 GCCTGACTAGCTACTGGAATACAA 59.900 45.833 10.40 0.00 0.00 2.41
4398 5018 3.637229 GCCTGACTAGCTACTGGAATACA 59.363 47.826 10.40 0.00 0.00 2.29
4399 5019 3.892588 AGCCTGACTAGCTACTGGAATAC 59.107 47.826 10.40 0.00 39.29 1.89
4400 5020 3.891977 CAGCCTGACTAGCTACTGGAATA 59.108 47.826 10.40 0.00 38.95 1.75
4401 5021 2.697751 CAGCCTGACTAGCTACTGGAAT 59.302 50.000 10.40 0.00 38.95 3.01
4402 5022 2.103373 CAGCCTGACTAGCTACTGGAA 58.897 52.381 10.40 0.00 38.95 3.53
4403 5023 1.006043 ACAGCCTGACTAGCTACTGGA 59.994 52.381 0.00 0.00 38.95 3.86
4404 5024 1.479709 ACAGCCTGACTAGCTACTGG 58.520 55.000 0.00 7.17 38.95 4.00
4405 5025 3.546724 TCTACAGCCTGACTAGCTACTG 58.453 50.000 0.00 5.49 38.95 2.74
4413 5075 2.260822 ACATGGTTCTACAGCCTGACT 58.739 47.619 0.00 0.00 0.00 3.41
4429 5091 3.075884 CCAAGGGATTTTTGCCAACATG 58.924 45.455 0.00 0.00 0.00 3.21
4430 5092 2.978278 TCCAAGGGATTTTTGCCAACAT 59.022 40.909 0.00 0.00 0.00 2.71
4434 5096 1.824230 CGATCCAAGGGATTTTTGCCA 59.176 47.619 0.00 0.00 43.27 4.92
4439 5101 3.433306 TCACACGATCCAAGGGATTTT 57.567 42.857 0.00 0.00 43.27 1.82
4440 5102 3.009033 TCTTCACACGATCCAAGGGATTT 59.991 43.478 0.00 0.00 43.27 2.17
4442 5104 2.187958 TCTTCACACGATCCAAGGGAT 58.812 47.619 0.00 0.00 46.28 3.85
4444 5106 2.283298 CATCTTCACACGATCCAAGGG 58.717 52.381 0.00 0.00 0.00 3.95
4445 5107 1.667724 GCATCTTCACACGATCCAAGG 59.332 52.381 0.00 0.00 0.00 3.61
4446 5108 1.325640 CGCATCTTCACACGATCCAAG 59.674 52.381 0.00 0.00 0.00 3.61
4447 5109 1.337728 ACGCATCTTCACACGATCCAA 60.338 47.619 0.00 0.00 0.00 3.53
4449 5111 0.647410 CACGCATCTTCACACGATCC 59.353 55.000 0.00 0.00 0.00 3.36
4450 5112 0.647410 CCACGCATCTTCACACGATC 59.353 55.000 0.00 0.00 0.00 3.69
4453 5115 3.027170 GCCCACGCATCTTCACACG 62.027 63.158 0.00 0.00 34.03 4.49
4454 5116 0.391130 TAGCCCACGCATCTTCACAC 60.391 55.000 0.00 0.00 37.52 3.82
4458 5120 2.246719 AGATTAGCCCACGCATCTTC 57.753 50.000 0.00 0.00 37.52 2.87
4463 5125 2.806745 GCTGATTAGATTAGCCCACGCA 60.807 50.000 0.00 0.00 36.02 5.24
4464 5126 1.801178 GCTGATTAGATTAGCCCACGC 59.199 52.381 0.00 0.00 36.02 5.34
4466 5128 2.802816 CGTGCTGATTAGATTAGCCCAC 59.197 50.000 2.78 0.00 40.80 4.61
4477 8487 0.824109 CCTGTCCCTCGTGCTGATTA 59.176 55.000 0.00 0.00 0.00 1.75
4483 8493 2.680352 TCCTCCTGTCCCTCGTGC 60.680 66.667 0.00 0.00 0.00 5.34
4515 8525 2.351210 GAAATGGCGATCGCGTGC 60.351 61.111 31.76 19.61 43.06 5.34
4548 8558 0.537188 GCCTCAGATTCCGTGGAGAA 59.463 55.000 0.00 0.00 0.00 2.87
4582 8603 1.153901 GAGTGCGTGCGCTAAGGTA 60.154 57.895 17.49 0.00 42.51 3.08
4598 8619 3.078837 GCTTATAGAGAGGGACGGAGAG 58.921 54.545 0.00 0.00 0.00 3.20
4626 8647 0.683973 ATCCGTCCAGATGGCTCATC 59.316 55.000 0.66 6.98 40.80 2.92
4632 8653 1.898472 AGATGCTATCCGTCCAGATGG 59.102 52.381 0.00 0.00 38.85 3.51
4636 8657 1.332195 TCCAGATGCTATCCGTCCAG 58.668 55.000 0.00 0.00 0.00 3.86
4637 8658 1.895798 GATCCAGATGCTATCCGTCCA 59.104 52.381 0.00 0.00 0.00 4.02
4641 8662 1.133982 CCGAGATCCAGATGCTATCCG 59.866 57.143 0.00 0.00 0.00 4.18
4683 8713 1.606480 CGCTCTCTTTCTGTTGCCTGA 60.606 52.381 0.00 0.00 0.00 3.86
4763 8794 1.298190 GTAGTCGTCGGCGGATGTC 60.298 63.158 10.62 7.83 38.89 3.06
4764 8795 2.796651 GTAGTCGTCGGCGGATGT 59.203 61.111 10.62 0.00 38.89 3.06
4854 8891 6.148976 GGTGAAAAGTTAATGTGGAGTAGGAC 59.851 42.308 0.00 0.00 0.00 3.85
4855 8892 6.235664 GGTGAAAAGTTAATGTGGAGTAGGA 58.764 40.000 0.00 0.00 0.00 2.94
4861 8898 4.710324 AGACGGTGAAAAGTTAATGTGGA 58.290 39.130 0.00 0.00 0.00 4.02
4880 8917 9.298774 GATTTCTGAATCAAATGAAATGGAGAC 57.701 33.333 11.90 0.00 41.10 3.36
4885 8922 7.274904 AGTGCGATTTCTGAATCAAATGAAATG 59.725 33.333 11.90 7.24 41.43 2.32
4886 8923 7.318141 AGTGCGATTTCTGAATCAAATGAAAT 58.682 30.769 8.18 8.18 41.43 2.17
4887 8924 6.680810 AGTGCGATTTCTGAATCAAATGAAA 58.319 32.000 0.00 0.00 41.43 2.69
4888 8925 6.258230 AGTGCGATTTCTGAATCAAATGAA 57.742 33.333 0.00 0.00 41.43 2.57
4889 8926 5.885230 AGTGCGATTTCTGAATCAAATGA 57.115 34.783 0.00 0.00 41.43 2.57
5036 10868 1.153369 CCAGCCGTAGACCATGGTG 60.153 63.158 25.52 8.65 35.49 4.17


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

AutoCloner maintained by Alex Coulton.