Multiple sequence alignment - TraesCS3D01G307800

Loading Multiple Alignment...

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 TraesCS3D01G307800 chr3D 100.000 5507 0 0 1 5507 421656883 421662389 0.000000e+00 10170.0
1 TraesCS3D01G307800 chr3D 89.600 125 13 0 1 125 378665978 378666102 5.710000e-35 159.0
2 TraesCS3D01G307800 chr3A 92.750 2869 118 40 155 2966 529219085 529216250 0.000000e+00 4063.0
3 TraesCS3D01G307800 chr3A 97.100 1276 32 2 3246 4520 529215782 529214511 0.000000e+00 2146.0
4 TraesCS3D01G307800 chr3A 90.769 390 24 2 5130 5507 529214504 529214115 1.370000e-140 510.0
5 TraesCS3D01G307800 chr3A 95.223 314 12 1 2967 3277 529216193 529215880 1.380000e-135 494.0
6 TraesCS3D01G307800 chr3A 97.059 34 1 0 128 161 201776959 201776926 2.140000e-04 58.4
7 TraesCS3D01G307800 chr3A 97.059 34 1 0 128 161 201857377 201857344 2.140000e-04 58.4
8 TraesCS3D01G307800 chr3B 95.113 1596 56 9 3085 4678 548886978 548888553 0.000000e+00 2495.0
9 TraesCS3D01G307800 chr3B 95.486 1152 43 7 1781 2929 548885833 548886978 0.000000e+00 1831.0
10 TraesCS3D01G307800 chr3B 94.978 896 19 7 863 1747 548884958 548885838 0.000000e+00 1382.0
11 TraesCS3D01G307800 chr3B 88.960 779 55 18 122 875 548954681 548955453 0.000000e+00 933.0
12 TraesCS3D01G307800 chr3B 83.673 490 57 8 5013 5485 549022037 549022520 1.820000e-119 440.0
13 TraesCS3D01G307800 chr3B 93.600 125 8 0 1 125 548954510 548954634 2.620000e-43 187.0
14 TraesCS3D01G307800 chr3B 85.000 180 26 1 4829 5008 549021823 549022001 1.220000e-41 182.0
15 TraesCS3D01G307800 chr3B 89.683 126 13 0 1 126 322726111 322726236 1.590000e-35 161.0
16 TraesCS3D01G307800 chr3B 90.244 123 12 0 5 127 385459421 385459299 1.590000e-35 161.0
17 TraesCS3D01G307800 chr4B 91.200 125 11 0 4 128 658985698 658985574 2.640000e-38 171.0
18 TraesCS3D01G307800 chr7D 91.129 124 11 0 4 127 425034500 425034377 9.490000e-38 169.0
19 TraesCS3D01G307800 chr7D 92.500 40 1 2 5084 5123 130233563 130233526 7.710000e-04 56.5
20 TraesCS3D01G307800 chr4D 90.551 127 12 0 1 127 310493334 310493460 9.490000e-38 169.0
21 TraesCS3D01G307800 chr5D 91.129 124 10 1 4 127 102450891 102450769 3.410000e-37 167.0
22 TraesCS3D01G307800 chr5D 82.682 179 27 4 4831 5008 63108187 63108362 7.390000e-34 156.0
23 TraesCS3D01G307800 chr5D 81.955 133 23 1 4832 4964 420709158 420709289 1.620000e-20 111.0
24 TraesCS3D01G307800 chr5D 100.000 28 0 0 5087 5114 88359270 88359243 1.000000e-02 52.8
25 TraesCS3D01G307800 chr6D 90.400 125 10 2 4 127 102492821 102492944 4.410000e-36 163.0
26 TraesCS3D01G307800 chr5B 80.769 182 25 9 4832 5008 9048095 9047919 3.460000e-27 134.0
27 TraesCS3D01G307800 chr5B 80.337 178 33 2 4832 5009 506786409 506786584 3.460000e-27 134.0
28 TraesCS3D01G307800 chr5A 79.888 179 25 7 4833 5008 552079987 552080157 2.690000e-23 121.0
29 TraesCS3D01G307800 chr4A 78.846 156 28 5 4856 5009 717000940 717001092 3.510000e-17 100.0
30 TraesCS3D01G307800 chr6A 79.070 129 13 6 42 157 330023179 330023052 5.920000e-10 76.8
31 TraesCS3D01G307800 chr2A 100.000 33 0 0 128 160 151202333 151202301 1.660000e-05 62.1
32 TraesCS3D01G307800 chr7B 97.222 36 0 1 5080 5114 531662175 531662210 5.960000e-05 60.2
33 TraesCS3D01G307800 chr2D 92.683 41 2 1 122 161 219672377 219672337 2.140000e-04 58.4
34 TraesCS3D01G307800 chr2D 94.595 37 0 2 128 162 129701145 129701109 7.710000e-04 56.5
35 TraesCS3D01G307800 chr1D 100.000 31 0 0 128 158 111497860 111497830 2.140000e-04 58.4
36 TraesCS3D01G307800 chr1D 100.000 31 0 0 128 158 442941157 442941127 2.140000e-04 58.4


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 TraesCS3D01G307800 chr3D 421656883 421662389 5506 False 10170.000000 10170 100.000000 1 5507 1 chr3D.!!$F2 5506
1 TraesCS3D01G307800 chr3A 529214115 529219085 4970 True 1803.250000 4063 93.960500 155 5507 4 chr3A.!!$R3 5352
2 TraesCS3D01G307800 chr3B 548884958 548888553 3595 False 1902.666667 2495 95.192333 863 4678 3 chr3B.!!$F2 3815
3 TraesCS3D01G307800 chr3B 548954510 548955453 943 False 560.000000 933 91.280000 1 875 2 chr3B.!!$F3 874
4 TraesCS3D01G307800 chr3B 549021823 549022520 697 False 311.000000 440 84.336500 4829 5485 2 chr3B.!!$F4 656

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
266 318 1.749063 TGTATCTCGCAGTGTACCAGG 59.251 52.381 0.0 0.0 0.00 4.45 F
1018 1109 1.117150 TCCCGATCCCCGAGTTAAAG 58.883 55.000 0.0 0.0 41.76 1.85 F
1337 1434 1.920325 CAGGCAAGAGTCTCCCCCA 60.920 63.158 0.0 0.0 0.00 4.96 F
2965 3085 1.436600 AAGCATCACACGAAGCTCAG 58.563 50.000 0.0 0.0 45.15 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1645 1.234615 TAACGCAGCTGAAGGCAACC 61.235 55.0 20.43 0.0 44.79 3.77 R
2585 2697 0.533032 GCTAGAGCTCCTGGTCGTTT 59.467 55.0 10.93 0.0 44.65 3.60 R
3022 3199 0.603065 GGGAAACATCCAACAGGCAC 59.397 55.0 0.00 0.0 0.00 5.01 R
4689 5000 0.035881 CTCCAGCATGCATATCCGGT 59.964 55.0 21.98 0.0 31.97 5.28 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
29 30 7.597743 AGTCTTCACATCAATTTCATCAAAAGC 59.402 33.333 0.00 0.00 0.00 3.51
30 31 6.869913 TCTTCACATCAATTTCATCAAAAGCC 59.130 34.615 0.00 0.00 0.00 4.35
31 32 6.099159 TCACATCAATTTCATCAAAAGCCA 57.901 33.333 0.00 0.00 0.00 4.75
125 126 6.126739 ACCAAATCTTCAGGGACTATAACTCC 60.127 42.308 0.00 0.00 36.02 3.85
168 220 6.491394 TGATGCACTTACACTTTACAACAAC 58.509 36.000 0.00 0.00 0.00 3.32
253 305 9.615295 GAAAGAAACTCTATACGGATGTATCTC 57.385 37.037 0.00 0.00 41.50 2.75
266 318 1.749063 TGTATCTCGCAGTGTACCAGG 59.251 52.381 0.00 0.00 0.00 4.45
356 408 5.721960 TGTTGAAGGAATAGAGTAGGAGCTT 59.278 40.000 0.00 0.00 0.00 3.74
424 481 2.098607 CACACATGCATCTGATGGGTTC 59.901 50.000 18.60 3.23 35.16 3.62
425 482 2.025605 ACACATGCATCTGATGGGTTCT 60.026 45.455 18.60 0.00 33.48 3.01
426 483 2.617308 CACATGCATCTGATGGGTTCTC 59.383 50.000 18.60 2.20 0.00 2.87
427 484 2.508716 ACATGCATCTGATGGGTTCTCT 59.491 45.455 18.60 0.00 0.00 3.10
428 485 2.996249 TGCATCTGATGGGTTCTCTC 57.004 50.000 18.60 0.84 0.00 3.20
429 486 2.475155 TGCATCTGATGGGTTCTCTCT 58.525 47.619 18.60 0.00 0.00 3.10
430 487 2.169978 TGCATCTGATGGGTTCTCTCTG 59.830 50.000 18.60 0.00 0.00 3.35
431 488 2.170187 GCATCTGATGGGTTCTCTCTGT 59.830 50.000 18.60 0.00 0.00 3.41
478 536 2.358737 GCGACCCCCTCACAACTG 60.359 66.667 0.00 0.00 0.00 3.16
679 748 9.952030 TTTGAAATTTGGGTCTTTTTAGAAGTT 57.048 25.926 0.00 0.00 0.00 2.66
1018 1109 1.117150 TCCCGATCCCCGAGTTAAAG 58.883 55.000 0.00 0.00 41.76 1.85
1337 1434 1.920325 CAGGCAAGAGTCTCCCCCA 60.920 63.158 0.00 0.00 0.00 4.96
1422 1519 3.317436 TTTGGGGTTGTGGTGGGCA 62.317 57.895 0.00 0.00 0.00 5.36
1463 1560 5.405063 AAGATCAGCTAACCCCTACTAGA 57.595 43.478 0.00 0.00 0.00 2.43
1548 1645 2.159099 TGTCCAGGCGCATTACTAGAAG 60.159 50.000 10.83 0.00 0.00 2.85
1761 1869 7.840342 TCAGAATTTTTCAGCTATCACTCTC 57.160 36.000 0.00 0.00 0.00 3.20
1762 1870 7.619050 TCAGAATTTTTCAGCTATCACTCTCT 58.381 34.615 0.00 0.00 0.00 3.10
1848 1956 4.082571 GCATTAAGCAACATTCTGGACTGT 60.083 41.667 0.00 0.00 44.79 3.55
1972 2081 6.754193 TGTACATGTCTTTTCCATTTTTCCC 58.246 36.000 0.00 0.00 0.00 3.97
2222 2331 5.924475 ACACACCGAAGAATTACTCTTTG 57.076 39.130 0.00 0.00 44.82 2.77
2375 2486 8.340443 AGTTGTTTCCGTAAGTGAGAAATAAAC 58.660 33.333 0.00 0.00 34.02 2.01
2585 2697 4.261994 GCATAGTTGAGCTTTGTTTTGGGA 60.262 41.667 0.00 0.00 0.00 4.37
2728 2847 1.467734 CTGTCAGGCTGCTCACAAATC 59.532 52.381 10.34 0.00 0.00 2.17
2854 2973 2.224548 GGTTTGTTGTGGGCTCTCTACT 60.225 50.000 2.11 0.00 0.00 2.57
2902 3021 8.565416 TCATACGTAGTCATTTCAGTATACCTG 58.435 37.037 0.08 0.00 43.93 4.00
2904 3023 5.360144 ACGTAGTCATTTCAGTATACCTGCT 59.640 40.000 0.00 0.00 37.33 4.24
2906 3025 5.028549 AGTCATTTCAGTATACCTGCTGG 57.971 43.478 8.29 8.29 41.25 4.85
2912 3031 3.844640 TCAGTATACCTGCTGGCTCATA 58.155 45.455 9.95 2.61 41.25 2.15
2930 3049 5.583854 GCTCATATCATGTGTATCCCATCAC 59.416 44.000 0.00 0.00 35.43 3.06
2963 3083 3.242543 CCATAAAGCATCACACGAAGCTC 60.243 47.826 0.00 0.00 45.15 4.09
2964 3084 1.882912 AAAGCATCACACGAAGCTCA 58.117 45.000 0.00 0.00 45.15 4.26
2965 3085 1.436600 AAGCATCACACGAAGCTCAG 58.563 50.000 0.00 0.00 45.15 3.35
2974 3151 4.160439 TCACACGAAGCTCAGAAATCCTAT 59.840 41.667 0.00 0.00 0.00 2.57
3031 3208 3.564511 CTTTGGTTTATCGTGCCTGTTG 58.435 45.455 0.00 0.00 0.00 3.33
3047 3224 4.560716 GCCTGTTGGATGTTTCCCTTTAAC 60.561 45.833 0.00 0.00 41.83 2.01
3049 3226 5.278957 CCTGTTGGATGTTTCCCTTTAACAG 60.279 44.000 12.54 12.54 44.36 3.16
3130 3310 4.522789 ACAGTTTCTTGGTTGTGTCTTGTT 59.477 37.500 0.00 0.00 0.00 2.83
3148 3328 1.916000 GTTACGTCGTACTGGCATCAC 59.084 52.381 4.17 0.00 0.00 3.06
3503 3813 6.223852 TGTCTCTTACATCTTCCAAGTGTTC 58.776 40.000 0.00 0.00 31.43 3.18
3564 3874 3.759581 ACTTGACAAGGAGCATGTGAAT 58.240 40.909 19.16 0.00 0.00 2.57
3637 3947 2.376808 AGTCGTCCTTGCTCAAGATG 57.623 50.000 10.94 3.83 40.79 2.90
3678 3988 2.736347 TGCTAGGGGTCTTGAGAGTAC 58.264 52.381 0.00 0.00 0.00 2.73
3781 4091 4.574674 AGCATTCCCAGTAAACAGATCA 57.425 40.909 0.00 0.00 0.00 2.92
4003 4313 3.633986 CCAGAGGTATTTTGCCTGATTCC 59.366 47.826 0.00 0.00 36.29 3.01
4004 4314 4.530875 CAGAGGTATTTTGCCTGATTCCT 58.469 43.478 0.00 0.00 36.29 3.36
4005 4315 5.397899 CCAGAGGTATTTTGCCTGATTCCTA 60.398 44.000 0.00 0.00 36.29 2.94
4006 4316 5.762218 CAGAGGTATTTTGCCTGATTCCTAG 59.238 44.000 0.00 0.00 36.29 3.02
4072 4382 5.473162 TGCTACAGTTACTGCATTCATTTGT 59.527 36.000 12.80 0.00 34.37 2.83
4149 4459 1.272490 TGCGTCTACAACAAGAGAGGG 59.728 52.381 0.00 0.00 0.00 4.30
4376 4687 7.969314 TGGTTGTTCTTTGCAAAAGTAATTTC 58.031 30.769 13.84 1.16 0.00 2.17
4547 4858 4.517285 TGGATTGTGATCAAAGCCTACTC 58.483 43.478 18.97 0.00 37.11 2.59
4614 4925 4.037446 ACCAATCGTAATTGTTTGTGCAGT 59.963 37.500 0.00 0.00 40.63 4.40
4617 4928 4.624336 TCGTAATTGTTTGTGCAGTTGT 57.376 36.364 0.00 0.00 0.00 3.32
4619 4930 9.787243 CAATCGTAATTGTTTGTGCAGTTGTGC 62.787 40.741 0.00 0.00 42.42 4.57
4639 4950 4.031611 TGCATTCCATTCCATTCCATGAA 58.968 39.130 0.00 0.00 0.00 2.57
4668 4979 1.429423 GCCTGCGAGTTATGCAACC 59.571 57.895 0.00 0.00 42.70 3.77
4678 4989 4.010349 GAGTTATGCAACCTACCTGCTTT 58.990 43.478 0.00 0.00 40.59 3.51
4679 4990 3.758554 AGTTATGCAACCTACCTGCTTTG 59.241 43.478 0.00 0.00 40.59 2.77
4680 4991 1.549203 ATGCAACCTACCTGCTTTGG 58.451 50.000 0.00 0.00 40.59 3.28
4681 4992 0.539438 TGCAACCTACCTGCTTTGGG 60.539 55.000 0.00 0.00 40.59 4.12
4682 4993 0.539669 GCAACCTACCTGCTTTGGGT 60.540 55.000 0.00 0.00 40.53 4.51
4683 4994 1.271707 GCAACCTACCTGCTTTGGGTA 60.272 52.381 0.00 0.00 38.19 3.69
4684 4995 2.433436 CAACCTACCTGCTTTGGGTAC 58.567 52.381 0.00 0.00 38.19 3.34
4685 4996 2.039879 CAACCTACCTGCTTTGGGTACT 59.960 50.000 0.00 0.00 38.19 2.73
4686 4997 3.194904 ACCTACCTGCTTTGGGTACTA 57.805 47.619 0.00 0.00 38.19 1.82
4687 4998 3.105283 ACCTACCTGCTTTGGGTACTAG 58.895 50.000 0.00 0.00 38.19 2.57
4688 4999 3.105283 CCTACCTGCTTTGGGTACTAGT 58.895 50.000 0.00 0.00 38.19 2.57
4689 5000 4.264532 ACCTACCTGCTTTGGGTACTAGTA 60.265 45.833 0.00 0.00 38.19 1.82
4690 5001 4.099113 CCTACCTGCTTTGGGTACTAGTAC 59.901 50.000 22.53 22.53 38.19 2.73
4702 5013 4.995124 GGTACTAGTACCGGATATGCATG 58.005 47.826 31.26 0.00 45.21 4.06
4703 5014 3.594603 ACTAGTACCGGATATGCATGC 57.405 47.619 9.46 11.82 0.00 4.06
4704 5015 3.165875 ACTAGTACCGGATATGCATGCT 58.834 45.455 20.33 7.07 0.00 3.79
4705 5016 2.462456 AGTACCGGATATGCATGCTG 57.538 50.000 20.33 6.35 0.00 4.41
4706 5017 1.002430 AGTACCGGATATGCATGCTGG 59.998 52.381 20.33 21.30 0.00 4.85
4707 5018 1.001974 GTACCGGATATGCATGCTGGA 59.998 52.381 26.79 13.37 0.00 3.86
4708 5019 0.035881 ACCGGATATGCATGCTGGAG 59.964 55.000 26.79 8.92 0.00 3.86
4709 5020 0.035881 CCGGATATGCATGCTGGAGT 59.964 55.000 20.33 0.06 0.00 3.85
4710 5021 1.276138 CCGGATATGCATGCTGGAGTA 59.724 52.381 20.33 0.00 0.00 2.59
4711 5022 2.614779 CGGATATGCATGCTGGAGTAG 58.385 52.381 20.33 1.28 0.00 2.57
4712 5023 2.028658 CGGATATGCATGCTGGAGTAGT 60.029 50.000 20.33 0.00 0.00 2.73
4713 5024 3.193479 CGGATATGCATGCTGGAGTAGTA 59.807 47.826 20.33 0.00 0.00 1.82
4714 5025 4.676459 CGGATATGCATGCTGGAGTAGTAG 60.676 50.000 20.33 0.00 0.00 2.57
4715 5026 4.464244 GGATATGCATGCTGGAGTAGTAGA 59.536 45.833 20.33 0.00 0.00 2.59
4716 5027 5.047021 GGATATGCATGCTGGAGTAGTAGAA 60.047 44.000 20.33 0.00 0.00 2.10
4717 5028 4.760530 ATGCATGCTGGAGTAGTAGAAA 57.239 40.909 20.33 0.00 0.00 2.52
4718 5029 4.551702 TGCATGCTGGAGTAGTAGAAAA 57.448 40.909 20.33 0.00 0.00 2.29
4719 5030 4.507710 TGCATGCTGGAGTAGTAGAAAAG 58.492 43.478 20.33 0.00 0.00 2.27
4720 5031 4.222810 TGCATGCTGGAGTAGTAGAAAAGA 59.777 41.667 20.33 0.00 0.00 2.52
4721 5032 5.178797 GCATGCTGGAGTAGTAGAAAAGAA 58.821 41.667 11.37 0.00 0.00 2.52
4722 5033 5.643777 GCATGCTGGAGTAGTAGAAAAGAAA 59.356 40.000 11.37 0.00 0.00 2.52
4723 5034 6.183360 GCATGCTGGAGTAGTAGAAAAGAAAG 60.183 42.308 11.37 0.00 0.00 2.62
4724 5035 6.420913 TGCTGGAGTAGTAGAAAAGAAAGT 57.579 37.500 0.00 0.00 0.00 2.66
4725 5036 6.827727 TGCTGGAGTAGTAGAAAAGAAAGTT 58.172 36.000 0.00 0.00 0.00 2.66
4726 5037 7.959175 TGCTGGAGTAGTAGAAAAGAAAGTTA 58.041 34.615 0.00 0.00 0.00 2.24
4727 5038 8.088981 TGCTGGAGTAGTAGAAAAGAAAGTTAG 58.911 37.037 0.00 0.00 0.00 2.34
4728 5039 7.546316 GCTGGAGTAGTAGAAAAGAAAGTTAGG 59.454 40.741 0.00 0.00 0.00 2.69
4729 5040 7.904205 TGGAGTAGTAGAAAAGAAAGTTAGGG 58.096 38.462 0.00 0.00 0.00 3.53
4730 5041 7.731688 TGGAGTAGTAGAAAAGAAAGTTAGGGA 59.268 37.037 0.00 0.00 0.00 4.20
4731 5042 8.252417 GGAGTAGTAGAAAAGAAAGTTAGGGAG 58.748 40.741 0.00 0.00 0.00 4.30
4732 5043 7.613585 AGTAGTAGAAAAGAAAGTTAGGGAGC 58.386 38.462 0.00 0.00 0.00 4.70
4733 5044 5.480205 AGTAGAAAAGAAAGTTAGGGAGCG 58.520 41.667 0.00 0.00 0.00 5.03
4734 5045 4.353383 AGAAAAGAAAGTTAGGGAGCGT 57.647 40.909 0.00 0.00 0.00 5.07
4735 5046 4.715713 AGAAAAGAAAGTTAGGGAGCGTT 58.284 39.130 0.00 0.00 0.00 4.84
4736 5047 4.755629 AGAAAAGAAAGTTAGGGAGCGTTC 59.244 41.667 0.00 0.00 0.00 3.95
4737 5048 2.365408 AGAAAGTTAGGGAGCGTTCG 57.635 50.000 0.00 0.00 0.00 3.95
4738 5049 1.067071 AGAAAGTTAGGGAGCGTTCGG 60.067 52.381 0.00 0.00 0.00 4.30
4739 5050 0.683412 AAAGTTAGGGAGCGTTCGGT 59.317 50.000 0.00 0.00 0.00 4.69
4740 5051 1.549203 AAGTTAGGGAGCGTTCGGTA 58.451 50.000 0.00 0.00 0.00 4.02
4741 5052 1.101331 AGTTAGGGAGCGTTCGGTAG 58.899 55.000 0.00 0.00 0.00 3.18
4742 5053 0.527169 GTTAGGGAGCGTTCGGTAGC 60.527 60.000 0.00 0.00 0.00 3.58
4743 5054 1.669999 TTAGGGAGCGTTCGGTAGCC 61.670 60.000 0.00 0.00 0.00 3.93
4744 5055 2.563013 TAGGGAGCGTTCGGTAGCCT 62.563 60.000 0.00 0.00 0.00 4.58
4745 5056 2.202756 GGAGCGTTCGGTAGCCTG 60.203 66.667 0.00 0.00 0.00 4.85
4746 5057 2.886124 GAGCGTTCGGTAGCCTGC 60.886 66.667 0.00 0.00 0.00 4.85
4747 5058 3.642778 GAGCGTTCGGTAGCCTGCA 62.643 63.158 0.00 0.00 0.00 4.41
4748 5059 2.511600 GCGTTCGGTAGCCTGCAT 60.512 61.111 0.00 0.00 0.00 3.96
4749 5060 2.813179 GCGTTCGGTAGCCTGCATG 61.813 63.158 0.00 0.00 0.00 4.06
4750 5061 1.153647 CGTTCGGTAGCCTGCATGA 60.154 57.895 0.00 0.00 0.00 3.07
4751 5062 0.739462 CGTTCGGTAGCCTGCATGAA 60.739 55.000 0.00 0.00 0.00 2.57
4752 5063 1.668419 GTTCGGTAGCCTGCATGAAT 58.332 50.000 0.00 0.00 0.00 2.57
4753 5064 2.017049 GTTCGGTAGCCTGCATGAATT 58.983 47.619 0.00 0.00 0.00 2.17
4754 5065 2.418368 TCGGTAGCCTGCATGAATTT 57.582 45.000 0.00 0.00 0.00 1.82
4755 5066 2.722094 TCGGTAGCCTGCATGAATTTT 58.278 42.857 0.00 0.00 0.00 1.82
4756 5067 3.879998 TCGGTAGCCTGCATGAATTTTA 58.120 40.909 0.00 0.00 0.00 1.52
4757 5068 3.876914 TCGGTAGCCTGCATGAATTTTAG 59.123 43.478 0.00 0.00 0.00 1.85
4758 5069 3.003689 CGGTAGCCTGCATGAATTTTAGG 59.996 47.826 0.00 0.00 0.00 2.69
4763 5074 4.460948 CCTGCATGAATTTTAGGCACTT 57.539 40.909 0.00 0.00 41.75 3.16
4764 5075 4.824289 CCTGCATGAATTTTAGGCACTTT 58.176 39.130 0.00 0.00 41.75 2.66
4765 5076 4.628333 CCTGCATGAATTTTAGGCACTTTG 59.372 41.667 0.00 0.00 41.75 2.77
4766 5077 3.995705 TGCATGAATTTTAGGCACTTTGC 59.004 39.130 0.00 0.00 44.08 3.68
4777 5088 2.514205 GCACTTTGCATCTTTGTGGT 57.486 45.000 0.00 0.00 44.26 4.16
4778 5089 2.825205 GCACTTTGCATCTTTGTGGTT 58.175 42.857 0.00 0.00 44.26 3.67
4779 5090 3.197265 GCACTTTGCATCTTTGTGGTTT 58.803 40.909 0.00 0.00 44.26 3.27
4780 5091 3.001533 GCACTTTGCATCTTTGTGGTTTG 59.998 43.478 0.00 0.00 44.26 2.93
4781 5092 4.431809 CACTTTGCATCTTTGTGGTTTGA 58.568 39.130 0.00 0.00 0.00 2.69
4782 5093 4.268405 CACTTTGCATCTTTGTGGTTTGAC 59.732 41.667 0.00 0.00 0.00 3.18
4783 5094 4.160252 ACTTTGCATCTTTGTGGTTTGACT 59.840 37.500 0.00 0.00 0.00 3.41
4784 5095 3.988379 TGCATCTTTGTGGTTTGACTC 57.012 42.857 0.00 0.00 0.00 3.36
4785 5096 3.286353 TGCATCTTTGTGGTTTGACTCA 58.714 40.909 0.00 0.00 0.00 3.41
4786 5097 3.698539 TGCATCTTTGTGGTTTGACTCAA 59.301 39.130 0.00 0.00 0.00 3.02
4787 5098 4.044426 GCATCTTTGTGGTTTGACTCAAC 58.956 43.478 0.00 0.00 0.00 3.18
4788 5099 4.610945 CATCTTTGTGGTTTGACTCAACC 58.389 43.478 0.00 0.00 0.00 3.77
4789 5100 3.691575 TCTTTGTGGTTTGACTCAACCA 58.308 40.909 1.00 1.00 0.00 3.67
4790 5101 3.694072 TCTTTGTGGTTTGACTCAACCAG 59.306 43.478 5.52 0.00 30.02 4.00
4791 5102 2.051334 TGTGGTTTGACTCAACCAGG 57.949 50.000 5.52 0.00 30.02 4.45
4792 5103 0.668535 GTGGTTTGACTCAACCAGGC 59.331 55.000 5.52 0.00 30.02 4.85
4793 5104 0.257328 TGGTTTGACTCAACCAGGCA 59.743 50.000 1.00 0.00 39.02 4.75
4794 5105 0.668535 GGTTTGACTCAACCAGGCAC 59.331 55.000 0.00 0.00 41.36 5.01
4795 5106 1.680338 GTTTGACTCAACCAGGCACT 58.320 50.000 0.00 0.00 41.36 4.40
4796 5107 2.024414 GTTTGACTCAACCAGGCACTT 58.976 47.619 0.00 0.00 41.36 3.16
4797 5108 2.427095 GTTTGACTCAACCAGGCACTTT 59.573 45.455 0.00 0.00 41.36 2.66
4798 5109 1.679139 TGACTCAACCAGGCACTTTG 58.321 50.000 0.00 0.00 33.83 2.77
4799 5110 0.312102 GACTCAACCAGGCACTTTGC 59.688 55.000 0.00 0.00 44.08 3.68
4809 5120 3.780925 GCACTTTGCATCTGTGGTC 57.219 52.632 13.54 0.00 44.26 4.02
4810 5121 0.242017 GCACTTTGCATCTGTGGTCC 59.758 55.000 13.54 0.00 44.26 4.46
4811 5122 0.518636 CACTTTGCATCTGTGGTCCG 59.481 55.000 0.00 0.00 0.00 4.79
4812 5123 0.606401 ACTTTGCATCTGTGGTCCGG 60.606 55.000 0.00 0.00 0.00 5.14
4813 5124 1.926511 CTTTGCATCTGTGGTCCGGC 61.927 60.000 0.00 0.00 0.00 6.13
4814 5125 2.410322 TTTGCATCTGTGGTCCGGCT 62.410 55.000 0.00 0.00 0.00 5.52
4815 5126 2.512515 GCATCTGTGGTCCGGCTC 60.513 66.667 0.00 0.00 0.00 4.70
4816 5127 2.981302 CATCTGTGGTCCGGCTCA 59.019 61.111 0.00 0.00 0.00 4.26
4817 5128 1.296392 CATCTGTGGTCCGGCTCAA 59.704 57.895 0.00 0.00 0.00 3.02
4818 5129 1.021390 CATCTGTGGTCCGGCTCAAC 61.021 60.000 0.00 0.00 0.00 3.18
4819 5130 2.185310 ATCTGTGGTCCGGCTCAACC 62.185 60.000 0.00 0.00 36.03 3.77
4820 5131 3.164977 TGTGGTCCGGCTCAACCA 61.165 61.111 8.62 8.62 43.20 3.67
4821 5132 2.358737 GTGGTCCGGCTCAACCAG 60.359 66.667 12.79 0.00 45.91 4.00
4822 5133 3.636231 TGGTCCGGCTCAACCAGG 61.636 66.667 8.62 0.00 40.60 4.45
4824 5135 4.021925 GTCCGGCTCAACCAGGCT 62.022 66.667 0.00 0.00 45.92 4.58
4825 5136 4.020617 TCCGGCTCAACCAGGCTG 62.021 66.667 7.75 7.75 45.92 4.85
4826 5137 4.020617 CCGGCTCAACCAGGCTGA 62.021 66.667 17.94 0.00 45.92 4.26
4827 5138 2.435586 CGGCTCAACCAGGCTGAG 60.436 66.667 17.94 14.82 45.92 3.35
4830 5141 0.833287 GGCTCAACCAGGCTGAGATA 59.167 55.000 22.24 0.00 44.64 1.98
4836 5147 4.326826 TCAACCAGGCTGAGATACAAAAG 58.673 43.478 17.94 0.00 0.00 2.27
4838 5149 4.851639 ACCAGGCTGAGATACAAAAGAT 57.148 40.909 17.94 0.00 0.00 2.40
4840 5151 4.225942 ACCAGGCTGAGATACAAAAGATCA 59.774 41.667 17.94 0.00 0.00 2.92
4847 5158 7.408123 GCTGAGATACAAAAGATCATGTTCTG 58.592 38.462 7.06 0.00 0.00 3.02
4852 5163 4.863491 ACAAAAGATCATGTTCTGCACAC 58.137 39.130 7.06 0.00 38.61 3.82
4854 5165 4.494350 AAAGATCATGTTCTGCACACAC 57.506 40.909 7.06 0.00 38.61 3.82
4858 5169 3.696281 TCATGTTCTGCACACACTTTG 57.304 42.857 0.00 0.00 38.61 2.77
4865 5176 3.739077 GCACACACTTTGTTTGCCT 57.261 47.368 6.22 0.00 45.43 4.75
4869 5180 1.280066 CACACTTTGTTTGCCTGCAC 58.720 50.000 0.00 0.00 0.00 4.57
4876 5187 3.185203 TTTGCCTGCACCCCCTCT 61.185 61.111 0.00 0.00 0.00 3.69
4882 5193 1.075226 CTGCACCCCCTCTAGCCTA 60.075 63.158 0.00 0.00 0.00 3.93
4889 5200 1.184970 CCCCTCTAGCCTAGCTGAGC 61.185 65.000 0.00 0.00 40.10 4.26
4891 5202 1.523154 CCTCTAGCCTAGCTGAGCGG 61.523 65.000 0.00 0.00 40.10 5.52
4897 5208 0.673644 GCCTAGCTGAGCGGAAACAA 60.674 55.000 2.37 0.00 0.00 2.83
4906 5217 2.360483 TGAGCGGAAACAAAAGCATTGA 59.640 40.909 9.00 0.00 0.00 2.57
4922 5233 3.395639 CATTGATGTTTGGTTGCAAGCT 58.604 40.909 27.31 8.59 0.00 3.74
4929 5240 2.860136 GTTTGGTTGCAAGCTTGTTCTC 59.140 45.455 27.31 14.76 0.00 2.87
4959 5270 4.686554 TGCAAAGTGTTGTTGTTTGGTTAC 59.313 37.500 0.00 0.00 37.06 2.50
4974 5285 7.421599 TGTTTGGTTACATACAAGACAATGTG 58.578 34.615 0.00 0.00 35.95 3.21
4977 5288 7.609760 TGGTTACATACAAGACAATGTGATC 57.390 36.000 0.00 0.00 36.96 2.92
4980 5291 7.201644 GGTTACATACAAGACAATGTGATCTGG 60.202 40.741 0.00 0.00 36.96 3.86
4984 5295 8.049117 ACATACAAGACAATGTGATCTGGTAAT 58.951 33.333 0.00 0.00 35.47 1.89
4987 5298 6.820656 ACAAGACAATGTGATCTGGTAATCTC 59.179 38.462 0.00 0.00 26.63 2.75
4993 5304 7.335422 ACAATGTGATCTGGTAATCTCTTGTTC 59.665 37.037 0.00 0.00 0.00 3.18
5001 5312 3.927142 GGTAATCTCTTGTTCGAGTGGTG 59.073 47.826 0.00 0.00 32.83 4.17
5008 5319 3.576982 TCTTGTTCGAGTGGTGAGGTTAT 59.423 43.478 0.00 0.00 0.00 1.89
5009 5320 4.768448 TCTTGTTCGAGTGGTGAGGTTATA 59.232 41.667 0.00 0.00 0.00 0.98
5010 5321 4.713824 TGTTCGAGTGGTGAGGTTATAG 57.286 45.455 0.00 0.00 0.00 1.31
5011 5322 3.446161 TGTTCGAGTGGTGAGGTTATAGG 59.554 47.826 0.00 0.00 0.00 2.57
5025 5367 8.202137 GTGAGGTTATAGGCAAGACAACTAATA 58.798 37.037 0.00 0.00 0.00 0.98
5027 5369 8.959705 AGGTTATAGGCAAGACAACTAATAAC 57.040 34.615 0.00 0.00 0.00 1.89
5043 5385 9.730420 CAACTAATAACAGGCATAACATAAACC 57.270 33.333 0.00 0.00 0.00 3.27
5054 5396 8.107095 AGGCATAACATAAACCAGAGTCTTAAA 58.893 33.333 0.00 0.00 0.00 1.52
5056 5398 8.947115 GCATAACATAAACCAGAGTCTTAAACT 58.053 33.333 0.00 0.00 42.42 2.66
5066 5408 5.921408 CCAGAGTCTTAAACTGTACTCACAC 59.079 44.000 9.58 0.00 40.65 3.82
5067 5409 6.461092 CCAGAGTCTTAAACTGTACTCACACA 60.461 42.308 9.58 0.00 40.65 3.72
5086 5433 6.041637 TCACACACAGTTAAACTACTCCATCT 59.958 38.462 0.00 0.00 0.00 2.90
5119 5466 6.833041 TGTTGTTGATTTAGTACAAGAGGGA 58.167 36.000 0.00 0.00 32.89 4.20
5258 5617 0.754957 CTTGGCCACCAACTCAACCA 60.755 55.000 3.88 0.00 38.75 3.67
5260 5619 1.454847 GGCCACCAACTCAACCACA 60.455 57.895 0.00 0.00 0.00 4.17
5266 5625 1.140052 ACCAACTCAACCACATCGTCA 59.860 47.619 0.00 0.00 0.00 4.35
5361 5720 3.501040 GAAACGGTGAAGGGGGCCA 62.501 63.158 4.39 0.00 0.00 5.36
5390 5749 2.917933 TCAAGGGTGAGTCTGTTGTTG 58.082 47.619 0.00 0.00 0.00 3.33
5403 5762 0.320073 GTTGTTGATCGTCCGGACCA 60.320 55.000 28.52 17.72 0.00 4.02
5412 5771 1.749033 GTCCGGACCATGATCCTCC 59.251 63.158 24.75 0.00 36.52 4.30
5446 5805 0.994995 CTCGTCCTCAGCACGAATTG 59.005 55.000 0.00 0.00 45.27 2.32
5474 5833 2.362077 GACAATGGTCAAGTGCTTGGTT 59.638 45.455 11.47 1.07 43.73 3.67
5492 5851 1.476845 TTAAGTCACAGGGCGGCAGA 61.477 55.000 12.47 0.00 0.00 4.26
5503 5862 1.292223 GCGGCAGACACTCCAACTA 59.708 57.895 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.125906 CTTTTGATGAAATTGATGTGAAGACTC 57.874 33.333 0.00 0.00 0.00 3.36
78 79 1.064825 AACCCATGAAAGACGACCCT 58.935 50.000 0.00 0.00 0.00 4.34
83 84 4.839668 TTGGTTTAACCCATGAAAGACG 57.160 40.909 12.02 0.00 37.50 4.18
89 90 5.480073 CCTGAAGATTTGGTTTAACCCATGA 59.520 40.000 12.02 0.00 37.50 3.07
125 126 4.487714 TCAAGTGCCCCTTAGTGATTAG 57.512 45.455 0.00 0.00 0.00 1.73
242 294 2.604855 GGTACACTGCGAGATACATCCG 60.605 54.545 0.00 0.00 0.00 4.18
253 305 3.852286 TGTAATTACCTGGTACACTGCG 58.148 45.455 13.01 0.00 0.00 5.18
266 318 7.914346 AGACGCCGCTATAGATATTGTAATTAC 59.086 37.037 8.75 8.75 0.00 1.89
282 334 2.905880 GGCTCCTAGACGCCGCTA 60.906 66.667 6.52 0.00 36.45 4.26
314 366 8.829612 CCTTCAACAAAGAATTGCTTGTAAAAT 58.170 29.630 2.92 0.00 40.34 1.82
356 408 3.834489 TGTTTAGGTCGTTTGTGGGTA 57.166 42.857 0.00 0.00 0.00 3.69
1240 1337 1.672529 GGTTAGGGTTAGGGTTGGGA 58.327 55.000 0.00 0.00 0.00 4.37
1422 1519 2.738587 TATCTCGGAGCTCACCTTCT 57.261 50.000 17.19 0.00 0.00 2.85
1463 1560 2.942376 TCATCGTTTAGGCAATGCGATT 59.058 40.909 0.00 0.00 39.80 3.34
1548 1645 1.234615 TAACGCAGCTGAAGGCAACC 61.235 55.000 20.43 0.00 44.79 3.77
1560 1668 6.771076 TCAATTAAAGCATACAGTAACGCAG 58.229 36.000 7.82 0.00 0.00 5.18
1607 1715 1.264557 CATACGGACTAGAGACAGGCG 59.735 57.143 0.00 0.00 0.00 5.52
1848 1956 4.155280 GCTAAGCCCTTTCACGATTTGTTA 59.845 41.667 0.00 0.00 0.00 2.41
1972 2081 2.224066 ACTGACAACCGAGTTCTGGAAG 60.224 50.000 0.00 0.00 0.00 3.46
2222 2331 6.397272 TGGCACAAAATCCTTGAACATATTC 58.603 36.000 0.00 0.00 31.92 1.75
2335 2444 5.578776 GGAAACAACTGATCTCAACGTTTT 58.421 37.500 0.00 0.00 0.00 2.43
2336 2445 4.260620 CGGAAACAACTGATCTCAACGTTT 60.261 41.667 0.00 0.00 0.00 3.60
2375 2486 8.876275 AGCATATATTGGTAAAACAAGCATTG 57.124 30.769 0.00 0.00 43.05 2.82
2507 2618 4.601084 TGAGGACTCGGACTCTAGAATTT 58.399 43.478 0.00 0.00 34.84 1.82
2567 2679 3.305897 CGTTTCCCAAAACAAAGCTCAAC 59.694 43.478 0.00 0.00 44.13 3.18
2585 2697 0.533032 GCTAGAGCTCCTGGTCGTTT 59.467 55.000 10.93 0.00 44.65 3.60
2630 2742 7.815068 CAGACCTGGACTATATATAAACTGTGC 59.185 40.741 0.00 0.00 0.00 4.57
2728 2847 1.171308 TAGTTCGACAAGAGGACCCG 58.829 55.000 0.00 0.00 0.00 5.28
2854 2973 7.840342 TGAAGTTGCTTGCAAAATCTAAAAA 57.160 28.000 9.75 0.00 0.00 1.94
2902 3021 3.937706 GGATACACATGATATGAGCCAGC 59.062 47.826 0.00 0.00 0.00 4.85
2904 3023 3.909364 TGGGATACACATGATATGAGCCA 59.091 43.478 0.00 0.00 39.74 4.75
2906 3025 5.583854 GTGATGGGATACACATGATATGAGC 59.416 44.000 0.00 0.00 37.05 4.26
2963 3083 7.646314 CCATCAACTAGCAAATAGGATTTCTG 58.354 38.462 0.00 0.00 35.63 3.02
2964 3084 6.264067 GCCATCAACTAGCAAATAGGATTTCT 59.736 38.462 0.00 0.00 35.63 2.52
2965 3085 6.264067 AGCCATCAACTAGCAAATAGGATTTC 59.736 38.462 0.00 0.00 35.63 2.17
2974 3151 7.938140 AATTAACTAGCCATCAACTAGCAAA 57.062 32.000 0.00 0.00 40.70 3.68
3022 3199 0.603065 GGGAAACATCCAACAGGCAC 59.397 55.000 0.00 0.00 0.00 5.01
3047 3224 4.334481 CGTTAGTTATTGCCCTTAACCCTG 59.666 45.833 0.00 0.00 31.31 4.45
3049 3226 4.264253 ACGTTAGTTATTGCCCTTAACCC 58.736 43.478 0.00 0.00 31.31 4.11
3130 3310 1.166989 TGTGATGCCAGTACGACGTA 58.833 50.000 2.97 2.97 0.00 3.57
3148 3328 4.355543 AGGCAACAGCATAAAACGTATG 57.644 40.909 0.00 0.00 41.41 2.39
3503 3813 5.264395 AGGGGAAAGGTGAATTTACATGAG 58.736 41.667 0.00 0.00 0.00 2.90
3564 3874 1.163554 TGCTAATCATTGTGCGCACA 58.836 45.000 37.86 37.86 39.98 4.57
3637 3947 4.094146 GCAATCTTGAGAGTTGTCTTAGCC 59.906 45.833 0.00 0.00 30.97 3.93
4033 4343 1.075542 TAGCAAGCAACGGATCAACG 58.924 50.000 0.00 0.00 40.31 4.10
4072 4382 2.575735 TGAATAAGGTGCCATCAGGTCA 59.424 45.455 0.00 0.00 37.19 4.02
4149 4459 1.819632 ATGCGTCCCTTGATTCGGC 60.820 57.895 0.00 0.00 0.00 5.54
4297 4607 1.552337 GGCTGGAGTCAGAATCTGTCA 59.448 52.381 10.36 4.56 43.49 3.58
4563 4874 7.234371 TCATCCAAACAAGGATTTTTGGTCATA 59.766 33.333 11.78 0.00 46.12 2.15
4588 4899 6.318628 TGCACAAACAATTACGATTGGTATC 58.681 36.000 0.00 0.00 42.27 2.24
4614 4925 3.171528 TGGAATGGAATGGAATGCACAA 58.828 40.909 0.00 0.00 0.00 3.33
4617 4928 3.644335 TCATGGAATGGAATGGAATGCA 58.356 40.909 0.00 0.00 46.73 3.96
4619 4930 5.864418 AGTTCATGGAATGGAATGGAATG 57.136 39.130 0.00 0.00 46.73 2.67
4620 4931 5.395990 GCAAGTTCATGGAATGGAATGGAAT 60.396 40.000 0.00 0.00 46.73 3.01
4621 4932 4.081531 GCAAGTTCATGGAATGGAATGGAA 60.082 41.667 0.00 0.00 46.73 3.53
4622 4933 3.448301 GCAAGTTCATGGAATGGAATGGA 59.552 43.478 0.00 0.00 46.73 3.41
4623 4934 3.449737 AGCAAGTTCATGGAATGGAATGG 59.550 43.478 0.00 0.00 46.73 3.16
4624 4935 4.430007 CAGCAAGTTCATGGAATGGAATG 58.570 43.478 0.00 0.00 46.73 2.67
4625 4936 3.118884 GCAGCAAGTTCATGGAATGGAAT 60.119 43.478 0.00 0.00 46.73 3.01
4626 4937 2.231964 GCAGCAAGTTCATGGAATGGAA 59.768 45.455 0.00 0.00 46.73 3.53
4627 4938 1.820519 GCAGCAAGTTCATGGAATGGA 59.179 47.619 0.00 0.00 46.73 3.41
4628 4939 1.546923 TGCAGCAAGTTCATGGAATGG 59.453 47.619 0.00 0.00 46.73 3.16
4655 4966 1.933853 GCAGGTAGGTTGCATAACTCG 59.066 52.381 0.00 0.00 41.17 4.18
4663 4974 0.539669 ACCCAAAGCAGGTAGGTTGC 60.540 55.000 0.00 0.00 41.83 4.17
4668 4979 5.259832 GTACTAGTACCCAAAGCAGGTAG 57.740 47.826 20.47 0.00 40.53 3.18
4681 4992 4.158025 AGCATGCATATCCGGTACTAGTAC 59.842 45.833 22.53 22.53 35.40 2.73
4682 4993 4.157840 CAGCATGCATATCCGGTACTAGTA 59.842 45.833 21.98 0.00 0.00 1.82
4683 4994 3.056536 CAGCATGCATATCCGGTACTAGT 60.057 47.826 21.98 0.00 0.00 2.57
4684 4995 3.515630 CAGCATGCATATCCGGTACTAG 58.484 50.000 21.98 0.00 0.00 2.57
4685 4996 2.233676 CCAGCATGCATATCCGGTACTA 59.766 50.000 21.98 0.00 31.97 1.82
4686 4997 1.002430 CCAGCATGCATATCCGGTACT 59.998 52.381 21.98 0.00 31.97 2.73
4687 4998 1.001974 TCCAGCATGCATATCCGGTAC 59.998 52.381 21.98 0.00 31.97 3.34
4688 4999 1.276138 CTCCAGCATGCATATCCGGTA 59.724 52.381 21.98 0.00 31.97 4.02
4689 5000 0.035881 CTCCAGCATGCATATCCGGT 59.964 55.000 21.98 0.00 31.97 5.28
4690 5001 0.035881 ACTCCAGCATGCATATCCGG 59.964 55.000 21.98 9.94 31.97 5.14
4691 5002 2.028658 ACTACTCCAGCATGCATATCCG 60.029 50.000 21.98 5.36 31.97 4.18
4692 5003 3.692257 ACTACTCCAGCATGCATATCC 57.308 47.619 21.98 0.00 31.97 2.59
4693 5004 5.651387 TCTACTACTCCAGCATGCATATC 57.349 43.478 21.98 0.00 31.97 1.63
4694 5005 6.425210 TTTCTACTACTCCAGCATGCATAT 57.575 37.500 21.98 2.76 31.97 1.78
4695 5006 5.869649 TTTCTACTACTCCAGCATGCATA 57.130 39.130 21.98 3.30 31.97 3.14
4696 5007 4.760530 TTTCTACTACTCCAGCATGCAT 57.239 40.909 21.98 1.69 31.97 3.96
4697 5008 4.222810 TCTTTTCTACTACTCCAGCATGCA 59.777 41.667 21.98 0.00 31.97 3.96
4698 5009 4.759782 TCTTTTCTACTACTCCAGCATGC 58.240 43.478 10.51 10.51 31.97 4.06
4699 5010 6.876257 ACTTTCTTTTCTACTACTCCAGCATG 59.124 38.462 0.00 0.00 0.00 4.06
4700 5011 7.010339 ACTTTCTTTTCTACTACTCCAGCAT 57.990 36.000 0.00 0.00 0.00 3.79
4701 5012 6.420913 ACTTTCTTTTCTACTACTCCAGCA 57.579 37.500 0.00 0.00 0.00 4.41
4702 5013 7.546316 CCTAACTTTCTTTTCTACTACTCCAGC 59.454 40.741 0.00 0.00 0.00 4.85
4703 5014 8.035984 CCCTAACTTTCTTTTCTACTACTCCAG 58.964 40.741 0.00 0.00 0.00 3.86
4704 5015 7.731688 TCCCTAACTTTCTTTTCTACTACTCCA 59.268 37.037 0.00 0.00 0.00 3.86
4705 5016 8.131847 TCCCTAACTTTCTTTTCTACTACTCC 57.868 38.462 0.00 0.00 0.00 3.85
4706 5017 7.760794 GCTCCCTAACTTTCTTTTCTACTACTC 59.239 40.741 0.00 0.00 0.00 2.59
4707 5018 7.577236 CGCTCCCTAACTTTCTTTTCTACTACT 60.577 40.741 0.00 0.00 0.00 2.57
4708 5019 6.530887 CGCTCCCTAACTTTCTTTTCTACTAC 59.469 42.308 0.00 0.00 0.00 2.73
4709 5020 6.210185 ACGCTCCCTAACTTTCTTTTCTACTA 59.790 38.462 0.00 0.00 0.00 1.82
4710 5021 5.011840 ACGCTCCCTAACTTTCTTTTCTACT 59.988 40.000 0.00 0.00 0.00 2.57
4711 5022 5.236282 ACGCTCCCTAACTTTCTTTTCTAC 58.764 41.667 0.00 0.00 0.00 2.59
4712 5023 5.479124 ACGCTCCCTAACTTTCTTTTCTA 57.521 39.130 0.00 0.00 0.00 2.10
4713 5024 4.353383 ACGCTCCCTAACTTTCTTTTCT 57.647 40.909 0.00 0.00 0.00 2.52
4714 5025 4.377124 CGAACGCTCCCTAACTTTCTTTTC 60.377 45.833 0.00 0.00 0.00 2.29
4715 5026 3.497262 CGAACGCTCCCTAACTTTCTTTT 59.503 43.478 0.00 0.00 0.00 2.27
4716 5027 3.064931 CGAACGCTCCCTAACTTTCTTT 58.935 45.455 0.00 0.00 0.00 2.52
4717 5028 2.612221 CCGAACGCTCCCTAACTTTCTT 60.612 50.000 0.00 0.00 0.00 2.52
4718 5029 1.067071 CCGAACGCTCCCTAACTTTCT 60.067 52.381 0.00 0.00 0.00 2.52
4719 5030 1.337541 ACCGAACGCTCCCTAACTTTC 60.338 52.381 0.00 0.00 0.00 2.62
4720 5031 0.683412 ACCGAACGCTCCCTAACTTT 59.317 50.000 0.00 0.00 0.00 2.66
4721 5032 1.475682 CTACCGAACGCTCCCTAACTT 59.524 52.381 0.00 0.00 0.00 2.66
4722 5033 1.101331 CTACCGAACGCTCCCTAACT 58.899 55.000 0.00 0.00 0.00 2.24
4723 5034 0.527169 GCTACCGAACGCTCCCTAAC 60.527 60.000 0.00 0.00 0.00 2.34
4724 5035 1.669999 GGCTACCGAACGCTCCCTAA 61.670 60.000 0.00 0.00 0.00 2.69
4725 5036 2.123428 GGCTACCGAACGCTCCCTA 61.123 63.158 0.00 0.00 0.00 3.53
4726 5037 3.459063 GGCTACCGAACGCTCCCT 61.459 66.667 0.00 0.00 0.00 4.20
4727 5038 3.459063 AGGCTACCGAACGCTCCC 61.459 66.667 0.00 0.00 0.00 4.30
4728 5039 2.202756 CAGGCTACCGAACGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
4729 5040 2.886124 GCAGGCTACCGAACGCTC 60.886 66.667 0.00 0.00 0.00 5.03
4730 5041 3.019003 ATGCAGGCTACCGAACGCT 62.019 57.895 0.00 0.00 0.00 5.07
4731 5042 2.511600 ATGCAGGCTACCGAACGC 60.512 61.111 0.00 0.00 0.00 4.84
4732 5043 0.739462 TTCATGCAGGCTACCGAACG 60.739 55.000 0.00 0.00 0.00 3.95
4733 5044 1.668419 ATTCATGCAGGCTACCGAAC 58.332 50.000 0.00 0.00 0.00 3.95
4734 5045 2.418368 AATTCATGCAGGCTACCGAA 57.582 45.000 0.00 0.00 0.00 4.30
4735 5046 2.418368 AAATTCATGCAGGCTACCGA 57.582 45.000 0.00 0.00 0.00 4.69
4736 5047 3.003689 CCTAAAATTCATGCAGGCTACCG 59.996 47.826 0.00 0.00 0.00 4.02
4737 5048 3.243535 GCCTAAAATTCATGCAGGCTACC 60.244 47.826 3.69 0.00 46.70 3.18
4738 5049 3.969899 GCCTAAAATTCATGCAGGCTAC 58.030 45.455 3.69 0.00 46.70 3.58
4742 5053 4.460948 AAGTGCCTAAAATTCATGCAGG 57.539 40.909 0.00 0.00 31.69 4.85
4743 5054 4.092383 GCAAAGTGCCTAAAATTCATGCAG 59.908 41.667 0.00 0.00 37.42 4.41
4744 5055 3.995705 GCAAAGTGCCTAAAATTCATGCA 59.004 39.130 0.00 0.00 37.42 3.96
4745 5056 3.995705 TGCAAAGTGCCTAAAATTCATGC 59.004 39.130 0.00 0.00 44.23 4.06
4746 5057 6.103997 AGATGCAAAGTGCCTAAAATTCATG 58.896 36.000 0.00 0.00 44.23 3.07
4747 5058 6.290294 AGATGCAAAGTGCCTAAAATTCAT 57.710 33.333 0.00 0.00 44.23 2.57
4748 5059 5.726980 AGATGCAAAGTGCCTAAAATTCA 57.273 34.783 0.00 0.00 44.23 2.57
4749 5060 6.424812 ACAAAGATGCAAAGTGCCTAAAATTC 59.575 34.615 0.00 0.00 44.23 2.17
4750 5061 6.203338 CACAAAGATGCAAAGTGCCTAAAATT 59.797 34.615 0.00 0.00 44.23 1.82
4751 5062 5.697633 CACAAAGATGCAAAGTGCCTAAAAT 59.302 36.000 0.00 0.00 44.23 1.82
4752 5063 5.049167 CACAAAGATGCAAAGTGCCTAAAA 58.951 37.500 0.00 0.00 44.23 1.52
4753 5064 4.501229 CCACAAAGATGCAAAGTGCCTAAA 60.501 41.667 0.00 0.00 44.23 1.85
4754 5065 3.005684 CCACAAAGATGCAAAGTGCCTAA 59.994 43.478 0.00 0.00 44.23 2.69
4755 5066 2.557924 CCACAAAGATGCAAAGTGCCTA 59.442 45.455 0.00 0.00 44.23 3.93
4756 5067 1.342174 CCACAAAGATGCAAAGTGCCT 59.658 47.619 0.00 0.00 44.23 4.75
4757 5068 1.069049 ACCACAAAGATGCAAAGTGCC 59.931 47.619 0.00 0.00 44.23 5.01
4758 5069 2.514205 ACCACAAAGATGCAAAGTGC 57.486 45.000 0.00 0.00 45.29 4.40
4759 5070 4.268405 GTCAAACCACAAAGATGCAAAGTG 59.732 41.667 0.00 0.00 0.00 3.16
4760 5071 4.160252 AGTCAAACCACAAAGATGCAAAGT 59.840 37.500 0.00 0.00 0.00 2.66
4761 5072 4.685924 AGTCAAACCACAAAGATGCAAAG 58.314 39.130 0.00 0.00 0.00 2.77
4762 5073 4.159321 TGAGTCAAACCACAAAGATGCAAA 59.841 37.500 0.00 0.00 0.00 3.68
4763 5074 3.698539 TGAGTCAAACCACAAAGATGCAA 59.301 39.130 0.00 0.00 0.00 4.08
4764 5075 3.286353 TGAGTCAAACCACAAAGATGCA 58.714 40.909 0.00 0.00 0.00 3.96
4765 5076 3.988379 TGAGTCAAACCACAAAGATGC 57.012 42.857 0.00 0.00 0.00 3.91
4776 5087 1.680338 AGTGCCTGGTTGAGTCAAAC 58.320 50.000 14.26 14.26 0.00 2.93
4777 5088 2.426738 CAAAGTGCCTGGTTGAGTCAAA 59.573 45.455 7.25 0.00 0.00 2.69
4778 5089 2.023673 CAAAGTGCCTGGTTGAGTCAA 58.976 47.619 0.08 0.08 0.00 3.18
4779 5090 1.679139 CAAAGTGCCTGGTTGAGTCA 58.321 50.000 0.00 0.00 0.00 3.41
4780 5091 0.312102 GCAAAGTGCCTGGTTGAGTC 59.688 55.000 0.00 0.00 37.42 3.36
4781 5092 0.395586 TGCAAAGTGCCTGGTTGAGT 60.396 50.000 0.00 0.00 44.23 3.41
4782 5093 0.963962 ATGCAAAGTGCCTGGTTGAG 59.036 50.000 0.00 0.00 44.23 3.02
4783 5094 0.961019 GATGCAAAGTGCCTGGTTGA 59.039 50.000 0.00 0.00 44.23 3.18
4784 5095 0.963962 AGATGCAAAGTGCCTGGTTG 59.036 50.000 0.00 0.00 44.23 3.77
4785 5096 0.963962 CAGATGCAAAGTGCCTGGTT 59.036 50.000 0.00 0.00 44.23 3.67
4786 5097 0.178981 ACAGATGCAAAGTGCCTGGT 60.179 50.000 10.08 0.00 44.23 4.00
4787 5098 0.242825 CACAGATGCAAAGTGCCTGG 59.757 55.000 10.08 0.00 44.23 4.45
4788 5099 0.242825 CCACAGATGCAAAGTGCCTG 59.757 55.000 10.10 1.76 44.23 4.85
4789 5100 0.178981 ACCACAGATGCAAAGTGCCT 60.179 50.000 10.10 0.00 44.23 4.75
4790 5101 0.242017 GACCACAGATGCAAAGTGCC 59.758 55.000 10.10 2.65 44.23 5.01
4791 5102 0.242017 GGACCACAGATGCAAAGTGC 59.758 55.000 10.10 0.00 45.29 4.40
4792 5103 0.518636 CGGACCACAGATGCAAAGTG 59.481 55.000 8.95 8.95 0.00 3.16
4793 5104 0.606401 CCGGACCACAGATGCAAAGT 60.606 55.000 0.00 0.00 0.00 2.66
4794 5105 1.926511 GCCGGACCACAGATGCAAAG 61.927 60.000 5.05 0.00 0.00 2.77
4795 5106 1.971167 GCCGGACCACAGATGCAAA 60.971 57.895 5.05 0.00 0.00 3.68
4796 5107 2.359850 GCCGGACCACAGATGCAA 60.360 61.111 5.05 0.00 0.00 4.08
4797 5108 3.315142 GAGCCGGACCACAGATGCA 62.315 63.158 5.05 0.00 0.00 3.96
4798 5109 2.512515 GAGCCGGACCACAGATGC 60.513 66.667 5.05 0.00 0.00 3.91
4799 5110 1.021390 GTTGAGCCGGACCACAGATG 61.021 60.000 5.05 0.00 0.00 2.90
4800 5111 1.296715 GTTGAGCCGGACCACAGAT 59.703 57.895 5.05 0.00 0.00 2.90
4801 5112 2.741092 GTTGAGCCGGACCACAGA 59.259 61.111 5.05 0.00 0.00 3.41
4802 5113 2.358737 GGTTGAGCCGGACCACAG 60.359 66.667 5.05 0.00 35.95 3.66
4803 5114 3.164977 TGGTTGAGCCGGACCACA 61.165 61.111 5.05 0.00 40.85 4.17
4804 5115 2.358737 CTGGTTGAGCCGGACCAC 60.359 66.667 5.05 0.00 46.81 4.16
4805 5116 3.636231 CCTGGTTGAGCCGGACCA 61.636 66.667 5.05 9.47 46.81 4.02
4807 5118 4.021925 AGCCTGGTTGAGCCGGAC 62.022 66.667 5.05 0.00 46.81 4.79
4808 5119 4.020617 CAGCCTGGTTGAGCCGGA 62.021 66.667 5.05 0.00 46.81 5.14
4809 5120 3.965539 CTCAGCCTGGTTGAGCCGG 62.966 68.421 24.62 0.00 43.41 6.13
4810 5121 2.249413 ATCTCAGCCTGGTTGAGCCG 62.249 60.000 29.31 12.64 40.00 5.52
4811 5122 0.833287 TATCTCAGCCTGGTTGAGCC 59.167 55.000 29.31 0.00 40.00 4.70
4812 5123 1.208052 TGTATCTCAGCCTGGTTGAGC 59.792 52.381 29.31 18.73 40.00 4.26
4813 5124 3.616956 TTGTATCTCAGCCTGGTTGAG 57.383 47.619 28.55 28.55 41.21 3.02
4814 5125 4.041567 TCTTTTGTATCTCAGCCTGGTTGA 59.958 41.667 12.85 12.85 0.00 3.18
4815 5126 4.326826 TCTTTTGTATCTCAGCCTGGTTG 58.673 43.478 3.88 3.88 0.00 3.77
4816 5127 4.640771 TCTTTTGTATCTCAGCCTGGTT 57.359 40.909 0.00 0.00 0.00 3.67
4817 5128 4.225942 TGATCTTTTGTATCTCAGCCTGGT 59.774 41.667 0.00 0.00 0.00 4.00
4818 5129 4.774124 TGATCTTTTGTATCTCAGCCTGG 58.226 43.478 0.00 0.00 0.00 4.45
4819 5130 5.821470 ACATGATCTTTTGTATCTCAGCCTG 59.179 40.000 0.00 0.00 0.00 4.85
4820 5131 5.999044 ACATGATCTTTTGTATCTCAGCCT 58.001 37.500 0.00 0.00 0.00 4.58
4821 5132 6.541641 AGAACATGATCTTTTGTATCTCAGCC 59.458 38.462 0.00 0.00 0.00 4.85
4822 5133 7.408123 CAGAACATGATCTTTTGTATCTCAGC 58.592 38.462 2.17 0.00 0.00 4.26
4823 5134 7.065443 TGCAGAACATGATCTTTTGTATCTCAG 59.935 37.037 2.17 0.00 0.00 3.35
4824 5135 6.880529 TGCAGAACATGATCTTTTGTATCTCA 59.119 34.615 2.17 0.00 0.00 3.27
4825 5136 7.148356 TGTGCAGAACATGATCTTTTGTATCTC 60.148 37.037 2.17 0.00 32.36 2.75
4826 5137 6.656270 TGTGCAGAACATGATCTTTTGTATCT 59.344 34.615 2.17 0.18 32.36 1.98
4827 5138 6.744537 GTGTGCAGAACATGATCTTTTGTATC 59.255 38.462 2.17 0.00 41.97 2.24
4830 5141 4.338964 TGTGTGCAGAACATGATCTTTTGT 59.661 37.500 2.17 0.00 41.97 2.83
4836 5147 4.224433 CAAAGTGTGTGCAGAACATGATC 58.776 43.478 0.00 0.00 41.97 2.92
4838 5149 3.016031 ACAAAGTGTGTGCAGAACATGA 58.984 40.909 0.00 0.00 41.97 3.07
4840 5151 4.175516 CAAACAAAGTGTGTGCAGAACAT 58.824 39.130 5.50 0.00 40.60 2.71
4852 5163 0.530431 GGGTGCAGGCAAACAAAGTG 60.530 55.000 0.00 0.00 0.00 3.16
4854 5165 1.069596 GGGGTGCAGGCAAACAAAG 59.930 57.895 0.00 0.00 0.00 2.77
4858 5169 2.137177 TAGAGGGGGTGCAGGCAAAC 62.137 60.000 0.00 0.00 0.00 2.93
4864 5175 1.075226 TAGGCTAGAGGGGGTGCAG 60.075 63.158 0.00 0.00 0.00 4.41
4865 5176 1.075226 CTAGGCTAGAGGGGGTGCA 60.075 63.158 16.70 0.00 0.00 4.57
4869 5180 0.541764 CTCAGCTAGGCTAGAGGGGG 60.542 65.000 25.37 9.15 36.40 5.40
4876 5187 0.460311 GTTTCCGCTCAGCTAGGCTA 59.540 55.000 0.00 0.00 36.40 3.93
4882 5193 0.312102 GCTTTTGTTTCCGCTCAGCT 59.688 50.000 0.00 0.00 0.00 4.24
4889 5200 5.433855 CAAACATCAATGCTTTTGTTTCCG 58.566 37.500 10.55 1.26 39.55 4.30
4891 5202 6.362210 ACCAAACATCAATGCTTTTGTTTC 57.638 33.333 10.55 0.00 39.55 2.78
4897 5208 3.806380 TGCAACCAAACATCAATGCTTT 58.194 36.364 0.00 0.00 34.97 3.51
4906 5217 2.985957 ACAAGCTTGCAACCAAACAT 57.014 40.000 26.27 0.00 0.00 2.71
4922 5233 1.536766 CTTTGCATCTGCGGAGAACAA 59.463 47.619 11.77 15.57 45.83 2.83
4929 5240 0.311790 ACAACACTTTGCATCTGCGG 59.688 50.000 0.00 0.00 45.83 5.69
4959 5270 7.848223 TTACCAGATCACATTGTCTTGTATG 57.152 36.000 0.00 0.00 0.00 2.39
4974 5285 5.746245 CACTCGAACAAGAGATTACCAGATC 59.254 44.000 0.62 0.00 40.57 2.75
4977 5288 4.177026 CCACTCGAACAAGAGATTACCAG 58.823 47.826 0.62 0.00 40.57 4.00
4980 5291 4.806330 TCACCACTCGAACAAGAGATTAC 58.194 43.478 0.62 0.00 40.57 1.89
4984 5295 1.613925 CCTCACCACTCGAACAAGAGA 59.386 52.381 0.62 0.00 40.57 3.10
4987 5298 2.240493 AACCTCACCACTCGAACAAG 57.760 50.000 0.00 0.00 0.00 3.16
4993 5304 1.754803 TGCCTATAACCTCACCACTCG 59.245 52.381 0.00 0.00 0.00 4.18
5001 5312 9.043079 GTTATTAGTTGTCTTGCCTATAACCTC 57.957 37.037 0.00 0.00 0.00 3.85
5008 5319 5.183228 GCCTGTTATTAGTTGTCTTGCCTA 58.817 41.667 0.00 0.00 0.00 3.93
5009 5320 4.010349 GCCTGTTATTAGTTGTCTTGCCT 58.990 43.478 0.00 0.00 0.00 4.75
5010 5321 3.756434 TGCCTGTTATTAGTTGTCTTGCC 59.244 43.478 0.00 0.00 0.00 4.52
5011 5322 5.567138 ATGCCTGTTATTAGTTGTCTTGC 57.433 39.130 0.00 0.00 0.00 4.01
5025 5367 5.570320 ACTCTGGTTTATGTTATGCCTGTT 58.430 37.500 0.00 0.00 0.00 3.16
5027 5369 5.431765 AGACTCTGGTTTATGTTATGCCTG 58.568 41.667 0.00 0.00 0.00 4.85
5043 5385 6.418226 GTGTGTGAGTACAGTTTAAGACTCTG 59.582 42.308 0.00 0.00 39.27 3.35
5056 5398 7.104043 AGTAGTTTAACTGTGTGTGAGTACA 57.896 36.000 8.00 0.00 0.00 2.90
5057 5399 6.640092 GGAGTAGTTTAACTGTGTGTGAGTAC 59.360 42.308 8.00 0.00 0.00 2.73
5098 5445 6.681729 ACTCCCTCTTGTACTAAATCAACA 57.318 37.500 0.00 0.00 0.00 3.33
5100 5447 8.092687 GTGTTACTCCCTCTTGTACTAAATCAA 58.907 37.037 0.00 0.00 0.00 2.57
5101 5448 7.233962 TGTGTTACTCCCTCTTGTACTAAATCA 59.766 37.037 0.00 0.00 0.00 2.57
5119 5466 8.472413 TGACTCTTTTAGTAAGTGTGTGTTACT 58.528 33.333 1.47 1.47 42.23 2.24
5266 5625 2.768253 TGCTGGTGATCGTCTTCAAT 57.232 45.000 0.00 0.00 0.00 2.57
5361 5720 5.163088 ACAGACTCACCCTTGATAAAGGTTT 60.163 40.000 8.14 0.00 38.28 3.27
5381 5740 0.963225 TCCGGACGATCAACAACAGA 59.037 50.000 0.00 0.00 0.00 3.41
5390 5749 0.038159 GGATCATGGTCCGGACGATC 60.038 60.000 28.88 28.88 33.30 3.69
5403 5762 1.047596 AGCTGCGTCTGGAGGATCAT 61.048 55.000 0.00 0.00 36.25 2.45
5446 5805 1.247567 CTTGACCATTGTCCCACCAC 58.752 55.000 0.00 0.00 41.01 4.16
5474 5833 1.911269 TCTGCCGCCCTGTGACTTA 60.911 57.895 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.