Multiple sequence alignment - TraesCS3D01G332100

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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 TraesCS3D01G332100 chr3D 100.000 5030 0 0 1 5030 444078550 444073521 0.000000e+00 9289.0
1 TraesCS3D01G332100 chr3A 94.011 2037 89 12 742 2755 585040126 585038100 0.000000e+00 3055.0
2 TraesCS3D01G332100 chr3A 94.055 1413 64 6 3047 4451 585038100 585036700 0.000000e+00 2126.0
3 TraesCS3D01G332100 chr3A 89.088 724 68 5 7 728 585318929 585318215 0.000000e+00 889.0
4 TraesCS3D01G332100 chr3A 94.366 142 8 0 4545 4686 585036383 585036242 8.480000e-53 219.0
5 TraesCS3D01G332100 chr3A 82.805 221 27 4 4719 4928 585036026 585035806 2.390000e-43 187.0
6 TraesCS3D01G332100 chr3B 93.775 2040 99 19 837 2853 581980416 581978382 0.000000e+00 3038.0
7 TraesCS3D01G332100 chr3B 90.836 873 52 7 2859 3712 581977988 581977125 0.000000e+00 1144.0
8 TraesCS3D01G332100 chr3B 92.487 772 45 5 3699 4464 581977106 581976342 0.000000e+00 1092.0
9 TraesCS3D01G332100 chr3B 87.743 873 70 13 1 858 581981328 581980478 0.000000e+00 985.0
10 TraesCS3D01G332100 chr1D 90.222 225 10 6 1123 1347 476430276 476430064 2.960000e-72 283.0
11 TraesCS3D01G332100 chr6B 89.286 224 12 3 1123 1346 78645657 78645868 2.310000e-68 270.0
12 TraesCS3D01G332100 chr6B 88.444 225 14 2 1123 1347 119108417 119108205 1.390000e-65 261.0
13 TraesCS3D01G332100 chr7B 88.889 225 13 2 1123 1347 706223626 706223838 2.990000e-67 267.0
14 TraesCS3D01G332100 chr6D 81.915 94 17 0 4937 5030 458532003 458531910 4.170000e-11 80.5
15 TraesCS3D01G332100 chr2B 86.154 65 9 0 2785 2849 383646726 383646662 2.510000e-08 71.3
16 TraesCS3D01G332100 chr5B 96.875 32 1 0 2786 2817 518957883 518957914 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G332100 chr3D 444073521 444078550 5029 True 9289.00 9289 100.00000 1 5030 1 chr3D.!!$R1 5029
1 TraesCS3D01G332100 chr3A 585035806 585040126 4320 True 1396.75 3055 91.30925 742 4928 4 chr3A.!!$R2 4186
2 TraesCS3D01G332100 chr3A 585318215 585318929 714 True 889.00 889 89.08800 7 728 1 chr3A.!!$R1 721
3 TraesCS3D01G332100 chr3B 581976342 581981328 4986 True 1564.75 3038 91.21025 1 4464 4 chr3B.!!$R1 4463

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
76 79 0.029035 GCTGGCTCATTCAAGCATCG 59.971 55.0 0.00 0.00 44.35 3.84 F
149 152 0.463833 GGAAATACTGGTGGCGAGGG 60.464 60.0 0.00 0.00 0.00 4.30 F
692 697 0.657312 TGTTTTCGCTGTGACTGCTG 59.343 50.0 12.54 6.45 0.00 4.41 F
2073 2197 0.787787 TTTCGAAGACACCGAATGCG 59.212 50.0 0.00 0.00 44.15 4.73 F
2939 3477 0.253044 GCAGGGCACTCATGGTTCTA 59.747 55.0 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1786 1.571460 GGCACAAACAGCACTCGAG 59.429 57.895 11.84 11.84 0.00 4.04 R
2098 2222 2.300152 TCTCAACCTCACTGTTAGCTGG 59.700 50.000 0.00 0.00 0.00 4.85 R
2507 2647 1.078759 GAGAGCATCCACCAACGACG 61.079 60.000 0.00 0.00 33.66 5.12 R
3865 4458 1.635817 AACCGGTAGCCATGCCAGAT 61.636 55.000 8.00 0.00 0.00 2.90 R
4723 5603 0.808453 GGGTATGCGTGCACGTATGT 60.808 55.000 40.85 26.23 44.05 2.29 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
38 39 2.743928 CTCACAAGCACCCTCCGC 60.744 66.667 0.00 0.00 0.00 5.54
59 60 1.546476 CTCAGGTACCTCTTCAACGCT 59.454 52.381 12.84 0.00 0.00 5.07
76 79 0.029035 GCTGGCTCATTCAAGCATCG 59.971 55.000 0.00 0.00 44.35 3.84
115 118 3.837355 AGAACCACTTCAAGCCTTCATT 58.163 40.909 0.00 0.00 0.00 2.57
149 152 0.463833 GGAAATACTGGTGGCGAGGG 60.464 60.000 0.00 0.00 0.00 4.30
271 274 2.379634 GCAAATCAAAACGCCGGGC 61.380 57.895 9.54 9.54 0.00 6.13
290 293 3.316573 CTCAACCCTCAGCGACCCC 62.317 68.421 0.00 0.00 0.00 4.95
291 294 3.322466 CAACCCTCAGCGACCCCT 61.322 66.667 0.00 0.00 0.00 4.79
292 295 3.322466 AACCCTCAGCGACCCCTG 61.322 66.667 0.00 0.00 0.00 4.45
293 296 3.846405 AACCCTCAGCGACCCCTGA 62.846 63.158 0.00 0.00 39.42 3.86
294 297 3.003173 CCCTCAGCGACCCCTGAA 61.003 66.667 0.00 0.00 41.02 3.02
295 298 2.581354 CCTCAGCGACCCCTGAAG 59.419 66.667 0.00 0.00 41.02 3.02
296 299 2.581354 CTCAGCGACCCCTGAAGG 59.419 66.667 0.00 0.00 41.02 3.46
368 371 6.142817 GTGGCTTGTAATAGTTTGTGTTGAG 58.857 40.000 0.00 0.00 0.00 3.02
385 388 1.977854 TGAGAACTTCTAAGGGCTGCA 59.022 47.619 0.50 0.00 0.00 4.41
468 471 1.247567 GGCTGTGGTTGTAGTGCAAT 58.752 50.000 0.00 0.00 39.55 3.56
481 484 6.358118 TGTAGTGCAATCCGTCAATTTATC 57.642 37.500 0.00 0.00 0.00 1.75
527 530 7.426929 AATATCGTGCATCTTGATAAACCTC 57.573 36.000 0.00 0.00 0.00 3.85
590 595 6.995511 TTTCTCTAATGGGGAATAAACACG 57.004 37.500 0.00 0.00 0.00 4.49
657 662 2.421424 GCTTGTCCAGCTCTTATTGTGG 59.579 50.000 0.00 0.00 46.27 4.17
671 676 2.869101 TTGTGGAATTGACCGATCCA 57.131 45.000 0.00 0.00 40.84 3.41
680 685 3.822594 TTGACCGATCCAATGTTTTCG 57.177 42.857 0.00 0.00 0.00 3.46
684 689 1.468520 CCGATCCAATGTTTTCGCTGT 59.531 47.619 0.00 0.00 0.00 4.40
692 697 0.657312 TGTTTTCGCTGTGACTGCTG 59.343 50.000 12.54 6.45 0.00 4.41
792 812 5.508489 CGTGTTTTACTGGTCCTCTACTTCA 60.508 44.000 0.00 0.00 0.00 3.02
800 820 7.741554 ACTGGTCCTCTACTTCAGAAATAAT 57.258 36.000 0.00 0.00 31.12 1.28
985 1104 1.132332 TCCCCTCTGTAAAACCCCTCA 60.132 52.381 0.00 0.00 0.00 3.86
1048 1167 2.286121 TCCTCCTCCCGGCCATTT 60.286 61.111 2.24 0.00 0.00 2.32
1248 1367 2.025969 CACTCAGGTGCGCTGTCTG 61.026 63.158 9.73 13.46 36.61 3.51
1300 1419 2.595655 GTGGTATGGGAGGCCACC 59.404 66.667 11.39 11.39 44.95 4.61
1367 1486 3.499537 TCGCTGCATTGTCATGGAATATC 59.500 43.478 0.00 0.00 28.90 1.63
1428 1547 4.173256 CCTTCTGTTGTCACCAAAAACAC 58.827 43.478 0.00 0.00 30.94 3.32
1663 1786 7.427606 GGTATACATCGTTATCGCACTATGTAC 59.572 40.741 5.01 0.00 36.56 2.90
1694 1817 2.125753 GTGCCGCCTCTCACTCAG 60.126 66.667 0.00 0.00 0.00 3.35
1771 1894 8.887036 ATTAATTTCTCCAAACAAGGTTTGAC 57.113 30.769 20.13 0.00 0.00 3.18
2073 2197 0.787787 TTTCGAAGACACCGAATGCG 59.212 50.000 0.00 0.00 44.15 4.73
2098 2222 6.774354 ACATGTTTCAGCAATTCAACAATC 57.226 33.333 0.00 0.00 33.02 2.67
2312 2444 2.045926 GCGAGCATTGGGACTGGT 60.046 61.111 0.00 0.00 0.00 4.00
2464 2604 4.709397 TCAACAACTTCACCCATTTTCTGT 59.291 37.500 0.00 0.00 0.00 3.41
2493 2633 8.893219 TTTTTCCAATGTTGTTGCATTACATA 57.107 26.923 8.66 0.00 37.00 2.29
2507 2647 9.185192 GTTGCATTACATATTAATTCTTCTGCC 57.815 33.333 0.00 0.00 0.00 4.85
2624 2766 8.680820 AGGGCCAGTATAAATATACAGTACAT 57.319 34.615 6.18 0.00 40.70 2.29
2643 2785 8.668353 CAGTACATGCAGAAATATGTACAAACT 58.332 33.333 21.75 6.14 46.93 2.66
2727 2870 1.421268 TCTGAGTGTTGCTCCATTGGT 59.579 47.619 1.86 0.00 43.48 3.67
2760 2903 4.358841 TTGCCCATCCCACCCACG 62.359 66.667 0.00 0.00 0.00 4.94
2764 2907 4.838152 CCATCCCACCCACGCGAG 62.838 72.222 15.93 4.16 0.00 5.03
2783 2927 2.843352 GCCTAGCCTCCGACGGTAC 61.843 68.421 14.79 4.61 0.00 3.34
2797 2941 1.227556 GGTACGGATGCAAGCGGAT 60.228 57.895 0.00 0.00 0.00 4.18
2813 2957 4.094646 ATGGCGTCCGCATGTCCA 62.095 61.111 14.19 2.06 44.11 4.02
2844 2988 6.581166 GTCCGCAAACAGGAAAATTAAACTAG 59.419 38.462 0.00 0.00 39.84 2.57
2853 2997 9.005777 ACAGGAAAATTAAACTAGCACGATTAA 57.994 29.630 0.00 0.00 0.00 1.40
2854 2998 9.834628 CAGGAAAATTAAACTAGCACGATTAAA 57.165 29.630 0.00 0.00 0.00 1.52
2883 3414 8.986477 ATGAGGATTAGTGCAATTTTTGTTAC 57.014 30.769 0.00 0.00 0.00 2.50
2885 3416 6.977213 AGGATTAGTGCAATTTTTGTTACGT 58.023 32.000 0.00 0.00 0.00 3.57
2937 3475 1.303561 TGCAGGGCACTCATGGTTC 60.304 57.895 0.00 0.00 31.71 3.62
2939 3477 0.253044 GCAGGGCACTCATGGTTCTA 59.747 55.000 0.00 0.00 0.00 2.10
2940 3478 1.340017 GCAGGGCACTCATGGTTCTAA 60.340 52.381 0.00 0.00 0.00 2.10
2941 3479 2.879756 GCAGGGCACTCATGGTTCTAAA 60.880 50.000 0.00 0.00 0.00 1.85
2972 3514 4.282195 GCCATAGGTGCTAGTGTCTATTCT 59.718 45.833 0.00 0.00 0.00 2.40
2976 3518 4.605183 AGGTGCTAGTGTCTATTCTCTGT 58.395 43.478 0.00 0.00 0.00 3.41
2981 3523 5.246203 TGCTAGTGTCTATTCTCTGTTGGTT 59.754 40.000 0.00 0.00 0.00 3.67
2987 3529 7.389053 AGTGTCTATTCTCTGTTGGTTGAATTC 59.611 37.037 0.00 0.00 32.33 2.17
2988 3530 7.389053 GTGTCTATTCTCTGTTGGTTGAATTCT 59.611 37.037 7.05 0.00 32.33 2.40
2994 3536 6.042143 TCTCTGTTGGTTGAATTCTTTTTGC 58.958 36.000 7.05 0.00 0.00 3.68
2995 3537 5.115480 TCTGTTGGTTGAATTCTTTTTGCC 58.885 37.500 7.05 1.10 0.00 4.52
2996 3538 4.195416 TGTTGGTTGAATTCTTTTTGCCC 58.805 39.130 7.05 0.00 0.00 5.36
2997 3539 4.080638 TGTTGGTTGAATTCTTTTTGCCCT 60.081 37.500 7.05 0.00 0.00 5.19
3011 3553 1.185315 TGCCCTTTTATTGCTCTGCC 58.815 50.000 0.00 0.00 0.00 4.85
3055 3597 8.927675 TTTTGAAGTAAAACATAGGCCTTAGA 57.072 30.769 12.58 0.00 33.48 2.10
3072 3614 4.202264 CCTTAGATGGAAATAGCTCACCGT 60.202 45.833 0.00 0.00 0.00 4.83
3082 3624 0.969894 AGCTCACCGTTCTGCTACTT 59.030 50.000 0.00 0.00 33.64 2.24
3083 3625 1.071605 GCTCACCGTTCTGCTACTTG 58.928 55.000 0.00 0.00 0.00 3.16
3104 3646 6.151144 ACTTGGATGTACTGCTTTACCATTTC 59.849 38.462 0.00 0.00 0.00 2.17
3123 3668 9.528489 ACCATTTCTGTAATTTAGCTTTTAGGA 57.472 29.630 0.00 0.00 0.00 2.94
3137 3682 4.381292 GCTTTTAGGAGAACTTGCATGCAT 60.381 41.667 23.37 6.60 0.00 3.96
3235 3788 4.344104 ACATTCCATAACCTGAAACCTGG 58.656 43.478 0.00 0.00 0.00 4.45
3238 3791 4.028993 TCCATAACCTGAAACCTGGAAC 57.971 45.455 0.00 0.00 30.15 3.62
3416 3977 8.093307 TGGATGTATTTGAGAGATGAGCTTATC 58.907 37.037 10.42 10.42 0.00 1.75
3424 3985 6.907741 TGAGAGATGAGCTTATCGAATACAG 58.092 40.000 12.39 0.00 32.33 2.74
3435 3996 4.696479 ATCGAATACAGCTTCCTTGGAT 57.304 40.909 0.00 0.00 0.00 3.41
3442 4003 3.771216 ACAGCTTCCTTGGATTTGACAT 58.229 40.909 0.00 0.00 0.00 3.06
3443 4004 3.508793 ACAGCTTCCTTGGATTTGACATG 59.491 43.478 0.00 0.00 0.00 3.21
3447 4008 5.954150 AGCTTCCTTGGATTTGACATGTTAT 59.046 36.000 0.00 0.00 0.00 1.89
3451 4012 6.923012 TCCTTGGATTTGACATGTTATTGTG 58.077 36.000 0.00 0.00 0.00 3.33
3452 4013 6.071447 TCCTTGGATTTGACATGTTATTGTGG 60.071 38.462 0.00 0.00 0.00 4.17
3526 4087 1.541588 GTGAAGGTCTGGAATGCAACC 59.458 52.381 6.38 6.38 0.00 3.77
3541 4102 6.183360 GGAATGCAACCCTAGTATTCTGTTTC 60.183 42.308 0.00 0.00 37.94 2.78
3846 4439 2.218953 TGCGGTGAGATATTTCCGTC 57.781 50.000 0.00 0.00 44.07 4.79
3865 4458 3.637432 GTCGATTTGAACATGTTGCCAA 58.363 40.909 17.58 12.07 0.00 4.52
3969 4566 3.054361 TCCCCAGCTTTGGAGAAAGATAC 60.054 47.826 0.37 0.00 41.12 2.24
4114 4711 1.970114 CAAGCAGGGCTGAGGTGTG 60.970 63.158 0.00 0.00 39.62 3.82
4151 4748 4.440127 GGGCGCGGGTCGTAGAAA 62.440 66.667 8.83 0.00 39.69 2.52
4154 4751 1.131218 GCGCGGGTCGTAGAAAAAC 59.869 57.895 8.83 0.00 39.69 2.43
4164 4761 7.013529 CGGGTCGTAGAAAAACTTTGAAATAG 58.986 38.462 0.00 0.00 39.69 1.73
4271 4868 7.368059 TGTTGTATACTGTATTATCTGCCTCG 58.632 38.462 5.52 0.00 0.00 4.63
4382 4981 6.674694 ACAGACTTGTCATCTGATATTTGC 57.325 37.500 9.89 0.00 45.46 3.68
4409 5008 8.423906 TGATCTTACTAAATGGTCTCCTATCC 57.576 38.462 0.00 0.00 0.00 2.59
4502 5217 1.824852 TGCATACTCTCTCCTTTGCGA 59.175 47.619 0.00 0.00 32.90 5.10
4534 5249 2.955022 ATCGTAGTCCCTCCGTCCCG 62.955 65.000 0.00 0.00 0.00 5.14
4549 5371 4.704540 TCCGTCCCGACTACTAAATTTGTA 59.295 41.667 0.00 1.15 0.00 2.41
4594 5416 4.189639 ACGAGTGATTTCTGTTACCTCC 57.810 45.455 0.00 0.00 0.00 4.30
4608 5430 2.165319 ACCTCCGCTGTTCTTTGTAC 57.835 50.000 0.00 0.00 0.00 2.90
4609 5431 1.414919 ACCTCCGCTGTTCTTTGTACA 59.585 47.619 0.00 0.00 0.00 2.90
4640 5462 8.418662 TGTGTTCTTTGTACTATAGTGACAGTT 58.581 33.333 15.90 0.00 0.00 3.16
4740 5745 2.456989 AGTACATACGTGCACGCATAC 58.543 47.619 37.35 29.29 44.43 2.39
4751 5756 2.186903 CGCATACCCTTCGGCTGT 59.813 61.111 0.00 0.00 0.00 4.40
4753 5758 1.220749 GCATACCCTTCGGCTGTGA 59.779 57.895 0.00 0.00 0.00 3.58
4784 5800 2.593468 TAGGGTTGCTCGCATCCTGC 62.593 60.000 18.43 6.07 40.69 4.85
4848 5864 5.965202 TCGAACATTTGTAGTAAACACGTG 58.035 37.500 15.48 15.48 38.00 4.49
4863 5879 2.573802 CGTGCACGTATACCCTTCG 58.426 57.895 30.50 0.20 34.11 3.79
4865 5881 3.470393 CGTGCACGTATACCCTTCGGT 62.470 57.143 30.50 0.00 39.31 4.69
4869 5885 0.179129 ACGTATACCCTTCGGTTGCG 60.179 55.000 0.00 0.00 40.58 4.85
4887 5903 1.333931 GCGACTTAAGGCAATTAGGGC 59.666 52.381 9.49 0.00 0.00 5.19
4923 5939 2.108168 GGTGCCACTGTAGGTCTATCA 58.892 52.381 0.00 0.00 0.00 2.15
4928 5944 3.243907 GCCACTGTAGGTCTATCATGTCC 60.244 52.174 0.00 0.00 0.00 4.02
4929 5945 3.960755 CCACTGTAGGTCTATCATGTCCA 59.039 47.826 0.00 0.00 0.00 4.02
4930 5946 4.405680 CCACTGTAGGTCTATCATGTCCAA 59.594 45.833 0.00 0.00 0.00 3.53
4931 5947 5.352284 CACTGTAGGTCTATCATGTCCAAC 58.648 45.833 0.00 0.00 0.00 3.77
4932 5948 5.127845 CACTGTAGGTCTATCATGTCCAACT 59.872 44.000 0.00 0.00 0.00 3.16
4933 5949 5.361285 ACTGTAGGTCTATCATGTCCAACTC 59.639 44.000 0.00 0.00 0.00 3.01
4934 5950 5.519808 TGTAGGTCTATCATGTCCAACTCT 58.480 41.667 0.00 0.00 0.00 3.24
4935 5951 5.360999 TGTAGGTCTATCATGTCCAACTCTG 59.639 44.000 0.00 0.00 0.00 3.35
4936 5952 4.357325 AGGTCTATCATGTCCAACTCTGT 58.643 43.478 0.00 0.00 0.00 3.41
4937 5953 4.780021 AGGTCTATCATGTCCAACTCTGTT 59.220 41.667 0.00 0.00 0.00 3.16
4938 5954 5.249393 AGGTCTATCATGTCCAACTCTGTTT 59.751 40.000 0.00 0.00 0.00 2.83
4939 5955 5.940470 GGTCTATCATGTCCAACTCTGTTTT 59.060 40.000 0.00 0.00 0.00 2.43
4940 5956 7.038302 AGGTCTATCATGTCCAACTCTGTTTTA 60.038 37.037 0.00 0.00 0.00 1.52
4941 5957 7.278868 GGTCTATCATGTCCAACTCTGTTTTAG 59.721 40.741 0.00 0.00 0.00 1.85
4942 5958 7.278868 GTCTATCATGTCCAACTCTGTTTTAGG 59.721 40.741 0.00 0.00 0.00 2.69
4943 5959 5.304686 TCATGTCCAACTCTGTTTTAGGT 57.695 39.130 0.00 0.00 0.00 3.08
4944 5960 5.063204 TCATGTCCAACTCTGTTTTAGGTG 58.937 41.667 0.00 0.00 0.00 4.00
4945 5961 4.497291 TGTCCAACTCTGTTTTAGGTGT 57.503 40.909 0.00 0.00 29.18 4.16
4946 5962 4.448210 TGTCCAACTCTGTTTTAGGTGTC 58.552 43.478 0.00 0.00 29.18 3.67
4947 5963 4.163458 TGTCCAACTCTGTTTTAGGTGTCT 59.837 41.667 0.00 0.00 29.18 3.41
4948 5964 5.123936 GTCCAACTCTGTTTTAGGTGTCTT 58.876 41.667 0.00 0.00 29.18 3.01
4949 5965 5.589050 GTCCAACTCTGTTTTAGGTGTCTTT 59.411 40.000 0.00 0.00 29.18 2.52
4950 5966 6.095021 GTCCAACTCTGTTTTAGGTGTCTTTT 59.905 38.462 0.00 0.00 29.18 2.27
4951 5967 6.661805 TCCAACTCTGTTTTAGGTGTCTTTTT 59.338 34.615 0.00 0.00 29.18 1.94
4952 5968 6.972901 CCAACTCTGTTTTAGGTGTCTTTTTC 59.027 38.462 0.00 0.00 29.18 2.29
4953 5969 7.148069 CCAACTCTGTTTTAGGTGTCTTTTTCT 60.148 37.037 0.00 0.00 29.18 2.52
4954 5970 7.321745 ACTCTGTTTTAGGTGTCTTTTTCTG 57.678 36.000 0.00 0.00 0.00 3.02
4955 5971 6.884836 ACTCTGTTTTAGGTGTCTTTTTCTGT 59.115 34.615 0.00 0.00 0.00 3.41
4956 5972 7.393515 ACTCTGTTTTAGGTGTCTTTTTCTGTT 59.606 33.333 0.00 0.00 0.00 3.16
4957 5973 8.117813 TCTGTTTTAGGTGTCTTTTTCTGTTT 57.882 30.769 0.00 0.00 0.00 2.83
4958 5974 8.241367 TCTGTTTTAGGTGTCTTTTTCTGTTTC 58.759 33.333 0.00 0.00 0.00 2.78
4959 5975 8.117813 TGTTTTAGGTGTCTTTTTCTGTTTCT 57.882 30.769 0.00 0.00 0.00 2.52
4960 5976 8.581578 TGTTTTAGGTGTCTTTTTCTGTTTCTT 58.418 29.630 0.00 0.00 0.00 2.52
4961 5977 9.419297 GTTTTAGGTGTCTTTTTCTGTTTCTTT 57.581 29.630 0.00 0.00 0.00 2.52
4964 5980 7.334844 AGGTGTCTTTTTCTGTTTCTTTAGG 57.665 36.000 0.00 0.00 0.00 2.69
4965 5981 5.977725 GGTGTCTTTTTCTGTTTCTTTAGGC 59.022 40.000 0.00 0.00 0.00 3.93
4966 5982 6.183360 GGTGTCTTTTTCTGTTTCTTTAGGCT 60.183 38.462 0.00 0.00 0.00 4.58
4967 5983 7.258441 GTGTCTTTTTCTGTTTCTTTAGGCTT 58.742 34.615 0.00 0.00 0.00 4.35
4968 5984 7.759886 GTGTCTTTTTCTGTTTCTTTAGGCTTT 59.240 33.333 0.00 0.00 0.00 3.51
4969 5985 7.759433 TGTCTTTTTCTGTTTCTTTAGGCTTTG 59.241 33.333 0.00 0.00 0.00 2.77
4970 5986 7.759886 GTCTTTTTCTGTTTCTTTAGGCTTTGT 59.240 33.333 0.00 0.00 0.00 2.83
4971 5987 7.759433 TCTTTTTCTGTTTCTTTAGGCTTTGTG 59.241 33.333 0.00 0.00 0.00 3.33
4972 5988 6.524101 TTTCTGTTTCTTTAGGCTTTGTGT 57.476 33.333 0.00 0.00 0.00 3.72
4973 5989 6.524101 TTCTGTTTCTTTAGGCTTTGTGTT 57.476 33.333 0.00 0.00 0.00 3.32
4974 5990 6.131544 TCTGTTTCTTTAGGCTTTGTGTTC 57.868 37.500 0.00 0.00 0.00 3.18
4975 5991 5.885912 TCTGTTTCTTTAGGCTTTGTGTTCT 59.114 36.000 0.00 0.00 0.00 3.01
4976 5992 5.890334 TGTTTCTTTAGGCTTTGTGTTCTG 58.110 37.500 0.00 0.00 0.00 3.02
4977 5993 4.568152 TTCTTTAGGCTTTGTGTTCTGC 57.432 40.909 0.00 0.00 0.00 4.26
4978 5994 3.820557 TCTTTAGGCTTTGTGTTCTGCT 58.179 40.909 0.00 0.00 0.00 4.24
4979 5995 3.815401 TCTTTAGGCTTTGTGTTCTGCTC 59.185 43.478 0.00 0.00 0.00 4.26
4980 5996 2.928801 TAGGCTTTGTGTTCTGCTCA 57.071 45.000 0.00 0.00 0.00 4.26
4981 5997 2.283145 AGGCTTTGTGTTCTGCTCAT 57.717 45.000 0.00 0.00 0.00 2.90
4982 5998 3.423539 AGGCTTTGTGTTCTGCTCATA 57.576 42.857 0.00 0.00 0.00 2.15
4983 5999 3.754965 AGGCTTTGTGTTCTGCTCATAA 58.245 40.909 0.00 0.00 0.00 1.90
4984 6000 4.144297 AGGCTTTGTGTTCTGCTCATAAA 58.856 39.130 0.00 0.00 0.00 1.40
4985 6001 4.217118 AGGCTTTGTGTTCTGCTCATAAAG 59.783 41.667 9.57 9.57 42.56 1.85
5004 6020 1.949257 CCAAGACGGCAACAGTTCC 59.051 57.895 0.00 0.00 0.00 3.62
5005 6021 1.515521 CCAAGACGGCAACAGTTCCC 61.516 60.000 0.00 0.00 0.00 3.97
5006 6022 0.535102 CAAGACGGCAACAGTTCCCT 60.535 55.000 0.00 0.00 0.00 4.20
5007 6023 0.535102 AAGACGGCAACAGTTCCCTG 60.535 55.000 0.00 0.00 44.68 4.45
5008 6024 1.070786 GACGGCAACAGTTCCCTGA 59.929 57.895 0.00 0.00 41.50 3.86
5009 6025 0.951040 GACGGCAACAGTTCCCTGAG 60.951 60.000 0.00 0.00 41.50 3.35
5010 6026 1.672356 CGGCAACAGTTCCCTGAGG 60.672 63.158 0.00 0.00 41.50 3.86
5011 6027 1.761174 GGCAACAGTTCCCTGAGGA 59.239 57.895 0.00 0.00 41.50 3.71
5012 6028 0.329596 GGCAACAGTTCCCTGAGGAT 59.670 55.000 0.00 0.00 43.54 3.24
5013 6029 1.457346 GCAACAGTTCCCTGAGGATG 58.543 55.000 0.00 0.00 43.54 3.51
5014 6030 1.952367 GCAACAGTTCCCTGAGGATGG 60.952 57.143 0.00 0.00 43.54 3.51
5015 6031 1.630369 CAACAGTTCCCTGAGGATGGA 59.370 52.381 0.00 0.00 43.54 3.41
5016 6032 2.040278 CAACAGTTCCCTGAGGATGGAA 59.960 50.000 0.00 0.00 43.54 3.53
5017 6033 2.566746 ACAGTTCCCTGAGGATGGAAT 58.433 47.619 0.00 0.00 43.54 3.01
5018 6034 3.736094 ACAGTTCCCTGAGGATGGAATA 58.264 45.455 0.00 0.00 43.54 1.75
5019 6035 4.111577 ACAGTTCCCTGAGGATGGAATAA 58.888 43.478 0.00 0.00 43.54 1.40
5020 6036 4.728860 ACAGTTCCCTGAGGATGGAATAAT 59.271 41.667 0.00 0.00 43.54 1.28
5021 6037 5.068636 CAGTTCCCTGAGGATGGAATAATG 58.931 45.833 0.00 0.00 43.54 1.90
5022 6038 4.728860 AGTTCCCTGAGGATGGAATAATGT 59.271 41.667 0.00 0.00 43.54 2.71
5023 6039 5.194537 AGTTCCCTGAGGATGGAATAATGTT 59.805 40.000 0.00 0.00 43.54 2.71
5024 6040 5.310409 TCCCTGAGGATGGAATAATGTTC 57.690 43.478 0.00 0.00 37.19 3.18
5025 6041 4.977739 TCCCTGAGGATGGAATAATGTTCT 59.022 41.667 0.00 0.00 37.19 3.01
5026 6042 5.072329 TCCCTGAGGATGGAATAATGTTCTC 59.928 44.000 0.00 0.00 37.19 2.87
5027 6043 5.312079 CCTGAGGATGGAATAATGTTCTCC 58.688 45.833 0.00 0.00 0.00 3.71
5028 6044 5.310409 TGAGGATGGAATAATGTTCTCCC 57.690 43.478 0.00 0.00 0.00 4.30
5029 6045 4.104738 TGAGGATGGAATAATGTTCTCCCC 59.895 45.833 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.065926 GTGAGGATGATGGTGCAGTCA 60.066 52.381 0.00 0.00 0.00 3.41
16 17 0.615331 GAGGGTGCTTGTGAGGATGA 59.385 55.000 0.00 0.00 0.00 2.92
38 39 1.404315 GCGTTGAAGAGGTACCTGAGG 60.404 57.143 22.10 0.00 0.00 3.86
59 60 1.378882 GCCGATGCTTGAATGAGCCA 61.379 55.000 0.00 0.00 42.01 4.75
115 118 6.122277 CAGTATTTCCTGGCCTGAAAATCTA 58.878 40.000 20.15 9.42 35.52 1.98
149 152 0.033208 TTGGGCTTCATCATCCACCC 60.033 55.000 0.00 0.00 37.88 4.61
271 274 2.266055 GGTCGCTGAGGGTTGAGG 59.734 66.667 0.00 0.00 0.00 3.86
290 293 6.150140 ACATAAGTTTAAGCTTCAGCCTTCAG 59.850 38.462 7.93 1.11 43.38 3.02
291 294 6.003950 ACATAAGTTTAAGCTTCAGCCTTCA 58.996 36.000 7.93 0.00 43.38 3.02
292 295 6.502136 ACATAAGTTTAAGCTTCAGCCTTC 57.498 37.500 7.93 0.00 43.38 3.46
293 296 6.901081 AACATAAGTTTAAGCTTCAGCCTT 57.099 33.333 7.93 4.10 36.72 4.35
294 297 6.490040 TCAAACATAAGTTTAAGCTTCAGCCT 59.510 34.615 7.93 0.00 45.80 4.58
295 298 6.677913 TCAAACATAAGTTTAAGCTTCAGCC 58.322 36.000 7.93 0.00 45.80 4.85
296 299 8.574196 TTTCAAACATAAGTTTAAGCTTCAGC 57.426 30.769 7.93 0.00 45.80 4.26
368 371 3.006247 CTCTTGCAGCCCTTAGAAGTTC 58.994 50.000 0.00 0.00 0.00 3.01
385 388 2.574006 TCAAGTGCTTGATGGCTCTT 57.426 45.000 10.26 0.00 43.90 2.85
468 471 7.598189 TTCATACAAACGATAAATTGACGGA 57.402 32.000 0.00 0.00 0.00 4.69
500 503 8.686334 AGGTTTATCAAGATGCACGATATTTTT 58.314 29.630 0.00 0.00 0.00 1.94
509 512 6.012658 TGTTTGAGGTTTATCAAGATGCAC 57.987 37.500 0.00 0.00 40.16 4.57
527 530 1.795170 CTCCCTGCCCACGTTGTTTG 61.795 60.000 0.00 0.00 0.00 2.93
650 655 4.495690 TGGATCGGTCAATTCCACAATA 57.504 40.909 0.00 0.00 34.65 1.90
651 656 3.364460 TGGATCGGTCAATTCCACAAT 57.636 42.857 0.00 0.00 34.65 2.71
653 658 2.869101 TTGGATCGGTCAATTCCACA 57.131 45.000 0.00 0.00 39.21 4.17
657 662 4.793216 CGAAAACATTGGATCGGTCAATTC 59.207 41.667 0.00 0.00 33.08 2.17
671 676 1.949525 AGCAGTCACAGCGAAAACATT 59.050 42.857 0.00 0.00 37.01 2.71
680 685 1.168407 TCTTTGCCAGCAGTCACAGC 61.168 55.000 0.00 0.00 0.00 4.40
684 689 1.761449 TTGTTCTTTGCCAGCAGTCA 58.239 45.000 0.00 0.00 0.00 3.41
692 697 3.065648 TCCGTGTACTTTTGTTCTTTGCC 59.934 43.478 0.00 0.00 0.00 4.52
778 794 8.041323 GTCAATTATTTCTGAAGTAGAGGACCA 58.959 37.037 0.00 0.00 36.61 4.02
779 795 7.222999 CGTCAATTATTTCTGAAGTAGAGGACC 59.777 40.741 10.94 0.00 36.61 4.46
780 796 7.760340 ACGTCAATTATTTCTGAAGTAGAGGAC 59.240 37.037 7.09 7.82 36.61 3.85
1248 1367 3.193479 GGAAACACAATCAGGATGGGAAC 59.807 47.826 0.00 0.00 36.16 3.62
1300 1419 9.398170 CCATAATACAAAATCTTAATGGCTTCG 57.602 33.333 0.00 0.00 0.00 3.79
1339 1458 1.675641 GACAATGCAGCGAACCCCT 60.676 57.895 0.00 0.00 0.00 4.79
1462 1581 3.664107 TCACATAGGTTGCTTCACAGAC 58.336 45.455 0.00 0.00 0.00 3.51
1466 1585 4.095483 CCAATCTCACATAGGTTGCTTCAC 59.905 45.833 0.00 0.00 43.86 3.18
1663 1786 1.571460 GGCACAAACAGCACTCGAG 59.429 57.895 11.84 11.84 0.00 4.04
1694 1817 6.476706 GCTTAATGCAATCCTGGAAAACATAC 59.523 38.462 0.00 0.00 42.31 2.39
2015 2139 4.591498 TGTCAACAGCTCCTTTTAGTCCTA 59.409 41.667 0.00 0.00 0.00 2.94
2073 2197 7.148755 GGATTGTTGAATTGCTGAAACATGTAC 60.149 37.037 0.00 0.00 32.90 2.90
2098 2222 2.300152 TCTCAACCTCACTGTTAGCTGG 59.700 50.000 0.00 0.00 0.00 4.85
2312 2444 2.267642 GTGCCGGTGATAGTGCCA 59.732 61.111 1.90 0.00 0.00 4.92
2421 2553 9.891828 TTGTTGACACAATAACATAGTCATTTC 57.108 29.630 0.00 0.00 38.03 2.17
2424 2556 8.621532 AGTTGTTGACACAATAACATAGTCAT 57.378 30.769 19.89 2.21 44.85 3.06
2425 2557 8.445275 AAGTTGTTGACACAATAACATAGTCA 57.555 30.769 19.89 0.00 44.85 3.41
2426 2558 8.556194 TGAAGTTGTTGACACAATAACATAGTC 58.444 33.333 19.89 13.60 44.85 2.59
2427 2559 8.342634 GTGAAGTTGTTGACACAATAACATAGT 58.657 33.333 19.89 7.59 44.85 2.12
2428 2560 7.803189 GGTGAAGTTGTTGACACAATAACATAG 59.197 37.037 19.89 0.00 44.85 2.23
2429 2561 7.255312 GGGTGAAGTTGTTGACACAATAACATA 60.255 37.037 19.89 8.08 44.85 2.29
2493 2633 3.374058 CCAACGACGGCAGAAGAATTAAT 59.626 43.478 0.00 0.00 0.00 1.40
2507 2647 1.078759 GAGAGCATCCACCAACGACG 61.079 60.000 0.00 0.00 33.66 5.12
2624 2766 5.815581 AGGGAGTTTGTACATATTTCTGCA 58.184 37.500 0.00 0.00 0.00 4.41
2635 2777 7.933215 ACCATTGTTATAAGGGAGTTTGTAC 57.067 36.000 0.00 0.00 0.00 2.90
2776 2919 2.514013 CGCTTGCATCCGTACCGTC 61.514 63.158 0.00 0.00 0.00 4.79
2779 2923 1.227556 ATCCGCTTGCATCCGTACC 60.228 57.895 5.90 0.00 0.00 3.34
2783 2927 3.957535 GCCATCCGCTTGCATCCG 61.958 66.667 0.00 0.00 0.00 4.18
2801 2945 2.094659 CAGTCGTGGACATGCGGAC 61.095 63.158 0.00 0.00 34.60 4.79
2813 2957 1.594293 CCTGTTTGCGGACAGTCGT 60.594 57.895 15.49 0.00 44.34 4.34
2844 2988 9.599322 CACTAATCCTCATTATTTTAATCGTGC 57.401 33.333 0.00 0.00 0.00 5.34
2858 3002 7.754924 CGTAACAAAAATTGCACTAATCCTCAT 59.245 33.333 0.00 0.00 0.00 2.90
2860 3004 7.060633 CACGTAACAAAAATTGCACTAATCCTC 59.939 37.037 0.00 0.00 0.00 3.71
2862 3006 6.088883 CCACGTAACAAAAATTGCACTAATCC 59.911 38.462 0.00 0.00 0.00 3.01
2863 3007 6.858993 TCCACGTAACAAAAATTGCACTAATC 59.141 34.615 0.00 0.00 0.00 1.75
2951 3489 6.264292 ACAGAGAATAGACACTAGCACCTATG 59.736 42.308 0.00 0.00 0.00 2.23
2972 3514 5.115480 GGCAAAAAGAATTCAACCAACAGA 58.885 37.500 8.44 0.00 0.00 3.41
2976 3518 4.769345 AGGGCAAAAAGAATTCAACCAA 57.231 36.364 8.44 0.00 0.00 3.67
2981 3523 6.997476 AGCAATAAAAGGGCAAAAAGAATTCA 59.003 30.769 8.44 0.00 0.00 2.57
2987 3529 4.152938 GCAGAGCAATAAAAGGGCAAAAAG 59.847 41.667 0.00 0.00 0.00 2.27
2988 3530 4.064388 GCAGAGCAATAAAAGGGCAAAAA 58.936 39.130 0.00 0.00 0.00 1.94
2994 3536 3.959535 TTTGGCAGAGCAATAAAAGGG 57.040 42.857 0.00 0.00 0.00 3.95
2995 3537 5.178067 CACTTTTTGGCAGAGCAATAAAAGG 59.822 40.000 17.66 12.43 36.73 3.11
2996 3538 5.984926 TCACTTTTTGGCAGAGCAATAAAAG 59.015 36.000 13.80 13.80 37.53 2.27
2997 3539 5.911752 TCACTTTTTGGCAGAGCAATAAAA 58.088 33.333 0.00 0.00 0.00 1.52
3011 3553 9.217223 CTTCAAAATTCTGCATTTCACTTTTTG 57.783 29.630 0.00 0.00 33.60 2.44
3055 3597 3.535561 CAGAACGGTGAGCTATTTCCAT 58.464 45.455 0.00 0.00 0.00 3.41
3072 3614 3.515502 AGCAGTACATCCAAGTAGCAGAA 59.484 43.478 0.00 0.00 0.00 3.02
3082 3624 5.647658 CAGAAATGGTAAAGCAGTACATCCA 59.352 40.000 0.00 0.00 0.00 3.41
3083 3625 5.648092 ACAGAAATGGTAAAGCAGTACATCC 59.352 40.000 0.00 0.00 0.00 3.51
3122 3667 9.226345 GTTAAATAGTAATGCATGCAAGTTCTC 57.774 33.333 26.68 11.85 0.00 2.87
3123 3668 8.960591 AGTTAAATAGTAATGCATGCAAGTTCT 58.039 29.630 26.68 19.51 0.00 3.01
3124 3669 9.573133 AAGTTAAATAGTAATGCATGCAAGTTC 57.427 29.630 26.68 13.38 0.00 3.01
3152 3697 7.534085 TTGATATCAACCTTGTACGTTCATC 57.466 36.000 14.23 0.00 0.00 2.92
3416 3977 4.635765 TCAAATCCAAGGAAGCTGTATTCG 59.364 41.667 0.00 0.00 0.00 3.34
3424 3985 4.525912 AACATGTCAAATCCAAGGAAGC 57.474 40.909 0.00 0.00 0.00 3.86
3435 3996 7.436933 TGTTATTGCCACAATAACATGTCAAA 58.563 30.769 28.81 13.77 43.91 2.69
3442 4003 7.710676 ATAACCTGTTATTGCCACAATAACA 57.289 32.000 29.68 29.68 45.51 2.41
3447 4008 6.892456 TGGAATATAACCTGTTATTGCCACAA 59.108 34.615 7.77 0.00 37.07 3.33
3451 4012 6.040391 TGCTTGGAATATAACCTGTTATTGCC 59.960 38.462 7.77 7.79 37.07 4.52
3452 4013 7.038154 TGCTTGGAATATAACCTGTTATTGC 57.962 36.000 7.77 0.04 37.07 3.56
3526 4087 6.801539 TGCAAACAGAAACAGAATACTAGG 57.198 37.500 0.00 0.00 0.00 3.02
3541 4102 6.551385 AGAGTGAACTAAATCTGCAAACAG 57.449 37.500 0.00 0.00 45.95 3.16
3559 4120 3.247173 GCTGACAAGAACTGTGAAGAGTG 59.753 47.826 0.00 0.00 38.84 3.51
3706 4267 5.069318 TGTGAATGCCAAACTGATAACTCA 58.931 37.500 0.00 0.00 0.00 3.41
3865 4458 1.635817 AACCGGTAGCCATGCCAGAT 61.636 55.000 8.00 0.00 0.00 2.90
3969 4566 3.242870 GCCGGAACAAAATGCTAGAGATG 60.243 47.826 5.05 0.00 0.00 2.90
4138 4735 2.545106 TCAAAGTTTTTCTACGACCCGC 59.455 45.455 0.00 0.00 0.00 6.13
4149 4746 3.898741 TCCGCCCCTATTTCAAAGTTTTT 59.101 39.130 0.00 0.00 0.00 1.94
4150 4747 3.502356 TCCGCCCCTATTTCAAAGTTTT 58.498 40.909 0.00 0.00 0.00 2.43
4151 4748 3.089284 CTCCGCCCCTATTTCAAAGTTT 58.911 45.455 0.00 0.00 0.00 2.66
4154 4751 2.420058 ACTCCGCCCCTATTTCAAAG 57.580 50.000 0.00 0.00 0.00 2.77
4202 4799 4.038162 TCGGGTTTTTATGGAACCAAGTTG 59.962 41.667 8.15 0.00 46.65 3.16
4271 4868 1.574134 TCACCGAGTTCCAAACGTTC 58.426 50.000 0.00 0.00 36.23 3.95
4310 4907 5.662674 ACAAAGATCCTAAGCGAACTACT 57.337 39.130 0.00 0.00 0.00 2.57
4382 4981 6.739331 AGGAGACCATTTAGTAAGATCAGG 57.261 41.667 0.00 0.00 0.00 3.86
4409 5008 4.062293 TGAACGAACCAATCACCAACTAG 58.938 43.478 0.00 0.00 0.00 2.57
4474 5189 5.753721 AGGAGAGAGTATGCAATATTCCC 57.246 43.478 0.00 0.00 36.30 3.97
4475 5190 6.072783 GCAAAGGAGAGAGTATGCAATATTCC 60.073 42.308 0.00 0.00 36.30 3.01
4502 5217 7.255871 GGAGGGACTACGATTCATACTACAAAT 60.256 40.741 0.00 0.00 41.55 2.32
4549 5371 8.804743 CGTATTCAATATCGTTAGTTTGACAGT 58.195 33.333 0.00 0.00 0.00 3.55
4594 5416 5.050363 ACACATTACTGTACAAAGAACAGCG 60.050 40.000 0.00 0.00 46.73 5.18
4688 5510 9.647797 TGTTCAATCTATCAACTACACGTATTT 57.352 29.630 0.00 0.00 0.00 1.40
4690 5512 9.817809 AATGTTCAATCTATCAACTACACGTAT 57.182 29.630 0.00 0.00 0.00 3.06
4691 5513 9.647797 AAATGTTCAATCTATCAACTACACGTA 57.352 29.630 0.00 0.00 0.00 3.57
4692 5514 8.443160 CAAATGTTCAATCTATCAACTACACGT 58.557 33.333 0.00 0.00 0.00 4.49
4693 5515 8.443160 ACAAATGTTCAATCTATCAACTACACG 58.557 33.333 0.00 0.00 0.00 4.49
4721 5601 1.519758 GGTATGCGTGCACGTATGTAC 59.480 52.381 40.85 32.96 44.05 2.90
4723 5603 0.808453 GGGTATGCGTGCACGTATGT 60.808 55.000 40.85 26.23 44.05 2.29
4790 5806 4.162320 ACTGTCATTATAGACCTGTGGTGG 59.838 45.833 0.00 0.00 35.25 4.61
4794 5810 9.599866 TTAATCAACTGTCATTATAGACCTGTG 57.400 33.333 0.00 0.00 37.73 3.66
4826 5842 4.605594 GCACGTGTTTACTACAAATGTTCG 59.394 41.667 18.38 0.00 38.80 3.95
4830 5846 3.897778 CGTGCACGTGTTTACTACAAATG 59.102 43.478 30.50 0.00 38.80 2.32
4863 5879 3.181500 CCTAATTGCCTTAAGTCGCAACC 60.181 47.826 17.81 0.00 46.96 3.77
4869 5885 2.359214 GCAGCCCTAATTGCCTTAAGTC 59.641 50.000 0.97 0.00 34.28 3.01
4899 5915 4.015406 CCTACAGTGGCACCGGCA 62.015 66.667 15.27 0.00 43.71 5.69
4900 5916 3.952628 GACCTACAGTGGCACCGGC 62.953 68.421 15.27 3.33 40.13 6.13
4901 5917 0.968901 TAGACCTACAGTGGCACCGG 60.969 60.000 15.27 12.21 0.00 5.28
4905 5921 3.374764 ACATGATAGACCTACAGTGGCA 58.625 45.455 0.00 0.00 0.00 4.92
4911 5927 5.360999 CAGAGTTGGACATGATAGACCTACA 59.639 44.000 0.00 0.00 33.34 2.74
4923 5939 5.048846 ACACCTAAAACAGAGTTGGACAT 57.951 39.130 0.00 0.00 0.00 3.06
4928 5944 7.698130 CAGAAAAAGACACCTAAAACAGAGTTG 59.302 37.037 0.00 0.00 0.00 3.16
4929 5945 7.393515 ACAGAAAAAGACACCTAAAACAGAGTT 59.606 33.333 0.00 0.00 0.00 3.01
4930 5946 6.884836 ACAGAAAAAGACACCTAAAACAGAGT 59.115 34.615 0.00 0.00 0.00 3.24
4931 5947 7.321745 ACAGAAAAAGACACCTAAAACAGAG 57.678 36.000 0.00 0.00 0.00 3.35
4932 5948 7.696992 AACAGAAAAAGACACCTAAAACAGA 57.303 32.000 0.00 0.00 0.00 3.41
4933 5949 8.244113 AGAAACAGAAAAAGACACCTAAAACAG 58.756 33.333 0.00 0.00 0.00 3.16
4934 5950 8.117813 AGAAACAGAAAAAGACACCTAAAACA 57.882 30.769 0.00 0.00 0.00 2.83
4935 5951 8.981724 AAGAAACAGAAAAAGACACCTAAAAC 57.018 30.769 0.00 0.00 0.00 2.43
4938 5954 8.899771 CCTAAAGAAACAGAAAAAGACACCTAA 58.100 33.333 0.00 0.00 0.00 2.69
4939 5955 7.012989 GCCTAAAGAAACAGAAAAAGACACCTA 59.987 37.037 0.00 0.00 0.00 3.08
4940 5956 6.183360 GCCTAAAGAAACAGAAAAAGACACCT 60.183 38.462 0.00 0.00 0.00 4.00
4941 5957 5.977725 GCCTAAAGAAACAGAAAAAGACACC 59.022 40.000 0.00 0.00 0.00 4.16
4942 5958 6.796426 AGCCTAAAGAAACAGAAAAAGACAC 58.204 36.000 0.00 0.00 0.00 3.67
4943 5959 7.404671 AAGCCTAAAGAAACAGAAAAAGACA 57.595 32.000 0.00 0.00 0.00 3.41
4944 5960 7.759886 ACAAAGCCTAAAGAAACAGAAAAAGAC 59.240 33.333 0.00 0.00 0.00 3.01
4945 5961 7.759433 CACAAAGCCTAAAGAAACAGAAAAAGA 59.241 33.333 0.00 0.00 0.00 2.52
4946 5962 7.545615 ACACAAAGCCTAAAGAAACAGAAAAAG 59.454 33.333 0.00 0.00 0.00 2.27
4947 5963 7.382898 ACACAAAGCCTAAAGAAACAGAAAAA 58.617 30.769 0.00 0.00 0.00 1.94
4948 5964 6.930731 ACACAAAGCCTAAAGAAACAGAAAA 58.069 32.000 0.00 0.00 0.00 2.29
4949 5965 6.524101 ACACAAAGCCTAAAGAAACAGAAA 57.476 33.333 0.00 0.00 0.00 2.52
4950 5966 6.377146 AGAACACAAAGCCTAAAGAAACAGAA 59.623 34.615 0.00 0.00 0.00 3.02
4951 5967 5.885912 AGAACACAAAGCCTAAAGAAACAGA 59.114 36.000 0.00 0.00 0.00 3.41
4952 5968 5.973565 CAGAACACAAAGCCTAAAGAAACAG 59.026 40.000 0.00 0.00 0.00 3.16
4953 5969 5.678616 GCAGAACACAAAGCCTAAAGAAACA 60.679 40.000 0.00 0.00 0.00 2.83
4954 5970 4.740205 GCAGAACACAAAGCCTAAAGAAAC 59.260 41.667 0.00 0.00 0.00 2.78
4955 5971 4.644685 AGCAGAACACAAAGCCTAAAGAAA 59.355 37.500 0.00 0.00 0.00 2.52
4956 5972 4.207165 AGCAGAACACAAAGCCTAAAGAA 58.793 39.130 0.00 0.00 0.00 2.52
4957 5973 3.815401 GAGCAGAACACAAAGCCTAAAGA 59.185 43.478 0.00 0.00 0.00 2.52
4958 5974 3.565482 TGAGCAGAACACAAAGCCTAAAG 59.435 43.478 0.00 0.00 0.00 1.85
4959 5975 3.550820 TGAGCAGAACACAAAGCCTAAA 58.449 40.909 0.00 0.00 0.00 1.85
4960 5976 3.207265 TGAGCAGAACACAAAGCCTAA 57.793 42.857 0.00 0.00 0.00 2.69
4961 5977 2.928801 TGAGCAGAACACAAAGCCTA 57.071 45.000 0.00 0.00 0.00 3.93
4962 5978 2.283145 ATGAGCAGAACACAAAGCCT 57.717 45.000 0.00 0.00 0.00 4.58
4963 5979 4.479619 CTTTATGAGCAGAACACAAAGCC 58.520 43.478 0.00 0.00 27.89 4.35
4986 6002 1.515521 GGGAACTGTTGCCGTCTTGG 61.516 60.000 15.44 0.00 42.50 3.61
4987 6003 1.949257 GGGAACTGTTGCCGTCTTG 59.051 57.895 15.44 0.00 0.00 3.02
4988 6004 4.475527 GGGAACTGTTGCCGTCTT 57.524 55.556 15.44 0.00 0.00 3.01
4999 6015 4.728860 ACATTATTCCATCCTCAGGGAACT 59.271 41.667 0.00 0.00 45.20 3.01
5000 6016 5.053978 ACATTATTCCATCCTCAGGGAAC 57.946 43.478 0.00 0.00 45.20 3.62
5001 6017 5.433051 AGAACATTATTCCATCCTCAGGGAA 59.567 40.000 0.00 0.00 46.41 3.97
5002 6018 4.977739 AGAACATTATTCCATCCTCAGGGA 59.022 41.667 0.00 0.00 46.81 4.20
5003 6019 5.312079 GAGAACATTATTCCATCCTCAGGG 58.688 45.833 0.00 0.00 0.00 4.45
5004 6020 5.312079 GGAGAACATTATTCCATCCTCAGG 58.688 45.833 0.00 0.00 0.00 3.86
5005 6021 5.312079 GGGAGAACATTATTCCATCCTCAG 58.688 45.833 0.00 0.00 32.50 3.35
5006 6022 4.104738 GGGGAGAACATTATTCCATCCTCA 59.895 45.833 0.00 0.00 32.50 3.86
5007 6023 4.657013 GGGGAGAACATTATTCCATCCTC 58.343 47.826 0.00 0.00 32.50 3.71
5008 6024 4.731313 GGGGAGAACATTATTCCATCCT 57.269 45.455 0.00 0.00 32.50 3.24


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

AutoCloner maintained by Alex Coulton.