Multiple sequence alignment - TraesCS4D01G025700

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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 TraesCS4D01G025700 chr4D 100.000 4384 0 0 1 4384 11078197 11082580 0.000000e+00 8096.0
1 TraesCS4D01G025700 chr4D 92.356 798 60 1 3588 4384 163759166 163758369 0.000000e+00 1134.0
2 TraesCS4D01G025700 chr4D 86.517 801 100 7 3586 4384 128842968 128842174 0.000000e+00 874.0
3 TraesCS4D01G025700 chr4D 86.211 805 101 9 3586 4384 128895837 128895037 0.000000e+00 863.0
4 TraesCS4D01G025700 chr4D 95.652 46 0 2 3543 3587 10808343 10808299 6.080000e-09 73.1
5 TraesCS4D01G025700 chr4B 92.009 1389 45 19 2084 3440 21148102 21149456 0.000000e+00 1890.0
6 TraesCS4D01G025700 chr4B 88.889 729 31 22 915 1626 21146846 21147541 0.000000e+00 852.0
7 TraesCS4D01G025700 chr4B 88.955 335 29 5 1 329 21145503 21145835 1.470000e-109 407.0
8 TraesCS4D01G025700 chr4B 88.060 335 22 13 377 698 21146509 21146838 8.900000e-102 381.0
9 TraesCS4D01G025700 chr4B 87.963 216 23 2 1719 1934 21147764 21147976 7.280000e-63 252.0
10 TraesCS4D01G025700 chr4B 95.652 46 0 2 3543 3587 20324041 20323997 6.080000e-09 73.1
11 TraesCS4D01G025700 chr4A 91.281 1296 56 30 2158 3440 591920773 591922024 0.000000e+00 1714.0
12 TraesCS4D01G025700 chr4A 90.791 847 28 20 786 1626 591919383 591920185 0.000000e+00 1086.0
13 TraesCS4D01G025700 chr4A 91.000 500 27 5 1622 2112 591920284 591920774 0.000000e+00 658.0
14 TraesCS4D01G025700 chr4A 90.663 332 24 5 1 327 591918191 591918520 6.730000e-118 435.0
15 TraesCS4D01G025700 chr4A 95.238 210 5 5 363 567 591919178 591919387 1.180000e-85 327.0
16 TraesCS4D01G025700 chr3D 88.986 799 77 7 3586 4384 231989746 231988959 0.000000e+00 977.0
17 TraesCS4D01G025700 chr3D 87.547 803 92 7 3588 4384 419823055 419822255 0.000000e+00 922.0
18 TraesCS4D01G025700 chr3D 87.422 803 93 7 3588 4384 419832626 419831826 0.000000e+00 917.0
19 TraesCS4D01G025700 chr3D 87.532 778 86 11 3591 4362 414545956 414545184 0.000000e+00 889.0
20 TraesCS4D01G025700 chr3D 90.169 295 20 5 1042 1336 63799679 63799964 4.140000e-100 375.0
21 TraesCS4D01G025700 chr3B 91.168 702 40 9 1689 2380 360430044 360429355 0.000000e+00 933.0
22 TraesCS4D01G025700 chr3B 90.000 300 21 6 1040 1339 706503606 706503316 3.200000e-101 379.0
23 TraesCS4D01G025700 chr3B 85.484 186 12 7 1426 1605 360430249 360430073 3.480000e-41 180.0
24 TraesCS4D01G025700 chr3B 86.111 72 7 3 490 561 495837047 495836979 1.690000e-09 75.0
25 TraesCS4D01G025700 chr7D 89.052 749 74 8 3578 4320 95957893 95957147 0.000000e+00 922.0
26 TraesCS4D01G025700 chr2A 88.315 736 80 6 3586 4319 111553567 111554298 0.000000e+00 878.0
27 TraesCS4D01G025700 chr5D 90.444 293 19 6 1044 1336 326028054 326028337 1.150000e-100 377.0
28 TraesCS4D01G025700 chr6A 90.411 292 18 6 1042 1333 29281649 29281930 4.140000e-100 375.0
29 TraesCS4D01G025700 chr6D 89.831 295 21 5 1042 1336 42970308 42970593 1.930000e-98 370.0
30 TraesCS4D01G025700 chr1B 90.068 292 20 5 1042 1333 614436292 614436574 1.930000e-98 370.0
31 TraesCS4D01G025700 chr1B 94.872 39 2 0 525 563 105731879 105731841 1.320000e-05 62.1
32 TraesCS4D01G025700 chr1A 89.333 300 22 5 1040 1339 18828269 18827980 6.930000e-98 368.0
33 TraesCS4D01G025700 chr5B 76.190 105 24 1 451 554 620008282 620008386 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G025700 chr4D 11078197 11082580 4383 False 8096.0 8096 100.0000 1 4384 1 chr4D.!!$F1 4383
1 TraesCS4D01G025700 chr4D 163758369 163759166 797 True 1134.0 1134 92.3560 3588 4384 1 chr4D.!!$R4 796
2 TraesCS4D01G025700 chr4D 128842174 128842968 794 True 874.0 874 86.5170 3586 4384 1 chr4D.!!$R2 798
3 TraesCS4D01G025700 chr4D 128895037 128895837 800 True 863.0 863 86.2110 3586 4384 1 chr4D.!!$R3 798
4 TraesCS4D01G025700 chr4B 21145503 21149456 3953 False 756.4 1890 89.1752 1 3440 5 chr4B.!!$F1 3439
5 TraesCS4D01G025700 chr4A 591918191 591922024 3833 False 844.0 1714 91.7946 1 3440 5 chr4A.!!$F1 3439
6 TraesCS4D01G025700 chr3D 231988959 231989746 787 True 977.0 977 88.9860 3586 4384 1 chr3D.!!$R1 798
7 TraesCS4D01G025700 chr3D 419822255 419823055 800 True 922.0 922 87.5470 3588 4384 1 chr3D.!!$R3 796
8 TraesCS4D01G025700 chr3D 419831826 419832626 800 True 917.0 917 87.4220 3588 4384 1 chr3D.!!$R4 796
9 TraesCS4D01G025700 chr3D 414545184 414545956 772 True 889.0 889 87.5320 3591 4362 1 chr3D.!!$R2 771
10 TraesCS4D01G025700 chr3B 360429355 360430249 894 True 556.5 933 88.3260 1426 2380 2 chr3B.!!$R3 954
11 TraesCS4D01G025700 chr7D 95957147 95957893 746 True 922.0 922 89.0520 3578 4320 1 chr7D.!!$R1 742
12 TraesCS4D01G025700 chr2A 111553567 111554298 731 False 878.0 878 88.3150 3586 4319 1 chr2A.!!$F1 733

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
798 1556 0.104855 GTCATCATGTCGCCAGCCTA 59.895 55.0 0.0 0.0 0.0 3.93 F
2195 3183 0.032130 GAGACGAGTTGTGGTGAGCA 59.968 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 3281 0.107508 AGGAAGCACACATAGCGCAT 60.108 50.0 11.47 0.0 37.01 4.73 R
3498 4527 0.173708 GAGAGTACGTCCCCAAGCAG 59.826 60.0 0.00 0.0 0.00 4.24 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
41 42 1.358152 TTGGTGTTGGACCTAGGAGG 58.642 55.000 17.98 0.00 46.32 4.30
48 49 1.076485 GGACCTAGGAGGCGGTGTA 60.076 63.158 17.98 0.00 39.63 2.90
52 53 1.399744 CCTAGGAGGCGGTGTATGCA 61.400 60.000 1.05 0.00 0.00 3.96
90 91 4.973168 TCAGATATGGGTGGATGCTTTAC 58.027 43.478 0.00 0.00 0.00 2.01
101 102 0.796312 ATGCTTTACGCGACTTGGTG 59.204 50.000 15.93 0.00 43.27 4.17
148 149 5.447818 CGCTCATGGTCTTTGGAGTATTTTC 60.448 44.000 0.00 0.00 0.00 2.29
201 206 3.504863 GCGACTTACTAAATCGTGACCA 58.495 45.455 1.98 0.00 38.13 4.02
217 223 0.608640 ACCATCGGTGTCTTCTGTCC 59.391 55.000 0.00 0.00 32.98 4.02
252 258 1.029681 TCGCCGCTGCTTCTATAAGA 58.970 50.000 0.00 0.00 34.37 2.10
255 261 2.608016 CGCCGCTGCTTCTATAAGATCA 60.608 50.000 0.00 0.00 34.37 2.92
343 966 2.223852 GCGCCCCTGAAACTGTTTTTAA 60.224 45.455 7.28 0.00 0.00 1.52
346 969 3.493699 GCCCCTGAAACTGTTTTTAACCC 60.494 47.826 7.28 0.00 0.00 4.11
349 972 5.243060 CCCCTGAAACTGTTTTTAACCCTAG 59.757 44.000 7.28 0.00 0.00 3.02
489 1238 7.104326 ACAAAGCATTTTTGTAAACTATGCG 57.896 32.000 3.64 6.67 40.47 4.73
643 1401 7.225784 TGTATAGCAATTTCAAAAAGCCTCA 57.774 32.000 0.00 0.00 0.00 3.86
644 1402 7.090173 TGTATAGCAATTTCAAAAAGCCTCAC 58.910 34.615 0.00 0.00 0.00 3.51
682 1440 9.307121 TGAAACACACGAACATTTTTGAAATAT 57.693 25.926 0.00 0.00 0.00 1.28
686 1444 7.381139 ACACACGAACATTTTTGAAATATCACC 59.619 33.333 0.00 0.00 34.61 4.02
688 1446 8.788806 ACACGAACATTTTTGAAATATCACCTA 58.211 29.630 0.00 0.00 34.61 3.08
732 1490 9.642327 TCGTAATAGTTGCACTTAGTTTTATGA 57.358 29.630 0.00 0.00 0.00 2.15
777 1535 5.968387 AAAGGAAGAATACGAACATAGCG 57.032 39.130 0.00 0.00 0.00 4.26
778 1536 3.381949 AGGAAGAATACGAACATAGCGC 58.618 45.455 0.00 0.00 0.00 5.92
779 1537 2.153247 GGAAGAATACGAACATAGCGCG 59.847 50.000 0.00 0.00 0.00 6.86
780 1538 2.486951 AGAATACGAACATAGCGCGT 57.513 45.000 8.43 0.00 41.58 6.01
781 1539 2.382519 AGAATACGAACATAGCGCGTC 58.617 47.619 8.43 0.00 39.24 5.19
782 1540 2.114056 GAATACGAACATAGCGCGTCA 58.886 47.619 8.43 0.00 39.24 4.35
783 1541 2.417339 ATACGAACATAGCGCGTCAT 57.583 45.000 8.43 0.00 39.24 3.06
784 1542 1.750351 TACGAACATAGCGCGTCATC 58.250 50.000 8.43 0.00 39.24 2.92
785 1543 0.179148 ACGAACATAGCGCGTCATCA 60.179 50.000 8.43 0.00 31.98 3.07
786 1544 1.131771 CGAACATAGCGCGTCATCAT 58.868 50.000 8.43 0.00 0.00 2.45
787 1545 1.136803 CGAACATAGCGCGTCATCATG 60.137 52.381 8.43 6.96 0.00 3.07
788 1546 1.860950 GAACATAGCGCGTCATCATGT 59.139 47.619 8.43 7.60 0.00 3.21
789 1547 1.491670 ACATAGCGCGTCATCATGTC 58.508 50.000 8.43 0.00 0.00 3.06
798 1556 0.104855 GTCATCATGTCGCCAGCCTA 59.895 55.000 0.00 0.00 0.00 3.93
873 1631 2.728817 CGGGACATAGACTCGGCC 59.271 66.667 0.00 0.00 0.00 6.13
1026 1790 3.134127 GATTTTGCCGCTCCCGCT 61.134 61.111 0.00 0.00 0.00 5.52
1210 1982 0.980231 CCTCTCCTCTCCTTGGGTGG 60.980 65.000 0.00 0.00 0.00 4.61
1488 2283 2.826287 CTCTCGCCTCCTCTCGCA 60.826 66.667 0.00 0.00 0.00 5.10
1493 2288 4.154347 GCCTCCTCTCGCAGTGGG 62.154 72.222 0.00 0.00 30.13 4.61
1498 2304 4.463879 CTCTCGCAGTGGGGCTGG 62.464 72.222 7.42 0.00 45.14 4.85
1523 2329 4.891037 GCTGGGGCTGGGCTGATC 62.891 72.222 0.00 0.00 35.22 2.92
1524 2330 4.559063 CTGGGGCTGGGCTGATCG 62.559 72.222 0.00 0.00 0.00 3.69
1635 2569 8.903820 GGTAGTATTACATGCTGAATTTTCCTT 58.096 33.333 0.00 0.00 0.00 3.36
1687 2629 2.909504 TATCCCTCTGGCTAGCCTAG 57.090 55.000 33.07 27.22 36.94 3.02
1712 2654 9.771534 AGCCTATTCTCTTCATTAACTTCATAC 57.228 33.333 0.00 0.00 0.00 2.39
1717 2662 8.873215 TTCTCTTCATTAACTTCATACGATCC 57.127 34.615 0.00 0.00 0.00 3.36
1917 2866 1.012486 AGTTTGCGTGCGGTACTAGC 61.012 55.000 6.87 6.87 0.00 3.42
1945 2903 0.183492 TGCCCCATGATCTGGTTAGC 59.817 55.000 0.00 9.37 44.30 3.09
1973 2934 1.003262 TCGTTTGTGTACGCGCTACC 61.003 55.000 5.73 3.61 41.16 3.18
2006 2972 7.099764 TGTCAGATGATCCAGTTAAGTTTCTC 58.900 38.462 0.00 0.00 0.00 2.87
2134 3115 5.205759 AGAAAGTCTTGCATTTTTCTGGG 57.794 39.130 11.88 0.00 38.18 4.45
2138 3119 3.823304 AGTCTTGCATTTTTCTGGGTCTC 59.177 43.478 0.00 0.00 0.00 3.36
2180 3168 5.140747 ACCAAGACAACTGATGTAGAGAC 57.859 43.478 0.00 0.00 44.12 3.36
2187 3175 4.278669 ACAACTGATGTAGAGACGAGTTGT 59.721 41.667 0.00 0.00 42.47 3.32
2188 3176 4.427096 ACTGATGTAGAGACGAGTTGTG 57.573 45.455 0.00 0.00 0.00 3.33
2189 3177 3.191581 ACTGATGTAGAGACGAGTTGTGG 59.808 47.826 0.00 0.00 0.00 4.17
2190 3178 3.154710 TGATGTAGAGACGAGTTGTGGT 58.845 45.455 0.00 0.00 0.00 4.16
2191 3179 3.057526 TGATGTAGAGACGAGTTGTGGTG 60.058 47.826 0.00 0.00 0.00 4.17
2192 3180 2.578786 TGTAGAGACGAGTTGTGGTGA 58.421 47.619 0.00 0.00 0.00 4.02
2193 3181 2.552743 TGTAGAGACGAGTTGTGGTGAG 59.447 50.000 0.00 0.00 0.00 3.51
2194 3182 0.315568 AGAGACGAGTTGTGGTGAGC 59.684 55.000 0.00 0.00 0.00 4.26
2195 3183 0.032130 GAGACGAGTTGTGGTGAGCA 59.968 55.000 0.00 0.00 0.00 4.26
2200 3188 1.221414 GAGTTGTGGTGAGCAGTGAC 58.779 55.000 0.00 0.00 0.00 3.67
2201 3189 0.833287 AGTTGTGGTGAGCAGTGACT 59.167 50.000 0.00 0.00 0.00 3.41
2202 3190 1.210478 AGTTGTGGTGAGCAGTGACTT 59.790 47.619 0.00 0.00 0.00 3.01
2205 3193 1.065491 TGTGGTGAGCAGTGACTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
2287 3281 6.183360 GCTTTCAGTTTATCACATGAATCGGA 60.183 38.462 0.00 0.00 32.13 4.55
2492 3497 5.692928 AGATGAGGCAAGCAATTCTCTTAT 58.307 37.500 0.00 0.00 0.00 1.73
2495 3500 5.255687 TGAGGCAAGCAATTCTCTTATGAA 58.744 37.500 0.00 0.00 0.00 2.57
2496 3501 5.889853 TGAGGCAAGCAATTCTCTTATGAAT 59.110 36.000 0.00 0.00 38.19 2.57
2497 3502 6.379133 TGAGGCAAGCAATTCTCTTATGAATT 59.621 34.615 0.00 0.00 44.57 2.17
2498 3503 7.093640 TGAGGCAAGCAATTCTCTTATGAATTT 60.094 33.333 0.00 0.00 42.63 1.82
2584 3593 0.923911 GATTGCGCCGTTAACGATGC 60.924 55.000 28.79 27.66 43.02 3.91
2588 3597 1.631072 CGCCGTTAACGATGCTCTG 59.369 57.895 28.79 11.32 43.02 3.35
2596 3605 5.034797 CGTTAACGATGCTCTGTCTCAATA 58.965 41.667 23.35 0.00 43.02 1.90
2661 3670 4.461198 GGCCTGTTGTAAGTATAGCCAAT 58.539 43.478 0.00 0.00 39.01 3.16
2791 3800 2.047769 GACAGAGATGATTACGCGCTC 58.952 52.381 5.73 2.24 0.00 5.03
2906 3919 3.695830 TTCCACTCTTTTCAGCGGTAT 57.304 42.857 0.00 0.00 0.00 2.73
3068 4085 1.749634 GCTTCTTGCAGAGATGCCATT 59.250 47.619 17.94 0.00 45.21 3.16
3210 4231 1.612726 GGATGCTTCTGGCTGTGAAGT 60.613 52.381 13.66 0.32 41.94 3.01
3217 4242 3.188159 TCTGGCTGTGAAGTACGTTTT 57.812 42.857 0.00 0.00 0.00 2.43
3223 4248 4.319261 GGCTGTGAAGTACGTTTTAGTTGG 60.319 45.833 0.00 0.00 0.00 3.77
3302 4327 6.876789 TGTGGTCGACAACATACATTTCTAAT 59.123 34.615 21.95 0.00 0.00 1.73
3303 4328 7.148490 TGTGGTCGACAACATACATTTCTAATG 60.148 37.037 21.95 0.00 0.00 1.90
3304 4329 7.064134 GTGGTCGACAACATACATTTCTAATGA 59.936 37.037 18.41 0.00 0.00 2.57
3305 4330 7.277760 TGGTCGACAACATACATTTCTAATGAG 59.722 37.037 18.91 0.00 0.00 2.90
3306 4331 7.491372 GGTCGACAACATACATTTCTAATGAGA 59.509 37.037 18.91 0.00 0.00 3.27
3307 4332 9.035607 GTCGACAACATACATTTCTAATGAGAT 57.964 33.333 11.55 0.00 0.00 2.75
3308 4333 9.249457 TCGACAACATACATTTCTAATGAGATC 57.751 33.333 6.42 0.00 0.00 2.75
3309 4334 9.254133 CGACAACATACATTTCTAATGAGATCT 57.746 33.333 0.00 0.00 0.00 2.75
3339 4368 1.409064 TGGTAGCGATAGGAGCACAAG 59.591 52.381 0.00 0.00 37.01 3.16
3358 4387 8.682710 AGCACAAGTCAGAAGTTGTTAAATTTA 58.317 29.630 0.00 0.00 44.83 1.40
3359 4388 9.296400 GCACAAGTCAGAAGTTGTTAAATTTAA 57.704 29.630 6.54 6.54 44.83 1.52
3396 4425 7.433680 TGAGTGCGTTAACATGATATATGTCT 58.566 34.615 6.39 0.00 0.00 3.41
3429 4458 5.359860 TGTATGAGATTGTCATCTACGGTGT 59.640 40.000 0.00 0.00 42.80 4.16
3440 4469 1.553248 TCTACGGTGTTCATCCTTGGG 59.447 52.381 0.00 0.00 0.00 4.12
3441 4470 1.278127 CTACGGTGTTCATCCTTGGGT 59.722 52.381 0.00 0.00 0.00 4.51
3442 4471 0.476771 ACGGTGTTCATCCTTGGGTT 59.523 50.000 0.00 0.00 0.00 4.11
3443 4472 1.133606 ACGGTGTTCATCCTTGGGTTT 60.134 47.619 0.00 0.00 0.00 3.27
3444 4473 2.106857 ACGGTGTTCATCCTTGGGTTTA 59.893 45.455 0.00 0.00 0.00 2.01
3445 4474 3.245122 ACGGTGTTCATCCTTGGGTTTAT 60.245 43.478 0.00 0.00 0.00 1.40
3446 4475 4.019141 ACGGTGTTCATCCTTGGGTTTATA 60.019 41.667 0.00 0.00 0.00 0.98
3447 4476 5.130350 CGGTGTTCATCCTTGGGTTTATAT 58.870 41.667 0.00 0.00 0.00 0.86
3448 4477 6.126710 ACGGTGTTCATCCTTGGGTTTATATA 60.127 38.462 0.00 0.00 0.00 0.86
3449 4478 6.768861 CGGTGTTCATCCTTGGGTTTATATAA 59.231 38.462 0.00 0.00 0.00 0.98
3450 4479 7.447238 CGGTGTTCATCCTTGGGTTTATATAAT 59.553 37.037 0.00 0.00 0.00 1.28
3451 4480 9.802039 GGTGTTCATCCTTGGGTTTATATAATA 57.198 33.333 0.00 0.00 0.00 0.98
3459 4488 8.984855 TCCTTGGGTTTATATAATAGATACCGG 58.015 37.037 0.00 0.00 0.00 5.28
3460 4489 8.765517 CCTTGGGTTTATATAATAGATACCGGT 58.234 37.037 13.98 13.98 0.00 5.28
3474 4503 6.912951 AGATACCGGTTTACATATGTAGCT 57.087 37.500 15.04 0.00 0.00 3.32
3475 4504 7.299246 AGATACCGGTTTACATATGTAGCTT 57.701 36.000 15.04 1.05 0.00 3.74
3476 4505 7.152645 AGATACCGGTTTACATATGTAGCTTG 58.847 38.462 15.04 7.70 0.00 4.01
3477 4506 3.875134 ACCGGTTTACATATGTAGCTTGC 59.125 43.478 14.96 5.88 0.00 4.01
3478 4507 4.127171 CCGGTTTACATATGTAGCTTGCT 58.873 43.478 14.96 0.00 0.00 3.91
3479 4508 4.574828 CCGGTTTACATATGTAGCTTGCTT 59.425 41.667 14.96 0.00 0.00 3.91
3480 4509 5.501715 CGGTTTACATATGTAGCTTGCTTG 58.498 41.667 14.96 0.00 0.00 4.01
3481 4510 5.504010 CGGTTTACATATGTAGCTTGCTTGG 60.504 44.000 14.96 0.00 0.00 3.61
3482 4511 5.221048 GGTTTACATATGTAGCTTGCTTGGG 60.221 44.000 14.96 0.00 0.00 4.12
3483 4512 2.936202 ACATATGTAGCTTGCTTGGGG 58.064 47.619 6.56 0.00 0.00 4.96
3484 4513 2.509548 ACATATGTAGCTTGCTTGGGGA 59.490 45.455 6.56 0.00 0.00 4.81
3485 4514 3.053693 ACATATGTAGCTTGCTTGGGGAA 60.054 43.478 6.56 0.00 0.00 3.97
3486 4515 2.603075 ATGTAGCTTGCTTGGGGAAA 57.397 45.000 0.00 0.00 0.00 3.13
3487 4516 2.603075 TGTAGCTTGCTTGGGGAAAT 57.397 45.000 0.00 0.00 0.00 2.17
3488 4517 2.446435 TGTAGCTTGCTTGGGGAAATC 58.554 47.619 0.00 0.00 0.00 2.17
3489 4518 2.224992 TGTAGCTTGCTTGGGGAAATCA 60.225 45.455 0.00 0.00 0.00 2.57
3490 4519 2.242882 AGCTTGCTTGGGGAAATCAT 57.757 45.000 0.00 0.00 0.00 2.45
3491 4520 1.829222 AGCTTGCTTGGGGAAATCATG 59.171 47.619 0.00 0.00 0.00 3.07
3492 4521 1.134610 GCTTGCTTGGGGAAATCATGG 60.135 52.381 0.00 0.00 0.00 3.66
3493 4522 2.181975 CTTGCTTGGGGAAATCATGGT 58.818 47.619 0.00 0.00 0.00 3.55
3494 4523 1.851304 TGCTTGGGGAAATCATGGTC 58.149 50.000 0.00 0.00 0.00 4.02
3495 4524 0.740737 GCTTGGGGAAATCATGGTCG 59.259 55.000 0.00 0.00 0.00 4.79
3496 4525 1.392589 CTTGGGGAAATCATGGTCGG 58.607 55.000 0.00 0.00 0.00 4.79
3497 4526 0.682855 TTGGGGAAATCATGGTCGGC 60.683 55.000 0.00 0.00 0.00 5.54
3498 4527 1.828224 GGGGAAATCATGGTCGGCC 60.828 63.158 0.00 0.00 0.00 6.13
3499 4528 1.227383 GGGAAATCATGGTCGGCCT 59.773 57.895 7.97 0.00 35.27 5.19
3500 4529 1.103398 GGGAAATCATGGTCGGCCTG 61.103 60.000 7.97 3.05 35.27 4.85
3501 4530 1.728490 GGAAATCATGGTCGGCCTGC 61.728 60.000 7.97 0.00 35.27 4.85
3502 4531 0.749454 GAAATCATGGTCGGCCTGCT 60.749 55.000 7.97 0.00 35.27 4.24
3503 4532 0.323725 AAATCATGGTCGGCCTGCTT 60.324 50.000 7.97 0.00 35.27 3.91
3504 4533 1.033746 AATCATGGTCGGCCTGCTTG 61.034 55.000 7.97 0.00 35.27 4.01
3505 4534 2.898920 ATCATGGTCGGCCTGCTTGG 62.899 60.000 7.97 0.00 39.35 3.61
3506 4535 4.431131 ATGGTCGGCCTGCTTGGG 62.431 66.667 7.97 0.00 36.00 4.12
3512 4541 3.712907 GGCCTGCTTGGGGACGTA 61.713 66.667 0.00 0.00 36.00 3.57
3513 4542 2.436115 GCCTGCTTGGGGACGTAC 60.436 66.667 0.00 0.00 36.00 3.67
3514 4543 2.955881 GCCTGCTTGGGGACGTACT 61.956 63.158 0.00 0.00 36.00 2.73
3515 4544 1.218316 CCTGCTTGGGGACGTACTC 59.782 63.158 0.00 0.00 0.00 2.59
3516 4545 1.258445 CCTGCTTGGGGACGTACTCT 61.258 60.000 0.00 0.00 0.00 3.24
3517 4546 0.173708 CTGCTTGGGGACGTACTCTC 59.826 60.000 0.00 0.00 0.00 3.20
3518 4547 0.541063 TGCTTGGGGACGTACTCTCA 60.541 55.000 0.00 0.00 0.00 3.27
3519 4548 0.824759 GCTTGGGGACGTACTCTCAT 59.175 55.000 0.00 0.00 0.00 2.90
3520 4549 1.202428 GCTTGGGGACGTACTCTCATC 60.202 57.143 0.00 0.00 0.00 2.92
3521 4550 1.409427 CTTGGGGACGTACTCTCATCC 59.591 57.143 0.00 0.00 0.00 3.51
3523 4552 3.516911 GGGACGTACTCTCATCCCT 57.483 57.895 0.00 0.00 46.43 4.20
3524 4553 1.777941 GGGACGTACTCTCATCCCTT 58.222 55.000 0.00 0.00 46.43 3.95
3525 4554 2.108970 GGGACGTACTCTCATCCCTTT 58.891 52.381 0.00 0.00 46.43 3.11
3526 4555 2.101082 GGGACGTACTCTCATCCCTTTC 59.899 54.545 0.00 0.00 46.43 2.62
3527 4556 2.101082 GGACGTACTCTCATCCCTTTCC 59.899 54.545 0.00 0.00 0.00 3.13
3528 4557 2.758979 GACGTACTCTCATCCCTTTCCA 59.241 50.000 0.00 0.00 0.00 3.53
3529 4558 2.761208 ACGTACTCTCATCCCTTTCCAG 59.239 50.000 0.00 0.00 0.00 3.86
3530 4559 2.761208 CGTACTCTCATCCCTTTCCAGT 59.239 50.000 0.00 0.00 0.00 4.00
3531 4560 3.195825 CGTACTCTCATCCCTTTCCAGTT 59.804 47.826 0.00 0.00 0.00 3.16
3532 4561 4.322801 CGTACTCTCATCCCTTTCCAGTTT 60.323 45.833 0.00 0.00 0.00 2.66
3533 4562 5.105473 CGTACTCTCATCCCTTTCCAGTTTA 60.105 44.000 0.00 0.00 0.00 2.01
3534 4563 5.843019 ACTCTCATCCCTTTCCAGTTTAA 57.157 39.130 0.00 0.00 0.00 1.52
3535 4564 6.394345 ACTCTCATCCCTTTCCAGTTTAAT 57.606 37.500 0.00 0.00 0.00 1.40
3536 4565 6.183347 ACTCTCATCCCTTTCCAGTTTAATG 58.817 40.000 0.00 0.00 0.00 1.90
3537 4566 6.012508 ACTCTCATCCCTTTCCAGTTTAATGA 60.013 38.462 0.00 0.00 0.00 2.57
3538 4567 6.789268 TCTCATCCCTTTCCAGTTTAATGAA 58.211 36.000 0.00 0.00 0.00 2.57
3539 4568 7.237982 TCTCATCCCTTTCCAGTTTAATGAAA 58.762 34.615 0.00 0.00 0.00 2.69
3540 4569 7.895429 TCTCATCCCTTTCCAGTTTAATGAAAT 59.105 33.333 0.00 0.00 0.00 2.17
3541 4570 9.189156 CTCATCCCTTTCCAGTTTAATGAAATA 57.811 33.333 0.00 0.00 0.00 1.40
3542 4571 9.540538 TCATCCCTTTCCAGTTTAATGAAATAA 57.459 29.630 0.00 0.00 0.00 1.40
3562 4591 2.632987 AAAACACGAGTAGGGCAAGT 57.367 45.000 0.00 0.00 0.00 3.16
3563 4592 1.878953 AAACACGAGTAGGGCAAGTG 58.121 50.000 0.00 0.00 38.63 3.16
3564 4593 0.602905 AACACGAGTAGGGCAAGTGC 60.603 55.000 0.00 0.00 36.38 4.40
3565 4594 2.094659 CACGAGTAGGGCAAGTGCG 61.095 63.158 0.00 0.00 43.26 5.34
3566 4595 2.273179 ACGAGTAGGGCAAGTGCGA 61.273 57.895 0.00 0.00 43.26 5.10
3567 4596 1.080093 CGAGTAGGGCAAGTGCGAA 60.080 57.895 0.00 0.00 43.26 4.70
3568 4597 0.669318 CGAGTAGGGCAAGTGCGAAA 60.669 55.000 0.00 0.00 43.26 3.46
3569 4598 1.519408 GAGTAGGGCAAGTGCGAAAA 58.481 50.000 0.00 0.00 43.26 2.29
3570 4599 1.197036 GAGTAGGGCAAGTGCGAAAAC 59.803 52.381 0.00 0.00 43.26 2.43
3571 4600 1.202770 AGTAGGGCAAGTGCGAAAACT 60.203 47.619 0.00 0.00 43.26 2.66
3572 4601 2.038033 AGTAGGGCAAGTGCGAAAACTA 59.962 45.455 0.00 0.00 43.26 2.24
3573 4602 1.975660 AGGGCAAGTGCGAAAACTAA 58.024 45.000 0.00 0.00 43.26 2.24
3574 4603 2.303175 AGGGCAAGTGCGAAAACTAAA 58.697 42.857 0.00 0.00 43.26 1.85
3575 4604 2.691011 AGGGCAAGTGCGAAAACTAAAA 59.309 40.909 0.00 0.00 43.26 1.52
3576 4605 3.049912 GGGCAAGTGCGAAAACTAAAAG 58.950 45.455 0.00 0.00 43.26 2.27
3583 4612 2.952978 TGCGAAAACTAAAAGGGAGCAA 59.047 40.909 0.00 0.00 0.00 3.91
3612 4642 4.111375 GTGGTAATCTCACGTCAGATGT 57.889 45.455 1.51 0.00 33.13 3.06
3653 4683 2.583593 GAGCCATGAGGACGTCGC 60.584 66.667 9.92 6.10 36.89 5.19
3713 4743 1.805345 CACGAGACGTACTCAGGTTCT 59.195 52.381 13.14 0.00 45.14 3.01
3719 4749 0.608640 CGTACTCAGGTTCTGGGCTT 59.391 55.000 0.00 0.00 34.91 4.35
3738 4768 2.544844 TTCCGGAGAGATAACACCCT 57.455 50.000 3.34 0.00 0.00 4.34
3752 4782 1.486726 ACACCCTTACTCCTGCTATGC 59.513 52.381 0.00 0.00 0.00 3.14
3758 4788 3.492309 CCTTACTCCTGCTATGCTGACTG 60.492 52.174 0.00 0.00 0.00 3.51
3762 4792 1.205655 TCCTGCTATGCTGACTGTGAC 59.794 52.381 0.00 0.00 0.00 3.67
3773 4803 5.555966 TGCTGACTGTGACCAAATGTATAA 58.444 37.500 0.00 0.00 0.00 0.98
3776 4806 7.176515 TGCTGACTGTGACCAAATGTATAAAAT 59.823 33.333 0.00 0.00 0.00 1.82
3888 4927 1.304713 CCTTTGCATGGGTGAGCCT 60.305 57.895 1.06 0.00 34.45 4.58
4123 5166 2.680352 AGGGTCGCGTCATGGACT 60.680 61.111 5.77 0.00 33.70 3.85
4196 5239 0.952280 CTATAGCCACGCTCTTCCGA 59.048 55.000 0.00 0.00 40.44 4.55
4233 5276 2.582498 GCACTGTAGCTACGCCCG 60.582 66.667 18.74 9.55 0.00 6.13
4244 5287 2.482296 CTACGCCCGGTCTTGTCGTT 62.482 60.000 0.00 0.00 34.97 3.85
4320 5364 4.452733 CCCCGACCCGTCTTCTGC 62.453 72.222 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.490693 CCAGACGATGCATACACCGC 61.491 60.000 0.00 0.00 0.00 5.68
101 102 1.227263 CCATCACCCCGACGACATC 60.227 63.158 0.00 0.00 0.00 3.06
148 149 2.094762 AAAACATCGAAGAGGACCCG 57.905 50.000 0.00 0.00 43.16 5.28
181 182 4.436847 CGATGGTCACGATTTAGTAAGTCG 59.563 45.833 21.91 21.91 40.91 4.18
201 206 1.338107 TGTGGACAGAAGACACCGAT 58.662 50.000 0.00 0.00 34.33 4.18
217 223 1.590238 GGCGAAGAAGTCATCGATGTG 59.410 52.381 24.09 2.07 39.14 3.21
252 258 9.362151 TGGAGAAAACTTGTTTAAACCTATGAT 57.638 29.630 15.59 0.00 0.00 2.45
255 261 7.562088 TGGTGGAGAAAACTTGTTTAAACCTAT 59.438 33.333 15.59 0.00 0.00 2.57
329 335 9.027202 AGTTTTCTAGGGTTAAAAACAGTTTCA 57.973 29.630 15.24 0.00 42.52 2.69
624 1382 3.181476 ACGTGAGGCTTTTTGAAATTGCT 60.181 39.130 0.00 0.00 0.00 3.91
625 1383 3.123050 ACGTGAGGCTTTTTGAAATTGC 58.877 40.909 0.00 0.00 0.00 3.56
643 1401 6.946165 TCGTGTGTTTCAAAAATATGTACGT 58.054 32.000 0.00 0.00 0.00 3.57
644 1402 7.373703 TGTTCGTGTGTTTCAAAAATATGTACG 59.626 33.333 0.00 0.00 0.00 3.67
753 1511 6.674760 GCGCTATGTTCGTATTCTTCCTTTTT 60.675 38.462 0.00 0.00 0.00 1.94
754 1512 5.220605 GCGCTATGTTCGTATTCTTCCTTTT 60.221 40.000 0.00 0.00 0.00 2.27
755 1513 4.270325 GCGCTATGTTCGTATTCTTCCTTT 59.730 41.667 0.00 0.00 0.00 3.11
756 1514 3.802685 GCGCTATGTTCGTATTCTTCCTT 59.197 43.478 0.00 0.00 0.00 3.36
757 1515 3.381949 GCGCTATGTTCGTATTCTTCCT 58.618 45.455 0.00 0.00 0.00 3.36
758 1516 2.153247 CGCGCTATGTTCGTATTCTTCC 59.847 50.000 5.56 0.00 0.00 3.46
759 1517 2.787680 ACGCGCTATGTTCGTATTCTTC 59.212 45.455 5.73 0.00 34.41 2.87
760 1518 2.787680 GACGCGCTATGTTCGTATTCTT 59.212 45.455 5.73 0.00 36.50 2.52
761 1519 2.223409 TGACGCGCTATGTTCGTATTCT 60.223 45.455 5.73 0.00 36.50 2.40
762 1520 2.114056 TGACGCGCTATGTTCGTATTC 58.886 47.619 5.73 0.00 36.50 1.75
763 1521 2.197792 TGACGCGCTATGTTCGTATT 57.802 45.000 5.73 0.00 36.50 1.89
764 1522 2.287368 TGATGACGCGCTATGTTCGTAT 60.287 45.455 5.73 0.00 36.50 3.06
765 1523 1.064357 TGATGACGCGCTATGTTCGTA 59.936 47.619 5.73 0.00 36.50 3.43
766 1524 0.179148 TGATGACGCGCTATGTTCGT 60.179 50.000 5.73 0.00 39.33 3.85
767 1525 1.131771 ATGATGACGCGCTATGTTCG 58.868 50.000 5.73 0.00 0.00 3.95
768 1526 1.860950 ACATGATGACGCGCTATGTTC 59.139 47.619 5.73 0.00 0.00 3.18
769 1527 1.860950 GACATGATGACGCGCTATGTT 59.139 47.619 5.73 0.00 32.58 2.71
770 1528 1.491670 GACATGATGACGCGCTATGT 58.508 50.000 5.73 9.98 34.91 2.29
771 1529 0.432361 CGACATGATGACGCGCTATG 59.568 55.000 5.73 6.56 0.00 2.23
772 1530 2.801388 CGACATGATGACGCGCTAT 58.199 52.632 5.73 0.00 0.00 2.97
773 1531 4.302154 CGACATGATGACGCGCTA 57.698 55.556 5.73 0.00 0.00 4.26
778 1536 2.528743 GGCTGGCGACATGATGACG 61.529 63.158 12.62 12.62 41.51 4.35
779 1537 0.104855 TAGGCTGGCGACATGATGAC 59.895 55.000 0.00 0.00 41.51 3.06
780 1538 0.829990 TTAGGCTGGCGACATGATGA 59.170 50.000 0.00 0.00 41.51 2.92
781 1539 0.940126 GTTAGGCTGGCGACATGATG 59.060 55.000 0.00 0.00 41.51 3.07
782 1540 0.530650 CGTTAGGCTGGCGACATGAT 60.531 55.000 0.00 0.00 41.51 2.45
783 1541 1.153647 CGTTAGGCTGGCGACATGA 60.154 57.895 0.00 0.00 41.51 3.07
784 1542 0.739462 TTCGTTAGGCTGGCGACATG 60.739 55.000 13.31 0.00 41.51 3.21
785 1543 0.036765 TTTCGTTAGGCTGGCGACAT 60.037 50.000 13.31 0.00 41.51 3.06
786 1544 0.947180 GTTTCGTTAGGCTGGCGACA 60.947 55.000 13.31 0.00 34.21 4.35
787 1545 0.947180 TGTTTCGTTAGGCTGGCGAC 60.947 55.000 13.31 6.20 34.21 5.19
788 1546 0.947180 GTGTTTCGTTAGGCTGGCGA 60.947 55.000 10.39 10.39 0.00 5.54
789 1547 1.225376 TGTGTTTCGTTAGGCTGGCG 61.225 55.000 0.00 1.18 0.00 5.69
798 1556 4.747605 GCCCATTAAACATTGTGTTTCGTT 59.252 37.500 10.97 0.00 46.61 3.85
1510 2316 4.864334 CACCGATCAGCCCAGCCC 62.864 72.222 0.00 0.00 0.00 5.19
1511 2317 4.101448 ACACCGATCAGCCCAGCC 62.101 66.667 0.00 0.00 0.00 4.85
1512 2318 2.821366 CACACCGATCAGCCCAGC 60.821 66.667 0.00 0.00 0.00 4.85
1513 2319 2.821366 GCACACCGATCAGCCCAG 60.821 66.667 0.00 0.00 0.00 4.45
1514 2320 4.408821 GGCACACCGATCAGCCCA 62.409 66.667 0.00 0.00 41.25 5.36
1515 2321 4.408821 TGGCACACCGATCAGCCC 62.409 66.667 0.00 0.00 46.45 5.19
1635 2569 9.206870 CTAGTTAAACGATTTGGTACCAACTAA 57.793 33.333 27.08 13.40 35.46 2.24
1687 2629 8.704234 CGTATGAAGTTAATGAAGAGAATAGGC 58.296 37.037 0.00 0.00 0.00 3.93
1688 2630 9.967346 TCGTATGAAGTTAATGAAGAGAATAGG 57.033 33.333 0.00 0.00 0.00 2.57
1693 2635 8.007405 TGGATCGTATGAAGTTAATGAAGAGA 57.993 34.615 0.00 0.00 0.00 3.10
1712 2654 3.380004 AGTTCAGTAGCTTCTCTGGATCG 59.620 47.826 0.00 0.00 33.13 3.69
1717 2662 4.274147 TCCCTAGTTCAGTAGCTTCTCTG 58.726 47.826 0.00 0.00 0.00 3.35
1807 2752 1.876156 GCAGATATTCCAAGGGCTTCG 59.124 52.381 0.00 0.00 0.00 3.79
1917 2866 4.262292 CCAGATCATGGGGCAATAATTGTG 60.262 45.833 0.00 0.00 46.36 3.33
1945 2903 3.479231 GCGTACACAAACGAACGACATAG 60.479 47.826 0.14 0.00 45.68 2.23
1973 2934 4.108336 CTGGATCATCTGACAGTAACACG 58.892 47.826 1.59 0.00 0.00 4.49
2129 3110 3.165875 CTCCAAACTACTGAGACCCAGA 58.834 50.000 0.00 0.00 45.78 3.86
2134 3115 4.039366 ACAACCTCTCCAAACTACTGAGAC 59.961 45.833 0.00 0.00 32.07 3.36
2138 3119 4.039973 TGGTACAACCTCTCCAAACTACTG 59.960 45.833 0.00 0.00 39.58 2.74
2180 3168 0.249447 TCACTGCTCACCACAACTCG 60.249 55.000 0.00 0.00 0.00 4.18
2187 3175 2.434336 AGTAACAAGTCACTGCTCACCA 59.566 45.455 0.00 0.00 0.00 4.17
2188 3176 3.113260 AGTAACAAGTCACTGCTCACC 57.887 47.619 0.00 0.00 0.00 4.02
2189 3177 3.871594 ACAAGTAACAAGTCACTGCTCAC 59.128 43.478 0.00 0.00 0.00 3.51
2190 3178 4.137116 ACAAGTAACAAGTCACTGCTCA 57.863 40.909 0.00 0.00 0.00 4.26
2191 3179 5.177696 CCTAACAAGTAACAAGTCACTGCTC 59.822 44.000 0.00 0.00 0.00 4.26
2192 3180 5.057149 CCTAACAAGTAACAAGTCACTGCT 58.943 41.667 0.00 0.00 0.00 4.24
2193 3181 5.054477 TCCTAACAAGTAACAAGTCACTGC 58.946 41.667 0.00 0.00 0.00 4.40
2194 3182 6.147821 CCATCCTAACAAGTAACAAGTCACTG 59.852 42.308 0.00 0.00 0.00 3.66
2195 3183 6.042781 TCCATCCTAACAAGTAACAAGTCACT 59.957 38.462 0.00 0.00 0.00 3.41
2200 3188 7.066284 CCTTGATCCATCCTAACAAGTAACAAG 59.934 40.741 0.00 0.00 37.02 3.16
2201 3189 6.884295 CCTTGATCCATCCTAACAAGTAACAA 59.116 38.462 0.00 0.00 37.02 2.83
2202 3190 6.012858 ACCTTGATCCATCCTAACAAGTAACA 60.013 38.462 0.00 0.00 37.02 2.41
2205 3193 5.724370 TGACCTTGATCCATCCTAACAAGTA 59.276 40.000 0.00 0.00 37.02 2.24
2287 3281 0.107508 AGGAAGCACACATAGCGCAT 60.108 50.000 11.47 0.00 37.01 4.73
2588 3597 7.982354 GGAGCCAATATACCTACATATTGAGAC 59.018 40.741 14.46 6.46 45.60 3.36
2596 3605 6.299141 CAAACTGGAGCCAATATACCTACAT 58.701 40.000 0.00 0.00 0.00 2.29
2661 3670 3.370978 CCGCTCTTCTCGAATAAGCAAAA 59.629 43.478 11.99 0.00 32.03 2.44
2791 3800 1.699656 CGTCTCCCATTGCAAGCTCG 61.700 60.000 4.94 0.00 0.00 5.03
2906 3919 2.166664 ACAAACCGCAGCTTAAAAACCA 59.833 40.909 0.00 0.00 0.00 3.67
3068 4085 5.620206 TGTGAATACAGAGGAGCAAAAAGA 58.380 37.500 0.00 0.00 31.91 2.52
3237 4262 3.930336 TCAACCACTCTGAAGCTACATG 58.070 45.455 0.00 0.00 0.00 3.21
3238 4263 4.623932 TTCAACCACTCTGAAGCTACAT 57.376 40.909 0.00 0.00 0.00 2.29
3302 4327 6.265422 TCGCTACCATTAGAAATGAGATCTCA 59.735 38.462 27.03 27.03 44.59 3.27
3303 4328 6.682746 TCGCTACCATTAGAAATGAGATCTC 58.317 40.000 16.21 16.21 0.00 2.75
3304 4329 6.656632 TCGCTACCATTAGAAATGAGATCT 57.343 37.500 0.00 0.00 0.00 2.75
3305 4330 7.704472 CCTATCGCTACCATTAGAAATGAGATC 59.296 40.741 1.23 0.00 0.00 2.75
3306 4331 7.397476 TCCTATCGCTACCATTAGAAATGAGAT 59.603 37.037 1.23 0.00 0.00 2.75
3307 4332 6.719829 TCCTATCGCTACCATTAGAAATGAGA 59.280 38.462 1.23 0.00 0.00 3.27
3308 4333 6.925211 TCCTATCGCTACCATTAGAAATGAG 58.075 40.000 1.23 0.00 0.00 2.90
3309 4334 6.572509 GCTCCTATCGCTACCATTAGAAATGA 60.573 42.308 1.23 0.00 0.00 2.57
3310 4335 5.578727 GCTCCTATCGCTACCATTAGAAATG 59.421 44.000 0.00 0.00 0.00 2.32
3311 4336 5.246203 TGCTCCTATCGCTACCATTAGAAAT 59.754 40.000 0.00 0.00 0.00 2.17
3312 4337 4.587262 TGCTCCTATCGCTACCATTAGAAA 59.413 41.667 0.00 0.00 0.00 2.52
3313 4338 4.022242 GTGCTCCTATCGCTACCATTAGAA 60.022 45.833 0.00 0.00 0.00 2.10
3314 4339 3.506455 GTGCTCCTATCGCTACCATTAGA 59.494 47.826 0.00 0.00 0.00 2.10
3315 4340 3.255888 TGTGCTCCTATCGCTACCATTAG 59.744 47.826 0.00 0.00 0.00 1.73
3316 4341 3.227614 TGTGCTCCTATCGCTACCATTA 58.772 45.455 0.00 0.00 0.00 1.90
3317 4342 2.039418 TGTGCTCCTATCGCTACCATT 58.961 47.619 0.00 0.00 0.00 3.16
3318 4343 1.704641 TGTGCTCCTATCGCTACCAT 58.295 50.000 0.00 0.00 0.00 3.55
3396 4425 6.655078 TGACAATCTCATACATGCTAGCTA 57.345 37.500 17.23 2.58 0.00 3.32
3448 4477 9.032624 AGCTACATATGTAAACCGGTATCTATT 57.967 33.333 8.00 0.00 0.00 1.73
3449 4478 8.591114 AGCTACATATGTAAACCGGTATCTAT 57.409 34.615 8.00 3.37 0.00 1.98
3450 4479 8.301720 CAAGCTACATATGTAAACCGGTATCTA 58.698 37.037 8.00 0.00 0.00 1.98
3451 4480 6.912951 AGCTACATATGTAAACCGGTATCT 57.087 37.500 8.00 0.00 0.00 1.98
3452 4481 6.128634 GCAAGCTACATATGTAAACCGGTATC 60.129 42.308 8.00 1.57 0.00 2.24
3453 4482 5.699458 GCAAGCTACATATGTAAACCGGTAT 59.301 40.000 8.00 0.00 0.00 2.73
3454 4483 5.051816 GCAAGCTACATATGTAAACCGGTA 58.948 41.667 8.00 0.00 0.00 4.02
3455 4484 3.875134 GCAAGCTACATATGTAAACCGGT 59.125 43.478 16.17 0.00 0.00 5.28
3456 4485 4.127171 AGCAAGCTACATATGTAAACCGG 58.873 43.478 16.17 0.00 0.00 5.28
3457 4486 5.501715 CAAGCAAGCTACATATGTAAACCG 58.498 41.667 16.17 6.30 0.00 4.44
3458 4487 5.221048 CCCAAGCAAGCTACATATGTAAACC 60.221 44.000 16.17 8.06 0.00 3.27
3459 4488 5.221048 CCCCAAGCAAGCTACATATGTAAAC 60.221 44.000 16.17 11.31 0.00 2.01
3460 4489 4.887071 CCCCAAGCAAGCTACATATGTAAA 59.113 41.667 16.17 0.00 0.00 2.01
3461 4490 4.165180 TCCCCAAGCAAGCTACATATGTAA 59.835 41.667 16.17 1.63 0.00 2.41
3462 4491 3.714280 TCCCCAAGCAAGCTACATATGTA 59.286 43.478 14.75 14.75 0.00 2.29
3463 4492 2.509548 TCCCCAAGCAAGCTACATATGT 59.490 45.455 13.93 13.93 0.00 2.29
3464 4493 3.213206 TCCCCAAGCAAGCTACATATG 57.787 47.619 0.00 0.00 0.00 1.78
3465 4494 3.951563 TTCCCCAAGCAAGCTACATAT 57.048 42.857 0.00 0.00 0.00 1.78
3466 4495 3.730215 TTTCCCCAAGCAAGCTACATA 57.270 42.857 0.00 0.00 0.00 2.29
3467 4496 2.603075 TTTCCCCAAGCAAGCTACAT 57.397 45.000 0.00 0.00 0.00 2.29
3468 4497 2.224992 TGATTTCCCCAAGCAAGCTACA 60.225 45.455 0.00 0.00 0.00 2.74
3469 4498 2.446435 TGATTTCCCCAAGCAAGCTAC 58.554 47.619 0.00 0.00 0.00 3.58
3470 4499 2.897271 TGATTTCCCCAAGCAAGCTA 57.103 45.000 0.00 0.00 0.00 3.32
3471 4500 1.829222 CATGATTTCCCCAAGCAAGCT 59.171 47.619 0.00 0.00 33.51 3.74
3472 4501 1.134610 CCATGATTTCCCCAAGCAAGC 60.135 52.381 0.00 0.00 33.51 4.01
3473 4502 2.167075 GACCATGATTTCCCCAAGCAAG 59.833 50.000 0.00 0.00 33.51 4.01
3474 4503 2.178580 GACCATGATTTCCCCAAGCAA 58.821 47.619 0.00 0.00 33.51 3.91
3475 4504 1.851304 GACCATGATTTCCCCAAGCA 58.149 50.000 0.00 0.00 34.56 3.91
3476 4505 0.740737 CGACCATGATTTCCCCAAGC 59.259 55.000 0.00 0.00 0.00 4.01
3477 4506 1.392589 CCGACCATGATTTCCCCAAG 58.607 55.000 0.00 0.00 0.00 3.61
3478 4507 0.682855 GCCGACCATGATTTCCCCAA 60.683 55.000 0.00 0.00 0.00 4.12
3479 4508 1.077068 GCCGACCATGATTTCCCCA 60.077 57.895 0.00 0.00 0.00 4.96
3480 4509 1.828224 GGCCGACCATGATTTCCCC 60.828 63.158 0.00 0.00 35.26 4.81
3481 4510 1.103398 CAGGCCGACCATGATTTCCC 61.103 60.000 0.00 0.00 39.06 3.97
3482 4511 1.728490 GCAGGCCGACCATGATTTCC 61.728 60.000 0.00 0.00 39.06 3.13
3483 4512 0.749454 AGCAGGCCGACCATGATTTC 60.749 55.000 0.00 0.00 39.06 2.17
3484 4513 0.323725 AAGCAGGCCGACCATGATTT 60.324 50.000 0.00 0.00 39.06 2.17
3485 4514 1.033746 CAAGCAGGCCGACCATGATT 61.034 55.000 0.00 0.00 39.06 2.57
3486 4515 1.452651 CAAGCAGGCCGACCATGAT 60.453 57.895 0.00 0.00 39.06 2.45
3487 4516 2.046023 CAAGCAGGCCGACCATGA 60.046 61.111 0.00 0.00 39.06 3.07
3488 4517 3.136123 CCAAGCAGGCCGACCATG 61.136 66.667 0.00 0.00 39.06 3.66
3489 4518 4.431131 CCCAAGCAGGCCGACCAT 62.431 66.667 0.00 0.00 39.06 3.55
3495 4524 3.712907 TACGTCCCCAAGCAGGCC 61.713 66.667 0.00 0.00 35.39 5.19
3496 4525 2.436115 GTACGTCCCCAAGCAGGC 60.436 66.667 0.00 0.00 35.39 4.85
3497 4526 1.218316 GAGTACGTCCCCAAGCAGG 59.782 63.158 0.00 0.00 37.03 4.85
3498 4527 0.173708 GAGAGTACGTCCCCAAGCAG 59.826 60.000 0.00 0.00 0.00 4.24
3499 4528 0.541063 TGAGAGTACGTCCCCAAGCA 60.541 55.000 0.00 0.00 0.00 3.91
3500 4529 0.824759 ATGAGAGTACGTCCCCAAGC 59.175 55.000 0.00 0.00 0.00 4.01
3501 4530 1.409427 GGATGAGAGTACGTCCCCAAG 59.591 57.143 0.00 0.00 39.33 3.61
3502 4531 1.481871 GGATGAGAGTACGTCCCCAA 58.518 55.000 0.00 0.00 39.33 4.12
3503 4532 3.202548 GGATGAGAGTACGTCCCCA 57.797 57.895 0.00 0.00 39.33 4.96
3506 4535 2.101082 GGAAAGGGATGAGAGTACGTCC 59.899 54.545 0.00 0.00 43.11 4.79
3507 4536 2.758979 TGGAAAGGGATGAGAGTACGTC 59.241 50.000 0.00 0.00 0.00 4.34
3508 4537 2.761208 CTGGAAAGGGATGAGAGTACGT 59.239 50.000 0.00 0.00 0.00 3.57
3509 4538 2.761208 ACTGGAAAGGGATGAGAGTACG 59.239 50.000 0.00 0.00 0.00 3.67
3510 4539 4.828072 AACTGGAAAGGGATGAGAGTAC 57.172 45.455 0.00 0.00 0.00 2.73
3511 4540 6.945636 TTAAACTGGAAAGGGATGAGAGTA 57.054 37.500 0.00 0.00 0.00 2.59
3512 4541 5.843019 TTAAACTGGAAAGGGATGAGAGT 57.157 39.130 0.00 0.00 0.00 3.24
3513 4542 6.418101 TCATTAAACTGGAAAGGGATGAGAG 58.582 40.000 0.00 0.00 0.00 3.20
3514 4543 6.387192 TCATTAAACTGGAAAGGGATGAGA 57.613 37.500 0.00 0.00 0.00 3.27
3515 4544 7.466746 TTTCATTAAACTGGAAAGGGATGAG 57.533 36.000 0.00 0.00 0.00 2.90
3516 4545 9.540538 TTATTTCATTAAACTGGAAAGGGATGA 57.459 29.630 0.00 0.00 34.38 2.92
3542 4571 2.616842 CACTTGCCCTACTCGTGTTTTT 59.383 45.455 0.00 0.00 0.00 1.94
3543 4572 2.218603 CACTTGCCCTACTCGTGTTTT 58.781 47.619 0.00 0.00 0.00 2.43
3544 4573 1.878953 CACTTGCCCTACTCGTGTTT 58.121 50.000 0.00 0.00 0.00 2.83
3545 4574 0.602905 GCACTTGCCCTACTCGTGTT 60.603 55.000 0.00 0.00 34.31 3.32
3546 4575 1.004918 GCACTTGCCCTACTCGTGT 60.005 57.895 0.00 0.00 34.31 4.49
3547 4576 2.094659 CGCACTTGCCCTACTCGTG 61.095 63.158 0.00 0.00 37.91 4.35
3548 4577 1.812686 TTCGCACTTGCCCTACTCGT 61.813 55.000 0.00 0.00 37.91 4.18
3549 4578 0.669318 TTTCGCACTTGCCCTACTCG 60.669 55.000 0.00 0.00 37.91 4.18
3550 4579 1.197036 GTTTTCGCACTTGCCCTACTC 59.803 52.381 0.00 0.00 37.91 2.59
3551 4580 1.202770 AGTTTTCGCACTTGCCCTACT 60.203 47.619 0.00 0.00 37.91 2.57
3552 4581 1.235724 AGTTTTCGCACTTGCCCTAC 58.764 50.000 0.00 0.00 37.91 3.18
3553 4582 2.843401 TAGTTTTCGCACTTGCCCTA 57.157 45.000 0.00 0.00 37.91 3.53
3554 4583 1.975660 TTAGTTTTCGCACTTGCCCT 58.024 45.000 0.00 0.00 37.91 5.19
3555 4584 2.785713 TTTAGTTTTCGCACTTGCCC 57.214 45.000 0.00 0.00 37.91 5.36
3556 4585 3.049912 CCTTTTAGTTTTCGCACTTGCC 58.950 45.455 0.00 0.00 37.91 4.52
3557 4586 3.049912 CCCTTTTAGTTTTCGCACTTGC 58.950 45.455 0.00 0.00 37.78 4.01
3558 4587 4.537015 CTCCCTTTTAGTTTTCGCACTTG 58.463 43.478 0.00 0.00 0.00 3.16
3559 4588 3.004419 GCTCCCTTTTAGTTTTCGCACTT 59.996 43.478 0.00 0.00 0.00 3.16
3560 4589 2.552743 GCTCCCTTTTAGTTTTCGCACT 59.447 45.455 0.00 0.00 0.00 4.40
3561 4590 2.292292 TGCTCCCTTTTAGTTTTCGCAC 59.708 45.455 0.00 0.00 0.00 5.34
3562 4591 2.577700 TGCTCCCTTTTAGTTTTCGCA 58.422 42.857 0.00 0.00 0.00 5.10
3563 4592 3.243267 TGTTGCTCCCTTTTAGTTTTCGC 60.243 43.478 0.00 0.00 0.00 4.70
3564 4593 4.036380 AGTGTTGCTCCCTTTTAGTTTTCG 59.964 41.667 0.00 0.00 0.00 3.46
3565 4594 5.163550 ACAGTGTTGCTCCCTTTTAGTTTTC 60.164 40.000 0.00 0.00 0.00 2.29
3566 4595 4.709886 ACAGTGTTGCTCCCTTTTAGTTTT 59.290 37.500 0.00 0.00 0.00 2.43
3567 4596 4.278310 ACAGTGTTGCTCCCTTTTAGTTT 58.722 39.130 0.00 0.00 0.00 2.66
3568 4597 3.883489 GACAGTGTTGCTCCCTTTTAGTT 59.117 43.478 0.00 0.00 0.00 2.24
3569 4598 3.477530 GACAGTGTTGCTCCCTTTTAGT 58.522 45.455 0.00 0.00 0.00 2.24
3570 4599 2.480419 CGACAGTGTTGCTCCCTTTTAG 59.520 50.000 0.00 0.00 0.00 1.85
3571 4600 2.158871 ACGACAGTGTTGCTCCCTTTTA 60.159 45.455 10.62 0.00 0.00 1.52
3572 4601 1.308998 CGACAGTGTTGCTCCCTTTT 58.691 50.000 0.00 0.00 0.00 2.27
3573 4602 0.180406 ACGACAGTGTTGCTCCCTTT 59.820 50.000 10.62 0.00 0.00 3.11
3574 4603 0.532862 CACGACAGTGTTGCTCCCTT 60.533 55.000 10.62 0.00 43.15 3.95
3575 4604 1.069765 CACGACAGTGTTGCTCCCT 59.930 57.895 10.62 0.00 43.15 4.20
3576 4605 1.961277 CCACGACAGTGTTGCTCCC 60.961 63.158 10.62 0.00 46.56 4.30
3583 4612 3.299340 GTGAGATTACCACGACAGTGT 57.701 47.619 0.00 0.00 46.56 3.55
3612 4642 1.306654 ACGATAAGCCACCCCCTGA 60.307 57.895 0.00 0.00 0.00 3.86
3713 4743 1.485066 GTTATCTCTCCGGAAAGCCCA 59.515 52.381 5.23 0.00 34.14 5.36
3719 4749 2.544844 AGGGTGTTATCTCTCCGGAA 57.455 50.000 5.23 0.00 0.00 4.30
3738 4768 3.099905 ACAGTCAGCATAGCAGGAGTAA 58.900 45.455 0.00 0.00 0.00 2.24
3752 4782 8.514594 ACATTTTATACATTTGGTCACAGTCAG 58.485 33.333 0.00 0.00 0.00 3.51
3758 4788 7.275560 GGAGCAACATTTTATACATTTGGTCAC 59.724 37.037 11.96 0.83 41.18 3.67
3762 4792 8.034215 TCAAGGAGCAACATTTTATACATTTGG 58.966 33.333 0.00 0.00 0.00 3.28
4123 5166 1.752198 GTGGGACTGTAGCCACACA 59.248 57.895 0.00 0.00 31.25 3.72
4171 5214 0.179111 GAGCGTGGCTATAGTGTGCA 60.179 55.000 0.84 0.00 39.88 4.57
4196 5239 1.690219 CGCCTGCTACCCCTGAATCT 61.690 60.000 0.00 0.00 0.00 2.40
4233 5276 0.179067 TCACCCACAACGACAAGACC 60.179 55.000 0.00 0.00 0.00 3.85
4244 5287 3.970332 AGTCTGCACTCACCCACA 58.030 55.556 0.00 0.00 0.00 4.17
4353 5406 1.749033 CCTTAGAAGGCGGCCTAGG 59.251 63.158 24.16 20.93 39.76 3.02


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

AutoCloner maintained by Alex Coulton.