Multiple sequence alignment - TraesCS4D01G267400

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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 TraesCS4D01G267400 chr4D 100.000 5308 0 0 729 6036 438141748 438147055 0.000000e+00 9803.0
1 TraesCS4D01G267400 chr4D 100.000 431 0 0 1 431 438141020 438141450 0.000000e+00 797.0
2 TraesCS4D01G267400 chr4D 85.714 77 7 4 4603 4675 75264074 75264150 1.800000e-10 78.7
3 TraesCS4D01G267400 chr4A 92.699 3890 213 36 730 4569 27567845 27571713 0.000000e+00 5544.0
4 TraesCS4D01G267400 chr4A 87.849 1325 81 32 4646 5957 27571945 27573202 0.000000e+00 1482.0
5 TraesCS4D01G267400 chr4A 89.447 199 16 4 1 196 27556844 27557040 4.670000e-61 246.0
6 TraesCS4D01G267400 chr4A 89.024 164 15 3 732 892 27557196 27557359 3.690000e-47 200.0
7 TraesCS4D01G267400 chr4A 91.304 69 4 2 4609 4675 594534179 594534247 6.440000e-15 93.5
8 TraesCS4D01G267400 chr4A 90.909 55 3 2 4623 4675 669374635 669374581 8.390000e-09 73.1
9 TraesCS4D01G267400 chr4B 90.595 3817 244 59 835 4601 541900269 541904020 0.000000e+00 4953.0
10 TraesCS4D01G267400 chr4B 85.514 1284 87 41 4731 5974 541904113 541905337 0.000000e+00 1249.0
11 TraesCS4D01G267400 chr4B 91.224 433 29 4 1 430 541898987 541899413 1.130000e-161 580.0
12 TraesCS4D01G267400 chr3B 89.139 534 31 12 5033 5547 713870579 713870054 1.830000e-179 640.0
13 TraesCS4D01G267400 chr3B 88.951 534 32 13 5033 5547 713802651 713802126 8.530000e-178 634.0
14 TraesCS4D01G267400 chr3B 88.931 533 32 12 5033 5546 713836588 713836064 3.070000e-177 632.0
15 TraesCS4D01G267400 chr3B 88.073 545 37 11 5033 5557 713767451 713766915 6.640000e-174 621.0
16 TraesCS4D01G267400 chrUn 87.890 545 38 11 5033 5557 176723040 176723576 3.090000e-172 616.0
17 TraesCS4D01G267400 chrUn 87.500 544 42 15 5033 5557 176757370 176757906 6.690000e-169 604.0
18 TraesCS4D01G267400 chr1D 86.607 112 13 2 5916 6025 23973961 23973850 8.220000e-24 122.0
19 TraesCS4D01G267400 chr2D 82.906 117 17 3 5921 6036 632051174 632051060 1.070000e-17 102.0
20 TraesCS4D01G267400 chr5B 83.019 106 17 1 5926 6030 551461191 551461296 1.790000e-15 95.3
21 TraesCS4D01G267400 chr5B 84.722 72 6 2 4606 4675 580101420 580101488 3.900000e-07 67.6
22 TraesCS4D01G267400 chr6B 90.278 72 4 2 4606 4675 545202877 545202807 2.320000e-14 91.6
23 TraesCS4D01G267400 chr2B 80.328 122 23 1 5916 6036 422512417 422512296 2.320000e-14 91.6
24 TraesCS4D01G267400 chr6D 90.141 71 4 2 4607 4675 363033206 363033137 8.330000e-14 89.8
25 TraesCS4D01G267400 chr3D 82.243 107 15 4 5920 6024 523838267 523838371 8.330000e-14 89.8
26 TraesCS4D01G267400 chr3D 79.508 122 24 1 5916 6036 124294303 124294424 1.080000e-12 86.1
27 TraesCS4D01G267400 chr1B 90.769 65 3 3 4617 4678 446029215 446029279 3.880000e-12 84.2
28 TraesCS4D01G267400 chr7B 81.308 107 15 4 5920 6022 641362616 641362721 1.390000e-11 82.4
29 TraesCS4D01G267400 chr7B 79.130 115 22 2 5920 6033 328521386 328521273 1.800000e-10 78.7
30 TraesCS4D01G267400 chr7A 100.000 42 0 0 4606 4647 692917725 692917684 1.800000e-10 78.7
31 TraesCS4D01G267400 chr3A 91.228 57 4 1 4606 4661 117319656 117319712 6.490000e-10 76.8


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 TraesCS4D01G267400 chr4D 438141020 438147055 6035 False 5300.000000 9803 100.0000 1 6036 2 chr4D.!!$F2 6035
1 TraesCS4D01G267400 chr4A 27567845 27573202 5357 False 3513.000000 5544 90.2740 730 5957 2 chr4A.!!$F3 5227
2 TraesCS4D01G267400 chr4A 27556844 27557359 515 False 223.000000 246 89.2355 1 892 2 chr4A.!!$F2 891
3 TraesCS4D01G267400 chr4B 541898987 541905337 6350 False 2260.666667 4953 89.1110 1 5974 3 chr4B.!!$F1 5973
4 TraesCS4D01G267400 chr3B 713870054 713870579 525 True 640.000000 640 89.1390 5033 5547 1 chr3B.!!$R4 514
5 TraesCS4D01G267400 chr3B 713802126 713802651 525 True 634.000000 634 88.9510 5033 5547 1 chr3B.!!$R2 514
6 TraesCS4D01G267400 chr3B 713836064 713836588 524 True 632.000000 632 88.9310 5033 5546 1 chr3B.!!$R3 513
7 TraesCS4D01G267400 chr3B 713766915 713767451 536 True 621.000000 621 88.0730 5033 5557 1 chr3B.!!$R1 524
8 TraesCS4D01G267400 chrUn 176723040 176723576 536 False 616.000000 616 87.8900 5033 5557 1 chrUn.!!$F1 524
9 TraesCS4D01G267400 chrUn 176757370 176757906 536 False 604.000000 604 87.5000 5033 5557 1 chrUn.!!$F2 524

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
422 426 0.037790 GGCGCTCTTTGTCACTCTCT 60.038 55.000 7.64 0.00 0.00 3.10 F
903 1607 0.519961 ATTTAAAGCACACGGCCGAC 59.480 50.000 35.90 17.91 46.50 4.79 F
1841 2575 0.391597 TCCTTTCCGGGTGCGATATC 59.608 55.000 0.00 0.00 0.00 1.63 F
2773 3517 0.539438 TGTGTGGCCCATCAAGGTTC 60.539 55.000 0.00 0.00 34.66 3.62 F
3093 3837 1.134250 TGCTTAGTGGACAACTGTGCA 60.134 47.619 0.00 0.00 44.12 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 2186 0.798776 GGATGCTATACATGTGGCGC 59.201 55.000 9.11 0.0 39.84 6.53 R
2288 3026 1.086696 TTATGGCTTTGCTGAGCGAC 58.913 50.000 0.00 0.0 43.62 5.19 R
3633 4379 0.899720 ATTGGTGCAAAGCCATCAGG 59.100 50.000 0.00 0.0 35.71 3.86 R
4762 5722 0.962489 CTACATCCTACGCCTCCAGG 59.038 60.000 0.00 0.0 38.53 4.45 R
5047 6025 3.900388 TTTTTAATCCCGTTCGTGGTG 57.100 42.857 0.00 0.0 0.00 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.547279 AAAGACTATTTGGATTCCTTTACCATT 57.453 29.630 3.95 0.00 33.56 3.16
73 74 7.059945 GTCGCTTGTTTGATTTCACTTATCAAG 59.940 37.037 0.00 0.00 41.53 3.02
243 247 4.514577 CCCGGTGCTACGAGGCAG 62.515 72.222 0.00 0.00 43.25 4.85
284 288 1.288127 CAAGGCTGGAGCTGCAAAC 59.712 57.895 9.92 4.98 41.70 2.93
309 313 2.047844 CGATGGCTAGGGATGCGG 60.048 66.667 0.00 0.00 0.00 5.69
336 340 2.110213 GGTGGTGCCTCAACGACA 59.890 61.111 0.00 0.00 31.04 4.35
342 346 1.541670 GGTGCCTCAACGACAAAGGTA 60.542 52.381 0.00 0.00 32.49 3.08
387 391 3.803082 CCTTGCGCGTCCATGGTG 61.803 66.667 12.58 7.02 0.00 4.17
397 401 4.586235 CCATGGTGGGGGATCGGC 62.586 72.222 2.57 0.00 32.67 5.54
398 402 4.935495 CATGGTGGGGGATCGGCG 62.935 72.222 0.00 0.00 0.00 6.46
422 426 0.037790 GGCGCTCTTTGTCACTCTCT 60.038 55.000 7.64 0.00 0.00 3.10
426 430 1.066502 GCTCTTTGTCACTCTCTCCCC 60.067 57.143 0.00 0.00 0.00 4.81
427 431 1.203523 CTCTTTGTCACTCTCTCCCCG 59.796 57.143 0.00 0.00 0.00 5.73
428 432 0.969894 CTTTGTCACTCTCTCCCCGT 59.030 55.000 0.00 0.00 0.00 5.28
429 433 0.679505 TTTGTCACTCTCTCCCCGTG 59.320 55.000 0.00 0.00 0.00 4.94
745 749 3.792736 CGGAGGGGGATGGCGAAA 61.793 66.667 0.00 0.00 0.00 3.46
775 780 1.938125 CAACGGACGTGTGAATGCA 59.062 52.632 0.00 0.00 0.00 3.96
782 788 1.100463 ACGTGTGAATGCAACTGCCA 61.100 50.000 0.00 0.00 41.18 4.92
815 821 4.142687 CCGGTCATCCAAAATAACAGTGAC 60.143 45.833 0.00 0.00 35.11 3.67
866 1569 8.148807 TGAAAATAACTGAATCGAGACAAACA 57.851 30.769 0.00 0.00 0.00 2.83
903 1607 0.519961 ATTTAAAGCACACGGCCGAC 59.480 50.000 35.90 17.91 46.50 4.79
942 1667 7.569240 TCAAAAGAACCTTCTCTTCTTCTCTT 58.431 34.615 0.00 0.00 37.04 2.85
1286 2014 2.344500 CCGCAACGGGGTTAGTCA 59.656 61.111 0.00 0.00 44.15 3.41
1291 2019 0.682852 CAACGGGGTTAGTCAGTCCA 59.317 55.000 0.00 0.00 0.00 4.02
1297 2030 2.638363 GGGGTTAGTCAGTCCATATCCC 59.362 54.545 0.00 0.00 0.00 3.85
1313 2046 5.221823 CCATATCCCCTCCTCTCTTTTTCTC 60.222 48.000 0.00 0.00 0.00 2.87
1319 2052 0.732880 CCTCTCTTTTTCTCGCGCGA 60.733 55.000 32.60 32.60 0.00 5.87
1331 2064 2.876879 CGCGCGACAGGTGTTTGAA 61.877 57.895 28.94 0.00 0.00 2.69
1453 2186 1.030457 GGCATTGCCTCCTGATCTTG 58.970 55.000 20.66 0.00 46.69 3.02
1471 2204 1.511850 TGCGCCACATGTATAGCATC 58.488 50.000 14.63 6.96 35.19 3.91
1503 2236 5.873179 TTGATTTTGGTTAGTAGAAGCCG 57.127 39.130 0.00 0.00 0.00 5.52
1615 2348 6.144402 GCCTTCAATAATTGCGTTATTCCATG 59.856 38.462 4.46 0.00 40.23 3.66
1712 2445 6.824305 AAGTTAATTGAAGTGGTGATCTGG 57.176 37.500 0.00 0.00 0.00 3.86
1719 2452 1.722034 AGTGGTGATCTGGTGACTGT 58.278 50.000 0.00 0.00 0.00 3.55
1737 2470 5.105269 TGACTGTGTTAGGTAGTTCACAACA 60.105 40.000 0.00 0.00 39.69 3.33
1791 2524 9.630098 TCTCTCAAAAAGCAAATAACATCAATC 57.370 29.630 0.00 0.00 0.00 2.67
1802 2535 7.753132 GCAAATAACATCAATCGGTTTAAGTCA 59.247 33.333 0.00 0.00 0.00 3.41
1841 2575 0.391597 TCCTTTCCGGGTGCGATATC 59.608 55.000 0.00 0.00 0.00 1.63
1853 2587 5.491982 GGGTGCGATATCTCTTATTTCCAT 58.508 41.667 0.34 0.00 0.00 3.41
1917 2651 5.121611 TGTTATATGGTGTCGCAGTTTTGAG 59.878 40.000 0.00 0.00 0.00 3.02
1962 2700 0.748005 AATGCCGGTATGCAGGTGAC 60.748 55.000 5.55 0.00 45.93 3.67
2124 2862 5.314923 TGCTTACAAAGGCATTTCTCATC 57.685 39.130 0.00 0.00 33.23 2.92
2202 2940 5.047872 TGCAACAAATCAGTCAGCATATTGT 60.048 36.000 0.00 0.00 30.68 2.71
2214 2952 9.507329 CAGTCAGCATATTGTATAAATACCCTT 57.493 33.333 0.00 0.00 32.33 3.95
2218 2956 9.283768 CAGCATATTGTATAAATACCCTTGTCA 57.716 33.333 0.00 0.00 32.33 3.58
2219 2957 9.507329 AGCATATTGTATAAATACCCTTGTCAG 57.493 33.333 0.00 0.00 32.33 3.51
2245 2983 9.744468 GTTAAAACTATGATTGTCCAAAGTTGT 57.256 29.630 0.00 0.00 0.00 3.32
2250 2988 5.633830 ATGATTGTCCAAAGTTGTAGCTG 57.366 39.130 0.00 0.00 0.00 4.24
2253 2991 0.881796 GTCCAAAGTTGTAGCTGCCC 59.118 55.000 0.00 0.00 0.00 5.36
2261 2999 1.807142 GTTGTAGCTGCCCTGTTTCTC 59.193 52.381 0.00 0.00 0.00 2.87
2281 3019 8.437575 GTTTCTCTATGGGAGGGTTTATTCATA 58.562 37.037 0.00 0.00 42.10 2.15
2288 3026 8.884124 ATGGGAGGGTTTATTCATATTATGTG 57.116 34.615 3.67 0.00 0.00 3.21
2314 3052 4.023365 GCTCAGCAAAGCCATAAATCTAGG 60.023 45.833 0.00 0.00 36.22 3.02
2342 3080 8.814235 CCTGAAATTGATAAATTTGCTCATGAC 58.186 33.333 5.44 0.00 32.92 3.06
2454 3192 1.674962 GACAGAATGCTGATCCCAAGC 59.325 52.381 8.02 0.00 45.17 4.01
2462 3200 3.634504 TGCTGATCCCAAGCATTATTGT 58.365 40.909 2.24 0.00 33.24 2.71
2531 3269 6.295292 GGAAAACCTTGCTCCTTTCATGTATT 60.295 38.462 0.00 0.00 30.89 1.89
2532 3270 6.670695 AAACCTTGCTCCTTTCATGTATTT 57.329 33.333 0.00 0.00 0.00 1.40
2533 3271 7.775053 AAACCTTGCTCCTTTCATGTATTTA 57.225 32.000 0.00 0.00 0.00 1.40
2576 3319 9.749490 GCATTGATCAAAAGTCAAAACATATTG 57.251 29.630 13.09 1.35 38.89 1.90
2583 3327 8.681806 TCAAAAGTCAAAACATATTGTCTGACA 58.318 29.630 6.36 6.36 36.49 3.58
2625 3369 5.741982 GTCAAAATAACGATACATTGGCCAC 59.258 40.000 3.88 0.00 0.00 5.01
2773 3517 0.539438 TGTGTGGCCCATCAAGGTTC 60.539 55.000 0.00 0.00 34.66 3.62
2787 3531 3.138304 CAAGGTTCGATGAGTTGGACAA 58.862 45.455 0.00 0.00 0.00 3.18
2807 3551 6.402983 GGACAACATGCTCTTGAACATTAGAG 60.403 42.308 1.85 0.00 40.66 2.43
2809 3553 6.370994 ACAACATGCTCTTGAACATTAGAGAG 59.629 38.462 0.00 3.25 40.24 3.20
2880 3624 1.544724 GTGCCAATAAAGTGGGAGCA 58.455 50.000 0.00 0.00 40.04 4.26
2965 3709 6.821665 TGGTTGAAGCAGGTTATGTAGATAAC 59.178 38.462 13.10 13.10 42.29 1.89
2996 3740 7.011669 GGCAAGCGTTTAATAAGTATCTTGGTA 59.988 37.037 0.00 0.00 32.65 3.25
3026 3770 1.522676 CTGCATATGCCACGTAAGTCG 59.477 52.381 24.54 0.00 45.39 4.18
3060 3804 5.776744 ACTTCTTTCCATTGAGCATTTCAC 58.223 37.500 0.00 0.00 34.94 3.18
3061 3805 5.302568 ACTTCTTTCCATTGAGCATTTCACA 59.697 36.000 0.00 0.00 34.94 3.58
3082 3826 4.217118 ACAGCTGAGAAAAATGCTTAGTGG 59.783 41.667 23.35 0.00 33.03 4.00
3093 3837 1.134250 TGCTTAGTGGACAACTGTGCA 60.134 47.619 0.00 0.00 44.12 4.57
3195 3939 1.935799 CCCACCCATGGTCATTGAAA 58.064 50.000 11.73 0.00 45.66 2.69
3207 3951 3.108144 GTCATTGAAAAATCCGGATGCG 58.892 45.455 19.95 0.00 0.00 4.73
3208 3952 2.098934 TCATTGAAAAATCCGGATGCGG 59.901 45.455 21.08 21.08 0.00 5.69
3228 3972 3.017442 GGTCATTAGGTCCTTGAAAGGC 58.983 50.000 0.00 0.20 46.06 4.35
3281 4025 3.788142 AGTGATGGGAAGGTTGATGGTAT 59.212 43.478 0.00 0.00 0.00 2.73
3286 4030 5.725551 TGGGAAGGTTGATGGTATGTATT 57.274 39.130 0.00 0.00 0.00 1.89
3312 4058 5.618561 GCTTGCACAGTTGTAGTACATAAC 58.381 41.667 3.28 0.17 0.00 1.89
3317 4063 5.519206 GCACAGTTGTAGTACATAACTAGGC 59.481 44.000 3.28 8.65 41.42 3.93
3318 4064 6.627243 CACAGTTGTAGTACATAACTAGGCA 58.373 40.000 3.28 0.00 41.42 4.75
3320 4066 7.764443 CACAGTTGTAGTACATAACTAGGCAAT 59.236 37.037 3.28 0.00 41.42 3.56
3321 4067 8.319146 ACAGTTGTAGTACATAACTAGGCAATT 58.681 33.333 3.28 0.00 41.42 2.32
3389 4135 3.056107 TCGTTAGCATTAACTCTGCAGGT 60.056 43.478 15.13 7.99 42.15 4.00
3464 4210 3.420893 TCATGGAAAAGGCACGAAAGAT 58.579 40.909 0.00 0.00 0.00 2.40
3503 4249 7.061752 AGAAGTTAAGCTTGCTATTACAACG 57.938 36.000 9.86 0.00 37.59 4.10
3508 4254 4.404507 AGCTTGCTATTACAACGTTGTG 57.595 40.909 37.43 24.19 42.31 3.33
3607 4353 1.210478 TGCTGCCAATCTAGGGAAGAC 59.790 52.381 0.00 0.00 36.93 3.01
3633 4379 8.807581 CACTTAAGTTTGGACAACTTTCAAATC 58.192 33.333 5.07 0.00 40.58 2.17
3809 4555 7.767250 TGACCATGTCCAACAATGTATTTTA 57.233 32.000 0.00 0.00 0.00 1.52
3820 4566 7.014230 CCAACAATGTATTTTACCCTATCCAGG 59.986 40.741 0.00 0.00 42.22 4.45
3861 4608 7.390440 TCAATACCCACATTTTACTCTGTTCTG 59.610 37.037 0.00 0.00 0.00 3.02
3884 4637 2.683211 ACAGCCCATCAGACCTTTTT 57.317 45.000 0.00 0.00 0.00 1.94
3948 4701 9.748708 ATTGAATGGGTCATTGATATTTTAACG 57.251 29.630 0.00 0.00 35.70 3.18
4002 4755 4.526970 ACACTCAAATAGGCACCATTAGG 58.473 43.478 0.00 0.00 42.21 2.69
4015 4768 3.638160 CACCATTAGGGCATGCAAGTATT 59.362 43.478 21.36 1.23 42.05 1.89
4044 4798 9.965902 ACTGTTTCTTTAATGAGATATCACCTT 57.034 29.630 5.32 0.80 0.00 3.50
4057 4814 9.159254 TGAGATATCACCTTTCTATAACCACAT 57.841 33.333 5.32 0.00 0.00 3.21
4129 4886 9.878667 AAAATCATATTCATTGTGCATCTTCAA 57.121 25.926 0.00 0.00 0.00 2.69
4197 4955 2.364324 TGTGTAGTTCCAGTCAGTGTCC 59.636 50.000 0.00 0.00 0.00 4.02
4198 4956 2.364324 GTGTAGTTCCAGTCAGTGTCCA 59.636 50.000 0.00 0.00 0.00 4.02
4215 4973 4.787551 TGTCCATTAACACACAGGTTCTT 58.212 39.130 0.00 0.00 32.29 2.52
4234 4992 6.701841 GGTTCTTTTTGAGGAATTTGGTCTTC 59.298 38.462 0.00 0.00 0.00 2.87
4245 5004 5.178067 GGAATTTGGTCTTCATGTGCTTTTG 59.822 40.000 0.00 0.00 0.00 2.44
4250 5009 4.036734 TGGTCTTCATGTGCTTTTGAGTTC 59.963 41.667 0.00 0.00 0.00 3.01
4258 5018 4.858935 TGTGCTTTTGAGTTCATACTTGC 58.141 39.130 0.00 0.00 33.84 4.01
4284 5044 8.292448 CGACCATATGCTTTGCTAATAAATTCT 58.708 33.333 0.00 0.00 0.00 2.40
4294 5054 9.358872 CTTTGCTAATAAATTCTTGGAACTTCC 57.641 33.333 0.20 0.20 36.96 3.46
4296 5056 6.094881 TGCTAATAAATTCTTGGAACTTCCCG 59.905 38.462 5.30 0.00 35.03 5.14
4359 5119 8.133024 TGAATTTGACTGGCCAAATAAGTTAT 57.867 30.769 7.01 0.00 43.61 1.89
4365 5125 6.597672 TGACTGGCCAAATAAGTTATGTACAG 59.402 38.462 7.01 3.66 0.00 2.74
4391 5152 8.431593 GCTTAGCTTCTTATTCATCGTAATCTG 58.568 37.037 0.00 0.00 0.00 2.90
4463 5224 4.907269 AGGTTCATGGAATCCAACCTTTTT 59.093 37.500 16.37 0.00 41.69 1.94
4464 5225 4.996758 GGTTCATGGAATCCAACCTTTTTG 59.003 41.667 5.89 0.00 36.95 2.44
4511 5274 9.850628 ATCAAATAATGGATATTCATTTCTGCG 57.149 29.630 14.51 1.44 38.24 5.18
4538 5301 3.814005 ATGCTCATTGGGCAGAATTTC 57.186 42.857 17.55 0.00 43.15 2.17
4795 5758 7.490000 CGTAGGATGTAGAAAATCTTACACCT 58.510 38.462 6.53 0.00 36.77 4.00
4911 5887 7.275920 AGCAACTAATAGAGGACTTATGGTTG 58.724 38.462 0.00 0.00 36.31 3.77
5031 6008 4.202245 TGAGTTGGCATACAGGAAGTAC 57.798 45.455 0.00 0.00 35.05 2.73
5136 6119 2.908073 GCCAAGGCCAACACTGTCG 61.908 63.158 5.01 0.00 34.56 4.35
5167 6150 2.348666 GGTGCTGCGTCAGTAAGTAATG 59.651 50.000 8.32 0.00 33.43 1.90
5201 6188 8.908786 AATGAATCCTATTGTTATGTCGTCAT 57.091 30.769 0.00 0.00 38.00 3.06
5465 6454 2.301346 CACTAATCCATGTTGGCCTCC 58.699 52.381 3.32 0.00 37.47 4.30
5719 6720 1.878775 GGCTGCTTTGTGTGCCTAG 59.121 57.895 0.00 0.00 41.92 3.02
5721 6722 0.239347 GCTGCTTTGTGTGCCTAGTG 59.761 55.000 0.00 0.00 0.00 2.74
5722 6723 0.239347 CTGCTTTGTGTGCCTAGTGC 59.761 55.000 0.00 0.00 41.77 4.40
5723 6724 1.172180 TGCTTTGTGTGCCTAGTGCC 61.172 55.000 1.42 0.00 40.16 5.01
5724 6725 0.890996 GCTTTGTGTGCCTAGTGCCT 60.891 55.000 1.42 0.00 40.16 4.75
5725 6726 1.610624 GCTTTGTGTGCCTAGTGCCTA 60.611 52.381 1.42 0.00 40.16 3.93
5726 6727 2.076863 CTTTGTGTGCCTAGTGCCTAC 58.923 52.381 1.42 1.90 40.16 3.18
5727 6728 1.348064 TTGTGTGCCTAGTGCCTACT 58.652 50.000 1.42 0.00 40.16 2.57
5728 6729 2.225382 TGTGTGCCTAGTGCCTACTA 57.775 50.000 1.42 0.00 40.16 1.82
5782 6783 2.146920 TTGCCTGATGATGCCAATGA 57.853 45.000 0.00 0.00 0.00 2.57
5841 6842 1.001378 ACAAGACGTGGATTTGCTTGC 60.001 47.619 9.95 0.00 39.51 4.01
5844 6845 0.593128 GACGTGGATTTGCTTGCAGT 59.407 50.000 0.00 0.00 0.00 4.40
5872 6873 5.757850 CCAGAACTATAGGCACCAAAATC 57.242 43.478 4.43 0.00 0.00 2.17
5875 6876 5.006746 CAGAACTATAGGCACCAAAATCGTC 59.993 44.000 4.43 0.00 0.00 4.20
5905 6906 3.242011 ACTTGCTGAAATGGGTTTGGAT 58.758 40.909 0.00 0.00 0.00 3.41
5981 6988 6.305693 GAGCATCTCAAACACAGTAAAAGT 57.694 37.500 0.00 0.00 0.00 2.66
5982 6989 6.699575 AGCATCTCAAACACAGTAAAAGTT 57.300 33.333 0.00 0.00 0.00 2.66
5983 6990 7.801716 AGCATCTCAAACACAGTAAAAGTTA 57.198 32.000 0.00 0.00 0.00 2.24
5984 6991 7.639945 AGCATCTCAAACACAGTAAAAGTTAC 58.360 34.615 0.00 0.00 0.00 2.50
5985 6992 6.573725 GCATCTCAAACACAGTAAAAGTTACG 59.426 38.462 0.00 0.00 0.00 3.18
5986 6993 7.627340 CATCTCAAACACAGTAAAAGTTACGT 58.373 34.615 0.00 0.00 0.00 3.57
5987 6994 7.225523 TCTCAAACACAGTAAAAGTTACGTC 57.774 36.000 0.00 0.00 0.00 4.34
5988 6995 6.812656 TCTCAAACACAGTAAAAGTTACGTCA 59.187 34.615 0.00 0.00 0.00 4.35
5989 6996 7.331440 TCTCAAACACAGTAAAAGTTACGTCAA 59.669 33.333 0.00 0.00 0.00 3.18
5990 6997 7.457868 TCAAACACAGTAAAAGTTACGTCAAG 58.542 34.615 0.00 0.00 0.00 3.02
5991 6998 7.331440 TCAAACACAGTAAAAGTTACGTCAAGA 59.669 33.333 0.00 0.00 0.00 3.02
5992 6999 7.781548 AACACAGTAAAAGTTACGTCAAGAT 57.218 32.000 0.00 0.00 0.00 2.40
5993 7000 7.781548 ACACAGTAAAAGTTACGTCAAGATT 57.218 32.000 0.00 0.00 0.00 2.40
5994 7001 7.848491 ACACAGTAAAAGTTACGTCAAGATTC 58.152 34.615 0.00 0.00 0.00 2.52
5995 7002 7.709613 ACACAGTAAAAGTTACGTCAAGATTCT 59.290 33.333 0.00 0.00 0.00 2.40
5996 7003 8.004344 CACAGTAAAAGTTACGTCAAGATTCTG 58.996 37.037 0.00 0.00 0.00 3.02
5997 7004 7.924412 ACAGTAAAAGTTACGTCAAGATTCTGA 59.076 33.333 0.00 0.00 0.00 3.27
5998 7005 8.428536 CAGTAAAAGTTACGTCAAGATTCTGAG 58.571 37.037 0.00 0.00 0.00 3.35
5999 7006 8.358148 AGTAAAAGTTACGTCAAGATTCTGAGA 58.642 33.333 0.00 0.00 0.00 3.27
6000 7007 7.409465 AAAAGTTACGTCAAGATTCTGAGAC 57.591 36.000 0.00 8.67 0.00 3.36
6001 7008 5.061920 AGTTACGTCAAGATTCTGAGACC 57.938 43.478 11.69 1.82 0.00 3.85
6002 7009 4.523173 AGTTACGTCAAGATTCTGAGACCA 59.477 41.667 11.69 1.40 0.00 4.02
6003 7010 5.186021 AGTTACGTCAAGATTCTGAGACCAT 59.814 40.000 11.69 5.58 0.00 3.55
6004 7011 4.116747 ACGTCAAGATTCTGAGACCATC 57.883 45.455 11.69 0.00 0.00 3.51
6005 7012 3.111838 CGTCAAGATTCTGAGACCATCG 58.888 50.000 11.69 0.69 0.00 3.84
6006 7013 3.181496 CGTCAAGATTCTGAGACCATCGA 60.181 47.826 11.69 0.00 0.00 3.59
6007 7014 4.675408 CGTCAAGATTCTGAGACCATCGAA 60.675 45.833 11.69 0.00 0.00 3.71
6008 7015 4.564769 GTCAAGATTCTGAGACCATCGAAC 59.435 45.833 7.84 0.00 0.00 3.95
6009 7016 3.428746 AGATTCTGAGACCATCGAACG 57.571 47.619 0.00 0.00 0.00 3.95
6010 7017 3.017442 AGATTCTGAGACCATCGAACGA 58.983 45.455 0.00 0.00 0.00 3.85
6011 7018 3.634448 AGATTCTGAGACCATCGAACGAT 59.366 43.478 3.80 3.80 34.81 3.73
6012 7019 3.422417 TTCTGAGACCATCGAACGATC 57.578 47.619 6.74 0.00 31.62 3.69
6013 7020 2.365582 TCTGAGACCATCGAACGATCA 58.634 47.619 6.74 2.52 31.62 2.92
6014 7021 2.097629 TCTGAGACCATCGAACGATCAC 59.902 50.000 6.74 2.56 31.62 3.06
6015 7022 2.092323 TGAGACCATCGAACGATCACT 58.908 47.619 6.74 6.83 31.62 3.41
6016 7023 3.275999 TGAGACCATCGAACGATCACTA 58.724 45.455 6.74 0.00 31.62 2.74
6017 7024 3.064958 TGAGACCATCGAACGATCACTAC 59.935 47.826 6.74 1.25 31.62 2.73
6018 7025 2.358267 AGACCATCGAACGATCACTACC 59.642 50.000 6.74 0.00 31.62 3.18
6019 7026 1.065102 ACCATCGAACGATCACTACCG 59.935 52.381 6.74 0.00 31.62 4.02
6020 7027 1.121240 CATCGAACGATCACTACCGC 58.879 55.000 6.74 0.00 31.62 5.68
6021 7028 0.030369 ATCGAACGATCACTACCGCC 59.970 55.000 3.80 0.00 0.00 6.13
6022 7029 1.937846 CGAACGATCACTACCGCCG 60.938 63.158 0.00 0.00 0.00 6.46
6023 7030 2.202703 AACGATCACTACCGCCGC 60.203 61.111 0.00 0.00 0.00 6.53
6024 7031 3.711541 AACGATCACTACCGCCGCC 62.712 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.542020 TCAAACAAGCGACTCCATGA 57.458 45.000 0.00 0.00 0.00 3.07
47 48 6.370593 TGATAAGTGAAATCAAACAAGCGAC 58.629 36.000 0.00 0.00 30.52 5.19
73 74 5.297527 GGCCATTCCAAATCATTTTCCATTC 59.702 40.000 0.00 0.00 34.01 2.67
110 111 1.456287 GACTCCTGGCCACCACTTT 59.544 57.895 0.00 0.00 0.00 2.66
160 161 1.437573 CGCCCATTGTCGAGCTCTA 59.562 57.895 12.85 0.00 0.00 2.43
181 184 1.228245 ATGGTTGCAGCTTCGGTGT 60.228 52.632 0.00 0.00 33.19 4.16
242 246 4.927782 TTGCCGCTCAACACCGCT 62.928 61.111 0.00 0.00 0.00 5.52
284 288 1.080230 CCTAGCCATCGCCATCTCG 60.080 63.158 0.00 0.00 34.57 4.04
359 363 1.973812 GCGCAAGGCCTCTTCCTTT 60.974 57.895 5.23 0.00 43.62 3.11
400 404 4.430423 GTGACAAAGAGCGCCGCG 62.430 66.667 8.83 8.83 0.00 6.46
401 405 3.016474 GAGTGACAAAGAGCGCCGC 62.016 63.158 2.29 0.00 0.00 6.53
402 406 1.347817 GAGAGTGACAAAGAGCGCCG 61.348 60.000 2.29 0.00 0.00 6.46
728 732 3.792736 TTTCGCCATCCCCCTCCG 61.793 66.667 0.00 0.00 0.00 4.63
729 733 2.124278 GTTTCGCCATCCCCCTCC 60.124 66.667 0.00 0.00 0.00 4.30
730 734 0.610785 TTTGTTTCGCCATCCCCCTC 60.611 55.000 0.00 0.00 0.00 4.30
731 735 0.611896 CTTTGTTTCGCCATCCCCCT 60.612 55.000 0.00 0.00 0.00 4.79
745 749 0.375803 GTCCGTTGCGTTGTCTTTGT 59.624 50.000 0.00 0.00 0.00 2.83
789 795 2.096248 GTTATTTTGGATGACCGGCCA 58.904 47.619 0.00 0.00 39.42 5.36
903 1607 0.878416 TTTTGATGTTCCCGGCTTCG 59.122 50.000 0.00 0.00 0.00 3.79
942 1667 0.253020 GGTCAAGGGGGAGGAAGGTA 60.253 60.000 0.00 0.00 0.00 3.08
979 1704 2.115266 AGGGTTTGGGAGGTTGCG 59.885 61.111 0.00 0.00 0.00 4.85
1286 2014 2.448708 AGAGAGGAGGGGATATGGACT 58.551 52.381 0.00 0.00 0.00 3.85
1291 2019 4.591072 CGAGAAAAAGAGAGGAGGGGATAT 59.409 45.833 0.00 0.00 0.00 1.63
1297 2030 1.634702 CGCGAGAAAAAGAGAGGAGG 58.365 55.000 0.00 0.00 0.00 4.30
1313 2046 2.368131 TTTCAAACACCTGTCGCGCG 62.368 55.000 26.76 26.76 0.00 6.86
1331 2064 2.545742 GCCGAACCTCACAAGCATTTTT 60.546 45.455 0.00 0.00 0.00 1.94
1453 2186 0.798776 GGATGCTATACATGTGGCGC 59.201 55.000 9.11 0.00 39.84 6.53
1471 2204 7.239763 ACTAACCAAAATCAAACCAATAGGG 57.760 36.000 0.00 0.00 44.81 3.53
1503 2236 6.852664 ACAAGTTAACAATACAAGCCTATGC 58.147 36.000 8.61 0.00 37.95 3.14
1662 2395 3.195002 CTGTGTGCCCATACCGCG 61.195 66.667 0.00 0.00 0.00 6.46
1712 2445 4.940463 TGTGAACTACCTAACACAGTCAC 58.060 43.478 0.00 0.00 38.14 3.67
1719 2452 4.709250 TGCATGTTGTGAACTACCTAACA 58.291 39.130 0.00 0.00 35.93 2.41
1737 2470 9.783081 AAAAAGGAAAAGAAGACAATAATGCAT 57.217 25.926 0.00 0.00 0.00 3.96
1824 2558 1.341531 AGAGATATCGCACCCGGAAAG 59.658 52.381 0.73 0.00 34.56 2.62
1853 2587 5.350365 GCAGACATCCGTAACAGAAACATTA 59.650 40.000 0.00 0.00 0.00 1.90
1962 2700 4.362932 TGATCTGTTAGAGCGAGAACTG 57.637 45.455 0.00 0.41 32.29 3.16
2170 2908 7.028962 GCTGACTGATTTGTTGCATTGTAATA 58.971 34.615 0.00 0.00 0.00 0.98
2214 2952 8.684386 TTGGACAATCATAGTTTTAACTGACA 57.316 30.769 5.41 0.00 40.07 3.58
2218 2956 9.965824 CAACTTTGGACAATCATAGTTTTAACT 57.034 29.630 0.29 0.29 37.01 2.24
2219 2957 9.744468 ACAACTTTGGACAATCATAGTTTTAAC 57.256 29.630 0.00 0.00 37.01 2.01
2223 2961 7.448469 AGCTACAACTTTGGACAATCATAGTTT 59.552 33.333 0.00 0.00 37.01 2.66
2245 2983 2.435805 CCATAGAGAAACAGGGCAGCTA 59.564 50.000 0.00 0.00 0.00 3.32
2250 2988 1.141858 CCTCCCATAGAGAAACAGGGC 59.858 57.143 0.00 0.00 46.50 5.19
2253 2991 4.576330 AAACCCTCCCATAGAGAAACAG 57.424 45.455 0.00 0.00 46.50 3.16
2281 3019 2.096496 GCTTTGCTGAGCGACACATAAT 59.904 45.455 0.00 0.00 32.23 1.28
2285 3023 2.253758 GGCTTTGCTGAGCGACACA 61.254 57.895 0.00 0.00 43.62 3.72
2288 3026 1.086696 TTATGGCTTTGCTGAGCGAC 58.913 50.000 0.00 0.00 43.62 5.19
2314 3052 6.108015 TGAGCAAATTTATCAATTTCAGGCC 58.892 36.000 0.00 0.00 40.09 5.19
2416 3154 6.691754 TCTGTCAAGATAAAACAGCAAACA 57.308 33.333 0.00 0.00 40.15 2.83
2433 3171 2.942752 GCTTGGGATCAGCATTCTGTCA 60.943 50.000 0.00 0.00 41.10 3.58
2510 3248 7.615365 TGATAAATACATGAAAGGAGCAAGGTT 59.385 33.333 0.00 0.00 0.00 3.50
2576 3319 7.766278 ACAGAAATCACTTATACCATGTCAGAC 59.234 37.037 0.00 0.00 0.00 3.51
2773 3517 2.079158 AGCATGTTGTCCAACTCATCG 58.921 47.619 11.14 0.00 41.67 3.84
2787 3531 5.426504 CCTCTCTAATGTTCAAGAGCATGT 58.573 41.667 0.06 0.00 39.30 3.21
2807 3551 2.649614 GCGTAGGTATCGCCCCTC 59.350 66.667 0.00 0.00 46.61 4.30
2880 3624 5.431765 CCTCACCAGCAATCTTAGTTACAT 58.568 41.667 0.00 0.00 0.00 2.29
2965 3709 3.124636 ACTTATTAAACGCTTGCCTGACG 59.875 43.478 0.00 0.00 0.00 4.35
2996 3740 1.263356 GCATATGCAGGGCCATCATT 58.737 50.000 22.84 2.60 41.59 2.57
3042 3786 3.575256 AGCTGTGAAATGCTCAATGGAAA 59.425 39.130 0.00 0.00 35.22 3.13
3060 3804 4.456911 TCCACTAAGCATTTTTCTCAGCTG 59.543 41.667 7.63 7.63 37.41 4.24
3061 3805 4.457257 GTCCACTAAGCATTTTTCTCAGCT 59.543 41.667 0.00 0.00 39.37 4.24
3082 3826 4.618489 GCAGAAAATACATGCACAGTTGTC 59.382 41.667 0.00 0.00 39.75 3.18
3093 3837 4.225942 TCACTCCCTCTGCAGAAAATACAT 59.774 41.667 18.85 0.00 0.00 2.29
3228 3972 1.202568 TCCATAGCATGAAGACCAGCG 60.203 52.381 0.00 0.00 0.00 5.18
3281 4025 2.616376 ACAACTGTGCAAGCGAAATACA 59.384 40.909 0.00 0.00 0.00 2.29
3286 4030 1.948104 ACTACAACTGTGCAAGCGAA 58.052 45.000 0.00 0.00 0.00 4.70
3312 4058 9.927668 TCTCCTTTTATTTTGAAAATTGCCTAG 57.072 29.630 8.60 1.40 0.00 3.02
3351 4097 8.801715 ATGCTAACGAAATAAATATTTGGCAG 57.198 30.769 11.05 5.01 36.13 4.85
3389 4135 9.383519 CCATACTTCTCAGCTAATTGACTAAAA 57.616 33.333 0.00 0.00 0.00 1.52
3464 4210 2.307768 ACTTCTCCAACGTCAGTCTCA 58.692 47.619 0.00 0.00 0.00 3.27
3607 4353 8.702163 ATTTGAAAGTTGTCCAAACTTAAGTG 57.298 30.769 9.34 0.00 39.36 3.16
3633 4379 0.899720 ATTGGTGCAAAGCCATCAGG 59.100 50.000 0.00 0.00 35.71 3.86
3809 4555 2.127708 GGAACACATCCTGGATAGGGT 58.872 52.381 9.27 8.40 45.56 4.34
3820 4566 4.636206 GGGTATTGAGTTGAGGAACACATC 59.364 45.833 0.00 0.00 33.38 3.06
3861 4608 2.789409 AGGTCTGATGGGCTGTTAAC 57.211 50.000 0.00 0.00 0.00 2.01
3884 4637 5.241285 TCAGCAACATCATCAGCTAACAAAA 59.759 36.000 0.00 0.00 35.19 2.44
3948 4701 5.946486 ACCATCCAGGAATAGGAATTCTTC 58.054 41.667 11.84 1.49 41.18 2.87
4002 4755 3.855689 ACAGTTGAATACTTGCATGCC 57.144 42.857 16.68 0.00 33.85 4.40
4031 4784 8.547481 TGTGGTTATAGAAAGGTGATATCTCA 57.453 34.615 3.98 0.00 0.00 3.27
4044 4798 6.883756 TGTGCTTCATTCATGTGGTTATAGAA 59.116 34.615 0.00 0.00 0.00 2.10
4057 4814 8.969260 AGAGTAATTGATATGTGCTTCATTCA 57.031 30.769 0.89 3.18 37.91 2.57
4129 4886 8.985315 TCCAAAATGTCTGCAATAGAAGATAT 57.015 30.769 0.00 0.00 37.12 1.63
4177 4935 2.364324 TGGACACTGACTGGAACTACAC 59.636 50.000 0.00 0.00 0.00 2.90
4197 4955 6.697019 CCTCAAAAAGAACCTGTGTGTTAATG 59.303 38.462 0.00 0.00 0.00 1.90
4198 4956 6.605594 TCCTCAAAAAGAACCTGTGTGTTAAT 59.394 34.615 0.00 0.00 0.00 1.40
4209 4967 6.161855 AGACCAAATTCCTCAAAAAGAACC 57.838 37.500 0.00 0.00 0.00 3.62
4215 4973 6.514947 CACATGAAGACCAAATTCCTCAAAA 58.485 36.000 0.00 0.00 0.00 2.44
4234 4992 5.344128 GCAAGTATGAACTCAAAAGCACATG 59.656 40.000 0.00 0.00 33.75 3.21
4245 5004 4.084328 GCATATGGTCGCAAGTATGAACTC 60.084 45.833 4.56 0.00 33.75 3.01
4250 5009 4.530388 CAAAGCATATGGTCGCAAGTATG 58.470 43.478 8.07 0.00 39.48 2.39
4258 5018 8.292448 AGAATTTATTAGCAAAGCATATGGTCG 58.708 33.333 8.07 3.98 0.00 4.79
4284 5044 4.042435 AGGAAATCTTACGGGAAGTTCCAA 59.958 41.667 23.33 8.47 38.64 3.53
4322 5082 7.116805 GGCCAGTCAAATTCATTTCACTAAAAG 59.883 37.037 0.00 0.00 29.02 2.27
4359 5119 6.697455 CGATGAATAAGAAGCTAAGCTGTACA 59.303 38.462 0.00 0.00 39.62 2.90
4365 5125 8.431593 CAGATTACGATGAATAAGAAGCTAAGC 58.568 37.037 0.00 0.00 0.00 3.09
4382 5143 1.022735 GCTCGTCCCTCAGATTACGA 58.977 55.000 0.00 0.00 41.63 3.43
4391 5152 1.232119 GTAGAGCTAGCTCGTCCCTC 58.768 60.000 33.31 19.01 46.90 4.30
4489 5252 8.394971 TCACGCAGAAATGAATATCCATTATT 57.605 30.769 0.00 0.00 35.86 1.40
4511 5274 2.292569 CTGCCCAATGAGCATACATCAC 59.707 50.000 0.00 0.00 40.04 3.06
4556 5319 6.379703 TCTCAGGAAACAAAGGAAACATGAAA 59.620 34.615 0.00 0.00 0.00 2.69
4619 5382 9.820229 TGAACTGCAAAAACGTCTTATATTTAG 57.180 29.630 0.00 0.00 0.00 1.85
4621 5384 9.522804 TTTGAACTGCAAAAACGTCTTATATTT 57.477 25.926 0.00 0.00 43.18 1.40
4636 5399 9.820229 CTAAATATAAGACGTTTTGAACTGCAA 57.180 29.630 0.83 0.00 33.88 4.08
4637 5400 9.210329 TCTAAATATAAGACGTTTTGAACTGCA 57.790 29.630 0.83 0.00 0.00 4.41
4712 5649 6.040729 TCAAACATGAAGCTGAAAATTGAGGA 59.959 34.615 0.00 0.00 0.00 3.71
4762 5722 0.962489 CTACATCCTACGCCTCCAGG 59.038 60.000 0.00 0.00 38.53 4.45
4862 5826 8.982685 GCTTATTTTGATCGTTCTCATATCTCA 58.017 33.333 0.00 0.00 0.00 3.27
4863 5827 8.982685 TGCTTATTTTGATCGTTCTCATATCTC 58.017 33.333 0.00 0.00 0.00 2.75
4954 5931 6.494491 ACAAAAGGATCATGTTTCAGGATTGA 59.506 34.615 0.00 0.00 34.96 2.57
5031 6008 7.844169 CGTTCGTGGTGTATTCAACTTATTATG 59.156 37.037 0.00 0.00 31.63 1.90
5047 6025 3.900388 TTTTTAATCCCGTTCGTGGTG 57.100 42.857 0.00 0.00 0.00 4.17
5052 6030 7.916552 AGATCACTTATTTTTAATCCCGTTCG 58.083 34.615 0.00 0.00 0.00 3.95
5136 6119 3.982241 GCAGCACCACAACAGGGC 61.982 66.667 0.00 0.00 0.00 5.19
5201 6188 8.832735 ACCAAAGGATCAAGTAGAAAATAGGTA 58.167 33.333 0.00 0.00 0.00 3.08
5225 6212 6.691508 AGGAATTTTTATTGCAGAACTGACC 58.308 36.000 5.97 0.00 0.00 4.02
5527 6527 6.415573 GGTGGAGATAATGTTCTAAACTGGT 58.584 40.000 0.00 0.00 0.00 4.00
5719 6720 7.171337 CAGCTTAGTAGTAGTAGTAGTAGGCAC 59.829 44.444 24.82 7.28 35.60 5.01
5721 6722 6.650390 CCAGCTTAGTAGTAGTAGTAGTAGGC 59.350 46.154 19.32 19.32 34.23 3.93
5722 6723 7.734942 ACCAGCTTAGTAGTAGTAGTAGTAGG 58.265 42.308 5.12 5.12 0.00 3.18
5723 6724 8.641541 AGACCAGCTTAGTAGTAGTAGTAGTAG 58.358 40.741 0.00 0.00 0.00 2.57
5724 6725 8.546083 AGACCAGCTTAGTAGTAGTAGTAGTA 57.454 38.462 0.00 0.00 0.00 1.82
5725 6726 7.436320 AGACCAGCTTAGTAGTAGTAGTAGT 57.564 40.000 0.00 0.00 0.00 2.73
5726 6727 9.480053 CTTAGACCAGCTTAGTAGTAGTAGTAG 57.520 40.741 0.00 0.00 0.00 2.57
5727 6728 9.206690 TCTTAGACCAGCTTAGTAGTAGTAGTA 57.793 37.037 0.00 0.00 0.00 1.82
5728 6729 8.088463 TCTTAGACCAGCTTAGTAGTAGTAGT 57.912 38.462 0.00 0.00 0.00 2.73
5782 6783 2.827921 CAGCTAACCAATGGAGGCTTTT 59.172 45.455 6.16 0.00 0.00 2.27
5796 6797 0.917259 CAGCGTCGATGACAGCTAAC 59.083 55.000 9.31 0.00 39.12 2.34
5841 6842 3.244249 GCCTATAGTTCTGGCCCTAACTG 60.244 52.174 23.41 11.91 40.71 3.16
5844 6845 2.704065 GTGCCTATAGTTCTGGCCCTAA 59.296 50.000 0.00 0.00 45.56 2.69
5939 6946 5.297547 TGCTCTGTACTTCGATGAACTTTT 58.702 37.500 5.16 0.00 0.00 2.27
5974 6981 8.426251 GTCTCAGAATCTTGACGTAACTTTTAC 58.574 37.037 0.00 0.00 0.00 2.01
5975 6982 7.597743 GGTCTCAGAATCTTGACGTAACTTTTA 59.402 37.037 0.00 0.00 0.00 1.52
5976 6983 6.424207 GGTCTCAGAATCTTGACGTAACTTTT 59.576 38.462 0.00 0.00 0.00 2.27
5977 6984 5.927115 GGTCTCAGAATCTTGACGTAACTTT 59.073 40.000 0.00 0.00 0.00 2.66
5978 6985 5.010719 TGGTCTCAGAATCTTGACGTAACTT 59.989 40.000 0.00 0.00 0.00 2.66
5979 6986 4.523173 TGGTCTCAGAATCTTGACGTAACT 59.477 41.667 0.00 0.00 0.00 2.24
5980 6987 4.806330 TGGTCTCAGAATCTTGACGTAAC 58.194 43.478 0.00 0.00 0.00 2.50
5981 6988 5.651530 GATGGTCTCAGAATCTTGACGTAA 58.348 41.667 0.00 0.00 0.00 3.18
5982 6989 4.201920 CGATGGTCTCAGAATCTTGACGTA 60.202 45.833 0.00 1.33 0.00 3.57
5983 6990 3.428180 CGATGGTCTCAGAATCTTGACGT 60.428 47.826 0.00 0.00 0.00 4.34
5984 6991 3.111838 CGATGGTCTCAGAATCTTGACG 58.888 50.000 6.95 0.00 0.00 4.35
5985 6992 4.377839 TCGATGGTCTCAGAATCTTGAC 57.622 45.455 5.05 5.05 0.00 3.18
5986 6993 4.675408 CGTTCGATGGTCTCAGAATCTTGA 60.675 45.833 0.00 0.00 0.00 3.02
5987 6994 3.549471 CGTTCGATGGTCTCAGAATCTTG 59.451 47.826 0.00 0.00 0.00 3.02
5988 6995 3.444034 TCGTTCGATGGTCTCAGAATCTT 59.556 43.478 0.00 0.00 0.00 2.40
5989 6996 3.017442 TCGTTCGATGGTCTCAGAATCT 58.983 45.455 0.00 0.00 0.00 2.40
5990 6997 3.422417 TCGTTCGATGGTCTCAGAATC 57.578 47.619 0.00 0.00 0.00 2.52
5991 6998 3.381590 TGATCGTTCGATGGTCTCAGAAT 59.618 43.478 12.42 0.00 0.00 2.40
5992 6999 2.752903 TGATCGTTCGATGGTCTCAGAA 59.247 45.455 12.42 0.00 0.00 3.02
5993 7000 2.097629 GTGATCGTTCGATGGTCTCAGA 59.902 50.000 12.42 0.00 0.00 3.27
5994 7001 2.098280 AGTGATCGTTCGATGGTCTCAG 59.902 50.000 12.42 0.00 0.00 3.35
5995 7002 2.092323 AGTGATCGTTCGATGGTCTCA 58.908 47.619 12.42 2.23 0.00 3.27
5996 7003 2.853731 AGTGATCGTTCGATGGTCTC 57.146 50.000 12.42 0.00 0.00 3.36
5997 7004 2.358267 GGTAGTGATCGTTCGATGGTCT 59.642 50.000 12.42 9.57 0.00 3.85
5998 7005 2.728922 GGTAGTGATCGTTCGATGGTC 58.271 52.381 12.42 0.29 0.00 4.02
5999 7006 1.065102 CGGTAGTGATCGTTCGATGGT 59.935 52.381 12.42 0.07 0.00 3.55
6000 7007 1.755161 CGGTAGTGATCGTTCGATGG 58.245 55.000 12.42 0.00 0.00 3.51
6001 7008 1.121240 GCGGTAGTGATCGTTCGATG 58.879 55.000 12.42 0.00 0.00 3.84
6002 7009 0.030369 GGCGGTAGTGATCGTTCGAT 59.970 55.000 7.43 7.43 0.00 3.59
6003 7010 1.430632 GGCGGTAGTGATCGTTCGA 59.569 57.895 0.00 0.00 0.00 3.71
6004 7011 1.937846 CGGCGGTAGTGATCGTTCG 60.938 63.158 0.00 0.00 0.00 3.95
6005 7012 2.228914 GCGGCGGTAGTGATCGTTC 61.229 63.158 9.78 0.00 0.00 3.95
6006 7013 2.202703 GCGGCGGTAGTGATCGTT 60.203 61.111 9.78 0.00 0.00 3.85
6007 7014 4.203076 GGCGGCGGTAGTGATCGT 62.203 66.667 9.78 0.00 0.00 3.73
6009 7016 4.944372 CCGGCGGCGGTAGTGATC 62.944 72.222 39.30 0.00 0.00 2.92
6014 7021 4.745751 TTGTTCCGGCGGCGGTAG 62.746 66.667 43.56 23.60 0.00 3.18
6015 7022 4.745751 CTTGTTCCGGCGGCGGTA 62.746 66.667 43.56 35.21 0.00 4.02


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

AutoCloner maintained by Alex Coulton.